Citrus Sinensis ID: 022724

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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---
Protein Sequence
MAAATAMRRRGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQFP
Secondary Structure (PSIPRED)
ccHHHHHHHccccccccccccccccccccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHccccEEEEccccccHHHHHHHHHHHHcccccccEEEEEEcccHHHHHHHHHHHHHHHcccccEEEEEEccccHHHHHHHHcccccEEEcccHHHHHHccccccccccccEEEEEccccccccccHHHHHHHHHHcccccEEEEEEccccHHHHHHHHHHccccEEEEEEccccccccEEEEEEEEccccHHHHHHHHHHHHccccEEEEEEcccccHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccEEEEccccccccccHHHccccHHHHHHHHHcccccccccHHHHHHHHHccccEEEEccccHHHHHHHHHHHHHHcccccccccEEEEcccHHHHHHHHHHHHHHcccccccEEEEcccccHHHHHHHHHHccEEEEEcHHHHHHHHcccccccccccEEEEccHHHHHccccHHHHHHHHHccccccEEEEEEccccHHHHHHHHHHccccEEEEcEcccccccccEEEEEEEccHHHHHHHHHHHHHcccccEEEEEEccHHHHHHHHHccc
Coil and Loop (DISEMBL)
MAAATAMRrrgggggmdddkMVFETTEGVeaitsfdamgiKDDLLRGIYQygfekpsaiqqravmpiikgrDVIAqaqsgtgktSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFiniqahacvggksvgedIRKLehgvhvvsgtpgrvcdmIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTkfmtdpvkILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQFP
Flexible Loop (DISEMBL)
maaatamrrrgggggmdddkMVFETTEGVEaitsfdamgiKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAqsgtgktsmIALTVCQTVDTSSREVQALIlsptrelatQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEhgvhvvsgtpgrvcdmikrkTLRTRAIKLlvldesdemlSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMttkfmtdpVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQFP
Low Complexity Region (SEG)
maaatamrrrgggggmdddKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQFP
Disordered region (IsUnstruct)
***********************ETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQ**
Disordered Region (DISOPRED)
**************************EGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQFP
Disordered Region (DISEMBL)
*************GGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQFP
Disordered Region (DISPRO)
******************DKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQFP
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAAATAMRRRGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQFP
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	293	2.2.26 [Sep-21-2011]
Q5VNM3	404	DEAD-box ATP-dependent RN	yes	no	0.965	0.700	0.863	1e-145
Q10I26	404	DEAD-box ATP-dependent RN	yes	no	0.965	0.700	0.856	1e-144
Q94A52	408	DEAD-box ATP-dependent RN	yes	no	0.924	0.664	0.889	1e-143
P41380	391	Eukaryotic initiation fac	N/A	no	0.921	0.690	0.888	1e-142
Q4P184	397	ATP-dependent RNA helicas	N/A	no	0.938	0.692	0.734	1e-124
Q3B8Q2	411	Eukaryotic initiation fac	yes	no	0.918	0.654	0.758	1e-122
A6M931	411	Eukaryotic initiation fac	yes	no	0.918	0.654	0.758	1e-122
Q2NL22	411	Eukaryotic initiation fac	yes	no	0.918	0.654	0.758	1e-122
P38919	411	Eukaryotic initiation fac	yes	no	0.918	0.654	0.758	1e-122
Q91VC3	411	Eukaryotic initiation fac	yes	no	0.918	0.654	0.758	1e-122

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

 Score =  515 bits (1326), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 246/285 (86%), 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 LTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKV 285
           LTLEGIKQFFVAVE+EEWKFDTLCDLYDTLTITQAVIFCNTKRKV
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 =  512 bits (1318), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 244/285 (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 LTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKV 285
           LTLEGIKQFFVAVE+EEWKFDTLCDLYDTLTITQAVIFCNTKRKV
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 = 241/271 (88%), Positives = 260/271 (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 REEWKFDTLCDLYDTLTITQAVIFCNTKRKV 285
           +EEWKFDTLCDLYDTLTITQAVIFCNTKRKV
Sbjct: 257 KEEWKFDTLCDLYDTLTITQAVIFCNTKRKV 287

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 =  504 bits (1298), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 240/270 (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 EEWKFDTLCDLYDTLTITQAVIFCNTKRKV 285
           EEWKFDTLCDLYDTLTITQAVIFCNTKRKV
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 =  445 bits (1144), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 202/275 (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 VAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKV 285
           VAVE+EEWKFDTLCDLYDTLTITQAVIFCNT+RKV
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|Q3B8Q2|IF4A3_RAT Eukaryotic initiation factor 4A-III OS=Rattus norvegicus GN=Eif4a3 PE=1 SV=1

 Score =  437 bits (1124), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 204/269 (75%), Positives = 240/269 (89%)

Query: 17  DDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQ 76
           D  K+ FET+E V+   +FD MG+++DLLRGIY YGFEKPSAIQQRA+  IIKGRDVIAQ
Sbjct: 22  DMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQ 81

Query: 77  AQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACV 136
           +QSGTGKT+  +++V Q +D   RE QALIL+PTRELA Q +K +LA+GD++N+Q HAC+
Sbjct: 82  SQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACI 141

Query: 137 GGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQI 196
           GG +VGEDIRKL++G HVV+GTPGRV DMI+R++LRTRAIK+LVLDE+DEML++GFK+QI
Sbjct: 142 GGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQI 201

Query: 197 YDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVERE 256
           YDVYRYLPP  QVVLISATLPHEILEMT KFMTDP++ILVKRDELTLEGIKQFFVAVERE
Sbjct: 202 YDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVERE 261

Query: 257 EWKFDTLCDLYDTLTITQAVIFCNTKRKV 285
           EWKFDTLCDLYDTLTITQAVIFCNTKRKV
Sbjct: 262 EWKFDTLCDLYDTLTITQAVIFCNTKRKV 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 =  437 bits (1124), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 204/269 (75%), Positives = 240/269 (89%)

Query: 17  DDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQ 76
           D  K+ FET+E V+   +FD MG+++DLLRGIY YGFEKPSAIQQRA+  IIKGRDVIAQ
Sbjct: 22  DMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQ 81

Query: 77  AQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACV 136
           +QSGTGKT+  +++V Q +D   RE QALIL+PTRELA Q +K +LA+GD++N+Q HAC+
Sbjct: 82  SQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACI 141

Query: 137 GGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQI 196
           GG +VGEDIRKL++G HVV+GTPGRV DMI+R++LRTRAIK+LVLDE+DEML++GFK+QI
Sbjct: 142 GGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQI 201

Query: 197 YDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVERE 256
           YDVYRYLPP  QVVLISATLPHEILEMT KFMTDP++ILVKRDELTLEGIKQFFVAVERE
Sbjct: 202 YDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVERE 261

Query: 257 EWKFDTLCDLYDTLTITQAVIFCNTKRKV 285
           EWKFDTLCDLYDTLTITQAVIFCNTKRKV
Sbjct: 262 EWKFDTLCDLYDTLTITQAVIFCNTKRKV 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 =  437 bits (1124), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 204/269 (75%), Positives = 240/269 (89%)

Query: 17  DDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQ 76
           D  K+ FET+E V+   +FD MG+++DLLRGIY YGFEKPSAIQQRA+  IIKGRDVIAQ
Sbjct: 22  DMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQ 81

Query: 77  AQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACV 136
           +QSGTGKT+  +++V Q +D   RE QALIL+PTRELA Q +K +LA+GD++N+Q HAC+
Sbjct: 82  SQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACI 141

Query: 137 GGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQI 196
           GG +VGEDIRKL++G HVV+GTPGRV DMI+R++LRTRAIK+LVLDE+DEML++GFK+QI
Sbjct: 142 GGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQI 201

Query: 197 YDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVERE 256
           YDVYRYLPP  QVVLISATLPHEILEMT KFMTDP++ILVKRDELTLEGIKQFFVAVERE
Sbjct: 202 YDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVERE 261

Query: 257 EWKFDTLCDLYDTLTITQAVIFCNTKRKV 285
           EWKFDTLCDLYDTLTITQAVIFCNTKRKV
Sbjct: 262 EWKFDTLCDLYDTLTITQAVIFCNTKRKV 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

>sp|P38919|IF4A3_HUMAN Eukaryotic initiation factor 4A-III OS=Homo sapiens GN=EIF4A3 PE=1 SV=4

 Score =  437 bits (1123), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 204/269 (75%), Positives = 240/269 (89%)

Query: 17  DDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQ 76
           D  K+ FET+E V+   +FD MG+++DLLRGIY YGFEKPSAIQQRA+  IIKGRDVIAQ
Sbjct: 22  DMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQ 81

Query: 77  AQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACV 136
           +QSGTGKT+  +++V Q +D   RE QALIL+PTRELA Q +K +LA+GD++N+Q HAC+
Sbjct: 82  SQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACI 141

Query: 137 GGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQI 196
           GG +VGEDIRKL++G HVV+GTPGRV DMI+R++LRTRAIK+LVLDE+DEML++GFK+QI
Sbjct: 142 GGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQI 201

Query: 197 YDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVERE 256
           YDVYRYLPP  QVVLISATLPHEILEMT KFMTDP++ILVKRDELTLEGIKQFFVAVERE
Sbjct: 202 YDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVERE 261

Query: 257 EWKFDTLCDLYDTLTITQAVIFCNTKRKV 285
           EWKFDTLCDLYDTLTITQAVIFCNTKRKV
Sbjct: 262 EWKFDTLCDLYDTLTITQAVIFCNTKRKV 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.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q91VC3|IF4A3_MOUSE Eukaryotic initiation factor 4A-III OS=Mus musculus GN=Eif4a3 PE=2 SV=3

 Score =  437 bits (1123), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 204/269 (75%), Positives = 240/269 (89%)

Query: 17  DDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQ 76
           D  K+ FET+E V+   +FD MG+++DLLRGIY YGFEKPSAIQQRA+  IIKGRDVIAQ
Sbjct: 22  DMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQ 81

Query: 77  AQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACV 136
           +QSGTGKT+  +++V Q +D   RE QALIL+PTRELA Q +K +LA+GD++N+Q HAC+
Sbjct: 82  SQSGTGKTATFSVSVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACI 141

Query: 137 GGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQI 196
           GG +VGEDIRKL++G HVV+GTPGRV DMI+R++LRTRAIK+LVLDE+DEML++GFK+QI
Sbjct: 142 GGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQI 201

Query: 197 YDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVERE 256
           YDVYRYLPP  QVVLISATLPHEILEMT KFMTDP++ILVKRDELTLEGIKQFFVAVERE
Sbjct: 202 YDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVERE 261

Query: 257 EWKFDTLCDLYDTLTITQAVIFCNTKRKV 285
           EWKFDTLCDLYDTLTITQAVIFCNTKRKV
Sbjct: 262 EWKFDTLCDLYDTLTITQAVIFCNTKRKV 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.

Mus musculus (taxid: 10090)

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	293
225464928	412	PREDICTED: eukaryotic initiation factor	0.969	0.689	0.892	1e-147
255559772	407	dead box ATP-dependent RNA helicase, put	0.918	0.660	0.929	1e-145
356530272	407	PREDICTED: DEAD-box ATP-dependent RNA he	0.959	0.690	0.901	1e-145
356556161	406	PREDICTED: DEAD-box ATP-dependent RNA he	0.955	0.689	0.897	1e-144
115438787	404	Os01g0639100 [Oryza sativa Japonica Grou	0.965	0.700	0.863	1e-143
118574850	406	DH [Medicago sativa]	0.972	0.701	0.879	1e-143
147785805	398	hypothetical protein VITISV_037577 [Viti	0.904	0.665	0.928	1e-143
317159567	395	DEAD box RNA helicase RH2b [Hevea brasil	0.918	0.681	0.918	1e-143
125586856	394	hypothetical protein OsJ_11472 [Oryza sa	0.965	0.718	0.856	1e-143
115453811	404	Os03g0566800 [Oryza sativa Japonica Grou	0.965	0.700	0.856	1e-143

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

 Score =  526 bits (1354), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 258/289 (89%), 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 KRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKV 285
           KRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKV
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 =  521 bits (1341), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 250/269 (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 EWKFDTLCDLYDTLTITQAVIFCNTKRKV 285
           EWKFDTLCDLYDTLTITQAVIFCNTKRKV
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 =  519 bits (1336), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 255/283 (90%), Positives = 264/283 (93%), Gaps = 2/283 (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 IKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLL 288
           IKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKV  L
Sbjct: 247 IKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWL 289

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 =  517 bits (1331), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 254/283 (89%), Positives = 264/283 (93%), Gaps = 3/283 (1%)

Query: 6   AMRRRGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVM 65
           A RRR        ++M FETTEGV+AI SF+ MGIKDDLLRGIYQYGFEKPSAIQQRAV 
Sbjct: 9   ANRRRAANPA---EEMDFETTEGVKAIASFEEMGIKDDLLRGIYQYGFEKPSAIQQRAVT 65

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

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

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

Query: 246 IKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLL 288
           IKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKV  L
Sbjct: 246 IKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWL 288

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 =  515 bits (1326), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 246/285 (86%), 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 LTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKV 285
           LTLEGIKQFFVAVE+EEWKFDTLCDLYDTLTITQAVIFCNTKRKV
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 =  514 bits (1323), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 256/291 (87%), Positives = 266/291 (91%), Gaps = 6/291 (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 RDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLL 288
           RDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKV  L
Sbjct: 238 RDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWL 288

Source: Medicago sativa

Species: Medicago sativa

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  513 bits (1320), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 246/265 (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 DTLCDLYDTLTITQAVIFCNTKRKV 285
           DTLCDLYDTLTITQAVIFCNTKRKV
Sbjct: 250 DTLCDLYDTLTITQAVIFCNTKRKV 274

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|317159567|gb|ADV04058.1| DEAD box RNA helicase RH2b [Hevea brasiliensis]

 Score =  512 bits (1319), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 247/269 (91%), Positives = 260/269 (96%)

Query: 17  DDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQ 76
           +D+K+ F TTEG+E ITSFD MGIK+DLLRGIY YGFEKP AIQQRAVMPIIKGRDVIAQ
Sbjct: 6   EDEKLAFGTTEGIEPITSFDEMGIKNDLLRGIYAYGFEKPPAIQQRAVMPIIKGRDVIAQ 65

Query: 77  AQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACV 136
           AQSGTG+TSMIALTVCQ VDTSSREVQALILSPTRELA QTEKVILAIGD+INIQAHAC+
Sbjct: 66  AQSGTGRTSMIALTVCQLVDTSSREVQALILSPTRELAAQTEKVILAIGDYINIQAHACI 125

Query: 137 GGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQI 196
           GGKSVGEDIRKLE GVHVVSGTPGRVCDMIKR+TLRTRAI+LLVLDESDEMLSRGFKDQI
Sbjct: 126 GGKSVGEDIRKLEFGVHVVSGTPGRVCDMIKRRTLRTRAIRLLVLDESDEMLSRGFKDQI 185

Query: 197 YDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVERE 256
           YDVYRYLPP+LQVVLISATLP+EILEMT+KFMTDPVKILVKRDELTLEGIKQFFVAVERE
Sbjct: 186 YDVYRYLPPELQVVLISATLPNEILEMTSKFMTDPVKILVKRDELTLEGIKQFFVAVERE 245

Query: 257 EWKFDTLCDLYDTLTITQAVIFCNTKRKV 285
           EWKFDTLCDLYDTLTITQAVIFCNTKRKV
Sbjct: 246 EWKFDTLCDLYDTLTITQAVIFCNTKRKV 274

Source: Hevea brasiliensis

Species: Hevea brasiliensis

Genus: Hevea

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  512 bits (1319), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 244/285 (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 LTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKV 285
           LTLEGIKQFFVAVE+EEWKFDTLCDLYDTLTITQAVIFCNTKRKV
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|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 =  512 bits (1318), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 244/285 (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 LTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKV 285
           LTLEGIKQFFVAVE+EEWKFDTLCDLYDTLTITQAVIFCNTKRKV
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	293
TAIR|locus:2091191	408	EIF4A-III "eukaryotic initiati	0.907	0.651	0.890	2.6e-125
FB|FBgn0037573	399	eIF4AIII "eIF4AIII" [Drosophil	0.897	0.659	0.771	4.8e-110
UNIPROTKB|Q5ZM36	412	EIF4A3 "Eukaryotic initiation	0.907	0.645	0.763	5.5e-109
UNIPROTKB|Q2NL22	411	EIF4A3 "Eukaryotic initiation	0.907	0.647	0.763	5.5e-109
UNIPROTKB|E2RDZ4	411	EIF4A3 "Uncharacterized protei	0.907	0.647	0.763	5.5e-109
UNIPROTKB|P38919	411	EIF4A3 "Eukaryotic initiation	0.907	0.647	0.763	5.5e-109
UNIPROTKB|A6M931	411	EIF4A3 "Eukaryotic initiation	0.907	0.647	0.763	5.5e-109
RGD|1591139	411	Eif4a3 "eukaryotic translation	0.907	0.647	0.763	5.5e-109
ZFIN|ZDB-GENE-040426-915	406	eif4a3 "eukaryotic translation	0.907	0.655	0.763	9e-109
WB|WBGene00018007	399	F33D11.10 [Caenorhabditis eleg	0.897	0.659	0.756	1e-107

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

 Score = 1231 (438.4 bits), Expect = 2.6e-125, P = 2.6e-125
 Identities = 237/266 (89%), Positives = 256/266 (96%)

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 FDTLCDLYDTLTITQAVIFCNTKRKV 285
             FDTLCDLYDTLTITQAVIFCNTKRKV
Sbjct:   262 FDTLCDLYDTLTITQAVIFCNTKRKV 287

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 = 1087 (387.7 bits), Expect = 4.8e-110, P = 4.8e-110
 Identities = 203/263 (77%), 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 LCDLYDTLTITQAVIFCNTKRKV 285
             LCDLYDTLTITQAVIFCNTKRKV
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 = 1077 (384.2 bits), Expect = 5.5e-109, P = 5.5e-109
 Identities = 203/266 (76%), 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 FDTLCDLYDTLTITQAVIFCNTKRKV 285
             FDTLCDLYDTLTITQAVIFCNTKRKV
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 = 1077 (384.2 bits), Expect = 5.5e-109, P = 5.5e-109
 Identities = 203/266 (76%), 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 FDTLCDLYDTLTITQAVIFCNTKRKV 285
             FDTLCDLYDTLTITQAVIFCNTKRKV
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 = 1077 (384.2 bits), Expect = 5.5e-109, P = 5.5e-109
 Identities = 203/266 (76%), 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 FDTLCDLYDTLTITQAVIFCNTKRKV 285
             FDTLCDLYDTLTITQAVIFCNTKRKV
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 = 1077 (384.2 bits), Expect = 5.5e-109, P = 5.5e-109
 Identities = 203/266 (76%), 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 FDTLCDLYDTLTITQAVIFCNTKRKV 285
             FDTLCDLYDTLTITQAVIFCNTKRKV
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 = 1077 (384.2 bits), Expect = 5.5e-109, P = 5.5e-109
 Identities = 203/266 (76%), 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 FDTLCDLYDTLTITQAVIFCNTKRKV 285
             FDTLCDLYDTLTITQAVIFCNTKRKV
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 = 1077 (384.2 bits), Expect = 5.5e-109, P = 5.5e-109
 Identities = 203/266 (76%), 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 FDTLCDLYDTLTITQAVIFCNTKRKV 285
             FDTLCDLYDTLTITQAVIFCNTKRKV
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 = 1075 (383.5 bits), Expect = 9.0e-109, P = 9.0e-109
 Identities = 203/266 (76%), 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 FDTLCDLYDTLTITQAVIFCNTKRKV 285
             FDTLCDLYDTLTITQAVIFCNTKRKV
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 = 1065 (380.0 bits), Expect = 1.0e-107, P = 1.0e-107
 Identities = 199/263 (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 LCDLYDTLTITQAVIFCNTKRKV 285
             L DLYDTLTITQAV+FCNT+RKV
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	0.7226	0.9351	0.6919	N/A	no
P0CQ72	FAL1_CRYNJ	3, ., 6, ., 4, ., 1, 3	0.7226	0.9351	0.6919	yes	no
Q4IAA0	FAL1_GIBZE	3, ., 6, ., 4, ., 1, 3	0.6630	0.9419	0.6882	yes	no
Q2NL22	IF4A3_BOVIN	3, ., 6, ., 4, ., 1, 3	0.7583	0.9180	0.6545	yes	no
Q5VNM3	RH2_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.8631	0.9658	0.7004	yes	no
B5FZY7	IF4A3_TAEGU	3, ., 6, ., 4, ., 1, 3	0.7583	0.9180	0.6560	yes	no
Q55D61	IF4A_DICDI	3, ., 6, ., 4, ., 1, 3	0.6666	0.8907	0.6444	yes	no
O42226	I4A3B_XENLA	3, ., 6, ., 4, ., 1, 3	0.7566	0.8976	0.6352	N/A	no
P41380	IF4A3_NICPL	3, ., 6, ., 4, ., 1, 3	0.8888	0.9215	0.6905	N/A	no
A6M931	IF4A3_PIG	3, ., 6, ., 4, ., 1, 3	0.7583	0.9180	0.6545	yes	no
Q6BT27	FAL1_DEBHA	3, ., 6, ., 4, ., 1, 3	0.6064	0.9385	0.6892	yes	no
Q2UAK1	FAL1_ASPOR	3, ., 6, ., 4, ., 1, 3	0.6824	0.9351	0.6884	yes	no
B5DG42	IF4A3_SALSA	3, ., 6, ., 4, ., 1, 3	0.7298	0.9726	0.7019	N/A	no
Q91VC3	IF4A3_MOUSE	3, ., 6, ., 4, ., 1, 3	0.7583	0.9180	0.6545	yes	no
A5AAE5	FAL1_ASPNC	3, ., 6, ., 4, ., 1, 3	0.6900	0.9249	0.6791	yes	no
Q5U526	I4A3A_XENLA	3, ., 6, ., 4, ., 1, 3	0.7583	0.9180	0.6481	N/A	no
Q7ZVA6	IF4A3_DANRE	3, ., 6, ., 4, ., 1, 3	0.7583	0.9180	0.6625	yes	no
P38919	IF4A3_HUMAN	3, ., 6, ., 4, ., 1, 3	0.7583	0.9180	0.6545	yes	no
Q5ZM36	IF4A3_CHICK	3, ., 6, ., 4, ., 1, 3	0.7583	0.9180	0.6529	yes	no
B7ZTW1	IF4A3_XENTR	3, ., 6, ., 4, ., 1, 3	0.7583	0.9180	0.6481	yes	no
Q4R3Q1	IF4A3_MACFA	3, ., 6, ., 4, ., 1, 3	0.7509	0.9180	0.6545	N/A	no
Q6C347	FAL1_YARLI	3, ., 6, ., 4, ., 1, 3	0.6642	0.9351	0.6901	yes	no
Q10I26	RH34_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.8561	0.9658	0.7004	yes	no
Q94A52	RH2_ARATH	3, ., 6, ., 4, ., 1, 3	0.8892	0.9249	0.6642	yes	no
Q4P184	FAL1_USTMA	3, ., 6, ., 4, ., 1, 3	0.7345	0.9385	0.6926	N/A	no
Q3B8Q2	IF4A3_RAT	3, ., 6, ., 4, ., 1, 3	0.7583	0.9180	0.6545	yes	no
Q10055	FAL1_SCHPO	3, ., 6, ., 4, ., 1, 3	0.6856	0.9010	0.6700	yes	no
Q5AUL4	FAL1_EMENI	3, ., 6, ., 4, ., 1, 3	0.6937	0.9249	0.6791	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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	293
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	1e-138
cd00268	203	cd00268, DEADc, DEAD-box helicases	2e-92
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	1e-85
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	5e-61
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	5e-50
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	6e-47
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	2e-45
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	5e-44
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	2e-34
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	3e-33
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	9e-33
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	1e-30
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	2e-30
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	2e-29
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	3e-28
COG1205	851	COG1205, COG1205, Distinct helicase family with a	7e-07

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

 Score =  395 bits (1017), Expect = e-138
 Identities = 170/262 (64%), Positives = 211/262 (80%)

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 LTITQAVIFCNTKRKVLLLVLQ 291
           LTITQA+I+CNT+RKV  L  +
Sbjct: 265 LTITQAIIYCNTRRKVDYLTKK 286

Length = 401

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

 Score =  272 bits (697), Expect = 2e-92
 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 =  265 bits (678), Expect = 1e-85
 Identities = 106/261 (40%), Positives = 155/261 (59%), Gaps = 5/261 (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 DTLTITQAVIFCNTKRKVLLL 288
                 + ++F  TKR V  L
Sbjct: 269 KDEDEGRVIVFVRTKRLVEEL 289

Length = 513

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

 Score =  200 bits (510), Expect = 5e-61
 Identities = 98/256 (38%), Positives = 142/256 (55%), Gaps = 7/256 (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 LTITQAVIFCNTKRKV 285
                 V+FCNTK++ 
Sbjct: 240 HQPESCVVFCNTKKEC 255

Length = 460

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

 Score =  162 bits (413), Expect = 5e-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 (395), Expect = 6e-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 =  158 bits (402), Expect = 2e-45
 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 =  158 bits (400), Expect = 5e-44
 Identities = 91/261 (34%), Positives = 135/261 (51%), Gaps = 8/261 (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 LYDTLTITQAVIFCNTKRKVL 286
             +      A+IF  TK   L
Sbjct: 239 FLEAEDFDAAIIFVRTKNATL 259

Length = 629

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

 Score =  130 bits (327), Expect = 2e-34
 Identities = 76/269 (28%), Positives = 135/269 (50%), Gaps = 11/269 (4%)

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 EWKFDTLCDLYDTLTITQAVIFCNTKRKV 285
           + K+  L +L       + ++F N K +V
Sbjct: 321 D-KYKLLYNLVTQNPWERVMVFANRKDEV 348

Length = 475

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

 Score =  126 bits (319), Expect = 3e-33
 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 =  117 bits (295), Expect = 9e-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 =  120 bits (302), Expect = 1e-30
 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 =  119 bits (299), Expect = 2e-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 =  115 bits (290), Expect = 2e-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 =  111 bits (281), Expect = 3e-28
 Identities = 77/265 (29%), Positives = 126/265 (47%), Gaps = 11/265 (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 DLYDTLTITQAVIFCNTKRKVLLLV 289
            L     +T++++F  T+ +V  L 
Sbjct: 238 HLLKQPEVTRSIVFVRTRERVHELA 262

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 = 7e-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	293
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	100.0
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	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
PLN00206	518	DEAD-box ATP-dependent RNA helicase; 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
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	100.0
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0326	459	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0346	569	consensus RNA helicase [RNA processing and modific	100.0
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	100.0
PTZ00424	401	helicase 45; Provisional	100.0
KOG0343	758	consensus RNA Helicase [RNA processing and modific	100.0
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	100.0
KOG0340	442	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0342	543	consensus ATP-dependent RNA helicase pitchoune [RN	100.0
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0327	397	consensus Translation initiation factor 4F, helica	100.0
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0334	997	consensus RNA helicase [RNA processing and modific	100.0
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	100.0
KOG0337	529	consensus ATP-dependent RNA helicase [RNA processi	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
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	100.0
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	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
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK09401	1176	reverse gyrase; Reviewed	99.98
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.97
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.97
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.97
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.97
COG1204	766	Superfamily II helicase [General function predicti	99.97
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.97
PRK14701	1638	reverse gyrase; Provisional	99.97
COG1205	851	Distinct helicase family with a unique C-terminal	99.97
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.96
COG1202	830	Superfamily II helicase, archaea-specific [General	99.96
PRK10689	1147	transcription-repair coupling factor; Provisional	99.96
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.96
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.96
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.95
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	99.95
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.95
PHA02653	675	RNA helicase NPH-II; Provisional	99.94
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.94
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.93
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.92
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.92
KOG0349	725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	99.92
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.92
PHA02558	501	uvsW UvsW helicase; Provisional	99.91
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.91
PRK13766	773	Hef nuclease; Provisional	99.9
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.89
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.89
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.89
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.88
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.88
PRK09694	878	helicase Cas3; Provisional	99.87
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.87
PRK05580	679	primosome assembly protein PriA; Validated	99.86
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.86
KOG0353	695	consensus ATP-dependent DNA helicase [General func	99.86
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.85
KOG0354	746	consensus DEAD-box like helicase [General function	99.85
KOG0351	941	consensus ATP-dependent DNA helicase [Replication,	99.84
KOG0947	1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	99.84
KOG0352	641	consensus ATP-dependent DNA helicase [Replication,	99.84
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.82
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.82
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.82
KOG0948	1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	99.81
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.8
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.79
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.79
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.78
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.76
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	99.75
KOG0950	1008	consensus DNA polymerase theta/eta, DEAD-box super	99.74
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.74
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.73
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.72
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	99.71
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.7
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.67
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.64
COG1198	730	PriA Primosomal protein N' (replication factor Y)	99.62
COG4096	875	HsdR Type I site-specific restriction-modification	99.6
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	99.58
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	99.57
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.54
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.53
KOG0949	1330	consensus Predicted helicase, DEAD-box superfamily	99.5
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.45
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.43
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.43
KOG0920	924	consensus ATP-dependent RNA helicase A [RNA proces	99.42
KOG0922	674	consensus DEAH-box RNA helicase [RNA processing an	99.42
PRK04914	956	ATP-dependent helicase HepA; Validated	99.4
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	99.38
PRK12326	764	preprotein translocase subunit SecA; Reviewed	99.34
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	99.31
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	99.31
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	99.3
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	99.23
KOG0925	699	consensus mRNA splicing factor ATP-dependent RNA h	99.22
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	99.2
KOG0926	1172	consensus DEAH-box RNA helicase [RNA processing an	99.19
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	99.18
PRK14873	665	primosome assembly protein PriA; Provisional	99.12
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	99.09
KOG1123	776	consensus RNA polymerase II transcription initiati	99.08
CHL00122	870	secA preprotein translocase subunit SecA; Validate	99.06
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	99.06
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	99.04
KOG0923	902	consensus mRNA splicing factor ATP-dependent RNA h	99.02
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	98.98
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	98.98
COG4889	1518	Predicted helicase [General function prediction on	98.94
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	98.94
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	98.91
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	98.82
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	98.81
KOG0385	971	consensus Chromatin remodeling complex WSTF-ISWI,	98.79
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.73
COG0610	962	Type I site-specific restriction-modification syst	98.73
PRK15483	986	type III restriction-modification system StyLTI en	98.72
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	98.65
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	98.63
KOG0389	941	consensus SNF2 family DNA-dependent ATPase [Chroma	98.62
KOG4150	1034	consensus Predicted ATP-dependent RNA helicase [RN	98.62
KOG0387	923	consensus Transcription-coupled repair protein CSB	98.58
PRK10536	262	hypothetical protein; Provisional	98.55
KOG0390	776	consensus DNA repair protein, SNF2 family [Replica	98.54
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	98.44
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	98.4
PF13872	303	AAA_34: P-loop containing NTP hydrolase pore-1	98.4
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	98.35
PRK10875	615	recD exonuclease V subunit alpha; Provisional	98.34
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	98.32
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	98.3
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	98.29
KOG0392	1549	consensus SNF2 family DNA-dependent ATPase domain-	98.27
PF13245	76	AAA_19: Part of AAA domain	98.19
KOG0384	1373	consensus Chromodomain-helicase DNA-binding protei	98.19
KOG1802	935	consensus RNA helicase nonsense mRNA reducing fact	98.19
TIGR00376	637	DNA helicase, putative. The gene product may repre	98.18
KOG1000	689	consensus Chromatin remodeling protein HARP/SMARCA	98.18
KOG1002	791	consensus Nucleotide excision repair protein RAD16	98.15
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	98.09
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	98.05
COG3587	985	Restriction endonuclease [Defense mechanisms]	98.04
PRK13889	988	conjugal transfer relaxase TraA; Provisional	98.04
KOG4439	901	consensus RNA polymerase II transcription terminat	98.03
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	97.96
KOG1803	649	consensus DNA helicase [Replication, recombination	97.95
KOG0391	1958	consensus SNF2 family DNA-dependent ATPase [Genera	97.93
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	97.91
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	97.9
KOG2340	698	consensus Uncharacterized conserved protein [Funct	97.85
PRK13826	1102	Dtr system oriT relaxase; Provisional	97.8
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	97.77
PRK04296	190	thymidine kinase; Provisional	97.73
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	97.7
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.7
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	97.7
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	97.65
KOG1132	945	consensus Helicase of the DEAD superfamily [Replic	97.63
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	97.62
smart00382	148	AAA ATPases associated with a variety of cellular	97.62
PRK08181	269	transposase; Validated	97.6
PRK06526	254	transposase; Provisional	97.53
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	97.42
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	97.4
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	97.39
KOG1805	1100	consensus DNA replication helicase [Replication, r	97.38
KOG0953	700	consensus Mitochondrial RNA helicase SUV3, DEAD-bo	97.38
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	97.36
PRK06921	266	hypothetical protein; Provisional	97.36
KOG0388	1185	consensus SNF2 family DNA-dependent ATPase [Replic	97.35
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.35
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.34
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	97.31
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	97.29
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	97.26
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	97.25
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	97.24
PRK05642	234	DNA replication initiation factor; Validated	97.24
PRK14974	336	cell division protein FtsY; Provisional	97.24
KOG0386	1157	consensus Chromatin remodeling complex SWI/SNF, co	97.23
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	97.23
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.22
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.21
PF03354	477	Terminase_1: Phage Terminase ; InterPro: IPR005021	97.19
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	97.15
PHA02533	534	17 large terminase protein; Provisional	97.14
PRK14088	440	dnaA chromosomal replication initiation protein; P	97.13
PRK07952	244	DNA replication protein DnaC; Validated	97.13
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	97.11
KOG1131	755	consensus RNA polymerase II transcription initiati	97.1
PRK00411	394	cdc6 cell division control protein 6; Reviewed	97.1
PRK14087	450	dnaA chromosomal replication initiation protein; P	97.1
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	97.09
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	97.09
PRK11054	684	helD DNA helicase IV; Provisional	97.07
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	97.06
COG1484	254	DnaC DNA replication protein [DNA replication, rec	97.06
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	97.05
PRK05707	328	DNA polymerase III subunit delta'; Validated	97.04
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	97.03
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	97.02
PRK06893	229	DNA replication initiation factor; Validated	96.99
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	96.99
PRK08116	268	hypothetical protein; Validated	96.98
PRK08727	233	hypothetical protein; Validated	96.98
PRK12377	248	putative replication protein; Provisional	96.97
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	96.97
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	96.97
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	96.96
PRK13833	323	conjugal transfer protein TrbB; Provisional	96.96
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	96.95
CHL00181	287	cbbX CbbX; Provisional	96.95
PRK06835	329	DNA replication protein DnaC; Validated	96.92
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	96.91
PF05127	177	Helicase_RecD: Helicase; InterPro: IPR007807 This	96.91
PF13173	128	AAA_14: AAA domain	96.89
PRK08084	235	DNA replication initiation factor; Provisional	96.85
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	96.85
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	96.84
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	96.83
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	96.82
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	96.81
PRK12422	445	chromosomal replication initiation protein; Provis	96.79
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	96.79
PRK12402	337	replication factor C small subunit 2; Reviewed	96.77
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	96.76
PF00004	132	AAA: ATPase family associated with various cellula	96.74
PLN03025	319	replication factor C subunit; Provisional	96.74
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	96.73
PRK14086	617	dnaA chromosomal replication initiation protein; P	96.72
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	96.7
COG1435	201	Tdk Thymidine kinase [Nucleotide transport and met	96.69
COG4626	546	Phage terminase-like protein, large subunit [Gener	96.68
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	96.67
COG1444	758	Predicted P-loop ATPase fused to an acetyltransfer	96.67
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	96.66
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	96.65
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	96.65
PHA03333	752	putative ATPase subunit of terminase; Provisional	96.64
PRK08903	227	DnaA regulatory inactivator Hda; Validated	96.63
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	96.62
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	96.61
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	96.61
PHA03368	738	DNA packaging terminase subunit 1; Provisional	96.6
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	96.59
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	96.57
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	96.55
PRK00771	437	signal recognition particle protein Srp54; Provisi	96.55
PRK05973	237	replicative DNA helicase; Provisional	96.55
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	96.54
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	96.54
PHA02544	316	44 clamp loader, small subunit; Provisional	96.54
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	96.52
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	96.5
PRK08533	230	flagellar accessory protein FlaH; Reviewed	96.47
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	96.47
PF05729	166	NACHT: NACHT domain	96.44
PTZ00293	211	thymidine kinase; Provisional	96.44
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	96.43
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	96.42
PRK08769	319	DNA polymerase III subunit delta'; Validated	96.42
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	96.4
PRK05298	652	excinuclease ABC subunit B; Provisional	96.36
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	96.34
KOG1015	1567	consensus Transcription regulator XNP/ATRX, DEAD-b	96.33
KOG0298	1394	consensus DEAD box-containing helicase-like transc	96.33
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	96.32
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	96.32
PTZ00112	1164	origin recognition complex 1 protein; Provisional	96.31
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	96.29
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	96.27
PRK09183	259	transposase/IS protein; Provisional	96.27
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	96.25
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	96.23
PRK06871	325	DNA polymerase III subunit delta'; Validated	96.23
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	96.22
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	96.19
PRK08699	325	DNA polymerase III subunit delta'; Validated	96.18
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	96.18
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	96.16
PHA00729	226	NTP-binding motif containing protein	96.14
COG2256	436	MGS1 ATPase related to the helicase subunit of the	96.1
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	96.09
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	96.09
COG3973	747	Superfamily I DNA and RNA helicases [General funct	96.09
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	96.08
PHA03372	668	DNA packaging terminase subunit 1; Provisional	96.07
PRK00440	319	rfc replication factor C small subunit; Reviewed	96.06
PRK06964	342	DNA polymerase III subunit delta'; Validated	96.06
PF03237	384	Terminase_6: Terminase-like family; InterPro: IPR0	96.04
COG3421	812	Uncharacterized protein conserved in bacteria [Fun	96.03
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	96.02
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.02
PRK07993	334	DNA polymerase III subunit delta'; Validated	96.01
PRK13851	344	type IV secretion system protein VirB11; Provision	95.99
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	95.98
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	95.98
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	95.97
PRK13342	413	recombination factor protein RarA; Reviewed	95.97
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	95.96
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	95.96
PRK11823	446	DNA repair protein RadA; Provisional	95.95
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	95.93
TIGR00064	272	ftsY signal recognition particle-docking protein F	95.93
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	95.92
PRK09112	351	DNA polymerase III subunit delta'; Validated	95.92
PRK04195	482	replication factor C large subunit; Provisional	95.92
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	95.89
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	95.88
PRK08939	306	primosomal protein DnaI; Reviewed	95.87
KOG1001	674	consensus Helicase-like transcription factor HLTF/	95.87
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	95.86
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	95.83
PRK06904	472	replicative DNA helicase; Validated	95.81
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	95.8
COG3972	660	Superfamily I DNA and RNA helicases [General funct	95.8
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	95.78
PRK13341	725	recombination factor protein RarA/unknown domain f	95.75
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	95.68
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	95.67
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	95.66
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	95.66
COG0593	408	DnaA ATPase involved in DNA replication initiation	95.64
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	95.61
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	95.6
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	95.59
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	95.55
PRK06620	214	hypothetical protein; Validated	95.55
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	95.53
PRK07471	365	DNA polymerase III subunit delta'; Validated	95.5
PRK04328	249	hypothetical protein; Provisional	95.48
PRK06090	319	DNA polymerase III subunit delta'; Validated	95.44
TIGR00767	415	rho transcription termination factor Rho. Members	95.43
PRK04841	903	transcriptional regulator MalT; Provisional	95.42
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	95.41
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	95.36
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	95.33
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	95.32
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	95.32
PF02572	172	CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase	95.29
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	95.27
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	95.27
PRK06067	234	flagellar accessory protein FlaH; Validated	95.26
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	95.25
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	95.24
PRK13764	602	ATPase; Provisional	95.21
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	95.18
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	95.16
KOG0058	716	consensus Peptide exporter, ABC superfamily [Intra	95.12
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	95.12
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	95.12
KOG1133	821	consensus Helicase of the DEAD superfamily [Replic	95.06
cd03115	173	SRP The signal recognition particle (SRP) mediates	95.05
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	95.05
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	95.0
PRK09354	349	recA recombinase A; Provisional	94.98
PRK05748	448	replicative DNA helicase; Provisional	94.96
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	94.96
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	94.95
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	94.91
TIGR02237	209	recomb_radB DNA repair and recombination protein R	94.87
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	94.82
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	94.81
COG1132	567	MdlB ABC-type multidrug transport system, ATPase a	94.81
PRK09376	416	rho transcription termination factor Rho; Provisio	94.78
PF00265	176	TK: Thymidine kinase; InterPro: IPR001267 Thymidin	94.72
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	94.71
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	94.68
cd00983	325	recA RecA is a bacterial enzyme which has roles in	94.67
PRK07940	394	DNA polymerase III subunit delta'; Validated	94.66
TIGR00959	428	ffh signal recognition particle protein. This mode	94.59
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	94.57
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	94.56
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	94.54
PRK10867	433	signal recognition particle protein; Provisional	94.53
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	94.48
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	94.47
PF12846	304	AAA_10: AAA-like domain	94.45
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	94.43
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	94.42
PRK09087	226	hypothetical protein; Validated	94.42
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	94.41
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	94.28
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	94.26
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	94.19
COG2109	198	BtuR ATP:corrinoid adenosyltransferase [Coenzyme m	94.19
PRK08058	329	DNA polymerase III subunit delta'; Validated	94.19
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	94.14
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	94.14
PRK08506	472	replicative DNA helicase; Provisional	94.13
PRK08840	464	replicative DNA helicase; Provisional	94.12
PRK10865	857	protein disaggregation chaperone; Provisional	94.09
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	94.06
PRK08006	471	replicative DNA helicase; Provisional	94.0
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	93.96
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	93.96
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	93.95
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	93.95
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	93.95
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	93.94
PRK07004	460	replicative DNA helicase; Provisional	93.93
cd01128	249	rho_factor Transcription termination factor rho is	93.91
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	93.88
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	93.87
KOG1016	1387	consensus Predicted DNA helicase, DEAD-box superfa	93.87
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	93.86
COG0552	340	FtsY Signal recognition particle GTPase [Intracell	93.83
PRK12608	380	transcription termination factor Rho; Provisional	93.8
PRK08760	476	replicative DNA helicase; Provisional	93.78
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	93.78
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	93.77
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	93.75
PRK10436	462	hypothetical protein; Provisional	93.75
PRK06321	472	replicative DNA helicase; Provisional	93.71
TIGR02533	486	type_II_gspE general secretory pathway protein E.	93.7
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	93.69
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	93.69
PRK07414	178	cob(I)yrinic acid a,c-diamide adenosyltransferase;	93.65
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	93.65
TIGR00665	434	DnaB replicative DNA helicase. This model describe	93.6
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	93.57
KOG2028	554	consensus ATPase related to the helicase subunit o	93.57
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	93.55
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	93.39
PRK13695	174	putative NTPase; Provisional	93.29
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	93.28
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	93.23
COG1702	348	PhoH Phosphate starvation-inducible protein PhoH,	93.21
PRK09165	497	replicative DNA helicase; Provisional	93.18
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	93.14
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	93.08
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	93.06
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	93.04
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	92.99
COG1074	1139	RecB ATP-dependent exoDNAse (exonuclease V) beta s	92.96
PRK10689	1147	transcription-repair coupling factor; Provisional	92.95
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	92.93
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	92.92
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	92.88
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	92.87
TIGR03375	694	type_I_sec_LssB type I secretion system ATPase, Ls	92.81
COG1221	403	PspF Transcriptional regulators containing an AAA-	92.75
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	92.72
TIGR03743	634	SXT_TraD conjugative coupling factor TraD, SXT/TOL	92.71
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	92.66
KOG1806	1320	consensus DEAD box containing helicases [Replicati	92.66
TIGR02203	571	MsbA_lipidA lipid A export permease/ATP-binding pr	92.64
PRK07399	314	DNA polymerase III subunit delta'; Validated	92.64
cd03239	178	ABC_SMC_head The structural maintenance of chromos	92.64
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	92.62
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	92.59
PRK05595	444	replicative DNA helicase; Provisional	92.58
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	92.57
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	92.54
KOG1513	1300	consensus Nuclear helicase MOP-3/SNO (DEAD-box sup	92.54
TIGR02204	576	MsbA_rel ABC transporter, permease/ATP-binding pro	92.53
PF13555	62	AAA_29: P-loop containing region of AAA domain	92.5
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	92.49
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	92.44
PHA02535	581	P terminase ATPase subunit; Provisional	92.43
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	92.41
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	92.34
PRK10416	318	signal recognition particle-docking protein FtsY;	92.34
PF14516	331	AAA_35: AAA-like domain	92.31
PF06733	174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	92.29
PRK13897	606	type IV secretion system component VirD4; Provisio	92.28
cd03289	275	ABCC_CFTR2 The CFTR subfamily domain 2. The cystic	92.21
PRK11176	582	lipid transporter ATP-binding/permease protein; Pr	92.2
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	92.19
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	92.17
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	92.14
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	92.12

>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=3.5e-51  Score=329.04  Aligned_cols=283  Identities=74%  Similarity=1.131  Sum_probs=271.9

Q ss_pred             hCCCCCCCCCcceeecccCCccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHH
Q 022724           10 RGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIAL   89 (293)
Q Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~   89 (293)
                      +..+....++...+++++...++++|++++++++++++++..||+.|+.+|+.|++.+++|+|++..+.+|+|||.+|.+
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            44556677889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcC
Q 022724           90 TVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK  169 (293)
Q Consensus        90 ~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~  169 (293)
                      .+++.+.-..+..+++|+.|||+|+.|+.+.+..++...++++..+.||.+..++++++..+.+++.+||++++.+++++
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            99999888878889999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEE
Q 022724          170 TLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQF  249 (293)
Q Consensus       170 ~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~  249 (293)
                      .+.-+.++++|+||+|.|++.+|..++-.+.+++++..|++++|||+|.++.++..+++.+|..+.+.+.+.+.+++.|+
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             EEEecCcccHHHHHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          250 FVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       250 ~~~~~~~~~k~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ++.++.++||...|.++++.....+++|||||+..+.++.+.+
T Consensus       244 ~v~ve~EewKfdtLcdLYd~LtItQavIFcnTk~kVdwLtekm  286 (400)
T KOG0328|consen  244 FVAVEKEEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKM  286 (400)
T ss_pred             eeeechhhhhHhHHHHHhhhhehheEEEEecccchhhHHHHHH
Confidence            9999999999999999999999999999999999999988754

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

Probab=100.00  E-value=9.6e-50  Score=333.29  Aligned_cols=263  Identities=31%  Similarity=0.512  Sum_probs=251.5

Q ss_pred             CccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEc
Q 022724           29 VEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (293)
Q Consensus        29 ~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~  108 (293)
                      .+...+|.++++.+++.+++++.||..||++|++++|..+.|+|++..|.||||||.+|++|+++++...+..++++|++
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            44567899999999999999999999999999999999999999999999999999999999999999999899999999


Q ss_pred             CCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHh-cCCCCCCCccEEEecchhhh
Q 022724          109 PTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIK-RKTLRTRAIKLLVLDESDEM  187 (293)
Q Consensus       109 P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~-~~~~~~~~l~~iViDE~h~~  187 (293)
                      |+|||+.|+.+.++.++..+|+++..+.||.+...+...+.+.++|+|+||++|...+. .+.+.+..++++|+||||.+
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            99999999999999999999999999999999999999999999999999999999888 57899999999999999999


Q ss_pred             hccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHH
Q 022724          188 LSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLY  267 (293)
Q Consensus       188 ~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~  267 (293)
                      ++..|...+..+++.++...|.+++|||++..+.++....+.+|..+.+.........+.|.|.+++... |...|.+++
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            9999999999999999999999999999999999999999999999999999999999999999999887 999999999


Q ss_pred             hhCCCCcEEEEcccchhHHHHHhhC
Q 022724          268 DTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       268 ~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      +...++++||||++...++.++-.|
T Consensus       296 ~e~~g~s~iVF~~t~~tt~~la~~L  320 (476)
T KOG0330|consen  296 NELAGNSVIVFCNTCNTTRFLALLL  320 (476)
T ss_pred             HhhcCCcEEEEEeccchHHHHHHHH
Confidence            9999999999999999999887554

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

Probab=100.00  E-value=7.1e-49  Score=346.75  Aligned_cols=258  Identities=31%  Similarity=0.568  Sum_probs=239.9

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhcc------CCCceeEEEE
Q 022724           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT------SSREVQALIL  107 (293)
Q Consensus        34 ~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~------~~~~~~~lil  107 (293)
                      .|++++++++...+++..||+.|+|+|.+.||.+++|+|++..+.||||||++|++|++.++..      ...+|++|||
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      4567999999


Q ss_pred             cCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhh
Q 022724          108 SPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (293)
Q Consensus       108 ~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~  187 (293)
                      +||||||.|+...+.++.....++..+++||.+...|.+.+.++++|+|+||+++.+++..+..+++++.++|+||||.|
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 022724          188 LSRGFKDQIYDVYRYL-PPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDE--LTLEGIKQFFVAVEREEWKFDTLC  264 (293)
Q Consensus       188 ~~~~~~~~~~~i~~~l-~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~i~~~~~~~~~~~~k~~~l~  264 (293)
                      ++.+|..+++.++..+ ++..|++++|||||..++.++..++.+|..+.+...+  ....++.|....++... |...+.
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 5566899999999999999999999999999988653  45678999999999555 888888


Q ss_pred             HHHhhC---CCCcEEEEcccchhHHHHHhhC
Q 022724          265 DLYDTL---TITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       265 ~l~~~~---~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      .++...   +.+|+||||+|++.|++++..|
T Consensus       331 ~lL~~~~~~~~~KvIIFc~tkr~~~~l~~~l  361 (519)
T KOG0331|consen  331 KLLEDISSDSEGKVIIFCETKRTCDELARNL  361 (519)
T ss_pred             HHHHHHhccCCCcEEEEecchhhHHHHHHHH
Confidence            888765   3569999999999999998875

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

Probab=100.00  E-value=3.8e-47  Score=347.28  Aligned_cols=260  Identities=40%  Similarity=0.652  Sum_probs=243.2

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhcc--CCCceeEEEEcCC
Q 022724           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT--SSREVQALILSPT  110 (293)
Q Consensus        33 ~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~--~~~~~~~lil~P~  110 (293)
                      ..|+++++++++++++.+.||..|||+|.+++|.++.|+|+++.++||+|||++|++|+++.+..  ......+||++||
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            78999999999999999999999999999999999999999999999999999999999999874  3222229999999


Q ss_pred             HHHHHHHHHHHHHhhccC-CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhc
Q 022724          111 RELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (293)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~  189 (293)
                      ||||.|+++.+..+.... ++++..++||.+...+...+..+++|+|+||+++++++.++.++++++.++|+||||.|++
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 7999999999999999988888899999999999999999999999999999999999999


Q ss_pred             cccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcc--cCCCceEEEEEecCcccHHHHHHHHH
Q 022724          190 RGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDEL--TLEGIKQFFVAVEREEWKFDTLCDLY  267 (293)
Q Consensus       190 ~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~i~~~~~~~~~~~~k~~~l~~l~  267 (293)
                      .||.+.+..+++.++...|++++|||+|+.+..+.+.++.+|..+.+.....  ....+.|+++.++....|...|..++
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            9999999999999999999999999999999999999999999888885555  77899999999998767999999999


Q ss_pred             hhCCCCcEEEEcccchhHHHHHhhC
Q 022724          268 DTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       268 ~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      +.....++||||+|++.|+.++..|
T Consensus       269 ~~~~~~~~IVF~~tk~~~~~l~~~l  293 (513)
T COG0513         269 KDEDEGRVIVFVRTKRLVEELAESL  293 (513)
T ss_pred             hcCCCCeEEEEeCcHHHHHHHHHHH
Confidence            9888889999999999999998765

>PTZ00110 helicase; Provisional

Probab=100.00  E-value=5.3e-46  Score=342.67  Aligned_cols=268  Identities=29%  Similarity=0.440  Sum_probs=238.2

Q ss_pred             ecccCCccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccC-----
Q 022724           24 ETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-----   98 (293)
Q Consensus        24 ~~~~~~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~-----   98 (293)
                      +....|.++.+|+++++++++++++.++||..|||+|.++||.+++|+|+++++|||||||++|++|++..+...     
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            456678889999999999999999999999999999999999999999999999999999999999998876542     


Q ss_pred             CCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccE
Q 022724           99 SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKL  178 (293)
Q Consensus        99 ~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~  178 (293)
                      ..++++|||+||++||.|+.+.++++....++++..++|+.+...+...+.++++|+|+||++|.+++..+...++++++
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            24678999999999999999999999988899999999999888888888889999999999999999998888999999


Q ss_pred             EEecchhhhhccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCC-CCEEEEecCCc-ccCCCceEEEEEecCc
Q 022724          179 LVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMT-DPVKILVKRDE-LTLEGIKQFFVAVERE  256 (293)
Q Consensus       179 iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~-~~~~~~~~~~~-~~~~~i~~~~~~~~~~  256 (293)
                      |||||||++++.+|...+..++..+++..|++++|||++..+..+...++. ++..+.+...+ ....++.+.+..++..
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            999999999999999999999999999999999999999999999888875 57777765544 2345677777777665


Q ss_pred             ccHHHHHHHHHhhC--CCCcEEEEcccchhHHHHHhhC
Q 022724          257 EWKFDTLCDLYDTL--TITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       257 ~~k~~~l~~l~~~~--~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      . |...+..+++..  ...++||||++++.|+.++..|
T Consensus       361 ~-k~~~L~~ll~~~~~~~~k~LIF~~t~~~a~~l~~~L  397 (545)
T PTZ00110        361 E-KRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKEL  397 (545)
T ss_pred             h-HHHHHHHHHHHhcccCCeEEEEecChHHHHHHHHHH
Confidence            5 888888887654  4569999999999999998876

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=2e-45  Score=331.51  Aligned_cols=261  Identities=30%  Similarity=0.425  Sum_probs=234.0

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccC-------CCcee
Q 022724           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-------SREVQ  103 (293)
Q Consensus        31 ~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~-------~~~~~  103 (293)
                      ...+|+++++++++++++.++||..|+|+|+++||.+++|+|++++||||||||++|++|+++.+...       ..+++
T Consensus         6 ~~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~~~   85 (423)
T PRK04837          6 TEQKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPR   85 (423)
T ss_pred             CCCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhcccccccccCCce
Confidence            34689999999999999999999999999999999999999999999999999999999999887542       23578


Q ss_pred             EEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecc
Q 022724          104 ALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDE  183 (293)
Q Consensus       104 ~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE  183 (293)
                      +|||+|+++||.|+.+.+..+....++++..++|+.+...+...+.++++|+|+||+++.+++.++.+.+++++++||||
T Consensus        86 ~lil~PtreLa~Qi~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~TP~~l~~~l~~~~~~l~~v~~lViDE  165 (423)
T PRK04837         86 ALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDE  165 (423)
T ss_pred             EEEECCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccccEEEEec
Confidence            99999999999999999999999999999999999988888888888899999999999999999889999999999999


Q ss_pred             hhhhhccccHHHHHHHHhhCCC--CccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHH
Q 022724          184 SDEMLSRGFKDQIYDVYRYLPP--DLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFD  261 (293)
Q Consensus       184 ~h~~~~~~~~~~~~~i~~~l~~--~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~  261 (293)
                      ||++++.+|...+..++..++.  ..+.+++|||++..+..+....+.+|..+.+.........+.+.+....... |..
T Consensus       166 ad~l~~~~f~~~i~~i~~~~~~~~~~~~~l~SAT~~~~~~~~~~~~~~~p~~i~v~~~~~~~~~i~~~~~~~~~~~-k~~  244 (423)
T PRK04837        166 ADRMFDLGFIKDIRWLFRRMPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTGHRIKEELFYPSNEE-KMR  244 (423)
T ss_pred             HHHHhhcccHHHHHHHHHhCCCccceeEEEEeccCCHHHHHHHHHHCCCCEEEEEcCCCcCCCceeEEEEeCCHHH-HHH
Confidence            9999999999999999999874  4668999999999999999889999988887766655666777766655444 888


Q ss_pred             HHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          262 TLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       262 ~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      .+..+++.....++||||++++.|+.+++.|
T Consensus       245 ~l~~ll~~~~~~~~lVF~~t~~~~~~l~~~L  275 (423)
T PRK04837        245 LLQTLIEEEWPDRAIIFANTKHRCEEIWGHL  275 (423)
T ss_pred             HHHHHHHhcCCCeEEEEECCHHHHHHHHHHH
Confidence            8888888777789999999999999998876

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=100.00  E-value=2.4e-45  Score=334.33  Aligned_cols=259  Identities=38%  Similarity=0.616  Sum_probs=238.0

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCH
Q 022724           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (293)
Q Consensus        32 ~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~  111 (293)
                      ..+|+++++++.+.+++.++||..|+|+|.++||.+++|+|++++||||+|||++|++|+++.+......++++|++||+
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            35899999999999999999999999999999999999999999999999999999999999997766667999999999


Q ss_pred             HHHHHHHHHHHHhhccC-CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcc
Q 022724          112 ELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (293)
Q Consensus       112 ~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~  190 (293)
                      +|+.|+.+.++.+.... ++++..++|+.+...+...+..+++|+|+||+++..++.++.+.++++++||+||+|.+++.
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            99999999999887654 78899999999998888888889999999999999999998888999999999999999999


Q ss_pred             ccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHhhC
Q 022724          191 GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL  270 (293)
Q Consensus       191 ~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~  270 (293)
                      +|...+..++..++...|++++|||+++.+..+...++.+|..+.+.... ....+.+.+..++... |...+..++...
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            99999999999999999999999999999999999999999988876544 3455888888888776 999999999888


Q ss_pred             CCCcEEEEcccchhHHHHHhhC
Q 022724          271 TITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       271 ~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      .+.++||||++++.|+.+++.|
T Consensus       241 ~~~~~lVF~~t~~~~~~l~~~L  262 (460)
T PRK11776        241 QPESCVVFCNTKKECQEVADAL  262 (460)
T ss_pred             CCCceEEEECCHHHHHHHHHHH
Confidence            8889999999999999999876

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

Probab=100.00  E-value=5.5e-45  Score=334.86  Aligned_cols=269  Identities=29%  Similarity=0.488  Sum_probs=238.5

Q ss_pred             eeecccCCccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhcc----
Q 022724           22 VFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT----   97 (293)
Q Consensus        22 ~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~----   97 (293)
                      .+.+...|.++.+|+++++++.++++|.+.||..|||+|.++||.+++|+|+++++|||||||++|++|++..+..    
T Consensus       110 ~~~g~~~p~pi~~f~~~~l~~~l~~~L~~~g~~~ptpiQ~~aip~il~g~dviv~ApTGSGKTlayllPil~~l~~~~~~  189 (518)
T PLN00206        110 HVKGEAVPPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSG  189 (518)
T ss_pred             EecCCCCCchhcCHHhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEecCCCCccHHHHHHHHHHHHhhccc
Confidence            3456667889999999999999999999999999999999999999999999999999999999999999987642    


Q ss_pred             ---CCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCC
Q 022724           98 ---SSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTR  174 (293)
Q Consensus        98 ---~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~  174 (293)
                         ...++++||++||++|+.|+.+.++.+....++++..+.||.....+...+..+++|+|+||+++.+++..+...++
T Consensus       190 ~~~~~~~~~aLIL~PTreLa~Qi~~~~~~l~~~~~~~~~~~~gG~~~~~q~~~l~~~~~IiV~TPgrL~~~l~~~~~~l~  269 (518)
T PLN00206        190 HPSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELD  269 (518)
T ss_pred             cccccCCceEEEEeCCHHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHHHhcCCCCEEEECHHHHHHHHHcCCccch
Confidence               22567999999999999999999999998888999999999988888888888899999999999999998888999


Q ss_pred             CccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEec
Q 022724          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVE  254 (293)
Q Consensus       175 ~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~  254 (293)
                      ++++|||||||.|++++|...+..++..++ ..|++++|||+++.+..+...++.++..+.+.........+.+.+..+.
T Consensus       270 ~v~~lViDEad~ml~~gf~~~i~~i~~~l~-~~q~l~~SATl~~~v~~l~~~~~~~~~~i~~~~~~~~~~~v~q~~~~~~  348 (518)
T PLN00206        270 NVSVLVLDEVDCMLERGFRDQVMQIFQALS-QPQVLLFSATVSPEVEKFASSLAKDIILISIGNPNRPNKAVKQLAIWVE  348 (518)
T ss_pred             heeEEEeecHHHHhhcchHHHHHHHHHhCC-CCcEEEEEeeCCHHHHHHHHHhCCCCEEEEeCCCCCCCcceeEEEEecc
Confidence            999999999999999999999999998885 6899999999999999999999999988888766655566788888777


Q ss_pred             CcccHHHHHHHHHhhCC--CCcEEEEcccchhHHHHHhhC
Q 022724          255 REEWKFDTLCDLYDTLT--ITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       255 ~~~~k~~~l~~l~~~~~--~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ... |...+..++....  ..++||||+++..|+.+++.|
T Consensus       349 ~~~-k~~~l~~~l~~~~~~~~~~iVFv~s~~~a~~l~~~L  387 (518)
T PLN00206        349 TKQ-KKQKLFDILKSKQHFKPPAVVFVSSRLGADLLANAI  387 (518)
T ss_pred             chh-HHHHHHHHHHhhcccCCCEEEEcCCchhHHHHHHHH
Confidence            666 6677777776433  358999999999999998765

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=100.00  E-value=5.6e-45  Score=330.83  Aligned_cols=258  Identities=35%  Similarity=0.573  Sum_probs=235.0

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCC------CceeEEEE
Q 022724           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS------REVQALIL  107 (293)
Q Consensus        34 ~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~------~~~~~lil  107 (293)
                      +|++++|++++.+++.++||..||++|.++||.+++|+|+++++|||+|||++|++|+++.+....      ..+++|||
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            699999999999999999999999999999999999999999999999999999999999885432      23589999


Q ss_pred             cCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhh
Q 022724          108 SPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (293)
Q Consensus       108 ~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~  187 (293)
                      +||++|+.|+.+.++.+....++++..++|+.+...+...+..+++|+|+||++|.+++....+.++++++|||||+|++
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            99999999999999999999999999999999988888888888999999999999999888888999999999999999


Q ss_pred             hccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHH
Q 022724          188 LSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLY  267 (293)
Q Consensus       188 ~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~  267 (293)
                      ++++|...+..++..++...|++++|||+++.+..+...++.+|..+.+.........+.+.+..++... +...+..++
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            9999999999999999999999999999999999999999999988887766666677888888777665 778888888


Q ss_pred             hhCCCCcEEEEcccchhHHHHHhhC
Q 022724          268 DTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       268 ~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ......++||||++++.|+.+++.|
T Consensus       241 ~~~~~~~~lVF~~t~~~~~~l~~~L  265 (456)
T PRK10590        241 GKGNWQQVLVFTRTKHGANHLAEQL  265 (456)
T ss_pred             HcCCCCcEEEEcCcHHHHHHHHHHH
Confidence            8777789999999999999998875

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=100.00  E-value=6.4e-45  Score=338.59  Aligned_cols=260  Identities=33%  Similarity=0.546  Sum_probs=238.9

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCH
Q 022724           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (293)
Q Consensus        32 ~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~  111 (293)
                      ..+|++++|++.++++|.++||..|+|+|.++||.+++|+|+++.||||+|||++|.+|+++.+.....++++||++||+
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            45799999999999999999999999999999999999999999999999999999999999987766678999999999


Q ss_pred             HHHHHHHHHHHHhhccC-CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcc
Q 022724          112 ELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (293)
Q Consensus       112 ~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~  190 (293)
                      +|+.|+.+.+..+.... ++.+..++|+.+...+.+.+..+++|+|+||+++.+++.++.+.++++++||+||||.+++.
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            99999999999887665 78999999999988888888888999999999999999998899999999999999999999


Q ss_pred             ccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHhhC
Q 022724          191 GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL  270 (293)
Q Consensus       191 ~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~  270 (293)
                      +|...+..++..++...|++++|||+|+.+..+...++.+|..+.+.........+.+.+..+.... |...+..++...
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            9999999999999999999999999999999999999999998888766666677888888777665 888898988887


Q ss_pred             CCCcEEEEcccchhHHHHHhhC
Q 022724          271 TITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       271 ~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ...++||||+|+..|+.++..|
T Consensus       244 ~~~~~IVF~~tk~~a~~l~~~L  265 (629)
T PRK11634        244 DFDAAIIFVRTKNATLEVAEAL  265 (629)
T ss_pred             CCCCEEEEeccHHHHHHHHHHH
Confidence            7789999999999999998876

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=1.1e-44  Score=335.00  Aligned_cols=259  Identities=32%  Similarity=0.465  Sum_probs=232.4

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccC-------CCceeEE
Q 022724           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-------SREVQAL  105 (293)
Q Consensus        33 ~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~-------~~~~~~l  105 (293)
                      .+|+++++++.++++|.++||..|||+|.++||.+++|+|+++++|||+|||++|++|+++.+...       ..++++|
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            479999999999999999999999999999999999999999999999999999999999987542       1247999


Q ss_pred             EEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcC-CCCCCCccEEEecch
Q 022724          106 ILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK-TLRTRAIKLLVLDES  184 (293)
Q Consensus       106 il~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~-~~~~~~l~~iViDE~  184 (293)
                      ||+|+++|+.|+++.+..+....++++..++|+.....+...+.++++|+|+||++|.+++.+. .+.+..+++|||||+
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            9999999999999999999999999999999999988888878888999999999999988774 567889999999999


Q ss_pred             hhhhccccHHHHHHHHhhCCC--CccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHH
Q 022724          185 DEMLSRGFKDQIYDVYRYLPP--DLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDT  262 (293)
Q Consensus       185 h~~~~~~~~~~~~~i~~~l~~--~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~  262 (293)
                      |++++.+|...+..+++.++.  ..|++++|||+++.+..+...++.+|..+.+.........+.+.+..+.... |...
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  6899999999999999999999988888777665555667788877766555 8888


Q ss_pred             HHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          263 LCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       263 l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      +..++....+.++||||||++.|+.+++.|
T Consensus       248 L~~ll~~~~~~k~LVF~nt~~~ae~l~~~L  277 (572)
T PRK04537        248 LLGLLSRSEGARTMVFVNTKAFVERVARTL  277 (572)
T ss_pred             HHHHHhcccCCcEEEEeCCHHHHHHHHHHH
Confidence            888888877789999999999999999876

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=100.00  E-value=8.8e-44  Score=322.05  Aligned_cols=259  Identities=29%  Similarity=0.473  Sum_probs=235.8

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccC----CCceeEEEEcC
Q 022724           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS----SREVQALILSP  109 (293)
Q Consensus        34 ~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~----~~~~~~lil~P  109 (293)
                      +|+++++++.+++.+.++||..|+++|.++|+.+++|+|+++++|||+|||++|++|+++.+...    ...+++||++|
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            69999999999999999999999999999999999999999999999999999999999887532    23468999999


Q ss_pred             CHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhc
Q 022724          110 TRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (293)
Q Consensus       110 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~  189 (293)
                      +++|+.|+.+.+..+....++++..++|+.....+...+.++++|+|+||++|.+++..+.+++.++++|||||+|.+++
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            99999999999999999999999999999988888777888899999999999999999889999999999999999999


Q ss_pred             cccHHHHHHHHhhCCCCccEEEEEeecCh-hHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHh
Q 022724          190 RGFKDQIYDVYRYLPPDLQVVLISATLPH-EILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYD  268 (293)
Q Consensus       190 ~~~~~~~~~i~~~l~~~~q~v~~SAt~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~  268 (293)
                      ++|...+..+...++...|++++|||++. .+..+...++.+|..+...........+.+.+..++....|...+..+++
T Consensus       162 ~~~~~~~~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~  241 (434)
T PRK11192        162 MGFAQDIETIAAETRWRKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRERKKIHQWYYRADDLEHKTALLCHLLK  241 (434)
T ss_pred             CCcHHHHHHHHHhCccccEEEEEEeecCHHHHHHHHHHHccCCEEEEecCCcccccCceEEEEEeCCHHHHHHHHHHHHh
Confidence            99999999999999989999999999985 57888888888999888877666667788888888776668888999998


Q ss_pred             hCCCCcEEEEcccchhHHHHHhhC
Q 022724          269 TLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       269 ~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      .....++||||+++++|+.++..|
T Consensus       242 ~~~~~~~lVF~~s~~~~~~l~~~L  265 (434)
T PRK11192        242 QPEVTRSIVFVRTRERVHELAGWL  265 (434)
T ss_pred             cCCCCeEEEEeCChHHHHHHHHHH
Confidence            767789999999999999999876

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

Probab=100.00  E-value=3.7e-45  Score=314.96  Aligned_cols=259  Identities=30%  Similarity=0.496  Sum_probs=239.6

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCc---eeEEEEc
Q 022724           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSRE---VQALILS  108 (293)
Q Consensus        32 ~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~---~~~lil~  108 (293)
                      ..+|.+++|+..+++++..+||..|||+|..+||..+-|+|++.||.||+|||.+|++|+++++.-.+.+   .|+|||+
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            4589999999999999999999999999999999999999999999999999999999999998766543   5999999


Q ss_pred             CCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc-CCCCCCCccEEEecchhhh
Q 022724          109 PTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-KTLRTRAIKLLVLDESDEM  187 (293)
Q Consensus       109 P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~-~~~~~~~l~~iViDE~h~~  187 (293)
                      |||+|+.|+..+.+++..+.++.++++.||-+...|...+...|||+|+||++|...+++ ..+.++++..+|+||||.|
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            999999999999999999999999999999999999999999999999999999999877 6789999999999999999


Q ss_pred             hccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEec--CcccHHHHHHH
Q 022724          188 LSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVE--REEWKFDTLCD  265 (293)
Q Consensus       188 ~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~--~~~~k~~~l~~  265 (293)
                      ++.+|...+..+++.++++.|.++||||+++.+++++...+..|+.+.+++....+..+.|.++.+.  .+.++..++..
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            9999999999999999999999999999999999999999999999999998888888888777554  34457777888


Q ss_pred             HHhhCCCCcEEEEcccchhHHHHHh
Q 022724          266 LYDTLTITQAVIFCNTKRKVLLLVL  290 (293)
Q Consensus       266 l~~~~~~~~~iIF~~s~~~a~~l~~  290 (293)
                      ++...-..+++||+.|++.|..+.-
T Consensus       420 l~~rtf~~~~ivFv~tKk~AHRl~I  444 (691)
T KOG0338|consen  420 LITRTFQDRTIVFVRTKKQAHRLRI  444 (691)
T ss_pred             HHHHhcccceEEEEehHHHHHHHHH
Confidence            8876656799999999999998764

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

Probab=100.00  E-value=3.9e-45  Score=298.74  Aligned_cols=258  Identities=37%  Similarity=0.646  Sum_probs=247.2

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCH
Q 022724           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (293)
Q Consensus        32 ~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~  111 (293)
                      ...|+++.|..+++..+.+.||++|+|+|.+++|..+.|+|++..|..|+|||-+|.+|.++++.......+++|++|++
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            34699999999999999999999999999999999999999999999999999999999999999988889999999999


Q ss_pred             HHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccc
Q 022724          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG  191 (293)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~  191 (293)
                      +||.|+...++.+.+..++.+....||++..+++-.+.+..+++|+||++++++.+.+.-+++++.++|+||||.+++..
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            99999999999999999999999999999999988899999999999999999999999999999999999999999999


Q ss_pred             cHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHhhCC
Q 022724          192 FKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLT  271 (293)
Q Consensus       192 ~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~  271 (293)
                      |...+..++..+|+..|++++|||+|-.+..+...++.+|..+..- .+.++.++.|+|.++.+.. |..-|..++.+..
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            9999999999999999999999999999999999999999999876 4577889999999999988 9999999999999


Q ss_pred             CCcEEEEcccchhHHHHHhh
Q 022724          272 ITQAVIFCNTKRKVLLLVLQ  291 (293)
Q Consensus       272 ~~~~iIF~~s~~~a~~l~~~  291 (293)
                      ..+.||||||.+.++.+|..
T Consensus       322 INQsIIFCNS~~rVELLAkK  341 (459)
T KOG0326|consen  322 INQSIIFCNSTNRVELLAKK  341 (459)
T ss_pred             ccceEEEeccchHhHHHHHH
Confidence            99999999999999999874

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=5.5e-44  Score=302.88  Aligned_cols=259  Identities=29%  Similarity=0.449  Sum_probs=227.4

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccC------CCceeEEE
Q 022724           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS------SREVQALI  106 (293)
Q Consensus        33 ~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~------~~~~~~li  106 (293)
                      ..|++++|++++++++.+.||..||-+|+.+||.++.|+|++..|.||||||.+|++|+++.+...      ..++.++|
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            689999999999999999999999999999999999999999999999999999999999988543      35789999


Q ss_pred             EcCCHHHHHHHHHHHHHhhccCC--ceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCC-CCCCCccEEEecc
Q 022724          107 LSPTRELATQTEKVILAIGDFIN--IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT-LRTRAIKLLVLDE  183 (293)
Q Consensus       107 l~P~~~l~~q~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~-~~~~~l~~iViDE  183 (293)
                      ++||+||+.|++..+.++.....  +++.-+.++.+.....-.+.+.++|+|+||++++.++..+. ..+..++++|+||
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            99999999999999998865553  45555555554444445667889999999999999998876 6789999999999


Q ss_pred             hhhhhccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCccc-CCCceEEEEEecCcccHHHH
Q 022724          184 SDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELT-LEGIKQFFVAVEREEWKFDT  262 (293)
Q Consensus       184 ~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~i~~~~~~~~~~~~k~~~  262 (293)
                      ||.++..||.+++..+.+.+|+..|-++||||+++++..+...++.+|..+.....+.. +..+.|+++.|..++ |...
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            99999999999999999999999999999999999999999999999999988776654 466999999999555 9988


Q ss_pred             HHHHHhh-CCCCcEEEEcccchhHHHHHhhC
Q 022724          263 LCDLYDT-LTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       263 l~~l~~~-~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      +..+++- .-.++.|||+||++.|.++.-.|
T Consensus       258 lyallKL~LI~gKsliFVNtIdr~YrLkLfL  288 (569)
T KOG0346|consen  258 LYALLKLRLIRGKSLIFVNTIDRCYRLKLFL  288 (569)
T ss_pred             HHHHHHHHHhcCceEEEEechhhhHHHHHHH
Confidence            8888873 34579999999999999886543

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

Probab=100.00  E-value=3.4e-43  Score=300.36  Aligned_cols=260  Identities=31%  Similarity=0.516  Sum_probs=235.0

Q ss_pred             cCcccCC--CCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCC-----CceeEE
Q 022724           33 TSFDAMG--IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-----REVQAL  105 (293)
Q Consensus        33 ~~f~~~~--l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~-----~~~~~l  105 (293)
                      .+|++++  |+++++.++.++||...||+|..++|.+++++|+++.++||||||+||++|+++.+....     ...-++
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            4677775  569999999999999999999999999999999999999999999999999999983321     123689


Q ss_pred             EEcCCHHHHHHHHHHHHHhhcc-CCceEEEEECCcchHHHHHHHh-cCCcEEEeChHHHHHHHhcC--CCCCCCccEEEe
Q 022724          106 ILSPTRELATQTEKVILAIGDF-INIQAHACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRK--TLRTRAIKLLVL  181 (293)
Q Consensus       106 il~P~~~l~~q~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~-~~~~ilV~Tp~~l~~~l~~~--~~~~~~l~~iVi  181 (293)
                      |++|||||+.|+.+++..+... .++++.++.||.+..+++..+. ++++|+||||++|.+++.+.  .+++++++++|+
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 6889999999999998888764 67899999999999999873  455679999999


Q ss_pred             cchhhhhccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcc--cCCCceEEEEEecCcccH
Q 022724          182 DESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDEL--TLEGIKQFFVAVEREEWK  259 (293)
Q Consensus       182 DE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~i~~~~~~~~~~~~k  259 (293)
                      ||||.+++.||...++.|++++|+.++.=++|||.+.++.++....+++|..+.+.....  ++.++..+|..|+... |
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            999999999999999999999999999999999999999999999999999999987765  7888999999999888 9


Q ss_pred             HHHHHHHHhhCCCCcEEEEcccchhHHHHHhhCC
Q 022724          260 FDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQFP  293 (293)
Q Consensus       260 ~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L~  293 (293)
                      ...+.+++.....+++|||..|...++..+..|+
T Consensus       243 ~~~lv~~L~~~~~kK~iVFF~TCasVeYf~~~~~  276 (567)
T KOG0345|consen  243 LSQLVHLLNNNKDKKCIVFFPTCASVEYFGKLFS  276 (567)
T ss_pred             HHHHHHHHhccccccEEEEecCcchHHHHHHHHH
Confidence            9999999999988999999999999999887653

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=2.3e-42  Score=315.64  Aligned_cols=261  Identities=27%  Similarity=0.483  Sum_probs=230.9

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCC-------Ccee
Q 022724           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-------REVQ  103 (293)
Q Consensus        31 ~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~-------~~~~  103 (293)
                      ....|.++++++.+.++|.++||..|+++|.++|+.+.+|+|+++.+|||||||++|++|+++.+...+       .+++
T Consensus        85 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~~  164 (475)
T PRK01297         85 GKTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPR  164 (475)
T ss_pred             CCCCHhHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCce
Confidence            345788999999999999999999999999999999999999999999999999999999999886543       1468


Q ss_pred             EEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHh-cCCcEEEeChHHHHHHHhcCCCCCCCccEEEec
Q 022724          104 ALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLD  182 (293)
Q Consensus       104 ~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViD  182 (293)
                      +|||+||++|+.|+.+.++.+.+..++++..++|+.+...+.+.+. +.++|+|+||++|..++..+...++++++||||
T Consensus       165 aLil~PtreLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~~~~~~~~Iiv~TP~~Ll~~~~~~~~~l~~l~~lViD  244 (475)
T PRK01297        165 ALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLD  244 (475)
T ss_pred             EEEEeCcHHHHHHHHHHHHHhhccCCCEEEEEEccCChHHHHHHHhCCCCCEEEECHHHHHHHHHcCCcccccCceEEec
Confidence            9999999999999999999999889999999999988777766664 568999999999999988888889999999999


Q ss_pred             chhhhhccccHHHHHHHHhhCCC--CccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHH
Q 022724          183 ESDEMLSRGFKDQIYDVYRYLPP--DLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKF  260 (293)
Q Consensus       183 E~h~~~~~~~~~~~~~i~~~l~~--~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~  260 (293)
                      |+|.+.+.++...+..+++.++.  ..|++++|||++..+..+...++.++..+.+.........+.+.+..+.... |.
T Consensus       245 Eah~l~~~~~~~~l~~i~~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~-k~  323 (475)
T PRK01297        245 EADRMLDMGFIPQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTVEQHVYAVAGSD-KY  323 (475)
T ss_pred             hHHHHHhcccHHHHHHHHHhCCCCCCceEEEEEeecCHHHHHHHHHhccCCEEEEeccCcCCCCcccEEEEEecchh-HH
Confidence            99999999999999999988864  5799999999999999999999999988877766555566777777666655 88


Q ss_pred             HHHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          261 DTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       261 ~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ..+..++......++||||+++++|+.+++.|
T Consensus       324 ~~l~~ll~~~~~~~~IVF~~s~~~~~~l~~~L  355 (475)
T PRK01297        324 KLLYNLVTQNPWERVMVFANRKDEVRRIEERL  355 (475)
T ss_pred             HHHHHHHHhcCCCeEEEEeCCHHHHHHHHHHH
Confidence            88888888777789999999999999998765

>PTZ00424 helicase 45; Provisional

Probab=100.00  E-value=2.6e-42  Score=309.94  Aligned_cols=263  Identities=65%  Similarity=1.069  Sum_probs=237.1

Q ss_pred             ccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcC
Q 022724           30 EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (293)
Q Consensus        30 ~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P  109 (293)
                      +...+|+++++++.+.+++.++||..|+|+|.++|+.+.+|+|+++++|||+|||++|++|++..+.....+.++||++|
T Consensus        25 ~~~~~~~~l~l~~~~~~~l~~~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~~~~~~~lil~P  104 (401)
T PTZ00424         25 EIVDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDLNACQALILAP  104 (401)
T ss_pred             cccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCCCCCceEEEECC
Confidence            34678999999999999999999999999999999999999999999999999999999999998876556779999999


Q ss_pred             CHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhc
Q 022724          110 TRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (293)
Q Consensus       110 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~  189 (293)
                      +++|+.|+.+.+..+....+..+..+.|+.....+...+.++++|+|+||+++.+++..+...++++++|||||+|++.+
T Consensus       105 t~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~l~~i~lvViDEah~~~~  184 (401)
T PTZ00424        105 TRELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLS  184 (401)
T ss_pred             CHHHHHHHHHHHHHHhhhcCceEEEEECCcCHHHHHHHHcCCCCEEEECcHHHHHHHHhCCcccccccEEEEecHHHHHh
Confidence            99999999999999988888888889999888777777878889999999999999988888899999999999999999


Q ss_pred             cccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHhh
Q 022724          190 RGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDT  269 (293)
Q Consensus       190 ~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~  269 (293)
                      .++...+..+++.+++..|++++|||+++....+...++.++..+.+...+....++.+++..++....+...+..++..
T Consensus       185 ~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  264 (401)
T PTZ00424        185 RGFKGQIYDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKEEWKFDTLCDLYET  264 (401)
T ss_pred             cchHHHHHHHHhhCCCCcEEEEEEecCCHHHHHHHHHHcCCCEEEEeCCCCcccCCceEEEEecChHHHHHHHHHHHHHh
Confidence            89988899999999999999999999999999998889988888877766666677888888777766677778888877


Q ss_pred             CCCCcEEEEcccchhHHHHHhhC
Q 022724          270 LTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       270 ~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ....++||||+++++|+.+++.|
T Consensus       265 ~~~~~~ivF~~t~~~~~~l~~~l  287 (401)
T PTZ00424        265 LTITQAIIYCNTRRKVDYLTKKM  287 (401)
T ss_pred             cCCCeEEEEecCcHHHHHHHHHH
Confidence            77789999999999999998765

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=100.00  E-value=4.9e-43  Score=304.45  Aligned_cols=261  Identities=29%  Similarity=0.471  Sum_probs=239.9

Q ss_pred             ccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCC----CceeEE
Q 022724           30 EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS----REVQAL  105 (293)
Q Consensus        30 ~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~----~~~~~l  105 (293)
                      ..+..|.++||+....++|++.+|..+|.+|+.+||..+.|+|++..|.||||||+||++|+++.+...+    .|.-+|
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            3455899999999999999999999999999999999999999999999999999999999999986543    456799


Q ss_pred             EEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc-CCCCCCCccEEEecch
Q 022724          106 ILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-KTLRTRAIKLLVLDES  184 (293)
Q Consensus       106 il~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~-~~~~~~~l~~iViDE~  184 (293)
                      |+.|||+||.|+++++.++++.++++...+.||.........+ ++++|+||||++|++.+.. ..++..++.++|+|||
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            9999999999999999999999999999999999877766655 4679999999999998876 5678899999999999


Q ss_pred             hhhhccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecC--CcccCCCceEEEEEecCcccHHHH
Q 022724          185 DEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKR--DELTLEGIKQFFVAVEREEWKFDT  262 (293)
Q Consensus       185 h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~i~~~~~~~~~~~~k~~~  262 (293)
                      |.+++.||...+..+++.+++..|.++||||.+..+.++++..+.+|..+.+..  ....|.++.|+|+.++... |+.+
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            999999999999999999999999999999999999999999999999887763  3467888999999999888 9999


Q ss_pred             HHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          263 LCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       263 l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      |-.+++.+...++|||+.|.+++..+++.+
T Consensus       304 L~sFI~shlk~K~iVF~SscKqvkf~~e~F  333 (758)
T KOG0343|consen  304 LWSFIKSHLKKKSIVFLSSCKQVKFLYEAF  333 (758)
T ss_pred             HHHHHHhccccceEEEEehhhHHHHHHHHH
Confidence            999999999899999999999999998764

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

Probab=100.00  E-value=2.3e-42  Score=298.61  Aligned_cols=280  Identities=25%  Similarity=0.384  Sum_probs=256.5

Q ss_pred             CCCCCCCcceeecccCCccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHH
Q 022724           13 GGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVC   92 (293)
Q Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~   92 (293)
                      ..-..+-....++..-+.|+.+|++.+++.++++.+.+.||..|+|+|.+++|..++++|+|.++.||||||.+|++|++
T Consensus       225 ri~redynis~kg~~lpnplrnwEE~~~P~e~l~~I~~~~y~eptpIqR~aipl~lQ~rD~igvaETgsGktaaf~ipLl  304 (673)
T KOG0333|consen  225 RIFREDYNISIKGGRLPNPLRNWEESGFPLELLSVIKKPGYKEPTPIQRQAIPLGLQNRDPIGVAETGSGKTAAFLIPLL  304 (673)
T ss_pred             eeeecceeeeecCCCCCccccChhhcCCCHHHHHHHHhcCCCCCchHHHhhccchhccCCeeeEEeccCCccccchhhHH
Confidence            33334445666788889999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhccC---------CCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHH
Q 022724           93 QTVDTS---------SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVC  163 (293)
Q Consensus        93 ~~l~~~---------~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~  163 (293)
                      ..+...         ..||++++++||++|+.|+.+.-.++++.+++++..+.||.+.+++--.+..+|+|+|+||++|.
T Consensus       305 ~~IsslP~~~~~en~~~gpyaiilaptReLaqqIeeEt~kf~~~lg~r~vsvigg~s~EEq~fqls~gceiviatPgrLi  384 (673)
T KOG0333|consen  305 IWISSLPPMARLENNIEGPYAIILAPTRELAQQIEEETNKFGKPLGIRTVSVIGGLSFEEQGFQLSMGCEIVIATPGRLI  384 (673)
T ss_pred             HHHHcCCCcchhhhcccCceeeeechHHHHHHHHHHHHHHhcccccceEEEEecccchhhhhhhhhccceeeecCchHHH
Confidence            877443         34789999999999999999999999999999999999999999888888899999999999999


Q ss_pred             HHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCC-------------------------CccEEEEEeecCh
Q 022724          164 DMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP-------------------------DLQVVLISATLPH  218 (293)
Q Consensus       164 ~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~-------------------------~~q~v~~SAt~~~  218 (293)
                      ..|.+..+.++++.++|+||||.|+|.+|..++..++..++.                         -.|.+.||||+|+
T Consensus       385 d~Lenr~lvl~qctyvvldeadrmiDmgfE~dv~~iL~~mPssn~k~~tde~~~~~~~~~~~~~~k~yrqT~mftatm~p  464 (673)
T KOG0333|consen  385 DSLENRYLVLNQCTYVVLDEADRMIDMGFEPDVQKILEQMPSSNAKPDTDEKEGEERVRKNFSSSKKYRQTVMFTATMPP  464 (673)
T ss_pred             HHHHHHHHHhccCceEeccchhhhhcccccHHHHHHHHhCCccccCCCccchhhHHHHHhhcccccceeEEEEEecCCCh
Confidence            999999999999999999999999999999999999999863                         1689999999999


Q ss_pred             hHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHhhCCCCcEEEEcccchhHHHHHhhCC
Q 022724          219 EILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQFP  293 (293)
Q Consensus       219 ~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L~  293 (293)
                      .+..+++.|+.+|..+.+.......+.+.|.+..+.... |...|..+++.....++|||+|+++.|+.+|+.|+
T Consensus       465 ~verlar~ylr~pv~vtig~~gk~~~rveQ~v~m~~ed~-k~kkL~eil~~~~~ppiIIFvN~kk~~d~lAk~Le  538 (673)
T KOG0333|consen  465 AVERLARSYLRRPVVVTIGSAGKPTPRVEQKVEMVSEDE-KRKKLIEILESNFDPPIIIFVNTKKGADALAKILE  538 (673)
T ss_pred             HHHHHHHHHhhCCeEEEeccCCCCccchheEEEEecchH-HHHHHHHHHHhCCCCCEEEEEechhhHHHHHHHHh
Confidence            999999999999999999988888888999999888777 89999999998877899999999999999998763

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

Probab=100.00  E-value=1e-42  Score=288.16  Aligned_cols=261  Identities=31%  Similarity=0.460  Sum_probs=237.2

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCC
Q 022724           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (293)
Q Consensus        31 ~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~  110 (293)
                      ...+|+.+|+++|+.+.++++|+..|||+|+.++|.|+.|+|.+-+|.||||||.+|.+|+++++..++.|..++|++||
T Consensus         5 t~~~F~~LGl~~Wlve~l~~l~i~~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLsedP~giFalvlTPT   84 (442)
T KOG0340|consen    5 TAKPFSILGLSPWLVEQLKALGIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSEDPYGIFALVLTPT   84 (442)
T ss_pred             ccCchhhcCccHHHHHHHHHhcCCCCCchHhhhhHHHhcccccccccccCCCcchhhhHHHHHhhccCCCcceEEEecch
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcC----CCCCCCccEEEecchhh
Q 022724          111 RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK----TLRTRAIKLLVLDESDE  186 (293)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~----~~~~~~l~~iViDE~h~  186 (293)
                      ++|+-|+.+++..+++..++++..++||++.-.+...+..+++++|+||+++...+.++    ...+++++++|+||||.
T Consensus        85 rELA~QiaEQF~alGk~l~lK~~vivGG~d~i~qa~~L~~rPHvVvatPGRlad~l~sn~~~~~~~~~rlkflVlDEADr  164 (442)
T KOG0340|consen   85 RELALQIAEQFIALGKLLNLKVSVIVGGTDMIMQAAILSDRPHVVVATPGRLADHLSSNLGVCSWIFQRLKFLVLDEADR  164 (442)
T ss_pred             HHHHHHHHHHHHHhcccccceEEEEEccHHHhhhhhhcccCCCeEecCccccccccccCCccchhhhhceeeEEecchhh
Confidence            99999999999999999999999999999999999999999999999999999988775    34579999999999999


Q ss_pred             hhccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCC--CEEEEecCCcccCCCceEEEEEecCcccHHHHHH
Q 022724          187 MLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTD--PVKILVKRDELTLEGIKQFFVAVEREEWKFDTLC  264 (293)
Q Consensus       187 ~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~  264 (293)
                      +++.+|.+.+..+.+.+|...|.+++|||+++.+.++.......  .......+....+..+.+.|+.++... |...+.
T Consensus       165 vL~~~f~d~L~~i~e~lP~~RQtLlfSATitd~i~ql~~~~i~k~~a~~~e~~~~vstvetL~q~yI~~~~~v-kdaYLv  243 (442)
T KOG0340|consen  165 VLAGCFPDILEGIEECLPKPRQTLLFSATITDTIKQLFGCPITKSIAFELEVIDGVSTVETLYQGYILVSIDV-KDAYLV  243 (442)
T ss_pred             hhccchhhHHhhhhccCCCccceEEEEeehhhHHHHhhcCCcccccceEEeccCCCCchhhhhhheeecchhh-hHHHHH
Confidence            99999999999999999999999999999999988887766665  344455555667778899999998877 888888


Q ss_pred             HHHhhCC---CCcEEEEcccchhHHHHHhhC
Q 022724          265 DLYDTLT---ITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       265 ~l~~~~~---~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ++++...   .+.++||+|+..+|+.++..|
T Consensus       244 ~~Lr~~~~~~~~simIFvnttr~cQ~l~~~l  274 (442)
T KOG0340|consen  244 HLLRDFENKENGSIMIFVNTTRECQLLSMTL  274 (442)
T ss_pred             HHHhhhhhccCceEEEEeehhHHHHHHHHHH
Confidence            8887554   458999999999999998654

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

Probab=100.00  E-value=1.6e-42  Score=301.68  Aligned_cols=280  Identities=30%  Similarity=0.417  Sum_probs=250.0

Q ss_pred             CCCCCCCCcceeecccCCccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHH
Q 022724           12 GGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTV   91 (293)
Q Consensus        12 ~~~~~~~~~~~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~   91 (293)
                      ...+..+-........-|.++..|++-.+.+.+..+++..+|..|+|+|+.++|.+..|++++.||+||+|||.+|++|+
T Consensus        53 nfd~~~~i~v~~~G~~~p~~i~~f~~~~l~~~l~~ni~~~~~~~ptpvQk~sip~i~~Grdl~acAqTGsGKT~aFLiPi  132 (482)
T KOG0335|consen   53 NFDKYNDIPVKVSGRDVPPHIPTFDEAILGEALAGNIKRSGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAAFLIPI  132 (482)
T ss_pred             ccCCccceeeeccCCccCCCcccccccchhHHHhhccccccccCCCcceeeccceeecCCceEEEccCCCcchHHHHHHH
Confidence            34445455556667777888889998899999999999999999999999999999999999999999999999999999


Q ss_pred             HhhhccCC----------CceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHH
Q 022724           92 CQTVDTSS----------REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGR  161 (293)
Q Consensus        92 ~~~l~~~~----------~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~  161 (293)
                      +..+....          ..|+++|++||++||.|++++.+++.-..+++....+|+.+...+.+.+.++|+|+|+||++
T Consensus       133 i~~~~~~~~~~~~~~~~~~~P~~lIlapTReL~~Qi~nea~k~~~~s~~~~~~~ygg~~~~~q~~~~~~gcdIlvaTpGr  212 (482)
T KOG0335|consen  133 ISYLLDEGPEDRGESGGGVYPRALILAPTRELVDQIYNEARKFSYLSGMKSVVVYGGTDLGAQLRFIKRGCDILVATPGR  212 (482)
T ss_pred             HHHHHhcCcccCcccCCCCCCceEEEeCcHHHhhHHHHHHHhhcccccceeeeeeCCcchhhhhhhhccCccEEEecCch
Confidence            99885542          35899999999999999999999999889999999999999999999999999999999999


Q ss_pred             HHHHHhcCCCCCCCccEEEecchhhhhc-cccHHHHHHHHhhCCC----CccEEEEEeecChhHHHHHHhcCCC-CEEEE
Q 022724          162 VCDMIKRKTLRTRAIKLLVLDESDEMLS-RGFKDQIYDVYRYLPP----DLQVVLISATLPHEILEMTTKFMTD-PVKIL  235 (293)
Q Consensus       162 l~~~l~~~~~~~~~l~~iViDE~h~~~~-~~~~~~~~~i~~~l~~----~~q~v~~SAt~~~~~~~~~~~~~~~-~~~~~  235 (293)
                      |.+++..+.+.++++.++|+||||.|+| .+|..+++.++.....    ..|.++||||+|..+..++..++.+ ...+.
T Consensus       213 L~d~~e~g~i~l~~~k~~vLDEADrMlD~mgF~p~Ir~iv~~~~~~~~~~~qt~mFSAtfp~~iq~l~~~fl~~~yi~la  292 (482)
T KOG0335|consen  213 LKDLIERGKISLDNCKFLVLDEADRMLDEMGFEPQIRKIVEQLGMPPKNNRQTLLFSATFPKEIQRLAADFLKDNYIFLA  292 (482)
T ss_pred             hhhhhhcceeehhhCcEEEecchHHhhhhccccccHHHHhcccCCCCccceeEEEEeccCChhhhhhHHHHhhccceEEE
Confidence            9999999999999999999999999999 8999999999998864    7899999999999999988888776 77788


Q ss_pred             ecCCcccCCCceEEEEEecCcccHHHHHHHHHhhCC----CC-----cEEEEcccchhHHHHHhhC
Q 022724          236 VKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLT----IT-----QAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       236 ~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~----~~-----~~iIF~~s~~~a~~l~~~L  292 (293)
                      +........++.|...++.+.. |...|.+++....    .+     +++|||.|++.|..++..|
T Consensus       293 V~rvg~~~~ni~q~i~~V~~~~-kr~~Lldll~~~~~~~~~~~~~~e~tlvFvEt~~~~d~l~~~l  357 (482)
T KOG0335|consen  293 VGRVGSTSENITQKILFVNEME-KRSKLLDLLNKDDGPPSDGEPKWEKTLVFVETKRGADELAAFL  357 (482)
T ss_pred             EeeeccccccceeEeeeecchh-hHHHHHHHhhcccCCcccCCcccceEEEEeeccchhhHHHHHH
Confidence            8888888999999999999888 7677766665322    23     8999999999999998876

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

Probab=100.00  E-value=1.2e-41  Score=293.18  Aligned_cols=271  Identities=30%  Similarity=0.439  Sum_probs=253.3

Q ss_pred             eeecccCCccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccC---
Q 022724           22 VFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS---   98 (293)
Q Consensus        22 ~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~---   98 (293)
                      .+....++.++.+|+.++++..+..+..+..|++|||+|.+++|..++|++++-.|-||||||-+|++|++.++...   
T Consensus       212 rv~g~s~~rpvtsfeh~gfDkqLm~airk~Ey~kptpiq~qalptalsgrdvigIAktgSgktaAfi~pm~~himdq~eL  291 (731)
T KOG0339|consen  212 RVSGSSPPRPVTSFEHFGFDKQLMTAIRKSEYEKPTPIQCQALPTALSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPEL  291 (731)
T ss_pred             eeccCCCCCCcchhhhcCchHHHHHHHhhhhcccCCcccccccccccccccchheeeccCcchhHHHHHHHHHhcchhhh
Confidence            34577889999999999999999999999999999999999999999999999999999999999999999887543   


Q ss_pred             --CCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCc
Q 022724           99 --SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (293)
Q Consensus        99 --~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l  176 (293)
                        ..+|..||++||++|+.|++..++++++..|++++.+|||.+..+|.+.+..++.|+|+||++|.++++-+..++.++
T Consensus       292 ~~g~gPi~vilvPTrela~Qi~~eaKkf~K~ygl~~v~~ygGgsk~eQ~k~Lk~g~EivVaTPgRlid~VkmKatn~~rv  371 (731)
T KOG0339|consen  292 KPGEGPIGVILVPTRELASQIFSEAKKFGKAYGLRVVAVYGGGSKWEQSKELKEGAEIVVATPGRLIDMVKMKATNLSRV  371 (731)
T ss_pred             cCCCCCeEEEEeccHHHHHHHHHHHHHhhhhccceEEEeecCCcHHHHHHhhhcCCeEEEechHHHHHHHHhhcccceee
Confidence              468999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCc
Q 022724          177 KLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVERE  256 (293)
Q Consensus       177 ~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~  256 (293)
                      .++|+||+|.|.+.||..+++.|...+++..|.++||||++..++.+++..+.+|+.+...........|.|.+..|...
T Consensus       372 S~LV~DEadrmfdmGfe~qVrSI~~hirpdrQtllFsaTf~~kIe~lard~L~dpVrvVqg~vgean~dITQ~V~V~~s~  451 (731)
T KOG0339|consen  372 SYLVLDEADRMFDMGFEPQVRSIKQHIRPDRQTLLFSATFKKKIEKLARDILSDPVRVVQGEVGEANEDITQTVSVCPSE  451 (731)
T ss_pred             eEEEEechhhhhccccHHHHHHHHhhcCCcceEEEeeccchHHHHHHHHHHhcCCeeEEEeehhccccchhheeeeccCc
Confidence            99999999999999999999999999999999999999999999999999999999998887778888999999999999


Q ss_pred             ccHHHHHH-HHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          257 EWKFDTLC-DLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       257 ~~k~~~l~-~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ..|++-+. +|......+++|||+.....++.++..|
T Consensus       452 ~~Kl~wl~~~L~~f~S~gkvlifVTKk~~~e~i~a~L  488 (731)
T KOG0339|consen  452 EKKLNWLLRHLVEFSSEGKVLIFVTKKADAEEIAANL  488 (731)
T ss_pred             HHHHHHHHHHhhhhccCCcEEEEEeccCCHHHHHHHh
Confidence            88888754 4555566679999999999999998876

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

Probab=100.00  E-value=2.5e-41  Score=290.46  Aligned_cols=262  Identities=27%  Similarity=0.443  Sum_probs=235.1

Q ss_pred             ccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccC----CCceeEE
Q 022724           30 EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS----SREVQAL  105 (293)
Q Consensus        30 ~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~----~~~~~~l  105 (293)
                      .....|++..|++..+++++++||...|++|+..++.++.|+|+++.|-||+|||+||++|+++.+...    +.+..++
T Consensus        79 ~~~~~f~~~~LS~~t~kAi~~~GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r~~~~vl  158 (543)
T KOG0342|consen   79 TTTFRFEEGSLSPLTLKAIKEMGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFKPRNGTGVL  158 (543)
T ss_pred             hhhhHhhccccCHHHHHHHHhcCccchhHHHHhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhcccCCCCCeeEE
Confidence            345578889999999999999999999999999999999999999999999999999999999988654    3456799


Q ss_pred             EEcCCHHHHHHHHHHHHHhhccC-CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc-CCCCCCCccEEEecc
Q 022724          106 ILSPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-KTLRTRAIKLLVLDE  183 (293)
Q Consensus       106 il~P~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~-~~~~~~~l~~iViDE  183 (293)
                      |+||||+|+.|++...+++.+.+ ++.+..+.||.......+.+..+++|+|+||++|...+.+ ..+-+++++++|+||
T Consensus       159 Ii~PTRELA~Q~~~eak~Ll~~h~~~~v~~viGG~~~~~e~~kl~k~~niliATPGRLlDHlqNt~~f~~r~~k~lvlDE  238 (543)
T KOG0342|consen  159 IICPTRELAMQIFAEAKELLKYHESITVGIVIGGNNFSVEADKLVKGCNILIATPGRLLDHLQNTSGFLFRNLKCLVLDE  238 (543)
T ss_pred             EecccHHHHHHHHHHHHHHHhhCCCcceEEEeCCccchHHHHHhhccccEEEeCCchHHhHhhcCCcchhhccceeEeec
Confidence            99999999999999999999888 8999999999999988888888999999999999999988 446678889999999


Q ss_pred             hhhhhccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCC-CCEEEEecCCc--ccCCCceEEEEEecCcccHH
Q 022724          184 SDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMT-DPVKILVKRDE--LTLEGIKQFFVAVEREEWKF  260 (293)
Q Consensus       184 ~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~-~~~~~~~~~~~--~~~~~i~~~~~~~~~~~~k~  260 (293)
                      ||++++.+|...+..++..+++..|.+++|||.++.++++.+..+. +|..+.+....  .+..++.|.|+.++... ++
T Consensus       239 ADrlLd~GF~~di~~Ii~~lpk~rqt~LFSAT~~~kV~~l~~~~L~~d~~~v~~~d~~~~~The~l~Qgyvv~~~~~-~f  317 (543)
T KOG0342|consen  239 ADRLLDIGFEEDVEQIIKILPKQRQTLLFSATQPSKVKDLARGALKRDPVFVNVDDGGERETHERLEQGYVVAPSDS-RF  317 (543)
T ss_pred             chhhhhcccHHHHHHHHHhccccceeeEeeCCCcHHHHHHHHHhhcCCceEeecCCCCCcchhhcccceEEeccccc-hH
Confidence            9999999999999999999999999999999999999999987766 47777776543  35677999899888777 68


Q ss_pred             HHHHHHHhhCCC-CcEEEEcccchhHHHHHhhC
Q 022724          261 DTLCDLYDTLTI-TQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       261 ~~l~~l~~~~~~-~~~iIF~~s~~~a~~l~~~L  292 (293)
                      -.+..+++++.. .++||||.|...+..+++.|
T Consensus       318 ~ll~~~LKk~~~~~KiiVF~sT~~~vk~~~~lL  350 (543)
T KOG0342|consen  318 SLLYTFLKKNIKRYKIIVFFSTCMSVKFHAELL  350 (543)
T ss_pred             HHHHHHHHHhcCCceEEEEechhhHHHHHHHHH
Confidence            888888888776 79999999999999988765

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

Probab=100.00  E-value=1.6e-41  Score=285.93  Aligned_cols=263  Identities=29%  Similarity=0.466  Sum_probs=235.9

Q ss_pred             CCccccCccc-CCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccC------CC
Q 022724           28 GVEAITSFDA-MGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS------SR  100 (293)
Q Consensus        28 ~~~~~~~f~~-~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~------~~  100 (293)
                      .|.|.-+|++ +.-.+++..++++.||.+|+|+|+++||.+++|.|++.++.||+|||++|++|.+.++...      ..
T Consensus       214 IPnP~ctFddAFq~~pevmenIkK~GFqKPtPIqSQaWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr~  293 (629)
T KOG0336|consen  214 IPNPVCTFDDAFQCYPEVMENIKKTGFQKPTPIQSQAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQRN  293 (629)
T ss_pred             CCCCcCcHHHHHhhhHHHHHHHHhccCCCCCcchhcccceeecCcceEEEEecCCCcCHHHhccceeeeeccchhhhccC
Confidence            5777888887 5788999999999999999999999999999999999999999999999999988777443      45


Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEE
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLV  180 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iV  180 (293)
                      ++.+|++.|+++|+.|+.-.+.++. .-|+...+++|+.+...+.+.+..+.+|+++||++|..+...+.+++..+.|+|
T Consensus       294 ~p~~lvl~ptreLalqie~e~~kys-yng~ksvc~ygggnR~eqie~lkrgveiiiatPgrlndL~~~n~i~l~siTYlV  372 (629)
T KOG0336|consen  294 GPGVLVLTPTRELALQIEGEVKKYS-YNGLKSVCVYGGGNRNEQIEDLKRGVEIIIATPGRLNDLQMDNVINLASITYLV  372 (629)
T ss_pred             CCceEEEeccHHHHHHHHhHHhHhh-hcCcceEEEecCCCchhHHHHHhcCceEEeeCCchHhhhhhcCeeeeeeeEEEE
Confidence            7899999999999999998887764 457888899999999999999999999999999999999999999999999999


Q ss_pred             ecchhhhhccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCccc-CCCceEEEEEecCcccH
Q 022724          181 LDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELT-LEGIKQFFVAVEREEWK  259 (293)
Q Consensus       181 iDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~i~~~~~~~~~~~~k  259 (293)
                      +||||.|++.+|..++..++-.+++..|.++.|||||+.+..+...|+.+|..+.+...+.. ...+.|++ .+..+..|
T Consensus       373 lDEADrMLDMgFEpqIrkilldiRPDRqtvmTSATWP~~VrrLa~sY~Kep~~v~vGsLdL~a~~sVkQ~i-~v~~d~~k  451 (629)
T KOG0336|consen  373 LDEADRMLDMGFEPQIRKILLDIRPDRQTVMTSATWPEGVRRLAQSYLKEPMIVYVGSLDLVAVKSVKQNI-IVTTDSEK  451 (629)
T ss_pred             ecchhhhhcccccHHHHHHhhhcCCcceeeeecccCchHHHHHHHHhhhCceEEEecccceeeeeeeeeeE-EecccHHH
Confidence            99999999999999999999999999999999999999999999999999999998877654 46677777 56666669


Q ss_pred             HHHHHHHHhhCCC-CcEEEEcccchhHHHHHhhC
Q 022724          260 FDTLCDLYDTLTI-TQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       260 ~~~l~~l~~~~~~-~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ...+..+++.... .++||||.++..|+.+...|
T Consensus       452 ~~~~~~f~~~ms~ndKvIiFv~~K~~AD~LSSd~  485 (629)
T KOG0336|consen  452 LEIVQFFVANMSSNDKVIIFVSRKVMADHLSSDF  485 (629)
T ss_pred             HHHHHHHHHhcCCCceEEEEEechhhhhhccchh
Confidence            9999998887654 59999999999998887654

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

Probab=100.00  E-value=3.7e-41  Score=280.50  Aligned_cols=283  Identities=35%  Similarity=0.565  Sum_probs=250.5

Q ss_pred             hhhhhHHhCCCCCCCCCcceeecccCCccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcC--CcEEEEcCCC
Q 022724            3 AATAMRRRGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG--RDVIAQAQSG   80 (293)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~--~~~li~~~Tg   80 (293)
                      +.+++.+.-.+.+....    +.+++..+..+|++|+|.|+++++++.|+|.+|+.+|..++|.++..  +|++.++.+|
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            34455554444444333    37788889999999999999999999999999999999999999865  7999999999


Q ss_pred             ChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChH
Q 022724           81 TGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPG  160 (293)
Q Consensus        81 ~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~  160 (293)
                      +|||.||.+.++.++...-..|+++.|+|+++||.|+.+.+.++++..++...+...+....+... +  ..+|+|+||+
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            999999999999999988888999999999999999999999999999888877776652222111 1  1379999999


Q ss_pred             HHHHHHhc-CCCCCCCccEEEecchhhhhcc-ccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecC
Q 022724          161 RVCDMIKR-KTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKR  238 (293)
Q Consensus       161 ~l~~~l~~-~~~~~~~l~~iViDE~h~~~~~-~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~  238 (293)
                      .+.+++.. ..+++..++.+|+||||.|++. ||.++-..+.+.+++++|++++|||+.+.+..+.....+++-.+....
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 8889999999999999999765 799999999999999999999999999999999999999999999999


Q ss_pred             CcccCCCceEEEEEecCcccHHHHHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          239 DELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       239 ~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      .+....+|.|+|..|..+++|++.+..++.....++.||||.|++.|.+++..|
T Consensus       297 eel~L~~IkQlyv~C~~~~~K~~~l~~lyg~~tigqsiIFc~tk~ta~~l~~~m  350 (477)
T KOG0332|consen  297 EELALDNIKQLYVLCACRDDKYQALVNLYGLLTIGQSIIFCHTKATAMWLYEEM  350 (477)
T ss_pred             hhccccchhhheeeccchhhHHHHHHHHHhhhhhhheEEEEeehhhHHHHHHHH
Confidence            999999999999999999999999999998888899999999999999999865

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

Probab=100.00  E-value=2.6e-40  Score=277.01  Aligned_cols=261  Identities=62%  Similarity=1.008  Sum_probs=243.9

Q ss_pred             CccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEc
Q 022724           29 VEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (293)
Q Consensus        29 ~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~  108 (293)
                      .+.+.+|++++|++.+++.++..||++|+.+|+.|+..+.+|.|+.+.+++|+|||.+|.+++++.+.......++++++
T Consensus        22 ~evvdsfddm~L~e~LLrgiy~yGFekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~~ke~qalila  101 (397)
T KOG0327|consen   22 NEVVDSFDDMNLKESLLRGIYAYGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMSVKETQALILA  101 (397)
T ss_pred             HHHhhhhhhcCCCHHHHhHHHhhccCCchHHHhccccccccCCceeEeeeccccchhhhHHHHHhhcCcchHHHHHHHhc
Confidence            45577999999999999999999999999999999999999999999999999999999999999998887888999999


Q ss_pred             CCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH-hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhh
Q 022724          109 PTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL-EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (293)
Q Consensus       109 P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~  187 (293)
                      |+++|+.|+..+...++...+.++..+.|+.....+...+ ...++|+|+||+++.+++..+.+..+.++++|+||+|.+
T Consensus       102 PtreLa~qi~~v~~~lg~~~~~~v~~~igg~~~~~~~~~i~~~~~hivvGTpgrV~dml~~~~l~~~~iKmfvlDEaDEm  181 (397)
T KOG0327|consen  102 PTRELAQQIQKVVRALGDHMDVSVHACIGGTNVRREDQALLKDKPHIVVGTPGRVFDMLNRGSLSTDGIKMFVLDEADEM  181 (397)
T ss_pred             chHHHHHHHHHHHHhhhcccceeeeeecCcccchhhhhhhhccCceeecCCchhHHHhhccccccccceeEEeecchHhh
Confidence            9999999999999999999999999999998877555444 456899999999999999999888889999999999999


Q ss_pred             hccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHH
Q 022724          188 LSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLY  267 (293)
Q Consensus       188 ~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~  267 (293)
                      +..++.+++..++..++++.|++++|||.|.++....+.++.+|..+.+...+.+...+.|+++.+..++ |+..+..++
T Consensus       182 Ls~gfkdqI~~if~~lp~~vQv~l~SAT~p~~vl~vt~~f~~~pv~i~vkk~~ltl~gikq~~i~v~k~~-k~~~l~dl~  260 (397)
T KOG0327|consen  182 LSRGFKDQIYDIFQELPSDVQVVLLSATMPSDVLEVTKKFMREPVRILVKKDELTLEGIKQFYINVEKEE-KLDTLCDLY  260 (397)
T ss_pred             hccchHHHHHHHHHHcCcchhheeecccCcHHHHHHHHHhccCceEEEecchhhhhhheeeeeeeccccc-cccHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999889999999999999888 999999999


Q ss_pred             hhCCCCcEEEEcccchhHHHHHhhC
Q 022724          268 DTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       268 ~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      +  .-.+.+||||+++.+..+...|
T Consensus       261 ~--~~~q~~if~nt~r~v~~l~~~L  283 (397)
T KOG0327|consen  261 R--RVTQAVIFCNTRRKVDNLTDKL  283 (397)
T ss_pred             H--hhhcceEEecchhhHHHHHHHH
Confidence            8  5569999999999999887664

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

Probab=100.00  E-value=1.2e-39  Score=282.34  Aligned_cols=270  Identities=26%  Similarity=0.429  Sum_probs=223.4

Q ss_pred             eeecccCCccccCcccCCCCHHHHHHHHH-CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhcc---
Q 022724           22 VFETTEGVEAITSFDAMGIKDDLLRGIYQ-YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT---   97 (293)
Q Consensus        22 ~~~~~~~~~~~~~f~~~~l~~~i~~~l~~-~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~---   97 (293)
                      ..+..+.+-....|.++++++.+.+.|+. +++..||.+|+++||.+++|+|++|.++||||||++|++|+++.+..   
T Consensus       125 vk~v~e~~fts~~f~~LGL~~~lv~~L~~~m~i~~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~  204 (708)
T KOG0348|consen  125 VKQVSEAPFTSAAFASLGLHPHLVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEP  204 (708)
T ss_pred             hccccccccccccchhcCCCHHHHHHHHHHhccCccchHhhcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCc
Confidence            33444455567789999999999999974 79999999999999999999999999999999999999999998843   


Q ss_pred             ---CCCceeEEEEcCCHHHHHHHHHHHHHhhccCC-ceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc-CCCC
Q 022724           98 ---SSREVQALILSPTRELATQTEKVILAIGDFIN-IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-KTLR  172 (293)
Q Consensus        98 ---~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~-~~~~  172 (293)
                         ...|+.++|++||||||.|+++.++++.+.+. +-.+.+.||.....+...+.++++|+|+||++|++.+.+ ..+.
T Consensus       205 ki~Rs~G~~ALVivPTREL~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARLRKGiNILIgTPGRLvDHLknT~~i~  284 (708)
T KOG0348|consen  205 KIQRSDGPYALVIVPTRELALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKARLRKGINILIGTPGRLVDHLKNTKSIK  284 (708)
T ss_pred             cccccCCceEEEEechHHHHHHHHHHHHHHhcCceEEeeceeecccccccHHHHHhcCceEEEcCchHHHHHHhccchhe
Confidence               34678999999999999999999999887654 334567888888888888999999999999999998877 6688


Q ss_pred             CCCccEEEecchhhhhccccHHHHHHHHhhCC-------------CCccEEEEEeecChhHHHHHHhcCCCCEEEEecCC
Q 022724          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP-------------PDLQVVLISATLPHEILEMTTKFMTDPVKILVKRD  239 (293)
Q Consensus       173 ~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~-------------~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~  239 (293)
                      ++++.++|+||+|.+++.||...+..|++.+.             ...|-+++|||+++.+..+....+.||..+..+..
T Consensus       285 ~s~LRwlVlDEaDrlleLGfekdit~Il~~v~~~~~~e~~~~~lp~q~q~mLlSATLtd~V~rLa~~sLkDpv~I~ld~s  364 (708)
T KOG0348|consen  285 FSRLRWLVLDEADRLLELGFEKDITQILKAVHSIQNAECKDPKLPHQLQNMLLSATLTDGVNRLADLSLKDPVYISLDKS  364 (708)
T ss_pred             eeeeeEEEecchhHHHhccchhhHHHHHHHHhhccchhcccccccHHHHhHhhhhhhHHHHHHHhhccccCceeeeccch
Confidence            99999999999999999999999999888872             13688999999999999999999999998872210


Q ss_pred             -------------------------cccCCCceEEEEEecCcccHHHHHHHHHh----hCCCCcEEEEcccchhHHHHHh
Q 022724          240 -------------------------ELTLEGIKQFFVAVEREEWKFDTLCDLYD----TLTITQAVIFCNTKRKVLLLVL  290 (293)
Q Consensus       240 -------------------------~~~~~~i~~~~~~~~~~~~k~~~l~~l~~----~~~~~~~iIF~~s~~~a~~l~~  290 (293)
                                               ...+.++.|.|..++..- .+..|..++.    .....++|||..+.+.++.=+.
T Consensus       365 ~~~~~p~~~a~~ev~~~~~~~~l~~~~iPeqL~qry~vVPpKL-RLV~Laa~L~~~~k~~~~qk~iVF~S~~d~VeFHy~  443 (708)
T KOG0348|consen  365 HSQLNPKDKAVQEVDDGPAGDKLDSFAIPEQLLQRYTVVPPKL-RLVALAALLLNKVKFEEKQKMIVFFSCSDSVEFHYS  443 (708)
T ss_pred             hhhcCcchhhhhhcCCcccccccccccCcHHhhhceEecCCch-hHHHHHHHHHHHhhhhhhceeEEEEechhHHHHHHH
Confidence                                     123445667777777666 5555555553    3344599999999999887665


Q ss_pred             hC
Q 022724          291 QF  292 (293)
Q Consensus       291 ~L  292 (293)
                      .|
T Consensus       444 lf  445 (708)
T KOG0348|consen  444 LF  445 (708)
T ss_pred             HH
Confidence            54

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1.2e-39  Score=302.42  Aligned_cols=272  Identities=31%  Similarity=0.508  Sum_probs=249.5

Q ss_pred             ceeecccCCccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccC--
Q 022724           21 MVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS--   98 (293)
Q Consensus        21 ~~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~--   98 (293)
                      ..+.+..-+.|+.+|...|++..++..++++||..|+|+|.+|||+|++|+++|.+|-||||||++|++|++.++...  
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            677888889999999999999999999999999999999999999999999999999999999999999999776432  


Q ss_pred             ---CCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCC---CC
Q 022724           99 ---SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT---LR  172 (293)
Q Consensus        99 ---~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~---~~  172 (293)
                         ..||-+||++||++|+.|+.+.++.+.+.+++++++++|+....+++..+++++.|+||||++...++-.+.   ..
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               358999999999999999999999999999999999999999999999999999999999999999775543   34


Q ss_pred             CCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEE
Q 022724          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVA  252 (293)
Q Consensus       173 ~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~  252 (293)
                      +.++.++|+||+|.|.+.+|..++..|+..+++..|.+++|||+|..+..+....+..|..+.+.........+.|.+..
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            56667999999999999999999999999999999999999999999999999999999999998777777889999999


Q ss_pred             ecCcccHHHHHHHHHhhC-CCCcEEEEcccchhHHHHHhhC
Q 022724          253 VEREEWKFDTLCDLYDTL-TITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       253 ~~~~~~k~~~l~~l~~~~-~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ++.+..|+..|.+++... ...++||||.+.+.|..+.+.|
T Consensus       593 ~~~e~eKf~kL~eLl~e~~e~~~tiiFv~~qe~~d~l~~~L  633 (997)
T KOG0334|consen  593 CAIENEKFLKLLELLGERYEDGKTIIFVDKQEKADALLRDL  633 (997)
T ss_pred             ecCchHHHHHHHHHHHHHhhcCCEEEEEcCchHHHHHHHHH
Confidence            997777999999999754 4569999999999999998766

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

Probab=100.00  E-value=4e-41  Score=281.80  Aligned_cols=270  Identities=30%  Similarity=0.474  Sum_probs=245.1

Q ss_pred             ceeecccCCccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhc----
Q 022724           21 MVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVD----   96 (293)
Q Consensus        21 ~~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~----   96 (293)
                      ..+++...|.|+.+|.++.++..+++.|++.|+.+|||+|.+-+|.+++|+|.+-.|-||||||+.|.+|++....    
T Consensus       158 I~veGd~ipPPIksF~eMKFP~~~L~~lk~KGI~~PTpIQvQGlPvvLsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~  237 (610)
T KOG0341|consen  158 ILVEGDDIPPPIKSFKEMKFPKPLLRGLKKKGIVHPTPIQVQGLPVVLSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEM  237 (610)
T ss_pred             EEeeCCCCCCchhhhhhccCCHHHHHHHHhcCCCCCCceeecCcceEeecCceeeEEeecCCceEEEeHHHHHHHHHHHh
Confidence            3457888899999999999999999999999999999999999999999999999999999999999999876542    


Q ss_pred             ----cCCCceeEEEEcCCHHHHHHHHHHHHHhhccC------CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHH
Q 022724           97 ----TSSREVQALILSPTRELATQTEKVILAIGDFI------NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMI  166 (293)
Q Consensus        97 ----~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l  166 (293)
                          ....||..+|+||+|+|+.|+++.+..+...+      .++...+.||.+..++...+..+.+|+|+||++|.++|
T Consensus       238 ~lPf~~~EGP~gLiicPSRELArQt~~iie~~~~~L~e~g~P~lRs~LciGG~~v~eql~~v~~GvHivVATPGRL~DmL  317 (610)
T KOG0341|consen  238 MLPFARGEGPYGLIICPSRELARQTHDIIEQYVAALQEAGYPELRSLLCIGGVPVREQLDVVRRGVHIVVATPGRLMDML  317 (610)
T ss_pred             cCccccCCCCeeEEEcCcHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhhcCccHHHHHHHHhcCeeEEEcCcchHHHHH
Confidence                23468899999999999999999988765333      46888999999999999999999999999999999999


Q ss_pred             hcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCc
Q 022724          167 KRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGI  246 (293)
Q Consensus       167 ~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  246 (293)
                      .....++.-+.++++||||+|.+.+|..+++.++..+...+|.++||||+|..+..+++..+-.|..+++.+.....-++
T Consensus       318 ~KK~~sLd~CRyL~lDEADRmiDmGFEddir~iF~~FK~QRQTLLFSATMP~KIQ~FAkSALVKPvtvNVGRAGAAsldV  397 (610)
T KOG0341|consen  318 AKKIMSLDACRYLTLDEADRMIDMGFEDDIRTIFSFFKGQRQTLLFSATMPKKIQNFAKSALVKPVTVNVGRAGAASLDV  397 (610)
T ss_pred             HHhhccHHHHHHhhhhhHHHHhhccchhhHHHHHHHHhhhhheeeeeccccHHHHHHHHhhcccceEEecccccccchhH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999888777778


Q ss_pred             eEEEEEecCcccHHHHHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          247 KQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       247 ~~~~~~~~~~~~k~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      .|.+.++..+. |+..+.+.+++.+ .+++|||..+.+++.++++|
T Consensus       398 iQevEyVkqEa-KiVylLeCLQKT~-PpVLIFaEkK~DVD~IhEYL  441 (610)
T KOG0341|consen  398 IQEVEYVKQEA-KIVYLLECLQKTS-PPVLIFAEKKADVDDIHEYL  441 (610)
T ss_pred             HHHHHHHHhhh-hhhhHHHHhccCC-CceEEEeccccChHHHHHHH
Confidence            88887787777 8888888776654 59999999999999998875

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

Probab=100.00  E-value=3e-39  Score=272.79  Aligned_cols=260  Identities=31%  Similarity=0.498  Sum_probs=237.8

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCC-CceeEEEEcCC
Q 022724           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-REVQALILSPT  110 (293)
Q Consensus        32 ~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~-~~~~~lil~P~  110 (293)
                      ..+|..++|+..+.+++.+.||..|+|+|+..+|.++++++++-.+-||||||.||++|+++++.... .|.|++++.|+
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            57899999999999999999999999999999999999999999999999999999999999987653 56799999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcc
Q 022724          111 RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (293)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~  190 (293)
                      ++|+.|+.+..+.+++.++++..+++|+.+..++...+..++|||++||+++.++.-.-.+.++.+.|+|+||+|.+.+.
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            99999999999999999999999999999999999999988999999999999988777788999999999999999999


Q ss_pred             ccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHhhC
Q 022724          191 GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL  270 (293)
Q Consensus       191 ~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~  270 (293)
                      ||.+++..++++++...|.++||||+|..+.++.+..+.+|..+..+-...........+..+...+ |...|..++...
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            9999999999999999999999999999999999999999999987765555556666677677666 999999998765


Q ss_pred             C-CCcEEEEcccchhHHHHHhhC
Q 022724          271 T-ITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       271 ~-~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      . ..+++|||.|...++.+...|
T Consensus       259 ~~~~~t~vf~~tk~hve~~~~ll  281 (529)
T KOG0337|consen  259 IKDKQTIVFVATKHHVEYVRGLL  281 (529)
T ss_pred             ccccceeEEecccchHHHHHHHH
Confidence            4 459999999999999887643

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=5.8e-39  Score=279.00  Aligned_cols=265  Identities=26%  Similarity=0.423  Sum_probs=222.3

Q ss_pred             ccCCccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcC-CcEEEEcCCCChhHHHHHHHHHhhhccC------
Q 022724           26 TEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG-RDVIAQAQSGTGKTSMIALTVCQTVDTS------   98 (293)
Q Consensus        26 ~~~~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~-~~~li~~~Tg~GKT~~~~~~~~~~l~~~------   98 (293)
                      +.....++-|..|+++.+++++|..+||..||++|...+|+...| .|++.-|.||||||+||-+|+++.+...      
T Consensus       174 ~~~~~DvsAW~~l~lp~~iL~aL~~~gFs~Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e  253 (731)
T KOG0347|consen  174 DSSKVDVSAWKNLFLPMEILRALSNLGFSRPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLESSDDSQE  253 (731)
T ss_pred             cccccChHHHhcCCCCHHHHHHHHhcCCCCCccchhhcccHhhccchhcccccccCCCceeeecchhhhhhhhccchHhh
Confidence            334455778999999999999999999999999999999999988 6999999999999999999999965432      


Q ss_pred             -----CCcee--EEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCC-
Q 022724           99 -----SREVQ--ALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT-  170 (293)
Q Consensus        99 -----~~~~~--~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~-  170 (293)
                           ..+++  ++|++|||+||.|+...+..+....++++..+.||.....|.+.+...++|+|+||++|+.++..+. 
T Consensus       254 ~~~~~~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQqRlL~~~p~IVVATPGRlweli~e~n~  333 (731)
T KOG0347|consen  254 LSNTSAKYVKPIALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQRLLNQRPDIVVATPGRLWELIEEDNT  333 (731)
T ss_pred             hhhHHhccCcceeEEecChHHHHHHHHHHHHHhccccCeEEEEeechhHHHHHHHHHhcCCCEEEecchHHHHHHHhhhh
Confidence                 12344  9999999999999999999999999999999999999999999999999999999999999997743 


Q ss_pred             --CCCCCccEEEecchhhhhccccHHHHHHHHhhCC-----CCccEEEEEeecChh---------------------HHH
Q 022724          171 --LRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP-----PDLQVVLISATLPHE---------------------ILE  222 (293)
Q Consensus       171 --~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~-----~~~q~v~~SAt~~~~---------------------~~~  222 (293)
                        -.++++.++|+||+|+|.+.|+...+..++..+.     ...|.+.+|||++-.                     +..
T Consensus       334 ~l~~~k~vkcLVlDEaDRmvekghF~Els~lL~~L~e~~~~~qrQTlVFSATlt~~~~~~~~~~~k~~~k~~~~~~kiq~  413 (731)
T KOG0347|consen  334 HLGNFKKVKCLVLDEADRMVEKGHFEELSKLLKHLNEEQKNRQRQTLVFSATLTLVLQQPLSSSRKKKDKEDELNAKIQH  413 (731)
T ss_pred             hhhhhhhceEEEEccHHHHhhhccHHHHHHHHHHhhhhhcccccceEEEEEEeehhhcChhHHhhhccchhhhhhHHHHH
Confidence              4678899999999999999998888888888775     457999999998432                     122


Q ss_pred             HHHh--cCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          223 MTTK--FMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       223 ~~~~--~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ++..  +...|..+...+.......+....+.|+..+ |.-.+.+++..++ +++|||||+++.+.+++..|
T Consensus       414 Lmk~ig~~~kpkiiD~t~q~~ta~~l~Es~I~C~~~e-KD~ylyYfl~ryP-GrTlVF~NsId~vKRLt~~L  483 (731)
T KOG0347|consen  414 LMKKIGFRGKPKIIDLTPQSATASTLTESLIECPPLE-KDLYLYYFLTRYP-GRTLVFCNSIDCVKRLTVLL  483 (731)
T ss_pred             HHHHhCccCCCeeEecCcchhHHHHHHHHhhcCCccc-cceeEEEEEeecC-CceEEEechHHHHHHHHHHH
Confidence            2222  2345677777777667777777788886665 7767777776665 79999999999999998765

>KOG4284 consensus DEAD box protein [Transcription]

Probab=100.00  E-value=4.4e-38  Score=277.90  Aligned_cols=263  Identities=29%  Similarity=0.526  Sum_probs=242.8

Q ss_pred             ccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcC
Q 022724           30 EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (293)
Q Consensus        30 ~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P  109 (293)
                      .....|+++.+...++..|+..+|..|+++|..|||+++.+.|+||.+-.|+|||++|...+++.+......++++|++|
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            34578999999999999999999999999999999999999999999999999999999999999988888899999999


Q ss_pred             CHHHHHHHHHHHHHhhcc-CCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhh
Q 022724          110 TRELATQTEKVILAIGDF-INIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (293)
Q Consensus       110 ~~~l~~q~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~  188 (293)
                      ||+++-|+.+.+.+++.. .|+++..+.||+........++ .++|+||||+++.+++..+.++.++++++|+||||.++
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            999999999999998864 5899999999998877766664 46899999999999999999999999999999999998


Q ss_pred             c-cccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcc-------cHH
Q 022724          189 S-RGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREE-------WKF  260 (293)
Q Consensus       189 ~-~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~-------~k~  260 (293)
                      + ..|..++..++..++...|++++|||.|..+.+.+.++|.+|..+..+..+...-++.|++......+       .|.
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 57999999999999999999999999999999999999999999999999888999999998877653       377


Q ss_pred             HHHHHHHhhCCCCcEEEEcccchhHHHHHhhCC
Q 022724          261 DTLCDLYDTLTITQAVIFCNTKRKVLLLVLQFP  293 (293)
Q Consensus       261 ~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L~  293 (293)
                      +.|.+++...+-.++||||+....|+.++..|.
T Consensus       261 q~L~~vf~~ipy~QAlVF~~~~sra~~~a~~L~  293 (980)
T KOG4284|consen  261 QKLTHVFKSIPYVQALVFCDQISRAEPIATHLK  293 (980)
T ss_pred             HHHHHHHhhCchHHHHhhhhhhhhhhHHHHHhh
Confidence            788889999888899999999999999998773

>cd00268 DEADc DEAD-box helicases

Probab=100.00  E-value=5.6e-36  Score=244.42  Aligned_cols=200  Identities=47%  Similarity=0.812  Sum_probs=184.7

Q ss_pred             cccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccC--CCceeEEEEcCCHH
Q 022724           35 FDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS--SREVQALILSPTRE  112 (293)
Q Consensus        35 f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~--~~~~~~lil~P~~~  112 (293)
                      |+++++++.+.+.+.++|++.|+++|+++++.+.+|+|+++++|||+|||++|++|+++.+...  ..+++++|++|+++
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            7899999999999999999999999999999999999999999999999999999999998876  56789999999999


Q ss_pred             HHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcccc
Q 022724          113 LATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF  192 (293)
Q Consensus       113 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~  192 (293)
                      |+.|+...++.+....++.+..++|+.+.......+.++++|+|+||+++..++.++...+.+++++|+||+|.+.+.++
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            99999999999988888899999999887777666766889999999999999988888889999999999999988888


Q ss_pred             HHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEE
Q 022724          193 KDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKI  234 (293)
Q Consensus       193 ~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~  234 (293)
                      ...+..+.+.++..+|++++|||+++....++..++.+|..+
T Consensus       161 ~~~~~~~~~~l~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~  202 (203)
T cd00268         161 EDQIREILKLLPKDRQTLLFSATMPKEVRDLARKFLRNPVRI  202 (203)
T ss_pred             HHHHHHHHHhCCcccEEEEEeccCCHHHHHHHHHHCCCCEEe
Confidence            999999999999899999999999999999998888887665

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.

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

Probab=100.00  E-value=6.2e-36  Score=283.56  Aligned_cols=244  Identities=20%  Similarity=0.243  Sum_probs=185.3

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHH
Q 022724           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (293)
Q Consensus        40 l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~  119 (293)
                      +++++.++|++.||..|+++|.++++.+.+|+|+++++|||||||+||++|+++.+... .+.++|||+|+++|+.|+.+
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            79999999999999999999999999999999999999999999999999999998764 35799999999999999999


Q ss_pred             HHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHH-hcC---CCCCCCccEEEecchhhhhccccHHH
Q 022724          120 VILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMI-KRK---TLRTRAIKLLVLDESDEMLSRGFKDQ  195 (293)
Q Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l-~~~---~~~~~~l~~iViDE~h~~~~~~~~~~  195 (293)
                      .++.+. ..++++..+.|+.+.. +.+.+.++++|+|+||+.+...+ ...   ...++++++|||||+|.+.+ .|+..
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 4578888888877654 44556667899999999997533 221   12378999999999999865 35555


Q ss_pred             HHHHHhh-------CCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecC-------------
Q 022724          196 IYDVYRY-------LPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVER-------------  255 (293)
Q Consensus       196 ~~~i~~~-------l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~-------------  255 (293)
                      +..++++       .+...|++++|||+++... .+..++..+..+. ... ..+....+.....+.             
T Consensus       177 ~~~il~rL~ri~~~~g~~~q~i~~SATi~n~~~-~~~~l~g~~~~~i-~~~-~~~~~~~~~~~~~p~~~~~~~~~~~~~r  253 (742)
T TIGR03817       177 VALVLRRLRRLCARYGASPVFVLASATTADPAA-AASRLIGAPVVAV-TED-GSPRGARTVALWEPPLTELTGENGAPVR  253 (742)
T ss_pred             HHHHHHHHHHHHHhcCCCCEEEEEecCCCCHHH-HHHHHcCCCeEEE-CCC-CCCcCceEEEEecCCccccccccccccc
Confidence            4444333       4567899999999998754 5677777775543 222 222222223222221             


Q ss_pred             ---cccHHHHHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          256 ---EEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       256 ---~~~k~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                         ...+...+..+++.  +.++||||||++.|+.++..|
T Consensus       254 ~~~~~~~~~~l~~l~~~--~~~~IVF~~sr~~ae~l~~~l  291 (742)
T TIGR03817       254 RSASAEAADLLADLVAE--GARTLTFVRSRRGAELVAAIA  291 (742)
T ss_pred             cchHHHHHHHHHHHHHC--CCCEEEEcCCHHHHHHHHHHH
Confidence               01244456666653  569999999999999998764

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.

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

Probab=100.00  E-value=4.6e-37  Score=244.47  Aligned_cols=252  Identities=35%  Similarity=0.615  Sum_probs=233.5

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCH
Q 022724           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (293)
Q Consensus        32 ~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~  111 (293)
                      .+.|.++-|.+++++++-++||..|+..|.+++|...-|.|++..|.+|.|||..|.++-++.+...+....++++|++|
T Consensus        41 ssgfrdfllkpellraivdcgfehpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqiepv~g~vsvlvmchtr  120 (387)
T KOG0329|consen   41 SSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPVDGQVSVLVMCHTR  120 (387)
T ss_pred             ccchhhhhcCHHHHHHHHhccCCCchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcCCCCCeEEEEEEeccH
Confidence            45799999999999999999999999999999999999999999999999999999999999999888888999999999


Q ss_pred             HHHHHHHHHHHHhhccC-CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcc
Q 022724          112 ELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (293)
Q Consensus       112 ~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~  190 (293)
                      +|+-|+.....++.+.. ++++...+||.+.......+.+.++|+|+||++++.+.+++.+++++++.+|+||+|.|++.
T Consensus       121 elafqi~~ey~rfskymP~vkvaVFfGG~~Ikkdee~lk~~PhivVgTPGrilALvr~k~l~lk~vkhFvlDEcdkmle~  200 (387)
T KOG0329|consen  121 ELAFQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELLKNCPHIVVGTPGRILALVRNRSLNLKNVKHFVLDECDKMLEQ  200 (387)
T ss_pred             HHHHHHHHHHHHHHhhCCCceEEEEEcceeccccHHHHhCCCeEEEcCcHHHHHHHHhccCchhhcceeehhhHHHHHHH
Confidence            99999999998887776 68999999999999888889899999999999999999999999999999999999998865


Q ss_pred             -ccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCc-ccCCCceEEEEEecCcccHHHHHHHHHh
Q 022724          191 -GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDE-LTLEGIKQFFVAVEREEWKFDTLCDLYD  268 (293)
Q Consensus       191 -~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~i~~~~~~~~~~~~k~~~l~~l~~  268 (293)
                       ..+.++..+.+..+...|++.+|||++.++...++++|.+|..+.++... ....++.|+|....+.+ |...+.++++
T Consensus       201 lDMrRDvQEifr~tp~~KQvmmfsatlskeiRpvC~kFmQdPmEi~vDdE~KLtLHGLqQ~YvkLke~e-KNrkl~dLLd  279 (387)
T KOG0329|consen  201 LDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCHKFMQDPMEIFVDDEAKLTLHGLQQYYVKLKENE-KNRKLNDLLD  279 (387)
T ss_pred             HHHHHHHHHHhhcCcccceeeeeeeecchhhHHHHHhhhcCchhhhccchhhhhhhhHHHHHHhhhhhh-hhhhhhhhhh
Confidence             67889999999999999999999999999999999999999999887653 46788999999998887 8888888888


Q ss_pred             hCCCCcEEEEcccchh
Q 022724          269 TLTITQAVIFCNTKRK  284 (293)
Q Consensus       269 ~~~~~~~iIF~~s~~~  284 (293)
                      ....++++||+.++..
T Consensus       280 ~LeFNQVvIFvKsv~R  295 (387)
T KOG0329|consen  280 VLEFNQVVIFVKSVQR  295 (387)
T ss_pred             hhhhcceeEeeehhhh
Confidence            8888899999999876

>PRK02362 ski2-like helicase; Provisional

Probab=100.00  E-value=3.7e-35  Score=280.46  Aligned_cols=248  Identities=18%  Similarity=0.248  Sum_probs=183.8

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHh-hhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHH
Q 022724           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (293)
Q Consensus        34 ~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~-i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~  112 (293)
                      .|+++++++++.+.+++.||..|+|+|.++++. +.+|+|+++++|||+|||++|.+|++..+..   +.++||++|+++
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 7789999999999999999999999998863   568999999999


Q ss_pred             HHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcccc
Q 022724          113 LATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF  192 (293)
Q Consensus       113 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~  192 (293)
                      |+.|+++.++++.. .++++..++|+......   ....++|+|+||+++..+++++...+++++++|+||+|++.+.++
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            99999999998653 58899889888754432   224579999999999999987666688999999999999988888


Q ss_pred             HHHHHHHHhhC---CCCccEEEEEeecChhHHHHHHhcCCC-------CEEE--EecCCcc-cCCCceEEEEEecCcccH
Q 022724          193 KDQIYDVYRYL---PPDLQVVLISATLPHEILEMTTKFMTD-------PVKI--LVKRDEL-TLEGIKQFFVAVEREEWK  259 (293)
Q Consensus       193 ~~~~~~i~~~l---~~~~q~v~~SAt~~~~~~~~~~~~~~~-------~~~~--~~~~~~~-~~~~i~~~~~~~~~~~~k  259 (293)
                      +..++.++.++   .+..|+|++|||+++. .++..+....       |..+  .+..... .... .+...........
T Consensus       155 g~~le~il~rl~~~~~~~qii~lSATl~n~-~~la~wl~~~~~~~~~rpv~l~~~v~~~~~~~~~~-~~~~~~~~~~~~~  232 (737)
T PRK02362        155 GPTLEVTLAKLRRLNPDLQVVALSATIGNA-DELADWLDAELVDSEWRPIDLREGVFYGGAIHFDD-SQREVEVPSKDDT  232 (737)
T ss_pred             hHHHHHHHHHHHhcCCCCcEEEEcccCCCH-HHHHHHhCCCcccCCCCCCCCeeeEecCCeecccc-ccccCCCccchHH
Confidence            87777766554   4678999999999763 3344333211       1111  0000000 0000 0111111111112


Q ss_pred             HHHHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          260 FDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       260 ~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ...+...+.  .++++||||+|+++|+.++..|
T Consensus       233 ~~~~~~~~~--~~~~~LVF~~sr~~~~~~a~~L  263 (737)
T PRK02362        233 LNLVLDTLE--EGGQCLVFVSSRRNAEGFAKRA  263 (737)
T ss_pred             HHHHHHHHH--cCCCeEEEEeCHHHHHHHHHHH
Confidence            333333333  4579999999999999988765

>PRK00254 ski2-like helicase; Provisional

Probab=100.00  E-value=1.1e-34  Score=276.45  Aligned_cols=245  Identities=16%  Similarity=0.201  Sum_probs=188.7

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHh-hhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHH
Q 022724           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (293)
Q Consensus        34 ~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~-i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~  112 (293)
                      +|+++++++.+.+.+++.||..|+|+|.++++. +.+|+|+++++|||+|||++|.+|++..+...  +.++||++|+++
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            578999999999999999999999999999996 78999999999999999999999999887653  458999999999


Q ss_pred             HHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcccc
Q 022724          113 LATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF  192 (293)
Q Consensus       113 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~  192 (293)
                      |+.|+++.++.+. ..++++..++|+.+....   ....++|+|+||+++..+++.+...++++++||+||+|.+.+.++
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            9999999998864 468899999988764432   234579999999999999887766789999999999999988888


Q ss_pred             HHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCce-----EEEEEecCcc-c-----HHH
Q 022724          193 KDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIK-----QFFVAVEREE-W-----KFD  261 (293)
Q Consensus       193 ~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~-----~~~~~~~~~~-~-----k~~  261 (293)
                      +..+..+++.+....|+|++|||+++. .++..++....  +...   ..+..+.     +.+....... .     ...
T Consensus       156 g~~le~il~~l~~~~qiI~lSATl~n~-~~la~wl~~~~--~~~~---~rpv~l~~~~~~~~~~~~~~~~~~~~~~~~~~  229 (720)
T PRK00254        156 GATLEMILTHMLGRAQILGLSATVGNA-EELAEWLNAEL--VVSD---WRPVKLRKGVFYQGFLFWEDGKIERFPNSWES  229 (720)
T ss_pred             hHHHHHHHHhcCcCCcEEEEEccCCCH-HHHHHHhCCcc--ccCC---CCCCcceeeEecCCeeeccCcchhcchHHHHH
Confidence            999999999998899999999999863 55555432221  1111   1111111     1111111111 0     112


Q ss_pred             HHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          262 TLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       262 ~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      .+.+.++  .++++||||+|++.|+.++..|
T Consensus       230 ~~~~~i~--~~~~vLVF~~sr~~~~~~a~~l  258 (720)
T PRK00254        230 LVYDAVK--KGKGALVFVNTRRSAEKEALEL  258 (720)
T ss_pred             HHHHHHH--hCCCEEEEEcChHHHHHHHHHH
Confidence            2333343  3579999999999999887554

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

Probab=100.00  E-value=2.7e-34  Score=247.52  Aligned_cols=260  Identities=20%  Similarity=0.329  Sum_probs=209.9

Q ss_pred             ccCcccCCCCHHHH----------HHHHHCCCCCCcHHHHHHHHhhh---------cCCcEEEEcCCCChhHHHHHHHHH
Q 022724           32 ITSFDAMGIKDDLL----------RGIYQYGFEKPSAIQQRAVMPII---------KGRDVIAQAQSGTGKTSMIALTVC   92 (293)
Q Consensus        32 ~~~f~~~~l~~~i~----------~~l~~~~~~~~~~~Q~~~~~~i~---------~~~~~li~~~Tg~GKT~~~~~~~~   92 (293)
                      ...|+.++++....          +++.++++....|+|..++|.++         .++|+.|.||||||||+||.+|++
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            34567776665443          44888999999999999999885         257999999999999999999999


Q ss_pred             hhhccCC-CceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcC-----CcEEEeChHHHHHHH
Q 022724           93 QTVDTSS-REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG-----VHVVSGTPGRVCDMI  166 (293)
Q Consensus        93 ~~l~~~~-~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~ilV~Tp~~l~~~l  166 (293)
                      +.+...+ +..|+||++|+++|+.|+++.+.++....|+.|+.+.|..+..++.+.+.+.     .||+|+||++|.+.+
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            9987763 3479999999999999999999999999999999999999988888877532     389999999999999


Q ss_pred             hc-CCCCCCCccEEEecchhhhhccccHHHHHHHHhhC----------------------------------CCCccEEE
Q 022724          167 KR-KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL----------------------------------PPDLQVVL  211 (293)
Q Consensus       167 ~~-~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l----------------------------------~~~~q~v~  211 (293)
                      ++ ..++++++.|+||||||++++..|..-+..+...+                                  .+..+.++
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            85 78999999999999999998765443332222221                                  12346888


Q ss_pred             EEeecChhHHHHHHhcCCCCEEEEec----CCcccCCCceEEEEEecCcccHHHHHHHHHhhCCCCcEEEEcccchhHHH
Q 022724          212 ISATLPHEILEMTTKFMTDPVKILVK----RDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLL  287 (293)
Q Consensus       212 ~SAt~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~~iIF~~s~~~a~~  287 (293)
                      +|||++.+-..+...-+..|..+.+.    .....+..+.++++.++... |.-.+..++......++|+|+|+.+.+.+
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            99999777666666666677555554    23455667888888887766 78888899999999999999999999999


Q ss_pred             HHhhC
Q 022724          288 LVLQF  292 (293)
Q Consensus       288 l~~~L  292 (293)
                      ++..|
T Consensus       445 l~~~L  449 (620)
T KOG0350|consen  445 LAHVL  449 (620)
T ss_pred             HHHHH
Confidence            98765

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

Probab=100.00  E-value=1e-33  Score=263.66  Aligned_cols=246  Identities=18%  Similarity=0.220  Sum_probs=192.8

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccC-----CCceeEEEEcCCHHHH
Q 022724           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-----SREVQALILSPTRELA  114 (293)
Q Consensus        40 l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~-----~~~~~~lil~P~~~l~  114 (293)
                      +++.+.+.+++. |..||+.|.+|||.+.+|+|++++||||||||+++.+|++..+...     ..+..+||++|.++|.
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            689999999987 9999999999999999999999999999999999999999998766     3457899999999999


Q ss_pred             HHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCC--CCCCCccEEEecchhhhhcccc
Q 022724          115 TQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT--LRTRAIKLLVLDESDEMLSRGF  192 (293)
Q Consensus       115 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~--~~~~~l~~iViDE~h~~~~~~~  192 (293)
                      +++.+.++.+....|+.+...+|+++..+..+...+++||+|+||+.|.-++....  -.+.++.++||||+|.+.+...
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            99999999999999999999999999888888889999999999999998886632  3479999999999999987766


Q ss_pred             HHHHHHHHhhCC---CCccEEEEEeecChhHHHHHHhcCCC--CEEEEecCCcccCCCceEEEEEecCc--------ccH
Q 022724          193 KDQIYDVYRYLP---PDLQVVLISATLPHEILEMTTKFMTD--PVKILVKRDELTLEGIKQFFVAVERE--------EWK  259 (293)
Q Consensus       193 ~~~~~~i~~~l~---~~~q~v~~SAt~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~i~~~~~~~~~~--------~~k  259 (293)
                      +.++...+.++.   ...|.|++|||+.+. ....+++.+.  +..+..... .....+  .+......        ..-
T Consensus       167 G~~Lsl~LeRL~~l~~~~qRIGLSATV~~~-~~varfL~g~~~~~~Iv~~~~-~k~~~i--~v~~p~~~~~~~~~~~~~~  242 (814)
T COG1201         167 GVQLALSLERLRELAGDFQRIGLSATVGPP-EEVAKFLVGFGDPCEIVDVSA-AKKLEI--KVISPVEDLIYDEELWAAL  242 (814)
T ss_pred             chhhhhhHHHHHhhCcccEEEeehhccCCH-HHHHHHhcCCCCceEEEEccc-CCcceE--EEEecCCccccccchhHHH
Confidence            665544333332   389999999999743 5555555544  333333222 222222  22222111        112


Q ss_pred             HHHHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          260 FDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       260 ~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      +..+.++++++.  .++||+||+..|+.++..|
T Consensus       243 ~~~i~~~v~~~~--ttLIF~NTR~~aE~l~~~L  273 (814)
T COG1201         243 YERIAELVKKHR--TTLIFTNTRSGAERLAFRL  273 (814)
T ss_pred             HHHHHHHHhhcC--cEEEEEeChHHHHHHHHHH
Confidence            444555666654  9999999999999998765

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

Probab=100.00  E-value=2.6e-32  Score=255.55  Aligned_cols=237  Identities=20%  Similarity=0.245  Sum_probs=179.5

Q ss_pred             HHHHH-CCCCCCcHHHHHHHHhhhcCC-cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEE-EcCCHHHHHHHHHHHH
Q 022724           46 RGIYQ-YGFEKPSAIQQRAVMPIIKGR-DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALI-LSPTRELATQTEKVIL  122 (293)
Q Consensus        46 ~~l~~-~~~~~~~~~Q~~~~~~i~~~~-~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~li-l~P~~~l~~q~~~~~~  122 (293)
                      +.+++ .||+ |+|+|.++++.++.|+ ++++.+|||||||.++.++++.. ......++.+| ++|+++|+.|+++.++
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            34443 5888 9999999999999998 67788999999998766555432 22233455555 7799999999999999


Q ss_pred             HhhccC-----------------------CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCC--------
Q 022724          123 AIGDFI-----------------------NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL--------  171 (293)
Q Consensus       123 ~~~~~~-----------------------~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~--------  171 (293)
                      ++.+.+                       ++++..++||.+...+...+..+++|+|+|++.+.    ++.+        
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            988755                       47889999999999999999999999999975443    3333        


Q ss_pred             --------CCCCccEEEecchhhhhccccHHHHHHHHhhC--CC---CccEEEEEeecChhHHHHHHhcCCCCEEEEecC
Q 022724          172 --------RTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL--PP---DLQVVLISATLPHEILEMTTKFMTDPVKILVKR  238 (293)
Q Consensus       172 --------~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l--~~---~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~  238 (293)
                              .+.++++||+||||  ++.+|...+..+++.+  ++   ..|+++||||++.++......++.++..+.+..
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   269999999999988888777777777666655


Q ss_pred             CcccCCCceEEEEEecCcccHHHHHHHHH---hhCCCCcEEEEcccchhHHHHHhhC
Q 022724          239 DELTLEGIKQFFVAVEREEWKFDTLCDLY---DTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       239 ~~~~~~~i~~~~~~~~~~~~k~~~l~~l~---~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ......++.++ ..++.+. |...+...+   ....++++||||||+++|+.+++.|
T Consensus       238 ~~l~a~ki~q~-v~v~~e~-Kl~~lv~~L~~ll~e~g~~vLVF~NTv~~Aq~L~~~L  292 (844)
T TIGR02621       238 KRLAAKKIVKL-VPPSDEK-FLSTMVKELNLLMKDSGGAILVFCRTVKHVRKVFAKL  292 (844)
T ss_pred             ccccccceEEE-EecChHH-HHHHHHHHHHHHHhhCCCcEEEEECCHHHHHHHHHHH
Confidence            55555566664 3333332 443322221   1234579999999999999999876

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=2.3e-32  Score=263.94  Aligned_cols=248  Identities=19%  Similarity=0.243  Sum_probs=174.5

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccC------CCceeEEEEcCCHHH
Q 022724           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS------SREVQALILSPTREL  113 (293)
Q Consensus        40 l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~------~~~~~~lil~P~~~l  113 (293)
                      +++.+.+.+.+ +|..|+|+|.++|+.+.+|+|+++++|||||||++|.+|+++.+...      ..+.++||++|+++|
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            57778887776 78999999999999999999999999999999999999999887532      245789999999999


Q ss_pred             HHHHHHHHHH-------hh----ccC-CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCC--CCCCccEE
Q 022724          114 ATQTEKVILA-------IG----DFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL--RTRAIKLL  179 (293)
Q Consensus       114 ~~q~~~~~~~-------~~----~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~--~~~~l~~i  179 (293)
                      +.|+.+.+..       +.    ... ++++...+|+.+.....+.+.++++|+|+||+++..++.+..+  .++++++|
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       21    222 6788889999988877777778899999999999888766443  47899999


Q ss_pred             EecchhhhhccccHHHHHHH----HhhCCCCccEEEEEeecChhHHHHHHhcCC-------CCEEEEecCCcccCCCceE
Q 022724          180 VLDESDEMLSRGFKDQIYDV----YRYLPPDLQVVLISATLPHEILEMTTKFMT-------DPVKILVKRDELTLEGIKQ  248 (293)
Q Consensus       180 ViDE~h~~~~~~~~~~~~~i----~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~i~~  248 (293)
                      ||||+|.+.+..++..+...    ....+...|++++|||+++. .....+...       .+..+. .........+..
T Consensus       177 VIDE~H~l~~~~RG~~l~~~L~rL~~l~~~~~q~IglSATl~~~-~~va~~L~~~~~~~~~r~~~iv-~~~~~k~~~i~v  254 (876)
T PRK13767        177 IVDEIHSLAENKRGVHLSLSLERLEELAGGEFVRIGLSATIEPL-EEVAKFLVGYEDDGEPRDCEIV-DARFVKPFDIKV  254 (876)
T ss_pred             EEechhhhccCccHHHHHHHHHHHHHhcCCCCeEEEEecccCCH-HHHHHHhcCccccCCCCceEEE-ccCCCccceEEE
Confidence            99999999877666554443    33334678999999999762 333332221       122221 111111111110


Q ss_pred             E-----EEEecCcc---cHHHHHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          249 F-----FVAVEREE---WKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       249 ~-----~~~~~~~~---~k~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      .     ........   .....+..+++  .++++||||||++.|+.++..|
T Consensus       255 ~~p~~~l~~~~~~~~~~~l~~~L~~~i~--~~~~~LVF~nTr~~ae~la~~L  304 (876)
T PRK13767        255 ISPVDDLIHTPAEEISEALYETLHELIK--EHRTTLIFTNTRSGAERVLYNL  304 (876)
T ss_pred             eccCccccccccchhHHHHHHHHHHHHh--cCCCEEEEeCCHHHHHHHHHHH
Confidence            0     00011111   11222333333  2469999999999999998765

>PRK01172 ski2-like helicase; Provisional

Probab=100.00  E-value=1.9e-32  Score=260.06  Aligned_cols=245  Identities=17%  Similarity=0.210  Sum_probs=181.0

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHH
Q 022724           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (293)
Q Consensus        34 ~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l  113 (293)
                      .|+++++++.+.+.+.+.+|. ++++|.++++.+.+|+|+++++|||+|||+++.++++..+..   +.++||++|+++|
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            578899999999999998887 999999999999999999999999999999999999988765   4589999999999


Q ss_pred             HHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccH
Q 022724          114 ATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFK  193 (293)
Q Consensus       114 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~  193 (293)
                      +.|+++.++++. ..|.++....|+......   ....++|+|+||+++..++++....+++++++|+||+|++.+.+++
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            999999998864 467888888887654322   2245799999999999988877666899999999999999887777


Q ss_pred             HHHHHHHhh---CCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEE-----EecCcccHHHHHHH
Q 022724          194 DQIYDVYRY---LPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFV-----AVEREEWKFDTLCD  265 (293)
Q Consensus       194 ~~~~~i~~~---l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~-----~~~~~~~k~~~l~~  265 (293)
                      ..++.++..   +++..|+|++|||+++. .++..++....  +...   ..+..+.....     ..+........+..
T Consensus       154 ~~le~ll~~~~~~~~~~riI~lSATl~n~-~~la~wl~~~~--~~~~---~r~vpl~~~i~~~~~~~~~~~~~~~~~~~~  227 (674)
T PRK01172        154 PTLETVLSSARYVNPDARILALSATVSNA-NELAQWLNASL--IKSN---FRPVPLKLGILYRKRLILDGYERSQVDINS  227 (674)
T ss_pred             HHHHHHHHHHHhcCcCCcEEEEeCccCCH-HHHHHHhCCCc--cCCC---CCCCCeEEEEEecCeeeecccccccccHHH
Confidence            777666544   45688999999999764 45554432211  1100   11111111110     11111101111223


Q ss_pred             HHhh--CCCCcEEEEcccchhHHHHHhhC
Q 022724          266 LYDT--LTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       266 l~~~--~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ++..  ..++++||||+++++|+.++..|
T Consensus       228 ~i~~~~~~~~~vLVF~~sr~~~~~~a~~L  256 (674)
T PRK01172        228 LIKETVNDGGQVLVFVSSRKNAEDYAEML  256 (674)
T ss_pred             HHHHHHhCCCcEEEEeccHHHHHHHHHHH
Confidence            3332  24579999999999999998765

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

Probab=100.00  E-value=8.7e-33  Score=242.91  Aligned_cols=272  Identities=25%  Similarity=0.341  Sum_probs=234.1

Q ss_pred             ceeecccCCccccCcccC----CCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhc
Q 022724           21 MVFETTEGVEAITSFDAM----GIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVD   96 (293)
Q Consensus        21 ~~~~~~~~~~~~~~f~~~----~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~   96 (293)
                      ..+.+...+.++.+|.++    ..++.+++++...+|..|+|+|.+++|.++.+++++.|+|||+|||++|.+|++.++.
T Consensus       120 ~~v~G~~~~~~l~~f~~lt~~~~~~~~ll~nl~~~~F~~Pt~iq~~aipvfl~~r~~lAcapTGsgKtlaf~~Pil~~L~  199 (593)
T KOG0344|consen  120 INVDGFHLPPPLLSFSDLTYDYSMNKRLLENLQELGFDEPTPIQKQAIPVFLEKRDVLACAPTGSGKTLAFNLPILQHLK  199 (593)
T ss_pred             eeccCCCCCCccccccccchhhhhcHHHHHhHhhCCCCCCCcccchhhhhhhcccceEEeccCCCcchhhhhhHHHHHHH
Confidence            344566778889999984    5788999999999999999999999999999999999999999999999999999885


Q ss_pred             cC-----CCceeEEEEcCCHHHHHHHHHHHHHhh--ccCCceEEEEECCcchHH-HHHHHhcCCcEEEeChHHHHHHHhc
Q 022724           97 TS-----SREVQALILSPTRELATQTEKVILAIG--DFINIQAHACVGGKSVGE-DIRKLEHGVHVVSGTPGRVCDMIKR  168 (293)
Q Consensus        97 ~~-----~~~~~~lil~P~~~l~~q~~~~~~~~~--~~~~~~~~~~~~~~~~~~-~~~~~~~~~~ilV~Tp~~l~~~l~~  168 (293)
                      ..     ..|.+++|+.|+++|+.|++..+.++.  ...+.++..........+ ........++++|+||.++...+..
T Consensus       200 ~~~~~~~~~gl~a~Il~ptreLa~Qi~re~~k~~~~~~t~~~a~~~~~~~~~~qk~a~~~~~k~dili~TP~ri~~~~~~  279 (593)
T KOG0344|consen  200 DLSQEKHKVGLRALILSPTRELAAQIYREMRKYSIDEGTSLRAAQFSKPAYPSQKPAFLSDEKYDILISTPMRIVGLLGL  279 (593)
T ss_pred             HhhcccCccceEEEEecchHHHHHHHHHHHHhcCCCCCCchhhhhcccccchhhccchhHHHHHHHHhcCHHHHHHHhcC
Confidence            43     457899999999999999999999998  555555554443322111 1112223468999999999999888


Q ss_pred             CC--CCCCCccEEEecchhhhhcc-ccHHHHHHHHhhCC-CCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCC
Q 022724          169 KT--LRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLP-PDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLE  244 (293)
Q Consensus       169 ~~--~~~~~l~~iViDE~h~~~~~-~~~~~~~~i~~~l~-~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (293)
                      +.  +++..+.++|+||+|++.+. .|..++..+++.+. +...+=+||||++..++++++..+.++..+.+...+....
T Consensus       280 ~~~~idl~~V~~lV~dEaD~lfe~~~f~~Qla~I~sac~s~~i~~a~FSat~~~~VEE~~~~i~~~~~~vivg~~~sa~~  359 (593)
T KOG0344|consen  280 GKLNIDLSKVEWLVVDEADLLFEPEFFVEQLADIYSACQSPDIRVALFSATISVYVEEWAELIKSDLKRVIVGLRNSANE  359 (593)
T ss_pred             CCccchhheeeeEeechHHhhhChhhHHHHHHHHHHHhcCcchhhhhhhccccHHHHHHHHHhhccceeEEEecchhHhh
Confidence            65  78999999999999999988 89999999988876 5677889999999999999999999999999998888888


Q ss_pred             CceEEEEEecCcccHHHHHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          245 GIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       245 ~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      .+.|...+|-.+..|.-++.++++..-..+++||+.+.++|.+|+..|
T Consensus       360 ~V~QelvF~gse~~K~lA~rq~v~~g~~PP~lIfVQs~eRak~L~~~L  407 (593)
T KOG0344|consen  360 TVDQELVFCGSEKGKLLALRQLVASGFKPPVLIFVQSKERAKQLFEEL  407 (593)
T ss_pred             hhhhhheeeecchhHHHHHHHHHhccCCCCeEEEEecHHHHHHHHHHh
Confidence            899999999999989999999999877779999999999999999887

>PRK09401 reverse gyrase; Reviewed

Probab=99.98  E-value=2.2e-30  Score=253.88  Aligned_cols=235  Identities=19%  Similarity=0.235  Sum_probs=179.7

Q ss_pred             HHHHHH-CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 022724           45 LRGIYQ-YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA  123 (293)
Q Consensus        45 ~~~l~~-~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~  123 (293)
                      .+.+++ .|+ .|+++|+.+++.+++|+|++++||||+|||. |.+++...+..  .+.+++|++||++|+.|+.+.++.
T Consensus        70 ~~~f~~~~G~-~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~-f~l~~~~~l~~--~g~~alIL~PTreLa~Qi~~~l~~  145 (1176)
T PRK09401         70 EKFFKKKTGS-KPWSLQRTWAKRLLLGESFAIIAPTGVGKTT-FGLVMSLYLAK--KGKKSYIIFPTRLLVEQVVEKLEK  145 (1176)
T ss_pred             HHHHHHhcCC-CCcHHHHHHHHHHHCCCcEEEEcCCCCCHHH-HHHHHHHHHHh--cCCeEEEEeccHHHHHHHHHHHHH
Confidence            334433 466 7999999999999999999999999999996 55555444433  367999999999999999999999


Q ss_pred             hhccCCceEEEEECCcch-----HHHHHHHh-cCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhc--------
Q 022724          124 IGDFINIQAHACVGGKSV-----GEDIRKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS--------  189 (293)
Q Consensus       124 ~~~~~~~~~~~~~~~~~~-----~~~~~~~~-~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~--------  189 (293)
                      +....++.+..+.++...     .+....+. .+++|+|+||+++.+.+.  .+...+++++||||||.+++        
T Consensus       146 l~~~~~~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~~~~--~l~~~~~~~lVvDEaD~~L~~~k~id~~  223 (1176)
T PRK09401        146 FGEKVGCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFD--ELPKKKFDFVFVDDVDAVLKSSKNIDKL  223 (1176)
T ss_pred             HhhhcCceEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECHHHHHHHHH--hccccccCEEEEEChHHhhhcccchhhH
Confidence            998888888777766532     22333444 458999999999998776  45566799999999999986        


Q ss_pred             ---cccH-HHHHHHHhhCCC------------------------CccEEEEEeecChh-HHHHHHhcCCCCEEEEecCCc
Q 022724          190 ---RGFK-DQIYDVYRYLPP------------------------DLQVVLISATLPHE-ILEMTTKFMTDPVKILVKRDE  240 (293)
Q Consensus       190 ---~~~~-~~~~~i~~~l~~------------------------~~q~v~~SAt~~~~-~~~~~~~~~~~~~~~~~~~~~  240 (293)
                         .||. ..+..++..++.                        ..|++++|||+++. +..   .++.++..+.+....
T Consensus       224 l~~lGF~~~~i~~i~~~i~~~~~~~~~~~~i~~l~~~i~~~~~~~~q~ilfSAT~~~~~~~~---~l~~~ll~~~v~~~~  300 (1176)
T PRK09401        224 LYLLGFSEEDIEKAMELIRLKRKYEEIYEKIRELEEKIAELKDKKGVLVVSSATGRPRGNRV---KLFRELLGFEVGSPV  300 (1176)
T ss_pred             HHhCCCCHHHHHHHHHhcccccccchhhhHHHHHHHhhhhcccCCceEEEEeCCCCccchHH---HHhhccceEEecCcc
Confidence               4564 567777666653                        68999999999864 332   233455556666655


Q ss_pred             ccCCCceEEEEEecCcccHHHHHHHHHhhCCCCcEEEEcccchh---HHHHHhhC
Q 022724          241 LTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRK---VLLLVLQF  292 (293)
Q Consensus       241 ~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~~iIF~~s~~~---a~~l~~~L  292 (293)
                      ....++.+.++.++   ++...+..+++... .++||||++++.   |+.+++.|
T Consensus       301 ~~~rnI~~~yi~~~---~k~~~L~~ll~~l~-~~~LIFv~t~~~~~~ae~l~~~L  351 (1176)
T PRK09401        301 FYLRNIVDSYIVDE---DSVEKLVELVKRLG-DGGLIFVPSDKGKEYAEELAEYL  351 (1176)
T ss_pred             cccCCceEEEEEcc---cHHHHHHHHHHhcC-CCEEEEEecccChHHHHHHHHHH
Confidence            66678888888765   37777888887654 589999999887   99998775

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

Probab=99.97  E-value=1.3e-30  Score=206.42  Aligned_cols=165  Identities=27%  Similarity=0.474  Sum_probs=144.0

Q ss_pred             cHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEE
Q 022724           57 SAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACV  136 (293)
Q Consensus        57 ~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~  136 (293)
                      ||+|.++|+.+.+|+++++.+|||+|||++|+++++..+... ...++++++|+++|++|+.+.+..+....++++..++
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            689999999999999999999999999999999999998876 4459999999999999999999999988888999999


Q ss_pred             CCcchH-HHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCC--CCccEEEEE
Q 022724          137 GGKSVG-EDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP--PDLQVVLIS  213 (293)
Q Consensus       137 ~~~~~~-~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~--~~~q~v~~S  213 (293)
                      ++.... .....+.++++|+|+||+++.+++..+..++.++++|||||+|.+.++.+...+..+...+.  .+.|++++|
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            988755 34444556799999999999999988656777899999999999988778888888888873  368999999


Q ss_pred             eecChhHHH
Q 022724          214 ATLPHEILE  222 (293)
Q Consensus       214 At~~~~~~~  222 (293)
                      ||+++.+++
T Consensus       160 AT~~~~~~~  168 (169)
T PF00270_consen  160 ATLPSNVEK  168 (169)
T ss_dssp             SSSTHHHHH
T ss_pred             eCCChhHhh
Confidence            999966554

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 ....

