Citrus Sinensis ID: 027749

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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-------22
Protein Sequence
MAAATAMRRRGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFLFD
Secondary Structure (PSIPRED)
ccHHHHHHHccccccccccccccccccccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHccccEEEEcccccHHHHHHHHHHHHHHcccccccEEEEEcccHHHHHHHHHHHHHHHcccccEEEEEEccccHHHHHHHHcccccEEEEccHHHHHHHcccccccccccEEEEEccHHHcccccHHHHHHHHHHcccccEEEEEEEccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccHHHHccccEEEEccccccccccHHHccccHHHHHHHHHcccccccccHHHHHHHHHccccEEEEccccHHHHHHHHHHHHHHcccccccccEEEEcccHHHHHHHHHHHHHHcccccccEEEEcccccHHHHHHHHHHccEEEEEcHHHHHHHHcccccccccccEEEEccHHHHHccccHHHHHHHHHccccccEEEEEEcccccc
Coil and Loop (DISEMBL)
MAAATAMRrrgggggmdddkMVFETTEGVeaitsfdamgiKDDLLRGIYQygfekpsaiqqravmpiikgrDVIAqaqsgtgktSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFiniqahacvggksvgedIRKLehgvhvvsgtpgrvcdmIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDvyrylppdlqvccpgscflfd
Flexible Loop (DISEMBL)
maaatamrrrgggggmdddkMVFETTEGVEaitsfdamgiKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAqsgtgktsmIALTVCQTVDTSSREVQALIlsptrelatQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEhgvhvvsgtpgrvcdmikrkTLRTRAIKLlvldesdemlSRGFKDQIYDVYRYLPPDLQVCCPGSCFLFD
Low Complexity Region (SEG)
maaatamrrrgggggmdddKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFLFD
Disordered region (IsUnstruct)
***********************ETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFLF*
Disordered Region (DISOPRED)
**************************EGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFLF*
Disordered Region (DISEMBL)
*************GGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFLFD
Disordered Region (DISPRO)
***********GGG*MDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSC****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAAATAMRRRGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFLFD
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	219	2.2.26 [Sep-21-2011]
Q5VNM3	404	DEAD-box ATP-dependent RN	yes	no	0.949	0.514	0.833	1e-101
Q10I26	404	DEAD-box ATP-dependent RN	yes	no	0.949	0.514	0.823	1e-100
Q94A52	408	DEAD-box ATP-dependent RN	yes	no	0.894	0.480	0.872	2e-99
P41380	391	Eukaryotic initiation fac	N/A	no	0.890	0.498	0.866	1e-97
Q9C8J1	392	DEAD-box ATP-dependent RN	no	no	0.899	0.502	0.720	1e-82
Q4P184	397	ATP-dependent RNA helicas	N/A	no	0.913	0.503	0.67	1e-80
P0CQ72	396	ATP-dependent RNA helicas	yes	no	0.949	0.525	0.629	4e-78
P0CQ73	396	ATP-dependent RNA helicas	N/A	no	0.949	0.525	0.629	4e-78
B5DG42	406	Eukaryotic initiation fac	N/A	no	0.958	0.517	0.652	1e-77
Q7ZVA6	406	Eukaryotic initiation fac	yes	no	0.958	0.517	0.652	2e-77

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

 Score =  367 bits (941), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 175/210 (83%), Positives = 192/210 (91%), Gaps = 2/210 (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 LDESDEMLSRGFKDQIYDVYRYLPPDLQVC 210
           LDE+DEML RGFKDQIYDVYRYLPP+LQVC
Sbjct: 179 LDEADEMLGRGFKDQIYDVYRYLPPELQVC 208

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 =  364 bits (934), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 173/210 (82%), Positives = 192/210 (91%), Gaps = 2/210 (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 LDESDEMLSRGFKDQIYDVYRYLPPDLQVC 210
           LDE+DEML RGFKDQIYDVYRYLPP+LQVC
Sbjct: 179 LDEADEMLGRGFKDQIYDVYRYLPPELQVC 208

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 =  361 bits (927), Expect = 2e-99,   Method: Compositional matrix adjust.
 Identities = 171/196 (87%), Positives = 186/196 (94%)

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 QIYDVYRYLPPDLQVC 210
           QIYDVYRYLPPDLQVC
Sbjct: 197 QIYDVYRYLPPDLQVC 212

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 =  355 bits (911), Expect = 1e-97,   Method: Compositional matrix adjust.
 Identities = 169/195 (86%), Positives = 183/195 (93%)

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 IYDVYRYLPPDLQVC 210
           IYDVYRYLPP+LQV 
Sbjct: 181 IYDVYRYLPPELQVV 195

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|Q9C8J1|RH34_ARATH DEAD-box ATP-dependent RNA helicase 34 OS=Arabidopsis thaliana GN=RH34 PE=2 SV=2

 Score =  305 bits (782), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 142/197 (72%), Positives = 173/197 (87%)

Query: 14  GGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDV 73
           G +D++ +VFETT+G++ I SFD MG+ D +LRG+Y YG++KPS IQQRA++PI+KGRDV
Sbjct: 3   GTLDEENLVFETTKGIKPIKSFDDMGMNDKVLRGVYDYGYKKPSEIQQRALVPILKGRDV 62

Query: 74  IAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAH 133
           IAQAQSGTGKTSMIA++VCQ V+ SSR+VQ L+LSP+RELA+QTEK I AIG   NIQAH
Sbjct: 63  IAQAQSGTGKTSMIAISVCQIVNISSRKVQVLVLSPSRELASQTEKTIQAIGAHTNIQAH 122

Query: 134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFK 193
           AC+GGKS+GEDI+KLE GVH VSGTPGRV DMIKR +L+T+A+KLLVLDESDEMLS+G K
Sbjct: 123 ACIGGKSIGEDIKKLERGVHAVSGTPGRVYDMIKRGSLQTKAVKLLVLDESDEMLSKGLK 182

Query: 194 DQIYDVYRYLPPDLQVC 210
           DQIYDVYR LP D+QVC
Sbjct: 183 DQIYDVYRALPHDIQVC 199

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

 Score =  299 bits (765), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 134/200 (67%), Positives = 170/200 (85%)

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 GFKDQIYDVYRYLPPDLQVC 210
           GFKDQIYDVYRYLPP  QV 
Sbjct: 182 GFKDQIYDVYRYLPPSTQVV 201

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

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

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

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

 Score =  290 bits (743), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 131/208 (62%), Positives = 169/208 (81%)

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

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

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

Query: 192 FKDQIYDVYRYLPPDLQVCCPGSCFLFD 219
           FKDQIYD+YRYLPP  QV    +    D
Sbjct: 182 FKDQIYDIYRYLPPATQVVVVSATLPHD 209

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

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

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

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

 Score =  290 bits (743), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 131/208 (62%), Positives = 169/208 (81%)

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

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

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

Query: 192 FKDQIYDVYRYLPPDLQVCCPGSCFLFD 219
           FKDQIYD+YRYLPP  QV    +    D
Sbjct: 182 FKDQIYDIYRYLPPATQVVVVSATLPHD 209

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

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

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|B5DG42|IF4A3_SALSA Eukaryotic initiation factor 4A-III OS=Salmo salar GN=eif4a3 PE=2 SV=1

 Score =  288 bits (738), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 137/210 (65%), Positives = 171/210 (81%)

Query: 1   MAAATAMRRRGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQ 60
           M  AT  R R      D  K+ FET+E V+   +FD MG+++DLLRGIY YGFEKPSAIQ
Sbjct: 1   MEVATVPRTRRLLKEEDMTKIEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQ 60

Query: 61  QRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKV 120
           QRA+  IIKGRDVIAQ+QSGTGKT+   ++V Q +D   RE QALIL+PTRELA Q +KV
Sbjct: 61  QRAIKQIIKGRDVIAQSQSGTGKTATFCVSVLQCLDIQVRETQALILAPTRELAGQIQKV 120

Query: 121 ILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLV 180
           +LA+GD++N+Q H+C+GG +VGEDIRKL++G HVV+GTPGRV DMI+R++LRTRAIK+LV
Sbjct: 121 LLALGDYMNVQCHSCIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLV 180

Query: 181 LDESDEMLSRGFKDQIYDVYRYLPPDLQVC 210
           LDE+DEML++GFK+QIYDVYRYLPP  QVC
Sbjct: 181 LDEADEMLNKGFKEQIYDVYRYLPPATQVC 210

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. Binds spliced mRNA in sequence-independent manner, 20-24 nucleotides upstream of mRNA exon-exon junctions.

Salmo salar (taxid: 8030)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q7ZVA6|IF4A3_DANRE Eukaryotic initiation factor 4A-III OS=Danio rerio GN=eif4a3 PE=2 SV=1

 Score =  288 bits (737), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 137/210 (65%), Positives = 171/210 (81%)

Query: 1   MAAATAMRRRGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQ 60
           MA A    R+      D  K+ FET+E V+   +FD MG+++DLLRGIY YGFEKPSAIQ
Sbjct: 1   MATAVVPVRKRILKEEDMTKIEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQ 60

Query: 61  QRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKV 120
           QRA+  IIKGRDVIAQ+QSGTGKT+   ++V Q +D   RE QALIL+PTRELA Q +KV
Sbjct: 61  QRAIKQIIKGRDVIAQSQSGTGKTATFCVSVLQCLDIQVRETQALILAPTRELAGQIQKV 120

Query: 121 ILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLV 180
           +LA+GD++N+Q HAC+GG +VGEDIRKL++G HVV+GTPGRV DMI+R++LRTRAIK+LV
Sbjct: 121 LLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLV 180

Query: 181 LDESDEMLSRGFKDQIYDVYRYLPPDLQVC 210
           LDE+DEML++GFK+QIYDVYRYLPP  QVC
Sbjct: 181 LDEADEMLNKGFKEQIYDVYRYLPPATQVC 210

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. Binds spliced mRNA in sequence-independent manner, 20-24 nucleotides upstream of mRNA exon-exon junctions.

Danio rerio (taxid: 7955)

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	219
225464928	412	PREDICTED: eukaryotic initiation factor	0.954	0.507	0.869	1e-102
356530272	407	PREDICTED: DEAD-box ATP-dependent RNA he	0.926	0.498	0.887	1e-100
255559772	407	dead box ATP-dependent RNA helicase, put	0.885	0.476	0.912	1e-100
356556161	406	PREDICTED: DEAD-box ATP-dependent RNA he	0.922	0.497	0.882	1e-100
115438787	404	Os01g0639100 [Oryza sativa Japonica Grou	0.949	0.514	0.833	3e-99
388500968	406	unknown [Medicago truncatula]	0.945	0.509	0.863	3e-99
118574850	406	DH [Medicago sativa]	0.945	0.509	0.859	8e-99
297830638	408	hypothetical protein ARALYDRAFT_479492 [	0.890	0.477	0.887	1e-98
115453811	404	Os03g0566800 [Oryza sativa Japonica Grou	0.949	0.514	0.823	2e-98
125586856	394	hypothetical protein OsJ_11472 [Oryza sa	0.949	0.527	0.823	2e-98

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

 Score =  376 bits (965), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 186/214 (86%), Positives = 198/214 (92%), Gaps = 5/214 (2%)

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 KLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVC 210
           KLLVLDESDEMLSRGFKDQIYDVYRYLPP+LQV 
Sbjct: 183 KLLVLDESDEMLSRGFKDQIYDVYRYLPPELQVV 216

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  370 bits (950), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 182/205 (88%), Positives = 190/205 (92%), Gaps = 2/205 (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 EMLSRGFKDQIYDVYRYLPPDLQVC 210
           EMLSRGFKDQIYDVYRYLPPDLQVC
Sbjct: 187 EMLSRGFKDQIYDVYRYLPPDLQVC 211

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  369 bits (946), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 177/194 (91%), Positives = 187/194 (96%)

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 YDVYRYLPPDLQVC 210
           YDVYRYLPP+LQV 
Sbjct: 198 YDVYRYLPPELQVV 211

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  368 bits (945), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 181/205 (88%), Positives = 190/205 (92%), Gaps = 3/205 (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 EMLSRGFKDQIYDVYRYLPPDLQVC 210
           EMLSRGFKDQIYDVYRYLPPDLQVC
Sbjct: 186 EMLSRGFKDQIYDVYRYLPPDLQVC 210

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 =  367 bits (941), Expect = 3e-99,   Method: Compositional matrix adjust.
 Identities = 175/210 (83%), Positives = 192/210 (91%), Gaps = 2/210 (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 LDESDEMLSRGFKDQIYDVYRYLPPDLQVC 210
           LDE+DEML RGFKDQIYDVYRYLPP+LQVC
Sbjct: 179 LDEADEMLGRGFKDQIYDVYRYLPPELQVC 208

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388500968|gb|AFK38550.1| unknown [Medicago truncatula]

 Score =  366 bits (940), Expect = 3e-99,   Method: Compositional matrix adjust.
 Identities = 184/213 (86%), Positives = 192/213 (90%), Gaps = 6/213 (2%)

Query: 1   MAAAT---AMRRRGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPS 57
           MA A+   A RRR      D D   FETTEGV+AI SF+ MGIKDDLLRGIYQYGFEKPS
Sbjct: 1   MATASVVPANRRRTVTANEDMD---FETTEGVKAIGSFEEMGIKDDLLRGIYQYGFEKPS 57

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

Query: 118 EKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIK 177
           EKVIL IGDFINIQAHAC+GGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR+TLRTRAIK
Sbjct: 118 EKVILTIGDFINIQAHACIGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRRTLRTRAIK 177

Query: 178 LLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVC 210
           LLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVC
Sbjct: 178 LLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVC 210

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  365 bits (937), Expect = 8e-99,   Method: Compositional matrix adjust.
 Identities = 183/213 (85%), Positives = 192/213 (90%), Gaps = 6/213 (2%)

Query: 1   MAAAT---AMRRRGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPS 57
           MA A+   A RRR      D D   FETTEGV+AI SF+ MGIKDDLLRGIY YGFEKPS
Sbjct: 1   MATASVVPANRRRTVTANEDMD---FETTEGVKAIGSFEEMGIKDDLLRGIYNYGFEKPS 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 LLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVC 210
           LLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVC
Sbjct: 178 LLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVC 210

Source: Medicago sativa

Species: Medicago sativa

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  364 bits (935), Expect = 1e-98,   Method: Compositional matrix adjust.
 Identities = 173/195 (88%), Positives = 187/195 (95%)

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

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

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

Query: 196 IYDVYRYLPPDLQVC 210
           IYDVYRYLPPDLQVC
Sbjct: 198 IYDVYRYLPPDLQVC 212

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 =  364 bits (934), Expect = 2e-98,   Method: Compositional matrix adjust.
 Identities = 173/210 (82%), Positives = 192/210 (91%), Gaps = 2/210 (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 LDESDEMLSRGFKDQIYDVYRYLPPDLQVC 210
           LDE+DEML RGFKDQIYDVYRYLPP+LQVC
Sbjct: 179 LDEADEMLGRGFKDQIYDVYRYLPPELQVC 208

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  363 bits (933), Expect = 2e-98,   Method: Compositional matrix adjust.
 Identities = 173/210 (82%), Positives = 192/210 (91%), Gaps = 2/210 (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 LDESDEMLSRGFKDQIYDVYRYLPPDLQVC 210
           LDE+DEML RGFKDQIYDVYRYLPP+LQVC
Sbjct: 179 LDEADEMLGRGFKDQIYDVYRYLPPELQVC 208

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	219
TAIR|locus:2091191	408	EIF4A-III "eukaryotic initiati	0.872	0.468	0.874	7.7e-87
TAIR|locus:2008296	392	AT1G51380 [Arabidopsis thalian	0.867	0.484	0.736	4.6e-73
ZFIN|ZDB-GENE-040426-915	406	eif4a3 "eukaryotic translation	0.872	0.470	0.691	5.5e-70
FB|FBgn0037573	399	eIF4AIII "eIF4AIII" [Drosophil	0.853	0.468	0.695	1.1e-69
WB|WBGene00018007	399	F33D11.10 [Caenorhabditis eleg	0.853	0.468	0.700	1.8e-69
WB|WBGene00022029	399	Y65B4A.6 [Caenorhabditis elega	0.853	0.468	0.695	3e-69
UNIPROTKB|Q5ZM36	412	EIF4A3 "Eukaryotic initiation	0.867	0.461	0.684	1e-68
UNIPROTKB|Q2NL22	411	EIF4A3 "Eukaryotic initiation	0.867	0.462	0.684	1e-68
UNIPROTKB|E2RDZ4	411	EIF4A3 "Uncharacterized protei	0.867	0.462	0.684	1e-68
UNIPROTKB|P38919	411	EIF4A3 "Eukaryotic initiation	0.867	0.462	0.684	1e-68

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

 Score = 868 (310.6 bits), Expect = 7.7e-87, P = 7.7e-87
 Identities = 167/191 (87%), Positives = 182/191 (95%)

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

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

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

Query:   200 YRYLPPDLQVC 210
             YRYLPPDLQVC
Sbjct:   202 YRYLPPDLQVC 212

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

TAIR|locus:2008296 AT1G51380 [Arabidopsis thaliana (taxid:3702)]

 Score = 738 (264.8 bits), Expect = 4.6e-73, P = 4.6e-73
 Identities = 140/190 (73%), Positives = 168/190 (88%)

Query:    21 MVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSG 80
             +VFETT+G++ I SFD MG+ D +LRG+Y YG++KPS IQQRA++PI+KGRDVIAQAQSG
Sbjct:    10 LVFETTKGIKPIKSFDDMGMNDKVLRGVYDYGYKKPSEIQQRALVPILKGRDVIAQAQSG 69

Query:    81 TGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKS 140
             TGKTSMIA++VCQ V+ SSR+VQ L+LSP+RELA+QTEK I AIG   NIQAHAC+GGKS
Sbjct:    70 TGKTSMIAISVCQIVNISSRKVQVLVLSPSRELASQTEKTIQAIGAHTNIQAHACIGGKS 129

Query:   141 VGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVY 200
             +GEDI+KLE GVH VSGTPGRV DMIKR +L+T+A+KLLVLDESDEMLS+G KDQIYDVY
Sbjct:   130 IGEDIKKLERGVHAVSGTPGRVYDMIKRGSLQTKAVKLLVLDESDEMLSKGLKDQIYDVY 189

Query:   201 RYLPPDLQVC 210
             R LP D+QVC
Sbjct:   190 RALPHDIQVC 199

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

GO:0009560 "embryo sac egg cell differentiation" evidence=RCA

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

 Score = 709 (254.6 bits), Expect = 5.5e-70, P = 5.5e-70
 Identities = 132/191 (69%), Positives = 165/191 (86%)

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 YRYLPPDLQVC 210
             YRYLPP  QVC
Sbjct:   200 YRYLPPATQVC 210

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

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

 Score = 706 (253.6 bits), Expect = 1.1e-69, P = 1.1e-69
 Identities = 130/187 (69%), Positives = 163/187 (87%)

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 LPPDLQV 209
             LPP  QV
Sbjct:   196 LPPATQV 202

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

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

 Score = 704 (252.9 bits), Expect = 1.8e-69, P = 1.8e-69
 Identities = 131/187 (70%), Positives = 163/187 (87%)

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 LPPDLQV 209
             LPP  QV
Sbjct:   196 LPPGAQV 202

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

WB|WBGene00022029 Y65B4A.6 [Caenorhabditis elegans (taxid:6239)]

 Score = 702 (252.2 bits), Expect = 3.0e-69, P = 3.0e-69
 Identities = 130/187 (69%), Positives = 163/187 (87%)

Query:    23 FETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTG 82
             FE++E V  I +FD MG+++DLLRGIY YGFEKPSAIQQRA+  I+K RDVIAQAQSGTG
Sbjct:    16 FESSEEVSIIPTFDKMGLREDLLRGIYAYGFEKPSAIQQRAIPAILKARDVIAQAQSGTG 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 LPPDLQV 209
             LPP  QV
Sbjct:   196 LPPGAQV 202

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:0018991 "oviposition" 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:0040011 "locomotion" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

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

GO:0042127 "regulation of cell proliferation" evidence=IMP

GO:0040020 "regulation of meiosis" evidence=IMP

GO:0007281 "germ cell development" evidence=IMP

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

 Score = 697 (250.4 bits), Expect = 1.0e-68, P = 1.0e-68
 Identities = 130/190 (68%), Positives = 164/190 (86%)

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 YRYLPPDLQV 209
             YRYLPP  QV
Sbjct:   206 YRYLPPATQV 215

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 = 697 (250.4 bits), Expect = 1.0e-68, P = 1.0e-68
 Identities = 130/190 (68%), Positives = 164/190 (86%)

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 YRYLPPDLQV 209
             YRYLPP  QV
Sbjct:   205 YRYLPPATQV 214

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 = 697 (250.4 bits), Expect = 1.0e-68, P = 1.0e-68
 Identities = 130/190 (68%), Positives = 164/190 (86%)

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 YRYLPPDLQV 209
             YRYLPP  QV
Sbjct:   205 YRYLPPATQV 214

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 = 697 (250.4 bits), Expect = 1.0e-68, P = 1.0e-68
 Identities = 130/190 (68%), Positives = 164/190 (86%)

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 YRYLPPDLQV 209
             YRYLPP  QV
Sbjct:   205 YRYLPPATQV 214

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

---

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)
Q5VNM3	RH2_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.8333	0.9497	0.5148	yes	no
Q10I26	RH34_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.8238	0.9497	0.5148	yes	no
Q94A52	RH2_ARATH	3, ., 6, ., 4, ., 1, 3	0.8724	0.8949	0.4803	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	0.914
3rd Layer	3.6.4	0.921

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

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

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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	219
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	5e-86
cd00268	203	cd00268, DEADc, DEAD-box helicases	1e-82
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	1e-59
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	1e-46
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	3e-45
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	1e-38
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	2e-37
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	5e-34
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	1e-30
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	2e-27
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	8e-27
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	2e-24
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	9e-24
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	1e-23
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	6e-21
COG1205	851	COG1205, COG1205, Distinct helicase family with a	4e-05

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

 Score =  259 bits (664), Expect = 5e-86
 Identities = 109/180 (60%), Positives = 137/180 (76%)

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

Length = 401

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

 Score =  244 bits (625), Expect = 1e-82
 Identities = 82/177 (46%), Positives = 117/177 (66%), Gaps = 2/177 (1%)

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 HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQV 209
           H+V  TPGR+ D+++R  L    +K LVLDE+D ML  GF+DQI ++ + LP D Q 
Sbjct: 121 HIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRMLDMGFEDQIREILKLLPKDRQT 177

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 =  194 bits (495), Expect = 1e-59
 Identities = 74/180 (41%), Positives = 106/180 (58%), Gaps = 3/180 (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

Length = 513

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

 Score =  151 bits (384), Expect = 1e-46
 Identities = 58/157 (36%), Positives = 93/157 (59%), Gaps = 2/157 (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 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCC 211
            +KLLVLDE+  +L  GF D + ++   LPPD Q+  
Sbjct: 121 NLKLLVLDEAHRLLDMGFGDDLEEILSRLPPDRQILL 157

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

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

 Score =  155 bits (395), Expect = 3e-45
 Identities = 73/177 (41%), Positives = 106/177 (59%), Gaps = 1/177 (0%)

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 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ 208
            H++ GTPGR+ D +++ TL   A+  LVLDE+D ML  GF+D I  + R  P   Q
Sbjct: 124 AHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMGFQDAIDAIIRQAPARRQ 180

Length = 460

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

 Score =  131 bits (332), Expect = 1e-38
 Identities = 54/166 (32%), Positives = 91/166 (54%), Gaps = 3/166 (1%)

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 IKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCC 211
           ++   L    + L++LDE+  +L  GF DQ+  + + LP ++Q+  
Sbjct: 120 LENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLL 165

Length = 201

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

 Score =  134 bits (340), Expect = 2e-37
 Identities = 70/181 (38%), Positives = 110/181 (60%), Gaps = 6/181 (3%)

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 Q 208
           Q
Sbjct: 182 Q 182

Length = 456

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

 Score =  127 bits (320), Expect = 5e-34
 Identities = 69/183 (37%), Positives = 101/183 (55%), Gaps = 7/183 (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 DLQ 208
             Q
Sbjct: 180 GHQ 182

Length = 629

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

 Score =  109 bits (275), Expect = 1e-30
 Identities = 47/139 (33%), Positives = 76/139 (54%), Gaps = 2/139 (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 GFKDQIYDVYRYLPPDLQV 209
           GF      +   LP D QV
Sbjct: 119 GFGLLGLKILLKLPKDRQV 137

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

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

 Score =  107 bits (270), Expect = 2e-27
 Identities = 57/180 (31%), Positives = 101/180 (56%), Gaps = 7/180 (3%)

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

Length = 518

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

 Score =  106 bits (266), Expect = 8e-27
 Identities = 58/187 (31%), Positives = 94/187 (50%), Gaps = 8/187 (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 205
           + R  P 
Sbjct: 261 IIRQTPR 267

Length = 475

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

 Score = 99.8 bits (249), Expect = 2e-24
 Identities = 59/185 (31%), Positives = 92/185 (49%), Gaps = 11/185 (5%)

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 PPDLQ 208
            PD Q
Sbjct: 306 RPDRQ 310

Length = 545

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

 Score = 97.3 bits (243), Expect = 9e-24
 Identities = 57/182 (31%), Positives = 90/182 (49%), Gaps = 11/182 (6%)

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 PP 205
           PP
Sbjct: 186 PP 187

Length = 423

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

 Score = 97.3 bits (243), Expect = 1e-23
 Identities = 54/164 (32%), Positives = 81/164 (49%), Gaps = 4/164 (2%)

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 EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF 192
                +V  TPGR+   IK +    RA++ L+LDE+D ML  GF
Sbjct: 121 SENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRMLDMGF 164

Length = 434

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

 Score = 90.0 bits (223), Expect = 6e-21
 Identities = 59/179 (32%), Positives = 88/179 (49%), Gaps = 8/179 (4%)

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-KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP 204
            L+ GV V+  TPGR+ D +K+ K +   A ++ VLDE+D M   GF   I  + R +P
Sbjct: 130 LLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFDLGFIKDIRFLLRRMP 188

Length = 572

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

 Score = 43.5 bits (103), Expect = 4e-05
 Identities = 41/170 (24%), Positives = 66/170 (38%), Gaps = 15/170 (8%)

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 183
            E    + +   ++   P    DM+    LR         R +K LV+DE
Sbjct: 158 EERRAIIRNPPDILLTNP----DMLHYLLLRNHDAWLWLLRNLKYLVVDE 203

Length = 851

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	219
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	100.0
PTZ00110	545	helicase; Provisional	100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	100.0
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	100.0
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	100.0
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	100.0
PRK11776	460	ATP-dependent RNA helicase DbpA; 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
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
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	100.0
PTZ00424	401	helicase 45; Provisional	100.0
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	100.0
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0346	569	consensus RNA helicase [RNA processing and modific	100.0
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0343	758	consensus RNA Helicase [RNA processing and modific	100.0
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0340	442	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0334	997	consensus RNA helicase [RNA processing and modific	100.0
KOG0326	459	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	100.0
KOG0347	731	consensus RNA helicase [RNA processing and modific	100.0
KOG0337	529	consensus ATP-dependent RNA helicase [RNA processi	100.0
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.98
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.98
PRK00254	720	ski2-like helicase; Provisional	99.97
PRK02362	737	ski2-like helicase; Provisional	99.97
KOG0327	397	consensus Translation initiation factor 4F, helica	99.97
KOG4284	980	consensus DEAD box protein [Transcription]	99.97
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	99.96
KOG0350	620	consensus DEAD-box ATP-dependent RNA helicase [RNA	99.96
PRK13767	876	ATP-dependent helicase; Provisional	99.96
PRK01172	674	ski2-like helicase; Provisional	99.96
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	99.96
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.96
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.95
PRK09401	1176	reverse gyrase; Reviewed	99.94
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.94
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.94
COG1205	851	Distinct helicase family with a unique C-terminal	99.93
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.92
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.92
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	99.92
PRK14701	1638	reverse gyrase; Provisional	99.92
COG1204	766	Superfamily II helicase [General function predicti	99.92
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.92
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.92
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.92
PRK10689	1147	transcription-repair coupling factor; Provisional	99.91
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.91
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.91
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.9
PHA02558	501	uvsW UvsW helicase; Provisional	99.89
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	99.88
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.88
COG1202	830	Superfamily II helicase, archaea-specific [General	99.86
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.86
KOG0354	746	consensus DEAD-box like helicase [General function	99.86
PRK13766	773	Hef nuclease; Provisional	99.85
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.85
PHA02653	675	RNA helicase NPH-II; Provisional	99.84
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.84
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.84
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.84
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.84
KOG0349	725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	99.83
PRK05580	679	primosome assembly protein PriA; Validated	99.82
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.81
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.8
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	99.78
KOG0947	1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	99.77
PRK09694	878	helicase Cas3; Provisional	99.76
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.75
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.73
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.72
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.72
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.71
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.71
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.7
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.7
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.68
KOG0352	641	consensus ATP-dependent DNA helicase [Replication,	99.67
KOG0948	1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	99.66
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.66
KOG0353	695	consensus ATP-dependent DNA helicase [General func	99.66
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.64
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.64
KOG0351	941	consensus ATP-dependent DNA helicase [Replication,	99.63
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.61
KOG0949	1330	consensus Predicted helicase, DEAD-box superfamily	99.6
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.58
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.58
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	99.56
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.54
KOG0950	1008	consensus DNA polymerase theta/eta, DEAD-box super	99.51
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.5
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	99.48
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.43
KOG0920	924	consensus ATP-dependent RNA helicase A [RNA proces	99.42
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.41
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	99.4
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	99.38
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.37
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.37
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	99.36
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	99.36
COG1198	730	PriA Primosomal protein N' (replication factor Y)	99.35
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	99.35
COG4096	875	HsdR Type I site-specific restriction-modification	99.34
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	99.25
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	99.24
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	99.23
PRK04914	956	ATP-dependent helicase HepA; Validated	99.17
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.16
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.15
PRK12326	764	preprotein translocase subunit SecA; Reviewed	99.14
KOG0922	674	consensus DEAH-box RNA helicase [RNA processing an	99.13
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	99.13
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	99.08
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	99.07
KOG0925	699	consensus mRNA splicing factor ATP-dependent RNA h	99.01
KOG1123	776	consensus RNA polymerase II transcription initiati	98.96
COG0610	962	Type I site-specific restriction-modification syst	98.95
CHL00122	870	secA preprotein translocase subunit SecA; Validate	98.94
KOG0926	1172	consensus DEAH-box RNA helicase [RNA processing an	98.93
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.93
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	98.93
KOG0385	971	consensus Chromatin remodeling complex WSTF-ISWI,	98.92
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	98.91
COG4889	1518	Predicted helicase [General function prediction on	98.9
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	98.88
KOG0389	941	consensus SNF2 family DNA-dependent ATPase [Chroma	98.85
PRK15483	986	type III restriction-modification system StyLTI en	98.83
KOG0390	776	consensus DNA repair protein, SNF2 family [Replica	98.81
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	98.81
KOG0923	902	consensus mRNA splicing factor ATP-dependent RNA h	98.78
KOG0387	923	consensus Transcription-coupled repair protein CSB	98.74
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	98.73
PRK14873	665	primosome assembly protein PriA; Provisional	98.73
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	98.7
PRK10875	615	recD exonuclease V subunit alpha; Provisional	98.7
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	98.66
KOG1000	689	consensus Chromatin remodeling protein HARP/SMARCA	98.63
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	98.6
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	98.58
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	98.56
KOG1802	935	consensus RNA helicase nonsense mRNA reducing fact	98.48
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	98.47
PF13872	303	AAA_34: P-loop containing NTP hydrolase pore-1	98.43
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	98.41
PRK10536	262	hypothetical protein; Provisional	98.4
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	98.35
KOG4439	901	consensus RNA polymerase II transcription terminat	98.32
TIGR00376	637	DNA helicase, putative. The gene product may repre	98.3
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	98.3
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	98.27
PRK13889	988	conjugal transfer relaxase TraA; Provisional	98.27
KOG1803	649	consensus DNA helicase [Replication, recombination	98.26
KOG0392	1549	consensus SNF2 family DNA-dependent ATPase domain-	98.25
KOG1132	945	consensus Helicase of the DEAD superfamily [Replic	98.23
PF13245	76	AAA_19: Part of AAA domain	98.23
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	98.22
KOG1002	791	consensus Nucleotide excision repair protein RAD16	98.21
COG3587	985	Restriction endonuclease [Defense mechanisms]	98.21
KOG0384	1373	consensus Chromodomain-helicase DNA-binding protei	98.15
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	98.08
PRK13826	1102	Dtr system oriT relaxase; Provisional	98.08
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	98.08
KOG2340	698	consensus Uncharacterized conserved protein [Funct	98.08
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	97.97
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	97.95
KOG0391	1958	consensus SNF2 family DNA-dependent ATPase [Genera	97.92
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	97.9
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.86
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	97.86
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	97.83
KOG1805	1100	consensus DNA replication helicase [Replication, r	97.83
KOG0388	1185	consensus SNF2 family DNA-dependent ATPase [Replic	97.8
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	97.8
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	97.75
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	97.72
KOG0386	1157	consensus Chromatin remodeling complex SWI/SNF, co	97.7
KOG4150	1034	consensus Predicted ATP-dependent RNA helicase [RN	97.69
smart00382	148	AAA ATPases associated with a variety of cellular	97.67
KOG1131	755	consensus RNA polymerase II transcription initiati	97.66
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	97.64
PF03354	477	Terminase_1: Phage Terminase ; InterPro: IPR005021	97.62
KOG1015	1567	consensus Transcription regulator XNP/ATRX, DEAD-b	97.61
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	97.61
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	97.6
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	97.58
PHA03368	738	DNA packaging terminase subunit 1; Provisional	97.55
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	97.53
PRK11054	684	helD DNA helicase IV; Provisional	97.51
PF05127	177	Helicase_RecD: Helicase; InterPro: IPR007807 This	97.5
PRK04296	190	thymidine kinase; Provisional	97.5
PHA02533	534	17 large terminase protein; Provisional	97.46
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.46
PRK08181	269	transposase; Validated	97.45
COG3421	812	Uncharacterized protein conserved in bacteria [Fun	97.43
PRK05642	234	DNA replication initiation factor; Validated	97.41
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	97.41
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	97.4
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.35
PRK06893	229	DNA replication initiation factor; Validated	97.34
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	97.33
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	97.31
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	97.3
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	97.28
PRK00411	394	cdc6 cell division control protein 6; Reviewed	97.28
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	97.26
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	97.24
PHA03333	752	putative ATPase subunit of terminase; Provisional	97.24
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.24
PRK08084	235	DNA replication initiation factor; Provisional	97.23
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	97.21
PRK14087	450	dnaA chromosomal replication initiation protein; P	97.2
PRK05707	328	DNA polymerase III subunit delta'; Validated	97.19
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	97.19
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	97.19
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	97.18
PRK08769	319	DNA polymerase III subunit delta'; Validated	97.17
PRK06921	266	hypothetical protein; Provisional	97.16
PRK14974	336	cell division protein FtsY; Provisional	97.15
PRK06526	254	transposase; Provisional	97.14
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	97.14
PRK14088	440	dnaA chromosomal replication initiation protein; P	97.13
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.13
COG1444	758	Predicted P-loop ATPase fused to an acetyltransfer	97.13
COG4626	546	Phage terminase-like protein, large subunit [Gener	97.12
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	97.11
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	97.11
PRK08727	233	hypothetical protein; Validated	97.11
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	97.1
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	97.07
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	97.06
PLN03025	319	replication factor C subunit; Provisional	97.06
PRK12402	337	replication factor C small subunit 2; Reviewed	97.04
PHA03372	668	DNA packaging terminase subunit 1; Provisional	97.01
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	97.0
PRK08116	268	hypothetical protein; Validated	97.0
PRK08903	227	DnaA regulatory inactivator Hda; Validated	97.0
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	96.96
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	96.96
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	96.93
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	96.93
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	96.93
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	96.9
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	96.89
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	96.89
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	96.88
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	96.85
KOG0953	700	consensus Mitochondrial RNA helicase SUV3, DEAD-bo	96.82
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	96.82
PHA02544	316	44 clamp loader, small subunit; Provisional	96.81
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	96.8
PRK13833	323	conjugal transfer protein TrbB; Provisional	96.79
PRK07952	244	DNA replication protein DnaC; Validated	96.78
PRK06835	329	DNA replication protein DnaC; Validated	96.78
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	96.77
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	96.77
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	96.76
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	96.75
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	96.74
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	96.74
COG2256	436	MGS1 ATPase related to the helicase subunit of the	96.71
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	96.7
PRK14086	617	dnaA chromosomal replication initiation protein; P	96.69
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	96.69
PRK12377	248	putative replication protein; Provisional	96.67
PF13173	128	AAA_14: AAA domain	96.65
PF05729	166	NACHT: NACHT domain	96.64
KOG1001	674	consensus Helicase-like transcription factor HLTF/	96.64
PRK00440	319	rfc replication factor C small subunit; Reviewed	96.62
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	96.59
PRK04195	482	replication factor C large subunit; Provisional	96.56
PRK12422	445	chromosomal replication initiation protein; Provis	96.55
PRK06871	325	DNA polymerase III subunit delta'; Validated	96.55
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	96.54
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	96.54
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	96.52
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	96.51
CHL00181	287	cbbX CbbX; Provisional	96.49
PRK05298	652	excinuclease ABC subunit B; Provisional	96.48
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	96.47
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	96.46
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	96.46
PRK06904	472	replicative DNA helicase; Validated	96.46
PF03237	384	Terminase_6: Terminase-like family; InterPro: IPR0	96.45
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	96.44
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	96.41
PTZ00112	1164	origin recognition complex 1 protein; Provisional	96.41
PRK09112	351	DNA polymerase III subunit delta'; Validated	96.4
PRK06090	319	DNA polymerase III subunit delta'; Validated	96.4
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	96.39
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	96.34
PF00004	132	AAA: ATPase family associated with various cellula	96.32
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	96.32
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	96.29
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	96.29
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	96.29
PRK07004	460	replicative DNA helicase; Provisional	96.25
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	96.24
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	96.24
COG3973	747	Superfamily I DNA and RNA helicases [General funct	96.23
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	96.22
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	96.2
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	96.2
PRK06964	342	DNA polymerase III subunit delta'; Validated	96.19
PRK07993	334	DNA polymerase III subunit delta'; Validated	96.19
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	96.17
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	96.16
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	96.15
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	96.15
PRK08939	306	primosomal protein DnaI; Reviewed	96.13
PRK08699	325	DNA polymerase III subunit delta'; Validated	96.12
PRK08506	472	replicative DNA helicase; Provisional	96.11
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	96.09
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	96.07
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	96.02
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	96.0
PRK08533	230	flagellar accessory protein FlaH; Reviewed	95.97
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	95.96
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	95.96
PRK13851	344	type IV secretion system protein VirB11; Provision	95.95
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	95.93
KOG0298	1394	consensus DEAD box-containing helicase-like transc	95.91
PRK05748	448	replicative DNA helicase; Provisional	95.89
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	95.89
PRK05973	237	replicative DNA helicase; Provisional	95.88
PRK08006	471	replicative DNA helicase; Provisional	95.87
TIGR00767	415	rho transcription termination factor Rho. Members	95.87
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	95.86
COG1435	201	Tdk Thymidine kinase [Nucleotide transport and met	95.86
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	95.78
PRK07471	365	DNA polymerase III subunit delta'; Validated	95.78
PRK00771	437	signal recognition particle protein Srp54; Provisi	95.77
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	95.75
PRK08840	464	replicative DNA helicase; Provisional	95.75
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	95.7
PTZ00293	211	thymidine kinase; Provisional	95.68
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	95.65
PRK06620	214	hypothetical protein; Validated	95.65
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	95.6
PRK04841	903	transcriptional regulator MalT; Provisional	95.59
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	95.57
PRK09183	259	transposase/IS protein; Provisional	95.55
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	95.5
KOG2028	554	consensus ATPase related to the helicase subunit o	95.49
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	95.47
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	95.47
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	95.46
PRK13342	413	recombination factor protein RarA; Reviewed	95.46
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	95.44
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	95.37
PRK07940	394	DNA polymerase III subunit delta'; Validated	95.37
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	95.36
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	95.36
PRK08760	476	replicative DNA helicase; Provisional	95.33
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	95.3
TIGR00064	272	ftsY signal recognition particle-docking protein F	95.27
PRK11823	446	DNA repair protein RadA; Provisional	95.27
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	95.24
PRK05636	505	replicative DNA helicase; Provisional	95.24
PRK06321	472	replicative DNA helicase; Provisional	95.23
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	95.19
PRK09376	416	rho transcription termination factor Rho; Provisio	95.15
COG0593	408	DnaA ATPase involved in DNA replication initiation	95.1
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	95.08
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	95.08
TIGR00665	434	DnaB replicative DNA helicase. This model describe	95.05
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	95.05
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	95.04
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	95.03
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	94.99
KOG1133	821	consensus Helicase of the DEAD superfamily [Replic	94.96
PRK04328	249	hypothetical protein; Provisional	94.95
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	94.94
PRK09165	497	replicative DNA helicase; Provisional	94.9
cd01128	249	rho_factor Transcription termination factor rho is	94.86
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	94.85
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	94.79
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	94.75
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	94.72
PRK13764	602	ATPase; Provisional	94.72
COG0210	655	UvrD Superfamily I DNA and RNA helicases [DNA repl	94.7
PHA02535	581	P terminase ATPase subunit; Provisional	94.69
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	94.67
PRK07399	314	DNA polymerase III subunit delta'; Validated	94.67
COG1074	1139	RecB ATP-dependent exoDNAse (exonuclease V) beta s	94.66
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	94.65
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	94.54
PRK06067	234	flagellar accessory protein FlaH; Validated	94.53
COG1485	367	Predicted ATPase [General function prediction only	94.52
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	94.52
TIGR02237	209	recomb_radB DNA repair and recombination protein R	94.49
PRK05595	444	replicative DNA helicase; Provisional	94.48
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	94.47
PF14516	331	AAA_35: AAA-like domain	94.47
TIGR02784	1141	addA_alphas double-strand break repair helicase Ad	94.44
PRK10436	462	hypothetical protein; Provisional	94.42
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	94.4
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	94.4
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	94.39
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	94.39
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	94.39
PF06733	174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	94.38
COG1484	254	DnaC DNA replication protein [DNA replication, rec	94.36
PRK08058	329	DNA polymerase III subunit delta'; Validated	94.35
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	94.35
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	94.33
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	94.3
PRK13341	725	recombination factor protein RarA/unknown domain f	94.28
cd03115	173	SRP The signal recognition particle (SRP) mediates	94.26
KOG1806	1320	consensus DEAD box containing helicases [Replicati	94.17
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	94.17
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	94.16
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	94.16
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	94.02
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	93.97
TIGR00959	428	ffh signal recognition particle protein. This mode	93.86
PRK09087	226	hypothetical protein; Validated	93.85
cd03239	178	ABC_SMC_head The structural maintenance of chromos	93.82
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	93.76
PRK13897	606	type IV secretion system component VirD4; Provisio	93.75
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	93.72
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	93.65
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	93.63
PRK10689	1147	transcription-repair coupling factor; Provisional	93.57
COG0305	435	DnaB Replicative DNA helicase [DNA replication, re	93.54
PRK12608	380	transcription termination factor Rho; Provisional	93.52
PRK13695	174	putative NTPase; Provisional	93.5
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	93.48
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	93.47
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	93.47
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	93.45
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	93.4
TIGR02533	486	type_II_gspE general secretory pathway protein E.	93.36
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	93.35
PRK05564	313	DNA polymerase III subunit delta'; Validated	93.35
PHA00350	399	putative assembly protein	93.34
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	93.29
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	93.29
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	93.23
PHA00729	226	NTP-binding motif containing protein	93.21
KOG1016	1387	consensus Predicted DNA helicase, DEAD-box superfa	93.2
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	93.19
PHA02542	473	41 41 helicase; Provisional	93.15
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	93.1
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	93.08
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	93.04
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	93.01
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	92.95
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	92.9
PRK06749	428	replicative DNA helicase; Provisional	92.87
PF13479	213	AAA_24: AAA domain	92.86
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	92.86
COG3972	660	Superfamily I DNA and RNA helicases [General funct	92.8
PRK05917	290	DNA polymerase III subunit delta'; Validated	92.74
PRK13850	670	type IV secretion system protein VirD4; Provisiona	92.72
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	92.67
PRK07773	886	replicative DNA helicase; Validated	92.66
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	92.64
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	92.57
PF12846	304	AAA_10: AAA-like domain	92.57
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	92.52
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	92.5
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	92.46
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	92.46
TIGR02773	1158	addB_Gpos ATP-dependent nuclease subunit B. DNA re	92.35
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	92.34
cd03289	275	ABCC_CFTR2 The CFTR subfamily domain 2. The cystic	92.32
CHL00176	638	ftsH cell division protein; Validated	92.32
PF01935	229	DUF87: Domain of unknown function DUF87; InterPro:	92.31
PTZ00110	545	helicase; Provisional	92.3
COG0552	340	FtsY Signal recognition particle GTPase [Intracell	92.28
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	92.27
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	92.22
PRK10416	318	signal recognition particle-docking protein FtsY;	92.16
TIGR03743	634	SXT_TraD conjugative coupling factor TraD, SXT/TOL	92.16
PRK10867	433	signal recognition particle protein; Provisional	92.15
COG1132	567	MdlB ABC-type multidrug transport system, ATPase a	92.06
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	92.06
PLN03232	1495	ABC transporter C family member; Provisional	92.03
TIGR00609	1087	recB exodeoxyribonuclease V, beta subunit. All pro	91.91
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	91.87
PHA00012	361	I assembly protein	91.8
COG5008	375	PilU Tfp pilus assembly protein, ATPase PilU [Cell	91.77
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	91.7
cd01127	410	TrwB Bacterial conjugation protein TrwB, ATP bindi	91.65
PRK10865	857	protein disaggregation chaperone; Provisional	91.58
TIGR03754	643	conj_TOL_TraD conjugative coupling factor TraD, TO	91.45

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

Probab=100.00  E-value=1.8e-41  Score=272.56  Aligned_cols=190  Identities=32%  Similarity=0.513  Sum_probs=182.9

Q ss_pred             CCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEc
Q 027749           29 VEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (219)
Q Consensus        29 ~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~  108 (219)
                      .+...+|.++++.+.+.+++++.||..|+++|++++|.++.|+++|..|.||||||.+|++|+++.+...+..++++|++
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            34557899999999999999999999999999999999999999999999999999999999999999988889999999


Q ss_pred             CCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHH-cCCCCCCCccEEEeccchhh
Q 027749          109 PTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIK-RKTLRTRAIKLLVLDESDEM  187 (219)
Q Consensus       109 P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~-~~~~~~~~l~~lVvDE~h~l  187 (219)
                      ||++||.|+.+.++.++...++++..+.||.+...+...+.+.++|+|+||++|.+.+. .+.+.++.++++|+||||++
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            99999999999999999999999999999999999999999999999999999999998 57889999999999999999


Q ss_pred             hccccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          188 LSRGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       188 ~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      +++.|...+.+|++.+|.+.|.++||||+|.
T Consensus       217 Ld~dF~~~ld~ILk~ip~erqt~LfsATMt~  247 (476)
T KOG0330|consen  217 LDMDFEEELDYILKVIPRERQTFLFSATMTK  247 (476)
T ss_pred             hhhhhHHHHHHHHHhcCccceEEEEEeecch
Confidence            9999999999999999999999999999985

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

Probab=100.00  E-value=2.6e-41  Score=285.45  Aligned_cols=185  Identities=32%  Similarity=0.564  Sum_probs=177.3

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhcc------CCCceeEEEE
Q 027749           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT------SSREVQALIL  107 (219)
Q Consensus        34 ~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~------~~~~~~~lil  107 (219)
                      .|.++++++....+++..||..|+|+|.+.||.++.|+|++..+.||+|||++|++|++.++..      ...+|.+||+
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            6888999999999999999999999999999999999999999999999999999999998875      4457999999


Q ss_pred             cCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhh
Q 027749          108 SPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (219)
Q Consensus       108 ~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l  187 (219)
                      +|||+||.|+...+.++.....++..|++||.+...+.+.+.++.+|+|+||++|.++++.+.++++++.|+|+||||+|
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-CCCCeEEEEeecccC
Q 027749          188 LSRGFKDQIYDVYRYL-PPDLQVCCPGSCFLF  218 (219)
Q Consensus       188 ~~~~~~~~~~~i~~~~-~~~~q~i~~SATl~~  218 (219)
                      ++++|+.++++|++.+ ++..|++++|||+|.
T Consensus       252 ldmGFe~qI~~Il~~i~~~~rQtlm~saTwp~  283 (519)
T KOG0331|consen  252 LDMGFEPQIRKILSQIPRPDRQTLMFSATWPK  283 (519)
T ss_pred             hccccHHHHHHHHHhcCCCcccEEEEeeeccH
Confidence            9999999999999999 556689999999985

>PTZ00110 helicase; Provisional

Probab=100.00  E-value=2.9e-40  Score=288.96  Aligned_cols=194  Identities=29%  Similarity=0.446  Sum_probs=181.2

Q ss_pred             ccCCCCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccC-----C
Q 027749           25 TTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-----S   99 (219)
Q Consensus        25 ~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~-----~   99 (219)
                      ....|+++.+|+++++++.++++|.+.||..|+|+|.++||.+++|+|+++++|||+|||++|++|++..+...     .
T Consensus       122 g~~~p~p~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~~~~  201 (545)
T PTZ00110        122 GENVPKPVVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYG  201 (545)
T ss_pred             CCCCCcccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEEeCCCChHHHHHHHHHHHHHHhcccccCC
Confidence            34558899999999999999999999999999999999999999999999999999999999999998876432     3


Q ss_pred             CceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEE
Q 027749          100 REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLL  179 (219)
Q Consensus       100 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~l  179 (219)
                      .++.+|||+||++||.|+.+.+.++....++++.+++|+.+...+...+..+++|+|+||++|.+++.++..+++++++|
T Consensus       202 ~gp~~LIL~PTreLa~Qi~~~~~~~~~~~~i~~~~~~gg~~~~~q~~~l~~~~~IlVaTPgrL~d~l~~~~~~l~~v~~l  281 (545)
T PTZ00110        202 DGPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQIYALRRGVEILIACPGRLIDFLESNVTNLRRVTYL  281 (545)
T ss_pred             CCcEEEEECChHHHHHHHHHHHHHHhcccCccEEEEeCCCCHHHHHHHHHcCCCEEEECHHHHHHHHHcCCCChhhCcEE
Confidence            46889999999999999999999999888999999999999888888888999999999999999999888889999999


Q ss_pred             EeccchhhhccccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          180 VLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       180 VvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      |+||||+|++++|...+..++..++++.|++++|||+|.
T Consensus       282 ViDEAd~mld~gf~~~i~~il~~~~~~~q~l~~SAT~p~  320 (545)
T PTZ00110        282 VLDEADRMLDMGFEPQIRKIVSQIRPDRQTLMWSATWPK  320 (545)
T ss_pred             EeehHHhhhhcchHHHHHHHHHhCCCCCeEEEEEeCCCH
Confidence            999999999999999999999999999999999999985

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

Probab=100.00  E-value=9.7e-40  Score=283.44  Aligned_cols=186  Identities=39%  Similarity=0.628  Sum_probs=176.1

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhcc--CCCceeEEEEcCC
Q 027749           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT--SSREVQALILSPT  110 (219)
Q Consensus        33 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~--~~~~~~~lil~P~  110 (219)
                      .+|+++++++.+++++.+.||..|+|+|..++|.++.|+|+++.++||+|||.+|++|+++.+..  ......+||++||
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            67999999999999999999999999999999999999999999999999999999999999773  3222229999999


Q ss_pred             HHHHHHHHHHHHHhcccc-ceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhc
Q 027749          111 RELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (219)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~  189 (219)
                      ++||.|+++.+.++.... ++++.+++||.+...+...+..+++|+|+||+++++++.++.++++.++++|+||||+|++
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 7999999999999999988988999999999999999999999999999999999999999


Q ss_pred             cccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          190 RGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       190 ~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      +||.+.+..|++.+|.+.|+++||||+|.
T Consensus       189 ~Gf~~~i~~I~~~~p~~~qtllfSAT~~~  217 (513)
T COG0513         189 MGFIDDIEKILKALPPDRQTLLFSATMPD  217 (513)
T ss_pred             CCCHHHHHHHHHhCCcccEEEEEecCCCH
Confidence            99999999999999999999999999985

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

Probab=100.00  E-value=5.8e-39  Score=279.71  Aligned_cols=194  Identities=30%  Similarity=0.529  Sum_probs=178.6

Q ss_pred             eccCCCCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhcc------
Q 027749           24 ETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT------   97 (219)
Q Consensus        24 ~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~------   97 (219)
                      .....|+++.+|+++++++.++++|.+.||..|+|+|.++||.+++|+|+++++|||+|||++|++|++..+..      
T Consensus       112 ~g~~~p~pi~~f~~~~l~~~l~~~L~~~g~~~ptpiQ~~aip~il~g~dviv~ApTGSGKTlayllPil~~l~~~~~~~~  191 (518)
T PLN00206        112 KGEAVPPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHP  191 (518)
T ss_pred             cCCCCCchhcCHHhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEecCCCCccHHHHHHHHHHHHhhccccc
Confidence            33455789999999999999999999999999999999999999999999999999999999999999987642      


Q ss_pred             -CCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCc
Q 027749           98 -SSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (219)
Q Consensus        98 -~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l  176 (219)
                       ...++++||++||++||.|+.+.++.+.+..++.+..++|+.....+...+..+++|+|+||++|.+++..+.+.++++
T Consensus       192 ~~~~~~~aLIL~PTreLa~Qi~~~~~~l~~~~~~~~~~~~gG~~~~~q~~~l~~~~~IiV~TPgrL~~~l~~~~~~l~~v  271 (518)
T PLN00206        192 SEQRNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDNV  271 (518)
T ss_pred             cccCCceEEEEeCCHHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHHHhcCCCCEEEECHHHHHHHHHcCCccchhe
Confidence             2246899999999999999999999998888899999999999888888888899999999999999999888899999


Q ss_pred             cEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          177 KLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       177 ~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      ++||+||||+|++++|...+..++..++ +.|++++|||+|.
T Consensus       272 ~~lViDEad~ml~~gf~~~i~~i~~~l~-~~q~l~~SATl~~  312 (518)
T PLN00206        272 SVLVLDEVDCMLERGFRDQVMQIFQALS-QPQVLLFSATVSP  312 (518)
T ss_pred             eEEEeecHHHHhhcchHHHHHHHHHhCC-CCcEEEEEeeCCH
Confidence            9999999999999999999999999885 6899999999985

>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=1.3e-39  Score=252.56  Aligned_cols=209  Identities=65%  Similarity=1.010  Sum_probs=199.2

Q ss_pred             CCCCCCCCCcceeeccCCCCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHH
Q 027749           11 GGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALT   90 (219)
Q Consensus        11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~   90 (219)
                      ........+..+++.+...+.+.+|+++++..++++..-..||++|..+|+++++.+++|+|++.++..|+|||.+|.+.
T Consensus         5 ~~~~~~~~~~~~feTs~~~~v~~~F~~Mgl~edlLrgiY~yGfekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~~si~   84 (400)
T KOG0328|consen    5 ELFTMEDMDTVEFETSEKVKVIPTFDDMGLKEDLLRGIYAYGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSIS   84 (400)
T ss_pred             hhcccccccceeEeeccCcccccchhhcCchHHHHHHHHHhccCCchHHHhhhhhhhhcccceEEEecCCCCceEEEEee
Confidence            34556677888999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCC
Q 027749           91 VCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT  170 (219)
Q Consensus        91 ~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~  170 (219)
                      +++.+.-+....+++|+.||++|+.|+.+.+..++...++.+..+.||++..++++++..|+.++.+||++.+++++.+.
T Consensus        85 vlq~~d~~~r~tQ~lilsPTRELa~Qi~~vi~alg~~mnvq~hacigg~n~gedikkld~G~hvVsGtPGrv~dmikr~~  164 (400)
T KOG0328|consen   85 VLQSLDISVRETQALILSPTRELAVQIQKVILALGDYMNVQCHACIGGKNLGEDIKKLDYGQHVVSGTPGRVLDMIKRRS  164 (400)
T ss_pred             eeeecccccceeeEEEecChHHHHHHHHHHHHHhcccccceEEEEecCCccchhhhhhcccceEeeCCCchHHHHHHhcc
Confidence            99988877777889999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEeecccCC
Q 027749          171 LRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFLFD  219 (219)
Q Consensus       171 ~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~~  219 (219)
                      +..+.++++|+||+|.|++.+|..++..+.+.+|++.|++++|||+|.|
T Consensus       165 L~tr~vkmlVLDEaDemL~kgfk~Qiydiyr~lp~~~Qvv~~SATlp~e  213 (400)
T KOG0328|consen  165 LRTRAVKMLVLDEADEMLNKGFKEQIYDIYRYLPPGAQVVLVSATLPHE  213 (400)
T ss_pred             ccccceeEEEeccHHHHHHhhHHHHHHHHHHhCCCCceEEEEeccCcHH
Confidence            9999999999999999999999999999999999999999999999964

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

Probab=100.00  E-value=8.1e-40  Score=270.74  Aligned_cols=186  Identities=31%  Similarity=0.513  Sum_probs=176.9

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCc---eeEEEEcC
Q 027749           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSRE---VQALILSP  109 (219)
Q Consensus        33 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~---~~~lil~P  109 (219)
                      .+|.+++|+.++++++...||..|+|+|..+||..+-|++++-||.||+|||.+|.+|++.++...+.+   -++||++|
T Consensus       181 ~sF~~mNLSRPlLka~~~lGy~~PTpIQ~a~IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~~~~TRVLVL~P  260 (691)
T KOG0338|consen  181 ESFQSMNLSRPLLKACSTLGYKKPTPIQVATIPVALLGKDICACAATGSGKTAAFALPILERLLYRPKKVAATRVLVLVP  260 (691)
T ss_pred             hhHHhcccchHHHHHHHhcCCCCCCchhhhcccHHhhcchhhheecccCCchhhhHHHHHHHHhcCcccCcceeEEEEec
Confidence            489999999999999999999999999999999999999999999999999999999999999776543   57999999


Q ss_pred             CHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcC-CCCCCCccEEEeccchhhh
Q 027749          110 TRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK-TLRTRAIKLLVLDESDEML  188 (219)
Q Consensus       110 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~-~~~~~~l~~lVvDE~h~l~  188 (219)
                      |++|+.|+++..+++..+.++.+++++||.+...+-..++..++|+|+||++|.+.+.+. .++++++..+|+||||+|+
T Consensus       261 TRELaiQv~sV~~qlaqFt~I~~~L~vGGL~lk~QE~~LRs~PDIVIATPGRlIDHlrNs~sf~ldsiEVLvlDEADRML  340 (691)
T KOG0338|consen  261 TRELAIQVHSVTKQLAQFTDITVGLAVGGLDLKAQEAVLRSRPDIVIATPGRLIDHLRNSPSFNLDSIEVLVLDEADRML  340 (691)
T ss_pred             cHHHHHHHHHHHHHHHhhccceeeeeecCccHHHHHHHHhhCCCEEEecchhHHHHhccCCCccccceeEEEechHHHHH
Confidence            999999999999999999999999999999999999999999999999999999998874 5789999999999999999


Q ss_pred             ccccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          189 SRGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       189 ~~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      +.+|.+.|..|++.+|+++|.++||||++.
T Consensus       341 eegFademnEii~lcpk~RQTmLFSATMte  370 (691)
T KOG0338|consen  341 EEGFADEMNEIIRLCPKNRQTMLFSATMTE  370 (691)
T ss_pred             HHHHHHHHHHHHHhccccccceeehhhhHH
Confidence            999999999999999999999999999875

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=2.1e-38  Score=270.71  Aligned_cols=188  Identities=29%  Similarity=0.456  Sum_probs=173.5

Q ss_pred             ccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccC-------CCcee
Q 027749           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-------SREVQ  103 (219)
Q Consensus        31 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~-------~~~~~  103 (219)
                      ...+|+++++++.++++|.++||..|+|+|.++||.+++|+|++++||||+|||++|++|+++.+...       ..+++
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            34689999999999999999999999999999999999999999999999999999999999877532       23578


Q ss_pred             EEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEecc
Q 027749          104 ALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDE  183 (219)
Q Consensus       104 ~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE  183 (219)
                      +||++||++||.|+++.+..+....++++..++|+.+...+...+..+++|+|+||++|.+++.+..+.++++++||+||
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            99999999999999999999998889999999999998888888888999999999999999998888999999999999


Q ss_pred             chhhhccccHHHHHHHHHhCCC--CCeEEEEeecccC
Q 027749          184 SDEMLSRGFKDQIYDVYRYLPP--DLQVCCPGSCFLF  218 (219)
Q Consensus       184 ~h~l~~~~~~~~~~~i~~~~~~--~~q~i~~SATl~~  218 (219)
                      ||++++++|...+..+++.++.  ..|.+++|||++.
T Consensus       166 ad~l~~~~f~~~i~~i~~~~~~~~~~~~~l~SAT~~~  202 (423)
T PRK04837        166 ADRMFDLGFIKDIRWLFRRMPPANQRLNMLFSATLSY  202 (423)
T ss_pred             HHHHhhcccHHHHHHHHHhCCCccceeEEEEeccCCH
Confidence            9999999999999999999975  5678999999974

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=100.00  E-value=2.6e-38  Score=272.23  Aligned_cols=185  Identities=38%  Similarity=0.626  Sum_probs=173.6

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCC------CceeEEEE
Q 027749           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS------REVQALIL  107 (219)
Q Consensus        34 ~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~------~~~~~lil  107 (219)
                      +|+++++++++.++|.+.||..|+|+|.++||.+++|+|+++++|||+|||++|++|+++.+....      ..+++||+
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~~~~~aLil   81 (456)
T PRK10590          2 SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALIL   81 (456)
T ss_pred             CHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhcccccccCCCceEEEE
Confidence            699999999999999999999999999999999999999999999999999999999999875432      23589999


Q ss_pred             cCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhh
Q 027749          108 SPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (219)
Q Consensus       108 ~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l  187 (219)
                      +||++||.|+.+.+..+....++.+..++|+.+...+...+..+++|+|+||++|++++....+.++++++|||||||++
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            99999999999999999988899999999999998888888889999999999999999888888999999999999999


Q ss_pred             hccccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          188 LSRGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       188 ~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      ++++|...+..++..++...|+++||||++.
T Consensus       162 l~~~~~~~i~~il~~l~~~~q~l~~SAT~~~  192 (456)
T PRK10590        162 LDMGFIHDIRRVLAKLPAKRQNLLFSATFSD  192 (456)
T ss_pred             hccccHHHHHHHHHhCCccCeEEEEeCCCcH
Confidence            9999999999999999999999999999985

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=100.00  E-value=2.8e-38  Score=272.63  Aligned_cols=186  Identities=39%  Similarity=0.629  Sum_probs=175.2

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHH
Q 027749           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (219)
Q Consensus        33 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  112 (219)
                      .+|+++++++.+.+++.+.||..|+|+|.++||.+++|+|+++++|||+|||++|++|+++.+......++++|++||++
T Consensus         4 ~~f~~l~l~~~l~~~l~~~g~~~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~~~~~~~lil~Ptre   83 (460)
T PRK11776          4 TAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTRE   83 (460)
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhhccCCceEEEEeCCHH
Confidence            57999999999999999999999999999999999999999999999999999999999999876666778999999999


Q ss_pred             HHHHHHHHHHHhcccc-ceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccc
Q 027749          113 LATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG  191 (219)
Q Consensus       113 l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~  191 (219)
                      |+.|+.+.++.+.... ++++..++|+.+...+...+..+++|+|+||++|.+++.++.+.++++++||+||||+|++++
T Consensus        84 La~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~~~~~IvV~Tp~rl~~~l~~~~~~l~~l~~lViDEad~~l~~g  163 (460)
T PRK11776         84 LADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMG  163 (460)
T ss_pred             HHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhcCCCCEEEEChHHHHHHHHcCCccHHHCCEEEEECHHHHhCcC
Confidence            9999999999887654 688889999999988888888999999999999999999888889999999999999999999


Q ss_pred             cHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          192 FKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       192 ~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      |...+..+++.+++..|+++||||+|+
T Consensus       164 ~~~~l~~i~~~~~~~~q~ll~SAT~~~  190 (460)
T PRK11776        164 FQDAIDAIIRQAPARRQTLLFSATYPE  190 (460)
T ss_pred             cHHHHHHHHHhCCcccEEEEEEecCcH
Confidence            999999999999999999999999985

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=100.00  E-value=6.6e-38  Score=276.95  Aligned_cols=188  Identities=34%  Similarity=0.567  Sum_probs=176.0

Q ss_pred             ccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCC
Q 027749           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (219)
Q Consensus        31 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~  110 (219)
                      ...+|.++++++.++++|.++||..|+|+|.++||.++.+++++++||||+|||++|.+|+++.+......+++||++||
T Consensus         4 ~~~~f~~l~L~~~ll~al~~~G~~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~~~~~~~LIL~PT   83 (629)
T PRK11634          4 FETTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPT   83 (629)
T ss_pred             ccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhccCCCeEEEEeCc
Confidence            34579999999999999999999999999999999999999999999999999999999999988766667899999999


Q ss_pred             HHHHHHHHHHHHHhcccc-ceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhc
Q 027749          111 RELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (219)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~  189 (219)
                      ++|+.|+.+.+..+.... ++.+..++|+.+...+...+..+++|+|+||+++.+++....+.++++++||+||||.|++
T Consensus        84 reLa~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l~~~~~IVVgTPgrl~d~l~r~~l~l~~l~~lVlDEAd~ml~  163 (629)
T PRK11634         84 RELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLR  163 (629)
T ss_pred             HHHHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcchhhceEEEeccHHHHhh
Confidence            999999999999887654 7889999999998888888888999999999999999998888999999999999999999


Q ss_pred             cccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          190 RGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       190 ~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      ++|...+..+++.+|...|+++||||+|.
T Consensus       164 ~gf~~di~~Il~~lp~~~q~llfSAT~p~  192 (629)
T PRK11634        164 MGFIEDVETIMAQIPEGHQTALFSATMPE  192 (629)
T ss_pred             cccHHHHHHHHHhCCCCCeEEEEEccCCh
Confidence            99999999999999999999999999985

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=3.4e-37  Score=270.64  Aligned_cols=186  Identities=31%  Similarity=0.463  Sum_probs=171.2

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccC-------CCceeEE
Q 027749           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-------SREVQAL  105 (219)
Q Consensus        33 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~-------~~~~~~l  105 (219)
                      .+|+++++++.++++|.+.||..|+|+|.++||.+++|+|+++++|||+|||++|++|+++.+...       ...+++|
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            469999999999999999999999999999999999999999999999999999999999987532       1247899


Q ss_pred             EEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcC-CCCCCCccEEEeccc
Q 027749          106 ILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK-TLRTRAIKLLVLDES  184 (219)
Q Consensus       106 il~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~-~~~~~~l~~lVvDE~  184 (219)
                      |++||++|+.|+++.+.++....++++..++|+.+...+...+..+++|+|+||++|++++.+. .+.++.+++||||||
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            9999999999999999999998899999999999988887778888999999999999988765 467889999999999


Q ss_pred             hhhhccccHHHHHHHHHhCCC--CCeEEEEeecccC
Q 027749          185 DEMLSRGFKDQIYDVYRYLPP--DLQVCCPGSCFLF  218 (219)
Q Consensus       185 h~l~~~~~~~~~~~i~~~~~~--~~q~i~~SATl~~  218 (219)
                      |+|++++|...+..+++.++.  ..|+++||||++.
T Consensus       169 h~lld~gf~~~i~~il~~lp~~~~~q~ll~SATl~~  204 (572)
T PRK04537        169 DRMFDLGFIKDIRFLLRRMPERGTRQTLLFSATLSH  204 (572)
T ss_pred             HHHhhcchHHHHHHHHHhcccccCceEEEEeCCccH
Confidence            999999999999999999987  7899999999975

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=100.00  E-value=1.7e-36  Score=259.79  Aligned_cols=185  Identities=30%  Similarity=0.449  Sum_probs=172.7

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccC----CCceeEEEEcC
Q 027749           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS----SREVQALILSP  109 (219)
Q Consensus        34 ~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~----~~~~~~lil~P  109 (219)
                      +|+++++++.++++|.+.||..|+++|.++|+.+++|+|+++++|||+|||++|++|+++.+...    ...+++||++|
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            69999999999999999999999999999999999999999999999999999999999877532    23468999999


Q ss_pred             CHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhc
Q 027749          110 TRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (219)
Q Consensus       110 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~  189 (219)
                      |++|+.|+.+.+..+....++++..+.|+.....+...+..+++|+|+||++|++++.++.+.++++++||+||||+|++
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            99999999999999999989999999999998888777888899999999999999998888899999999999999999


Q ss_pred             cccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          190 RGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       190 ~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      ++|...+..+...++...|+++||||++.
T Consensus       162 ~~~~~~~~~i~~~~~~~~q~~~~SAT~~~  190 (434)
T PRK11192        162 MGFAQDIETIAAETRWRKQTLLFSATLEG  190 (434)
T ss_pred             CCcHHHHHHHHHhCccccEEEEEEeecCH
Confidence            99999999999999989999999999863

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

Probab=100.00  E-value=7.9e-38  Score=260.63  Aligned_cols=204  Identities=28%  Similarity=0.433  Sum_probs=185.4

Q ss_pred             CCCCcceeecc--CCCCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHh
Q 027749           16 MDDDKMVFETT--EGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQ   93 (219)
Q Consensus        16 ~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~   93 (219)
                      ...++...+.+  ..|.++..|.+..+.+.+..++...++..|+|+|+.++|.+..|++.++||+||+|||.+|++|++.
T Consensus        55 d~~~~i~v~~~G~~~p~~i~~f~~~~l~~~l~~ni~~~~~~~ptpvQk~sip~i~~Grdl~acAqTGsGKT~aFLiPii~  134 (482)
T KOG0335|consen   55 DKYNDIPVKVSGRDVPPHIPTFDEAILGEALAGNIKRSGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAAFLIPIIS  134 (482)
T ss_pred             CCccceeeeccCCccCCCcccccccchhHHHhhccccccccCCCcceeeccceeecCCceEEEccCCCcchHHHHHHHHH
Confidence            33444444444  4478888999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccCC----------CceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHH
Q 027749           94 TVDTSS----------REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVC  163 (219)
Q Consensus        94 ~~~~~~----------~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~  163 (219)
                      .+....          ..|.++|++||++||.|++++++++.-..+++.+..+|+.+...+...+.++|+|+|+||++|.
T Consensus       135 ~~~~~~~~~~~~~~~~~~P~~lIlapTReL~~Qi~nea~k~~~~s~~~~~~~ygg~~~~~q~~~~~~gcdIlvaTpGrL~  214 (482)
T KOG0335|consen  135 YLLDEGPEDRGESGGGVYPRALILAPTRELVDQIYNEARKFSYLSGMKSVVVYGGTDLGAQLRFIKRGCDILVATPGRLK  214 (482)
T ss_pred             HHHhcCcccCcccCCCCCCceEEEeCcHHHhhHHHHHHHhhcccccceeeeeeCCcchhhhhhhhccCccEEEecCchhh
Confidence            886542          2589999999999999999999999988899999999999999999999999999999999999


Q ss_pred             HHHHcCCCCCCCccEEEeccchhhhc-cccHHHHHHHHHhCCC----CCeEEEEeecccCC
Q 027749          164 DMIKRKTLRTRAIKLLVLDESDEMLS-RGFKDQIYDVYRYLPP----DLQVCCPGSCFLFD  219 (219)
Q Consensus       164 ~~l~~~~~~~~~l~~lVvDE~h~l~~-~~~~~~~~~i~~~~~~----~~q~i~~SATl~~~  219 (219)
                      ++++.+.+.+++++++|+||||+|++ ++|..+++.|+.+...    ..|.++||||+|.+
T Consensus       215 d~~e~g~i~l~~~k~~vLDEADrMlD~mgF~p~Ir~iv~~~~~~~~~~~qt~mFSAtfp~~  275 (482)
T KOG0335|consen  215 DLIERGKISLDNCKFLVLDEADRMLDEMGFEPQIRKIVEQLGMPPKNNRQTLLFSATFPKE  275 (482)
T ss_pred             hhhhcceeehhhCcEEEecchHHhhhhccccccHHHHhcccCCCCccceeEEEEeccCChh
Confidence            99999999999999999999999999 8999999999999743    78999999999964

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

Probab=100.00  E-value=3.4e-37  Score=255.15  Aligned_cols=195  Identities=32%  Similarity=0.480  Sum_probs=185.7

Q ss_pred             eccCCCCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccC-----
Q 027749           24 ETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-----   98 (219)
Q Consensus        24 ~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~-----   98 (219)
                      ...+.++++.+|+.++++..+..+.++..|.+|+|+|.+++|..++|++++-.|-||+|||.+|+.|++..+..+     
T Consensus       214 ~g~s~~rpvtsfeh~gfDkqLm~airk~Ey~kptpiq~qalptalsgrdvigIAktgSgktaAfi~pm~~himdq~eL~~  293 (731)
T KOG0339|consen  214 SGSSPPRPVTSFEHFGFDKQLMTAIRKSEYEKPTPIQCQALPTALSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPELKP  293 (731)
T ss_pred             ccCCCCCCcchhhhcCchHHHHHHHhhhhcccCCcccccccccccccccchheeeccCcchhHHHHHHHHHhcchhhhcC
Confidence            344568899999999999999999999999999999999999999999999999999999999999999888653     


Q ss_pred             CCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccE
Q 027749           99 SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKL  178 (219)
Q Consensus        99 ~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~  178 (219)
                      ..+|..+|++||++|+.|++.+++++++..++++++++||.+..++...|..++.||||||++|.++++-+..++.++.|
T Consensus       294 g~gPi~vilvPTrela~Qi~~eaKkf~K~ygl~~v~~ygGgsk~eQ~k~Lk~g~EivVaTPgRlid~VkmKatn~~rvS~  373 (731)
T KOG0339|consen  294 GEGPIGVILVPTRELASQIFSEAKKFGKAYGLRVVAVYGGGSKWEQSKELKEGAEIVVATPGRLIDMVKMKATNLSRVSY  373 (731)
T ss_pred             CCCCeEEEEeccHHHHHHHHHHHHHhhhhccceEEEeecCCcHHHHHHhhhcCCeEEEechHHHHHHHHhhcccceeeeE
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeccchhhhccccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          179 LVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       179 lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      ||+||+|+|+++||..+++.|..+..++.|.|+||||++.
T Consensus       374 LV~DEadrmfdmGfe~qVrSI~~hirpdrQtllFsaTf~~  413 (731)
T KOG0339|consen  374 LVLDEADRMFDMGFEPQVRSIKQHIRPDRQTLLFSATFKK  413 (731)
T ss_pred             EEEechhhhhccccHHHHHHHHhhcCCcceEEEeeccchH
Confidence            9999999999999999999999999999999999999974

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

Probab=100.00  E-value=6.1e-37  Score=252.66  Aligned_cols=188  Identities=29%  Similarity=0.467  Sum_probs=174.9

Q ss_pred             cCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccC----CCceeEEEE
Q 027749           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS----SREVQALIL  107 (219)
Q Consensus        32 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~----~~~~~~lil  107 (219)
                      ...|++.++++..++++.++||...|++|+..++.++.|+|+++.|-||+|||++|++|+++.+...    +.+..++|+
T Consensus        81 ~~~f~~~~LS~~t~kAi~~~GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r~~~~vlIi  160 (543)
T KOG0342|consen   81 TFRFEEGSLSPLTLKAIKEMGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFKPRNGTGVLII  160 (543)
T ss_pred             hhHhhccccCHHHHHHHHhcCccchhHHHHhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhcccCCCCCeeEEEe
Confidence            4567888999999999999999999999999999999999999999999999999999999988643    345679999


Q ss_pred             cCCHHHHHHHHHHHHHhcccc-ceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCC-CCCCCccEEEeccch
Q 027749          108 SPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT-LRTRAIKLLVLDESD  185 (219)
Q Consensus       108 ~P~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~-~~~~~l~~lVvDE~h  185 (219)
                      +||++||.|++.+++++.... ++.+..++||.+...+.+++.++|+|+|+||++|++.+.+.. +.+++++++|+||||
T Consensus       161 ~PTRELA~Q~~~eak~Ll~~h~~~~v~~viGG~~~~~e~~kl~k~~niliATPGRLlDHlqNt~~f~~r~~k~lvlDEAD  240 (543)
T KOG0342|consen  161 CPTRELAMQIFAEAKELLKYHESITVGIVIGGNNFSVEADKLVKGCNILIATPGRLLDHLQNTSGFLFRNLKCLVLDEAD  240 (543)
T ss_pred             cccHHHHHHHHHHHHHHHhhCCCcceEEEeCCccchHHHHHhhccccEEEeCCchHHhHhhcCCcchhhccceeEeecch
Confidence            999999999999999999888 899999999999999999999999999999999999998754 556788999999999


Q ss_pred             hhhccccHHHHHHHHHhCCCCCeEEEEeecccCC
Q 027749          186 EMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFLFD  219 (219)
Q Consensus       186 ~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~~  219 (219)
                      ++++.||.+.++.|++.+|+..|.++||||.|++
T Consensus       241 rlLd~GF~~di~~Ii~~lpk~rqt~LFSAT~~~k  274 (543)
T KOG0342|consen  241 RLLDIGFEEDVEQIIKILPKQRQTLLFSATQPSK  274 (543)
T ss_pred             hhhhcccHHHHHHHHHhccccceeeEeeCCCcHH
Confidence            9999999999999999999999999999999864

>cd00268 DEADc DEAD-box helicases

Probab=100.00  E-value=9.4e-36  Score=230.70  Aligned_cols=184  Identities=45%  Similarity=0.741  Sum_probs=170.8

Q ss_pred             cccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccC--CCceeEEEEcCCHH
Q 027749           35 FDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS--SREVQALILSPTRE  112 (219)
Q Consensus        35 ~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~--~~~~~~lil~P~~~  112 (219)
                      |+++++++.+.+.|.+.|+..|+++|.++++.+.+|+++++++|||+|||++|+++++..+...  ..+++++|++|+++
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            7889999999999999999999999999999999999999999999999999999999988876  56789999999999


Q ss_pred             HHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhcccc
Q 027749          113 LATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF  192 (219)
Q Consensus       113 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~  192 (219)
                      |+.|+...++.+....++.+..+.|+.+.......+..+++|+|+||+++...+.+....+++++++|+||+|.+.+.++
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            99999999999988778888889998887777666767899999999999999988878889999999999999998889


Q ss_pred             HHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          193 KDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       193 ~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      ...+..+++.+++++|++++|||+++
T Consensus       161 ~~~~~~~~~~l~~~~~~~~~SAT~~~  186 (203)
T cd00268         161 EDQIREILKLLPKDRQTLLFSATMPK  186 (203)
T ss_pred             HHHHHHHHHhCCcccEEEEEeccCCH
Confidence            99999999999999999999999985

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.

>PTZ00424 helicase 45; Provisional

Probab=100.00  E-value=6.3e-36  Score=253.98  Aligned_cols=188  Identities=57%  Similarity=0.950  Sum_probs=174.4

Q ss_pred             ccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCC
Q 027749           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (219)
Q Consensus        31 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~  110 (219)
                      ...+|+++++++.+.++|.++|+..|+|+|.++|+.+.+|+++++++|||+|||++|++|++..+.....+.++||++|+
T Consensus        26 ~~~~~~~l~l~~~~~~~l~~~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~~~~~~~lil~Pt  105 (401)
T PTZ00424         26 IVDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDLNACQALILAPT  105 (401)
T ss_pred             ccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCCCCCceEEEECCC
Confidence            46789999999999999999999999999999999999999999999999999999999999988765567789999999


Q ss_pred             HHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhcc
Q 027749          111 RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (219)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~  190 (219)
                      ++|+.|+.+.+..+....+..+..+.|+.....+...+..+++|+|+||+++.+++..+...++++++||+||+|++.++
T Consensus       106 ~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~l~~i~lvViDEah~~~~~  185 (401)
T PTZ00424        106 RELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSR  185 (401)
T ss_pred             HHHHHHHHHHHHHHhhhcCceEEEEECCcCHHHHHHHHcCCCCEEEECcHHHHHHHHhCCcccccccEEEEecHHHHHhc
Confidence            99999999999999887788888888988887777788888999999999999999888888999999999999999999


Q ss_pred             ccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          191 GFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       191 ~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      +|...+..+++.++++.|++++|||+|.
T Consensus       186 ~~~~~~~~i~~~~~~~~~~i~~SAT~~~  213 (401)
T PTZ00424        186 GFKGQIYDVFKKLPPDVQVALFSATMPN  213 (401)
T ss_pred             chHHHHHHHHhhCCCCcEEEEEEecCCH
Confidence            9999999999999999999999999985

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

Probab=100.00  E-value=9.9e-37  Score=253.13  Aligned_cols=214  Identities=26%  Similarity=0.385  Sum_probs=195.6

Q ss_pred             hhhhhcCCCCCCCCCcceeeccCCCCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchh
Q 027749            5 TAMRRRGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKT   84 (219)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT   84 (219)
                      ..|+.+.-..-..+=.+..+....++++.+|++.+++..+++.+.+.||..|+|+|..++|..++.+|+|..+.||||||
T Consensus       217 ~Em~~rdwri~redynis~kg~~lpnplrnwEE~~~P~e~l~~I~~~~y~eptpIqR~aipl~lQ~rD~igvaETgsGkt  296 (673)
T KOG0333|consen  217 AEMTERDWRIFREDYNISIKGGRLPNPLRNWEESGFPLELLSVIKKPGYKEPTPIQRQAIPLGLQNRDPIGVAETGSGKT  296 (673)
T ss_pred             HhcCCccceeeecceeeeecCCCCCccccChhhcCCCHHHHHHHHhcCCCCCchHHHhhccchhccCCeeeEEeccCCcc
Confidence            34555555555555666777788899999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhHHHHHhhhcc---------CCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEE
Q 027749           85 SMIALTVCQTVDT---------SSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVV  155 (219)
Q Consensus        85 ~~~~~~~~~~~~~---------~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~  155 (219)
                      .+|++|++..+..         .-.+|+++|++||++|++|+.++..++++..+++++.++||.+.+++...+..+|.|+
T Consensus       297 aaf~ipLl~~IsslP~~~~~en~~~gpyaiilaptReLaqqIeeEt~kf~~~lg~r~vsvigg~s~EEq~fqls~gceiv  376 (673)
T KOG0333|consen  297 AAFLIPLLIWISSLPPMARLENNIEGPYAIILAPTRELAQQIEEETNKFGKPLGIRTVSVIGGLSFEEQGFQLSMGCEIV  376 (673)
T ss_pred             ccchhhHHHHHHcCCCcchhhhcccCceeeeechHHHHHHHHHHHHHHhcccccceEEEEecccchhhhhhhhhccceee
Confidence            9999999877643         3357999999999999999999999999999999999999999999988999999999


Q ss_pred             EeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCC---C----------------------CeEE
Q 027749          156 SGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP---D----------------------LQVC  210 (219)
Q Consensus       156 v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~---~----------------------~q~i  210 (219)
                      |+||++|.+.+.++.+.++++.++|+||||+|++++|+.++..++.+||.   .                      .|.+
T Consensus       377 iatPgrLid~Lenr~lvl~qctyvvldeadrmiDmgfE~dv~~iL~~mPssn~k~~tde~~~~~~~~~~~~~~k~yrqT~  456 (673)
T KOG0333|consen  377 IATPGRLIDSLENRYLVLNQCTYVVLDEADRMIDMGFEPDVQKILEQMPSSNAKPDTDEKEGEERVRKNFSSSKKYRQTV  456 (673)
T ss_pred             ecCchHHHHHHHHHHHHhccCceEeccchhhhhcccccHHHHHHHHhCCccccCCCccchhhHHHHHhhcccccceeEEE
Confidence            99999999999999999999999999999999999999999999999964   1                      6999


Q ss_pred             EEeecccC
Q 027749          211 CPGSCFLF  218 (219)
Q Consensus       211 ~~SATl~~  218 (219)
                      .||||+|+
T Consensus       457 mftatm~p  464 (673)
T KOG0333|consen  457 MFTATMPP  464 (673)
T ss_pred             EEecCCCh
Confidence            99999986

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

Probab=100.00  E-value=5.8e-37  Score=255.06  Aligned_cols=189  Identities=28%  Similarity=0.488  Sum_probs=169.9

Q ss_pred             CCccCccccCCCCHHHHHHHH-HCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhcc------CCCc
Q 027749           29 VEAITSFDAMGIKDDLLRGIY-QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT------SSRE  101 (219)
Q Consensus        29 ~~~~~~~~~~~l~~~~~~~l~-~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~------~~~~  101 (219)
                      +=....|.++++++.+...|. .+++..||.+|+++||.+++|+|++|.++||+|||++|++|+++.+..      ...+
T Consensus       132 ~fts~~f~~LGL~~~lv~~L~~~m~i~~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~G  211 (708)
T KOG0348|consen  132 PFTSAAFASLGLHPHLVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRSDG  211 (708)
T ss_pred             ccccccchhcCCCHHHHHHHHHHhccCccchHhhcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCccccccCC
Confidence            445578999999999999998 679999999999999999999999999999999999999999998854      3457


Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhcccc-ceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHc-CCCCCCCccEE
Q 027749          102 VQALILSPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-KTLRTRAIKLL  179 (219)
Q Consensus       102 ~~~lil~P~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~-~~~~~~~l~~l  179 (219)
                      +.++|++||++||.|+++.+.++.+.+ .+..+.++||.....+..++++|++|+|+||++|.+.+.+ ..+.++++++|
T Consensus       212 ~~ALVivPTREL~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARLRKGiNILIgTPGRLvDHLknT~~i~~s~LRwl  291 (708)
T KOG0348|consen  212 PYALVIVPTRELALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKARLRKGINILIGTPGRLVDHLKNTKSIKFSRLRWL  291 (708)
T ss_pred             ceEEEEechHHHHHHHHHHHHHHhcCceEEeeceeecccccccHHHHHhcCceEEEcCchHHHHHHhccchheeeeeeEE
Confidence            999999999999999999999998765 4666788999999888899999999999999999998887 55788999999


Q ss_pred             EeccchhhhccccHHHHHHHHHhCCC-------------CCeEEEEeeccc
Q 027749          180 VLDESDEMLSRGFKDQIYDVYRYLPP-------------DLQVCCPGSCFL  217 (219)
Q Consensus       180 VvDE~h~l~~~~~~~~~~~i~~~~~~-------------~~q~i~~SATl~  217 (219)
                      |+||+|++++.||+..+..|++.+..             ..|.+++|||+.
T Consensus       292 VlDEaDrlleLGfekdit~Il~~v~~~~~~e~~~~~lp~q~q~mLlSATLt  342 (708)
T KOG0348|consen  292 VLDEADRLLELGFEKDITQILKAVHSIQNAECKDPKLPHQLQNMLLSATLT  342 (708)
T ss_pred             EecchhHHHhccchhhHHHHHHHHhhccchhcccccccHHHHhHhhhhhhH
Confidence            99999999999999999988887621             267899999986

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=7.4e-37  Score=249.35  Aligned_cols=187  Identities=28%  Similarity=0.421  Sum_probs=167.3

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhcc------CCCceeEEE
Q 027749           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT------SSREVQALI  106 (219)
Q Consensus        33 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~------~~~~~~~li  106 (219)
                      .+|+++++++++++++.+.||.+||-+|..+||.++.|+|++..|.||||||.+|++|+++.+..      ...++.++|
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            68999999999999999999999999999999999999999999999999999999999998854      234689999


Q ss_pred             EcCCHHHHHHHHHHHHHhccccc--eeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCC-CCCCCccEEEecc
Q 027749          107 LSPTRELATQTEKVILAIGDFIN--IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT-LRTRAIKLLVLDE  183 (219)
Q Consensus       107 l~P~~~l~~q~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~-~~~~~l~~lVvDE  183 (219)
                      ++||++||.|++..+.++....+  +++.-+.+..+.......+...++|+|+||++++.++..+. ..+..+.++|+||
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            99999999999999988876653  55555555555555556677889999999999999998877 6788999999999


Q ss_pred             chhhhccccHHHHHHHHHhCCCCCeEEEEeecccCC
Q 027749          184 SDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFLFD  219 (219)
Q Consensus       184 ~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~~  219 (219)
                      ||.+++.||++++..+.+++|+.+|-+++|||++.|
T Consensus       179 ADLllsfGYeedlk~l~~~LPr~~Q~~LmSATl~dD  214 (569)
T KOG0346|consen  179 ADLLLSFGYEEDLKKLRSHLPRIYQCFLMSATLSDD  214 (569)
T ss_pred             hhhhhhcccHHHHHHHHHhCCchhhheeehhhhhhH
Confidence            999999999999999999999999999999999754

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=1.9e-35  Score=255.77  Aligned_cols=188  Identities=29%  Similarity=0.479  Sum_probs=170.7

Q ss_pred             ccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCC-------Ccee
Q 027749           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-------REVQ  103 (219)
Q Consensus        31 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~-------~~~~  103 (219)
                      ....|.++++++.+.++|.++||..|+++|.++|+.+.+|+|+++.+|||+|||++|++|+++.+....       ..++
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            346788999999999999999999999999999999999999999999999999999999999876542       2578


Q ss_pred             EEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhc-CCCeEEEeChHHHHHHHHcCCCCCCCccEEEec
Q 027749          104 ALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLD  182 (219)
Q Consensus       104 ~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvD  182 (219)
                      +||++||++|+.|+.+.+..+.+..++.+..++|+.+...+...+. ..++|+|+||++|+.++..+...++++++||||
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            9999999999999999999999888999999999988777766664 468999999999999988888889999999999


Q ss_pred             cchhhhccccHHHHHHHHHhCCC--CCeEEEEeecccC
Q 027749          183 ESDEMLSRGFKDQIYDVYRYLPP--DLQVCCPGSCFLF  218 (219)
Q Consensus       183 E~h~l~~~~~~~~~~~i~~~~~~--~~q~i~~SATl~~  218 (219)
                      |+|.+.+++|...+..+++.++.  +.|++++|||++.
T Consensus       245 Eah~l~~~~~~~~l~~i~~~~~~~~~~q~i~~SAT~~~  282 (475)
T PRK01297        245 EADRMLDMGFIPQVRQIIRQTPRKEERQTLLFSATFTD  282 (475)
T ss_pred             hHHHHHhcccHHHHHHHHHhCCCCCCceEEEEEeecCH
Confidence            99999999999999999999864  6799999999874

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

Probab=100.00  E-value=1.8e-35  Score=242.97  Aligned_cols=185  Identities=33%  Similarity=0.567  Sum_probs=165.8

Q ss_pred             CccccCC--CCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCC-----CceeEE
Q 027749           33 TSFDAMG--IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-----REVQAL  105 (219)
Q Consensus        33 ~~~~~~~--l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~-----~~~~~l  105 (219)
                      .+|++++  |++++++++..+||+..||+|..++|.+++++|+++.++||||||++|++|++..+....     ....++
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            4677764  669999999999999999999999999999999999999999999999999999884321     124699


Q ss_pred             EEcCCHHHHHHHHHHHHHhccc-cceeEEEEECCcccHHHHHHhc-CCCeEEEeChHHHHHHHHcCC--CCCCCccEEEe
Q 027749          106 ILSPTRELATQTEKVILAIGDF-INIQAHACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRKT--LRTRAIKLLVL  181 (219)
Q Consensus       106 il~P~~~l~~q~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~l~-~~~~I~v~Tp~~l~~~l~~~~--~~~~~l~~lVv  181 (219)
                      |++||++|+.|+.+.+..+... .++++.+++||.+..++...+. ++++|+||||++|.+++.+..  ++++.+.++|+
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 6789999999999988887774 589999999999999998744  55679999999


Q ss_pred             ccchhhhccccHHHHHHHHHhCCCCCeEEEEeeccc
Q 027749          182 DESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFL  217 (219)
Q Consensus       182 DE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl~  217 (219)
                      ||||+++++||...++.|++.+|+.+++=+||||-.
T Consensus       164 DEADrLldmgFe~~~n~ILs~LPKQRRTGLFSATq~  199 (567)
T KOG0345|consen  164 DEADRLLDMGFEASVNTILSFLPKQRRTGLFSATQT  199 (567)
T ss_pred             cchHhHhcccHHHHHHHHHHhcccccccccccchhh
Confidence            999999999999999999999999999999999964

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=100.00  E-value=3.8e-36  Score=251.00  Aligned_cols=188  Identities=29%  Similarity=0.476  Sum_probs=173.0

Q ss_pred             CCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCC----CceeE
Q 027749           29 VEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS----REVQA  104 (219)
Q Consensus        29 ~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~----~~~~~  104 (219)
                      ...+..|.++|++....+.|++.+|..++.+|+.+||..+.|++++-.+.||||||++|++|+++.+...+    .+..+
T Consensus        65 ~~~~~kF~dlpls~~t~kgLke~~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~kWs~~DGlGa  144 (758)
T KOG0343|consen   65 STTIKKFADLPLSQKTLKGLKEAKFVKMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLKWSPTDGLGA  144 (758)
T ss_pred             hhhhhhHHhCCCchHHHHhHhhcCCccHHHHHHhhcchhccCcccccccccCCCceeeehHHHHHHHHHcCCCCCCCcee
Confidence            34567899999999999999999999999999999999999999999999999999999999999886543    45779


Q ss_pred             EEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcC-CCCCCCccEEEecc
Q 027749          105 LILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK-TLRTRAIKLLVLDE  183 (219)
Q Consensus       105 lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~-~~~~~~l~~lVvDE  183 (219)
                      ||+.||++||.|.++.+.+.++..+++..+++||.+...+..++ ++++|+||||++|+..+... .++..++.++|+||
T Consensus       145 lIISPTRELA~QtFevL~kvgk~h~fSaGLiiGG~~~k~E~eRi-~~mNILVCTPGRLLQHmde~~~f~t~~lQmLvLDE  223 (758)
T KOG0343|consen  145 LIISPTRELALQTFEVLNKVGKHHDFSAGLIIGGKDVKFELERI-SQMNILVCTPGRLLQHMDENPNFSTSNLQMLVLDE  223 (758)
T ss_pred             EEecchHHHHHHHHHHHHHHhhccccccceeecCchhHHHHHhh-hcCCeEEechHHHHHHhhhcCCCCCCcceEEEecc
Confidence            99999999999999999999999999999999999987776555 46899999999999977654 57889999999999


Q ss_pred             chhhhccccHHHHHHHHHhCCCCCeEEEEeeccc
Q 027749          184 SDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFL  217 (219)
Q Consensus       184 ~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl~  217 (219)
                      ||+++++||...+..|++.+|+.+|.++||||-+
T Consensus       224 ADR~LDMGFk~tL~~Ii~~lP~~RQTLLFSATqt  257 (758)
T KOG0343|consen  224 ADRMLDMGFKKTLNAIIENLPKKRQTLLFSATQT  257 (758)
T ss_pred             HHHHHHHhHHHHHHHHHHhCChhheeeeeecccc
Confidence            9999999999999999999999999999999964

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

Probab=100.00  E-value=4.7e-36  Score=243.16  Aligned_cols=191  Identities=31%  Similarity=0.486  Sum_probs=177.9

Q ss_pred             CCCCccCcccc-CCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhcc------CC
Q 027749           27 EGVEAITSFDA-MGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT------SS   99 (219)
Q Consensus        27 ~~~~~~~~~~~-~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~------~~   99 (219)
                      .-|+|.-+|++ +...+.++.++.+.||.+|+|+|.++||.+++|++.+.++.||+|||++|++|-+-.+..      +.
T Consensus       213 pIPnP~ctFddAFq~~pevmenIkK~GFqKPtPIqSQaWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr  292 (629)
T KOG0336|consen  213 PIPNPVCTFDDAFQCYPEVMENIKKTGFQKPTPIQSQAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQR  292 (629)
T ss_pred             cCCCCcCcHHHHHhhhHHHHHHHHhccCCCCCcchhcccceeecCcceEEEEecCCCcCHHHhccceeeeeccchhhhcc
Confidence            34888889987 578999999999999999999999999999999999999999999999999998776643      34


Q ss_pred             CceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEE
Q 027749          100 REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLL  179 (219)
Q Consensus       100 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~l  179 (219)
                      .+|..|+++||++|+.|+.-++.++. +.+....|++|+.+..+++..++++.+|+++||++|.++...+.+++..+.|+
T Consensus       293 ~~p~~lvl~ptreLalqie~e~~kys-yng~ksvc~ygggnR~eqie~lkrgveiiiatPgrlndL~~~n~i~l~siTYl  371 (629)
T KOG0336|consen  293 NGPGVLVLTPTRELALQIEGEVKKYS-YNGLKSVCVYGGGNRNEQIEDLKRGVEIIIATPGRLNDLQMDNVINLASITYL  371 (629)
T ss_pred             CCCceEEEeccHHHHHHHHhHHhHhh-hcCcceEEEecCCCchhHHHHHhcCceEEeeCCchHhhhhhcCeeeeeeeEEE
Confidence            57899999999999999999998875 44889999999999999999999999999999999999999999999999999


Q ss_pred             EeccchhhhccccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          180 VLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       180 VvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      |+||||+|++++|+.++.+|+-...+++|+++-|||+|+
T Consensus       372 VlDEADrMLDMgFEpqIrkilldiRPDRqtvmTSATWP~  410 (629)
T KOG0336|consen  372 VLDEADRMLDMGFEPQIRKILLDIRPDRQTVMTSATWPE  410 (629)
T ss_pred             EecchhhhhcccccHHHHHHhhhcCCcceeeeecccCch
Confidence            999999999999999999999999999999999999996

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

Probab=100.00  E-value=4e-35  Score=233.70  Aligned_cols=187  Identities=32%  Similarity=0.503  Sum_probs=178.7

Q ss_pred             ccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCC
Q 027749           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (219)
Q Consensus        31 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~  110 (219)
                      ....|+++++++++.+.|+.+|+..|+|+|..++|.++.|+|++-+|.||||||.+|.+|+++++...+.+.+++|++||
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            45689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCC----CCCCCccEEEeccchh
Q 027749          111 RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT----LRTRAIKLLVLDESDE  186 (219)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~----~~~~~l~~lVvDE~h~  186 (219)
                      ++|+-|+.+.+..+++..+.+++.++||.+.-.+...+...++++|+||+++.+.+.++.    ..+++++++|+||||+
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            999999999999999999999999999999999999999999999999999999988763    3468899999999999


Q ss_pred             hhccccHHHHHHHHHhCCCCCeEEEEeeccc
Q 027749          187 MLSRGFKDQIYDVYRYLPPDLQVCCPGSCFL  217 (219)
Q Consensus       187 l~~~~~~~~~~~i~~~~~~~~q~i~~SATl~  217 (219)
                      +++..|.+.+..+.+.+|+.+|.++||||+.
T Consensus       165 vL~~~f~d~L~~i~e~lP~~RQtLlfSATit  195 (442)
T KOG0340|consen  165 VLAGCFPDILEGIEECLPKPRQTLLFSATIT  195 (442)
T ss_pred             hhccchhhHHhhhhccCCCccceEEEEeehh
Confidence            9999999999999999999999999999985

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=3e-35  Score=260.80  Aligned_cols=198  Identities=32%  Similarity=0.538  Sum_probs=183.9

Q ss_pred             ceeeccCCCCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccC--
Q 027749           21 MVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS--   98 (219)
Q Consensus        21 ~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~--   98 (219)
                      +.......+.|+.+|.+.+++..++..++++|+.+|+|+|.+|||++.+|+++|.+|-||+|||++|++|++.....+  
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            566777789999999999999999999999999999999999999999999999999999999999999999776543  


Q ss_pred             ---CCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCC---CC
Q 027749           99 ---SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT---LR  172 (219)
Q Consensus        99 ---~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~---~~  172 (219)
                         ..+|-+||++||++|+.|+.+.++++.+..++++++++|+....+++..+++++.|+||||+++.+++-.+.   .+
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               358999999999999999999999999999999999999999999999999999999999999999775433   45


Q ss_pred             CCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       173 ~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      +.++.++|+||+|+|++.+|..++..|++.+++..|+++||||+|.
T Consensus       513 lrR~t~lv~deaDrmfdmgfePq~~~Ii~nlrpdrQtvlfSatfpr  558 (997)
T KOG0334|consen  513 LRRVTYLVLDEADRMFDMGFEPQITRILQNLRPDRQTVLFSATFPR  558 (997)
T ss_pred             ccccceeeechhhhhheeccCcccchHHhhcchhhhhhhhhhhhhH
Confidence            6677799999999999999999999999999999999999999985

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

Probab=100.00  E-value=2.1e-35  Score=232.69  Aligned_cols=188  Identities=36%  Similarity=0.617  Sum_probs=181.4

Q ss_pred             ccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCC
Q 027749           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (219)
Q Consensus        31 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~  110 (219)
                      .-..|+++.+...++..+.+.||++|.|+|.+++|.++.|+|++..|..|+|||-+|.+|+++.+.......+++|++||
T Consensus        83 kG~efEd~~Lkr~LLmgIfe~G~ekPSPiQeesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~~~~~IQ~~ilVPt  162 (459)
T KOG0326|consen   83 KGNEFEDYCLKRELLMGIFEKGFEKPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLEKIDPKKNVIQAIILVPT  162 (459)
T ss_pred             cCccHHHhhhhHHHHHHHHHhccCCCCCccccccceeecchhhhhhccCCCCCccceechhhhhcCccccceeEEEEeec
Confidence            34679999999999999999999999999999999999999999999999999999999999999998888999999999


Q ss_pred             HHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhcc
Q 027749          111 RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (219)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~  190 (219)
                      ++||.|....|.++.+..++.+....||.+...++.++..+..++|+||++++++.+.+...++++.++|+||||.+++.
T Consensus       163 relALQtSqvc~~lskh~~i~vmvttGGT~lrDDI~Rl~~~VH~~vgTPGRIlDL~~KgVa~ls~c~~lV~DEADKlLs~  242 (459)
T KOG0326|consen  163 RELALQTSQVCKELSKHLGIKVMVTTGGTSLRDDIMRLNQTVHLVVGTPGRILDLAKKGVADLSDCVILVMDEADKLLSV  242 (459)
T ss_pred             chhhHHHHHHHHHHhcccCeEEEEecCCcccccceeeecCceEEEEcCChhHHHHHhcccccchhceEEEechhhhhhch
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          191 GFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       191 ~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      .|...+..++..+|++.|++++|||+|.
T Consensus       243 ~F~~~~e~li~~lP~~rQillySATFP~  270 (459)
T KOG0326|consen  243 DFQPIVEKLISFLPKERQILLYSATFPL  270 (459)
T ss_pred             hhhhHHHHHHHhCCccceeeEEecccch
Confidence            9999999999999999999999999984

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

Probab=100.00  E-value=7.8e-36  Score=240.51  Aligned_cols=198  Identities=31%  Similarity=0.519  Sum_probs=183.1

Q ss_pred             ceeeccCCCCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhc----
Q 027749           21 MVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVD----   96 (219)
Q Consensus        21 ~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~----   96 (219)
                      +..+-...|.|+.+|.++.++..+++.|++.|+..|+|+|.+-+|.+++|++.|-.+-||||||++|.+|++.+..    
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            3455667799999999999999999999999999999999999999999999999999999999999999987663    


Q ss_pred             ----cCCCceeEEEEcCCHHHHHHHHHHHHHhcccc------ceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHH
Q 027749           97 ----TSSREVQALILSPTRELATQTEKVILAIGDFI------NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMI  166 (219)
Q Consensus        97 ----~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l  166 (219)
                          ....+|..+|+||+++||.|.++.+.++....      .++..+++||.+..++....++|..|+|+||++|.+++
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                34568999999999999999999998875543      47888899999999999999999999999999999999


Q ss_pred             HcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          167 KRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       167 ~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      ..+.+.+.-++|+++||||+|.++||.++++.|+..+..-+|.++||||.|.
T Consensus       318 ~KK~~sLd~CRyL~lDEADRmiDmGFEddir~iF~~FK~QRQTLLFSATMP~  369 (610)
T KOG0341|consen  318 AKKIMSLDACRYLTLDEADRMIDMGFEDDIRTIFSFFKGQRQTLLFSATMPK  369 (610)
T ss_pred             HHhhccHHHHHHhhhhhHHHHhhccchhhHHHHHHHHhhhhheeeeeccccH
Confidence            9999999999999999999999999999999999999999999999999985

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1.7e-33  Score=235.09  Aligned_cols=193  Identities=26%  Similarity=0.470  Sum_probs=173.1

Q ss_pred             cCCCCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCC-CcEEEEcCCCCchhHHhHHHHHhhhccCC-----
Q 027749           26 TEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG-RDVIAQAQSGTGKTSMIALTVCQTVDTSS-----   99 (219)
Q Consensus        26 ~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~-~~~lv~~~tG~GKT~~~~~~~~~~~~~~~-----   99 (219)
                      .+....+..|..++++..++++|...||..|+++|...+|.+..| .|++--|.||||||++|-+|+++.+....     
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            344567788999999999999999999999999999999999999 69999999999999999999999664321     


Q ss_pred             ------C--ceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCC
Q 027749          100 ------R--EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL  171 (219)
Q Consensus       100 ------~--~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~  171 (219)
                            .  .+.+||++|||+||.|+...+..+....++++..++||.....+.+.++..++|+|+||++|..++.....
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                  1  24499999999999999999999999999999999999999999899999999999999999999987543


Q ss_pred             ---CCCCccEEEeccchhhhccccHHHHHHHHHhCC-----CCCeEEEEeecccC
Q 027749          172 ---RTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP-----PDLQVCCPGSCFLF  218 (219)
Q Consensus       172 ---~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~-----~~~q~i~~SATl~~  218 (219)
                         ++++++++|+||+|+|.+.|+...+..+++.+.     ...|.+.|||||+-
T Consensus       334 ~l~~~k~vkcLVlDEaDRmvekghF~Els~lL~~L~e~~~~~qrQTlVFSATlt~  388 (731)
T KOG0347|consen  334 HLGNFKKVKCLVLDEADRMVEKGHFEELSKLLKHLNEEQKNRQRQTLVFSATLTL  388 (731)
T ss_pred             hhhhhhhceEEEEccHHHHhhhccHHHHHHHHHHhhhhhcccccceEEEEEEeeh
Confidence               678899999999999999999999999998875     35799999999973

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

Probab=100.00  E-value=7.9e-34  Score=230.58  Aligned_cols=187  Identities=32%  Similarity=0.534  Sum_probs=177.4

Q ss_pred             cCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccC-CCceeEEEEcCC
Q 027749           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-SREVQALILSPT  110 (219)
Q Consensus        32 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~-~~~~~~lil~P~  110 (219)
                      .-+|.+++|+..+.+++++.||..|+|+|++.+|.++.+++++-.+-||+|||.||++|++..+... ..+.+++++.||
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            4689999999999999999999999999999999999999999999999999999999999988653 456789999999


Q ss_pred             HHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhcc
Q 027749          111 RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (219)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~  190 (219)
                      ++|+.|....++++++..+.+..+++|+.+.++++..+..++|||++||++++.+.-.-.+.++.+.|||+||+|.++++
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            99999999999999999999999999999999999999999999999999999877666688999999999999999999


Q ss_pred             ccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          191 GFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       191 ~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      ||.+++..++..+|.+.|.++||||+|.
T Consensus       180 gfqeql~e~l~rl~~~~QTllfSatlp~  207 (529)
T KOG0337|consen  180 GFQEQLHEILSRLPESRQTLLFSATLPR  207 (529)
T ss_pred             hhHHHHHHHHHhCCCcceEEEEeccCch
Confidence            9999999999999999999999999995

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

Probab=99.98  E-value=5.5e-31  Score=197.97  Aligned_cols=160  Identities=24%  Similarity=0.416  Sum_probs=141.2

Q ss_pred             hHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEE
Q 027749           57 SAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACV  136 (219)
Q Consensus        57 ~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~  136 (219)
                      ||+|.++|+.+.+++++++.+|||+|||++++++++..+... ...++++++|++++++|+.+.+.+++...++++..++
T Consensus         1 t~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~-~~~~~lii~P~~~l~~q~~~~~~~~~~~~~~~~~~~~   79 (169)
T PF00270_consen    1 TPLQQEAIEAIISGKNVLISAPTGSGKTLAYILPALNRLQEG-KDARVLIIVPTRALAEQQFERLRKFFSNTNVRVVLLH   79 (169)
T ss_dssp             -HHHHHHHHHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTT-SSSEEEEEESSHHHHHHHHHHHHHHTTTTTSSEEEES
T ss_pred             CHHHHHHHHHHHcCCCEEEECCCCCccHHHHHHHHHhhhccC-CCceEEEEeeccccccccccccccccccccccccccc
Confidence            689999999999999999999999999999999999988776 5568999999999999999999999988788999988


Q ss_pred             CCcccH-HHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCC--CCCeEEEEe
Q 027749          137 GGKSVG-EDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP--PDLQVCCPG  213 (219)
Q Consensus       137 ~~~~~~-~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~--~~~q~i~~S  213 (219)
                      ++.+.. .....+.++++|+|+||++|.+++..+..++.++++||+||+|.+.++.+...+..+++.+.  ++.|++++|
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            888755 33344556899999999999999988666778899999999999998888888999988873  368999999


Q ss_pred             eccc
Q 027749          214 SCFL  217 (219)
Q Consensus       214 ATl~  217 (219)
                      ||++
T Consensus       160 AT~~  163 (169)
T PF00270_consen  160 ATLP  163 (169)
T ss_dssp             SSST
T ss_pred             eCCC
Confidence            9997

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 ....

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

Probab=99.98  E-value=8.2e-31  Score=235.89  Aligned_cols=185  Identities=18%  Similarity=0.205  Sum_probs=148.4

Q ss_pred             CccCccccCC--CCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEE
Q 027749           30 EAITSFDAMG--IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALIL  107 (219)
Q Consensus        30 ~~~~~~~~~~--l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil  107 (219)
                      .....+..++  +++.+.++|.+.|+..|+++|.++++.+++|+|+++++|||||||++|++|+++.+... .++++||+
T Consensus         9 ~~~a~~~~~~~~l~~~l~~~L~~~g~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~~-~~~~aL~l   87 (742)
T TIGR03817         9 ARAGRTAPWPAWAHPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADD-PRATALYL   87 (742)
T ss_pred             CCCcccCCCCCcCCHHHHHHHHHcCCCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhhC-CCcEEEEE
Confidence            3334444443  89999999999999999999999999999999999999999999999999999988764 45789999


Q ss_pred             cCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcC----CCCCCCccEEEecc
Q 027749          108 SPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK----TLRTRAIKLLVLDE  183 (219)
Q Consensus       108 ~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~----~~~~~~l~~lVvDE  183 (219)
                      +||++|+.|+.+.++++. ..++++..+.|+.+. .+...+..+++|+|+||+.+...+...    ...++++++||+||
T Consensus        88 ~PtraLa~q~~~~l~~l~-~~~i~v~~~~Gdt~~-~~r~~i~~~~~IivtTPd~L~~~~L~~~~~~~~~l~~l~~vViDE  165 (742)
T TIGR03817        88 APTKALAADQLRAVRELT-LRGVRPATYDGDTPT-EERRWAREHARYVLTNPDMLHRGILPSHARWARFLRRLRYVVIDE  165 (742)
T ss_pred             cChHHHHHHHHHHHHHhc-cCCeEEEEEeCCCCH-HHHHHHhcCCCEEEEChHHHHHhhccchhHHHHHHhcCCEEEEeC
Confidence            999999999999999987 346777666666654 444566778999999999987533211    12378999999999


Q ss_pred             chhhhccccHHHHHHHHH-------hCCCCCeEEEEeecccC
Q 027749          184 SDEMLSRGFKDQIYDVYR-------YLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       184 ~h~l~~~~~~~~~~~i~~-------~~~~~~q~i~~SATl~~  218 (219)
                      +|.+.+ .|...+..+++       ..+.++|++++|||++.
T Consensus       166 ah~~~g-~fg~~~~~il~rL~ri~~~~g~~~q~i~~SATi~n  206 (742)
T TIGR03817       166 CHSYRG-VFGSHVALVLRRLRRLCARYGASPVFVLASATTAD  206 (742)
T ss_pred             hhhccC-ccHHHHHHHHHHHHHHHHhcCCCCEEEEEecCCCC
Confidence            999865 35555444433       34667899999999975

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.

>PRK00254 ski2-like helicase; Provisional

Probab=99.97  E-value=1.3e-30  Score=235.31  Aligned_cols=179  Identities=13%  Similarity=0.189  Sum_probs=158.7

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHHHHHH-HhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHH
Q 027749           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (219)
Q Consensus        34 ~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~-~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  112 (219)
                      +|+++++++.+.+.+.+.|+..|+|+|.++++. +.+|+|+++++|||+|||++|.+|+++.+...  +.++||++|+++
T Consensus         2 ~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~~--~~~~l~l~P~~a   79 (720)
T PRK00254          2 KVDELRVDERIKRVLKERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLRE--GGKAVYLVPLKA   79 (720)
T ss_pred             cHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHhc--CCeEEEEeChHH
Confidence            578999999999999999999999999999986 78999999999999999999999999887653  457999999999


Q ss_pred             HHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhcccc
Q 027749          113 LATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF  192 (219)
Q Consensus       113 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~  192 (219)
                      |+.|+++.+.++. ..++++..+.|+.+....   ....++|+|+||+++..++.++...++++++||+||+|.+.+.++
T Consensus        80 La~q~~~~~~~~~-~~g~~v~~~~Gd~~~~~~---~~~~~~IiV~Tpe~~~~ll~~~~~~l~~l~lvViDE~H~l~~~~r  155 (720)
T PRK00254         80 LAEEKYREFKDWE-KLGLRVAMTTGDYDSTDE---WLGKYDIIIATAEKFDSLLRHGSSWIKDVKLVVADEIHLIGSYDR  155 (720)
T ss_pred             HHHHHHHHHHHHh-hcCCEEEEEeCCCCCchh---hhccCCEEEEcHHHHHHHHhCCchhhhcCCEEEEcCcCccCCccc
Confidence            9999999998764 357888888888765432   235689999999999999887777789999999999999998888


Q ss_pred             HHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          193 KDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       193 ~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      ...+..++..++.+.|++++|||++.
T Consensus       156 g~~le~il~~l~~~~qiI~lSATl~n  181 (720)
T PRK00254        156 GATLEMILTHMLGRAQILGLSATVGN  181 (720)
T ss_pred             hHHHHHHHHhcCcCCcEEEEEccCCC
Confidence            89999999999989999999999963

>PRK02362 ski2-like helicase; Provisional

Probab=99.97  E-value=1e-30  Score=236.58  Aligned_cols=178  Identities=17%  Similarity=0.240  Sum_probs=153.2

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHHHHHH-HhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHH
Q 027749           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (219)
Q Consensus        34 ~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~-~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  112 (219)
                      .|+++++++.+.+++.+.|+..|+|+|.++++. +.+|+|+++++|||+|||++|.+++++.+..   +.+++|++|+++
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 7789999999999999999999999998853   457999999999


Q ss_pred             HHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhcccc
Q 027749          113 LATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF  192 (219)
Q Consensus       113 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~  192 (219)
                      |+.|+++.+.++.. .++++..+.|+......   ....++|+|+||+++..++.+...+++++++||+||+|.+.+.++
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            99999999997654 47888888887664432   234689999999999999887666789999999999999988777


Q ss_pred             HHHHHHHHHhC---CCCCeEEEEeecccC
Q 027749          193 KDQIYDVYRYL---PPDLQVCCPGSCFLF  218 (219)
Q Consensus       193 ~~~~~~i~~~~---~~~~q~i~~SATl~~  218 (219)
                      +..++.++..+   ++..|++++|||++.
T Consensus       155 g~~le~il~rl~~~~~~~qii~lSATl~n  183 (737)
T PRK02362        155 GPTLEVTLAKLRRLNPDLQVVALSATIGN  183 (737)
T ss_pred             hHHHHHHHHHHHhcCCCCcEEEEcccCCC
Confidence            77776665544   568999999999974

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

Probab=99.97  E-value=1.5e-31  Score=215.37  Aligned_cols=190  Identities=57%  Similarity=0.928  Sum_probs=177.0

Q ss_pred             CccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcC
Q 027749           30 EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (219)
Q Consensus        30 ~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P  109 (219)
                      +-..+|++++|.+.+++.+...||++|+.+|++|+..+..|+|+.+.+++|+|||.+|.+++++.+........+++++|
T Consensus        23 evvdsfddm~L~e~LLrgiy~yGFekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~~ke~qalilaP  102 (397)
T KOG0327|consen   23 EVVDSFDDMNLKESLLRGIYAYGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMSVKETQALILAP  102 (397)
T ss_pred             HHhhhhhhcCCCHHHHhHHHhhccCCchHHHhccccccccCCceeEeeeccccchhhhHHHHHhhcCcchHHHHHHHhcc
Confidence            44569999999999999999999999999999999999999999999999999999999999999988777888999999


Q ss_pred             CHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh-cCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhh
Q 027749          110 TRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL-EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (219)
Q Consensus       110 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l-~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~  188 (219)
                      +++|+.|+......++...++++..+.|+.+...+...+ ..++.|+|+||++..+++....+..+.++++|+||+|.|+
T Consensus       103 treLa~qi~~v~~~lg~~~~~~v~~~igg~~~~~~~~~i~~~~~hivvGTpgrV~dml~~~~l~~~~iKmfvlDEaDEmL  182 (397)
T KOG0327|consen  103 TRELAQQIQKVVRALGDHMDVSVHACIGGTNVRREDQALLKDKPHIVVGTPGRVFDMLNRGSLSTDGIKMFVLDEADEML  182 (397)
T ss_pred             hHHHHHHHHHHHHhhhcccceeeeeecCcccchhhhhhhhccCceeecCCchhHHHhhccccccccceeEEeecchHhhh
Confidence            999999999999999999999999999999988555554 4568999999999999999888888889999999999999


Q ss_pred             ccccHHHHHHHHHhCCCCCeEEEEeecccCC
Q 027749          189 SRGFKDQIYDVYRYLPPDLQVCCPGSCFLFD  219 (219)
Q Consensus       189 ~~~~~~~~~~i~~~~~~~~q~i~~SATl~~~  219 (219)
                      +.+|.+++..+++.+|++.|++++|||.|.|
T Consensus       183 s~gfkdqI~~if~~lp~~vQv~l~SAT~p~~  213 (397)
T KOG0327|consen  183 SRGFKDQIYDIFQELPSDVQVVLLSATMPSD  213 (397)
T ss_pred             ccchHHHHHHHHHHcCcchhheeecccCcHH
Confidence            9999999999999999999999999999864

>KOG4284 consensus DEAD box protein [Transcription]

Probab=99.97  E-value=5.3e-31  Score=223.77  Aligned_cols=191  Identities=27%  Similarity=0.491  Sum_probs=177.1

Q ss_pred             CCCCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEE
Q 027749           27 EGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALI  106 (219)
Q Consensus        27 ~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~li  106 (219)
                      ..+.....|+++.|...++..|+..+|..|+++|..|||.++.+.|+||++..|+|||++|.+.+++.+......++++|
T Consensus        19 V~~~~~~~fe~l~l~r~vl~glrrn~f~~ptkiQaaAIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~~~~~~q~~I   98 (980)
T KOG4284|consen   19 VQSNCTPGFEQLALWREVLLGLRRNAFALPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDSRSSHIQKVI   98 (980)
T ss_pred             cccCCCCCHHHHHHHHHHHHHHHhhcccCCCchhhhhhhhhhcccceEEEecCCCCceEEEEeeeehhcCcccCcceeEE
Confidence            34666788999999999999999999999999999999999999999999999999999999999998887777899999


Q ss_pred             EcCCHHHHHHHHHHHHHhcccc-ceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccch
Q 027749          107 LSPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESD  185 (219)
Q Consensus       107 l~P~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h  185 (219)
                      |+||++++.|+.+.+.+++..+ +.++..++||.....+...+ +.|.|+|+||+++..+++.+.++.+.++++|+||||
T Consensus        99 v~PTREiaVQI~~tv~~v~~sf~g~~csvfIGGT~~~~d~~rl-k~~rIvIGtPGRi~qL~el~~~n~s~vrlfVLDEAD  177 (980)
T KOG4284|consen   99 VTPTREIAVQIKETVRKVAPSFTGARCSVFIGGTAHKLDLIRL-KQTRIVIGTPGRIAQLVELGAMNMSHVRLFVLDEAD  177 (980)
T ss_pred             EecchhhhhHHHHHHHHhcccccCcceEEEecCchhhhhhhhh-hhceEEecCchHHHHHHHhcCCCccceeEEEeccHH
Confidence            9999999999999999998754 89999999999988776665 458899999999999999999999999999999999


Q ss_pred             hhhcc-ccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          186 EMLSR-GFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       186 ~l~~~-~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      .|++. .|...+..|++.||+..|++.||||.|.
T Consensus       178 kL~~t~sfq~~In~ii~slP~~rQv~a~SATYp~  211 (980)
T KOG4284|consen  178 KLMDTESFQDDINIIINSLPQIRQVAAFSATYPR  211 (980)
T ss_pred             hhhchhhHHHHHHHHHHhcchhheeeEEeccCch
Confidence            99984 7999999999999999999999999985

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

Probab=99.96  E-value=3.1e-29  Score=192.65  Aligned_cols=188  Identities=31%  Similarity=0.543  Sum_probs=174.7

Q ss_pred             cCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCH
Q 027749           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (219)
Q Consensus        32 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~  111 (219)
                      .+.|.++-+.+.+++++.+.||+.|..+|.+++|...-|.+++++|..|.|||.+|.++-++.+....+...++++|.|+
T Consensus        41 ssgfrdfllkpellraivdcgfehpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqiepv~g~vsvlvmchtr  120 (387)
T KOG0329|consen   41 SSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPVDGQVSVLVMCHTR  120 (387)
T ss_pred             ccchhhhhcCHHHHHHHHhccCCCchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcCCCCCeEEEEEEeccH
Confidence            35688888999999999999999999999999999999999999999999999999999999998888888899999999


Q ss_pred             HHHHHHHHHHHHhcccc-ceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhcc
Q 027749          112 ELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (219)
Q Consensus       112 ~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~  190 (219)
                      +||-|+..+...+.++. ++.+..++||.+.......+.+.+.|+|+||++++.+.+++.+++++++.+|+||||.|+++
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            99999999998888776 57888899999988877778888899999999999999999999999999999999999976


Q ss_pred             -ccHHHHHHHHHhCCCCCeEEEEeecccCC
Q 027749          191 -GFKDQIYDVYRYLPPDLQVCCPGSCFLFD  219 (219)
Q Consensus       191 -~~~~~~~~i~~~~~~~~q~i~~SATl~~~  219 (219)
                       .++.+++.+.+..|...|+..||||++.|
T Consensus       201 lDMrRDvQEifr~tp~~KQvmmfsatlske  230 (387)
T KOG0329|consen  201 LDMRRDVQEIFRMTPHEKQVMMFSATLSKE  230 (387)
T ss_pred             HHHHHHHHHHhhcCcccceeeeeeeecchh
Confidence             68899999999999999999999999864

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

Probab=99.96  E-value=3.2e-29  Score=207.50  Aligned_cols=174  Identities=21%  Similarity=0.433  Sum_probs=146.9

Q ss_pred             CCccCccccCCCCHH----------HHHHHHHCCCCCChHHHHHHHHHHh---------CCCcEEEEcCCCCchhHHhHH
Q 027749           29 VEAITSFDAMGIKDD----------LLRGIYQYGFEKPSAIQQRAVMPII---------KGRDVIAQAQSGTGKTSMIAL   89 (219)
Q Consensus        29 ~~~~~~~~~~~l~~~----------~~~~l~~~~~~~~~~~Q~~~~~~~~---------~~~~~lv~~~tG~GKT~~~~~   89 (219)
                      .....-|+.++.+..          +.+++.++++....|+|..++|.++         ..+|+.|.||||||||++|.+
T Consensus       123 ~nslq~~s~l~~se~k~~~d~lea~~~q~l~k~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~i  202 (620)
T KOG0350|consen  123 NNSLQIFSVLGKSEMKNLEDTLEATIDQLLVKMAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVI  202 (620)
T ss_pred             CCceeeeeccchhHHHHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehh
Confidence            344455666665554          3445889999999999999999874         357999999999999999999


Q ss_pred             HHHhhhccC-CCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCC-----CeEEEeChHHHH
Q 027749           90 TVCQTVDTS-SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG-----VHVVSGTPGRVC  163 (219)
Q Consensus        90 ~~~~~~~~~-~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~-----~~I~v~Tp~~l~  163 (219)
                      |+.+.+... -...+|+|++|+++|+.|++..+.++....++.|+.+.|..+...+.+.+.+.     .+|+|+||++|.
T Consensus       203 PIVQ~L~~R~v~~LRavVivPtr~L~~QV~~~f~~~~~~tgL~V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPGRLV  282 (620)
T KOG0350|consen  203 PIVQLLSSRPVKRLRAVVIVPTRELALQVYDTFKRLNSGTGLAVCSLSGQNSLEDEARQLASDPPECRIDILVATPGRLV  282 (620)
T ss_pred             HHHHHHccCCccceEEEEEeeHHHHHHHHHHHHHHhccCCceEEEecccccchHHHHHHHhcCCCccccceEEcCchHHH
Confidence            999988766 34578999999999999999999999999999999999999999988888653     389999999999


Q ss_pred             HHHHc-CCCCCCCccEEEeccchhhhccccHHHHHHHHHh
Q 027749          164 DMIKR-KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRY  202 (219)
Q Consensus       164 ~~l~~-~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~  202 (219)
                      +.+.+ ..+++++++|+||||||+|++..|...+-.++..
T Consensus       283 DHl~~~k~f~Lk~LrfLVIDEADRll~qsfQ~Wl~~v~~~  322 (620)
T KOG0350|consen  283 DHLNNTKSFDLKHLRFLVIDEADRLLDQSFQEWLDTVMSL  322 (620)
T ss_pred             HhccCCCCcchhhceEEEechHHHHHHHHHHHHHHHHHHH
Confidence            99985 6789999999999999999987766655544443

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.96  E-value=9.9e-29  Score=226.26  Aligned_cols=178  Identities=17%  Similarity=0.223  Sum_probs=142.7

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccC------CCceeEEEEcCCHHH
Q 027749           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS------SREVQALILSPTREL  113 (219)
Q Consensus        40 l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~------~~~~~~lil~P~~~l  113 (219)
                      +++.+.+.+.+ +|..|+|+|.++|+.+++|+|+++++|||+|||++|.+|+++.+...      ..++++||++|+++|
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            56667776655 78899999999999999999999999999999999999999877532      235789999999999


Q ss_pred             HHHHHHHHHH-------hc----ccc-ceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCC--CCCCccEE
Q 027749          114 ATQTEKVILA-------IG----DFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL--RTRAIKLL  179 (219)
Q Consensus       114 ~~q~~~~~~~-------~~----~~~-~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~--~~~~l~~l  179 (219)
                      ++|+++.+..       +.    ... ++++....|+.+..++...+.+.++|+|+||++|..++.+...  .++++++|
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            9999886643       21    222 6778888888888777777778899999999999887765432  47899999


Q ss_pred             EeccchhhhccccHHH----HHHHHHhCCCCCeEEEEeecccC
Q 027749          180 VLDESDEMLSRGFKDQ----IYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       180 VvDE~h~l~~~~~~~~----~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      |+||+|.+.+..+...    +.++....+...|++++|||+++
T Consensus       177 VIDE~H~l~~~~RG~~l~~~L~rL~~l~~~~~q~IglSATl~~  219 (876)
T PRK13767        177 IVDEIHSLAENKRGVHLSLSLERLEELAGGEFVRIGLSATIEP  219 (876)
T ss_pred             EEechhhhccCccHHHHHHHHHHHHHhcCCCCeEEEEecccCC
Confidence            9999999997654444    33444444467899999999875

>PRK01172 ski2-like helicase; Provisional

Probab=99.96  E-value=4.1e-28  Score=218.00  Aligned_cols=177  Identities=19%  Similarity=0.255  Sum_probs=149.6

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHH
Q 027749           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (219)
Q Consensus        34 ~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l  113 (219)
                      +|+++++++.+.+.+.+.++. ++++|.++++.+.+++++++++|||+|||+++.+++++.+..   +.++||++|+++|
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            578899999999999998886 999999999999999999999999999999999999887764   3569999999999


Q ss_pred             HHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccH
Q 027749          114 ATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFK  193 (219)
Q Consensus       114 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~  193 (219)
                      +.|+++.+.++. ..+.++....|+......   ..+.++|+|+||+++..++.+....++++++||+||+|.+.+.++.
T Consensus        78 a~q~~~~~~~l~-~~g~~v~~~~G~~~~~~~---~~~~~dIiv~Tpek~~~l~~~~~~~l~~v~lvViDEaH~l~d~~rg  153 (674)
T PRK01172         78 AMEKYEELSRLR-SLGMRVKISIGDYDDPPD---FIKRYDVVILTSEKADSLIHHDPYIINDVGLIVADEIHIIGDEDRG  153 (674)
T ss_pred             HHHHHHHHHHHh-hcCCeEEEEeCCCCCChh---hhccCCEEEECHHHHHHHHhCChhHHhhcCEEEEecchhccCCCcc
Confidence            999999998764 357788777877654332   2246899999999999998877667899999999999999887766


Q ss_pred             HHHHHHHH---hCCCCCeEEEEeecccC
Q 027749          194 DQIYDVYR---YLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       194 ~~~~~i~~---~~~~~~q~i~~SATl~~  218 (219)
                      ..+..++.   .++++.|+|++|||++.
T Consensus       154 ~~le~ll~~~~~~~~~~riI~lSATl~n  181 (674)
T PRK01172        154 PTLETVLSSARYVNPDARILALSATVSN  181 (674)
T ss_pred             HHHHHHHHHHHhcCcCCcEEEEeCccCC
Confidence            66665544   45678999999999963

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

Probab=99.96  E-value=5.2e-29  Score=200.03  Aligned_cols=190  Identities=37%  Similarity=0.592  Sum_probs=168.7

Q ss_pred             ccCCCCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCC--CcEEEEcCCCCchhHHhHHHHHhhhccCCCce
Q 027749           25 TTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREV  102 (219)
Q Consensus        25 ~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~--~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~  102 (219)
                      ..++.....+|++++|.+.+++.+-.++|.+|+.+|..++|.++..  +|.|.++..|+|||.||.+.++.++......|
T Consensus        82 pnsPlyS~ksFeeL~LkPellkgly~M~F~kPskIQe~aLPlll~~Pp~nlIaQsqsGtGKTaaFvL~MLsrvd~~~~~P  161 (477)
T KOG0332|consen   82 PNSPLYSAKSFEELRLKPELLKGLYAMKFQKPSKIQETALPLLLAEPPQNLIAQSQSGTGKTAAFVLTMLSRVDPDVVVP  161 (477)
T ss_pred             CCCCccccccHHhhCCCHHHHhHHHHhccCCcchHHHhhcchhhcCCchhhhhhhcCCCchhHHHHHHHHHhcCccccCC
Confidence            3445567789999999999999999999999999999999999876  68999999999999999999999999888889


Q ss_pred             eEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHc-CCCCCCCccEEEe
Q 027749          103 QALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-KTLRTRAIKLLVL  181 (219)
Q Consensus       103 ~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~-~~~~~~~l~~lVv  181 (219)
                      +++.++|+++||.|.-+.+.+.++..++...+.+.+.....- ..+  ..+|+|+||+.+.+++.. +.++++.++.+|+
T Consensus       162 Q~iCLaPtrELA~Q~~eVv~eMGKf~~ita~yair~sk~~rG-~~i--~eqIviGTPGtv~Dlm~klk~id~~kikvfVl  238 (477)
T KOG0332|consen  162 QCICLAPTRELAPQTGEVVEEMGKFTELTASYAIRGSKAKRG-NKL--TEQIVIGTPGTVLDLMLKLKCIDLEKIKVFVL  238 (477)
T ss_pred             CceeeCchHHHHHHHHHHHHHhcCceeeeEEEEecCcccccC-Ccc--hhheeeCCCccHHHHHHHHHhhChhhceEEEe
Confidence            999999999999999999999999998888887766522111 111  358999999999998887 8889999999999


Q ss_pred             ccchhhhcc-ccHHHHHHHHHhCCCCCeEEEEeeccc
Q 027749          182 DESDEMLSR-GFKDQIYDVYRYLPPDLQVCCPGSCFL  217 (219)
Q Consensus       182 DE~h~l~~~-~~~~~~~~i~~~~~~~~q~i~~SATl~  217 (219)
                      ||||.|++. ||.+.-.+|.+.+|+++|+++||||+.
T Consensus       239 DEAD~Mi~tqG~~D~S~rI~~~lP~~~QllLFSATf~  275 (477)
T KOG0332|consen  239 DEADVMIDTQGFQDQSIRIMRSLPRNQQLLLFSATFV  275 (477)
T ss_pred             cchhhhhhcccccccchhhhhhcCCcceEEeeechhH
Confidence            999999976 899999999999999999999999985

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

Probab=99.96  E-value=5.6e-28  Score=214.77  Aligned_cols=177  Identities=17%  Similarity=0.189  Sum_probs=154.5

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccC-----CCceeEEEEcCCHHHH
Q 027749           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-----SREVQALILSPTRELA  114 (219)
Q Consensus        40 l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~-----~~~~~~lil~P~~~l~  114 (219)
                      +++.+.+.+.+. |..|||.|.++||.+.+|+|++|.||||+|||+++.+|++..+...     ..+..+||+.|.++|.
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            788999999887 8999999999999999999999999999999999999999988766     2357899999999999


Q ss_pred             HHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCC--CCCCCccEEEeccchhhhcccc
Q 027749          115 TQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT--LRTRAIKLLVLDESDEMLSRGF  192 (219)
Q Consensus       115 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~--~~~~~l~~lVvDE~h~l~~~~~  192 (219)
                      +++...+..++...|+.+..-+|.++..+..+..++.++|+++||++|.-++....  -.+++++++||||+|.+.+..-
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            99999999999999999988888888888888888899999999999999887643  3578999999999999987642


Q ss_pred             H----HHHHHHHHhCCCCCeEEEEeecccC
Q 027749          193 K----DQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       193 ~----~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      +    -.++++.+..+ +.|.|++|||+.+
T Consensus       167 G~~Lsl~LeRL~~l~~-~~qRIGLSATV~~  195 (814)
T COG1201         167 GVQLALSLERLRELAG-DFQRIGLSATVGP  195 (814)
T ss_pred             chhhhhhHHHHHhhCc-ccEEEeehhccCC
Confidence            2    33455555555 8999999999875

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

Probab=99.95  E-value=6.5e-27  Score=208.97  Aligned_cols=161  Identities=23%  Similarity=0.285  Sum_probs=131.8

Q ss_pred             CCCCCChHHHHHHHHHHhCCC-cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEE-EEcCCHHHHHHHHHHHHHhcccc
Q 027749           51 YGFEKPSAIQQRAVMPIIKGR-DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQAL-ILSPTRELATQTEKVILAIGDFI  128 (219)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~-~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~l-il~P~~~l~~q~~~~~~~~~~~~  128 (219)
                      .||. |+|+|.++++.++.|+ ++++++|||+|||.++.++++.. ......++.| +++|+++|+.|+++.+.++.+..
T Consensus        12 ~G~~-PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafll~~-~~~~~~~~rLv~~vPtReLa~Qi~~~~~~~~k~l   89 (844)
T TIGR02621        12 HGYS-PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWLLAV-EIGAKVPRRLVYVVNRRTVVDQVTEEAEKIGERL   89 (844)
T ss_pred             hCCC-CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhhccc-cccccccceEEEeCchHHHHHHHHHHHHHHHHHh
Confidence            4776 9999999999999998 57788999999998776555533 2223334444 57799999999999999988754


Q ss_pred             -----------------------ceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCC-------------
Q 027749          129 -----------------------NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLR-------------  172 (219)
Q Consensus       129 -----------------------~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~-------------  172 (219)
                                             ++++..++||.+...++..+..+++|+|+|+    +++.++.++             
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~GG~~~~~q~~~l~~~p~IIVgT~----D~i~sr~L~~gYg~~~~~~pi~  165 (844)
T TIGR02621        90 PDVPEVEAALWALCSTRPEKKDRPLAISTLRGQFADNDEWMLDPHRPAVIVGTV----DMIGSRLLFSGYGCGFKSRPLH  165 (844)
T ss_pred             cccchhhhhhhhhhccccccccCCeEEEEEECCCChHHHHHhcCCCCcEEEECH----HHHcCCccccccccccccccch
Confidence                                   4888999999999999999999999999996    555555442             


Q ss_pred             ---CCCccEEEeccchhhhccccHHHHHHHHHhC--CCC---CeEEEEeecccCC
Q 027749          173 ---TRAIKLLVLDESDEMLSRGFKDQIYDVYRYL--PPD---LQVCCPGSCFLFD  219 (219)
Q Consensus       173 ---~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~--~~~---~q~i~~SATl~~~  219 (219)
                         ++++++||+||||  ++++|...+..|++.+  ++.   +|+++||||+|.+
T Consensus       166 ag~L~~v~~LVLDEAD--Ld~gF~~~l~~Il~~l~rp~~~rprQtLLFSAT~p~e  218 (844)
T TIGR02621       166 AGFLGQDALIVHDEAH--LEPAFQELLKQIMNEQQRPPDFLPLRVVELTATSRTD  218 (844)
T ss_pred             hhhhccceEEEEehhh--hccccHHHHHHHHHhcccCcccccceEEEEecCCCcc
Confidence               6889999999999  6789999999999975  432   6999999999853

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

>PRK09401 reverse gyrase; Reviewed

Probab=99.94  E-value=6.8e-26  Score=210.98  Aligned_cols=167  Identities=17%  Similarity=0.237  Sum_probs=132.2

Q ss_pred             HHHHH-CCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 027749           46 RGIYQ-YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (219)
Q Consensus        46 ~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (219)
                      +.+.+ .|+ .|+++|..++|.++.|+|++++||||+|||. |.++++..+..  .+++++|++||++|+.|+.+.++++
T Consensus        71 ~~f~~~~G~-~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~-f~l~~~~~l~~--~g~~alIL~PTreLa~Qi~~~l~~l  146 (1176)
T PRK09401         71 KFFKKKTGS-KPWSLQRTWAKRLLLGESFAIIAPTGVGKTT-FGLVMSLYLAK--KGKKSYIIFPTRLLVEQVVEKLEKF  146 (1176)
T ss_pred             HHHHHhcCC-CCcHHHHHHHHHHHCCCcEEEEcCCCCCHHH-HHHHHHHHHHh--cCCeEEEEeccHHHHHHHHHHHHHH
Confidence            34443 355 8999999999999999999999999999995 54555444433  3678999999999999999999999


Q ss_pred             ccccceeEEEEECCccc-----HHHHHHhc-CCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhc---------
Q 027749          125 GDFINIQAHACVGGKSV-----GEDIRKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS---------  189 (219)
Q Consensus       125 ~~~~~~~~~~~~~~~~~-----~~~~~~l~-~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~---------  189 (219)
                      +...++.+..+.|+.+.     .+....+. .+++|+|+||++|.+.+.  .+...++++||+||||+|++         
T Consensus       147 ~~~~~~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~~~~--~l~~~~~~~lVvDEaD~~L~~~k~id~~l  224 (1176)
T PRK09401        147 GEKVGCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFD--ELPKKKFDFVFVDDVDAVLKSSKNIDKLL  224 (1176)
T ss_pred             hhhcCceEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECHHHHHHHHH--hccccccCEEEEEChHHhhhcccchhhHH
Confidence            98888887777766542     22333444 468999999999998876  34556799999999999996         


Q ss_pred             --cccH-HHHHHHHHhCCC------------------------CCeEEEEeecccC
Q 027749          190 --RGFK-DQIYDVYRYLPP------------------------DLQVCCPGSCFLF  218 (219)
Q Consensus       190 --~~~~-~~~~~i~~~~~~------------------------~~q~i~~SATl~~  218 (219)
                        .||. +.+..+++.++.                        ..|++++|||.++
T Consensus       225 ~~lGF~~~~i~~i~~~i~~~~~~~~~~~~i~~l~~~i~~~~~~~~q~ilfSAT~~~  280 (1176)
T PRK09401        225 YLLGFSEEDIEKAMELIRLKRKYEEIYEKIRELEEKIAELKDKKGVLVVSSATGRP  280 (1176)
T ss_pred             HhCCCCHHHHHHHHHhcccccccchhhhHHHHHHHhhhhcccCCceEEEEeCCCCc
Confidence              4674 677777777654                        6899999999986

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.94  E-value=7.2e-26  Score=195.74  Aligned_cols=158  Identities=18%  Similarity=0.264  Sum_probs=122.0

Q ss_pred             HCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccc
Q 027749           50 QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (219)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (219)
                      .+|+..|+|+|.++++.+++|+++++++|||+|||++|++|++..      +..+||++|+++|+.|+...+...    +
T Consensus         6 ~~g~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~~------~~~~lVi~P~~~L~~dq~~~l~~~----g   75 (470)
T TIGR00614         6 VFGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALCS------DGITLVISPLISLMEDQVLQLKAS----G   75 (470)
T ss_pred             hcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHHHc------CCcEEEEecHHHHHHHHHHHHHHc----C
Confidence            579999999999999999999999999999999999999998753      345999999999999998888754    5


Q ss_pred             eeEEEEECCcccHHHHH---Hh-cCCCeEEEeChHHHHHHH-HcCCC-CCCCccEEEeccchhhhccc--cHHHHHHH--
Q 027749          130 IQAHACVGGKSVGEDIR---KL-EHGVHVVSGTPGRVCDMI-KRKTL-RTRAIKLLVLDESDEMLSRG--FKDQIYDV--  199 (219)
Q Consensus       130 ~~~~~~~~~~~~~~~~~---~l-~~~~~I~v~Tp~~l~~~l-~~~~~-~~~~l~~lVvDE~h~l~~~~--~~~~~~~i--  199 (219)
                      +....+.++.+..+...   .+ ....+|+++||+++.... ....+ ...++++|||||||++.+|+  |...+..+  
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            66666666665543221   22 235899999999875321 01111 46789999999999999886  56555443  


Q ss_pred             -HHhCCCCCeEEEEeecccC
Q 027749          200 -YRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       200 -~~~~~~~~q~i~~SATl~~  218 (219)
                       .+.+ ++.+++++|||.++
T Consensus       156 l~~~~-~~~~~l~lTAT~~~  174 (470)
T TIGR00614       156 LKQKF-PNVPIMALTATASP  174 (470)
T ss_pred             HHHHc-CCCceEEEecCCCH
Confidence             3344 57889999999875

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=99.94  E-value=3.3e-25  Score=201.42  Aligned_cols=176  Identities=18%  Similarity=0.223  Sum_probs=136.2

Q ss_pred             Cccc--cCCCCHHHHHHHH-HCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcC
Q 027749           33 TSFD--AMGIKDDLLRGIY-QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (219)
Q Consensus        33 ~~~~--~~~l~~~~~~~l~-~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P  109 (219)
                      .+|.  .++++..+...++ .+|+..++|.|.++|+.++.|+|+++++|||+|||+||++|++..      ...+|||+|
T Consensus       435 ~~W~~~~fpw~~~L~~~lk~~FG~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL~~------~GiTLVISP  508 (1195)
T PLN03137        435 KKWSSRNFPWTKKLEVNNKKVFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALIC------PGITLVISP  508 (1195)
T ss_pred             ccccccCCCchHHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHHHHHHHc------CCcEEEEeC
Confidence            4465  4677888887777 578999999999999999999999999999999999999999863      246999999


Q ss_pred             CHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhc------CCCeEEEeChHHHHH---HHHc--CCCCCCCccE
Q 027749          110 TRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE------HGVHVVSGTPGRVCD---MIKR--KTLRTRAIKL  178 (219)
Q Consensus       110 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~------~~~~I~v~Tp~~l~~---~l~~--~~~~~~~l~~  178 (219)
                      +++|+.++...+...    ++....+.++.+..++...+.      ..++|+++||+++..   ++..  .......+.+
T Consensus       509 LiSLmqDQV~~L~~~----GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTPERL~~~d~ll~~L~~L~~~~~Lsl  584 (1195)
T PLN03137        509 LVSLIQDQIMNLLQA----NIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTPEKVAKSDSLLRHLENLNSRGLLAR  584 (1195)
T ss_pred             HHHHHHHHHHHHHhC----CCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEChHHhhcchHHHHHHHhhhhccccce
Confidence            999998666655543    677888888877665544332      468999999999862   2221  1112345889


Q ss_pred             EEeccchhhhccc--cHHHHHHH--HHhCCCCCeEEEEeecccC
Q 027749          179 LVLDESDEMLSRG--FKDQIYDV--YRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       179 lVvDE~h~l~~~~--~~~~~~~i--~~~~~~~~q~i~~SATl~~  218 (219)
                      |||||||++.+||  |+..+..+  +....++.|+++||||.++
T Consensus       585 IVIDEAHcVSqWGhDFRpdYr~L~~Lr~~fp~vPilALTATAT~  628 (1195)
T PLN03137        585 FVIDEAHCVSQWGHDFRPDYQGLGILKQKFPNIPVLALTATATA  628 (1195)
T ss_pred             eccCcchhhhhcccchHHHHHHHHHHHHhCCCCCeEEEEecCCH
Confidence            9999999999997  77766653  4444457889999999875

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

Probab=99.93  E-value=8e-25  Score=198.51  Aligned_cols=177  Identities=20%  Similarity=0.266  Sum_probs=143.9

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHH
Q 027749           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (219)
Q Consensus        40 l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~  119 (219)
                      ....+..++.+.|...++++|.+|+..+.+|+|++|..|||||||.+|++|+++.+...... ++|+|.||++|++++.+
T Consensus        55 ~~~~l~~~l~~~g~~~lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~~a-~AL~lYPtnALa~DQ~~  133 (851)
T COG1205          55 RDESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSA-RALLLYPTNALANDQAE  133 (851)
T ss_pred             hhhHHHHHHHHhccccccHHHHHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhhCcCc-cEEEEechhhhHhhHHH
Confidence            44556888999999999999999999999999999999999999999999999999876553 79999999999999999


Q ss_pred             HHHHhccccc--eeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCC----CCCCCccEEEeccchhhhccccH
Q 027749          120 VILAIGDFIN--IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT----LRTRAIKLLVLDESDEMLSRGFK  193 (219)
Q Consensus       120 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~----~~~~~l~~lVvDE~h~l~~~~~~  193 (219)
                      ++.++....+  +......|.....+......+.++|++++|+.|..++....    ..++++++|||||+|. +.-.|+
T Consensus       134 rl~~~~~~~~~~v~~~~y~Gdt~~~~r~~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDElHt-YrGv~G  212 (851)
T COG1205         134 RLRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHT-YRGVQG  212 (851)
T ss_pred             HHHHHHHhCCCcceeeeecCCCChHHHHHHHhCCCCEEEeCHHHHHHHhccCcchHHHHHhcCcEEEEeccee-ccccch
Confidence            9999988776  66666666666666556678899999999999998554322    3457799999999995 433345


Q ss_pred             HHHHHHHHh-------CCCCCeEEEEeecccC
Q 027749          194 DQIYDVYRY-------LPPDLQVCCPGSCFLF  218 (219)
Q Consensus       194 ~~~~~i~~~-------~~~~~q~i~~SATl~~  218 (219)
                      ..+..+++.       .+.+.|+|+.|||+..
T Consensus       213 S~vA~llRRL~~~~~~~~~~~q~i~~SAT~~n  244 (851)
T COG1205         213 SEVALLLRRLLRRLRRYGSPLQIICTSATLAN  244 (851)
T ss_pred             hHHHHHHHHHHHHHhccCCCceEEEEeccccC
Confidence            444433333       3458899999999864

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.92  E-value=3.8e-24  Score=195.32  Aligned_cols=166  Identities=17%  Similarity=0.187  Sum_probs=132.7

Q ss_pred             CCCHHHHHHHHH-CCCCCChHHHHHHHHHHhCC------CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCH
Q 027749           39 GIKDDLLRGIYQ-YGFEKPSAIQQRAVMPIIKG------RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (219)
Q Consensus        39 ~l~~~~~~~l~~-~~~~~~~~~Q~~~~~~~~~~------~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~  111 (219)
                      +.+..+.+.+.+ ++| .||+.|..+++.+.++      ++.+++|+||+|||.+|+.+++..+..   +.+++|++||+
T Consensus       435 ~~~~~~~~~~~~~~~f-~~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~---g~qvlvLvPT~  510 (926)
T TIGR00580       435 PPDLEWQQEFEDSFPF-EETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLD---GKQVAVLVPTT  510 (926)
T ss_pred             CCCHHHHHHHHHhCCC-CCCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHh---CCeEEEEeCcH
Confidence            345566666664 577 6999999999999875      689999999999999999999887754   36799999999


Q ss_pred             HHHHHHHHHHHHhccccceeEEEEECCcccHHH---HHHhcC-CCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhh
Q 027749          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGED---IRKLEH-GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (219)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~l~~-~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l  187 (219)
                      +||.|+++.+.++....++++..+.|..+..++   ...+.. .++|+|+||..    + ++.+.++++++||+||+|++
T Consensus       511 ~LA~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~l----l-~~~v~f~~L~llVIDEahrf  585 (926)
T TIGR00580       511 LLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKL----L-QKDVKFKDLGLLIIDEEQRF  585 (926)
T ss_pred             HHHHHHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHH----h-hCCCCcccCCEEEeeccccc
Confidence            999999999999888888888888877664433   233333 58999999942    2 35567899999999999984


Q ss_pred             hccccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          188 LSRGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       188 ~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                           .......++.++++.|+++||||..+
T Consensus       586 -----gv~~~~~L~~~~~~~~vL~~SATpip  611 (926)
T TIGR00580       586 -----GVKQKEKLKELRTSVDVLTLSATPIP  611 (926)
T ss_pred             -----chhHHHHHHhcCCCCCEEEEecCCCH
Confidence                 33455667778888999999999654

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.