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.97  E-value=3.2e-30  Score=235.03  Aligned_cols=227  Identities=16%  Similarity=0.256  Sum_probs=162.2

Q ss_pred             HCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCC
Q 022724           50 QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (293)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (293)
                      .+||..|+|+|.++++.+++|+|+++++|||+|||++|++|++..      +..+||++|+++|+.|+.+.+..    .+
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------DGITLVISPLISLMEDQVLQLKA----SG   75 (470)
T ss_pred             hcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHHHc------CCcEEEEecHHHHHHHHHHHHHH----cC
Confidence            469999999999999999999999999999999999999998753      34799999999999999888765    35


Q ss_pred             ceEEEEECCcchHHHHH---HH-hcCCcEEEeChHHHHHHH-hcCCC-CCCCccEEEecchhhhhccc--cHHHHHH---
Q 022724          130 IQAHACVGGKSVGEDIR---KL-EHGVHVVSGTPGRVCDMI-KRKTL-RTRAIKLLVLDESDEMLSRG--FKDQIYD---  198 (293)
Q Consensus       130 ~~~~~~~~~~~~~~~~~---~~-~~~~~ilV~Tp~~l~~~l-~~~~~-~~~~l~~iViDE~h~~~~~~--~~~~~~~---  198 (293)
                      +.+..+.++....+...   .+ ...++|+++||+++.... ....+ ...++++|||||||++.+|+  |...+..   
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            67777777765543322   22 345799999999976422 11111 46789999999999998876  4555443   


Q ss_pred             HHhhCCCCccEEEEEeecChhHHHHHHhcC--CCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHh-hCCCCcE
Q 022724          199 VYRYLPPDLQVVLISATLPHEILEMTTKFM--TDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYD-TLTITQA  275 (293)
Q Consensus       199 i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~-~~~~~~~  275 (293)
                      +...+ +..+++++|||+++.+...+...+  .+|..+....   ...++...+  ..........+..++. ...+.++
T Consensus       156 l~~~~-~~~~~l~lTAT~~~~~~~di~~~l~l~~~~~~~~s~---~r~nl~~~v--~~~~~~~~~~l~~~l~~~~~~~~~  229 (470)
T TIGR00614       156 LKQKF-PNVPIMALTATASPSVREDILRQLNLKNPQIFCTSF---DRPNLYYEV--RRKTPKILEDLLRFIRKEFKGKSG  229 (470)
T ss_pred             HHHHc-CCCceEEEecCCCHHHHHHHHHHcCCCCCcEEeCCC---CCCCcEEEE--EeCCccHHHHHHHHHHHhcCCCce
Confidence            33444 578999999999998766554443  3454443322   122222221  2222124555666665 4555677


Q ss_pred             EEEcccchhHHHHHhhC
Q 022724          276 VIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       276 iIF~~s~~~a~~l~~~L  292 (293)
                      ||||+|+++|+.++..|
T Consensus       230 IIF~~s~~~~e~la~~L  246 (470)
T TIGR00614       230 IIYCPSRKKSEQVTASL  246 (470)
T ss_pred             EEEECcHHHHHHHHHHH
Confidence            99999999999999876

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

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

Probab=99.97  E-value=9e-30  Score=242.30  Aligned_cols=244  Identities=16%  Similarity=0.220  Sum_probs=174.1

Q ss_pred             Ccc--cCCCCHHHHHHHHH-CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCC
Q 022724           34 SFD--AMGIKDDLLRGIYQ-YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (293)
Q Consensus        34 ~f~--~~~l~~~i~~~l~~-~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~  110 (293)
                      .|.  .+++...+...+++ +||..|+|.|.++|+.++.|+|+++++|||+|||+||++|++..      +..+|||+|+
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  46777777777765 79999999999999999999999999999999999999999864      3479999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHh------cCCcEEEeChHHHHH---HHhc--CCCCCCCccEE
Q 022724          111 RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE------HGVHVVSGTPGRVCD---MIKR--KTLRTRAIKLL  179 (293)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~ilV~Tp~~l~~---~l~~--~~~~~~~l~~i  179 (293)
                      ++|+.++...+..    .++....+.++....++...+.      ..++|+++||+++..   ++..  .......+.+|
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            9999866555543    4788888898887766654432      457999999999863   2221  11123558999


Q ss_pred             Eecchhhhhccc--cHHHHHHH--HhhCCCCccEEEEEeecChhHHHHHHhcCC--CCEEEEecCCcccCCCceEEEEEe
Q 022724          180 VLDESDEMLSRG--FKDQIYDV--YRYLPPDLQVVLISATLPHEILEMTTKFMT--DPVKILVKRDELTLEGIKQFFVAV  253 (293)
Q Consensus       180 ViDE~h~~~~~~--~~~~~~~i--~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~i~~~~~~~  253 (293)
                      ||||||++.+||  |+..+..+  +...-+..+++++|||+++.+...+...+.  ++..+..   .....++.  +...
T Consensus       586 VIDEAHcVSqWGhDFRpdYr~L~~Lr~~fp~vPilALTATAT~~V~eDI~~~L~l~~~~vfr~---Sf~RpNL~--y~Vv  660 (1195)
T PLN03137        586 VIDEAHCVSQWGHDFRPDYQGLGILKQKFPNIPVLALTATATASVKEDVVQALGLVNCVVFRQ---SFNRPNLW--YSVV  660 (1195)
T ss_pred             ccCcchhhhhcccchHHHHHHHHHHHHhCCCCCeEEEEecCCHHHHHHHHHHcCCCCcEEeec---ccCccceE--EEEe
Confidence            999999999987  66655542  333335789999999999988875555443  2322221   12223332  2222


Q ss_pred             cCcccHHHHHHHHHhhC-CCCcEEEEcccchhHHHHHhhC
Q 022724          254 EREEWKFDTLCDLYDTL-TITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       254 ~~~~~k~~~l~~l~~~~-~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      .........+..++... ...+.||||+|+++|+.++..|
T Consensus       661 ~k~kk~le~L~~~I~~~~~~esgIIYC~SRke~E~LAe~L  700 (1195)
T PLN03137        661 PKTKKCLEDIDKFIKENHFDECGIIYCLSRMDCEKVAERL  700 (1195)
T ss_pred             ccchhHHHHHHHHHHhcccCCCceeEeCchhHHHHHHHHH
Confidence            32221234566666543 3568999999999999999876

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.97  E-value=3.2e-29  Score=234.38  Aligned_cols=236  Identities=17%  Similarity=0.263  Sum_probs=168.0

Q ss_pred             CCHHHHHHHHH-CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHH
Q 022724           40 IKDDLLRGIYQ-YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE  118 (293)
Q Consensus        40 l~~~i~~~l~~-~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~  118 (293)
                      .+....+.|++ +||..|+|+|+++++.++.|+|+++++|||+|||++|++|++..      +..+||++|+++|+.|+.
T Consensus         9 ~~~~~~~~l~~~fG~~~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y~lpal~~------~g~tlVisPl~sL~~dqv   82 (607)
T PRK11057          9 LESLAKQVLQETFGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVL------DGLTLVVSPLISLMKDQV   82 (607)
T ss_pred             chhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHc------CCCEEEEecHHHHHHHHH
Confidence            33344445544 69999999999999999999999999999999999999999854      247999999999999999


Q ss_pred             HHHHHhhccCCceEEEEECCcchHHHHHH---H-hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccc--c
Q 022724          119 KVILAIGDFINIQAHACVGGKSVGEDIRK---L-EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG--F  192 (293)
Q Consensus       119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~-~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~--~  192 (293)
                      +.++.+    ++.+..+.++.........   + ....+++++||+++........+...++++|||||||++.+++  |
T Consensus        83 ~~l~~~----gi~~~~~~s~~~~~~~~~~~~~~~~g~~~il~~tPe~l~~~~~~~~l~~~~l~~iVIDEaH~i~~~G~~f  158 (607)
T PRK11057         83 DQLLAN----GVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMDNFLEHLAHWNPALLAVDEAHCISQWGHDF  158 (607)
T ss_pred             HHHHHc----CCcEEEEcCCCCHHHHHHHHHHHhCCCCcEEEEChHHhcChHHHHHHhhCCCCEEEEeCccccccccCcc
Confidence            888754    5667677776655443322   2 2456899999999874222222334678999999999998876  4


Q ss_pred             HHHH---HHHHhhCCCCccEEEEEeecChhHHHHHHhc--CCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHH
Q 022724          193 KDQI---YDVYRYLPPDLQVVLISATLPHEILEMTTKF--MTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLY  267 (293)
Q Consensus       193 ~~~~---~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~  267 (293)
                      ...+   ..+...+ +..+++++|||+++.....+...  +.+|.......   ...++.  +....... +...+..++
T Consensus       159 r~~y~~L~~l~~~~-p~~~~v~lTAT~~~~~~~di~~~l~l~~~~~~~~~~---~r~nl~--~~v~~~~~-~~~~l~~~l  231 (607)
T PRK11057        159 RPEYAALGQLRQRF-PTLPFMALTATADDTTRQDIVRLLGLNDPLIQISSF---DRPNIR--YTLVEKFK-PLDQLMRYV  231 (607)
T ss_pred             cHHHHHHHHHHHhC-CCCcEEEEecCCChhHHHHHHHHhCCCCeEEEECCC---CCCcce--eeeeeccc-hHHHHHHHH
Confidence            4443   3334444 57899999999998876544333  34554433221   122332  22222222 556677777


Q ss_pred             hhCCCCcEEEEcccchhHHHHHhhC
Q 022724          268 DTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       268 ~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ....+.++||||+|+++|+.++..|
T Consensus       232 ~~~~~~~~IIFc~tr~~~e~la~~L  256 (607)
T PRK11057        232 QEQRGKSGIIYCNSRAKVEDTAARL  256 (607)
T ss_pred             HhcCCCCEEEEECcHHHHHHHHHHH
Confidence            7777789999999999999999876

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.97  E-value=6.5e-30  Score=240.68  Aligned_cols=247  Identities=17%  Similarity=0.189  Sum_probs=186.6

Q ss_pred             CCCHHHHHHHHHCCCCCCcHHHHHHHHhhh-cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHH
Q 022724           39 GIKDDLLRGIYQYGFEKPSAIQQRAVMPII-KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQT  117 (293)
Q Consensus        39 ~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~-~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~  117 (293)
                      .+++.+..-+...++....+.|+.++.... +++|+++++|||+|||+.++++++..+...  +.++||+||+++|+.++
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            467788888888899889899998888754 569999999999999999999999999876  45899999999999999


Q ss_pred             HHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHH
Q 022724          118 EKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIY  197 (293)
Q Consensus       118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~  197 (293)
                      ++.+++ ...+|+++...+|+.+....   ...+++|+|+|||++-.++++.......++++||||+|.+.+...+..++
T Consensus        93 ~~~~~~-~~~~GirV~~~TgD~~~~~~---~l~~~~ViVtT~EK~Dsl~R~~~~~~~~V~lvViDEiH~l~d~~RG~~lE  168 (766)
T COG1204          93 YEEFSR-LEELGIRVGISTGDYDLDDE---RLARYDVIVTTPEKLDSLTRKRPSWIEEVDLVVIDEIHLLGDRTRGPVLE  168 (766)
T ss_pred             HHHhhh-HHhcCCEEEEecCCcccchh---hhccCCEEEEchHHhhHhhhcCcchhhcccEEEEeeeeecCCcccCceeh
Confidence            999994 45789999999999875542   12457999999999999999877788999999999999998887777777


Q ss_pred             HHHhhCC---CCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccC-CCceEEEEEecCccc-----H-HHHHHHHH
Q 022724          198 DVYRYLP---PDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTL-EGIKQFFVAVEREEW-----K-FDTLCDLY  267 (293)
Q Consensus       198 ~i~~~l~---~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~i~~~~~~~~~~~~-----k-~~~l~~l~  267 (293)
                      .+..++.   ...|++++|||+|+. .+++.+.-.++......+..... ....+.+........     . ...+...+
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            7776665   347999999999985 66666665554432222222211 112233333332220     1 22233333


Q ss_pred             hh-CCCCcEEEEcccchhHHHHHhhC
Q 022724          268 DT-LTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       268 ~~-~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      .. ..+++++|||+|++.+...++.|
T Consensus       248 ~~~~~~~qvLvFv~sR~~a~~~A~~l  273 (766)
T COG1204         248 ESLAEGGQVLVFVHSRKEAEKTAKKL  273 (766)
T ss_pred             HHHhcCCeEEEEEecCchHHHHHHHH
Confidence            33 24579999999999999988764

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.97  E-value=4e-29  Score=234.03  Aligned_cols=229  Identities=17%  Similarity=0.251  Sum_probs=169.1

Q ss_pred             HHHH-CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhh
Q 022724           47 GIYQ-YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIG  125 (293)
Q Consensus        47 ~l~~-~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  125 (293)
                      .|++ +||..|+|.|.++++.++.|+|+++++|||+|||++|++|++..      +..++|++|+++|+.|+.+.++.+ 
T Consensus         4 ~l~~~fg~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~lpal~~------~g~~lVisPl~sL~~dq~~~l~~~-   76 (591)
T TIGR01389         4 VLKRTFGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALLL------KGLTVVISPLISLMKDQVDQLRAA-   76 (591)
T ss_pred             HHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHHHHHHHc------CCcEEEEcCCHHHHHHHHHHHHHc-
Confidence            3443 79999999999999999999999999999999999999998753      346899999999999999988764 


Q ss_pred             ccCCceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccc--cHHHHHH-
Q 022724          126 DFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG--FKDQIYD-  198 (293)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~--~~~~~~~-  198 (293)
                         ++.+..++++.+..+....+    ....+|+++||+++........+...++++|||||+|++.+|+  |...+.. 
T Consensus        77 ---gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe~l~~~~~~~~l~~~~l~~iViDEaH~i~~~g~~frp~y~~l  153 (591)
T TIGR01389        77 ---GVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQDYFLNMLQRIPIALVAVDEAHCVSQWGHDFRPEYQRL  153 (591)
T ss_pred             ---CCcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChhHhcChHHHHHHhcCCCCEEEEeCCcccccccCccHHHHHHH
Confidence               57787888877655443322    3567999999999875333334456789999999999998875  5544443 


Q ss_pred             --HHhhCCCCccEEEEEeecChhHHHHHHhcCC--CCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHhhCCCCc
Q 022724          199 --VYRYLPPDLQVVLISATLPHEILEMTTKFMT--DPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQ  274 (293)
Q Consensus       199 --i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~  274 (293)
                        +...++ ..+++++|||.++.+...+...+.  ++..+...   ....++.  +...... .+...+..++....+.+
T Consensus       154 ~~l~~~~~-~~~vi~lTAT~~~~~~~~i~~~l~~~~~~~~~~~---~~r~nl~--~~v~~~~-~~~~~l~~~l~~~~~~~  226 (591)
T TIGR01389       154 GSLAERFP-QVPRIALTATADAETRQDIRELLRLADANEFITS---FDRPNLR--FSVVKKN-NKQKFLLDYLKKHRGQS  226 (591)
T ss_pred             HHHHHhCC-CCCEEEEEeCCCHHHHHHHHHHcCCCCCCeEecC---CCCCCcE--EEEEeCC-CHHHHHHHHHHhcCCCC
Confidence              344443 456999999999988776655543  33333211   1222222  2222223 36677778887777789


Q ss_pred             EEEEcccchhHHHHHhhC
Q 022724          275 AVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       275 ~iIF~~s~~~a~~l~~~L  292 (293)
                      +||||+|+++|+.+++.|
T Consensus       227 ~IIf~~sr~~~e~la~~L  244 (591)
T TIGR01389       227 GIIYASSRKKVEELAERL  244 (591)
T ss_pred             EEEEECcHHHHHHHHHHH
Confidence            999999999999999876

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.

>PRK14701 reverse gyrase; Provisional

Probab=99.97  E-value=6.6e-29  Score=248.41  Aligned_cols=239  Identities=17%  Similarity=0.204  Sum_probs=177.4

Q ss_pred             HHHHHHHH-CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHH
Q 022724           43 DLLRGIYQ-YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVI  121 (293)
Q Consensus        43 ~i~~~l~~-~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~  121 (293)
                      ++.+.+++ +|| .|+++|+++++.+++|+|++++||||+|||++++++++....   .+.+++|++||++|+.|+.+.+
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            45555665 799 599999999999999999999999999999976666554422   3568999999999999999999


Q ss_pred             HHhhccC--CceEEEEECCcchHHHHH---HHhc-CCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhc------
Q 022724          122 LAIGDFI--NIQAHACVGGKSVGEDIR---KLEH-GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS------  189 (293)
Q Consensus       122 ~~~~~~~--~~~~~~~~~~~~~~~~~~---~~~~-~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~------  189 (293)
                      +.+....  ++++..++|+.+..++..   .+.+ .++|+|+||+.+...+... . ..++++|||||||+|++      
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  456777888887766533   3333 5899999999998765542 2 27799999999999986      


Q ss_pred             -----cccHHHHHH----HHh----------------------hCCCCcc-EEEEEeecChhHHHHHHhcCCCCEEEEec
Q 022724          190 -----RGFKDQIYD----VYR----------------------YLPPDLQ-VVLISATLPHEILEMTTKFMTDPVKILVK  237 (293)
Q Consensus       190 -----~~~~~~~~~----i~~----------------------~l~~~~q-~v~~SAt~~~~~~~~~~~~~~~~~~~~~~  237 (293)
                           .+|..++..    +++                      .+++..| ++++|||.++.  .....++.++..+.+.
T Consensus       221 ~~L~llGF~~e~~~~~~~il~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ll~~SAT~~~r--~~~~~l~~~~l~f~v~  298 (1638)
T PRK14701        221 RSLQLLGFYEEIIEKAWKIIYLKKQGNIEDAMEKREILNKEIEKIGNKIGCLIVASATGKAK--GDRVKLYRELLGFEVG  298 (1638)
T ss_pred             hhhhcCCChHHHHHHHHHhhhcccccccchhhhhhhhhhhhhhhcCCCccEEEEEecCCCch--hHHHHHhhcCeEEEec
Confidence                 366666543    321                      2334455 67799999863  1112334567777777


Q ss_pred             CCcccCCCceEEEEEecCcccHHHHHHHHHhhCCCCcEEEEcccchh---HHHHHhhC
Q 022724          238 RDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRK---VLLLVLQF  292 (293)
Q Consensus       238 ~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~~iIF~~s~~~---a~~l~~~L  292 (293)
                      .......++.+.++.++... + ..+..+++.. +.++||||+|++.   |+.+++.|
T Consensus       299 ~~~~~lr~i~~~yi~~~~~~-k-~~L~~ll~~~-g~~gIVF~~t~~~~e~ae~la~~L  353 (1638)
T PRK14701        299 SGRSALRNIVDVYLNPEKII-K-EHVRELLKKL-GKGGLIFVPIDEGAEKAEEIEKYL  353 (1638)
T ss_pred             CCCCCCCCcEEEEEECCHHH-H-HHHHHHHHhC-CCCeEEEEeccccchHHHHHHHHH
Confidence            76666778888888765443 4 4677777766 4689999999876   47877765

>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=1.8e-28  Score=233.91  Aligned_cols=245  Identities=20%  Similarity=0.273  Sum_probs=187.1

Q ss_pred             CHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHH
Q 022724           41 KDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKV  120 (293)
Q Consensus        41 ~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~  120 (293)
                      ...+..++.+.|...++++|.+|+..+.+|+|++|+.|||||||++|++|+++.+...+.. ++|+|.||++|++++.++
T Consensus        56 ~~~l~~~l~~~g~~~lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~~a-~AL~lYPtnALa~DQ~~r  134 (851)
T COG1205          56 DESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSA-RALLLYPTNALANDQAER  134 (851)
T ss_pred             hhHHHHHHHHhccccccHHHHHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhhCcCc-cEEEEechhhhHhhHHHH
Confidence            4456888888899999999999999999999999999999999999999999999887665 899999999999999999


Q ss_pred             HHHhhccCC--ceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcC----CCCCCCccEEEecchhhhhccccHH
Q 022724          121 ILAIGDFIN--IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK----TLRTRAIKLLVLDESDEMLSRGFKD  194 (293)
Q Consensus       121 ~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~----~~~~~~l~~iViDE~h~~~~~~~~~  194 (293)
                      ++++....+  +.+..+.|+....+....+.++++|++|||+++..++...    .+.++++++||+||+|.+- ..++.
T Consensus       135 l~~~~~~~~~~v~~~~y~Gdt~~~~r~~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDElHtYr-Gv~GS  213 (851)
T COG1205         135 LRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYR-GVQGS  213 (851)
T ss_pred             HHHHHHhCCCcceeeeecCCCChHHHHHHHhCCCCEEEeCHHHHHHHhccCcchHHHHHhcCcEEEEecceecc-ccchh
Confidence            999987777  7777888888777766777899999999999999955432    2345889999999999873 23444


Q ss_pred             HHHHHHhh-------CCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecC--------cccH
Q 022724          195 QIYDVYRY-------LPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVER--------EEWK  259 (293)
Q Consensus       195 ~~~~i~~~-------l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~--------~~~k  259 (293)
                      ++..++++       .+.+.|+|+.|||+.+. .++...+........+. .+..+.....++..-+.        ...+
T Consensus       214 ~vA~llRRL~~~~~~~~~~~q~i~~SAT~~np-~e~~~~l~~~~f~~~v~-~~g~~~~~~~~~~~~p~~~~~~~~~r~s~  291 (851)
T COG1205         214 EVALLLRRLLRRLRRYGSPLQIICTSATLANP-GEFAEELFGRDFEVPVD-EDGSPRGLRYFVRREPPIRELAESIRRSA  291 (851)
T ss_pred             HHHHHHHHHHHHHhccCCCceEEEEeccccCh-HHHHHHhcCCcceeecc-CCCCCCCceEEEEeCCcchhhhhhcccch
Confidence            44443333       34578999999999776 55666666655555333 33334444444443330        1124


Q ss_pred             HHHHHHHHhhC--CCCcEEEEcccchhHHHHH
Q 022724          260 FDTLCDLYDTL--TITQAVIFCNTKRKVLLLV  289 (293)
Q Consensus       260 ~~~l~~l~~~~--~~~~~iIF~~s~~~a~~l~  289 (293)
                      ...+..+....  .+-++|+||.+++.++.++
T Consensus       292 ~~~~~~~~~~~~~~~~~tL~F~~sr~~~e~~~  323 (851)
T COG1205         292 LAELATLAALLVRNGIQTLVFFRSRKQVELLY  323 (851)
T ss_pred             HHHHHHHHHHHHHcCceEEEEEehhhhhhhhh
Confidence            55555555432  4559999999999999886

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.96  E-value=6.7e-28  Score=231.44  Aligned_cols=234  Identities=19%  Similarity=0.178  Sum_probs=171.8

Q ss_pred             CCHHHHHHHH-HCCCCCCcHHHHHHHHhhhcC------CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHH
Q 022724           40 IKDDLLRGIY-QYGFEKPSAIQQRAVMPIIKG------RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (293)
Q Consensus        40 l~~~i~~~l~-~~~~~~~~~~Q~~~~~~i~~~------~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~  112 (293)
                      .+....+.+. .++|. ||+.|.++++.+.++      +|.+++||||+|||.+|+++++..+..   +.+++|++||++
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            4455666654 46785 999999999999875      799999999999999999999988765   468999999999


Q ss_pred             HHHHHHHHHHHhhccCCceEEEEECCcchHHHH---HHHhc-CCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhh
Q 022724          113 LATQTEKVILAIGDFINIQAHACVGGKSVGEDI---RKLEH-GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (293)
Q Consensus       113 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~-~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~  188 (293)
                      ||.|+++.++++....++++..++++.+..+..   +.+.+ .++|+||||..    + +....+++++++||||+|++.
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            999999999998888889998888877654433   33333 58999999942    2 345678999999999999863


Q ss_pred             ccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHh
Q 022724          189 SRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYD  268 (293)
Q Consensus       189 ~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~  268 (293)
                           ......++.++...|+++||||+.+....+......++..+...+.+  ...+..++...+... -...+...+ 
T Consensus       587 -----v~~~~~L~~~~~~~~vL~~SATpiprtl~~~l~g~~d~s~I~~~p~~--R~~V~t~v~~~~~~~-i~~~i~~el-  657 (926)
T TIGR00580       587 -----VKQKEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPED--RLPVRTFVMEYDPEL-VREAIRREL-  657 (926)
T ss_pred             -----hhHHHHHHhcCCCCCEEEEecCCCHHHHHHHHhcCCCcEEEecCCCC--ccceEEEEEecCHHH-HHHHHHHHH-
Confidence                 22344556667789999999998777666665566677666654432  223444444222111 111222222 


Q ss_pred             hCCCCcEEEEcccchhHHHHHhhC
Q 022724          269 TLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       269 ~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                       ..+++++||||++++++.+++.|
T Consensus       658 -~~g~qv~if~n~i~~~e~l~~~L  680 (926)
T TIGR00580       658 -LRGGQVFYVHNRIESIEKLATQL  680 (926)
T ss_pred             -HcCCeEEEEECCcHHHHHHHHHH
Confidence             24579999999999999988765

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.

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

Probab=99.96  E-value=7.5e-29  Score=217.44  Aligned_cols=251  Identities=19%  Similarity=0.234  Sum_probs=199.5

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHh-hhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCH
Q 022724           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (293)
Q Consensus        33 ~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~-i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~  111 (293)
                      ...+++++++++.+-|+..|++.+.|+|.-++.. ++.|.|.+|+++|+||||++..++.+..+...  +.+.+|++|..
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            4678899999999999999999999999999998 88999999999999999999999999988775  45899999999


Q ss_pred             HHHHHHHHHHHHhhccCCceEEEEECCcchHHHH----HHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhh
Q 022724          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDI----RKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (293)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~  187 (293)
                      +||+|-++.++.-...+++.+..-.|..-.....    -....+.||||+|.+-+-++++.+ .++.++..+||||+|.+
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            9999999999876677888887766653222211    111235699999999999999988 66899999999999999


Q ss_pred             hccccHHHHHHHH---hhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHH
Q 022724          188 LSRGFKDQIYDVY---RYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLC  264 (293)
Q Consensus       188 ~~~~~~~~~~~i~---~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~  264 (293)
                      .+...+..+.-++   +++-+..|+|++|||+.+. ..+++.+...+...     +..|-.+....+++..+..|...+.
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-EELAKKLGAKLVLY-----DERPVPLERHLVFARNESEKWDIIA  424 (830)
T ss_pred             cchhcccchhhHHHHHHHhCCCCeEEEEEeecCCh-HHHHHHhCCeeEee-----cCCCCChhHeeeeecCchHHHHHHH
Confidence            7765555554444   4444689999999999775 56666654443333     2334456666777887777999988


Q ss_pred             HHHhhC-----C---CCcEEEEcccchhHHHHHhhC
Q 022724          265 DLYDTL-----T---ITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       265 ~l~~~~-----~---~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      .+.+..     +   .++||||.+|++.|..++..|
T Consensus       425 ~L~k~E~~~~sskg~rGQtIVFT~SRrr~h~lA~~L  460 (830)
T COG1202         425 RLVKREFSTESSKGYRGQTIVFTYSRRRCHELADAL  460 (830)
T ss_pred             HHHHHHHhhhhccCcCCceEEEecchhhHHHHHHHh
Confidence            887531     1   359999999999999999886

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.96  E-value=6.6e-28  Score=236.02  Aligned_cols=231  Identities=16%  Similarity=0.159  Sum_probs=174.7

Q ss_pred             HHHHHHHHCCCCCCcHHHHHHHHhhhcC------CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHH
Q 022724           43 DLLRGIYQYGFEKPSAIQQRAVMPIIKG------RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQ  116 (293)
Q Consensus        43 ~i~~~l~~~~~~~~~~~Q~~~~~~i~~~------~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q  116 (293)
                      +..+....+.| .||+.|.++|+.+..+      +|++++|+||+|||.+|+.+++..+..   +.+++|++||++|+.|
T Consensus       589 ~~~~~~~~~~~-~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~~---g~qvlvLvPT~eLA~Q  664 (1147)
T PRK10689        589 QYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVEN---HKQVAVLVPTTLLAQQ  664 (1147)
T ss_pred             HHHHHHHhCCC-CCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHHc---CCeEEEEeCcHHHHHH
Confidence            44444567777 5999999999999886      799999999999999999888776643   6799999999999999


Q ss_pred             HHHHHHHhhccCCceEEEEECCcchHHHHHHHh----cCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcccc
Q 022724          117 TEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF  192 (293)
Q Consensus       117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~  192 (293)
                      +++.+++.....++++..++++.+..++.+.+.    ..++|+|+||+.+    . ....+.+++++||||+|++.   +
T Consensus       665 ~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL----~-~~v~~~~L~lLVIDEahrfG---~  736 (1147)
T PRK10689        665 HYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLL----Q-SDVKWKDLGLLIVDEEHRFG---V  736 (1147)
T ss_pred             HHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHH----h-CCCCHhhCCEEEEechhhcc---h
Confidence            999999877777888888888877666554432    4689999999633    2 34567899999999999972   2


Q ss_pred             HHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHhhCCC
Q 022724          193 KDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTI  272 (293)
Q Consensus       193 ~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~  272 (293)
                      .  ....++.++.++|++++|||+.+....+....+.++..+......  ...+.+++........+...+.++.   .+
T Consensus       737 ~--~~e~lk~l~~~~qvLl~SATpiprtl~l~~~gl~d~~~I~~~p~~--r~~v~~~~~~~~~~~~k~~il~el~---r~  809 (1147)
T PRK10689        737 R--HKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPAR--RLAVKTFVREYDSLVVREAILREIL---RG  809 (1147)
T ss_pred             h--HHHHHHhcCCCCcEEEEcCCCCHHHHHHHHhhCCCcEEEecCCCC--CCCceEEEEecCcHHHHHHHHHHHh---cC
Confidence            2  234456677889999999999888788777778888877665433  2235555544332222333333333   35


Q ss_pred             CcEEEEcccchhHHHHHhhC
Q 022724          273 TQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       273 ~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ++++||||+++.++.+++.|
T Consensus       810 gqv~vf~n~i~~ie~la~~L  829 (1147)
T PRK10689        810 GQVYYLYNDVENIQKAAERL  829 (1147)
T ss_pred             CeEEEEECCHHHHHHHHHHH
Confidence            79999999999988888765

>TIGR01054 rgy reverse gyrase

Probab=99.96  E-value=5e-28  Score=237.62  Aligned_cols=238  Identities=18%  Similarity=0.240  Sum_probs=173.0

Q ss_pred             HHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHH
Q 022724           42 DDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVI  121 (293)
Q Consensus        42 ~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~  121 (293)
                      .++.+.+.+.....|+++|+.+++.++.|+|++++||||+|||. |.+++...+...  +++++|++||++|+.|+.+.+
T Consensus        65 ~~f~~~f~~~~g~~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~-f~l~~~~~l~~~--g~~vLIL~PTreLa~Qi~~~l  141 (1171)
T TIGR01054        65 KEFEEFFKKAVGSEPWSIQKMWAKRVLRGDSFAIIAPTGVGKTT-FGLAMSLFLAKK--GKRCYIILPTTLLVIQVAEKI  141 (1171)
T ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHHHhCCCeEEEECCCCCCHHH-HHHHHHHHHHhc--CCeEEEEeCHHHHHHHHHHHH
Confidence            34555555544457999999999999999999999999999996 666666555432  679999999999999999999


Q ss_pred             HHhhccCCceEE---EEECCcchHHHH---HHHh-cCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhc-----
Q 022724          122 LAIGDFINIQAH---ACVGGKSVGEDI---RKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS-----  189 (293)
Q Consensus       122 ~~~~~~~~~~~~---~~~~~~~~~~~~---~~~~-~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~-----  189 (293)
                      +.+....++.+.   .++|+.+..++.   ..+. ++++|+|+||+++...+..-  .. +++++|+||||.|++     
T Consensus       142 ~~l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~~~l--~~-~~~~iVvDEaD~~L~~~k~v  218 (1171)
T TIGR01054       142 SSLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDEL--GP-KFDFIFVDDVDALLKASKNV  218 (1171)
T ss_pred             HHHHHhcCCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHHHHh--cC-CCCEEEEeChHhhhhccccH
Confidence            999887776543   467877665542   2333 35899999999998876542  12 899999999999987     


Q ss_pred             ------cccHHH-HHHHH----------------------hhCCCCcc--EEEEEee-cChhHHHHHHhcCCCCEEEEec
Q 022724          190 ------RGFKDQ-IYDVY----------------------RYLPPDLQ--VVLISAT-LPHEILEMTTKFMTDPVKILVK  237 (293)
Q Consensus       190 ------~~~~~~-~~~i~----------------------~~l~~~~q--~v~~SAt-~~~~~~~~~~~~~~~~~~~~~~  237 (293)
                            .||..+ +..++                      +.+++..|  ++++||| .|..+..   .++.++..+.+.
T Consensus       219 d~il~llGF~~e~i~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~li~~SAT~~p~~~~~---~l~r~ll~~~v~  295 (1171)
T TIGR01054       219 DKLLKLLGFSEELIEKAWKLIRLRLKLYRALHAKKRLELLEAIPGKKRGCLIVSSATGRPRGKRA---KLFRELLGFEVG  295 (1171)
T ss_pred             HHHHHHcCCCHHHHHHHHHHhhhccccchHHHHHHHHHHHHhhhhccCcEEEEEeCCCCccccHH---HHcccccceEec
Confidence                  456543 34332                      23344444  6778999 5655432   234555666666


Q ss_pred             CCcccCCCceEEEEEecCcccHHHHHHHHHhhCCCCcEEEEcccc---hhHHHHHhhC
Q 022724          238 RDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTK---RKVLLLVLQF  292 (293)
Q Consensus       238 ~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~~iIF~~s~---~~a~~l~~~L  292 (293)
                      .......++.+.+...+.   +...+.++++.. +.++||||+++   +.|+.+++.|
T Consensus       296 ~~~~~~r~I~~~~~~~~~---~~~~L~~ll~~l-~~~~IVFv~t~~~~~~a~~l~~~L  349 (1171)
T TIGR01054       296 GGSDTLRNVVDVYVEDED---LKETLLEIVKKL-GTGGIVYVSIDYGKEKAEEIAEFL  349 (1171)
T ss_pred             CccccccceEEEEEeccc---HHHHHHHHHHHc-CCCEEEEEeccccHHHHHHHHHHH
Confidence            655666778888775543   234566777665 36899999999   9999999876

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.

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.96  E-value=2e-27  Score=234.34  Aligned_cols=215  Identities=16%  Similarity=0.212  Sum_probs=152.3

Q ss_pred             EEcCCCChhHHHHHHHHHhhhccC----------CCceeEEEEcCCHHHHHHHHHHHHHhh------------ccCCceE
Q 022724           75 AQAQSGTGKTSMIALTVCQTVDTS----------SREVQALILSPTRELATQTEKVILAIG------------DFINIQA  132 (293)
Q Consensus        75 i~~~Tg~GKT~~~~~~~~~~l~~~----------~~~~~~lil~P~~~l~~q~~~~~~~~~------------~~~~~~~  132 (293)
                      |++|||||||++|.+|+++.+...          ..+.++|||+|+++|+.|+.+.++...            ...++++
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            579999999999999999988643          235799999999999999999887521            1347889


Q ss_pred             EEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcC-CCCCCCccEEEecchhhhhccccHH----HHHHHHhhCCCCc
Q 022724          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK-TLRTRAIKLLVLDESDEMLSRGFKD----QIYDVYRYLPPDL  207 (293)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~-~~~~~~l~~iViDE~h~~~~~~~~~----~~~~i~~~l~~~~  207 (293)
                      ...+|+++..++.+.+.++++|+|+||+++..++.++ ...++++++|||||+|.+.+..++.    .+..+...++.+.
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 3468999999999999998765443    4555556666789


Q ss_pred             cEEEEEeecChhHHHHHHhcCC-CCEEEEecCCcccCCCceEEEEEecCcc-------------------cHHHH-HHHH
Q 022724          208 QVVLISATLPHEILEMTTKFMT-DPVKILVKRDELTLEGIKQFFVAVEREE-------------------WKFDT-LCDL  266 (293)
Q Consensus       208 q~v~~SAt~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~i~~~~~~~~~~~-------------------~k~~~-l~~l  266 (293)
                      |+|++|||+++. ++..+++.. ++..+.. ........+. .++...+..                   ..... ...+
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 555555443 3544432 2222222232 222211100                   00011 1123


Q ss_pred             Hhh-CCCCcEEEEcccchhHHHHHhhC
Q 022724          267 YDT-LTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       267 ~~~-~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      +.. ....++||||||++.|+.++..|
T Consensus       238 l~~i~~~~stLVFvNSR~~AE~La~~L  264 (1490)
T PRK09751        238 LDEVLRHRSTIVFTNSRGLAEKLTARL  264 (1490)
T ss_pred             HHHHhcCCCEEEECCCHHHHHHHHHHH
Confidence            322 23569999999999999998765

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.95  E-value=6.7e-26  Score=199.37  Aligned_cols=226  Identities=13%  Similarity=0.098  Sum_probs=151.3

Q ss_pred             HHHHHHHhhhcCCc--EEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcc----CCceE
Q 022724           59 IQQRAVMPIIKGRD--VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDF----INIQA  132 (293)
Q Consensus        59 ~Q~~~~~~i~~~~~--~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~----~~~~~  132 (293)
                      +|.++|+.+.++++  +++++|||+|||++|++|++..      +.+++|++|+++|++|+++.++.+...    .+..+
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  8899999999999999998852      346899999999999999999887633    24556


Q ss_pred             EEEECCcchH--HHH------------------HHHhcCCcEEEeChHHHHHHHhcC----C-C---CCCCccEEEecch
Q 022724          133 HACVGGKSVG--EDI------------------RKLEHGVHVVSGTPGRVCDMIKRK----T-L---RTRAIKLLVLDES  184 (293)
Q Consensus       133 ~~~~~~~~~~--~~~------------------~~~~~~~~ilV~Tp~~l~~~l~~~----~-~---~~~~l~~iViDE~  184 (293)
                      ..+.|....+  ...                  ....+.+.|+++||+.+..+++..    . .   .+.++++|||||+
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            6666652221  000                  011246789999999998776542    1 1   2478999999999


Q ss_pred             hhhhcccc-----HHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhc--CCCCEEEEecCCc----------c------
Q 022724          185 DEMLSRGF-----KDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKF--MTDPVKILVKRDE----------L------  241 (293)
Q Consensus       185 h~~~~~~~-----~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~--~~~~~~~~~~~~~----------~------  241 (293)
                      |.+..+..     .-....+++......+++++|||+++.+...+...  +..+.........          .      
T Consensus       155 H~~~~~~~~~~~~~l~~~~~~~~~~~~~~~i~lSAT~~~~~~~~l~~~~~~~~~~~~v~g~~~~~~~~~~~~~~~~~~~~  234 (357)
T TIGR03158       155 HLYDAKQLVGMLFLLAYMQLIRFFECRRKFVFLSATPDPALILRLQNAKQAGVKIAPIDGEKYQFPDNPELEADNKTQSF  234 (357)
T ss_pred             cccCcccchhhhhhhHHHHHHHhhhcCCcEEEEecCCCHHHHHHHHhccccCceeeeecCcccccCCChhhhcccccccc
Confidence            99864321     11233444444446799999999999888877765  4444433222200          0      


Q ss_pred             --cCCCceEEEEEecCcccHHHHHHHHH-------hhCCCCcEEEEcccchhHHHHHhhC
Q 022724          242 --TLEGIKQFFVAVEREEWKFDTLCDLY-------DTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       242 --~~~~i~~~~~~~~~~~~k~~~l~~l~-------~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                        ..+.+.+.+.. . ...|...+..++       +..+++++||||||++.|+.++..|
T Consensus       235 ~~~~~~i~~~~~~-~-~~~~~~~l~~l~~~i~~~~~~~~~~k~LIf~nt~~~~~~l~~~L  292 (357)
T TIGR03158       235 RPVLPPVELELIP-A-PDFKEEELSELAEEVIERFRQLPGERGAIILDSLDEVNRLSDLL  292 (357)
T ss_pred             ceeccceEEEEEe-C-CchhHHHHHHHHHHHHHHHhccCCCeEEEEECCHHHHHHHHHHH
Confidence              01245554443 2 222444333322       2235679999999999999999876

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.

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

Probab=99.95  E-value=4.3e-27  Score=218.16  Aligned_cols=238  Identities=13%  Similarity=0.222  Sum_probs=175.4

Q ss_pred             HCCCCCCcHHHHHHHHhhh-cCCcEEEEcCCCChhHHHHHHHHHhhhcc-------CCCceeEEEEcCCHHHHHHHHHHH
Q 022724           50 QYGFEKPSAIQQRAVMPII-KGRDVIAQAQSGTGKTSMIALTVCQTVDT-------SSREVQALILSPTRELATQTEKVI  121 (293)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~i~-~~~~~li~~~Tg~GKT~~~~~~~~~~l~~-------~~~~~~~lil~P~~~l~~q~~~~~  121 (293)
                      -++|..++.+|++++|... ++.|.+||||||+|||-.|++.+++.+..       ...+.++||++|+++||.++.+.+
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       234679999999999999999999


Q ss_pred             HHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCC---CCCCCccEEEecchhhhhccccHHHHHH
Q 022724          122 LAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT---LRTRAIKLLVLDESDEMLSRGFKDQIYD  198 (293)
Q Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~---~~~~~l~~iViDE~h~~~~~~~~~~~~~  198 (293)
                      .+-....|+++..+.|+++...-.   -..++|+|+|||++--.-+...   ..++.+.++||||+|++.+. .+..++.
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            887778899999999998765432   2357999999999864433322   22577899999999988644 5666666


Q ss_pred             HHhhC-------CCCccEEEEEeecChhHHHHHHhcCCCC-EEEEecCCcccCCCceEEEEEecCcc--cHHHHH-----
Q 022724          199 VYRYL-------PPDLQVVLISATLPHEILEMTTKFMTDP-VKILVKRDELTLEGIKQFFVAVEREE--WKFDTL-----  263 (293)
Q Consensus       199 i~~~l-------~~~~q~v~~SAt~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~i~~~~~~~~~~~--~k~~~l-----  263 (293)
                      +..++       ....++|++|||+|+- .+.+.++--+| ..+..-.....+-.+.+.++-+....  .+...+     
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            65554       3568999999999985 66666555443 33333333345556777777666551  122222     


Q ss_pred             HHHHhh-CCCCcEEEEcccchhHHHHHhhC
Q 022724          264 CDLYDT-LTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       264 ~~l~~~-~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ....+. ..+.+++|||++++++.+.|+.|
T Consensus       340 ~kv~e~~~~g~qVlvFvhsR~~Ti~tA~~l  369 (1230)
T KOG0952|consen  340 DKVVEFLQEGHQVLVFVHSRNETIRTAKKL  369 (1230)
T ss_pred             HHHHHHHHcCCeEEEEEecChHHHHHHHHH
Confidence            122222 23569999999999999988765

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.95  E-value=9.4e-26  Score=213.30  Aligned_cols=225  Identities=20%  Similarity=0.226  Sum_probs=156.2

Q ss_pred             HHHHHHH-HHCCCCCCcHHHHHHHHhhhcC------CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHH
Q 022724           42 DDLLRGI-YQYGFEKPSAIQQRAVMPIIKG------RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELA  114 (293)
Q Consensus        42 ~~i~~~l-~~~~~~~~~~~Q~~~~~~i~~~------~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~  114 (293)
                      ..+.+.+ ..++|. ||+.|+++++.+.++      ++.+++||||||||++|++|++..+..   +.+++|++||++|+
T Consensus       248 ~~~~~~~~~~l~f~-lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~~---g~q~lilaPT~~LA  323 (681)
T PRK10917        248 GELLKKFLASLPFE-LTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEA---GYQAALMAPTEILA  323 (681)
T ss_pred             hHHHHHHHHhCCCC-CCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHHc---CCeEEEEeccHHHH
Confidence            3444444 456775 999999999999876      489999999999999999999988754   67899999999999


Q ss_pred             HHHHHHHHHhhccCCceEEEEECCcchHHHH---HHHhc-CCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcc
Q 022724          115 TQTEKVILAIGDFINIQAHACVGGKSVGEDI---RKLEH-GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (293)
Q Consensus       115 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~-~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~  190 (293)
                      .|+++.++++....++++..++|+.+..+..   ..+.+ .++|+||||+.+..     ...+.+++++||||+|++...
T Consensus       324 ~Q~~~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~-----~v~~~~l~lvVIDE~Hrfg~~  398 (681)
T PRK10917        324 EQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQD-----DVEFHNLGLVIIDEQHRFGVE  398 (681)
T ss_pred             HHHHHHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcc-----cchhcccceEEEechhhhhHH
Confidence            9999999999988899999999998754433   33433 58999999976643     345789999999999997422


Q ss_pred             ccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHhhC
Q 022724          191 GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL  270 (293)
Q Consensus       191 ~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~  270 (293)
                           ....+.......++++||||+.+....+......++..+....  .....+...+............+...+  .
T Consensus       399 -----qr~~l~~~~~~~~iL~~SATp~prtl~~~~~g~~~~s~i~~~p--~~r~~i~~~~~~~~~~~~~~~~i~~~~--~  469 (681)
T PRK10917        399 -----QRLALREKGENPHVLVMTATPIPRTLAMTAYGDLDVSVIDELP--PGRKPITTVVIPDSRRDEVYERIREEI--A  469 (681)
T ss_pred             -----HHHHHHhcCCCCCEEEEeCCCCHHHHHHHHcCCCceEEEecCC--CCCCCcEEEEeCcccHHHHHHHHHHHH--H
Confidence                 2222333455689999999987765554432222333222211  112234444433222221122233322  3


Q ss_pred             CCCcEEEEcccchh
Q 022724          271 TITQAVIFCNTKRK  284 (293)
Q Consensus       271 ~~~~~iIF~~s~~~  284 (293)
                      .+.+++|||+++++
T Consensus       470 ~g~q~~v~~~~ie~  483 (681)
T PRK10917        470 KGRQAYVVCPLIEE  483 (681)
T ss_pred             cCCcEEEEEccccc
Confidence            45799999997654

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.94  E-value=1.7e-25  Score=208.30  Aligned_cols=223  Identities=19%  Similarity=0.143  Sum_probs=158.0

Q ss_pred             cHHHHHHHHhhhcCCcEEEEcCCCChhHHH---------HHHHHHhhhc---cCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 022724           57 SAIQQRAVMPIIKGRDVIAQAQSGTGKTSM---------IALTVCQTVD---TSSREVQALILSPTRELATQTEKVILAI  124 (293)
Q Consensus        57 ~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~---------~~~~~~~~l~---~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (293)
                      -.+|.++++.+.+|++++++|+||+|||.+         |++|.+..+.   ....+.++++++|+++|+.|+...+.+.
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            457899999999999999999999999987         5555555543   2334568999999999999999988765


Q ss_pred             hcc---CCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHh
Q 022724          125 GDF---INIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYR  201 (293)
Q Consensus       125 ~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~  201 (293)
                      ...   .+..+...+|+.+. ..........+|+|+|++.       ....++++++||+||||.+...+  +.+..+++
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   35677888888763 2222222356899999742       12347889999999999986554  44555555


Q ss_pred             hCC-CCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecC---------cccHHHHHHHHHhh--
Q 022724          202 YLP-PDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVER---------EEWKFDTLCDLYDT--  269 (293)
Q Consensus       202 ~l~-~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~---------~~~k~~~l~~l~~~--  269 (293)
                      .+. ...|+++||||+++++..+ ..++.++..+.+..  .....+.+.+.....         ...+...+..+...  
T Consensus       316 ~~~~~~rq~ILmSATl~~dv~~l-~~~~~~p~~I~I~g--rt~~pV~~~yi~~~~~~~~~~~y~~~~k~~~l~~L~~~~~  392 (675)
T PHA02653        316 KHIDKIRSLFLMTATLEDDRDRI-KEFFPNPAFVHIPG--GTLFPISEVYVKNKYNPKNKRAYIEEEKKNIVTALKKYTP  392 (675)
T ss_pred             HhhhhcCEEEEEccCCcHhHHHH-HHHhcCCcEEEeCC--CcCCCeEEEEeecCcccccchhhhHHHHHHHHHHHHHhhc
Confidence            443 3459999999999887776 57888888887752  234567777764331         11122223333322  


Q ss_pred             CCCCcEEEEcccchhHHHHHhhC
Q 022724          270 LTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       270 ~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ..++++||||+++++++.+++.|
T Consensus       393 ~~~g~iLVFlpg~~ei~~l~~~L  415 (675)
T PHA02653        393 PKGSSGIVFVASVSQCEEYKKYL  415 (675)
T ss_pred             ccCCcEEEEECcHHHHHHHHHHH
Confidence            23468999999999999998876

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.94  E-value=6.1e-25  Score=206.47  Aligned_cols=223  Identities=19%  Similarity=0.170  Sum_probs=151.9

Q ss_pred             HHHHHHHCCCCCCcHHHHHHHHhhhcC------CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHH
Q 022724           44 LLRGIYQYGFEKPSAIQQRAVMPIIKG------RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQT  117 (293)
Q Consensus        44 i~~~l~~~~~~~~~~~Q~~~~~~i~~~------~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~  117 (293)
                      +.+.+..++| .||+.|+++++.+.++      .+.+++||||||||.+|++|++..+..   +.+++|++||++|+.|+
T Consensus       225 ~~~~~~~lpf-~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~---g~qvlilaPT~~LA~Q~  300 (630)
T TIGR00643       225 LTKFLASLPF-KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEA---GYQVALMAPTEILAEQH  300 (630)
T ss_pred             HHHHHHhCCC-CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHHc---CCcEEEECCHHHHHHHH
Confidence            4455667788 5999999999999865      368999999999999999999988764   56899999999999999


Q ss_pred             HHHHHHhhccCCceEEEEECCcchHHHH---HHHh-cCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccH
Q 022724          118 EKVILAIGDFINIQAHACVGGKSVGEDI---RKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFK  193 (293)
Q Consensus       118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~  193 (293)
                      ++.++++....++++..++|+....+..   ..+. ..++|+|+||+.+..     ...+.+++++||||+|.+....  
T Consensus       301 ~~~~~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~-----~~~~~~l~lvVIDEaH~fg~~q--  373 (630)
T TIGR00643       301 YNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQE-----KVEFKRLALVIIDEQHRFGVEQ--  373 (630)
T ss_pred             HHHHHHHhcccCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhc-----cccccccceEEEechhhccHHH--
Confidence            9999999988899999999998765532   3333 357999999987653     3567899999999999864321  


Q ss_pred             HHHHHHHhhCC--CCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHhh-C
Q 022724          194 DQIYDVYRYLP--PDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDT-L  270 (293)
Q Consensus       194 ~~~~~i~~~l~--~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~-~  270 (293)
                        ...+.....  ...++++||||+.+....+......+...+..  .......+...+..  ... +...+..+.+. .
T Consensus       374 --r~~l~~~~~~~~~~~~l~~SATp~prtl~l~~~~~l~~~~i~~--~p~~r~~i~~~~~~--~~~-~~~~~~~i~~~l~  446 (630)
T TIGR00643       374 --RKKLREKGQGGFTPHVLVMSATPIPRTLALTVYGDLDTSIIDE--LPPGRKPITTVLIK--HDE-KDIVYEFIEEEIA  446 (630)
T ss_pred             --HHHHHHhcccCCCCCEEEEeCCCCcHHHHHHhcCCcceeeecc--CCCCCCceEEEEeC--cch-HHHHHHHHHHHHH
Confidence              122222222  26899999999866544433221112111111  11111223333332  222 32223222222 2


Q ss_pred             CCCcEEEEcccchh
Q 022724          271 TITQAVIFCNTKRK  284 (293)
Q Consensus       271 ~~~~~iIF~~s~~~  284 (293)
                      .+.+++|||+++++
T Consensus       447 ~g~q~~v~~~~i~~  460 (630)
T TIGR00643       447 KGRQAYVVYPLIEE  460 (630)
T ss_pred             hCCcEEEEEccccc
Confidence            46799999998743

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.93  E-value=2.1e-25  Score=197.36  Aligned_cols=215  Identities=18%  Similarity=0.121  Sum_probs=139.1

Q ss_pred             cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchH---------
Q 022724           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVG---------  142 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~---------  142 (293)
                      ++++++|||+|||++|++++++.+... .+.+++|++|+++|+.|+.+++..+...   .+..++++....         
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~~-~~~~ii~v~P~~~L~~q~~~~l~~~f~~---~~~~~~~~~~~~~~~~~~~~~   76 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKSQ-KADRVIIALPTRATINAMYRRAKELFGS---NLGLLHSSSSFKRIKEMGDSE   76 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhhC-CCCeEEEEeehHHHHHHHHHHHHHHhCc---ccEEeeccHHHHHHhccCCch
Confidence            589999999999999999999887543 3568999999999999999999987432   333444432210         


Q ss_pred             ---HHHHHH-h-----cCCcEEEeChHHHHHHHhcCC----CCC--CCccEEEecchhhhhccccHHHHHHHHhhCC-CC
Q 022724          143 ---EDIRKL-E-----HGVHVVSGTPGRVCDMIKRKT----LRT--RAIKLLVLDESDEMLSRGFKDQIYDVYRYLP-PD  206 (293)
Q Consensus       143 ---~~~~~~-~-----~~~~ilV~Tp~~l~~~l~~~~----~~~--~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~-~~  206 (293)
                         ...... .     ...+|+|+||+++.+.+..+.    ..+  -..+++|+||+|.+.+.++.. +..+++.+. .+
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               000000 0     235799999999988765521    111  123789999999998765443 555554443 47


Q ss_pred             ccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEE-ecCcccHHHHHHHHHhhC-CCCcEEEEcccchh
Q 022724          207 LQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVA-VEREEWKFDTLCDLYDTL-TITQAVIFCNTKRK  284 (293)
Q Consensus       207 ~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~-~~~~~~k~~~l~~l~~~~-~~~~~iIF~~s~~~  284 (293)
                      .|+++||||+|+.+.++.......+.....+..... ....+.+.. ......+...+..+++.. .++++||||||+++
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            899999999998877777655433211111111000 011222222 222223566666666543 46799999999999


Q ss_pred             HHHHHhhC
Q 022724          285 VLLLVLQF  292 (293)
Q Consensus       285 a~~l~~~L  292 (293)
                      |+.+++.|
T Consensus       235 ~~~~~~~L  242 (358)
T TIGR01587       235 AQEFYQQL  242 (358)
T ss_pred             HHHHHHHH
Confidence            99998776

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.

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.92  E-value=1.1e-23  Score=200.90  Aligned_cols=216  Identities=19%  Similarity=0.261  Sum_probs=156.5

Q ss_pred             HHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHH-HhhccCCceEEEEEC
Q 022724           59 IQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL-AIGDFINIQAHACVG  137 (293)
Q Consensus        59 ~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~-~~~~~~~~~~~~~~~  137 (293)
                      +-.+.+..+.++++++++||||||||.+|.+++++....   ..+++++.|++++|.|+.+++. .+....|..+....+
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            334566777788999999999999999999999976432   2489999999999999999985 455556777776666


Q ss_pred             CcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhh-hccc-cHHHHHHHHhhCCCCccEEEEEee
Q 022724          138 GKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM-LSRG-FKDQIYDVYRYLPPDLQVVLISAT  215 (293)
Q Consensus       138 ~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~-~~~~-~~~~~~~i~~~l~~~~q~v~~SAt  215 (293)
                      +.+..      ....+|+|+||+.+.+++... ..++++++|||||+|.. ++.. ....+..+.+.++++.|+++||||
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 AESKV------GPNTRLEVVTEGILTRMIQRD-PELSGVGLVILDEFHERSLQADLALALLLDVQQGLRDDLKLLIMSAT  158 (812)
T ss_pred             Ccccc------CCCCcEEEEChhHHHHHHhhC-CCcCcCcEEEEcCCCccccccchHHHHHHHHHHhCCccceEEEEecC
Confidence            54321      234589999999999988763 57899999999999973 3322 223345566777788999999999


Q ss_pred             cChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHH-----HHHHHHhhCCCCcEEEEcccchhHHHHHh
Q 022724          216 LPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFD-----TLCDLYDTLTITQAVIFCNTKRKVLLLVL  290 (293)
Q Consensus       216 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~-----~l~~l~~~~~~~~~iIF~~s~~~a~~l~~  290 (293)
                      ++...   ...++.++..+.....   ...+.++|..++... +..     .+..++.. ..+++||||+++++++.+++
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   3456665555544322   234677776655443 332     24444443 35799999999999999988


Q ss_pred             hC
Q 022724          291 QF  292 (293)
Q Consensus       291 ~L  292 (293)
                      .|
T Consensus       231 ~L  232 (812)
T PRK11664        231 QL  232 (812)
T ss_pred             HH
Confidence            76

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.92  E-value=3.7e-23  Score=196.99  Aligned_cols=217  Identities=17%  Similarity=0.217  Sum_probs=155.9

Q ss_pred             HHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHH-HhhccCCceEEEEEC
Q 022724           59 IQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL-AIGDFINIQAHACVG  137 (293)
Q Consensus        59 ~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~-~~~~~~~~~~~~~~~  137 (293)
                      +-.+.+..+.++++++++|+||||||.+|.+++++...   .+.+++++.|++++|.|+.+++. .+....|..+....+
T Consensus         6 ~~~~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~---~~~~ilvlqPrR~aA~qiA~rva~~~~~~~g~~VGy~vr   82 (819)
T TIGR01970         6 VLPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPG---IGGKIIMLEPRRLAARSAAQRLASQLGEAVGQTVGYRVR   82 (819)
T ss_pred             HHHHHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhhc---cCCeEEEEeCcHHHHHHHHHHHHHHhCCCcCcEEEEEEc
Confidence            34456677778899999999999999999999998763   24589999999999999999885 455555666655544


Q ss_pred             CcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhh-hhccccHH-HHHHHHhhCCCCccEEEEEee
Q 022724          138 GKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDE-MLSRGFKD-QIYDVYRYLPPDLQVVLISAT  215 (293)
Q Consensus       138 ~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~-~~~~~~~~-~~~~i~~~l~~~~q~v~~SAt  215 (293)
                      +..      ......+|+|+||+.|.+++.. ...++++++|||||+|. .++.++.- .+..+.+.+++..|+|+||||
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      2234568999999999998876 35789999999999995 55544432 344566667788999999999


Q ss_pred             cChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHH----HHHHHHHhhCCCCcEEEEcccchhHHHHHhh
Q 022724          216 LPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKF----DTLCDLYDTLTITQAVIFCNTKRKVLLLVLQ  291 (293)
Q Consensus       216 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~----~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~  291 (293)
                      ++...   ...++.++..+.....   ...+.++|..........    ..+..+++. ..+++||||+++++++.+++.
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            98753   3456655555544322   234666766554433111    234444443 357899999999999999876


Q ss_pred             C
Q 022724          292 F  292 (293)
Q Consensus       292 L  292 (293)
                      |
T Consensus       229 L  229 (819)
T TIGR01970       229 L  229 (819)
T ss_pred             H
Confidence            5

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.

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

Probab=99.92  E-value=1.2e-24  Score=185.45  Aligned_cols=193  Identities=28%  Similarity=0.393  Sum_probs=146.0

Q ss_pred             CceeEEEEcCCHHHHHHHHHHHHHhh---ccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCc
Q 022724          100 REVQALILSPTRELATQTEKVILAIG---DFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (293)
Q Consensus       100 ~~~~~lil~P~~~l~~q~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l  176 (293)
                      +.++++|+-|+++|++|+.+.++++.   .+..++...+.||.-...+.+.+.++.+|+|+||+++.+++..+...+.++
T Consensus       285 Nap~avivepsrelaEqt~N~i~~Fk~h~~np~~r~lLmiggv~~r~Q~~ql~~g~~ivvGtpgRl~~~is~g~~~lt~c  364 (725)
T KOG0349|consen  285 NAPEAVIVEPSRELAEQTHNQIEEFKMHTSNPEVRSLLMIGGVLKRTQCKQLKDGTHIVVGTPGRLLQPISKGLVTLTHC  364 (725)
T ss_pred             CCcceeEecCcHHHHHHHHhhHHHHHhhcCChhhhhhhhhhhHHhHHHHHHhhcCceeeecCchhhhhhhhccceeeeee
Confidence            34789999999999999999777665   344566667888888888999999999999999999999999999999999


Q ss_pred             cEEEecchhhhhccccHHHHHHHHhhCC------CCccEEEEEeecCh-hHHHHHHhcCCCCEEEEecCCcccCCCceEE
Q 022724          177 KLLVLDESDEMLSRGFKDQIYDVYRYLP------PDLQVVLISATLPH-EILEMTTKFMTDPVKILVKRDELTLEGIKQF  249 (293)
Q Consensus       177 ~~iViDE~h~~~~~~~~~~~~~i~~~l~------~~~q~v~~SAt~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~  249 (293)
                      .++|+||+|.++..+|.+.+.++...++      .+.|.++.|||+.. +++.+.+..|.=|..+.....+..+..+++.
T Consensus       365 rFlvlDead~lL~qgy~d~I~r~h~qip~~tsdg~rlq~~vCsatlh~feVkk~~ervmhfptwVdLkgeD~vpetvHhv  444 (725)
T KOG0349|consen  365 RFLVLDEADLLLGQGYDDKIYRFHGQIPHMTSDGFRLQSPVCSATLHIFEVKKVGERVMHFPTWVDLKGEDLVPETVHHV  444 (725)
T ss_pred             EEEEecchhhhhhcccHHHHHHHhccchhhhcCCcccccceeeeEEeEEEeeehhhhhccCceeEecccccccchhhccc
Confidence            9999999999999999999988888776      36899999999853 3455666666656666555554455555444


Q ss_pred             EEEecCcc-----------------------------cHHHH---------HHHHHhhCCCCcEEEEcccchhHHHHHhh
Q 022724          250 FVAVEREE-----------------------------WKFDT---------LCDLYDTLTITQAVIFCNTKRKVLLLVLQ  291 (293)
Q Consensus       250 ~~~~~~~~-----------------------------~k~~~---------l~~l~~~~~~~~~iIF~~s~~~a~~l~~~  291 (293)
                      +..+...-                             .....         -...++++...++||||.|+.+|+.+.++
T Consensus       445 v~lv~p~~d~sw~~lr~~i~td~vh~kdn~~pg~~Spe~~s~a~kilkgEy~v~ai~~h~mdkaiifcrtk~dcDnLer~  524 (725)
T KOG0349|consen  445 VKLVCPSVDGSWCDLRQFIETDKVHTKDNLLPGQVSPENPSSATKILKGEYGVVAIRRHAMDKAIIFCRTKQDCDNLERM  524 (725)
T ss_pred             eeecCCccCccHHHHhhhhccCCcccccccccccCCCCChhhhhHHhcCchhhhhhhhhccCceEEEEeccccchHHHHH
Confidence            33322110                             01111         11223455667999999999999988776


Q ss_pred             C
Q 022724          292 F  292 (293)
Q Consensus       292 L  292 (293)
                      +
T Consensus       525 ~  525 (725)
T KOG0349|consen  525 M  525 (725)
T ss_pred             H
Confidence            4

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

Probab=99.92  E-value=6.7e-24  Score=191.75  Aligned_cols=232  Identities=18%  Similarity=0.207  Sum_probs=165.3

Q ss_pred             HHHHH-CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 022724           46 RGIYQ-YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (293)
Q Consensus        46 ~~l~~-~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (293)
                      ..|++ +||..+++-|.++|..+++|+|+++..|||+||++||.+|++-.     .| -+|||+|..+|..++.+.++..
T Consensus         7 ~~L~~~fGy~~FR~gQ~evI~~~l~g~d~lvvmPTGgGKSlCyQiPAll~-----~G-~TLVVSPLiSLM~DQV~~l~~~   80 (590)
T COG0514           7 QVLKQVFGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLL-----EG-LTLVVSPLISLMKDQVDQLEAA   80 (590)
T ss_pred             HHHHHHhCccccCCCHHHHHHHHHcCCcEEEEccCCCCcchHhhhHHHhc-----CC-CEEEECchHHHHHHHHHHHHHc
Confidence            34543 69999999999999999999999999999999999999999765     23 6999999999999999988764


Q ss_pred             hccCCceEEEEECCcchHHHHHHH---h-cCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccc--cHHHHHH
Q 022724          125 GDFINIQAHACVGGKSVGEDIRKL---E-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG--FKDQIYD  198 (293)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~~---~-~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~--~~~~~~~  198 (293)
                          |+.+..+++.-+.++....+   . ...+++.-+||++..--....+.-..+.++||||||++.+||  |+..+..
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                57777888776655543332   2 346899999999975222222335678999999999999997  7766655


Q ss_pred             H---HhhCCCCccEEEEEeecChhHHHHHHhcCC--CCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHhhCCCC
Q 022724          199 V---YRYLPPDLQVVLISATLPHEILEMTTKFMT--DPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTIT  273 (293)
Q Consensus       199 i---~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~~  273 (293)
                      +   ...++ +..++++|||.++.+..-+...+.  .+..+...   ...+++...+........+...+.. ......+
T Consensus       157 lg~l~~~~~-~~p~~AlTATA~~~v~~DI~~~L~l~~~~~~~~s---fdRpNi~~~v~~~~~~~~q~~fi~~-~~~~~~~  231 (590)
T COG0514         157 LGRLRAGLP-NPPVLALTATATPRVRDDIREQLGLQDANIFRGS---FDRPNLALKVVEKGEPSDQLAFLAT-VLPQLSK  231 (590)
T ss_pred             HHHHHhhCC-CCCEEEEeCCCChHHHHHHHHHhcCCCcceEEec---CCCchhhhhhhhcccHHHHHHHHHh-hccccCC
Confidence            4   44454 789999999999988886665443  33333332   2223333222222211223332222 1144456


Q ss_pred             cEEEEcccchhHHHHHhhC
Q 022724          274 QAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       274 ~~iIF~~s~~~a~~l~~~L  292 (293)
                      +.||||.|++.|+.+++.|
T Consensus       232 ~GIIYc~sRk~~E~ia~~L  250 (590)
T COG0514         232 SGIIYCLTRKKVEELAEWL  250 (590)
T ss_pred             CeEEEEeeHHhHHHHHHHH
Confidence            8999999999999999876

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.91  E-value=1.3e-23  Score=192.90  Aligned_cols=151  Identities=17%  Similarity=0.134  Sum_probs=114.8

Q ss_pred             CCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceE
Q 022724           53 FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQA  132 (293)
Q Consensus        53 ~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  132 (293)
                      ...|+++|+++++.++.+++.++++|||+|||+++...+...+..  ...+++|++|+++|+.|+.+.++++.......+
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  234899999999999999999998765444445


Q ss_pred             EEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEE
Q 022724          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLI  212 (293)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~  212 (293)
                      ..+.+|....       .+.+|+|+||+++.+...   ..++++++||+||+|++....    +..++..+++..+++++
T Consensus       190 ~~i~~g~~~~-------~~~~I~VaT~qsl~~~~~---~~~~~~~~iIvDEaH~~~~~~----~~~il~~~~~~~~~lGL  255 (501)
T PHA02558        190 HKIYSGTAKD-------TDAPIVVSTWQSAVKQPK---EWFDQFGMVIVDECHLFTGKS----LTSIITKLDNCKFKFGL  255 (501)
T ss_pred             eEEecCcccC-------CCCCEEEeeHHHHhhchh---hhccccCEEEEEchhcccchh----HHHHHHhhhccceEEEE
Confidence            4555554322       246899999999876432   246789999999999986543    45666666667889999


Q ss_pred             EeecChh
Q 022724          213 SATLPHE  219 (293)
Q Consensus       213 SAt~~~~  219 (293)
                      |||+.+.
T Consensus       256 TATp~~~  262 (501)
T PHA02558        256 TGSLRDG  262 (501)
T ss_pred             eccCCCc
Confidence            9999654

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.91  E-value=2.5e-22  Score=162.35  Aligned_cols=187  Identities=35%  Similarity=0.591  Sum_probs=153.7

Q ss_pred             CCCCCCcHHHHHHHHhhhcC-CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCC
Q 022724           51 YGFEKPSAIQQRAVMPIIKG-RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (293)
Q Consensus        51 ~~~~~~~~~Q~~~~~~i~~~-~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (293)
                      .++..|+++|.++++.+..+ +++++.+|||+|||.++..+++..+.... ..++++++|+..++.|+...+..+.....
T Consensus         4 ~~~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~~-~~~~l~~~p~~~~~~~~~~~~~~~~~~~~   82 (201)
T smart00487        4 FGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGK-GKRVLVLVPTRELAEQWAEELKKLGPSLG   82 (201)
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhcccC-CCcEEEEeCCHHHHHHHHHHHHHHhccCC
Confidence            46788999999999999988 99999999999999999999988877653 34799999999999999999988776554


Q ss_pred             ceEEEEECCcchHHHHHHHhcCC-cEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCcc
Q 022724          130 IQAHACVGGKSVGEDIRKLEHGV-HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ  208 (293)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~-~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q  208 (293)
                      .......++.........+.++. +++++|++.+.+.+........+++++|+||+|.+....+...+..++..+++..+
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~v~~~t~~~l~~~~~~~~~~~~~~~~iIiDE~h~~~~~~~~~~~~~~~~~~~~~~~  162 (201)
T smart00487       83 LKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDLLELSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQ  162 (201)
T ss_pred             eEEEEEeCCcchHHHHHHHhcCCCCEEEeChHHHHHHHHcCCcCHhHCCEEEEECHHHHhcCCcHHHHHHHHHhCCccce
Confidence            33344444444344555555555 99999999999988887777888999999999999765778888888888888899


Q ss_pred             EEEEEeecChhHHHHHHhcCCCCEEEEecC
Q 022724          209 VVLISATLPHEILEMTTKFMTDPVKILVKR  238 (293)
Q Consensus       209 ~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~  238 (293)
                      ++++|||+++........++.+...+....
T Consensus       163 ~v~~saT~~~~~~~~~~~~~~~~~~~~~~~  192 (201)
T smart00487      163 LLLLSATPPEEIENLLELFLNDPVFIDVGP  192 (201)
T ss_pred             EEEEecCCchhHHHHHHHhcCCCEEEeCCc
Confidence            999999999998888888887666665543

>PRK13766 Hef nuclease; Provisional

Probab=99.90  E-value=2.7e-22  Score=193.93  Aligned_cols=162  Identities=18%  Similarity=0.207  Sum_probs=128.6

Q ss_pred             CCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCce
Q 022724           52 GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ  131 (293)
Q Consensus        52 ~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  131 (293)
                      +.-.|+++|++++...+.+ |+++++|||+|||+++++++...+..  .+.++||++|+++|+.|+.+.++.+....+.+
T Consensus        12 ~~~~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~~--~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~~~~   88 (773)
T PRK13766         12 NTIEARLYQQLLAATALKK-NTLVVLPTGLGKTAIALLVIAERLHK--KGGKVLILAPTKPLVEQHAEFFRKFLNIPEEK   88 (773)
T ss_pred             CcCCccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHHh--CCCeEEEEeCcHHHHHHHHHHHHHHhCCCCce
Confidence            4457999999999988776 99999999999999999988887742  34689999999999999999999876554557


Q ss_pred             EEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEE
Q 022724          132 AHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVL  211 (293)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~  211 (293)
                      +..++|+.+..... .+..+.+|+|+||+.+...+..+.+.+.++++|||||||++........+........+..++++
T Consensus        89 v~~~~g~~~~~~r~-~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~~liVvDEaH~~~~~~~~~~i~~~~~~~~~~~~il~  167 (773)
T PRK13766         89 IVVFTGEVSPEKRA-ELWEKAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKNPLVLG  167 (773)
T ss_pred             EEEEeCCCCHHHHH-HHHhCCCEEEECHHHHHHHHHcCCCChhhCcEEEEECCccccccccHHHHHHHHHhcCCCCEEEE
Confidence            77788877665443 33345799999999999887777888899999999999998655333334444444445678999


Q ss_pred             EEeecC
Q 022724          212 ISATLP  217 (293)
Q Consensus       212 ~SAt~~  217 (293)
                      +|||+.
T Consensus       168 lTaTP~  173 (773)
T PRK13766        168 LTASPG  173 (773)
T ss_pred             EEcCCC
Confidence            999974

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.89  E-value=4.1e-22  Score=183.42  Aligned_cols=231  Identities=17%  Similarity=0.210  Sum_probs=171.3

Q ss_pred             CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q 022724           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (293)
Q Consensus        51 ~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (293)
                      .|. .|+++|..+++.+..|+  +..+.||+|||++|.+|++.....   |++++|++||++||.|.++.+..+...+|+
T Consensus       100 lg~-~p~~VQ~~~~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al~---G~~v~VvTptreLA~qdae~~~~l~~~lGl  173 (656)
T PRK12898        100 LGQ-RHFDVQLMGGLALLSGR--LAEMQTGEGKTLTATLPAGTAALA---GLPVHVITVNDYLAERDAELMRPLYEALGL  173 (656)
T ss_pred             hCC-CCChHHHHHHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhhc---CCeEEEEcCcHHHHHHHHHHHHHHHhhcCC
Confidence            454 49999999999999999  999999999999999999987654   568999999999999999999999999999


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcCC-------------------------CCCCCccEEEecch
Q 022724          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRKT-------------------------LRTRAIKLLVLDES  184 (293)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l-~~~l~~~~-------------------------~~~~~l~~iViDE~  184 (293)
                      ++..++|+.+..  .+....+++|+++|...+ .++|+.+.                         ...+.+.+.||||+
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  344456789999999887 44554431                         11366899999999


Q ss_pred             hhhh-ccc-----------------cHHHHHHHHhhC--------------------------------CC---------
Q 022724          185 DEML-SRG-----------------FKDQIYDVYRYL--------------------------------PP---------  205 (293)
Q Consensus       185 h~~~-~~~-----------------~~~~~~~i~~~l--------------------------------~~---------  205 (293)
                      |.++ |..                 .......+...+                                +.         
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            9974 110                 000011110000                                00         


Q ss_pred             ----------------------------------------------------------------------------CccE
Q 022724          206 ----------------------------------------------------------------------------DLQV  209 (293)
Q Consensus       206 ----------------------------------------------------------------------------~~q~  209 (293)
                                                                                                  -.++
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                                                                                        1368


Q ss_pred             EEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHhhC--CCCcEEEEcccchhHHH
Q 022724          210 VLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL--TITQAVIFCNTKRKVLL  287 (293)
Q Consensus       210 v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~--~~~~~iIF~~s~~~a~~  287 (293)
                      .+||||.+....++...|..++..+......  .....+.++.++... |...+.+++...  .+.++||||+|++.++.
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            8999999988888888887776665544332  222344455565544 888888888753  35689999999999999


Q ss_pred             HHhhC
Q 022724          288 LVLQF  292 (293)
Q Consensus       288 l~~~L  292 (293)
                      ++..|
T Consensus       489 L~~~L  493 (656)
T PRK12898        489 LSALL  493 (656)
T ss_pred             HHHHH
Confidence            98876

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

Probab=99.89  E-value=3.1e-22  Score=188.56  Aligned_cols=247  Identities=15%  Similarity=0.255  Sum_probs=178.8

Q ss_pred             CCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcC-CcEEEEcCCCChhHHHHHHHHHhhhccCCC--------ceeEEEEcC
Q 022724           39 GIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG-RDVIAQAQSGTGKTSMIALTVCQTVDTSSR--------EVQALILSP  109 (293)
Q Consensus        39 ~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~-~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~--------~~~~lil~P  109 (293)
                      .+|.+-..++.  |..+++++|..+.+..+.+ .|+++|||||+|||-.+++.+++.+..+.+        ..+++|++|
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            45666666664  6778999999999997765 699999999999999999999999865432        348999999


Q ss_pred             CHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCC--CCCCCccEEEecchhhh
Q 022724          110 TRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT--LRTRAIKLLVLDESDEM  187 (293)
Q Consensus       110 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~--~~~~~l~~iViDE~h~~  187 (293)
                      .++|++++...+.+....+|+.|...+|+.....+.  + .+.+|+||||++.--.-++..  -..+-++++|+||+|++
T Consensus       373 mKaLvqE~VgsfSkRla~~GI~V~ElTgD~~l~~~q--i-eeTqVIV~TPEK~DiITRk~gdraY~qlvrLlIIDEIHLL  449 (1674)
T KOG0951|consen  373 MKALVQEMVGSFSKRLAPLGITVLELTGDSQLGKEQ--I-EETQVIVTTPEKWDIITRKSGDRAYEQLVRLLIIDEIHLL  449 (1674)
T ss_pred             HHHHHHHHHHHHHhhccccCcEEEEecccccchhhh--h-hcceeEEeccchhhhhhcccCchhHHHHHHHHhhhhhhhc
Confidence            999999999999998889999999999987543221  1 346899999998854433321  12245788999999988


Q ss_pred             hccccHHHHHHHHhhC-------CCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCccc--
Q 022724          188 LSRGFKDQIYDVYRYL-------PPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEW--  258 (293)
Q Consensus       188 ~~~~~~~~~~~i~~~l-------~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~--  258 (293)
                      .|. .+..++.+..+.       ...++++++|||+|+. .+....+.-++..+.....+..+..+.|.++.+...+.  
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            544 455555544433       2478999999999985 23222223344444444455666778888888876542  


Q ss_pred             HHHHH-----HHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          259 KFDTL-----CDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       259 k~~~l-----~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      +.+++     ...++....+++|||+++|+++-+.|+++
T Consensus       528 ~~qamNe~~yeKVm~~agk~qVLVFVHsRkET~ktA~aI  566 (1674)
T KOG0951|consen  528 RFQAMNEACYEKVLEHAGKNQVLVFVHSRKETAKTARAI  566 (1674)
T ss_pred             HHHHHHHHHHHHHHHhCCCCcEEEEEEechHHHHHHHHH
Confidence            22232     23334445579999999999999988764

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

Probab=99.89  E-value=1.4e-21  Score=185.47  Aligned_cols=178  Identities=22%  Similarity=0.286  Sum_probs=145.3

Q ss_pred             HHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhc
Q 022724           47 GIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGD  126 (293)
Q Consensus        47 ~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~  126 (293)
                      .....+|. +.++|++++..+..|.+++++||||+|||+....++...+..   +.+++|..|.++|.+|.++.+.....
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            33456776 999999999999999999999999999999988888777665   34699999999999999998876544


Q ss_pred             cCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCC
Q 022724          127 FINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPD  206 (293)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~  206 (293)
                      ...-.+....|+.+..       .+..++|.|-+.|-+++.++...+..+.+||+||+|.|.+...+-..+.++-.++..
T Consensus       188 dv~~~vGL~TGDv~IN-------~~A~clvMTTEILRnMlyrg~~~~~~i~~ViFDEvHyi~D~eRG~VWEE~Ii~lP~~  260 (1041)
T COG4581         188 DVADMVGLMTGDVSIN-------PDAPCLVMTTEILRNMLYRGSESLRDIEWVVFDEVHYIGDRERGVVWEEVIILLPDH  260 (1041)
T ss_pred             hhhhhccceecceeeC-------CCCceEEeeHHHHHHHhccCcccccccceEEEEeeeeccccccchhHHHHHHhcCCC
Confidence            3322345666666543       457899999999999999999999999999999999999998999999999999999


Q ss_pred             ccEEEEEeecChhHHHHHHhc---CCCCEEEEe
Q 022724          207 LQVVLISATLPHEILEMTTKF---MTDPVKILV  236 (293)
Q Consensus       207 ~q~v~~SAt~~~~~~~~~~~~---~~~~~~~~~  236 (293)
                      .++|++|||+|+. .++..|.   -..|..+..
T Consensus       261 v~~v~LSATv~N~-~EF~~Wi~~~~~~~~~vv~  292 (1041)
T COG4581         261 VRFVFLSATVPNA-EEFAEWIQRVHSQPIHVVS  292 (1041)
T ss_pred             CcEEEEeCCCCCH-HHHHHHHHhccCCCeEEEe
Confidence            9999999999886 3333333   234444444

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

Probab=99.88  E-value=5.2e-21  Score=166.69  Aligned_cols=167  Identities=16%  Similarity=0.175  Sum_probs=138.4

Q ss_pred             CCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceE
Q 022724           53 FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQA  132 (293)
Q Consensus        53 ~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  132 (293)
                      .-.++.+|.......+.+ |++++.|||.|||+++++.+...+...++  ++|+++||+.|+.|..+.|+++..-..-.+
T Consensus        13 ~ie~R~YQ~~i~a~al~~-NtLvvlPTGLGKT~IA~~V~~~~l~~~~~--kvlfLAPTKPLV~Qh~~~~~~v~~ip~~~i   89 (542)
T COG1111          13 TIEPRLYQLNIAAKALFK-NTLVVLPTGLGKTFIAAMVIANRLRWFGG--KVLFLAPTKPLVLQHAEFCRKVTGIPEDEI   89 (542)
T ss_pred             cccHHHHHHHHHHHHhhc-CeEEEecCCccHHHHHHHHHHHHHHhcCC--eEEEecCCchHHHHHHHHHHHHhCCChhhe
Confidence            346888999888777665 99999999999999999988888877543  899999999999999999999887777788


Q ss_pred             EEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEE
Q 022724          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLI  212 (293)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~  212 (293)
                      ..++|.....+....|..+ +|+|+||+.+.+-+..+.+++.++.++||||||+...+.-.-.+......-.+++.++++
T Consensus        90 ~~ltGev~p~~R~~~w~~~-kVfvaTPQvveNDl~~Grid~~dv~~lifDEAHRAvGnyAYv~Va~~y~~~~k~~~ilgL  168 (542)
T COG1111          90 AALTGEVRPEEREELWAKK-KVFVATPQVVENDLKAGRIDLDDVSLLIFDEAHRAVGNYAYVFVAKEYLRSAKNPLILGL  168 (542)
T ss_pred             eeecCCCChHHHHHHHhhC-CEEEeccHHHHhHHhcCccChHHceEEEechhhhccCcchHHHHHHHHHHhccCceEEEE
Confidence            8999998888777777654 899999999999999999999999999999999986554333343333334467899999


Q ss_pred             EeecChhHHHH
Q 022724          213 SATLPHEILEM  223 (293)
Q Consensus       213 SAt~~~~~~~~  223 (293)
                      |||+..+.+..
T Consensus       169 TASPGs~~ekI  179 (542)
T COG1111         169 TASPGSDLEKI  179 (542)
T ss_pred             ecCCCCCHHHH
Confidence            99997765543

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.88  E-value=7.4e-22  Score=185.20  Aligned_cols=148  Identities=18%  Similarity=0.304  Sum_probs=131.0

Q ss_pred             ccCCCCHHHHHHHH-----HCCCCCC---cHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEE
Q 022724           36 DAMGIKDDLLRGIY-----QYGFEKP---SAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALIL  107 (293)
Q Consensus        36 ~~~~l~~~i~~~l~-----~~~~~~~---~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil  107 (293)
                      +.+++..++...+.     .+||..|   +|+|.++++.+..+++++..++||+|||++|++|++..+...   ..++||
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            45678888888876     6799999   999999999999999999999999999999999999877643   248899


Q ss_pred             cCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcCCCCCC-------CccEE
Q 022724          108 SPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRKTLRTR-------AIKLL  179 (293)
Q Consensus       108 ~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l-~~~l~~~~~~~~-------~l~~i  179 (293)
                      +|+++||.|..+.+..+.+.+++++..+.||.+...+...+  +++|+|+||++| .++++.+.+.++       .+.++
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            99999999999999999999999999999999888776555  489999999999 999998766655       56899


Q ss_pred             Eecchhhhh
Q 022724          180 VLDESDEML  188 (293)
Q Consensus       180 ViDE~h~~~  188 (293)
                      ||||||.|+
T Consensus       220 IIDEADsmL  228 (970)
T PRK12899        220 IIDEVDSIL  228 (970)
T ss_pred             EEechhhhh
Confidence            999999986

>PRK09694 helicase Cas3; Provisional

Probab=99.87  E-value=9.5e-21  Score=180.79  Aligned_cols=238  Identities=14%  Similarity=0.086  Sum_probs=143.7

Q ss_pred             CCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccC--Cc
Q 022724           53 FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI--NI  130 (293)
Q Consensus        53 ~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~--~~  130 (293)
                      ...|+|+|+.+-.....+..+++.+|||+|||.+++..+...+. .....+++|..||++.+++++++++++....  ..
T Consensus       284 ~~~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~~l~~-~~~~~gi~~aLPT~Atan~m~~Rl~~~~~~~f~~~  362 (878)
T PRK09694        284 GYQPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAWRLID-QGLADSIIFALPTQATANAMLSRLEALASKLFPSP  362 (878)
T ss_pred             CCCChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHHHHHH-hCCCCeEEEECcHHHHHHHHHHHHHHHHHHhcCCC
Confidence            34799999988655445678999999999999998776654333 3334589999999999999999998643322  34


Q ss_pred             eEEEEECCcchHHHHH--------------------HHh----c---CCcEEEeChHHHHHHHhc-CCCCCCCc----cE
Q 022724          131 QAHACVGGKSVGEDIR--------------------KLE----H---GVHVVSGTPGRVCDMIKR-KTLRTRAI----KL  178 (293)
Q Consensus       131 ~~~~~~~~~~~~~~~~--------------------~~~----~---~~~ilV~Tp~~l~~~l~~-~~~~~~~l----~~  178 (293)
                      ++...+|.........                    .+.    +   -.+|+|||+++++..+-. +...++.+    ++
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            5666776543221100                    111    1   158999999999863322 22222333    48


Q ss_pred             EEecchhhhhccccHHHHHHHHhhCC-CCccEEEEEeecChhHHHHHHhcCCCC----------EEEEecC---Ccc--c
Q 022724          179 LVLDESDEMLSRGFKDQIYDVYRYLP-PDLQVVLISATLPHEILEMTTKFMTDP----------VKILVKR---DEL--T  242 (293)
Q Consensus       179 iViDE~h~~~~~~~~~~~~~i~~~l~-~~~q~v~~SAt~~~~~~~~~~~~~~~~----------~~~~~~~---~~~--~  242 (293)
                      |||||+|.+ +......+..+++.+. ...++|+||||+|....+.+...+...          .......   ...  .
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            999999987 3434455566665543 467899999999988776443322110          0000000   000  0


Q ss_pred             C----CCceEEEE--Ee--cCcccHHHHHHHHHhh-CCCCcEEEEcccchhHHHHHhhC
Q 022724          243 L----EGIKQFFV--AV--EREEWKFDTLCDLYDT-LTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       243 ~----~~i~~~~~--~~--~~~~~k~~~l~~l~~~-~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      .    ....+.+.  ..  .........+..+++. ..+++++|||||++.|+.+++.|
T Consensus       522 ~~~~~~~~~~~v~v~~~~~~~~~~~~~~l~~i~~~~~~g~~vLVf~NTV~~Aq~ly~~L  580 (878)
T PRK09694        522 AHPEQLPARFTIQLEPICLADMLPDLTLLQRMIAAANAGAQVCLICNLVDDAQKLYQRL  580 (878)
T ss_pred             ccccccCcceEEEEEeeccccccCHHHHHHHHHHHHhcCCEEEEEECCHHHHHHHHHHH
Confidence            0    00111111  11  1111123344444443 34679999999999999999876

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.87  E-value=1.7e-20  Score=174.77  Aligned_cols=132  Identities=17%  Similarity=0.256  Sum_probs=100.5

Q ss_pred             CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q 022724           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (293)
Q Consensus        51 ~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (293)
                      .|. .|++.|......+.+|  .++.++||+|||++|++|++.....   +..++|++|+++||.|..+.+..+...+|+
T Consensus        67 lgl-rpydVQlig~l~l~~G--~Iaem~TGeGKTLta~Lpa~l~aL~---g~~V~VVTpn~yLA~Rdae~m~~l~~~LGL  140 (762)
T TIGR03714        67 LGM-FPYDVQVLGAIVLHQG--NIAEMKTGEGKTLTATMPLYLNALT---GKGAMLVTTNDYLAKRDAEEMGPVYEWLGL  140 (762)
T ss_pred             cCC-CccHHHHHHHHHhcCC--ceeEecCCcchHHHHHHHHHHHhhc---CCceEEeCCCHHHHHHHHHHHHHHHhhcCC
Confidence            354 4555555555544444  6999999999999999998766554   346999999999999999999999999999


Q ss_pred             eEEEEECCc---chHHHHHHHhcCCcEEEeChHHH-HHHHhc------CCCCCCCccEEEecchhhhh
Q 022724          131 QAHACVGGK---SVGEDIRKLEHGVHVVSGTPGRV-CDMIKR------KTLRTRAIKLLVLDESDEML  188 (293)
Q Consensus       131 ~~~~~~~~~---~~~~~~~~~~~~~~ilV~Tp~~l-~~~l~~------~~~~~~~l~~iViDE~h~~~  188 (293)
                      ++...+++.   ......+....+++|+++||+++ ..+++.      ....++.+.++|+||||.++
T Consensus       141 sv~~~~~~s~~~~~~~~~rr~~y~~dIvygTp~~LgfDyLrD~l~~~~~~~~~r~l~~~IVDEaDsIL  208 (762)
T TIGR03714       141 TVSLGVVDDPDEEYDANEKRKIYNSDIVYTTNSALGFDYLIDNLASNKEGKFLRPFNYVIVDEVDSVL  208 (762)
T ss_pred             cEEEEECCCCccccCHHHHHHhCCCCEEEECchhhhhhHHHHHhhcchhhcccccCcEEEEecHhhHh
Confidence            998877652   12233334445789999999999 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.

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.86  E-value=7.2e-20  Score=172.90  Aligned_cols=156  Identities=24%  Similarity=0.253  Sum_probs=119.0

Q ss_pred             CCcHHHHHHHHhhhcC---CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCce
Q 022724           55 KPSAIQQRAVMPIIKG---RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ  131 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~---~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  131 (293)
                      .+++.|+++++.+.++   +++++.++||+|||.+|+.++...+..   +.+++|++|+++|+.|+.+.+++..   +.+
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   789999999999999999887777654   5689999999999999999888643   567


Q ss_pred             EEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccc-----c-HHHHHHHHh
Q 022724          132 AHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG-----F-KDQIYDVYR  201 (293)
Q Consensus       132 ~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~-----~-~~~~~~i~~  201 (293)
                      +..++|+.+..+..+.+    ...++|+|+|+..+.       ..+.++++|||||+|...-..     | ...+. +.+
T Consensus       218 v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~-------~p~~~l~liVvDEeh~~s~~~~~~p~y~~r~va-~~r  289 (679)
T PRK05580        218 VAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALF-------LPFKNLGLIIVDEEHDSSYKQQEGPRYHARDLA-VVR  289 (679)
T ss_pred             EEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHhc-------ccccCCCEEEEECCCccccccCcCCCCcHHHHH-HHH
Confidence            88899987765554333    245799999997653       347889999999999764221     1 12222 233


Q ss_pred             hCCCCccEEEEEeecChhHHHHH
Q 022724          202 YLPPDLQVVLISATLPHEILEMT  224 (293)
Q Consensus       202 ~l~~~~q~v~~SAt~~~~~~~~~  224 (293)
                      ....+.+++++|||++.......
T Consensus       290 a~~~~~~~il~SATps~~s~~~~  312 (679)
T PRK05580        290 AKLENIPVVLGSATPSLESLANA  312 (679)
T ss_pred             hhccCCCEEEEcCCCCHHHHHHH
Confidence            33468899999999875544443

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.86  E-value=3.6e-20  Score=174.07  Aligned_cols=131  Identities=16%  Similarity=0.284  Sum_probs=109.4

Q ss_pred             CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q 022724           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (293)
Q Consensus        51 ~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (293)
                      +|. .|+++|..+.+.+.+|+  +..+.||+|||+++++|++.....   |.++.|++|+++||.|.++.+..+...+|+
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 69999999999998887  999999999999999999865554   568999999999999999999999999999


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcCC------CCCCCccEEEecchhhhh
Q 022724          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRKT------LRTRAIKLLVLDESDEML  188 (293)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l-~~~l~~~~------~~~~~l~~iViDE~h~~~  188 (293)
                      ++....|+.+...+.+.. .+++|+++||+.+ .++++.+.      ..++.+.++||||+|.++
T Consensus       149 ~v~~i~g~~~~~~~r~~~-y~~dIvygT~~~l~fDyLrd~~~~~~~~~~~r~~~~~IvDEaDsiL  212 (790)
T PRK09200        149 TVGLNFSDIDDASEKKAI-YEADIIYTTNSELGFDYLRDNLADSKEDKVQRPLNYAIIDEIDSIL  212 (790)
T ss_pred             eEEEEeCCCCcHHHHHHh-cCCCEEEECCccccchhHHhccccchhhhcccccceEEEeccccce
Confidence            999999998733333333 4589999999999 45554432      356889999999999975

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

Probab=99.86  E-value=1.9e-20  Score=157.69  Aligned_cols=249  Identities=16%  Similarity=0.228  Sum_probs=171.4

Q ss_pred             cCcccCCCCHHHHHHHHH-CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCH
Q 022724           33 TSFDAMGIKDDLLRGIYQ-YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (293)
Q Consensus        33 ~~f~~~~l~~~i~~~l~~-~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~  111 (293)
                      ..-+++|++.+..+-|++ +..+.++|.|..+++....|++.+++.|||.||++||.+|++-.      ...++++||..
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            345678999998888875 56779999999999999999999999999999999999998753      34799999999


Q ss_pred             HHHHHHHHHHHHhhccCCceEEEEECCcchHHHH---HHH---hcCCcEEEeChHHHHH---HHhc--CCCCCCCccEEE
Q 022724          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDI---RKL---EHGVHVVSGTPGRVCD---MIKR--KTLRTRAIKLLV  180 (293)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~---~~~~~ilV~Tp~~l~~---~l~~--~~~~~~~l~~iV  180 (293)
                      .|++++.-+++.++    +....+..+.+..+..   ..+   .....++..||+++..   ++..  ..+....+.+|-
T Consensus       145 slmedqil~lkqlg----i~as~lnansske~~k~v~~~i~nkdse~kliyvtpekiaksk~~mnkleka~~~~~~~~ia  220 (695)
T KOG0353|consen  145 SLMEDQILQLKQLG----IDASMLNANSSKEEAKRVEAAITNKDSEFKLIYVTPEKIAKSKKFMNKLEKALEAGFFKLIA  220 (695)
T ss_pred             HHHHHHHHHHHHhC----cchhhccCcccHHHHHHHHHHHcCCCceeEEEEecHHHHHHHHHHHHHHHHHhhcceeEEEe
Confidence            99999888887664    4333444444333221   111   1234688899999865   2222  445678889999


Q ss_pred             ecchhhhhccc--cHHHHHH--HHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEE-ecC
Q 022724          181 LDESDEMLSRG--FKDQIYD--VYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVA-VER  255 (293)
Q Consensus       181 iDE~h~~~~~~--~~~~~~~--i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~-~~~  255 (293)
                      |||+|+...||  |+.++..  ++++-=++..+++++||.++.+..-.+..+.-...+.+.. ....+++...+.- ...
T Consensus       221 idevhccsqwghdfr~dy~~l~ilkrqf~~~~iigltatatn~vl~d~k~il~ie~~~tf~a-~fnr~nl~yev~qkp~n  299 (695)
T KOG0353|consen  221 IDEVHCCSQWGHDFRPDYKALGILKRQFKGAPIIGLTATATNHVLDDAKDILCIEAAFTFRA-GFNRPNLKYEVRQKPGN  299 (695)
T ss_pred             ecceeehhhhCcccCcchHHHHHHHHhCCCCceeeeehhhhcchhhHHHHHHhHHhhheeec-ccCCCCceeEeeeCCCC
Confidence            99999998886  4444432  3444446889999999998887776665543222222211 1222232222221 112


Q ss_pred             cccHHHHHHHHHh-hCCCCcEEEEcccchhHHHHHhhC
Q 022724          256 EEWKFDTLCDLYD-TLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       256 ~~~k~~~l~~l~~-~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      +++-.+.+..+++ ...+...||||-++++|++++..|
T Consensus       300 ~dd~~edi~k~i~~~f~gqsgiiyc~sq~d~ekva~al  337 (695)
T KOG0353|consen  300 EDDCIEDIAKLIKGDFAGQSGIIYCFSQKDCEKVAKAL  337 (695)
T ss_pred             hHHHHHHHHHHhccccCCCcceEEEeccccHHHHHHHH
Confidence            2234445555554 556779999999999999998865

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.85  E-value=5.6e-20  Score=170.47  Aligned_cols=130  Identities=21%  Similarity=0.324  Sum_probs=110.1

Q ss_pred             CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q 022724           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (293)
Q Consensus        51 ~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (293)
                      +|. .|++.|......+.+|+  +..++||+|||+++.+|++-....   |.++.|++|+.+||.|.++.+..+...+|+
T Consensus        53 lg~-~p~~vQlig~~~l~~G~--Iaem~TGeGKTLva~lpa~l~aL~---G~~V~VvTpt~~LA~qdae~~~~l~~~LGL  126 (745)
T TIGR00963        53 LGM-RPFDVQLIGGIALHKGK--IAEMKTGEGKTLTATLPAYLNALT---GKGVHVVTVNDYLAQRDAEWMGQVYRFLGL  126 (745)
T ss_pred             hCC-CccchHHhhhhhhcCCc--eeeecCCCccHHHHHHHHHHHHHh---CCCEEEEcCCHHHHHHHHHHHHHHhccCCC
Confidence            454 49999999999888887  999999999999999999543333   346999999999999999999999999999


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcC------CCCCCCccEEEecchhhhh
Q 022724          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRK------TLRTRAIKLLVLDESDEML  188 (293)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l-~~~l~~~------~~~~~~l~~iViDE~h~~~  188 (293)
                      ++..+.|+.+........  .++|++|||++| .++++.+      ...++.+.++||||+|.++
T Consensus       127 sv~~i~g~~~~~~r~~~y--~~dIvyGT~~rlgfDyLrd~~~~~~~~~~~r~l~~aIIDEaDs~L  189 (745)
T TIGR00963       127 SVGLILSGMSPEERREAY--ACDITYGTNNELGFDYLRDNMAHSKEEKVQRPFHFAIIDEVDSIL  189 (745)
T ss_pred             eEEEEeCCCCHHHHHHhc--CCCEEEECCCchhhHHHhcccccchhhhhccccceeEeecHHHHh
Confidence            999999998765444333  479999999999 8888776      3567899999999999985

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.

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

Probab=99.85  E-value=1.9e-20  Score=171.79  Aligned_cols=167  Identities=16%  Similarity=0.186  Sum_probs=128.4

Q ss_pred             CCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCce
Q 022724           52 GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ  131 (293)
Q Consensus        52 ~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  131 (293)
                      ..-.++.+|.+.....+ |+|++|++|||+|||++++..+.+++...+. .++|+++|++.|+.|+...+..++..  ..
T Consensus        59 ~~~~lR~YQ~eivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p~-~KiVF~aP~~pLv~QQ~a~~~~~~~~--~~  134 (746)
T KOG0354|consen   59 TNLELRNYQEELVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWRPK-GKVVFLAPTRPLVNQQIACFSIYLIP--YS  134 (746)
T ss_pred             CcccccHHHHHHhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhcCCc-ceEEEeeCCchHHHHHHHHHhhccCc--cc
Confidence            34468999999998888 9999999999999999999999999888766 58999999999999999666655533  44


Q ss_pred             EEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCC-CCCccEEEecchhhhhccc-cHHHHHHHHhhCCCCccE
Q 022724          132 AHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLR-TRAIKLLVLDESDEMLSRG-FKDQIYDVYRYLPPDLQV  209 (293)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~-~~~l~~iViDE~h~~~~~~-~~~~~~~i~~~l~~~~q~  209 (293)
                      +....||.........+-...+|+|.||+.+.+.|.++..+ ++.+.++||||||+...+. |...+..++..-....|+
T Consensus       135 ~T~~l~~~~~~~~r~~i~~s~~vff~TpQil~ndL~~~~~~~ls~fs~iv~DE~Hra~kn~~Y~~Vmr~~l~~k~~~~qI  214 (746)
T KOG0354|consen  135 VTGQLGDTVPRSNRGEIVASKRVFFRTPQILENDLKSGLHDELSDFSLIVFDECHRTSKNHPYNNIMREYLDLKNQGNQI  214 (746)
T ss_pred             ceeeccCccCCCchhhhhcccceEEeChHhhhhhcccccccccceEEEEEEcccccccccccHHHHHHHHHHhhhccccE
Confidence            44555553322222233345699999999999988876544 5999999999999987664 444444666555556699


Q ss_pred             EEEEeecChhHHH
Q 022724          210 VLISATLPHEILE  222 (293)
Q Consensus       210 v~~SAt~~~~~~~  222 (293)
                      +++|||++.+...
T Consensus       215 LgLTASpG~~~~~  227 (746)
T KOG0354|consen  215 LGLTASPGSKLEQ  227 (746)
T ss_pred             EEEecCCCccHHH
Confidence            9999999765444

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

Probab=99.84  E-value=4.9e-20  Score=175.72  Aligned_cols=235  Identities=15%  Similarity=0.178  Sum_probs=165.0

Q ss_pred             HHHHH-HHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHH
Q 022724           44 LLRGI-YQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL  122 (293)
Q Consensus        44 i~~~l-~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~  122 (293)
                      ....+ ..+|...+++-|.+++..++.|++.++..|||.||++||.+|++-.      ++-.|+|.|..+|+..+...+.
T Consensus       252 ~~~~l~~~Fg~~~FR~~Q~eaI~~~l~Gkd~fvlmpTG~GKSLCYQlPA~l~------~gitvVISPL~SLm~DQv~~L~  325 (941)
T KOG0351|consen  252 LELLLKEVFGHKGFRPNQLEAINATLSGKDCFVLMPTGGGKSLCYQLPALLL------GGVTVVISPLISLMQDQVTHLS  325 (941)
T ss_pred             HHHHHHHHhccccCChhHHHHHHHHHcCCceEEEeecCCceeeEeecccccc------CCceEEeccHHHHHHHHHHhhh
Confidence            44443 4579999999999999999999999999999999999999988543      3479999999999998877552


Q ss_pred             HhhccCCceEEEEECCcchHHHHH---HHhc---CCcEEEeChHHHHH--HHhcCCCCCCC---ccEEEecchhhhhccc
Q 022724          123 AIGDFINIQAHACVGGKSVGEDIR---KLEH---GVHVVSGTPGRVCD--MIKRKTLRTRA---IKLLVLDESDEMLSRG  191 (293)
Q Consensus       123 ~~~~~~~~~~~~~~~~~~~~~~~~---~~~~---~~~ilV~Tp~~l~~--~l~~~~~~~~~---l~~iViDE~h~~~~~~  191 (293)
                          ..++....++++....++..   .+.+   .++|+-.||+++..  .+.....++..   +.++||||||+...|+
T Consensus       326 ----~~~I~a~~L~s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~~~~~~L~~~~~lal~vIDEAHCVSqWg  401 (941)
T KOG0351|consen  326 ----KKGIPACFLSSIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLYARGLLALFVIDEAHCVSQWG  401 (941)
T ss_pred             ----hcCcceeeccccccHHHHHHHHHHHhCCCCeEEEEEeCHHHhhcccchhhHHHhccCCCeeEEEEecHHHHhhhhc
Confidence                45677778888776654433   3333   46899999999976  22323334444   8999999999999886


Q ss_pred             --cHHHHHHHHhhCC--CCccEEEEEeecChhHHHHHHhcC--CCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHH
Q 022724          192 --FKDQIYDVYRYLP--PDLQVVLISATLPHEILEMTTKFM--TDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCD  265 (293)
Q Consensus       192 --~~~~~~~i~~~l~--~~~q~v~~SAt~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~  265 (293)
                        |+..+..+.....  +...++++|||.+..+..-+-..+  .++..+...   ..+.++...+. .+........+..
T Consensus       402 HdFRp~Yk~l~~l~~~~~~vP~iALTATAT~~v~~DIi~~L~l~~~~~~~~s---fnR~NL~yeV~-~k~~~~~~~~~~~  477 (941)
T KOG0351|consen  402 HDFRPSYKRLGLLRIRFPGVPFIALTATATERVREDVIRSLGLRNPELFKSS---FNRPNLKYEVS-PKTDKDALLDILE  477 (941)
T ss_pred             ccccHHHHHHHHHHhhCCCCCeEEeehhccHHHHHHHHHHhCCCCcceeccc---CCCCCceEEEE-eccCccchHHHHH
Confidence              6666655433322  358999999999988887555443  345533222   22233333322 2221223333333


Q ss_pred             HHh-hCCCCcEEEEcccchhHHHHHhhC
Q 022724          266 LYD-TLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       266 l~~-~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ..+ .+.....||||.++.+|+.++..|
T Consensus       478 ~~~~~~~~~s~IIYC~sr~~ce~vs~~L  505 (941)
T KOG0351|consen  478 ESKLRHPDQSGIIYCLSRKECEQVSAVL  505 (941)
T ss_pred             HhhhcCCCCCeEEEeCCcchHHHHHHHH
Confidence            343 455679999999999999998765

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

Probab=99.84  E-value=9.8e-20  Score=168.19  Aligned_cols=161  Identities=20%  Similarity=0.271  Sum_probs=136.2

Q ss_pred             CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q 022724           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (293)
Q Consensus        51 ~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (293)
                      ..|. |..+|++|+-++.+|.+++|.|+|++|||.++..++.-..   .++.|+||-+|-++|-+|-++.++.-....| 
T Consensus       294 ~pFe-lD~FQk~Ai~~lerg~SVFVAAHTSAGKTvVAEYAialaq---~h~TR~iYTSPIKALSNQKfRDFk~tF~Dvg-  368 (1248)
T KOG0947|consen  294 YPFE-LDTFQKEAIYHLERGDSVFVAAHTSAGKTVVAEYAIALAQ---KHMTRTIYTSPIKALSNQKFRDFKETFGDVG-  368 (1248)
T ss_pred             CCCC-ccHHHHHHHHHHHcCCeEEEEecCCCCcchHHHHHHHHHH---hhccceEecchhhhhccchHHHHHHhccccc-
Confidence            3444 8999999999999999999999999999988766553332   2356899999999999999999987665544 


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEE
Q 022724          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVV  210 (293)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v  210 (293)
                         .++|+.+...       ...++|.|-+.|-++|.++..-.++++++|+||+|.+.|...+-.++.++-++|...++|
T Consensus       369 ---LlTGDvqinP-------eAsCLIMTTEILRsMLYrgadliRDvE~VIFDEVHYiND~eRGvVWEEViIMlP~HV~~I  438 (1248)
T KOG0947|consen  369 ---LLTGDVQINP-------EASCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYINDVERGVVWEEVIIMLPRHVNFI  438 (1248)
T ss_pred             ---eeecceeeCC-------CcceEeehHHHHHHHHhcccchhhccceEEEeeeeecccccccccceeeeeeccccceEE
Confidence               6777765543       368999999999999999988899999999999999999889999999999999999999


Q ss_pred             EEEeecChhHHHHHHhc
Q 022724          211 LISATLPHEILEMTTKF  227 (293)
Q Consensus       211 ~~SAt~~~~~~~~~~~~  227 (293)
                      ++|||+|+. .+++.|.
T Consensus       439 lLSATVPN~-~EFA~WI  454 (1248)
T KOG0947|consen  439 LLSATVPNT-LEFADWI  454 (1248)
T ss_pred             EEeccCCCh-HHHHHHh
Confidence            999999987 4455443

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

Probab=99.84  E-value=3.1e-20  Score=158.44  Aligned_cols=237  Identities=16%  Similarity=0.193  Sum_probs=154.3

Q ss_pred             HHHHHHHH-CCCCCC-cHHHHHHHHhhhcC-CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHH
Q 022724           43 DLLRGIYQ-YGFEKP-SAIQQRAVMPIIKG-RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (293)
Q Consensus        43 ~i~~~l~~-~~~~~~-~~~Q~~~~~~i~~~-~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~  119 (293)
                      .+.++|++ +|+..+ ++.|.+++..+.++ +|+.|++|||+||++||.+|.+-.      +...|++.|..+|..++.+
T Consensus         6 ~VreaLKK~FGh~kFKs~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~~------~gITIV~SPLiALIkDQiD   79 (641)
T KOG0352|consen    6 KVREALKKLFGHKKFKSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPALVH------GGITIVISPLIALIKDQID   79 (641)
T ss_pred             HHHHHHHHHhCchhhcChHHHHHHHHHHhccCcEEEeccCCCchhhhhhchHHHh------CCeEEEehHHHHHHHHHHH
Confidence            56677776 477755 89999999998865 699999999999999999998764      3479999999999999988


Q ss_pred             HHHHhhccCCceEEEEECCcchHHHHHHH------hcCCcEEEeChHHHHHHH----hcCCCCCCCccEEEecchhhhhc
Q 022724          120 VILAIGDFINIQAHACVGGKSVGEDIRKL------EHGVHVVSGTPGRVCDMI----KRKTLRTRAIKLLVLDESDEMLS  189 (293)
Q Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~ilV~Tp~~l~~~l----~~~~~~~~~l~~iViDE~h~~~~  189 (293)
                      .+..+.    +++..+++..+..+..+.+      .....++--||+....-.    -++...-..+.++|+||||+..+
T Consensus        80 HL~~LK----Vp~~SLNSKlSt~ER~ri~~DL~~ekp~~K~LYITPE~AAt~~FQ~lLn~L~~r~~L~Y~vVDEAHCVSQ  155 (641)
T KOG0352|consen   80 HLKRLK----VPCESLNSKLSTVERSRIMGDLAKEKPTIKMLYITPEGAATDGFQKLLNGLANRDVLRYIVVDEAHCVSQ  155 (641)
T ss_pred             HHHhcC----CchhHhcchhhHHHHHHHHHHHHhcCCceeEEEEchhhhhhhhHHHHHHHHhhhceeeeEEechhhhHhh
Confidence            777653    3444455555544433322      223468888998775422    12222345589999999999998


Q ss_pred             cc--cHHHHHH---HHhhCCCCccEEEEEeecChhHHHHHH--hcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHH
Q 022724          190 RG--FKDQIYD---VYRYLPPDLQVVLISATLPHEILEMTT--KFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDT  262 (293)
Q Consensus       190 ~~--~~~~~~~---i~~~l~~~~q~v~~SAt~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~  262 (293)
                      ||  |+.++..   +.+.+ ....-++++||.++.+++-+-  ..+.+|+.+.-.+.-  ..++..-...-+...+-+..
T Consensus       156 WGHDFRPDYL~LG~LRS~~-~~vpwvALTATA~~~VqEDi~~qL~L~~PVAiFkTP~F--R~NLFYD~~~K~~I~D~~~~  232 (641)
T KOG0352|consen  156 WGHDFRPDYLTLGSLRSVC-PGVPWVALTATANAKVQEDIAFQLKLRNPVAIFKTPTF--RDNLFYDNHMKSFITDCLTV  232 (641)
T ss_pred             hccccCcchhhhhhHHhhC-CCCceEEeecccChhHHHHHHHHHhhcCcHHhccCcch--hhhhhHHHHHHHHhhhHhHh
Confidence            86  5655544   34444 467889999999988877433  334566554332110  01100000000011122333


Q ss_pred             HHHHHhhC-------------CCCcEEEEcccchhHHHHHhhC
Q 022724          263 LCDLYDTL-------------TITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       263 l~~l~~~~-------------~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      |.++....             ..+..||||.|+++|++++-.|
T Consensus       233 LaDF~~~~LG~~~~~~~~~K~~~GCGIVYCRTR~~cEq~AI~l  275 (641)
T KOG0352|consen  233 LADFSSSNLGKHEKASQNKKTFTGCGIVYCRTRNECEQVAIML  275 (641)
T ss_pred             HHHHHHHhcCChhhhhcCCCCcCcceEEEeccHHHHHHHHHHh
Confidence            44433211             1348999999999999998765

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.82  E-value=8.8e-19  Score=171.10  Aligned_cols=215  Identities=20%  Similarity=0.273  Sum_probs=133.5

Q ss_pred             cHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHH-HHhhhccCCCceeEEEEcCC----HHHHHHHHHHHHH-hhccCCc
Q 022724           57 SAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALT-VCQTVDTSSREVQALILSPT----RELATQTEKVILA-IGDFINI  130 (293)
Q Consensus        57 ~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~-~~~~l~~~~~~~~~lil~P~----~~l~~q~~~~~~~-~~~~~~~  130 (293)
                      +..-.+++..+.+++.++|+|+||||||.  .+| ++....... ...+++.-|.    ++++.++.+.+.. ++...|+
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--QLPKICLELGRGV-KGLIGHTQPRRLAARTVANRIAEELETELGGCVGY  152 (1294)
T ss_pred             HHHHHHHHHHHHhCCeEEEECCCCCCHHH--HHHHHHHHcCCCC-CCceeeCCCcHHHHHHHHHHHHHHHhhhhcceece
Confidence            44444666777778888999999999998  355 333332221 1244445585    4666666665553 3433343


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhh-hhccccHH-HHHHHHhhCCCCcc
Q 022724          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDE-MLSRGFKD-QIYDVYRYLPPDLQ  208 (293)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~-~~~~~~~~-~~~~i~~~l~~~~q  208 (293)
                      .+.    .   ..   ...++++|+++||+.|++.+....+ ++++++|||||+|. +++.++.. .+..++.. .+..|
T Consensus       153 ~vr----f---~~---~~s~~t~I~v~TpG~LL~~l~~d~~-Ls~~~~IIIDEAHERsLn~DfLLg~Lk~lL~~-rpdlK  220 (1294)
T PRK11131        153 KVR----F---ND---QVSDNTMVKLMTDGILLAEIQQDRL-LMQYDTIIIDEAHERSLNIDFILGYLKELLPR-RPDLK  220 (1294)
T ss_pred             eec----C---cc---ccCCCCCEEEEChHHHHHHHhcCCc-cccCcEEEecCccccccccchHHHHHHHhhhc-CCCce
Confidence            321    1   11   1234679999999999998876544 89999999999994 66665543 23333332 24689


Q ss_pred             EEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcc-----cHHHHHHHHHh---hCCCCcEEEEcc
Q 022724          209 VVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREE-----WKFDTLCDLYD---TLTITQAVIFCN  280 (293)
Q Consensus       209 ~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~-----~k~~~l~~l~~---~~~~~~~iIF~~  280 (293)
                      +|+||||++.  ..+.+.+...|. +.+...   ...+..+|.......     +....+...+.   ....+.+||||+
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            9999999975  355555554553 444322   234566666553321     12222332222   234579999999


Q ss_pred             cchhHHHHHhhC
Q 022724          281 TKRKVLLLVLQF  292 (293)
Q Consensus       281 s~~~a~~l~~~L  292 (293)
                      +.++++.+++.|
T Consensus       295 g~~EIe~lae~L  306 (1294)
T PRK11131        295 GEREIRDTADAL  306 (1294)
T ss_pred             CHHHHHHHHHHH
Confidence            999999998876

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.82  E-value=1.4e-18  Score=132.47  Aligned_cols=144  Identities=35%  Similarity=0.523  Sum_probs=113.1

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhc
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH  150 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  150 (293)
                      +++++.+|||+|||..++..+....... ...+++|++|++.++.|+.+.+...... +..+..+.+.............
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~~-~~~~~lv~~p~~~l~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~   78 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDSL-KGGQVLVLAPTRELANQVAERLKELFGE-GIKVGYLIGGTSIKQQEKLLSG   78 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhcc-cCCCEEEEcCcHHHHHHHHHHHHHHhhC-CcEEEEEecCcchhHHHHHhcC
Confidence            4789999999999999988887776653 3458999999999999999999887665 6777777777666555555566


Q ss_pred             CCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEeec
Q 022724          151 GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATL  216 (293)
Q Consensus       151 ~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~  216 (293)
                      +.+|+++|++.+..............+++|+||+|.+....................+++++|||+
T Consensus        79 ~~~i~i~t~~~~~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~~~~~~~~~~~~i~~saTp  144 (144)
T cd00046          79 KTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQGFGLLGLKILLKLPKDRQVLLLSATP  144 (144)
T ss_pred             CCCEEEECcHHHHHHHHcCCcchhcCCEEEEeCHHHHhhcchHHHHHHHHhhCCccceEEEEeccC
Confidence            789999999999987777655667889999999999976554443223344455788999999995

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

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.82  E-value=7e-19  Score=164.00  Aligned_cols=221  Identities=17%  Similarity=0.135  Sum_probs=139.7

Q ss_pred             CCcHHHHHHHHhhhc-C--CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCce
Q 022724           55 KPSAIQQRAVMPIIK-G--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ  131 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~-~--~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  131 (293)
                      .++|+|.+++..+.. |  ++.+++.|||+|||+..+..+.. +     +.++|||||+..|+.|+.+.+.++.......
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            589999999999874 4  47899999999999988765543 2     2369999999999999999999886444445


Q ss_pred             EEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc--------CCCCCCCccEEEecchhhhhccccHHHHHHHHhhC
Q 022724          132 AHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR--------KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL  203 (293)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~--------~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l  203 (293)
                      +..+.|+....     ......|+|+|++.+.....+        ..+.-..+++||+||+|++....    +..++..+
T Consensus       329 I~~~tg~~k~~-----~~~~~~VvVtTYq~l~~~~~r~~~~~~~l~~l~~~~~gLII~DEvH~lpA~~----fr~il~~l  399 (732)
T TIGR00603       329 ICRFTSDAKER-----FHGEAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPAAM----FRRVLTIV  399 (732)
T ss_pred             EEEEecCcccc-----cccCCcEEEEEHHHhhcccccchhhhHHHHHhccccCCEEEEEccccccHHH----HHHHHHhc
Confidence            55555543221     112358999999877543221        12233568899999999985433    44445544


Q ss_pred             CCCccEEEEEeecChh--HHHHHHhcCCCCEEEEecCCcc----cCCCceEEEEEec----------------------C
Q 022724          204 PPDLQVVLISATLPHE--ILEMTTKFMTDPVKILVKRDEL----TLEGIKQFFVAVE----------------------R  255 (293)
Q Consensus       204 ~~~~q~v~~SAt~~~~--~~~~~~~~~~~~~~~~~~~~~~----~~~~i~~~~~~~~----------------------~  255 (293)
                      . ....+++|||+...  ....+..++ .|..+..+..+.    -...+.-..+.|+                      .
T Consensus       400 ~-a~~RLGLTATP~ReD~~~~~L~~Li-GP~vye~~~~eLi~~G~LA~~~~~ev~v~~t~~~~~~yl~~~~~~k~~l~~~  477 (732)
T TIGR00603       400 Q-AHCKLGLTATLVREDDKITDLNFLI-GPKLYEANWMELQKKGFIANVQCAEVWCPMTPEFYREYLRENSRKRMLLYVM  477 (732)
T ss_pred             C-cCcEEEEeecCcccCCchhhhhhhc-CCeeeecCHHHHHhCCccccceEEEEEecCCHHHHHHHHHhcchhhhHHhhh
Confidence            3 45689999998532  111222222 233332221110    0011111111111                      1


Q ss_pred             cccHHHHHHHHHhhC--CCCcEEEEcccchhHHHHHhhC
Q 022724          256 EEWKFDTLCDLYDTL--TITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       256 ~~~k~~~l~~l~~~~--~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ...|...+..+++.+  .+.++||||++...+..++..|
T Consensus       478 np~K~~~~~~Li~~he~~g~kiLVF~~~~~~l~~~a~~L  516 (732)
T TIGR00603       478 NPNKFRACQFLIRFHEQRGDKIIVFSDNVFALKEYAIKL  516 (732)
T ss_pred             ChHHHHHHHHHHHHHhhcCCeEEEEeCCHHHHHHHHHHc
Confidence            123566666677654  6679999999999999998765

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).

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

Probab=99.81  E-value=3.7e-19  Score=160.88  Aligned_cols=168  Identities=18%  Similarity=0.259  Sum_probs=137.8

Q ss_pred             CCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q 022724           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (293)
                      .+.|+|+.++..+-++.+++|.|.|++|||.++..++...+..   .-|+||-.|-++|-+|-++.+..=++.    |..
T Consensus       129 ~LDpFQ~~aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~---kQRVIYTSPIKALSNQKYREl~~EF~D----VGL  201 (1041)
T KOG0948|consen  129 TLDPFQSTAIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLRE---KQRVIYTSPIKALSNQKYRELLEEFKD----VGL  201 (1041)
T ss_pred             ccCchHhhhhhhhcCCceEEEEeecCCCcchHHHHHHHHHHHh---cCeEEeeChhhhhcchhHHHHHHHhcc----cce
Confidence            4789999999999999999999999999999988888777765   358999999999999999988754444    344


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEe
Q 022724          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (293)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SA  214 (293)
                      .+|+....       .....+|.|-+.|-.++.++.--.+.+.++|+||+|.|-|...+-.++.-+-.++++.+.+++||
T Consensus       202 MTGDVTIn-------P~ASCLVMTTEILRsMLYRGSEvmrEVaWVIFDEIHYMRDkERGVVWEETIIllP~~vr~VFLSA  274 (1041)
T KOG0948|consen  202 MTGDVTIN-------PDASCLVMTTEILRSMLYRGSEVMREVAWVIFDEIHYMRDKERGVVWEETIILLPDNVRFVFLSA  274 (1041)
T ss_pred             eecceeeC-------CCCceeeeHHHHHHHHHhccchHhheeeeEEeeeehhccccccceeeeeeEEeccccceEEEEec
Confidence            55555433       34578999999999999999888999999999999999888777778888888999999999999


Q ss_pred             ecChhHH--HHHHhcCCCCEEEEe
Q 022724          215 TLPHEIL--EMTTKFMTDPVKILV  236 (293)
Q Consensus       215 t~~~~~~--~~~~~~~~~~~~~~~  236 (293)
                      |+|++.+  +++...-..|.++..
T Consensus       275 TiPNA~qFAeWI~~ihkQPcHVVY  298 (1041)
T KOG0948|consen  275 TIPNARQFAEWICHIHKQPCHVVY  298 (1041)
T ss_pred             cCCCHHHHHHHHHHHhcCCceEEe
Confidence            9999743  244444456666544

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.80  E-value=2.8e-18  Score=161.49  Aligned_cols=127  Identities=20%  Similarity=0.281  Sum_probs=104.9

Q ss_pred             CCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q 022724           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (293)
                      .|++.|--.--.+..|  -+..++||+|||++|.+|++.....   |..+.|++|+++||.|.++.+..+...+|+++..
T Consensus        82 ~~ydvQliGg~~Lh~G--~Iaem~TGeGKTL~a~Lpa~~~al~---G~~V~VvTpn~yLA~qd~e~m~~l~~~lGLtv~~  156 (896)
T PRK13104         82 RHFDVQLIGGMVLHEG--NIAEMRTGEGKTLVATLPAYLNAIS---GRGVHIVTVNDYLAKRDSQWMKPIYEFLGLTVGV  156 (896)
T ss_pred             CcchHHHhhhhhhccC--ccccccCCCCchHHHHHHHHHHHhc---CCCEEEEcCCHHHHHHHHHHHHHHhcccCceEEE
Confidence            3777776644444444  4889999999999999999977654   3468999999999999999999999999999999


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcC-CCCC-----CCccEEEecchhhhh
Q 022724          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRK-TLRT-----RAIKLLVLDESDEML  188 (293)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l-~~~l~~~-~~~~-----~~l~~iViDE~h~~~  188 (293)
                      +.|+.+.......+  .++|+++||++| .++++.+ .+++     +.+.++||||+|.++
T Consensus       157 i~gg~~~~~r~~~y--~~dIvygT~grlgfDyLrd~~~~~~~~~v~r~l~~~IvDEaDsiL  215 (896)
T PRK13104        157 IYPDMSHKEKQEAY--KADIVYGTNNEYGFDYLRDNMAFSLTDKVQRELNFAIVDEVDSIL  215 (896)
T ss_pred             EeCCCCHHHHHHHh--CCCEEEECChhhhHHHHhcCCccchHhhhccccceEEeccHhhhh
Confidence            99998776654444  579999999999 8888876 3444     689999999999985

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

Probab=99.79  E-value=1.9e-18  Score=156.01  Aligned_cols=147  Identities=18%  Similarity=0.176  Sum_probs=101.8

Q ss_pred             CCCcHHHHHHHHhhhc----CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCC
Q 022724           54 EKPSAIQQRAVMPIIK----GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (293)
Q Consensus        54 ~~~~~~Q~~~~~~i~~----~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (293)
                      ..++++|++++..+.+    ++..+++.|||+|||..++..+...      +.+++||||+++|+.|+.+.+.+..... 
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            3599999999999988    8899999999999998877665443      2249999999999999987666544322 


Q ss_pred             ceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccE
Q 022724          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQV  209 (293)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~  209 (293)
                      ..+..+.++.....      . ..|.|+|.+.+........+...++++||+||+|++....+......+...    ..+
T Consensus       108 ~~~g~~~~~~~~~~------~-~~i~vat~qtl~~~~~l~~~~~~~~~liI~DE~Hh~~a~~~~~~~~~~~~~----~~~  176 (442)
T COG1061         108 DEIGIYGGGEKELE------P-AKVTVATVQTLARRQLLDEFLGNEFGLIIFDEVHHLPAPSYRRILELLSAA----YPR  176 (442)
T ss_pred             cccceecCceeccC------C-CcEEEEEhHHHhhhhhhhhhcccccCEEEEEccccCCcHHHHHHHHhhhcc----cce
Confidence            12223333322111      0 369999998887742112333457899999999999766544433333222    229


Q ss_pred             EEEEeecCh
Q 022724          210 VLISATLPH  218 (293)
Q Consensus       210 v~~SAt~~~  218 (293)
                      +++|||++.
T Consensus       177 LGLTATp~R  185 (442)
T COG1061         177 LGLTATPER  185 (442)
T ss_pred             eeeccCcee
Confidence            999999753

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.79  E-value=7.6e-18  Score=158.29  Aligned_cols=129  Identities=20%  Similarity=0.329  Sum_probs=107.3

Q ss_pred             CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHH-hhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCC
Q 022724           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVC-QTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (293)
Q Consensus        51 ~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~-~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (293)
                      .|. .|++.|--.--.+.+|+  +..+.||+|||+++.+|++ ..+ .   |..+-|++|+..||.|-.+.+..+...+|
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 LGM-RHFDVQLIGGMVLHEGK--IAEMKTGEGKTLVATLPAYLNAL-T---GKGVHVVTVNDYLAKRDAEWMGPLYEFLG  150 (830)
T ss_pred             hCC-CCCccHHHhhHHhcCCc--hhhhhcCCCcHHHHHHHHHHHHH-c---CCCEEEEecCHHHHHHHHHHHHHHHhhcC
Confidence            454 48888888776666665  8999999999999999996 554 3   23467999999999999999999999999


Q ss_pred             ceEEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcCC------CCCCCccEEEecchhhhh
Q 022724          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRKT------LRTRAIKLLVLDESDEML  188 (293)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l-~~~l~~~~------~~~~~l~~iViDE~h~~~  188 (293)
                      +++..+.++.+..++...+  .++|+++||..+ .++++.+.      ...+.+.++||||+|.++
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  379999999999 88887754      246789999999999985

>TIGR00595 priA primosomal protein N'

Probab=99.78  E-value=2e-17  Score=151.30  Aligned_cols=136  Identities=21%  Similarity=0.191  Sum_probs=97.5

Q ss_pred             EEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----h
Q 022724           74 IAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----E  149 (293)
Q Consensus        74 li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~  149 (293)
                      ++.||||+|||.+|+..+.+.+..   +.+++|++|+++|+.|+.+.+++..   +.++..++++.+..+..+.+    .
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   5589999999999999999888643   45778888887665543333    2


Q ss_pred             cCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccc-----c-HHHHHHHHhhCCCCccEEEEEeecChhHHHH
Q 022724          150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG-----F-KDQIYDVYRYLPPDLQVVLISATLPHEILEM  223 (293)
Q Consensus       150 ~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~-----~-~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~  223 (293)
                      ...+|+|||+..+.       ..+.++++|||||.|...-++     | ...+...... ..+.++|++|||++.+....
T Consensus        75 g~~~IVVGTrsalf-------~p~~~l~lIIVDEeh~~sykq~~~p~y~ar~~a~~ra~-~~~~~vil~SATPsles~~~  146 (505)
T TIGR00595        75 GEILVVIGTRSALF-------LPFKNLGLIIVDEEHDSSYKQEEGPRYHARDVAVYRAK-KFNCPVVLGSATPSLESYHN  146 (505)
T ss_pred             CCCCEEECChHHHc-------CcccCCCEEEEECCCccccccccCCCCcHHHHHHHHHH-hcCCCEEEEeCCCCHHHHHH
Confidence            45789999997653       347889999999999865221     1 1223333333 35789999999976544333

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).

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

Probab=99.76  E-value=1.1e-16  Score=145.30  Aligned_cols=231  Identities=18%  Similarity=0.212  Sum_probs=162.0

Q ss_pred             CCCHHHHHHH-HHCCCCCCcHHHHHHHHhhhcC------CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCH
Q 022724           39 GIKDDLLRGI-YQYGFEKPSAIQQRAVMPIIKG------RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (293)
Q Consensus        39 ~l~~~i~~~l-~~~~~~~~~~~Q~~~~~~i~~~------~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~  111 (293)
                      +...++.+.+ ..+.|. +|..|++++..|..+      .+-+++|.-|||||.+++++++..+..   |.++..++||.
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            4455555554 556666 999999999999854      478999999999999999999988877   67999999999


Q ss_pred             HHHHHHHHHHHHhhccCCceEEEEECCcchHHHHH---HHhc-CCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhh
Q 022724          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIR---KLEH-GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (293)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~  187 (293)
                      -||+|-++.+.++....|+++..+.|.....+...   .+.+ ..+|+|||-     .|-+....++++.++|+||-|++
T Consensus       322 ILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTH-----ALiQd~V~F~~LgLVIiDEQHRF  396 (677)
T COG1200         322 ILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTH-----ALIQDKVEFHNLGLVIIDEQHRF  396 (677)
T ss_pred             HHHHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcc-----hhhhcceeecceeEEEEeccccc
Confidence            99999999999999999999999999876554433   3334 489999995     44455677999999999999997


Q ss_pred             hccccHHHHHHHHhhCCC-CccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHH
Q 022724          188 LSRGFKDQIYDVYRYLPP-DLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDL  266 (293)
Q Consensus       188 ~~~~~~~~~~~i~~~l~~-~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l  266 (293)
                      .-.     =+..+..-.. .+.++.||||+-|..-.+.  .+.+-..-.++....-+..|.-..+..+..+.-++.+..-
T Consensus       397 GV~-----QR~~L~~KG~~~Ph~LvMTATPIPRTLAlt--~fgDldvS~IdElP~GRkpI~T~~i~~~~~~~v~e~i~~e  469 (677)
T COG1200         397 GVH-----QRLALREKGEQNPHVLVMTATPIPRTLALT--AFGDLDVSIIDELPPGRKPITTVVIPHERRPEVYERIREE  469 (677)
T ss_pred             cHH-----HHHHHHHhCCCCCcEEEEeCCCchHHHHHH--HhccccchhhccCCCCCCceEEEEeccccHHHHHHHHHHH
Confidence            422     2223333344 5789999999866544433  3333222222222222233555555443333223333333


Q ss_pred             HhhCCCCcEEEEcccchhHHH
Q 022724          267 YDTLTITQAVIFCNTKRKVLL  287 (293)
Q Consensus       267 ~~~~~~~~~iIF~~s~~~a~~  287 (293)
                      +.  .+.++.|.|+-+++.+.
T Consensus       470 i~--~GrQaY~VcPLIeESE~  488 (677)
T COG1200         470 IA--KGRQAYVVCPLIEESEK  488 (677)
T ss_pred             HH--cCCEEEEEecccccccc
Confidence            33  56799999999887763

>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=99.75  E-value=1.8e-17  Score=132.67  Aligned_cols=152  Identities=19%  Similarity=0.171  Sum_probs=101.1

Q ss_pred             CCcHHHHHHHHhhhc-------CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcc
Q 022724           55 KPSAIQQRAVMPIIK-------GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDF  127 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~-------~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (293)
                      .++++|.+++..+.+       ++++++.+|||+|||.+++..+.....      ++++++|+..|+.|+.+.+..+...
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            489999999999873       589999999999999888754444433      8999999999999999999665433


Q ss_pred             CCceE-----------EEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCC-----------CCCCCccEEEecchh
Q 022724          128 INIQA-----------HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT-----------LRTRAIKLLVLDESD  185 (293)
Q Consensus       128 ~~~~~-----------~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~-----------~~~~~l~~iViDE~h  185 (293)
                      .....           ....................+++++|.+.+........           ......++||+||+|
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~vI~DEaH  156 (184)
T PF04851_consen   77 KYNFFEKSIKPAYDSKEFISIQDDISDKSESDNNDKDIILTTYQSLQSDIKEEKKIDESARRSYKLLKNKFDLVIIDEAH  156 (184)
T ss_dssp             SEEEEE--GGGCCE-SEEETTTTEEEHHHHHCBSS-SEEEEEHHHHHHHHHH---------GCHHGGGGSESEEEEETGG
T ss_pred             hhhhcccccccccccccccccccccccccccccccccchhhHHHHHHhhcccccccccchhhhhhhccccCCEEEEehhh
Confidence            21100           00111111112222234566899999999988765421           123467899999999


Q ss_pred             hhhccccHHHHHHHHhhCCCCccEEEEEeecC
Q 022724          186 EMLSRGFKDQIYDVYRYLPPDLQVVLISATLP  217 (293)
Q Consensus       186 ~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~  217 (293)
                      ++....-   ...+..  .+...+++||||+.
T Consensus       157 ~~~~~~~---~~~i~~--~~~~~~l~lTATp~  183 (184)
T PF04851_consen  157 HYPSDSS---YREIIE--FKAAFILGLTATPF  183 (184)
T ss_dssp             CTHHHHH---HHHHHH--SSCCEEEEEESS-S
T ss_pred             hcCCHHH---HHHHHc--CCCCeEEEEEeCcc
Confidence            9865431   333333  45778999999975

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 ....

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

Probab=99.74  E-value=1.3e-17  Score=154.87  Aligned_cols=174  Identities=14%  Similarity=0.167  Sum_probs=138.7

Q ss_pred             CCHHHHH-HHHHCCCCCCcHHHHHHHH--hhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHH
Q 022724           40 IKDDLLR-GIYQYGFEKPSAIQQRAVM--PIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQ  116 (293)
Q Consensus        40 l~~~i~~-~l~~~~~~~~~~~Q~~~~~--~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q  116 (293)
                      +++.+.+ ..+..|....+.||.+++.  .++.++|++...||+.|||+++.+-++..+...  +..++++.|....+.+
T Consensus       207 ~~~k~~~~~~~~kgi~~~fewq~ecls~~~~~e~~nliys~Pts~gktlvaeilml~~~l~~--rr~~llilp~vsiv~E  284 (1008)
T KOG0950|consen  207 LPTKVSHLYAKDKGILKLFEWQAECLSLPRLLERKNLIYSLPTSAGKTLVAEILMLREVLCR--RRNVLLILPYVSIVQE  284 (1008)
T ss_pred             CchHHHHHHHHhhhHHHHHHHHHHHhcchhhhcccceEEeCCCccchHHHHHHHHHHHHHHH--hhceeEecceeehhHH
Confidence            3444433 3456688899999999884  577899999999999999999998888876654  3368999999999999


Q ss_pred             HHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc--CCCCCCCccEEEecchhhhhccccHH
Q 022724          117 TEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR--KTLRTRAIKLLVLDESDEMLSRGFKD  194 (293)
Q Consensus       117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~--~~~~~~~l~~iViDE~h~~~~~~~~~  194 (293)
                      -...+..+....|+.+-.++|..+.....    +.-++.|+|.++...++..  ...++..+++|||||.|++.+.+.+.
T Consensus       285 k~~~l~~~~~~~G~~ve~y~g~~~p~~~~----k~~sv~i~tiEkanslin~lie~g~~~~~g~vvVdElhmi~d~~rg~  360 (1008)
T KOG0950|consen  285 KISALSPFSIDLGFPVEEYAGRFPPEKRR----KRESVAIATIEKANSLINSLIEQGRLDFLGMVVVDELHMIGDKGRGA  360 (1008)
T ss_pred             HHhhhhhhccccCCcchhhcccCCCCCcc----cceeeeeeehHhhHhHHHHHHhcCCccccCcEEEeeeeeeeccccch
Confidence            99999999999999998888766544332    2348999999998876654  33456779999999999999999888


Q ss_pred             HHHHHHhhC-----CCCccEEEEEeecChh
Q 022724          195 QIYDVYRYL-----PPDLQVVLISATLPHE  219 (293)
Q Consensus       195 ~~~~i~~~l-----~~~~q~v~~SAt~~~~  219 (293)
                      .++.++.++     ....|+|+||||+++.
T Consensus       361 ~lE~~l~k~~y~~~~~~~~iIGMSATi~N~  390 (1008)
T KOG0950|consen  361 ILELLLAKILYENLETSVQIIGMSATIPNN  390 (1008)
T ss_pred             HHHHHHHHHHHhccccceeEeeeecccCCh
Confidence            888776664     2347899999999863

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.74  E-value=4.8e-16  Score=152.61  Aligned_cols=226  Identities=17%  Similarity=0.199  Sum_probs=139.0

Q ss_pred             CCCCCCcHHHH---HHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHH-hhc
Q 022724           51 YGFEKPSAIQQ---RAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA-IGD  126 (293)
Q Consensus        51 ~~~~~~~~~Q~---~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~-~~~  126 (293)
                      ..|...-|+..   +++..+.+++.++|+|+||||||... ..++...... ...++++.-|.+--+..+..++.+ ++.
T Consensus        60 ~~~~~~LPi~~~~~~Il~~l~~~~vvii~g~TGSGKTTql-Pq~lle~~~~-~~~~I~~tQPRRlAA~svA~RvA~elg~  137 (1283)
T TIGR01967        60 IRYPDNLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQL-PKICLELGRG-SHGLIGHTQPRRLAARTVAQRIAEELGT  137 (1283)
T ss_pred             ccCCCCCCHHHHHHHHHHHHHhCceEEEeCCCCCCcHHHH-HHHHHHcCCC-CCceEecCCccHHHHHHHHHHHHHHhCC
Confidence            34554445544   56666777788999999999999743 2222222211 223566677999888888876654 333


Q ss_pred             cCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhh-hhccccHH-HHHHHHhhCC
Q 022724          127 FINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDE-MLSRGFKD-QIYDVYRYLP  204 (293)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~-~~~~~~~~-~~~~i~~~l~  204 (293)
                      ..|-.+.......+   .   ......|.++|++.|++.+.... .+.++++|||||+|. .++.++.- .+..++... 
T Consensus       138 ~lG~~VGY~vR~~~---~---~s~~T~I~~~TdGiLLr~l~~d~-~L~~~~~IIIDEaHERsL~~D~LL~lLk~il~~r-  209 (1283)
T TIGR01967       138 PLGEKVGYKVRFHD---Q---VSSNTLVKLMTDGILLAETQQDR-FLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPRR-  209 (1283)
T ss_pred             CcceEEeeEEcCCc---c---cCCCceeeeccccHHHHHhhhCc-ccccCcEEEEcCcchhhccchhHHHHHHHHHhhC-
Confidence            33433333221111   1   12456899999999999876643 489999999999994 66655543 345554443 


Q ss_pred             CCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCc-----ccHHHHHHHHHh---hCCCCcEE
Q 022724          205 PDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVERE-----EWKFDTLCDLYD---TLTITQAV  276 (293)
Q Consensus       205 ~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~-----~~k~~~l~~l~~---~~~~~~~i  276 (293)
                      +..|+|+||||+..  ..+.+.+...|. +.+...   ...+..+|......     .++...+...+.   ....+.+|
T Consensus       210 pdLKlIlmSATld~--~~fa~~F~~apv-I~V~Gr---~~PVev~Y~~~~~~~~~~~~~~~~~i~~~I~~l~~~~~GdIL  283 (1283)
T TIGR01967       210 PDLKIIITSATIDP--ERFSRHFNNAPI-IEVSGR---TYPVEVRYRPLVEEQEDDDLDQLEAILDAVDELFAEGPGDIL  283 (1283)
T ss_pred             CCCeEEEEeCCcCH--HHHHHHhcCCCE-EEECCC---cccceeEEecccccccchhhhHHHHHHHHHHHHHhhCCCCEE
Confidence            57899999999974  445555444443 444322   12344455443221     123333333332   22457999


Q ss_pred             EEcccchhHHHHHhhC
Q 022724          277 IFCNTKRKVLLLVLQF  292 (293)
Q Consensus       277 IF~~s~~~a~~l~~~L  292 (293)
                      |||++.++++.+++.|
T Consensus       284 VFLpg~~EI~~l~~~L  299 (1283)
T TIGR01967       284 IFLPGEREIRDAAEIL  299 (1283)
T ss_pred             EeCCCHHHHHHHHHHH
Confidence            9999999999998765

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.

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

Probab=99.73  E-value=3.8e-17  Score=160.38  Aligned_cols=159  Identities=16%  Similarity=0.144  Sum_probs=106.2

Q ss_pred             CCcHHHHHHHHhhh----c-CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCC
Q 022724           55 KPSAIQQRAVMPII----K-GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~----~-~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (293)
                      .++++|.+|+..+.    + .+..+++++||+|||.+++ .++..+.......++|||+|+.+|+.|..+.++.+.....
T Consensus       413 ~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai-~li~~L~~~~~~~rVLfLvDR~~L~~Qa~~~F~~~~~~~~  491 (1123)
T PRK11448        413 GLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAI-ALMYRLLKAKRFRRILFLVDRSALGEQAEDAFKDTKIEGD  491 (1123)
T ss_pred             CCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHHH-HHHHHHHhcCccCeEEEEecHHHHHHHHHHHHHhcccccc
Confidence            48999999998775    2 3689999999999998744 3445554444456999999999999999999887642222


Q ss_pred             ceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc-----CCCCCCCccEEEecchhhhhc------c--------
Q 022724          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-----KTLRTRAIKLLVLDESDEMLS------R--------  190 (293)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~-----~~~~~~~l~~iViDE~h~~~~------~--------  190 (293)
                      ......++......  ........|+|+|.+++...+..     ..+...++++|||||||+-..      .        
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            11111111110010  01123468999999999875432     124567889999999998531      0        


Q ss_pred             -ccHHHHHHHHhhCCCCccEEEEEeecCh
Q 022724          191 -GFKDQIYDVYRYLPPDLQVVLISATLPH  218 (293)
Q Consensus       191 -~~~~~~~~i~~~l~~~~q~v~~SAt~~~  218 (293)
                       .+...+..++.+.  +...|++|||+-.
T Consensus       570 ~~~~~~yr~iL~yF--dA~~IGLTATP~r  596 (1123)
T PRK11448        570 LDYVSKYRRVLDYF--DAVKIGLTATPAL  596 (1123)
T ss_pred             hhHHHHHHHHHhhc--CccEEEEecCCcc
Confidence             1134566666655  3578999999854

>COG1197 Mfd Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]

Probab=99.72  E-value=7e-16  Score=147.38  Aligned_cols=235  Identities=19%  Similarity=0.179  Sum_probs=174.3

Q ss_pred             CCCHHHHHHHHH-CCCCCCcHHHHHHHHhhhcC------CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCH
Q 022724           39 GIKDDLLRGIYQ-YGFEKPSAIQQRAVMPIIKG------RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (293)
Q Consensus        39 ~l~~~i~~~l~~-~~~~~~~~~Q~~~~~~i~~~------~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~  111 (293)
                      +.+.+.++.+.+ +.|. -|+-|..|+..+.+.      +|-+|||--|-|||.+++-+++..+..   |.++.+|+||-
T Consensus       578 ~~d~~~q~~F~~~FPye-ET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~~---GKQVAvLVPTT  653 (1139)
T COG1197         578 PPDTEWQEEFEASFPYE-ETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVMD---GKQVAVLVPTT  653 (1139)
T ss_pred             CCChHHHHHHHhcCCCc-CCHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHHHHHHHHHhcC---CCeEEEEcccH
Confidence            345555666554 3444 799999999998843      589999999999999999999888776   57999999999


Q ss_pred             HHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHh----cCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhh
Q 022724          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (293)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~  187 (293)
                      -||+|-++.++.-+.++.+++..++.-.+..++...+.    ...||+|||-     -|-+..+.+++++++||||-|++
T Consensus       654 lLA~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTH-----rLL~kdv~FkdLGLlIIDEEqRF  728 (1139)
T COG1197         654 LLAQQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTH-----RLLSKDVKFKDLGLLIIDEEQRF  728 (1139)
T ss_pred             HhHHHHHHHHHHHhcCCCeeEEEecccCCHHHHHHHHHHHhcCCccEEEech-----HhhCCCcEEecCCeEEEechhhc
Confidence            99999999999999999999999888777766654442    4679999995     33345678999999999999997


Q ss_pred             hccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHH
Q 022724          188 LSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLY  267 (293)
Q Consensus       188 ~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~  267 (293)
                      . ....+.    ++.+..+.-++-||||+-|..-.+.-..+++...+..++.+.  ..++-++..-++.--+...+.++ 
T Consensus       729 G-Vk~KEk----LK~Lr~~VDvLTLSATPIPRTL~Msm~GiRdlSvI~TPP~~R--~pV~T~V~~~d~~~ireAI~REl-  800 (1139)
T COG1197         729 G-VKHKEK----LKELRANVDVLTLSATPIPRTLNMSLSGIRDLSVIATPPEDR--LPVKTFVSEYDDLLIREAILREL-  800 (1139)
T ss_pred             C-ccHHHH----HHHHhccCcEEEeeCCCCcchHHHHHhcchhhhhccCCCCCC--cceEEEEecCChHHHHHHHHHHH-
Confidence            4 223333    444456778999999997777777777777777776665443  23444444333222222223332 


Q ss_pred             hhCCCCcEEEEcccchhHHHHHhhC
Q 022724          268 DTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       268 ~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                        .+++++...+|.++..+.+++.|
T Consensus       801 --~RgGQvfYv~NrV~~Ie~~~~~L  823 (1139)
T COG1197         801 --LRGGQVFYVHNRVESIEKKAERL  823 (1139)
T ss_pred             --hcCCEEEEEecchhhHHHHHHHH
Confidence              34689999999999988888765

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

Probab=99.71  E-value=4.3e-16  Score=145.75  Aligned_cols=232  Identities=17%  Similarity=0.232  Sum_probs=151.7

Q ss_pred             HHHHHC-CCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 022724           46 RGIYQY-GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (293)
Q Consensus        46 ~~l~~~-~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (293)
                      +.+.+. |+ .|+..|+-....+.+|+++-+.||||.|||.-.++..+..   ..+|.+++|++||..|+.|+.+.++++
T Consensus        73 ~fF~k~~G~-~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTfg~~~sl~~---a~kgkr~yii~PT~~Lv~Q~~~kl~~~  148 (1187)
T COG1110          73 EFFKKATGF-RPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFGLLMSLYL---AKKGKRVYIIVPTTTLVRQVYERLKKF  148 (1187)
T ss_pred             HHHHHhhCC-CchHHHHHHHHHHHcCCceEEEcCCCCchhHHHHHHHHHH---HhcCCeEEEEecCHHHHHHHHHHHHHH
Confidence            333433 55 7999999999999999999999999999995444333332   223569999999999999999999998


Q ss_pred             hccCC-ceEEE-EECCcchHH---HHHHHh-cCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccc-------
Q 022724          125 GDFIN-IQAHA-CVGGKSVGE---DIRKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG-------  191 (293)
Q Consensus       125 ~~~~~-~~~~~-~~~~~~~~~---~~~~~~-~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~-------  191 (293)
                      ....+ ..+.. +|+..+..+   ....+. .+.||+|+|.+-|..-...  +.--+++++.+|++|.++..+       
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            86665 44433 555544333   233343 4689999998655543322  112467999999999987543       


Q ss_pred             ----cHHH-------HHHHHhhC------------------------CCCccEEEEEeecChhHH--HHHHhcCCCCEEE
Q 022724          192 ----FKDQ-------IYDVYRYL------------------------PPDLQVVLISATLPHEIL--EMTTKFMTDPVKI  234 (293)
Q Consensus       192 ----~~~~-------~~~i~~~l------------------------~~~~q~v~~SAt~~~~~~--~~~~~~~~~~~~~  234 (293)
                          |...       +..+...+                        .+..++|+.|||..+.-.  .+.+.++    .+
T Consensus       227 ~LlGf~eE~i~~a~~~~~lr~~~~~~~~~~~~~e~~~~~e~~~~~~r~k~g~LvvsSATg~~rg~R~~LfReLl----gF  302 (1187)
T COG1110         227 RLLGFSEEVIESAYELIKLRRKLYGEKRAERVREELREVEREREKKRRKLGILVVSSATGKPRGSRLKLFRELL----GF  302 (1187)
T ss_pred             HHcCCCHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhccCCceEEEeeccCCCCCchHHHHHHHh----CC
Confidence                1110       11111111                        134689999999855421  2333332    23


Q ss_pred             EecCCcccCCCceEEEEEecCcccHHHHHHHHHhhCCCCcEEEEccc---chhHHHHHhhC
Q 022724          235 LVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNT---KRKVLLLVLQF  292 (293)
Q Consensus       235 ~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~~iIF~~s---~~~a~~l~~~L  292 (293)
                      .+........+|...|...    .-...+..+++... .-.|||++.   ++.+++++++|
T Consensus       303 evG~~~~~LRNIvD~y~~~----~~~e~~~elvk~lG-~GgLIfV~~d~G~e~aeel~e~L  358 (1187)
T COG1110         303 EVGSGGEGLRNIVDIYVES----ESLEKVVELVKKLG-DGGLIFVPIDYGREKAEELAEYL  358 (1187)
T ss_pred             ccCccchhhhheeeeeccC----ccHHHHHHHHHHhC-CCeEEEEEcHHhHHHHHHHHHHH
Confidence            4444445556677776655    24445556666654 478999999   99999998875

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

Probab=99.70  E-value=3e-15  Score=125.02  Aligned_cols=216  Identities=17%  Similarity=0.125  Sum_probs=146.4

Q ss_pred             CCcHHHHHHHHhhh----cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q 022724           55 KPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~----~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (293)
                      ++++.|+.+-+.+.    +.+++++.|-||+|||.+..-.+-..+..   |.++.+.+|....+.+++.+++.-..+  .
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---GGRVCIASPRVDVCLELYPRLKQAFSN--C  171 (441)
T ss_pred             ccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhhhHHHHHHHHhc---CCeEEEecCcccchHHHHHHHHHhhcc--C
Confidence            68999998777654    56899999999999997755444444433   678999999999999999999876543  4


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEE
Q 022724          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVV  210 (293)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v  210 (293)
                      .+..++|+.+...       ..+++|+|-.+++++       -+.++++||||+|.+.-..-...-..+.+...+..-.|
T Consensus       172 ~I~~Lyg~S~~~f-------r~plvVaTtHQLlrF-------k~aFD~liIDEVDAFP~~~d~~L~~Av~~ark~~g~~I  237 (441)
T COG4098         172 DIDLLYGDSDSYF-------RAPLVVATTHQLLRF-------KQAFDLLIIDEVDAFPFSDDQSLQYAVKKARKKEGATI  237 (441)
T ss_pred             CeeeEecCCchhc-------cccEEEEehHHHHHH-------HhhccEEEEeccccccccCCHHHHHHHHHhhcccCceE
Confidence            5677787765332       148999999888774       24578999999998742222233334445555677899


Q ss_pred             EEEeecChhHHHHHHhcCCCCEEEEecCCc-ccCCCceEEEEEecCcccHHH------HHHHHHhhC--CCCcEEEEccc
Q 022724          211 LISATLPHEILEMTTKFMTDPVKILVKRDE-LTLEGIKQFFVAVEREEWKFD------TLCDLYDTL--TITQAVIFCNT  281 (293)
Q Consensus       211 ~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~i~~~~~~~~~~~~k~~------~l~~l~~~~--~~~~~iIF~~s  281 (293)
                      ++|||.+...+.-+...  +...+..+... ..+-.+..+ .++..-..++.      .+...+++.  .+.+++||+++
T Consensus       238 ylTATp~k~l~r~~~~g--~~~~~klp~RfH~~pLpvPkf-~w~~~~~k~l~r~kl~~kl~~~lekq~~~~~P~liF~p~  314 (441)
T COG4098         238 YLTATPTKKLERKILKG--NLRILKLPARFHGKPLPVPKF-VWIGNWNKKLQRNKLPLKLKRWLEKQRKTGRPVLIFFPE  314 (441)
T ss_pred             EEecCChHHHHHHhhhC--CeeEeecchhhcCCCCCCCce-EEeccHHHHhhhccCCHHHHHHHHHHHhcCCcEEEEecc
Confidence            99999998877665443  22223333222 222223333 33433332321      355556543  35699999999


Q ss_pred             chhHHHHHhhC
Q 022724          282 KRKVLLLVLQF  292 (293)
Q Consensus       282 ~~~a~~l~~~L  292 (293)
                      ++..+++++.|
T Consensus       315 I~~~eq~a~~l  325 (441)
T COG4098         315 IETMEQVAAAL  325 (441)
T ss_pred             hHHHHHHHHHH
Confidence            99999998876

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.67  E-value=9.6e-16  Score=146.36  Aligned_cols=237  Identities=16%  Similarity=0.146  Sum_probs=144.0

Q ss_pred             CCcHHHHHHHHhhhcC---C-cEEEEcCCCChhHHHHHHHHHhhhcc-CCCceeEEEEcCCHHHHHHHHHHHHHhhccCC
Q 022724           55 KPSAIQQRAVMPIIKG---R-DVIAQAQSGTGKTSMIALTVCQTVDT-SSREVQALILSPTRELATQTEKVILAIGDFIN  129 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~---~-~~li~~~Tg~GKT~~~~~~~~~~l~~-~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (293)
                      .+.+.|..++..+.+.   . .+++.+|||+|||++.+.++...+.. .....+++++.|++.++++++++++.+....+
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            3499999999987743   4 78999999999999999999888776 44567999999999999999999998765554


Q ss_pred             ceEEEEECCcchHHHHHH-----H---------hcCCcEEEeChHHHHHHHh-cCCCC-C--CCccEEEecchhhhhccc
Q 022724          130 IQAHACVGGKSVGEDIRK-----L---------EHGVHVVSGTPGRVCDMIK-RKTLR-T--RAIKLLVLDESDEMLSRG  191 (293)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~-----~---------~~~~~ilV~Tp~~l~~~l~-~~~~~-~--~~l~~iViDE~h~~~~~~  191 (293)
                      ......++.....-....     .         ..-..+.++||........ ...+. +  --.+.+|+||+|.+.+..
T Consensus       275 ~~~~~~h~~~~~~~~~~~~~~~~~~~~~~ds~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~S~vIlDE~h~~~~~~  354 (733)
T COG1203         275 VIGKSLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILIFSVKGFKFEFLALLLTSLVILDEVHLYADET  354 (733)
T ss_pred             cccccccccccchhhhccccccceeEEecccccceeccccccCHhHhhhhhccccchHHHHHHHhhchhhccHHhhcccc
Confidence            433322332211110000     0         0012345555554444211 11111 1  123679999999997764


Q ss_pred             cHHHHHHHHhhCC-CCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCc---ccCCCceEEEE-EecCcccHHHHHHHH
Q 022724          192 FKDQIYDVYRYLP-PDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDE---LTLEGIKQFFV-AVEREEWKFDTLCDL  266 (293)
Q Consensus       192 ~~~~~~~i~~~l~-~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~i~~~~~-~~~~~~~k~~~l~~l  266 (293)
                      ....+..++..+. .+..+|+||||+|+..+..+.........+......   ..-..+.+... ...... ........
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            3444444444433 478999999999999999888877654444333110   00011111100 000010 00111111


Q ss_pred             Hh-hCCCCcEEEEcccchhHHHHHhhC
Q 022724          267 YD-TLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       267 ~~-~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      .. -..+.+++|.|||+..|.+++..|
T Consensus       434 ~~~~~~~~kvlvI~NTV~~Aie~Y~~L  460 (733)
T COG1203         434 SEEVKEGKKVLVIVNTVDRAIELYEKL  460 (733)
T ss_pred             hhhhccCCcEEEEEecHHHHHHHHHHH
Confidence            22 234569999999999999999876

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.64  E-value=6.2e-15  Score=138.83  Aligned_cols=127  Identities=19%  Similarity=0.254  Sum_probs=101.7

Q ss_pred             CCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q 022724           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (293)
                      .|++.|--.--.+.  +.-+..++||.|||+++.+|++......   ..+.|++|+..||.+..+.+..+...+|+++..
T Consensus        82 ~~ydVQliGgl~L~--~G~IaEm~TGEGKTL~a~lp~~l~al~g---~~VhIvT~ndyLA~RD~e~m~~l~~~lGlsv~~  156 (908)
T PRK13107         82 RHFDVQLLGGMVLD--SNRIAEMRTGEGKTLTATLPAYLNALTG---KGVHVITVNDYLARRDAENNRPLFEFLGLTVGI  156 (908)
T ss_pred             CcCchHHhcchHhc--CCccccccCCCCchHHHHHHHHHHHhcC---CCEEEEeCCHHHHHHHHHHHHHHHHhcCCeEEE
Confidence            37777765433333  4458899999999999999998776553   349999999999999999999999999999999


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcC-CCCC-----CCccEEEecchhhhh
Q 022724          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRK-TLRT-----RAIKLLVLDESDEML  188 (293)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l-~~~l~~~-~~~~-----~~l~~iViDE~h~~~  188 (293)
                      ..++.+.......  -.++|+++||+.+ .++|+.+ ..+.     +.+.+.||||+|.++
T Consensus       157 i~~~~~~~~r~~~--Y~~dI~YgT~~e~gfDyLrdnm~~~~~~~vqr~~~~aIvDEvDsiL  215 (908)
T PRK13107        157 NVAGLGQQEKKAA--YNADITYGTNNEFGFDYLRDNMAFSPQERVQRPLHYALIDEVDSIL  215 (908)
T ss_pred             ecCCCCHHHHHhc--CCCCeEEeCCCcccchhhhccCccchhhhhccccceeeecchhhhc
Confidence            9888775433222  2579999999999 8888776 3333     788999999999986

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

Probab=99.62  E-value=3.1e-14  Score=132.95  Aligned_cols=216  Identities=19%  Similarity=0.167  Sum_probs=144.3

Q ss_pred             CCCcHHHHHHHHhhhcC----CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCC
Q 022724           54 EKPSAIQQRAVMPIIKG----RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (293)
Q Consensus        54 ~~~~~~Q~~~~~~i~~~----~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (293)
                      ..+++-|+.+++.+.+.    +..++.|.||||||.+|+-.+-..+..   |.++|+|+|.++|..|+..+++..+   |
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            35788999999998765    679999999999999998877777766   5689999999999999999888754   4


Q ss_pred             ceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhh---ccc---cHHHHHHH
Q 022724          130 IQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML---SRG---FKDQIYDV  199 (293)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~---~~~---~~~~~~~i  199 (293)
                      .++..++++-+..+..+.+    .....|+|||-..+.       ..++++++|||||-|.-.   +++   ...++...
T Consensus       271 ~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSAlF-------~Pf~~LGLIIvDEEHD~sYKq~~~prYhARdvA~~  343 (730)
T COG1198         271 AKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSALF-------LPFKNLGLIIVDEEHDSSYKQEDGPRYHARDVAVL  343 (730)
T ss_pred             CChhhhcccCChHHHHHHHHHHhcCCceEEEEechhhc-------CchhhccEEEEeccccccccCCcCCCcCHHHHHHH
Confidence            6788888887666555444    356789999974333       357899999999999642   111   22333333


Q ss_pred             HhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHH-----HHHHHHHhh--CCC
Q 022724          200 YRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKF-----DTLCDLYDT--LTI  272 (293)
Q Consensus       200 ~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~-----~~l~~l~~~--~~~  272 (293)
                      ... ..++++|+-|||.+  ++.+..-.-+....+..........-....++.+..+..+.     ..+.+.+++  ..+
T Consensus       344 Ra~-~~~~pvvLgSATPS--LES~~~~~~g~y~~~~L~~R~~~a~~p~v~iiDmr~e~~~~~~~lS~~Ll~~i~~~l~~g  420 (730)
T COG1198         344 RAK-KENAPVVLGSATPS--LESYANAESGKYKLLRLTNRAGRARLPRVEIIDMRKEPLETGRSLSPALLEAIRKTLERG  420 (730)
T ss_pred             HHH-HhCCCEEEecCCCC--HHHHHhhhcCceEEEEccccccccCCCcceEEeccccccccCccCCHHHHHHHHHHHhcC
Confidence            333 35899999999965  44444432222333333332221112223333444333222     345555532  356


Q ss_pred             CcEEEEcccchhH
Q 022724          273 TQAVIFCNTKRKV  285 (293)
Q Consensus       273 ~~~iIF~~s~~~a  285 (293)
                      +++|+|.|++.-+
T Consensus       421 eQ~llflnRRGys  433 (730)
T COG1198         421 EQVLLFLNRRGYA  433 (730)
T ss_pred             CeEEEEEccCCcc
Confidence            7999999998654

>COG4096 HsdR Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

Probab=99.60  E-value=2e-14  Score=132.58  Aligned_cols=149  Identities=19%  Similarity=0.211  Sum_probs=106.7

Q ss_pred             CCcHHHHHHHHhhh----cCC-cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCC
Q 022724           55 KPSAIQQRAVMPII----KGR-DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~----~~~-~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (293)
                      .|+.+|..|+..+.    +|+ .+++++.||+|||..+ ++++..|.+.....|+|+|+-+++|+.|.+..+..+..+..
T Consensus       165 ~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTA-iaii~rL~r~~~~KRVLFLaDR~~Lv~QA~~af~~~~P~~~  243 (875)
T COG4096         165 GPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTA-IAIIDRLIKSGWVKRVLFLADRNALVDQAYGAFEDFLPFGT  243 (875)
T ss_pred             cchHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeH-HHHHHHHHhcchhheeeEEechHHHHHHHHHHHHHhCCCcc
Confidence            68999999997654    553 5999999999999764 46778888877778999999999999999998888765432


Q ss_pred             ceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcC-----CCCCCCccEEEecchhhhhccccHHHHHHHHhhCC
Q 022724          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK-----TLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP  204 (293)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~-----~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~  204 (293)
                       .+..+.+.. .       ...+.|.|+|.+.+...+...     .+...++++|||||||+=    .......++.++.
T Consensus       244 -~~n~i~~~~-~-------~~s~~i~lsTyqt~~~~~~~~~~~~~~f~~g~FDlIvIDEaHRg----i~~~~~~I~dYFd  310 (875)
T COG4096         244 -KMNKIEDKK-G-------DTSSEIYLSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHRG----IYSEWSSILDYFD  310 (875)
T ss_pred             -ceeeeeccc-C-------CcceeEEEeehHHHHhhhhccccccccCCCCceeEEEechhhhh----HHhhhHHHHHHHH
Confidence             222222111 1       114689999999998866553     455677999999999963    3333445666653


Q ss_pred             CCccEEEEEeecChh
Q 022724          205 PDLQVVLISATLPHE  219 (293)
Q Consensus       205 ~~~q~v~~SAt~~~~  219 (293)
                      .  -.++++||+.+.
T Consensus       311 A--~~~gLTATP~~~  323 (875)
T COG4096         311 A--ATQGLTATPKET  323 (875)
T ss_pred             H--HHHhhccCcccc
Confidence            2  233448887653

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

Probab=99.58  E-value=6.2e-14  Score=132.70  Aligned_cols=152  Identities=17%  Similarity=0.165  Sum_probs=99.9

Q ss_pred             CCcHHHHHHHHhhh----c------CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 022724           55 KPSAIQQRAVMPII----K------GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~----~------~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (293)
                      .++.+|.+++..+.    +      ++..++..+||||||+..+..+...+ .....+++|||+|+.+|..|+.+.+..+
T Consensus       238 ~~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~~l~-~~~~~~~vl~lvdR~~L~~Q~~~~f~~~  316 (667)
T TIGR00348       238 YQRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKAL-ELLKNPKVFFVVDRRELDYQLMKEFQSL  316 (667)
T ss_pred             ehHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHHHHH-hhcCCCeEEEEECcHHHHHHHHHHHHhh
Confidence            37899999998764    2      25799999999999988766554333 3344579999999999999999999887


Q ss_pred             hccCCceEEEEECCcchHHHHHHHh-cCCcEEEeChHHHHHHHhcC--CCCCCCc-cEEEecchhhhhccccHHHHHHHH
Q 022724          125 GDFINIQAHACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRK--TLRTRAI-KLLVLDESDEMLSRGFKDQIYDVY  200 (293)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ilV~Tp~~l~~~l~~~--~~~~~~l-~~iViDE~h~~~~~~~~~~~~~i~  200 (293)
                      .... .     .+..+.......+. ....|+|+|.+++...+...  .+...+- -+||+||||+.....+...+   .
T Consensus       317 ~~~~-~-----~~~~s~~~L~~~l~~~~~~iivtTiQk~~~~~~~~~~~~~~~~~~~lvIvDEaHrs~~~~~~~~l---~  387 (667)
T TIGR00348       317 QKDC-A-----ERIESIAELKRLLEKDDGGIIITTIQKFDKKLKEEEEKFPVDRKEVVVIFDEAHRSQYGELAKNL---K  387 (667)
T ss_pred             CCCC-C-----cccCCHHHHHHHHhCCCCCEEEEEhHHhhhhHhhhhhccCCCCCCEEEEEEcCccccchHHHHHH---H
Confidence            5321 0     11112222222332 23589999999998644331  1111111 28999999986433333222   2


Q ss_pred             hhCCCCccEEEEEeecC
Q 022724          201 RYLPPDLQVVLISATLP  217 (293)
Q Consensus       201 ~~l~~~~q~v~~SAt~~  217 (293)
                      ..+ ++...+++|||+-
T Consensus       388 ~~~-p~a~~lGfTaTP~  403 (667)
T TIGR00348       388 KAL-KNASFFGFTGTPI  403 (667)
T ss_pred             hhC-CCCcEEEEeCCCc
Confidence            344 4678999999984

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

>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]

Probab=99.57  E-value=3.9e-13  Score=127.54  Aligned_cols=221  Identities=15%  Similarity=0.201  Sum_probs=145.5

Q ss_pred             cHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHH-hhccCCceEEEE
Q 022724           57 SAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA-IGDFINIQAHAC  135 (293)
Q Consensus        57 ~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~-~~~~~~~~~~~~  135 (293)
                      +....+...++.+++-++|+||||||||...-..+++.-.  ..+..+.+.-|.|--|..+.+++.. ++...|-.|.+.
T Consensus        52 ~~~~~~i~~ai~~~~vvii~getGsGKTTqlP~~lle~g~--~~~g~I~~tQPRRlAArsvA~RvAeel~~~~G~~VGY~  129 (845)
T COG1643          52 TAVRDEILKAIEQNQVVIIVGETGSGKTTQLPQFLLEEGL--GIAGKIGCTQPRRLAARSVAERVAEELGEKLGETVGYS  129 (845)
T ss_pred             HHHHHHHHHHHHhCCEEEEeCCCCCChHHHHHHHHHhhhc--ccCCeEEecCchHHHHHHHHHHHHHHhCCCcCceeeEE
Confidence            5556677778888999999999999999776555655544  2234677888999888888887754 555455444443


Q ss_pred             ECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhh-ccc-cHHHHHHHHhhCCCCccEEEEE
Q 022724          136 VGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML-SRG-FKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~-~~~-~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      ....+      ....+..|-+.|.+.|++.+..... ++.+++|||||+|.=. +-. ....+..++...+...++|.||
T Consensus       130 iRfe~------~~s~~Trik~mTdGiLlrei~~D~~-Ls~ys~vIiDEaHERSl~tDilLgllk~~~~~rr~DLKiIimS  202 (845)
T COG1643         130 IRFES------KVSPRTRIKVMTDGILLREIQNDPL-LSGYSVVIIDEAHERSLNTDILLGLLKDLLARRRDDLKLIIMS  202 (845)
T ss_pred             EEeec------cCCCCceeEEeccHHHHHHHhhCcc-cccCCEEEEcchhhhhHHHHHHHHHHHHHHhhcCCCceEEEEe
Confidence            32221      1123457999999999998876544 8999999999999721 111 2234555666677679999999


Q ss_pred             eecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCccc-HHHHHHHHHh---hCCCCcEEEEcccchhHHHHH
Q 022724          214 ATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEW-KFDTLCDLYD---TLTITQAVIFCNTKRKVLLLV  289 (293)
Q Consensus       214 At~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~-k~~~l~~l~~---~~~~~~~iIF~~s~~~a~~l~  289 (293)
                      ||+..+   ....++.+.-.+.+.-   ..+.+..+|......+. -...+...++   ....+.+|||.+-..+.+.++
T Consensus       203 ATld~~---rfs~~f~~apvi~i~G---R~fPVei~Y~~~~~~d~~l~~ai~~~v~~~~~~~~GdILvFLpG~~EI~~~~  276 (845)
T COG1643         203 ATLDAE---RFSAYFGNAPVIEIEG---RTYPVEIRYLPEAEADYILLDAIVAAVDIHLREGSGSILVFLPGQREIERTA  276 (845)
T ss_pred             cccCHH---HHHHHcCCCCEEEecC---CccceEEEecCCCCcchhHHHHHHHHHHHhccCCCCCEEEECCcHHHHHHHH
Confidence            999754   3334444443444432   22345555544443333 3333444443   334679999999999999887


Q ss_pred             hhC
Q 022724          290 LQF  292 (293)
Q Consensus       290 ~~L  292 (293)
                      +.|
T Consensus       277 ~~L  279 (845)
T COG1643         277 EWL  279 (845)
T ss_pred             HHH
Confidence            765

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

Probab=99.54  E-value=2.1e-13  Score=132.90  Aligned_cols=94  Identities=22%  Similarity=0.237  Sum_probs=71.8

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHH----hhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHH
Q 022724           40 IKDDLLRGIYQYGFEKPSAIQQRAVM----PIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELAT  115 (293)
Q Consensus        40 l~~~i~~~l~~~~~~~~~~~Q~~~~~----~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~  115 (293)
                      +++.....+...||+ +++.|.+.++    .+.+++++++.||||+|||++|++|++....   .+.+++|.+||++|..
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            345677777778888 8899998666    4557899999999999999999999988765   2458999999999999


Q ss_pred             HHHH-HHHHhhccCC--ceEEEEEC
Q 022724          116 QTEK-VILAIGDFIN--IQAHACVG  137 (293)
Q Consensus       116 q~~~-~~~~~~~~~~--~~~~~~~~  137 (293)
                      |+.. .+..+.+.++  +++..+.|
T Consensus       307 Ql~~~~~~~l~~~~~~~~~~~~~kG  331 (850)
T TIGR01407       307 QLLEKDIPLLNEILNFKINAALIKG  331 (850)
T ss_pred             HHHHHHHHHHHHHcCCCceEEEEEc
Confidence            9865 4555544433  44444443

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.

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

Probab=99.53  E-value=1.4e-13  Score=131.15  Aligned_cols=224  Identities=16%  Similarity=0.214  Sum_probs=151.3

Q ss_pred             CCCCcHHHHHHHHhhhc-CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHH-HhhccCCc
Q 022724           53 FEKPSAIQQRAVMPIIK-GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL-AIGDFINI  130 (293)
Q Consensus        53 ~~~~~~~Q~~~~~~i~~-~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~-~~~~~~~~  130 (293)
                      |....|+|.++++-+.+ +.++++.+|+|+|||.|+.++++.    .....+++++.|..+.+..++..|. ++.+..|.
T Consensus      1141 f~~~n~iqtqVf~~~y~~nd~v~vga~~gsgkt~~ae~a~l~----~~~~~~~vyi~p~~~i~~~~~~~w~~~f~~~~G~ 1216 (1674)
T KOG0951|consen 1141 FQDFNPIQTQVFTSLYNTNDNVLVGAPNGSGKTACAELALLR----PDTIGRAVYIAPLEEIADEQYRDWEKKFSKLLGL 1216 (1674)
T ss_pred             ccccCCceEEEEeeeecccceEEEecCCCCchhHHHHHHhcC----CccceEEEEecchHHHHHHHHHHHHHhhccccCc
Confidence            44558999999998764 568999999999999999998887    2234699999999999999988886 47777888


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHH------HHHHHHhhCC
Q 022724          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKD------QIYDVYRYLP  204 (293)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~------~~~~i~~~l~  204 (293)
                      .+..+.|..+.+-.   +....+|+|+||+++-.+ .    ..+.++++|.||.|++.+. ++.      .++.+-+.+-
T Consensus      1217 ~~~~l~ge~s~~lk---l~~~~~vii~tpe~~d~l-q----~iQ~v~l~i~d~lh~igg~-~g~v~evi~S~r~ia~q~~ 1287 (1674)
T KOG0951|consen 1217 RIVKLTGETSLDLK---LLQKGQVIISTPEQWDLL-Q----SIQQVDLFIVDELHLIGGV-YGAVYEVICSMRYIASQLE 1287 (1674)
T ss_pred             eEEecCCccccchH---HhhhcceEEechhHHHHH-h----hhhhcceEeeehhhhhccc-CCceEEEEeeHHHHHHHHH
Confidence            88888888766532   233458999999998765 2    5678899999999998743 221      1556666677


Q ss_pred             CCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCccc-CCCceEEEEEecCcccHHHH-----HHHHHh-hCCCCcEEE
Q 022724          205 PDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELT-LEGIKQFFVAVEREEWKFDT-----LCDLYD-TLTITQAVI  277 (293)
Q Consensus       205 ~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~i~~~~~~~~~~~~k~~~-----l~~l~~-~~~~~~~iI  277 (293)
                      +..+++.+|..+.+. .+++  ++.....++....... |..+.-..............     ...+.+ ...+++++|
T Consensus      1288 k~ir~v~ls~~lana-~d~i--g~s~~~v~Nf~p~~R~~Pl~i~i~~~~~~~~~~~~~am~~~~~~ai~~~a~~~k~~~v 1364 (1674)
T KOG0951|consen 1288 KKIRVVALSSSLANA-RDLI--GASSSGVFNFSPSVRPVPLEIHIQSVDISHFESRMLAMTKPTYTAIVRHAGNRKPAIV 1364 (1674)
T ss_pred             hheeEEEeehhhccc-hhhc--cccccceeecCcccCCCceeEEEEEeccchhHHHHHHhhhhHHHHHHHHhcCCCCeEE
Confidence            889999999998765 3332  2222233333322222 11122111111111111111     111121 124569999


Q ss_pred             EcccchhHHHHHhhC
Q 022724          278 FCNTKRKVLLLVLQF  292 (293)
Q Consensus       278 F~~s~~~a~~l~~~L  292 (293)
                      |+++++.|..++..|
T Consensus      1365 f~p~rk~~~~~a~~~ 1379 (1674)
T KOG0951|consen 1365 FLPTRKHARLVAVDL 1379 (1674)
T ss_pred             Eeccchhhhhhhhcc
Confidence            999999999887643

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

Probab=99.50  E-value=9.7e-14  Score=129.38  Aligned_cols=160  Identities=14%  Similarity=0.156  Sum_probs=114.0

Q ss_pred             CCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCc-eEE
Q 022724           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI-QAH  133 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~-~~~  133 (293)
                      .|..||++.+..+=.+++.+|+|||.+|||++-.-.+ +++.+.....-+|+++|+++|+.|+...+......... +..
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            5899999999999999999999999999997654444 44444444457999999999999998877765433221 111


Q ss_pred             EEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc---CCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEE
Q 022724          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR---KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVV  210 (293)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~---~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v  210 (293)
                      .+.|....  +.+.-.-.|+|+|+-|+.+..++..   ..-...++.++|+||+|.+....-....+.++...  .|.++
T Consensus       590 sl~g~ltq--EYsinp~nCQVLITvPecleslLlspp~~q~~cerIRyiIfDEVH~iG~~ed~l~~Eqll~li--~CP~L  665 (1330)
T KOG0949|consen  590 SLLGDLTQ--EYSINPWNCQVLITVPECLESLLLSPPHHQKFCERIRYIIFDEVHLIGNEEDGLLWEQLLLLI--PCPFL  665 (1330)
T ss_pred             hhHhhhhH--HhcCCchhceEEEEchHHHHHHhcCchhhhhhhhcceEEEechhhhccccccchHHHHHHHhc--CCCee
Confidence            22222211  1111112589999999999998876   44557899999999999997654444444444443  58899


Q ss_pred             EEEeecChh
Q 022724          211 LISATLPHE  219 (293)
Q Consensus       211 ~~SAt~~~~  219 (293)
                      ++|||+.+.
T Consensus       666 ~LSATigN~  674 (1330)
T KOG0949|consen  666 VLSATIGNP  674 (1330)
T ss_pred             EEecccCCH
Confidence            999999654

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.45  E-value=2.9e-12  Score=120.57  Aligned_cols=130  Identities=18%  Similarity=0.281  Sum_probs=102.9

Q ss_pred             CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q 022724           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (293)
Q Consensus        51 ~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (293)
                      .|. .|++.|.-.--.+.+|+  +....||+|||+++.+|++.....   |..+-+++|+..||.|=++.+..+...+|+
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 48999988766676776  899999999999999998877666   557899999999999999999999999999


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHHH-HHHhcCC------CCCCCccEEEecchhhhh
Q 022724          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVC-DMIKRKT------LRTRAIKLLVLDESDEML  188 (293)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~-~~l~~~~------~~~~~l~~iViDE~h~~~  188 (293)
                      ++..+.++.+..+....+  .+||+-+|...+- ++|+.+.      ...+.+.+.||||+|.++
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  4699999987764 3444421      123668999999999974

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

Probab=99.43  E-value=2.8e-12  Score=119.00  Aligned_cols=61  Identities=18%  Similarity=0.201  Sum_probs=51.7

Q ss_pred             HHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhh
Q 022724           64 VMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIG  125 (293)
Q Consensus        64 ~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  125 (293)
                      ...+.+++.+++.+|||+|||++|++|++..+... .+.++||++||++|..|+.+.+..+.
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.

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

Probab=99.43  E-value=3.2e-12  Score=123.28  Aligned_cols=83  Identities=25%  Similarity=0.329  Sum_probs=65.9

Q ss_pred             CCCCCCcHHHHHHHHhh----hcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHH-HHHHHHhh
Q 022724           51 YGFEKPSAIQQRAVMPI----IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQT-EKVILAIG  125 (293)
Q Consensus        51 ~~~~~~~~~Q~~~~~~i----~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~-~~~~~~~~  125 (293)
                      .||+ +++-|.+....+    .+++++++.|+||+|||++|++|++...    .+.++||++||++|++|+ ...+..+.
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 899999855544    4678899999999999999999988754    246899999999999999 46677777


Q ss_pred             ccCCceEEEEECC
Q 022724          126 DFINIQAHACVGG  138 (293)
Q Consensus       126 ~~~~~~~~~~~~~  138 (293)
                      +..++++..+.|+
T Consensus       317 ~~~~~~~~~~kg~  329 (820)
T PRK07246        317 EVFHIDCHSLKGP  329 (820)
T ss_pred             HhcCCcEEEEECC
Confidence            7777766665554

>KOG0920 consensus ATP-dependent RNA helicase A [RNA processing and modification]

Probab=99.42  E-value=2.5e-11  Score=115.27  Aligned_cols=226  Identities=17%  Similarity=0.182  Sum_probs=144.9

Q ss_pred             CcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHH-hhccCCceEEE
Q 022724           56 PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA-IGDFINIQAHA  134 (293)
Q Consensus        56 ~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~-~~~~~~~~~~~  134 (293)
                      .+..+.++++++.+++.++|.|.||+|||.-..-.+++.....+...++++--|.|--|..+++++.+ .+...|-.|..
T Consensus       174 a~~~r~~Il~~i~~~qVvvIsGeTGcGKTTQvpQfiLd~~~~~~~~~~IicTQPRRIsAIsvAeRVa~ER~~~~g~~VGY  253 (924)
T KOG0920|consen  174 AYKMRDTILDAIEENQVVVISGETGCGKTTQVPQFILDEAIESGAACNIICTQPRRISAISVAERVAKERGESLGEEVGY  253 (924)
T ss_pred             cHHHHHHHHHHHHhCceEEEeCCCCCCchhhhhHHHHHHHHhcCCCCeEEecCCchHHHHHHHHHHHHHhccccCCeeeE
Confidence            57788889999999999999999999999877777777765555666788888999999999888753 34444444433


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhh-ccccHHHHHHHHhhCCCCccEEEEE
Q 022724          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML-SRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~-~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      -.+..+.      ......+++||.+.|++.+.. .-.+..+..+|+||+|.=. +..|.-.+...+-..++..++|+||
T Consensus       254 qvrl~~~------~s~~t~L~fcTtGvLLr~L~~-~~~l~~vthiivDEVHER~i~~DflLi~lk~lL~~~p~LkvILMS  326 (924)
T KOG0920|consen  254 QVRLESK------RSRETRLLFCTTGVLLRRLQS-DPTLSGVTHIIVDEVHERSINTDFLLILLKDLLPRNPDLKVILMS  326 (924)
T ss_pred             EEeeecc------cCCceeEEEecHHHHHHHhcc-CcccccCceeeeeeEEEccCCcccHHHHHHHHhhhCCCceEEEee
Confidence            3222211      112257999999999998877 4458899999999999742 1223333333333334789999999


Q ss_pred             eecChhHHHHHHhcCCCCEEEEecCCccc----------------CCCceEE------------EEEecCcccHHHHHHH
Q 022724          214 ATLPHEILEMTTKFMTDPVKILVKRDELT----------------LEGIKQF------------FVAVEREEWKFDTLCD  265 (293)
Q Consensus       214 At~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------~~~i~~~------------~~~~~~~~~k~~~l~~  265 (293)
                      ||+..+   ....|++....+.+.-....                .....++            ......+ .....+.+
T Consensus       327 AT~dae---~fs~YF~~~pvi~i~grtfpV~~~fLEDil~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-id~~Li~~  402 (924)
T KOG0920|consen  327 ATLDAE---LFSDYFGGCPVITIPGRTFPVKEYFLEDILSKTGYVSEDDSARSGPERSQLRLARLKLWEPE-IDYDLIED  402 (924)
T ss_pred             eecchH---HHHHHhCCCceEeecCCCcchHHHHHHHHHHHhcccccccccccccccCccccccchhcccc-ccHHHHHH
Confidence            999833   44445544434433211000                0000111            0000111 13334444


Q ss_pred             HH----hhCCCCcEEEEcccchhHHHHHhhC
Q 022724          266 LY----DTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       266 l~----~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ++    +....+.+|||.+...+...+.+.|
T Consensus       403 li~~I~~~~~~GaILVFLPG~~eI~~~~~~L  433 (924)
T KOG0920|consen  403 LIEYIDEREFEGAILVFLPGWEEILQLKELL  433 (924)
T ss_pred             HHHhcccCCCCceEEEEcCCHHHHHHHHHHh
Confidence            43    3334579999999999999988876

>KOG0922 consensus DEAH-box RNA helicase [RNA processing and modification]

Probab=99.42  E-value=3.5e-11  Score=109.01  Aligned_cols=220  Identities=13%  Similarity=0.168  Sum_probs=133.6

Q ss_pred             cHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHH-HhhccCCceEEEE
Q 022724           57 SAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL-AIGDFINIQAHAC  135 (293)
Q Consensus        57 ~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~-~~~~~~~~~~~~~  135 (293)
                      ..+-.+.+..+.+++-++|.|+||||||.-.--.+.+.-.. ..| ++-+.-|.|--|..+..+.. +.+..+|-.|...
T Consensus        53 ~~~r~~il~~ve~nqvlIviGeTGsGKSTQipQyL~eaG~~-~~g-~I~~TQPRRVAavslA~RVAeE~~~~lG~~VGY~  130 (674)
T KOG0922|consen   53 YKYRDQILYAVEDNQVLIVIGETGSGKSTQIPQYLAEAGFA-SSG-KIACTQPRRVAAVSLAKRVAEEMGCQLGEEVGYT  130 (674)
T ss_pred             HHHHHHHHHHHHHCCEEEEEcCCCCCccccHhHHHHhcccc-cCC-cEEeecCchHHHHHHHHHHHHHhCCCcCceeeeE
Confidence            44555777888889999999999999996432223222222 223 47777799988888776664 4555555544432


Q ss_pred             ECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhh--hccccHHHHHHHHhhCCCCccEEEEE
Q 022724          136 VGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM--LSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~--~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      ..-.+..      .....|...|.+.|++-+... -.+++.++||+||||.=  ..+-....++.+++.. +..++|+||
T Consensus       131 IRFed~t------s~~TrikymTDG~LLRE~l~D-p~LskYsvIIlDEAHERsl~TDiLlGlLKki~~~R-~~LklIimS  202 (674)
T KOG0922|consen  131 IRFEDST------SKDTRIKYMTDGMLLREILKD-PLLSKYSVIILDEAHERSLHTDILLGLLKKILKKR-PDLKLIIMS  202 (674)
T ss_pred             EEecccC------CCceeEEEecchHHHHHHhcC-CccccccEEEEechhhhhhHHHHHHHHHHHHHhcC-CCceEEEEe
Confidence            2111111      123479999999999855443 23789999999999962  1111222333333333 468999999


Q ss_pred             eecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHH---hhCCCCcEEEEcccchhHHHHHh
Q 022724          214 ATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLY---DTLTITQAVIFCNTKRKVLLLVL  290 (293)
Q Consensus       214 At~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~---~~~~~~~~iIF~~s~~~a~~l~~  290 (293)
                      ||+..+   ....++.+-..+.+.   .....+..+|..-+..+.-.+.+...+   ...+++-+|||....++.+.+++
T Consensus       203 ATlda~---kfS~yF~~a~i~~i~---GR~fPVei~y~~~p~~dYv~a~~~tv~~Ih~~E~~GDILvFLtGqeEIe~~~~  276 (674)
T KOG0922|consen  203 ATLDAE---KFSEYFNNAPILTIP---GRTFPVEILYLKEPTADYVDAALITVIQIHLTEPPGDILVFLTGQEEIEAACE  276 (674)
T ss_pred             eeecHH---HHHHHhcCCceEeec---CCCCceeEEeccCCchhhHHHHHHHHHHHHccCCCCCEEEEeCCHHHHHHHHH
Confidence            999743   334444443333333   222345556665444442233333333   34556799999999999998887


Q ss_pred             hC
Q 022724          291 QF  292 (293)
Q Consensus       291 ~L  292 (293)
                      .|
T Consensus       277 ~l  278 (674)
T KOG0922|consen  277 LL  278 (674)
T ss_pred             HH
Confidence            64

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.40  E-value=2.6e-11  Score=117.42  Aligned_cols=158  Identities=18%  Similarity=0.083  Sum_probs=96.1

Q ss_pred             CCcHHHHHHHHhhhcC--CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceE
Q 022724           55 KPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQA  132 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~--~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  132 (293)
                      .|.|+|.++...+.+.  ..+++.-.+|.|||.-+.+.+...+... ...+++|+||. .|..|+...+.+..   ++..
T Consensus       152 ~l~pHQl~~~~~vl~~~~~R~LLADEvGLGKTIeAglil~~l~~~g-~~~rvLIVvP~-sL~~QW~~El~~kF---~l~~  226 (956)
T PRK04914        152 SLIPHQLYIAHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQLLTG-RAERVLILVPE-TLQHQWLVEMLRRF---NLRF  226 (956)
T ss_pred             CCCHHHHHHHHHHhhccCCCEEEEeCCcCcHHHHHHHHHHHHHHcC-CCCcEEEEcCH-HHHHHHHHHHHHHh---CCCe
Confidence            5999999998777643  4789999999999977765554444443 33489999997 89999988775432   3444


Q ss_pred             EEEECCcchHHHHH--HHhcCCcEEEeChHHHHHHH-hcCCCCCCCccEEEecchhhhhcc--ccHHHHHHHHhhCCCCc
Q 022724          133 HACVGGKSVGEDIR--KLEHGVHVVSGTPGRVCDMI-KRKTLRTRAIKLLVLDESDEMLSR--GFKDQIYDVYRYLPPDL  207 (293)
Q Consensus       133 ~~~~~~~~~~~~~~--~~~~~~~ilV~Tp~~l~~~l-~~~~~~~~~l~~iViDE~h~~~~~--~~~~~~~~i~~~l~~~~  207 (293)
                      ..+.++........  .-....+++|++.+.+...- ....+.-..++++||||||++-..  .-......+........
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            33333221110000  00123579999987765411 111122346899999999998521  11112222222222345


Q ss_pred             cEEEEEeecC
Q 022724          208 QVVLISATLP  217 (293)
Q Consensus       208 q~v~~SAt~~  217 (293)
                      .++++|||+.
T Consensus       307 ~~LLLTATP~  316 (956)
T PRK04914        307 GVLLLTATPE  316 (956)
T ss_pred             CEEEEEcCcc
Confidence            7899999973

>PF07652 Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR011492 This is the Flavivirus DEAD domain

Probab=99.38  E-value=9.2e-13  Score=98.24  Aligned_cols=136  Identities=15%  Similarity=0.230  Sum_probs=81.5

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  148 (293)
                      +|+-.++...+|+|||--.+.-++......  +.|+|+|.|||.++..+.+.++..    .+++.  ..-..  .   ..
T Consensus         3 kg~~~~~d~hpGaGKTr~vlp~~~~~~i~~--~~rvLvL~PTRvva~em~~aL~~~----~~~~~--t~~~~--~---~~   69 (148)
T PF07652_consen    3 KGELTVLDLHPGAGKTRRVLPEIVREAIKR--RLRVLVLAPTRVVAEEMYEALKGL----PVRFH--TNARM--R---TH   69 (148)
T ss_dssp             TTEEEEEE--TTSSTTTTHHHHHHHHHHHT--T--EEEEESSHHHHHHHHHHTTTS----SEEEE--STTSS--------
T ss_pred             CCceeEEecCCCCCCcccccHHHHHHHHHc--cCeEEEecccHHHHHHHHHHHhcC----CcccC--ceeee--c---cc
Confidence            566788999999999987776666554443  568999999999999999977533    22221  11110  0   11


Q ss_pred             hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccc--cHHHHHHHHhhCCCCccEEEEEeecChhH
Q 022724          149 EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG--FKDQIYDVYRYLPPDLQVVLISATLPHEI  220 (293)
Q Consensus       149 ~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~--~~~~~~~i~~~l~~~~q~v~~SAt~~~~~  220 (293)
                      ..+.-|-|.|-..+.+.+.+ .....++++||+||+|..-...  ....+... ... ....+|+||||+|...
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-PCRLKNYDVIIMDECHFTDPTSIAARGYLREL-AES-GEAKVIFMTATPPGSE  140 (148)
T ss_dssp             -SSSSEEEEEHHHHHHHHHT-SSCTTS-SEEEECTTT--SHHHHHHHHHHHHH-HHT-TS-EEEEEESS-TT--
T ss_pred             cCCCcccccccHHHHHHhcC-cccccCccEEEEeccccCCHHHHhhheeHHHh-hhc-cCeeEEEEeCCCCCCC
Confidence            23446888898888887766 4457899999999999863221  12222222 222 2468999999998754

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 ....

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=99.34  E-value=1.2e-10  Score=107.97  Aligned_cols=130  Identities=15%  Similarity=0.240  Sum_probs=103.3

Q ss_pred             CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q 022724           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (293)
Q Consensus        51 ~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (293)
                      .|. .|++.|--..-.+.+|+  +....||.|||+++.+|++.....   |..+-+++|+..||.+=++.+..+...+|+
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 LGL-RPFDVQLLGALRLLAGD--VIEMATGEGKTLAGAIAAAGYALQ---GRRVHVITVNDYLARRDAEWMGPLYEALGL  148 (764)
T ss_pred             cCC-CcchHHHHHHHHHhCCC--cccccCCCCHHHHHHHHHHHHHHc---CCCeEEEcCCHHHHHHHHHHHHHHHHhcCC
Confidence            454 49999999888888775  679999999999999998877655   557899999999999999999999999999


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHHH-HHHhcC------CCCCCCccEEEecchhhhh
Q 022724          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVC-DMIKRK------TLRTRAIKLLVLDESDEML  188 (293)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~-~~l~~~------~~~~~~l~~iViDE~h~~~  188 (293)
                      ++....++.+..+....+  .+||.-+|...+- ++|+.+      ....+.+.+.||||+|.++
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            999988887655444333  4799999987653 344332      2234668999999999975

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=99.31  E-value=4.4e-11  Score=102.31  Aligned_cols=70  Identities=19%  Similarity=0.199  Sum_probs=56.5

Q ss_pred             CCcHHHHHHHH----hhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCC---ceeEEEEcCCHHHHHHHHHHHHHh
Q 022724           55 KPSAIQQRAVM----PIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR---EVQALILSPTRELATQTEKVILAI  124 (293)
Q Consensus        55 ~~~~~Q~~~~~----~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~---~~~~lil~P~~~l~~q~~~~~~~~  124 (293)
                      .|+|.|.+.+.    .+..|+++++.+|||+|||++|+.|++..+...+.   +.+++|.++|..+..|....++++
T Consensus         8 ~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00488        8 EPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhc
Confidence            37999999554    45578999999999999999999999876654332   248999999999988887777665

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=99.31  E-value=4.4e-11  Score=102.31  Aligned_cols=70  Identities=19%  Similarity=0.199  Sum_probs=56.5

Q ss_pred             CCcHHHHHHHH----hhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCC---ceeEEEEcCCHHHHHHHHHHHHHh
Q 022724           55 KPSAIQQRAVM----PIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR---EVQALILSPTRELATQTEKVILAI  124 (293)
Q Consensus        55 ~~~~~Q~~~~~----~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~---~~~~lil~P~~~l~~q~~~~~~~~  124 (293)
                      .|+|.|.+.+.    .+..|+++++.+|||+|||++|+.|++..+...+.   +.+++|.++|..+..|....++++
T Consensus         8 ~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00489        8 EPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhc
Confidence            37999999554    45578999999999999999999999876654332   248999999999988887777665

>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=99.30  E-value=6.6e-11  Score=102.06  Aligned_cols=143  Identities=19%  Similarity=0.141  Sum_probs=84.1

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCC--ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSR--EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRK  147 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~--~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (293)
                      .+..+++-.+|+|||...+..+.......+.  ...+||+||. .+..++...+.++.....+++..+.++.........
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            4679999999999997766544322222211  1259999999 888999999999886556677666666522222222


Q ss_pred             HhcCCcEEEeChHHHHHHHhc---CCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEeec
Q 022724          148 LEHGVHVVSGTPGRVCDMIKR---KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATL  216 (293)
Q Consensus       148 ~~~~~~ilV~Tp~~l~~~l~~---~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~  216 (293)
                      .....+++|+|.+.+...-..   ..+...+.++||+||+|.+-  +........+..+. ....+++|||+
T Consensus       104 ~~~~~~vvi~ty~~~~~~~~~~~~~~l~~~~~~~vIvDEaH~~k--~~~s~~~~~l~~l~-~~~~~lLSgTP  172 (299)
T PF00176_consen  104 QLPKYDVVITTYETLRKARKKKDKEDLKQIKWDRVIVDEAHRLK--NKDSKRYKALRKLR-ARYRWLLSGTP  172 (299)
T ss_dssp             SCCCSSEEEEEHHHHH--TSTHTTHHHHTSEEEEEEETTGGGGT--TTTSHHHHHHHCCC-ECEEEEE-SS-
T ss_pred             ccccceeeeccccccccccccccccccccccceeEEEecccccc--cccccccccccccc-cceEEeecccc
Confidence            334568999999988810000   01111348999999999983  22333333444455 66788899996

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=2.1e-10  Score=112.73  Aligned_cols=65  Identities=20%  Similarity=0.217  Sum_probs=53.7

Q ss_pred             CCCCCcHHHHHHHHhhh----cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHH
Q 022724           52 GFEKPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (293)
Q Consensus        52 ~~~~~~~~Q~~~~~~i~----~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~  119 (293)
                      || .+++-|.+....+.    +++++++.||||+|||++|++|++......  +.++||-++|+.|-+|+..
T Consensus       255 ~~-e~R~~Q~~m~~~v~~~l~~~~~~~iEA~TGtGKTlaYLlpa~~~a~~~--~~~vvIsT~T~~LQ~Ql~~  323 (928)
T PRK08074        255 KY-EKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAYLLPAAYFAKKK--EEPVVISTYTIQLQQQLLE  323 (928)
T ss_pred             CC-cCCHHHHHHHHHHHHHHhcCCCEEEECCCCCchhHHHHHHHHHHhhcc--CCeEEEEcCCHHHHHHHHH
Confidence            44 49999999666544    678999999999999999999998655433  4589999999999999865

>KOG0925 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.22  E-value=2.2e-09  Score=94.13  Aligned_cols=237  Identities=14%  Similarity=0.166  Sum_probs=140.2

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCC-cHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCC
Q 022724           32 ITSFDAMGIKDDLLRGIYQYGFEKP-SAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (293)
Q Consensus        32 ~~~f~~~~l~~~i~~~l~~~~~~~~-~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~  110 (293)
                      +..|+..+.++.-.+-+++.. .-| +..+.+....+.+++-++++|.||||||.-.--..+.......  ..+..--|.
T Consensus        24 ~Npf~~~p~s~rY~~ilk~R~-~LPvw~~k~~F~~~l~~nQ~~v~vGetgsGKttQiPq~~~~~~~~~~--~~v~CTQpr  100 (699)
T KOG0925|consen   24 INPFNGKPYSQRYYDILKKRR-ELPVWEQKEEFLKLLLNNQIIVLVGETGSGKTTQIPQFVLEYELSHL--TGVACTQPR  100 (699)
T ss_pred             cCCCCCCcCcHHHHHHHHHHh-cCchHHhHHHHHHHHhcCceEEEEecCCCCccccCcHHHHHHHHhhc--cceeecCch
Confidence            778999999999999888753 334 3333444455567788999999999999554333333333332  346666798


Q ss_pred             HHHHHHHHHHHH-HhhccCCceEEEEECCcchHHHHHHHhcCC-----cEEEeChHHHHHHHhcCCCCCCCccEEEecch
Q 022724          111 RELATQTEKVIL-AIGDFINIQAHACVGGKSVGEDIRKLEHGV-----HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDES  184 (293)
Q Consensus       111 ~~l~~q~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~  184 (293)
                      +--+.++..+.. .+.-.+|-.|.....-           ++|     -+-.+|.+.|++-.-+. -.+.+.+.||+|||
T Consensus       101 rvaamsva~RVadEMDv~lG~EVGysIrf-----------EdC~~~~T~Lky~tDgmLlrEams~-p~l~~y~viiLDea  168 (699)
T KOG0925|consen  101 RVAAMSVAQRVADEMDVTLGEEVGYSIRF-----------EDCTSPNTLLKYCTDGMLLREAMSD-PLLGRYGVIILDEA  168 (699)
T ss_pred             HHHHHHHHHHHHHHhccccchhccccccc-----------cccCChhHHHHHhcchHHHHHHhhC-cccccccEEEechh
Confidence            888888776553 3332333222111100           111     01113444444422222 23688999999999


Q ss_pred             hhh--hccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHH
Q 022724          185 DEM--LSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDT  262 (293)
Q Consensus       185 h~~--~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~  262 (293)
                      |.=  ..+-....+..+.... +..++|.||||+-.   .....|+.++-.+.++.    .+.+..+|..-...+ ..+.
T Consensus       169 hERtlATDiLmGllk~v~~~r-pdLk~vvmSatl~a---~Kfq~yf~n~Pll~vpg----~~PvEi~Yt~e~erD-ylEa  239 (699)
T KOG0925|consen  169 HERTLATDILMGLLKEVVRNR-PDLKLVVMSATLDA---EKFQRYFGNAPLLAVPG----THPVEIFYTPEPERD-YLEA  239 (699)
T ss_pred             hhhhHHHHHHHHHHHHHHhhC-CCceEEEeecccch---HHHHHHhCCCCeeecCC----CCceEEEecCCCChh-HHHH
Confidence            962  2222333445555554 58999999999853   35556777777776654    123444444333333 4444


Q ss_pred             -HHHHH---hhCCCCcEEEEcccchhHHHHHhhC
Q 022724          263 -LCDLY---DTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       263 -l~~l~---~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                       ++..+   .....+-+++|....++.+..++.+
T Consensus       240 airtV~qih~~ee~GDilvFLtgeeeIe~aC~~i  273 (699)
T KOG0925|consen  240 AIRTVLQIHMCEEPGDILVFLTGEEEIEDACRKI  273 (699)
T ss_pred             HHHHHHHHHhccCCCCEEEEecCHHHHHHHHHHH
Confidence             33333   3345679999999999888877643

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=99.20  E-value=6.9e-10  Score=108.23  Aligned_cols=153  Identities=14%  Similarity=0.125  Sum_probs=102.0

Q ss_pred             CCcHHHHHHHHhhh----cCCcEEEEcCCCChhHHHHHHHHHhhhc-cCCCceeEEEEcCCHHHHHHHHHHHHHhhccCC
Q 022724           55 KPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVD-TSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~----~~~~~li~~~Tg~GKT~~~~~~~~~~l~-~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (293)
                      .++++|.+.+..+.    .|.+.|+.-.+|.|||+..+..+ ..+. .......+|||||. .+..++.+.+.++..  .
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    57789999999999997654333 3332 22223468999995 667889999988864  3


Q ss_pred             ceEEEEECCcchHHHHHH---HhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCC
Q 022724          130 IQAHACVGGKSVGEDIRK---LEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPD  206 (293)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~---~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~  206 (293)
                      +++..++|+.........   .....+|+|+|.+.+.....  .+.--..++||+||+|.+-..  ...+...+..+. .
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            566667766443222211   12457899999988865321  222345789999999998432  333444555554 3


Q ss_pred             ccEEEEEeec
Q 022724          207 LQVVLISATL  216 (293)
Q Consensus       207 ~q~v~~SAt~  216 (293)
                      ...+++|+|+
T Consensus       320 ~~RLLLTGTP  329 (1033)
T PLN03142        320 NYRLLITGTP  329 (1033)
T ss_pred             CcEEEEecCC
Confidence            4567899997

>KOG0926 consensus DEAH-box RNA helicase [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.19  E-value=2.7e-10  Score=104.96  Aligned_cols=217  Identities=18%  Similarity=0.189  Sum_probs=124.9

Q ss_pred             HHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccC---CCceeEEEEcCCHHHHHHHHHHHH-HhhccCCceEEE--
Q 022724           61 QRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS---SREVQALILSPTRELATQTEKVIL-AIGDFINIQAHA--  134 (293)
Q Consensus        61 ~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~---~~~~~~lil~P~~~l~~q~~~~~~-~~~~~~~~~~~~--  134 (293)
                      +++..+|..+.-++|||.||||||.-.--.+.+.=...   ..+.-+=|--|.|--|..+..+.. .++. ++-.|..  
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            35566677777899999999999954322222221111   112234455599888877776654 3444 4333332  


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcc-----ccHHHHHHHHhhCCC----
Q 022724          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-----GFKDQIYDVYRYLPP----  205 (293)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~-----~~~~~~~~i~~~l~~----  205 (293)
                      -+.++        +.....|.+.|.+-|++-+.+ .+.+...+.||+||||.=.-+     |....+..+.+.+.+    
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            23222        223458999999999987665 356899999999999963110     222333333333333    


Q ss_pred             --CccEEEEEeecChhHHHHHHhcCCC-CEEEEecCCcccCCCceEEEEEecCccc--HHHHHHHH---HhhCCCCcEEE
Q 022724          206 --DLQVVLISATLPHEILEMTTKFMTD-PVKILVKRDELTLEGIKQFFVAVEREEW--KFDTLCDL---YDTLTITQAVI  277 (293)
Q Consensus       206 --~~q~v~~SAt~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~i~~~~~~~~~~~~--k~~~l~~l---~~~~~~~~~iI  277 (293)
                        ..++|+||||+--+-..-.+.+++. |-.+.++.....     -..++-....+  --.+....   =++.+.+-+||
T Consensus       412 ~kpLKLIIMSATLRVsDFtenk~LFpi~pPlikVdARQfP-----VsIHF~krT~~DYi~eAfrKtc~IH~kLP~G~ILV  486 (1172)
T KOG0926|consen  412 IKPLKLIIMSATLRVSDFTENKRLFPIPPPLIKVDARQFP-----VSIHFNKRTPDDYIAEAFRKTCKIHKKLPPGGILV  486 (1172)
T ss_pred             cCceeEEEEeeeEEecccccCceecCCCCceeeeecccCc-----eEEEeccCCCchHHHHHHHHHHHHhhcCCCCcEEE
Confidence              6789999999853322222333432 334445433221     11222222211  11222222   23557789999


Q ss_pred             EcccchhHHHHHhhC
Q 022724          278 FCNTKRKVLLLVLQF  292 (293)
Q Consensus       278 F~~s~~~a~~l~~~L  292 (293)
                      |+....++.++++.|
T Consensus       487 FvTGQqEV~qL~~kL  501 (1172)
T KOG0926|consen  487 FVTGQQEVDQLCEKL  501 (1172)
T ss_pred             EEeChHHHHHHHHHH
Confidence            999999999998865

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

Probab=99.18  E-value=2.7e-12  Score=120.82  Aligned_cols=228  Identities=14%  Similarity=0.190  Sum_probs=149.1

Q ss_pred             CCCCcHHHHHHHHhhhc-CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCce
Q 022724           53 FEKPSAIQQRAVMPIIK-GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ  131 (293)
Q Consensus        53 ~~~~~~~Q~~~~~~i~~-~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  131 (293)
                      +..+.|.|.+.+..+.. ..+.++-+|||+|||.+|.++++..+...+. .++++++|.++|+..-.+.+++.....|++
T Consensus       925 ~~~fn~~q~~if~~~y~td~~~~~g~ptgsgkt~~ae~a~~~~~~~~p~-~kvvyIap~kalvker~~Dw~~r~~~~g~k 1003 (1230)
T KOG0952|consen  925 YKYFNPIQTQIFHCLYHTDLNFLLGAPTGSGKTVVAELAIFRALSYYPG-SKVVYIAPDKALVKERSDDWSKRDELPGIK 1003 (1230)
T ss_pred             hcccCCccceEEEEEeecchhhhhcCCccCcchhHHHHHHHHHhccCCC-ccEEEEcCCchhhcccccchhhhcccCCce
Confidence            33566777777766553 5789999999999999999999988877765 689999999999999999888765555899


Q ss_pred             EEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc--CCCCCCCccEEEecchhhhhccccHHHHHHHHhh-------
Q 022724          132 AHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR--KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRY-------  202 (293)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~--~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~-------  202 (293)
                      +..+.|+...+  .... ...+++|+||++.-...++  ..-.+.++..+|+||.|++.+. ++..++.+.+.       
T Consensus      1004 ~ie~tgd~~pd--~~~v-~~~~~~ittpek~dgi~Rsw~~r~~v~~v~~iv~de~hllg~~-rgPVle~ivsr~n~~s~~ 1079 (1230)
T KOG0952|consen 1004 VIELTGDVTPD--VKAV-READIVITTPEKWDGISRSWQTRKYVQSVSLIVLDEIHLLGED-RGPVLEVIVSRMNYISSQ 1079 (1230)
T ss_pred             eEeccCccCCC--hhhe-ecCceEEcccccccCccccccchhhhccccceeecccccccCC-CcceEEEEeeccccCccc
Confidence            99999887655  2222 2468999999999888774  5556789999999999987543 34433333222       


Q ss_pred             CCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCC------cccCCCceEEEEEecCcccHHHHHHHHHhhCC-CCcE
Q 022724          203 LPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRD------ELTLEGIKQFFVAVEREEWKFDTLCDLYDTLT-ITQA  275 (293)
Q Consensus       203 l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~-~~~~  275 (293)
                      ..+..|.+++|.-+.+. .++..++...+. ......      +....+..- ..+|+....+.....+.++.++ ..++
T Consensus      1080 t~~~vr~~glsta~~na-~dla~wl~~~~~-~nf~~svrpvp~~~~i~gfp~-~~~cprm~smnkpa~qaik~~sp~~p~ 1156 (1230)
T KOG0952|consen 1080 TEEPVRYLGLSTALANA-NDLADWLNIKDM-YNFRPSVRPVPLEVHIDGFPG-QHYCPRMMSMNKPAFQAIKTHSPIKPV 1156 (1230)
T ss_pred             cCcchhhhhHhhhhhcc-HHHHHHhCCCCc-CCCCcccccCCceEeecCCCc-hhcchhhhhcccHHHHHHhcCCCCCce
Confidence            23456777776555332 344444322222 111100      000011111 1233433334444455566554 4599


Q ss_pred             EEEcccchhHHHH
Q 022724          276 VIFCNTKRKVLLL  288 (293)
Q Consensus       276 iIF~~s~~~a~~l  288 (293)
                      +||+.+++....-
T Consensus      1157 lifv~srrqtrlt 1169 (1230)
T KOG0952|consen 1157 LIFVSSRRQTRLT 1169 (1230)
T ss_pred             EEEeecccccccc
Confidence            9999998865443

>PRK14873 primosome assembly protein PriA; Provisional

Probab=99.12  E-value=1.5e-09  Score=102.10  Aligned_cols=138  Identities=14%  Similarity=0.142  Sum_probs=96.2

Q ss_pred             EEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----h
Q 022724           74 IAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----E  149 (293)
Q Consensus        74 li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~  149 (293)
                      +..+.+|||||..|+-.+-..+..   |.++|+|+|.+.|+.|+...++..+.  +..+..++++.+..+..+.+    .
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            334446999999998877666665   56899999999999999999987553  24688888887766655444    3


Q ss_pred             cCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhh--cc-c---cHHHHHHHHhhCCCCccEEEEEeecChhHHHH
Q 022724          150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML--SR-G---FKDQIYDVYRYLPPDLQVVLISATLPHEILEM  223 (293)
Q Consensus       150 ~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~--~~-~---~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~  223 (293)
                      ....|+|||-..+.       ..+.++++|||||-|.-.  +. .   ...++...... ..+..+|+.|||.+-+....
T Consensus       239 G~~~IViGtRSAvF-------aP~~~LgLIIvdEEhd~sykq~~~p~yhaRdvA~~Ra~-~~~~~lvLgSaTPSles~~~  310 (665)
T PRK14873        239 GQARVVVGTRSAVF-------APVEDLGLVAIWDDGDDLLAEPRAPYPHAREVALLRAH-QHGCALLIGGHARTAEAQAL  310 (665)
T ss_pred             CCCcEEEEcceeEE-------eccCCCCEEEEEcCCchhhcCCCCCCccHHHHHHHHHH-HcCCcEEEECCCCCHHHHHH
Confidence            44789999963332       357899999999998642  11 1   11223333333 35889999999987554443


Q ss_pred             H
Q 022724          224 T  224 (293)
Q Consensus       224 ~  224 (293)
                      .
T Consensus       311 ~  311 (665)
T PRK14873        311 V  311 (665)
T ss_pred             H
Confidence            3

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=99.09  E-value=1.8e-09  Score=103.63  Aligned_cols=168  Identities=20%  Similarity=0.159  Sum_probs=102.5

Q ss_pred             CCcHHHHHHHHhhhc--------CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhc
Q 022724           55 KPSAIQQRAVMPIIK--------GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGD  126 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~--------~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~  126 (293)
                      ....||-.|++.+..        |--++-.|.||+|||++=+- |+..+.....|.|..|..-.|.|..|+-+.+++-..
T Consensus       408 ~rF~WQdkA~d~a~~~r~~~~~~GfF~vNMASTGcGKT~aNAR-ImyaLsd~~~g~RfsiALGLRTLTLQTGda~r~rL~  486 (1110)
T TIGR02562       408 PRFRWQNKAFNLAQKLRQKSPEQGAFGVNMASTGCGKTLANAR-AMYALRDDKQGARFAIALGLRSLTLQTGHALKTRLN  486 (1110)
T ss_pred             CCcchHHHHHHHHHHHHhhcccCCeEEEEecCCCcchHHHHHH-HHHHhCCCCCCceEEEEccccceeccchHHHHHhcC
Confidence            457899999998763        11245559999999987543 445556666778999999999999998877765322


Q ss_pred             cCCceEEEEECCcchH-------------------------------------------HHHHHHhc--------CCcEE
Q 022724          127 FINIQAHACVGGKSVG-------------------------------------------EDIRKLEH--------GVHVV  155 (293)
Q Consensus       127 ~~~~~~~~~~~~~~~~-------------------------------------------~~~~~~~~--------~~~il  155 (293)
                      -.+-...++.|+....                                           .....+.+        ...++
T Consensus       487 L~~ddLAVlIGs~Av~~L~e~~~~~~~~~~~~GSeS~e~l~~e~~~~~~~~~~g~l~~~~l~~~l~~~~k~~rll~apv~  566 (1110)
T TIGR02562       487 LSDDDLAVLIGGTAVQTLFDLSKEKIEQVDEDGSESAPIFLAEGQDCNLPDWDGPLDTIELLGRLSLDDKEKTLLAAPVL  566 (1110)
T ss_pred             CCccceEEEECHHHHHHHHHHHhhhccccccCCCccchhhhcccCcCCeeeccCCccchhhhhhhccChhhhhhhcCCeE
Confidence            2222222233321110                                           00011110        14699


Q ss_pred             EeChHHHHHHHhc---CCCCCCC----ccEEEecchhhhhccccHHHHHHHHhhCC-CCccEEEEEeecChhHHHHH
Q 022724          156 SGTPGRVCDMIKR---KTLRTRA----IKLLVLDESDEMLSRGFKDQIYDVYRYLP-PDLQVVLISATLPHEILEMT  224 (293)
Q Consensus       156 V~Tp~~l~~~l~~---~~~~~~~----l~~iViDE~h~~~~~~~~~~~~~i~~~l~-~~~q~v~~SAt~~~~~~~~~  224 (293)
                      |||++.++.....   +...+..    =+.|||||+|.+-.. ....+..++..+. ...++++||||+|+.+...+
T Consensus       567 V~TIDQlL~a~~~~r~~~~~l~ll~La~svlVlDEVHaYD~~-~~~~L~rlL~w~~~lG~~VlLmSATLP~~l~~~L  642 (1110)
T TIGR02562       567 VCTIDHLIPATESHRGGHHIAPMLRLMSSDLILDEPDDYEPE-DLPALLRLVQLAGLLGSRVLLSSATLPPALVKTL  642 (1110)
T ss_pred             EecHHHHHHHhhhcccchhHHHHHHhcCCCEEEECCccCCHH-HHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHH
Confidence            9999999886522   1111111    256999999987332 2333444444322 36889999999999876633

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.

>KOG1123 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription; Replication, recombination and repair]

Probab=99.08  E-value=1.9e-10  Score=101.07  Aligned_cols=147  Identities=22%  Similarity=0.219  Sum_probs=105.5

Q ss_pred             CCcHHHHHHHHhhhc-C--CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCce
Q 022724           55 KPSAIQQRAVMPIIK-G--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ  131 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~-~--~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  131 (293)
                      .++|+|...+..... |  ++-+|+.|.|+|||++..-+++..      ..++|+||.+--.+.|+..+++.|...-.-.
T Consensus       302 ~iRpYQEksL~KMFGNgRARSGiIVLPCGAGKtLVGvTAa~ti------kK~clvLcts~VSVeQWkqQfk~wsti~d~~  375 (776)
T KOG1123|consen  302 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGVTAACTI------KKSCLVLCTSAVSVEQWKQQFKQWSTIQDDQ  375 (776)
T ss_pred             ccCchHHHHHHHHhCCCcccCceEEEecCCCCceeeeeeeeee------cccEEEEecCccCHHHHHHHHHhhcccCccc
Confidence            589999999999874 4  589999999999998765444322      3479999999999999999999887655555


Q ss_pred             EEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcC--------CCCCCCccEEEecchhhhhccccHHHHHHHHhhC
Q 022724          132 AHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK--------TLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL  203 (293)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~--------~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l  203 (293)
                      ++...++...     ....++.|+|+|...+.+--++.        .+.-+..+++++||+|.+...-|+..+..+...+
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            6655554432     12356789999986654322111        1123567899999999986665666666555554


Q ss_pred             CCCccEEEEEeecC
Q 022724          204 PPDLQVVLISATLP  217 (293)
Q Consensus       204 ~~~~q~v~~SAt~~  217 (293)
                           .++++||+-
T Consensus       451 -----KLGLTATLv  459 (776)
T KOG1123|consen  451 -----KLGLTATLV  459 (776)
T ss_pred             -----hccceeEEe
Confidence                 578999973

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=99.06  E-value=4.6e-09  Score=99.39  Aligned_cols=130  Identities=19%  Similarity=0.235  Sum_probs=98.4

Q ss_pred             CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q 022724           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (293)
Q Consensus        51 ~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (293)
                      .|.. |++.|--..-.+  .+.-+..+.||.|||+++.+|+.-....   |..+-|++++..||.+-.+.+..+...+|+
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-HFDVQLIGGLVL--NDGKIAEMKTGEGKTLVATLPAYLNALT---GKGVHIVTVNDYLAKRDQEWMGQIYRFLGL  146 (870)
T ss_pred             hCCC-CCchHhhhhHhh--cCCccccccCCCCchHHHHHHHHHHHhc---CCceEEEeCCHHHHHHHHHHHHHHHHHcCC
Confidence            4554 888777654333  4568899999999999999998644333   456899999999999999999999999999


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHHH-HHHhcCC------CCCCCccEEEecchhhhh
Q 022724          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVC-DMIKRKT------LRTRAIKLLVLDESDEML  188 (293)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~-~~l~~~~------~~~~~l~~iViDE~h~~~  188 (293)
                      .+....++.+..+.....  .++|+-+|...+- ++|+.+.      ...+.+.+.||||+|.++
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            999888777765544444  3689999986553 3444431      124678999999999975

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=99.06  E-value=8.7e-10  Score=104.68  Aligned_cols=130  Identities=18%  Similarity=0.249  Sum_probs=99.6

Q ss_pred             CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q 022724           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (293)
Q Consensus        51 ~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (293)
                      .|. .|+++|--.--.+  .+.-+....||.|||+++.+|++-....   |..+-+++|+..||.+=++.+..+...+|+
T Consensus        79 lGm-~~ydVQliGg~~L--h~G~iaEM~TGEGKTLvA~l~a~l~al~---G~~VhvvT~ndyLA~RD~e~m~~l~~~lGl  152 (913)
T PRK13103         79 MGM-RHFDVQLIGGMTL--HEGKIAEMRTGEGKTLVGTLAVYLNALS---GKGVHVVTVNDYLARRDANWMRPLYEFLGL  152 (913)
T ss_pred             hCC-CcchhHHHhhhHh--ccCccccccCCCCChHHHHHHHHHHHHc---CCCEEEEeCCHHHHHHHHHHHHHHhcccCC
Confidence            353 4777776544344  3456889999999999999998866555   457899999999999999999999999999


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcCC------CCCCCccEEEecchhhhh
Q 022724          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRKT------LRTRAIKLLVLDESDEML  188 (293)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l-~~~l~~~~------~~~~~l~~iViDE~h~~~  188 (293)
                      ++.++.++.+..+....+.  ++|++||...+ .++|+.+.      ...+.+.+.||||+|.++
T Consensus       153 ~v~~i~~~~~~~err~~Y~--~dI~YGT~~e~gFDYLrD~~~~~~~~~vqr~l~~aIVDEvDsiL  215 (913)
T PRK13103        153 SVGIVTPFQPPEEKRAAYA--ADITYGTNNEFGFDYLRDNMAFSLDDKFQRELNFAVIDEVDSIL  215 (913)
T ss_pred             EEEEECCCCCHHHHHHHhc--CCEEEEcccccccchhhccceechhhhcccccceeEechhhhee
Confidence            9999888776555444443  79999998776 33444321      123789999999999975

>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=99.04  E-value=1.2e-08  Score=85.47  Aligned_cols=130  Identities=20%  Similarity=0.319  Sum_probs=97.5

Q ss_pred             CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q 022724           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (293)
Q Consensus        51 ~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (293)
                      .|+ .|++.|..+.-.+.+|+  +....||-|||++..+|+.-....   |..+=|++.+..|+..=.+.+..+...+|+
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 49999999888887766  999999999999988877655544   457889999999999999999999999999


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHHHH-HHhcCC------CCCCCccEEEecchhhhh
Q 022724          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCD-MIKRKT------LRTRAIKLLVLDESDEML  188 (293)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~-~l~~~~------~~~~~l~~iViDE~h~~~  188 (293)
                      ++....++.+..+......  ++|+-+|...+.- +|+.+.      ...+.+.++||||+|.++
T Consensus       148 sv~~~~~~~~~~~r~~~Y~--~dI~Y~t~~~~~fD~Lrd~~~~~~~~~~~r~~~~~ivDEvDs~L  210 (266)
T PF07517_consen  148 SVGIITSDMSSEERREAYA--ADIVYGTNSEFGFDYLRDNLALSKNEQVQRGFDFAIVDEVDSIL  210 (266)
T ss_dssp             -EEEEETTTEHHHHHHHHH--SSEEEEEHHHHHHHHHHHTT-SSGGG--SSSSSEEEECTHHHHT
T ss_pred             ccccCccccCHHHHHHHHh--CcccccccchhhHHHHHHHHhhccchhccCCCCEEEEeccceEE
Confidence            9999999887654433333  5799999988864 554421      124788999999999975

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 ....

>KOG0923 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.02  E-value=1.9e-08  Score=91.38  Aligned_cols=220  Identities=13%  Similarity=0.185  Sum_probs=130.7

Q ss_pred             CcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHH-HhhccCCceEEE
Q 022724           56 PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL-AIGDFINIQAHA  134 (293)
Q Consensus        56 ~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~-~~~~~~~~~~~~  134 (293)
                      .+++-.+.+.++...+-++|.|.||||||.-.--.+.+.=.. +.+.++-+--|.|--|..+..+.. .++..+|-.|..
T Consensus       266 Vy~ykdell~av~e~QVLiI~GeTGSGKTTQiPQyL~EaGyt-k~gk~IgcTQPRRVAAmSVAaRVA~EMgvkLG~eVGY  344 (902)
T KOG0923|consen  266 VYPYKDELLKAVKEHQVLIIVGETGSGKTTQIPQYLYEAGYT-KGGKKIGCTQPRRVAAMSVAARVAEEMGVKLGHEVGY  344 (902)
T ss_pred             chhhHHHHHHHHHhCcEEEEEcCCCCCccccccHHHHhcccc-cCCceEeecCcchHHHHHHHHHHHHHhCcccccccce
Confidence            355666777888888999999999999996532222222122 234456677799988888876654 455444433322


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHH---HhhCCCCccEEE
Q 022724          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDV---YRYLPPDLQVVL  211 (293)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i---~~~l~~~~q~v~  211 (293)
                      ...-.+.      -.+..-|=..|.+.|++-+.. ..++.+.++|||||||.=.-  .-+.+..+   +.+.++..++++
T Consensus       345 sIRFEdc------TSekTvlKYMTDGmLlREfL~-epdLasYSViiiDEAHERTL--~TDILfgLvKDIar~RpdLKllI  415 (902)
T KOG0923|consen  345 SIRFEDC------TSEKTVLKYMTDGMLLREFLS-EPDLASYSVIIVDEAHERTL--HTDILFGLVKDIARFRPDLKLLI  415 (902)
T ss_pred             EEEeccc------cCcceeeeeecchhHHHHHhc-cccccceeEEEeehhhhhhh--hhhHHHHHHHHHHhhCCcceEEe
Confidence            1111000      012235667899998884433 45688999999999996210  11112222   233457899999


Q ss_pred             EEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHh---hCCCCcEEEEcccchhHHHH
Q 022724          212 ISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYD---TLTITQAVIFCNTKRKVLLL  288 (293)
Q Consensus       212 ~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~---~~~~~~~iIF~~s~~~a~~l  288 (293)
                      +|||+..+  .+. .++.+...+.++.   ....+.-+|...+..+.-.+.+...++   ..+.+-+|||..-.++.+.+
T Consensus       416 sSAT~DAe--kFS-~fFDdapIF~iPG---RRyPVdi~Yt~~PEAdYldAai~tVlqIH~tqp~GDILVFltGQeEIEt~  489 (902)
T KOG0923|consen  416 SSATMDAE--KFS-AFFDDAPIFRIPG---RRYPVDIFYTKAPEADYLDAAIVTVLQIHLTQPLGDILVFLTGQEEIETV  489 (902)
T ss_pred             eccccCHH--HHH-HhccCCcEEeccC---cccceeeecccCCchhHHHHHHhhheeeEeccCCccEEEEeccHHHHHHH
Confidence            99998643  333 3444433333332   223566677766666633444444443   23557899999888877665


Q ss_pred             Hhh
Q 022724          289 VLQ  291 (293)
Q Consensus       289 ~~~  291 (293)
                      .+.
T Consensus       490 ~e~  492 (902)
T KOG0923|consen  490 KEN  492 (902)
T ss_pred             HHH
Confidence            544

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=98.98  E-value=7.5e-09  Score=98.82  Aligned_cols=64  Identities=27%  Similarity=0.330  Sum_probs=52.0

Q ss_pred             CCCCCcHHHHHHHHhhh----c-----CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHH
Q 022724           52 GFEKPSAIQQRAVMPII----K-----GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE  118 (293)
Q Consensus        52 ~~~~~~~~Q~~~~~~i~----~-----~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~  118 (293)
                      ||. +++-|.+....+.    .     ++.++|.||||+|||++|++|++......  +.++||-++|+.|-+|+.
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     36789999999999999999998765443  457999999999999985

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=98.98  E-value=4.1e-08  Score=89.53  Aligned_cols=218  Identities=15%  Similarity=0.140  Sum_probs=127.2

Q ss_pred             CcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHH-HhhccCCceEEE
Q 022724           56 PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL-AIGDFINIQAHA  134 (293)
Q Consensus        56 ~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~-~~~~~~~~~~~~  134 (293)
                      ....+.+.+..+..++-++|+|.||||||.-..-.+++.=... .| -+-+--|.+.-|..+..+.. .++..+|-.|..
T Consensus       357 vf~~R~~ll~~ir~n~vvvivgETGSGKTTQl~QyL~edGY~~-~G-mIGcTQPRRvAAiSVAkrVa~EM~~~lG~~VGY  434 (1042)
T KOG0924|consen  357 VFACRDQLLSVIRENQVVVIVGETGSGKTTQLAQYLYEDGYAD-NG-MIGCTQPRRVAAISVAKRVAEEMGVTLGDTVGY  434 (1042)
T ss_pred             hHHHHHHHHHHHhhCcEEEEEecCCCCchhhhHHHHHhccccc-CC-eeeecCchHHHHHHHHHHHHHHhCCccccccce
Confidence            4566777777787888999999999999965433333322221 12 34444599999999887775 454444443332


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHH-HHhcCCCCCCCccEEEecchhhhhcc-c-cHHHHHHHHhhCCCCccEEE
Q 022724          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCD-MIKRKTLRTRAIKLLVLDESDEMLSR-G-FKDQIYDVYRYLPPDLQVVL  211 (293)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~-~l~~~~~~~~~l~~iViDE~h~~~~~-~-~~~~~~~i~~~l~~~~q~v~  211 (293)
                      ...-.+..      .....|=..|.+.|++ .|..  -++.+.+.||+||||.=.-+ . ....+..+++.. .+.++|.
T Consensus       435 sIRFEdvT------~~~T~IkymTDGiLLrEsL~d--~~L~kYSviImDEAHERslNtDilfGllk~~larR-rdlKliV  505 (1042)
T KOG0924|consen  435 SIRFEDVT------SEDTKIKYMTDGILLRESLKD--RDLDKYSVIIMDEAHERSLNTDILFGLLKKVLARR-RDLKLIV  505 (1042)
T ss_pred             EEEeeecC------CCceeEEEeccchHHHHHhhh--hhhhheeEEEechhhhcccchHHHHHHHHHHHHhh-ccceEEE
Confidence            22111110      0123577788888877 3332  34678999999999973211 1 112233333333 4789999


Q ss_pred             EEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHhhC---CCCcEEEEcccchhHHHH
Q 022724          212 ISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL---TITQAVIFCNTKRKVLLL  288 (293)
Q Consensus       212 ~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~---~~~~~iIF~~s~~~a~~l  288 (293)
                      +|||+..  ..+...+...|...+..+.    ..+.-++...+.++.-...+.+.+.-+   ..+-.+||....++.+-.
T Consensus       506 tSATm~a--~kf~nfFgn~p~f~IpGRT----yPV~~~~~k~p~eDYVeaavkq~v~Ihl~~~~GdilIfmtGqediE~t  579 (1042)
T KOG0924|consen  506 TSATMDA--QKFSNFFGNCPQFTIPGRT----YPVEIMYTKTPVEDYVEAAVKQAVQIHLSGPPGDILIFMTGQEDIECT  579 (1042)
T ss_pred             eeccccH--HHHHHHhCCCceeeecCCc----cceEEEeccCchHHHHHHHHhhheEeeccCCCCCEEEecCCCcchhHH
Confidence            9999864  3344333334544443321    234555555555553344455554422   346899999888776655


Q ss_pred             Hh
Q 022724          289 VL  290 (293)
Q Consensus       289 ~~  290 (293)
                      +.
T Consensus       580 ~~  581 (1042)
T KOG0924|consen  580 CD  581 (1042)
T ss_pred             HH
Confidence            54

>COG4889 Predicted helicase [General function prediction only]

Probab=98.94  E-value=7.3e-10  Score=103.12  Aligned_cols=149  Identities=20%  Similarity=0.228  Sum_probs=96.8

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCC----cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEc
Q 022724           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGR----DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (293)
Q Consensus        33 ~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~----~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~  108 (293)
                      -.|+.+. +.++..++.-..-.+|+|+|+.|+++...|-    .-=+.+..|+|||+..+- +.+.+..    .++++|+
T Consensus       140 IDW~~f~-p~e~~~nl~l~~~kk~R~hQq~Aid~a~~~F~~n~RGkLIMAcGTGKTfTsLk-isEala~----~~iL~Lv  213 (1518)
T COG4889         140 IDWDIFD-PTELQDNLPLKKPKKPRPHQQTAIDAAKEGFSDNDRGKLIMACGTGKTFTSLK-ISEALAA----ARILFLV  213 (1518)
T ss_pred             CChhhcC-ccccccccccCCCCCCChhHHHHHHHHHhhcccccCCcEEEecCCCccchHHH-HHHHHhh----hheEeec
Confidence            3455542 2466666665566789999999999987541    122334569999987653 3344433    5899999


Q ss_pred             CCHHHHHHHHHHHHHhhccCCceEEEEECCcchHH-----------------------HHHHH--hcCCcEEEeChHHHH
Q 022724          109 PTRELATQTEKVILAIGDFINIQAHACVGGKSVGE-----------------------DIRKL--EHGVHVVSGTPGRVC  163 (293)
Q Consensus       109 P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------------~~~~~--~~~~~ilV~Tp~~l~  163 (293)
                      |+++|..|..+.+..= +...++...+.++....+                       .+...  .++--|+++|.+.+.
T Consensus       214 PSIsLLsQTlrew~~~-~~l~~~a~aVcSD~kvsrs~eDik~sdl~~p~sT~~~~il~~~~~~~k~~~~~vvFsTYQSl~  292 (1518)
T COG4889         214 PSISLLSQTLREWTAQ-KELDFRASAVCSDDKVSRSAEDIKASDLPIPVSTDLEDILSEMEHRQKANGLTVVFSTYQSLP  292 (1518)
T ss_pred             chHHHHHHHHHHHhhc-cCccceeEEEecCccccccccccccccCCCCCcccHHHHHHHHHHhhccCCcEEEEEcccchH
Confidence            9999999999877542 223333333333221111                       11111  123458999999988


Q ss_pred             HHHhcCCCCCCCccEEEecchhhhh
Q 022724          164 DMIKRKTLRTRAIKLLVLDESDEML  188 (293)
Q Consensus       164 ~~l~~~~~~~~~l~~iViDE~h~~~  188 (293)
                      ..-.....-+..+++||.||||+-.
T Consensus       293 ~i~eAQe~G~~~fDliicDEAHRTt  317 (1518)
T COG4889         293 RIKEAQEAGLDEFDLIICDEAHRTT  317 (1518)
T ss_pred             HHHHHHHcCCCCccEEEecchhccc
Confidence            7766656668889999999999964

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=98.94  E-value=7.8e-08  Score=90.35  Aligned_cols=148  Identities=12%  Similarity=0.127  Sum_probs=97.3

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhc
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH  150 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  150 (293)
                      .-.+|.+|.|+|||.+..-++-+.+..  .+.+++++..+++|+.++..+++...- .++..+.-.++....      ..
T Consensus        50 ~V~vVRSpMGTGKTtaLi~wLk~~l~~--~~~~VLvVShRrSL~~sL~~rf~~~~l-~gFv~Y~d~~~~~i~------~~  120 (824)
T PF02399_consen   50 GVLVVRSPMGTGKTTALIRWLKDALKN--PDKSVLVVSHRRSLTKSLAERFKKAGL-SGFVNYLDSDDYIID------GR  120 (824)
T ss_pred             CeEEEECCCCCCcHHHHHHHHHHhccC--CCCeEEEEEhHHHHHHHHHHHHhhcCC-Ccceeeecccccccc------cc
Confidence            457888999999997765544444432  245899999999999999998875421 122222111111111      01


Q ss_pred             CCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcccc-------HHHHHHHHhhCCCCccEEEEEeecChhHHHH
Q 022724          151 GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF-------KDQIYDVYRYLPPDLQVVLISATLPHEILEM  223 (293)
Q Consensus       151 ~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~-------~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~  223 (293)
                      ..+-+++..+.|.+..   ...+.+.++|||||+-..+..-+       ...+..+...+.....+|++-|++++...++
T Consensus       121 ~~~rLivqIdSL~R~~---~~~l~~yDvVIIDEv~svL~qL~S~Tm~~~~~v~~~L~~lI~~ak~VI~~DA~ln~~tvdF  197 (824)
T PF02399_consen  121 PYDRLIVQIDSLHRLD---GSLLDRYDVVIIDEVMSVLNQLFSPTMRQREEVDNLLKELIRNAKTVIVMDADLNDQTVDF  197 (824)
T ss_pred             ccCeEEEEehhhhhcc---cccccccCEEEEehHHHHHHHHhHHHHhhHHHHHHHHHHHHHhCCeEEEecCCCCHHHHHH
Confidence            2356667777776643   22466789999999988764422       2223334445566789999999999999999


Q ss_pred             HHhcCCC
Q 022724          224 TTKFMTD  230 (293)
Q Consensus       224 ~~~~~~~  230 (293)
                      +..+.++
T Consensus       198 l~~~Rp~  204 (824)
T PF02399_consen  198 LASCRPD  204 (824)
T ss_pred             HHHhCCC
Confidence            9887654

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=98.91  E-value=9e-08  Score=90.58  Aligned_cols=130  Identities=15%  Similarity=0.210  Sum_probs=97.9

Q ss_pred             CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q 022724           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (293)
Q Consensus        51 ~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (293)
                      .|. .|++.|--.--.+..|+  +....||-|||+++.+|+.-....   |..+-|++.+..||..=.+.+..+...+|+
T Consensus        75 lG~-r~ydVQliGglvLh~G~--IAEMkTGEGKTLvAtLpayLnAL~---GkgVhVVTvNdYLA~RDae~mg~vy~fLGL  148 (925)
T PRK12903         75 LGK-RPYDVQIIGGIILDLGS--VAEMKTGEGKTITSIAPVYLNALT---GKGVIVSTVNEYLAERDAEEMGKVFNFLGL  148 (925)
T ss_pred             hCC-CcCchHHHHHHHHhcCC--eeeecCCCCccHHHHHHHHHHHhc---CCceEEEecchhhhhhhHHHHHHHHHHhCC
Confidence            354 58888887666666664  789999999999999888654333   345778889999999999999999999999


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHHH-HHHhcCC------CCCCCccEEEecchhhhh
Q 022724          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVC-DMIKRKT------LRTRAIKLLVLDESDEML  188 (293)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~-~~l~~~~------~~~~~l~~iViDE~h~~~  188 (293)
                      ++.....+.+..+.....  .+||.-+|...|- .+|+.+.      ...+.+.+.||||+|.++
T Consensus       149 svG~i~~~~~~~~rr~aY--~~DItYgTn~E~gFDYLRDnm~~~~~~~vqR~~~faIVDEVDSIL  211 (925)
T PRK12903        149 SVGINKANMDPNLKREAY--ACDITYSVHSELGFDYLRDNMVSSKEEKVQRGLNFCLIDEVDSIL  211 (925)
T ss_pred             ceeeeCCCCChHHHHHhc--cCCCeeecCcccchhhhhhcccccHHHhcCcccceeeeccchhee
Confidence            999887776655443433  4799999987663 3555432      224778999999999975

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

Probab=98.82  E-value=3.1e-08  Score=94.75  Aligned_cols=73  Identities=21%  Similarity=0.226  Sum_probs=59.2

Q ss_pred             HHCCCCCCcHHHHHHHHhhh----cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 022724           49 YQYGFEKPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA  123 (293)
Q Consensus        49 ~~~~~~~~~~~Q~~~~~~i~----~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~  123 (293)
                      ..+....|++.|.+.+..+.    +++.+++.||||+|||++|+.|++......+  .+++|.++|+.+-+|+.+....
T Consensus         9 ~~~~~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~~~--~~viist~t~~lq~q~~~~~~~   85 (654)
T COG1199           9 VAFPGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEG--KKVIISTRTKALQEQLLEEDLP   85 (654)
T ss_pred             hhCCCCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHHcC--CcEEEECCCHHHHHHHHHhhcc
Confidence            34455679999999886654    4567999999999999999999998876653  5799999999999998765543

>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=98.81  E-value=3.7e-08  Score=79.23  Aligned_cols=141  Identities=15%  Similarity=0.223  Sum_probs=75.8

Q ss_pred             CCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHH-------HHHHHh--
Q 022724           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE-------KVILAI--  124 (293)
Q Consensus        54 ~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~-------~~~~~~--  124 (293)
                      .-.++.|..++.++.+.+-+++.||.|+|||+.++..+++.+... ...+++|.-|..+..+++-       +.+..+  
T Consensus         3 ~p~~~~Q~~~~~al~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g-~~~kiii~Rp~v~~~~~lGflpG~~~eK~~p~~~   81 (205)
T PF02562_consen    3 KPKNEEQKFALDALLNNDLVIVNGPAGTGKTFLALAAALELVKEG-EYDKIIITRPPVEAGEDLGFLPGDLEEKMEPYLR   81 (205)
T ss_dssp             ---SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTT-S-SEEEEEE-S--TT----SS---------TTTH
T ss_pred             cCCCHHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHHHHhC-CCcEEEEEecCCCCccccccCCCCHHHHHHHHHH
Confidence            345889999999999888999999999999999998888888773 3447888888776422221       111100  


Q ss_pred             --hccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhh
Q 022724          125 --GDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRY  202 (293)
Q Consensus       125 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~  202 (293)
                        .+.+..-    .+.    ...+.+.....|-+..+    .+++...++   -++||+|||+.+    -...+..++.+
T Consensus        82 p~~d~l~~~----~~~----~~~~~~~~~~~Ie~~~~----~~iRGrt~~---~~~iIvDEaQN~----t~~~~k~ilTR  142 (205)
T PF02562_consen   82 PIYDALEEL----FGK----EKLEELIQNGKIEIEPL----AFIRGRTFD---NAFIIVDEAQNL----TPEELKMILTR  142 (205)
T ss_dssp             HHHHHHTTT----S-T----TCHHHHHHTTSEEEEEG----GGGTT--B----SEEEEE-SGGG------HHHHHHHHTT
T ss_pred             HHHHHHHHH----hCh----HhHHHHhhcCeEEEEeh----hhhcCcccc---ceEEEEecccCC----CHHHHHHHHcc
Confidence              0000000    011    11122222334544444    333433332   289999999876    35678899999


Q ss_pred             CCCCccEEEEEe
Q 022724          203 LPPDLQVVLISA  214 (293)
Q Consensus       203 l~~~~q~v~~SA  214 (293)
                      +..++++|++--
T Consensus       143 ~g~~skii~~GD  154 (205)
T PF02562_consen  143 IGEGSKIIITGD  154 (205)
T ss_dssp             B-TT-EEEEEE-
T ss_pred             cCCCcEEEEecC
Confidence            998899887743

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

>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]

Probab=98.79  E-value=1.3e-07  Score=87.29  Aligned_cols=152  Identities=17%  Similarity=0.191  Sum_probs=101.1

Q ss_pred             CCcHHHHHHHHhhh----cCCcEEEEcCCCChhHHHH--HHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccC
Q 022724           55 KPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMI--ALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI  128 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~----~~~~~li~~~Tg~GKT~~~--~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~  128 (293)
                      .++++|.+-++-+.    .|-|.|+.-..|-|||+-.  ++.-+...... .| .-+|+||...| ..+.+.++++.+  
T Consensus       167 ~lr~YQveGlnWLi~l~engingILaDEMGLGKTlQtIs~l~yl~~~~~~-~G-PfLVi~P~StL-~NW~~Ef~rf~P--  241 (971)
T KOG0385|consen  167 ELRDYQLEGLNWLISLYENGINGILADEMGLGKTLQTISLLGYLKGRKGI-PG-PFLVIAPKSTL-DNWMNEFKRFTP--  241 (971)
T ss_pred             ccchhhhccHHHHHHHHhcCcccEeehhcccchHHHHHHHHHHHHHhcCC-CC-CeEEEeeHhhH-HHHHHHHHHhCC--
Confidence            58899999887654    5779999999999999542  22223332222 23 47999997776 456666777765  


Q ss_pred             CceEEEEECCcchHHHHHH-H--hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCC
Q 022724          129 NIQAHACVGGKSVGEDIRK-L--EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP  205 (293)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~-~--~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~  205 (293)
                      ++++..++|+......... +  ..+.+|+|+|.+....-  ...+.--...++||||+|++-.  ....+..+++.+..
T Consensus       242 ~l~~~~~~Gdk~eR~~~~r~~~~~~~fdV~iTsYEi~i~d--k~~lk~~~W~ylvIDEaHRiKN--~~s~L~~~lr~f~~  317 (971)
T KOG0385|consen  242 SLNVVVYHGDKEERAALRRDIMLPGRFDVCITSYEIAIKD--KSFLKKFNWRYLVIDEAHRIKN--EKSKLSKILREFKT  317 (971)
T ss_pred             CcceEEEeCCHHHHHHHHHHhhccCCCceEeehHHHHHhh--HHHHhcCCceEEEechhhhhcc--hhhHHHHHHHHhcc
Confidence            5688888888754443322 2  24679999999887753  1222334568999999999843  34455566777764


Q ss_pred             CccEEEEEeec
Q 022724          206 DLQVVLISATL  216 (293)
Q Consensus       206 ~~q~v~~SAt~  216 (293)
                      ..+ +++|.|+
T Consensus       318 ~nr-LLlTGTP  327 (971)
T KOG0385|consen  318 DNR-LLLTGTP  327 (971)
T ss_pred             cce-eEeeCCc
Confidence            444 4556664

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

Probab=98.73  E-value=6.5e-08  Score=80.14  Aligned_cols=67  Identities=19%  Similarity=0.345  Sum_probs=50.2

Q ss_pred             CcHHHHHHHHhhhcCCc-EEEEcCCCChhHHHHHHHHHhhh------ccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 022724           56 PSAIQQRAVMPIIKGRD-VIAQAQSGTGKTSMIALTVCQTV------DTSSREVQALILSPTRELATQTEKVILA  123 (293)
Q Consensus        56 ~~~~Q~~~~~~i~~~~~-~li~~~Tg~GKT~~~~~~~~~~l------~~~~~~~~~lil~P~~~l~~q~~~~~~~  123 (293)
                      +++.|.+|+..+++... .+|.||.|+|||.... .++..+      .....+.++++++|+..-++.+.+.+.+
T Consensus         2 ln~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~l~-~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen    2 LNESQREAIQSALSSNGITLIQGPPGTGKTTTLA-SIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             --HHHHHHHHHHCTSSE-EEEE-STTSSHHHHHH-HHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHcCCCCEEEECCCCCChHHHHH-HHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            67899999999999888 9999999999995433 333333      1234466899999999999999998877

>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

Probab=98.73  E-value=1.5e-07  Score=92.58  Aligned_cols=137  Identities=15%  Similarity=0.160  Sum_probs=93.1

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhc
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH  150 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  150 (293)
                      +..+|.--+|||||+.....+-..+.. ..-+.++||+-+++|-.|+.+.+..+........    ...+..+..+.+.+
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            468999999999998866555333333 5567999999999999999999998875443211    33444444444543


Q ss_pred             C-CcEEEeChHHHHHHHhcC-CCCC-CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEeec
Q 022724          151 G-VHVVSGTPGRVCDMIKRK-TLRT-RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATL  216 (293)
Q Consensus       151 ~-~~ilV~Tp~~l~~~l~~~-~~~~-~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~  216 (293)
                      + -.|+|||.++|...+... .... .+==.||+||||+-   .++..-..+...+ ++...++||+|+
T Consensus       349 ~~~~ii~TTIQKf~~~~~~~~~~~~~~~~ivvI~DEaHRS---Q~G~~~~~~~~~~-~~a~~~gFTGTP  413 (962)
T COG0610         349 GKGKIIVTTIQKFNKAVKEDELELLKRKNVVVIIDEAHRS---QYGELAKLLKKAL-KKAIFIGFTGTP  413 (962)
T ss_pred             CCCcEEEEEecccchhhhcccccccCCCcEEEEEechhhc---cccHHHHHHHHHh-ccceEEEeeCCc
Confidence            3 389999999999877654 1112 22235899999984   2333333334444 358899999997

>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional

Probab=98.72  E-value=3e-07  Score=88.71  Aligned_cols=143  Identities=17%  Similarity=0.263  Sum_probs=86.2

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHH-----H-hhc---cCCceEEEEECCc--
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL-----A-IGD---FINIQAHACVGGK--  139 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~-----~-~~~---~~~~~~~~~~~~~--  139 (293)
                      .++.+.++||+|||.+|+-.+++.....+ ..+.||+||+.++-+.+...+.     . +..   ...+....+.++.  
T Consensus        60 ~n~~~~M~TGtGKT~~~~~~i~~l~~~~~-~~~fii~vp~~aI~egv~~~l~s~~~k~hF~~~y~~~~~~~~~~~S~k~~  138 (986)
T PRK15483         60 ANIDIKMETGTGKTYVYTRLMYELHQKYG-LFKFIIVVPTPAIKEGTRNFIQSDYAKQHFSQFYENTRIELYVINAGDKK  138 (986)
T ss_pred             ceEEEEeCCCCCHHHHHHHHHHHHHHHcC-CcEEEEEeCCHHHHHHHHHHhhHHHHHHHHHHHcCCceeEEEEEecCccc
Confidence            48999999999999999888766554433 3589999999999888876664     1 111   1123444444332  


Q ss_pred             -----chHHHHHHHh-------cCCcEEEeChHHHHHHHh-cCC----------CCCCC----ccEEEecchhhhhcccc
Q 022724          140 -----SVGEDIRKLE-------HGVHVVSGTPGRVCDMIK-RKT----------LRTRA----IKLLVLDESDEMLSRGF  192 (293)
Q Consensus       140 -----~~~~~~~~~~-------~~~~ilV~Tp~~l~~~l~-~~~----------~~~~~----l~~iViDE~h~~~~~~~  192 (293)
                           +....++..-       +..+|+|.|.+.+..-.. +..          ..+..    =-.+|+||.|++...  
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       146899999988865211 110          01111    135999999998432  


Q ss_pred             HHHHHHHHhhCCCCccEEEEEeecCh
Q 022724          193 KDQIYDVYRYLPPDLQVVLISATLPH  218 (293)
Q Consensus       193 ~~~~~~i~~~l~~~~q~v~~SAt~~~  218 (293)
                      ......+ ..+++-+ ++.+|||++.
T Consensus       217 ~k~~~~i-~~lnpl~-~lrysAT~~~  240 (986)
T PRK15483        217 NKFYQAI-EALKPQM-IIRFGATFPD  240 (986)
T ss_pred             hHHHHHH-HhcCccc-EEEEeeecCC
Confidence            2223333 4454333 5669999986

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

Probab=98.65  E-value=2.9e-07  Score=74.35  Aligned_cols=123  Identities=20%  Similarity=0.272  Sum_probs=72.6

Q ss_pred             CCcHHHHHHHHhhhcC--CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceE
Q 022724           55 KPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQA  132 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~--~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  132 (293)
                      ++++-|.+++..++.+  +-.++.||.|+|||.. +-.+...+...  +.++++++||...+..+.+..       +...
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            3688999999998643  3577889999999964 33344445443  468999999999888877742       1111


Q ss_pred             EEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcC----CCCCCCccEEEecchhhhhccccHHHHHHHHhhCCC-Cc
Q 022724          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK----TLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP-DL  207 (293)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~----~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~-~~  207 (293)
                                              .|-.+++......    ...+...++|||||+-++.    ...+..++..... ..
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                                    2222222211111    1114566899999999874    3456666666665 56


Q ss_pred             cEEEEEee
Q 022724          208 QVVLISAT  215 (293)
Q Consensus       208 q~v~~SAt  215 (293)
                      ++|++-=+
T Consensus       123 klilvGD~  130 (196)
T PF13604_consen  123 KLILVGDP  130 (196)
T ss_dssp             EEEEEE-T
T ss_pred             EEEEECCc
Confidence            77766443

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=98.63  E-value=2e-07  Score=88.54  Aligned_cols=130  Identities=18%  Similarity=0.241  Sum_probs=97.5

Q ss_pred             CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q 022724           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (293)
Q Consensus        51 ~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (293)
                      .|. .|++.|--.--.+  .+.-+..+.||-|||+++.+|+.-....   |..+-|++++..||..=.+.+..+...+|+
T Consensus        82 lG~-r~ydVQliGgl~L--h~G~IAEM~TGEGKTL~atlpaylnAL~---GkgVhVVTvNdYLA~RDae~m~~vy~~LGL  155 (939)
T PRK12902         82 LGM-RHFDVQLIGGMVL--HEGQIAEMKTGEGKTLVATLPSYLNALT---GKGVHVVTVNDYLARRDAEWMGQVHRFLGL  155 (939)
T ss_pred             hCC-CcchhHHHhhhhh--cCCceeeecCCCChhHHHHHHHHHHhhc---CCCeEEEeCCHHHHHhHHHHHHHHHHHhCC
Confidence            354 3777776644444  4556889999999999999988765444   446899999999999999999999999999


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhc------CCCCCCCccEEEecchhhhh
Q 022724          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKR------KTLRTRAIKLLVLDESDEML  188 (293)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l-~~~l~~------~~~~~~~l~~iViDE~h~~~  188 (293)
                      .+....++.+..+....  -.+||+.+|+..+ .++|+.      .....+.+.+.||||+|.++
T Consensus       156 tvg~i~~~~~~~err~a--Y~~DItYgTn~e~gFDYLRDnm~~~~~~~vqR~~~faIVDEvDSIL  218 (939)
T PRK12902        156 SVGLIQQDMSPEERKKN--YACDITYATNSELGFDYLRDNMATDISEVVQRPFNYCVIDEVDSIL  218 (939)
T ss_pred             eEEEECCCCChHHHHHh--cCCCeEEecCCcccccchhhhhcccccccccCccceEEEeccccee
Confidence            99988776655443333  3579999999877 223332      22345778999999999975

>KOG0389 consensus SNF2 family DNA-dependent ATPase [Chromatin structure and dynamics]

Probab=98.62  E-value=2.7e-07  Score=85.51  Aligned_cols=162  Identities=14%  Similarity=0.163  Sum_probs=102.4

Q ss_pred             CcHHHHHHHHhhh----cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCce
Q 022724           56 PSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ  131 (293)
Q Consensus        56 ~~~~Q~~~~~~i~----~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  131 (293)
                      +-++|.--++.+.    ++-+.|+.-..|-|||. -.++.+..+...+....-+|+||...| +.+.+.+.+|+.  .++
T Consensus       400 LkdYQlvGvNWL~Llyk~~l~gILADEMGLGKTi-QvIaFlayLkq~g~~gpHLVVvPsSTl-eNWlrEf~kwCP--sl~  475 (941)
T KOG0389|consen  400 LKDYQLVGVNWLLLLYKKKLNGILADEMGLGKTI-QVIAFLAYLKQIGNPGPHLVVVPSSTL-ENWLREFAKWCP--SLK  475 (941)
T ss_pred             ccchhhhhHHHHHHHHHccccceehhhccCcchh-HHHHHHHHHHHcCCCCCcEEEecchhH-HHHHHHHHHhCC--ceE
Confidence            7889998877643    45688999999999993 233333434333323357999998775 456666777765  468


Q ss_pred             EEEEECCcchHHHHHHHh----cCCcEEEeChHHHHHHHh-cCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCC
Q 022724          132 AHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIK-RKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPD  206 (293)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~----~~~~ilV~Tp~~l~~~l~-~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~  206 (293)
                      +..++|.......++...    .+.+|+|+|...+..--. +..+.-.++.++|+||.|++-+.. ...+..+.+-  +.
T Consensus       476 Ve~YyGSq~ER~~lR~~i~~~~~~ydVllTTY~la~~~kdDRsflk~~~~n~viyDEgHmLKN~~-SeRy~~LM~I--~A  552 (941)
T KOG0389|consen  476 VEPYYGSQDERRELRERIKKNKDDYDVLLTTYNLAASSKDDRSFLKNQKFNYVIYDEGHMLKNRT-SERYKHLMSI--NA  552 (941)
T ss_pred             EEeccCcHHHHHHHHHHHhccCCCccEEEEEeecccCChHHHHHHHhccccEEEecchhhhhccc-hHHHHHhccc--cc
Confidence            888899887777666542    367999999865542111 112234677899999999885442 2223322222  24


Q ss_pred             ccEEEEEeec-ChhHHHHH
Q 022724          207 LQVVLISATL-PHEILEMT  224 (293)
Q Consensus       207 ~q~v~~SAt~-~~~~~~~~  224 (293)
                      .+.+++|.|+ -+.+.+++
T Consensus       553 n~RlLLTGTPLQNNL~ELi  571 (941)
T KOG0389|consen  553 NFRLLLTGTPLQNNLKELI  571 (941)
T ss_pred             cceEEeeCCcccccHHHHH
Confidence            4566777775 55555543

>KOG4150 consensus Predicted ATP-dependent RNA helicase [RNA processing and modification]

Probab=98.62  E-value=4.5e-07  Score=81.42  Aligned_cols=240  Identities=11%  Similarity=0.020  Sum_probs=152.4

Q ss_pred             HHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcc
Q 022724           48 IYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDF  127 (293)
Q Consensus        48 l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (293)
                      ++.+.-+....+|.+++..+.+|++.++...|.+||.++|.++....+...+. ...++..|++++++...+-+.-....
T Consensus       279 ~~~~~~E~~~~~~~~~~~~~~~G~~~~~~~~~~~GK~~~~~~~s~~~~~~~~~-s~~~~~~~~~~~~~~~~~~~~V~~~~  357 (1034)
T KOG4150|consen  279 LNKNTGESGIAISLELLKFASEGRADGGNEARQAGKGTCPTSGSRKFQTLCHA-TNSLLPSEMVEHLRNGSKGQVVHVEV  357 (1034)
T ss_pred             HhcccccchhhhhHHHHhhhhhcccccccchhhcCCccCcccchhhhhhcCcc-cceecchhHHHHhhccCCceEEEEEe
Confidence            34455567899999999999999999999999999999999988877766544 36789999999988765533211111


Q ss_pred             C---CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCC----CCCCccEEEecchhhhhcc--c-cHHHHH
Q 022724          128 I---NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL----RTRAIKLLVLDESDEMLSR--G-FKDQIY  197 (293)
Q Consensus       128 ~---~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~----~~~~l~~iViDE~h~~~~~--~-~~~~~~  197 (293)
                      .   .--++..+++.+.......+..+.+++.+.|+......--+..    .+-+..+.++||+|.....  . ...+++
T Consensus       358 I~~~K~A~V~~~D~~sE~~~~A~~R~~~~~~~s~~~~~~s~~L~~~~~~~~~~~~~~~~~~~~~~~Y~~~~~~~~~~~~R  437 (1034)
T KOG4150|consen  358 IKARKSAYVEMSDKLSETTKSALKRIGLNTLYSHQAEAISAALAKSLCYNVPVFEELCKDTNSCALYLFPTKALAQDQLR  437 (1034)
T ss_pred             hhhhhcceeecccCCCchhHHHHHhcCcceeecCHHHHHHHHhhhccccccHHHHHHHhcccceeeeecchhhHHHHHHH
Confidence            0   1122333444444444444456778999999888774432222    1234567899999986432  1 122333


Q ss_pred             HHHhhC-----CCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcc--------cHHHHHH
Q 022724          198 DVYRYL-----PPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREE--------WKFDTLC  264 (293)
Q Consensus       198 ~i~~~l-----~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~--------~k~~~l~  264 (293)
                      ++.+.+     +.+.|++-.+||+.+.+.-.......+-..+...  +..+.+-.+++.+-+...        .+.....
T Consensus       438 ~L~~L~~~F~~~~~~~~~~~~~~~K~~~~~~~~~~~~~E~~Li~~--DGSPs~~K~~V~WNP~~~P~~~~~~~~~i~E~s  515 (1034)
T KOG4150|consen  438 ALSDLIKGFEASINMGVYDGDTPYKDRTRLRSELANLSELELVTI--DGSPSSEKLFVLWNPSAPPTSKSEKSSKVVEVS  515 (1034)
T ss_pred             HHHHHHHHHHhhcCcceEeCCCCcCCHHHHHHHhcCCcceEEEEe--cCCCCccceEEEeCCCCCCcchhhhhhHHHHHH
Confidence            333332     2478999999999877665554443343433332  344555567777665422        1333334


Q ss_pred             HHHhhC--CCCcEEEEcccchhHHHHHh
Q 022724          265 DLYDTL--TITQAVIFCNTKRKVLLLVL  290 (293)
Q Consensus       265 ~l~~~~--~~~~~iIF~~s~~~a~~l~~  290 (293)
                      .++.+.  .+-++|-||.+++-|+.+..
T Consensus       516 ~~~~~~i~~~~R~IAFC~~R~~CEL~~~  543 (1034)
T KOG4150|consen  516 HLFAEMVQHGLRCIAFCPSRKLCELVLC  543 (1034)
T ss_pred             HHHHHHHHcCCcEEEeccHHHHHHHHHH
Confidence            444332  34599999999999987654

>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]

Probab=98.58  E-value=9e-07  Score=82.23  Aligned_cols=158  Identities=16%  Similarity=0.111  Sum_probs=100.1

Q ss_pred             CCcHHHHHHHHhhh----cCCcEEEEcCCCChhH---HHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcc
Q 022724           55 KPSAIQQRAVMPII----KGRDVIAQAQSGTGKT---SMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDF  127 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~----~~~~~li~~~Tg~GKT---~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (293)
                      .+.++|++.+.-+.    ++..-|+--..|-|||   .+|+-++.+.-   .-...+||+|| ..+..|+.+.+..+...
T Consensus       205 ~Lf~yQreGV~WL~~L~~q~~GGILgDeMGLGKTIQiisFLaaL~~S~---k~~~paLIVCP-~Tii~qW~~E~~~w~p~  280 (923)
T KOG0387|consen  205 KLFPYQREGVQWLWELYCQRAGGILGDEMGLGKTIQIISFLAALHHSG---KLTKPALIVCP-ATIIHQWMKEFQTWWPP  280 (923)
T ss_pred             HhhHHHHHHHHHHHHHHhccCCCeecccccCccchhHHHHHHHHhhcc---cccCceEEEcc-HHHHHHHHHHHHHhCcc
Confidence            57889999887654    5667888889999999   33443333321   12247999999 56678999989888654


Q ss_pred             CCceEEEEECCcch--------HHHHHH-----HhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHH
Q 022724          128 INIQAHACVGGKSV--------GEDIRK-----LEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKD  194 (293)
Q Consensus       128 ~~~~~~~~~~~~~~--------~~~~~~-----~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~  194 (293)
                        +++..+++..+.        ......     ...+..|+++|.+.+--.  ...+.-...+++|+||.|.+-..  -.
T Consensus       281 --~rv~ilh~t~s~~r~~~~~~~~~~~~~L~r~~~~~~~ilitty~~~r~~--~d~l~~~~W~y~ILDEGH~IrNp--ns  354 (923)
T KOG0387|consen  281 --FRVFILHGTGSGARYDASHSSHKKDKLLIRKVATDGGILITTYDGFRIQ--GDDLLGILWDYVILDEGHRIRNP--NS  354 (923)
T ss_pred             --eEEEEEecCCcccccccchhhhhhhhhheeeecccCcEEEEehhhhccc--CcccccccccEEEecCcccccCC--cc
Confidence              567777766542        111111     113457999998655421  12333456799999999998433  34


Q ss_pred             HHHHHHhhCCCCccEEEEEeec-ChhHHHH
Q 022724          195 QIYDVYRYLPPDLQVVLISATL-PHEILEM  223 (293)
Q Consensus       195 ~~~~i~~~l~~~~q~v~~SAt~-~~~~~~~  223 (293)
                      .+...+..++. .+.|++|.|+ -+.+.++
T Consensus       355 ~islackki~T-~~RiILSGTPiQNnL~EL  383 (923)
T KOG0387|consen  355 KISLACKKIRT-VHRIILSGTPIQNNLTEL  383 (923)
T ss_pred             HHHHHHHhccc-cceEEeeCccccchHHHH
Confidence            45556666654 4455566665 4444443

>PRK10536 hypothetical protein; Provisional

Probab=98.55  E-value=2.7e-06  Score=70.52  Aligned_cols=142  Identities=13%  Similarity=0.145  Sum_probs=85.5

Q ss_pred             CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHH-----------HHH
Q 022724           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQ-----------TEK  119 (293)
Q Consensus        51 ~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q-----------~~~  119 (293)
                      .++.-.+..|...+..+.++..+++.||+|+|||+.....+++.+.... -.++++.=|..+..+.           +.-
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 SPILARNEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKAAEALIHKD-VDRIIVTRPVLQADEDLGFLPGDIAEKFAP  133 (262)
T ss_pred             ccccCCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHhcCC-eeEEEEeCCCCCchhhhCcCCCCHHHHHHH
Confidence            3555568899999999998889999999999999887777776664432 3355555576543222           222


Q ss_pred             HHHHhhccCCceEEEEECCcchHHHHHHH-h-cCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHH
Q 022724          120 VILAIGDFINIQAHACVGGKSVGEDIRKL-E-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIY  197 (293)
Q Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~-~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~  197 (293)
                      .+..+.+.+...    .+.    ...+.+ . ..-.|-|...    .+++...++   -++||+||++.+.    ..++.
T Consensus       134 ~~~pi~D~L~~~----~~~----~~~~~~~~~~~~~Iei~~l----~ymRGrtl~---~~~vIvDEaqn~~----~~~~k  194 (262)
T PRK10536        134 YFRPVYDVLVRR----LGA----SFMQYCLRPEIGKVEIAPF----AYMRGRTFE---NAVVILDEAQNVT----AAQMK  194 (262)
T ss_pred             HHHHHHHHHHHH----hCh----HHHHHHHHhccCcEEEecH----HHhcCCccc---CCEEEEechhcCC----HHHHH
Confidence            222222221110    111    111211 1 1113333333    344544442   2899999999873    46788


Q ss_pred             HHHhhCCCCccEEEE
Q 022724          198 DVYRYLPPDLQVVLI  212 (293)
Q Consensus       198 ~i~~~l~~~~q~v~~  212 (293)
                      .++.+++.+.++|+.
T Consensus       195 ~~ltR~g~~sk~v~~  209 (262)
T PRK10536        195 MFLTRLGENVTVIVN  209 (262)
T ss_pred             HHHhhcCCCCEEEEe
Confidence            889999988888865

>KOG0390 consensus DNA repair protein, SNF2 family [Replication, recombination and repair]

Probab=98.54  E-value=2.6e-06  Score=80.45  Aligned_cols=164  Identities=16%  Similarity=0.096  Sum_probs=106.8

Q ss_pred             CCcHHHHHHHHhhhc---CC-------cEEEEcCCCChhHHHHHHHHHhhhccCCC----ceeEEEEcCCHHHHHHHHHH
Q 022724           55 KPSAIQQRAVMPIIK---GR-------DVIAQAQSGTGKTSMIALTVCQTVDTSSR----EVQALILSPTRELATQTEKV  120 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~---~~-------~~li~~~Tg~GKT~~~~~~~~~~l~~~~~----~~~~lil~P~~~l~~q~~~~  120 (293)
                      ..+|+|++.|.-+.+   |.       ..++.-..|+|||+-...-+...+...+.    -.++||++| ..|+..+.+.
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            589999999987653   21       34555668999997655444444444332    147999999 6788999999


Q ss_pred             HHHhhccCCceEEEEECCcch--HHHHHHHh-----cCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccH
Q 022724          121 ILAIGDFINIQAHACVGGKSV--GEDIRKLE-----HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFK  193 (293)
Q Consensus       121 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~-----~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~  193 (293)
                      +.+|.....+....+++....  ......+.     -...|++-+.+.+.+..+.  +....++++|+||.|..  ..-.
T Consensus       317 F~KWl~~~~i~~l~~~~~~~~~w~~~~sil~~~~~~~~~~vli~sye~~~~~~~~--il~~~~glLVcDEGHrl--kN~~  392 (776)
T KOG0390|consen  317 FGKWLGNHRINPLDFYSTKKSSWIKLKSILFLGYKQFTTPVLIISYETASDYCRK--ILLIRPGLLVCDEGHRL--KNSD  392 (776)
T ss_pred             HHHhccccccceeeeecccchhhhhhHHHHHhhhhheeEEEEeccHHHHHHHHHH--HhcCCCCeEEECCCCCc--cchh
Confidence            999887666777777777653  11111111     1124677788887654443  33567899999999987  3334


Q ss_pred             HHHHHHHhhCCCCccEEEEEeec-ChhHHHHH
Q 022724          194 DQIYDVYRYLPPDLQVVLISATL-PHEILEMT  224 (293)
Q Consensus       194 ~~~~~i~~~l~~~~q~v~~SAt~-~~~~~~~~  224 (293)
                      ..+...+..+. -.+.|++|.|+ -+++.++.
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            55666666665 45566778886 45555543

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=98.44  E-value=4.2e-06  Score=78.27  Aligned_cols=141  Identities=18%  Similarity=0.216  Sum_probs=85.6

Q ss_pred             cHHHHHHHHhhhcCCcEEEEcCCCChhHHHHH--HHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q 022724           57 SAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIA--LTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (293)
Q Consensus        57 ~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~--~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (293)
                      .++|+.++...+.++-.+|.|+.|+|||....  +..+........+.++++.+||-.-+..+.+.+......+...   
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            37999999999999999999999999996532  2223222222123579999999988888888765533222110   


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc------CCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCcc
Q 022724          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR------KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ  208 (293)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~------~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q  208 (293)
                             ....    ....+-..|-.+++.....      .......+++|||||+-++.    ...+..+++.++...+
T Consensus       224 -------~~~~----~~~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIiDEaSMvd----~~l~~~ll~al~~~~r  288 (586)
T TIGR01447       224 -------EALI----AALPSEAVTIHRLLGIKPDTKRFRHHERNPLPLDVLVVDEASMVD----LPLMAKLLKALPPNTK  288 (586)
T ss_pred             -------hhhh----hccccccchhhhhhcccCCcchhhhcccCCCcccEEEEcccccCC----HHHHHHHHHhcCCCCE
Confidence                   0000    0011112333333322110      11123457999999998763    3456677788888888


Q ss_pred             EEEEEee
Q 022724          209 VVLISAT  215 (293)
Q Consensus       209 ~v~~SAt  215 (293)
                      +|++-=.
T Consensus       289 lIlvGD~  295 (586)
T TIGR01447       289 LILLGDK  295 (586)
T ss_pred             EEEECCh
Confidence            8877543

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.

>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=98.40  E-value=3.9e-05  Score=68.66  Aligned_cols=192  Identities=17%  Similarity=0.190  Sum_probs=114.4

Q ss_pred             CceeEEEEcCCHHHHHHHHHHHHHhhcc-C------------Cce------EEEEECCcchHHHHHHHh-----------
Q 022724          100 REVQALILSPTRELATQTEKVILAIGDF-I------------NIQ------AHACVGGKSVGEDIRKLE-----------  149 (293)
Q Consensus       100 ~~~~~lil~P~~~l~~q~~~~~~~~~~~-~------------~~~------~~~~~~~~~~~~~~~~~~-----------  149 (293)
                      ..|++|||+|+|..|-++.+.+.++... .            ++.      ...-........+.+.+.           
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            4589999999999999998888766543 1            100      000000001111122221           


Q ss_pred             --------------cCCcEEEeChHHHHHHHhc------CCCCCCCccEEEecchhhhhccccHHHHHHHHhhCC---C-
Q 022724          150 --------------HGVHVVSGTPGRVCDMIKR------KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP---P-  205 (293)
Q Consensus       150 --------------~~~~ilV~Tp~~l~~~l~~------~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~---~-  205 (293)
                                    ..+||||++|=-|-..+..      ....++.++++|+|.+|.++-. ..+++..++..++   + 
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                          1368999999888877763      2233689999999999998533 2344455555443   1 


Q ss_pred             --------------------CccEEEEEeecChhHHHHHHhcCCCCEE-EEe--cCC-----cccCCCceEEEEEecCcc
Q 022724          206 --------------------DLQVVLISATLPHEILEMTTKFMTDPVK-ILV--KRD-----ELTLEGIKQFFVAVEREE  257 (293)
Q Consensus       206 --------------------~~q~v~~SAt~~~~~~~~~~~~~~~~~~-~~~--~~~-----~~~~~~i~~~~~~~~~~~  257 (293)
                                          -+|.|++|+..++++..+......+... +.+  ...     .....++.|.+...+...
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                                2699999999999999988875554322 221  111     123456777777655432


Q ss_pred             ------cHHHH-----HHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          258 ------WKFDT-----LCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       258 ------~k~~~-----l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                            ...+.     +-.+.+....+.+|||++|--+=..+.++|
T Consensus       275 ~~~~~d~Rf~yF~~~iLP~l~~~~~~~~~LIfIPSYfDfVRlRN~l  320 (442)
T PF06862_consen  275 PADDPDARFKYFTKKILPQLKRDSKMSGTLIFIPSYFDFVRLRNYL  320 (442)
T ss_pred             cchhhhHHHHHHHHHHHHHhhhccCCCcEEEEecchhhhHHHHHHH
Confidence                  12222     222222334569999999976655555443

; GO: 0005634 nucleus

>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1

Probab=98.40  E-value=4.1e-06  Score=70.69  Aligned_cols=173  Identities=21%  Similarity=0.172  Sum_probs=109.7

Q ss_pred             cCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhh----------cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEE
Q 022724           37 AMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII----------KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALI  106 (293)
Q Consensus        37 ~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~----------~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~li  106 (293)
                      .+.|++.+.+    .|  .++..|-+++-...          ++..+++-=.||.||.-...-.|++.+....  .++|+
T Consensus        25 ~~~lp~~~~~----~g--~LS~~QLEaV~yA~q~h~~~Lp~~~R~Gf~lGDGtGvGKGR~iAgiI~~n~l~Gr--~r~vw   96 (303)
T PF13872_consen   25 RLHLPEEVID----SG--LLSALQLEAVIYACQRHEQILPGGSRAGFFLGDGTGVGKGRQIAGIILENWLRGR--KRAVW   96 (303)
T ss_pred             ccCCCHHHHh----cc--cccHHHHHHHHHHHHHHHhhcccccCcEEEeccCCCcCccchhHHHHHHHHHcCC--CceEE
Confidence            3356655443    22  46788887775433          2356788888999999776667777777653  37999


Q ss_pred             EcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcC---CCC---------CC
Q 022724          107 LSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK---TLR---------TR  174 (293)
Q Consensus       107 l~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~---~~~---------~~  174 (293)
                      +..+..|-.+..+.++.++.. .+.+..+..-...    ....-...|+++|...|...-..+   ...         -.
T Consensus        97 vS~s~dL~~Da~RDl~DIG~~-~i~v~~l~~~~~~----~~~~~~~GvlF~TYs~L~~~~~~~~~~~sRl~ql~~W~g~d  171 (303)
T PF13872_consen   97 VSVSNDLKYDAERDLRDIGAD-NIPVHPLNKFKYG----DIIRLKEGVLFSTYSTLISESQSGGKYRSRLDQLVDWCGED  171 (303)
T ss_pred             EECChhhhhHHHHHHHHhCCC-cccceechhhccC----cCCCCCCCccchhHHHHHhHHhccCCccchHHHHHHHHhcC
Confidence            999999999999999988754 3333332221000    001113469999998887654221   111         12


Q ss_pred             CccEEEecchhhhhcccc--------HHHHHHHHhhCCCCccEEEEEeecChhHHHH
Q 022724          175 AIKLLVLDESDEMLSRGF--------KDQIYDVYRYLPPDLQVVLISATLPHEILEM  223 (293)
Q Consensus       175 ~l~~iViDE~h~~~~~~~--------~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~  223 (293)
                      .=.+||+||+|.+-...-        +.....+...+ ++.+++++|||--.+.+++
T Consensus       172 fdgvivfDEcH~akn~~~~~~~~sk~g~avl~LQ~~L-P~ARvvY~SATgasep~Nm  227 (303)
T PF13872_consen  172 FDGVIVFDECHKAKNLSSGSKKPSKTGIAVLELQNRL-PNARVVYASATGASEPRNM  227 (303)
T ss_pred             CCceEEeccchhcCCCCccCccccHHHHHHHHHHHhC-CCCcEEEecccccCCCcee
Confidence            236899999999854321        23444555666 4678999999976554444

>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=98.35  E-value=1.3e-05  Score=65.31  Aligned_cols=128  Identities=20%  Similarity=0.282  Sum_probs=85.4

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhc---CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcC
Q 022724           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIK---GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (293)
Q Consensus        33 ~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~---~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P  109 (293)
                      .+|+....|.+++=.+.. ++. .++.|.++...+.+   |+|.+...-+|.|||.+.+ |++..+..++. .-+.+++|
T Consensus         3 ~~w~p~~~P~wLl~E~e~-~il-iR~~Q~~ia~~mi~~~~~~n~v~QlnMGeGKTsVI~-Pmla~~LAdg~-~LvrviVp   78 (229)
T PF12340_consen    3 RNWDPMEYPDWLLFEIES-NIL-IRPVQVEIAREMISPPSGKNSVMQLNMGEGKTSVIV-PMLALALADGS-RLVRVIVP   78 (229)
T ss_pred             CCCCchhChHHHHHHHHc-Cce-eeHHHHHHHHHHhCCCCCCCeEeeecccCCccchHH-HHHHHHHcCCC-cEEEEEcC
Confidence            357777777777766653 444 89999999888774   6899999999999997654 66655555433 24556666


Q ss_pred             CHHHHHHHHHHHHH-hhccCCceEEEEECC--cchH----HHHHH----HhcCCcEEEeChHHHHHH
Q 022724          110 TRELATQTEKVILA-IGDFINIQAHACVGG--KSVG----EDIRK----LEHGVHVVSGTPGRVCDM  165 (293)
Q Consensus       110 ~~~l~~q~~~~~~~-~~~~~~~~~~~~~~~--~~~~----~~~~~----~~~~~~ilV~Tp~~l~~~  165 (293)
                       ++|..|+...++. ++.-.+-++..+.-+  ....    ..+..    ....-.|+++||+.+.++
T Consensus        79 -k~Ll~q~~~~L~~~lg~l~~r~i~~lpFsR~~~~~~~~~~~~~~l~~~~~~~~gill~~PEhilSf  144 (229)
T PF12340_consen   79 -KALLEQMRQMLRSRLGGLLNRRIYHLPFSRSTPLTPETLEKIRQLLEECMRSGGILLATPEHILSF  144 (229)
T ss_pred             -HHHHHHHHHHHHHHHHHHhCCeeEEecccCCCCCCHHHHHHHHHHHHHHHHcCCEEEeChHHHHHH
Confidence             7799999988874 555556566554433  2221    11111    122347999999999763

There are two conserved sequence motifs: LLE and NMG.

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=98.34  E-value=7.8e-06  Score=76.75  Aligned_cols=140  Identities=16%  Similarity=0.210  Sum_probs=85.4

Q ss_pred             cHHHHHHHHhhhcCCcEEEEcCCCChhHHHHH--HHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q 022724           57 SAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIA--LTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (293)
Q Consensus        57 ~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~--~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (293)
                      .++|+.|+-....++-.+|.|++|+|||....  +..+..... ....++.+.+||..-+..+.+.+.......+..   
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            58999999999999999999999999996532  222222211 123578888999998999888776533322210   


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc------CCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCcc
Q 022724          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR------KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ  208 (293)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~------~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q  208 (293)
                              ....   .....-..|-.+++.....      +....-..+++||||+-++-    ...+..+++.+++..+
T Consensus       230 --------~~~~---~~~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIvDEaSMvd----~~lm~~ll~al~~~~r  294 (615)
T PRK10875        230 --------DEQK---KRIPEEASTLHRLLGAQPGSQRLRYHAGNPLHLDVLVVDEASMVD----LPMMARLIDALPPHAR  294 (615)
T ss_pred             --------hhhh---hcCCCchHHHHHHhCcCCCccchhhccccCCCCCeEEEChHhccc----HHHHHHHHHhcccCCE
Confidence                    0000   0001112233333221111      11122346899999998762    4456677788888888


Q ss_pred             EEEEEee
Q 022724          209 VVLISAT  215 (293)
Q Consensus       209 ~v~~SAt  215 (293)
                      +|++-=.
T Consensus       295 lIlvGD~  301 (615)
T PRK10875        295 VIFLGDR  301 (615)
T ss_pred             EEEecch
Confidence            8887544

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=98.32  E-value=2.7e-06  Score=81.92  Aligned_cols=74  Identities=19%  Similarity=0.183  Sum_probs=62.4

Q ss_pred             CCCCCcHHHHHHHHhhh----cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhh
Q 022724           52 GFEKPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIG  125 (293)
Q Consensus        52 ~~~~~~~~Q~~~~~~i~----~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  125 (293)
                      -|..++|.|.+....+.    .|++.++.+|||+|||++.+.+++......+...+++|.+.|..-..|+.+.++++.
T Consensus         7 Py~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~~~~kIiy~sRThsQl~q~i~Elk~~~   84 (705)
T TIGR00604         7 PYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKPEVRKIIYASRTHSQLEQATEELRKLM   84 (705)
T ss_pred             CCCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhccccccEEEEcccchHHHHHHHHHHhhh
Confidence            45666999998776644    688999999999999999999999887655545699999999999999999998853

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).

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=98.30  E-value=1.6e-05  Score=76.42  Aligned_cols=126  Identities=22%  Similarity=0.235  Sum_probs=78.9

Q ss_pred             CCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEE
Q 022724           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAH  133 (293)
Q Consensus        54 ~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~  133 (293)
                      ..+++.|++|+..+..++-+++.|+.|+|||... -.++..+........+++++||-.-+..+.+..       +... 
T Consensus       322 ~~l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~l-~~i~~~~~~~~~~~~v~l~ApTg~AA~~L~e~~-------g~~a-  392 (720)
T TIGR01448       322 KGLSEEQKQALDTAIQHKVVILTGGPGTGKTTIT-RAIIELAEELGGLLPVGLAAPTGRAAKRLGEVT-------GLTA-  392 (720)
T ss_pred             CCCCHHHHHHHHHHHhCCeEEEECCCCCCHHHHH-HHHHHHHHHcCCCceEEEEeCchHHHHHHHHhc-------CCcc-
Confidence            3589999999999998899999999999999543 234444433321246888899988777554421       2111 


Q ss_pred             EEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc-----CCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCcc
Q 022724          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-----KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ  208 (293)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~-----~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q  208 (293)
                                             .|-.+++.....     ..-.....++|||||++++..    ..+..+++.++...+
T Consensus       393 -----------------------~Tih~lL~~~~~~~~~~~~~~~~~~~llIvDEaSMvd~----~~~~~Ll~~~~~~~r  445 (720)
T TIGR01448       393 -----------------------STIHRLLGYGPDTFRHNHLEDPIDCDLLIVDESSMMDT----WLALSLLAALPDHAR  445 (720)
T ss_pred             -----------------------ccHHHHhhccCCccchhhhhccccCCEEEEeccccCCH----HHHHHHHHhCCCCCE
Confidence                                   111111111000     001124568999999998742    345666777777788


Q ss_pred             EEEEEee
Q 022724          209 VVLISAT  215 (293)
Q Consensus       209 ~v~~SAt  215 (293)
                      +|++-=.
T Consensus       446 lilvGD~  452 (720)
T TIGR01448       446 LLLVGDT  452 (720)
T ss_pred             EEEECcc
Confidence            8876543

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.

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=98.29  E-value=6.1e-06  Score=72.97  Aligned_cols=108  Identities=13%  Similarity=0.206  Sum_probs=68.0

Q ss_pred             cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcC
Q 022724           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG  151 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (293)
                      -++|.|..|||||+..+ -++..+.....+.++++++++.+|...+...+..-...                      ..
T Consensus         3 v~~I~G~aGTGKTvla~-~l~~~l~~~~~~~~~~~l~~n~~l~~~l~~~l~~~~~~----------------------~~   59 (352)
T PF09848_consen    3 VILITGGAGTGKTVLAL-NLAKELQNSEEGKKVLYLCGNHPLRNKLREQLAKKYNP----------------------KL   59 (352)
T ss_pred             EEEEEecCCcCHHHHHH-HHHHHhhccccCCceEEEEecchHHHHHHHHHhhhccc----------------------ch
Confidence            47889999999996654 33344422334568999999999999888877543200                      00


Q ss_pred             CcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccc-------cHHHHHHHHhh
Q 022724          152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG-------FKDQIYDVYRY  202 (293)
Q Consensus       152 ~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~-------~~~~~~~i~~~  202 (293)
                      ....+..+..+..............++|||||||.+.+.+       ....+..+++.
T Consensus        60 ~~~~~~~~~~~i~~~~~~~~~~~~~DviivDEAqrl~~~~~~~~~~~~~~~L~~i~~~  117 (352)
T PF09848_consen   60 KKSDFRKPTSFINNYSESDKEKNKYDVIIVDEAQRLRTKGDQYNNFSEPNQLDEIIKR  117 (352)
T ss_pred             hhhhhhhhHHHHhhcccccccCCcCCEEEEehhHhhhhccccccccccHHHHHHHHhc
Confidence            1223344444444333223446788999999999997631       23556666665

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>KOG0392 consensus SNF2 family DNA-dependent ATPase domain-containing protein [Transcription]

Probab=98.27  E-value=6e-06  Score=80.15  Aligned_cols=168  Identities=18%  Similarity=0.200  Sum_probs=108.6

Q ss_pred             CCcHHHHHHHHhhh--c--CCcEEEEcCCCChhHHHHHHHHHhhhccC-C-----CceeEEEEcCCHHHHHHHHHHHHHh
Q 022724           55 KPSAIQQRAVMPII--K--GRDVIAQAQSGTGKTSMIALTVCQTVDTS-S-----REVQALILSPTRELATQTEKVILAI  124 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~--~--~~~~li~~~Tg~GKT~~~~~~~~~~l~~~-~-----~~~~~lil~P~~~l~~q~~~~~~~~  124 (293)
                      .++.+|++-++.+.  +  +-+-|+|-..|-|||+-.+-.+....... .     ...-++|+|| ..|+-.+...+.++
T Consensus       975 ~LRkYQqEGVnWLaFLnky~LHGILcDDMGLGKTLQticilAsd~y~r~s~~~e~~~~PSLIVCP-sTLtGHW~~E~~kf 1053 (1549)
T KOG0392|consen  975 KLRKYQQEGVNWLAFLNKYKLHGILCDDMGLGKTLQTICILASDHYKRRSESSEFNRLPSLIVCP-STLTGHWKSEVKKF 1053 (1549)
T ss_pred             HHHHHHHhccHHHHHHHHhcccceeeccccccHHHHHHHHHHHHHHhhcccchhhccCCeEEECC-chhhhHHHHHHHHh
Confidence            46889999887643  2  45899999999999976543333222221 0     1223899999 57889999999998


Q ss_pred             hccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCC
Q 022724          125 GDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP  204 (293)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~  204 (293)
                      ...  +++..+.|+.......+.-.++.+|+|++.+.+-+-+..  +.-....|.|+||-|-+- + -...+....+.+.
T Consensus      1054 ~pf--L~v~~yvg~p~~r~~lR~q~~~~~iiVtSYDv~RnD~d~--l~~~~wNYcVLDEGHVik-N-~ktkl~kavkqL~ 1127 (1549)
T KOG0392|consen 1054 FPF--LKVLQYVGPPAERRELRDQYKNANIIVTSYDVVRNDVDY--LIKIDWNYCVLDEGHVIK-N-SKTKLTKAVKQLR 1127 (1549)
T ss_pred             cch--hhhhhhcCChHHHHHHHhhccccceEEeeHHHHHHHHHH--HHhcccceEEecCcceec-c-hHHHHHHHHHHHh
Confidence            876  667777777666655555556679999999877542211  112345799999999873 2 2444555556665


Q ss_pred             CCccEEEEEeec-ChhHHH---HHHhcCCC
Q 022724          205 PDLQVVLISATL-PHEILE---MTTKFMTD  230 (293)
Q Consensus       205 ~~~q~v~~SAt~-~~~~~~---~~~~~~~~  230 (293)
                      .+.++ .+|.|+ .+.+.+   +...+|+.
T Consensus      1128 a~hRL-ILSGTPIQNnvleLWSLFdFLMPG 1156 (1549)
T KOG0392|consen 1128 ANHRL-ILSGTPIQNNVLELWSLFDFLMPG 1156 (1549)
T ss_pred             hcceE-EeeCCCcccCHHHHHHHHHHhccc
Confidence            44444 466665 444443   44455543

>PF13245 AAA_19: Part of AAA domain

Probab=98.19  E-value=8.7e-06  Score=54.89  Aligned_cols=51  Identities=25%  Similarity=0.429  Sum_probs=38.4

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhc--cCCCceeEEEEcCCHHHHHHHHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVD--TSSREVQALILSPTRELATQTEKVI  121 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~--~~~~~~~~lil~P~~~l~~q~~~~~  121 (293)
                      +.-++|.||.|+|||...+-.+...+.  ... +.++++++|++..++++.+.+
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            344666999999999665555555542  233 568999999999999999877

>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]

Probab=98.19  E-value=6.8e-06  Score=79.80  Aligned_cols=159  Identities=16%  Similarity=0.222  Sum_probs=101.5

Q ss_pred             CCCcHHHHHHHHhhh----cCCcEEEEcCCCChhH---HHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhc
Q 022724           54 EKPSAIQQRAVMPII----KGRDVIAQAQSGTGKT---SMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGD  126 (293)
Q Consensus        54 ~~~~~~Q~~~~~~i~----~~~~~li~~~Tg~GKT---~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~  126 (293)
                      ..++.+|-+-++-++    +++|.|+.-..|-|||   .+|+-.+++.....  || .|+++|...+ ..+.+.+..+. 
T Consensus       369 ~~LRdyQLeGlNWl~~~W~~~~n~ILADEmgLgktvqti~fl~~l~~~~~~~--gp-flvvvplst~-~~W~~ef~~w~-  443 (1373)
T KOG0384|consen  369 NELRDYQLEGLNWLLYSWYKRNNCILADEMGLGKTVQTITFLSYLFHSLQIH--GP-FLVVVPLSTI-TAWEREFETWT-  443 (1373)
T ss_pred             chhhhhhcccchhHHHHHHhcccceehhhcCCCcchHHHHHHHHHHHhhhcc--CC-eEEEeehhhh-HHHHHHHHHHh-
Confidence            578999999887654    6889999999999999   34554555544332  33 6888896654 33445555554 


Q ss_pred             cCCceEEEEECCcchHHHHHHHh----c-----CCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHH
Q 022724          127 FINIQAHACVGGKSVGEDIRKLE----H-----GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIY  197 (293)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~----~-----~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~  197 (293)
                        ..+++.++|+....+.++...    .     ..+++++|.+.++.-  ...+.--...+++|||||.+-..  ...+.
T Consensus       444 --~mn~i~y~g~~~sr~~i~~ye~~~~~~~~~lkf~~lltTye~~LkD--k~~L~~i~w~~~~vDeahrLkN~--~~~l~  517 (1373)
T KOG0384|consen  444 --DMNVIVYHGNLESRQLIRQYEFYHSSNTKKLKFNALLTTYEIVLKD--KAELSKIPWRYLLVDEAHRLKND--ESKLY  517 (1373)
T ss_pred             --hhceeeeecchhHHHHHHHHHheecCCccccccceeehhhHHHhcc--HhhhccCCcceeeecHHhhcCch--HHHHH
Confidence              678888888876666555442    2     368999999877641  11222234578999999998422  22333


Q ss_pred             HHHhhCCCCccEEEEEee-cChhHHHHH
Q 022724          198 DVYRYLPPDLQVVLISAT-LPHEILEMT  224 (293)
Q Consensus       198 ~i~~~l~~~~q~v~~SAt-~~~~~~~~~  224 (293)
                      ..+..+..+.+++ +|.| +-+.++++.
T Consensus       518 ~~l~~f~~~~rll-itgTPlQNsikEL~  544 (1373)
T KOG0384|consen  518 ESLNQFKMNHRLL-ITGTPLQNSLKELW  544 (1373)
T ss_pred             HHHHHhcccceee-ecCCCccccHHHHH
Confidence            3344454444554 5555 456666544

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

Probab=98.19  E-value=1.3e-05  Score=73.48  Aligned_cols=76  Identities=22%  Similarity=0.186  Sum_probs=61.6

Q ss_pred             HHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 022724           47 GIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (293)
Q Consensus        47 ~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (293)
                      .+...++..++..|..|+.+++++.-.+|+||.|+|||....-.+++.... . +..+++.+|+..-++|+.+.+.+.
T Consensus       402 ~~s~~~lpkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa~IVyhl~~~-~-~~~VLvcApSNiAVDqLaeKIh~t  477 (935)
T KOG1802|consen  402 RFSVPNLPKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSATIVYHLARQ-H-AGPVLVCAPSNIAVDQLAEKIHKT  477 (935)
T ss_pred             hhcCCCchhhchHHHHHHHHHHcCCceeeecCCCCCceehhHHHHHHHHHh-c-CCceEEEcccchhHHHHHHHHHhc
Confidence            344457788999999999999999999999999999997765444444443 3 447999999999999999988654

>TIGR00376 DNA helicase, putative

Probab=98.18  E-value=2.3e-05  Score=74.26  Aligned_cols=66  Identities=18%  Similarity=0.212  Sum_probs=52.0

Q ss_pred             CCcHHHHHHHHhhhcC-CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 022724           55 KPSAIQQRAVMPIIKG-RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA  123 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~-~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~  123 (293)
                      .+++.|..++...... ..++|.||+|+|||....-.+.+.+..   +.++++++||..-+.++.+.+..
T Consensus       157 ~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~~~ii~~~~~~---g~~VLv~a~sn~Avd~l~e~l~~  223 (637)
T TIGR00376       157 NLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTLVELIRQLVKR---GLRVLVTAPSNIAVDNLLERLAL  223 (637)
T ss_pred             CCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHHHHHHHHHHHc---CCCEEEEcCcHHHHHHHHHHHHh
Confidence            5689999999998865 678999999999996544333333332   45899999999999999988865

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.

>KOG1000 consensus Chromatin remodeling protein HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure and dynamics]

Probab=98.18  E-value=1.3e-05  Score=71.06  Aligned_cols=152  Identities=16%  Similarity=0.146  Sum_probs=95.0

Q ss_pred             CCCCcHHHHHHHHh-hhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCce
Q 022724           53 FEKPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ  131 (293)
Q Consensus        53 ~~~~~~~Q~~~~~~-i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  131 (293)
                      +..+.|+|.+-+.. +.+|..+++.-..|-|||.-++-.+ .....   ..-.+|+||.. +-..+.+.++.+.....- 
T Consensus       196 vs~LlPFQreGv~faL~RgGR~llADeMGLGKTiQAlaIA-~yyra---EwplliVcPAs-vrftWa~al~r~lps~~p-  269 (689)
T KOG1000|consen  196 VSRLLPFQREGVIFALERGGRILLADEMGLGKTIQALAIA-RYYRA---EWPLLIVCPAS-VRFTWAKALNRFLPSIHP-  269 (689)
T ss_pred             HHhhCchhhhhHHHHHhcCCeEEEecccccchHHHHHHHH-HHHhh---cCcEEEEecHH-HhHHHHHHHHHhcccccc-
Confidence            34578899998876 5578889999999999997655332 22222   22479999943 334566666666554322 


Q ss_pred             EEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEE
Q 022724          132 AHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVL  211 (293)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~  211 (293)
                      +....++.+....   +.....|.|.+.+.+..+-.  .+.-....++|+||.|++-+ +-......+...+..-.++|+
T Consensus       270 i~vv~~~~D~~~~---~~t~~~v~ivSye~ls~l~~--~l~~~~~~vvI~DEsH~Lk~-sktkr~Ka~~dllk~akhvIL  343 (689)
T KOG1000|consen  270 IFVVDKSSDPLPD---VCTSNTVAIVSYEQLSLLHD--ILKKEKYRVVIFDESHMLKD-SKTKRTKAATDLLKVAKHVIL  343 (689)
T ss_pred             eEEEecccCCccc---cccCCeEEEEEHHHHHHHHH--HHhcccceEEEEechhhhhc-cchhhhhhhhhHHHHhhheEE
Confidence            4444444332211   11234678888876654321  12234478999999998743 334446666666666678999


Q ss_pred             EEeec
Q 022724          212 ISATL  216 (293)
Q Consensus       212 ~SAt~  216 (293)
                      +|.|+
T Consensus       344 LSGTP  348 (689)
T KOG1000|consen  344 LSGTP  348 (689)
T ss_pred             ecCCc
Confidence            99996

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]

Probab=98.15  E-value=3e-05  Score=68.89  Aligned_cols=151  Identities=20%  Similarity=0.184  Sum_probs=95.3

Q ss_pred             CCcHHHHHHHHhhhcCC-----cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCC
Q 022724           55 KPSAIQQRAVMPIIKGR-----DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~-----~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (293)
                      .+-|+|.+.+..+.+..     .-++.-..|+|||.-....++..+    .+...++++|+.+| .|+.+.+..... -.
T Consensus       184 ~LL~fQkE~l~Wl~~QE~Ss~~GGiLADEMGMGKTIQtIaLllae~----~ra~tLVvaP~VAl-mQW~nEI~~~T~-gs  257 (791)
T KOG1002|consen  184 PLLPFQKEGLAWLTSQEESSVAGGILADEMGMGKTIQTIALLLAEV----DRAPTLVVAPTVAL-MQWKNEIERHTS-GS  257 (791)
T ss_pred             cchhhhHHHHHHHHHhhhhhhccceehhhhccchHHHHHHHHHhcc----ccCCeeEEccHHHH-HHHHHHHHHhcc-Cc
Confidence            46789999877655432     356667799999966544444433    33458999999996 688888887765 45


Q ss_pred             ceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCC-------------CCCCcc--EEEecchhhhhccccHH
Q 022724          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL-------------RTRAIK--LLVLDESDEMLSRGFKD  194 (293)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~-------------~~~~l~--~iViDE~h~~~~~~~~~  194 (293)
                      +++..++|.. .....+.+. +.|++.+|...+.+..+....             .+.+++  -||+||||.+-+.  ..
T Consensus       258 lkv~~YhG~~-R~~nikel~-~YDvVLTty~vvEs~yRk~~~GfrrKngv~ke~SlLHsi~~~RiIlDEAH~IK~R--~s  333 (791)
T KOG1002|consen  258 LKVYIYHGAK-RDKNIKELM-NYDVVLTTYAVVESVYRKQDYGFRRKNGVDKEKSLLHSIKFYRIILDEAHNIKDR--QS  333 (791)
T ss_pred             eEEEEEeccc-ccCCHHHhh-cCcEEEEecHHHHHHHHhccccccccCCcccccchhhhceeeeeehhhhcccccc--cc
Confidence            7777777653 223334443 479999999888776554211             123344  3999999998543  22


Q ss_pred             HHHHHHhhCCCCccEEEEEeec
Q 022724          195 QIYDVYRYLPPDLQVVLISATL  216 (293)
Q Consensus       195 ~~~~i~~~l~~~~q~v~~SAt~  216 (293)
                      ...+..-.+. ......+|.|+
T Consensus       334 nTArAV~~L~-tt~rw~LSGTP  354 (791)
T KOG1002|consen  334 NTARAVFALE-TTYRWCLSGTP  354 (791)
T ss_pred             cHHHHHHhhH-hhhhhhccCCc
Confidence            2222222221 33456777775

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=98.09  E-value=3.8e-05  Score=66.09  Aligned_cols=144  Identities=15%  Similarity=0.182  Sum_probs=91.3

Q ss_pred             HCCCCCCcHHHHHHHHhhhcCC--cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHH-------HH
Q 022724           50 QYGFEKPSAIQQRAVMPIIKGR--DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE-------KV  120 (293)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~i~~~~--~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~-------~~  120 (293)
                      -+|+.--+..|..|+..++...  -+.+.|+.|+|||+-++.+.+++....+...++|+.=|+..+-+++-       +.
T Consensus       223 vwGi~prn~eQ~~ALdlLld~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~~y~KiiVtRp~vpvG~dIGfLPG~eEeK  302 (436)
T COG1875         223 VWGIRPRNAEQRVALDLLLDDDIDLVSLGGKAGTGKTLLALAAGLEQVLERKRYRKIIVTRPTVPVGEDIGFLPGTEEEK  302 (436)
T ss_pred             hhccCcccHHHHHHHHHhcCCCCCeEEeeccCCccHhHHHHHHHHHHHHHHhhhceEEEecCCcCcccccCcCCCchhhh
Confidence            3577777888999999998763  57788999999999988888888777666667788778877654431       11


Q ss_pred             HHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCC----------ccEEEecchhhhhcc
Q 022724          121 ILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRA----------IKLLVLDESDEMLSR  190 (293)
Q Consensus       121 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~----------l~~iViDE~h~~~~~  190 (293)
                      +..|.+..             .+-.+.+.+..+   ++.+.+...+....+.+..          =.|+|||||+.+   
T Consensus       303 m~PWmq~i-------------~DnLE~L~~~~~---~~~~~l~~~l~~~~iev~alt~IRGRSl~~~FiIIDEaQNL---  363 (436)
T COG1875         303 MGPWMQAI-------------FDNLEVLFSPNE---PGDRALEEILSRGRIEVEALTYIRGRSLPDSFIIIDEAQNL---  363 (436)
T ss_pred             ccchHHHH-------------HhHHHHHhcccc---cchHHHHHHHhccceeeeeeeeecccccccceEEEehhhcc---
Confidence            11111000             000111110000   1233444444443333221          268999999977   


Q ss_pred             ccHHHHHHHHhhCCCCccEEEEE
Q 022724          191 GFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       191 ~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                       -..++..++.+..+..++|++.
T Consensus       364 -TpheikTiltR~G~GsKIVl~g  385 (436)
T COG1875         364 -TPHELKTILTRAGEGSKIVLTG  385 (436)
T ss_pred             -CHHHHHHHHHhccCCCEEEEcC
Confidence             3678999999999999998763

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=98.05  E-value=0.00011  Score=71.05  Aligned_cols=121  Identities=19%  Similarity=0.175  Sum_probs=74.4

Q ss_pred             CCcHHHHHHHHhhhc-CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEE
Q 022724           55 KPSAIQQRAVMPIIK-GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAH  133 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~-~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~  133 (293)
                      .+++-|++++..+.. ++-+++.|+.|+|||... -++...+...  +.++++++||--.+..+.+       ..++.. 
T Consensus       352 ~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtll-~~i~~~~~~~--g~~V~~~ApTg~Aa~~L~~-------~~g~~a-  420 (744)
T TIGR02768       352 RLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTML-KAAREAWEAA--GYRVIGAALSGKAAEGLQA-------ESGIES-  420 (744)
T ss_pred             CCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHHH-HHHHHHHHhC--CCeEEEEeCcHHHHHHHHh-------ccCCce-
Confidence            489999999999886 467899999999999542 2333444332  5689999999876666553       122211 


Q ss_pred             EEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhC-CCCccEEEE
Q 022724          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL-PPDLQVVLI  212 (293)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l-~~~~q~v~~  212 (293)
                                             .|-.++..-...+...+...++|||||+-++....    +..+++.. ....++|++
T Consensus       421 -----------------------~Ti~~~~~~~~~~~~~~~~~~llIvDEasMv~~~~----~~~Ll~~~~~~~~kliLV  473 (744)
T TIGR02768       421 -----------------------RTLASLEYAWANGRDLLSDKDVLVIDEAGMVGSRQ----MARVLKEAEEAGAKVVLV  473 (744)
T ss_pred             -----------------------eeHHHHHhhhccCcccCCCCcEEEEECcccCCHHH----HHHHHHHHHhcCCEEEEE
Confidence                                   12222211112223335678999999998874333    33344422 245667666


Q ss_pred             E
Q 022724          213 S  213 (293)
Q Consensus       213 S  213 (293)
                      -
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.

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=98.04  E-value=1.7e-05  Score=74.65  Aligned_cols=145  Identities=14%  Similarity=0.123  Sum_probs=78.3

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcc-----C-CceEEEEECCcchHHH
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDF-----I-NIQAHACVGGKSVGED  144 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~-----~-~~~~~~~~~~~~~~~~  144 (293)
                      -|+=|.+.||+|||.+|+-.+++--.. -.-.+-||+||+.+.-..+.-..+.....     . +.+.-.+.-+......
T Consensus        75 lNiDI~METGTGKTy~YlrtmfeLhk~-YG~~KFIivVPs~AIkeGv~~~s~~~~ehF~k~~Yent~~e~~i~~~~~~~~  153 (985)
T COG3587          75 LNIDILMETGTGKTYTYLRTMFELHKK-YGLFKFIIVVPSLAIKEGVFLTSKETTEHFFKSEYENTRLESYIYDEDIEKF  153 (985)
T ss_pred             ceeeEEEecCCCceeeHHHHHHHHHHH-hCceeEEEEeccHHHHhhhHHHHHHHHHHHhhhhccCcceeEEeechHHHHH
Confidence            478899999999999998766543222 22357899999998877754433322111     1 2222222221111111


Q ss_pred             HHHHhcCCcEEEeChHHHHH------HHhcCCCCCCC---------------ccEEEecchhhhhcc-ccHHHHHHHHhh
Q 022724          145 IRKLEHGVHVVSGTPGRVCD------MIKRKTLRTRA---------------IKLLVLDESDEMLSR-GFKDQIYDVYRY  202 (293)
Q Consensus       145 ~~~~~~~~~ilV~Tp~~l~~------~l~~~~~~~~~---------------l~~iViDE~h~~~~~-~~~~~~~~i~~~  202 (293)
                      .-...+.+.+++.|...+..      ++.+......+               =-.+||||-|.|... .....+..+   
T Consensus       154 ~~~~~~~~~vLl~~~~Afnk~~inan~iN~~s~~~~~~~~~~~spvd~la~~rPIvIvDEPh~f~~~~k~~~~i~~l---  230 (985)
T COG3587         154 KFKSNNKPCVLLIFVSAFNKEEINANMINSESMENTNLFNGATSPVDALASMRPIVIVDEPHRFLGDDKTYGAIKQL---  230 (985)
T ss_pred             hhccCCCceEEEEehhhhccccccccccchhhhcccCccccccCHHHHHHhcCCEEEecChhhcccchHHHHHHHhh---
Confidence            12223566777777655532      22221111111               135999999999753 222222222   


Q ss_pred             CCCCccEEEEEeecChhHH
Q 022724          203 LPPDLQVVLISATLPHEIL  221 (293)
Q Consensus       203 l~~~~q~v~~SAt~~~~~~  221 (293)
                      .  ..-++=++||+++...
T Consensus       231 ~--pl~ilRfgATfkd~y~  247 (985)
T COG3587         231 N--PLLILRFGATFKDEYN  247 (985)
T ss_pred             C--ceEEEEecccchhhhc
Confidence            1  2336678999876544

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=98.04  E-value=0.00011  Score=72.32  Aligned_cols=123  Identities=20%  Similarity=0.122  Sum_probs=76.2

Q ss_pred             CCcHHHHHHHHhhhcCC-cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEE
Q 022724           55 KPSAIQQRAVMPIIKGR-DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAH  133 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~-~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~  133 (293)
                      .+++-|.+++..++.++ -+++.|+.|+|||.. +-++...+...  |.+++.++||-.-+..+.+       ..|+.. 
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-LGVAREAWEAA--GYEVRGAALSGIAAENLEG-------GSGIAS-  414 (988)
T ss_pred             CCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHH-HHHHHHHHHHc--CCeEEEecCcHHHHHHHhh-------ccCcch-
Confidence            48999999999998865 578999999999965 33344444332  5689999999876655543       122211 


Q ss_pred             EEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhC-CCCccEEEE
Q 022724          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL-PPDLQVVLI  212 (293)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l-~~~~q~v~~  212 (293)
                                             .|..++..-...+...+...++|||||+-++...    .+..+++.. ....++|++
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                                   1222222211122334566789999999977433    344444433 346677766


Q ss_pred             Eee
Q 022724          213 SAT  215 (293)
Q Consensus       213 SAt  215 (293)
                      -=+
T Consensus       468 GD~  470 (988)
T PRK13889        468 GDP  470 (988)
T ss_pred             CCH
Confidence            543

>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=98.03  E-value=1.7e-05  Score=73.10  Aligned_cols=132  Identities=17%  Similarity=0.128  Sum_probs=85.3

Q ss_pred             CCcHHHHHHHHhhhc-----CCcEEEEcCCCChhHHHHHHHHHhhhc-----cC--CCceeEEEEcCCHHHHHHHHHHHH
Q 022724           55 KPSAIQQRAVMPIIK-----GRDVIAQAQSGTGKTSMIALTVCQTVD-----TS--SREVQALILSPTRELATQTEKVIL  122 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~-----~~~~li~~~Tg~GKT~~~~~~~~~~l~-----~~--~~~~~~lil~P~~~l~~q~~~~~~  122 (293)
                      .+-|+|..++..+.-     +..-|+.-..|-|||+...-.+++.-.     ..  ......+|+|| ..|..|+...+.
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            467899988877652     245788888999999865544443321     10  11125899999 567888888887


Q ss_pred             HhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHH----HHhc--CCCCCCC--ccEEEecchhhhh
Q 022724          123 AIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCD----MIKR--KTLRTRA--IKLLVLDESDEML  188 (293)
Q Consensus       123 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~----~l~~--~~~~~~~--l~~iViDE~h~~~  188 (293)
                      .-.....++|+.+||....+-..+.+ ..+||+|+|..-+..    -+..  ....+.+  ...||+||||.+-
T Consensus       404 ~rl~~n~LsV~~~HG~n~r~i~~~~L-~~YDvViTTY~lva~~~~~e~~~~~~~spL~~I~W~RVILDEAH~Ir  476 (901)
T KOG4439|consen  404 RRLEQNALSVYLYHGPNKREISAKEL-RKYDVVITTYNLVANKPDDELEEGKNSSPLARIAWSRVILDEAHNIR  476 (901)
T ss_pred             HHHhhcceEEEEecCCccccCCHHHH-hhcceEEEeeeccccCCchhhhcccCccHHHHhhHHHhhhhhhhhhc
Confidence            65556678999988887533233333 457999999865554    1111  1111222  3569999999984

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=97.96  E-value=1.5e-05  Score=76.88  Aligned_cols=127  Identities=17%  Similarity=0.214  Sum_probs=91.6

Q ss_pred             CCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q 022724           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (293)
                      .|+++|--.=-.+  .+.-+....||-|||+++.+|++-.....   .-+=+++.+..||..=.+.+..+...+|++|.+
T Consensus       138 ~~ydVQLiGgivL--h~G~IAEM~TGEGKTLvatlp~yLnAL~G---~gVHvVTvNDYLA~RDaewm~p~y~flGLtVg~  212 (1025)
T PRK12900        138 VPYDVQLIGGIVL--HSGKISEMATGEGKTLVSTLPTFLNALTG---RGVHVVTVNDYLAQRDKEWMNPVFEFHGLSVGV  212 (1025)
T ss_pred             cccchHHhhhHHh--hcCCccccCCCCCcchHhHHHHHHHHHcC---CCcEEEeechHhhhhhHHHHHHHHHHhCCeeee
Confidence            3666665533333  34457899999999999999986655553   346778888999999999999999999999998


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcC------CCCCCCccEEEecchhhhh
Q 022724          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRK------TLRTRAIKLLVLDESDEML  188 (293)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l-~~~l~~~------~~~~~~l~~iViDE~h~~~  188 (293)
                      ...+.+.......  -.|||.-||...| .++|+.+      ....+.+.|.||||+|.++
T Consensus       213 i~~~~~~~~Rr~a--Y~~DItYgTn~EfGFDYLRDnma~~~~~~vqR~~~faIVDEvDSvL  271 (1025)
T PRK12900        213 ILNTMRPEERREQ--YLCDITYGTNNEFGFDYLRDNMAGTPEEMVQRDFYFAIVDEVDSVL  271 (1025)
T ss_pred             eCCCCCHHHHHHh--CCCcceecCCCccccccchhccccchhhhhccCCceEEEechhhhh
Confidence            8766555443333  3479999998666 2344432      1224778999999999975

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

Probab=97.95  E-value=2.9e-05  Score=70.63  Aligned_cols=64  Identities=22%  Similarity=0.293  Sum_probs=52.4

Q ss_pred             CCcHHHHHHHHhhhcCC-cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHH
Q 022724           55 KPSAIQQRAVMPIIKGR-DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVI  121 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~-~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~  121 (293)
                      .+.+-|..|+......+ -.++.||+|+|||......+.+.+..   +.++++.+||..-++.+.+++
T Consensus       185 ~ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvEiI~qlvk~---~k~VLVcaPSn~AVdNiverl  249 (649)
T KOG1803|consen  185 NLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVKQ---KKRVLVCAPSNVAVDNIVERL  249 (649)
T ss_pred             cccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHHHHHHHHHc---CCeEEEEcCchHHHHHHHHHh
Confidence            57889999999887764 57888999999998766666666655   358999999999999988864

>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]

Probab=97.93  E-value=8.5e-05  Score=72.18  Aligned_cols=158  Identities=16%  Similarity=0.207  Sum_probs=100.0

Q ss_pred             CCcHHHHHHHHhhh----cCCcEEEEcCCCChhHHHHHHHHHhhh--ccCCCceeEEEEcCCHHHHHHHHHHHHHhhccC
Q 022724           55 KPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTV--DTSSREVQALILSPTRELATQTEKVILAIGDFI  128 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~----~~~~~li~~~Tg~GKT~~~~~~~~~~l--~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~  128 (293)
                      .++.||..-++.+.    ++-|-|+.-..|-|||.- .+.++.++  .....|+ -+|++||--+. .+.=.+++|..  
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            47789998877654    345889999999999943 33344443  2334454 58888876543 34445677754  


Q ss_pred             CceEEEEECCcchHHHHH-HHh--cCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCC
Q 022724          129 NIQAHACVGGKSVGEDIR-KLE--HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP  205 (293)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~-~~~--~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~  205 (293)
                      ++++..++|........+ .|.  +..+|.|++...+.+-+.  .|.-.+..|+|+||+|.+-.+. ...+..++...  
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            678888898865443332 232  446889998877776443  4455778999999999984432 23345554443  


Q ss_pred             CccEEEEEeec-ChhHHH
Q 022724          206 DLQVVLISATL-PHEILE  222 (293)
Q Consensus       206 ~~q~v~~SAt~-~~~~~~  222 (293)
                      ..|.++++.|. .+.+.+
T Consensus       765 sqrRLLLtgTPLqNslmE  782 (1958)
T KOG0391|consen  765 SQRRLLLTGTPLQNSLME  782 (1958)
T ss_pred             hhheeeecCCchhhHHHH
Confidence            34556666664 444333

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.91  E-value=0.00044  Score=61.47  Aligned_cols=129  Identities=19%  Similarity=0.220  Sum_probs=70.2

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhh-ccCCCceeEEEEc--CCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHH
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTV-DTSSREVQALILS--PTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRK  147 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l-~~~~~~~~~lil~--P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (293)
                      +.++++||||+|||....--+.... .....+.++.++.  +.+.-+..+   ++.+....++.+..             
T Consensus       175 ~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQ---L~~~a~~lgvpv~~-------------  238 (388)
T PRK12723        175 RVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQ---IQTYGDIMGIPVKA-------------  238 (388)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHH---HHHHhhcCCcceEe-------------
Confidence            4689999999999976543332221 1111233444444  334444333   33444444443321             


Q ss_pred             HhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccc-cHHHHHHHHhhCCCC-ccEEEEEeecC-hhHHHHH
Q 022724          148 LEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG-FKDQIYDVYRYLPPD-LQVVLISATLP-HEILEMT  224 (293)
Q Consensus       148 ~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~-~~~~~~~i~~~l~~~-~q~v~~SAt~~-~~~~~~~  224 (293)
                              +-+++.+...+..    +.+.++|+||++....... ....+..++...... -.++.+|||.. +++.+..
T Consensus       239 --------~~~~~~l~~~L~~----~~~~DlVLIDTaGr~~~~~~~l~el~~~l~~~~~~~e~~LVlsat~~~~~~~~~~  306 (388)
T PRK12723        239 --------IESFKDLKEEITQ----SKDFDLVLVDTIGKSPKDFMKLAEMKELLNACGRDAEFHLAVSSTTKTSDVKEIF  306 (388)
T ss_pred             --------eCcHHHHHHHHHH----hCCCCEEEEcCCCCCccCHHHHHHHHHHHHhcCCCCeEEEEEcCCCCHHHHHHHH
Confidence                    1234444444432    3567999999998874321 223445555544433 46788999985 4455555


Q ss_pred             Hhc
Q 022724          225 TKF  227 (293)
Q Consensus       225 ~~~  227 (293)
                      ..+
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=4.4e-05  Score=66.13  Aligned_cols=122  Identities=16%  Similarity=0.167  Sum_probs=74.6

Q ss_pred             CcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccC-CCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q 022724           56 PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-SREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (293)
Q Consensus        56 ~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~-~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (293)
                      +++-|.+++..  .+.+++|.|+.|||||.+.+--+...+... -...+++++++|+..+.++.+++...........  
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            46789998888  788999999999999987766665555544 2345899999999999999999987643321100  


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHH-HHhcCCCCC-CCccEEEecchh
Q 022724          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCD-MIKRKTLRT-RAIKLLVLDESD  185 (293)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~-~l~~~~~~~-~~l~~iViDE~h  185 (293)
                          ...............+.|+|-..+.. +++...... -.-.+-++|+..
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                00001111112234678888887776 333321111 122455666665

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 ....

>KOG2340 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.85  E-value=0.0003  Score=63.25  Aligned_cols=176  Identities=18%  Similarity=0.238  Sum_probs=111.8

Q ss_pred             CCCcHHHHHHHHhhhcCCcEEEEcCC-CChh--HHHHHHHHHhhhccC----------------------------CCce
Q 022724           54 EKPSAIQQRAVMPIIKGRDVIAQAQS-GTGK--TSMIALTVCQTVDTS----------------------------SREV  102 (293)
Q Consensus        54 ~~~~~~Q~~~~~~i~~~~~~li~~~T-g~GK--T~~~~~~~~~~l~~~----------------------------~~~~  102 (293)
                      ..+|+.|.+.+....+.+|++..-.| +.|+  +-.|.+.+++++.+.                            -..|
T Consensus       215 ~pltalQ~~L~~~m~~YrDl~y~~~s~kn~~e~R~lYclH~lNHi~K~r~~IL~Nn~r~~Sqk~g~~~~~~frDQG~tRp  294 (698)
T KOG2340|consen  215 EPLTALQKELFKIMFNYRDLLYPTRSQKNGEEYRSLYCLHALNHILKTRDLILGNNRRLASQKEGENPDESFRDQGFTRP  294 (698)
T ss_pred             CcchHHHHHHHHHHHhhhhhccccccccccchhhhhHHHHHHHHHHHHHHHHhcchHhhhhhhcCCCCchhhhhcCCCCc
Confidence            46899999999999999998765443 3444  456777777766211                            1347


Q ss_pred             eEEEEcCCHHHHHHHHHHHHHhhccCCc---------eEEEEECCc--------chHHHHHHH-----------------
Q 022724          103 QALILSPTRELATQTEKVILAIGDFINI---------QAHACVGGK--------SVGEDIRKL-----------------  148 (293)
Q Consensus       103 ~~lil~P~~~l~~q~~~~~~~~~~~~~~---------~~~~~~~~~--------~~~~~~~~~-----------------  148 (293)
                      ++||+||+++-|-.+.+.+..+....+-         +...-+++.        +.....+.+                 
T Consensus       295 kVLivvpfRe~A~riVn~lis~l~G~~q~k~~V~Nk~RF~~eys~~te~~~~~~~kP~D~~~lf~GNtDD~FriGl~ftk  374 (698)
T KOG2340|consen  295 KVLIVVPFRESAYRIVNLLISLLSGDDQGKSEVWNKKRFEGEYSGPTELPPPRAKKPEDFEELFSGNTDDAFRIGLAFTK  374 (698)
T ss_pred             eEEEEecchHHHHHHHHHHHHHhcCccccchhhhhhhhhchhcCCCcccCCCCCCCchhHHHHhcCCCcchhhhhHHHHH
Confidence            8999999999999999988776322110         111111110        000111111                 


Q ss_pred             --------hcCCcEEEeChHHHHHHHhcC-----CC-CCCCccEEEecchhhhhccccHHHHHHHHhhCCC---------
Q 022724          149 --------EHGVHVVSGTPGRVCDMIKRK-----TL-RTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP---------  205 (293)
Q Consensus       149 --------~~~~~ilV~Tp~~l~~~l~~~-----~~-~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~---------  205 (293)
                              ....||+||+|--|-.++.+.     .+ .++.+.++|||-+|.++-..|. ++..++..+..         
T Consensus       375 KtikLys~fy~SDIlVaSPLGLRmil~n~gdkkrd~dfLSSIEl~iIDQa~~~l~QNwE-hl~~ifdHLn~~P~k~h~~D  453 (698)
T KOG2340|consen  375 KTIKLYSKFYKSDILVASPLGLRMILGNTGDKKRDFDFLSSIELLIIDQADIMLMQNWE-HLLHIFDHLNLQPSKQHDVD  453 (698)
T ss_pred             HHHHHHhhhcccCeEEecchhhhhhhcCCCcccccchhhhhhhhhhhhhHHHHHHhhHH-HHHHHHHHhhcCcccccCCC
Confidence                    124689999998777766531     12 2588899999999998755443 44445544421         


Q ss_pred             ---------------CccEEEEEeecChhHHHHHHhcCCC
Q 022724          206 ---------------DLQVVLISATLPHEILEMTTKFMTD  230 (293)
Q Consensus       206 ---------------~~q~v~~SAt~~~~~~~~~~~~~~~  230 (293)
                                     -.|.+++|+--.+....+...+..+
T Consensus       454 fSRVR~wyL~~qsr~~rQtl~Fs~y~~~~~nS~fn~~c~N  493 (698)
T KOG2340|consen  454 FSRVRMWYLDGQSRYFRQTLLFSRYSHPLFNSLFNQYCQN  493 (698)
T ss_pred             hhheehheeccHHHHHHHHHHHHhhccHHHHHHHHHhhhh
Confidence                           2588888888888777777666543

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=97.80  E-value=0.00052  Score=68.26  Aligned_cols=137  Identities=18%  Similarity=0.170  Sum_probs=82.2

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHhhhc-CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHH
Q 022724           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPIIK-GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE  118 (293)
Q Consensus        40 l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~-~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~  118 (293)
                      .++..+......+ ..+++-|.+++..+.. ++-.++.|+.|+|||.+. -++...+...  |.+++.++||-.-+..+.
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 VREAVLAATFARH-ARLSDEQKTAIEHVAGPARIAAVVGRAGAGKTTMM-KAAREAWEAA--GYRVVGGALAGKAAEGLE  442 (1102)
T ss_pred             CCHHHHHHHHhcC-CCCCHHHHHHHHHHhccCCeEEEEeCCCCCHHHHH-HHHHHHHHHc--CCeEEEEcCcHHHHHHHH
Confidence            4444444443333 3599999999998864 567899999999999543 2343434332  568999999977776654


Q ss_pred             HHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHH
Q 022724          119 KVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYD  198 (293)
Q Consensus       119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~  198 (293)
                      +       ..|+...                        |-.++..-...+...+..-++|||||+.++..    ..+..
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       2232221                        22222111112223456678999999998743    33444


Q ss_pred             HHhhCC-CCccEEEEEee
Q 022724          199 VYRYLP-PDLQVVLISAT  215 (293)
Q Consensus       199 i~~~l~-~~~q~v~~SAt  215 (293)
                      +++... ...++|++-=+
T Consensus       488 Ll~~~~~~garvVLVGD~  505 (1102)
T PRK13826        488 FVEAVTRAGAKLVLVGDP  505 (1102)
T ss_pred             HHHHHHhcCCEEEEECCH
Confidence            555543 45677776544

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=97.77  E-value=4.9e-05  Score=73.70  Aligned_cols=126  Identities=19%  Similarity=0.225  Sum_probs=89.2

Q ss_pred             CcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEE
Q 022724           56 PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC  135 (293)
Q Consensus        56 ~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~  135 (293)
                      |+++|--  -.+.=.+.-+..+.||-|||+++.+|+.-.....   .-+-+++.+..||..=.+.+..+...+|+.+.+.
T Consensus       170 ~yDVQli--GgivLh~G~IAEM~TGEGKTLvAtlp~yLnAL~G---kgVHvVTVNDYLA~RDaewmgply~fLGLsvg~i  244 (1112)
T PRK12901        170 HYDVQLI--GGVVLHQGKIAEMATGEGKTLVATLPVYLNALTG---NGVHVVTVNDYLAKRDSEWMGPLYEFHGLSVDCI  244 (1112)
T ss_pred             ccchHHh--hhhhhcCCceeeecCCCCchhHHHHHHHHHHHcC---CCcEEEEechhhhhccHHHHHHHHHHhCCceeec
Confidence            5555544  4444445568899999999999999887665553   3467788889999998999999999999999877


Q ss_pred             ECC-cchHHHHHHHhcCCcEEEeChHHH-HHHHhcC------CCCCCCccEEEecchhhhh
Q 022724          136 VGG-KSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRK------TLRTRAIKLLVLDESDEML  188 (293)
Q Consensus       136 ~~~-~~~~~~~~~~~~~~~ilV~Tp~~l-~~~l~~~------~~~~~~l~~iViDE~h~~~  188 (293)
                      ... .+..+. +.. -.+||.-+|...| .++|+.+      ....+.+.|.||||+|.++
T Consensus       245 ~~~~~~~~~r-r~a-Y~~DItYgTn~EfGFDYLRDnm~~~~~~~vqR~~~fAIVDEvDSIL  303 (1112)
T PRK12901        245 DKHQPNSEAR-RKA-YNADITYGTNNEFGFDYLRDNMAHSPEDLVQRKHNYAIVDEVDSVL  303 (1112)
T ss_pred             CCCCCCHHHH-HHh-CCCcceecCCCccccccchhccccchHhhhCcCCceeEeechhhhh
Confidence            653 333322 222 3479999997665 2344432      1234668999999999975

>PRK04296 thymidine kinase; Provisional

Probab=97.73  E-value=0.00034  Score=56.25  Aligned_cols=110  Identities=12%  Similarity=0.163  Sum_probs=56.9

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCC---HHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT---RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIR  146 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~---~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  146 (293)
                      |.-.++.||+|+|||...+- .+.++...  +.+++++-|.   +....       .+....++...             
T Consensus         2 g~i~litG~~GsGKTT~~l~-~~~~~~~~--g~~v~i~k~~~d~~~~~~-------~i~~~lg~~~~-------------   58 (190)
T PRK04296          2 AKLEFIYGAMNSGKSTELLQ-RAYNYEER--GMKVLVFKPAIDDRYGEG-------KVVSRIGLSRE-------------   58 (190)
T ss_pred             cEEEEEECCCCCHHHHHHHH-HHHHHHHc--CCeEEEEeccccccccCC-------cEecCCCCccc-------------
Confidence            34578899999999965443 33443332  4577777662   21111       11111121110             


Q ss_pred             HHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEee
Q 022724          147 KLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISAT  215 (293)
Q Consensus       147 ~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt  215 (293)
                            .+.+..++.+...+..   .-.+.++|||||+|.+..    .++..+++.+.+....+++++-
T Consensus        59 ------~~~~~~~~~~~~~~~~---~~~~~dvviIDEaq~l~~----~~v~~l~~~l~~~g~~vi~tgl  114 (190)
T PRK04296         59 ------AIPVSSDTDIFELIEE---EGEKIDCVLIDEAQFLDK----EQVVQLAEVLDDLGIPVICYGL  114 (190)
T ss_pred             ------ceEeCChHHHHHHHHh---hCCCCCEEEEEccccCCH----HHHHHHHHHHHHcCCeEEEEec
Confidence                  1223445555555444   335678999999987522    2344455554333344555544

>PF14617 CMS1: U3-containing 90S pre-ribosomal complex subunit

Probab=97.70  E-value=0.00013  Score=60.64  Aligned_cols=87  Identities=21%  Similarity=0.311  Sum_probs=66.9

Q ss_pred             CCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECC-cchHHHHHHHh-cCCcEEEeChHHHHHHHhcCCCCCCCc
Q 022724           99 SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGG-KSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (293)
Q Consensus        99 ~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~-~~~~ilV~Tp~~l~~~l~~~~~~~~~l  176 (293)
                      +..|.+|||+.+---|-++.+.++.+.. -+..+..++.. ....++...+. ...+|.||||+++..++..+.+.++++
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            4468999999987777788887776631 12344444433 46777877776 478999999999999999999999999


Q ss_pred             cEEEecchhh
Q 022724          177 KLLVLDESDE  186 (293)
Q Consensus       177 ~~iViDE~h~  186 (293)
                      .+||||--|.
T Consensus       203 ~~ivlD~s~~  212 (252)
T PF14617_consen  203 KRIVLDWSYL  212 (252)
T ss_pred             eEEEEcCCcc
Confidence            9999997553

>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=97.70  E-value=0.00079  Score=50.86  Aligned_cols=17  Identities=29%  Similarity=0.616  Sum_probs=15.1

Q ss_pred             CCcEEEEcCCCChhHHH
Q 022724           70 GRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~   86 (293)
                      ++.+++.||+|+|||..
T Consensus        19 ~~~v~i~G~~G~GKT~l   35 (151)
T cd00009          19 PKNLLLYGPPGTGKTTL   35 (151)
T ss_pred             CCeEEEECCCCCCHHHH
Confidence            67899999999999953

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.

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=97.70  E-value=0.0002  Score=60.27  Aligned_cols=55  Identities=22%  Similarity=0.327  Sum_probs=35.9

Q ss_pred             CCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEeec---ChhHHHHHHhc
Q 022724          172 RTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATL---PHEILEMTTKF  227 (293)
Q Consensus       172 ~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~---~~~~~~~~~~~  227 (293)
                      ....++.||+||+|.|....+ ..+.+.+...+...+++++.-.+   ++.+...+.++
T Consensus       126 ~~~~fKiiIlDEcdsmtsdaq-~aLrr~mE~~s~~trFiLIcnylsrii~pi~SRC~Kf  183 (346)
T KOG0989|consen  126 PCPPFKIIILDECDSMTSDAQ-AALRRTMEDFSRTTRFILICNYLSRIIRPLVSRCQKF  183 (346)
T ss_pred             CCCcceEEEEechhhhhHHHH-HHHHHHHhccccceEEEEEcCChhhCChHHHhhHHHh
Confidence            356679999999999965543 34556666666677888876654   33344444443

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=97.65  E-value=0.0003  Score=52.65  Aligned_cols=20  Identities=30%  Similarity=0.556  Sum_probs=12.7

Q ss_pred             cCCcEEEEcCCCChhHHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~   88 (293)
                      +++.+++.||+|+|||....
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            35678999999999996543

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

Probab=97.63  E-value=0.00053  Score=65.18  Aligned_cols=70  Identities=16%  Similarity=0.187  Sum_probs=48.8

Q ss_pred             CCcHHHHHHHHhhh----cCCcEEEEcCCCChhHHHHHHHHHh---hhc-----------c--------C----------
Q 022724           55 KPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQ---TVD-----------T--------S----------   98 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~----~~~~~li~~~Tg~GKT~~~~~~~~~---~l~-----------~--------~----------   98 (293)
                      .|++.|...+..++    ...+.++..|||+|||++.+=..+.   .+.           .        .          
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            58999998777765    4578999999999999776544332   221           0        0          


Q ss_pred             --C-----CceeEEEEcCCHHHHHHHHHHHHHh
Q 022724           99 --S-----REVQALILSPTRELATQTEKVILAI  124 (293)
Q Consensus        99 --~-----~~~~~lil~P~~~l~~q~~~~~~~~  124 (293)
                        +     .-+++.|-.-|..-..|+.+.+++.
T Consensus       101 ~e~~~~~~~ipkIyyaSRTHsQltQvvrElrrT  133 (945)
T KOG1132|consen  101 GEPIACYTGIPKIYYASRTHSQLTQVVRELRRT  133 (945)
T ss_pred             cCccccccCCceEEEecchHHHHHHHHHHHhhc
Confidence              0     1256777777888788888777654

>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]

Probab=97.62  E-value=0.00015  Score=65.26  Aligned_cols=73  Identities=22%  Similarity=0.277  Sum_probs=55.2

Q ss_pred             CCcHHHHHHHHhhhcC-----CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCC
Q 022724           55 KPSAIQQRAVMPIIKG-----RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~-----~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (293)
                      .|.--|-+||..+..|     +.-.+-|.||||||+...-.+ ..+.     .-++|++|++.||.|++..++.++....
T Consensus        12 ~PaGDQP~AI~~Lv~gi~~g~~~QtLLGvTGSGKTfT~AnVI-~~~~-----rPtLV~AhNKTLAaQLy~Efk~fFP~Na   85 (663)
T COG0556          12 KPAGDQPEAIAELVEGIENGLKHQTLLGVTGSGKTFTMANVI-AKVQ-----RPTLVLAHNKTLAAQLYSEFKEFFPENA   85 (663)
T ss_pred             CCCCCcHHHHHHHHHHHhcCceeeEEeeeccCCchhHHHHHH-HHhC-----CCeEEEecchhHHHHHHHHHHHhCcCcc
Confidence            3777788888877643     477888999999997754333 2222     2489999999999999999999987765


Q ss_pred             ceEE
Q 022724          130 IQAH  133 (293)
Q Consensus       130 ~~~~  133 (293)
                      +...
T Consensus        86 VEYF   89 (663)
T COG0556          86 VEYF   89 (663)
T ss_pred             eEEE
Confidence            5443

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.62  E-value=0.00028  Score=52.93  Aligned_cols=41  Identities=15%  Similarity=0.321  Sum_probs=25.1

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l  113 (293)
                      +..+++.||+|+|||.... .+...+....  ..++++.+....
T Consensus         2 ~~~~~l~G~~G~GKTtl~~-~l~~~~~~~~--~~~~~~~~~~~~   42 (148)
T smart00382        2 GEVILIVGPPGSGKTTLAR-ALARELGPPG--GGVIYIDGEDIL   42 (148)
T ss_pred             CCEEEEECCCCCcHHHHHH-HHHhccCCCC--CCEEEECCEEcc
Confidence            5689999999999995543 2223332221  246777765443

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.

>PRK08181 transposase; Validated

Probab=97.60  E-value=0.0008  Score=56.96  Aligned_cols=58  Identities=21%  Similarity=0.322  Sum_probs=33.0

Q ss_pred             cHHHHHHHHh----hhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHH
Q 022724           57 SAIQQRAVMP----IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE  118 (293)
Q Consensus        57 ~~~Q~~~~~~----i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~  118 (293)
                      .+.|..++..    +..++++++.||+|+|||.... ++...+...  |.++++ ++..+|+.++.
T Consensus        89 ~~~~~~~L~~~~~~~~~~~nlll~Gp~GtGKTHLa~-Aia~~a~~~--g~~v~f-~~~~~L~~~l~  150 (269)
T PRK08181         89 SKAQVMAIAAGDSWLAKGANLLLFGPPGGGKSHLAA-AIGLALIEN--GWRVLF-TRTTDLVQKLQ  150 (269)
T ss_pred             CHHHHHHHHHHHHHHhcCceEEEEecCCCcHHHHHH-HHHHHHHHc--CCceee-eeHHHHHHHHH
Confidence            4555555532    3367899999999999994433 222222222  334444 44455555553

>PRK06526 transposase; Provisional

Probab=97.53  E-value=0.00051  Score=57.75  Aligned_cols=21  Identities=29%  Similarity=0.406  Sum_probs=17.2

Q ss_pred             hcCCcEEEEcCCCChhHHHHH
Q 022724           68 IKGRDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        68 ~~~~~~li~~~Tg~GKT~~~~   88 (293)
                      ..+.++++.||+|+|||....
T Consensus        96 ~~~~nlll~Gp~GtGKThLa~  116 (254)
T PRK06526         96 TGKENVVFLGPPGTGKTHLAI  116 (254)
T ss_pred             hcCceEEEEeCCCCchHHHHH
Confidence            356799999999999995543

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.42  E-value=0.0032  Score=55.75  Aligned_cols=128  Identities=13%  Similarity=0.245  Sum_probs=67.0

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEc--CCH-HHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHH
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS--PTR-ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRK  147 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~--P~~-~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (293)
                      +.++++||||+|||.....-+.. +...  +.++.++.  |.+ ..+.|+..    +....++.+               
T Consensus       242 ~vI~LVGptGvGKTTTiaKLA~~-L~~~--GkkVglI~aDt~RiaAvEQLk~----yae~lgipv---------------  299 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAKMAWQ-FHGK--KKTVGFITTDHSRIGTVQQLQD----YVKTIGFEV---------------  299 (436)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHH-HHHc--CCcEEEEecCCcchHHHHHHHH----HhhhcCCcE---------------
Confidence            56899999999999655433332 3222  33444444  333 23334333    222222222               


Q ss_pred             HhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcc-ccHHHHHHHHhhCCCCccEEEEEeecC-hhHHHHHH
Q 022724          148 LEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPPDLQVVLISATLP-HEILEMTT  225 (293)
Q Consensus       148 ~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~-~~~~~~~~i~~~l~~~~q~v~~SAt~~-~~~~~~~~  225 (293)
                            +.+.+|..+...+..-.- ..+.++|+||-+=..... .....+..+++...+..-++.+|||.. .++.+.+.
T Consensus       300 ------~v~~d~~~L~~aL~~lk~-~~~~DvVLIDTaGRs~kd~~lm~EL~~~lk~~~PdevlLVLsATtk~~d~~~i~~  372 (436)
T PRK11889        300 ------IAVRDEAAMTRALTYFKE-EARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASMKSKDMIEIIT  372 (436)
T ss_pred             ------EecCCHHHHHHHHHHHHh-ccCCCEEEEeCccccCcCHHHHHHHHHHHhhcCCCeEEEEECCccChHHHHHHHH
Confidence                  223466666655533111 124789999988654322 223334455544444445667888765 45566665


Q ss_pred             hc
Q 022724          226 KF  227 (293)
Q Consensus       226 ~~  227 (293)
                      .+
T Consensus       373 ~F  374 (436)
T PRK11889        373 NF  374 (436)
T ss_pred             Hh
Confidence            54

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=97.40  E-value=0.00062  Score=60.51  Aligned_cols=59  Identities=22%  Similarity=0.327  Sum_probs=42.5

Q ss_pred             CcHHHHHHHHhh------hcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHH
Q 022724           56 PSAIQQRAVMPI------IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQT  117 (293)
Q Consensus        56 ~~~~Q~~~~~~i------~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~  117 (293)
                      +++-|++++..+      .++.++.+.|+-|+|||..+- .+.+.+..  .+..+++++||-.-|..+
T Consensus         2 Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~~-~i~~~~~~--~~~~~~~~a~tg~AA~~i   66 (364)
T PF05970_consen    2 LNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFLIK-AIIDYLRS--RGKKVLVTAPTGIAAFNI   66 (364)
T ss_pred             CCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChhHHHH-HHHHHhcc--ccceEEEecchHHHHHhc
Confidence            677899998888      577899999999999995432 22233333  345788888987766555

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=97.39  E-value=0.00088  Score=64.33  Aligned_cols=69  Identities=17%  Similarity=0.185  Sum_probs=53.7

Q ss_pred             CCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCC-CceeEEEEcCCHHHHHHHHHHHHHhh
Q 022724           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-REVQALILSPTRELATQTEKVILAIG  125 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~-~~~~~lil~P~~~l~~q~~~~~~~~~  125 (293)
                      .+++-|++++...  +.+++|.|+.|||||.+..--+.+.+.... ...++++++-|+..|.++.+++..+.
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 RLNPGQQQAVEFV--TGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVAQTL   71 (672)
T ss_pred             CCCHHHHHHHhCC--CCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeeeEechHHHHHHHHHHHHHHh
Confidence            3788999988763  567899999999999876655555554322 23479999999999999999988754

>KOG1805 consensus DNA replication helicase [Replication, recombination and repair]

Probab=97.38  E-value=0.0014  Score=63.02  Aligned_cols=135  Identities=16%  Similarity=0.168  Sum_probs=83.0

Q ss_pred             CCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcC-CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHH
Q 022724           39 GIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG-RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQT  117 (293)
Q Consensus        39 ~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~-~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~  117 (293)
                      .+.+++...    -...++.-|++|+-..+.- ...+|.|-+|+|||..... ++..+...  |.++++.+=|..-++.+
T Consensus       657 ~~~p~~~~~----~~~~LN~dQr~A~~k~L~aedy~LI~GMPGTGKTTtI~~-LIkiL~~~--gkkVLLtsyThsAVDNI  729 (1100)
T KOG1805|consen  657 VLIPKIKKI----ILLRLNNDQRQALLKALAAEDYALILGMPGTGKTTTISL-LIKILVAL--GKKVLLTSYTHSAVDNI  729 (1100)
T ss_pred             ccCchhhHH----HHhhcCHHHHHHHHHHHhccchheeecCCCCCchhhHHH-HHHHHHHc--CCeEEEEehhhHHHHHH
Confidence            345555443    2346889999999987765 4578889999999955432 22333332  45788888899888888


Q ss_pred             HHHHHHhhccCCceEEEEE---------------CCc--chHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEE
Q 022724          118 EKVILAIGDFINIQAHACV---------------GGK--SVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLV  180 (293)
Q Consensus       118 ~~~~~~~~~~~~~~~~~~~---------------~~~--~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iV  180 (293)
                      .-.++.+.    +.+.-+-               .+.  ..-+..+...+.+.|+.+|=-.+.+    ..+..+.+++.|
T Consensus       730 LiKL~~~~----i~~lRLG~~~kih~~v~e~~~~~~~s~ks~~~l~~~~~~~~IVa~TClgi~~----plf~~R~FD~cI  801 (1100)
T KOG1805|consen  730 LIKLKGFG----IYILRLGSEEKIHPDVEEFTLTNETSEKSYADLKKFLDQTSIVACTCLGINH----PLFVNRQFDYCI  801 (1100)
T ss_pred             HHHHhccC----cceeecCCccccchHHHHHhcccccchhhHHHHHHHhCCCcEEEEEccCCCc----hhhhccccCEEE
Confidence            87776542    2111111               111  1112233444567788777422222    234456689999


Q ss_pred             ecchhhhh
Q 022724          181 LDESDEML  188 (293)
Q Consensus       181 iDE~h~~~  188 (293)
                      ||||-++.
T Consensus       802 iDEASQI~  809 (1100)
T KOG1805|consen  802 IDEASQIL  809 (1100)
T ss_pred             Eccccccc
Confidence            99999875

>KOG0953 consensus Mitochondrial RNA helicase SUV3, DEAD-box superfamily [RNA processing and modification]

Probab=97.38  E-value=0.00021  Score=64.55  Aligned_cols=102  Identities=20%  Similarity=0.153  Sum_probs=64.9

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHh
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE  149 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  149 (293)
                      ++-++=+|||.||||--    +++++...+   ..+|-.|.+-||.++++++.+.+    +.+..+.|..-.....  -.
T Consensus       191 RkIi~H~GPTNSGKTy~----ALqrl~~ak---sGvycGPLrLLA~EV~~r~na~g----ipCdL~TGeE~~~~~~--~~  257 (700)
T KOG0953|consen  191 RKIIMHVGPTNSGKTYR----ALQRLKSAK---SGVYCGPLRLLAHEVYDRLNALG----IPCDLLTGEERRFVLD--NG  257 (700)
T ss_pred             heEEEEeCCCCCchhHH----HHHHHhhhc---cceecchHHHHHHHHHHHhhhcC----CCccccccceeeecCC--CC
Confidence            34566779999999954    567776654   45899999999999999888754    4443444332111000  01


Q ss_pred             cCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcccc
Q 022724          150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF  192 (293)
Q Consensus       150 ~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~  192 (293)
                      +.++.+=||.|+..        --..++..||||+++|-+...
T Consensus       258 ~~a~hvScTVEM~s--------v~~~yeVAViDEIQmm~Dp~R  292 (700)
T KOG0953|consen  258 NPAQHVSCTVEMVS--------VNTPYEVAVIDEIQMMRDPSR  292 (700)
T ss_pred             CcccceEEEEEEee--------cCCceEEEEehhHHhhcCccc
Confidence            23455666664332        124568899999999876543

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=97.36  E-value=0.008  Score=53.11  Aligned_cols=130  Identities=18%  Similarity=0.251  Sum_probs=70.3

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCC-H-HHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT-R-ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRK  147 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~-~-~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (293)
                      ++.+.++||||.|||...+=-+........+..-+||-.-+ | .-++|+....    +-.++.+               
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYRIGA~EQLk~Ya----~im~vp~---------------  263 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRIGAVEQLKTYA----DIMGVPL---------------  263 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEEeccchhhHHHHHHHHH----HHhCCce---------------
Confidence            67899999999999965433222222222223345666654 3 3344443333    2333333               


Q ss_pred             HhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhh-ccccHHHHHHHHhhCCCCccEEEEEeecC-hhHHHHHH
Q 022724          148 LEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML-SRGFKDQIYDVYRYLPPDLQVVLISATLP-HEILEMTT  225 (293)
Q Consensus       148 ~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~-~~~~~~~~~~i~~~l~~~~q~v~~SAt~~-~~~~~~~~  225 (293)
                            .+|-+|.-|...+.    .+.+.++|.||=+-+=. +......+..++....+.-..+.+|||.. .+++....
T Consensus       264 ------~vv~~~~el~~ai~----~l~~~d~ILVDTaGrs~~D~~~i~el~~~~~~~~~i~~~Lvlsat~K~~dlkei~~  333 (407)
T COG1419         264 ------EVVYSPKELAEAIE----ALRDCDVILVDTAGRSQYDKEKIEELKELIDVSHSIEVYLVLSATTKYEDLKEIIK  333 (407)
T ss_pred             ------EEecCHHHHHHHHH----HhhcCCEEEEeCCCCCccCHHHHHHHHHHHhccccceEEEEEecCcchHHHHHHHH
Confidence                  34455655555443    24555777777664321 12234455555555544455677888874 55666666


Q ss_pred             hcC
Q 022724          226 KFM  228 (293)
Q Consensus       226 ~~~  228 (293)
                      .+.
T Consensus       334 ~f~  336 (407)
T COG1419         334 QFS  336 (407)
T ss_pred             Hhc
Confidence            654

>PRK06921 hypothetical protein; Provisional

Probab=97.36  E-value=0.003  Score=53.54  Aligned_cols=45  Identities=18%  Similarity=0.237  Sum_probs=26.6

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQT  117 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~  117 (293)
                      ++++++.|++|+|||.... ++...+... .+..++++. ..++..++
T Consensus       117 ~~~l~l~G~~G~GKThLa~-aia~~l~~~-~g~~v~y~~-~~~l~~~l  161 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLT-AAANELMRK-KGVPVLYFP-FVEGFGDL  161 (266)
T ss_pred             CCeEEEECCCCCcHHHHHH-HHHHHHhhh-cCceEEEEE-HHHHHHHH
Confidence            5789999999999994432 344444332 134455554 34444443

>KOG0388 consensus SNF2 family DNA-dependent ATPase [Replication, recombination and repair]

Probab=97.35  E-value=0.00076  Score=62.78  Aligned_cols=154  Identities=18%  Similarity=0.194  Sum_probs=96.0

Q ss_pred             CcHHHHHHHHhhh----cCCcEEEEcCCCChhHHHHHHHHHhhhccCC--CceeEEEEcCCHHHHHHHHHHHHHhhccCC
Q 022724           56 PSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVDTSS--REVQALILSPTRELATQTEKVILAIGDFIN  129 (293)
Q Consensus        56 ~~~~Q~~~~~~i~----~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~--~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (293)
                      +..+|-..++.+.    +|-|-|+.-..|-|||.-.+ .++.++....  .|| -++++|...| ..+...+.++..  .
T Consensus       568 LKEYQlkGLnWLvnlYdqGiNGILADeMGLGKTVQsi-svlAhLaE~~nIwGP-FLVVtpaStL-~NWaqEisrFlP--~  642 (1185)
T KOG0388|consen  568 LKEYQLKGLNWLVNLYDQGINGILADEMGLGKTVQSI-SVLAHLAETHNIWGP-FLVVTPASTL-HNWAQEISRFLP--S  642 (1185)
T ss_pred             hHHHhhccHHHHHHHHHccccceehhhhccchhHHHH-HHHHHHHHhccCCCc-eEEeehHHHH-hHHHHHHHHhCc--c
Confidence            4567777766554    67899999999999995433 4444443332  233 6788886554 344555555543  4


Q ss_pred             ceEEEEECCcchHHHHHH---------HhcCCcEEEeChHHHHH---HHhcCCCCCCCccEEEecchhhhhccccHHHHH
Q 022724          130 IQAHACVGGKSVGEDIRK---------LEHGVHVVSGTPGRVCD---MIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIY  197 (293)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~---------~~~~~~ilV~Tp~~l~~---~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~  197 (293)
                      ++++-+.|+.+.....++         -..+.+|+|++.+.++.   ++.     --+..+.|+|||+.+-.. ....+.
T Consensus       643 ~k~lpywGs~~eRkiLrKfw~rKnmY~rna~fhVviTSYQlvVtDeky~q-----kvKWQYMILDEAQAIKSS-sS~RWK  716 (1185)
T KOG0388|consen  643 FKVLPYWGSPSERKILRKFWNRKNMYRRNAPFHVVITSYQLVVTDEKYLQ-----KVKWQYMILDEAQAIKSS-SSSRWK  716 (1185)
T ss_pred             ceeecCcCChhhhHHHHHhcchhhhhccCCCceEEEEeeeeeechHHHHH-----hhhhhheehhHHHHhhhh-hhhHHH
Confidence            678888888877666555         23457899998866643   222     234578999999988432 233444


Q ss_pred             HHHhhCCCCccEEEEEeec-ChhHHH
Q 022724          198 DVYRYLPPDLQVVLISATL-PHEILE  222 (293)
Q Consensus       198 ~i~~~l~~~~q~v~~SAt~-~~~~~~  222 (293)
                      .+++.-  ..-.++++.|+ -+.+.+
T Consensus       717 tLLsF~--cRNRLLLTGTPIQNsMqE  740 (1185)
T KOG0388|consen  717 TLLSFK--CRNRLLLTGTPIQNSMQE  740 (1185)
T ss_pred             HHhhhh--ccceeeecCCccchHHHH
Confidence            444432  33466777776 344333

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.35  E-value=0.0016  Score=59.57  Aligned_cols=46  Identities=9%  Similarity=0.203  Sum_probs=27.1

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHH
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE  118 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~  118 (293)
                      +.+++.||+|+|||... -++...+.....+.+++++ +..++..+..
T Consensus       149 ~~l~l~G~~G~GKThL~-~ai~~~~~~~~~~~~v~yi-~~~~~~~~~~  194 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLL-HAIGNYILEKNPNAKVVYV-TSEKFTNDFV  194 (450)
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHHHHHhCCCCeEEEE-EHHHHHHHHH
Confidence            46899999999999443 2344444443334456665 4445544433

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.34  E-value=0.0016  Score=57.50  Aligned_cols=129  Identities=18%  Similarity=0.211  Sum_probs=62.0

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcC-C-HHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP-T-RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRK  147 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P-~-~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (293)
                      |..++++||||+|||....--+........ ..++.++.. + +.-+.   +.++.+....++.+..             
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~~~~~~~G-~~~V~lit~D~~R~ga~---EqL~~~a~~~gv~~~~-------------  199 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAARCVMRFG-ASKVALLTTDSYRIGGH---EQLRIFGKILGVPVHA-------------  199 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcC-CCeEEEEecccccccHH---HHHHHHHHHcCCceEe-------------
Confidence            568999999999999665433333222211 123444432 2 22222   2333333333443322             


Q ss_pred             HhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcc-ccHHHHHHHHhhCCCCccEEEEEeecChhH-HHHHH
Q 022724          148 LEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPPDLQVVLISATLPHEI-LEMTT  225 (293)
Q Consensus       148 ~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~-~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~-~~~~~  225 (293)
                              +-+++.+...+..    +.+.++++||++-....+ .....+..+.........++.+|||..... .+..+
T Consensus       200 --------~~~~~~l~~~l~~----l~~~DlVLIDTaG~~~~d~~l~e~La~L~~~~~~~~~lLVLsAts~~~~l~evi~  267 (374)
T PRK14722        200 --------VKDGGDLQLALAE----LRNKHMVLIDTIGMSQRDRTVSDQIAMLHGADTPVQRLLLLNATSHGDTLNEVVQ  267 (374)
T ss_pred             --------cCCcccHHHHHHH----hcCCCEEEEcCCCCCcccHHHHHHHHHHhccCCCCeEEEEecCccChHHHHHHHH
Confidence                    2333333333321    345578889988543211 122333333222223345788899985443 33444


Q ss_pred             hc
Q 022724          226 KF  227 (293)
Q Consensus       226 ~~  227 (293)
                      .+
T Consensus       268 ~f  269 (374)
T PRK14722        268 AY  269 (374)
T ss_pred             HH
Confidence            33

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=97.31  E-value=0.0041  Score=48.01  Aligned_cols=38  Identities=16%  Similarity=0.326  Sum_probs=23.1

Q ss_pred             EEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHH
Q 022724           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (293)
Q Consensus        73 ~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l  113 (293)
                      +++.||+|+|||......+ .....  .+..++++......
T Consensus         2 ~~i~G~~G~GKT~l~~~i~-~~~~~--~~~~v~~~~~e~~~   39 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLA-LNIAT--KGGKVVYVDIEEEI   39 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHH-HHHHh--cCCEEEEEECCcch
Confidence            6899999999996543332 22222  24467777654443

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.

>TIGR01075 uvrD DNA helicase II

Probab=97.29  E-value=0.0014  Score=63.65  Aligned_cols=71  Identities=17%  Similarity=0.195  Sum_probs=54.5

Q ss_pred             CCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCC-CceeEEEEcCCHHHHHHHHHHHHHhhc
Q 022724           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-REVQALILSPTRELATQTEKVILAIGD  126 (293)
Q Consensus        54 ~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~-~~~~~lil~P~~~l~~q~~~~~~~~~~  126 (293)
                      ..+++-|++++...  ..+++|.|+.|||||.+..--+.+.+.... ...++++++-|+..|.++.+++.++..
T Consensus         3 ~~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~~L~~Ria~Li~~~~v~p~~IL~lTFTnkAA~em~~Rl~~~~~   74 (715)
T TIGR01075         3 DGLNDKQREAVAAP--PGNLLVLAGAGSGKTRVLTHRIAWLLSVENASPHSIMAVTFTNKAAAEMRHRIGALLG   74 (715)
T ss_pred             cccCHHHHHHHcCC--CCCEEEEecCCCCHHHHHHHHHHHHHHcCCCCHHHeEeeeccHHHHHHHHHHHHHHhc
Confidence            35899999988753  568999999999999775555544443322 234899999999999999999988653

Designed to identify uvrD members of the uvrD/rep subfamily.