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.92  E-value=2.5e-24  Score=190.98  Aligned_cols=168  Identities=16%  Similarity=0.202  Sum_probs=126.4

Q ss_pred             CCHHHHHHHH-HCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHH
Q 027749           40 IKDDLLRGIY-QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE  118 (219)
Q Consensus        40 l~~~~~~~l~-~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~  118 (219)
                      ......+.|+ .+|+..|+|+|.++++.+++|+++++++|||+|||++|++|++..      ...+||++|+++|+.|+.
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            3444445555 469999999999999999999999999999999999999998753      235999999999999999


Q ss_pred             HHHHHhccccceeEEEEECCcccHHHHHH---h-cCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccc--c
Q 027749          119 KVILAIGDFINIQAHACVGGKSVGEDIRK---L-EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG--F  192 (219)
Q Consensus       119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---l-~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~--~  192 (219)
                      +.+...    ++....+.+..+.......   + ....+++++||+++........+...++++|||||||++.+|+  |
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            888765    5666666666555443222   2 2357899999999874221122334579999999999999986  5


Q ss_pred             HHHHH---HHHHhCCCCCeEEEEeecccC
Q 027749          193 KDQIY---DVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       193 ~~~~~---~i~~~~~~~~q~i~~SATl~~  218 (219)
                      ...+.   .+.+.+ ++.+++++|||.+.
T Consensus       159 r~~y~~L~~l~~~~-p~~~~v~lTAT~~~  186 (607)
T PRK11057        159 RPEYAALGQLRQRF-PTLPFMALTATADD  186 (607)
T ss_pred             cHHHHHHHHHHHhC-CCCcEEEEecCCCh
Confidence            55443   334444 47899999999875

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

Probab=99.92  E-value=2.5e-25  Score=187.70  Aligned_cols=192  Identities=26%  Similarity=0.386  Sum_probs=157.6

Q ss_pred             CCCCccCcccc----CCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccC----
Q 027749           27 EGVEAITSFDA----MGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS----   98 (219)
Q Consensus        27 ~~~~~~~~~~~----~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~----   98 (219)
                      ..+.++.+|.+    ...+..+++.+.+.+|..|+|.|.+++|.++.+++++.|+|||+|||++|.+|++..+...    
T Consensus       126 ~~~~~l~~f~~lt~~~~~~~~ll~nl~~~~F~~Pt~iq~~aipvfl~~r~~lAcapTGsgKtlaf~~Pil~~L~~~~~~~  205 (593)
T KOG0344|consen  126 HLPPPLLSFSDLTYDYSMNKRLLENLQELGFDEPTPIQKQAIPVFLEKRDVLACAPTGSGKTLAFNLPILQHLKDLSQEK  205 (593)
T ss_pred             CCCCccccccccchhhhhcHHHHHhHhhCCCCCCCcccchhhhhhhcccceEEeccCCCcchhhhhhHHHHHHHHhhccc
Confidence            34778888887    4578999999999999999999999999999999999999999999999999999988542    


Q ss_pred             -CCceeEEEEcCCHHHHHHHHHHHHHhc--cccceeEEEEECCcccHHH-HHHhcCCCeEEEeChHHHHHHHHcCC--CC
Q 027749           99 -SREVQALILSPTRELATQTEKVILAIG--DFINIQAHACVGGKSVGED-IRKLEHGVHVVSGTPGRVCDMIKRKT--LR  172 (219)
Q Consensus        99 -~~~~~~lil~P~~~l~~q~~~~~~~~~--~~~~~~~~~~~~~~~~~~~-~~~l~~~~~I~v~Tp~~l~~~l~~~~--~~  172 (219)
                       ..+.+++|+.|+++|+.|++.++.++.  ...+.+............. .......++|+|+||.++..++....  ++
T Consensus       206 ~~~gl~a~Il~ptreLa~Qi~re~~k~~~~~~t~~~a~~~~~~~~~~qk~a~~~~~k~dili~TP~ri~~~~~~~~~~id  285 (593)
T KOG0344|consen  206 HKVGLRALILSPTRELAAQIYREMRKYSIDEGTSLRAAQFSKPAYPSQKPAFLSDEKYDILISTPMRIVGLLGLGKLNID  285 (593)
T ss_pred             CccceEEEEecchHHHHHHHHHHHHhcCCCCCCchhhhhcccccchhhccchhHHHHHHHHhcCHHHHHHHhcCCCccch
Confidence             456899999999999999999999998  4444444333222111111 11122358999999999999998765  78


Q ss_pred             CCCccEEEeccchhhhcc-ccHHHHHHHHHhCC-CCCeEEEEeecccC
Q 027749          173 TRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLP-PDLQVCCPGSCFLF  218 (219)
Q Consensus       173 ~~~l~~lVvDE~h~l~~~-~~~~~~~~i~~~~~-~~~q~i~~SATl~~  218 (219)
                      +..+.++|+||+|.+++. .|..++-.|+..+. ++..+=+||||+|.
T Consensus       286 l~~V~~lV~dEaD~lfe~~~f~~Qla~I~sac~s~~i~~a~FSat~~~  333 (593)
T KOG0344|consen  286 LSKVEWLVVDEADLLFEPEFFVEQLADIYSACQSPDIRVALFSATISV  333 (593)
T ss_pred             hheeeeEeechHHhhhChhhHHHHHHHHHHHhcCcchhhhhhhccccH
Confidence            899999999999999999 89999999988874 47788899999985

>PRK14701 reverse gyrase; Provisional

Probab=99.92  E-value=4.8e-24  Score=202.75  Aligned_cols=170  Identities=16%  Similarity=0.193  Sum_probs=130.7

Q ss_pred             HHHHHHHH-CCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHH
Q 027749           43 DLLRGIYQ-YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVI  121 (219)
Q Consensus        43 ~~~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~  121 (219)
                      .+.+.+++ .|+ .|+++|..+++.+++|+++++++|||+|||++++++.+....   .+.+++||+||++|+.|+.+.+
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            34455655 788 699999999999999999999999999999876665554422   3567999999999999999999


Q ss_pred             HHhcccc--ceeEEEEECCcccHHHH---HHhcC-CCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhc------
Q 027749          122 LAIGDFI--NIQAHACVGGKSVGEDI---RKLEH-GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS------  189 (219)
Q Consensus       122 ~~~~~~~--~~~~~~~~~~~~~~~~~---~~l~~-~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~------  189 (219)
                      +.++...  ++++..++|+.+..++.   ..+.. +++|+|+||+.|.+.+... . ..++++|||||||+|++      
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  46667778888766553   33444 5899999999988766542 1 26799999999999986      


Q ss_pred             -----cccHHHHHH----HHH----------------------hCCCCCe-EEEEeecccC
Q 027749          190 -----RGFKDQIYD----VYR----------------------YLPPDLQ-VCCPGSCFLF  218 (219)
Q Consensus       190 -----~~~~~~~~~----i~~----------------------~~~~~~q-~i~~SATl~~  218 (219)
                           .+|..++..    +++                      .+++..| ++++|||.++
T Consensus       221 ~~L~llGF~~e~~~~~~~il~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ll~~SAT~~~  281 (1638)
T PRK14701        221 RSLQLLGFYEEIIEKAWKIIYLKKQGNIEDAMEKREILNKEIEKIGNKIGCLIVASATGKA  281 (1638)
T ss_pred             hhhhcCCChHHHHHHHHHhhhcccccccchhhhhhhhhhhhhhhcCCCccEEEEEecCCCc
Confidence                 367766653    322                      2345556 6789999985

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.92  E-value=8.9e-25  Score=195.90  Aligned_cols=174  Identities=16%  Similarity=0.220  Sum_probs=144.8

Q ss_pred             CCCHHHHHHHHHCCCCCChHHHHHHHHH-HhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHH
Q 027749           39 GIKDDLLRGIYQYGFEKPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQT  117 (219)
Q Consensus        39 ~l~~~~~~~l~~~~~~~~~~~Q~~~~~~-~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~  117 (219)
                      .++..+...+...++...++.|+.++.. +.+++|++|++|||+|||+.+++.+++.+...  +.+++|+||+++||.+.
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            3778888888888887888888888766 44669999999999999999999999988876  45699999999999999


Q ss_pred             HHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHH
Q 027749          118 EKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIY  197 (219)
Q Consensus       118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~  197 (219)
                      ++.++ .....|+++....|......+   ...+++|+|+||+++..++++.......+++||+||+|.+.+......++
T Consensus        93 ~~~~~-~~~~~GirV~~~TgD~~~~~~---~l~~~~ViVtT~EK~Dsl~R~~~~~~~~V~lvViDEiH~l~d~~RG~~lE  168 (766)
T COG1204          93 YEEFS-RLEELGIRVGISTGDYDLDDE---RLARYDVIVTTPEKLDSLTRKRPSWIEEVDLVVIDEIHLLGDRTRGPVLE  168 (766)
T ss_pred             HHHhh-hHHhcCCEEEEecCCcccchh---hhccCCEEEEchHHhhHhhhcCcchhhcccEEEEeeeeecCCcccCceeh
Confidence            99999 445569999999888775542   23579999999999999999988889999999999999988875455555


Q ss_pred             HHHHhC---CCCCeEEEEeecccC
Q 027749          198 DVYRYL---PPDLQVCCPGSCFLF  218 (219)
Q Consensus       198 ~i~~~~---~~~~q~i~~SATl~~  218 (219)
                      .++..+   ...+|++++|||+|.
T Consensus       169 ~iv~r~~~~~~~~rivgLSATlpN  192 (766)
T COG1204         169 SIVARMRRLNELIRIVGLSATLPN  192 (766)
T ss_pred             hHHHHHHhhCcceEEEEEeeecCC
Confidence            555544   445899999999985

>TIGR01054 rgy reverse gyrase

Probab=99.92  E-value=7.5e-24  Score=197.61  Aligned_cols=140  Identities=16%  Similarity=0.214  Sum_probs=109.8

Q ss_pred             HHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 027749           44 LLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA  123 (219)
Q Consensus        44 ~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~  123 (219)
                      +.+.+.+.....|+++|..+++.++.|++++++||||+|||. |.+++...+...  +++++|++||++|+.|+.+.+.+
T Consensus        67 f~~~f~~~~g~~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~-f~l~~~~~l~~~--g~~vLIL~PTreLa~Qi~~~l~~  143 (1171)
T TIGR01054        67 FEEFFKKAVGSEPWSIQKMWAKRVLRGDSFAIIAPTGVGKTT-FGLAMSLFLAKK--GKRCYIILPTTLLVIQVAEKISS  143 (1171)
T ss_pred             HHHHHHHhcCCCCcHHHHHHHHHHhCCCeEEEECCCCCCHHH-HHHHHHHHHHhc--CCeEEEEeCHHHHHHHHHHHHHH
Confidence            444454444458999999999999999999999999999996 656666555433  57899999999999999999999


Q ss_pred             hccccceeEE---EEECCcccHHH---HHHhc-CCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhc
Q 027749          124 IGDFINIQAH---ACVGGKSVGED---IRKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (219)
Q Consensus       124 ~~~~~~~~~~---~~~~~~~~~~~---~~~l~-~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~  189 (219)
                      +....++.+.   .++|+.+..++   ...+. ++++|+|+||++|.+.+....  . +++++|+||||+|++
T Consensus       144 l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~~~l~--~-~~~~iVvDEaD~~L~  213 (1171)
T TIGR01054       144 LAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDELG--P-KFDFIFVDDVDALLK  213 (1171)
T ss_pred             HHHhcCCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHHHHhc--C-CCCEEEEeChHhhhh
Confidence            9877665543   45677766543   23333 359999999999998776422  2 899999999999998

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.

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.92  E-value=4.8e-24  Score=189.20  Aligned_cols=161  Identities=16%  Similarity=0.204  Sum_probs=125.8

Q ss_pred             HHH-HCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhc
Q 027749           47 GIY-QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIG  125 (219)
Q Consensus        47 ~l~-~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  125 (219)
                      .|+ .+||..++|.|.++++.+++|+|+++++|||+|||++|++|++..      ...++|++|+.+|+.|+...+..+ 
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            454 479999999999999999999999999999999999999998742      235899999999999999988775 


Q ss_pred             cccceeEEEEECCcccHHHHHH----hcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccc--cHHHHHHH
Q 027749          126 DFINIQAHACVGGKSVGEDIRK----LEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG--FKDQIYDV  199 (219)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~----l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~--~~~~~~~i  199 (219)
                         ++.+..+.++.+..+....    .....+|+++||+++........+...++++|||||||++.+|+  |+..+..+
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               5667777777665543322    23568999999999875333333456789999999999999886  66554444


Q ss_pred             ---HHhCCCCCeEEEEeecccC
Q 027749          200 ---YRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       200 ---~~~~~~~~q~i~~SATl~~  218 (219)
                         .+.++. .+++++|||.++
T Consensus       154 ~~l~~~~~~-~~vi~lTAT~~~  174 (591)
T TIGR01389       154 GSLAERFPQ-VPRIALTATADA  174 (591)
T ss_pred             HHHHHhCCC-CCEEEEEeCCCH
Confidence               444544 459999999875

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.

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.92  E-value=1.2e-23  Score=188.68  Aligned_cols=163  Identities=20%  Similarity=0.253  Sum_probs=129.2

Q ss_pred             HHHHHHHH-HCCCCCChHHHHHHHHHHhCC------CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHH
Q 027749           42 DDLLRGIY-QYGFEKPSAIQQRAVMPIIKG------RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELA  114 (219)
Q Consensus        42 ~~~~~~l~-~~~~~~~~~~Q~~~~~~~~~~------~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~  114 (219)
                      ..+.+.+. ..+| .||+.|+++++.+.++      ++.+++|+||+|||++|+++++..+..   +.+++|++||++||
T Consensus       248 ~~~~~~~~~~l~f-~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~~---g~q~lilaPT~~LA  323 (681)
T PRK10917        248 GELLKKFLASLPF-ELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEA---GYQAALMAPTEILA  323 (681)
T ss_pred             hHHHHHHHHhCCC-CCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHHc---CCeEEEEeccHHHH
Confidence            44555554 5556 7999999999999876      479999999999999999999887754   56799999999999


Q ss_pred             HHHHHHHHHhccccceeEEEEECCcccHHH---HHHhcC-CCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhcc
Q 027749          115 TQTEKVILAIGDFINIQAHACVGGKSVGED---IRKLEH-GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (219)
Q Consensus       115 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~l~~-~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~  190 (219)
                      .|+++.+++++...++++..+.|+.+..++   ...+.. .++|+|+||+.+.     ..+.+++++++|+||+|++.  
T Consensus       324 ~Q~~~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~-----~~v~~~~l~lvVIDE~Hrfg--  396 (681)
T PRK10917        324 EQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQ-----DDVEFHNLGLVIIDEQHRFG--  396 (681)
T ss_pred             HHHHHHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhc-----ccchhcccceEEEechhhhh--
Confidence            999999999998889999999999885443   333433 5999999997664     34567899999999999853  


Q ss_pred             ccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          191 GFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       191 ~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                         ......+.......++++||||..+
T Consensus       397 ---~~qr~~l~~~~~~~~iL~~SATp~p  421 (681)
T PRK10917        397 ---VEQRLALREKGENPHVLVMTATPIP  421 (681)
T ss_pred             ---HHHHHHHHhcCCCCCEEEEeCCCCH
Confidence               2233344444557899999999643

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.91  E-value=4.6e-23  Score=191.85  Aligned_cols=164  Identities=16%  Similarity=0.203  Sum_probs=129.5

Q ss_pred             CHHHHHH-HHHCCCCCChHHHHHHHHHHhCC------CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHH
Q 027749           41 KDDLLRG-IYQYGFEKPSAIQQRAVMPIIKG------RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (219)
Q Consensus        41 ~~~~~~~-l~~~~~~~~~~~Q~~~~~~~~~~------~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l  113 (219)
                      +....+. ...+.| .|++.|.++|+.++.+      ++.+++++||+|||.+|+.+++..+..   +.+++|++||++|
T Consensus       586 ~~~~~~~~~~~~~~-~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~~---g~qvlvLvPT~eL  661 (1147)
T PRK10689        586 DREQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVEN---HKQVAVLVPTTLL  661 (1147)
T ss_pred             CHHHHHHHHHhCCC-CCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHHc---CCeEEEEeCcHHH
Confidence            3334444 456667 7999999999999876      799999999999999998887666542   5679999999999


Q ss_pred             HHHHHHHHHHhccccceeEEEEECCcccHHHHHHh---c-CCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhc
Q 027749          114 ATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL---E-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (219)
Q Consensus       114 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l---~-~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~  189 (219)
                      |.|+++.+.+.....++++..+.|+.+..++...+   . .+++|+|+||+.+     +..+.++++++|||||+|++  
T Consensus       662 A~Q~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL-----~~~v~~~~L~lLVIDEahrf--  734 (1147)
T PRK10689        662 AQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLL-----QSDVKWKDLGLLIVDEEHRF--  734 (1147)
T ss_pred             HHHHHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHH-----hCCCCHhhCCEEEEechhhc--
Confidence            99999999987777778888888877766654433   2 4689999999633     24456789999999999996  


Q ss_pred             cccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          190 RGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       190 ~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                       ++.  ....++.++.++|+++||||.++
T Consensus       735 -G~~--~~e~lk~l~~~~qvLl~SATpip  760 (1147)
T PRK10689        735 -GVR--HKERIKAMRADVDILTLTATPIP  760 (1147)
T ss_pred             -chh--HHHHHHhcCCCCcEEEEcCCCCH
Confidence             322  34556778889999999999764

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.91  E-value=5.8e-23  Score=183.02  Aligned_cols=162  Identities=19%  Similarity=0.239  Sum_probs=126.2

Q ss_pred             HHHHHHHCCCCCChHHHHHHHHHHhCC------CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHH
Q 027749           44 LLRGIYQYGFEKPSAIQQRAVMPIIKG------RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQT  117 (219)
Q Consensus        44 ~~~~l~~~~~~~~~~~Q~~~~~~~~~~------~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~  117 (219)
                      +.+.+...+| .||+.|+++++.+.++      .+.+++|+||+|||.+|+++++..+..   +.+++|++||++||.|+
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            3445567777 7999999999998865      368999999999999999999887754   45799999999999999


Q ss_pred             HHHHHHhccccceeEEEEECCcccHHH---HHHhc-CCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccH
Q 027749          118 EKVILAIGDFINIQAHACVGGKSVGED---IRKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFK  193 (219)
Q Consensus       118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~l~-~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~  193 (219)
                      ++.+.+++...++++..+.|+.+..++   ...+. ..++|+|+||+.+.+     ...+++++++|+||+|++...   
T Consensus       301 ~~~~~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~-----~~~~~~l~lvVIDEaH~fg~~---  372 (630)
T TIGR00643       301 YNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQE-----KVEFKRLALVIIDEQHRFGVE---  372 (630)
T ss_pred             HHHHHHHhcccCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhc-----cccccccceEEEechhhccHH---
Confidence            999999998889999999998876553   23333 358999999986642     356789999999999985321   


Q ss_pred             HHHHHHHHhCC--CCCeEEEEeecccC
Q 027749          194 DQIYDVYRYLP--PDLQVCCPGSCFLF  218 (219)
Q Consensus       194 ~~~~~i~~~~~--~~~q~i~~SATl~~  218 (219)
                       ....+.+...  ..+++++||||..+
T Consensus       373 -qr~~l~~~~~~~~~~~~l~~SATp~p  398 (630)
T TIGR00643       373 -QRKKLREKGQGGFTPHVLVMSATPIP  398 (630)
T ss_pred             -HHHHHHHhcccCCCCCEEEEeCCCCc
Confidence             1122222222  26789999999654

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.91  E-value=2.7e-22  Score=153.30  Aligned_cols=168  Identities=32%  Similarity=0.532  Sum_probs=139.9

Q ss_pred             HCCCCCChHHHHHHHHHHhCC-CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhcccc
Q 027749           50 QYGFEKPSAIQQRAVMPIIKG-RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI  128 (219)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~~~~~-~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~  128 (219)
                      .+++..++++|.++++.+..+ ++.++.++||+|||.++..+++..+.... ..++++++|+..++.|+...+.+.....
T Consensus         3 ~~~~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~~-~~~~l~~~p~~~~~~~~~~~~~~~~~~~   81 (201)
T smart00487        3 KFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGK-GKRVLVLVPTRELAEQWAEELKKLGPSL   81 (201)
T ss_pred             ccCCCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhcccC-CCcEEEEeCCHHHHHHHHHHHHHHhccC
Confidence            346778999999999999988 99999999999999988888888776543 3469999999999999999998887655


Q ss_pred             ceeEEEEECCcccHHHHHHhcCCC-eEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCC
Q 027749          129 NIQAHACVGGKSVGEDIRKLEHGV-HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDL  207 (219)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~l~~~~-~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~  207 (219)
                      ........++......+..+..+. +++++|++.+.+.+........+++++|+||+|.+....+...+..++..+++..
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~t~~~l~~~~~~~~~~~~~~~~iIiDE~h~~~~~~~~~~~~~~~~~~~~~~  161 (201)
T smart00487       82 GLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDLLELSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNV  161 (201)
T ss_pred             CeEEEEEeCCcchHHHHHHHhcCCCCEEEeChHHHHHHHHcCCcCHhHCCEEEEECHHHHhcCCcHHHHHHHHHhCCccc
Confidence            434444555555555666666665 9999999999998888766778899999999999887577889999999888889


Q ss_pred             eEEEEeecccC
Q 027749          208 QVCCPGSCFLF  218 (219)
Q Consensus       208 q~i~~SATl~~  218 (219)
                      +++++|||.+.
T Consensus       162 ~~v~~saT~~~  172 (201)
T smart00487      162 QLLLLSATPPE  172 (201)
T ss_pred             eEEEEecCCch
Confidence            99999999864

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.90  E-value=4e-23  Score=193.98  Aligned_cols=144  Identities=15%  Similarity=0.175  Sum_probs=118.5

Q ss_pred             EEcCCCCchhHHhHHHHHhhhccC----------CCceeEEEEcCCHHHHHHHHHHHHHhc------------cccceeE
Q 027749           75 AQAQSGTGKTSMIALTVCQTVDTS----------SREVQALILSPTRELATQTEKVILAIG------------DFINIQA  132 (219)
Q Consensus        75 v~~~tG~GKT~~~~~~~~~~~~~~----------~~~~~~lil~P~~~l~~q~~~~~~~~~------------~~~~~~~  132 (219)
                      |++|||||||++|.+|++..+...          ..+.++|||+|+++|+.|+.+.++...            ...++++
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            579999999999999999987643          235789999999999999999886421            1246888


Q ss_pred             EEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCC-CCCCCccEEEeccchhhhccc----cHHHHHHHHHhCCCCC
Q 027749          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT-LRTRAIKLLVLDESDEMLSRG----FKDQIYDVYRYLPPDL  207 (219)
Q Consensus       133 ~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~-~~~~~l~~lVvDE~h~l~~~~----~~~~~~~i~~~~~~~~  207 (219)
                      ....|+.+..++.+.+.+.++|+|+||++|..++.++. ..++++++|||||+|.+.+..    +...+.++...++.+.
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            88899998888777777889999999999999876543 468999999999999998753    3455666666677889


Q ss_pred             eEEEEeecccC
Q 027749          208 QVCCPGSCFLF  218 (219)
Q Consensus       208 q~i~~SATl~~  218 (219)
                      |+|++|||+++
T Consensus       161 QrIgLSATI~n  171 (1490)
T PRK09751        161 QRIGLSATVRS  171 (1490)
T ss_pred             eEEEEEeeCCC
Confidence            99999999975

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.89  E-value=3.1e-22  Score=174.24  Aligned_cols=150  Identities=17%  Similarity=0.092  Sum_probs=115.4

Q ss_pred             CCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeE
Q 027749           53 FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQA  132 (219)
Q Consensus        53 ~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  132 (219)
                      ...|+++|.++++.++.+++.++++|||+|||+++...+ ...... ...++||++||++|+.|+.+.+.++.......+
T Consensus       112 ~~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~l~-~~~~~~-~~~~vLilvpt~eL~~Q~~~~l~~~~~~~~~~~  189 (501)
T PHA02558        112 KIEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLLS-RYYLEN-YEGKVLIIVPTTSLVTQMIDDFVDYRLFPREAM  189 (501)
T ss_pred             cCCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHHHH-HHHHhc-CCCeEEEEECcHHHHHHHHHHHHHhccccccce
Confidence            358999999999999999999999999999998765432 222222 234799999999999999999999875544445


Q ss_pred             EEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEE
Q 027749          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCP  212 (219)
Q Consensus       133 ~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~  212 (219)
                      ..+.++....       .+.+|+|+||+++.+...   ..++++++||+||||++...    .+..+++.+++..++++|
T Consensus       190 ~~i~~g~~~~-------~~~~I~VaT~qsl~~~~~---~~~~~~~~iIvDEaH~~~~~----~~~~il~~~~~~~~~lGL  255 (501)
T PHA02558        190 HKIYSGTAKD-------TDAPIVVSTWQSAVKQPK---EWFDQFGMVIVDECHLFTGK----SLTSIITKLDNCKFKFGL  255 (501)
T ss_pred             eEEecCcccC-------CCCCEEEeeHHHHhhchh---hhccccCEEEEEchhcccch----hHHHHHHhhhccceEEEE
Confidence            4555554432       357899999999876432   24678999999999998754    456777777777899999


Q ss_pred             eecccC
Q 027749          213 GSCFLF  218 (219)
Q Consensus       213 SATl~~  218 (219)
                      |||++.
T Consensus       256 TATp~~  261 (501)
T PHA02558        256 TGSLRD  261 (501)
T ss_pred             eccCCC
Confidence            999863

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

Probab=99.88  E-value=2.8e-22  Score=178.28  Aligned_cols=164  Identities=13%  Similarity=0.206  Sum_probs=129.7

Q ss_pred             CCCCCChHHHHHHHHHHh-CCCcEEEEcCCCCchhHHhHHHHHhhhcc-------CCCceeEEEEcCCHHHHHHHHHHHH
Q 027749           51 YGFEKPSAIQQRAVMPII-KGRDVIAQAQSGTGKTSMIALTVCQTVDT-------SSREVQALILSPTRELATQTEKVIL  122 (219)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~-~~~~~lv~~~tG~GKT~~~~~~~~~~~~~-------~~~~~~~lil~P~~~l~~q~~~~~~  122 (219)
                      +++..++.+|..++|.+- ++.|.+||||||+|||..+++.+++.+..       .....+++|++|.++||.++.+.+.
T Consensus       106 f~f~~fN~iQS~vFp~aY~SneNMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKALa~Em~~~~~  185 (1230)
T KOG0952|consen  106 FSFEEFNRIQSEVFPVAYKSNENMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAAEMVDKFS  185 (1230)
T ss_pred             ccHHHHHHHHHHhhhhhhcCCCCEEEECCCCCCchHHHHHHHHHHHHhhccccccccCCceEEEEechHHHHHHHHHHHh
Confidence            456788999999999865 56799999999999999999999988864       2346789999999999999999998


Q ss_pred             HhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCC---CCCCCccEEEeccchhhhccccHHHHHHH
Q 027749          123 AIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT---LRTRAIKLLVLDESDEMLSRGFKDQIYDV  199 (219)
Q Consensus       123 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~---~~~~~l~~lVvDE~h~l~~~~~~~~~~~i  199 (219)
                      +-+...++.+..+.|.......-   -..|+|+|+||+++--.-+...   ..++.+++||+||+|.+-+. .+..++.|
T Consensus       186 kkl~~~gi~v~ELTGD~ql~~te---i~~tqiiVTTPEKwDvvTRk~~~d~~l~~~V~LviIDEVHlLhd~-RGpvlEti  261 (1230)
T KOG0952|consen  186 KKLAPLGISVRELTGDTQLTKTE---IADTQIIVTTPEKWDVVTRKSVGDSALFSLVRLVIIDEVHLLHDD-RGPVLETI  261 (1230)
T ss_pred             hhcccccceEEEecCcchhhHHH---HHhcCEEEecccceeeeeeeeccchhhhhheeeEEeeeehhhcCc-ccchHHHH
Confidence            88888899999999877654432   2369999999999865544332   23577899999999987765 23333333


Q ss_pred             H-------HhCCCCCeEEEEeecccC
Q 027749          200 Y-------RYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       200 ~-------~~~~~~~q~i~~SATl~~  218 (219)
                      +       +......+++++|||+|.
T Consensus       262 VaRtlr~vessqs~IRivgLSATlPN  287 (1230)
T KOG0952|consen  262 VARTLRLVESSQSMIRIVGLSATLPN  287 (1230)
T ss_pred             HHHHHHHHHhhhhheEEEEeeccCCC
Confidence            3       334557889999999995

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.88  E-value=1.1e-21  Score=175.63  Aligned_cols=149  Identities=18%  Similarity=0.302  Sum_probs=129.3

Q ss_pred             ccCCCCHHHHHHHH-----HCCCCCC---hHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEE
Q 027749           36 DAMGIKDDLLRGIY-----QYGFEKP---SAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALIL  107 (219)
Q Consensus        36 ~~~~l~~~~~~~l~-----~~~~~~~---~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil  107 (219)
                      +.+.+...+.+.+.     ..|+..|   +|+|.++++.+..+++++.+++||+|||++|++|++..+....   .++||
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 EAYGVVKNVCRRLAGTPVEVSGYHQQWDMVPYDVQILGAIAMHKGFITEMQTGEGKTLTAVMPLYLNALTGK---PVHLV  141 (970)
T ss_pred             HHhCCCHHHHHHHhccccccccccCCCCCChHHHHHhhhhhcCCCeEEEeCCCCChHHHHHHHHHHHHhhcC---CeEEE
Confidence            44567777776665     5688888   9999999999999999999999999999999999998776532   38999


Q ss_pred             cCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHH-HHHHHcCCCCCC-------CccEE
Q 027749          108 SPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRKTLRTR-------AIKLL  179 (219)
Q Consensus       108 ~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l-~~~l~~~~~~~~-------~l~~l  179 (219)
                      +|+++||.|..+.+..+.+..++++.+++|+.+..++...+  +|+|+|+||++| .++++.+.+.++       .+.++
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            99999999999999999999999999999999988876555  599999999999 999988766655       45899


Q ss_pred             Eeccchhhhc
Q 027749          180 VLDESDEMLS  189 (219)
Q Consensus       180 VvDE~h~l~~  189 (219)
                      |+||||.|+-
T Consensus       220 IIDEADsmLi  229 (970)
T PRK12899        220 IIDEVDSILI  229 (970)
T ss_pred             EEechhhhhh
Confidence            9999998874

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

Probab=99.86  E-value=4.5e-21  Score=162.01  Aligned_cols=183  Identities=18%  Similarity=0.199  Sum_probs=149.3

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCChHHHHHHHHH-HhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCH
Q 027749           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (219)
Q Consensus        33 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~-~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~  111 (219)
                      -..+++++++.+...|+..|+..+.|+|..++.. ++.|.|.+|+++|+||||++.-++-+..+...  +.+-+|++|..
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            4678899999999999999999999999999987 88999999999999999999999999988875  34599999999


Q ss_pred             HHHHHHHHHHHHhccccceeEEEEECCcccHHHH----HHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhh
Q 027749          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDI----RKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (219)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l  187 (219)
                      +||+|.++.+++-....++.+..-+|..-....-    ..-..++||||+|.+.+-.+++.+ -++.+++.||+||+|.+
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            9999999999877777787776666544322211    111236899999999999999876 57899999999999988


Q ss_pred             hccc---cHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          188 LSRG---FKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       188 ~~~~---~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      -+..   ..+-+...++.+-++.|.|.+|||+-.
T Consensus       351 ~deERG~RLdGLI~RLr~l~~~AQ~i~LSATVgN  384 (830)
T COG1202         351 EDEERGPRLDGLIGRLRYLFPGAQFIYLSATVGN  384 (830)
T ss_pred             cchhcccchhhHHHHHHHhCCCCeEEEEEeecCC
Confidence            8753   223345555666668999999999853

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

Probab=99.86  E-value=9.1e-21  Score=158.26  Aligned_cols=161  Identities=16%  Similarity=0.129  Sum_probs=130.6

Q ss_pred             CCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEE
Q 027749           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAH  133 (219)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~  133 (219)
                      -.++.+|.......+.+ |++|+.|||-|||..+.+-+..++...++  ++||++||+.|+.|..+.|.+......-.+.
T Consensus        14 ie~R~YQ~~i~a~al~~-NtLvvlPTGLGKT~IA~~V~~~~l~~~~~--kvlfLAPTKPLV~Qh~~~~~~v~~ip~~~i~   90 (542)
T COG1111          14 IEPRLYQLNIAAKALFK-NTLVVLPTGLGKTFIAAMVIANRLRWFGG--KVLFLAPTKPLVLQHAEFCRKVTGIPEDEIA   90 (542)
T ss_pred             ccHHHHHHHHHHHHhhc-CeEEEecCCccHHHHHHHHHHHHHHhcCC--eEEEecCCchHHHHHHHHHHHHhCCChhhee
Confidence            46788898888777755 99999999999999888887777776644  7999999999999999999999877677788


Q ss_pred             EEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       134 ~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      .+.|....+++...+ ...+|+|+||+.+.+-+..+.+++.++.++||||||+-...+-.-.+....-.-.+++.++++|
T Consensus        91 ~ltGev~p~~R~~~w-~~~kVfvaTPQvveNDl~~Grid~~dv~~lifDEAHRAvGnyAYv~Va~~y~~~~k~~~ilgLT  169 (542)
T COG1111          91 ALTGEVRPEEREELW-AKKKVFVATPQVVENDLKAGRIDLDDVSLLIFDEAHRAVGNYAYVFVAKEYLRSAKNPLILGLT  169 (542)
T ss_pred             eecCCCChHHHHHHH-hhCCEEEeccHHHHhHHhcCccChHHceEEEechhhhccCcchHHHHHHHHHHhccCceEEEEe
Confidence            888888777664444 5579999999999999999999999999999999999665543333333333335678999999


Q ss_pred             ecccC
Q 027749          214 SCFLF  218 (219)
Q Consensus       214 ATl~~  218 (219)
                      ||.-.
T Consensus       170 ASPGs  174 (542)
T COG1111         170 ASPGS  174 (542)
T ss_pred             cCCCC
Confidence            99643

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

Probab=99.86  E-value=6.4e-21  Score=166.87  Aligned_cols=174  Identities=15%  Similarity=0.138  Sum_probs=133.5

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHH
Q 027749           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (219)
Q Consensus        40 l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~  119 (219)
                      +.....+...--....++.+|.+.+-..+ |+|+||++|||+|||+++...++.++..... .++||++|++.|+.|+..
T Consensus        47 ~~~s~~~~~~~p~~~~lR~YQ~eivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p~-~KiVF~aP~~pLv~QQ~a  124 (746)
T KOG0354|consen   47 LDESAAQRWIYPTNLELRNYQEELVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWRPK-GKVVFLAPTRPLVNQQIA  124 (746)
T ss_pred             CChhhhccccccCcccccHHHHHHhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhcCCc-ceEEEeeCCchHHHHHHH
Confidence            44444444443344478999999998888 9999999999999999998888887776654 789999999999999997


Q ss_pred             HHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCC-CCCccEEEeccchhhhcc-ccHHHHH
Q 027749          120 VILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLR-TRAIKLLVLDESDEMLSR-GFKDQIY  197 (219)
Q Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~-~~~l~~lVvDE~h~l~~~-~~~~~~~  197 (219)
                      .+..++..  .++....|+.........+-...+|+|+||+.+.+.+.+...+ ++++.++||||||+-... .|..-++
T Consensus       125 ~~~~~~~~--~~~T~~l~~~~~~~~r~~i~~s~~vff~TpQil~ndL~~~~~~~ls~fs~iv~DE~Hra~kn~~Y~~Vmr  202 (746)
T KOG0354|consen  125 CFSIYLIP--YSVTGQLGDTVPRSNRGEIVASKRVFFRTPQILENDLKSGLHDELSDFSLIVFDECHRTSKNHPYNNIMR  202 (746)
T ss_pred             HHhhccCc--ccceeeccCccCCCchhhhhcccceEEeChHhhhhhcccccccccceEEEEEEcccccccccccHHHHHH
Confidence            66666654  4555555554433333355567899999999999988876544 489999999999997755 4666666


Q ss_pred             HHHHhCCCCCeEEEEeeccc
Q 027749          198 DVYRYLPPDLQVCCPGSCFL  217 (219)
Q Consensus       198 ~i~~~~~~~~q~i~~SATl~  217 (219)
                      .++..-....|+|++|||+.
T Consensus       203 ~~l~~k~~~~qILgLTASpG  222 (746)
T KOG0354|consen  203 EYLDLKNQGNQILGLTASPG  222 (746)
T ss_pred             HHHHhhhccccEEEEecCCC
Confidence            77777655669999999975

>PRK13766 Hef nuclease; Provisional

Probab=99.85  E-value=3.7e-20  Score=169.19  Aligned_cols=160  Identities=18%  Similarity=0.182  Sum_probs=127.9

Q ss_pred             CCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeE
Q 027749           53 FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQA  132 (219)
Q Consensus        53 ~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  132 (219)
                      ...|+++|..+...++.+ ++++++|||+|||.++++++...+.  ..+.++||++|+++|+.|+.+.++++....+..+
T Consensus        13 ~~~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~--~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~~~~v   89 (773)
T PRK13766         13 TIEARLYQQLLAATALKK-NTLVVLPTGLGKTAIALLVIAERLH--KKGGKVLILAPTKPLVEQHAEFFRKFLNIPEEKI   89 (773)
T ss_pred             cCCccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHH--hCCCeEEEEeCcHHHHHHHHHHHHHHhCCCCceE
Confidence            347899999999888776 9999999999999999888877763  2346799999999999999999998765444566


Q ss_pred             EEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEE
Q 027749          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCP  212 (219)
Q Consensus       133 ~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~  212 (219)
                      ..+.|+.+... ...+..+++|+|+||+.+...+..+.+.+.++++|||||||++........+........+.+++++|
T Consensus        90 ~~~~g~~~~~~-r~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~~liVvDEaH~~~~~~~~~~i~~~~~~~~~~~~il~l  168 (773)
T PRK13766         90 VVFTGEVSPEK-RAELWEKAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKNPLVLGL  168 (773)
T ss_pred             EEEeCCCCHHH-HHHHHhCCCEEEECHHHHHHHHHcCCCChhhCcEEEEECCccccccccHHHHHHHHHhcCCCCEEEEE
Confidence            66777666554 34445578999999999998877777888999999999999987654444455555555567789999


Q ss_pred             eecc
Q 027749          213 GSCF  216 (219)
Q Consensus       213 SATl  216 (219)
                      |||.
T Consensus       169 TaTP  172 (773)
T PRK13766        169 TASP  172 (773)
T ss_pred             EcCC
Confidence            9995

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

Probab=99.85  E-value=1.3e-20  Score=170.56  Aligned_cols=160  Identities=19%  Similarity=0.218  Sum_probs=134.5

Q ss_pred             HHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccc
Q 027749           48 IYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDF  127 (219)
Q Consensus        48 l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (219)
                      -...+| .+.++|++++-.+..|.+++|+||||+|||++.-.++...+....   +++|+.|.++|.+|.++.+......
T Consensus       113 ~~~~~F-~LD~fQ~~a~~~Ler~esVlV~ApTssGKTvVaeyAi~~al~~~q---rviYTsPIKALsNQKyrdl~~~fgd  188 (1041)
T COG4581         113 AREYPF-ELDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIALALRDGQ---RVIYTSPIKALSNQKYRDLLAKFGD  188 (1041)
T ss_pred             HHhCCC-CcCHHHHHHHHHHhCCCcEEEEccCCCCcchHHHHHHHHHHHcCC---ceEeccchhhhhhhHHHHHHHHhhh
Confidence            345666 799999999999999999999999999999988887766655543   3999999999999999999766544


Q ss_pred             cceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCC
Q 027749          128 INIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDL  207 (219)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~  207 (219)
                      ..-.+.++.|..+.+       .++.++|.|.+-|.+++..+...+.++.+||+||+|.|.+...+...+.++-.+|++.
T Consensus       189 v~~~vGL~TGDv~IN-------~~A~clvMTTEILRnMlyrg~~~~~~i~~ViFDEvHyi~D~eRG~VWEE~Ii~lP~~v  261 (1041)
T COG4581         189 VADMVGLMTGDVSIN-------PDAPCLVMTTEILRNMLYRGSESLRDIEWVVFDEVHYIGDRERGVVWEEVIILLPDHV  261 (1041)
T ss_pred             hhhhccceecceeeC-------CCCceEEeeHHHHHHHhccCcccccccceEEEEeeeeccccccchhHHHHHHhcCCCC
Confidence            322233444444443       3678999999999999999888899999999999999999988889999999999999


Q ss_pred             eEEEEeecccC
Q 027749          208 QVCCPGSCFLF  218 (219)
Q Consensus       208 q~i~~SATl~~  218 (219)
                      |+++||||+|.
T Consensus       262 ~~v~LSATv~N  272 (1041)
T COG4581         262 RFVFLSATVPN  272 (1041)
T ss_pred             cEEEEeCCCCC
Confidence            99999999985

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.84  E-value=2.2e-20  Score=165.73  Aligned_cols=152  Identities=18%  Similarity=0.077  Sum_probs=111.9

Q ss_pred             hHHHHHHHHHHhCCCcEEEEcCCCCchhHH---------hHHHHHhhhcc---CCCceeEEEEcCCHHHHHHHHHHHHHh
Q 027749           57 SAIQQRAVMPIIKGRDVIAQAQSGTGKTSM---------IALTVCQTVDT---SSREVQALILSPTRELATQTEKVILAI  124 (219)
Q Consensus        57 ~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~---------~~~~~~~~~~~---~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (219)
                      -.+|.++++.+.++++++++|+||+|||.+         |+++.+..+..   ...+.++++++|++++|.|+...+.+.
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            347999999999999999999999999976         33444444321   334567999999999999999998775


Q ss_pred             ccc---cceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHH
Q 027749          125 GDF---INIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYR  201 (219)
Q Consensus       125 ~~~---~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~  201 (219)
                      ...   .+..+...+|+.+. .......++.+|+|+|++.       ....++++++||+||||.+...+  +.+..+++
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            543   35667778888773 2222233467999999742       11247889999999999987664  45556665


Q ss_pred             hCC-CCCeEEEEeecccC
Q 027749          202 YLP-PDLQVCCPGSCFLF  218 (219)
Q Consensus       202 ~~~-~~~q~i~~SATl~~  218 (219)
                      ... +..|+++||||++.
T Consensus       316 ~~~~~~rq~ILmSATl~~  333 (675)
T PHA02653        316 KHIDKIRSLFLMTATLED  333 (675)
T ss_pred             HhhhhcCEEEEEccCCcH
Confidence            543 34699999999975

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.84  E-value=6.2e-20  Score=166.47  Aligned_cols=150  Identities=19%  Similarity=0.239  Sum_probs=116.2

Q ss_pred             HHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHH-HhccccceeEEEEEC
Q 027749           59 IQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL-AIGDFINIQAHACVG  137 (219)
Q Consensus        59 ~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~-~~~~~~~~~~~~~~~  137 (219)
                      +-.+.+..+.++++++++|+||||||.+|.+++++....   ..+++++.|++++|.|+.+.+. .+....+..+...++
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            334566667788999999999999999999999876432   2479999999999999999985 445556667776666


Q ss_pred             CcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchh-hhcccc-HHHHHHHHHhCCCCCeEEEEeec
Q 027749          138 GKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDE-MLSRGF-KDQIYDVYRYLPPDLQVCCPGSC  215 (219)
Q Consensus       138 ~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~-l~~~~~-~~~~~~i~~~~~~~~q~i~~SAT  215 (219)
                      +.+...      ...+|+|+||+.|.+++.+. ..++++++||+||+|. .++.++ ...+..+++.++++.|+++||||
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 AESKVG------PNTRLEVVTEGILTRMIQRD-PELSGVGLVILDEFHERSLQADLALALLLDVQQGLRDDLKLLIMSAT  158 (812)
T ss_pred             CccccC------CCCcEEEEChhHHHHHHhhC-CCcCcCcEEEEcCCCccccccchHHHHHHHHHHhCCccceEEEEecC
Confidence            554322      34689999999999988764 4789999999999996 344332 23345667778889999999999


Q ss_pred             ccC
Q 027749          216 FLF  218 (219)
Q Consensus       216 l~~  218 (219)
                      ++.
T Consensus       159 l~~  161 (812)
T PRK11664        159 LDN  161 (812)
T ss_pred             CCH
Confidence            974

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.84  E-value=6.6e-20  Score=153.33  Aligned_cols=154  Identities=12%  Similarity=0.075  Sum_probs=108.8

Q ss_pred             HHHHHHHHHhCCCc--EEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhcccc----ceeE
Q 027749           59 IQQRAVMPIIKGRD--VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI----NIQA  132 (219)
Q Consensus        59 ~Q~~~~~~~~~~~~--~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~----~~~~  132 (219)
                      +|.++++.+.++.+  +++++|||+|||++|+++++..      ..+++|++|+++|++|+++.+.++....    +..+
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            48999999998864  7889999999999999998742      2358999999999999999998876432    4555


Q ss_pred             EEEECCcccHH-HH-------------------HHhcCCCeEEEeChHHHHHHHHcCCC--------CCCCccEEEeccc
Q 027749          133 HACVGGKSVGE-DI-------------------RKLEHGVHVVSGTPGRVCDMIKRKTL--------RTRAIKLLVLDES  184 (219)
Q Consensus       133 ~~~~~~~~~~~-~~-------------------~~l~~~~~I~v~Tp~~l~~~l~~~~~--------~~~~l~~lVvDE~  184 (219)
                      ..+.|....+. ..                   ......+.|+++||+.|..++.....        .+..+++||+||+
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            55555422110 00                   01123678899999999877653211        2478999999999


Q ss_pred             hhhhccc-----cHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          185 DEMLSRG-----FKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       185 h~l~~~~-----~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      |.+..+.     +......+++......+++++|||+|+
T Consensus       155 H~~~~~~~~~~~~~l~~~~~~~~~~~~~~~i~lSAT~~~  193 (357)
T TIGR03158       155 HLYDAKQLVGMLFLLAYMQLIRFFECRRKFVFLSATPDP  193 (357)
T ss_pred             cccCcccchhhhhhhHHHHHHHhhhcCCcEEEEecCCCH
Confidence            9866432     112333444444446799999999975

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.

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.84  E-value=9.6e-20  Score=165.05  Aligned_cols=150  Identities=19%  Similarity=0.239  Sum_probs=116.6

Q ss_pred             HHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHH-HhccccceeEEEEEC
Q 027749           59 IQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL-AIGDFINIQAHACVG  137 (219)
Q Consensus        59 ~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~-~~~~~~~~~~~~~~~  137 (219)
                      +-.+.+..+.++.+++++|+||+|||.+|.+++++...   .+.+++++.|++++|.|+.+++. .+....+..+...++
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            33456667778889999999999999999999988763   23579999999999999999985 444455555655554


Q ss_pred             CcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchh-hhccccHH-HHHHHHHhCCCCCeEEEEeec
Q 027749          138 GKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDE-MLSRGFKD-QIYDVYRYLPPDLQVCCPGSC  215 (219)
Q Consensus       138 ~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~-l~~~~~~~-~~~~i~~~~~~~~q~i~~SAT  215 (219)
                      +.+      ....+.+|+|+||+.|++.+.+. ..++++++||+||+|. +++.++.. .+..+.+.++++.|+|+||||
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------KVSRRTRLEVVTEGILTRMIQDD-PELDGVGALIFDEFHERSLDADLGLALALDVQSSLREDLKILAMSAT  155 (819)
T ss_pred             ccc------ccCCCCcEEEECCcHHHHHHhhC-cccccCCEEEEeccchhhhccchHHHHHHHHHHhcCCCceEEEEeCC
Confidence            433      22345789999999999988764 4789999999999994 67665543 345566778889999999999


Q ss_pred             ccC
Q 027749          216 FLF  218 (219)
Q Consensus       216 l~~  218 (219)
                      ++.
T Consensus       156 l~~  158 (819)
T TIGR01970       156 LDG  158 (819)
T ss_pred             CCH
Confidence            974

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.

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.84  E-value=3.5e-19  Score=128.60  Aligned_cols=144  Identities=33%  Similarity=0.473  Sum_probs=113.1

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcC
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH  150 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  150 (219)
                      +++++.+|||+|||..++..+...... ....+++|++|+..++.++.+.+...... +..+..+.+.............
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~-~~~~~~lv~~p~~~l~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~   78 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDS-LKGGQVLVLAPTRELANQVAERLKELFGE-GIKVGYLIGGTSIKQQEKLLSG   78 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhc-ccCCCEEEEcCcHHHHHHHHHHHHHHhhC-CcEEEEEecCcchhHHHHHhcC
Confidence            468999999999998888877776654 23457999999999999999999888765 5667777777666665555667


Q ss_pred             CCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEeecc
Q 027749          151 GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCF  216 (219)
Q Consensus       151 ~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl  216 (219)
                      +.+|+++|++.+..............+++|+||+|.+....................+++++|||.
T Consensus        79 ~~~i~i~t~~~~~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~~~~~~~~~~~~i~~saTp  144 (144)
T cd00046          79 KTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQGFGLLGLKILLKLPKDRQVLLLSATP  144 (144)
T ss_pred             CCCEEEECcHHHHHHHHcCCcchhcCCEEEEeCHHHHhhcchHHHHHHHHhhCCccceEEEEeccC
Confidence            899999999999987776655567789999999999887654444333344456788999999995

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

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

Probab=99.83  E-value=1.2e-20  Score=154.98  Aligned_cols=116  Identities=31%  Similarity=0.507  Sum_probs=103.4

Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhcccc---ceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccE
Q 027749          102 VQALILSPTRELATQTEKVILAIGDFI---NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKL  178 (219)
Q Consensus       102 ~~~lil~P~~~l~~q~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~  178 (219)
                      |.++|+-|+++|++|.++.++++....   .++..++.|+.-.+.+...+..+.+|+|+||+++...+..+.+.+..+.+
T Consensus       287 p~avivepsrelaEqt~N~i~~Fk~h~~np~~r~lLmiggv~~r~Q~~ql~~g~~ivvGtpgRl~~~is~g~~~lt~crF  366 (725)
T KOG0349|consen  287 PEAVIVEPSRELAEQTHNQIEEFKMHTSNPEVRSLLMIGGVLKRTQCKQLKDGTHIVVGTPGRLLQPISKGLVTLTHCRF  366 (725)
T ss_pred             cceeEecCcHHHHHHHHhhHHHHHhhcCChhhhhhhhhhhHHhHHHHHHhhcCceeeecCchhhhhhhhccceeeeeeEE
Confidence            569999999999999999777765443   45666888999999999999999999999999999999999999999999


Q ss_pred             EEeccchhhhccccHHHHHHHHHhCCC------CCeEEEEeeccc
Q 027749          179 LVLDESDEMLSRGFKDQIYDVYRYLPP------DLQVCCPGSCFL  217 (219)
Q Consensus       179 lVvDE~h~l~~~~~~~~~~~i~~~~~~------~~q~i~~SATl~  217 (219)
                      +|+||+|.++..++.+.+.++..++|.      ..|.+++|||++
T Consensus       367 lvlDead~lL~qgy~d~I~r~h~qip~~tsdg~rlq~~vCsatlh  411 (725)
T KOG0349|consen  367 LVLDEADLLLGQGYDDKIYRFHGQIPHMTSDGFRLQSPVCSATLH  411 (725)
T ss_pred             EEecchhhhhhcccHHHHHHHhccchhhhcCCcccccceeeeEEe
Confidence            999999999999999999999888864      579999999986

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.82  E-value=7e-19  Score=157.72  Aligned_cols=150  Identities=21%  Similarity=0.246  Sum_probs=114.2

Q ss_pred             CChHHHHHHHHHHhCC---CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhcccccee
Q 027749           55 KPSAIQQRAVMPIIKG---RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ  131 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~---~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  131 (219)
                      .+++.|+++++.+.++   +++++.++||+|||.+|+.++...+..   +.++||++|+++|+.|+.+.+++..   +..
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   789999999999999998877666543   4579999999999999999998754   467


Q ss_pred             EEEEECCcccHHHH---HHh-cCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccc-----c-HHHHHHHHH
Q 027749          132 AHACVGGKSVGEDI---RKL-EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG-----F-KDQIYDVYR  201 (219)
Q Consensus       132 ~~~~~~~~~~~~~~---~~l-~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~-----~-~~~~~~i~~  201 (219)
                      +..++|+.+..++.   ..+ .+..+|+|+|+..+.       ..++++++|||||+|......     | ...+ .+.+
T Consensus       218 v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~-------~p~~~l~liVvDEeh~~s~~~~~~p~y~~r~v-a~~r  289 (679)
T PRK05580        218 VAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALF-------LPFKNLGLIIVDEEHDSSYKQQEGPRYHARDL-AVVR  289 (679)
T ss_pred             EEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHhc-------ccccCCCEEEEECCCccccccCcCCCCcHHHH-HHHH
Confidence            77888887765443   333 346899999997653       457899999999999754321     1 1222 2334


Q ss_pred             hCCCCCeEEEEeecccC
Q 027749          202 YLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       202 ~~~~~~q~i~~SATl~~  218 (219)
                      ....+.+++++|||.+.
T Consensus       290 a~~~~~~~il~SATps~  306 (679)
T PRK05580        290 AKLENIPVVLGSATPSL  306 (679)
T ss_pred             hhccCCCEEEEcCCCCH
Confidence            44568899999999764

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.81  E-value=1.1e-19  Score=152.30  Aligned_cols=142  Identities=15%  Similarity=0.075  Sum_probs=99.1

Q ss_pred             cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccH---------
Q 027749           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVG---------  142 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~---------  142 (219)
                      ++++.+|||+|||.+|++++++.+.. ....+++|++|+++|+.|+.+.+..+...   .+...+++....         
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~-~~~~~ii~v~P~~~L~~q~~~~l~~~f~~---~~~~~~~~~~~~~~~~~~~~~   76 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKS-QKADRVIIALPTRATINAMYRRAKELFGS---NLGLLHSSSSFKRIKEMGDSE   76 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhh-CCCCeEEEEeehHHHHHHHHHHHHHHhCc---ccEEeeccHHHHHHhccCCch
Confidence            47999999999999999999987654 34568999999999999999999887432   222333322210         


Q ss_pred             ---HHHHHh------cCCCeEEEeChHHHHHHHHcCC----CCCC--CccEEEeccchhhhccccHHHHHHHHHhCC-CC
Q 027749          143 ---EDIRKL------EHGVHVVSGTPGRVCDMIKRKT----LRTR--AIKLLVLDESDEMLSRGFKDQIYDVYRYLP-PD  206 (219)
Q Consensus       143 ---~~~~~l------~~~~~I~v~Tp~~l~~~l~~~~----~~~~--~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~-~~  206 (219)
                         ......      ....+|+|+||+++...+....    ..+.  ..++||+||+|.+.+.++.. +..+++.++ .+
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               000011      1246799999999998766521    1111  23789999999988765333 566665554 47


Q ss_pred             CeEEEEeecccC
Q 027749          207 LQVCCPGSCFLF  218 (219)
Q Consensus       207 ~q~i~~SATl~~  218 (219)
                      .|++++|||+|.
T Consensus       156 ~~~i~~SATlp~  167 (358)
T TIGR01587       156 VPILLMSATLPK  167 (358)
T ss_pred             CCEEEEecCchH
Confidence            899999999973

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.

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

Probab=99.80  E-value=5e-19  Score=152.98  Aligned_cols=162  Identities=19%  Similarity=0.214  Sum_probs=127.1

Q ss_pred             HHHH-HCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 027749           46 RGIY-QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (219)
Q Consensus        46 ~~l~-~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (219)
                      ..|+ -+|+..+.+-|.++|..+++|+++++..|||+||++||.+|.+-.     .+ -+|||.|..+|...+.+.++..
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            4454 468999999999999999999999999999999999999998766     22 4999999999999988888776


Q ss_pred             ccccceeEEEEECCcccHHHHHHh---c-CCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccc--cHHHHHH
Q 027749          125 GDFINIQAHACVGGKSVGEDIRKL---E-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG--FKDQIYD  198 (219)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~l---~-~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~--~~~~~~~  198 (219)
                          |+...++.+..+..+....+   . ...+++..+||++..--....+.-..+.++|||||||+.+||  |+..+.+
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                57777777776665543332   2 347999999999875322222224578899999999999996  8877665


Q ss_pred             H---HHhCCCCCeEEEEeecccC
Q 027749          199 V---YRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       199 i---~~~~~~~~q~i~~SATl~~  218 (219)
                      +   ...+| +..++.+|||-++
T Consensus       157 lg~l~~~~~-~~p~~AlTATA~~  178 (590)
T COG0514         157 LGRLRAGLP-NPPVLALTATATP  178 (590)
T ss_pred             HHHHHhhCC-CCCEEEEeCCCCh
Confidence            5   44455 7899999999765

>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=99.78  E-value=7e-18  Score=127.94  Aligned_cols=153  Identities=18%  Similarity=0.155  Sum_probs=102.3

Q ss_pred             CChHHHHHHHHHHhC-------CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccc
Q 027749           55 KPSAIQQRAVMPIIK-------GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDF  127 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~-------~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (219)
                      +++++|.+++..+..       .+++++.+|||+|||.+++..+.+...      +++|++|+..++.|+.+.+..+...
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            578999999988773       588999999999999888754444433      6999999999999999999766543


Q ss_pred             cceeEEE-----------EECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCC-----------CCCCCccEEEeccch
Q 027749          128 INIQAHA-----------CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT-----------LRTRAIKLLVLDESD  185 (219)
Q Consensus       128 ~~~~~~~-----------~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~-----------~~~~~l~~lVvDE~h  185 (219)
                      .......           ................+.+++++|.+.+........           ......++||+||||
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            2111100           111111112222334577899999999998765321           223467899999999


Q ss_pred             hhhccccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          186 EMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       186 ~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      +.....   ....+++  .+...+|+||||.++
T Consensus       157 ~~~~~~---~~~~i~~--~~~~~~l~lTATp~r  184 (184)
T PF04851_consen  157 HYPSDS---SYREIIE--FKAAFILGLTATPFR  184 (184)
T ss_dssp             CTHHHH---HHHHHHH--SSCCEEEEEESS-S-
T ss_pred             hcCCHH---HHHHHHc--CCCCeEEEEEeCccC
Confidence            876543   1444544  456779999999863

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

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

Probab=99.77  E-value=1.7e-18  Score=153.18  Aligned_cols=154  Identities=16%  Similarity=0.181  Sum_probs=130.5

Q ss_pred             HCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccc
Q 027749           50 QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (219)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (219)
                      .+.| .+..+|++|+-++.+|.++.|.|+|.+|||+++-.++...   ....-++||..|-++|.+|.++.+++.....+
T Consensus       293 ~~pF-elD~FQk~Ai~~lerg~SVFVAAHTSAGKTvVAEYAiala---q~h~TR~iYTSPIKALSNQKfRDFk~tF~Dvg  368 (1248)
T KOG0947|consen  293 IYPF-ELDTFQKEAIYHLERGDSVFVAAHTSAGKTVVAEYAIALA---QKHMTRTIYTSPIKALSNQKFRDFKETFGDVG  368 (1248)
T ss_pred             hCCC-CccHHHHHHHHHHHcCCeEEEEecCCCCcchHHHHHHHHH---HhhccceEecchhhhhccchHHHHHHhccccc
Confidence            4455 7899999999999999999999999999998876654332   22345699999999999999999988766554


Q ss_pred             eeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeE
Q 027749          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQV  209 (219)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~  209 (219)
                          ++.|.....       ..+.++|+|.+-|..++.++.-.++++++||+||+|.+.+...+-.++.++-.+|++.++
T Consensus       369 ----LlTGDvqin-------PeAsCLIMTTEILRsMLYrgadliRDvE~VIFDEVHYiND~eRGvVWEEViIMlP~HV~~  437 (1248)
T KOG0947|consen  369 ----LLTGDVQIN-------PEASCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYINDVERGVVWEEVIIMLPRHVNF  437 (1248)
T ss_pred             ----eeecceeeC-------CCcceEeehHHHHHHHHhcccchhhccceEEEeeeeecccccccccceeeeeeccccceE
Confidence                455554433       347899999999999999888778999999999999999988888899999999999999


Q ss_pred             EEEeecccC
Q 027749          210 CCPGSCFLF  218 (219)
Q Consensus       210 i~~SATl~~  218 (219)
                      |++|||+|.
T Consensus       438 IlLSATVPN  446 (1248)
T KOG0947|consen  438 ILLSATVPN  446 (1248)
T ss_pred             EEEeccCCC
Confidence            999999985

>PRK09694 helicase Cas3; Provisional

Probab=99.76  E-value=7.3e-18  Score=153.22  Aligned_cols=164  Identities=13%  Similarity=0.060  Sum_probs=113.5

Q ss_pred             CCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhcccc--ce
Q 027749           53 FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI--NI  130 (219)
Q Consensus        53 ~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~--~~  130 (219)
                      ...|+|+|..+.........+++.+|||+|||.+++..+...+ ......+++|.+||+++++++++++.++....  ..
T Consensus       284 ~~~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~~l~-~~~~~~gi~~aLPT~Atan~m~~Rl~~~~~~~f~~~  362 (878)
T PRK09694        284 GYQPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAWRLI-DQGLADSIIFALPTQATANAMLSRLEALASKLFPSP  362 (878)
T ss_pred             CCCChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHHHHH-HhCCCCeEEEECcHHHHHHHHHHHHHHHHHHhcCCC
Confidence            3479999998855444456799999999999999877655433 33334579999999999999999997654322  34


Q ss_pred             eEEEEECCcccHHHHH--------------------Hh----cC---CCeEEEeChHHHHHHHHc-CCCCCCCc----cE
Q 027749          131 QAHACVGGKSVGEDIR--------------------KL----EH---GVHVVSGTPGRVCDMIKR-KTLRTRAI----KL  178 (219)
Q Consensus       131 ~~~~~~~~~~~~~~~~--------------------~l----~~---~~~I~v~Tp~~l~~~l~~-~~~~~~~l----~~  178 (219)
                      ++.+.+|.........                    .+    .+   -.+|+|||.++++..... +...++.+    ++
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            5666666544221110                    11    11   268999999998864433 32223333    48


Q ss_pred             EEeccchhhhccccHHHHHHHHHhCC-CCCeEEEEeecccC
Q 027749          179 LVLDESDEMLSRGFKDQIYDVYRYLP-PDLQVCCPGSCFLF  218 (219)
Q Consensus       179 lVvDE~h~l~~~~~~~~~~~i~~~~~-~~~q~i~~SATl~~  218 (219)
                      |||||+|.. +..+...+..+++.+. ....+|+||||+|.
T Consensus       443 vIiDEVHAy-D~ym~~lL~~~L~~l~~~g~~vIllSATLP~  482 (878)
T PRK09694        443 LIVDEVHAY-DAYMYGLLEAVLKAQAQAGGSVILLSATLPA  482 (878)
T ss_pred             EEEechhhC-CHHHHHHHHHHHHHHHhcCCcEEEEeCCCCH
Confidence            999999974 5556667777777753 36789999999985

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.75  E-value=1.4e-17  Score=147.44  Aligned_cols=131  Identities=21%  Similarity=0.314  Sum_probs=110.3

Q ss_pred             CCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccce
Q 027749           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (219)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (219)
                      .|. .|++.|....+.+..|+  +.+++||+|||+++.+|++......   ..+.|++||..||.|.++.+.++.+..++
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--IAEMKTGEGKTLTATLPAYLNALTG---KGVHVVTVNDYLAQRDAEWMGQVYRFLGL  126 (745)
T ss_pred             hCC-CccchHHhhhhhhcCCc--eeeecCCCccHHHHHHHHHHHHHhC---CCEEEEcCCHHHHHHHHHHHHHHhccCCC
Confidence            454 79999999988887775  9999999999999999996544442   34999999999999999999999999999


Q ss_pred             eEEEEECCcccHHHHHHhcCCCeEEEeChHHH-HHHHHcC------CCCCCCccEEEeccchhhhc
Q 027749          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRK------TLRTRAIKLLVLDESDEMLS  189 (219)
Q Consensus       131 ~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l-~~~l~~~------~~~~~~l~~lVvDE~h~l~~  189 (219)
                      ++.++.|+.+..++...  ..++|+++||++| .++++.+      ...++.+.++|+||+|.|+-
T Consensus       127 sv~~i~g~~~~~~r~~~--y~~dIvyGT~~rlgfDyLrd~~~~~~~~~~~r~l~~aIIDEaDs~LI  190 (745)
T TIGR00963       127 SVGLILSGMSPEERREA--YACDITYGTNNELGFDYLRDNMAHSKEEKVQRPFHFAIIDEVDSILI  190 (745)
T ss_pred             eEEEEeCCCCHHHHHHh--cCCCEEEECCCchhhHHHhcccccchhhhhccccceeEeecHHHHhH
Confidence            99999999886654433  3589999999999 7777655      34678899999999999875

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.

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.73  E-value=8.9e-17  Score=143.10  Aligned_cols=130  Identities=17%  Similarity=0.237  Sum_probs=99.2

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEE
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (219)
                      .|+++|......+.+|  .+++++||+|||++|.+|++......   ..++|++|++.||.|..+.+..+....++++.+
T Consensus        70 rpydVQlig~l~l~~G--~Iaem~TGeGKTLta~Lpa~l~aL~g---~~V~VVTpn~yLA~Rdae~m~~l~~~LGLsv~~  144 (762)
T TIGR03714        70 FPYDVQVLGAIVLHQG--NIAEMKTGEGKTLTATMPLYLNALTG---KGAMLVTTNDYLAKRDAEEMGPVYEWLGLTVSL  144 (762)
T ss_pred             CccHHHHHHHHHhcCC--ceeEecCCcchHHHHHHHHHHHhhcC---CceEEeCCCHHHHHHHHHHHHHHHhhcCCcEEE
Confidence            5666665555544444  69999999999999999987766543   359999999999999999999999999999888


Q ss_pred             EECCcc---cHHHHHHhcCCCeEEEeChHHH-HHHHHc------CCCCCCCccEEEeccchhhhc
Q 027749          135 CVGGKS---VGEDIRKLEHGVHVVSGTPGRV-CDMIKR------KTLRTRAIKLLVLDESDEMLS  189 (219)
Q Consensus       135 ~~~~~~---~~~~~~~l~~~~~I~v~Tp~~l-~~~l~~------~~~~~~~l~~lVvDE~h~l~~  189 (219)
                      .+++..   .....+....+|+|+++||++| .+.+..      ....++.+.++|+||||.|+-
T Consensus       145 ~~~~s~~~~~~~~~rr~~y~~dIvygTp~~LgfDyLrD~l~~~~~~~~~r~l~~~IVDEaDsILi  209 (762)
T TIGR03714       145 GVVDDPDEEYDANEKRKIYNSDIVYTTNSALGFDYLIDNLASNKEGKFLRPFNYVIVDEVDSVLL  209 (762)
T ss_pred             EECCCCccccCHHHHHHhCCCCEEEECchhhhhhHHHHHhhcchhhcccccCcEEEEecHhhHhh
Confidence            776521   2222334446899999999999 444422      234567899999999999864

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.

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.72  E-value=7.5e-17  Score=144.58  Aligned_cols=131  Identities=16%  Similarity=0.272  Sum_probs=108.3

Q ss_pred             CCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccce
Q 027749           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (219)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (219)
                      .|. .|+++|..+.+.+.+|+  +.++.||+|||+++.+|++.....   +..+.|++||+.||.|.++.+..+....++
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            455 89999999999888876  999999999999999999866664   456999999999999999999999999999


Q ss_pred             eEEEEECCcccHHHHHHhcCCCeEEEeChHHH-HHHHHcC------CCCCCCccEEEeccchhhh
Q 027749          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRK------TLRTRAIKLLVLDESDEML  188 (219)
Q Consensus       131 ~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l-~~~l~~~------~~~~~~l~~lVvDE~h~l~  188 (219)
                      ++.++.|+.+...+.+ ...+++|+++||+.| .+++..+      ....+.+.++||||+|.|+
T Consensus       149 ~v~~i~g~~~~~~~r~-~~y~~dIvygT~~~l~fDyLrd~~~~~~~~~~~r~~~~~IvDEaDsiL  212 (790)
T PRK09200        149 TVGLNFSDIDDASEKK-AIYEADIIYTTNSELGFDYLRDNLADSKEDKVQRPLNYAIIDEIDSIL  212 (790)
T ss_pred             eEEEEeCCCCcHHHHH-HhcCCCEEEECCccccchhHHhccccchhhhcccccceEEEeccccce
Confidence            9999999988433333 335799999999999 4444332      1345789999999999876

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.72  E-value=8.4e-17  Score=141.55  Aligned_cols=130  Identities=19%  Similarity=0.327  Sum_probs=107.7

Q ss_pred             CCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccce
Q 027749           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (219)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (219)
                      .|. .|+++|..+++.++.|+  |.++.||+|||++|.+|++.....   ++.++|++||++||.|.++.+.++....++
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            344 79999999999999998  999999999999999999987654   467999999999999999999999999999


Q ss_pred             eEEEEECCcccHHHHHHhcCCCeEEEeChHHHH-HHHHcCC-------------------------CCCCCccEEEeccc
Q 027749          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVC-DMIKRKT-------------------------LRTRAIKLLVLDES  184 (219)
Q Consensus       131 ~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~-~~l~~~~-------------------------~~~~~l~~lVvDE~  184 (219)
                      ++.+++|+.+..  .+....+|+|+++|+..|- +++..+-                         .....+.+.||||+
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  3455578999999999884 3443221                         11245789999999


Q ss_pred             hhhh
Q 027749          185 DEML  188 (219)
Q Consensus       185 h~l~  188 (219)
                      |-++
T Consensus       252 DSiL  255 (656)
T PRK12898        252 DSVL  255 (656)
T ss_pred             ccee
Confidence            9765

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

Probab=99.71  E-value=2.4e-16  Score=136.76  Aligned_cols=164  Identities=20%  Similarity=0.246  Sum_probs=132.7

Q ss_pred             CCCHHHHHHHH-HCCCCCChHHHHHHHHHHhCC------CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCH
Q 027749           39 GIKDDLLRGIY-QYGFEKPSAIQQRAVMPIIKG------RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (219)
Q Consensus        39 ~l~~~~~~~l~-~~~~~~~~~~Q~~~~~~~~~~------~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~  111 (219)
                      +....+.+.+. ...| ++|..|++++..+..+      .+-+++|..|||||++++++++..+..   +.++..++||.
T Consensus       246 ~~~~~l~~~~~~~LPF-~LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~~---G~Q~ALMAPTE  321 (677)
T COG1200         246 PANGELLAKFLAALPF-KLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEA---GYQAALMAPTE  321 (677)
T ss_pred             CccHHHHHHHHHhCCC-CccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHHc---CCeeEEeccHH
Confidence            34555555554 5555 7999999999998744      367999999999999999998887766   45699999999


Q ss_pred             HHHHHHHHHHHHhccccceeEEEEECCcccHHHHHH---hcC-CCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhh
Q 027749          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRK---LEH-GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (219)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---l~~-~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l  187 (219)
                      -||+|.+..+.++....++++..+.|..+...+...   +.+ ..+|+|+|     ..+-+..+.++++.++|+||-|+ 
T Consensus       322 ILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGT-----HALiQd~V~F~~LgLVIiDEQHR-  395 (677)
T COG1200         322 ILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGT-----HALIQDKVEFHNLGLVIIDEQHR-  395 (677)
T ss_pred             HHHHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEc-----chhhhcceeecceeEEEEecccc-
Confidence            999999999999999999999999988776554333   333 58999999     55667778899999999999998 


Q ss_pred             hccccHHHHHHHHHhCCC-CCeEEEEeecc
Q 027749          188 LSRGFKDQIYDVYRYLPP-DLQVCCPGSCF  216 (219)
Q Consensus       188 ~~~~~~~~~~~i~~~~~~-~~q~i~~SATl  216 (219)
                          |+-.-+..+..... .+.++.||||.
T Consensus       396 ----FGV~QR~~L~~KG~~~Ph~LvMTATP  421 (677)
T COG1200         396 ----FGVHQRLALREKGEQNPHVLVMTATP  421 (677)
T ss_pred             ----ccHHHHHHHHHhCCCCCcEEEEeCCC
Confidence                45566666666666 67899999995

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

Probab=99.71  E-value=1.4e-16  Score=136.56  Aligned_cols=146  Identities=17%  Similarity=0.195  Sum_probs=100.1

Q ss_pred             CChHHHHHHHHHHhC----CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccce
Q 027749           55 KPSAIQQRAVMPIIK----GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~----~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (219)
                      .++++|++++..+.+    ++..+++.|||+|||.+++..+. .+...     +|||+|+.+|+.|+.+.+.+.....  
T Consensus        36 ~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~-~~~~~-----~Lvlv~~~~L~~Qw~~~~~~~~~~~--  107 (442)
T COG1061          36 ELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIA-ELKRS-----TLVLVPTKELLDQWAEALKKFLLLN--  107 (442)
T ss_pred             CCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHH-HhcCC-----EEEEECcHHHHHHHHHHHHHhcCCc--
Confidence            689999999999887    88999999999999977665443 33222     9999999999999998777665432  


Q ss_pred             eEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEE
Q 027749          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVC  210 (219)
Q Consensus       131 ~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i  210 (219)
                      .....+|+......      +..|.|+|.+.+..............++||+||||++....+..    +.+.+.....++
T Consensus       108 ~~~g~~~~~~~~~~------~~~i~vat~qtl~~~~~l~~~~~~~~~liI~DE~Hh~~a~~~~~----~~~~~~~~~~~L  177 (442)
T COG1061         108 DEIGIYGGGEKELE------PAKVTVATVQTLARRQLLDEFLGNEFGLIIFDEVHHLPAPSYRR----ILELLSAAYPRL  177 (442)
T ss_pred             cccceecCceeccC------CCcEEEEEhHHHhhhhhhhhhcccccCEEEEEccccCCcHHHHH----HHHhhhccccee
Confidence            12222333332211      13699999988876421122233478999999999988654333    333333222299


Q ss_pred             EEeecccC
Q 027749          211 CPGSCFLF  218 (219)
Q Consensus       211 ~~SATl~~  218 (219)
                      +||||.+.
T Consensus       178 GLTATp~R  185 (442)
T COG1061         178 GLTATPER  185 (442)
T ss_pred             eeccCcee
Confidence            99999753

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

Probab=99.70  E-value=1e-16  Score=145.25  Aligned_cols=174  Identities=14%  Similarity=0.216  Sum_probs=132.1

Q ss_pred             CCCHHHHHHHHHCCCCCChHHHHHHHHHHhCC-CcEEEEcCCCCchhHHhHHHHHhhhccCC--------CceeEEEEcC
Q 027749           39 GIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG-RDVIAQAQSGTGKTSMIALTVCQTVDTSS--------REVQALILSP  109 (219)
Q Consensus        39 ~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~-~~~lv~~~tG~GKT~~~~~~~~~~~~~~~--------~~~~~lil~P  109 (219)
                      +++.+-..++.  |...++++|..+.+..+.+ .++++|||||+|||-.+++.+++.+....        ...++++++|
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            35555555665  4456999999999998866 58999999999999999999999886532        2358999999


Q ss_pred             CHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCC--CCCCCccEEEeccchhh
Q 027749          110 TRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT--LRTRAIKLLVLDESDEM  187 (219)
Q Consensus       110 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~--~~~~~l~~lVvDE~h~l  187 (219)
                      ..+|++.+...+.+.....++.|....|......+.   -.+.+|+|+||+++--+-++..  -+.+-++++|+||.|.+
T Consensus       373 mKaLvqE~VgsfSkRla~~GI~V~ElTgD~~l~~~q---ieeTqVIV~TPEK~DiITRk~gdraY~qlvrLlIIDEIHLL  449 (1674)
T KOG0951|consen  373 MKALVQEMVGSFSKRLAPLGITVLELTGDSQLGKEQ---IEETQVIVTTPEKWDIITRKSGDRAYEQLVRLLIIDEIHLL  449 (1674)
T ss_pred             HHHHHHHHHHHHHhhccccCcEEEEecccccchhhh---hhcceeEEeccchhhhhhcccCchhHHHHHHHHhhhhhhhc
Confidence            999999999999999999999999999887754332   2368999999999755444322  22345789999999977


Q ss_pred             hccccHHHHHHH----HHhC---CCCCeEEEEeecccC
Q 027749          188 LSRGFKDQIYDV----YRYL---PPDLQVCCPGSCFLF  218 (219)
Q Consensus       188 ~~~~~~~~~~~i----~~~~---~~~~q~i~~SATl~~  218 (219)
                      -+. .+..++.+    ++..   ...++++++|||||.
T Consensus       450 hDd-RGpvLESIVaRt~r~ses~~e~~RlVGLSATLPN  486 (1674)
T KOG0951|consen  450 HDD-RGPVLESIVARTFRRSESTEEGSRLVGLSATLPN  486 (1674)
T ss_pred             ccc-cchHHHHHHHHHHHHhhhcccCceeeeecccCCc
Confidence            543 23444333    2222   347899999999995

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.70  E-value=3.5e-16  Score=140.57  Aligned_cols=128  Identities=20%  Similarity=0.277  Sum_probs=105.2

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEE
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (219)
                      .|+++|...--.+..|  -|..++||+|||++|.+|++..+...   ..+.|++||+.||.|.++.+..+....++++.+
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--NIAEMRTGEGKTLVATLPAYLNAISG---RGVHIVTVNDYLAKRDSQWMKPIYEFLGLTVGV  156 (896)
T ss_pred             CcchHHHhhhhhhccC--ccccccCCCCchHHHHHHHHHHHhcC---CCEEEEcCCHHHHHHHHHHHHHHhcccCceEEE
Confidence            6788885544444444  58899999999999999999877653   349999999999999999999999999999999


Q ss_pred             EECCcccHHHHHHhcCCCeEEEeChHHH-HHHHHcC-CCCC-----CCccEEEeccchhhhc
Q 027749          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRK-TLRT-----RAIKLLVLDESDEMLS  189 (219)
Q Consensus       135 ~~~~~~~~~~~~~l~~~~~I~v~Tp~~l-~~~l~~~-~~~~-----~~l~~lVvDE~h~l~~  189 (219)
                      +.|+.+...+...+  .++|+++||+.| .+++..+ .+++     +.+.++||||||.|+-
T Consensus       157 i~gg~~~~~r~~~y--~~dIvygT~grlgfDyLrd~~~~~~~~~v~r~l~~~IvDEaDsiLI  216 (896)
T PRK13104        157 IYPDMSHKEKQEAY--KADIVYGTNNEYGFDYLRDNMAFSLTDKVQRELNFAIVDEVDSILI  216 (896)
T ss_pred             EeCCCCHHHHHHHh--CCCEEEECChhhhHHHHhcCCccchHhhhccccceEEeccHhhhhh
Confidence            99998877654443  689999999999 8888765 3334     5899999999998773

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.68  E-value=8.7e-16  Score=136.68  Aligned_cols=148  Identities=18%  Similarity=0.167  Sum_probs=103.5

Q ss_pred             CChHHHHHHHHHHh-CC--CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhcccccee
Q 027749           55 KPSAIQQRAVMPII-KG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ  131 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~-~~--~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  131 (219)
                      .++|+|++++..+. +|  ++.+++.|||+|||+..+..+.. +.     .++|||||+..|+.|+.+.+.++.......
T Consensus       255 ~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa~~-l~-----k~tLILvps~~Lv~QW~~ef~~~~~l~~~~  328 (732)
T TIGR00603       255 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACT-VK-----KSCLVLCTSAVSVEQWKQQFKMWSTIDDSQ  328 (732)
T ss_pred             CcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHHHH-hC-----CCEEEEeCcHHHHHHHHHHHHHhcCCCCce
Confidence            57999999998876 34  47899999999999887765443 21     349999999999999999999986543445


Q ss_pred             EEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHc--------CCCCCCCccEEEeccchhhhccccHHHHHHHHHhC
Q 027749          132 AHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR--------KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL  203 (219)
Q Consensus       132 ~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~--------~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~  203 (219)
                      +..+.|+...     .......|+|+|++.+......        ..+.-...++||+||||++-.    .....++..+
T Consensus       329 I~~~tg~~k~-----~~~~~~~VvVtTYq~l~~~~~r~~~~~~~l~~l~~~~~gLII~DEvH~lpA----~~fr~il~~l  399 (732)
T TIGR00603       329 ICRFTSDAKE-----RFHGEAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPA----AMFRRVLTIV  399 (732)
T ss_pred             EEEEecCccc-----ccccCCcEEEEEHHHhhcccccchhhhHHHHHhccccCCEEEEEccccccH----HHHHHHHHhc
Confidence            5555554322     1123478999999876532211        112224678999999999754    3444566665


Q ss_pred             CCCCeEEEEeecccC
Q 027749          204 PPDLQVCCPGSCFLF  218 (219)
Q Consensus       204 ~~~~q~i~~SATl~~  218 (219)
                      +. ...++||||+-.
T Consensus       400 ~a-~~RLGLTATP~R  413 (732)
T TIGR00603       400 QA-HCKLGLTATLVR  413 (732)
T ss_pred             Cc-CcEEEEeecCcc
Confidence            43 457999999864

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).

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

Probab=99.67  E-value=5.9e-16  Score=127.32  Aligned_cols=166  Identities=16%  Similarity=0.236  Sum_probs=117.0

Q ss_pred             HHHHHHHH-CCCC-CChHHHHHHHHHHhCC-CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHH
Q 027749           43 DLLRGIYQ-YGFE-KPSAIQQRAVMPIIKG-RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (219)
Q Consensus        43 ~~~~~l~~-~~~~-~~~~~Q~~~~~~~~~~-~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~  119 (219)
                      .+..+|++ +|+. .-++.|..++..+..+ +|+.|+.|||+||++||.+|.+..      +.-.|++.|..+|..++.+
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            35556664 3443 3378999999998765 699999999999999999998754      2258999999999998888


Q ss_pred             HHHHhccccceeEEEEECCcccHHHHHHh------cCCCeEEEeChHHHHH-----HHHcCCCCCCCccEEEeccchhhh
Q 027749          120 VILAIGDFINIQAHACVGGKSVGEDIRKL------EHGVHVVSGTPGRVCD-----MIKRKTLRTRAIKLLVLDESDEML  188 (219)
Q Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l------~~~~~I~v~Tp~~l~~-----~l~~~~~~~~~l~~lVvDE~h~l~  188 (219)
                      .+..+    .+.+..+.+..+..++.+.+      +-...++..||+....     ++. ....-..+.|+||||||+..
T Consensus        80 HL~~L----KVp~~SLNSKlSt~ER~ri~~DL~~ekp~~K~LYITPE~AAt~~FQ~lLn-~L~~r~~L~Y~vVDEAHCVS  154 (641)
T KOG0352|consen   80 HLKRL----KVPCESLNSKLSTVERSRIMGDLAKEKPTIKMLYITPEGAATDGFQKLLN-GLANRDVLRYIVVDEAHCVS  154 (641)
T ss_pred             HHHhc----CCchhHhcchhhHHHHHHHHHHHHhcCCceeEEEEchhhhhhhhHHHHHH-HHhhhceeeeEEechhhhHh
Confidence            88776    45555555555544432222      1256799999986542     222 22234568999999999999


Q ss_pred             ccc--cHHHHHHH--HHhCCCCCeEEEEeecccCC
Q 027749          189 SRG--FKDQIYDV--YRYLPPDLQVCCPGSCFLFD  219 (219)
Q Consensus       189 ~~~--~~~~~~~i--~~~~~~~~q~i~~SATl~~~  219 (219)
                      .||  |+.+..++  ++..-.+..-+.++||-+++
T Consensus       155 QWGHDFRPDYL~LG~LRS~~~~vpwvALTATA~~~  189 (641)
T KOG0352|consen  155 QWGHDFRPDYLTLGSLRSVCPGVPWVALTATANAK  189 (641)
T ss_pred             hhccccCcchhhhhhHHhhCCCCceEEeecccChh
Confidence            995  66665554  33333467789999997653

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

Probab=99.66  E-value=1.6e-16  Score=138.05  Aligned_cols=150  Identities=16%  Similarity=0.210  Sum_probs=127.1

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEE
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (219)
                      .+.|+|..++..+-++.+++|.|.|.+|||.++-.++...+..+   .++||..|-++|.+|-++++..-.+..|+    
T Consensus       129 ~LDpFQ~~aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~k---QRVIYTSPIKALSNQKYREl~~EF~DVGL----  201 (1041)
T KOG0948|consen  129 TLDPFQSTAIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLREK---QRVIYTSPIKALSNQKYRELLEEFKDVGL----  201 (1041)
T ss_pred             ccCchHhhhhhhhcCCceEEEEeecCCCcchHHHHHHHHHHHhc---CeEEeeChhhhhcchhHHHHHHHhcccce----
Confidence            56899999999999999999999999999999988887777664   35999999999999999999776555443    


Q ss_pred             EECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEee
Q 027749          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGS  214 (219)
Q Consensus       135 ~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SA  214 (219)
                      ..|..+.+.       ++.-+|.|.+-|..++.++.-..+.+.+||+||+|.|-+...+-.++.-+--+|++.+.+++||
T Consensus       202 MTGDVTInP-------~ASCLVMTTEILRsMLYRGSEvmrEVaWVIFDEIHYMRDkERGVVWEETIIllP~~vr~VFLSA  274 (1041)
T KOG0948|consen  202 MTGDVTINP-------DASCLVMTTEILRSMLYRGSEVMREVAWVIFDEIHYMRDKERGVVWEETIILLPDNVRFVFLSA  274 (1041)
T ss_pred             eecceeeCC-------CCceeeeHHHHHHHHHhccchHhheeeeEEeeeehhccccccceeeeeeEEeccccceEEEEec
Confidence            445544433       4678999999999999988888899999999999999987656666666777899999999999


Q ss_pred             cccC
Q 027749          215 CFLF  218 (219)
Q Consensus       215 Tl~~  218 (219)
                      |+|.
T Consensus       275 TiPN  278 (1041)
T KOG0948|consen  275 TIPN  278 (1041)
T ss_pred             cCCC
Confidence            9996

>TIGR00595 priA primosomal protein N'

Probab=99.66  E-value=7.8e-16  Score=133.81  Aligned_cols=131  Identities=21%  Similarity=0.234  Sum_probs=93.1

Q ss_pred             EEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHH---HHHhc-
Q 027749           74 IAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGED---IRKLE-  149 (219)
Q Consensus        74 lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~l~-  149 (219)
                      ++.|+||+|||.+|+..+.+.+..   +.++||++|+.+|+.|+.+.+++..   +..+..++++.+..++   +..+. 
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            478999999999997665444433   3469999999999999999998754   4556677777665544   33332 


Q ss_pred             CCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccc-----cH-HHHHHHHHhCCCCCeEEEEeecccC
Q 027749          150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG-----FK-DQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       150 ~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~-----~~-~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      +.++|+|+|+..+.       ..++++++|||||.|......     |. .++. +++....+.++|++|||.+.
T Consensus        75 g~~~IVVGTrsalf-------~p~~~l~lIIVDEeh~~sykq~~~p~y~ar~~a-~~ra~~~~~~vil~SATPsl  141 (505)
T TIGR00595        75 GEILVVIGTRSALF-------LPFKNLGLIIVDEEHDSSYKQEEGPRYHARDVA-VYRAKKFNCPVVLGSATPSL  141 (505)
T ss_pred             CCCCEEECChHHHc-------CcccCCCEEEEECCCccccccccCCCCcHHHHH-HHHHHhcCCCEEEEeCCCCH
Confidence            45799999987553       357899999999999765322     11 2222 23333457899999999653

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).

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

Probab=99.66  E-value=1.6e-15  Score=123.38  Aligned_cols=174  Identities=19%  Similarity=0.224  Sum_probs=130.0

Q ss_pred             CccccCCCCHHHHHHHH-HCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCH
Q 027749           33 TSFDAMGIKDDLLRGIY-QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (219)
Q Consensus        33 ~~~~~~~l~~~~~~~l~-~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~  111 (219)
                      ..-+++|++....+.|+ .+.+++++|.|..+++....|++.++..|||.||++||.+|.+-.      ...+++++|..
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            45567899999998887 567889999999999999999999999999999999999987642      34699999999


Q ss_pred             HHHHHHHHHHHHhccccceeEEEEECCcccHHHHH---Hh---cCCCeEEEeChHHHHH---HHH--cCCCCCCCccEEE
Q 027749          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIR---KL---EHGVHVVSGTPGRVCD---MIK--RKTLRTRAIKLLV  180 (219)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~l---~~~~~I~v~Tp~~l~~---~l~--~~~~~~~~l~~lV  180 (219)
                      +|++.+.-.++.+    ++....+..+.+.++..+   .+   .....++..||+++..   ++.  .+.+....+++|-
T Consensus       145 slmedqil~lkql----gi~as~lnansske~~k~v~~~i~nkdse~kliyvtpekiaksk~~mnkleka~~~~~~~~ia  220 (695)
T KOG0353|consen  145 SLMEDQILQLKQL----GIDASMLNANSSKEEAKRVEAAITNKDSEFKLIYVTPEKIAKSKKFMNKLEKALEAGFFKLIA  220 (695)
T ss_pred             HHHHHHHHHHHHh----CcchhhccCcccHHHHHHHHHHHcCCCceeEEEEecHHHHHHHHHHHHHHHHHhhcceeEEEe
Confidence            9999877777776    444444443333332211   11   2246789999999875   222  2446678899999


Q ss_pred             eccchhhhccc--cHHHHH---HHHHhCCCCCeEEEEeeccc
Q 027749          181 LDESDEMLSRG--FKDQIY---DVYRYLPPDLQVCCPGSCFL  217 (219)
Q Consensus       181 vDE~h~l~~~~--~~~~~~---~i~~~~~~~~q~i~~SATl~  217 (219)
                      +||+|+-..||  |+.+..   -+.+++ ++..+|+++||-+
T Consensus       221 idevhccsqwghdfr~dy~~l~ilkrqf-~~~~iigltatat  261 (695)
T KOG0353|consen  221 IDEVHCCSQWGHDFRPDYKALGILKRQF-KGAPIIGLTATAT  261 (695)
T ss_pred             ecceeehhhhCcccCcchHHHHHHHHhC-CCCceeeeehhhh
Confidence            99999988885  555543   334444 4678999999864

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

Probab=99.64  E-value=3.1e-15  Score=139.58  Aligned_cols=158  Identities=15%  Similarity=0.108  Sum_probs=106.3

Q ss_pred             CChHHHHHHHHHHh----CC-CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccc
Q 027749           55 KPSAIQQRAVMPII----KG-RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~----~~-~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (219)
                      .++++|.+++..+.    +| ++.+++++||+|||.+++. ++..+.......++|||+|+.+|+.|..+.+..+.....
T Consensus       413 ~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai~-li~~L~~~~~~~rVLfLvDR~~L~~Qa~~~F~~~~~~~~  491 (1123)
T PRK11448        413 GLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAIA-LMYRLLKAKRFRRILFLVDRSALGEQAEDAFKDTKIEGD  491 (1123)
T ss_pred             CCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHHHH-HHHHHHhcCccCeEEEEecHHHHHHHHHHHHHhcccccc
Confidence            58999999997764    33 6799999999999977544 445454444456899999999999999999987643222


Q ss_pred             eeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcC-----CCCCCCccEEEeccchhhhcc--------------
Q 027749          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK-----TLRTRAIKLLVLDESDEMLSR--------------  190 (219)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~-----~~~~~~l~~lVvDE~h~l~~~--------------  190 (219)
                      ......++......  ........|+|+|.++|...+...     ...+.++++||+||||+-...              
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            11111111111011  011235789999999998765321     235678899999999985310              


Q ss_pred             -ccHHHHHHHHHhCCCCCeEEEEeeccc
Q 027749          191 -GFKDQIYDVYRYLPPDLQVCCPGSCFL  217 (219)
Q Consensus       191 -~~~~~~~~i~~~~~~~~q~i~~SATl~  217 (219)
                       .+...+..+++.+.  .-.|+||||.-
T Consensus       570 ~~~~~~yr~iL~yFd--A~~IGLTATP~  595 (1123)
T PRK11448        570 LDYVSKYRRVLDYFD--AVKIGLTATPA  595 (1123)
T ss_pred             hhHHHHHHHHHhhcC--ccEEEEecCCc
Confidence             12356777777663  46899999963

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.64  E-value=5.6e-15  Score=137.77  Aligned_cols=147  Identities=18%  Similarity=0.241  Sum_probs=95.2

Q ss_pred             hHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHH-HHhhhccCCCceeEEEEcCC----HHHHHHHHHHHHH-hccccce
Q 027749           57 SAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALT-VCQTVDTSSREVQALILSPT----RELATQTEKVILA-IGDFINI  130 (219)
Q Consensus        57 ~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~-~~~~~~~~~~~~~~lil~P~----~~l~~q~~~~~~~-~~~~~~~  130 (219)
                      +....+.+..+..+..++|+|+||||||.  .+| ++.... ......+++.-|.    +++|.++.+++.. ++...|+
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--QLPKICLELG-RGVKGLIGHTQPRRLAARTVANRIAEELETELGGCVGY  152 (1294)
T ss_pred             HHHHHHHHHHHHhCCeEEEECCCCCCHHH--HHHHHHHHcC-CCCCCceeeCCCcHHHHHHHHHHHHHHHhhhhcceece
Confidence            44445566666677778899999999996  455 333222 2112234445575    4666666666653 3443343


Q ss_pred             eEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccch-hhhccccHHH-HHHHHHhCCCCCe
Q 027749          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESD-EMLSRGFKDQ-IYDVYRYLPPDLQ  208 (219)
Q Consensus       131 ~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h-~l~~~~~~~~-~~~i~~~~~~~~q  208 (219)
                      .+.    ..+      ....++.|+|+||+.|++.+.... .++++++||+|||| ++++.+|... +..++.. .++.|
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----FND------QVSDNTMVKLMTDGILLAEIQQDR-LLMQYDTIIIDEAHERSLNIDFILGYLKELLPR-RPDLK  220 (1294)
T ss_pred             eec----Ccc------ccCCCCCEEEEChHHHHHHHhcCC-ccccCcEEEecCccccccccchHHHHHHHhhhc-CCCce
Confidence            321    111      113468999999999999887654 48999999999999 5777776643 3333332 24789


Q ss_pred             EEEEeecccC
Q 027749          209 VCCPGSCFLF  218 (219)
Q Consensus       209 ~i~~SATl~~  218 (219)
                      +|+||||++.
T Consensus       221 vILmSATid~  230 (1294)
T PRK11131        221 VIITSATIDP  230 (1294)
T ss_pred             EEEeeCCCCH
Confidence            9999999974

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

Probab=99.63  E-value=1.6e-15  Score=138.18  Aligned_cols=164  Identities=18%  Similarity=0.208  Sum_probs=123.3

Q ss_pred             HHHHHH-HHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHH
Q 027749           43 DLLRGI-YQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVI  121 (219)
Q Consensus        43 ~~~~~l-~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~  121 (219)
                      .....+ ..+|...+.+-|.+++...+.|++++|..|||.||++||.+|++-.      ++-.|+|.|..+|.+.+...+
T Consensus       251 ~~~~~l~~~Fg~~~FR~~Q~eaI~~~l~Gkd~fvlmpTG~GKSLCYQlPA~l~------~gitvVISPL~SLm~DQv~~L  324 (941)
T KOG0351|consen  251 ELELLLKEVFGHKGFRPNQLEAINATLSGKDCFVLMPTGGGKSLCYQLPALLL------GGVTVVISPLISLMQDQVTHL  324 (941)
T ss_pred             HHHHHHHHHhccccCChhHHHHHHHHHcCCceEEEeecCCceeeEeecccccc------CCceEEeccHHHHHHHHHHhh
Confidence            344444 4779999999999999999999999999999999999999987553      236999999999998777766


Q ss_pred             HHhccccceeEEEEECCcccHHHH---HHhcC---CCeEEEeChHHHHHH--HHcCCCCCCC---ccEEEeccchhhhcc
Q 027749          122 LAIGDFINIQAHACVGGKSVGEDI---RKLEH---GVHVVSGTPGRVCDM--IKRKTLRTRA---IKLLVLDESDEMLSR  190 (219)
Q Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~~~---~~l~~---~~~I~v~Tp~~l~~~--l~~~~~~~~~---l~~lVvDE~h~l~~~  190 (219)
                      .+    .++....+.++....++.   ..+..   .++|+..||+++...  +......+..   +.++|+||||+...|
T Consensus       325 ~~----~~I~a~~L~s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~~~~~~L~~~~~lal~vIDEAHCVSqW  400 (941)
T KOG0351|consen  325 SK----KGIPACFLSSIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLYARGLLALFVIDEAHCVSQW  400 (941)
T ss_pred             hh----cCcceeeccccccHHHHHHHHHHHhCCCCeEEEEEeCHHHhhcccchhhHHHhccCCCeeEEEEecHHHHhhhh
Confidence            33    367777787777765443   22322   578999999988752  2222223333   789999999999999


Q ss_pred             c--cHHHHHHH---HHhCCCCCeEEEEeeccc
Q 027749          191 G--FKDQIYDV---YRYLPPDLQVCCPGSCFL  217 (219)
Q Consensus       191 ~--~~~~~~~i---~~~~~~~~q~i~~SATl~  217 (219)
                      +  |+....++   ....+ ...+|.+|||-+
T Consensus       401 gHdFRp~Yk~l~~l~~~~~-~vP~iALTATAT  431 (941)
T KOG0351|consen  401 GHDFRPSYKRLGLLRIRFP-GVPFIALTATAT  431 (941)
T ss_pred             cccccHHHHHHHHHHhhCC-CCCeEEeehhcc
Confidence            5  77666655   33333 478999999975

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

Probab=99.61  E-value=2.1e-14  Score=131.02  Aligned_cols=164  Identities=19%  Similarity=0.208  Sum_probs=130.7

Q ss_pred             CCCHHHHHHHHH-CCCCCChHHHHHHHHHHhC----C--CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCH
Q 027749           39 GIKDDLLRGIYQ-YGFEKPSAIQQRAVMPIIK----G--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (219)
Q Consensus        39 ~l~~~~~~~l~~-~~~~~~~~~Q~~~~~~~~~----~--~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~  111 (219)
                      +-+......+.. +.| .-|+.|..||..+.+    +  .|-+|||-.|-|||.+++-++...+...   .++.++|||.
T Consensus       578 ~~d~~~q~~F~~~FPy-eET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~~G---KQVAvLVPTT  653 (1139)
T COG1197         578 PPDTEWQEEFEASFPY-EETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVMDG---KQVAVLVPTT  653 (1139)
T ss_pred             CCChHHHHHHHhcCCC-cCCHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHHHHHHHHHhcCC---CeEEEEcccH
Confidence            344555555553 344 569999999998874    3  4889999999999999988887776654   5699999999


Q ss_pred             HHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh---c-CCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhh
Q 027749          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL---E-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (219)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l---~-~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l  187 (219)
                      -||+|.++.+++.+...++++..+..-.+..++...+   . +..||+|||     .-+.++.+.+++++++||||-|+ 
T Consensus       654 lLA~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGT-----HrLL~kdv~FkdLGLlIIDEEqR-  727 (1139)
T COG1197         654 LLAQQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGT-----HRLLSKDVKFKDLGLLIIDEEQR-  727 (1139)
T ss_pred             HhHHHHHHHHHHHhcCCCeeEEEecccCCHHHHHHHHHHHhcCCccEEEec-----hHhhCCCcEEecCCeEEEechhh-
Confidence            9999999999999999999999887666665554333   2 368999999     44456778899999999999998 


Q ss_pred             hccccHHHHHHHHHhCCCCCeEEEEeecc
Q 027749          188 LSRGFKDQIYDVYRYLPPDLQVCCPGSCF  216 (219)
Q Consensus       188 ~~~~~~~~~~~i~~~~~~~~q~i~~SATl  216 (219)
                          |+-.-+.-++.+..+.-++-+|||.
T Consensus       728 ----FGVk~KEkLK~Lr~~VDvLTLSATP  752 (1139)
T COG1197         728 ----FGVKHKEKLKELRANVDVLTLSATP  752 (1139)
T ss_pred             ----cCccHHHHHHHHhccCcEEEeeCCC
Confidence                4555667777778888999999995

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

Probab=99.60  E-value=3.8e-15  Score=132.62  Aligned_cols=159  Identities=13%  Similarity=0.098  Sum_probs=120.6

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhc-cccceeEE
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIG-DFINIQAH  133 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~-~~~~~~~~  133 (219)
                      .|..||.+.+..+-.+.+.+|+|||.+|||++- ..++....+.....-+|+++|+.+|++|+...+.... ...-.+..
T Consensus       511 ~Pd~WQ~elLDsvDr~eSavIVAPTSaGKTfis-fY~iEKVLResD~~VVIyvaPtKaLVnQvsa~VyaRF~~~t~~rg~  589 (1330)
T KOG0949|consen  511 CPDEWQRELLDSVDRNESAVIVAPTSAGKTFIS-FYAIEKVLRESDSDVVIYVAPTKALVNQVSANVYARFDTKTFLRGV  589 (1330)
T ss_pred             CCcHHHHHHhhhhhcccceEEEeeccCCceecc-HHHHHHHHhhcCCCEEEEecchHHHhhhhhHHHHHhhccCccccch
Confidence            688999999999999999999999999999443 4455655555555679999999999999998886655 22223334


Q ss_pred             EEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHc---CCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEE
Q 027749          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR---KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVC  210 (219)
Q Consensus       134 ~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~---~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i  210 (219)
                      .+.|..+.+.+..  ...|+|+|+-|+.+..++..   ..-+..+++++|+||+|.+.+..-....+.++-..  .|.++
T Consensus       590 sl~g~ltqEYsin--p~nCQVLITvPecleslLlspp~~q~~cerIRyiIfDEVH~iG~~ed~l~~Eqll~li--~CP~L  665 (1330)
T KOG0949|consen  590 SLLGDLTQEYSIN--PWNCQVLITVPECLESLLLSPPHHQKFCERIRYIIFDEVHLIGNEEDGLLWEQLLLLI--PCPFL  665 (1330)
T ss_pred             hhHhhhhHHhcCC--chhceEEEEchHHHHHHhcCchhhhhhhhcceEEEechhhhccccccchHHHHHHHhc--CCCee
Confidence            4445545444332  34799999999999998877   45678999999999999988765444455555444  47899


Q ss_pred             EEeecccC
Q 027749          211 CPGSCFLF  218 (219)
Q Consensus       211 ~~SATl~~  218 (219)
                      ++|||+-+
T Consensus       666 ~LSATigN  673 (1330)
T KOG0949|consen  666 VLSATIGN  673 (1330)
T ss_pred             EEecccCC
Confidence            99999854

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.58  E-value=2e-14  Score=129.05  Aligned_cols=130  Identities=20%  Similarity=0.302  Sum_probs=106.1

Q ss_pred             CCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccce
Q 027749           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (219)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (219)
                      .|. .|+++|....-.+.+|  -+..+.||+|||+++.+|++.......   .+-|++|+..||.|.++.+..+....++
T Consensus        78 lg~-~~~dvQlig~l~L~~G--~Iaem~TGeGKTLva~lpa~l~aL~G~---~V~IvTpn~yLA~rd~e~~~~l~~~LGl  151 (830)
T PRK12904         78 LGM-RHFDVQLIGGMVLHEG--KIAEMKTGEGKTLVATLPAYLNALTGK---GVHVVTVNDYLAKRDAEWMGPLYEFLGL  151 (830)
T ss_pred             hCC-CCCccHHHhhHHhcCC--chhhhhcCCCcHHHHHHHHHHHHHcCC---CEEEEecCHHHHHHHHHHHHHHHhhcCC
Confidence            444 7899997766555555  489999999999999999975444332   3679999999999999999999999999


Q ss_pred             eEEEEECCcccHHHHHHhcCCCeEEEeChHHH-HHHHHcCC------CCCCCccEEEeccchhhh
Q 027749          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRKT------LRTRAIKLLVLDESDEML  188 (219)
Q Consensus       131 ~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l-~~~l~~~~------~~~~~l~~lVvDE~h~l~  188 (219)
                      ++.++.|+.+..++...+  .++|+++||+.| .++++.+.      ...+.+.++||||||.|+
T Consensus       152 sv~~i~~~~~~~er~~~y--~~dI~ygT~~elgfDyLrd~~~~~~~~~~~r~~~~aIvDEaDsiL  214 (830)
T PRK12904        152 SVGVILSGMSPEERREAY--AADITYGTNNEFGFDYLRDNMVFSLEERVQRGLNYAIVDEVDSIL  214 (830)
T ss_pred             eEEEEcCCCCHHHHHHhc--CCCeEEECCcchhhhhhhcccccchhhhcccccceEEEechhhhe
Confidence            999999988887765554  589999999999 77876543      235778999999999876

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.58  E-value=4.5e-14  Score=132.10  Aligned_cols=148  Identities=16%  Similarity=0.077  Sum_probs=99.5

Q ss_pred             HHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhc-cccceeEEEEECCc
Q 027749           61 QRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIG-DFINIQAHACVGGK  139 (219)
Q Consensus        61 ~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~-~~~~~~~~~~~~~~  139 (219)
                      .+.+..+.++..++|+|+||||||..  +|.+-.-.......++++.-|.+..|..+...+.+.. ...|-.+.+.+...
T Consensus        73 ~~Il~~l~~~~vvii~g~TGSGKTTq--lPq~lle~~~~~~~~I~~tQPRRlAA~svA~RvA~elg~~lG~~VGY~vR~~  150 (1283)
T TIGR01967        73 EDIAEAIAENQVVIIAGETGSGKTTQ--LPKICLELGRGSHGLIGHTQPRRLAARTVAQRIAEELGTPLGEKVGYKVRFH  150 (1283)
T ss_pred             HHHHHHHHhCceEEEeCCCCCCcHHH--HHHHHHHcCCCCCceEecCCccHHHHHHHHHHHHHHhCCCcceEEeeEEcCC
Confidence            34555666677889999999999963  3433222222223356777899998888887775443 33333333322222


Q ss_pred             ccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccch-hhhccccHHH-HHHHHHhCCCCCeEEEEeeccc
Q 027749          140 SVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESD-EMLSRGFKDQ-IYDVYRYLPPDLQVCCPGSCFL  217 (219)
Q Consensus       140 ~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h-~l~~~~~~~~-~~~i~~~~~~~~q~i~~SATl~  217 (219)
                      +.      ...+..|.|+|++.|+..+.+.. .++++++||+||+| ++++.+|... +..++... ++.|+|+||||++
T Consensus       151 ~~------~s~~T~I~~~TdGiLLr~l~~d~-~L~~~~~IIIDEaHERsL~~D~LL~lLk~il~~r-pdLKlIlmSATld  222 (1283)
T TIGR01967       151 DQ------VSSNTLVKLMTDGILLAETQQDR-FLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPRR-PDLKIIITSATID  222 (1283)
T ss_pred             cc------cCCCceeeeccccHHHHHhhhCc-ccccCcEEEEcCcchhhccchhHHHHHHHHHhhC-CCCeEEEEeCCcC
Confidence            21      12457899999999999887654 48999999999999 5887776654 55665443 5789999999986


Q ss_pred             C
Q 027749          218 F  218 (219)
Q Consensus       218 ~  218 (219)
                      .
T Consensus       223 ~  223 (1283)
T TIGR01967       223 P  223 (1283)
T ss_pred             H
Confidence            4

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.

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

Probab=99.56  E-value=5.2e-14  Score=126.35  Aligned_cols=151  Identities=17%  Similarity=0.145  Sum_probs=99.6

Q ss_pred             CChHHHHHHHHHHh----C------CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 027749           55 KPSAIQQRAVMPII----K------GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~----~------~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (219)
                      -+.++|.+++..+.    +      .+..+++.+||||||+.++..+...+ .....+++|||+|+.+|..|+.+.+..+
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            47889999997753    2      25799999999999977766543333 4445678999999999999999999887


Q ss_pred             ccccceeEEEEECCcccHHHHHHhc-CCCeEEEeChHHHHHHHHcC--CCCCCCc-cEEEeccchhhhccccHHHHHHHH
Q 027749          125 GDFINIQAHACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRK--TLRTRAI-KLLVLDESDEMLSRGFKDQIYDVY  200 (219)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~l~-~~~~I~v~Tp~~l~~~l~~~--~~~~~~l-~~lVvDE~h~l~~~~~~~~~~~i~  200 (219)
                      .... +     .+..+.......+. .+..|+|+|.++|...+...  .....+- -+||+||||+.....    +...+
T Consensus       317 ~~~~-~-----~~~~s~~~L~~~l~~~~~~iivtTiQk~~~~~~~~~~~~~~~~~~~lvIvDEaHrs~~~~----~~~~l  386 (667)
T TIGR00348       317 QKDC-A-----ERIESIAELKRLLEKDDGGIIITTIQKFDKKLKEEEEKFPVDRKEVVVIFDEAHRSQYGE----LAKNL  386 (667)
T ss_pred             CCCC-C-----cccCCHHHHHHHHhCCCCCEEEEEhHHhhhhHhhhhhccCCCCCCEEEEEEcCccccchH----HHHHH
Confidence            5321 0     11122222223332 24689999999998644321  1111111 279999999865332    33333


Q ss_pred             -HhCCCCCeEEEEeeccc
Q 027749          201 -RYLPPDLQVCCPGSCFL  217 (219)
Q Consensus       201 -~~~~~~~q~i~~SATl~  217 (219)
                       +.+| +...++||||.-
T Consensus       387 ~~~~p-~a~~lGfTaTP~  403 (667)
T TIGR00348       387 KKALK-NASFFGFTGTPI  403 (667)
T ss_pred             HhhCC-CCcEEEEeCCCc
Confidence             3444 468999999973

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

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

Probab=99.54  E-value=2.4e-13  Score=125.38  Aligned_cols=95  Identities=22%  Similarity=0.236  Sum_probs=71.4

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHH----HHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHH
Q 027749           40 IKDDLLRGIYQYGFEKPSAIQQRAVM----PIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELAT  115 (219)
Q Consensus        40 l~~~~~~~l~~~~~~~~~~~Q~~~~~----~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~  115 (219)
                      +++...+.+...|+. +++.|.+.+.    .+.+++++++.||||+|||++|++|++..+. .  +.+++|.+||++|..
T Consensus       231 ~~~~~~~~~~~~~~~-~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~-~--~~~vvi~t~t~~Lq~  306 (850)
T TIGR01407       231 LSSLFSKNIDRLGLE-YRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAI-T--EKPVVISTNTKVLQS  306 (850)
T ss_pred             ccHHHHHhhhhcCCc-cCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhc-C--CCeEEEEeCcHHHHH
Confidence            444666777777885 7899998666    4557889999999999999999999988766 2  346999999999999


Q ss_pred             HHHH-HHHHhccccc--eeEEEEECC
Q 027749          116 QTEK-VILAIGDFIN--IQAHACVGG  138 (219)
Q Consensus       116 q~~~-~~~~~~~~~~--~~~~~~~~~  138 (219)
                      |+.. .+..+.+..+  +++..+.|+
T Consensus       307 Ql~~~~~~~l~~~~~~~~~~~~~kG~  332 (850)
T TIGR01407       307 QLLEKDIPLLNEILNFKINAALIKGK  332 (850)
T ss_pred             HHHHHHHHHHHHHcCCCceEEEEEcc
Confidence            9865 4544443333  555555544

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.

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

Probab=99.51  E-value=5.6e-14  Score=125.22  Aligned_cols=165  Identities=13%  Similarity=0.128  Sum_probs=131.2

Q ss_pred             HHHCCCCCChHHHHHHH--HHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhc
Q 027749           48 IYQYGFEKPSAIQQRAV--MPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIG  125 (219)
Q Consensus        48 l~~~~~~~~~~~Q~~~~--~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  125 (219)
                      ++..|..+.+.||.+++  +.++.++|.+...||+.|||++.-+-++......+.  .++++.|..+.+.+-.+.+..+.
T Consensus       216 ~~~kgi~~~fewq~ecls~~~~~e~~nliys~Pts~gktlvaeilml~~~l~~rr--~~llilp~vsiv~Ek~~~l~~~~  293 (1008)
T KOG0950|consen  216 AKDKGILKLFEWQAECLSLPRLLERKNLIYSLPTSAGKTLVAEILMLREVLCRRR--NVLLILPYVSIVQEKISALSPFS  293 (1008)
T ss_pred             HHhhhHHHHHHHHHHHhcchhhhcccceEEeCCCccchHHHHHHHHHHHHHHHhh--ceeEecceeehhHHHHhhhhhhc
Confidence            34667888999999988  567788999999999999999999888887765533  49999999999999999999999


Q ss_pred             cccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHc--CCCCCCCccEEEeccchhhhccccHHHHHHHHHhC
Q 027749          126 DFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR--KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL  203 (219)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~--~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~  203 (219)
                      ...|+.+....|........    +.-.+.|+|-++-..+++.  ..-.+..+++|||||.|.+.+.+.+..++.++...
T Consensus       294 ~~~G~~ve~y~g~~~p~~~~----k~~sv~i~tiEkanslin~lie~g~~~~~g~vvVdElhmi~d~~rg~~lE~~l~k~  369 (1008)
T KOG0950|consen  294 IDLGFPVEEYAGRFPPEKRR----KRESVAIATIEKANSLINSLIEQGRLDFLGMVVVDELHMIGDKGRGAILELLLAKI  369 (1008)
T ss_pred             cccCCcchhhcccCCCCCcc----cceeeeeeehHhhHhHHHHHHhcCCccccCcEEEeeeeeeeccccchHHHHHHHHH
Confidence            99999999888777765443    3458999999987765543  22346789999999999999887665555555442


Q ss_pred             -----CCCCeEEEEeecccC
Q 027749          204 -----PPDLQVCCPGSCFLF  218 (219)
Q Consensus       204 -----~~~~q~i~~SATl~~  218 (219)
                           ....|+|++|||+|.
T Consensus       370 ~y~~~~~~~~iIGMSATi~N  389 (1008)
T KOG0950|consen  370 LYENLETSVQIIGMSATIPN  389 (1008)
T ss_pred             HHhccccceeEeeeecccCC
Confidence                 234679999999985

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.50  E-value=1.8e-13  Score=123.14  Aligned_cols=131  Identities=19%  Similarity=0.275  Sum_probs=104.3

Q ss_pred             CCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccce
Q 027749           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (219)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (219)
                      .|. .|+++|...--.+.+  .-|.+++||.|||+++.+|++..+.....   +.||+|+..||.+..+.+..+....++
T Consensus        79 lgm-~~ydVQliGgl~L~~--G~IaEm~TGEGKTL~a~lp~~l~al~g~~---VhIvT~ndyLA~RD~e~m~~l~~~lGl  152 (908)
T PRK13107         79 FEM-RHFDVQLLGGMVLDS--NRIAEMRTGEGKTLTATLPAYLNALTGKG---VHVITVNDYLARRDAENNRPLFEFLGL  152 (908)
T ss_pred             hCC-CcCchHHhcchHhcC--CccccccCCCCchHHHHHHHHHHHhcCCC---EEEEeCCHHHHHHHHHHHHHHHHhcCC
Confidence            344 678888554433433  45889999999999999999887765433   999999999999999999999999999


Q ss_pred             eEEEEECCcccHHHHHHhcCCCeEEEeChHHH-HHHHHcC-CCCC-----CCccEEEeccchhhhc
Q 027749          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRK-TLRT-----RAIKLLVLDESDEMLS  189 (219)
Q Consensus       131 ~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l-~~~l~~~-~~~~-----~~l~~lVvDE~h~l~~  189 (219)
                      ++.++.++.+....  .-..+|+|+++||+.| .++++.+ ....     ..+.+.||||+|.++-
T Consensus       153 sv~~i~~~~~~~~r--~~~Y~~dI~YgT~~e~gfDyLrdnm~~~~~~~vqr~~~~aIvDEvDsiLi  216 (908)
T PRK13107        153 TVGINVAGLGQQEK--KAAYNADITYGTNNEFGFDYLRDNMAFSPQERVQRPLHYALIDEVDSILI  216 (908)
T ss_pred             eEEEecCCCCHHHH--HhcCCCCeEEeCCCcccchhhhccCccchhhhhccccceeeecchhhhcc
Confidence            99999888776443  2234799999999999 7777665 3333     6788999999998774

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

Probab=99.48  E-value=2.6e-12  Score=115.57  Aligned_cols=138  Identities=14%  Similarity=0.196  Sum_probs=97.4

Q ss_pred             HHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccc
Q 027749           48 IYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDF  127 (219)
Q Consensus        48 l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (219)
                      +.+.....||..|+.....+.+|+++-+.||||.|||..-++..+. +...  +.++++++||..|+.|+++.+.++...
T Consensus        75 F~k~~G~~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTfg~~~sl~-~a~k--gkr~yii~PT~~Lv~Q~~~kl~~~~e~  151 (1187)
T COG1110          75 FKKATGFRPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFGLLMSLY-LAKK--GKRVYIIVPTTTLVRQVYERLKKFAED  151 (1187)
T ss_pred             HHHhhCCCchHHHHHHHHHHHcCCceEEEcCCCCchhHHHHHHHHH-HHhc--CCeEEEEecCHHHHHHHHHHHHHHHhh
Confidence            3333334899999988899999999999999999999443333332 2222  357999999999999999999999876


Q ss_pred             cc-eeEEE-EECCcccHH---HHHHh-cCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhcc
Q 027749          128 IN-IQAHA-CVGGKSVGE---DIRKL-EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (219)
Q Consensus       128 ~~-~~~~~-~~~~~~~~~---~~~~l-~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~  190 (219)
                      .+ ..+.. .++..+..+   ....+ .++.+|+|+|.+-|......-.  -.++++|+||++|.++..
T Consensus       152 ~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~FL~k~~e~L~--~~kFdfifVDDVDA~Lka  218 (1187)
T COG1110         152 AGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLSKRFEELS--KLKFDFIFVDDVDAILKA  218 (1187)
T ss_pred             cCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHHHHhhHHHhc--ccCCCEEEEccHHHHHhc
Confidence            65 33333 444433322   22333 3479999999877665544311  146889999999987753

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

Probab=99.43  E-value=3.1e-12  Score=113.07  Aligned_cols=60  Identities=18%  Similarity=0.194  Sum_probs=50.9

Q ss_pred             HHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhc
Q 027749           65 MPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIG  125 (219)
Q Consensus        65 ~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  125 (219)
                      ..+.+++.++++++||+|||++|++|++..+... .+.++||.+||++|+.|+.+.+..+.
T Consensus        11 ~al~~~~~lliEA~TGtGKTlAYLlpal~~~~~~-~~~rvlIstpT~~Lq~Ql~~~l~~l~   70 (636)
T TIGR03117        11 TSLRQKRIGMLEASTGVGKTLAMIMAALTMLKER-PDQKIAIAVPTLALMGQLWSELERLT   70 (636)
T ss_pred             HHHhcCCeEEEEcCCCCcHHHHHHHHHHHHHHhc-cCceEEEECCcHHHHHHHHHHHHHHH
Confidence            4455778899999999999999999998877532 24679999999999999999888776

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.

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

Probab=99.42  E-value=7e-12  Score=113.38  Aligned_cols=173  Identities=13%  Similarity=0.110  Sum_probs=122.9

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHH
Q 027749           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (219)
Q Consensus        40 l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~  119 (219)
                      .++...+.+....-...+..+...+..+.+...+++.|.||+|||.-..-.++.....++...++++.-|++--|..+.+
T Consensus       158 ~s~~~~~~~~~R~~LPa~~~r~~Il~~i~~~qVvvIsGeTGcGKTTQvpQfiLd~~~~~~~~~~IicTQPRRIsAIsvAe  237 (924)
T KOG0920|consen  158 KSESYKEMLRFRESLPAYKMRDTILDAIEENQVVVISGETGCGKTTQVPQFILDEAIESGAACNIICTQPRRISAISVAE  237 (924)
T ss_pred             hhhHHHHHHHHHHhCccHHHHHHHHHHHHhCceEEEeCCCCCCchhhhhHHHHHHHHhcCCCCeEEecCCchHHHHHHHH
Confidence            33444444443333456778888899999999999999999999977777777777666677789999999999999988


Q ss_pred             HHH-HhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhh-ccccHHHHH
Q 027749          120 VIL-AIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML-SRGFKDQIY  197 (219)
Q Consensus       120 ~~~-~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~-~~~~~~~~~  197 (219)
                      ++. +.+...+-.+....+..+...      ....+.+||.+.|++.+.. .-.+..+..||+||+|.=. +.+|...+.
T Consensus       238 RVa~ER~~~~g~~VGYqvrl~~~~s------~~t~L~fcTtGvLLr~L~~-~~~l~~vthiivDEVHER~i~~DflLi~l  310 (924)
T KOG0920|consen  238 RVAKERGESLGEEVGYQVRLESKRS------RETRLLFCTTGVLLRRLQS-DPTLSGVTHIIVDEVHERSINTDFLLILL  310 (924)
T ss_pred             HHHHHhccccCCeeeEEEeeecccC------CceeEEEecHHHHHHHhcc-CcccccCceeeeeeEEEccCCcccHHHHH
Confidence            883 333444444444433333221      2367999999999998876 4457899999999999522 223444444


Q ss_pred             HHHHhCCCCCeEEEEeecccCC
Q 027749          198 DVYRYLPPDLQVCCPGSCFLFD  219 (219)
Q Consensus       198 ~i~~~~~~~~q~i~~SATl~~~  219 (219)
                      +.+-...++.++|+||||+..|
T Consensus       311 k~lL~~~p~LkvILMSAT~dae  332 (924)
T KOG0920|consen  311 KDLLPRNPDLKVILMSATLDAE  332 (924)
T ss_pred             HHHhhhCCCceEEEeeeecchH
Confidence            4444446799999999998753

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

Probab=99.41  E-value=4.5e-12  Score=116.03  Aligned_cols=84  Identities=24%  Similarity=0.313  Sum_probs=65.0

Q ss_pred             CCCCCChHHHHHHHHH----HhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHH-HHHHHHhc
Q 027749           51 YGFEKPSAIQQRAVMP----IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQT-EKVILAIG  125 (219)
Q Consensus        51 ~~~~~~~~~Q~~~~~~----~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~-~~~~~~~~  125 (219)
                      .|+ .+++-|.+....    +..++.++++|+||+|||++|++|++...    .+.++||.+||++|++|+ .+.+..+.
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 LGL-EERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLLAQS----DQRQIIVSVPTKILQDQIMAEEVKAIQ  316 (820)
T ss_pred             CCC-ccCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHHHHHhc----CCCcEEEEeCcHHHHHHHHHHHHHHHH
Confidence            345 688999985544    34677899999999999999999988754    245799999999999999 46677776


Q ss_pred             cccceeEEEEECCc
Q 027749          126 DFINIQAHACVGGK  139 (219)
Q Consensus       126 ~~~~~~~~~~~~~~  139 (219)
                      +..++++..+.|+.
T Consensus       317 ~~~~~~~~~~kg~~  330 (820)
T PRK07246        317 EVFHIDCHSLKGPQ  330 (820)
T ss_pred             HhcCCcEEEEECCc
Confidence            66666666666543

>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=99.40  E-value=5.6e-12  Score=102.78  Aligned_cols=138  Identities=16%  Similarity=0.111  Sum_probs=85.7

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCc---eeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHH
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSRE---VQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDI  145 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~---~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  145 (219)
                      ..+..+++..+|.|||...+..+ ..+......   ..+|||+|. .+..++.+++.++......++....|........
T Consensus        24 ~~~g~lL~de~GlGKT~~~i~~~-~~l~~~~~~~~~~~~LIv~P~-~l~~~W~~E~~~~~~~~~~~v~~~~~~~~~~~~~  101 (299)
T PF00176_consen   24 PPRGGLLADEMGLGKTITAIALI-SYLKNEFPQRGEKKTLIVVPS-SLLSQWKEEIEKWFDPDSLRVIIYDGDSERRRLS  101 (299)
T ss_dssp             TT-EEEE---TTSSHHHHHHHHH-HHHHHCCTTSS-S-EEEEE-T-TTHHHHHHHHHHHSGT-TS-EEEESSSCHHHHTT
T ss_pred             CCCCEEEEECCCCCchhhhhhhh-hhhhhccccccccceeEeecc-chhhhhhhhhcccccccccccccccccccccccc
Confidence            34578999999999996665544 333322221   249999999 8889999999999865456666666555222222


Q ss_pred             HHhcCCCeEEEeChHHHH--------HHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEeecc
Q 027749          146 RKLEHGVHVVSGTPGRVC--------DMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCF  216 (219)
Q Consensus       146 ~~l~~~~~I~v~Tp~~l~--------~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl  216 (219)
                      .......+++|+|.+.+.        ..+..     -+.++||+||+|.+-+.  .......+..+. ...++++|||.
T Consensus       102 ~~~~~~~~vvi~ty~~~~~~~~~~~~~~l~~-----~~~~~vIvDEaH~~k~~--~s~~~~~l~~l~-~~~~~lLSgTP  172 (299)
T PF00176_consen  102 KNQLPKYDVVITTYETLRKARKKKDKEDLKQ-----IKWDRVIVDEAHRLKNK--DSKRYKALRKLR-ARYRWLLSGTP  172 (299)
T ss_dssp             SSSCCCSSEEEEEHHHHH--TSTHTTHHHHT-----SEEEEEEETTGGGGTTT--TSHHHHHHHCCC-ECEEEEE-SS-
T ss_pred             ccccccceeeecccccccccccccccccccc-----ccceeEEEecccccccc--cccccccccccc-cceEEeecccc
Confidence            333456889999999888        22222     23788999999998543  334444444455 56789999995

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.

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

Probab=99.38  E-value=3.2e-12  Score=91.73  Aligned_cols=133  Identities=14%  Similarity=0.164  Sum_probs=82.8

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  148 (219)
                      +|+-.++...+|+|||.-.+.-++......  +.++|+|.||+.++..+.+.++..    .+++....-.       ...
T Consensus         3 kg~~~~~d~hpGaGKTr~vlp~~~~~~i~~--~~rvLvL~PTRvva~em~~aL~~~----~~~~~t~~~~-------~~~   69 (148)
T PF07652_consen    3 KGELTVLDLHPGAGKTRRVLPEIVREAIKR--RLRVLVLAPTRVVAEEMYEALKGL----PVRFHTNARM-------RTH   69 (148)
T ss_dssp             TTEEEEEE--TTSSTTTTHHHHHHHHHHHT--T--EEEEESSHHHHHHHHHHTTTS----SEEEESTTSS----------
T ss_pred             CCceeEEecCCCCCCcccccHHHHHHHHHc--cCeEEEecccHHHHHHHHHHHhcC----CcccCceeee-------ccc
Confidence            455678999999999987777776655554  456999999999999988887543    3333211100       011


Q ss_pred             cCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccc--cHHHHHHHHHhCCCCCeEEEEeeccc
Q 027749          149 EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG--FKDQIYDVYRYLPPDLQVCCPGSCFL  217 (219)
Q Consensus       149 ~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~--~~~~~~~i~~~~~~~~q~i~~SATl~  217 (219)
                      ..+.-|-|+|...+.+.+.+ .....+.++||+||+|..-...  +...+...-. . ....+|++|||-|
T Consensus        70 ~g~~~i~vMc~at~~~~~~~-p~~~~~yd~II~DEcH~~Dp~sIA~rg~l~~~~~-~-g~~~~i~mTATPP  137 (148)
T PF07652_consen   70 FGSSIIDVMCHATYGHFLLN-PCRLKNYDVIIMDECHFTDPTSIAARGYLRELAE-S-GEAKVIFMTATPP  137 (148)
T ss_dssp             -SSSSEEEEEHHHHHHHHHT-SSCTTS-SEEEECTTT--SHHHHHHHHHHHHHHH-T-TS-EEEEEESS-T
T ss_pred             cCCCcccccccHHHHHHhcC-cccccCccEEEEeccccCCHHHHhhheeHHHhhh-c-cCeeEEEEeCCCC
Confidence            23556788999998887665 4557889999999999743222  2333333322 1 3468999999987

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 ....