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]

Probab=97.26  E-value=0.0017  Score=62.06  Aligned_cols=144  Identities=22%  Similarity=0.279  Sum_probs=89.5

Q ss_pred             HHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCc--eeEEEEcCCHHHHHHHHHHHHH-----hhccCCceEE
Q 022724           61 QRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSRE--VQALILSPTRELATQTEKVILA-----IGDFINIQAH  133 (293)
Q Consensus        61 ~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~--~~~lil~P~~~l~~q~~~~~~~-----~~~~~~~~~~  133 (293)
                      ..++..+..+.-++|.+.||+|||.-+.--+++.+.....+  ..+.+--|++..+..+.+++-.     .+...+.++.
T Consensus       384 ~~i~q~v~dn~v~~I~getgcgk~tq~aq~iLe~~~~ns~g~~~na~v~qprrisaisiaerva~er~e~~g~tvgy~vR  463 (1282)
T KOG0921|consen  384 SEILQAVAENRVVIIKGETGCGKSTQVAQFLLESFLENSNGASFNAVVSQPRRISAISLAERVANERGEEVGETCGYNVR  463 (1282)
T ss_pred             HHHHHHHhcCceeeEeecccccchhHHHHHHHHHHhhccccccccceeccccccchHHHHHHHHHhhHHhhccccccccc
Confidence            34555566677889999999999999888888887665443  3456666998888887776632     2222222221


Q ss_pred             EEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhC---CCCccEE
Q 022724          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL---PPDLQVV  210 (293)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l---~~~~q~v  210 (293)
                      .. +..+..       . -.|+.+|-+-+++++.++   +..+.++|+||+|...-.  ...+..+++.+   .....++
T Consensus       464 f~-Sa~prp-------y-g~i~fctvgvllr~~e~g---lrg~sh~i~deiherdv~--~dfll~~lr~m~~ty~dl~v~  529 (1282)
T KOG0921|consen  464 FD-SATPRP-------Y-GSIMFCTVGVLLRMMENG---LRGISHVIIDEIHERDVD--TDFVLIVLREMISTYRDLRVV  529 (1282)
T ss_pred             cc-cccccc-------c-cceeeeccchhhhhhhhc---ccccccccchhhhhhccc--hHHHHHHHHhhhccchhhhhh
Confidence            10 011100       0 158999999999988876   455789999999986322  22222222222   2345566


Q ss_pred             EEEeecCh
Q 022724          211 LISATLPH  218 (293)
Q Consensus       211 ~~SAt~~~  218 (293)
                      +||||+..
T Consensus       530 lmsatIdT  537 (1282)
T KOG0921|consen  530 LMSATIDT  537 (1282)
T ss_pred             hhhcccch
Confidence            66666543

>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=97.25  E-value=0.0012  Score=54.26  Aligned_cols=107  Identities=19%  Similarity=0.331  Sum_probs=59.0

Q ss_pred             cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcC
Q 022724           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG  151 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (293)
                      .+++.||+|+|||- -+-++.+.+.....+.+++++.. .+......+.++.                            
T Consensus        36 ~l~l~G~~G~GKTH-LL~Ai~~~~~~~~~~~~v~y~~~-~~f~~~~~~~~~~----------------------------   85 (219)
T PF00308_consen   36 PLFLYGPSGLGKTH-LLQAIANEAQKQHPGKRVVYLSA-EEFIREFADALRD----------------------------   85 (219)
T ss_dssp             EEEEEESTTSSHHH-HHHHHHHHHHHHCTTS-EEEEEH-HHHHHHHHHHHHT----------------------------
T ss_pred             ceEEECCCCCCHHH-HHHHHHHHHHhccccccceeecH-HHHHHHHHHHHHc----------------------------
Confidence            48999999999995 34445555544333556776654 2333333332221                            


Q ss_pred             CcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccc-cHHHHHHHHhhCC-CCccEEEEEeecChhH
Q 022724          152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG-FKDQIYDVYRYLP-PDLQVVLISATLPHEI  220 (293)
Q Consensus       152 ~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~-~~~~~~~i~~~l~-~~~q~v~~SAt~~~~~  220 (293)
                           ...+.+.+.       +...++++||++|.+.... +...+..++..+. ...++|+.|...|..+
T Consensus        86 -----~~~~~~~~~-------~~~~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l  144 (219)
T PF00308_consen   86 -----GEIEEFKDR-------LRSADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSEL  144 (219)
T ss_dssp             -----TSHHHHHHH-------HCTSSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTTT
T ss_pred             -----ccchhhhhh-------hhcCCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCccc
Confidence                 112222222       3467899999999986542 3444444444443 4566766665665543

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.

>COG0553 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]

Probab=97.24  E-value=0.0024  Score=63.27  Aligned_cols=158  Identities=18%  Similarity=0.125  Sum_probs=96.2

Q ss_pred             CCCcHHHHHHHHhhh-----cCCcEEEEcCCCChhHHHHHHHHHhhhccCCC-ceeEEEEcCCHHHHHHHHHHHHHhhcc
Q 022724           54 EKPSAIQQRAVMPII-----KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR-EVQALILSPTRELATQTEKVILAIGDF  127 (293)
Q Consensus        54 ~~~~~~Q~~~~~~i~-----~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~-~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (293)
                      ..+.++|.+.++.+.     .+.+-++.-..|.|||...+..+......... .+.++++||+ +++..+.+.+.++...
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            457888998886644     25678888999999997655555442222222 3478999995 4456777777776655


Q ss_pred             CCceEEEEECCcch----HHHHHHHhcC-----CcEEEeChHHHHHHH-hcCCCCCCCccEEEecchhhhhccccHHHHH
Q 022724          128 INIQAHACVGGKSV----GEDIRKLEHG-----VHVVSGTPGRVCDMI-KRKTLRTRAIKLLVLDESDEMLSRGFKDQIY  197 (293)
Q Consensus       128 ~~~~~~~~~~~~~~----~~~~~~~~~~-----~~ilV~Tp~~l~~~l-~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~  197 (293)
                      ... +...+|....    .+....+...     .+++++|.+.+.... ....+.-.....+|+||+|.+-... .....
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            443 5556665541    3333333321     689999998887732 1223444667899999999974332 22222


Q ss_pred             HHHhhCCCCccEEEEEeec
Q 022724          198 DVYRYLPPDLQVVLISATL  216 (293)
Q Consensus       198 ~i~~~l~~~~q~v~~SAt~  216 (293)
                      .+. .+....+ +.+|.|+
T Consensus       494 ~l~-~~~~~~~-~~LtgTP  510 (866)
T COG0553         494 ALQ-FLKALNR-LDLTGTP  510 (866)
T ss_pred             HHH-HHhhcce-eeCCCCh
Confidence            222 3332233 6777776

>PRK05642 DNA replication initiation factor; Validated

Probab=97.24  E-value=0.0011  Score=55.10  Aligned_cols=44  Identities=16%  Similarity=0.399  Sum_probs=28.1

Q ss_pred             CccEEEecchhhhhcc-ccHHHHHHHHhhCCCCccEEEEEeecCh
Q 022724          175 AIKLLVLDESDEMLSR-GFKDQIYDVYRYLPPDLQVVLISATLPH  218 (293)
Q Consensus       175 ~l~~iViDE~h~~~~~-~~~~~~~~i~~~l~~~~q~v~~SAt~~~  218 (293)
                      +.+++|+||+|.+... .+...+-.++..+..+...++++++.++
T Consensus        97 ~~d~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p  141 (234)
T PRK05642         97 QYELVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSP  141 (234)
T ss_pred             hCCEEEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCCCH
Confidence            4578999999987433 3445566666555544455667777544

>PRK14974 cell division protein FtsY; Provisional

Probab=97.24  E-value=0.009  Score=52.24  Aligned_cols=129  Identities=21%  Similarity=0.311  Sum_probs=72.2

Q ss_pred             cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCC---HHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH
Q 022724           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT---RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~---~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  148 (293)
                      -++++|++|+|||....-.+ ..+...  +.+++++...   .....|+.....    ..++.+.....+.         
T Consensus       142 vi~~~G~~GvGKTTtiakLA-~~l~~~--g~~V~li~~Dt~R~~a~eqL~~~a~----~lgv~v~~~~~g~---------  205 (336)
T PRK14974        142 VIVFVGVNGTGKTTTIAKLA-YYLKKN--GFSVVIAAGDTFRAGAIEQLEEHAE----RLGVKVIKHKYGA---------  205 (336)
T ss_pred             EEEEEcCCCCCHHHHHHHHH-HHHHHc--CCeEEEecCCcCcHHHHHHHHHHHH----HcCCceecccCCC---------
Confidence            47889999999996544333 233322  3456665543   334444443333    3444443211111         


Q ss_pred             hcCCcEEEeChHHH-HHHHhcCCCCCCCccEEEecchhhhhc-cccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHh
Q 022724          149 EHGVHVVSGTPGRV-CDMIKRKTLRTRAIKLLVLDESDEMLS-RGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTK  226 (293)
Q Consensus       149 ~~~~~ilV~Tp~~l-~~~l~~~~~~~~~l~~iViDE~h~~~~-~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~  226 (293)
                               .|..+ ...+...  ...+.++|+||.+..+.. ......+..+.+...+...++.++|+...+....+..
T Consensus       206 ---------dp~~v~~~ai~~~--~~~~~DvVLIDTaGr~~~~~~lm~eL~~i~~~~~pd~~iLVl~a~~g~d~~~~a~~  274 (336)
T PRK14974        206 ---------DPAAVAYDAIEHA--KARGIDVVLIDTAGRMHTDANLMDELKKIVRVTKPDLVIFVGDALAGNDAVEQARE  274 (336)
T ss_pred             ---------CHHHHHHHHHHHH--HhCCCCEEEEECCCccCCcHHHHHHHHHHHHhhCCceEEEeeccccchhHHHHHHH
Confidence                     11111 1111110  123457999999998753 3456667777777777788899999887766655554


Q ss_pred             c
Q 022724          227 F  227 (293)
Q Consensus       227 ~  227 (293)
                      +
T Consensus       275 f  275 (336)
T PRK14974        275 F  275 (336)
T ss_pred             H
Confidence            4

>KOG0386 consensus Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics; Transcription]

Probab=97.23  E-value=0.001  Score=64.10  Aligned_cols=155  Identities=14%  Similarity=0.127  Sum_probs=87.9

Q ss_pred             CCCcHHHHHHHHhhh---cC-CcEEEEcCCCChhHHHHHHHHHhhhccCC-CceeEEEEcCCHHHHHHHHHHHHHhhccC
Q 022724           54 EKPSAIQQRAVMPII---KG-RDVIAQAQSGTGKTSMIALTVCQTVDTSS-REVQALILSPTRELATQTEKVILAIGDFI  128 (293)
Q Consensus        54 ~~~~~~Q~~~~~~i~---~~-~~~li~~~Tg~GKT~~~~~~~~~~l~~~~-~~~~~lil~P~~~l~~q~~~~~~~~~~~~  128 (293)
                      ..+.++|...+....   ++ -|-++.-.+|-|||..-.--+..-+.... .|| -+|++|+-.|.+=. ..+..|... 
T Consensus       393 G~Lk~YQl~GLqWmVSLyNNnLNGILADEMGLGKTIQtIsLitYLmE~K~~~GP-~LvivPlstL~NW~-~Ef~kWaPS-  469 (1157)
T KOG0386|consen  393 GELKEYQLHGLQWMVSLYNNNLNGILADEMGLGKTIQTISLITYLMEHKQMQGP-FLIIVPLSTLVNWS-SEFPKWAPS-  469 (1157)
T ss_pred             CCCchhhhhhhHHHhhccCCCcccccchhcccchHHHHHHHHHHHHHHcccCCC-eEEeccccccCCch-hhccccccc-
Confidence            368899999887654   23 47888899999999554333333222222 243 68889988876533 334444432 


Q ss_pred             CceEEEEECCcchHHHH--HHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCC
Q 022724          129 NIQAHACVGGKSVGEDI--RKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPD  206 (293)
Q Consensus       129 ~~~~~~~~~~~~~~~~~--~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~  206 (293)
                       +....+.|........  +......+|+++|.+.+..  ....+.--+..++||||-|.|-.  ....+...+.-....
T Consensus       470 -v~~i~YkGtp~~R~~l~~qir~gKFnVLlTtyEyiik--dk~lLsKI~W~yMIIDEGHRmKN--a~~KLt~~L~t~y~~  544 (1157)
T KOG0386|consen  470 -VQKIQYKGTPQQRSGLTKQQRHGKFNVLLTTYEYIIK--DKALLSKISWKYMIIDEGHRMKN--AICKLTDTLNTHYRA  544 (1157)
T ss_pred             -eeeeeeeCCHHHHhhHHHHHhcccceeeeeeHHHhcC--CHHHHhccCCcceeecccccccc--hhhHHHHHhhccccc
Confidence             3333333332222211  1122567999999987665  11222334567899999999832  223333333322234


Q ss_pred             ccEEEEEeec
Q 022724          207 LQVVLISATL  216 (293)
Q Consensus       207 ~q~v~~SAt~  216 (293)
                      ...++++.|.
T Consensus       545 q~RLLLTGTP  554 (1157)
T KOG0386|consen  545 QRRLLLTGTP  554 (1157)
T ss_pred             hhhhhhcCCh
Confidence            4556677775

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=97.23  E-value=0.033  Score=59.64  Aligned_cols=206  Identities=12%  Similarity=0.124  Sum_probs=107.0

Q ss_pred             CCcHHHHHHHHhhhcC--CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceE
Q 022724           55 KPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQA  132 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~--~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  132 (293)
                      .+++-|++++..++..  +-.+|.|+.|+|||... -.++..+..  .|.+++.++|+-.-+..+.+....-.       
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--QGYEIQIITAGSLSAQELRQKIPRLA-------  498 (1960)
T ss_pred             CCCHHHHHHHHHHHhCCCCeEEEEECCCCCHHHHH-HHHHHHHHh--cCCeEEEEeCCHHHHHHHHHHhcchh-------
Confidence            4789999999998764  57899999999999542 233333333  25689999999887777665322100       


Q ss_pred             EEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhC-CCCccEEE
Q 022724          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL-PPDLQVVL  211 (293)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l-~~~~q~v~  211 (293)
                            .........+.++  .-..|...+.    .....+..-++|||||+-++..    ..+..+++.. ..+.++|+
T Consensus       499 ------~Ti~~~l~~l~~~--~~~~tv~~fl----~~~~~l~~~~vlIVDEAsMl~~----~~~~~Ll~~a~~~garvVl  562 (1960)
T TIGR02760       499 ------STFITWVKNLFND--DQDHTVQGLL----DKSSPFSNKDIFVVDEANKLSN----NELLKLIDKAEQHNSKLIL  562 (1960)
T ss_pred             ------hhHHHHHHhhccc--ccchhHHHhh----cccCCCCCCCEEEEECCCCCCH----HHHHHHHHHHhhcCCEEEE
Confidence                  0000111111111  1112222222    1223345678999999997743    3455555544 35788887


Q ss_pred             EEee--cC----hhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHH-hhC-CCCcEEEEcccch
Q 022724          212 ISAT--LP----HEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLY-DTL-TITQAVIFCNTKR  283 (293)
Q Consensus       212 ~SAt--~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~-~~~-~~~~~iIF~~s~~  283 (293)
                      +-=+  ++    ..+...+.... -+.. ...........+  .+...+. ......+..-+ ... ...+++|+..+.+
T Consensus       563 vGD~~QL~sV~aG~~f~~L~~~g-v~t~-~l~~i~rq~~~v--~i~~~~~-~~r~~~ia~~y~~L~~~r~~tliv~~t~~  637 (1960)
T TIGR02760       563 LNDSAQRQGMSAGSAIDLLKEGG-VTTY-AWVDTKQQKASV--EISEAVD-KLRVDYIASAWLDLTPDRQNSQVLATTHR  637 (1960)
T ss_pred             EcChhhcCccccchHHHHHHHCC-CcEE-EeecccccCcce--eeeccCc-hHHHHHHHHHHHhcccccCceEEEcCCcH
Confidence            7654  21    12233333321 1111 111111111111  1222222 22333443333 322 3346999999988


Q ss_pred             hHHHHHhh
Q 022724          284 KVLLLVLQ  291 (293)
Q Consensus       284 ~a~~l~~~  291 (293)
                      +.+.+...
T Consensus       638 dr~~Ln~~  645 (1960)
T TIGR02760       638 EQQDLTQI  645 (1960)
T ss_pred             HHHHHHHH
Confidence            87776543

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.

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.22  E-value=0.0029  Score=57.14  Aligned_cols=37  Identities=14%  Similarity=0.267  Sum_probs=23.8

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEc
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~  108 (293)
                      +.+++.||+|+|||... .++.+.+.....+.+++++.
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            35889999999999543 34445554433345666664

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).

>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=97.21  E-value=0.0025  Score=51.45  Aligned_cols=127  Identities=18%  Similarity=0.280  Sum_probs=64.5

Q ss_pred             cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEc--CCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHh
Q 022724           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS--PTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE  149 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~--P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  149 (293)
                      -++++||||+|||....--+......   +.++.+++  ..|.=+.++.+   .+....++.+.......+         
T Consensus         3 vi~lvGptGvGKTTt~aKLAa~~~~~---~~~v~lis~D~~R~ga~eQL~---~~a~~l~vp~~~~~~~~~---------   67 (196)
T PF00448_consen    3 VIALVGPTGVGKTTTIAKLAARLKLK---GKKVALISADTYRIGAVEQLK---TYAEILGVPFYVARTESD---------   67 (196)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHT---T--EEEEEESTSSTHHHHHHH---HHHHHHTEEEEESSTTSC---------
T ss_pred             EEEEECCCCCchHhHHHHHHHHHhhc---cccceeecCCCCCccHHHHHH---HHHHHhccccchhhcchh---------
Confidence            47899999999997654433333333   23444444  23443333333   333333444433221111         


Q ss_pred             cCCcEEEeChHHHH-HHHhcCCCCCCCccEEEecchhhhhc-cccHHHHHHHHhhCCCCccEEEEEeecChhHHHHH
Q 022724          150 HGVHVVSGTPGRVC-DMIKRKTLRTRAIKLLVLDESDEMLS-RGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMT  224 (293)
Q Consensus       150 ~~~~ilV~Tp~~l~-~~l~~~~~~~~~l~~iViDE~h~~~~-~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~  224 (293)
                               |..+. +.++.  ...++.++|+||-+-+... ......+..+.....+..-.+.+|||...+.....
T Consensus        68 ---------~~~~~~~~l~~--~~~~~~D~vlIDT~Gr~~~d~~~~~el~~~~~~~~~~~~~LVlsa~~~~~~~~~~  133 (196)
T PF00448_consen   68 ---------PAEIAREALEK--FRKKGYDLVLIDTAGRSPRDEELLEELKKLLEALNPDEVHLVLSATMGQEDLEQA  133 (196)
T ss_dssp             ---------HHHHHHHHHHH--HHHTTSSEEEEEE-SSSSTHHHHHHHHHHHHHHHSSSEEEEEEEGGGGGHHHHHH
T ss_pred             ---------hHHHHHHHHHH--HhhcCCCEEEEecCCcchhhHHHHHHHHHHhhhcCCccceEEEecccChHHHHHH
Confidence                     21211 12221  1124467888888765422 23345666666666666778889999876544433

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 ....

>PF03354 Terminase_1: Phage Terminase ; InterPro: IPR005021 This entry is represented by Lactococcus phage bIL285, Orf41 (terminase)

Probab=97.19  E-value=0.0018  Score=59.74  Aligned_cols=149  Identities=15%  Similarity=0.113  Sum_probs=82.2

Q ss_pred             HHHHHHHHhhh-----cC----CcEEEEcCCCChhHHHHHHHHHhhh-ccCCCceeEEEEcCCHHHHHHHHHHHHHhhcc
Q 022724           58 AIQQRAVMPII-----KG----RDVIAQAQSGTGKTSMIALTVCQTV-DTSSREVQALILSPTRELATQTEKVILAIGDF  127 (293)
Q Consensus        58 ~~Q~~~~~~i~-----~~----~~~li~~~Tg~GKT~~~~~~~~~~l-~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (293)
                      |||+-++-.+.     .|    +.+++..|=|.|||......++..+ .....+..+++.+++++-+..+++.++.+...
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     12    3688888999999966554444444 33344678999999999999999988876543


Q ss_pred             CCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc--CCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCC
Q 022724          128 INIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR--KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP  205 (293)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~--~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~  205 (293)
                      ...... ...     ...... ..-.|.....+.....+..  ...+=.+.+++|+||+|.+-+......+..-.... +
T Consensus        81 ~~~l~~-~~~-----~~~~~~-~~~~i~~~~~~s~~~~~s~~~~~~dG~~~~~~i~DE~h~~~~~~~~~~l~~g~~~r-~  152 (477)
T PF03354_consen   81 SPELRK-RKK-----PKIIKS-NKKEIEFPKTGSFFKALSSDADSLDGLNPSLAIFDELHAHKDDELYDALESGMGAR-P  152 (477)
T ss_pred             Chhhcc-chh-----hhhhhh-hceEEEEcCCCcEEEEEecCCCCccCCCCceEEEeCCCCCCCHHHHHHHHhhhccC-C
Confidence            211000 000     000000 0112222221222222211  22222457899999999986544444444444442 3


Q ss_pred             CccEEEEEe
Q 022724          206 DLQVVLISA  214 (293)
Q Consensus       206 ~~q~v~~SA  214 (293)
                      +.+++.+|.
T Consensus       153 ~pl~~~IST  161 (477)
T PF03354_consen  153 NPLIIIIST  161 (477)
T ss_pred             CceEEEEeC
Confidence            555555543

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=97.15  E-value=0.0022  Score=62.25  Aligned_cols=70  Identities=16%  Similarity=0.175  Sum_probs=53.8

Q ss_pred             CCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccC-CCceeEEEEcCCHHHHHHHHHHHHHhhc
Q 022724           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-SREVQALILSPTRELATQTEKVILAIGD  126 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~-~~~~~~lil~P~~~l~~q~~~~~~~~~~  126 (293)
                      .+++-|++++...  ..+++|.|+.|||||.+..--+.+.+... -...++++++-|+..|.++.+++.++..
T Consensus         9 ~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~vl~~Ria~Li~~~~v~p~~IL~lTFT~kAA~Em~~Rl~~~~~   79 (721)
T PRK11773          9 SLNDKQREAVAAP--LGNMLVLAGAGSGKTRVLVHRIAWLMQVENASPYSIMAVTFTNKAAAEMRHRIEQLLG   79 (721)
T ss_pred             hcCHHHHHHHhCC--CCCEEEEecCCCCHHHHHHHHHHHHHHcCCCChhHeEeeeccHHHHHHHHHHHHHHhc
Confidence            5899999988753  46899999999999977555454444322 2234799999999999999999988653

>PHA02533 17 large terminase protein; Provisional

Probab=97.14  E-value=0.005  Score=57.29  Aligned_cols=148  Identities=14%  Similarity=0.167  Sum_probs=85.1

Q ss_pred             CCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCC--ceE
Q 022724           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN--IQA  132 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~--~~~  132 (293)
                      .+.|+|...+..+..++-.++..+=..|||.+....++...... .+.++++++|+..-+..+.+.++.+.....  .+.
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            47899999998876666667888889999977765444333322 245899999999999999888876543221  010


Q ss_pred             EEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCC--CccEE
Q 022724          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP--DLQVV  210 (293)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~--~~q~v  210 (293)
                      .....+    ...-.+.++..|.+.|.+.       ....=.+.+++|+||+|.+.+  ....+..+...+..  ..+++
T Consensus       138 ~i~~~~----~~~I~l~NGS~I~~lss~~-------~t~rG~~~~~liiDE~a~~~~--~~e~~~ai~p~lasg~~~r~i  204 (534)
T PHA02533        138 GIVEWN----KGSIELENGSKIGAYASSP-------DAVRGNSFAMIYIDECAFIPN--FIDFWLAIQPVISSGRSSKII  204 (534)
T ss_pred             ceeecC----ccEEEeCCCCEEEEEeCCC-------CccCCCCCceEEEeccccCCC--HHHHHHHHHHHHHcCCCceEE
Confidence            000000    0001123555554444320       111123467899999998643  22333333333322  34566


Q ss_pred             EEEeec
Q 022724          211 LISATL  216 (293)
Q Consensus       211 ~~SAt~  216 (293)
                      ++|++-
T Consensus       205 iiSTp~  210 (534)
T PHA02533        205 ITSTPN  210 (534)
T ss_pred             EEECCC
Confidence            666664

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=97.13  E-value=0.0058  Score=55.68  Aligned_cols=38  Identities=13%  Similarity=0.307  Sum_probs=24.3

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcC
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P  109 (293)
                      +.+++.||+|+|||... -++.+.+.....+.+++|+..
T Consensus       131 n~l~lyG~~G~GKTHLl-~ai~~~l~~~~~~~~v~yi~~  168 (440)
T PRK14088        131 NPLFIYGGVGLGKTHLL-QSIGNYVVQNEPDLRVMYITS  168 (440)
T ss_pred             CeEEEEcCCCCcHHHHH-HHHHHHHHHhCCCCeEEEEEH
Confidence            46999999999999443 234444444333446776653

>PRK07952 DNA replication protein DnaC; Validated

Probab=97.13  E-value=0.0076  Score=50.28  Aligned_cols=104  Identities=14%  Similarity=0.232  Sum_probs=53.7

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhc
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH  150 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  150 (293)
                      ..+++.|++|+|||.... ++...+...  +..++++ +..++...+...+.   ..                       
T Consensus       100 ~~~~l~G~~GtGKThLa~-aia~~l~~~--g~~v~~i-t~~~l~~~l~~~~~---~~-----------------------  149 (244)
T PRK07952        100 ASFIFSGKPGTGKNHLAA-AICNELLLR--GKSVLII-TVADIMSAMKDTFS---NS-----------------------  149 (244)
T ss_pred             ceEEEECCCCCCHHHHHH-HHHHHHHhc--CCeEEEE-EHHHHHHHHHHHHh---hc-----------------------
Confidence            479999999999995443 344444432  3345554 43344333322110   00                       


Q ss_pred             CCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHH-HHHHHHhhCCC-CccEEEEEeecC
Q 022724          151 GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKD-QIYDVYRYLPP-DLQVVLISATLP  217 (293)
Q Consensus       151 ~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~-~~~~i~~~l~~-~~q~v~~SAt~~  217 (293)
                        +   .+.+.+.+.       +.+.++|||||++......+.. .+..++..... ...++ +|..++
T Consensus       150 --~---~~~~~~l~~-------l~~~dlLvIDDig~~~~s~~~~~~l~~Ii~~Ry~~~~~ti-itSNl~  205 (244)
T PRK07952        150 --E---TSEEQLLND-------LSNVDLLVIDEIGVQTESRYEKVIINQIVDRRSSSKRPTG-MLTNSN  205 (244)
T ss_pred             --c---ccHHHHHHH-------hccCCEEEEeCCCCCCCCHHHHHHHHHHHHHHHhCCCCEE-EeCCCC
Confidence              0   122233322       4467899999999875443433 34445544332 34444 444443

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=97.11  E-value=0.0061  Score=63.64  Aligned_cols=63  Identities=24%  Similarity=0.287  Sum_probs=45.4

Q ss_pred             CCcHHHHHHHHhhhcC--CcEEEEcCCCChhHHHHHHHHHhhhc--cCCCceeEEEEcCCHHHHHHHH
Q 022724           55 KPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVD--TSSREVQALILSPTRELATQTE  118 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~--~~~li~~~Tg~GKT~~~~~~~~~~l~--~~~~~~~~lil~P~~~l~~q~~  118 (293)
                      .+++.|++++..++.+  +-++|.|..|+|||... -.++..+.  ....+.+++.++||-.-+..+.
T Consensus       967 ~Lt~~Q~~Av~~il~s~dr~~~I~G~AGTGKTT~l-~~v~~~~~~l~~~~~~~V~glAPTgrAAk~L~ 1033 (1747)
T PRK13709        967 GLTSGQRAATRMILESTDRFTVVQGYAGVGKTTQF-RAVMSAVNTLPESERPRVVGLGPTHRAVGEMR 1033 (1747)
T ss_pred             CCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHHH-HHHHHHHHHhhcccCceEEEECCcHHHHHHHH
Confidence            5899999999998864  57899999999999553 22323222  1223457888999988776654

>KOG1131 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 5'-3' helicase subunit RAD3 [Transcription; Replication, recombination and repair]

Probab=97.10  E-value=0.0027  Score=57.22  Aligned_cols=71  Identities=13%  Similarity=0.028  Sum_probs=43.8

Q ss_pred             CCCCCcHHHHHHHHhhh----cCCcEEEEcCCCChhHHHHHHHHHhhhccCC-CceeEEEEcCCHHHHHHHHHHHH
Q 022724           52 GFEKPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-REVQALILSPTRELATQTEKVIL  122 (293)
Q Consensus        52 ~~~~~~~~Q~~~~~~i~----~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~-~~~~~lil~P~~~l~~q~~~~~~  122 (293)
                      -|...+|-|.+-.-.+.    .+.+.++..|+|+|||.+.+-.++......+ ...+.|+-.-|..-++.....++
T Consensus        13 PY~~iYPEQ~~YM~elKrsLDakGh~llEMPSGTGKTvsLLSli~aYq~~~p~~~~KliYCSRTvpEieK~l~El~   88 (755)
T KOG1131|consen   13 PYDYIYPEQYEYMRELKRSLDAKGHCLLEMPSGTGKTVSLLSLIIAYQLHYPDEHRKLIYCSRTVPEIEKALEELK   88 (755)
T ss_pred             CCcccCHHHHHHHHHHHHhhccCCcEEEECCCCCCcchHHHHHHHHHHHhCCcccceEEEecCcchHHHHHHHHHH
Confidence            45667888877665554    3568999999999999776555554433333 23355555555544444444443

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=97.10  E-value=0.0046  Score=55.55  Aligned_cols=36  Identities=22%  Similarity=0.358  Sum_probs=22.3

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEE
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALIL  107 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil  107 (293)
                      .+++|.||+|+|||... -.++..+.....+...+++
T Consensus        56 ~~~lI~G~~GtGKT~l~-~~v~~~l~~~~~~~~~v~i   91 (394)
T PRK00411         56 LNVLIYGPPGTGKTTTV-KKVFEELEEIAVKVVYVYI   91 (394)
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHHHHHhcCCcEEEEE
Confidence            57999999999999543 3344444333223345554

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=97.10  E-value=0.0021  Score=58.67  Aligned_cols=49  Identities=16%  Similarity=0.332  Sum_probs=30.0

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHH
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVI  121 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~  121 (293)
                      +.+++.|++|+|||... -++.+.+.....+.+++++.+ .++..++...+
T Consensus       142 npl~i~G~~G~GKTHLl-~Ai~~~l~~~~~~~~v~yv~~-~~f~~~~~~~l  190 (450)
T PRK14087        142 NPLFIYGESGMGKTHLL-KAAKNYIESNFSDLKVSYMSG-DEFARKAVDIL  190 (450)
T ss_pred             CceEEECCCCCcHHHHH-HHHHHHHHHhCCCCeEEEEEH-HHHHHHHHHHH
Confidence            45899999999999332 344455544334556666555 55555554433

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=97.09  E-value=0.0045  Score=63.85  Aligned_cols=64  Identities=22%  Similarity=0.293  Sum_probs=46.5

Q ss_pred             CCcHHHHHHHHhhhc--CCcEEEEcCCCChhHHHH--HHHHHhhhccCCCceeEEEEcCCHHHHHHHHH
Q 022724           55 KPSAIQQRAVMPIIK--GRDVIAQAQSGTGKTSMI--ALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~--~~~~li~~~Tg~GKT~~~--~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~  119 (293)
                      .+++-|++++..++.  ++-++|.|..|+|||...  ++.++..+.. ..+.+++.++||-.-+..+.+
T Consensus       835 ~Lt~~Qr~Av~~iLts~dr~~~IqG~AGTGKTT~l~~i~~~~~~l~e-~~g~~V~glAPTgkAa~~L~e  902 (1623)
T PRK14712        835 KLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPE-SERPRVVGLGPTHRAVGEMRS  902 (1623)
T ss_pred             ccCHHHHHHHHHHHhCCCceEEEEeCCCCCHHHHHHHHHHHHHHHhh-ccCceEEEEechHHHHHHHHH
Confidence            589999999999885  477999999999999653  2223333222 234578899999887776643

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=97.09  E-value=0.0039  Score=63.91  Aligned_cols=122  Identities=15%  Similarity=0.172  Sum_probs=79.3

Q ss_pred             CcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhc-cCCceEEE
Q 022724           56 PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGD-FINIQAHA  134 (293)
Q Consensus        56 ~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~-~~~~~~~~  134 (293)
                      .|+-|++++.  ..+++++|.|+.|||||.+..--++..+.....-.++++++=|+..+.++.+++.+... ...-    
T Consensus         2 ~t~~Q~~ai~--~~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~~~~~~il~~tFt~~aa~e~~~ri~~~l~~~~~~----   75 (1232)
T TIGR02785         2 WTDEQWQAIY--TRGQNILVSASAGSGKTAVLVERIIKKILRGVDIDRLLVVTFTNAAAREMKERIEEALQKALQQ----   75 (1232)
T ss_pred             CCHHHHHHHh--CCCCCEEEEecCCCcHHHHHHHHHHHHHhcCCCHhhEEEEeccHHHHHHHHHHHHHHHHHHHhc----
Confidence            5889999997  46889999999999999876666666554432224799999999999999998876332 1110    


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHH-HHhcCCCCC-CCccEEEecchhh
Q 022724          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCD-MIKRKTLRT-RAIKLLVLDESDE  186 (293)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~-~l~~~~~~~-~~l~~iViDE~h~  186 (293)
                         .....+..+.+..-...-|+|...++. +++.....+ =+..+=|.||...
T Consensus        76 ---~p~~~~L~~q~~~~~~~~i~Tihsf~~~~~~~~~~~l~ldP~F~i~de~e~  126 (1232)
T TIGR02785        76 ---EPNSKHLRRQLALLNTANISTLHSFCLKVIRKHYYLLDLDPSFRILTDTEQ  126 (1232)
T ss_pred             ---CchhHHHHHHHhhccCCeEeeHHHHHHHHHHHhhhhcCCCCCceeCCHHHH
Confidence               001111112222234678899999986 555432221 1225566888876

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.

>PRK11054 helD DNA helicase IV; Provisional

Probab=97.07  E-value=0.0032  Score=60.40  Aligned_cols=70  Identities=23%  Similarity=0.242  Sum_probs=52.2

Q ss_pred             CCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccC-CCceeEEEEcCCHHHHHHHHHHHHHhh
Q 022724           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-SREVQALILSPTRELATQTEKVILAIG  125 (293)
Q Consensus        54 ~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~-~~~~~~lil~P~~~l~~q~~~~~~~~~  125 (293)
                      ..+++-|++++..  ...+++|.|+.|||||.+..--+...+... ..+.++++++.++..+..+.+++....
T Consensus       195 ~~L~~~Q~~av~~--~~~~~lV~agaGSGKT~vl~~r~ayLl~~~~~~~~~IL~ltft~~AA~em~eRL~~~l  265 (684)
T PRK11054        195 SPLNPSQARAVVN--GEDSLLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRQAAEEMDERIRERL  265 (684)
T ss_pred             CCCCHHHHHHHhC--CCCCeEEEEeCCCCHHHHHHHHHHHHHHhCCCCHHHeEEEeccHHHHHHHHHHHHHhc
Confidence            4689999998864  345789999999999977554443333322 224589999999999999999887644

>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=97.06  E-value=0.0091  Score=47.53  Aligned_cols=48  Identities=15%  Similarity=0.160  Sum_probs=31.7

Q ss_pred             EEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 022724           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (293)
Q Consensus        73 ~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (293)
                      ++|.||+|+|||...+-.+...+..   +.+++|+.. .+...++.+.+..+
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            6899999999996554444444322   456777754 45567777766655

A related protein is found in archaea.

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=97.06  E-value=0.0034  Score=52.79  Aligned_cols=67  Identities=15%  Similarity=0.306  Sum_probs=42.5

Q ss_pred             CCCCCcHHHHHHHHhhh-------cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHH
Q 022724           52 GFEKPSAIQQRAVMPII-------KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL  122 (293)
Q Consensus        52 ~~~~~~~~Q~~~~~~i~-------~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~  122 (293)
                      .|......+..++..+.       +++++++.||+|+|||..+.. +...+..  .| ..++.+++.+++.++...+.
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            44445555555554432       578999999999999955442 3333332  23 45666787888887777443

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.05  E-value=0.021  Score=51.77  Aligned_cols=128  Identities=15%  Similarity=0.234  Sum_probs=65.6

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhh-ccCCCceeEEEEc--CCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTV-DTSSREVQALILS--PTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIR  146 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l-~~~~~~~~~lil~--P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  146 (293)
                      ++.++++||||+|||....--+.... ...  +.++.++.  |.+.-+.   +.++.+....++.+              
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~--g~~V~li~~D~~r~~a~---eqL~~~a~~~~vp~--------------  281 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYG--KKKVALITLDTYRIGAV---EQLKTYAKIMGIPV--------------  281 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcC--CCeEEEEECCccHHHHH---HHHHHHHHHhCCce--------------
Confidence            46789999999999965443222222 121  23455444  2333222   22333333333322              


Q ss_pred             HHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcc-ccHHHHHHHHhhC-CCCccEEEEEeecCh-hHHHH
Q 022724          147 KLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYL-PPDLQVVLISATLPH-EILEM  223 (293)
Q Consensus       147 ~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~-~~~~~~~~i~~~l-~~~~q~v~~SAt~~~-~~~~~  223 (293)
                             ..+.+++.+...+..    +.+.++|+||.+-..... .....+..++... .+....+++|||... ++.+.
T Consensus       282 -------~~~~~~~~l~~~l~~----~~~~DlVlIDt~G~~~~d~~~~~~L~~ll~~~~~~~~~~LVl~a~~~~~~l~~~  350 (424)
T PRK05703        282 -------EVVYDPKELAKALEQ----LRDCDVILIDTAGRSQRDKRLIEELKALIEFSGEPIDVYLVLSATTKYEDLKDI  350 (424)
T ss_pred             -------EccCCHHhHHHHHHH----hCCCCEEEEeCCCCCCCCHHHHHHHHHHHhccCCCCeEEEEEECCCCHHHHHHH
Confidence                   122345555554443    235789999988553221 2233455555522 233457889998864 44555


Q ss_pred             HHhc
Q 022724          224 TTKF  227 (293)
Q Consensus       224 ~~~~  227 (293)
                      ...+
T Consensus       351 ~~~f  354 (424)
T PRK05703        351 YKHF  354 (424)
T ss_pred             HHHh
Confidence            4444

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=97.04  E-value=0.0067  Score=53.02  Aligned_cols=33  Identities=18%  Similarity=0.207  Sum_probs=26.5

Q ss_pred             CcHHHHHHHHhhhcC-C---cEEEEcCCCChhHHHHH
Q 022724           56 PSAIQQRAVMPIIKG-R---DVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        56 ~~~~Q~~~~~~i~~~-~---~~li~~~Tg~GKT~~~~   88 (293)
                      .+|||...|..+... +   -+++.||.|.|||..+.
T Consensus         4 ~yPWl~~~~~~~~~~~r~~ha~Lf~G~~G~GK~~~A~   40 (328)
T PRK05707          4 IYPWQQSLWQQLAGRGRHPHAYLLHGPAGIGKRALAE   40 (328)
T ss_pred             CCCCcHHHHHHHHHCCCcceeeeeECCCCCCHHHHHH
Confidence            579999999998743 2   48899999999995543

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=97.03  E-value=0.0032  Score=60.38  Aligned_cols=126  Identities=18%  Similarity=0.257  Sum_probs=92.4

Q ss_pred             CcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEE
Q 022724           56 PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC  135 (293)
Q Consensus        56 ~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~  135 (293)
                      |..+|.  +-.+.-...-+...-||-|||+.+.+|+.-.-..   |..+-++....-|+..-.+.+..+...+|+++...
T Consensus        81 ~~dVQl--iG~i~lh~g~iaEM~TGEGKTL~atlp~ylnaL~---gkgVhvVTvNdYLA~RDae~m~~l~~~LGlsvG~~  155 (822)
T COG0653          81 HFDVQL--LGGIVLHLGDIAEMRTGEGKTLVATLPAYLNALA---GKGVHVVTVNDYLARRDAEWMGPLYEFLGLSVGVI  155 (822)
T ss_pred             hhhHHH--hhhhhhcCCceeeeecCCchHHHHHHHHHHHhcC---CCCcEEeeehHHhhhhCHHHHHHHHHHcCCceeec
Confidence            444444  4555555667889999999999999887655444   23477888899999999999999999999999998


Q ss_pred             ECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcC------CCCCCCccEEEecchhhhh
Q 022724          136 VGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRK------TLRTRAIKLLVLDESDEML  188 (293)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~ilV~Tp~~l-~~~l~~~------~~~~~~l~~iViDE~h~~~  188 (293)
                      ..+.+..+....+  .|||.-+|...+ .++++.+      ......+.+-|+||+|.++
T Consensus       156 ~~~m~~~ek~~aY--~~DItY~TnnElGFDYLRDNm~~~~ee~vqr~~~faIvDEvDSIL  213 (822)
T COG0653         156 LAGMSPEEKRAAY--ACDITYGTNNELGFDYLRDNMVTSQEEKVQRGLNFAIVDEVDSIL  213 (822)
T ss_pred             cCCCChHHHHHHH--hcCceeccccccCcchhhhhhhccHHHhhhccCCeEEEcchhhee
Confidence            8888766555554  368999997665 2233222      1223568899999999874

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=97.02  E-value=0.0028  Score=57.07  Aligned_cols=135  Identities=16%  Similarity=0.219  Sum_probs=77.8

Q ss_pred             cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHH-HHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhc
Q 022724           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE-LATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH  150 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~-l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  150 (293)
                      -.++.|+.|||||.+...-++..+...+.+.+++++-|+.. +-..+...+.......++....-....+.  .+ .+.+
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            36788999999999888877777666423468899989865 77777887776655555432111111100  00 0112


Q ss_pred             -CCcEEEeCh-HHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCC--CCccEEEEEeecCh
Q 022724          151 -GVHVVSGTP-GRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP--PDLQVVLISATLPH  218 (293)
Q Consensus       151 -~~~ilV~Tp-~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~--~~~q~v~~SAt~~~  218 (293)
                       +..|++..- +.... ++    ....++++.+||+..+...    .+..++.+++  .....+++|.++..
T Consensus        80 ~g~~i~f~g~~d~~~~-ik----~~~~~~~~~idEa~~~~~~----~~~~l~~rlr~~~~~~~i~~t~NP~~  142 (396)
T TIGR01547        80 TGKKFIFKGLNDKPNK-LK----SGAGIAIIWFEEASQLTFE----DIKELIPRLRETGGKKFIIFSSNPES  142 (396)
T ss_pred             CCeEEEeecccCChhH-hh----CcceeeeehhhhhhhcCHH----HHHHHHHHhhccCCccEEEEEcCcCC
Confidence             334555443 22211 11    1233689999999988433    3444444443  22224778888754

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.

>PRK06893 DNA replication initiation factor; Validated

Probab=96.99  E-value=0.0027  Score=52.60  Aligned_cols=46  Identities=20%  Similarity=0.387  Sum_probs=29.0

Q ss_pred             CCccEEEecchhhhhcc-ccHHHHHHHHhhCC-CCccEEEEEeecChh
Q 022724          174 RAIKLLVLDESDEMLSR-GFKDQIYDVYRYLP-PDLQVVLISATLPHE  219 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~-~~~~~~~~i~~~l~-~~~q~v~~SAt~~~~  219 (293)
                      .+.+++|+||+|.+... .+...+..++..+. ...+++++|++.++.
T Consensus        90 ~~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~  137 (229)
T PRK06893         90 EQQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPH  137 (229)
T ss_pred             ccCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChH
Confidence            45689999999987533 33334445454443 345677888876544

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=96.99  E-value=0.0054  Score=50.51  Aligned_cols=20  Identities=25%  Similarity=0.424  Sum_probs=16.3

Q ss_pred             cCCcEEEEcCCCChhHHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~   88 (293)
                      .+.++++.||+|+|||....
T Consensus        37 ~~~~lll~G~~G~GKT~la~   56 (226)
T TIGR03420        37 GDRFLYLWGESGSGKSHLLQ   56 (226)
T ss_pred             CCCeEEEECCCCCCHHHHHH
Confidence            45689999999999995543

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.

>PRK08116 hypothetical protein; Validated

Probab=96.98  E-value=0.013  Score=49.83  Aligned_cols=44  Identities=18%  Similarity=0.271  Sum_probs=26.3

Q ss_pred             cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHH
Q 022724           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~  119 (293)
                      .+++.|++|+|||..+. ++.+.+...  +..++ ..+..++...+..
T Consensus       116 gl~l~G~~GtGKThLa~-aia~~l~~~--~~~v~-~~~~~~ll~~i~~  159 (268)
T PRK08116        116 GLLLWGSVGTGKTYLAA-CIANELIEK--GVPVI-FVNFPQLLNRIKS  159 (268)
T ss_pred             eEEEECCCCCCHHHHHH-HHHHHHHHc--CCeEE-EEEHHHHHHHHHH
Confidence            49999999999995433 455555443  33344 4444555544433

>PRK08727 hypothetical protein; Validated

Probab=96.98  E-value=0.0047  Score=51.33  Aligned_cols=35  Identities=20%  Similarity=0.356  Sum_probs=21.4

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEc
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~  108 (293)
                      +.+++.||+|+|||.... ++.+.+...  +.+++|+.
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            459999999999994322 333333332  34566654

>PRK12377 putative replication protein; Provisional

Probab=96.97  E-value=0.013  Score=48.95  Aligned_cols=46  Identities=13%  Similarity=0.265  Sum_probs=27.6

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~  119 (293)
                      ..++++.||+|+|||.... ++...+...  +..+ +.++..++..++..
T Consensus       101 ~~~l~l~G~~GtGKThLa~-AIa~~l~~~--g~~v-~~i~~~~l~~~l~~  146 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLAA-AIGNRLLAK--GRSV-IVVTVPDVMSRLHE  146 (248)
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHHHHc--CCCe-EEEEHHHHHHHHHH
Confidence            3689999999999994332 334444432  3334 44455566665544

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=96.97  E-value=0.011  Score=50.11  Aligned_cols=18  Identities=33%  Similarity=0.514  Sum_probs=15.1

Q ss_pred             CcEEEEcCCCChhHHHHH
Q 022724           71 RDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~   88 (293)
                      .++++.||+|+|||..+-
T Consensus        43 ~~vll~GppGtGKTtlA~   60 (261)
T TIGR02881        43 LHMIFKGNPGTGKTTVAR   60 (261)
T ss_pred             ceEEEEcCCCCCHHHHHH
Confidence            579999999999996543

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.

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=96.97  E-value=0.0099  Score=56.78  Aligned_cols=67  Identities=22%  Similarity=0.301  Sum_probs=51.6

Q ss_pred             CCcHHHHHHHHhhhcC-----CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcc
Q 022724           55 KPSAIQQRAVMPIIKG-----RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDF  127 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~-----~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (293)
                      .|+-.|..++..+.++     ++.++.|-||||||+...- ++..+     +..+||++|++.+|.|+++.++.+...
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            4888999999887643     3667999999999976442 33322     225899999999999999999988754

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

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=96.96  E-value=0.0057  Score=58.92  Aligned_cols=69  Identities=17%  Similarity=0.151  Sum_probs=53.7

Q ss_pred             CcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccC-CCceeEEEEcCCHHHHHHHHHHHHHhhc
Q 022724           56 PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-SREVQALILSPTRELATQTEKVILAIGD  126 (293)
Q Consensus        56 ~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~-~~~~~~lil~P~~~l~~q~~~~~~~~~~  126 (293)
                      +++-|++++..  .+.+++|.|+.|||||.+..--+.+.+... ....++++++.|+..+.++.+++.+...
T Consensus         2 Ln~~Q~~av~~--~~~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~~~p~~IL~vTFt~~Aa~em~~Rl~~~l~   71 (664)
T TIGR01074         2 LNPQQQEAVEY--VTGPCLVLAGAGSGKTRVITNKIAYLIQNCGYKARNIAAVTFTNKAAREMKERVAKTLG   71 (664)
T ss_pred             CCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHhC
Confidence            67889998865  356899999999999987666666666432 2335789999999999999999987543

Designed to identify rep members of the uvrD/rep subfamily.

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=96.96  E-value=0.0039  Score=54.13  Aligned_cols=64  Identities=22%  Similarity=0.279  Sum_probs=42.1

Q ss_pred             HHHHCCCCCCcHHHHHHHHh-hhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHH
Q 022724           47 GIYQYGFEKPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (293)
Q Consensus        47 ~l~~~~~~~~~~~Q~~~~~~-i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l  113 (293)
                      .+.+.|.  .++.|...+.. +..+++++|+|+||||||. ++-+++..+...+.+.+++.+=...||
T Consensus       122 ~lv~~g~--~~~~~~~~L~~~v~~~~nilI~G~tGSGKTT-ll~aL~~~i~~~~~~~rivtiEd~~El  186 (323)
T PRK13833        122 DYVTSKI--MTEAQASVIRSAIDSRLNIVISGGTGSGKTT-LANAVIAEIVASAPEDRLVILEDTAEI  186 (323)
T ss_pred             HHHHcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHH-HHHHHHHHHhcCCCCceEEEecCCccc
Confidence            3444443  56677766655 4567899999999999994 344555655433334577777767776

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=96.95  E-value=0.0039  Score=53.03  Aligned_cols=132  Identities=14%  Similarity=0.231  Sum_probs=65.9

Q ss_pred             CcHHHHHHHHhhh---cC------CcEEEEcCCCChhHHHHHHHHHhhhcc-CC---CceeEEEEcCCHHHHHHHHHHHH
Q 022724           56 PSAIQQRAVMPII---KG------RDVIAQAQSGTGKTSMIALTVCQTVDT-SS---REVQALILSPTRELATQTEKVIL  122 (293)
Q Consensus        56 ~~~~Q~~~~~~i~---~~------~~~li~~~Tg~GKT~~~~~~~~~~l~~-~~---~~~~~lil~P~~~l~~q~~~~~~  122 (293)
                      .+|.=.+++..+.   ..      .+++++|+|+.|||...--..-.+-.. ..   .-|-+.+-+|...-....+..+-
T Consensus        38 gY~~A~~~L~~L~~Ll~~P~~~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL  117 (302)
T PF05621_consen   38 GYPRAKEALDRLEELLEYPKRHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAIL  117 (302)
T ss_pred             cCHHHHHHHHHHHHHHhCCcccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHH
Confidence            4555555555443   21      489999999999996432111111000 00   12445666677666666555443


Q ss_pred             HhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcccc--HHHHHHHH
Q 022724          123 AIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF--KDQIYDVY  200 (293)
Q Consensus       123 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~--~~~~~~i~  200 (293)
                      .   .++.....   ..... ..             -....++++     .-.++++||||+|.++....  ...+..++
T Consensus       118 ~---~lgaP~~~---~~~~~-~~-------------~~~~~~llr-----~~~vrmLIIDE~H~lLaGs~~~qr~~Ln~L  172 (302)
T PF05621_consen  118 E---ALGAPYRP---RDRVA-KL-------------EQQVLRLLR-----RLGVRMLIIDEFHNLLAGSYRKQREFLNAL  172 (302)
T ss_pred             H---HhCcccCC---CCCHH-HH-------------HHHHHHHHH-----HcCCcEEEeechHHHhcccHHHHHHHHHHH
Confidence            2   22211100   00000 00             011223333     34568999999999876543  34455566


Q ss_pred             hhCCCC--ccEEEE
Q 022724          201 RYLPPD--LQVVLI  212 (293)
Q Consensus       201 ~~l~~~--~q~v~~  212 (293)
                      +.+.+.  ..+|++
T Consensus       173 K~L~NeL~ipiV~v  186 (302)
T PF05621_consen  173 KFLGNELQIPIVGV  186 (302)
T ss_pred             HHHhhccCCCeEEe
Confidence            666654  445544

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>CHL00181 cbbX CbbX; Provisional

Probab=96.95  E-value=0.017  Score=49.58  Aligned_cols=19  Identities=32%  Similarity=0.455  Sum_probs=15.8

Q ss_pred             CCcEEEEcCCCChhHHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~   88 (293)
                      |.++++.||+|+|||..+-
T Consensus        59 ~~~ill~G~pGtGKT~lAr   77 (287)
T CHL00181         59 GLHMSFTGSPGTGKTTVAL   77 (287)
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            4579999999999996654

>PRK06835 DNA replication protein DnaC; Validated

Probab=96.92  E-value=0.012  Score=51.35  Aligned_cols=46  Identities=15%  Similarity=0.237  Sum_probs=27.7

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE  118 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~  118 (293)
                      .++++++.||||+|||.... ++...+...  +..+++ .+..++..++.
T Consensus       182 ~~~~Lll~G~~GtGKThLa~-aIa~~l~~~--g~~V~y-~t~~~l~~~l~  227 (329)
T PRK06835        182 NNENLLFYGNTGTGKTFLSN-CIAKELLDR--GKSVIY-RTADELIEILR  227 (329)
T ss_pred             cCCcEEEECCCCCcHHHHHH-HHHHHHHHC--CCeEEE-EEHHHHHHHHH
Confidence            35799999999999995433 344444332  334554 44455554443

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=96.91  E-value=0.0038  Score=60.69  Aligned_cols=70  Identities=16%  Similarity=0.207  Sum_probs=54.2

Q ss_pred             CCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCC-CceeEEEEcCCHHHHHHHHHHHHHhh
Q 022724           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-REVQALILSPTRELATQTEKVILAIG  125 (293)
Q Consensus        54 ~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~-~~~~~lil~P~~~l~~q~~~~~~~~~  125 (293)
                      ..+++-|.+++...  ..+++|.|+.|||||.+..--+.+.+.... ...++++++-|+..+.++.+++.++.
T Consensus         3 ~~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~~l~~ria~Li~~~~i~P~~IL~lTFT~kAA~em~~Rl~~~~   73 (726)
T TIGR01073         3 AHLNPEQREAVKTT--EGPLLIMAGAGSGKTRVLTHRIAHLIAEKNVAPWNILAITFTNKAAREMKERVEKLL   73 (726)
T ss_pred             cccCHHHHHHHhCC--CCCEEEEeCCCCCHHHHHHHHHHHHHHcCCCCHHHeeeeeccHHHHHHHHHHHHHHh
Confidence            35899999998753  578999999999999776655555554322 22479999999999999999988764

Designed to identify pcrA members of the uvrD/rep subfamily.

>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=96.91  E-value=0.0011  Score=52.29  Aligned_cols=124  Identities=15%  Similarity=0.196  Sum_probs=51.0

Q ss_pred             EEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCc
Q 022724           74 IAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVH  153 (293)
Q Consensus        74 li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  153 (293)
                      ++.|+-|-|||.+.-+.+...+...  ..+++|.+|+.+-+..+.+.+..-.+..+++.......   ........++..
T Consensus         1 VltA~RGRGKSa~lGl~~a~l~~~~--~~~I~vtAP~~~~~~~lf~~~~~~l~~~~~~~~~~~~~---~~~~~~~~~~~~   75 (177)
T PF05127_consen    1 VLTADRGRGKSAALGLAAAALIQKG--KIRILVTAPSPENVQTLFEFAEKGLKALGYKEEKKKRI---GQIIKLRFNKQR   75 (177)
T ss_dssp             -EEE-TTSSHHHHHHHCCCCSSS-------EEEE-SS--S-HHHHHCC-----------------------------CCC
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHhc--CceEEEecCCHHHHHHHHHHHHhhcccccccccccccc---ccccccccccce
Confidence            5789999999954433332222222  25799999999999998887665444443332000000   000001112345


Q ss_pred             EEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEeecC
Q 022724          154 VVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLP  217 (293)
Q Consensus       154 ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~  217 (293)
                      |-...|+.+...       ....+++|||||=.+.    ...+..+++    ....+++|.|+.
T Consensus        76 i~f~~Pd~l~~~-------~~~~DlliVDEAAaIp----~p~L~~ll~----~~~~vv~stTi~  124 (177)
T PF05127_consen   76 IEFVAPDELLAE-------KPQADLLIVDEAAAIP----LPLLKQLLR----RFPRVVFSTTIH  124 (177)
T ss_dssp             --B--HHHHCCT-----------SCEEECTGGGS-----HHHHHHHHC----CSSEEEEEEEBS
T ss_pred             EEEECCHHHHhC-------cCCCCEEEEechhcCC----HHHHHHHHh----hCCEEEEEeecc
Confidence            666666544432       1234899999997652    233444433    334677788874

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.

>PF13173 AAA_14: AAA domain

Probab=96.89  E-value=0.024  Score=42.27  Aligned_cols=38  Identities=16%  Similarity=0.347  Sum_probs=25.7

Q ss_pred             CccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEee
Q 022724          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISAT  215 (293)
Q Consensus       175 ~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt  215 (293)
                      .-.++++||+|.+.  .+...+..+...- ++.++++.+..
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            45789999999984  4566666666654 45666655443

>PRK08084 DNA replication initiation factor; Provisional

Probab=96.85  E-value=0.0045  Score=51.49  Aligned_cols=37  Identities=8%  Similarity=0.240  Sum_probs=22.2

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcC
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P  109 (293)
                      +.++++.||+|+|||.... ++.+.+...  +.+++|+.-
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            3689999999999994433 233333322  345555533

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=96.85  E-value=0.0066  Score=52.37  Aligned_cols=66  Identities=21%  Similarity=0.395  Sum_probs=42.3

Q ss_pred             HHHHHHCCCCCCcHHHHHHHHh-hhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHH
Q 022724           45 LRGIYQYGFEKPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (293)
Q Consensus        45 ~~~l~~~~~~~~~~~Q~~~~~~-i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l  113 (293)
                      ++.+.+.|.  +++.|...+.. +..+++++|+|+||||||. ++-+++..+.......+++.+-...|+
T Consensus       108 l~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTT-ll~al~~~i~~~~~~~ri~tiEd~~El  174 (299)
T TIGR02782       108 LDDYVEAGI--MTAAQRDVLREAVLARKNILVVGGTGSGKTT-LANALLAEIAKNDPTDRVVIIEDTREL  174 (299)
T ss_pred             HHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHH-HHHHHHHHhhccCCCceEEEECCchhh
Confidence            444444443  44555555554 5567899999999999994 344555665543334477777777776

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.

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

Probab=96.84  E-value=0.0091  Score=50.72  Aligned_cols=143  Identities=15%  Similarity=0.150  Sum_probs=65.5

Q ss_pred             HHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHH
Q 022724           43 DLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL  122 (293)
Q Consensus        43 ~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~  122 (293)
                      ++.++|..-+..+..+---+.+.-+..|..+++.|++|+|||....-.+.+....  .+..++|+.-- .-..++..++.
T Consensus         3 ~~~~~~~~~~~~tg~~~Ld~~~gG~~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~--~g~~vl~iS~E-~~~~~~~~r~~   79 (271)
T cd01122           3 EIREALSNEEVWWPFPVLNKLTKGLRKGELIILTAGTGVGKTTFLREYALDLITQ--HGVRVGTISLE-EPVVRTARRLL   79 (271)
T ss_pred             hhhccccccCCCCCcceeeeeeEEEcCCcEEEEEcCCCCCHHHHHHHHHHHHHHh--cCceEEEEEcc-cCHHHHHHHHH
Confidence            3445555333333222222233345567889999999999995433333332222  14467777642 23445555444


Q ss_pred             HhhccCCceEEEEECCcchHHH---HHHHhcCCcEE-Ee-----ChHHHHHHHhcCCCCCCCccEEEecchhhhhc
Q 022724          123 AIGDFINIQAHACVGGKSVGED---IRKLEHGVHVV-SG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (293)
Q Consensus       123 ~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~il-V~-----Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~  189 (293)
                      .......+..............   ...+.....+. +-     +++.+...++.-. .-..+++||||.++.+..
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~d~~~~~~~~~i~~~i~~~~-~~~~~~~vvID~l~~l~~  154 (271)
T cd01122          80 GQYAGKRLHLPDTVFIYTLEEFDAAFDEFEGTGRLFMYDSFGEYSMDSVLEKVRYMA-VSHGIQHIIIDNLSIMVS  154 (271)
T ss_pred             HHHhCCCcccCCccccccHHHHHHHHHHhcCCCcEEEEcCCCccCHHHHHHHHHHHH-hcCCceEEEECCHHHHhc
Confidence            3322222211100001111111   11222112222 21     4555555444311 123578999999998854

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

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=96.83  E-value=0.0055  Score=55.24  Aligned_cols=33  Identities=21%  Similarity=0.361  Sum_probs=26.5

Q ss_pred             CcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHH
Q 022724           56 PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        56 ~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~   88 (293)
                      +.......+..+..++++++.||+|+|||..+-
T Consensus       180 ~e~~le~l~~~L~~~~~iil~GppGtGKT~lA~  212 (459)
T PRK11331        180 PETTIETILKRLTIKKNIILQGPPGVGKTFVAR  212 (459)
T ss_pred             CHHHHHHHHHHHhcCCCEEEECCCCCCHHHHHH
Confidence            455566677778889999999999999996553

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.82  E-value=0.016  Score=54.66  Aligned_cols=39  Identities=13%  Similarity=0.352  Sum_probs=24.1

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      .+.+++||||+|++....+ ..+...+..-+....+|+.+
T Consensus       117 gk~KV~IIDEVh~LS~~A~-NALLKtLEEPP~~v~FILaT  155 (702)
T PRK14960        117 GRFKVYLIDEVHMLSTHSF-NALLKTLEEPPEHVKFLFAT  155 (702)
T ss_pred             CCcEEEEEechHhcCHHHH-HHHHHHHhcCCCCcEEEEEE
Confidence            4568999999998854432 33444455444455566544

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=96.81  E-value=0.0053  Score=53.35  Aligned_cols=66  Identities=20%  Similarity=0.352  Sum_probs=43.5

Q ss_pred             HHHHHHCCCCCCcHHHHHHHHh-hhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHH
Q 022724           45 LRGIYQYGFEKPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (293)
Q Consensus        45 ~~~l~~~~~~~~~~~Q~~~~~~-i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l  113 (293)
                      ++.+.+.|.  +++.|.+.+.. +..+++++++|+|||||| .++-+++..+...+...+++++-.+.|+
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            344445554  55677777765 456789999999999999 4445555554322334477777777765

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=96.79  E-value=0.013  Score=53.35  Aligned_cols=108  Identities=15%  Similarity=0.314  Sum_probs=55.7

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhc
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH  150 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  150 (293)
                      +.+++.||+|+|||.... ++...+...  +.+++++.. ..+..+....++.                           
T Consensus       142 npl~L~G~~G~GKTHLl~-Ai~~~l~~~--~~~v~yi~~-~~f~~~~~~~l~~---------------------------  190 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQ-AAVHALRES--GGKILYVRS-ELFTEHLVSAIRS---------------------------  190 (445)
T ss_pred             ceEEEEcCCCCCHHHHHH-HHHHHHHHc--CCCEEEeeH-HHHHHHHHHHHhc---------------------------
Confidence            468999999999994322 444444332  446666653 3443333222210                           


Q ss_pred             CCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccc-cHHHHHHHHhhC-CCCccEEEEEeecChhHHH
Q 022724          151 GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG-FKDQIYDVYRYL-PPDLQVVLISATLPHEILE  222 (293)
Q Consensus       151 ~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~-~~~~~~~i~~~l-~~~~q~v~~SAt~~~~~~~  222 (293)
                            ...+.+...       ..+.++++|||+|.+.... ....+..++..+ ....++|+.|-..|..+..
T Consensus       191 ------~~~~~f~~~-------~~~~dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~~  251 (445)
T PRK12422        191 ------GEMQRFRQF-------YRNVDALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDLKA  251 (445)
T ss_pred             ------chHHHHHHH-------cccCCEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHHhh
Confidence                  011111111       2457899999999985432 233333443322 2345555555444554443

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.79  E-value=0.01  Score=51.85  Aligned_cols=56  Identities=27%  Similarity=0.501  Sum_probs=36.6

Q ss_pred             cccCcccCCCCHHHHHHHHHC--------------CCCCCcHHHHHH------HHhhhcC-----CcEEEEcCCCChhHH
Q 022724           31 AITSFDAMGIKDDLLRGIYQY--------------GFEKPSAIQQRA------VMPIIKG-----RDVIAQAQSGTGKTS   85 (293)
Q Consensus        31 ~~~~f~~~~l~~~i~~~l~~~--------------~~~~~~~~Q~~~------~~~i~~~-----~~~li~~~Tg~GKT~   85 (293)
                      ....|+.++....+.+.|+.-              |....-..=++|      +|.+++|     +.+++.||.|+|||+
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            356788888898898888651              111112222222      2455565     689999999999995


Q ss_pred             H
Q 022724           86 M   86 (293)
Q Consensus        86 ~   86 (293)
                      .
T Consensus       261 L  261 (491)
T KOG0738|consen  261 L  261 (491)
T ss_pred             H
Confidence            3

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=96.77  E-value=0.023  Score=49.84  Aligned_cols=40  Identities=8%  Similarity=0.223  Sum_probs=25.4

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEe
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SA  214 (293)
                      ....+||+||+|.+.+. ....+..++...+...++|+.+.
T Consensus       124 ~~~~vlilDe~~~l~~~-~~~~L~~~le~~~~~~~~Il~~~  163 (337)
T PRK12402        124 ADYKTILLDNAEALRED-AQQALRRIMEQYSRTCRFIIATR  163 (337)
T ss_pred             CCCcEEEEeCcccCCHH-HHHHHHHHHHhccCCCeEEEEeC
Confidence            45679999999987432 23445555555555666665443

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.76  E-value=0.0063  Score=55.42  Aligned_cols=17  Identities=29%  Similarity=0.440  Sum_probs=14.4

Q ss_pred             EEEEcCCCChhHHHHHH
Q 022724           73 VIAQAQSGTGKTSMIAL   89 (293)
Q Consensus        73 ~li~~~Tg~GKT~~~~~   89 (293)
                      ++++||.|+|||.++.+
T Consensus        43 ~Lf~GP~GtGKTTlAri   59 (484)
T PRK14956         43 YIFFGPRGVGKTTIARI   59 (484)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            79999999999966543

>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=96.74  E-value=0.037  Score=40.98  Aligned_cols=17  Identities=24%  Similarity=0.464  Sum_probs=13.6

Q ss_pred             CccEEEecchhhhhccc
Q 022724          175 AIKLLVLDESDEMLSRG  191 (293)
Q Consensus       175 ~l~~iViDE~h~~~~~~  191 (293)
                      ...+++|||+|.+....
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 ....

>PLN03025 replication factor C subunit; Provisional

Probab=96.74  E-value=0.024  Score=49.48  Aligned_cols=39  Identities=21%  Similarity=0.307  Sum_probs=24.2

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      ...+++|+||+|.+.... ...+...+...+....+++.+
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            347899999999985433 344445555545555555543

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.73  E-value=0.05  Score=49.91  Aligned_cols=21  Identities=29%  Similarity=0.316  Sum_probs=16.4

Q ss_pred             CCcEEEEcCCCChhHHHHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIALT   90 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~   90 (293)
                      |+-+.++||||+|||.....-
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKL  276 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKL  276 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHH
Confidence            456889999999999765433

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=96.72  E-value=0.016  Score=54.38  Aligned_cols=107  Identities=16%  Similarity=0.231  Sum_probs=55.9

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhc
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH  150 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  150 (293)
                      +.+++.|++|+|||.. +-++.+.+.....+.+++|+. ..+++.+....+..   .                       
T Consensus       315 NpL~LyG~sGsGKTHL-L~AIa~~a~~~~~g~~V~Yit-aeef~~el~~al~~---~-----------------------  366 (617)
T PRK14086        315 NPLFIYGESGLGKTHL-LHAIGHYARRLYPGTRVRYVS-SEEFTNEFINSIRD---G-----------------------  366 (617)
T ss_pred             CcEEEECCCCCCHHHH-HHHHHHHHHHhCCCCeEEEee-HHHHHHHHHHHHHh---c-----------------------
Confidence            3489999999999943 223444444333344555554 45555444332211   0                       


Q ss_pred             CCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccc-cHHHHHHHHhhCC-CCccEEEEEeecChh
Q 022724          151 GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG-FKDQIYDVYRYLP-PDLQVVLISATLPHE  219 (293)
Q Consensus       151 ~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~-~~~~~~~i~~~l~-~~~q~v~~SAt~~~~  219 (293)
                             ..+.+...       +.++++|||||+|.+.... ....+..++..+. .+.++|+.|-..+..
T Consensus       367 -------~~~~f~~~-------y~~~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~P~e  423 (617)
T PRK14086        367 -------KGDSFRRR-------YREMDILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDRPPKQ  423 (617)
T ss_pred             -------cHHHHHHH-------hhcCCEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCCChHh
Confidence                   01111111       3457899999999885432 2333444444443 345666544444443

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.70  E-value=0.013  Score=57.16  Aligned_cols=38  Identities=13%  Similarity=0.253  Sum_probs=22.8

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEE
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLI  212 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~  212 (293)
                      .+.+++||||+|+|.... ...+...+..-+..+.+|+.
T Consensus       118 gk~KViIIDEAh~LT~eA-qNALLKtLEEPP~~vrFILa  155 (944)
T PRK14949        118 GRFKVYLIDEVHMLSRSS-FNALLKTLEEPPEHVKFLLA  155 (944)
T ss_pred             CCcEEEEEechHhcCHHH-HHHHHHHHhccCCCeEEEEE
Confidence            457899999999985332 23333344443445556654

>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]

Probab=96.69  E-value=0.023  Score=45.07  Aligned_cols=106  Identities=14%  Similarity=0.129  Sum_probs=61.1

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHh
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE  149 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  149 (293)
                      |+-.+++||..||||...+-.+- +....  +.++++..|-..             ...+........|.+.        
T Consensus         4 g~l~~i~gpM~SGKT~eLl~r~~-~~~~~--g~~v~vfkp~iD-------------~R~~~~~V~Sr~G~~~--------   59 (201)
T COG1435           4 GWLEFIYGPMFSGKTEELLRRAR-RYKEA--GMKVLVFKPAID-------------TRYGVGKVSSRIGLSS--------   59 (201)
T ss_pred             EEEEEEEccCcCcchHHHHHHHH-HHHHc--CCeEEEEecccc-------------cccccceeeeccCCcc--------
Confidence            44578999999999975443332 22222  457888888332             2333333333333322        


Q ss_pred             cCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhC
Q 022724          150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL  203 (293)
Q Consensus       150 ~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l  203 (293)
                        .-+.|-.+..+...+.....+.. ++.|.|||++.+ +......+..+...+
T Consensus        60 --~A~~i~~~~~i~~~i~~~~~~~~-~~~v~IDEaQF~-~~~~v~~l~~lad~l  109 (201)
T COG1435          60 --EAVVIPSDTDIFDEIAALHEKPP-VDCVLIDEAQFF-DEELVYVLNELADRL  109 (201)
T ss_pred             --cceecCChHHHHHHHHhcccCCC-cCEEEEehhHhC-CHHHHHHHHHHHhhc
Confidence              24566666677766655333222 789999999876 334455555555554

>COG4626 Phage terminase-like protein, large subunit [General function prediction only]

Probab=96.68  E-value=0.019  Score=52.59  Aligned_cols=147  Identities=14%  Similarity=0.131  Sum_probs=85.5

Q ss_pred             CCcHHHHHHHHhhhc------C----CcEEEEcCCCChhHHHHH-HHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 022724           55 KPSAIQQRAVMPIIK------G----RDVIAQAQSGTGKTSMIA-LTVCQTVDTSSREVQALILSPTRELATQTEKVILA  123 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~------~----~~~li~~~Tg~GKT~~~~-~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~  123 (293)
                      ..-|||+-++-.+..      |    +-.+|..|-+-|||.... +.....+.....+....|++|+.+-+.+..+.++.
T Consensus        61 ~l~PwQkFiia~l~G~~~k~T~~rrf~e~fI~v~RkngKt~l~A~i~~~~~l~~~~~~~~~~i~A~s~~qa~~~F~~ar~  140 (546)
T COG4626          61 SLEPWQKFIVAALFGFYDKQTGIRRFKEAFIFIPRKNGKSTLAAGIMMTALLLNWRSGAGIYILAPSVEQAANSFNPARD  140 (546)
T ss_pred             ccchHHHHHHHHHhceeecCCCceEEEEEEEEEecCCchHHHHHHHHHHHHHhhhhcCCcEEEEeccHHHHHHhhHHHHH
Confidence            468999999998871      1    357888999999994433 33333343345566889999999999998888876


Q ss_pred             hhccCCceEEEEECCcchHHHHHHHh-cCCcEEEeChHHHHHHHhc--CCCCCCCccEEEecchhhhhccccHHHHHHHH
Q 022724          124 IGDFINIQAHACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKR--KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVY  200 (293)
Q Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ilV~Tp~~l~~~l~~--~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~  200 (293)
                      ......          +.... ..+. +...|...--......+..  +..+=.+..+.|+||.|.+.+.+  ..+..+.
T Consensus       141 mv~~~~----------~l~~~-~~~q~~s~~i~~~~~~s~ik~~aa~~~~~Dg~~~~~~I~DEih~f~~~~--~~~~~~~  207 (546)
T COG4626         141 MVKRDD----------DLRDL-CNVQTHSRTITHRKTDSTIKAVAADPNTVDGLNSVGAIIDELHLFGKQE--DMYSEAK  207 (546)
T ss_pred             HHHhCc----------chhhh-hccccceeEEEecccceeeeeeccCCCcccCCCcceEEEehhhhhcCHH--HHHHHHH
Confidence            543221          00000 0000 0111222111112222222  33444667899999999986553  4444444


Q ss_pred             hhCC--CCccEEEEEe
Q 022724          201 RYLP--PDLQVVLISA  214 (293)
Q Consensus       201 ~~l~--~~~q~v~~SA  214 (293)
                      .-+.  ++.++++.|.
T Consensus       208 ~g~~ar~~~l~~~ITT  223 (546)
T COG4626         208 GGLGARPEGLVVYITT  223 (546)
T ss_pred             hhhccCcCceEEEEec
Confidence            4443  4667777776

>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=96.67  E-value=0.014  Score=45.48  Aligned_cols=43  Identities=16%  Similarity=0.381  Sum_probs=28.5

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEeecC
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLP  217 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~  217 (293)
                      ...+++||||+|.|.... ...+...+..-+....++++|....
T Consensus       101 ~~~KviiI~~ad~l~~~a-~NaLLK~LEepp~~~~fiL~t~~~~  143 (162)
T PF13177_consen  101 GKYKVIIIDEADKLTEEA-QNALLKTLEEPPENTYFILITNNPS  143 (162)
T ss_dssp             SSSEEEEEETGGGS-HHH-HHHHHHHHHSTTTTEEEEEEES-GG
T ss_pred             CCceEEEeehHhhhhHHH-HHHHHHHhcCCCCCEEEEEEECChH
Confidence            568999999999985443 4445556666666777777766543

...

>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]

Probab=96.67  E-value=0.024  Score=54.23  Aligned_cols=157  Identities=16%  Similarity=0.245  Sum_probs=89.4

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCC--cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHH
Q 022724           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGR--DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQT  117 (293)
Q Consensus        40 l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~--~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~  117 (293)
                      .++..-..+.....+.+..-|.+.+..+.+.+  -+++.|.-|=|||.+.=+++ ..+.......+++|.+|+.+-++.+
T Consensus       199 ~~~~~~~~l~~l~~T~dQ~~~l~~~~~l~~~~~~~~vlTAdRGRGKSA~lGi~~-~~~~~~~~~~~iiVTAP~~~nv~~L  277 (758)
T COG1444         199 LDPVFPRELYELCLTEDQAEALEILERLLDAPKRALVLTADRGRGKSAALGIAL-AAAARLAGSVRIIVTAPTPANVQTL  277 (758)
T ss_pred             CCCCCCHHHhhhhcChhHHHHHHHHHHHHcCCCceEEEEcCCCCcHhHHHhHHH-HHHHHhcCCceEEEeCCCHHHHHHH
Confidence            33333444555555566666666777777543  58889999999996544333 2221111145899999999999999


Q ss_pred             HHHHHHhhccCCceEEEEECCcchHHHHHHH-hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHH
Q 022724          118 EKVILAIGDFINIQAHACVGGKSVGEDIRKL-EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQI  196 (293)
Q Consensus       118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~  196 (293)
                      ...+.+-....|++-.........   .... .+...|=.-.|....          ..-+++|||||=.+.    ...+
T Consensus       278 f~fa~~~l~~lg~~~~v~~d~~g~---~~~~~~~~~~i~y~~P~~a~----------~~~DllvVDEAAaIp----lplL  340 (758)
T COG1444         278 FEFAGKGLEFLGYKRKVAPDALGE---IREVSGDGFRIEYVPPDDAQ----------EEADLLVVDEAAAIP----LPLL  340 (758)
T ss_pred             HHHHHHhHHHhCCccccccccccc---eeeecCCceeEEeeCcchhc----------ccCCEEEEehhhcCC----hHHH
Confidence            888876555555432221111000   0000 011123333443222          115899999996652    3344


Q ss_pred             HHHHhhCCCCccEEEEEeecCh
Q 022724          197 YDVYRYLPPDLQVVLISATLPH  218 (293)
Q Consensus       197 ~~i~~~l~~~~q~v~~SAt~~~  218 (293)
                      ..++..    .+.++||.|+..
T Consensus       341 ~~l~~~----~~rv~~sTTIhG  358 (758)
T COG1444         341 HKLLRR----FPRVLFSTTIHG  358 (758)
T ss_pred             HHHHhh----cCceEEEeeecc
Confidence            444443    357889999853

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=96.66  E-value=0.016  Score=62.00  Aligned_cols=63  Identities=32%  Similarity=0.420  Sum_probs=45.5

Q ss_pred             CCCcHHHHHHHHhhhcC--CcEEEEcCCCChhHHHHH---HHHHhhhccCCCceeEEEEcCCHHHHHHHH
Q 022724           54 EKPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIA---LTVCQTVDTSSREVQALILSPTRELATQTE  118 (293)
Q Consensus        54 ~~~~~~Q~~~~~~i~~~--~~~li~~~Tg~GKT~~~~---~~~~~~l~~~~~~~~~lil~P~~~l~~q~~  118 (293)
                      ..+++.|++++..++.+  +-++|.|+.|+|||...-   -++...+..  .+.+++.++||..-+..+.
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            35899999999998754  567889999999995541   123233322  2567899999988776664

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.

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=96.65  E-value=0.015  Score=49.79  Aligned_cols=18  Identities=28%  Similarity=0.370  Sum_probs=15.5

Q ss_pred             CCcEEEEcCCCChhHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~   87 (293)
                      +.++++.||+|+|||..+
T Consensus        58 ~~~vll~G~pGTGKT~lA   75 (284)
T TIGR02880        58 TLHMSFTGNPGTGKTTVA   75 (284)
T ss_pred             CceEEEEcCCCCCHHHHH
Confidence            458999999999999665

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.

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.65  E-value=0.02  Score=52.12  Aligned_cols=61  Identities=11%  Similarity=0.301  Sum_probs=38.8

Q ss_pred             CCCCCccEEEecchhhhhcc--------c-cHHHHHHHHhhCC-----CCccEEEEEeecChhHHHHHHhcCCCCEEEEe
Q 022724          171 LRTRAIKLLVLDESDEMLSR--------G-FKDQIYDVYRYLP-----PDLQVVLISATLPHEILEMTTKFMTDPVKILV  236 (293)
Q Consensus       171 ~~~~~l~~iViDE~h~~~~~--------~-~~~~~~~i~~~l~-----~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~  236 (293)
                      ..-+.+..||+||+|.+...        + .-..++.+++++.     ++.-+|+||--     .+++...+..|..+.+
T Consensus       320 g~~SgLHIIIFDEiDAICKqRGS~~g~TGVhD~VVNQLLsKmDGVeqLNNILVIGMTNR-----~DlIDEALLRPGRlEV  394 (744)
T KOG0741|consen  320 GANSGLHIIIFDEIDAICKQRGSMAGSTGVHDTVVNQLLSKMDGVEQLNNILVIGMTNR-----KDLIDEALLRPGRLEV  394 (744)
T ss_pred             CccCCceEEEehhhHHHHHhcCCCCCCCCccHHHHHHHHHhcccHHhhhcEEEEeccCc-----hhhHHHHhcCCCceEE
Confidence            34577899999999998632        1 2345667777764     35566777543     5566666656655544

>PHA03333 putative ATPase subunit of terminase; Provisional

Probab=96.64  E-value=0.059  Score=50.98  Aligned_cols=144  Identities=13%  Similarity=0.156  Sum_probs=82.9

Q ss_pred             CCcHHHHHHHHhhh---cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCc-
Q 022724           55 KPSAIQQRAVMPII---KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI-  130 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~---~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~-  130 (293)
                      .|+|.=.+-++++.   +.+-.++.+|=|.|||++..+.+...+..  .+.++++.+|...-+.++.+.++......+. 
T Consensus       169 ~~~~~~~~~id~~~~~fkq~~tV~taPRqrGKS~iVgi~l~~La~f--~Gi~IlvTAH~~~ts~evF~rv~~~le~lg~~  246 (752)
T PHA03333        169 APSPRTLREIDRIFDEYGKCYTAATVPRRCGKTTIMAIILAAMISF--LEIDIVVQAQRKTMCLTLYNRVETVVHAYQHK  246 (752)
T ss_pred             CCChhhHHHHHHHHHHHhhcceEEEeccCCCcHHHHHHHHHHHHHh--cCCeEEEECCChhhHHHHHHHHHHHHHHhccc
Confidence            45555555556554   56788999999999998766555443332  2568999999999999998888776553321 


Q ss_pred             -------eEEEEECCcchHHHHHHHhcCCcEEEeChHHHH----H--HH--hcCCCCCCCccEEEecchhhhhccccHHH
Q 022724          131 -------QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVC----D--MI--KRKTLRTRAIKLLVLDESDEMLSRGFKDQ  195 (293)
Q Consensus       131 -------~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~----~--~l--~~~~~~~~~l~~iViDE~h~~~~~~~~~~  195 (293)
                             .+....|+.            -.|.+..|....    .  +.  ..+...-...+++|+|||..+...    .
T Consensus       247 ~~fp~~~~iv~vkgg~------------E~I~f~~p~gak~G~sti~F~Ars~~s~RG~~~DLLIVDEAAfI~~~----~  310 (752)
T PHA03333        247 PWFPEEFKIVTLKGTD------------ENLEYISDPAAKEGKTTAHFLASSPNAARGQNPDLVIVDEAAFVNPG----A  310 (752)
T ss_pred             cccCCCceEEEeeCCe------------eEEEEecCcccccCcceeEEecccCCCcCCCCCCEEEEECcccCCHH----H
Confidence                   111111111            012222211110    0  00  011122235689999999987543    3


Q ss_pred             HHHHHhhCC-CCccEEEEEeec
Q 022724          196 IYDVYRYLP-PDLQVVLISATL  216 (293)
Q Consensus       196 ~~~i~~~l~-~~~q~v~~SAt~  216 (293)
                      +..++-.+. ...+++++|.+-
T Consensus       311 l~aIlP~l~~~~~k~IiISS~~  332 (752)
T PHA03333        311 LLSVLPLMAVKGTKQIHISSPV  332 (752)
T ss_pred             HHHHHHHHccCCCceEEEeCCC
Confidence            444444443 467778888775

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=96.63  E-value=0.014  Score=48.11  Aligned_cols=43  Identities=9%  Similarity=0.261  Sum_probs=25.2

Q ss_pred             CccEEEecchhhhhccccHHHHHHHHhhCCCCcc-EEEEEeecCh
Q 022724          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ-VVLISATLPH  218 (293)
Q Consensus       175 ~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q-~v~~SAt~~~  218 (293)
                      ..+++||||+|.+... ....+..++........ +++++++.++
T Consensus        90 ~~~~liiDdi~~l~~~-~~~~L~~~~~~~~~~~~~~vl~~~~~~~  133 (227)
T PRK08903         90 EAELYAVDDVERLDDA-QQIALFNLFNRVRAHGQGALLVAGPAAP  133 (227)
T ss_pred             cCCEEEEeChhhcCch-HHHHHHHHHHHHHHcCCcEEEEeCCCCH
Confidence            4578999999987432 23334444444333333 5677777554

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.62  E-value=0.045  Score=52.79  Aligned_cols=128  Identities=15%  Similarity=0.142  Sum_probs=63.8

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCC--HHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT--RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~--~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  148 (293)
                      +-+.++||||+|||.....-+........ +.++.++.-.  +.=+   .+.++.+....++.+                
T Consensus       186 ~Vi~lVGpnGvGKTTTiaKLA~~~~~~~G-~kkV~lit~Dt~RigA---~eQL~~~a~~~gvpv----------------  245 (767)
T PRK14723        186 GVLALVGPTGVGKTTTTAKLAARCVAREG-ADQLALLTTDSFRIGA---LEQLRIYGRILGVPV----------------  245 (767)
T ss_pred             eEEEEECCCCCcHHHHHHHHHhhHHHHcC-CCeEEEecCcccchHH---HHHHHHHHHhCCCCc----------------
Confidence            45789999999999665433322212221 1244444432  2212   223333333333322                


Q ss_pred             hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcc-ccHHHHHHHHhhCCCCccEEEEEeecCh-hHHHHHHh
Q 022724          149 EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPPDLQVVLISATLPH-EILEMTTK  226 (293)
Q Consensus       149 ~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~-~~~~~~~~i~~~l~~~~q~v~~SAt~~~-~~~~~~~~  226 (293)
                           ..+.+|+.+...+..    +.+.++|+||=+=+.... .....+..+.....+...++.++||... .+.+....
T Consensus       246 -----~~~~~~~~l~~al~~----~~~~D~VLIDTAGRs~~d~~l~eel~~l~~~~~p~e~~LVLsAt~~~~~l~~i~~~  316 (767)
T PRK14723        246 -----HAVKDAADLRFALAA----LGDKHLVLIDTVGMSQRDRNVSEQIAMLCGVGRPVRRLLLLNAASHGDTLNEVVHA  316 (767)
T ss_pred             -----cccCCHHHHHHHHHH----hcCCCEEEEeCCCCCccCHHHHHHHHHHhccCCCCeEEEEECCCCcHHHHHHHHHH
Confidence                 223466666555543    334578888877654222 2233333344334445567888888743 34444444


Q ss_pred             c
Q 022724          227 F  227 (293)
Q Consensus       227 ~  227 (293)
                      |
T Consensus       317 f  317 (767)
T PRK14723        317 Y  317 (767)
T ss_pred             H
Confidence            4

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=96.61  E-value=0.012  Score=57.30  Aligned_cols=87  Identities=10%  Similarity=0.031  Sum_probs=70.6

Q ss_pred             CcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEeecCh------hHHHHHH
Q 022724          152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPH------EILEMTT  225 (293)
Q Consensus       152 ~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~------~~~~~~~  225 (293)
                      ..|++.||..+..-+-.+.+++..+..|||||||++.+..-...+..+.+.-++..-+.+|||.+..      .+...++
T Consensus         8 ggi~~~T~rIl~~DlL~~ri~~~~itgiiv~~Ahr~~~~~~eaFI~rlyr~~n~~gfIkafSdsP~~~~~g~~~l~~vmk   87 (814)
T TIGR00596         8 GGIFSITSRILVVDLLTGIIPPELITGILVLRADRIIESSQEAFILRLYRQKNKTGFIKAFSDNPEAFTMGFSPLETKMR   87 (814)
T ss_pred             CCEEEEechhhHhHHhcCCCCHHHccEEEEeecccccccccHHHHHHHHHHhCCCcceEEecCCCcccccchHHHHHHHH
Confidence            4799999999998888888999999999999999998777777788888887788889999999864      4566666


Q ss_pred             hcCCCCEEEEecC
Q 022724          226 KFMTDPVKILVKR  238 (293)
Q Consensus       226 ~~~~~~~~~~~~~  238 (293)
                      .++-.-..+....
T Consensus        88 ~L~i~~v~l~prf  100 (814)
T TIGR00596        88 NLFLRHVYLWPRF  100 (814)
T ss_pred             HhCcCeEEEeCCC
Confidence            6665555555443

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

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=96.61  E-value=0.014  Score=48.63  Aligned_cols=53  Identities=15%  Similarity=0.226  Sum_probs=36.0

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhh
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIG  125 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  125 (293)
                      .|..++|.||+|+|||...+-.+...+..   +-+++|++ +.+-..++.+.+..++
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            35689999999999997655555555533   44677777 4455667777666543

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.

>PHA03368 DNA packaging terminase subunit 1; Provisional

Probab=96.60  E-value=0.023  Score=53.43  Aligned_cols=136  Identities=14%  Similarity=0.188  Sum_probs=81.1

Q ss_pred             hcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccC-Cce-EEEEECCcchHHHH
Q 022724           68 IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI-NIQ-AHACVGGKSVGEDI  145 (293)
Q Consensus        68 ~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~-~~~-~~~~~~~~~~~~~~  145 (293)
                      .+.+-.++..|=-.|||+... +++..+...-.|.++++.+|.+..++.+++.+....... .-. +....| ...   .
T Consensus       252 fkqk~tVflVPRR~GKTwivv-~iI~~ll~s~~Gi~IgytAH~~~ts~~vF~eI~~~le~~f~~~~v~~vkG-e~I---~  326 (738)
T PHA03368        252 FRQRATVFLVPRRHGKTWFLV-PLIALALATFRGIKIGYTAHIRKATEPVFEEIGARLRQWFGASRVDHVKG-ETI---S  326 (738)
T ss_pred             hhccceEEEecccCCchhhHH-HHHHHHHHhCCCCEEEEEcCcHHHHHHHHHHHHHHHhhhcchhheeeecC-cEE---E
Confidence            345788999999999998766 666655544447799999999999999998887654321 111 111111 100   0


Q ss_pred             HHHhcC--CcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCC-CCccEEEEEeecCh
Q 022724          146 RKLEHG--VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP-PDLQVVLISATLPH  218 (293)
Q Consensus       146 ~~~~~~--~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~-~~~q~v~~SAt~~~  218 (293)
                      -...++  ..|.+.+-      -..+...=..++++|||||+.+-+..+..    ++-.+. .+.++|++|.|-+.
T Consensus       327 i~f~nG~kstI~FaSa------rntNsiRGqtfDLLIVDEAqFIk~~al~~----ilp~l~~~n~k~I~ISS~Ns~  392 (738)
T PHA03368        327 FSFPDGSRSTIVFASS------HNTNGIRGQDFNLLFVDEANFIRPDAVQT----IMGFLNQTNCKIIFVSSTNTG  392 (738)
T ss_pred             EEecCCCccEEEEEec------cCCCCccCCcccEEEEechhhCCHHHHHH----HHHHHhccCccEEEEecCCCC
Confidence            001112  13444321      01122333478999999999886544333    333322 47899999988543

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.59  E-value=0.026  Score=50.87  Aligned_cols=130  Identities=15%  Similarity=0.188  Sum_probs=60.4

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCC-HHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT-RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~-~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  148 (293)
                      |.-+.++||||+|||.....-+-..+.......-.++...+ +.-+.++   +..+....|+.+..              
T Consensus       191 g~vi~lvGpnG~GKTTtlakLA~~~~~~~~~~~v~~i~~d~~rigalEQ---L~~~a~ilGvp~~~--------------  253 (420)
T PRK14721        191 GGVYALIGPTGVGKTTTTAKLAARAVIRHGADKVALLTTDSYRIGGHEQ---LRIYGKLLGVSVRS--------------  253 (420)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecCCcchhHHHH---HHHHHHHcCCceec--------------
Confidence            45689999999999966543222222221111234555544 2222222   33333333443322              


Q ss_pred             hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcc-ccHHHHHHHHhhCCCCccEEEEEeecC-hhHHHHHHh
Q 022724          149 EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPPDLQVVLISATLP-HEILEMTTK  226 (293)
Q Consensus       149 ~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~-~~~~~~~~i~~~l~~~~q~v~~SAt~~-~~~~~~~~~  226 (293)
                             +.++..+...+.    .+.+.+.+.||.+-+.... .....+..+.....+...++.+|||.. ..+.+....
T Consensus       254 -------v~~~~dl~~al~----~l~~~d~VLIDTaGrsqrd~~~~~~l~~l~~~~~~~~~~LVl~at~~~~~~~~~~~~  322 (420)
T PRK14721        254 -------IKDIADLQLMLH----ELRGKHMVLIDTVGMSQRDQMLAEQIAMLSQCGTQVKHLLLLNATSSGDTLDEVISA  322 (420)
T ss_pred             -------CCCHHHHHHHHH----HhcCCCEEEecCCCCCcchHHHHHHHHHHhccCCCceEEEEEcCCCCHHHHHHHHHH
Confidence                   223333332222    1445677888875322111 112233333222223345778999974 445555554


Q ss_pred             c
Q 022724          227 F  227 (293)
Q Consensus       227 ~  227 (293)
                      +
T Consensus       323 f  323 (420)
T PRK14721        323 Y  323 (420)
T ss_pred             h
Confidence            4

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=96.57  E-value=0.014  Score=55.93  Aligned_cols=40  Identities=18%  Similarity=0.432  Sum_probs=24.4

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEe
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SA  214 (293)
                      .+.+++||||+|+|....+.. +.+.+..-+....+|+.+-
T Consensus       118 gr~KVIIIDEah~LT~~A~NA-LLKtLEEPP~~v~FILaTt  157 (830)
T PRK07003        118 ARFKVYMIDEVHMLTNHAFNA-MLKTLEEPPPHVKFILATT  157 (830)
T ss_pred             CCceEEEEeChhhCCHHHHHH-HHHHHHhcCCCeEEEEEEC
Confidence            457899999999986544333 3334444444555655543

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.55  E-value=0.021  Score=53.05  Aligned_cols=39  Identities=15%  Similarity=0.366  Sum_probs=25.0

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      .+.+++||||+|++....+. .+...+..-+..+.+|+.+
T Consensus       118 ~~~kV~iIDE~~~ls~~a~n-aLLk~LEepp~~~~fIlat  156 (509)
T PRK14958        118 GRFKVYLIDEVHMLSGHSFN-ALLKTLEEPPSHVKFILAT  156 (509)
T ss_pred             CCcEEEEEEChHhcCHHHHH-HHHHHHhccCCCeEEEEEE
Confidence            45789999999998654432 3334445545566666654

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=96.55  E-value=0.038  Score=50.12  Aligned_cols=128  Identities=12%  Similarity=0.208  Sum_probs=61.0

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcC--CHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP--TRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P--~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  148 (293)
                      ..++++|++|+|||....-.+ ..+...  +.+++++..  .+.-+   .++++.+....++.+.......         
T Consensus        96 ~vI~lvG~~GsGKTTtaakLA-~~L~~~--g~kV~lV~~D~~R~aa---~eQL~~la~~~gvp~~~~~~~~---------  160 (437)
T PRK00771         96 QTIMLVGLQGSGKTTTAAKLA-RYFKKK--GLKVGLVAADTYRPAA---YDQLKQLAEKIGVPFYGDPDNK---------  160 (437)
T ss_pred             eEEEEECCCCCcHHHHHHHHH-HHHHHc--CCeEEEecCCCCCHHH---HHHHHHHHHHcCCcEEecCCcc---------
Confidence            358899999999996654333 233332  335555553  23322   2333334434444432211111         


Q ss_pred             hcCCcEEEeChHH-HHHHHhcCCCCCCCccEEEecchhhhh-ccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHh
Q 022724          149 EHGVHVVSGTPGR-VCDMIKRKTLRTRAIKLLVLDESDEML-SRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTK  226 (293)
Q Consensus       149 ~~~~~ilV~Tp~~-l~~~l~~~~~~~~~l~~iViDE~h~~~-~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~  226 (293)
                               .|.. +...+..    +...++||||.+-... +......+..+.....+..-++.++|+...+..+.+..
T Consensus       161 ---------d~~~i~~~al~~----~~~~DvVIIDTAGr~~~d~~lm~El~~l~~~~~pdevlLVvda~~gq~av~~a~~  227 (437)
T PRK00771        161 ---------DAVEIAKEGLEK----FKKADVIIVDTAGRHALEEDLIEEMKEIKEAVKPDEVLLVIDATIGQQAKNQAKA  227 (437)
T ss_pred             ---------CHHHHHHHHHHH----hhcCCEEEEECCCcccchHHHHHHHHHHHHHhcccceeEEEeccccHHHHHHHHH
Confidence                     1111 1122221    1112678888774332 22233445555555555556667777766554444444

>PRK05973 replicative DNA helicase; Provisional

Probab=96.55  E-value=0.031  Score=46.33  Aligned_cols=82  Identities=15%  Similarity=0.190  Sum_probs=48.0

Q ss_pred             CCCCHHHHHHHHHCCCC----------CCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEE
Q 022724           38 MGIKDDLLRGIYQYGFE----------KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALIL  107 (293)
Q Consensus        38 ~~l~~~i~~~l~~~~~~----------~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil  107 (293)
                      .++++.+-+...+-||.          .++|.. +...-+..|.-++|.|++|+|||...+-.+.+....   |.+++|+
T Consensus        23 ~~~~~~~~~~a~~~g~~~w~~~~~~~~~~~p~~-~l~GGl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~~---Ge~vlyf   98 (237)
T PRK05973         23 IPLHEALDRIAAEEGFSSWSLLAAKAAATTPAE-ELFSQLKPGDLVLLGARPGHGKTLLGLELAVEAMKS---GRTGVFF   98 (237)
T ss_pred             CcHHHHHHHHHHHhccchHHHHHHhccCCCCHH-HhcCCCCCCCEEEEEeCCCCCHHHHHHHHHHHHHhc---CCeEEEE
Confidence            34444444444445655          345522 233445567789999999999996555444444432   4467777


Q ss_pred             cCCHHHHHHHHHHHHHh
Q 022724          108 SPTRELATQTEKVILAI  124 (293)
Q Consensus       108 ~P~~~l~~q~~~~~~~~  124 (293)
                      +-- +-..|+.+++..+
T Consensus        99 SlE-es~~~i~~R~~s~  114 (237)
T PRK05973         99 TLE-YTEQDVRDRLRAL  114 (237)
T ss_pred             EEe-CCHHHHHHHHHHc
Confidence            543 3356777777665

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=96.54  E-value=0.046  Score=48.01  Aligned_cols=51  Identities=18%  Similarity=0.184  Sum_probs=34.7

Q ss_pred             hhhHHhCCCCCCCCCcceeecccCCccccCcccCCCCHHHHHHHHHCCCCC
Q 022724            5 TAMRRRGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEK   55 (293)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~~~~~   55 (293)
                      +++...........+....+....+.++......++++...+.|++.||.+
T Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~~~~kL~~~g~~t   54 (344)
T PLN03187          4 SAQADEGAQLQLVEAEEVDEEEDLFESIDKLISQGINAGDVKKLQDAGIYT   54 (344)
T ss_pred             hhhhhhhhhhhhhhhhhhhhhhhcccCHHHHhhCCCCHHHHHHHHHcCCCc
Confidence            334444444555555555555556777777778889999999998888873

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.54  E-value=0.014  Score=53.51  Aligned_cols=40  Identities=15%  Similarity=0.398  Sum_probs=23.2

Q ss_pred             CCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       173 ~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      ..+.+++||||+|++....+ ..+...+..-++...+|+.+
T Consensus       114 ~~~~KVvIIDEah~Ls~~A~-NaLLK~LEePp~~v~fIlat  153 (491)
T PRK14964        114 SSKFKVYIIDEVHMLSNSAF-NALLKTLEEPAPHVKFILAT  153 (491)
T ss_pred             cCCceEEEEeChHhCCHHHH-HHHHHHHhCCCCCeEEEEEe
Confidence            35778999999999854332 22333333333445555544

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=96.54  E-value=0.021  Score=49.69  Aligned_cols=39  Identities=10%  Similarity=0.198  Sum_probs=26.0

Q ss_pred             CccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       175 ~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      ..+++||||+|.+........+..++...+..+++|+.+
T Consensus       100 ~~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~  138 (316)
T PHA02544        100 GGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITA  138 (316)
T ss_pred             CCeEEEEECcccccCHHHHHHHHHHHHhcCCCceEEEEc
Confidence            457999999998833333455666666666666666644

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=96.52  E-value=0.016  Score=56.67  Aligned_cols=39  Identities=15%  Similarity=0.405  Sum_probs=25.8

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      .+.+++||||+|+|.... ...+..++...+..+.+|+.+
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            567899999999996443 333445555555566666655

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA

Probab=96.50  E-value=0.0098  Score=55.82  Aligned_cols=68  Identities=15%  Similarity=0.241  Sum_probs=53.9

Q ss_pred             CCcHHHHHHHHhhhcC--CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHH-HHHHHh
Q 022724           55 KPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE-KVILAI  124 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~--~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~-~~~~~~  124 (293)
                      ..+|+|.+..+.+...  +.++++.++-+|||.+.+-.+...+...+.  .++++.||.+.+.... +++..+
T Consensus        16 ~~~Py~~eimd~~~~~~v~~Vv~~k~aQ~GkT~~~~n~~g~~i~~~P~--~~l~v~Pt~~~a~~~~~~rl~Pm   86 (557)
T PF05876_consen   16 DRTPYLREIMDALSDPSVREVVVMKSAQVGKTELLLNWIGYSIDQDPG--PMLYVQPTDDAAKDFSKERLDPM   86 (557)
T ss_pred             CCChhHHHHHHhcCCcCccEEEEEEcchhhHhHHHHhhceEEEEeCCC--CEEEEEEcHHHHHHHHHHHHHHH
Confidence            5789999999998865  589999999999998766666566666543  5899999999999876 555443

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 [].

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=96.47  E-value=0.045  Score=45.36  Aligned_cols=54  Identities=15%  Similarity=0.181  Sum_probs=32.9

Q ss_pred             hhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 022724           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (293)
                      +..|.-+++.|++|+|||...+-.+...+..   +.++++++. .+-..+..+.+..+
T Consensus        21 i~~g~~~~i~G~~G~GKTtl~~~~~~~~~~~---g~~~~yi~~-e~~~~~~~~~~~~~   74 (230)
T PRK08533         21 IPAGSLILIEGDESTGKSILSQRLAYGFLQN---GYSVSYVST-QLTTTEFIKQMMSL   74 (230)
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHHHhC---CCcEEEEeC-CCCHHHHHHHHHHh
Confidence            3456789999999999996543333333222   456788874 33345555555443

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=96.47  E-value=0.035  Score=48.34  Aligned_cols=40  Identities=18%  Similarity=0.403  Sum_probs=23.8

Q ss_pred             CCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       173 ~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      ....+++||||||.|... -...+...+..-+.+..+++.+
T Consensus       107 ~~~~kviiidead~mt~~-A~nallk~lEep~~~~~~il~~  146 (325)
T COG0470         107 EGGYKVVIIDEADKLTED-AANALLKTLEEPPKNTRFILIT  146 (325)
T ss_pred             CCCceEEEeCcHHHHhHH-HHHHHHHHhccCCCCeEEEEEc
Confidence            367899999999998643 2333333444334445555444

>PF05729 NACHT: NACHT domain

Probab=96.44  E-value=0.021  Score=44.16  Aligned_cols=38  Identities=29%  Similarity=0.548  Sum_probs=23.6

Q ss_pred             EEEecchhhhhccc-------cHHHHHHHHhh-CCCCccEEEEEee
Q 022724          178 LLVLDESDEMLSRG-------FKDQIYDVYRY-LPPDLQVVLISAT  215 (293)
Q Consensus       178 ~iViDE~h~~~~~~-------~~~~~~~i~~~-l~~~~q~v~~SAt  215 (293)
                      +||+|-+|.+.+..       ....+..++.. +.++.++++.|.+
T Consensus        84 llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~  129 (166)
T PF05729_consen   84 LLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRP  129 (166)
T ss_pred             EEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcC
Confidence            49999999986532       22344455555 4456777666554

>PTZ00293 thymidine kinase; Provisional

Probab=96.44  E-value=0.029  Score=45.47  Aligned_cols=39  Identities=15%  Similarity=0.191  Sum_probs=25.7

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCH
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~  111 (293)
                      |.-.++.||.++|||.-.+-. +......  +.+++++-|..
T Consensus         4 G~i~vi~GpMfSGKTteLLr~-i~~y~~a--g~kv~~~kp~~   42 (211)
T PTZ00293          4 GTISVIIGPMFSGKTTELMRL-VKRFTYS--EKKCVVIKYSK   42 (211)
T ss_pred             eEEEEEECCCCChHHHHHHHH-HHHHHHc--CCceEEEEecc
Confidence            556788999999999544433 3333332  44688888844

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=96.43  E-value=0.072  Score=42.54  Aligned_cols=40  Identities=13%  Similarity=0.405  Sum_probs=23.3

Q ss_pred             CCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       173 ~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      .....++||||+|.+.... ...+...+..-++..-+|+.+
T Consensus        94 ~~~~kviiide~~~l~~~~-~~~Ll~~le~~~~~~~~il~~  133 (188)
T TIGR00678        94 ESGRRVVIIEDAERMNEAA-ANALLKTLEEPPPNTLFILIT  133 (188)
T ss_pred             cCCeEEEEEechhhhCHHH-HHHHHHHhcCCCCCeEEEEEE
Confidence            3567899999999985432 233444444434444555543

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.

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.42  E-value=0.098  Score=44.35  Aligned_cols=129  Identities=13%  Similarity=0.243  Sum_probs=67.8

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcC--CH-HHHHHHHHHHHHhhccCCceEEEEECCcchHHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP--TR-ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIR  146 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P--~~-~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  146 (293)
                      +..+.++|++|+|||..+...+.. +...  +.++.++.-  .+ ..+.|+....    ...++.+.             
T Consensus        75 ~~~i~~~G~~g~GKTtl~~~l~~~-l~~~--~~~v~~i~~D~~ri~~~~ql~~~~----~~~~~~~~-------------  134 (270)
T PRK06731         75 VQTIALIGPTGVGKTTTLAKMAWQ-FHGK--KKTVGFITTDHSRIGTVQQLQDYV----KTIGFEVI-------------  134 (270)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHHH-HHHc--CCeEEEEecCCCCHHHHHHHHHHh----hhcCceEE-------------
Confidence            357899999999999765533322 2221  234444443  22 4444444322    22232221             


Q ss_pred             HHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhc-cccHHHHHHHHhhCCCCccEEEEEeecC-hhHHHHH
Q 022724          147 KLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS-RGFKDQIYDVYRYLPPDLQVVLISATLP-HEILEMT  224 (293)
Q Consensus       147 ~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~-~~~~~~~~~i~~~l~~~~q~v~~SAt~~-~~~~~~~  224 (293)
                              ...+|+.+...+..- -...+.++++||.+=.... ......+..+++...+..-++.+|||.. .++.+.+
T Consensus       135 --------~~~~~~~l~~~l~~l-~~~~~~D~ViIDt~Gr~~~~~~~l~el~~~~~~~~~~~~~LVl~a~~~~~d~~~~~  205 (270)
T PRK06731        135 --------AVRDEAAMTRALTYF-KEEARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASMKSKDMIEII  205 (270)
T ss_pred             --------ecCCHHHHHHHHHHH-HhcCCCCEEEEECCCCCcCCHHHHHHHHHHHhhhCCCeEEEEEcCccCHHHHHHHH
Confidence                    113455554444321 1123578999998865432 1223344445554444445777999874 4666666


Q ss_pred             Hhc
Q 022724          225 TKF  227 (293)
Q Consensus       225 ~~~  227 (293)
                      +.+
T Consensus       206 ~~f  208 (270)
T PRK06731        206 TNF  208 (270)
T ss_pred             HHh
Confidence            654

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=96.42  E-value=0.056  Score=46.99  Aligned_cols=36  Identities=28%  Similarity=0.314  Sum_probs=28.4

Q ss_pred             CCCCcHHHHHHHHhhh----cCC---cEEEEcCCCChhHHHHH
Q 022724           53 FEKPSAIQQRAVMPII----KGR---DVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        53 ~~~~~~~Q~~~~~~i~----~~~---~~li~~~Tg~GKT~~~~   88 (293)
                      +..++|||..+|..+.    +|+   -+++.||.|.||+..+.
T Consensus         2 ~~~~yPW~~~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~   44 (319)
T PRK08769          2 TSAFSPWQQRAYDQTVAALDAGRLGHGLLICGPEGLGKRAVAL   44 (319)
T ss_pred             CccccccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHH
Confidence            4568999999998876    344   48999999999995543

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=96.40  E-value=0.029  Score=49.82  Aligned_cols=24  Identities=29%  Similarity=0.454  Sum_probs=17.5

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhh
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTV   95 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l   95 (293)
                      .+++|.||+|+|||... -.++..+
T Consensus        41 ~~i~I~G~~GtGKT~l~-~~~~~~l   64 (365)
T TIGR02928        41 SNVFIYGKTGTGKTAVT-KYVMKEL   64 (365)
T ss_pred             CcEEEECCCCCCHHHHH-HHHHHHH
Confidence            58999999999999543 3344444

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.

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=96.36  E-value=0.043  Score=52.69  Aligned_cols=67  Identities=24%  Similarity=0.312  Sum_probs=52.0

Q ss_pred             CCcHHHHHHHHhhhcC-----CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcc
Q 022724           55 KPSAIQQRAVMPIIKG-----RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDF  127 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~-----~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (293)
                      .|+..|..++..+.++     +..++.|.+|+|||+.+. .++...     +..+|||+|+...+.++++.++.+...
T Consensus        12 ~~~~~Q~~ai~~l~~~~~~~~~~~ll~Gl~gs~ka~lia-~l~~~~-----~r~vLIVt~~~~~A~~l~~dL~~~~~~   83 (652)
T PRK05298         12 KPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMA-NVIARL-----QRPTLVLAHNKTLAAQLYSEFKEFFPE   83 (652)
T ss_pred             CCChHHHHHHHHHHHhhhcCCCcEEEEcCCCcHHHHHHH-HHHHHh-----CCCEEEEECCHHHHHHHHHHHHHhcCC
Confidence            5999999999987632     257799999999997643 232222     236999999999999999999888643

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.34  E-value=0.041  Score=51.96  Aligned_cols=41  Identities=15%  Similarity=0.353  Sum_probs=24.6

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEee
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISAT  215 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt  215 (293)
                      .+.+++||||+|+|....+.. +.+.+..-+..+.+|+.|..
T Consensus       123 gr~KViIIDEah~Ls~~AaNA-LLKTLEEPP~~v~FILaTte  163 (700)
T PRK12323        123 GRFKVYMIDEVHMLTNHAFNA-MLKTLEEPPEHVKFILATTD  163 (700)
T ss_pred             CCceEEEEEChHhcCHHHHHH-HHHhhccCCCCceEEEEeCC
Confidence            467899999999986543322 22233333445666666543

>KOG1015 consensus Transcription regulator XNP/ATRX, DEAD-box superfamily [Transcription]

Probab=96.33  E-value=0.037  Score=53.67  Aligned_cols=144  Identities=14%  Similarity=0.124  Sum_probs=74.3

Q ss_pred             cEEEEcCCCChhHHHH---HHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccC----CceEEEEECCcchHHH
Q 022724           72 DVIAQAQSGTGKTSMI---ALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI----NIQAHACVGGKSVGED  144 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~---~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~----~~~~~~~~~~~~~~~~  144 (293)
                      ..|+.--.|-|||+-.   +..++.....  .-.++||+||... +..+.+.|.+|...+    .+.|..+..-......
T Consensus       698 GcILAHcMGLGKTlQVvtflhTvL~c~kl--g~ktaLvV~PlNt-~~NW~~EFekWm~~~e~~~~leV~eL~~vkr~e~R  774 (1567)
T KOG1015|consen  698 GCILAHCMGLGKTLQVVTFLHTVLLCDKL--GFKTALVVCPLNT-ALNWMNEFEKWMEGLEDDEKLEVSELATVKRPEER  774 (1567)
T ss_pred             chHHHHhhcccceehhhHHHHHHHHhhcc--CCceEEEEcchHH-HHHHHHHHHHhcccccccccceeehhhhccChHHH
Confidence            4555556799999643   3333322221  1248999999665 456677777776542    3445444333322222


Q ss_pred             ---HHHHhcCCcEEEeChHHHHHHHhcC-------------CCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCcc
Q 022724          145 ---IRKLEHGVHVVSGTPGRVCDMIKRK-------------TLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ  208 (293)
Q Consensus       145 ---~~~~~~~~~ilV~Tp~~l~~~l~~~-------------~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q  208 (293)
                         ...|.+.-.|.|.-.+.+-.+-...             .+.-...+++|.||+|.+-..  ...+...+..+... +
T Consensus       775 ~~~L~~W~~~ggVmIiGYdmyRnLa~gr~vk~rk~ke~f~k~lvdpGPD~vVCDE~HiLKNe--ksa~Skam~~irtk-R  851 (1567)
T KOG1015|consen  775 SYMLQRWQEDGGVMIIGYDMYRNLAQGRNVKSRKLKEIFNKALVDPGPDFVVCDEGHILKNE--KSAVSKAMNSIRTK-R  851 (1567)
T ss_pred             HHHHHHHHhcCCEEEEehHHHHHHhcccchhhhHHHHHHHHhccCCCCCeEEecchhhhccc--hHHHHHHHHHHHhh-e
Confidence               2334443355555444443322111             111245699999999987432  23333333344333 3


Q ss_pred             EEEEEeec-ChhHH
Q 022724          209 VVLISATL-PHEIL  221 (293)
Q Consensus       209 ~v~~SAt~-~~~~~  221 (293)
                      .|++|.|+ -+.+.
T Consensus       852 RI~LTGTPLQNNLm  865 (1567)
T KOG1015|consen  852 RIILTGTPLQNNLM  865 (1567)
T ss_pred             eEEeecCchhhhhH
Confidence            45566664 44433

>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]

Probab=96.33  E-value=0.02  Score=56.90  Aligned_cols=143  Identities=15%  Similarity=0.022  Sum_probs=84.2

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhcc-----------C----CCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDT-----------S----SREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~-----------~----~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (293)
                      |+.++..-..|+|||.+-+...+...-.           .    ...+-+||+|| .++..|+.+.+.+-... ++++..
T Consensus       374 g~~~~~ade~~~qk~~~~l~~~l~~~~k~~~~~cS~~~~e~~n~~~tgaTLII~P-~aIl~QW~~EI~kH~~~-~lKv~~  451 (1394)
T KOG0298|consen  374 GKRVQCADEMGWQKTSEKLILELSDLPKLCPSCCSELVKEGENLVETGATLIICP-NAILMQWFEEIHKHISS-LLKVLL  451 (1394)
T ss_pred             CcceeehhhhhccchHHHHHHHHhcccccchhhhhHHHhcccceeecCceEEECc-HHHHHHHHHHHHHhccc-cceEEE
Confidence            4566777788999998766554433211           0    11235899999 46678988888764433 377877


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCC--CC----------------CCCccE--EEecchhhhhccccHH
Q 022724          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT--LR----------------TRAIKL--LVLDESDEMLSRGFKD  194 (293)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~--~~----------------~~~l~~--iViDE~h~~~~~~~~~  194 (293)
                      +.|-....-......-.+||++||...|-.-+....  .+                +-.+.+  |++|||+++-.  -..
T Consensus       452 Y~Girk~~~~~~~el~~yDIVlTtYdiLr~El~hte~~~~~R~lR~qsr~~~~~SPL~~v~wWRIclDEaQMves--ssS  529 (1394)
T KOG0298|consen  452 YFGIRKTFWLSPFELLQYDIVLTTYDILRNELYHTEDFGSDRQLRHQSRYMRPNSPLLMVNWWRICLDEAQMVES--SSS  529 (1394)
T ss_pred             EechhhhcccCchhhhccCEEEeehHHHHhHhhcccccCChhhhhcccCCCCCCCchHHHHHHHHhhhHHHhhcc--hHH
Confidence            776533221111222357999999988876443221  00                111122  89999998744  334


Q ss_pred             HHHHHHhhCCCCccEEEEEeecC
Q 022724          195 QIYDVYRYLPPDLQVVLISATLP  217 (293)
Q Consensus       195 ~~~~i~~~l~~~~q~v~~SAt~~  217 (293)
                      .......+++ ....-.+|+|+-
T Consensus       530 ~~a~M~~rL~-~in~W~VTGTPi  551 (1394)
T KOG0298|consen  530 AAAEMVRRLH-AINRWCVTGTPI  551 (1394)
T ss_pred             HHHHHHHHhh-hhceeeecCCch
Confidence            4444555553 344567778853

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=96.32  E-value=0.15  Score=45.28  Aligned_cols=27  Identities=30%  Similarity=0.513  Sum_probs=18.7

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccC
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTS   98 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~   98 (293)
                      .|+++.|+||+|||...- -++..+...
T Consensus        43 ~n~~iyG~~GTGKT~~~~-~v~~~l~~~   69 (366)
T COG1474          43 SNIIIYGPTGTGKTATVK-FVMEELEES   69 (366)
T ss_pred             ccEEEECCCCCCHhHHHH-HHHHHHHhh
Confidence            379999999999996543 344444443

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=96.32  E-value=0.031  Score=53.20  Aligned_cols=39  Identities=15%  Similarity=0.358  Sum_probs=24.2

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      .+.+++||||+|.+....+ ..+...+..-+..+.+|+.+
T Consensus       118 gk~KVIIIDEad~Ls~~A~-NALLKtLEEPp~~v~fILaT  156 (709)
T PRK08691        118 GKYKVYIIDEVHMLSKSAF-NAMLKTLEEPPEHVKFILAT  156 (709)
T ss_pred             CCcEEEEEECccccCHHHH-HHHHHHHHhCCCCcEEEEEe
Confidence            4678999999998754332 23444444444566666655

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=96.31  E-value=0.097  Score=51.13  Aligned_cols=38  Identities=21%  Similarity=0.585  Sum_probs=21.6

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCC-CCccEEEE
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLP-PDLQVVLI  212 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~-~~~q~v~~  212 (293)
                      ....+||+||+|.+.... ...+..+++... ...+++++
T Consensus       868 r~v~IIILDEID~L~kK~-QDVLYnLFR~~~~s~SKLiLI  906 (1164)
T PTZ00112        868 RNVSILIIDEIDYLITKT-QKVLFTLFDWPTKINSKLVLI  906 (1164)
T ss_pred             ccceEEEeehHhhhCccH-HHHHHHHHHHhhccCCeEEEE
Confidence            456789999999997542 333444444322 23444443

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.29  E-value=0.035  Score=52.42  Aligned_cols=40  Identities=13%  Similarity=0.360  Sum_probs=23.7

Q ss_pred             CCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       173 ~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      ..+.+++||||+|++.... ...+...+..-+....+|+.+
T Consensus       117 ~~~~KVvIIdev~~Lt~~a-~naLLk~LEepp~~~~fIl~t  156 (576)
T PRK14965        117 RSRYKIFIIDEVHMLSTNA-FNALLKTLEEPPPHVKFIFAT  156 (576)
T ss_pred             cCCceEEEEEChhhCCHHH-HHHHHHHHHcCCCCeEEEEEe
Confidence            3567899999999985433 223333444434445555544

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=96.27  E-value=0.011  Score=50.56  Aligned_cols=19  Identities=32%  Similarity=0.511  Sum_probs=15.3

Q ss_pred             CCcEEEEcCCCChhHHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~   88 (293)
                      ++.++++||||+|||....
T Consensus       194 ~~vi~~vGptGvGKTTt~~  212 (282)
T TIGR03499       194 GGVIALVGPTGVGKTTTLA  212 (282)
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            3478899999999996544

>PRK09183 transposase/IS protein; Provisional

Probab=96.27  E-value=0.035  Score=46.91  Aligned_cols=21  Identities=29%  Similarity=0.534  Sum_probs=17.5

Q ss_pred             hhcCCcEEEEcCCCChhHHHH
Q 022724           67 IIKGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~~~   87 (293)
                      +.++.++++.||+|+|||...
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa  119 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLA  119 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHH
Confidence            446789999999999999443

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=96.25  E-value=0.012  Score=47.98  Aligned_cols=37  Identities=22%  Similarity=0.372  Sum_probs=23.5

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEE
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVL  211 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~  211 (293)
                      .+-+.+|+||||.|-+ +-...+++......+.+++.+
T Consensus       112 grhKIiILDEADSMT~-gAQQAlRRtMEiyS~ttRFal  148 (333)
T KOG0991|consen  112 GRHKIIILDEADSMTA-GAQQALRRTMEIYSNTTRFAL  148 (333)
T ss_pred             CceeEEEeeccchhhh-HHHHHHHHHHHHHcccchhhh
Confidence            5668899999999853 334445555555554455443

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.23  E-value=0.1  Score=46.34  Aligned_cols=22  Identities=27%  Similarity=0.280  Sum_probs=16.8

Q ss_pred             CCcEEEEcCCCChhHHHHHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIALTV   91 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~   91 (293)
                      ++.++++||+|+|||....-.+
T Consensus       206 ~~ii~lvGptGvGKTTt~akLA  227 (407)
T PRK12726        206 HRIISLIGQTGVGKTTTLVKLG  227 (407)
T ss_pred             CeEEEEECCCCCCHHHHHHHHH
Confidence            5678999999999996554333

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=96.23  E-value=0.061  Score=46.89  Aligned_cols=33  Identities=24%  Similarity=0.298  Sum_probs=24.9

Q ss_pred             CcHHHHHHHHhhh----cCC---cEEEEcCCCChhHHHHH
Q 022724           56 PSAIQQRAVMPII----KGR---DVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        56 ~~~~Q~~~~~~i~----~~~---~~li~~~Tg~GKT~~~~   88 (293)
                      .+|||+..|..+.    +|+   -.++.||.|.||+..+.
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            3688888888765    443   47799999999995543

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.22  E-value=0.066  Score=49.47  Aligned_cols=129  Identities=16%  Similarity=0.252  Sum_probs=61.0

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEc--CCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS--PTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIR  146 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~--P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  146 (293)
                      .|+.+.++||||+|||......+...... ..+.++.++.  +.+.-+.   +.++.+....++.+..            
T Consensus       349 ~G~vIaLVGPtGvGKTTtaakLAa~la~~-~~gkkVaLIdtDtyRigA~---EQLk~ya~iLgv~v~~------------  412 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTIAKLAQRFAAQ-HAPRDVALVTTDTQRVGGR---EQLHSYGRQLGIAVHE------------  412 (559)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHh-cCCCceEEEecccccccHH---HHHHHhhcccCceeEe------------
Confidence            46789999999999996553322222222 1122344443  2233222   2233333333332221            


Q ss_pred             HHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcc-ccHHHHHHHHhhCCCCccEEEEEeecC-hhHHHHH
Q 022724          147 KLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPPDLQVVLISATLP-HEILEMT  224 (293)
Q Consensus       147 ~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~-~~~~~~~~i~~~l~~~~q~v~~SAt~~-~~~~~~~  224 (293)
                               +.+++.+...+..    +.+.++|+||.+-..... .....+..+... .....+++++++.. .++...+
T Consensus       413 ---------a~d~~~L~~aL~~----l~~~DLVLIDTaG~s~~D~~l~eeL~~L~aa-~~~a~lLVLpAtss~~Dl~eii  478 (559)
T PRK12727        413 ---------ADSAESLLDLLER----LRDYKLVLIDTAGMGQRDRALAAQLNWLRAA-RQVTSLLVLPANAHFSDLDEVV  478 (559)
T ss_pred             ---------cCcHHHHHHHHHH----hccCCEEEecCCCcchhhHHHHHHHHHHHHh-hcCCcEEEEECCCChhHHHHHH
Confidence                     1233344444432    245688999988654211 112223333222 23456777888764 3444444


Q ss_pred             Hhc
Q 022724          225 TKF  227 (293)
Q Consensus       225 ~~~  227 (293)
                      +.+
T Consensus       479 ~~f  481 (559)
T PRK12727        479 RRF  481 (559)
T ss_pred             HHH
Confidence            443

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=96.19  E-value=0.069  Score=44.09  Aligned_cols=52  Identities=15%  Similarity=0.149  Sum_probs=31.2

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (293)
                      .|..+++.|++|+|||....-.+.+.+..   +..++++.- .+...++.+..+.+
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            46789999999999995544333333332   335666664 33445555554443

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.

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=96.18  E-value=0.06  Score=47.03  Aligned_cols=33  Identities=21%  Similarity=0.214  Sum_probs=26.0

Q ss_pred             CcHHHHHHHHhhhc--CC---cEEEEcCCCChhHHHHH
Q 022724           56 PSAIQQRAVMPIIK--GR---DVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        56 ~~~~Q~~~~~~i~~--~~---~~li~~~Tg~GKT~~~~   88 (293)
                      .+|||+..|..+..  ++   .+++.||.|.|||..+.
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            36899999998873  33   58899999999996544

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.18  E-value=0.059  Score=49.54  Aligned_cols=18  Identities=33%  Similarity=0.484  Sum_probs=14.6

Q ss_pred             cEEEEcCCCChhHHHHHH
Q 022724           72 DVIAQAQSGTGKTSMIAL   89 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~   89 (293)
                      .+++.||.|+|||..+..
T Consensus        38 ~~Lf~GPpGtGKTTlA~~   55 (472)
T PRK14962         38 AYIFAGPRGTGKTTVARI   55 (472)
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            379999999999966543

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=96.16  E-value=0.017  Score=51.34  Aligned_cols=39  Identities=13%  Similarity=0.241  Sum_probs=24.5

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEc
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~  108 (293)
                      .+..++|+||||||||.. +-.++..+.......+++.+=
T Consensus       148 ~~GlilI~G~TGSGKTT~-l~al~~~i~~~~~~~~IvtiE  186 (372)
T TIGR02525       148 AAGLGLICGETGSGKSTL-AASIYQHCGETYPDRKIVTYE  186 (372)
T ss_pred             cCCEEEEECCCCCCHHHH-HHHHHHHHHhcCCCceEEEEe
Confidence            455799999999999944 345556554332233455543

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).

>PHA00729 NTP-binding motif containing protein

Probab=96.14  E-value=0.051  Score=44.60  Aligned_cols=74  Identities=14%  Similarity=0.232  Sum_probs=38.3

Q ss_pred             cEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcc-ccH----HHHHHHHhhCCCCccEEEEEeecChhHHHHHHh
Q 022724          153 HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFK----DQIYDVYRYLPPDLQVVLISATLPHEILEMTTK  226 (293)
Q Consensus       153 ~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~-~~~----~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~  226 (293)
                      ..++.+.+.+...+....-...+.+++||||+-.-... .+.    .....+...+...++++.+...-++++...++.
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            45555556666655432112234678999994322211 111    112223333344566777777766777766665

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=96.10  E-value=0.025  Score=49.84  Aligned_cols=18  Identities=33%  Similarity=0.516  Sum_probs=14.9

Q ss_pred             CcEEEEcCCCChhHHHHH
Q 022724           71 RDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~   88 (293)
                      .+.|+.||.|+|||..+-
T Consensus        49 ~SmIl~GPPG~GKTTlA~   66 (436)
T COG2256          49 HSMILWGPPGTGKTTLAR   66 (436)
T ss_pred             ceeEEECCCCCCHHHHHH
Confidence            389999999999996543

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.09  E-value=0.037  Score=52.23  Aligned_cols=20  Identities=20%  Similarity=0.365  Sum_probs=15.9

Q ss_pred             cEEEEcCCCChhHHHHHHHH
Q 022724           72 DVIAQAQSGTGKTSMIALTV   91 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~~~   91 (293)
                      .+++.||.|+|||.++...+
T Consensus        40 a~Lf~GPpG~GKTtiArilA   59 (624)
T PRK14959         40 AYLFSGTRGVGKTTIARIFA   59 (624)
T ss_pred             eEEEECCCCCCHHHHHHHHH
Confidence            58899999999997765433

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.09  E-value=0.045  Score=48.67  Aligned_cols=39  Identities=15%  Similarity=0.371  Sum_probs=23.1

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      .+..++||||+|.+....+. .+...+..-+....+|+.+
T Consensus       118 ~~~kviIIDEa~~l~~~a~n-aLLk~lEe~~~~~~fIl~t  156 (363)
T PRK14961        118 SRFKVYLIDEVHMLSRHSFN-ALLKTLEEPPQHIKFILAT  156 (363)
T ss_pred             CCceEEEEEChhhcCHHHHH-HHHHHHhcCCCCeEEEEEc
Confidence            45689999999998543322 2333344434455566554

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=96.09  E-value=0.04  Score=50.97  Aligned_cols=90  Identities=22%  Similarity=0.311  Sum_probs=56.0

Q ss_pred             cCCCCHHH-HHHHHHCCCCCC----cHHHHHHHHhhh--cCCcEEEEcCCCChhHHHHHHHHHhhhccCC---CceeEEE
Q 022724           37 AMGIKDDL-LRGIYQYGFEKP----SAIQQRAVMPII--KGRDVIAQAQSGTGKTSMIALTVCQTVDTSS---REVQALI  106 (293)
Q Consensus        37 ~~~l~~~i-~~~l~~~~~~~~----~~~Q~~~~~~i~--~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~---~~~~~li  106 (293)
                      +.+...++ +..|++..-...    .-+|.+==+.+.  .++-++|+|..|||||.+++--+...+...+   .+..+++
T Consensus       186 d~~~~dEvL~~~Lek~ss~~mrdIV~TIQkEQneIIR~ek~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vlv  265 (747)
T COG3973         186 DTGGRDEVLQRVLEKNSSAKMRDIVETIQKEQNEIIRFEKNKILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLV  265 (747)
T ss_pred             CCchHHHHHHHHHHhccchhHHHHHHHhhHhHHHHHhccCCCeEEEecCCCCCchhHHHHHHHHHHhccccccccCceEE
Confidence            34455554 444654322221    234444333444  3456899999999999877655444443322   2334999


Q ss_pred             EcCCHHHHHHHHHHHHHhhc
Q 022724          107 LSPTRELATQTEKVILAIGD  126 (293)
Q Consensus       107 l~P~~~l~~q~~~~~~~~~~  126 (293)
                      +.|++-...-+.+++-.++.
T Consensus       266 l~PN~vFleYis~VLPeLGe  285 (747)
T COG3973         266 LGPNRVFLEYISRVLPELGE  285 (747)
T ss_pred             EcCcHHHHHHHHHhchhhcc
Confidence            99999999999988877764

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=96.08  E-value=0.037  Score=52.57  Aligned_cols=38  Identities=16%  Similarity=0.338  Sum_probs=22.5

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEE
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLI  212 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~  212 (293)
                      .+.+++||||+|+|....+. .+...+..-+....+|+.
T Consensus       118 g~~KV~IIDEah~Ls~~a~N-ALLKtLEEPp~~v~FIL~  155 (647)
T PRK07994        118 GRFKVYLIDEVHMLSRHSFN-ALLKTLEEPPEHVKFLLA  155 (647)
T ss_pred             CCCEEEEEechHhCCHHHHH-HHHHHHHcCCCCeEEEEe
Confidence            46789999999998644332 233344443344455554

>PHA03372 DNA packaging terminase subunit 1; Provisional

Probab=96.07  E-value=0.084  Score=49.18  Aligned_cols=126  Identities=12%  Similarity=0.142  Sum_probs=79.6

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHH----HhhccCCceEEEEECCcchHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL----AIGDFINIQAHACVGGKSVGEDI  145 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~  145 (293)
                      .|-.+.-.|--.|||| ++.|++..+...-.+.++-|+++-+-.++-+.+.+.    +|.+...+  ...          
T Consensus       202 QkaTVFLVPRRHGKTW-f~VpiIsllL~s~~gI~IGYvAHqKhvs~~Vf~EI~~~lrrwF~~~~v--i~~----------  268 (668)
T PHA03372        202 QKATVFLVPRRHGKTW-FIIPIISFLLKNIIGISIGYVAHQKHVSQFVLKEVEFRCRRMFPRKHT--IEN----------  268 (668)
T ss_pred             ccceEEEecccCCcee-hHHHHHHHHHHhhcCceEEEEeeHHHHHHHHHHHHHHHHhhhcCccce--eee----------
Confidence            3678888999999997 466787877777778899999998877666555543    34322111  100          


Q ss_pred             HHHhcCCcEEEeChHHH-----HHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCC-CCccEEEEEeec
Q 022724          146 RKLEHGVHVVSGTPGRV-----CDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP-PDLQVVLISATL  216 (293)
Q Consensus       146 ~~~~~~~~ilV~Tp~~l-----~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~-~~~q~v~~SAt~  216 (293)
                          ++..|.+.-|+.=     ......+...=+++.+++|||||.+-.    ..+..++..+. +++++|+.|.|=
T Consensus       269 ----k~~tI~~s~pg~Kst~~fasc~n~NsiRGQ~fnll~VDEA~FI~~----~a~~tilgfm~q~~~KiIfISS~N  337 (668)
T PHA03372        269 ----KDNVISIDHRGAKSTALFASCYNTNSIRGQNFHLLLVDEAHFIKK----DAFNTILGFLAQNTTKIIFISSTN  337 (668)
T ss_pred             ----cCcEEEEecCCCcceeeehhhccCccccCCCCCEEEEehhhccCH----HHHHHhhhhhcccCceEEEEeCCC
Confidence                1113444433221     111222344457789999999998743    34555555554 678899998874

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=96.06  E-value=0.061  Score=46.70  Aligned_cols=38  Identities=18%  Similarity=0.388  Sum_probs=24.4

Q ss_pred             CccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       175 ~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      ...+++|||+|.+.... ...+..++...+....+|+.+
T Consensus       102 ~~~vviiDe~~~l~~~~-~~~L~~~le~~~~~~~lIl~~  139 (319)
T PRK00440        102 PFKIIFLDEADNLTSDA-QQALRRTMEMYSQNTRFILSC  139 (319)
T ss_pred             CceEEEEeCcccCCHHH-HHHHHHHHhcCCCCCeEEEEe
Confidence            45799999999884432 334555555555566666654

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=96.06  E-value=0.067  Score=46.98  Aligned_cols=33  Identities=18%  Similarity=0.210  Sum_probs=25.9

Q ss_pred             CcHHHHHHHHhhhc--CC---cEEEEcCCCChhHHHHH
Q 022724           56 PSAIQQRAVMPIIK--GR---DVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        56 ~~~~Q~~~~~~i~~--~~---~~li~~~Tg~GKT~~~~   88 (293)
                      .+|||...|..+..  ++   -+++.||.|.||+..+.
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            37899999988764  33   58899999999995543

>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=96.04  E-value=0.21  Score=44.04  Aligned_cols=144  Identities=17%  Similarity=0.160  Sum_probs=64.8

Q ss_pred             EEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCC-HHHHHHHHH---HHHHhhccCCceEEEE--ECCcchHHHHHH
Q 022724           74 IAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT-RELATQTEK---VILAIGDFINIQAHAC--VGGKSVGEDIRK  147 (293)
Q Consensus        74 li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~-~~l~~q~~~---~~~~~~~~~~~~~~~~--~~~~~~~~~~~~  147 (293)
                      ++.++.|+|||......++..+...+...++++. |+ ..+...+..   .+..+... .+....-  ....-.      
T Consensus         1 ~i~~~r~~GKT~~~~~~~~~~~~~~~~~~~vi~~-~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~------   72 (384)
T PF03237_consen    1 LINGGRGSGKTTLIAIWFLWWALTRPPGRRVIIA-STYRQARDIFGRFWKGIIELLPS-WFEIKFNEWNDRKII------   72 (384)
T ss_dssp             -EEE-SSS-HHHHHHHHHHHHHHSSSS--EEEEE-ESSHHHHHHHHHHHHHHHHTS-T-TTS--EEEE-SSEEE------
T ss_pred             CCcCCccccHHHHHHHHHHHHHhhCCCCcEEEEe-cCHHHHHHHHHHhHHHHHHHHHH-hcCcccccCCCCcEE------
Confidence            4778999999988887777776665544455555 65 455554333   33333333 2222111  111100      


Q ss_pred             HhcCCcEEEeChHHH--HHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEeec--ChhHHHH
Q 022724          148 LEHGVHVVSGTPGRV--CDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATL--PHEILEM  223 (293)
Q Consensus       148 ~~~~~~ilV~Tp~~l--~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~--~~~~~~~  223 (293)
                      +.++..|.+.+-+.-  ..-++.     ..++++++||+-.+.+..+...+........ ....+..|.+.  ......+
T Consensus        73 ~~nG~~i~~~~~~~~~~~~~~~G-----~~~~~i~iDE~~~~~~~~~~~~~~~~~~~~~-~~~~~~~s~p~~~~~~~~~~  146 (384)
T PF03237_consen   73 LPNGSRIQFRGADSPDSGDNIRG-----FEYDLIIIDEAAKVPDDAFSELIRRLRATWG-GSIRMYISTPPNPGGWFYEI  146 (384)
T ss_dssp             ETTS-EEEEES-----SHHHHHT-----S--SEEEEESGGGSTTHHHHHHHHHHHHCST-T--EEEEEE---SSSHHHHH
T ss_pred             ecCceEEEEeccccccccccccc-----cccceeeeeecccCchHHHHHHHHhhhhccc-CcceEEeecCCCCCCceeee
Confidence            135556666653221  111121     5568999999988755544444444433332 22222555544  3344445


Q ss_pred             HHhcCCCC
Q 022724          224 TTKFMTDP  231 (293)
Q Consensus       224 ~~~~~~~~  231 (293)
                      ......+.
T Consensus       147 ~~~~~~~~  154 (384)
T PF03237_consen  147 FQRNLDDD  154 (384)
T ss_dssp             HHHHHCTS
T ss_pred             eehhhcCC
Confidence            55444443

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.

>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.03  E-value=0.02  Score=52.77  Aligned_cols=142  Identities=18%  Similarity=0.229  Sum_probs=77.7

Q ss_pred             EEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHH------h-hccC-----CceEEEEECCcchH
Q 022724           75 AQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA------I-GDFI-----NIQAHACVGGKSVG  142 (293)
Q Consensus        75 i~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~------~-~~~~-----~~~~~~~~~~~~~~  142 (293)
                      +.+.||||||++.+-.|++....+-+  .-|+.|..-..++.....+..      + ....     .+.+-.+. ..+. 
T Consensus         2 f~matgsgkt~~ma~lil~~y~kgyr--~flffvnq~nilekt~~nftd~~s~kylf~e~i~~~d~~i~ikkvn-~fse-   77 (812)
T COG3421           2 FEMATGSGKTLVMAGLILECYKKGYR--NFLFFVNQANILEKTKLNFTDSVSSKYLFSENININDENIEIKKVN-NFSE-   77 (812)
T ss_pred             cccccCCChhhHHHHHHHHHHHhchh--hEEEEecchhHHHHHHhhcccchhhhHhhhhhhhcCCceeeeeeec-ccCc-
Confidence            46789999998887777777666433  467777766655554433211      0 0000     11111111 1111 


Q ss_pred             HHHHHHhcCCcEEEeChHHHHHHHhcC---CC---CCCCccE-EEecchhhhhccc-------------cHHHHHHHHhh
Q 022724          143 EDIRKLEHGVHVVSGTPGRVCDMIKRK---TL---RTRAIKL-LVLDESDEMLSRG-------------FKDQIYDVYRY  202 (293)
Q Consensus       143 ~~~~~~~~~~~ilV~Tp~~l~~~l~~~---~~---~~~~l~~-iViDE~h~~~~~~-------------~~~~~~~i~~~  202 (293)
                           -.++..|.++|.+.|...+.+.   .+   ++.+..+ ++-||+|++....             +...+...++.
T Consensus        78 -----hnd~iei~fttiq~l~~d~~~~ken~itledl~~~klvfl~deahhln~~tkkk~~de~~~~~~we~~v~la~~~  152 (812)
T COG3421          78 -----HNDAIEIYFTTIQGLFSDFTRAKENAITLEDLKDQKLVFLADEAHHLNTETKKKLNDEASEKRNWESVVKLALEQ  152 (812)
T ss_pred             -----cCCceEEEEeehHHHHHHHHhhccccccHhhHhhCceEEEechhhhhhhhhhhhcccHHHHHhhHHHHHHHHHhc
Confidence                 1245689999999998876542   22   3344444 5679999985321             22222222222


Q ss_pred             CCCCccEEEEEeecChhHHHHHHhc
Q 022724          203 LPPDLQVVLISATLPHEILEMTTKF  227 (293)
Q Consensus       203 l~~~~q~v~~SAt~~~~~~~~~~~~  227 (293)
                       ++..-++.+|||.+.+ +....+|
T Consensus       153 -nkd~~~lef~at~~k~-k~v~~ky  175 (812)
T COG3421         153 -NKDNLLLEFSATIPKE-KSVEDKY  175 (812)
T ss_pred             -CCCceeehhhhcCCcc-ccHHHHh
Confidence             2455677899999833 4444444

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.02  E-value=0.065  Score=50.02  Aligned_cols=39  Identities=13%  Similarity=0.246  Sum_probs=24.5

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      .+..++||||+|.+.... ...+...+..-+....+|+.+
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            456899999999985433 233444444444556666655

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.02  E-value=0.24  Score=44.74  Aligned_cols=59  Identities=12%  Similarity=0.026  Sum_probs=31.4

Q ss_pred             cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcC--CHHHHHHHHHHHHHhhccCCceEEEEE
Q 022724           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP--TRELATQTEKVILAIGDFINIQAHACV  136 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P--~~~l~~q~~~~~~~~~~~~~~~~~~~~  136 (293)
                      -++++|++|+|||....--+. .+...  +.++++++.  .+.-+.++.   +.+....++.+....
T Consensus       102 vi~lvG~~GvGKTTtaaKLA~-~l~~~--G~kV~lV~~D~~R~aA~eQL---k~~a~~~~vp~~~~~  162 (429)
T TIGR01425       102 VIMFVGLQGSGKTTTCTKLAY-YYQRK--GFKPCLVCADTFRAGAFDQL---KQNATKARIPFYGSY  162 (429)
T ss_pred             EEEEECCCCCCHHHHHHHHHH-HHHHC--CCCEEEEcCcccchhHHHHH---HHHhhccCCeEEeec
Confidence            478999999999955432222 22222  345666653  454444333   334444555554433

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.

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=96.01  E-value=0.058  Score=47.30  Aligned_cols=33  Identities=21%  Similarity=0.305  Sum_probs=25.5

Q ss_pred             CcHHHHHHHHhhh----cCC---cEEEEcCCCChhHHHHH
Q 022724           56 PSAIQQRAVMPII----KGR---DVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        56 ~~~~Q~~~~~~i~----~~~---~~li~~~Tg~GKT~~~~   88 (293)
                      .+|||+..|..+.    +|+   -.++.||.|.||+..+.
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            5788998888765    343   57899999999995543

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=95.99  E-value=0.015  Score=51.10  Aligned_cols=44  Identities=18%  Similarity=0.333  Sum_probs=30.5

Q ss_pred             hhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHH
Q 022724           66 PIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (293)
Q Consensus        66 ~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l  113 (293)
                      .+..+++++|+||||||||. ++-+++..+..   ..+++.+-.+.|+
T Consensus       158 ~v~~~~nilI~G~tGSGKTT-ll~aLl~~i~~---~~rivtiEd~~El  201 (344)
T PRK13851        158 CVVGRLTMLLCGPTGSGKTT-MSKTLISAIPP---QERLITIEDTLEL  201 (344)
T ss_pred             HHHcCCeEEEECCCCccHHH-HHHHHHcccCC---CCCEEEECCCccc
Confidence            34578899999999999994 34445555433   3366777677765

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=95.98  E-value=0.25  Score=41.76  Aligned_cols=34  Identities=26%  Similarity=0.397  Sum_probs=24.3

Q ss_pred             CCcHHHHHHHHhhh----cCC-cEEEEcCCCChhHHHHH
Q 022724           55 KPSAIQQRAVMPII----KGR-DVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~----~~~-~~li~~~Tg~GKT~~~~   88 (293)
                      .+++.+.+++..+.    .+. .+++.||+|+|||...-
T Consensus        23 ~~~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~~   61 (269)
T TIGR03015        23 YPSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLIR   61 (269)
T ss_pred             CCCHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHH
Confidence            46667777776653    333 68899999999995543

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.

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=95.98  E-value=0.04  Score=51.22  Aligned_cols=40  Identities=13%  Similarity=0.294  Sum_probs=25.8

Q ss_pred             CCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       173 ~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      .....++||||+|.+.... ...+...+..-++...+|+.+
T Consensus       115 ~~~~KVvIIDEad~Lt~~A-~NALLK~LEEpp~~t~FIL~t  154 (535)
T PRK08451        115 MARFKIFIIDEVHMLTKEA-FNALLKTLEEPPSYVKFILAT  154 (535)
T ss_pred             cCCeEEEEEECcccCCHHH-HHHHHHHHhhcCCceEEEEEE
Confidence            3567899999999985433 233444444445666777665

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=95.97  E-value=0.093  Score=40.67  Aligned_cols=53  Identities=28%  Similarity=0.538  Sum_probs=41.0

Q ss_pred             CCCccEEEecchhhhhcccc--HHHHHHHHhhCCCCccEEEEEeecChhHHHHHH
Q 022724          173 TRAIKLLVLDESDEMLSRGF--KDQIYDVYRYLPPDLQVVLISATLPHEILEMTT  225 (293)
Q Consensus       173 ~~~l~~iViDE~h~~~~~~~--~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~  225 (293)
                      ...++++|+||+-...+.++  .+.+..+++..+...-+|+.+-..|+.+.+.+.
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            45679999999988866664  456777888888777888888888888777653

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.

>PRK13342 recombination factor protein RarA; Reviewed

Probab=95.97  E-value=0.055  Score=49.05  Aligned_cols=18  Identities=33%  Similarity=0.501  Sum_probs=14.8

Q ss_pred             CcEEEEcCCCChhHHHHH
Q 022724           71 RDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~   88 (293)
                      .++++.||+|+|||..+.
T Consensus        37 ~~ilL~GppGtGKTtLA~   54 (413)
T PRK13342         37 SSMILWGPPGTGKTTLAR   54 (413)
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            379999999999995543

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=95.96  E-value=0.1  Score=43.44  Aligned_cols=40  Identities=20%  Similarity=0.184  Sum_probs=26.2

Q ss_pred             hcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcC
Q 022724           68 IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (293)
Q Consensus        68 ~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P  109 (293)
                      ..|.-++|.|++|+|||...+--+.+.....  +..+++++.
T Consensus        11 ~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~--g~~vly~s~   50 (242)
T cd00984          11 QPGDLIIIAARPSMGKTAFALNIAENIAKKQ--GKPVLFFSL   50 (242)
T ss_pred             CCCeEEEEEeCCCCCHHHHHHHHHHHHHHhC--CCceEEEeC
Confidence            4567899999999999954443344433332  346777774

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.

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.96  E-value=0.1  Score=46.96  Aligned_cols=18  Identities=28%  Similarity=0.366  Sum_probs=14.9

Q ss_pred             cEEEEcCCCChhHHHHHH
Q 022724           72 DVIAQAQSGTGKTSMIAL   89 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~   89 (293)
                      .+++.||.|+|||.++..
T Consensus        40 a~lf~Gp~G~GKtt~A~~   57 (397)
T PRK14955         40 GYIFSGLRGVGKTTAARV   57 (397)
T ss_pred             eEEEECCCCCCHHHHHHH
Confidence            388999999999976653

>PRK11823 DNA repair protein RadA; Provisional

Probab=95.95  E-value=0.062  Score=49.12  Aligned_cols=95  Identities=18%  Similarity=0.212  Sum_probs=54.3

Q ss_pred             HHHhhhc-----CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEC
Q 022724           63 AVMPIIK-----GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVG  137 (293)
Q Consensus        63 ~~~~i~~-----~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~  137 (293)
                      -++.++.     |.-+++.|++|+|||...+-.+ ..+..  .+.+++|+.- .+-..|+..+.+.+.....        
T Consensus        68 ~LD~~LgGGi~~Gs~~lI~G~pG~GKTtL~lq~a-~~~a~--~g~~vlYvs~-Ees~~qi~~ra~rlg~~~~--------  135 (446)
T PRK11823         68 ELDRVLGGGLVPGSVVLIGGDPGIGKSTLLLQVA-ARLAA--AGGKVLYVSG-EESASQIKLRAERLGLPSD--------  135 (446)
T ss_pred             HHHHHhcCCccCCEEEEEECCCCCCHHHHHHHHH-HHHHh--cCCeEEEEEc-cccHHHHHHHHHHcCCChh--------
Confidence            4455554     4578999999999995433333 23222  2457888874 4445677666655532111        


Q ss_pred             CcchHHHHHHHhcCCcEEEe---ChHHHHHHHhcCCCCCCCccEEEecchhhhhc
Q 022724          138 GKSVGEDIRKLEHGVHVVSG---TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (293)
Q Consensus       138 ~~~~~~~~~~~~~~~~ilV~---Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~  189 (293)
                                     .+.+.   ..+.+.+.+..     .+.+++|||+++.+..
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                           02222   22334444332     3568999999998753

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.93  E-value=0.061  Score=50.68  Aligned_cols=39  Identities=15%  Similarity=0.443  Sum_probs=24.1

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      .+.+++||||+|+|....+ ..+...+..-+....+|+.+
T Consensus       117 ~~~KVvIIDEah~Lt~~A~-NALLK~LEEpp~~~~fIL~t  155 (584)
T PRK14952        117 SRYRIFIVDEAHMVTTAGF-NALLKIVEEPPEHLIFIFAT  155 (584)
T ss_pred             CCceEEEEECCCcCCHHHH-HHHHHHHhcCCCCeEEEEEe
Confidence            5678999999999864432 23334444444455566555

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=95.93  E-value=0.19  Score=42.70  Aligned_cols=35  Identities=20%  Similarity=0.291  Sum_probs=21.8

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEc
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~  108 (293)
                      +-++++||+|+|||....-.+.. +..  .+.++.++.
T Consensus        73 ~vi~l~G~~G~GKTTt~akLA~~-l~~--~g~~V~li~  107 (272)
T TIGR00064        73 NVILFVGVNGVGKTTTIAKLANK-LKK--QGKSVLLAA  107 (272)
T ss_pred             eEEEEECCCCCcHHHHHHHHHHH-HHh--cCCEEEEEe
Confidence            45788899999999765433322 222  234566665

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.

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.92  E-value=0.037  Score=51.32  Aligned_cols=16  Identities=25%  Similarity=0.378  Sum_probs=13.8

Q ss_pred             EEEEcCCCChhHHHHH
Q 022724           73 VIAQAQSGTGKTSMIA   88 (293)
Q Consensus        73 ~li~~~Tg~GKT~~~~   88 (293)
                      +++.||.|+|||..+.
T Consensus        39 ~Lf~GppGtGKTTlA~   54 (504)
T PRK14963         39 YLFSGPRGVGKTTTAR   54 (504)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            5999999999997654

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=95.92  E-value=0.13  Score=45.39  Aligned_cols=39  Identities=21%  Similarity=0.381  Sum_probs=24.9

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      ....++||||+|.|.... ...+...+..-+.+..++++|
T Consensus       140 g~~rVviIDeAd~l~~~a-anaLLk~LEEpp~~~~fiLit  178 (351)
T PRK09112        140 GNWRIVIIDPADDMNRNA-ANAILKTLEEPPARALFILIS  178 (351)
T ss_pred             CCceEEEEEchhhcCHHH-HHHHHHHHhcCCCCceEEEEE
Confidence            467899999999985443 333444555544455566665

>PRK04195 replication factor C large subunit; Provisional

Probab=95.92  E-value=0.067  Score=49.50  Aligned_cols=18  Identities=28%  Similarity=0.497  Sum_probs=15.3

Q ss_pred             CCcEEEEcCCCChhHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~   87 (293)
                      .+.+++.||+|+|||...
T Consensus        39 ~~~lLL~GppG~GKTtla   56 (482)
T PRK04195         39 KKALLLYGPPGVGKTSLA   56 (482)
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            468999999999999554

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=95.89  E-value=0.021  Score=54.75  Aligned_cols=45  Identities=20%  Similarity=0.322  Sum_probs=38.8

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEeecCh
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPH  218 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~  218 (293)
                      .+.-++|+|+-|.+.+.....-+..+++..+++...++.|-+-|+
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            334699999999998888888899999999999999999987554

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=95.88  E-value=0.071  Score=50.47  Aligned_cols=40  Identities=13%  Similarity=0.339  Sum_probs=25.0

Q ss_pred             CCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       173 ~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      +...+++||||+|.+.... ...+...+..-+..+.+|+.+
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            4567899999999985433 223333344444566677655

>PRK08939 primosomal protein DnaI; Reviewed

Probab=95.87  E-value=0.071  Score=46.15  Aligned_cols=46  Identities=15%  Similarity=0.284  Sum_probs=26.0

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~  119 (293)
                      ++++++.||+|+|||.... ++...+...  +..+.++ ...+++.++..
T Consensus       156 ~~gl~L~G~~G~GKThLa~-Aia~~l~~~--g~~v~~~-~~~~l~~~lk~  201 (306)
T PRK08939        156 VKGLYLYGDFGVGKSYLLA-AIANELAKK--GVSSTLL-HFPEFIRELKN  201 (306)
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHHHHc--CCCEEEE-EHHHHHHHHHH
Confidence            4689999999999994433 333444332  3334433 32345544443

>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=95.87  E-value=0.066  Score=51.17  Aligned_cols=124  Identities=19%  Similarity=0.168  Sum_probs=75.1

Q ss_pred             HHHHHHHHhhhcC-----CcEEEEcCCCChhHHHHHHHHHhh-hccC-----CCceeEEEEcCCHHHHHHHHHHHHHhhc
Q 022724           58 AIQQRAVMPIIKG-----RDVIAQAQSGTGKTSMIALTVCQT-VDTS-----SREVQALILSPTRELATQTEKVILAIGD  126 (293)
Q Consensus        58 ~~Q~~~~~~i~~~-----~~~li~~~Tg~GKT~~~~~~~~~~-l~~~-----~~~~~~lil~P~~~l~~q~~~~~~~~~~  126 (293)
                      ..|...|-.....     +-.|+.-..|-|||..-+..++.. ....     ......+++||+. +..|....+.+..+
T Consensus       135 ~~~~~~~~~~~~~~~~~~~ggIladd~glgkt~~ti~l~l~~~~~~~~~~~~~~~kttLivcp~s-~~~qW~~elek~~~  213 (674)
T KOG1001|consen  135 LKQKYRWSLLKSREQQSLRGGILADDMGLGKTVKTIALILKQKLKSKEEDRQKEFKTTLIVCPTS-LLTQWKTELEKVTE  213 (674)
T ss_pred             HHHHHHHHhhcccccCccccceEeeccccchHHHHHHHHHhcccCCcchhhccccCceeEecchH-HHHHHHHHHhccCC
Confidence            5566655554432     346777778999997655444433 2222     1344678888854 45676666666666


Q ss_pred             cCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcc
Q 022724          127 FINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (293)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~  190 (293)
                      ...+.+..++| ..  .. ....++.+|+++|++.+..    ..+..-..-.+|+||+|.+-..
T Consensus       214 ~~~l~v~v~~g-r~--kd-~~el~~~dVVltTy~il~~----~~l~~i~w~Riildea~~ikn~  269 (674)
T KOG1001|consen  214 EDKLSIYVYHG-RT--KD-KSELNSYDVVLTTYDILKN----SPLVKIKWLRIVLDEAHTIKNK  269 (674)
T ss_pred             ccceEEEEecc-cc--cc-cchhcCCceEEeeHHHhhc----ccccceeEEEEEeccccccCCc
Confidence            66777777777 11  11 1222456899999977764    1111223345999999998544

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=95.86  E-value=0.12  Score=47.95  Aligned_cols=18  Identities=22%  Similarity=0.361  Sum_probs=15.2

Q ss_pred             cEEEEcCCCChhHHHHHH
Q 022724           72 DVIAQAQSGTGKTSMIAL   89 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~   89 (293)
                      .++++||.|+|||..+.+
T Consensus        45 a~Lf~Gp~G~GKTT~Ari   62 (507)
T PRK06645         45 GYLLTGIRGVGKTTSARI   62 (507)
T ss_pred             eEEEECCCCCCHHHHHHH
Confidence            699999999999966543

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=95.83  E-value=0.039  Score=48.33  Aligned_cols=43  Identities=19%  Similarity=0.376  Sum_probs=28.9

Q ss_pred             hhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHH
Q 022724           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l  113 (293)
                      +..+++++|+|+||||||. ++-+++..+..   ..+++.+=-+.|+
T Consensus       157 v~~~~nili~G~tgSGKTT-ll~aL~~~ip~---~~ri~tiEd~~El  199 (332)
T PRK13900        157 VISKKNIIISGGTSTGKTT-FTNAALREIPA---IERLITVEDAREI  199 (332)
T ss_pred             HHcCCcEEEECCCCCCHHH-HHHHHHhhCCC---CCeEEEecCCCcc
Confidence            4468899999999999994 34455555543   3356665455554

>PRK06904 replicative DNA helicase; Validated

Probab=95.81  E-value=0.21  Score=46.03  Aligned_cols=149  Identities=19%  Similarity=0.232  Sum_probs=70.4

Q ss_pred             hhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEC-CcchHHH-
Q 022724           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVG-GKSVGED-  144 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~-~~~~~~~-  144 (293)
                      +..|.-+++.|.+|+|||. |++-+...+... .+..++|++.- --..|+..++-.........-. ..| ..+..+. 
T Consensus       218 l~~G~LiiIaarPg~GKTa-falnia~~~a~~-~g~~Vl~fSlE-Ms~~ql~~Rlla~~s~v~~~~i-~~g~~l~~~e~~  293 (472)
T PRK06904        218 LQPSDLIIVAARPSMGKTT-FAMNLCENAAMA-SEKPVLVFSLE-MPAEQIMMRMLASLSRVDQTKI-RTGQNLDQQDWA  293 (472)
T ss_pred             cCCCcEEEEEeCCCCChHH-HHHHHHHHHHHh-cCCeEEEEecc-CCHHHHHHHHHHhhCCCCHHHh-ccCCCCCHHHHH
Confidence            3345668888999999995 444444433221 13356666543 3344555444332222111110 122 1111111 


Q ss_pred             -----HHHHhcCCcEEEe-----ChHHHHHHHhcCCCCCCCccEEEecchhhhhccc----cHHHHHHHHhhCC-----C
Q 022724          145 -----IRKLEHGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG----FKDQIYDVYRYLP-----P  205 (293)
Q Consensus       145 -----~~~~~~~~~ilV~-----Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~----~~~~~~~i~~~l~-----~  205 (293)
                           ...+...+.+.|-     |+..+....++.......+++||||-.+.+...+    ....+..+-+.+.     .
T Consensus       294 ~~~~a~~~l~~~~~l~I~d~~~~t~~~i~~~~r~~~~~~~~~~lvvIDYLqli~~~~~~~~r~~ei~~isr~LK~lAkel  373 (472)
T PRK06904        294 KISSTVGMFKQKPNLYIDDSSGLTPTELRSRARRVYRENGGLSLIMVDYLQLMRAPGFEDNRTLEIAEISRSLKALAKEL  373 (472)
T ss_pred             HHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHHHhCCCCCEEEEecHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHh
Confidence                 1122233446652     5555554333211112357899999999885322    2223333333331     2


Q ss_pred             CccEEEEEeecChhH
Q 022724          206 DLQVVLISATLPHEI  220 (293)
Q Consensus       206 ~~q~v~~SAt~~~~~  220 (293)
                      ++.++++| -++..+
T Consensus       374 ~ipVi~ls-QLnR~~  387 (472)
T PRK06904        374 KVPVVALS-QLNRTL  387 (472)
T ss_pred             CCeEEEEE-ecCchh
Confidence            56777776 444443

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.80  E-value=0.079  Score=49.52  Aligned_cols=40  Identities=15%  Similarity=0.360  Sum_probs=24.4

Q ss_pred             CCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       173 ~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      ..+.+++||||+|.|....+ ..+...+..-+....+|+.+
T Consensus       117 ~~~~kVvIIDEad~ls~~a~-naLLK~LEepp~~~~fIL~t  156 (527)
T PRK14969        117 RGRFKVYIIDEVHMLSKSAF-NAMLKTLEEPPEHVKFILAT  156 (527)
T ss_pred             cCCceEEEEcCcccCCHHHH-HHHHHHHhCCCCCEEEEEEe
Confidence            35678999999999854332 22333344444556666655

>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=95.80  E-value=0.059  Score=48.73  Aligned_cols=80  Identities=18%  Similarity=0.184  Sum_probs=57.5

Q ss_pred             HHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHH
Q 022724           43 DLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL  122 (293)
Q Consensus        43 ~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~  122 (293)
                      .+++.++. .+-.+...|.++.-..-.|+. .|.|=.|||||...++-+ ..+...+...+++|-+-|+.|+.++.+.+.
T Consensus       151 a~l~~ies-kIanfD~~Q~kaa~~~~~G~q-rIrGLAGSGKT~~La~Ka-a~lh~knPd~~I~~Tfftk~L~s~~r~lv~  227 (660)
T COG3972         151 ALLDTIES-KIANFDTDQTKAAFQSGFGKQ-RIRGLAGSGKTELLAHKA-AELHSKNPDSRIAFTFFTKILASTMRTLVP  227 (660)
T ss_pred             HHHHHHHH-HHhcccchhheeeeecCCchh-hhhcccCCCchhHHHHHH-HHHhcCCCCceEEEEeehHHHHHHHHHHHH
Confidence            44555544 455677788887666667777 788999999996544333 344444455699999999999999998887


Q ss_pred             Hhh
Q 022724          123 AIG  125 (293)
Q Consensus       123 ~~~  125 (293)
                      ++.
T Consensus       228 ~F~  230 (660)
T COG3972         228 EFF  230 (660)
T ss_pred             HHH
Confidence            764

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

Probab=95.78  E-value=0.022  Score=45.20  Aligned_cols=46  Identities=20%  Similarity=0.330  Sum_probs=26.2

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE  118 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~  118 (293)
                      +++++++.||+|+|||..+.. +...+...  +..+++ ++..+|...+.
T Consensus        46 ~~~~l~l~G~~G~GKThLa~a-i~~~~~~~--g~~v~f-~~~~~L~~~l~   91 (178)
T PF01695_consen   46 NGENLILYGPPGTGKTHLAVA-IANEAIRK--GYSVLF-ITASDLLDELK   91 (178)
T ss_dssp             C--EEEEEESTTSSHHHHHHH-HHHHHHHT--T--EEE-EEHHHHHHHHH
T ss_pred             cCeEEEEEhhHhHHHHHHHHH-HHHHhccC--CcceeE-eecCceecccc
Confidence            578999999999999965443 33333332  334544 45555655543

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.

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=95.75  E-value=0.054  Score=52.40  Aligned_cols=40  Identities=18%  Similarity=0.223  Sum_probs=24.6

Q ss_pred             CccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEeecChh
Q 022724          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHE  219 (293)
Q Consensus       175 ~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~  219 (293)
                      +..+++|||+|.+....    -..++..+ ...+++++++|-++.
T Consensus       109 ~~~IL~IDEIh~Ln~~q----QdaLL~~l-E~g~IiLI~aTTenp  148 (725)
T PRK13341        109 KRTILFIDEVHRFNKAQ----QDALLPWV-ENGTITLIGATTENP  148 (725)
T ss_pred             CceEEEEeChhhCCHHH----HHHHHHHh-cCceEEEEEecCCCh
Confidence            45689999999984322    22333333 246788888875543

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.68  E-value=0.037  Score=52.34  Aligned_cols=39  Identities=21%  Similarity=0.370  Sum_probs=22.4

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      .+.+++||||+|+|....+.. +...+..-+....+|+.+
T Consensus       123 g~~KV~IIDEvh~Ls~~a~Na-LLKtLEEPP~~~~fIL~T  161 (618)
T PRK14951        123 GRFKVFMIDEVHMLTNTAFNA-MLKTLEEPPEYLKFVLAT  161 (618)
T ss_pred             CCceEEEEEChhhCCHHHHHH-HHHhcccCCCCeEEEEEE
Confidence            467899999999986443222 222233333345555544

>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair

Probab=95.67  E-value=0.016  Score=47.31  Aligned_cols=16  Identities=25%  Similarity=0.472  Sum_probs=14.0

Q ss_pred             cEEEEcCCCChhHHHH
Q 022724           72 DVIAQAQSGTGKTSMI   87 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~   87 (293)
                      ++++.||.|+|||..+
T Consensus        52 h~lf~GPPG~GKTTLA   67 (233)
T PF05496_consen   52 HMLFYGPPGLGKTTLA   67 (233)
T ss_dssp             EEEEESSTTSSHHHHH
T ss_pred             eEEEECCCccchhHHH
Confidence            7999999999999544

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.

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

Probab=95.66  E-value=0.031  Score=47.42  Aligned_cols=29  Identities=10%  Similarity=0.295  Sum_probs=21.3

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCC
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSR  100 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~  100 (293)
                      .-++|.||||||||.. +.++++.+.....
T Consensus       126 GLILVTGpTGSGKSTT-lAamId~iN~~~~  154 (353)
T COG2805         126 GLILVTGPTGSGKSTT-LAAMIDYINKHKA  154 (353)
T ss_pred             ceEEEeCCCCCcHHHH-HHHHHHHHhccCC
Confidence            3588999999999954 4467777766543

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=95.66  E-value=0.06  Score=50.61  Aligned_cols=18  Identities=33%  Similarity=0.468  Sum_probs=14.7

Q ss_pred             cEEEEcCCCChhHHHHHH
Q 022724           72 DVIAQAQSGTGKTSMIAL   89 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~   89 (293)
                      .+++.||.|+|||..+..
T Consensus        40 A~Lf~GP~GvGKTTlA~~   57 (605)
T PRK05896         40 AYIFSGPRGIGKTSIAKI   57 (605)
T ss_pred             eEEEECCCCCCHHHHHHH
Confidence            488999999999965543

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=95.64  E-value=0.077  Score=47.43  Aligned_cols=47  Identities=21%  Similarity=0.420  Sum_probs=30.7

Q ss_pred             CccEEEecchhhhhcc-ccHHHHHHHHhhCC-CCccEEEEEeecChhHH
Q 022724          175 AIKLLVLDESDEMLSR-GFKDQIYDVYRYLP-PDLQVVLISATLPHEIL  221 (293)
Q Consensus       175 ~l~~iViDE~h~~~~~-~~~~~~~~i~~~l~-~~~q~v~~SAt~~~~~~  221 (293)
                      ++++++||+++.+... .....+-.++..+. ...|+++.|-..|..+.
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            6789999999998654 33444444444443 44577777777665544

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

Probab=95.61  E-value=0.05  Score=47.09  Aligned_cols=58  Identities=16%  Similarity=0.245  Sum_probs=39.7

Q ss_pred             CCCCCcHHHHHHHHhhhcC-CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHH
Q 022724           52 GFEKPSAIQQRAVMPIIKG-RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (293)
Q Consensus        52 ~~~~~~~~Q~~~~~~i~~~-~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l  113 (293)
                      .|...++-|...+-.+... .|++++|.||||||.. +-++...+..   .-|+|.+=-+.||
T Consensus       154 ~~gt~~~~~a~~L~~av~~r~NILisGGTGSGKTTl-LNal~~~i~~---~eRvItiEDtaEL  212 (355)
T COG4962         154 IFGTMIRRAAKFLRRAVGIRCNILISGGTGSGKTTL-LNALSGFIDS---DERVITIEDTAEL  212 (355)
T ss_pred             HcCCcCHHHHHHHHHHHhhceeEEEeCCCCCCHHHH-HHHHHhcCCC---cccEEEEeehhhh
Confidence            3557888888877776655 5999999999999942 2222223222   2278888777776

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=95.60  E-value=0.13  Score=45.77  Aligned_cols=97  Identities=12%  Similarity=0.166  Sum_probs=53.1

Q ss_pred             HHHhhhc-----CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEC
Q 022724           63 AVMPIIK-----GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVG  137 (293)
Q Consensus        63 ~~~~i~~-----~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~  137 (293)
                      -++.++.     |.-+++.|++|+|||...+..+ ..+...  +.+++|+.-. +...|+..+.+++.-... ++ .+..
T Consensus        70 eLD~vLgGGi~~GslvLI~G~pG~GKStLllq~a-~~~a~~--g~~VlYvs~E-Es~~qi~~Ra~rlg~~~~-~l-~l~~  143 (372)
T cd01121          70 ELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVA-ARLAKR--GGKVLYVSGE-ESPEQIKLRADRLGISTE-NL-YLLA  143 (372)
T ss_pred             HHHHhhcCCccCCeEEEEEeCCCCCHHHHHHHHH-HHHHhc--CCeEEEEECC-cCHHHHHHHHHHcCCCcc-cE-EEEc
Confidence            4455553     4678999999999995443333 333222  3478887653 345666665555432110 00 0110


Q ss_pred             CcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhh
Q 022724          138 GKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (293)
Q Consensus       138 ~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~  188 (293)
                      .                  ...+.+...+..     .+.+++|||+++.+.
T Consensus       144 e------------------~~le~I~~~i~~-----~~~~lVVIDSIq~l~  171 (372)
T cd01121         144 E------------------TNLEDILASIEE-----LKPDLVIIDSIQTVY  171 (372)
T ss_pred             c------------------CcHHHHHHHHHh-----cCCcEEEEcchHHhh
Confidence            0                  123444444432     356899999999874

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.

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=95.59  E-value=0.034  Score=49.21  Aligned_cols=28  Identities=14%  Similarity=0.382  Sum_probs=20.5

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhcc
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDT   97 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~   97 (293)
                      .+..++|+||||||||... -.++..+..
T Consensus       133 ~~glilI~GpTGSGKTTtL-~aLl~~i~~  160 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTLL-AAIIRELAE  160 (358)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHHhh
Confidence            5678999999999999543 445555543

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.

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.55  E-value=0.33  Score=43.71  Aligned_cols=126  Identities=13%  Similarity=0.133  Sum_probs=62.2

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEc--CCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS--PTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~--P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  148 (293)
                      .-++++||+|+|||....--+.......  +.++.++.  +.+..+..+.   +.+....++....              
T Consensus       224 ~vi~lvGptGvGKTTtaaKLA~~~~~~~--G~~V~Lit~Dt~R~aA~eQL---k~yAe~lgvp~~~--------------  284 (432)
T PRK12724        224 KVVFFVGPTGSGKTTSIAKLAAKYFLHM--GKSVSLYTTDNYRIAAIEQL---KRYADTMGMPFYP--------------  284 (432)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHhc--CCeEEEecccchhhhHHHHH---HHHHHhcCCCeee--------------
Confidence            3478999999999966554443322221  33444444  3344433322   2333333332211              


Q ss_pred             hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhh-ccccHHHHHHHHhhCC---CCccEEEEEeecCh-hHHHH
Q 022724          149 EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML-SRGFKDQIYDVYRYLP---PDLQVVLISATLPH-EILEM  223 (293)
Q Consensus       149 ~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~-~~~~~~~~~~i~~~l~---~~~q~v~~SAt~~~-~~~~~  223 (293)
                             +..+..+...+.     ..+.++|+||=+-... +......+..+++...   +.-.++.+|||... ++.+.
T Consensus       285 -------~~~~~~l~~~l~-----~~~~D~VLIDTaGr~~rd~~~l~eL~~~~~~~~~~~~~e~~LVLsAt~~~~~~~~~  352 (432)
T PRK12724        285 -------VKDIKKFKETLA-----RDGSELILIDTAGYSHRNLEQLERMQSFYSCFGEKDSVENLLVLSSTSSYHHTLTV  352 (432)
T ss_pred             -------hHHHHHHHHHHH-----hCCCCEEEEeCCCCCccCHHHHHHHHHHHHhhcCCCCCeEEEEEeCCCCHHHHHHH
Confidence                   111233333333     1456889999665432 1222334444444432   22467888999876 45555


Q ss_pred             HHhc
Q 022724          224 TTKF  227 (293)
Q Consensus       224 ~~~~  227 (293)
                      ...+
T Consensus       353 ~~~f  356 (432)
T PRK12724        353 LKAY  356 (432)
T ss_pred             HHHh
Confidence            5444

>PRK06620 hypothetical protein; Validated

Probab=95.55  E-value=0.035  Score=45.48  Aligned_cols=16  Identities=25%  Similarity=0.412  Sum_probs=13.7

Q ss_pred             CcEEEEcCCCChhHHH
Q 022724           71 RDVIAQAQSGTGKTSM   86 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~   86 (293)
                      +.+++.||+|+|||..
T Consensus        45 ~~l~l~Gp~G~GKThL   60 (214)
T PRK06620         45 FTLLIKGPSSSGKTYL   60 (214)
T ss_pred             ceEEEECCCCCCHHHH
Confidence            5689999999999943

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=95.53  E-value=0.083  Score=42.13  Aligned_cols=144  Identities=16%  Similarity=0.170  Sum_probs=75.4

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHH-HHHHHHHHhhccCCceEEEEECCcchHHHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELAT-QTEKVILAIGDFINIQAHACVGGKSVGEDIRK  147 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~-q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (293)
                      ...++.+..++|.|||.+++--++..+..   |.+++++-=.+.-.. .=...++++   .++.....-.+......   
T Consensus        21 ~~g~v~v~~g~GkGKtt~a~g~a~ra~g~---G~~V~ivQFlKg~~~~GE~~~l~~l---~~v~~~~~g~~~~~~~~---   91 (191)
T PRK05986         21 EKGLLIVHTGNGKGKSTAAFGMALRAVGH---GKKVGVVQFIKGAWSTGERNLLEFG---GGVEFHVMGTGFTWETQ---   91 (191)
T ss_pred             cCCeEEEECCCCCChHHHHHHHHHHHHHC---CCeEEEEEEecCCCccCHHHHHhcC---CCcEEEECCCCCcccCC---
Confidence            55689999999999998877666665544   446666543222100 111112221   12222221111110000   


Q ss_pred             HhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcccc--HHHHHHHHhhCCCCccEEEEEeecChhHHHHHH
Q 022724          148 LEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF--KDQIYDVYRYLPPDLQVVLISATLPHEILEMTT  225 (293)
Q Consensus       148 ~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~--~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~  225 (293)
                         ...--.......+...+. .+.-..++++|+||+-..++.++  ...+..++...+...-+|+.--..|+.+.+.+.
T Consensus        92 ---~~~e~~~~~~~~~~~a~~-~l~~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~~p~~Lie~AD  167 (191)
T PRK05986         92 ---DRERDIAAAREGWEEAKR-MLADESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRGAPRELIEAAD  167 (191)
T ss_pred             ---CcHHHHHHHHHHHHHHHH-HHhCCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCCCCHHHHHhCc
Confidence               000000001111111111 12235678999999998887774  456777777777777777776677887776654

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=95.50  E-value=0.13  Score=45.72  Aligned_cols=42  Identities=19%  Similarity=0.355  Sum_probs=24.8

Q ss_pred             CCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEee
Q 022724          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISAT  215 (293)
Q Consensus       173 ~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt  215 (293)
                      .....++||||+|.+.... ...+...+..-+....+|++|..
T Consensus       139 ~~~~kVviIDead~m~~~a-anaLLK~LEepp~~~~~IL~t~~  180 (365)
T PRK07471        139 EGGWRVVIVDTADEMNANA-ANALLKVLEEPPARSLFLLVSHA  180 (365)
T ss_pred             cCCCEEEEEechHhcCHHH-HHHHHHHHhcCCCCeEEEEEECC
Confidence            3567899999999985332 33344444544444555555443

>PRK04328 hypothetical protein; Provisional

Probab=95.48  E-value=0.14  Score=42.96  Aligned_cols=53  Identities=15%  Similarity=0.213  Sum_probs=33.8

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhh
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIG  125 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  125 (293)
                      .|..+++.|++|+|||.-.+-.+.+.+..   +.+++|+. +.+-..++.+.++.++
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            45679999999999996554445454433   34566666 4445556666665543

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=95.44  E-value=0.14  Score=44.50  Aligned_cols=34  Identities=18%  Similarity=0.213  Sum_probs=26.4

Q ss_pred             CCcHHHHHHHHhhh----cCC---cEEEEcCCCChhHHHHH
Q 022724           55 KPSAIQQRAVMPII----KGR---DVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~----~~~---~~li~~~Tg~GKT~~~~   88 (293)
                      .++|||+..|..+.    +|+   -+++.||.|.||+..+.
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            46789999988866    343   58999999999995443

>TIGR00767 rho transcription termination factor Rho

Probab=95.43  E-value=0.11  Score=46.27  Aligned_cols=31  Identities=26%  Similarity=0.387  Sum_probs=21.7

Q ss_pred             hhcCCcEEEEcCCCChhHHHHHHHHHhhhccC
Q 022724           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS   98 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~   98 (293)
                      +-.|+-++|+||+|+|||... -.+...+...
T Consensus       165 ig~Gq~~~IvG~~g~GKTtL~-~~i~~~I~~n  195 (415)
T TIGR00767       165 IGKGQRGLIVAPPKAGKTVLL-QKIAQAITRN  195 (415)
T ss_pred             eCCCCEEEEECCCCCChhHHH-HHHHHhhccc
Confidence            347889999999999999643 3344544443

Members of this family differ in the specificity of RNA binding.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=95.42  E-value=0.13  Score=51.50  Aligned_cols=45  Identities=22%  Similarity=0.345  Sum_probs=35.5

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEeecCh
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPH  218 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~  218 (293)
                      ..--+||||++|.+.+......+..+++..+....+|+.|-+.++
T Consensus       120 ~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~sR~~~~  164 (903)
T PRK04841        120 HQPLYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVLSRNLPP  164 (903)
T ss_pred             CCCEEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEEeCCCCC
Confidence            344689999999986555667888899999888999888877543

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=95.41  E-value=0.032  Score=45.99  Aligned_cols=132  Identities=13%  Similarity=0.164  Sum_probs=65.5

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccC-------CceEEEEECCcch
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI-------NIQAHACVGGKSV  141 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~-------~~~~~~~~~~~~~  141 (293)
                      .|..+++.|++|+|||.-.+-.+.+.+...  +-++++++- .+-..++.+.++.++-..       .+.+.........
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--GEKVLYVSF-EEPPEELIENMKSFGWDLEEYEDSGKLKIIDAFPERIG   94 (226)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHH--T--EEEEES-SS-HHHHHHHHHTTTS-HHHHHHTTSEEEEESSGGGST
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHhhhhc--CCcEEEEEe-cCCHHHHHHHHHHcCCcHHHHhhcCCEEEEeccccccc
Confidence            456899999999999966555555554441  235677763 333466666665443111       1111111100000


Q ss_pred             HHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcc----ccHHHHHHHHhhCCCCccEEEEEeec
Q 022724          142 GEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR----GFKDQIYDVYRYLPPDLQVVLISATL  216 (293)
Q Consensus       142 ~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~----~~~~~~~~i~~~l~~~~q~v~~SAt~  216 (293)
                      .          .  -..++.+...+... +.-.+.+.+|||-+..+...    .+...+..+...+.....+.++++..
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  12233343333221 00112289999999988221    24455666666665555566666663

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 ....

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=95.36  E-value=0.074  Score=50.09  Aligned_cols=19  Identities=32%  Similarity=0.382  Sum_probs=15.1

Q ss_pred             cEEEEcCCCChhHHHHHHH
Q 022724           72 DVIAQAQSGTGKTSMIALT   90 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~~   90 (293)
                      -++++||.|+|||.++-..
T Consensus        40 ayLf~Gp~GtGKTt~Ak~l   58 (559)
T PRK05563         40 AYLFSGPRGTGKTSAAKIF   58 (559)
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            4789999999999665443

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=95.33  E-value=0.11  Score=43.78  Aligned_cols=38  Identities=16%  Similarity=0.112  Sum_probs=25.8

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcC
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P  109 (293)
                      .|.-++|.|++|+|||...+-.+.+.+..   +.+++|+.-
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            45678999999999996555444444332   446777773

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=95.32  E-value=0.16  Score=39.94  Aligned_cols=52  Identities=21%  Similarity=0.463  Sum_probs=40.3

Q ss_pred             CCccEEEecchhhhhcccc--HHHHHHHHhhCCCCccEEEEEeecChhHHHHHH
Q 022724          174 RAIKLLVLDESDEMLSRGF--KDQIYDVYRYLPPDLQVVLISATLPHEILEMTT  225 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~--~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~  225 (293)
                      ..++++|+||+-...+.++  ...+..+++..++..-+|+..-..|+.+.+.+.
T Consensus        96 ~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~p~~l~e~AD  149 (173)
T TIGR00708        96 PELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGCPQDLLELAD  149 (173)
T ss_pred             CCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhCc
Confidence            5679999999998877764  456677778777777888887778888777664

Alternate name: corrinoid adenosyltransferase.

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

Probab=95.32  E-value=0.12  Score=48.20  Aligned_cols=65  Identities=18%  Similarity=0.197  Sum_probs=39.4

Q ss_pred             EEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcc-------ccHHHHHHHHhhCC---CCccEEEEEeecChh
Q 022724          154 VVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-------GFKDQIYDVYRYLP---PDLQVVLISATLPHE  219 (293)
Q Consensus       154 ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~-------~~~~~~~~i~~~l~---~~~q~v~~SAt~~~~  219 (293)
                      -+||--++..+.+..+.- .+..+.|.|||+|.+...       .-...++.++..+.   ....+..+.||=-++
T Consensus       584 kYVGESErAVR~vFqRAR-~saPCVIFFDEiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPD  658 (802)
T KOG0733|consen  584 KYVGESERAVRQVFQRAR-ASAPCVIFFDEIDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRPD  658 (802)
T ss_pred             HHhhhHHHHHHHHHHHhh-cCCCeEEEecchhhcCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCCc
Confidence            345556666664443221 355789999999998532       12344555555553   456788888885444

>PF02572 CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP; InterPro: IPR003724 ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2

Probab=95.29  E-value=0.56  Score=36.83  Aligned_cols=141  Identities=17%  Similarity=0.242  Sum_probs=64.7

Q ss_pred             EEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCC
Q 022724           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGV  152 (293)
Q Consensus        73 ~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  152 (293)
                      +.|-...|-|||.+++=-++..+-.   +.+++++-=.+.-.  .......+....++.+...-.+.........    .
T Consensus         6 i~vytG~GKGKTTAAlGlalRA~G~---G~rV~ivQFlKg~~--~~GE~~~l~~l~~~~~~~~g~~f~~~~~~~~----~   76 (172)
T PF02572_consen    6 IQVYTGDGKGKTTAALGLALRAAGH---GMRVLIVQFLKGGR--YSGELKALKKLPNVEIERFGKGFVWRMNEEE----E   76 (172)
T ss_dssp             EEEEESSSS-HHHHHHHHHHHHHCT---T--EEEEESS--SS----HHHHHHGGGT--EEEE--TT----GGGHH----H
T ss_pred             EEEEeCCCCCchHHHHHHHHHHHhC---CCEEEEEEEecCCC--CcCHHHHHHhCCeEEEEEcCCcccccCCCcH----H
Confidence            5566788999999877666665544   56777776544411  1122222222222322221111100000000    0


Q ss_pred             cEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcccc--HHHHHHHHhhCCCCccEEEEEeecChhHHHHHH
Q 022724          153 HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF--KDQIYDVYRYLPPDLQVVLISATLPHEILEMTT  225 (293)
Q Consensus       153 ~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~--~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~  225 (293)
                      +  .......++..+ ..+.-..+++||+||+-...+.++  ...+..++...+...-+|+.--..|+.+.+.+.
T Consensus        77 ~--~~~~~~~~~~a~-~~i~~~~~dlvILDEi~~a~~~gll~~~~v~~~l~~rp~~~evVlTGR~~~~~l~e~AD  148 (172)
T PF02572_consen   77 D--RAAAREGLEEAK-EAISSGEYDLVILDEINYAVDYGLLSEEEVLDLLENRPESLEVVLTGRNAPEELIEAAD  148 (172)
T ss_dssp             H--HHHHHHHHHHHH-HHTT-TT-SEEEEETHHHHHHTTSS-HHHHHHHHHTS-TT-EEEEE-SS--HHHHHH-S
T ss_pred             H--HHHHHHHHHHHH-HHHhCCCCCEEEEcchHHHhHCCCccHHHHHHHHHcCCCCeEEEEECCCCCHHHHHhCC
Confidence            0  000111112111 123346789999999998877765  456777777777777788777778888777663

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.

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=95.27  E-value=0.21  Score=45.38  Aligned_cols=120  Identities=18%  Similarity=0.199  Sum_probs=56.9

Q ss_pred             HHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHH
Q 022724           64 VMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGE  143 (293)
Q Consensus        64 ~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~  143 (293)
                      +.-+..|.-+++.|++|+|||...+-.+.+.....  +..++|++.- --..|+..++-...  .++....+..+.-...
T Consensus       188 ~~G~~~g~liviag~pg~GKT~~al~ia~~~a~~~--g~~v~~fSlE-m~~~~l~~Rl~~~~--~~v~~~~~~~~~l~~~  262 (421)
T TIGR03600       188 TNGLVKGDLIVIGARPSMGKTTLALNIAENVALRE--GKPVLFFSLE-MSAEQLGERLLASK--SGINTGNIRTGRFNDS  262 (421)
T ss_pred             hcCCCCCceEEEEeCCCCCHHHHHHHHHHHHHHhC--CCcEEEEECC-CCHHHHHHHHHHHH--cCCCHHHHhcCCCCHH
Confidence            33344567789999999999954433332322122  3456676632 23444444433221  1222111111111111


Q ss_pred             HH-------HHHhcCCcEEEe-----ChHHHHHHHhcCCCCCCCccEEEecchhhhhc
Q 022724          144 DI-------RKLEHGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (293)
Q Consensus       144 ~~-------~~~~~~~~ilV~-----Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~  189 (293)
                      +.       ..+.+ ..+.|.     |++.+...++.-......+++||||=.+.+..
T Consensus       263 ~~~~~~~~~~~l~~-~~l~i~d~~~~t~~~i~~~~r~~~~~~~~~~lvvIDyLql~~~  319 (421)
T TIGR03600       263 DFNRLLNAVDRLSE-KDLYIDDTGGLTVAQIRSIARRIKRKKGGLDLIVVDYIQLMAP  319 (421)
T ss_pred             HHHHHHHHHHHHhc-CCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEecccccCC
Confidence            11       22222 244443     44455444432111123588999999998853

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.

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

Probab=95.27  E-value=0.033  Score=47.30  Aligned_cols=44  Identities=14%  Similarity=0.338  Sum_probs=30.5

Q ss_pred             hhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHH
Q 022724           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l  113 (293)
                      +..+.+++++|+||||||.. +-.++..+...  ..+++.+-...|+
T Consensus       124 v~~~~~ili~G~tGSGKTT~-l~all~~i~~~--~~~iv~iEd~~E~  167 (270)
T PF00437_consen  124 VRGRGNILISGPTGSGKTTL-LNALLEEIPPE--DERIVTIEDPPEL  167 (270)
T ss_dssp             HHTTEEEEEEESTTSSHHHH-HHHHHHHCHTT--TSEEEEEESSS-S
T ss_pred             cccceEEEEECCCccccchH-HHHHhhhcccc--ccceEEeccccce
Confidence            34578999999999999954 45566666554  2467777666664

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 ....

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=95.26  E-value=0.38  Score=39.87  Aligned_cols=51  Identities=12%  Similarity=0.206  Sum_probs=31.6

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (293)
                      |.-+++.|++|+|||.-....+...+..   +.+++|+.-.. -..++.+.+..+
T Consensus        25 g~~~~i~G~~GsGKt~l~~~~~~~~~~~---g~~~~y~~~e~-~~~~~~~~~~~~   75 (234)
T PRK06067         25 PSLILIEGDHGTGKSVLSQQFVYGALKQ---GKKVYVITTEN-TSKSYLKQMESV   75 (234)
T ss_pred             CcEEEEECCCCCChHHHHHHHHHHHHhC---CCEEEEEEcCC-CHHHHHHHHHHC
Confidence            4578999999999995544334443332   44677776543 345565655554

>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=95.25  E-value=0.15  Score=43.06  Aligned_cols=141  Identities=17%  Similarity=0.180  Sum_probs=67.7

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHH---
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDI---  145 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---  145 (293)
                      .|.-+++.|++|.|||...+-.+.+.....  +..++|++.-.. ..++..++-........  ..+..+.....+.   
T Consensus        18 ~g~L~vi~a~pg~GKT~~~l~ia~~~a~~~--~~~vly~SlEm~-~~~l~~R~la~~s~v~~--~~i~~g~l~~~e~~~~   92 (259)
T PF03796_consen   18 PGELTVIAARPGVGKTAFALQIALNAALNG--GYPVLYFSLEMS-EEELAARLLARLSGVPY--NKIRSGDLSDEEFERL   92 (259)
T ss_dssp             TT-EEEEEESTTSSHHHHHHHHHHHHHHTT--SSEEEEEESSS--HHHHHHHHHHHHHTSTH--HHHHCCGCHHHHHHHH
T ss_pred             cCcEEEEEecccCCchHHHHHHHHHHHHhc--CCeEEEEcCCCC-HHHHHHHHHHHhhcchh--hhhhccccCHHHHHHH
Confidence            456789999999999955444444444332  356888875322 12333333221111111  1111111111111   


Q ss_pred             ----HHHhcCCcEEE-e----ChHHHHHHHhcCCCCCCCccEEEecchhhhhcc----ccHHHHHHHHhhCC-----CCc
Q 022724          146 ----RKLEHGVHVVS-G----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR----GFKDQIYDVYRYLP-----PDL  207 (293)
Q Consensus       146 ----~~~~~~~~ilV-~----Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~----~~~~~~~~i~~~l~-----~~~  207 (293)
                          ..+.+. .+.| .    |++.+...++.-......+++||||-+|.+...    .....+..+.+.+.     .++
T Consensus        93 ~~~~~~l~~~-~l~i~~~~~~~~~~i~~~i~~~~~~~~~~~~v~IDyl~ll~~~~~~~~~~~~~~~i~~~Lk~lA~~~~i  171 (259)
T PF03796_consen   93 QAAAEKLSDL-PLYIEDTPSLTIDDIESKIRRLKREGKKVDVVFIDYLQLLKSEDSSDNRRQEIGEISRELKALAKELNI  171 (259)
T ss_dssp             HHHHHHHHTS-EEEEEESSS-BHHHHHHHHHHHHHHSTTEEEEEEEEGGGSBTSCSSSCCHHHHHHHHHHHHHHHHHHTS
T ss_pred             HHHHHHHhhC-cEEEECCCCCCHHHHHHHHHHHHhhccCCCEEEechHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHcCC
Confidence                122222 3443 3    455666655442222367899999999998553    23333433333322     245


Q ss_pred             cEEEEEee
Q 022724          208 QVVLISAT  215 (293)
Q Consensus       208 q~v~~SAt  215 (293)
                      .++++|..
T Consensus       172 ~vi~~sQl  179 (259)
T PF03796_consen  172 PVIALSQL  179 (259)
T ss_dssp             EEEEEEEB
T ss_pred             eEEEcccc
Confidence            66666553

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 ....

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=95.24  E-value=0.14  Score=48.58  Aligned_cols=48  Identities=25%  Similarity=0.315  Sum_probs=34.0

Q ss_pred             cEEEe-ChHHHHHHHhc-CCCCCCCccEEEecchhhhhccccHHHHHHHHhhCC
Q 022724          153 HVVSG-TPGRVCDMIKR-KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP  204 (293)
Q Consensus       153 ~ilV~-Tp~~l~~~l~~-~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~  204 (293)
                      .-+|| -|+++.+-++. +..+    -++++||+|.|.....++--..++.-+.
T Consensus       397 RTYIGamPGrIiQ~mkka~~~N----Pv~LLDEIDKm~ss~rGDPaSALLEVLD  446 (782)
T COG0466         397 RTYIGAMPGKIIQGMKKAGVKN----PVFLLDEIDKMGSSFRGDPASALLEVLD  446 (782)
T ss_pred             ccccccCChHHHHHHHHhCCcC----CeEEeechhhccCCCCCChHHHHHhhcC
Confidence            34444 69999998876 3333    3799999999987666666666666664

>PRK13764 ATPase; Provisional

Probab=95.21  E-value=0.045  Score=51.50  Aligned_cols=28  Identities=14%  Similarity=0.383  Sum_probs=21.0

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhcc
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDT   97 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~   97 (293)
                      .+++++++||||||||. ++-+++..+..
T Consensus       256 ~~~~ILIsG~TGSGKTT-ll~AL~~~i~~  283 (602)
T PRK13764        256 RAEGILIAGAPGAGKST-FAQALAEFYAD  283 (602)
T ss_pred             cCCEEEEECCCCCCHHH-HHHHHHHHHhh
Confidence            46789999999999995 34556666543

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=95.18  E-value=0.035  Score=52.01  Aligned_cols=40  Identities=25%  Similarity=0.313  Sum_probs=26.2

Q ss_pred             CCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEE
Q 022724          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLI  212 (293)
Q Consensus       173 ~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~  212 (293)
                      +++-+.+|+||+-.-+|......+...+..+.++.-+|..
T Consensus       486 l~~~~iliLDE~TSaLD~~te~~I~~~l~~~~~~~TvIiI  525 (529)
T TIGR02868       486 LADAPILLLDEPTEHLDAGTESELLEDLLAALSGKTVVVI  525 (529)
T ss_pred             hcCCCEEEEeCCcccCCHHHHHHHHHHHHHhcCCCEEEEE
Confidence            3667889999998877776666666666555444444443

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.

>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=95.16  E-value=0.04  Score=45.17  Aligned_cols=55  Identities=16%  Similarity=0.298  Sum_probs=28.8

Q ss_pred             ChHHHHHHHhcCCCCCCCccEEEecchhhhh-c----cccHHHHHHHHhhCCC-CccEEEEEeec
Q 022724          158 TPGRVCDMIKRKTLRTRAIKLLVLDESDEML-S----RGFKDQIYDVYRYLPP-DLQVVLISATL  216 (293)
Q Consensus       158 Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~-~----~~~~~~~~~i~~~l~~-~~q~v~~SAt~  216 (293)
                      +...+...+......    -+|||||+|.+. .    ..+...+..++..... ....++++++-
T Consensus       105 ~l~~~~~~l~~~~~~----~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~v~~~S~  165 (234)
T PF01637_consen  105 ALERLLEKLKKKGKK----VIIVIDEFQYLAIASEEDKDFLKSLRSLLDSLLSQQNVSIVITGSS  165 (234)
T ss_dssp             -HHHHHHHHHHCHCC----EEEEEETGGGGGBCTTTTHHHHHHHHHHHHH----TTEEEEEEESS
T ss_pred             HHHHHHHHHHhcCCc----EEEEEecHHHHhhcccchHHHHHHHHHHHhhccccCCceEEEECCc
Confidence            344555555443222    689999999998 2    2344556666665322 22334455553

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>KOG0058 consensus Peptide exporter, ABC superfamily [Intracellular trafficking, secretion, and vesicular transport]

Probab=95.12  E-value=0.073  Score=50.35  Aligned_cols=41  Identities=24%  Similarity=0.313  Sum_probs=31.5

Q ss_pred             CCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEe
Q 022724          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (293)
Q Consensus       173 ~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SA  214 (293)
                      +++...+|+|||-..+|..-...++..+..+..+ +.++.-|
T Consensus       620 lr~P~VLILDEATSALDaeSE~lVq~aL~~~~~~-rTVlvIA  660 (716)
T KOG0058|consen  620 LRNPRVLILDEATSALDAESEYLVQEALDRLMQG-RTVLVIA  660 (716)
T ss_pred             hcCCCEEEEechhhhcchhhHHHHHHHHHHhhcC-CeEEEEe
Confidence            4678899999999999887788888888777666 4444434

>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=95.12  E-value=0.52  Score=41.85  Aligned_cols=109  Identities=15%  Similarity=0.185  Sum_probs=61.2

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHh
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE  149 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  149 (293)
                      .+.+-+.|+.|.|||+.  +-++........+.|+    +..+-..++...+.++...          ..+.        
T Consensus        62 ~~GlYl~G~vG~GKT~L--md~f~~~lp~~~k~R~----HFh~Fm~~vh~~l~~~~~~----------~~~l--------  117 (362)
T PF03969_consen   62 PKGLYLWGPVGRGKTML--MDLFYDSLPIKRKRRV----HFHEFMLDVHSRLHQLRGQ----------DDPL--------  117 (362)
T ss_pred             CceEEEECCCCCchhHH--HHHHHHhCCccccccc----cccHHHHHHHHHHHHHhCC----------CccH--------
Confidence            46899999999999953  2333332222222222    6667777777777765410          0000        


Q ss_pred             cCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhC-CCCccEEEEEeecChh
Q 022724          150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL-PPDLQVVLISATLPHE  219 (293)
Q Consensus       150 ~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l-~~~~q~v~~SAt~~~~  219 (293)
                                ..+.+.+      .+...+|.+||+|.- |.+-...+..+++.+ ....-+|+.|-+.|++
T Consensus       118 ----------~~va~~l------~~~~~lLcfDEF~V~-DiaDAmil~rLf~~l~~~gvvlVaTSN~~P~~  171 (362)
T PF03969_consen  118 ----------PQVADEL------AKESRLLCFDEFQVT-DIADAMILKRLFEALFKRGVVLVATSNRPPED  171 (362)
T ss_pred             ----------HHHHHHH------HhcCCEEEEeeeecc-chhHHHHHHHHHHHHHHCCCEEEecCCCChHH
Confidence                      1111221      234568999999863 444445555555554 3456666666666655

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

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.12  E-value=0.13  Score=48.70  Aligned_cols=18  Identities=28%  Similarity=0.392  Sum_probs=14.6

Q ss_pred             cEEEEcCCCChhHHHHHH
Q 022724           72 DVIAQAQSGTGKTSMIAL   89 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~   89 (293)
                      .+++.||.|+|||.....
T Consensus        40 a~Lf~Gp~G~GKTtlA~~   57 (585)
T PRK14950         40 AYLFTGPRGVGKTSTARI   57 (585)
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            469999999999966543

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

Probab=95.06  E-value=0.034  Score=52.05  Aligned_cols=41  Identities=22%  Similarity=0.310  Sum_probs=32.8

Q ss_pred             CCcHHHHHHHHhhh----cCCcEEEEcCCCChhHHHHHHHHHhhh
Q 022724           55 KPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTV   95 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~----~~~~~li~~~Tg~GKT~~~~~~~~~~l   95 (293)
                      +|+.+|.+....+.    .|+--|+.+|||+|||++.+=+.+..+
T Consensus        15 ~PYdIQ~~lM~elyrvLe~GkIgIfESPTGTGKSLSLiCaaltWL   59 (821)
T KOG1133|consen   15 TPYDIQEDLMRELYRVLEEGKIGIFESPTGTGKSLSLICAALTWL   59 (821)
T ss_pred             CchhHHHHHHHHHHHHHhcCCeeeeeCCCCCCchHHHHHHHHHHH
Confidence            59999998877654    789999999999999987665555444

>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=95.05  E-value=1.1  Score=35.05  Aligned_cols=54  Identities=11%  Similarity=0.364  Sum_probs=28.6

Q ss_pred             CCccEEEecchhhhh-ccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhc
Q 022724          174 RAIKLLVLDESDEML-SRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKF  227 (293)
Q Consensus       174 ~~l~~iViDE~h~~~-~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~  227 (293)
                      .+.+++|+|...... +......+..+........-++.+++.-+.+..+....+
T Consensus        81 ~~~d~viiDt~g~~~~~~~~l~~l~~l~~~~~~~~~~lVv~~~~~~~~~~~~~~~  135 (173)
T cd03115          81 ENFDVVIVDTAGRLQIDENLMEELKKIKRVVKPDEVLLVVDAMTGQDAVNQAKAF  135 (173)
T ss_pred             CCCCEEEEECcccchhhHHHHHHHHHHHhhcCCCeEEEEEECCCChHHHHHHHHH
Confidence            346788888887642 122333344444333345556667776555544444443

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.

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

Probab=95.05  E-value=0.061  Score=48.93  Aligned_cols=42  Identities=17%  Similarity=0.313  Sum_probs=29.7

Q ss_pred             CcHHHHHHHHhhhcCC--cEEEEcCCCChhHHHHHHHHHhhhccC
Q 022724           56 PSAIQQRAVMPIIKGR--DVIAQAQSGTGKTSMIALTVCQTVDTS   98 (293)
Q Consensus        56 ~~~~Q~~~~~~i~~~~--~~li~~~Tg~GKT~~~~~~~~~~l~~~   98 (293)
                      .++.|...+..+.+..  =+++.||||||||.. +..++..+...
T Consensus       242 ~~~~~~~~~~~~~~~p~GliLvTGPTGSGKTTT-LY~~L~~ln~~  285 (500)
T COG2804         242 MSPFQLARLLRLLNRPQGLILVTGPTGSGKTTT-LYAALSELNTP  285 (500)
T ss_pred             CCHHHHHHHHHHHhCCCeEEEEeCCCCCCHHHH-HHHHHHHhcCC
Confidence            3577777787777654  488899999999954 44555665554

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=95.00  E-value=0.22  Score=44.77  Aligned_cols=48  Identities=21%  Similarity=0.186  Sum_probs=28.9

Q ss_pred             CHHHHHHHHHCCCC--CCcHHHH-H----HHHhhhcCCcEEEEcCCCChhHHHHH
Q 022724           41 KDDLLRGIYQYGFE--KPSAIQQ-R----AVMPIIKGRDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        41 ~~~i~~~l~~~~~~--~~~~~Q~-~----~~~~i~~~~~~li~~~Tg~GKT~~~~   88 (293)
                      .+|+---+...||.  .++.-|+ .    .++.+.++.|++..||+|+|||-.|.
T Consensus       173 dEWid~LlrSiG~~P~~~~~r~k~~~L~rl~~fve~~~Nli~lGp~GTGKThla~  227 (449)
T TIGR02688       173 EEWIDVLIRSIGYEPEGFEARQKLLLLARLLPLVEPNYNLIELGPKGTGKSYIYN  227 (449)
T ss_pred             HHHHHHHHHhcCCCcccCChHHHHHHHHhhHHHHhcCCcEEEECCCCCCHHHHHH
Confidence            33444445556766  2222222 1    12445578899999999999995443

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

>PRK09354 recA recombinase A; Provisional

Probab=94.98  E-value=0.072  Score=46.75  Aligned_cols=43  Identities=19%  Similarity=0.257  Sum_probs=30.1

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELAT  115 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~  115 (293)
                      |.-+.|.||+|+|||...+..+.+....   +..++|+-.-..+-.
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            4578899999999997665555444433   457888887665543

>PRK05748 replicative DNA helicase; Provisional

Probab=94.96  E-value=0.26  Score=45.22  Aligned_cols=114  Identities=19%  Similarity=0.205  Sum_probs=54.2

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHH---
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDI---  145 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---  145 (293)
                      .|.-++|.|++|+|||.- .+-+....... .+..++|++. ..-..|+..++-.....  +....+..+.-...+.   
T Consensus       202 ~G~livIaarpg~GKT~~-al~ia~~~a~~-~g~~v~~fSl-Ems~~~l~~R~l~~~~~--v~~~~i~~~~l~~~e~~~~  276 (448)
T PRK05748        202 PNDLIIVAARPSVGKTAF-ALNIAQNVATK-TDKNVAIFSL-EMGAESLVMRMLCAEGN--IDAQRLRTGQLTDDDWPKL  276 (448)
T ss_pred             CCceEEEEeCCCCCchHH-HHHHHHHHHHh-CCCeEEEEeC-CCCHHHHHHHHHHHhcC--CCHHHhhcCCCCHHHHHHH
Confidence            456788899999999944 44444333221 1334566543 33344555544322111  1111111111111121   


Q ss_pred             ----HHHhcCCcEEEe-----ChHHHHHHHhcCCCCCCCccEEEecchhhhh
Q 022724          146 ----RKLEHGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (293)
Q Consensus       146 ----~~~~~~~~ilV~-----Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~  188 (293)
                          ..+.+ ..+.|.     |++.+...++.-......+++||||=.+.+.
T Consensus       277 ~~a~~~l~~-~~~~i~d~~~~ti~~i~~~~r~~~~~~~~~~~vvIDyL~li~  327 (448)
T PRK05748        277 TIAMGSLSD-APIYIDDTPGIKVTEIRARCRRLAQEHGGLGLILIDYLQLIQ  327 (448)
T ss_pred             HHHHHHHhc-CCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEccchhcC
Confidence                12222 235442     4455554433311111258899999999884

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=94.96  E-value=0.1  Score=46.05  Aligned_cols=16  Identities=38%  Similarity=0.515  Sum_probs=13.5

Q ss_pred             cEEEEcCCCChhHHHH
Q 022724           72 DVIAQAQSGTGKTSMI   87 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~   87 (293)
                      .+++.||.|+|||...
T Consensus        38 ~~Ll~G~~G~GKt~~a   53 (355)
T TIGR02397        38 AYLFSGPRGTGKTSIA   53 (355)
T ss_pred             EEEEECCCCCCHHHHH
Confidence            5789999999999554

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.

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.95  E-value=0.24  Score=47.05  Aligned_cols=18  Identities=28%  Similarity=0.366  Sum_probs=14.9

Q ss_pred             cEEEEcCCCChhHHHHHH
Q 022724           72 DVIAQAQSGTGKTSMIAL   89 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~   89 (293)
                      .++++||.|+|||.++..
T Consensus        40 a~Lf~Gp~GvGKttlA~~   57 (620)
T PRK14954         40 GYIFSGLRGVGKTTAARV   57 (620)
T ss_pred             eEEEECCCCCCHHHHHHH
Confidence            488999999999976543

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=94.91  E-value=0.24  Score=46.62  Aligned_cols=18  Identities=33%  Similarity=0.329  Sum_probs=14.8

Q ss_pred             cEEEEcCCCChhHHHHHH
Q 022724           72 DVIAQAQSGTGKTSMIAL   89 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~   89 (293)
                      -+++.||.|+|||.++..
T Consensus        40 ayLf~Gp~G~GKTt~Ar~   57 (563)
T PRK06647         40 AYIFSGPRGVGKTSSARA   57 (563)
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            479999999999976543

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=94.87  E-value=0.22  Score=40.40  Aligned_cols=39  Identities=13%  Similarity=0.256  Sum_probs=26.1

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCC
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~  110 (293)
                      .|.-+.+.||+|+|||...+..+.+....   +.+++|+.-.
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            35678999999999996655444443332   3467777654

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>TIGR00763 lon ATP-dependent protease La

Probab=94.82  E-value=0.19  Score=49.45  Aligned_cols=18  Identities=33%  Similarity=0.372  Sum_probs=15.0

Q ss_pred             CCcEEEEcCCCChhHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~   87 (293)
                      +..+++.||+|+|||..+
T Consensus       347 ~~~lll~GppG~GKT~lA  364 (775)
T TIGR00763       347 GPILCLVGPPGVGKTSLG  364 (775)
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            457999999999999544

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.

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=94.81  E-value=1.6  Score=38.07  Aligned_cols=58  Identities=14%  Similarity=0.304  Sum_probs=35.8

Q ss_pred             HHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhC---CCCccEEEEEeecC
Q 022724          160 GRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL---PPDLQVVLISATLP  217 (293)
Q Consensus       160 ~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l---~~~~q~v~~SAt~~  217 (293)
                      .+++..++.+...-+.--.+|+||+|.+........+-.++..-   +..+-++++|..+.
T Consensus       122 ~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~rQtllYnlfDisqs~r~Piciig~Ttrld  182 (408)
T KOG2228|consen  122 SKLLEALKKGDETTSGKVIFILDEFDLFAPHSRQTLLYNLFDISQSARAPICIIGVTTRLD  182 (408)
T ss_pred             HHHHHHHhcCCCCCCceEEEEeehhhccccchhhHHHHHHHHHHhhcCCCeEEEEeecccc
Confidence            45666666654444444679999999987665544444444433   34566777777653

>COG1132 MdlB ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]

Probab=94.81  E-value=0.084  Score=49.94  Aligned_cols=39  Identities=26%  Similarity=0.342  Sum_probs=27.1

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEE
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLI  212 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~  212 (293)
                      ++-..+|+||+..-+|......+...+..+.+++.++..
T Consensus       482 ~~~~ILILDEaTSalD~~tE~~I~~~l~~l~~~rT~iiI  520 (567)
T COG1132         482 RNPPILILDEATSALDTETEALIQDALKKLLKGRTTLII  520 (567)
T ss_pred             cCCCEEEEeccccccCHHhHHHHHHHHHHHhcCCEEEEE
Confidence            556899999999888877777777766655544333333

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=94.78  E-value=0.19  Score=44.74  Aligned_cols=68  Identities=21%  Similarity=0.329  Sum_probs=37.0

Q ss_pred             CcHHHHHHHHhhh---cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhh
Q 022724           56 PSAIQQRAVMPII---KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIG  125 (293)
Q Consensus        56 ~~~~Q~~~~~~i~---~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  125 (293)
                      +.+.=.++++.+.   +|+-.+|.||.|+|||.. +-.+...+........++|++ ..+--+++.+..+.+.
T Consensus       152 ~~~~~~rvID~l~PIGkGQR~lIvgppGvGKTTL-aK~Ian~I~~nhFDv~~~VvL-IgER~~EVtdiqrsIl  222 (416)
T PRK09376        152 PEDLSTRIIDLIAPIGKGQRGLIVAPPKAGKTVL-LQNIANSITTNHPEVHLIVLL-IDERPEEVTDMQRSVK  222 (416)
T ss_pred             CcccceeeeeeecccccCceEEEeCCCCCChhHH-HHHHHHHHHhhcCCeEEEEEE-eCCchhHHHHHHHHhc
Confidence            3444456666544   788999999999999953 333444444432233333322 3333334444444443

>PF00265 TK: Thymidine kinase; InterPro: IPR001267 Thymidine kinase (TK) (2

Probab=94.72  E-value=0.07  Score=42.21  Aligned_cols=38  Identities=11%  Similarity=0.164  Sum_probs=25.2

Q ss_pred             cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHH
Q 022724           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~  112 (293)
                      -.++.||.+||||.- ++-.++++...  +.+++++-|...
T Consensus         3 l~~i~GpM~sGKS~e-Li~~~~~~~~~--~~~v~~~kp~~D   40 (176)
T PF00265_consen    3 LEFITGPMFSGKSTE-LIRRIHRYEIA--GKKVLVFKPAID   40 (176)
T ss_dssp             EEEEEESTTSSHHHH-HHHHHHHHHHT--T-EEEEEEESTS
T ss_pred             EEEEECCcCChhHHH-HHHHHHHHHhC--CCeEEEEEeccc
Confidence            467899999999954 33444444443  457888888543

7.1.21 from EC) is an ubiquitous enzyme that catalyzes the ATP-dependent phosphorylation of thymidine. Two different families of Thymidine kinase have been identified [, ] and are represented in this entry; one groups together Thymidine kinase from herpesviruses, as well as cytosolic thymidylate kinases and the second family groups Thymidine kinase from various sources that include, vertebrates, bacteria, the Bacteriophage T4, poxviruses, African swine fever virus (ASFV) and Fish lymphocystis disease virus (FLDV). The major capsid protein of insect iridescent viruses also belongs to this family.; GO: 0004797 thymidine kinase activity, 0005524 ATP binding; PDB: 1XX6_B 2J9R_A 2J87_B 3E2I_A 2JA1_A 2UZ3_B 2B8T_B 2WVJ_A 1W4R_F 1XBT_F ....

>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=94.71  E-value=0.14  Score=44.56  Aligned_cols=72  Identities=21%  Similarity=0.260  Sum_probs=44.8

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCCcHHHHH-HHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCH
Q 022724           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQR-AVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (293)
Q Consensus        33 ~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~-~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~  111 (293)
                      ..+...+++..-+.   +.|  .+++.|.. .|-.+..+++++++|+|||||| .++.+++..+-..   .+.+.+=-+.
T Consensus       110 Rk~~~~~~t~~~l~---~~g--t~~~~~~ayL~~~ie~~~siii~G~t~sGKT-t~lnall~~Ip~~---~rivtIEdt~  180 (312)
T COG0630         110 RKFSDEPITPEDLI---EYG--TISPEQAAYLWLAIEARKSIIICGGTASGKT-TLLNALLDFIPPE---ERIVTIEDTP  180 (312)
T ss_pred             EcCCCCCCCHHHHh---hcC--CCCHHHHHHHHHHHHcCCcEEEECCCCCCHH-HHHHHHHHhCCch---hcEEEEeccc
Confidence            34555555543333   223  45555543 6677788999999999999999 4555666655442   3566665555


Q ss_pred             HH
Q 022724          112 EL  113 (293)
Q Consensus       112 ~l  113 (293)
                      ++
T Consensus       181 E~  182 (312)
T COG0630         181 EL  182 (312)
T ss_pred             cc
Confidence            54

>TIGR02012 tigrfam_recA protein RecA

Probab=94.68  E-value=0.11  Score=45.13  Aligned_cols=44  Identities=16%  Similarity=0.269  Sum_probs=28.8

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELAT  115 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~  115 (293)
                      .|.-+.|.||+|+|||...+..+.+....   +.+++|+-.-..+-.
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            34678999999999996655444444332   456788766544443

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.

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=94.67  E-value=0.076  Score=46.19  Aligned_cols=43  Identities=14%  Similarity=0.222  Sum_probs=29.4

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELAT  115 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~  115 (293)
                      |.-+.|.||+|+|||...+..+.+....   +.+++|+..-..+-.
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            4678899999999996555444443332   457888887665543

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=94.66  E-value=0.3  Score=43.92  Aligned_cols=18  Identities=11%  Similarity=0.274  Sum_probs=14.7

Q ss_pred             CcEEEEcCCCChhHHHHH
Q 022724           71 RDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~   88 (293)
                      +.+++.||.|+|||..+.
T Consensus        37 ha~Lf~Gp~G~GKt~lA~   54 (394)
T PRK07940         37 HAWLFTGPPGSGRSVAAR   54 (394)
T ss_pred             eEEEEECCCCCcHHHHHH
Confidence            458999999999995544

>TIGR00959 ffh signal recognition particle protein

Probab=94.59  E-value=0.68  Score=42.05  Aligned_cols=86  Identities=21%  Similarity=0.284  Sum_probs=41.7

Q ss_pred             cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEc--CCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHH----H
Q 022724           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS--PTRELATQTEKVILAIGDFINIQAHACVGGKSVGED----I  145 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~--P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~  145 (293)
                      -++++|++|+|||....--+.......  +.+++++.  +.|.-+.++   ++.+....++.+...........-    .
T Consensus       101 vi~~vG~~GsGKTTtaakLA~~l~~~~--g~kV~lV~~D~~R~~a~~Q---L~~~a~~~gvp~~~~~~~~~P~~i~~~al  175 (428)
T TIGR00959       101 VILMVGLQGSGKTTTCGKLAYYLKKKQ--GKKVLLVACDLYRPAAIEQ---LKVLGQQVGVPVFALGKGQSPVEIARRAL  175 (428)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHhC--CCeEEEEeccccchHHHHH---HHHHHHhcCCceEecCCCCCHHHHHHHHH
Confidence            478999999999976543333321122  33555554  334443333   333344455555443332222111    1


Q ss_pred             HH-HhcCCc-EEEeChHHH
Q 022724          146 RK-LEHGVH-VVSGTPGRV  162 (293)
Q Consensus       146 ~~-~~~~~~-ilV~Tp~~l  162 (293)
                      +. ..++++ |+|=||+++
T Consensus       176 ~~~~~~~~DvVIIDTaGr~  194 (428)
T TIGR00959       176 EYAKENGFDVVIVDTAGRL  194 (428)
T ss_pred             HHHHhcCCCEEEEeCCCcc
Confidence            11 123444 666777654

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.

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.57  E-value=0.17  Score=48.21  Aligned_cols=18  Identities=33%  Similarity=0.355  Sum_probs=14.9

Q ss_pred             CcEEEEcCCCChhHHHHH
Q 022724           71 RDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~   88 (293)
                      ..+++.||.|+|||..+.
T Consensus        39 ~a~Lf~Gp~G~GKttlA~   56 (620)
T PRK14948         39 PAYLFTGPRGTGKTSSAR   56 (620)
T ss_pred             ceEEEECCCCCChHHHHH
Confidence            467999999999996654

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=94.56  E-value=0.37  Score=44.34  Aligned_cols=49  Identities=20%  Similarity=0.338  Sum_probs=30.8

Q ss_pred             CCccEEEecchhhhhccc-------cHHHHHHHHhhCC---CCccEEEEEee-cChhHHH
Q 022724          174 RAIKLLVLDESDEMLSRG-------FKDQIYDVYRYLP---PDLQVVLISAT-LPHEILE  222 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~-------~~~~~~~i~~~l~---~~~q~v~~SAt-~~~~~~~  222 (293)
                      +..+.|.|||+|.+...-       ....++.++..+.   .+--+|++.|| +|+++..
T Consensus       395 ~APcIIFIDEiDavG~kR~~~~~~y~kqTlNQLLvEmDGF~qNeGiIvigATNfpe~LD~  454 (752)
T KOG0734|consen  395 RAPCIIFIDEIDAVGGKRNPSDQHYAKQTLNQLLVEMDGFKQNEGIIVIGATNFPEALDK  454 (752)
T ss_pred             cCCeEEEEechhhhcccCCccHHHHHHHHHHHHHHHhcCcCcCCceEEEeccCChhhhhH
Confidence            456889999999986431       1233455555553   34568888888 3544433

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=94.54  E-value=0.38  Score=48.00  Aligned_cols=79  Identities=10%  Similarity=0.112  Sum_probs=60.9

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHHhcCCCCCCCc
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l~~~~~~~~~l  176 (293)
                      +.+++|++|+++-+..+.+.++++.  .+.++..+||+.+..+..+.+    ....+|+|+|.     .+ ...+++.++
T Consensus       660 g~qv~if~n~i~~~e~l~~~L~~~~--p~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~-----ii-e~GIDIp~v  731 (926)
T TIGR00580       660 GGQVFYVHNRIESIEKLATQLRELV--PEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTT-----II-ETGIDIPNA  731 (926)
T ss_pred             CCeEEEEECCcHHHHHHHHHHHHhC--CCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECC-----hh-hcccccccC
Confidence            5689999999999999888888764  357899999998766544333    24679999995     22 336889999


Q ss_pred             cEEEecchhhh
Q 022724          177 KLLVLDESDEM  187 (293)
Q Consensus       177 ~~iViDE~h~~  187 (293)
                      +++|++.++.+
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.

>PRK10867 signal recognition particle protein; Provisional

Probab=94.53  E-value=0.7  Score=42.01  Aligned_cols=58  Identities=16%  Similarity=0.284  Sum_probs=30.7

Q ss_pred             cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEc--CCHHHHHHHHHHHHHhhccCCceEEE
Q 022724           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS--PTRELATQTEKVILAIGDFINIQAHA  134 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~--P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (293)
                      -++++|++|+|||....--+.. +... .+.+++++.  +.+.-+.++   ++.+....++.+..
T Consensus       102 vI~~vG~~GsGKTTtaakLA~~-l~~~-~G~kV~lV~~D~~R~aa~eQ---L~~~a~~~gv~v~~  161 (433)
T PRK10867        102 VIMMVGLQGAGKTTTAGKLAKY-LKKK-KKKKVLLVAADVYRPAAIEQ---LKTLGEQIGVPVFP  161 (433)
T ss_pred             EEEEECCCCCcHHHHHHHHHHH-HHHh-cCCcEEEEEccccchHHHHH---HHHHHhhcCCeEEe
Confidence            4788999999999665433332 2222 133455554  345544332   33344455555544

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=94.48  E-value=0.36  Score=47.97  Aligned_cols=17  Identities=24%  Similarity=0.567  Sum_probs=14.8

Q ss_pred             CcEEEEcCCCChhHHHH
Q 022724           71 RDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~   87 (293)
                      +|.++.||+|+|||...
T Consensus       195 ~n~lL~G~pGvGKT~l~  211 (852)
T TIGR03346       195 NNPVLIGEPGVGKTAIV  211 (852)
T ss_pred             CceEEEcCCCCCHHHHH
Confidence            58999999999999554

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.

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=94.47  E-value=0.18  Score=49.07  Aligned_cols=27  Identities=26%  Similarity=0.486  Sum_probs=18.9

Q ss_pred             HHHHHhhhc--CCcEEEEcCCCChhHHHH
Q 022724           61 QRAVMPIIK--GRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        61 ~~~~~~i~~--~~~~li~~~Tg~GKT~~~   87 (293)
                      .+.+..+.+  ..|+++.||+|+|||...
T Consensus       196 ~~~i~iL~r~~~~n~LLvGppGvGKT~la  224 (758)
T PRK11034        196 ERAIQVLCRRRKNNPLLVGESGVGKTAIA  224 (758)
T ss_pred             HHHHHHHhccCCCCeEEECCCCCCHHHHH
Confidence            334444433  469999999999999554

>PF12846 AAA_10: AAA-like domain

Probab=94.45  E-value=0.054  Score=46.44  Aligned_cols=41  Identities=15%  Similarity=0.389  Sum_probs=27.3

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l  113 (293)
                      +.|++|.|+||+|||.... .++..+...  +..++++=|..+.
T Consensus         1 n~h~~i~G~tGsGKT~~~~-~l~~~~~~~--g~~~~i~D~~g~~   41 (304)
T PF12846_consen    1 NPHTLILGKTGSGKTTLLK-NLLEQLIRR--GPRVVIFDPKGDY   41 (304)
T ss_pred             CCeEEEECCCCCcHHHHHH-HHHHHHHHc--CCCEEEEcCCchH
Confidence            3689999999999997666 444444333  3456666555443

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=94.43  E-value=0.19  Score=49.08  Aligned_cols=52  Identities=17%  Similarity=0.228  Sum_probs=29.0

Q ss_pred             ccCcccCCCCHHHHHHHHHC-CCCCCcHHHHHHHHh--hhcCCcEEEEcCCCChhHHH
Q 022724           32 ITSFDAMGIKDDLLRGIYQY-GFEKPSAIQQRAVMP--IIKGRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        32 ~~~f~~~~l~~~i~~~l~~~-~~~~~~~~Q~~~~~~--i~~~~~~li~~~Tg~GKT~~   86 (293)
                      -.+|++++-.....+.+.++ .+....|   +.+..  +..++.+++.||+|+|||..
T Consensus       174 ~~~~~di~G~~~~~~~l~~~i~~~~~~~---~~~~~~gi~~~~giLL~GppGtGKT~l  228 (733)
T TIGR01243       174 KVTYEDIGGLKEAKEKIREMVELPMKHP---ELFEHLGIEPPKGVLLYGPPGTGKTLL  228 (733)
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHHhhCH---HHHHhcCCCCCceEEEECCCCCChHHH
Confidence            35677775555555555432 1111111   11222  23467899999999999954

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.

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=94.42  E-value=0.46  Score=39.06  Aligned_cols=53  Identities=21%  Similarity=0.250  Sum_probs=33.3

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhh
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIG  125 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  125 (293)
                      .|..+++.|++|+|||...+-.+...+..   +.+++|+.-. +-.+++.+.+..+.
T Consensus        15 ~g~~~li~G~~G~GKt~~~~~~~~~~~~~---g~~~~y~s~e-~~~~~l~~~~~~~~   67 (224)
T TIGR03880        15 EGHVIVVIGEYGTGKTTFSLQFLYQGLKN---GEKAMYISLE-EREERILGYAKSKG   67 (224)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEECC-CCHHHHHHHHHHcC
Confidence            35678999999999985433334343333   4467776653 34677777666543

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.

>PRK09087 hypothetical protein; Validated

Probab=94.42  E-value=0.15  Score=42.19  Aligned_cols=16  Identities=31%  Similarity=0.443  Sum_probs=13.6

Q ss_pred             CCcEEEEcCCCChhHH
Q 022724           70 GRDVIAQAQSGTGKTS   85 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~   85 (293)
                      ++.+++.||+|+|||.
T Consensus        44 ~~~l~l~G~~GsGKTh   59 (226)
T PRK09087         44 SPVVVLAGPVGSGKTH   59 (226)
T ss_pred             CCeEEEECCCCCCHHH
Confidence            3459999999999994

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.41  E-value=0.23  Score=42.72  Aligned_cols=67  Identities=21%  Similarity=0.240  Sum_probs=38.4

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhc--cCCCcee-EEEEcC-----------CHHHHHHHHHHHHHhhccCCceEEEE
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVD--TSSREVQ-ALILSP-----------TRELATQTEKVILAIGDFINIQAHAC  135 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~--~~~~~~~-~lil~P-----------~~~l~~q~~~~~~~~~~~~~~~~~~~  135 (293)
                      ++-+++.||+|+|||. ..-++.+++.  ...+..+ .+|=..           +--|+.++++.+..+.+.-+.-++.+
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            4568999999999992 2223444442  1111112 222222           33567777788887776666655555


Q ss_pred             EC
Q 022724          136 VG  137 (293)
Q Consensus       136 ~~  137 (293)
                      .+
T Consensus       256 ID  257 (423)
T KOG0744|consen  256 ID  257 (423)
T ss_pred             eH
Confidence            43

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=94.28  E-value=0.57  Score=39.01  Aligned_cols=31  Identities=19%  Similarity=0.381  Sum_probs=21.0

Q ss_pred             HhhhcCC-cEEEEcCCCChhHHHHHHHHHhhhc
Q 022724           65 MPIIKGR-DVIAQAQSGTGKTSMIALTVCQTVD   96 (293)
Q Consensus        65 ~~i~~~~-~~li~~~Tg~GKT~~~~~~~~~~l~   96 (293)
                      +.+..|+ -+.++|+-|||||...= ++...+.
T Consensus        45 ~~i~d~qg~~~vtGevGsGKTv~~R-al~~s~~   76 (269)
T COG3267          45 AAIADGQGILAVTGEVGSGKTVLRR-ALLASLN   76 (269)
T ss_pred             HHHhcCCceEEEEecCCCchhHHHH-HHHHhcC
Confidence            4455666 78899999999996544 3433333

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

Probab=94.26  E-value=0.14  Score=43.45  Aligned_cols=60  Identities=13%  Similarity=0.263  Sum_probs=35.1

Q ss_pred             HHHHCCCCCCcHHHHHHHHhhhc--CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHH
Q 022724           47 GIYQYGFEKPSAIQQRAVMPIIK--GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (293)
Q Consensus        47 ~l~~~~~~~~~~~Q~~~~~~i~~--~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~  112 (293)
                      .+.++|+   .+.|.+.+..+..  +..++|.||||||||.. +-.++..+...  +.+++.+-...|
T Consensus        58 ~l~~lg~---~~~~~~~l~~~~~~~~GlilisG~tGSGKTT~-l~all~~i~~~--~~~iitiEdp~E  119 (264)
T cd01129          58 DLEKLGL---KPENLEIFRKLLEKPHGIILVTGPTGSGKTTT-LYSALSELNTP--EKNIITVEDPVE  119 (264)
T ss_pred             CHHHcCC---CHHHHHHHHHHHhcCCCEEEEECCCCCcHHHH-HHHHHhhhCCC--CCeEEEECCCce
Confidence            3555663   4556666665543  34689999999999954 34455555432  224555443333

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.

>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth

Probab=94.19  E-value=0.39  Score=36.53  Aligned_cols=31  Identities=19%  Similarity=0.229  Sum_probs=23.0

Q ss_pred             CCCccEEEecchhhhhccccHHHHHHHHhhC
Q 022724          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYL  203 (293)
Q Consensus       173 ~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l  203 (293)
                      ..+.+++++||.-.-+|......+..+++.+
T Consensus        86 ~~~p~illlDEP~~~LD~~~~~~l~~~l~~~  116 (144)
T cd03221          86 LENPNLLLLDEPTNHLDLESIEALEEALKEY  116 (144)
T ss_pred             hcCCCEEEEeCCccCCCHHHHHHHHHHHHHc
Confidence            3456899999998777776666676677666

EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.

>COG2109 BtuR ATP:corrinoid adenosyltransferase [Coenzyme metabolism]

Probab=94.19  E-value=0.66  Score=36.76  Aligned_cols=143  Identities=15%  Similarity=0.210  Sum_probs=72.8

Q ss_pred             cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHH-HHHHHHHhhccCCceEEEEECCcchHHHHHHHhc
Q 022724           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQ-TEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH  150 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  150 (293)
                      -++|....|-|||.+++=-++..+-.   |.++.|+-=.+--... -...+..+  ..++....+..+...+.+.+.   
T Consensus        30 li~V~TG~GKGKTTAAlG~alRa~Gh---G~rv~vvQFiKg~~~~GE~~~~~~~--~~~v~~~~~~~g~tw~~~~~~---  101 (198)
T COG2109          30 LIIVFTGNGKGKTTAALGLALRALGH---GLRVGVVQFIKGGWKYGEEAALEKF--GLGVEFHGMGEGFTWETQDRE---  101 (198)
T ss_pred             eEEEEecCCCChhHHHHHHHHHHhcC---CCEEEEEEEeecCcchhHHHHHHhh--ccceeEEecCCceeCCCcCcH---
Confidence            36777889999998887767666544   4566665422211111 11122222  122222222222111111000   


Q ss_pred             CCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcccc--HHHHHHHHhhCCCCccEEEEEeecChhHHHHHHh
Q 022724          151 GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF--KDQIYDVYRYLPPDLQVVLISATLPHEILEMTTK  226 (293)
Q Consensus       151 ~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~--~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~  226 (293)
                       .++  ..+......... .+.-..++++|+||+...+..++  .+.+..++...|...-+|+.--..|+.+.+.+..
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--AAAKAGWEHAKE-ALADGKYDLVILDELNYALRYGLLPLEEVVALLKARPEHTHVIITGRGAPPELIELADL  175 (198)
T ss_pred             -HHH--HHHHHHHHHHHH-HHhCCCCCEEEEehhhHHHHcCCCCHHHHHHHHhcCCCCcEEEEECCCCCHHHHHHHHH
Confidence             011  112222211111 12223678999999999887765  3556667776666666776666678877776543

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=94.19  E-value=0.65  Score=40.73  Aligned_cols=41  Identities=10%  Similarity=0.267  Sum_probs=24.1

Q ss_pred             CCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEe
Q 022724          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (293)
Q Consensus       173 ~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SA  214 (293)
                      ....+++||||+|.+.... ...+...+..-+....+|+.+.
T Consensus       108 ~~~~kvviI~~a~~~~~~a-~NaLLK~LEEPp~~~~~Il~t~  148 (329)
T PRK08058        108 ESNKKVYIIEHADKMTASA-ANSLLKFLEEPSGGTTAILLTE  148 (329)
T ss_pred             ccCceEEEeehHhhhCHHH-HHHHHHHhcCCCCCceEEEEeC
Confidence            3567899999999985432 2233334444344555665443

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=94.14  E-value=0.17  Score=49.46  Aligned_cols=53  Identities=19%  Similarity=0.255  Sum_probs=28.9

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHh--hhcCCcEEEEcCCCChhHHHH
Q 022724           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMP--IIKGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        33 ~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~--i~~~~~~li~~~Tg~GKT~~~   87 (293)
                      .+|++.+-.+.+.+.+.+. +..|..++. .+..  +...+.+++.||+|+|||+.+
T Consensus       450 ~~~~di~g~~~~k~~l~~~-v~~~~~~~~-~~~~~g~~~~~giLL~GppGtGKT~la  504 (733)
T TIGR01243       450 VRWSDIGGLEEVKQELREA-VEWPLKHPE-IFEKMGIRPPKGVLLFGPPGTGKTLLA  504 (733)
T ss_pred             cchhhcccHHHHHHHHHHH-HHhhhhCHH-HHHhcCCCCCceEEEECCCCCCHHHHH
Confidence            4566666666666666542 111111111 1111  123467999999999999543

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.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=94.14  E-value=0.51  Score=43.74  Aligned_cols=60  Identities=17%  Similarity=0.227  Sum_probs=40.6

Q ss_pred             HHHHhhhc-----CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhh
Q 022724           62 RAVMPIIK-----GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIG  125 (293)
Q Consensus        62 ~~~~~i~~-----~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  125 (293)
                      ..++.++.     |--+++.||+|+|||...+-.+...+..   +.+++|++ ..+-..|+..+++.++
T Consensus       250 ~~lD~~lgGG~~~gs~~li~G~~G~GKt~l~~~f~~~~~~~---ge~~~y~s-~eEs~~~i~~~~~~lg  314 (484)
T TIGR02655       250 VRLDEMCGGGFFKDSIILATGATGTGKTLLVSKFLENACAN---KERAILFA-YEESRAQLLRNAYSWG  314 (484)
T ss_pred             HhHHHHhcCCccCCcEEEEECCCCCCHHHHHHHHHHHHHHC---CCeEEEEE-eeCCHHHHHHHHHHcC
Confidence            44566554     3579999999999996554444443332   44677776 5677788888887664

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.

>PRK08506 replicative DNA helicase; Provisional

Probab=94.13  E-value=0.59  Score=43.14  Aligned_cols=113  Identities=19%  Similarity=0.147  Sum_probs=55.7

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEE-ECCcchHH----
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC-VGGKSVGE----  143 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~-~~~~~~~~----  143 (293)
                      .|.-+++.|.+|+|||...+-.+.+ ...  .+..++|++.- .-..|+..++-....  ++....+ .+..+..+    
T Consensus       191 ~G~LivIaarpg~GKT~fal~ia~~-~~~--~g~~V~~fSlE-Ms~~ql~~Rlla~~s--~v~~~~i~~~~l~~~e~~~~  264 (472)
T PRK08506        191 KGDLIIIAARPSMGKTTLCLNMALK-ALN--QDKGVAFFSLE-MPAEQLMLRMLSAKT--SIPLQNLRTGDLDDDEWERL  264 (472)
T ss_pred             CCceEEEEcCCCCChHHHHHHHHHH-HHh--cCCcEEEEeCc-CCHHHHHHHHHHHhc--CCCHHHHhcCCCCHHHHHHH
Confidence            4567888999999999544433333 322  24456666543 334555554433222  2211111 12212111    


Q ss_pred             --HHHHHhcCCcEEEe-----ChHHHHHHHhcCCCCCCCccEEEecchhhhh
Q 022724          144 --DIRKLEHGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (293)
Q Consensus       144 --~~~~~~~~~~ilV~-----Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~  188 (293)
                        ....+.+. .+.|-     |+..+...++.-......+++||||=.+.+.
T Consensus       265 ~~a~~~l~~~-~l~I~d~~~~ti~~I~~~~r~l~~~~~~~~lvvIDyLql~~  315 (472)
T PRK08506        265 SDACDELSKK-KLFVYDSGYVNIHQVRAQLRKLKSQHPEIGLAVIDYLQLMS  315 (472)
T ss_pred             HHHHHHHHcC-CeEEECCCCCCHHHHHHHHHHHHHhCCCCCEEEEcChhhcc
Confidence              11222233 34442     4555554443311112357999999999885

>PRK08840 replicative DNA helicase; Provisional

Probab=94.12  E-value=0.86  Score=41.96  Aligned_cols=148  Identities=19%  Similarity=0.214  Sum_probs=67.5

Q ss_pred             hhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEE-ECCcchHHH
Q 022724           66 PIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC-VGGKSVGED  144 (293)
Q Consensus        66 ~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~-~~~~~~~~~  144 (293)
                      -+..|.-+++.|.+|+|||.-. +-+....... .+..++|+..-.. ..|+..++-....  ++....+ .|..+..+.
T Consensus       213 G~~~g~LiviaarPg~GKTafa-lnia~~~a~~-~~~~v~~fSlEMs-~~ql~~Rlla~~s--~v~~~~i~~~~l~~~e~  287 (464)
T PRK08840        213 GLQGSDLIIVAARPSMGKTTFA-MNLCENAAMD-QDKPVLIFSLEMP-AEQLMMRMLASLS--RVDQTKIRTGQLDDEDW  287 (464)
T ss_pred             CCCCCceEEEEeCCCCchHHHH-HHHHHHHHHh-CCCeEEEEeccCC-HHHHHHHHHHhhC--CCCHHHHhcCCCCHHHH
Confidence            3445567888899999999443 3333333211 1335666654322 3444444432211  1111111 111121111


Q ss_pred             ------HHHHhcCCcEEEe-----ChHHHHHHHhcCCCCCCCccEEEecchhhhhccc----cHHHHHHHHhhCC-----
Q 022724          145 ------IRKLEHGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG----FKDQIYDVYRYLP-----  204 (293)
Q Consensus       145 ------~~~~~~~~~ilV~-----Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~----~~~~~~~i~~~l~-----  204 (293)
                            ...+.+...+.|-     |+..+....+.-......+++||||-.|.+...+    ....+..+-+.+.     
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                  1122122345443     3444443332211112357999999999884222    1222333333332     


Q ss_pred             CCccEEEEEeecChh
Q 022724          205 PDLQVVLISATLPHE  219 (293)
Q Consensus       205 ~~~q~v~~SAt~~~~  219 (293)
                      .++.++++| -++..
T Consensus       368 l~ipVi~Ls-QLnR~  381 (464)
T PRK08840        368 LNVPVVALS-QLNRS  381 (464)
T ss_pred             hCCeEEEEE-ecCcc
Confidence            256777776 44443

>PRK10865 protein disaggregation chaperone; Provisional

Probab=94.09  E-value=0.45  Score=47.33  Aligned_cols=17  Identities=24%  Similarity=0.567  Sum_probs=14.8

Q ss_pred             CcEEEEcCCCChhHHHH
Q 022724           71 RDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~   87 (293)
                      .|.++.||+|+|||...
T Consensus       200 ~n~lL~G~pGvGKT~l~  216 (857)
T PRK10865        200 NNPVLIGEPGVGKTAIV  216 (857)
T ss_pred             CceEEECCCCCCHHHHH
Confidence            48999999999999554

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.06  E-value=0.49  Score=43.53  Aligned_cols=67  Identities=22%  Similarity=0.284  Sum_probs=39.1

Q ss_pred             CCCCHHHHHHHHHCCCCCCcHHHHHHHHh-------hhc-C----CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEE
Q 022724           38 MGIKDDLLRGIYQYGFEKPSAIQQRAVMP-------IIK-G----RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQAL  105 (293)
Q Consensus        38 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~-------i~~-~----~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~l  105 (293)
                      +|.+++.++.+...|.-.-.+.=.+.+..       +.. .    ..+++.||.|+|||.-+     ..+.....-|.+=
T Consensus       494 FG~see~l~~~~~~Gmi~~g~~v~~il~~G~llv~qvk~s~~s~lvSvLl~Gp~~sGKTaLA-----A~iA~~S~FPFvK  568 (744)
T KOG0741|consen  494 FGISEEDLERFVMNGMINWGPPVTRILDDGKLLVQQVKNSERSPLVSVLLEGPPGSGKTALA-----AKIALSSDFPFVK  568 (744)
T ss_pred             cCCCHHHHHHHHhCCceeecccHHHHHhhHHHHHHHhhccccCcceEEEEecCCCCChHHHH-----HHHHhhcCCCeEE
Confidence            57888888887766554333333333321       111 1    36899999999999322     2222233456677


Q ss_pred             EEcC
Q 022724          106 ILSP  109 (293)
Q Consensus       106 il~P  109 (293)
                      ++.|
T Consensus       569 iiSp  572 (744)
T KOG0741|consen  569 IISP  572 (744)
T ss_pred             EeCh
Confidence            7777

>PRK08006 replicative DNA helicase; Provisional

Probab=94.00  E-value=1.2  Score=41.03  Aligned_cols=147  Identities=20%  Similarity=0.193  Sum_probs=68.6

Q ss_pred             hhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEE-CCcchHHH-
Q 022724           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACV-GGKSVGED-  144 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~-~~~~~~~~-  144 (293)
                      +..|.-++|.|.+|+|||. |++-+...+... .+..++|++.- --..|+..++-.....  +....+. +..+..+. 
T Consensus       221 l~~G~LiiIaarPgmGKTa-falnia~~~a~~-~g~~V~~fSlE-M~~~ql~~Rlla~~~~--v~~~~i~~~~l~~~e~~  295 (471)
T PRK08006        221 LQPSDLIIVAARPSMGKTT-FAMNLCENAAML-QDKPVLIFSLE-MPGEQIMMRMLASLSR--VDQTRIRTGQLDDEDWA  295 (471)
T ss_pred             CCCCcEEEEEeCCCCCHHH-HHHHHHHHHHHh-cCCeEEEEecc-CCHHHHHHHHHHHhcC--CCHHHhhcCCCCHHHHH
Confidence            3345667888999999994 444443333211 13356666543 2234444444322211  1111111 22222211 


Q ss_pred             -----HHHHhcCCcEEEe-----ChHHHHHHHhcCCCCCCCccEEEecchhhhhcc----ccHHHHHHHHhhCC-----C
Q 022724          145 -----IRKLEHGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR----GFKDQIYDVYRYLP-----P  205 (293)
Q Consensus       145 -----~~~~~~~~~ilV~-----Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~----~~~~~~~~i~~~l~-----~  205 (293)
                           ...+.....+.|-     |+..+....+.-......+++||||=.|.+...    .....+..+-+.+.     .
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                 1122123345543     455554443321111235899999999988422    12223344433332     2


Q ss_pred             CccEEEEEeecChh
Q 022724          206 DLQVVLISATLPHE  219 (293)
Q Consensus       206 ~~q~v~~SAt~~~~  219 (293)
                      ++.+|++| -++..
T Consensus       376 ~ipVi~Ls-QLnR~  388 (471)
T PRK08006        376 QVPVVALS-QLNRS  388 (471)
T ss_pred             CCeEEEEE-ecCcc
Confidence            56778776 34443

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

Probab=93.96  E-value=0.11  Score=41.45  Aligned_cols=40  Identities=15%  Similarity=0.302  Sum_probs=27.8

Q ss_pred             CCcHHHHHHHHh-hhcCCcEEEEcCCCChhHHHHHHHHHhhh
Q 022724           55 KPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTV   95 (293)
Q Consensus        55 ~~~~~Q~~~~~~-i~~~~~~li~~~Tg~GKT~~~~~~~~~~l   95 (293)
                      ..++-|...+.. +..|.+++++||||+|||... -.++..+
T Consensus         9 ~~~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTll-~aL~~~i   49 (186)
T cd01130           9 TFSPLQAAYLWLAVEARKNILISGGTGSGKTTLL-NALLAFI   49 (186)
T ss_pred             CCCHHHHHHHHHHHhCCCEEEEECCCCCCHHHHH-HHHHhhc
Confidence            456667776665 446889999999999999543 2344443

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.

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

Probab=93.96  E-value=0.037  Score=47.36  Aligned_cols=57  Identities=14%  Similarity=0.250  Sum_probs=33.0

Q ss_pred             ccCcccCCCCHHHHHHHHHC--CCC--------CCcHHHHHHHHh-----h-hcCCcEEEEcCCCChhHHHHH
Q 022724           32 ITSFDAMGIKDDLLRGIYQY--GFE--------KPSAIQQRAVMP-----I-IKGRDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        32 ~~~f~~~~l~~~i~~~l~~~--~~~--------~~~~~Q~~~~~~-----i-~~~~~~li~~~Tg~GKT~~~~   88 (293)
                      ..+.+++|-|.+|.+.|.+.  |-.        ..+.+-++.-..     + ++.-|+++.||||||||+.+.
T Consensus        43 ~~~~~~lPtP~eik~~Ld~YVIGQe~AKKvLsVAVYNHYKRl~~~~~~~dvEL~KSNILLiGPTGsGKTlLAq  115 (408)
T COG1219          43 EKELSELPTPKEIKAHLDEYVIGQEQAKKVLSVAVYNHYKRLNNKEDNDDVELSKSNILLIGPTGSGKTLLAQ  115 (408)
T ss_pred             chhhccCCChHHHHHHhhhheecchhhhceeeeeehhHHHHHhccCCCCceeeeeccEEEECCCCCcHHHHHH
Confidence            34666788888888888552  111        111122221111     1 123489999999999996543

>PF05707 Zot: Zonular occludens toxin (Zot); InterPro: IPR008900 This entry consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot)

Probab=93.95  E-value=0.41  Score=38.40  Aligned_cols=51  Identities=18%  Similarity=0.325  Sum_probs=25.5

Q ss_pred             CccEEEecchhhhhccc-cH----HHHHHHHhhCCC-CccEEEEEeecChhHHHHHHh
Q 022724          175 AIKLLVLDESDEMLSRG-FK----DQIYDVYRYLPP-DLQVVLISATLPHEILEMTTK  226 (293)
Q Consensus       175 ~l~~iViDE~h~~~~~~-~~----~~~~~i~~~l~~-~~q~v~~SAt~~~~~~~~~~~  226 (293)
                      .-.++||||||.+.... ..    ......+...+. ...++++|-.+. .+...++.
T Consensus        79 ~~~liviDEa~~~~~~r~~~~~~~~~~~~~l~~hRh~g~diiliTQ~~~-~id~~ir~  135 (193)
T PF05707_consen   79 KGSLIVIDEAQNFFPSRSWKGKKVPEIIEFLAQHRHYGWDIILITQSPS-QIDKFIRD  135 (193)
T ss_dssp             TT-EEEETTGGGTSB---T-T----HHHHGGGGCCCTT-EEEEEES-GG-GB-HHHHC
T ss_pred             CCcEEEEECChhhcCCCccccccchHHHHHHHHhCcCCcEEEEEeCCHH-HHhHHHHH
Confidence            45799999999986442 21    122244444443 456777766653 34444443

Zot is elaborated by bacteriophage present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers.; PDB: 2R2A_B.

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=93.95  E-value=0.19  Score=41.23  Aligned_cols=43  Identities=16%  Similarity=0.157  Sum_probs=26.7

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccC---CCceeEEEEcCCH
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTS---SREVQALILSPTR  111 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~---~~~~~~lil~P~~  111 (293)
                      .|.-+.|.||+|+|||...+..+.......   .....++++....
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            356789999999999965554443333221   0124678877643

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.

>TIGR00416 sms DNA repair protein RadA

Probab=93.95  E-value=0.65  Score=42.62  Aligned_cols=98  Identities=13%  Similarity=0.211  Sum_probs=54.7

Q ss_pred             HHHHhhhc-----CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEE
Q 022724           62 RAVMPIIK-----GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACV  136 (293)
Q Consensus        62 ~~~~~i~~-----~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~  136 (293)
                      .-++.++.     |.-+++.|++|+|||...+..+ ..+...  +.+++|+... +-..|+..+..++.-..  .-..+.
T Consensus        81 ~~LD~vLgGGi~~GsvilI~G~pGsGKTTL~lq~a-~~~a~~--g~kvlYvs~E-Es~~qi~~ra~rlg~~~--~~l~~~  154 (454)
T TIGR00416        81 GELDRVLGGGIVPGSLILIGGDPGIGKSTLLLQVA-CQLAKN--QMKVLYVSGE-ESLQQIKMRAIRLGLPE--PNLYVL  154 (454)
T ss_pred             HHHHHHhcCCccCCeEEEEEcCCCCCHHHHHHHHH-HHHHhc--CCcEEEEECc-CCHHHHHHHHHHcCCCh--HHeEEc
Confidence            34455553     4678999999999996544333 333322  3468888753 44567666555543111  000000


Q ss_pred             CCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhh
Q 022724          137 GGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (293)
Q Consensus       137 ~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~  188 (293)
                      ..                  .+.+.+...+..     .+.+++|||.+..+.
T Consensus       155 ~e------------------~~~~~I~~~i~~-----~~~~~vVIDSIq~l~  183 (454)
T TIGR00416       155 SE------------------TNWEQICANIEE-----ENPQACVIDSIQTLY  183 (454)
T ss_pred             CC------------------CCHHHHHHHHHh-----cCCcEEEEecchhhc
Confidence            00                  134455554433     346799999998874

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)).

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=93.94  E-value=0.22  Score=43.87  Aligned_cols=63  Identities=17%  Similarity=0.250  Sum_probs=39.3

Q ss_pred             HHHHHHCCCCCCcHHHHHHHHhhh-cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHH
Q 022724           45 LRGIYQYGFEKPSAIQQRAVMPII-KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (293)
Q Consensus        45 ~~~l~~~~~~~~~~~Q~~~~~~i~-~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l  113 (293)
                      ++.+.+.|+  +++.+...+..+. .+++++++|+||+|||.. +-.++..+..   ..+.+.+-...|+
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  4456666666544 567999999999999943 3334444432   2356666666665

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.

>PRK07004 replicative DNA helicase; Provisional

Probab=93.93  E-value=0.56  Score=43.14  Aligned_cols=141  Identities=17%  Similarity=0.236  Sum_probs=63.6

Q ss_pred             hcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEE-ECCcchHHH--
Q 022724           68 IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC-VGGKSVGED--  144 (293)
Q Consensus        68 ~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~-~~~~~~~~~--  144 (293)
                      ..|.-+++.|.+|+|||.- ++-+...+... .+..+++++.- --..|+..++-....  ++....+ .|..+..+.  
T Consensus       211 ~~g~liviaarpg~GKT~~-al~ia~~~a~~-~~~~v~~fSlE-M~~~ql~~R~la~~~--~v~~~~i~~g~l~~~e~~~  285 (460)
T PRK07004        211 HGGELIIVAGRPSMGKTAF-SMNIGEYVAVE-YGLPVAVFSME-MPGTQLAMRMLGSVG--RLDQHRMRTGRLTDEDWPK  285 (460)
T ss_pred             CCCceEEEEeCCCCCccHH-HHHHHHHHHHH-cCCeEEEEeCC-CCHHHHHHHHHHhhc--CCCHHHHhcCCCCHHHHHH
Confidence            3456788899999999944 33333332211 13345555532 223344333321111  1111111 122121111  


Q ss_pred             ----HHHHhcCCcEEEe-----ChHHHHHHHhcCCCCCCCccEEEecchhhhhccc----cHHHHHHHHhhCC-----CC
Q 022724          145 ----IRKLEHGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG----FKDQIYDVYRYLP-----PD  206 (293)
Q Consensus       145 ----~~~~~~~~~ilV~-----Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~----~~~~~~~i~~~l~-----~~  206 (293)
                          ...+.+ ..+.|.     |+..+....++-......+++||||=.+.+...+    ....+..+.+.+.     .+
T Consensus       286 ~~~a~~~l~~-~~l~I~d~~~~~~~~i~~~~r~l~~~~~~~~lviIDYLql~~~~~~~~~r~~ei~~Isr~LK~lAkel~  364 (460)
T PRK07004        286 LTHAVQKMSE-AQLFIDETGGLNPMELRSRARRLARQCGKLGLIIIDYLQLMSGSSQGENRATEISEISRSLKSLAKELD  364 (460)
T ss_pred             HHHHHHHHhc-CCEEEECCCCCCHHHHHHHHHHHHHhCCCCCEEEEChhhhccCCCCCCcHHHHHHHHHHHHHHHHHHhC
Confidence                122222 345552     4444444332211112357899999999985321    2223333333332     25


Q ss_pred             ccEEEEEe
Q 022724          207 LQVVLISA  214 (293)
Q Consensus       207 ~q~v~~SA  214 (293)
                      +.++++|.
T Consensus       365 ipVi~lsQ  372 (460)
T PRK07004        365 VPVIALSQ  372 (460)
T ss_pred             CeEEEEec
Confidence            67777754

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=93.91  E-value=0.35  Score=40.55  Aligned_cols=30  Identities=23%  Similarity=0.370  Sum_probs=21.0

Q ss_pred             hhcCCcEEEEcCCCChhHHHHHHHHHhhhcc
Q 022724           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDT   97 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~   97 (293)
                      +..|+.+++.||.|+|||.. +-.+++.+..
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            34789999999999999943 2334444433

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.

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=93.88  E-value=1.5  Score=37.20  Aligned_cols=22  Identities=14%  Similarity=0.261  Sum_probs=16.9

Q ss_pred             HHhhh-cC--CcEEEEcCCCChhHH
Q 022724           64 VMPII-KG--RDVIAQAQSGTGKTS   85 (293)
Q Consensus        64 ~~~i~-~~--~~~li~~~Tg~GKT~   85 (293)
                      ++.+. ++  +++++.||+|+|||.
T Consensus       102 l~~l~~~~~~~~~~i~g~~g~GKtt  126 (270)
T TIGR02858       102 LPYLVRNNRVLNTLIISPPQCGKTT  126 (270)
T ss_pred             HHHHHhCCCeeEEEEEcCCCCCHHH
Confidence            44444 33  689999999999994

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.

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.87  E-value=0.32  Score=46.40  Aligned_cols=40  Identities=13%  Similarity=0.179  Sum_probs=23.2

Q ss_pred             CCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       173 ~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      +...+++||||+|.+.... ...+...+..-+....+|+.+
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            4567899999999985432 223334444434444444443

>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [General function prediction only]

Probab=93.87  E-value=0.76  Score=44.17  Aligned_cols=180  Identities=13%  Similarity=0.101  Sum_probs=100.7

Q ss_pred             CCHHHHHHHHHC---CCCCCcHHHHHHHHhhh--cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHH
Q 022724           40 IKDDLLRGIYQY---GFEKPSAIQQRAVMPII--KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELA  114 (293)
Q Consensus        40 l~~~i~~~l~~~---~~~~~~~~Q~~~~~~i~--~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~  114 (293)
                      +-+.+.+.++-.   |+..++.-=.+.+....  +|-..|+.-..|-|||+-.. ..++.+.+.-....+++++|-..| 
T Consensus       247 lapqla~v~kPHQiGGiRFlYDN~iESl~rykkSsGFGCILAHSMGLGKTlQVi-sF~diflRhT~AKtVL~ivPiNTl-  324 (1387)
T KOG1016|consen  247 LAPQLAHVLKPHQIGGIRFLYDNTIESLGRYKKSSGFGCILAHSMGLGKTLQVI-SFSDIFLRHTKAKTVLVIVPINTL-  324 (1387)
T ss_pred             ehhhhHhhcCccccCcEEEehhhHHHHHhhccccCCcceeeeeccccCceeEEe-ehhHHHhhcCccceEEEEEehHHH-
Confidence            455666666432   45555555455555543  45678888999999995422 223333344445689999996665 


Q ss_pred             HHHHHHHHHhhcc----C-----CceEEEEECCcchHHH-HHHH---hcCCcEEEeChHHHHHHHhc-----CC------
Q 022724          115 TQTEKVILAIGDF----I-----NIQAHACVGGKSVGED-IRKL---EHGVHVVSGTPGRVCDMIKR-----KT------  170 (293)
Q Consensus       115 ~q~~~~~~~~~~~----~-----~~~~~~~~~~~~~~~~-~~~~---~~~~~ilV~Tp~~l~~~l~~-----~~------  170 (293)
                      ..++..+..|...    .     .+.+..+.++.....+ .+-+   -..-.|+..-.+.+--+...     +.      
T Consensus       325 QNWlsEfnmWiP~y~sD~~vrpR~F~vf~LnD~~KT~~~Rakvi~~Wv~~GGVlLvGYemfRLL~lk~~~~~grpkkt~k  404 (1387)
T KOG1016|consen  325 QNWLSEFNMWIPKYFSDTGVRPRSFEVFLLNDGVKTFDQRAKVIEQWVQTGGVLLVGYEMFRLLILKTLPKKGRPKKTLK  404 (1387)
T ss_pred             HHHHHHhhhhcCCCcccCCCccceeEEEEecCchhhHHHHHHHHHHHhccCCEEEehHHHHHHHHHhcccccCCcccccc
Confidence            3344445444332    1     2456666666443332 2222   22224555555444222111     00      


Q ss_pred             ------CC-------------------CCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEeecChhHHHH
Q 022724          171 ------LR-------------------TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEM  223 (293)
Q Consensus       171 ------~~-------------------~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~  223 (293)
                            ++                   -...+++|.||-|.+-.  ....+...++.++.++++|+....+-+.+.++
T Consensus       405 r~~~~~i~~d~eD~~qe~~~li~~AL~~PGPDlVICDEGHrIKN--~~A~iS~aLk~IrtrRRiVLTGYPLQNNLlEY  480 (1387)
T KOG1016|consen  405 RISSGFIKDDSEDQRQEAYSLIRSALLEPGPDLVICDEGHRIKN--ITAEISMALKAIRTRRRIVLTGYPLQNNLLEY  480 (1387)
T ss_pred             ccCCcccCCchhhhHHHHHHHHHHHhcCCCCCeEEecCCceecc--chHHHHHHHHHhhhceeEEEeccccccchHHH
Confidence                  00                   02358899999999833  34445566677777788888888887665543

>cd01131 PilT Pilus retraction ATPase PilT

Probab=93.86  E-value=0.11  Score=42.05  Aligned_cols=39  Identities=15%  Similarity=0.325  Sum_probs=23.6

Q ss_pred             cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHH
Q 022724           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~  112 (293)
                      -++++||||||||... ..++..+.... +.+++.+-...+
T Consensus         3 lilI~GptGSGKTTll-~~ll~~~~~~~-~~~i~t~e~~~E   41 (198)
T cd01131           3 LVLVTGPTGSGKSTTL-AAMIDYINKNK-THHILTIEDPIE   41 (198)
T ss_pred             EEEEECCCCCCHHHHH-HHHHHHhhhcC-CcEEEEEcCCcc
Confidence            3789999999999653 34455554332 235555554333

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.

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=93.83  E-value=1.4  Score=38.24  Aligned_cols=129  Identities=20%  Similarity=0.345  Sum_probs=70.2

Q ss_pred             cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcC--CHHHHHHHHHHHHHhhccCCceEEEE-ECCcchHHHHHHH
Q 022724           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP--TRELATQTEKVILAIGDFINIQAHAC-VGGKSVGEDIRKL  148 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P--~~~l~~q~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~  148 (293)
                      -++++|-.|+|||....=.+ +.+...  |.++++.+-  .|+-|.++.+.|   ....|..+..- .|+.         
T Consensus       141 Vil~vGVNG~GKTTTIaKLA-~~l~~~--g~~VllaA~DTFRAaAiEQL~~w---~er~gv~vI~~~~G~D---------  205 (340)
T COG0552         141 VILFVGVNGVGKTTTIAKLA-KYLKQQ--GKSVLLAAGDTFRAAAIEQLEVW---GERLGVPVISGKEGAD---------  205 (340)
T ss_pred             EEEEEecCCCchHhHHHHHH-HHHHHC--CCeEEEEecchHHHHHHHHHHHH---HHHhCCeEEccCCCCC---------
Confidence            47889999999997643222 222222  445665553  377766665544   44556655542 1222         


Q ss_pred             hcCCcEEEeChHHHH-HHHhcCCCCCCCccEEEecchhhhhcc-ccHHHHHHHHhhCCCCc------cEEEEEeecChhH
Q 022724          149 EHGVHVVSGTPGRVC-DMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPPDL------QVVLISATLPHEI  220 (293)
Q Consensus       149 ~~~~~ilV~Tp~~l~-~~l~~~~~~~~~l~~iViDE~h~~~~~-~~~~~~~~i~~~l~~~~------q~v~~SAt~~~~~  220 (293)
                                |..+. +.+..  -..++++++++|=|-++... .....+..+.+-+.+..      -++.+-||...+.
T Consensus       206 ----------pAaVafDAi~~--Akar~~DvvliDTAGRLhnk~nLM~EL~KI~rV~~k~~~~ap~e~llvlDAttGqna  273 (340)
T COG0552         206 ----------PAAVAFDAIQA--AKARGIDVVLIDTAGRLHNKKNLMDELKKIVRVIKKDDPDAPHEILLVLDATTGQNA  273 (340)
T ss_pred             ----------cHHHHHHHHHH--HHHcCCCEEEEeCcccccCchhHHHHHHHHHHHhccccCCCCceEEEEEEcccChhH
Confidence                      22111 11111  11355677888877776543 34555666666665433      3555589987765


Q ss_pred             HHHHHhc
Q 022724          221 LEMTTKF  227 (293)
Q Consensus       221 ~~~~~~~  227 (293)
                      .+.++.+
T Consensus       274 l~QAk~F  280 (340)
T COG0552         274 LSQAKIF  280 (340)
T ss_pred             HHHHHHH
Confidence            5544443

>PRK12608 transcription termination factor Rho; Provisional

Probab=93.80  E-value=0.97  Score=40.11  Aligned_cols=39  Identities=23%  Similarity=0.346  Sum_probs=27.6

Q ss_pred             HHHHHHHHhhh---cCCcEEEEcCCCChhHHHHHHHHHhhhcc
Q 022724           58 AIQQRAVMPII---KGRDVIAQAQSGTGKTSMIALTVCQTVDT   97 (293)
Q Consensus        58 ~~Q~~~~~~i~---~~~~~li~~~Tg~GKT~~~~~~~~~~l~~   97 (293)
                      .+-.++++.+.   +|+..+|.||.|+|||... .-+...+..
T Consensus       118 ~~~~RvID~l~PiGkGQR~LIvG~pGtGKTTLl-~~la~~i~~  159 (380)
T PRK12608        118 DLSMRVVDLVAPIGKGQRGLIVAPPRAGKTVLL-QQIAAAVAA  159 (380)
T ss_pred             chhHhhhhheeecCCCceEEEECCCCCCHHHHH-HHHHHHHHh
Confidence            45566888766   7889999999999999543 234444443

>PRK08760 replicative DNA helicase; Provisional

Probab=93.78  E-value=0.77  Score=42.44  Aligned_cols=114  Identities=18%  Similarity=0.185  Sum_probs=55.0

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHH----
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGED----  144 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~----  144 (293)
                      .|.-++|.|.+|+|||...+ -+....... .+..++|++.-. -..|+..++..........- ...|..+..+.    
T Consensus       228 ~G~LivIaarPg~GKTafal-~iA~~~a~~-~g~~V~~fSlEM-s~~ql~~Rl~a~~s~i~~~~-i~~g~l~~~e~~~~~  303 (476)
T PRK08760        228 PTDLIILAARPAMGKTTFAL-NIAEYAAIK-SKKGVAVFSMEM-SASQLAMRLISSNGRINAQR-LRTGALEDEDWARVT  303 (476)
T ss_pred             CCceEEEEeCCCCChhHHHH-HHHHHHHHh-cCCceEEEeccC-CHHHHHHHHHHhhCCCcHHH-HhcCCCCHHHHHHHH
Confidence            45668889999999995443 333333211 133566665432 23455555544332222111 01122111111    


Q ss_pred             --HHHHhcCCcEEEe-----ChHHHHHHHhcCCCCCCCccEEEecchhhhh
Q 022724          145 --IRKLEHGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (293)
Q Consensus       145 --~~~~~~~~~ilV~-----Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~  188 (293)
                        ...+.+ ..+.|.     |++.+...++.-.. -..+++||||=.+.+.
T Consensus       304 ~a~~~l~~-~~l~I~d~~~~t~~~I~~~~r~l~~-~~~~~lVvIDyLql~~  352 (476)
T PRK08760        304 GAIKMLKE-TKIFIDDTPGVSPEVLRSKCRRLKR-EHDLGLIVIDYLQLMS  352 (476)
T ss_pred             HHHHHHhc-CCEEEeCCCCCCHHHHHHHHHHHHH-hcCCCEEEEecHHhcC
Confidence              122222 344443     45555544433111 1347999999999884

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=93.78  E-value=0.041  Score=49.32  Aligned_cols=47  Identities=21%  Similarity=0.144  Sum_probs=36.1

Q ss_pred             cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 022724           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA  123 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~  123 (293)
                      +++++||||+|||.++++|-+-..     +..+||+=|.-++........+.
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll~~-----~~s~vv~D~Kge~~~~t~~~r~~   47 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLLTW-----PGSVVVLDPKGENFELTSEHRRA   47 (384)
T ss_pred             CeeEecCCCCCCccEEEccchhcC-----CCCEEEEccchhHHHHHHHHHHH
Confidence            579999999999999887765432     23578888988888877766554

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.

>COG1197 Mfd Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]

Probab=93.77  E-value=2  Score=43.30  Aligned_cols=162  Identities=12%  Similarity=0.152  Sum_probs=111.6

Q ss_pred             cccCCccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhh---------
Q 022724           25 TTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTV---------   95 (293)
Q Consensus        25 ~~~~~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l---------   95 (293)
                      +..-....-.|.++||-  |++.=+++|.     -|++-+..+...-|++--..|--=.|+-..+..+..+         
T Consensus       704 THrLL~kdv~FkdLGLl--IIDEEqRFGV-----k~KEkLK~Lr~~VDvLTLSATPIPRTL~Msm~GiRdlSvI~TPP~~  776 (1139)
T COG1197         704 THRLLSKDVKFKDLGLL--IIDEEQRFGV-----KHKEKLKELRANVDVLTLSATPIPRTLNMSLSGIRDLSVIATPPED  776 (1139)
T ss_pred             chHhhCCCcEEecCCeE--EEechhhcCc-----cHHHHHHHHhccCcEEEeeCCCCcchHHHHHhcchhhhhccCCCCC
Confidence            33334445567777653  3333344444     3677777777777888888888778866554444333         


Q ss_pred             ---------------------ccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hc
Q 022724           96 ---------------------DTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EH  150 (293)
Q Consensus        96 ---------------------~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~  150 (293)
                                           ..-.+|+++.|+.|..+-..++.+.++.+-.  ..++...||.+...+..+..    ..
T Consensus       777 R~pV~T~V~~~d~~~ireAI~REl~RgGQvfYv~NrV~~Ie~~~~~L~~LVP--EarI~vaHGQM~e~eLE~vM~~F~~g  854 (1139)
T COG1197         777 RLPVKTFVSEYDDLLIREAILRELLRGGQVFYVHNRVESIEKKAERLRELVP--EARIAVAHGQMRERELEEVMLDFYNG  854 (1139)
T ss_pred             CcceEEEEecCChHHHHHHHHHHHhcCCEEEEEecchhhHHHHHHHHHHhCC--ceEEEEeecCCCHHHHHHHHHHHHcC
Confidence                                 1113578999999999999999999998865  46789999998876654433    35


Q ss_pred             CCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCC
Q 022724          151 GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP  205 (293)
Q Consensus       151 ~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~  205 (293)
                      ..||+|||-     .+ ...++..+-..||||.||++.    ..++..+..+...
T Consensus       855 ~~dVLv~TT-----II-EtGIDIPnANTiIIe~AD~fG----LsQLyQLRGRVGR  899 (1139)
T COG1197         855 EYDVLVCTT-----II-ETGIDIPNANTIIIERADKFG----LAQLYQLRGRVGR  899 (1139)
T ss_pred             CCCEEEEee-----ee-ecCcCCCCCceEEEecccccc----HHHHHHhccccCC
Confidence            789999994     33 345889999999999999974    3445555555543

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=93.75  E-value=0.15  Score=44.34  Aligned_cols=20  Identities=30%  Similarity=0.637  Sum_probs=17.1

Q ss_pred             hhcCCcEEEEcCCCChhHHH
Q 022724           67 IIKGRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~~   86 (293)
                      +..+.+++++||||+|||..
T Consensus       141 v~~~~~ili~G~tGsGKTTl  160 (308)
T TIGR02788       141 IASRKNIIISGGTGSGKTTF  160 (308)
T ss_pred             hhCCCEEEEECCCCCCHHHH
Confidence            44688999999999999953

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.

>PRK10436 hypothetical protein; Provisional

Probab=93.75  E-value=0.17  Score=46.42  Aligned_cols=46  Identities=20%  Similarity=0.323  Sum_probs=29.7

Q ss_pred             HHHCCCCCCcHHHHHHHHhhh--cCCcEEEEcCCCChhHHHHHHHHHhhhcc
Q 022724           48 IYQYGFEKPSAIQQRAVMPII--KGRDVIAQAQSGTGKTSMIALTVCQTVDT   97 (293)
Q Consensus        48 l~~~~~~~~~~~Q~~~~~~i~--~~~~~li~~~Tg~GKT~~~~~~~~~~l~~   97 (293)
                      |.++|+   .+.|.+.+..+.  .+.-++++||||||||... ..++..+..
T Consensus       197 L~~LG~---~~~~~~~l~~~~~~~~GliLvtGpTGSGKTTtL-~a~l~~~~~  244 (462)
T PRK10436        197 LETLGM---TPAQLAQFRQALQQPQGLILVTGPTGSGKTVTL-YSALQTLNT  244 (462)
T ss_pred             HHHcCc---CHHHHHHHHHHHHhcCCeEEEECCCCCChHHHH-HHHHHhhCC
Confidence            445553   455666666554  3457999999999999653 345555543

>PRK06321 replicative DNA helicase; Provisional

Probab=93.71  E-value=0.89  Score=41.94  Aligned_cols=119  Identities=16%  Similarity=0.195  Sum_probs=56.5

Q ss_pred             HHHhhhc----CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEE-EC
Q 022724           63 AVMPIIK----GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC-VG  137 (293)
Q Consensus        63 ~~~~i~~----~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~-~~  137 (293)
                      .++.+..    |.-++|.|.+|+|||.- .+-+...+... .+..++|++. .--..|+..++-....  ++....+ .+
T Consensus       215 ~LD~~t~Gl~~G~LiiiaarPgmGKTaf-al~ia~~~a~~-~g~~v~~fSL-EMs~~ql~~Rlla~~s--~v~~~~i~~~  289 (472)
T PRK06321        215 DLDKMINGFSPSNLMILAARPAMGKTAL-ALNIAENFCFQ-NRLPVGIFSL-EMTVDQLIHRIICSRS--EVESKKISVG  289 (472)
T ss_pred             HHHHHhcCCCCCcEEEEEeCCCCChHHH-HHHHHHHHHHh-cCCeEEEEec-cCCHHHHHHHHHHhhc--CCCHHHhhcC
Confidence            3455443    45578889999999944 44444443221 1334556553 2223444444432221  2221111 12


Q ss_pred             CcchHHH------HHHHhcCCcEEEe-----ChHHHHHHHhcCCCCCCCccEEEecchhhhh
Q 022724          138 GKSVGED------IRKLEHGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (293)
Q Consensus       138 ~~~~~~~------~~~~~~~~~ilV~-----Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~  188 (293)
                      ..+..+.      ...+.+. .+.|-     |.+.+...++.-.. -..+++||||=.+.+.
T Consensus       290 ~l~~~e~~~~~~a~~~l~~~-~~~idd~~~~ti~~i~~~~r~~~~-~~~~~lvvIDyLql~~  349 (472)
T PRK06321        290 DLSGRDFQRIVSVVNEMQEH-TLLIDDQPGLKITDLRARARRMKE-SYDIQFLIIDYLQLLS  349 (472)
T ss_pred             CCCHHHHHHHHHHHHHHHcC-CEEEeCCCCCCHHHHHHHHHHHHH-hcCCCEEEEcchHHcC
Confidence            2221111      1222232 45553     44455444333111 1347899999999885

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=93.70  E-value=0.17  Score=46.85  Aligned_cols=47  Identities=17%  Similarity=0.316  Sum_probs=30.3

Q ss_pred             HHHHCCCCCCcHHHHHHHHhhhcC-C-cEEEEcCCCChhHHHHHHHHHhhhcc
Q 022724           47 GIYQYGFEKPSAIQQRAVMPIIKG-R-DVIAQAQSGTGKTSMIALTVCQTVDT   97 (293)
Q Consensus        47 ~l~~~~~~~~~~~Q~~~~~~i~~~-~-~~li~~~Tg~GKT~~~~~~~~~~l~~   97 (293)
                      .|.++|+   .+-|.+.+..+... + -++++||||||||... -.++..+..
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            3455554   46677777766543 3 4789999999999543 345565543

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.

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=93.69  E-value=0.14  Score=45.26  Aligned_cols=43  Identities=9%  Similarity=0.268  Sum_probs=27.1

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l  113 (293)
                      .+..++++||||||||... -.++..+.... +.+++.+-...+.
T Consensus       121 ~~g~ili~G~tGSGKTT~l-~al~~~i~~~~-~~~i~tiEdp~E~  163 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTL-ASMIDYINKNA-AGHIITIEDPIEY  163 (343)
T ss_pred             cCcEEEEECCCCCCHHHHH-HHHHHhhCcCC-CCEEEEEcCChhh
Confidence            4578999999999999543 34455554332 3356666544443

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.

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional

Probab=93.69  E-value=0.12  Score=45.53  Aligned_cols=35  Identities=17%  Similarity=0.336  Sum_probs=22.2

Q ss_pred             EEeChHHHHHHHhcCCC----CCCCccEEEecchhhhhc
Q 022724          155 VSGTPGRVCDMIKRKTL----RTRAIKLLVLDESDEMLS  189 (293)
Q Consensus       155 lV~Tp~~l~~~l~~~~~----~~~~l~~iViDE~h~~~~  189 (293)
                      .++-|+++++.+....-    .-...+.|+|||+|.+..
T Consensus       188 ~vGEsEk~IR~~F~~A~~~a~~~~aPcVLFIDEIDA~~g  226 (413)
T PLN00020        188 NAGEPGKLIRQRYREAADIIKKKGKMSCLFINDLDAGAG  226 (413)
T ss_pred             cCCcHHHHHHHHHHHHHHHhhccCCCeEEEEehhhhcCC
Confidence            44666777664433211    124578999999998753

>PRK07414 cob(I)yrinic acid a,c-diamide adenosyltransferase; Validated

Probab=93.65  E-value=1.1  Score=35.32  Aligned_cols=52  Identities=21%  Similarity=0.449  Sum_probs=39.7

Q ss_pred             CCCccEEEecchhhhhcccc--HHHHHHHHhhCCCCccEEEEEeecChhHHHHH
Q 022724          173 TRAIKLLVLDESDEMLSRGF--KDQIYDVYRYLPPDLQVVLISATLPHEILEMT  224 (293)
Q Consensus       173 ~~~l~~iViDE~h~~~~~~~--~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~  224 (293)
                      -..++++|+||+-...+.++  ...+..+++..+...-+|+.--..|+.+.+.+
T Consensus       113 ~~~~dlvVLDEi~~Al~~gli~~eeVl~~L~~rp~~~evILTGR~~p~~Lie~A  166 (178)
T PRK07414        113 EGRYSLVVLDELSLAIQFGLIPETEVLEFLEKRPSHVDVILTGPEMPESLLAIA  166 (178)
T ss_pred             CCCCCEEEEehhHHHHHCCCccHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhC
Confidence            35678999999998887775  45677778877777777777777788776655

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.65  E-value=0.42  Score=44.21  Aligned_cols=17  Identities=35%  Similarity=0.536  Sum_probs=13.8

Q ss_pred             EEEEcCCCChhHHHHHH
Q 022724           73 VIAQAQSGTGKTSMIAL   89 (293)
Q Consensus        73 ~li~~~Tg~GKT~~~~~   89 (293)
                      +++.||.|+|||.++.+
T Consensus        41 yLf~Gp~G~GKTtlAr~   57 (486)
T PRK14953         41 YIFAGPRGTGKTTIARI   57 (486)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            57899999999966543

>TIGR00665 DnaB replicative DNA helicase

Probab=93.60  E-value=1.1  Score=40.82  Aligned_cols=140  Identities=18%  Similarity=0.142  Sum_probs=64.9

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHH----
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGED----  144 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~----  144 (293)
                      .|.-++|.|++|+|||...+--+.+.....  +..+++++.- .-..++..++..........-. ..|.....+.    
T Consensus       194 ~G~l~vi~g~pg~GKT~~~l~~a~~~a~~~--g~~vl~~SlE-m~~~~i~~R~~~~~~~v~~~~~-~~g~l~~~~~~~~~  269 (434)
T TIGR00665       194 PSDLIILAARPSMGKTAFALNIAENAAIKE--GKPVAFFSLE-MSAEQLAMRMLSSESRVDSQKL-RTGKLSDEDWEKLT  269 (434)
T ss_pred             CCeEEEEEeCCCCChHHHHHHHHHHHHHhC--CCeEEEEeCc-CCHHHHHHHHHHHhcCCCHHHh-ccCCCCHHHHHHHH
Confidence            456788999999999954333333322222  3356666543 2344554444333222211111 1121121111    


Q ss_pred             --HHHHhcCCcEEE-e----ChHHHHHHHhcCCCCCCCccEEEecchhhhhccc----cHHHHHHHHhhCC-----CCcc
Q 022724          145 --IRKLEHGVHVVS-G----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG----FKDQIYDVYRYLP-----PDLQ  208 (293)
Q Consensus       145 --~~~~~~~~~ilV-~----Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~----~~~~~~~i~~~l~-----~~~q  208 (293)
                        ...+.+ ..+.| .    |++.+...++.-... ..+++||||=.+.+....    ....+..+.+.+.     .++.
T Consensus       270 ~a~~~l~~-~~l~i~d~~~~~~~~i~~~i~~~~~~-~~~~~vvID~l~~i~~~~~~~~r~~~i~~i~~~Lk~lA~e~~i~  347 (434)
T TIGR00665       270 SAAGKLSE-APLYIDDTPGLTITELRAKARRLKRE-HGLGLIVIDYLQLMSGSGRSENRQQEVSEISRSLKALAKELNVP  347 (434)
T ss_pred             HHHHHHhc-CCEEEECCCCCCHHHHHHHHHHHHHh-cCCCEEEEcchHhcCCCCCCCCHHHHHHHHHHHHHHHHHHhCCe
Confidence              122223 23444 2    455555443321111 247899999999874222    2223333333332     3566


Q ss_pred             EEEEEe
Q 022724          209 VVLISA  214 (293)
Q Consensus       209 ~v~~SA  214 (293)
                      ++++|.
T Consensus       348 vi~lsq  353 (434)
T TIGR00665       348 VIALSQ  353 (434)
T ss_pred             EEEEec
Confidence            776664

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.

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=93.57  E-value=0.093  Score=45.36  Aligned_cols=16  Identities=25%  Similarity=0.509  Sum_probs=13.9

Q ss_pred             CcEEEEcCCCChhHHH
Q 022724           71 RDVIAQAQSGTGKTSM   86 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~   86 (293)
                      .++++.||+|+|||..
T Consensus        31 ~~~ll~Gp~G~GKT~l   46 (305)
T TIGR00635        31 DHLLLYGPPGLGKTTL   46 (305)
T ss_pred             CeEEEECCCCCCHHHH
Confidence            4799999999999944

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.

>KOG2028 consensus ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]

Probab=93.57  E-value=0.51  Score=41.43  Aligned_cols=50  Identities=20%  Similarity=0.267  Sum_probs=29.8

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA  123 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~  123 (293)
                      .++++.||.|+|||..+-+.+-.  . ....-+-|=+..+.+-+.++...+++
T Consensus       163 pSmIlWGppG~GKTtlArlia~t--s-k~~SyrfvelSAt~a~t~dvR~ife~  212 (554)
T KOG2028|consen  163 PSMILWGPPGTGKTTLARLIAST--S-KKHSYRFVELSATNAKTNDVRDIFEQ  212 (554)
T ss_pred             CceEEecCCCCchHHHHHHHHhh--c-CCCceEEEEEeccccchHHHHHHHHH
Confidence            37999999999999543322211  1 11123556666677666666665543

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=93.55  E-value=0.39  Score=44.00  Aligned_cols=18  Identities=28%  Similarity=0.460  Sum_probs=14.8

Q ss_pred             cEEEEcCCCChhHHHHHH
Q 022724           72 DVIAQAQSGTGKTSMIAL   89 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~   89 (293)
                      .+++.||.|+|||..+..
T Consensus        41 a~Lf~Gp~G~GKtt~A~~   58 (451)
T PRK06305         41 AYLFSGIRGTGKTTLARI   58 (451)
T ss_pred             EEEEEcCCCCCHHHHHHH
Confidence            478999999999966543

>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]

Probab=93.39  E-value=1.2  Score=39.27  Aligned_cols=64  Identities=16%  Similarity=0.237  Sum_probs=41.0

Q ss_pred             CCccEEEecchhhhhccc--cHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecC
Q 022724          174 RAIKLLVLDESDEMLSRG--FKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKR  238 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~--~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~  238 (293)
                      +.--++|+|-+|.+-|.+  ....+..+-..++...-.+.+|++..+... .......++..+.++.
T Consensus       114 d~~~~liLDnad~lrD~~a~ll~~l~~L~el~~~~~i~iils~~~~e~~y-~~n~g~~~i~~l~fP~  179 (438)
T KOG2543|consen  114 DQKVFLILDNADALRDMDAILLQCLFRLYELLNEPTIVIILSAPSCEKQY-LINTGTLEIVVLHFPQ  179 (438)
T ss_pred             CceEEEEEcCHHhhhccchHHHHHHHHHHHHhCCCceEEEEeccccHHHh-hcccCCCCceEEecCC
Confidence            445689999999997654  344555566666666667788888877532 2222334566666654

>PRK13695 putative NTPase; Provisional

Probab=93.29  E-value=1.3  Score=34.67  Aligned_cols=17  Identities=24%  Similarity=0.474  Sum_probs=14.2

Q ss_pred             cEEEEcCCCChhHHHHH
Q 022724           72 DVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~   88 (293)
                      .+++.|+.|+|||....
T Consensus         2 ~i~ltG~~G~GKTTll~   18 (174)
T PRK13695          2 KIGITGPPGVGKTTLVL   18 (174)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            57899999999996544

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=93.28  E-value=0.75  Score=45.02  Aligned_cols=17  Identities=24%  Similarity=0.493  Sum_probs=14.9

Q ss_pred             CcEEEEcCCCChhHHHH
Q 022724           71 RDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~   87 (293)
                      .|+++.||+|+|||...
T Consensus       204 ~n~lL~G~pG~GKT~l~  220 (731)
T TIGR02639       204 NNPLLVGEPGVGKTAIA  220 (731)
T ss_pred             CceEEECCCCCCHHHHH
Confidence            58999999999999554

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

Probab=93.23  E-value=0.086  Score=48.60  Aligned_cols=49  Identities=18%  Similarity=0.239  Sum_probs=37.2

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (293)
                      .++++.||||||||..+.+|.+-.   .+ + -+||.=|--++.......+++.
T Consensus        45 ~h~lvig~tgSGKt~~~viP~ll~---~~-~-s~iV~D~KgEl~~~t~~~r~~~   93 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNLLN---YP-G-SMIVTDPKGELYEKTAGYRKKR   93 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHHHh---cc-C-CEEEEECCCcHHHHHHHHHHHC
Confidence            479999999999999998887632   21 2 5677778888888777766554

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

>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]

Probab=93.21  E-value=0.6  Score=40.51  Aligned_cols=56  Identities=16%  Similarity=0.153  Sum_probs=40.5

Q ss_pred             CCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcC
Q 022724           53 FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (293)
Q Consensus        53 ~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P  109 (293)
                      +.--++-|..=+.++.+..-++..||-|+|||.-......+.+....- .++|.-=|
T Consensus       126 I~~kt~~Q~~y~eai~~~di~fGiGpAGTGKTyLava~av~al~~~~v-~rIiLtRP  181 (348)
T COG1702         126 IIPKTPGQNMYPEAIEEHDIVFGIGPAGTGKTYLAVAKAVDALGAGQV-RRIILTRP  181 (348)
T ss_pred             eEecChhHHHHHHHHHhcCeeeeecccccCChhhhHHhHhhhhhhccc-ceeeecCc
Confidence            445688999988888888888999999999997766666666655432 23443335

>PRK09165 replicative DNA helicase; Provisional

Probab=93.18  E-value=0.61  Score=43.36  Aligned_cols=115  Identities=17%  Similarity=0.140  Sum_probs=55.5

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccC------------CCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEE
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTS------------SREVQALILSPTRELATQTEKVILAIGDFINIQAHACV  136 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~------------~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~  136 (293)
                      .|.-++|.|++|+|||.-.+-.+.+.....            ..+..++|++. ..-..|+..++-........  ..+.
T Consensus       216 ~g~livIaarpg~GKT~~al~ia~~~a~~~~~~~~~~~~~~~~~g~~vl~fSl-EMs~~ql~~R~la~~s~v~~--~~i~  292 (497)
T PRK09165        216 PSDLIILAGRPSMGKTALATNIAFNAAKAYRREAQPDGSKKAVNGGVVGFFSL-EMSAEQLATRILSEQSEISS--SKIR  292 (497)
T ss_pred             CCceEEEEeCCCCChHHHHHHHHHHHHHhhcccccccccccccCCCeEEEEeC-cCCHHHHHHHHHHHhcCCCH--HHHh
Confidence            345688899999999954433332222111            12445666653 33345666655433222211  1111


Q ss_pred             CCcchHHHH-------HHHhcCCcEEEe-----ChHHHHHHHhcCCCCCCCccEEEecchhhhh
Q 022724          137 GGKSVGEDI-------RKLEHGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (293)
Q Consensus       137 ~~~~~~~~~-------~~~~~~~~ilV~-----Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~  188 (293)
                      .+.-...+.       ..+.+ ..+.|-     |++.+...+++-.. -..+++||||=.+.+.
T Consensus       293 ~~~l~~~e~~~l~~a~~~l~~-~~l~I~d~~~~ti~~i~~~ir~l~~-~~~~~lvvIDyLqli~  354 (497)
T PRK09165        293 RGKISEEDFEKLVDASQELQK-LPLYIDDTPALSISQLRARARRLKR-QHGLDLLVVDYLQLIR  354 (497)
T ss_pred             cCCCCHHHHHHHHHHHHHHhc-CCeEEeCCCCCCHHHHHHHHHHHHH-hcCCCEEEEcchHhcc
Confidence            121111111       12222 234443     45555544433111 1357999999999885

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=93.14  E-value=0.055  Score=44.69  Aligned_cols=14  Identities=21%  Similarity=0.729  Sum_probs=12.0

Q ss_pred             EEEEcCCCChhHHH
Q 022724           73 VIAQAQSGTGKTSM   86 (293)
Q Consensus        73 ~li~~~Tg~GKT~~   86 (293)
                      ++|.|+.|+|||..
T Consensus         1 ~vv~G~pGsGKSt~   14 (234)
T PF01443_consen    1 IVVHGVPGSGKSTL   14 (234)
T ss_pred             CEEEcCCCCCHHHH
Confidence            47899999999964

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

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=93.08  E-value=0.24  Score=46.84  Aligned_cols=45  Identities=24%  Similarity=0.377  Sum_probs=29.9

Q ss_pred             HHHCCCCCCcHHHHHHHHhhhc--CCcEEEEcCCCChhHHHHHHHHHhhhc
Q 022724           48 IYQYGFEKPSAIQQRAVMPIIK--GRDVIAQAQSGTGKTSMIALTVCQTVD   96 (293)
Q Consensus        48 l~~~~~~~~~~~Q~~~~~~i~~--~~~~li~~~Tg~GKT~~~~~~~~~~l~   96 (293)
                      +.++|+   .+.|.+.+..+..  +..++++||||||||... ..++..+.
T Consensus       295 l~~lg~---~~~~~~~l~~~~~~~~Glilv~G~tGSGKTTtl-~a~l~~~~  341 (564)
T TIGR02538       295 IDKLGF---EPDQKALFLEAIHKPQGMVLVTGPTGSGKTVSL-YTALNILN  341 (564)
T ss_pred             HHHcCC---CHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHH-HHHHHhhC
Confidence            455664   4566666666543  456889999999999653 34556554

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.

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=93.06  E-value=0.11  Score=44.08  Aligned_cols=26  Identities=31%  Similarity=0.404  Sum_probs=20.3

Q ss_pred             HHHhhhcCCcEEEEcCCCChhHHHHH
Q 022724           63 AVMPIIKGRDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        63 ~~~~i~~~~~~li~~~Tg~GKT~~~~   88 (293)
                      +...+..|+++++.||+|+|||..+.
T Consensus        14 ~l~~l~~g~~vLL~G~~GtGKT~lA~   39 (262)
T TIGR02640        14 ALRYLKSGYPVHLRGPAGTGKTTLAM   39 (262)
T ss_pred             HHHHHhcCCeEEEEcCCCCCHHHHHH
Confidence            33445578999999999999996654

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).

>KOG0732 consensus AAA+-type ATPase containing the bromodomain [Posttranslational modification, protein turnover, chaperones]

Probab=93.04  E-value=0.28  Score=48.74  Aligned_cols=143  Identities=17%  Similarity=0.189  Sum_probs=77.6

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCC-CCcHHHHHHHH-hhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEc
Q 022724           31 AITSFDAMGIKDDLLRGIYQYGFE-KPSAIQQRAVM-PIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (293)
Q Consensus        31 ~~~~f~~~~l~~~i~~~l~~~~~~-~~~~~Q~~~~~-~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~  108 (293)
                      ....|++.|....+.+-|+++-.. -.+|-+.+  + .+..-+.++++||.|+|||+.+-.-+ ........  ++-+  
T Consensus       260 ~~v~fd~vggl~~~i~~LKEmVl~PLlyPE~f~--~~~itpPrgvL~~GppGTGkTl~araLa-~~~s~~~~--kisf--  332 (1080)
T KOG0732|consen  260 SSVGFDSVGGLENYINQLKEMVLLPLLYPEFFD--NFNITPPRGVLFHGPPGTGKTLMARALA-AACSRGNR--KISF--  332 (1080)
T ss_pred             cccCccccccHHHHHHHHHHHHHhHhhhhhHhh--hcccCCCcceeecCCCCCchhHHHHhhh-hhhccccc--ccch--
Confidence            345789998888888888887432 22221111  1 13345779999999999996532111 11111000  0000  


Q ss_pred             CCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhh
Q 022724          109 PTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (293)
Q Consensus       109 P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~  188 (293)
                                 ..++     |                   ...-..-|+.+++=++++.... .-.....+-+||+|-+.
T Consensus       333 -----------fmrk-----g-------------------aD~lskwvgEaERqlrllFeeA-~k~qPSIIffdeIdGla  376 (1080)
T KOG0732|consen  333 -----------FMRK-----G-------------------ADCLSKWVGEAERQLRLLFEEA-QKTQPSIIFFDEIDGLA  376 (1080)
T ss_pred             -----------hhhc-----C-------------------chhhccccCcHHHHHHHHHHHH-hccCceEEecccccccc
Confidence                       0000     0                   0011345677776666654421 12445778899999542


Q ss_pred             cc----------ccHHHHHHHHhhCCCCccEEEEEeec
Q 022724          189 SR----------GFKDQIYDVYRYLPPDLQVVLISATL  216 (293)
Q Consensus       189 ~~----------~~~~~~~~i~~~l~~~~q~v~~SAt~  216 (293)
                      -.          .....+..+..-+....|+++++||-
T Consensus       377 pvrSskqEqih~SIvSTLLaLmdGldsRgqVvvigATn  414 (1080)
T KOG0732|consen  377 PVRSSKQEQIHASIVSTLLALMDGLDSRGQVVVIGATN  414 (1080)
T ss_pred             ccccchHHHhhhhHHHHHHHhccCCCCCCceEEEcccC
Confidence            11          12233344444556789999999996

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=92.99  E-value=0.36  Score=45.32  Aligned_cols=55  Identities=24%  Similarity=0.337  Sum_probs=34.4

Q ss_pred             ccccCcccCCCCHHHHHHHHHC---CCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHH
Q 022724           30 EAITSFDAMGIKDDLLRGIYQY---GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        30 ~~~~~f~~~~l~~~i~~~l~~~---~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~   87 (293)
                      .+-.+|++.|=-+++...|++.   ...+|-.+....   +..-+.+++.||.|+|||+.+
T Consensus       428 ~p~v~W~dIGGlE~lK~elq~~V~~p~~~pe~F~r~G---i~ppkGVLlyGPPGC~KT~lA  485 (693)
T KOG0730|consen  428 MPNVSWDDIGGLEELKRELQQAVEWPLKHPEKFARFG---ISPPKGVLLYGPPGCGKTLLA  485 (693)
T ss_pred             CCCCChhhccCHHHHHHHHHHHHhhhhhchHHHHHhc---CCCCceEEEECCCCcchHHHH
Confidence            3456788887556666666542   222333332222   234478999999999999654

>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]

Probab=92.96  E-value=0.19  Score=51.42  Aligned_cols=55  Identities=25%  Similarity=0.320  Sum_probs=45.3

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccC--CCceeEEEEcCCHHHHHHHHHHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTS--SREVQALILSPTRELATQTEKVILA  123 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~--~~~~~~lil~P~~~l~~q~~~~~~~  123 (293)
                      .+++++|.|..|||||.+..--++..+...  -.-.++++++-|++-+.++..++..
T Consensus        15 ~~~~~lveASAGSGKT~vL~~r~lrlLl~~~~~~v~~ILvvTFT~aAa~Emk~RI~~   71 (1139)
T COG1074          15 PGQSVLVEASAGTGKTFVLAERVLRLLLEGGPLDVDEILVVTFTKAAAAEMKERIRD   71 (1139)
T ss_pred             CCCcEEEEEcCCCCchhHHHHHHHHHHhhcCCCChhHeeeeeccHHHHHHHHHHHHH
Confidence            567999999999999988777777777663  2335899999999999999888864

>PRK10689 transcription-repair coupling factor; Provisional

Probab=92.95  E-value=0.56  Score=48.03  Aligned_cols=79  Identities=13%  Similarity=0.130  Sum_probs=60.4

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHHhcCCCCCCCc
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l~~~~~~~~~l  176 (293)
                      +.+++|++|+++-+..+.+.+++...  +.++..+||+.+..+..+.+    ....+|+|+|.     .+ ...+++.++
T Consensus       809 ~gqv~vf~n~i~~ie~la~~L~~~~p--~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaTd-----Ii-erGIDIP~v  880 (1147)
T PRK10689        809 GGQVYYLYNDVENIQKAAERLAELVP--EARIAIGHGQMRERELERVMNDFHHQRFNVLVCTT-----II-ETGIDIPTA  880 (1147)
T ss_pred             CCeEEEEECCHHHHHHHHHHHHHhCC--CCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEECc-----hh-hcccccccC
Confidence            45899999999988888888887643  46788899998776544333    25679999995     22 236889999


Q ss_pred             cEEEecchhhh
Q 022724          177 KLLVLDESDEM  187 (293)
Q Consensus       177 ~~iViDE~h~~  187 (293)
                      +++|++.+|++
T Consensus       881 ~~VIi~~ad~f  891 (1147)
T PRK10689        881 NTIIIERADHF  891 (1147)
T ss_pred             CEEEEecCCCC
Confidence            99999998864

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=92.93  E-value=0.17  Score=42.01  Aligned_cols=36  Identities=17%  Similarity=0.310  Sum_probs=23.9

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcC
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P  109 (293)
                      -.++|+|++||||| .++.-++..+...-  ..+++++|
T Consensus        14 fr~viIG~sGSGKT-~li~~lL~~~~~~f--~~I~l~t~   49 (241)
T PF04665_consen   14 FRMVIIGKSGSGKT-TLIKSLLYYLRHKF--DHIFLITP   49 (241)
T ss_pred             ceEEEECCCCCCHH-HHHHHHHHhhcccC--CEEEEEec
Confidence            37999999999999 44555555544432  34555566

This is thought to be an ATPase involved in viral DNA packaging [].

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=92.92  E-value=1.6  Score=43.36  Aligned_cols=17  Identities=29%  Similarity=0.618  Sum_probs=14.8

Q ss_pred             CcEEEEcCCCChhHHHH
Q 022724           71 RDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~   87 (293)
                      .|.++.||.|+|||...
T Consensus       209 ~n~lLvG~pGvGKTal~  225 (852)
T TIGR03345       209 NNPILTGEAGVGKTAVV  225 (852)
T ss_pred             CceeEECCCCCCHHHHH
Confidence            58999999999999544

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.

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

Probab=92.88  E-value=0.71  Score=42.59  Aligned_cols=83  Identities=18%  Similarity=0.181  Sum_probs=59.7

Q ss_pred             HHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHh----cCCcEEEeChHHHH
Q 022724           88 ALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVC  163 (293)
Q Consensus        88 ~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~ilV~Tp~~l~  163 (293)
                      +..++..+. ...+.++||.|.|+--|+++...++..    +.++..+||+.+..+....+.    ..+.|+|+|.    
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            444555555 334568999999999999999877653    367889999987766655553    4578999995    


Q ss_pred             HHHhcCCCCCCCccEEEe
Q 022724          164 DMIKRKTLRTRAIKLLVL  181 (293)
Q Consensus       164 ~~l~~~~~~~~~l~~iVi  181 (293)
                        +..+.+++.+++++|-
T Consensus       400 --VAaRGLDi~dV~lVIn  415 (519)
T KOG0331|consen  400 --VAARGLDVPDVDLVIN  415 (519)
T ss_pred             --cccccCCCccccEEEe
Confidence              2334677888888764

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=92.87  E-value=0.41  Score=40.80  Aligned_cols=51  Identities=22%  Similarity=0.354  Sum_probs=32.7

Q ss_pred             ccEEEecchhhhhccccHHHHHHHHhhCC-------CCccEEEEEeecChhHHHHHHhc
Q 022724          176 IKLLVLDESDEMLSRGFKDQIYDVYRYLP-------PDLQVVLISATLPHEILEMTTKF  227 (293)
Q Consensus       176 l~~iViDE~h~~~~~~~~~~~~~i~~~l~-------~~~q~v~~SAt~~~~~~~~~~~~  227 (293)
                      =.++|+||+|.|. .+..+.+.-++.+.+       .+.=+|++|-+-...+.+.....
T Consensus       179 rslFIFDE~DKmp-~gLld~lkpfLdyyp~v~gv~frkaIFIfLSN~gg~eI~~~aL~~  236 (344)
T KOG2170|consen  179 RSLFIFDEVDKLP-PGLLDVLKPFLDYYPQVSGVDFRKAIFIFLSNAGGSEIARIALEN  236 (344)
T ss_pred             CceEEechhhhcC-HhHHHHHhhhhccccccccccccceEEEEEcCCcchHHHHHHHHH
Confidence            3689999999984 344445555555432       23458899988777666555443

>TIGR03375 type_I_sec_LssB type I secretion system ATPase, LssB family

Probab=92.81  E-value=0.073  Score=51.65  Aligned_cols=41  Identities=20%  Similarity=0.306  Sum_probs=28.5

Q ss_pred             CCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       173 ~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      +++-+++|+||+-.-+|......+...+..+.+++.++..|
T Consensus       617 l~~p~iliLDE~Ts~LD~~te~~i~~~l~~~~~~~T~iiIt  657 (694)
T TIGR03375       617 LRDPPILLLDEPTSAMDNRSEERFKDRLKRWLAGKTLVLVT  657 (694)
T ss_pred             hcCCCEEEEeCCCCCCCHHHHHHHHHHHHHHhCCCEEEEEe
Confidence            36678999999987777766666766666665455555544

Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. This model is related to models TIGR01842 and TIGR01846, and to bacteriocin ABC transporters that cleave their substrates during export.

>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=92.75  E-value=0.58  Score=41.86  Aligned_cols=39  Identities=15%  Similarity=0.229  Sum_probs=27.2

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccC-CCceeEEEEcC
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTS-SREVQALILSP  109 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~-~~~~~~lil~P  109 (293)
                      .|.++++.|+||+||++.+.  .++.+... ..+|.+-|=|-
T Consensus       100 ~~~~vLi~GetGtGKel~A~--~iH~~s~r~~~~PFI~~NCa  139 (403)
T COG1221         100 SGLPVLIIGETGTGKELFAR--LIHALSARRAEAPFIAFNCA  139 (403)
T ss_pred             CCCcEEEecCCCccHHHHHH--HHHHhhhcccCCCEEEEEHH
Confidence            67899999999999997654  33444444 45666666553

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=92.72  E-value=0.38  Score=38.37  Aligned_cols=58  Identities=17%  Similarity=0.216  Sum_probs=34.7

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhcc-------CCCceeEEEEcCCHHHHHHHHHHHHHhhcc
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDT-------SSREVQALILSPTRELATQTEKVILAIGDF  127 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~-------~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (293)
                      .|.-+++.||+|+|||...+-.+......       ...+.+++++..-.. ..++.+++..+...
T Consensus        31 ~g~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~-~~~~~~rl~~~~~~   95 (193)
T PF13481_consen   31 RGELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS-ESQIARRLRALLQD   95 (193)
T ss_dssp             TTSEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS--HHHHHHHHHHHHTT
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC-HHHHHHHHHHHhcc
Confidence            56779999999999996544333333321       113457777776555 66777888776543

>TIGR03743 SXT_TraD conjugative coupling factor TraD, SXT/TOL subfamily

Probab=92.71  E-value=0.28  Score=46.86  Aligned_cols=53  Identities=17%  Similarity=0.309  Sum_probs=37.0

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCH--HHHHHHHHHHHHhh
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR--ELATQTEKVILAIG  125 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~--~l~~q~~~~~~~~~  125 (293)
                      ..|++|.|+||+|||..+.+.+.+.+..   +..++++=|--  ++...+...++..+
T Consensus       176 ~~H~lv~G~TGsGKT~l~~~l~~q~i~~---g~~viv~DpKgD~~l~~~~~~~~~~~G  230 (634)
T TIGR03743       176 VGHTLVLGTTGVGKTRLAELLITQDIRR---GDVVIVIDPKGDADLKRRMRAEAKRAG  230 (634)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEeCCCchHHHHHHHHHHHHhC
Confidence            3689999999999997775555555543   33566666764  47777777776654

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.

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=92.66  E-value=0.18  Score=49.76  Aligned_cols=83  Identities=13%  Similarity=0.098  Sum_probs=51.9

Q ss_pred             ccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHhhC--CCCcEEEEcccchh
Q 022724          207 LQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL--TITQAVIFCNTKRK  284 (293)
Q Consensus       207 ~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~--~~~~~iIF~~s~~~  284 (293)
                      .++-+||.|......++..-|-.+...+-.. ......+... .++.... .|...+...+...  .+.|+||||+|++.
T Consensus       534 ~kLaGMTGTA~te~~Ef~~iY~L~Vv~IPTn-rP~~R~D~~d-~vy~t~~-eK~~Ali~~I~~~~~~grpVLIft~Sve~  610 (1025)
T PRK12900        534 KKLAGMTGTAETEASEFFEIYKLDVVVIPTN-KPIVRKDMDD-LVYKTRR-EKYNAIVLKVEELQKKGQPVLVGTASVEV  610 (1025)
T ss_pred             hhhcccCCCChhHHHHHHHHhCCcEEECCCC-CCcceecCCC-eEecCHH-HHHHHHHHHHHHHhhCCCCEEEEeCcHHH
Confidence            4688999998777666765554333222221 1111111121 2223333 4888888888543  56799999999999


Q ss_pred             HHHHHhhC
Q 022724          285 VLLLVLQF  292 (293)
Q Consensus       285 a~~l~~~L  292 (293)
                      ++.+++.|
T Consensus       611 sE~Ls~~L  618 (1025)
T PRK12900        611 SETLSRML  618 (1025)
T ss_pred             HHHHHHHH
Confidence            99999876

>KOG1806 consensus DEAD box containing helicases [Replication, recombination and repair]

Probab=92.66  E-value=0.22  Score=48.88  Aligned_cols=72  Identities=19%  Similarity=0.230  Sum_probs=55.4

Q ss_pred             CCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 022724           52 GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (293)
Q Consensus        52 ~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (293)
                      ++-.++|-|-+++-.-.+...+.++||+|+|||-... -++..+...-...+++|++.+..-.+|..+.+.++
T Consensus       735 n~v~ft~~qveai~sg~qpgltmvvgppgtgktd~av-qil~~lyhn~p~qrTlivthsnqaln~lfeKi~~~  806 (1320)
T KOG1806|consen  735 NQVKFTPTQVEAILSGMQPGLTMVVGPPGTGKTDVAV-QILSVLYHNSPNQRTLIVTHSNQALNQLFEKIMAL  806 (1320)
T ss_pred             chhccCHHHHHHHHhcCCCCceeeecCCCCCCcchhh-hhhhhhhhcCCCcceEEEEecccchhHHHHHHHhc
Confidence            4456788999888877778899999999999995543 34444444444579999999999999998877654

>TIGR02203 MsbA_lipidA lipid A export permease/ATP-binding protein MsbA

Probab=92.64  E-value=0.18  Score=47.70  Aligned_cols=41  Identities=17%  Similarity=0.252  Sum_probs=28.4

Q ss_pred             CCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       173 ~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      +++-+.+++||.-.-+|......+...+....++.-+|..|
T Consensus       485 l~~~~illLDEpts~LD~~~~~~i~~~L~~~~~~~tiIiit  525 (571)
T TIGR02203       485 LKDAPILILDEATSALDNESERLVQAALERLMQGRTTLVIA  525 (571)
T ss_pred             hcCCCEEEEeCccccCCHHHHHHHHHHHHHHhCCCEEEEEe
Confidence            35668899999988888777777776666664454455443

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=92.64  E-value=1.5  Score=38.14  Aligned_cols=58  Identities=12%  Similarity=0.227  Sum_probs=31.9

Q ss_pred             EEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEe
Q 022724          154 VVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (293)
Q Consensus       154 ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SA  214 (293)
                      |-|-....+.+.+....+ ....+++|||++|.|.... ...+...+..-+ +..+|+++.
T Consensus       104 I~id~ir~i~~~l~~~p~-~~~~kVvII~~ae~m~~~a-aNaLLK~LEEPp-~~~fILi~~  161 (314)
T PRK07399        104 IRLEQIREIKRFLSRPPL-EAPRKVVVIEDAETMNEAA-ANALLKTLEEPG-NGTLILIAP  161 (314)
T ss_pred             CcHHHHHHHHHHHccCcc-cCCceEEEEEchhhcCHHH-HHHHHHHHhCCC-CCeEEEEEC
Confidence            333334445454444333 3578999999999985433 233344444444 555555544

>cd03239 ABC_SMC_head The structural maintenance of chromosomes (SMC) proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms

Probab=92.64  E-value=0.18  Score=40.01  Aligned_cols=41  Identities=22%  Similarity=0.351  Sum_probs=27.6

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCC-CccEEEEEe
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP-DLQVVLISA  214 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~-~~q~v~~SA  214 (293)
                      .+.+++++||...-++......+..++..+.. ..++++.|-
T Consensus       115 ~~p~llilDEp~~~LD~~~~~~i~~~L~~~~~~g~tiIiiSH  156 (178)
T cd03239         115 KPSPFYVLDEIDAALDPTNRRRVSDMIKEMAKHTSQFIVITL  156 (178)
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHHHHHHhCCCEEEEEEC
Confidence            56789999999988877666666555555433 355655543

SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and each has five distinct domains: amino- and carboxy-terminal globular domains, which contain sequences characteristic of ATPases, two coiled-coil regions separating the terminal domains , and a central flexible hinge. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair, and epigenetic silencing of gene expression.

>KOG2004 consensus Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]

Probab=92.62  E-value=0.86  Score=43.52  Aligned_cols=110  Identities=21%  Similarity=0.327  Sum_probs=63.0

Q ss_pred             CcHHHHHHHHhhh--------cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcc
Q 022724           56 PSAIQQRAVMPII--------KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDF  127 (293)
Q Consensus        56 ~~~~Q~~~~~~i~--------~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (293)
                      ...+-.++++.+.        +|+-+.++||+|.|||.+.                           ..+.+.+.+  ++
T Consensus       416 m~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~---------------------------kSIA~ALnR--kF  466 (906)
T KOG2004|consen  416 MEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIA---------------------------KSIARALNR--KF  466 (906)
T ss_pred             hHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHH---------------------------HHHHHHhCC--ce
Confidence            4455555665543        4677899999999999432                           222222211  01


Q ss_pred             CCceEEEEECCcchHHHHHHHhcCCcEEEe-ChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCC
Q 022724          128 INIQAHACVGGKSVGEDIRKLEHGVHVVSG-TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP  204 (293)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~-Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~  204 (293)
                          .....||..-..+   ++...+-+|| -|+++.+.|+.-....   -++.|||+|.+.....++--..++..+.
T Consensus       467 ----fRfSvGG~tDvAe---IkGHRRTYVGAMPGkiIq~LK~v~t~N---PliLiDEvDKlG~g~qGDPasALLElLD  534 (906)
T KOG2004|consen  467 ----FRFSVGGMTDVAE---IKGHRRTYVGAMPGKIIQCLKKVKTEN---PLILIDEVDKLGSGHQGDPASALLELLD  534 (906)
T ss_pred             ----EEEeccccccHHh---hcccceeeeccCChHHHHHHHhhCCCC---ceEEeehhhhhCCCCCCChHHHHHHhcC
Confidence                1123345433322   3333345555 6999999998743222   3789999999974444555555555553

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.59  E-value=1.2  Score=39.59  Aligned_cols=18  Identities=22%  Similarity=0.359  Sum_probs=14.7

Q ss_pred             CcEEEEcCCCChhHHHHH
Q 022724           71 RDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~   88 (293)
                      +.+++.||.|+|||....
T Consensus        40 ~~~L~~G~~G~GKt~~a~   57 (367)
T PRK14970         40 QALLFCGPRGVGKTTCAR   57 (367)
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            368999999999995544

>PRK05595 replicative DNA helicase; Provisional

Probab=92.58  E-value=1.3  Score=40.59  Aligned_cols=114  Identities=15%  Similarity=0.185  Sum_probs=52.8

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  148 (293)
                      .|.-++|.|.||+|||... +-+...+... .+.+++++..- .-..|+..++-.......  ...+..+.-...+...+
T Consensus       200 ~g~liviaarpg~GKT~~a-l~ia~~~a~~-~g~~vl~fSlE-ms~~~l~~R~~a~~~~v~--~~~~~~~~l~~~e~~~~  274 (444)
T PRK05595        200 KGDMILIAARPSMGKTTFA-LNIAEYAALR-EGKSVAIFSLE-MSKEQLAYKLLCSEANVD--MLRLRTGNLEDKDWENI  274 (444)
T ss_pred             CCcEEEEEecCCCChHHHH-HHHHHHHHHH-cCCcEEEEecC-CCHHHHHHHHHHHhcCCC--HHHHhcCCCCHHHHHHH
Confidence            3456788899999999443 3333332211 13456666543 234455554433222221  11111111111111111


Q ss_pred             h------cCCcEEEe-----ChHHHHHHHhcCCCCCCCccEEEecchhhhh
Q 022724          149 E------HGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (293)
Q Consensus       149 ~------~~~~ilV~-----Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~  188 (293)
                      .      ....+.|-     |++.+...++.-.. -..+++||||=.+.+.
T Consensus       275 ~~~~~~l~~~~l~i~d~~~~t~~~i~~~~r~~~~-~~~~~~vvIDylql~~  324 (444)
T PRK05595        275 ARASGPLAAAKIFIDDTAGVSVMEMRSKCRRLKI-EHGIDMILIDYLQLMS  324 (444)
T ss_pred             HHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHH-hcCCCEEEEeHHHhcc
Confidence            1      11234332     34444443333111 1347899999999985

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=92.57  E-value=1.1  Score=43.47  Aligned_cols=16  Identities=25%  Similarity=0.468  Sum_probs=13.9

Q ss_pred             cEEEEcCCCChhHHHH
Q 022724           72 DVIAQAQSGTGKTSMI   87 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~   87 (293)
                      ++++.||||.|||..+
T Consensus       523 sFlF~GPTGVGKTELA  538 (786)
T COG0542         523 SFLFLGPTGVGKTELA  538 (786)
T ss_pred             EEEeeCCCcccHHHHH
Confidence            7899999999999544

>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=92.54  E-value=0.091  Score=44.71  Aligned_cols=20  Identities=50%  Similarity=0.747  Sum_probs=17.1

Q ss_pred             hhcCCcEEEEcCCCChhHHH
Q 022724           67 IIKGRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~~   86 (293)
                      +..+++++++||+|+|||..
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            34678999999999999954

>KOG1513 consensus Nuclear helicase MOP-3/SNO (DEAD-box superfamily) [Transcription; Signal transduction mechanisms]

Probab=92.54  E-value=0.2  Score=47.92  Aligned_cols=155  Identities=23%  Similarity=0.202  Sum_probs=91.5

Q ss_pred             CCcHHHHHHHHhhh--------cCC--cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 022724           55 KPSAIQQRAVMPII--------KGR--DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~--------~~~--~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (293)
                      .++..|.+++-...        +|.  .++|--..|.||--...-.|++...+.  ..++|.+.-+..|--+..+.++.+
T Consensus       264 ~lSALQLEav~YAcQ~He~llPsG~RaGfLiGDGAGVGKGRTvAgiIfeNyLkG--RKrAlW~SVSsDLKfDAERDL~Di  341 (1300)
T KOG1513|consen  264 HLSALQLEAVTYACQAHEVLLPSGQRAGFLIGDGAGVGKGRTVAGIIFENYLKG--RKRALWFSVSSDLKFDAERDLRDI  341 (1300)
T ss_pred             chhHHHHHHHHHHHhhhhhcCCCCccceeeeccCcccCCCceeEEEEehhhhcc--cceeEEEEeccccccchhhchhhc
Confidence            57778887775433        232  456665556665533333355555554  348999999999988888888877


Q ss_pred             hccCCceEEEEECC----cchHHHHHHHhcCCcEEEeChHHHHHHHhc--CC-----------CCCCCccEEEecchhhh
Q 022724          125 GDFINIQAHACVGG----KSVGEDIRKLEHGVHVVSGTPGRVCDMIKR--KT-----------LRTRAIKLLVLDESDEM  187 (293)
Q Consensus       125 ~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~--~~-----------~~~~~l~~iViDE~h~~  187 (293)
                      +. +++.|..+..-    .+.++.   -.-.-.|+++|...|.---..  +.           +--..=.+||+||+|..
T Consensus       342 gA-~~I~V~alnK~KYakIss~en---~n~krGViFaTYtaLIGEs~~~~~kyrtR~rQllqW~Ge~feGvIvfDECHkA  417 (1300)
T KOG1513|consen  342 GA-TGIAVHALNKFKYAKISSKEN---TNTKRGVIFATYTALIGESQGKGGKYRTRFRQLLQWCGEDFEGVIVFDECHKA  417 (1300)
T ss_pred             CC-CCccceehhhccccccccccc---CCccceeEEEeeHhhhhhccccCchHHHHHHHHHHHhhhccceeEEehhhhhh
Confidence            53 34555443311    000000   001126899998766532211  00           00122378999999996


Q ss_pred             hcc---------ccHHHHHHHHhhCCCCccEEEEEeec
Q 022724          188 LSR---------GFKDQIYDVYRYLPPDLQVVLISATL  216 (293)
Q Consensus       188 ~~~---------~~~~~~~~i~~~l~~~~q~v~~SAt~  216 (293)
                      -..         ..+.-+..+.+.++ +.++|.-|||=
T Consensus       418 KNL~p~~~~k~TKtG~tVLdLQk~LP-~ARVVYASATG  454 (1300)
T KOG1513|consen  418 KNLVPTAGAKSTKTGKTVLDLQKKLP-NARVVYASATG  454 (1300)
T ss_pred             cccccccCCCcCcccHhHHHHHHhCC-CceEEEeeccC
Confidence            321         24566667777775 78999999994

>TIGR02204 MsbA_rel ABC transporter, permease/ATP-binding protein

Probab=92.53  E-value=0.16  Score=48.08  Aligned_cols=41  Identities=17%  Similarity=0.262  Sum_probs=26.9

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEe
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SA  214 (293)
                      ++-+.+++||+-.-+|......+...+..+.++..+|..|-
T Consensus       493 ~~~~ililDEpts~lD~~~~~~i~~~l~~~~~~~t~IiitH  533 (576)
T TIGR02204       493 KDAPILLLDEATSALDAESEQLVQQALETLMKGRTTLIIAH  533 (576)
T ss_pred             hCCCeEEEeCcccccCHHHHHHHHHHHHHHhCCCEEEEEec
Confidence            56688999999887777666666555555544444554443

This protein is related to a Proteobacterial ATP transporter that exports lipid A and to eukaryotic P-glycoproteins.

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=92.50  E-value=0.12  Score=33.00  Aligned_cols=19  Identities=21%  Similarity=0.629  Sum_probs=15.6

Q ss_pred             cCCcEEEEcCCCChhHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~   87 (293)
                      .|+.+++.+++|+|||..+
T Consensus        22 ~g~~tli~G~nGsGKSTll   40 (62)
T PF13555_consen   22 RGDVTLITGPNGSGKSTLL   40 (62)
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            3557999999999999543

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=92.49  E-value=0.76  Score=36.00  Aligned_cols=41  Identities=27%  Similarity=0.384  Sum_probs=28.8

Q ss_pred             CCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEe
Q 022724          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (293)
Q Consensus       173 ~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SA  214 (293)
                      ..+.+++++||.-.-+|......+..++..+... ..++++.
T Consensus       112 ~~~p~llllDEP~~gLD~~~~~~l~~~l~~~~~~-~tii~~s  152 (171)
T cd03228         112 LRDPPILILDEATSALDPETEALILEALRALAKG-KTVIVIA  152 (171)
T ss_pred             hcCCCEEEEECCCcCCCHHHHHHHHHHHHHhcCC-CEEEEEe
Confidence            3567899999998777777677777777766544 4444543

They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=92.44  E-value=1.7  Score=36.10  Aligned_cols=55  Identities=18%  Similarity=0.151  Sum_probs=31.1

Q ss_pred             cEEEEcCCCChhHHHHHHHHHhhhc---------cCCCceeEEEEcCCHHHHHHHHHHHHHhhcc
Q 022724           72 DVIAQAQSGTGKTSMIALTVCQTVD---------TSSREVQALILSPTRELATQTEKVILAIGDF  127 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~~~~~~l~---------~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (293)
                      -.++.||.|+|||+..+-.++....         ....+.+++|+.--. -..++.+++..+...
T Consensus         3 ~~ll~g~~G~GKS~lal~la~~va~G~~~~g~~~~~~~~~~Vlyi~~Ed-~~~~i~~Rl~~i~~~   66 (239)
T cd01125           3 VSALVAPGGTGKSSLLLVLALAMALGKNLFGGGLKVTEPGRVVYLSAED-PREEIHRRLEAILQH   66 (239)
T ss_pred             eeEEEcCCCCCHHHHHHHHHHHHhcCccccCCccccCCCceEEEEECCC-CHHHHHHHHHHHHhh
Confidence            3689999999999665544433211         112345788887322 223455555555443

RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.

>PHA02535 P terminase ATPase subunit; Provisional

Probab=92.43  E-value=1.8  Score=40.69  Aligned_cols=86  Identities=14%  Similarity=0.065  Sum_probs=61.2

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHH
Q 022724           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (293)
Q Consensus        40 l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~  119 (293)
                      +++.....|.+.....+.++|+..+..=...+.-++.-.=-.|||+.|..-++......  |...++|.|+++.+....+
T Consensus       123 ~s~~~~~~l~~~~~~~l~~YQ~~W~~~~~~~r~r~ilKSRQiG~T~~fA~EA~~dal~~--G~nqiflSas~~QA~~f~~  200 (581)
T PHA02535        123 ISDEQTEKLIEAFLDSLFDYQKHWYRAGLHHRTRNILKSRQIGATYYFAREALEDALLT--GRNQIFLSASKAQAHVFKQ  200 (581)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHhCccccceeeEeeecccchHHHHHHHHHHHHHhc--CCceEEECCCHHHHHHHHH
Confidence            56667777776555689999999886522234445555566799998876665544442  4578999999999999888


Q ss_pred             HHHHhhcc
Q 022724          120 VILAIGDF  127 (293)
Q Consensus       120 ~~~~~~~~  127 (293)
                      .+..+.+.
T Consensus       201 yi~~~a~~  208 (581)
T PHA02535        201 YIIAFARE  208 (581)
T ss_pred             HHHHHHHh
Confidence            88777543

>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=92.41  E-value=0.6  Score=41.63  Aligned_cols=16  Identities=38%  Similarity=0.648  Sum_probs=14.5

Q ss_pred             CcEEEEcCCCChhHHH
Q 022724           71 RDVIAQAQSGTGKTSM   86 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~   86 (293)
                      +|+++-||+|+|||+.
T Consensus       385 RNilfyGPPGTGKTm~  400 (630)
T KOG0742|consen  385 RNILFYGPPGTGKTMF  400 (630)
T ss_pred             hheeeeCCCCCCchHH
Confidence            6999999999999954

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=92.34  E-value=1.5  Score=34.47  Aligned_cols=39  Identities=15%  Similarity=0.165  Sum_probs=26.9

Q ss_pred             CCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEE
Q 022724          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLI  212 (293)
Q Consensus       173 ~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~  212 (293)
                      ..+.+++++||.-.-+|......+..++..+... ..+++
T Consensus       114 ~~~p~~lllDEP~~~LD~~~~~~l~~~l~~~~~~-~tii~  152 (178)
T cd03247         114 LQDAPIVLLDEPTVGLDPITERQLLSLIFEVLKD-KTLIW  152 (178)
T ss_pred             hcCCCEEEEECCcccCCHHHHHHHHHHHHHHcCC-CEEEE
Confidence            3667899999998877776666666666666443 34444

The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=92.34  E-value=0.84  Score=39.79  Aligned_cols=54  Identities=19%  Similarity=0.449  Sum_probs=28.6

Q ss_pred             CCccEEEecchhhhhcc-ccHHHHHHHHhhC------CCCccEEEEEeecChhHHHHHHhc
Q 022724          174 RAIKLLVLDESDEMLSR-GFKDQIYDVYRYL------PPDLQVVLISATLPHEILEMTTKF  227 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~-~~~~~~~~i~~~l------~~~~q~v~~SAt~~~~~~~~~~~~  227 (293)
                      .+.++||||=+-.+... .....+..+.+..      .+.-.++.++||...+....+..+
T Consensus       195 ~~~D~ViIDTaGr~~~~~~l~~eL~~~~~v~~~~~~~~p~~~~LVl~a~~g~~~~~~a~~f  255 (318)
T PRK10416        195 RGIDVLIIDTAGRLHNKTNLMEELKKIKRVIKKADPDAPHEVLLVLDATTGQNALSQAKAF  255 (318)
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHHHHHHhhhcCCCCceEEEEEECCCChHHHHHHHHH
Confidence            45678888877654322 2233444443322      233457888888765433334433

>PF14516 AAA_35: AAA-like domain

Probab=92.31  E-value=1.5  Score=38.52  Aligned_cols=49  Identities=18%  Similarity=0.312  Sum_probs=36.5

Q ss_pred             cHHHHHHHHhhhc-CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEc
Q 022724           57 SAIQQRAVMPIIK-GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (293)
Q Consensus        57 ~~~Q~~~~~~i~~-~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~  108 (293)
                      .|..++++..+.+ |..+.|.||-.+|||. .+..+.+.+...  +-+++++-
T Consensus        17 ~~~e~~~~~~i~~~G~~~~I~apRq~GKTS-ll~~l~~~l~~~--~~~~v~id   66 (331)
T PF14516_consen   17 PPAEQECYQEIVQPGSYIRIKAPRQMGKTS-LLLRLLERLQQQ--GYRCVYID   66 (331)
T ss_pred             hHHHHHHHHHHhcCCCEEEEECcccCCHHH-HHHHHHHHHHHC--CCEEEEEE
Confidence            3589999999987 9999999999999994 455566666554  34555543

>PF06733 DEAD_2: DEAD_2; InterPro: IPR010614 This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin

Probab=92.29  E-value=0.097  Score=41.28  Aligned_cols=45  Identities=20%  Similarity=0.262  Sum_probs=27.5

Q ss_pred             HHHhcCCcEEEeChHHHHHHHhcCCC--CCCCccEEEecchhhhhcc
Q 022724          146 RKLEHGVHVVSGTPGRVCDMIKRKTL--RTRAIKLLVLDESDEMLSR  190 (293)
Q Consensus       146 ~~~~~~~~ilV~Tp~~l~~~l~~~~~--~~~~l~~iViDE~h~~~~~  190 (293)
                      +.....++|+|++...++.-.....+  ...+-.+|||||||.+.+.
T Consensus       114 r~~~~~adivi~~y~yl~~~~~~~~~~~~~~~~~ivI~DEAHNL~~~  160 (174)
T PF06733_consen  114 RELAKNADIVICNYNYLFDPSIRKSLFGIDLKDNIVIFDEAHNLEDA  160 (174)
T ss_dssp             HHCGGG-SEEEEETHHHHSHHHHHHHCT--CCCEEEEETTGGGCGGG
T ss_pred             HHhcccCCEEEeCHHHHhhHHHHhhhccccccCcEEEEecccchHHH
Confidence            33345679999998777653222111  1234478999999998654

RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast [].; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 3CRV_A 3CRW_1 2VL7_A 4A15_A 2VSF_A.

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=92.28  E-value=0.14  Score=48.44  Aligned_cols=49  Identities=14%  Similarity=-0.005  Sum_probs=38.7

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (293)
                      .++++.||||||||..+.+|-+-..     +.-+||+=|--|+...+....++.
T Consensus       159 ~hvLviapTgSGKg~g~VIPnLL~~-----~~S~VV~DpKGEl~~~Ta~~R~~~  207 (606)
T PRK13897        159 QHALLFAPTGSGKGVGFVIPNLLFW-----EDSVVVHDIKLENYELTSGWREKQ  207 (606)
T ss_pred             ceEEEEcCCCCCcceEEehhhHHhC-----CCCEEEEeCcHHHHHHHHHHHHHC
Confidence            5899999999999999998877653     224777778889888877766553

>cd03289 ABCC_CFTR2 The CFTR subfamily domain 2

Probab=92.21  E-value=0.48  Score=40.41  Aligned_cols=42  Identities=24%  Similarity=0.204  Sum_probs=28.9

Q ss_pred             CCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEe
Q 022724          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (293)
Q Consensus       173 ~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SA  214 (293)
                      +.+-+++++||.-.-+|......+..++......+.+|+.|-
T Consensus       154 l~~p~illlDEpts~LD~~~~~~l~~~l~~~~~~~tii~isH  195 (275)
T cd03289         154 LSKAKILLLDEPSAHLDPITYQVIRKTLKQAFADCTVILSEH  195 (275)
T ss_pred             hcCCCEEEEECccccCCHHHHHHHHHHHHHhcCCCEEEEEEC
Confidence            356789999999887777766777777776544444544443

The cystic fibrosis transmembrane regulator (CFTR), the product of the gene mutated in patients with cystic fibrosis, has adapted the ABC transporter structural motif to form a tightly regulated anion channel at the apical surface of many epithelia. Use of the term assembly of a functional ion channel implies the coming together of subunits or at least smaller not-yet functional components of the active whole. In fact, on the basis of current knowledge only the CFTR polypeptide itself is required to form an ATP- and protein kinase A-dependent low-conductance chloride channel of the type present in the apical membrane of many epithelial cells. CFTR displays the typical organization (IM-ABC)2 and carries a characteristic hydrophilic R-domain that separates IM1-ABC1 from IM2-ABC2.

>PRK11176 lipid transporter ATP-binding/permease protein; Provisional

Probab=92.20  E-value=0.23  Score=47.20  Aligned_cols=42  Identities=21%  Similarity=0.281  Sum_probs=29.4

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEee
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISAT  215 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt  215 (293)
                      ++-+.+|+||.-.-+|......+...+..+..++-+|+.|--
T Consensus       497 ~~~~ililDEptsaLD~~t~~~i~~~l~~~~~~~tvI~VtHr  538 (582)
T PRK11176        497 RDSPILILDEATSALDTESERAIQAALDELQKNRTSLVIAHR  538 (582)
T ss_pred             hCCCEEEEECccccCCHHHHHHHHHHHHHHhCCCEEEEEecc
Confidence            566889999998888876666666666666555556666543

>PF10412 TrwB_AAD_bind: Type IV secretion-system coupling protein DNA-binding domain; InterPro: IPR019476 The plasmid conjugative coupling protein TraD (also known as TrwB) is a basic integral inner-membrane nucleoside-triphosphate-binding protein

Probab=92.19  E-value=0.19  Score=45.17  Aligned_cols=48  Identities=19%  Similarity=0.325  Sum_probs=29.4

Q ss_pred             hhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHH
Q 022724           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQT  117 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~  117 (293)
                      -...+++++.|.||+|||. ++..++..+...  +.++||.=|.-+.....
T Consensus        12 ~~e~~~~li~G~~GsGKT~-~i~~ll~~~~~~--g~~~iI~D~kg~~~~~f   59 (386)
T PF10412_consen   12 DSENRHILIIGATGSGKTQ-AIRHLLDQIRAR--GDRAIIYDPKGEFTERF   59 (386)
T ss_dssp             GGGGG-EEEEE-TTSSHHH-HHHHHHHHHHHT--T-EEEEEEETTHHHHHH
T ss_pred             chhhCcEEEECCCCCCHHH-HHHHHHHHHHHc--CCEEEEEECCchHHHHh
Confidence            3456899999999999996 445666666444  33555555655554433

It is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells []. This protein forms hexamers from six structurally very similar protomers []. This hexamer contains a central channel running from the cytosolic pole (formed by the all-alpha domains) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB all-alpha domain appears to be the DNA-binding domain of the structure. ; PDB: 1E9S_D 1E9R_F 1GKI_B 1GL7_G 1GL6_A.

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=92.17  E-value=0.32  Score=46.83  Aligned_cols=18  Identities=33%  Similarity=0.486  Sum_probs=14.5

Q ss_pred             cEEEEcCCCChhHHHHHH
Q 022724           72 DVIAQAQSGTGKTSMIAL   89 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~   89 (293)
                      -+++.||.|+|||.++..
T Consensus        42 AYLF~GP~GtGKTt~Ari   59 (725)
T PRK07133         42 AYLFSGPRGTGKTSVAKI   59 (725)
T ss_pred             EEEEECCCCCcHHHHHHH
Confidence            368999999999976543

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=92.14  E-value=0.7  Score=45.90  Aligned_cols=16  Identities=31%  Similarity=0.366  Sum_probs=13.7

Q ss_pred             cEEEEcCCCChhHHHH
Q 022724           72 DVIAQAQSGTGKTSMI   87 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~   87 (293)
                      .+++.||||+|||..+
T Consensus       598 ~~lf~Gp~GvGKT~lA  613 (852)
T TIGR03345       598 VFLLVGPSGVGKTETA  613 (852)
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4899999999999654

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.