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

Probab=99.37  E-value=1.2e-11  Score=99.60  Aligned_cols=145  Identities=17%  Similarity=0.109  Sum_probs=106.8

Q ss_pred             CChHHHHHHHHHH----hCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccce
Q 027749           55 KPSAIQQRAVMPI----IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (219)
Q Consensus        55 ~~~~~Q~~~~~~~----~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (219)
                      ++++.|+.+-..+    .+.++++|+|.||+|||.. +...++....+  +.++.+..|+...+.+++.+++.-..  +.
T Consensus        97 ~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEM-if~~i~~al~~--G~~vciASPRvDVclEl~~Rlk~aF~--~~  171 (441)
T COG4098          97 TLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEM-IFQGIEQALNQ--GGRVCIASPRVDVCLELYPRLKQAFS--NC  171 (441)
T ss_pred             ccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhh-hHHHHHHHHhc--CCeEEEecCcccchHHHHHHHHHhhc--cC
Confidence            6788898877654    4668999999999999954 45555655554  45699999999999999999987654  46


Q ss_pred             eEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEE
Q 027749          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVC  210 (219)
Q Consensus       131 ~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i  210 (219)
                      .+.+++|+.....+       ..++|+|...|++.-       +.++++|+||+|.+--..-...-..+.+...++..+|
T Consensus       172 ~I~~Lyg~S~~~fr-------~plvVaTtHQLlrFk-------~aFD~liIDEVDAFP~~~d~~L~~Av~~ark~~g~~I  237 (441)
T COG4098         172 DIDLLYGDSDSYFR-------APLVVATTHQLLRFK-------QAFDLLIIDEVDAFPFSDDQSLQYAVKKARKKEGATI  237 (441)
T ss_pred             CeeeEecCCchhcc-------ccEEEEehHHHHHHH-------hhccEEEEeccccccccCCHHHHHHHHHhhcccCceE
Confidence            77778877765432       689999998887653       4578999999997543322233334444455677899


Q ss_pred             EEeecccC
Q 027749          211 CPGSCFLF  218 (219)
Q Consensus       211 ~~SATl~~  218 (219)
                      .+|||-+.
T Consensus       238 ylTATp~k  245 (441)
T COG4098         238 YLTATPTK  245 (441)
T ss_pred             EEecCChH
Confidence            99999873

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.37  E-value=3.3e-12  Score=115.98  Aligned_cols=164  Identities=13%  Similarity=0.131  Sum_probs=107.4

Q ss_pred             CChHHHHHHHHHHhCC---C-cEEEEcCCCCchhHHhHHHHHhhhcc-CCCceeEEEEcCCHHHHHHHHHHHHHhccccc
Q 027749           55 KPSAIQQRAVMPIIKG---R-DVIAQAQSGTGKTSMIALTVCQTVDT-SSREVQALILSPTRELATQTEKVILAIGDFIN  129 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~---~-~~lv~~~tG~GKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (219)
                      ...+.|..++..+.+.   . .+++.+|||.|||.+.+.+....+.. .....+++++.|++.+++++++++.++....+
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            4588999999887643   3 68899999999999999988887766 45678999999999999999999998766554


Q ss_pred             eeEEEEECCcccHHHHHH-----h---------cCCCeEEEeChHHHHHHHHcC-CCC-CC--CccEEEeccchhhhccc
Q 027749          130 IQAHACVGGKSVGEDIRK-----L---------EHGVHVVSGTPGRVCDMIKRK-TLR-TR--AIKLLVLDESDEMLSRG  191 (219)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~-----l---------~~~~~I~v~Tp~~l~~~l~~~-~~~-~~--~l~~lVvDE~h~l~~~~  191 (219)
                      +.....+|..........     .         .....+.++||.......... ... +.  ....+|+||+|.+.+..
T Consensus       275 ~~~~~~h~~~~~~~~~~~~~~~~~~~~~~ds~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~S~vIlDE~h~~~~~~  354 (733)
T COG1203         275 VIGKSLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILIFSVKGFKFEFLALLLTSLVILDEVHLYADET  354 (733)
T ss_pred             cccccccccccchhhhccccccceeEEecccccceeccccccCHhHhhhhhccccchHHHHHHHhhchhhccHHhhcccc
Confidence            433322322221111000     0         002345566665555422211 111 11  12579999999877663


Q ss_pred             cHHHHHHHHHhCC-CCCeEEEEeecccC
Q 027749          192 FKDQIYDVYRYLP-PDLQVCCPGSCFLF  218 (219)
Q Consensus       192 ~~~~~~~i~~~~~-~~~q~i~~SATl~~  218 (219)
                      ....+..++..+. .+..+|++|||+|+
T Consensus       355 ~~~~l~~~i~~l~~~g~~ill~SATlP~  382 (733)
T COG1203         355 MLAALLALLEALAEAGVPVLLMSATLPP  382 (733)
T ss_pred             hHHHHHHHHHHHHhCCCCEEEEecCCCH
Confidence            3444444444442 36789999999996

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=99.36  E-value=1.5e-11  Score=100.14  Aligned_cols=70  Identities=19%  Similarity=0.200  Sum_probs=57.1

Q ss_pred             CChHHHHHHH----HHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCC---ceeEEEEcCCHHHHHHHHHHHHHh
Q 027749           55 KPSAIQQRAV----MPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR---EVQALILSPTRELATQTEKVILAI  124 (219)
Q Consensus        55 ~~~~~Q~~~~----~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~---~~~~lil~P~~~l~~q~~~~~~~~  124 (219)
                      .|+|.|.+.+    ..+..|+++++.+|||+|||++++.|++..+...+.   +.+++|.++|..+..|....+++.
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            4699999954    445678899999999999999999999877654333   247999999999998887777665

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=99.36  E-value=1.5e-11  Score=100.14  Aligned_cols=70  Identities=19%  Similarity=0.200  Sum_probs=57.1

Q ss_pred             CChHHHHHHH----HHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCC---ceeEEEEcCCHHHHHHHHHHHHHh
Q 027749           55 KPSAIQQRAV----MPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR---EVQALILSPTRELATQTEKVILAI  124 (219)
Q Consensus        55 ~~~~~Q~~~~----~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~---~~~~lil~P~~~l~~q~~~~~~~~  124 (219)
                      .|+|.|.+.+    ..+..|+++++.+|||+|||++++.|++..+...+.   +.+++|.++|..+..|....+++.
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            4699999954    445678899999999999999999999877654333   247999999999998887777665

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

Probab=99.35  E-value=1.2e-11  Score=110.36  Aligned_cols=151  Identities=21%  Similarity=0.210  Sum_probs=110.4

Q ss_pred             CChHHHHHHHHHHhCC----CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccce
Q 027749           55 KPSAIQQRAVMPIIKG----RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~----~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (219)
                      .+++-|..++..+...    +..++.|.||||||.+|+-.+-..+...   ..+|+++|-.+|-.|+.++++...   +.
T Consensus       198 ~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~i~~~L~~G---kqvLvLVPEI~Ltpq~~~rf~~rF---g~  271 (730)
T COG1198         198 ALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLEAIAKVLAQG---KQVLVLVPEIALTPQLLARFKARF---GA  271 (730)
T ss_pred             ccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHHHHHHHHHcC---CEEEEEeccccchHHHHHHHHHHh---CC
Confidence            5678899999888655    6799999999999999988766666553   459999999999999999998765   36


Q ss_pred             eEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhc-----cccHHHHHHHHH
Q 027749          131 QAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS-----RGFKDQIYDVYR  201 (219)
Q Consensus       131 ~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~-----~~~~~~~~~i~~  201 (219)
                      ++..++++.+..++...+    .+...|+|||--.       -...++++++|||||-|.-.-     +.|...=..+++
T Consensus       272 ~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSA-------lF~Pf~~LGLIIvDEEHD~sYKq~~~prYhARdvA~~R  344 (730)
T COG1198         272 KVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSA-------LFLPFKNLGLIIVDEEHDSSYKQEDGPRYHARDVAVLR  344 (730)
T ss_pred             ChhhhcccCChHHHHHHHHHHhcCCceEEEEechh-------hcCchhhccEEEEeccccccccCCcCCCcCHHHHHHHH
Confidence            666677777765554333    3578999999311       124679999999999996331     112222233344


Q ss_pred             hCCCCCeEEEEeecccC
Q 027749          202 YLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       202 ~~~~~~q~i~~SATl~~  218 (219)
                      .-..++++|+-|||-+-
T Consensus       345 a~~~~~pvvLgSATPSL  361 (730)
T COG1198         345 AKKENAPVVLGSATPSL  361 (730)
T ss_pred             HHHhCCCEEEecCCCCH
Confidence            43457899999999764

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

Probab=99.35  E-value=1.9e-11  Score=110.64  Aligned_cols=155  Identities=15%  Similarity=0.155  Sum_probs=108.8

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh-ccccceeEE
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI-GDFINIQAH  133 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~-~~~~~~~~~  133 (219)
                      .-+....+.+..+.+..-++|+|+||+|||...-..+++.-.  ..+..+.++=|++--|..+.+++.+- ....|-.|.
T Consensus        50 Pv~~~~~~i~~ai~~~~vvii~getGsGKTTqlP~~lle~g~--~~~g~I~~tQPRRlAArsvA~RvAeel~~~~G~~VG  127 (845)
T COG1643          50 PVTAVRDEILKAIEQNQVVIIVGETGSGKTTQLPQFLLEEGL--GIAGKIGCTQPRRLAARSVAERVAEELGEKLGETVG  127 (845)
T ss_pred             CcHHHHHHHHHHHHhCCEEEEeCCCCCChHHHHHHHHHhhhc--ccCCeEEecCchHHHHHHHHHHHHHHhCCCcCceee
Confidence            445666667777788888999999999999665555555444  23446889999998888888888444 333343333


Q ss_pred             EEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchh-hhcccc-HHHHHHHHHhCCCCCeEEE
Q 027749          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDE-MLSRGF-KDQIYDVYRYLPPDLQVCC  211 (219)
Q Consensus       134 ~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~-l~~~~~-~~~~~~i~~~~~~~~q~i~  211 (219)
                      +.+...+.      ...+..|-+.|.+.|+..+.+... ++.+++||+||+|. .++..+ ...+..++...+.+..+|+
T Consensus       128 Y~iRfe~~------~s~~Trik~mTdGiLlrei~~D~~-Ls~ys~vIiDEaHERSl~tDilLgllk~~~~~rr~DLKiIi  200 (845)
T COG1643         128 YSIRFESK------VSPRTRIKVMTDGILLREIQNDPL-LSGYSVVIIDEAHERSLNTDILLGLLKDLLARRRDDLKLII  200 (845)
T ss_pred             EEEEeecc------CCCCceeEEeccHHHHHHHhhCcc-cccCCEEEEcchhhhhHHHHHHHHHHHHHHhhcCCCceEEE
Confidence            33222221      123468999999999998876653 89999999999995 222222 3445666777777899999


Q ss_pred             EeecccC
Q 027749          212 PGSCFLF  218 (219)
Q Consensus       212 ~SATl~~  218 (219)
                      +|||+..
T Consensus       201 mSATld~  207 (845)
T COG1643         201 MSATLDA  207 (845)
T ss_pred             EecccCH
Confidence            9999865

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

Probab=99.34  E-value=7e-12  Score=110.96  Aligned_cols=149  Identities=17%  Similarity=0.165  Sum_probs=106.5

Q ss_pred             CCChHHHHHHHHHH----hCCC-cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhcccc
Q 027749           54 EKPSAIQQRAVMPI----IKGR-DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI  128 (219)
Q Consensus        54 ~~~~~~Q~~~~~~~----~~~~-~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~  128 (219)
                      ..|+++|..|+..+    .+|+ .+++++.||+|||..+ +.++.++.+.+...++|||+-+++|+.|.+..+..+....
T Consensus       164 i~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTA-iaii~rL~r~~~~KRVLFLaDR~~Lv~QA~~af~~~~P~~  242 (875)
T COG4096         164 IGPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTA-IAIIDRLIKSGWVKRVLFLADRNALVDQAYGAFEDFLPFG  242 (875)
T ss_pred             ccchHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeH-HHHHHHHHhcchhheeeEEechHHHHHHHHHHHHHhCCCc
Confidence            36899999999765    3453 5999999999999665 4577888877777889999999999999999988876553


Q ss_pred             ceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcC-----CCCCCCccEEEeccchhhhccccHHHHHHHHHhC
Q 027749          129 NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK-----TLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL  203 (219)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~-----~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~  203 (219)
                      . ....+.+...        ...++|.|+|..++...+.+.     .+....+++||+||||+-+    ....+.|+.++
T Consensus       243 ~-~~n~i~~~~~--------~~s~~i~lsTyqt~~~~~~~~~~~~~~f~~g~FDlIvIDEaHRgi----~~~~~~I~dYF  309 (875)
T COG4096         243 T-KMNKIEDKKG--------DTSSEIYLSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHRGI----YSEWSSILDYF  309 (875)
T ss_pred             c-ceeeeecccC--------CcceeEEEeehHHHHhhhhccccccccCCCCceeEEEechhhhhH----HhhhHHHHHHH
Confidence            2 2222211111        115899999999999887765     3455678999999999844    33344666665


Q ss_pred             CCCCeEEEEeecccC
Q 027749          204 PPDLQVCCPGSCFLF  218 (219)
Q Consensus       204 ~~~~q~i~~SATl~~  218 (219)
                      ..-  .++++||...
T Consensus       310 dA~--~~gLTATP~~  322 (875)
T COG4096         310 DAA--TQGLTATPKE  322 (875)
T ss_pred             HHH--HHhhccCccc
Confidence            432  3344887643

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=99.25  E-value=2.2e-10  Score=106.10  Aligned_cols=153  Identities=12%  Similarity=0.076  Sum_probs=102.8

Q ss_pred             CChHHHHHHHHHHh----CCCcEEEEcCCCCchhHHhHHHHHhhhc-cCCCceeEEEEcCCHHHHHHHHHHHHHhccccc
Q 027749           55 KPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVD-TSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~----~~~~~lv~~~tG~GKT~~~~~~~~~~~~-~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (219)
                      .+.++|...+..+.    +|.+.|+.-.+|.|||+..+..+ ..+. .......+|||||. ++..++.+++.+++.  .
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            67899999987764    67789999999999997654433 3332 22222348999995 566889999999875  3


Q ss_pred             eeEEEEECCcccHHHHHH---hcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCC
Q 027749          130 IQAHACVGGKSVGEDIRK---LEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPD  206 (219)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~---l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~  206 (219)
                      +++..+.|..........   ....++|+|+|.+.+.....  .+.--..++|||||||++-+.  ...+...++.+.. 
T Consensus       245 l~v~~~~G~~~eR~~~~~~~~~~~~~dVvITSYe~l~~e~~--~L~k~~W~~VIvDEAHrIKN~--~Sklskalr~L~a-  319 (1033)
T PLN03142        245 LRAVKFHGNPEERAHQREELLVAGKFDVCVTSFEMAIKEKT--ALKRFSWRYIIIDEAHRIKNE--NSLLSKTMRLFST-  319 (1033)
T ss_pred             CceEEEeCCHHHHHHHHHHHhcccCCCcceecHHHHHHHHH--HhccCCCCEEEEcCccccCCH--HHHHHHHHHHhhc-
Confidence            566666665543322211   13468999999988765322  111224578999999997764  3445556666643 


Q ss_pred             CeEEEEeecc
Q 027749          207 LQVCCPGSCF  216 (219)
Q Consensus       207 ~q~i~~SATl  216 (219)
                      ...+++|+|.
T Consensus       320 ~~RLLLTGTP  329 (1033)
T PLN03142        320 NYRLLITGTP  329 (1033)
T ss_pred             CcEEEEecCC
Confidence            4568899995

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

Probab=99.24  E-value=1.9e-10  Score=107.10  Aligned_cols=63  Identities=21%  Similarity=0.193  Sum_probs=53.0

Q ss_pred             CChHHHHHHHHHH----hCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHH
Q 027749           55 KPSAIQQRAVMPI----IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (219)
Q Consensus        55 ~~~~~Q~~~~~~~----~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~  119 (219)
                      .++|-|.+....+    .+++.+++.||||+|||++|++|++......  +.+++|-++|..|-+|+..
T Consensus       257 e~R~~Q~~m~~~v~~~l~~~~~~~iEA~TGtGKTlaYLlpa~~~a~~~--~~~vvIsT~T~~LQ~Ql~~  323 (928)
T PRK08074        257 EKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAYLLPAAYFAKKK--EEPVVISTYTIQLQQQLLE  323 (928)
T ss_pred             cCCHHHHHHHHHHHHHHhcCCCEEEECCCCCchhHHHHHHHHHHhhcc--CCeEEEEcCCHHHHHHHHH
Confidence            7899999966554    4678899999999999999999998766544  3469999999999999876

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=99.23  E-value=9.6e-11  Score=105.90  Aligned_cols=127  Identities=18%  Similarity=0.242  Sum_probs=98.2

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEE
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (219)
                      .|+++|...--.+..  .-|....||.|||+++.+|++.......   .+-+++|+.-||.+-++.+..+....++++.+
T Consensus        82 ~~ydVQliGg~~Lh~--G~iaEM~TGEGKTLvA~l~a~l~al~G~---~VhvvT~ndyLA~RD~e~m~~l~~~lGl~v~~  156 (913)
T PRK13103         82 RHFDVQLIGGMTLHE--GKIAEMRTGEGKTLVGTLAVYLNALSGK---GVHVVTVNDYLARRDANWMRPLYEFLGLSVGI  156 (913)
T ss_pred             CcchhHHHhhhHhcc--CccccccCCCCChHHHHHHHHHHHHcCC---CEEEEeCCHHHHHHHHHHHHHHhcccCCEEEE
Confidence            788888655444433  4688999999999999999887766643   48999999999999999999999999999999


Q ss_pred             EECCcccHHHHHHhcCCCeEEEeChHHHH-HHHHcC------CCCCCCccEEEeccchhhh
Q 027749          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVC-DMIKRK------TLRTRAIKLLVLDESDEML  188 (219)
Q Consensus       135 ~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~-~~l~~~------~~~~~~l~~lVvDE~h~l~  188 (219)
                      +.++.+..++...+  .|+|+++|...|- ++|..+      ......+.+.||||+|.++
T Consensus       157 i~~~~~~~err~~Y--~~dI~YGT~~e~gFDYLrD~~~~~~~~~vqr~l~~aIVDEvDsiL  215 (913)
T PRK13103        157 VTPFQPPEEKRAAY--AADITYGTNNEFGFDYLRDNMAFSLDDKFQRELNFAVIDEVDSIL  215 (913)
T ss_pred             ECCCCCHHHHHHHh--cCCEEEEcccccccchhhccceechhhhcccccceeEechhhhee
Confidence            88877766554443  4999999988762 223221      1123778999999999866

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.17  E-value=3.5e-10  Score=104.36  Aligned_cols=157  Identities=18%  Similarity=0.078  Sum_probs=94.4

Q ss_pred             CChHHHHHHHHHHhCC--CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeE
Q 027749           55 KPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQA  132 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~--~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  132 (219)
                      .|.|+|.++...+...  ..+++.-.+|.|||.-+.+.+...+... ...++|||||. .|..|+..++.+..   ++..
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            6899999998776543  4789999999999977766544444433 33469999997 79999999986543   2222


Q ss_pred             EEEECCcccHHHHH---HhcCCCeEEEeChHHHHHHHH-cCCCCCCCccEEEeccchhhhcc-ccHHHHHHHHHhC-CCC
Q 027749          133 HACVGGKSVGEDIR---KLEHGVHVVSGTPGRVCDMIK-RKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYL-PPD  206 (219)
Q Consensus       133 ~~~~~~~~~~~~~~---~l~~~~~I~v~Tp~~l~~~l~-~~~~~~~~l~~lVvDE~h~l~~~-~~~~~~~~i~~~~-~~~  206 (219)
                      ..+ ++........   ......+++|+|.+.+...-. ...+.-...++|||||||++-.. +-.......++.+ .+.
T Consensus       227 ~i~-~~~~~~~~~~~~~~pf~~~~~vI~S~~~l~~~~~~~~~l~~~~wdlvIvDEAH~lk~~~~~~s~~y~~v~~La~~~  305 (956)
T PRK04914        227 SLF-DEERYAEAQHDADNPFETEQLVICSLDFLRRNKQRLEQALAAEWDLLVVDEAHHLVWSEEAPSREYQVVEQLAEVI  305 (956)
T ss_pred             EEE-cCcchhhhcccccCccccCcEEEEEHHHhhhCHHHHHHHhhcCCCEEEEechhhhccCCCCcCHHHHHHHHHhhcc
Confidence            222 2211111000   111246899999876653110 01122246789999999998631 1011112223333 234


Q ss_pred             CeEEEEeeccc
Q 027749          207 LQVCCPGSCFL  217 (219)
Q Consensus       207 ~q~i~~SATl~  217 (219)
                      ..++++|||.-
T Consensus       306 ~~~LLLTATP~  316 (956)
T PRK04914        306 PGVLLLTATPE  316 (956)
T ss_pred             CCEEEEEcCcc
Confidence            46899999963

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

Probab=99.16  E-value=8e-11  Score=107.80  Aligned_cols=150  Identities=17%  Similarity=0.226  Sum_probs=117.0

Q ss_pred             CChHHHHHHHHHHh-CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHH-HhccccceeE
Q 027749           55 KPSAIQQRAVMPII-KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL-AIGDFINIQA  132 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~-~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~-~~~~~~~~~~  132 (219)
                      ..+|+|.++++.+- .+.+++|.+|+|+|||.|+-++++.    .....++++++|..+.+..+++.+. ++.+..|..+
T Consensus      1143 ~~n~iqtqVf~~~y~~nd~v~vga~~gsgkt~~ae~a~l~----~~~~~~~vyi~p~~~i~~~~~~~w~~~f~~~~G~~~ 1218 (1674)
T KOG0951|consen 1143 DFNPIQTQVFTSLYNTNDNVLVGAPNGSGKTACAELALLR----PDTIGRAVYIAPLEEIADEQYRDWEKKFSKLLGLRI 1218 (1674)
T ss_pred             ccCCceEEEEeeeecccceEEEecCCCCchhHHHHHHhcC----CccceEEEEecchHHHHHHHHHHHHHhhccccCceE
Confidence            44888999998865 4568999999999999999888776    3345679999999999998888884 4555567777


Q ss_pred             EEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccc------cHHHHHHHHHhCCCC
Q 027749          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG------FKDQIYDVYRYLPPD  206 (219)
Q Consensus       133 ~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~------~~~~~~~i~~~~~~~  206 (219)
                      ..+.|..+.+-   ++....+|+|+||+++..+-     ..+.+++.|+||+|.+...+      ... ++++-.++-++
T Consensus      1219 ~~l~ge~s~~l---kl~~~~~vii~tpe~~d~lq-----~iQ~v~l~i~d~lh~igg~~g~v~evi~S-~r~ia~q~~k~ 1289 (1674)
T KOG0951|consen 1219 VKLTGETSLDL---KLLQKGQVIISTPEQWDLLQ-----SIQQVDLFIVDELHLIGGVYGAVYEVICS-MRYIASQLEKK 1289 (1674)
T ss_pred             EecCCccccch---HHhhhcceEEechhHHHHHh-----hhhhcceEeeehhhhhcccCCceEEEEee-HHHHHHHHHhh
Confidence            77777666542   34455799999999998772     57889999999999877432      113 77888888888


Q ss_pred             CeEEEEeeccc
Q 027749          207 LQVCCPGSCFL  217 (219)
Q Consensus       207 ~q~i~~SATl~  217 (219)
                      .+++.+|..+.
T Consensus      1290 ir~v~ls~~la 1300 (1674)
T KOG0951|consen 1290 IRVVALSSSLA 1300 (1674)
T ss_pred             eeEEEeehhhc
Confidence            89999987764

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.15  E-value=3.3e-10  Score=101.90  Aligned_cols=130  Identities=17%  Similarity=0.261  Sum_probs=102.0

Q ss_pred             CCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccce
Q 027749           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (219)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (219)
                      .|. .|++.|....-.+..|+  +....||.|||+++.+|++..+....   .+-+++|+.-||.+-++.+..+....|+
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--IAEMKTGEGKTLTATLPVYLNALTGK---GVHVVTVNEYLSSRDATEMGELYRWLGL  150 (796)
T ss_pred             hCC-CCchhHHHHHHHHhcCC--cccccCCCCCcHHHHHHHHHHHHcCC---CeEEEeccHHHHHhhHHHHHHHHHhcCC
Confidence            344 78999977766665664  89999999999999999888777654   3899999999999999999999999999


Q ss_pred             eEEEEECCcccHHHHHHhcCCCeEEEeChHHHHH-HHHcC------CCCCCCccEEEeccchhhh
Q 027749          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCD-MIKRK------TLRTRAIKLLVLDESDEML  188 (219)
Q Consensus       131 ~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~-~l~~~------~~~~~~l~~lVvDE~h~l~  188 (219)
                      ++.++.++.+..++...  ..|+|..+|...|-. +++.+      ......+.+.||||+|.++
T Consensus       151 ~vg~i~~~~~~~~r~~~--y~~dI~Y~t~~e~gfDyLRD~m~~~~~~~v~r~~~~aIvDEvDSiL  213 (796)
T PRK12906        151 TVGLNLNSMSPDEKRAA--YNCDITYSTNSELGFDYLRDNMVVYKEQMVQRPLNYAIVDEVDSIL  213 (796)
T ss_pred             eEEEeCCCCCHHHHHHH--hcCCCeecCCccccccchhhccccchhhhhccCcceeeeccchhee
Confidence            99999887766554333  378999999887753 33321      1123567899999999765

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=99.14  E-value=5.3e-10  Score=99.08  Aligned_cols=130  Identities=14%  Similarity=0.217  Sum_probs=102.6

Q ss_pred             CCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccce
Q 027749           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (219)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (219)
                      .|. .|++.|....-.+++|  -+.+..||.|||++..+|++.......   .+-+++|+.-||.+-++.+..+....++
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-RPFDVQLLGALRLLAG--DVIEMATGEGKTLAGAIAAAGYALQGR---RVHVITVNDYLARRDAEWMGPLYEALGL  148 (764)
T ss_pred             cCC-CcchHHHHHHHHHhCC--CcccccCCCCHHHHHHHHHHHHHHcCC---CeEEEcCCHHHHHHHHHHHHHHHHhcCC
Confidence            344 7899998888888776  377999999999999999888776643   4999999999999999999999999999


Q ss_pred             eEEEEECCcccHHHHHHhcCCCeEEEeChHHHHH-HHHcC------CCCCCCccEEEeccchhhh
Q 027749          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCD-MIKRK------TLRTRAIKLLVLDESDEML  188 (219)
Q Consensus       131 ~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~-~l~~~------~~~~~~l~~lVvDE~h~l~  188 (219)
                      ++.+..++.+..+....+  .|+|..+|...|-. +++.+      ......+.+.||||+|.++
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            999988877765544333  68999999887643 33221      1123567899999999766

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

Probab=99.13  E-value=1.5e-09  Score=94.39  Aligned_cols=154  Identities=14%  Similarity=0.157  Sum_probs=99.1

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHH-hccccceeEE
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA-IGDFINIQAH  133 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~-~~~~~~~~~~  133 (219)
                      .-+..-.+.+..+.++.-++|.|+||+|||.-.--.+.+.-....+  ++-+.-|+|..|..+..++.. ..-..|-.|.
T Consensus        51 PI~~~r~~il~~ve~nqvlIviGeTGsGKSTQipQyL~eaG~~~~g--~I~~TQPRRVAavslA~RVAeE~~~~lG~~VG  128 (674)
T KOG0922|consen   51 PIYKYRDQILYAVEDNQVLIVIGETGSGKSTQIPQYLAEAGFASSG--KIACTQPRRVAAVSLAKRVAEEMGCQLGEEVG  128 (674)
T ss_pred             CHHHHHHHHHHHHHHCCEEEEEcCCCCCccccHhHHHHhcccccCC--cEEeecCchHHHHHHHHHHHHHhCCCcCceee
Confidence            3455566677777888889999999999994443333333333322  388889999988888877743 3333344443


Q ss_pred             EEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhh--hccccHHHHHHHHHhCCCCCeEEE
Q 027749          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM--LSRGFKDQIYDVYRYLPPDLQVCC  211 (219)
Q Consensus       134 ~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l--~~~~~~~~~~~i~~~~~~~~q~i~  211 (219)
                      ..+.-.+...      ....|.+.|-+.|++-+.... .+++..+||+||||.=  ..+-....++++++. +++..+|+
T Consensus       129 Y~IRFed~ts------~~TrikymTDG~LLRE~l~Dp-~LskYsvIIlDEAHERsl~TDiLlGlLKki~~~-R~~LklIi  200 (674)
T KOG0922|consen  129 YTIRFEDSTS------KDTRIKYMTDGMLLREILKDP-LLSKYSVIILDEAHERSLHTDILLGLLKKILKK-RPDLKLII  200 (674)
T ss_pred             eEEEecccCC------CceeEEEecchHHHHHHhcCC-ccccccEEEEechhhhhhHHHHHHHHHHHHHhc-CCCceEEE
Confidence            3321111111      246899999999998666544 4789999999999951  111122333344333 34688999


Q ss_pred             EeecccC
Q 027749          212 PGSCFLF  218 (219)
Q Consensus       212 ~SATl~~  218 (219)
                      +|||+..
T Consensus       201 mSATlda  207 (674)
T KOG0922|consen  201 MSATLDA  207 (674)
T ss_pred             EeeeecH
Confidence            9999865

>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=99.13  E-value=2.7e-09  Score=85.24  Aligned_cols=131  Identities=20%  Similarity=0.315  Sum_probs=96.8

Q ss_pred             HCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccc
Q 027749           50 QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (219)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (219)
                      ..|+ .|++.|..++-.+..|+  +++..||-|||++..++++......   ..+=|++.+..||..=.+.+..+....|
T Consensus        73 ~~g~-~p~~vQll~~l~L~~G~--laEm~TGEGKTli~~l~a~~~AL~G---~~V~vvT~NdyLA~RD~~~~~~~y~~LG  146 (266)
T PF07517_consen   73 TLGL-RPYDVQLLGALALHKGR--LAEMKTGEGKTLIAALPAALNALQG---KGVHVVTSNDYLAKRDAEEMRPFYEFLG  146 (266)
T ss_dssp             HTS-----HHHHHHHHHHHTTS--EEEESTTSHHHHHHHHHHHHHHTTS---S-EEEEESSHHHHHHHHHHHHHHHHHTT
T ss_pred             HcCC-cccHHHHhhhhhcccce--eEEecCCCCcHHHHHHHHHHHHHhc---CCcEEEeccHHHhhccHHHHHHHHHHhh
Confidence            3444 79999988887776664  9999999999999888877766653   3488999999999999999999999999


Q ss_pred             eeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHH-HHHcCC------CCCCCccEEEeccchhhh
Q 027749          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCD-MIKRKT------LRTRAIKLLVLDESDEML  188 (219)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~-~l~~~~------~~~~~l~~lVvDE~h~l~  188 (219)
                      +++....++.+..++...  ..++|+.+|...|.. .++.+.      .....+.++||||+|.++
T Consensus       147 lsv~~~~~~~~~~~r~~~--Y~~dI~Y~t~~~~~fD~Lrd~~~~~~~~~~~r~~~~~ivDEvDs~L  210 (266)
T PF07517_consen  147 LSVGIITSDMSSEERREA--YAADIVYGTNSEFGFDYLRDNLALSKNEQVQRGFDFAIVDEVDSIL  210 (266)
T ss_dssp             --EEEEETTTEHHHHHHH--HHSSEEEEEHHHHHHHHHHHTT-SSGGG--SSSSSEEEECTHHHHT
T ss_pred             hccccCccccCHHHHHHH--HhCcccccccchhhHHHHHHHHhhccchhccCCCCEEEEeccceEE
Confidence            999999988876543333  357899999998865 443221      123678899999999876

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 ....

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=99.08  E-value=1.7e-09  Score=98.35  Aligned_cols=73  Identities=19%  Similarity=0.194  Sum_probs=62.4

Q ss_pred             CCCCChHHHHHHHHHH----hCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 027749           52 GFEKPSAIQQRAVMPI----IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (219)
Q Consensus        52 ~~~~~~~~Q~~~~~~~----~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (219)
                      -|..++|.|.+.+..+    ..+++.++.+|||+|||++.+.+.+......+..++++|.+.|+....|+.+++++.
T Consensus         7 Py~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~~~~kIiy~sRThsQl~q~i~Elk~~   83 (705)
T TIGR00604         7 PYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKPEVRKIIYASRTHSQLEQATEELRKL   83 (705)
T ss_pred             CCCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhccccccEEEEcccchHHHHHHHHHHhh
Confidence            4556699999877654    477899999999999999999999988776555578999999999999999999885

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).

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=99.07  E-value=1.5e-09  Score=99.44  Aligned_cols=163  Identities=17%  Similarity=0.103  Sum_probs=96.7

Q ss_pred             CCChHHHHHHHHHHhC--------CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhc
Q 027749           54 EKPSAIQQRAVMPIIK--------GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIG  125 (219)
Q Consensus        54 ~~~~~~Q~~~~~~~~~--------~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  125 (219)
                      ...+.||.+|+..+..        |--++-.|.||+|||++=.- +++.+.....+.+..|-...|.|--|--+.+++-.
T Consensus       407 ~~rF~WQdkA~d~a~~~r~~~~~~GfF~vNMASTGcGKT~aNAR-ImyaLsd~~~g~RfsiALGLRTLTLQTGda~r~rL  485 (1110)
T TIGR02562       407 HPRFRWQNKAFNLAQKLRQKSPEQGAFGVNMASTGCGKTLANAR-AMYALRDDKQGARFAIALGLRSLTLQTGHALKTRL  485 (1110)
T ss_pred             CCCcchHHHHHHHHHHHHhhcccCCeEEEEecCCCcchHHHHHH-HHHHhCCCCCCceEEEEccccceeccchHHHHHhc
Confidence            3557799999988752        22355668999999965433 34444455556666666666666666666665544


Q ss_pred             cccceeEEEEECCcccHHH-------------------------------------------HHHhcC--------CCeE
Q 027749          126 DFINIQAHACVGGKSVGED-------------------------------------------IRKLEH--------GVHV  154 (219)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~-------------------------------------------~~~l~~--------~~~I  154 (219)
                      .-.+-....++|+....+.                                           ...+.+        .+.|
T Consensus       486 ~L~~ddLAVlIGs~Av~~L~e~~~~~~~~~~~~GSeS~e~l~~e~~~~~~~~~~g~l~~~~l~~~l~~~~k~~rll~apv  565 (1110)
T TIGR02562       486 NLSDDDLAVLIGGTAVQTLFDLSKEKIEQVDEDGSESAPIFLAEGQDCNLPDWDGPLDTIELLGRLSLDDKEKTLLAAPV  565 (1110)
T ss_pred             CCCccceEEEECHHHHHHHHHHHhhhccccccCCCccchhhhcccCcCCeeeccCCccchhhhhhhccChhhhhhhcCCe
Confidence            3322222233332221110                                           000100        2579


Q ss_pred             EEeChHHHHHHHHc-C--CCCCC--C--ccEEEeccchhhhccccHHHHHHHHHhCC-CCCeEEEEeecccC
Q 027749          155 VSGTPGRVCDMIKR-K--TLRTR--A--IKLLVLDESDEMLSRGFKDQIYDVYRYLP-PDLQVCCPGSCFLF  218 (219)
Q Consensus       155 ~v~Tp~~l~~~l~~-~--~~~~~--~--l~~lVvDE~h~l~~~~~~~~~~~i~~~~~-~~~q~i~~SATl~~  218 (219)
                      +|||++.++..... +  ...+.  .  =+.|||||+|. ++......+.+++..+. ....++++|||+|+
T Consensus       566 ~V~TIDQlL~a~~~~r~~~~~l~ll~La~svlVlDEVHa-YD~~~~~~L~rlL~w~~~lG~~VlLmSATLP~  636 (1110)
T TIGR02562       566 LVCTIDHLIPATESHRGGHHIAPMLRLMSSDLILDEPDD-YEPEDLPALLRLVQLAGLLGSRVLLSSATLPP  636 (1110)
T ss_pred             EEecHHHHHHHhhhcccchhHHHHHHhcCCCEEEECCcc-CCHHHHHHHHHHHHHHHHcCCCEEEEeCCCCH
Confidence            99999999987632 1  11111  1  24699999996 44444555666666432 26789999999996

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.

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

Probab=99.01  E-value=5.6e-09  Score=87.97  Aligned_cols=179  Identities=13%  Similarity=0.093  Sum_probs=114.0

Q ss_pred             CccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcC
Q 027749           30 EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (219)
Q Consensus        30 ~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P  109 (219)
                      +.+..|+..|++++..+.|+++.-...|..+.+.+..+.++.-++++|.||+|||.-.--+++........  .+...-|
T Consensus        22 k~~Npf~~~p~s~rY~~ilk~R~~LPvw~~k~~F~~~l~~nQ~~v~vGetgsGKttQiPq~~~~~~~~~~~--~v~CTQp   99 (699)
T KOG0925|consen   22 KAINPFNGKPYSQRYYDILKKRRELPVWEQKEEFLKLLLNNQIIVLVGETGSGKTTQIPQFVLEYELSHLT--GVACTQP   99 (699)
T ss_pred             hhcCCCCCCcCcHHHHHHHHHHhcCchHHhHHHHHHHHhcCceEEEEecCCCCccccCcHHHHHHHHhhcc--ceeecCc
Confidence            34788999999999999999876556677777777778888889999999999996665566665554432  3777889


Q ss_pred             CHHHHHHHHHHHHHhcc-ccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhh
Q 027749          110 TRELATQTEKVILAIGD-FINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (219)
Q Consensus       110 ~~~l~~q~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~  188 (219)
                      .+..|.++..+..+-+. ..|..+...+.-.+......      -.-.+|.+.|++-..+.. .+.+.+.||+||||.=.
T Consensus       100 rrvaamsva~RVadEMDv~lG~EVGysIrfEdC~~~~T------~Lky~tDgmLlrEams~p-~l~~y~viiLDeahERt  172 (699)
T KOG0925|consen  100 RRVAAMSVAQRVADEMDVTLGEEVGYSIRFEDCTSPNT------LLKYCTDGMLLREAMSDP-LLGRYGVIILDEAHERT  172 (699)
T ss_pred             hHHHHHHHHHHHHHHhccccchhccccccccccCChhH------HHHHhcchHHHHHHhhCc-ccccccEEEechhhhhh
Confidence            99988888877744321 11222211111111000000      011234444444222222 36788999999999521


Q ss_pred             --ccccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          189 --SRGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       189 --~~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                        ..-....++.++..- ++..+|.+|||+-+
T Consensus       173 lATDiLmGllk~v~~~r-pdLk~vvmSatl~a  203 (699)
T KOG0925|consen  173 LATDILMGLLKEVVRNR-PDLKLVVMSATLDA  203 (699)
T ss_pred             HHHHHHHHHHHHHHhhC-CCceEEEeecccch
Confidence              122344556666655 48999999999854

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

Probab=98.96  E-value=7.5e-10  Score=93.48  Aligned_cols=148  Identities=20%  Similarity=0.204  Sum_probs=101.0

Q ss_pred             CChHHHHHHHHHHh-CC--CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhcccccee
Q 027749           55 KPSAIQQRAVMPII-KG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ  131 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~-~~--~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  131 (219)
                      .++|+|..++..+. +|  ++.+|+.|.|+|||++-+-+++..      +..+|+++.+...+.|+...+..|...-+-.
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            56899999998876 33  589999999999997765544322      2349999999999999999999997665555


Q ss_pred             EEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCC---------CCCCCccEEEeccchhhhccccHHHHHHHHHh
Q 027749          132 AHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT---------LRTRAIKLLVLDESDEMLSRGFKDQIYDVYRY  202 (219)
Q Consensus       132 ~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~---------~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~  202 (219)
                      ++.+.+..+     .....++.|+|+|...+..--+ +.         +.-+.-+++++||+|.+-..-|+..+.-+-.+
T Consensus       376 i~rFTsd~K-----e~~~~~~gvvvsTYsMva~t~k-RS~eaek~m~~l~~~EWGllllDEVHvvPA~MFRRVlsiv~aH  449 (776)
T KOG1123|consen  376 ICRFTSDAK-----ERFPSGAGVVVTTYSMVAYTGK-RSHEAEKIMDFLRGREWGLLLLDEVHVVPAKMFRRVLSIVQAH  449 (776)
T ss_pred             eEEeecccc-----ccCCCCCcEEEEeeehhhhccc-ccHHHHHHHHHHhcCeeeeEEeehhccchHHHHHHHHHHHHHH
Confidence            554443322     1234589999999754332111 11         11133578999999987655555555544444


Q ss_pred             CCCCCeEEEEeecccCC
Q 027749          203 LPPDLQVCCPGSCFLFD  219 (219)
Q Consensus       203 ~~~~~q~i~~SATl~~~  219 (219)
                      +     .++++|||=.|
T Consensus       450 c-----KLGLTATLvRE  461 (776)
T KOG1123|consen  450 C-----KLGLTATLVRE  461 (776)
T ss_pred             h-----hccceeEEeec
Confidence            4     38999998543

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

Probab=98.95  E-value=9.6e-09  Score=95.66  Aligned_cols=137  Identities=14%  Similarity=0.116  Sum_probs=95.1

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcC
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH  150 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  150 (219)
                      +..+||.-+|||||+.....+ +.+......|.++||+-++.|-.|..+.+..+........    ...+..+....+..
T Consensus       274 ~~G~IWHtqGSGKTlTm~~~A-~~l~~~~~~~~v~fvvDR~dLd~Q~~~~f~~~~~~~~~~~----~~~s~~~Lk~~l~~  348 (962)
T COG0610         274 KGGYIWHTQGSGKTLTMFKLA-RLLLELPKNPKVLFVVDRKDLDDQTSDEFQSFGKVAFNDP----KAESTSELKELLED  348 (962)
T ss_pred             CceEEEeecCCchHHHHHHHH-HHHHhccCCCeEEEEechHHHHHHHHHHHHHHHHhhhhcc----cccCHHHHHHHHhc
Confidence            468999999999997765543 3343346778999999999999999999998865532222    34455555555554


Q ss_pred             C-CeEEEeChHHHHHHHHcC-CCCCCCc-cEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEeecc
Q 027749          151 G-VHVVSGTPGRVCDMIKRK-TLRTRAI-KLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCF  216 (219)
Q Consensus       151 ~-~~I~v~Tp~~l~~~l~~~-~~~~~~l-~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl  216 (219)
                      + -.|+|+|-++|....... .....+- -.||+||||+-.   ++..-..+...++ +...++||+|.
T Consensus       349 ~~~~ii~TTIQKf~~~~~~~~~~~~~~~~ivvI~DEaHRSQ---~G~~~~~~~~~~~-~a~~~gFTGTP  413 (962)
T COG0610         349 GKGKIIVTTIQKFNKAVKEDELELLKRKNVVVIIDEAHRSQ---YGELAKLLKKALK-KAIFIGFTGTP  413 (962)
T ss_pred             CCCcEEEEEecccchhhhcccccccCCCcEEEEEechhhcc---ccHHHHHHHHHhc-cceEEEeeCCc
Confidence            4 489999999999988664 1112222 268999999843   3333344444444 37899999985

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=98.94  E-value=5.8e-09  Score=94.20  Aligned_cols=131  Identities=18%  Similarity=0.214  Sum_probs=98.5

Q ss_pred             HCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccc
Q 027749           50 QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (219)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (219)
                      ..|. .|++.|....  +.-.+.-+....||-|||+++.+|++......   ..+-|++++..||.+-.+.+..+....|
T Consensus        72 ~lG~-r~ydvQlig~--l~L~~G~IaEm~TGEGKTL~a~l~ayl~aL~G---~~VhVvT~NdyLA~RD~e~m~pvy~~LG  145 (870)
T CHL00122         72 TLGL-RHFDVQLIGG--LVLNDGKIAEMKTGEGKTLVATLPAYLNALTG---KGVHIVTVNDYLAKRDQEWMGQIYRFLG  145 (870)
T ss_pred             HhCC-CCCchHhhhh--HhhcCCccccccCCCCchHHHHHHHHHHHhcC---CceEEEeCCHHHHHHHHHHHHHHHHHcC
Confidence            3455 6888886554  33345678999999999999999987655543   3489999999999999999999999999


Q ss_pred             eeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHH-HHHcC------CCCCCCccEEEeccchhhh
Q 027749          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCD-MIKRK------TLRTRAIKLLVLDESDEML  188 (219)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~-~l~~~------~~~~~~l~~lVvDE~h~l~  188 (219)
                      +++.+..++.+..++...  ..|+|..+|...|-. .++-+      ......+.+.||||+|.++
T Consensus       146 Lsvg~i~~~~~~~err~a--Y~~DItYgTn~e~gFDyLRDnm~~~~~~~v~r~~~faIVDEvDSiL  209 (870)
T CHL00122        146 LTVGLIQEGMSSEERKKN--YLKDITYVTNSELGFDYLRDNMALSLSDVVQRPFNYCIIDEVDSIL  209 (870)
T ss_pred             CceeeeCCCCChHHHHHh--cCCCCEecCCccccccchhhccCcChHHhhccccceeeeecchhhe
Confidence            999988877776654433  468999999876642 33221      1123568899999999766

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

Probab=98.93  E-value=1e-08  Score=90.93  Aligned_cols=151  Identities=17%  Similarity=0.130  Sum_probs=91.6

Q ss_pred             HHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCC---CceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEEC
Q 027749           61 QRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS---REVQALILSPTRELATQTEKVILAIGDFINIQAHACVG  137 (219)
Q Consensus        61 ~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~---~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~  137 (219)
                      ++++..+..+.-+||||.||+|||.-.---++..=..+.   .+.-+=|.-|+|..|..+..+...-+...+..+...+.
T Consensus       262 q~IMEaIn~n~vvIIcGeTGsGKTTQvPQFLYEAGf~s~~~~~~gmIGITqPRRVAaiamAkRVa~EL~~~~~eVsYqIR  341 (1172)
T KOG0926|consen  262 QRIMEAINENPVVIICGETGSGKTTQVPQFLYEAGFASEQSSSPGMIGITQPRRVAAIAMAKRVAFELGVLGSEVSYQIR  341 (1172)
T ss_pred             HHHHHHhhcCCeEEEecCCCCCccccchHHHHHcccCCccCCCCCeeeecCchHHHHHHHHHHHHHHhccCccceeEEEE
Confidence            345555666667999999999999443222222212221   12246677899988887777764443334444444331


Q ss_pred             CcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhh--cc---ccHHHHHHHHHhCCC------C
Q 027749          138 GKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML--SR---GFKDQIYDVYRYLPP------D  206 (219)
Q Consensus       138 ~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~--~~---~~~~~~~~i~~~~~~------~  206 (219)
                      -..      ....+..|-++|-+.|++-+.+.. .++....||+||||.=.  ..   |+...+..+-..+.+      .
T Consensus       342 fd~------ti~e~T~IkFMTDGVLLrEi~~Df-lL~kYSvIIlDEAHERSvnTDILiGmLSRiV~LR~k~~ke~~~~kp  414 (1172)
T KOG0926|consen  342 FDG------TIGEDTSIKFMTDGVLLREIENDF-LLTKYSVIILDEAHERSVNTDILIGMLSRIVPLRQKYYKEQCQIKP  414 (1172)
T ss_pred             ecc------ccCCCceeEEecchHHHHHHHHhH-hhhhceeEEechhhhccchHHHHHHHHHHHHHHHHHHhhhhcccCc
Confidence            111      112356899999999999887654 47889999999999511  11   222223333333322      5


Q ss_pred             CeEEEEeecccC
Q 027749          207 LQVCCPGSCFLF  218 (219)
Q Consensus       207 ~q~i~~SATl~~  218 (219)
                      ..+|+|||||.-
T Consensus       415 LKLIIMSATLRV  426 (1172)
T KOG0926|consen  415 LKLIIMSATLRV  426 (1172)
T ss_pred             eeEEEEeeeEEe
Confidence            679999999863

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

Probab=98.93  E-value=1.6e-08  Score=79.22  Aligned_cols=68  Identities=21%  Similarity=0.356  Sum_probs=50.6

Q ss_pred             CChHHHHHHHHHHhCCCc-EEEEcCCCCchhHHhHHHHHhhh------ccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 027749           55 KPSAIQQRAVMPIIKGRD-VIAQAQSGTGKTSMIALTVCQTV------DTSSREVQALILSPTRELATQTEKVILA  123 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~-~lv~~~tG~GKT~~~~~~~~~~~------~~~~~~~~~lil~P~~~l~~q~~~~~~~  123 (219)
                      ++++.|..++..+++... .+|+||.|+|||.... .++..+      .....+.++++++|++..++.+.+.+.+
T Consensus         1 ~ln~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~l~-~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen    1 KLNESQREAIQSALSSNGITLIQGPPGTGKTTTLA-SIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             ---HHHHHHHHHHCTSSE-EEEE-STTSSHHHHHH-HHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHcCCCCEEEECCCCCChHHHHH-HHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            357889999999998888 9999999999994433 334433      1234566799999999999999999887

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=98.93  E-value=2.3e-08  Score=90.64  Aligned_cols=64  Identities=27%  Similarity=0.331  Sum_probs=51.9

Q ss_pred             CCCCChHHHHHHHHHHh---C------CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHH
Q 027749           52 GFEKPSAIQQRAVMPII---K------GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE  118 (219)
Q Consensus        52 ~~~~~~~~Q~~~~~~~~---~------~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~  118 (219)
                      || .+++-|.+....+.   .      ++..+|.||||+|||++|++|++......+  .++||=+.|..|-+|+.
T Consensus        23 ~~-e~R~~Q~~M~~~V~~al~~~~~~~~~~lviEAgTGtGKTlaYLlPai~~A~~~~--k~vVIST~T~~LQeQL~   95 (697)
T PRK11747         23 GF-IPRAGQRQMIAEVAKTLAGEYLKDGRILVIEAGTGVGKTLSYLLAGIPIARAEK--KKLVISTATVALQEQLV   95 (697)
T ss_pred             CC-CcCHHHHHHHHHHHHHHhcccccccceEEEECCCCcchhHHHHHHHHHHHHHcC--CeEEEEcCCHHHHHHHH
Confidence            44 68999999766543   3      367899999999999999999988766543  45999999999998886

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

Probab=98.92  E-value=2.2e-08  Score=88.34  Aligned_cols=152  Identities=16%  Similarity=0.148  Sum_probs=102.9

Q ss_pred             CChHHHHHHHHHHh----CCCcEEEEcCCCCchhHHhHHHHHhhhcc--CCCceeEEEEcCCHHHHHHHHHHHHHhcccc
Q 027749           55 KPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVDT--SSREVQALILSPTRELATQTEKVILAIGDFI  128 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~----~~~~~lv~~~tG~GKT~~~~~~~~~~~~~--~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~  128 (219)
                      .+.++|.+.++.+.    +|-+.|+.-.+|-|||+--+ .++..+..  ...+| -+|++|...|. .+.+++.+++.  
T Consensus       167 ~lr~YQveGlnWLi~l~engingILaDEMGLGKTlQtI-s~l~yl~~~~~~~GP-fLVi~P~StL~-NW~~Ef~rf~P--  241 (971)
T KOG0385|consen  167 ELRDYQLEGLNWLISLYENGINGILADEMGLGKTLQTI-SLLGYLKGRKGIPGP-FLVIAPKSTLD-NWMNEFKRFTP--  241 (971)
T ss_pred             ccchhhhccHHHHHHHHhcCcccEeehhcccchHHHHH-HHHHHHHHhcCCCCC-eEEEeeHhhHH-HHHHHHHHhCC--
Confidence            67888988776643    67789999999999995433 33333322  22344 78999987774 57888888876  


Q ss_pred             ceeEEEEECCcccHHHHHH---hcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCC
Q 027749          129 NIQAHACVGGKSVGEDIRK---LEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP  205 (219)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~---l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~  205 (219)
                      ++++..++|.........+   .....+|+|+|.+..++--  ..+.--.-+|+||||+|++-+.  ...+..+++.+..
T Consensus       242 ~l~~~~~~Gdk~eR~~~~r~~~~~~~fdV~iTsYEi~i~dk--~~lk~~~W~ylvIDEaHRiKN~--~s~L~~~lr~f~~  317 (971)
T KOG0385|consen  242 SLNVVVYHGDKEERAALRRDIMLPGRFDVCITSYEIAIKDK--SFLKKFNWRYLVIDEAHRIKNE--KSKLSKILREFKT  317 (971)
T ss_pred             CcceEEEeCCHHHHHHHHHHhhccCCCceEeehHHHHHhhH--HHHhcCCceEEEechhhhhcch--hhHHHHHHHHhcc
Confidence            4788888888764443222   1347899999987665431  1111123468999999998876  4666678888754


Q ss_pred             CCeEEEEeecc
Q 027749          206 DLQVCCPGSCF  216 (219)
Q Consensus       206 ~~q~i~~SATl  216 (219)
                      . ..+++|+|.
T Consensus       318 ~-nrLLlTGTP  327 (971)
T KOG0385|consen  318 D-NRLLLTGTP  327 (971)
T ss_pred             c-ceeEeeCCc
Confidence            3 456677773

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

Probab=98.91  E-value=7.7e-09  Score=93.46  Aligned_cols=74  Identities=22%  Similarity=0.241  Sum_probs=60.8

Q ss_pred             HHCCCCCChHHHHHHHHHHh----CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 027749           49 YQYGFEKPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (219)
Q Consensus        49 ~~~~~~~~~~~Q~~~~~~~~----~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (219)
                      ..+....|++.|.+.+..+.    .++..+++||||+|||++|+.|.+......+  .+++|.++|+.+-.|+.+....+
T Consensus         9 ~~~~~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~~~--~~viist~t~~lq~q~~~~~~~~   86 (654)
T COG1199           9 VAFPGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEG--KKVIISTRTKALQEQLLEEDLPI   86 (654)
T ss_pred             hhCCCCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHHcC--CcEEEECCCHHHHHHHHHhhcch
Confidence            34556689999999886543    5566999999999999999999999887664  56999999999999998877554

>COG4889 Predicted helicase [General function prediction only]

Probab=98.90  E-value=8.5e-09  Score=92.22  Aligned_cols=150  Identities=21%  Similarity=0.222  Sum_probs=96.6

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCC----CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEc
Q 027749           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG----RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (219)
Q Consensus        33 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~----~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~  108 (219)
                      ..|+.+.. ..+..++.-..-++|+|+|+.++.....+    ...-+...+|+|||+..+- +.+.+..    .++|+++
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 IDWDIFDP-TELQDNLPLKKPKKPRPHQQTAIDAAKEGFSDNDRGKLIMACGTGKTFTSLK-ISEALAA----ARILFLV  213 (1518)
T ss_pred             CChhhcCc-cccccccccCCCCCCChhHHHHHHHHHhhcccccCCcEEEecCCCccchHHH-HHHHHhh----hheEeec
Confidence            44555422 34444444445568999999999988754    1234566789999966644 2333332    5699999


Q ss_pred             CCHHHHHHHHHHHHHhccccceeEEEEECCcccHHH-------------------------HHHhcCCCeEEEeChHHHH
Q 027749          109 PTRELATQTEKVILAIGDFINIQAHACVGGKSVGED-------------------------IRKLEHGVHVVSGTPGRVC  163 (219)
Q Consensus       109 P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------------------~~~l~~~~~I~v~Tp~~l~  163 (219)
                      |+.+|..|-.+++..-. ...++...+++..+....                         .+.-..+--|+++|.+++.
T Consensus       214 PSIsLLsQTlrew~~~~-~l~~~a~aVcSD~kvsrs~eDik~sdl~~p~sT~~~~il~~~~~~~k~~~~~vvFsTYQSl~  292 (1518)
T COG4889         214 PSISLLSQTLREWTAQK-ELDFRASAVCSDDKVSRSAEDIKASDLPIPVSTDLEDILSEMEHRQKANGLTVVFSTYQSLP  292 (1518)
T ss_pred             chHHHHHHHHHHHhhcc-CccceeEEEecCccccccccccccccCCCCCcccHHHHHHHHHHhhccCCcEEEEEcccchH
Confidence            99999998887775432 234555555543332110                         1111235569999999888


Q ss_pred             HHHHcCCCCCCCccEEEeccchhhhc
Q 027749          164 DMIKRKTLRTRAIKLLVLDESDEMLS  189 (219)
Q Consensus       164 ~~l~~~~~~~~~l~~lVvDE~h~l~~  189 (219)
                      ..-.-...-+..+++||+||||+...
T Consensus       293 ~i~eAQe~G~~~fDliicDEAHRTtG  318 (1518)
T COG4889         293 RIKEAQEAGLDEFDLIICDEAHRTTG  318 (1518)
T ss_pred             HHHHHHHcCCCCccEEEecchhcccc
Confidence            76554444578899999999998654

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=98.88  E-value=2.5e-08  Score=90.20  Aligned_cols=130  Identities=19%  Similarity=0.231  Sum_probs=99.0

Q ss_pred             CCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccce
Q 027749           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (219)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (219)
                      .|. .|+++|...--.+.  ..-|....||-|||+++.+|++......++   +-||+++.-||..=.+.+..+....|+
T Consensus        82 lG~-r~ydVQliGgl~Lh--~G~IAEM~TGEGKTL~atlpaylnAL~Gkg---VhVVTvNdYLA~RDae~m~~vy~~LGL  155 (939)
T PRK12902         82 LGM-RHFDVQLIGGMVLH--EGQIAEMKTGEGKTLVATLPSYLNALTGKG---VHVVTVNDYLARRDAEWMGQVHRFLGL  155 (939)
T ss_pred             hCC-CcchhHHHhhhhhc--CCceeeecCCCChhHHHHHHHHHHhhcCCC---eEEEeCCHHHHHhHHHHHHHHHHHhCC
Confidence            344 78888865544443  446889999999999999998877766433   999999999999999999999999999


Q ss_pred             eEEEEECCcccHHHHHHhcCCCeEEEeChHHH-----HHHHHc--CCCCCCCccEEEeccchhhh
Q 027749          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-----CDMIKR--KTLRTRAIKLLVLDESDEML  188 (219)
Q Consensus       131 ~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l-----~~~l~~--~~~~~~~l~~lVvDE~h~l~  188 (219)
                      ++.+..++.+..+.  +-...|+|+.+|+..|     .+.+..  .......+.+.||||+|.++
T Consensus       156 tvg~i~~~~~~~er--r~aY~~DItYgTn~e~gFDYLRDnm~~~~~~~vqR~~~faIVDEvDSIL  218 (939)
T PRK12902        156 SVGLIQQDMSPEER--KKNYACDITYATNSELGFDYLRDNMATDISEVVQRPFNYCVIDEVDSIL  218 (939)
T ss_pred             eEEEECCCCChHHH--HHhcCCCeEEecCCcccccchhhhhcccccccccCccceEEEeccccee
Confidence            99988776665543  3345899999999888     332221  11234678899999999765

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

Probab=98.85  E-value=1.5e-08  Score=89.53  Aligned_cols=155  Identities=13%  Similarity=0.107  Sum_probs=102.5

Q ss_pred             CChHHHHHHHHHHh----CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccce
Q 027749           55 KPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~----~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (219)
                      .+-++|.-.++.+.    ++-+.|+.-.+|-||| |-.++.+..+...+....-|||||...| +.|.+++.+|+..  +
T Consensus       399 ~LkdYQlvGvNWL~Llyk~~l~gILADEMGLGKT-iQvIaFlayLkq~g~~gpHLVVvPsSTl-eNWlrEf~kwCPs--l  474 (941)
T KOG0389|consen  399 QLKDYQLVGVNWLLLLYKKKLNGILADEMGLGKT-IQVIAFLAYLKQIGNPGPHLVVVPSSTL-ENWLREFAKWCPS--L  474 (941)
T ss_pred             cccchhhhhHHHHHHHHHccccceehhhccCcch-hHHHHHHHHHHHcCCCCCcEEEecchhH-HHHHHHHHHhCCc--e
Confidence            36778887776542    5567899999999999 5556666666554444447999998777 4588888888875  7


Q ss_pred             eEEEEECCcccHHHHHHhc----CCCeEEEeChHHHHHHHH-cCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCC
Q 027749          131 QAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIK-RKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP  205 (219)
Q Consensus       131 ~~~~~~~~~~~~~~~~~l~----~~~~I~v~Tp~~l~~~l~-~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~  205 (219)
                      ++..++|......+.+...    .+++|+|+|..-....-. +..+.-.++.++|+||.|.+-+.. ......++..-  
T Consensus       475 ~Ve~YyGSq~ER~~lR~~i~~~~~~ydVllTTY~la~~~kdDRsflk~~~~n~viyDEgHmLKN~~-SeRy~~LM~I~--  551 (941)
T KOG0389|consen  475 KVEPYYGSQDERRELRERIKKNKDDYDVLLTTYNLAASSKDDRSFLKNQKFNYVIYDEGHMLKNRT-SERYKHLMSIN--  551 (941)
T ss_pred             EEEeccCcHHHHHHHHHHHhccCCCccEEEEEeecccCChHHHHHHHhccccEEEecchhhhhccc-hHHHHHhcccc--
Confidence            7888888876555544432    268999999743321000 011223567899999999877653 33444444332  


Q ss_pred             CCeEEEEeecc
Q 027749          206 DLQVCCPGSCF  216 (219)
Q Consensus       206 ~~q~i~~SATl  216 (219)
                      ..+.|++|+|.
T Consensus       552 An~RlLLTGTP  562 (941)
T KOG0389|consen  552 ANFRLLLTGTP  562 (941)
T ss_pred             ccceEEeeCCc
Confidence            45678888884

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

Probab=98.83  E-value=1e-07  Score=87.53  Aligned_cols=143  Identities=16%  Similarity=0.220  Sum_probs=86.7

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHH-----Hhc----cccceeEEEEECCc--
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL-----AIG----DFINIQAHACVGGK--  139 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~-----~~~----~~~~~~~~~~~~~~--  139 (219)
                      .++.+..+||+|||.+|+-.+++.....+ ..+.||+||+.+.-+.+...+.     ...    ....+....+.++.  
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            47899999999999999888766554433 3679999999998887776653     111    11224444444332  


Q ss_pred             -----ccHHHHHHhc-------CCCeEEEeChHHHHHHHH-cCC----------CCCCCc----cEEEeccchhhhcccc
Q 027749          140 -----SVGEDIRKLE-------HGVHVVSGTPGRVCDMIK-RKT----------LRTRAI----KLLVLDESDEMLSRGF  192 (219)
Q Consensus       140 -----~~~~~~~~l~-------~~~~I~v~Tp~~l~~~l~-~~~----------~~~~~l----~~lVvDE~h~l~~~~~  192 (219)
                           +.....+..-       ++.+|+|+|-+.|..-.. +..          ..+..+    -.||+||.|++...  
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       157899999988865221 110          111111    27999999997542  


Q ss_pred             HHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          193 KDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       193 ~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      ......| ..+.+-+ ++.+|||++.
T Consensus       217 ~k~~~~i-~~lnpl~-~lrysAT~~~  240 (986)
T PRK15483        217 NKFYQAI-EALKPQM-IIRFGATFPD  240 (986)
T ss_pred             hHHHHHH-HhcCccc-EEEEeeecCC
Confidence            2233334 5554332 5779999975

>KOG0390 consensus DNA repair protein, SNF2 family [Replication, recombination and repair]

Probab=98.81  E-value=1.4e-07  Score=84.72  Aligned_cols=153  Identities=15%  Similarity=0.057  Sum_probs=105.5

Q ss_pred             CChHHHHHHHHHHh----------CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCc-----eeEEEEcCCHHHHHHHHH
Q 027749           55 KPSAIQQRAVMPII----------KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSRE-----VQALILSPTRELATQTEK  119 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~----------~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~-----~~~lil~P~~~l~~q~~~  119 (219)
                      .++|+|++.+.-+-          .....|+.-.+|+|||+-.+. ++..+....+.     .++|||+| ..|+..+..
T Consensus       238 ~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq~Is-flwtlLrq~P~~~~~~~k~lVV~P-~sLv~nWkk  315 (776)
T KOG0390|consen  238 ILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQCIS-FIWTLLRQFPQAKPLINKPLVVAP-SSLVNNWKK  315 (776)
T ss_pred             hcCchHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHHHHH-HHHHHHHhCcCccccccccEEEcc-HHHHHHHHH
Confidence            56899999886542          123467788899999965543 44444444334     67999999 678899999


Q ss_pred             HHHHhccccceeEEEEECCcccHHHHHHh---------cCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhcc
Q 027749          120 VILAIGDFINIQAHACVGGKSVGEDIRKL---------EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (219)
Q Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l---------~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~  190 (219)
                      ++.+|.....+....+++..+.  .+.++         .....|++.+.+.+.+....  +....++++|+||.|++-+.
T Consensus       316 EF~KWl~~~~i~~l~~~~~~~~--~w~~~~sil~~~~~~~~~~vli~sye~~~~~~~~--il~~~~glLVcDEGHrlkN~  391 (776)
T KOG0390|consen  316 EFGKWLGNHRINPLDFYSTKKS--SWIKLKSILFLGYKQFTTPVLIISYETASDYCRK--ILLIRPGLLVCDEGHRLKNS  391 (776)
T ss_pred             HHHHhccccccceeeeecccch--hhhhhHHHHHhhhhheeEEEEeccHHHHHHHHHH--HhcCCCCeEEECCCCCccch
Confidence            9999987656777777776664  11111         11346778888888755443  33567899999999986654


Q ss_pred             ccHHHHHHHHHhCCCCCeEEEEeecc
Q 027749          191 GFKDQIYDVYRYLPPDLQVCCPGSCF  216 (219)
Q Consensus       191 ~~~~~~~~i~~~~~~~~q~i~~SATl  216 (219)
                        ...+...+..+. ....|++|+|+
T Consensus       392 --~s~~~kaL~~l~-t~rRVLLSGTp  414 (776)
T KOG0390|consen  392 --DSLTLKALSSLK-TPRRVLLTGTP  414 (776)
T ss_pred             --hhHHHHHHHhcC-CCceEEeeCCc
Confidence              355566666663 45678899985

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

Probab=98.81  E-value=3.4e-08  Score=76.07  Aligned_cols=120  Identities=20%  Similarity=0.227  Sum_probs=72.5

Q ss_pred             ChHHHHHHHHHHhCCC--cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEE
Q 027749           56 PSAIQQRAVMPIIKGR--DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAH  133 (219)
Q Consensus        56 ~~~~Q~~~~~~~~~~~--~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~  133 (219)
                      +++-|..++..++.+.  -.+++|+.|+|||.+ +-.+...+...  +.++++++||...+..+.+...       +.. 
T Consensus         2 L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~-l~~~~~~~~~~--g~~v~~~apT~~Aa~~L~~~~~-------~~a-   70 (196)
T PF13604_consen    2 LNEEQREAVRAILTSGDRVSVLQGPAGTGKTTL-LKALAEALEAA--GKRVIGLAPTNKAAKELREKTG-------IEA-   70 (196)
T ss_dssp             S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHH-HHHHHHHHHHT--T--EEEEESSHHHHHHHHHHHT-------S-E-
T ss_pred             CCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHH-HHHHHHHHHhC--CCeEEEECCcHHHHHHHHHhhC-------cch-
Confidence            6788999999986443  477889999999953 33455555544  4679999999999887666531       111 


Q ss_pred             EEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcC----CCCCCCccEEEeccchhhhccccHHHHHHHHHhCCC-CCe
Q 027749          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK----TLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP-DLQ  208 (219)
Q Consensus       134 ~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~----~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~-~~q  208 (219)
                                             .|-.+++......    .......++|||||+-++.    ...+..+++..+. +.+
T Consensus        71 -----------------------~Ti~~~l~~~~~~~~~~~~~~~~~~vliVDEasmv~----~~~~~~ll~~~~~~~~k  123 (196)
T PF13604_consen   71 -----------------------QTIHSFLYRIPNGDDEGRPELPKKDVLIVDEASMVD----SRQLARLLRLAKKSGAK  123 (196)
T ss_dssp             -----------------------EEHHHHTTEECCEECCSSCC-TSTSEEEESSGGG-B----HHHHHHHHHHS-T-T-E
T ss_pred             -----------------------hhHHHHHhcCCcccccccccCCcccEEEEecccccC----HHHHHHHHHHHHhcCCE
Confidence                                   1222221111110    0014556799999998655    4567777777766 667


Q ss_pred             EEEEe
Q 027749          209 VCCPG  213 (219)
Q Consensus       209 ~i~~S  213 (219)
                      +|++.
T Consensus       124 lilvG  128 (196)
T PF13604_consen  124 LILVG  128 (196)
T ss_dssp             EEEEE
T ss_pred             EEEEC
Confidence            77664

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

Probab=98.78  E-value=1.3e-07  Score=82.54  Aligned_cols=160  Identities=13%  Similarity=0.117  Sum_probs=101.1

Q ss_pred             CCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHH-hccccc
Q 027749           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA-IGDFIN  129 (219)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~-~~~~~~  129 (219)
                      +.....+++-.+.+..+....-++|.|.||||||.-.--.+...=.. ..+.++=+.-|++..|..+..++.+ ++-..|
T Consensus       261 RksLPVy~ykdell~av~e~QVLiI~GeTGSGKTTQiPQyL~EaGyt-k~gk~IgcTQPRRVAAmSVAaRVA~EMgvkLG  339 (902)
T KOG0923|consen  261 RKSLPVYPYKDELLKAVKEHQVLIIVGETGSGKTTQIPQYLYEAGYT-KGGKKIGCTQPRRVAAMSVAARVAEEMGVKLG  339 (902)
T ss_pred             HhcCCchhhHHHHHHHHHhCcEEEEEcCCCCCccccccHHHHhcccc-cCCceEeecCcchHHHHHHHHHHHHHhCcccc
Confidence            34456677888888888888899999999999995433333332222 2344477888999999988887743 333333


Q ss_pred             eeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhh-cc-ccHHHHHHHHHhCCCCC
Q 027749          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML-SR-GFKDQIYDVYRYLPPDL  207 (219)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~-~~-~~~~~~~~i~~~~~~~~  207 (219)
                      ..|..-+.-.+.-.      ...-|=+.|.+.|++-+... .++.....|||||||.=. .. -....+..|.+. .++.
T Consensus       340 ~eVGYsIRFEdcTS------ekTvlKYMTDGmLlREfL~e-pdLasYSViiiDEAHERTL~TDILfgLvKDIar~-RpdL  411 (902)
T KOG0923|consen  340 HEVGYSIRFEDCTS------EKTVLKYMTDGMLLREFLSE-PDLASYSVIIVDEAHERTLHTDILFGLVKDIARF-RPDL  411 (902)
T ss_pred             cccceEEEeccccC------cceeeeeecchhHHHHHhcc-ccccceeEEEeehhhhhhhhhhHHHHHHHHHHhh-CCcc
Confidence            22222111111100      12346689999998855443 367889999999999511 11 122333444333 5689


Q ss_pred             eEEEEeecccCC
Q 027749          208 QVCCPGSCFLFD  219 (219)
Q Consensus       208 q~i~~SATl~~~  219 (219)
                      .+++.|||+.++
T Consensus       412 KllIsSAT~DAe  423 (902)
T KOG0923|consen  412 KLLISSATMDAE  423 (902)
T ss_pred             eEEeeccccCHH
Confidence            999999998653

>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]

Probab=98.74  E-value=1.5e-07  Score=83.50  Aligned_cols=153  Identities=16%  Similarity=0.076  Sum_probs=95.3

Q ss_pred             CChHHHHHHHHHH----hCCCcEEEEcCCCCchhHHhHHHHHhhhccC-CCceeEEEEcCCHHHHHHHHHHHHHhccccc
Q 027749           55 KPSAIQQRAVMPI----IKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-SREVQALILSPTRELATQTEKVILAIGDFIN  129 (219)
Q Consensus        55 ~~~~~Q~~~~~~~----~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~-~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (219)
                      .+.++|+..+..+    .++..-|+--.+|-|||.- .+..+..+..+ .....+|||||. .+..|+..++..+...  
T Consensus       205 ~Lf~yQreGV~WL~~L~~q~~GGILgDeMGLGKTIQ-iisFLaaL~~S~k~~~paLIVCP~-Tii~qW~~E~~~w~p~--  280 (923)
T KOG0387|consen  205 KLFPYQREGVQWLWELYCQRAGGILGDEMGLGKTIQ-IISFLAALHHSGKLTKPALIVCPA-TIIHQWMKEFQTWWPP--  280 (923)
T ss_pred             HhhHHHHHHHHHHHHHHhccCCCeecccccCccchh-HHHHHHHHhhcccccCceEEEccH-HHHHHHHHHHHHhCcc--
Confidence            5578899877554    3667789999999999922 22222222222 222449999995 6778999999999765  


Q ss_pred             eeEEEEECCccc--------HHHHHHh-----cCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHH
Q 027749          130 IQAHACVGGKSV--------GEDIRKL-----EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQI  196 (219)
Q Consensus       130 ~~~~~~~~~~~~--------~~~~~~l-----~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~  196 (219)
                      +++..+++..+.        ......+     ..+..|+++|.+.|.-.  ...+.-..-+|+|+||.|.+-+++  ..+
T Consensus       281 ~rv~ilh~t~s~~r~~~~~~~~~~~~~L~r~~~~~~~ilitty~~~r~~--~d~l~~~~W~y~ILDEGH~IrNpn--s~i  356 (923)
T KOG0387|consen  281 FRVFILHGTGSGARYDASHSSHKKDKLLIRKVATDGGILITTYDGFRIQ--GDDLLGILWDYVILDEGHRIRNPN--SKI  356 (923)
T ss_pred             eEEEEEecCCcccccccchhhhhhhhhheeeecccCcEEEEehhhhccc--CcccccccccEEEecCcccccCCc--cHH
Confidence            556656554442        1111111     12456899997654322  112222234689999999988875  445


Q ss_pred             HHHHHhCCCCCeEEEEeecc
Q 027749          197 YDVYRYLPPDLQVCCPGSCF  216 (219)
Q Consensus       197 ~~i~~~~~~~~q~i~~SATl  216 (219)
                      ....+.++ ..+.|++|+|.
T Consensus       357 slackki~-T~~RiILSGTP  375 (923)
T KOG0387|consen  357 SLACKKIR-TVHRIILSGTP  375 (923)
T ss_pred             HHHHHhcc-ccceEEeeCcc
Confidence            55555554 45678888874

>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=98.73  E-value=2.3e-08  Score=76.92  Aligned_cols=145  Identities=14%  Similarity=0.182  Sum_probs=74.9

Q ss_pred             CCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHH-------HHHHHhcc
Q 027749           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE-------KVILAIGD  126 (219)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~-------~~~~~~~~  126 (219)
                      ...+..|..++..+.+..-+++.||.|+|||+.++...++.+.. +.-.+++++-|..+..+.+-       +.+..+..
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 KPKNEEQKFALDALLNNDLVIVNGPAGTGKTFLALAAALELVKE-GEYDKIIITRPPVEAGEDLGFLPGDLEEKMEPYLR   81 (205)
T ss_dssp             ---SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHT-TS-SEEEEEE-S--TT----SS---------TTTH
T ss_pred             cCCCHHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHHHHh-CCCcEEEEEecCCCCccccccCCCCHHHHHHHHHH
Confidence            45678899999999988889999999999999988888887766 44456888888765422111       11100000


Q ss_pred             ccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCC
Q 027749          127 FINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPD  206 (219)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~  206 (219)
                      ..--....+.+..    ....+.....|-+..+.    .++.+.  ++ -.+||+|||.++.    ...+..++..+..+
T Consensus        82 p~~d~l~~~~~~~----~~~~~~~~~~Ie~~~~~----~iRGrt--~~-~~~iIvDEaQN~t----~~~~k~ilTR~g~~  146 (205)
T PF02562_consen   82 PIYDALEELFGKE----KLEELIQNGKIEIEPLA----FIRGRT--FD-NAFIIVDEAQNLT----PEELKMILTRIGEG  146 (205)
T ss_dssp             HHHHHHTTTS-TT----CHHHHHHTTSEEEEEGG----GGTT----B--SEEEEE-SGGG------HHHHHHHHTTB-TT
T ss_pred             HHHHHHHHHhChH----hHHHHhhcCeEEEEehh----hhcCcc--cc-ceEEEEecccCCC----HHHHHHHHcccCCC
Confidence            0000000000111    11222223445555542    222222  22 2789999999766    57888888888888


Q ss_pred             CeEEEEee
Q 027749          207 LQVCCPGS  214 (219)
Q Consensus       207 ~q~i~~SA  214 (219)
                      ++++++.-
T Consensus       147 skii~~GD  154 (205)
T PF02562_consen  147 SKIIITGD  154 (205)
T ss_dssp             -EEEEEE-
T ss_pred             cEEEEecC
Confidence            88888753

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

>PRK14873 primosome assembly protein PriA; Provisional

Probab=98.73  E-value=6.8e-08  Score=86.64  Aligned_cols=133  Identities=15%  Similarity=0.090  Sum_probs=88.7

Q ss_pred             EEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHH---Hhc-
Q 027749           74 IAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIR---KLE-  149 (219)
Q Consensus        74 lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~l~-  149 (219)
                      +..+.+|+|||.+|+-.+-..+..   +..+||++|...+..|+.+.++..+..  ..+..++++.+..++..   ... 
T Consensus       164 i~~~~~GSGKTevyl~~i~~~l~~---Gk~vLvLvPEi~lt~q~~~rl~~~f~~--~~v~~lhS~l~~~~R~~~w~~~~~  238 (665)
T PRK14873        164 VWQALPGEDWARRLAAAAAATLRA---GRGALVVVPDQRDVDRLEAALRALLGA--GDVAVLSAGLGPADRYRRWLAVLR  238 (665)
T ss_pred             HhhcCCCCcHHHHHHHHHHHHHHc---CCeEEEEecchhhHHHHHHHHHHHcCC--CcEEEECCCCCHHHHHHHHHHHhC
Confidence            344446999999998766555554   335999999999999999999877641  34666777776655433   333 


Q ss_pred             CCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhcc-----ccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-----GFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       150 ~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~-----~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      +...|+|||-..       -...++++++|||||-|.-.-.     .|...=..+++.-..++.+|+-|||-+-
T Consensus       239 G~~~IViGtRSA-------vFaP~~~LgLIIvdEEhd~sykq~~~p~yhaRdvA~~Ra~~~~~~lvLgSaTPSl  305 (665)
T PRK14873        239 GQARVVVGTRSA-------VFAPVEDLGLVAIWDDGDDLLAEPRAPYPHAREVALLRAHQHGCALLIGGHARTA  305 (665)
T ss_pred             CCCcEEEEccee-------EEeccCCCCEEEEEcCCchhhcCCCCCCccHHHHHHHHHHHcCCcEEEECCCCCH
Confidence            357999999311       1246789999999999853211     1222212223333457889999999764

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=98.70  E-value=2.6e-07  Score=82.01  Aligned_cols=139  Identities=18%  Similarity=0.199  Sum_probs=87.8

Q ss_pred             hHHHHHHHHHHhCCCcEEEEcCCCCchhHHhH--HHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEE
Q 027749           57 SAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIA--LTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (219)
Q Consensus        57 ~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~--~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (219)
                      ..+|+.++..++.++-++|.|+.|+|||....  +.++........++++++.+||...+..+.+.+..........   
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            37899999999999999999999999995432  2222222222123579999999999998888776543222110   


Q ss_pred             EECCcccHHHHHHhcCCCeEEEeChHHHHHHHHc------CCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCe
Q 027749          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR------KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ  208 (219)
Q Consensus       135 ~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~------~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q  208 (219)
                             ....    ....+-..|-.+|+.....      ...+...+++|||||+-++.    ...+..+++.++++.+
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    0111223454444433211      11123457899999998544    4567788888898999


Q ss_pred             EEEEe
Q 027749          209 VCCPG  213 (219)
Q Consensus       209 ~i~~S  213 (219)
                      +|++.
T Consensus       289 lIlvG  293 (586)
T TIGR01447       289 LILLG  293 (586)
T ss_pred             EEEEC
Confidence            88874

This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model.

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=98.70  E-value=5.7e-07  Score=80.12  Aligned_cols=138  Identities=17%  Similarity=0.178  Sum_probs=87.7

Q ss_pred             hHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhcc--CCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEE
Q 027749           57 SAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT--SSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (219)
Q Consensus        57 ~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~--~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (219)
                      .++|+.|+...+.++-.+|.|++|+|||....- ++..+..  .....++.+++||...+..+.+.+.......+..   
T Consensus       154 ~d~Qk~Av~~a~~~~~~vItGgpGTGKTt~v~~-ll~~l~~~~~~~~~~i~l~APTgkAA~rL~e~~~~~~~~~~~~---  229 (615)
T PRK10875        154 VDWQKVAAAVALTRRISVISGGPGTGKTTTVAK-LLAALIQLADGERCRIRLAAPTGKAAARLTESLGKALRQLPLT---  229 (615)
T ss_pred             CHHHHHHHHHHhcCCeEEEEeCCCCCHHHHHHH-HHHHHHHhcCCCCcEEEEECCcHHHHHHHHHHHHhhhhccccc---
Confidence            479999999999989999999999999955322 2222221  1223578899999999999988876543322210   


Q ss_pred             EECCcccHHHHHHhcCCCeEEEeChHHHHHHHHc------CCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCe
Q 027749          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR------KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ  208 (219)
Q Consensus       135 ~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~------~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q  208 (219)
                             ....    .....-..|-.+|+.....      ...+.-.+++|||||+.++-    ...+..+++.++++.+
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    0111122344444332111      11123346899999998543    5778888889999999


Q ss_pred             EEEEe
Q 027749          209 VCCPG  213 (219)
Q Consensus       209 ~i~~S  213 (219)
                      +|++.
T Consensus       295 lIlvG  299 (615)
T PRK10875        295 VIFLG  299 (615)
T ss_pred             EEEec
Confidence            98875

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

Probab=98.66  E-value=4e-07  Score=79.84  Aligned_cols=155  Identities=14%  Similarity=0.114  Sum_probs=94.4

Q ss_pred             CCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhc-ccccee
Q 027749           53 FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIG-DFINIQ  131 (219)
Q Consensus        53 ~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~-~~~~~~  131 (219)
                      +......+.+.+..+..+.-++|.+.||||||.-..-.++..=+..  ..-+-+.-|.+..|..+..++.+-+ ...|-.
T Consensus       354 ~LPvf~~R~~ll~~ir~n~vvvivgETGSGKTTQl~QyL~edGY~~--~GmIGcTQPRRvAAiSVAkrVa~EM~~~lG~~  431 (1042)
T KOG0924|consen  354 YLPVFACRDQLLSVIRENQVVVIVGETGSGKTTQLAQYLYEDGYAD--NGMIGCTQPRRVAAISVAKRVAEEMGVTLGDT  431 (1042)
T ss_pred             hcchHHHHHHHHHHHhhCcEEEEEecCCCCchhhhHHHHHhccccc--CCeeeecCchHHHHHHHHHHHHHHhCCccccc
Confidence            3455667777777788888899999999999955444444433332  2245667799999998888874433 222322


Q ss_pred             EEEEECCcccHHHHHHhcCCCeEEEeChHHHHH-HHHcCCCCCCCccEEEeccchhhh-ccc-cHHHHHHHHHhCCCCCe
Q 027749          132 AHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCD-MIKRKTLRTRAIKLLVLDESDEML-SRG-FKDQIYDVYRYLPPDLQ  208 (219)
Q Consensus       132 ~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~-~l~~~~~~~~~l~~lVvDE~h~l~-~~~-~~~~~~~i~~~~~~~~q  208 (219)
                      +.+.+.-.+...      ....|-+.|-+.|+. .+..+  .+.+...||+||||.=. +.. ....++.++.. ..+..
T Consensus       432 VGYsIRFEdvT~------~~T~IkymTDGiLLrEsL~d~--~L~kYSviImDEAHERslNtDilfGllk~~lar-RrdlK  502 (1042)
T KOG0924|consen  432 VGYSIRFEDVTS------EDTKIKYMTDGILLRESLKDR--DLDKYSVIIMDEAHERSLNTDILFGLLKKVLAR-RRDLK  502 (1042)
T ss_pred             cceEEEeeecCC------CceeEEEeccchHHHHHhhhh--hhhheeEEEechhhhcccchHHHHHHHHHHHHh-hccce
Confidence            222211111100      234677899998886 33332  46788999999999521 111 11222222222 34788


Q ss_pred             EEEEeecccC
Q 027749          209 VCCPGSCFLF  218 (219)
Q Consensus       209 ~i~~SATl~~  218 (219)
                      +|..|||+..
T Consensus       503 liVtSATm~a  512 (1042)
T KOG0924|consen  503 LIVTSATMDA  512 (1042)
T ss_pred             EEEeeccccH
Confidence            9999999864

>KOG1000 consensus Chromatin remodeling protein HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure and dynamics]

Probab=98.63  E-value=2.8e-07  Score=78.05  Aligned_cols=151  Identities=13%  Similarity=0.108  Sum_probs=98.5

Q ss_pred             CCChHHHHHHHHHHh-CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeE
Q 027749           54 EKPSAIQQRAVMPII-KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQA  132 (219)
Q Consensus        54 ~~~~~~Q~~~~~~~~-~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  132 (219)
                      ..+.|+|.+-+...+ +|..+++.-.+|-|||.-++. +....... . | .+||||.. +--.+.+.+..++..... +
T Consensus       197 s~LlPFQreGv~faL~RgGR~llADeMGLGKTiQAla-IA~yyraE-w-p-lliVcPAs-vrftWa~al~r~lps~~p-i  270 (689)
T KOG1000|consen  197 SRLLPFQREGVIFALERGGRILLADEMGLGKTIQALA-IARYYRAE-W-P-LLIVCPAS-VRFTWAKALNRFLPSIHP-I  270 (689)
T ss_pred             HhhCchhhhhHHHHHhcCCeEEEecccccchHHHHHH-HHHHHhhc-C-c-EEEEecHH-HhHHHHHHHHHhcccccc-e
Confidence            356788999887754 678899999999999955433 22222222 2 2 89999964 445678888888765433 4


Q ss_pred             EEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEE
Q 027749          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCP  212 (219)
Q Consensus       133 ~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~  212 (219)
                      ..+.++......   +..-..|.|.+.+.+..+-.  .+.....++||+||.|.+-+.. -...+.++.-+..-..+|++
T Consensus       271 ~vv~~~~D~~~~---~~t~~~v~ivSye~ls~l~~--~l~~~~~~vvI~DEsH~Lk~sk-tkr~Ka~~dllk~akhvILL  344 (689)
T KOG1000|consen  271 FVVDKSSDPLPD---VCTSNTVAIVSYEQLSLLHD--ILKKEKYRVVIFDESHMLKDSK-TKRTKAATDLLKVAKHVILL  344 (689)
T ss_pred             EEEecccCCccc---cccCCeEEEEEHHHHHHHHH--HHhcccceEEEEechhhhhccc-hhhhhhhhhHHHHhhheEEe
Confidence            555555544322   12235688888776654322  2223457899999999876543 34466666666666779999


Q ss_pred             eecc
Q 027749          213 GSCF  216 (219)
Q Consensus       213 SATl  216 (219)
                      |+|.
T Consensus       345 SGTP  348 (689)
T KOG1000|consen  345 SGTP  348 (689)
T ss_pred             cCCc
Confidence            9985

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=98.60  E-value=1.2e-06  Score=79.89  Aligned_cols=124  Identities=22%  Similarity=0.209  Sum_probs=80.6

Q ss_pred             CCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEE
Q 027749           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAH  133 (219)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~  133 (219)
                      ..+++.|+.++..+..++-+++.|+.|+|||... -.++..+........+++++||...+..+.+..       +... 
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            4789999999999998889999999999999433 334444443322246888999998887655432       1110 


Q ss_pred             EEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHc-----CCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCe
Q 027749          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-----KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ  208 (219)
Q Consensus       134 ~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~-----~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q  208 (219)
                                             .|-.+++.....     ..-.....++|||||++++.    ...+..+++.++.+.+
T Consensus       393 -----------------------~Tih~lL~~~~~~~~~~~~~~~~~~~llIvDEaSMvd----~~~~~~Ll~~~~~~~r  445 (720)
T TIGR01448       393 -----------------------STIHRLLGYGPDTFRHNHLEDPIDCDLLIVDESSMMD----TWLALSLLAALPDHAR  445 (720)
T ss_pred             -----------------------ccHHHHhhccCCccchhhhhccccCCEEEEeccccCC----HHHHHHHHHhCCCCCE
Confidence                                   122222111000     00112457899999999754    3456777788888888


Q ss_pred             EEEEe
Q 027749          209 VCCPG  213 (219)
Q Consensus       209 ~i~~S  213 (219)
                      +|++.
T Consensus       446 lilvG  450 (720)
T TIGR01448       446 LLLVG  450 (720)
T ss_pred             EEEEC
Confidence            88875

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.

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=98.58  E-value=6.4e-07  Score=81.14  Aligned_cols=129  Identities=15%  Similarity=0.187  Sum_probs=96.8

Q ss_pred             CCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhcccccee
Q 027749           52 GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ  131 (219)
Q Consensus        52 ~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  131 (219)
                      |. .|+++|....-.+..|  -|....||=|||+++.+|++-.....++   +-||+...-||..=.+.+..+....|++
T Consensus        76 G~-r~ydVQliGglvLh~G--~IAEMkTGEGKTLvAtLpayLnAL~Gkg---VhVVTvNdYLA~RDae~mg~vy~fLGLs  149 (925)
T PRK12903         76 GK-RPYDVQIIGGIILDLG--SVAEMKTGEGKTITSIAPVYLNALTGKG---VIVSTVNEYLAERDAEEMGKVFNFLGLS  149 (925)
T ss_pred             CC-CcCchHHHHHHHHhcC--CeeeecCCCCccHHHHHHHHHHHhcCCc---eEEEecchhhhhhhHHHHHHHHHHhCCc
Confidence            44 7899997766555555  4799999999999999988776665433   7888888999998888888888888999


Q ss_pred             EEEEECCcccHHHHHHhcCCCeEEEeChHHHHH-HHHcCC------CCCCCccEEEeccchhhh
Q 027749          132 AHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCD-MIKRKT------LRTRAIKLLVLDESDEML  188 (219)
Q Consensus       132 ~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~-~l~~~~------~~~~~l~~lVvDE~h~l~  188 (219)
                      +.+...+.+..+....  ..|+|..+|...|-. +++-+-      .....+.+.||||+|.++
T Consensus       150 vG~i~~~~~~~~rr~a--Y~~DItYgTn~E~gFDYLRDnm~~~~~~~vqR~~~faIVDEVDSIL  211 (925)
T PRK12903        150 VGINKANMDPNLKREA--YACDITYSVHSELGFDYLRDNMVSSKEEKVQRGLNFCLIDEVDSIL  211 (925)
T ss_pred             eeeeCCCCChHHHHHh--ccCCCeeecCcccchhhhhhcccccHHHhcCcccceeeeccchhee
Confidence            9888776666554333  469999999887754 443211      123567899999999765

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=98.56  E-value=6e-07  Score=75.33  Aligned_cols=108  Identities=13%  Similarity=0.195  Sum_probs=69.9

Q ss_pred             cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCC
Q 027749           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG  151 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  151 (219)
                      -++|.|..|||||+..+- ++..+.....+..++++++...+...+.+.+......                      ..
T Consensus         3 v~~I~G~aGTGKTvla~~-l~~~l~~~~~~~~~~~l~~n~~l~~~l~~~l~~~~~~----------------------~~   59 (352)
T PF09848_consen    3 VILITGGAGTGKTVLALN-LAKELQNSEEGKKVLYLCGNHPLRNKLREQLAKKYNP----------------------KL   59 (352)
T ss_pred             EEEEEecCCcCHHHHHHH-HHHHhhccccCCceEEEEecchHHHHHHHHHhhhccc----------------------ch
Confidence            478999999999955543 4455433334566999999999999888877553200                      01


Q ss_pred             CeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccc-------cHHHHHHHHHh
Q 027749          152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG-------FKDQIYDVYRY  202 (219)
Q Consensus       152 ~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~-------~~~~~~~i~~~  202 (219)
                      ....+..+..+...+..........++|||||||++...+       ....+..+++.
T Consensus        60 ~~~~~~~~~~~i~~~~~~~~~~~~~DviivDEAqrl~~~~~~~~~~~~~~~L~~i~~~  117 (352)
T PF09848_consen   60 KKSDFRKPTSFINNYSESDKEKNKYDVIIVDEAQRLRTKGDQYNNFSEPNQLDEIIKR  117 (352)
T ss_pred             hhhhhhhhHHHHhhcccccccCCcCCEEEEehhHhhhhccccccccccHHHHHHHHhc
Confidence            1223344554444333223346788999999999998731       24667777776

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

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

Probab=98.48  E-value=1.1e-06  Score=76.87  Aligned_cols=76  Identities=22%  Similarity=0.186  Sum_probs=61.3

Q ss_pred             HHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 027749           47 GIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (219)
Q Consensus        47 ~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (219)
                      .+...++.+++.-|..|+.++++..=.+++||.|+|||+...--+++.+...  ...+|+++|+...++|+.+.+.+-
T Consensus       402 ~~s~~~lpkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa~IVyhl~~~~--~~~VLvcApSNiAVDqLaeKIh~t  477 (935)
T KOG1802|consen  402 RFSVPNLPKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSATIVYHLARQH--AGPVLVCAPSNIAVDQLAEKIHKT  477 (935)
T ss_pred             hhcCCCchhhchHHHHHHHHHHcCCceeeecCCCCCceehhHHHHHHHHHhc--CCceEEEcccchhHHHHHHHHHhc
Confidence            3444567788999999999999998999999999999977665555554443  334999999999999999988665

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

Probab=98.47  E-value=1.3e-07  Score=86.04  Aligned_cols=132  Identities=15%  Similarity=0.208  Sum_probs=100.8

Q ss_pred             CChHHHHHHHHHHh-CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEE
Q 027749           55 KPSAIQQRAVMPII-KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAH  133 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~-~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~  133 (219)
                      ...|.|.+.+-... -..++++-+|||+|||.++-+.+...+...+ +.++++++|..+|+..-.+.+.+.....|+++.
T Consensus       927 ~fn~~q~~if~~~y~td~~~~~g~ptgsgkt~~ae~a~~~~~~~~p-~~kvvyIap~kalvker~~Dw~~r~~~~g~k~i 1005 (1230)
T KOG0952|consen  927 YFNPIQTQIFHCLYHTDLNFLLGAPTGSGKTVVAELAIFRALSYYP-GSKVVYIAPDKALVKERSDDWSKRDELPGIKVI 1005 (1230)
T ss_pred             ccCCccceEEEEEeecchhhhhcCCccCcchhHHHHHHHHHhccCC-CccEEEEcCCchhhcccccchhhhcccCCceeE
Confidence            34455555543332 2357888999999999999998877776654 478999999999999888888666555588888


Q ss_pred             EEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHc--CCCCCCCccEEEeccchhhhcc
Q 027749          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR--KTLRTRAIKLLVLDESDEMLSR  190 (219)
Q Consensus       134 ~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~--~~~~~~~l~~lVvDE~h~l~~~  190 (219)
                      .+.|....+..   -...++++|+||+++....++  ..-.++++..+|+||.|++.+.
T Consensus      1006 e~tgd~~pd~~---~v~~~~~~ittpek~dgi~Rsw~~r~~v~~v~~iv~de~hllg~~ 1061 (1230)
T KOG0952|consen 1006 ELTGDVTPDVK---AVREADIVITTPEKWDGISRSWQTRKYVQSVSLIVLDEIHLLGED 1061 (1230)
T ss_pred             eccCccCCChh---heecCceEEcccccccCccccccchhhhccccceeecccccccCC
Confidence            88888777622   124689999999999888774  4456889999999999987654

>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1

Probab=98.43  E-value=6.2e-06  Score=66.63  Aligned_cols=155  Identities=19%  Similarity=0.129  Sum_probs=99.6

Q ss_pred             CChHHHHHHHHHHh----------CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 027749           55 KPSAIQQRAVMPII----------KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~----------~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (219)
                      .+...|.+++-...          .+..+++--.||.||--...--+++.+...+  .++|++..+..|..+..+.++.+
T Consensus        37 ~LS~~QLEaV~yA~q~h~~~Lp~~~R~Gf~lGDGtGvGKGR~iAgiI~~n~l~Gr--~r~vwvS~s~dL~~Da~RDl~DI  114 (303)
T PF13872_consen   37 LLSALQLEAVIYACQRHEQILPGGSRAGFFLGDGTGVGKGRQIAGIILENWLRGR--KRAVWVSVSNDLKYDAERDLRDI  114 (303)
T ss_pred             cccHHHHHHHHHHHHHHHhhcccccCcEEEeccCCCcCccchhHHHHHHHHHcCC--CceEEEECChhhhhHHHHHHHHh
Confidence            35777888775543          2345788888999988666555666666543  35999999999999999999988


Q ss_pred             ccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcC---CCCC---------CCccEEEeccchhhhcccc
Q 027749          125 GDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK---TLRT---------RAIKLLVLDESDEMLSRGF  192 (219)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~---~~~~---------~~l~~lVvDE~h~l~~~~~  192 (219)
                      +.. .+.+..+..- +..   ....-+-.|+++|...|...-..+   ...+         ..-.+||+||||.+-+..-
T Consensus       115 G~~-~i~v~~l~~~-~~~---~~~~~~~GvlF~TYs~L~~~~~~~~~~~sRl~ql~~W~g~dfdgvivfDEcH~akn~~~  189 (303)
T PF13872_consen  115 GAD-NIPVHPLNKF-KYG---DIIRLKEGVLFSTYSTLISESQSGGKYRSRLDQLVDWCGEDFDGVIVFDECHKAKNLSS  189 (303)
T ss_pred             CCC-cccceechhh-ccC---cCCCCCCCccchhHHHHHhHHhccCCccchHHHHHHHHhcCCCceEEeccchhcCCCCc
Confidence            654 3444333211 100   001124469999998877654321   1111         1234899999998776532


Q ss_pred             --------HHHHHHHHHhCCCCCeEEEEeeccc
Q 027749          193 --------KDQIYDVYRYLPPDLQVCCPGSCFL  217 (219)
Q Consensus       193 --------~~~~~~i~~~~~~~~q~i~~SATl~  217 (219)
                              ...+..+.+.+|+ -+++.+|||--
T Consensus       190 ~~~~~sk~g~avl~LQ~~LP~-ARvvY~SATga  221 (303)
T PF13872_consen  190 GSKKPSKTGIAVLELQNRLPN-ARVVYASATGA  221 (303)
T ss_pred             cCccccHHHHHHHHHHHhCCC-CcEEEeccccc
Confidence                    2345566667764 46999999964

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

Probab=98.41  E-value=2e-06  Score=77.36  Aligned_cols=135  Identities=11%  Similarity=0.091  Sum_probs=83.7

Q ss_pred             cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCC
Q 027749           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG  151 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  151 (219)
                      -.+|.+|+|+|||.+.+-++-+.+...  ..+++++..+++|+.++...++...-. ++....-.++....      ...
T Consensus        51 V~vVRSpMGTGKTtaLi~wLk~~l~~~--~~~VLvVShRrSL~~sL~~rf~~~~l~-gFv~Y~d~~~~~i~------~~~  121 (824)
T PF02399_consen   51 VLVVRSPMGTGKTTALIRWLKDALKNP--DKSVLVVSHRRSLTKSLAERFKKAGLS-GFVNYLDSDDYIID------GRP  121 (824)
T ss_pred             eEEEECCCCCCcHHHHHHHHHHhccCC--CCeEEEEEhHHHHHHHHHHHHhhcCCC-cceeeecccccccc------ccc
Confidence            468999999999966655554444332  456999999999999999988755321 22211111111110      012


Q ss_pred             CeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHH------HHHHHH-hCCCCCeEEEEeecccC
Q 027749          152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQ------IYDVYR-YLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       152 ~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~------~~~i~~-~~~~~~q~i~~SATl~~  218 (219)
                      ++-+++..++|.+.-.   -.+.+.++||+||+...+..-|...      +..++. .+.....+|++-|++..
T Consensus       122 ~~rLivqIdSL~R~~~---~~l~~yDvVIIDEv~svL~qL~S~Tm~~~~~v~~~L~~lI~~ak~VI~~DA~ln~  192 (824)
T PF02399_consen  122 YDRLIVQIDSLHRLDG---SLLDRYDVVIIDEVMSVLNQLFSPTMRQREEVDNLLKELIRNAKTVIVMDADLND  192 (824)
T ss_pred             cCeEEEEehhhhhccc---ccccccCEEEEehHHHHHHHHhHHHHhhHHHHHHHHHHHHHhCCeEEEecCCCCH
Confidence            4567777777766532   2466789999999987776532222      222222 23456679999999864

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

>PRK10536 hypothetical protein; Provisional

Probab=98.40  E-value=2.6e-06  Score=67.65  Aligned_cols=147  Identities=13%  Similarity=0.097  Sum_probs=83.6

Q ss_pred             CCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHH-------HHHHHHH
Q 027749           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQ-------TEKVILA  123 (219)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q-------~~~~~~~  123 (219)
                      .++..-+..|...+..+.+...+++.||+|+|||+......++.+... .-.++++.-|..+..+.       ..+.+..
T Consensus        55 ~~i~p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~a~a~~~l~~~-~~~kIiI~RP~v~~ge~LGfLPG~~~eK~~p  133 (262)
T PRK10536         55 SPILARNEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKAAEALIHK-DVDRIIVTRPVLQADEDLGFLPGDIAEKFAP  133 (262)
T ss_pred             ccccCCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHhcC-CeeEEEEeCCCCCchhhhCcCCCCHHHHHHH
Confidence            355667889999999888888899999999999977777666555443 23446666565432211       1111111


Q ss_pred             hccccceeEEEEECCcccHHHHHHh--cCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHH
Q 027749          124 IGDFINIQAHACVGGKSVGEDIRKL--EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYR  201 (219)
Q Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~~~l--~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~  201 (219)
                      +....--....+.+.    .....+  .....|-|...    ..++.+.+   +-++||+|||+++.    ...+..++.
T Consensus       134 ~~~pi~D~L~~~~~~----~~~~~~~~~~~~~Iei~~l----~ymRGrtl---~~~~vIvDEaqn~~----~~~~k~~lt  198 (262)
T PRK10536        134 YFRPVYDVLVRRLGA----SFMQYCLRPEIGKVEIAPF----AYMRGRTF---ENAVVILDEAQNVT----AAQMKMFLT  198 (262)
T ss_pred             HHHHHHHHHHHHhCh----HHHHHHHHhccCcEEEecH----HHhcCCcc---cCCEEEEechhcCC----HHHHHHHHh
Confidence            111100000000111    111111  11223444432    34444443   23799999999755    478888888


Q ss_pred             hCCCCCeEEEEe
Q 027749          202 YLPPDLQVCCPG  213 (219)
Q Consensus       202 ~~~~~~q~i~~S  213 (219)
                      .++.+.++|+..
T Consensus       199 R~g~~sk~v~~G  210 (262)
T PRK10536        199 RLGENVTVIVNG  210 (262)
T ss_pred             hcCCCCEEEEeC
Confidence            888888887754

>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=9.4e-06  Score=63.26  Aligned_cols=152  Identities=22%  Similarity=0.242  Sum_probs=93.0

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhC---CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcC
Q 027749           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIK---GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (219)
Q Consensus        33 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~---~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P  109 (219)
                      .+|+-...+.+++=.+.. ++ -.++.|.++...+.+   |+|.+.+.-+|.|||.+. +|++..+...+. .-+.+++|
T Consensus         3 ~~w~p~~~P~wLl~E~e~-~i-liR~~Q~~ia~~mi~~~~~~n~v~QlnMGeGKTsVI-~Pmla~~LAdg~-~LvrviVp   78 (229)
T PF12340_consen    3 RNWDPMEYPDWLLFEIES-NI-LIRPVQVEIAREMISPPSGKNSVMQLNMGEGKTSVI-VPMLALALADGS-RLVRVIVP   78 (229)
T ss_pred             CCCCchhChHHHHHHHHc-Cc-eeeHHHHHHHHHHhCCCCCCCeEeeecccCCccchH-HHHHHHHHcCCC-cEEEEEcC
Confidence            356666677777766653 33 578889998887764   578999999999999554 556665555433 34666777


Q ss_pred             CHHHHHHHHHHHHHhccc-cceeEEEE--ECCcccH-H---HHH----HhcCCCeEEEeChHHHHHHHHcC-------CC
Q 027749          110 TRELATQTEKVILAIGDF-INIQAHAC--VGGKSVG-E---DIR----KLEHGVHVVSGTPGRVCDMIKRK-------TL  171 (219)
Q Consensus       110 ~~~l~~q~~~~~~~~~~~-~~~~~~~~--~~~~~~~-~---~~~----~l~~~~~I~v~Tp~~l~~~l~~~-------~~  171 (219)
                       ++|..|.++.+...... .+-++..+  ....... .   ...    .-.....|+++||+.++......       ..
T Consensus        79 -k~Ll~q~~~~L~~~lg~l~~r~i~~lpFsR~~~~~~~~~~~~~~l~~~~~~~~gill~~PEhilSf~L~~le~l~~~~~  157 (229)
T PF12340_consen   79 -KALLEQMRQMLRSRLGGLLNRRIYHLPFSRSTPLTPETLEKIRQLLEECMRSGGILLATPEHILSFKLKGLERLQDGKP  157 (229)
T ss_pred             -HHHHHHHHHHHHHHHHHHhCCeeEEecccCCCCCCHHHHHHHHHHHHHHHHcCCEEEeChHHHHHHHHHHHHHHHhcCH
Confidence             67899999888655433 22233222  2222211 1   111    11234579999999987633211       10


Q ss_pred             -----------CCCCccEEEeccchhhhc
Q 027749          172 -----------RTRAIKLLVLDESDEMLS  189 (219)
Q Consensus       172 -----------~~~~l~~lVvDE~h~l~~  189 (219)
                                 .++.-..=|+||+|.++.
T Consensus       158 ~~~~~l~~~q~~l~~~~rdilDEsDe~L~  186 (229)
T PF12340_consen  158 EEARELLKIQKWLDEHSRDILDESDEILS  186 (229)
T ss_pred             HHHHHHHHHHHHHHhcCCeEeECchhccC
Confidence                       112233469999998776

There are two conserved sequence motifs: LLE and NMG.

>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=98.32  E-value=1.3e-06  Score=76.81  Aligned_cols=134  Identities=17%  Similarity=0.145  Sum_probs=88.8

Q ss_pred             CChHHHHHHHHHHhC-----CCcEEEEcCCCCchhHHhHHHHHhh-hcc---C---CCceeEEEEcCCHHHHHHHHHHHH
Q 027749           55 KPSAIQQRAVMPIIK-----GRDVIAQAQSGTGKTSMIALTVCQT-VDT---S---SREVQALILSPTRELATQTEKVIL  122 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~-----~~~~lv~~~tG~GKT~~~~~~~~~~-~~~---~---~~~~~~lil~P~~~l~~q~~~~~~  122 (219)
                      .+.|+|+.++..+.-     ....|+....|-|||+..+-.+++. ...   .   ......||||| ..|..|+..++.
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            457889888876652     2357889999999997665544432 110   0   11124999999 678899999998


Q ss_pred             HhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHH----HHHc--CCCCCCCcc--EEEeccchhhhcc
Q 027749          123 AIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCD----MIKR--KTLRTRAIK--LLVLDESDEMLSR  190 (219)
Q Consensus       123 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~----~l~~--~~~~~~~l~--~lVvDE~h~l~~~  190 (219)
                      .......++|..++|....+-..+.+ ..+||||+|..-...    -...  ....+.++.  .||+||||.+-+.
T Consensus       404 ~rl~~n~LsV~~~HG~n~r~i~~~~L-~~YDvViTTY~lva~~~~~e~~~~~~~spL~~I~W~RVILDEAH~IrN~  478 (901)
T KOG4439|consen  404 RRLEQNALSVYLYHGPNKREISAKEL-RKYDVVITTYNLVANKPDDELEEGKNSSPLARIAWSRVILDEAHNIRNS  478 (901)
T ss_pred             HHHhhcceEEEEecCCccccCCHHHH-hhcceEEEeeeccccCCchhhhcccCccHHHHhhHHHhhhhhhhhhccc
Confidence            88777789999998877644333333 468999999754333    1111  112233443  4999999987654

>TIGR00376 DNA helicase, putative

Probab=98.30  E-value=1.1e-05  Score=72.53  Aligned_cols=66  Identities=18%  Similarity=0.212  Sum_probs=52.0

Q ss_pred             CChHHHHHHHHHHhCC-CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 027749           55 KPSAIQQRAVMPIIKG-RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA  123 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~-~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~  123 (219)
                      .+++.|..++..++.. ..++|.||+|+|||....-.+.+.+. .  +.++++++||+..+.++.+.+..
T Consensus       157 ~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~~~ii~~~~~-~--g~~VLv~a~sn~Avd~l~e~l~~  223 (637)
T TIGR00376       157 NLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTLVELIRQLVK-R--GLRVLVTAPSNIAVDNLLERLAL  223 (637)
T ss_pred             CCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHHHHHHHHHHH-c--CCCEEEEcCcHHHHHHHHHHHHh
Confidence            5689999999998866 67899999999999554433333333 2  34799999999999999998876

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.

>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=98.30  E-value=5e-06  Score=70.87  Aligned_cols=118  Identities=19%  Similarity=0.199  Sum_probs=79.1

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhcccc-c----------ee--------EEEEECCcccHHHHHHhcC-----------
Q 027749          101 EVQALILSPTRELATQTEKVILAIGDFI-N----------IQ--------AHACVGGKSVGEDIRKLEH-----------  150 (219)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~-~----------~~--------~~~~~~~~~~~~~~~~l~~-----------  150 (219)
                      .|++|||+|++..|-++.+.+.++.... .          +.        ...-........++..+..           
T Consensus        37 RPkVLIL~P~R~~A~~~V~~Li~l~~~~~~~~nk~RF~~efg~~~~~~~~~~~~~~~~~kP~D~~~~F~GN~DD~FrlGi  116 (442)
T PF06862_consen   37 RPKVLILLPFRNSALRIVETLISLLPPGKQVENKKRFEEEFGLPEDEDDDEEPPEFKKSKPEDFKALFSGNNDDCFRLGI  116 (442)
T ss_pred             CceEEEEcccHHHHHHHHHHHHHHcCccchHHHHHHHHHHcCCCccccchhhhccccCCCchhHHHhcCCCccceEEEeE
Confidence            5899999999999999999988776551 1          10        0000001112223333322           


Q ss_pred             --------------CCeEEEeChHHHHHHHHc------CCCCCCCccEEEeccchhhhccccHHHHHHHHHhC---CCC-
Q 027749          151 --------------GVHVVSGTPGRVCDMIKR------KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL---PPD-  206 (219)
Q Consensus       151 --------------~~~I~v~Tp~~l~~~l~~------~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~---~~~-  206 (219)
                                    .+|||||+|-.|...+..      ..-.++.++++|+|.+|.|.-.+ ++.+..+++.+   |++ 
T Consensus       117 k~trk~ikLys~Fy~SDIIiASPLGLr~~i~~~~~~~~d~DFLSSIEv~iiD~ad~l~MQN-W~Hv~~v~~~lN~~P~~~  195 (442)
T PF06862_consen  117 KFTRKSIKLYSDFYSSDIIIASPLGLRMIIGEEGEKKRDYDFLSSIEVLIIDQADVLLMQN-WEHVLHVFEHLNLQPKKS  195 (442)
T ss_pred             EEecCeeeeecccccCCEEEEChHHHHHHhccccccccccchhheeeeEeechhhHHHHhh-HHHHHHHHHHhccCCCCC
Confidence                          379999999999988874      12346889999999999877544 56666666665   331 


Q ss_pred             --------------------CeEEEEeecccCC
Q 027749          207 --------------------LQVCCPGSCFLFD  219 (219)
Q Consensus       207 --------------------~q~i~~SATl~~~  219 (219)
                                          +|+|++|+...|+
T Consensus       196 ~~~DfsRVR~w~Ldg~a~~~RQtii~S~~~~pe  228 (442)
T PF06862_consen  196 HDTDFSRVRPWYLDGQAKYYRQTIIFSSFQTPE  228 (442)
T ss_pred             CCCCHHHHHHHHHcCcchheeEeEEecCCCCHH
Confidence                                6999999987764

; GO: 0005634 nucleus

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=98.27  E-value=2e-06  Score=79.00  Aligned_cols=127  Identities=16%  Similarity=0.196  Sum_probs=92.1

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEE
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (219)
                      .|+++|...--.+.+  .-|....||-|||+++.+|++-.....++   +-+|+..--||..=.+.+..+....|+++.+
T Consensus       138 ~~ydVQLiGgivLh~--G~IAEM~TGEGKTLvatlp~yLnAL~G~g---VHvVTvNDYLA~RDaewm~p~y~flGLtVg~  212 (1025)
T PRK12900        138 VPYDVQLIGGIVLHS--GKISEMATGEGKTLVSTLPTFLNALTGRG---VHVVTVNDYLAQRDKEWMNPVFEFHGLSVGV  212 (1025)
T ss_pred             cccchHHhhhHHhhc--CCccccCCCCCcchHhHHHHHHHHHcCCC---cEEEeechHhhhhhHHHHHHHHHHhCCeeee
Confidence            577787544433434  45789999999999999999887776543   6777777889988788888888888999998


Q ss_pred             EECCcccHHHHHHhcCCCeEEEeChHHHHH-HHHcC------CCCCCCccEEEeccchhhh
Q 027749          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCD-MIKRK------TLRTRAIKLLVLDESDEML  188 (219)
Q Consensus       135 ~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~-~l~~~------~~~~~~l~~lVvDE~h~l~  188 (219)
                      ...+.+..++  +-...|||..+|...|-. +|+-+      ...-..+.+.||||+|-++
T Consensus       213 i~~~~~~~~R--r~aY~~DItYgTn~EfGFDYLRDnma~~~~~~vqR~~~faIVDEvDSvL  271 (1025)
T PRK12900        213 ILNTMRPEER--REQYLCDITYGTNNEFGFDYLRDNMAGTPEEMVQRDFYFAIVDEVDSVL  271 (1025)
T ss_pred             eCCCCCHHHH--HHhCCCcceecCCCccccccchhccccchhhhhccCCceEEEechhhhh
Confidence            8665555443  344689999999876642 33211      1123567899999999755

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=98.27  E-value=2.6e-05  Score=72.89  Aligned_cols=121  Identities=18%  Similarity=0.095  Sum_probs=76.9

Q ss_pred             CChHHHHHHHHHHhCCC-cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEE
Q 027749           55 KPSAIQQRAVMPIIKGR-DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAH  133 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~-~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~  133 (219)
                      .+++-|..++..++.++ -++|.|+.|+|||.. +-.+...+...  +.+++.++||...+..+.+.       .++.. 
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--GYEVRGAALSGIAAENLEGG-------SGIAS-  414 (988)
T ss_pred             CCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHH-HHHHHHHHHHc--CCeEEEecCcHHHHHHHhhc-------cCcch-
Confidence            68999999999999865 478999999999954 33444444433  46699999998877655431       12110 


Q ss_pred             EEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhC-CCCCeEEEE
Q 027749          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL-PPDLQVCCP  212 (219)
Q Consensus       134 ~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~-~~~~q~i~~  212 (219)
                                             .|-.+|+.-.......+...++|||||+-++..    ..+..+++.. +...++|++
T Consensus       415 -----------------------~TI~sll~~~~~~~~~l~~~~vlIVDEASMv~~----~~m~~LL~~a~~~garvVLV  467 (988)
T PRK13889        415 -----------------------RTIASLEHGWGQGRDLLTSRDVLVIDEAGMVGT----RQLERVLSHAADAGAKVVLV  467 (988)
T ss_pred             -----------------------hhHHHHHhhhcccccccccCcEEEEECcccCCH----HHHHHHHHhhhhCCCEEEEE
Confidence                                   133333221112223356678999999986543    3455666544 446777776


Q ss_pred             e
Q 027749          213 G  213 (219)
Q Consensus       213 S  213 (219)
                      .
T Consensus       468 G  468 (988)
T PRK13889        468 G  468 (988)
T ss_pred             C
Confidence            4

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

Probab=98.26  E-value=3.2e-06  Score=73.40  Aligned_cols=66  Identities=21%  Similarity=0.278  Sum_probs=51.3

Q ss_pred             CCChHHHHHHHHHHhCCC-cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHH
Q 027749           54 EKPSAIQQRAVMPIIKGR-DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL  122 (219)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~~-~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~  122 (219)
                      +.+.+-|..++....+.+ -.+++||+|+|||.....-+.+.+...   .++++.+||+..++.+.+++.
T Consensus       184 ~~ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvEiI~qlvk~~---k~VLVcaPSn~AVdNiverl~  250 (649)
T KOG1803|consen  184 KNLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVKQK---KRVLVCAPSNVAVDNIVERLT  250 (649)
T ss_pred             ccccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHHHHHHHHHcC---CeEEEEcCchHHHHHHHHHhc
Confidence            466788999998877764 578999999999966655444454443   469999999999999998754

>KOG0392 consensus SNF2 family DNA-dependent ATPase domain-containing protein [Transcription]

Probab=98.25  E-value=6.9e-06  Score=76.22  Aligned_cols=154  Identities=16%  Similarity=0.136  Sum_probs=102.0

Q ss_pred             CChHHHHHHHHHH--hC--CCcEEEEcCCCCchhHHhHHHHHhhhccCC-----Cce-eEEEEcCCHHHHHHHHHHHHHh
Q 027749           55 KPSAIQQRAVMPI--IK--GRDVIAQAQSGTGKTSMIALTVCQTVDTSS-----REV-QALILSPTRELATQTEKVILAI  124 (219)
Q Consensus        55 ~~~~~Q~~~~~~~--~~--~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~-----~~~-~~lil~P~~~l~~q~~~~~~~~  124 (219)
                      .++.+|++-++.+  ++  +-+.|+|-.+|-|||+-.+--+.......+     ..+ -.||||| ..|+-.+..++.++
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            3467888877664  22  237899999999999765444443333221     012 2899999 56888999999999


Q ss_pred             ccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCC
Q 027749          125 GDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP  204 (219)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~  204 (219)
                      ...  .++...+|+.......+..-++.+|+|++.+.+.+-+..  +.-.+-.|+|+||-|.|-+.  ...+-+..+++.
T Consensus      1054 ~pf--L~v~~yvg~p~~r~~lR~q~~~~~iiVtSYDv~RnD~d~--l~~~~wNYcVLDEGHVikN~--ktkl~kavkqL~ 1127 (1549)
T KOG0392|consen 1054 FPF--LKVLQYVGPPAERRELRDQYKNANIIVTSYDVVRNDVDY--LIKIDWNYCVLDEGHVIKNS--KTKLTKAVKQLR 1127 (1549)
T ss_pred             cch--hhhhhhcCChHHHHHHHhhccccceEEeeHHHHHHHHHH--HHhcccceEEecCcceecch--HHHHHHHHHHHh
Confidence            876  566667777666655555566789999999877642211  01123458999999987654  455556666664


Q ss_pred             CCCeEEEEeecc
Q 027749          205 PDLQVCCPGSCF  216 (219)
Q Consensus       205 ~~~q~i~~SATl  216 (219)
                      .+ ..+.+|+|.
T Consensus      1128 a~-hRLILSGTP 1138 (1549)
T KOG0392|consen 1128 AN-HRLILSGTP 1138 (1549)
T ss_pred             hc-ceEEeeCCC
Confidence            43 356677773

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

Probab=98.23  E-value=8.9e-06  Score=73.32  Aligned_cols=73  Identities=15%  Similarity=0.147  Sum_probs=52.6

Q ss_pred             CChHHHHHHHHHHh----CCCcEEEEcCCCCchhHHhHHHHHhhh---cc---------CC-------------------
Q 027749           55 KPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTV---DT---------SS-------------------   99 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~----~~~~~lv~~~tG~GKT~~~~~~~~~~~---~~---------~~-------------------   99 (219)
                      .|++.|...+..++    +..+.++..|||+|||++.+-..+...   ..         +.                   
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            68999988776654    456899999999999977654443322   10         00                   


Q ss_pred             --------CceeEEEEcCCHHHHHHHHHHHHHhccc
Q 027749          100 --------REVQALILSPTRELATQTEKVILAIGDF  127 (219)
Q Consensus       100 --------~~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (219)
                              ..|+++|-.-|+....|+.+++++..-.
T Consensus       101 ~e~~~~~~~ipkIyyaSRTHsQltQvvrElrrT~Y~  136 (945)
T KOG1132|consen  101 GEPIACYTGIPKIYYASRTHSQLTQVVRELRRTGYR  136 (945)
T ss_pred             cCccccccCCceEEEecchHHHHHHHHHHHhhcCCC
Confidence                    1378899999999999999998776433

>PF13245 AAA_19: Part of AAA domain

Probab=98.23  E-value=7.1e-06  Score=53.12  Aligned_cols=52  Identities=25%  Similarity=0.419  Sum_probs=38.1

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhhcc-CCCceeEEEEcCCHHHHHHHHHHH
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTVDT-SSREVQALILSPTRELATQTEKVI  121 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~l~~q~~~~~  121 (219)
                      ++-++|.||.|+|||....-.+...+.. ...+.++++++|++..++++.+.+
T Consensus        10 ~~~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen   10 SPLFVVQGPPGTGKTTTLAARIAELLAARADPGKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCCCeEEEECCCHHHHHHHHHHH
Confidence            3446669999999996655555444421 112567999999999999998888

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=98.22  E-value=4.6e-05  Score=69.85  Aligned_cols=121  Identities=18%  Similarity=0.153  Sum_probs=74.8

Q ss_pred             CChHHHHHHHHHHhCC-CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEE
Q 027749           55 KPSAIQQRAVMPIIKG-RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAH  133 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~-~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~  133 (219)
                      .+++-|+.++..+..+ +-++|.|+.|+|||... -.+...+...  +..+++++||...+..+.+..       ++.. 
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--GYRVIGAALSGKAAEGLQAES-------GIES-  420 (744)
T ss_pred             CCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHHH-HHHHHHHHhC--CCeEEEEeCcHHHHHHHHhcc-------CCce-
Confidence            5899999999998874 56899999999999443 3344444433  456999999988776654321       2211 


Q ss_pred             EEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhC-CCCCeEEEE
Q 027749          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL-PPDLQVCCP  212 (219)
Q Consensus       134 ~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~-~~~~q~i~~  212 (219)
                                             .|-.+++.-.......+...++|||||+-++...    .+..+++.. +...++|++
T Consensus       421 -----------------------~Ti~~~~~~~~~~~~~~~~~~llIvDEasMv~~~----~~~~Ll~~~~~~~~kliLV  473 (744)
T TIGR02768       421 -----------------------RTLASLEYAWANGRDLLSDKDVLVIDEAGMVGSR----QMARVLKEAEEAGAKVVLV  473 (744)
T ss_pred             -----------------------eeHHHHHhhhccCcccCCCCcEEEEECcccCCHH----HHHHHHHHHHhcCCEEEEE
Confidence                                   1222222111222223567889999999865533    344455532 345667766


Q ss_pred             e
Q 027749          213 G  213 (219)
Q Consensus       213 S  213 (219)
                      .
T Consensus       474 G  474 (744)
T TIGR02768       474 G  474 (744)
T ss_pred             C
Confidence            4

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.

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]

Probab=98.21  E-value=1.1e-05  Score=68.85  Aligned_cols=128  Identities=20%  Similarity=0.227  Sum_probs=85.0

Q ss_pred             CChHHHHHHHHHHhCC-----CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccc
Q 027749           55 KPSAIQQRAVMPIIKG-----RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~-----~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (219)
                      .+-|+|.+.+-.+...     ...++.-.+|.|||.-.+..++..    ..+...|+|+|+.++ .|+.+++..... -.
T Consensus       184 ~LL~fQkE~l~Wl~~QE~Ss~~GGiLADEMGMGKTIQtIaLllae----~~ra~tLVvaP~VAl-mQW~nEI~~~T~-gs  257 (791)
T KOG1002|consen  184 PLLPFQKEGLAWLTSQEESSVAGGILADEMGMGKTIQTIALLLAE----VDRAPTLVVAPTVAL-MQWKNEIERHTS-GS  257 (791)
T ss_pred             cchhhhHHHHHHHHHhhhhhhccceehhhhccchHHHHHHHHHhc----cccCCeeEEccHHHH-HHHHHHHHHhcc-Cc
Confidence            5578899877655432     246788889999995554444442    223349999999887 578899988776 35


Q ss_pred             eeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCC-------------CCCCCccE--EEeccchhhhcc
Q 027749          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT-------------LRTRAIKL--LVLDESDEMLSR  190 (219)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~-------------~~~~~l~~--lVvDE~h~l~~~  190 (219)
                      .++...+|.. ......++ .+++++.+|...+....+...             ..+..+++  ||+||||.+-+.
T Consensus       258 lkv~~YhG~~-R~~nikel-~~YDvVLTty~vvEs~yRk~~~GfrrKngv~ke~SlLHsi~~~RiIlDEAH~IK~R  331 (791)
T KOG1002|consen  258 LKVYIYHGAK-RDKNIKEL-MNYDVVLTTYAVVESVYRKQDYGFRRKNGVDKEKSLLHSIKFYRIILDEAHNIKDR  331 (791)
T ss_pred             eEEEEEeccc-ccCCHHHh-hcCcEEEEecHHHHHHHHhccccccccCCcccccchhhhceeeeeehhhhcccccc
Confidence            6666666543 33333333 468999999988877665311             12344444  999999987653

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=98.21  E-value=5.2e-06  Score=74.59  Aligned_cols=144  Identities=13%  Similarity=0.105  Sum_probs=78.5

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHH---Hhc---cccceeEEEEECCcccHHH
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL---AIG---DFINIQAHACVGGKSVGED  144 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~---~~~---~~~~~~~~~~~~~~~~~~~  144 (219)
                      -++-|.+.||+|||.||+-.++..=...+ -.+-|||||+.+.-.-++-...   +..   .+.+.+...+.-.......
T Consensus        75 lNiDI~METGTGKTy~YlrtmfeLhk~YG-~~KFIivVPs~AIkeGv~~~s~~~~ehF~k~~Yent~~e~~i~~~~~~~~  153 (985)
T COG3587          75 LNIDILMETGTGKTYTYLRTMFELHKKYG-LFKFIIVVPSLAIKEGVFLTSKETTEHFFKSEYENTRLESYIYDEDIEKF  153 (985)
T ss_pred             ceeeEEEecCCCceeeHHHHHHHHHHHhC-ceeEEEEeccHHHHhhhHHHHHHHHHHHhhhhccCcceeEEeechHHHHH
Confidence            47889999999999999876655333322 3568999999987665443331   111   1112333333222222222


Q ss_pred             HHHhcCCCeEEEeChHHHHHH------HHcCCCCCCC--------------c-cEEEeccchhhhccccHHHHHHHHHhC
Q 027749          145 IRKLEHGVHVVSGTPGRVCDM------IKRKTLRTRA--------------I-KLLVLDESDEMLSRGFKDQIYDVYRYL  203 (219)
Q Consensus       145 ~~~l~~~~~I~v~Tp~~l~~~------l~~~~~~~~~--------------l-~~lVvDE~h~l~~~~~~~~~~~i~~~~  203 (219)
                      ...-.+.+.+++.|...+..-      +.+......+              + -.+|+||-|+|...  ......+...-
T Consensus       154 ~~~~~~~~~vLl~~~~Afnk~~inan~iN~~s~~~~~~~~~~~spvd~la~~rPIvIvDEPh~f~~~--~k~~~~i~~l~  231 (985)
T COG3587         154 KFKSNNKPCVLLIFVSAFNKEEINANMINSESMENTNLFNGATSPVDALASMRPIVIVDEPHRFLGD--DKTYGAIKQLN  231 (985)
T ss_pred             hhccCCCceEEEEehhhhccccccccccchhhhcccCccccccCHHHHHHhcCCEEEecChhhcccc--hHHHHHHHhhC
Confidence            222234677888776555322      2211111111              1 37999999998864  12222232221


Q ss_pred             CCCCeEEEEeecccCC
Q 027749          204 PPDLQVCCPGSCFLFD  219 (219)
Q Consensus       204 ~~~~q~i~~SATl~~~  219 (219)
                        ..-++=+|||++.+
T Consensus       232 --pl~ilRfgATfkd~  245 (985)
T COG3587         232 --PLLILRFGATFKDE  245 (985)
T ss_pred             --ceEEEEecccchhh
Confidence              12367799998753

>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]

Probab=98.15  E-value=8.9e-06  Score=75.51  Aligned_cols=148  Identities=14%  Similarity=0.173  Sum_probs=98.2

Q ss_pred             CCChHHHHHHHHHHh----CCCcEEEEcCCCCchh---HHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhcc
Q 027749           54 EKPSAIQQRAVMPII----KGRDVIAQAQSGTGKT---SMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGD  126 (219)
Q Consensus        54 ~~~~~~Q~~~~~~~~----~~~~~lv~~~tG~GKT---~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~  126 (219)
                      ..++.+|.+-++-++    ++.+.|+.-.+|-|||   .+|+-.+.+.....  +| .|+|+|...+. .+...+..+. 
T Consensus       369 ~~LRdyQLeGlNWl~~~W~~~~n~ILADEmgLgktvqti~fl~~l~~~~~~~--gp-flvvvplst~~-~W~~ef~~w~-  443 (1373)
T KOG0384|consen  369 NELRDYQLEGLNWLLYSWYKRNNCILADEMGLGKTVQTITFLSYLFHSLQIH--GP-FLVVVPLSTIT-AWEREFETWT-  443 (1373)
T ss_pred             chhhhhhcccchhHHHHHHhcccceehhhcCCCcchHHHHHHHHHHHhhhcc--CC-eEEEeehhhhH-HHHHHHHHHh-
Confidence            467788888776654    6789999999999999   34444444443332  44 68888976654 4667777765 


Q ss_pred             ccceeEEEEECCcccHHHHHHhc----C-----CCeEEEeChHHHHHHHHcCCCCCCCc--cEEEeccchhhhccccHHH
Q 027749          127 FINIQAHACVGGKSVGEDIRKLE----H-----GVHVVSGTPGRVCDMIKRKTLRTRAI--KLLVLDESDEMLSRGFKDQ  195 (219)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~l~----~-----~~~I~v~Tp~~l~~~l~~~~~~~~~l--~~lVvDE~h~l~~~~~~~~  195 (219)
                        .+++++++|.....+.++...    .     ..+++++|.+.++.    ..-.++.+  .+++|||||+|-+..  ..
T Consensus       444 --~mn~i~y~g~~~sr~~i~~ye~~~~~~~~~lkf~~lltTye~~Lk----Dk~~L~~i~w~~~~vDeahrLkN~~--~~  515 (1373)
T KOG0384|consen  444 --DMNVIVYHGNLESRQLIRQYEFYHSSNTKKLKFNALLTTYEIVLK----DKAELSKIPWRYLLVDEAHRLKNDE--SK  515 (1373)
T ss_pred             --hhceeeeecchhHHHHHHHHHheecCCccccccceeehhhHHHhc----cHhhhccCCcceeeecHHhhcCchH--HH
Confidence              689999999888776655542    1     47899999876653    22224444  479999999987653  33


Q ss_pred             HHHHHHhCCCCCeEEEEeec
Q 027749          196 IYDVYRYLPPDLQVCCPGSC  215 (219)
Q Consensus       196 ~~~i~~~~~~~~q~i~~SAT  215 (219)
                      +...+..+.-+ ..+++|+|
T Consensus       516 l~~~l~~f~~~-~rllitgT  534 (1373)
T KOG0384|consen  516 LYESLNQFKMN-HRLLITGT  534 (1373)
T ss_pred             HHHHHHHhccc-ceeeecCC
Confidence            44445555433 24556665

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=98.08  E-value=8.7e-06  Score=75.12  Aligned_cols=127  Identities=17%  Similarity=0.208  Sum_probs=89.9

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEE
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (219)
                      .|+++|...  .+.-...-|....||-|||+++.+|++......++   +-+|+.+--||..=.+.+..+....|+++.+
T Consensus       169 ~~yDVQliG--givLh~G~IAEM~TGEGKTLvAtlp~yLnAL~Gkg---VHvVTVNDYLA~RDaewmgply~fLGLsvg~  243 (1112)
T PRK12901        169 VHYDVQLIG--GVVLHQGKIAEMATGEGKTLVATLPVYLNALTGNG---VHVVTVNDYLAKRDSEWMGPLYEFHGLSVDC  243 (1112)
T ss_pred             cccchHHhh--hhhhcCCceeeecCCCCchhHHHHHHHHHHHcCCC---cEEEEechhhhhccHHHHHHHHHHhCCceee
Confidence            567777443  33333446889999999999999999888777544   7777888889987777888888888999987


Q ss_pred             EEC-CcccHHHHHHhcCCCeEEEeChHHHHH-HHHcC------CCCCCCccEEEeccchhhh
Q 027749          135 CVG-GKSVGEDIRKLEHGVHVVSGTPGRVCD-MIKRK------TLRTRAIKLLVLDESDEML  188 (219)
Q Consensus       135 ~~~-~~~~~~~~~~l~~~~~I~v~Tp~~l~~-~l~~~------~~~~~~l~~lVvDE~h~l~  188 (219)
                      ... ..+..+  ++-...|||..+|...|-. +|+-+      ......+.+.||||+|-++
T Consensus       244 i~~~~~~~~~--rr~aY~~DItYgTn~EfGFDYLRDnm~~~~~~~vqR~~~fAIVDEvDSIL  303 (1112)
T PRK12901        244 IDKHQPNSEA--RRKAYNADITYGTNNEFGFDYLRDNMAHSPEDLVQRKHNYAIVDEVDSVL  303 (1112)
T ss_pred             cCCCCCCHHH--HHHhCCCcceecCCCccccccchhccccchHhhhCcCCceeEeechhhhh
Confidence            765 323333  3344589999999876642 33211      1123557899999999755

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=98.08  E-value=0.00011  Score=69.20  Aligned_cols=135  Identities=16%  Similarity=0.136  Sum_probs=83.2

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHHhC-CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHH
Q 027749           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPIIK-GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE  118 (219)
Q Consensus        40 l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~  118 (219)
                      +++..++.....++ .+++-|..++..+.. ++-.+|.|+.|+|||.+ +-.+...+...  +.+++-++||..-+..+.
T Consensus       367 v~~~~l~a~~~~~~-~Ls~eQ~~Av~~i~~~~r~~~v~G~AGTGKTt~-l~~~~~~~e~~--G~~V~g~ApTgkAA~~L~  442 (1102)
T PRK13826        367 VREAVLAATFARHA-RLSDEQKTAIEHVAGPARIAAVVGRAGAGKTTM-MKAAREAWEAA--GYRVVGGALAGKAAEGLE  442 (1102)
T ss_pred             CCHHHHHHHHhcCC-CCCHHHHHHHHHHhccCCeEEEEeCCCCCHHHH-HHHHHHHHHHc--CCeEEEEcCcHHHHHHHH
Confidence            44555554444343 689999999998864 45689999999999933 33444444443  456999999988876654


Q ss_pred             HHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHH
Q 027749          119 KVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYD  198 (219)
Q Consensus       119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~  198 (219)
                      +..       ++..                        .|-.+|+.-.......+..-++|||||+.++.    ...+..
T Consensus       443 e~~-------Gi~a------------------------~TIas~ll~~~~~~~~l~~~~vlVIDEAsMv~----~~~m~~  487 (1102)
T PRK13826        443 KEA-------GIQS------------------------RTLSSWELRWNQGRDQLDNKTVFVLDEAGMVA----SRQMAL  487 (1102)
T ss_pred             Hhh-------CCCe------------------------eeHHHHHhhhccCccCCCCCcEEEEECcccCC----HHHHHH
Confidence            322       2221                        12222221111122235566799999998654    345556


Q ss_pred             HHHhCC-CCCeEEEEe
Q 027749          199 VYRYLP-PDLQVCCPG  213 (219)
Q Consensus       199 i~~~~~-~~~q~i~~S  213 (219)
                      +++..+ ...++|++.
T Consensus       488 Ll~~~~~~garvVLVG  503 (1102)
T PRK13826        488 FVEAVTRAGAKLVLVG  503 (1102)
T ss_pred             HHHHHHhcCCEEEEEC
Confidence            666654 467777765

>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=98.08  E-value=1.4e-05  Score=65.44  Aligned_cols=69  Identities=17%  Similarity=0.215  Sum_probs=53.2

Q ss_pred             ChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccC-CCceeEEEEcCCHHHHHHHHHHHHHhcc
Q 027749           56 PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-SREVQALILSPTRELATQTEKVILAIGD  126 (219)
Q Consensus        56 ~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~-~~~~~~lil~P~~~l~~q~~~~~~~~~~  126 (219)
                      +++-|.+++..  ..++++|.|+.|||||.+.+--+...+... ....+++++++|+..+.++.+++.....
T Consensus         1 l~~eQ~~~i~~--~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~~~~~~Il~lTft~~aa~e~~~ri~~~l~   70 (315)
T PF00580_consen    1 LTDEQRRIIRS--TEGPLLVNAGAGSGKTTTLLERIAYLLYEGGVPPERILVLTFTNAAAQEMRERIRELLE   70 (315)
T ss_dssp             S-HHHHHHHHS---SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHhC--CCCCEEEEeCCCCCchHHHHHHHHHhhccccCChHHheecccCHHHHHHHHHHHHHhcC
Confidence            36778888887  667999999999999987766666655544 3456799999999999999999987643

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=98.08  E-value=2.5e-05  Score=67.04  Aligned_cols=150  Identities=19%  Similarity=0.252  Sum_probs=98.1

Q ss_pred             CCCChHHHHHHHHHHhCCCcEEEEcCC-CCch--hHHhHHHHHhhhccC----------------------------CCc
Q 027749           53 FEKPSAIQQRAVMPIIKGRDVIAQAQS-GTGK--TSMIALTVCQTVDTS----------------------------SRE  101 (219)
Q Consensus        53 ~~~~~~~Q~~~~~~~~~~~~~lv~~~t-G~GK--T~~~~~~~~~~~~~~----------------------------~~~  101 (219)
                      -..+++.|.+.+....+.++++..-.+ +.|+  +..|.+.++.++...                            -..
T Consensus       214 s~pltalQ~~L~~~m~~YrDl~y~~~s~kn~~e~R~lYclH~lNHi~K~r~~IL~Nn~r~~Sqk~g~~~~~~frDQG~tR  293 (698)
T KOG2340|consen  214 SEPLTALQKELFKIMFNYRDLLYPTRSQKNGEEYRSLYCLHALNHILKTRDLILGNNRRLASQKEGENPDESFRDQGFTR  293 (698)
T ss_pred             cCcchHHHHHHHHHHHhhhhhccccccccccchhhhhHHHHHHHHHHHHHHHHhcchHhhhhhhcCCCCchhhhhcCCCC
Confidence            357899999999999998887654332 3344  346777777665321                            013


Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhccccce---eE------EEEECC--------cccHHHHHH-----------------
Q 027749          102 VQALILSPTRELATQTEKVILAIGDFINI---QA------HACVGG--------KSVGEDIRK-----------------  147 (219)
Q Consensus       102 ~~~lil~P~~~l~~q~~~~~~~~~~~~~~---~~------~~~~~~--------~~~~~~~~~-----------------  147 (219)
                      |++|||||+++-|-.+.+.+..++...+-   .+      ..-+++        .+..++...                 
T Consensus       294 pkVLivvpfRe~A~riVn~lis~l~G~~q~k~~V~Nk~RF~~eys~~te~~~~~~~kP~D~~~lf~GNtDD~FriGl~ft  373 (698)
T KOG2340|consen  294 PKVLIVVPFRESAYRIVNLLISLLSGDDQGKSEVWNKKRFEGEYSGPTELPPPRAKKPEDFEELFSGNTDDAFRIGLAFT  373 (698)
T ss_pred             ceEEEEecchHHHHHHHHHHHHHhcCccccchhhhhhhhhchhcCCCcccCCCCCCCchhHHHHhcCCCcchhhhhHHHH
Confidence            89999999999999999988777433210   00      000111        011111111                 


Q ss_pred             -----h---cCCCeEEEeChHHHHHHHHcCC------CCCCCccEEEeccchhhhccccHHHHHHHHHhC
Q 027749          148 -----L---EHGVHVVSGTPGRVCDMIKRKT------LRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL  203 (219)
Q Consensus       148 -----l---~~~~~I~v~Tp~~l~~~l~~~~------~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~  203 (219)
                           +   ...++|+||+|-.|.-++.+.+      -.++.+.++|||.+|.++..+ ++.+..++++|
T Consensus       374 kKtikLys~fy~SDIlVaSPLGLRmil~n~gdkkrd~dfLSSIEl~iIDQa~~~l~QN-wEhl~~ifdHL  442 (698)
T KOG2340|consen  374 KKTIKLYSKFYKSDILVASPLGLRMILGNTGDKKRDFDFLSSIELLIIDQADIMLMQN-WEHLLHIFDHL  442 (698)
T ss_pred             HHHHHHHhhhcccCeEEecchhhhhhhcCCCcccccchhhhhhhhhhhhhHHHHHHhh-HHHHHHHHHHh
Confidence                 1   1357999999999988887432      235778899999999888665 67788888886

>PF14617 CMS1: U3-containing 90S pre-ribosomal complex subunit

Probab=97.97  E-value=2.4e-05  Score=62.11  Aligned_cols=86  Identities=21%  Similarity=0.331  Sum_probs=67.9

Q ss_pred             CCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCc-ccHHHHHHhc-CCCeEEEeChHHHHHHHHcCCCCCCCc
Q 027749           99 SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGK-SVGEDIRKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (219)
Q Consensus        99 ~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~l~-~~~~I~v~Tp~~l~~~l~~~~~~~~~l  176 (219)
                      .+.|.+|||+..---|-.+.+.++.+... +..+..++..+ ...++...+. ....|.||||+++..++.++.+.++++
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 KGSPHVLVVSSSALRAADLIRALRSFKGK-DCKVAKLFAKHIKLEEQVKLLKKTRVHIAVGTPGRLSKLLENGALSLSNL  202 (252)
T ss_pred             CCCCEEEEEcchHHHHHHHHHHHHhhccC-CchHHHHHHhhccHHHHHHHHHhCCceEEEeChHHHHHHHHcCCCCcccC
Confidence            35689999999988888888888876422 24444455444 6667766665 378999999999999999999999999


Q ss_pred             cEEEeccch
Q 027749          177 KLLVLDESD  185 (219)
Q Consensus       177 ~~lVvDE~h  185 (219)
                      .+||||--|
T Consensus       203 ~~ivlD~s~  211 (252)
T PF14617_consen  203 KRIVLDWSY  211 (252)
T ss_pred             eEEEEcCCc
Confidence            999999865

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=97.95  E-value=0.00013  Score=51.87  Aligned_cols=21  Identities=29%  Similarity=0.495  Sum_probs=13.0

Q ss_pred             CCCcEEEEcCCCCchhHHhHH
Q 027749           69 KGRDVIAQAQSGTGKTSMIAL   89 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~   89 (219)
                      +++.++|.|++|+|||.....
T Consensus         3 ~~~~~~i~G~~G~GKT~~~~~   23 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLIKR   23 (131)
T ss_dssp             ----EEEEE-TTSSHHHHHHH
T ss_pred             CCcccEEEcCCCCCHHHHHHH
Confidence            346789999999999955433

>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]

Probab=97.92  E-value=7.2e-05  Score=69.57  Aligned_cols=151  Identities=15%  Similarity=0.140  Sum_probs=96.5

Q ss_pred             CChHHHHHHHHHHh----CCCcEEEEcCCCCchhHHhHHHHHhhhc--cCCCceeEEEEcCCHHHHHHHHHHHHHhcccc
Q 027749           55 KPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVD--TSSREVQALILSPTRELATQTEKVILAIGDFI  128 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~----~~~~~lv~~~tG~GKT~~~~~~~~~~~~--~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~  128 (219)
                      .++.+|...+..+.    ++-|.|+.-.+|-||| +-.+.++.++.  ....+| -|||+||..+.+ |.=++++|+.  
T Consensus       615 qLReYQkiGLdWLatLYeknlNGILADEmGLGKT-IQtISllAhLACeegnWGP-HLIVVpTsviLn-WEMElKRwcP--  689 (1958)
T KOG0391|consen  615 QLREYQKIGLDWLATLYEKNLNGILADEMGLGKT-IQTISLLAHLACEEGNWGP-HLIVVPTSVILN-WEMELKRWCP--  689 (1958)
T ss_pred             HHHHHHHhhHHHHHHHHHhcccceehhhhcccch-hHHHHHHHHHHhcccCCCC-ceEEeechhhhh-hhHHHhhhCC--
Confidence            44667877776543    4457899999999999 44444555553  334566 688889887654 5667788876  


Q ss_pred             ceeEEEEECCcccHHHHHHhcC---CCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCC
Q 027749          129 NIQAHACVGGKSVGEDIRKLEH---GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP  205 (219)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~l~~---~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~  205 (219)
                      ++.+..++|........+.-..   ...|-|++...+..-+.  .+.-++-.|+|+||||++-++. ...++.++..-  
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            5788888887765544433322   34566666544433221  1222456799999999988774 45566666552  


Q ss_pred             CCeEEEEeec
Q 027749          206 DLQVCCPGSC  215 (219)
Q Consensus       206 ~~q~i~~SAT  215 (219)
                      ..+.++++.|
T Consensus       765 sqrRLLLtgT  774 (1958)
T KOG0391|consen  765 SQRRLLLTGT  774 (1958)
T ss_pred             hhheeeecCC
Confidence            3467777776

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=97.90  E-value=7.4e-05  Score=61.71  Aligned_cols=144  Identities=14%  Similarity=0.162  Sum_probs=87.6

Q ss_pred             HCCCCCChHHHHHHHHHHhCCC--cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHH-------HH
Q 027749           50 QYGFEKPSAIQQRAVMPIIKGR--DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE-------KV  120 (219)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~~~~~~--~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~-------~~  120 (219)
                      -+|+..-+..|..|+..++...  =+.+.|+.|+|||+-++.+.++.....+.-.++|+.=|+..+.+++-       +.
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            4577777888999999888653  36688999999998888888887777666677888888766653221       11


Q ss_pred             HHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCC----------ccEEEeccchhhhcc
Q 027749          121 ILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRA----------IKLLVLDESDEMLSR  190 (219)
Q Consensus       121 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~----------l~~lVvDE~h~l~~~  190 (219)
                      +..|++..           ...-+.-...+.|     +-+.+..++....+.+..          =.+||+|||.++.  
T Consensus       303 m~PWmq~i-----------~DnLE~L~~~~~~-----~~~~l~~~l~~~~iev~alt~IRGRSl~~~FiIIDEaQNLT--  364 (436)
T COG1875         303 MGPWMQAI-----------FDNLEVLFSPNEP-----GDRALEEILSRGRIEVEALTYIRGRSLPDSFIIIDEAQNLT--  364 (436)
T ss_pred             ccchHHHH-----------HhHHHHHhccccc-----chHHHHHHHhccceeeeeeeeecccccccceEEEehhhccC--
Confidence            11111110           0000000001112     133333444333322211          2489999999876  


Q ss_pred             ccHHHHHHHHHhCCCCCeEEEEe
Q 027749          191 GFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       191 ~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                        ..++..++....+...++++.
T Consensus       365 --pheikTiltR~G~GsKIVl~g  385 (436)
T COG1875         365 --PHELKTILTRAGEGSKIVLTG  385 (436)
T ss_pred             --HHHHHHHHHhccCCCEEEEcC
Confidence              578899999888877777653

>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=97.86  E-value=0.00038  Score=49.79  Aligned_cols=25  Identities=24%  Similarity=0.510  Sum_probs=17.9

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhh
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTV   95 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~   95 (219)
                      ++.+++.||+|+|||. .+-.++..+
T Consensus        19 ~~~v~i~G~~G~GKT~-l~~~i~~~~   43 (151)
T cd00009          19 PKNLLLYGPPGTGKTT-LARAIANEL   43 (151)
T ss_pred             CCeEEEECCCCCCHHH-HHHHHHHHh
Confidence            6789999999999994 333344433

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.

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=97.86  E-value=9.4e-05  Score=62.39  Aligned_cols=59  Identities=22%  Similarity=0.263  Sum_probs=43.2

Q ss_pred             ChHHHHHHHHHH------hCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHH
Q 027749           56 PSAIQQRAVMPI------IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQT  117 (219)
Q Consensus        56 ~~~~Q~~~~~~~------~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~  117 (219)
                      +++-|++++..+      ..+.++.|.|+.|+|||  |++-.+...... .+..+++++||...|..+
T Consensus         2 Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs--~l~~~i~~~~~~-~~~~~~~~a~tg~AA~~i   66 (364)
T PF05970_consen    2 LNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKS--FLIKAIIDYLRS-RGKKVLVTAPTGIAAFNI   66 (364)
T ss_pred             CCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChh--HHHHHHHHHhcc-ccceEEEecchHHHHHhc
Confidence            567789998887      67788999999999999  444333333332 245699999998777655

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]

Probab=97.83  E-value=4.3e-05  Score=65.77  Aligned_cols=73  Identities=23%  Similarity=0.277  Sum_probs=55.1

Q ss_pred             CChHHHHHHHHHHhCC-----CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccc
Q 027749           55 KPSAIQQRAVMPIIKG-----RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~-----~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (219)
                      .|...|-+||..+..|     +.-.+.|.||||||+...- ++....    .| +||++|.+.||.|++.+++.+.....
T Consensus        12 ~PaGDQP~AI~~Lv~gi~~g~~~QtLLGvTGSGKTfT~An-VI~~~~----rP-tLV~AhNKTLAaQLy~Efk~fFP~Na   85 (663)
T COG0556          12 KPAGDQPEAIAELVEGIENGLKHQTLLGVTGSGKTFTMAN-VIAKVQ----RP-TLVLAHNKTLAAQLYSEFKEFFPENA   85 (663)
T ss_pred             CCCCCcHHHHHHHHHHHhcCceeeEEeeeccCCchhHHHH-HHHHhC----CC-eEEEecchhHHHHHHHHHHHhCcCcc
Confidence            6778888888876543     4678899999999955433 233222    22 99999999999999999999988765


Q ss_pred             eeEE
Q 027749          130 IQAH  133 (219)
Q Consensus       130 ~~~~  133 (219)
                      +...
T Consensus        86 VEYF   89 (663)
T COG0556          86 VEYF   89 (663)
T ss_pred             eEEE
Confidence            5544

>KOG1805 consensus DNA replication helicase [Replication, recombination and repair]

Probab=97.83  E-value=0.00014  Score=66.60  Aligned_cols=143  Identities=16%  Similarity=0.183  Sum_probs=88.1

Q ss_pred             cCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCc-EEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHH
Q 027749           37 AMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRD-VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELAT  115 (219)
Q Consensus        37 ~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~-~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~  115 (219)
                      ...+.+.+.+.    -...++..|++|+..++..++ .+|.|=+|+|||..... +++.+...  +.++|..+-|+..+.
T Consensus       655 ~~~~~p~~~~~----~~~~LN~dQr~A~~k~L~aedy~LI~GMPGTGKTTtI~~-LIkiL~~~--gkkVLLtsyThsAVD  727 (1100)
T KOG1805|consen  655 SKVLIPKIKKI----ILLRLNNDQRQALLKALAAEDYALILGMPGTGKTTTISL-LIKILVAL--GKKVLLTSYTHSAVD  727 (1100)
T ss_pred             ccccCchhhHH----HHhhcCHHHHHHHHHHHhccchheeecCCCCCchhhHHH-HHHHHHHc--CCeEEEEehhhHHHH
Confidence            44456665554    223578889999998886654 78899999999955443 44555444  345999999999888


Q ss_pred             HHHHHHHHhcccc---c--eeE------EEEECCc--ccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEec
Q 027749          116 QTEKVILAIGDFI---N--IQA------HACVGGK--SVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLD  182 (219)
Q Consensus       116 q~~~~~~~~~~~~---~--~~~------~~~~~~~--~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvD  182 (219)
                      .+.-.+..+.-..   |  ..+      .+.....  ..-+...+..+...|+.+|--.+.+-+.    ..+.++|.|||
T Consensus       728 NILiKL~~~~i~~lRLG~~~kih~~v~e~~~~~~~s~ks~~~l~~~~~~~~IVa~TClgi~~plf----~~R~FD~cIiD  803 (1100)
T KOG1805|consen  728 NILIKLKGFGIYILRLGSEEKIHPDVEEFTLTNETSEKSYADLKKFLDQTSIVACTCLGINHPLF----VNRQFDYCIID  803 (1100)
T ss_pred             HHHHHHhccCcceeecCCccccchHHHHHhcccccchhhHHHHHHHhCCCcEEEEEccCCCchhh----hccccCEEEEc
Confidence            7777666543221   0  000      0001111  1112233444567899998654443332    23568999999


Q ss_pred             cchhhhcc
Q 027749          183 ESDEMLSR  190 (219)
Q Consensus       183 E~h~l~~~  190 (219)
                      ||-++..+
T Consensus       804 EASQI~lP  811 (1100)
T KOG1805|consen  804 EASQILLP  811 (1100)
T ss_pred             cccccccc
Confidence            99987754

>KOG0388 consensus SNF2 family DNA-dependent ATPase [Replication, recombination and repair]

Probab=97.80  E-value=7.5e-05  Score=66.32  Aligned_cols=148  Identities=16%  Similarity=0.131  Sum_probs=92.9

Q ss_pred             HHHHHHHHH----HhCCCcEEEEcCCCCchhHHhHHHHHhhhccCC-CceeEEEEcCCHHHHHHHHHHHHHhccccceeE
Q 027749           58 AIQQRAVMP----IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-REVQALILSPTRELATQTEKVILAIGDFINIQA  132 (219)
Q Consensus        58 ~~Q~~~~~~----~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~-~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  132 (219)
                      .+|.+.+..    .-+|-+.|+.-.+|-|||.-.+..+.+...... .+| .|+|+|...| +.+..++.+++.  .+.+
T Consensus       570 EYQlkGLnWLvnlYdqGiNGILADeMGLGKTVQsisvlAhLaE~~nIwGP-FLVVtpaStL-~NWaqEisrFlP--~~k~  645 (1185)
T KOG0388|consen  570 EYQLKGLNWLVNLYDQGINGILADEMGLGKTVQSISVLAHLAETHNIWGP-FLVVTPASTL-HNWAQEISRFLP--SFKV  645 (1185)
T ss_pred             HHhhccHHHHHHHHHccccceehhhhccchhHHHHHHHHHHHHhccCCCc-eEEeehHHHH-hHHHHHHHHhCc--ccee
Confidence            455555443    347889999999999999655544444443332 355 6888997666 557777777765  4778


Q ss_pred             EEEECCcccHHHHHHh---------cCCCeEEEeChHHHHHHHHcCCCCCCCc--cEEEeccchhhhccccHHHHHHHHH
Q 027749          133 HACVGGKSVGEDIRKL---------EHGVHVVSGTPGRVCDMIKRKTLRTRAI--KLLVLDESDEMLSRGFKDQIYDVYR  201 (219)
Q Consensus       133 ~~~~~~~~~~~~~~~l---------~~~~~I~v~Tp~~l~~~l~~~~~~~~~l--~~lVvDE~h~l~~~~~~~~~~~i~~  201 (219)
                      +...|+.+.....++.         ..+.+|+|+|.+.+..-    .-.++++  .|.|+|||..+-+.. ......++.
T Consensus       646 lpywGs~~eRkiLrKfw~rKnmY~rna~fhVviTSYQlvVtD----eky~qkvKWQYMILDEAQAIKSSs-S~RWKtLLs  720 (1185)
T KOG0388|consen  646 LPYWGSPSERKILRKFWNRKNMYRRNAPFHVVITSYQLVVTD----EKYLQKVKWQYMILDEAQAIKSSS-SSRWKTLLS  720 (1185)
T ss_pred             ecCcCChhhhHHHHHhcchhhhhccCCCceEEEEeeeeeech----HHHHHhhhhhheehhHHHHhhhhh-hhHHHHHhh
Confidence            8888887755544441         23578888886544310    0112333  479999999876543 455666665


Q ss_pred             hCCCCCeEEEEeecc
Q 027749          202 YLPPDLQVCCPGSCF  216 (219)
Q Consensus       202 ~~~~~~q~i~~SATl  216 (219)
                      .-  .+..+++++|.
T Consensus       721 F~--cRNRLLLTGTP  733 (1185)
T KOG0388|consen  721 FK--CRNRLLLTGTP  733 (1185)
T ss_pred             hh--ccceeeecCCc
Confidence            52  23367777773

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=97.80  E-value=0.00014  Score=58.70  Aligned_cols=45  Identities=16%  Similarity=0.178  Sum_probs=34.2

Q ss_pred             CCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEeec
Q 027749          170 TLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSC  215 (219)
Q Consensus       170 ~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SAT  215 (219)
                      .-....++.+|+||||.|... .+..+.+.++..+....+++.+.-
T Consensus       124 ~~~~~~fKiiIlDEcdsmtsd-aq~aLrr~mE~~s~~trFiLIcny  168 (346)
T KOG0989|consen  124 GYPCPPFKIIILDECDSMTSD-AQAALRRTMEDFSRTTRFILICNY  168 (346)
T ss_pred             CCCCCcceEEEEechhhhhHH-HHHHHHHHHhccccceEEEEEcCC
Confidence            345567899999999998865 377888888888777777666543

>COG0553 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]

Probab=97.75  E-value=0.00027  Score=65.92  Aligned_cols=135  Identities=19%  Similarity=0.144  Sum_probs=86.6

Q ss_pred             CCChHHHHHHHHHHh-----CCCcEEEEcCCCCchhHHhHHHHHhhhccCCC-ceeEEEEcCCHHHHHHHHHHHHHhccc
Q 027749           54 EKPSAIQQRAVMPII-----KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR-EVQALILSPTRELATQTEKVILAIGDF  127 (219)
Q Consensus        54 ~~~~~~Q~~~~~~~~-----~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~-~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (219)
                      ..+.++|.+.++.+.     .+.+.++...+|.|||+..+..+.+....... .+.+++++|+. ++.++.+++.++...
T Consensus       337 ~~lr~yq~~g~~wl~~~l~~~~~~~ilaD~mglGKTiq~i~~l~~~~~~~~~~~~~~liv~p~s-~~~nw~~e~~k~~~~  415 (866)
T COG0553         337 AELRPYQLEGVNWLSELLRSNLLGGILADDMGLGKTVQTIALLLSLLESIKVYLGPALIVVPAS-LLSNWKREFEKFAPD  415 (866)
T ss_pred             hhhHHHHHHHHHHHHHHHHhccCCCcccccccchhHHHHHHHHHhhhhcccCCCCCeEEEecHH-HHHHHHHHHhhhCcc
Confidence            356778888776543     35678888999999996655544442322222 34699999964 556788888777665


Q ss_pred             cceeEEEEECCccc----HHHHHHhcCC-----CeEEEeChHHHHHHH-HcCCCCCCCccEEEeccchhhhcc
Q 027749          128 INIQAHACVGGKSV----GEDIRKLEHG-----VHVVSGTPGRVCDMI-KRKTLRTRAIKLLVLDESDEMLSR  190 (219)
Q Consensus       128 ~~~~~~~~~~~~~~----~~~~~~l~~~-----~~I~v~Tp~~l~~~l-~~~~~~~~~l~~lVvDE~h~l~~~  190 (219)
                      ... +....|....    .+....+...     .+++++|.+.+.... ....+.-....++|+||+|.+-+.
T Consensus       416 ~~~-~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~v~itty~~l~~~~~~~~~l~~~~~~~~v~DEa~~ikn~  487 (866)
T COG0553         416 LRL-VLVYHGEKSELDKKREALRDLLKLHLVIIFDVVITTYELLRRFLVDHGGLKKIEWDRVVLDEAHRIKND  487 (866)
T ss_pred             ccc-eeeeeCCcccccHHHHHHHHHhhhcccceeeEEechHHHHHHhhhhHHHHhhceeeeeehhhHHHHhhh
Confidence            433 5556665541    3333333322     789999998877632 112233345678999999997655

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.72  E-value=0.00054  Score=58.08  Aligned_cols=119  Identities=18%  Similarity=0.105  Sum_probs=64.1

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhcc--CCCceeEEEEcCC-HHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHH
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDT--SSREVQALILSPT-RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRK  147 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~--~~~~~~~lil~P~-~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (219)
                      +.+++.||||+|||....-.+......  .....-+++-+.+ +.-+..+   ++.++...++.+..             
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            468899999999996654333222211  1122223444443 2323222   44444443443321             


Q ss_pred             hcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccc-cHHHHHHHHHhCCCC-CeEEEEeeccc
Q 027749          148 LEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG-FKDQIYDVYRYLPPD-LQVCCPGSCFL  217 (219)
Q Consensus       148 l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~-~~~~~~~i~~~~~~~-~q~i~~SATl~  217 (219)
                              +-++..+...+..    ..+.++|+||++.++.... ....+..+++..... .-++.+|||..
T Consensus       239 --------~~~~~~l~~~L~~----~~~~DlVLIDTaGr~~~~~~~l~el~~~l~~~~~~~e~~LVlsat~~  298 (388)
T PRK12723        239 --------IESFKDLKEEITQ----SKDFDLVLVDTIGKSPKDFMKLAEMKELLNACGRDAEFHLAVSSTTK  298 (388)
T ss_pred             --------eCcHHHHHHHHHH----hCCCCEEEEcCCCCCccCHHHHHHHHHHHHhcCCCCeEEEEEcCCCC
Confidence                    1235555554443    3568899999998765321 234556666655433 45788999864

>KOG0386 consensus Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics; Transcription]

Probab=97.70  E-value=6.5e-05  Score=68.77  Aligned_cols=152  Identities=14%  Similarity=0.092  Sum_probs=89.8

Q ss_pred             CCChHHHHHHHHHHh---C-CCcEEEEcCCCCchhHHhHHHHHhhhccCC-CceeEEEEcCCHHHHHHHHHHHHHhcccc
Q 027749           54 EKPSAIQQRAVMPII---K-GRDVIAQAQSGTGKTSMIALTVCQTVDTSS-REVQALILSPTRELATQTEKVILAIGDFI  128 (219)
Q Consensus        54 ~~~~~~Q~~~~~~~~---~-~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~-~~~~~lil~P~~~l~~q~~~~~~~~~~~~  128 (219)
                      ..+.++|...+..+.   + .-+-|+.-.+|-|||..-+.-+.+.+...+ .+| -+|+||+..|.+ +..++.++..  
T Consensus       393 G~Lk~YQl~GLqWmVSLyNNnLNGILADEMGLGKTIQtIsLitYLmE~K~~~GP-~LvivPlstL~N-W~~Ef~kWaP--  468 (1157)
T KOG0386|consen  393 GELKEYQLHGLQWMVSLYNNNLNGILADEMGLGKTIQTISLITYLMEHKQMQGP-FLIIVPLSTLVN-WSSEFPKWAP--  468 (1157)
T ss_pred             CCCchhhhhhhHHHhhccCCCcccccchhcccchHHHHHHHHHHHHHHcccCCC-eEEeccccccCC-chhhcccccc--
Confidence            367788888776543   2 347889999999999555444444444333 344 688999998876 5556666643  


Q ss_pred             ceeEEEEECCcccHHHHHH--hcCCCeEEEeChHHHHHHHHcCCCCCCCc--cEEEeccchhhhccccHHHHHHHHHhCC
Q 027749          129 NIQAHACVGGKSVGEDIRK--LEHGVHVVSGTPGRVCDMIKRKTLRTRAI--KLLVLDESDEMLSRGFKDQIYDVYRYLP  204 (219)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~--l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l--~~lVvDE~h~l~~~~~~~~~~~i~~~~~  204 (219)
                      .+..+...|..........  .....+|+++|.+.+.+    ..-.++.+  .|+||||-|+|-+.  ...+...+...-
T Consensus       469 Sv~~i~YkGtp~~R~~l~~qir~gKFnVLlTtyEyiik----dk~lLsKI~W~yMIIDEGHRmKNa--~~KLt~~L~t~y  542 (1157)
T KOG0386|consen  469 SVQKIQYKGTPQQRSGLTKQQRHGKFNVLLTTYEYIIK----DKALLSKISWKYMIIDEGHRMKNA--ICKLTDTLNTHY  542 (1157)
T ss_pred             ceeeeeeeCCHHHHhhHHHHHhcccceeeeeeHHHhcC----CHHHHhccCCcceeecccccccch--hhHHHHHhhccc
Confidence            2444444443332222111  12578999999876553    22223444  47999999998764  344444444322


Q ss_pred             CCCeEEEEeec
Q 027749          205 PDLQVCCPGSC  215 (219)
Q Consensus       205 ~~~q~i~~SAT  215 (219)
                      .....+++++|
T Consensus       543 ~~q~RLLLTGT  553 (1157)
T KOG0386|consen  543 RAQRRLLLTGT  553 (1157)
T ss_pred             cchhhhhhcCC
Confidence            22335555555

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

Probab=97.69  E-value=4.2e-05  Score=66.40  Aligned_cols=172  Identities=12%  Similarity=-0.025  Sum_probs=112.1

Q ss_pred             HHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 027749           44 LLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA  123 (219)
Q Consensus        44 ~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~  123 (219)
                      +...+.++.-+....+|.+++..+.+|++.++.-.+.+||.++|.+.....+..... ...++..|+.++++.......-
T Consensus       275 ~~~~~~~~~~E~~~~~~~~~~~~~~~G~~~~~~~~~~~GK~~~~~~~s~~~~~~~~~-s~~~~~~~~~~~~~~~~~~~~V  353 (1034)
T KOG4150|consen  275 IRSLLNKNTGESGIAISLELLKFASEGRADGGNEARQAGKGTCPTSGSRKFQTLCHA-TNSLLPSEMVEHLRNGSKGQVV  353 (1034)
T ss_pred             HHHHHhcccccchhhhhHHHHhhhhhcccccccchhhcCCccCcccchhhhhhcCcc-cceecchhHHHHhhccCCceEE
Confidence            444555566678899999999999999999999999999999999887776654433 3478888888887755443321


Q ss_pred             hcccc---ceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCC----CCCCCccEEEeccchhhhccccH---
Q 027749          124 IGDFI---NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT----LRTRAIKLLVLDESDEMLSRGFK---  193 (219)
Q Consensus       124 ~~~~~---~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~----~~~~~l~~lVvDE~h~l~~~~~~---  193 (219)
                      .....   .-.++..+.+.+........+.+..++++.|+.....+.-+.    ..+-.+.++++||+|.-. .-|.   
T Consensus       354 ~~~~I~~~K~A~V~~~D~~sE~~~~A~~R~~~~~~~s~~~~~~s~~L~~~~~~~~~~~~~~~~~~~~~~~Y~-~~~~~~~  432 (1034)
T KOG4150|consen  354 HVEVIKARKSAYVEMSDKLSETTKSALKRIGLNTLYSHQAEAISAALAKSLCYNVPVFEELCKDTNSCALYL-FPTKALA  432 (1034)
T ss_pred             EEEehhhhhcceeecccCCCchhHHHHHhcCcceeecCHHHHHHHHhhhccccccHHHHHHHhcccceeeee-cchhhHH
Confidence            11111   122333445555555555556789999999988876443322    223345679999999533 2233   


Q ss_pred             -HHHHHHHHhC-----CCCCeEEEEeeccc
Q 027749          194 -DQIYDVYRYL-----PPDLQVCCPGSCFL  217 (219)
Q Consensus       194 -~~~~~i~~~~-----~~~~q~i~~SATl~  217 (219)
                       ..++++.+-+     ..+.|++-.|||+.
T Consensus       433 ~~~~R~L~~L~~~F~~~~~~~~~~~~~~~K  462 (1034)
T KOG4150|consen  433 QDQLRALSDLIKGFEASINMGVYDGDTPYK  462 (1034)
T ss_pred             HHHHHHHHHHHHHHHhhcCcceEeCCCCcC
Confidence             2333333322     33678888888874

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.67  E-value=0.00025  Score=50.28  Aligned_cols=41  Identities=15%  Similarity=0.306  Sum_probs=25.1

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHH
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l  113 (219)
                      +..+++.||+|+|||..... ++..+....  ..++++.+....
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~-l~~~~~~~~--~~~~~~~~~~~~   42 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARA-LARELGPPG--GGVIYIDGEDIL   42 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHH-HHhccCCCC--CCEEEECCEEcc
Confidence            56789999999999944332 333333322  236666665543

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.

>KOG1131 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 5'-3' helicase subunit RAD3 [Transcription; Replication, recombination and repair]

Probab=97.66  E-value=0.001  Score=57.46  Aligned_cols=73  Identities=12%  Similarity=0.037  Sum_probs=47.0

Q ss_pred             CCCCChHHHHHHHHHHh----CCCcEEEEcCCCCchhHHhHHHHHhhhccCC-CceeEEEEcCCHHHHHHHHHHHHHh
Q 027749           52 GFEKPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-REVQALILSPTRELATQTEKVILAI  124 (219)
Q Consensus        52 ~~~~~~~~Q~~~~~~~~----~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~-~~~~~lil~P~~~l~~q~~~~~~~~  124 (219)
                      -+...+|-|..=+..+.    .+.+.++..|+|+|||.+.+..++......+ .-.+.|+..-|..-.+....+++.+
T Consensus        13 PY~~iYPEQ~~YM~elKrsLDakGh~llEMPSGTGKTvsLLSli~aYq~~~p~~~~KliYCSRTvpEieK~l~El~~l   90 (755)
T KOG1131|consen   13 PYDYIYPEQYEYMRELKRSLDAKGHCLLEMPSGTGKTVSLLSLIIAYQLHYPDEHRKLIYCSRTVPEIEKALEELKRL   90 (755)
T ss_pred             CCcccCHHHHHHHHHHHHhhccCCcEEEECCCCCCcchHHHHHHHHHHHhCCcccceEEEecCcchHHHHHHHHHHHH
Confidence            34556777766554433    4578999999999999666554444443333 3456777777776666666666554

>TIGR01075 uvrD DNA helicase II

Probab=97.64  E-value=0.00024  Score=65.22  Aligned_cols=108  Identities=16%  Similarity=0.183  Sum_probs=73.1

Q ss_pred             CCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccC-CCceeEEEEcCCHHHHHHHHHHHHHhccccceeE
Q 027749           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-SREVQALILSPTRELATQTEKVILAIGDFINIQA  132 (219)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~-~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  132 (219)
                      ..+++-|++++.+.  ..+++|.|+.|||||.+...-+.+.+... -...++++++.|+..|.++.+++.++....    
T Consensus         3 ~~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~~L~~Ria~Li~~~~v~p~~IL~lTFTnkAA~em~~Rl~~~~~~~----   76 (715)
T TIGR01075         3 DGLNDKQREAVAAP--PGNLLVLAGAGSGKTRVLTHRIAWLLSVENASPHSIMAVTFTNKAAAEMRHRIGALLGTS----   76 (715)
T ss_pred             cccCHHHHHHHcCC--CCCEEEEecCCCCHHHHHHHHHHHHHHcCCCCHHHeEeeeccHHHHHHHHHHHHHHhccc----
Confidence            35889999998653  46899999999999977665555555432 234579999999999999999998864310    


Q ss_pred             EEEECCcccHHHHHHhcCCCeEEEeChHHHHH-HHHcCC--CCCCCccEEEeccchh
Q 027749          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCD-MIKRKT--LRTRAIKLLVLDESDE  186 (219)
Q Consensus       133 ~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~-~l~~~~--~~~~~l~~lVvDE~h~  186 (219)
                                        ...+.|+|-+.|.. +++...  ..+. -.+-|+|+.+.
T Consensus        77 ------------------~~~~~i~TfHs~~~~iLr~~~~~~g~~-~~f~i~d~~d~  114 (715)
T TIGR01075        77 ------------------ARGMWIGTFHGLAHRLLRAHHLDAGLP-QDFQILDSDDQ  114 (715)
T ss_pred             ------------------ccCcEEEcHHHHHHHHHHHHHHHhCCC-CCCeecCHHHH
Confidence                              12467888888775 333221  1111 12456777654

Designed to identify uvrD members of the uvrD/rep subfamily.

>PF03354 Terminase_1: Phage Terminase ; InterPro: IPR005021 This entry is represented by Lactococcus phage bIL285, Orf41 (terminase)

Probab=97.62  E-value=0.00044  Score=60.48  Aligned_cols=70  Identities=16%  Similarity=0.131  Sum_probs=51.2

Q ss_pred             HHHHHHHHHHh-----CC----CcEEEEcCCCCchhHHhHHHHHhhh-ccCCCceeEEEEcCCHHHHHHHHHHHHHhccc
Q 027749           58 AIQQRAVMPII-----KG----RDVIAQAQSGTGKTSMIALTVCQTV-DTSSREVQALILSPTRELATQTEKVILAIGDF  127 (219)
Q Consensus        58 ~~Q~~~~~~~~-----~~----~~~lv~~~tG~GKT~~~~~~~~~~~-~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (219)
                      |||+.++-.+.     .|    +.+++..|=|.|||.......+..+ .....+..++++++++..|..+++.+..+...
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            57777776655     22    3588899999999955544334333 34445678999999999999999999887655

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>KOG1015 consensus Transcription regulator XNP/ATRX, DEAD-box superfamily [Transcription]

Probab=97.61  E-value=0.0006  Score=62.58  Aligned_cols=140  Identities=12%  Similarity=0.021  Sum_probs=80.7

Q ss_pred             CcEEEEcCCCCchhHHh---HHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhcccc----ceeEEEEECCcccHH
Q 027749           71 RDVIAQAQSGTGKTSMI---ALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI----NIQAHACVGGKSVGE  143 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~---~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~----~~~~~~~~~~~~~~~  143 (219)
                      -..|+..-+|-|||+-.   +..++..-.  .+-.++|||+|...+ ..++.++.+|....    .+.+..+..-.....
T Consensus       697 sGcILAHcMGLGKTlQVvtflhTvL~c~k--lg~ktaLvV~PlNt~-~NW~~EFekWm~~~e~~~~leV~eL~~vkr~e~  773 (1567)
T KOG1015|consen  697 SGCILAHCMGLGKTLQVVTFLHTVLLCDK--LGFKTALVVCPLNTA-LNWMNEFEKWMEGLEDDEKLEVSELATVKRPEE  773 (1567)
T ss_pred             cchHHHHhhcccceehhhHHHHHHHHhhc--cCCceEEEEcchHHH-HHHHHHHHHhcccccccccceeehhhhccChHH
Confidence            35777888999999543   333332222  223469999997655 56899999998753    345554444444344


Q ss_pred             HHHH---hcCCCeEEEeChHHHHHHHHcCCCC-------------CCCccEEEeccchhhhccccHHHHHHHHHhCCCCC
Q 027749          144 DIRK---LEHGVHVVSGTPGRVCDMIKRKTLR-------------TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDL  207 (219)
Q Consensus       144 ~~~~---l~~~~~I~v~Tp~~l~~~l~~~~~~-------------~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~  207 (219)
                      +...   +.+.-.|.|.-.+.+..+-..+...             -..-++||+||+|.+-+.  ...+...+..+. ..
T Consensus       774 R~~~L~~W~~~ggVmIiGYdmyRnLa~gr~vk~rk~ke~f~k~lvdpGPD~vVCDE~HiLKNe--ksa~Skam~~ir-tk  850 (1567)
T KOG1015|consen  774 RSYMLQRWQEDGGVMIIGYDMYRNLAQGRNVKSRKLKEIFNKALVDPGPDFVVCDEGHILKNE--KSAVSKAMNSIR-TK  850 (1567)
T ss_pred             HHHHHHHHHhcCCEEEEehHHHHHHhcccchhhhHHHHHHHHhccCCCCCeEEecchhhhccc--hHHHHHHHHHHH-hh
Confidence            4433   3344456665565554443322211             123479999999987665  233444444432 23


Q ss_pred             eEEEEeecc
Q 027749          208 QVCCPGSCF  216 (219)
Q Consensus       208 q~i~~SATl  216 (219)
                      +.|++++|.
T Consensus       851 RRI~LTGTP  859 (1567)
T KOG1015|consen  851 RRIILTGTP  859 (1567)
T ss_pred             eeEEeecCc
Confidence            467777763

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=97.61  E-value=0.00031  Score=63.88  Aligned_cols=87  Identities=15%  Similarity=0.098  Sum_probs=64.3

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCC-CceeEEEEcCCHHHHHHHHHHHHHhccccceeEE
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-REVQALILSPTRELATQTEKVILAIGDFINIQAH  133 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~-~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~  133 (219)
                      .+++-|++++.+.  ..+++|.|+.|||||.+...-+.+.+...+ ...++++++.|+..|.++.+++.......     
T Consensus         2 ~Ln~~Q~~av~~~--~g~~lV~AgpGSGKT~vL~~Ria~Li~~~~v~p~~IL~lTFT~kAA~em~~Rl~~~l~~~-----   74 (672)
T PRK10919          2 RLNPGQQQAVEFV--TGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVAQTLGRK-----   74 (672)
T ss_pred             CCCHHHHHHHhCC--CCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeeeEechHHHHHHHHHHHHHHhCcc-----
Confidence            4788899998653  468899999999999777666666554322 34579999999999999999997764210     


Q ss_pred             EEECCcccHHHHHHhcCCCeEEEeChHHHHH
Q 027749          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCD  164 (219)
Q Consensus       134 ~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~  164 (219)
                                      ....+.|+|.+.|..
T Consensus        75 ----------------~~~~v~i~TfHS~~~   89 (672)
T PRK10919         75 ----------------EARGLMISTFHTLGL   89 (672)
T ss_pred             ----------------cccCcEEEcHHHHHH
Confidence                            012467888888875

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=97.60  E-value=0.00047  Score=63.33  Aligned_cols=108  Identities=15%  Similarity=0.163  Sum_probs=73.0

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccC-CCceeEEEEcCCHHHHHHHHHHHHHhccccceeEE
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-SREVQALILSPTRELATQTEKVILAIGDFINIQAH  133 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~-~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~  133 (219)
                      .+++-|++++.+.  ..+++|.|+.|||||.+...-+.+.+... -...++++|+-|+..|.++.+++.++....     
T Consensus         9 ~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~vl~~Ria~Li~~~~v~p~~IL~lTFT~kAA~Em~~Rl~~~~~~~-----   81 (721)
T PRK11773          9 SLNDKQREAVAAP--LGNMLVLAGAGSGKTRVLVHRIAWLMQVENASPYSIMAVTFTNKAAAEMRHRIEQLLGTS-----   81 (721)
T ss_pred             hcCHHHHHHHhCC--CCCEEEEecCCCCHHHHHHHHHHHHHHcCCCChhHeEeeeccHHHHHHHHHHHHHHhccC-----
Confidence            5899999998653  46899999999999977665555554432 234569999999999999999998764310     


Q ss_pred             EEECCcccHHHHHHhcCCCeEEEeChHHHHH-HHHcCCCCCC-CccEEEeccchh
Q 027749          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCD-MIKRKTLRTR-AIKLLVLDESDE  186 (219)
Q Consensus       134 ~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~-~l~~~~~~~~-~l~~lVvDE~h~  186 (219)
                                       ...+.|+|-+.|.. +++....... .-.+-|+|+.++
T Consensus        82 -----------------~~~~~i~TfHs~~~~iLr~~~~~~g~~~~f~i~d~~d~  119 (721)
T PRK11773         82 -----------------QGGMWVGTFHGLAHRLLRAHWQDANLPQDFQILDSDDQ  119 (721)
T ss_pred             -----------------CCCCEEEcHHHHHHHHHHHHHHHhCCCCCCeecCHHHH
Confidence                             12467899888876 3333211000 112457787664

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=97.58  E-value=0.00079  Score=65.77  Aligned_cols=63  Identities=22%  Similarity=0.289  Sum_probs=46.0

Q ss_pred             CChHHHHHHHHHHhCC--CcEEEEcCCCCchhHHhH--HHHHhhhccCCCceeEEEEcCCHHHHHHHH
Q 027749           55 KPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIA--LTVCQTVDTSSREVQALILSPTRELATQTE  118 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~--~~~lv~~~tG~GKT~~~~--~~~~~~~~~~~~~~~~lil~P~~~l~~q~~  118 (219)
                      .+++-|..++..++.+  +-++|.|..|+|||...-  +.++..+. ...+..++.++||...+..+.
T Consensus       835 ~Lt~~Qr~Av~~iLts~dr~~~IqG~AGTGKTT~l~~i~~~~~~l~-e~~g~~V~glAPTgkAa~~L~  901 (1623)
T PRK14712        835 KLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLP-ESERPRVVGLGPTHRAVGEMR  901 (1623)
T ss_pred             ccCHHHHHHHHHHHhCCCceEEEEeCCCCCHHHHHHHHHHHHHHHh-hccCceEEEEechHHHHHHHH
Confidence            6899999999998854  679999999999995532  22222222 223466889999998887664

>PHA03368 DNA packaging terminase subunit 1; Provisional

Probab=97.55  E-value=0.00098  Score=59.46  Aligned_cols=135  Identities=13%  Similarity=0.134  Sum_probs=84.9

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhcccc--ceeEEEEECCcccHHHHH
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI--NIQAHACVGGKSVGEDIR  146 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~  146 (219)
                      +.+-.++..|--.|||+... +++..+...-.+.++++++|....++.+++++....+..  +-.+....| ...   ..
T Consensus       253 kqk~tVflVPRR~GKTwivv-~iI~~ll~s~~Gi~IgytAH~~~ts~~vF~eI~~~le~~f~~~~v~~vkG-e~I---~i  327 (738)
T PHA03368        253 RQRATVFLVPRRHGKTWFLV-PLIALALATFRGIKIGYTAHIRKATEPVFEEIGARLRQWFGASRVDHVKG-ETI---SF  327 (738)
T ss_pred             hccceEEEecccCCchhhHH-HHHHHHHHhCCCCEEEEEcCcHHHHHHHHHHHHHHHhhhcchhheeeecC-cEE---EE
Confidence            45678999999999997665 666666655557889999999999999999998775532  111111111 111   01


Q ss_pred             HhcCC--CeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhC-CCCCeEEEEeecccC
Q 027749          147 KLEHG--VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL-PPDLQVCCPGSCFLF  218 (219)
Q Consensus       147 ~l~~~--~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~-~~~~q~i~~SATl~~  218 (219)
                      .+.++  ..|.++|.      -..+.+.=..++++|||||+-+-+.    .+..++-.+ ..++++|++|.|-+.
T Consensus       328 ~f~nG~kstI~FaSa------rntNsiRGqtfDLLIVDEAqFIk~~----al~~ilp~l~~~n~k~I~ISS~Ns~  392 (738)
T PHA03368        328 SFPDGSRSTIVFASS------HNTNGIRGQDFNLLFVDEANFIRPD----AVQTIMGFLNQTNCKIIFVSSTNTG  392 (738)
T ss_pred             EecCCCccEEEEEec------cCCCCccCCcccEEEEechhhCCHH----HHHHHHHHHhccCccEEEEecCCCC
Confidence            12223  25666642      0122334457899999999976643    334444333 237899999988543

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=97.53  E-value=0.0012  Score=65.17  Aligned_cols=122  Identities=20%  Similarity=0.228  Sum_probs=74.1

Q ss_pred             CChHHHHHHHHHHhCC--CcEEEEcCCCCchhHHhHHHHHhhhc--cCCCceeEEEEcCCHHHHHHHHHHHHHhccccce
Q 027749           55 KPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVD--TSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~--~~~lv~~~tG~GKT~~~~~~~~~~~~--~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (219)
                      .+++.|+.++..++.+  +-++|.|..|+|||... -.++..+.  ....+..++.++||...+..+.+    .    ++
T Consensus       967 ~Lt~~Q~~Av~~il~s~dr~~~I~G~AGTGKTT~l-~~v~~~~~~l~~~~~~~V~glAPTgrAAk~L~e----~----Gi 1037 (1747)
T PRK13709        967 GLTSGQRAATRMILESTDRFTVVQGYAGVGKTTQF-RAVMSAVNTLPESERPRVVGLGPTHRAVGEMRS----A----GV 1037 (1747)
T ss_pred             CCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHHH-HHHHHHHHHhhcccCceEEEECCcHHHHHHHHh----c----Cc
Confidence            6899999999998875  56899999999999443 23333332  12234568889999988876543    1    22


Q ss_pred             eEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHH----cCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCC-
Q 027749          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIK----RKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP-  205 (219)
Q Consensus       131 ~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~----~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~-  205 (219)
                      ..                        .|-.+|+....    +.......-++|||||+-++.    ...+..+++..+. 
T Consensus      1038 ~A------------------------~TI~s~L~~~~~~~~~~~~~~~~~~llIVDEaSMv~----~~~m~~Ll~~~~~~ 1089 (1747)
T PRK13709       1038 DA------------------------QTLASFLHDTQLQQRSGETPDFSNTLFLLDESSMVG----NTDMARAYALIAAG 1089 (1747)
T ss_pred             ch------------------------hhHHHHhcccccccccccCCCCCCcEEEEEcccccc----HHHHHHHHHhhhcC
Confidence            11                        12222222110    111112234789999998654    3455566666553 


Q ss_pred             CCeEEEEe
Q 027749          206 DLQVCCPG  213 (219)
Q Consensus       206 ~~q~i~~S  213 (219)
                      +.++|++.
T Consensus      1090 garvVLVG 1097 (1747)
T PRK13709       1090 GGRAVSSG 1097 (1747)
T ss_pred             CCEEEEec
Confidence            57777764

>PRK11054 helD DNA helicase IV; Provisional

Probab=97.51  E-value=0.0015  Score=59.53  Aligned_cols=70  Identities=23%  Similarity=0.226  Sum_probs=52.8

Q ss_pred             CCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccC-CCceeEEEEcCCHHHHHHHHHHHHHhc
Q 027749           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-SREVQALILSPTRELATQTEKVILAIG  125 (219)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~-~~~~~~lil~P~~~l~~q~~~~~~~~~  125 (219)
                      ..+++-|++++..-  ..+++|.|+.|||||.+..--+...+... ..+.++++++.++..|..+.+++....
T Consensus       195 ~~L~~~Q~~av~~~--~~~~lV~agaGSGKT~vl~~r~ayLl~~~~~~~~~IL~ltft~~AA~em~eRL~~~l  265 (684)
T PRK11054        195 SPLNPSQARAVVNG--EDSLLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRQAAEEMDERIRERL  265 (684)
T ss_pred             CCCCHHHHHHHhCC--CCCeEEEEeCCCCHHHHHHHHHHHHHHhCCCCHHHeEEEeccHHHHHHHHHHHHHhc
Confidence            47899999988543  35789999999999976655444444332 234479999999999999999987654

>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=97.50  E-value=8.5e-05  Score=55.93  Aligned_cols=122  Identities=14%  Similarity=0.183  Sum_probs=53.3

Q ss_pred             EEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHH-HHhcCCC
Q 027749           74 IAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDI-RKLEHGV  152 (219)
Q Consensus        74 lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~l~~~~  152 (219)
                      ++.|+-|-|||.+.-+.+...+...  ..+++|.+|+.+-++.+++.+..-.+..+++...    ....... .....+.
T Consensus         1 VltA~RGRGKSa~lGl~~a~l~~~~--~~~I~vtAP~~~~~~~lf~~~~~~l~~~~~~~~~----~~~~~~~~~~~~~~~   74 (177)
T PF05127_consen    1 VLTADRGRGKSAALGLAAAALIQKG--KIRILVTAPSPENVQTLFEFAEKGLKALGYKEEK----KKRIGQIIKLRFNKQ   74 (177)
T ss_dssp             -EEE-TTSSHHHHHHHCCCCSSS-------EEEE-SS--S-HHHHHCC------------------------------CC
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHhc--CceEEEecCCHHHHHHHHHHHHhhcccccccccc----ccccccccccccccc
Confidence            5789999999955555443333332  2569999999999998888776655544443300    0000000 0111245


Q ss_pred             eEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEeecc
Q 027749          153 HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCF  216 (219)
Q Consensus       153 ~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl  216 (219)
                      .|-+..|+.+...       ....+++|||||=.+-    ...+..+++..+    .++||.|+
T Consensus        75 ~i~f~~Pd~l~~~-------~~~~DlliVDEAAaIp----~p~L~~ll~~~~----~vv~stTi  123 (177)
T PF05127_consen   75 RIEFVAPDELLAE-------KPQADLLIVDEAAAIP----LPLLKQLLRRFP----RVVFSTTI  123 (177)
T ss_dssp             C--B--HHHHCCT-----------SCEEECTGGGS-----HHHHHHHHCCSS----EEEEEEEB
T ss_pred             eEEEECCHHHHhC-------cCCCCEEEEechhcCC----HHHHHHHHhhCC----EEEEEeec
Confidence            6777778654422       1235789999996543    455556654433    56777775

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.

>PRK04296 thymidine kinase; Provisional

Probab=97.50  E-value=0.00036  Score=53.41  Aligned_cols=36  Identities=11%  Similarity=0.230  Sum_probs=23.1

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcC
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P  109 (219)
                      .-.++.||+|+|||...+- ++.++...  +.+++++-|
T Consensus         3 ~i~litG~~GsGKTT~~l~-~~~~~~~~--g~~v~i~k~   38 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQ-RAYNYEER--GMKVLVFKP   38 (190)
T ss_pred             EEEEEECCCCCHHHHHHHH-HHHHHHHc--CCeEEEEec
Confidence            3468899999999954443 44444433  345777755

>PHA02533 17 large terminase protein; Provisional

Probab=97.46  E-value=0.0018  Score=57.21  Aligned_cols=123  Identities=15%  Similarity=0.160  Sum_probs=77.1

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccc--eeE
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN--IQA  132 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~--~~~  132 (219)
                      .+.|+|...+..+..++-.++..+=..|||.+....++..+... .+..+++++|+...+..+++.++.......  ...
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            57899999998876667778999999999977665444433322 245799999999999999988876544321  110


Q ss_pred             EEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhc
Q 027749          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (219)
Q Consensus       133 ~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~  189 (219)
                      ....    .......+.+++.|.+.|..       .+...=....++|+||+|.+-+
T Consensus       138 ~i~~----~~~~~I~l~NGS~I~~lss~-------~~t~rG~~~~~liiDE~a~~~~  183 (534)
T PHA02533        138 GIVE----WNKGSIELENGSKIGAYASS-------PDAVRGNSFAMIYIDECAFIPN  183 (534)
T ss_pred             ceee----cCccEEEeCCCCEEEEEeCC-------CCccCCCCCceEEEeccccCCC
Confidence            0000    00111223467777665532       1111223466899999997543

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.46  E-value=0.00093  Score=58.01  Aligned_cols=105  Identities=10%  Similarity=0.161  Sum_probs=54.9

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcC
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH  150 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  150 (219)
                      ..+++.||+|+|||.. +..+...+.....+.+++++.. ..+..+....+..                           
T Consensus       149 ~~l~l~G~~G~GKThL-~~ai~~~~~~~~~~~~v~yi~~-~~~~~~~~~~~~~---------------------------  199 (450)
T PRK00149        149 NPLFIYGGVGLGKTHL-LHAIGNYILEKNPNAKVVYVTS-EKFTNDFVNALRN---------------------------  199 (450)
T ss_pred             CeEEEECCCCCCHHHH-HHHHHHHHHHhCCCCeEEEEEH-HHHHHHHHHHHHc---------------------------
Confidence            4589999999999933 2334444444333445666633 3444333322211                           


Q ss_pred             CCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccc-cHHHHHHHHHhCCC-CCeEEEEeecccC
Q 027749          151 GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG-FKDQIYDVYRYLPP-DLQVCCPGSCFLF  218 (219)
Q Consensus       151 ~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~-~~~~~~~i~~~~~~-~~q~i~~SATl~~  218 (219)
                      +      +.+.+...       +...++|++||+|.+.... ....+..+++.+.. ..+ ++++++.++
T Consensus       200 ~------~~~~~~~~-------~~~~dlLiiDDi~~l~~~~~~~~~l~~~~n~l~~~~~~-iiits~~~p  255 (450)
T PRK00149        200 N------TMEEFKEK-------YRSVDVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQ-IVLTSDRPP  255 (450)
T ss_pred             C------cHHHHHHH-------HhcCCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCc-EEEECCCCH
Confidence            0      11222222       2246799999999876432 23445555554422 334 555555443

>PRK08181 transposase; Validated

Probab=97.45  E-value=0.0017  Score=52.38  Aligned_cols=57  Identities=21%  Similarity=0.271  Sum_probs=31.2

Q ss_pred             hHHHHHHHH----HHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHH
Q 027749           57 SAIQQRAVM----PIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQT  117 (219)
Q Consensus        57 ~~~Q~~~~~----~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~  117 (219)
                      ...|..++.    .+..+++++++||+|+|||.... .+...+...  +..++|+ +..+|+.++
T Consensus        89 ~~~~~~~L~~~~~~~~~~~nlll~Gp~GtGKTHLa~-Aia~~a~~~--g~~v~f~-~~~~L~~~l  149 (269)
T PRK08181         89 SKAQVMAIAAGDSWLAKGANLLLFGPPGGGKSHLAA-AIGLALIEN--GWRVLFT-RTTDLVQKL  149 (269)
T ss_pred             CHHHHHHHHHHHHHHhcCceEEEEecCCCcHHHHHH-HHHHHHHHc--CCceeee-eHHHHHHHH
Confidence            445555442    23467899999999999993332 233333332  2335444 334444443

>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=97.43  E-value=0.0004  Score=60.81  Aligned_cols=135  Identities=12%  Similarity=0.108  Sum_probs=71.9

Q ss_pred             EEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHH-H----Hhc--cc-----cceeEEEEECCcccH
Q 027749           75 AQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVI-L----AIG--DF-----INIQAHACVGGKSVG  142 (219)
Q Consensus        75 v~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~-~----~~~--~~-----~~~~~~~~~~~~~~~  142 (219)
                      ....||+|||++....+++.....  -..-|+.|.....++.-..-+ .    +++  ..     ..+.+..+       
T Consensus         2 f~matgsgkt~~ma~lil~~y~kg--yr~flffvnq~nilekt~~nftd~~s~kylf~e~i~~~d~~i~ikkv-------   72 (812)
T COG3421           2 FEMATGSGKTLVMAGLILECYKKG--YRNFLFFVNQANILEKTKLNFTDSVSSKYLFSENININDENIEIKKV-------   72 (812)
T ss_pred             cccccCCChhhHHHHHHHHHHHhc--hhhEEEEecchhHHHHHHhhcccchhhhHhhhhhhhcCCceeeeeee-------
Confidence            467899999987766666655432  223555555444433222211 0    000  00     01111111       


Q ss_pred             HHHHHhcCCCeEEEeChHHHHHHHHcC---CC---CCCCccE-EEeccchhhhccc-------------cHHHHHHHHHh
Q 027749          143 EDIRKLEHGVHVVSGTPGRVCDMIKRK---TL---RTRAIKL-LVLDESDEMLSRG-------------FKDQIYDVYRY  202 (219)
Q Consensus       143 ~~~~~l~~~~~I~v~Tp~~l~~~l~~~---~~---~~~~l~~-lVvDE~h~l~~~~-------------~~~~~~~i~~~  202 (219)
                      ........+..|.++|.+.|...+.+.   .+   ++.+.++ ++-||+|++....             +...+..-++.
T Consensus        73 n~fsehnd~iei~fttiq~l~~d~~~~ken~itledl~~~klvfl~deahhln~~tkkk~~de~~~~~~we~~v~la~~~  152 (812)
T COG3421          73 NNFSEHNDAIEIYFTTIQGLFSDFTRAKENAITLEDLKDQKLVFLADEAHHLNTETKKKLNDEASEKRNWESVVKLALEQ  152 (812)
T ss_pred             cccCccCCceEEEEeehHHHHHHHHhhccccccHhhHhhCceEEEechhhhhhhhhhhhcccHHHHHhhHHHHHHHHHhc
Confidence            111223456899999999998766542   22   3455554 6779999987531             11222222222


Q ss_pred             CCCCCeEEEEeecccCC
Q 027749          203 LPPDLQVCCPGSCFLFD  219 (219)
Q Consensus       203 ~~~~~q~i~~SATl~~~  219 (219)
                       .++.-++.+|||.|.+
T Consensus       153 -nkd~~~lef~at~~k~  168 (812)
T COG3421         153 -NKDNLLLEFSATIPKE  168 (812)
T ss_pred             -CCCceeehhhhcCCcc
Confidence             3456688999999853

>PRK05642 DNA replication initiation factor; Validated

Probab=97.41  E-value=0.00051  Score=54.36  Aligned_cols=45  Identities=11%  Similarity=0.219  Sum_probs=30.0

Q ss_pred             CCccEEEeccchhhhcc-ccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          174 RAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~-~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      .++++||+|++|.+... .....+..+++.+......++++++.++
T Consensus        96 ~~~d~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p  141 (234)
T PRK05642         96 EQYELVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSP  141 (234)
T ss_pred             hhCCEEEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCCCH
Confidence            35578999999976533 3456677887776554445677776543

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=97.41  E-value=0.0029  Score=63.81  Aligned_cols=133  Identities=14%  Similarity=0.153  Sum_probs=81.1

Q ss_pred             CChHHHHHHHHHHhCC--CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeE
Q 027749           55 KPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQA  132 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~--~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  132 (219)
                      .+++-|..++..++.+  +-.+|.|+.|+|||.. +-.+...+...  +..++.++||...+..+.+......       
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 ALSPSNKDAVSTLFTSTKRFIIINGFGGTGSTEI-AQLLLHLASEQ--GYEIQIITAGSLSAQELRQKIPRLA-------  498 (1960)
T ss_pred             CCCHHHHHHHHHHHhCCCCeEEEEECCCCCHHHH-HHHHHHHHHhc--CCeEEEEeCCHHHHHHHHHHhcchh-------
Confidence            5788999999998865  5688999999999933 33444444443  4579999999988877666432110       


Q ss_pred             EEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhC-CCCCeEEE
Q 027749          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL-PPDLQVCC  211 (219)
Q Consensus       133 ~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~-~~~~q~i~  211 (219)
                            .+.......+..+  .-..|...|+    +....+..-++|||||+.++.    ...+..+++.. +.+.++|+
T Consensus       499 ------~Ti~~~l~~l~~~--~~~~tv~~fl----~~~~~l~~~~vlIVDEAsMl~----~~~~~~Ll~~a~~~garvVl  562 (1960)
T TIGR02760       499 ------STFITWVKNLFND--DQDHTVQGLL----DKSSPFSNKDIFVVDEANKLS----NNELLKLIDKAEQHNSKLIL  562 (1960)
T ss_pred             ------hhHHHHHHhhccc--ccchhHHHhh----cccCCCCCCCEEEEECCCCCC----HHHHHHHHHHHhhcCCEEEE
Confidence                  0000111111111  1122333333    222334567899999998654    45677777665 35778887


Q ss_pred             Ee
Q 027749          212 PG  213 (219)
Q Consensus       212 ~S  213 (219)
                      +.
T Consensus       563 vG  564 (1960)
T TIGR02760       563 LN  564 (1960)
T ss_pred             Ec
Confidence            65

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.

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=97.40  E-value=0.0007  Score=61.73  Aligned_cols=127  Identities=17%  Similarity=0.240  Sum_probs=92.9

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEE
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (219)
                      .|+.+|  .+-.+.-...-+....||-|||++..+|+.-.....++   +.+|+-..-|+..-.+....+....++++..
T Consensus        80 ~~~dVQ--liG~i~lh~g~iaEM~TGEGKTL~atlp~ylnaL~gkg---VhvVTvNdYLA~RDae~m~~l~~~LGlsvG~  154 (822)
T COG0653          80 RHFDVQ--LLGGIVLHLGDIAEMRTGEGKTLVATLPAYLNALAGKG---VHVVTVNDYLARRDAEWMGPLYEFLGLSVGV  154 (822)
T ss_pred             ChhhHH--HhhhhhhcCCceeeeecCCchHHHHHHHHHHHhcCCCC---cEEeeehHHhhhhCHHHHHHHHHHcCCceee
Confidence            566666  44444444557889999999999999998777766543   7888888889998888888888888999998


Q ss_pred             EECCcccHHHHHHhcCCCeEEEeChHHHHH-HHH-c-----CCCCCCCccEEEeccchhhh
Q 027749          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCD-MIK-R-----KTLRTRAIKLLVLDESDEML  188 (219)
Q Consensus       135 ~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~-~l~-~-----~~~~~~~l~~lVvDE~h~l~  188 (219)
                      ...+.+..++...  ..|+|..+|...|-. .+. +     .......+.+-|+||+|-++
T Consensus       155 ~~~~m~~~ek~~a--Y~~DItY~TnnElGFDYLRDNm~~~~ee~vqr~~~faIvDEvDSIL  213 (822)
T COG0653         155 ILAGMSPEEKRAA--YACDITYGTNNELGFDYLRDNMVTSQEEKVQRGLNFAIVDEVDSIL  213 (822)
T ss_pred             ccCCCChHHHHHH--HhcCceeccccccCcchhhhhhhccHHHhhhccCCeEEEcchhhee
Confidence            8888776665444  378999999876632 221 1     11223457899999999655

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.35  E-value=0.0014  Score=56.21  Aligned_cols=37  Identities=14%  Similarity=0.267  Sum_probs=23.5

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEc
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~  108 (219)
                      ..+++.|++|+|||... ..+...+.....+..++++.
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            35789999999999333 34445554433344566664

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).

>PRK06893 DNA replication initiation factor; Validated

Probab=97.34  E-value=0.00064  Score=53.59  Aligned_cols=45  Identities=11%  Similarity=0.197  Sum_probs=30.3

Q ss_pred             CCccEEEeccchhhhcc-ccHHHHHHHHHhCCC-CCeEEEEeecccC
Q 027749          174 RAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPP-DLQVCCPGSCFLF  218 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~-~~~~~~~~i~~~~~~-~~q~i~~SATl~~  218 (219)
                      .+.++||+||+|.+... .+...+..+++.... +.+++++|++.++
T Consensus        90 ~~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p  136 (229)
T PRK06893         90 EQQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSP  136 (229)
T ss_pred             ccCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCCh
Confidence            46789999999987633 334456666665543 4567788887654

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=97.33  E-value=0.0021  Score=47.08  Aligned_cols=38  Identities=16%  Similarity=0.334  Sum_probs=22.4

Q ss_pred             EEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHH
Q 027749           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (219)
Q Consensus        73 ~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l  113 (219)
                      +++.|++|+|||..... ++..+...  +..++++......
T Consensus         2 ~~i~G~~G~GKT~l~~~-i~~~~~~~--~~~v~~~~~e~~~   39 (165)
T cd01120           2 ILVFGPTGSGKTTLALQ-LALNIATK--GGKVVYVDIEEEI   39 (165)
T ss_pred             eeEeCCCCCCHHHHHHH-HHHHHHhc--CCEEEEEECCcch
Confidence            68999999999954433 33333222  3346666554443

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.

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=97.31  E-value=0.0019  Score=59.51  Aligned_cols=109  Identities=16%  Similarity=0.217  Sum_probs=73.0

Q ss_pred             CCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCC-CceeEEEEcCCHHHHHHHHHHHHHhccccceeE
Q 027749           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-REVQALILSPTRELATQTEKVILAIGDFINIQA  132 (219)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~-~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  132 (219)
                      ..+++-|.+++.+.  ..+++|.|+.|||||.+..--+.+.+...+ ..-++++++-|+..+.++.+++.++...     
T Consensus         3 ~~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~~l~~ria~Li~~~~i~P~~IL~lTFT~kAA~em~~Rl~~~~~~-----   75 (726)
T TIGR01073         3 AHLNPEQREAVKTT--EGPLLIMAGAGSGKTRVLTHRIAHLIAEKNVAPWNILAITFTNKAAREMKERVEKLLGP-----   75 (726)
T ss_pred             cccCHHHHHHHhCC--CCCEEEEeCCCCCHHHHHHHHHHHHHHcCCCCHHHeeeeeccHHHHHHHHHHHHHHhcc-----
Confidence            35789999998753  468999999999999776665555554322 2346999999999999999999776421     


Q ss_pred             EEEECCcccHHHHHHhcCCCeEEEeChHHHHH-HHHcCCCCCC-CccEEEeccchh
Q 027749          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCD-MIKRKTLRTR-AIKLLVLDESDE  186 (219)
Q Consensus       133 ~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~-~l~~~~~~~~-~l~~lVvDE~h~  186 (219)
                                       ...++.|+|-+.|.. ++........ .-.+-|+|+.+.
T Consensus        76 -----------------~~~~~~i~TFHs~~~~iLr~~~~~~g~~~~f~i~d~~~~  114 (726)
T TIGR01073        76 -----------------VAEDIWISTFHSMCVRILRRDIDRIGINRNFSIIDPTDQ  114 (726)
T ss_pred             -----------------ccCCcEEEcHHHHHHHHHHHHHHHhCCCCCCCcCCHHHH
Confidence                             013577888888876 3332111000 122446777663

Designed to identify pcrA members of the uvrD/rep subfamily.

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=97.30  E-value=0.0021  Score=62.43  Aligned_cols=122  Identities=16%  Similarity=0.172  Sum_probs=77.5

Q ss_pred             ChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEE
Q 027749           56 PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC  135 (219)
Q Consensus        56 ~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~  135 (219)
                      .|+-|.+++.  ..+++++|.|..|||||.+..--++..+......-++++|+-|+..+.++.+++.+.....--.    
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            5788999987  4688999999999999977666666655443333469999999999999999997654321000    


Q ss_pred             ECCcccHHHHHHhcCCCeEEEeChHHHHH-HHHcCCCCCCCc--cEEEeccchh
Q 027749          136 VGGKSVGEDIRKLEHGVHVVSGTPGRVCD-MIKRKTLRTRAI--KLLVLDESDE  186 (219)
Q Consensus       136 ~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~-~l~~~~~~~~~l--~~lVvDE~h~  186 (219)
                        ........+.+..-...-|+|-+.|.. ++++.. ..-++  .+=|.||...
T Consensus        76 --~p~~~~L~~q~~~~~~~~i~Tihsf~~~~~~~~~-~~l~ldP~F~i~de~e~  126 (1232)
T TIGR02785        76 --EPNSKHLRRQLALLNTANISTLHSFCLKVIRKHY-YLLDLDPSFRILTDTEQ  126 (1232)
T ss_pred             --CchhHHHHHHHhhccCCeEeeHHHHHHHHHHHhh-hhcCCCCCceeCCHHHH
Confidence              000011111122224567999999986 444432 12222  3446888775

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.

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=97.28  E-value=0.0013  Score=56.12  Aligned_cols=136  Identities=16%  Similarity=0.160  Sum_probs=77.1

Q ss_pred             cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHH-HHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcC
Q 027749           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE-LATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH  150 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~-l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  150 (219)
                      -.++.|+.|||||.+...-++..+.....+.+++++-++.. +-..++..+.......++....-....+.  .+ .+..
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            36789999999998888877776666433567899989887 55566777766555444432211111110  11 1222


Q ss_pred             -CCeEEEeCh-HHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEeeccc
Q 027749          151 -GVHVVSGTP-GRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFL  217 (219)
Q Consensus       151 -~~~I~v~Tp-~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl~  217 (219)
                       +..|++..- +...++. +    ...+.++.+|||..+....+...+.+ ++. +.....+++|.+.+
T Consensus        80 ~g~~i~f~g~~d~~~~ik-~----~~~~~~~~idEa~~~~~~~~~~l~~r-lr~-~~~~~~i~~t~NP~  141 (396)
T TIGR01547        80 TGKKFIFKGLNDKPNKLK-S----GAGIAIIWFEEASQLTFEDIKELIPR-LRE-TGGKKFIIFSSNPE  141 (396)
T ss_pred             CCeEEEeecccCChhHhh-C----cceeeeehhhhhhhcCHHHHHHHHHH-hhc-cCCccEEEEEcCcC
Confidence             566777654 3222221 1    23368999999998754333333322 333 22222467776643

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.

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=97.28  E-value=0.0023  Score=54.41  Aligned_cols=36  Identities=22%  Similarity=0.330  Sum_probs=22.3

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEE
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALIL  107 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil  107 (219)
                      .+++|.||+|+|||.. +-.++..+.....+...+++
T Consensus        56 ~~~lI~G~~GtGKT~l-~~~v~~~l~~~~~~~~~v~i   91 (394)
T PRK00411         56 LNVLIYGPPGTGKTTT-VKKVFEELEEIAVKVVYVYI   91 (394)
T ss_pred             CeEEEECCCCCCHHHH-HHHHHHHHHHhcCCcEEEEE
Confidence            5799999999999944 33445554433223334444

>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=97.26  E-value=0.0024  Score=50.02  Aligned_cols=105  Identities=15%  Similarity=0.232  Sum_probs=58.2

Q ss_pred             cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCC
Q 027749           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG  151 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  151 (219)
                      .+.++||+|+|||- .+.++...+.....+.+++++.. .+......+.+..                            
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            58999999999993 33344454444334455666643 2222222222211                            


Q ss_pred             CeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhcc-ccHHHHHHHHHhCCC-CCeEEEEeecccC
Q 027749          152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPP-DLQVCCPGSCFLF  218 (219)
Q Consensus       152 ~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~-~~~~~~~~i~~~~~~-~~q~i~~SATl~~  218 (219)
                           ...+.+.+-       +...++|++|++|.+... .....+..+++.+.. +.++|+.|...|.
T Consensus        86 -----~~~~~~~~~-------~~~~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~  142 (219)
T PF00308_consen   86 -----GEIEEFKDR-------LRSADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPS  142 (219)
T ss_dssp             -----TSHHHHHHH-------HCTSSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TT
T ss_pred             -----ccchhhhhh-------hhcCCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCc
Confidence                 122333322       346789999999987754 345667777766533 4566666655554

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.

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=97.24  E-value=0.0024  Score=58.21  Aligned_cols=68  Identities=18%  Similarity=0.153  Sum_probs=53.4

Q ss_pred             ChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccC-CCceeEEEEcCCHHHHHHHHHHHHHhc
Q 027749           56 PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-SREVQALILSPTRELATQTEKVILAIG  125 (219)
Q Consensus        56 ~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~-~~~~~~lil~P~~~l~~q~~~~~~~~~  125 (219)
                      +++-|++++.+  ...+++|.|+.|||||.+..--+.+.+... ....++++|+.|+..+.++.+++.+..
T Consensus         2 Ln~~Q~~av~~--~~~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~~~p~~IL~vTFt~~Aa~em~~Rl~~~l   70 (664)
T TIGR01074         2 LNPQQQEAVEY--VTGPCLVLAGAGSGKTRVITNKIAYLIQNCGYKARNIAAVTFTNKAAREMKERVAKTL   70 (664)
T ss_pred             CCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHh
Confidence            67889888765  346899999999999977766666666432 234579999999999999999997764

Designed to identify rep members of the uvrD/rep subfamily.

>PHA03333 putative ATPase subunit of terminase; Provisional

Probab=97.24  E-value=0.012  Score=53.08  Aligned_cols=138  Identities=9%  Similarity=0.037  Sum_probs=77.2

Q ss_pred             hCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccce--------eEEEEECCc
Q 027749           68 IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI--------QAHACVGGK  139 (219)
Q Consensus        68 ~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~--------~~~~~~~~~  139 (219)
                      .+.+-.++.+|-|.|||++..+.+...+..  .+.++++++|....+.++++++.......+.        .+....|+.
T Consensus       185 fkq~~tV~taPRqrGKS~iVgi~l~~La~f--~Gi~IlvTAH~~~ts~evF~rv~~~le~lg~~~~fp~~~~iv~vkgg~  262 (752)
T PHA03333        185 YGKCYTAATVPRRCGKTTIMAIILAAMISF--LEIDIVVQAQRKTMCLTLYNRVETVVHAYQHKPWFPEEFKIVTLKGTD  262 (752)
T ss_pred             HhhcceEEEeccCCCcHHHHHHHHHHHHHh--cCCeEEEECCChhhHHHHHHHHHHHHHHhccccccCCCceEEEeeCCe
Confidence            355678899999999997766554443321  2467999999999999999998877763321        111111111


Q ss_pred             cc-HHHH-HHhc-CCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCC-CCCeEEEEeec
Q 027749          140 SV-GEDI-RKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP-PDLQVCCPGSC  215 (219)
Q Consensus       140 ~~-~~~~-~~l~-~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~-~~~q~i~~SAT  215 (219)
                      .. .-.. .... .+..|.+++..       .+...-...+++|||||.-+-.    ..+..++-.+. .+..++++|.+
T Consensus       263 E~I~f~~p~gak~G~sti~F~Ars-------~~s~RG~~~DLLIVDEAAfI~~----~~l~aIlP~l~~~~~k~IiISS~  331 (752)
T PHA03333        263 ENLEYISDPAAKEGKTTAHFLASS-------PNAARGQNPDLVIVDEAAFVNP----GALLSVLPLMAVKGTKQIHISSP  331 (752)
T ss_pred             eEEEEecCcccccCcceeEEeccc-------CCCcCCCCCCEEEEECcccCCH----HHHHHHHHHHccCCCceEEEeCC
Confidence            00 0000 0000 01233332211       1222223568999999987654    33334444433 36677888876


Q ss_pred             ccC
Q 027749          216 FLF  218 (219)
Q Consensus       216 l~~  218 (219)
                      -+.
T Consensus       332 ~~~  334 (752)
T PHA03333        332 VDA  334 (752)
T ss_pred             CCc
Confidence            543

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.24  E-value=0.0048  Score=52.03  Aligned_cols=22  Identities=27%  Similarity=0.303  Sum_probs=17.2

Q ss_pred             CCcEEEEcCCCCchhHHhHHHH
Q 027749           70 GRDVIAQAQSGTGKTSMIALTV   91 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~   91 (219)
                      ++.+++.||||+|||....--+
T Consensus       137 g~ii~lvGptGvGKTTtiakLA  158 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLA  158 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHH
Confidence            5678999999999996654433

>PRK08084 DNA replication initiation factor; Provisional

Probab=97.23  E-value=0.0013  Score=52.16  Aligned_cols=43  Identities=12%  Similarity=0.100  Sum_probs=25.6

Q ss_pred             ccEEEeccchhhhcc-ccHHHHHHHHHhCCC-CCeEEEEeecccC
Q 027749          176 IKLLVLDESDEMLSR-GFKDQIYDVYRYLPP-DLQVCCPGSCFLF  218 (219)
Q Consensus       176 l~~lVvDE~h~l~~~-~~~~~~~~i~~~~~~-~~q~i~~SATl~~  218 (219)
                      .++|++||+|.+... .....+..+++.+.. +...+++|++.|+
T Consensus        98 ~dlliiDdi~~~~~~~~~~~~lf~l~n~~~e~g~~~li~ts~~~p  142 (235)
T PRK08084         98 LSLVCIDNIECIAGDELWEMAIFDLYNRILESGRTRLLITGDRPP  142 (235)
T ss_pred             CCEEEEeChhhhcCCHHHHHHHHHHHHHHHHcCCCeEEEeCCCCh
Confidence            468999999987643 345556666655432 2223555665553

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]

Probab=97.21  E-value=0.0013  Score=60.10  Aligned_cols=145  Identities=18%  Similarity=0.176  Sum_probs=90.2

Q ss_pred             HHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCC--ceeEEEEcCCHHHHHHHHHHHHHh-----ccccceeEEEE
Q 027749           63 AVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR--EVQALILSPTRELATQTEKVILAI-----GDFINIQAHAC  135 (219)
Q Consensus        63 ~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~--~~~~lil~P~~~l~~q~~~~~~~~-----~~~~~~~~~~~  135 (219)
                      .+..+....-+++-+.||+||+.-+.-.++..+..+..  ...+.+--|++..+..+.+++.+-     +.-.+.++.. 
T Consensus       386 i~q~v~dn~v~~I~getgcgk~tq~aq~iLe~~~~ns~g~~~na~v~qprrisaisiaerva~er~e~~g~tvgy~vRf-  464 (1282)
T KOG0921|consen  386 ILQAVAENRVVIIKGETGCGKSTQVAQFLLESFLENSNGASFNAVVSQPRRISAISLAERVANERGEEVGETCGYNVRF-  464 (1282)
T ss_pred             HHHHHhcCceeeEeecccccchhHHHHHHHHHHhhccccccccceeccccccchHHHHHHHHHhhHHhhcccccccccc-
Confidence            33444455668899999999999888888887765543  244777778888887777766322     2111221110 


Q ss_pred             ECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhcc-ccHHHHHHHHHhCCCCCeEEEEee
Q 027749          136 VGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPPDLQVCCPGS  214 (219)
Q Consensus       136 ~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~-~~~~~~~~i~~~~~~~~q~i~~SA  214 (219)
                      .+..+..        ---|+++|-+.+++++.+..   ..+.++|+||.|...-. .|...+.+=+.....+..++++||
T Consensus       465 ~Sa~prp--------yg~i~fctvgvllr~~e~gl---rg~sh~i~deiherdv~~dfll~~lr~m~~ty~dl~v~lmsa  533 (1282)
T KOG0921|consen  465 DSATPRP--------YGSIMFCTVGVLLRMMENGL---RGISHVIIDEIHERDVDTDFVLIVLREMISTYRDLRVVLMSA  533 (1282)
T ss_pred             ccccccc--------ccceeeeccchhhhhhhhcc---cccccccchhhhhhccchHHHHHHHHhhhccchhhhhhhhhc
Confidence            0111111        12588999999999887653   56778999999964432 233333333333344667788888


Q ss_pred             cccCC
Q 027749          215 CFLFD  219 (219)
Q Consensus       215 Tl~~~  219 (219)
                      |+..|
T Consensus       534 tIdTd  538 (1282)
T KOG0921|consen  534 TIDTD  538 (1282)
T ss_pred             ccchh
Confidence            87543

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=97.20  E-value=0.0013  Score=57.01  Aligned_cols=106  Identities=12%  Similarity=0.190  Sum_probs=56.7

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcC
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH  150 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  150 (219)
                      ..+++.|++|+|||- .+..+.+.+.....+.+++++.. ..+..++...+..-.                         
T Consensus       142 npl~i~G~~G~GKTH-Ll~Ai~~~l~~~~~~~~v~yv~~-~~f~~~~~~~l~~~~-------------------------  194 (450)
T PRK14087        142 NPLFIYGESGMGKTH-LLKAAKNYIESNFSDLKVSYMSG-DEFARKAVDILQKTH-------------------------  194 (450)
T ss_pred             CceEEECCCCCcHHH-HHHHHHHHHHHhCCCCeEEEEEH-HHHHHHHHHHHHHhh-------------------------
Confidence            458899999999992 22344444444334455666655 445444444332100                         


Q ss_pred             CCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhcc-ccHHHHHHHHHhCCC-CCeEEEEeeccc
Q 027749          151 GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPP-DLQVCCPGSCFL  217 (219)
Q Consensus       151 ~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~-~~~~~~~~i~~~~~~-~~q~i~~SATl~  217 (219)
                               +.+.....    .+.+.++||+||+|.+... ...+.+..+++.+.. ..|+| +|+..+
T Consensus       195 ---------~~~~~~~~----~~~~~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iI-ltsd~~  249 (450)
T PRK14087        195 ---------KEIEQFKN----EICQNDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLF-FSSDKS  249 (450)
T ss_pred             ---------hHHHHHHH----HhccCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEE-EECCCC
Confidence                     11111111    1346779999999977532 234556666666533 33554 444433

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=97.19  E-value=0.0045  Score=51.47  Aligned_cols=134  Identities=8%  Similarity=0.027  Sum_probs=67.2

Q ss_pred             ChHHHHHHHHHHhCC----CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhcccccee
Q 027749           56 PSAIQQRAVMPIIKG----RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ  131 (219)
Q Consensus        56 ~~~~Q~~~~~~~~~~----~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  131 (219)
                      .+|||...|..+...    +..+++||.|.||+..+.. +...+.......  .  .|     =..+..|+.+.......
T Consensus         4 ~yPWl~~~~~~~~~~~r~~ha~Lf~G~~G~GK~~~A~~-~A~~llC~~~~~--~--~~-----Cg~C~sC~~~~~g~HPD   73 (328)
T PRK05707          4 IYPWQQSLWQQLAGRGRHPHAYLLHGPAGIGKRALAER-LAAALLCEAPQG--G--GA-----CGSCKGCQLLRAGSHPD   73 (328)
T ss_pred             CCCCcHHHHHHHHHCCCcceeeeeECCCCCCHHHHHHH-HHHHHcCCCCCC--C--CC-----CCCCHHHHHHhcCCCCC
Confidence            478999999887643    2478999999999954433 334333221100  0  00     01234444443332222


Q ss_pred             EEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcC--CCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeE
Q 027749          132 AHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK--TLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQV  209 (219)
Q Consensus       132 ~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~--~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~  209 (219)
                      +..+......          ..|   .-+.+..+...-  .-.....+++||||+|.|.... .+.+.+.++.-|.+.-+
T Consensus        74 ~~~i~~~~~~----------~~i---~id~iR~l~~~~~~~~~~~~~kv~iI~~a~~m~~~a-aNaLLK~LEEPp~~~~f  139 (328)
T PRK05707         74 NFVLEPEEAD----------KTI---KVDQVRELVSFVVQTAQLGGRKVVLIEPAEAMNRNA-ANALLKSLEEPSGDTVL  139 (328)
T ss_pred             EEEEeccCCC----------CCC---CHHHHHHHHHHHhhccccCCCeEEEECChhhCCHHH-HHHHHHHHhCCCCCeEE
Confidence            2222110000          000   012222222211  1123467889999999988654 55566677776655555


Q ss_pred             EEEe
Q 027749          210 CCPG  213 (219)
Q Consensus       210 i~~S  213 (219)
                      |+.|
T Consensus       140 iL~t  143 (328)
T PRK05707        140 LLIS  143 (328)
T ss_pred             EEEE
Confidence            5544

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=97.19  E-value=0.0035  Score=48.94  Aligned_cols=41  Identities=10%  Similarity=0.233  Sum_probs=24.1

Q ss_pred             ccEEEeccchhhhcc-ccHHHHHHHHHhCCCCCeEEEEeecc
Q 027749          176 IKLLVLDESDEMLSR-GFKDQIYDVYRYLPPDLQVCCPGSCF  216 (219)
Q Consensus       176 l~~lVvDE~h~l~~~-~~~~~~~~i~~~~~~~~q~i~~SATl  216 (219)
                      .++||+||+|.+... .....+..+++........+++|++.
T Consensus        91 ~~lLvIDdi~~l~~~~~~~~~L~~~l~~~~~~~~~iIits~~  132 (226)
T TIGR03420        91 ADLVCLDDVEAIAGQPEWQEALFHLYNRVREAGGRLLIAGRA  132 (226)
T ss_pred             CCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCeEEEECCC
Confidence            468999999987643 23455666655532222245556553

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.

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=97.19  E-value=0.0059  Score=55.38  Aligned_cols=67  Identities=22%  Similarity=0.301  Sum_probs=51.1

Q ss_pred             CChHHHHHHHHHHhCC-----CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccc
Q 027749           55 KPSAIQQRAVMPIIKG-----RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDF  127 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~-----~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (219)
                      .|+..|..++..+.++     ++.++.|.||+|||+...- ++...     +..+|||+|+..+|.|+++.++.+...
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            6888999999877533     3667999999999955432 33322     123899999999999999999998754

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

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.18  E-value=0.0023  Score=55.49  Aligned_cols=19  Identities=26%  Similarity=0.366  Sum_probs=15.2

Q ss_pred             cEEEEcCCCCchhHHhHHH
Q 027749           72 DVIAQAQSGTGKTSMIALT   90 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~~~   90 (219)
                      ..+++||.|+|||.++.+.
T Consensus        42 a~Lf~GP~GtGKTTlAriL   60 (484)
T PRK14956         42 AYIFFGPRGVGKTTIARIL   60 (484)
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            3799999999999665543

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=97.17  E-value=0.004  Score=51.49  Aligned_cols=140  Identities=12%  Similarity=0.159  Sum_probs=71.1

Q ss_pred             CCChHHHHHHHHHHh----CCC---cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhcc
Q 027749           54 EKPSAIQQRAVMPII----KGR---DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGD  126 (219)
Q Consensus        54 ~~~~~~Q~~~~~~~~----~~~---~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~  126 (219)
                      ..++|||..+|..+.    +|+   -.++.||.|.||+..+. .+...+......+     ++       .+..++.+..
T Consensus         3 ~~~yPW~~~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~-~lA~~LlC~~~~~-----~~-------~c~~c~~~~~   69 (319)
T PRK08769          3 SAFSPWQQRAYDQTVAALDAGRLGHGLLICGPEGLGKRAVAL-ALAEHVLASGPDP-----AA-------AQRTRQLIAA   69 (319)
T ss_pred             ccccccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHH-HHHHHHhCCCCCC-----CC-------cchHHHHHhc
Confidence            367899999998765    343   48899999999995443 3444443322111     00       1122222222


Q ss_pred             ccceeEEEE--ECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCC
Q 027749          127 FINIQAHAC--VGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP  204 (219)
Q Consensus       127 ~~~~~~~~~--~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~  204 (219)
                      .....+..+  ...... .     .....|.|---..+.+.+.... .....+++|||++|.|.... .+.+.+.++.-|
T Consensus        70 g~HPD~~~i~~~p~~~~-~-----k~~~~I~idqIR~l~~~~~~~p-~~g~~kV~iI~~ae~m~~~A-aNaLLKtLEEPp  141 (319)
T PRK08769         70 GTHPDLQLVSFIPNRTG-D-----KLRTEIVIEQVREISQKLALTP-QYGIAQVVIVDPADAINRAA-CNALLKTLEEPS  141 (319)
T ss_pred             CCCCCEEEEecCCCccc-c-----cccccccHHHHHHHHHHHhhCc-ccCCcEEEEeccHhhhCHHH-HHHHHHHhhCCC
Confidence            221222222  100000 0     0001222222222222222221 23467899999999987554 556666778777


Q ss_pred             CCCeEEEEee
Q 027749          205 PDLQVCCPGS  214 (219)
Q Consensus       205 ~~~q~i~~SA  214 (219)
                      .++.+|+.|.
T Consensus       142 ~~~~fiL~~~  151 (319)
T PRK08769        142 PGRYLWLISA  151 (319)
T ss_pred             CCCeEEEEEC
Confidence            7777777664

>PRK06921 hypothetical protein; Provisional

Probab=97.16  E-value=0.011  Score=47.64  Aligned_cols=38  Identities=18%  Similarity=0.342  Sum_probs=23.3

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEc
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~  108 (219)
                      .+.++++.|++|+|||... ..+...+.... +..++++.
T Consensus       116 ~~~~l~l~G~~G~GKThLa-~aia~~l~~~~-g~~v~y~~  153 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLL-TAAANELMRKK-GVPVLYFP  153 (266)
T ss_pred             CCCeEEEECCCCCcHHHHH-HHHHHHHhhhc-CceEEEEE
Confidence            3568999999999999332 23344444321 34456654

>PRK14974 cell division protein FtsY; Provisional

Probab=97.15  E-value=0.011  Score=49.28  Aligned_cols=43  Identities=19%  Similarity=0.339  Sum_probs=30.5

Q ss_pred             CccEEEeccchhhhc-cccHHHHHHHHHhCCCCCeEEEEeeccc
Q 027749          175 AIKLLVLDESDEMLS-RGFKDQIYDVYRYLPPDLQVCCPGSCFL  217 (219)
Q Consensus       175 ~l~~lVvDE~h~l~~-~~~~~~~~~i~~~~~~~~q~i~~SATl~  217 (219)
                      +.++|++|.+.++.. ..+...+..+.+...++.-++.++|+..
T Consensus       222 ~~DvVLIDTaGr~~~~~~lm~eL~~i~~~~~pd~~iLVl~a~~g  265 (336)
T PRK14974        222 GIDVVLIDTAGRMHTDANLMDELKKIVRVTKPDLVIFVGDALAG  265 (336)
T ss_pred             CCCEEEEECCCccCCcHHHHHHHHHHHHhhCCceEEEeeccccc
Confidence            456888888887653 3456677777777777777788887654

>PRK06526 transposase; Provisional

Probab=97.14  E-value=0.0017  Score=52.01  Aligned_cols=22  Identities=27%  Similarity=0.434  Sum_probs=17.5

Q ss_pred             HhCCCcEEEEcCCCCchhHHhH
Q 027749           67 IIKGRDVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        67 ~~~~~~~lv~~~tG~GKT~~~~   88 (219)
                      +..+++++++||+|+|||....
T Consensus        95 i~~~~nlll~Gp~GtGKThLa~  116 (254)
T PRK06526         95 VTGKENVVFLGPPGTGKTHLAI  116 (254)
T ss_pred             hhcCceEEEEeCCCCchHHHHH
Confidence            3456799999999999994443

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=97.14  E-value=0.0078  Score=54.92  Aligned_cols=39  Identities=15%  Similarity=0.355  Sum_probs=26.2

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      .+.+++||||+|.|....+ +.+.+.++.-+.+..+|+.+
T Consensus       118 gr~KVIIIDEah~LT~~A~-NALLKtLEEPP~~v~FILaT  156 (830)
T PRK07003        118 ARFKVYMIDEVHMLTNHAF-NAMLKTLEEPPPHVKFILAT  156 (830)
T ss_pred             CCceEEEEeChhhCCHHHH-HHHHHHHHhcCCCeEEEEEE
Confidence            4578999999998876543 44555666666655555544

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=97.13  E-value=0.0034  Score=54.33  Aligned_cols=38  Identities=13%  Similarity=0.307  Sum_probs=24.3

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcC
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P  109 (219)
                      ..+++.||+|+|||-.. ..+.+.+.....+.+++++..
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            46899999999999332 334444444433456777653

>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=97.13  E-value=0.011  Score=45.44  Aligned_cols=120  Identities=16%  Similarity=0.233  Sum_probs=54.1

Q ss_pred             EEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCC-HHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCC
Q 027749           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT-RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG  151 (219)
Q Consensus        73 ~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~-~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  151 (219)
                      ++++||||+|||....=.+.+.... +.+ -+++-+-+ |.=+.   +.++.+.+..++.+.......+           
T Consensus         4 i~lvGptGvGKTTt~aKLAa~~~~~-~~~-v~lis~D~~R~ga~---eQL~~~a~~l~vp~~~~~~~~~-----------   67 (196)
T PF00448_consen    4 IALVGPTGVGKTTTIAKLAARLKLK-GKK-VALISADTYRIGAV---EQLKTYAEILGVPFYVARTESD-----------   67 (196)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHT-T---EEEEEESTSSTHHH---HHHHHHHHHHTEEEEESSTTSC-----------
T ss_pred             EEEECCCCCchHhHHHHHHHHHhhc-ccc-ceeecCCCCCccHH---HHHHHHHHHhccccchhhcchh-----------
Confidence            6789999999996654433333333 222 34444443 32222   3333343333555443322221           


Q ss_pred             CeEEEeChHHHH-HHHHcCCCCCCCccEEEeccchhhhc-cccHHHHHHHHHhCCCCCeEEEEeeccc
Q 027749          152 VHVVSGTPGRVC-DMIKRKTLRTRAIKLLVLDESDEMLS-RGFKDQIYDVYRYLPPDLQVCCPGSCFL  217 (219)
Q Consensus       152 ~~I~v~Tp~~l~-~~l~~~~~~~~~l~~lVvDE~h~l~~-~~~~~~~~~i~~~~~~~~q~i~~SATl~  217 (219)
                             |..+. ..+...  ..++.++|+||-+-+... ......+..+++.+.+..-.+.+|||..
T Consensus        68 -------~~~~~~~~l~~~--~~~~~D~vlIDT~Gr~~~d~~~~~el~~~~~~~~~~~~~LVlsa~~~  126 (196)
T PF00448_consen   68 -------PAEIAREALEKF--RKKGYDLVLIDTAGRSPRDEELLEELKKLLEALNPDEVHLVLSATMG  126 (196)
T ss_dssp             -------HHHHHHHHHHHH--HHTTSSEEEEEE-SSSSTHHHHHHHHHHHHHHHSSSEEEEEEEGGGG
T ss_pred             -------hHHHHHHHHHHH--hhcCCCEEEEecCCcchhhHHHHHHHHHHhhhcCCccceEEEecccC
Confidence                   11111 111110  113355666666543221 1234455555555555555666666654

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 ....

>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]

Probab=97.13  E-value=0.012  Score=53.52  Aligned_cols=152  Identities=14%  Similarity=0.240  Sum_probs=90.0

Q ss_pred             HHHHHHHCCCCCChHHHHHHHHHHhCCC--cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHH
Q 027749           44 LLRGIYQYGFEKPSAIQQRAVMPIIKGR--DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVI  121 (219)
Q Consensus        44 ~~~~l~~~~~~~~~~~Q~~~~~~~~~~~--~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~  121 (219)
                      .-..+.+.....+..-|.+.+..+...+  -+++.|.-|-|||.+.-+.+....... ....++|.+|+.+-++.+++.+
T Consensus       203 ~~~~l~~l~~T~dQ~~~l~~~~~l~~~~~~~~vlTAdRGRGKSA~lGi~~~~~~~~~-~~~~iiVTAP~~~nv~~Lf~fa  281 (758)
T COG1444         203 FPRELYELCLTEDQAEALEILERLLDAPKRALVLTADRGRGKSAALGIALAAAARLA-GSVRIIVTAPTPANVQTLFEFA  281 (758)
T ss_pred             CCHHHhhhhcChhHHHHHHHHHHHHcCCCceEEEEcCCCCcHhHHHhHHHHHHHHhc-CCceEEEeCCCHHHHHHHHHHH
Confidence            3344555444445555555665555443  588999999999977666552222222 1457999999999999999988


Q ss_pred             HHhccccceeEEEEECCcccHHHHHHh-cCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHH
Q 027749          122 LAIGDFINIQAHACVGGKSVGEDIRKL-EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVY  200 (219)
Q Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~~~~~l-~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~  200 (219)
                      .+-....++.........   ...... .+...|=+..|....          ..-+++|||||=.+-    ...+.+++
T Consensus       282 ~~~l~~lg~~~~v~~d~~---g~~~~~~~~~~~i~y~~P~~a~----------~~~DllvVDEAAaIp----lplL~~l~  344 (758)
T COG1444         282 GKGLEFLGYKRKVAPDAL---GEIREVSGDGFRIEYVPPDDAQ----------EEADLLVVDEAAAIP----LPLLHKLL  344 (758)
T ss_pred             HHhHHHhCCccccccccc---cceeeecCCceeEEeeCcchhc----------ccCCEEEEehhhcCC----hHHHHHHH
Confidence            776655554322111000   000011 122345556663211          116789999996543    56677777


Q ss_pred             HhCCCCCeEEEEeeccc
Q 027749          201 RYLPPDLQVCCPGSCFL  217 (219)
Q Consensus       201 ~~~~~~~q~i~~SATl~  217 (219)
                      +..+    .++||.|+.
T Consensus       345 ~~~~----rv~~sTTIh  357 (758)
T COG1444         345 RRFP----RVLFSTTIH  357 (758)
T ss_pred             hhcC----ceEEEeeec
Confidence            7654    588888864

>COG4626 Phage terminase-like protein, large subunit [General function prediction only]

Probab=97.12  E-value=0.0056  Score=53.47  Aligned_cols=145  Identities=12%  Similarity=0.094  Sum_probs=86.0

Q ss_pred             CChHHHHHHHHHHh------CC----CcEEEEcCCCCchhHHhH-HHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 027749           55 KPSAIQQRAVMPII------KG----RDVIAQAQSGTGKTSMIA-LTVCQTVDTSSREVQALILSPTRELATQTEKVILA  123 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~------~~----~~~lv~~~tG~GKT~~~~-~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~  123 (219)
                      ..-|||+.++-.+.      .+    +..+|..|-+.|||.... +.....+.....+....|++|+.+.+.+.+..++.
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            66899999998876      11    357899999999994433 44444454556667899999999999999998877


Q ss_pred             hccccc-eeEEEEECCcccHHHHHHhcC-CCeEEEeChHHHHHHHHc--CCCCCCCccEEEeccchhhhccccHHHHHHH
Q 027749          124 IGDFIN-IQAHACVGGKSVGEDIRKLEH-GVHVVSGTPGRVCDMIKR--KTLRTRAIKLLVLDESDEMLSRGFKDQIYDV  199 (219)
Q Consensus       124 ~~~~~~-~~~~~~~~~~~~~~~~~~l~~-~~~I~v~Tp~~l~~~l~~--~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i  199 (219)
                      ...... ++..            ..... ...|...--....+.+..  +..+-.+....|+||.|.....+  ..+..+
T Consensus       141 mv~~~~~l~~~------------~~~q~~s~~i~~~~~~s~ik~~aa~~~~~Dg~~~~~~I~DEih~f~~~~--~~~~~~  206 (546)
T COG4626         141 MVKRDDDLRDL------------CNVQTHSRTITHRKTDSTIKAVAADPNTVDGLNSVGAIIDELHLFGKQE--DMYSEA  206 (546)
T ss_pred             HHHhCcchhhh------------hccccceeEEEecccceeeeeeccCCCcccCCCcceEEEehhhhhcCHH--HHHHHH
Confidence            654432 1100            00000 111111111111122222  23444566789999999866543  555555


Q ss_pred             HHhCC--CCCeEEEEe
Q 027749          200 YRYLP--PDLQVCCPG  213 (219)
Q Consensus       200 ~~~~~--~~~q~i~~S  213 (219)
                      ..-+.  ++.+++..|
T Consensus       207 ~~g~~ar~~~l~~~IT  222 (546)
T COG4626         207 KGGLGARPEGLVVYIT  222 (546)
T ss_pred             HhhhccCcCceEEEEe
Confidence            55553  355666555

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.11  E-value=0.011  Score=50.21  Aligned_cols=20  Identities=25%  Similarity=0.415  Sum_probs=15.5

Q ss_pred             CcEEEEcCCCCchhHHhHHH
Q 027749           71 RDVIAQAQSGTGKTSMIALT   90 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~   90 (219)
                      +.+.+.||+|+|||.....-
T Consensus       242 ~vI~LVGptGvGKTTTiaKL  261 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAKM  261 (436)
T ss_pred             cEEEEECCCCCcHHHHHHHH
Confidence            46789999999999555443

>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=97.11  E-value=0.0022  Score=47.72  Aligned_cols=41  Identities=12%  Similarity=0.230  Sum_probs=30.8

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEeec
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSC  215 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SAT  215 (219)
                      ...+++|+||+|.|... ....+.+.++.-|.+..+|++|..
T Consensus       101 ~~~KviiI~~ad~l~~~-a~NaLLK~LEepp~~~~fiL~t~~  141 (162)
T PF13177_consen  101 GKYKVIIIDEADKLTEE-AQNALLKTLEEPPENTYFILITNN  141 (162)
T ss_dssp             SSSEEEEEETGGGS-HH-HHHHHHHHHHSTTTTEEEEEEES-
T ss_pred             CCceEEEeehHhhhhHH-HHHHHHHHhcCCCCCEEEEEEECC
Confidence            56889999999998755 367788888887777777776654

...

>PRK08727 hypothetical protein; Validated

Probab=97.11  E-value=0.0028  Score=50.12  Aligned_cols=43  Identities=9%  Similarity=0.089  Sum_probs=23.7

Q ss_pred             CCccEEEeccchhhhcc-ccHHHHHHHHHhCCC-CCeEEEEeeccc
Q 027749          174 RAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPP-DLQVCCPGSCFL  217 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~-~~~~~~~~i~~~~~~-~~q~i~~SATl~  217 (219)
                      .+.++||+||+|.+... .....+..+++.... ..+ +++|+..+
T Consensus        92 ~~~dlLiIDDi~~l~~~~~~~~~lf~l~n~~~~~~~~-vI~ts~~~  136 (233)
T PRK08727         92 EGRSLVALDGLESIAGQREDEVALFDFHNRARAAGIT-LLYTARQM  136 (233)
T ss_pred             hcCCEEEEeCcccccCChHHHHHHHHHHHHHHHcCCe-EEEECCCC
Confidence            44578999999987643 223344455554422 234 44444433

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=97.10  E-value=0.0045  Score=62.46  Aligned_cols=63  Identities=32%  Similarity=0.420  Sum_probs=45.6

Q ss_pred             CCChHHHHHHHHHHhCC--CcEEEEcCCCCchhHHhH---HHHHhhhccCCCceeEEEEcCCHHHHHHHH
Q 027749           54 EKPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIA---LTVCQTVDTSSREVQALILSPTRELATQTE  118 (219)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~--~~~lv~~~tG~GKT~~~~---~~~~~~~~~~~~~~~~lil~P~~~l~~q~~  118 (219)
                      ..+++.|..++..++.+  +-++|.|+.|+|||....   -++...+..  .+..++.++||...+..+.
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            36899999999998765  557889999999995441   223333332  2456889999988877664

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.

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.07  E-value=0.0042  Score=55.78  Aligned_cols=39  Identities=13%  Similarity=0.283  Sum_probs=27.2

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      .+.+++||||+|+|....+ +.+.+.++.-+.++.+|+.|
T Consensus       123 gr~KViIIDEah~Ls~~Aa-NALLKTLEEPP~~v~FILaT  161 (700)
T PRK12323        123 GRFKVYMIDEVHMLTNHAF-NAMLKTLEEPPEHVKFILAT  161 (700)
T ss_pred             CCceEEEEEChHhcCHHHH-HHHHHhhccCCCCceEEEEe
Confidence            4678999999999876554 34445566656677666665

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=97.06  E-value=0.0081  Score=49.47  Aligned_cols=39  Identities=13%  Similarity=0.253  Sum_probs=27.4

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ...+++|+||||.|... -...+.+.++.-+.+..+++.+
T Consensus       108 ~~~kviiidead~mt~~-A~nallk~lEep~~~~~~il~~  146 (325)
T COG0470         108 GGYKVVIIDEADKLTED-AANALLKTLEEPPKNTRFILIT  146 (325)
T ss_pred             CCceEEEeCcHHHHhHH-HHHHHHHHhccCCCCeEEEEEc
Confidence            67889999999998853 3556666666655555555554

>PLN03025 replication factor C subunit; Provisional

Probab=97.06  E-value=0.0072  Score=50.06  Aligned_cols=38  Identities=18%  Similarity=0.279  Sum_probs=26.0

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEE
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCP  212 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~  212 (219)
                      ...+++|+||+|.|.... ...+.+.++..++...+++.
T Consensus        98 ~~~kviiiDE~d~lt~~a-q~aL~~~lE~~~~~t~~il~  135 (319)
T PLN03025         98 GRHKIVILDEADSMTSGA-QQALRRTMEIYSNTTRFALA  135 (319)
T ss_pred             CCeEEEEEechhhcCHHH-HHHHHHHHhcccCCceEEEE
Confidence            357899999999987543 45566667666655555543

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=97.04  E-value=0.014  Score=48.51  Aligned_cols=39  Identities=8%  Similarity=0.152  Sum_probs=26.8

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ...++||+||+|.+... ....+..+++..+..+.+|+.+
T Consensus       124 ~~~~vlilDe~~~l~~~-~~~~L~~~le~~~~~~~~Il~~  162 (337)
T PRK12402        124 ADYKTILLDNAEALRED-AQQALRRIMEQYSRTCRFIIAT  162 (337)
T ss_pred             CCCcEEEEeCcccCCHH-HHHHHHHHHHhccCCCeEEEEe
Confidence            45678999999987543 3456677777766666666544

>PHA03372 DNA packaging terminase subunit 1; Provisional

Probab=97.01  E-value=0.0056  Score=54.17  Aligned_cols=132  Identities=12%  Similarity=0.114  Sum_probs=85.8

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  148 (219)
                      +.+-.+...|--.||| +++.|++..+..+-.+.++-|++.-+..++-+++++...+..-       ++....     ..
T Consensus       201 KQkaTVFLVPRRHGKT-Wf~VpiIsllL~s~~gI~IGYvAHqKhvs~~Vf~EI~~~lrrw-------F~~~~v-----i~  267 (668)
T PHA03372        201 KQKATVFLVPRRHGKT-WFIIPIISFLLKNIIGISIGYVAHQKHVSQFVLKEVEFRCRRM-------FPRKHT-----IE  267 (668)
T ss_pred             hccceEEEecccCCce-ehHHHHHHHHHHhhcCceEEEEeeHHHHHHHHHHHHHHHHhhh-------cCccce-----ee
Confidence            3456788899999999 7888899988888788999999999999988888774333221       000000     00


Q ss_pred             cCCCeEEEeChHHH-----HHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCC-CCCeEEEEeeccc
Q 027749          149 EHGVHVVSGTPGRV-----CDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP-PDLQVCCPGSCFL  217 (219)
Q Consensus       149 ~~~~~I~v~Tp~~l-----~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~-~~~q~i~~SATl~  217 (219)
                      .++-.|.+.-|+.=     ..-.+.+.+.-++..+++|||||-+-    .+.+..++..|. +++.+|+.|.|=+
T Consensus       268 ~k~~tI~~s~pg~Kst~~fasc~n~NsiRGQ~fnll~VDEA~FI~----~~a~~tilgfm~q~~~KiIfISS~Ns  338 (668)
T PHA03372        268 NKDNVISIDHRGAKSTALFASCYNTNSIRGQNFHLLLVDEAHFIK----KDAFNTILGFLAQNTTKIIFISSTNT  338 (668)
T ss_pred             ecCcEEEEecCCCcceeeehhhccCccccCCCCCEEEEehhhccC----HHHHHHhhhhhcccCceEEEEeCCCC
Confidence            01122333333211     11112244555778999999999544    466778888864 5788999988743

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.00  E-value=0.0043  Score=55.73  Aligned_cols=39  Identities=15%  Similarity=0.294  Sum_probs=25.6

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      .+.+++||||+|+|....+ +.+.+.++..|.++.+|+.+
T Consensus       123 g~~KV~IIDEvh~Ls~~a~-NaLLKtLEEPP~~~~fIL~T  161 (618)
T PRK14951        123 GRFKVFMIDEVHMLTNTAF-NAMLKTLEEPPEYLKFVLAT  161 (618)
T ss_pred             CCceEEEEEChhhCCHHHH-HHHHHhcccCCCCeEEEEEE
Confidence            4678999999999876553 33445555555555555543

>PRK08116 hypothetical protein; Validated

Probab=97.00  E-value=0.0037  Score=50.48  Aligned_cols=43  Identities=16%  Similarity=0.238  Sum_probs=24.8

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHH
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQT  117 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~  117 (219)
                      ..++++|++|+|||..+ ..+.+.+...  +..++++ +...+...+
T Consensus       115 ~gl~l~G~~GtGKThLa-~aia~~l~~~--~~~v~~~-~~~~ll~~i  157 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLA-ACIANELIEK--GVPVIFV-NFPQLLNRI  157 (268)
T ss_pred             ceEEEECCCCCCHHHHH-HHHHHHHHHc--CCeEEEE-EHHHHHHHH
Confidence            34999999999999333 2345555443  2234444 344444433

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=97.00  E-value=0.0044  Score=48.63  Aligned_cols=42  Identities=7%  Similarity=0.129  Sum_probs=25.5

Q ss_pred             CccEEEeccchhhhccccHHHHHHHHHhCCCCCe-EEEEeeccc
Q 027749          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ-VCCPGSCFL  217 (219)
Q Consensus       175 ~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q-~i~~SATl~  217 (219)
                      ..++||+||+|.+.... ...+..+++....... +++++++.+
T Consensus        90 ~~~~liiDdi~~l~~~~-~~~L~~~~~~~~~~~~~~vl~~~~~~  132 (227)
T PRK08903         90 EAELYAVDDVERLDDAQ-QIALFNLFNRVRAHGQGALLVAGPAA  132 (227)
T ss_pred             cCCEEEEeChhhcCchH-HHHHHHHHHHHHHcCCcEEEEeCCCC
Confidence            45689999999865432 4455566655433333 466666543

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.96  E-value=0.017  Score=49.77  Aligned_cols=20  Identities=35%  Similarity=0.456  Sum_probs=15.9

Q ss_pred             CCcEEEEcCCCCchhHHhHH
Q 027749           70 GRDVIAQAQSGTGKTSMIAL   89 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~   89 (219)
                      ++.+++.||||+|||....-
T Consensus       221 ~~~i~~vGptGvGKTTt~~k  240 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAK  240 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHH
Confidence            45688999999999965543

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.96  E-value=0.0083  Score=52.44  Aligned_cols=117  Identities=13%  Similarity=0.151  Sum_probs=58.8

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCccc-HHHHHHhc
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSV-GEDIRKLE  149 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~l~  149 (219)
                      +..+++||.|+|||.++.+.+ ..+... .++       +..-+ ..+..|..+.......+..+.+..+. -++++.+ 
T Consensus        36 ha~Lf~Gp~G~GKTT~ArilA-k~LnC~-~~~-------~~~pC-g~C~~C~~i~~~~~~Dv~eidaas~~~vddIR~I-  104 (491)
T PRK14964         36 QSILLVGASGVGKTTCARIIS-LCLNCS-NGP-------TSDPC-GTCHNCISIKNSNHPDVIEIDAASNTSVDDIKVI-  104 (491)
T ss_pred             ceEEEECCCCccHHHHHHHHH-HHHcCc-CCC-------CCCCc-cccHHHHHHhccCCCCEEEEecccCCCHHHHHHH-
Confidence            368999999999996655432 222111 111       00001 12445555554445555554432211 1112221 


Q ss_pred             CCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       150 ~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                                   .+...... ...+.+++|+||+|.|.... .+.+.+.++..|++..+|+.+
T Consensus       105 -------------ie~~~~~P-~~~~~KVvIIDEah~Ls~~A-~NaLLK~LEePp~~v~fIlat  153 (491)
T PRK14964        105 -------------LENSCYLP-ISSKFKVYIIDEVHMLSNSA-FNALLKTLEEPAPHVKFILAT  153 (491)
T ss_pred             -------------HHHHHhcc-ccCCceEEEEeChHhCCHHH-HHHHHHHHhCCCCCeEEEEEe
Confidence                         11111122 23578899999999877544 344555566656555555543

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=96.93  E-value=0.0069  Score=48.67  Aligned_cols=18  Identities=33%  Similarity=0.514  Sum_probs=14.9

Q ss_pred             CcEEEEcCCCCchhHHhH
Q 027749           71 RDVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~   88 (219)
                      .++++.||+|+|||..+-
T Consensus        43 ~~vll~GppGtGKTtlA~   60 (261)
T TIGR02881        43 LHMIFKGNPGTGKTTVAR   60 (261)
T ss_pred             ceEEEEcCCCCCHHHHHH
Confidence            478999999999995543

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.

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=96.93  E-value=0.011  Score=55.07  Aligned_cols=39  Identities=15%  Similarity=0.333  Sum_probs=29.3

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      .+.+++||||+|.|.... .+.+.++++..+.++-+|+.+
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            567899999999988654 456677777777776666655

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.93  E-value=0.0088  Score=52.72  Aligned_cols=39  Identities=13%  Similarity=0.283  Sum_probs=27.9

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      .+.+++|+||+|.|....+ +.+.+.++..|+++.+|+.+
T Consensus       118 ~~~kV~iIDE~~~ls~~a~-naLLk~LEepp~~~~fIlat  156 (509)
T PRK14958        118 GRFKVYLIDEVHMLSGHSF-NALLKTLEEPPSHVKFILAT  156 (509)
T ss_pred             CCcEEEEEEChHhcCHHHH-HHHHHHHhccCCCeEEEEEE
Confidence            4678999999998876543 45556777777776666654

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=96.90  E-value=0.0065  Score=51.33  Aligned_cols=89  Identities=19%  Similarity=0.261  Sum_probs=50.7

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhc
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE  149 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  149 (219)
                      ++-+.+.||||.|||....=.+.......+...-+||.+-|--.+.  .+.++-++...++.+..+............+.
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYRIGA--~EQLk~Ya~im~vp~~vv~~~~el~~ai~~l~  280 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRIGA--VEQLKTYADIMGVPLEVVYSPKELAEAIEALR  280 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEEeccchhhH--HHHHHHHHHHhCCceEEecCHHHHHHHHHHhh
Confidence            6789999999999996554333333322223344677766654432  24444455555677776666666555554444


Q ss_pred             CCCeEEEeChH
Q 027749          150 HGVHVVSGTPG  160 (219)
Q Consensus       150 ~~~~I~v~Tp~  160 (219)
                      +.--|+|-|.+
T Consensus       281 ~~d~ILVDTaG  291 (407)
T COG1419         281 DCDVILVDTAG  291 (407)
T ss_pred             cCCEEEEeCCC
Confidence            43334455543

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=96.89  E-value=0.0076  Score=49.09  Aligned_cols=117  Identities=15%  Similarity=0.241  Sum_probs=60.5

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhcc----CCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHH
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDT----SSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIR  146 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~----~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  146 (219)
                      .+.+++|+++.|||...---.-.+-..    ...-|-+.+-+|...-....+..+-....   ....    ...      
T Consensus        62 p~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL~~lg---aP~~----~~~------  128 (302)
T PF05621_consen   62 PNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAILEALG---APYR----PRD------  128 (302)
T ss_pred             CceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHHHHhC---cccC----CCC------
Confidence            489999999999995331111111000    11126677778887777766666643321   1110    000      


Q ss_pred             HhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccH--HHHHHHHHhCCCCC--eEEEE
Q 027749          147 KLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFK--DQIYDVYRYLPPDL--QVCCP  212 (219)
Q Consensus       147 ~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~--~~~~~i~~~~~~~~--q~i~~  212 (219)
                                 +...+..... ..+..-++++|||||+|.++.....  ..+.+.++.+.+..  .++++
T Consensus       129 -----------~~~~~~~~~~-~llr~~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~ipiV~v  186 (302)
T PF05621_consen  129 -----------RVAKLEQQVL-RLLRRLGVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNELQIPIVGV  186 (302)
T ss_pred             -----------CHHHHHHHHH-HHHHHcCCcEEEeechHHHhcccHHHHHHHHHHHHHHhhccCCCeEEe
Confidence                       1111111111 1111235789999999998865433  34555566665543  34443

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

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

Probab=96.89  E-value=0.007  Score=48.75  Aligned_cols=121  Identities=17%  Similarity=0.162  Sum_probs=56.5

Q ss_pred             HHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccH---
Q 027749           66 PIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVG---  142 (219)
Q Consensus        66 ~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~---  142 (219)
                      -+..|.-+++.|++|+|||......+.+.+...  +..++|+.- ..-..++...+........+.........+..   
T Consensus        26 G~~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~~--g~~vl~iS~-E~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~  102 (271)
T cd01122          26 GLRKGELIILTAGTGVGKTTFLREYALDLITQH--GVRVGTISL-EEPVVRTARRLLGQYAGKRLHLPDTVFIYTLEEFD  102 (271)
T ss_pred             EEcCCcEEEEEcCCCCCHHHHHHHHHHHHHHhc--CceEEEEEc-ccCHHHHHHHHHHHHhCCCcccCCccccccHHHHH
Confidence            345667899999999999954443333333321  334666653 22334444444332211121110000011111   


Q ss_pred             HHHHHhcCCCeEEEe------ChHHHHHHHHcCCCCCCCccEEEeccchhhhcc
Q 027749          143 EDIRKLEHGVHVVSG------TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (219)
Q Consensus       143 ~~~~~l~~~~~I~v~------Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~  190 (219)
                      .....+.....+++.      +++.+...+..-. .-.++++||||..+.+...
T Consensus       103 ~~~~~~~~~~~l~i~d~~~~~~~~~i~~~i~~~~-~~~~~~~vvID~l~~l~~~  155 (271)
T cd01122         103 AAFDEFEGTGRLFMYDSFGEYSMDSVLEKVRYMA-VSHGIQHIIIDNLSIMVSD  155 (271)
T ss_pred             HHHHHhcCCCcEEEEcCCCccCHHHHHHHHHHHH-hcCCceEEEECCHHHHhcc
Confidence            111222221222221      4555555444211 1135789999999987643

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

>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=96.88  E-value=0.01  Score=44.83  Aligned_cols=48  Identities=15%  Similarity=0.166  Sum_probs=30.0

Q ss_pred             EEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 027749           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (219)
Q Consensus        73 ~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (219)
                      ++|.||+|+|||...+--+...+ ..  +.+++|+.. .+...++.+.+..+
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~-~~--g~~v~~~s~-e~~~~~~~~~~~~~   49 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGL-AR--GEPGLYVTL-EESPEELIENAESL   49 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHH-HC--CCcEEEEEC-CCCHHHHHHHHHHc
Confidence            68999999999954443333333 22  344777754 45566666666555

A related protein is found in archaea.

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA

Probab=96.85  E-value=0.0064  Score=54.21  Aligned_cols=125  Identities=16%  Similarity=0.185  Sum_probs=74.7

Q ss_pred             CChHHHHHHHHHHhCC--CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHH-HHHHHhcccccee
Q 027749           55 KPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE-KVILAIGDFINIQ  131 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~--~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~-~~~~~~~~~~~~~  131 (219)
                      ..+|+|.+.+..+...  +.+.++.++.+|||.+.+..+...+...+.  .++++.||...+.... ..+..+......-
T Consensus        16 ~~~Py~~eimd~~~~~~v~~Vv~~k~aQ~GkT~~~~n~~g~~i~~~P~--~~l~v~Pt~~~a~~~~~~rl~Pmi~~sp~l   93 (557)
T PF05876_consen   16 DRTPYLREIMDALSDPSVREVVVMKSAQVGKTELLLNWIGYSIDQDPG--PMLYVQPTDDAAKDFSKERLDPMIRASPVL   93 (557)
T ss_pred             CCChhHHHHHHhcCCcCccEEEEEEcchhhHhHHHHhhceEEEEeCCC--CEEEEEEcHHHHHHHHHHHHHHHHHhCHHH
Confidence            5688999998887654  579999999999998666655555555543  3999999999999765 5555554433210


Q ss_pred             EEEEEC---CcccH-HHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhh
Q 027749          132 AHACVG---GKSVG-EDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (219)
Q Consensus       132 ~~~~~~---~~~~~-~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~  188 (219)
                      -..+..   ....+ ....... +..+.++...+      -..+.-..++++++||+|..-
T Consensus        94 ~~~~~~~~~~~~~~t~~~k~f~-gg~l~~~ga~S------~~~l~s~~~r~~~~DEvD~~p  147 (557)
T PF05876_consen   94 RRKLSPSKSRDSGNTILYKRFP-GGFLYLVGANS------PSNLRSRPARYLLLDEVDRYP  147 (557)
T ss_pred             HHHhCchhhcccCCchhheecC-CCEEEEEeCCC------CcccccCCcCEEEEechhhcc
Confidence            011111   00100 1111122 34444433210      122334568899999999874

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 [].

>KOG0953 consensus Mitochondrial RNA helicase SUV3, DEAD-box superfamily [RNA processing and modification]

Probab=96.82  E-value=0.0018  Score=56.32  Aligned_cols=97  Identities=20%  Similarity=0.178  Sum_probs=64.0

Q ss_pred             EEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCC
Q 027749           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGV  152 (219)
Q Consensus        73 ~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  152 (219)
                      ++=+|||.||||    ..+++++...+.   .+|--|.+-||.++++.+...    ++.+.++.|.......-.  .+.+
T Consensus       194 i~H~GPTNSGKT----y~ALqrl~~aks---GvycGPLrLLA~EV~~r~na~----gipCdL~TGeE~~~~~~~--~~~a  260 (700)
T KOG0953|consen  194 IMHVGPTNSGKT----YRALQRLKSAKS---GVYCGPLRLLAHEVYDRLNAL----GIPCDLLTGEERRFVLDN--GNPA  260 (700)
T ss_pred             EEEeCCCCCchh----HHHHHHHhhhcc---ceecchHHHHHHHHHHHhhhc----CCCccccccceeeecCCC--CCcc
Confidence            556799999999    445677666544   789999999999999988766    566666665544322211  1234


Q ss_pred             eEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhcc
Q 027749          153 HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (219)
Q Consensus       153 ~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~  190 (219)
                      +.+-||-+...        .-..++..|+||+.+|-+.
T Consensus       261 ~hvScTVEM~s--------v~~~yeVAViDEIQmm~Dp  290 (700)
T KOG0953|consen  261 QHVSCTVEMVS--------VNTPYEVAVIDEIQMMRDP  290 (700)
T ss_pred             cceEEEEEEee--------cCCceEEEEehhHHhhcCc
Confidence            55666643210        1235678889998887765

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.82  E-value=0.0086  Score=55.58  Aligned_cols=38  Identities=11%  Similarity=0.186  Sum_probs=25.8

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEE
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCP  212 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~  212 (219)
                      .+.+++||||+|+|.... .+.+.+.++.-|.++.+|+.
T Consensus       118 gk~KViIIDEAh~LT~eA-qNALLKtLEEPP~~vrFILa  155 (944)
T PRK14949        118 GRFKVYLIDEVHMLSRSS-FNALLKTLEEPPEHVKFLLA  155 (944)
T ss_pred             CCcEEEEEechHhcCHHH-HHHHHHHHhccCCCeEEEEE
Confidence            467899999999986443 45555666665666665554

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=96.81  E-value=0.0089  Score=49.29  Aligned_cols=39  Identities=10%  Similarity=0.130  Sum_probs=28.0

Q ss_pred             CccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       175 ~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ..++||+||+|.+........+..+++..+.++++|+.+
T Consensus       100 ~~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~  138 (316)
T PHA02544        100 GGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITA  138 (316)
T ss_pred             CCeEEEEECcccccCHHHHHHHHHHHHhcCCCceEEEEc
Confidence            457899999998844434566777788777777766644

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=96.80  E-value=0.0093  Score=48.98  Aligned_cols=67  Identities=21%  Similarity=0.372  Sum_probs=42.0

Q ss_pred             HHHHHHHCCCCCChHHHHHHHHH-HhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHH
Q 027749           44 LLRGIYQYGFEKPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (219)
Q Consensus        44 ~~~~l~~~~~~~~~~~Q~~~~~~-~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l  113 (219)
                      -+..|.+.|.  .++.|...+.. +..+++++++|+||+||| .++-.++..+......-+++++-...++
T Consensus       107 tl~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKT-Tll~al~~~i~~~~~~~ri~tiEd~~El  174 (299)
T TIGR02782       107 TLDDYVEAGI--MTAAQRDVLREAVLARKNILVVGGTGSGKT-TLANALLAEIAKNDPTDRVVIIEDTREL  174 (299)
T ss_pred             CHHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHH-HHHHHHHHHhhccCCCceEEEECCchhh
Confidence            3445555554  34444444444 556779999999999999 5555566666543233457777666665

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.

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=96.79  E-value=0.0074  Score=49.99  Aligned_cols=65  Identities=22%  Similarity=0.262  Sum_probs=41.5

Q ss_pred             HHHHHCCCCCChHHHHHHHHH-HhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHH
Q 027749           46 RGIYQYGFEKPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (219)
Q Consensus        46 ~~l~~~~~~~~~~~Q~~~~~~-~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l  113 (219)
                      ..+.+.|.  .++.|...+.. +..+++++++|+||+||| .++-.++..+......-+++.+=.+.++
T Consensus       121 ~~lv~~g~--~~~~~~~~L~~~v~~~~nilI~G~tGSGKT-Tll~aL~~~i~~~~~~~rivtiEd~~El  186 (323)
T PRK13833        121 DDYVTSKI--MTEAQASVIRSAIDSRLNIVISGGTGSGKT-TLANAVIAEIVASAPEDRLVILEDTAEI  186 (323)
T ss_pred             HHHHHcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHH-HHHHHHHHHHhcCCCCceEEEecCCccc
Confidence            34555554  45566666555 456679999999999999 4555666665433333456666666655

>PRK07952 DNA replication protein DnaC; Validated

Probab=96.78  E-value=0.019  Score=45.72  Aligned_cols=34  Identities=26%  Similarity=0.477  Sum_probs=21.4

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEE
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALIL  107 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil  107 (219)
                      ..+++.|++|+|||.... .+...+...  +..++++
T Consensus       100 ~~~~l~G~~GtGKThLa~-aia~~l~~~--g~~v~~i  133 (244)
T PRK07952        100 ASFIFSGKPGTGKNHLAA-AICNELLLR--GKSVLII  133 (244)
T ss_pred             ceEEEECCCCCCHHHHHH-HHHHHHHhc--CCeEEEE
Confidence            479999999999994333 344444443  2335555

>PRK06835 DNA replication protein DnaC; Validated

Probab=96.78  E-value=0.0079  Score=50.04  Aligned_cols=44  Identities=16%  Similarity=0.219  Sum_probs=25.8

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHH
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQ  116 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q  116 (219)
                      .++++++.|++|+|||... ..+...+...  +..++++ +...+..+
T Consensus       182 ~~~~Lll~G~~GtGKThLa-~aIa~~l~~~--g~~V~y~-t~~~l~~~  225 (329)
T PRK06835        182 NNENLLFYGNTGTGKTFLS-NCIAKELLDR--GKSVIYR-TADELIEI  225 (329)
T ss_pred             cCCcEEEECCCCCcHHHHH-HHHHHHHHHC--CCeEEEE-EHHHHHHH
Confidence            3578999999999999432 2334444433  3345554 33444443

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=96.77  E-value=0.016  Score=48.76  Aligned_cols=24  Identities=29%  Similarity=0.454  Sum_probs=17.4

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhh
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTV   95 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~   95 (219)
                      .+++|.||+|+|||... -.++..+
T Consensus        41 ~~i~I~G~~GtGKT~l~-~~~~~~l   64 (365)
T TIGR02928        41 SNVFIYGKTGTGKTAVT-KYVMKEL   64 (365)
T ss_pred             CcEEEECCCCCCHHHHH-HHHHHHH
Confidence            57999999999999443 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.

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=96.77  E-value=0.0024  Score=59.00  Aligned_cols=67  Identities=10%  Similarity=-0.017  Sum_probs=58.9

Q ss_pred             CCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEeeccc
Q 027749          151 GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFL  217 (219)
Q Consensus       151 ~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl~  217 (219)
                      ...|+++||..+..-+..+.++++++..|||||||++....-...+.++.+.-.+..-+.+|||...
T Consensus         7 ~ggi~~~T~rIl~~DlL~~ri~~~~itgiiv~~Ahr~~~~~~eaFI~rlyr~~n~~gfIkafSdsP~   73 (814)
T TIGR00596         7 EGGIFSITSRILVVDLLTGIIPPELITGILVLRADRIIESSQEAFILRLYRQKNKTGFIKAFSDNPE   73 (814)
T ss_pred             cCCEEEEechhhHhHHhcCCCCHHHccEEEEeecccccccccHHHHHHHHHHhCCCcceEEecCCCc
Confidence            4689999999999877788899999999999999999888777888888888888888999999754

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

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

Probab=96.76  E-value=0.01  Score=48.21  Aligned_cols=26  Identities=12%  Similarity=0.348  Sum_probs=18.0

Q ss_pred             cEEEEcCCCCchhHHhHHHHHhhhccC
Q 027749           72 DVIAQAQSGTGKTSMIALTVCQTVDTS   98 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~~~~~~~~~~~   98 (219)
                      =++|.||||||||.. +.+++..+...
T Consensus       127 LILVTGpTGSGKSTT-lAamId~iN~~  152 (353)
T COG2805         127 LILVTGPTGSGKSTT-LAAMIDYINKH  152 (353)
T ss_pred             eEEEeCCCCCcHHHH-HHHHHHHHhcc
Confidence            388999999999943 34455555443

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.75  E-value=0.051  Score=47.51  Aligned_cols=91  Identities=18%  Similarity=0.219  Sum_probs=46.2

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhc
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE  149 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  149 (219)
                      |+-+.+.||||+|||......+.......+...-.++-+-+.-..  ..+.++.+....++.+...............+.
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~G~~kV~LI~~Dt~Rig--A~EQLr~~AeilGVpv~~~~~~~Dl~~aL~~L~  333 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAARCVMRHGASKVALLTTDSYRIG--GHEQLRIYGKILGVPVHAVKDAADLRLALSELR  333 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHHHHHhcCCCeEEEEeCCccchh--HHHHHHHHHHHhCCCeeccCCchhHHHHHHhcc
Confidence            345789999999999776554433323322212233333332111  234444444444554443333333333344444


Q ss_pred             CCCeEEEeChHHH
Q 027749          150 HGVHVVSGTPGRV  162 (219)
Q Consensus       150 ~~~~I~v~Tp~~l  162 (219)
                      ....++|-|+++.
T Consensus       334 d~d~VLIDTaGr~  346 (484)
T PRK06995        334 NKHIVLIDTIGMS  346 (484)
T ss_pred             CCCeEEeCCCCcC
Confidence            4456888888843

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.74  E-value=0.012  Score=52.97  Aligned_cols=39  Identities=10%  Similarity=0.199  Sum_probs=26.5

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      .+.+++||||+|+|.... ...+.+.++..+.+..+|+.+
T Consensus       117 gk~KV~IIDEVh~LS~~A-~NALLKtLEEPP~~v~FILaT  155 (702)
T PRK14960        117 GRFKVYLIDEVHMLSTHS-FNALLKTLEEPPEHVKFLFAT  155 (702)
T ss_pred             CCcEEEEEechHhcCHHH-HHHHHHHHhcCCCCcEEEEEE
Confidence            356899999999876554 455666677766666555543

>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=96.74  E-value=0.024  Score=47.85  Aligned_cols=108  Identities=13%  Similarity=0.108  Sum_probs=59.4

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhc
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE  149 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  149 (219)
                      .+.+.++|+.|.|||+  ++.++........+.+    ++..+...++.+.+.++.           |+.+.        
T Consensus        62 ~~GlYl~G~vG~GKT~--Lmd~f~~~lp~~~k~R----~HFh~Fm~~vh~~l~~~~-----------~~~~~--------  116 (362)
T PF03969_consen   62 PKGLYLWGPVGRGKTM--LMDLFYDSLPIKRKRR----VHFHEFMLDVHSRLHQLR-----------GQDDP--------  116 (362)
T ss_pred             CceEEEECCCCCchhH--HHHHHHHhCCcccccc----ccccHHHHHHHHHHHHHh-----------CCCcc--------
Confidence            4679999999999993  4433333222222222    245666777777776653           11110        


Q ss_pred             CCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhC-CCCCeEEEEeecccC
Q 027749          150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL-PPDLQVCCPGSCFLF  218 (219)
Q Consensus       150 ~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~-~~~~q~i~~SATl~~  218 (219)
                               ...+.+.+      .+...+|++||.|. .+.+-...+.++++.+ ..+.-++.-|-+.|.
T Consensus       117 ---------l~~va~~l------~~~~~lLcfDEF~V-~DiaDAmil~rLf~~l~~~gvvlVaTSN~~P~  170 (362)
T PF03969_consen  117 ---------LPQVADEL------AKESRLLCFDEFQV-TDIADAMILKRLFEALFKRGVVLVATSNRPPE  170 (362)
T ss_pred             ---------HHHHHHHH------HhcCCEEEEeeeec-cchhHHHHHHHHHHHHHHCCCEEEecCCCChH
Confidence                     11111221      24456899999984 4444456666676665 335556665555553

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

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=96.71  E-value=0.0048  Score=51.85  Aligned_cols=19  Identities=37%  Similarity=0.559  Sum_probs=15.3

Q ss_pred             CcEEEEcCCCCchhHHhHH
Q 027749           71 RDVIAQAQSGTGKTSMIAL   89 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~   89 (219)
                      .+.|++||.|+|||..+-+
T Consensus        49 ~SmIl~GPPG~GKTTlA~l   67 (436)
T COG2256          49 HSMILWGPPGTGKTTLARL   67 (436)
T ss_pred             ceeEEECCCCCCHHHHHHH
Confidence            4799999999999955433

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.70  E-value=0.016  Score=49.61  Aligned_cols=40  Identities=10%  Similarity=0.154  Sum_probs=24.7

Q ss_pred             CCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       173 ~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ...-+++||||+|.|.... ...+...++..++...+|+.+
T Consensus       125 ~~~~kvvIIdea~~l~~~~-~~~LLk~LEep~~~t~~Il~t  164 (397)
T PRK14955        125 KGRYRVYIIDEVHMLSIAA-FNAFLKTLEEPPPHAIFIFAT  164 (397)
T ss_pred             cCCeEEEEEeChhhCCHHH-HHHHHHHHhcCCCCeEEEEEe
Confidence            4567899999999987543 334445555555444444433

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=96.69  E-value=0.013  Score=52.37  Aligned_cols=42  Identities=14%  Similarity=0.324  Sum_probs=26.4

Q ss_pred             CCccEEEeccchhhhcc-ccHHHHHHHHHhCCC-CCeEEEEeecc
Q 027749          174 RAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPP-DLQVCCPGSCF  216 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~-~~~~~~~~i~~~~~~-~~q~i~~SATl  216 (219)
                      .++++|||||+|.+... .....+..+++.+.. +.++|+ |+..
T Consensus       376 ~~~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~III-TSd~  419 (617)
T PRK14086        376 REMDILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVL-SSDR  419 (617)
T ss_pred             hcCCEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEE-ecCC
Confidence            45789999999987653 234556666666543 455665 4443

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=96.69  E-value=0.012  Score=52.72  Aligned_cols=40  Identities=13%  Similarity=0.268  Sum_probs=27.8

Q ss_pred             CCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       173 ~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ..+.+++||||+|.|.... .+.+.+.++..+.++.+|+.+
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            4567899999999887543 345555566666676666654

>PRK12377 putative replication protein; Provisional

Probab=96.67  E-value=0.033  Score=44.42  Aligned_cols=45  Identities=9%  Similarity=0.251  Sum_probs=25.9

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHH
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~  119 (219)
                      .++++.|++|+|||-.. ..+...+...  +..++ .++..++..++..
T Consensus       102 ~~l~l~G~~GtGKThLa-~AIa~~l~~~--g~~v~-~i~~~~l~~~l~~  146 (248)
T PRK12377        102 TNFVFSGKPGTGKNHLA-AAIGNRLLAK--GRSVI-VVTVPDVMSRLHE  146 (248)
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHHHHHc--CCCeE-EEEHHHHHHHHHH
Confidence            57999999999999332 3334444433  22243 3344555554443

>PF13173 AAA_14: AAA domain

Probab=96.65  E-value=0.037  Score=39.30  Aligned_cols=37  Identities=19%  Similarity=0.328  Sum_probs=26.1

Q ss_pred             CccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEee
Q 027749          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGS  214 (219)
Q Consensus       175 ~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SA  214 (219)
                      .-.+|++||+|.+-  ++...+..+.+.- ++.++++.+.
T Consensus        61 ~~~~i~iDEiq~~~--~~~~~lk~l~d~~-~~~~ii~tgS   97 (128)
T PF13173_consen   61 GKKYIFIDEIQYLP--DWEDALKFLVDNG-PNIKIILTGS   97 (128)
T ss_pred             CCcEEEEehhhhhc--cHHHHHHHHHHhc-cCceEEEEcc
Confidence            55689999999865  4567788877765 4556665543

>PF05729 NACHT: NACHT domain

Probab=96.64  E-value=0.018  Score=42.28  Aligned_cols=38  Identities=26%  Similarity=0.443  Sum_probs=24.3

Q ss_pred             EEEeccchhhhccc-------cHHHHHHHHHh-CCCCCeEEEEeec
Q 027749          178 LLVLDESDEMLSRG-------FKDQIYDVYRY-LPPDLQVCCPGSC  215 (219)
Q Consensus       178 ~lVvDE~h~l~~~~-------~~~~~~~i~~~-~~~~~q~i~~SAT  215 (219)
                      +||+|-.|.+....       +...+..++.. ++++.++++.|.+
T Consensus        84 llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~  129 (166)
T PF05729_consen   84 LLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRP  129 (166)
T ss_pred             EEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcC
Confidence            49999999887642       23345555555 4556777666654

>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=96.64  E-value=0.0099  Score=53.91  Aligned_cols=109  Identities=21%  Similarity=0.179  Sum_probs=69.4

Q ss_pred             cEEEEcCCCCchhHHhHHHHHhh-hccC-----CCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHH
Q 027749           72 DVIAQAQSGTGKTSMIALTVCQT-VDTS-----SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDI  145 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~~~~~~~-~~~~-----~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  145 (219)
                      -.|+.-..|-|||..-+..++.. ....     ......+||+|+. +..|+..++.+..+.....+..++|   .....
T Consensus       154 ggIladd~glgkt~~ti~l~l~~~~~~~~~~~~~~~kttLivcp~s-~~~qW~~elek~~~~~~l~v~v~~g---r~kd~  229 (674)
T KOG1001|consen  154 GGILADDMGLGKTVKTIALILKQKLKSKEEDRQKEFKTTLIVCPTS-LLTQWKTELEKVTEEDKLSIYVYHG---RTKDK  229 (674)
T ss_pred             cceEeeccccchHHHHHHHHHhcccCCcchhhccccCceeEecchH-HHHHHHHHHhccCCccceEEEEecc---ccccc
Confidence            47888899999997665544432 2222     1344588888865 5567777776666666677777776   11111


Q ss_pred             HHhcCCCeEEEeChHHHHHHHHcCCCCCCCcc--EEEeccchhhhccc
Q 027749          146 RKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIK--LLVLDESDEMLSRG  191 (219)
Q Consensus       146 ~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~--~lVvDE~h~l~~~~  191 (219)
                       ....+++|+++|++.+..      ..+..+.  .+|+||+|.+.+..
T Consensus       230 -~el~~~dVVltTy~il~~------~~l~~i~w~Riildea~~ikn~~  270 (674)
T KOG1001|consen  230 -SELNSYDVVLTTYDILKN------SPLVKIKWLRIVLDEAHTIKNKD  270 (674)
T ss_pred             -chhcCCceEEeeHHHhhc------ccccceeEEEEEeccccccCCcc
Confidence             122467899999976653      1222343  49999999877643

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=96.62  E-value=0.024  Score=46.57  Aligned_cols=38  Identities=16%  Similarity=0.304  Sum_probs=25.7

Q ss_pred             CccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       175 ~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ..++|++||+|.+.... ...+..+++..+..+.+|+.+
T Consensus       102 ~~~vviiDe~~~l~~~~-~~~L~~~le~~~~~~~lIl~~  139 (319)
T PRK00440        102 PFKIIFLDEADNLTSDA-QQALRRTMEMYSQNTRFILSC  139 (319)
T ss_pred             CceEEEEeCcccCCHHH-HHHHHHHHhcCCCCCeEEEEe
Confidence            46789999999875432 455666677666666666544

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=96.59  E-value=0.026  Score=50.99  Aligned_cols=38  Identities=11%  Similarity=0.193  Sum_probs=25.9

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEE
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCP  212 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~  212 (219)
                      .+.+++||||+|+|.... .+.+.+.++.-|.+..+|+.
T Consensus       118 g~~KV~IIDEah~Ls~~a-~NALLKtLEEPp~~v~FIL~  155 (647)
T PRK07994        118 GRFKVYLIDEVHMLSRHS-FNALLKTLEEPPEHVKFLLA  155 (647)
T ss_pred             CCCEEEEEechHhCCHHH-HHHHHHHHHcCCCCeEEEEe
Confidence            467899999999887654 44455566665655555554

>PRK04195 replication factor C large subunit; Provisional

Probab=96.56  E-value=0.031  Score=49.05  Aligned_cols=18  Identities=28%  Similarity=0.497  Sum_probs=15.0

Q ss_pred             CCcEEEEcCCCCchhHHh
Q 027749           70 GRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~   87 (219)
                      .+.+++.||.|+|||...
T Consensus        39 ~~~lLL~GppG~GKTtla   56 (482)
T PRK04195         39 KKALLLYGPPGVGKTSLA   56 (482)
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            467999999999999444

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=96.55  E-value=0.015  Score=50.38  Aligned_cols=42  Identities=10%  Similarity=0.250  Sum_probs=24.7

Q ss_pred             CCccEEEeccchhhhcc-ccHHHHHHHHHhCC-CCCeEEEEeecc
Q 027749          174 RAIKLLVLDESDEMLSR-GFKDQIYDVYRYLP-PDLQVCCPGSCF  216 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~-~~~~~~~~i~~~~~-~~~q~i~~SATl  216 (219)
                      ...++|++||+|.+... .....+..+++.+. ...| ++++++.
T Consensus       201 ~~~dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~-IIlts~~  244 (445)
T PRK12422        201 RNVDALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKL-IVISSTC  244 (445)
T ss_pred             ccCCEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCc-EEEecCC
Confidence            35789999999987653 22445555555432 2344 4555544

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=96.55  E-value=0.0034  Score=52.00  Aligned_cols=133  Identities=11%  Similarity=0.091  Sum_probs=67.4

Q ss_pred             ChHHHHHHHHHHh----CC---CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhcccc
Q 027749           56 PSAIQQRAVMPII----KG---RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI  128 (219)
Q Consensus        56 ~~~~Q~~~~~~~~----~~---~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~  128 (219)
                      .+|||+..|..+.    +|   +-.++.||.|.||+..+.. +...+.......  .  -|    + ..+..|+.+....
T Consensus         3 ~yPW~~~~~~~l~~~~~~~rl~HA~Lf~G~~G~GK~~lA~~-~A~~llC~~~~~--~--~~----C-g~C~sC~~~~~g~   72 (325)
T PRK06871          3 LYPWLQPTYQQITQAFQQGLGHHALLFKADSGLGTEQLIRA-LAQWLMCQTPQG--D--QP----C-GQCHSCHLFQAGN   72 (325)
T ss_pred             CCcchHHHHHHHHHHHHcCCcceeEEeECCCCCCHHHHHHH-HHHHHcCCCCCC--C--CC----C-CCCHHHHHHhcCC
Confidence            3677888887654    34   3577999999999954433 334433221100  0  00    0 1234444444333


Q ss_pred             ceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHc--CCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCC
Q 027749          129 NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR--KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPD  206 (219)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~--~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~  206 (219)
                      ...+..+....           +..|   .-+.+.++...  ..-.-...+++|+|+||.|.... .+.+.+.++.-|++
T Consensus        73 HPD~~~i~p~~-----------~~~I---~id~iR~l~~~~~~~~~~g~~KV~iI~~a~~m~~~A-aNaLLKtLEEPp~~  137 (325)
T PRK06871         73 HPDFHILEPID-----------NKDI---GVDQVREINEKVSQHAQQGGNKVVYIQGAERLTEAA-ANALLKTLEEPRPN  137 (325)
T ss_pred             CCCEEEEcccc-----------CCCC---CHHHHHHHHHHHhhccccCCceEEEEechhhhCHHH-HHHHHHHhcCCCCC
Confidence            33332221100           0011   12222222221  11123567899999999988553 56667777776666


Q ss_pred             CeEEEEe
Q 027749          207 LQVCCPG  213 (219)
Q Consensus       207 ~q~i~~S  213 (219)
                      .-+|+.|
T Consensus       138 ~~fiL~t  144 (325)
T PRK06871        138 TYFLLQA  144 (325)
T ss_pred             eEEEEEE
Confidence            6555554

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.54  E-value=0.024  Score=49.50  Aligned_cols=33  Identities=12%  Similarity=0.231  Sum_probs=20.2

Q ss_pred             CCCccEEEeccchhhhccccHHHHHHHHHhCCCC
Q 027749          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPD  206 (219)
Q Consensus       173 ~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~  206 (219)
                      ..+.++||+||+|.+.... ...+...++..+.+
T Consensus       115 ~~~~kVvIIDE~h~Lt~~a-~~~LLk~LE~p~~~  147 (472)
T PRK14962        115 EGKYKVYIIDEVHMLTKEA-FNALLKTLEEPPSH  147 (472)
T ss_pred             cCCeEEEEEEChHHhHHHH-HHHHHHHHHhCCCc
Confidence            3567899999999986433 23344444444433

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.54  E-value=0.025  Score=50.11  Aligned_cols=39  Identities=10%  Similarity=0.187  Sum_probs=26.8

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      .+.+++||||+|.|.... .+.+.+.++..|.+..+|+.+
T Consensus       118 ~~~kVvIIDEad~ls~~a-~naLLK~LEepp~~~~fIL~t  156 (527)
T PRK14969        118 GRFKVYIIDEVHMLSKSA-FNAMLKTLEEPPEHVKFILAT  156 (527)
T ss_pred             CCceEEEEcCcccCCHHH-HHHHHHHHhCCCCCEEEEEEe
Confidence            467899999999887544 344555566666666666654

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=96.52  E-value=0.018  Score=49.68  Aligned_cols=34  Identities=21%  Similarity=0.330  Sum_probs=26.4

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhH
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~   88 (219)
                      .+.......+..+..++++++.||+|+|||..+.
T Consensus       179 i~e~~le~l~~~L~~~~~iil~GppGtGKT~lA~  212 (459)
T PRK11331        179 IPETTIETILKRLTIKKNIILQGPPGVGKTFVAR  212 (459)
T ss_pred             CCHHHHHHHHHHHhcCCCEEEECCCCCCHHHHHH
Confidence            3445556667777789999999999999995553

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=96.51  E-value=0.014  Score=48.29  Aligned_cols=67  Identities=19%  Similarity=0.341  Sum_probs=43.2

Q ss_pred             HHHHHHHCCCCCChHHHHHHHHH-HhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHH
Q 027749           44 LLRGIYQYGFEKPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (219)
Q Consensus        44 ~~~~l~~~~~~~~~~~Q~~~~~~-~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l  113 (219)
                      -+..|.+.|.  +++.|...+.. +..+++++++|+||+||| .++-.++..+.......+++++-.+.++
T Consensus       123 tl~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKT-Tll~aL~~~~~~~~~~~rivtIEd~~El  190 (319)
T PRK13894        123 TLDQYVERGI--MTAAQREAIIAAVRAHRNILVIGGTGSGKT-TLVNAIINEMVIQDPTERVFIIEDTGEI  190 (319)
T ss_pred             CHHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHH-HHHHHHHHhhhhcCCCceEEEEcCCCcc
Confidence            3455555565  45566666654 556789999999999999 5555566554322233456776666665

>CHL00181 cbbX CbbX; Provisional

Probab=96.49  E-value=0.029  Score=45.80  Aligned_cols=20  Identities=30%  Similarity=0.398  Sum_probs=16.0

Q ss_pred             CCcEEEEcCCCCchhHHhHH
Q 027749           70 GRDVIAQAQSGTGKTSMIAL   89 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~   89 (219)
                      +.++++.||+|+|||..+-.
T Consensus        59 ~~~ill~G~pGtGKT~lAr~   78 (287)
T CHL00181         59 GLHMSFTGSPGTGKTTVALK   78 (287)
T ss_pred             CceEEEECCCCCCHHHHHHH
Confidence            45689999999999965544

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=96.48  E-value=0.032  Score=50.78  Aligned_cols=67  Identities=24%  Similarity=0.312  Sum_probs=51.3

Q ss_pred             CChHHHHHHHHHHhC----C-CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccc
Q 027749           55 KPSAIQQRAVMPIIK----G-RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDF  127 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~----~-~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (219)
                      .|++.|..++..+.+    + ++.++.|.+|+||++.+. .++...     +..+|||+|+...+.++++.+..+...
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            789999999988753    2 257799999999995543 233221     234999999999999999999888654

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=96.47  E-value=0.025  Score=51.36  Aligned_cols=39  Identities=10%  Similarity=0.175  Sum_probs=26.4

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      .+.+++||||+|.|.... ...+.+.++..+.++.+|+.+
T Consensus       118 gk~KVIIIDEad~Ls~~A-~NALLKtLEEPp~~v~fILaT  156 (709)
T PRK08691        118 GKYKVYIIDEVHMLSKSA-FNAMLKTLEEPPEHVKFILAT  156 (709)
T ss_pred             CCcEEEEEECccccCHHH-HHHHHHHHHhCCCCcEEEEEe
Confidence            467899999999876433 345566666666666666554

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.46  E-value=0.05  Score=48.33  Aligned_cols=39  Identities=10%  Similarity=0.151  Sum_probs=27.7

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      .+.+++||||+|.|.... .+.+.+.++..|.+..+|+.+
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            466899999999987543 455666777766666666654

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.46  E-value=0.029  Score=50.32  Aligned_cols=39  Identities=13%  Similarity=0.299  Sum_probs=26.9

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      .+.+++||||+|.|.... .+.+.+.++..|.+.-+|+.+
T Consensus       118 ~~~KVvIIdev~~Lt~~a-~naLLk~LEepp~~~~fIl~t  156 (576)
T PRK14965        118 SRYKIFIIDEVHMLSTNA-FNALLKTLEEPPPHVKFIFAT  156 (576)
T ss_pred             CCceEEEEEChhhCCHHH-HHHHHHHHHcCCCCeEEEEEe
Confidence            567899999999877543 456666666666665555544

>PRK06904 replicative DNA helicase; Validated

Probab=96.46  E-value=0.04  Score=48.17  Aligned_cols=140  Identities=20%  Similarity=0.226  Sum_probs=70.1

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEE-EC-CcccHHHHH
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC-VG-GKSVGEDIR  146 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~-~~-~~~~~~~~~  146 (219)
                      .|.=++|.|.+|.||| ++.+-++..+.... +..++|.. ...-..|+..++-.....  +....+ .| ..+. +++.
T Consensus       220 ~G~LiiIaarPg~GKT-afalnia~~~a~~~-g~~Vl~fS-lEMs~~ql~~Rlla~~s~--v~~~~i~~g~~l~~-~e~~  293 (472)
T PRK06904        220 PSDLIIVAARPSMGKT-TFAMNLCENAAMAS-EKPVLVFS-LEMPAEQIMMRMLASLSR--VDQTKIRTGQNLDQ-QDWA  293 (472)
T ss_pred             CCcEEEEEeCCCCChH-HHHHHHHHHHHHhc-CCeEEEEe-ccCCHHHHHHHHHHhhCC--CCHHHhccCCCCCH-HHHH
Confidence            4455788899999999 45555555443221 22355553 345556666665433222  221111 22 1222 2222


Q ss_pred             -------HhcCCCeEEE-----eChHHHHHHHHcCCCCCCCccEEEeccchhhhccc----cHHHHHHHHHhC---C--C
Q 027749          147 -------KLEHGVHVVS-----GTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG----FKDQIYDVYRYL---P--P  205 (219)
Q Consensus       147 -------~l~~~~~I~v-----~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~----~~~~~~~i~~~~---~--~  205 (219)
                             .+.....+.|     .|+..+....+.-......+++||||-.+.|...+    ....+..+.+.+   -  .
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                   2222344555     35555554332211111358899999998775332    223344444443   2  2


Q ss_pred             CCeEEEEee
Q 027749          206 DLQVCCPGS  214 (219)
Q Consensus       206 ~~q~i~~SA  214 (219)
                      ++.++++|.
T Consensus       374 ~ipVi~lsQ  382 (472)
T PRK06904        374 KVPVVALSQ  382 (472)
T ss_pred             CCeEEEEEe
Confidence            677888874

>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=96.45  E-value=0.057  Score=44.98  Aligned_cols=118  Identities=18%  Similarity=0.164  Sum_probs=57.3

Q ss_pred             EEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHH----HHHHHHhccccceeEEEE-ECCcccHHHHHHh
Q 027749           74 IAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQT----EKVILAIGDFINIQAHAC-VGGKSVGEDIRKL  148 (219)
Q Consensus        74 lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~----~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~l  148 (219)
                      ++.++.|+|||......++..+........+++. ++...+...    ...+..+... .+....- .....     ..+
T Consensus         1 ~i~~~r~~GKT~~~~~~~~~~~~~~~~~~~vi~~-~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~-----~~~   73 (384)
T PF03237_consen    1 LINGGRGSGKTTLIAIWFLWWALTRPPGRRVIIA-STYRQARDIFGRFWKGIIELLPS-WFEIKFNEWNDRK-----IIL   73 (384)
T ss_dssp             -EEE-SSS-HHHHHHHHHHHHHHSSSS--EEEEE-ESSHHHHHHHHHHHHHHHHTS-T-TTS--EEEE-SSE-----EEE
T ss_pred             CCcCCccccHHHHHHHHHHHHHhhCCCCcEEEEe-cCHHHHHHHHHHhHHHHHHHHHH-hcCcccccCCCCc-----EEe
Confidence            4678999999988887777777666544556666 665555542    2333333333 2222211 00000     011


Q ss_pred             cCCCeEEEeChHH--HHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhC
Q 027749          149 EHGVHVVSGTPGR--VCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL  203 (219)
Q Consensus       149 ~~~~~I~v~Tp~~--l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~  203 (219)
                      .++..|.+.+-+.  -...+..     ..++++++||+-.+.+..+...+.......
T Consensus        74 ~nG~~i~~~~~~~~~~~~~~~G-----~~~~~i~iDE~~~~~~~~~~~~~~~~~~~~  125 (384)
T PF03237_consen   74 PNGSRIQFRGADSPDSGDNIRG-----FEYDLIIIDEAAKVPDDAFSELIRRLRATW  125 (384)
T ss_dssp             TTS-EEEEES-----SHHHHHT-----S--SEEEEESGGGSTTHHHHHHHHHHHHCS
T ss_pred             cCceEEEEeccccccccccccc-----cccceeeeeecccCchHHHHHHHHhhhhcc
Confidence            4567777766332  1122222     467799999988765554445454444443

The large subunit heterodimerises with the small terminase protein, which is docked on the capsid portal protein. The latter forms a ring through which genomic DNA is translocated into the capsid. The terminase protein may have or induce an endonuclease activity to cleave DNA after encapsidation. This entry represents a family of terminase large subunits found in a variety of the Caudovirales and prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) [], including ORFg2 (RCAP_rcc01683) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in ].; PDB: 2O0K_A 3CPE_A 2O0J_A 2O0H_A 3C6H_A 3C6A_A.