>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []

Probab=92.12  E-value=0.15  Score=39.93  Aligned_cols=40  Identities=20%  Similarity=0.410  Sum_probs=20.9

Q ss_pred             CCccEEEecchhhhhc--cccHHHHHHHHhhCCCCccEEEEEeecChh
Q 022724          174 RAIKLLVLDESDEMLS--RGFKDQIYDVYRYLPPDLQVVLISATLPHE  219 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~--~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~  219 (293)
                      .+-+++|+||+=.|.-  .+|...+..++.   .+..++   ||++..
T Consensus        94 ~~~~liviDEIG~mEl~~~~F~~~v~~~l~---s~~~vi---~vv~~~  135 (168)
T PF03266_consen   94 SSSDLIVIDEIGKMELKSPGFREAVEKLLD---SNKPVI---GVVHKR  135 (168)
T ss_dssp             HCCHEEEE---STTCCC-CHHHHHHHHHHC---TTSEEE---EE--SS
T ss_pred             CCCCEEEEeccchhhhcCHHHHHHHHHHHc---CCCcEE---EEEecC
Confidence            4668999999988743  245665655555   444544   455443

It includes proteins from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase []. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme []. The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue [].; GO: 0005524 ATP binding, 0016740 transferase activity, 0019204 nucleotide phosphatase activity; PDB: 1YE8_A 2I3B_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	293
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		1e-123
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		1e-123
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		1e-123
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		1e-123
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		1e-120
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		1e-119
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		1e-95
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		3e-95
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		2e-89
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		1e-84
3bor_A	237	Crystal Structure Of The Deadc Domain Of Human Tran		4e-71
1qde_A	224	Crystal Structure Of The Atpase Domain Of Translati		9e-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		1e-51
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		4e-44
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		6e-44
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		2e-43
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		2e-43
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		2e-43
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		2e-43
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		5e-38
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		1e-37
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		1e-37
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		2e-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		3e-34
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		9e-34
2oxc_A	230	Human Dead-Box Rna Helicase Ddx20, Dead Domain In C		4e-31
1t6n_A	220	Crystal Structure Of The N-Terminal Domain Of Human		9e-31
3fhc_B	235	Crystal Structure Of Human Dbp5 In Complex With Nup		1e-30
3fmo_B	300	Crystal Structure Of The Nucleoporin Nup214 In Comp		6e-30
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		7e-30
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		2e-28
1q0u_A	219	Crystal Structure Of The Bstdead N-Terminal Domain		3e-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		1e-24
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		1e-23
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		1e-23
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		2e-23
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		5e-23
3ly5_A	262	Ddx18 Dead-Domain Length = 262		5e-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		2e-18
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		4e-16
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		3e-15
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		3e-15
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		4e-15
1fuk_A	165	Crystal Structure Of The Carboxy Terminal Domain Of		2e-13
2rb4_A	175	Crystal Structure Of The Helicase Domain Of Human D		2e-07
2wax_A	193	Structure Of The Human Ddx6 C-Terminal Domain In Co		1e-04

>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 =  437 bits (1124), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 203/266 (76%), 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 FDTLCDLYDTLTITQAVIFCNTKRKV 285
           FDTLCDLYDTLTITQAVIFCNTKRKV
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 =  437 bits (1124), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 204/269 (75%), Positives = 240/269 (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 FDTLCDLYDTLTITQAVIFCNTKRKVLLL 288
           FDTLCDLYDTLTITQAVIFCNTKRKV  L
Sbjct: 264 FDTLCDLYDTLTITQAVIFCNTKRKVDWL 292

>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 =  437 bits (1124), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 203/266 (76%), 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 FDTLCDLYDTLTITQAVIFCNTKRKV 285
           FDTLCDLYDTLTITQAVIFCNTKRKV
Sbjct: 265 FDTLCDLYDTLTITQAVIFCNTKRKV 290

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

Iteration: 1
 Score =  436 bits (1121), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 203/266 (76%), 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 FDTLCDLYDTLTITQAVIFCNTKRKV 285
           FDTLCDLYDTLTITQAVIFCNTKRKV
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 =  427 bits (1097), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 196/252 (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 QAVIFCNTKRKV 285
           QAVIFCNTKRKV
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 =  425 bits (1093), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 197/252 (78%), 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 QAVIFCNTKRKV 285
           QAVIFCNTKRKV
Sbjct: 242 QAVIFCNTKRKV 253

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score =  346 bits (887), Expect = 1e-95,   Method: Compositional matrix adjust.
 Identities = 157/257 (61%), 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 TLTITQAVIFCNTKRKV 285
           TLTITQAVIF NT+RKV
Sbjct: 251 TLTITQAVIFINTRRKV 267

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score =  344 bits (883), Expect = 3e-95,   Method: Compositional matrix adjust.
 Identities = 157/257 (61%), 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 TLTITQAVIFCNTKRKV 285
           TLTITQAVIF NT+RKV
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 = 150/254 (59%), 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 ITQAVIFCNTKRKV 285
           +TQAVIFCNT+RKV
Sbjct: 260 VTQAVIFCNTRRKV 273

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score =  309 bits (792), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 146/254 (57%), Positives = 192/254 (75%), Gaps = 1/254 (0%)
Query: 32  ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTV 91
           +  FD   + ++LLRG++ YGFE+PSAIQQRA+ PII+G DV+AQAQSGTGKT   ++  
Sbjct: 20  VYKFDDXELDENLLRGVFGYGFEEPSAIQQRAIXPIIEGHDVLAQAQSGTGKTGTFSIAA 79
Query: 92  CQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG 151
            Q +DTS +  QAL L+PTRELA Q +KV+ A+    +I+ HAC+GG S  ED   L   
Sbjct: 80  LQRIDTSVKAPQALXLAPTRELALQIQKVVXALAFHXDIKVHACIGGTSFVEDAEGLRDA 139
Query: 152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVL 211
             +V GTPGRV D I+R+  RT  IK  +LDE+DE LS GFK+QIY ++  LPP  QVVL
Sbjct: 140 -QIVVGTPGRVFDNIQRRRFRTDKIKXFILDEADEXLSSGFKEQIYQIFTLLPPTTQVVL 198
Query: 212 ISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLT 271
           +SAT P+++LE+TTKF  +PV+ILVK+DELTLEGIKQF+V VE EE+K++ L DLYD+++
Sbjct: 199 LSATXPNDVLEVTTKFXRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLYDSIS 258
Query: 272 ITQAVIFCNTKRKV 285
           +TQAVIFCNT+RKV
Sbjct: 259 VTQAVIFCNTRRKV 272

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

Iteration: 1
 Score =  264 bits (675), Expect = 4e-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 =  259 bits (663), Expect = 9e-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 =  244 bits (624), 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 =  199 bits (507), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 106/257 (41%), Positives = 154/257 (59%), Gaps = 2/257 (0%)
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 TQAVIFCNTKRKVLLLV 289
            QA+IFCN+  +V LL 
Sbjct: 259 NQAIIFCNSTNRVELLA 275

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score =  174 bits (442), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 97/258 (37%), Positives = 154/258 (59%), Gaps = 7/258 (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 TITQAVIFCNTKRKVLLL 288
           TI  ++IF  TK+   +L
Sbjct: 242 TIGSSIIFVATKKTANVL 259

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score =  174 bits (441), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 97/258 (37%), Positives = 154/258 (59%), Gaps = 7/258 (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 TITQAVIFCNTKRKVLLL 288
           TI  ++IF  TK+   +L
Sbjct: 242 TIGSSIIFVATKKTANVL 259

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

Iteration: 1
 Score =  172 bits (437), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 105/270 (38%), Positives = 160/270 (59%), Gaps = 14/270 (5%)
Query: 31  AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG---RDVIAQAQSGTGKTSMI 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 LCDLYDTLTITQAVIFCNTKRKVLLLVLQF 292
           LC+LY  +TI QA+IFC+T++    L  + 
Sbjct: 324 LCNLYGAITIAQAMIFCHTRKTASWLAAEL 353

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score =  172 bits (437), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 105/270 (38%), Positives = 160/270 (59%), Gaps = 14/270 (5%)
Query: 31  AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG---RDVIAQAQSGTGKTSMI 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 LCDLYDTLTITQAVIFCNTKRKVLLLVLQF 292
           LC+LY  +TI QA+IFC+T++    L  + 
Sbjct: 257 LCNLYGAITIAQAMIFCHTRKTASWLAAEL 286

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

Iteration: 1
 Score =  172 bits (437), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 105/270 (38%), Positives = 160/270 (59%), Gaps = 14/270 (5%)
Query: 31  AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG---RDVIAQAQSGTGKTSMI 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 LCDLYDTLTITQAVIFCNTKRKVLLLVLQF 292
           LC+LY  +TI QA+IFC+T++    L  + 
Sbjct: 273 LCNLYGAITIAQAMIFCHTRKTASWLAAEL 302

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

Iteration: 1
 Score =  172 bits (436), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 105/270 (38%), Positives = 160/270 (59%), Gaps = 14/270 (5%)
Query: 31  AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG---RDVIAQAQSGTGKTSMI 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 LCDLYDTLTITQAVIFCNTKRKVLLLVLQF 292
           LC+LY  +TI QA+IFC+T++    L  + 
Sbjct: 294 LCNLYGAITIAQAMIFCHTRKTASWLAAEL 323

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score =  154 bits (390), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 92/261 (35%), Positives = 148/261 (56%), Gaps = 5/261 (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 DTLTITQAVIFCNTKRKVLLL 288
           D L   Q VIF  + ++ + L
Sbjct: 245 DVLEFNQVVIFVKSVQRCIAL 265

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score =  153 bits (386), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 92/260 (35%), Positives = 146/260 (56%), Gaps = 5/260 (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 TLTITQAVIFCNTKRKVLLL 288
            L   Q VIF  + ++ + L
Sbjct: 247 VLEFNQVVIFVKSVQRCIAL 266

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score =  153 bits (386), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 92/260 (35%), Positives = 146/260 (56%), Gaps = 5/260 (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 TLTITQAVIFCNTKRKVLLL 288
            L   Q VIF  + ++ + L
Sbjct: 247 VLEFNQVVIFVKSVQRCIAL 266

>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  SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTV 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-GIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALKN- 123
Query: 152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVL 211
            ++V GTPGR+ D I R TL  + +K  +LDE+DE L+ GF   +  +      D +++L
Sbjct: 124 ANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEXLNXGFIKDVEKILNACNKDKRILL 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 (357), Expect = 3e-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 (353), Expect = 9e-34,   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 =  131 bits (330), Expect = 4e-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 = 9e-31,   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 =  129 bits (325), Expect = 1e-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|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 300

Iteration: 1
 Score =  127 bits (320), Expect = 6e-30,   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|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score =  127 bits (319), Expect = 7e-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|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score =  126 bits (316), 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 (306), Expect = 2e-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 = 3e-27,   Method: Compositional matrix adjust.
 Identities = 70/210 (33%), Positives = 106/210 (50%), Gaps = 4/210 (1%)
Query: 31  AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALT 90
           A T F     +  ++  I    F KP+ IQ+R +   ++G   + Q+Q+GTGKT    L 
Sbjct: 2   AETQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESXVGQSQTGTGKTHAYLLP 61
Query: 91  VCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI----NIQAHACVGGKSVGEDIR 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 LQVVLISATLPHEILEMTTKFMTDPVKILV 236
           LQ ++ SAT+P ++     K+  +P  + V
Sbjct: 182 LQXLVFSATIPEKLKPFLKKYXENPTFVHV 211

>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 (274), Expect = 1e-24,   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 =  106 bits (265), Expect = 1e-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 =  106 bits (265), Expect = 1e-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 (263), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 64/212 (30%), Positives = 105/212 (49%), Gaps = 5/212 (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 PDLQVVLISATLPHEILEMTTKFMTDPVKILV 236
           PD Q ++ SAT P E+ ++   F+ D + I +
Sbjct: 220 PDRQTLMWSATWPKEVRQLAEDFLKDYIHINI 251

>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 = 98.2 bits (243), Expect = 5e-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  VCQTV----DTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA---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 = 95.1 bits (235), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 61/214 (28%), Positives = 113/214 (52%), Gaps = 6/214 (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 LPPDLQVVLISATLPHEILEMTTKFMTDPVKILV 236
           LP   Q +L SAT    + ++    + +P  + V
Sbjct: 199 LPKKRQTLLFSATQTKSVKDLARLSLKNPEYVWV 232

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

Iteration: 1
 Score = 89.7 bits (221), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 63/249 (25%), Positives = 127/249 (51%), Gaps = 17/249 (6%)
Query: 46  RGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQAL 105
           + I + GF+  + +Q + +  +++G++V+ +A++G+GKT+  A+ + +        +++L
Sbjct: 7   QAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL------GMKSL 60
Query: 106 ILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDM 165
           +++PTREL  Q    I  IG +++ +     GG      I ++ +   +V  TPGR+ D+
Sbjct: 61  VVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVRNA-DIVVATPGRLLDL 119
Query: 166 IKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTT 225
             +  +   + +++++DE+D M   GF D I  +           L SAT+P EI ++  
Sbjct: 120 WSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITGLFSATIPEEIRKVVK 179
Query: 226 KFMTDPVKILVKRDELTLEGIKQFFVAVEREEW--KFDTLCDLYDTLTITQAVIFCNTKR 283
            F+T+  +I      + L  ++  FV V +++W  K   L +  D       ++F  T+ 
Sbjct: 180 DFITNYEEIEAC---IGLANVEHKFVHV-KDDWRSKVQALRENKD----KGVIVFVRTRN 231
Query: 284 KVLLLVLQF 292
           +V  LV  F
Sbjct: 232 RVAKLVRLF 240

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

Iteration: 1
 Score = 81.6 bits (200), Expect = 4e-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|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion) Bound To Ssrna And Amp-Pnp Length = 512

Iteration: 1
 Score = 79.0 bits (193), Expect = 3e-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|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 79.0 bits (193), Expect = 3e-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|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast Eif4a Length = 165

Iteration: 1
 Score = 72.8 bits (177), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 30/43 (69%), Positives = 39/43 (90%)
Query: 243 LEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKV 285
           LEGIKQF+V VE EE+K++ L DLYD++++TQAVIFCNT+RKV
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 = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 21/52 (40%), Positives = 34/52 (65%)
Query: 241 LTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF 292
           LTL  I+Q++V  E  + K+  LC++Y ++TI QA+IFC T+R    L ++ 
Sbjct: 3   LTLNNIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRNAKWLTVEM 54

>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 = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/60 (40%), Positives = 37/60 (61%), Gaps = 2/60 (3%)
Query: 230 DPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLV 289
           DP +I +  +ELTL+G+ Q++  V  E  K   L  L+  L I Q++IFCN+ ++V LL 
Sbjct: 4   DPYEINLM-EELTLKGVTQYYAYVT-ERQKVHCLNTLFSRLQINQSIIFCNSSQRVELLA 61

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	293
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	1e-168
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	1e-165
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	1e-162
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-150
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	1e-146
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-134
3bor_A	237	Human initiation factor 4A-II; translation initiat	1e-130
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	1e-115
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	1e-111
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	1e-100
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	9e-97
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-79
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	1e-74
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	1e-70
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	1e-69
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	3e-68
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	2e-63
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-56
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	3e-55
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	3e-55
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	3e-55
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	3e-55
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	8e-52
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	9e-49
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	6e-26
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	8e-25
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	2e-21
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	3e-20
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	1e-13
3b6e_A	216	Interferon-induced helicase C domain-containing P;	3e-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
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-07
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	4e-07
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	6e-07
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	2e-06
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	4e-06
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	4e-06
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	2e-05
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	1e-04
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	2e-04
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	3e-04
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	7e-04
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	7e-04
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	8e-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 =  470 bits (1213), Expect = e-168
 Identities = 207/288 (71%), Positives = 245/288 (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 TLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLV 289
           TLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKV  L 
Sbjct: 246 TLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLT 293

>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 =  464 bits (1197), Expect = e-165
 Identities = 160/282 (56%), Positives = 213/282 (75%), Gaps = 1/282 (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 QFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLV 289
           QF++ VEREEWK DTLCDLY+TLTITQAVIF NT+RKV  L 
Sbjct: 256 QFYINVEREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLT 297

>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 =  455 bits (1174), Expect = e-162
 Identities = 154/276 (55%), Positives = 209/276 (75%), Gaps = 2/276 (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 EREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLV 289
           E EE+K++ L DLYD++++TQAVIFCNT+RKV  L 
Sbjct: 241 EEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELT 276

>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 =  430 bits (1108), Expect = e-152
 Identities = 108/266 (40%), Positives = 157/266 (59%), Gaps = 4/266 (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 CDLYDTLTITQAVIFCNTKRKVLLLV 289
             L+  L I QA+IFCN+  +V LL 
Sbjct: 250 NTLFSKLQINQAIIFCNSTNRVELLA 275

>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 =  425 bits (1094), Expect = e-150
 Identities = 100/278 (35%), Positives = 159/278 (57%), Gaps = 8/278 (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 AVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLV 289
                + KF  LC+LY  +TI QA+IFC+T++    L 
Sbjct: 246 LCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLA 283

>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 =  419 bits (1079), Expect = e-146
 Identities = 100/278 (35%), Positives = 159/278 (57%), Gaps = 8/278 (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 AVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLV 289
                + KF  LC+LY  +TI QA+IFC+T++    L 
Sbjct: 313 LCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLA 350

>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 = 96/257 (37%), Positives = 152/257 (59%), Gaps = 7/257 (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 TLTITQAVIFCNTKRKV 285
            +TI  ++IF  TK+  
Sbjct: 240 LMTIGSSIIFVATKKTA 256

>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 =  395 bits (1016), Expect = e-138
 Identities = 91/264 (34%), Positives = 146/264 (55%), Gaps = 5/264 (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 LYDTLTITQAVIFCNTKRKVLLLV 289
           L D L   Q VIF  + ++ + L 
Sbjct: 244 LLDVLEFNQVVIFVKSVQRCIALA 267

>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 =  378 bits (974), Expect = e-134
 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 =  368 bits (948), Expect = e-130
 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 =  330 bits (848), Expect = e-115
 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 =  323 bits (829), Expect = e-111
 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 =  291 bits (747), Expect = e-100
 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 =  282 bits (725), Expect = 9e-97
 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 = 87/259 (33%), Positives = 143/259 (55%), Gaps = 9/259 (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 TITQAVIFCNTKRKVLLLV 289
                ++FC TKR    L 
Sbjct: 238 EF-YGLVFCKTKRDTKELA 255

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score =  238 bits (611), Expect = 2e-79
 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 =  230 bits (590), Expect = 1e-74
 Identities = 58/250 (23%), Positives = 123/250 (49%), Gaps = 13/250 (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 NTKRKVLLLV 289
            T+ +V  LV
Sbjct: 228 RTRNRVAKLV 237

>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 (580), Expect = 1e-70
 Identities = 68/294 (23%), Positives = 134/294 (45%), Gaps = 28/294 (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-----DTLCDLYDTLTITQAVIFCNTKRKVLLLV 289
              E I Q  V  E+               + +  +  +A+IF  T +    L 
Sbjct: 252 EAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLC 305

>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 =  224 bits (573), Expect = 1e-69
 Identities = 68/297 (22%), Positives = 134/297 (45%), Gaps = 28/297 (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-----DTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF 292
              E I Q  V  E+               + +  +  +A+IF  T +    L    
Sbjct: 303 EAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSIL 359

>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 =  210 bits (536), Expect = 3e-68
 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 =  199 bits (507), Expect = 2e-63
 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 = 71/264 (26%), Positives = 125/264 (47%), Gaps = 11/264 (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 TLCDLYDTLTITQAVIFCNTKRKV 285
            L ++         ++F  TKR  
Sbjct: 291 KLIEILSE-QADGTIVFVETKRGA 313

>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 = 87/280 (31%), Positives = 134/280 (47%), Gaps = 26/280 (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-LYDTLTITQAVIFCNTKRKV 285
            Q  V VE  + K   L D L  T   +  ++F  TK+  
Sbjct: 251 TQKVVWVEESD-KRSFLLDLLNATGKDSLTLVFVETKKGA 289

>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 =  180 bits (460), Expect = 2e-56
 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

>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 (453), Expect = 3e-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

>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 =  178 bits (453), Expect = 3e-55
 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

>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 =  178 bits (453), Expect = 3e-55
 Identities = 67/232 (28%), Positives = 116/232 (50%), Gaps = 13/232 (5%)

Query: 30  EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKT----- 84
             I +FD + +   +   I    +++P+ IQ+ A+  I++ RD++A AQ+G+GKT     
Sbjct: 20  NVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLI 79

Query: 85  ----SMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKS 140
                ++   + Q   + +   + LIL+PTRELA Q             +++    GG  
Sbjct: 80  PIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGAD 139

Query: 141 VGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVY 200
               IR+++ G H++  TPGR+ D I++  +     K +VLDE+D ML  GF+ QI  + 
Sbjct: 140 THSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKII 199

Query: 201 RYLPP----DLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQ 248
                    + Q ++ SAT P EI ++   F+ + + + V R   T + IKQ
Sbjct: 200 EESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVGSTSDSIKQ 251

>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 =  177 bits (451), Expect = 3e-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

>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 = 8e-52
 Identities = 39/273 (14%), Positives = 88/273 (32%), Gaps = 36/273 (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 EWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLV 289
           E K   L +++    +    IF  T+ +   L 
Sbjct: 242 E-KLVELLEIFRDGIL----IFAQTEEEGKELY 269

>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 =  162 bits (411), Expect = 9e-49
 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 =   99 bits (250), Expect = 6e-26
 Identities = 21/50 (42%), Positives = 32/50 (64%)

Query: 240 ELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLV 289
            LTL  I+Q++V  E  + K+  LC++Y ++TI QA+IFC T+R    L 
Sbjct: 2   MLTLNNIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRNAKWLT 51

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19 Length = 165

 Score = 96.5 bits (241), Expect = 8e-25
 Identities = 31/47 (65%), Positives = 40/47 (85%)

Query: 243 LEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLV 289
           LEGIKQF+V VE EE+K++ L DLYD++++TQAVIFCNT+RKV  L 
Sbjct: 1   LEGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELT 47

>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 = 87.6 bits (218), Expect = 2e-21
 Identities = 15/48 (31%), Positives = 27/48 (56%), Gaps = 1/48 (2%)

Query: 242 TLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLV 289
           +L G++Q++V ++ +  K   L DL D L   Q VIF  + ++ + L 
Sbjct: 2   SLHGLQQYYVKLK-DNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALA 48

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis} Length = 163

 Score = 84.1 bits (209), Expect = 3e-20
 Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 1/46 (2%)

Query: 240 ELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKV 285
            LT   I+   + V REE KF  L D+  T      +IFC TK  V
Sbjct: 4   GLTTRNIEHAVIQV-REENKFSLLKDVLMTENPDSCIIFCRTKEHV 48

>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 = 52.1 bits (125), Expect = 3e-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 = 51.5 bits (122), 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

>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 = 51.0 bits (121), Expect = 2e-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

>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 = 50.2 bits (120), Expect = 4e-07
 Identities = 51/275 (18%), Positives = 99/275 (36%), Gaps = 56/275 (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------QAVIFCNTKRKV 285
             F T   + ++ L           ++F +T+R  
Sbjct: 221 GAFSTSRRVKFEELVEECVAENGGVLVFESTRRGA 255

>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

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 48.0 bits (113), 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

>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

>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 = 46.9 bits (111), Expect = 4e-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

>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 = 50/271 (18%), Positives = 108/271 (39%), Gaps = 44/271 (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-TITQAVIFCNTKRKVLLLVLQ 291
             +L YD +     A+IF N +RK   + L+
Sbjct: 226 WEELVYDAIRKKKGALIFVNMRRKAERVALE 256

>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 = 41.1 bits (97), Expect = 1e-04
 Identities = 8/40 (20%), Positives = 17/40 (42%), Gaps = 1/40 (2%)

Query: 246 IKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKV 285
            ++  V       + + L DL    +  +A++F  TK + 
Sbjct: 6   YEEEAVPAPVRG-RLEVLSDLLYVASPDRAMVFTRTKAET 44

>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 = 41.7 bits (98), Expect = 2e-04
 Identities = 8/40 (20%), Positives = 17/40 (42%), Gaps = 1/40 (2%)

Query: 246 IKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKV 285
            ++  V       + + L DL    +  +A++F  TK + 
Sbjct: 3   YEEEAVPAPVRG-RLEVLSDLLYVASPDRAMVFTRTKAET 41

>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 = 3e-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

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens} Length = 191

 Score = 38.8 bits (91), Expect = 7e-04
 Identities = 10/69 (14%), Positives = 17/69 (24%), Gaps = 15/69 (21%)

Query: 227 FMTDPVKILVKRDELTL-------EGIKQFFVAVEREEWKFDTLCDL---YDTLTITQAV 276
                  + +  + L           + Q    V+ E  K   L +         +    
Sbjct: 4   HHHHSSGVDLGTENLYFQSMGAASLDVIQEVEYVKEEA-KMVYLLECLQKTPPPVL---- 58

Query: 277 IFCNTKRKV 285
           IF   K  V
Sbjct: 59  IFAEKKADV 67

>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 = 40.2 bits (93), Expect = 7e-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

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli} Length = 170

 Score = 38.3 bits (90), Expect = 8e-04
 Identities = 9/42 (21%), Positives = 19/42 (45%)

Query: 244 EGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKV 285
           + I Q++   +  E K   L  L      T++++F   + +V
Sbjct: 2   KKIHQWYYRADDLEHKTALLVHLLKQPEATRSIVFVRKRERV 43

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	293
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
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	100.0
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	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
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	100.0
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	100.0
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	100.0
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	100.0
3bor_A	237	Human initiation factor 4A-II; translation initiat	100.0
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	100.0
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	100.0
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	100.0
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	100.0
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	100.0
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	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
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	100.0
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	100.0
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	100.0
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	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
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	100.0
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	100.0
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	100.0
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	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
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.97
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.97
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.97
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.97
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	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
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.97
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.96
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	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	99.94
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.94
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.94
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.94
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.94
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.93
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	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	99.92
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.92
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.92
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.91
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.9
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.89
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.89
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.89
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.89
3h1t_A	590	Type I site-specific restriction-modification syst	99.88
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.87
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.85
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.85
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.79
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.77
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.76
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	99.68
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.67
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.61
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.54
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	99.15
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.13
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.05
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	98.8
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	98.54
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	98.54
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	98.5
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	98.49
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	98.42
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	98.37
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	97.75
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	97.7
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	97.6
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	97.5
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	97.5
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	97.45
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	97.44
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	97.33
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	97.25
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	97.24
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	97.2
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	97.2
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	97.11
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	97.08
2chg_A	226	Replication factor C small subunit; DNA-binding pr	97.08
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	97.06
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	97.05
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	97.05
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	96.97
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	96.96
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	96.95
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	96.92
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	96.89
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	96.85
3co5_A	143	Putative two-component system transcriptional RES	96.81
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	96.77
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	96.76
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	96.68
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	96.64
3bos_A	242	Putative DNA replication factor; P-loop containing	96.61
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	96.58
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	96.57
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	96.56
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	96.55
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	96.52
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	96.46
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	96.43
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	96.35
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	96.35
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	96.33
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	96.33
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	96.19
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	96.18
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	96.09
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	95.95
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	95.91
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	95.88
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	95.79
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	95.68
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	95.61
2qgz_A	308	Helicase loader, putative primosome component; str	95.57
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	95.51
2r6a_A	454	DNAB helicase, replicative helicase; replication,	95.02
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	95.01
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	95.01
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	94.99
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	94.95
2chq_A	319	Replication factor C small subunit; DNA-binding pr	94.93
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	94.85
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	94.77
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	94.74
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	94.61
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	94.46
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	94.44
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	94.44
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	94.4
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	94.31
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	94.31
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	94.19
3pvs_A	447	Replication-associated recombination protein A; ma	94.14
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	93.99
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	93.98
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	93.95
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	93.77
1xp8_A	366	RECA protein, recombinase A; recombination, radior	93.63
2z43_A	324	DNA repair and recombination protein RADA; archaea	93.56
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	93.52
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	93.44
3io5_A	333	Recombination and repair protein; storage dimer, i	93.4
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	93.21
2fna_A	357	Conserved hypothetical protein; structural genomic	93.12
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	93.11
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	93.03
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	92.97
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	92.95
3u4q_B	1166	ATP-dependent helicase/deoxyribonuclease subunit;	92.85
2l8b_A	189	Protein TRAI, DNA helicase I; RECD, hydrolase; NMR	92.7
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	92.41
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	92.09
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	92.03
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	92.0
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	91.88
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	91.8
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	91.74
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	91.7
1u94_A	356	RECA protein, recombinase A; homologous recombinat	91.67
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	91.03
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	90.76
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	90.72
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	90.68
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	90.55
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	90.55
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	90.21
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	90.21
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	90.09
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	89.73
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	89.72
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	89.61
1p9r_A	418	General secretion pathway protein E; bacterial typ	89.57
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	89.36
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	89.34
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	89.33
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	89.28
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	89.26
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	89.06
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	88.93
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	88.93
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	88.91
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	88.89
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	88.83
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	88.71
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	88.58
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	88.48
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	88.2
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	88.36
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	88.28
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	88.21
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	88.18
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	88.06
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	88.05
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	88.03
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	87.88
2eyu_A	261	Twitching motility protein PILT; pilus retraction	87.81
2r44_A	331	Uncharacterized protein; putative ATPase, structur	87.68
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	87.65
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	87.59
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	87.43
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	87.37
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	87.3
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	87.29
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	87.27
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	87.22
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	87.0
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	86.86
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	86.82
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	86.75
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	86.74
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	86.73
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	86.66
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	86.38
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	86.32
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	86.31
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	86.26
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	86.14
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	86.07
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	86.01
1w36_B	1180	RECB, exodeoxyribonuclease V beta chain; recombina	85.95
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	85.91
2cvh_A	220	DNA repair and recombination protein RADB; filamen	85.59
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	85.59
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	85.57
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	85.56
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	85.56
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	85.52
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	85.4
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	85.39
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	85.2
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	85.19
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	85.17
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	85.14
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	85.06
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	84.96
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	84.75
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	84.65
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	84.64
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	84.62
1tue_A	212	Replication protein E1; helicase, replication, E1E	84.5
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	84.35
2ewv_A	372	Twitching motility protein PILT; pilus retraction	84.27
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	84.14
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	84.13
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	83.94
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	83.9
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	83.88
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	83.76
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	83.69
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	83.67
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	83.66
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	83.62
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	83.18
1yks_A	440	Genome polyprotein [contains: flavivirin protease	83.16
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	82.93
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	82.79
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	82.75
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	82.26
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	82.15
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	82.1
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	82.03
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	81.94
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	81.93
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	81.91
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	81.84
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	81.79
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	81.76
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	81.49
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	81.46
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	81.33
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	80.94
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	80.89
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	80.73
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	80.6
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	80.26
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	80.21
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	80.07

>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=336.74  Aligned_cols=271  Identities=27%  Similarity=0.406  Sum_probs=246.7

Q ss_pred             cceeecccCCccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCC
Q 022724           20 KMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS   99 (293)
Q Consensus        20 ~~~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~   99 (293)
                      ++.+.....+.++.+|+++++++.++++++++||..|+|+|+++||.+++|+|+++++|||+|||++|++|++..+...+
T Consensus        43 ~~~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~~  122 (434)
T 2db3_A           43 PVKVTGSDVPQPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDP  122 (434)
T ss_dssp             CEEEESSSCCCCCCCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSC
T ss_pred             eeEecCCCCCCCcCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHhcc
Confidence            45566777888999999999999999999999999999999999999999999999999999999999999999886432


Q ss_pred             -----CceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCC
Q 022724          100 -----REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTR  174 (293)
Q Consensus       100 -----~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~  174 (293)
                           .++++||++|+++|+.|+.+.++++....++++..++|+.....+...+..+++|+|+||++|.+++.++...+.
T Consensus       123 ~~~~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Ivv~Tp~~l~~~l~~~~~~l~  202 (434)
T 2db3_A          123 HELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTFITFE  202 (434)
T ss_dssp             CCCCTTCCSEEEECSSHHHHHHHHHHHHHHTTTSSCCCCEECTTSCHHHHHHHHTTCCSEEEECHHHHHHHHHTTSCCCT
T ss_pred             cccccCCccEEEEecCHHHHHHHHHHHHHHhccCCcEEEEEECCCCHHHHHHHhhcCCCEEEEChHHHHHHHHhCCcccc
Confidence                 367999999999999999999999998888999999999998888888888999999999999999998888899


Q ss_pred             CccEEEecchhhhhccccHHHHHHHHhhC--CCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEE
Q 022724          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYL--PPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVA  252 (293)
Q Consensus       175 ~l~~iViDE~h~~~~~~~~~~~~~i~~~l--~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~  252 (293)
                      +++++|+||||++++.+|...+..++..+  ++..|++++|||+++.+..+...++.++..+.+........++.+.+..
T Consensus       203 ~~~~lVlDEah~~~~~gf~~~~~~i~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~  282 (434)
T 2db3_A          203 DTRFVVLDEADRMLDMGFSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTIYE  282 (434)
T ss_dssp             TCCEEEEETHHHHTSTTTHHHHHHHHHCTTSCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEEESSTTCCCTTEEEEEEE
T ss_pred             cCCeEEEccHhhhhccCcHHHHHHHHHhcCCCCCceEEEEeccCCHHHHHHHHHhccCCEEEEeccccccccccceEEEE
Confidence            99999999999999999999999999885  5689999999999999999999999999999888777777888999888


Q ss_pred             ecCcccHHHHHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          253 VEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       253 ~~~~~~k~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      +.... |...+.+++..... ++||||++++.|+.+++.|
T Consensus       283 ~~~~~-k~~~l~~~l~~~~~-~~lVF~~t~~~a~~l~~~L  320 (434)
T 2db3_A          283 VNKYA-KRSKLIEILSEQAD-GTIVFVETKRGADFLASFL  320 (434)
T ss_dssp             CCGGG-HHHHHHHHHHHCCT-TEEEECSSHHHHHHHHHHH
T ss_pred             eCcHH-HHHHHHHHHHhCCC-CEEEEEeCcHHHHHHHHHH
Confidence            88776 88888888887654 4999999999999999875

>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=2.7e-44  Score=322.28  Aligned_cols=273  Identities=75%  Similarity=1.170  Sum_probs=249.5

Q ss_pred             cceeecccCCccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCC
Q 022724           20 KMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS   99 (293)
Q Consensus        20 ~~~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~   99 (293)
                      ....+....+++..+|+++++++.+.++++++||..|+|+|+++++.+.+|+++++++|||+|||++|++|+++.+....
T Consensus        24 ~~~~~~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~  103 (410)
T 2j0s_A           24 KVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQV  103 (410)
T ss_dssp             SCCCCCCTTCCCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTS
T ss_pred             ccccCCCCCccCCCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHHHHHHHHHhhcc
Confidence            44445566667788999999999999999999999999999999999999999999999999999999999999987666


Q ss_pred             CceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEE
Q 022724          100 REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLL  179 (293)
Q Consensus       100 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~i  179 (293)
                      .+.++||++|+++|+.|+.+.++++....++.+..++|+.....+...+..+++|+|+||+++.+++..+...+.++++|
T Consensus       104 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ivv~Tp~~l~~~l~~~~~~~~~~~~v  183 (410)
T 2j0s_A          104 RETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKML  183 (410)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEE
T ss_pred             CCceEEEEcCcHHHHHHHHHHHHHHhccCCeEEEEEECCCCHHHHHHHhhcCCCEEEcCHHHHHHHHHhCCccHhheeEE
Confidence            67899999999999999999999999889999999999998888888888889999999999999999888888999999


Q ss_pred             EecchhhhhccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccH
Q 022724          180 VLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWK  259 (293)
Q Consensus       180 ViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k  259 (293)
                      |+||+|.+.+.++...+..+++.+++..|++++|||+++.+..+...++.+|..+...........+.+.+..+.....|
T Consensus       184 ViDEah~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k  263 (410)
T 2j0s_A          184 VLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWK  263 (410)
T ss_dssp             EEETHHHHTSTTTHHHHHHHHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECCCGGGCSCTTEEEEEEEESSTTHH
T ss_pred             EEccHHHHHhhhhHHHHHHHHHhCccCceEEEEEcCCCHHHHHHHHHHcCCCEEEEecCccccCCCceEEEEEeCcHHhH
Confidence            99999999999999999999999999999999999999999888889999999888777677778889999988888778


Q ss_pred             HHHHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          260 FDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       260 ~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ...+..+++....+++||||++++.++.+++.|
T Consensus       264 ~~~l~~~~~~~~~~~~lVf~~~~~~~~~l~~~L  296 (410)
T 2j0s_A          264 FDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKM  296 (410)
T ss_dssp             HHHHHHHHHHHTSSEEEEECSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCcEEEEEcCHHHHHHHHHHH
Confidence            999999998877789999999999999998765

>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=1.7e-43  Score=317.60  Aligned_cols=271  Identities=30%  Similarity=0.430  Sum_probs=237.5

Q ss_pred             ceeecccCCccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCC-
Q 022724           21 MVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-   99 (293)
Q Consensus        21 ~~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~-   99 (293)
                      ....+...+.++.+|+++++++.+.+++.++||..|+|+|.++++.+.+|+|+++++|||+|||++|++|++..+.... 
T Consensus         3 ~~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~   82 (417)
T 2i4i_A            3 VEATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGP   82 (417)
T ss_dssp             EEEESTTCCCCCSSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCC
T ss_pred             cccCCCcCCcccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHhccc
Confidence            3445566678889999999999999999999999999999999999999999999999999999999999998875322 


Q ss_pred             -----------------CceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHH
Q 022724          100 -----------------REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV  162 (293)
Q Consensus       100 -----------------~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l  162 (293)
                                       .++++||++|+++|+.|+.+.++++....++++..++|+.....+...+..+++|+|+||+++
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l  162 (417)
T 2i4i_A           83 GEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRL  162 (417)
T ss_dssp             CHHHHHHHHCBTTBSCSBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCHHHHHHHHTTCCSEEEECHHHH
T ss_pred             cchhhccccccccccccCCccEEEECCcHHHHHHHHHHHHHHhCcCCceEEEEECCCCHHHHHHHhhCCCCEEEEChHHH
Confidence                             236899999999999999999999988889999999999988888888888899999999999


Q ss_pred             HHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhC--CC--CccEEEEEeecChhHHHHHHhcCCCCEEEEecC
Q 022724          163 CDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL--PP--DLQVVLISATLPHEILEMTTKFMTDPVKILVKR  238 (293)
Q Consensus       163 ~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l--~~--~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~  238 (293)
                      .+++..+.+.+.++++||+||+|.+.++++...+..++...  +.  ..|++++|||+++.+..+...++.++..+....
T Consensus       163 ~~~l~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~  242 (417)
T 2i4i_A          163 VDMMERGKIGLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGR  242 (417)
T ss_dssp             HHHHHTTSBCCTTCCEEEESSHHHHHHTTCHHHHHHHHTSSSCCCBTTBEEEEEESCCCHHHHHHHHHHCSSCEEEEEC-
T ss_pred             HHHHHcCCcChhhCcEEEEEChhHhhccCcHHHHHHHHHhccCCCcCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEeCC
Confidence            99999888889999999999999999999999999988853  22  679999999999999999999999998888776


Q ss_pred             CcccCCCceEEEEEecCcccHHHHHHHHHhhC-CCCcEEEEcccchhHHHHHhhC
Q 022724          239 DELTLEGIKQFFVAVEREEWKFDTLCDLYDTL-TITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       239 ~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~-~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      .......+.+.+..+.... +...+..+++.. .++++||||+++++++.+++.|
T Consensus       243 ~~~~~~~i~~~~~~~~~~~-~~~~l~~~l~~~~~~~~~lVf~~~~~~~~~l~~~L  296 (417)
T 2i4i_A          243 VGSTSENITQKVVWVEESD-KRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFL  296 (417)
T ss_dssp             ---CCSSEEEEEEECCGGG-HHHHHHHHHHTCCTTCEEEEECSSHHHHHHHHHHH
T ss_pred             CCCCccCceEEEEEeccHh-HHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHH
Confidence            6666778888888877666 888888888876 4569999999999999998865

>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=8.2e-43  Score=291.21  Aligned_cols=220  Identities=29%  Similarity=0.459  Sum_probs=204.2

Q ss_pred             cceeecccCCccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccC-
Q 022724           20 KMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-   98 (293)
Q Consensus        20 ~~~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~-   98 (293)
                      ...+.+...+.++.+|+++++++.+.+++.++||..|+++|.++++.+.+|+|+++++|||+|||++|++|++..+... 
T Consensus        16 ~i~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~~~l~~l~~l~~~~   95 (242)
T 3fe2_A           16 EITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQP   95 (242)
T ss_dssp             TEEEESSCCCCCCSSTTTTTCCHHHHHHHHTTTCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHHHHHHHHHHHHHTSC
T ss_pred             ceEEeCCCCCCccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHHHHHHHHHHHHHhcc
Confidence            4455667788899999999999999999999999999999999999999999999999999999999999999987643 


Q ss_pred             ----CCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCC
Q 022724           99 ----SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTR  174 (293)
Q Consensus        99 ----~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~  174 (293)
                          ..++++||++|+++|+.|+.+.++++....++++..++|+.+...+...+.++++|+|+||+++.+++..+...+.
T Consensus        96 ~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~  175 (242)
T 3fe2_A           96 FLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLR  175 (242)
T ss_dssp             CCCTTCCCSEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHHTSCCCT
T ss_pred             ccccCCCCEEEEEeCcHHHHHHHHHHHHHHHhhcCceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCCcc
Confidence                3467899999999999999999999998889999999999998888888888899999999999999988888899


Q ss_pred             CccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCC
Q 022724          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRD  239 (293)
Q Consensus       175 ~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~  239 (293)
                      +++++|+||+|++.+++|...+..+++.+++..|++++|||+++.+..++..++.+|..+.+...
T Consensus       176 ~~~~lViDEah~l~~~~~~~~~~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~l~~~~~i~~~~~  240 (242)
T 3fe2_A          176 RTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIGAL  240 (242)
T ss_dssp             TCCEEEETTHHHHHHTTCHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEEEECC-
T ss_pred             cccEEEEeCHHHHhhhCcHHHHHHHHHhCCccceEEEEEeecCHHHHHHHHHHCCCCEEEEecCC
Confidence            99999999999999999999999999999999999999999999999999999999999988754

>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=309.21  Aligned_cols=267  Identities=59%  Similarity=0.993  Sum_probs=244.9

Q ss_pred             ccCCccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEE
Q 022724           26 TEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQAL  105 (293)
Q Consensus        26 ~~~~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~l  105 (293)
                      ....+...+|+++++++.+.+.+.++||..|+++|.++++.+.+|+++++++|||+|||++|++++++.+.....+.+++
T Consensus        33 ~~~~~~~~~f~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~l  112 (414)
T 3eiq_A           33 SNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQAL  112 (414)
T ss_dssp             CCCCCCCCCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCTTSCSCCEE
T ss_pred             CCccchhcCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhhcCCceeEE
Confidence            33445667899999999999999999999999999999999999999999999999999999999999988766678999


Q ss_pred             EEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHh-cCCcEEEeChHHHHHHHhcCCCCCCCccEEEecch
Q 022724          106 ILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDES  184 (293)
Q Consensus       106 il~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~  184 (293)
                      |++|+++|+.|+.+.++++....+..+..+.|+.....+...+. .+++|+|+||+++.+.+..+.+.+.++++||+||+
T Consensus       113 il~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~~~vViDEa  192 (414)
T 3eiq_A          113 VLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEA  192 (414)
T ss_dssp             EECSSHHHHHHHHHHHHHHGGGSCCCEEECCCCTTHHHHHHHHTTTCCSEEEECHHHHHHHHHHTSSCSTTCCEEEECSH
T ss_pred             EEeChHHHHHHHHHHHHHHhcccCceEEEEECCcchHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccCcEEEEECH
Confidence            99999999999999999999888999999999988777776665 67899999999999999888888899999999999


Q ss_pred             hhhhccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHH
Q 022724          185 DEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLC  264 (293)
Q Consensus       185 h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~  264 (293)
                      |.+.+.++...+..++..+++..|++++|||+++.+......++.++..+...........+.+.+..+.....+...+.
T Consensus       193 h~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  272 (414)
T 3eiq_A          193 DEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLC  272 (414)
T ss_dssp             HHHHHTTTHHHHHHHHTTSCTTCEEEEECSCCCHHHHHHHTTTCSSCEEECCCCCCCCTTSCCEEEEECSSSTTHHHHHH
T ss_pred             HHhhccCcHHHHHHHHHhCCCCCeEEEEEEecCHHHHHHHHHHcCCCEEEEecCCccCCCCceEEEEEeChHHhHHHHHH
Confidence            99999999999999999999999999999999999999999999999988887777777888999998888887999999


Q ss_pred             HHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          265 DLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       265 ~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      .+++....+++||||+++++++.+++.|
T Consensus       273 ~~~~~~~~~~~lvf~~~~~~~~~l~~~l  300 (414)
T 3eiq_A          273 DLYETLTITQAVIFINTRRKVDWLTEKM  300 (414)
T ss_dssp             HHHHSSCCSSCEEECSCHHHHHHHHHHH
T ss_pred             HHHHhCCCCcEEEEeCCHHHHHHHHHHH
Confidence            9999888889999999999999998865

>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=3.3e-41  Score=301.21  Aligned_cols=260  Identities=40%  Similarity=0.681  Sum_probs=232.5

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCC
Q 022724           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (293)
Q Consensus        31 ~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~  110 (293)
                      ...+|+++++++.+.+++.++||..|+|+|.++++.+.+|+++++++|||+|||++|++|++..+.....+.+++|++|+
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            45689999999999999999999999999999999999999999999999999999999999988776667799999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcc
Q 022724          111 RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (293)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~  190 (293)
                      ++|+.|+.+.++++....++++....|+.....+...+..+++|+|+||+++.+.+......+.+++++|+||+|++.+.
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            99999999999999988899999999998887777777788899999999999998888788999999999999999888


Q ss_pred             ccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHhhC
Q 022724          191 GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL  270 (293)
Q Consensus       191 ~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~  270 (293)
                      ++...+..+...+++..|++++|||++..+..+....+.++..+.... ......+.+++..+.... |...+..+++..
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            888999999999988999999999999999999988888887765543 344566778877777665 888899999888


Q ss_pred             CCCcEEEEcccchhHHHHHhhC
Q 022724          271 TITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       271 ~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ..+++||||+++++++.+++.|
T Consensus       257 ~~~~~lVf~~~~~~~~~l~~~L  278 (400)
T 1s2m_A          257 QINQAIIFCNSTNRVELLAKKI  278 (400)
T ss_dssp             CCSEEEEECSSHHHHHHHHHHH
T ss_pred             CCCcEEEEEecHHHHHHHHHHH
Confidence            8889999999999999998865

>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=9.5e-42  Score=303.81  Aligned_cols=262  Identities=58%  Similarity=0.965  Sum_probs=191.8

Q ss_pred             ccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcC
Q 022724           30 EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (293)
Q Consensus        30 ~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P  109 (293)
                      +...+|+++++++.+.+++..+||..|+|+|+++++.+.+|+++++++|||+|||++|++|++..+.....+++++|++|
T Consensus        18 ~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P   97 (394)
T 1fuu_A           18 KVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAP   97 (394)
T ss_dssp             CCCCSSGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTTCCSCCEEEECS
T ss_pred             cccCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhccCCCCCEEEEcC
Confidence            44678999999999999999999999999999999999999999999999999999999999999887767789999999


Q ss_pred             CHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhc
Q 022724          110 TRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (293)
Q Consensus       110 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~  189 (293)
                      +++|+.|+.+.++++....++++..++|+.........+. +++|+|+||+++...+......+.+++++|+||+|.+.+
T Consensus        98 ~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-~~~i~v~T~~~l~~~~~~~~~~~~~~~~vIiDEah~~~~  176 (394)
T 1fuu_A           98 TRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLS  176 (394)
T ss_dssp             SHHHHHHHHHHHHHHTTTSCCCEEEECSSCCHHHHHHHHH-HCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHH
T ss_pred             CHHHHHHHHHHHHHHhccCCeeEEEEeCCCchHHHHhhcC-CCCEEEECHHHHHHHHHhCCcchhhCcEEEEEChHHhhC
Confidence            9999999999999998888999999999988766655554 579999999999999988888889999999999999998


Q ss_pred             cccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHhh
Q 022724          190 RGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDT  269 (293)
Q Consensus       190 ~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~  269 (293)
                      .++...+..++..+++..|++++|||+++.+......++.+|..+...........+.+.+..+.....+...+..+++.
T Consensus       177 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  256 (394)
T 1fuu_A          177 SGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLYDS  256 (394)
T ss_dssp             TTCHHHHHHHHHHSCTTCEEEEECSSCCHHHHHHHHHHCCSCEEEEECC-------------------------------
T ss_pred             CCcHHHHHHHHHhCCCCceEEEEEEecCHHHHHHHHHhcCCCeEEEecCccccCCCceEEEEEcCchhhHHHHHHHHHhc
Confidence            89999999999999999999999999999999999999999998888776666677777777777666677788888887


Q ss_pred             CCCCcEEEEcccchhHHHHHhhC
Q 022724          270 LTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       270 ~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ...+++||||+++++++.+++.|
T Consensus       257 ~~~~~~lVf~~~~~~~~~l~~~L  279 (394)
T 1fuu_A          257 ISVTQAVIFCNTRRKVEELTTKL  279 (394)
T ss_dssp             -----------------------
T ss_pred             CCCCcEEEEECCHHHHHHHHHHH
Confidence            77789999999999999998876

>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=1.6e-41  Score=285.18  Aligned_cols=230  Identities=29%  Similarity=0.466  Sum_probs=196.2

Q ss_pred             cceeecccCCc--cccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhcc
Q 022724           20 KMVFETTEGVE--AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT   97 (293)
Q Consensus        20 ~~~~~~~~~~~--~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~   97 (293)
                      +........+.  ++.+|+++++++.+.+++.++||..|+++|.++++.+.+|+|+++++|||+|||++|++|++..+..
T Consensus         8 ~~~~~~~~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~~~~l~~l~~   87 (253)
T 1wrb_A            8 PVSVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVC   87 (253)
T ss_dssp             CCCEECCSSSCCSCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             ceeeeCCCCCCCCccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHh
Confidence            34444444444  7789999999999999999999999999999999999999999999999999999999999988754


Q ss_pred             CC---------CceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc
Q 022724           98 SS---------REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR  168 (293)
Q Consensus        98 ~~---------~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~  168 (293)
                      ..         .++++||++|+++|+.|+.+.++++....++.+..++|+.....+...+..+++|+|+||+++.+.+..
T Consensus        88 ~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~  167 (253)
T 1wrb_A           88 QDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEK  167 (253)
T ss_dssp             TCC------CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHT
T ss_pred             hccccccccccCCceEEEEECCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhCCCCCEEEECHHHHHHHHHc
Confidence            32         346899999999999999999999988888999999999988888888888899999999999999988


Q ss_pred             CCCCCCCccEEEecchhhhhccccHHHHHHHHhhC--CC--CccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCC
Q 022724          169 KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL--PP--DLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLE  244 (293)
Q Consensus       169 ~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l--~~--~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (293)
                      +...+.+++++|+||+|++.+++|...+..++..+  +.  ..|++++|||+++.+..+...++.+|..+.+...+....
T Consensus       168 ~~~~~~~~~~lViDEah~~~~~~~~~~~~~i~~~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~  247 (253)
T 1wrb_A          168 NKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVGSTSD  247 (253)
T ss_dssp             TSBCCTTCCEEEEETHHHHHHTTCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEEC-------
T ss_pred             CCCChhhCCEEEEeCHHHHHhCchHHHHHHHHhhccCCCCCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEECCCCCCcC
Confidence            88889999999999999999999999999999854  33  679999999999999999999999999998887666666


Q ss_pred             CceEE
Q 022724          245 GIKQF  249 (293)
Q Consensus       245 ~i~~~  249 (293)
                      ++.|+
T Consensus       248 ~i~q~  252 (253)
T 1wrb_A          248 SIKQE  252 (253)
T ss_dssp             -----
T ss_pred             Cceec
Confidence            66654

>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=7.9e-41  Score=299.56  Aligned_cols=266  Identities=37%  Similarity=0.629  Sum_probs=233.5

Q ss_pred             ecccCCccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcC--CcEEEEcCCCChhHHHHHHHHHhhhccCCCc
Q 022724           24 ETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSRE  101 (293)
Q Consensus        24 ~~~~~~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~--~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~  101 (293)
                      ..+.+..+..+|+++++++.+.+++.++||..|+|+|.++++.+.++  +++++++|||+|||++|++|++..+.....+
T Consensus        16 ~~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~   95 (412)
T 3fht_A           16 DPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKY   95 (412)
T ss_dssp             CTTSTTCCSSCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTSCS
T ss_pred             cCCCCccccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhhhcCCC
Confidence            34445566789999999999999999999999999999999999987  8999999999999999999999999877777


Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhhccC-CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc-CCCCCCCccEE
Q 022724          102 VQALILSPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-KTLRTRAIKLL  179 (293)
Q Consensus       102 ~~~lil~P~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~-~~~~~~~l~~i  179 (293)
                      ++++|++|+++|+.|+.+.++++.... +..+....++.......   ..+++|+|+||+++.+++.+ +.+.+.++++|
T Consensus        96 ~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~~i  172 (412)
T 3fht_A           96 PQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ---KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVF  172 (412)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTCCCCTTC---CCCCSEEEECHHHHHHHHTTSCSSCGGGCCEE
T ss_pred             CCEEEECCCHHHHHHHHHHHHHHHhhcccceEEEeecCcchhhhh---cCCCCEEEECchHHHHHHHhcCCcChhhCcEE
Confidence            899999999999999999999987654 57777777776543321   34579999999999998865 56677899999


Q ss_pred             Eecchhhhhc-cccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCccc
Q 022724          180 VLDESDEMLS-RGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEW  258 (293)
Q Consensus       180 ViDE~h~~~~-~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~  258 (293)
                      |+||+|++.+ .++...+..+...++...|++++|||+++.+..+...++.++..+...........+.+.+..+.....
T Consensus       173 ViDEah~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  252 (412)
T 3fht_A          173 VLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDE  252 (412)
T ss_dssp             EEETHHHHHSTTTTHHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSSSCEEECCCGGGSSCTTEEEEEEECSSHHH
T ss_pred             EEeCHHHHhhcCCcHHHHHHHHhhCCCCceEEEEEeecCHHHHHHHHHhcCCCeEEeeccccccccCceEEEEEcCChHH
Confidence            9999999987 578888889999999999999999999999999999999999988887777777888899888888777


Q ss_pred             HHHHHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          259 KFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       259 k~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      +...+..++....++++||||+++++|+.+++.|
T Consensus       253 ~~~~l~~~~~~~~~~~~lvf~~~~~~~~~l~~~L  286 (412)
T 3fht_A          253 KFQALCNLYGAITIAQAMIFCHTRKTASWLAAEL  286 (412)
T ss_dssp             HHHHHHHHHHHHSSSEEEEECSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhcCCCCEEEEeCCHHHHHHHHHHH
Confidence            8999999998888889999999999999999875

>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=4.5e-41  Score=288.85  Aligned_cols=209  Identities=37%  Similarity=0.593  Sum_probs=187.4

Q ss_pred             cCCccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcC--CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeE
Q 022724           27 EGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQA  104 (293)
Q Consensus        27 ~~~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~--~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~  104 (293)
                      .+..+..+|+++++++.+++++.++||..|+++|.++||.++.|  +|+++++|||+|||++|++|+++.+.....++++
T Consensus        86 ~p~~~~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~~~~~~~  165 (300)
T 3fmo_B           86 SPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQC  165 (300)
T ss_dssp             CCCCCCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCE
T ss_pred             CCcCCcCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhhhccCCCceE
Confidence            34446789999999999999999999999999999999999987  9999999999999999999999999887778899


Q ss_pred             EEEcCCHHHHHHHHHHHHHhhccC-CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc-CCCCCCCccEEEec
Q 022724          105 LILSPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-KTLRTRAIKLLVLD  182 (293)
Q Consensus       105 lil~P~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~-~~~~~~~l~~iViD  182 (293)
                      ||++|+++|+.|+.+.++.+.... ++.+....++.......   ..+++|+|+||+++.+++.+ +.+.++++++||||
T Consensus       166 lil~PtreLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~TP~~l~~~l~~~~~~~l~~l~~lVlD  242 (300)
T 3fmo_B          166 LCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ---KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLD  242 (300)
T ss_dssp             EEECSSHHHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTTC---CCCCSEEEECHHHHHHHHTTTCCCCGGGCSEEEET
T ss_pred             EEEcCcHHHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhhh---cCCCCEEEECHHHHHHHHHhcCCCChhhceEEEEe
Confidence            999999999999999999988764 67888888876544322   35679999999999999866 66778999999999


Q ss_pred             chhhhhc-cccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecC
Q 022724          183 ESDEMLS-RGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKR  238 (293)
Q Consensus       183 E~h~~~~-~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~  238 (293)
                      |+|.+++ .++...+..+.+.+++.+|++++|||+++.+..++..++.+|..+.+..
T Consensus       243 Ead~l~~~~~~~~~~~~i~~~~~~~~q~i~~SAT~~~~v~~~a~~~l~~p~~i~~~~  299 (300)
T 3fmo_B          243 EADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKR  299 (300)
T ss_dssp             THHHHHHSTTHHHHHHHHHTTSCTTCEEEEEESCCCHHHHHHHHHHSSSCEEEEECC
T ss_pred             CHHHHhhccCcHHHHHHHHHhCCCCCEEEEEeccCCHHHHHHHHHHCCCCeEEEecC
Confidence            9999987 6899999999999999999999999999999999999999999887753

>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=2.8e-40  Score=294.18  Aligned_cols=259  Identities=36%  Similarity=0.612  Sum_probs=229.0

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHH
Q 022724           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (293)
Q Consensus        33 ~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~  112 (293)
                      .+|+++++++.+.++|.++||..|+|+|.++++.+.+|+++++.+|||+|||++|++|++..+.....+.++||++|+++
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            57999999999999999999999999999999999999999999999999999999999999877666779999999999


Q ss_pred             HHHHHHHHHHHhhccC-CceEEEEECCcchHHHHHHHhc-CCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcc
Q 022724          113 LATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEH-GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (293)
Q Consensus       113 l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~-~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~  190 (293)
                      |+.|+.+.++++.... ++++..++|+.........+.+ .++|+|+||+++..++......+.+++++|+||+|++.++
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 7889999999887766665543 4799999999999999888888999999999999999874


Q ss_pred             -ccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCc-ccCCCceEEEEEecCcccHHHHHHHHHh
Q 022724          191 -GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDE-LTLEGIKQFFVAVEREEWKFDTLCDLYD  268 (293)
Q Consensus       191 -~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~i~~~~~~~~~~~~k~~~l~~l~~  268 (293)
                       ++...+..++...++..|++++|||+++.+......++.+|..+...... .....+.+.+..+.... +...+..+++
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             77888888898888899999999999999999999999999888776543 34456777777776665 8888999998


Q ss_pred             hCCCCcEEEEcccchhHHHHHhhC
Q 022724          269 TLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       269 ~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ...++++||||+++++++.+++.|
T Consensus       247 ~~~~~~~lvf~~~~~~~~~l~~~L  270 (391)
T 1xti_A          247 VLEFNQVVIFVKSVQRCIALAQLL  270 (391)
T ss_dssp             HSCCSEEEEECSCHHHHHHHHHHH
T ss_pred             hcCCCcEEEEeCcHHHHHHHHHHH
Confidence            888889999999999999998865

>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=5.3e-41  Score=277.77  Aligned_cols=212  Identities=31%  Similarity=0.485  Sum_probs=187.8

Q ss_pred             ecccCCccccCccc-CCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccC----
Q 022724           24 ETTEGVEAITSFDA-MGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS----   98 (293)
Q Consensus        24 ~~~~~~~~~~~f~~-~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~----   98 (293)
                      +....+++..+|++ +++++++.+++.++||..|+++|.++++.+.+|+|+++++|||+|||++|++|++..+...    
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            44556778899999 7999999999999999999999999999999999999999999999999999999887542    


Q ss_pred             --CCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCc
Q 022724           99 --SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (293)
Q Consensus        99 --~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l  176 (293)
                        ..++++||++|+++|+.|+.+.++++. ..++++..++|+.....+...+.++++|+|+||+++.+++......+.++
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              256789999999999999999999986 45788889999988888888888889999999999999998888889999


Q ss_pred             cEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEe
Q 022724          177 KLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILV  236 (293)
Q Consensus       177 ~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~  236 (293)
                      +++|+||+|++.++++...+..++..++++.|++++|||+++.+.+++..++.+|..+.+
T Consensus       169 ~~lViDEah~~~~~~~~~~~~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~l~~p~~i~v  228 (228)
T 3iuy_A          169 TYLVIDEADKMLDMEFEPQIRKILLDVRPDRQTVMTSATWPDTVRQLALSYLKDPMIVYV  228 (228)
T ss_dssp             CEEEECCHHHHHHTTCHHHHHHHHHHSCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEEC
T ss_pred             eEEEEECHHHHhccchHHHHHHHHHhCCcCCeEEEEEeeCCHHHHHHHHHHCCCCEEEeC
Confidence            999999999999999999999999999999999999999999999999999999987753

>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=3.5e-41  Score=280.48  Aligned_cols=214  Identities=57%  Similarity=0.945  Sum_probs=182.2

Q ss_pred             ecccCCccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCcee
Q 022724           24 ETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQ  103 (293)
Q Consensus        24 ~~~~~~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~  103 (293)
                      ..+..+++..+|+++++++++.+++.++||..|+++|.++++.+.+|+|+++++|||+|||++|++|++..+.....+++
T Consensus        21 ~~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~~~~~~~  100 (237)
T 3bor_A           21 IESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEFKETQ  100 (237)
T ss_dssp             ------CCCCSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCTTSCSCC
T ss_pred             ccCCCCCccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCce
Confidence            34445667889999999999999999999999999999999999999999999999999999999999999877666779


Q ss_pred             EEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcC-CcEEEeChHHHHHHHhcCCCCCCCccEEEec
Q 022724          104 ALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG-VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLD  182 (293)
Q Consensus       104 ~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViD  182 (293)
                      +||++|+++|+.|+.+.++++....+..+..+.|+.....+...+..+ ++|+|+||+++.+++..+...+.++++||+|
T Consensus       101 ~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~~~~lViD  180 (237)
T 3bor_A          101 ALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLD  180 (237)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECC-------------CCCSEEEECHHHHHHHHHTTSSCSTTCCEEEEE
T ss_pred             EEEEECcHHHHHHHHHHHHHHhhhcCceEEEEECCCchHHHHHHHhcCCCCEEEECHHHHHHHHHhCCcCcccCcEEEEC
Confidence            999999999999999999999888888998899988777666666554 8999999999999998888888999999999


Q ss_pred             chhhhhccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEec
Q 022724          183 ESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVK  237 (293)
Q Consensus       183 E~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~  237 (293)
                      |+|.+.+.++...+..+++.++...|++++|||+++.+.+++..++.+|..+.+.
T Consensus       181 Eah~~~~~~~~~~l~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~l~~p~~i~v~  235 (237)
T 3bor_A          181 EADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVK  235 (237)
T ss_dssp             SHHHHHHTTCHHHHHHHHHHSCTTCEEEEECSSCCHHHHHHHHHHCSSCEEEC--
T ss_pred             CchHhhccCcHHHHHHHHHhCCCCCeEEEEEEecCHHHHHHHHHHCCCCEEEEec
Confidence            9999999999999999999999999999999999999999999999999887654

>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=2.6e-40  Score=294.41  Aligned_cols=258  Identities=38%  Similarity=0.626  Sum_probs=230.7

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcC--CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEc
Q 022724           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (293)
Q Consensus        31 ~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~--~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~  108 (293)
                      ...+|+++++++.+.+++.+.||..|+|+|.++++.+.++  +++++++|||+|||++|+++++..+.....++++||++
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  89999999999999999999999988776778999999


Q ss_pred             CCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhh
Q 022724          109 PTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (293)
Q Consensus       109 P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~  188 (293)
                      |+++|+.|+.+.++++....++.+....++......    ..+++|+|+||+++...+......+.++++||+||+|.+.
T Consensus        83 P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~  158 (395)
T 3pey_A           83 PSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKNK----QINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNML  158 (395)
T ss_dssp             SSHHHHHHHHHHHHHHTTTSCCCEEEESTTSSCTTS----CBCCSEEEECHHHHHHHHHTTCBCCTTCCEEEEETHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhcccCeeEEEEecCchhhhc----cCCCCEEEEcHHHHHHHHHcCCcccccCCEEEEEChhhhc
Confidence            999999999999999988888888887776543221    2367999999999999998888889999999999999998


Q ss_pred             c-cccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHH
Q 022724          189 S-RGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLY  267 (293)
Q Consensus       189 ~-~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~  267 (293)
                      + .++...+..+...+++..|++++|||+++.+..+...++.++..+...........+.+.+..+.....+...+..++
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 578888889999999999999999999999999999999998888877777777788888888877777888899999


Q ss_pred             hhCCCCcEEEEcccchhHHHHHhhC
Q 022724          268 DTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       268 ~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      .....+++||||++++.|+.+++.|
T Consensus       239 ~~~~~~~~lvf~~~~~~~~~l~~~l  263 (395)
T 3pey_A          239 GLMTIGSSIIFVATKKTANVLYGKL  263 (395)
T ss_dssp             TTTTSSEEEEECSCHHHHHHHHHHH
T ss_pred             HhccCCCEEEEeCCHHHHHHHHHHH
Confidence            8888889999999999999998865

>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=2e-40  Score=269.92  Aligned_cols=202  Identities=34%  Similarity=0.640  Sum_probs=188.8

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHH
Q 022724           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (293)
Q Consensus        33 ~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~  112 (293)
                      .+|+++++++++++++.++||..|+++|.++++.+.+|+++++++|||+|||++|++|++..+.....++++||++|+++
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            57999999999999999999999999999999999999999999999999999999999999877667789999999999


Q ss_pred             HHHHHHHHHHHhhccC-CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccc
Q 022724          113 LATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG  191 (293)
Q Consensus       113 l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~  191 (293)
                      |+.|+.+.++.+.... +.++..++|+.....+...+.++++|+|+||+++.+.+.++...+.+++++|+||+|.+.+.+
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            9999999999988776 788999999988887777777889999999999999998888889999999999999999889


Q ss_pred             cHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEE
Q 022724          192 FKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKI  234 (293)
Q Consensus       192 ~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~  234 (293)
                      +...+..++..+++..|++++|||+++.+.+++..++.+|..+
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

>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=1.1e-40  Score=279.33  Aligned_cols=209  Identities=33%  Similarity=0.541  Sum_probs=193.7

Q ss_pred             CccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEc
Q 022724           29 VEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (293)
Q Consensus        29 ~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~  108 (293)
                      ..+..+|+++++++.+.++++++||..|+++|.++++.+.+|+++++++|||+|||++|++|++..+.....++++||++
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            34567899999999999999999999999999999999999999999999999999999999999988776778999999


Q ss_pred             CCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc-CCCCCCCccEEEecchhhh
Q 022724          109 PTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-KTLRTRAIKLLVLDESDEM  187 (293)
Q Consensus       109 P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~-~~~~~~~l~~iViDE~h~~  187 (293)
                      |+++|+.|+.+.++++....++++..++|+.....+...+.++++|+|+||+++.+.+.+ ..+.+.++++||+||+|++
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            999999999999999998889999999999888777777778899999999999998876 5567899999999999999


Q ss_pred             hccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEec
Q 022724          188 LSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVK  237 (293)
Q Consensus       188 ~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~  237 (293)
                      .+.++...+..+++.+++..|++++|||+++.+.++++.++.+|..+.+.
T Consensus       199 ~~~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~p~~i~v~  248 (249)
T 3ber_A          199 LNMDFETEVDKILKVIPRDRKTFLFSATMTKKVQKLQRAALKNPVKCAVS  248 (249)
T ss_dssp             HHTTCHHHHHHHHHSSCSSSEEEEEESSCCHHHHHHHHHHCSSCEEEECC
T ss_pred             hccChHHHHHHHHHhCCCCCeEEEEeccCCHHHHHHHHHHCCCCEEEEec
Confidence            99999999999999999899999999999999999999999999887653

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=100.00  E-value=5.6e-41  Score=275.96  Aligned_cols=207  Identities=34%  Similarity=0.557  Sum_probs=189.2

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCH
Q 022724           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (293)
Q Consensus        32 ~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~  111 (293)
                      ..+|+++++++++.+++.++||..|+++|.++++.+.+|+++++++|||+|||++|++|++..+.....+++++|++|++
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            46799999999999999999999999999999999999999999999999999999999999988766678999999999


Q ss_pred             HHHHHHHHHHHHhhccC----CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhh
Q 022724          112 ELATQTEKVILAIGDFI----NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (293)
Q Consensus       112 ~l~~q~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~  187 (293)
                      +|+.|+.+.++++....    ++.+..++|+.......+.+.++++|+|+||+++.+.+..+...+.+++++|+||+|.+
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    67888889988776665556667899999999999999888888899999999999999


Q ss_pred             hccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecC
Q 022724          188 LSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKR  238 (293)
Q Consensus       188 ~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~  238 (293)
                      .++++...+..++..+++..|++++|||+++++.++++.++.+|..+.+..
T Consensus       163 ~~~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~~~~p~~~~~~~  213 (219)
T 1q0u_A          163 LDMGFITDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPTFVHVLE  213 (219)
T ss_dssp             HHTTCHHHHHHHHHTSCTTCEEEEEESCCCGGGHHHHHHHCSSCEEEECC-
T ss_pred             hhhChHHHHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHcCCCeEEEeec
Confidence            999999999999999998999999999999999999999999998876653

>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=5.5e-41  Score=306.74  Aligned_cols=260  Identities=38%  Similarity=0.639  Sum_probs=180.9

Q ss_pred             ccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcC--CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEE
Q 022724           30 EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALIL  107 (293)
Q Consensus        30 ~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~--~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil  107 (293)
                      .+..+|+++++++.+.++++++||..|+|+|.++++.++.+  +++++++|||+|||++|++|++..+.....++++||+
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            44678999999999999999999999999999999999987  8999999999999999999999999887777899999


Q ss_pred             cCCHHHHHHHHHHHHHhhccC-CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc-CCCCCCCccEEEecchh
Q 022724          108 SPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-KTLRTRAIKLLVLDESD  185 (293)
Q Consensus       108 ~P~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~-~~~~~~~l~~iViDE~h  185 (293)
                      +|+++|+.|+.+.++.+.... ++.+....++.......   ..+++|+|+||+++.+++.+ +.+.+.++++|||||+|
T Consensus       169 ~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEah  245 (479)
T 3fmp_B          169 SPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ---KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEAD  245 (479)
T ss_dssp             CSSHHHHHHHHHHHHHHHTTSTTCCEEEESTTCCCCTTC---CCCCSEEEECHHHHHHHHTTSCCCCGGGCCEEEECCHH
T ss_pred             eChHHHHHHHHHHHHHHHhhCCCceEEEEeCCccccccc---cCCCCEEEECchHHHHHHHhcCCcCcccCCEEEEECHH
Confidence            999999999999999887654 56777777665443221   23568999999999998866 55677999999999999


Q ss_pred             hhhc-cccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHH
Q 022724          186 EMLS-RGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLC  264 (293)
Q Consensus       186 ~~~~-~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~  264 (293)
                      .+.+ .++...+..+.+.++..+|++++|||+++.+..+...++.++..+...........+.+.+..+.....+...+.
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 578888889999999999999999999999999999999999999888777777788888888887777888888


Q ss_pred             HHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          265 DLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       265 ~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      .++......++||||++++.|+.++..|
T Consensus       326 ~~~~~~~~~~~lvF~~s~~~~~~l~~~L  353 (479)
T 3fmp_B          326 NLYGAITIAQAMIFCHTRKTASWLAAEL  353 (479)
T ss_dssp             ----------------------------
T ss_pred             HHHhhccCCceEEEeCcHHHHHHHHHHH
Confidence            8888777789999999999999999876

>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=1.9e-40  Score=273.58  Aligned_cols=212  Identities=55%  Similarity=0.922  Sum_probs=185.1

Q ss_pred             cCCccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEE
Q 022724           27 EGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALI  106 (293)
Q Consensus        27 ~~~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~li  106 (293)
                      .-+.+..+|+++++++.+.+.+.++||..|+++|.++++.+.+|+++++++|||+|||++|++|+++.+.....++++||
T Consensus         8 ~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~~~~~~~li   87 (224)
T 1qde_A            8 NYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALM   87 (224)
T ss_dssp             SCCCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEE
T ss_pred             ccCcccCChhhcCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhccCCCceEEE
Confidence            34556789999999999999999999999999999999999999999999999999999999999999887777789999


Q ss_pred             EcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhh
Q 022724          107 LSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDE  186 (293)
Q Consensus       107 l~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~  186 (293)
                      ++|+++|+.|+.+.++++....++++..++|+.....+...+.+ ++|+|+||+++.+.+.++...+.+++++|+||+|+
T Consensus        88 l~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~-~~iiv~Tp~~l~~~~~~~~~~~~~~~~iViDEah~  166 (224)
T 1qde_A           88 LAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLRD-AQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADE  166 (224)
T ss_dssp             ECSSHHHHHHHHHHHHHHTTTSCCCEEEECC----------CTT-CSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHH
T ss_pred             EECCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHhcCCC-CCEEEECHHHHHHHHHhCCcchhhCcEEEEcChhH
Confidence            99999999999999999988889999999998877666555544 89999999999999988888899999999999999


Q ss_pred             hhccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCC
Q 022724          187 MLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRD  239 (293)
Q Consensus       187 ~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~  239 (293)
                      +.++++...+..++..+++..|++++|||+++.+.++...++.+|..+.+...
T Consensus       167 ~~~~~~~~~l~~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~~p~~i~~~~~  219 (224)
T 1qde_A          167 MLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKD  219 (224)
T ss_dssp             HHHTTCHHHHHHHHHHSCTTCEEEEEESSCCHHHHHHHHHHCSSCEEEC----
T ss_pred             HhhhhhHHHHHHHHHhCCccCeEEEEEeecCHHHHHHHHHHCCCCEEEEecCC
Confidence            99999999999999999999999999999999999999999999988876543

>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=2.4e-40  Score=274.19  Aligned_cols=211  Identities=34%  Similarity=0.561  Sum_probs=186.6

Q ss_pred             cccCCccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeE
Q 022724           25 TTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQA  104 (293)
Q Consensus        25 ~~~~~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~  104 (293)
                      ....+.+..+|+++++++.+.++++++||..|+++|.++++.+.+|+|+++++|||+|||++|++|++..+.....++++
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            44455667889999999999999999999999999999999999999999999999999999999999998776667899


Q ss_pred             EEEcCCHHHHHHHHHHHHHhhccC-CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecc
Q 022724          105 LILSPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDE  183 (293)
Q Consensus       105 lil~P~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE  183 (293)
                      ||++|+++|+.|+.+.++++.... ++++..++|+.....+...+ .+++|+|+||+++.+++..+.+.+.+++++|+||
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            999999999999999999987665 78899999988776665555 4689999999999999988888889999999999


Q ss_pred             hhhhhccc-cHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEe
Q 022724          184 SDEMLSRG-FKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILV  236 (293)
Q Consensus       184 ~h~~~~~~-~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~  236 (293)
                      +|++.+++ |...+..+++.+++..|++++|||+++.+.+++..++.+|..+.+
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 999999999999989999999999999999999999999987754

>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=3.3e-39  Score=268.36  Aligned_cols=208  Identities=28%  Similarity=0.499  Sum_probs=186.6

Q ss_pred             CccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccC----CCceeE
Q 022724           29 VEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS----SREVQA  104 (293)
Q Consensus        29 ~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~----~~~~~~  104 (293)
                      +.+..+|+++++++.+.+++.+.||..|+++|.++++.+.+|+++++++|||+|||++|++|++..+...    ..++++
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            4567789999999999999999999999999999999999999999999999999999999999887542    235689


Q ss_pred             EEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcC-CCCCCCccEEEecc
Q 022724          105 LILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK-TLRTRAIKLLVLDE  183 (293)
Q Consensus       105 lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~-~~~~~~l~~iViDE  183 (293)
                      +|++|+++|+.|+.+.++.+....++++..++|+.....+...+ .+++|+|+||+++.+.+... .+.+.+++++|+||
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            99999999999999999999888889999999998777666555 46899999999999987664 56788999999999


Q ss_pred             hhhhhccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEec
Q 022724          184 SDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVK  237 (293)
Q Consensus       184 ~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~  237 (293)
                      +|++.++++...+..+++.+++..|++++|||+++.+.++.+.++.+|..+.+.
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            999999999999999999999999999999999999999999999999888765

>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=5.3e-39  Score=261.67  Aligned_cols=201  Identities=35%  Similarity=0.584  Sum_probs=184.5

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccC---CCceeEEEEcCC
Q 022724           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS---SREVQALILSPT  110 (293)
Q Consensus        34 ~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~---~~~~~~lil~P~  110 (293)
                      +|+++++++++.+++.+.||..|+++|.++++.+.+|+++++++|||+|||++|++|++..+...   ..+++++|++|+
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            69999999999999999999999999999999999999999999999999999999999988642   346789999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcc
Q 022724          111 RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (293)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~  190 (293)
                      ++|+.|+.+.++++...  +++..++|+.....+...+.++++|+|+||+++.+.+..+...+.+++++|+||+|.+.+.
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            99999999999988654  6778888888877777777778999999999999999888888999999999999999999


Q ss_pred             ccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEe
Q 022724          191 GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILV  236 (293)
Q Consensus       191 ~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~  236 (293)
                      ++...+..+++.+++..|++++|||+++.+.++.+.++.+|..+.+
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            9999999999999989999999999999999999999999988765

>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=4.7e-39  Score=264.61  Aligned_cols=206  Identities=35%  Similarity=0.594  Sum_probs=185.3

Q ss_pred             ccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcC
Q 022724           30 EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (293)
Q Consensus        30 ~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P  109 (293)
                      ....+|+++++++.+.+++.++||..|+++|.++++.+.+|+++++++|||+|||++|++|++..+.....+++++|++|
T Consensus        11 ~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P   90 (220)
T 1t6n_A           11 IHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCH   90 (220)
T ss_dssp             ---CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECS
T ss_pred             ccCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhccCCCEEEEEEeC
Confidence            34467999999999999999999999999999999999999999999999999999999999999877666679999999


Q ss_pred             CHHHHHHHHHHHHHhhccC-CceEEEEECCcchHHHHHHHhc-CCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhh
Q 022724          110 TRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEH-GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (293)
Q Consensus       110 ~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~-~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~  187 (293)
                      +++|+.|+.+.++++.... ++++..++|+.....+...+.+ .++|+|+||+++..++......+.+++++|+||+|++
T Consensus        91 t~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDEah~~  170 (220)
T 1t6n_A           91 TRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKM  170 (220)
T ss_dssp             CHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEESHHHH
T ss_pred             CHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHHHhcCCCCEEEeCHHHHHHHHHhCCCCcccCCEEEEcCHHHH
Confidence            9999999999999988766 7899999999887776666653 5699999999999999888888999999999999999


Q ss_pred             hc-cccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEE
Q 022724          188 LS-RGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKIL  235 (293)
Q Consensus       188 ~~-~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~  235 (293)
                      .+ .++...+..+++.+++..|++++|||+++.+.++.+.++.+|..+.
T Consensus       171 ~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~p~~i~  219 (220)
T 1t6n_A          171 LEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIF  219 (220)
T ss_dssp             HSSHHHHHHHHHHHHTSCSSSEEEEEESCCCTTTHHHHHTTCSSCEEEE
T ss_pred             hcccCcHHHHHHHHHhCCCcCeEEEEEeecCHHHHHHHHHHcCCCeEEe
Confidence            87 4788889999999988999999999999999999999999998764

>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=3e-38  Score=278.35  Aligned_cols=253  Identities=34%  Similarity=0.592  Sum_probs=221.1

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcC-CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCC
Q 022724           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG-RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (293)
Q Consensus        32 ~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~-~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~  110 (293)
                      ..+|+++++++.+.+++++.||..|+|+|.++++.+.++ +++++.+|||+|||++|+++++..+... .+.+++|++|+
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 7999999999999999999999887654 35689999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcc
Q 022724          111 RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (293)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~  190 (293)
                      ++|+.|+.+.++++....++.+...+|+.....+...+. +++|+|+||+++.+.+..+...+.+++++|+||+|.+.+.
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            999999999999998888889999999988776666554 5799999999999999888888899999999999999999


Q ss_pred             ccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHhhC
Q 022724          191 GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL  270 (293)
Q Consensus       191 ~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~  270 (293)
                      ++...+..++..+++..+++++|||+++........++.++..+.....    ..+.+.+..+.... +...+..+++ .
T Consensus       163 ~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~-~~~~l~~~l~-~  236 (367)
T 1hv8_A          163 GFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKAKIN----ANIEQSYVEVNENE-RFEALCRLLK-N  236 (367)
T ss_dssp             TTHHHHHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEECCSS----SSSEEEEEECCGGG-HHHHHHHHHC-S
T ss_pred             chHHHHHHHHHhCCCCceEEEEeeccCHHHHHHHHHHcCCCeEEEecCC----CCceEEEEEeChHH-HHHHHHHHHh-c
Confidence            9999999999999889999999999999998888888887666554322    35677777776655 8888888886 4


Q ss_pred             CCCcEEEEcccchhHHHHHhhC
Q 022724          271 TITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       271 ~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      .+.++||||+++++++.+++.|
T Consensus       237 ~~~~~lvf~~~~~~~~~l~~~L  258 (367)
T 1hv8_A          237 KEFYGLVFCKTKRDTKELASML  258 (367)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHH
T ss_pred             CCCcEEEEECCHHHHHHHHHHH
Confidence            4579999999999999998865

>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=1.1e-38  Score=269.07  Aligned_cols=200  Identities=29%  Similarity=0.509  Sum_probs=179.0

Q ss_pred             cCcccCC--CCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCC----CceeEEE
Q 022724           33 TSFDAMG--IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS----REVQALI  106 (293)
Q Consensus        33 ~~f~~~~--l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~----~~~~~li  106 (293)
                      .+|++++  +++.++++++++||..|+++|.++++.+..|+|+++++|||+|||++|++|++..+....    .+.++||
T Consensus        52 ~~f~~l~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~~~~li  131 (262)
T 3ly5_A           52 TSFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLI  131 (262)
T ss_dssp             GCC-----CCCHHHHHHHHHTTCCBCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEE
T ss_pred             CChhHhccccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhccccccCCceEEE
Confidence            4566666  999999999999999999999999999999999999999999999999999998876422    3568999


Q ss_pred             EcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcC-CCCCCCccEEEecchh
Q 022724          107 LSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK-TLRTRAIKLLVLDESD  185 (293)
Q Consensus       107 l~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~-~~~~~~l~~iViDE~h  185 (293)
                      ++|+++|+.|+.+.++++....+..+..+.|+.....+...+..+++|+|+||+++...+... .+.+.++++|||||+|
T Consensus       132 l~Pt~~La~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~~~~~~~~~~~~l~~lViDEah  211 (262)
T 3ly5_A          132 LSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEAD  211 (262)
T ss_dssp             ECSSHHHHHHHHHHHHHHTTTCCSCEEEECSSSCHHHHHHHHHHCCSEEEECHHHHHHHHHHCTTCCCTTCCEEEECSHH
T ss_pred             EeCCHHHHHHHHHHHHHHHhhcCceEEEEECCCCHHHHHHHhcCCCCEEEEcHHHHHHHHHccCCcccccCCEEEEcChH
Confidence            999999999999999999988899999999999888888888788999999999999977664 4678999999999999


Q ss_pred             hhhccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCE
Q 022724          186 EMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPV  232 (293)
Q Consensus       186 ~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~  232 (293)
                      ++.+++|...+..+++.+++.+|++++|||+++.+.++.+.++.++.
T Consensus       212 ~l~~~~~~~~l~~i~~~~~~~~q~l~~SAT~~~~v~~~~~~~l~~~~  258 (262)
T 3ly5_A          212 RILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEP  258 (262)
T ss_dssp             HHHHTTCHHHHHHHHHHSCSSSEEEEECSSCCHHHHHHHHHHCSSCC
T ss_pred             HHhhhhHHHHHHHHHHhCCCCCeEEEEEecCCHHHHHHHHHHcCCCC
Confidence            99999999999999999999999999999999999999998876543

>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=9.4e-39  Score=267.07  Aligned_cols=220  Identities=24%  Similarity=0.451  Sum_probs=188.5

Q ss_pred             cceeecccCCccccCcccC----CCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhh
Q 022724           20 KMVFETTEGVEAITSFDAM----GIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTV   95 (293)
Q Consensus        20 ~~~~~~~~~~~~~~~f~~~----~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l   95 (293)
                      ...++....+.++.+|+++    ++++++.+++.++||..|+++|.++++.+.+|+++++++|||+|||++|++|++..+
T Consensus        12 ~i~~~~~~~p~~~~~f~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l   91 (245)
T 3dkp_A           12 KIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQL   91 (245)
T ss_dssp             TEEEESSSCCCCCSSHHHHHHHHCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             ceEecCCCCCCcccCHHHhhhccCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHH
Confidence            3455667778889999987    899999999999999999999999999999999999999999999999999999988


Q ss_pred             ccC-CCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHH-HHHhcCCcEEEeChHHHHHHHhcC--CC
Q 022724           96 DTS-SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDI-RKLEHGVHVVSGTPGRVCDMIKRK--TL  171 (293)
Q Consensus        96 ~~~-~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~ilV~Tp~~l~~~l~~~--~~  171 (293)
                      ... ..++++||++|+++|+.|+.+.++++....++++..++++....... .....+++|+|+||+++..++...  ..
T Consensus        92 ~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~  171 (245)
T 3dkp_A           92 KQPANKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGI  171 (245)
T ss_dssp             CSCCSSSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEECCCHHHHHHTTTSTTSCCCCCEEEECHHHHHHHHHSSSCSC
T ss_pred             hhcccCCceEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEecCccHHHHhhhhhcCCCCEEEECHHHHHHHHHhCCCCc
Confidence            643 35678999999999999999999999888888887777664333222 122456799999999999998775  56


Q ss_pred             CCCCccEEEecchhhhhcc---ccHHHHHHHHhhCC-CCccEEEEEeecChhHHHHHHhcCCCCEEEEecCC
Q 022724          172 RTRAIKLLVLDESDEMLSR---GFKDQIYDVYRYLP-PDLQVVLISATLPHEILEMTTKFMTDPVKILVKRD  239 (293)
Q Consensus       172 ~~~~l~~iViDE~h~~~~~---~~~~~~~~i~~~l~-~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~  239 (293)
                      .+.+++++|+||+|.+.++   ++...+..++..+. ...|++++|||+++++..+++.++.+|..+.+...
T Consensus       172 ~~~~~~~lViDEah~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~SAT~~~~v~~~~~~~l~~p~~i~~~~~  243 (245)
T 3dkp_A          172 DLASVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISVSIGAR  243 (245)
T ss_dssp             CCTTCCEEEESSHHHHHHHC--CHHHHHHHHHHHCCCTTCEEEEEESSCCHHHHHHHHHHSSSCEEEEECC-
T ss_pred             ccccCcEEEEeChHHhcccccccHHHHHHHHHHhcCCCCcEEEEEeccCCHHHHHHHHHhCCCCEEEEeCCC
Confidence            7899999999999999874   67788888877764 57899999999999999999999999999988653

>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=6.8e-38  Score=292.41  Aligned_cols=263  Identities=25%  Similarity=0.387  Sum_probs=210.5

Q ss_pred             ccccCcccCC----CCHHHHHHHHHCCCCCCcHHHHHHHHhhh--cCCcEEEEcCCCChhHHHHHHHHHhhhccCC----
Q 022724           30 EAITSFDAMG----IKDDLLRGIYQYGFEKPSAIQQRAVMPII--KGRDVIAQAQSGTGKTSMIALTVCQTVDTSS----   99 (293)
Q Consensus        30 ~~~~~f~~~~----l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~--~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~----   99 (293)
                      ....+|+++.    +++++++++.++||..|+|+|.++++.++  .|+++++++|||+|||++|++|+++.+....    
T Consensus        14 ~~~~~~~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~~~~   93 (579)
T 3sqw_A           14 SKEVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQ   93 (579)
T ss_dssp             CCCCCHHHHHHTTSSCHHHHHHHHTTTCSSCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSST
T ss_pred             CCCcCHHHHhhcCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhcccccc
Confidence            3344555553    99999999999999999999999999999  7889999999999999999999998876542    


Q ss_pred             CceeEEEEcCCHHHHHHHHHHHHHhhc----cCCceEEEEECCcchHHHHHHHh-cCCcEEEeChHHHHHHHhcC-CCCC
Q 022724          100 REVQALILSPTRELATQTEKVILAIGD----FINIQAHACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRK-TLRT  173 (293)
Q Consensus       100 ~~~~~lil~P~~~l~~q~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~-~~~~ilV~Tp~~l~~~l~~~-~~~~  173 (293)
                      .++++||++|+++|+.|+.+.++++..    .....+....|+.....+...+. .+++|+|+||+++..++... ...+
T Consensus        94 ~~~~~lvl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~  173 (579)
T 3sqw_A           94 YMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFF  173 (579)
T ss_dssp             TSCCEEEECSSHHHHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHC
T ss_pred             CCCeEEEEcchHHHHHHHHHHHHHHHhhcccccceEEEEEECCccHHHHHHHHhcCCCCEEEECHHHHHHHHHhcccccc
Confidence            356899999999999999999998753    23467788888888777776664 47899999999999988764 4457


Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCC-------CCccEEEEEeecChhHHHHHHhcCCCCEEEEecCC----ccc
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLP-------PDLQVVLISATLPHEILEMTTKFMTDPVKILVKRD----ELT  242 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~-------~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~----~~~  242 (293)
                      +++++|||||||++.+++|...+..+...++       ...|++++|||+++.+..+...++.++..+.+...    ...
T Consensus       174 ~~~~~lViDEah~l~~~gf~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~  253 (579)
T 3sqw_A          174 RFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEA  253 (579)
T ss_dssp             TTCCEEEEETHHHHTSTTTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSS
T ss_pred             ccCCEEEEEChHHhhcCCCHHHHHHHHHHhhhhhcccccCceEEEEeccCChHHHHHHHHHcCCCceEEEeecCcccccc
Confidence            8899999999999999999988888877653       36799999999999999999999998877766432    223


Q ss_pred             CCCceEEEEEecCcccHH-HH---HHHHHhh-CCCCcEEEEcccchhHHHHHhhC
Q 022724          243 LEGIKQFFVAVEREEWKF-DT---LCDLYDT-LTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       243 ~~~i~~~~~~~~~~~~k~-~~---l~~l~~~-~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ...+.+.+........+. ..   +...+.. ..+.++||||+|++.|+.++..|
T Consensus       254 ~~~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iVF~~t~~~~~~l~~~L  308 (579)
T 3sqw_A          254 HERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSIL  308 (579)
T ss_dssp             CTTEEEEEEEESSTTHHHHHHHHHHHHHHHHTTTCCEEEEECSSHHHHHHHHHHH
T ss_pred             ccccceEEEEecchhhhHHHHHHHHHHHHhhcCCCCcEEEECCcHHHHHHHHHHH
Confidence            445667776666543232 22   2333333 45679999999999999998765

>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=8e-37  Score=266.33  Aligned_cols=241  Identities=24%  Similarity=0.454  Sum_probs=207.9

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHH
Q 022724           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (293)
Q Consensus        40 l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~  119 (293)
                      +++++.++++++||..|+|+|+++++.+.+|+++++.+|||+|||++|++|++..      +.+++|++|+++|+.|+.+
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      4689999999999999999


Q ss_pred             HHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHH
Q 022724          120 VILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDV  199 (293)
Q Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i  199 (293)
                      .++++....+.++..++|+.....+...+.+ ++|+|+||+++.+.+......+.+++++|+||+|++.++++...+..+
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~~  153 (337)
T 2z0m_A           75 HIRDIGRYMDTKVAEVYGGMPYKAQINRVRN-ADIVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKII  153 (337)
T ss_dssp             HHHHHTTTSCCCEEEECTTSCHHHHHHHHTT-CSEEEECHHHHHHHHHTTSCCGGGCSEEEEESHHHHHHTTCHHHHHHH
T ss_pred             HHHHHhhhcCCcEEEEECCcchHHHHhhcCC-CCEEEECHHHHHHHHHcCCcchhhCcEEEEEChHHhhccccHHHHHHH
Confidence            9999988888999999999887776666544 799999999999998887778899999999999999999999999999


Q ss_pred             HhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHhhCCCCcEEEEc
Q 022724          200 YRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFC  279 (293)
Q Consensus       200 ~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~~iIF~  279 (293)
                      +...+...+++++|||+++........++.++..+...   .....+.+.+..+.... +.  ....+....++++||||
T Consensus       154 ~~~~~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~-~~--~~~~~~~~~~~~~lvf~  227 (337)
T 2z0m_A          154 LAQTSNRKITGLFSATIPEEIRKVVKDFITNYEEIEAC---IGLANVEHKFVHVKDDW-RS--KVQALRENKDKGVIVFV  227 (337)
T ss_dssp             HHHCTTCSEEEEEESCCCHHHHHHHHHHSCSCEEEECS---GGGGGEEEEEEECSSSS-HH--HHHHHHTCCCSSEEEEC
T ss_pred             HhhCCcccEEEEEeCcCCHHHHHHHHHhcCCceeeecc---cccCCceEEEEEeChHH-HH--HHHHHHhCCCCcEEEEE
Confidence            99999899999999999999999998888887766433   23345566666665543 22  23555666778999999


Q ss_pred             ccchhHHHHHhhCC
Q 022724          280 NTKRKVLLLVLQFP  293 (293)
Q Consensus       280 ~s~~~a~~l~~~L~  293 (293)
                      +++++++.+++.|.
T Consensus       228 ~~~~~~~~l~~~l~  241 (337)
T 2z0m_A          228 RTRNRVAKLVRLFD  241 (337)
T ss_dssp             SCHHHHHHHHTTCT
T ss_pred             cCHHHHHHHHHHhh
Confidence            99999999998773

>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=4.9e-37  Score=285.89  Aligned_cols=253  Identities=26%  Similarity=0.394  Sum_probs=204.2

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHhhh--cCCcEEEEcCCCChhHHHHHHHHHhhhccCC----CceeEEEEcCCHHH
Q 022724           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPII--KGRDVIAQAQSGTGKTSMIALTVCQTVDTSS----REVQALILSPTREL  113 (293)
Q Consensus        40 l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~--~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~----~~~~~lil~P~~~l  113 (293)
                      +++++.+++.++||..|+|+|.++++.++  .++++++++|||+|||++|++|+++.+....    .++++||++|+++|
T Consensus        79 l~~~l~~~l~~~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lil~Ptr~L  158 (563)
T 3i5x_A           79 LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDL  158 (563)
T ss_dssp             SCHHHHHHHHTTCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhccccccCCeeEEEEcCcHHH
Confidence            99999999999999999999999999999  6789999999999999999999999886543    24689999999999


Q ss_pred             HHHHHHHHHHhhcc----CCceEEEEECCcchHHHHHHH-hcCCcEEEeChHHHHHHHhcC-CCCCCCccEEEecchhhh
Q 022724          114 ATQTEKVILAIGDF----INIQAHACVGGKSVGEDIRKL-EHGVHVVSGTPGRVCDMIKRK-TLRTRAIKLLVLDESDEM  187 (293)
Q Consensus       114 ~~q~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~-~~~~~ilV~Tp~~l~~~l~~~-~~~~~~l~~iViDE~h~~  187 (293)
                      +.|+.+.++++...    ....+..+.|+.....+...+ ..+++|+|+||+++.+++.+. ...++++++|||||||++
T Consensus       159 a~Q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~l  238 (563)
T 3i5x_A          159 ALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRL  238 (563)
T ss_dssp             HHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTCCEEEEETHHHH
T ss_pred             HHHHHHHHHHHHhhccccCceeEEEEECCcCHHHHHHHHhcCCCCEEEECcHHHHHHHHhccccccccceEEEEeCHHHH
Confidence            99999999987532    245677888888777776665 457899999999999988664 345788999999999999


Q ss_pred             hccccHHHHHHHHhhCC-------CCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCc----ccCCCceEEEEEecCc
Q 022724          188 LSRGFKDQIYDVYRYLP-------PDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDE----LTLEGIKQFFVAVERE  256 (293)
Q Consensus       188 ~~~~~~~~~~~i~~~l~-------~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~i~~~~~~~~~~  256 (293)
                      .+++|...+..+...++       ...|++++|||+++.+..+...++.++..+......    .....+.+.+......
T Consensus       239 ~~~~f~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  318 (563)
T 3i5x_A          239 LEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKF  318 (563)
T ss_dssp             TSTTTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEESST
T ss_pred             hccchHHHHHHHHHhhhhccccCccCceEEEEEccCCHHHHHHHHHhcCCCceEEEeccCCCCccccccCceEEEECchh
Confidence            99999988888776653       367999999999999999999999888777654322    2334566777666654


Q ss_pred             ccHHHH----HHHHHhh-CCCCcEEEEcccchhHHHHHhhC
Q 022724          257 EWKFDT----LCDLYDT-LTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       257 ~~k~~~----l~~l~~~-~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ..+...    +...+.. ..+.++||||+|++.|+.++..|
T Consensus       319 ~~~~~~~~~~l~~~~~~~~~~~~~iVF~~s~~~~~~l~~~L  359 (563)
T 3i5x_A          319 ANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSIL  359 (563)
T ss_dssp             THHHHHHHHHHHHHHHHTTTCCEEEEECSCHHHHHHHHHHH
T ss_pred             HhhHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHHHHHHH
Confidence            433322    2233333 45679999999999999998865

>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=2.7e-35  Score=264.23  Aligned_cols=234  Identities=18%  Similarity=0.219  Sum_probs=181.7

Q ss_pred             HHHHHHHH-CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHH
Q 022724           43 DLLRGIYQ-YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVI  121 (293)
Q Consensus        43 ~i~~~l~~-~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~  121 (293)
                      ++.+.+++ +|| .|+|+|.++++.+.+|+|+++++|||+|||++|+++++..+.   .+++++|++|+++|+.|+.+.+
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            45555655 466 699999999999999999999999999999999999888763   3578999999999999999999


Q ss_pred             HHhhccCCceEEEEECCcch---HHHHHHHhcC-CcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhc--------
Q 022724          122 LAIGDFINIQAHACVGGKSV---GEDIRKLEHG-VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS--------  189 (293)
Q Consensus       122 ~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~-~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~--------  189 (293)
                      +++.. .++++..++|+.+.   ..+...+..+ ++|+|+||+++.+.+..  +.+.++++||+||+|++.+        
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 88999999999887   4555666555 89999999999887764  5677899999999997754        


Q ss_pred             ---cccHHH-HHHHHhhCC-----------CCccEEEEEee-cChhHH-HHHHhcCCCCEEEEecCCcccCCCceEEEEE
Q 022724          190 ---RGFKDQ-IYDVYRYLP-----------PDLQVVLISAT-LPHEIL-EMTTKFMTDPVKILVKRDELTLEGIKQFFVA  252 (293)
Q Consensus       190 ---~~~~~~-~~~i~~~l~-----------~~~q~v~~SAt-~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~  252 (293)
                         .+|... +..+++.++           ...|++++||| .++.+. .+...++.    +.+........++.+.+..
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 777777765           78999999999 565443 22222221    2222333445567777665


Q ss_pred             ecCcccHHHHHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          253 VEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       253 ~~~~~~k~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      +    .+...+..+++. .++++||||++++.|+.++..|
T Consensus       238 ~----~~~~~l~~~l~~-~~~~~lVF~~~~~~~~~l~~~L  272 (414)
T 3oiy_A          238 S----RSKEKLVELLEI-FRDGILIFAQTEEEGKELYEYL  272 (414)
T ss_dssp             S----CCHHHHHHHHHH-HCSSEEEEESSHHHHHHHHHHH
T ss_pred             c----CHHHHHHHHHHH-cCCCEEEEECCHHHHHHHHHHH
Confidence            4    255666777766 3479999999999999998865

>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=4.6e-34  Score=265.61  Aligned_cols=247  Identities=13%  Similarity=0.193  Sum_probs=184.3

Q ss_pred             CcccCCCCHHHHHHHHH-CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHH
Q 022724           34 SFDAMGIKDDLLRGIYQ-YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (293)
Q Consensus        34 ~f~~~~l~~~i~~~l~~-~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~  112 (293)
                      .+.++++++.+.+.|++ +||..|+|+|.++++.+++|+|+++++|||+|||++|++|++..      ++++||++|+++
T Consensus        22 ~~~~~~l~~~l~~~L~~~fg~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~lpal~~------~g~~lVisP~~~   95 (591)
T 2v1x_A           22 NKEDFPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCS------DGFTLVICPLIS   95 (591)
T ss_dssp             CCSCSTTHHHHHHHHHHTSCCCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHHHHHHTS------SSEEEEECSCHH
T ss_pred             ccccCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHHHHHHHc------CCcEEEEeCHHH
Confidence            44468899999999998 69999999999999999999999999999999999999999763      358999999999


Q ss_pred             HHHHHHHHHHHhhccCCceEEEEECCcchHHHHHH---H---hcCCcEEEeChHHHHH------HHhcCCCCCCCccEEE
Q 022724          113 LATQTEKVILAIGDFINIQAHACVGGKSVGEDIRK---L---EHGVHVVSGTPGRVCD------MIKRKTLRTRAIKLLV  180 (293)
Q Consensus       113 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~---~~~~~ilV~Tp~~l~~------~l~~~~~~~~~l~~iV  180 (293)
                      |+.|+.+.++++    ++++..++++....+....   +   ...++|+|+||+++..      .+. ....+.++++||
T Consensus        96 L~~q~~~~l~~~----gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L~~~~~~~~~l~-~~~~~~~i~~iV  170 (591)
T 2v1x_A           96 LMEDQLMVLKQL----GISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLE-KAYEARRFTRIA  170 (591)
T ss_dssp             HHHHHHHHHHHH----TCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHHHHHSCHHHHHHHH-HHHHTTCEEEEE
T ss_pred             HHHHHHHHHHhc----CCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChhHhhccHHHHHHHH-hhhhccCCcEEE
Confidence            999999999886    6778888888766544322   2   3568999999998742      222 234467899999


Q ss_pred             ecchhhhhccc--cHHHHHH--HHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecC-
Q 022724          181 LDESDEMLSRG--FKDQIYD--VYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVER-  255 (293)
Q Consensus       181 iDE~h~~~~~~--~~~~~~~--i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~-  255 (293)
                      |||||++.+++  |...+..  .+....+..+++++|||+++.+...+..++..+....+.. .....++...+..... 
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            99999998876  5554433  2333335789999999999988877776665433222221 1223344333332221 


Q ss_pred             cccHHHHHHHHHhh-CCCCcEEEEcccchhHHHHHhhC
Q 022724          256 EEWKFDTLCDLYDT-LTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       256 ~~~k~~~l~~l~~~-~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ...+...+..++.. ..+.++||||+|+++|+.++..|
T Consensus       250 ~~~~~~~l~~~l~~~~~~~~~IVf~~sr~~~e~la~~L  287 (591)
T 2v1x_A          250 TEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSL  287 (591)
T ss_dssp             HHHHHHHHHHHHTTTTTTCEEEEECSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccCCCeEEEeCcHHHHHHHHHHH
Confidence            12345566666654 36679999999999999999875

>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=5.2e-34  Score=272.40  Aligned_cols=245  Identities=16%  Similarity=0.207  Sum_probs=190.2

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHh-hhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHH
Q 022724           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (293)
Q Consensus        34 ~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~-i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~  112 (293)
                      +|+++++++++.+.+++.||..|+++|.++++. +.+++++++++|||+|||++|.+++++.+...  +.+++|++|+++
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 88999999999999999999999999887643  468999999999


Q ss_pred             HHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcccc
Q 022724          113 LATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF  192 (293)
Q Consensus       113 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~  192 (293)
                      |+.|+.+.++++.. .++++..++|+......   ...+++|+|+||+++..++......++++++|||||+|.+.+.++
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 48899999987654432   123579999999999998888766688999999999999988888


Q ss_pred             HHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEE------EecC----cccHHHH
Q 022724          193 KDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFV------AVER----EEWKFDT  262 (293)
Q Consensus       193 ~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~------~~~~----~~~k~~~  262 (293)
                      +..+..++..++...|+|++|||+++. ..+..++. .+ .+...   ..+..+...+.      ....    ...+...
T Consensus       156 ~~~~~~ll~~l~~~~~ii~lSATl~n~-~~~~~~l~-~~-~~~~~---~rp~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  229 (720)
T 2zj8_A          156 GATLEVILAHMLGKAQIIGLSATIGNP-EELAEWLN-AE-LIVSD---WRPVKLRRGVFYQGFVTWEDGSIDRFSSWEEL  229 (720)
T ss_dssp             HHHHHHHHHHHBTTBEEEEEECCCSCH-HHHHHHTT-EE-EEECC---CCSSEEEEEEEETTEEEETTSCEEECSSTTHH
T ss_pred             cHHHHHHHHHhhcCCeEEEEcCCcCCH-HHHHHHhC-Cc-ccCCC---CCCCcceEEEEeCCeeeccccchhhhhHHHHH
Confidence            999999988887789999999999863 44554432 11 11111   11111222111      1110    1224555


Q ss_pred             HHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          263 LCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       263 l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      +.+.+.  .++++||||+++++|+.++..|
T Consensus       230 ~~~~~~--~~~~~LVF~~sr~~~~~~a~~L  257 (720)
T 2zj8_A          230 VYDAIR--KKKGALIFVNMRRKAERVALEL  257 (720)
T ss_dssp             HHHHHH--TTCCEEEECSCHHHHHHHHHHH
T ss_pred             HHHHHh--CCCCEEEEecCHHHHHHHHHHH
Confidence            555554  3579999999999999998764

>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=4.3e-33  Score=256.32  Aligned_cols=243  Identities=15%  Similarity=0.236  Sum_probs=185.0

Q ss_pred             cCcccCCCCHHHHHHHHH-CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCH
Q 022724           33 TSFDAMGIKDDLLRGIYQ-YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (293)
Q Consensus        33 ~~f~~~~l~~~i~~~l~~-~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~  111 (293)
                      .+|+++++++++.+.|++ +||..|+|+|.++++.+++|+|+++++|||+|||++|++|++..      ..++||++|++
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            579999999999999998 89999999999999999999999999999999999999999854      24799999999


Q ss_pred             HHHHHHHHHHHHhhccCCceEEEEECCcchHHHHH---H-HhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhh
Q 022724          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIR---K-LEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (293)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~-~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~  187 (293)
                      +|+.|+.+.++.+    ++.+..++++........   . ....++|+++||+++........+...++++|||||+|++
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            9999999988864    677778888776554332   2 2356899999999996422222234578999999999999


Q ss_pred             hccc--cHHHHH---HHHhhCCCCccEEEEEeecChhHHHHHH-hc-CCCCEEEEecCCcccCCCceEEEEEecCcccHH
Q 022724          188 LSRG--FKDQIY---DVYRYLPPDLQVVLISATLPHEILEMTT-KF-MTDPVKILVKRDELTLEGIKQFFVAVEREEWKF  260 (293)
Q Consensus       188 ~~~~--~~~~~~---~i~~~l~~~~q~v~~SAt~~~~~~~~~~-~~-~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~  260 (293)
                      .+++  |...+.   .+...+ +..+++++|||+++.+...+. .+ +.++..+...   ....++...  ..... .+.
T Consensus       152 ~~~g~~fr~~~~~l~~l~~~~-~~~~~i~lSAT~~~~~~~~i~~~l~~~~~~~~~~~---~~r~~l~~~--v~~~~-~~~  224 (523)
T 1oyw_A          152 SQWGHDFRPEYAALGQLRQRF-PTLPFMALTATADDTTRQDIVRLLGLNDPLIQISS---FDRPNIRYM--LMEKF-KPL  224 (523)
T ss_dssp             CTTSSCCCHHHHGGGGHHHHC-TTSCEEEEESCCCHHHHHHHHHHHTCCSCEEEECC---CCCTTEEEE--EEECS-SHH
T ss_pred             CcCCCccHHHHHHHHHHHHhC-CCCCEEEEeCCCCHHHHHHHHHHhCCCCCeEEeCC---CCCCceEEE--EEeCC-CHH
Confidence            8876  544443   344455 468999999999988665333 33 3345443322   122333322  22333 377


Q ss_pred             HHHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          261 DTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       261 ~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ..+..++....+.++||||+|+++++.+++.|
T Consensus       225 ~~l~~~l~~~~~~~~IVf~~sr~~~e~l~~~L  256 (523)
T 1oyw_A          225 DQLMRYVQEQRGKSGIIYCNSRAKVEDTAARL  256 (523)
T ss_dssp             HHHHHHHHHTTTCCEEEECSSHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCCcEEEEeCCHHHHHHHHHHH
Confidence            78888888877789999999999999999875

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

Probab=100.00  E-value=9.2e-33  Score=263.73  Aligned_cols=245  Identities=13%  Similarity=0.175  Sum_probs=188.6

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHh-hhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCH
Q 022724           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (293)
Q Consensus        33 ~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~-i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~  111 (293)
                      .+|+++++++++.+.+++.||..|+|+|.++++. +.+++++++++|||+|||+++.+++++.+...  +.+++|++|++
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  46999999999


Q ss_pred             HHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccc
Q 022724          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG  191 (293)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~  191 (293)
                      +|+.|+.+.++.+. ..|+++...+|+......  .+ .+++|+|+||+++..++.+....++++++|||||+|.+.+..
T Consensus        86 ~La~q~~~~~~~~~-~~g~~v~~~~G~~~~~~~--~~-~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~~  161 (715)
T 2va8_A           86 ALTNEKYLTFKDWE-LIGFKVAMTSGDYDTDDA--WL-KNYDIIITTYEKLDSLWRHRPEWLNEVNYFVLDELHYLNDPE  161 (715)
T ss_dssp             HHHHHHHHHHGGGG-GGTCCEEECCSCSSSCCG--GG-GGCSEEEECHHHHHHHHHHCCGGGGGEEEEEECSGGGGGCTT
T ss_pred             HHHHHHHHHHHHhh-cCCCEEEEEeCCCCCchh--hc-CCCCEEEEcHHHHHHHHhCChhHhhccCEEEEechhhcCCcc
Confidence            99999999996554 458888888887654432  12 367999999999999888876668899999999999998778


Q ss_pred             cHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEE------------EEec-----
Q 022724          192 FKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFF------------VAVE-----  254 (293)
Q Consensus       192 ~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~------------~~~~-----  254 (293)
                      ++..+..++.+++ ..|+|++|||+++. ..+..++.. + .+...   ..+..+...+            ...+     
T Consensus       162 ~~~~l~~i~~~~~-~~~ii~lSATl~n~-~~~~~~l~~-~-~~~~~---~r~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  234 (715)
T 2va8_A          162 RGPVVESVTIRAK-RRNLLALSATISNY-KQIAKWLGA-E-PVATN---WRPVPLIEGVIYPERKKKEYNVIFKDNTTKK  234 (715)
T ss_dssp             THHHHHHHHHHHH-TSEEEEEESCCTTH-HHHHHHHTC-E-EEECC---CCSSCEEEEEEEECSSTTEEEEEETTSCEEE
T ss_pred             cchHHHHHHHhcc-cCcEEEEcCCCCCH-HHHHHHhCC-C-ccCCC---CCCCCceEEEEecCCcccceeeecCcchhhh
Confidence            8888888887776 89999999999763 445544421 1 11111   1111121111            1111     


Q ss_pred             --CcccHHHHHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          255 --REEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       255 --~~~~k~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                        ....+...+.+.+.  .++++||||+++++++.++..|
T Consensus       235 ~~~~~~~~~~~~~~~~--~~~~~LVF~~s~~~~~~~a~~L  272 (715)
T 2va8_A          235 VHGDDAIIAYTLDSLS--KNGQVLVFRNSRKMAESTALKI  272 (715)
T ss_dssp             EESSSHHHHHHHHHHT--TTCCEEEECSSHHHHHHHHHHH
T ss_pred             cccchHHHHHHHHHHh--cCCCEEEEECCHHHHHHHHHHH
Confidence              01224455555553  4579999999999999998764

>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=9e-33  Score=272.01  Aligned_cols=246  Identities=17%  Similarity=0.221  Sum_probs=194.4

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCH
Q 022724           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (293)
Q Consensus        32 ~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~  111 (293)
                      ...|+.+++++.+...+...++..|+++|.++++.+.+|+++++++|||+|||++|++|++..+..   +.+++|++|++
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            346777888877777776666777999999999999999999999999999999999999988854   56899999999


Q ss_pred             HHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccc
Q 022724          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG  191 (293)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~  191 (293)
                      +|+.|+++.+.++..    .+..++|+.+..       .+++|+|+||++|.+++.++...+.++++|||||+|.+.+++
T Consensus       238 aLa~Q~~~~l~~~~~----~VglltGd~~~~-------~~~~IlV~Tpe~L~~~L~~~~~~l~~l~lVVIDEaH~l~d~~  306 (1108)
T 3l9o_A          238 ALSNQKYRELLAEFG----DVGLMTGDITIN-------PDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKE  306 (1108)
T ss_dssp             HHHHHHHHHHHHHTS----SEEEECSSCBCC-------CSCSEEEEEHHHHHHHHHHCSSHHHHEEEEEEETGGGTTSHH
T ss_pred             HHHHHHHHHHHHHhC----CccEEeCccccC-------CCCCEEEeChHHHHHHHHcCccccccCCEEEEhhhhhccccc
Confidence            999999999998765    566677776533       457999999999999998887778899999999999999999


Q ss_pred             cHHHHHHHHhhCCCCccEEEEEeecChh--HHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecC---------c----
Q 022724          192 FKDQIYDVYRYLPPDLQVVLISATLPHE--ILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVER---------E----  256 (293)
Q Consensus       192 ~~~~~~~i~~~l~~~~q~v~~SAt~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~---------~----  256 (293)
                      ++..+..++..+++..|+++||||+++.  +..++......+..+......  +..+.+++.....         .    
T Consensus       307 rg~~~e~ii~~l~~~~qvl~lSATipn~~e~a~~l~~~~~~~~~vi~~~~r--p~pl~~~~~~~~~~~~~~~vd~~~~~~  384 (1108)
T 3l9o_A          307 RGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNFR--PTPLQHYLFPAHGDGIYLVVDEKSTFR  384 (1108)
T ss_dssp             HHHHHHHHHHHSCTTSEEEEEECSCSSCHHHHHHHHHHTCSCEEEEEECCC--SSCEEEEEEETTSSCCEEEEETTTEEC
T ss_pred             hHHHHHHHHHhcCCCceEEEEcCCCCCHHHHHHHHHhhcCCCeEEEecCCC--cccceEEEeecCCcceeeeeccccchh
Confidence            9999999999999999999999999875  446666666666666554322  2223333221110         0    


Q ss_pred             -----------------------------------------ccHHHHHHHHHhhCCCCcEEEEcccchhHHHHHhhCC
Q 022724          257 -----------------------------------------EWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQFP  293 (293)
Q Consensus       257 -----------------------------------------~~k~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L~  293 (293)
                                                               ..+...+...+......++||||++++.|+.++..|.
T Consensus       385 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~li~~l~~~~~~~vIVF~~sr~~~e~la~~L~  462 (1108)
T 3l9o_A          385 EENFQKAMASISNQIGDDPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMS  462 (1108)
T ss_dssp             HHHHHHHHTTC-----------------------------CHHHHHHHHHHHHHTTCCCEEEEESCHHHHHHHHHHTC
T ss_pred             hhhHHHHHHHHHhhhcccccccccccccccccccccccccchhHHHHHHHHHHhcCCCCEEEEeCcHHHHHHHHHHHH
Confidence                                                     1122234444455566799999999999999998763

>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=7.4e-34  Score=270.64  Aligned_cols=244  Identities=14%  Similarity=0.161  Sum_probs=184.4

Q ss_pred             CcccCC--CCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCH
Q 022724           34 SFDAMG--IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (293)
Q Consensus        34 ~f~~~~--l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~  111 (293)
                      +|++++  +++.+.+.+++.||..|+|+|.++++.+.+++++++++|||+|||++|.+++++.+..   +.+++|++|++
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   46899999999


Q ss_pred             HHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccc
Q 022724          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG  191 (293)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~  191 (293)
                      +|+.|+.+.++.+. ..|+++...+|+......   ...+++|+|+||+++..++.+....++++++|||||+|.+.+++
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            99999999996554 458889999888655432   12367999999999999988876668899999999999998877


Q ss_pred             cHHHHHHHHhhC---CCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEE------EecC------c
Q 022724          192 FKDQIYDVYRYL---PPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFV------AVER------E  256 (293)
Q Consensus       192 ~~~~~~~i~~~l---~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~------~~~~------~  256 (293)
                      ++..+..++..+   ++..|+|++|||+++ ...+..++. .+ .+...   ..+..+...+.      ..+.      .
T Consensus       155 r~~~~~~ll~~l~~~~~~~~ii~lSATl~n-~~~~~~~l~-~~-~~~~~---~r~~~l~~~~~~~~~~~~~~~~~~~~~~  228 (702)
T 2p6r_A          155 RGATLEILVTKMRRMNKALRVIGLSATAPN-VTEIAEWLD-AD-YYVSD---WRPVPLVEGVLCEGTLELFDGAFSTSRR  228 (702)
T ss_dssp             THHHHHHHHHHHHHHCTTCEEEEEECCCTT-HHHHHHHTT-CE-EEECC---CCSSCEEEEEECSSEEEEEETTEEEEEE
T ss_pred             cccHHHHHHHHHHhcCcCceEEEECCCcCC-HHHHHHHhC-CC-cccCC---CCCccceEEEeeCCeeeccCcchhhhhh
Confidence            777777766655   578999999999986 355555443 22 12111   11112222111      1111      0


Q ss_pred             ccHHHHHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          257 EWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       257 ~~k~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ..+...+.+.+.  .++++||||+++++++.++..|
T Consensus       229 ~~~~~~~~~~~~--~~~~~LVF~~s~~~~~~~a~~L  262 (702)
T 2p6r_A          229 VKFEELVEECVA--ENGGVLVFESTRRGAEKTAVKL  262 (702)
T ss_dssp             CCHHHHHHHHHH--TTCCEEEECSSHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHh--cCCCEEEEcCCHHHHHHHHHHH
Confidence            114455555554  4579999999999999998764

>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=1.5e-32  Score=270.35  Aligned_cols=227  Identities=17%  Similarity=0.227  Sum_probs=181.8

Q ss_pred             HCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCC
Q 022724           50 QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (293)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (293)
                      .+|| .|+|+|.++++.+++|+|+++++|||+|||++|+++++..+.   .++++||++|+++|+.|+.+.++++. ..+
T Consensus        74 ~~gf-~pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~~---~~~~~Lil~PtreLa~Q~~~~l~~l~-~~~  148 (1104)
T 4ddu_A           74 KFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLAR---KGKKSALVFPTVTLVKQTLERLQKLA-DEK  148 (1104)
T ss_dssp             HSSS-CCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHHT---TTCCEEEEESSHHHHHHHHHHHHTTS-CTT
T ss_pred             hcCC-CCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHHh---cCCeEEEEechHHHHHHHHHHHHHhh-CCC
Confidence            4688 599999999999999999999999999999999988888773   36789999999999999999999977 778


Q ss_pred             ceEEEEECCcch---HHHHHHHhcC-CcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhc-----------cccHH
Q 022724          130 IQAHACVGGKSV---GEDIRKLEHG-VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS-----------RGFKD  194 (293)
Q Consensus       130 ~~~~~~~~~~~~---~~~~~~~~~~-~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~-----------~~~~~  194 (293)
                      +++..++|+.+.   ..+...+.++ ++|+|+||+++.+++..  +.+.++++|||||+|++..           .+|..
T Consensus       149 i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~--l~~~~l~~lViDEaH~l~~~~r~~Dr~L~~~gf~~  226 (1104)
T 4ddu_A          149 VKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK--LSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGIPE  226 (1104)
T ss_dssp             SCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHH--HHTSCCSEEEESCHHHHTTSSHHHHHHHHTSSCCH
T ss_pred             CeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHh--hcccCcCEEEEeCCCccccccccchhhhHhcCCCH
Confidence            999999999887   5566667665 89999999999887764  5678899999999986553           67777


Q ss_pred             H-HHHHHhhCC-----------CCccEEEEEee-cChhHHH-HHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHH
Q 022724          195 Q-IYDVYRYLP-----------PDLQVVLISAT-LPHEILE-MTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKF  260 (293)
Q Consensus       195 ~-~~~i~~~l~-----------~~~q~v~~SAt-~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~  260 (293)
                      . +..+++.++           ...|++++||| .+..+.. +....+.    +.+........++.+.+..++    +.
T Consensus       227 ~~i~~il~~l~~~~~~~~~~~~~~~q~ll~SAT~~p~~~~~~~~~~~l~----i~v~~~~~~~~~i~~~~~~~~----k~  298 (1104)
T 4ddu_A          227 EIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLN----FTVGRLVSVARNITHVRISSR----SK  298 (1104)
T ss_dssp             HHHHHHHHHHHHTSCCCCCSSCCCCEEEEECBSSCCCSSTTHHHHHHTC----CCCCBCCCCCCCEEEEEESCC----CH
T ss_pred             HHHHHHHHhcccchhhhhhccCCCceEEEEcCCCCcHHHHHHHhhccee----EEeccCCCCcCCceeEEEecC----HH
Confidence            7 788888776           78999999999 5555442 3333322    233334445667778777552    56


Q ss_pred             HHHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          261 DTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       261 ~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ..+..+++.. ++++||||++++.|+.++..|
T Consensus       299 ~~L~~ll~~~-~~~~LVF~~s~~~a~~l~~~L  329 (1104)
T 4ddu_A          299 EKLVELLEIF-RDGILIFAQTEEEGKELYEYL  329 (1104)
T ss_dssp             HHHHHHHHHH-CSSEEEEESSSHHHHHHHHHH
T ss_pred             HHHHHHHHhc-CCCEEEEECcHHHHHHHHHHH
Confidence            6667777663 489999999999999999875

>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=7e-33  Score=272.58  Aligned_cols=230  Identities=16%  Similarity=0.213  Sum_probs=181.7

Q ss_pred             HHHH-HCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 022724           46 RGIY-QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (293)
Q Consensus        46 ~~l~-~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (293)
                      +.+. .+||. | ++|.++++.+++|+|+++++|||+|||+ |.+|++..+...  ++++||++|+++|+.|+.+.++++
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 47999 9 9999999999999999999999999998 888888877653  579999999999999999999999


Q ss_pred             hccCCc----eEEEEECCcchHHH---HHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHH
Q 022724          125 GDFINI----QAHACVGGKSVGED---IRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIY  197 (293)
Q Consensus       125 ~~~~~~----~~~~~~~~~~~~~~---~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~  197 (293)
                      ....++    ++..++|+.+...+   ...+.+ ++|+|+||++|.+++.+    ++++++|||||+|++++  ++..+.
T Consensus       123 ~~~~~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~-~~IlV~TP~~L~~~l~~----L~~l~~lViDEah~~l~--~~~~~~  195 (1054)
T 1gku_B          123 AEKAGVGTENLIGYYHGRIPKREKENFMQNLRN-FKIVITTTQFLSKHYRE----LGHFDFIFVDDVDAILK--ASKNVD  195 (1054)
T ss_dssp             HTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGG-CSEEEEEHHHHHHCSTT----SCCCSEEEESCHHHHHT--STHHHH
T ss_pred             HhhcCCCccceEEEEeCCCChhhHHHHHhhccC-CCEEEEcHHHHHHHHHH----hccCCEEEEeChhhhhh--ccccHH
Confidence            988888    89999999877663   344455 89999999999987665    66899999999999987  567777


Q ss_pred             HHHhhCC-----------CCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHH
Q 022724          198 DVYRYLP-----------PDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDL  266 (293)
Q Consensus       198 ~i~~~l~-----------~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l  266 (293)
                      .+...++           ...|++++|||+++. ..+...++.++..+.+........++.+.+.   . ..+...+..+
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            7777773           467899999999887 4333333333333333434444556777666   2 2366667777


Q ss_pred             HhhCCCCcEEEEcccchhHHHHHhhCC
Q 022724          267 YDTLTITQAVIFCNTKRKVLLLVLQFP  293 (293)
Q Consensus       267 ~~~~~~~~~iIF~~s~~~a~~l~~~L~  293 (293)
                      ++.. ++++||||+++++|+.+++.|.
T Consensus       271 l~~~-~~~~LVF~~t~~~a~~l~~~L~  296 (1054)
T 1gku_B          271 LEKL-GTGGIIYARTGEEAEEIYESLK  296 (1054)
T ss_dssp             HTTS-CSCEEEEESSHHHHHHHHHTTT
T ss_pred             Hhhc-CCCEEEEEcCHHHHHHHHHHHh
Confidence            7765 4789999999999999998874

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.97  E-value=1.8e-31  Score=254.28  Aligned_cols=173  Identities=16%  Similarity=0.237  Sum_probs=140.6

Q ss_pred             HHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCC--ceeEEEEcCCHHHHHHHHHHHH
Q 022724           45 LRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR--EVQALILSPTRELATQTEKVIL  122 (293)
Q Consensus        45 ~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~--~~~~lil~P~~~l~~q~~~~~~  122 (293)
                      ..++..+||..|+++|.++++.+++|+|+++++|||+|||++|++|+++.+...+.  +.++||++|+++|+.|+.+.++
T Consensus         3 ~~~l~~~g~~~lr~~Q~~~i~~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~lvl~Pt~~L~~Q~~~~~~   82 (696)
T 2ykg_A            3 VSDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQNKSVFS   82 (696)
T ss_dssp             ----CTTC--CCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCTTCCCCEEEECSSHHHHHHHHHHHH
T ss_pred             CCcccccCCCCccHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHHHHhCccCCCCeEEEEECCHHHHHHHHHHHH
Confidence            45677889999999999999999999999999999999999999999988765432  2689999999999999999999


Q ss_pred             HhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCC-CCCCccEEEecchhhhhccc-cHHHHHHHH
Q 022724          123 AIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL-RTRAIKLLVLDESDEMLSRG-FKDQIYDVY  200 (293)
Q Consensus       123 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~-~~~~l~~iViDE~h~~~~~~-~~~~~~~i~  200 (293)
                      ++....++++..++|+.....+...+..+++|+|+||++|.+.+..+.+ .+.++++|||||||++.+.. +...+...+
T Consensus        83 ~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~L~~~l~~~~~~~l~~~~~vViDEaH~~~~~~~~~~i~~~~l  162 (696)
T 2ykg_A           83 KYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYL  162 (696)
T ss_dssp             HHTTTTTCCEEEECSSSCSSSCHHHHHHTCSEEEECHHHHHHHHHTTSSCCGGGCSEEEEETGGGCSTTCHHHHHHHHHH
T ss_pred             HHhccCCceEEEEeCCccccccHHHhccCCCEEEECHHHHHHHHhcCcccccccccEEEEeCCCcccCcccHHHHHHHHH
Confidence            9988888999999999876666666666789999999999999988766 78899999999999986553 233332222


Q ss_pred             hh-----CCCCccEEEEEeecC
Q 022724          201 RY-----LPPDLQVVLISATLP  217 (293)
Q Consensus       201 ~~-----l~~~~q~v~~SAt~~  217 (293)
                      ..     .++..+++++|||+.
T Consensus       163 ~~~~~~~~~~~~~il~LTATp~  184 (696)
T 2ykg_A          163 DQKLGGSSGPLPQVIGLTASVG  184 (696)
T ss_dssp             HHHHTTCCSCCCEEEEEESCCC
T ss_pred             HHhhcccCCCCCeEEEEeCccc
Confidence            22     246789999999996

>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=3.3e-30  Score=239.15  Aligned_cols=166  Identities=15%  Similarity=0.183  Sum_probs=133.5

Q ss_pred             CCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCC--ceeEEEEcCCHHHHHHHHHHHHHhhccCC
Q 022724           52 GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR--EVQALILSPTRELATQTEKVILAIGDFIN  129 (293)
Q Consensus        52 ~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~--~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (293)
                      +...|+|+|.++++.+++|+++++++|||+|||++|++|+++.+...+.  ++++||++|+++|+.|+.+.++++....+
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            4457999999999999999999999999999999999999998876542  56899999999999999999999988889


Q ss_pred             ceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCC-CCCCccEEEecchhhhhccccHHHH-HHHHhh----C
Q 022724          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL-RTRAIKLLVLDESDEMLSRGFKDQI-YDVYRY----L  203 (293)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~-~~~~l~~iViDE~h~~~~~~~~~~~-~~i~~~----l  203 (293)
                      +++..++|+.....+...+..+++|+|+||+++.+.+..+.+ .+.++++|||||+|++.+++....+ ..++..    .
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            999999999877766666666789999999999999988777 7899999999999999876543332 222222    1


Q ss_pred             CCCccEEEEEeecC
Q 022724          204 PPDLQVVLISATLP  217 (293)
Q Consensus       204 ~~~~q~v~~SAt~~  217 (293)
                      .+..|++++|||++
T Consensus       164 ~~~~~~l~lSAT~~  177 (556)
T 4a2p_A          164 SQLPQILGLTASVG  177 (556)
T ss_dssp             --CCEEEEEESCCC
T ss_pred             CCCCeEEEEeCCcc
Confidence            35689999999995

>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=6.1e-30  Score=249.94  Aligned_cols=228  Identities=18%  Similarity=0.274  Sum_probs=176.7

Q ss_pred             HHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccC
Q 022724           49 YQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI  128 (293)
Q Consensus        49 ~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~  128 (293)
                      ..++|. |+++|.++++.+.+|+++++++|||+|||++|.++++..+..   +.+++|++|+++|+.|+++.+.++..  
T Consensus        81 ~~~~f~-L~~~Q~eai~~l~~g~~vLV~apTGSGKTlva~lai~~~l~~---g~rvL~l~PtkaLa~Q~~~~l~~~~~--  154 (1010)
T 2xgj_A           81 RTYPFT-LDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKN---KQRVIYTSPIKALSNQKYRELLAEFG--  154 (1010)
T ss_dssp             CCCSSC-CCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHHT---TCEEEEEESSHHHHHHHHHHHHHHHS--
T ss_pred             HhCCCC-CCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhcc---CCeEEEECChHHHHHHHHHHHHHHhC--
Confidence            345666 999999999999999999999999999999999999887754   56999999999999999999998765  


Q ss_pred             CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCcc
Q 022724          129 NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ  208 (293)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q  208 (293)
                        ++..++|+.+..       .+++|+|+||+++.+++.++...+.++++|||||+|.+.+.+++..+..++..++...|
T Consensus       155 --~vglltGd~~~~-------~~~~IvV~Tpe~L~~~L~~~~~~l~~l~lVViDEaH~l~d~~rg~~~e~il~~l~~~~~  225 (1010)
T 2xgj_A          155 --DVGLMTGDITIN-------PDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVR  225 (1010)
T ss_dssp             --CEEEECSSCEEC-------TTCSEEEEEHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCTTTHHHHHHHHHHSCTTCE
T ss_pred             --CEEEEeCCCccC-------CCCCEEEEcHHHHHHHHHcCcchhhcCCEEEEechhhhcccchhHHHHHHHHhcCCCCe
Confidence              566778876543       34789999999999999888778899999999999999998889999999999999999


Q ss_pred             EEEEEeecChhHH--HHHHhcCCCCEEEEecCCcccCCCceEEEEEec---------Cc---------------------
Q 022724          209 VVLISATLPHEIL--EMTTKFMTDPVKILVKRDELTLEGIKQFFVAVE---------RE---------------------  256 (293)
Q Consensus       209 ~v~~SAt~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~---------~~---------------------  256 (293)
                      ++++|||+++...  .++......+..+.....  .+..+.+++....         ..                     
T Consensus       226 il~LSATi~n~~e~a~~l~~~~~~~~~vi~~~~--rp~pl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  303 (1010)
T 2xgj_A          226 YVFLSATIPNAMEFAEWICKIHSQPCHIVYTNF--RPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASISNQIGD  303 (1010)
T ss_dssp             EEEEECCCTTHHHHHHHHHHHHTSCEEEEEECC--CSSCEEEEEEETTSSCCEEEECTTCCBCHHHHHHHHHTCC-----
T ss_pred             EEEEcCCCCCHHHHHHHHHhhcCCCeEEEecCC--CcccceEEEEecCCcceeeeeccccccchHHHHHHHHHHhhhhcc
Confidence            9999999987532  344333445555544432  2223444433211         00                     


Q ss_pred             ------------------------ccHHHHHHHHHhhCCCCcEEEEcccchhHHHHHhhCC
Q 022724          257 ------------------------EWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQFP  293 (293)
Q Consensus       257 ------------------------~~k~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L~  293 (293)
                                              ......+...+......++||||++++.|+.++..|.
T Consensus       304 ~~~~~~~~g~~~~~~k~~~~~~~~~~~l~~l~~~l~~~~~~~~IVF~~sr~~~e~la~~L~  364 (1010)
T 2xgj_A          304 DPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMS  364 (1010)
T ss_dssp             -------------------------CHHHHHHHHHHHHTCCSEEEEESSHHHHHHHHHTTT
T ss_pred             cccccccccccccccccccccccchHHHHHHHHHHHhcCCCCEEEEECCHHHHHHHHHHHH
Confidence                                    1122234444444455699999999999999998763

>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=3.2e-30  Score=262.13  Aligned_cols=247  Identities=15%  Similarity=0.190  Sum_probs=180.8

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHhhhc-CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHH
Q 022724           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPIIK-GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE  118 (293)
Q Consensus        40 l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~-~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~  118 (293)
                      +.+...+++...+|..|+|+|.++++.+.. ++|++++||||||||++|.+|+++.+...+ +.++||++|+++|+.|++
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            455677777778899999999999999875 578999999999999999999999987654 358999999999999999


Q ss_pred             HHHHH-hhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCC--CCCCCccEEEecchhhhhccccHHH
Q 022724          119 KVILA-IGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT--LRTRAIKLLVLDESDEMLSRGFKDQ  195 (293)
Q Consensus       119 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~--~~~~~l~~iViDE~h~~~~~~~~~~  195 (293)
                      +.+++ +....|+++..++|+...+..   ...+++|+|+||+++..++++..  ..+++++++|+||+|.+.+. .+..
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 566789999999988754432   22347999999999988877632  33688999999999998764 4554


Q ss_pred             HHHHHh-------hCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHH------HH
Q 022724          196 IYDVYR-------YLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKF------DT  262 (293)
Q Consensus       196 ~~~i~~-------~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~------~~  262 (293)
                      +..++.       .+++..|+|++|||+++. .++..|+..++..+.....+..+..+...+...+......      ..
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            444433       456789999999999874 6666666544333332223334444555544444332111      11


Q ss_pred             HHHHHh-hCCCCcEEEEcccchhHHHHHhhC
Q 022724          263 LCDLYD-TLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       263 l~~l~~-~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      +...+. ...++++||||+|++.|+.++..|
T Consensus      1145 ~~~~i~~~~~~~~~lVF~~sR~~~~~~A~~L 1175 (1724)
T 4f92_B         1145 VYHAITKHSPKKPVIVFVPSRKQTRLTAIDI 1175 (1724)
T ss_dssp             HHHHHHHHCSSSCEEEEESSHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCCeeeeCCCHHHHHHHHHHH
Confidence            222333 345679999999999999988653

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.97  E-value=1.5e-29  Score=234.51  Aligned_cols=164  Identities=16%  Similarity=0.225  Sum_probs=139.4

Q ss_pred             CCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCC--ceeEEEEcCCHHHHHHHHHHHHHhhccCCceE
Q 022724           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR--EVQALILSPTRELATQTEKVILAIGDFINIQA  132 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~--~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  132 (293)
                      .|+|+|.++++.+++|+++++++|||+|||++|++|+++.+...+.  ++++||++|+++|+.|+.+.++++....++++
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            5999999999999999999999999999999999999998876542  56899999999999999999999988889999


Q ss_pred             EEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCC-CCCCccEEEecchhhhhccc-cHHHHHHHHhhC-----CC
Q 022724          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL-RTRAIKLLVLDESDEMLSRG-FKDQIYDVYRYL-----PP  205 (293)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~-~~~~l~~iViDE~h~~~~~~-~~~~~~~i~~~l-----~~  205 (293)
                      ..++|+.....+...+..+++|+|+||+++...+..+.+ .+.++++|||||||++.+.+ +...+...+...     .+
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 78899999999999997664 333333333332     24


Q ss_pred             CccEEEEEeecCh
Q 022724          206 DLQVVLISATLPH  218 (293)
Q Consensus       206 ~~q~v~~SAt~~~  218 (293)
                      ..|++++|||++.
T Consensus       164 ~~~~l~lSAT~~~  176 (555)
T 3tbk_A          164 LPQVVGLTASVGV  176 (555)
T ss_dssp             CCEEEEEESCCCC
T ss_pred             CCeEEEEecCccc
Confidence            5799999999954

>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=2.8e-30  Score=262.54  Aligned_cols=246  Identities=15%  Similarity=0.238  Sum_probs=178.4

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHhhh-cCCcEEEEcCCCChhHHHHHHHHHhhhccC--------CCceeEEEEcCC
Q 022724           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPII-KGRDVIAQAQSGTGKTSMIALTVCQTVDTS--------SREVQALILSPT  110 (293)
Q Consensus        40 l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~-~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~--------~~~~~~lil~P~  110 (293)
                      |+++....+  .||++++++|++++|.++ +++|++++||||+|||++|.+++++.+...        ..+.++||++|+
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            444444333  279999999999999876 578999999999999999999999988642        245689999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCC--CCCCccEEEecchhhhh
Q 022724          111 RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL--RTRAIKLLVLDESDEML  188 (293)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~--~~~~l~~iViDE~h~~~  188 (293)
                      ++|+.|+.+.+++.....|+++..++|+.+....   ...+++|+|+|||++..++++...  .++++++|||||+|++.
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            9999999999998888899999999998765432   124579999999999777765432  36889999999999886


Q ss_pred             ccccHHHHHHHHh-------hCCCCccEEEEEeecChhHHHHHHhcCCCCE-EEEecCCcccCCCceEEEEEecCccc--
Q 022724          189 SRGFKDQIYDVYR-------YLPPDLQVVLISATLPHEILEMTTKFMTDPV-KILVKRDELTLEGIKQFFVAVEREEW--  258 (293)
Q Consensus       189 ~~~~~~~~~~i~~-------~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~i~~~~~~~~~~~~--  258 (293)
                      + .++..++.++.       .+++..|+|++|||+|+. .+++.++..++. .+.....+..+-.+.+.++.......  
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 46666655544       346789999999999863 566665544321 12222223344456666555544331  


Q ss_pred             HHHHH----HHHHhh-CCCCcEEEEcccchhHHHHHhhC
Q 022724          259 KFDTL----CDLYDT-LTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       259 k~~~l----~~l~~~-~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ....+    ...+.+ ..++++||||+|++.|+.+++.|
T Consensus       299 ~~~~~~~~~~~~v~~~~~~~~~LVF~~sR~~~~~~A~~l  337 (1724)
T 4f92_B          299 RFQIMNEIVYEKIMEHAGKNQVLVFVHSRKETGKTARAI  337 (1724)
T ss_dssp             HHHHHHHHHHHHHTTCCSSCCEEEECSSTTTTHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHhcCCcEEEECCCHHHHHHHHHHH
Confidence            12222    222222 34569999999999999988754

>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=1e-29  Score=245.14  Aligned_cols=168  Identities=15%  Similarity=0.188  Sum_probs=135.9

Q ss_pred             HCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCC--ceeEEEEcCCHHHHHHHHHHHHHhhcc
Q 022724           50 QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR--EVQALILSPTRELATQTEKVILAIGDF  127 (293)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~--~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (293)
                      .+|+..|+|+|.++++.+++|+++++++|||+|||++|++|++..+...+.  ++++||++|+++|+.|+.+.++++...
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            457889999999999999999999999999999999999999998876542  568999999999999999999999888


Q ss_pred             CCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCC-CCCCccEEEecchhhhhcccc-HHHHHHHHhh---
Q 022724          128 INIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL-RTRAIKLLVLDESDEMLSRGF-KDQIYDVYRY---  202 (293)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~-~~~~l~~iViDE~h~~~~~~~-~~~~~~i~~~---  202 (293)
                      .++++..++|+.....+...+..+++|+|+||+++.+.+..+.+ .+.++++|||||||++.+.+. ...+..+...   
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            89999999999877776667777899999999999999988766 788999999999999876543 3333233332   


Q ss_pred             -CCCCccEEEEEeecC
Q 022724          203 -LPPDLQVVLISATLP  217 (293)
Q Consensus       203 -l~~~~q~v~~SAt~~  217 (293)
                       ..+..|++++|||++
T Consensus       403 ~~~~~~~~l~lSATp~  418 (797)
T 4a2q_A          403 SASQLPQILGLTASVG  418 (797)
T ss_dssp             TCCCCCEEEEEESCCC
T ss_pred             cCCCCCeEEEEcCCcc
Confidence             145689999999995

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

Probab=99.97  E-value=1.7e-29  Score=246.68  Aligned_cols=158  Identities=20%  Similarity=0.284  Sum_probs=137.9

Q ss_pred             HCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCC
Q 022724           50 QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (293)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (293)
                      .++|. |+++|.++++.+.+|+++++++|||+|||++|++++...+..   +.+++|++|+++|+.|+++.++++..  +
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            34565 899999999999999999999999999999999998876543   56899999999999999999987643  5


Q ss_pred             ceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccE
Q 022724          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQV  209 (293)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~  209 (293)
                      +++..++|+.+..       ...+|+|+||++|.+++......+.++++|||||+|++.+++++..+..++..+++..|+
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            7788888887543       347999999999999998887778999999999999999999998999999999999999


Q ss_pred             EEEEeecChhH
Q 022724          210 VLISATLPHEI  220 (293)
Q Consensus       210 v~~SAt~~~~~  220 (293)
                      |++|||+++..
T Consensus       182 IlLSAT~~n~~  192 (997)
T 4a4z_A          182 ILLSATVPNTY  192 (997)
T ss_dssp             EEEECCCTTHH
T ss_pred             EEEcCCCCChH
Confidence            99999998653

>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=1.8e-28  Score=239.28  Aligned_cols=168  Identities=15%  Similarity=0.206  Sum_probs=134.4

Q ss_pred             HCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCC--ceeEEEEcCCHHHHHHHHHHHHHhhcc
Q 022724           50 QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR--EVQALILSPTRELATQTEKVILAIGDF  127 (293)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~--~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (293)
                      -.|+..|+++|.++++.+++|+++++.+|||+|||++|++|++..+...+.  +.++||++|+++|+.|+.+.++++...
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            346788999999999999999999999999999999999999998876532  568999999999999999999999888


Q ss_pred             CCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCC-CCCCccEEEecchhhhhccc-cHHHHHHHHhh---
Q 022724          128 INIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL-RTRAIKLLVLDESDEMLSRG-FKDQIYDVYRY---  202 (293)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~-~~~~l~~iViDE~h~~~~~~-~~~~~~~i~~~---  202 (293)
                      .++++..++|+.+...+...+..+++|+|+||+++.+.+..+.+ .+.++++|||||||++...+ +...+..+...   
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            89999999999876665555556789999999999999988766 78899999999999987653 33333333332   


Q ss_pred             -CCCCccEEEEEeecC
Q 022724          203 -LPPDLQVVLISATLP  217 (293)
Q Consensus       203 -l~~~~q~v~~SAt~~  217 (293)
                       ..+..|++++|||++
T Consensus       403 ~~~~~~~~l~LSATp~  418 (936)
T 4a2w_A          403 SASQLPQILGLTASVG  418 (936)
T ss_dssp             TCSCCCEEEEEESCCC
T ss_pred             cCCCcCeEEEecCCcc
Confidence             145689999999995

>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=2.4e-27  Score=215.70  Aligned_cols=169  Identities=18%  Similarity=0.201  Sum_probs=136.7

Q ss_pred             CCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q 022724           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (293)
                      .|+|+|.++++.+.++ ++++.+|||+|||++++.++...+..  .+.++||++|+++|+.|+.+.++++....+.++..
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            5999999999999998 99999999999999999999887762  35689999999999999999999887545568888


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEe
Q 022724          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (293)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SA  214 (293)
                      ++|+......... ..+++|+|+||+.+...+..+.+.+.++++||+||+|++.+......+...+....+..+++++||
T Consensus        86 ~~g~~~~~~~~~~-~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~~~~~~~~~~~~~~~~~~~~~l~lTa  164 (494)
T 1wp9_A           86 LTGEKSPEERSKA-WARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTA  164 (494)
T ss_dssp             ECSCSCHHHHHHH-HHHCSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTTCHHHHHHHHHHHHCSSCCEEEEES
T ss_pred             eeCCcchhhhhhh-ccCCCEEEecHHHHHHHHhcCCcchhhceEEEEECCcccCCCCcHHHHHHHHHhcCCCCeEEEEec
Confidence            8888766544333 335799999999999988888788899999999999999765444445555555567889999999


Q ss_pred             ecChh---HHHHHHhc
Q 022724          215 TLPHE---ILEMTTKF  227 (293)
Q Consensus       215 t~~~~---~~~~~~~~  227 (293)
                      |+.+.   +..+...+
T Consensus       165 Tp~~~~~~~~~l~~~l  180 (494)
T 1wp9_A          165 SPGSTPEKIMEVINNL  180 (494)
T ss_dssp             CSCSSHHHHHHHHHHT
T ss_pred             CCCCCcHHHHHHHHhc
Confidence            99743   34444443

>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=9.4e-28  Score=225.18  Aligned_cols=161  Identities=20%  Similarity=0.244  Sum_probs=135.6

Q ss_pred             HCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCC
Q 022724           50 QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (293)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (293)
                      .+|| .|+++|..++|.+.+|+  +..++||+|||++|.+|++.....   +..++||+||++||.|..+.+..+...+|
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            4799 89999999999999999  999999999999999999854332   45799999999999999999999999999


Q ss_pred             ceEEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcC------CCCCCCccEEEecchhhhh-ccc----------
Q 022724          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRK------TLRTRAIKLLVLDESDEML-SRG----------  191 (293)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l-~~~l~~~------~~~~~~l~~iViDE~h~~~-~~~----------  191 (293)
                      +++..++||.+...+..  ..+++|+|+||++| .++++.+      ...++.+.++|+||||.|+ +.+          
T Consensus       153 l~v~~i~gg~~~~~r~~--~~~~dIv~gTpgrlgfD~L~D~m~~~~~~l~lr~~~~lVlDEaD~mLiDea~tplIisg~~  230 (844)
T 1tf5_A          153 LTVGLNLNSMSKDEKRE--AYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQA  230 (844)
T ss_dssp             CCEEECCTTSCHHHHHH--HHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTTTCEEEEEEEE
T ss_pred             CeEEEEeCCCCHHHHHH--hcCCCEEEECchhhhHHHHHHhhhcchhhhcccCCCEEEECchhhhhhhccccchhhcCCc
Confidence            99999999987654333  34689999999999 6666543      3567899999999999997 553          


Q ss_pred             -----cHHHHHHHHhhCC---------CCccEE-----------------EEEeecCh
Q 022724          192 -----FKDQIYDVYRYLP---------PDLQVV-----------------LISATLPH  218 (293)
Q Consensus       192 -----~~~~~~~i~~~l~---------~~~q~v-----------------~~SAt~~~  218 (293)
                           +...+..+++.++         +..|+.                 ++|||.+.
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                 6678889999986         367777                 88999764

>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=8.9e-28  Score=224.86  Aligned_cols=147  Identities=16%  Similarity=0.230  Sum_probs=114.1

Q ss_pred             CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q 022724           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (293)
Q Consensus        51 ~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (293)
                      +|. .|+++|..+++.+.+|+  +..++||+|||++|++|++.....   +.+++|++||++||.|..+.+..+...+++
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 79999999999999998  999999999999999999865433   468999999999999999999999999999


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcCC------CCCCCccEEEecchhhhh-ccc-----------
Q 022724          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRKT------LRTRAIKLLVLDESDEML-SRG-----------  191 (293)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l-~~~l~~~~------~~~~~l~~iViDE~h~~~-~~~-----------  191 (293)
                      ++..++||.+...  +....+++|+||||++| .++++.+.      ..++++.++|+||+|.|+ +.+           
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 77777542      567999999999999998 433           


Q ss_pred             ----cHHHHHHHHhhCCC
Q 022724          192 ----FKDQIYDVYRYLPP  205 (293)
Q Consensus       192 ----~~~~~~~i~~~l~~  205 (293)
                          +...+..++..+++
T Consensus       223 ~~~~~y~~i~~iv~~L~~  240 (853)
T 2fsf_A          223 DSSEMYKRVNKIIPHLIR  240 (853)
T ss_dssp             ------------------
T ss_pred             cchhHHHHHHHHHHhchh
Confidence                45667777777753

>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=99.94  E-value=7.9e-26  Score=223.94  Aligned_cols=235  Identities=16%  Similarity=0.161  Sum_probs=169.7

Q ss_pred             CCCCHHHHHHHH-HCCCCCCcHHHHHHHHhhhc----CC--cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCC
Q 022724           38 MGIKDDLLRGIY-QYGFEKPSAIQQRAVMPIIK----GR--DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (293)
Q Consensus        38 ~~l~~~i~~~l~-~~~~~~~~~~Q~~~~~~i~~----~~--~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~  110 (293)
                      ++.+....+.+. .++|. |+|+|.++++.+.+    |+  ++++++|||+|||++|+.+++..+..   +.+++|++||
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            455666666664 46776 79999999999875    65  99999999999999999888876654   4699999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEECCcchHHHH---HHHhc-CCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhh
Q 022724          111 RELATQTEKVILAIGDFINIQAHACVGGKSVGEDI---RKLEH-GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDE  186 (293)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~-~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~  186 (293)
                      ++|+.|+++.+++.....++++..+++..+..+..   ..+.. .++|+|+||+.+.     ....+.++++|||||+|+
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            99999999999988877888888888776554432   33333 5899999997553     346688999999999999


Q ss_pred             hhccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHH
Q 022724          187 MLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDL  266 (293)
Q Consensus       187 ~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l  266 (293)
                      +.     ......+..+....++++||||+.+....+....+.++..+....  .....+..++....    +......+
T Consensus       737 ~g-----~~~~~~l~~l~~~~~vl~lSATp~p~~l~~~~~~~~~~~~i~~~~--~~r~~i~~~~~~~~----~~~i~~~i  805 (1151)
T 2eyq_A          737 FG-----VRHKERIKAMRANVDILTLTATPIPRTLNMAMSGMRDLSIIATPP--ARRLAVKTFVREYD----SMVVREAI  805 (1151)
T ss_dssp             SC-----HHHHHHHHHHHTTSEEEEEESSCCCHHHHHHHTTTSEEEECCCCC--CBCBCEEEEEEECC----HHHHHHHH
T ss_pred             cC-----hHHHHHHHHhcCCCCEEEEcCCCChhhHHHHHhcCCCceEEecCC--CCccccEEEEecCC----HHHHHHHH
Confidence            63     233444555566789999999998777766666555544332222  12223444444322    22222233


Q ss_pred             Hhh-CCCCcEEEEcccchhHHHHHhhC
Q 022724          267 YDT-LTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       267 ~~~-~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ++. ..+++++||||++++++.+++.|
T Consensus       806 l~~l~~g~qvlvf~~~v~~~~~l~~~L  832 (1151)
T 2eyq_A          806 LREILRGGQVYYLYNDVENIQKAAERL  832 (1151)
T ss_dssp             HHHHTTTCEEEEECCCSSCHHHHHHHH
T ss_pred             HHHHhcCCeEEEEECCHHHHHHHHHHH
Confidence            322 34679999999999999998765

>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=99.94  E-value=6.5e-26  Score=212.71  Aligned_cols=161  Identities=17%  Similarity=0.219  Sum_probs=136.5

Q ss_pred             HCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCC
Q 022724           50 QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (293)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (293)
                      .+|+ .|+++|..+++.+.+|+  +..++||+|||++|.+|++.....   +.+++|++||++||.|..+.+..+...+|
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 89999999999999998  999999999999999999754433   45799999999999999999999999999


Q ss_pred             ceEEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcC------CCCCCCccEEEecchhhhh-cc-----------
Q 022724          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRK------TLRTRAIKLLVLDESDEML-SR-----------  190 (293)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l-~~~l~~~------~~~~~~l~~iViDE~h~~~-~~-----------  190 (293)
                      +++..++|+.+.....  ...+++|+++||++| .++|+.+      ...++.+.++||||+|.|+ +.           
T Consensus       181 Lsv~~i~gg~~~~~r~--~~y~~DIvygTpgrlgfDyLrD~m~~~~~~l~lr~l~~lIVDEaDsmLiDeartPLiiSg~~  258 (922)
T 1nkt_A          181 LQVGVILATMTPDERR--VAYNADITYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVDEVDSILIDEARTPLIISGPA  258 (922)
T ss_dssp             CCEEECCTTCCHHHHH--HHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEETTHHHHHTTGGGSCEEEEEEC
T ss_pred             CeEEEEeCCCCHHHHH--HhcCCCEEEECchHhhHHHHHhhhhccHhhhccCCCCEEEEeChHHHHHhcCccceeecCCC
Confidence            9999999998754333  333589999999999 6777654      3667899999999999998 42           


Q ss_pred             ----ccHHHHHHHHhhCC---------CCccEE-----------------EEEeecCh
Q 022724          191 ----GFKDQIYDVYRYLP---------PDLQVV-----------------LISATLPH  218 (293)
Q Consensus       191 ----~~~~~~~~i~~~l~---------~~~q~v-----------------~~SAt~~~  218 (293)
                          ++...+..++..++         +..|+.                 ++|||.++
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                46788999999997         678888                 88999764

>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=5.5e-27  Score=191.54  Aligned_cols=164  Identities=14%  Similarity=0.157  Sum_probs=120.5

Q ss_pred             CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccC---CCceeEEEEcCCHHHHHH-HHHHHHHhhc
Q 022724           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS---SREVQALILSPTRELATQ-TEKVILAIGD  126 (293)
Q Consensus        51 ~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~---~~~~~~lil~P~~~l~~q-~~~~~~~~~~  126 (293)
                      .....|+++|.++++.+.+++++++.+|||+|||+++++++...+...   ..+.+++|++|+++|+.| +.+.++.+..
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            345579999999999999999999999999999999999998776432   235689999999999999 7788887765


Q ss_pred             cCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCC------CCCCCccEEEecchhhhhccccHHHH-HHH
Q 022724          127 FINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT------LRTRAIKLLVLDESDEMLSRGFKDQI-YDV  199 (293)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~------~~~~~l~~iViDE~h~~~~~~~~~~~-~~i  199 (293)
                      . ++++..++|+.........+..+++|+|+||+.+.+.+....      ..+.++++|||||+|++.+.++...+ ..+
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 678888888766555544444568999999999999887643      55788999999999999876544443 333


Q ss_pred             HhhC-------------CCCccEEEEEee
Q 022724          200 YRYL-------------PPDLQVVLISAT  215 (293)
Q Consensus       200 ~~~l-------------~~~~q~v~~SAt  215 (293)
                      +...             .+..+++++|||
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

>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=1.7e-26  Score=219.58  Aligned_cols=231  Identities=17%  Similarity=0.190  Sum_probs=157.9

Q ss_pred             HHHHHHHHHCCCCCCcHHHHHHHHhhhcC------CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHH
Q 022724           42 DDLLRGIYQYGFEKPSAIQQRAVMPIIKG------RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELAT  115 (293)
Q Consensus        42 ~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~------~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~  115 (293)
                      +.+.+.+..++| .|+++|+++++.+.++      +++++++|||||||++|++|++..+..   +.+++|++|+++|+.
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            445555678899 7999999999998865      699999999999999999999988765   468999999999999


Q ss_pred             HHHHHHHHhhccCCceEEEEECCcchHHHH---HHHhc-CCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccc
Q 022724          116 QTEKVILAIGDFINIQAHACVGGKSVGEDI---RKLEH-GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG  191 (293)
Q Consensus       116 q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~-~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~  191 (293)
                      |+++.++++....++++..++|+.+..+..   ..+.+ .++|+|+||+.+.+     ...+.+++++||||+|.+....
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            999999999888899999999998765543   33333 48999999987754     4568899999999999973221


Q ss_pred             cHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHh-h-
Q 022724          192 FKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYD-T-  269 (293)
Q Consensus       192 ~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~-~-  269 (293)
                           ...+.......++++||||+.+....+..  ..+.....+.........+...+.   ... +...+...+. . 
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                 11122223568999999998766554433  222211122211111122332222   122 2333333333 2 


Q ss_pred             CCCCcEEEEcccchh--------HHHHHhhC
Q 022724          270 LTITQAVIFCNTKRK--------VLLLVLQF  292 (293)
Q Consensus       270 ~~~~~~iIF~~s~~~--------a~~l~~~L  292 (293)
                      ..+++++|||+++++        ++.+++.|
T Consensus       576 ~~g~qvlVf~~~ie~se~l~~~~a~~l~~~L  606 (780)
T 1gm5_A          576 MRGGQAFIVYPLIEESDKLNVKSAVEMYEYL  606 (780)
T ss_dssp             TTSCCBCCBCCCC--------CHHHHHHHSG
T ss_pred             hcCCcEEEEecchhhhhhhhHHHHHHHHHHH
Confidence            345699999997754        55555544

>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=1.5e-27  Score=227.33  Aligned_cols=163  Identities=13%  Similarity=0.177  Sum_probs=127.3

Q ss_pred             CCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCC---CceeEEEEcCCHHHHHHH-HHHHHHhhccCCc
Q 022724           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS---REVQALILSPTRELATQT-EKVILAIGDFINI  130 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~---~~~~~lil~P~~~l~~q~-~~~~~~~~~~~~~  130 (293)
                      .|+++|.++++.+++|+++++.+|||+|||++|++|++..+....   .+.++||++|+++|+.|+ .+.++++... ++
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            599999999999999999999999999999999999998775431   235899999999999999 9999998765 57


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHH------hcCCCCCCCccEEEecchhhhhccc-cHHHHHHHHhhC
Q 022724          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMI------KRKTLRTRAIKLLVLDESDEMLSRG-FKDQIYDVYRYL  203 (293)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l------~~~~~~~~~l~~iViDE~h~~~~~~-~~~~~~~i~~~l  203 (293)
                      ++..++|+.........+..+++|+|+||++|.+.+      ....+.+.++++|||||||++...+ +...+..++...
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            888999987766655666677899999999999988      4455678899999999999985543 333333222221


Q ss_pred             -------------CCCccEEEEEeecCh
Q 022724          204 -------------PPDLQVVLISATLPH  218 (293)
Q Consensus       204 -------------~~~~q~v~~SAt~~~  218 (293)
                                   .+..+++++|||++.
T Consensus       166 ~~~~~~~~~~~~~~~~~~il~lTATp~~  193 (699)
T 4gl2_A          166 LKNNRLKKENKPVIPLPQILGLTASPGV  193 (699)
T ss_dssp             HHHHHHHC----CCCCCEEEEECSCCCC
T ss_pred             hcccccccccccCCCCCEEEEecccccc
Confidence                         156799999999986

>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=2.7e-26  Score=211.02  Aligned_cols=155  Identities=21%  Similarity=0.190  Sum_probs=128.8

Q ss_pred             CCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEE
Q 022724           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAH  133 (293)
Q Consensus        54 ~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~  133 (293)
                      ..|+++|.++++.+.++++.++++|||+|||++|+.++...+...  +.+++|++|+++|+.|+.+.++++....+..+.
T Consensus       112 ~~l~~~Q~~ai~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~--~~~vlvl~P~~~L~~Q~~~~~~~~~~~~~~~v~  189 (510)
T 2oca_A          112 IEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENY--EGKILIIVPTTALTTQMADDFVDYRLFSHAMIK  189 (510)
T ss_dssp             ECCCHHHHHHHHHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHHC--SSEEEEEESSHHHHHHHHHHHHHTTSSCGGGEE
T ss_pred             CCCCHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhCC--CCeEEEEECcHHHHHHHHHHHHHhhcCCccceE
Confidence            379999999999999999999999999999999999988877543  348999999999999999999988766667888


Q ss_pred             EEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      .++++.+...+   .....+|+|+||+.+..   .....+.++++|||||+|.+..    ..+..+++.+.+..+++++|
T Consensus       190 ~~~~~~~~~~~---~~~~~~I~i~T~~~l~~---~~~~~~~~~~liIiDE~H~~~~----~~~~~il~~~~~~~~~l~lS  259 (510)
T 2oca_A          190 KIGGGASKDDK---YKNDAPVVVGTWQTVVK---QPKEWFSQFGMMMNDECHLATG----KSISSIISGLNNCMFKFGLS  259 (510)
T ss_dssp             ECGGGCCTTGG---GCTTCSEEEEEHHHHTT---SCGGGGGGEEEEEEETGGGCCH----HHHHHHGGGCTTCCEEEEEE
T ss_pred             EEecCCccccc---cccCCcEEEEeHHHHhh---chhhhhhcCCEEEEECCcCCCc----ccHHHHHHhcccCcEEEEEE
Confidence            88888765543   34567999999996543   3334567899999999999854    45667778887888999999


Q ss_pred             eecChhH
Q 022724          214 ATLPHEI  220 (293)
Q Consensus       214 At~~~~~  220 (293)
                      ||+++..
T Consensus       260 ATp~~~~  266 (510)
T 2oca_A          260 GSLRDGK  266 (510)
T ss_dssp             SCGGGCS
T ss_pred             eCCCCCc
Confidence            9997653

>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=4.3e-25  Score=201.16  Aligned_cols=136  Identities=15%  Similarity=0.136  Sum_probs=112.2

Q ss_pred             CCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCce-EE
Q 022724           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ-AH  133 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~-~~  133 (293)
                      .|+|+|.++++.+.+++++++++|||+|||++|+.++...      +.++||++|+++|+.|+.+.++++    +++ +.
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            5899999999999999999999999999999999888764      458999999999999999988773    677 77


Q ss_pred             EEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      .++|+...         ..+|+|+||+.+...+..-   ..++++|||||+|.+.+..+..    +...+ +..+++++|
T Consensus       163 ~~~g~~~~---------~~~Ivv~T~~~l~~~~~~~---~~~~~liIvDEaH~~~~~~~~~----~~~~~-~~~~~l~lS  225 (472)
T 2fwr_A          163 EFSGRIKE---------LKPLTVSTYDSAYVNAEKL---GNRFMLLIFDEVHHLPAESYVQ----IAQMS-IAPFRLGLT  225 (472)
T ss_dssp             EBSSSCBC---------CCSEEEEEHHHHHHTHHHH---TTTCSEEEEETGGGTTSTTTHH----HHHTC-CCSEEEEEE
T ss_pred             EECCCcCC---------cCCEEEEEcHHHHHHHHHh---cCCCCEEEEECCcCCCChHHHH----HHHhc-CCCeEEEEe
Confidence            77776542         4689999999988765421   2458999999999998776654    44444 467899999


Q ss_pred             eecC
Q 022724          214 ATLP  217 (293)
Q Consensus       214 At~~  217 (293)
                      ||+.
T Consensus       226 ATp~  229 (472)
T 2fwr_A          226 ATFE  229 (472)
T ss_dssp             SCCC
T ss_pred             cCcc
Confidence            9996

>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=6.3e-24  Score=202.83  Aligned_cols=246  Identities=15%  Similarity=0.177  Sum_probs=165.0

Q ss_pred             ccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhh-cCCcEEEEcCCCChhHHHHHHHHH--hhhccCCCceeEEE
Q 022724           30 EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII-KGRDVIAQAQSGTGKTSMIALTVC--QTVDTSSREVQALI  106 (293)
Q Consensus        30 ~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~-~~~~~li~~~Tg~GKT~~~~~~~~--~~l~~~~~~~~~li  106 (293)
                      .++.+|+++++++.+.+.+.+.+ ..|++.|+++++.++ .+++++++||||+|||+  ++|++  ........+.++++
T Consensus        69 ~~~~~f~~~~l~~~~~~~l~~r~-~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTt--llp~ll~~~~~~~~~g~~ilv  145 (773)
T 2xau_A           69 GKINPFTGREFTPKYVDILKIRR-ELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTT--QIPQFVLFDEMPHLENTQVAC  145 (773)
T ss_dssp             SSBCTTTCSBCCHHHHHHHHHHT-TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHH--HHHHHHHHHHCGGGGTCEEEE
T ss_pred             CCCCCccccCCCHHHHHHHHHhh-cCChHHHHHHHHHHHhCCCeEEEECCCCCCHHH--HHHHHHHHhccccCCCceEEe
Confidence            34678999999999999999887 789999999999876 56789999999999998  34444  21111222567999


Q ss_pred             EcCCHHHHHHHHHHHHHhh-ccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchh
Q 022724          107 LSPTRELATQTEKVILAIG-DFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESD  185 (293)
Q Consensus       107 l~P~~~l~~q~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h  185 (293)
                      ++|+++|+.|+.+.+.... ...+..+........      ....+.+|+++||+++.+.+... ..+.++++||+||+|
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            9999999999988775432 222322322111111      11235689999999999876654 458899999999999


Q ss_pred             h-hhccc-cHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHH--
Q 022724          186 E-MLSRG-FKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFD--  261 (293)
Q Consensus       186 ~-~~~~~-~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~--  261 (293)
                      . .++.. ....+..+.... +..|+++||||++..  .+. .++.+...+.+...   ...+.+++......+....  
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 44432 233444555444 578999999999643  333 34444444444322   2345666554444432222  


Q ss_pred             -HHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          262 -TLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       262 -~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                       .+..+.....++++||||+++++++.+++.|
T Consensus       292 ~~l~~~~~~~~~g~iLVF~~~~~~i~~l~~~L  323 (773)
T 2xau_A          292 RTVLQIHATEEAGDILLFLTGEDEIEDAVRKI  323 (773)
T ss_dssp             HHHHHHHHHSCSCEEEEECSCHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCCCEEEECCCHHHHHHHHHHH
Confidence             2333344456789999999999999998765

>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=99.92  E-value=3e-24  Score=177.95  Aligned_cols=166  Identities=19%  Similarity=0.243  Sum_probs=124.7

Q ss_pred             CCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCC--ceeEEEEcCCHHHHHHHHHHHHHhh-ccCCce
Q 022724           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR--EVQALILSPTRELATQTEKVILAIG-DFINIQ  131 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~--~~~~lil~P~~~l~~q~~~~~~~~~-~~~~~~  131 (293)
                      .++++|.++++.+.+|++++++||||||||.++.++++........  +.++++++|+++++.|+.+.+.... ...+..
T Consensus        61 p~~~~q~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~~~~~~~~~~~~~~~~  140 (235)
T 3llm_A           61 PVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPGKS  140 (235)
T ss_dssp             GGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHHHHHHHHTTTCCTTSS
T ss_pred             ChHHHHHHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHHHHHHHHHhccccCce
Confidence            4789999999999999999999999999999998888887654433  4589999999999999998887543 233433


Q ss_pred             EEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhh-hccccH-HHHHHHHhhCCCCccE
Q 022724          132 AHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM-LSRGFK-DQIYDVYRYLPPDLQV  209 (293)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~-~~~~~~-~~~~~i~~~l~~~~q~  209 (293)
                      +........     .....+++|+|+||+++.+.+..   .++++++||+||+|.+ .+.++. ..+..+.... ++.|+
T Consensus       141 ~g~~~~~~~-----~~~~~~~~Ivv~Tpg~l~~~l~~---~l~~~~~lVlDEah~~~~~~~~~~~~l~~i~~~~-~~~~~  211 (235)
T 3llm_A          141 CGYSVRFES-----ILPRPHASIMFCTVGVLLRKLEA---GIRGISHVIVDEIHERDINTDFLLVVLRDVVQAY-PEVRI  211 (235)
T ss_dssp             EEEEETTEE-----ECCCSSSEEEEEEHHHHHHHHHH---CCTTCCEEEECCTTSCCHHHHHHHHHHHHHHHHC-TTSEE
T ss_pred             EEEeechhh-----ccCCCCCeEEEECHHHHHHHHHh---hhcCCcEEEEECCccCCcchHHHHHHHHHHHhhC-CCCeE
Confidence            333221111     00113478999999999998876   3889999999999985 555555 4566666665 47899


Q ss_pred             EEEEeecChhHHHHHHhcCCCC
Q 022724          210 VLISATLPHEILEMTTKFMTDP  231 (293)
Q Consensus       210 v~~SAt~~~~~~~~~~~~~~~~  231 (293)
                      +++|||++...  +.+.+...|
T Consensus       212 il~SAT~~~~~--~~~~~~~~p  231 (235)
T 3llm_A          212 VLMSATIDTSM--FCEYFFNCP  231 (235)
T ss_dssp             EEEECSSCCHH--HHHHTTSCC
T ss_pred             EEEecCCCHHH--HHHHcCCCC
Confidence            99999999775  444444444

>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=1.3e-25  Score=203.19  Aligned_cols=206  Identities=15%  Similarity=0.112  Sum_probs=137.6

Q ss_pred             CCCCCcHHHHHHHHhhhcCCcE-EEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q 022724           52 GFEKPSAIQQRAVMPIIKGRDV-IAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (293)
Q Consensus        52 ~~~~~~~~Q~~~~~~i~~~~~~-li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (293)
                      |+.+|+|+|+ ++|.+++++++ ++++|||||||++|++|++..+...  +++++|++|+++|+.|+.+.+.      +.
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            6789999985 79999988876 9999999999999999998876553  5689999999999999999774      22


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHh-hCCCCccE
Q 022724          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYR-YLPPDLQV  209 (293)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~-~l~~~~q~  209 (293)
                      .+.........     ....+..|.++|++.+.+.+.+. ..+.++++|||||+|++ +..+......+.. ...+..|+
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     11234478899999998876554 45789999999999987 3333332322222 23457999


Q ss_pred             EEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHhhCCCCcEEEEcccchhHHHHH
Q 022724          210 VLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLV  289 (293)
Q Consensus       210 v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~  289 (293)
                      ++||||+++....+   +..++..+.....  .+.  .           ....+...+... .+++||||+|+++|+.++
T Consensus       145 i~~SAT~~~~~~~~---~~~~~~~~~~~~~--~p~--~-----------~~~~~~~~l~~~-~~~~lVF~~s~~~a~~l~  205 (451)
T 2jlq_A          145 IFMTATPPGSTDPF---PQSNSPIEDIERE--IPE--R-----------SWNTGFDWITDY-QGKTVWFVPSIKAGNDIA  205 (451)
T ss_dssp             EEECSSCTTCCCSS---CCCSSCEEEEECC--CCS--S-----------CCSSSCHHHHHC-CSCEEEECSSHHHHHHHH
T ss_pred             EEEccCCCccchhh---hcCCCceEecCcc--CCc--h-----------hhHHHHHHHHhC-CCCEEEEcCCHHHHHHHH
Confidence            99999998754332   2233333333210  000  0           000111223333 469999999999999999


Q ss_pred             hhC
Q 022724          290 LQF  292 (293)
Q Consensus       290 ~~L  292 (293)
                      +.|
T Consensus       206 ~~L  208 (451)
T 2jlq_A          206 NCL  208 (451)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            875

>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=2.7e-26  Score=214.14  Aligned_cols=220  Identities=15%  Similarity=0.102  Sum_probs=147.1

Q ss_pred             CCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHH
Q 022724           38 MGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQT  117 (293)
Q Consensus        38 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~  117 (293)
                      +++++.+.+++... ...|+|+|+.+++.+.+|+++++++|||||||++|++|+++.+...  +.++||++|+++|+.|+
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            45666666555543 4788999888999999999999999999999999999999887653  56899999999999999


Q ss_pred             HHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHH
Q 022724          118 EKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIY  197 (293)
Q Consensus       118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~  197 (293)
                      .+.++.      ..+. +.+.. ..   ..-..+..+.+.|.+.+.+.+... ..+.++++||+||||++ +.++...+.
T Consensus       232 ~~~l~~------~~v~-~~~~~-l~---~~~tp~~~i~~~t~~~l~~~l~~~-~~l~~~~~iViDEah~~-~~~~~~~~~  298 (618)
T 2whx_A          232 EEALRG------LPIR-YQTPA-VK---SDHTGREIVDLMCHATFTTRLLSS-TRVPNYNLIVMDEAHFT-DPCSVAARG  298 (618)
T ss_dssp             HHHTTT------SCEE-ECCTT-SS---CCCCSSSCEEEEEHHHHHHHHHHC-SSCCCCSEEEEESTTCC-SHHHHHHHH
T ss_pred             HHHhcC------Ccee-Eeccc-ce---eccCCCceEEEEChHHHHHHHhcc-ccccCCeEEEEECCCCC-CccHHHHHH
Confidence            987752      2232 11111 00   001122356777888887755544 45889999999999998 566666777


Q ss_pred             HHHhhCC-CCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHhhCCCCcEE
Q 022724          198 DVYRYLP-PDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAV  276 (293)
Q Consensus       198 ~i~~~l~-~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~~i  276 (293)
                      .+...++ +..|+++||||+++.+..+..   .++..+.+....             +...  ...+...+.+. .+++|
T Consensus       299 ~i~~~l~~~~~q~il~SAT~~~~~~~~~~---~~~~~~~v~~~~-------------~~~~--~~~ll~~l~~~-~~~~L  359 (618)
T 2whx_A          299 YISTRVEMGEAAAIFMTATPPGSTDPFPQ---SNSPIEDIEREI-------------PERS--WNTGFDWITDY-QGKTV  359 (618)
T ss_dssp             HHHHHHHHTSCEEEEECSSCTTCCCSSCC---CSSCEEEEECCC-------------CSSC--CSSSCHHHHHC-CSCEE
T ss_pred             HHHHHhcccCccEEEEECCCchhhhhhhc---cCCceeeecccC-------------CHHH--HHHHHHHHHhC-CCCEE
Confidence            7776664 679999999999877443222   123333322110             1111  11112222232 56999


Q ss_pred             EEcccchhHHHHHhhC
Q 022724          277 IFCNTKRKVLLLVLQF  292 (293)
Q Consensus       277 IF~~s~~~a~~l~~~L  292 (293)
                      |||+|+++|+.+++.|
T Consensus       360 VF~~s~~~a~~l~~~L  375 (618)
T 2whx_A          360 WFVPSIKAGNDIANCL  375 (618)
T ss_dssp             EECSSHHHHHHHHHHH
T ss_pred             EEECChhHHHHHHHHH
Confidence            9999999999999875

>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=99.91  E-value=3.4e-25  Score=205.79  Aligned_cols=197  Identities=17%  Similarity=0.180  Sum_probs=139.9

Q ss_pred             CcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEE
Q 022724           56 PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC  135 (293)
Q Consensus        56 ~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~  135 (293)
                      +++.|.++++.+.++++++++||||+|||.+|.+++++.      +.+++|++|+++|+.|+.+.+.+..   +..+...
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            455666666667788999999999999999999998863      4589999999999999998776543   3445556


Q ss_pred             ECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCcc--EEEEE
Q 022724          136 VGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ--VVLIS  213 (293)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q--~v~~S  213 (293)
                      .|+..       ...+.+|+|+||++|   +....+.++++++|||||+|++ +.++...+..+++.++...+  ++++|
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            66643       245689999999997   4567778899999999999764 56777788888998886666  78889


Q ss_pred             eecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          214 ATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       214 At~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ||+++.+.      ...+....+....   .....+   ..... .       ++...++++|||||++++|+.+++.|
T Consensus       358 AT~~~~i~------~~~p~i~~v~~~~---~~~i~~---~~~~~-~-------l~~~~~~~vLVFv~Tr~~ae~la~~L  416 (666)
T 3o8b_A          358 ATPPGSVT------VPHPNIEEVALSN---TGEIPF---YGKAI-P-------IEAIRGGRHLIFCHSKKKCDELAAKL  416 (666)
T ss_dssp             SSCTTCCC------CCCTTEEEEECBS---CSSEEE---TTEEE-C-------GGGSSSSEEEEECSCHHHHHHHHHHH
T ss_pred             CCCCcccc------cCCcceEEEeecc---cchhHH---HHhhh-h-------hhhccCCcEEEEeCCHHHHHHHHHHH
Confidence            99987421      1111111111000   000111   01000 0       22345679999999999999999875

>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=4.7e-24  Score=181.55  Aligned_cols=154  Identities=21%  Similarity=0.198  Sum_probs=124.4

Q ss_pred             CCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q 022724           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (293)
                      .|+++|.++++.+.++++.++++|||+|||++++.++...+...  +.+++|++|+++|+.|+.+.++++....+..+..
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            79999999999999888899999999999999988887766542  3489999999999999999999987766677777


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEe
Q 022724          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (293)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SA  214 (293)
                      +.++.....   ....+.+|+|+||+.+.+.   ....+.+++++|+||+|++.+    ..+..+++.+....+++++||
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            777764432   1224579999999876543   223467889999999999863    367778888877899999999


Q ss_pred             ecChhH
Q 022724          215 TLPHEI  220 (293)
Q Consensus       215 t~~~~~  220 (293)
                      |+++..
T Consensus       261 Tp~~~~  266 (282)
T 1rif_A          261 SLRDGK  266 (282)
T ss_dssp             SCCTTS
T ss_pred             CCCCcc
Confidence            997653

>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=99.89  E-value=2.9e-25  Score=200.18  Aligned_cols=185  Identities=14%  Similarity=0.145  Sum_probs=117.6

Q ss_pred             hhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHH
Q 022724           66 PIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDI  145 (293)
Q Consensus        66 ~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  145 (293)
                      .+.+|+|+++++|||||||++|++|++..+...  +++++|++||++|+.|+++.++.+      .+....+..      
T Consensus         4 ~l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~~--~~~~lil~Ptr~La~Q~~~~l~~~------~v~~~~~~~------   69 (440)
T 1yks_A            4 MLKKGMTTVLDFHPGAGKTRRFLPQILAECARR--RLRTLVLAPTRVVLSEMKEAFHGL------DVKFHTQAF------   69 (440)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTTTS------CEEEESSCC------
T ss_pred             HhhCCCCEEEEcCCCCCHHHHHHHHHHHHHHhc--CCeEEEEcchHHHHHHHHHHHhcC------CeEEecccc------
Confidence            467899999999999999999999999877654  568999999999999999987633      222111110      


Q ss_pred             HHHhcCCcEEEeChHHHHHHHhc--------CCCCCCCccEEEecchhhhhccccHHHHHHHHhhC-CCCccEEEEEeec
Q 022724          146 RKLEHGVHVVSGTPGRVCDMIKR--------KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL-PPDLQVVLISATL  216 (293)
Q Consensus       146 ~~~~~~~~ilV~Tp~~l~~~l~~--------~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l-~~~~q~v~~SAt~  216 (293)
                              -.|+||+++..++..        ....+.+++++|+||+|.+ +.++...+..+...+ +...|+++||||+
T Consensus        70 --------~~v~Tp~~l~~~l~~~~l~~~~~~~~~~~~l~~vViDEah~~-~~~~~~~~~~~~~~~~~~~~~~l~~SAT~  140 (440)
T 1yks_A           70 --------SAHGSGREVIDAMCHATLTYRMLEPTRVVNWEVIIMDEAHFL-DPASIAARGWAAHRARANESATILMTATP  140 (440)
T ss_dssp             --------CCCCCSSCCEEEEEHHHHHHHHTSSSCCCCCSEEEETTTTCC-SHHHHHHHHHHHHHHHTTSCEEEEECSSC
T ss_pred             --------eeccCCccceeeecccchhHhhhCcccccCccEEEEECcccc-CcchHHHHHHHHHHhccCCceEEEEeCCC
Confidence                    035666555432221        2244789999999999998 333332232222222 3579999999999


Q ss_pred             ChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          217 PHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       217 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ++.+..+....  .+.              ......++... +...+..+. +. ++++||||++++.|+.+++.|
T Consensus       141 ~~~~~~~~~~~--~~~--------------~~~~~~~~~~~-~~~~~~~l~-~~-~~~~lVF~~s~~~a~~l~~~L  197 (440)
T 1yks_A          141 PGTSDEFPHSN--GEI--------------EDVQTDIPSEP-WNTGHDWIL-AD-KRPTAWFLPSIRAANVMAASL  197 (440)
T ss_dssp             TTCCCSSCCCS--SCE--------------EEEECCCCSSC-CSSSCHHHH-HC-CSCEEEECSCHHHHHHHHHHH
T ss_pred             CchhhhhhhcC--CCe--------------eEeeeccChHH-HHHHHHHHH-hc-CCCEEEEeCCHHHHHHHHHHH
Confidence            87644332210  111              11111111111 111122222 22 579999999999999999875

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.89  E-value=4.3e-23  Score=185.54  Aligned_cols=190  Identities=13%  Similarity=0.116  Sum_probs=120.8

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  148 (293)
                      +|+++++++|||||||++|++|+++.+...  +.+++|++|+++|+.|+.+.++      ++.+....++...     .-
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            478999999999999999999999666543  5689999999999999998664      3444443333211     11


Q ss_pred             hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhC-CCCccEEEEEeecChhHHHHHHhc
Q 022724          149 EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL-PPDLQVVLISATLPHEILEMTTKF  227 (293)
Q Consensus       149 ~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l-~~~~q~v~~SAt~~~~~~~~~~~~  227 (293)
                      ..+..+.+.|.+.+.+.+.. ...+.++++|||||+|.+ +..+......+.... +...|+++||||+++.+..+... 
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            12345677788888776655 456889999999999997 333333333333332 46799999999998753221110 


Q ss_pred             CCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          228 MTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       228 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                       ..|              +.......+..  +...+..++... ++++||||+++++|+.+++.|
T Consensus       145 -~~~--------------i~~~~~~~~~~--~~~~~~~~l~~~-~~~~lVF~~~~~~~~~l~~~L  191 (431)
T 2v6i_A          145 -NSP--------------IIDEETRIPDK--AWNSGYEWITEF-DGRTVWFVHSIKQGAEIGTCL  191 (431)
T ss_dssp             -SSC--------------CEEEECCCCSS--CCSSCCHHHHSC-SSCEEEECSSHHHHHHHHHHH
T ss_pred             -CCc--------------eeeccccCCHH--HHHHHHHHHHcC-CCCEEEEeCCHHHHHHHHHHH
Confidence             011              11100001111  111222334333 569999999999999999875

>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=2.7e-24  Score=202.00  Aligned_cols=211  Identities=16%  Similarity=0.168  Sum_probs=130.5

Q ss_pred             HHHHCCCC-----CCcHHHH-----HHHHhhh------cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCC
Q 022724           47 GIYQYGFE-----KPSAIQQ-----RAVMPII------KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (293)
Q Consensus        47 ~l~~~~~~-----~~~~~Q~-----~~~~~i~------~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~  110 (293)
                      ++...||.     .|+++|+     +++|.++      +|+|+++++|||||||++|++|++..+...  +.+++|++||
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            34455666     8999999     9999888      899999999999999999999999887653  5689999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHh-cCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhc
Q 022724          111 RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (293)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~  189 (293)
                      ++|+.|+.+.++.+.    +.  ...+.      ..... .+.-+-..+.+.+.+.+... ..++++++|||||+|.+ +
T Consensus       280 r~La~Q~~~~l~~~~----i~--~~~~~------l~~v~tp~~ll~~l~~~~l~~~l~~~-~~l~~l~lvViDEaH~~-~  345 (673)
T 2wv9_A          280 RVVAAEMAEALRGLP----VR--YLTPA------VQREHSGNEIVDVMCHATLTHRLMSP-LRVPNYNLFVMDEAHFT-D  345 (673)
T ss_dssp             HHHHHHHHHHTTTSC----CE--ECCC---------CCCCSCCCEEEEEHHHHHHHHHSS-SCCCCCSEEEEESTTCC-C
T ss_pred             HHHHHHHHHHHhcCC----ee--eeccc------ccccCCHHHHHHHHHhhhhHHHHhcc-cccccceEEEEeCCccc-C
Confidence            999999999876442    21  10000      00000 11123333444444433332 56889999999999998 2


Q ss_pred             cccHHHHHHHHhhC-CCCccEEEEEeecChhHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHh
Q 022724          190 RGFKDQIYDVYRYL-PPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYD  268 (293)
Q Consensus       190 ~~~~~~~~~i~~~l-~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~  268 (293)
                      ..+...+..+...+ +...|+++||||+++.+..+...  ..+..              .......... ....+..+.+
T Consensus       346 ~~~~~~~~~l~~~~~~~~~~vl~~SAT~~~~i~~~~~~--~~~i~--------------~v~~~~~~~~-~~~~l~~l~~  408 (673)
T 2wv9_A          346 PASIAARGYIATRVEAGEAAAIFMTATPPGTSDPFPDT--NSPVH--------------DVSSEIPDRA-WSSGFEWITD  408 (673)
T ss_dssp             HHHHHHHHHHHHHHHTTSCEEEEECSSCTTCCCSSCCC--SSCEE--------------EEECCCCSSC-CSSCCHHHHS
T ss_pred             ccHHHHHHHHHHhccccCCcEEEEcCCCChhhhhhccc--CCceE--------------EEeeecCHHH-HHHHHHHHHh
Confidence            22222333333333 25789999999998764322211  01111              1110011111 1111222222


Q ss_pred             hCCCCcEEEEcccchhHHHHHhhC
Q 022724          269 TLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       269 ~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                        .++++||||+++++|+.+++.|
T Consensus       409 --~~~~~lVF~~s~~~~e~la~~L  430 (673)
T 2wv9_A          409 --YAGKTVWFVASVKMSNEIAQCL  430 (673)
T ss_dssp             --CCSCEEEECSSHHHHHHHHHHH
T ss_pred             --CCCCEEEEECCHHHHHHHHHHH
Confidence              4679999999999999999875

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.89  E-value=2.5e-21  Score=181.46  Aligned_cols=130  Identities=19%  Similarity=0.239  Sum_probs=112.5

Q ss_pred             CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q 022724           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (293)
Q Consensus        51 ~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (293)
                      +|+ .|+++|..+++.+.+|+  +..+.||+|||++|.+|++.....   +.+++|++||++||.|.++.+..+...+|+
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 89999999999999998  999999999999999999644433   457999999999999999999999999999


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcCC------CCCC---CccEEEecchhhhh
Q 022724          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRKT------LRTR---AIKLLVLDESDEML  188 (293)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l-~~~l~~~~------~~~~---~l~~iViDE~h~~~  188 (293)
                      ++..++|+.+...  +....+++|+|+||+.+ .++++.+.      ..++   ++.++||||+|.++
T Consensus       150 sv~~i~Gg~~~~~--r~~ay~~DIvyGTpgrlgfDyLrd~m~~~~~~l~~r~d~~l~~lIIDEaDsmL  215 (997)
T 2ipc_A          150 SVGVIQHASTPAE--RRKAYLADVTYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAIIDEVDSIL  215 (997)
T ss_dssp             CEEECCTTCCHHH--HHHHHTSSEEEEEHHHHHHHHHHHTSCSSTTTCCSCSSSSSCEEEETTHHHHT
T ss_pred             eEEEEeCCCCHHH--HHHHcCCCEEEECchhhhhHHHHHhhhcchhhcccccCCCcceEEEechHHHH
Confidence            9999999987443  33334689999999999 78887653      4567   89999999999986

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.88  E-value=4.3e-23  Score=192.94  Aligned_cols=150  Identities=20%  Similarity=0.270  Sum_probs=90.8

Q ss_pred             CCcHHHHHHHHhhhc----C-CcEEEEcCCCChhHHHHHHHHHhhhccCC-------CceeEEEEcCCHHHHHHHH-HHH
Q 022724           55 KPSAIQQRAVMPIIK----G-RDVIAQAQSGTGKTSMIALTVCQTVDTSS-------REVQALILSPTRELATQTE-KVI  121 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~----~-~~~li~~~Tg~GKT~~~~~~~~~~l~~~~-------~~~~~lil~P~~~l~~q~~-~~~  121 (293)
                      .|+++|.++++.+..    | +++++++|||+|||++++..+ ..+....       .++++|||+|+++|+.|+. +.+
T Consensus       178 ~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~~~~~-~~l~~~~~~~~~~~~~~~vlil~P~~~L~~Q~~~~~~  256 (590)
T 3h1t_A          178 SPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVAFQIS-WKLWSARWNRTGDYRKPRILFLADRNVLVDDPKDKTF  256 (590)
T ss_dssp             -CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHH-HHHHHTTCCSSCSSSCCCEEEEEC-----------CC
T ss_pred             CchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHHHHHH-HHHHhcccccccccCCCeEEEEeCCHHHHHHHHHHHH
Confidence            699999999998875    4 679999999999999965544 4443332       5679999999999999998 666


Q ss_pred             HHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc----CCCCCCCccEEEecchhhhhccccHHHHH
Q 022724          122 LAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR----KTLRTRAIKLLVLDESDEMLSRGFKDQIY  197 (293)
Q Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~----~~~~~~~l~~iViDE~h~~~~~~~~~~~~  197 (293)
                      +.+.    ..+..+.++        ....+.+|+|+||+++......    ..+...++++||+||||++.... ...+.
T Consensus       257 ~~~~----~~~~~~~~~--------~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~lvIiDEaH~~~~~~-~~~~~  323 (590)
T 3h1t_A          257 TPFG----DARHKIEGG--------KVVKSREIYFAIYQSIASDERRPGLYKEFPQDFFDLIIIDECHRGSARD-NSNWR  323 (590)
T ss_dssp             TTTC----SSEEECCC----------CCSSCSEEEEEGGGC------CCGGGGSCTTSCSEEEESCCC----------CH
T ss_pred             Hhcc----hhhhhhhcc--------CCCCCCcEEEEEhhhhccccccccccccCCCCccCEEEEECCccccccc-hHHHH
Confidence            5443    233333322        1234579999999999886542    33556789999999999986532 23455