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=96.44  E-value=0.02  Score=44.90  Aligned_cols=132  Identities=13%  Similarity=0.113  Sum_probs=66.0

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhcccc-------ceeEEEEECCccc
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI-------NIQAHACVGGKSV  141 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~-------~~~~~~~~~~~~~  141 (219)
                      .|..++|.|++|+|||...+-.+...+...+  -++++++- .+-..++.+.+..+....       .+.+.-.   ...
T Consensus        18 ~gs~~li~G~~GsGKT~l~~q~l~~~~~~~g--e~vlyvs~-ee~~~~l~~~~~s~g~d~~~~~~~g~l~~~d~---~~~   91 (226)
T PF06745_consen   18 KGSVVLISGPPGSGKTTLALQFLYNGLKNFG--EKVLYVSF-EEPPEELIENMKSFGWDLEEYEDSGKLKIIDA---FPE   91 (226)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHHT----EEEEES-SS-HHHHHHHHHTTTS-HHHHHHTTSEEEEES---SGG
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHhhhhcC--CcEEEEEe-cCCHHHHHHHHHHcCCcHHHHhhcCCEEEEec---ccc
Confidence            3457899999999999555444445544412  23777764 444466666665553211       0111100   000


Q ss_pred             HHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhcc----ccHHHHHHHHHhCCCCCeEEEEeecc
Q 027749          142 GEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR----GFKDQIYDVYRYLPPDLQVCCPGSCF  216 (219)
Q Consensus       142 ~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~----~~~~~~~~i~~~~~~~~q~i~~SATl  216 (219)
                      ....       .  -..++.+...+.+.. .-.+.+.+|+|-...+...    .+...+..+...+.....+.++++..
T Consensus        92 ~~~~-------~--~~~~~~l~~~i~~~i-~~~~~~~vVIDsls~l~~~~~~~~~r~~l~~l~~~l~~~~~t~llt~~~  160 (226)
T PF06745_consen   92 RIGW-------S--PNDLEELLSKIREAI-EELKPDRVVIDSLSALLLYDDPEELRRFLRALIKFLKSRGVTTLLTSEM  160 (226)
T ss_dssp             GST--------T--SCCHHHHHHHHHHHH-HHHTSSEEEEETHHHHTTSSSGGGHHHHHHHHHHHHHHTTEEEEEEEEE
T ss_pred             cccc-------c--ccCHHHHHHHHHHHH-HhcCCCEEEEECHHHHhhcCCHHHHHHHHHHHHHHHHHCCCEEEEEEcc
Confidence            0000       0  112344444333210 0112278999999988221    35566666776665555566666653

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 ....

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.41  E-value=0.018  Score=48.66  Aligned_cols=39  Identities=13%  Similarity=0.288  Sum_probs=25.3

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      .+.+++|+||+|.|....+ +.+.+.++..|.+..+|+.+
T Consensus       118 ~~~kviIIDEa~~l~~~a~-naLLk~lEe~~~~~~fIl~t  156 (363)
T PRK14961        118 SRFKVYLIDEVHMLSRHSF-NALLKTLEEPPQHIKFILAT  156 (363)
T ss_pred             CCceEEEEEChhhcCHHHH-HHHHHHHhcCCCCeEEEEEc
Confidence            4568999999998875433 33555556555566555544

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=96.41  E-value=0.087  Score=49.22  Aligned_cols=29  Identities=17%  Similarity=0.625  Sum_probs=20.3

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhC
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYL  203 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~  203 (219)
                      ....+||+||+|.+.... ...+..+++..
T Consensus       868 r~v~IIILDEID~L~kK~-QDVLYnLFR~~  896 (1164)
T PTZ00112        868 RNVSILIIDEIDYLITKT-QKVLFTLFDWP  896 (1164)
T ss_pred             ccceEEEeehHhhhCccH-HHHHHHHHHHh
Confidence            446689999999988642 45566666653

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=96.40  E-value=0.049  Score=45.79  Aligned_cols=39  Identities=13%  Similarity=0.227  Sum_probs=27.5

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ...+++||||+|.|.... .+.+.+.++..+.+.-+|++|
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            467899999999987554 455666777766666566655

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=96.40  E-value=0.018  Score=47.65  Aligned_cols=135  Identities=12%  Similarity=0.120  Sum_probs=68.7

Q ss_pred             CChHHHHHHHHHHh----CCC---cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccc
Q 027749           55 KPSAIQQRAVMPII----KGR---DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDF  127 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~----~~~---~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (219)
                      .++|||...|..+.    +++   -.++.||.|.||+..+.. +.+.+........     |    + ..+..|+.+...
T Consensus         3 ~~yPWl~~~~~~l~~~~~~~rl~hA~L~~G~~G~Gk~~lA~~-~a~~llC~~~~~~-----~----C-g~C~sC~~~~~g   71 (319)
T PRK06090          3 NDYPWLVPVWQNWKAGLDAGRIPGALLLQSDEGLGVESLVEL-FSRALLCQNYQSE-----A----C-GFCHSCELMQSG   71 (319)
T ss_pred             cCcccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHH-HHHHHcCCCCCCC-----C----C-CCCHHHHHHHcC
Confidence            46788888887765    343   589999999999944433 3333332211100     1    0 112344444333


Q ss_pred             cceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHc--CCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCC
Q 027749          128 INIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR--KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP  205 (219)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~--~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~  205 (219)
                      ....+..+.....          +..|   +-+.+..+...  ........+++|||+||.|.... .+.+.+.++.-|+
T Consensus        72 ~HPD~~~i~p~~~----------~~~I---~vdqiR~l~~~~~~~~~~~~~kV~iI~~ae~m~~~A-aNaLLKtLEEPp~  137 (319)
T PRK06090         72 NHPDLHVIKPEKE----------GKSI---TVEQIRQCNRLAQESSQLNGYRLFVIEPADAMNESA-SNALLKTLEEPAP  137 (319)
T ss_pred             CCCCEEEEecCcC----------CCcC---CHHHHHHHHHHHhhCcccCCceEEEecchhhhCHHH-HHHHHHHhcCCCC
Confidence            2222222221100          0011   11222222111  11123567899999999988543 5666677777666


Q ss_pred             CCeEEEEee
Q 027749          206 DLQVCCPGS  214 (219)
Q Consensus       206 ~~q~i~~SA  214 (219)
                      +.-+|+.|.
T Consensus       138 ~t~fiL~t~  146 (319)
T PRK06090        138 NCLFLLVTH  146 (319)
T ss_pred             CeEEEEEEC
Confidence            655555554

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=96.39  E-value=0.028  Score=49.50  Aligned_cols=37  Identities=14%  Similarity=0.265  Sum_probs=22.2

Q ss_pred             CCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEE
Q 027749          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVC  210 (219)
Q Consensus       173 ~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i  210 (219)
                      ..+.+++|+||+|.+.... ...+.+.++..+.+.-+|
T Consensus       126 ~~~~KVvIIDEa~~Ls~~a-~naLLk~LEepp~~~vfI  162 (507)
T PRK06645        126 QGKHKIFIIDEVHMLSKGA-FNALLKTLEEPPPHIIFI  162 (507)
T ss_pred             cCCcEEEEEEChhhcCHHH-HHHHHHHHhhcCCCEEEE
Confidence            3567899999999876543 333444455544443333

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.34  E-value=0.045  Score=50.28  Aligned_cols=21  Identities=24%  Similarity=0.232  Sum_probs=16.1

Q ss_pred             CcEEEEcCCCCchhHHhHHHH
Q 027749           71 RDVIAQAQSGTGKTSMIALTV   91 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~   91 (219)
                      +-+.++||||+|||.....-+
T Consensus       186 ~Vi~lVGpnGvGKTTTiaKLA  206 (767)
T PRK14723        186 GVLALVGPTGVGKTTTTAKLA  206 (767)
T ss_pred             eEEEEECCCCCcHHHHHHHHH
Confidence            347899999999996665543

>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=96.32  E-value=0.066  Score=37.62  Aligned_cols=16  Identities=25%  Similarity=0.501  Sum_probs=13.1

Q ss_pred             ccEEEeccchhhhccc
Q 027749          176 IKLLVLDESDEMLSRG  191 (219)
Q Consensus       176 l~~lVvDE~h~l~~~~  191 (219)
                      -.+|++||+|.+....
T Consensus        59 ~~vl~iDe~d~l~~~~   74 (132)
T PF00004_consen   59 PCVLFIDEIDKLFPKS   74 (132)
T ss_dssp             SEEEEEETGGGTSHHC
T ss_pred             ceeeeeccchhccccc
Confidence            4789999999988654

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 ....

>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=96.32  E-value=0.023  Score=45.57  Aligned_cols=141  Identities=17%  Similarity=0.196  Sum_probs=68.9

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  148 (219)
                      .|.=+++.|++|.|||. +++-+...+.... +..++|+..-. -..++..++-.....  +....+..+.-...++..+
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 PGELTVIAARPGVGKTA-FALQIALNAALNG-GYPVLYFSLEM-SEEELAARLLARLSG--VPYNKIRSGDLSDEEFERL   92 (259)
T ss_dssp             TT-EEEEEESTTSSHHH-HHHHHHHHHHHTT-SSEEEEEESSS--HHHHHHHHHHHHHT--STHHHHHCCGCHHHHHHHH
T ss_pred             cCcEEEEEecccCCchH-HHHHHHHHHHHhc-CCeEEEEcCCC-CHHHHHHHHHHHhhc--chhhhhhccccCHHHHHHH
Confidence            34458899999999994 4444444443332 24477776532 222333333222211  1111111111111222221


Q ss_pred             ------cCCCeEEE-e----ChHHHHHHHHcCCCCCCCccEEEeccchhhhcc----ccHHHHHHHHHhCC-----CCCe
Q 027749          149 ------EHGVHVVS-G----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR----GFKDQIYDVYRYLP-----PDLQ  208 (219)
Q Consensus       149 ------~~~~~I~v-~----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~----~~~~~~~~i~~~~~-----~~~q  208 (219)
                            .....++| .    |++.+...+..-.....++++||||-.|.+-..    +....+..+.+.+.     .++.
T Consensus        93 ~~~~~~l~~~~l~i~~~~~~~~~~i~~~i~~~~~~~~~~~~v~IDyl~ll~~~~~~~~~~~~~~~i~~~Lk~lA~~~~i~  172 (259)
T PF03796_consen   93 QAAAEKLSDLPLYIEDTPSLTIDDIESKIRRLKREGKKVDVVFIDYLQLLKSEDSSDNRRQEIGEISRELKALAKELNIP  172 (259)
T ss_dssp             HHHHHHHHTSEEEEEESSS-BHHHHHHHHHHHHHHSTTEEEEEEEEGGGSBTSCSSSCCHHHHHHHHHHHHHHHHHHTSE
T ss_pred             HHHHHHHhhCcEEEECCCCCCHHHHHHHHHHHHhhccCCCEEEechHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHcCCe
Confidence                  12333443 3    455666555432222267899999999987763    33444555444432     2667


Q ss_pred             EEEEee
Q 027749          209 VCCPGS  214 (219)
Q Consensus       209 ~i~~SA  214 (219)
                      ++++|.
T Consensus       173 vi~~sQ  178 (259)
T PF03796_consen  173 VIALSQ  178 (259)
T ss_dssp             EEEEEE
T ss_pred             EEEccc
Confidence            777775

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 ....

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.29  E-value=0.034  Score=48.99  Aligned_cols=22  Identities=27%  Similarity=0.436  Sum_probs=16.1

Q ss_pred             EEEEcCCCCchhHHhHHHHHhhh
Q 027749           73 VIAQAQSGTGKTSMIALTVCQTV   95 (219)
Q Consensus        73 ~lv~~~tG~GKT~~~~~~~~~~~   95 (219)
                      .+++||.|+|||.++.. +...+
T Consensus        39 ~Lf~GppGtGKTTlA~~-lA~~l   60 (504)
T PRK14963         39 YLFSGPRGVGKTTTARL-IAMAV   60 (504)
T ss_pred             EEEECCCCCCHHHHHHH-HHHHH
Confidence            59999999999966543 33444

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=96.29  E-value=0.042  Score=44.82  Aligned_cols=18  Identities=28%  Similarity=0.370  Sum_probs=15.3

Q ss_pred             CCcEEEEcCCCCchhHHh
Q 027749           70 GRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~   87 (219)
                      +.++++.||+|+|||.++
T Consensus        58 ~~~vll~G~pGTGKT~lA   75 (284)
T TIGR02880        58 TLHMSFTGNPGTGKTTVA   75 (284)
T ss_pred             CceEEEEcCCCCCHHHHH
Confidence            457999999999999655

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.

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.29  E-value=0.08  Score=42.81  Aligned_cols=19  Identities=26%  Similarity=0.447  Sum_probs=15.6

Q ss_pred             CcEEEEcCCCCchhHHhHH
Q 027749           71 RDVIAQAQSGTGKTSMIAL   89 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~   89 (219)
                      ..+.+.+++|+|||..+..
T Consensus        76 ~~i~~~G~~g~GKTtl~~~   94 (270)
T PRK06731         76 QTIALIGPTGVGKTTTLAK   94 (270)
T ss_pred             CEEEEECCCCCcHHHHHHH
Confidence            5789999999999965554

>PRK07004 replicative DNA helicase; Provisional

Probab=96.25  E-value=0.021  Score=49.71  Aligned_cols=141  Identities=18%  Similarity=0.218  Sum_probs=67.3

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  148 (219)
                      .|.-++|.|.+|.||| ++.+-+...+..... ..++|.. ...-..|+..++-....  ++....+..+.-..+++..+
T Consensus       212 ~g~liviaarpg~GKT-~~al~ia~~~a~~~~-~~v~~fS-lEM~~~ql~~R~la~~~--~v~~~~i~~g~l~~~e~~~~  286 (460)
T PRK07004        212 GGELIIVAGRPSMGKT-AFSMNIGEYVAVEYG-LPVAVFS-MEMPGTQLAMRMLGSVG--RLDQHRMRTGRLTDEDWPKL  286 (460)
T ss_pred             CCceEEEEeCCCCCcc-HHHHHHHHHHHHHcC-CeEEEEe-CCCCHHHHHHHHHHhhc--CCCHHHHhcCCCCHHHHHHH
Confidence            3456788999999999 444444443322212 2244443 33344455554422111  12211111122222222221


Q ss_pred             ------cCCCeEEE-----eChHHHHHHHHcCCCCCCCccEEEeccchhhhcc----ccHHHHHHHHHhCC-----CCCe
Q 027749          149 ------EHGVHVVS-----GTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR----GFKDQIYDVYRYLP-----PDLQ  208 (219)
Q Consensus       149 ------~~~~~I~v-----~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~----~~~~~~~~i~~~~~-----~~~q  208 (219)
                            ..+..+.|     .|+..+....+.-......+++||||=.+.|...    +....+..+.+.++     -++.
T Consensus       287 ~~a~~~l~~~~l~I~d~~~~~~~~i~~~~r~l~~~~~~~~lviIDYLql~~~~~~~~~r~~ei~~Isr~LK~lAkel~ip  366 (460)
T PRK07004        287 THAVQKMSEAQLFIDETGGLNPMELRSRARRLARQCGKLGLIIIDYLQLMSGSSQGENRATEISEISRSLKSLAKELDVP  366 (460)
T ss_pred             HHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHhCCCCCEEEEChhhhccCCCCCCcHHHHHHHHHHHHHHHHHHhCCe
Confidence                  12345665     3444444433221111235889999999987532    12233445544442     2678


Q ss_pred             EEEEee
Q 027749          209 VCCPGS  214 (219)
Q Consensus       209 ~i~~SA  214 (219)
                      ++++|.
T Consensus       367 Vi~lsQ  372 (460)
T PRK07004        367 VIALSQ  372 (460)
T ss_pred             EEEEec
Confidence            888875

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.24  E-value=0.04  Score=49.36  Aligned_cols=39  Identities=13%  Similarity=0.283  Sum_probs=27.2

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      .+.+++||||+|.|.... .+.+.+.++..|.+.-+|+.+
T Consensus       117 ~~~KVvIIDEah~Lt~~A-~NALLK~LEEpp~~~~fIL~t  155 (584)
T PRK14952        117 SRYRIFIVDEAHMVTTAG-FNALLKIVEEPPEHLIFIFAT  155 (584)
T ss_pred             CCceEEEEECCCcCCHHH-HHHHHHHHhcCCCCeEEEEEe
Confidence            567899999999887554 445566666666666666554

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=96.24  E-value=0.029  Score=50.21  Aligned_cols=39  Identities=10%  Similarity=0.166  Sum_probs=25.1

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      .+-+++|+||+|.|.... ...+...++..|.+.-+|+.+
T Consensus       118 ~~~KVIIIDEad~Lt~~A-~NaLLKtLEEPp~~tvfIL~T  156 (605)
T PRK05896        118 FKYKVYIIDEAHMLSTSA-WNALLKTLEEPPKHVVFIFAT  156 (605)
T ss_pred             CCcEEEEEechHhCCHHH-HHHHHHHHHhCCCcEEEEEEC
Confidence            346789999999876433 445666666655554455444

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=96.23  E-value=0.037  Score=49.07  Aligned_cols=59  Identities=22%  Similarity=0.363  Sum_probs=42.7

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCC---CceeEEEEcCCHHHHHHHHHHHHHhccc
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSS---REVQALILSPTRELATQTEKVILAIGDF  127 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~---~~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (219)
                      .++-++|+|..|||||.+++--+...+...+   ....++|+.|.+....-+.+.+=.++..
T Consensus       225 k~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vlvl~PN~vFleYis~VLPeLGe~  286 (747)
T COG3973         225 KNKILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLGPNRVFLEYISRVLPELGEE  286 (747)
T ss_pred             CCCeEEEecCCCCCchhHHHHHHHHHHhccccccccCceEEEcCcHHHHHHHHHhchhhccC
Confidence            3456899999999999887765544443322   2233999999999998888887666543

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=96.22  E-value=0.039  Score=48.82  Aligned_cols=39  Identities=10%  Similarity=0.211  Sum_probs=28.4

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ...+++|+||+|.|.... ...+.+.++..|+++.+|+.+
T Consensus       116 ~~~KVvIIDEad~Lt~~A-~NALLK~LEEpp~~t~FIL~t  154 (535)
T PRK08451        116 ARFKIFIIDEVHMLTKEA-FNALLKTLEEPPSYVKFILAT  154 (535)
T ss_pred             CCeEEEEEECcccCCHHH-HHHHHHHHhhcCCceEEEEEE
Confidence            567899999999887543 455666777767777666654

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=96.20  E-value=0.26  Score=39.42  Aligned_cols=34  Identities=26%  Similarity=0.397  Sum_probs=22.5

Q ss_pred             CChHHHHHHHHHHh----CCC-cEEEEcCCCCchhHHhH
Q 027749           55 KPSAIQQRAVMPII----KGR-DVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~----~~~-~~lv~~~tG~GKT~~~~   88 (219)
                      .+++.+.+++..+.    .+. .+++.||.|+|||....
T Consensus        23 ~~~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~~   61 (269)
T TIGR03015        23 YPSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLIR   61 (269)
T ss_pred             CCCHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHH
Confidence            34555566665543    333 58899999999994443

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.

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=96.20  E-value=0.051  Score=43.02  Aligned_cols=53  Identities=15%  Similarity=0.226  Sum_probs=34.6

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhc
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIG  125 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  125 (219)
                      .|..++|.|++|+|||...+--+...+..   +-+++|++ +.+-..++.+.+..+.
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            35679999999999995544444444432   33477777 4556667777666554

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.

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=96.19  E-value=0.032  Score=46.62  Aligned_cols=40  Identities=10%  Similarity=0.179  Sum_probs=28.0

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEee
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGS  214 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SA  214 (219)
                      ...+++|||++|.|.... .+.+.+.++.-|++.-+|+.|.
T Consensus       131 ~~~kV~iI~~ae~m~~~A-aNaLLKtLEEPp~~t~fiL~t~  170 (342)
T PRK06964        131 GGARVVVLYPAEALNVAA-ANALLKTLEEPPPGTVFLLVSA  170 (342)
T ss_pred             CCceEEEEechhhcCHHH-HHHHHHHhcCCCcCcEEEEEEC
Confidence            567899999999988554 4556666776666655555553

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=96.19  E-value=0.014  Score=48.63  Aligned_cols=135  Identities=10%  Similarity=0.069  Sum_probs=68.4

Q ss_pred             ChHHHHHHHHHHh----CCC---cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhcccc
Q 027749           56 PSAIQQRAVMPII----KGR---DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI  128 (219)
Q Consensus        56 ~~~~Q~~~~~~~~----~~~---~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~  128 (219)
                      .+|||+..|..+.    +|+   -.++.||.|.||+..+.. +...+.........    |    + ..+..|+.+....
T Consensus         3 ~yPWl~~~~~~l~~~~~~~rl~HA~Lf~G~~G~Gk~~lA~~-~A~~LlC~~~~~~~----~----C-g~C~sC~~~~~g~   72 (334)
T PRK07993          3 WYPWLRPDYEQLVGSYQAGRGHHALLIQALPGMGDDALIYA-LSRWLMCQQPQGHK----S----C-GHCRGCQLMQAGT   72 (334)
T ss_pred             CCCCChHHHHHHHHHHHcCCcceEEeeECCCCCCHHHHHHH-HHHHHcCCCCCCCC----C----C-CCCHHHHHHHcCC
Confidence            5678888887764    343   578999999999954433 33434322110000    0    0 0234444444333


Q ss_pred             ceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHc--CCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCC
Q 027749          129 NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR--KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPD  206 (219)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~--~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~  206 (219)
                      ...+..+....+          +..|   +-+.+..+...  ..-.-...+++|+|+||.|.... .+.+.+.++.-|.+
T Consensus        73 HPD~~~i~p~~~----------~~~I---~idqiR~l~~~~~~~~~~g~~kV~iI~~ae~m~~~A-aNaLLKtLEEPp~~  138 (334)
T PRK07993         73 HPDYYTLTPEKG----------KSSL---GVDAVREVTEKLYEHARLGGAKVVWLPDAALLTDAA-ANALLKTLEEPPEN  138 (334)
T ss_pred             CCCEEEEecccc----------cccC---CHHHHHHHHHHHhhccccCCceEEEEcchHhhCHHH-HHHHHHHhcCCCCC
Confidence            233332221110          0011   12222222221  11123567899999999988553 56666677775555


Q ss_pred             CeEEEEee
Q 027749          207 LQVCCPGS  214 (219)
Q Consensus       207 ~q~i~~SA  214 (219)
                      .-+|+.|.
T Consensus       139 t~fiL~t~  146 (334)
T PRK07993        139 TWFFLACR  146 (334)
T ss_pred             eEEEEEEC
Confidence            55555553

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=96.17  E-value=0.054  Score=42.77  Aligned_cols=40  Identities=20%  Similarity=0.184  Sum_probs=24.7

Q ss_pred             hCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcC
Q 027749           68 IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (219)
Q Consensus        68 ~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P  109 (219)
                      ..|.-++|.|++|+|||...+--+.+.+...  +..++|+..
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            4566789999999999944433333333332  234777764

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.

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.16  E-value=0.04  Score=49.50  Aligned_cols=20  Identities=20%  Similarity=0.348  Sum_probs=15.9

Q ss_pred             CcEEEEcCCCCchhHHhHHH
Q 027749           71 RDVIAQAQSGTGKTSMIALT   90 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~   90 (219)
                      +..|++||.|+|||.++.+.
T Consensus        39 ha~Lf~GPpG~GKTtiAril   58 (624)
T PRK14959         39 PAYLFSGTRGVGKTTIARIF   58 (624)
T ss_pred             ceEEEECCCCCCHHHHHHHH
Confidence            35789999999999666553

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=96.15  E-value=0.037  Score=47.66  Aligned_cols=142  Identities=20%  Similarity=0.261  Sum_probs=67.3

Q ss_pred             HhCCCcEEEEcCCCCchhHHhHHHHHhhhc-cCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHH
Q 027749           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVD-TSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDI  145 (219)
Q Consensus        67 ~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~-~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  145 (219)
                      +..|.-++|.|++|.||| ++.+.+...+. ..  +..++|+. ...-..|+..++.....  ++....+..+.-...++
T Consensus       191 ~~~g~liviag~pg~GKT-~~al~ia~~~a~~~--g~~v~~fS-lEm~~~~l~~Rl~~~~~--~v~~~~~~~~~l~~~~~  264 (421)
T TIGR03600       191 LVKGDLIVIGARPSMGKT-TLALNIAENVALRE--GKPVLFFS-LEMSAEQLGERLLASKS--GINTGNIRTGRFNDSDF  264 (421)
T ss_pred             CCCCceEEEEeCCCCCHH-HHHHHHHHHHHHhC--CCcEEEEE-CCCCHHHHHHHHHHHHc--CCCHHHHhcCCCCHHHH
Confidence            334556889999999999 44444443332 32  22356664 23344455444432211  22221111111112222


Q ss_pred             HHhc------CCCeEEEe-----ChHHHHHHHHcCCCCCCCccEEEeccchhhhcc---ccHHHHHHHHHhCC-----CC
Q 027749          146 RKLE------HGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR---GFKDQIYDVYRYLP-----PD  206 (219)
Q Consensus       146 ~~l~------~~~~I~v~-----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~---~~~~~~~~i~~~~~-----~~  206 (219)
                      ..+.      .+..+.|.     |++.+...++.-......+++||||-.+.|...   +....+..+.+.+.     .+
T Consensus       265 ~~~~~~~~~l~~~~l~i~d~~~~t~~~i~~~~r~~~~~~~~~~lvvIDyLql~~~~~~~~~~~~~~~i~~~Lk~lAke~~  344 (421)
T TIGR03600       265 NRLLNAVDRLSEKDLYIDDTGGLTVAQIRSIARRIKRKKGGLDLIVVDYIQLMAPTRGRDRNEELGGISRGLKALAKELD  344 (421)
T ss_pred             HHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEecccccCCCCCCCHHHHHHHHHHHHHHHHHHhC
Confidence            2211      23345553     344444433321111235889999999887631   22233444433332     26


Q ss_pred             CeEEEEee
Q 027749          207 LQVCCPGS  214 (219)
Q Consensus       207 ~q~i~~SA  214 (219)
                      +.++++|.
T Consensus       345 i~Vi~lsQ  352 (421)
T TIGR03600       345 VPVVLLAQ  352 (421)
T ss_pred             CcEEEecc
Confidence            67777775

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.

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=96.15  E-value=0.044  Score=49.00  Aligned_cols=37  Identities=14%  Similarity=0.284  Sum_probs=22.3

Q ss_pred             CCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEE
Q 027749          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVC  210 (219)
Q Consensus       173 ~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i  210 (219)
                      ..+.+++||||+|.|....+ ..+.+.++..|.+.-+|
T Consensus       117 ~~~~kViIIDE~~~Lt~~a~-naLLKtLEepp~~~ifI  153 (559)
T PRK05563        117 EAKYKVYIIDEVHMLSTGAF-NALLKTLEEPPAHVIFI  153 (559)
T ss_pred             cCCeEEEEEECcccCCHHHH-HHHHHHhcCCCCCeEEE
Confidence            35678999999998865433 34444455544443333

>PRK08939 primosomal protein DnaI; Reviewed

Probab=96.13  E-value=0.033  Score=45.91  Aligned_cols=16  Identities=19%  Similarity=0.258  Sum_probs=14.1

Q ss_pred             CCcEEEEcCCCCchhH
Q 027749           70 GRDVIAQAQSGTGKTS   85 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~   85 (219)
                      ++++++.|++|+|||.
T Consensus       156 ~~gl~L~G~~G~GKTh  171 (306)
T PRK08939        156 VKGLYLYGDFGVGKSY  171 (306)
T ss_pred             CCeEEEECCCCCCHHH
Confidence            4679999999999993

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=96.12  E-value=0.07  Score=44.37  Aligned_cols=144  Identities=10%  Similarity=0.084  Sum_probs=69.1

Q ss_pred             ChHHHHHHHHHHhC--C---CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccce
Q 027749           56 PSAIQQRAVMPIIK--G---RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (219)
Q Consensus        56 ~~~~Q~~~~~~~~~--~---~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (219)
                      .+|||+..|..+..  +   +..++.||.|.||+..+.. +...+.........   .|    + ..+..|+.+......
T Consensus         2 ~yPW~~~~w~~l~~~~~r~~hA~Lf~G~~G~GK~~la~~-~a~~llC~~~~~~~---~~----C-g~C~~C~~~~~~~Hp   72 (325)
T PRK08699          2 IYPWHQEQWRQIAEHWERRPNAWLFAGKKGIGKTAFARF-AAQALLCETPAPGH---KP----C-GECMSCHLFGQGSHP   72 (325)
T ss_pred             CCCccHHHHHHHHHhcCCcceEEEeECCCCCCHHHHHHH-HHHHHcCCCCCCCC---CC----C-CcCHHHHHHhcCCCC
Confidence            36888888888762  3   2588999999999955433 33333321110000   00    0 123445555444333


Q ss_pred             eEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEE
Q 027749          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVC  210 (219)
Q Consensus       131 ~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i  210 (219)
                      .+..+.......+..   +....|-|-.-..+.+.+.... .....+++|+|++|.|... ....+.+.++..+.+..+|
T Consensus        73 D~~~~~p~~~~~~~g---~~~~~I~id~iR~l~~~~~~~p-~~~~~kV~iiEp~~~Ld~~-a~naLLk~LEep~~~~~~I  147 (325)
T PRK08699         73 DFYEITPLSDEPENG---RKLLQIKIDAVREIIDNVYLTS-VRGGLRVILIHPAESMNLQ-AANSLLKVLEEPPPQVVFL  147 (325)
T ss_pred             CEEEEeccccccccc---ccCCCcCHHHHHHHHHHHhhCc-ccCCceEEEEechhhCCHH-HHHHHHHHHHhCcCCCEEE
Confidence            333332111000000   0001121111122222222221 2356788999999987644 4666777777776555555


Q ss_pred             EEe
Q 027749          211 CPG  213 (219)
Q Consensus       211 ~~S  213 (219)
                      +.|
T Consensus       148 lvt  150 (325)
T PRK08699        148 LVS  150 (325)
T ss_pred             EEe
Confidence            544

>PRK08506 replicative DNA helicase; Provisional

Probab=96.11  E-value=0.036  Score=48.49  Aligned_cols=138  Identities=20%  Similarity=0.195  Sum_probs=68.6

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEE-ECCcccHHHHH-
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC-VGGKSVGEDIR-  146 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~-  146 (219)
                      .|.-+++.|.+|.||| ++.+-+...+...  +..++|... -.-..|+..++-....  ++....+ .|..+ ..++. 
T Consensus       191 ~G~LivIaarpg~GKT-~fal~ia~~~~~~--g~~V~~fSl-EMs~~ql~~Rlla~~s--~v~~~~i~~~~l~-~~e~~~  263 (472)
T PRK08506        191 KGDLIIIAARPSMGKT-TLCLNMALKALNQ--DKGVAFFSL-EMPAEQLMLRMLSAKT--SIPLQNLRTGDLD-DDEWER  263 (472)
T ss_pred             CCceEEEEcCCCCChH-HHHHHHHHHHHhc--CCcEEEEeC-cCCHHHHHHHHHHHhc--CCCHHHHhcCCCC-HHHHHH
Confidence            3445788999999999 5555455444333  233555533 4455566665533222  2211111 12222 12222 


Q ss_pred             ------HhcCCCeEEEe-----ChHHHHHHHHcCCCCCCCccEEEeccchhhhccc----cHHHHHHHHHhC---C--CC
Q 027749          147 ------KLEHGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG----FKDQIYDVYRYL---P--PD  206 (219)
Q Consensus       147 ------~l~~~~~I~v~-----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~----~~~~~~~i~~~~---~--~~  206 (219)
                            .+. +..+.|-     |+..+...++.-......+++||||-.+.|...+    -...+..+.+.+   -  .+
T Consensus       264 ~~~a~~~l~-~~~l~I~d~~~~ti~~I~~~~r~l~~~~~~~~lvvIDyLql~~~~~~~~~r~~ev~~isr~LK~lAkel~  342 (472)
T PRK08506        264 LSDACDELS-KKKLFVYDSGYVNIHQVRAQLRKLKSQHPEIGLAVIDYLQLMSGSGNFKDRHLQISEISRGLKLLARELD  342 (472)
T ss_pred             HHHHHHHHH-cCCeEEECCCCCCHHHHHHHHHHHHHhCCCCCEEEEcChhhccCCCCCCCHHHHHHHHHHHHHHHHHHhC
Confidence                  222 2345542     4555554443211112358999999999775322    123344443333   2  26


Q ss_pred             CeEEEEee
Q 027749          207 LQVCCPGS  214 (219)
Q Consensus       207 ~q~i~~SA  214 (219)
                      +.++++|.
T Consensus       343 ipVi~lsQ  350 (472)
T PRK08506        343 IPIIALSQ  350 (472)
T ss_pred             CcEEEEee
Confidence            77888774

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.09  E-value=0.035  Score=50.08  Aligned_cols=122  Identities=10%  Similarity=0.098  Sum_probs=58.7

Q ss_pred             cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCC
Q 027749           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG  151 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  151 (219)
                      ..|++||.|+|||.++..-. ..+.........-+.-++..-| ..+..|+.+......++..+.+....          
T Consensus        40 a~Lf~Gp~GvGKttlA~~lA-k~L~c~~~~~~~~~~~~~~~~C-g~C~sC~~~~~g~~~n~~~~d~~s~~----------  107 (620)
T PRK14954         40 GYIFSGLRGVGKTTAARVFA-KAVNCQRMIDDPVYLQEVTEPC-GECESCRDFDAGTSLNISEFDAASNN----------  107 (620)
T ss_pred             eEEEECCCCCCHHHHHHHHH-HHhCCCCcCCccccccccCCCC-ccCHHHHHHhccCCCCeEEecccccC----------
Confidence            48899999999996665433 3332211000000000000101 12455665555545555444332221          


Q ss_pred             CeEEEeChHHHHHHHH---cCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          152 VHVVSGTPGRVCDMIK---RKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       152 ~~I~v~Tp~~l~~~l~---~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                            ..+.+..+..   ... ...+-+++||||+|.|.... .+.+...++..|...-+|+.+
T Consensus       108 ------~vd~Ir~l~e~~~~~P-~~~~~KVvIIdEad~Lt~~a-~naLLK~LEePp~~tv~IL~t  164 (620)
T PRK14954        108 ------SVDDIRQLRENVRYGP-QKGRYRVYIIDEVHMLSTAA-FNAFLKTLEEPPPHAIFIFAT  164 (620)
T ss_pred             ------CHHHHHHHHHHHHhhh-hcCCCEEEEEeChhhcCHHH-HHHHHHHHhCCCCCeEEEEEe
Confidence                  0122222221   112 34567899999999987543 344555566655554455444

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=96.07  E-value=0.022  Score=48.22  Aligned_cols=27  Identities=19%  Similarity=0.304  Sum_probs=19.6

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhc
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVD   96 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~   96 (219)
                      .+..++|+|||||||| ..+..++..+.
T Consensus       148 ~~GlilI~G~TGSGKT-T~l~al~~~i~  174 (372)
T TIGR02525       148 AAGLGLICGETGSGKS-TLAASIYQHCG  174 (372)
T ss_pred             cCCEEEEECCCCCCHH-HHHHHHHHHHH
Confidence            4457899999999999 44455555554

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).

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=96.02  E-value=0.028  Score=51.50  Aligned_cols=44  Identities=14%  Similarity=0.160  Sum_probs=38.8

Q ss_pred             CccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       175 ~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      +--++|+|+-|.+.++....-+.+++++.|.+..+++.|-+-|+
T Consensus       129 ~pl~LVlDDyHli~~~~l~~~l~fLl~~~P~~l~lvv~SR~rP~  172 (894)
T COG2909         129 GPLYLVLDDYHLISDPALHEALRFLLKHAPENLTLVVTSRSRPQ  172 (894)
T ss_pred             CceEEEeccccccCcccHHHHHHHHHHhCCCCeEEEEEeccCCC
Confidence            34589999999999998889999999999999999999877663

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.00  E-value=0.087  Score=44.65  Aligned_cols=20  Identities=30%  Similarity=0.385  Sum_probs=15.6

Q ss_pred             CCcEEEEcCCCCchhHHhHH
Q 027749           70 GRDVIAQAQSGTGKTSMIAL   89 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~   89 (219)
                      ++.+++.||+|+|||....-
T Consensus       206 ~~ii~lvGptGvGKTTt~ak  225 (407)
T PRK12726        206 HRIISLIGQTGVGKTTTLVK  225 (407)
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            45678999999999955444

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=95.97  E-value=0.14  Score=40.33  Aligned_cols=53  Identities=13%  Similarity=0.162  Sum_probs=31.3

Q ss_pred             hCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 027749           68 IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (219)
Q Consensus        68 ~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (219)
                      ..|.-+++.|++|+|||....-.+...+. .  +.+++++.. .+-..+..+.+..+
T Consensus        22 ~~g~~~~i~G~~G~GKTtl~~~~~~~~~~-~--g~~~~yi~~-e~~~~~~~~~~~~~   74 (230)
T PRK08533         22 PAGSLILIEGDESTGKSILSQRLAYGFLQ-N--GYSVSYVST-QLTTTEFIKQMMSL   74 (230)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHHh-C--CCcEEEEeC-CCCHHHHHHHHHHh
Confidence            44667999999999999553333333322 2  345777774 33444555555443

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.96  E-value=0.082  Score=47.85  Aligned_cols=37  Identities=16%  Similarity=0.257  Sum_probs=22.4

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEE
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCC  211 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~  211 (219)
                      .+.+++||||+|.|.... ...+.+.++.-+...-+|+
T Consensus       120 ~~~KViIIDEad~Lt~~a-~naLLK~LEePp~~tvfIL  156 (620)
T PRK14948        120 ARWKVYVIDECHMLSTAA-FNALLKTLEEPPPRVVFVL  156 (620)
T ss_pred             CCceEEEEECccccCHHH-HHHHHHHHhcCCcCeEEEE
Confidence            456899999999886533 3444555555444443333

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=95.96  E-value=0.16  Score=38.56  Aligned_cols=40  Identities=8%  Similarity=0.248  Sum_probs=25.7

Q ss_pred             CCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       173 ~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ...-+++||||+|.+.... ...+...++..+++.-+|+.+
T Consensus        94 ~~~~kviiide~~~l~~~~-~~~Ll~~le~~~~~~~~il~~  133 (188)
T TIGR00678        94 ESGRRVVIIEDAERMNEAA-ANALLKTLEEPPPNTLFILIT  133 (188)
T ss_pred             cCCeEEEEEechhhhCHHH-HHHHHHHhcCCCCCeEEEEEE
Confidence            3567899999999987543 445556666655554455443

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.

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=95.95  E-value=0.02  Score=47.91  Aligned_cols=45  Identities=18%  Similarity=0.294  Sum_probs=30.2

Q ss_pred             HHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHH
Q 027749           65 MPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (219)
Q Consensus        65 ~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l  113 (219)
                      ..+..+++++|+|+||+||| .++-.++..+...   .+++.+-.+.++
T Consensus       157 ~~v~~~~nilI~G~tGSGKT-Tll~aLl~~i~~~---~rivtiEd~~El  201 (344)
T PRK13851        157 ACVVGRLTMLLCGPTGSGKT-TMSKTLISAIPPQ---ERLITIEDTLEL  201 (344)
T ss_pred             HHHHcCCeEEEECCCCccHH-HHHHHHHcccCCC---CCEEEECCCccc
Confidence            34557789999999999999 5555555555332   236666666555

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.93  E-value=0.069  Score=48.08  Aligned_cols=38  Identities=13%  Similarity=0.203  Sum_probs=23.1

Q ss_pred             CCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEE
Q 027749          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCC  211 (219)
Q Consensus       173 ~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~  211 (219)
                      ....++|||||+|.|.... .+.+.+.++..+.+.-+|+
T Consensus       118 ~~~~kVvIIDEa~~L~~~a-~naLLk~LEepp~~tv~Il  155 (585)
T PRK14950        118 LARYKVYIIDEVHMLSTAA-FNALLKTLEEPPPHAIFIL  155 (585)
T ss_pred             cCCeEEEEEeChHhCCHHH-HHHHHHHHhcCCCCeEEEE
Confidence            3567899999999877543 3334444555444443443

>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]

Probab=95.91  E-value=0.018  Score=54.64  Aligned_cols=97  Identities=14%  Similarity=-0.000  Sum_probs=63.4

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccC-----------C----CceeEEEEcCCHHHHHHHHHHHHHhccccceeEE
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTS-----------S----REVQALILSPTRELATQTEKVILAIGDFINIQAH  133 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~-----------~----~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~  133 (219)
                      .|+.+++.-..|.|||.+-+...+......           .    ...-+||++| .++..|+++++.+..... +.+.
T Consensus       373 ~g~~~~~ade~~~qk~~~~l~~~l~~~~k~~~~~cS~~~~e~~n~~~tgaTLII~P-~aIl~QW~~EI~kH~~~~-lKv~  450 (1394)
T KOG0298|consen  373 HGKRVQCADEMGWQKTSEKLILELSDLPKLCPSCCSELVKEGENLVETGATLIICP-NAILMQWFEEIHKHISSL-LKVL  450 (1394)
T ss_pred             CCcceeehhhhhccchHHHHHHHHhcccccchhhhhHHHhcccceeecCceEEECc-HHHHHHHHHHHHHhcccc-ceEE
Confidence            456678888899999988776555443111           1    1234899999 567789999998876553 6676


Q ss_pred             EEECCcccHHHHHHhcCCCeEEEeChHHHHHHHH
Q 027749          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIK  167 (219)
Q Consensus       134 ~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~  167 (219)
                      ...|-.+..-....-.-.+|||++|...|..-+.
T Consensus       451 ~Y~Girk~~~~~~~el~~yDIVlTtYdiLr~El~  484 (1394)
T KOG0298|consen  451 LYFGIRKTFWLSPFELLQYDIVLTTYDILRNELY  484 (1394)
T ss_pred             EEechhhhcccCchhhhccCEEEeehHHHHhHhh
Confidence            6665333221111122368999999998876553

>PRK05748 replicative DNA helicase; Provisional

Probab=95.89  E-value=0.079  Score=46.08  Aligned_cols=142  Identities=20%  Similarity=0.224  Sum_probs=67.3

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  148 (219)
                      .|.-++|.|++|.||| ++.+.++....... +..++|+. ...-..|+..++.....  ++....+..+.-...++..+
T Consensus       202 ~G~livIaarpg~GKT-~~al~ia~~~a~~~-g~~v~~fS-lEms~~~l~~R~l~~~~--~v~~~~i~~~~l~~~e~~~~  276 (448)
T PRK05748        202 PNDLIIVAARPSVGKT-AFALNIAQNVATKT-DKNVAIFS-LEMGAESLVMRMLCAEG--NIDAQRLRTGQLTDDDWPKL  276 (448)
T ss_pred             CCceEEEEeCCCCCch-HHHHHHHHHHHHhC-CCeEEEEe-CCCCHHHHHHHHHHHhc--CCCHHHhhcCCCCHHHHHHH
Confidence            3456888999999999 55555554443221 22355543 33444555555532211  11111111121112222221


Q ss_pred             ------cCCCeEEEe-----ChHHHHHHHHcCCCCCCCccEEEeccchhhhccc-----cHHHHHHHHHhCC-----CCC
Q 027749          149 ------EHGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG-----FKDQIYDVYRYLP-----PDL  207 (219)
Q Consensus       149 ------~~~~~I~v~-----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~-----~~~~~~~i~~~~~-----~~~  207 (219)
                            ..+..+.|.     |++.+...++.-.....++++||||-.+.|...+     ....+..+.+.+.     -++
T Consensus       277 ~~a~~~l~~~~~~i~d~~~~ti~~i~~~~r~~~~~~~~~~~vvIDyL~li~~~~~~~~~r~~~i~~i~~~LK~lAke~~i  356 (448)
T PRK05748        277 TIAMGSLSDAPIYIDDTPGIKVTEIRARCRRLAQEHGGLGLILIDYLQLIQGSGRSGENRQQEVSEISRSLKALAKELKV  356 (448)
T ss_pred             HHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEccchhcCCCCCCCcCHHHHHHHHHHHHHHHHHHhCC
Confidence                  123345542     4455554333211111268899999999874221     1233444444441     267


Q ss_pred             eEEEEeec
Q 027749          208 QVCCPGSC  215 (219)
Q Consensus       208 q~i~~SAT  215 (219)
                      .++++|..
T Consensus       357 ~vi~lsQl  364 (448)
T PRK05748        357 PVIALSQL  364 (448)
T ss_pred             eEEEeccc
Confidence            78877753

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

Probab=95.89  E-value=0.037  Score=45.83  Aligned_cols=61  Identities=16%  Similarity=0.315  Sum_probs=40.2

Q ss_pred             HHHHCCCCCChHHHHHHHHHHhCCC-cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHH
Q 027749           47 GIYQYGFEKPSAIQQRAVMPIIKGR-DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (219)
Q Consensus        47 ~l~~~~~~~~~~~Q~~~~~~~~~~~-~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l  113 (219)
                      .|-++|  ..++.|-..+..+..++ |++++|.|||||| ..+-.+...+....   ++|.+=-|.+|
T Consensus       151 dli~~g--t~~~~~a~~L~~av~~r~NILisGGTGSGKT-TlLNal~~~i~~~e---RvItiEDtaEL  212 (355)
T COG4962         151 DLIIFG--TMIRRAAKFLRRAVGIRCNILISGGTGSGKT-TLLNALSGFIDSDE---RVITIEDTAEL  212 (355)
T ss_pred             HHHHcC--CcCHHHHHHHHHHHhhceeEEEeCCCCCCHH-HHHHHHHhcCCCcc---cEEEEeehhhh
Confidence            444444  67777888887777665 9999999999999 33333434443332   46766666555

>PRK05973 replicative DNA helicase; Provisional

Probab=95.88  E-value=0.18  Score=39.93  Aligned_cols=84  Identities=15%  Similarity=0.190  Sum_probs=49.0

Q ss_pred             ccCCCCHHHHHHHHHCCCC----------CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEE
Q 027749           36 DAMGIKDDLLRGIYQYGFE----------KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQAL  105 (219)
Q Consensus        36 ~~~~l~~~~~~~l~~~~~~----------~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~l  105 (219)
                      ...+++..+-+.-.+.||.          .++|. .+..--+..|.-++|.|++|+|||...+--+.+.+. +  +.+++
T Consensus        21 ~~~~~~~~~~~~a~~~g~~~w~~~~~~~~~~~p~-~~l~GGl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~-~--Ge~vl   96 (237)
T PRK05973         21 QNIPLHEALDRIAAEEGFSSWSLLAAKAAATTPA-EELFSQLKPGDLVLLGARPGHGKTLLGLELAVEAMK-S--GRTGV   96 (237)
T ss_pred             cCCcHHHHHHHHHHHhccchHHHHHHhccCCCCH-HHhcCCCCCCCEEEEEeCCCCCHHHHHHHHHHHHHh-c--CCeEE
Confidence            4456677777666676764          33442 222233445667899999999999544443333332 2  33466


Q ss_pred             EEcCCHHHHHHHHHHHHHh
Q 027749          106 ILSPTRELATQTEKVILAI  124 (219)
Q Consensus       106 il~P~~~l~~q~~~~~~~~  124 (219)
                      |+.-- +-..++.+.+..+
T Consensus        97 yfSlE-es~~~i~~R~~s~  114 (237)
T PRK05973         97 FFTLE-YTEQDVRDRLRAL  114 (237)
T ss_pred             EEEEe-CCHHHHHHHHHHc
Confidence            66543 3356667776655

>PRK08006 replicative DNA helicase; Provisional

Probab=95.87  E-value=0.11  Score=45.52  Aligned_cols=140  Identities=20%  Similarity=0.207  Sum_probs=69.2

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEE-ECCcccHHHHHH
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC-VGGKSVGEDIRK  147 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~  147 (219)
                      .|.-++|-|.+|.||| +|.+-+...+.... +..++|... -.-..|+..++-....  ++....+ .|..+. +++.+
T Consensus       223 ~G~LiiIaarPgmGKT-afalnia~~~a~~~-g~~V~~fSl-EM~~~ql~~Rlla~~~--~v~~~~i~~~~l~~-~e~~~  296 (471)
T PRK08006        223 PSDLIIVAARPSMGKT-TFAMNLCENAAMLQ-DKPVLIFSL-EMPGEQIMMRMLASLS--RVDQTRIRTGQLDD-EDWAR  296 (471)
T ss_pred             CCcEEEEEeCCCCCHH-HHHHHHHHHHHHhc-CCeEEEEec-cCCHHHHHHHHHHHhc--CCCHHHhhcCCCCH-HHHHH
Confidence            3445778899999999 55555554443221 223555433 3444555555533222  2222111 122222 22222


Q ss_pred             -------hcCCCeEEEe-----ChHHHHHHHHcCCCCCCCccEEEeccchhhhcc----ccHHHHHHHHHhCC-----CC
Q 027749          148 -------LEHGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR----GFKDQIYDVYRYLP-----PD  206 (219)
Q Consensus       148 -------l~~~~~I~v~-----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~----~~~~~~~~i~~~~~-----~~  206 (219)
                             +.....+.|-     |+..+....+.-......+++||||=.+.|...    +-...+..+.+.++     -+
T Consensus       297 ~~~a~~~~~~~~~l~I~d~~~~t~~~i~~~~r~~~~~~~~~~lvvIDYLqli~~~~~~~~r~~ei~~isr~LK~lAkel~  376 (471)
T PRK08006        297 ISGTMGILLEKRNMYIDDSSGLTPTEVRSRARRIFREHGGLSLIMIDYLQLMRVPSLSDNRTLEIAEISRSLKALAKELQ  376 (471)
T ss_pred             HHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEccHHHccCCCCCCCcHHHHHHHHHHHHHHHHHhC
Confidence                   2133445553     455554433221111135899999999987532    22334455544442     26


Q ss_pred             CeEEEEee
Q 027749          207 LQVCCPGS  214 (219)
Q Consensus       207 ~q~i~~SA  214 (219)
                      +.+|++|.
T Consensus       377 ipVi~LsQ  384 (471)
T PRK08006        377 VPVVALSQ  384 (471)
T ss_pred             CeEEEEEe
Confidence            77888874

>TIGR00767 rho transcription termination factor Rho

Probab=95.87  E-value=0.093  Score=44.70  Aligned_cols=41  Identities=24%  Similarity=0.323  Sum_probs=25.5

Q ss_pred             hCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcC
Q 027749           68 IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (219)
Q Consensus        68 ~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P  109 (219)
                      -.|..+++.||+|+|||.. +..+...+..+.....+++++.
T Consensus       166 g~Gq~~~IvG~~g~GKTtL-~~~i~~~I~~nhfdv~v~VlLI  206 (415)
T TIGR00767       166 GKGQRGLIVAPPKAGKTVL-LQKIAQAITRNHPEVELIVLLI  206 (415)
T ss_pred             CCCCEEEEECCCCCChhHH-HHHHHHhhcccCCceEEEEEEc
Confidence            4678899999999999953 3334455444423334444443

Members of this family differ in the specificity of RNA binding.

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=95.86  E-value=0.042  Score=45.83  Aligned_cols=44  Identities=18%  Similarity=0.360  Sum_probs=28.8

Q ss_pred             HHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHH
Q 027749           66 PIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (219)
Q Consensus        66 ~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l  113 (219)
                      .+..+++++|+|+||+||| .++-.++..+...   -+++.+=-+.++
T Consensus       156 ~v~~~~nili~G~tgSGKT-Tll~aL~~~ip~~---~ri~tiEd~~El  199 (332)
T PRK13900        156 AVISKKNIIISGGTSTGKT-TFTNAALREIPAI---ERLITVEDAREI  199 (332)
T ss_pred             HHHcCCcEEEECCCCCCHH-HHHHHHHhhCCCC---CeEEEecCCCcc
Confidence            3457789999999999999 5555666655432   235555444443

>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]

Probab=95.86  E-value=0.19  Score=38.36  Aligned_cols=104  Identities=13%  Similarity=0.120  Sum_probs=55.9

Q ss_pred             cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCC
Q 027749           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG  151 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  151 (219)
                      =.++.+|+.+|||...+- ..++....  +.++++..|-..-             ..+...+...-|.          +.
T Consensus         6 l~~i~gpM~SGKT~eLl~-r~~~~~~~--g~~v~vfkp~iD~-------------R~~~~~V~Sr~G~----------~~   59 (201)
T COG1435           6 LEFIYGPMFSGKTEELLR-RARRYKEA--GMKVLVFKPAIDT-------------RYGVGKVSSRIGL----------SS   59 (201)
T ss_pred             EEEEEccCcCcchHHHHH-HHHHHHHc--CCeEEEEeccccc-------------ccccceeeeccCC----------cc
Confidence            357899999999954333 33333333  3447777774211             0011111111111          11


Q ss_pred             CeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhC
Q 027749          152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL  203 (219)
Q Consensus       152 ~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~  203 (219)
                      .-++|-.+..+.+.+....-.. .++.|.||||+- ++......+.++.+.+
T Consensus        60 ~A~~i~~~~~i~~~i~~~~~~~-~~~~v~IDEaQF-~~~~~v~~l~~lad~l  109 (201)
T COG1435          60 EAVVIPSDTDIFDEIAALHEKP-PVDCVLIDEAQF-FDEELVYVLNELADRL  109 (201)
T ss_pred             cceecCChHHHHHHHHhcccCC-CcCEEEEehhHh-CCHHHHHHHHHHHhhc
Confidence            3456667777777666543222 288999999974 4444455566665554

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=95.78  E-value=0.049  Score=44.35  Aligned_cols=19  Identities=26%  Similarity=0.359  Sum_probs=15.0

Q ss_pred             CcEEEEcCCCCchhHHhHH
Q 027749           71 RDVIAQAQSGTGKTSMIAL   89 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~   89 (219)
                      +.++++||||+|||....-
T Consensus       195 ~vi~~vGptGvGKTTt~~k  213 (282)
T TIGR03499       195 GVIALVGPTGVGKTTTLAK  213 (282)
T ss_pred             eEEEEECCCCCCHHHHHHH
Confidence            4688999999999955543

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=95.78  E-value=0.087  Score=44.54  Aligned_cols=40  Identities=15%  Similarity=0.245  Sum_probs=27.5

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEee
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGS  214 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SA  214 (219)
                      ...+++||||+|.|.... .+.+.+.++..+.+..+|++|.
T Consensus       140 ~~~kVviIDead~m~~~a-anaLLK~LEepp~~~~~IL~t~  179 (365)
T PRK07471        140 GGWRVVIVDTADEMNANA-ANALLKVLEEPPARSLFLLVSH  179 (365)
T ss_pred             CCCEEEEEechHhcCHHH-HHHHHHHHhcCCCCeEEEEEEC
Confidence            567789999999876443 4556666777665665666553

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=95.77  E-value=0.078  Score=45.87  Aligned_cols=18  Identities=28%  Similarity=0.423  Sum_probs=14.4

Q ss_pred             cEEEEcCCCCchhHHhHH
Q 027749           72 DVIAQAQSGTGKTSMIAL   89 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~~   89 (219)
                      .++++|++|+|||....-
T Consensus        97 vI~lvG~~GsGKTTtaak  114 (437)
T PRK00771         97 TIMLVGLQGSGKTTTAAK  114 (437)
T ss_pred             EEEEECCCCCcHHHHHHH
Confidence            478999999999965543

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=95.75  E-value=0.036  Score=43.64  Aligned_cols=35  Identities=17%  Similarity=0.282  Sum_probs=23.8

Q ss_pred             CCCccEEEeccchhhhccccHHHHHHHHHhCCCCCe
Q 027749          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ  208 (219)
Q Consensus       173 ~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q  208 (219)
                      ..+-+.||+||||-|.+. ....+++.++.-.+.++
T Consensus       111 ~grhKIiILDEADSMT~g-AQQAlRRtMEiyS~ttR  145 (333)
T KOG0991|consen  111 PGRHKIIILDEADSMTAG-AQQALRRTMEIYSNTTR  145 (333)
T ss_pred             CCceeEEEeeccchhhhH-HHHHHHHHHHHHcccch
Confidence            467789999999987743 35566666665544443

>PRK08840 replicative DNA helicase; Provisional

Probab=95.75  E-value=0.12  Score=45.26  Aligned_cols=142  Identities=20%  Similarity=0.221  Sum_probs=68.2

Q ss_pred             HhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEE-ECCcccHHHH
Q 027749           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC-VGGKSVGEDI  145 (219)
Q Consensus        67 ~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~  145 (219)
                      +..|.-+++.|.+|.||| ++.+-+...+.... +..++|... ..-..|+..++-....  ++....+ .|..+. +++
T Consensus       214 ~~~g~LiviaarPg~GKT-afalnia~~~a~~~-~~~v~~fSl-EMs~~ql~~Rlla~~s--~v~~~~i~~~~l~~-~e~  287 (464)
T PRK08840        214 LQGSDLIIVAARPSMGKT-TFAMNLCENAAMDQ-DKPVLIFSL-EMPAEQLMMRMLASLS--RVDQTKIRTGQLDD-EDW  287 (464)
T ss_pred             CCCCceEEEEeCCCCchH-HHHHHHHHHHHHhC-CCeEEEEec-cCCHHHHHHHHHHhhC--CCCHHHHhcCCCCH-HHH
Confidence            334456788899999999 44454444443222 223554433 3445556555533222  1211111 122222 222


Q ss_pred             HH-------hcCCCeEEEe-----ChHHHHHHHHcCCCCCCCccEEEeccchhhhccc----cHHHHHHHHHhCC-----
Q 027749          146 RK-------LEHGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG----FKDQIYDVYRYLP-----  204 (219)
Q Consensus       146 ~~-------l~~~~~I~v~-----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~----~~~~~~~i~~~~~-----  204 (219)
                      ..       +.....+.|-     |+..+....+.-......+++||||-.+.|...+    ....+..+.+.++     
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            22       2123345552     3444443322211111358899999999875222    1233444444432     


Q ss_pred             CCCeEEEEee
Q 027749          205 PDLQVCCPGS  214 (219)
Q Consensus       205 ~~~q~i~~SA  214 (219)
                      -++.++++|.
T Consensus       368 l~ipVi~LsQ  377 (464)
T PRK08840        368 LNVPVVALSQ  377 (464)
T ss_pred             hCCeEEEEEe
Confidence            2677888874

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=95.70  E-value=0.13  Score=43.45  Aligned_cols=28  Identities=21%  Similarity=0.453  Sum_probs=19.2

Q ss_pred             CccEEEeccchhhhccccHHHHHHHHHhC
Q 027749          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYL  203 (219)
Q Consensus       175 ~l~~lVvDE~h~l~~~~~~~~~~~i~~~~  203 (219)
                      ..-+||+||+|.|.+..- ..+..+++..
T Consensus       123 ~~~IvvLDEid~L~~~~~-~~LY~L~r~~  150 (366)
T COG1474         123 KTVIVILDEVDALVDKDG-EVLYSLLRAP  150 (366)
T ss_pred             CeEEEEEcchhhhccccc-hHHHHHHhhc
Confidence            445799999999987643 5555555554

>PTZ00293 thymidine kinase; Provisional

Probab=95.68  E-value=0.11  Score=40.36  Aligned_cols=38  Identities=16%  Similarity=0.188  Sum_probs=24.2

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCC
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~  110 (219)
                      |+=.++.||+++||| .-++-.+++....  +.+++++-|.
T Consensus         4 G~i~vi~GpMfSGKT-teLLr~i~~y~~a--g~kv~~~kp~   41 (211)
T PTZ00293          4 GTISVIIGPMFSGKT-TELMRLVKRFTYS--EKKCVVIKYS   41 (211)
T ss_pred             eEEEEEECCCCChHH-HHHHHHHHHHHHc--CCceEEEEec
Confidence            334578999999999 4344444444433  2347777774

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.65  E-value=0.14  Score=45.18  Aligned_cols=21  Identities=33%  Similarity=0.501  Sum_probs=16.6

Q ss_pred             CCCcEEEEcCCCCchhHHhHH
Q 027749           69 KGRDVIAQAQSGTGKTSMIAL   89 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~   89 (219)
                      .|+.+.++||+|+|||.....
T Consensus       349 ~G~vIaLVGPtGvGKTTtaak  369 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTIAK  369 (559)
T ss_pred             CCCEEEEECCCCCCHHHHHHH
Confidence            456788999999999965533

>PRK06620 hypothetical protein; Validated

Probab=95.65  E-value=0.028  Score=43.82  Aligned_cols=14  Identities=29%  Similarity=0.449  Sum_probs=12.8

Q ss_pred             CcEEEEcCCCCchh
Q 027749           71 RDVIAQAQSGTGKT   84 (219)
Q Consensus        71 ~~~lv~~~tG~GKT   84 (219)
                      +.++++||+|+|||
T Consensus        45 ~~l~l~Gp~G~GKT   58 (214)
T PRK06620         45 FTLLIKGPSSSGKT   58 (214)
T ss_pred             ceEEEECCCCCCHH
Confidence            45899999999999

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=95.60  E-value=0.14  Score=42.38  Aligned_cols=55  Identities=13%  Similarity=0.255  Sum_probs=31.7

Q ss_pred             HHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCC---CCCeEEEEee
Q 027749          160 GRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP---PDLQVCCPGS  214 (219)
Q Consensus       160 ~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~---~~~q~i~~SA  214 (219)
                      .+++..++.+....+.=-.+|+||.|-.........+..+++...   ..+=++++|.
T Consensus       122 ~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~rQtllYnlfDisqs~r~Piciig~Tt  179 (408)
T KOG2228|consen  122 SKLLEALKKGDETTSGKVIFILDEFDLFAPHSRQTLLYNLFDISQSARAPICIIGVTT  179 (408)
T ss_pred             HHHHHHHhcCCCCCCceEEEEeehhhccccchhhHHHHHHHHHHhhcCCCeEEEEeec
Confidence            455556665544333334689999997666655556666666543   2333555543

>PRK04841 transcriptional regulator MalT; Provisional

Probab=95.59  E-value=0.17  Score=47.72  Aligned_cols=41  Identities=15%  Similarity=0.195  Sum_probs=34.1

Q ss_pred             cEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEeeccc
Q 027749          177 KLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFL  217 (219)
Q Consensus       177 ~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl~  217 (219)
                      -+||||++|.+-+......+..+++.+|.+..+|+.|-+.|
T Consensus       123 ~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~sR~~~  163 (903)
T PRK04841        123 LYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVLSRNLP  163 (903)
T ss_pred             EEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEEeCCCC
Confidence            47999999998666667789999999998889888887644

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.57  E-value=0.13  Score=46.59  Aligned_cols=40  Identities=10%  Similarity=0.086  Sum_probs=26.3

Q ss_pred             CCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       173 ~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ....+++||||+|.|.... ...+...++..|.+.-+|+.+
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            4567899999999986543 455666666655554444433

>PRK09183 transposase/IS protein; Provisional

Probab=95.55  E-value=0.072  Score=42.82  Aligned_cols=21  Identities=29%  Similarity=0.534  Sum_probs=17.3

Q ss_pred             HhCCCcEEEEcCCCCchhHHh
Q 027749           67 IIKGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        67 ~~~~~~~lv~~~tG~GKT~~~   87 (219)
                      +..+.++++.||+|+|||...
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa  119 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLA  119 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHH
Confidence            456789999999999999443

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=95.50  E-value=0.21  Score=39.06  Aligned_cols=52  Identities=15%  Similarity=0.153  Sum_probs=29.8

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (219)
                      .|..+++.|++|+|||.....-+.+.+. .  +..++++.- .+...++.+....+
T Consensus        19 ~G~~~~i~G~~G~GKT~l~~~~~~~~~~-~--g~~~~~is~-e~~~~~i~~~~~~~   70 (229)
T TIGR03881        19 RGFFVAVTGEPGTGKTIFCLHFAYKGLR-D--GDPVIYVTT-EESRESIIRQAAQF   70 (229)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHHHHHh-c--CCeEEEEEc-cCCHHHHHHHHHHh
Confidence            4567999999999999544333333332 2  234666654 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.

>KOG2028 consensus ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]

Probab=95.49  E-value=0.061  Score=45.10  Aligned_cols=48  Identities=23%  Similarity=0.306  Sum_probs=25.8

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHH
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVI  121 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~  121 (219)
                      .++|+|||.|+|||..+-+.+ ...  .....+.|=+..|.+-++++...+
T Consensus       163 pSmIlWGppG~GKTtlArlia-~ts--k~~SyrfvelSAt~a~t~dvR~if  210 (554)
T KOG2028|consen  163 PSMILWGPPGTGKTTLARLIA-STS--KKHSYRFVELSATNAKTNDVRDIF  210 (554)
T ss_pred             CceEEecCCCCchHHHHHHHH-hhc--CCCceEEEEEeccccchHHHHHHH
Confidence            379999999999994332211 111  111234455555555554444443

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=95.47  E-value=0.18  Score=43.90  Aligned_cols=39  Identities=10%  Similarity=0.211  Sum_probs=25.1

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      .+-+++||||+|.|.... ...+.+.++..+....+|+.+
T Consensus       120 ~~~kvvIIdead~lt~~~-~n~LLk~lEep~~~~~~Il~t  158 (451)
T PRK06305        120 SRYKIYIIDEVHMLTKEA-FNSLLKTLEEPPQHVKFFLAT  158 (451)
T ss_pred             CCCEEEEEecHHhhCHHH-HHHHHHHhhcCCCCceEEEEe
Confidence            456789999999887543 344555566655555555543

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=95.47  E-value=0.11  Score=43.47  Aligned_cols=39  Identities=10%  Similarity=0.174  Sum_probs=22.7

Q ss_pred             CCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEE
Q 027749          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCP  212 (219)
Q Consensus       173 ~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~  212 (219)
                      ...-++||+||+|.+.... ...+.+.++..|.+..+|+.
T Consensus       115 ~~~~~vviidea~~l~~~~-~~~Ll~~le~~~~~~~lIl~  153 (355)
T TIGR02397       115 SGKYKVYIIDEVHMLSKSA-FNALLKTLEEPPEHVVFILA  153 (355)
T ss_pred             cCCceEEEEeChhhcCHHH-HHHHHHHHhCCccceeEEEE
Confidence            3456789999999876433 23344444554444444443

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.

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=95.46  E-value=0.42  Score=40.07  Aligned_cols=39  Identities=18%  Similarity=0.212  Sum_probs=27.3

Q ss_pred             CCCCcceeeccCCCCccCccccCCCCHHHHHHHHHCCCC
Q 027749           16 MDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFE   54 (219)
Q Consensus        16 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~   54 (219)
                      .+.++...+.+..+.++......++++...+.|++.|+.
T Consensus        15 ~~~~~~~~~~~~~~~~~~~l~~~g~~~~~~~kL~~~g~~   53 (344)
T PLN03187         15 LVEAEEVDEEEDLFESIDKLISQGINAGDVKKLQDAGIY   53 (344)
T ss_pred             hhhhhhhhhhhhcccCHHHHhhCCCCHHHHHHHHHcCCC
Confidence            333334444444466777777888999999999988886

>PRK13342 recombination factor protein RarA; Reviewed

Probab=95.46  E-value=0.075  Score=45.71  Aligned_cols=18  Identities=33%  Similarity=0.501  Sum_probs=14.7

Q ss_pred             CcEEEEcCCCCchhHHhH
Q 027749           71 RDVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~   88 (219)
                      .++++.||.|+|||..+.
T Consensus        37 ~~ilL~GppGtGKTtLA~   54 (413)
T PRK13342         37 SSMILWGPPGTGKTTLAR   54 (413)
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            379999999999995443

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.44  E-value=0.069  Score=45.88  Aligned_cols=42  Identities=21%  Similarity=0.219  Sum_probs=23.9

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCH
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~  111 (219)
                      |+-+.+.||+|+|||....................++...+.
T Consensus       191 g~vi~lvGpnG~GKTTtlakLA~~~~~~~~~~~v~~i~~d~~  232 (420)
T PRK14721        191 GGVYALIGPTGVGKTTTTAKLAARAVIRHGADKVALLTTDSY  232 (420)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecCCc
Confidence            455889999999999665433322222222222355555553

>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=95.37  E-value=0.2  Score=38.76  Aligned_cols=42  Identities=19%  Similarity=0.335  Sum_probs=25.9

Q ss_pred             ChHHHHHHHHcCCCCCCCccEEEeccchhhh-c----cccHHHHHHHHHhC
Q 027749          158 TPGRVCDMIKRKTLRTRAIKLLVLDESDEML-S----RGFKDQIYDVYRYL  203 (219)
Q Consensus       158 Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~-~----~~~~~~~~~i~~~~  203 (219)
                      +...+...+.....   + -+||+||+|.+. .    ..+...+..+++..
T Consensus       105 ~l~~~~~~l~~~~~---~-~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~~  151 (234)
T PF01637_consen  105 ALERLLEKLKKKGK---K-VIIVIDEFQYLAIASEEDKDFLKSLRSLLDSL  151 (234)
T ss_dssp             -HHHHHHHHHHCHC---C-EEEEEETGGGGGBCTTTTHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHhcCC---c-EEEEEecHHHHhhcccchHHHHHHHHHHHhhc
Confidence            44555555554331   1 679999999998 2    24566677777763

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=95.37  E-value=0.12  Score=44.12  Aligned_cols=39  Identities=13%  Similarity=0.273  Sum_probs=25.2

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      .+.+++||||+|.|.... .+.+.+.++.-+++.-+|+.+
T Consensus       116 ~~~kViiIDead~m~~~a-anaLLk~LEep~~~~~fIL~a  154 (394)
T PRK07940        116 GRWRIVVIEDADRLTERA-ANALLKAVEEPPPRTVWLLCA  154 (394)
T ss_pred             CCcEEEEEechhhcCHHH-HHHHHHHhhcCCCCCeEEEEE
Confidence            567899999999987543 345555666655554444433

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=95.36  E-value=0.046  Score=44.81  Aligned_cols=16  Identities=25%  Similarity=0.509  Sum_probs=13.7

Q ss_pred             CcEEEEcCCCCchhHH
Q 027749           71 RDVIAQAQSGTGKTSM   86 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~   86 (219)
                      .+++++||.|+|||..
T Consensus        31 ~~~ll~Gp~G~GKT~l   46 (305)
T TIGR00635        31 DHLLLYGPPGLGKTTL   46 (305)
T ss_pred             CeEEEECCCCCCHHHH
Confidence            4699999999999933

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.

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=95.36  E-value=0.29  Score=39.02  Aligned_cols=31  Identities=19%  Similarity=0.381  Sum_probs=20.9

Q ss_pred             HHHhCCC-cEEEEcCCCCchhHHhHHHHHhhhc
Q 027749           65 MPIIKGR-DVIAQAQSGTGKTSMIALTVCQTVD   96 (219)
Q Consensus        65 ~~~~~~~-~~lv~~~tG~GKT~~~~~~~~~~~~   96 (219)
                      +.+..|+ -+.++|+.|+|||...- .+.....
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            3445555 67899999999996665 4444433

>PRK08760 replicative DNA helicase; Provisional

Probab=95.33  E-value=0.21  Score=43.88  Aligned_cols=140  Identities=21%  Similarity=0.238  Sum_probs=67.6

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  148 (219)
                      .|.-++|.|.+|.||| ++.+-+...+.... +..++|... ..-..|+..++..........-. ..|..+ ..++..+
T Consensus       228 ~G~LivIaarPg~GKT-afal~iA~~~a~~~-g~~V~~fSl-EMs~~ql~~Rl~a~~s~i~~~~i-~~g~l~-~~e~~~~  302 (476)
T PRK08760        228 PTDLIILAARPAMGKT-TFALNIAEYAAIKS-KKGVAVFSM-EMSASQLAMRLISSNGRINAQRL-RTGALE-DEDWARV  302 (476)
T ss_pred             CCceEEEEeCCCCChh-HHHHHHHHHHHHhc-CCceEEEec-cCCHHHHHHHHHHhhCCCcHHHH-hcCCCC-HHHHHHH
Confidence            3445788999999999 55554544443221 223555533 33445566655433222221111 112222 2222211


Q ss_pred             ------cCCCeEEEe-----ChHHHHHHHHcCCCCCCCccEEEeccchhhhccc----cHHHHHHHHHhCC---C--CCe
Q 027749          149 ------EHGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG----FKDQIYDVYRYLP---P--DLQ  208 (219)
Q Consensus       149 ------~~~~~I~v~-----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~----~~~~~~~i~~~~~---~--~~q  208 (219)
                            ..+..+.|.     |++.+...++.-. .-..+++||||-.+.|...+    ....+..+.+.+.   +  ++.
T Consensus       303 ~~a~~~l~~~~l~I~d~~~~t~~~I~~~~r~l~-~~~~~~lVvIDyLql~~~~~~~~~r~~ei~~Isr~LK~lAkel~ip  381 (476)
T PRK08760        303 TGAIKMLKETKIFIDDTPGVSPEVLRSKCRRLK-REHDLGLIVIDYLQLMSVPGNSENRATEISEISRSLKGLAKELNVP  381 (476)
T ss_pred             HHHHHHHhcCCEEEeCCCCCCHHHHHHHHHHHH-HhcCCCEEEEecHHhcCCCCCCcccHHHHHHHHHHHHHHHHHhCCE
Confidence                  122345543     4555554333211 11358899999998774322    2233444444432   2  677


Q ss_pred             EEEEee
Q 027749          209 VCCPGS  214 (219)
Q Consensus       209 ~i~~SA  214 (219)
                      ++++|.
T Consensus       382 Vi~lsQ  387 (476)
T PRK08760        382 VIALSQ  387 (476)
T ss_pred             EEEeec
Confidence            787774

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=95.30  E-value=0.056  Score=45.55  Aligned_cols=26  Identities=15%  Similarity=0.365  Sum_probs=19.1

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhh
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTV   95 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~   95 (219)
                      .+..++|+||||+|||.. +..++..+
T Consensus       133 ~~glilI~GpTGSGKTTt-L~aLl~~i  158 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTL-LAAIIREL  158 (358)
T ss_pred             cCCEEEEECCCCCCHHHH-HHHHHHHH
Confidence            566899999999999943 34455544

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.

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=95.27  E-value=0.21  Score=40.45  Aligned_cols=21  Identities=29%  Similarity=0.355  Sum_probs=15.5

Q ss_pred             CcEEEEcCCCCchhHHhHHHH
Q 027749           71 RDVIAQAQSGTGKTSMIALTV   91 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~   91 (219)
                      +-++++|++|+|||....-.+
T Consensus        73 ~vi~l~G~~G~GKTTt~akLA   93 (272)
T TIGR00064        73 NVILFVGVNGVGKTTTIAKLA   93 (272)
T ss_pred             eEEEEECCCCCcHHHHHHHHH
Confidence            357788999999996554433

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.

>PRK11823 DNA repair protein RadA; Provisional

Probab=95.27  E-value=0.27  Score=42.75  Aligned_cols=88  Identities=20%  Similarity=0.235  Sum_probs=49.9

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhc
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE  149 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  149 (219)
                      |.-+++.|++|+|||...+. ++..+...  +.+++|+.- .+...|+......+....  .                  
T Consensus        80 Gs~~lI~G~pG~GKTtL~lq-~a~~~a~~--g~~vlYvs~-Ees~~qi~~ra~rlg~~~--~------------------  135 (446)
T PRK11823         80 GSVVLIGGDPGIGKSTLLLQ-VAARLAAA--GGKVLYVSG-EESASQIKLRAERLGLPS--D------------------  135 (446)
T ss_pred             CEEEEEECCCCCCHHHHHHH-HHHHHHhc--CCeEEEEEc-cccHHHHHHHHHHcCCCh--h------------------
Confidence            45688999999999944433 33333322  345788775 344566666655543211  0                  


Q ss_pred             CCCeEEEeC---hHHHHHHHHcCCCCCCCccEEEeccchhhhc
Q 027749          150 HGVHVVSGT---PGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (219)
Q Consensus       150 ~~~~I~v~T---p~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~  189 (219)
                         ++.+..   .+.+...+..     .+.++||+|+++.+..
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               022222   2333444332     3567999999998764

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

Probab=95.24  E-value=0.12  Score=45.39  Aligned_cols=94  Identities=17%  Similarity=0.145  Sum_probs=68.4

Q ss_pred             HhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhc----CCCeEEEeChHH
Q 027749           86 MIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGR  161 (219)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~----~~~~I~v~Tp~~  161 (219)
                      .-+..++.... ...+.++||.|.|+--|.++...++..    +....+++|..+..++-..+.    ..+.|+|+|.  
T Consensus       327 ~~l~~lL~~~~-~~~~~KvIIFc~tkr~~~~l~~~l~~~----~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATd--  399 (519)
T KOG0331|consen  327 RKLGKLLEDIS-SDSEGKVIIFCETKRTCDELARNLRRK----GWPAVAIHGDKSQSERDWVLKGFREGKSPVLVATD--  399 (519)
T ss_pred             HHHHHHHHHHh-ccCCCcEEEEecchhhHHHHHHHHHhc----CcceeeecccccHHHHHHHHHhcccCCcceEEEcc--
Confidence            34445555555 344568999999999998888877654    478889999999887755553    3689999994  


Q ss_pred             HHHHHHcCCCCCCCccEEEe--------ccchhhhcc
Q 027749          162 VCDMIKRKTLRTRAIKLLVL--------DESDEMLSR  190 (219)
Q Consensus       162 l~~~l~~~~~~~~~l~~lVv--------DE~h~l~~~  190 (219)
                          +-.+++++.++++||-        |-+|++...
T Consensus       400 ----VAaRGLDi~dV~lVInydfP~~vEdYVHRiGRT  432 (519)
T KOG0331|consen  400 ----VAARGLDVPDVDLVINYDFPNNVEDYVHRIGRT  432 (519)
T ss_pred             ----cccccCCCccccEEEeCCCCCCHHHHHhhcCcc
Confidence                2347789999999874        456766543

>PRK05636 replicative DNA helicase; Provisional

Probab=95.24  E-value=0.099  Score=46.13  Aligned_cols=138  Identities=18%  Similarity=0.238  Sum_probs=63.4

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhc-
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE-  149 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-  149 (219)
                      .-++|.|.+|.|||.. .+.++..+.... +..++|. ....-..|+..++-....  ++....+..+.-..+++..+. 
T Consensus       266 ~Liiiaarpg~GKT~~-al~~a~~~a~~~-g~~v~~f-SlEMs~~ql~~R~ls~~s--~v~~~~i~~g~l~~~e~~~~~~  340 (505)
T PRK05636        266 QMIIVAARPGVGKSTL-ALDFMRSASIKH-NKASVIF-SLEMSKSEIVMRLLSAEA--EVRLSDMRGGKMDEDAWEKLVQ  340 (505)
T ss_pred             ceEEEEeCCCCCHHHH-HHHHHHHHHHhC-CCeEEEE-EeeCCHHHHHHHHHHHhc--CCCHHHHhcCCCCHHHHHHHHH
Confidence            4468899999999944 444444332221 2234554 223333444444422211  121111122222222322221 


Q ss_pred             -----CCCeEEEe-----ChHHHHHHHHcCCCCCCCccEEEeccchhhhccc----cHHHHHHHHHhC---CC--CCeEE
Q 027749          150 -----HGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG----FKDQIYDVYRYL---PP--DLQVC  210 (219)
Q Consensus       150 -----~~~~I~v~-----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~----~~~~~~~i~~~~---~~--~~q~i  210 (219)
                           ....+.|-     |...+....+.-.. -..+++||||-.+.|....    ....+..+.+.+   -+  ++.+|
T Consensus       341 a~~~l~~~~l~I~d~~~~ti~~I~~~~r~~~~-~~~~~lvvIDYLql~~~~~~~~~r~~ei~~isr~LK~lAkel~ipVi  419 (505)
T PRK05636        341 RLGKIAQAPIFIDDSANLTMMEIRSKARRLKQ-KHDLKLIVVDYLQLMSSGKRVESRQQEVSEFSRQLKLLAKELDVPLI  419 (505)
T ss_pred             HHHHHhcCCEEEECCCCCCHHHHHHHHHHHHH-hcCCCEEEEcchHhcCCCCCCCcHHHHHHHHHHHHHHHHHHhCCeEE
Confidence                 23445552     33334332222111 1358899999999875321    123344444443   22  67788


Q ss_pred             EEee
Q 027749          211 CPGS  214 (219)
Q Consensus       211 ~~SA  214 (219)
                      ++|.
T Consensus       420 ~lsQ  423 (505)
T PRK05636        420 AISQ  423 (505)
T ss_pred             EEee
Confidence            8874

>PRK06321 replicative DNA helicase; Provisional

Probab=95.23  E-value=0.22  Score=43.62  Aligned_cols=151  Identities=18%  Similarity=0.274  Sum_probs=72.8

Q ss_pred             ChHHHHHHHHHHhCC----CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhcccccee
Q 027749           56 PSAIQQRAVMPIIKG----RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ  131 (219)
Q Consensus        56 ~~~~Q~~~~~~~~~~----~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  131 (219)
                      ||.+.  .+..+..|    .=++|.|.+|.||| +|.+-+...+....+. .++|.. ...-..|+..++.....  ++.
T Consensus       210 ~tG~~--~LD~~t~Gl~~G~LiiiaarPgmGKT-afal~ia~~~a~~~g~-~v~~fS-LEMs~~ql~~Rlla~~s--~v~  282 (472)
T PRK06321        210 PTHFI--DLDKMINGFSPSNLMILAARPAMGKT-ALALNIAENFCFQNRL-PVGIFS-LEMTVDQLIHRIICSRS--EVE  282 (472)
T ss_pred             ccCcH--HHHHHhcCCCCCcEEEEEeCCCCChH-HHHHHHHHHHHHhcCC-eEEEEe-ccCCHHHHHHHHHHhhc--CCC
Confidence            45443  44555443    34678899999999 5555555554322122 244443 23344455555432211  222


Q ss_pred             EEEEECCcccHHHHHHhc------CCCeEEEe-----ChHHHHHHHHcCCCCCCCccEEEeccchhhhccc-------cH
Q 027749          132 AHACVGGKSVGEDIRKLE------HGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG-------FK  193 (219)
Q Consensus       132 ~~~~~~~~~~~~~~~~l~------~~~~I~v~-----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~-------~~  193 (219)
                      ...+..+.-...++..+.      .+..+.|-     |.+.+...++.-. .-..+++||||-.+.|...+       ..
T Consensus       283 ~~~i~~~~l~~~e~~~~~~a~~~l~~~~~~idd~~~~ti~~i~~~~r~~~-~~~~~~lvvIDyLql~~~~~~~~~~~~r~  361 (472)
T PRK06321        283 SKKISVGDLSGRDFQRIVSVVNEMQEHTLLIDDQPGLKITDLRARARRMK-ESYDIQFLIIDYLQLLSGSGNLRNSESRQ  361 (472)
T ss_pred             HHHhhcCCCCHHHHHHHHHHHHHHHcCCEEEeCCCCCCHHHHHHHHHHHH-HhcCCCEEEEcchHHcCCCCccCCcchHH
Confidence            211111221222232211      12345553     4445544333211 11358899999999875321       12


Q ss_pred             HHHHHHHHhCC-----CCCeEEEEee
Q 027749          194 DQIYDVYRYLP-----PDLQVCCPGS  214 (219)
Q Consensus       194 ~~~~~i~~~~~-----~~~q~i~~SA  214 (219)
                      ..+..+.+.++     -++.+|++|.
T Consensus       362 ~ei~~Isr~LK~lAkel~vpVi~lsQ  387 (472)
T PRK06321        362 TEISEISRMLKNLARELNIPILCLSQ  387 (472)
T ss_pred             HHHHHHHHHHHHHHHHhCCcEEEEee
Confidence            34445544443     2677888775

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.19  E-value=0.14  Score=45.00  Aligned_cols=69  Identities=23%  Similarity=0.292  Sum_probs=39.2

Q ss_pred             CCCCHHHHHHHHHCCCCCChHHHHHHHHH-------HhCC-----CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEE
Q 027749           38 MGIKDDLLRGIYQYGFEKPSAIQQRAVMP-------IIKG-----RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQAL  105 (219)
Q Consensus        38 ~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~-------~~~~-----~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~l  105 (219)
                      ++.++.-++.+...|.-.-.+.-.+.+..       +...     .++++.||.|+|||..+.     .+......|++=
T Consensus       494 FG~see~l~~~~~~Gmi~~g~~v~~il~~G~llv~qvk~s~~s~lvSvLl~Gp~~sGKTaLAA-----~iA~~S~FPFvK  568 (744)
T KOG0741|consen  494 FGISEEDLERFVMNGMINWGPPVTRILDDGKLLVQQVKNSERSPLVSVLLEGPPGSGKTALAA-----KIALSSDFPFVK  568 (744)
T ss_pred             cCCCHHHHHHHHhCCceeecccHHHHHhhHHHHHHHhhccccCcceEEEEecCCCCChHHHHH-----HHHhhcCCCeEE
Confidence            46777777777776654333322333322       1111     368999999999993221     222233457777


Q ss_pred             EEcCCH
Q 027749          106 ILSPTR  111 (219)
Q Consensus       106 il~P~~  111 (219)
                      ++.|..
T Consensus       569 iiSpe~  574 (744)
T KOG0741|consen  569 IISPED  574 (744)
T ss_pred             EeChHH
Confidence            777743

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=95.15  E-value=0.22  Score=42.46  Aligned_cols=65  Identities=20%  Similarity=0.291  Sum_probs=35.3

Q ss_pred             HHHHHHHHHH---hCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 027749           58 AIQQRAVMPI---IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (219)
Q Consensus        58 ~~Q~~~~~~~---~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (219)
                      +.-.+++..+   -.|...+|.||.|+|||.. +-.+...+..+.....++|++ ..+-...+.+..+.+
T Consensus       154 ~~~~rvID~l~PIGkGQR~lIvgppGvGKTTL-aK~Ian~I~~nhFDv~~~VvL-IgER~~EVtdiqrsI  221 (416)
T PRK09376        154 DLSTRIIDLIAPIGKGQRGLIVAPPKAGKTVL-LQNIANSITTNHPEVHLIVLL-IDERPEEVTDMQRSV  221 (416)
T ss_pred             ccceeeeeeecccccCceEEEeCCCCCChhHH-HHHHHHHHHhhcCCeEEEEEE-eCCchhHHHHHHHHh
Confidence            3334455543   3788899999999999943 333445444432233333332 333334444444444

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=95.10  E-value=0.18  Score=43.01  Aligned_cols=43  Identities=12%  Similarity=0.273  Sum_probs=29.7

Q ss_pred             CccEEEeccchhhhcc-ccHHHHHHHHHhCCCC-CeEEEEeeccc
Q 027749          175 AIKLLVLDESDEMLSR-GFKDQIYDVYRYLPPD-LQVCCPGSCFL  217 (219)
Q Consensus       175 ~l~~lVvDE~h~l~~~-~~~~~~~~i~~~~~~~-~q~i~~SATl~  217 (219)
                      .++++++|+++.+... .....+..+++.+..+ .|+++-|...|
T Consensus       175 ~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P  219 (408)
T COG0593         175 SLDLLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPP  219 (408)
T ss_pred             ccCeeeechHhHhcCChhHHHHHHHHHHHHHhcCCEEEEEcCCCc
Confidence            6889999999987754 4466677777776543 36666665554

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=95.08  E-value=0.3  Score=41.43  Aligned_cols=88  Identities=16%  Similarity=0.195  Sum_probs=49.3

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhc
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE  149 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  149 (219)
                      |.-+++.|++|+|||...+. ++..+...  +.+++|+.-. +-..|+..+...+....  .                  
T Consensus        82 GslvLI~G~pG~GKStLllq-~a~~~a~~--g~~VlYvs~E-Es~~qi~~Ra~rlg~~~--~------------------  137 (372)
T cd01121          82 GSVILIGGDPGIGKSTLLLQ-VAARLAKR--GGKVLYVSGE-ESPEQIKLRADRLGIST--E------------------  137 (372)
T ss_pred             CeEEEEEeCCCCCHHHHHHH-HHHHHHhc--CCeEEEEECC-cCHHHHHHHHHHcCCCc--c------------------
Confidence            45688999999999944433 33333332  2357887654 33456655554442110  0                  


Q ss_pred             CCCeEEEe---ChHHHHHHHHcCCCCCCCccEEEeccchhhhc
Q 027749          150 HGVHVVSG---TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (219)
Q Consensus       150 ~~~~I~v~---Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~  189 (219)
                         ++.+.   ..+.+...+..     .+.++||||+++.+..
T Consensus       138 ---~l~l~~e~~le~I~~~i~~-----~~~~lVVIDSIq~l~~  172 (372)
T cd01121         138 ---NLYLLAETNLEDILASIEE-----LKPDLVIIDSIQTVYS  172 (372)
T ss_pred             ---cEEEEccCcHHHHHHHHHh-----cCCcEEEEcchHHhhc
Confidence               11111   23444444432     3578999999998763

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.08  E-value=0.36  Score=41.53  Aligned_cols=21  Identities=33%  Similarity=0.376  Sum_probs=15.8

Q ss_pred             cEEEEcCCCCchhHHhHHHHH
Q 027749           72 DVIAQAQSGTGKTSMIALTVC   92 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~~~~~   92 (219)
                      -+++.||+|+|||....-.+.
T Consensus       225 vi~lvGptGvGKTTtaaKLA~  245 (432)
T PRK12724        225 VVFFVGPTGSGKTTSIAKLAA  245 (432)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            377999999999966554433

>TIGR00665 DnaB replicative DNA helicase

Probab=95.05  E-value=0.29  Score=42.38  Aligned_cols=139  Identities=19%  Similarity=0.191  Sum_probs=66.5

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHH---
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDI---  145 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---  145 (219)
                      .|.-++|.|++|+||| ++.+-++..+.... +..++|+.. ..-..++..++......  +....+..+.-...++   
T Consensus       194 ~G~l~vi~g~pg~GKT-~~~l~~a~~~a~~~-g~~vl~~Sl-Em~~~~i~~R~~~~~~~--v~~~~~~~g~l~~~~~~~~  268 (434)
T TIGR00665       194 PSDLIILAARPSMGKT-AFALNIAENAAIKE-GKPVAFFSL-EMSAEQLAMRMLSSESR--VDSQKLRTGKLSDEDWEKL  268 (434)
T ss_pred             CCeEEEEEeCCCCChH-HHHHHHHHHHHHhC-CCeEEEEeC-cCCHHHHHHHHHHHhcC--CCHHHhccCCCCHHHHHHH
Confidence            3456789999999999 44444444432211 223555543 33445555555333222  2211111121111222   


Q ss_pred             ----HHhcCCCeEEE-----eChHHHHHHHHcCCCCCCCccEEEeccchhhhccc----cHHHHHHHHHhCC-----CCC
Q 027749          146 ----RKLEHGVHVVS-----GTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG----FKDQIYDVYRYLP-----PDL  207 (219)
Q Consensus       146 ----~~l~~~~~I~v-----~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~----~~~~~~~i~~~~~-----~~~  207 (219)
                          ..+. +..+.|     .|++.+...+..-.. -..+++||||-.+.+...+    ....+..+.+.+.     .++
T Consensus       269 ~~a~~~l~-~~~l~i~d~~~~~~~~i~~~i~~~~~-~~~~~~vvID~l~~i~~~~~~~~r~~~i~~i~~~Lk~lA~e~~i  346 (434)
T TIGR00665       269 TSAAGKLS-EAPLYIDDTPGLTITELRAKARRLKR-EHGLGLIVIDYLQLMSGSGRSENRQQEVSEISRSLKALAKELNV  346 (434)
T ss_pred             HHHHHHHh-cCCEEEECCCCCCHHHHHHHHHHHHH-hcCCCEEEEcchHhcCCCCCCCCHHHHHHHHHHHHHHHHHHhCC
Confidence                2222 234444     244555543332111 1247899999998775322    2233444444432     367


Q ss_pred             eEEEEee
Q 027749          208 QVCCPGS  214 (219)
Q Consensus       208 q~i~~SA  214 (219)
                      .++++|.
T Consensus       347 ~vi~lsq  353 (434)
T TIGR00665       347 PVIALSQ  353 (434)
T ss_pred             eEEEEec
Confidence            7777774

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.

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=95.05  E-value=0.11  Score=48.17  Aligned_cols=51  Identities=20%  Similarity=0.334  Sum_probs=27.9

Q ss_pred             CccccCCCCHHHHHHHHHC---CCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHH
Q 027749           33 TSFDAMGIKDDLLRGIYQY---GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSM   86 (219)
Q Consensus        33 ~~~~~~~l~~~~~~~l~~~---~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~   86 (219)
                      .+|++++-....++.+.+.   -+..|.-++..   .+..++.+++.||+|+|||..
T Consensus       175 ~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~---gi~~~~giLL~GppGtGKT~l  228 (733)
T TIGR01243       175 VTYEDIGGLKEAKEKIREMVELPMKHPELFEHL---GIEPPKGVLLYGPPGTGKTLL  228 (733)
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhc---CCCCCceEEEECCCCCChHHH
Confidence            4566665555555555432   11122111111   123457899999999999943

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.

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.04  E-value=0.32  Score=42.80  Aligned_cols=38  Identities=13%  Similarity=0.228  Sum_probs=23.3

Q ss_pred             CCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEE
Q 027749          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCC  211 (219)
Q Consensus       173 ~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~  211 (219)
                      ..+.+++|+||+|.|.... .+.+...++..|.+.-+|+
T Consensus       117 ~~~~KVvIIDEad~Lt~~a-~naLLk~LEepp~~~v~Il  154 (486)
T PRK14953        117 KGKYKVYIIDEAHMLTKEA-FNALLKTLEEPPPRTIFIL  154 (486)
T ss_pred             cCCeeEEEEEChhhcCHHH-HHHHHHHHhcCCCCeEEEE
Confidence            3567899999999876443 3344455555444443443

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

Probab=95.03  E-value=0.069  Score=46.44  Aligned_cols=41  Identities=17%  Similarity=0.323  Sum_probs=27.8

Q ss_pred             hHHHHHHHHHHhCCC--cEEEEcCCCCchhHHhHHHHHhhhccC
Q 027749           57 SAIQQRAVMPIIKGR--DVIAQAQSGTGKTSMIALTVCQTVDTS   98 (219)
Q Consensus        57 ~~~Q~~~~~~~~~~~--~~lv~~~tG~GKT~~~~~~~~~~~~~~   98 (219)
                      .+.|...+..+.+..  =++|.|||||||| .-+..++..+...
T Consensus       243 ~~~~~~~~~~~~~~p~GliLvTGPTGSGKT-TTLY~~L~~ln~~  285 (500)
T COG2804         243 SPFQLARLLRLLNRPQGLILVTGPTGSGKT-TTLYAALSELNTP  285 (500)
T ss_pred             CHHHHHHHHHHHhCCCeEEEEeCCCCCCHH-HHHHHHHHHhcCC
Confidence            566666776666543  3789999999999 4445555655443

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=94.99  E-value=0.19  Score=44.98  Aligned_cols=38  Identities=11%  Similarity=0.235  Sum_probs=22.8

Q ss_pred             CCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEE
Q 027749          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCC  211 (219)
Q Consensus       173 ~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~  211 (219)
                      ..+.+++|+||+|.|.... .+.+.+.++..|...-+|+
T Consensus       117 ~~~~KVvIIDEa~~Ls~~a-~naLLK~LEepp~~~vfI~  154 (563)
T PRK06647        117 SSRYRVYIIDEVHMLSNSA-FNALLKTIEEPPPYIVFIF  154 (563)
T ss_pred             cCCCEEEEEEChhhcCHHH-HHHHHHhhccCCCCEEEEE
Confidence            3567899999999886543 3334444555444433333

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

Probab=94.96  E-value=0.043  Score=49.26  Aligned_cols=41  Identities=22%  Similarity=0.294  Sum_probs=32.5

Q ss_pred             CChHHHHHHHHHH----hCCCcEEEEcCCCCchhHHhHHHHHhhh
Q 027749           55 KPSAIQQRAVMPI----IKGRDVIAQAQSGTGKTSMIALTVCQTV   95 (219)
Q Consensus        55 ~~~~~Q~~~~~~~----~~~~~~lv~~~tG~GKT~~~~~~~~~~~   95 (219)
                      +|+.+|...+..+    ..|+=.|+.+|||+|||+..+=..+..+
T Consensus        15 ~PYdIQ~~lM~elyrvLe~GkIgIfESPTGTGKSLSLiCaaltWL   59 (821)
T KOG1133|consen   15 TPYDIQEDLMRELYRVLEEGKIGIFESPTGTGKSLSLICAALTWL   59 (821)
T ss_pred             CchhHHHHHHHHHHHHHhcCCeeeeeCCCCCCchHHHHHHHHHHH
Confidence            7889998877654    4788889999999999987765555544

>PRK04328 hypothetical protein; Provisional

Probab=94.95  E-value=0.39  Score=38.35  Aligned_cols=53  Identities=15%  Similarity=0.213  Sum_probs=32.1

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhc
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIG  125 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  125 (219)
                      .|..++|.|++|+|||...+--+...+..   +-+++|+. +.+-..++.+.+..+.
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            35678999999999995443334443333   22366665 4445555666665554

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

Probab=94.94  E-value=0.14  Score=38.93  Aligned_cols=45  Identities=16%  Similarity=0.302  Sum_probs=29.6

Q ss_pred             HHHCCCCCChHHHHHHHHH-HhCCCcEEEEcCCCCchhHHhHHHHHhhh
Q 027749           48 IYQYGFEKPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTV   95 (219)
Q Consensus        48 l~~~~~~~~~~~Q~~~~~~-~~~~~~~lv~~~tG~GKT~~~~~~~~~~~   95 (219)
                      |.+.|.  .++.|...+.. +..+..+++.||||+|||... -.++..+
T Consensus         4 l~~~g~--~~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTll-~aL~~~i   49 (186)
T cd01130           4 LIAQGT--FSPLQAAYLWLAVEARKNILISGGTGSGKTTLL-NALLAFI   49 (186)
T ss_pred             HHHcCC--CCHHHHHHHHHHHhCCCEEEEECCCCCCHHHHH-HHHHhhc
Confidence            445554  45556666655 456789999999999999443 3344444

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.

>PRK09165 replicative DNA helicase; Provisional

Probab=94.90  E-value=0.22  Score=43.92  Aligned_cols=141  Identities=16%  Similarity=0.130  Sum_probs=67.1

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhhccC------------CCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEEC
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTS------------SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVG  137 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~~~~------------~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~  137 (219)
                      |.-++|.|++|.|||...+--+.+.....            ..+..++|+ ....-..|+..++..........  .+..
T Consensus       217 g~livIaarpg~GKT~~al~ia~~~a~~~~~~~~~~~~~~~~~g~~vl~f-SlEMs~~ql~~R~la~~s~v~~~--~i~~  293 (497)
T PRK09165        217 SDLIILAGRPSMGKTALATNIAFNAAKAYRREAQPDGSKKAVNGGVVGFF-SLEMSAEQLATRILSEQSEISSS--KIRR  293 (497)
T ss_pred             CceEEEEeCCCCChHHHHHHHHHHHHHhhcccccccccccccCCCeEEEE-eCcCCHHHHHHHHHHHhcCCCHH--HHhc
Confidence            34578899999999944433222222221            113345555 34445566666654332222211  1111


Q ss_pred             CcccHHHHHHhc------CCCeEEEe-----ChHHHHHHHHcCCCCCCCccEEEeccchhhhccc------cHHHHHHHH
Q 027749          138 GKSVGEDIRKLE------HGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG------FKDQIYDVY  200 (219)
Q Consensus       138 ~~~~~~~~~~l~------~~~~I~v~-----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~------~~~~~~~i~  200 (219)
                      +.-...++..+.      ....+.|-     |++.+...++.-.. -..+++||||=.+.|...+      ....+..+.
T Consensus       294 ~~l~~~e~~~l~~a~~~l~~~~l~I~d~~~~ti~~i~~~ir~l~~-~~~~~lvvIDyLqli~~~~~~~~~~r~~ev~~is  372 (497)
T PRK09165        294 GKISEEDFEKLVDASQELQKLPLYIDDTPALSISQLRARARRLKR-QHGLDLLVVDYLQLIRGSSKRSSDNRVQEISEIT  372 (497)
T ss_pred             CCCCHHHHHHHHHHHHHHhcCCeEEeCCCCCCHHHHHHHHHHHHH-hcCCCEEEEcchHhccCCCCCCCCchHHHHHHHH
Confidence            221222222221      12345542     45555544432111 1358899999999775322      112344443


Q ss_pred             Hh---CC--CCCeEEEEee
Q 027749          201 RY---LP--PDLQVCCPGS  214 (219)
Q Consensus       201 ~~---~~--~~~q~i~~SA  214 (219)
                      +.   +-  .++.++++|.
T Consensus       373 ~~LK~lAkel~ipVi~lsQ  391 (497)
T PRK09165        373 QGLKALAKELNIPVIALSQ  391 (497)
T ss_pred             HHHHHHHHHhCCeEEEeec
Confidence            33   32  2677777775

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=94.86  E-value=0.24  Score=39.55  Aligned_cols=30  Identities=23%  Similarity=0.370  Sum_probs=21.1

Q ss_pred             HhCCCcEEEEcCCCCchhHHhHHHHHhhhcc
Q 027749           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDT   97 (219)
Q Consensus        67 ~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~   97 (219)
                      +-.|..+++.|+.|+|||. .+-.++..+..
T Consensus        13 i~~Gqr~~I~G~~G~GKTT-Llr~I~n~l~~   42 (249)
T cd01128          13 IGKGQRGLIVAPPKAGKTT-LLQSIANAITK   42 (249)
T ss_pred             cCCCCEEEEECCCCCCHHH-HHHHHHhcccc
Confidence            3478899999999999994 33334444443

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.

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=94.85  E-value=0.099  Score=47.86  Aligned_cols=40  Identities=10%  Similarity=0.159  Sum_probs=25.5

Q ss_pred             CCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       173 ~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ..+.+++|+||+|.|.... ...+...++..|....+|+.+
T Consensus       116 ~g~~KV~IIDEa~~LT~~A-~NALLKtLEEPP~~tifILaT  155 (725)
T PRK07133        116 QSKYKIYIIDEVHMLSKSA-FNALLKTLEEPPKHVIFILAT  155 (725)
T ss_pred             cCCCEEEEEEChhhCCHHH-HHHHHHHhhcCCCceEEEEEc
Confidence            3567899999999876443 444555566655555444443

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

Probab=94.79  E-value=0.06  Score=43.38  Aligned_cols=44  Identities=14%  Similarity=0.322  Sum_probs=29.6

Q ss_pred             HhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHH
Q 027749           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (219)
Q Consensus        67 ~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l  113 (219)
                      +..+.+++++|+|||||| .++-.++..+...  ..+++++-...++
T Consensus       124 v~~~~~ili~G~tGSGKT-T~l~all~~i~~~--~~~iv~iEd~~E~  167 (270)
T PF00437_consen  124 VRGRGNILISGPTGSGKT-TLLNALLEEIPPE--DERIVTIEDPPEL  167 (270)
T ss_dssp             HHTTEEEEEEESTTSSHH-HHHHHHHHHCHTT--TSEEEEEESSS-S
T ss_pred             cccceEEEEECCCccccc-hHHHHHhhhcccc--ccceEEeccccce
Confidence            345789999999999999 4445566665554  2346666655554

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 ....

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=94.75  E-value=0.86  Score=39.39  Aligned_cols=85  Identities=13%  Similarity=0.121  Sum_probs=41.2

Q ss_pred             cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcC--CHHHHHHHHHHHHHhccccceeEEEEECCcccHH----HH
Q 027749           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP--TRELATQTEKVILAIGDFINIQAHACVGGKSVGE----DI  145 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P--~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~  145 (219)
                      -++++|++|+|||....--+ ..+...  +.+++++.-  .+.-+.   +.++.+....++.+....+..+...    ..
T Consensus       102 vi~lvG~~GvGKTTtaaKLA-~~l~~~--G~kV~lV~~D~~R~aA~---eQLk~~a~~~~vp~~~~~~~~dp~~i~~~~l  175 (429)
T TIGR01425       102 VIMFVGLQGSGKTTTCTKLA-YYYQRK--GFKPCLVCADTFRAGAF---DQLKQNATKARIPFYGSYTESDPVKIASEGV  175 (429)
T ss_pred             EEEEECCCCCCHHHHHHHHH-HHHHHC--CCCEEEEcCcccchhHH---HHHHHHhhccCCeEEeecCCCCHHHHHHHHH
Confidence            36799999999995543322 223322  224454443  233332   3333344444555554443333211    12


Q ss_pred             HHhc-CCCe-EEEeChHHH
Q 027749          146 RKLE-HGVH-VVSGTPGRV  162 (219)
Q Consensus       146 ~~l~-~~~~-I~v~Tp~~l  162 (219)
                      .... .+++ |+|=||+++
T Consensus       176 ~~~~~~~~DvViIDTaGr~  194 (429)
T TIGR01425       176 EKFKKENFDIIIVDTSGRH  194 (429)
T ss_pred             HHHHhCCCCEEEEECCCCC
Confidence            2222 3455 667888765

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.

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=94.72  E-value=0.14  Score=45.37  Aligned_cols=40  Identities=20%  Similarity=0.217  Sum_probs=29.0

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ++=+.+|+||+---+|..-+..+...+..+.++.-+|..|
T Consensus       487 ~~~~iliLDE~TSaLD~~te~~I~~~l~~~~~~~TvIiIt  526 (529)
T TIGR02868       487 ADAPILLLDEPTEHLDAGTESELLEDLLAALSGKTVVVIT  526 (529)
T ss_pred             cCCCEEEEeCCcccCCHHHHHHHHHHHHHhcCCCEEEEEe
Confidence            5667999999988777766777777777765555555544

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.

>PRK13764 ATPase; Provisional

Probab=94.72  E-value=0.082  Score=47.45  Aligned_cols=28  Identities=14%  Similarity=0.358  Sum_probs=21.0

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhcc
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDT   97 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~   97 (219)
                      .+++++++||||+||| .++..++..+..
T Consensus       256 ~~~~ILIsG~TGSGKT-Tll~AL~~~i~~  283 (602)
T PRK13764        256 RAEGILIAGAPGAGKS-TFAQALAEFYAD  283 (602)
T ss_pred             cCCEEEEECCCCCCHH-HHHHHHHHHHhh
Confidence            4678999999999999 444556665543

>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]

Probab=94.70  E-value=0.098  Score=47.71  Aligned_cols=70  Identities=20%  Similarity=0.253  Sum_probs=55.0

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccC-CCceeEEEEcCCHHHHHHHHHHHHHhcc
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-SREVQALILSPTRELATQTEKVILAIGD  126 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~-~~~~~~lil~P~~~l~~q~~~~~~~~~~  126 (219)
                      .+++-|.+++...  ....+|.|+.|+|||.+..--+.+.+... -....++.++=|+..|.++.+++.++..
T Consensus         2 ~Ln~~Q~~av~~~--~gp~lV~AGaGsGKT~vlt~Ria~li~~~~v~p~~Il~vTFTnkAA~em~~Rl~~~~~   72 (655)
T COG0210           2 KLNPEQREAVLHP--DGPLLVLAGAGSGKTRVLTERIAYLIAAGGVDPEQILAITFTNKAAAEMRERLLKLLG   72 (655)
T ss_pred             CCCHHHHHHHhcC--CCCeEEEECCCCCchhhHHHHHHHHHHcCCcChHHeeeeechHHHHHHHHHHHHHHhC
Confidence            4788899988766  56899999999999977766655555443 2234599999999999999999988865

>PHA02535 P terminase ATPase subunit; Provisional

Probab=94.69  E-value=0.59  Score=41.77  Aligned_cols=86  Identities=14%  Similarity=0.065  Sum_probs=63.8

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHH
Q 027749           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (219)
Q Consensus        40 l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~  119 (219)
                      ++......|.+.....+.++|+.-+..-...+.-++.-.--.|||+.|..-++......  +...+|+.|+...+....+
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            67777777776656788999999775522345566677788899998887666655543  3358999999999999888


Q ss_pred             HHHHhccc
Q 027749          120 VILAIGDF  127 (219)
Q Consensus       120 ~~~~~~~~  127 (219)
                      .+..+.+.
T Consensus       201 yi~~~a~~  208 (581)
T PHA02535        201 YIIAFARE  208 (581)
T ss_pred             HHHHHHHh
Confidence            88777554

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

Probab=94.67  E-value=0.074  Score=40.22  Aligned_cols=45  Identities=20%  Similarity=0.352  Sum_probs=25.3

Q ss_pred             hCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHH
Q 027749           68 IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQ  116 (219)
Q Consensus        68 ~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q  116 (219)
                      .+++++++.|++|+|||..+.. +...+...  +..++|+ ...+|+..
T Consensus        45 ~~~~~l~l~G~~G~GKThLa~a-i~~~~~~~--g~~v~f~-~~~~L~~~   89 (178)
T PF01695_consen   45 ENGENLILYGPPGTGKTHLAVA-IANEAIRK--GYSVLFI-TASDLLDE   89 (178)
T ss_dssp             SC--EEEEEESTTSSHHHHHHH-HHHHHHHT--T--EEEE-EHHHHHHH
T ss_pred             ccCeEEEEEhhHhHHHHHHHHH-HHHHhccC--CcceeEe-ecCceecc
Confidence            4678999999999999954433 33444433  3335554 44445444

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.

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=94.67  E-value=0.86  Score=37.75  Aligned_cols=51  Identities=10%  Similarity=0.175  Sum_probs=32.2

Q ss_pred             HHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          160 GRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       160 ~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ..+...+..... ....+++|+|++|.|.... .+.+.+.++..| +.-+|+++
T Consensus       110 r~i~~~l~~~p~-~~~~kVvII~~ae~m~~~a-aNaLLK~LEEPp-~~~fILi~  160 (314)
T PRK07399        110 REIKRFLSRPPL-EAPRKVVVIEDAETMNEAA-ANALLKTLEEPG-NGTLILIA  160 (314)
T ss_pred             HHHHHHHccCcc-cCCceEEEEEchhhcCHHH-HHHHHHHHhCCC-CCeEEEEE
Confidence            334444433332 3578899999999987543 566777777766 55555554

>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]

Probab=94.66  E-value=0.067  Score=51.83  Aligned_cols=58  Identities=24%  Similarity=0.268  Sum_probs=47.1

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccC--CCceeEEEEcCCHHHHHHHHHHHHHhcc
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTS--SREVQALILSPTRELATQTEKVILAIGD  126 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~--~~~~~~lil~P~~~l~~q~~~~~~~~~~  126 (219)
                      .+.+++|.|..|||||.+..--++..+...  -.-..+++|+.|+.-+.++..++.+-..
T Consensus        15 ~~~~~lveASAGSGKT~vL~~r~lrlLl~~~~~~v~~ILvvTFT~aAa~Emk~RI~~~L~   74 (1139)
T COG1074          15 PGQSVLVEASAGTGKTFVLAERVLRLLLEGGPLDVDEILVVTFTKAAAAEMKERIRDRLK   74 (1139)
T ss_pred             CCCcEEEEEcCCCCchhHHHHHHHHHHhhcCCCChhHeeeeeccHHHHHHHHHHHHHHHH
Confidence            567999999999999988777777777664  2446799999999999999998865543

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.65  E-value=0.38  Score=40.62  Aligned_cols=18  Identities=22%  Similarity=0.359  Sum_probs=14.5

Q ss_pred             CcEEEEcCCCCchhHHhH
Q 027749           71 RDVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~   88 (219)
                      +..+++||.|+|||....
T Consensus        40 ~~~L~~G~~G~GKt~~a~   57 (367)
T PRK14970         40 QALLFCGPRGVGKTTCAR   57 (367)
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            368899999999995443

>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=94.54  E-value=0.19  Score=41.55  Aligned_cols=59  Identities=22%  Similarity=0.270  Sum_probs=36.8

Q ss_pred             cCccccCCCCHHHHHHHHHCCCCCChHHHHH-HHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhc
Q 027749           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQR-AVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVD   96 (219)
Q Consensus        32 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~-~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~   96 (219)
                      +.++..-+++...+   .+.|.  +.+.|.. .|-.+..+++++++|+||+||| .++.+++..+-
T Consensus       109 IRk~~~~~~t~~~l---~~~gt--~~~~~~ayL~~~ie~~~siii~G~t~sGKT-t~lnall~~Ip  168 (312)
T COG0630         109 IRKFSDEPITPEDL---IEYGT--ISPEQAAYLWLAIEARKSIIICGGTASGKT-TLLNALLDFIP  168 (312)
T ss_pred             EEcCCCCCCCHHHH---hhcCC--CCHHHHHHHHHHHHcCCcEEEECCCCCCHH-HHHHHHHHhCC
Confidence            34455545554433   33343  3444433 5556778899999999999999 55566665554

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=94.53  E-value=0.9  Score=35.69  Aligned_cols=51  Identities=12%  Similarity=0.207  Sum_probs=30.0

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (219)
                      |.-+++.|++|+|||.....-+...+. +  +.+++|+.-.. -..++.+.+..+
T Consensus        25 g~~~~i~G~~GsGKt~l~~~~~~~~~~-~--g~~~~y~~~e~-~~~~~~~~~~~~   75 (234)
T PRK06067         25 PSLILIEGDHGTGKSVLSQQFVYGALK-Q--GKKVYVITTEN-TSKSYLKQMESV   75 (234)
T ss_pred             CcEEEEECCCCCChHHHHHHHHHHHHh-C--CCEEEEEEcCC-CHHHHHHHHHHC
Confidence            456889999999999444333333333 2  34466666543 345555555554

>COG1485 Predicted ATPase [General function prediction only]

Probab=94.52  E-value=0.69  Score=38.63  Aligned_cols=107  Identities=11%  Similarity=0.107  Sum_probs=60.7

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcC
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH  150 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  150 (219)
                      +.+-++|+.|.|||  +++...........+    .-++...-...+.+++..+-           |.            
T Consensus        66 ~GlYl~GgVGrGKT--~LMD~Fy~~lp~~~k----~R~HFh~FM~~vH~~l~~l~-----------g~------------  116 (367)
T COG1485          66 RGLYLWGGVGRGKT--MLMDLFYESLPGERK----RRLHFHRFMARVHQRLHTLQ-----------GQ------------  116 (367)
T ss_pred             ceEEEECCCCccHH--HHHHHHHhhCCcccc----ccccHHHHHHHHHHHHHHHc-----------CC------------
Confidence            46889999999999  444443333222121    22455667777777776553           11            


Q ss_pred             CCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhC-CCCCeEEEEeecccC
Q 027749          151 GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL-PPDLQVCCPGSCFLF  218 (219)
Q Consensus       151 ~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~-~~~~q~i~~SATl~~  218 (219)
                       .+.+   +....++       ..+.++|++||.+. .|-+-...+.++++.+ ..++.++.-|-|-|.
T Consensus       117 -~dpl---~~iA~~~-------~~~~~vLCfDEF~V-tDI~DAMiL~rL~~~Lf~~GV~lvaTSN~~P~  173 (367)
T COG1485         117 -TDPL---PPIADEL-------AAETRVLCFDEFEV-TDIADAMILGRLLEALFARGVVLVATSNTAPD  173 (367)
T ss_pred             -CCcc---HHHHHHH-------HhcCCEEEeeeeee-cChHHHHHHHHHHHHHHHCCcEEEEeCCCChH
Confidence             1111   1000111       34567899999874 4444445566666664 457777777777664

>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.52  E-value=0.78  Score=37.68  Aligned_cols=49  Identities=14%  Similarity=0.270  Sum_probs=29.4

Q ss_pred             HHHhCCC-----cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHH
Q 027749           65 MPIIKGR-----DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKV  120 (219)
Q Consensus        65 ~~~~~~~-----~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~  120 (219)
                      |++..|+     .+++-+|.|+||+  |+.-...   ....  ...|-+.+..|+..+..+
T Consensus       156 PqlFtGkR~PwrgiLLyGPPGTGKS--YLAKAVA---TEAn--STFFSvSSSDLvSKWmGE  209 (439)
T KOG0739|consen  156 PQLFTGKRKPWRGILLYGPPGTGKS--YLAKAVA---TEAN--STFFSVSSSDLVSKWMGE  209 (439)
T ss_pred             hhhhcCCCCcceeEEEeCCCCCcHH--HHHHHHH---hhcC--CceEEeehHHHHHHHhcc
Confidence            5666664     5899999999999  4332211   1211  256666666666554443

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=94.49  E-value=0.66  Score=35.67  Aligned_cols=39  Identities=13%  Similarity=0.258  Sum_probs=24.3

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCC
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~  110 (219)
                      .|.-+.+.|++|+|||...+..+..... .  +.+++|+.-.
T Consensus        11 ~g~i~~i~G~~GsGKT~l~~~~~~~~~~-~--g~~v~yi~~e   49 (209)
T TIGR02237        11 RGTITQIYGPPGSGKTNICMILAVNAAR-Q--GKKVVYIDTE   49 (209)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHh-C--CCeEEEEECC
Confidence            3456889999999999555443333322 2  3346776654

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PRK05595 replicative DNA helicase; Provisional

Probab=94.48  E-value=0.24  Score=43.00  Aligned_cols=150  Identities=13%  Similarity=0.152  Sum_probs=70.9

Q ss_pred             ChHHHHHHHHHHhC----CCcEEEEcCCCCchhHHhHHHHHhhh-ccCCCceeEEEEcCCHHHHHHHHHHHHHhccccce
Q 027749           56 PSAIQQRAVMPIIK----GRDVIAQAQSGTGKTSMIALTVCQTV-DTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (219)
Q Consensus        56 ~~~~Q~~~~~~~~~----~~~~lv~~~tG~GKT~~~~~~~~~~~-~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (219)
                      |++++  .+..+..    |.-++|.|.+|.||| ++.+.+...+ ...  +..++|+.. ..-..|+..++......  +
T Consensus       185 ~tg~~--~ld~~~~G~~~g~liviaarpg~GKT-~~al~ia~~~a~~~--g~~vl~fSl-Ems~~~l~~R~~a~~~~--v  256 (444)
T PRK05595        185 ASGFR--ELDAKTSGFQKGDMILIAARPSMGKT-TFALNIAEYAALRE--GKSVAIFSL-EMSKEQLAYKLLCSEAN--V  256 (444)
T ss_pred             cCChH--HHHHhcCCCCCCcEEEEEecCCCChH-HHHHHHHHHHHHHc--CCcEEEEec-CCCHHHHHHHHHHHhcC--C
Confidence            45443  4444443    345778999999999 5545444433 232  233555544 33444555554332222  2


Q ss_pred             eEEEEECCcccHHHHHHhc------CCCeEEEe-----ChHHHHHHHHcCCCCCCCccEEEeccchhhhccc----cHHH
Q 027749          131 QAHACVGGKSVGEDIRKLE------HGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG----FKDQ  195 (219)
Q Consensus       131 ~~~~~~~~~~~~~~~~~l~------~~~~I~v~-----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~----~~~~  195 (219)
                      ....+..+.-...++..+.      ....+.|-     |++.+...++.-.. -..+++||||=.+.|....    ....
T Consensus       257 ~~~~~~~~~l~~~e~~~~~~~~~~l~~~~l~i~d~~~~t~~~i~~~~r~~~~-~~~~~~vvIDylql~~~~~~~~~r~~~  335 (444)
T PRK05595        257 DMLRLRTGNLEDKDWENIARASGPLAAAKIFIDDTAGVSVMEMRSKCRRLKI-EHGIDMILIDYLQLMSGGKGSESRQQE  335 (444)
T ss_pred             CHHHHhcCCCCHHHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHH-hcCCCEEEEeHHHhccCCCCCccHHHH
Confidence            2111111211222222221      12234442     34444433332111 1358899999999876321    1233


Q ss_pred             HHHHHHhCC-----CCCeEEEEee
Q 027749          196 IYDVYRYLP-----PDLQVCCPGS  214 (219)
Q Consensus       196 ~~~i~~~~~-----~~~q~i~~SA  214 (219)
                      +..+.+.++     .++.++++|.
T Consensus       336 v~~is~~LK~lAke~~i~vi~lsQ  359 (444)
T PRK05595        336 VSEISRSIKALAKEMECPVIALSQ  359 (444)
T ss_pred             HHHHHHHHHHHHHHhCCeEEEeec
Confidence            444433332     2677887764

>TIGR03689 pup_AAA proteasome ATPase

Probab=94.47  E-value=0.37  Score=42.55  Aligned_cols=17  Identities=29%  Similarity=0.472  Sum_probs=14.6

Q ss_pred             CCcEEEEcCCCCchhHH
Q 027749           70 GRDVIAQAQSGTGKTSM   86 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~   86 (219)
                      .+.+++.||+|+|||..
T Consensus       216 p~GILLyGPPGTGKT~L  232 (512)
T TIGR03689       216 PKGVLLYGPPGCGKTLI  232 (512)
T ss_pred             CcceEEECCCCCcHHHH
Confidence            46799999999999954

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.

>PF14516 AAA_35: AAA-like domain

Probab=94.47  E-value=0.03  Score=46.71  Aligned_cols=47  Identities=17%  Similarity=0.294  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHhC-CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEE
Q 027749           58 AIQQRAVMPIIK-GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALIL  107 (219)
Q Consensus        58 ~~Q~~~~~~~~~-~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil  107 (219)
                      |..++++..+.+ |..+.|.||-.+||| +.+..+++.+...  +.+++++
T Consensus        18 ~~e~~~~~~i~~~G~~~~I~apRq~GKT-Sll~~l~~~l~~~--~~~~v~i   65 (331)
T PF14516_consen   18 PAEQECYQEIVQPGSYIRIKAPRQMGKT-SLLLRLLERLQQQ--GYRCVYI   65 (331)
T ss_pred             HHHHHHHHHHhcCCCEEEEECcccCCHH-HHHHHHHHHHHHC--CCEEEEE
Confidence            578889988887 889999999999999 5555566666554  3344444

>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type

Probab=94.44  E-value=0.12  Score=50.34  Aligned_cols=58  Identities=17%  Similarity=0.205  Sum_probs=45.8

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhcc
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGD  126 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~  126 (219)
                      -.++++|.|+.|||||....--++..+......-.+++++-|+.-+.++.+++.+...
T Consensus         9 p~~~~~~~a~agsgkt~~l~~~~~~~~~~~~~~~~i~~~t~t~~aa~em~~Ri~~~L~   66 (1141)
T TIGR02784         9 PKTSAWVSANAGSGKTHVLTQRVIRLLLNGVPPSKILCLTYTKAAAAEMQNRVFDRLG   66 (1141)
T ss_pred             CCCCEEEEEECCCCHHHHHHHHHHHHHHcCCCCCeEEEEecCHHHHHHHHHHHHHHHH
Confidence            3568999999999999776666666555444445799999999999999999876654

AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the alphaproteobacteria (as modeled here) and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species.

>PRK10436 hypothetical protein; Provisional

Probab=94.42  E-value=0.14  Score=44.59  Aligned_cols=45  Identities=18%  Similarity=0.312  Sum_probs=27.7

Q ss_pred             HHHCCCCCChHHHHHHHHHHh--CCCcEEEEcCCCCchhHHhHHHHHhhhc
Q 027749           48 IYQYGFEKPSAIQQRAVMPII--KGRDVIAQAQSGTGKTSMIALTVCQTVD   96 (219)
Q Consensus        48 l~~~~~~~~~~~Q~~~~~~~~--~~~~~lv~~~tG~GKT~~~~~~~~~~~~   96 (219)
                      |.+.|+   .+.|...+..+.  .+.-++++||||||||... ..++..+.
T Consensus       197 L~~LG~---~~~~~~~l~~~~~~~~GliLvtGpTGSGKTTtL-~a~l~~~~  243 (462)
T PRK10436        197 LETLGM---TPAQLAQFRQALQQPQGLILVTGPTGSGKTVTL-YSALQTLN  243 (462)
T ss_pred             HHHcCc---CHHHHHHHHHHHHhcCCeEEEECCCCCChHHHH-HHHHHhhC
Confidence            445553   344555555543  3456899999999999543 44555543

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

Probab=94.40  E-value=0.071  Score=46.52  Aligned_cols=50  Identities=20%  Similarity=0.277  Sum_probs=37.8

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhc
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIG  125 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  125 (219)
                      .++++.||||+|||..+++|-+-.   ...  -+||.=|-.++.......+++.+
T Consensus        45 ~h~lvig~tgSGKt~~~viP~ll~---~~~--s~iV~D~KgEl~~~t~~~r~~~G   94 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNLLN---YPG--SMIVTDPKGELYEKTAGYRKKRG   94 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHHHh---ccC--CEEEEECCCcHHHHHHHHHHHCC
Confidence            479999999999999998886533   222  38888898888877666665553

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

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=94.40  E-value=0.27  Score=45.59  Aligned_cols=40  Identities=18%  Similarity=0.247  Sum_probs=24.0

Q ss_pred             cEEEeccchhhhcccc----HHHHHHHHHhCCCCCeEEEEeecc
Q 027749          177 KLLVLDESDEMLSRGF----KDQIYDVYRYLPPDLQVCCPGSCF  216 (219)
Q Consensus       177 ~~lVvDE~h~l~~~~~----~~~~~~i~~~~~~~~q~i~~SATl  216 (219)
                      .+|++||+|.+...+-    ...+..+++.+-...++.++.||=
T Consensus       280 ~ILfIDEIh~L~g~g~~~~g~~d~~nlLkp~L~~g~i~vIgATt  323 (758)
T PRK11034        280 SILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIGSTT  323 (758)
T ss_pred             CEEEeccHHHHhccCCCCCcHHHHHHHHHHHHhCCCeEEEecCC
Confidence            4899999999875431    234444555443344556666654

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=94.39  E-value=0.034  Score=47.32  Aligned_cols=47  Identities=21%  Similarity=0.143  Sum_probs=34.7

Q ss_pred             cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 027749           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA  123 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~  123 (219)
                      ++++.||||+|||.++++|-+....     ..+||+=|..++........++
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll~~~-----~s~vv~D~Kge~~~~t~~~r~~   47 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLLTWP-----GSVVVLDPKGENFELTSEHRRA   47 (384)
T ss_pred             CeeEecCCCCCCccEEEccchhcCC-----CCEEEEccchhHHHHHHHHHHH
Confidence            5789999999999988877655432     2388888888888665555444

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.

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

Probab=94.39  E-value=0.29  Score=43.75  Aligned_cols=46  Identities=17%  Similarity=0.099  Sum_probs=27.8

Q ss_pred             CCccEEEeccchhhhcc---ccH----HHHHHHH---HhCCCCCeEEEEeecccCC
Q 027749          174 RAIKLLVLDESDEMLSR---GFK----DQIYDVY---RYLPPDLQVCCPGSCFLFD  219 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~---~~~----~~~~~i~---~~~~~~~q~i~~SATl~~~  219 (219)
                      +.-+.|.|||+|.|.-.   +-.    ..+..++   +-+....+++.+.||=.||
T Consensus       603 saPCVIFFDEiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPD  658 (802)
T KOG0733|consen  603 SAPCVIFFDEIDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRPD  658 (802)
T ss_pred             CCCeEEEecchhhcCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCCc
Confidence            34567999999988742   112    2222332   2234456789999987665

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=94.39  E-value=0.053  Score=42.45  Aligned_cols=14  Identities=21%  Similarity=0.729  Sum_probs=11.8

Q ss_pred             EEEEcCCCCchhHH
Q 027749           73 VIAQAQSGTGKTSM   86 (219)
Q Consensus        73 ~lv~~~tG~GKT~~   86 (219)
                      ++|.|+.|+|||..
T Consensus         1 ~vv~G~pGsGKSt~   14 (234)
T PF01443_consen    1 IVVHGVPGSGKSTL   14 (234)
T ss_pred             CEEEcCCCCCHHHH
Confidence            47899999999943

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

>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=94.38  E-value=0.029  Score=42.14  Aligned_cols=46  Identities=17%  Similarity=0.235  Sum_probs=28.7

Q ss_pred             HHHHhcCCCeEEEeChHHHHHHHHcCC---CCCCCccEEEeccchhhhcc
Q 027749          144 DIRKLEHGVHVVSGTPGRVCDMIKRKT---LRTRAIKLLVLDESDEMLSR  190 (219)
Q Consensus       144 ~~~~l~~~~~I~v~Tp~~l~~~l~~~~---~~~~~l~~lVvDE~h~l~~~  190 (219)
                      ..+.....++|+|++..-|++-.....   +.. +-.+|||||||++.+.
T Consensus       112 ~~r~~~~~adivi~~y~yl~~~~~~~~~~~~~~-~~~ivI~DEAHNL~~~  160 (174)
T PF06733_consen  112 LARELAKNADIVICNYNYLFDPSIRKSLFGIDL-KDNIVIFDEAHNLEDA  160 (174)
T ss_dssp             HHHHCGGG-SEEEEETHHHHSHHHHHHHCT--C-CCEEEEETTGGGCGGG
T ss_pred             HHHHhcccCCEEEeCHHHHhhHHHHhhhccccc-cCcEEEEecccchHHH
Confidence            334555678999999877765322211   223 3468999999998764

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.