Q ss_pred             HHHhhCCCCccEEEEEeecChh
Q 022724          198 DVYRYLPPDLQVVLISATLPHE  219 (293)
Q Consensus       198 ~i~~~l~~~~q~v~~SAt~~~~  219 (293)
                      .++..++ ..+++++|||+...
T Consensus       324 ~il~~~~-~~~~l~lTATP~~~  344 (590)
T 3h1t_A          324 EILEYFE-PAFQIGMTATPLRE  344 (590)
T ss_dssp             HHHHHST-TSEEEEEESSCSCT
T ss_pred             HHHHhCC-cceEEEeccccccc
Confidence            6666665 57899999998643

>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=99.87  E-value=2e-22  Score=182.67  Aligned_cols=191  Identities=14%  Similarity=0.170  Sum_probs=121.3

Q ss_pred             HHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHH
Q 022724           64 VMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGE  143 (293)
Q Consensus        64 ~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~  143 (293)
                      -..+.+++++++++|||||||++|++|++..+...  ++++||++|+++|+.|+.+.++      +..+....+....  
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            34466789999999999999999999999887653  5689999999999999999876      2222221111110  


Q ss_pred             HHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhh-----hccccHHHHHHHHhhCCCCccEEEEEeecCh
Q 022724          144 DIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM-----LSRGFKDQIYDVYRYLPPDLQVVLISATLPH  218 (293)
Q Consensus       144 ~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~-----~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~  218 (293)
                         .-..+..+.+.|.+.+.+.+... ..++++++|||||+|.+     ...++.....     ..+..|+++||||+++
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               01123357778888887755543 55889999999999983     3333322211     1357899999999987


Q ss_pred             hHHHHHHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          219 EILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       219 ~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      .+..+...  ..|.......              .+..  +...+..++... ++++||||+++++|+.+++.|
T Consensus       156 ~~~~~~~~--~~pi~~~~~~--------------~~~~--~~~~~~~~l~~~-~~~~LVF~~s~~~~~~l~~~L  210 (459)
T 2z83_A          156 TTDPFPDS--NAPIHDLQDE--------------IPDR--AWSSGYEWITEY-AGKTVWFVASVKMGNEIAMCL  210 (459)
T ss_dssp             CCCSSCCC--SSCEEEEECC--------------CCSS--CCSSCCHHHHHC-CSCEEEECSCHHHHHHHHHHH
T ss_pred             chhhhccC--CCCeEEeccc--------------CCcc--hhHHHHHHHHhc-CCCEEEEeCChHHHHHHHHHH
Confidence            64332211  1222221110              0000  001111223333 579999999999999999875

>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=99.85  E-value=1.6e-21  Score=190.06  Aligned_cols=153  Identities=12%  Similarity=0.082  Sum_probs=115.4

Q ss_pred             CCcHHHHHHHHhhhc--------------CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHH
Q 022724           55 KPSAIQQRAVMPIIK--------------GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKV  120 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~--------------~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~  120 (293)
                      .|+|+|.++++.+..              +++.+++++||||||+++ ++++..+...+...++|||+|+++|+.|+.+.
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 55555555444446999999999999999999


Q ss_pred             HHHhhccCCceEEEEECCcchHHHHHHHh-cCCcEEEeChHHHHHHHhcCC--CCCCCccEEEecchhhhhccccHHHHH
Q 022724          121 ILAIGDFINIQAHACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRKT--LRTRAIKLLVLDESDEMLSRGFKDQIY  197 (293)
Q Consensus       121 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ilV~Tp~~l~~~l~~~~--~~~~~l~~iViDE~h~~~~~~~~~~~~  197 (293)
                      ++.+...      .+.++.+.......+. .+.+|+|+||+++...+....  ..+....+||+||||++...   ....
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            8887543      1223444444445553 467999999999998876532  23557899999999997532   3345


Q ss_pred             HHHhhCCCCccEEEEEeecCh
Q 022724          198 DVYRYLPPDLQVVLISATLPH  218 (293)
Q Consensus       198 ~i~~~l~~~~q~v~~SAt~~~  218 (293)
                      .+...++ +.++++||||+..
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            5666665 5899999999864

>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=1.6e-20  Score=155.53  Aligned_cols=138  Identities=16%  Similarity=0.144  Sum_probs=109.2

Q ss_pred             CCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCce-EE
Q 022724           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ-AH  133 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~-~~  133 (293)
                      .|+++|.++++.+.+++++++++|||+|||.+++.++...      +.+++|++|+++|+.|+.+.+.++    ++. +.
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      357999999999999999988763    566 66


Q ss_pred             EEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      .+.|+...         ..+|+|+|++.+......-   ..++++|||||+|++.+..+.    .+...++ ..+++++|
T Consensus       163 ~~~g~~~~---------~~~i~v~T~~~l~~~~~~~---~~~~~llIiDEaH~l~~~~~~----~i~~~~~-~~~~l~LS  225 (237)
T 2fz4_A          163 EFSGRIKE---------LKPLTVSTYDSAYVNAEKL---GNRFMLLIFDEVHHLPAESYV----QIAQMSI-APFRLGLT  225 (237)
T ss_dssp             EESSSCBC---------CCSEEEEEHHHHHHTHHHH---TTTCSEEEEECSSCCCTTTHH----HHHHTCC-CSEEEEEE
T ss_pred             EEeCCCCC---------cCCEEEEeHHHHHhhHHHh---cccCCEEEEECCccCCChHHH----HHHHhcc-CCEEEEEe
Confidence            66666532         4689999999987755421   245899999999999766543    3445554 67899999


Q ss_pred             eecChh
Q 022724          214 ATLPHE  219 (293)
Q Consensus       214 At~~~~  219 (293)
                      ||++..
T Consensus       226 ATp~r~  231 (237)
T 2fz4_A          226 ATFERE  231 (237)
T ss_dssp             ESCC--
T ss_pred             cCCCCC
Confidence            998754

>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=99.79  E-value=2.4e-18  Score=157.66  Aligned_cols=148  Identities=13%  Similarity=0.138  Sum_probs=106.7

Q ss_pred             CCcHHHHHHHHhh----hcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q 022724           55 KPSAIQQRAVMPI----IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (293)
Q Consensus        55 ~~~~~Q~~~~~~i----~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (293)
                      .|+|+|.++++.+    ..+++.++..+||+|||+.++..+. .+.......++||+|| ..|+.|+.+.++++..  +.
T Consensus        37 ~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai~~i~-~~~~~~~~~~~LIv~P-~~l~~qw~~e~~~~~~--~~  112 (500)
T 1z63_A           37 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFS-DAKKENELTPSLVICP-LSVLKNWEEELSKFAP--HL  112 (500)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHH-HHHHTTCCSSEEEEEC-STTHHHHHHHHHHHCT--TS
T ss_pred             cchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHHHHHH-HHHhcCCCCCEEEEcc-HHHHHHHHHHHHHHCC--Cc
Confidence            6999999999876    3578999999999999988765444 4433333458999999 5699999999998865  35


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEE
Q 022724          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVV  210 (293)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v  210 (293)
                      ++..++|+...     ....+.+|+|+|++.+.....   +...++++||+||+|++.+..  ......+..++ ..+.+
T Consensus       113 ~v~~~~g~~~~-----~~~~~~~ivi~t~~~l~~~~~---l~~~~~~~vIvDEaH~~kn~~--~~~~~~l~~l~-~~~~l  181 (500)
T 1z63_A          113 RFAVFHEDRSK-----IKLEDYDIILTTYAVLLRDTR---LKEVEWKYIVIDEAQNIKNPQ--TKIFKAVKELK-SKYRI  181 (500)
T ss_dssp             CEEECSSSTTS-----CCGGGSSEEEEEHHHHTTCHH---HHTCCEEEEEEETGGGGSCTT--SHHHHHHHTSC-EEEEE
T ss_pred             eEEEEecCchh-----ccccCCcEEEeeHHHHhccch---hcCCCcCEEEEeCccccCCHh--HHHHHHHHhhc-cCcEE
Confidence            56666655421     112356899999998876433   334567999999999985443  22334444553 56789


Q ss_pred             EEEeecC
Q 022724          211 LISATLP  217 (293)
Q Consensus       211 ~~SAt~~  217 (293)
                      ++|||+.
T Consensus       182 ~LTaTP~  188 (500)
T 1z63_A          182 ALTGTPI  188 (500)
T ss_dssp             EECSSCS
T ss_pred             EEecCCC
Confidence            9999983

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.77  E-value=2.5e-19  Score=168.08  Aligned_cols=190  Identities=16%  Similarity=0.142  Sum_probs=124.3

Q ss_pred             HhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHH
Q 022724           65 MPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGED  144 (293)
Q Consensus        65 ~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  144 (293)
                      ...++|++++++||||+|||..    ++..+...   .+.+|++|+++|+.|+++.+++.    ++++..+.|+..... 
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 ARAMQRKIIFHSGPTNSGKTYH----AIQKYFSA---KSGVYCGPLKLLAHEIFEKSNAA----GVPCDLVTGEERVTV-  217 (677)
T ss_dssp             HHTSCCEEEEEECCTTSSHHHH----HHHHHHHS---SSEEEEESSHHHHHHHHHHHHHT----TCCEEEECSSCEECC-
T ss_pred             HHhcCCCEEEEEcCCCCCHHHH----HHHHHHhc---CCeEEEeCHHHHHHHHHHHHHhc----CCcEEEEECCeeEEe-
Confidence            3446889999999999999983    33333333   24599999999999999998775    667778887754310 


Q ss_pred             HHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCC-CCccEEEEEeecChhHHHH
Q 022724          145 IRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP-PDLQVVLISATLPHEILEM  223 (293)
Q Consensus       145 ~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~-~~~q~v~~SAt~~~~~~~~  223 (293)
                       ..-....+++++|++.+.        ....++++||||+|++.+.+++..+..++..++ ...+++++|||. +.+..+
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--------VTTPYEVAVIDEIQMIRDPARGWAWTRALLGLCAEEVHLCGEPAAI-DLVMEL  287 (677)
T ss_dssp             -STTCCCCSEEEEEGGGCC--------SSSCEEEEEECSGGGGGCTTTHHHHHHHHHHCCEEEEEEEECGGGH-HHHHHH
T ss_pred             -cCCCcccceeEecHhHhh--------hcccCCEEEEecceecCCccchHHHHHHHHccCccceEEEeccchH-HHHHHH
Confidence             000112567777774332        246789999999999998889999998888887 678999999995 334444


Q ss_pred             HHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          224 TTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       224 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      .... .....+.....   ....  . . ....      + ..+... ....+|||+++++++.+++.|
T Consensus       288 ~~~~-~~~~~v~~~~r---~~~l--~-~-~~~~------l-~~l~~~-~~g~iIf~~s~~~ie~la~~L  340 (677)
T 3rc3_A          288 MYTT-GEEVEVRDYKR---LTPI--S-V-LDHA------L-ESLDNL-RPGDCIVCFSKNDIYSVSRQI  340 (677)
T ss_dssp             HHHH-TCCEEEEECCC---SSCE--E-E-CSSC------C-CSGGGC-CTTEEEECSSHHHHHHHHHHH
T ss_pred             HHhc-CCceEEEEeee---cchH--H-H-HHHH------H-HHHHhc-CCCCEEEEcCHHHHHHHHHHH
Confidence            4443 23333322110   0010  0 0 0000      0 011122 245689999999999998865

>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=99.76  E-value=1.8e-18  Score=169.28  Aligned_cols=158  Identities=16%  Similarity=0.098  Sum_probs=106.6

Q ss_pred             CCcHHHHHHHHhhhc--CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceE
Q 022724           55 KPSAIQQRAVMPIIK--GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQA  132 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~--~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  132 (293)
                      .|+|+|.+++..+..  +.+.+++.+||+|||+.++..+...+.... ..+++|+||+ .|+.|+.+.+.+..   ++++
T Consensus       153 ~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g~-~~rvLIVvP~-sLl~Qw~~E~~~~f---~l~v  227 (968)
T 3dmq_A          153 SLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSGA-AERVLIIVPE-TLQHQWLVEMLRRF---NLRF  227 (968)
T ss_dssp             CCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHTSS-CCCEEEECCT-TTHHHHHHHHHHHS---CCCC
T ss_pred             CCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHhCC-CCeEEEEeCH-HHHHHHHHHHHHHh---CCCE
Confidence            699999999998775  458999999999999998877766655443 3479999999 99999999886544   5566


Q ss_pred             EEEECCcchHHHHH--HHhcCCcEEEeChHHHHHHHhc-CCCCCCCccEEEecchhhhhccccH--HHHHHHHhhCCCCc
Q 022724          133 HACVGGKSVGEDIR--KLEHGVHVVSGTPGRVCDMIKR-KTLRTRAIKLLVLDESDEMLSRGFK--DQIYDVYRYLPPDL  207 (293)
Q Consensus       133 ~~~~~~~~~~~~~~--~~~~~~~ilV~Tp~~l~~~l~~-~~~~~~~l~~iViDE~h~~~~~~~~--~~~~~i~~~l~~~~  207 (293)
                      ..+.++........  ......+|+|+|++.+...... ..+...++++|||||+|++...+..  .....+........
T Consensus       228 ~v~~~~~~~~~~~~~~~~~~~~dIvI~T~~~L~~~~~~~~~l~~~~~dlVIvDEAH~~kn~~~~~s~~~~~l~~L~~~~~  307 (968)
T 3dmq_A          228 ALFDDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLVWSEDAPSREYQAIEQLAEHVP  307 (968)
T ss_dssp             EECCHHHHHHHHHTTCSSSTTCSEEEECHHHHHTSTTTTHHHHTSCCCEEEECCSSCCCCBTTBCCHHHHHHHHHHTTCS
T ss_pred             EEEccchhhhhhhhcccccccCCEEEEcHHHHhhCHHHHHHhhhcCCCEEEehhhHhhcCCCCcchHHHHHHHHHhhcCC
Confidence            55554432221111  1112468999999877542111 1133457899999999999644321  11222222222456


Q ss_pred             cEEEEEeecC
Q 022724          208 QVVLISATLP  217 (293)
Q Consensus       208 q~v~~SAt~~  217 (293)
                      +++++|||+.
T Consensus       308 ~~L~LTATPi  317 (968)
T 3dmq_A          308 GVLLLTATPE  317 (968)
T ss_dssp             SEEESCSSCS
T ss_pred             cEEEEEcCCc
Confidence            7999999973

>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=3e-17  Score=151.95  Aligned_cols=129  Identities=18%  Similarity=0.057  Sum_probs=100.3

Q ss_pred             CCcHHHHHHHHh----hhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q 022724           55 KPSAIQQRAVMP----IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (293)
Q Consensus        55 ~~~~~Q~~~~~~----i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (293)
                      .|+|.|.+++..    +..|+++++.+|||+|||++|++|++.      .+++++|++||++|+.|+.+.+..+....++
T Consensus         3 ~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~------~~~~v~i~~pt~~l~~q~~~~~~~l~~~~~~   76 (551)
T 3crv_A            3 KLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLE------VKPKVLFVVRTHNEFYPIYRDLTKIREKRNI   76 (551)
T ss_dssp             SCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHH------HCSEEEEEESSGGGHHHHHHHHTTCCCSSCC
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHh------CCCeEEEEcCCHHHHHHHHHHHHHHhhhcCc
Confidence            599999997765    457899999999999999999999998      2568999999999999999999888777778


Q ss_pred             eEEEEECCcch---------------------------------HHHH------------------HHHhcCCcEEEeCh
Q 022724          131 QAHACVGGKSV---------------------------------GEDI------------------RKLEHGVHVVSGTP  159 (293)
Q Consensus       131 ~~~~~~~~~~~---------------------------------~~~~------------------~~~~~~~~ilV~Tp  159 (293)
                      ++..+.|..+.                                 ....                  +.....++|+|+|+
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            88776653211                                 1111                  22234679999999


Q ss_pred             HHHHHHHhcCCCCC-CCccEEEecchhhhhc
Q 022724          160 GRVCDMIKRKTLRT-RAIKLLVLDESDEMLS  189 (293)
Q Consensus       160 ~~l~~~l~~~~~~~-~~l~~iViDE~h~~~~  189 (293)
                      ..+.....+..+.+ ....++||||||.+.+
T Consensus       157 ~~l~~~~~~~~~~~~~~~~~vIiDEAHnl~d  187 (551)
T 3crv_A          157 PYFFIDRYREFIDIDLREYMIVIDEAHNLDK  187 (551)
T ss_dssp             HHHHCHHHHTTSCCCSTTEEEEETTGGGGGG
T ss_pred             hHhcCHHHHHhcCCCcCCeEEEEecccchHH
Confidence            99988543333323 4678899999999976

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=99.68  E-value=1.3e-15  Score=146.79  Aligned_cols=154  Identities=14%  Similarity=0.169  Sum_probs=110.0

Q ss_pred             CCcHHHHHHHHhhh----cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q 022724           55 KPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~----~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (293)
                      .++|+|.+++..+.    .+++.++..+||.|||+.++..+...+........+||+|| ..++.|+.+.+.++..  ++
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            58899999998655    78899999999999998876666554433333456899999 7889999999998864  46


Q ss_pred             eEEEEECCcchHHHHHHH------------hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHH
Q 022724          131 QAHACVGGKSVGEDIRKL------------EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYD  198 (293)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~------------~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~  198 (293)
                      ++..++|+..........            ....+|+|+|++.+......  +...++++||+||+|++-..  ......
T Consensus       313 ~v~~~~g~~~~r~~~~~~~~~~~~~~~~~~~~~~dvvitTy~~l~~~~~~--l~~~~w~~vIvDEaH~lkn~--~s~~~~  388 (800)
T 3mwy_W          313 NCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRAE--LGSIKWQFMAVDEAHRLKNA--ESSLYE  388 (800)
T ss_dssp             CEEECCCSSHHHHHHHHHHSCSCC-----CCCCCSEEEECTTHHHHTHHH--HHTSEEEEEEETTGGGGCCS--SSHHHH
T ss_pred             eEEEEeCCHHHHHHHHHHHhhccccccccccccCCEEEecHHHHHhhHHH--HhcCCcceeehhhhhhhcCc--hhHHHH
Confidence            677777766544443322            13468999999998764322  12235789999999998432  233444


Q ss_pred             HHhhCCCCccEEEEEeec
Q 022724          199 VYRYLPPDLQVVLISATL  216 (293)
Q Consensus       199 i~~~l~~~~q~v~~SAt~  216 (293)
                      .+..+. ....+++|||+
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            455553 55678899997

>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=99.67  E-value=6.1e-15  Score=136.34  Aligned_cols=130  Identities=16%  Similarity=0.193  Sum_probs=101.1

Q ss_pred             CCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q 022724           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (293)
Q Consensus        51 ~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (293)
                      +|.. |++.|....-.+.+|+  +....||.|||+++.+|++-....   |..+.|++|+..||.|-.+.+..+...+|+
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            4654 9999999988888888  899999999999999998754433   456899999999999999999999999999


Q ss_pred             eEEEEECC--------------------------------------------------cchHHHHHHHhcCCcEEEeChH
Q 022724          131 QAHACVGG--------------------------------------------------KSVGEDIRKLEHGVHVVSGTPG  160 (293)
Q Consensus       131 ~~~~~~~~--------------------------------------------------~~~~~~~~~~~~~~~ilV~Tp~  160 (293)
                      ++.+..+.                                                  .+..+.....  .|||.-+|..
T Consensus       146 svg~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~err~aY--~~DItYgTn~  223 (822)
T 3jux_A          146 RVGVINSLGKSYEVVWKNPDLARKAIEENWSVWPDGFNGEVLKEESMNKEAVEAFQVELKEITRKEAY--LCDVTYGTNN  223 (822)
T ss_dssp             CEEEEETTTEEEEEEESSHHHHHHHHHTTCCSSCTTCCSSSCCGGGSCHHHHTTTCEECCBCCHHHHH--HSSEEEEEHH
T ss_pred             EEEEEcCCCcccccccccchhhhhhhcccccccccccccccccccccccccchhccccCCHHHHHHHh--cCCCEEccCc
Confidence            99988872                                                  1111111222  3699999988


Q ss_pred             HHH-HHHhcC------CCCCCCccEEEecchhhhh
Q 022724          161 RVC-DMIKRK------TLRTRAIKLLVLDESDEML  188 (293)
Q Consensus       161 ~l~-~~l~~~------~~~~~~l~~iViDE~h~~~  188 (293)
                      .+- ++|+.+      ....+.+.+.||||+|.++
T Consensus       224 EfgFDYLRDnm~~~~~~~vqR~~~~aIVDEvDSiL  258 (822)
T 3jux_A          224 EFGFDYLRDNLVLDYNDKVQRGHFYAIVDEADSVL  258 (822)
T ss_dssp             HHHHHHHHHTSCSSTTSCCCCCCCEEEEETHHHHH
T ss_pred             chhhHhHHhhccCCHHHhccCCCCeEEEeccccee
Confidence            774 465543      2234678999999999975

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.61  E-value=7.5e-16  Score=142.12  Aligned_cols=127  Identities=17%  Similarity=0.199  Sum_probs=85.8

Q ss_pred             CCCCCCcHHHHHHHHh----hhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhc
Q 022724           51 YGFEKPSAIQQRAVMP----IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGD  126 (293)
Q Consensus        51 ~~~~~~~~~Q~~~~~~----i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~  126 (293)
                      .|| .|+|+|.+++..    +..|+++++.+|||+|||++|++|++..      +.+++|++||++|+.|+.+.+..+  
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            467 699999998654    4578999999999999999999998764      468999999999999999887764  


Q ss_pred             cCCceEEEEECCcc--------hH------------------------HH---------------HHHHhcCCcEEEeCh
Q 022724          127 FINIQAHACVGGKS--------VG------------------------ED---------------IRKLEHGVHVVSGTP  159 (293)
Q Consensus       127 ~~~~~~~~~~~~~~--------~~------------------------~~---------------~~~~~~~~~ilV~Tp  159 (293)
                        ++++..+.|...        ..                        +.               .+.....++|+|+|+
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              333333222110        00                        00               011123569999999


Q ss_pred             HHHHHHHhcCCC-------CCCCccEEEecchhhhh
Q 022724          160 GRVCDMIKRKTL-------RTRAIKLLVLDESDEML  188 (293)
Q Consensus       160 ~~l~~~l~~~~~-------~~~~l~~iViDE~h~~~  188 (293)
                      ..+..-...+.+       .+....++||||||.+.
T Consensus       153 ~~l~~~~~~~~~~~~~~~~~~~~~~~vIiDEAHnl~  188 (540)
T 2vl7_A          153 PYLFQKPIRNSVFCNKDDCLKLEDYLIVIDEAHNLL  188 (540)
T ss_dssp             HHHHSHHHHHHHSCSSTTSCCGGGEEEEETTGGGGG
T ss_pred             HHhcCHHHHHhhCcccccccCcCCCEEEEEccccHH
Confidence            999873322211       24567899999999994

>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=99.54  E-value=1.2e-13  Score=129.90  Aligned_cols=155  Identities=16%  Similarity=0.115  Sum_probs=107.3

Q ss_pred             CCcHHHHHHHHhhh---------cCCcEEEEcCCCChhHHHHHHHHHhhhccCC----CceeEEEEcCCHHHHHHHHHHH
Q 022724           55 KPSAIQQRAVMPII---------KGRDVIAQAQSGTGKTSMIALTVCQTVDTSS----REVQALILSPTRELATQTEKVI  121 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~---------~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~----~~~~~lil~P~~~l~~q~~~~~  121 (293)
                      .++|+|.+++..+.         .+++.++..+||+|||+.++..+...+...+    ...++||+||+ .|+.|+.+.+
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            58999999998864         4567999999999999887766655544332    23469999996 8999999999


Q ss_pred             HHhhccCCceEEEEECCcchHH--HHHHHh------cCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccH
Q 022724          122 LAIGDFINIQAHACVGGKSVGE--DIRKLE------HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFK  193 (293)
Q Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~--~~~~~~------~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~  193 (293)
                      .++... .+.+..++++.....  ......      ...+|+|+|++.+....  ..+....+++||+||+|++-... .
T Consensus       134 ~~~~~~-~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~vvi~ty~~l~~~~--~~l~~~~~~~vI~DEaH~ikn~~-~  209 (644)
T 1z3i_X          134 GKWLGG-RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHA--EVLHKGKVGLVICDEGHRLKNSD-N  209 (644)
T ss_dssp             HHHHGG-GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHT--TTTTTSCCCEEEETTGGGCCTTC-H
T ss_pred             HHHcCC-CeeEEEEeCCCHHHHHHHHHHHHHhcCCCCCCcEEEeeHHHHHhhH--HHhhcCCccEEEEECceecCChh-h
Confidence            988754 455666666643321  112211      13689999999887543  23444678999999999984332 2


Q ss_pred             HHHHHHHhhCCCCccEEEEEeec
Q 022724          194 DQIYDVYRYLPPDLQVVLISATL  216 (293)
Q Consensus       194 ~~~~~i~~~l~~~~q~v~~SAt~  216 (293)
                      . ....+..+. ....+++|||+
T Consensus       210 ~-~~~al~~l~-~~~rl~LTgTP  230 (644)
T 1z3i_X          210 Q-TYLALNSMN-AQRRVLISGTP  230 (644)
T ss_dssp             H-HHHHHHHHC-CSEEEEECSSC
T ss_pred             H-HHHHHHhcc-cCcEEEEecCc
Confidence            2 222333343 56789999997

>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=99.15  E-value=1.2e-10  Score=108.60  Aligned_cols=146  Identities=16%  Similarity=0.215  Sum_probs=92.5

Q ss_pred             cHHHHHHHHhhhcCCcEEEEcCCCChhH--HHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q 022724           57 SAIQQRAVMPIIKGRDVIAQAQSGTGKT--SMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (293)
Q Consensus        57 ~~~Q~~~~~~i~~~~~~li~~~Tg~GKT--~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (293)
                      +++|+.+++.++.++.+++.|++|+|||  .+++++.+..+... .+.++++++||..++.++.+.+.......++....
T Consensus       151 ~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~~-~~~~vll~APTg~AA~~L~e~~~~~~~~l~l~~~~  229 (608)
T 1w36_D          151 INWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMADG-ERCRIRLAAPTGKAAARLTESLGKALRQLPLTDEQ  229 (608)
T ss_dssp             CCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCSS-CCCCEEEEBSSHHHHHHHHHHHTHHHHHSSCCSCC
T ss_pred             CHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhhc-CCCeEEEEeCChhHHHHHHHHHHHHHhcCCCCHHH
Confidence            7899999999999999999999999999  66777777665322 35689999999999999998887655444332110


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEe
Q 022724          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (293)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SA  214 (293)
                      . .+..  .....+   ..++-.+|+.. . +........+++++||||++++ +   ...+..+++.++...|+|++.=
T Consensus       230 ~-~~~~--~~~~Ti---h~ll~~~~~~~-~-~~~~~~~~l~~d~lIIDEAsml-~---~~~~~~Ll~~l~~~~~liLvGD  297 (608)
T 1w36_D          230 K-KRIP--EDASTL---HRLLGAQPGSQ-R-LRHHAGNPLHLDVLVVDEASMI-D---LPMMSRLIDALPDHARVIFLGD  297 (608)
T ss_dssp             C-CSCS--CCCBTT---TSCC-------------CTTSCCSCSEEEECSGGGC-B---HHHHHHHHHTCCTTCEEEEEEC
T ss_pred             H-hccc--hhhhhh---HhhhccCCCch-H-HHhccCCCCCCCEEEEechhhC-C---HHHHHHHHHhCCCCCEEEEEcc
Confidence            0 0000  000000   01222223211 1 1111222337899999999955 3   4567788888888899988864


Q ss_pred             e
Q 022724          215 T  215 (293)
Q Consensus       215 t  215 (293)
                      .
T Consensus       298 ~  298 (608)
T 1w36_D          298 R  298 (608)
T ss_dssp             T
T ss_pred             h
Confidence            3

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=99.13  E-value=8.1e-11  Score=109.98  Aligned_cols=82  Identities=22%  Similarity=0.225  Sum_probs=68.3

Q ss_pred             CCcHHHHHHHHh----hhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q 022724           55 KPSAIQQRAVMP----IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (293)
Q Consensus        55 ~~~~~Q~~~~~~----i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (293)
                      .|+|.|.+.+..    +.+|+++++.+|||+|||++|++|++..+...  +.+++|++||++++.|+.+.+..+....++
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            589999998864    45799999999999999999999999887653  468999999999999999999988776667


Q ss_pred             eEEEEECC
Q 022724          131 QAHACVGG  138 (293)
Q Consensus       131 ~~~~~~~~  138 (293)
                      ++..+.|.
T Consensus        81 ~~~~l~gr   88 (620)
T 4a15_A           81 RAIPMQGR   88 (620)
T ss_dssp             CEEECCCH
T ss_pred             EEEEEECC
Confidence            76665553

>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=99.05  E-value=3.6e-09  Score=99.66  Aligned_cols=68  Identities=28%  Similarity=0.386  Sum_probs=52.6

Q ss_pred             CCCCCcHHHHHHHHhhhc----CC-cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhc
Q 022724           52 GFEKPSAIQQRAVMPIIK----GR-DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGD  126 (293)
Q Consensus        52 ~~~~~~~~Q~~~~~~i~~----~~-~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~  126 (293)
                      +| .|+..|..++..+.+    |. ..++.|.||||||+.+.-.+ ...     +..+|||+|+..+|.|+++.++.+..
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            55 799999999887653    43 46788999999997665332 332     12489999999999999999999864

>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=98.80  E-value=1.1e-07  Score=89.43  Aligned_cols=67  Identities=21%  Similarity=0.298  Sum_probs=50.8

Q ss_pred             CCcHHHHHHHHhhh----cCC-cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcc
Q 022724           55 KPSAIQQRAVMPII----KGR-DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDF  127 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~----~~~-~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (293)
                      .|+..|..++..+.    +|. ...+.|.||+|||+...- ++....     ..+|||+|+..+|.|+++.++.+...
T Consensus        12 ~p~~~Q~~~i~~l~~~~~~~~~~~~l~g~~gs~k~~~~a~-~~~~~~-----~~~lvv~~~~~~A~~l~~el~~~~~~   83 (661)
T 2d7d_A           12 QPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTVSN-LIKEVN-----KPTLVIAHNKTLAGQLYSEFKEFFPN   83 (661)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHH-HHHHHC-----CCEEEECSSHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEECcCCcHHHHHHHH-HHHHhC-----CCEEEEECCHHHHHHHHHHHHHHcCC
Confidence            59999998888655    343 467889999999976543 223321     24899999999999999999998643

>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=98.54  E-value=1.3e-06  Score=81.71  Aligned_cols=69  Identities=20%  Similarity=0.187  Sum_probs=54.3

Q ss_pred             CCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 022724           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (293)
Q Consensus        54 ~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (293)
                      ..+++.|.+++..++.+...+|.||+|+|||....- ++..+... .+.++++++||...++++.+.+.+.
T Consensus       179 ~~ln~~Q~~av~~~l~~~~~li~GppGTGKT~~~~~-~i~~l~~~-~~~~ilv~a~tn~A~~~l~~~l~~~  247 (624)
T 2gk6_A          179 PDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSAT-IVYHLARQ-GNGPVLVCAPSNIAVDQLTEKIHQT  247 (624)
T ss_dssp             CCCCHHHHHHHHHHHTCSEEEEECCTTSCHHHHHHH-HHHHHHTS-SSCCEEEEESSHHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHhcCCCeEEECCCCCCHHHHHHH-HHHHHHHc-CCCeEEEEeCcHHHHHHHHHHHHhc
Confidence            357899999999988888899999999999976443 33333332 3458999999999999999887653

>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=98.54  E-value=7.4e-07  Score=82.44  Aligned_cols=125  Identities=21%  Similarity=0.261  Sum_probs=80.3

Q ss_pred             CCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q 022724           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (293)
                      .+++.|++++..+..++.+++.||.|+|||... ..++..+...  +.++++++||...+..+.+.+.       .....
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 GLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTT-KAVADLAESL--GLEVGLCAPTGKAARRLGEVTG-------RTAST  258 (574)
T ss_dssp             TCCHHHHHHHHHHTTCSEEEEECCTTSCHHHHH-HHHHHHHHHT--TCCEEEEESSHHHHHHHHHHHT-------SCEEE
T ss_pred             CCCHHHHHHHHHHHhCCEEEEEcCCCCCHHHHH-HHHHHHHHhc--CCeEEEecCcHHHHHHhHhhhc-------ccHHH
Confidence            478999999999999999999999999999653 2333444332  4579999999998888776431       11111


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      ++      .   .+.    .   .|+    ............++|||||++++.    ...+..+++.++...+++++.
T Consensus       259 ih------~---ll~----~---~~~----~~~~~~~~~~~~dvlIIDEasml~----~~~~~~Ll~~~~~~~~lilvG  313 (574)
T 3e1s_A          259 VH------R---LLG----Y---GPQ----GFRHNHLEPAPYDLLIVDEVSMMG----DALMLSLLAAVPPGARVLLVG  313 (574)
T ss_dssp             HH------H---HTT----E---ETT----EESCSSSSCCSCSEEEECCGGGCC----HHHHHHHHTTSCTTCEEEEEE
T ss_pred             HH------H---HHc----C---Ccc----hhhhhhcccccCCEEEEcCccCCC----HHHHHHHHHhCcCCCEEEEEe
Confidence            00      0   000    0   000    011112233467899999999873    335666777777777777764

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=98.50  E-value=1.7e-06  Score=83.01  Aligned_cols=69  Identities=19%  Similarity=0.224  Sum_probs=54.0

Q ss_pred             CCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 022724           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (293)
Q Consensus        54 ~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (293)
                      ..+++.|.+|+..++.+..++|.||.|+|||....-.+ ..+... .+.++++++||...++++.+++.+.
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 AQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSATIV-YHLSKI-HKDRILVCAPSNVAVDHLAAKLRDL  427 (802)
T ss_dssp             CCCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHHHHHH-HHHHHH-HCCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             ccCCHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHH-HHHHhC-CCCeEEEEcCcHHHHHHHHHHHHhh
Confidence            35689999999999888889999999999996644333 332221 2458999999999999999988764

>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=98.49  E-value=1.1e-06  Score=79.43  Aligned_cols=134  Identities=15%  Similarity=0.206  Sum_probs=80.6

Q ss_pred             HCCCCCCcHHHHHHHHhhhc----C-CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 022724           50 QYGFEKPSAIQQRAVMPIIK----G-RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (293)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~i~~----~-~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (293)
                      -+.|..+++-|++++..+..    + ..++|.|+.|+|||... ..++..+..... .++++++||...+..+.+.+   
T Consensus        20 p~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll-~~~~~~l~~~~~-~~il~~a~T~~Aa~~l~~~~---   94 (459)
T 3upu_A           20 HMTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLT-KFIIEALISTGE-TGIILAAPTHAAKKILSKLS---   94 (459)
T ss_dssp             -CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHH-HHHHHHHHHTTC-CCEEEEESSHHHHHHHHHHH---
T ss_pred             CCccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHH-HHHHHHHHhcCC-ceEEEecCcHHHHHHHHhhh---
Confidence            35788999999999997653    2 38999999999999543 344444444322 36899999999888877654   


Q ss_pred             hccCCceEEEEECCcchHHHHHHHh----cCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHH
Q 022724          125 GDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVY  200 (293)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~  200 (293)
                          +..+..++      ... .+.    .....+..          .....+...+++||||++++.    ...+..+.
T Consensus        95 ----~~~~~T~h------~~~-~~~~~~~~~~~~~~~----------~~~~~~~~~~~iiiDE~~~~~----~~~~~~l~  149 (459)
T 3upu_A           95 ----GKEASTIH------SIL-KINPVTYEENVLFEQ----------KEVPDLAKCRVLICDEVSMYD----RKLFKILL  149 (459)
T ss_dssp             ----SSCEEEHH------HHH-TEEEEECSSCEEEEE----------CSCCCCSSCSEEEESCGGGCC----HHHHHHHH
T ss_pred             ----ccchhhHH------HHh-ccCcccccccchhcc----------cccccccCCCEEEEECchhCC----HHHHHHHH
Confidence                11111111      000 000    00000000          122345678999999999763    23455566


Q ss_pred             hhCCCCccEEEEE
Q 022724          201 RYLPPDLQVVLIS  213 (293)
Q Consensus       201 ~~l~~~~q~v~~S  213 (293)
                      ..++...+++++.
T Consensus       150 ~~~~~~~~~~~vG  162 (459)
T 3upu_A          150 STIPPWCTIIGIG  162 (459)
T ss_dssp             HHSCTTCEEEEEE
T ss_pred             HhccCCCEEEEEC
Confidence            6666556666554

>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=3.7e-06  Score=80.59  Aligned_cols=68  Identities=22%  Similarity=0.211  Sum_probs=53.9

Q ss_pred             CCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 022724           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (293)
                      .+++.|.+|+..++.+...+|.||.|+|||.... .++..+... .+.++++++||...+.++.+.+...
T Consensus       356 ~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~ti~-~~i~~l~~~-~~~~ilv~a~tn~A~~~l~~~l~~~  423 (800)
T 2wjy_A          356 DLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSA-TIVYHLARQ-GNGPVLVCAPSNIAVDQLTEKIHQT  423 (800)
T ss_dssp             CCCHHHHHHHHHHHTSSEEEEECCTTSCHHHHHH-HHHHHHHTT-CSSCEEEEESSHHHHHHHHHHHHTT
T ss_pred             CCCHHHHHHHHHhccCCeEEEEcCCCCCHHHHHH-HHHHHHHHc-CCCcEEEEcCcHHHHHHHHHHHHHh
Confidence            4689999999999888889999999999996643 333444332 3458999999999999999887653

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=98.37  E-value=9.3e-07  Score=83.21  Aligned_cols=67  Identities=19%  Similarity=0.232  Sum_probs=53.1

Q ss_pred             CCcHHHHHHHHhhhcCC-cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 022724           55 KPSAIQQRAVMPIIKGR-DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~-~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (293)
                      .+++.|.+|+...+..+ -.+|.||.|+|||....-.+.+.+..   +.++++++||..-++++.+++...
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            47899999999987655 57899999999997655444444433   458999999999999999888654

>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=97.75  E-value=0.00085  Score=58.66  Aligned_cols=71  Identities=13%  Similarity=0.123  Sum_probs=56.4

Q ss_pred             CCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhc
Q 022724           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGD  126 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~  126 (293)
                      .++|+|...+..+...+-+++..+-+.|||......++..+... .+.++++++|+.+.+..+.+.++.+..
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            68999999998876567789999999999987766665544333 345899999999999988888877653

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=97.70  E-value=4.7e-05  Score=60.09  Aligned_cols=67  Identities=13%  Similarity=0.070  Sum_probs=41.3

Q ss_pred             HHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          224 TTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       224 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      .+.++.+|..+.+...+....++.|.+..++... |...+.+++.... +++||||++++.++.++..|
T Consensus         8 ~~~~~~~p~~i~v~~~~~~~~~i~q~~~~~~~~~-K~~~L~~~l~~~~-~~~lVF~~~~~~~~~l~~~L   74 (191)
T 2p6n_A            8 SSGVDLGTENLYFQSMGAASLDVIQEVEYVKEEA-KMVYLLECLQKTP-PPVLIFAEKKADVDAIHEYL   74 (191)
T ss_dssp             --------------------CCSEEEEEECCGGG-HHHHHHHHHTTSC-SCEEEECSCHHHHHHHHHHH
T ss_pred             cccccCCCEEEEECCCCCCCcCceEEEEEcChHH-HHHHHHHHHHhCC-CCEEEEECCHHHHHHHHHHH
Confidence            3457788988888877777889999999988776 9999999997754 58999999999999998865

>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=97.60  E-value=0.00075  Score=62.69  Aligned_cols=143  Identities=12%  Similarity=0.183  Sum_probs=87.3

Q ss_pred             CCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCC--ceE
Q 022724           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN--IQA  132 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~--~~~  132 (293)
                      .++|+|..++..+...+..++..+-|.|||.+....++..+...+ +.+++++.|+.+.+..+.+.++.+.....  +..
T Consensus       163 ~l~p~Q~~i~~~l~~~r~~~i~~~Rq~GKS~~~a~~~l~~~~~~~-~~~i~~va~t~~qA~~~~~~i~~~i~~~p~~~~~  241 (592)
T 3cpe_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFNK-DKAVGILAHKGSMSAEVLDRTKQAIELLPDFLQP  241 (592)
T ss_dssp             CCCHHHHHHHHHHHHCSEEEEEECSSSCHHHHHHHHHHHHHHTSS-SCEEEEEESSHHHHHHHHHHHHHHHTTSCTTTSC
T ss_pred             cCCHHHHHHHHhhccccEEEEEEcCccChHHHHHHHHHHHHHhCC-CCeEEEEECCHHHHHHHHHHHHHHHHhChHhhcc
Confidence            479999999988766678999999999999876655555544433 45899999999999999988887654432  111


Q ss_pred             EEE-ECCcchHHHHHHHhcCCcEEEe--ChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCC--CCc
Q 022724          133 HAC-VGGKSVGEDIRKLEHGVHVVSG--TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP--PDL  207 (293)
Q Consensus       133 ~~~-~~~~~~~~~~~~~~~~~~ilV~--Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~--~~~  207 (293)
                      ... .+...    + .+.++..|.+.  .|+.+..    .     +.+++|+||+|.+-+.  ...+..+...+.  ...
T Consensus       242 ~~~~~~~~~----i-~~~nGs~i~~~s~~~~~lrG----~-----~~~~~iiDE~~~~~~~--~~l~~~~~~~l~~~~~~  305 (592)
T 3cpe_A          242 GIVEWNKGS----I-ELDNGSSIGAYASSPDAVRG----N-----SFAMIYIEDCAFIPNF--HDSWLAIQPVISSGRRS  305 (592)
T ss_dssp             CEEEECSSE----E-EETTSCEEEEEECCHHHHHH----S-----CCSEEEEETGGGCTTH--HHHHHHHHHHHSSSSCC
T ss_pred             ccccCCccE----E-EecCCCEEEEEeCCCCCccC----C-----CcceEEEehhccCCch--hHHHHHHHHHhccCCCc
Confidence            000 01110    0 11234444433  2443322    1     3578999999987432  233344443343  235


Q ss_pred             cEEEEEe
Q 022724          208 QVVLISA  214 (293)
Q Consensus       208 q~v~~SA  214 (293)
                      +++++|.
T Consensus       306 ~ii~isT  312 (592)
T 3cpe_A          306 KIIITTT  312 (592)
T ss_dssp             EEEEEEC
T ss_pred             eEEEEeC
Confidence            5555543

>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=97.50  E-value=0.00041  Score=53.87  Aligned_cols=31  Identities=29%  Similarity=0.493  Sum_probs=22.1

Q ss_pred             cHHHHHHHHhhh---------cCCcEEEEcCCCChhHHHH
Q 022724           57 SAIQQRAVMPII---------KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        57 ~~~Q~~~~~~i~---------~~~~~li~~~Tg~GKT~~~   87 (293)
                      .+.|.+++..+.         .|+.+++.||+|+|||...
T Consensus        16 ~~~~~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~   55 (180)
T 3ec2_A           16 NVSQNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLA   55 (180)
T ss_dssp             SHHHHHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHH
Confidence            445665555432         4788999999999999543

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=97.50  E-value=0.00042  Score=61.45  Aligned_cols=85  Identities=24%  Similarity=0.185  Sum_probs=52.8

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhc
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH  150 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  150 (293)
                      +-.++.|+.|+|||....    +.+..    .+.+|++|+++++.++.+.+.+....                      .
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            357899999999996532    22221    25699999999999988866432100                      0


Q ss_pred             CCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhh
Q 022724          151 GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (293)
Q Consensus       151 ~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~  187 (293)
                      ....-|.|-++++.  +.........+.+||||+-++
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            01233566665542  222222234799999999865

>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=97.45  E-value=0.00029  Score=66.14  Aligned_cols=70  Identities=16%  Similarity=0.212  Sum_probs=55.0

Q ss_pred             CCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCC-CceeEEEEcCCHHHHHHHHHHHHHhh
Q 022724           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-REVQALILSPTRELATQTEKVILAIG  125 (293)
Q Consensus        54 ~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~-~~~~~lil~P~~~l~~q~~~~~~~~~  125 (293)
                      ..+++-|.+++..  .+..++|.|+.|||||....--+.+.+.... ...+++++++|+..+.++.+++..+.
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            4689999999983  3678999999999999776555555554322 23489999999999999999998764

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=97.44  E-value=0.00066  Score=53.09  Aligned_cols=40  Identities=15%  Similarity=0.223  Sum_probs=26.6

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCH
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~  111 (293)
                      +|+-.++.||.|+|||...+-.+ ......  +.+++++.|..
T Consensus         2 ~g~i~vi~G~~gsGKTT~ll~~~-~~~~~~--g~~v~~~~~~~   41 (184)
T 2orw_A            2 SGKLTVITGPMYSGKTTELLSFV-EIYKLG--KKKVAVFKPKI   41 (184)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHH-HHHHHT--TCEEEEEEEC-
T ss_pred             ccEEEEEECCCCCCHHHHHHHHH-HHHHHC--CCeEEEEeecc
Confidence            46678899999999997654333 333222  34788888874

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=97.33  E-value=0.00029  Score=53.94  Aligned_cols=51  Identities=33%  Similarity=0.454  Sum_probs=44.2

Q ss_pred             ccCCCceEEEEEecCcccHHHHHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          241 LTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       241 ~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ..+.++.|.+..++... |...+..+++...++++||||++++.++.++..|
T Consensus         5 ~~~~~i~~~~~~~~~~~-K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L   55 (163)
T 2hjv_A            5 LTTRNIEHAVIQVREEN-KFSLLKDVLMTENPDSCIIFCRTKEHVNQLTDEL   55 (163)
T ss_dssp             -CCCCEEEEEEECCGGG-HHHHHHHHHHHHCCSSEEEECSSHHHHHHHHHHH
T ss_pred             cCcccceEEEEECChHH-HHHHHHHHHHhcCCCcEEEEECCHHHHHHHHHHH
Confidence            45567999999988766 9999999998888889999999999999998865

>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=97.25  E-value=0.0005  Score=64.94  Aligned_cols=70  Identities=17%  Similarity=0.158  Sum_probs=54.4

Q ss_pred             CCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhcc-CCCceeEEEEcCCHHHHHHHHHHHHHhhc
Q 022724           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT-SSREVQALILSPTRELATQTEKVILAIGD  126 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~-~~~~~~~lil~P~~~l~~q~~~~~~~~~~  126 (293)
                      .+++-|++++...  +.+++|.|+.|||||....--+.+.+.. .-...++++++.|+..+.++.+++.....
T Consensus         2 ~L~~~Q~~av~~~--~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~~~~~~IL~lTfT~~Aa~em~~Rl~~~l~   72 (673)
T 1uaa_A            2 RLNPGQQQAVEFV--TGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLG   72 (673)
T ss_dssp             CCCHHHHHHHHCC--SSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHSC
T ss_pred             CCCHHHHHHHhCC--CCCEEEEeCCCCChHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHcC
Confidence            4789999999863  6789999999999997765545444433 22335899999999999999999987643

>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=97.24  E-value=0.00088  Score=54.03  Aligned_cols=91  Identities=15%  Similarity=0.179  Sum_probs=52.2

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  148 (293)
                      .|.-+++.|++|+|||...+-.+ .++...  +.+++++.|...-  . .  ...+....|+..                
T Consensus        11 ~G~i~litG~mGsGKTT~ll~~~-~r~~~~--g~kVli~~~~~d~--r-~--~~~i~srlG~~~----------------   66 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAELIRRL-HRLEYA--DVKYLVFKPKIDT--R-S--IRNIQSRTGTSL----------------   66 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHHHHHH-HHHHHT--TCCEEEEEECCCG--G-G--CSSCCCCCCCSS----------------
T ss_pred             CcEEEEEECCCCCcHHHHHHHHH-HHHHhc--CCEEEEEEeccCc--h-H--HHHHHHhcCCCc----------------
Confidence            45678889999999997654433 333332  4578888775531  0 0  001122222111                


Q ss_pred             hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhh
Q 022724          149 EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (293)
Q Consensus       149 ~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~  187 (293)
                         ..+-+.+.+.+...+.... .-.+.++|||||++.+
T Consensus        67 ---~~~~~~~~~~i~~~i~~~~-~~~~~dvViIDEaQ~l  101 (223)
T 2b8t_A           67 ---PSVEVESAPEILNYIMSNS-FNDETKVIGIDEVQFF  101 (223)
T ss_dssp             ---CCEEESSTHHHHHHHHSTT-SCTTCCEEEECSGGGS
T ss_pred             ---cccccCCHHHHHHHHHHHh-hCCCCCEEEEecCccC
Confidence               1234566666766665432 2345799999999975

>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=97.20  E-value=0.0011  Score=52.03  Aligned_cols=40  Identities=10%  Similarity=0.148  Sum_probs=27.4

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCH
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~  111 (293)
                      +|+-.++.||+|+|||...+-. ..+....  +.+++++.|..
T Consensus         7 ~g~i~v~~G~mgsGKTT~ll~~-a~r~~~~--g~kV~v~k~~~   46 (191)
T 1xx6_A            7 HGWVEVIVGPMYSGKSEELIRR-IRRAKIA--KQKIQVFKPEI   46 (191)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHH-HHHHHHT--TCCEEEEEEC-
T ss_pred             CCEEEEEECCCCCcHHHHHHHH-HHHHHHC--CCEEEEEEecc
Confidence            4567889999999999765543 3443332  45789998874

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=97.20  E-value=0.00022  Score=53.79  Aligned_cols=18  Identities=22%  Similarity=0.510  Sum_probs=16.0

Q ss_pred             cCCcEEEEcCCCChhHHH
Q 022724           69 KGRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~   86 (293)
                      .|+.+++.||+|+|||..
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            688999999999999943

>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=97.11  E-value=0.0008  Score=52.63  Aligned_cols=52  Identities=29%  Similarity=0.224  Sum_probs=43.7

Q ss_pred             cccCCCceEEEEEecCcccHHHHHHHHHhhC-CCCcEEEEcccchhHHHHHhhC
Q 022724          240 ELTLEGIKQFFVAVEREEWKFDTLCDLYDTL-TITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       240 ~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~-~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ...+.++.|.+..++... |...|.++++.. .++++||||++++.++.++..|
T Consensus        14 ~~~~~~i~q~~~~v~~~~-K~~~L~~ll~~~~~~~k~lVF~~~~~~~~~l~~~L   66 (185)
T 2jgn_A           14 GSTSENITQKVVWVEESD-KRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFL   66 (185)
T ss_dssp             --CCTTEEEEEEECCGGG-HHHHHHHHHHHC-CCSCEEEEESCHHHHHHHHHHH
T ss_pred             CCCCCCceEEEEEeCcHH-HHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHH
Confidence            345678999999998776 999999999876 4679999999999999998865

>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=97.08  E-value=0.0016  Score=51.88  Aligned_cols=40  Identities=18%  Similarity=0.189  Sum_probs=26.7

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHH
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~  112 (293)
                      |+-.+++|+.|+|||...+-.+......   +.+++++.|.+.
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            4556789999999997655444433333   457899998764

>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=97.08  E-value=0.0061  Score=48.21  Aligned_cols=40  Identities=15%  Similarity=0.292  Sum_probs=25.6

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEe
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SA  214 (293)
                      ..-.+|||||+|.+... ....+..++...+....+|+.|.
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 23445555666555566665543

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=97.06  E-value=0.003  Score=53.69  Aligned_cols=25  Identities=8%  Similarity=0.137  Sum_probs=18.5

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhh
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTV   95 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l   95 (293)
                      +.++++.||+|+|||...- .++..+
T Consensus        45 ~~~lli~GpPGTGKT~~v~-~v~~~L   69 (318)
T 3te6_A           45 NKLFYITNADDSTKFQLVN-DVMDEL   69 (318)
T ss_dssp             CCEEEEECCCSHHHHHHHH-HHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHH
Confidence            4689999999999996543 344444

>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=97.05  E-value=0.0013  Score=66.25  Aligned_cols=67  Identities=19%  Similarity=0.300  Sum_probs=55.4

Q ss_pred             CCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCC---CceeEEEEcCCHHHHHHHHHHHHH
Q 022724           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS---REVQALILSPTRELATQTEKVILA  123 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~~  123 (293)
                      .+|+-|.+++..-  +++++|.|+.|||||.+.+--++..+....   ...+++++++|++.+.++.+++..
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            5899999998865  889999999999999876666666665532   345899999999999999998876

>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=97.05  E-value=0.0029  Score=53.90  Aligned_cols=18  Identities=28%  Similarity=0.440  Sum_probs=15.3

Q ss_pred             CCcEEEEcCCCChhHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~   87 (293)
                      ++.+++.||+|+|||...
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            468999999999999543

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=96.97  E-value=0.0076  Score=44.86  Aligned_cols=20  Identities=20%  Similarity=0.155  Sum_probs=16.9

Q ss_pred             hcCCcEEEEcCCCChhHHHH
Q 022724           68 IKGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        68 ~~~~~~li~~~Tg~GKT~~~   87 (293)
                      ..+.++++.||+|+|||..+
T Consensus        22 ~~~~~vll~G~~GtGKt~lA   41 (145)
T 3n70_A           22 ETDIAVWLYGAPGTGRMTGA   41 (145)
T ss_dssp             TCCSCEEEESSTTSSHHHHH
T ss_pred             CCCCCEEEECCCCCCHHHHH
Confidence            35679999999999999654

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=96.96  E-value=0.0063  Score=52.17  Aligned_cols=33  Identities=21%  Similarity=0.313  Sum_probs=24.9

Q ss_pred             CcHHHHHHHHhhh----cCC---cEEEEcCCCChhHHHHH
Q 022724           56 PSAIQQRAVMPII----KGR---DVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        56 ~~~~Q~~~~~~i~----~~~---~~li~~~Tg~GKT~~~~   88 (293)
                      .+|||.+++..+.    +|+   .+++.||.|+|||....
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            4688888877654    443   38999999999996544

>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=96.95  E-value=0.0023  Score=60.92  Aligned_cols=70  Identities=17%  Similarity=0.194  Sum_probs=54.8

Q ss_pred             CCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCC-CceeEEEEcCCHHHHHHHHHHHHHhh
Q 022724           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-REVQALILSPTRELATQTEKVILAIG  125 (293)
Q Consensus        54 ~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~-~~~~~lil~P~~~l~~q~~~~~~~~~  125 (293)
                      ..+++-|++++..  .+.+++|.|+.|||||.+..--+.+.+.... ...++++++.|+..+.++.+++..+.
T Consensus        10 ~~Ln~~Q~~av~~--~~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~~~p~~IL~vTFTnkAA~Em~~Rl~~~l   80 (724)
T 1pjr_A           10 AHLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLL   80 (724)
T ss_dssp             TTSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             hhCCHHHHHHHhC--CCCCEEEEEcCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHh
Confidence            4689999999886  3578999999999999776555555554322 33579999999999999999988764

>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=96.92  E-value=0.0053  Score=49.44  Aligned_cols=41  Identities=12%  Similarity=0.191  Sum_probs=28.5

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHH
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~  112 (293)
                      .|+-.++.|+.|+|||...+-.+......   +.+++++-|.+.
T Consensus        18 ~g~l~v~~G~MgsGKTT~lL~~~~r~~~~---g~kvli~kp~~D   58 (234)
T 2orv_A           18 RGQIQVILGPMFSGKSTELMRRVRRFQIA---QYKCLVIKYAKD   58 (234)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHHTT---TCCEEEEEETTC
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHHHHHHC---CCeEEEEeecCC
Confidence            46778889999999997655444443322   457888888653

>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=96.89  E-value=0.0045  Score=55.24  Aligned_cols=18  Identities=22%  Similarity=0.324  Sum_probs=15.2

Q ss_pred             CCcEEEEcCCCChhHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~   87 (293)
                      .+++++.||+|+|||...
T Consensus       130 ~~~lll~Gp~G~GKTtLa  147 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLL  147 (440)
T ss_dssp             SCCEEEECSSSSSHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            368999999999999543

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=96.85  E-value=0.0039  Score=54.11  Aligned_cols=19  Identities=32%  Similarity=0.480  Sum_probs=15.7

Q ss_pred             cCCcEEEEcCCCChhHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~   87 (293)
                      .+.++++.||+|+|||...
T Consensus        43 ~~~~vll~G~~G~GKT~l~   61 (387)
T 2v1u_A           43 KPSNALLYGLTGTGKTAVA   61 (387)
T ss_dssp             CCCCEEECBCTTSSHHHHH
T ss_pred             CCCcEEEECCCCCCHHHHH
Confidence            3468999999999999543

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=96.81  E-value=0.0025  Score=47.45  Aligned_cols=19  Identities=11%  Similarity=0.200  Sum_probs=16.1

Q ss_pred             hcCCcEEEEcCCCChhHHH
Q 022724           68 IKGRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        68 ~~~~~~li~~~Tg~GKT~~   86 (293)
                      ..+.++++.||+|+|||..
T Consensus        25 ~~~~~vll~G~~GtGKt~l   43 (143)
T 3co5_A           25 KRTSPVFLTGEAGSPFETV   43 (143)
T ss_dssp             TCSSCEEEEEETTCCHHHH
T ss_pred             CCCCcEEEECCCCccHHHH
Confidence            4567999999999999943

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=96.77  E-value=0.0071  Score=56.37  Aligned_cols=113  Identities=14%  Similarity=0.219  Sum_probs=72.6

Q ss_pred             CCcHHHHHHHHhhhc--CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceE
Q 022724           55 KPSAIQQRAVMPIIK--GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQA  132 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~--~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  132 (293)
                      .+|.-|++++..+..  ....++.|+-|.|||.+.-+ ++..+..     +++|.+|+.+-+..+.+...+         
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            689999999998875  34579999999999944333 3333322     468899998877765553211         


Q ss_pred             EEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEE
Q 022724          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLI  212 (293)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~  212 (293)
                                          .+-...|+.+..       ...+.+++|||||=.+.    ...+..++..    ...++|
T Consensus       240 --------------------~i~~~~Pd~~~~-------~~~~~dlliVDEAAaIp----~pll~~ll~~----~~~v~~  284 (671)
T 2zpa_A          240 --------------------KFRFIAPDALLA-------SDEQADWLVVDEAAAIP----APLLHQLVSR----FPRTLL  284 (671)
T ss_dssp             --------------------GCCBCCHHHHHH-------SCCCCSEEEEETGGGSC----HHHHHHHHTT----SSEEEE
T ss_pred             --------------------CeEEeCchhhhh-------CcccCCEEEEEchhcCC----HHHHHHHHhh----CCeEEE
Confidence                                122235655332       13458999999997763    3445555543    336778


Q ss_pred             EeecC
Q 022724          213 SATLP  217 (293)
Q Consensus       213 SAt~~  217 (293)
                      |.|+.
T Consensus       285 ~tTv~  289 (671)
T 2zpa_A          285 TTTVQ  289 (671)
T ss_dssp             EEEBS
T ss_pred             EecCC
Confidence            88873

>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=96.76  E-value=0.0094  Score=49.36  Aligned_cols=17  Identities=24%  Similarity=0.421  Sum_probs=14.7

Q ss_pred             CcEEEEcCCCChhHHHH
Q 022724           71 RDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~   87 (293)
                      .++++.||+|+|||..+
T Consensus        65 ~~vLl~G~~GtGKT~la   81 (272)
T 1d2n_A           65 VSVLLEGPPHSGKTALA   81 (272)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             eEEEEECCCCCcHHHHH
Confidence            57999999999999654

>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=96.68  E-value=0.0027  Score=55.26  Aligned_cols=37  Identities=30%  Similarity=0.524  Sum_probs=22.1

Q ss_pred             EEEecchhhhhccccHHH-HHHHHhhCCCCccEEEEEee
Q 022724          178 LLVLDESDEMLSRGFKDQ-IYDVYRYLPPDLQVVLISAT  215 (293)
Q Consensus       178 ~iViDE~h~~~~~~~~~~-~~~i~~~l~~~~q~v~~SAt  215 (293)
                      +|||||+|.+........ +..+.... ....+|+.|..
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            999999999865432334 44555444 34455554433

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=96.64  E-value=0.0056  Score=47.98  Aligned_cols=39  Identities=13%  Similarity=0.154  Sum_probs=26.9

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCC
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~  110 (293)
                      .|+-.++.||.|+|||.-.+-.+-+....   +.+++++.|.
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            36678999999999995544444333333   3578998886

>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=0.0035  Score=50.52  Aligned_cols=19  Identities=16%  Similarity=0.237  Sum_probs=16.0

Q ss_pred             cCCcEEEEcCCCChhHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~   87 (293)
                      .++++++.||+|+|||...
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            4678999999999999543

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=96.58  E-value=0.011  Score=49.11  Aligned_cols=54  Identities=19%  Similarity=0.255  Sum_probs=33.0

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHh--hhcCCcEEEEcCCCChhHHHH
Q 022724           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMP--IIKGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        32 ~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~--i~~~~~~li~~~Tg~GKT~~~   87 (293)
                      ..+|+++.-.+...+.+.+.- ..|. ...+.+..  +..++++++.||+|+|||...
T Consensus        13 ~~~~~~i~G~~~~~~~l~~~~-~~~~-~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la   68 (285)
T 3h4m_A           13 NVRYEDIGGLEKQMQEIREVV-ELPL-KHPELFEKVGIEPPKGILLYGPPGTGKTLLA   68 (285)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHT-HHHH-HCHHHHHHHCCCCCSEEEEESSSSSSHHHHH
T ss_pred             CCCHHHhcCHHHHHHHHHHHH-HHHh-hCHHHHHhcCCCCCCeEEEECCCCCcHHHHH
Confidence            467888877777777776531 1111 11122222  235678999999999999543

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=96.57  E-value=0.0027  Score=53.56  Aligned_cols=18  Identities=28%  Similarity=0.370  Sum_probs=15.1

Q ss_pred             CCcEEEEcCCCChhHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~   87 (293)
                      +.++++.||+|+|||...
T Consensus        67 ~~~vll~G~~GtGKT~la   84 (309)
T 3syl_A           67 TLHMSFTGNPGTGKTTVA   84 (309)
T ss_dssp             CCEEEEEECTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            347999999999999654

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=96.56  E-value=0.024  Score=44.41  Aligned_cols=25  Identities=20%  Similarity=0.442  Sum_probs=18.0

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhc
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVD   96 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~   96 (293)
                      +++++.||+|+|||.... .+...+.
T Consensus        55 ~~~~l~G~~GtGKT~la~-~i~~~~~   79 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLA-AIANELA   79 (202)
T ss_dssp             CEEEEECSTTSSHHHHHH-HHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHH-HHHHHHH
Confidence            789999999999995432 3334443

>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=96.55  E-value=0.01  Score=50.20  Aligned_cols=39  Identities=15%  Similarity=0.380  Sum_probs=24.8

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      .+-.++|+||+|.+... ....+..++...+....+|+.+
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            45679999999998533 2334555555555556666554

>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=0.01  Score=50.96  Aligned_cols=43  Identities=5%  Similarity=0.345  Sum_probs=28.3

Q ss_pred             CCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEeec
Q 022724          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATL  216 (293)
Q Consensus       173 ~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~  216 (293)
                      ..+.+++|+||+|.+ +......+..++...+....+|+.|-..
T Consensus       132 ~~~~~vlilDE~~~L-~~~~~~~L~~~le~~~~~~~~Il~t~~~  174 (354)
T 1sxj_E          132 AHRYKCVIINEANSL-TKDAQAALRRTMEKYSKNIRLIMVCDSM  174 (354)
T ss_dssp             --CCEEEEEECTTSS-CHHHHHHHHHHHHHSTTTEEEEEEESCS
T ss_pred             CCCCeEEEEeCcccc-CHHHHHHHHHHHHhhcCCCEEEEEeCCH
Confidence            346789999999994 4444555666666666666666666544

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=96.46  E-value=0.011  Score=45.34  Aligned_cols=18  Identities=28%  Similarity=0.523  Sum_probs=15.2

Q ss_pred             CCcEEEEcCCCChhHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~   87 (293)
                      ..++++.||+|+|||...
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            468999999999999543

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=96.43  E-value=0.0051  Score=49.01  Aligned_cols=99  Identities=6%  Similarity=0.004  Sum_probs=53.0

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  148 (293)
                      .|.-.+++||.|+|||...+-.+ .+....  +.+++++.|...--..    -..+....|+...               
T Consensus        27 ~G~I~vitG~M~sGKTT~Llr~~-~r~~~~--g~kvli~kp~~D~R~~----~~~I~Sr~G~~~~---------------   84 (219)
T 3e2i_A           27 SGWIECITGSMFSGKSEELIRRL-RRGIYA--KQKVVVFKPAIDDRYH----KEKVVSHNGNAIE---------------   84 (219)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHH-HHHHHT--TCCEEEEEEC---------------CBTTBCCE---------------
T ss_pred             CceEEEEECCCCCCHHHHHHHHH-HHHHHc--CCceEEEEeccCCcch----hhhHHHhcCCcee---------------
Confidence            46678999999999996554443 444333  4578999886541100    0112222232211               


Q ss_pred             hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHH
Q 022724          149 EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVY  200 (293)
Q Consensus       149 ~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~  200 (293)
                          -+.|..+..+...+      ..+.++|+|||++.+. ......+..+.
T Consensus        85 ----a~~v~~~~di~~~i------~~~~dvV~IDEaQFf~-~~~v~~l~~la  125 (219)
T 3e2i_A           85 ----AINISKASEIMTHD------LTNVDVIGIDEVQFFD-DEIVSIVEKLS  125 (219)
T ss_dssp             ----EEEESSGGGGGGSC------CTTCSEEEECCGGGSC-THHHHHHHHHH
T ss_pred             ----eEEeCCHHHHHHHH------hcCCCEEEEechhcCC-HHHHHHHHHHH
Confidence                23444443333221      2467899999999764 34555566555

>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=96.35  E-value=0.0079  Score=52.11  Aligned_cols=18  Identities=28%  Similarity=0.558  Sum_probs=15.3

Q ss_pred             CCcEEEEcCCCChhHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~   87 (293)
                      +..+++.||+|+|||...
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            568999999999999543

>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=96.35  E-value=0.036  Score=43.43  Aligned_cols=141  Identities=16%  Similarity=0.193  Sum_probs=70.3

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHH-HHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE-LATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~-l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  148 (293)
                      ...+++..++|.|||.+++-.++..+..   |.+++|+.=.+. .-..=.+.++.+    ++.+...-.+.....+...-
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            3589999999999998887766666655   557788743221 000001111122    22222111111110000000


Q ss_pred             hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcccc--HHHHHHHHhhCCCCccEEEEEeecChhHHHHH
Q 022724          149 EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF--KDQIYDVYRYLPPDLQVVLISATLPHEILEMT  224 (293)
Q Consensus       149 ~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~--~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~  224 (293)
                          +.  ......+..... .+.-..+++||+||+-.....++  ...+..++...+...-+|+.+--.|+.+.+.+
T Consensus       101 ----~~--~~a~~~l~~a~~-~l~~~~yDlvILDEi~~al~~g~l~~~ev~~~l~~Rp~~~~vIlTGr~ap~~l~e~A  171 (196)
T 1g5t_A          101 ----DT--AACMAVWQHGKR-MLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCHRDILDLA  171 (196)
T ss_dssp             ----HH--HHHHHHHHHHHH-HTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSCCHHHHHHC
T ss_pred             ----HH--HHHHHHHHHHHH-HHhcCCCCEEEEeCCCccccCCCCCHHHHHHHHHhCcCCCEEEEECCCCcHHHHHhC
Confidence                00  000111111111 12235689999999987655543  34566667766656666665555677666655

>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=96.33  E-value=0.0069  Score=52.68  Aligned_cols=16  Identities=31%  Similarity=0.447  Sum_probs=14.0

Q ss_pred             cEEEEcCCCChhHHHH
Q 022724           72 DVIAQAQSGTGKTSMI   87 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~   87 (293)
                      .+++.||+|+|||...
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            7999999999999543

>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=96.33  E-value=0.0093  Score=50.70  Aligned_cols=40  Identities=13%  Similarity=0.187  Sum_probs=24.3

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      ....+++|||+|.+........+..++...+...++|+.+
T Consensus       104 ~~~~vliiDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~  143 (324)
T 3u61_B          104 GRQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITA  143 (324)
T ss_dssp             SCEEEEEEESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEE
T ss_pred             CCCeEEEEECCcccCcHHHHHHHHHHHHhCCCCcEEEEEe
Confidence            3678999999999852223334444455444455666543

>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=96.19  E-value=0.026  Score=50.03  Aligned_cols=128  Identities=14%  Similarity=0.270  Sum_probs=66.8

Q ss_pred             cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEc--CCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHh
Q 022724           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS--PTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE  149 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~--P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  149 (293)
                      -++++|++|+|||....--+ ..+...  +.+++++.  +.+.-+.+   .+..+....++.+.....+.          
T Consensus        99 vI~lvG~~GsGKTTt~~kLA-~~l~~~--G~kVllv~~D~~r~~a~e---qL~~~~~~~gv~~~~~~~~~----------  162 (433)
T 3kl4_A           99 IIMLVGVQGSGKTTTAGKLA-YFYKKR--GYKVGLVAADVYRPAAYD---QLLQLGNQIGVQVYGEPNNQ----------  162 (433)
T ss_dssp             EEEECCCTTSCHHHHHHHHH-HHHHHT--TCCEEEEEECCSCHHHHH---HHHHHHHTTTCCEECCTTCS----------
T ss_pred             EEEEECCCCCCHHHHHHHHH-HHHHHc--CCeEEEEecCccchhHHH---HHHHHHHhcCCceeeccccC----------
Confidence            57888999999996543222 222222  44566655  34443332   33334444444433221111          


Q ss_pred             cCCcEEEeChHHHH-HHHhcCCCCCCCccEEEecchhhhh---ccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHH
Q 022724          150 HGVHVVSGTPGRVC-DMIKRKTLRTRAIKLLVLDESDEML---SRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTT  225 (293)
Q Consensus       150 ~~~~ilV~Tp~~l~-~~l~~~~~~~~~l~~iViDE~h~~~---~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~  225 (293)
                              .|..+. ..+..  ....+.+++|||++-...   +..+...+..+.+...+..-++.++|+...+....+.
T Consensus       163 --------dp~~i~~~al~~--a~~~~~DvvIIDTaGr~~~~~d~~lm~el~~i~~~~~pd~vlLVlDa~~gq~a~~~a~  232 (433)
T 3kl4_A          163 --------NPIEIAKKGVDI--FVKNKMDIIIVDTAGRHGYGEETKLLEEMKEMYDVLKPDDVILVIDASIGQKAYDLAS  232 (433)
T ss_dssp             --------CHHHHHHHHHHH--TTTTTCSEEEEEECCCSSSCCTTHHHHHHHHHHHHHCCSEEEEEEEGGGGGGGHHHHH
T ss_pred             --------CHHHHHHHHHHH--HHhcCCCEEEEECCCCccccCCHHHHHHHHHHHHhhCCcceEEEEeCccchHHHHHHH
Confidence                    122222 12221  112467889999987543   2334555666666666666677888887655444443

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=96.18  E-value=0.054  Score=46.15  Aligned_cols=17  Identities=24%  Similarity=0.518  Sum_probs=14.8

Q ss_pred             CcEEEEcCCCChhHHHH
Q 022724           71 RDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~   87 (293)
                      .++++.||+|+|||..+
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=96.09  E-value=0.076  Score=42.26  Aligned_cols=40  Identities=13%  Similarity=0.238  Sum_probs=22.8

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEe
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SA  214 (293)
                      ..-.+|||||+|.+... ....+...+...+....+|+.|.
T Consensus       125 ~~~~vlviDe~~~l~~~-~~~~l~~~l~~~~~~~~~i~~t~  164 (250)
T 1njg_A          125 GRFKVYLIDEVHMLSRH-SFNALLKTLEEPPEHVKFLLATT  164 (250)
T ss_dssp             SSSEEEEEETGGGSCHH-HHHHHHHHHHSCCTTEEEEEEES
T ss_pred             CCceEEEEECcccccHH-HHHHHHHHHhcCCCceEEEEEeC
Confidence            34578999999987432 23334444444444455555543

>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=95.95  E-value=0.047  Score=46.68  Aligned_cols=39  Identities=21%  Similarity=0.425  Sum_probs=25.5

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      ...+++|+||+|.+... ....+..++...+....+++.+
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            44789999999988543 2344555666655566666554

>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=95.91  E-value=0.025  Score=48.39  Aligned_cols=40  Identities=20%  Similarity=0.295  Sum_probs=25.3

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEe
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SA  214 (293)
                      ....++++||+|.+... ....+..++...+....+++.+.
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            34579999999988533 23445555665555566666543

>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=95.88  E-value=0.09  Score=44.34  Aligned_cols=39  Identities=13%  Similarity=0.234  Sum_probs=23.3

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      ...+++||||+|.|.... ...+...+..-++...+|+.+
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            457899999999985433 233344444434445555554

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=95.79  E-value=0.02  Score=48.68  Aligned_cols=50  Identities=8%  Similarity=0.082  Sum_probs=32.2

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhh-----cCCcEEEEcCCCChhHHHH
Q 022724           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII-----KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        32 ~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~-----~~~~~li~~~Tg~GKT~~~   87 (293)
                      ..+|+++.-...+.+.+.+.- .  .|   ...+.+.     ..+++++.||+|+|||..+
T Consensus        14 ~~~~~di~G~~~~~~~l~~~i-~--~~---~~~~~~~~~~~~~~~~vLl~GppGtGKT~la   68 (322)
T 3eie_A           14 NVKWEDVAGLEGAKEALKEAV-I--LP---VKFPHLFKGNRKPTSGILLYGPPGTGKSYLA   68 (322)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHT-H--HH---HHCGGGCCTTCCCCCEEEEECSSSSCHHHHH
T ss_pred             CCCHHHhcChHHHHHHHHHHH-H--HH---HhCHHHHhcCCCCCCeEEEECCCCCcHHHHH
Confidence            457899877777777776531 1  11   1112222     2357999999999999654

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=95.68  E-value=0.07  Score=42.98  Aligned_cols=52  Identities=13%  Similarity=0.131  Sum_probs=31.0

Q ss_pred             hcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 022724           68 IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA  123 (293)
Q Consensus        68 ~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~  123 (293)
                      ..|.-+++.||+|+|||...+-.+......   +.+++++.-.. ...++.+.+..
T Consensus        21 ~~G~~~~i~G~~GsGKTtl~~~~~~~~~~~---~~~v~~~~~e~-~~~~~~~~~~~   72 (247)
T 2dr3_A           21 PERNVVLLSGGPGTGKTIFSQQFLWNGLKM---GEPGIYVALEE-HPVQVRQNMAQ   72 (247)
T ss_dssp             ETTCEEEEEECTTSSHHHHHHHHHHHHHHT---TCCEEEEESSS-CHHHHHHHHHT
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHHhc---CCeEEEEEccC-CHHHHHHHHHH
Confidence            356789999999999996543333333222   34577776432 24555555543

>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=95.61  E-value=0.044  Score=46.16  Aligned_cols=39  Identities=15%  Similarity=0.298  Sum_probs=24.2

Q ss_pred             CccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEe
Q 022724          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (293)
Q Consensus       175 ~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SA  214 (293)
                      +-.++||||+|.+.... ...+..++...+....+|+.|.
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            46899999999985432 2334445555555566666553

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=95.57  E-value=0.032  Score=47.22  Aligned_cols=18  Identities=17%  Similarity=0.390  Sum_probs=15.6

Q ss_pred             CCcEEEEcCCCChhHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~   87 (293)
                      ++++++.||+|+|||...
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            579999999999999543

>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=95.51  E-value=0.07  Score=45.96  Aligned_cols=39  Identities=13%  Similarity=0.267  Sum_probs=23.1

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      ..-.++||||+|.+.... ...+...+...+....+|+.+
T Consensus       118 ~~~~vliiDe~~~l~~~~-~~~Ll~~le~~~~~~~~Il~~  156 (373)
T 1jr3_A          118 GRFKVYLIDEVHMLSRHS-FNALLKTLEEPPEHVKFLLAT  156 (373)
T ss_dssp             SSSEEEEEECGGGSCHHH-HHHHHHHHHSCCSSEEEEEEE
T ss_pred             CCeEEEEEECcchhcHHH-HHHHHHHHhcCCCceEEEEEe
Confidence            456799999999985332 333444455444444455544

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=95.02  E-value=0.18  Score=44.97  Aligned_cols=51  Identities=18%  Similarity=0.136  Sum_probs=28.8

Q ss_pred             hhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHH
Q 022724           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKV  120 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~  120 (293)
                      +..|.-+++.|++|+|||...+-.+.......  +..++|+..... ..++..+
T Consensus       200 l~~G~liiI~G~pG~GKTtl~l~ia~~~~~~~--g~~Vl~~s~E~s-~~~l~~r  250 (454)
T 2r6a_A          200 FQRSDLIIVAARPSVGKTAFALNIAQNVATKT--NENVAIFSLEMS-AQQLVMR  250 (454)
T ss_dssp             BCTTCEEEEECCTTSCHHHHHHHHHHHHHHHS--SCCEEEEESSSC-HHHHHHH
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHHHHhC--CCcEEEEECCCC-HHHHHHH
Confidence            33567799999999999954433333322222  335777764322 2344444

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=95.01  E-value=0.11  Score=45.41  Aligned_cols=18  Identities=28%  Similarity=0.497  Sum_probs=15.6

Q ss_pred             CCcEEEEcCCCChhHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~   87 (293)
                      .+++++.||+|+|||..+
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

>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=95.01  E-value=0.067  Score=46.74  Aligned_cols=17  Identities=29%  Similarity=0.481  Sum_probs=13.8

Q ss_pred             CcEEE--EcCCCChhHHHH
Q 022724           71 RDVIA--QAQSGTGKTSMI   87 (293)
Q Consensus        71 ~~~li--~~~Tg~GKT~~~   87 (293)
                      ..++|  .||.|+|||...
T Consensus        51 ~~~li~i~G~~G~GKT~L~   69 (412)
T 1w5s_A           51 VNMIYGSIGRVGIGKTTLA   69 (412)
T ss_dssp             EEEEEECTTCCSSSHHHHH
T ss_pred             CEEEEeCcCcCCCCHHHHH
Confidence            46888  899999999543

>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=94.99  E-value=0.33  Score=43.04  Aligned_cols=57  Identities=16%  Similarity=0.146  Sum_probs=32.0

Q ss_pred             cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEc--CCHHHHHHHHHHHHHhhccCCceEEE
Q 022724           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS--PTRELATQTEKVILAIGDFINIQAHA  134 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~--P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (293)
                      -++++|++|+|||....--+ ..+...  +.+++++.  |.+.-+.   +.++.+....++.+..
T Consensus       102 vIlivG~~G~GKTTt~~kLA-~~l~~~--G~kVllv~~D~~R~aa~---eqL~~~~~~~gvpv~~  160 (443)
T 3dm5_A          102 ILLMVGIQGSGKTTTVAKLA-RYFQKR--GYKVGVVCSDTWRPGAY---HQLRQLLDRYHIEVFG  160 (443)
T ss_dssp             EEEEECCTTSSHHHHHHHHH-HHHHTT--TCCEEEEECCCSSTHHH---HHHHHHHGGGTCEEEC
T ss_pred             EEEEECcCCCCHHHHHHHHH-HHHHHC--CCeEEEEeCCCcchhHH---HHHHHHHHhcCCcEEe
Confidence            57889999999996543222 223332  44566655  4455443   3344455555655543

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=94.95  E-value=0.13  Score=40.84  Aligned_cols=20  Identities=30%  Similarity=0.350  Sum_probs=16.1

Q ss_pred             hcCCcEEEEcCCCChhHHHH
Q 022724           68 IKGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        68 ~~~~~~li~~~Tg~GKT~~~   87 (293)
                      ..|.-+++.||+|+|||...
T Consensus        21 ~~G~~~~i~G~~GsGKTtl~   40 (235)
T 2w0m_A           21 PQGFFIALTGEPGTGKTIFS   40 (235)
T ss_dssp             ETTCEEEEECSTTSSHHHHH
T ss_pred             cCCCEEEEEcCCCCCHHHHH
Confidence            35678999999999999543

>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=94.93  E-value=0.057  Score=45.35  Aligned_cols=16  Identities=31%  Similarity=0.515  Sum_probs=13.9

Q ss_pred             cEEEEcCCCChhHHHH
Q 022724           72 DVIAQAQSGTGKTSMI   87 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~   87 (293)
                      ++++.||+|+|||...
T Consensus        40 ~~ll~G~~G~GKt~la   55 (319)
T 2chq_A           40 HLLFSGPPGTGKTATA   55 (319)
T ss_dssp             CEEEESSSSSSHHHHH
T ss_pred             eEEEECcCCcCHHHHH
Confidence            6999999999999543

>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=94.85  E-value=0.21  Score=40.01  Aligned_cols=23  Identities=22%  Similarity=0.121  Sum_probs=17.8

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTV   91 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~   91 (293)
                      .|.-+++.||+|+|||......+
T Consensus        23 ~G~~~~i~G~~GsGKTtl~~~l~   45 (243)
T 1n0w_A           23 TGSITEMFGEFRTGKTQICHTLA   45 (243)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHH
Confidence            56789999999999996544333

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=94.77  E-value=0.19  Score=37.81  Aligned_cols=74  Identities=12%  Similarity=0.156  Sum_probs=54.0

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHHhcCCCCCCCc
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l~~~~~~~~~l  176 (293)
                      +.++||.|+++.-+..+.+.+...    ++.+..++|+.+..+....+    ....+|+|+|.     .+ ...+++.++
T Consensus        35 ~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~-~~Gld~~~~  104 (163)
T 2hjv_A           35 PDSCIIFCRTKEHVNQLTDELDDL----GYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATD-----VA-ARGIDIENI  104 (163)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECG-----GG-TTTCCCSCC
T ss_pred             CCcEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEECC-----hh-hcCCchhcC
Confidence            347999999999999999888764    67888899987765544333    24568999994     22 335778888


Q ss_pred             cEEEecch
Q 022724          177 KLLVLDES  184 (293)
Q Consensus       177 ~~iViDE~  184 (293)
                      +++|.-+.
T Consensus       105 ~~Vi~~~~  112 (163)
T 2hjv_A          105 SLVINYDL  112 (163)
T ss_dssp             SEEEESSC
T ss_pred             CEEEEeCC
Confidence            88876543

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=94.74  E-value=0.031  Score=58.36  Aligned_cols=40  Identities=15%  Similarity=0.217  Sum_probs=28.5

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHH
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~  112 (293)
                      ++++++.||+|+|||..+...+.+...   .+.+++|+.....
T Consensus      1427 g~~vll~GppGtGKT~LA~ala~ea~~---~G~~v~Fi~~e~~ 1466 (2050)
T 3cmu_A         1427 GRIVEIYGPESSGKTTLTLQVIAAAQR---EGKTCAFIDAEHA 1466 (2050)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHHHHT---TTCCEEEECTTSC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHH---cCCcEEEEEcccc
Confidence            689999999999999765544444332   2557888876543

>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=94.61  E-value=0.24  Score=37.72  Aligned_cols=73  Identities=16%  Similarity=0.132  Sum_probs=53.7

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHHhcCCCCCCCc
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l~~~~~~~~~l  176 (293)
                      +.++||.|+++..+..+.+.+..    .++.+..++|+.+..+....+    ....+|+|+|.     . -...+++..+
T Consensus        34 ~~~~lVF~~~~~~~~~l~~~L~~----~~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~-----~-~~~Gid~~~~  103 (175)
T 2rb4_A           34 IGQAIIFCQTRRNAKWLTVEMIQ----DGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTN-----V-CARGIDVKQV  103 (175)
T ss_dssp             CSEEEEECSCHHHHHHHHHHHHT----TTCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECC-----S-CCTTTCCTTE
T ss_pred             CCCEEEEECCHHHHHHHHHHHHH----cCCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEec-----c-hhcCCCcccC
Confidence            45899999999999998887764    367888899998766554333    24578999994     2 2345778888


Q ss_pred             cEEEecc
Q 022724          177 KLLVLDE  183 (293)
Q Consensus       177 ~~iViDE  183 (293)
                      +++|.-+
T Consensus       104 ~~Vi~~d  110 (175)
T 2rb4_A          104 TIVVNFD  110 (175)
T ss_dssp             EEEEESS
T ss_pred             CEEEEeC
Confidence            8888543

>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=94.46  E-value=0.066  Score=44.77  Aligned_cols=41  Identities=15%  Similarity=0.152  Sum_probs=24.5

Q ss_pred             hhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcC
Q 022724           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P  109 (293)
                      +..|.-+++.||+|+|||..... +...+... .|.+++++..
T Consensus        32 l~~G~~~~i~G~~G~GKTTl~~~-ia~~~~~~-~G~~v~~~~~   72 (296)
T 1cr0_A           32 ARGGEVIMVTSGSGMGKSTFVRQ-QALQWGTA-MGKKVGLAML   72 (296)
T ss_dssp             BCTTCEEEEEESTTSSHHHHHHH-HHHHHHHT-SCCCEEEEES
T ss_pred             CCCCeEEEEEeCCCCCHHHHHHH-HHHHHHHH-cCCeEEEEeC
Confidence            44678899999999999954332 22222222 1335666653

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=94.44  E-value=0.33  Score=43.18  Aligned_cols=50  Identities=22%  Similarity=0.102  Sum_probs=28.3

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVI  121 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~  121 (293)
                      .|.-+++.|++|+|||...+-.+.+.....  +..++|+..-.. ..|+..++
T Consensus       199 ~G~l~ii~G~pg~GKT~lal~ia~~~a~~~--g~~vl~~slE~~-~~~l~~R~  248 (444)
T 2q6t_A          199 PGSLNIIAARPAMGKTAFALTIAQNAALKE--GVGVGIYSLEMP-AAQLTLRM  248 (444)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHHHHHHHTT--CCCEEEEESSSC-HHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHhC--CCeEEEEECCCC-HHHHHHHH
Confidence            456789999999999954433333332222  335777664322 33444443

>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=94.44  E-value=0.16  Score=46.16  Aligned_cols=41  Identities=20%  Similarity=0.210  Sum_probs=25.7

Q ss_pred             CCccEEEecchhhhhccc--cHHHHHHHHhhCCCCccEEEEEeec
Q 022724          174 RAIKLLVLDESDEMLSRG--FKDQIYDVYRYLPPDLQVVLISATL  216 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~--~~~~~~~i~~~l~~~~q~v~~SAt~  216 (293)
                      ..-.+|+|||+|.+....  ....+..++..  ....+|+++++.
T Consensus       147 ~~~~vliIDEid~l~~~~~~~l~~L~~~l~~--~~~~iIli~~~~  189 (516)
T 1sxj_A          147 GKHFVIIMDEVDGMSGGDRGGVGQLAQFCRK--TSTPLILICNER  189 (516)
T ss_dssp             TTSEEEEECSGGGCCTTSTTHHHHHHHHHHH--CSSCEEEEESCT
T ss_pred             CCCeEEEEECCCccchhhHHHHHHHHHHHHh--cCCCEEEEEcCC
Confidence            445789999999986432  22344444444  245677777764

>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=94.40  E-value=0.21  Score=45.11  Aligned_cols=43  Identities=19%  Similarity=0.289  Sum_probs=26.3

Q ss_pred             ccEEEecchhhhhccc----------cHHHHHHHHhhCCCCccEEEEEeecCh
Q 022724          176 IKLLVLDESDEMLSRG----------FKDQIYDVYRYLPPDLQVVLISATLPH  218 (293)
Q Consensus       176 l~~iViDE~h~~~~~~----------~~~~~~~i~~~l~~~~q~v~~SAt~~~  218 (293)
                      .+.|++||+|.+....          ....+..++........++++.||=.+
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            3689999999986421          123344444545556667777777433

>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=94.31  E-value=0.06  Score=45.48  Aligned_cols=18  Identities=22%  Similarity=0.353  Sum_probs=15.3

Q ss_pred             CCcEEEEcCCCChhHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~   87 (293)
                      ..++++.||+|+|||...
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            368999999999999543

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=94.19  E-value=0.34  Score=36.43  Aligned_cols=74  Identities=12%  Similarity=0.118  Sum_probs=53.6

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHHhcCCCCCCCc
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l~~~~~~~~~l  176 (293)
                      +.++||.++++.-+..+...++..    ++.+..++|+.+..+....+    .....|+|+|.     . -...+++.++
T Consensus        30 ~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~-~~~G~d~~~~   99 (165)
T 1fuk_A           30 VTQAVIFCNTRRKVEELTTKLRND----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTD-----L-LARGIDVQQV   99 (165)
T ss_dssp             CSCEEEEESSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEG-----G-GTTTCCCCSC
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHc----CCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEEcC-----h-hhcCCCcccC
Confidence            358999999999999998887653    66788899987765544333    24568999994     2 2335678888


Q ss_pred             cEEEecch
Q 022724          177 KLLVLDES  184 (293)
Q Consensus       177 ~~iViDE~  184 (293)
                      +++|.-+.
T Consensus       100 ~~Vi~~~~  107 (165)
T 1fuk_A          100 SLVINYDL  107 (165)
T ss_dssp             SEEEESSC
T ss_pred             CEEEEeCC
Confidence            88876543

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=94.14  E-value=0.043  Score=49.00  Aligned_cols=17  Identities=35%  Similarity=0.558  Sum_probs=14.5

Q ss_pred             CcEEEEcCCCChhHHHH
Q 022724           71 RDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~   87 (293)
                      .++++.||+|+|||...
T Consensus        51 ~~vLL~GppGtGKTtlA   67 (447)
T 3pvs_A           51 HSMILWGPPGTGKTTLA   67 (447)
T ss_dssp             CEEEEECSTTSSHHHHH
T ss_pred             cEEEEECCCCCcHHHHH
Confidence            47999999999999554

>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=93.99  E-value=0.24  Score=40.95  Aligned_cols=24  Identities=17%  Similarity=0.249  Sum_probs=19.1

Q ss_pred             HhhhcCCcEEEEcCCCChhHHHHH
Q 022724           65 MPIIKGRDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        65 ~~i~~~~~~li~~~Tg~GKT~~~~   88 (293)
                      .-+..|.-+++.||+|+|||....
T Consensus        25 ggl~~G~i~~i~G~~GsGKTtl~~   48 (279)
T 1nlf_A           25 PNMVAGTVGALVSPGGAGKSMLAL   48 (279)
T ss_dssp             TTEETTSEEEEEESTTSSHHHHHH
T ss_pred             CCccCCCEEEEEcCCCCCHHHHHH
Confidence            345578889999999999995543

>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=93.98  E-value=0.092  Score=44.51  Aligned_cols=55  Identities=11%  Similarity=0.126  Sum_probs=32.0

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccC---------CCc----eeEEEEcCCHHH-HHHHHHHHHHh
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTS---------SRE----VQALILSPTREL-ATQTEKVILAI  124 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~---------~~~----~~~lil~P~~~l-~~q~~~~~~~~  124 (293)
                      |.-+++.|++|+|||...+-.+.+.....         ..+    .+++|+.-...+ ..++...++.+
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            35789999999999965444443322111         112    578888755432 45555555444

>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=93.95  E-value=0.29  Score=38.68  Aligned_cols=71  Identities=24%  Similarity=0.308  Sum_probs=53.1

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHHhcCCCCCCCc
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l~~~~~~~~~l  176 (293)
                      +.++||.|+++.-+..+.+.+...    ++.+..++|+.+..++...+    ....+|+|+|.     . -...+++.++
T Consensus        31 ~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~-----~-~~~Gidi~~v  100 (212)
T 3eaq_A           31 PDRAMVFTRTKAETEEIAQGLLRL----GHPAQALHGDLSQGERERVLGAFRQGEVRVLVATD-----V-AARGLDIPQV  100 (212)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHH----TCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECT-----T-TTCSSSCCCB
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHc----CCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecC-----h-hhcCCCCccC
Confidence            348999999999999998887764    67888899998766554433    24568999994     2 2345778888


Q ss_pred             cEEEe
Q 022724          177 KLLVL  181 (293)
Q Consensus       177 ~~iVi  181 (293)
                      +++|.
T Consensus       101 ~~Vi~  105 (212)
T 3eaq_A          101 DLVVH  105 (212)
T ss_dssp             SEEEE
T ss_pred             cEEEE
Confidence            88874

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=93.77  E-value=0.51  Score=36.59  Aligned_cols=72  Identities=22%  Similarity=0.260  Sum_probs=52.9

Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHHhcCCCCCCCcc
Q 022724          102 VQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAIK  177 (293)
Q Consensus       102 ~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~  177 (293)
                      .++||.|+++.-+..+.+.++..    ++.+..++|+.+..+....+    ....+|+|+|.     .+. ..+++.+++
T Consensus        55 ~~~lVF~~~~~~~~~l~~~L~~~----g~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~-----~~~-~Gldi~~v~  124 (191)
T 2p6n_A           55 PPVLIFAEKKADVDAIHEYLLLK----GVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATD-----VAS-KGLDFPAIQ  124 (191)
T ss_dssp             SCEEEECSCHHHHHHHHHHHHHH----TCCEEEECTTSCHHHHHHHHHHHHHTSCSEEEECH-----HHH-TTCCCCCCS
T ss_pred             CCEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEcC-----chh-cCCCcccCC
Confidence            47999999999999999888764    67888899987765544333    24578999993     222 356788888


Q ss_pred             EEEecc
Q 022724          178 LLVLDE  183 (293)
Q Consensus       178 ~iViDE  183 (293)
                      ++|.-+
T Consensus       125 ~VI~~d  130 (191)
T 2p6n_A          125 HVINYD  130 (191)
T ss_dssp             EEEESS
T ss_pred             EEEEeC
Confidence            887643

>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=93.63  E-value=0.15  Score=44.22  Aligned_cols=40  Identities=13%  Similarity=0.199  Sum_probs=25.2

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCH
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~  111 (293)
                      .|.-++|.|++|+|||...+- +...+...  +.+++|+....
T Consensus        73 ~G~li~I~G~pGsGKTtlal~-la~~~~~~--g~~vlyi~~E~  112 (366)
T 1xp8_A           73 RGRITEIYGPESGGKTTLALA-IVAQAQKA--GGTCAFIDAEH  112 (366)
T ss_dssp             TTSEEEEEESTTSSHHHHHHH-HHHHHHHT--TCCEEEEESSC
T ss_pred             CCcEEEEEcCCCCChHHHHHH-HHHHHHHC--CCeEEEEECCC
Confidence            346789999999999954443 33333222  34677777543

>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=93.56  E-value=0.28  Score=41.57  Aligned_cols=55  Identities=13%  Similarity=0.067  Sum_probs=31.2

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccC---CCceeEEEEcCCHHH-HHHHHHHHHHh
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTS---SREVQALILSPTREL-ATQTEKVILAI  124 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~---~~~~~~lil~P~~~l-~~q~~~~~~~~  124 (293)
                      |.-+++.||+|+|||...+-.+.......   ..+.+++|+.-...+ ..++...++.+
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            46799999999999965444333322210   113467887754432 34444444443

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=93.52  E-value=0.19  Score=43.03  Aligned_cols=51  Identities=25%  Similarity=0.179  Sum_probs=29.7

Q ss_pred             hhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHH
Q 022724           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVI  121 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~  121 (293)
                      +..|.-+++.|++|+|||...+-.+ ..+..  .+..++|+..-. -..|+..++
T Consensus        43 l~~G~LiiIaG~pG~GKTt~al~ia-~~~a~--~g~~Vl~fSlEm-s~~ql~~Rl   93 (338)
T 4a1f_A           43 FNKGSLVIIGARPSMGKTSLMMNMV-LSALN--DDRGVAVFSLEM-SAEQLALRA   93 (338)
T ss_dssp             BCTTCEEEEEECTTSCHHHHHHHHH-HHHHH--TTCEEEEEESSS-CHHHHHHHH
T ss_pred             CCCCcEEEEEeCCCCCHHHHHHHHH-HHHHH--cCCeEEEEeCCC-CHHHHHHHH
Confidence            3355679999999999995443333 33322  244677776432 234444444

>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=93.44  E-value=0.093  Score=45.16  Aligned_cols=39  Identities=18%  Similarity=0.234  Sum_probs=25.3

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCC
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~  110 (293)
                      .|.-+++.||+|+|||...+..+......   +.+++|+.-.
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            45779999999999996544333333222   3467777654

>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=93.40  E-value=0.099  Score=44.23  Aligned_cols=90  Identities=11%  Similarity=0.127  Sum_probs=50.2

Q ss_pred             cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcC
Q 022724           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG  151 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (293)
                      -+++.+|+|+|||...+-.+...... ..+.+++|+..-..+...   ++++++-..                       
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            58899999999996555444443332 124578888876555322   344443211                       


Q ss_pred             CcEEEeCh---HHH-HHHHhc-CCCCCCCccEEEecchhhhh
Q 022724          152 VHVVSGTP---GRV-CDMIKR-KTLRTRAIKLLVLDESDEML  188 (293)
Q Consensus       152 ~~ilV~Tp---~~l-~~~l~~-~~~~~~~l~~iViDE~h~~~  188 (293)
                      .++++..|   +.+ +..+.. ..+.-..+++||||-+..+.
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            12444433   333 222211 11223468999999999875

>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=93.21  E-value=0.29  Score=37.74  Aligned_cols=89  Identities=12%  Similarity=0.155  Sum_probs=51.0

Q ss_pred             CChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHH---H-hcCCcEE
Q 022724           80 GTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRK---L-EHGVHVV  155 (293)
Q Consensus        80 g~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~-~~~~~il  155 (293)
                      ...|- ..+.-++...   ..+.++||.|+++.-+..+.+.++..    ++.+..++|+.+..+....   . ....+|+
T Consensus        29 ~~~K~-~~L~~ll~~~---~~~~k~lVF~~~~~~~~~l~~~L~~~----g~~~~~lhg~~~~~~r~~~~~~f~~g~~~vL  100 (185)
T 2jgn_A           29 ESDKR-SFLLDLLNAT---GKDSLTLVFVETKKGADSLEDFLYHE----GYACTSIHGDRSQRDREEALHQFRSGKSPIL  100 (185)
T ss_dssp             GGGHH-HHHHHHHHHC----CCSCEEEEESCHHHHHHHHHHHHHT----TCCEEEEC--------CHHHHHHHHTSSSEE
T ss_pred             cHHHH-HHHHHHHHhc---CCCCeEEEEECCHHHHHHHHHHHHHc----CCceEEEeCCCCHHHHHHHHHHHHcCCCeEE
Confidence            34565 3344444432   23458999999999999999887753    6778888888654443222   2 2456899


Q ss_pred             EeChHHHHHHHhcCCCCCCCccEEEec
Q 022724          156 SGTPGRVCDMIKRKTLRTRAIKLLVLD  182 (293)
Q Consensus       156 V~Tp~~l~~~l~~~~~~~~~l~~iViD  182 (293)
                      |+|. .+     ...+++.+++++|.=
T Consensus       101 vaT~-~~-----~~Gldi~~~~~VI~~  121 (185)
T 2jgn_A          101 VATA-VA-----ARGLDISNVKHVINF  121 (185)
T ss_dssp             EEEC------------CCCSBSEEEES
T ss_pred             EEcC-hh-----hcCCCcccCCEEEEe
Confidence            9994 22     224677788887763

>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=93.12  E-value=2.7  Score=35.35  Aligned_cols=51  Identities=14%  Similarity=0.273  Sum_probs=29.2

Q ss_pred             hHHHHHHHhcCCCCCCCccEEEecchhhhhc---cccHHHHHHHHhhCCCCccEEEEE
Q 022724          159 PGRVCDMIKRKTLRTRAIKLLVLDESDEMLS---RGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       159 p~~l~~~l~~~~~~~~~l~~iViDE~h~~~~---~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      ...+...+....-   .--+|||||+|.+.+   ..+...+..+.... .+..+|+.+
T Consensus       124 ~~~l~~~l~~~~~---~~~vlvlDe~~~~~~~~~~~~~~~l~~~~~~~-~~~~~i~~g  177 (357)
T 2fna_A          124 FANLLESFEQASK---DNVIIVLDEAQELVKLRGVNLLPALAYAYDNL-KRIKFIMSG  177 (357)
T ss_dssp             HHHHHHHHHHTCS---SCEEEEEETGGGGGGCTTCCCHHHHHHHHHHC-TTEEEEEEE
T ss_pred             HHHHHHHHHhcCC---CCeEEEEECHHHhhccCchhHHHHHHHHHHcC-CCeEEEEEc
Confidence            4455555544211   245899999999864   34555666665554 244555443

>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=93.11  E-value=1.5  Score=39.97  Aligned_cols=96  Identities=6%  Similarity=0.055  Sum_probs=65.4

Q ss_pred             hhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hcCCcEEEe
Q 022724           82 GKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSG  157 (293)
Q Consensus        82 GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~  157 (293)
                      .+....+-.+...+.....+.++||.|+++.-+..+.+.++.... .++.+..++++.+..+....+    ....+|+|+
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            333333334444444434456899999999999999998887542 367788899988766554333    246789999


Q ss_pred             ChHHHHHHHhcCCCCCCCccEEEecch
Q 022724          158 TPGRVCDMIKRKTLRTRAIKLLVLDES  184 (293)
Q Consensus       158 Tp~~l~~~l~~~~~~~~~l~~iViDE~  184 (293)
                      |.     . -...+++.+++++|.-..
T Consensus       399 T~-----~-~~~GiDip~v~~VI~~~~  419 (563)
T 3i5x_A          399 TD-----V-GARGMDFPNVHEVLQIGV  419 (563)
T ss_dssp             CG-----G-GTSSCCCTTCCEEEEESC
T ss_pred             cc-----h-hhcCCCcccCCEEEEECC
Confidence            96     2 234678888998886554

>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=93.03  E-value=0.52  Score=40.28  Aligned_cols=54  Identities=9%  Similarity=-0.010  Sum_probs=30.2

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccC---CCceeEEEEcCCHHH-HHHHHHHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTS---SREVQALILSPTREL-ATQTEKVILA  123 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~---~~~~~~lil~P~~~l-~~q~~~~~~~  123 (293)
                      |.-+++.||+|+|||...+-.+.......   ..+.+++|+.-...+ ..++...++.
T Consensus       122 G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~~~~~~l~~~~~~  179 (343)
T 1v5w_A          122 MAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRDIADR  179 (343)
T ss_dssp             SEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            34689999999999965443333322211   023467887754431 3344444443

>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=92.97  E-value=0.12  Score=44.54  Aligned_cols=42  Identities=24%  Similarity=0.283  Sum_probs=26.5

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l  113 (293)
                      .|.-++|.||+|+|||... +.++..+...  +.+++|+.....+
T Consensus        60 ~G~i~~I~GppGsGKSTLa-l~la~~~~~~--gg~VlyId~E~s~  101 (356)
T 3hr8_A           60 RGRIVEIFGQESSGKTTLA-LHAIAEAQKM--GGVAAFIDAEHAL  101 (356)
T ss_dssp             TTEEEEEEESTTSSHHHHH-HHHHHHHHHT--TCCEEEEESSCCC
T ss_pred             CCcEEEEECCCCCCHHHHH-HHHHHHHHhc--CCeEEEEeccccc
Confidence            3467899999999999543 3333333322  3467888764433

>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=92.95  E-value=0.08  Score=48.48  Aligned_cols=19  Identities=37%  Similarity=0.496  Sum_probs=16.1

Q ss_pred             cCCcEEEEcCCCChhHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~   87 (293)
                      .|..+++.||+|+|||..+
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            4678999999999999543

>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=92.85  E-value=0.16  Score=51.05  Aligned_cols=40  Identities=20%  Similarity=0.311  Sum_probs=30.4

Q ss_pred             EEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHH
Q 022724           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (293)
Q Consensus        73 ~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~  112 (293)
                      -+|.|+.|||||...+--+.+.+.....+.++++++|...
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            3788999999998776666665655555568999999764

>2l8b_A Protein TRAI, DNA helicase I; RECD, hydrolase; NMR {Escherichia coli}

Probab=92.70  E-value=0.33  Score=37.42  Aligned_cols=122  Identities=10%  Similarity=0.090  Sum_probs=71.9

Q ss_pred             CcHHHHHHHHhhhc--CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEE
Q 022724           56 PSAIQQRAVMPIIK--GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAH  133 (293)
Q Consensus        56 ~~~~Q~~~~~~i~~--~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~  133 (293)
                      ..+-|..++..++.  .+-.+|.++-|++|+-..+-.++..-..  .|.++.+|+|+..-...+.+       ..++.- 
T Consensus        35 ~~~~~~~a~~~l~~s~~~~~iv~g~ggs~~~~~~~a~L~~~a~~--~Gr~V~vLAp~~~s~~~l~~-------~~~l~~-  104 (189)
T 2l8b_A           35 RTAGYSDAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMARE--QGREVQIIAADRRSQMNMKQ-------DERLSG-  104 (189)
T ss_dssp             CHHHHHHHHHHHHHHSCCEECCBCSSCSHHHHHHHHHHHHHHHH--TTCCEEEECSTTHHHHHHSC-------TTTCSS-
T ss_pred             cCccchhHHHHHhccCCceEEEecccchHHHHHHHHHHHHHHHh--cCeEEEEEcCchHHHHHHHh-------hcCcCc-
Confidence            45779999998864  3467788999999997754444443333  35689999999876555443       211110 


Q ss_pred             EEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                                         +++ +.     ..+......+..=+.+||||+.++.-......+....+   .+.|+|++-
T Consensus       105 -------------------~t~-t~-----~~ll~~~~~~tp~s~lIVD~AekLS~kE~~~Lld~A~~---~naqvvll~  156 (189)
T 2l8b_A          105 -------------------ELI-TG-----RRQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAAR---HNVQVLITD  156 (189)
T ss_dssp             -------------------CSS-ST-----TTTTTTSCCCCCCCEEEEEESSSHHHHHHHHHHHHHHH---TTCCEEEEE
T ss_pred             -------------------cee-eh-----hhhhcCCCCCCCCCEEEEechhhcCHHHHHHHHHHHHh---cCCEEEEeC
Confidence                               011 11     11222233334556899999998854433333333322   457888875


Q ss_pred             ee
Q 022724          214 AT  215 (293)
Q Consensus       214 At  215 (293)
                      -+
T Consensus       157 ~~  158 (189)
T 2l8b_A          157 SG  158 (189)
T ss_dssp             SS
T ss_pred             Cc
Confidence            54

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=92.41  E-value=2.1  Score=39.26  Aligned_cols=87  Identities=7%  Similarity=0.088  Sum_probs=61.7

Q ss_pred             HHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHH
Q 022724           91 VCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMI  166 (293)
Q Consensus        91 ~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l  166 (293)
                      +...+.....+.++||.|+++.-+..+.+.++.... .++.+..++|+.+..+..+.+    ....+|+|+|.     . 
T Consensus       278 l~~~~~~~~~~~~~iVF~~t~~~~~~l~~~L~~~~~-~~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVaT~-----~-  350 (579)
T 3sqw_A          278 IKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFK-KDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD-----V-  350 (579)
T ss_dssp             HHHHHHHTTTCCEEEEECSSHHHHHHHHHHHHHHHT-TTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECG-----G-
T ss_pred             HHHHHhhcCCCCcEEEECCcHHHHHHHHHHHHHhhc-CCCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEEcc-----h-
Confidence            334444334456899999999999999998887542 367788899988766554333    24678999995     2 


Q ss_pred             hcCCCCCCCccEEEecch
Q 022724          167 KRKTLRTRAIKLLVLDES  184 (293)
Q Consensus       167 ~~~~~~~~~l~~iViDE~  184 (293)
                      -...+++.+++++|.-+.
T Consensus       351 ~~~GiDip~v~~VI~~~~  368 (579)
T 3sqw_A          351 GARGMDFPNVHEVLQIGV  368 (579)
T ss_dssp             GTSSCCCTTCCEEEEESC
T ss_pred             hhcCCCcccCCEEEEcCC
Confidence            234678888999887654

>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=92.09  E-value=1.2  Score=40.08  Aligned_cols=52  Identities=13%  Similarity=0.230  Sum_probs=39.3

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhc
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGD  126 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~  126 (293)
                      .|....+.|-||+|||+...-.+ ..   .  +..+|||+|+...|.++++.++.+..
T Consensus        13 ~~~~~~l~g~~gs~ka~~~a~l~-~~---~--~~p~lvv~~~~~~A~~l~~~l~~~~~   64 (483)
T 3hjh_A           13 AGEQRLLGELTGAACATLVAEIA-ER---H--AGPVVLIAPDMQNALRLHDEISQFTD   64 (483)
T ss_dssp             TTCEEEEECCCTTHHHHHHHHHH-HH---S--SSCEEEEESSHHHHHHHHHHHHHTCS
T ss_pred             CCCeEEEeCCCchHHHHHHHHHH-HH---h--CCCEEEEeCCHHHHHHHHHHHHhhCC
Confidence            45678999999999996533222 21   1  22589999999999999999998764

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=92.03  E-value=1.1  Score=38.79  Aligned_cols=72  Identities=14%  Similarity=0.195  Sum_probs=53.6

Q ss_pred             CceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHHhcCCCCCCC
Q 022724          100 REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRA  175 (293)
Q Consensus       100 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l~~~~~~~~~  175 (293)
                      .+.++||.++++.-+..+.+.++..    ++.+..++|+.+..+....+    ....+|+|+|.     .+ ...+++.+
T Consensus       275 ~~~~~lVf~~~~~~~~~l~~~L~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlvaT~-----~~-~~Gidip~  344 (417)
T 2i4i_A          275 KDSLTLVFVETKKGADSLEDFLYHE----GYACTSIHGDRSQRDREEALHQFRSGKSPILVATA-----VA-ARGLDISN  344 (417)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHHTSSCEEEECH-----HH-HTTSCCCC
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHHC----CCCeeEecCCCCHHHHHHHHHHHHcCCCCEEEECC-----hh-hcCCCccc
Confidence            4568999999999999999888753    67888899988765544333    24578999995     22 23577888


Q ss_pred             ccEEEe
Q 022724          176 IKLLVL  181 (293)
Q Consensus       176 l~~iVi  181 (293)
                      ++++|.
T Consensus       345 v~~Vi~  350 (417)
T 2i4i_A          345 VKHVIN  350 (417)
T ss_dssp             EEEEEE
T ss_pred             CCEEEE
Confidence            888875

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=92.00  E-value=0.37  Score=40.70  Aligned_cols=53  Identities=15%  Similarity=0.080  Sum_probs=31.0

Q ss_pred             hhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 022724           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA  123 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~  123 (293)
                      +..|.-+++.|++|+|||...+-.+.+....   +..++|++-- .-..|+..++..
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            3356779999999999995443333333322   2467777643 334455554443

>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11

Probab=91.88  E-value=0.68  Score=39.68  Aligned_cols=18  Identities=22%  Similarity=0.217  Sum_probs=14.6

Q ss_pred             CcEEEEcCCCChhHHHHH
Q 022724           71 RDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~   88 (293)
                      .-+.+.||+|+|||....
T Consensus       132 ~i~~I~G~~GsGKTTL~~  149 (349)
T 1pzn_A          132 AITEVFGEFGSGKTQLAH  149 (349)
T ss_dssp             EEEEEEESTTSSHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            468899999999995443

>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=91.80  E-value=0.63  Score=35.29  Aligned_cols=74  Identities=11%  Similarity=0.107  Sum_probs=53.7

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHHhcCCCCCCCc
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l~~~~~~~~~l  176 (293)
                      +.++||.|+++.-+..+.+.+...    ++.+..++|+.+..+....+    ....+|+|+|.-      -...+++..+
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            347999999999999999888764    67888899987765544333    245789999951      2235677788


Q ss_pred             cEEEecch
Q 022724          177 KLLVLDES  184 (293)
Q Consensus       177 ~~iViDE~  184 (293)
                      +++|.-+.
T Consensus       101 ~~Vi~~d~  108 (172)
T 1t5i_A          101 NIAFNYDM  108 (172)
T ss_dssp             SEEEESSC
T ss_pred             CEEEEECC
Confidence            88876443

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=91.74  E-value=0.61  Score=44.46  Aligned_cols=17  Identities=29%  Similarity=0.452  Sum_probs=14.4

Q ss_pred             cEEEEcCCCChhHHHHH
Q 022724           72 DVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~   88 (293)
                      ++++.||||+|||..+-
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

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=91.70  E-value=0.062  Score=47.62  Aligned_cols=55  Identities=15%  Similarity=0.274  Sum_probs=36.0

Q ss_pred             ccccCcccCCCCHHHHHHHHHCC---CCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHH
Q 022724           30 EAITSFDAMGIKDDLLRGIYQYG---FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        30 ~~~~~f~~~~l~~~i~~~l~~~~---~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~   87 (293)
                      .|..+|++.+-.++..+.+.+.=   +..|.-++..-   +...+.+++.||+|+|||+.+
T Consensus       175 ~p~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g---~~~prGvLLyGPPGTGKTllA  232 (434)
T 4b4t_M          175 KPTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMG---IRAPKGALMYGPPGTGKTLLA  232 (434)
T ss_dssp             SCSCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHC---CCCCCEEEEESCTTSSHHHHH
T ss_pred             CCCCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCCeeEEECcCCCCHHHHH
Confidence            35568999988888877776531   12333333221   123478999999999999653

>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=91.67  E-value=0.11  Score=44.74  Aligned_cols=40  Identities=15%  Similarity=0.201  Sum_probs=26.0

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCH
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~  111 (293)
                      .|.-+++.|++|+|||...+-.+......   +.+++|+....
T Consensus        62 ~G~ii~I~G~pGsGKTtLal~la~~~~~~---g~~vlyid~E~  101 (356)
T 1u94_A           62 MGRIVEIYGPESSGKTTLTLQVIAAAQRE---GKTCAFIDAEH  101 (356)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHHT---TCCEEEEESSC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHC---CCeEEEEeCCC
Confidence            45679999999999996554433333322   34677777643

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=91.03  E-value=1.6  Score=38.18  Aligned_cols=27  Identities=15%  Similarity=0.249  Sum_probs=20.8

Q ss_pred             CccccCcccCCCCHHHHHHHHHCCCCC
Q 022724           29 VEAITSFDAMGIKDDLLRGIYQYGFEK   55 (293)
Q Consensus        29 ~~~~~~f~~~~l~~~i~~~l~~~~~~~   55 (293)
                      +.++..++..++++..++.|++.||.+
T Consensus        80 ~~~~~~l~~~gi~~~~~~~L~~ag~~t  106 (400)
T 3lda_A           80 FVPIEKLQVNGITMADVKKLRESGLHT  106 (400)
T ss_dssp             SCBGGGGCCTTCCHHHHHHHHHTTCCB
T ss_pred             ccCHHHHHhCCCCHHHHHHHHHcCCCc
Confidence            445666777789999999998888773

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=90.76  E-value=0.88  Score=38.10  Aligned_cols=71  Identities=23%  Similarity=0.306  Sum_probs=52.1

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHHhcCCCCCCCc
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l~~~~~~~~~l  176 (293)
                      +.++||.|+++.-++.+.+.+..    .++.+..++|+.+..++...+    ....+|+|+|.     . -...+++.++
T Consensus        28 ~~~~LVF~~t~~~~~~l~~~L~~----~g~~~~~lhg~l~~~~r~~~~~~f~~g~~~vLVaT~-----v-a~~Gidi~~v   97 (300)
T 3i32_A           28 PDRAMVFTRTKAETEEIAQGLLR----LGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATD-----V-AARGLDIPQV   97 (300)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHT----TTCCEEEECSCCCTHHHHHHHHHHHHTSCCEEEECS-----T-TTCSTTCCCC
T ss_pred             CCCEEEEECCHHHHHHHHHHHHh----CCCCEEEEeCCCCHHHHHHHHHHhhcCCceEEEEec-----h-hhcCccccce
Confidence            45899999999999888887654    367888999998766554433    24578999994     2 2335677888


Q ss_pred             cEEEe
Q 022724          177 KLLVL  181 (293)
Q Consensus       177 ~~iVi  181 (293)
                      +++|.
T Consensus        98 ~~VI~  102 (300)
T 3i32_A           98 DLVVH  102 (300)
T ss_dssp             SEEEE
T ss_pred             eEEEE
Confidence            88774

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=90.72  E-value=0.48  Score=49.76  Aligned_cols=47  Identities=13%  Similarity=0.114  Sum_probs=31.7

Q ss_pred             hcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHH
Q 022724           68 IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE  118 (293)
Q Consensus        68 ~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~  118 (293)
                      ..|.++++.+|+|+|||......+.+.+..   |.+++|+.- .++.+++.
T Consensus      1079 ~~g~~vll~G~~GtGKT~la~~~~~ea~k~---Ge~~~Fit~-ee~~~~L~ 1125 (2050)
T 3cmu_A         1079 PMGRIVEIYGPESSGKTTLTLQVIAAAQRE---GKTCAFIDA-EHALDPIY 1125 (2050)
T ss_dssp             ETTSEEEEECCTTSSHHHHHHHHHHHHHTT---TCCEEEECT-TSCCCHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEEc-cccHHHHH
Confidence            356899999999999997666555555544   446777763 34444444

>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=90.68  E-value=0.29  Score=47.43  Aligned_cols=18  Identities=22%  Similarity=0.516  Sum_probs=15.0

Q ss_pred             CCcEEEEcCCCChhHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~   87 (293)
                      .++++++||+|+|||...
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            358999999999999543

>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=90.55  E-value=0.38  Score=41.36  Aligned_cols=19  Identities=21%  Similarity=0.434  Sum_probs=16.0

Q ss_pred             cCCcEEEEcCCCChhHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~   87 (293)
                      .+.++++.||+|+|||..+
T Consensus        50 ~~~~vll~GppGtGKT~la   68 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTLLA   68 (363)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            3568999999999999654

>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=90.55  E-value=7.3  Score=33.07  Aligned_cols=76  Identities=12%  Similarity=0.069  Sum_probs=56.5

Q ss_pred             CceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH---h-cCCcEEEeChHHHHHHHhcCCCCCCC
Q 022724          100 REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL---E-HGVHVVSGTPGRVCDMIKRKTLRTRA  175 (293)
Q Consensus       100 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~-~~~~ilV~Tp~~l~~~l~~~~~~~~~  175 (293)
                      .+.++||.++++.-+..+.+.++..    +..+..++|+.+..+..+.+   . ...+|+|+|.     . -...+++.+
T Consensus       242 ~~~~~lvf~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~-~~~Gidip~  311 (395)
T 3pey_A          242 TIGSSIIFVATKKTANVLYGKLKSE----GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTN-----V-LARGIDIPT  311 (395)
T ss_dssp             TSSEEEEECSCHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECG-----G-GSSSCCCTT
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHHhc----CCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECC-----h-hhcCCCccc
Confidence            3468999999999999999888754    56788899987765544333   2 4568999995     2 234678889


Q ss_pred             ccEEEecchh
Q 022724          176 IKLLVLDESD  185 (293)
Q Consensus       176 l~~iViDE~h  185 (293)
                      ++++|.-+..
T Consensus       312 ~~~Vi~~~~p  321 (395)
T 3pey_A          312 VSMVVNYDLP  321 (395)
T ss_dssp             EEEEEESSCC
T ss_pred             CCEEEEcCCC
Confidence            9999876654

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=90.21  E-value=0.88  Score=41.20  Aligned_cols=40  Identities=15%  Similarity=0.099  Sum_probs=25.8

Q ss_pred             HHHHHHCCCCCCcHHHHHHHH-hhhcCCcEEEEcCCCChhHHH
Q 022724           45 LRGIYQYGFEKPSAIQQRAVM-PIIKGRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        45 ~~~l~~~~~~~~~~~Q~~~~~-~i~~~~~~li~~~Tg~GKT~~   86 (293)
                      ...+.+.|.  +++.+...+. .+..|.+++++||||||||..
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            344555552  3333444333 356788999999999999953

>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=90.21  E-value=3.1  Score=38.39  Aligned_cols=82  Identities=10%  Similarity=0.135  Sum_probs=57.2

Q ss_pred             HHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHH
Q 022724           91 VCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMI  166 (293)
Q Consensus        91 ~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l  166 (293)
                      ++..+.....+.++||.|+++.-++++.+.++..    ++.+..++++.+..+..+.+    ....+|+|+|.      .
T Consensus       257 l~~~l~~~~~~~~~IVf~~sr~~~e~la~~L~~~----g~~~~~~h~~l~~~~R~~~~~~F~~g~~~VlVAT~------a  326 (591)
T 2v1x_A          257 IVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNL----GIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATV------A  326 (591)
T ss_dssp             HHHHHTTTTTTCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEECT------T
T ss_pred             HHHHHHHhccCCCeEEEeCcHHHHHHHHHHHHHC----CCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEec------h
Confidence            3344433334568999999999999999988753    67888999998766554333    24568999994      1


Q ss_pred             hcCCCCCCCccEEEec
Q 022724          167 KRKTLRTRAIKLLVLD  182 (293)
Q Consensus       167 ~~~~~~~~~l~~iViD  182 (293)
                      -...+++.+++++|.-
T Consensus       327 ~~~GID~p~V~~VI~~  342 (591)
T 2v1x_A          327 FGMGIDKPDVRFVIHH  342 (591)
T ss_dssp             SCTTCCCSCEEEEEES
T ss_pred             hhcCCCcccccEEEEe
Confidence            2345677788887743

>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=90.09  E-value=0.25  Score=43.74  Aligned_cols=19  Identities=26%  Similarity=0.648  Sum_probs=16.5

Q ss_pred             cCCcEEEEcCCCChhHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~   87 (293)
                      ...|++|.|+||+|||...
T Consensus        52 ~~~h~~i~G~tGsGKs~~~   70 (437)
T 1e9r_A           52 EPRHLLVNGATGTGKSVLL   70 (437)
T ss_dssp             GGGCEEEEECTTSSHHHHH
T ss_pred             CcceEEEECCCCCCHHHHH
Confidence            4579999999999999764

>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=89.73  E-value=0.27  Score=50.77  Aligned_cols=86  Identities=15%  Similarity=0.269  Sum_probs=54.2

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHh
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE  149 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  149 (293)
                      |+-+.+.+|.|||||...+..+-+....   +..++|+.+-.++....   +++++-+++                    
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            4679999999999997765544443333   55789999877765554   444433221                    


Q ss_pred             cCCcEEEeChHH---HHH----HHhcCCCCCCCccEEEecchhhhhc
Q 022724          150 HGVHVVSGTPGR---VCD----MIKRKTLRTRAIKLLVLDESDEMLS  189 (293)
Q Consensus       150 ~~~~ilV~Tp~~---l~~----~l~~~~~~~~~l~~iViDE~h~~~~  189 (293)
                         ++++.-|+.   .+.    +++++     .+++||||.+..+..
T Consensus      1485 ---~l~~~~p~~~e~~l~~~~~~~~s~-----~~~~vvvDsv~al~~ 1523 (1706)
T 3cmw_A         1485 ---NLLCSQPDTGEQALEICDALARSG-----AVDVIVVDSVAALTP 1523 (1706)
T ss_dssp             ---GCEEECCSSHHHHHHHHHHHHHHT-----CCSEEEESCSTTCCC
T ss_pred             ---HeEEeCCCcHHHHHHHHHHHHHcC-----CCCEEEEccHHhCCc
Confidence               355555532   222    33333     367899999988753

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=89.72  E-value=0.16  Score=44.37  Aligned_cols=54  Identities=22%  Similarity=0.334  Sum_probs=33.2

Q ss_pred             cccCcccCCCCHHHHHHHHHCC---CCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHH
Q 022724           31 AITSFDAMGIKDDLLRGIYQYG---FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        31 ~~~~f~~~~l~~~i~~~l~~~~---~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~   87 (293)
                      |..+|++.+=-++..+.+++.=   +..|.-++..-   +...+.+++.||+|+|||+.+
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            4568999876667777776531   11222222111   223478999999999999653

>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=89.61  E-value=0.11  Score=43.52  Aligned_cols=54  Identities=17%  Similarity=0.329  Sum_probs=31.7

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHh--hhcCCcEEEEcCCCChhHHHH
Q 022724           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMP--IIKGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        32 ~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~--i~~~~~~li~~~Tg~GKT~~~   87 (293)
                      ..+|+++.-.+.+.+.+.+. ...|.... +.+..  +..++.+++.||+|+|||...
T Consensus        11 ~~~~~di~G~~~~~~~l~~~-v~~~~~~~-~~~~~~~~~~~~~vLL~Gp~GtGKT~la   66 (301)
T 3cf0_A           11 QVTWEDIGGLEDVKRELQEL-VQYPVEHP-DKFLKFGMTPSKGVLFYGPPGCGKTLLA   66 (301)
T ss_dssp             CCCGGGSCSCHHHHHHHHHH-HHHHHHCH-HHHHHHCCCCCSEEEEECSSSSSHHHHH
T ss_pred             CCCHHHhCCHHHHHHHHHHH-HHHHhhCH-HHHHHcCCCCCceEEEECCCCcCHHHHH
Confidence            46788887666666666542 11111000 11111  234678999999999999654

>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=89.57  E-value=0.58  Score=41.24  Aligned_cols=28  Identities=14%  Similarity=0.296  Sum_probs=19.2

Q ss_pred             HHHHHHHhhh--cCCcEEEEcCCCChhHHH
Q 022724           59 IQQRAVMPII--KGRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        59 ~Q~~~~~~i~--~~~~~li~~~Tg~GKT~~   86 (293)
                      -+..++..+.  .|..++|.||||||||..
T Consensus       154 ~~~~~L~~l~~~~ggii~I~GpnGSGKTTl  183 (418)
T 1p9r_A          154 HNHDNFRRLIKRPHGIILVTGPTGSGKSTT  183 (418)
T ss_dssp             HHHHHHHHHHTSSSEEEEEECSTTSCHHHH
T ss_pred             HHHHHHHHHHHhcCCeEEEECCCCCCHHHH
Confidence            3444555444  345689999999999953

>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=89.36  E-value=1.4  Score=38.06  Aligned_cols=73  Identities=16%  Similarity=0.130  Sum_probs=54.5

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHHhcCCCCCCCc
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l~~~~~~~~~l  176 (293)
                      +.++||.|+++.-+..+.+.+...    +..+..++|+.+..+....+    ....+|+|+|.     . -...+++.++
T Consensus       266 ~~~~lvf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~-~~~Gidip~~  335 (412)
T 3fht_A          266 IAQAMIFCHTRKTASWLAAELSKE----GHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTN-----V-CARGIDVEQV  335 (412)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECG-----G-GTSSCCCTTE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhC----CCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcC-----c-cccCCCccCC
Confidence            358999999999999999988764    56788899988766554433    24568999995     2 2346788899


Q ss_pred             cEEEecc
Q 022724          177 KLLVLDE  183 (293)
Q Consensus       177 ~~iViDE  183 (293)
                      +++|.-+
T Consensus       336 ~~Vi~~~  342 (412)
T 3fht_A          336 SVVINFD  342 (412)
T ss_dssp             EEEEESS
T ss_pred             CEEEEEC
Confidence            9988533

>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=89.34  E-value=0.21  Score=50.71  Aligned_cols=40  Identities=20%  Similarity=0.292  Sum_probs=28.0

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      ++-+.+|+||+-.-+|..-...+...++...+++-+|..+
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            4557899999987777766777777777765555555543

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=89.33  E-value=0.49  Score=37.32  Aligned_cols=30  Identities=27%  Similarity=0.244  Sum_probs=25.4

Q ss_pred             cHHHHHHHHhhhcCCcEEEEcCCCChhHHH
Q 022724           57 SAIQQRAVMPIIKGRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        57 ~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~   86 (293)
                      +.-|..++..+..|.-+.+.||+|+|||..
T Consensus         9 ~~g~~~~l~~i~~Ge~~~liG~nGsGKSTL   38 (208)
T 3b85_A            9 TLGQKHYVDAIDTNTIVFGLGPAGSGKTYL   38 (208)
T ss_dssp             SHHHHHHHHHHHHCSEEEEECCTTSSTTHH
T ss_pred             CHhHHHHHHhccCCCEEEEECCCCCCHHHH
Confidence            455677888888999999999999999954

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=89.28  E-value=0.16  Score=45.20  Aligned_cols=55  Identities=16%  Similarity=0.209  Sum_probs=34.3

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhh--hcCCcEEEEcCCCChhHHHH
Q 022724           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPI--IKGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        31 ~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i--~~~~~~li~~~Tg~GKT~~~   87 (293)
                      |..+|++.+=-+++.+.+++.= ..|.. ..+.+..+  ...+.+++.||+|+|||+.+
T Consensus       204 P~vt~~DIgGl~~~k~~L~e~V-~~pl~-~pe~f~~~Gi~pprGILLyGPPGTGKTlLA  260 (467)
T 4b4t_H          204 PDVTYSDVGGCKDQIEKLREVV-ELPLL-SPERFATLGIDPPKGILLYGPPGTGKTLCA  260 (467)
T ss_dssp             CSCCCSSCTTCHHHHHHHHHHT-HHHHH-CHHHHHHHTCCCCSEEEECSCTTSSHHHHH
T ss_pred             CCCCHHHhccHHHHHHHHHHHH-HHHhc-CHHHHHHCCCCCCCceEeeCCCCCcHHHHH
Confidence            4467999887777777777631 11110 11222222  24578999999999999653

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=89.26  E-value=0.53  Score=42.53  Aligned_cols=42  Identities=17%  Similarity=0.294  Sum_probs=27.4

Q ss_pred             HHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHH
Q 022724           44 LLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        44 i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~   86 (293)
                      +.+.+.+ .+.--...=..+.-.+..+.++++.||+|+|||..
T Consensus        16 l~~~l~~-~ivGq~~~i~~l~~al~~~~~VLL~GpPGtGKT~L   57 (500)
T 3nbx_X           16 LSSSLEK-GLYERSHAIRLCLLAALSGESVFLLGPPGIAKSLI   57 (500)
T ss_dssp             HHHHHHT-TCSSCHHHHHHHHHHHHHTCEEEEECCSSSSHHHH
T ss_pred             HHHHHHh-hhHHHHHHHHHHHHHHhcCCeeEeecCchHHHHHH
Confidence            3444443 33323333345555667889999999999999954

>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=89.06  E-value=2.9  Score=35.37  Aligned_cols=52  Identities=21%  Similarity=0.394  Sum_probs=29.0

Q ss_pred             ccEEEecchhhhh-ccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhc
Q 022724          176 IKLLVLDESDEML-SRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKF  227 (293)
Q Consensus       176 l~~iViDE~h~~~-~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~  227 (293)
                      .+++++|.+-... +......+..+.+.+.+...++.+.++...+..+.++.+
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            3566777765432 123344455555555556667777777766555555443

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=88.93  E-value=0.14  Score=45.42  Aligned_cols=54  Identities=24%  Similarity=0.377  Sum_probs=32.6

Q ss_pred             cccCcccCCCCHHHHHHHHHCC---CCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHH
Q 022724           31 AITSFDAMGIKDDLLRGIYQYG---FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        31 ~~~~f~~~~l~~~i~~~l~~~~---~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~   87 (293)
                      |..+|++.+=-++..+.+.+.=   +..|.-++..-   +...+.+++.||+|+|||+.+
T Consensus       176 p~v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g---~~~prGvLL~GPPGtGKTllA  232 (437)
T 4b4t_L          176 GEITFDGIGGLTEQIRELREVIELPLKNPEIFQRVG---IKPPKGVLLYGPPGTGKTLLA  232 (437)
T ss_dssp             CSSCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHC---CCCCCEEEEESCTTSSHHHHH
T ss_pred             CCCChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCCeEEEECCCCCcHHHHH
Confidence            4567999876666666665531   11222221111   223478999999999999653

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=88.93  E-value=0.38  Score=36.51  Aligned_cols=18  Identities=22%  Similarity=0.516  Sum_probs=15.2

Q ss_pred             CCcEEEEcCCCChhHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~   87 (293)
                      ++++++.||+|+|||...
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            368999999999999543

>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=88.91  E-value=7.2  Score=36.43  Aligned_cols=77  Identities=16%  Similarity=0.228  Sum_probs=58.5

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH---h-cCCcEEEeChHHHHHHHhcCCCCCCCc
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL---E-HGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~-~~~~ilV~Tp~~l~~~l~~~~~~~~~l  176 (293)
                      +.++||.|+++.-++.+.+.++..    ++++..++++.+..+..+.+   . ...+|+|+|.     . -...+++.++
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-----L-LREGLDIPEV  514 (661)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESC-----C-CSTTCCCTTE
T ss_pred             CCeEEEEECCHHHHHHHHHHHHhc----CCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecc-----h-hhCCcccCCC
Confidence            458999999999999998887764    67788888887655544432   2 4578999995     2 2456788899


Q ss_pred             cEEEecchhhh
Q 022724          177 KLLVLDESDEM  187 (293)
Q Consensus       177 ~~iViDE~h~~  187 (293)
                      +++|+-|++..
T Consensus       515 ~lVi~~d~d~~  525 (661)
T 2d7d_A          515 SLVAILDADKE  525 (661)
T ss_dssp             EEEEETTTTCC
T ss_pred             CEEEEeCcccc
Confidence            99999998764

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=88.89  E-value=0.22  Score=38.17  Aligned_cols=18  Identities=11%  Similarity=0.381  Sum_probs=15.5

Q ss_pred             cCCcEEEEcCCCChhHHH
Q 022724           69 KGRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~   86 (293)
                      .|+-++++||+|+|||..
T Consensus         4 ~g~~i~i~GpsGsGKSTL   21 (180)
T 1kgd_A            4 MRKTLVLLGAHGVGRRHI   21 (180)
T ss_dssp             CCCEEEEECCTTSSHHHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            567899999999999954

>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=88.83  E-value=0.52  Score=45.09  Aligned_cols=16  Identities=38%  Similarity=0.632  Sum_probs=14.4

Q ss_pred             CcEEEEcCCCChhHHH
Q 022724           71 RDVIAQAQSGTGKTSM   86 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~   86 (293)
                      +.+++.||.|+|||+.
T Consensus       239 ~GILL~GPPGTGKT~L  254 (806)
T 3cf2_A          239 RGILLYGPPGTGKTLI  254 (806)
T ss_dssp             CEEEEECCTTSCHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            6899999999999954

>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=88.71  E-value=0.44  Score=40.54  Aligned_cols=19  Identities=42%  Similarity=0.712  Sum_probs=16.9

Q ss_pred             hhcCCcEEEEcCCCChhHH
Q 022724           67 IIKGRDVIAQAQSGTGKTS   85 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~   85 (293)
                      +..|..++++||||+|||.
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            4478999999999999995

>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=88.58  E-value=2.2  Score=36.70  Aligned_cols=73  Identities=11%  Similarity=0.102  Sum_probs=53.3

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHHhcCCCCCCCc
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l~~~~~~~~~l  176 (293)
                      +.++||.|+++.-+..+.+.++..    ++.+..++|+.+..+....+    ....+|+|+|.     . -...+++..+
T Consensus       258 ~~~~lVf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~-----~-~~~Gidip~~  327 (400)
T 1s2m_A          258 INQAIIFCNSTNRVELLAKKITDL----GYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSD-----L-LTRGIDIQAV  327 (400)
T ss_dssp             CSEEEEECSSHHHHHHHHHHHHHH----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESS-----C-SSSSCCCTTE
T ss_pred             CCcEEEEEecHHHHHHHHHHHHhc----CCCeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC-----c-cccCCCccCC
Confidence            358999999999999999888764    56788888887765544333    24568999994     2 2345778888


Q ss_pred             cEEEecc
Q 022724          177 KLLVLDE  183 (293)
Q Consensus       177 ~~iViDE  183 (293)
                      +++|.-+
T Consensus       328 ~~Vi~~~  334 (400)
T 1s2m_A          328 NVVINFD  334 (400)
T ss_dssp             EEEEESS
T ss_pred             CEEEEeC
Confidence            8887543

>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=88.48  E-value=3.2  Score=36.49  Aligned_cols=70  Identities=13%  Similarity=0.180  Sum_probs=52.8

Q ss_pred             eEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHHhcCCCCCCCccE
Q 022724          103 QALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAIKL  178 (293)
Q Consensus       103 ~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~  178 (293)
                      ++||.|+++.-+..+.+.+...    ++.+..++|+.+..+....+    ....+|+|+|.      +-...+++.++++
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            4999999999999998887653    67888899997766554433    24578999996      2334678889998


Q ss_pred             EEec
Q 022724          179 LVLD  182 (293)
Q Consensus       179 iViD  182 (293)
                      +|.-
T Consensus       372 VI~~  375 (434)
T 2db3_A          372 VINY  375 (434)
T ss_dssp             EEES
T ss_pred             EEEE
Confidence            8753

>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=88.20  E-value=0.087  Score=40.09  Aligned_cols=75  Identities=12%  Similarity=0.139  Sum_probs=49.7

Q ss_pred             CceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHHhcCCCCCCC
Q 022724          100 REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRA  175 (293)
Q Consensus       100 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l~~~~~~~~~  175 (293)
                      .+.++||.|+++.-+..+.+.++..    ++.+..++|+.+..+....+    ....+|+|+|. .+.     ..+++..
T Consensus        29 ~~~~~iVF~~~~~~~~~l~~~L~~~----~~~~~~~~g~~~~~~r~~~~~~f~~g~~~vLvaT~-~~~-----~Gid~~~   98 (170)
T 2yjt_D           29 EATRSIVFVRKRERVHELANWLREA----GINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATD-VAA-----RGIDIPD   98 (170)
Confidence            3458999999999999888877653    56777888886654443332    13457999983 222     2456667


Q ss_pred             ccEEEecch
Q 022724          176 IKLLVLDES  184 (293)
Q Consensus       176 l~~iViDE~  184 (293)
                      ++++|.-+.
T Consensus        99 ~~~Vi~~~~  107 (170)
T 2yjt_D           99 VSHVFNFDM  107 (170)
Confidence            777765443

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=88.36  E-value=0.18  Score=44.62  Aligned_cols=54  Identities=22%  Similarity=0.240  Sum_probs=32.2

Q ss_pred             cccCcccCCCCHHHHHHHHHC---CCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHH
Q 022724           31 AITSFDAMGIKDDLLRGIYQY---GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        31 ~~~~f~~~~l~~~i~~~l~~~---~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~   87 (293)
                      |..+|++.+=-.++.+.+.+.   -+..|.-++..-   +...+.+++.||+|+|||+.+
T Consensus       167 p~v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g---~~~prGiLL~GPPGtGKT~la  223 (428)
T 4b4t_K          167 PDVTYADVGGLDMQKQEIREAVELPLVQADLYEQIG---IDPPRGVLLYGPPGTGKTMLV  223 (428)
T ss_dssp             CSCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHC---CCCCCEEEEESCTTTTHHHHH
T ss_pred             CCCCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCceEEEECCCCCCHHHHH
Confidence            346889987666666666542   111222222111   223478999999999999653

>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=88.28  E-value=2.2  Score=35.97  Aligned_cols=73  Identities=12%  Similarity=0.202  Sum_probs=52.5

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHHhcCCCCCCCc
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l~~~~~~~~~l  176 (293)
                      +.++||.|+++.-+..+.+.++..    +..+..++|+.+..+....+    ....+|+|+|. .+..     .+++.++
T Consensus       238 ~~~~lvf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~-~~~~-----Gid~~~~  307 (367)
T 1hv8_A          238 EFYGLVFCKTKRDTKELASMLRDI----GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATD-VMSR-----GIDVNDL  307 (367)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECT-THHH-----HCCCSCC
T ss_pred             CCcEEEEECCHHHHHHHHHHHHhc----CCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECC-hhhc-----CCCcccC
Confidence            457999999999999999888764    56788889887765544333    24568999995 2222     4667788


Q ss_pred             cEEEecc
Q 022724          177 KLLVLDE  183 (293)
Q Consensus       177 ~~iViDE  183 (293)
                      +++|.-+
T Consensus       308 ~~Vi~~~  314 (367)
T 1hv8_A          308 NCVINYH  314 (367)
T ss_dssp             SEEEESS
T ss_pred             CEEEEec
Confidence            8887644

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=88.21  E-value=0.53  Score=40.55  Aligned_cols=20  Identities=25%  Similarity=0.577  Sum_probs=17.4

Q ss_pred             hhcCCcEEEEcCCCChhHHH
Q 022724           67 IIKGRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~~   86 (293)
                      +..|..++++||||+|||..
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            45789999999999999953

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=88.18  E-value=0.26  Score=38.44  Aligned_cols=19  Identities=21%  Similarity=0.237  Sum_probs=16.5

Q ss_pred             cCCcEEEEcCCCChhHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~   87 (293)
                      .++.++++|++|+|||...
T Consensus        24 ~~~~i~l~G~~GsGKsTl~   42 (199)
T 3vaa_A           24 AMVRIFLTGYMGAGKTTLG   42 (199)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHH
Confidence            5778999999999999654

>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=88.06  E-value=1.1  Score=48.55  Aligned_cols=67  Identities=15%  Similarity=0.094  Sum_probs=40.4

Q ss_pred             CHHHHHHHHHCCCCCCcHHHH-H---HHHhhhcCCcEEEEcCCCChhHHHHHHH--HHhhhccCCCceeEEEEcCC
Q 022724           41 KDDLLRGIYQYGFEKPSAIQQ-R---AVMPIIKGRDVIAQAQSGTGKTSMIALT--VCQTVDTSSREVQALILSPT  110 (293)
Q Consensus        41 ~~~i~~~l~~~~~~~~~~~Q~-~---~~~~i~~~~~~li~~~Tg~GKT~~~~~~--~~~~l~~~~~~~~~lil~P~  110 (293)
                      ...+.+.+.+.|+. +++.+. .   ....+..+..++++||||+|||.++-..  ++..+..  ...+..++-|.
T Consensus       891 ~~~i~~~~~~~~l~-~~~~~~~K~~ql~e~~~~r~gvmlvGptgsGKTt~~~~La~al~~l~~--~~~~~~~inpk  963 (2695)
T 4akg_A          891 VQCLKDAGQRSGFS-MSEEFLKKCMQFYYMQKTQQALILVGKAGCGKTATWKTVIDAMAIFDG--HANVVYVIDTK  963 (2695)
T ss_dssp             HHHHHHHHHHHTCC-CCHHHHHHHHHHHHHHHHCSEEEEECSTTSSHHHHHHHHHHHHHHHTC--CEEEEEEECTT
T ss_pred             HHHHHHHHHHcCCc-ccHHHHHHHHHHHHHHHhcceEEEECCCCCCHHHHHHHHHHHHHHhcC--CCceEEEeCCC
Confidence            34566667777766 666553 2   3334456788999999999999876432  2333322  23345555564

>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=88.05  E-value=2.1  Score=36.59  Aligned_cols=74  Identities=11%  Similarity=0.132  Sum_probs=54.7

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH---h-cCCcEEEeChHHHHHHHhcCCCCCCCc
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL---E-HGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~-~~~~ilV~Tp~~l~~~l~~~~~~~~~l  176 (293)
                      +.++||.++++.-+..+.+.++..    ++.+..++|+.+..+....+   . ....|+|+|.     . -...+++..+
T Consensus       250 ~~~~lvf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~-----~-~~~Gidi~~~  319 (391)
T 1xti_A          250 FNQVVIFVKSVQRCIALAQLLVEQ----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATN-----L-FGRGMDIERV  319 (391)
T ss_dssp             CSEEEEECSCHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESC-----C-CSSCBCCTTE
T ss_pred             CCcEEEEeCcHHHHHHHHHHHHhC----CCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECC-----h-hhcCCCcccC
Confidence            458999999999999999887753    67788889887765544333   2 3568999994     1 2346788889


Q ss_pred             cEEEecch
Q 022724          177 KLLVLDES  184 (293)
Q Consensus       177 ~~iViDE~  184 (293)
                      +++|.-+.
T Consensus       320 ~~Vi~~~~  327 (391)
T 1xti_A          320 NIAFNYDM  327 (391)
T ss_dssp             EEEEESSC
T ss_pred             CEEEEeCC
Confidence            99887554

>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=88.03  E-value=1.8  Score=38.03  Aligned_cols=96  Identities=19%  Similarity=0.186  Sum_probs=59.1

Q ss_pred             CCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEC--------CcchHHHHHHH--
Q 022724           79 SGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVG--------GKSVGEDIRKL--  148 (293)
Q Consensus        79 Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~--  148 (293)
                      ..++|... +.-++........+.++||.++++.-+..+.+.++..    ++++..++|        +.+..++...+  
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            44556533 3334443321123568999999999999998888765    677888888        54443333222  


Q ss_pred             --hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchh
Q 022724          149 --EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESD  185 (293)
Q Consensus       149 --~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h  185 (293)
                        ....+|+|+|.     .+ ...+++..++++|+-+..
T Consensus       415 F~~~~~~vLv~T~-----~~-~~Gldl~~~~~Vi~~d~~  447 (494)
T 1wp9_A          415 FARGEFNVLVATS-----VG-EEGLDVPEVDLVVFYEPV  447 (494)
T ss_dssp             HHHTSCSEEEECG-----GG-GGGGGSTTCCEEEESSCC
T ss_pred             HhcCCceEEEECC-----cc-ccCCCchhCCEEEEeCCC
Confidence              24568999994     22 235678888888866543

>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=87.88  E-value=1.1  Score=36.30  Aligned_cols=19  Identities=26%  Similarity=0.420  Sum_probs=16.1

Q ss_pred             cCCcEEEEcCCCChhHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~   87 (293)
                      .+.++++.||+|+|||...
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            4679999999999999543

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=87.81  E-value=0.27  Score=40.31  Aligned_cols=20  Identities=20%  Similarity=0.305  Sum_probs=16.9

Q ss_pred             hhcCCcEEEEcCCCChhHHH
Q 022724           67 IIKGRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~~   86 (293)
                      +..|.-++++||||+|||..
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            45678899999999999954

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=87.68  E-value=0.3  Score=41.33  Aligned_cols=26  Identities=23%  Similarity=0.413  Sum_probs=19.9

Q ss_pred             HHHHhhhcCCcEEEEcCCCChhHHHH
Q 022724           62 RAVMPIIKGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        62 ~~~~~i~~~~~~li~~~Tg~GKT~~~   87 (293)
                      .+...+..++++++.||+|+|||...
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            33344557899999999999999543

>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=87.65  E-value=0.52  Score=41.00  Aligned_cols=43  Identities=16%  Similarity=0.182  Sum_probs=27.5

Q ss_pred             CccEEEecchhhhhcc---ccHHHHHHHHhhCCC-CccEEEEEeecC
Q 022724          175 AIKLLVLDESDEMLSR---GFKDQIYDVYRYLPP-DLQVVLISATLP  217 (293)
Q Consensus       175 ~l~~iViDE~h~~~~~---~~~~~~~~i~~~l~~-~~q~v~~SAt~~  217 (293)
                      .-.++|+||+|.++..   .....+..+.+..++ +.-+++.|-.+.
T Consensus       262 ~~~~i~iDEa~~~~~~~~~~~~~~l~~~~~~~Rk~g~~~~~~tQ~~~  308 (392)
T 4ag6_A          262 ERTVLVVDEAWMLVDPQTPQAIAFLRDTSKRIRKYNGSLIVISQNVI  308 (392)
T ss_dssp             TTCEEEETTGGGGCCTTCTHHHHHHHHHHHHGGGGTCEEEEEESCGG
T ss_pred             ccEEEEEecHHHHhCcCchHHHHHHHHHHHHhhhhCeEEEEEcCCHH
Confidence            4578999999999852   244556666666553 455666655553

>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=87.59  E-value=2.3  Score=36.77  Aligned_cols=72  Identities=15%  Similarity=0.159  Sum_probs=53.3

Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHHhcCCCCCCCcc
Q 022724          102 VQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAIK  177 (293)
Q Consensus       102 ~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~  177 (293)
                      .++||.|+++.-+..+.+.++..    ++.+..++|+.+..+....+    ....+|+|+|.     . -...+++.+++
T Consensus       277 ~~~lVf~~~~~~~~~l~~~L~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~-~~~Gidi~~v~  346 (410)
T 2j0s_A          277 TQAVIFCNTKRKVDWLTEKMREA----NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTD-----V-WARGLDVPQVS  346 (410)
T ss_dssp             SEEEEECSSHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECG-----G-GSSSCCCTTEE
T ss_pred             CcEEEEEcCHHHHHHHHHHHHhC----CCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECC-----h-hhCcCCcccCC
Confidence            48999999999999998887753    56788899987765544333    24568999995     2 23467888899


Q ss_pred             EEEecc
Q 022724          178 LLVLDE  183 (293)
Q Consensus       178 ~iViDE  183 (293)
                      ++|.-+
T Consensus       347 ~Vi~~~  352 (410)
T 2j0s_A          347 LIINYD  352 (410)
T ss_dssp             EEEESS
T ss_pred             EEEEEC
Confidence            888643

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=87.43  E-value=0.11  Score=44.22  Aligned_cols=50  Identities=12%  Similarity=0.127  Sum_probs=31.2

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhh-----cCCcEEEEcCCCChhHHHH
Q 022724           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII-----KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        32 ~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~-----~~~~~li~~~Tg~GKT~~~   87 (293)
                      ..+|++++=.+.+.+.+.+.- .  .|..   .+.+.     ..+.+++.||+|+|||..+
T Consensus         8 ~~~~~di~G~~~~k~~l~~~v-~--~p~~---~~~~~~~~~~~~~~iLL~GppGtGKT~la   62 (322)
T 1xwi_A            8 NVKWSDVAGLEGAKEALKEAV-I--LPIK---FPHLFTGKRTPWRGILLFGPPGTGKSYLA   62 (322)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHH-H--HHHH---CGGGSCTTCCCCSEEEEESSSSSCHHHHH
T ss_pred             CCCHHHhcCHHHHHHHHHHHH-H--HHHh---CHHHHhCCCCCCceEEEECCCCccHHHHH
Confidence            467898876777777765421 0  1111   12222     2368999999999999544

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=87.37  E-value=0.3  Score=38.15  Aligned_cols=19  Identities=32%  Similarity=0.613  Sum_probs=14.8

Q ss_pred             cCCcEEEEcCCCChhHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~   87 (293)
                      .|+-++++||+|+|||...
T Consensus         3 ~g~~i~lvGpsGaGKSTLl   21 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTLL   21 (198)
T ss_dssp             --CCEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4678999999999999543

>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=87.30  E-value=2.7  Score=38.06  Aligned_cols=73  Identities=14%  Similarity=0.124  Sum_probs=53.5

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHHhcCCCCCCCc
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l~~~~~~~~~l  176 (293)
                      +.++||.|+++.-++.+.+.++..    ++.+..++++.+..+.....    .+..+|+|+|.      .-...+++.++
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            457999999999999999988764    67888899988765543332    24578999996      12345677888


Q ss_pred             cEEEecc
Q 022724          177 KLLVLDE  183 (293)
Q Consensus       177 ~~iViDE  183 (293)
                      +++|.-+
T Consensus       306 ~~VI~~~  312 (523)
T 1oyw_A          306 RFVVHFD  312 (523)
T ss_dssp             CEEEESS
T ss_pred             cEEEEEC
Confidence            8887533

>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=87.29  E-value=4.4  Score=33.64  Aligned_cols=18  Identities=22%  Similarity=0.198  Sum_probs=14.0

Q ss_pred             CCcEEEEcCCCChhHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~   87 (293)
                      ++-+.+++++|+|||...
T Consensus        98 ~~~i~i~g~~G~GKTT~~  115 (295)
T 1ls1_A           98 RNLWFLVGLQGSGKTTTA  115 (295)
T ss_dssp             SEEEEEECCTTTTHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            446778899999999543

>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=87.27  E-value=1.4  Score=36.54  Aligned_cols=18  Identities=22%  Similarity=0.542  Sum_probs=15.5

Q ss_pred             CCcEEEEcCCCChhHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~   87 (293)
                      ..++++.||+|+|||...
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            578999999999999544

>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=87.22  E-value=0.31  Score=38.29  Aligned_cols=19  Identities=26%  Similarity=0.471  Sum_probs=15.7

Q ss_pred             cCCcEEEEcCCCChhHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~   87 (293)
                      .|+-++++||+|+|||...
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            4677999999999999543

>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=87.00  E-value=0.29  Score=37.32  Aligned_cols=21  Identities=19%  Similarity=0.338  Sum_probs=17.1

Q ss_pred             hcCCcEEEEcCCCChhHHHHH
Q 022724           68 IKGRDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        68 ~~~~~~li~~~Tg~GKT~~~~   88 (293)
                      .+++.++++|++|+|||...-
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            456789999999999996543

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=86.86  E-value=0.13  Score=42.60  Aligned_cols=54  Identities=15%  Similarity=0.231  Sum_probs=27.9

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhh--cCCcEEEEcCCCChhHHH
Q 022724           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII--KGRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        31 ~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~--~~~~~li~~~Tg~GKT~~   86 (293)
                      +..+|++++-.+++.+.+.+. +..|.. ..+++..+.  -.+.+++.||+|+|||..
T Consensus         5 ~~~~~~di~g~~~~~~~l~~~-i~~~~~-~~~~l~~~~l~~~~GvlL~Gp~GtGKTtL   60 (274)
T 2x8a_A            5 PNVTWADIGALEDIREELTMA-ILAPVR-NPDQFKALGLVTPAGVLLAGPPGCGKTLL   60 (274)
T ss_dssp             -------CCHHHHHHHHHHHH-HTHHHH-SHHHHHHTTCCCCSEEEEESSTTSCHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHH-HHHHhh-CHHHHHHcCCCCCCeEEEECCCCCcHHHH
Confidence            346789988777777777653 111111 122333321  234599999999999954

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=86.82  E-value=0.33  Score=37.10  Aligned_cols=19  Identities=26%  Similarity=0.253  Sum_probs=15.8

Q ss_pred             CCcEEEEcCCCChhHHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~   88 (293)
                      ++.++++|++|+|||...-
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            5689999999999996543

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=86.75  E-value=0.31  Score=38.07  Aligned_cols=21  Identities=24%  Similarity=0.430  Sum_probs=17.6

Q ss_pred             hhcCCcEEEEcCCCChhHHHH
Q 022724           67 IIKGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~~~   87 (293)
                      ...|+-++++||+|+|||...
T Consensus         9 ~~~~~~i~l~G~sGsGKsTl~   29 (204)
T 2qor_A            9 MARIPPLVVCGPSGVGKGTLI   29 (204)
T ss_dssp             CCCCCCEEEECCTTSCHHHHH
T ss_pred             cccCCEEEEECCCCCCHHHHH
Confidence            457889999999999999643

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=86.74  E-value=0.41  Score=38.37  Aligned_cols=52  Identities=19%  Similarity=0.308  Sum_probs=29.1

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA  123 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~  123 (293)
                      .|.-+++.|++|+|||...+-.+.+.....  +..++|+.-. .-..++..++..
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            356799999999999954433333333222  2246666533 224455555443

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=86.73  E-value=0.35  Score=41.22  Aligned_cols=18  Identities=22%  Similarity=0.438  Sum_probs=14.7

Q ss_pred             CCcEEEEcCCCChhHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~   87 (293)
                      ++.++|+||||+|||...
T Consensus        40 ~~lIvI~GPTgsGKTtLa   57 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLS   57 (339)
T ss_dssp             CEEEEEECSTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            346899999999999543

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=86.66  E-value=2.4  Score=46.69  Aligned_cols=75  Identities=16%  Similarity=0.135  Sum_probs=43.7

Q ss_pred             CHHHHHHHHHCCCCCCcHHHH-HHHH---hhhcCCcEEEEcCCCChhHHHHHH--HHHhhhccCCCceeEEEEcCCHHHH
Q 022724           41 KDDLLRGIYQYGFEKPSAIQQ-RAVM---PIIKGRDVIAQAQSGTGKTSMIAL--TVCQTVDTSSREVQALILSPTRELA  114 (293)
Q Consensus        41 ~~~i~~~l~~~~~~~~~~~Q~-~~~~---~i~~~~~~li~~~Tg~GKT~~~~~--~~~~~l~~~~~~~~~lil~P~~~l~  114 (293)
                      ...+.+.+.+.|+. |.+.+. +++.   .+..+..++++||||+|||.++-.  -++..+.  .......++-|----.
T Consensus       874 ~~ai~~~~~~~~L~-~~~~~v~KviQLye~~~vRhGvmlVGp~gsGKTt~~~~L~~al~~l~--~~~~~~~~iNPKait~  950 (3245)
T 3vkg_A          874 RKKIQEIAKQRHLV-TKQEWVEKILQLHQILNINHGVMMVGPSGGGKTTSWEVYLEAIEQVD--NIKSEAHVMDPKAITK  950 (3245)
T ss_dssp             HHHHHHHHHHTTCC-CCHHHHHHHHHHHHHHTTCSEEEEECSSSSSHHHHHHHHHHHHTTTT--TCEEEEEEECTTTSCH
T ss_pred             HHHHHHHHHHcCCc-cCHHHHHHHHHHHHHHHheeeEEEECCCCCCHHHHHHHHHHHHHHhh--CCCceEEEECCCCCch
Confidence            34566666778876 555554 3333   344567899999999999988642  2222222  1233455666744334


Q ss_pred             HHHH
Q 022724          115 TQTE  118 (293)
Q Consensus       115 ~q~~  118 (293)
                      .|++
T Consensus       951 ~eLy  954 (3245)
T 3vkg_A          951 DQLF  954 (3245)
T ss_dssp             HHHH
T ss_pred             hhhc
Confidence            4443

>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=86.38  E-value=0.37  Score=36.52  Aligned_cols=18  Identities=28%  Similarity=0.505  Sum_probs=15.0

Q ss_pred             CCcEEEEcCCCChhHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~   87 (293)
                      ++.++++|++|+|||...
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            467899999999999654

>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=86.32  E-value=0.97  Score=40.88  Aligned_cols=19  Identities=16%  Similarity=0.354  Sum_probs=16.2

Q ss_pred             cCCcEEEEcCCCChhHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~   87 (293)
                      ++.+++|.|+||||||.+.
T Consensus       166 ~~pHlLIaG~TGSGKSt~L  184 (512)
T 2ius_A          166 KMPHLLVAGTTGSGASVGV  184 (512)
T ss_dssp             GSCSEEEECCTTSSHHHHH
T ss_pred             cCceEEEECCCCCCHHHHH
Confidence            4579999999999999654

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=86.31  E-value=0.49  Score=40.75  Aligned_cols=18  Identities=22%  Similarity=0.405  Sum_probs=15.0

Q ss_pred             cCCcEEEEcCCCChhHHH
Q 022724           69 KGRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~   86 (293)
                      .+..++++||||||||..
T Consensus       122 ~~g~i~I~GptGSGKTTl  139 (356)
T 3jvv_A          122 PRGLVLVTGPTGSGKSTT  139 (356)
T ss_dssp             SSEEEEEECSTTSCHHHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            455899999999999943

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=86.26  E-value=0.34  Score=37.67  Aligned_cols=20  Identities=30%  Similarity=0.411  Sum_probs=16.6

Q ss_pred             hcCCcEEEEcCCCChhHHHH
Q 022724           68 IKGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        68 ~~~~~~li~~~Tg~GKT~~~   87 (293)
                      ..|.-++++||+|||||...
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            45778999999999999543

>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=86.14  E-value=1.4  Score=36.77  Aligned_cols=19  Identities=26%  Similarity=0.536  Sum_probs=15.4

Q ss_pred             CCcEEEEcCCCChhHHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~   88 (293)
                      ++.++++||+|+|||....
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            5578999999999996543

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=86.07  E-value=0.22  Score=43.89  Aligned_cols=54  Identities=22%  Similarity=0.337  Sum_probs=33.2

Q ss_pred             cccCcccCCCCHHHHHHHHHC---CCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHH
Q 022724           31 AITSFDAMGIKDDLLRGIYQY---GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        31 ~~~~f~~~~l~~~i~~~l~~~---~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~   87 (293)
                      +..+|++.+=-++..+.+.+.   -+..|.-++..-   +...+.+++.||+|+|||+.+
T Consensus       177 p~v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~G---i~~prGvLLyGPPGTGKTlLA  233 (437)
T 4b4t_I          177 PTESYSDIGGLESQIQEIKESVELPLTHPELYEEMG---IKPPKGVILYGAPGTGKTLLA  233 (437)
T ss_dssp             CCCCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHT---CCCCSEEEEESSTTTTHHHHH
T ss_pred             CCCcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCCCCceECCCCchHHHHH
Confidence            457899997555666666542   122333332221   123478999999999999643

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=86.01  E-value=0.26  Score=37.89  Aligned_cols=20  Identities=20%  Similarity=0.503  Sum_probs=16.6

Q ss_pred             hhcCCcEEEEcCCCChhHHH
Q 022724           67 IIKGRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~~   86 (293)
                      +.+|.-+++.||+|+|||..
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            44677899999999999954

>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=85.95  E-value=1.5  Score=44.06  Aligned_cols=53  Identities=21%  Similarity=0.152  Sum_probs=41.1

Q ss_pred             cEEEEcCCCChhHHHHHHHHHhhhccC---------CCceeEEEEcCCHHHHHHHHHHHHHh
Q 022724           72 DVIAQAQSGTGKTSMIALTVCQTVDTS---------SREVQALILSPTRELATQTEKVILAI  124 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~~~~~~l~~~---------~~~~~~lil~P~~~l~~q~~~~~~~~  124 (293)
                      ..+|.|+.|||||.+..--++..+...         -...++|+|+=|++-+.++.+++...
T Consensus        18 ~~lV~AsAGSGKT~~L~~r~lrLll~~g~~~~~~~~~~~~~ILvvTFT~aAA~EMr~RI~~~   79 (1180)
T 1w36_B           18 ERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSN   79 (1180)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHHhcCCcccccCCCCCHHHEEEEeccHHHHHHHHHHHHHH
Confidence            459999999999987666666666432         12247999999999999999988753

>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=85.91  E-value=0.29  Score=39.66  Aligned_cols=53  Identities=11%  Similarity=0.084  Sum_probs=30.8

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhh--cCCcEEEEcCCCChhHHH
Q 022724           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII--KGRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        31 ~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~--~~~~~li~~~Tg~GKT~~   86 (293)
                      +..+|+++.-.+.....++..-..  . -...++..+.  -.+.+++.||+|+|||..
T Consensus        11 ~~~~~~~i~g~~~~~~~l~~l~~~--~-~~~~~~~~~~~~~~~g~ll~G~~G~GKTtl   65 (254)
T 1ixz_A           11 PKVTFKDVAGAEEAKEELKEIVEF--L-KNPSRFHEMGARIPKGVLLVGPPGVGKTHL   65 (254)
T ss_dssp             CSCCGGGCCSCHHHHHHHHHHHHH--H-HCHHHHHHTTCCCCSEEEEECCTTSSHHHH
T ss_pred             CCCCHHHhCCcHHHHHHHHHHHHH--H-HCHHHHHHcCCCCCCeEEEECCCCCCHHHH
Confidence            446788887666666666543110  0 0112333322  134599999999999954

>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=85.59  E-value=0.51  Score=37.02  Aligned_cols=35  Identities=14%  Similarity=0.031  Sum_probs=22.9

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcC
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P  109 (293)
                      .|.-+++.||+|+|||......+.   .   .+..++++.-
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            467799999999999955433332   1   2345666653

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=85.59  E-value=0.43  Score=37.06  Aligned_cols=19  Identities=47%  Similarity=0.623  Sum_probs=15.9

Q ss_pred             cCCcEEEEcCCCChhHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~   87 (293)
                      .|.-+.+.||+|+|||...
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            5778899999999999543

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=85.57  E-value=0.45  Score=37.76  Aligned_cols=20  Identities=20%  Similarity=0.290  Sum_probs=16.0

Q ss_pred             hhcCCcEEEEcCCCChhHHH
Q 022724           67 IIKGRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~~   86 (293)
                      +..|+-+.++||+|+|||..
T Consensus        20 i~~G~~~~lvGpsGsGKSTL   39 (218)
T 1z6g_A           20 MNNIYPLVICGPSGVGKGTL   39 (218)
T ss_dssp             --CCCCEEEECSTTSSHHHH
T ss_pred             cCCCCEEEEECCCCCCHHHH
Confidence            34688899999999999954

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=85.56  E-value=1.3  Score=37.09  Aligned_cols=19  Identities=32%  Similarity=0.480  Sum_probs=16.1

Q ss_pred             cCCcEEEEcCCCChhHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~   87 (293)
                      .+.++++.||+|+|||..+
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            4578999999999999654

>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=85.56  E-value=0.43  Score=36.63  Aligned_cols=19  Identities=47%  Similarity=0.749  Sum_probs=16.2

Q ss_pred             cCCcEEEEcCCCChhHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~   87 (293)
                      +++.++++|++|+|||...
T Consensus         9 ~~~~I~l~G~~GsGKSTv~   27 (184)
T 1y63_A            9 KGINILITGTPGTGKTSMA   27 (184)
T ss_dssp             SSCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4678999999999999654

>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=85.52  E-value=0.41  Score=38.78  Aligned_cols=52  Identities=15%  Similarity=0.205  Sum_probs=28.0

Q ss_pred             cCcccCCCCHHHHHHHHHCC--CCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHH
Q 022724           33 TSFDAMGIKDDLLRGIYQYG--FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        33 ~~f~~~~l~~~i~~~l~~~~--~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~   87 (293)
                      .+|+++.=.+.+.+.+.++-  +..|..+...   .+...+.+++.||+|+|||...
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            46777755555665554420  1112111111   1123468999999999999544

>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=85.40  E-value=0.4  Score=37.59  Aligned_cols=18  Identities=33%  Similarity=0.536  Sum_probs=15.0

Q ss_pred             cCCcEEEEcCCCChhHHH
Q 022724           69 KGRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~   86 (293)
                      .|+-+++.||||+|||..
T Consensus        33 ~g~~ilI~GpsGsGKStL   50 (205)
T 2qmh_A           33 YGLGVLITGDSGVGKSET   50 (205)
T ss_dssp             TTEEEEEECCCTTTTHHH
T ss_pred             CCEEEEEECCCCCCHHHH
Confidence            456799999999999843

>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=85.39  E-value=0.46  Score=37.18  Aligned_cols=18  Identities=17%  Similarity=0.457  Sum_probs=15.8

Q ss_pred             cCCcEEEEcCCCChhHHH
Q 022724           69 KGRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~   86 (293)
                      +|+-++++||+|+|||..
T Consensus        18 ~g~~ivl~GPSGaGKsTL   35 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHI   35 (197)
T ss_dssp             SCCEEEEECCTTSSHHHH
T ss_pred             CCCEEEEECcCCCCHHHH
Confidence            678899999999999954

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=85.20  E-value=0.4  Score=39.80  Aligned_cols=53  Identities=9%  Similarity=0.092  Sum_probs=30.6

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCCcHHH-HHHHHhhh-cCCcEEEEcCCCChhHHHH
Q 022724           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQ-QRAVMPII-KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        32 ~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q-~~~~~~i~-~~~~~li~~~Tg~GKT~~~   87 (293)
                      ..+|+++.=.+...+.+.+.- .  .+.. .+.+..+. .++.+++.||+|+|||..+
T Consensus        17 ~~~~~~i~G~~~~~~~l~~~i-~--~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la   71 (297)
T 3b9p_A           17 KVEWTDIAGQDVAKQALQEMV-I--LPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLA   71 (297)
T ss_dssp             CCCGGGSCCCHHHHHHHHHHT-H--HHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHH
T ss_pred             CCCHHHhCChHHHHHHHHHHH-H--hhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHH
Confidence            457888766666666665431 1  0000 00111111 3578999999999999544

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=85.19  E-value=7.8  Score=34.60  Aligned_cols=75  Identities=8%  Similarity=-0.004  Sum_probs=50.1

Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHHhcCCCCCCCcc
Q 022724          102 VQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAIK  177 (293)
Q Consensus       102 ~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~  177 (293)
                      .+.++++....-+..+.+.+..    .+.++..++|+.+..+..+.+    ....+|+|+|+..+..     .+++.+++
T Consensus       348 ~~~~ivf~~~~~~~~l~~~L~~----~~~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv~T~~~~~~-----GiDip~v~  418 (510)
T 2oca_A          348 ENAFVMFKHVSHGKAIFDLIKN----EYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFST-----GISVKNLH  418 (510)
T ss_dssp             CEEEEEESSHHHHHHHHHHHHT----TCSSEEEESSSTTHHHHHHHHHHHHHCCSCEEEEEHHHHHH-----SCCCCSEE
T ss_pred             CCeEEEEecHHHHHHHHHHHHH----cCCCeEEEECCCCHHHHHHHHHHHhCCCCCEEEEEcChhhc-----ccccccCc
Confidence            3455555556666666665544    334788888887755443322    3456899999866554     57888999


Q ss_pred             EEEecchh
Q 022724          178 LLVLDESD  185 (293)
Q Consensus       178 ~iViDE~h  185 (293)
                      ++|+.+..
T Consensus       419 ~vi~~~~~  426 (510)
T 2oca_A          419 HVVLAHGV  426 (510)
T ss_dssp             EEEESSCC
T ss_pred             EEEEeCCC
Confidence            99998876

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=85.17  E-value=0.48  Score=35.65  Aligned_cols=18  Identities=22%  Similarity=0.447  Sum_probs=15.1

Q ss_pred             CCcEEEEcCCCChhHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~   87 (293)
                      ++.+++.||.|||||...
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            567999999999999543

>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=85.14  E-value=1.8  Score=43.34  Aligned_cols=78  Identities=12%  Similarity=0.090  Sum_probs=58.7

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHHhcCCCCCCCc
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l~~~~~~~~~l  176 (293)
                      +.+++|+||+++-+..+.+.+++..  .+.++..++|+.+..+..+.+    .+..+|+|+|.     . -...+++.++
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-----I-IETGIDIPTA  883 (1151)
T ss_dssp             TCEEEEECCCSSCHHHHHHHHHHHC--TTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESS-----T-TGGGSCCTTE
T ss_pred             CCeEEEEECCHHHHHHHHHHHHHhC--CCCeEEEEeCCCCHHHHHHHHHHHHcCCCcEEEECC-----c-ceeeecccCC
Confidence            5689999999999999999888763  256788899988765544332    24679999995     2 2345788899


Q ss_pred             cEEEecchhh
Q 022724          177 KLLVLDESDE  186 (293)
Q Consensus       177 ~~iViDE~h~  186 (293)
                      +++|+..++.
T Consensus       884 ~~VIi~~~~~  893 (1151)
T 2eyq_A          884 NTIIIERADH  893 (1151)
T ss_dssp             EEEEETTTTS
T ss_pred             cEEEEeCCCC
Confidence            9999877754

>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=85.06  E-value=0.4  Score=40.44  Aligned_cols=18  Identities=22%  Similarity=0.196  Sum_probs=14.1

Q ss_pred             CCcEEEEcCCCChhHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~   87 (293)
                      ++-++|.||||+|||...
T Consensus         3 ~~~i~i~GptgsGKt~la   20 (322)
T 3exa_A            3 EKLVAIVGPTAVGKTKTS   20 (322)
T ss_dssp             CEEEEEECCTTSCHHHHH
T ss_pred             CcEEEEECCCcCCHHHHH
Confidence            345788999999999543

>1c9k_A COBU, adenosylcobinamide kinase; alpha/beta structure rossmann fold P-loop, transferase; HET: 5GP; 2.20A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1cbu_A

Probab=84.96  E-value=0.98  Score=34.72  Aligned_cols=43  Identities=14%  Similarity=0.215  Sum_probs=23.2

Q ss_pred             EEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHH
Q 022724           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL  122 (293)
Q Consensus        73 ~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~  122 (293)
                      ++|.|++|||||.-+. -+    ...  +..++|+......-.++.+++.
T Consensus         2 ilV~Gg~~SGKS~~A~-~l----a~~--~~~~~yiaT~~~~d~e~~~rI~   44 (180)
T 1c9k_A            2 ILVTGGARSGKSRHAE-AL----IGD--APQVLYIATSQILDDEMAARIQ   44 (180)
T ss_dssp             EEEEECTTSSHHHHHH-HH----HCS--CSSEEEEECCCC------CHHH
T ss_pred             EEEECCCCCcHHHHHH-HH----Hhc--CCCeEEEecCCCCCHHHHHHHH
Confidence            6899999999994332 22    122  3357888875544444444443

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=84.75  E-value=0.49  Score=36.63  Aligned_cols=16  Identities=38%  Similarity=0.767  Sum_probs=13.7

Q ss_pred             CcEEEEcCCCChhHHH
Q 022724           71 RDVIAQAQSGTGKTSM   86 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~   86 (293)
                      +-++++||+|+|||..
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            5689999999999953

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=84.65  E-value=0.45  Score=38.62  Aligned_cols=53  Identities=23%  Similarity=0.246  Sum_probs=28.9

Q ss_pred             ccCcccCCCCHHHHHHHHHCC--CCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHH
Q 022724           32 ITSFDAMGIKDDLLRGIYQYG--FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        32 ~~~f~~~~l~~~i~~~l~~~~--~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~   87 (293)
                      ...|+++.-.+.+.+.+.+.-  +..+..++..   .....+.+++.||+|+|||...
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            457888866666666654320  0111100000   0112457999999999999543

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=84.64  E-value=2  Score=37.01  Aligned_cols=18  Identities=28%  Similarity=0.506  Sum_probs=15.4

Q ss_pred             CCcEEEEcCCCChhHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~   87 (293)
                      ..++++.||+|+|||..+
T Consensus        72 ~~~ill~Gp~GtGKT~la   89 (376)
T 1um8_A           72 KSNILLIGPTGSGKTLMA   89 (376)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CCCEEEECCCCCCHHHHH
Confidence            468999999999999654