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=94.36  E-value=0.12  Score=41.48  Aligned_cols=50  Identities=12%  Similarity=0.316  Sum_probs=33.8

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHH
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL  122 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~  122 (219)
                      ++.++++.||+|+|||..+.. +...+...  +. -++.+++.+++.++.....
T Consensus       104 ~~~nl~l~G~~G~GKThLa~A-i~~~l~~~--g~-sv~f~~~~el~~~Lk~~~~  153 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIA-IGNELLKA--GI-SVLFITAPDLLSKLKAAFD  153 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHH-HHHHHHHc--CC-eEEEEEHHHHHHHHHHHHh
Confidence            677999999999999944333 33444432  22 5566677888887777554

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=94.35  E-value=0.31  Score=40.62  Aligned_cols=40  Identities=8%  Similarity=0.129  Sum_probs=28.6

Q ss_pred             CCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       173 ~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ....+++||||+|.|.... .+.+.+.++..|++..+|+.+
T Consensus       108 ~~~~kvviI~~a~~~~~~a-~NaLLK~LEEPp~~~~~Il~t  147 (329)
T PRK08058        108 ESNKKVYIIEHADKMTASA-ANSLLKFLEEPSGGTTAILLT  147 (329)
T ss_pred             ccCceEEEeehHhhhCHHH-HHHHHHHhcCCCCCceEEEEe
Confidence            3567899999999987543 556667777766666666654

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=94.35  E-value=0.35  Score=38.82  Aligned_cols=38  Identities=16%  Similarity=0.112  Sum_probs=23.9

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcC
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P  109 (219)
                      .|.-++|.|++|+|||...+--+.+.+..   +-+++|+.-
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            34568999999999995444433333332   334677663

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=94.33  E-value=0.5  Score=43.81  Aligned_cols=17  Identities=24%  Similarity=0.493  Sum_probs=14.7

Q ss_pred             CcEEEEcCCCCchhHHh
Q 027749           71 RDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~   87 (219)
                      .|.++.||+|+|||...
T Consensus       204 ~n~lL~G~pG~GKT~l~  220 (731)
T TIGR02639       204 NNPLLVGEPGVGKTAIA  220 (731)
T ss_pred             CceEEECCCCCCHHHHH
Confidence            58999999999999544

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=94.30  E-value=0.37  Score=43.35  Aligned_cols=75  Identities=8%  Similarity=0.143  Sum_probs=55.9

Q ss_pred             CceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCC
Q 027749          100 REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRA  175 (219)
Q Consensus       100 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~  175 (219)
                      .+.++||.++++..++++++.+.+.    ++.+..++|+.+..++...+    ....+|+|+|.     .+ ..++++.+
T Consensus       256 ~~~k~LVF~nt~~~ae~l~~~L~~~----g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaTd-----v~-arGIDip~  325 (572)
T PRK04537        256 EGARTMVFVNTKAFVERVARTLERH----GYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATD-----VA-ARGLHIDG  325 (572)
T ss_pred             cCCcEEEEeCCHHHHHHHHHHHHHc----CCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEeh-----hh-hcCCCccC
Confidence            3457999999999999998888654    67888889887766554333    23679999993     33 46778888


Q ss_pred             ccEEEeccc
Q 027749          176 IKLLVLDES  184 (219)
Q Consensus       176 l~~lVvDE~  184 (219)
                      +++||.-+.
T Consensus       326 V~~VInyd~  334 (572)
T PRK04537        326 VKYVYNYDL  334 (572)
T ss_pred             CCEEEEcCC
Confidence            988876544

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=94.28  E-value=0.13  Score=47.29  Aligned_cols=18  Identities=28%  Similarity=0.462  Sum_probs=14.8

Q ss_pred             CcEEEEcCCCCchhHHhH
Q 027749           71 RDVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~   88 (219)
                      .++++.||+|+|||....
T Consensus        53 ~slLL~GPpGtGKTTLA~   70 (725)
T PRK13341         53 GSLILYGPPGVGKTTLAR   70 (725)
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            479999999999995443

>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=94.26  E-value=1.4  Score=32.69  Aligned_cols=17  Identities=29%  Similarity=0.425  Sum_probs=13.5

Q ss_pred             EEEEcCCCCchhHHhHH
Q 027749           73 VIAQAQSGTGKTSMIAL   89 (219)
Q Consensus        73 ~lv~~~tG~GKT~~~~~   89 (219)
                      +++.|++|+|||.....
T Consensus         3 ~~~~G~~G~GKTt~~~~   19 (173)
T cd03115           3 ILLVGLQGVGKTTTAAK   19 (173)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            57899999999955433

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.

>KOG1806 consensus DEAD box containing helicases [Replication, recombination and repair]

Probab=94.17  E-value=0.1  Score=48.92  Aligned_cols=72  Identities=19%  Similarity=0.223  Sum_probs=56.0

Q ss_pred             CCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 027749           52 GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (219)
Q Consensus        52 ~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (219)
                      +.-..+|-|.+++-.-.+-..+++.+|+|+|||....- ++..+......++++|++.+....+|.++.+.+.
T Consensus       735 n~v~ft~~qveai~sg~qpgltmvvgppgtgktd~avq-il~~lyhn~p~qrTlivthsnqaln~lfeKi~~~  806 (1320)
T KOG1806|consen  735 NQVKFTPTQVEAILSGMQPGLTMVVGPPGTGKTDVAVQ-ILSVLYHNSPNQRTLIVTHSNQALNQLFEKIMAL  806 (1320)
T ss_pred             chhccCHHHHHHHHhcCCCCceeeecCCCCCCcchhhh-hhhhhhhcCCCcceEEEEecccchhHHHHHHHhc
Confidence            33456888988887766667999999999999955533 4555566666788999999999999988877554

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=94.17  E-value=0.24  Score=41.45  Aligned_cols=64  Identities=16%  Similarity=0.192  Sum_probs=38.9

Q ss_pred             HHHHHHHCCCCCChHHHHHHHHH-HhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHH
Q 027749           44 LLRGIYQYGFEKPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (219)
Q Consensus        44 ~~~~l~~~~~~~~~~~Q~~~~~~-~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l  113 (219)
                      -+..|.+.|.  ..+.+...+.. +..+++++++|+||+||| .++-.++..+...   .+.+++-.+.++
T Consensus       153 tl~~l~~~g~--~~~~~~~~L~~~v~~~~~ili~G~tGsGKT-Tll~al~~~i~~~---~riv~iEd~~El  217 (340)
T TIGR03819       153 TLDELVASGT--FPPGVARLLRAIVAARLAFLISGGTGSGKT-TLLSALLALVAPD---ERIVLVEDAAEL  217 (340)
T ss_pred             CHHHHHHcCC--CCHHHHHHHHHHHhCCCeEEEECCCCCCHH-HHHHHHHccCCCC---CcEEEECCccee
Confidence            3555666665  34455555554 446679999999999999 4444455444322   346666555555

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.

>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=94.16  E-value=0.065  Score=40.16  Aligned_cols=28  Identities=25%  Similarity=0.478  Sum_probs=18.7

Q ss_pred             CCccEEEeccchhhhc--cccHHHHHHHHH
Q 027749          174 RAIKLLVLDESDEMLS--RGFKDQIYDVYR  201 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~--~~~~~~~~~i~~  201 (219)
                      ..-+++|+||+=.|-.  .+|...+..+++
T Consensus        94 ~~~~liviDEIG~mEl~~~~F~~~v~~~l~  123 (168)
T PF03266_consen   94 SSSDLIVIDEIGKMELKSPGFREAVEKLLD  123 (168)
T ss_dssp             HCCHEEEE---STTCCC-CHHHHHHHHHHC
T ss_pred             CCCCEEEEeccchhhhcCHHHHHHHHHHHc
Confidence            4567999999987554  468888888887

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.

>KOG0732 consensus AAA+-type ATPase containing the bromodomain [Posttranslational modification, protein turnover, chaperones]

Probab=94.16  E-value=0.15  Score=48.30  Aligned_cols=146  Identities=17%  Similarity=0.146  Sum_probs=80.4

Q ss_pred             ccCccccCCCCHHHHHHHHHCCCCC-ChHHHHHHHHH-HhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEc
Q 027749           31 AITSFDAMGIKDDLLRGIYQYGFEK-PSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (219)
Q Consensus        31 ~~~~~~~~~l~~~~~~~l~~~~~~~-~~~~Q~~~~~~-~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~  108 (219)
                      ....|++.+--..+++.|+++-+.. .+|-+  ..+. +..-+.+++++|.|+|||+..-..+..-.....+        
T Consensus       260 ~~v~fd~vggl~~~i~~LKEmVl~PLlyPE~--f~~~~itpPrgvL~~GppGTGkTl~araLa~~~s~~~~k--------  329 (1080)
T KOG0732|consen  260 SSVGFDSVGGLENYINQLKEMVLLPLLYPEF--FDNFNITPPRGVLFHGPPGTGKTLMARALAAACSRGNRK--------  329 (1080)
T ss_pred             cccCccccccHHHHHHHHHHHHHhHhhhhhH--hhhcccCCCcceeecCCCCCchhHHHHhhhhhhcccccc--------
Confidence            3457888888888888888775422 12211  1111 2234679999999999995543221111111000        


Q ss_pred             CCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhh
Q 027749          109 PTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (219)
Q Consensus       109 P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~  188 (219)
                                  +..+.                    ++....-..-|+.+++=+.++.... .-.....+.+||+|=+.
T Consensus       330 ------------isffm--------------------rkgaD~lskwvgEaERqlrllFeeA-~k~qPSIIffdeIdGla  376 (1080)
T KOG0732|consen  330 ------------ISFFM--------------------RKGADCLSKWVGEAERQLRLLFEEA-QKTQPSIIFFDEIDGLA  376 (1080)
T ss_pred             ------------cchhh--------------------hcCchhhccccCcHHHHHHHHHHHH-hccCceEEecccccccc
Confidence                        00000                    0000011234777776666554321 12345678899998221


Q ss_pred             -------cc---ccHHHHHHHHHhCCCCCeEEEEeecccCC
Q 027749          189 -------SR---GFKDQIYDVYRYLPPDLQVCCPGSCFLFD  219 (219)
Q Consensus       189 -------~~---~~~~~~~~i~~~~~~~~q~i~~SATl~~~  219 (219)
                             +.   .-...+..++.-++...|+++++||-.+|
T Consensus       377 pvrSskqEqih~SIvSTLLaLmdGldsRgqVvvigATnRpd  417 (1080)
T KOG0732|consen  377 PVRSSKQEQIHASIVSTLLALMDGLDSRGQVVVIGATNRPD  417 (1080)
T ss_pred             ccccchHHHhhhhHHHHHHHhccCCCCCCceEEEcccCCcc
Confidence                   11   23455667777788899999999996653

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

Probab=94.02  E-value=0.23  Score=43.46  Aligned_cols=81  Identities=15%  Similarity=0.180  Sum_probs=60.8

Q ss_pred             CceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhc----CCCeEEEeChHHHHHHHHcCCCCCCC
Q 027749          100 REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRA  175 (219)
Q Consensus       100 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~----~~~~I~v~Tp~~l~~~l~~~~~~~~~  175 (219)
                      ..|.+||.+++..-|+-+..-+.+.    +++++.++|+++.+++-..+.    +..+|+|||.     . -.++++..+
T Consensus       516 ~~ppiIIFvN~kk~~d~lAk~LeK~----g~~~~tlHg~k~qeQRe~aL~~fr~~t~dIlVaTD-----v-AgRGIDIpn  585 (673)
T KOG0333|consen  516 FDPPIIIFVNTKKGADALAKILEKA----GYKVTTLHGGKSQEQRENALADFREGTGDILVATD-----V-AGRGIDIPN  585 (673)
T ss_pred             CCCCEEEEEechhhHHHHHHHHhhc----cceEEEeeCCccHHHHHHHHHHHHhcCCCEEEEec-----c-cccCCCCCc
Confidence            3567999999998887766666554    799999999999887765552    3689999994     2 357788899


Q ss_pred             ccEEE--------eccchhhhcc
Q 027749          176 IKLLV--------LDESDEMLSR  190 (219)
Q Consensus       176 l~~lV--------vDE~h~l~~~  190 (219)
                      +.+||        .|-.|++...
T Consensus       586 VSlVinydmaksieDYtHRIGRT  608 (673)
T KOG0333|consen  586 VSLVINYDMAKSIEDYTHRIGRT  608 (673)
T ss_pred             cceeeecchhhhHHHHHHHhccc
Confidence            88774        5667776643

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=93.97  E-value=0.18  Score=46.66  Aligned_cols=17  Identities=35%  Similarity=0.519  Sum_probs=14.2

Q ss_pred             CCcEEEEcCCCCchhHH
Q 027749           70 GRDVIAQAQSGTGKTSM   86 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~   86 (219)
                      .+.+++.||+|+|||..
T Consensus       487 ~~giLL~GppGtGKT~l  503 (733)
T TIGR01243       487 PKGVLLFGPPGTGKTLL  503 (733)
T ss_pred             CceEEEECCCCCCHHHH
Confidence            35699999999999943

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.

>TIGR00959 ffh signal recognition particle protein

Probab=93.86  E-value=0.95  Score=39.18  Aligned_cols=87  Identities=20%  Similarity=0.235  Sum_probs=41.0

Q ss_pred             cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCH-HHHHHHHHHHHHhccccceeEEEEECCcccHHH----HH
Q 027749           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR-ELATQTEKVILAIGDFINIQAHACVGGKSVGED----IR  146 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~-~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~  146 (219)
                      -++++|++|+|||....-.+.......+ ..-+++-+-+. ..+.   +.+..+....++.+.......+...-    ..
T Consensus       101 vi~~vG~~GsGKTTtaakLA~~l~~~~g-~kV~lV~~D~~R~~a~---~QL~~~a~~~gvp~~~~~~~~~P~~i~~~al~  176 (428)
T TIGR00959       101 VILMVGLQGSGKTTTCGKLAYYLKKKQG-KKVLLVACDLYRPAAI---EQLKVLGQQVGVPVFALGKGQSPVEIARRALE  176 (428)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHhCC-CeEEEEeccccchHHH---HHHHHHHHhcCCceEecCCCCCHHHHHHHHHH
Confidence            3789999999999665443333221222 22233444332 2222   22333333345554443322232111    11


Q ss_pred             H-hcCCCe-EEEeChHHH
Q 027749          147 K-LEHGVH-VVSGTPGRV  162 (219)
Q Consensus       147 ~-l~~~~~-I~v~Tp~~l  162 (219)
                      . ..++++ |+|=||+++
T Consensus       177 ~~~~~~~DvVIIDTaGr~  194 (428)
T TIGR00959       177 YAKENGFDVVIVDTAGRL  194 (428)
T ss_pred             HHHhcCCCEEEEeCCCcc
Confidence            1 134565 778888754

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.

>PRK09087 hypothetical protein; Validated

Probab=93.85  E-value=0.18  Score=39.63  Aligned_cols=38  Identities=5%  Similarity=-0.048  Sum_probs=22.4

Q ss_pred             cEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEeecc
Q 027749          177 KLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCF  216 (219)
Q Consensus       177 ~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl  216 (219)
                      ++|++|++|.+. . -...+..+++.+......++++++.
T Consensus        89 ~~l~iDDi~~~~-~-~~~~lf~l~n~~~~~g~~ilits~~  126 (226)
T PRK09087         89 GPVLIEDIDAGG-F-DETGLFHLINSVRQAGTSLLMTSRL  126 (226)
T ss_pred             CeEEEECCCCCC-C-CHHHHHHHHHHHHhCCCeEEEECCC
Confidence            379999999753 2 2455666666654433345555543

>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=93.82  E-value=0.13  Score=38.82  Aligned_cols=40  Identities=20%  Similarity=0.243  Sum_probs=28.5

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCC-CCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP-DLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~-~~q~i~~S  213 (219)
                      .+-+++++||...-++......+...+..+.+ +.++|+.|
T Consensus       115 ~~p~llilDEp~~~LD~~~~~~i~~~L~~~~~~g~tiIiiS  155 (178)
T cd03239         115 KPSPFYVLDEIDAALDPTNRRRVSDMIKEMAKHTSQFIVIT  155 (178)
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHHHHHHhCCCEEEEEE
Confidence            45688999999988877666666666666533 36777765

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.

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=93.76  E-value=0.65  Score=38.52  Aligned_cols=65  Identities=18%  Similarity=0.197  Sum_probs=37.5

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhcc--CCCc-eeEEEEcCCHH-----------HHHHHHHHHHHhccccceeEEEEE
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDT--SSRE-VQALILSPTRE-----------LATQTEKVILAIGDFINIQAHACV  136 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~--~~~~-~~~lil~P~~~-----------l~~q~~~~~~~~~~~~~~~~~~~~  136 (219)
                      |=+++.||+|+||| ...-++.+.+.-  .... ...+|=.....           |+.++++.++++...-+.-++.+.
T Consensus       178 RliLlhGPPGTGKT-SLCKaLaQkLSIR~~~~y~~~~liEinshsLFSKWFsESgKlV~kmF~kI~ELv~d~~~lVfvLI  256 (423)
T KOG0744|consen  178 RLILLHGPPGTGKT-SLCKALAQKLSIRTNDRYYKGQLIEINSHSLFSKWFSESGKLVAKMFQKIQELVEDRGNLVFVLI  256 (423)
T ss_pred             eEEEEeCCCCCChh-HHHHHHHHhheeeecCccccceEEEEehhHHHHHHHhhhhhHHHHHHHHHHHHHhCCCcEEEEEe
Confidence            44789999999999 444455555421  1111 22444444444           555666666666666555555554

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=93.75  E-value=0.076  Score=47.81  Aligned_cols=49  Identities=12%  Similarity=0.009  Sum_probs=38.1

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (219)
                      .++++.||||+|||..+++|-+.....     -+||+=|-.++........++.
T Consensus       159 ~hvLviapTgSGKg~g~VIPnLL~~~~-----S~VV~DpKGEl~~~Ta~~R~~~  207 (606)
T PRK13897        159 QHALLFAPTGSGKGVGFVIPNLLFWED-----SVVVHDIKLENYELTSGWREKQ  207 (606)
T ss_pred             ceEEEEcCCCCCcceEEehhhHHhCCC-----CEEEEeCcHHHHHHHHHHHHHC
Confidence            478999999999999998887765432     2888888888887666666554

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

Probab=93.72  E-value=0.22  Score=40.13  Aligned_cols=46  Identities=11%  Similarity=0.271  Sum_probs=28.7

Q ss_pred             HHHHCCCCCChHHHHHHHHHHhC--CCcEEEEcCCCCchhHHhHHHHHhhhc
Q 027749           47 GIYQYGFEKPSAIQQRAVMPIIK--GRDVIAQAQSGTGKTSMIALTVCQTVD   96 (219)
Q Consensus        47 ~l~~~~~~~~~~~Q~~~~~~~~~--~~~~lv~~~tG~GKT~~~~~~~~~~~~   96 (219)
                      .|.+.|+   .+.|.+.+..+..  +..+++.|+||+|||. .+..++..+.
T Consensus        58 ~l~~lg~---~~~~~~~l~~~~~~~~GlilisG~tGSGKTT-~l~all~~i~  105 (264)
T cd01129          58 DLEKLGL---KPENLEIFRKLLEKPHGIILVTGPTGSGKTT-TLYSALSELN  105 (264)
T ss_pred             CHHHcCC---CHHHHHHHHHHHhcCCCEEEEECCCCCcHHH-HHHHHHhhhC
Confidence            3556654   4445556655442  3468999999999994 4444555543

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.

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=93.65  E-value=0.18  Score=41.67  Aligned_cols=29  Identities=21%  Similarity=0.481  Sum_probs=20.9

Q ss_pred             HHhCCCcEEEEcCCCCchhHHhHHHHHhhh
Q 027749           66 PIIKGRDVIAQAQSGTGKTSMIALTVCQTV   95 (219)
Q Consensus        66 ~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~   95 (219)
                      .+..+.++++.|+||+|||. ++-.++..+
T Consensus       140 ~v~~~~~ili~G~tGsGKTT-ll~al~~~~  168 (308)
T TIGR02788       140 AIASRKNIIISGGTGSGKTT-FLKSLVDEI  168 (308)
T ss_pred             HhhCCCEEEEECCCCCCHHH-HHHHHHccC
Confidence            34577899999999999994 334444444

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.

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=93.63  E-value=0.2  Score=44.12  Aligned_cols=36  Identities=14%  Similarity=0.325  Sum_probs=21.9

Q ss_pred             CCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeE
Q 027749          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQV  209 (219)
Q Consensus       173 ~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~  209 (219)
                      ..+.+..|+||+|++....|.. +.+.++.-|.+.-+
T Consensus       117 ~~ryKVyiIDEvHMLS~~afNA-LLKTLEEPP~hV~F  152 (515)
T COG2812         117 EGRYKVYIIDEVHMLSKQAFNA-LLKTLEEPPSHVKF  152 (515)
T ss_pred             cccceEEEEecHHhhhHHHHHH-HhcccccCccCeEE
Confidence            4678899999999877554433 33333444444333

>PRK10689 transcription-repair coupling factor; Provisional

Probab=93.57  E-value=0.36  Score=46.83  Aligned_cols=78  Identities=13%  Similarity=0.124  Sum_probs=60.0

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCCc
Q 027749          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (219)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~l  176 (219)
                      +.+++|++|+.+-+..+.+.+.+...  +.++..++|+.+..++...+    .+..+|+|||     .++ .+++++.++
T Consensus       809 ~gqv~vf~n~i~~ie~la~~L~~~~p--~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaT-----dIi-erGIDIP~v  880 (1147)
T PRK10689        809 GGQVYYLYNDVENIQKAAERLAELVP--EARIAIGHGQMRERELERVMNDFHHQRFNVLVCT-----TII-ETGIDIPTA  880 (1147)
T ss_pred             CCeEEEEECCHHHHHHHHHHHHHhCC--CCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEEC-----chh-hcccccccC
Confidence            34699999999999988888887654  35777788888776543332    2478999999     333 467899999


Q ss_pred             cEEEeccchh
Q 027749          177 KLLVLDESDE  186 (219)
Q Consensus       177 ~~lVvDE~h~  186 (219)
                      ++||++.+|+
T Consensus       881 ~~VIi~~ad~  890 (1147)
T PRK10689        881 NTIIIERADH  890 (1147)
T ss_pred             CEEEEecCCC
Confidence            9999999986

>COG0305 DnaB Replicative DNA helicase [DNA replication, recombination, and repair]

Probab=93.54  E-value=0.46  Score=41.00  Aligned_cols=138  Identities=20%  Similarity=0.245  Sum_probs=71.5

Q ss_pred             cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcC-
Q 027749           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH-  150 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~-  150 (219)
                      =+++.|.+|-||| ++.+.++..+......+-++|-  ...-+.|+..++-.  ...++....+..+.-.+++|..+.. 
T Consensus       198 Lii~AaRP~mGKT-afalnia~n~a~~~~~~v~iFS--LEM~~eql~~R~Ls--~~s~v~~~kirtg~l~~~d~~~l~~a  272 (435)
T COG0305         198 LIIVAARPGMGKT-ALALNIALNAAADGRKPVAIFS--LEMSEEQLVMRLLS--SESGIESSKLRTGRLSDDEWERLIKA  272 (435)
T ss_pred             EEEEccCCCCChH-HHHHHHHHHHHHhcCCCeEEEE--ccCCHHHHHHHhhc--cccccchhccccccccHHHHHHHHHH
Confidence            3667788999999 6666666666555445534443  34445566655532  2334444444444444444444321 


Q ss_pred             -----CCeEEE-eChHHHHHHHHcC--C-CCCCCccEEEeccchhhhccc----cHHHHHHHHHhCC-----CCCeEEEE
Q 027749          151 -----GVHVVS-GTPGRVCDMIKRK--T-LRTRAIKLLVLDESDEMLSRG----FKDQIYDVYRYLP-----PDLQVCCP  212 (219)
Q Consensus       151 -----~~~I~v-~Tp~~l~~~l~~~--~-~~~~~l~~lVvDE~h~l~~~~----~~~~~~~i~~~~~-----~~~q~i~~  212 (219)
                           ...|.| -||+.=..-++.+  . -.-..++++++|-.+.|...+    ....+..+-+.+.     -+++++.+
T Consensus       273 ~~~l~~~~i~IdD~~~~si~eir~~aRrlk~~~~l~~i~iDYLqLm~~~~~~~~r~qevs~iSr~LK~lAkEl~vpvial  352 (435)
T COG0305         273 ASELSEAPIFIDDTPGLTITEIRSKARRLKLKHNLGLIVIDYLQLMTGGKKSENRKQEVSEISRSLKGLAKELGVPVIAL  352 (435)
T ss_pred             HHHHhhCCeeecCCCcCCHHHHHHHHHHHHHhcCccEEEEEEEEeecccccchhHHHHHHHHHHHHHHHHHhcCCcEEeh
Confidence                 233444 3443222212111  1 111339999999999877654    3333444433332     15677776


Q ss_pred             ee
Q 027749          213 GS  214 (219)
Q Consensus       213 SA  214 (219)
                      |.
T Consensus       353 SQ  354 (435)
T COG0305         353 SQ  354 (435)
T ss_pred             hh
Confidence            63

>PRK12608 transcription termination factor Rho; Provisional

Probab=93.52  E-value=0.63  Score=39.40  Aligned_cols=40  Identities=23%  Similarity=0.312  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHh---CCCcEEEEcCCCCchhHHhHHHHHhhhccC
Q 027749           58 AIQQRAVMPII---KGRDVIAQAQSGTGKTSMIALTVCQTVDTS   98 (219)
Q Consensus        58 ~~Q~~~~~~~~---~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~   98 (219)
                      +.-.++++.+.   .|...+|.|+.|+|||.. +..+++.+..+
T Consensus       118 ~~~~RvID~l~PiGkGQR~LIvG~pGtGKTTL-l~~la~~i~~~  160 (380)
T PRK12608        118 DLSMRVVDLVAPIGKGQRGLIVAPPRAGKTVL-LQQIAAAVAAN  160 (380)
T ss_pred             chhHhhhhheeecCCCceEEEECCCCCCHHHH-HHHHHHHHHhc
Confidence            44456777655   778999999999999944 33345555443

>PRK13695 putative NTPase; Provisional

Probab=93.50  E-value=1.8  Score=32.21  Aligned_cols=24  Identities=17%  Similarity=0.394  Sum_probs=16.4

Q ss_pred             cEEEEcCCCCchhHHhHHHHHhhhc
Q 027749           72 DVIAQAQSGTGKTSMIALTVCQTVD   96 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~~~~~~~~~   96 (219)
                      .+.+.++.|+|||..... +...+.
T Consensus         2 ~i~ltG~~G~GKTTll~~-i~~~l~   25 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLK-IAELLK   25 (174)
T ss_pred             EEEEECCCCCCHHHHHHH-HHHHHH
Confidence            478999999999955443 334333

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=93.48  E-value=0.36  Score=45.83  Aligned_cols=79  Identities=10%  Similarity=0.120  Sum_probs=61.1

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCCc
Q 027749          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (219)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~l  176 (219)
                      +.+++|++|+.+-+..+++.+++...  ++++..++|+.+..+....+    .+..+|+|+|.     ++ ..++++.++
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 GGQVFYVHNRIESIEKLATQLRELVP--EARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTT-----II-ETGIDIPNA  731 (926)
T ss_pred             CCeEEEEECCcHHHHHHHHHHHHhCC--CCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECC-----hh-hcccccccC
Confidence            35699999999999998888887643  57888889988766554332    34689999994     33 467899999


Q ss_pred             cEEEeccchhh
Q 027749          177 KLLVLDESDEM  187 (219)
Q Consensus       177 ~~lVvDE~h~l  187 (219)
                      ++||++.+++.
T Consensus       732 ~~VIi~~a~~~  742 (926)
T TIGR00580       732 NTIIIERADKF  742 (926)
T ss_pred             CEEEEecCCCC
Confidence            99999999763

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.

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=93.47  E-value=0.44  Score=34.15  Aligned_cols=20  Identities=25%  Similarity=0.431  Sum_probs=15.6

Q ss_pred             HhCCCcEEEEcCCCCchhHH
Q 027749           67 IIKGRDVIAQAQSGTGKTSM   86 (219)
Q Consensus        67 ~~~~~~~lv~~~tG~GKT~~   86 (219)
                      ...+.++++.|+.|+||+.+
T Consensus        18 a~~~~pvli~GE~GtGK~~~   37 (138)
T PF14532_consen   18 AKSSSPVLITGEPGTGKSLL   37 (138)
T ss_dssp             HCSSS-EEEECCTTSSHHHH
T ss_pred             hCCCCcEEEEcCCCCCHHHH
Confidence            34567899999999999943

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

Probab=93.47  E-value=0.62  Score=41.18  Aligned_cols=99  Identities=17%  Similarity=0.167  Sum_probs=72.3

Q ss_pred             cCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHH---hc-CCC
Q 027749           77 AQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRK---LE-HGV  152 (219)
Q Consensus        77 ~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---l~-~~~  152 (219)
                      .-.++|++..-++++.+.+... -.|.++|-+-+.+-|.|++..+.   ...++++..++|..+..++-..   .+ ...
T Consensus       364 elvF~gse~~K~lA~rq~v~~g-~~PP~lIfVQs~eRak~L~~~L~---~~~~i~v~vIh~e~~~~qrde~~~~FR~g~I  439 (593)
T KOG0344|consen  364 ELVFCGSEKGKLLALRQLVASG-FKPPVLIFVQSKERAKQLFEELE---IYDNINVDVIHGERSQKQRDETMERFRIGKI  439 (593)
T ss_pred             hheeeecchhHHHHHHHHHhcc-CCCCeEEEEecHHHHHHHHHHhh---hccCcceeeEecccchhHHHHHHHHHhccCe
Confidence            3457888877777766666554 45668999999999999999886   3446788888888665544322   22 356


Q ss_pred             eEEEeChHHHHHHHHcCCCCCCCccEEEeccch
Q 027749          153 HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESD  185 (219)
Q Consensus       153 ~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h  185 (219)
                      .++|||     +++. +++++.++.+||-++.-
T Consensus       440 wvLicT-----dll~-RGiDf~gvn~VInyD~p  466 (593)
T KOG0344|consen  440 WVLICT-----DLLA-RGIDFKGVNLVINYDFP  466 (593)
T ss_pred             eEEEeh-----hhhh-ccccccCcceEEecCCC
Confidence            899999     5554 55899999999998864

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

Probab=93.45  E-value=0.092  Score=42.53  Aligned_cols=28  Identities=39%  Similarity=0.593  Sum_probs=20.2

Q ss_pred             HhCCCcEEEEcCCCCchhHHhHHHHHhhh
Q 027749           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTV   95 (219)
Q Consensus        67 ~~~~~~~lv~~~tG~GKT~~~~~~~~~~~   95 (219)
                      +.++++++++||+|+|||... -..+..+
T Consensus        30 ~~~~~pvLl~G~~GtGKT~li-~~~l~~l   57 (272)
T PF12775_consen   30 LSNGRPVLLVGPSGTGKTSLI-QNFLSSL   57 (272)
T ss_dssp             HHCTEEEEEESSTTSSHHHHH-HHHHHCS
T ss_pred             HHcCCcEEEECCCCCchhHHH-HhhhccC
Confidence            457789999999999999433 3344443

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=93.40  E-value=0.094  Score=42.18  Aligned_cols=26  Identities=31%  Similarity=0.404  Sum_probs=20.4

Q ss_pred             HHHHHhCCCcEEEEcCCCCchhHHhH
Q 027749           63 AVMPIIKGRDVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        63 ~~~~~~~~~~~lv~~~tG~GKT~~~~   88 (219)
                      +...+..++++++.||+|+|||..+.
T Consensus        14 ~l~~l~~g~~vLL~G~~GtGKT~lA~   39 (262)
T TIGR02640        14 ALRYLKSGYPVHLRGPAGTGKTTLAM   39 (262)
T ss_pred             HHHHHhcCCeEEEEcCCCCCHHHHHH
Confidence            44455678999999999999995543

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).

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=93.36  E-value=0.23  Score=43.72  Aligned_cols=46  Identities=15%  Similarity=0.276  Sum_probs=28.5

Q ss_pred             HHHHCCCCCChHHHHHHHHHHhCC-C-cEEEEcCCCCchhHHhHHHHHhhhc
Q 027749           47 GIYQYGFEKPSAIQQRAVMPIIKG-R-DVIAQAQSGTGKTSMIALTVCQTVD   96 (219)
Q Consensus        47 ~l~~~~~~~~~~~Q~~~~~~~~~~-~-~~lv~~~tG~GKT~~~~~~~~~~~~   96 (219)
                      .|.+.|+   .+.|...+..+... + -++++||||+|||.. +..++..+.
T Consensus       220 ~l~~Lg~---~~~~~~~l~~~~~~~~GlilitGptGSGKTTt-L~a~L~~l~  267 (486)
T TIGR02533       220 DLETLGM---SPELLSRFERLIRRPHGIILVTGPTGSGKTTT-LYAALSRLN  267 (486)
T ss_pred             CHHHcCC---CHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHH-HHHHHhccC
Confidence            3445554   45566666655543 3 478999999999944 344555554

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.

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

Probab=93.35  E-value=0.56  Score=41.60  Aligned_cols=71  Identities=17%  Similarity=0.212  Sum_probs=54.3

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhc----CCCeEEEeChHHHHHHHHcCCCCCCCc
Q 027749          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (219)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~----~~~~I~v~Tp~~l~~~l~~~~~~~~~l  176 (219)
                      ..++||.+.|...++.+...+...    ++.+..++|+.+..++...+.    ...+|+|+|-     .. .+++++.++
T Consensus       273 ~~~~IVF~~tk~~~~~l~~~l~~~----g~~~~~lhG~l~q~~R~~~l~~F~~g~~~vLVaTD-----va-aRGiDi~~v  342 (513)
T COG0513         273 EGRVIVFVRTKRLVEELAESLRKR----GFKVAALHGDLPQEERDRALEKFKDGELRVLVATD-----VA-ARGLDIPDV  342 (513)
T ss_pred             CCeEEEEeCcHHHHHHHHHHHHHC----CCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEEec-----hh-hccCCcccc
Confidence            346999999999999988777665    588999999999877655542    4789999993     32 466777777


Q ss_pred             cEEEe
Q 027749          177 KLLVL  181 (219)
Q Consensus       177 ~~lVv  181 (219)
                      .+||=
T Consensus       343 ~~Vin  347 (513)
T COG0513         343 SHVIN  347 (513)
T ss_pred             ceeEE
Confidence            76653

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=93.35  E-value=0.91  Score=37.46  Aligned_cols=40  Identities=10%  Similarity=0.184  Sum_probs=26.5

Q ss_pred             CCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       173 ~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ...-+++|||++|.|.... .+.+.+.++..|++.-+|+.+
T Consensus        91 ~~~~kv~iI~~ad~m~~~a-~naLLK~LEepp~~t~~il~~  130 (313)
T PRK05564         91 EGDKKVIIIYNSEKMTEQA-QNAFLKTIEEPPKGVFIILLC  130 (313)
T ss_pred             cCCceEEEEechhhcCHHH-HHHHHHHhcCCCCCeEEEEEe
Confidence            3567899999999887543 455666666655555555444

>PHA00350 putative assembly protein

Probab=93.34  E-value=1  Score=38.47  Aligned_cols=17  Identities=12%  Similarity=0.085  Sum_probs=13.9

Q ss_pred             EEEEcCCCCchhHHhHH
Q 027749           73 VIAQAQSGTGKTSMIAL   89 (219)
Q Consensus        73 ~lv~~~tG~GKT~~~~~   89 (219)
                      .++.|..|+|||+..+-
T Consensus         4 ~l~tG~pGSGKT~~aV~   20 (399)
T PHA00350          4 YAIVGRPGSYKSYEAVV   20 (399)
T ss_pred             EEEecCCCCchhHHHHH
Confidence            47899999999976654

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=93.29  E-value=0.55  Score=40.43  Aligned_cols=73  Identities=14%  Similarity=0.148  Sum_probs=53.6

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCCc
Q 027749          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (219)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~l  176 (219)
                      ..++||.++++..+..+.+.+...    ++.+..++|+.+..++...+    .+..+|+|+|.     . ..+++++.++
T Consensus       255 ~~~~lVF~~t~~~~~~l~~~L~~~----g~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLVaTd-----v-~~rGiDip~v  324 (423)
T PRK04837        255 PDRAIIFANTKHRCEEIWGHLAAD----GHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATD-----V-AARGLHIPAV  324 (423)
T ss_pred             CCeEEEEECCHHHHHHHHHHHHhC----CCcEEEecCCCChhHHHHHHHHHHcCCCcEEEEec-----h-hhcCCCcccc
Confidence            457999999999998888877643    67888888887765554333    24689999994     2 2467888888


Q ss_pred             cEEEecc
Q 027749          177 KLLVLDE  183 (219)
Q Consensus       177 ~~lVvDE  183 (219)
                      ++||.-+
T Consensus       325 ~~VI~~d  331 (423)
T PRK04837        325 THVFNYD  331 (423)
T ss_pred             CEEEEeC
Confidence            8776544

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=93.29  E-value=0.57  Score=40.47  Aligned_cols=79  Identities=10%  Similarity=0.112  Sum_probs=55.6

Q ss_pred             hhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhc----CCCeEEEeChHHHHHHHHc
Q 027749           93 QTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKR  168 (219)
Q Consensus        93 ~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~----~~~~I~v~Tp~~l~~~l~~  168 (219)
                      ..+.......++||.+++++-+..+.+.+.+.    ++.+..+.|+.+..++...+.    ...+|+|+|.     . ..
T Consensus       237 ~~l~~~~~~~~~lVF~~s~~~~~~l~~~L~~~----~~~~~~l~g~~~~~~R~~~l~~f~~G~~~vLVaTd-----~-~~  306 (434)
T PRK11192        237 CHLLKQPEVTRSIVFVRTRERVHELAGWLRKA----GINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATD-----V-AA  306 (434)
T ss_pred             HHHHhcCCCCeEEEEeCChHHHHHHHHHHHhC----CCCEEEecCCCCHHHHHHHHHHHhCCCCcEEEEcc-----c-cc
Confidence            33333334567999999999999998888763    678888888877666544332    3678999993     2 24


Q ss_pred             CCCCCCCccEEEe
Q 027749          169 KTLRTRAIKLLVL  181 (219)
Q Consensus       169 ~~~~~~~l~~lVv  181 (219)
                      .++++.++.+||.
T Consensus       307 ~GiDip~v~~VI~  319 (434)
T PRK11192        307 RGIDIDDVSHVIN  319 (434)
T ss_pred             cCccCCCCCEEEE
Confidence            5677888887763

>TIGR00416 sms DNA repair protein RadA

Probab=93.23  E-value=1.4  Score=38.46  Aligned_cols=91  Identities=16%  Similarity=0.243  Sum_probs=50.5

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhc
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE  149 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  149 (219)
                      |.-+++.|++|+|||...+. ++..+...  +.+++|+..- +-..|+......+...  .....+..            
T Consensus        94 GsvilI~G~pGsGKTTL~lq-~a~~~a~~--g~kvlYvs~E-Es~~qi~~ra~rlg~~--~~~l~~~~------------  155 (454)
T TIGR00416        94 GSLILIGGDPGIGKSTLLLQ-VACQLAKN--QMKVLYVSGE-ESLQQIKMRAIRLGLP--EPNLYVLS------------  155 (454)
T ss_pred             CeEEEEEcCCCCCHHHHHHH-HHHHHHhc--CCcEEEEECc-CCHHHHHHHHHHcCCC--hHHeEEcC------------
Confidence            45689999999999954443 33333332  2358888754 4456666555544211  00000000            


Q ss_pred             CCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhc
Q 027749          150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (219)
Q Consensus       150 ~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~  189 (219)
                       .     .+.+.+...+..     .+.++||||....+..
T Consensus       156 -e-----~~~~~I~~~i~~-----~~~~~vVIDSIq~l~~  184 (454)
T TIGR00416       156 -E-----TNWEQICANIEE-----ENPQACVIDSIQTLYS  184 (454)
T ss_pred             -C-----CCHHHHHHHHHh-----cCCcEEEEecchhhcc
Confidence             0     134555555443     2467899999987653

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)).

>PHA00729 NTP-binding motif containing protein

Probab=93.21  E-value=0.2  Score=39.35  Aligned_cols=16  Identities=25%  Similarity=0.488  Sum_probs=13.7

Q ss_pred             cEEEEcCCCCchhHHh
Q 027749           72 DVIAQAQSGTGKTSMI   87 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~   87 (219)
                      ++++.|++|+|||..+
T Consensus        19 nIlItG~pGvGKT~LA   34 (226)
T PHA00729         19 SAVIFGKQGSGKTTYA   34 (226)
T ss_pred             EEEEECCCCCCHHHHH
Confidence            7999999999999433

>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [General function prediction only]

Probab=93.20  E-value=1.1  Score=41.33  Aligned_cols=94  Identities=13%  Similarity=0.033  Sum_probs=55.2

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhcccc---------ceeEEEEECCc
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI---------NIQAHACVGGK  139 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~---------~~~~~~~~~~~  139 (219)
                      +|-..|+...+|-|||+-. +..+..+........+|+++|-..| +.+..++..|....         .+.+..+..+.
T Consensus       281 sGFGCILAHSMGLGKTlQV-isF~diflRhT~AKtVL~ivPiNTl-QNWlsEfnmWiP~y~sD~~vrpR~F~vf~LnD~~  358 (1387)
T KOG1016|consen  281 SGFGCILAHSMGLGKTLQV-ISFSDIFLRHTKAKTVLVIVPINTL-QNWLSEFNMWIPKYFSDTGVRPRSFEVFLLNDGV  358 (1387)
T ss_pred             CCcceeeeeccccCceeEE-eehhHHHhhcCccceEEEEEehHHH-HHHHHHhhhhcCCCcccCCCccceeEEEEecCch
Confidence            3446888899999999443 2334444443344569999997776 45777777665442         25666666655


Q ss_pred             ccHHHHHHh----cCCCeEEEeChHHHHH
Q 027749          140 SVGEDIRKL----EHGVHVVSGTPGRVCD  164 (219)
Q Consensus       140 ~~~~~~~~l----~~~~~I~v~Tp~~l~~  164 (219)
                      +...+..++    -....|+..-.+.+.-
T Consensus       359 KT~~~Rakvi~~Wv~~GGVlLvGYemfRL  387 (1387)
T KOG1016|consen  359 KTFDQRAKVIEQWVQTGGVLLVGYEMFRL  387 (1387)
T ss_pred             hhHHHHHHHHHHHhccCCEEEehHHHHHH
Confidence            544333222    2234455555665543

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=93.19  E-value=0.61  Score=40.66  Aligned_cols=74  Identities=23%  Similarity=0.255  Sum_probs=53.1

Q ss_pred             CceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh---c-CCCeEEEeChHHHHHHHHcCCCCCCC
Q 027749          100 REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL---E-HGVHVVSGTPGRVCDMIKRKTLRTRA  175 (219)
Q Consensus       100 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l---~-~~~~I~v~Tp~~l~~~l~~~~~~~~~  175 (219)
                      ...++||.++++.-++.+.+.+.+.    ++.+..++|+.+..++...+   . ...+|+|+|.     .+ ..++++.+
T Consensus       244 ~~~~~lVF~~t~~~~~~l~~~L~~~----g~~~~~lhg~~~~~~R~~~l~~F~~g~~~iLVaTd-----v~-~rGiDip~  313 (456)
T PRK10590        244 NWQQVLVFTRTKHGANHLAEQLNKD----GIRSAAIHGNKSQGARTRALADFKSGDIRVLVATD-----IA-ARGLDIEE  313 (456)
T ss_pred             CCCcEEEEcCcHHHHHHHHHHHHHC----CCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcc-----HH-hcCCCccc
Confidence            3456999999999999888877653    67788888888765554333   2 3678999993     33 36678888


Q ss_pred             ccEEEecc
Q 027749          176 IKLLVLDE  183 (219)
Q Consensus       176 l~~lVvDE  183 (219)
                      +++||.=+
T Consensus       314 v~~VI~~~  321 (456)
T PRK10590        314 LPHVVNYE  321 (456)
T ss_pred             CCEEEEeC
Confidence            88776433

>PHA02542 41 41 helicase; Provisional

Probab=93.15  E-value=0.43  Score=41.86  Aligned_cols=40  Identities=13%  Similarity=0.058  Sum_probs=24.7

Q ss_pred             CccEEEeccchhhhcc-------ccHHHHHHHHHhCCC-----CCeEEEEee
Q 027749          175 AIKLLVLDESDEMLSR-------GFKDQIYDVYRYLPP-----DLQVCCPGS  214 (219)
Q Consensus       175 ~l~~lVvDE~h~l~~~-------~~~~~~~~i~~~~~~-----~~q~i~~SA  214 (219)
                      .+++||||-.+.|...       +....+..|.+.++.     ++.++++|.
T Consensus       301 ~~dlVvIDYLqL~~~~~~~~~~~nr~~ei~~Isr~LK~lAkel~vpVi~lsQ  352 (473)
T PHA02542        301 KPDVIIVDYLGICASSRLRVSSENSYTYVKAIAEELRGLAVEHDVVVWTAAQ  352 (473)
T ss_pred             CCCEEEEechhhccCCcccCCCCChHHHHHHHHHHHHHHHHHhCCeEEEEEe
Confidence            3789999999887522       223334444444322     677888875

>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=93.10  E-value=0.17  Score=40.20  Aligned_cols=35  Identities=17%  Similarity=0.349  Sum_probs=23.6

Q ss_pred             cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcC
Q 027749           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P  109 (219)
                      +++|.|++||||| .++..++..+...-  ..+++++|
T Consensus        15 r~viIG~sGSGKT-~li~~lL~~~~~~f--~~I~l~t~   49 (241)
T PF04665_consen   15 RMVIIGKSGSGKT-TLIKSLLYYLRHKF--DHIFLITP   49 (241)
T ss_pred             eEEEECCCCCCHH-HHHHHHHHhhcccC--CEEEEEec
Confidence            6899999999999 66666666544332  33455555

This is thought to be an ATPase involved in viral DNA packaging [].

>PF00931 NB-ARC: NB-ARC domain; InterPro: IPR002182 This is the NB-ARC domain, a novel signalling motif found in bacteria and eukaryotes, shared by plant resistance gene products and regulators of cell death in animals []

Probab=93.08  E-value=0.76  Score=37.05  Aligned_cols=23  Identities=30%  Similarity=0.393  Sum_probs=16.5

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhh
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQT   94 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~   94 (219)
                      +-+.|+|..|.|||..+.- +++.
T Consensus        20 ~~v~I~G~~G~GKT~LA~~-~~~~   42 (287)
T PF00931_consen   20 RVVAIVGMGGIGKTTLARQ-VARD   42 (287)
T ss_dssp             EEEEEEESTTSSHHHHHHH-HHCH
T ss_pred             EEEEEEcCCcCCcceeeee-cccc
Confidence            3578999999999955544 3344

This domain has been structurally characterised in the human protein apoptotic protease-activating factor 1 (Apaf-1) []. It contains the three-layered alpha-beta fold and subsequent short alpha-helical region characteristic of the AAA+ ATPase domain superfamily. While this domain is thought to bind and hyrolyse ATP, only ADP binding has been experimentally verified. It is proposed that binding and hydrolysis of ATP by this domain induces conformational changes the the overall protein, leading to formation of the apoptosome.; GO: 0043531 ADP binding; PDB: 3IZA_E 1Z6T_D 3SFZ_A 3SHF_A 1VT4_M 3IZ8_G 3LQR_A 2A5Y_C 3LQQ_A.

>TIGR00763 lon ATP-dependent protease La

Probab=93.04  E-value=0.48  Score=44.25  Aligned_cols=18  Identities=33%  Similarity=0.372  Sum_probs=14.6

Q ss_pred             CCcEEEEcCCCCchhHHh
Q 027749           70 GRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~   87 (219)
                      +..+++.||+|+|||..+
T Consensus       347 ~~~lll~GppG~GKT~lA  364 (775)
T TIGR00763       347 GPILCLVGPPGVGKTSLG  364 (775)
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            456999999999999443

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.

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=93.01  E-value=1.4  Score=33.62  Aligned_cols=41  Identities=24%  Similarity=0.387  Sum_probs=30.6

Q ss_pred             CCCccEEEeccchhhhcccc--HHHHHHHHHhCCCCCeEEEEe
Q 027749          173 TRAIKLLVLDESDEMLSRGF--KDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       173 ~~~l~~lVvDE~h~l~~~~~--~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      -..+++||+||+-..++.++  .+.+..+++.-|.+.-+|+-.
T Consensus       113 ~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTG  155 (191)
T PRK05986        113 DESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITG  155 (191)
T ss_pred             CCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEEC
Confidence            35789999999998888764  466888888877665555543

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=92.95  E-value=1.9  Score=38.03  Aligned_cols=52  Identities=19%  Similarity=0.296  Sum_probs=34.6

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhc
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIG  125 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  125 (219)
                      |.-++|.+|+|+|||...+.-+...+ .+  +-+++|+. ..+-..|+...++.++
T Consensus       263 gs~~li~G~~G~GKt~l~~~f~~~~~-~~--ge~~~y~s-~eEs~~~i~~~~~~lg  314 (484)
T TIGR02655       263 DSIILATGATGTGKTLLVSKFLENAC-AN--KERAILFA-YEESRAQLLRNAYSWG  314 (484)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHH-HC--CCeEEEEE-eeCCHHHHHHHHHHcC
Confidence            45689999999999954444333332 22  33577776 5667778888877664

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.

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=92.90  E-value=1.7  Score=34.22  Aligned_cols=54  Identities=19%  Similarity=0.155  Sum_probs=30.1

Q ss_pred             cEEEEcCCCCchhHHhHHHHHhhhc---------cCCCceeEEEEcCCHHHHHHHHHHHHHhcc
Q 027749           72 DVIAQAQSGTGKTSMIALTVCQTVD---------TSSREVQALILSPTRELATQTEKVILAIGD  126 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~~~~~~~~~---------~~~~~~~~lil~P~~~l~~q~~~~~~~~~~  126 (219)
                      -.++.||.|+|||...+-.++....         ....+.+++|+.--. -..++.+++..+..
T Consensus         3 ~~ll~g~~G~GKS~lal~la~~va~G~~~~g~~~~~~~~~~Vlyi~~Ed-~~~~i~~Rl~~i~~   65 (239)
T cd01125           3 VSALVAPGGTGKSSLLLVLALAMALGKNLFGGGLKVTEPGRVVYLSAED-PREEIHRRLEAILQ   65 (239)
T ss_pred             eeEEEcCCCCCHHHHHHHHHHHHhcCccccCCccccCCCceEEEEECCC-CHHHHHHHHHHHHh
Confidence            3689999999999655544443221         112344677777322 22344555555543

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.

>PRK06749 replicative DNA helicase; Provisional

Probab=92.87  E-value=0.97  Score=39.14  Aligned_cols=49  Identities=27%  Similarity=0.218  Sum_probs=27.9

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHH
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVI  121 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~  121 (219)
                      .|.-++|-|.+|.||| ++.+-+...+...  +..++|... ..-..|+..++
T Consensus       185 ~G~LiiIaarPgmGKT-afal~ia~~~a~~--g~~v~~fSl-EMs~~ql~~R~  233 (428)
T PRK06749        185 EGDFVVLGARPSMGKT-AFALNVGLHAAKS--GAAVGLFSL-EMSSKQLLKRM  233 (428)
T ss_pred             CCcEEEEEeCCCCCch-HHHHHHHHHHHhc--CCCEEEEEe-eCCHHHHHHHH
Confidence            3445788899999999 5555555554433  223444433 33344555544

>PF13479 AAA_24: AAA domain

Probab=92.86  E-value=0.19  Score=39.12  Aligned_cols=35  Identities=6%  Similarity=-0.003  Sum_probs=21.6

Q ss_pred             eEEEeChHHHHHHHHcCCCCCCCccEEEeccchhh
Q 027749          153 HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (219)
Q Consensus       153 ~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l  187 (219)
                      .|-|.+++.+.+.+..-.-....++.||||-++.+
T Consensus        46 ~i~i~s~~~~~~~~~~l~~~~~~y~tiVIDsis~~   80 (213)
T PF13479_consen   46 VIPITSWEDFLEALDELEEDEADYDTIVIDSISWL   80 (213)
T ss_pred             eeCcCCHHHHHHHHHHHHhccCCCCEEEEECHHHH
Confidence            34455777777765432122567888888877754

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=92.86  E-value=1.1  Score=34.82  Aligned_cols=51  Identities=20%  Similarity=0.208  Sum_probs=31.3

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (219)
                      |..+++.|++|+|||...+--+...+..   +-+++|+.-. +-..++.+.+..+
T Consensus        16 g~~~li~G~~G~GKt~~~~~~~~~~~~~---g~~~~y~s~e-~~~~~l~~~~~~~   66 (224)
T TIGR03880        16 GHVIVVIGEYGTGKTTFSLQFLYQGLKN---GEKAMYISLE-EREERILGYAKSK   66 (224)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEECC-CCHHHHHHHHHHc
Confidence            4578999999999994433333333332   3346776554 4566666666555

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.

>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=92.80  E-value=0.15  Score=44.33  Aligned_cols=155  Identities=17%  Similarity=0.185  Sum_probs=88.4

Q ss_pred             HHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHH
Q 027749           42 DDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVI  121 (219)
Q Consensus        42 ~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~  121 (219)
                      ..+++.+++ .+-.+...|.++.-..-.|+. .+.|-.|||||...+. -...+...++.-+++|.+-|+.|+.++...+
T Consensus       150 ~a~l~~ies-kIanfD~~Q~kaa~~~~~G~q-rIrGLAGSGKT~~La~-Kaa~lh~knPd~~I~~Tfftk~L~s~~r~lv  226 (660)
T COG3972         150 NALLDTIES-KIANFDTDQTKAAFQSGFGKQ-RIRGLAGSGKTELLAH-KAAELHSKNPDSRIAFTFFTKILASTMRTLV  226 (660)
T ss_pred             HHHHHHHHH-HHhcccchhheeeeecCCchh-hhhcccCCCchhHHHH-HHHHHhcCCCCceEEEEeehHHHHHHHHHHH
Confidence            345566654 355677788887655556665 6789999999944433 3445666667778999999999999999888


Q ss_pred             HHhcccc--------ceeEEEEECCcccHHH---HHHhcCCCeEEEeC----hHHHHH-HHHcCCCCCCCccEEEeccch
Q 027749          122 LAIGDFI--------NIQAHACVGGKSVGED---IRKLEHGVHVVSGT----PGRVCD-MIKRKTLRTRAIKLLVLDESD  185 (219)
Q Consensus       122 ~~~~~~~--------~~~~~~~~~~~~~~~~---~~~l~~~~~I~v~T----p~~l~~-~l~~~~~~~~~l~~lVvDE~h  185 (219)
                      .+++-..        ..-++.-.||.+...-   .+...+-..+=++-    -....+ ++. ..-+.+-+++|.+||..
T Consensus       227 ~~F~f~~~e~~pdW~~~l~~h~wgG~t~~g~y~~~~~~~~~~~~~fsg~g~~F~~aC~eli~-~~~~~~~yD~ilIDE~Q  305 (660)
T COG3972         227 PEFFFMRVEKQPDWGTKLFCHNWGGLTKEGFYGMYRYICHYYEIPFSGFGNGFDAACKELIA-DINNKKAYDYILIDESQ  305 (660)
T ss_pred             HHHHHHHhhcCCCccceEEEeccCCCCCCcchHHHHHHhcccccccCCCCcchHHHHHHHHH-hhhccccccEEEecccc
Confidence            7775211        1233333455554321   11111101111110    111111 221 11125668999999998


Q ss_pred             hhhccccHHHHHHHHH
Q 027749          186 EMLSRGFKDQIYDVYR  201 (219)
Q Consensus       186 ~l~~~~~~~~~~~i~~  201 (219)
                      .+- .+|.+.+..+.+
T Consensus       306 DFP-~~F~~Lcf~~tk  320 (660)
T COG3972         306 DFP-QSFIDLCFMVTK  320 (660)
T ss_pred             cCC-HHHHHHHHHHhc
Confidence            643 345555555544

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=92.74  E-value=3  Score=34.17  Aligned_cols=41  Identities=15%  Similarity=0.182  Sum_probs=30.2

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEeec
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSC  215 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SAT  215 (219)
                      ...+++|+|++|.|.... ...+.++++.-|++.-+|++|..
T Consensus        94 ~~~kv~ii~~ad~mt~~A-aNaLLK~LEEPp~~~~fiL~~~~  134 (290)
T PRK05917         94 SPYKIYIIHEADRMTLDA-ISAFLKVLEDPPQHGVIILTSAK  134 (290)
T ss_pred             CCceEEEEechhhcCHHH-HHHHHHHhhcCCCCeEEEEEeCC
Confidence            567899999999988543 67777777886666666666543

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=92.72  E-value=0.14  Score=46.71  Aligned_cols=48  Identities=19%  Similarity=0.165  Sum_probs=34.7

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA  123 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~  123 (219)
                      .++++.||||+|||..+++|-+-.+..     .+||+=|-.++........++
T Consensus       140 ~hvlviApTgSGKgvg~VIPnLL~~~g-----S~VV~DpKGE~~~~Ta~~R~~  187 (670)
T PRK13850        140 PHSLVVAPTRAGKGVGVVIPTLLTFKG-----SVIALDVKGELFELTSRARKA  187 (670)
T ss_pred             ceEEEEecCCCCceeeehHhHHhcCCC-----CEEEEeCCchHHHHHHHHHHh
Confidence            489999999999999998887655322     377777777776654444443

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

Probab=92.67  E-value=0.084  Score=43.43  Aligned_cols=18  Identities=22%  Similarity=0.495  Sum_probs=15.1

Q ss_pred             CcEEEEcCCCCchhHHhH
Q 027749           71 RDVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~   88 (219)
                      -|+++.||||||||+.+.
T Consensus        98 SNILLiGPTGsGKTlLAq  115 (408)
T COG1219          98 SNILLIGPTGSGKTLLAQ  115 (408)
T ss_pred             ccEEEECCCCCcHHHHHH
Confidence            379999999999996553

>PRK07773 replicative DNA helicase; Validated

Probab=92.66  E-value=0.44  Score=45.17  Aligned_cols=138  Identities=19%  Similarity=0.198  Sum_probs=66.0

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhc-
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE-  149 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-  149 (219)
                      .-++|.|++|.||| ++.+.++..+..... ..++|.. .-.-..|+..++..........-. -.|..+ ..++..+. 
T Consensus       218 ~livIagrPg~GKT-~fal~ia~~~a~~~~-~~V~~fS-lEms~~ql~~R~~s~~~~i~~~~i-~~g~l~-~~~~~~~~~  292 (886)
T PRK07773        218 QLIIVAARPSMGKT-TFGLDFARNCAIRHR-LAVAIFS-LEMSKEQLVMRLLSAEAKIKLSDM-RSGRMS-DDDWTRLAR  292 (886)
T ss_pred             cEEEEEeCCCCCcH-HHHHHHHHHHHHhcC-CeEEEEe-cCCCHHHHHHHHHHHhcCCCHHHH-hcCCCC-HHHHHHHHH
Confidence            44788999999999 444544444432222 2244443 344455666555433222211111 012222 12222211 


Q ss_pred             -----CCCeEEE-----eChHHHHHHHHcCCCCCCCccEEEeccchhhhcc----ccHHHHHHHHHhCC-----CCCeEE
Q 027749          150 -----HGVHVVS-----GTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR----GFKDQIYDVYRYLP-----PDLQVC  210 (219)
Q Consensus       150 -----~~~~I~v-----~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~----~~~~~~~~i~~~~~-----~~~q~i  210 (219)
                           .+..+.|     .|++.+...+..-.- -..+++||||-.+.|...    +....+..+.+.++     -++.+|
T Consensus       293 a~~~l~~~~i~i~d~~~~~i~~i~~~~r~~~~-~~~~~lvvIDyLql~~~~~~~~~r~~ei~~isr~LK~lAkel~vpvi  371 (886)
T PRK07773        293 AMGEISEAPIFIDDTPNLTVMEIRAKARRLRQ-EANLGLIVVDYLQLMTSGKKYENRQQEVSEISRHLKLLAKELEVPVV  371 (886)
T ss_pred             HHHHHhcCCEEEECCCCCCHHHHHHHHHHHHH-hcCCCEEEEcchhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHCCcEE
Confidence                 2334555     245555443221110 135889999999977532    12233444444442     266777


Q ss_pred             EEee
Q 027749          211 CPGS  214 (219)
Q Consensus       211 ~~SA  214 (219)
                      ++|.
T Consensus       372 ~lsQ  375 (886)
T PRK07773        372 ALSQ  375 (886)
T ss_pred             Eecc
Confidence            7764

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=92.64  E-value=1.9  Score=39.51  Aligned_cols=63  Identities=25%  Similarity=0.335  Sum_probs=42.8

Q ss_pred             EECCcccHHHHHHhcCCCeEEEe-ChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhC
Q 027749          135 CVGGKSVGEDIRKLEHGVHVVSG-TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL  203 (219)
Q Consensus       135 ~~~~~~~~~~~~~l~~~~~I~v~-Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~  203 (219)
                      ..||...+.+++..++.   .|+ -|+++...+...+.   .=-++.+||+|.|.+...++.-..+++.+
T Consensus       382 sLGGvrDEAEIRGHRRT---YIGamPGrIiQ~mkka~~---~NPv~LLDEIDKm~ss~rGDPaSALLEVL  445 (782)
T COG0466         382 SLGGVRDEAEIRGHRRT---YIGAMPGKIIQGMKKAGV---KNPVFLLDEIDKMGSSFRGDPASALLEVL  445 (782)
T ss_pred             ecCccccHHHhcccccc---ccccCChHHHHHHHHhCC---cCCeEEeechhhccCCCCCChHHHHHhhc
Confidence            35777777776666553   344 49999988776432   12369999999999876556666666665

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=92.57  E-value=3.5  Score=33.41  Aligned_cols=24  Identities=13%  Similarity=0.224  Sum_probs=17.2

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhh
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTV   95 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~   95 (219)
                      +++++.+|+|+||| .++-.+...+
T Consensus       112 ~~~~i~g~~g~GKt-tl~~~l~~~~  135 (270)
T TIGR02858       112 LNTLIISPPQCGKT-TLLRDLARIL  135 (270)
T ss_pred             eEEEEEcCCCCCHH-HHHHHHhCcc
Confidence            58999999999999 3333344443

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.

>PF12846 AAA_10: AAA-like domain

Probab=92.57  E-value=0.27  Score=39.75  Aligned_cols=41  Identities=17%  Similarity=0.211  Sum_probs=25.7

Q ss_pred             CccEEEeccchhhhcc-ccHHHHHHHHHhCCC-CCeEEEEeec
Q 027749          175 AIKLLVLDESDEMLSR-GFKDQIYDVYRYLPP-DLQVCCPGSC  215 (219)
Q Consensus       175 ~l~~lVvDE~h~l~~~-~~~~~~~~i~~~~~~-~~q~i~~SAT  215 (219)
                      .-.++++||+|.+... .....+..+++..++ ..-+++.|.+
T Consensus       220 ~~~~i~iDEa~~~~~~~~~~~~~~~~~~~~Rk~g~~~~l~tQ~  262 (304)
T PF12846_consen  220 RPKIIVIDEAHNFLSNPSGAEFLDELLREGRKYGVGLILATQS  262 (304)
T ss_pred             ceEEEEeCCccccccccchhhhhhHHHHHHHhcCCEEEEeeCC
Confidence            3457899999998876 344556666666544 4445555544

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=92.52  E-value=0.35  Score=43.42  Aligned_cols=46  Identities=24%  Similarity=0.369  Sum_probs=28.9

Q ss_pred             HHHHCCCCCChHHHHHHHHHHhC--CCcEEEEcCCCCchhHHhHHHHHhhhc
Q 027749           47 GIYQYGFEKPSAIQQRAVMPIIK--GRDVIAQAQSGTGKTSMIALTVCQTVD   96 (219)
Q Consensus        47 ~l~~~~~~~~~~~Q~~~~~~~~~--~~~~lv~~~tG~GKT~~~~~~~~~~~~   96 (219)
                      .|.+.|+   .+.|...+..+..  +..++++||||||||... ..++..+.
T Consensus       294 ~l~~lg~---~~~~~~~l~~~~~~~~Glilv~G~tGSGKTTtl-~a~l~~~~  341 (564)
T TIGR02538       294 DIDKLGF---EPDQKALFLEAIHKPQGMVLVTGPTGSGKTVSL-YTALNILN  341 (564)
T ss_pred             CHHHcCC---CHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHH-HHHHHhhC
Confidence            3555664   3445556655443  346889999999999543 44555553

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.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=92.50  E-value=1.4  Score=41.70  Aligned_cols=17  Identities=24%  Similarity=0.567  Sum_probs=14.6

Q ss_pred             CcEEEEcCCCCchhHHh
Q 027749           71 RDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~   87 (219)
                      .+.++.||+|+|||...
T Consensus       195 ~n~lL~G~pGvGKT~l~  211 (852)
T TIGR03346       195 NNPVLIGEPGVGKTAIV  211 (852)
T ss_pred             CceEEEcCCCCCHHHHH
Confidence            58999999999999444

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.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=92.46  E-value=0.94  Score=42.75  Aligned_cols=17  Identities=29%  Similarity=0.618  Sum_probs=14.5

Q ss_pred             CcEEEEcCCCCchhHHh
Q 027749           71 RDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~   87 (219)
                      .|.++.||.|+|||...
T Consensus       209 ~n~lLvG~pGvGKTal~  225 (852)
T TIGR03345       209 NNPILTGEAGVGKTAVV  225 (852)
T ss_pred             CceeEECCCCCCHHHHH
Confidence            58999999999999444

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.

>cd01131 PilT Pilus retraction ATPase PilT

Probab=92.46  E-value=0.25  Score=37.96  Aligned_cols=36  Identities=14%  Similarity=0.339  Sum_probs=21.3

Q ss_pred             cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcC
Q 027749           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P  109 (219)
                      -++++||||+|||... ..++..+.... +.+++.+-.
T Consensus         3 lilI~GptGSGKTTll-~~ll~~~~~~~-~~~i~t~e~   38 (198)
T cd01131           3 LVLVTGPTGSGKSTTL-AAMIDYINKNK-THHILTIED   38 (198)
T ss_pred             EEEEECCCCCCHHHHH-HHHHHHhhhcC-CcEEEEEcC
Confidence            3689999999999543 44455443322 223444443

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.

>TIGR02773 addB_Gpos ATP-dependent nuclease subunit B

Probab=92.35  E-value=0.93  Score=44.33  Aligned_cols=41  Identities=15%  Similarity=0.263  Sum_probs=31.5

Q ss_pred             EEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHH
Q 027749           74 IAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELA  114 (219)
Q Consensus        74 lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~  114 (219)
                      +|.|+.|||||...+--+.+.+...+.++..|+++|.+...
T Consensus         5 fi~G~aGSGKT~~l~~ri~~~l~~~~~~~~~illVPeq~TF   45 (1158)
T TIGR02773         5 FIYGRAGTGKSTFCIDEIKQKIKENPLGKPIILIVPDQMTF   45 (1158)
T ss_pred             EEEeCCCCChHHHHHHHHHHHHhhCCCCCcEEEEcCCcccH
Confidence            68899999999666556666665655678899999988644

DNA repair is accomplished by several different systems in prokaryotes. Recombinational repair of double-stranded DNA breaks involves the RecBCD pathway in some lineages, and AddAB (also called RexAB) in other. The AddA protein is conserved between the firmicutes and the alphaproteobacteria, while the partner protein is not. Nevertheless, the partner is designated AddB in both systems. This model describes the AddB protein as found Bacillus subtilis and related species. Although the RexB protein of Streptococcus and Lactococcus is considered to be orthologous, functionally equivalent, and merely named differently, all members of this protein family have a P-loop nucleotide binding motif GxxGxGK[ST] at the N-terminus, unlike RexB proteins, and a CxxCxxxxxC motif at the C-terminus, both of which may be relevant to function.

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=92.34  E-value=0.25  Score=41.46  Aligned_cols=42  Identities=10%  Similarity=0.230  Sum_probs=25.2

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHH
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  112 (219)
                      .+..++++||||+|||.. +..++..+... .+.+++.+-...+
T Consensus       121 ~~g~ili~G~tGSGKTT~-l~al~~~i~~~-~~~~i~tiEdp~E  162 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTT-LASMIDYINKN-AAGHIITIEDPIE  162 (343)
T ss_pred             cCcEEEEECCCCCCHHHH-HHHHHHhhCcC-CCCEEEEEcCChh
Confidence            456899999999999944 34455544332 1234555544333

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.

>cd03289 ABCC_CFTR2 The CFTR subfamily domain 2

Probab=92.32  E-value=0.56  Score=38.07  Aligned_cols=40  Identities=23%  Similarity=0.161  Sum_probs=29.8

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      .+=+++++||.-.-++......+..++.....++.+|+.|
T Consensus       155 ~~p~illlDEpts~LD~~~~~~l~~~l~~~~~~~tii~is  194 (275)
T cd03289         155 SKAKILLLDEPSAHLDPITYQVIRKTLKQAFADCTVILSE  194 (275)
T ss_pred             cCCCEEEEECccccCCHHHHHHHHHHHHHhcCCCEEEEEE
Confidence            4457899999988788777777888887765556666655

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.

>CHL00176 ftsH cell division protein; Validated

Probab=92.32  E-value=0.8  Score=41.73  Aligned_cols=18  Identities=33%  Similarity=0.495  Sum_probs=14.8

Q ss_pred             CCcEEEEcCCCCchhHHh
Q 027749           70 GRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~   87 (219)
                      .+.+++.||+|+|||...
T Consensus       216 p~gVLL~GPpGTGKT~LA  233 (638)
T CHL00176        216 PKGVLLVGPPGTGKTLLA  233 (638)
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            357999999999999443

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

Probab=92.31  E-value=0.22  Score=38.96  Aligned_cols=43  Identities=19%  Similarity=0.406  Sum_probs=28.0

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHH
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELA  114 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~  114 (219)
                      ++++.|.|.||+|||... -.+++.+.. ..+..++|+=|..+=+
T Consensus        23 ~~H~~I~G~TGsGKS~~~-~~ll~~l~~-~~~~~~ii~D~~GEY~   65 (229)
T PF01935_consen   23 NRHIAIFGTTGSGKSNTV-KVLLEELLK-KKGAKVIIFDPHGEYA   65 (229)
T ss_pred             cceEEEECCCCCCHHHHH-HHHHHHHHh-cCCCCEEEEcCCCcch
Confidence            478999999999999444 445555552 2233477776665443

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

>PTZ00110 helicase; Provisional

Probab=92.30  E-value=1.3  Score=39.60  Aligned_cols=74  Identities=18%  Similarity=0.123  Sum_probs=53.9

Q ss_pred             CceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh---c-CCCeEEEeChHHHHHHHHcCCCCCCC
Q 027749          100 REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL---E-HGVHVVSGTPGRVCDMIKRKTLRTRA  175 (219)
Q Consensus       100 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l---~-~~~~I~v~Tp~~l~~~l~~~~~~~~~  175 (219)
                      .+.++||.|+++..++.+...+...    ++.+..++|+.+..++...+   . ....|+|+|.     . ..+++++.+
T Consensus       376 ~~~k~LIF~~t~~~a~~l~~~L~~~----g~~~~~ihg~~~~~eR~~il~~F~~G~~~ILVaTd-----v-~~rGIDi~~  445 (545)
T PTZ00110        376 DGDKILIFVETKKGADFLTKELRLD----GWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATD-----V-ASRGLDVKD  445 (545)
T ss_pred             cCCeEEEEecChHHHHHHHHHHHHc----CCcEEEEECCCcHHHHHHHHHHHhcCCCcEEEEcc-----h-hhcCCCccc
Confidence            3567999999999999888887643    56777888887766554332   2 3578999993     2 256788888


Q ss_pred             ccEEEecc
Q 027749          176 IKLLVLDE  183 (219)
Q Consensus       176 l~~lVvDE  183 (219)
                      +++||.=+
T Consensus       446 v~~VI~~d  453 (545)
T PTZ00110        446 VKYVINFD  453 (545)
T ss_pred             CCEEEEeC
Confidence            98877543

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=92.28  E-value=2.3  Score=35.35  Aligned_cols=107  Identities=19%  Similarity=0.356  Sum_probs=54.2

Q ss_pred             EEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCC--HHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcC
Q 027749           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT--RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH  150 (219)
Q Consensus        73 ~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~--~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  150 (219)
                      ++++|..|+|||....= +.+.+..+  +.++++.+--  |+-|.   +.++.|.+..++.++..-.|..          
T Consensus       142 il~vGVNG~GKTTTIaK-LA~~l~~~--g~~VllaA~DTFRAaAi---EQL~~w~er~gv~vI~~~~G~D----------  205 (340)
T COG0552         142 ILFVGVNGVGKTTTIAK-LAKYLKQQ--GKSVLLAAGDTFRAAAI---EQLEVWGERLGVPVISGKEGAD----------  205 (340)
T ss_pred             EEEEecCCCchHhHHHH-HHHHHHHC--CCeEEEEecchHHHHHH---HHHHHHHHHhCCeEEccCCCCC----------
Confidence            67899999999955433 33444433  3345555543  23332   3344444455666654211111          


Q ss_pred             CCeEEEeChHHH-HHHHHcCCCCCCCccEEEeccchhhhcc-ccHHHHHHHHHhCCC
Q 027749          151 GVHVVSGTPGRV-CDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPP  205 (219)
Q Consensus       151 ~~~I~v~Tp~~l-~~~l~~~~~~~~~l~~lVvDE~h~l~~~-~~~~~~~~i~~~~~~  205 (219)
                              |... .+.+....  .+++++|++|=|=+|... +.-..+.+|.+.+.+
T Consensus       206 --------pAaVafDAi~~Ak--ar~~DvvliDTAGRLhnk~nLM~EL~KI~rV~~k  252 (340)
T COG0552         206 --------PAAVAFDAIQAAK--ARGIDVVLIDTAGRLHNKKNLMDELKKIVRVIKK  252 (340)
T ss_pred             --------cHHHHHHHHHHHH--HcCCCEEEEeCcccccCchhHHHHHHHHHHHhcc
Confidence                    2211 12222211  245666777776666543 455566666666544

>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]

Probab=92.27  E-value=3.1  Score=35.37  Aligned_cols=45  Identities=16%  Similarity=0.176  Sum_probs=31.4

Q ss_pred             CCccEEEeccchhhhccc--cHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          174 RAIKLLVLDESDEMLSRG--FKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~--~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      +..-+||+|.+|.+-+.+  ....+.++-+-++.+.-.|.+|++..+
T Consensus       114 d~~~~liLDnad~lrD~~a~ll~~l~~L~el~~~~~i~iils~~~~e  160 (438)
T KOG2543|consen  114 DQKVFLILDNADALRDMDAILLQCLFRLYELLNEPTIVIILSAPSCE  160 (438)
T ss_pred             CceEEEEEcCHHhhhccchHHHHHHHHHHHHhCCCceEEEEeccccH
Confidence            345689999999998875  334455555556666667888887764

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

Probab=92.22  E-value=0.29  Score=37.60  Aligned_cols=28  Identities=14%  Similarity=0.324  Sum_probs=16.9

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhc
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVD   96 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~   96 (219)
                      ...+++|.|.||+|||.+....+...+.
T Consensus        37 ~~~h~li~G~tgsGKS~~l~~ll~~l~~   64 (205)
T PF01580_consen   37 KNPHLLIAGATGSGKSTLLRTLLLSLAL   64 (205)
T ss_dssp             GS-SEEEE--TTSSHHHHHHHHHHHHHT
T ss_pred             CCceEEEEcCCCCCccHHHHHHHHHHHH
Confidence            3458999999999999554443444443

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

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=92.16  E-value=6  Score=32.85  Aligned_cols=18  Identities=28%  Similarity=0.420  Sum_probs=14.1

Q ss_pred             CcEEEEcCCCCchhHHhH
Q 027749           71 RDVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~   88 (219)
                      +-+.+.||+|+|||....
T Consensus       115 ~vi~lvGpnGsGKTTt~~  132 (318)
T PRK10416        115 FVILVVGVNGVGKTTTIG  132 (318)
T ss_pred             eEEEEECCCCCcHHHHHH
Confidence            347789999999995543

>TIGR03743 SXT_TraD conjugative coupling factor TraD, SXT/TOL subfamily

Probab=92.16  E-value=0.59  Score=42.53  Aligned_cols=55  Identities=16%  Similarity=0.273  Sum_probs=36.8

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHH--HHHHHHHHHHHhccc
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE--LATQTEKVILAIGDF  127 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~--l~~q~~~~~~~~~~~  127 (219)
                      .++++|.|+||+|||..+...+.+.+..   +..++++=|-..  +...+...++..+..
T Consensus       176 ~~H~lv~G~TGsGKT~l~~~l~~q~i~~---g~~viv~DpKgD~~l~~~~~~~~~~~G~~  232 (634)
T TIGR03743       176 VGHTLVLGTTGVGKTRLAELLITQDIRR---GDVVIVIDPKGDADLKRRMRAEAKRAGRP  232 (634)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEeCCCchHHHHHHHHHHHHhCCC
Confidence            3689999999999996664444444443   234777777654  666777777666543

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.

>PRK10867 signal recognition particle protein; Provisional

Probab=92.15  E-value=3  Score=36.22  Aligned_cols=18  Identities=22%  Similarity=0.357  Sum_probs=14.3

Q ss_pred             EEEEcCCCCchhHHhHHH
Q 027749           73 VIAQAQSGTGKTSMIALT   90 (219)
Q Consensus        73 ~lv~~~tG~GKT~~~~~~   90 (219)
                      ++++|++|+|||....-.
T Consensus       103 I~~vG~~GsGKTTtaakL  120 (433)
T PRK10867        103 IMMVGLQGAGKTTTAGKL  120 (433)
T ss_pred             EEEECCCCCcHHHHHHHH
Confidence            679999999999655443

>COG1132 MdlB ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]

Probab=92.06  E-value=0.43  Score=42.77  Aligned_cols=39  Identities=23%  Similarity=0.225  Sum_probs=27.1

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEE
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCP  212 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~  212 (219)
                      ++=.++|+||+.--+|..-+..+.+.++.+.++..++..
T Consensus       482 ~~~~ILILDEaTSalD~~tE~~I~~~l~~l~~~rT~iiI  520 (567)
T COG1132         482 RNPPILILDEATSALDTETEALIQDALKKLLKGRTTLII  520 (567)
T ss_pred             cCCCEEEEeccccccCHHhHHHHHHHHHHHhcCCEEEEE
Confidence            444799999999888876677777777655555444433

>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=92.06  E-value=0.2  Score=42.67  Aligned_cols=43  Identities=21%  Similarity=0.403  Sum_probs=25.1

Q ss_pred             hCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHH
Q 027749           68 IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (219)
Q Consensus        68 ~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l  113 (219)
                      ...+++++.|.||+|||. ++..++..+...+  -++||.=|..+.
T Consensus        13 ~e~~~~li~G~~GsGKT~-~i~~ll~~~~~~g--~~~iI~D~kg~~   55 (386)
T PF10412_consen   13 SENRHILIIGATGSGKTQ-AIRHLLDQIRARG--DRAIIYDPKGEF   55 (386)
T ss_dssp             GGGG-EEEEE-TTSSHHH-HHHHHHHHHHHTT---EEEEEEETTHH
T ss_pred             hhhCcEEEECCCCCCHHH-HHHHHHHHHHHcC--CEEEEEECCchH
Confidence            455799999999999995 5556666554432  234444444333

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.

>PLN03232 ABC transporter C family member; Provisional

Probab=92.03  E-value=0.3  Score=48.88  Aligned_cols=39  Identities=23%  Similarity=0.146  Sum_probs=27.6

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEE
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCP  212 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~  212 (219)
                      ++=+.+|+||+---+|..-...+++.++...+++-+|..
T Consensus      1388 r~~~ILILDEATSaLD~~Te~~Iq~~L~~~~~~~TvI~I 1426 (1495)
T PLN03232       1388 RRSKILVLDEATASVDVRTDSLIQRTIREEFKSCTMLVI 1426 (1495)
T ss_pred             hCCCEEEEECCcccCCHHHHHHHHHHHHHHcCCCEEEEE
Confidence            445789999998777776677787777776555555544

>TIGR00609 recB exodeoxyribonuclease V, beta subunit

Probab=91.91  E-value=0.41  Score=46.37  Aligned_cols=54  Identities=20%  Similarity=0.167  Sum_probs=42.4

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhccC--CCceeEEEEcCCHHHHHHHHHHHHHh
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDTS--SREVQALILSPTRELATQTEKVILAI  124 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~~--~~~~~~lil~P~~~l~~q~~~~~~~~  124 (219)
                      ...+|.|..|+|||.+...-.+..+...  -...++|+|+=|++-+.++.+++++.
T Consensus        10 G~~lieAsAGtGKT~ti~~~~lrll~~~~~~~~~~iLvvTFT~aAt~el~~RIr~r   65 (1087)
T TIGR00609        10 GTFLIEASAGTGKTFTIAQLYLRLLLEGGPLTVEEILVVTFTNAATEELKTRIRGR   65 (1087)
T ss_pred             CCEEEEECCCCCHHHHHHHHHHHHHhcCCCCChhhEEEEehhHHHHHHHHHHHHHH
Confidence            3678999999999977766666655543  23357999999999999999998764

All proteins in this family for which functions are known are DNA-DNA helicases that are used as part of an exonuclease-helicase complex (made up of RecBCD homologs) that function to generate substrates for the initiation of recombination and recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=91.87  E-value=3.6  Score=30.99  Aligned_cols=44  Identities=20%  Similarity=0.348  Sum_probs=31.9

Q ss_pred             CCCccEEEeccchhhhcccc--HHHHHHHHHhCCCCCeEEEEeecc
Q 027749          173 TRAIKLLVLDESDEMLSRGF--KDQIYDVYRYLPPDLQVCCPGSCF  216 (219)
Q Consensus       173 ~~~l~~lVvDE~h~l~~~~~--~~~~~~i~~~~~~~~q~i~~SATl  216 (219)
                      -..+++||+||+-..++.++  .+.+..+++.-|.+.-+|+-.-..
T Consensus        95 ~~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~  140 (173)
T TIGR00708        95 DPELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGC  140 (173)
T ss_pred             cCCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCC
Confidence            35789999999998887763  356778888877776666544433

Alternate name: corrinoid adenosyltransferase.

>PHA00012 I assembly protein

Probab=91.80  E-value=2.1  Score=35.65  Aligned_cols=25  Identities=16%  Similarity=0.251  Sum_probs=19.1

Q ss_pred             EEEEcCCCCchhHHhHHHHHhhhcc
Q 027749           73 VIAQAQSGTGKTSMIALTVCQTVDT   97 (219)
Q Consensus        73 ~lv~~~tG~GKT~~~~~~~~~~~~~   97 (219)
                      .++.|..|+|||+.....+...+.+
T Consensus         4 ylITGkPGSGKSl~aV~~I~~~L~~   28 (361)
T PHA00012          4 YVVTGKLGAGKTLVAVSRIQDKLVK   28 (361)
T ss_pred             EEEecCCCCCchHHHHHHHHHHHHc
Confidence            4789999999998777766555544

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

Probab=91.77  E-value=0.31  Score=39.26  Aligned_cols=17  Identities=35%  Similarity=0.552  Sum_probs=13.8

Q ss_pred             cEEEEcCCCCchhHHhH
Q 027749           72 DVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~   88 (219)
                      =++++|+|||||+....
T Consensus       129 LviiVGaTGSGKSTtmA  145 (375)
T COG5008         129 LVIIVGATGSGKSTTMA  145 (375)
T ss_pred             eEEEECCCCCCchhhHH
Confidence            47899999999995543

>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=91.70  E-value=1.7  Score=31.45  Aligned_cols=38  Identities=21%  Similarity=0.221  Sum_probs=25.6

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      .+-+++++||.-.=++......+..+++.+.  ..+++.|
T Consensus        87 ~~p~illlDEP~~~LD~~~~~~l~~~l~~~~--~til~~t  124 (144)
T cd03221          87 ENPNLLLLDEPTNHLDLESIEALEEALKEYP--GTVILVS  124 (144)
T ss_pred             cCCCEEEEeCCccCCCHHHHHHHHHHHHHcC--CEEEEEE
Confidence            4557899999887677666677777777663  3444443

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.

>cd01127 TrwB Bacterial conjugation protein TrwB, ATP binding domain

Probab=91.65  E-value=0.23  Score=42.71  Aligned_cols=28  Identities=18%  Similarity=0.251  Sum_probs=19.8

Q ss_pred             HhCCCcEEEEcCCCCchhHHhHHHHHhhh
Q 027749           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTV   95 (219)
Q Consensus        67 ~~~~~~~lv~~~tG~GKT~~~~~~~~~~~   95 (219)
                      -...+++++.|+||+|||.. +..++..+
T Consensus        39 ~~~~~h~~i~g~tGsGKt~~-i~~l~~~~   66 (410)
T cd01127          39 DAEEAHTMIIGTTGTGKTTQ-IRELLASI   66 (410)
T ss_pred             chhhccEEEEcCCCCCHHHH-HHHHHHHH
Confidence            34457999999999999964 44444443

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

>PRK10865 protein disaggregation chaperone; Provisional

Probab=91.58  E-value=1.7  Score=41.19  Aligned_cols=17  Identities=24%  Similarity=0.567  Sum_probs=14.5

Q ss_pred             CcEEEEcCCCCchhHHh
Q 027749           71 RDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~   87 (219)
                      .+.++.||+|+|||...
T Consensus       200 ~n~lL~G~pGvGKT~l~  216 (857)
T PRK10865        200 NNPVLIGEPGVGKTAIV  216 (857)
T ss_pred             CceEEECCCCCCHHHHH
Confidence            48999999999999444

>TIGR03754 conj_TOL_TraD conjugative coupling factor TraD, TOL family

Probab=91.45  E-value=0.89  Score=41.28  Aligned_cols=55  Identities=15%  Similarity=0.236  Sum_probs=39.3

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCH--HHHHHHHHHHHHhccc
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR--ELATQTEKVILAIGDF  127 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~--~l~~q~~~~~~~~~~~  127 (219)
                      ..+++|.|+||+|||......+.+.+..   +..++++=|..  ++...++..++..+..
T Consensus       180 ~gHtlV~GtTGsGKT~l~~~li~q~i~~---g~~vi~fDpkgD~el~~~~~~~~~~~GR~  236 (643)
T TIGR03754       180 VGHTLVLGTTRVGKTRLAELLITQDIRR---GDVVIVFDPKGDADLLKRMYAEAKRAGRL  236 (643)
T ss_pred             cCceEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEeCCCCHHHHHHHHHHHHHhCCC
Confidence            3589999999999997766655555543   34577777766  4667777777777653

Members of this protein are assigned by homology to the TraD family of conjugative coupling factor. This particular clade serves as a marker for an extended gene region that occurs occasionally on plasmids, including the toluene catabolism TOL plasmid. More commonly, the gene region is chromosomal, flanked by various markers of conjugative transfer and insertion.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	219
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		4e-77
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		5e-77
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		5e-77
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		7e-77
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		4e-74
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		1e-73
3bor_A	237	Crystal Structure Of The Deadc Domain Of Human Tran		3e-59
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		2e-58
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		4e-58
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		4e-54
1qde_A	224	Crystal Structure Of The Atpase Domain Of Translati		5e-54
1qva_A	223	Yeast Initiation Factor 4a N-Terminal Domain Length		1e-53
2g9n_A	221	Structure Of The Dead Domain Of Human Eukaryotic In		6e-53
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		2e-50
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		1e-36
2kbe_A	226	Solution Structure Of Amino-Terminal Domain Of Dbp5		4e-32
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		6e-32
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		7e-32
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		5e-31
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		4e-26
2oxc_A	230	Human Dead-Box Rna Helicase Ddx20, Dead Domain In C		9e-26
3fhc_B	235	Crystal Structure Of Human Dbp5 In Complex With Nup		4e-25
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		5e-25
3fmo_B	300	Crystal Structure Of The Nucleoporin Nup214 In Comp		5e-25
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		7e-25
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		8e-25
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		8e-25
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		8e-25
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		2e-24
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		7e-24
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		7e-24
1t6n_A	220	Crystal Structure Of The N-Terminal Domain Of Human		8e-24
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		2e-23
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		2e-23
1q0u_A	219	Crystal Structure Of The Bstdead N-Terminal Domain		3e-23
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		4e-22
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		2e-20
3ly5_A	262	Ddx18 Dead-Domain Length = 262		2e-19
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		2e-19
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		1e-18
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		3e-18
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		3e-18
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		3e-18
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		8e-18
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		9e-17
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		6e-15
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		2e-14
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		2e-14
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		2e-14

>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 =  283 bits (725), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 130/191 (68%), Positives = 164/191 (85%)
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 YRYLPPDLQVC 210
           YRYLPP  QV 
Sbjct: 205 YRYLPPATQVV 215

>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 =  283 bits (724), Expect = 5e-77,   Method: Compositional matrix adjust.
 Identities = 130/191 (68%), Positives = 164/191 (85%)
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 YRYLPPDLQVC 210
           YRYLPP  QV 
Sbjct: 205 YRYLPPATQVV 215

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

Iteration: 1
 Score =  283 bits (724), Expect = 5e-77,   Method: Compositional matrix adjust.
 Identities = 130/191 (68%), Positives = 164/191 (85%)
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 YRYLPPDLQVC 210
           YRYLPP  QV 
Sbjct: 204 YRYLPPATQVV 214

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

Iteration: 1
 Score =  283 bits (723), Expect = 7e-77,   Method: Compositional matrix adjust.
 Identities = 130/191 (68%), Positives = 164/191 (85%)
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 YRYLPPDLQVC 210
           YRYLPP  QV 
Sbjct: 183 YRYLPPATQVV 193

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

Iteration: 1
 Score =  273 bits (699), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 124/177 (70%), Positives = 156/177 (88%)
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 VVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVC 210
           VV+GTPGRV DMI+R++LRTRAIK+LVLDE+DEML++GFK+QIYDVYRYLPP  QV 
Sbjct: 122 VVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVV 178

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

Iteration: 1
 Score =  272 bits (695), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 124/176 (70%), Positives = 155/176 (88%)
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 VVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQV 209
           VV+GTPGRV DMI+R++LRTRAIK+LVLDE+DEML++GFK+QIYDVYRYLPP  QV
Sbjct: 122 VVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQV 177

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

Iteration: 1
 Score =  224 bits (570), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 104/181 (57%), Positives = 140/181 (77%), Gaps = 1/181 (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 V 209
           V
Sbjct: 207 V 207

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score =  221 bits (563), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 101/182 (55%), Positives = 138/182 (75%), Gaps = 1/182 (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 VC 210
           V 
Sbjct: 191 VV 192

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score =  221 bits (562), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 101/182 (55%), Positives = 138/182 (75%), Gaps = 1/182 (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 VC 210
           V 
Sbjct: 217 VV 218

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score =  207 bits (527), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 97/182 (53%), Positives = 131/182 (71%), Gaps = 1/182 (0%)
Query: 30  EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIAL 89
           + +  FD M + ++LLRG++ YGFE+PSAIQQRA+MPII+G DV+AQAQSGTGKT   ++
Sbjct: 19  KVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSI 78
Query: 90  TVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE 149
              Q +DTS +  QAL+L+PTRELA Q +KV++A+   ++I+ HAC+GG S  ED   L 
Sbjct: 79  AALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR 138
Query: 150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQV 209
               +V GTPGRV D I+R+  RT  IK+ +LDE+DEMLS GFK+QIY ++  LPP  QV
Sbjct: 139 DA-QIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQV 197
Query: 210 CC 211
Sbjct: 198 VL 199

>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 =  207 bits (526), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 97/182 (53%), Positives = 131/182 (71%), Gaps = 1/182 (0%)
Query: 30  EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIAL 89
           + +  FD M + ++LLRG++ YGFE+PSAIQQRA+MPII+G DV+AQAQSGTGKT   ++
Sbjct: 11  KVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSI 70
Query: 90  TVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE 149
              Q +DTS +  QAL+L+PTRELA Q +KV++A+   ++I+ HAC+GG S  ED   L 
Sbjct: 71  AALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR 130
Query: 150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQV 209
               +V GTPGRV D I+R+  RT  IK+ +LDE+DEMLS GFK+QIY ++  LPP  QV
Sbjct: 131 DA-QIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQV 189
Query: 210 CC 211
Sbjct: 190 VL 191

>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain Length = 223

Iteration: 1
 Score =  205 bits (522), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 97/182 (53%), Positives = 130/182 (71%), Gaps = 1/182 (0%)
Query: 30  EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIAL 89
           + +  FD M + + LLRG++ YGFE+PSAIQQRA+MPII+G DV+AQAQSGTGKT   ++
Sbjct: 18  KVVYKFDDMELDEQLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSI 77
Query: 90  TVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE 149
              Q +DTS +  QAL+L+PTRELA Q +KV++A+   ++I+ HAC+GG S  ED   L 
Sbjct: 78  AALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR 137
Query: 150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQV 209
               +V GTPGRV D I+R+  RT  IK+ +LDE+DEMLS GFK+QIY ++  LPP  QV
Sbjct: 138 DA-QIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQV 196
Query: 210 CC 211
Sbjct: 197 VL 198

>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic Initiation Factor 4a, Eif4a Length = 221

Iteration: 1
 Score =  203 bits (517), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 94/181 (51%), Positives = 129/181 (71%), Gaps = 1/181 (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 V 209
           V
Sbjct: 192 V 192

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score =  194 bits (494), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 94/180 (52%), Positives = 123/180 (68%), Gaps = 1/180 (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 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCC 211
             +V GTPGRV D I+R+  RT  IK  +LDE+DE LS GFK+QIY ++  LPP  QV  
Sbjct: 140 -QIVVGTPGRVFDNIQRRRFRTDKIKXFILDEADEXLSSGFKEQIYQIFTLLPPTTQVVL 198

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

Iteration: 1
 Score =  149 bits (375), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 74/184 (40%), Positives = 110/184 (59%)
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 HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCP 212
           H++ GTPGRV D+  RK        L ++DE+D+MLSR FK  I  +  +LPP  Q    
Sbjct: 141 HILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSLLF 200
Query: 213 GSCF 216
            + F
Sbjct: 201 SATF 204

>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p Length = 226

Iteration: 1
 Score =  134 bits (337), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 75/187 (40%), Positives = 113/187 (60%), Gaps = 9/187 (4%)
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         +  + 
Sbjct: 82  MLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFE----KNKQI 137
Query: 151 GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML-SRGFKDQIYDVYRYLPPDLQV 209
              V+ GTPG V D+++RK ++ + IK+ VLDE+D ML  +G  DQ   V R+LP D Q+
Sbjct: 138 NAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQL 197
Query: 210 CCPGSCF 216
               + F
Sbjct: 198 VLFSATF 204

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score =  133 bits (335), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 74/186 (39%), Positives = 112/186 (60%), Gaps = 7/186 (3%)
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-SRGFKDQIYDVYRYLPPDLQVC 210
             V+ GTPG V D+++RK ++ + IK+ VLDE+D ML  +G  DQ   V R+LP D Q+ 
Sbjct: 122 AQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLV 181
Query: 211 CPGSCF 216
              + F
Sbjct: 182 LFSATF 187

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score =  133 bits (335), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 74/186 (39%), Positives = 112/186 (60%), Gaps = 7/186 (3%)
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-SRGFKDQIYDVYRYLPPDLQVC 210
             V+ GTPG V D+++RK ++ + IK+ VLDE+D ML  +G  DQ   V R+LP D Q+ 
Sbjct: 122 AQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLV 181
Query: 211 CPGSCF 216
              + F
Sbjct: 182 LFSATF 187

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

Iteration: 1
 Score =  130 bits (328), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 62/185 (33%), Positives = 114/185 (61%), Gaps = 1/185 (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 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCC 211
           VHVV  TPGR+ D+IK+   +   ++++VLDE+D++LS+ F   + D+   LP + Q+  
Sbjct: 123 VHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILL 182
Query: 212 PGSCF 216
             + F
Sbjct: 183 YSATF 187

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

Iteration: 1
 Score =  114 bits (285), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 59/161 (36%), Positives = 103/161 (63%), Gaps = 5/161 (3%)
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-GIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALKNA 124
Query: 152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF 192
            ++V GTPGR+ D I R TL  + +K  +LDE+DE L+ GF
Sbjct: 125 -NIVVGTPGRILDHINRGTLNLKNVKYFILDEADEXLNXGF 164

>pdb|2OXC|A Chain A, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex With Adp Length = 230

Iteration: 1
 Score =  113 bits (282), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 64/178 (35%), Positives = 107/178 (60%), Gaps = 5/178 (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-FKDQIYDVYRYLPPDLQV 209
           H+  G+PGR+  +I+   L   +I+L +LDE+D++L  G F++QI  +Y  LP   Q+
Sbjct: 144 HIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQM 201

>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214 Length = 235

Iteration: 1
 Score =  110 bits (276), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 74/194 (38%), Positives = 113/194 (58%), Gaps = 14/194 (7%)
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-KRKTLRTRAIKLLVLDESDEML-SRGFKDQIYDVYRY 202
           I +      +V GTPG V D   K K +  + IK+ VLDE+D M+ ++G +DQ   + R 
Sbjct: 142 ISE-----QIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRM 196
Query: 203 LPPDLQVCCPGSCF 216
           LP + Q+    + F
Sbjct: 197 LPRNCQMLLFSATF 210

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

Iteration: 1
 Score =  110 bits (276), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 60/178 (33%), Positives = 99/178 (55%), Gaps = 1/178 (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-KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPD 206
              H++  TPGR+ D ++  K    RA+K LV+DE+D +L+  F+ ++  + + +P D
Sbjct: 160 KKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRILNMDFETEVDKILKVIPRD 217

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

Iteration: 1
 Score =  110 bits (276), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 74/196 (37%), Positives = 112/196 (57%), Gaps = 18/196 (9%)
Query: 31  AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII---KGRDVIAQAQSGTGKTSMI 87
           ++ SF+ + +K  LL+G+Y  GF +PS IQ+ A +P++     +++IAQ+QSGTGKT+  
Sbjct: 90  SVKSFEELRLKPQLLQGVYAMGFNRPSKIQENA-LPLMLAEPPQNLIAQSQSGTGKTAAF 148
Query: 88  ALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIR 146
            L +   V+ +++  Q L LSPT ELA QT KVI  +G F   ++    V G        
Sbjct: 149 VLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRG-------N 201
Query: 147 KLEHGV----HVVSGTPGRVCDMI-KRKTLRTRAIKLLVLDESDEML-SRGFKDQIYDVY 200
           KLE G      +V GTPG V D   K K +  + IK+ VLDE+D M+ ++G +DQ   + 
Sbjct: 202 KLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQ 261
Query: 201 RYLPPDLQVCCPGSCF 216
           R LP + Q+    + F
Sbjct: 262 RMLPRNCQMLLFSATF 277

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

Iteration: 1
 Score =  110 bits (274), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 74/196 (37%), Positives = 112/196 (57%), Gaps = 18/196 (9%)
Query: 31  AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG---RDVIAQAQSGTGKTSMI 87
           ++ SF+ + +K  LL+G+Y  GF +PS IQ+ A +P++     +++IAQ+QSGTGKT+  
Sbjct: 90  SVKSFEELRLKPQLLQGVYAMGFNRPSKIQENA-LPLMLAEPPQNLIAQSQSGTGKTAAF 148
Query: 88  ALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIR 146
            L +   V+ +++  Q L LSPT ELA QT KVI  +G F   ++    V G        
Sbjct: 149 VLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGN------- 201
Query: 147 KLEHGV----HVVSGTPGRVCDMI-KRKTLRTRAIKLLVLDESDEML-SRGFKDQIYDVY 200
           KLE G      +V GTPG V D   K K +  + IK+ VLDE+D M+ ++G +DQ   + 
Sbjct: 202 KLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQ 261
Query: 201 RYLPPDLQVCCPGSCF 216
           R LP + Q+    + F
Sbjct: 262 RMLPRNCQMLLFSATF 277

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

Iteration: 1
 Score =  110 bits (274), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 74/196 (37%), Positives = 112/196 (57%), Gaps = 18/196 (9%)
Query: 31  AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG---RDVIAQAQSGTGKTSMI 87
           ++ SF+ + +K  LL+G+Y  GF +PS IQ+ A +P++     +++IAQ+QSGTGKT+  
Sbjct: 60  SVKSFEELRLKPQLLQGVYAMGFNRPSKIQENA-LPLMLAEPPQNLIAQSQSGTGKTAAF 118
Query: 88  ALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIR 146
            L +   V+ +++  Q L LSPT ELA QT KVI  +G F   ++    V G        
Sbjct: 119 VLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGN------- 171
Query: 147 KLEHGV----HVVSGTPGRVCDMI-KRKTLRTRAIKLLVLDESDEML-SRGFKDQIYDVY 200
           KLE G      +V GTPG V D   K K +  + IK+ VLDE+D M+ ++G +DQ   + 
Sbjct: 172 KLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQ 231
Query: 201 RYLPPDLQVCCPGSCF 216
           R LP + Q+    + F
Sbjct: 232 RMLPRNCQMLLFSATF 247

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

Iteration: 1
 Score =  110 bits (274), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 74/196 (37%), Positives = 112/196 (57%), Gaps = 18/196 (9%)
Query: 31  AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG---RDVIAQAQSGTGKTSMI 87
           ++ SF+ + +K  LL+G+Y  GF +PS IQ+ A +P++     +++IAQ+QSGTGKT+  
Sbjct: 39  SVKSFEELRLKPQLLQGVYAMGFNRPSKIQENA-LPLMLAEPPQNLIAQSQSGTGKTAAF 97
Query: 88  ALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIR 146
            L +   V+ +++  Q L LSPT ELA QT KVI  +G F   ++    V G        
Sbjct: 98  VLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGN------- 150
Query: 147 KLEHGV----HVVSGTPGRVCDMI-KRKTLRTRAIKLLVLDESDEML-SRGFKDQIYDVY 200
           KLE G      +V GTPG V D   K K +  + IK+ VLDE+D M+ ++G +DQ   + 
Sbjct: 151 KLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQ 210
Query: 201 RYLPPDLQVCCPGSCF 216
           R LP + Q+    + F
Sbjct: 211 RMLPRNCQMLLFSATF 226

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score =  110 bits (274), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 74/196 (37%), Positives = 112/196 (57%), Gaps = 18/196 (9%)
Query: 31  AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG---RDVIAQAQSGTGKTSMI 87
           ++ SF+ + +K  LL+G+Y  GF +PS IQ+ A +P++     +++IAQ+QSGTGKT+  
Sbjct: 23  SVKSFEELRLKPQLLQGVYAMGFNRPSKIQENA-LPLMLAEPPQNLIAQSQSGTGKTAAF 81
Query: 88  ALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIR 146
            L +   V+ +++  Q L LSPT ELA QT KVI  +G F   ++    V G        
Sbjct: 82  VLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGN------- 134
Query: 147 KLEHGV----HVVSGTPGRVCDMI-KRKTLRTRAIKLLVLDESDEML-SRGFKDQIYDVY 200
           KLE G      +V GTPG V D   K K +  + IK+ VLDE+D M+ ++G +DQ   + 
Sbjct: 135 KLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQ 194
Query: 201 RYLPPDLQVCCPGSCF 216
           R LP + Q+    + F
Sbjct: 195 RMLPRNCQMLLFSATF 210

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

Iteration: 1
 Score =  108 bits (270), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 60/180 (33%), Positives = 97/180 (53%), Gaps = 5/180 (2%)
Query: 35  FDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQT 94
           F    +K ++L  ++  G   P+ IQ  A+   ++G+D+I QA++GTGKT   AL + + 
Sbjct: 3   FKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAER 62
Query: 95  VDTSS---REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG 151
           +  S    R+ +AL+L+PTRELA Q    + A+   + + A    GG   G+    L  G
Sbjct: 63  LAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVVA--VYGGTGYGKQKEALLRG 120
Query: 152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCC 211
              V  TPGR  D +++  L    +++ VLDE+DEMLS GF++++  +    PP  Q   
Sbjct: 121 ADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLL 180

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

Iteration: 1
 Score =  107 bits (266), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 59/180 (32%), Positives = 97/180 (53%), Gaps = 5/180 (2%)
Query: 35  FDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQT 94
           F    +K ++L  ++  G   P+ I+  A+   ++G+D+I QA++GTGKT   AL + + 
Sbjct: 3   FKDFPLKPEILEALHGRGLTTPTPIEAAALPLALEGKDLIGQARTGTGKTLAFALPIAER 62
Query: 95  VDTSS---REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG 151
           +  S    R+ +AL+L+PTRELA Q    + A+   + + A    GG   G+    L  G
Sbjct: 63  LAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVVA--VYGGTGYGKQKEALLRG 120
Query: 152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCC 211
              V  TPGR  D +++  L    +++ VLDE+DEMLS GF++++  +    PP  Q   
Sbjct: 121 ADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLL 180

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score =  107 bits (266), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 61/181 (33%), Positives = 100/181 (55%), Gaps = 3/181 (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 V 209
           V
Sbjct: 186 V 186

>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56 Length = 220

Iteration: 1
 Score =  106 bits (265), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 61/180 (33%), Positives = 98/180 (54%), Gaps = 3/180 (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

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score =  105 bits (263), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 61/180 (33%), Positives = 98/180 (54%), Gaps = 3/180 (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

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score =  105 bits (262), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 61/180 (33%), Positives = 98/180 (54%), Gaps = 3/180 (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

>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain Length = 219

Iteration: 1
 Score =  104 bits (260), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 63/182 (34%), Positives = 91/182 (50%), Gaps = 4/182 (2%)
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 LQ 208
           LQ
Sbjct: 182 LQ 183

>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 =  101 bits (251), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 60/181 (33%), Positives = 100/181 (55%), Gaps = 15/181 (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 I 196
           I
Sbjct: 195 I 195

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

Iteration: 1
 Score = 92.0 bits (227), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 53/182 (29%), Positives = 102/182 (56%), Gaps = 13/182 (7%)
Query: 33  TSFDAM--GIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALT 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 DIRKLEHGVHVVSGTPGRVCDMIKRKT-LRTRAIKLLVLDESDEMLSRGFKDQIYDVYRY 202
           + +KL +G++++  TPGR+ D ++       + ++ LV+DE+D +L  GF++++  + + 
Sbjct: 169 EAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKL 228
Query: 203 LP 204
           LP
Sbjct: 229 LP 230

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

Iteration: 1
 Score = 92.0 bits (227), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 61/184 (33%), Positives = 96/184 (52%), Gaps = 20/184 (10%)
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 KDQI 196
           + QI
Sbjct: 193 EPQI 196

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

Iteration: 1
 Score = 89.4 bits (220), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 61/187 (32%), Positives = 97/187 (51%), Gaps = 7/187 (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 CCPGSCF 216
               + +
Sbjct: 202 VMTSATW 208

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

Iteration: 1
 Score = 88.6 bits (218), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 55/174 (31%), Positives = 90/174 (51%), Gaps = 9/174 (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 EDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQI 196
                +  G HVV  TPGR+ D + R  +     + +VLDE+D ML  GF + +
Sbjct: 171 HQNECITRGCHVVIATPGRLLDFVDRTFITFEDTRFVVLDEADRMLDMGFSEDM 224

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

Iteration: 1
 Score = 88.2 bits (217), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 56/184 (30%), Positives = 89/184 (48%), Gaps = 5/184 (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 PDLQ 208
           PD Q
Sbjct: 206 PDRQ 209

>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 = 88.2 bits (217), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 56/184 (30%), Positives = 89/184 (48%), Gaps = 5/184 (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 PDLQ 208
           PD Q
Sbjct: 220 PDRQ 223

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

Iteration: 1
 Score = 87.0 bits (214), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 55/189 (29%), Positives = 100/189 (52%), Gaps = 6/189 (3%)
Query: 28  GVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI 87
            V  IT F    +    L+G+ +  +   + IQ++ +   ++G+DV+  A++G+GKT   
Sbjct: 20  NVNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAF 79
Query: 88  ALTVCQTV----DTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGE 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 LPPDLQVCC 211
           LP   Q   
Sbjct: 199 LPKKRQTLL 207

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

Iteration: 1
 Score = 83.2 bits (204), Expect = 9e-17,   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|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 77.0 bits (188), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 39/157 (24%), Positives = 88/157 (56%), Gaps = 7/157 (4%)
Query: 40  IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS 99
           + + + + I + GF+  + +Q + +  +++G++V+ +A++G+GKT+  A+ + +      
Sbjct: 1   MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL----- 55
Query: 100 REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTP 159
             +++L+++PTREL  Q    I  IG +++ +     GG      I ++ +   +V  TP
Sbjct: 56  -GMKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVRNA-DIVVATP 113
Query: 160 GRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQI 196
           GR+ D+  +  +   + +++++DE+D M   GF D I
Sbjct: 114 GRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDI 150

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 75.9 bits (185), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 53/166 (31%), Positives = 93/166 (56%), Gaps = 12/166 (7%)
Query: 43  DLLRGIYQYGFEKPSAIQQRAVMPII--KGRDVIAQAQSGTGKTSMIALTVCQ----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-TRAIKLLVLDESDEMLSRGFKDQI 196
            ++V  TPGR+ D++++ + +  R +   VLDE+D +L  GF+D +
Sbjct: 202 PNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDL 247

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

Iteration: 1
 Score = 75.9 bits (185), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 53/166 (31%), Positives = 93/166 (56%), Gaps = 12/166 (7%)
Query: 43  DLLRGIYQYGFEKPSAIQQRAVMPII--KGRDVIAQAQSGTGKTSMIALTVCQ----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-TRAIKLLVLDESDEMLSRGFKDQI 196
            ++V  TPGR+ D++++ + +  R +   VLDE+D +L  GF+D +
Sbjct: 151 PNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDL 196

>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 = 75.9 bits (185), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 53/166 (31%), Positives = 93/166 (56%), Gaps = 12/166 (7%)
Query: 43  DLLRGIYQYGFEKPSAIQQRAVMPII--KGRDVIAQAQSGTGKTSMIALTVCQ----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-TRAIKLLVLDESDEMLSRGFKDQI 196
            ++V  TPGR+ D++++ + +  R +   VLDE+D +L  GF+D +
Sbjct: 151 PNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDL 196

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	219
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	1e-112
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	1e-111
3bor_A	237	Human initiation factor 4A-II; translation initiat	1e-111
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	1e-110
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	1e-107
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	1e-103
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	4e-99
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	1e-95
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	7e-95
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	2e-93
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	2e-93
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	3e-90
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	7e-88
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	2e-83
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	4e-82
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	5e-68
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	9e-58
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	2e-56
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	6e-55
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	2e-51
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	3e-51
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	5e-51
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	9e-50
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	8e-47
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	4e-46
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	5e-46
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	9e-46
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	1e-45
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	4e-44
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	8e-43
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	4e-38
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	1e-12
3b6e_A	216	Interferon-induced helicase C domain-containing P;	6e-09
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	2e-08
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	3e-08
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	3e-07
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	6e-07
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	7e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	3e-04
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	4e-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 =  326 bits (839), Expect = e-112
 Identities = 133/209 (63%), Positives = 169/209 (80%)

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 DESDEMLSRGFKDQIYDVYRYLPPDLQVC 210
           DE+DEML++GFK+QIYDVYRYLPP  QV 
Sbjct: 186 DEADEMLNKGFKEQIYDVYRYLPPATQVV 214

>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 =  317 bits (816), Expect = e-111
 Identities = 98/192 (51%), Positives = 135/192 (70%), Gaps = 2/192 (1%)

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 VYRYLPPDLQVC 210
           ++  LPP  QV 
Sbjct: 179 IFTLLPPTTQVV 190

>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 =  317 bits (815), Expect = e-111
 Identities = 107/200 (53%), Positives = 145/200 (72%), Gaps = 2/200 (1%)

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 GFKDQIYDVYRYLPPDLQVC 210
           GFKDQIY++++ L   +QV 
Sbjct: 189 GFKDQIYEIFQKLNTSIQVV 208

>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 =  319 bits (821), Expect = e-110
 Identities = 103/203 (50%), Positives = 142/203 (69%), Gaps = 1/203 (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 LSRGFKDQIYDVYRYLPPDLQVC 210
           LSRGFKDQIYD+++ L  + QV 
Sbjct: 196 LSRGFKDQIYDIFQKLNSNTQVV 218

>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 =  313 bits (804), Expect = e-107
 Identities = 100/197 (50%), Positives = 137/197 (69%), Gaps = 2/197 (1%)

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 DQIYDVYRYLPPDLQVC 210
           +QIY ++  LPP  QV 
Sbjct: 181 EQIYQIFTLLPPTTQVV 197

>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 =  301 bits (774), Expect = e-103
 Identities = 75/187 (40%), Positives = 111/187 (59%), Gaps = 2/187 (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 PPDLQVC 210
           PP  Q  
Sbjct: 192 PPTHQSL 198

>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 =  286 bits (734), Expect = 4e-99
 Identities = 65/199 (32%), Positives = 109/199 (54%), Gaps = 4/199 (2%)

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 FKDQIYDVYRYLPPDLQVC 210
           F++QI  +Y  LP   Q+ 
Sbjct: 184 FQEQINWIYSSLPASKQML 202

>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 =  284 bits (728), Expect = 1e-95
 Identities = 68/199 (34%), Positives = 111/199 (55%), Gaps = 8/199 (4%)

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 FKDQIYDVYRYLPPDLQVC 210
            +DQ   + R LP + Q+ 
Sbjct: 186 HQDQSIRIQRMLPRNCQML 204

>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 =  278 bits (712), Expect = 7e-95
 Identities = 68/199 (34%), Positives = 111/199 (55%), Gaps = 8/199 (4%)

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 FKDQIYDVYRYLPPDLQVC 210
            +DQ   + R LP + Q+ 
Sbjct: 253 HQDQSIRIQRMLPRNCQML 271

>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 =  280 bits (719), Expect = 2e-93
 Identities = 68/199 (34%), Positives = 111/199 (55%), Gaps = 8/199 (4%)

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 FKDQIYDVYRYLPPDLQVC 210
            +DQ   + R LP + Q+ 
Sbjct: 253 HQDQSIRIQRMLPRNCQML 271

>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 =  277 bits (712), Expect = 2e-93
 Identities = 73/182 (40%), Positives = 110/182 (60%), Gaps = 7/182 (3%)

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 VC 210
           + 
Sbjct: 180 LV 181

>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 =  269 bits (690), Expect = 3e-90
 Identities = 61/184 (33%), Positives = 98/184 (53%), Gaps = 3/184 (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 LQVC 210
            QV 
Sbjct: 185 KQVM 188

>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 =  257 bits (658), Expect = 7e-88
 Identities = 61/179 (34%), Positives = 112/179 (62%), Gaps = 1/179 (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 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVC 210
           VHVV  TPGR+ D+IK+   +   ++++VLDE+D++LS+ F   + D+   LP + Q+ 
Sbjct: 123 VHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQIL 181

>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 =  242 bits (621), Expect = 4e-82
 Identities = 61/180 (33%), Positives = 98/180 (54%), Gaps = 3/180 (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

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score =  207 bits (528), Expect = 5e-68
 Identities = 63/181 (34%), Positives = 94/181 (51%), Gaps = 4/181 (2%)

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 V 209
           +
Sbjct: 184 M 184

>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 =  185 bits (472), Expect = 9e-58
 Identities = 59/179 (32%), Positives = 105/179 (58%), Gaps = 3/179 (1%)

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 GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQV 209
             ++V GTPGR+ D I R TL  + +K  +LDE+DEML+ GF   +  +      D ++
Sbjct: 123 NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRI 181

>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 =  177 bits (451), Expect = 2e-56
 Identities = 60/179 (33%), Positives = 97/179 (54%), Gaps = 5/179 (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 GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQV 209
           G   V  TPGR  D +++  L    +++ VLDE+DEMLS GF++++  +    PP  Q 
Sbjct: 120 GADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQT 178

>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 =  174 bits (444), Expect = 6e-55
 Identities = 61/193 (31%), Positives = 102/193 (52%), Gaps = 1/193 (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 IYDVYRYLPPDLQ 208
           +  + + +P D +
Sbjct: 207 VDKILKVIPRDRK 219

>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 =  173 bits (441), Expect = 2e-51
 Identities = 51/195 (26%), Positives = 99/195 (50%), Gaps = 12/195 (6%)

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 FKDQIYDVYRYLPPD 206
           F+D +  +   L   
Sbjct: 192 FRDDLETISGILNEK 206

>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 =  173 bits (439), Expect = 3e-51
 Identities = 51/195 (26%), Positives = 99/195 (50%), Gaps = 12/195 (6%)

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 FKDQIYDVYRYLPPD 206
           F+D +  +   L   
Sbjct: 243 FRDDLETISGILNEK 257

>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 =  167 bits (425), Expect = 5e-51
 Identities = 39/170 (22%), Positives = 88/170 (51%), Gaps = 7/170 (4%)

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 GRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQV 209
           GR+ D+  +  +   + +++++DE+D M   GF D I  +          
Sbjct: 114 GRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKIT 163

>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 =  161 bits (409), Expect = 9e-50
 Identities = 56/196 (28%), Positives = 101/196 (51%), Gaps = 6/196 (3%)

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 KDQIYDVYRYLPPDLQ 208
            D +  V   LP   Q
Sbjct: 189 ADTMNAVIENLPKKRQ 204

>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 =  154 bits (391), Expect = 8e-47
 Identities = 53/176 (30%), Positives = 91/176 (51%), Gaps = 9/176 (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 VGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQI 196
               IR+++ G H++  TPGR+ D I++  +     K +VLDE+D ML  GF+ QI
Sbjct: 140 THSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQI 195

>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 =  152 bits (387), Expect = 4e-46
 Identities = 55/199 (27%), Positives = 101/199 (50%), Gaps = 7/199 (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 RGFKDQIYDVYRYLPPDLQ 208
            GF++++  + + LP   Q
Sbjct: 216 VGFEEELKQIIKLLPTRRQ 234

>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 =  151 bits (384), Expect = 5e-46
 Identities = 58/183 (31%), Positives = 87/183 (47%), Gaps = 7/183 (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 DLQ 208
           D Q
Sbjct: 207 DRQ 209

>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 =  150 bits (382), Expect = 9e-46
 Identities = 60/184 (32%), Positives = 91/184 (49%), Gaps = 8/184 (4%)

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 PDLQ 208
           PD Q
Sbjct: 197 PDRQ 200

>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 =  150 bits (382), Expect = 1e-45
 Identities = 48/188 (25%), Positives = 94/188 (50%), Gaps = 11/188 (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 VYRYLPPD 206
           ++      
Sbjct: 202 IFLACTSH 209

>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 =  151 bits (384), Expect = 4e-44
 Identities = 51/173 (29%), Positives = 88/173 (50%), Gaps = 7/173 (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 DIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQI 196
               +  G HVV  TPGR+ D + R  +     + +VLDE+D ML  GF + +
Sbjct: 172 QNECITRGCHVVIATPGRLLDFVDRTFITFEDTRFVVLDEADRMLDMGFSEDM 224

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  148 bits (375), Expect = 8e-43
 Identities = 61/186 (32%), Positives = 94/186 (50%), Gaps = 20/186 (10%)

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 GFKDQI 196
           GF+ QI
Sbjct: 191 GFEPQI 196

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score =  135 bits (341), Expect = 4e-38
 Identities = 25/171 (14%), Positives = 63/171 (36%), Gaps = 10/171 (5%)

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 TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ 208
           +   V     R+ L  +    + +D+ D +L          +   +P ++ 
Sbjct: 124 STQFVSK--NREKLSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGIPEEII 172

>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 = 64.8 bits (157), Expect = 1e-12
 Identities = 30/152 (19%), Positives = 59/152 (38%), Gaps = 3/152 (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 LDESDEMLSRGFKDQIYDVYRYLPPDLQVCCP 212
            DE+   +       I   Y+    +  V   
Sbjct: 131 FDEAHRAVGNYAYVFIAREYKRQAKNPLVIGL 162

>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 = 53.3 bits (128), Expect = 6e-09
 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

>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 = 53.1 bits (126), Expect = 2e-08
 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

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 52.3 bits (124), Expect = 3e-08
 Identities = 26/152 (17%), Positives = 59/152 (38%), Gaps = 5/152 (3%)

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 -RTRAIKLLVLDESDEMLSRGFKDQIYDVYRY 202
                  L++ DE      +   + I   Y  
Sbjct: 132 PSLSIFTLMIFDECHNTSKQHPYNMIMFNYLD 163

>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 = 49.2 bits (116), Expect = 3e-07
 Identities = 24/132 (18%), Positives = 48/132 (36%), Gaps = 3/132 (2%)

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 RTRAIKLLVLDE 183
                 L++ DE
Sbjct: 127 SLSIFTLMIFDE 138

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 48.4 bits (114), Expect = 6e-07
 Identities = 20/127 (15%), Positives = 46/127 (36%), Gaps = 3/127 (2%)

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 KLLVLDE 183
            L++ DE
Sbjct: 129 TLMIFDE 135

>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 = 48.4 bits (114), Expect = 7e-07
 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

>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 = 40.6 bits (94), Expect = 2e-04
 Identities = 24/147 (16%), Positives = 49/147 (33%), Gaps = 40/147 (27%)

Query: 61  QRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQT-------------VDTSSREVQALIL 107
           ++A++ +   ++V+     G+GKT + AL VC +             ++  +      +L
Sbjct: 141 RQALLELRPAKNVLIDGVLGSGKTWV-ALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVL 199

Query: 108 SPTRELATQTEKVILAIGDF-INIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMI 166
              ++L  Q +    +  D   NI+             I+               +  ++
Sbjct: 200 EMLQKLLYQIDPNWTSRSDHSSNIKLRI--------HSIQA-------------ELRRLL 238

Query: 167 KRKTLRTRAIKLLVLDE-SDEMLSRGF 192
           K K        LLVL    +      F
Sbjct: 239 KSKPYE-NC--LLVLLNVQNAKAWNAF 262

>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 = 40.2 bits (94), Expect = 3e-04
 Identities = 32/160 (20%), Positives = 60/160 (37%), Gaps = 19/160 (11%)

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----SDEMLSRG 191
             T  +   +I+ +    +A+  LV+DE      E   RG
Sbjct: 119 VTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSE--KRG 156

>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 = 40.0 bits (93), Expect = 4e-04
 Identities = 24/183 (13%), Positives = 52/183 (28%), Gaps = 39/183 (21%)

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 LQV 209
           L V
Sbjct: 352 LVV 354

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	219
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	100.0
3bor_A	237	Human initiation factor 4A-II; translation initiat	100.0
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	100.0
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	100.0
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	100.0
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	100.0
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	100.0
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	100.0
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	100.0
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	100.0
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	100.0
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	100.0
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	100.0
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	100.0
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	100.0
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	100.0
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	100.0
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	100.0
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
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	100.0
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	100.0
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	100.0
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	100.0
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	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
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.97
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.97
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.97
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.96
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.96
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.96
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.96
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.96
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.96
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.96
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.95
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.95
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.95
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.95
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.94
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.94
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.94
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.93
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.93
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.93
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.93
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.92
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.92
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.92
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.92
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.91
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.91
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.91
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.9
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.89
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.87
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.87
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.87
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.86
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.86
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.84
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.83
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.82
3h1t_A	590	Type I site-specific restriction-modification syst	99.82
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.81
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.81
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.8
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.79
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.75
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.7
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.69
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.65
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.62
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.59
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.58
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.47
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	99.27
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.2
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	98.75
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	98.71
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	98.7
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	98.66
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	98.64
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	98.62
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	97.98
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	97.89
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	97.75
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	97.66
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	97.65
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	97.52
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	97.4
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	97.4
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	97.34
2chg_A	226	Replication factor C small subunit; DNA-binding pr	97.33
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	97.32
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	97.3
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	97.25
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	97.19
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	97.16
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	97.15
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	97.13
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	97.1
3bos_A	242	Putative DNA replication factor; P-loop containing	97.01
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	96.97
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	96.96
3co5_A	143	Putative two-component system transcriptional RES	96.94
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	96.87
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	96.84
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	96.81
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	96.78
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	96.74
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	96.7
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	96.69
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	96.68
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	96.64
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	96.6
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	96.52
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	96.49
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	96.45
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	96.44
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	96.43
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	96.41
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	96.39
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	96.32
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	96.26
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	96.23
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	96.22
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	96.19
2qgz_A	308	Helicase loader, putative primosome component; str	96.06
2chq_A	319	Replication factor C small subunit; DNA-binding pr	95.86
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	95.83
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	95.6
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	95.56
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	95.53
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	95.46
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	95.36
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	95.25
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	95.23
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	95.18
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	95.07
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	94.99
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	94.96
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	94.91
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	94.91
3pvs_A	447	Replication-associated recombination protein A; ma	94.89
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	94.85
2r6a_A	454	DNAB helicase, replicative helicase; replication,	94.73
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	94.64
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	94.55
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	94.49
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	94.45
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	94.13
3u4q_B	1166	ATP-dependent helicase/deoxyribonuclease subunit;	94.13
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	94.04
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	94.02
2l8b_A	189	Protein TRAI, DNA helicase I; RECD, hydrolase; NMR	93.88
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	93.79
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	93.78
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	93.71
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	93.67
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	93.66
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	93.43
1w36_B	1180	RECB, exodeoxyribonuclease V beta chain; recombina	93.28
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	93.11
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	93.09
2fna_A	357	Conserved hypothetical protein; structural genomic	92.84
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	92.73
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	92.57
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	92.34
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	92.34
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	92.25
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	92.22
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	92.14
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	91.96
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	91.62
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	91.53
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	91.3
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	91.25
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	91.06
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	90.96
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	90.74
3io5_A	333	Recombination and repair protein; storage dimer, i	90.66
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	90.55
1tue_A	212	Replication protein E1; helicase, replication, E1E	90.23
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	90.13
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	90.1
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	90.08
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	90.06
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	89.96
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	89.86
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	89.85
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	89.39
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	89.35
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	89.33
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	89.13
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	89.09
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	88.95
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	88.93
1p9r_A	418	General secretion pathway protein E; bacterial typ	88.93
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	88.55
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	88.84
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	88.78
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	88.76
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	88.71
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	88.22
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	88.15
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	87.65
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	87.6
2r44_A	331	Uncharacterized protein; putative ATPase, structur	87.37
1yks_A	440	Genome polyprotein [contains: flavivirin protease	87.37
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	87.3
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	87.28
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	87.15
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	87.0
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	86.93
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	86.86
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	86.64
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	86.62
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	86.57
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	86.43
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	86.07
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	86.06
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	86.05
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	86.04
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	85.85
2eyu_A	261	Twitching motility protein PILT; pilus retraction	85.75
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	85.43
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	85.4
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	85.36
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	85.29
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	85.07
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	85.02
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	84.94
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	84.81
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	84.74
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	84.73
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	84.72
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	84.65
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	84.45
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	84.34
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	84.24
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	84.21
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	84.0
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	83.94
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	83.88
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	83.85
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	83.8
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	83.79
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	83.59
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	83.57
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	83.54
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	83.43
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	83.14
2ewv_A	372	Twitching motility protein PILT; pilus retraction	83.09
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	83.02
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	82.99
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	82.94
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	82.94
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	82.93
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	82.81
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	82.77
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	82.73
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	82.71
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	82.37
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	82.26
3ice_A	422	Transcription termination factor RHO; transcriptio	82.09
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	82.02
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	81.88
3nwn_A	359	Kinesin-like protein KIF9; motor domain, ADP, stru	81.87
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	81.67
2cvh_A	220	DNA repair and recombination protein RADB; filamen	81.63
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	81.58
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	81.44
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	81.31
3b5x_A	582	Lipid A export ATP-binding/permease protein MSBA;	81.25
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	81.1
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	81.1
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	81.0
1bg2_A	325	Kinesin; motor protein, ATPase, microtubule associ	80.95
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	80.84
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	80.74
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	80.63
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	80.59
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	80.49
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	80.44
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	80.32
3dc4_A	344	Kinesin-like protein NOD; catalytic domain, ATPase	80.27
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	80.11

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=100.00  E-value=4.5e-42  Score=271.80  Aligned_cols=199  Identities=28%  Similarity=0.424  Sum_probs=184.5

Q ss_pred             cceeeccCCCCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccC-
Q 027749           20 KMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-   98 (219)
Q Consensus        20 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~-   98 (219)
                      .+.......++++.+|+++++++.+.+++.+.|+..|+++|.++++.+.+|+++++++|||+|||++|++|++..+... 
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            4455566678899999999999999999999999999999999999999999999999999999999999999887642 


Q ss_pred             ----CCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCC
Q 027749           99 ----SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTR  174 (219)
Q Consensus        99 ----~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~  174 (219)
                          ..++++||++|+++|+.|+.+.++++....++.+..++|+.+...+...+.++++|+|+||++|.+++.++...++
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                3467899999999999999999999988889999999999998888888888999999999999999988888899


Q ss_pred             CccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       175 ~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      ++++||+||||++.+++|...+..+++.++++.|+++||||+|+
T Consensus       176 ~~~~lViDEah~l~~~~~~~~~~~i~~~~~~~~q~~~~SAT~~~  219 (242)
T 3fe2_A          176 RTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPK  219 (242)
T ss_dssp             TCCEEEETTHHHHHHTTCHHHHHHHHTTSCSSCEEEEEESCCCH
T ss_pred             cccEEEEeCHHHHhhhCcHHHHHHHHHhCCccceEEEEEeecCH
Confidence            99999999999999999999999999999999999999999985

>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=5.4e-41  Score=264.90  Aligned_cols=205  Identities=51%  Similarity=0.795  Sum_probs=166.2

Q ss_pred             CCCCCCcceeeccCCCCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHh
Q 027749           14 GGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQ   93 (219)
Q Consensus        14 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~   93 (219)
                      ......+.....+..+++..+|+++++++.+.+++.++|+..|+++|.++++.+++++++++++|||+|||++|++++++
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~   90 (237)
T 3bor_A           11 RENLYFQGGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQ   90 (237)
T ss_dssp             ----------------CCCCSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHH
T ss_pred             cccccCCCCcccCCCCCccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHH
Confidence            33333334444555567889999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCC-CeEEEeChHHHHHHHHcCCCC
Q 027749           94 TVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG-VHVVSGTPGRVCDMIKRKTLR  172 (219)
Q Consensus        94 ~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~-~~I~v~Tp~~l~~~l~~~~~~  172 (219)
                      .+.....++++||++|+++|+.|+.+.++++....+..+....|+.+...+...+..+ ++|+|+||+++.+++..+...
T Consensus        91 ~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~  170 (237)
T 3bor_A           91 QLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLS  170 (237)
T ss_dssp             HCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECC-------------CCCSEEEECHHHHHHHHHTTSSC
T ss_pred             HHHhcCCCceEEEEECcHHHHHHHHHHHHHHhhhcCceEEEEECCCchHHHHHHHhcCCCCEEEECHHHHHHHHHhCCcC
Confidence            8876666778999999999999999999999888888888889988877776666555 899999999999999888888


Q ss_pred             CCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       173 ~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      ++++++||+||||++.+++|...+..+++.++++.|++++|||+|+
T Consensus       171 ~~~~~~lViDEah~~~~~~~~~~l~~i~~~~~~~~~~i~~SAT~~~  216 (237)
T 3bor_A          171 PKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATMPT  216 (237)
T ss_dssp             STTCCEEEEESHHHHHHTTCHHHHHHHHHHSCTTCEEEEECSSCCH
T ss_pred             cccCcEEEECCchHhhccCcHHHHHHHHHhCCCCCeEEEEEEecCH
Confidence            8999999999999999999999999999999999999999999985

>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=5.4e-40  Score=253.41  Aligned_cols=186  Identities=33%  Similarity=0.628  Sum_probs=174.1

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHH
Q 027749           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (219)
Q Consensus        33 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  112 (219)
                      .+|+++++++.+++++.++|+..|+++|.++++.+.+++++++++|||+|||++|++|++..+.....++++||++|+++
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            57999999999999999999999999999999999999999999999999999999999998877667788999999999


Q ss_pred             HHHHHHHHHHHhcccc-ceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccc
Q 027749          113 LATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG  191 (219)
Q Consensus       113 l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~  191 (219)
                      |+.|+.+.+.++.... +..+....|+.+...+...+..+++|+|+||+++.+.+.++...++++++||+||||++.+.+
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            9999999999998776 788888999998888877888899999999999999998888888999999999999999999


Q ss_pred             cHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          192 FKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       192 ~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      |...+..+++.++++.|++++|||+|.
T Consensus       163 ~~~~l~~i~~~~~~~~~~l~~SAT~~~  189 (206)
T 1vec_A          163 FVQIMEDIILTLPKNRQILLYSATFPL  189 (206)
T ss_dssp             THHHHHHHHHHSCTTCEEEEEESCCCH
T ss_pred             cHHHHHHHHHhCCccceEEEEEeeCCH
Confidence            999999999999999999999999985

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=100.00  E-value=1.7e-40  Score=260.30  Aligned_cols=192  Identities=30%  Similarity=0.435  Sum_probs=170.1

Q ss_pred             cCCCCccCcccc-CCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccC------
Q 027749           26 TEGVEAITSFDA-MGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS------   98 (219)
Q Consensus        26 ~~~~~~~~~~~~-~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~------   98 (219)
                      ...|++..+|++ +++++.+.+++.+.|+..|+++|.++++.+.+|+++++++|||+|||++|++|++..+...      
T Consensus        12 ~~~p~p~~~f~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~~~   91 (228)
T 3iuy_A           12 RLIPKPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQ   91 (228)
T ss_dssp             CCCCCCCCSHHHHHTTCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC--------
T ss_pred             CcCCCChhhHhhhhccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccchhhc
Confidence            345788899999 7999999999999999999999999999999999999999999999999999999877542      


Q ss_pred             CCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccE
Q 027749           99 SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKL  178 (219)
Q Consensus        99 ~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~  178 (219)
                      ..++++||++|+++|+.|+.+.+.++. ..++.+..++|+.+...+...+.++++|+|+||+++.+++.+....++++++
T Consensus        92 ~~~~~~lil~Pt~~L~~q~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~Tp~~l~~~~~~~~~~~~~~~~  170 (228)
T 3iuy_A           92 RNGPGMLVLTPTRELALHVEAECSKYS-YKGLKSICIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMNNSVNLRSITY  170 (228)
T ss_dssp             -CCCSEEEECSSHHHHHHHHHHHHHHC-CTTCCEEEECC------CHHHHHSCCSEEEECHHHHHHHHHTTCCCCTTCCE
T ss_pred             cCCCcEEEEeCCHHHHHHHHHHHHHhc-ccCceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCcCcccceE
Confidence            256789999999999999999999986 4478888899998888888888889999999999999999888888999999


Q ss_pred             EEeccchhhhccccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          179 LVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       179 lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      ||+||||++.+++|...+..+++.+++++|++++|||+|+
T Consensus       171 lViDEah~~~~~~~~~~~~~i~~~~~~~~~~l~~SAT~~~  210 (228)
T 3iuy_A          171 LVIDEADKMLDMEFEPQIRKILLDVRPDRQTVMTSATWPD  210 (228)
T ss_dssp             EEECCHHHHHHTTCHHHHHHHHHHSCSSCEEEEEESCCCH
T ss_pred             EEEECHHHHhccchHHHHHHHHHhCCcCCeEEEEEeeCCH
Confidence            9999999999999999999999999999999999999985

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=100.00  E-value=2.3e-40  Score=258.14  Aligned_cols=188  Identities=34%  Similarity=0.515  Sum_probs=172.2

Q ss_pred             cCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCH
Q 027749           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (219)
Q Consensus        32 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~  111 (219)
                      ..+|+++++++.+.+++.++|+..|+++|.++++.+.+++++++++|||+|||++|++|++..+.....+++++|++|++
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            46799999999999999999999999999999999999999999999999999999999999988766678899999999


Q ss_pred             HHHHHHHHHHHHhcccc----ceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhh
Q 027749          112 ELATQTEKVILAIGDFI----NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (219)
Q Consensus       112 ~l~~q~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l  187 (219)
                      +|+.|+.+.+.++....    ++.+..+.|+.+.......+..+++|+|+||+++.+.+.++...++++++||+||||++
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    67888888888876666566678999999999999999888888899999999999999


Q ss_pred             hccccHHHHHHHHHhCCCCCeEEEEeecccCC
Q 027749          188 LSRGFKDQIYDVYRYLPPDLQVCCPGSCFLFD  219 (219)
Q Consensus       188 ~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~~  219 (219)
                      .+++|...+..+++.++++.|++++|||+|.+
T Consensus       163 ~~~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~  194 (219)
T 1q0u_A          163 LDMGFITDVDQIAARMPKDLQMLVFSATIPEK  194 (219)
T ss_dssp             HHTTCHHHHHHHHHTSCTTCEEEEEESCCCGG
T ss_pred             hhhChHHHHHHHHHhCCcccEEEEEecCCCHH
Confidence            99999999999999999999999999999863

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=100.00  E-value=3.3e-40  Score=262.26  Aligned_cols=190  Identities=32%  Similarity=0.511  Sum_probs=176.3

Q ss_pred             CCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEc
Q 027749           29 VEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (219)
Q Consensus        29 ~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~  108 (219)
                      +++..+|+++++++.+.++|.++|+..|+++|.++++.+.+|+++++++|||+|||++|++|++..+.....++++||++
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            34568899999999999999999999999999999999999999999999999999999999999887776678899999


Q ss_pred             CCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHc-CCCCCCCccEEEeccchhh
Q 027749          109 PTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-KTLRTRAIKLLVLDESDEM  187 (219)
Q Consensus       109 P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~-~~~~~~~l~~lVvDE~h~l  187 (219)
                      |+++|+.|+.+.++++....++++..+.|+.+...+...+..+++|+|+||+++.+.+.+ +.+.++++++||+||||++
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            999999999999999988888999999999888777777788999999999999998876 5567899999999999999


Q ss_pred             hccccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          188 LSRGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       188 ~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      .+++|...+..+++.++++.|+++||||+|+
T Consensus       199 ~~~~~~~~l~~i~~~~~~~~~~l~~SAT~~~  229 (249)
T 3ber_A          199 LNMDFETEVDKILKVIPRDRKTFLFSATMTK  229 (249)
T ss_dssp             HHTTCHHHHHHHHHSSCSSSEEEEEESSCCH
T ss_pred             hccChHHHHHHHHHhCCCCCeEEEEeccCCH
Confidence            9999999999999999999999999999985

>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=1.4e-39  Score=255.72  Aligned_cols=191  Identities=33%  Similarity=0.544  Sum_probs=170.1

Q ss_pred             CCCCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEE
Q 027749           27 EGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALI  106 (219)
Q Consensus        27 ~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~li  106 (219)
                      ..+.+..+|+++++++.+.+++.++|+..|+++|.++++.+.+|+++++++|||+|||++|++|++..+.....++++||
T Consensus        18 ~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~li   97 (230)
T 2oxc_A           18 VLLAEPADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILI   97 (230)
T ss_dssp             ------CCGGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEE
T ss_pred             CCCCCCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEE
Confidence            34567788999999999999999999999999999999999999999999999999999999999998877666788999


Q ss_pred             EcCCHHHHHHHHHHHHHhcccc-ceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccch
Q 027749          107 LSPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESD  185 (219)
Q Consensus       107 l~P~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h  185 (219)
                      ++|+++|+.|+.+.++++.... ++++..+.|+.+...+...+ .+++|+|+||+++.+++..+.+.++++++||+||||
T Consensus        98 l~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~Iiv~Tp~~l~~~~~~~~~~~~~~~~lViDEah  176 (230)
T 2oxc_A           98 LAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRL-KKCHIAVGSPGRIKQLIELDYLNPGSIRLFILDEAD  176 (230)
T ss_dssp             ECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHT-TSCSEEEECHHHHHHHHHTTSSCGGGCCEEEESSHH
T ss_pred             EeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhc-cCCCEEEECHHHHHHHHhcCCcccccCCEEEeCCch
Confidence            9999999999999999998665 78888888888876665544 579999999999999998888888999999999999


Q ss_pred             hhhccc-cHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          186 EMLSRG-FKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       186 ~l~~~~-~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      ++.+++ |...+..+++.++++.|++++|||+|.
T Consensus       177 ~~~~~~~~~~~~~~i~~~~~~~~~~l~lSAT~~~  210 (230)
T 2oxc_A          177 KLLEEGSFQEQINWIYSSLPASKQMLAVSATYPE  210 (230)
T ss_dssp             HHHSTTSSHHHHHHHHHHSCSSCEEEEEESCCCH
T ss_pred             HhhcCcchHHHHHHHHHhCCCCCeEEEEEeccCH
Confidence            999987 999999999999999999999999985

>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=1.3e-39  Score=254.52  Aligned_cols=191  Identities=51%  Similarity=0.836  Sum_probs=168.7

Q ss_pred             CCCCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEE
Q 027749           27 EGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALI  106 (219)
Q Consensus        27 ~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~li  106 (219)
                      ..++.+.+|+++++++.+.+.+.++|+..|+++|.++++.+.+++++++++|||+|||++|++++++.+.....++++||
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            34567789999999999999999999999999999999999999999999999999999999999999877767788999


Q ss_pred             EcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchh
Q 027749          107 LSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDE  186 (219)
Q Consensus       107 l~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~  186 (219)
                      ++|+++|+.|+.+.+.++....++.+..+.|+.+...+...+.+ ++|+|+||+++.+.+.++...++++++||+||||+
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            99999999999999999988888999999988887666555544 89999999999999988888889999999999999


Q ss_pred             hhccccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          187 MLSRGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       187 l~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      +.+++|...+..+++.++++.|++++|||+|+
T Consensus       167 ~~~~~~~~~l~~i~~~~~~~~~~i~lSAT~~~  198 (224)
T 1qde_A          167 MLSSGFKEQIYQIFTLLPPTTQVVLLSATMPN  198 (224)
T ss_dssp             HHHTTCHHHHHHHHHHSCTTCEEEEEESSCCH
T ss_pred             HhhhhhHHHHHHHHHhCCccCeEEEEEeecCH
Confidence            99999999999999999999999999999985

>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=1.2e-39  Score=278.18  Aligned_cols=197  Identities=27%  Similarity=0.423  Sum_probs=181.3

Q ss_pred             eeeccCCCCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCC--
Q 027749           22 VFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS--   99 (219)
Q Consensus        22 ~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~--   99 (219)
                      +......+.++.+|+++++++.+++++.++||..|+|+|.++||.+++|+++++++|||+|||++|++|+++.+....  
T Consensus        45 ~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~~~~  124 (434)
T 2db3_A           45 KVTGSDVPQPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHE  124 (434)
T ss_dssp             EEESSSCCCCCCCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCCC
T ss_pred             EecCCCCCCCcCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHhcccc
Confidence            344455688899999999999999999999999999999999999999999999999999999999999999876532  


Q ss_pred             ---CceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCc
Q 027749          100 ---REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (219)
Q Consensus       100 ---~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l  176 (219)
                         .++++||++||++|+.|+++.++++....++++..++|+.+...+...+..+++|+|+||++|.+++.+....++++
T Consensus       125 ~~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Ivv~Tp~~l~~~l~~~~~~l~~~  204 (434)
T 2db3_A          125 LELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTFITFEDT  204 (434)
T ss_dssp             CCTTCCSEEEECSSHHHHHHHHHHHHHHTTTSSCCCCEECTTSCHHHHHHHHTTCCSEEEECHHHHHHHHHTTSCCCTTC
T ss_pred             cccCCccEEEEecCHHHHHHHHHHHHHHhccCCcEEEEEECCCCHHHHHHHhhcCCCEEEEChHHHHHHHHhCCcccccC
Confidence               36789999999999999999999999888899999999999888888888899999999999999999888889999


Q ss_pred             cEEEeccchhhhccccHHHHHHHHHhC--CCCCeEEEEeecccC
Q 027749          177 KLLVLDESDEMLSRGFKDQIYDVYRYL--PPDLQVCCPGSCFLF  218 (219)
Q Consensus       177 ~~lVvDE~h~l~~~~~~~~~~~i~~~~--~~~~q~i~~SATl~~  218 (219)
                      ++||+||||+|.+++|...+..++..+  +++.|+++||||+|.
T Consensus       205 ~~lVlDEah~~~~~gf~~~~~~i~~~~~~~~~~q~l~~SAT~~~  248 (434)
T 2db3_A          205 RFVVLDEADRMLDMGFSEDMRRIMTHVTMRPEHQTLMFSATFPE  248 (434)
T ss_dssp             CEEEEETHHHHTSTTTHHHHHHHHHCTTSCSSCEEEEEESCCCH
T ss_pred             CeEEEccHhhhhccCcHHHHHHHHHhcCCCCCceEEEEeccCCH
Confidence            999999999999999999999999985  678999999999985

>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=7.4e-40  Score=266.85  Aligned_cols=187  Identities=36%  Similarity=0.571  Sum_probs=168.2

Q ss_pred             CCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCC--CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEE
Q 027749           29 VEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALI  106 (219)
Q Consensus        29 ~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~--~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~li  106 (219)
                      .....+|+++++++.++++|.++||..|+++|.++||.++.|  +++++++|||+|||++|++|+++.+.....++++||
T Consensus        88 ~~~~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~~~~~~~li  167 (300)
T 3fmo_B           88 LYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLC  167 (300)
T ss_dssp             CCCCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEE
T ss_pred             cCCcCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhhhccCCCceEEE
Confidence            335689999999999999999999999999999999999987  999999999999999999999999988777889999


Q ss_pred             EcCCHHHHHHHHHHHHHhcccc-ceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHc-CCCCCCCccEEEeccc
Q 027749          107 LSPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-KTLRTRAIKLLVLDES  184 (219)
Q Consensus       107 l~P~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~-~~~~~~~l~~lVvDE~  184 (219)
                      ++||++|+.|+++.+..+.... ++.+....|+.......   ..+++|+|+||++|.+++.+ +.++++++++||+|||
T Consensus       168 l~PtreLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~TP~~l~~~l~~~~~~~l~~l~~lVlDEa  244 (300)
T 3fmo_B          168 LSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ---KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEA  244 (300)
T ss_dssp             ECSSHHHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTTC---CCCCSEEEECHHHHHHHHTTTCCCCGGGCSEEEETTH
T ss_pred             EcCcHHHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhhh---cCCCCEEEECHHHHHHHHHhcCCCChhhceEEEEeCH
Confidence            9999999999999999998764 67888888877654322   45789999999999999866 5677899999999999


Q ss_pred             hhhhc-cccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          185 DEMLS-RGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       185 h~l~~-~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      |+|++ .+|...+..+++.+++++|+++||||+|.
T Consensus       245 d~l~~~~~~~~~~~~i~~~~~~~~q~i~~SAT~~~  279 (300)
T 3fmo_B          245 DVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFED  279 (300)
T ss_dssp             HHHHHSTTHHHHHHHHHTTSCTTCEEEEEESCCCH
T ss_pred             HHHhhccCcHHHHHHHHHhCCCCCEEEEEeccCCH
Confidence            99998 68999999999999999999999999985

>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=2e-39  Score=258.06  Aligned_cols=188  Identities=29%  Similarity=0.484  Sum_probs=173.0

Q ss_pred             ccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCC---------Cc
Q 027749           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS---------RE  101 (219)
Q Consensus        31 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~---------~~  101 (219)
                      ++.+|+++++++.+.++|.+.|+..|+++|.++++.+++++++++++|||+|||++|++|++..+....         .+
T Consensus        21 ~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~~~  100 (253)
T 1wrb_A           21 VIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAY  100 (253)
T ss_dssp             CCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBC
T ss_pred             ccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhhccccccccccCC
Confidence            778999999999999999999999999999999999999999999999999999999999998875432         34


Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEe
Q 027749          102 VQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVL  181 (219)
Q Consensus       102 ~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVv  181 (219)
                      +++||++|+++|+.|+.+.+.++....++.+..+.|+.+...+...+..+++|+|+||++|.+.+......++++++||+
T Consensus       101 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~lVi  180 (253)
T 1wrb_A          101 PKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVL  180 (253)
T ss_dssp             CSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCTTCCEEEE
T ss_pred             ceEEEEECCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhCCCCCEEEECHHHHHHHHHcCCCChhhCCEEEE
Confidence            68999999999999999999999888889999999999988888888889999999999999999888888899999999


Q ss_pred             ccchhhhccccHHHHHHHHHh--CCC--CCeEEEEeecccC
Q 027749          182 DESDEMLSRGFKDQIYDVYRY--LPP--DLQVCCPGSCFLF  218 (219)
Q Consensus       182 DE~h~l~~~~~~~~~~~i~~~--~~~--~~q~i~~SATl~~  218 (219)
                      ||||++.+++|...+..+++.  ++.  +.|+++||||+|+
T Consensus       181 DEah~~~~~~~~~~~~~i~~~~~~~~~~~~q~l~~SAT~~~  221 (253)
T 1wrb_A          181 DEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPK  221 (253)
T ss_dssp             ETHHHHHHTTCHHHHHHHHHSSCCCCGGGCEEEEEESSCCH
T ss_pred             eCHHHHHhCchHHHHHHHHhhccCCCCCCcEEEEEEEeCCH
Confidence            999999999999999999995  444  7899999999975

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=100.00  E-value=2.4e-38  Score=246.71  Aligned_cols=191  Identities=32%  Similarity=0.527  Sum_probs=170.1

Q ss_pred             CCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEc
Q 027749           29 VEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (219)
Q Consensus        29 ~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~  108 (219)
                      +....+|+++++++.+.+++.++|+..|+++|.++++.+.+++++++++|||+|||++|+++++..+.....++++||++
T Consensus        10 ~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~   89 (220)
T 1t6n_A           10 SIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMC   89 (220)
T ss_dssp             ----CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEEC
T ss_pred             cccCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhccCCCEEEEEEe
Confidence            33446799999999999999999999999999999999999999999999999999999999999887766667899999


Q ss_pred             CCHHHHHHHHHHHHHhcccc-ceeEEEEECCcccHHHHHHhcC-CCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchh
Q 027749          109 PTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEH-GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDE  186 (219)
Q Consensus       109 P~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l~~-~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~  186 (219)
                      |+++|+.|+.+.++++.... ++++..+.|+.+...+...+.. .++|+|+||+++...+.+....++++++||+||||+
T Consensus        90 Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDEah~  169 (220)
T 1t6n_A           90 HTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDK  169 (220)
T ss_dssp             SCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEESHHH
T ss_pred             CCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHHHhcCCCCEEEeCHHHHHHHHHhCCCCcccCCEEEEcCHHH
Confidence            99999999999999998765 7888888888887766665544 579999999999999988888889999999999999


Q ss_pred             hhc-cccHHHHHHHHHhCCCCCeEEEEeecccCC
Q 027749          187 MLS-RGFKDQIYDVYRYLPPDLQVCCPGSCFLFD  219 (219)
Q Consensus       187 l~~-~~~~~~~~~i~~~~~~~~q~i~~SATl~~~  219 (219)
                      +.+ .+|...+..+++.++++.|++++|||+|.+
T Consensus       170 ~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~  203 (220)
T 1t6n_A          170 MLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKE  203 (220)
T ss_dssp             HHSSHHHHHHHHHHHHTSCSSSEEEEEESCCCTT
T ss_pred             HhcccCcHHHHHHHHHhCCCcCeEEEEEeecCHH
Confidence            987 488899999999999999999999999864

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=100.00  E-value=1.5e-38  Score=250.47  Aligned_cols=189  Identities=28%  Similarity=0.472  Sum_probs=169.0

Q ss_pred             CCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccC----CCceeE
Q 027749           29 VEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS----SREVQA  104 (219)
Q Consensus        29 ~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~----~~~~~~  104 (219)
                      +++..+|+++++++.+.++|.++|+..|+++|.++++.+++|+++++++|||+|||++|++|++..+...    ..++++
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            4567889999999999999999999999999999999999999999999999999999999999877532    235789


Q ss_pred             EEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcC-CCCCCCccEEEecc
Q 027749          105 LILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK-TLRTRAIKLLVLDE  183 (219)
Q Consensus       105 lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~-~~~~~~l~~lVvDE  183 (219)
                      ||++|+++|+.|+.+.+.++....++.+..+.|+.+...+...+ .+++|+|+||+++.+.+... ...+.++++||+||
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            99999999999999999999888888999999988877665555 57899999999999988764 46778999999999


Q ss_pred             chhhhccccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          184 SDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       184 ~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      ||++.+++|...+..+++.+++++|+++||||+|+
T Consensus       180 ah~~~~~~~~~~~~~i~~~~~~~~~~l~~SAT~~~  214 (236)
T 2pl3_A          180 ADRILDMGFADTMNAVIENLPKKRQTLLFSATQTK  214 (236)
T ss_dssp             HHHHHHTTTHHHHHHHHHTSCTTSEEEEEESSCCH
T ss_pred             hHHHhcCCcHHHHHHHHHhCCCCCeEEEEEeeCCH
Confidence            99999999999999999999999999999999985

>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=5.2e-39  Score=257.20  Aligned_cols=186  Identities=28%  Similarity=0.496  Sum_probs=166.9

Q ss_pred             CccccCC--CCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCC----CceeEEE
Q 027749           33 TSFDAMG--IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS----REVQALI  106 (219)
Q Consensus        33 ~~~~~~~--l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~----~~~~~li  106 (219)
                      .+|++++  +++.+++++.++|+..|+++|.++++.+..++++++++|||+|||++|++|+++.+....    .+.++||
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            3456665  899999999999999999999999999999999999999999999999999998776422    3567999


Q ss_pred             EcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcC-CCCCCCccEEEeccch
Q 027749          107 LSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK-TLRTRAIKLLVLDESD  185 (219)
Q Consensus       107 l~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~-~~~~~~l~~lVvDE~h  185 (219)
                      ++|+++|+.|+++.++++....+..+..+.|+.....+...+..+++|+|+||+++.+.+... ...++++++||+||||
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            999999999999999999988889999999999988888888888999999999999987764 4678999999999999


Q ss_pred             hhhccccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          186 EMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       186 ~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      ++.+++|...+..+++.+++.+|+++||||+|+
T Consensus       212 ~l~~~~~~~~l~~i~~~~~~~~q~l~~SAT~~~  244 (262)
T 3ly5_A          212 RILDVGFEEELKQIIKLLPTRRQTMLFSATQTR  244 (262)
T ss_dssp             HHHHTTCHHHHHHHHHHSCSSSEEEEECSSCCH
T ss_pred             HHhhhhHHHHHHHHHHhCCCCCeEEEEEecCCH
Confidence            999999999999999999999999999999985

>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=2.1e-38  Score=244.55  Aligned_cols=183  Identities=33%  Similarity=0.535  Sum_probs=168.3

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccC---CCceeEEEEcCC
Q 027749           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS---SREVQALILSPT  110 (219)
Q Consensus        34 ~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~---~~~~~~lil~P~  110 (219)
                      +|+++++++.+.+++.+.|+..|+++|.++++.+.+++++++++|||+|||++|+++++..+...   ..+++++|++|+
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            69999999999999999999999999999999999999999999999999999999999987642   346789999999


Q ss_pred             HHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhcc
Q 027749          111 RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (219)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~  190 (219)
                      ++|+.|+.+.+.++...  +++..+.|+.+...+...+..+++|+|+||+++.+.+.++...++++++||+||||++.++
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            99999999999998765  6777888888887777777788999999999999999888888999999999999999999


Q ss_pred             ccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          191 GFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       191 ~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      +|...+..+++.++++.|++++|||+|+
T Consensus       160 ~~~~~~~~i~~~~~~~~~~i~~SAT~~~  187 (207)
T 2gxq_A          160 GFEEEVEALLSATPPSRQTLLFSATLPS  187 (207)
T ss_dssp             TCHHHHHHHHHTSCTTSEEEEECSSCCH
T ss_pred             chHHHHHHHHHhCCccCeEEEEEEecCH
Confidence            9999999999999999999999999985

>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=6e-38  Score=248.34  Aligned_cols=199  Identities=26%  Similarity=0.483  Sum_probs=169.5

Q ss_pred             cceeeccCCCCccCccccC----CCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhh
Q 027749           20 KMVFETTEGVEAITSFDAM----GIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTV   95 (219)
Q Consensus        20 ~~~~~~~~~~~~~~~~~~~----~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~   95 (219)
                      .+..+....+.++.+|+++    ++++.+++++.+.|+..|+++|.++++.+.+|+++++++|||+|||++|++|++..+
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            3445556678899999987    899999999999999999999999999999999999999999999999999999988


Q ss_pred             cc-CCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHH-HHhcCCCeEEEeChHHHHHHHHcC--CC
Q 027749           96 DT-SSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDI-RKLEHGVHVVSGTPGRVCDMIKRK--TL  171 (219)
Q Consensus        96 ~~-~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~l~~~~~I~v~Tp~~l~~~l~~~--~~  171 (219)
                      .. ...++++||++|+++|+.|+.+.+.++....++.+..+.|+....... .....+++|+|+||+++..++.+.  ..
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            64 334678999999999999999999999888888887776655433322 122457899999999999998876  46


Q ss_pred             CCCCccEEEeccchhhhc---cccHHHHHHHHHhC-CCCCeEEEEeecccC
Q 027749          172 RTRAIKLLVLDESDEMLS---RGFKDQIYDVYRYL-PPDLQVCCPGSCFLF  218 (219)
Q Consensus       172 ~~~~l~~lVvDE~h~l~~---~~~~~~~~~i~~~~-~~~~q~i~~SATl~~  218 (219)
                      .++++++||+||||++.+   .+|...+..++..+ +.+.|+++||||+|.
T Consensus       172 ~~~~~~~lViDEah~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~SAT~~~  222 (245)
T 3dkp_A          172 DLASVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAY  222 (245)
T ss_dssp             CCTTCCEEEESSHHHHHHHC--CHHHHHHHHHHHCCCTTCEEEEEESSCCH
T ss_pred             ccccCcEEEEeChHHhcccccccHHHHHHHHHHhcCCCCcEEEEEeccCCH
Confidence            788999999999999998   46889999998776 457899999999985

>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-37  Score=261.03  Aligned_cols=199  Identities=65%  Similarity=1.054  Sum_probs=183.4

Q ss_pred             cceeeccCCCCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCC
Q 027749           20 KMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS   99 (219)
Q Consensus        20 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~   99 (219)
                      ..+.+....++...+|+++++++.+.+++.++|+..|+|+|.++++.+++++++++++|||+|||++|++|+++.+....
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            44455556667788999999999999999999999999999999999999999999999999999999999999887666


Q ss_pred             CceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEE
Q 027749          100 REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLL  179 (219)
Q Consensus       100 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~l  179 (219)
                      .++++||++|+++|+.|+.+.+.++....++.+..+.|+.....+...+..+++|+|+||+++.+++..+...+.++++|
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            67789999999999999999999999888999999999999888888888889999999999999999888888999999


Q ss_pred             EeccchhhhccccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          180 VLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       180 VvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      |+||+|++.+++|...+..+++.++++.|++++|||+|.
T Consensus       184 ViDEah~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~  222 (410)
T 2j0s_A          184 VLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPH  222 (410)
T ss_dssp             EEETHHHHTSTTTHHHHHHHHTTSCTTCEEEEEESCCCH
T ss_pred             EEccHHHHHhhhhHHHHHHHHHhCccCceEEEEEcCCCH
Confidence            999999999999999999999999999999999999974

>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=9e-37  Score=258.14  Aligned_cols=197  Identities=30%  Similarity=0.459  Sum_probs=177.3

Q ss_pred             eeeccCCCCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCC--
Q 027749           22 VFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS--   99 (219)
Q Consensus        22 ~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~--   99 (219)
                      +......|+++.+|+++++++.+.++|...|+..|+|+|.++++.+.+++++++++|||+|||++|++|++..+....  
T Consensus         4 ~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~   83 (417)
T 2i4i_A            4 EATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPG   83 (417)
T ss_dssp             EEESTTCCCCCSSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCCC
T ss_pred             ccCCCcCCcccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHhcccc
Confidence            344455678889999999999999999999999999999999999999999999999999999999999998775432  


Q ss_pred             ----------------CceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHH
Q 027749          100 ----------------REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVC  163 (219)
Q Consensus       100 ----------------~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~  163 (219)
                                      .++++||++|+++|+.|+++.+.++....++++..+.|+.+...+...+..+++|+|+||++|.
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~  163 (417)
T 2i4i_A           84 EALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLV  163 (417)
T ss_dssp             HHHHHHHHCBTTBSCSBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCHHHHHHHHTTCCSEEEECHHHHH
T ss_pred             chhhccccccccccccCCccEEEECCcHHHHHHHHHHHHHHhCcCCceEEEEECCCCHHHHHHHhhCCCCEEEEChHHHH
Confidence                            2367999999999999999999999888889999999999988888888889999999999999


Q ss_pred             HHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHh--CCC--CCeEEEEeecccC
Q 027749          164 DMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRY--LPP--DLQVCCPGSCFLF  218 (219)
Q Consensus       164 ~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~--~~~--~~q~i~~SATl~~  218 (219)
                      +.+....+.+.++++||+||+|++.+++|...+..++..  ++.  ..|++++|||+|.
T Consensus       164 ~~l~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~SAT~~~  222 (417)
T 2i4i_A          164 DMMERGKIGLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPK  222 (417)
T ss_dssp             HHHHTTSBCCTTCCEEEESSHHHHHHTTCHHHHHHHHTSSSCCCBTTBEEEEEESCCCH
T ss_pred             HHHHcCCcChhhCcEEEEEChhHhhccCcHHHHHHHHHhccCCCcCCcEEEEEEEeCCH
Confidence            999888888899999999999999999999999999885  333  6899999999974

>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=3.2e-35  Score=248.25  Aligned_cols=190  Identities=53%  Similarity=0.896  Sum_probs=176.5

Q ss_pred             CCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEc
Q 027749           29 VEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (219)
Q Consensus        29 ~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~  108 (219)
                      .+...+|+++++++.+.+.+.++|+..|+++|.++++.+.+|+++++++|||+|||++|++++++.+.....+.+++|++
T Consensus        36 ~~~~~~f~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~  115 (414)
T 3eiq_A           36 NEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLA  115 (414)
T ss_dssp             CCCCCCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCTTSCSCCEEEEC
T ss_pred             cchhcCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhhcCCceeEEEEe
Confidence            45668899999999999999999999999999999999999999999999999999999999999887766678899999


Q ss_pred             CCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhc-CCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhh
Q 027749          109 PTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (219)
Q Consensus       109 P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l  187 (219)
                      |+++|+.|+.+.+.++....+..+....|+.....+...+. .+++|+|+||++|.+.+..+...+.++++||+||||++
T Consensus       116 P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~~~vViDEah~~  195 (414)
T 3eiq_A          116 PTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEM  195 (414)
T ss_dssp             SSHHHHHHHHHHHHHHGGGSCCCEEECCCCTTHHHHHHHHTTTCCSEEEECHHHHHHHHHHTSSCSTTCCEEEECSHHHH
T ss_pred             ChHHHHHHHHHHHHHHhcccCceEEEEECCcchHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccCcEEEEECHHHh
Confidence            99999999999999999888899999999988877776665 67899999999999999888888899999999999999


Q ss_pred             hccccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          188 LSRGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       188 ~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      .++++...+..++..++++.|++++|||++.
T Consensus       196 ~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~  226 (414)
T 3eiq_A          196 LSRGFKDQIYDIFQKLNSNTQVVLLSATMPS  226 (414)
T ss_dssp             HHTTTHHHHHHHHTTSCTTCEEEEECSCCCH
T ss_pred             hccCcHHHHHHHHHhCCCCCeEEEEEEecCH
Confidence            9999999999999999999999999999874

>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=4.3e-35  Score=246.69  Aligned_cols=189  Identities=39%  Similarity=0.651  Sum_probs=173.6

Q ss_pred             CccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcC
Q 027749           30 EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (219)
Q Consensus        30 ~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P  109 (219)
                      ....+|+++++++.+.++|.++|+..|+|+|.++++.+.+++++++++|||+|||++|++|++..+.....+.+++|++|
T Consensus        18 ~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P   97 (400)
T 1s2m_A           18 TKGNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVP   97 (400)
T ss_dssp             ---CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECS
T ss_pred             cccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhhccCCccEEEEcC
Confidence            44578999999999999999999999999999999999999999999999999999999999998876656778999999


Q ss_pred             CHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhc
Q 027749          110 TRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (219)
Q Consensus       110 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~  189 (219)
                      +++|+.|+.+.+.++....++.+....|+.....+...+..+++|+|+||++|.+.+......+.++++||+||+|++.+
T Consensus        98 ~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~  177 (400)
T 1s2m_A           98 TRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLS  177 (400)
T ss_dssp             SHHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEESHHHHSS
T ss_pred             CHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHHHhcCCCCEEEEchHHHHHHHHhCCcccccCCEEEEeCchHhhh
Confidence            99999999999999998888999999999888877777778899999999999999988878889999999999999999


Q ss_pred             cccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          190 RGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       190 ~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      .+|...+..++..+++..|++++|||+|.
T Consensus       178 ~~~~~~~~~i~~~~~~~~~~i~lSAT~~~  206 (400)
T 1s2m_A          178 RDFKTIIEQILSFLPPTHQSLLFSATFPL  206 (400)
T ss_dssp             HHHHHHHHHHHTTSCSSCEEEEEESCCCH
T ss_pred             hchHHHHHHHHHhCCcCceEEEEEecCCH
Confidence            88999999999999999999999999874

>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=1.2e-34  Score=243.16  Aligned_cols=189  Identities=51%  Similarity=0.850  Sum_probs=173.3

Q ss_pred             CCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEc
Q 027749           29 VEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (219)
Q Consensus        29 ~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~  108 (219)
                      .+...+|+++++++.+.+++.++|+..|+|+|.++++.+.+++++++++|||+|||++|++|++..+.....++++||++
T Consensus        17 ~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~   96 (394)
T 1fuu_A           17 DKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLA   96 (394)
T ss_dssp             CCCCCSSGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTTCCSCCEEEEC
T ss_pred             ccccCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhccCCCCCEEEEc
Confidence            35567899999999999999999999999999999999999999999999999999999999999888776778899999


Q ss_pred             CCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhh
Q 027749          109 PTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (219)
Q Consensus       109 P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~  188 (219)
                      |+++|+.|+.+.+.++....++.+..+.|+.+.......+. +++|+|+||++|...+......+.++++||+||+|++.
T Consensus        97 P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-~~~i~v~T~~~l~~~~~~~~~~~~~~~~vIiDEah~~~  175 (394)
T 1fuu_A           97 PTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEML  175 (394)
T ss_dssp             SSHHHHHHHHHHHHHHTTTSCCCEEEECSSCCHHHHHHHHH-HCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhccCCeeEEEEeCCCchHHHHhhcC-CCCEEEECHHHHHHHHHhCCcchhhCcEEEEEChHHhh
Confidence            99999999999999998888899999999888766655443 68999999999999998888888999999999999999


Q ss_pred             ccccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          189 SRGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       189 ~~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      ++++...+..++..+++..|++++|||+++
T Consensus       176 ~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~  205 (394)
T 1fuu_A          176 SSGFKEQIYQIFTLLPPTTQVVLLSATMPN  205 (394)
T ss_dssp             HTTCHHHHHHHHHHSCTTCEEEEECSSCCH
T ss_pred             CCCcHHHHHHHHHhCCCCceEEEEEEecCH
Confidence            999999999999999999999999999974

>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=3.6e-34  Score=240.13  Aligned_cols=187  Identities=33%  Similarity=0.556  Sum_probs=168.8

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHH
Q 027749           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (219)
Q Consensus        33 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  112 (219)
                      .+|+++++++.+.++|.++|+..|+|+|.++++.+.+++++++.+|||+|||++|+++++..+.....++++||++|+++
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            57999999999999999999999999999999999999999999999999999999999998877666778999999999


Q ss_pred             HHHHHHHHHHHhcccc-ceeEEEEECCcccHHHHHHhcC-CCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhcc
Q 027749          113 LATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEH-GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (219)
Q Consensus       113 l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l~~-~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~  190 (219)
                      |+.|+.+.+.++.... ++++..+.|+.+.......+.. .++|+|+||+++...+.+....+.++++||+||||++.++
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            9999999999998765 7888888998887666655543 4799999999999999888888899999999999999884


Q ss_pred             -ccHHHHHHHHHhCCCCCeEEEEeecccCC
Q 027749          191 -GFKDQIYDVYRYLPPDLQVCCPGSCFLFD  219 (219)
Q Consensus       191 -~~~~~~~~i~~~~~~~~q~i~~SATl~~~  219 (219)
                       ++...+..++...++..|++++|||++++
T Consensus       168 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~  197 (391)
T 1xti_A          168 LDMRRDVQEIFRMTPHEKQVMMFSATLSKE  197 (391)
T ss_dssp             HHHHHHHHHHHHTSCSSSEEEEEESSCCST
T ss_pred             cchHHHHHHHHhhCCCCceEEEEEeeCCHH
Confidence             78888999999999999999999999863

>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=1.8e-33  Score=235.73  Aligned_cols=184  Identities=40%  Similarity=0.643  Sum_probs=165.3

Q ss_pred             ccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCC--CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEc
Q 027749           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (219)
Q Consensus        31 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~--~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~  108 (219)
                      -..+|+++++++.+.+++.+.|+..|+|+|.++++.++++  +++++++|||+|||++|+++++..+.....++++||++
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            4578999999999999999999999999999999999988  89999999999999999999999888776778899999


Q ss_pred             CCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhh
Q 027749          109 PTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (219)
Q Consensus       109 P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~  188 (219)
                      |+++|+.|+.+.+.++....++.+....++......    ..+++|+|+||+++...+.+....+.++++||+||||++.
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            999999999999999988888888777766543221    3468999999999999998888889999999999999998


Q ss_pred             c-cccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          189 S-RGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       189 ~-~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      + .++...+..+.+.++++.|++++|||+++
T Consensus       159 ~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~  189 (395)
T 3pey_A          159 DQQGLGDQCIRVKRFLPKDTQLVLFSATFAD  189 (395)
T ss_dssp             HSTTHHHHHHHHHHTSCTTCEEEEEESCCCH
T ss_pred             CccccHHHHHHHHHhCCCCcEEEEEEecCCH
Confidence            7 67889999999999999999999999874

>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=1.6e-33  Score=237.47  Aligned_cols=190  Identities=36%  Similarity=0.561  Sum_probs=166.4

Q ss_pred             cCCCCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCC--CcEEEEcCCCCchhHHhHHHHHhhhccCCCcee
Q 027749           26 TEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQ  103 (219)
Q Consensus        26 ~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~--~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~  103 (219)
                      ..+..+..+|+++++++.+.++|.++|+..|+|+|.++++.+.++  +++++++|||+|||++|++|++..+.....+++
T Consensus        18 ~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~   97 (412)
T 3fht_A           18 NSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQ   97 (412)
T ss_dssp             TSTTCCSSCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCC
T ss_pred             CCCccccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhhhcCCCCC
Confidence            344567789999999999999999999999999999999999987  899999999999999999999999887777788


Q ss_pred             EEEEcCCHHHHHHHHHHHHHhcccc-ceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHc-CCCCCCCccEEEe
Q 027749          104 ALILSPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-KTLRTRAIKLLVL  181 (219)
Q Consensus       104 ~lil~P~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~-~~~~~~~l~~lVv  181 (219)
                      +||++|+++|+.|+.+.+.++.... +..+....++......   ...+++|+|+||+++.+.+.+ +.+.++++++||+
T Consensus        98 ~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~~iVi  174 (412)
T 3fht_A           98 CLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVL  174 (412)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTCCCCTT---CCCCCSEEEECHHHHHHHHTTSCSSCGGGCCEEEE
T ss_pred             EEEECCCHHHHHHHHHHHHHHHhhcccceEEEeecCcchhhh---hcCCCCEEEECchHHHHHHHhcCCcChhhCcEEEE
Confidence            9999999999999999999987754 5777777776654332   134679999999999998865 5567789999999


Q ss_pred             ccchhhhc-cccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          182 DESDEMLS-RGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       182 DE~h~l~~-~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      ||+|++.+ .++...+..+.+.++++.|++++|||++.
T Consensus       175 DEah~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~  212 (412)
T 3fht_A          175 DEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFED  212 (412)
T ss_dssp             ETHHHHHSTTTTHHHHHHHHHTSCTTCEEEEEESCCCH
T ss_pred             eCHHHHhhcCCcHHHHHHHHhhCCCCceEEEEEeecCH
Confidence            99999987 68889999999999999999999999874

>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=6.1e-33  Score=230.34  Aligned_cols=184  Identities=32%  Similarity=0.553  Sum_probs=167.4

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCC-CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCH
Q 027749           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG-RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (219)
Q Consensus        33 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~-~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~  111 (219)
                      .+|+++++++.+.++|.+.|+..|+|+|.++++.++++ +++++.+|||+|||++|+++++..+... .+.+++|++|++
T Consensus         6 ~~f~~~~l~~~~~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~~-~~~~~lil~P~~   84 (367)
T 1hv8_A            6 MNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNEN-NGIEAIILTPTR   84 (367)
T ss_dssp             CCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSS-SSCCEEEECSCH
T ss_pred             CchhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhccc-CCCcEEEEcCCH
Confidence            57999999999999999999999999999999999988 6999999999999999999998877653 456799999999


Q ss_pred             HHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccc
Q 027749          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG  191 (219)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~  191 (219)
                      +|+.|+.+.+.++....++.+....|+.....+...+. +++|+|+||++|.+.+......+.++++||+||+|.+.+++
T Consensus        85 ~L~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~-~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~~~~  163 (367)
T 1hv8_A           85 ELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMG  163 (367)
T ss_dssp             HHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHH-TCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHTTT
T ss_pred             HHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHhhcC-CCCEEEecHHHHHHHHHcCCcccccCCEEEEeCchHhhhhc
Confidence            99999999999998887888888898888776655554 68999999999999998888888999999999999999999


Q ss_pred             cHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          192 FKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       192 ~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      +...+..++..++++.+++++|||+++
T Consensus       164 ~~~~~~~~~~~~~~~~~~i~~SAT~~~  190 (367)
T 1hv8_A          164 FIKDVEKILNACNKDKRILLFSATMPR  190 (367)
T ss_dssp             THHHHHHHHHTSCSSCEEEEECSSCCH
T ss_pred             hHHHHHHHHHhCCCCceEEEEeeccCH
Confidence            999999999999999999999999874

>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=2.1e-33  Score=242.10  Aligned_cols=186  Identities=37%  Similarity=0.571  Sum_probs=162.9

Q ss_pred             CccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCC--CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEE
Q 027749           30 EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALIL  107 (219)
Q Consensus        30 ~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~--~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil  107 (219)
                      .+..+|+++++++.++++|.++||..|+|+|.++++.++.+  +++++++|||+|||++|++|++..+.....++++||+
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            34678999999999999999999999999999999999987  8999999999999999999999998877777889999


Q ss_pred             cCCHHHHHHHHHHHHHhcccc-ceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHc-CCCCCCCccEEEeccch
Q 027749          108 SPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-KTLRTRAIKLLVLDESD  185 (219)
Q Consensus       108 ~P~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~-~~~~~~~l~~lVvDE~h  185 (219)
                      +|+++|+.|+.+.+.++.... ++.+....++......   ...+++|+|+||++|.+++.+ +.+.++++++||+||+|
T Consensus       169 ~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEah  245 (479)
T 3fmp_B          169 SPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEAD  245 (479)
T ss_dssp             CSSHHHHHHHHHHHHHHHTTSTTCCEEEESTTCCCCTT---CCCCCSEEEECHHHHHHHHTTSCCCCGGGCCEEEECCHH
T ss_pred             eChHHHHHHHHHHHHHHHhhCCCceEEEEeCCcccccc---ccCCCCEEEECchHHHHHHHhcCCcCcccCCEEEEECHH
Confidence            999999999999999887653 5667767666554322   134679999999999998865 45677899999999999


Q ss_pred             hhhc-cccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          186 EMLS-RGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       186 ~l~~-~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      ++.+ .++...+..+.+.++.++|++++|||++.
T Consensus       246 ~~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~  279 (479)
T 3fmp_B          246 VMIATQGHQDQSIRIQRMLPRNCQMLLFSATFED  279 (479)
T ss_dssp             HHHTSTTHHHHHHHHHTTSCTTSEEEEEESCCCH
T ss_pred             HHhhcCCcHHHHHHHHhhCCccceEEEEeCCCCH
Confidence            9987 58889999999999999999999999974

>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=3.2e-33  Score=246.27  Aligned_cols=189  Identities=27%  Similarity=0.433  Sum_probs=160.1

Q ss_pred             CccCccccCC----CCHHHHHHHHHCCCCCChHHHHHHHHHHh--CCCcEEEEcCCCCchhHHhHHHHHhhhccCC----
Q 027749           30 EAITSFDAMG----IKDDLLRGIYQYGFEKPSAIQQRAVMPII--KGRDVIAQAQSGTGKTSMIALTVCQTVDTSS----   99 (219)
Q Consensus        30 ~~~~~~~~~~----l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~--~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~----   99 (219)
                      ....+|+++.    +++.+++++.++|+..|+|+|.++++.++  .++++++++|||+|||++|++|+++.+....    
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            3444566553    99999999999999999999999999999  7789999999999999999999998876542    


Q ss_pred             CceeEEEEcCCHHHHHHHHHHHHHhccc----cceeEEEEECCcccHHHHHHhc-CCCeEEEeChHHHHHHHHcC-CCCC
Q 027749          100 REVQALILSPTRELATQTEKVILAIGDF----INIQAHACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRK-TLRT  173 (219)
Q Consensus       100 ~~~~~lil~P~~~l~~q~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~l~-~~~~I~v~Tp~~l~~~l~~~-~~~~  173 (219)
                      .++++||++|+++|+.|+.+.+.++...    ..+.+....|+.....+...+. .+++|+|+||++|.+.+... ...+
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            3568999999999999999999987532    3467778888888777766664 47999999999999988764 3457


Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCC-------CCCeEEEEeecccC
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLP-------PDLQVCCPGSCFLF  218 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~-------~~~q~i~~SATl~~  218 (219)
                      +.+++||+||||++.+++|...+..++..++       .++|+++||||+++
T Consensus       174 ~~~~~lViDEah~l~~~gf~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~  225 (579)
T 3sqw_A          174 RFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDD  225 (579)
T ss_dssp             TTCCEEEEETHHHHTSTTTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCT
T ss_pred             ccCCEEEEEChHHhhcCCCHHHHHHHHHHhhhhhcccccCceEEEEeccCCh
Confidence            8899999999999999999999988887753       37799999999985

>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=3.7e-32  Score=223.34  Aligned_cols=172  Identities=23%  Similarity=0.458  Sum_probs=157.2

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHH
Q 027749           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (219)
Q Consensus        40 l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~  119 (219)
                      +++.+.++|.++|+..|+|+|.++++.+.+++++++.+|||+|||++|+++++..      +.+++|++|+++|+.|+.+
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            5788999999999999999999999999999999999999999999999998774      4569999999999999999


Q ss_pred             HHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHH
Q 027749          120 VILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDV  199 (219)
Q Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i  199 (219)
                      .+.++....+..+..+.|+.....+...+. +++|+|+||++|.+.+......+.++++||+||+|++.++++...+..+
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~~  153 (337)
T 2z0m_A           75 HIRDIGRYMDTKVAEVYGGMPYKAQINRVR-NADIVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKII  153 (337)
T ss_dssp             HHHHHTTTSCCCEEEECTTSCHHHHHHHHT-TCSEEEECHHHHHHHHHTTSCCGGGCSEEEEESHHHHHHTTCHHHHHHH
T ss_pred             HHHHHhhhcCCcEEEEECCcchHHHHhhcC-CCCEEEECHHHHHHHHHcCCcchhhCcEEEEEChHHhhccccHHHHHHH
Confidence            999998888889988999888776665554 4899999999999998887778889999999999999999999999999


Q ss_pred             HHhCCCCCeEEEEeecccC
Q 027749          200 YRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       200 ~~~~~~~~q~i~~SATl~~  218 (219)
                      +..++...+++++|||+|+
T Consensus       154 ~~~~~~~~~~~~~SAT~~~  172 (337)
T 2z0m_A          154 LAQTSNRKITGLFSATIPE  172 (337)
T ss_dssp             HHHCTTCSEEEEEESCCCH
T ss_pred             HhhCCcccEEEEEeCcCCH
Confidence            9999999999999999975

>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=2.4e-32  Score=239.77  Aligned_cols=186  Identities=27%  Similarity=0.448  Sum_probs=157.0

Q ss_pred             CccccCC----CCHHHHHHHHHCCCCCChHHHHHHHHHHh--CCCcEEEEcCCCCchhHHhHHHHHhhhccCC----Cce
Q 027749           33 TSFDAMG----IKDDLLRGIYQYGFEKPSAIQQRAVMPII--KGRDVIAQAQSGTGKTSMIALTVCQTVDTSS----REV  102 (219)
Q Consensus        33 ~~~~~~~----l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~--~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~----~~~  102 (219)
                      .+|+++.    +++.+.+++.++|+..|+|+|.++++.++  .++++++++|||+|||++|++|+++.+....    .++
T Consensus        68 ~~~~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~  147 (563)
T 3i5x_A           68 VTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMV  147 (563)
T ss_dssp             CCHHHHHHTTSSCHHHHHHHHTTCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSC
T ss_pred             cCHHHHhhcCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhccccccCCe
Confidence            3455543    99999999999999999999999999999  6789999999999999999999999886543    246


Q ss_pred             eEEEEcCCHHHHHHHHHHHHHhccc----cceeEEEEECCcccHHHHHHh-cCCCeEEEeChHHHHHHHHcC-CCCCCCc
Q 027749          103 QALILSPTRELATQTEKVILAIGDF----INIQAHACVGGKSVGEDIRKL-EHGVHVVSGTPGRVCDMIKRK-TLRTRAI  176 (219)
Q Consensus       103 ~~lil~P~~~l~~q~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~l-~~~~~I~v~Tp~~l~~~l~~~-~~~~~~l  176 (219)
                      ++||++|+++|+.|+.+.+.++...    ....+..+.|+.....+...+ ..+++|+|+||++|.+++.+. ...++.+
T Consensus       148 ~~lil~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~  227 (563)
T 3i5x_A          148 KAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFV  227 (563)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTC
T ss_pred             eEEEEcCcHHHHHHHHHHHHHHHhhccccCceeEEEEECCcCHHHHHHHHhcCCCCEEEECcHHHHHHHHhccccccccc
Confidence            8999999999999999999887432    245677788888877776666 458999999999999988754 3357889


Q ss_pred             cEEEeccchhhhccccHHHHHHHHHhC-------CCCCeEEEEeecccC
Q 027749          177 KLLVLDESDEMLSRGFKDQIYDVYRYL-------PPDLQVCCPGSCFLF  218 (219)
Q Consensus       177 ~~lVvDE~h~l~~~~~~~~~~~i~~~~-------~~~~q~i~~SATl~~  218 (219)
                      ++||+||||++.+++|...+..++..+       +.++|+++||||+|+
T Consensus       228 ~~lViDEah~l~~~~f~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~  276 (563)
T 3i5x_A          228 DYKVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDD  276 (563)
T ss_dssp             CEEEEETHHHHTSTTTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCT
T ss_pred             eEEEEeCHHHHhccchHHHHHHHHHhhhhccccCccCceEEEEEccCCH
Confidence            999999999999999999988887765       237899999999985

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.97  E-value=8.3e-31  Score=221.92  Aligned_cols=168  Identities=15%  Similarity=0.217  Sum_probs=140.4

Q ss_pred             HHHHHHHH-CCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHH
Q 027749           43 DLLRGIYQ-YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVI  121 (219)
Q Consensus        43 ~~~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~  121 (219)
                      .+.+.+++ +++ .|+|+|.++++.+++|+++++++|||+|||++|+++++...   ..++++||++|+++|+.|+.+.+
T Consensus         9 ~~~~~l~~~~~~-~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~---~~~~~~lil~Pt~~L~~q~~~~~   84 (414)
T 3oiy_A            9 DFRSFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLA---RKGKKSALVFPTVTLVKQTLERL   84 (414)
T ss_dssp             HHHHHHHHHHSS-CCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHH---TTTCCEEEEESSHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCC-CCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHh---cCCCEEEEEECCHHHHHHHHHHH
Confidence            34455554 355 89999999999999999999999999999999999988766   23567999999999999999999


Q ss_pred             HHhccccceeEEEEECCccc---HHHHHHhcCC-CeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhc--------
Q 027749          122 LAIGDFINIQAHACVGGKSV---GEDIRKLEHG-VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS--------  189 (219)
Q Consensus       122 ~~~~~~~~~~~~~~~~~~~~---~~~~~~l~~~-~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~--------  189 (219)
                      .+++. .++++..+.|+.+.   ..+...+..+ ++|+|+||++|.+.+..  +.+.++++||+||||++.+        
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            99888 78899999999887   4555666555 99999999999887764  5567999999999987654        


Q ss_pred             ---cccHHH-HHHHHHhCC-----------CCCeEEEEeeccc
Q 027749          190 ---RGFKDQ-IYDVYRYLP-----------PDLQVCCPGSCFL  217 (219)
Q Consensus       190 ---~~~~~~-~~~i~~~~~-----------~~~q~i~~SATl~  217 (219)
                         .+|... +..+++.++           .+.|++++|||++
T Consensus       162 l~~~~~~~~~~~~i~~~~~~~~~~~~l~~~~~~~~i~~SAT~~  204 (414)
T 3oiy_A          162 LMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAK  204 (414)
T ss_dssp             HHHTTCCHHHHHHHHHHHHHTCCCCCCTTCCCCEEEESSCCSS
T ss_pred             HhhcCCcHHHHHHHHHhcccchhhhhcccCCCceEEEEecCCC
Confidence               566666 778887766           7899999999943

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=99.97  E-value=5.8e-30  Score=230.62  Aligned_cols=179  Identities=15%  Similarity=0.212  Sum_probs=156.8

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHHHHHH-HhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHH
Q 027749           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (219)
Q Consensus        34 ~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~-~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  112 (219)
                      +|+++++++.+.+.+.+.|+..|+|+|.++++. +.+++++++++|||+|||+++.+++++.+...  +.+++|++|+++
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 88999999999999999999999999877643  467999999999


Q ss_pred             HHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhcccc
Q 027749          113 LATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF  192 (219)
Q Consensus       113 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~  192 (219)
                      |+.|+.+.++++.. .++++....|+......   ...+++|+|+||+++..++.+....++++++||+||+|.+.++++
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            99999999965543 47888888887655432   124689999999999998888776788999999999999998888


Q ss_pred             HHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          193 KDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       193 ~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      ...+..++..++++.|+|++|||++.
T Consensus       156 ~~~~~~ll~~l~~~~~ii~lSATl~n  181 (720)
T 2zj8_A          156 GATLEVILAHMLGKAQIIGLSATIGN  181 (720)
T ss_dssp             HHHHHHHHHHHBTTBEEEEEECCCSC
T ss_pred             cHHHHHHHHHhhcCCeEEEEcCCcCC
Confidence            88999998888778999999999973

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.96  E-value=2e-29  Score=227.05  Aligned_cols=178  Identities=13%  Similarity=0.186  Sum_probs=155.1

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCChHHHHHHHHH-HhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCH
Q 027749           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (219)
Q Consensus        33 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~-~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~  111 (219)
                      .+|+++++++.+.+.+.+.|+..|+|+|.++++. +.+++++++++|||+|||+++.+++++.+...  +.+++|++|++
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 78899999999999999999999999877643  45799999999


Q ss_pred             HHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccc
Q 027749          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG  191 (219)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~  191 (219)
                      +|+.|+.+.++.+. ..++++....|+.......   ..+++|+|+||++|..++.+....++++++||+||+|.+.+.+
T Consensus        86 ~La~q~~~~~~~~~-~~g~~v~~~~G~~~~~~~~---~~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~~  161 (715)
T 2va8_A           86 ALTNEKYLTFKDWE-LIGFKVAMTSGDYDTDDAW---LKNYDIIITTYEKLDSLWRHRPEWLNEVNYFVLDELHYLNDPE  161 (715)
T ss_dssp             HHHHHHHHHHGGGG-GGTCCEEECCSCSSSCCGG---GGGCSEEEECHHHHHHHHHHCCGGGGGEEEEEECSGGGGGCTT
T ss_pred             HHHHHHHHHHHHhh-cCCCEEEEEeCCCCCchhh---cCCCCEEEEcHHHHHHHHhCChhHhhccCEEEEechhhcCCcc
Confidence            99999999996543 3478888888876654431   2368999999999999988877668899999999999998878


Q ss_pred             cHHHHHHHHHhCCCCCeEEEEeeccc
Q 027749          192 FKDQIYDVYRYLPPDLQVCCPGSCFL  217 (219)
Q Consensus       192 ~~~~~~~i~~~~~~~~q~i~~SATl~  217 (219)
                      +...+..++..++ +.|+|++|||++
T Consensus       162 ~~~~l~~i~~~~~-~~~ii~lSATl~  186 (715)
T 2va8_A          162 RGPVVESVTIRAK-RRNLLALSATIS  186 (715)
T ss_dssp             THHHHHHHHHHHH-TSEEEEEESCCT
T ss_pred             cchHHHHHHHhcc-cCcEEEEcCCCC
Confidence            8888888887776 789999999997

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A

Probab=99.96  E-value=1.3e-29  Score=227.86  Aligned_cols=177  Identities=15%  Similarity=0.181  Sum_probs=149.8

Q ss_pred             ccccCC--CCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCH
Q 027749           34 SFDAMG--IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (219)
Q Consensus        34 ~~~~~~--l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~  111 (219)
                      +|++++  +++.+.+.+.++|+..|+|+|.++++.+.+++++++++|||+|||+++.+++++.+..   +.+++|++|++
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  9999999999999999999999999999999999999999999999999999987664   45799999999


Q ss_pred             HHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccc
Q 027749          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG  191 (219)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~  191 (219)
                      +|+.|+.+.++.+. ..++++....|+......   ...+++|+|+||++|..++.+....++++++||+||+|.+.+++
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            99999999996543 347888888887765442   12478999999999999998877668899999999999999877


Q ss_pred             cHHHHHHHHHhC---CCCCeEEEEeeccc
Q 027749          192 FKDQIYDVYRYL---PPDLQVCCPGSCFL  217 (219)
Q Consensus       192 ~~~~~~~i~~~~---~~~~q~i~~SATl~  217 (219)
                      +...+..++..+   +++.|+|++|||++
T Consensus       155 r~~~~~~ll~~l~~~~~~~~ii~lSATl~  183 (702)
T 2p6r_A          155 RGATLEILVTKMRRMNKALRVIGLSATAP  183 (702)
T ss_dssp             THHHHHHHHHHHHHHCTTCEEEEEECCCT
T ss_pred             cccHHHHHHHHHHhcCcCceEEEECCCcC
Confidence            777766665554   57899999999997

>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=99.96  E-value=2.2e-28  Score=213.58  Aligned_cols=166  Identities=14%  Similarity=0.151  Sum_probs=133.9

Q ss_pred             CCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCC--ceeEEEEcCCHHHHHHHHHHHHHhccccc
Q 027749           52 GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR--EVQALILSPTRELATQTEKVILAIGDFIN  129 (219)
Q Consensus        52 ~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~--~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (219)
                      +...|+|+|.++++.+++++++++++|||+|||++|++|+++.+.....  ++++||++|+++|+.|+.+.+.++....+
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            3458999999999999999999999999999999999999988866432  57799999999999999999999988888


Q ss_pred             eeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCC-CCCCccEEEeccchhhhccccHHHH-HHHHHh----C
Q 027749          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL-RTRAIKLLVLDESDEMLSRGFKDQI-YDVYRY----L  203 (219)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~-~~~~l~~lVvDE~h~l~~~~~~~~~-~~i~~~----~  203 (219)
                      +++..+.|+.+...++..+..+++|+|+||++|.+.+....+ .+.++++||+||||++.+++....+ ...+..    .
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            999999999887777677777899999999999999988777 7899999999999999887643333 233222    1


Q ss_pred             CCCCeEEEEeeccc
Q 027749          204 PPDLQVCCPGSCFL  217 (219)
Q Consensus       204 ~~~~q~i~~SATl~  217 (219)
                      ++..|++++|||++
T Consensus       164 ~~~~~~l~lSAT~~  177 (556)
T 4a2p_A          164 SQLPQILGLTASVG  177 (556)
T ss_dssp             --CCEEEEEESCCC
T ss_pred             CCCCeEEEEeCCcc
Confidence            45689999999985

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae}

Probab=99.96  E-value=4.2e-29  Score=232.64  Aligned_cols=172  Identities=16%  Similarity=0.168  Sum_probs=151.0

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHH
Q 027749           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (219)
Q Consensus        33 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  112 (219)
                      ..|..++++..+...+...+...|+|+|.++++.+.+|+++++++|||+|||++|.++++..+..   +.+++|++|+++
T Consensus       162 ~~~~~~~l~~~~~~~~~~~~~f~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~~---g~rvlvl~Ptra  238 (1108)
T 3l9o_A          162 PNYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKN---KQRVIYTSPIKA  238 (1108)
T ss_dssp             SCCCSSTTTTTCCCSCSSCCSSCCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHHT---TCEEEEEESSHH
T ss_pred             CCcccCCCChhhhHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHhc---CCeEEEEcCcHH
Confidence            46777778777777777667778999999999999999999999999999999999999988744   457999999999


Q ss_pred             HHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhcccc
Q 027749          113 LATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF  192 (219)
Q Consensus       113 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~  192 (219)
                      |+.|+++.+.++..    .+..+.|+.+.       ..+++|+|+||++|.+++.+....++++++|||||||++.++++
T Consensus       239 La~Q~~~~l~~~~~----~VglltGd~~~-------~~~~~IlV~Tpe~L~~~L~~~~~~l~~l~lVVIDEaH~l~d~~r  307 (1108)
T 3l9o_A          239 LSNQKYRELLAEFG----DVGLMTGDITI-------NPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKER  307 (1108)
T ss_dssp             HHHHHHHHHHHHTS----SEEEECSSCBC-------CCSCSEEEEEHHHHHHHHHHCSSHHHHEEEEEEETGGGTTSHHH
T ss_pred             HHHHHHHHHHHHhC----CccEEeCcccc-------CCCCCEEEeChHHHHHHHHcCccccccCCEEEEhhhhhccccch
Confidence            99999999998765    45556676663       34689999999999999988877788999999999999999999


Q ss_pred             HHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          193 KDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       193 ~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      ...+..++..++++.|+|+||||+|.
T Consensus       308 g~~~e~ii~~l~~~~qvl~lSATipn  333 (1108)
T 3l9o_A          308 GVVWEETIILLPDKVRYVFLSATIPN  333 (1108)
T ss_dssp             HHHHHHHHHHSCTTSEEEEEECSCSS
T ss_pred             HHHHHHHHHhcCCCceEEEEcCCCCC
Confidence            99999999999999999999999875

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A*

Probab=99.96  E-value=2.3e-28  Score=215.23  Aligned_cols=173  Identities=14%  Similarity=0.179  Sum_probs=140.4

Q ss_pred             cccCCCCHHHHHHHHH-CCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHH
Q 027749           35 FDAMGIKDDLLRGIYQ-YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (219)
Q Consensus        35 ~~~~~l~~~~~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l  113 (219)
                      ++++++++.+.+.|++ +|+..|+|+|.++++.+++|+++++.+|||+|||++|++|++..      ..++||++|+++|
T Consensus        23 ~~~~~l~~~l~~~L~~~fg~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~lpal~~------~g~~lVisP~~~L   96 (591)
T 2v1x_A           23 KEDFPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCS------DGFTLVICPLISL   96 (591)
T ss_dssp             CSCSTTHHHHHHHHHHTSCCCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHHHHHHTS------SSEEEEECSCHHH
T ss_pred             cccCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHHHHHHHc------CCcEEEEeCHHHH
Confidence            3458899999999997 79999999999999999999999999999999999999999763      3479999999999


Q ss_pred             HHHHHHHHHHhccccceeEEEEECCcccHHHHHH------hcCCCeEEEeChHHHH------HHHHcCCCCCCCccEEEe
Q 027749          114 ATQTEKVILAIGDFINIQAHACVGGKSVGEDIRK------LEHGVHVVSGTPGRVC------DMIKRKTLRTRAIKLLVL  181 (219)
Q Consensus       114 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------l~~~~~I~v~Tp~~l~------~~l~~~~~~~~~l~~lVv  181 (219)
                      +.|+.+.+.++    ++.+..+.|+.+..+....      ...+++|+|+||++|.      +.+.. ...+.++.+|||
T Consensus        97 ~~q~~~~l~~~----gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L~~~~~~~~~l~~-~~~~~~i~~iVi  171 (591)
T 2v1x_A           97 MEDQLMVLKQL----GISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEK-AYEARRFTRIAV  171 (591)
T ss_dssp             HHHHHHHHHHH----TCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHHHHHSCHHHHHHHHH-HHHTTCEEEEEE
T ss_pred             HHHHHHHHHhc----CCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChhHhhccHHHHHHHHh-hhhccCCcEEEE
Confidence            99999999887    6777778887776544322      2457899999999874      22222 334678999999


Q ss_pred             ccchhhhccc--cHHHHHH--HHHhCCCCCeEEEEeecccC
Q 027749          182 DESDEMLSRG--FKDQIYD--VYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       182 DE~h~l~~~~--~~~~~~~--i~~~~~~~~q~i~~SATl~~  218 (219)
                      ||||++.+|+  |...+..  ++....++.|+++||||+++
T Consensus       172 DEAH~is~~g~dfr~~~~~l~~l~~~~~~~~ii~lSAT~~~  212 (591)
T 2v1x_A          172 DEVHCCSQWGHDFRPDYKALGILKRQFPNASLIGLTATATN  212 (591)
T ss_dssp             ETGGGGSTTCTTCCGGGGGGGHHHHHCTTSEEEEEESSCCH
T ss_pred             ECcccccccccccHHHHHHHHHHHHhCCCCcEEEEecCCCH
Confidence            9999999987  6665543  34333457899999999875

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.96  E-value=4.4e-28  Score=211.33  Aligned_cols=164  Identities=15%  Similarity=0.197  Sum_probs=140.1

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCC--ceeEEEEcCCHHHHHHHHHHHHHhccccceeE
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR--EVQALILSPTRELATQTEKVILAIGDFINIQA  132 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~--~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  132 (219)
                      .|+|+|.++++.+++++++++++|||+|||++|++|+++.+.....  ++++||++|+++|+.|+.+.+.++....++++
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            7999999999999999999999999999999999999988876532  56799999999999999999999988888999


Q ss_pred             EEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCC-CCCCccEEEeccchhhhccc-cHHHHHHHHHhC-----CC
Q 027749          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL-RTRAIKLLVLDESDEMLSRG-FKDQIYDVYRYL-----PP  205 (219)
Q Consensus       133 ~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~-~~~~l~~lVvDE~h~l~~~~-~~~~~~~i~~~~-----~~  205 (219)
                      ..+.|+.+...++..+..+++|+|+||++|...+....+ .+.++++||+||||++.+.+ +...+...+...     .+
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            999999987777667777899999999999999988776 78899999999999998774 333333443332     24


Q ss_pred             CCeEEEEeecccC
Q 027749          206 DLQVCCPGSCFLF  218 (219)
Q Consensus       206 ~~q~i~~SATl~~  218 (219)
                      ..|++++|||++.
T Consensus       164 ~~~~l~lSAT~~~  176 (555)
T 3tbk_A          164 LPQVVGLTASVGV  176 (555)
T ss_dssp             CCEEEEEESCCCC
T ss_pred             CCeEEEEecCccc
Confidence            6799999999853

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.96  E-value=3.8e-28  Score=226.15  Aligned_cols=161  Identities=15%  Similarity=0.209  Sum_probs=139.0

Q ss_pred             HCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccc
Q 027749           50 QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (219)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (219)
                      ..|+ .|+|+|.++++.+++|+++++++|||+|||++|+++++..+   ..++++||++||++|+.|+++.+.++. ..+
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-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLA---RKGKKSALVFPTVTLVKQTLERLQKLA-DEK  148 (1104)
T ss_dssp             HSSS-CCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHH---TTTCCEEEEESSHHHHHHHHHHHHTTS-CTT
T ss_pred             hcCC-CCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHH---hcCCeEEEEechHHHHHHHHHHHHHhh-CCC
Confidence            4677 69999999999999999999999999999998888887776   335679999999999999999999977 668


Q ss_pred             eeEEEEECCccc---HHHHHHhcCC-CeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhh----------c-cccHH
Q 027749          130 IQAHACVGGKSV---GEDIRKLEHG-VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML----------S-RGFKD  194 (219)
Q Consensus       130 ~~~~~~~~~~~~---~~~~~~l~~~-~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~----------~-~~~~~  194 (219)
                      +++..++|+.+.   ..+...+..+ ++|+|+||++|.+++..  +.++++++||+||||++.          + ++|..
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            899999999987   5566667665 99999999999887764  567899999999997655          4 77777


Q ss_pred             H-HHHHHHhCC-----------CCCeEEEEeeccc
Q 027749          195 Q-IYDVYRYLP-----------PDLQVCCPGSCFL  217 (219)
Q Consensus       195 ~-~~~i~~~~~-----------~~~q~i~~SATl~  217 (219)
                      . +..+++.++           ++.|+++||||+.
T Consensus       227 ~~i~~il~~l~~~~~~~~~~~~~~~q~ll~SAT~~  261 (1104)
T 4ddu_A          227 EIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAK  261 (1104)
T ss_dssp             HHHHHHHHHHHHTSCCCCCSSCCCCEEEEECBSSC
T ss_pred             HHHHHHHHhcccchhhhhhccCCCceEEEEcCCCC
Confidence            7 888888877           7899999999954

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.95  E-value=6.1e-28  Score=216.53  Aligned_cols=173  Identities=16%  Similarity=0.205  Sum_probs=140.9

Q ss_pred             HHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCC--ceeEEEEcCCHHHHHHHHHHHH
Q 027749           45 LRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR--EVQALILSPTRELATQTEKVIL  122 (219)
Q Consensus        45 ~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~--~~~~lil~P~~~l~~q~~~~~~  122 (219)
                      ..++..+|+..|+++|.++++.+++|+++++++|||+|||++|++++++.+.....  +.++||++|+++|+.|+.+.+.
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            45677889999999999999999999999999999999999999999987765432  3679999999999999999999


Q ss_pred             HhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCC-CCCCccEEEeccchhhhccc-cHHHHHHHH
Q 027749          123 AIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL-RTRAIKLLVLDESDEMLSRG-FKDQIYDVY  200 (219)
Q Consensus       123 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~-~~~~l~~lVvDE~h~l~~~~-~~~~~~~i~  200 (219)
                      ++....++++..+.|+.....+...+..+++|+|+||++|.+.+....+ .+.++++|||||||++.+.. +...+...+
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            9988778999999998876666666666899999999999999988766 68899999999999987653 333333333


Q ss_pred             Hh-----CCCCCeEEEEeeccc
Q 027749          201 RY-----LPPDLQVCCPGSCFL  217 (219)
Q Consensus       201 ~~-----~~~~~q~i~~SATl~  217 (219)
                      ..     .++..+++++|||+.
T Consensus       163 ~~~~~~~~~~~~~il~LTATp~  184 (696)
T 2ykg_A          163 DQKLGGSSGPLPQVIGLTASVG  184 (696)
T ss_dssp             HHHHTTCCSCCCEEEEEESCCC
T ss_pred             HHhhcccCCCCCeEEEEeCccc
Confidence            32     246789999999986

>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=99.95  E-value=6.4e-28  Score=186.55  Aligned_cols=165  Identities=13%  Similarity=0.133  Sum_probs=120.9

Q ss_pred             HCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccC---CCceeEEEEcCCHHHHHH-HHHHHHHhc
Q 027749           50 QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS---SREVQALILSPTRELATQ-TEKVILAIG  125 (219)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~---~~~~~~lil~P~~~l~~q-~~~~~~~~~  125 (219)
                      ......|+++|.++++.+.+++++++++|||+|||++++.+++..+...   ..+.+++|++|+++|+.| +.+.+.++.
T Consensus        28 ~~~~~~l~~~Q~~~i~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~~lil~p~~~L~~q~~~~~~~~~~  107 (216)
T 3b6e_A           28 PEPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFL  107 (216)
T ss_dssp             CSCCCCCCHHHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCCCEEEEESSHHHHHHHHHHTHHHHH
T ss_pred             ccCCCCchHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhcccccCCCcEEEEECHHHHHHHHHHHHHHHHh
Confidence            3345589999999999999999999999999999999999988766432   235679999999999999 777888776


Q ss_pred             cccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCC------CCCCCccEEEeccchhhhccccHHHH-HH
Q 027749          126 DFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT------LRTRAIKLLVLDESDEMLSRGFKDQI-YD  198 (219)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~------~~~~~l~~lVvDE~h~l~~~~~~~~~-~~  198 (219)
                      .. ++.+..+.|+.........+..+++|+|+||+.|...+....      ..+.++++||+||||++.+.++...+ ..
T Consensus       108 ~~-~~~v~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~~~~~~~  186 (216)
T 3b6e_A          108 KK-WYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIMRH  186 (216)
T ss_dssp             TT-TSCEEECCC---CCCCHHHHHHHCSEEEEEHHHHHHHHHC-------CCCGGGCSEEEETTC-------CHHHHHHH
T ss_pred             cc-CceEEEEeCCcccchhHHhhccCCCEEEECHHHHHHHHhccCcccccccchhcccEEEEECchhhccCCcHHHHHHH
Confidence            54 677877887776655555555578999999999999887643      56788999999999999876555444 23


Q ss_pred             HHHhC-------------CCCCeEEEEeec
Q 027749          199 VYRYL-------------PPDLQVCCPGSC  215 (219)
Q Consensus       199 i~~~~-------------~~~~q~i~~SAT  215 (219)
                      ++...             .+..++|++|||
T Consensus       187 ~~~~~~~~~~~~~~~~~~~~~~~~l~lSAT  216 (216)
T 3b6e_A          187 YLMQKLKNNRLKKENKPVIPLPQILGLTAS  216 (216)
T ss_dssp             HHHHHHHHHHHHHTTCCCCCCCEEEEEECC
T ss_pred             HHHHhcccccccccccCCCCcceEEEeecC
Confidence            32221             157899999998

>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=99.95  E-value=2.7e-27  Score=215.32  Aligned_cols=168  Identities=15%  Similarity=0.157  Sum_probs=135.9

Q ss_pred             HCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCC--ceeEEEEcCCHHHHHHHHHHHHHhccc
Q 027749           50 QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR--EVQALILSPTRELATQTEKVILAIGDF  127 (219)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~--~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (219)
                      -+|+..|+|+|.++++.+++|+++++++|||+|||++|++|+++.+.....  ++++||++|+++|+.|+.+.+.++...
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            456789999999999999999999999999999999999999988876532  567999999999999999999999888


Q ss_pred             cceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCC-CCCCccEEEeccchhhhcccc-HHHHHHHHHh---
Q 027749          128 INIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL-RTRAIKLLVLDESDEMLSRGF-KDQIYDVYRY---  202 (219)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~-~~~~l~~lVvDE~h~l~~~~~-~~~~~~i~~~---  202 (219)
                      .++++..++|+.+...+...+..+++|+|+||++|.+.+....+ .+.++++|||||||++...+. ...+..++..   
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            88999999999987777777777899999999999999988776 788999999999999887643 3333333332   


Q ss_pred             -CCCCCeEEEEeeccc
Q 027749          203 -LPPDLQVCCPGSCFL  217 (219)
Q Consensus       203 -~~~~~q~i~~SATl~  217 (219)
                       ..+..|++++|||++
T Consensus       403 ~~~~~~~~l~lSATp~  418 (797)
T 4a2q_A          403 SASQLPQILGLTASVG  418 (797)
T ss_dssp             TCCCCCEEEEEESCCC
T ss_pred             cCCCCCeEEEEcCCcc
Confidence             245689999999985

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A*

Probab=99.95  E-value=5.1e-28  Score=210.63  Aligned_cols=176  Identities=14%  Similarity=0.193  Sum_probs=140.9

Q ss_pred             cCccccCCCCHHHHHHHHH-CCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCC
Q 027749           32 ITSFDAMGIKDDLLRGIYQ-YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (219)
Q Consensus        32 ~~~~~~~~l~~~~~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~  110 (219)
                      +.+|+++++++.+.+.|++ +|+..|+|+|.++++.+++|+++++++|||+|||++|++|++..      ...+||++|+
T Consensus         1 ~~~fe~l~L~~~~~~~l~~~~g~~~~r~~Q~~~i~~il~g~d~lv~apTGsGKTl~~~lp~l~~------~g~~lvi~P~   74 (523)
T 1oyw_A            1 MAQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL------NGLTVVVSPL   74 (523)
T ss_dssp             CCCCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS------SSEEEEECSC
T ss_pred             CCChhhCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHHh------CCCEEEECCh
Confidence            3679999999999999997 89999999999999999999999999999999999999998753      2469999999


Q ss_pred             HHHHHHHHHHHHHhccccceeEEEEECCcccHHHHH---Hh-cCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchh
Q 027749          111 RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIR---KL-EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDE  186 (219)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~l-~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~  186 (219)
                      ++|+.|+.+.+..+    ++.+..+.++.+..+...   .+ ...++|+|+||++|........+...++++|||||||+
T Consensus        75 ~aL~~q~~~~l~~~----gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~~~~~~l~~~~~~~vViDEaH~  150 (523)
T 1oyw_A           75 ISLMKDQVDQLQAN----GVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHC  150 (523)
T ss_dssp             HHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGGG
T ss_pred             HHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhChHHHHHHhhCCCCEEEEeCccc
Confidence            99999999999875    567777777766544322   22 34689999999998632111123347899999999999


Q ss_pred             hhccc--cHHHHH---HHHHhCCCCCeEEEEeecccC
Q 027749          187 MLSRG--FKDQIY---DVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       187 l~~~~--~~~~~~---~i~~~~~~~~q~i~~SATl~~  218 (219)
                      +.+|+  |...+.   .+.+.+| +.+++++|||.++
T Consensus       151 i~~~g~~fr~~~~~l~~l~~~~~-~~~~i~lSAT~~~  186 (523)
T 1oyw_A          151 ISQWGHDFRPEYAALGQLRQRFP-TLPFMALTATADD  186 (523)
T ss_dssp             GCTTSSCCCHHHHGGGGHHHHCT-TSCEEEEESCCCH
T ss_pred             cCcCCCccHHHHHHHHHHHHhCC-CCCEEEEeCCCCH
Confidence            99886  555443   4455554 6899999999874

>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=99.94  E-value=6.2e-27  Score=217.73  Aligned_cols=162  Identities=18%  Similarity=0.202  Sum_probs=137.6

Q ss_pred             HHHH-HCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 027749           46 RGIY-QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (219)
Q Consensus        46 ~~l~-~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (219)
                      +.+. .+|+. | ++|.++++.+++|+++++++|||+|||+ |.+|++..+...  ++++||++||++|+.|+.+.+.++
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 57998 9 9999999999999999999999999997 888888877653  567999999999999999999999


Q ss_pred             ccccce----eEEEEECCcccHHH---HHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHH
Q 027749          125 GDFINI----QAHACVGGKSVGED---IRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIY  197 (219)
Q Consensus       125 ~~~~~~----~~~~~~~~~~~~~~---~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~  197 (219)
                      +...++    ++..++|+.+...+   ...+.+ ++|+|+||++|.+.+.+    ++++++||+||||+|+++  ...+.
T Consensus       123 ~~~~~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~-~~IlV~TP~~L~~~l~~----L~~l~~lViDEah~~l~~--~~~~~  195 (1054)
T 1gku_B          123 AEKAGVGTENLIGYYHGRIPKREKENFMQNLRN-FKIVITTTQFLSKHYRE----LGHFDFIFVDDVDAILKA--SKNVD  195 (1054)
T ss_dssp             HTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGG-CSEEEEEHHHHHHCSTT----SCCCSEEEESCHHHHHTS--THHHH
T ss_pred             HhhcCCCccceEEEEeCCCChhhHHHHHhhccC-CCEEEEcHHHHHHHHHH----hccCCEEEEeChhhhhhc--cccHH
Confidence            988787    88899999887663   344555 99999999999987655    668999999999999984  57777


Q ss_pred             HHHHhC-----------CCCCeEEEEeecccCC
Q 027749          198 DVYRYL-----------PPDLQVCCPGSCFLFD  219 (219)
Q Consensus       198 ~i~~~~-----------~~~~q~i~~SATl~~~  219 (219)
                      .++..+           +...|++++|||++++
T Consensus       196 ~i~~~lgf~~~~~~~~~~~~~q~~l~SAT~t~~  228 (1054)
T 1gku_B          196 KLLHLLGFHYDLKTKSWVGEARGCLMVSTATAK  228 (1054)
T ss_dssp             HHHHHTTEEEETTTTEEEECCSSEEEECCCCSC
T ss_pred             HHHHHhCcchhhhhhhcccCCceEEEEecCCCc
Confidence            777776           3578999999999863

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.94  E-value=2.5e-26  Score=212.38  Aligned_cols=155  Identities=18%  Similarity=0.231  Sum_probs=136.1

Q ss_pred             HHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhcccc
Q 027749           49 YQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI  128 (219)
Q Consensus        49 ~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~  128 (219)
                      ..++| .|+++|.++++.+.+++++++++|||+|||++|.++++..+..   +.++||++|+++|++|+++.+.++..  
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 RTYPF-TLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKN---KQRVIYTSPIKALSNQKYRELLAEFG--  154 (1010)
T ss_dssp             CCCSS-CCCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHHT---TCEEEEEESSHHHHHHHHHHHHHHHS--
T ss_pred             HhCCC-CCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhcc---CCeEEEECChHHHHHHHHHHHHHHhC--
Confidence            34566 5999999999999999999999999999999999988877643   46799999999999999999988765  


Q ss_pred             ceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCe
Q 027749          129 NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ  208 (219)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q  208 (219)
                        .+..+.|+.+..       .+++|+|+||++|.+++.+....++++++|||||+|++.++++...+..++..++++.|
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              455567766543       35799999999999998887778899999999999999999888899999999999999


Q ss_pred             EEEEeecccC
Q 027749          209 VCCPGSCFLF  218 (219)
Q Consensus       209 ~i~~SATl~~  218 (219)
                      ++++|||+|.
T Consensus       226 il~LSATi~n  235 (1010)
T 2xgj_A          226 YVFLSATIPN  235 (1010)
T ss_dssp             EEEEECCCTT
T ss_pred             EEEEcCCCCC
Confidence            9999999974

>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=99.94  E-value=3.3e-26  Score=211.02  Aligned_cols=168  Identities=15%  Similarity=0.175  Sum_probs=134.4

Q ss_pred             HCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCC--ceeEEEEcCCHHHHHHHHHHHHHhccc
Q 027749           50 QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR--EVQALILSPTRELATQTEKVILAIGDF  127 (219)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~--~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (219)
                      -.++..|+|+|.++++.+++|+++++++|||+|||++|++++++.+.....  +.++||++|+++|+.|+.+.+.++...
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            345778999999999999999999999999999999999999888776432  567999999999999999999999887


Q ss_pred             cceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCC-CCCCccEEEeccchhhhccc-cHHHHHHHHHh---
Q 027749          128 INIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL-RTRAIKLLVLDESDEMLSRG-FKDQIYDVYRY---  202 (219)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~-~~~~l~~lVvDE~h~l~~~~-~~~~~~~i~~~---  202 (219)
                      .++++..++|+.+...+...+..+++|+|+||++|.+.+....+ .+.++++||+||||++...+ +...+..++..   
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            78999999999877665556666789999999999999987766 68889999999999988764 33333333333   


Q ss_pred             -CCCCCeEEEEeeccc
Q 027749          203 -LPPDLQVCCPGSCFL  217 (219)
Q Consensus       203 -~~~~~q~i~~SATl~  217 (219)
                       ..+..|++++|||.+
T Consensus       403 ~~~~~~~~l~LSATp~  418 (936)
T 4a2w_A          403 SASQLPQILGLTASVG  418 (936)
T ss_dssp             TCSCCCEEEEEESCCC
T ss_pred             cCCCcCeEEEecCCcc
Confidence             245689999999984

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.93  E-value=5.6e-26  Score=210.00  Aligned_cols=156  Identities=16%  Similarity=0.206  Sum_probs=135.8

Q ss_pred             HCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccc
Q 027749           50 QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (219)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (219)
                      .++| .|+++|.++++.+.+|+++++++|||+|||++|++++...+..   +.++||++|+++|+.|+++.+.++..  +
T Consensus        35 ~~~f-~l~~~Q~~aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~~---g~~vlvl~PtraLa~Q~~~~l~~~~~--~  108 (997)
T 4a4z_A           35 SWPF-ELDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHRN---MTKTIYTSPIKALSNQKFRDFKETFD--D  108 (997)
T ss_dssp             CCSS-CCCHHHHHHHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHHT---TCEEEEEESCGGGHHHHHHHHHTTC----
T ss_pred             hCCC-CCCHHHHHHHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHhc---CCeEEEEeCCHHHHHHHHHHHHHHcC--C
Confidence            3455 5899999999999999999999999999999999988776543   46799999999999999999988654  5


Q ss_pred             eeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeE
Q 027749          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQV  209 (219)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~  209 (219)
                      +++..+.|+.+..       ..++|+|+||+.|.+++......++++++|||||||++.++++...+..++..++++.|+
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            6777788877643       357999999999999988877778999999999999999999888999999999999999


Q ss_pred             EEEeecccC
Q 027749          210 CCPGSCFLF  218 (219)
Q Consensus       210 i~~SATl~~  218 (219)
                      |++|||+|.
T Consensus       182 IlLSAT~~n  190 (997)
T 4a4z_A          182 ILLSATVPN  190 (997)
T ss_dssp             EEEECCCTT
T ss_pred             EEEcCCCCC
Confidence            999999873

>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=99.93  E-value=1.1e-25  Score=216.35  Aligned_cols=163  Identities=13%  Similarity=0.211  Sum_probs=132.1

Q ss_pred             CCCCChHHHHHHHHHHh-CCCcEEEEcCCCCchhHHhHHHHHhhhccC--------CCceeEEEEcCCHHHHHHHHHHHH
Q 027749           52 GFEKPSAIQQRAVMPII-KGRDVIAQAQSGTGKTSMIALTVCQTVDTS--------SREVQALILSPTRELATQTEKVIL  122 (219)
Q Consensus        52 ~~~~~~~~Q~~~~~~~~-~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~--------~~~~~~lil~P~~~l~~q~~~~~~  122 (219)
                      ||+.++++|.+++|.++ +++|++++||||+|||+++.+++++.+...        ..+.++||++|+++|+.|+++.+.
T Consensus        76 g~~~ln~iQs~~~~~al~~~~N~lv~APTGsGKTlva~l~il~~l~~~~~~~~~~~~~~~k~lyiaP~kALa~e~~~~l~  155 (1724)
T 4f92_B           76 GFKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMVGSFG  155 (1724)
T ss_dssp             TCSBCCHHHHHTHHHHHTCCCCEEEECCTTSCCHHHHHHHHHHHHGGGCCTTSSCCTTSCEEEEECSSHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHcCCCcEEEEeCCcchHHHHHHHHHHHHHHhhccccccccCCCCEEEEECCHHHHHHHHHHHHH
Confidence            78899999999999876 578999999999999999999999887542        235789999999999999999999


Q ss_pred             HhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCC--CCCCCccEEEeccchhhhccccHHHHHHH-
Q 027749          123 AIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT--LRTRAIKLLVLDESDEMLSRGFKDQIYDV-  199 (219)
Q Consensus       123 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~--~~~~~l~~lVvDE~h~l~~~~~~~~~~~i-  199 (219)
                      +.....++++..+.|+.....+   ...+++|+|+|||++..++++..  ..++++++||+||+|.+.+ ..+..++.+ 
T Consensus       156 ~~~~~~gi~V~~~tGd~~~~~~---~~~~~~IlVtTpEkld~llr~~~~~~~l~~v~~vIiDEvH~l~d-~RG~~lE~~l  231 (1724)
T 4f92_B          156 KRLATYGITVAELTGDHQLCKE---EISATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLHD-DRGPVLEALV  231 (1724)
T ss_dssp             HHHTTTTCCEEECCSSCSSCCT---TGGGCSEEEECHHHHHHHTTSSTTHHHHTTEEEEEETTGGGGGS-TTHHHHHHHH
T ss_pred             HHHhhCCCEEEEEECCCCCCcc---ccCCCCEEEECHHHHHHHHcCCccchhhcCcCEEEEecchhcCC-ccHHHHHHHH
Confidence            8888889999999988765432   12468999999999876665433  2368899999999997765 333333332 


Q ss_pred             ------HHhCCCCCeEEEEeecccC
Q 027749          200 ------YRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       200 ------~~~~~~~~q~i~~SATl~~  218 (219)
                            .+..+++.|+|++|||+|+
T Consensus       232 ~rl~~~~~~~~~~~riI~LSATl~N  256 (1724)
T 4f92_B          232 ARAIRNIEMTQEDVRLIGLSATLPN  256 (1724)
T ss_dssp             HHHHHHHHHHTCCCEEEEEECSCTT
T ss_pred             HHHHHHHHhCCCCCcEEEEecccCC
Confidence                  3345778999999999984

>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=99.93  E-value=3e-25  Score=213.47  Aligned_cols=174  Identities=18%  Similarity=0.215  Sum_probs=139.8

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHHhC-CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHH
Q 027749           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPIIK-GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE  118 (219)
Q Consensus        40 l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~  118 (219)
                      +.+...+++...+|..++|+|.++++.+.. ++|++++||||+|||+++.+++++.+.... +.++||++|+++|+.|++
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            556777788777899999999999999875 578999999999999999999999887643 457999999999999999


Q ss_pred             HHHHH-hccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCC--CCCCCccEEEeccchhhhccccHHH
Q 027749          119 KVILA-IGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT--LRTRAIKLLVLDESDEMLSRGFKDQ  195 (219)
Q Consensus       119 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~--~~~~~l~~lVvDE~h~l~~~~~~~~  195 (219)
                      +.+.+ +....+.++..+.|+...+..   ...+++|+|+||+++..++++..  ..++++++||+||+|.+.+. .+..
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            99965 556678899888887665433   22458999999999988776533  34678999999999988764 2333


Q ss_pred             -------HHHHHHhCCCCCeEEEEeecccC
Q 027749          196 -------IYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       196 -------~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                             +..+....+++.|+|++|||++.
T Consensus      1066 le~il~rl~~i~~~~~~~~riI~lSATl~N 1095 (1724)
T 4f92_B         1066 LEVICSRMRYISSQIERPIRIVALSSSLSN 1095 (1724)
T ss_dssp             HHHHHHHHHHHHHTTSSCCEEEEEESCBTT
T ss_pred             HHHHHHHHHHHHhhcCCCceEEEEeCCCCC
Confidence                   33344456788999999999974

>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=99.93  E-value=2.8e-25  Score=174.72  Aligned_cols=158  Identities=16%  Similarity=0.158  Sum_probs=120.7

Q ss_pred             CCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCC--ceeEEEEcCCHHHHHHHHHHHHHhcc-cc
Q 027749           52 GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR--EVQALILSPTRELATQTEKVILAIGD-FI  128 (219)
Q Consensus        52 ~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~--~~~~lil~P~~~l~~q~~~~~~~~~~-~~  128 (219)
                      ....++++|.++++.+.+|++++++||||+|||..+..+++........  ..+++++.|+++++.|+.+.+..... ..
T Consensus        58 ~~~p~~~~q~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~~~~~~~~~~~~~  137 (235)
T 3llm_A           58 ELLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEP  137 (235)
T ss_dssp             HTSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHHHHHHHHTTTCCT
T ss_pred             hcCChHHHHHHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHHHHHHHHHhcccc
Confidence            3346799999999999999999999999999999888888876654433  45899999999999999988865543 22


Q ss_pred             ceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhh-hccccH-HHHHHHHHhCCCC
Q 027749          129 NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM-LSRGFK-DQIYDVYRYLPPD  206 (219)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l-~~~~~~-~~~~~i~~~~~~~  206 (219)
                      +..+........     .....+++|+|+||+++.+.+..   .++++++||+||+|.+ .+.+|. ..+..++... ++
T Consensus       138 ~~~~g~~~~~~~-----~~~~~~~~Ivv~Tpg~l~~~l~~---~l~~~~~lVlDEah~~~~~~~~~~~~l~~i~~~~-~~  208 (235)
T 3llm_A          138 GKSCGYSVRFES-----ILPRPHASIMFCTVGVLLRKLEA---GIRGISHVIVDEIHERDINTDFLLVVLRDVVQAY-PE  208 (235)
T ss_dssp             TSSEEEEETTEE-----ECCCSSSEEEEEEHHHHHHHHHH---CCTTCCEEEECCTTSCCHHHHHHHHHHHHHHHHC-TT
T ss_pred             CceEEEeechhh-----ccCCCCCeEEEECHHHHHHHHHh---hhcCCcEEEEECCccCCcchHHHHHHHHHHHhhC-CC
Confidence            333332221111     11124688999999999998876   3789999999999985 666666 4566666665 47


Q ss_pred             CeEEEEeecccC
Q 027749          207 LQVCCPGSCFLF  218 (219)
Q Consensus       207 ~q~i~~SATl~~  218 (219)
                      .|+++||||++.
T Consensus       209 ~~~il~SAT~~~  220 (235)
T 3llm_A          209 VRIVLMSATIDT  220 (235)
T ss_dssp             SEEEEEECSSCC
T ss_pred             CeEEEEecCCCH
Confidence            899999999986

>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=99.92  E-value=1.2e-24  Score=185.98  Aligned_cols=159  Identities=18%  Similarity=0.152  Sum_probs=132.4

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEE
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (219)
                      .|+|+|.++++.+.++ ++++.+|||+|||++++.+++..+.  ..+.++||++|+++|+.|+.+++.++......++..
T Consensus         9 ~l~~~Q~~~i~~~~~~-~~ll~~~tG~GKT~~~~~~~~~~~~--~~~~~~liv~P~~~L~~q~~~~~~~~~~~~~~~v~~   85 (494)
T 1wp9_A            9 QPRIYQEVIYAKCKET-NCLIVLPTGLGKTLIAMMIAEYRLT--KYGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVA   85 (494)
T ss_dssp             CCCHHHHHHHHHGGGS-CEEEECCTTSCHHHHHHHHHHHHHH--HSCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEE
T ss_pred             CccHHHHHHHHHHhhC-CEEEEcCCCCCHHHHHHHHHHHHHh--cCCCeEEEEECCHHHHHHHHHHHHHHhCcchhheEE
Confidence            6899999999999988 9999999999999999999888766  234579999999999999999999987544557777


Q ss_pred             EECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEee
Q 027749          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGS  214 (219)
Q Consensus       135 ~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SA  214 (219)
                      +.|+...... .....+++|+|+||+.|...+....+.+.++++||+||||++.+......+...+....+..+++++||
T Consensus        86 ~~g~~~~~~~-~~~~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~~~~~~~~~~~~~~~~~~~~~l~lTa  164 (494)
T 1wp9_A           86 LTGEKSPEER-SKAWARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTA  164 (494)
T ss_dssp             ECSCSCHHHH-HHHHHHCSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTTCHHHHHHHHHHHHCSSCCEEEEES
T ss_pred             eeCCcchhhh-hhhccCCCEEEecHHHHHHHHhcCCcchhhceEEEEECCcccCCCCcHHHHHHHHHhcCCCCeEEEEec
Confidence            7877765543 333346899999999999998887778899999999999998866445555566665567889999999


Q ss_pred             ccc
Q 027749          215 CFL  217 (219)
Q Consensus       215 Tl~  217 (219)
                      |.+
T Consensus       165 Tp~  167 (494)
T 1wp9_A          165 SPG  167 (494)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            986

>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=99.92  E-value=4.8e-25  Score=196.89  Aligned_cols=160  Identities=19%  Similarity=0.230  Sum_probs=136.1

Q ss_pred             HCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccc
Q 027749           50 QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (219)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (219)
                      ..|+ .|+|+|..++|.+++|+  +.+++||+|||++|.+|++.....   ++.++||+||++||.|..+.+..+....+
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 99999999999999998  999999999999999999855443   35699999999999999999999999999


Q ss_pred             eeEEEEECCcccHHHHHHhcCCCeEEEeChHHH-HHHHHcC------CCCCCCccEEEeccchhhh-ccc----------
Q 027749          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRK------TLRTRAIKLLVLDESDEML-SRG----------  191 (219)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l-~~~l~~~------~~~~~~l~~lVvDE~h~l~-~~~----------  191 (219)
                      +++.+++|+.+...+  ....+++|+|+||++| .+++..+      .+.++.+.++|+||||.|+ +.+          
T Consensus       153 l~v~~i~gg~~~~~r--~~~~~~dIv~gTpgrlgfD~L~D~m~~~~~~l~lr~~~~lVlDEaD~mLiDea~tplIisg~~  230 (844)
T 1tf5_A          153 LTVGLNLNSMSKDEK--REAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQA  230 (844)
T ss_dssp             CCEEECCTTSCHHHH--HHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTTTCEEEEEEEE
T ss_pred             CeEEEEeCCCCHHHH--HHhcCCCEEEECchhhhHHHHHHhhhcchhhhcccCCCEEEECchhhhhhhccccchhhcCCc
Confidence            999999999876543  3345799999999999 5655432      3567889999999999998 553          


Q ss_pred             -----cHHHHHHHHHhCC---------CCCeEE-----------------EEeeccc
Q 027749          192 -----FKDQIYDVYRYLP---------PDLQVC-----------------CPGSCFL  217 (219)
Q Consensus       192 -----~~~~~~~i~~~~~---------~~~q~i-----------------~~SATl~  217 (219)
                           |...+..+++.++         +..|++                 +||||.+
T Consensus       231 ~~~~~~~~~i~~iv~~l~~~~~y~vd~k~rq~~lt~~g~~~~e~~~~i~~Lfsat~~  287 (844)
T 1tf5_A          231 AKSTKLYVQANAFVRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHV  287 (844)
T ss_dssp             ECCCHHHHHHHHHHTTCCSSSSBCCCSSSCCCCBCHHHHHHHHHHTTCSCTTSGGGH
T ss_pred             ccchhHHHHHHHHHHhCcccccceeccccceEEecHHHHHHHHHHhCccccCCCccc
Confidence                 7788999999997         467887                 8999975

>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=99.92  E-value=4.2e-25  Score=178.13  Aligned_cols=152  Identities=20%  Similarity=0.174  Sum_probs=123.9

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEE
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (219)
                      .|+++|.++++.++++++.++++|||+|||.+++.++...+...  ..++||++|+++|+.|+.+.+.++.......+..
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            79999999999988888899999999999999988777665432  3369999999999999999999997766677777


Q ss_pred             EECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEee
Q 027749          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGS  214 (219)
Q Consensus       135 ~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SA  214 (219)
                      +.++.....   ....+++|+|+||+.+...   ....+.++++||+||||++.+    ..+..+++.+++..+++++||
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            777765432   2235689999999876532   223467889999999999874    477788888878899999999


Q ss_pred             cccC
Q 027749          215 CFLF  218 (219)
Q Consensus       215 Tl~~  218 (219)
                      |++.
T Consensus       261 Tp~~  264 (282)
T 1rif_A          261 SLRD  264 (282)
T ss_dssp             SCCT
T ss_pred             CCCC
Confidence            9975

>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=99.92  E-value=8.1e-26  Score=202.83  Aligned_cols=163  Identities=13%  Similarity=0.152  Sum_probs=127.0

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccC---CCceeEEEEcCCHHHHHHH-HHHHHHhccccce
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS---SREVQALILSPTRELATQT-EKVILAIGDFINI  130 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~---~~~~~~lil~P~~~l~~q~-~~~~~~~~~~~~~  130 (219)
                      .|+|+|.++++.+++|+++++++|||+|||++|++|+++.+...   ..+.++||++|+++|+.|+ .+.+.+++.. ++
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            79999999999999999999999999999999999998877543   1235799999999999999 9999998765 58


Q ss_pred             eEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHH------HcCCCCCCCccEEEeccchhhhccc-cHHHHHHHHHh-
Q 027749          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMI------KRKTLRTRAIKLLVLDESDEMLSRG-FKDQIYDVYRY-  202 (219)
Q Consensus       131 ~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l------~~~~~~~~~l~~lVvDE~h~l~~~~-~~~~~~~i~~~-  202 (219)
                      ++..+.|+.........+..+++|+|+||+.|...+      ....+.+.++++|||||||++.... +...+...+.. 
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            888888888777666666678999999999999887      3445677889999999999986543 22222222221 


Q ss_pred             ---C---------CCCCeEEEEeecccC
Q 027749          203 ---L---------PPDLQVCCPGSCFLF  218 (219)
Q Consensus       203 ---~---------~~~~q~i~~SATl~~  218 (219)
                         .         .+.++++++|||.+.
T Consensus       166 ~~~~~~~~~~~~~~~~~~il~lTATp~~  193 (699)
T 4gl2_A          166 LKNNRLKKENKPVIPLPQILGLTASPGV  193 (699)
T ss_dssp             HHHHHHHC----CCCCCEEEEECSCCCC
T ss_pred             hcccccccccccCCCCCEEEEecccccc
Confidence               1         156799999999875

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.91  E-value=3.8e-24  Score=185.58  Aligned_cols=153  Identities=20%  Similarity=0.166  Sum_probs=127.6

Q ss_pred             CCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEE
Q 027749           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAH  133 (219)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~  133 (219)
                      ..|+++|.++++.+++++++++++|||+|||++++.++...+...  +.+++|++|+++|+.|+.+.+.++....+..+.
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            379999999999999999999999999999999998888776543  347999999999999999999998766667788


Q ss_pred             EEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       134 ~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      .+.|+.+...+   +..+++|+|+||+.+..   .....++++++|||||+|++..    ..+..+++.+++..++++||
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            88877766543   45678999999996543   2334567899999999999774    55777888888889999999


Q ss_pred             ecccC
Q 027749          214 SCFLF  218 (219)
Q Consensus       214 ATl~~  218 (219)
                      ||.+.
T Consensus       260 ATp~~  264 (510)
T 2oca_A          260 GSLRD  264 (510)
T ss_dssp             SCGGG
T ss_pred             eCCCC
Confidence            99864

>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=99.91  E-value=7e-24  Score=191.14  Aligned_cols=163  Identities=19%  Similarity=0.199  Sum_probs=128.5

Q ss_pred             HHHHHHHHHCCCCCChHHHHHHHHHHhCC------CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHH
Q 027749           42 DDLLRGIYQYGFEKPSAIQQRAVMPIIKG------RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELAT  115 (219)
Q Consensus        42 ~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~------~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~  115 (219)
                      ..+.+.+..++| .|+++|.++++.+.++      +++++++|||+|||++|+++++..+..   +.+++|++||++|+.
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            334445568888 8999999999998765      589999999999999999999987764   356999999999999


Q ss_pred             HHHHHHHHhccccceeEEEEECCcccHHHH---HHhcC-CCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccc
Q 027749          116 QTEKVILAIGDFINIQAHACVGGKSVGEDI---RKLEH-GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG  191 (219)
Q Consensus       116 q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~l~~-~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~  191 (219)
                      |+++.+.++....++++..++|+.+..++.   ..+.. .++|+|+||+.|.+     ...+.++++||+||+|++... 
T Consensus       432 Q~~~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~-----~~~~~~l~lVVIDEaHr~g~~-  505 (780)
T 1gm5_A          432 QHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE-----DVHFKNLGLVIIDEQHRFGVK-  505 (780)
T ss_dssp             HHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH-----CCCCSCCCEEEEESCCCC----
T ss_pred             HHHHHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhh-----hhhccCCceEEecccchhhHH-
Confidence            999999999988889999999988765543   33333 59999999987743     456889999999999985321 


Q ss_pred             cHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          192 FKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       192 ~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                          ....+.....++++++||||.++
T Consensus       506 ----qr~~l~~~~~~~~vL~mSATp~p  528 (780)
T 1gm5_A          506 ----QREALMNKGKMVDTLVMSATPIP  528 (780)
T ss_dssp             ------CCCCSSSSCCCEEEEESSCCC
T ss_pred             ----HHHHHHHhCCCCCEEEEeCCCCH
Confidence                12222333457899999999764

>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=99.91  E-value=1.1e-23  Score=188.25  Aligned_cols=160  Identities=16%  Similarity=0.208  Sum_probs=136.9

Q ss_pred             HCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccc
Q 027749           50 QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (219)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (219)
                      ..|+ .|+++|..++|.+++|+  +.+++||+|||++|.+|++.....   +..++||+||++||.|..+.+..+....+
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            4687 99999999999999997  999999999999999999765543   34599999999999999999999999999


Q ss_pred             eeEEEEECCcccHHHHHHhcCCCeEEEeChHHH-HHHHHcC------CCCCCCccEEEeccchhhh-c------------
Q 027749          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRK------TLRTRAIKLLVLDESDEML-S------------  189 (219)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l-~~~l~~~------~~~~~~l~~lVvDE~h~l~-~------------  189 (219)
                      +++.+++|+.+...+  ....+|+|+|+||++| .+++..+      .+.++.+.++||||||.|+ +            
T Consensus       181 Lsv~~i~gg~~~~~r--~~~y~~DIvygTpgrlgfDyLrD~m~~~~~~l~lr~l~~lIVDEaDsmLiDeartPLiiSg~~  258 (922)
T 1nkt_A          181 LQVGVILATMTPDER--RVAYNADITYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVDEVDSILIDEARTPLIISGPA  258 (922)
T ss_dssp             CCEEECCTTCCHHHH--HHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEETTHHHHHTTGGGSCEEEEEEC
T ss_pred             CeEEEEeCCCCHHHH--HHhcCCCEEEECchHhhHHHHHhhhhccHhhhccCCCCEEEEeChHHHHHhcCccceeecCCC
Confidence            999999999875443  3344799999999999 6766543      3567889999999999998 3            


Q ss_pred             ---cccHHHHHHHHHhCC---------CCCeEE-----------------EEeeccc
Q 027749          190 ---RGFKDQIYDVYRYLP---------PDLQVC-----------------CPGSCFL  217 (219)
Q Consensus       190 ---~~~~~~~~~i~~~~~---------~~~q~i-----------------~~SATl~  217 (219)
                         .+|...+..++..++         +..|++                 ++|||.+
T Consensus       259 ~~~~~~y~~i~~iv~~L~~~~dy~vDek~rqv~Lte~G~~~~e~~l~i~~Lfsat~~  315 (922)
T 1nkt_A          259 DGASNWYTEFARLAPLMEKDVHYEVDLRKRTVGVHEKGVEFVEDQLGIDNLYEAANS  315 (922)
T ss_dssp             CCCHHHHHHHHHHHHHSCBTTTEEEETTTTEEEECHHHHHHHHHHHTCSSTTCSTTC
T ss_pred             CcchhHHHHHHHHHHhCcccccceeccCcceEEecHhHHHHHHHHhCCccccCCcch
Confidence               257889999999998         678998                 8999976

>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=99.90  E-value=7.5e-24  Score=188.90  Aligned_cols=147  Identities=16%  Similarity=0.229  Sum_probs=113.3

Q ss_pred             CCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccce
Q 027749           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (219)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (219)
                      .|. .|+++|..+++.+++|+  +.+++||+|||++|.+|++.....   +++++|++||++||.|..+.+..+....++
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            454 89999999999999997  999999999999999999865543   456999999999999999999999999999


Q ss_pred             eEEEEECCcccHHHHHHhcCCCeEEEeChHHH-HHHHHcC------CCCCCCccEEEeccchhhh-cc------------
Q 027749          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRK------TLRTRAIKLLVLDESDEML-SR------------  190 (219)
Q Consensus       131 ~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l-~~~l~~~------~~~~~~l~~lVvDE~h~l~-~~------------  190 (219)
                      ++.+++|+.+...  +.+..+++|+|+||++| .+++..+      ....+++.++|+||||.|+ +.            
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            9999999987643  34445799999999999 6777644      2567899999999999998 43            


Q ss_pred             ---ccHHHHHHHHHhCCC
Q 027749          191 ---GFKDQIYDVYRYLPP  205 (219)
Q Consensus       191 ---~~~~~~~~i~~~~~~  205 (219)
                         +|...+..++..+++
T Consensus       223 ~~~~~y~~i~~iv~~L~~  240 (853)
T 2fsf_A          223 DSSEMYKRVNKIIPHLIR  240 (853)
T ss_dssp             ------------------
T ss_pred             cchhHHHHHHHHHHhchh
Confidence               356778888888864

>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=99.89  E-value=4.4e-22  Score=186.43  Aligned_cols=167  Identities=15%  Similarity=0.180  Sum_probs=131.1

Q ss_pred             CCCCHHHHHHHH-HCCCCCChHHHHHHHHHHhC----CC--cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCC
Q 027749           38 MGIKDDLLRGIY-QYGFEKPSAIQQRAVMPIIK----GR--DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (219)
Q Consensus        38 ~~l~~~~~~~l~-~~~~~~~~~~Q~~~~~~~~~----~~--~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~  110 (219)
                      ++.+....+.+. .+++ .++|+|.++++.++.    ++  +++++++||+|||++++.+++..+..   +.+++|++||
T Consensus       586 ~~~~~~~~~~~~~~f~~-~~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~~---g~~vlvlvPt  661 (1151)
T 2eyq_A          586 FKHDREQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDN---HKQVAVLVPT  661 (1151)
T ss_dssp             CCCCHHHHHHHHHTCCS-CCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTT---TCEEEEECSS
T ss_pred             CCCCHHHHHHHHHhCCC-CCCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHHh---CCeEEEEech
Confidence            455666666665 5566 579999999999875    65  89999999999999999888776543   4579999999


Q ss_pred             HHHHHHHHHHHHHhccccceeEEEEECCcccHHH---HHHhcC-CCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchh
Q 027749          111 RELATQTEKVILAIGDFINIQAHACVGGKSVGED---IRKLEH-GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDE  186 (219)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~l~~-~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~  186 (219)
                      ++|+.|+++.+.+.....++++..+.+..+..+.   ...+.. .++|+|+||+.+.     +.+.++++++|||||+|+
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            9999999999998888778888888766554433   233434 5999999997552     456788999999999999


Q ss_pred             hhccccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          187 MLSRGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       187 l~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      +     ......+++.++.+.++++||||.++
T Consensus       737 ~-----g~~~~~~l~~l~~~~~vl~lSATp~p  763 (1151)
T 2eyq_A          737 F-----GVRHKERIKAMRANVDILTLTATPIP  763 (1151)
T ss_dssp             S-----CHHHHHHHHHHHTTSEEEEEESSCCC
T ss_pred             c-----ChHHHHHHHHhcCCCCEEEEcCCCCh
Confidence            4     23455666667778999999999764

>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=99.87  E-value=1.1e-22  Score=174.23  Aligned_cols=152  Identities=14%  Similarity=0.066  Sum_probs=111.6

Q ss_pred             CCCCChHHHHHHHHHHhCCCcE-EEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccce
Q 027749           52 GFEKPSAIQQRAVMPIIKGRDV-IAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (219)
Q Consensus        52 ~~~~~~~~Q~~~~~~~~~~~~~-lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (219)
                      |+..|+|+|. ++|.++++++. ++++|||+|||++|++|++..+...  +++++|++||++|+.|+.+.+.      +.
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            6778999985 79999988877 9999999999999999998876653  4679999999999999999874      22


Q ss_pred             eEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHh-CCCCCeE
Q 027749          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRY-LPPDLQV  209 (219)
Q Consensus       131 ~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~-~~~~~q~  209 (219)
                      .+....+....     ....+..|.++|++.+...+.+. ..++++++||+||+|++ +..+...+..+... .++++|+
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            22221111110     11234578899999998876654 45789999999999976 44433333333222 3557999


Q ss_pred             EEEeecccCC
Q 027749          210 CCPGSCFLFD  219 (219)
Q Consensus       210 i~~SATl~~~  219 (219)
                      ++||||+|.+
T Consensus       145 i~~SAT~~~~  154 (451)
T 2jlq_A          145 IFMTATPPGS  154 (451)
T ss_dssp             EEECSSCTTC
T ss_pred             EEEccCCCcc
Confidence            9999999863

>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=99.87  E-value=4.1e-21  Score=151.09  Aligned_cols=137  Identities=15%  Similarity=0.108  Sum_probs=108.5

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhcccccee-EE
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ-AH  133 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~-~~  133 (219)
                      .|+++|.++++.+.+++++++++|||+|||.+++.++...      +.+++|++|+++|+.|+.+.+.++    ++. +.
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            6899999999999999899999999999999988776553      346999999999999999999874    455 55


Q ss_pred             EEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       134 ~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      .+.|+..         ...+|+|+|++.+.......   ..++++||+||+|++.+..+.    .+++.++ ..+++++|
T Consensus       163 ~~~g~~~---------~~~~i~v~T~~~l~~~~~~~---~~~~~llIiDEaH~l~~~~~~----~i~~~~~-~~~~l~LS  225 (237)
T 2fz4_A          163 EFSGRIK---------ELKPLTVSTYDSAYVNAEKL---GNRFMLLIFDEVHHLPAESYV----QIAQMSI-APFRLGLT  225 (237)
T ss_dssp             EESSSCB---------CCCSEEEEEHHHHHHTHHHH---TTTCSEEEEECSSCCCTTTHH----HHHHTCC-CSEEEEEE
T ss_pred             EEeCCCC---------CcCCEEEEeHHHHHhhHHHh---cccCCEEEEECCccCCChHHH----HHHHhcc-CCEEEEEe
Confidence            5555543         25789999999987655421   246899999999998876543    3555554 67899999


Q ss_pred             ecccC
Q 027749          214 SCFLF  218 (219)
Q Consensus       214 ATl~~  218 (219)
                      ||.+.
T Consensus       226 ATp~r  230 (237)
T 2fz4_A          226 ATFER  230 (237)
T ss_dssp             ESCC-
T ss_pred             cCCCC
Confidence            99875

>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=99.87  E-value=2.9e-21  Score=165.99  Aligned_cols=136  Identities=15%  Similarity=0.111  Sum_probs=111.7

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhcccccee-EE
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ-AH  133 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~-~~  133 (219)
                      .|+|+|.++++.+.+++++++++|||+|||++++.++...      +.++||++|+++|+.|+.+++.++    +++ +.
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            6899999999999999999999999999999999887764      346999999999999999999884    566 66


Q ss_pred             EEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       134 ~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      .+.|+.+.         .++|+|+||+.+...+...   .+++++|||||+|++.+..|..    +++.+ +..+++++|
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            66666542         4789999999988765421   2468999999999999887654    45555 367899999


Q ss_pred             eccc
Q 027749          214 SCFL  217 (219)
Q Consensus       214 ATl~  217 (219)
                      ||.+
T Consensus       226 ATp~  229 (472)
T 2fwr_A          226 ATFE  229 (472)
T ss_dssp             SCCC
T ss_pred             cCcc
Confidence            9986

>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=99.86  E-value=5.7e-23  Score=181.66  Aligned_cols=166  Identities=16%  Similarity=0.056  Sum_probs=121.0

Q ss_pred             CCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHH
Q 027749           38 MGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQT  117 (219)
Q Consensus        38 ~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~  117 (219)
                      +++++.+.+++... ...++|+|+.+++.+.+++++++++|||+|||++|++|+++.+...  ++++||++||++|+.|+
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            45666666666543 4678888888899999999999999999999999999999887653  46799999999999999


Q ss_pred             HHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHH
Q 027749          118 EKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIY  197 (219)
Q Consensus       118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~  197 (219)
                      .+.+..      ..+.. .+.. ..   ..-..+..+.++|.+.+...+... ..++++++||+||||++ +.++...+.
T Consensus       232 ~~~l~~------~~v~~-~~~~-l~---~~~tp~~~i~~~t~~~l~~~l~~~-~~l~~~~~iViDEah~~-~~~~~~~~~  298 (618)
T 2whx_A          232 EEALRG------LPIRY-QTPA-VK---SDHTGREIVDLMCHATFTTRLLSS-TRVPNYNLIVMDEAHFT-DPCSVAARG  298 (618)
T ss_dssp             HHHTTT------SCEEE-CCTT-SS---CCCCSSSCEEEEEHHHHHHHHHHC-SSCCCCSEEEEESTTCC-SHHHHHHHH
T ss_pred             HHHhcC------CceeE-eccc-ce---eccCCCceEEEEChHHHHHHHhcc-ccccCCeEEEEECCCCC-CccHHHHHH
Confidence            988762      22221 1111 00   001123457788888887755544 35789999999999997 677788888


Q ss_pred             HHHHhCC-CCCeEEEEeecccCC
Q 027749          198 DVYRYLP-PDLQVCCPGSCFLFD  219 (219)
Q Consensus       198 ~i~~~~~-~~~q~i~~SATl~~~  219 (219)
                      .+++.++ ++.|+++||||++.+
T Consensus       299 ~i~~~l~~~~~q~il~SAT~~~~  321 (618)
T 2whx_A          299 YISTRVEMGEAAAIFMTATPPGS  321 (618)
T ss_dssp             HHHHHHHHTSCEEEEECSSCTTC
T ss_pred             HHHHHhcccCccEEEEECCCchh
Confidence            8887775 689999999999863

>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=99.86  E-value=3.7e-22  Score=176.19  Aligned_cols=144  Identities=13%  Similarity=0.063  Sum_probs=115.3

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEE
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (219)
                      .++++|..+++.+..++++++++|||+|||.+|.+++++.      +.+++|++|+++|+.|+.+.+.+..   +..+..
T Consensus       217 P~~~~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~~------g~~vLVl~PTReLA~Qia~~l~~~~---g~~vg~  287 (666)
T 3o8b_A          217 PVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAAQ------GYKVLVLNPSVAATLGFGAYMSKAH---GIDPNI  287 (666)
T ss_dssp             CSCCCCCSCCCCCSSCEEEEEECCTTSCTTTHHHHHHHHT------TCCEEEEESCHHHHHHHHHHHHHHH---SCCCEE
T ss_pred             CcHHHHHHHHHHHHcCCeEEEEeCCchhHHHHHHHHHHHC------CCeEEEEcchHHHHHHHHHHHHHHh---CCCeeE
Confidence            4455566666666788899999999999999999988762      4479999999999999998876554   344555


Q ss_pred             EECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCe--EEEE
Q 027749          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ--VCCP  212 (219)
Q Consensus       135 ~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q--~i~~  212 (219)
                      .+|+..       ...+++|+|+||++|   +....+.++++++||+||+| +++.+|...+..+++.++...|  ++++
T Consensus       288 ~vG~~~-------~~~~~~IlV~TPGrL---l~~~~l~l~~l~~lVlDEAH-~l~~~~~~~l~~Il~~l~~~~~~llil~  356 (666)
T 3o8b_A          288 RTGVRT-------ITTGAPVTYSTYGKF---LADGGCSGGAYDIIICDECH-STDSTTILGIGTVLDQAETAGARLVVLA  356 (666)
T ss_dssp             ECSSCE-------ECCCCSEEEEEHHHH---HHTTSCCTTSCSEEEETTTT-CCSHHHHHHHHHHHHHTTTTTCSEEEEE
T ss_pred             EECcEe-------ccCCCCEEEECcHHH---HhCCCcccCcccEEEEccch-hcCccHHHHHHHHHHhhhhcCCceEEEE
Confidence            566644       345789999999997   45667788899999999996 4667888889999999987777  7888


Q ss_pred             eecccC
Q 027749          213 GSCFLF  218 (219)
Q Consensus       213 SATl~~  218 (219)
                      |||++.
T Consensus       357 SAT~~~  362 (666)
T 3o8b_A          357 TATPPG  362 (666)
T ss_dssp             ESSCTT
T ss_pred             CCCCCc
Confidence            999985

>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=99.84  E-value=2.3e-20  Score=168.83  Aligned_cols=178  Identities=14%  Similarity=0.127  Sum_probs=126.9

Q ss_pred             CccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhC-CCcEEEEcCCCCchhHHhHHHHH--hhhccCCCceeEEE
Q 027749           30 EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIK-GRDVIAQAQSGTGKTSMIALTVC--QTVDTSSREVQALI  106 (219)
Q Consensus        30 ~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~~lv~~~tG~GKT~~~~~~~~--~~~~~~~~~~~~li  106 (219)
                      .++.+|+++++++.+.+.+...+ ..|++.|+.+++.++. +++++++||||+|||+  ++|++  ........+.++++
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            45678999999999999999887 6899999999988764 5679999999999997  34443  22222222567999


Q ss_pred             EcCCHHHHHHHHHHHHHhc-cccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccch
Q 027749          107 LSPTRELATQTEKVILAIG-DFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESD  185 (219)
Q Consensus       107 l~P~~~l~~q~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h  185 (219)
                      ++|+++++.|+.+.+.+.. ...+..+........      ....+.+|+|+||+.+.+.+... ..+.++++||+||+|
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            9999999999998775543 222222221111111      11246789999999999877654 358899999999999


Q ss_pred             h-hhccc-cHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          186 E-MLSRG-FKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       186 ~-l~~~~-~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      . .++.. +...+..+.... ++.|++++|||++.
T Consensus       219 ~R~ld~d~~~~~l~~l~~~~-~~~~iIl~SAT~~~  252 (773)
T 2xau_A          219 ERTLATDILMGLLKQVVKRR-PDLKIIIMSATLDA  252 (773)
T ss_dssp             GCCHHHHHHHHHHHHHHHHC-TTCEEEEEESCSCC
T ss_pred             ccccchHHHHHHHHHHHHhC-CCceEEEEeccccH
Confidence            6 55433 234444555444 57899999999864

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.83  E-value=3.6e-20  Score=165.64  Aligned_cols=132  Identities=19%  Similarity=0.228  Sum_probs=113.3

Q ss_pred             HCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccc
Q 027749           50 QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (219)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (219)
                      ..|+ .|+++|..++|.+++|+  +.++.||+|||++|.+|++.....   +.+++|++||++||.|.++.+..+....+
T Consensus        75 ~lG~-~Pt~VQ~~~ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~aL~---G~qv~VvTPTreLA~Qdae~m~~l~~~lG  148 (997)
T 2ipc_A           75 YLGM-RHFDVQLIGGAVLHEGK--IAEMKTGEGKTLVATLAVALNALT---GKGVHVVTVNDYLARRDAEWMGPVYRGLG  148 (997)
T ss_dssp             HTCC-CCCHHHHHHHHHHHTTS--EEECCSTHHHHHHHHHHHHHHHTT---CSCCEEEESSHHHHHHHHHHHHHHHHTTT
T ss_pred             HhCC-CCcHHHHhhcccccCCc--eeeccCCCchHHHHHHHHHHHHHh---CCCEEEEeCCHHHHHHHHHHHHHHHHhcC
Confidence            4688 99999999999999998  999999999999999999654443   34599999999999999999999999999


Q ss_pred             eeEEEEECCcccHHHHHHhcCCCeEEEeChHHH-HHHHHcC------CCCCC---CccEEEeccchhhhc
Q 027749          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRK------TLRTR---AIKLLVLDESDEMLS  189 (219)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l-~~~l~~~------~~~~~---~l~~lVvDE~h~l~~  189 (219)
                      +++.+++|+.+...  +....+++|+|+||+.| .+++..+      .+.++   .+.++|+||+|.|+.
T Consensus       149 Lsv~~i~Gg~~~~~--r~~ay~~DIvyGTpgrlgfDyLrd~m~~~~~~l~~r~d~~l~~lIIDEaDsmLi  216 (997)
T 2ipc_A          149 LSVGVIQHASTPAE--RRKAYLADVTYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAIIDEVDSILI  216 (997)
T ss_dssp             CCEEECCTTCCHHH--HHHHHTSSEEEEEHHHHHHHHHHHTSCSSTTTCCSCSSSSSCEEEETTHHHHTT
T ss_pred             CeEEEEeCCCCHHH--HHHHcCCCEEEECchhhhhHHHHHhhhcchhhcccccCCCcceEEEechHHHHH
Confidence            99999999987543  33445799999999999 7777654      24567   899999999999873

>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=99.82  E-value=5.8e-20  Score=169.74  Aligned_cols=153  Identities=12%  Similarity=0.086  Sum_probs=117.2

Q ss_pred             CChHHHHHHHHHHhC--------------CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHH
Q 027749           55 KPSAIQQRAVMPIIK--------------GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKV  120 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~--------------~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~  120 (219)
                      .|+|+|..+++.++.              +++.+++++||+|||+++ ++++..+.......++|||+|+++|+.|+.+.
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              368999999999999987 55666555444456899999999999999999


Q ss_pred             HHHhccccceeEEEEECCcccHHHHHHhc-CCCeEEEeChHHHHHHHHcCC--CCCCCccEEEeccchhhhccccHHHHH
Q 027749          121 ILAIGDFINIQAHACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRKT--LRTRAIKLLVLDESDEMLSRGFKDQIY  197 (219)
Q Consensus       121 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-~~~~I~v~Tp~~l~~~l~~~~--~~~~~l~~lVvDE~h~l~~~~~~~~~~  197 (219)
                      +..+...      .+.++.+.......+. .+.+|+|+||++|...+....  ..++...+||+||||++..   .....
T Consensus       350 f~~f~~~------~v~~~~s~~~l~~~L~~~~~~IiVtTiqkl~~~l~~~~~~~~~~~~~lvIiDEAHrs~~---~~~~~  420 (1038)
T 2w00_A          350 YQRFSPD------SVNGSENTAGLKRNLDKDDNKIIVTTIQKLNNLMKAESDLPVYNQQVVFIFDECHRSQF---GEAQK  420 (1038)
T ss_dssp             HHTTSTT------CSSSSCCCHHHHHHHHCSSCCEEEEEHHHHHHHHHHCCCCGGGGSCEEEEEESCCTTHH---HHHHH
T ss_pred             HHHhccc------ccccccCHHHHHHHhcCCCCCEEEEEHHHHHHHHhcccchhccccccEEEEEccchhcc---hHHHH
Confidence            9887643      1234455555555553 578999999999999876532  2355778999999999763   34456


Q ss_pred             HHHHhCCCCCeEEEEeecccC
Q 027749          198 DVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       198 ~i~~~~~~~~q~i~~SATl~~  218 (219)
                      .+.+.+| +.++++||||...
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            6777776 4799999999863

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.82  E-value=1.5e-20  Score=165.86  Aligned_cols=148  Identities=20%  Similarity=0.263  Sum_probs=90.1

Q ss_pred             CChHHHHHHHHHHhC----C-CcEEEEcCCCCchhHHhHHHHHhhhccCC-------CceeEEEEcCCHHHHHHHH-HHH
Q 027749           55 KPSAIQQRAVMPIIK----G-RDVIAQAQSGTGKTSMIALTVCQTVDTSS-------REVQALILSPTRELATQTE-KVI  121 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~----~-~~~lv~~~tG~GKT~~~~~~~~~~~~~~~-------~~~~~lil~P~~~l~~q~~-~~~  121 (219)
                      .|+++|.++++.+..    + ++++++++||+|||++++..+ ..+....       ..+++|||+|+++|+.|+. +.+
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            699999999998764    4 568999999999998865544 4443333       5678999999999999998 666


Q ss_pred             HHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHc----CCCCCCCccEEEeccchhhhccccHHHHH
Q 027749          122 LAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR----KTLRTRAIKLLVLDESDEMLSRGFKDQIY  197 (219)
Q Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~----~~~~~~~l~~lVvDE~h~l~~~~~~~~~~  197 (219)
                      ..+..    .+..+.++        ....+.+|+|+||++|......    ..+....+++||+||||++.... ...+.
T Consensus       257 ~~~~~----~~~~~~~~--------~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~lvIiDEaH~~~~~~-~~~~~  323 (590)
T 3h1t_A          257 TPFGD----ARHKIEGG--------KVVKSREIYFAIYQSIASDERRPGLYKEFPQDFFDLIIIDECHRGSARD-NSNWR  323 (590)
T ss_dssp             TTTCS----SEEECCC----------CCSSCSEEEEEGGGC------CCGGGGSCTTSCSEEEESCCC----------CH
T ss_pred             Hhcch----hhhhhhcc--------CCCCCCcEEEEEhhhhccccccccccccCCCCccCEEEEECCccccccc-hHHHH
Confidence            65532    22222221        2335689999999999887642    23456779999999999987543 35667


Q ss_pred             HHHHhCCCCCeEEEEeeccc
Q 027749          198 DVYRYLPPDLQVCCPGSCFL  217 (219)
Q Consensus       198 ~i~~~~~~~~q~i~~SATl~  217 (219)
                      .+++.++ ..++++||||..
T Consensus       324 ~il~~~~-~~~~l~lTATP~  342 (590)
T 3h1t_A          324 EILEYFE-PAFQIGMTATPL  342 (590)
T ss_dssp             HHHHHST-TSEEEEEESSCS
T ss_pred             HHHHhCC-cceEEEeccccc
Confidence            7777776 468999999965

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.81  E-value=1e-20  Score=168.49  Aligned_cols=158  Identities=16%  Similarity=0.128  Sum_probs=106.7

Q ss_pred             HHHHCCCC-----CChHHHH-----HHHHHHh------CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCC
Q 027749           47 GIYQYGFE-----KPSAIQQ-----RAVMPII------KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (219)
Q Consensus        47 ~l~~~~~~-----~~~~~Q~-----~~~~~~~------~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~  110 (219)
                      ++...||.     .|+++|+     +++|.++      +++++++++|||+|||++|++++++.+...  +++++|++||
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            34445555     8999999     9999887      899999999999999999999999876653  4679999999


Q ss_pred             HHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhcc
Q 027749          111 RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (219)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~  190 (219)
                      ++|+.|+++.+..+.    +.  ...+....     .-..+.-+-+.+.+.+...+.+. ..++++++||+||+|++ +.
T Consensus       280 r~La~Q~~~~l~~~~----i~--~~~~~l~~-----v~tp~~ll~~l~~~~l~~~l~~~-~~l~~l~lvViDEaH~~-~~  346 (673)
T 2wv9_A          280 RVVAAEMAEALRGLP----VR--YLTPAVQR-----EHSGNEIVDVMCHATLTHRLMSP-LRVPNYNLFVMDEAHFT-DP  346 (673)
T ss_dssp             HHHHHHHHHHTTTSC----CE--ECCC---C-----CCCSCCCEEEEEHHHHHHHHHSS-SCCCCCSEEEEESTTCC-CH
T ss_pred             HHHHHHHHHHHhcCC----ee--eecccccc-----cCCHHHHHHHHHhhhhHHHHhcc-cccccceEEEEeCCccc-Cc
Confidence            999999999887542    21  11110000     00011223445555555544443 56889999999999997 33


Q ss_pred             ccHHHHHHHHHhCC-CCCeEEEEeecccCC
Q 027749          191 GFKDQIYDVYRYLP-PDLQVCCPGSCFLFD  219 (219)
Q Consensus       191 ~~~~~~~~i~~~~~-~~~q~i~~SATl~~~  219 (219)
                      .+...+..+.+.++ ++.|+++||||++++
T Consensus       347 ~~~~~~~~l~~~~~~~~~~vl~~SAT~~~~  376 (673)
T 2wv9_A          347 ASIAARGYIATRVEAGEAAAIFMTATPPGT  376 (673)
T ss_dssp             HHHHHHHHHHHHHHTTSCEEEEECSSCTTC
T ss_pred             cHHHHHHHHHHhccccCCcEEEEcCCCChh
Confidence            33344444444443 678999999999863

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.81  E-value=1.4e-19  Score=154.02  Aligned_cols=135  Identities=13%  Similarity=0.051  Sum_probs=95.2

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  148 (219)
                      +|+++++++|||+|||++|++++++.+...  +.+++|++||++|+.|+++.+.      ++.+....|....     .-
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            478999999999999999999999666544  4579999999999999988775      3344443333211     11


Q ss_pred             cCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhC-CCCCeEEEEeecccC
Q 027749          149 EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL-PPDLQVCCPGSCFLF  218 (219)
Q Consensus       149 ~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~-~~~~q~i~~SATl~~  218 (219)
                      ..+..+.+.|.+.+...+.+ ...++++++||+||+|++ +.++......+.+.. ++++|+++||||+++
T Consensus        68 ~~~~~~~~~~~~~l~~~l~~-~~~~~~l~~vViDEaH~~-~~~~~~~~~~l~~~~~~~~~~~l~~SAT~~~  136 (431)
T 2v6i_A           68 TGNEIVDFMCHSTFTMKLLQ-GVRVPNYNLYIMDEAHFL-DPASVAARGYIETRVSMGDAGAIFMTATPPG  136 (431)
T ss_dssp             -CCCSEEEEEHHHHHHHHHH-TCCCCCCSEEEEESTTCC-SHHHHHHHHHHHHHHHTTSCEEEEEESSCTT
T ss_pred             CCCceEEEEchHHHHHHHhc-CccccCCCEEEEeCCccC-CccHHHHHHHHHHHhhCCCCcEEEEeCCCCc
Confidence            12345667788888776655 456889999999999997 444444444444332 568999999999986

>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=99.80  E-value=2.8e-21  Score=164.91  Aligned_cols=131  Identities=14%  Similarity=0.147  Sum_probs=91.4

Q ss_pred             HHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHH
Q 027749           66 PIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDI  145 (219)
Q Consensus        66 ~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  145 (219)
                      .+.+|+++++++|||+|||++|++|+++.+...  +++++|++||++|+.|+++.+..+    ++.  ...+...     
T Consensus         4 ~l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~~--~~~~lil~Ptr~La~Q~~~~l~~~----~v~--~~~~~~~-----   70 (440)
T 1yks_A            4 MLKKGMTTVLDFHPGAGKTRRFLPQILAECARR--RLRTLVLAPTRVVLSEMKEAFHGL----DVK--FHTQAFS-----   70 (440)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTTTS----CEE--EESSCCC-----
T ss_pred             HhhCCCCEEEEcCCCCCHHHHHHHHHHHHHHhc--CCeEEEEcchHHHHHHHHHHHhcC----CeE--Eecccce-----
Confidence            356889999999999999999999999877654  467999999999999999988743    222  1111100     


Q ss_pred             HHhcCCCeEEEeChHHHHHHH--------HcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhC-CCCCeEEEEeecc
Q 027749          146 RKLEHGVHVVSGTPGRVCDMI--------KRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL-PPDLQVCCPGSCF  216 (219)
Q Consensus       146 ~~l~~~~~I~v~Tp~~l~~~l--------~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~-~~~~q~i~~SATl  216 (219)
                               .++||+++.+++        ......++++++||+||+|++ +.++...+..+.+.. +.+.|+++||||+
T Consensus        71 ---------~v~Tp~~l~~~l~~~~l~~~~~~~~~~~~l~~vViDEah~~-~~~~~~~~~~~~~~~~~~~~~~l~~SAT~  140 (440)
T 1yks_A           71 ---------AHGSGREVIDAMCHATLTYRMLEPTRVVNWEVIIMDEAHFL-DPASIAARGWAAHRARANESATILMTATP  140 (440)
T ss_dssp             ---------CCCCSSCCEEEEEHHHHHHHHTSSSCCCCCSEEEETTTTCC-SHHHHHHHHHHHHHHHTTSCEEEEECSSC
T ss_pred             ---------eccCCccceeeecccchhHhhhCcccccCccEEEEECcccc-CcchHHHHHHHHHHhccCCceEEEEeCCC
Confidence                     255554443211        122345789999999999998 444444433333333 3579999999999


Q ss_pred             cCC
Q 027749          217 LFD  219 (219)
Q Consensus       217 ~~~  219 (219)
                      ++.
T Consensus       141 ~~~  143 (440)
T 1yks_A          141 PGT  143 (440)
T ss_dssp             TTC
T ss_pred             Cch
Confidence            763

>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=99.79  E-value=2.1e-19  Score=154.05  Aligned_cols=136  Identities=14%  Similarity=0.123  Sum_probs=94.5

Q ss_pred             HHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHH
Q 027749           65 MPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGED  144 (219)
Q Consensus        65 ~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  144 (219)
                      ..+.+++++++++|||+|||++|++|++..+...  ++++||++|+++|+.|+.+.+.      +..+....+....   
T Consensus        16 ~~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~~--~~~~lvl~Ptr~La~Q~~~~l~------g~~v~~~~~~~~~---   84 (459)
T 2z83_A           16 NMLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQQ--RLRTAVLAPTRVVAAEMAEALR------GLPVRYQTSAVQR---   84 (459)
T ss_dssp             GGGSTTCEEEECCCTTSCTTTTHHHHHHHHHHHT--TCCEEEEECSHHHHHHHHHHTT------TSCEEECC--------
T ss_pred             HHHhcCCcEEEECCCCCCHHHHHHHHHHHHHHhC--CCcEEEECchHHHHHHHHHHhc------CceEeEEeccccc---
Confidence            3456788999999999999999999999877653  4679999999999999999886      2222221111110   


Q ss_pred             HHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchh-----hhccccHHHHHHHHHhCCCCCeEEEEeecccCC
Q 027749          145 IRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDE-----MLSRGFKDQIYDVYRYLPPDLQVCCPGSCFLFD  219 (219)
Q Consensus       145 ~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~-----l~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~~  219 (219)
                        .-..+..+.++|.+.+...+... ..++++++||+||||.     +...++.....     .+++.|+++||||+|.+
T Consensus        85 --~~t~~~~i~~~~~~~l~~~l~~~-~~l~~~~~iViDEaH~~~~~~~~~~~~~~~~~-----~~~~~~~il~SAT~~~~  156 (459)
T 2z83_A           85 --EHQGNEIVDVMCHATLTHRLMSP-NRVPNYNLFVMDEAHFTDPASIAARGYIATKV-----ELGEAAAIFMTATPPGT  156 (459)
T ss_dssp             -----CCCSEEEEEHHHHHHHHHSC-C-CCCCSEEEESSTTCCSHHHHHHHHHHHHHH-----HTTSCEEEEECSSCTTC
T ss_pred             --CCCCCcEEEEEchHHHHHHhhcc-ccccCCcEEEEECCccCCchhhHHHHHHHHHh-----ccCCccEEEEEcCCCcc
Confidence              01123457788888887765544 4578999999999998     33333322221     13678999999999863

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.75  E-value=9.4e-18  Score=146.89  Aligned_cols=129  Identities=18%  Similarity=0.056  Sum_probs=100.8

Q ss_pred             CChHHHHHHHHH----HhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccce
Q 027749           55 KPSAIQQRAVMP----IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (219)
Q Consensus        55 ~~~~~Q~~~~~~----~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (219)
                      .|+|.|.+++..    +..|+++++++|||+|||++|++|++.      .+++++|++||++|+.|+.+.+..+.+..++
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            689999997764    457899999999999999999999988      2567999999999999999999888777677


Q ss_pred             eEEEEECCccc---------------------------------HHH------------------HHHhcCCCeEEEeCh
Q 027749          131 QAHACVGGKSV---------------------------------GED------------------IRKLEHGVHVVSGTP  159 (219)
Q Consensus       131 ~~~~~~~~~~~---------------------------------~~~------------------~~~l~~~~~I~v~Tp  159 (219)
                      ++..+.|..+.                                 ...                  .+....+++|+|+|+
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            77777664321                                 011                  122334689999999


Q ss_pred             HHHHHHHHcCCCCC-CCccEEEeccchhhhc
Q 027749          160 GRVCDMIKRKTLRT-RAIKLLVLDESDEMLS  189 (219)
Q Consensus       160 ~~l~~~l~~~~~~~-~~l~~lVvDE~h~l~~  189 (219)
                      +.|++......+.+ ....++||||||+|.+
T Consensus       157 ~~l~~~~~~~~~~~~~~~~~vIiDEAHnl~d  187 (551)
T 3crv_A          157 PYFFIDRYREFIDIDLREYMIVIDEAHNLDK  187 (551)
T ss_dssp             HHHHCHHHHTTSCCCSTTEEEEETTGGGGGG
T ss_pred             hHhcCHHHHHhcCCCcCCeEEEEecccchHH
Confidence            99988544333322 4667899999999987

>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=99.70  E-value=5.6e-17  Score=140.20  Aligned_cols=149  Identities=12%  Similarity=0.113  Sum_probs=107.0

Q ss_pred             CCChHHHHHHHHHH----hCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccc
Q 027749           54 EKPSAIQQRAVMPI----IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (219)
Q Consensus        54 ~~~~~~Q~~~~~~~----~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (219)
                      ..++|+|.++++.+    ..+++.++..+||+|||+.++..+ ..+.......++|||+| ..++.|+.+++.++...  
T Consensus        36 ~~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai~~i-~~~~~~~~~~~~LIv~P-~~l~~qw~~e~~~~~~~--  111 (500)
T 1z63_A           36 ANLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVF-SDAKKENELTPSLVICP-LSVLKNWEEELSKFAPH--  111 (500)
T ss_dssp             SCCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHH-HHHHHTTCCSSEEEEEC-STTHHHHHHHHHHHCTT--
T ss_pred             ccchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHHHHH-HHHHhcCCCCCEEEEcc-HHHHHHHHHHHHHHCCC--
Confidence            36899999998766    467899999999999998876544 43433333456999999 56889999999998753  


Q ss_pred             eeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeE
Q 027749          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQV  209 (219)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~  209 (219)
                      .++..+.|+...     ....+++|+|+|++.+.....   +.....++||+||||++.+.+  ......+..++ ..+.
T Consensus       112 ~~v~~~~g~~~~-----~~~~~~~ivi~t~~~l~~~~~---l~~~~~~~vIvDEaH~~kn~~--~~~~~~l~~l~-~~~~  180 (500)
T 1z63_A          112 LRFAVFHEDRSK-----IKLEDYDIILTTYAVLLRDTR---LKEVEWKYIVIDEAQNIKNPQ--TKIFKAVKELK-SKYR  180 (500)
T ss_dssp             SCEEECSSSTTS-----CCGGGSSEEEEEHHHHTTCHH---HHTCCEEEEEEETGGGGSCTT--SHHHHHHHTSC-EEEE
T ss_pred             ceEEEEecCchh-----ccccCCcEEEeeHHHHhccch---hcCCCcCEEEEeCccccCCHh--HHHHHHHHhhc-cCcE
Confidence            455555554422     122467999999998875432   223467899999999987654  33445555564 4578


Q ss_pred             EEEeeccc
Q 027749          210 CCPGSCFL  217 (219)
Q Consensus       210 i~~SATl~  217 (219)
                      +++|||..
T Consensus       181 l~LTaTP~  188 (500)
T 1z63_A          181 IALTGTPI  188 (500)
T ss_dssp             EEECSSCS
T ss_pred             EEEecCCC
Confidence            99999963

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.69  E-value=7.1e-17  Score=143.63  Aligned_cols=131  Identities=15%  Similarity=0.096  Sum_probs=99.6

Q ss_pred             HHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHH
Q 027749           66 PIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDI  145 (219)
Q Consensus        66 ~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  145 (219)
                      ..+++++++++||||+|||.    +++..+....   ..+|++|+++||.|+++.+.+.    ++.+..+.|+...... 
T Consensus       151 r~l~rk~vlv~apTGSGKT~----~al~~l~~~~---~gl~l~PtR~LA~Qi~~~l~~~----g~~v~lltG~~~~iv~-  218 (677)
T 3rc3_A          151 RAMQRKIIFHSGPTNSGKTY----HAIQKYFSAK---SGVYCGPLKLLAHEIFEKSNAA----GVPCDLVTGEERVTVQ-  218 (677)
T ss_dssp             HTSCCEEEEEECCTTSSHHH----HHHHHHHHSS---SEEEEESSHHHHHHHHHHHHHT----TCCEEEECSSCEECCS-
T ss_pred             HhcCCCEEEEEcCCCCCHHH----HHHHHHHhcC---CeEEEeCHHHHHHHHHHHHHhc----CCcEEEEECCeeEEec-
Confidence            34578899999999999997    3334333332   2599999999999999999876    5677777777664110 


Q ss_pred             HHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCC-CCCeEEEEeeccc
Q 027749          146 RKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP-PDLQVCCPGSCFL  217 (219)
Q Consensus       146 ~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~-~~~q~i~~SATl~  217 (219)
                       .-....+++++|++.+.        ....+++||+||+|++.+.++...+..++..++ ++.+++++|||.+
T Consensus       219 -TpGr~~~il~~T~e~~~--------l~~~v~lvVIDEaH~l~d~~~g~~~~~~l~~l~~~~i~il~~SAT~~  282 (677)
T 3rc3_A          219 -PNGKQASHVSCTVEMCS--------VTTPYEVAVIDEIQMIRDPARGWAWTRALLGLCAEEVHLCGEPAAID  282 (677)
T ss_dssp             -TTCCCCSEEEEEGGGCC--------SSSCEEEEEECSGGGGGCTTTHHHHHHHHHHCCEEEEEEEECGGGHH
T ss_pred             -CCCcccceeEecHhHhh--------hcccCCEEEEecceecCCccchHHHHHHHHccCccceEEEeccchHH
Confidence             00113678888875432        246789999999999999999999999999988 6889999999964

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.65  E-value=1.8e-16  Score=138.46  Aligned_cols=128  Identities=17%  Similarity=0.199  Sum_probs=86.2

Q ss_pred             CCCCCChHHHHHHHHH----HhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhcc
Q 027749           51 YGFEKPSAIQQRAVMP----IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGD  126 (219)
Q Consensus        51 ~~~~~~~~~Q~~~~~~----~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~  126 (219)
                      .|+ .|+|+|.+++..    +..|+++++++|||+|||++|++|++..      +.+++|++||++|+.|+.+.+..+  
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            356 799999998654    4688999999999999999999998764      467999999999999999888764  


Q ss_pred             ccceeEEEEECCcc--------cH---------------------------------------HHHHHhcCCCeEEEeCh
Q 027749          127 FINIQAHACVGGKS--------VG---------------------------------------EDIRKLEHGVHVVSGTP  159 (219)
Q Consensus       127 ~~~~~~~~~~~~~~--------~~---------------------------------------~~~~~l~~~~~I~v~Tp  159 (219)
                        ++++..+.|...        ..                                       ...+....+++|+|+|+
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              333333332211        00                                       00011224579999999


Q ss_pred             HHHHHHHHcCCC-------CCCCccEEEeccchhhhc
Q 027749          160 GRVCDMIKRKTL-------RTRAIKLLVLDESDEMLS  189 (219)
Q Consensus       160 ~~l~~~l~~~~~-------~~~~l~~lVvDE~h~l~~  189 (219)
                      +.|++-...+.+       .+....++||||||++.+
T Consensus       153 ~~l~~~~~~~~~~~~~~~~~~~~~~~vIiDEAHnl~~  189 (540)
T 2vl7_A          153 PYLFQKPIRNSVFCNKDDCLKLEDYLIVIDEAHNLLE  189 (540)
T ss_dssp             HHHHSHHHHHHHSCSSTTSCCGGGEEEEETTGGGGGG
T ss_pred             HHhcCHHHHHhhCcccccccCcCCCEEEEEccccHHH
Confidence            999873332211       235577999999999843

>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=99.62  E-value=4.8e-16  Score=143.84  Aligned_cols=158  Identities=16%  Similarity=0.074  Sum_probs=104.1

Q ss_pred             CCChHHHHHHHHHHhC--CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhcccccee
Q 027749           54 EKPSAIQQRAVMPIIK--GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ  131 (219)
Q Consensus        54 ~~~~~~Q~~~~~~~~~--~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  131 (219)
                      ..|+|+|.+++..+..  +.+++++++||+|||..++..+...+... ...++|||+|+ .|+.|+..++.+..   +..
T Consensus       152 ~~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g-~~~rvLIVvP~-sLl~Qw~~E~~~~f---~l~  226 (968)
T 3dmq_A          152 TSLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSG-AAERVLIIVPE-TLQHQWLVEMLRRF---NLR  226 (968)
T ss_dssp             SCCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHTS-SCCCEEEECCT-TTHHHHHHHHHHHS---CCC
T ss_pred             CCCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHhC-CCCeEEEEeCH-HHHHHHHHHHHHHh---CCC
Confidence            3789999999988775  35799999999999998877665555433 33469999999 99999999996655   444


Q ss_pred             EEEEECCcccHHHHHH---hcCCCeEEEeChHHHHHHHHc-CCCCCCCccEEEeccchhhhccccH-HHHHHHHHhC-CC
Q 027749          132 AHACVGGKSVGEDIRK---LEHGVHVVSGTPGRVCDMIKR-KTLRTRAIKLLVLDESDEMLSRGFK-DQIYDVYRYL-PP  205 (219)
Q Consensus       132 ~~~~~~~~~~~~~~~~---l~~~~~I~v~Tp~~l~~~l~~-~~~~~~~l~~lVvDE~h~l~~~~~~-~~~~~i~~~~-~~  205 (219)
                      +..+.+.... .....   .....+|+|+|++.+...... ..+...++++|||||||++.+.+.. ......+..+ .+
T Consensus       227 v~v~~~~~~~-~~~~~~~~~~~~~dIvI~T~~~L~~~~~~~~~l~~~~~dlVIvDEAH~~kn~~~~~s~~~~~l~~L~~~  305 (968)
T 3dmq_A          227 FALFDDERYA-EAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLVWSEDAPSREYQAIEQLAEH  305 (968)
T ss_dssp             CEECCHHHHH-HHHHTTCSSSTTCSEEEECHHHHHTSTTTTHHHHTSCCCEEEECCSSCCCCBTTBCCHHHHHHHHHHTT
T ss_pred             EEEEccchhh-hhhhhcccccccCCEEEEcHHHHhhCHHHHHHhhhcCCCEEEehhhHhhcCCCCcchHHHHHHHHHhhc
Confidence            4444332221 11111   123579999999877532111 1123457899999999998754311 1111222222 24


Q ss_pred             CCeEEEEeeccc
Q 027749          206 DLQVCCPGSCFL  217 (219)
Q Consensus       206 ~~q~i~~SATl~  217 (219)
                      ..+++++|||.-
T Consensus       306 ~~~~L~LTATPi  317 (968)
T 3dmq_A          306 VPGVLLLTATPE  317 (968)
T ss_dssp             CSSEEESCSSCS
T ss_pred             CCcEEEEEcCCc
Confidence            457999999963

>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=99.59  E-value=2.6e-14  Score=127.23  Aligned_cols=155  Identities=14%  Similarity=0.090  Sum_probs=107.5