>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=84.62  E-value=0.45  Score=35.62  Aligned_cols=17  Identities=18%  Similarity=0.495  Sum_probs=13.9

Q ss_pred             CcEEEEcCCCChhHHHH
Q 022724           71 RDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~   87 (293)
                      +.++++|++|||||...
T Consensus         2 ~~I~l~G~~GsGKsT~a   18 (179)
T 3lw7_A            2 KVILITGMPGSGKSEFA   18 (179)
T ss_dssp             CEEEEECCTTSCHHHHH
T ss_pred             cEEEEECCCCCCHHHHH
Confidence            35789999999999643

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=84.50  E-value=0.52  Score=37.16  Aligned_cols=50  Identities=14%  Similarity=0.147  Sum_probs=29.2

Q ss_pred             HHHHHHHHHCCCCCCcHHHHHHHHhhhcC----CcEEEEcCCCChhHHHHHHHHHhh
Q 022724           42 DDLLRGIYQYGFEKPSAIQQRAVMPIIKG----RDVIAQAQSGTGKTSMIALTVCQT   94 (293)
Q Consensus        42 ~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~----~~~li~~~Tg~GKT~~~~~~~~~~   94 (293)
                      ..|.+.|+--|+. +... ...+..+.++    +.+++.||.|+|||..+ ..+...
T Consensus        28 ~~I~~~l~yq~~~-~~~f-~~~l~~~~~~iPkkn~ili~GPPGtGKTt~a-~ala~~   81 (212)
T 1tue_A           28 RPIVQFLRYQQIE-FITF-LGALKSFLKGTPKKNCLVFCGPANTGKSYFG-MSFIHF   81 (212)
T ss_dssp             HHHHHHHHHTTCC-HHHH-HHHHHHHHHTCTTCSEEEEESCGGGCHHHHH-HHHHHH
T ss_pred             HHHHHHHHHcCcC-HHHH-HHHHHHHHhcCCcccEEEEECCCCCCHHHHH-HHHHHH
Confidence            3556665543433 3333 3444555544    36999999999999544 344443

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=84.35  E-value=2  Score=35.20  Aligned_cols=43  Identities=12%  Similarity=0.186  Sum_probs=29.5

Q ss_pred             HHHHHHHHCCCCCCcHHHHH-HHHhhhcCC-----cEEEEcCCCChhHHHHH
Q 022724           43 DLLRGIYQYGFEKPSAIQQR-AVMPIIKGR-----DVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        43 ~i~~~l~~~~~~~~~~~Q~~-~~~~i~~~~-----~~li~~~Tg~GKT~~~~   88 (293)
                      .+.+-|+-.||.   +.+-. ++..+++++     .+++.||.|+|||+.+.
T Consensus        74 ~i~~~l~~qg~~---~~~~~~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~  122 (267)
T 1u0j_A           74 RIYKILELNGYD---PQYAASVFLGWATKKFGKRNTIWLFGPATTGKTNIAE  122 (267)
T ss_dssp             HHHHHHHHTTCC---HHHHHHHHHHHHTTCSTTCCEEEEECSTTSSHHHHHH
T ss_pred             HHHHHHHHcCCC---HHHHHHHHHHHHhCCCCCCcEEEEECCCCCCHHHHHH
Confidence            678888777766   44432 344455442     59999999999996654

>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=84.27  E-value=0.47  Score=41.08  Aligned_cols=20  Identities=20%  Similarity=0.305  Sum_probs=16.5

Q ss_pred             hhcCCcEEEEcCCCChhHHH
Q 022724           67 IIKGRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~~   86 (293)
                      +..|..++++||||+|||..
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

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=84.14  E-value=0.45  Score=40.78  Aligned_cols=18  Identities=50%  Similarity=0.815  Sum_probs=15.2

Q ss_pred             CCcEEEEcCCCChhHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~   87 (293)
                      ++.+++.||+|+|||...
T Consensus        70 ~~~vLl~GppGtGKT~la   87 (368)
T 3uk6_A           70 GRAVLIAGQPGTGKTAIA   87 (368)
T ss_dssp             TCEEEEEESTTSSHHHHH
T ss_pred             CCEEEEECCCCCCHHHHH
Confidence            358999999999999654

>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=83.94  E-value=0.59  Score=47.50  Aligned_cols=34  Identities=21%  Similarity=0.245  Sum_probs=23.7

Q ss_pred             CCCccEEEecchhhhhccccHHHHHHHHhhCCCC
Q 022724          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPD  206 (293)
Q Consensus       173 ~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~  206 (293)
                      +++-+.+|+||+-.-+|..-...+...+..+.++
T Consensus       570 ~~~~~IliLDE~tSaLD~~te~~i~~~l~~~~~~  603 (1321)
T 4f4c_A          570 VRNPKILLLDEATSALDAESEGIVQQALDKAAKG  603 (1321)
T ss_dssp             TTCCSEEEEESTTTTSCTTTHHHHHHHHHHHHTT
T ss_pred             ccCCCEEEEecccccCCHHHHHHHHHHHHHHhCC
Confidence            3567899999998888776566666655554333

>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=83.90  E-value=0.52  Score=39.68  Aligned_cols=16  Identities=19%  Similarity=0.434  Sum_probs=13.2

Q ss_pred             cEEEEcCCCChhHHHH
Q 022724           72 DVIAQAQSGTGKTSMI   87 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~   87 (293)
                      -++|+||||+|||...
T Consensus        12 ~i~i~GptgsGKt~la   27 (316)
T 3foz_A           12 AIFLMGPTASGKTALA   27 (316)
T ss_dssp             EEEEECCTTSCHHHHH
T ss_pred             EEEEECCCccCHHHHH
Confidence            4788999999999543

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=83.88  E-value=0.57  Score=36.41  Aligned_cols=19  Identities=37%  Similarity=0.594  Sum_probs=16.0

Q ss_pred             cCCcEEEEcCCCChhHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~   87 (293)
                      .|+.+++.||.|+|||...
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            4678999999999999543

>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=83.76  E-value=0.57  Score=36.66  Aligned_cols=21  Identities=33%  Similarity=0.566  Sum_probs=16.2

Q ss_pred             hhhcCCcEEEEcCCCChhHHH
Q 022724           66 PIIKGRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        66 ~i~~~~~~li~~~Tg~GKT~~   86 (293)
                      .+..|.-+.+.||+|+|||..
T Consensus        16 ~i~~Gei~~l~GpnGsGKSTL   36 (207)
T 1znw_A           16 PAAVGRVVVLSGPSAVGKSTV   36 (207)
T ss_dssp             ---CCCEEEEECSTTSSHHHH
T ss_pred             CCCCCCEEEEECCCCCCHHHH
Confidence            567788999999999999954

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=83.69  E-value=0.48  Score=35.90  Aligned_cols=19  Identities=26%  Similarity=0.363  Sum_probs=15.8

Q ss_pred             cCCcEEEEcCCCChhHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~   87 (293)
                      .|.-+.++||+|+|||..+
T Consensus         8 ~gei~~l~G~nGsGKSTl~   26 (171)
T 4gp7_A            8 ELSLVVLIGSSGSGKSTFA   26 (171)
T ss_dssp             SSEEEEEECCTTSCHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHH
Confidence            5677899999999999543

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=83.67  E-value=0.51  Score=38.42  Aligned_cols=16  Identities=25%  Similarity=0.250  Sum_probs=13.3

Q ss_pred             cEEEEcCCCChhHHHH
Q 022724           72 DVIAQAQSGTGKTSMI   87 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~   87 (293)
                      .++++||+|||||..+
T Consensus         3 li~I~G~~GSGKSTla   18 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMA   18 (253)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEECCCCcCHHHHH
Confidence            4789999999999544

>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=83.66  E-value=18  Score=33.82  Aligned_cols=77  Identities=13%  Similarity=0.154  Sum_probs=57.5

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH---h-cCCcEEEeChHHHHHHHhcCCCCCCCc
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL---E-HGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~-~~~~ilV~Tp~~l~~~l~~~~~~~~~l  176 (293)
                      +.++||.|+++.-+..+.+.+...    ++++..++++.+..+....+   . ...+|+|+|.     .+ ...+++.++
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-----LL-REGLDIPEV  508 (664)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESC-----CC-CTTCCCTTE
T ss_pred             CCEEEEEECCHHHHHHHHHHHHhc----CCCceeecCCCCHHHHHHHHHHhhcCCceEEEccC-----hh-hcCccCCCC
Confidence            458999999999999998877764    56788888887655554432   2 4578999984     22 346788899


Q ss_pred             cEEEecchhhh
Q 022724          177 KLLVLDESDEM  187 (293)
Q Consensus       177 ~~iViDE~h~~  187 (293)
                      +++|+=|++..
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

>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=83.62  E-value=0.58  Score=35.74  Aligned_cols=19  Identities=26%  Similarity=0.414  Sum_probs=15.2

Q ss_pred             cCCcEEEEcCCCChhHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~   87 (293)
                      +++.+++.|+.|+|||...
T Consensus         2 ~~~~I~i~G~~GsGKsT~~   20 (192)
T 1kht_A            2 KNKVVVVTGVPGVGSTTSS   20 (192)
T ss_dssp             -CCEEEEECCTTSCHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            3567999999999999643

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=83.18  E-value=0.46  Score=39.14  Aligned_cols=53  Identities=11%  Similarity=0.084  Sum_probs=31.5

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhh--cCCcEEEEcCCCChhHHH
Q 022724           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII--KGRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        31 ~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~--~~~~~li~~~Tg~GKT~~   86 (293)
                      +..+|+++.-.+.+...++..-..  . -...++..+.  -.+.+++.||+|+|||..
T Consensus        35 ~~~~~~~i~g~~~~~~~l~~l~~~--~-~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl   89 (278)
T 1iy2_A           35 PKVTFKDVAGAEEAKEELKEIVEF--L-KNPSRFHEMGARIPKGVLLVGPPGVGKTHL   89 (278)
T ss_dssp             CCCCGGGSSSCHHHHHHHHHHHHH--H-HCHHHHHHTTCCCCCEEEEECCTTSSHHHH
T ss_pred             CCCCHHHhCChHHHHHHHHHHHHH--H-HCHHHHHHcCCCCCCeEEEECCCcChHHHH
Confidence            456788887777776666543111  0 0112233321  134599999999999954

>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=83.16  E-value=3  Score=36.84  Aligned_cols=68  Identities=4%  Similarity=0.000  Sum_probs=45.8

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHh-cCCcEEEeChHHHHHHHhcCCCCCCCccEE
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLL  179 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~i  179 (293)
                      +.+++|.||+++-+..+.+.++..    ++++..++|.. ....+.... ...+|+|+|.     .+ ...+++. ++++
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----GKSVVVLNRKT-FEREYPTIKQKKPDFILATD-----IA-EMGANLC-VERV  244 (440)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHT----TCCEEECCSSS-CC--------CCCSEEEESS-----ST-TCCTTCC-CSEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHc----CCCEEEecchh-HHHHHhhhcCCCceEEEECC-----hh-heeeccC-ceEE
Confidence            458999999999999999988764    57788888843 222233332 4578999995     22 3356777 8887


Q ss_pred             E
Q 022724          180 V  180 (293)
Q Consensus       180 V  180 (293)
                      |
T Consensus       245 I  245 (440)
T 1yks_A          245 L  245 (440)
T ss_dssp             E
T ss_pred             E
Confidence            6

>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=82.93  E-value=0.36  Score=42.93  Aligned_cols=54  Identities=11%  Similarity=0.067  Sum_probs=30.1

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCCcHHHH-HHHHh-hhcCCcEEEEcCCCChhHHHH
Q 022724           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQ-RAVMP-IIKGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        31 ~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~-~~~~~-i~~~~~~li~~~Tg~GKT~~~   87 (293)
                      +..+|+++.=...+.+.+.+.- .  .|... +.+.. ....+.+++.||+|+|||..+
T Consensus       129 ~~~~~~di~G~~~~k~~l~~~v-~--~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA  184 (444)
T 2zan_A          129 PNVKWSDVAGLEGAKEALKEAV-I--LPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLA  184 (444)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHH-T--HHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHH
T ss_pred             CCCCHHHhcCHHHHHHHHHHHH-H--HHhhCHHHhhccCCCCceEEEECCCCCCHHHHH
Confidence            3456777765666666665421 0  01100 00001 123478999999999999654

>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=82.79  E-value=0.53  Score=35.54  Aligned_cols=19  Identities=21%  Similarity=0.321  Sum_probs=15.5

Q ss_pred             cCCcEEEEcCCCChhHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~   87 (293)
                      .|..++++|+.|+|||...
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            3567899999999999643

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=82.75  E-value=0.91  Score=35.51  Aligned_cols=40  Identities=8%  Similarity=0.234  Sum_probs=23.4

Q ss_pred             ccEEEecchhhhhcc---cc--HHHHHHHHhhCCCCccEEEEEee
Q 022724          176 IKLLVLDESDEMLSR---GF--KDQIYDVYRYLPPDLQVVLISAT  215 (293)
Q Consensus       176 l~~iViDE~h~~~~~---~~--~~~~~~i~~~l~~~~q~v~~SAt  215 (293)
                      -.+|||||||.+...   ..  ...+..+........++|+++..
T Consensus        88 ~~vliIDEAq~l~~~~~~~~e~~rll~~l~~~r~~~~~iil~tq~  132 (199)
T 2r2a_A           88 GSIVIVDEAQDVWPARSAGSKIPENVQWLNTHRHQGIDIFVLTQG  132 (199)
T ss_dssp             TCEEEETTGGGTSBCCCTTCCCCHHHHGGGGTTTTTCEEEEEESC
T ss_pred             ceEEEEEChhhhccCccccchhHHHHHHHHhcCcCCeEEEEECCC
Confidence            568999999998432   11  12222222222345688888777

>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=82.26  E-value=0.72  Score=36.67  Aligned_cols=20  Identities=40%  Similarity=0.612  Sum_probs=16.0

Q ss_pred             hhcCCcEEEEcCCCChhHHH
Q 022724           67 IIKGRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~~   86 (293)
                      ...|+-+++.||+|+|||..
T Consensus        13 ~~~G~ii~l~GpsGsGKSTL   32 (219)
T 1s96_A           13 MAQGTLYIVSAPSGAGKSSL   32 (219)
T ss_dssp             --CCCEEEEECCTTSCHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHH
Confidence            45688899999999999954

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=82.15  E-value=0.59  Score=38.95  Aligned_cols=17  Identities=18%  Similarity=0.010  Sum_probs=14.3

Q ss_pred             CcEEEEcCCCChhHHHH
Q 022724           71 RDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~   87 (293)
                      +.+++.||+|+|||...
T Consensus        37 ~~lLl~GppGtGKT~la   53 (293)
T 3t15_A           37 LILGIWGGKGQGKSFQC   53 (293)
T ss_dssp             SEEEEEECTTSCHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            57899999999999543

>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=82.10  E-value=1.9  Score=39.49  Aligned_cols=41  Identities=12%  Similarity=0.308  Sum_probs=25.0

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhcc-CCCceeEEEEcCC
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDT-SSREVQALILSPT  110 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~-~~~~~~~lil~P~  110 (293)
                      ..+++|.|.||||||.+.-..++..+.. .+...+.+++=|-
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            4689999999999996544334333332 2233455555454

>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=82.03  E-value=0.95  Score=38.19  Aligned_cols=37  Identities=8%  Similarity=0.125  Sum_probs=22.2

Q ss_pred             CccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEe
Q 022724          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (293)
Q Consensus       175 ~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SA  214 (293)
                      ..+.+|++..|.+. ..  ..+...++.+.+...++..|-
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            35778888888763 22  455555555555566665543

>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=81.94  E-value=0.68  Score=34.64  Aligned_cols=16  Identities=13%  Similarity=0.079  Sum_probs=13.5

Q ss_pred             cEEEEcCCCChhHHHH
Q 022724           72 DVIAQAQSGTGKTSMI   87 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~   87 (293)
                      .+++.|+.|+|||...
T Consensus         3 ~i~l~G~~GsGKsT~~   18 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVA   18 (173)
T ss_dssp             EEEEECSSSSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4789999999999654

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=81.93  E-value=6.8  Score=35.43  Aligned_cols=51  Identities=18%  Similarity=0.284  Sum_probs=29.3

Q ss_pred             hhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHH
Q 022724           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVI  121 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~  121 (293)
                      +..|.-+++.||+|+|||..... ++.....  .+.+++++++... ..++...+
T Consensus       278 i~~G~i~~i~G~~GsGKSTLl~~-l~g~~~~--~G~~vi~~~~ee~-~~~l~~~~  328 (525)
T 1tf7_A          278 FFKDSIILATGATGTGKTLLVSR-FVENACA--NKERAILFAYEES-RAQLLRNA  328 (525)
T ss_dssp             EESSCEEEEEECTTSSHHHHHHH-HHHHHHT--TTCCEEEEESSSC-HHHHHHHH
T ss_pred             CCCCcEEEEEeCCCCCHHHHHHH-HHHHHHh--CCCCEEEEEEeCC-HHHHHHHH
Confidence            44667899999999999954332 2222222  2445777765432 23444433

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=81.91  E-value=0.51  Score=35.99  Aligned_cols=19  Identities=32%  Similarity=0.455  Sum_probs=15.6

Q ss_pred             cCCcEEEEcCCCChhHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~   87 (293)
                      .|..++++|+.|||||...
T Consensus         3 ~g~~I~l~G~~GsGKST~~   21 (186)
T 3cm0_A            3 VGQAVIFLGPPGAGKGTQA   21 (186)
T ss_dssp             CEEEEEEECCTTSCHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            3567899999999999654

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=81.84  E-value=2.6  Score=37.13  Aligned_cols=67  Identities=4%  Similarity=-0.058  Sum_probs=45.8

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH-hcCCcEEEeChHHHHHHHhcCCCCCCCccEE
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL-EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLL  179 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~i  179 (293)
                      +.+++|+||++.-++.+.+.+++.    +.++..++|+... ..+... ....+|+|+|.     .+.. .+++. ...+
T Consensus       171 ~~~~lVF~~~~~~~~~l~~~L~~~----~~~v~~lhg~~r~-~~~~~f~~g~~~vLVaT~-----v~e~-GiDip-~~~V  238 (431)
T 2v6i_A          171 DGRTVWFVHSIKQGAEIGTCLQKA----GKKVLYLNRKTFE-SEYPKCKSEKWDFVITTD-----ISEM-GANFK-ADRV  238 (431)
T ss_dssp             SSCEEEECSSHHHHHHHHHHHHHT----TCCEEEESTTTHH-HHTTHHHHSCCSEEEECG-----GGGT-SCCCC-CSEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHc----CCeEEEeCCccHH-HHHHhhcCCCCeEEEECc-----hHHc-CcccC-CcEE
Confidence            347999999999999999988765    6788888887322 222222 34679999995     3333 45565 5554

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=81.79  E-value=0.69  Score=34.90  Aligned_cols=16  Identities=19%  Similarity=0.385  Sum_probs=13.4

Q ss_pred             cEEEEcCCCChhHHHH
Q 022724           72 DVIAQAQSGTGKTSMI   87 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~   87 (293)
                      -++++|++|||||...
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            4789999999999643

>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=81.76  E-value=0.72  Score=39.60  Aligned_cols=18  Identities=22%  Similarity=0.427  Sum_probs=15.2

Q ss_pred             CCcEEEEcCCCChhHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~   87 (293)
                      .+.+++.||+|+|||..+
T Consensus        84 ~~~iLL~GppGtGKT~la  101 (355)
T 2qp9_X           84 TSGILLYGPPGTGKSYLA  101 (355)
T ss_dssp             CCCEEEECSTTSCHHHHH
T ss_pred             CceEEEECCCCCcHHHHH
Confidence            357999999999999654

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=81.49  E-value=2.8  Score=35.37  Aligned_cols=16  Identities=13%  Similarity=0.094  Sum_probs=13.2

Q ss_pred             cEEEEcCCCChhHHHH
Q 022724           72 DVIAQAQSGTGKTSMI   87 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~   87 (293)
                      -+.+.||+|||||...
T Consensus        94 iigI~GpsGSGKSTl~  109 (321)
T 3tqc_A           94 IIGIAGSVAVGKSTTS  109 (321)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4788899999999543

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=81.46  E-value=0.65  Score=36.08  Aligned_cols=19  Identities=32%  Similarity=0.529  Sum_probs=15.9

Q ss_pred             cCCcEEEEcCCCChhHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~   87 (293)
                      .|.-+.+.||+|+|||...
T Consensus        24 ~g~~i~l~G~sGsGKSTl~   42 (200)
T 3uie_A           24 KGCVIWVTGLSGSGKSTLA   42 (200)
T ss_dssp             CCEEEEEECSTTSSHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            5678999999999999543

>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=81.33  E-value=0.72  Score=41.09  Aligned_cols=20  Identities=40%  Similarity=0.657  Sum_probs=16.3

Q ss_pred             cCCcEEEEcCCCChhHHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~   88 (293)
                      .++++++.||+|+|||..+-
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

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=80.94  E-value=1.5  Score=38.93  Aligned_cols=38  Identities=18%  Similarity=0.138  Sum_probs=25.1

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcC
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P  109 (293)
                      .|.-++|.|++|+|||...+-.+.+....   +.+++|++-
T Consensus       196 ~G~liiIaG~pG~GKTtlal~ia~~~a~~---g~~vl~fSl  233 (444)
T 3bgw_A          196 RRNFVLIAARPSMGKTAFALKQAKNMSDN---DDVVNLHSL  233 (444)
T ss_dssp             SSCEEEEEECSSSSHHHHHHHHHHHHHHT---TCEEEEECS
T ss_pred             CCcEEEEEeCCCCChHHHHHHHHHHHHHc---CCEEEEEEC
Confidence            45679999999999995444333333333   446777764

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=80.89  E-value=0.7  Score=38.48  Aligned_cols=17  Identities=24%  Similarity=0.421  Sum_probs=14.5

Q ss_pred             CcEEEEcCCCChhHHHH
Q 022724           71 RDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~   87 (293)
                      ..+++.||+|+|||..+
T Consensus        48 ~~~ll~G~~GtGKt~la   64 (311)
T 4fcw_A           48 GSFLFLGPTGVGKTELA   64 (311)
T ss_dssp             EEEEEESCSSSSHHHHH
T ss_pred             eEEEEECCCCcCHHHHH
Confidence            37999999999999654

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=80.73  E-value=0.96  Score=38.28  Aligned_cols=16  Identities=19%  Similarity=0.403  Sum_probs=13.7

Q ss_pred             cEEEEcCCCChhHHHH
Q 022724           72 DVIAQAQSGTGKTSMI   87 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~   87 (293)
                      .++++||||+|||...
T Consensus         7 ~i~i~GptGsGKTtla   22 (323)
T 3crm_A            7 AIFLMGPTAAGKTDLA   22 (323)
T ss_dssp             EEEEECCTTSCHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            6899999999999544

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=80.60  E-value=0.64  Score=37.04  Aligned_cols=20  Identities=30%  Similarity=0.396  Sum_probs=12.7

Q ss_pred             hhcCCcEEEEcCCCChhHHH
Q 022724           67 IIKGRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~~   86 (293)
                      +..|+-+.+.||+|+|||..
T Consensus        24 v~~G~ii~l~Gp~GsGKSTl   43 (231)
T 3lnc_A           24 KSVGVILVLSSPSGCGKTTV   43 (231)
T ss_dssp             EECCCEEEEECSCC----CH
T ss_pred             cCCCCEEEEECCCCCCHHHH
Confidence            44678899999999999954

>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=80.26  E-value=0.82  Score=39.25  Aligned_cols=18  Identities=28%  Similarity=0.396  Sum_probs=15.4

Q ss_pred             CCcEEEEcCCCChhHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~   87 (293)
                      .+.+++.||+|+|||..+
T Consensus       117 ~~~vLl~GppGtGKT~la  134 (357)
T 3d8b_A          117 PKGILLFGPPGTGKTLIG  134 (357)
T ss_dssp             CSEEEEESSTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            468999999999999654

>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=80.21  E-value=8  Score=36.88  Aligned_cols=75  Identities=17%  Similarity=0.113  Sum_probs=53.6

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhh-------ccCCceEEEEECCcchHHHHHHHhc---------CCcEEEeChHHHHH
Q 022724          101 EVQALILSPTRELATQTEKVILAIG-------DFINIQAHACVGGKSVGEDIRKLEH---------GVHVVSGTPGRVCD  164 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~ilV~Tp~~l~~  164 (293)
                      +.++||.+|++.-+..+.+.+....       ...++.+..++++.+..++.+.+..         ...|+|+|. .+. 
T Consensus       303 ~g~iLVF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~~~eR~~v~~~f~~~~~~~g~~kVlVAT~-iae-  380 (773)
T 2xau_A          303 AGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNGRPGRKVVISTN-IAE-  380 (773)
T ss_dssp             SCEEEEECSCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECTTCCHHHHGGGGSCCCCCSSSSCCEEEEEECT-HHH-
T ss_pred             CCCEEEECCCHHHHHHHHHHHHHHHHhhcccccCCCeEEEEeCCCCCHHHHHHHHhhcccccCCCCceEEEEeCc-HHH-
Confidence            4589999999999999998887522       2357889999999887666544432         347999995 222 


Q ss_pred             HHhcCCCCCCCccEEEe
Q 022724          165 MIKRKTLRTRAIKLLVL  181 (293)
Q Consensus       165 ~l~~~~~~~~~l~~iVi  181 (293)
                          ..+++..+.+||-
T Consensus       381 ----~GidIp~v~~VId  393 (773)
T 2xau_A          381 ----TSLTIDGIVYVVD  393 (773)
T ss_dssp             ----HTCCCTTEEEEEE
T ss_pred             ----hCcCcCCeEEEEe
Confidence                2567778887663

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=80.07  E-value=4.2  Score=36.55  Aligned_cols=96  Identities=16%  Similarity=0.142  Sum_probs=53.1

Q ss_pred             ChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEC--------CcchHHHHHH---Hh
Q 022724           81 TGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVG--------GKSVGEDIRK---LE  149 (293)
Q Consensus        81 ~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~---~~  149 (293)
                      ++|-.. +.-++........+.++||.|+++.-+..+.+.++......++.+..++|        +.+..++.+.   ..
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            455532 33334333222334689999999999999999998765333344444443        4443333322   22


Q ss_pred             --cCCcEEEeChHHHHHHHhcCCCCCCCccEEEecc
Q 022724          150 --HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDE  183 (293)
Q Consensus       150 --~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE  183 (293)
                        ...+|+|+|.     . -...+++.+++++|.=+
T Consensus       449 ~~g~~~vLvaT~-----~-~~~GlDlp~v~~VI~~d  478 (555)
T 3tbk_A          449 ASGDNNILIATS-----V-ADEGIDIAECNLVILYE  478 (555)
T ss_dssp             ---CCSEEEECC-----C-TTCCEETTSCSEEEEES
T ss_pred             cCCCeeEEEEcc-----h-hhcCCccccCCEEEEeC
Confidence              3468999995     2 23457788888887643

---

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	293
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	2e-59
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	2e-52
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	5e-52
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	9e-50
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	3e-43
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	5e-43
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	5e-42
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	3e-39
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	1e-34
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	3e-22
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	2e-21
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	8e-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	5e-14
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	1e-11
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	4e-10
d1t5ia_	168	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	4e-08
d1s2ma2	171	c.37.1.19 (A:252-422) Putative ATP-dependent RNA h	6e-08
d1hv8a2	155	c.37.1.19 (A:211-365) Putative DEAD box RNA helica	5e-05
d1yksa1	140	c.37.1.14 (A:185-324) YFV helicase domain {Yellow	0.002

>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 =  187 bits (475), Expect = 2e-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 =  168 bits (427), Expect = 2e-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 =  168 bits (425), Expect = 5e-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 = 9e-50
 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 =  145 bits (365), Expect = 3e-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 =  144 bits (363), Expect = 5e-43
 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 =  143 bits (360), Expect = 5e-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 =  134 bits (338), Expect = 3e-39
 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 =  122 bits (306), Expect = 1e-34
 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 = 89.7 bits (221), Expect = 3e-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

>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 = 87.3 bits (215), Expect = 2e-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

>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 = 86.9 bits (214), Expect = 8e-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

>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 = 79.2 bits (194), Expect = 1e-17
 Identities = 30/164 (18%), Positives = 53/164 (32%), Gaps = 14/164 (8%)

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 SRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPV 232
                 + Y   R    +   + ++AT P               
Sbjct: 114 PASIAARGYISTRVEMGEAAGIFMTATPPGSRDPFPQSNAPIMD 157

>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 = 67.1 bits (162), Expect = 5e-14
 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 = 64.2 bits (155), Expect = 3e-13
 Identities = 47/47 (100%), Positives = 47/47 (100%)

Query: 239 DELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKV 285
           DELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKV
Sbjct: 1   DELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKV 47

>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 = 55.3 bits (132), Expect = 4e-10
 Identities = 25/38 (65%), Positives = 34/38 (89%)

Query: 246 IKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKR 283
           IKQF+V VE EE+K++ L DLYD++++TQAVIFCNT+R
Sbjct: 1   IKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRR 38

>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 = 50.1 bits (118), Expect = 4e-08
 Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 1/40 (2%)

Query: 245 GIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRK 284
           G++Q++V ++ +  K   L DL D L   Q VIF  + ++
Sbjct: 1   GLQQYYVKLK-DNEKNRKLFDLLDVLEFNQVVIFVKSVQR 39

>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 = 49.3 bits (116), Expect = 6e-08
 Identities = 21/43 (48%), Positives = 27/43 (62%), Gaps = 1/43 (2%)

Query: 240 ELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTK 282
           ELTL+GI Q++  VE E  K   L  L+  L I QA+IFCN+ 
Sbjct: 1   ELTLKGITQYYAFVE-ERQKLHCLNTLFSKLQINQAIIFCNST 42

>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 = 40.7 bits (94), Expect = 5e-05
 Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 2/40 (5%)

Query: 246 IKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKV 285
           I+Q +V V  E  +F+ LC L         ++FC TKR  
Sbjct: 4   IEQSYVEVN-ENERFEALCRLLKNKEF-YGLVFCKTKRDT 41

>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 = 35.8 bits (81), Expect = 0.002
 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	293
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	100.0
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	100.0
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	100.0
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	100.0
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	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	99.97
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:	99.89
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.86
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.84
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.82
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.79
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.78
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	99.7
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.23
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.19
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	98.86
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	98.75
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	98.51
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	97.96
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	97.83
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	97.72
d1ls1a2	207	GTPase domain of the signal sequence recognition p	97.39
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	97.29
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	97.25
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	97.11
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.1
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	97.08
d2qy9a2	211	GTPase domain of the signal recognition particle r	97.06
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	97.01
d1okkd2	207	GTPase domain of the signal recognition particle r	96.99
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	96.94
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.66
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	96.44
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	96.41
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	96.36
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	96.36
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.2
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	96.18
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	96.08
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	96.06
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	96.02
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	95.94
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	95.9
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	95.8
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	95.7
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	95.39
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	95.11
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	95.03
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	95.02
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	94.77
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	94.59
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	94.45
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	94.41
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	94.03
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	93.99
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	93.76
d1g5ta_	157	ATP:corrinoid adenosyltransferase CobA {Salmonella	93.36
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	93.18
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	93.07
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	93.0
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	92.97
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	92.74
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	92.7
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	92.68
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	92.34
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	92.26
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	92.2
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	92.16
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	92.01
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	91.32
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	91.06
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	90.83
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	90.72
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	90.58
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	90.57
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	90.26
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	90.01
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	89.81
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	89.45
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	89.38
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	89.19
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	89.06
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	89.05
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	88.78
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	88.42
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	88.3
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	88.16
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	87.99
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	87.82
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	87.56
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	87.49
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	86.82
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	86.77
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	86.58
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	86.5
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	86.42
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	86.27
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	85.85
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	85.78
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	85.7
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	85.52
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	85.38
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	85.36
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	85.04
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	84.92
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	84.89
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	84.86
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	84.72
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	84.43
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	84.38
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	84.16
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	83.95
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	83.94
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	83.86
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	83.86
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	83.73
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	83.71
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	83.61
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	83.23
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	83.23
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	83.22
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	83.22
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	83.21
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	82.6
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	82.51
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	82.48
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	82.45
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	82.13
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	81.95
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	81.31
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	81.09
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	81.07
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	80.92
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	80.37
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	80.35
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	80.31
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	80.01

>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=6e-49  Score=320.05  Aligned_cols=218  Identities=71%  Similarity=1.133  Sum_probs=206.6

Q ss_pred             cceeecccCCccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCC
Q 022724           20 KMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS   99 (293)
Q Consensus        20 ~~~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~   99 (293)
                      ....+.++..+...+|++++|+++++++|+++||..|||+|+++||.+++|+|+++.||||||||+||++|+++.+....
T Consensus         4 ~~~~~~~~~~~~~~sF~~l~L~~~l~~~L~~~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~~~   83 (222)
T d2j0sa1           4 KVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQV   83 (222)
T ss_dssp             SCCCCCCTTCCCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTS
T ss_pred             ccccccCCCCCCCCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhcccccccccccc
Confidence            44556667778888999999999999999999999999999999999999999999999999999999999999998888


Q ss_pred             CceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEE
Q 022724          100 REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLL  179 (293)
Q Consensus       100 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~i  179 (293)
                      .+++++|++|+++|+.|+++.++++.+..++++..++|+.....+...+..+++|+|+||+++.+++..+...+++++++
T Consensus        84 ~~~~~lil~PtreLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l~~~~~Ilv~TPgrl~~~~~~~~~~~~~l~~l  163 (222)
T d2j0sa1          84 RETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKML  163 (222)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEE
T ss_pred             cCceeEEecchHHHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHhccCCeEEeCCCCcHHhcccccccccccceee
Confidence            88999999999999999999999999999999999999999998888888899999999999999999999999999999


Q ss_pred             EecchhhhhccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEec
Q 022724          180 VLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVK  237 (293)
Q Consensus       180 ViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~  237 (293)
                      |+||||.+++.+|...+..+++.+++.+|++++|||+++++.++++.++.+|..+.+.
T Consensus       164 VlDEaD~ll~~~f~~~i~~I~~~l~~~~Q~ilfSAT~~~~v~~l~~~~l~~Pv~I~V~  221 (222)
T d2j0sa1         164 VLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVK  221 (222)
T ss_dssp             EEETHHHHTSTTTHHHHHHHHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECCC
T ss_pred             eecchhHhhhcCcHHHHHHHHHhCCCCCEEEEEEEeCCHHHHHHHHHHCCCCEEEEEe
Confidence            9999999999999999999999999999999999999999999999999999887653

>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=5.9e-46  Score=299.95  Aligned_cols=203  Identities=33%  Similarity=0.630  Sum_probs=191.3

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCH
Q 022724           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (293)
Q Consensus        32 ~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~  111 (293)
                      ..+|++++|++++++++.++||+.|||+|+++||.+++|+|++++||||||||+||++|+++++...+.+++++|++|++
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            46899999999999999999999999999999999999999999999999999999999999998888899999999999


Q ss_pred             HHHHHHHHHHHHhhccC-CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcc
Q 022724          112 ELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (293)
Q Consensus       112 ~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~  190 (293)
                      +|+.|+++.+..+.+.. +..+....|+.....+...+.++++|+|+||+++.+++..+...+++++++|+||||.|++.
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 022724          191 GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKI  234 (293)
Q Consensus       191 ~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~  234 (293)
                      +|...+..+++.+++++|++++|||+++++.++++.++.+|..+
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

>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=7.4e-46  Score=301.49  Aligned_cols=210  Identities=56%  Similarity=0.946  Sum_probs=193.4

Q ss_pred             CCccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEE
Q 022724           28 GVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALIL  107 (293)
Q Consensus        28 ~~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil  107 (293)
                      .++++.+|+++++++.+.+++.++||..|+++|+++||.+++|+|++++||||||||++|++|+++.+.....+++++|+
T Consensus         7 ~~e~i~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~~~~~~~alil   86 (218)
T d2g9na1           7 WNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVL   86 (218)
T ss_dssp             CCCCCCCGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEE
T ss_pred             CCCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhhhhheecccccCccEEEE
Confidence            35788999999999999999999999999999999999999999999999999999999999999999888889999999


Q ss_pred             cCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHH-HhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhh
Q 022724          108 SPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRK-LEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDE  186 (293)
Q Consensus       108 ~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~  186 (293)
                      +|+++|+.|+++.+..+....+.....+.++.....+... ..++++|+|+||+++..++.++...+++++++|+||||.
T Consensus        87 ~Pt~eL~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IvV~TP~rl~~~l~~~~~~~~~l~~lVlDEaD~  166 (218)
T d2g9na1          87 APTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADE  166 (218)
T ss_dssp             CSSHHHHHHHHHHHHHHHTTTTCCEEEECC--CCCSTTTSSSSCCCSEEEECHHHHHHHHHTTSSCSTTCCEEEEESHHH
T ss_pred             cccchhhhhHHHHHhhhccccceeEEeeecccchhHHHHHHhcCCCEEEEeCChhHHHHHhcCCcccccceEEEeeecch
Confidence            9999999999999999999999988888877655544333 345789999999999999999889999999999999999


Q ss_pred             hhccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEec
Q 022724          187 MLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVK  237 (293)
Q Consensus       187 ~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~~  237 (293)
                      +++.+|...+..+++.++++.|++++|||+++.+.++.+.++.+|..+.+.
T Consensus       167 ll~~~f~~~~~~Il~~~~~~~Q~il~SAT~~~~v~~~~~~~l~~pv~i~v~  217 (218)
T d2g9na1         167 MLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVK  217 (218)
T ss_dssp             HHHTTCHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEEECC
T ss_pred             hhcCchHHHHHHHHHhCCCCCeEEEEEecCCHHHHHHHHHHCCCCEEEEEe
Confidence            999999999999999999999999999999999999999999999988764

>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=2.6e-45  Score=296.43  Aligned_cols=204  Identities=36%  Similarity=0.613  Sum_probs=189.2

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHH
Q 022724           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (293)
Q Consensus        33 ~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~  112 (293)
                      ++|++++|++++++++.++||+.|||+|+++||.+++|+|+++.||||||||++|++|+++.+.....+++++|++|+++
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            47999999999999999999999999999999999999999999999999999999999999998888899999999999


Q ss_pred             HHHHHHHHHHHhhccCC-ceEEEEECCcchHHHHHHH-hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcc
Q 022724          113 LATQTEKVILAIGDFIN-IQAHACVGGKSVGEDIRKL-EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (293)
Q Consensus       113 l~~q~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~-~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~  190 (293)
                      |+.|+.+.++.+....+ +++..+.|+.....+...+ .++++|+|+||+++.++++++.++++++.++|+||||.+++.
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            99999999999887764 5677788888877776665 467899999999999999999999999999999999999975


Q ss_pred             -ccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEe
Q 022724          191 -GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILV  236 (293)
Q Consensus       191 -~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~  236 (293)
                       ++...+..+.+.+++.+|++++|||+++.++++++.++.+|..+.+
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

>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=2.1e-45  Score=297.72  Aligned_cols=208  Identities=55%  Similarity=0.918  Sum_probs=188.5

Q ss_pred             cCCccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEE
Q 022724           27 EGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALI  106 (293)
Q Consensus        27 ~~~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~li  106 (293)
                      .-++++.+|++++++++++++|.++||+.|||+|+++||.+++|+|+++++|||||||++|++|+++++.....+++++|
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            34677899999999999999999999999999999999999999999999999999999999999999998888999999


Q ss_pred             EcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhh
Q 022724          107 LSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDE  186 (293)
Q Consensus       107 l~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~  186 (293)
                      ++|+++++.|+...+..+.....+.+....++....++...+ ++++|+|+||+++..++..+.+.+++++++|+||||.
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            999999999999999999988888888888887776665554 4679999999999999999999999999999999999


Q ss_pred             hhccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEE
Q 022724          187 MLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKIL  235 (293)
Q Consensus       187 ~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~  235 (293)
                      +++.+|...+..+++.+++.+|++++|||+++.++++++.++.+|..+.
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

>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=2.9e-44  Score=296.06  Aligned_cols=212  Identities=29%  Similarity=0.483  Sum_probs=195.5

Q ss_pred             cccCCccccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccC------
Q 022724           25 TTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS------   98 (293)
Q Consensus        25 ~~~~~~~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~------   98 (293)
                      ....+.++.+|++++++++++++|.++||..|+|+|+.+||.+++|+|+++++|||+|||+||++|+++++...      
T Consensus        13 ~~~~~~~~~~F~~l~l~~~l~~~L~~~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~   92 (238)
T d1wrba1          13 DYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQR   92 (238)
T ss_dssp             SSSCCSCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC----
T ss_pred             CCCCCCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeHHHHHHHHHhccccccc
Confidence            33456678999999999999999999999999999999999999999999999999999999999999998432      


Q ss_pred             ---CCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCC
Q 022724           99 ---SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRA  175 (293)
Q Consensus        99 ---~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~  175 (293)
                         ..+++++|++|+++|+.|+.+.+..+....++++..+.|+.....+.+....+++|+|+||+++.++++.+...+.+
T Consensus        93 ~~~~~~~~alil~pt~el~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ivV~TP~~l~~~~~~~~~~l~~  172 (238)
T d1wrba1          93 YSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEF  172 (238)
T ss_dssp             --CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCTT
T ss_pred             ccCCCCceEEEeccchhhhcchheeeeecccCCCcEEEEEeccchhhHHHhhcccCCceeecCHHHHHhHHccCceeccc
Confidence               34678999999999999999999999999999999999999888888888889999999999999999999999999


Q ss_pred             ccEEEecchhhhhccccHHHHHHHHhhCC----CCccEEEEEeecChhHHHHHHhcCCCCEEEEe
Q 022724          176 IKLLVLDESDEMLSRGFKDQIYDVYRYLP----PDLQVVLISATLPHEILEMTTKFMTDPVKILV  236 (293)
Q Consensus       176 l~~iViDE~h~~~~~~~~~~~~~i~~~l~----~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~  236 (293)
                      ++++|+||+|.+++.+|..++..+++.+.    .++|++++|||++++++.+++.++.+|..+.+
T Consensus       173 v~~lViDEaD~ll~~~f~~~i~~Il~~~~~~~~~~~Q~il~SAT~~~~v~~l~~~~~~~p~~i~v  237 (238)
T d1wrba1         173 CKYIVLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTV  237 (238)
T ss_dssp             CCEEEEETHHHHHHTTCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEE
T ss_pred             cceeeeehhhhhhhhccHHHHHHHHHHhcCCCCCCCEEEEEeeeCCHHHHHHHHHHCCCCEEEEe
Confidence            99999999999999999999999998764    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=1.3e-43  Score=286.67  Aligned_cols=204  Identities=40%  Similarity=0.681  Sum_probs=196.2

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHH
Q 022724           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (293)
Q Consensus        33 ~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~  112 (293)
                      .+|++++|++.++++|+++||.+|||+|+++||.+++|+|+++.||||+|||++|++|+++.+.....+.++++++|+.+
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            37999999999999999999999999999999999999999999999999999999999999988888899999999999


Q ss_pred             HHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcccc
Q 022724          113 LATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF  192 (293)
Q Consensus       113 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~  192 (293)
                      ++.+....+..+....++++...+|+.....+...+..+++|+|+||+++.++++.+.+.+.+++++|+||||.+++.+|
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            99999999999999999999999999999888888889999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEe
Q 022724          193 KDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILV  236 (293)
Q Consensus       193 ~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~  236 (293)
                      ...+..+++.+++.+|++++|||+|+.+.+++..++.+|..+.+
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=1.6e-43  Score=286.30  Aligned_cols=203  Identities=35%  Similarity=0.605  Sum_probs=188.6

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCC-cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCC
Q 022724           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGR-DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (293)
Q Consensus        32 ~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~-~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~  110 (293)
                      ..+|+++++++++++++.++||.+|+|+|+++||.+++|+ |+++++|||+|||++|++|+++..... .+++++|++|+
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 YMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNEN-NGIEAIILTPT   81 (208)
T ss_dssp             CCCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSS-SSCCEEEECSC
T ss_pred             ccCHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeecccccccccc-cCcceEEEeec
Confidence            3589999999999999999999999999999999998875 999999999999999999999876554 56899999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcc
Q 022724          111 RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (293)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~  190 (293)
                      ++|+.|+.+.++.+....+.++..++|+.+...+.+.+. +++|+|+||+++.++++++.+++++++++|+||+|.+++.
T Consensus        82 ~~l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~-~~~IlV~TP~~l~~~l~~~~~~~~~l~~lViDEad~l~~~  160 (208)
T d1hv8a1          82 RELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNM  160 (208)
T ss_dssp             HHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHH-TCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHTT
T ss_pred             cccchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhcC-CCCEEEEChHHHHHHHHcCCCCcccCcEEEEEChHHhhcC
Confidence            999999999999999999999999999988887776664 6899999999999999999999999999999999999999


Q ss_pred             ccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEe
Q 022724          191 GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILV  236 (293)
Q Consensus       191 ~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~  236 (293)
                      ++...+..+++.+++++|++++|||+++.+.++++.++.+|..+.+
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            9999999999999999999999999999999999999999887764

>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=3.1e-41  Score=273.53  Aligned_cols=204  Identities=35%  Similarity=0.572  Sum_probs=185.7

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHH
Q 022724           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (293)
Q Consensus        33 ~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~  112 (293)
                      ++|++++|++++++++++.||..|+|+|+++||.+++|+|++++||||||||++|++|+++.+.....+...++++|+.+
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            47999999999999999999999999999999999999999999999999999999999999988888889999999999


Q ss_pred             HHHHHHHHHHHhhccC----CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhh
Q 022724          113 LATQTEKVILAIGDFI----NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (293)
Q Consensus       113 l~~q~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~  188 (293)
                      ++.+....+.......    ...+....++.+...+......+++|+|+||+++..++.+....+++++++|+||||.++
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            9999998887755443    345666667776666656667789999999999999999988889999999999999999


Q ss_pred             ccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcCCCCEEEEe
Q 022724          189 SRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILV  236 (293)
Q Consensus       189 ~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~~~~~~~~~  236 (293)
                      +++|...+..+++.++++.|++++|||+|+++.++++.++.+|..+.+
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            999999999999999999999999999999999999999999988765

>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=4.9e-31  Score=212.58  Aligned_cols=189  Identities=15%  Similarity=0.195  Sum_probs=143.7

Q ss_pred             cCcccCCCCHHHHHHHHHC-CCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCH
Q 022724           33 TSFDAMGIKDDLLRGIYQY-GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (293)
Q Consensus        33 ~~f~~~~l~~~i~~~l~~~-~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~  111 (293)
                      ...+.++|++.+.+.|++. ||..++|+|.++++++.+|+|+++++|||+|||++|.+|++..      ..++++++|++
T Consensus         2 ~~~e~~~l~~~~~~~l~~~fg~~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~~~~~~~~~------~~~~~~v~P~~   75 (206)
T d1oywa2           2 AQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL------NGLTVVVSPLI   75 (206)
T ss_dssp             CCCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS------SSEEEEECSCH
T ss_pred             CchhhCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcchhhhhhhhc------cCceEEeccch
Confidence            3567888999999999876 9999999999999999999999999999999999999998764      35799999999


Q ss_pred             HHHHHHHHHHHHhhccCCceEEEEECCcchHH----HHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhh
Q 022724          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGE----DIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (293)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~  187 (293)
                      +|+.|..+.++.++..    ............    .........+++++||+.+............+++++|+||+|.+
T Consensus        76 ~L~~q~~~~l~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~t~~~~~~~~~~~~~~~~~v~~lviDEaH~~  151 (206)
T d1oywa2          76 SLMKDQVDQLQANGVA----AACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCI  151 (206)
T ss_dssp             HHHHHHHHHHHHTTCC----EEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGGGG
T ss_pred             hhhhhHHHHHHhhccc----ccccccccccccchhHHHHHhcCCceEEEEechhhhchhhcccchhheeeeeeeeeeeee
Confidence            9999999999876533    222222222111    11223456789999999886654444556778999999999999


Q ss_pred             hccccH--H---HHHHHHhhCCCCccEEEEEeecChhHHH-HHHhc-CCCCE
Q 022724          188 LSRGFK--D---QIYDVYRYLPPDLQVVLISATLPHEILE-MTTKF-MTDPV  232 (293)
Q Consensus       188 ~~~~~~--~---~~~~i~~~l~~~~q~v~~SAt~~~~~~~-~~~~~-~~~~~  232 (293)
                      .++++.  .   .+..+...+ +++|++++|||+++.+.+ +.+.+ +.+|.
T Consensus       152 ~~~~~~~~~~~~~~~~l~~~~-~~~~ii~lSATl~~~v~~di~~~L~l~~p~  202 (206)
T d1oywa2         152 SQWGHDFRPEYAALGQLRQRF-PTLPFMALTATADDTTRQDIVRLLGLNDPL  202 (206)
T ss_dssp             CTTSSCCCHHHHGGGGHHHHC-TTSCEEEEESCCCHHHHHHHHHHHTCCSCE
T ss_pred             eccccchHHHHHHHHHHHHhC-CCCceEEEEeCCCHHHHHHHHHHcCCCCCc
Confidence            876532  1   233445555 478999999999998765 45443 67774

>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=99.97  E-value=1.4e-30  Score=209.15  Aligned_cols=180  Identities=18%  Similarity=0.227  Sum_probs=142.6

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHH
Q 022724           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (293)
Q Consensus        40 l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~  119 (293)
                      +++.+.+.|++.||..|+|+|.++++.+.+|+|+++++|||+|||+++.++++..+..   +.++|+++|+++|+.|+.+
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            5778899999999999999999999999999999999999999999999999888765   3579999999999999999


Q ss_pred             HHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHH
Q 022724          120 VILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDV  199 (293)
Q Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i  199 (293)
                      .++++.... .++....++.....   .....++++++||..+..++......+.++++||+||+|.+.+..+...+..+
T Consensus        87 ~~~~~~~~~-~~v~~~~~~~~~~~---~~~~~~~ii~~~~~~~~~~~~~~~~~~~~~~~ii~DE~h~~~~~~r~~~~~~~  162 (202)
T d2p6ra3          87 SFKKWEKIG-LRIGISTGDYESRD---EHLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEIL  162 (202)
T ss_dssp             HHTTTTTTT-CCEEEECSSCBCCS---SCSTTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCTTTHHHHHHH
T ss_pred             HHHHHhhcc-ccceeeccCccccc---ccccccceeeeccHHHHHHHhccchhhhhhhhccccHHHHhcccccchHHHHH
Confidence            998776433 45555555544322   12245789999999999999888878889999999999999877655444433


Q ss_pred             ---HhhCCCCccEEEEEeecChhHHHHHHhc
Q 022724          200 ---YRYLPPDLQVVLISATLPHEILEMTTKF  227 (293)
Q Consensus       200 ---~~~l~~~~q~v~~SAt~~~~~~~~~~~~  227 (293)
                         ++..+++.|+++||||+++ ..++..++
T Consensus       163 l~~i~~~~~~~~~l~lSATl~n-~~~~~~~l  192 (202)
T d2p6ra3         163 VTKMRRMNKALRVIGLSATAPN-VTEIAEWL  192 (202)
T ss_dssp             HHHHHHHCTTCEEEEEECCCTT-HHHHHHHT
T ss_pred             HHHHHhcCCCCcEEEEcCCCCc-HHHHHHHc
Confidence               4445678999999999976 35565444

>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=9e-30  Score=209.50  Aligned_cols=180  Identities=15%  Similarity=0.109  Sum_probs=131.9

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHH
Q 022724           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (293)
Q Consensus        33 ~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~  112 (293)
                      ..|.+..+.+.+.+.+ +.++..|+++|+++++.+++|+|+++++|||+|||++++++++.....   +.+++|++|+++
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            3444444444554444 457889999999999999999999999999999999999998876654   468999999999


Q ss_pred             HHHHHHHHHHHhhccCCceE----EEEECCcchHHHHHHH--hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhh
Q 022724          113 LATQTEKVILAIGDFINIQA----HACVGGKSVGEDIRKL--EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDE  186 (293)
Q Consensus       113 l~~q~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~--~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~  186 (293)
                      |+.|+.+.++++....++++    ....++.........+  ..+++|+|+||+.+.+.    ...+++++++||||+|.
T Consensus        98 La~Q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Ilv~Tp~~l~~~----~~~~~~~~~vVvDE~d~  173 (237)
T d1gkub1          98 LVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKH----YRELGHFDFIFVDDVDA  173 (237)
T ss_dssp             HHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHHC----STTSCCCSEEEESCHHH
T ss_pred             HHHHHHHHHHHHHHHcCCceEEEEeeeecccchhhhhhhhccccccceeccChHHHHHh----hhhcCCCCEEEEEChhh
Confidence            99999999999887766543    3333444333333332  34578999999876653    34567899999999999


Q ss_pred             hhccccHHHHHHHHhh-------------CCCCccEEEEEeecChhHHH
Q 022724          187 MLSRGFKDQIYDVYRY-------------LPPDLQVVLISATLPHEILE  222 (293)
Q Consensus       187 ~~~~~~~~~~~~i~~~-------------l~~~~q~v~~SAt~~~~~~~  222 (293)
                      +++.+.  .+..+...             .+...|++++|||+++....
T Consensus       174 ~l~~~~--~~~~~~~~~g~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~  220 (237)
T d1gkub1         174 ILKASK--NVDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAKKGKKA  220 (237)
T ss_dssp             HHTSTH--HHHHHHHHTTEEEETTTTEEEECCSSEEEECCCCSCCCTTH
T ss_pred             hhhccc--chhHHHHhcCChHHHHHHHhhCCCCCeEEEEeCCCCcccHH
Confidence            976542  22222222             23467899999999876544

>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=6.3e-27  Score=187.37  Aligned_cols=166  Identities=17%  Similarity=0.173  Sum_probs=133.5

Q ss_pred             CCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEE
Q 022724           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAH  133 (293)
Q Consensus        54 ~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~  133 (293)
                      -.|+++|.++++.+. ++|+++++|||+|||+++++++...+...  +.+++|++|+++|+.|+.+.++++....+.++.
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            369999999999875 56899999999999999998887766553  358999999999999999999999888888888


Q ss_pred             EEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                      ..+++.........+. ..+++++||+.+.+.+....+.+++++++|+||+|++........+...........+++++|
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            8887777665544443 358999999999999888888889999999999999866543343444444445678999999


Q ss_pred             eecChhHHHH
Q 022724          214 ATLPHEILEM  223 (293)
Q Consensus       214 At~~~~~~~~  223 (293)
                      ||++.....+
T Consensus       164 ATp~~~~~~~  173 (200)
T d1wp9a1         164 ASPGSTPEKI  173 (200)
T ss_dssp             SCSCSSHHHH
T ss_pred             ecCCCcHHHH
Confidence            9986554443

>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=99.89  E-value=5.4e-24  Score=180.87  Aligned_cols=192  Identities=15%  Similarity=0.052  Sum_probs=120.4

Q ss_pred             hhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHH
Q 022724           66 PIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDI  145 (293)
Q Consensus        66 ~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  145 (293)
                      .+.+|+++++.||||+|||++|+++++......  +.++||++|+++|+.|+.+.++.+.....  ....         .
T Consensus         5 ~~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~--~~~~lvi~Ptr~La~q~~~~l~~~~~~~~--~~~~---------~   71 (305)
T d2bmfa2           5 IFRKKRLTIMDLHPGAGKTKRYLPAIVREAIKR--GLRTLILAPTRVVAAEMEEALRGLPIRYQ--TPAI---------R   71 (305)
T ss_dssp             SSSTTCEEEECCCTTSSTTTTHHHHHHHHHHHH--TCCEEEEESSHHHHHHHHHHTTTSCCBCC--C-------------
T ss_pred             HhhcCCcEEEEECCCCCHHHHHHHHHHHHHHhc--CCEEEEEccHHHHHHHHHHHHhcCCccee--eeEE---------e
Confidence            356889999999999999999988888765543  56899999999999999987765432211  1000         0


Q ss_pred             HHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhC--CCCccEEEEEeecChhHHHH
Q 022724          146 RKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL--PPDLQVVLISATLPHEILEM  223 (293)
Q Consensus       146 ~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l--~~~~q~v~~SAt~~~~~~~~  223 (293)
                      ........++++|++.+...... ...+.+++++||||+|++.++++.  ...++..+  ....+++++|||++......
T Consensus        72 ~~~~~~~~i~~~t~~~l~~~~~~-~~~~~~~~~vViDE~H~~~~~~~~--~~~~l~~~~~~~~~~~v~~SAT~~~~~~~~  148 (305)
T d2bmfa2          72 AEHTGREIVDLMCHATFTMRLLS-PIRVPNYNLIIMDEAHFTDPASIA--ARGYISTRVEMGEAAGIFMTATPPGSRDPF  148 (305)
T ss_dssp             ----CCCSEEEEEHHHHHHHHTS-SSCCCCCSEEEEESTTCCSHHHHH--HHHHHHHHHHHTSCEEEEECSSCTTCCCSS
T ss_pred             ecccCccccccCCcHHHHHHHhc-CccccceeEEEeeeeeecchhhHH--HHHHHHHhhccccceEEEeecCCCcceeee
Confidence            11223457999999988776554 345788999999999998655422  12222221  25689999999987542111


Q ss_pred             HHhcCCCCEEEEecCCcccCCCceEEEEEecCcccHHHHHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          224 TTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       224 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      .   ...             ..+........... +...+.. + ...+++++|||+++++++.+++.|
T Consensus       149 ~---~~~-------------~~~~~~~~~~~~~~-~~~~~~~-~-~~~~~~~lvf~~~~~~~~~l~~~L  198 (305)
T d2bmfa2         149 P---QSN-------------APIMDEEREIPERS-WNSGHEW-V-TDFKGKTVWFVPSIKAGNDIAACL  198 (305)
T ss_dssp             C---CCS-------------SCEEEEECCCCCSC-CSSCCHH-H-HSSCSCEEEECSCHHHHHHHHHHH
T ss_pred             c---ccC-------------CcceEEEEeccHHH-HHHHHHH-H-HhhCCCEEEEeccHHHHHHHHHHH
Confidence            0   000             01111111111111 1111111 1 223579999999999999998875

>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=99.86  E-value=1.2e-20  Score=151.89  Aligned_cols=175  Identities=17%  Similarity=0.164  Sum_probs=134.4

Q ss_pred             CCCHHHHHHHHHCCCCCCcHHHHHHHHhhhc----C--CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHH
Q 022724           39 GIKDDLLRGIYQYGFEKPSAIQQRAVMPIIK----G--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (293)
Q Consensus        39 ~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~----~--~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~  112 (293)
                      ..+.+..+.+.+.-...+|+-|..++..+.+    +  .+.+++|.||||||.+|+.++...+..   |.++++++|+..
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            4456677776654344599999999988753    3  479999999999999999999888865   569999999999


Q ss_pred             HHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhh
Q 022724          113 LATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (293)
Q Consensus       113 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~  188 (293)
                      |+.|.++.++++....+.++..+++..+..+....+    ....+|+|||-..+.     ....++++++|||||-|.+.
T Consensus       116 La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~-----~~~~f~~LgLiIiDEeH~fg  190 (233)
T d2eyqa3         116 LAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ-----SDVKFKDLGLLIVDEEHRFG  190 (233)
T ss_dssp             HHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH-----SCCCCSSEEEEEEESGGGSC
T ss_pred             hHHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhc-----cCCccccccceeeechhhhh
Confidence            999999999999999999999999998766554433    345799999974333     35668999999999999753


Q ss_pred             ccccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHh
Q 022724          189 SRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTK  226 (293)
Q Consensus       189 ~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~  226 (293)
                         +.. -.. ++....++.++++|||+.+....+...
T Consensus       191 ---~kQ-~~~-l~~~~~~~~~l~~SATPiprtl~~~~~  223 (233)
T d2eyqa3         191 ---VRH-KER-IKAMRANVDILTLTATPIPRTLNMAMS  223 (233)
T ss_dssp             ---HHH-HHH-HHHHHTTSEEEEEESSCCCHHHHHHHT
T ss_pred             ---hHH-HHH-HHhhCCCCCEEEEecchhHHHHHHHHH
Confidence               222 122 233345788999999997765555443

>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=2.1e-20  Score=153.13  Aligned_cols=170  Identities=19%  Similarity=0.236  Sum_probs=129.0

Q ss_pred             HHHHHH-HHHCCCCCCcHHHHHHHHhhhc----C--CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHH
Q 022724           42 DDLLRG-IYQYGFEKPSAIQQRAVMPIIK----G--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELA  114 (293)
Q Consensus        42 ~~i~~~-l~~~~~~~~~~~Q~~~~~~i~~----~--~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~  114 (293)
                      ..+.+. ...+.|. +|+-|++++..+..    +  .+.+++|.||||||.+|+.++...+..   |.++++++||..|+
T Consensus        70 ~~l~~~f~~~LPFe-LT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~---g~q~~~m~Pt~~La  145 (264)
T d1gm5a3          70 GKLAEEFIKSLPFK-LTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA---GFQTAFMVPTSILA  145 (264)
T ss_dssp             THHHHHHHHHSSSC-CCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH---TSCEEEECSCHHHH
T ss_pred             hHHHHHHHhhcccc-CCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhc---ccceeEEeehHhhh
Confidence            344444 3455655 99999999999863    2  478999999999999999999888877   56899999999999


Q ss_pred             HHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcc
Q 022724          115 TQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (293)
Q Consensus       115 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~  190 (293)
                      .|.++.++++....++.+..++|+.+..+..+.+    .+.++|+|||-.-+..     ...+++++++||||-|.+.-.
T Consensus       146 ~Qh~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~~-----~~~f~~LglviiDEqH~fgv~  220 (264)
T d1gm5a3         146 IQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE-----DVHFKNLGLVIIDEQHRFGVK  220 (264)
T ss_dssp             HHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH-----CCCCSCCCEEEEESCCCC---
T ss_pred             HHHHHHHHHhhhhccccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhcC-----CCCccccceeeeccccccchh
Confidence            9999999999999999999999998766544333    2468999999744433     456789999999999987422


Q ss_pred             ccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHH
Q 022724          191 GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTT  225 (293)
Q Consensus       191 ~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~  225 (293)
                      ..     ..+......+.+++||||+-+....+..
T Consensus       221 Qr-----~~l~~~~~~~~~l~~SATPiprtl~~~~  250 (264)
T d1gm5a3         221 QR-----EALMNKGKMVDTLVMSATPIPRSMALAF  250 (264)
T ss_dssp             -------CCCCSSSSCCCEEEEESSCCCHHHHHHH
T ss_pred             hH-----HHHHHhCcCCCEEEEECCCCHHHHHHHH
Confidence            21     1122233468899999998766555543

>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=99.82  E-value=1.7e-20  Score=156.88  Aligned_cols=153  Identities=22%  Similarity=0.196  Sum_probs=112.9

Q ss_pred             CCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q 022724           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (293)
                      .|+++|.+++..+++++..++.+|||+|||+++...+.......  ..++||++|+++|+.|+.+.+.++.......+..
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            59999999999999999999999999999988665443333332  3489999999999999999999887655555555


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEe
Q 022724          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (293)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SA  214 (293)
                      ..++.....   ......+++|+|++.+....   ...++++++||+||||++.    ...+..++..+.+....+++||
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   12234689999998765432   2335678999999999874    3445666666655455699999


Q ss_pred             ecChh
Q 022724          215 TLPHE  219 (293)
Q Consensus       215 t~~~~  219 (293)
                      |+++.
T Consensus       261 T~~~~  265 (282)
T d1rifa_         261 SLRDG  265 (282)
T ss_dssp             SCCTT
T ss_pred             ecCCC
Confidence            98654

>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=4.5e-19  Score=141.67  Aligned_cols=136  Identities=16%  Similarity=0.150  Sum_probs=100.4

Q ss_pred             CCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q 022724           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (293)
                      .++++|++++..+.++++.++.+|||+|||++++..+ ..+     +.++||+||+++|+.|+.+.++.+...   .+..
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            5999999999999999999999999999998766444 332     347999999999999999988776432   2333


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEe
Q 022724          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (293)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SA  214 (293)
                      ..|+..         ...+++|+|.+.+.......   ..++++||+||+|++....    +..+...++ ....+++||
T Consensus       141 ~~~~~~---------~~~~i~i~t~~~~~~~~~~~---~~~~~lvIiDEaH~~~a~~----~~~i~~~~~-~~~~lgLTA  203 (206)
T d2fz4a1         141 FSGRIK---------ELKPLTVSTYDSAYVNAEKL---GNRFMLLIFDEVHHLPAES----YVQIAQMSI-APFRLGLTA  203 (206)
T ss_dssp             ESSSCB---------CCCSEEEEEHHHHHHTHHHH---TTTCSEEEEECSSCCCTTT----HHHHHHTCC-CSEEEEEEE
T ss_pred             cccccc---------cccccccceehhhhhhhHhh---CCcCCEEEEECCeeCCcHH----HHHHHhccC-CCcEEEEec
Confidence            333322         23579999998887654432   3567899999999985433    344455443 456789999


Q ss_pred             ec
Q 022724          215 TL  216 (293)
Q Consensus       215 t~  216 (293)
                      |+
T Consensus       204 Tl  205 (206)
T d2fz4a1         204 TF  205 (206)
T ss_dssp             SC
T ss_pred             CC
Confidence            97

>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=99.78  E-value=7.9e-20  Score=136.72  Aligned_cols=136  Identities=14%  Similarity=0.192  Sum_probs=91.2

Q ss_pred             hhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHH
Q 022724           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIR  146 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  146 (293)
                      +.+|+++++++|||+|||.+++.+++......  +.++++++|++++++|..+.+...    +..+........      
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            45789999999999999988877777666554  458999999999999998866432    222211111110      


Q ss_pred             HHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccH-HHHHHHHhhCCCCccEEEEEeecC
Q 022724          147 KLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFK-DQIYDVYRYLPPDLQVVLISATLP  217 (293)
Q Consensus       147 ~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~-~~~~~i~~~l~~~~q~v~~SAt~~  217 (293)
                       ......+.+.|...+.+.. .....+.+++++|+||+|++...++. ..+...+.. .++.++++||||+|
T Consensus        72 -~~~~~~~~~~~~~~l~~~~-~~~~~~~~~~lvIiDEaH~~~~~~~~~~~~~~~~~~-~~~~~~l~lTATPp  140 (140)
T d1yksa1          72 -GSGREVIDAMCHATLTYRM-LEPTRVVNWEVIIMDEAHFLDPASIAARGWAAHRAR-ANESATILMTATPP  140 (140)
T ss_dssp             -CCSSCCEEEEEHHHHHHHH-TSSSCCCCCSEEEETTTTCCSHHHHHHHHHHHHHHH-TTSCEEEEECSSCT
T ss_pred             -cccccchhhhhHHHHHHHH-hccccccceeEEEEccccccChhhHHHHHHHHHHhh-CCCCCEEEEEcCCC
Confidence             0123457777877776643 34456789999999999987444322 112222223 35789999999987

>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=99.70  E-value=3e-17  Score=122.23  Aligned_cols=127  Identities=17%  Similarity=0.129  Sum_probs=85.5

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHh
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE  149 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  149 (293)
                      .+..++.+|||+|||+.+...+.+      .+.+++|++|+++|++|+.+.+.+.....   .....++....       
T Consensus         8 ~~~~ll~apTGsGKT~~~~~~~~~------~~~~vli~~P~~~l~~q~~~~~~~~~~~~---~~~~~~~~~~~-------   71 (136)
T d1a1va1           8 FQVAHLHAPTGSGKSTKVPAAYAA------QGYKVLVLNPSVAATLGFGAYMSKAHGVD---PNIRTGVRTIT-------   71 (136)
T ss_dssp             CEEEEEECCTTSCTTTHHHHHHHT------TTCCEEEEESCHHHHHHHHHHHHHHHSCC---CEEECSSCEEC-------
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHHH------cCCcEEEEcChHHHHHHHHHHHHHHhhcc---ccccccccccc-------
Confidence            456899999999999765433321      25589999999999999999988764332   22333332211       


Q ss_pred             cCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCC--CCccEEEEEeec
Q 022724          150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP--PDLQVVLISATL  216 (293)
Q Consensus       150 ~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~--~~~q~v~~SAt~  216 (293)
                      ....+.++|.+.....   ....+++++++|+||+|++... ....+..+++.+.  ...+++++|||+
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            2346888888776543   3345678999999999987332 2223444555443  456899999995

>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=99.23  E-value=1.9e-10  Score=96.04  Aligned_cols=155  Identities=16%  Similarity=0.109  Sum_probs=96.2

Q ss_pred             CCcHHHHHHHHhhh---------cCCcEEEEcCCCChhHHHHHHHHHhhhccC----CCceeEEEEcCCHHHHHHHHHHH
Q 022724           55 KPSAIQQRAVMPII---------KGRDVIAQAQSGTGKTSMIALTVCQTVDTS----SREVQALILSPTRELATQTEKVI  121 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~---------~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~----~~~~~~lil~P~~~l~~q~~~~~  121 (293)
                      .++|+|.+++.-+.         .+...++.=.+|.|||+..+..+...+...    +...++||+||.. ++.|+.+.+
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            58899999987542         345688888999999975443222222222    1234699999964 889999999


Q ss_pred             HHhhccCCceEEEEECCcchHHHHH--HHh------cCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccH
Q 022724          122 LAIGDFINIQAHACVGGKSVGEDIR--KLE------HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFK  193 (293)
Q Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~~~~--~~~------~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~  193 (293)
                      .++.... ..+...+++.......+  ...      ...+++|+|.+.+.....  .+...+.+++|+||+|.+-... .
T Consensus       134 ~k~~~~~-~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i~sy~~~~~~~~--~l~~~~~~~vI~DEaH~ikn~~-s  209 (298)
T d1z3ix2         134 GKWLGGR-VQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAE--VLHKGKVGLVICDEGHRLKNSD-N  209 (298)
T ss_dssp             HHHHGGG-CCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTT--TTTTSCCCEEEETTGGGCCTTC-H
T ss_pred             HhhcCCc-eeEEEEeCchHHHHHHHHHHhhhccCccccceEEEEeecccccchh--cccccceeeeeccccccccccc-c
Confidence            8876542 34445555543222111  111      134689999887765322  2333467899999999985332 2


Q ss_pred             HHHHHHHhhCCCCccEEEEEeec
Q 022724          194 DQIYDVYRYLPPDLQVVLISATL  216 (293)
Q Consensus       194 ~~~~~i~~~l~~~~q~v~~SAt~  216 (293)
                      .... ....+ +....+++|||+
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 345678999998

>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=7.2e-11  Score=94.90  Aligned_cols=147  Identities=13%  Similarity=0.143  Sum_probs=94.1

Q ss_pred             CCcHHHHHHHHhhh----cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q 022724           55 KPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~----~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (293)
                      .+.|+|.+++..+.    .+...++.-++|.|||...+..+ ..+.......+++|+|| ..+..|..+.+.++....  
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i~~~-~~~~~~~~~~~~LIv~p-~~l~~~W~~e~~~~~~~~--   87 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVF-SDAKKENELTPSLVICP-LSVLKNWEEELSKFAPHL--   87 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHH-HHHHHTTCCSSEEEEEC-STTHHHHHHHHHHHCTTS--
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHHHhh-hhhhhcccccccceecc-hhhhhHHHHHHHhhcccc--
Confidence            58899999987543    45678999999999998765444 43333333457899999 667788888888776543  


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEE
Q 022724          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVV  210 (293)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v  210 (293)
                      .+...........     ..+.+++++|.+.+...-.   +.--..+++|+||+|.+-...  .........+. ....+
T Consensus        88 ~~~~~~~~~~~~~-----~~~~~vvi~~~~~~~~~~~---l~~~~~~~vI~DEah~~k~~~--s~~~~~~~~l~-a~~r~  156 (230)
T d1z63a1          88 RFAVFHEDRSKIK-----LEDYDIILTTYAVLLRDTR---LKEVEWKYIVIDEAQNIKNPQ--TKIFKAVKELK-SKYRI  156 (230)
T ss_dssp             CEEECSSSTTSCC-----GGGSSEEEEEHHHHTTCHH---HHTCCEEEEEEETGGGGSCTT--SHHHHHHHTSC-EEEEE
T ss_pred             cceeeccccchhh-----ccCcCEEEeeHHHHHhHHH---HhcccceEEEEEhhhcccccc--hhhhhhhhhhc-cceEE
Confidence            3322222211111     1235899999987754222   112356889999999985432  22223334443 45578


Q ss_pred             EEEeec
Q 022724          211 LISATL  216 (293)
Q Consensus       211 ~~SAt~  216 (293)
                      ++|||+
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=98.86  E-value=4.1e-08  Score=78.39  Aligned_cols=164  Identities=18%  Similarity=0.242  Sum_probs=120.5

Q ss_pred             CCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q 022724           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (293)
                      .|++.|.-.--.+.+|+  +....||-|||++..+|+.-....   |..+-|++.+..||..=.+.+..+...+|+++..
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            48888887766676774  889999999999998888766555   3457889999999999999999999999999998


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHH-HHHhcCC------CCCCCccEEEecchhhhh-ccccH-------------
Q 022724          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVC-DMIKRKT------LRTRAIKLLVLDESDEML-SRGFK-------------  193 (293)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~-~~l~~~~------~~~~~l~~iViDE~h~~~-~~~~~-------------  193 (293)
                      ...+.+..+.....  .+||+-+|...+- ++|+.+.      ...+.+.+.||||+|.++ |....             
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            88777666554444  3689999988774 4665432      234778999999999985 22110             


Q ss_pred             HHHHHHHhhCCCCccEEEEEeecChhHHHHHHhcC
Q 022724          194 DQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFM  228 (293)
Q Consensus       194 ~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~~~  228 (293)
                      -.+..+++..   .++-+||.|......++..-|-
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            0123334433   4788899998776666666554

>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=98.51  E-value=2.4e-07  Score=78.52  Aligned_cols=140  Identities=15%  Similarity=0.158  Sum_probs=85.1

Q ss_pred             CCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHH--HHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceE
Q 022724           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIAL--TVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQA  132 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~--~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  132 (293)
                      ....+|++|+...+.++-++|.||.|+|||....-  ..+..... ..+.++++++||..-+..+.+.+...........
T Consensus       148 ~~~~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i~~~l~~l~~~~~-~~~~~I~l~ApTgkAA~~L~e~~~~~~~~~~~~~  226 (359)
T d1w36d1         148 DEINWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMAD-GERCRIRLAAPTGKAAARLTESLGKALRQLPLTD  226 (359)
T ss_dssp             TSCCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCS-SCCCCEEEEBSSHHHHHHHHHHHTHHHHHSSCCS
T ss_pred             ccccHHHHHHHHHHcCCeEEEEcCCCCCceehHHHHHHHHHHHHh-ccCCeEEEecCcHHHHHHHHHHHHHHHhhcCchh
Confidence            45779999999999999999999999999966422  22222222 2456899999999988888877654332221100


Q ss_pred             EEEECCcchHHHHHHHhcCCcEEEeChHHHH------HHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCC
Q 022724          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVC------DMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPD  206 (293)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~------~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~  206 (293)
                      ..... .             ..-..|..++.      ..+.........++++||||+-++.    ...+..++..++..
T Consensus       227 ~~~~~-~-------------~~~~~t~~~ll~~~~~~~~~~~~~~~~l~~d~lIIDEaSmv~----~~l~~~ll~~~~~~  288 (359)
T d1w36d1         227 EQKKR-I-------------PEDASTLHRLLGAQPGSQRLRHHAGNPLHLDVLVVDEASMID----LPMMSRLIDALPDH  288 (359)
T ss_dssp             CCCCS-C-------------SCCCBTTTSCC-----------CTTSCCSCSEEEECSGGGCB----HHHHHHHHHTCCTT
T ss_pred             hhhhh-h-------------hhhhhHHHHHHhhhhcchHHHHhhhcccccceeeehhhhccC----HHHHHHHHHHhcCC
Confidence            00000 0             00001111111      1122233445568999999998763    34566778888888


Q ss_pred             ccEEEEE
Q 022724          207 LQVVLIS  213 (293)
Q Consensus       207 ~q~v~~S  213 (293)
                      .++|++-
T Consensus       289 ~~lILvG  295 (359)
T d1w36d1         289 ARVIFLG  295 (359)
T ss_dssp             CEEEEEE
T ss_pred             CEEEEEC
Confidence            8888774

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=97.96  E-value=9.1e-06  Score=66.79  Aligned_cols=69  Identities=17%  Similarity=0.137  Sum_probs=51.3

Q ss_pred             CCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhcc-CCCceeEEEEcCCHHHHHHHHHHHHHhh
Q 022724           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT-SSREVQALILSPTRELATQTEKVILAIG  125 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~-~~~~~~~lil~P~~~l~~q~~~~~~~~~  125 (293)
                      +++|-|++++..  ...+++|.|+.|||||.+.+--+...+.. .....+++++++|+.+++.+.+.+.++.
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            478999999975  34679999999999997655433333322 1123479999999999999998887754

>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=97.83  E-value=1.6e-05  Score=61.73  Aligned_cols=34  Identities=21%  Similarity=0.299  Sum_probs=25.6

Q ss_pred             CcHHHHHHHHhhh----cCC--c-EEEEcCCCChhHHHHHH
Q 022724           56 PSAIQQRAVMPII----KGR--D-VIAQAQSGTGKTSMIAL   89 (293)
Q Consensus        56 ~~~~Q~~~~~~i~----~~~--~-~li~~~Tg~GKT~~~~~   89 (293)
                      .+|||..+|..+.    +++  + +++.||.|+|||..+..
T Consensus         3 ~yPw~~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~~   43 (207)
T d1a5ta2           3 WYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYA   43 (207)
T ss_dssp             CCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHH
T ss_pred             CCcccHHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHHHH
Confidence            4578888888764    343  3 89999999999965543

>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=97.72  E-value=5.4e-05  Score=62.49  Aligned_cols=68  Identities=18%  Similarity=0.218  Sum_probs=51.8

Q ss_pred             CCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccCC-CceeEEEEcCCHHHHHHHHHHHHHh
Q 022724           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-REVQALILSPTRELATQTEKVILAI  124 (293)
Q Consensus        55 ~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~-~~~~~lil~P~~~l~~q~~~~~~~~  124 (293)
                      .+++-|++++...  +..++|.|+.|||||.+.+--+.+.+.... ...+++++++++..+..+...+...
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            4889999999853  457999999999999876554444443322 2247999999999999999888654

>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=97.39  E-value=0.00021  Score=55.02  Aligned_cols=131  Identities=17%  Similarity=0.240  Sum_probs=64.9

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcC--CHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP--TRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P--~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  148 (293)
                      +-++++||||+|||....--+... ...  +.++.+++.  .|.-+.++...+   .+..++.+...........-....
T Consensus        11 ~vi~lvGp~GvGKTTTiaKLA~~~-~~~--g~kV~lit~Dt~R~gA~eQL~~~---a~~l~v~~~~~~~~~~~~~~~~~~   84 (207)
T d1ls1a2          11 NLWFLVGLQGSGKTTTAAKLALYY-KGK--GRRPLLVAADTQRPAAREQLRLL---GEKVGVPVLEVMDGESPESIRRRV   84 (207)
T ss_dssp             EEEEEECCTTTTHHHHHHHHHHHH-HHT--TCCEEEEECCSSCHHHHHHHHHH---HHHHTCCEEECCTTCCHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHH-HHC--CCcEEEEecccccchHHHHHHHH---HHhcCCccccccccchhhHHHHHH
Confidence            336779999999996654433322 222  234555553  455555444433   333445554433333222111000


Q ss_pred             hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcc-ccHHHHHHHHhhCCCCccEEEEEeecChhHHHHHHh
Q 022724          149 EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTK  226 (293)
Q Consensus       149 ~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~-~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~~~  226 (293)
                                    ..+.     ...+.++++||=+-+...+ .....+..+.+..++..-++.++|+.+.+..+.+..
T Consensus        85 --------------~~~~-----~~~~~d~vlIDTaGr~~~d~~~~~el~~~~~~~~~~~~llv~~a~~~~~~~~~~~~  144 (207)
T d1ls1a2          85 --------------EEKA-----RLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARA  144 (207)
T ss_dssp             --------------HHHH-----HHHTCCEEEEECCCCSSCCHHHHHHHHHHHHHHCCSEEEEEEEGGGTHHHHHHHHH
T ss_pred             --------------HHHH-----hhccCcceeecccccchhhhhhHHHHHHHHhhcCCceEEEEeccccchhHHHHHHH
Confidence                          0000     1223345566655443211 233455556666666667788888887765555544

>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=97.25  E-value=0.0016  Score=49.54  Aligned_cols=112  Identities=13%  Similarity=0.181  Sum_probs=62.4

Q ss_pred             HHHHHHhhhc---CCcEEEEcCCCChhHHHHHHHHHhhhc-cCCCceeEEEEcCCHH--HHHHHHHHHHHhhccCCceEE
Q 022724           60 QQRAVMPIIK---GRDVIAQAQSGTGKTSMIALTVCQTVD-TSSREVQALILSPTRE--LATQTEKVILAIGDFINIQAH  133 (293)
Q Consensus        60 Q~~~~~~i~~---~~~~li~~~Tg~GKT~~~~~~~~~~l~-~~~~~~~~lil~P~~~--l~~q~~~~~~~~~~~~~~~~~  133 (293)
                      |.+.+..+.+   +.++++.||.|+|||..+...+ ..+. .....+-.+++.|...  -++|+.+              
T Consensus         2 ~~~~l~~~i~~~~~~~~l~~G~~g~gk~~~a~~l~-~~i~~~~~~h~D~~~i~~~~~~I~Id~IR~--------------   66 (198)
T d2gnoa2           2 QLETLKRIIEKSEGISILINGEDLSYPREVSLELP-EYVEKFPPKASDVLEIDPEGENIGIDDIRT--------------   66 (198)
T ss_dssp             HHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHH-HHHHTSCCCTTTEEEECCSSSCBCHHHHHH--------------
T ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHH-HHHhccccCCCCEEEEeCCcCCCCHHHHHH--------------
Confidence            4555555543   3489999999999996554322 2222 2223345677766311  1222222              


Q ss_pred             EEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEE
Q 022724          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (293)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~S  213 (293)
                                                  +.+.+.... .....+++||||||.|.... ...+..++..-+++..+++.|
T Consensus        67 ----------------------------i~~~~~~~~-~~~~~KviIId~ad~l~~~a-qNaLLK~LEEPp~~t~fiLit  116 (198)
T d2gnoa2          67 ----------------------------IKDFLNYSP-ELYTRKYVIVHDCERMTQQA-ANAFLKALEEPPEYAVIVLNT  116 (198)
T ss_dssp             ----------------------------HHHHHTSCC-SSSSSEEEEETTGGGBCHHH-HHHTHHHHHSCCTTEEEEEEE
T ss_pred             ----------------------------HHHHHhhCc-ccCCCEEEEEeCccccchhh-hhHHHHHHhCCCCCceeeecc
Confidence                                        112222211 23556899999999985432 334555555556677777776


Q ss_pred             eec
Q 022724          214 ATL  216 (293)
Q Consensus       214 At~  216 (293)
                      ..+
T Consensus       117 ~~~  119 (198)
T d2gnoa2         117 RRW  119 (198)
T ss_dssp             SCG
T ss_pred             CCh
Confidence            554

>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=97.11  E-value=0.0024  Score=49.46  Aligned_cols=43  Identities=19%  Similarity=0.413  Sum_probs=26.9

Q ss_pred             CCCCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEe
Q 022724          171 LRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (293)
Q Consensus       171 ~~~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SA  214 (293)
                      ........+|+||+|.+.... ...+..++...++...+++.+-
T Consensus        95 ~~~~~~kiiiiDe~d~~~~~~-~~~Ll~~le~~~~~~~~~~~~~  137 (227)
T d1sxjc2          95 IFSKGFKLIILDEADAMTNAA-QNALRRVIERYTKNTRFCVLAN  137 (227)
T ss_dssp             SSSCSCEEEEETTGGGSCHHH-HHHHHHHHHHTTTTEEEEEEES
T ss_pred             ccCCCeEEEEEeccccchhhH-HHHHHHHhhhcccceeeccccC
Confidence            334556799999999985443 3445556666655555555443

>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=97.10  E-value=0.002  Score=49.68  Aligned_cols=103  Identities=17%  Similarity=0.313  Sum_probs=54.2

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhc
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH  150 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  150 (293)
                      +.+++.||+|+|||--. .++.+.+...  +..++++ +...+..+....+..                           
T Consensus        37 n~l~l~G~~G~GKTHLl-~A~~~~~~~~--~~~~~~~-~~~~~~~~~~~~~~~---------------------------   85 (213)
T d1l8qa2          37 NPIFIYGSVGTGKTHLL-QAAGNEAKKR--GYRVIYS-SADDFAQAMVEHLKK---------------------------   85 (213)
T ss_dssp             SSEEEECSSSSSHHHHH-HHHHHHHHHT--TCCEEEE-EHHHHHHHHHHHHHH---------------------------
T ss_pred             CcEEEECCCCCcHHHHH-HHHHHHhccC--ccceEEe-chHHHHHHHHHHHHc---------------------------
Confidence            34899999999999422 2344444433  2334443 444444444443221                           


Q ss_pred             CCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcc-ccHHHHHHHHhhCC-CCccEEEEEeecC
Q 022724          151 GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLP-PDLQVVLISATLP  217 (293)
Q Consensus       151 ~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~-~~~~~~~~i~~~l~-~~~q~v~~SAt~~  217 (293)
                            ..+..+...       +...++++||++|.+... .+...+-.++..+. .+.++|+.|...|
T Consensus        86 ------~~~~~~~~~-------~~~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p  141 (213)
T d1l8qa2          86 ------GTINEFRNM-------YKSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHP  141 (213)
T ss_dssp             ------TCHHHHHHH-------HHTCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCG
T ss_pred             ------cchhhHHHH-------HhhccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcc
Confidence                  011222222       235689999999998654 33444444444443 4455555444333

>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=97.08  E-value=0.0047  Score=48.26  Aligned_cols=41  Identities=12%  Similarity=0.259  Sum_probs=25.6

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEee
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISAT  215 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt  215 (293)
                      ....++||||+|.|.... ...+...+..-+....+++.+-.
T Consensus       114 ~~~kviiIde~d~l~~~~-q~~Llk~lE~~~~~~~~il~tn~  154 (239)
T d1njfa_         114 GRFKVYLIDEVHMLSRHS-FNALLKTLEEPPEHVKFLLATTD  154 (239)
T ss_dssp             SSSEEEEEETGGGSCHHH-HHHHHHHHHSCCTTEEEEEEESC
T ss_pred             CCCEEEEEECcccCCHHH-HHHHHHHHhcCCCCeEEEEEcCC
Confidence            345799999999985332 33455555555555666665443

>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=97.06  E-value=0.0026  Score=48.79  Aligned_cols=61  Identities=21%  Similarity=0.249  Sum_probs=32.7

Q ss_pred             EEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEc-CC-HHHHHHHHHHHHHhhccCCceEEEEECCc
Q 022724           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS-PT-RELATQTEKVILAIGDFINIQAHACVGGK  139 (293)
Q Consensus        73 ~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~-P~-~~l~~q~~~~~~~~~~~~~~~~~~~~~~~  139 (293)
                      ++++||||+|||....=-+. .+...  +.++.+++ -+ |.=+.++.+   .+.+..++.+.......
T Consensus        12 i~lvGptGvGKTTTiAKLA~-~~~~~--g~kV~lit~Dt~R~gA~eQL~---~~a~~l~v~~~~~~~~~   74 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTIGKLAR-QFEQQ--GKSVMLAAGDTFRAAAVEQLQ---VWGQRNNIPVIAQHTGA   74 (211)
T ss_dssp             EEEECCTTSCHHHHHHHHHH-HHHTT--TCCEEEECCCTTCHHHHHHHH---HHHHHTTCCEECCSTTC
T ss_pred             EEEECCCCCCHHHHHHHHHH-HHHHC--CCcEEEEecccccccchhhhh---hhhhhcCCcccccccCC
Confidence            56799999999976554432 23332  23455554 33 444444333   44444556555444333

>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=97.01  E-value=0.00041  Score=54.84  Aligned_cols=50  Identities=16%  Similarity=0.317  Sum_probs=32.4

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhh
Q 022724           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTV   95 (293)
Q Consensus        33 ~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l   95 (293)
                      ..|+++.-.+++.+.++.+- ...           ....++++.||.|+|||..+. .+...+
T Consensus         8 ~~~~diig~~~~~~~L~~~~-~~~-----------~~~~~lll~Gp~G~GKTt~~~-~la~~l   57 (252)
T d1sxje2           8 KSLNALSHNEELTNFLKSLS-DQP-----------RDLPHLLLYGPNGTGKKTRCM-ALLESI   57 (252)
T ss_dssp             CSGGGCCSCHHHHHHHHTTT-TCT-----------TCCCCEEEECSTTSSHHHHHH-THHHHH
T ss_pred             CCHHHccCcHHHHHHHHHHH-HcC-----------CCCCeEEEECCCCCCHHHHHH-HHHHhh
Confidence            36888877888888886541 100           112369999999999996543 344444

>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=96.99  E-value=0.0021  Score=49.21  Aligned_cols=62  Identities=18%  Similarity=0.090  Sum_probs=33.7

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEc-C-CHHHHHHHHHHHHHhhccCCceEEEEEC
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS-P-TRELATQTEKVILAIGDFINIQAHACVG  137 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~-P-~~~l~~q~~~~~~~~~~~~~~~~~~~~~  137 (293)
                      ++-++++||||+|||....=-+. .+...  +.++.+++ - .|.-+.++.+.+-   ...++.+.....
T Consensus         6 ~~vi~lvGptGvGKTTTiaKLA~-~~~~~--g~kV~lit~Dt~R~gA~eQL~~~a---~~l~i~~~~~~~   69 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTIAKLGR-YYQNL--GKKVMFCAGDTFRAAGGTQLSEWG---KRLSIPVIQGPE   69 (207)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHH-HHHTT--TCCEEEECCCCSSTTHHHHHHHHH---HHHTCCEECCCT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH-HHHHC--CCcEEEEEeccccccchhhHhhcc---cccCceEEeccC
Confidence            45678899999999977554332 22222  33455555 3 3555555444333   333444444333

>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=96.94  E-value=0.0018  Score=50.11  Aligned_cols=45  Identities=13%  Similarity=0.234  Sum_probs=28.8

Q ss_pred             CCCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEeecCh
Q 022724          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPH  218 (293)
Q Consensus       173 ~~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~  218 (293)
                      .....++|+||+|.+.... ...+...+...+....+++.+.....
T Consensus        99 ~~~~kviiiDe~d~~~~~~-~~~ll~~~e~~~~~~~~i~~~~~~~~  143 (224)
T d1sxjb2          99 PGKHKIVILDEADSMTAGA-QQALRRTMELYSNSTRFAFACNQSNK  143 (224)
T ss_dssp             TTCCEEEEEESGGGSCHHH-HHTTHHHHHHTTTTEEEEEEESCGGG
T ss_pred             CcceEEEEEecccccchhH-HHHHhhhccccccceeeeeccCchhh
Confidence            3456799999999986543 33344455555566677776665543

>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=96.66  E-value=0.0078  Score=46.06  Aligned_cols=60  Identities=17%  Similarity=0.112  Sum_probs=31.4

Q ss_pred             cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcC-CHHHHHHHHHHHHHhhccCCceEEEEE
Q 022724           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP-TRELATQTEKVILAIGDFINIQAHACV  136 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P-~~~l~~q~~~~~~~~~~~~~~~~~~~~  136 (293)
                      -++++||||+|||....--+... ...+ ..-++|-+. .|.=+.++.+   .+....++.+....
T Consensus        13 vi~lvGptGvGKTTTiAKLAa~~-~~~~-~kV~lit~Dt~R~gA~eQL~---~~a~~l~i~~~~~~   73 (213)
T d1vmaa2          13 VIMVVGVNGTGKTTSCGKLAKMF-VDEG-KSVVLAAADTFRAAAIEQLK---IWGERVGATVISHS   73 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH-HHTT-CCEEEEEECTTCHHHHHHHH---HHHHHHTCEEECCS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH-HHCC-CceEEEeecccccchhHHHH---HHhhhcCccccccC
Confidence            36779999999997654333332 2222 223444444 3554444443   33334455554433

>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=96.44  E-value=0.0061  Score=47.93  Aligned_cols=54  Identities=11%  Similarity=0.136  Sum_probs=32.1

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhh--cCCcEEEEcCCCChhHHHH
Q 022724           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII--KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        31 ~~~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~--~~~~~li~~~Tg~GKT~~~   87 (293)
                      |..+|++++-.+++.+.+.+. . .+ ..+.+.+..+-  ..+.+++.||.|+|||+..
T Consensus         4 p~~~~~di~G~~~~k~~l~~~-i-~~-l~~~~~~~~~g~~~~~giLl~GppGtGKT~la   59 (247)
T d1ixza_           4 PKVTFKDVAGAEEAKEELKEI-V-EF-LKNPSRFHEMGARIPKGVLLVGPPGVGKTHLA   59 (247)
T ss_dssp             CSCCGGGCCSCHHHHHHHHHH-H-HH-HHCHHHHHHTTCCCCSEEEEECCTTSSHHHHH
T ss_pred             CCCcHHHHccHHHHHHHHHHH-H-HH-HHCHHHHHHcCCCCCceEEEecCCCCChhHHH
Confidence            447899997677666666542 1 11 01112222221  2357999999999999654

>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=96.41  E-value=0.0047  Score=47.00  Aligned_cols=92  Identities=12%  Similarity=0.096  Sum_probs=70.2

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHHhcCCCCCCCc
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l~~~~~~~~~l  176 (293)
                      +.++.|+||..+-...+.+.++++..  +.++..+||.++..+..+.+    ....+|+|+|.     .+. ..++..+.
T Consensus        31 GgQvy~V~p~I~~~e~~~~~l~~~~p--~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~Tt-----vIE-vGiDvpnA  102 (211)
T d2eyqa5          31 GGQVYYLYNDVENIQKAAERLAELVP--EARIAIGHGQMRERELERVMNDFHHQRFNVLVCTT-----IIE-TGIDIPTA  102 (211)
T ss_dssp             TCEEEEECCCSSCHHHHHHHHHHHCT--TSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESS-----TTG-GGSCCTTE
T ss_pred             CCeEEEEEcCccchhhHHHHHHHhCC--ceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEeh-----hhh-hccCCCCC
Confidence            67999999999999999998888754  56888899998766554333    35689999996     333 35788999


Q ss_pred             cEEEecchhhhhccccHHHHHHHHhhCC
Q 022724          177 KLLVLDESDEMLSRGFKDQIYDVYRYLP  204 (293)
Q Consensus       177 ~~iViDE~h~~~~~~~~~~~~~i~~~l~  204 (293)
                      .++||.+|+++.    ..++..+.-+..
T Consensus       103 ~~iiI~~a~rfG----LaQLhQLRGRVG  126 (211)
T d2eyqa5         103 NTIIIERADHFG----LAQLHQLRGRVG  126 (211)
T ss_dssp             EEEEETTTTSSC----HHHHHHHHTTCC
T ss_pred             cEEEEecchhcc----ccccccccceee
Confidence            999999999863    445666666664

>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=96.36  E-value=0.0038  Score=52.95  Aligned_cols=66  Identities=24%  Similarity=0.342  Sum_probs=48.0

Q ss_pred             CcHHHHHHHHhhh----cC-CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcc
Q 022724           56 PSAIQQRAVMPII----KG-RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDF  127 (293)
Q Consensus        56 ~~~~Q~~~~~~i~----~~-~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (293)
                      |+=-|-+++..+.    +| ++.++.|-||||||+... .++...     +..+|||+|+..+|.|+++.++.+...
T Consensus        12 p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~~iA-~l~~~~-----~rp~LVVt~n~~~A~qL~~dL~~~l~~   82 (413)
T d1t5la1          12 PQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTIS-NVIAQV-----NKPTLVIAHNKTLAGQLYSELKEFFPH   82 (413)
T ss_dssp             CCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHHHHH-HHHHHH-----TCCEEEECSSHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHHHHH-HHHHHh-----CCCEEEEeCCHHHHHHHHHHHHHHcCC
Confidence            5556666666554    34 578899999999996543 222332     225899999999999999999988644

>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=96.36  E-value=0.0046  Score=44.05  Aligned_cols=90  Identities=14%  Similarity=0.128  Sum_probs=52.3

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhc
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH  150 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  150 (293)
                      .-.++.||..||||.- ++-.+++....  +.+++++-|...-         +...    .+ ..+.+..          
T Consensus         3 ~L~~i~GpMfsGKTte-Li~~~~~~~~~--~~kv~~ikp~~D~---------R~~~----~i-~s~~g~~----------   55 (139)
T d2b8ta1           3 WIEFITGPMFAGKTAE-LIRRLHRLEYA--DVKYLVFKPKIDT---------RSIR----NI-QSRTGTS----------   55 (139)
T ss_dssp             EEEEEECSTTSCHHHH-HHHHHHHHHHT--TCCEEEEEECCCG---------GGCS----SC-CCCCCCS----------
T ss_pred             EEEEEEccccCHHHHH-HHHHHHHHHHC--CCcEEEEEEcccc---------cccc----eE-EcccCce----------
Confidence            3357899999999944 44445555443  4478889896541         0011    11 1111111          


Q ss_pred             CCcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhh
Q 022724          151 GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (293)
Q Consensus       151 ~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~  188 (293)
                      -..+.+.....+...+..... ..+.++|.|||++.+.
T Consensus        56 ~~~~~~~~~~~~~~~~~~~~~-~~~~dvI~IDE~QFf~   92 (139)
T d2b8ta1          56 LPSVEVESAPEILNYIMSNSF-NDETKVIGIDEVQFFD   92 (139)
T ss_dssp             SCCEEESSTHHHHHHHHSTTS-CTTCCEEEECSGGGSC
T ss_pred             eeeEEeccchhhHHHHHhhcc-ccCcCEEEechhhhcc
Confidence            123556666666665554433 4678999999999874

>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=96.20  E-value=0.004  Score=47.71  Aligned_cols=127  Identities=14%  Similarity=0.239  Sum_probs=54.2

Q ss_pred             EEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcC-CHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcC
Q 022724           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP-TRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG  151 (293)
Q Consensus        73 ~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P-~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (293)
                      ++++||||+|||....=-+. .+...+ ..-++|-+- .|.=+.++.+   .+.+..++.+...............    
T Consensus        15 i~lvGptGvGKTTTiAKLA~-~~~~~g-~kV~lit~Dt~R~ga~eQL~---~~a~~l~v~~~~~~~~~~~~~~~~~----   85 (211)
T d1j8yf2          15 IMLVGVQGTGKATTAGKLAY-FYKKKG-FKVGLVGADVYRPAALEQLQ---QLGQQIGVPVYGEPGEKDVVGIAKR----   85 (211)
T ss_dssp             EEEECSCCC----HHHHHHH-HHHHTT-CCEEEEECCCSSHHHHHHHH---HHHHHHTCCEECCTTCCCHHHHHHH----
T ss_pred             EEEECCCCCCHHHHHHHHHH-HHHHCC-CceEEEEeeccccchhHHHH---HhccccCcceeecccchhhhHHHHH----
Confidence            66789999999976543332 233322 223444443 3444444333   3333344444333322222111110    


Q ss_pred             CcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcc---ccHHHHHHHHhhCCCCccEEEEEeecChhHHHH
Q 022724          152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR---GFKDQIYDVYRYLPPDLQVVLISATLPHEILEM  223 (293)
Q Consensus       152 ~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~---~~~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~  223 (293)
                                .....     ...+.++|+||=+=+....   .....+..+.....+...++.++|+...+....
T Consensus        86 ----------a~~~~-----~~~~~d~IlIDTaGr~~~~~~~~~~~el~~~~~~~~~~~~~LVl~a~~~~~~~~~  145 (211)
T d1j8yf2          86 ----------GVEKF-----LSEKMEIIIVDTAGRHGYGEEAALLEEMKNIYEAIKPDEVTLVIDASIGQKAYDL  145 (211)
T ss_dssp             ----------HHHHH-----HHTTCSEEEEECCCSCCTTCHHHHHHHHHHHHHHHCCSEEEEEEEGGGGGGHHHH
T ss_pred             ----------HHHHh-----hccCCceEEEecCCcCccchhhHHHHHHHHHHhhcCCceEEEEEecccCcchHHH
Confidence                      00000     1123455666655321101   112345555555555566778888886554443

>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=96.18  E-value=0.0054  Score=43.75  Aligned_cols=41  Identities=10%  Similarity=0.159  Sum_probs=27.5

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHH
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~  112 (293)
                      .|.--+++||..||||. .++-.+++....  +.+++++-|...
T Consensus         6 ~G~l~lI~GpMfSGKTt-eLi~~~~~~~~~--g~~vl~i~~~~D   46 (141)
T d1xx6a1           6 HGWVEVIVGPMYSGKSE-ELIRRIRRAKIA--KQKIQVFKPEID   46 (141)
T ss_dssp             CCEEEEEECSTTSSHHH-HHHHHHHHHHHT--TCCEEEEEEC--
T ss_pred             ceeEEEEEeccccHHHH-HHHHHHHHhhhc--CCcEEEEEeccc
Confidence            34557889999999994 455555555443  447899999655

>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=96.08  E-value=0.013  Score=45.17  Aligned_cols=40  Identities=15%  Similarity=0.327  Sum_probs=26.9

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhhh--cCCcEEEEcCCCChhHHHHH
Q 022724           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII--KGRDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        34 ~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i~--~~~~~li~~~Tg~GKT~~~~   88 (293)
                      +|+++-..+++.+.|...               +.  +-.++++.||+|+|||..+-
T Consensus        22 ~~~diig~~~~~~~l~~~---------------i~~~~~~~lll~Gp~G~GKTtla~   63 (231)
T d1iqpa2          22 RLDDIVGQEHIVKRLKHY---------------VKTGSMPHLLFAGPPGVGKTTAAL   63 (231)
T ss_dssp             STTTCCSCHHHHHHHHHH---------------HHHTCCCEEEEESCTTSSHHHHHH
T ss_pred             CHHHccCcHHHHHHHHHH---------------HHcCCCCeEEEECCCCCcHHHHHH
Confidence            677776666666655442               11  22479999999999996543

>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=96.06  E-value=0.0067  Score=47.95  Aligned_cols=52  Identities=23%  Similarity=0.259  Sum_probs=30.4

Q ss_pred             cCcccCCCCHHHHHHHHHC--CCCCCcHHHHHHHHhhhcCCcEEEEcCCCChhHHHH
Q 022724           33 TSFDAMGIKDDLLRGIYQY--GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        33 ~~f~~~~l~~~i~~~l~~~--~~~~~~~~Q~~~~~~i~~~~~~li~~~Tg~GKT~~~   87 (293)
                      .+|+|.+-.+...+.+.+.  .+..|..+|..   -+...+.+++.||+|+|||+..
T Consensus         9 ~t~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~---g~~~~~~iLL~GppGtGKT~la   62 (256)
T d1lv7a_           9 TTFADVAGCDEAKEEVAELVEYLREPSRFQKL---GGKIPKGVLMVGPPGTGKTLLA   62 (256)
T ss_dssp             CCGGGSCSCHHHHHHTHHHHHHHHCGGGC--------CCCCEEEEECCTTSCHHHHH
T ss_pred             CCHHHHhchHHHHHHHHHHHHHHHCHHHHHHc---CCCCCCeEEeeCCCCCCccHHH
Confidence            5789988777777666542  01111111111   0112467999999999999653

>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=96.02  E-value=0.0059  Score=50.06  Aligned_cols=64  Identities=22%  Similarity=0.320  Sum_probs=40.3

Q ss_pred             HHHHHCCCCC---CcHHHHHHHHh-hhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHH
Q 022724           46 RGIYQYGFEK---PSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (293)
Q Consensus        46 ~~l~~~~~~~---~~~~Q~~~~~~-i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l  113 (293)
                      ..+.+.|+-.   ..+.+...+.. +..++|++|+||||||||.. +-+++..+..   ..+++.+-.+.|+
T Consensus       138 ~~l~~~g~~~~~~~~~~~~~~l~~~v~~~~nili~G~tgSGKTT~-l~al~~~i~~---~~rivtiEd~~El  205 (323)
T d1g6oa_         138 SFFEEQGFYNLLDNKEQAISAIKDGIAIGKNVIVCGGTGSGKTTY-IKSIMEFIPK---EERIISIEDTEEI  205 (323)
T ss_dssp             HHHHHTTTTTTCSSHHHHHHHHHHHHHHTCCEEEEESTTSSHHHH-HHHHGGGSCT---TCCEEEEESSCCC
T ss_pred             HHHHHHhhhcccccHHHHHHHHHHHHHhCCCEEEEeeccccchHH-HHHHhhhccc---ccceeeccchhhh
Confidence            3344444432   33444444444 45788999999999999954 4455555533   3467777777775

>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=95.94  E-value=0.12  Score=37.79  Aligned_cols=113  Identities=12%  Similarity=0.066  Sum_probs=74.1

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHHhcCCCCCCCc
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l~~~~~~~~~l  176 (293)
                      +.++||.|+++.-++.+.+.+..    .|+++..++|+.+..+..+.+    ....+|+|+|.      +-...++..++
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 GERTLVTVLTVRMAEELTSFLVE----HGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGIN------LLREGLDIPEV  100 (174)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHH----TTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESC------CCCTTCCCTTE
T ss_pred             CCcEEEEEcchhHHHHHHHHHHh----cCCceEEEecccchHHHHHHHHHHHCCCeEEEEeee------eeeeeccCCCC
Confidence            56899999999999999987775    478999999998877665544    25679999995      23446889999


Q ss_pred             cEEEecchhhhhcc-ccHHHHHHHHhhCCC-CccEEEEEeecChhHHHH
Q 022724          177 KLLVLDESDEMLSR-GFKDQIYDVYRYLPP-DLQVVLISATLPHEILEM  223 (293)
Q Consensus       177 ~~iViDE~h~~~~~-~~~~~~~~i~~~l~~-~~q~v~~SAt~~~~~~~~  223 (293)
                      +++|+=+++...-. .....+..+-+..+. ....+++.....+.+...
T Consensus       101 ~~Vi~~~~~~~~~~~~~~~~iq~~GR~gR~~~g~~~~~~~~~~~~~~~~  149 (174)
T d1c4oa2         101 SLVAILDADKEGFLRSERSLIQTIGRAARNARGEVWLYADRVSEAMQRA  149 (174)
T ss_dssp             EEEEETTTTSCSGGGSHHHHHHHHGGGTTSTTCEEEEECSSCCHHHHHH
T ss_pred             cEEEEeccccccccchhHHHHHHhhhhhhcCCCeeEEeecCCCHHHHHH
Confidence            99998777653211 112223333333322 234445544455554443

>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=95.90  E-value=0.011  Score=41.53  Aligned_cols=40  Identities=10%  Similarity=0.223  Sum_probs=27.3

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHH
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~  112 (293)
                      |.-.+++||..||||. -++-.++.....  +.+++++-|...
T Consensus         2 G~L~li~GpMfsGKTt-~Li~~~~~~~~~--g~~v~~ikp~~D   41 (133)
T d1xbta1           2 GQIQVILGPMFSGKST-ELMRRVRRFQIA--QYKCLVIKYAKD   41 (133)
T ss_dssp             CEEEEEECCTTSCHHH-HHHHHHHHHHTT--TCCEEEEEETTC
T ss_pred             cEEEEEEecccCHHHH-HHHHHHHHHHHc--CCcEEEEecccc
Confidence            4456889999999995 455555554443  446888888544

>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=95.80  E-value=0.019  Score=44.87  Aligned_cols=17  Identities=24%  Similarity=0.421  Sum_probs=14.4

Q ss_pred             CcEEEEcCCCChhHHHH
Q 022724           71 RDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~   87 (293)
                      +.+++.||+|+|||..+
T Consensus        41 ~~vLL~GppGtGKT~la   57 (246)
T d1d2na_          41 VSVLLEGPPHSGKTALA   57 (246)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             eEEEEECcCCCCHHHHH
Confidence            46999999999999554

>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=95.70  E-value=0.012  Score=45.36  Aligned_cols=43  Identities=19%  Similarity=0.308  Sum_probs=25.7

Q ss_pred             CccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEeecCh
Q 022724          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPH  218 (293)
Q Consensus       175 ~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt~~~  218 (293)
                      ....+|+||+|.+.... ...+..++...+....+++.+.....
T Consensus       108 ~~~viiiDe~d~l~~~~-~~~l~~~~~~~~~~~~~i~~~~~~~~  150 (237)
T d1sxjd2         108 PYKIIILDEADSMTADA-QSALRRTMETYSGVTRFCLICNYVTR  150 (237)
T ss_dssp             SCEEEEETTGGGSCHHH-HHHHHHHHHHTTTTEEEEEEESCGGG
T ss_pred             CceEEEEecccccCHHH-HHHHhhcccccccccccccccccccc
Confidence            45689999999986543 33344455555555556555444433

>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=95.39  E-value=0.0084  Score=49.97  Aligned_cols=17  Identities=29%  Similarity=0.558  Sum_probs=15.1

Q ss_pred             CcEEEEcCCCChhHHHH
Q 022724           71 RDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~   87 (293)
                      .|++++||||+|||..+
T Consensus        69 ~niLfiGPTGvGKTElA   85 (364)
T d1um8a_          69 SNILLIGPTGSGKTLMA   85 (364)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             cceeeeCCCCccHHHHH
Confidence            58999999999999664

>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=95.11  E-value=0.071  Score=38.56  Aligned_cols=74  Identities=12%  Similarity=0.122  Sum_probs=56.3

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHh----cCCcEEEeChHHHHHHHhcCCCCCCCc
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~ilV~Tp~~l~~~l~~~~~~~~~l  176 (293)
                      ..++||.|.++.-++++.+.+..    .++.+..++|+.+..+....+.    ....|+|+|.     . -...+++.++
T Consensus        27 ~~k~iIF~~s~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Td-----v-~~rGiDi~~v   96 (162)
T d1fuka_          27 VTQAVIFCNTRRKVEELTTKLRN----DKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTD-----L-LARGIDVQQV   96 (162)
T ss_dssp             CSCEEEEESSHHHHHHHHHHHHH----TTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEG-----G-GTTTCCCCSC
T ss_pred             CCcEEEEEEEEchHHHHHHHHhh----cCceEEEeccCCchhhHHHHHHHHhhcccceeeccc-----c-ccccccCCCc
Confidence            35799999999999999887654    4678889999988776655442    4578999996     2 2456889999


Q ss_pred             cEEEecch
Q 022724          177 KLLVLDES  184 (293)
Q Consensus       177 ~~iViDE~  184 (293)
                      +++|.=+.
T Consensus        97 ~~VI~~d~  104 (162)
T d1fuka_          97 SLVINYDL  104 (162)
T ss_dssp             SEEEESSC
T ss_pred             eEEEEecc
Confidence            99887554

>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=95.03  E-value=0.075  Score=38.77  Aligned_cols=75  Identities=11%  Similarity=0.052  Sum_probs=56.5

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHHhcCCCCCCCc
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l~~~~~~~~~l  176 (293)
                      +.++||.|+++.-++.+...+...    ++.+..++|+.+..+..+.+    ....+|+|+|.-      -...+++.++
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            458999999999999888877754    67888899988766655443    246789999972      2446788899


Q ss_pred             cEEEecchh
Q 022724          177 KLLVLDESD  185 (293)
Q Consensus       177 ~~iViDE~h  185 (293)
                      +++|.=++.
T Consensus       102 ~~VI~~d~p  110 (171)
T d1s2ma2         102 NVVINFDFP  110 (171)
T ss_dssp             EEEEESSCC
T ss_pred             EEEEecCCc
Confidence            988865553

>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=95.02  E-value=0.06  Score=39.81  Aligned_cols=76  Identities=16%  Similarity=0.201  Sum_probs=60.4

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHh----cCCcEEEeChHHHHHHHhcCCCCCCCc
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~ilV~Tp~~l~~~l~~~~~~~~~l  176 (293)
                      +.++||.|+++.-++.+...++    ..|+++..++|+.+..+..+.+.    ...+|+|+|.      +-...++..++
T Consensus        31 ~~~~iif~~~~~~~~~~~~~l~----~~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTd------v~~rGiDip~v  100 (181)
T d1t5la2          31 NERTLVTTLTKKMAEDLTDYLK----EAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN------LLREGLDIPEV  100 (181)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHH----TTTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESC------CCSSSCCCTTE
T ss_pred             CCeEEEEeehhhhhHHHHHHHH----hCCcceeEecCCccHHHHHHHHHHHHCCCCCEEEehh------HHHccCCCCCC
Confidence            4589999999999988888665    45889999999998776655442    4679999995      23456889999


Q ss_pred             cEEEecchhh
Q 022724          177 KLLVLDESDE  186 (293)
Q Consensus       177 ~~iViDE~h~  186 (293)
                      +++|.-++..
T Consensus       101 ~~VI~~d~p~  110 (181)
T d1t5la2         101 SLVAILDADK  110 (181)
T ss_dssp             EEEEETTTTS
T ss_pred             CEEEEecCCc
Confidence            9999988875

>d1jr6a_ c.37.1.14 (A:) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=94.77  E-value=0.0054  Score=43.60  Aligned_cols=25  Identities=24%  Similarity=0.486  Sum_probs=21.4

Q ss_pred             hhCCCCcEEEEcccchhHHHHHhhC
Q 022724          268 DTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       268 ~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      +...++++||||+|+++|+.+++.|
T Consensus        31 ~~~~~~k~IVFc~t~~~ae~la~~L   55 (138)
T d1jr6a_          31 EVIKGGRHLIFCHSKKKCDELAAKL   55 (138)
T ss_dssp             HHHTTSCEEEECSCHHHHHHHHHHH
T ss_pred             hhcCCCCEEEEeCcHHHHHHHHHHH
Confidence            3445679999999999999999876

>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=94.59  E-value=0.031  Score=47.06  Aligned_cols=41  Identities=17%  Similarity=0.285  Sum_probs=27.8

Q ss_pred             CcHHHHHHHHhhhcC--CcEEEEcCCCChhHHHHHHHHHhhhcc
Q 022724           56 PSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVDT   97 (293)
Q Consensus        56 ~~~~Q~~~~~~i~~~--~~~li~~~Tg~GKT~~~~~~~~~~l~~   97 (293)
                      +.+.|.+.+..+...  .-+++.||||||||.... .++..+..
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            346667777776654  358899999999996543 45555544

>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=94.45  E-value=0.016  Score=42.40  Aligned_cols=37  Identities=19%  Similarity=0.283  Sum_probs=23.6

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcC
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P  109 (293)
                      |++++.||+|+|||. .+-.++..+...... .+++.++
T Consensus         2 k~v~ItG~~GtGKTt-l~~~i~~~l~~~~~~-v~~~~~~   38 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTT-LIHKASEVLKSSGVP-VDGFYTE   38 (189)
T ss_dssp             CCEEEESCCSSCHHH-HHHHHHHHHHHTTCC-CEEEECC
T ss_pred             cEEEEECCCCCcHHH-HHHHHHHHHHHCCCE-EEEEEec
Confidence            789999999999996 333455555444322 3344444

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=94.41  E-value=0.008  Score=51.44  Aligned_cols=18  Identities=22%  Similarity=0.542  Sum_probs=15.5

Q ss_pred             CCcEEEEcCCCChhHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~   87 (293)
                      .+|++++||||+|||+.+
T Consensus        49 ksNILliGPTGvGKTlLA   66 (443)
T d1g41a_          49 PKNILMIGPTGVGKTEIA   66 (443)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             cccEEEECCCCCCHHHHH
Confidence            369999999999999654

>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=93.99  E-value=0.03  Score=45.33  Aligned_cols=18  Identities=22%  Similarity=0.542  Sum_probs=15.8

Q ss_pred             CCcEEEEcCCCChhHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~   87 (293)
                      .+++++.||||+|||+.+
T Consensus        49 ~~~iLl~GPpG~GKT~lA   66 (309)
T d1ofha_          49 PKNILMIGPTGVGKTEIA   66 (309)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            578999999999999654

>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=93.76  E-value=0.2  Score=37.46  Aligned_cols=72  Identities=14%  Similarity=0.113  Sum_probs=53.6

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH----hcCCcEEEeChHHHHHHHhcCCCCCCCc
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~l~~~~~~~~~l  176 (293)
                      +.++||.|+|+.-++.+...++.    .++.+..++|+.+.....+.+    ....+|+|+|.      +....+++.++
T Consensus        30 ~~~~IIF~~t~~~~~~l~~~l~~----~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd------~~~~GiD~p~v   99 (200)
T d1oywa3          30 GKSGIIYCNSRAKVEDTAARLQS----KGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATV------AFGMGINKPNV   99 (200)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHH----TTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECT------TSCTTTCCTTC
T ss_pred             CCCEEEEEeeehhhHHhhhhhcc----CCceeEEecCCCcHHHHHHHHHHHhcccceEEEecc------hhhhccCCCCC
Confidence            45799999999999999887765    367888899998766554433    24578999996      23346788889


Q ss_pred             cEEEec
Q 022724          177 KLLVLD  182 (293)
Q Consensus       177 ~~iViD  182 (293)
                      +++|.=
T Consensus       100 ~~VI~~  105 (200)
T d1oywa3         100 RFVVHF  105 (200)
T ss_dssp             CEEEES
T ss_pred             CEEEEC
Confidence            888643

>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=93.36  E-value=0.2  Score=35.87  Aligned_cols=138  Identities=15%  Similarity=0.171  Sum_probs=72.2

Q ss_pred             EEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHH-HHHhcC
Q 022724           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDI-RKLEHG  151 (293)
Q Consensus        73 ~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~  151 (293)
                      +.|-...|-|||.+++--++..+-.   |.+++++-=.+.-...-..   .+....++.+...-.+....... ..... 
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            5566778999999988777776654   4566766432211000001   11112233322211111111000 00000 


Q ss_pred             CcEEEeChHHHHHHHhcCCCCCCCccEEEecchhhhhcccc--HHHHHHHHhhCCCCccEEEEEeecChhHHHHH
Q 022724          152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF--KDQIYDVYRYLPPDLQVVLISATLPHEILEMT  224 (293)
Q Consensus       152 ~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~~~~~~~--~~~~~~i~~~l~~~~q~v~~SAt~~~~~~~~~  224 (293)
                            .........+ ..+.-..+++||+||+...+..++  ...+..+++..|...-+|+.--..|+.+.+.+
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                  0011122111 123345679999999999887764  45677777777777777777666788766654

>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=0.12  Score=40.12  Aligned_cols=26  Identities=19%  Similarity=0.245  Sum_probs=18.5

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhcc
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDT   97 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~   97 (293)
                      .++++.||+|+|||... -.+...+..
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            58999999999999553 234444433

>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=93.07  E-value=0.094  Score=44.03  Aligned_cols=67  Identities=28%  Similarity=0.334  Sum_probs=46.3

Q ss_pred             CCcHHHHHHHHhh----hcCC-cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcc
Q 022724           55 KPSAIQQRAVMPI----IKGR-DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDF  127 (293)
Q Consensus        55 ~~~~~Q~~~~~~i----~~~~-~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (293)
                      .|+--|-+++..+    .+|+ ...+.|.+||||++... .++...     +..+|||+|+...|.++++.++.+...
T Consensus         8 ~p~~dqp~aI~~l~~~L~~g~~~~~L~GlsgS~ka~~~A-~l~~~~-----~rp~LvVt~~~~~A~~l~~dL~~~l~~   79 (408)
T d1c4oa1           8 SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMA-KVIEAL-----GRPALVLAPNKILAAQLAAEFRELFPE   79 (408)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHH-HHHHHH-----TCCEEEEESSHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEecCCCCHHHHHHH-HHHHHh-----CCCEEEEeCCHHHHHHHHHHHHHhcCc
Confidence            4555565566654    3555 46889999999995432 222222     125899999999999999999987643

>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=93.00  E-value=0.26  Score=35.67  Aligned_cols=98  Identities=13%  Similarity=0.100  Sum_probs=66.6

Q ss_pred             cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHH---
Q 022724           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL---  148 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---  148 (293)
                      +..+..+....|- .++..++...    .+.++||.|+++.-++.+...++..    ++.+..++|+.+..+....+   
T Consensus        10 q~~v~v~~~~~K~-~~L~~ll~~~----~~~k~iiF~~~~~~~~~~~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f   80 (168)
T d2j0sa2          10 QFFVAVEREEWKF-DTLCDLYDTL----TITQAVIFCNTKRKVDWLTEKMREA----NFTVSSMHGDMPQKERESIMKEF   80 (168)
T ss_dssp             EEEEEESSTTHHH-HHHHHHHHHH----TSSEEEEECSSHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHH
T ss_pred             EEEEEecChHHHH-HHHHHHHHhC----CCCceEEEeeeHHHHHHHHHHhhhc----ccchhhhhhhhhHHHHHHHHHHH
Confidence            3444445555664 3344444443    2358999999999999988877654    56788889998877665444   


Q ss_pred             -hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEecch
Q 022724          149 -EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDES  184 (293)
Q Consensus       149 -~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~  184 (293)
                       ....+|+|+|.     . -...+++.+++++|.=++
T Consensus        81 k~g~~~iLv~Td-----~-~~rGiDi~~v~~VIn~d~  111 (168)
T d2j0sa2          81 RSGASRVLISTD-----V-WARGLDVPQVSLIINYDL  111 (168)
T ss_dssp             HHTSSCEEEECG-----G-GSSSCCCTTEEEEEESSC
T ss_pred             hcCCccEEeccc-----h-hcccccccCcceEEEecC
Confidence             24578999996     2 345688889998875443

>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=92.97  E-value=0.042  Score=46.42  Aligned_cols=42  Identities=19%  Similarity=0.356  Sum_probs=25.4

Q ss_pred             hcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHH
Q 022724           68 IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (293)
Q Consensus        68 ~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~  112 (293)
                      ...+|++|.|+||+|||.... .++..+...  +..++|+=|.-+
T Consensus        48 ~~~~H~~I~G~tGsGKT~~l~-~li~~~~~~--g~~~iiiD~kge   89 (433)
T d1e9ra_          48 AEPRHLLVNGATGTGKSVLLR-ELAYTGLLR--GDRMVIVDPNGD   89 (433)
T ss_dssp             GGGGCEEEEECTTSSHHHHHH-HHHHHHHHT--TCEEEEEEETTH
T ss_pred             cccceEEEEeCCCCcHHHHHH-HHHHHHHhC--CCCEEEEeCChh
Confidence            456799999999999997643 344333322  223444444443

>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=92.74  E-value=0.6  Score=32.97  Aligned_cols=73  Identities=12%  Similarity=0.196  Sum_probs=52.8

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHh----cCCcEEEeChHHHHHHHhcCCCCCCCc
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~ilV~Tp~~l~~~l~~~~~~~~~l  176 (293)
                      +.++||.|+++.-+.++...+++    .++.+..++++.+..+....+.    ....|+|+|. .+.+     .+++..+
T Consensus        28 ~~k~IIF~~s~~~~~~l~~~L~~----~g~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~-~~~~-----Gid~~~v   97 (155)
T d1hv8a2          28 EFYGLVFCKTKRDTKELASMLRD----IGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATD-VMSR-----GIDVNDL   97 (155)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHH----TTCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECT-THHH-----HCCCSCC
T ss_pred             CCCEEEEECchHHHHHHHhhhcc----cccccccccccchhhhhhhhhhhhhcccceeeeehh-HHhh-----hhhhccC
Confidence            34799999999999988887765    4678888999887666554442    4568999995 2222     4678888


Q ss_pred             cEEEecc
Q 022724          177 KLLVLDE  183 (293)
Q Consensus       177 ~~iViDE  183 (293)
                      +++|.=+
T Consensus        98 ~~Vi~~d  104 (155)
T d1hv8a2          98 NCVINYH  104 (155)
T ss_dssp             SEEEESS
T ss_pred             cEEEEec
Confidence            8887533

>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=92.70  E-value=0.28  Score=36.39  Aligned_cols=113  Identities=12%  Similarity=0.196  Sum_probs=57.9

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHhhhccC-----CCceeEEEEcCCHHHHH------HHHHHHHHhhccC---CceEEEEE
Q 022724           71 RDVIAQAQSGTGKTSMIALTVCQTVDTS-----SREVQALILSPTRELAT------QTEKVILAIGDFI---NIQAHACV  136 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~~~~~~~l~~~-----~~~~~~lil~P~~~l~~------q~~~~~~~~~~~~---~~~~~~~~  136 (293)
                      .|++++||.|.|||.... .+...+...     -.+ +-++-...-.|+.      +..++++.+....   .-++..+.
T Consensus        44 ~n~lLvG~pGVGKTalv~-~LA~ri~~~~vp~~L~~-~~i~~ld~~~LiAg~~~rG~~E~rl~~il~e~~~~~~~iILfI  121 (195)
T d1jbka_          44 NNPVLIGEPGVGKTAIVE-GLAQRIINGEVPEGLKG-RRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFI  121 (195)
T ss_dssp             CEEEEECCTTSCHHHHHH-HHHHHHHHTCSCGGGTT-CEEEEECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEE
T ss_pred             CCeEEEecCCcccHHHHH-HHHHHHHhCCCCHHHcC-ceEEEeeHHHHhccCCccHHHHHHHHHHHHHHhcCCCcEEEEc
Confidence            589999999999994432 222222221     112 3355554444432      4444454332211   11222222


Q ss_pred             C-------------CcchHHHHHHH-h-cCCc-EEEeChHHHHHHHhcCCCCCCCccEEEecchh
Q 022724          137 G-------------GKSVGEDIRKL-E-HGVH-VVSGTPGRVCDMIKRKTLRTRAIKLLVLDESD  185 (293)
Q Consensus       137 ~-------------~~~~~~~~~~~-~-~~~~-ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h  185 (293)
                      +             +.+.....+.. . .... |.-+||+.+..++....--.+++..|-|+|.+
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            1             22222333322 1 2233 34568988888776654445778889888875

>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=92.68  E-value=0.039  Score=39.31  Aligned_cols=19  Identities=21%  Similarity=0.414  Sum_probs=16.0

Q ss_pred             CCcEEEEcCCCChhHHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~   88 (293)
                      .|++++.||+|+|||..+-
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            4789999999999996544

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.34  E-value=0.24  Score=35.79  Aligned_cols=74  Identities=11%  Similarity=0.102  Sum_probs=54.3

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHh----cCCcEEEeChHHHHHHHhcCCCCCCCc
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~ilV~Tp~~l~~~l~~~~~~~~~l  176 (293)
                      +.++||.|+++.-++.+.+.+.+    .+..+..++|+.+..+....+.    ...+|+|+|.-      -...+++..+
T Consensus        27 ~~k~iIF~~~~~~~~~l~~~L~~----~~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T~~------~~~Gid~~~~   96 (168)
T d1t5ia_          27 FNQVVIFVKSVQRCIALAQLLVE----QNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNL------FGRGMDIERV   96 (168)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHH----TTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSC------CSTTCCGGGC
T ss_pred             CCeEEEEEeeeecchhhhhhhcc----ccccccccccccchhhhhhhhhhhccccceeeecccc------ccchhhcccc
Confidence            34799999999999888876664    4678889999987776654442    45789999941      2345677788


Q ss_pred             cEEEecch
Q 022724          177 KLLVLDES  184 (293)
Q Consensus       177 ~~iViDE~  184 (293)
                      +++|.=+.
T Consensus        97 ~~vi~~~~  104 (168)
T d1t5ia_          97 NIAFNYDM  104 (168)
T ss_dssp             SEEEESSC
T ss_pred             hhhhhhhc
Confidence            88776554

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=92.26  E-value=0.032  Score=40.41  Aligned_cols=19  Identities=47%  Similarity=0.749  Sum_probs=16.0

Q ss_pred             cCCcEEEEcCCCChhHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~   87 (293)
                      ++.++++.||+|+|||...
T Consensus         4 k~~~I~i~G~~GsGKTT~~   22 (174)
T d1y63a_           4 KGINILITGTPGTGKTSMA   22 (174)
T ss_dssp             SSCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHH
Confidence            3568999999999999654

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=92.20  E-value=0.19  Score=39.40  Aligned_cols=33  Identities=12%  Similarity=0.164  Sum_probs=25.2

Q ss_pred             EEEeChHHHHHHHhcCCCCCCCccEEEecchhh
Q 022724          154 VVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDE  186 (293)
Q Consensus       154 ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~  186 (293)
                      |.-+||+.+..++....-..+.+..|-|+|.+.
T Consensus       151 IgatT~eey~~~~e~d~al~rrF~~I~V~Eps~  183 (268)
T d1r6bx2         151 IGSTTYQEFSNIFEKDRALARRFQKIDITEPSI  183 (268)
T ss_dssp             EEEECHHHHHCCCCCTTSSGGGEEEEECCCCCH
T ss_pred             EEeCCHHHHHHHHhhcHHHHhhhcccccCCCCH
Confidence            455689888877766555568889999999874

>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=92.16  E-value=0.15  Score=43.13  Aligned_cols=54  Identities=20%  Similarity=0.170  Sum_probs=39.0

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCC---------CceeEEEEcCCHHHHHHHHHHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSS---------REVQALILSPTRELATQTEKVILA  123 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~---------~~~~~lil~P~~~l~~q~~~~~~~  123 (293)
                      ...++|.|+.|||||.+..--++..+....         ..-++++|+=|+.-+.++.+++..
T Consensus        16 ~g~~lv~A~AGsGKT~~l~~r~~~ll~~~~~~~~~~~~~~~~~IL~lTFT~kAA~Emk~RI~~   78 (485)
T d1w36b1          16 QGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRS   78 (485)
T ss_dssp             SSCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHH
T ss_pred             CCCeEEEEcCchHHHHHHHHHHHHHHhhCcccccccCCCCcccEeEeccHHHHHHHHHHHHHH
Confidence            457999999999999776555555543321         113588999899989998887754

>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=92.01  E-value=0.044  Score=42.18  Aligned_cols=18  Identities=28%  Similarity=0.481  Sum_probs=15.3

Q ss_pred             CcEEEEcCCCChhHHHHH
Q 022724           71 RDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~   88 (293)
                      .++++.||+|+|||..+-
T Consensus        36 ~~~L~~GPpGtGKT~lA~   53 (238)
T d1in4a2          36 DHVLLAGPPGLGKTTLAH   53 (238)
T ss_dssp             CCEEEESSTTSSHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHH
Confidence            489999999999996543

>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=91.32  E-value=0.058  Score=41.50  Aligned_cols=18  Identities=22%  Similarity=0.420  Sum_probs=15.3

Q ss_pred             CcEEEEcCCCChhHHHHH
Q 022724           71 RDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~   88 (293)
                      +++++.||+|+|||..+-
T Consensus        36 ~~~Ll~GPpG~GKTtla~   53 (239)
T d1ixsb2          36 EHLLLFGPPGLGKTTLAH   53 (239)
T ss_dssp             CCEEEECCTTSCHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHH
Confidence            589999999999996543

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=91.06  E-value=0.051  Score=39.14  Aligned_cols=17  Identities=24%  Similarity=0.503  Sum_probs=14.5

Q ss_pred             CcEEEEcCCCChhHHHH
Q 022724           71 RDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~   87 (293)
                      .+++++||.|||||...
T Consensus         5 ~~I~i~G~pGsGKTTia   21 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLG   21 (173)
T ss_dssp             CCEEEECSTTSSHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            57899999999999644

>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=90.83  E-value=0.065  Score=41.82  Aligned_cols=17  Identities=35%  Similarity=0.526  Sum_probs=14.3

Q ss_pred             CcEEEEcCCCChhHHHH
Q 022724           71 RDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~   87 (293)
                      +.+++.||+|+|||..+
T Consensus        33 ~~ilL~GpPGtGKT~la   49 (273)
T d1gvnb_          33 TAFLLGGQPGSGKTSLR   49 (273)
T ss_dssp             EEEEEECCTTSCTHHHH
T ss_pred             EEEEEECCCCCCHHHHH
Confidence            35999999999999654

>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=90.72  E-value=0.045  Score=39.87  Aligned_cols=16  Identities=19%  Similarity=0.368  Sum_probs=14.1

Q ss_pred             CcEEEEcCCCChhHHH
Q 022724           71 RDVIAQAQSGTGKTSM   86 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~   86 (293)
                      |.++|.||+|+|||..
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            6799999999999953

>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=90.58  E-value=0.044  Score=39.71  Aligned_cols=19  Identities=21%  Similarity=0.532  Sum_probs=15.8

Q ss_pred             cCCcEEEEcCCCChhHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~   87 (293)
                      .|+-+++.||+|||||...
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            4677899999999999643

>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=90.57  E-value=0.057  Score=38.11  Aligned_cols=15  Identities=20%  Similarity=0.428  Sum_probs=12.7

Q ss_pred             cEEEEcCCCChhHHH
Q 022724           72 DVIAQAQSGTGKTSM   86 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~   86 (293)
                      -++++|++|||||..
T Consensus         4 lIii~G~pGsGKTTl   18 (152)
T d1ly1a_           4 IILTIGCPGSGKSTW   18 (152)
T ss_dssp             EEEEECCTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            478899999999964

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=90.26  E-value=0.068  Score=38.49  Aligned_cols=18  Identities=17%  Similarity=0.477  Sum_probs=15.1

Q ss_pred             CcEEEEcCCCChhHHHHH
Q 022724           71 RDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~   88 (293)
                      ||++++|+.|+|||...-
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            579999999999996543

>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=90.01  E-value=0.054  Score=39.23  Aligned_cols=21  Identities=14%  Similarity=0.292  Sum_probs=17.2

Q ss_pred             hhcCCcEEEEcCCCChhHHHH
Q 022724           67 IIKGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~~~   87 (293)
                      -.+|.-++++|++|+|||..+
T Consensus         3 ~~~g~~I~l~G~~GsGKTTia   23 (183)
T d1m8pa3           3 ATQGFTIFLTGYMNSGKDAIA   23 (183)
T ss_dssp             TTCCEEEEEECSTTSSHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHH
Confidence            346777899999999999664

>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=89.81  E-value=0.069  Score=38.31  Aligned_cols=17  Identities=24%  Similarity=0.391  Sum_probs=13.9

Q ss_pred             CcEEEEcCCCChhHHHH
Q 022724           71 RDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~   87 (293)
                      +-+++.||+|+|||..+
T Consensus         3 klI~i~G~~GsGKTTva   19 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTC   19 (176)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            34789999999999653

>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=89.45  E-value=0.13  Score=38.62  Aligned_cols=32  Identities=9%  Similarity=0.063  Sum_probs=24.4

Q ss_pred             HHHHHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          259 KFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       259 k~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      ..+.+.+.+.+  ++++||||+|++.|+.+|..|
T Consensus        29 ~~~l~~~~i~~--~~~~LVF~~sRk~~~~~A~~L   60 (201)
T d2p6ra4          29 FEELVEECVAE--NGGVLVFESTRRGAEKTAVKL   60 (201)
T ss_dssp             HHHHHHHHHHT--TCCEEEECSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHc--CCcEEEEeCCHHHHHHHHHHH
Confidence            34455666654  579999999999999988764

>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=89.38  E-value=0.31  Score=38.03  Aligned_cols=42  Identities=14%  Similarity=0.124  Sum_probs=27.0

Q ss_pred             hhcCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCC
Q 022724           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~  110 (293)
                      +..|.-+++.|+||+|||...+-.+.+.....  +.+++++..-
T Consensus        32 ~~~G~l~vi~G~~G~GKT~~~~~la~~~a~~~--g~~v~~~s~E   73 (277)
T d1cr2a_          32 ARGGEVIMVTSGSGMGKSTFVRQQALQWGTAM--GKKVGLAMLE   73 (277)
T ss_dssp             BCTTCEEEEECSTTSSHHHHHHHHHHHHHHTS--CCCEEEEESS
T ss_pred             CCCCeEEEEEeCCCCCHHHHHHHHHHhhhhhc--ccceeEeeec
Confidence            45677899999999999954333333322222  4467888754

>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=89.19  E-value=0.19  Score=38.39  Aligned_cols=37  Identities=22%  Similarity=0.351  Sum_probs=25.0

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcC
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P  109 (293)
                      |.-+++.|++|+|||...+-.+.+.+..   +..+++++-
T Consensus        26 gsl~li~G~pGsGKT~l~~qia~~~~~~---~~~~~~is~   62 (242)
T d1tf7a2          26 DSIILATGATGTGKTLLVSRFVENACAN---KERAILFAY   62 (242)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHHTT---TCCEEEEES
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHh---ccccceeec
Confidence            4679999999999996655444443332   345677764

>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=89.06  E-value=0.11  Score=40.17  Aligned_cols=55  Identities=11%  Similarity=0.081  Sum_probs=31.7

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHhh-----hcCCcEEEEcCCCChhHHHHH
Q 022724           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPI-----IKGRDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        33 ~~f~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~i-----~~~~~~li~~~Tg~GKT~~~~   88 (293)
                      .+|+++-..+...+.|..+ +...-......+...     ...+++++.||+|+|||.+.-
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            4689988888887777652 000000011111111     112579999999999995543

>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=89.05  E-value=0.17  Score=39.84  Aligned_cols=43  Identities=19%  Similarity=0.249  Sum_probs=28.6

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELA  114 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~  114 (293)
                      .|+-+.+.||.|+|||...+..+......   +..++|+-.-..+-
T Consensus        59 ~g~i~e~~G~~~~GKT~l~l~~~~~~q~~---g~~~vyIDtE~~~~  101 (269)
T d1mo6a1          59 RGRVIEIYGPESSGKTTVALHAVANAQAA---GGVAAFIDAEHALD  101 (269)
T ss_dssp             SSSEEEEECSSSSSHHHHHHHHHHHHHHT---TCEEEEEESSCCCC
T ss_pred             cceeEEEecCCCcHHHHHHHHHHHHHhcC---CCEEEEEECCccCC
Confidence            35779999999999997665555444333   44677766544443

>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=88.78  E-value=0.23  Score=38.98  Aligned_cols=43  Identities=19%  Similarity=0.202  Sum_probs=27.5

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELAT  115 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l~~  115 (293)
                      |+-+.+.||.|+|||...+..+......   +..++|+---..+-.
T Consensus        57 g~itei~G~~~sGKT~l~l~~~~~aqk~---g~~v~yiDtE~~~~~   99 (268)
T d1xp8a1          57 GRITEIYGPESGGKTTLALAIVAQAQKA---GGTCAFIDAEHALDP   99 (268)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHT---TCCEEEEESSCCCCH
T ss_pred             ceEEEEecCCccchHHHHHHHHHHHHhC---CCEEEEEECCccCCH
Confidence            3578899999999997655444443332   346777765444433

>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=88.42  E-value=0.2  Score=35.63  Aligned_cols=35  Identities=20%  Similarity=0.224  Sum_probs=21.0

Q ss_pred             cEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcC
Q 022724           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P  109 (293)
                      -+.|+|+.|||||. .+-.++..+...  +.++.++..
T Consensus         4 vi~itG~~GSGKTT-L~~~L~~~l~~~--g~~v~v~~~   38 (170)
T d1np6a_           4 LLAFAAWSGTGKTT-LLKKLIPALCAR--GIRPGLIKH   38 (170)
T ss_dssp             EEEEECCTTSCHHH-HHHHHHHHHHHT--TCCEEEEEE
T ss_pred             EEEEEcCCCCCHHH-HHHHHHHHHHHC--CCeEEEecc
Confidence            36889999999994 333344444433  334555543

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=88.30  E-value=0.11  Score=37.33  Aligned_cols=19  Identities=26%  Similarity=0.480  Sum_probs=15.3

Q ss_pred             cCCcEEEEcCCCChhHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~   87 (293)
                      +.+-++++|++|||||..+
T Consensus         2 ~~kiI~l~G~~GsGKsTva   20 (178)
T d1qhxa_           2 TTRMIILNGGSSAGKSGIV   20 (178)
T ss_dssp             CCCEEEEECCTTSSHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            3566889999999999554

>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=88.16  E-value=0.12  Score=38.63  Aligned_cols=35  Identities=17%  Similarity=0.247  Sum_probs=31.6

Q ss_pred             cHHHHHHHHHhhCCCCcEEEEcccchhHHHHHhhC
Q 022724          258 WKFDTLCDLYDTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       258 ~k~~~l~~l~~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      .|...+.++++...+.++||||++.+.++.+++.|
T Consensus        79 ~K~~~l~~ll~~~~~~k~lvf~~~~~~~~~l~~~l  113 (200)
T d2fwra1          79 NKIRKLREILERHRKDKIIIFTRHNELVYRISKVF  113 (200)
T ss_dssp             HHHHHHHHHHHHTSSSCBCCBCSCHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhCCCCcEEEEeCcHHHHHHHHhhc
Confidence            48889999999988889999999999999998876

>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=87.99  E-value=0.18  Score=38.32  Aligned_cols=46  Identities=13%  Similarity=0.097  Sum_probs=27.0

Q ss_pred             HHHhhhc-----CCcEEEEcCCCChhHHHHHHHHHhhhcc---CCCceeEEEEc
Q 022724           63 AVMPIIK-----GRDVIAQAQSGTGKTSMIALTVCQTVDT---SSREVQALILS  108 (293)
Q Consensus        63 ~~~~i~~-----~~~~li~~~Tg~GKT~~~~~~~~~~l~~---~~~~~~~lil~  108 (293)
                      .++.++.     |+-+++.||+|+|||...+-.+.+....   ...+..++++.
T Consensus        22 ~LD~ll~GGi~~G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~   75 (251)
T d1szpa2          22 NLDTLLGGGVETGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYID   75 (251)
T ss_dssp             HHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEE
T ss_pred             HHHhhhCCCCcCCeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEe
Confidence            3455554     4689999999999996544333332221   12234566664

>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=87.82  E-value=0.36  Score=33.63  Aligned_cols=66  Identities=18%  Similarity=0.197  Sum_probs=48.1

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEE
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLV  180 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~l~~~~~~~~~l~~iV  180 (293)
                      +.++||.|+++.-|+++.+.+++.    ++++..++++....+.   .....+++|+|.     .+..+ ++ .+++++|
T Consensus        35 ~~k~IVFc~t~~~ae~la~~L~~~----G~~~~~~H~~~~~~~~---~~~~~~vlvaTd-----~~~~G-iD-~~v~~Vi  100 (138)
T d1jr6a_          35 GGRHLIFCHSKKKCDELAAKLVAL----GINAVAYYRGLDVSVI---PTNGDVVVVATD-----ALMTG-FT-GDFDSVI  100 (138)
T ss_dssp             TSCEEEECSCHHHHHHHHHHHHHH----TCEEEEECTTCCSCCC---TTSSCEEEEESS-----SSCSS-SC-CCBSEEE
T ss_pred             CCCEEEEeCcHHHHHHHHHHHhcc----ccchhhhhccchhhhh---hhhhcceeehhH-----HHHhc-cc-cccceEE
Confidence            347999999999999999988764    6788888988765433   235578999995     33333 55 5677764

>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=87.56  E-value=0.44  Score=37.91  Aligned_cols=55  Identities=7%  Similarity=-0.097  Sum_probs=38.9

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEECCcchHHHHHHHhcCCcEEEeCh
Q 022724          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTP  159 (293)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp  159 (293)
                      +.++++.||+..-++++.+.+++.    |.++..++|.....+..+......+|+|+|.
T Consensus        36 ~g~~~~F~~s~~~~~~~a~~L~~~----g~~V~~l~~~~~~~e~~~~~~~~~~~~~~t~   90 (299)
T d1yksa2          36 KRPTAWFLPSIRAANVMAASLRKA----GKSVVVLNRKTFEREYPTIKQKKPDFILATD   90 (299)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHT----TCCEEECCSSSCC--------CCCSEEEESS
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhc----CCeEEEEcCcCcHhHHhhhhcCCcCEEEEec
Confidence            347999999999999999988764    5678889988776665554556678999996

>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=87.49  E-value=0.14  Score=38.50  Aligned_cols=18  Identities=44%  Similarity=0.648  Sum_probs=15.5

Q ss_pred             cCCcEEEEcCCCChhHHH
Q 022724           69 KGRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~   86 (293)
                      +|+-++++||+|+|||..
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            477899999999999954

>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=86.82  E-value=0.36  Score=34.69  Aligned_cols=17  Identities=24%  Similarity=0.435  Sum_probs=14.1

Q ss_pred             CCcEEEEcCCCChhHHH
Q 022724           70 GRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~   86 (293)
                      +|-+++.|++|+|||..
T Consensus         1 ~kiI~i~G~~GsGKsT~   17 (190)
T d1khta_           1 NKVVVVTGVPGVGSTTS   17 (190)
T ss_dssp             CCEEEEECCTTSCHHHH
T ss_pred             CCEEEEECCCCCCHHHH
Confidence            35688999999999954

>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=86.77  E-value=0.16  Score=37.39  Aligned_cols=15  Identities=40%  Similarity=0.756  Sum_probs=13.4

Q ss_pred             CcEEEEcCCCChhHH
Q 022724           71 RDVIAQAQSGTGKTS   85 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~   85 (293)
                      +.++++||+|+|||.
T Consensus         2 rpIvl~GpsG~GK~t   16 (186)
T d1gkya_           2 RPIVISGPSGTGKST   16 (186)
T ss_dssp             CCEEEECCTTSSHHH
T ss_pred             CeEEEECCCCCCHHH
Confidence            568999999999995

>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=86.58  E-value=0.21  Score=37.04  Aligned_cols=25  Identities=20%  Similarity=0.104  Sum_probs=18.2

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhh
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQT   94 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~   94 (293)
                      |.-+++.||+|+|||...+-.+.+.
T Consensus        23 G~v~~i~G~~GsGKT~l~l~la~~~   47 (242)
T d1n0wa_          23 GSITEMFGEFRTGKTQICHTLAVTC   47 (242)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHHH
Confidence            5689999999999996544444433

>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=86.50  E-value=0.14  Score=36.73  Aligned_cols=18  Identities=22%  Similarity=0.375  Sum_probs=14.2

Q ss_pred             CcEEEEcCCCChhHHHHH
Q 022724           71 RDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~   88 (293)
                      +-++++||+|||||..+-
T Consensus         7 ~iivl~G~~GsGKsT~a~   24 (171)
T d1knqa_           7 HIYVLMGVSGSGKSAVAS   24 (171)
T ss_dssp             EEEEEECSTTSCHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            447889999999996543

>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=86.42  E-value=0.23  Score=36.39  Aligned_cols=20  Identities=25%  Similarity=0.410  Sum_probs=16.1

Q ss_pred             cCCcEEEEcCCCChhHHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~   88 (293)
                      +|..+++.||+|||||...-
T Consensus         2 ~~~riil~G~pGSGKsT~a~   21 (190)
T d1ak2a1           2 KGVRAVLLGPPGAGKGTQAP   21 (190)
T ss_dssp             CCCEEEEECCTTSSHHHHHH
T ss_pred             CccEEEEECCCCCCHHHHHH
Confidence            35678899999999996554

>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=86.27  E-value=0.17  Score=36.93  Aligned_cols=17  Identities=35%  Similarity=0.614  Sum_probs=14.8

Q ss_pred             CCcEEEEcCCCChhHHH
Q 022724           70 GRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~   86 (293)
                      |+-++++||+|+|||..
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            66789999999999954

>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=85.85  E-value=0.093  Score=38.57  Aligned_cols=19  Identities=37%  Similarity=0.457  Sum_probs=15.1

Q ss_pred             CCcEEEEcCCCChhHHHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~   88 (293)
                      |.-++++|++|||||..+-
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            4567799999999996543

>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=85.78  E-value=0.26  Score=35.48  Aligned_cols=18  Identities=17%  Similarity=0.252  Sum_probs=15.1

Q ss_pred             CcEEEEcCCCChhHHHHH
Q 022724           71 RDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~   88 (293)
                      +.+++.|+.|+|||...-
T Consensus         3 ~~Iil~G~~GsGKSTia~   20 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGR   20 (170)
T ss_dssp             CCEEEESCTTSSHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHH
Confidence            578899999999996554

>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=85.70  E-value=0.24  Score=35.59  Aligned_cols=41  Identities=17%  Similarity=0.067  Sum_probs=23.7

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEEEee
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISAT  215 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~SAt  215 (293)
                      .+.+++++||++...... ......+.+.+......++++..
T Consensus        98 ~~~~vlllDE~~~~~~~~-~~~~~~l~~~l~~~~~~il~~~h  138 (178)
T d1ye8a1          98 DRRKVIIIDEIGKMELFS-KKFRDLVRQIMHDPNVNVVATIP  138 (178)
T ss_dssp             CTTCEEEECCCSTTGGGC-HHHHHHHHHHHTCTTSEEEEECC
T ss_pred             cCCCceeecCCCccchhh-HHHHHHHHHHhccCCCEEEEEEc
Confidence            567899999987654322 33344444444444455555543

>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=85.52  E-value=0.076  Score=40.10  Aligned_cols=82  Identities=15%  Similarity=0.171  Sum_probs=50.8

Q ss_pred             CceeEEEEcCCHHHHHH-----HHHHHHHhhcc--CCceEEEEECCcchHHHHH---HHh-cCCcEEEeChHHHHHHHhc
Q 022724          100 REVQALILSPTRELATQ-----TEKVILAIGDF--INIQAHACVGGKSVGEDIR---KLE-HGVHVVSGTPGRVCDMIKR  168 (293)
Q Consensus       100 ~~~~~lil~P~~~l~~q-----~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~---~~~-~~~~ilV~Tp~~l~~~l~~  168 (293)
                      ++.++.++||..+-.+.     ..+....+.+.  .++++..+||.++..+..+   ... ...+|+|+|.     . -.
T Consensus        28 ~g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~~~iLVaTt-----V-iE  101 (206)
T d1gm5a4          28 RGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTT-----V-IE  101 (206)
T ss_dssp             TSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSS-----C-CC
T ss_pred             cCCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCCEEEEEEeh-----h-hh
Confidence            35689999998654332     22333333332  2667888999876554433   333 4579999995     2 33


Q ss_pred             CCCCCCCccEEEecchhhh
Q 022724          169 KTLRTRAIKLLVLDESDEM  187 (293)
Q Consensus       169 ~~~~~~~l~~iViDE~h~~  187 (293)
                      ..++..+..++|+.+++.+
T Consensus       102 ~GIDip~a~~iii~~a~~f  120 (206)
T d1gm5a4         102 VGIDVPRANVMVIENPERF  120 (206)
T ss_dssp             SCSCCTTCCEEEBCSCSSS
T ss_pred             ccccccCCcEEEEEccCCc
Confidence            4688999999999999875

>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=85.38  E-value=0.25  Score=35.73  Aligned_cols=17  Identities=18%  Similarity=0.389  Sum_probs=14.5

Q ss_pred             cEEEEcCCCChhHHHHH
Q 022724           72 DVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~   88 (293)
                      ++++.||+|||||....
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            58999999999997654

>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=85.36  E-value=3.4  Score=33.78  Aligned_cols=32  Identities=16%  Similarity=0.195  Sum_probs=23.4

Q ss_pred             EEEeChHHHHHHHhcCCCCCCCccEEEecchhh
Q 022724          154 VVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDE  186 (293)
Q Consensus       154 ilV~Tp~~l~~~l~~~~~~~~~l~~iViDE~h~  186 (293)
                      |.-+||+.+.. +....-..+++..|-|+|-+.
T Consensus       155 I~~tT~~ey~~-~e~d~al~rrF~~v~v~ep~~  186 (387)
T d1qvra2         155 IGATTLDEYRE-IEKDPALERRFQPVYVDEPTV  186 (387)
T ss_dssp             EEEECHHHHHH-HTTCTTTCSCCCCEEECCCCH
T ss_pred             eeecCHHHHHH-hcccHHHHHhcccccCCCCcH
Confidence            55668988865 454444468899999999875

>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=0.2  Score=36.37  Aligned_cols=16  Identities=31%  Similarity=0.518  Sum_probs=13.3

Q ss_pred             CcEEEEcCCCChhHHH
Q 022724           71 RDVIAQAQSGTGKTSM   86 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~   86 (293)
                      .-++++|++|||||..
T Consensus        15 ~liil~G~pGsGKST~   30 (172)
T d1yj5a2          15 EVVVAVGFPGAGKSTF   30 (172)
T ss_dssp             CEEEEECCTTSSHHHH
T ss_pred             EEEEEECCCCCCHHHH
Confidence            3588999999999953

>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=84.92  E-value=1.1  Score=34.46  Aligned_cols=39  Identities=18%  Similarity=0.236  Sum_probs=24.7

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcC
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P  109 (293)
                      .+..++|.|++|+|||..+-  .++........+.+.+-+.
T Consensus        22 ~~~pvlI~Ge~GtGK~~~A~--~ih~~s~~~~~~~~~~~~~   60 (247)
T d1ny5a2          22 AECPVLITGESGVGKEVVAR--LIHKLSDRSKEPFVALNVA   60 (247)
T ss_dssp             CCSCEEEECSTTSSHHHHHH--HHHHHSTTTTSCEEEEETT
T ss_pred             CCCCEEEECCCCcCHHHHHH--HHHHhcCCcccccccchhh
Confidence            46789999999999995432  4444444434444444443

>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=84.89  E-value=0.15  Score=41.31  Aligned_cols=19  Identities=26%  Similarity=0.400  Sum_probs=16.0

Q ss_pred             cCCcEEEEcCCCChhHHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~   87 (293)
                      .+.++++.||+|+|||..+
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            4578999999999999543

>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=84.86  E-value=0.2  Score=38.98  Aligned_cols=17  Identities=35%  Similarity=0.563  Sum_probs=14.8

Q ss_pred             CCcEEEEcCCCChhHHH
Q 022724           70 GRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~   86 (293)
                      .+.+++.||.|+|||+.
T Consensus        38 ~~giLL~GppGtGKT~l   54 (258)
T d1e32a2          38 PRGILLYGPPGTGKTLI   54 (258)
T ss_dssp             CCEEEEECCTTSSHHHH
T ss_pred             CceeEEecCCCCCchHH
Confidence            36799999999999964

>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=84.72  E-value=0.23  Score=36.63  Aligned_cols=16  Identities=38%  Similarity=0.725  Sum_probs=13.5

Q ss_pred             CcEEEEcCCCChhHHH
Q 022724           71 RDVIAQAQSGTGKTSM   86 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~   86 (293)
                      +-++++||+|+|||..
T Consensus         1 rpIvl~GPsGsGK~tl   16 (190)
T d1lvga_           1 RPVVLSGPSGAGKSTL   16 (190)
T ss_dssp             CCEEEECCTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            3589999999999954

>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=84.43  E-value=0.53  Score=35.77  Aligned_cols=25  Identities=16%  Similarity=0.097  Sum_probs=18.2

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhh
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQT   94 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~   94 (293)
                      |.-++|.||+|+|||...+-.+.+.
T Consensus        36 G~~~li~G~pGsGKT~~~lq~~~~~   60 (254)
T d1pzna2          36 QAITEVFGEFGSGKTQLAHTLAVMV   60 (254)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHHh
Confidence            4579999999999996554444443

>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=84.38  E-value=0.25  Score=36.10  Aligned_cols=17  Identities=12%  Similarity=0.431  Sum_probs=14.2

Q ss_pred             CCcEEEEcCCCChhHHH
Q 022724           70 GRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~   86 (293)
                      ++-++++||+|+||+..
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            35689999999999953

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC 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: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.16  E-value=0.34  Score=37.54  Aligned_cols=32  Identities=22%  Similarity=0.263  Sum_probs=24.3

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCC
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP  205 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~  205 (293)
                      .+-+++|+||.-.-+|......+..++..+.+
T Consensus       168 ~~p~ililDEpTs~LD~~~~~~i~~~l~~l~~  199 (251)
T d1jj7a_         168 RKPCVLILDDATSALDANSQLQVEQLLYESPE  199 (251)
T ss_dssp             TCCSEEEEESTTTTCCHHHHHHHHHHHHTCGG
T ss_pred             cCCcEEEecCcCcccChhhHHHHHHHHHHHhh
Confidence            66789999999887777666777777766653

>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=83.95  E-value=0.31  Score=36.66  Aligned_cols=39  Identities=21%  Similarity=0.264  Sum_probs=23.9

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcC
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P  109 (293)
                      .|.-++|.|++|+|||...+-.+.+.....  +..++++..
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            457899999999999955433333323222  224666654

>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=83.94  E-value=0.32  Score=35.33  Aligned_cols=17  Identities=18%  Similarity=0.409  Sum_probs=14.2

Q ss_pred             cEEEEcCCCChhHHHHH
Q 022724           72 DVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~   88 (293)
                      .+++.||+|||||...-
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            57899999999997553

>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=83.86  E-value=0.25  Score=35.87  Aligned_cols=17  Identities=24%  Similarity=0.384  Sum_probs=14.5

Q ss_pred             cEEEEcCCCChhHHHHH
Q 022724           72 DVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~   88 (293)
                      ++++.||.|||||...-
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            68999999999997554

>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=83.86  E-value=0.31  Score=37.21  Aligned_cols=45  Identities=11%  Similarity=-0.005  Sum_probs=26.7

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhhccC---CCceeEEEEcCCHHH
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTS---SREVQALILSPTREL  113 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~---~~~~~~lil~P~~~l  113 (293)
                      .|.-++|.||+|+|||...+-.+.+.....   .....++++......
T Consensus        36 ~G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (258)
T d1v5wa_          36 SMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTF   83 (258)
T ss_dssp             SSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCC
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEechHHHH
Confidence            346799999999999966554444433221   122345655554433

>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=83.73  E-value=0.48  Score=35.75  Aligned_cols=27  Identities=15%  Similarity=0.121  Sum_probs=19.9

Q ss_pred             cCCcEEEEcCCCChhHHHHHHHHHhhh
Q 022724           69 KGRDVIAQAQSGTGKTSMIALTVCQTV   95 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~~~~~~~~~l   95 (293)
                      .|.-++|.|++|+|||...+-.+.+..
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            356799999999999966555554443

>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=83.71  E-value=0.23  Score=35.96  Aligned_cols=16  Identities=19%  Similarity=0.219  Sum_probs=13.8

Q ss_pred             cEEEEcCCCChhHHHH
Q 022724           72 DVIAQAQSGTGKTSMI   87 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~   87 (293)
                      .+++.||+|||||...
T Consensus         2 ~I~i~G~pGSGKsT~~   17 (179)
T d1e4va1           2 RIILLGAPVAGKGTQA   17 (179)
T ss_dssp             EEEEEESTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            5789999999999654

>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=83.61  E-value=0.53  Score=38.54  Aligned_cols=36  Identities=14%  Similarity=0.129  Sum_probs=22.9

Q ss_pred             CCCCCcHHHHHHHHhhhc----CCcEEEEcCCCChhHHHH
Q 022724           52 GFEKPSAIQQRAVMPIIK----GRDVIAQAQSGTGKTSMI   87 (293)
Q Consensus        52 ~~~~~~~~Q~~~~~~i~~----~~~~li~~~Tg~GKT~~~   87 (293)
                      ++......-.+++..+..    ++.+++.||+|+|||..+
T Consensus       132 ~~~~~~~~i~~~l~~~~~~~~~~~~~~~~g~~~~gk~~~~  171 (362)
T d1svma_         132 LLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLA  171 (362)
T ss_dssp             TSTTHHHHHHHHHHHHHHCCTTCCEEEEECSTTSSHHHHH
T ss_pred             cccchHHHHHHHHHHHHhCCCCcCeEEEECCCCCCHHHHH
Confidence            444444443344444443    357999999999999543

>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=83.23  E-value=0.15  Score=39.65  Aligned_cols=15  Identities=27%  Similarity=0.366  Sum_probs=11.9

Q ss_pred             EEEEcCCCChhHHHH
Q 022724           73 VIAQAQSGTGKTSMI   87 (293)
Q Consensus        73 ~li~~~Tg~GKT~~~   87 (293)
                      +++.||+|+|||...
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

>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=83.23  E-value=0.26  Score=36.06  Aligned_cols=18  Identities=17%  Similarity=0.268  Sum_probs=14.8

Q ss_pred             CcEEEEcCCCChhHHHHH
Q 022724           71 RDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~   88 (293)
                      ..+++.||+|||||...-
T Consensus         4 m~I~i~GppGsGKsT~a~   21 (189)
T d1zaka1           4 LKVMISGAPASGKGTQCE   21 (189)
T ss_dssp             CCEEEEESTTSSHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            468999999999996543

>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=83.22  E-value=0.29  Score=34.98  Aligned_cols=18  Identities=17%  Similarity=0.329  Sum_probs=14.6

Q ss_pred             CcEEEEcCCCChhHHHHH
Q 022724           71 RDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        71 ~~~li~~~Tg~GKT~~~~   88 (293)
                      .++++.|+.|+|||...-
T Consensus         2 p~IvliG~~G~GKSTig~   19 (165)
T d2iyva1           2 PKAVLVGLPGSGKSTIGR   19 (165)
T ss_dssp             CSEEEECSTTSSHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHH
Confidence            357888999999996643

>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=83.22  E-value=0.43  Score=35.00  Aligned_cols=22  Identities=18%  Similarity=0.335  Sum_probs=17.5

Q ss_pred             hhcCCcEEEEcCCCChhHHHHH
Q 022724           67 IIKGRDVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        67 i~~~~~~li~~~Tg~GKT~~~~   88 (293)
                      +.+.+-+++.||+|||||...-
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            4566778999999999996543

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=83.21  E-value=0.39  Score=36.95  Aligned_cols=39  Identities=21%  Similarity=0.262  Sum_probs=25.2

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEE
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLI  212 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~  212 (293)
                      .+-+++|+||+-.-+|......+...+..+.+..-+|+.
T Consensus       156 ~~p~ililDEpts~LD~~~~~~i~~~l~~l~~~~Tvi~i  194 (241)
T d2pmka1         156 NNPKILIFDEATSALDYESEHVIMRNMHKICKGRTVIII  194 (241)
T ss_dssp             TCCSEEEECCCCSCCCHHHHHHHHHHHHHHHTTSEEEEE
T ss_pred             cccchhhhhCCccccCHHHHHHHHHHHHHHhCCCEEEEE
Confidence            567889999987777766566666555555444444443

>d1l2ta_ c.37.1.12 (A:) MJ0796 {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: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=82.60  E-value=0.44  Score=36.32  Aligned_cols=31  Identities=13%  Similarity=0.245  Sum_probs=21.8

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCC
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLP  204 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~  204 (293)
                      .+.+++++||.-.-+|......+..++..+.
T Consensus       162 ~~P~lLllDEPTs~LD~~~~~~i~~~l~~l~  192 (230)
T d1l2ta_         162 NNPPIILADQPTGALDSKTGEKIMQLLKKLN  192 (230)
T ss_dssp             TCCSEEEEESTTTTSCHHHHHHHHHHHHHHH
T ss_pred             cCCCEEEecCCccccCHHHHHHHHHHHHHHH
Confidence            5567888888877777666666666666653

>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=82.51  E-value=0.27  Score=39.58  Aligned_cols=16  Identities=25%  Similarity=0.476  Sum_probs=13.8

Q ss_pred             cEEEEcCCCChhHHHH
Q 022724           72 DVIAQAQSGTGKTSMI   87 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~   87 (293)
                      +++++||||+|||..+
T Consensus        54 ~~lf~Gp~GvGKT~la   69 (315)
T d1r6bx3          54 SFLFAGPTGVGKTEVT   69 (315)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCcchhHHHH
Confidence            6899999999999544

>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=82.48  E-value=0.49  Score=37.17  Aligned_cols=34  Identities=18%  Similarity=0.337  Sum_probs=26.4

Q ss_pred             HHHHHHHHH----hhCCCCcEEEEcccchhHHHHHhhC
Q 022724          259 KFDTLCDLY----DTLTITQAVIFCNTKRKVLLLVLQF  292 (293)
Q Consensus       259 k~~~l~~l~----~~~~~~~~iIF~~s~~~a~~l~~~L  292 (293)
                      |...+.+++    ....+.++||||+++..++.+++.|
T Consensus       144 K~~~l~~~l~~~~~~~~~~k~iiF~~~~~~~~~~~~~L  181 (286)
T d1wp9a2         144 KMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNEL  181 (286)
T ss_dssp             HHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCCcEEEEeCcHHhHHHHHHHH
Confidence            655555444    4567789999999999999998865

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=82.45  E-value=0.6  Score=33.14  Aligned_cols=33  Identities=9%  Similarity=-0.034  Sum_probs=19.5

Q ss_pred             EEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEc
Q 022724           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (293)
Q Consensus        73 ~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~  108 (293)
                      +.|+|+.|||||.. +-.++..+...  |.++.++-
T Consensus         4 i~I~G~~gSGKTTl-i~~l~~~L~~~--g~~v~vik   36 (165)
T d1xjca_           4 WQVVGYKHSGKTTL-MEKWVAAAVRE--GWRVGTVK   36 (165)
T ss_dssp             EEEECCTTSSHHHH-HHHHHHHHHHT--TCCEEEEE
T ss_pred             EEEEeCCCCCHHHH-HHHHHHHHHhC--CCeEEEEE
Confidence            45899999999943 33444444443  33444443

>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=82.13  E-value=0.51  Score=37.95  Aligned_cols=23  Identities=30%  Similarity=0.556  Sum_probs=17.3

Q ss_pred             HHhhhcCCc--EEEEcCCCChhHHH
Q 022724           64 VMPIIKGRD--VIAQAQSGTGKTSM   86 (293)
Q Consensus        64 ~~~i~~~~~--~li~~~Tg~GKT~~   86 (293)
                      ++.+++|.|  ++..|+||||||..
T Consensus        68 v~~~l~G~n~~i~aYGqtgSGKTyT   92 (323)
T d1bg2a_          68 VKDVLEGYNGTIFAYGQTSSGKTHT   92 (323)
T ss_dssp             HHHHHTTCCEEEEEECSTTSSHHHH
T ss_pred             HHHHHcCCCcceeeecccCCCCcee
Confidence            344567875  67779999999965

>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=81.95  E-value=0.29  Score=38.21  Aligned_cols=17  Identities=29%  Similarity=0.495  Sum_probs=14.9

Q ss_pred             CCcEEEEcCCCChhHHH
Q 022724           70 GRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~   86 (293)
                      .+.+++.||+|+|||+.
T Consensus        41 ~~giLL~Gp~GtGKT~l   57 (265)
T d1r7ra3          41 SKGVLFYGPPGCGKTLL   57 (265)
T ss_dssp             CCEEEEBCCTTSSHHHH
T ss_pred             CCeEEEECCCCCcchhH
Confidence            46899999999999954

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-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: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=81.31  E-value=0.65  Score=36.12  Aligned_cols=41  Identities=17%  Similarity=0.240  Sum_probs=27.3

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEEcCCHHH
Q 022724           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (293)
Q Consensus        70 ~~~~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil~P~~~l  113 (293)
                      |+-+.+.||+|+|||...+-.+......   +..++|+---...
T Consensus        54 g~itei~G~~gsGKTtl~l~~~~~~q~~---g~~~vyidtE~~~   94 (263)
T d1u94a1          54 GRIVEIYGPESSGKTTLTLQVIAAAQRE---GKTCAFIDAEHAL   94 (263)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHT---TCCEEEEESSCCC
T ss_pred             ceEEEEecCCCcHHHHHHHHHHHHHHcC---CCEEEEEcccccc
Confidence            4679999999999997665555554433   3456776644333

>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=81.09  E-value=0.45  Score=34.90  Aligned_cols=17  Identities=18%  Similarity=0.294  Sum_probs=13.6

Q ss_pred             cEEEEcCCCChhHHHHH
Q 022724           72 DVIAQAQSGTGKTSMIA   88 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~~   88 (293)
                      -+++.||+|||||..+-
T Consensus        10 iI~i~GppGSGKsT~a~   26 (196)
T d1ukza_          10 VIFVLGGPGAGKGTQCE   26 (196)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47888999999995543

>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=81.07  E-value=0.42  Score=34.97  Aligned_cols=16  Identities=25%  Similarity=0.337  Sum_probs=13.4

Q ss_pred             cEEEEcCCCChhHHHH
Q 022724           72 DVIAQAQSGTGKTSMI   87 (293)
Q Consensus        72 ~~li~~~Tg~GKT~~~   87 (293)
                      -+++.||.|||||...
T Consensus         8 iI~i~G~pGSGKsT~a   23 (194)
T d1qf9a_           8 VVFVLGGPGSGKGTQC   23 (194)
T ss_dssp             EEEEEESTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4788999999999654

>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=80.92  E-value=0.71  Score=35.68  Aligned_cols=63  Identities=13%  Similarity=0.181  Sum_probs=36.8

Q ss_pred             HHHhhhcCCcEEEEcCCCChhHHHHHHHHHhhhccC--------CCceeEEEEcCCHHHHHHHHHHHHHhhcc
Q 022724           63 AVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS--------SREVQALILSPTRELATQTEKVILAIGDF  127 (293)
Q Consensus        63 ~~~~i~~~~~~li~~~Tg~GKT~~~~~~~~~~l~~~--------~~~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (293)
                      +++-+..|.-+++.|++|+|||...+-.++ .+...        ..+.+++|+.- ..-..++..++..+...
T Consensus        22 li~G~~pg~~~~i~G~~G~GKS~l~l~la~-~ia~g~~~~~~~~~~~~~vl~~~~-E~~~~~~~~Rl~~~~~~   92 (274)
T d1nlfa_          22 VLPNMVAGTVGALVSPGGAGKSMLALQLAA-QIAGGPDLLEVGELPTGPVIYLPA-EDPPTAIHHRLHALGAH   92 (274)
T ss_dssp             EETTEETTSEEEEEESTTSSHHHHHHHHHH-HHHTCCCTTCCCCCCCCCEEEEES-SSCHHHHHHHHHHHHTT
T ss_pred             HhCCccCCcEEEEEeCCCCCHHHHHHHHHH-HHHcCCCcccccccCCCceEEEec-cchHHHHHHHHHHHhhc
Confidence            345555678899999999999955443333 22211        12335666653 22345666666665543

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=80.37  E-value=0.36  Score=35.15  Aligned_cols=14  Identities=29%  Similarity=0.373  Sum_probs=11.5

Q ss_pred             EEEEcCCCChhHHH
Q 022724           73 VIAQAQSGTGKTSM   86 (293)
Q Consensus        73 ~li~~~Tg~GKT~~   86 (293)
                      +.|.||+|||||..
T Consensus        25 IgI~G~~GSGKSTl   38 (198)
T d1rz3a_          25 LGIDGLSRSGKTTL   38 (198)
T ss_dssp             EEEEECTTSSHHHH
T ss_pred             EEEECCCCCCHHHH
Confidence            44899999999954

>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=80.35  E-value=0.38  Score=35.84  Aligned_cols=18  Identities=39%  Similarity=0.565  Sum_probs=15.8

Q ss_pred             cCCcEEEEcCCCChhHHH
Q 022724           69 KGRDVIAQAQSGTGKTSM   86 (293)
Q Consensus        69 ~~~~~li~~~Tg~GKT~~   86 (293)
                      +|.-+.+.||.|+|||..
T Consensus        26 ~Gei~~l~G~NGsGKSTL   43 (200)
T d1sgwa_          26 KGNVVNFHGPNGIGKTTL   43 (200)
T ss_dssp             TTCCEEEECCTTSSHHHH
T ss_pred             CCCEEEEECCCCChHHHH
Confidence            678899999999999953

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

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: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=80.31  E-value=0.54  Score=36.14  Aligned_cols=39  Identities=23%  Similarity=0.284  Sum_probs=26.2

Q ss_pred             CCccEEEecchhhhhccccHHHHHHHHhhCCCCccEEEE
Q 022724          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLI  212 (293)
Q Consensus       174 ~~l~~iViDE~h~~~~~~~~~~~~~i~~~l~~~~q~v~~  212 (293)
                      .+.+++|+||.-.-+|......+...+..+.+..-+|+.
T Consensus       156 ~~p~ililDEpts~LD~~~~~~i~~~l~~l~~~~Tvi~i  194 (242)
T d1mv5a_         156 RNPKILMLDEATASLDSESESMVQKALDSLMKGRTTLVI  194 (242)
T ss_dssp             HCCSEEEEECCSCSSCSSSCCHHHHHHHHHHTTSEEEEE
T ss_pred             cCCCEEEecCCccccCHHHHHHHHHHHHHHcCCCEEEEE
Confidence            456789999998877776666666666665444444443

>d1sq5a_ c.37.1.6 (A:) Pantothenate kinase PanK {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: Phosphoribulokinase/pantothenate kinase
domain: Pantothenate kinase PanK
species: Escherichia coli [TaxId: 562]

Probab=80.01  E-value=0.86  Score=36.28  Aligned_cols=34  Identities=6%  Similarity=0.116  Sum_probs=19.2

Q ss_pred             EEEEcCCCChhHHHHHHHHHhhhccCCCceeEEEE
Q 022724           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALIL  107 (293)
Q Consensus        73 ~li~~~Tg~GKT~~~~~~~~~~l~~~~~~~~~lil  107 (293)
                      +.|.|+.|+|||...- .+-..+.....++++.++
T Consensus        83 IGIaG~sgSGKSTla~-~L~~lL~~~~~~~~v~~I  116 (308)
T d1sq5a_          83 ISIAGSVAVGKSTTAR-VLQALLSRWPEHRRVELI  116 (308)
T ss_dssp             EEEEECTTSSHHHHHH-HHHHHHTTSTTCCCEEEE
T ss_pred             EEEeCCCCCCCcHHHH-HHHHHHhhhcCCCceEEE
Confidence            5678999999995432 122223333334555554