Q ss_pred             CChHHHHHHHHHHh---------CCCcEEEEcCCCCchhHHhHHHHHhhhccCC----CceeEEEEcCCHHHHHHHHHHH
Q 027749           55 KPSAIQQRAVMPII---------KGRDVIAQAQSGTGKTSMIALTVCQTVDTSS----REVQALILSPTRELATQTEKVI  121 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~---------~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~----~~~~~lil~P~~~l~~q~~~~~  121 (219)
                      .++|+|.+++..+.         .++..|+..+||.|||+.++..+...+....    ...++|||+|+ +++.|+.+++
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            68999999998763         4567899999999999887776655543321    22459999996 8899999999


Q ss_pred             HHhccccceeEEEEECCcccHHH--HHHh-c-----CCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccH
Q 027749          122 LAIGDFINIQAHACVGGKSVGED--IRKL-E-----HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFK  193 (219)
Q Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~~--~~~l-~-----~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~  193 (219)
                      .++... .+.+..+.++......  .... .     ..++|+|+|++.+....  ..+.....++||+||+|++-+..  
T Consensus       134 ~~~~~~-~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~vvi~ty~~l~~~~--~~l~~~~~~~vI~DEaH~ikn~~--  208 (644)
T 1z3i_X          134 GKWLGG-RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHA--EVLHKGKVGLVICDEGHRLKNSD--  208 (644)
T ss_dssp             HHHHGG-GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHT--TTTTTSCCCEEEETTGGGCCTTC--
T ss_pred             HHHcCC-CeeEEEEeCCCHHHHHHHHHHHHHhcCCCCCCcEEEeeHHHHHhhH--HHhhcCCccEEEEECceecCChh--
Confidence            998765 5666666666543221  1111 1     14789999999887543  22334567899999999987653  


Q ss_pred             HHHHHHHHhCCCCCeEEEEeecc
Q 027749          194 DQIYDVYRYLPPDLQVCCPGSCF  216 (219)
Q Consensus       194 ~~~~~i~~~~~~~~q~i~~SATl  216 (219)
                      ......+..++ ....+++|||.
T Consensus       209 ~~~~~al~~l~-~~~rl~LTgTP  230 (644)
T 1z3i_X          209 NQTYLALNSMN-AQRRVLISGTP  230 (644)
T ss_dssp             HHHHHHHHHHC-CSEEEEECSSC
T ss_pred             hHHHHHHHhcc-cCcEEEEecCc
Confidence            23333334443 45789999995

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=99.58  E-value=6.7e-15  Score=133.97  Aligned_cols=154  Identities=12%  Similarity=0.118  Sum_probs=110.2

Q ss_pred             CChHHHHHHHHHHh----CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccce
Q 027749           55 KPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~----~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (219)
                      .++|+|.+++..+.    .+++.|+..+||.|||+.++..+...+........+||||| .+++.|+.+++.++..  +.
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            67899999997654    78899999999999998876666554433333345899999 7788999999999874  46


Q ss_pred             eEEEEECCcccHHHHHHh------------cCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHH
Q 027749          131 QAHACVGGKSVGEDIRKL------------EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYD  198 (219)
Q Consensus       131 ~~~~~~~~~~~~~~~~~l------------~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~  198 (219)
                      ++....|...........            ...++|+|+|++.+......  +.....++|||||||++-+.+  .....
T Consensus       313 ~v~~~~g~~~~r~~~~~~~~~~~~~~~~~~~~~~dvvitTy~~l~~~~~~--l~~~~w~~vIvDEaH~lkn~~--s~~~~  388 (800)
T 3mwy_W          313 NCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRAE--LGSIKWQFMAVDEAHRLKNAE--SSLYE  388 (800)
T ss_dssp             CEEECCCSSHHHHHHHHHHSCSCC-----CCCCCSEEEECTTHHHHTHHH--HHTSEEEEEEETTGGGGCCSS--SHHHH
T ss_pred             eEEEEeCCHHHHHHHHHHHhhccccccccccccCCEEEecHHHHHhhHHH--HhcCCcceeehhhhhhhcCch--hHHHH
Confidence            677777766554433321            23578999999998764322  112256789999999986543  34455


Q ss_pred             HHHhCCCCCeEEEEeecc
Q 027749          199 VYRYLPPDLQVCCPGSCF  216 (219)
Q Consensus       199 i~~~~~~~~q~i~~SATl  216 (219)
                      .+..++ ....+++|||.
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            555553 45678999996

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=99.47  E-value=1.1e-13  Score=122.38  Aligned_cols=81  Identities=22%  Similarity=0.232  Sum_probs=66.3

Q ss_pred             CChHHHHHHHHH----HhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccce
Q 027749           55 KPSAIQQRAVMP----IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (219)
Q Consensus        55 ~~~~~Q~~~~~~----~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (219)
                      .|+|.|.+.+..    +.+|+++++++|||+|||++|++|++..+...  +.+++|++||++++.|+.+.+..+....++
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            689999998754    56889999999999999999999999987653  457999999999999999999888765556


Q ss_pred             eEEEEEC
Q 027749          131 QAHACVG  137 (219)
Q Consensus       131 ~~~~~~~  137 (219)
                      ++..+.|
T Consensus        81 ~~~~l~g   87 (620)
T 4a15_A           81 RAIPMQG   87 (620)
T ss_dssp             CEEECCC
T ss_pred             EEEEEEC
Confidence            6555444

>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=99.27  E-value=4.6e-11  Score=105.57  Aligned_cols=144  Identities=18%  Similarity=0.217  Sum_probs=90.9

Q ss_pred             hHHHHHHHHHHhCCCcEEEEcCCCCchh--HHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEE
Q 027749           57 SAIQQRAVMPIIKGRDVIAQAQSGTGKT--SMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (219)
Q Consensus        57 ~~~Q~~~~~~~~~~~~~lv~~~tG~GKT--~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (219)
                      ++.|+.+++.++.++.+++.|++|+|||  ++++++.+..+... .+.++++++||..++.++.+.+.......++....
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            6889999999999999999999999999  55666666654322 34679999999999999998887654433322110


Q ss_pred             EECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       135 ~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      . .+..  .....+   ..++-.+|+...  +.........+++|||||++ |.+   ...+..+++.++.+.|++++.
T Consensus       230 ~-~~~~--~~~~Ti---h~ll~~~~~~~~--~~~~~~~~l~~d~lIIDEAs-ml~---~~~~~~Ll~~l~~~~~liLvG  296 (608)
T 1w36_D          230 K-KRIP--EDASTL---HRLLGAQPGSQR--LRHHAGNPLHLDVLVVDEAS-MID---LPMMSRLIDALPDHARVIFLG  296 (608)
T ss_dssp             C-CSCS--CCCBTT---TSCC-------------CTTSCCSCSEEEECSGG-GCB---HHHHHHHHHTCCTTCEEEEEE
T ss_pred             H-hccc--hhhhhh---HhhhccCCCchH--HHhccCCCCCCCEEEEechh-hCC---HHHHHHHHHhCCCCCEEEEEc
Confidence            0 0000  000000   011212232210  11112223378999999999 454   467788899999999999886

>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=99.20  E-value=2.5e-10  Score=101.06  Aligned_cols=131  Identities=15%  Similarity=0.172  Sum_probs=100.6

Q ss_pred             HCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccc
Q 027749           50 QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (219)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  129 (219)
                      ..|. .|+++|....-.+..|+  |....||.|||+++.+|++-.....   ..+.|++|+..||.+-.+.+..+....|
T Consensus        71 ~lg~-r~~dvQligg~~L~~G~--iaEM~TGEGKTLva~lp~~lnAL~G---~~vhVvT~ndyLA~rdae~m~~l~~~Lg  144 (822)
T 3jux_A           71 TLGM-RPFDVQVMGGIALHEGK--VAEMKTGEGKTLAATMPIYLNALIG---KGVHLVTVNDYLARRDALWMGPVYLFLG  144 (822)
T ss_dssp             HTSC-CCCHHHHHHHHHHHTTC--EEECCTTSCHHHHTHHHHHHHHTTS---SCEEEEESSHHHHHHHHHHHHHHHHHTT
T ss_pred             HhCC-CCcHHHHHHHHHHhCCC--hhhccCCCCccHHHHHHHHHHHhcC---CceEEEeccHHHHHhHHHHHHHHHHHhC
Confidence            3455 79999988888887776  8999999999999999998766653   3499999999999999999999999999


Q ss_pred             eeEEEEECC--------------------------------------------------cccHHHHHHhcCCCeEEEeCh
Q 027749          130 IQAHACVGG--------------------------------------------------KSVGEDIRKLEHGVHVVSGTP  159 (219)
Q Consensus       130 ~~~~~~~~~--------------------------------------------------~~~~~~~~~l~~~~~I~v~Tp  159 (219)
                      +++.+....                                                  .+..++..  ...|+|..+|.
T Consensus       145 lsvg~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~err~--aY~~DItYgTn  222 (822)
T 3jux_A          145 LRVGVINSLGKSYEVVWKNPDLARKAIEENWSVWPDGFNGEVLKEESMNKEAVEAFQVELKEITRKE--AYLCDVTYGTN  222 (822)
T ss_dssp             CCEEEEETTTEEEEEEESSHHHHHHHHHTTCCSSCTTCCSSSCCGGGSCHHHHTTTCEECCBCCHHH--HHHSSEEEEEH
T ss_pred             CEEEEEcCCCcccccccccchhhhhhhcccccccccccccccccccccccccchhccccCCHHHHHH--HhcCCCEEccC
Confidence            999988872                                                  11111111  12589999999


Q ss_pred             HHHHH-HHHcC------CCCCCCccEEEeccchhhh
Q 027749          160 GRVCD-MIKRK------TLRTRAIKLLVLDESDEML  188 (219)
Q Consensus       160 ~~l~~-~l~~~------~~~~~~l~~lVvDE~h~l~  188 (219)
                      ..|-. .++-+      ......+.+.||||+|.++
T Consensus       223 ~EfgFDYLRDnm~~~~~~~vqR~~~~aIVDEvDSiL  258 (822)
T 3jux_A          223 NEFGFDYLRDNLVLDYNDKVQRGHFYAIVDEADSVL  258 (822)
T ss_dssp             HHHHHHHHHHTSCSSTTSCCCCCCCEEEEETHHHHH
T ss_pred             cchhhHhHHhhccCCHHHhccCCCCeEEEeccccee
Confidence            88754 44321      1223568899999999766

>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=98.75  E-value=6e-08  Score=82.89  Aligned_cols=136  Identities=15%  Similarity=0.184  Sum_probs=81.6

Q ss_pred             HHHCCCCCChHHHHHHHHHHhC----C-CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHH
Q 027749           48 IYQYGFEKPSAIQQRAVMPIIK----G-RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL  122 (219)
Q Consensus        48 l~~~~~~~~~~~Q~~~~~~~~~----~-~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~  122 (219)
                      +.-+.+..+++-|+.++..+..    + ..++|.|+.|+|||... ..++..+...+. ..+++++||...+..+.+.+.
T Consensus        18 ~~p~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll-~~~~~~l~~~~~-~~il~~a~T~~Aa~~l~~~~~   95 (459)
T 3upu_A           18 GSHMTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLT-KFIIEALISTGE-TGIILAAPTHAAKKILSKLSG   95 (459)
T ss_dssp             ---CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHH-HHHHHHHHHTTC-CCEEEEESSHHHHHHHHHHHS
T ss_pred             cCCCccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHH-HHHHHHHHhcCC-ceEEEecCcHHHHHHHHhhhc
Confidence            4455678899999999987643    2 38999999999999443 444555544322 359999999999887776551


Q ss_pred             HhccccceeEEEEECCcccHHHHHHhc----CCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHH
Q 027749          123 AIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYD  198 (219)
Q Consensus       123 ~~~~~~~~~~~~~~~~~~~~~~~~~l~----~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~  198 (219)
                             .....+       .....+.    .+...+..          .........++|||||++.+.    ...+..
T Consensus        96 -------~~~~T~-------h~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~iiiDE~~~~~----~~~~~~  147 (459)
T 3upu_A           96 -------KEASTI-------HSILKINPVTYEENVLFEQ----------KEVPDLAKCRVLICDEVSMYD----RKLFKI  147 (459)
T ss_dssp             -------SCEEEH-------HHHHTEEEEECSSCEEEEE----------CSCCCCSSCSEEEESCGGGCC----HHHHHH
T ss_pred             -------cchhhH-------HHHhccCcccccccchhcc----------cccccccCCCEEEEECchhCC----HHHHHH
Confidence                   111110       0000000    00111111          122345678999999999643    345566


Q ss_pred             HHHhCCCCCeEEEEe
Q 027749          199 VYRYLPPDLQVCCPG  213 (219)
Q Consensus       199 i~~~~~~~~q~i~~S  213 (219)
                      +++.++...+++++.
T Consensus       148 l~~~~~~~~~~~~vG  162 (459)
T 3upu_A          148 LLSTIPPWCTIIGIG  162 (459)
T ss_dssp             HHHHSCTTCEEEEEE
T ss_pred             HHHhccCCCEEEEEC
Confidence            666666666676654

>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=98.71  E-value=2.5e-07  Score=82.06  Aligned_cols=69  Identities=20%  Similarity=0.187  Sum_probs=54.0

Q ss_pred             CCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 027749           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (219)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (219)
                      ..+++.|..++..++.+...+|+||+|+|||....- ++..+... .+.++++++||...+.++.+.+.+.
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            356899999999988878899999999999965443 33333322 3456999999999999999988654

>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=98.70  E-value=1.4e-07  Score=82.68  Aligned_cols=125  Identities=22%  Similarity=0.259  Sum_probs=81.2

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEE
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (219)
                      .+++.|+.++..+..++.+++.|+.|+|||... ..++..+...  +.++++++||...+..+.+.+.       .....
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            578999999999998899999999999999543 3344444433  3569999999999987766542       11100


Q ss_pred             EECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       135 ~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                            . ..  .+..       .|..    ...........++|||||++++.    ...+..+++.++...+++++.
T Consensus       259 ------i-h~--ll~~-------~~~~----~~~~~~~~~~~dvlIIDEasml~----~~~~~~Ll~~~~~~~~lilvG  313 (574)
T 3e1s_A          259 ------V-HR--LLGY-------GPQG----FRHNHLEPAPYDLLIVDEVSMMG----DALMLSLLAAVPPGARVLLVG  313 (574)
T ss_dssp             ------H-HH--HTTE-------ETTE----ESCSSSSCCSCSEEEECCGGGCC----HHHHHHHHTTSCTTCEEEEEE
T ss_pred             ------H-HH--HHcC-------Ccch----hhhhhcccccCCEEEEcCccCCC----HHHHHHHHHhCcCCCEEEEEe
Confidence                  0 00  0000       0000    00111233467899999999654    356777788888777887764

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=98.66  E-value=5.4e-08  Score=86.63  Aligned_cols=67  Identities=19%  Similarity=0.233  Sum_probs=53.1

Q ss_pred             CChHHHHHHHHHHhCCC-cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 027749           55 KPSAIQQRAVMPIIKGR-DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~-~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (219)
                      .+++.|.+|+..++..+ -.+|+||.|||||.+..-.+.+.+. .  +.++|+++||+..++++.+.+...
T Consensus       189 ~LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti~~~I~~l~~-~--~~~ILv~a~TN~AvD~i~erL~~~  256 (646)
T 4b3f_X          189 CLDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAVK-Q--GLKVLCCAPSNIAVDNLVERLALC  256 (646)
T ss_dssp             TCCHHHHHHHHHHHHCSSEEEEECCTTSCHHHHHHHHHHHHHH-T--TCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHhcCCCceEEECCCCCCHHHHHHHHHHHHHh-C--CCeEEEEcCchHHHHHHHHHHHhc
Confidence            46899999999988655 5799999999999765544444443 3  356999999999999999988654

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=98.64  E-value=4.7e-07  Score=82.31  Aligned_cols=68  Identities=18%  Similarity=0.210  Sum_probs=53.3

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (219)
                      .+++.|..++..++.+...+|.||.|+|||....-. +..+... .+.++++++||...+.++.+.+.+.
T Consensus       360 ~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~~i~~~-i~~l~~~-~~~~ILv~a~tn~A~d~l~~rL~~~  427 (802)
T 2xzl_A          360 QLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSATI-VYHLSKI-HKDRILVCAPSNVAVDHLAAKLRDL  427 (802)
T ss_dssp             CCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHHHHH-HHHHHHH-HCCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             cCCHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHH-HHHHHhC-CCCeEEEEcCcHHHHHHHHHHHHhh
Confidence            468999999999888777899999999999654433 3333221 2346999999999999999998765

>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=98.62  E-value=5.9e-07  Score=81.61  Aligned_cols=68  Identities=22%  Similarity=0.211  Sum_probs=53.6

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (219)
                      .+++.|..++..++.+...+|.||.|+|||.... .++..+... .+.++++++||...+.++.+.+.+.
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            4689999999998888889999999999996543 334444332 3456999999999999999988654

>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=97.98  E-value=3.7e-05  Score=63.98  Aligned_cols=122  Identities=11%  Similarity=0.155  Sum_probs=77.2

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccc--eeE
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN--IQA  132 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~--~~~  132 (219)
                      .++|+|...+..+...+..++..+-+.|||......++..+... .+..+++++|+...|..+++.+..+.....  ++.
T Consensus       163 ~L~p~Qk~il~~l~~~R~~vi~~sRq~GKT~l~a~~~l~~a~~~-~g~~v~~vA~t~~qA~~vf~~i~~mi~~~P~ll~~  241 (385)
T 2o0j_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFN-KDKAVGILAHKGSMSAEVLDRTKQAIELLPDFLQP  241 (385)
T ss_dssp             CCCHHHHHHHHHHHHSSEEEEEECSSSCHHHHHHHHHHHHHHSS-SSCEEEEEESSHHHHHHHHHHHHHHHHHSCTTTSC
T ss_pred             CCCHHHHHHHHhhccCcEEEEEEcCcCChhHHHHHHHHHHHHhC-CCCeEEEEeCCHHHHHHHHHHHHHHHHhChHhhhh
Confidence            78999999998765556789999999999987766555544332 355799999999999999888877654322  110


Q ss_pred             -EEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhc
Q 027749          133 -HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (219)
Q Consensus       133 -~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~  189 (219)
                       ..-.+...     ..+.+|..|.+.+..  ...+..     ....++|+||+|.+-+
T Consensus       242 ~~~~~~~~~-----I~f~nGs~i~~lsa~--~~slrG-----~~~~~viiDE~a~~~~  287 (385)
T 2o0j_A          242 GIVEWNKGS-----IELDNGSSIGAYASS--PDAVRG-----NSFAMIYIEDCAFIPN  287 (385)
T ss_dssp             CEEEECSSE-----EEETTSCEEEEEECS--HHHHHT-----SCCSEEEEESGGGSTT
T ss_pred             hhccCCccE-----EEeCCCCEEEEEECC--CCCccC-----CCCCEEEechhhhcCC
Confidence             00001000     112345555544421  012222     2357899999998654

>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=97.89  E-value=0.00013  Score=64.70  Aligned_cols=109  Identities=15%  Similarity=0.194  Sum_probs=73.1

Q ss_pred             CCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCC-CceeEEEEcCCHHHHHHHHHHHHHhccccceeE
Q 027749           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-REVQALILSPTRELATQTEKVILAIGDFINIQA  132 (219)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~-~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  132 (219)
                      ..+++-|.+++..  .+..++|.|+.|||||.+..--+.+.+...+ ...+++++++|+..+.++.+++.+.....    
T Consensus         8 ~~Ln~~Q~~av~~--~~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~~~~~~iL~ltft~~aa~e~~~rl~~~~~~~----   81 (647)
T 3lfu_A            8 DSLNDKQREAVAA--PRSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFTNKAAAEMRHRIGQLMGTS----   81 (647)
T ss_dssp             TTCCHHHHHHHTC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTSCCCGGGEEEEESSHHHHHHHHHHHHHHHCSC----
T ss_pred             hcCCHHHHHHHhC--CCCCEEEEECCCCCHHHHHHHHHHHHHHhCCCChhhEEEEeccHHHHHHHHHHHHHHhccc----
Confidence            4689999999973  3568999999999999766555555554322 33479999999999999999998764210    


Q ss_pred             EEEECCcccHHHHHHhcCCCeEEEeChHHHHHH-HHcCCCCCC-CccEEEeccchh
Q 027749          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDM-IKRKTLRTR-AIKLLVLDESDE  186 (219)
Q Consensus       133 ~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~-l~~~~~~~~-~l~~lVvDE~h~  186 (219)
                                        ...+-|+|.+.|..- +........ .-.+-|+|+.+.
T Consensus        82 ------------------~~~~~v~Tfhs~~~~il~~~~~~~~~~~~~~i~~~~~~  119 (647)
T 3lfu_A           82 ------------------QGGMWVGTFHGLAHRLLRAHHMDANLPQDFQILDSEDQ  119 (647)
T ss_dssp             ------------------CTTCEEEEHHHHHHHHHHHTTGGGTCCTTCEEECHHHH
T ss_pred             ------------------cCCcEEEcHHHHHHHHHHHHHHHhCCCCCCEEeCHHHH
Confidence                              135678888888663 333221111 123456776653

>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=97.75  E-value=0.00052  Score=60.36  Aligned_cols=120  Identities=13%  Similarity=0.183  Sum_probs=78.0

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccc--eeE
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN--IQA  132 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~--~~~  132 (219)
                      .++|+|...+..+...+..++..+-|+|||......++..+... .+..+++++|+...+..+++.++.+....+  +..
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 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFN-KDKAVGILAHKGSMSAEVLDRTKQAIELLPDFLQP  241 (592)
T ss_dssp             CCCHHHHHHHHHHHHCSEEEEEECSSSCHHHHHHHHHHHHHHTS-SSCEEEEEESSHHHHHHHHHHHHHHHTTSCTTTSC
T ss_pred             cCCHHHHHHHHhhccccEEEEEEcCccChHHHHHHHHHHHHHhC-CCCeEEEEECCHHHHHHHHHHHHHHHHhChHhhcc
Confidence            57999999988775567799999999999977665555544433 345799999999999999988887765442  111


Q ss_pred             EEE-ECCcccHHHHHHhcCCCeEEEeC--hHHHHHHHHcCCCCCCCccEEEeccchhhhc
Q 027749          133 HAC-VGGKSVGEDIRKLEHGVHVVSGT--PGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (219)
Q Consensus       133 ~~~-~~~~~~~~~~~~l~~~~~I~v~T--p~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~  189 (219)
                      ... .+...     ..+.+|..|.+.+  |+++    ...     ...++|+||+|.+-+
T Consensus       242 ~~~~~~~~~-----i~~~nGs~i~~~s~~~~~l----rG~-----~~~~~iiDE~~~~~~  287 (592)
T 3cpe_A          242 GIVEWNKGS-----IELDNGSSIGAYASSPDAV----RGN-----SFAMIYIEDCAFIPN  287 (592)
T ss_dssp             CEEEECSSE-----EEETTSCEEEEEECCHHHH----HHS-----CCSEEEEETGGGCTT
T ss_pred             ccccCCccE-----EEecCCCEEEEEeCCCCCc----cCC-----CcceEEEehhccCCc
Confidence            000 01100     1123456555543  3322    222     357899999997644

>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=97.66  E-value=0.00031  Score=51.82  Aligned_cols=19  Identities=26%  Similarity=0.524  Sum_probs=15.9

Q ss_pred             CCCcEEEEcCCCCchhHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~   87 (219)
                      .|+.+++.||+|+|||...
T Consensus        37 ~g~~~~l~G~~G~GKTtL~   55 (180)
T 3ec2_A           37 EGKGLTFVGSPGVGKTHLA   55 (180)
T ss_dssp             GCCEEEECCSSSSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4678999999999999443

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=97.65  E-value=0.00028  Score=59.66  Aligned_cols=105  Identities=23%  Similarity=0.139  Sum_probs=61.4

Q ss_pred             cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCC
Q 027749           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG  151 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  151 (219)
                      -.++.|+.|+|||....    +.+..    ...+|++||++++.++.+.+.+....                      ..
T Consensus       163 v~~I~G~aGsGKTt~I~----~~~~~----~~~lVlTpT~~aa~~l~~kl~~~~~~----------------------~~  212 (446)
T 3vkw_A          163 VVLVDGVPGCGKTKEIL----SRVNF----EEDLILVPGRQAAEMIRRRANASGII----------------------VA  212 (446)
T ss_dssp             EEEEEECTTSCHHHHHH----HHCCT----TTCEEEESCHHHHHHHHHHHTTTSCC----------------------CC
T ss_pred             EEEEEcCCCCCHHHHHH----HHhcc----CCeEEEeCCHHHHHHHHHHhhhcCcc----------------------cc
Confidence            46899999999994432    22221    23699999999999888877432100                      01


Q ss_pred             CeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       152 ~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ...-|.|-++++.  .......-..++|||||+- |...+   .+..++...+. .+++++.
T Consensus       213 ~~~~V~T~dsfL~--~~~~~~~~~~d~liiDE~s-m~~~~---~l~~l~~~~~~-~~vilvG  267 (446)
T 3vkw_A          213 TKDNVRTVDSFLM--NYGKGARCQFKRLFIDEGL-MLHTG---CVNFLVEMSLC-DIAYVYG  267 (446)
T ss_dssp             CTTTEEEHHHHHH--TTTSSCCCCCSEEEEETGG-GSCHH---HHHHHHHHTTC-SEEEEEE
T ss_pred             ccceEEEeHHhhc--CCCCCCCCcCCEEEEeCcc-cCCHH---HHHHHHHhCCC-CEEEEec
Confidence            1223567665442  2222222347899999997 44443   33344444443 5666654

>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=97.52  E-value=0.00029  Score=62.86  Aligned_cols=69  Identities=29%  Similarity=0.371  Sum_probs=52.0

Q ss_pred             CCCCChHHHHHHHHHHh----CCC-cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhcc
Q 027749           52 GFEKPSAIQQRAVMPII----KGR-DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGD  126 (219)
Q Consensus        52 ~~~~~~~~Q~~~~~~~~----~~~-~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~  126 (219)
                      ++ .|++.|..++..+.    .|. ..++.+.||+|||+.+.- ++...  .  . .+|||+|+..+|.|+++.++.+..
T Consensus         6 ~~-~~~~~q~~ai~~l~~~~~~~~~~~~l~g~tgs~kt~~~a~-~~~~~--~--~-~~lvv~~~~~~A~ql~~el~~~~~   78 (664)
T 1c4o_A            6 GP-SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMAK-VIEAL--G--R-PALVLAPNKILAAQLAAEFRELFP   78 (664)
T ss_dssp             SC-CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHH-HHHHH--T--C-CEEEEESSHHHHHHHHHHHHHHCT
T ss_pred             CC-CCCCCChHHHHHHHHHHhcCCCcEEEEcCCCcHHHHHHHH-HHHHh--C--C-CEEEEecCHHHHHHHHHHHHHHCC
Confidence            45 89999998887654    343 467889999999965543 23332  1  1 399999999999999999999964


Q ss_pred             c
Q 027749          127 F  127 (219)
Q Consensus       127 ~  127 (219)
                      .
T Consensus        79 ~   79 (664)
T 1c4o_A           79 E   79 (664)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=97.40  E-value=0.00032  Score=62.61  Aligned_cols=70  Identities=17%  Similarity=0.158  Sum_probs=54.4

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhcc-CCCceeEEEEcCCHHHHHHHHHHHHHhcc
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT-SSREVQALILSPTRELATQTEKVILAIGD  126 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~l~~q~~~~~~~~~~  126 (219)
                      .+++-|++++...  +.+++|.|+.|||||.+..--+.+.+.. .....++++|+.|+..+.++.+++.+...
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            4789999998753  5789999999999997665555554443 22345699999999999999999987654

>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=97.40  E-value=0.00083  Score=54.28  Aligned_cols=18  Identities=28%  Similarity=0.440  Sum_probs=15.0

Q ss_pred             CCcEEEEcCCCCchhHHh
Q 027749           70 GRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~   87 (219)
                      +.++++.||+|+|||...
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            468999999999999443

>1pjr_A PCRA; DNA repair, DNA replication, SOS response, helicase, ATP- binding, DNA-binding; 2.50A {Geobacillus stearothermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1qhg_A* 3pjr_A* 2pjr_A* 1qhh_B* 1qhh_D* 1qhh_A* 1qhh_C* 2pjr_B*

Probab=97.34  E-value=0.00059  Score=61.43  Aligned_cols=70  Identities=17%  Similarity=0.194  Sum_probs=54.7

Q ss_pred             CCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCC-CceeEEEEcCCHHHHHHHHHHHHHhc
Q 027749           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-REVQALILSPTRELATQTEKVILAIG  125 (219)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~-~~~~~lil~P~~~l~~q~~~~~~~~~  125 (219)
                      ..+++-|++++..  .+.+++|.|+.|||||.+..--+.+.+...+ ...++++|+.|+..+.++.+++.+..
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            4689999999876  3568999999999999766555555554322 34569999999999999999997764

>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=97.33  E-value=0.0027  Score=47.52  Aligned_cols=39  Identities=13%  Similarity=0.221  Sum_probs=26.7

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ..-.+||+||+|.+... ....+..+++..+.+..+|+.|
T Consensus       101 ~~~~vliiDe~~~l~~~-~~~~l~~~l~~~~~~~~~i~~~  139 (226)
T 2chg_A          101 APFKIIFLDEADALTAD-AQAALRRTMEMYSKSCRFILSC  139 (226)
T ss_dssp             CSCEEEEEETGGGSCHH-HHHHHHHHHHHTTTTEEEEEEE
T ss_pred             cCceEEEEeChhhcCHH-HHHHHHHHHHhcCCCCeEEEEe
Confidence            45678999999987643 3556667777766666666554

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=97.32  E-value=0.0011  Score=58.81  Aligned_cols=113  Identities=12%  Similarity=0.167  Sum_probs=75.9

Q ss_pred             CChHHHHHHHHHHhC--CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeE
Q 027749           55 KPSAIQQRAVMPIIK--GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQA  132 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~--~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  132 (219)
                      .+|..|.+++..+..  ....++.|+-|.|||.+.-+.+ ..+..     .++|.+|+.+-+..+++...+         
T Consensus       175 ~~T~dQ~~al~~~~~~~~~~~vlta~RGRGKSa~lG~~~-a~~~~-----~~~vtAP~~~a~~~l~~~~~~---------  239 (671)
T 2zpa_A          175 APQPEQQQLLKQLMTMPPGVAAVTAARGRGKSALAGQLI-SRIAG-----RAIVTAPAKASTDVLAQFAGE---------  239 (671)
T ss_dssp             SCCHHHHHHHHHHTTCCSEEEEEEECTTSSHHHHHHHHH-HHSSS-----CEEEECSSCCSCHHHHHHHGG---------
T ss_pred             CCCHHHHHHHHHHHHhhhCeEEEecCCCCCHHHHHHHHH-HHHHh-----CcEEECCCHHHHHHHHHHhhC---------
Confidence            578899999988775  3357999999999995544433 43332     269999999988766554321         


Q ss_pred             EEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEE
Q 027749          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCP  212 (219)
Q Consensus       133 ~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~  212 (219)
                                          .|-+..|+.+.   .    ...+.++||||||=.+-    ...+..++...    ..++|
T Consensus       240 --------------------~i~~~~Pd~~~---~----~~~~~dlliVDEAAaIp----~pll~~ll~~~----~~v~~  284 (671)
T 2zpa_A          240 --------------------KFRFIAPDALL---A----SDEQADWLVVDEAAAIP----APLLHQLVSRF----PRTLL  284 (671)
T ss_dssp             --------------------GCCBCCHHHHH---H----SCCCCSEEEEETGGGSC----HHHHHHHHTTS----SEEEE
T ss_pred             --------------------CeEEeCchhhh---h----CcccCCEEEEEchhcCC----HHHHHHHHhhC----CeEEE
Confidence                                13334676533   1    13458999999997544    46667776643    35788


Q ss_pred             eeccc
Q 027749          213 GSCFL  217 (219)
Q Consensus       213 SATl~  217 (219)
                      |.|+.
T Consensus       285 ~tTv~  289 (671)
T 2zpa_A          285 TTTVQ  289 (671)
T ss_dssp             EEEBS
T ss_pred             EecCC
Confidence            88763

>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=97.30  E-value=0.00055  Score=65.15  Aligned_cols=69  Identities=19%  Similarity=0.266  Sum_probs=55.9

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCC---CceeEEEEcCCHHHHHHHHHHHHHhc
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS---REVQALILSPTRELATQTEKVILAIG  125 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~---~~~~~lil~P~~~l~~q~~~~~~~~~  125 (219)
                      .+++-|.+++..-  +++++|.|+.|||||.+.+--++..+....   ..-+++++++|+..+.++.+++....
T Consensus        10 ~~t~eQ~~~i~~~--~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~~~~~~~il~~Tft~~aa~e~~~ri~~~l   81 (1232)
T 3u4q_A           10 TWTDDQWNAIVST--GQDILVAAAAGSGKTAVLVERMIRKITAEENPIDVDRLLVVTFTNASAAEMKHRIAEAL   81 (1232)
T ss_dssp             CCCHHHHHHHHCC--SSCEEEEECTTCCHHHHHHHHHHHHHSCSSSCCCGGGEEEECSSHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHhCC--CCCEEEEecCCCcHHHHHHHHHHHHHhcCCCCCCccceEEEeccHHHHHHHHHHHHHHH
Confidence            5799999998764  789999999999999777666666665532   34579999999999999999997643

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=97.25  E-value=0.00016  Score=51.97  Aligned_cols=44  Identities=9%  Similarity=0.182  Sum_probs=26.3

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCC-CCeEEEEeecccC
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP-DLQVCCPGSCFLF  218 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~-~~q~i~~SATl~~  218 (219)
                      .+.+++|+||.+.+.... ...+..+++.+.. ...++++++..++
T Consensus        82 ~~~~lLilDE~~~~~~~~-~~~l~~li~~~~~~g~~~iiits~~~p  126 (149)
T 2kjq_A           82 FEAEYLAVDQVEKLGNEE-QALLFSIFNRFRNSGKGFLLLGSEYTP  126 (149)
T ss_dssp             GGCSEEEEESTTCCCSHH-HHHHHHHHHHHHHHTCCEEEEEESSCT
T ss_pred             hCCCEEEEeCccccChHH-HHHHHHHHHHHHHcCCcEEEEECCCCH
Confidence            346799999999755433 5556666555432 2343556666543

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=97.19  E-value=0.0021  Score=52.10  Aligned_cols=40  Identities=15%  Similarity=0.417  Sum_probs=24.9

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhC---CCCCeEEEEeecc
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYL---PPDLQVCCPGSCF  216 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~---~~~~q~i~~SATl  216 (219)
                      ....+|++||+|.+.+   ...+..++++.   ....-+|+.++|+
T Consensus       131 ~~~~ii~lDE~d~l~~---q~~L~~l~~~~~~~~s~~~vI~i~n~~  173 (318)
T 3te6_A          131 KRKTLILIQNPENLLS---EKILQYFEKWISSKNSKLSIICVGGHN  173 (318)
T ss_dssp             SCEEEEEEECCSSSCC---THHHHHHHHHHHCSSCCEEEEEECCSS
T ss_pred             CCceEEEEecHHHhhc---chHHHHHHhcccccCCcEEEEEEecCc
Confidence            3456899999999883   24444455432   2234566777775

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=97.16  E-value=0.0045  Score=43.88  Aligned_cols=36  Identities=11%  Similarity=0.131  Sum_probs=22.8

Q ss_pred             cEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          177 KLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       177 ~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      +.|++||+|.+... ....+..++...+.+.++|+-|
T Consensus        78 g~l~ldei~~l~~~-~q~~Ll~~l~~~~~~~~~I~~t  113 (145)
T 3n70_A           78 GTLVLSHPEHLTRE-QQYHLVQLQSQEHRPFRLIGIG  113 (145)
T ss_dssp             SCEEEECGGGSCHH-HHHHHHHHHHSSSCSSCEEEEE
T ss_pred             cEEEEcChHHCCHH-HHHHHHHHHhhcCCCEEEEEEC
Confidence            46999999987543 3445555555555566665544

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=97.15  E-value=0.0026  Score=52.13  Aligned_cols=29  Identities=34%  Similarity=0.441  Sum_probs=20.0

Q ss_pred             CccEEEeccchhhhccc-cHHHHHHHHHhC
Q 027749          175 AIKLLVLDESDEMLSRG-FKDQIYDVYRYL  203 (219)
Q Consensus       175 ~l~~lVvDE~h~l~~~~-~~~~~~~i~~~~  203 (219)
                      .-.+||+||+|.+.... ....+..+++..
T Consensus       130 ~~~vlilDEi~~l~~~~~~~~~l~~l~~~~  159 (387)
T 2v1u_A          130 GIYIIVLDEIDFLPKRPGGQDLLYRITRIN  159 (387)
T ss_dssp             SEEEEEEETTTHHHHSTTHHHHHHHHHHGG
T ss_pred             CeEEEEEccHhhhcccCCCChHHHhHhhch
Confidence            35589999999987542 345566666654

>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=97.13  E-value=0.0023  Score=54.24  Aligned_cols=40  Identities=15%  Similarity=0.426  Sum_probs=24.2

Q ss_pred             CccEEEeccchhhhcc-ccHHHHHHHHHhC-CCCCeEEEEeec
Q 027749          175 AIKLLVLDESDEMLSR-GFKDQIYDVYRYL-PPDLQVCCPGSC  215 (219)
Q Consensus       175 ~l~~lVvDE~h~l~~~-~~~~~~~~i~~~~-~~~~q~i~~SAT  215 (219)
                      ..++|++||+|.+... .....+..+++.+ ..+.++|+ ++.
T Consensus       194 ~~~vL~IDEi~~l~~~~~~q~~l~~~l~~l~~~~~~iIi-tt~  235 (440)
T 2z4s_A          194 KVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVI-CSD  235 (440)
T ss_dssp             TCSEEEEECGGGGSSCHHHHHHHHHHHHHHHTTTCEEEE-EES
T ss_pred             CCCEEEEeCcccccCChHHHHHHHHHHHHHHHCCCeEEE-EEC
Confidence            4678999999998753 2344455555543 33455555 444

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=97.10  E-value=0.002  Score=52.50  Aligned_cols=39  Identities=18%  Similarity=0.283  Sum_probs=25.9

Q ss_pred             ChHHHHHHHHHHh----CCC---cEEEEcCCCCchhHHhHHHHHhhh
Q 027749           56 PSAIQQRAVMPII----KGR---DVIAQAQSGTGKTSMIALTVCQTV   95 (219)
Q Consensus        56 ~~~~Q~~~~~~~~----~~~---~~lv~~~tG~GKT~~~~~~~~~~~   95 (219)
                      .+|||..++..+.    +|+   ..++.||.|+|||..... +...+
T Consensus         3 ~~pw~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~~-la~~l   48 (334)
T 1a5t_A            3 WYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYA-LSRYL   48 (334)
T ss_dssp             CCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHH-HHHHH
T ss_pred             CCCchHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHHHH-HHHHH
Confidence            3577777776543    443   389999999999955443 33444

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=97.01  E-value=0.00069  Score=51.78  Aligned_cols=19  Identities=16%  Similarity=0.237  Sum_probs=15.8

Q ss_pred             CCCcEEEEcCCCCchhHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~   87 (219)
                      .++++++.||+|+|||...
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            4678999999999999443

>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=96.97  E-value=0.012  Score=47.89  Aligned_cols=40  Identities=8%  Similarity=0.223  Sum_probs=28.4

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEee
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGS  214 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SA  214 (219)
                      .+-+++|+||+|. ++......+...++..+.+..+|+.|-
T Consensus       133 ~~~~vlilDE~~~-L~~~~~~~L~~~le~~~~~~~~Il~t~  172 (354)
T 1sxj_E          133 HRYKCVIINEANS-LTKDAQAALRRTMEKYSKNIRLIMVCD  172 (354)
T ss_dssp             -CCEEEEEECTTS-SCHHHHHHHHHHHHHSTTTEEEEEEES
T ss_pred             CCCeEEEEeCccc-cCHHHHHHHHHHHHhhcCCCEEEEEeC
Confidence            4567999999998 455556777778887766666666553

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=96.96  E-value=0.0013  Score=48.88  Aligned_cols=39  Identities=13%  Similarity=0.219  Sum_probs=25.1

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCH
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~  111 (219)
                      |+-.++.|++|+|||...+- ++..+...  +.+++++.|..
T Consensus         3 g~i~vi~G~~gsGKTT~ll~-~~~~~~~~--g~~v~~~~~~~   41 (184)
T 2orw_A            3 GKLTVITGPMYSGKTTELLS-FVEIYKLG--KKKVAVFKPKI   41 (184)
T ss_dssp             CCEEEEEESTTSSHHHHHHH-HHHHHHHT--TCEEEEEEEC-
T ss_pred             cEEEEEECCCCCCHHHHHHH-HHHHHHHC--CCeEEEEeecc
Confidence            45578999999999955543 33443333  23588887763

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=96.94  E-value=0.011  Score=41.82  Aligned_cols=18  Identities=11%  Similarity=0.182  Sum_probs=15.6

Q ss_pred             hCCCcEEEEcCCCCchhH
Q 027749           68 IKGRDVIAQAQSGTGKTS   85 (219)
Q Consensus        68 ~~~~~~lv~~~tG~GKT~   85 (219)
                      ..+.+++++|++|+|||.
T Consensus        25 ~~~~~vll~G~~GtGKt~   42 (143)
T 3co5_A           25 KRTSPVFLTGEAGSPFET   42 (143)
T ss_dssp             TCSSCEEEEEETTCCHHH
T ss_pred             CCCCcEEEECCCCccHHH
Confidence            456789999999999993

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=96.87  E-value=0.0045  Score=48.82  Aligned_cols=54  Identities=17%  Similarity=0.220  Sum_probs=32.6

Q ss_pred             cCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHH--HhCCCcEEEEcCCCCchhHHh
Q 027749           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMP--IIKGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        32 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~--~~~~~~~lv~~~tG~GKT~~~   87 (219)
                      -.+|+++.-.+..++.+.+.-. .+.. ....+..  +...+++++.||+|+|||...
T Consensus        13 ~~~~~~i~G~~~~~~~l~~~~~-~~~~-~~~~~~~~~~~~~~~~ll~G~~GtGKT~la   68 (285)
T 3h4m_A           13 NVRYEDIGGLEKQMQEIREVVE-LPLK-HPELFEKVGIEPPKGILLYGPPGTGKTLLA   68 (285)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHTH-HHHH-CHHHHHHHCCCCCSEEEEESSSSSSHHHHH
T ss_pred             CCCHHHhcCHHHHHHHHHHHHH-HHhh-CHHHHHhcCCCCCCeEEEECCCCCcHHHHH
Confidence            3568888777777777765321 1100 1112222  234578999999999999443

>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=96.84  E-value=0.0063  Score=46.69  Aligned_cols=113  Identities=14%  Similarity=0.115  Sum_probs=58.7

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  148 (219)
                      .|.-.++.|++|+|||...+- ++.++...  +.+++++.|...-  .   ....+....++..                
T Consensus        11 ~G~i~litG~mGsGKTT~ll~-~~~r~~~~--g~kVli~~~~~d~--r---~~~~i~srlG~~~----------------   66 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAELIR-RLHRLEYA--DVKYLVFKPKIDT--R---SIRNIQSRTGTSL----------------   66 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHHHH-HHHHHHHT--TCCEEEEEECCCG--G---GCSSCCCCCCCSS----------------
T ss_pred             CcEEEEEECCCCCcHHHHHHH-HHHHHHhc--CCEEEEEEeccCc--h---HHHHHHHhcCCCc----------------
Confidence            345578899999999955544 34444433  3347777665421  0   0001111111110                


Q ss_pred             cCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          149 EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       149 ~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                         ..+-+.+...+...+.... .-.+.++|||||++.+.. .....+..+.+.   +.++++..
T Consensus        67 ---~~~~~~~~~~i~~~i~~~~-~~~~~dvViIDEaQ~l~~-~~ve~l~~L~~~---gi~Vil~G  123 (223)
T 2b8t_A           67 ---PSVEVESAPEILNYIMSNS-FNDETKVIGIDEVQFFDD-RICEVANILAEN---GFVVIISG  123 (223)
T ss_dssp             ---CCEEESSTHHHHHHHHSTT-SCTTCCEEEECSGGGSCT-HHHHHHHHHHHT---TCEEEEEC
T ss_pred             ---cccccCCHHHHHHHHHHHh-hCCCCCEEEEecCccCcH-HHHHHHHHHHhC---CCeEEEEe
Confidence               1233456666766665432 234578999999986432 233344443332   45555543

>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=96.81  E-value=0.0019  Score=53.07  Aligned_cols=36  Identities=25%  Similarity=0.399  Sum_probs=22.0

Q ss_pred             EEEeccchhhhccccHHH-HHHHHHhCCCCCeEEEEee
Q 027749          178 LLVLDESDEMLSRGFKDQ-IYDVYRYLPPDLQVCCPGS  214 (219)
Q Consensus       178 ~lVvDE~h~l~~~~~~~~-~~~i~~~~~~~~q~i~~SA  214 (219)
                      +||+||+|.+........ +..+++.. .+..+|+.|.
T Consensus       136 vlilDEi~~l~~~~~~~~~l~~l~~~~-~~~~iI~~t~  172 (384)
T 2qby_B          136 IIYLDEVDTLVKRRGGDIVLYQLLRSD-ANISVIMISN  172 (384)
T ss_dssp             EEEEETTHHHHHSTTSHHHHHHHHTSS-SCEEEEEECS
T ss_pred             EEEEECHHHhccCCCCceeHHHHhcCC-cceEEEEEEC
Confidence            899999999875432344 55555554 3444554443

>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=96.78  E-value=0.015  Score=45.57  Aligned_cols=17  Identities=24%  Similarity=0.421  Sum_probs=14.5

Q ss_pred             CcEEEEcCCCCchhHHh
Q 027749           71 RDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~   87 (219)
                      +++++.||+|+|||..+
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            47999999999999544

>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=96.74  E-value=0.009  Score=44.65  Aligned_cols=39  Identities=10%  Similarity=0.148  Sum_probs=25.8

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCH
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~  111 (219)
                      |+=.++.|++|+|||...+ -++.++...  +.+++++.|..
T Consensus         8 g~i~v~~G~mgsGKTT~ll-~~a~r~~~~--g~kV~v~k~~~   46 (191)
T 1xx6_A            8 GWVEVIVGPMYSGKSEELI-RRIRRAKIA--KQKIQVFKPEI   46 (191)
T ss_dssp             CEEEEEECSTTSSHHHHHH-HHHHHHHHT--TCCEEEEEEC-
T ss_pred             CEEEEEECCCCCcHHHHHH-HHHHHHHHC--CCEEEEEEecc
Confidence            4457889999999995554 444544433  34588888763

>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=96.70  E-value=0.0085  Score=47.92  Aligned_cols=39  Identities=13%  Similarity=0.298  Sum_probs=26.5

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ..-++||+||+|.+... ....+...++..+.+..+|+.+
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            45678999999987643 3455666777766666665544

>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=96.69  E-value=0.007  Score=53.89  Aligned_cols=67  Identities=21%  Similarity=0.306  Sum_probs=50.0

Q ss_pred             CChHHHHHHHHHHh----CCC-cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccc
Q 027749           55 KPSAIQQRAVMPII----KGR-DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDF  127 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~----~~~-~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (219)
                      .|+..|..++..+.    .|. ...+.+.||+|||+...- ++...  .  . .+|||+|+..+|.|+++.++.+...
T Consensus        12 ~p~~~Q~~~i~~l~~~~~~~~~~~~l~g~~gs~k~~~~a~-~~~~~--~--~-~~lvv~~~~~~A~~l~~el~~~~~~   83 (661)
T 2d7d_A           12 QPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTVSN-LIKEV--N--K-PTLVIAHNKTLAGQLYSEFKEFFPN   83 (661)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHH-HHHHH--C--C-CEEEECSSHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEECcCCcHHHHHHHH-HHHHh--C--C-CEEEEECCHHHHHHHHHHHHHHcCC
Confidence            78889988887544    343 467889999999955432 23332  1  1 3999999999999999999999643

>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=96.68  E-value=0.0047  Score=49.75  Aligned_cols=40  Identities=13%  Similarity=0.120  Sum_probs=26.9

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ...++|++||+|.+........+...++..+.+.++|+.+
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            3678999999998862333556666666655566666644

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=96.64  E-value=0.0027  Score=50.72  Aligned_cols=37  Identities=22%  Similarity=0.227  Sum_probs=23.2

Q ss_pred             cEEEeccchhhhcc--------ccHHHHHHHHHhCCCCCeEEEEe
Q 027749          177 KLLVLDESDEMLSR--------GFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       177 ~~lVvDE~h~l~~~--------~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ++|++||+|.+...        .....+..+++..+.+..+|+.+
T Consensus       132 ~vl~iDEid~l~~~~~~~~~~~~~~~~Ll~~l~~~~~~~~~i~~~  176 (309)
T 3syl_A          132 GVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENNRDDLVVILAG  176 (309)
T ss_dssp             SEEEEETGGGSCCCC---CCTHHHHHHHHHHHHHCTTTCEEEEEE
T ss_pred             CEEEEEChhhhccCCCcccccHHHHHHHHHHHhcCCCCEEEEEeC
Confidence            58999999988521        23345556666655555555554

>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=96.60  E-value=0.0038  Score=51.28  Aligned_cols=24  Identities=21%  Similarity=0.278  Sum_probs=17.0

Q ss_pred             cEEEEcCCCCchhHHhHHHHHhhhc
Q 027749           72 DVIAQAQSGTGKTSMIALTVCQTVD   96 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~~~~~~~~~   96 (219)
                      .+++.||+|+|||... -.+...+.
T Consensus        46 ~~li~G~~G~GKTtl~-~~l~~~~~   69 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTL-RKLWELYK   69 (389)
T ss_dssp             EEEEECCTTSSHHHHH-HHHHHHHT
T ss_pred             eEEEECCCCCCHHHHH-HHHHHHHh
Confidence            7999999999999443 33444443

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=96.52  E-value=0.0048  Score=46.07  Aligned_cols=25  Identities=20%  Similarity=0.442  Sum_probs=17.7

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhc
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVD   96 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~   96 (219)
                      ++++++||+|+|||.... .+...+.
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            689999999999995432 3344443

>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=96.49  E-value=0.021  Score=46.58  Aligned_cols=18  Identities=28%  Similarity=0.558  Sum_probs=15.1

Q ss_pred             CCcEEEEcCCCCchhHHh
Q 027749           70 GRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~   87 (219)
                      ++.+++.||.|+|||...
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            568999999999999443

>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=96.45  E-value=0.012  Score=44.70  Aligned_cols=39  Identities=10%  Similarity=0.148  Sum_probs=24.7

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHH
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  112 (219)
                      +=.++.|++|+|||...+-. +.++...  +.+++++.|...
T Consensus        29 ~l~vitG~MgsGKTT~lL~~-a~r~~~~--g~kVli~k~~~d   67 (214)
T 2j9r_A           29 WIEVICGSMFSGKSEELIRR-VRRTQFA--KQHAIVFKPCID   67 (214)
T ss_dssp             EEEEEECSTTSCHHHHHHHH-HHHHHHT--TCCEEEEECC--
T ss_pred             EEEEEECCCCCcHHHHHHHH-HHHHHHC--CCEEEEEEeccC
Confidence            33568999999999555444 4444433  345888888653

>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=96.44  E-value=0.019  Score=44.13  Aligned_cols=39  Identities=10%  Similarity=0.214  Sum_probs=25.8

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCH
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~  111 (219)
                      |+=.++.|++|+|||...+-. +.+....  +.+++++-|..
T Consensus        19 g~l~v~~G~MgsGKTT~lL~~-~~r~~~~--g~kvli~kp~~   57 (234)
T 2orv_A           19 GQIQVILGPMFSGKSTELMRR-VRRFQIA--QYKCLVIKYAK   57 (234)
T ss_dssp             CEEEEEECCTTSCHHHHHHHH-HHHHHTT--TCCEEEEEETT
T ss_pred             eEEEEEECCCCCcHHHHHHHH-HHHHHHC--CCeEEEEeecC
Confidence            455778999999999555444 4444333  34588887764

>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=96.43  E-value=0.053  Score=40.73  Aligned_cols=38  Identities=11%  Similarity=0.164  Sum_probs=23.6

Q ss_pred             CccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       175 ~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      .-.+||+||+|.+... ....+...++..+....+|+.|
T Consensus       126 ~~~vlviDe~~~l~~~-~~~~l~~~l~~~~~~~~~i~~t  163 (250)
T 1njg_A          126 RFKVYLIDEVHMLSRH-SFNALLKTLEEPPEHVKFLLAT  163 (250)
T ss_dssp             SSEEEEEETGGGSCHH-HHHHHHHHHHSCCTTEEEEEEE
T ss_pred             CceEEEEECcccccHH-HHHHHHHHHhcCCCceEEEEEe
Confidence            3468999999986533 3445555666555555555544

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=96.41  E-value=0.0097  Score=45.32  Aligned_cols=99  Identities=6%  Similarity=-0.003  Sum_probs=51.0

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  148 (219)
                      .|.=.++.|++|+|||...+-. +.++...  +.+++++.|...--   +. -..+....+...                
T Consensus        27 ~G~I~vitG~M~sGKTT~Llr~-~~r~~~~--g~kvli~kp~~D~R---~~-~~~I~Sr~G~~~----------------   83 (219)
T 3e2i_A           27 SGWIECITGSMFSGKSEELIRR-LRRGIYA--KQKVVVFKPAIDDR---YH-KEKVVSHNGNAI----------------   83 (219)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHH-HHHHHHT--TCCEEEEEEC---------------CBTTBCC----------------
T ss_pred             CceEEEEECCCCCCHHHHHHHH-HHHHHHc--CCceEEEEeccCCc---ch-hhhHHHhcCCce----------------
Confidence            3455788999999999544444 4544443  34588888864311   00 011111112111                


Q ss_pred             cCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHH
Q 027749          149 EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVY  200 (219)
Q Consensus       149 ~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~  200 (219)
                         .-+.|..+..+...+      ..+.++|+|||++- ++......+..+.
T Consensus        84 ---~a~~v~~~~di~~~i------~~~~dvV~IDEaQF-f~~~~v~~l~~la  125 (219)
T 3e2i_A           84 ---EAINISKASEIMTHD------LTNVDVIGIDEVQF-FDDEIVSIVEKLS  125 (219)
T ss_dssp             ---EEEEESSGGGGGGSC------CTTCSEEEECCGGG-SCTHHHHHHHHHH
T ss_pred             ---eeEEeCCHHHHHHHH------hcCCCEEEEechhc-CCHHHHHHHHHHH
Confidence               123344443332221      24678999999985 4444566666665

>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=96.39  E-value=0.0082  Score=47.91  Aligned_cols=38  Identities=16%  Similarity=0.279  Sum_probs=25.9

Q ss_pred             CccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       175 ~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      +-.+||+||+|.+.... ...+...++..+.+..+|+.|
T Consensus       107 ~~~viiiDe~~~l~~~~-~~~L~~~le~~~~~~~~il~~  144 (323)
T 1sxj_B          107 KHKIVILDEADSMTAGA-QQALRRTMELYSNSTRFAFAC  144 (323)
T ss_dssp             CCEEEEEESGGGSCHHH-HHTTHHHHHHTTTTEEEEEEE
T ss_pred             CceEEEEECcccCCHHH-HHHHHHHHhccCCCceEEEEe
Confidence            46789999999876432 445566666666666666654

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=96.32  E-value=0.011  Score=47.83  Aligned_cols=38  Identities=18%  Similarity=0.297  Sum_probs=26.0

Q ss_pred             CccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       175 ~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ..++|++||+|.+... ....+..+++..+....+++.+
T Consensus       133 ~~~vliiDE~~~l~~~-~~~~Ll~~le~~~~~~~~il~~  170 (353)
T 1sxj_D          133 PYKIIILDEADSMTAD-AQSALRRTMETYSGVTRFCLIC  170 (353)
T ss_dssp             SCEEEEETTGGGSCHH-HHHHHHHHHHHTTTTEEEEEEE
T ss_pred             CceEEEEECCCccCHH-HHHHHHHHHHhcCCCceEEEEe
Confidence            4579999999987643 3456667777766665555544

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=96.26  E-value=0.012  Score=42.79  Aligned_cols=18  Identities=28%  Similarity=0.523  Sum_probs=15.0

Q ss_pred             CCcEEEEcCCCCchhHHh
Q 027749           70 GRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~   87 (219)
                      .+++++.||+|+|||...
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            467999999999999443

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=96.23  E-value=0.049  Score=44.10  Aligned_cols=39  Identities=23%  Similarity=0.459  Sum_probs=27.7

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ...+++|+||+|.|... ....+..+++..+.+..+++.+
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            45789999999987643 3556777777777666666544

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=96.22  E-value=0.02  Score=42.89  Aligned_cols=38  Identities=11%  Similarity=0.193  Sum_probs=25.1

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCC
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~  110 (219)
                      |+=.++.||+|+|||.- ++-.+.+....  +.+++++.|.
T Consensus        20 g~l~fiyG~MgsGKTt~-Ll~~i~n~~~~--~~kvl~~kp~   57 (195)
T 1w4r_A           20 GQIQVILGPMFSGKSTE-LMRRVRRFQIA--QYKCLVIKYA   57 (195)
T ss_dssp             CEEEEEEECTTSCHHHH-HHHHHHHHHHT--TCCEEEEEET
T ss_pred             eEEEEEECCCCCcHHHH-HHHHHHHHHHc--CCeEEEEccc
Confidence            45578899999999944 34344444333  2458888776

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=96.19  E-value=0.06  Score=43.18  Aligned_cols=40  Identities=8%  Similarity=0.138  Sum_probs=26.7

Q ss_pred             CCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       173 ~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ..+.+++|+||+|.|.... .+.+.+.++.-|++.-+|+.+
T Consensus        80 ~~~~kvviIdead~lt~~a-~naLLk~LEep~~~t~fIl~t  119 (305)
T 2gno_A           80 LYTRKYVIVHDCERMTQQA-ANAFLKALEEPPEYAVIVLNT  119 (305)
T ss_dssp             SSSSEEEEETTGGGBCHHH-HHHTHHHHHSCCTTEEEEEEE
T ss_pred             cCCceEEEeccHHHhCHHH-HHHHHHHHhCCCCCeEEEEEE
Confidence            3467899999999987544 345666666655555555544

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=96.06  E-value=0.0053  Score=49.41  Aligned_cols=18  Identities=17%  Similarity=0.390  Sum_probs=15.4

Q ss_pred             CCcEEEEcCCCCchhHHh
Q 027749           70 GRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~   87 (219)
                      ++++++.||+|+|||...
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            578999999999999443

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=95.86  E-value=0.04  Score=43.74  Aligned_cols=42  Identities=21%  Similarity=0.380  Sum_probs=25.8

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHh
Q 027749           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        33 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~   87 (219)
                      .+|+++--.+.+.+.+.+. +..            ....++++.||.|+|||...
T Consensus        14 ~~~~~~~g~~~~~~~l~~~-l~~------------~~~~~~ll~G~~G~GKt~la   55 (319)
T 2chq_A           14 RTLDEVVGQDEVIQRLKGY-VER------------KNIPHLLFSGPPGTGKTATA   55 (319)
T ss_dssp             SSGGGSCSCHHHHHHHHTT-TTT------------TCCCCEEEESSSSSSHHHHH
T ss_pred             CCHHHHhCCHHHHHHHHHH-HhC------------CCCCeEEEECcCCcCHHHHH
Confidence            4566655566666666543 111            11235999999999999443

>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=95.83  E-value=0.1  Score=44.89  Aligned_cols=41  Identities=17%  Similarity=0.080  Sum_probs=26.4

Q ss_pred             CCccEEEeccchhhhcc--ccHHHHHHHHHhCCCCCeEEEEeecc
Q 027749          174 RAIKLLVLDESDEMLSR--GFKDQIYDVYRYLPPDLQVCCPGSCF  216 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~--~~~~~~~~i~~~~~~~~q~i~~SATl  216 (219)
                      ..-.+|++||+|.+...  +....+..+++..  ...+|+.+++.
T Consensus       147 ~~~~vliIDEid~l~~~~~~~l~~L~~~l~~~--~~~iIli~~~~  189 (516)
T 1sxj_A          147 GKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKT--STPLILICNER  189 (516)
T ss_dssp             TTSEEEEECSGGGCCTTSTTHHHHHHHHHHHC--SSCEEEEESCT
T ss_pred             CCCeEEEEECCCccchhhHHHHHHHHHHHHhc--CCCEEEEEcCC
Confidence            34568999999998753  2335555666553  44577777653

>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=95.60  E-value=0.028  Score=45.24  Aligned_cols=50  Identities=8%  Similarity=0.141  Sum_probs=32.1

Q ss_pred             cCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHh-----CCCcEEEEcCCCCchhHHh
Q 027749           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII-----KGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        32 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~-----~~~~~lv~~~tG~GKT~~~   87 (219)
                      -.+|+++.-...+.+.+.+.-.   +|.   ..|...     ..+++++.||+|+|||...
T Consensus        14 ~~~~~di~G~~~~~~~l~~~i~---~~~---~~~~~~~~~~~~~~~vLl~GppGtGKT~la   68 (322)
T 3eie_A           14 NVKWEDVAGLEGAKEALKEAVI---LPV---KFPHLFKGNRKPTSGILLYGPPGTGKSYLA   68 (322)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHTH---HHH---HCGGGCCTTCCCCCEEEEECSSSSCHHHHH
T ss_pred             CCCHHHhcChHHHHHHHHHHHH---HHH---hCHHHHhcCCCCCCeEEEECCCCCcHHHHH
Confidence            3568888878888888875421   111   112211     2357999999999999544

>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=95.56  E-value=0.075  Score=43.21  Aligned_cols=39  Identities=10%  Similarity=0.179  Sum_probs=25.1

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ..-.+||+||+|.+.... ...+...++..+.+..+|+.+
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            456789999999876433 455566666655555555544

>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=95.53  E-value=0.039  Score=45.52  Aligned_cols=17  Identities=29%  Similarity=0.481  Sum_probs=13.6

Q ss_pred             CcEEE--EcCCCCchhHHh
Q 027749           71 RDVIA--QAQSGTGKTSMI   87 (219)
Q Consensus        71 ~~~lv--~~~tG~GKT~~~   87 (219)
                      ..++|  .|+.|+|||...
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            46788  899999999443

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=95.46  E-value=0.054  Score=43.64  Aligned_cols=17  Identities=24%  Similarity=0.518  Sum_probs=14.6

Q ss_pred             CcEEEEcCCCCchhHHh
Q 027749           71 RDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~   87 (219)
                      .++++.||+|+|||...
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            57999999999999544

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=95.36  E-value=0.059  Score=46.18  Aligned_cols=40  Identities=15%  Similarity=0.217  Sum_probs=26.7

Q ss_pred             cEEEeccchhhhcc----------ccHHHHHHHHHhCCCCCeEEEEeecc
Q 027749          177 KLLVLDESDEMLSR----------GFKDQIYDVYRYLPPDLQVCCPGSCF  216 (219)
Q Consensus       177 ~~lVvDE~h~l~~~----------~~~~~~~~i~~~~~~~~q~i~~SATl  216 (219)
                      .+|++||+|.+...          .....+...++.......++++.||=
T Consensus       299 ~iLfLDEId~l~~~~~~~~~~~~~~~~~~LL~~ld~~~~~~~v~vIaaTn  348 (489)
T 3hu3_A          299 AIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATN  348 (489)
T ss_dssp             EEEEEESHHHHCBCTTSCCCHHHHHHHHHHHHHHHHSCTTSCEEEEEEES
T ss_pred             cEEEecchhhhccccccccchHHHHHHHHHHHHhhccccCCceEEEEecC
Confidence            57999999988752          12344556666666666677777764

>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=95.25  E-value=0.16  Score=42.85  Aligned_cols=43  Identities=12%  Similarity=0.309  Sum_probs=26.2

Q ss_pred             CCccEEEeccchhhh---ccccHHHHHHHHHhCCCCCeEEEEeecc
Q 027749          174 RAIKLLVLDESDEML---SRGFKDQIYDVYRYLPPDLQVCCPGSCF  216 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~---~~~~~~~~~~i~~~~~~~~q~i~~SATl  216 (219)
                      .+.+++|+|++-++.   +..+...+..+.+...++.-++.++|+.
T Consensus       178 ~~~DvvIIDTaGr~~~~~d~~lm~el~~i~~~~~pd~vlLVlDa~~  223 (433)
T 3kl4_A          178 NKMDIIIVDTAGRHGYGEETKLLEEMKEMYDVLKPDDVILVIDASI  223 (433)
T ss_dssp             TTCSEEEEEECCCSSSCCTTHHHHHHHHHHHHHCCSEEEEEEEGGG
T ss_pred             cCCCEEEEECCCCccccCCHHHHHHHHHHHHhhCCcceEEEEeCcc
Confidence            456778888876543   2345556666666665555566666654

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=95.23  E-value=0.053  Score=43.29  Aligned_cols=18  Identities=22%  Similarity=0.353  Sum_probs=15.1

Q ss_pred             CCcEEEEcCCCCchhHHh
Q 027749           70 GRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~   87 (219)
                      ..++++.||+|+|||...
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            368999999999999443

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=95.18  E-value=0.097  Score=37.55  Aligned_cols=73  Identities=12%  Similarity=0.162  Sum_probs=54.4

Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCCcc
Q 027749          102 VQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAIK  177 (219)
Q Consensus       102 ~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~  177 (219)
                      .++||.++++..+..+.+.+.+.    ++.+..++|+.+..++...+    ....+|+|+|.     . ...++++..++
T Consensus        36 ~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T~-----~-~~~Gld~~~~~  105 (163)
T 2hjv_A           36 DSCIIFCRTKEHVNQLTDELDDL----GYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATD-----V-AARGIDIENIS  105 (163)
T ss_dssp             SSEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECG-----G-GTTTCCCSCCS
T ss_pred             CcEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEECC-----h-hhcCCchhcCC
Confidence            46999999999999999888765    67788888887765543333    23678999993     2 24677888899


Q ss_pred             EEEeccc
Q 027749          178 LLVLDES  184 (219)
Q Consensus       178 ~lVvDE~  184 (219)
                      +||.-+.
T Consensus       106 ~Vi~~~~  112 (163)
T 2hjv_A          106 LVINYDL  112 (163)
T ss_dssp             EEEESSC
T ss_pred             EEEEeCC
Confidence            8886544

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens}

Probab=95.07  E-value=0.13  Score=37.26  Aligned_cols=73  Identities=16%  Similarity=0.110  Sum_probs=54.0

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCCc
Q 027749          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (219)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~l  176 (219)
                      ..++||.++++..+..+...+...    ++.+..++|+.+..++...+    ....+|+|+|.-      ...++++..+
T Consensus        34 ~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~~------~~~Gid~~~~  103 (175)
T 2rb4_A           34 IGQAIIFCQTRRNAKWLTVEMIQD----GHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNV------CARGIDVKQV  103 (175)
T ss_dssp             CSEEEEECSCHHHHHHHHHHHHTT----TCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECCS------CCTTTCCTTE
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEecc------hhcCCCcccC
Confidence            457999999999999888888654    67788888887766554333    236789999941      2467788889


Q ss_pred             cEEEecc
Q 027749          177 KLLVLDE  183 (219)
Q Consensus       177 ~~lVvDE  183 (219)
                      .+||.-+
T Consensus       104 ~~Vi~~d  110 (175)
T 2rb4_A          104 TIVVNFD  110 (175)
T ss_dssp             EEEEESS
T ss_pred             CEEEEeC
Confidence            8888433

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=94.99  E-value=0.092  Score=43.39  Aligned_cols=18  Identities=28%  Similarity=0.497  Sum_probs=15.3

Q ss_pred             CCcEEEEcCCCCchhHHh
Q 027749           70 GRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~   87 (219)
                      .+++++.||+|+|||...
T Consensus       148 ~~~vLL~GppGtGKT~la  165 (389)
T 3vfd_A          148 ARGLLLFGPPGNGKTMLA  165 (389)
T ss_dssp             CSEEEEESSTTSCHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            468999999999999444

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=94.96  E-value=0.12  Score=43.69  Aligned_cols=140  Identities=21%  Similarity=0.201  Sum_probs=64.0

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  148 (219)
                      .|.-++|.|++|+|||. +.+-++..+.... +..++|+..-. -..|+..++..........-. ..|..+ ..++..+
T Consensus       199 ~G~l~ii~G~pg~GKT~-lal~ia~~~a~~~-g~~vl~~slE~-~~~~l~~R~~~~~~~i~~~~l-~~g~l~-~~~~~~~  273 (444)
T 2q6t_A          199 PGSLNIIAARPAMGKTA-FALTIAQNAALKE-GVGVGIYSLEM-PAAQLTLRMMCSEARIDMNRV-RLGQLT-DRDFSRL  273 (444)
T ss_dssp             TTCEEEEEECTTSCHHH-HHHHHHHHHHHTT-CCCEEEEESSS-CHHHHHHHHHHHHTTCCTTTC-CGGGCC-HHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHH-HHHHHHHHHHHhC-CCeEEEEECCC-CHHHHHHHHHHHHcCCCHHHH-hCCCCC-HHHHHHH
Confidence            44568999999999994 4444444333221 22366665432 233444443221111111000 011111 1222221


Q ss_pred             c------CCCeEEEe-----ChHHHHHHHHcCCCCCCCccEEEeccchhhhcc--c-----cHHHHHHHHHhCC-----C
Q 027749          149 E------HGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR--G-----FKDQIYDVYRYLP-----P  205 (219)
Q Consensus       149 ~------~~~~I~v~-----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~--~-----~~~~~~~i~~~~~-----~  205 (219)
                      .      ....+.+-     |++.+...+..-. .-..+++||||..+.+...  +     -...+..+.+.+.     .
T Consensus       274 ~~a~~~l~~~~l~i~d~~~~s~~~l~~~~~~l~-~~~~~~lIvID~l~~~~~~~~~~~~~~r~~~i~~i~~~Lk~lAke~  352 (444)
T 2q6t_A          274 VDVASRLSEAPIYIDDTPDLTLMEVRARARRLV-SQNQVGLIIIDYLQLMSGPGSGKSGENRQQEIAAISRGLKALAREL  352 (444)
T ss_dssp             HHHHHHHHTSCEEEECCTTCBHHHHHHHHHHHH-HHSCCCEEEEECGGGCBCC-------CHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHH-HHcCCCEEEEcChhhcCCCcCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence            1      12345552     3444544332210 0125889999999988643  1     1223334433331     2


Q ss_pred             CCeEEEEee
Q 027749          206 DLQVCCPGS  214 (219)
Q Consensus       206 ~~q~i~~SA  214 (219)
                      ++.++++|.
T Consensus       353 ~v~vi~lsq  361 (444)
T 2q6t_A          353 GIPIIALSQ  361 (444)
T ss_dssp             TSCEEEEEE
T ss_pred             CCeEEEEec
Confidence            567787765

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=94.91  E-value=0.25  Score=37.44  Aligned_cols=52  Identities=13%  Similarity=0.123  Sum_probs=30.0

Q ss_pred             hCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 027749           68 IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA  123 (219)
Q Consensus        68 ~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~  123 (219)
                      ..|.-+++.|++|+|||.....-+...+ ..  +.+++++.-.. ...++.+.+..
T Consensus        21 ~~G~~~~i~G~~GsGKTtl~~~~~~~~~-~~--~~~v~~~~~e~-~~~~~~~~~~~   72 (247)
T 2dr3_A           21 PERNVVLLSGGPGTGKTIFSQQFLWNGL-KM--GEPGIYVALEE-HPVQVRQNMAQ   72 (247)
T ss_dssp             ETTCEEEEEECTTSSHHHHHHHHHHHHH-HT--TCCEEEEESSS-CHHHHHHHHHT
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHH-hc--CCeEEEEEccC-CHHHHHHHHHH
Confidence            3566789999999999954333333332 22  22366665433 34555555543

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=94.91  E-value=0.15  Score=36.49  Aligned_cols=73  Identities=12%  Similarity=0.129  Sum_probs=53.6

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCCc
Q 027749          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (219)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~l  176 (219)
                      ..++||.++++..+..+...+.+.    ++.+..++|+.+..++...+    .....|+|+|.     . ...++++..+
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            356999999999999988888764    57788888887765543333    24678999994     1 2466788888


Q ss_pred             cEEEecc
Q 027749          177 KLLVLDE  183 (219)
Q Consensus       177 ~~lVvDE  183 (219)
                      ++||.-+
T Consensus       100 ~~Vi~~~  106 (165)
T 1fuk_A          100 SLVINYD  106 (165)
T ss_dssp             SEEEESS
T ss_pred             CEEEEeC
Confidence            8877654

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=94.89  E-value=0.017  Score=48.93  Aligned_cols=17  Identities=35%  Similarity=0.558  Sum_probs=14.3

Q ss_pred             CcEEEEcCCCCchhHHh
Q 027749           71 RDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~   87 (219)
                      .+++++||+|+|||...
T Consensus        51 ~~vLL~GppGtGKTtlA   67 (447)
T 3pvs_A           51 HSMILWGPPGTGKTTLA   67 (447)
T ss_dssp             CEEEEECSTTSSHHHHH
T ss_pred             cEEEEECCCCCcHHHHH
Confidence            47999999999999444

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=94.85  E-value=0.014  Score=47.61  Aligned_cols=49  Identities=24%  Similarity=0.220  Sum_probs=28.4

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHH
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVI  121 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~  121 (219)
                      .|.-+++.|++|+|||. +.+-++..+...  +..++|+..- .-..|+..++
T Consensus        45 ~G~LiiIaG~pG~GKTt-~al~ia~~~a~~--g~~Vl~fSlE-ms~~ql~~Rl   93 (338)
T 4a1f_A           45 KGSLVIIGARPSMGKTS-LMMNMVLSALND--DRGVAVFSLE-MSAEQLALRA   93 (338)
T ss_dssp             TTCEEEEEECTTSCHHH-HHHHHHHHHHHT--TCEEEEEESS-SCHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHH-HHHHHHHHHHHc--CCeEEEEeCC-CCHHHHHHHH
Confidence            44568999999999994 444444433332  3346666543 2334444444

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=94.73  E-value=0.18  Score=42.65  Aligned_cols=139  Identities=22%  Similarity=0.280  Sum_probs=63.3

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEE-ECCcccHHHHHH
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC-VGGKSVGEDIRK  147 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~  147 (219)
                      .|.-++|.|++|+|||. +++-++..+.... +..++|+..-.. ..++..++.....  ++....+ .|..+ ..++..
T Consensus       202 ~G~liiI~G~pG~GKTt-l~l~ia~~~~~~~-g~~Vl~~s~E~s-~~~l~~r~~~~~~--~~~~~~l~~g~l~-~~~~~~  275 (454)
T 2r6a_A          202 RSDLIIVAARPSVGKTA-FALNIAQNVATKT-NENVAIFSLEMS-AQQLVMRMLCAEG--NINAQNLRTGKLT-PEDWGK  275 (454)
T ss_dssp             TTCEEEEECCTTSCHHH-HHHHHHHHHHHHS-SCCEEEEESSSC-HHHHHHHHHHHHH--TCCHHHHHTSCCC-HHHHHH
T ss_pred             CCCEEEEECCCCCCHHH-HHHHHHHHHHHhC-CCcEEEEECCCC-HHHHHHHHHHHHc--CCCHHHHhcCCCC-HHHHHH
Confidence            45668999999999994 4444444333211 223666654322 2344444321000  1110000 11111 122211


Q ss_pred             hc------CCCeEEEe-----ChHHHHHHHHcCCCCCCCccEEEeccchhhhccc-----cHHHHHHHHHhCC-----CC
Q 027749          148 LE------HGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG-----FKDQIYDVYRYLP-----PD  206 (219)
Q Consensus       148 l~------~~~~I~v~-----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~-----~~~~~~~i~~~~~-----~~  206 (219)
                      +.      ....+.+-     |.+.+...+..-. .-..+++||||+.+.+....     ....+..+.+.+.     .+
T Consensus       276 ~~~a~~~l~~~~l~i~d~~~~s~~~i~~~~~~l~-~~~~~~livID~l~~~~~~~~~~~~~~~~i~~i~~~Lk~lAke~~  354 (454)
T 2r6a_A          276 LTMAMGSLSNAGIYIDDTPSIRVSDIRAKCRRLK-QESGLGMIVIDYLQLIQGSGRSKENRQQEVSEISRSLKALARELE  354 (454)
T ss_dssp             HHHHHHHHHSSCEEEECCTTCCHHHHHHHHHHHH-TTTCCCEEEEECGGGSCCSCC----CHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHH-HHcCCCEEEEccHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHhC
Confidence            10      12345553     4444444333210 11358899999999887432     2233334333331     25


Q ss_pred             CeEEEEee
Q 027749          207 LQVCCPGS  214 (219)
Q Consensus       207 ~q~i~~SA  214 (219)
                      +.++++|-
T Consensus       355 i~vi~~sq  362 (454)
T 2r6a_A          355 VPVIALSQ  362 (454)
T ss_dssp             CCEEEEEC
T ss_pred             CeEEEEec
Confidence            66777764

>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer, ATP-binding, helicase, hydrolase, nucleotide-binding; 2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A

Probab=94.64  E-value=0.14  Score=38.57  Aligned_cols=70  Identities=24%  Similarity=0.315  Sum_probs=52.8

Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCCcc
Q 027749          102 VQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAIK  177 (219)
Q Consensus       102 ~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~  177 (219)
                      .++||.++++.-+..+.+.+...    ++.+..++|+.+..++...+    .+..+|+|+|.     . -..++++.+++
T Consensus        32 ~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~-----~-~~~Gidi~~v~  101 (212)
T 3eaq_A           32 DRAMVFTRTKAETEEIAQGLLRL----GHPAQALHGDLSQGERERVLGAFRQGEVRVLVATD-----V-AARGLDIPQVD  101 (212)
T ss_dssp             SCEEEECSSHHHHHHHHHHHHHH----TCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECT-----T-TTCSSSCCCBS
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHc----CCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecC-----h-hhcCCCCccCc
Confidence            46999999999999998888765    67788889888766554333    24678999993     2 24677888888


Q ss_pred             EEEe
Q 027749          178 LLVL  181 (219)
Q Consensus       178 ~lVv  181 (219)
                      +||.
T Consensus       102 ~Vi~  105 (212)
T 3eaq_A          102 LVVH  105 (212)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            8774

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=94.55  E-value=0.12  Score=41.54  Aligned_cols=50  Identities=18%  Similarity=0.170  Sum_probs=29.0

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHH
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL  122 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~  122 (219)
                      .|.-++|.|++|+|||. +.+-+...+....  ..++|+.-- .-..++..++.
T Consensus        67 ~G~l~li~G~pG~GKTt-l~l~ia~~~a~~g--~~vl~~slE-~s~~~l~~R~~  116 (315)
T 3bh0_A           67 RRNFVLIAARPSMGKTA-FALKQAKNMSDND--DVVNLHSLE-MGKKENIKRLI  116 (315)
T ss_dssp             TTCEEEEECCTTSSHHH-HHHHHHHHHHTTT--CEEEEEESS-SCHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHH-HHHHHHHHHHHcC--CeEEEEECC-CCHHHHHHHHH
Confidence            45568999999999994 4343433333222  346666543 33445555543

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=94.49  E-value=0.46  Score=40.98  Aligned_cols=90  Identities=7%  Similarity=0.070  Sum_probs=63.2

Q ss_pred             HHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHH
Q 027749           88 ALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVC  163 (219)
Q Consensus        88 ~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~  163 (219)
                      +-.+...+.....+.++||.++++..+..+.+.+.+.... ++.+..++|+.+..++...+    ....+|+|+|.    
T Consensus       326 ~~~l~~~~~~~~~~~~~iVF~~s~~~~~~l~~~L~~~~~~-~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLvaT~----  400 (563)
T 3i5x_A          326 VEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKK-DLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD----  400 (563)
T ss_dssp             HHHHHHHHHHTTTCCEEEEECSCHHHHHHHHHHHHHHHTT-TSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECG----
T ss_pred             HHHHHHHHhhcCCCCcEEEEcCcHHHHHHHHHHHHHhccC-CceEEEecCCCCHHHHHHHHHHHhcCCCCEEEEcc----
Confidence            3334444444344567999999999999999999876432 57788888887766554333    24689999994    


Q ss_pred             HHHHcCCCCCCCccEEEeccc
Q 027749          164 DMIKRKTLRTRAIKLLVLDES  184 (219)
Q Consensus       164 ~~l~~~~~~~~~l~~lVvDE~  184 (219)
                       . -..++++.++++||.-..
T Consensus       401 -~-~~~GiDip~v~~VI~~~~  419 (563)
T 3i5x_A          401 -V-GARGMDFPNVHEVLQIGV  419 (563)
T ss_dssp             -G-GTSSCCCTTCCEEEEESC
T ss_pred             -h-hhcCCCcccCCEEEEECC
Confidence             2 346788888988876553

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=94.45  E-value=0.098  Score=39.31  Aligned_cols=19  Identities=32%  Similarity=0.413  Sum_probs=15.4

Q ss_pred             CCCcEEEEcCCCCchhHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~   87 (219)
                      .|.-+++.||+|+|||...
T Consensus        22 ~G~~~~i~G~~GsGKTtl~   40 (235)
T 2w0m_A           22 QGFFIALTGEPGTGKTIFS   40 (235)
T ss_dssp             TTCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHH
Confidence            4567899999999999443

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=94.13  E-value=0.33  Score=35.85  Aligned_cols=72  Identities=22%  Similarity=0.259  Sum_probs=53.7

Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCCcc
Q 027749          102 VQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAIK  177 (219)
Q Consensus       102 ~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~  177 (219)
                      .++||.++++..+..+.+.+...    ++.+..+.|+.+..++...+    ....+|+|+|.     .+ ..++++.+++
T Consensus        55 ~~~lVF~~~~~~~~~l~~~L~~~----g~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~-----~~-~~Gldi~~v~  124 (191)
T 2p6n_A           55 PPVLIFAEKKADVDAIHEYLLLK----GVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATD-----VA-SKGLDFPAIQ  124 (191)
T ss_dssp             SCEEEECSCHHHHHHHHHHHHHH----TCCEEEECTTSCHHHHHHHHHHHHHTSCSEEEECH-----HH-HTTCCCCCCS
T ss_pred             CCEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEcC-----ch-hcCCCcccCC
Confidence            46999999999999999888765    67788888887765543333    24688999993     32 3567888888


Q ss_pred             EEEecc
Q 027749          178 LLVLDE  183 (219)
Q Consensus       178 ~lVvDE  183 (219)
                      +||.=+
T Consensus       125 ~VI~~d  130 (191)
T 2p6n_A          125 HVINYD  130 (191)
T ss_dssp             EEEESS
T ss_pred             EEEEeC
Confidence            887644

>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=94.13  E-value=0.12  Score=48.89  Aligned_cols=87  Identities=13%  Similarity=0.136  Sum_probs=51.8

Q ss_pred             EEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCC
Q 027749           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGV  152 (219)
Q Consensus        73 ~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  152 (219)
                      -+|.|+.|||||.+.+--+.+.+.....+.+++++||.+.... +.+++....   +..                  ...
T Consensus         4 ~lV~agAGSGKT~~l~~ri~~ll~~~~~~~~il~lVP~q~TFt-~~~rl~~~l---~~~------------------~~~   61 (1166)
T 3u4q_B            4 EFLVGRSGSGKTKLIINSIQDELRRAPFGKPIIFLVPDQMTFL-MEYELAKTP---DMG------------------GMI   61 (1166)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHHHCTTSSCEEEECCGGGHHH-HHHHHTCCS---SCS------------------EES
T ss_pred             EEEEeCCCCChHHHHHHHHHHHHHhCCCCCcEEEEecCcccHH-HHHHHHHhh---hhc------------------cee
Confidence            3789999999997776666665555444567999999875544 333332221   100                  013


Q ss_pred             eEEEeChHHHHH-HHHcCCCCCCCccEEEeccch
Q 027749          153 HVVSGTPGRVCD-MIKRKTLRTRAIKLLVLDESD  185 (219)
Q Consensus       153 ~I~v~Tp~~l~~-~l~~~~~~~~~l~~lVvDE~h  185 (219)
                      ++-|+|-.+|.. ++...+    ....-++|+.+
T Consensus        62 ~~~V~TFhsla~~il~~~g----~~~~~ild~~~   91 (1166)
T 3u4q_B           62 RAQVFSFSRLAWRVLQHTG----GMSRPFLTSTG   91 (1166)
T ss_dssp             SEEEECHHHHHHHHHHHHS----CTTSCEECHHH
T ss_pred             eeEEecHHHHHHHHHHHcC----CCcccCcCHHH
Confidence            578889888876 333222    12234566655

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19

Probab=94.04  E-value=0.17  Score=36.64  Aligned_cols=74  Identities=11%  Similarity=0.107  Sum_probs=54.3

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCCc
Q 027749          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (219)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~l  176 (219)
                      ..++||.++++..+..+.+.+...    ++.+..++|+.+..++...+    .....|+|+|..      ...++++..+
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            346999999999999998888765    67788888887765543333    246789999941      2456788888


Q ss_pred             cEEEeccc
Q 027749          177 KLLVLDES  184 (219)
Q Consensus       177 ~~lVvDE~  184 (219)
                      ++||.-+.
T Consensus       101 ~~Vi~~d~  108 (172)
T 1t5i_A          101 NIAFNYDM  108 (172)
T ss_dssp             SEEEESSC
T ss_pred             CEEEEECC
Confidence            88776544

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=94.02  E-value=0.66  Score=40.31  Aligned_cols=87  Identities=7%  Similarity=0.084  Sum_probs=62.0

Q ss_pred             HHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHH
Q 027749           91 VCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMI  166 (219)
Q Consensus        91 ~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l  166 (219)
                      +...+.....+.++||.++++..+..+++.+.+.... ++.+..++|+.+..++...+    ....+|+|+|.     . 
T Consensus       278 l~~~~~~~~~~~~~iVF~~t~~~~~~l~~~L~~~~~~-~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVaT~-----~-  350 (579)
T 3sqw_A          278 IKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKK-DLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD-----V-  350 (579)
T ss_dssp             HHHHHHHTTTCCEEEEECSSHHHHHHHHHHHHHHHTT-TSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECG-----G-
T ss_pred             HHHHHhhcCCCCcEEEECCcHHHHHHHHHHHHHhhcC-CCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEEcc-----h-
Confidence            3334443344567999999999999999999876432 57788888887766553333    24689999994     2 


Q ss_pred             HcCCCCCCCccEEEeccc
Q 027749          167 KRKTLRTRAIKLLVLDES  184 (219)
Q Consensus       167 ~~~~~~~~~l~~lVvDE~  184 (219)
                      -..++++.++++||.-..
T Consensus       351 ~~~GiDip~v~~VI~~~~  368 (579)
T 3sqw_A          351 GARGMDFPNVHEVLQIGV  368 (579)
T ss_dssp             GTSSCCCTTCCEEEEESC
T ss_pred             hhcCCCcccCCEEEEcCC
Confidence            346788889998886654

>2l8b_A Protein TRAI, DNA helicase I; RECD, hydrolase; NMR {Escherichia coli}

Probab=93.88  E-value=0.066  Score=39.56  Aligned_cols=120  Identities=11%  Similarity=0.081  Sum_probs=71.6

Q ss_pred             ChHHHHHHHHHHhCC--CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEE
Q 027749           56 PSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAH  133 (219)
Q Consensus        56 ~~~~Q~~~~~~~~~~--~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~  133 (219)
                      ..+-|..++..+...  +-.+|.++-|++|+...+-.++......  +.++.+++|+..-.....+..       +..- 
T Consensus        35 ~~~~~~~a~~~l~~s~~~~~iv~g~ggs~~~~~~~a~L~~~a~~~--Gr~V~vLAp~~~s~~~l~~~~-------~l~~-  104 (189)
T 2l8b_A           35 RTAGYSDAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQ--GREVQIIAADRRSQMNMKQDE-------RLSG-  104 (189)
T ss_dssp             CHHHHHHHHHHHHHHSCCEECCBCSSCSHHHHHHHHHHHHHHHHT--TCCEEEECSTTHHHHHHSCTT-------TCSS-
T ss_pred             cCccchhHHHHHhccCCceEEEecccchHHHHHHHHHHHHHHHhc--CeEEEEEcCchHHHHHHHhhc-------CcCc-
Confidence            456788899888644  3577889999999977655555554444  456999999986654433322       1110 


Q ss_pred             EEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhC-CCCCeEEEE
Q 027749          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL-PPDLQVCCP  212 (219)
Q Consensus       134 ~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~-~~~~q~i~~  212 (219)
                                        . ++  |-    ..+......+..=+.+|||||..|.    ..++..+++.- ..+.|+|++
T Consensus       105 ------------------~-t~--t~----~~ll~~~~~~tp~s~lIVD~AekLS----~kE~~~Lld~A~~~naqvvll  155 (189)
T 2l8b_A          105 ------------------E-LI--TG----RRQLLEGMAFTPGSTVIVDQGEKLS----LKETLTLLDGAARHNVQVLIT  155 (189)
T ss_dssp             ------------------C-SS--ST----TTTTTTSCCCCCCCEEEEEESSSHH----HHHHHHHHHHHHHTTCCEEEE
T ss_pred             ------------------c-ee--eh----hhhhcCCCCCCCCCEEEEechhhcC----HHHHHHHHHHHHhcCCEEEEe
Confidence                              0 00  10    1111222223344489999999877    45556665553 235777776


Q ss_pred             ee
Q 027749          213 GS  214 (219)
Q Consensus       213 SA  214 (219)
                      --
T Consensus       156 ~~  157 (189)
T 2l8b_A          156 DS  157 (189)
T ss_dssp             ES
T ss_pred             CC
Confidence            43

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=93.79  E-value=0.62  Score=35.13  Aligned_cols=23  Identities=22%  Similarity=0.121  Sum_probs=17.4

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHH
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTV   91 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~   91 (219)
                      .|.-+.+.||+|+|||......+
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            45678999999999995544433

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens}

Probab=93.78  E-value=0.21  Score=36.72  Aligned_cols=90  Identities=12%  Similarity=0.175  Sum_probs=51.4

Q ss_pred             CCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHH---h-cCCCeEE
Q 027749           80 GTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRK---L-EHGVHVV  155 (219)
Q Consensus        80 G~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---l-~~~~~I~  155 (219)
                      ...|- ..+.-++...   ..+.++||.++++..+..+.+.+...    ++.+..+.|+.+..++...   . ....+|+
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            45565 3444444432   23456999999999999988888764    5777888887665443222   2 2467899


Q ss_pred             EeChHHHHHHHHcCCCCCCCccEEEecc
Q 027749          156 SGTPGRVCDMIKRKTLRTRAIKLLVLDE  183 (219)
Q Consensus       156 v~Tp~~l~~~l~~~~~~~~~l~~lVvDE  183 (219)
                      |+|.     . ...++++..+++||.=+
T Consensus       101 vaT~-----~-~~~Gldi~~~~~VI~~d  122 (185)
T 2jgn_A          101 VATA-----V-AARGLDISNVKHVINFD  122 (185)
T ss_dssp             EEEC------------CCCSBSEEEESS
T ss_pred             EEcC-----h-hhcCCCcccCCEEEEeC
Confidence            9993     2 23566788888877633

>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=93.71  E-value=0.72  Score=38.92  Aligned_cols=57  Identities=16%  Similarity=0.162  Sum_probs=30.5

Q ss_pred             cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEc--CCHHHHHHHHHHHHHhccccceeEEE
Q 027749           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS--PTRELATQTEKVILAIGDFINIQAHA  134 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~--P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (219)
                      -+++.|++|+|||....- +...+...  +.+++++.  |.+.-+   .+.+..+....++.+..
T Consensus       102 vIlivG~~G~GKTTt~~k-LA~~l~~~--G~kVllv~~D~~R~aa---~eqL~~~~~~~gvpv~~  160 (443)
T 3dm5_A          102 ILLMVGIQGSGKTTTVAK-LARYFQKR--GYKVGVVCSDTWRPGA---YHQLRQLLDRYHIEVFG  160 (443)
T ss_dssp             EEEEECCTTSSHHHHHHH-HHHHHHTT--TCCEEEEECCCSSTHH---HHHHHHHHGGGTCEEEC
T ss_pred             EEEEECcCCCCHHHHHHH-HHHHHHHC--CCeEEEEeCCCcchhH---HHHHHHHHHhcCCcEEe
Confidence            478899999999955443 33333333  23455544  334433   23344444444555443

>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=93.67  E-value=0.13  Score=44.60  Aligned_cols=19  Identities=37%  Similarity=0.496  Sum_probs=15.8

Q ss_pred             CCCcEEEEcCCCCchhHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~   87 (219)
                      .+..+++.||+|+|||...
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            4678999999999999443

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=93.66  E-value=0.44  Score=39.12  Aligned_cols=72  Identities=14%  Similarity=0.195  Sum_probs=54.2

Q ss_pred             CceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCC
Q 027749          100 REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRA  175 (219)
Q Consensus       100 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~  175 (219)
                      .+.++||.++++..+..+.+.+.+.    ++.+..++|+.+..++...+    ....+|+|+|.     .+ ..++++.+
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            4567999999999999998888764    67788888888765553333    24678999994     33 46778888


Q ss_pred             ccEEEe
Q 027749          176 IKLLVL  181 (219)
Q Consensus       176 l~~lVv  181 (219)
                      +++||.
T Consensus       345 v~~Vi~  350 (417)
T 2i4i_A          345 VKHVIN  350 (417)
T ss_dssp             EEEEEE
T ss_pred             CCEEEE
Confidence            888775

>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=93.43  E-value=2.7  Score=34.88  Aligned_cols=26  Identities=15%  Similarity=0.257  Sum_probs=21.4

Q ss_pred             CCccCccccCCCCHHHHHHHHHCCCC
Q 027749           29 VEAITSFDAMGIKDDLLRGIYQYGFE   54 (219)
Q Consensus        29 ~~~~~~~~~~~l~~~~~~~l~~~~~~   54 (219)
                      +.++..++..++++..++.|.+.|+.
T Consensus        80 ~~~~~~l~~~gi~~~~~~~L~~ag~~  105 (400)
T 3lda_A           80 FVPIEKLQVNGITMADVKKLRESGLH  105 (400)
T ss_dssp             SCBGGGGCCTTCCHHHHHHHHHTTCC
T ss_pred             ccCHHHHHhCCCCHHHHHHHHHcCCC
Confidence            44667777788999999999998886

>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=93.28  E-value=0.17  Score=47.99  Aligned_cols=55  Identities=20%  Similarity=0.114  Sum_probs=42.9

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhccC---------CCceeEEEEcCCHHHHHHHHHHHHHhc
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDTS---------SREVQALILSPTRELATQTEKVILAIG  125 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~~---------~~~~~~lil~P~~~l~~q~~~~~~~~~  125 (219)
                      .+.+|.|..|||||.+..--++..+...         -...++|+|+=|+.-+.++.+++.+..
T Consensus        17 g~~lV~AsAGSGKT~~L~~r~lrLll~~g~~~~~~~~~~~~~ILvvTFT~aAA~EMr~RI~~~L   80 (1180)
T 1w36_B           17 GERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSNI   80 (1180)
T ss_dssp             SCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCHHHHHHHHHHHHHhcCCcccccCCCCCHHHEEEEeccHHHHHHHHHHHHHHH
Confidence            3559999999999977766666666532         123469999999999999999997654

>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=93.09  E-value=0.66  Score=37.06  Aligned_cols=55  Identities=11%  Similarity=0.126  Sum_probs=30.7

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhhccC---------CCc----eeEEEEcCCHHH-HHHHHHHHHHh
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTS---------SRE----VQALILSPTREL-ATQTEKVILAI  124 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~~~~---------~~~----~~~lil~P~~~l-~~q~~~~~~~~  124 (219)
                      |.-+++.|++|+|||...+-.+.......         ..+    .+++|+.-...+ ..++.+.+..+
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            34689999999999954443333322211         111    467777755432 44555555443

>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=92.84  E-value=2.9  Score=33.12  Aligned_cols=51  Identities=16%  Similarity=0.276  Sum_probs=30.5

Q ss_pred             hHHHHHHHHcCCCCCCCccEEEeccchhhhc---cccHHHHHHHHHhCCCCCeEEEEe
Q 027749          159 PGRVCDMIKRKTLRTRAIKLLVLDESDEMLS---RGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       159 p~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~---~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ...+...+....-   .--+||+||+|.+..   ..+...+..+.+..+ +..+|+.+
T Consensus       124 ~~~l~~~l~~~~~---~~~vlvlDe~~~~~~~~~~~~~~~l~~~~~~~~-~~~~i~~g  177 (357)
T 2fna_A          124 FANLLESFEQASK---DNVIIVLDEAQELVKLRGVNLLPALAYAYDNLK-RIKFIMSG  177 (357)
T ss_dssp             HHHHHHHHHHTCS---SCEEEEEETGGGGGGCTTCCCHHHHHHHHHHCT-TEEEEEEE
T ss_pred             HHHHHHHHHhcCC---CCeEEEEECHHHhhccCchhHHHHHHHHHHcCC-CeEEEEEc
Confidence            4455555544221   234799999999864   356677777776643 44455444

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=92.73  E-value=0.12  Score=43.77  Aligned_cols=139  Identities=15%  Similarity=0.117  Sum_probs=64.4

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECC--ccc-----
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGG--KSV-----  141 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~--~~~-----  141 (219)
                      .|.-++|.|++|+|||. +.+-++..+...  +..++|+.-- .-..|+..++.......+..-. ..|.  .+.     
T Consensus       196 ~G~liiIaG~pG~GKTt-lal~ia~~~a~~--g~~vl~fSlE-ms~~ql~~R~~~~~~~i~~~~l-~~g~~~l~~~~~~~  270 (444)
T 3bgw_A          196 RRNFVLIAARPSMGKTA-FALKQAKNMSDN--DDVVNLHSLE-MGKKENIKRLIVTAGSINAQKI-KAARRDFASEDWGK  270 (444)
T ss_dssp             SSCEEEEEECSSSSHHH-HHHHHHHHHHHT--TCEEEEECSS-SCTTHHHHHHHHHHSCCCHHHH-HHTGGGTCCSCHHH
T ss_pred             CCcEEEEEeCCCCChHH-HHHHHHHHHHHc--CCEEEEEECC-CCHHHHHHHHHHHHcCCCHHHH-hcccCCCCHHHHHH
Confidence            44568999999999994 444444444333  3347776543 2233444443222111111000 0011  000     


Q ss_pred             -HHHHHHhcCCCeEEEe-----ChHHHHHHHHcCCCCCCCcc--EEEeccchhhhcc----ccHHHHHHHHHhCC-----
Q 027749          142 -GEDIRKLEHGVHVVSG-----TPGRVCDMIKRKTLRTRAIK--LLVLDESDEMLSR----GFKDQIYDVYRYLP-----  204 (219)
Q Consensus       142 -~~~~~~l~~~~~I~v~-----Tp~~l~~~l~~~~~~~~~l~--~lVvDE~h~l~~~----~~~~~~~~i~~~~~-----  204 (219)
                       ......+. ...+.|-     |++.+...+..-.. -..++  +||||-...|...    +....+..+.+.+.     
T Consensus       271 l~~a~~~l~-~~~l~i~d~~~~s~~~i~~~ir~l~~-~~~~~~~lIVID~Lq~~~~~~~~~~r~~~i~~i~~~Lk~lAke  348 (444)
T 3bgw_A          271 LSMAIGEIS-NSNINIFDKAGQSVNYIWSKTRQTKR-KNPGKRVIVMIDYLQLLEPAKANDSRTNQISQISRDLKKMARE  348 (444)
T ss_dssp             HHHHHHHHH-TSCEEEECCSSCBHHHHHHHHHHHHH-HSCSSCEEEEEECSTTSBCSCSSSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHh-cCCEEEECCCCCCHHHHHHHHHHHHH-HhCCCCeEEEEecHHhccCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence             01111221 2345542     45555543332100 12578  9999999877633    22233444433331     


Q ss_pred             CCCeEEEEee
Q 027749          205 PDLQVCCPGS  214 (219)
Q Consensus       205 ~~~q~i~~SA  214 (219)
                      .++.++++|.
T Consensus       349 ~~v~vi~lsq  358 (444)
T 3bgw_A          349 LDVVVIALSQ  358 (444)
T ss_dssp             HTCEEEEEEE
T ss_pred             hCCeEEEEec
Confidence            2667787775

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=92.57  E-value=0.36  Score=38.50  Aligned_cols=73  Identities=22%  Similarity=0.287  Sum_probs=53.7

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCCc
Q 027749          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (219)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~l  176 (219)
                      +.++||.++++..+..+.+.+...    ++.+..++|+.+..++...+    .+..+|+|+|.     . -..++++.++
T Consensus        28 ~~~~LVF~~t~~~~~~l~~~L~~~----g~~~~~lhg~l~~~~r~~~~~~f~~g~~~vLVaT~-----v-a~~Gidi~~v   97 (300)
T 3i32_A           28 PDRAMVFTRTKAETEEIAQGLLRL----GHPAQALHGDMSQGERERVMGAFRQGEVRVLVATD-----V-AARGLDIPQV   97 (300)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHTT----TCCEEEECSCCCTHHHHHHHHHHHHTSCCEEEECS-----T-TTCSTTCCCC
T ss_pred             CCCEEEEECCHHHHHHHHHHHHhC----CCCEEEEeCCCCHHHHHHHHHHhhcCCceEEEEec-----h-hhcCccccce
Confidence            346999999999998888877654    67888899987766554333    24678999993     2 2467788888


Q ss_pred             cEEEecc
Q 027749          177 KLLVLDE  183 (219)
Q Consensus       177 ~~lVvDE  183 (219)
                      ++||.=+
T Consensus        98 ~~VI~~d  104 (300)
T 3i32_A           98 DLVVHYR  104 (300)
T ss_dssp             SEEEESS
T ss_pred             eEEEEcC
Confidence            8877533

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=92.34  E-value=0.49  Score=40.70  Aligned_cols=48  Identities=13%  Similarity=0.098  Sum_probs=28.9

Q ss_pred             HHHHHHCCCCCChHHHHHHH-HHHhCCCcEEEEcCCCCchhHHhHHHHHhhh
Q 027749           45 LRGIYQYGFEKPSAIQQRAV-MPIIKGRDVIAQAQSGTGKTSMIALTVCQTV   95 (219)
Q Consensus        45 ~~~l~~~~~~~~~~~Q~~~~-~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~   95 (219)
                      ...|.+.|..  .+.+...+ -.+..|..+++.||||+|||. .+-.++..+
T Consensus       236 ~~~l~~~G~~--~~~~l~~l~~~v~~g~~i~I~GptGSGKTT-lL~aL~~~i  284 (511)
T 2oap_1          236 PIDLIEKGTV--PSGVLAYLWLAIEHKFSAIVVGETASGKTT-TLNAIMMFI  284 (511)
T ss_dssp             HHHHHHTTSS--CHHHHHHHHHHHHTTCCEEEEESTTSSHHH-HHHHHGGGS
T ss_pred             hhhHHhcCCC--CHHHHHHHHHHHhCCCEEEEECCCCCCHHH-HHHHHHhhC
Confidence            3445566632  23333333 335678899999999999993 334444444

>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=92.34  E-value=0.8  Score=37.05  Aligned_cols=76  Identities=13%  Similarity=0.089  Sum_probs=56.6

Q ss_pred             CceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCC
Q 027749          100 REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRA  175 (219)
Q Consensus       100 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~  175 (219)
                      ...++||.++++..+..+++.+.+.    ++.+..++|+.+..++...+    .+..+|+|+|.      .-..++++.+
T Consensus       242 ~~~~~lvf~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~------~~~~Gidip~  311 (395)
T 3pey_A          242 TIGSSIIFVATKKTANVLYGKLKSE----GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTN------VLARGIDIPT  311 (395)
T ss_dssp             TSSEEEEECSCHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECG------GGSSSCCCTT
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHHhc----CCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECC------hhhcCCCccc
Confidence            3467999999999999998888765    56778888887765543333    23678999994      2356788999


Q ss_pred             ccEEEeccch
Q 027749          176 IKLLVLDESD  185 (219)
Q Consensus       176 l~~lVvDE~h  185 (219)
                      +++||.-+..
T Consensus       312 ~~~Vi~~~~p  321 (395)
T 3pey_A          312 VSMVVNYDLP  321 (395)
T ss_dssp             EEEEEESSCC
T ss_pred             CCEEEEcCCC
Confidence            9998876554

>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=92.25  E-value=0.92  Score=38.72  Aligned_cols=52  Identities=13%  Similarity=0.256  Sum_probs=38.7

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhcc
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGD  126 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~  126 (219)
                      .+....+.+.+|+||++...- ++..   .  +..+|||+|+...|.++++.++.+..
T Consensus        13 ~~~~~~l~g~~gs~ka~~~a~-l~~~---~--~~p~lvv~~~~~~A~~l~~~l~~~~~   64 (483)
T 3hjh_A           13 AGEQRLLGELTGAACATLVAE-IAER---H--AGPVVLIAPDMQNALRLHDEISQFTD   64 (483)
T ss_dssp             TTCEEEEECCCTTHHHHHHHH-HHHH---S--SSCEEEEESSHHHHHHHHHHHHHTCS
T ss_pred             CCCeEEEeCCCchHHHHHHHH-HHHH---h--CCCEEEEeCCHHHHHHHHHHHHhhCC
Confidence            456788999999999944322 2222   1  12389999999999999999998864

>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=92.22  E-value=1.4  Score=32.86  Aligned_cols=35  Identities=20%  Similarity=0.181  Sum_probs=25.7

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEE
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALIL  107 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil  107 (219)
                      ...+++..+.|.|||.+++-..+..+..   +.+++|+
T Consensus        28 ~g~i~v~tG~GkGKTTaA~GlalRA~g~---G~rV~~v   62 (196)
T 1g5t_A           28 RGIIIVFTGNGKGKTTAAFGTAARAVGH---GKNVGVV   62 (196)
T ss_dssp             CCCEEEEESSSSCHHHHHHHHHHHHHHT---TCCEEEE
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHC---CCeEEEE
Confidence            3579999999999998777666665544   3447776

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=91.96  E-value=0.46  Score=42.81  Aligned_cols=26  Identities=12%  Similarity=0.198  Sum_probs=17.5

Q ss_pred             ccEEEeccchhhhccccHHHHHHHHHh
Q 027749          176 IKLLVLDESDEMLSRGFKDQIYDVYRY  202 (219)
Q Consensus       176 l~~lVvDE~h~l~~~~~~~~~~~i~~~  202 (219)
                      .++|++||+|.+.. .....+..+++.
T Consensus       580 ~~vl~lDEi~~~~~-~~~~~Ll~~le~  605 (758)
T 3pxi_A          580 YSVVLLDAIEKAHP-DVFNILLQVLED  605 (758)
T ss_dssp             SSEEEEECGGGSCH-HHHHHHHHHHHH
T ss_pred             CeEEEEeCccccCH-HHHHHHHHHhcc
Confidence            45899999998643 345555666655

>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=91.62  E-value=0.51  Score=42.90  Aligned_cols=43  Identities=14%  Similarity=0.137  Sum_probs=27.2

Q ss_pred             ccEEEeccchhhhcc------c----cHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          176 IKLLVLDESDEMLSR------G----FKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       176 l~~lVvDE~h~l~~~------~----~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      -..|++||+|.+...      .    ....+...++.+....+++++-||=.+
T Consensus       298 PsIIfIDEiDal~~~r~~~~~~~~~riv~~LL~~mdg~~~~~~V~VIaaTN~~  350 (806)
T 3cf2_A          298 PAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRP  350 (806)
T ss_dssp             SEEEEEESGGGTCCTTTTCCCTTHHHHHHHHHTHHHHCCGGGCEEEEEECSST
T ss_pred             CeEEEEehhcccccccCCCCChHHHHHHHHHHHHHhcccccCCEEEEEecCCh
Confidence            357999999988742      1    123344445556566678888887544

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=91.53  E-value=0.07  Score=44.98  Aligned_cols=55  Identities=13%  Similarity=0.268  Sum_probs=36.3

Q ss_pred             CccCccccCCCCHHHHHHHHHCC---CCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHh
Q 027749           30 EAITSFDAMGIKDDLLRGIYQYG---FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        30 ~~~~~~~~~~l~~~~~~~l~~~~---~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~   87 (219)
                      .+-.+|++.+--..+.+.+.+.-   +..|.-++..-+   ...+.+++.||.|+|||+.+
T Consensus       175 ~p~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~---~~prGvLLyGPPGTGKTllA  232 (434)
T 4b4t_M          175 KPTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGI---RAPKGALMYGPPGTGKTLLA  232 (434)
T ss_dssp             SCSCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCC---CCCCEEEEESCTTSSHHHHH
T ss_pred             CCCCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCCeeEEECcCCCCHHHHH
Confidence            45578999988888888887541   123333332222   23468999999999999443

>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=91.30  E-value=1.2  Score=39.00  Aligned_cols=83  Identities=10%  Similarity=0.140  Sum_probs=58.7

Q ss_pred             HHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHH
Q 027749           91 VCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMI  166 (219)
Q Consensus        91 ~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l  166 (219)
                      ++..+.....+.++||.++++..++++.+.+.+.    ++.+..++++.+..++...+    ....+|+|+|..      
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----GIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVA------  326 (591)
T ss_dssp             HHHHHTTTTTTCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEECTT------
T ss_pred             HHHHHHHhccCCCeEEEeCcHHHHHHHHHHHHHC----CCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEech------
Confidence            3344433334567999999999999999988764    67888889888766554333    246789999941      


Q ss_pred             HcCCCCCCCccEEEecc
Q 027749          167 KRKTLRTRAIKLLVLDE  183 (219)
Q Consensus       167 ~~~~~~~~~l~~lVvDE  183 (219)
                      -..++++.++++||.=.
T Consensus       327 ~~~GID~p~V~~VI~~~  343 (591)
T 2v1x_A          327 FGMGIDKPDVRFVIHHS  343 (591)
T ss_dssp             SCTTCCCSCEEEEEESS
T ss_pred             hhcCCCcccccEEEEeC
Confidence            24567888888877543

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=91.25  E-value=1  Score=37.55  Aligned_cols=69  Identities=13%  Similarity=0.187  Sum_probs=53.2

Q ss_pred             EEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCCccEE
Q 027749          104 ALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLL  179 (219)
Q Consensus       104 ~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~l  179 (219)
                      +||.++++..+..+.+.+.+.    ++.+..++|+.+..++...+    .....|+|+|.      +-.+++++.++++|
T Consensus       303 ~lVF~~t~~~a~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~------v~~rGlDi~~v~~V  372 (434)
T 2db3_A          303 TIVFVETKRGADFLASFLSEK----EFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATS------VASRGLDIKNIKHV  372 (434)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT----TCCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECG------GGTSSCCCTTCCEE
T ss_pred             EEEEEeCcHHHHHHHHHHHhC----CCCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEch------hhhCCCCcccCCEE
Confidence            999999999999988888764    67788888887766554333    23678999995      23577899999988


Q ss_pred             Eec
Q 027749          180 VLD  182 (219)
Q Consensus       180 VvD  182 (219)
                      |.=
T Consensus       373 I~~  375 (434)
T 2db3_A          373 INY  375 (434)
T ss_dssp             EES
T ss_pred             EEE
Confidence            753

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=91.06  E-value=0.2  Score=45.82  Aligned_cols=17  Identities=24%  Similarity=0.567  Sum_probs=14.4

Q ss_pred             CcEEEEcCCCCchhHHh
Q 027749           71 RDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~   87 (219)
                      ++++++||+|+|||...
T Consensus       192 ~~vlL~G~pG~GKT~la  208 (854)
T 1qvr_A          192 NNPVLIGEPGVGKTAIV  208 (854)
T ss_dssp             CCCEEEECTTSCHHHHH
T ss_pred             CceEEEcCCCCCHHHHH
Confidence            57999999999999443

>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=90.96  E-value=0.66  Score=37.89  Aligned_cols=72  Identities=17%  Similarity=0.144  Sum_probs=54.5

Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCCcc
Q 027749          102 VQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAIK  177 (219)
Q Consensus       102 ~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~  177 (219)
                      .++||.++++..+..+.+.+.+.    ++.+..++|+.+..++...+    .+..+|+|+|.     . -..++++.+++
T Consensus       267 ~~~lvf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~-~~~Gidip~~~  336 (412)
T 3fht_A          267 AQAMIFCHTRKTASWLAAELSKE----GHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTN-----V-CARGIDVEQVS  336 (412)
T ss_dssp             SEEEEECSSHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECG-----G-GTSSCCCTTEE
T ss_pred             CCEEEEeCCHHHHHHHHHHHHhC----CCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcC-----c-cccCCCccCCC
Confidence            57999999999999999988765    56778888887766554333    24678999994     2 35678889999


Q ss_pred             EEEecc
Q 027749          178 LLVLDE  183 (219)
Q Consensus       178 ~lVvDE  183 (219)
                      +||.-.
T Consensus       337 ~Vi~~~  342 (412)
T 3fht_A          337 VVINFD  342 (412)
T ss_dssp             EEEESS
T ss_pred             EEEEEC
Confidence            888533

>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=90.74  E-value=0.92  Score=36.97  Aligned_cols=73  Identities=11%  Similarity=0.102  Sum_probs=53.1

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCCc
Q 027749          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (219)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~l  176 (219)
                      ..++||.++++..+..+.+.+.+.    ++.+..++|+.+..++...+    ....+|+|+|.      .-..++++..+
T Consensus       258 ~~~~lVf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~------~~~~Gidip~~  327 (400)
T 1s2m_A          258 INQAIIFCNSTNRVELLAKKITDL----GYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSD------LLTRGIDIQAV  327 (400)
T ss_dssp             CSEEEEECSSHHHHHHHHHHHHHH----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESS------CSSSSCCCTTE
T ss_pred             CCcEEEEEecHHHHHHHHHHHHhc----CCCeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC------ccccCCCccCC
Confidence            357999999999999999888765    56777888887765543332    23578999994      12456788888


Q ss_pred             cEEEecc
Q 027749          177 KLLVLDE  183 (219)
Q Consensus       177 ~~lVvDE  183 (219)
                      ++||.-+
T Consensus       328 ~~Vi~~~  334 (400)
T 1s2m_A          328 NVVINFD  334 (400)
T ss_dssp             EEEEESS
T ss_pred             CEEEEeC
Confidence            8877543

>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=90.66  E-value=0.45  Score=38.44  Aligned_cols=42  Identities=10%  Similarity=-0.001  Sum_probs=26.9

Q ss_pred             cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHH
Q 027749           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELA  114 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~  114 (219)
                      -+++.+|.|+|||...+-. +........+.+++|+..-..+-
T Consensus        30 iteI~G~pGsGKTtL~Lq~-~~~~~~~g~g~~vlyId~E~s~~   71 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTM-VSSYMRQYPDAVCLFYDSEFGIT   71 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHH-HHHHHHHCTTCEEEEEESSCCCC
T ss_pred             eEEEECCCCCCHHHHHHHH-HHHHHhcCCCceEEEEeccchhh
Confidence            5789999999999554443 33333322244688887766553

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=90.55  E-value=0.56  Score=36.19  Aligned_cols=20  Identities=25%  Similarity=0.356  Sum_probs=16.2

Q ss_pred             hCCCcEEEEcCCCCchhHHh
Q 027749           68 IKGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        68 ~~~~~~lv~~~tG~GKT~~~   87 (219)
                      ..+.++++.|++|+|||...
T Consensus        27 ~~~~~vll~G~~GtGKt~la   46 (265)
T 2bjv_A           27 PLDKPVLIIGERGTGKELIA   46 (265)
T ss_dssp             TSCSCEEEECCTTSCHHHHH
T ss_pred             CCCCCEEEECCCCCcHHHHH
Confidence            35678999999999999433

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=90.23  E-value=0.49  Score=35.67  Aligned_cols=52  Identities=12%  Similarity=0.123  Sum_probs=31.1

Q ss_pred             CHHHHHHHHHCCCCCChHHHHHHHHHHhCC----CcEEEEcCCCCchhHHhHHHHHhhh
Q 027749           41 KDDLLRGIYQYGFEKPSAIQQRAVMPIIKG----RDVIAQAQSGTGKTSMIALTVCQTV   95 (219)
Q Consensus        41 ~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~----~~~lv~~~tG~GKT~~~~~~~~~~~   95 (219)
                      ...+.+-|.-.++ .+..+ ...+..+.++    +.+++.||.|+|||..+ ..++..+
T Consensus        27 w~~I~~~l~yq~~-~~~~f-~~~l~~~~~~iPkkn~ili~GPPGtGKTt~a-~ala~~l   82 (212)
T 1tue_A           27 WRPIVQFLRYQQI-EFITF-LGALKSFLKGTPKKNCLVFCGPANTGKSYFG-MSFIHFI   82 (212)
T ss_dssp             SHHHHHHHHHTTC-CHHHH-HHHHHHHHHTCTTCSEEEEESCGGGCHHHHH-HHHHHHH
T ss_pred             HHHHHHHHHHcCc-CHHHH-HHHHHHHHhcCCcccEEEEECCCCCCHHHHH-HHHHHHh
Confidence            3456666665554 34444 4445555544    35999999999999443 4444443

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=90.13  E-value=0.48  Score=47.21  Aligned_cols=42  Identities=17%  Similarity=0.226  Sum_probs=28.0

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHH
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l  113 (219)
                      .++++++.+|+|+|||......+.... ..  +.+++|+.....+
T Consensus      1426 ~g~~vll~GppGtGKT~LA~ala~ea~-~~--G~~v~Fi~~e~~~ 1467 (2050)
T 3cmu_A         1426 MGRIVEIYGPESSGKTTLTLQVIAAAQ-RE--GKTCAFIDAEHAL 1467 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHH-TT--TCCEEEECTTSCC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH-Hc--CCcEEEEEccccc
Confidence            367899999999999965544333322 22  4458888766544

>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=90.10  E-value=0.55  Score=38.19  Aligned_cols=19  Identities=21%  Similarity=0.434  Sum_probs=15.8

Q ss_pred             CCCcEEEEcCCCCchhHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~   87 (219)
                      ...++++.||+|+|||..+
T Consensus        50 ~~~~vll~GppGtGKT~la   68 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTLLA   68 (363)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            4568999999999999544

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=90.08  E-value=0.98  Score=36.98  Aligned_cols=72  Identities=15%  Similarity=0.166  Sum_probs=53.7

Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCCcc
Q 027749          102 VQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAIK  177 (219)
Q Consensus       102 ~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~  177 (219)
                      .++||.++++..+..+.+.+.+.    ++.+..++|+.+..++...+    .+..+|+|+|.      .-..++++.+++
T Consensus       277 ~~~lVf~~~~~~~~~l~~~L~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~------~~~~Gidi~~v~  346 (410)
T 2j0s_A          277 TQAVIFCNTKRKVDWLTEKMREA----NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTD------VWARGLDVPQVS  346 (410)
T ss_dssp             SEEEEECSSHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECG------GGSSSCCCTTEE
T ss_pred             CcEEEEEcCHHHHHHHHHHHHhC----CCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECC------hhhCcCCcccCC
Confidence            47999999999999988888764    56788888887765543332    23678999995      235678899999


Q ss_pred             EEEecc
Q 027749          178 LLVLDE  183 (219)
Q Consensus       178 ~lVvDE  183 (219)
                      +||.-+
T Consensus       347 ~Vi~~~  352 (410)
T 2j0s_A          347 LIINYD  352 (410)
T ss_dssp             EEEESS
T ss_pred             EEEEEC
Confidence            887543

>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=90.06  E-value=0.11  Score=41.41  Aligned_cols=55  Identities=16%  Similarity=0.294  Sum_probs=31.5

Q ss_pred             cCccccCCCCHHHHHHHHHCCCCCChHHHHHHHH-HHhCCCcEEEEcCCCCchhHHh
Q 027749           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVM-PIIKGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        32 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~-~~~~~~~~lv~~~tG~GKT~~~   87 (219)
                      -.+|+++.-...+.+.+.+.- ..|......... .+..++.+++.||+|+|||...
T Consensus        11 ~~~~~di~G~~~~~~~l~~~v-~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la   66 (301)
T 3cf0_A           11 QVTWEDIGGLEDVKRELQELV-QYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLA   66 (301)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHH-HHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHH
T ss_pred             CCCHHHhCCHHHHHHHHHHHH-HHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHH
Confidence            356888876777777776531 001000000111 1234578999999999999443

>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=89.96  E-value=1.2  Score=36.88  Aligned_cols=96  Identities=19%  Similarity=0.184  Sum_probs=60.6

Q ss_pred             CCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEEC--------CcccHHHHHHh--
Q 027749           79 SGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVG--------GKSVGEDIRKL--  148 (219)
Q Consensus        79 tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~l--  148 (219)
                      ..++|. ..+..++........+.++||.++++..+..+.+.+...    ++.+..+.|        +.+..++...+  
T Consensus       340 ~~~~k~-~~l~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~----~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~  414 (494)
T 1wp9_A          340 LDHPKM-DKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKD----GIKAKRFVGQASKENDRGLSQREQKLILDE  414 (494)
T ss_dssp             CSCHHH-HHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHT----TCCEEEECCSSCC-------CCHHHHHHHH
T ss_pred             CCChHH-HHHHHHHHHHhccCCCCeEEEEEccHHHHHHHHHHHHHc----CCCcEEEeccccccccccCCHHHHHHHHHH
Confidence            344555 333444444332233567999999999999988888765    677777887        44443332222  


Q ss_pred             --cCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccch
Q 027749          149 --EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESD  185 (219)
Q Consensus       149 --~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h  185 (219)
                        ...+.|+|+|.     . -..++++..+.+||+-+..
T Consensus       415 F~~~~~~vLv~T~-----~-~~~Gldl~~~~~Vi~~d~~  447 (494)
T 1wp9_A          415 FARGEFNVLVATS-----V-GEEGLDVPEVDLVVFYEPV  447 (494)
T ss_dssp             HHHTSCSEEEECG-----G-GGGGGGSTTCCEEEESSCC
T ss_pred             HhcCCceEEEECC-----c-cccCCCchhCCEEEEeCCC
Confidence              23578999993     2 2456788889988866554

>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=89.86  E-value=0.76  Score=47.17  Aligned_cols=74  Identities=15%  Similarity=0.121  Sum_probs=42.8

Q ss_pred             CCHHHHHHHHHCCCCCChHHH-HHH---HHHHhCCCcEEEEcCCCCchhHHhHHHH--HhhhccCCCceeEEEEcCCHHH
Q 027749           40 IKDDLLRGIYQYGFEKPSAIQ-QRA---VMPIIKGRDVIAQAQSGTGKTSMIALTV--CQTVDTSSREVQALILSPTREL  113 (219)
Q Consensus        40 l~~~~~~~l~~~~~~~~~~~Q-~~~---~~~~~~~~~~lv~~~tG~GKT~~~~~~~--~~~~~~~~~~~~~lil~P~~~l  113 (219)
                      +...+.+.+.+.++. +.+.+ .++   ...+...+.+++.||||+|||.++-..+  +..+.  +......++-|..--
T Consensus       890 l~~~i~~~~~~~~l~-~~~~~~~K~~ql~e~~~~r~gvmlvGptgsGKTt~~~~La~al~~l~--~~~~~~~~inpk~~t  966 (2695)
T 4akg_A          890 IVQCLKDAGQRSGFS-MSEEFLKKCMQFYYMQKTQQALILVGKAGCGKTATWKTVIDAMAIFD--GHANVVYVIDTKVLT  966 (2695)
T ss_dssp             HHHHHHHHHHHHTCC-CCHHHHHHHHHHHHHHHHCSEEEEECSTTSSHHHHHHHHHHHHHHHT--CCEEEEEEECTTTSC
T ss_pred             HHHHHHHHHHHcCCc-ccHHHHHHHHHHHHHHHhcceEEEECCCCCCHHHHHHHHHHHHHHhc--CCCceEEEeCCCCCC
Confidence            345566777777774 55544 222   2334567889999999999997764422  22222  223445556564333


Q ss_pred             HHH
Q 027749          114 ATQ  116 (219)
Q Consensus       114 ~~q  116 (219)
                      ..+
T Consensus       967 ~~e  969 (2695)
T 4akg_A          967 KES  969 (2695)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            333

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=89.85  E-value=1.5  Score=45.81  Aligned_cols=75  Identities=16%  Similarity=0.149  Sum_probs=44.8

Q ss_pred             CHHHHHHHHHCCCCCChHHH-HHHH---HHHhCCCcEEEEcCCCCchhHHhHHHH--HhhhccCCCceeEEEEcCCHHHH
Q 027749           41 KDDLLRGIYQYGFEKPSAIQ-QRAV---MPIIKGRDVIAQAQSGTGKTSMIALTV--CQTVDTSSREVQALILSPTRELA  114 (219)
Q Consensus        41 ~~~~~~~l~~~~~~~~~~~Q-~~~~---~~~~~~~~~lv~~~tG~GKT~~~~~~~--~~~~~~~~~~~~~lil~P~~~l~  114 (219)
                      ...+.+.+.+.|+. |.+.+ .+++   ..+...+.++++||||+|||.++-...  +..+.  +......++-|----.
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            45566677788874 55544 3333   334456789999999999998775422  22221  2234455667765555


Q ss_pred             HHHH
Q 027749          115 TQTE  118 (219)
Q Consensus       115 ~q~~  118 (219)
                      .|++
T Consensus       951 ~eLy  954 (3245)
T 3vkg_A          951 DQLF  954 (3245)
T ss_dssp             HHHH
T ss_pred             hhhc
Confidence            5555

>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=89.39  E-value=1.4  Score=37.89  Aligned_cols=73  Identities=14%  Similarity=0.130  Sum_probs=54.1

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCCc
Q 027749          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (219)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~l  176 (219)
                      +.++||.++++..++.+.+.+.+.    ++.+..++|+.+..++....    ....+|+|+|..      -..++++.++
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----GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVA------FGMGINKPNV  305 (523)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTT------SCTTTCCTTC
T ss_pred             CCcEEEEeCCHHHHHHHHHHHHHC----CCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEech------hhCCCCccCc
Confidence            446999999999999999988765    67788888888765543332    246789999951      2456788888


Q ss_pred             cEEEecc
Q 027749          177 KLLVLDE  183 (219)
Q Consensus       177 ~~lVvDE  183 (219)
                      ++||.-.
T Consensus       306 ~~VI~~~  312 (523)
T 1oyw_A          306 RFVVHFD  312 (523)
T ss_dssp             CEEEESS
T ss_pred             cEEEEEC
Confidence            8887644

>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=89.35  E-value=1.4  Score=35.73  Aligned_cols=74  Identities=11%  Similarity=0.139  Sum_probs=54.5

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCCc
Q 027749          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (219)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~l  176 (219)
                      +.++||.++++..+..+.+.+.+.    ++.+..++|+.+..++...+    .....|+|+|.     . -..++++..+
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            457999999999999998888764    56778888887765543332    23678999994     1 2456788889


Q ss_pred             cEEEeccc
Q 027749          177 KLLVLDES  184 (219)
Q Consensus       177 ~~lVvDE~  184 (219)
                      ++||.-+.
T Consensus       320 ~~Vi~~~~  327 (391)
T 1xti_A          320 NIAFNYDM  327 (391)
T ss_dssp             EEEEESSC
T ss_pred             CEEEEeCC
Confidence            88887554

>1e9r_A Conjugal transfer protein TRWB; coupling protein, bacterial conjugation, F1-ATPase-like quaternary structure, ring helicases; 2.4A {Escherichia coli} SCOP: c.37.1.11 PDB: 1e9s_A 1gki_A* 1gl7_A* 1gl6_A*

Probab=89.33  E-value=0.27  Score=41.14  Aligned_cols=19  Identities=26%  Similarity=0.648  Sum_probs=16.3

Q ss_pred             CCCcEEEEcCCCCchhHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~   87 (219)
                      ...+++|.|+||+|||...
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            4568999999999999764

>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=89.13  E-value=1  Score=35.24  Aligned_cols=18  Identities=22%  Similarity=0.542  Sum_probs=15.3

Q ss_pred             CCcEEEEcCCCCchhHHh
Q 027749           70 GRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~   87 (219)
                      .+++++.||+|+|||...
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            568999999999999443

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=89.09  E-value=0.61  Score=40.01  Aligned_cols=41  Identities=15%  Similarity=0.195  Sum_probs=26.4

Q ss_pred             HHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhH
Q 027749           44 LLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTS   85 (219)
Q Consensus        44 ~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~   85 (219)
                      +.+.+... +..-...-..+...+..+.++++.||+|+|||.
T Consensus        16 l~~~l~~~-ivGq~~~i~~l~~al~~~~~VLL~GpPGtGKT~   56 (500)
T 3nbx_X           16 LSSSLEKG-LYERSHAIRLCLLAALSGESVFLLGPPGIAKSL   56 (500)
T ss_dssp             HHHHHHTT-CSSCHHHHHHHHHHHHHTCEEEEECCSSSSHHH
T ss_pred             HHHHHHhh-hHHHHHHHHHHHHHHhcCCeeEeecCchHHHHH
Confidence            34444433 323333334455556788999999999999993

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=88.95  E-value=0.58  Score=35.11  Aligned_cols=33  Identities=24%  Similarity=0.202  Sum_probs=26.4

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHh
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~   87 (219)
                      .-+.-|..++..+..|.-+.+.||.|+|||...
T Consensus         7 pk~~g~~~~l~~i~~Ge~~~liG~nGsGKSTLl   39 (208)
T 3b85_A            7 PKTLGQKHYVDAIDTNTIVFGLGPAGSGKTYLA   39 (208)
T ss_dssp             CCSHHHHHHHHHHHHCSEEEEECCTTSSTTHHH
T ss_pred             cCCHhHHHHHHhccCCCEEEEECCCCCCHHHHH
Confidence            335557778888888888999999999999543

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=88.93  E-value=0.22  Score=35.80  Aligned_cols=18  Identities=22%  Similarity=0.516  Sum_probs=14.9

Q ss_pred             CCcEEEEcCCCCchhHHh
Q 027749           70 GRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~   87 (219)
                      .+++++.||+|+|||...
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            367999999999999543

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=88.93  E-value=0.83  Score=38.23  Aligned_cols=35  Identities=14%  Similarity=0.248  Sum_probs=21.3

Q ss_pred             HHHHHHHHh--CCCcEEEEcCCCCchhHHhHHHHHhhh
Q 027749           60 QQRAVMPII--KGRDVIAQAQSGTGKTSMIALTVCQTV   95 (219)
Q Consensus        60 Q~~~~~~~~--~~~~~lv~~~tG~GKT~~~~~~~~~~~   95 (219)
                      +..++..+.  .+.-++|.||||+|||.. +-.++..+
T Consensus       155 ~~~~L~~l~~~~ggii~I~GpnGSGKTTl-L~allg~l  191 (418)
T 1p9r_A          155 NHDNFRRLIKRPHGIILVTGPTGSGKSTT-LYAGLQEL  191 (418)
T ss_dssp             HHHHHHHHHTSSSEEEEEECSTTSCHHHH-HHHHHHHH
T ss_pred             HHHHHHHHHHhcCCeEEEECCCCCCHHHH-HHHHHhhc
Confidence            344444433  344588999999999943 33344444

>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=88.55  E-value=0.078  Score=38.33  Aligned_cols=74  Identities=11%  Similarity=0.144  Sum_probs=48.7

Q ss_pred             CceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhc----CCCeEEEeChHHHHHHHHcCCCCCCC
Q 027749          100 REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRA  175 (219)
Q Consensus       100 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~----~~~~I~v~Tp~~l~~~l~~~~~~~~~  175 (219)
                      .+.++||.++++..+..+.+.+...    ++.+..++|+.+..++...+.    ...+|+|+|.     .+ ..++++..
T Consensus        29 ~~~~~iVF~~~~~~~~~l~~~L~~~----~~~~~~~~g~~~~~~r~~~~~~f~~g~~~vLvaT~-----~~-~~Gid~~~   98 (170)
T 2yjt_D           29 EATRSIVFVRKRERVHELANWLREA----GINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATD-----VA-ARGIDIPD   98 (170)
Confidence            3457999999999998888877654    567777777766544433321    3567999983     22 34556666


Q ss_pred             ccEEEecc
Q 027749          176 IKLLVLDE  183 (219)
Q Consensus       176 l~~lVvDE  183 (219)
                      +++||.-+
T Consensus        99 ~~~Vi~~~  106 (170)
T 2yjt_D           99 VSHVFNFD  106 (170)
Confidence            66665533

>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=88.84  E-value=2.8  Score=34.00  Aligned_cols=17  Identities=29%  Similarity=0.540  Sum_probs=13.9

Q ss_pred             CCccEEEeccchhhhcc
Q 027749          174 RAIKLLVLDESDEMLSR  190 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~  190 (219)
                      .+.++||+||.-.+++.
T Consensus       230 ~~~~llIlDs~ta~ld~  246 (349)
T 1pzn_A          230 RPVKLLIVDSLTSHFRS  246 (349)
T ss_dssp             SCEEEEEEETSSTTHHH
T ss_pred             CCCCEEEEeCchHhhhh
Confidence            56889999999887754

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=88.78  E-value=0.24  Score=41.26  Aligned_cols=54  Identities=22%  Similarity=0.334  Sum_probs=33.3

Q ss_pred             ccCccccCCCCHHHHHHHHHCC---CCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHh
Q 027749           31 AITSFDAMGIKDDLLRGIYQYG---FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        31 ~~~~~~~~~l~~~~~~~l~~~~---~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~   87 (219)
                      |--+|++.+=-....+.+++.-   +..|.-++..-   +...+.+++.||.|+|||+.+
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            3467888876677777776542   11222222211   223468999999999999443

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=88.76  E-value=0.54  Score=38.46  Aligned_cols=19  Identities=26%  Similarity=0.559  Sum_probs=16.8

Q ss_pred             HhCCCcEEEEcCCCCchhH
Q 027749           67 IIKGRDVIAQAQSGTGKTS   85 (219)
Q Consensus        67 ~~~~~~~lv~~~tG~GKT~   85 (219)
                      +..|..+++.||||+|||.
T Consensus       172 i~~G~~i~ivG~sGsGKST  190 (361)
T 2gza_A          172 VQLERVIVVAGETGSGKTT  190 (361)
T ss_dssp             HHTTCCEEEEESSSSCHHH
T ss_pred             HhcCCEEEEECCCCCCHHH
Confidence            4578899999999999994

>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=88.71  E-value=0.95  Score=35.44  Aligned_cols=45  Identities=11%  Similarity=0.195  Sum_probs=30.2

Q ss_pred             CHHHHHHHHHCCCCCChHHHHH-HHHHHhCCC-----cEEEEcCCCCchhHHhH
Q 027749           41 KDDLLRGIYQYGFEKPSAIQQR-AVMPIIKGR-----DVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        41 ~~~~~~~l~~~~~~~~~~~Q~~-~~~~~~~~~-----~~lv~~~tG~GKT~~~~   88 (219)
                      ...+.+.|+..|+.   |.+.. ++..+++++     .+++.||.|+|||+.+.
T Consensus        72 ~n~i~~~l~~qg~~---~~~~~~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~  122 (267)
T 1u0j_A           72 SNRIYKILELNGYD---PQYAASVFLGWATKKFGKRNTIWLFGPATTGKTNIAE  122 (267)
T ss_dssp             GCHHHHHHHHTTCC---HHHHHHHHHHHHTTCSTTCCEEEEECSTTSSHHHHHH
T ss_pred             hHHHHHHHHHcCCC---HHHHHHHHHHHHhCCCCCCcEEEEECCCCCCHHHHHH
Confidence            34688888887763   43422 344455443     49999999999995554

>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=88.22  E-value=1.6  Score=38.77  Aligned_cols=76  Identities=16%  Similarity=0.240  Sum_probs=57.2

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh---c-CCCeEEEeChHHHHHHHHcCCCCCCCc
Q 027749          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL---E-HGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (219)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l---~-~~~~I~v~Tp~~l~~~l~~~~~~~~~l  176 (219)
                      +.++||.++++..+..+.+.+.+.    ++.+..++|+.+..++...+   . +..+|+|+|.     . ...++++.++
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            457999999999999988888765    56777778777655543332   2 4678999984     1 2567889999


Q ss_pred             cEEEeccchh
Q 027749          177 KLLVLDESDE  186 (219)
Q Consensus       177 ~~lVvDE~h~  186 (219)
                      +++|+-+++.
T Consensus       515 ~lVi~~d~d~  524 (661)
T 2d7d_A          515 SLVAILDADK  524 (661)
T ss_dssp             EEEEETTTTC
T ss_pred             CEEEEeCccc
Confidence            9999988864

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=88.15  E-value=0.18  Score=42.58  Aligned_cols=54  Identities=24%  Similarity=0.377  Sum_probs=32.4

Q ss_pred             ccCccccCCCCHHHHHHHHHCC---CCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHh
Q 027749           31 AITSFDAMGIKDDLLRGIYQYG---FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        31 ~~~~~~~~~l~~~~~~~l~~~~---~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~   87 (219)
                      +--+|++.+=-....+.+.+.-   +..|.-++..-   +...+.+++.||.|+|||+.+
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            4457888876667776665431   11222222111   123468999999999999443

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=87.65  E-value=0.25  Score=41.93  Aligned_cols=54  Identities=17%  Similarity=0.223  Sum_probs=33.8

Q ss_pred             ccCccccCCCCHHHHHHHHHCC---CCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHh
Q 027749           31 AITSFDAMGIKDDLLRGIYQYG---FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        31 ~~~~~~~~~l~~~~~~~l~~~~---~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~   87 (219)
                      |--+|++.+=-..+.+.|++.-   +..|.-++..-   +...+.+++.||.|+|||+.+
T Consensus       204 P~vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~G---i~pprGILLyGPPGTGKTlLA  260 (467)
T 4b4t_H          204 PDVTYSDVGGCKDQIEKLREVVELPLLSPERFATLG---IDPPKGILLYGPPGTGKTLCA  260 (467)
T ss_dssp             CSCCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHT---CCCCSEEEECSCTTSSHHHHH
T ss_pred             CCCCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHCC---CCCCCceEeeCCCCCcHHHHH
Confidence            4467888887777888887542   11222222111   123468999999999999443

>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=87.60  E-value=1.5  Score=35.03  Aligned_cols=74  Identities=12%  Similarity=0.223  Sum_probs=52.9

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCCc
Q 027749          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (219)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~l  176 (219)
                      +.++||.++++..+..+.+.+.+.    ++.+..++|+.+..++...+    .+..+|+|+|.     .+ ..++++.++
T Consensus       238 ~~~~lvf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~-----~~-~~Gid~~~~  307 (367)
T 1hv8_A          238 EFYGLVFCKTKRDTKELASMLRDI----GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATD-----VM-SRGIDVNDL  307 (367)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECT-----TH-HHHCCCSCC
T ss_pred             CCcEEEEECCHHHHHHHHHHHHhc----CCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECC-----hh-hcCCCcccC
Confidence            456999999999999998888765    56778888887765543332    24678999994     22 235677888


Q ss_pred             cEEEeccc
Q 027749          177 KLLVLDES  184 (219)
Q Consensus       177 ~~lVvDE~  184 (219)
                      ++||.-+.
T Consensus       308 ~~Vi~~~~  315 (367)
T 1hv8_A          308 NCVINYHL  315 (367)
T ss_dssp             SEEEESSC
T ss_pred             CEEEEecC
Confidence            88876443

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=87.37  E-value=0.3  Score=39.08  Aligned_cols=24  Identities=21%  Similarity=0.399  Sum_probs=18.8

Q ss_pred             HHHHhCCCcEEEEcCCCCchhHHh
Q 027749           64 VMPIIKGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        64 ~~~~~~~~~~lv~~~tG~GKT~~~   87 (219)
                      ...+..++++++.||+|+|||...
T Consensus        40 ~~~l~~~~~vll~G~pGtGKT~la   63 (331)
T 2r44_A           40 LIGICTGGHILLEGVPGLAKTLSV   63 (331)
T ss_dssp             HHHHHHTCCEEEESCCCHHHHHHH
T ss_pred             HHHHHcCCeEEEECCCCCcHHHHH
Confidence            344556889999999999999443

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A*

Probab=87.37  E-value=1.4  Score=36.96  Aligned_cols=67  Identities=4%  Similarity=-0.001  Sum_probs=46.3

Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh-cCCCeEEEeChHHHHHHHHcCCCCCCCccEEE
Q 027749          102 VQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL-EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLV  180 (219)
Q Consensus       102 ~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l-~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lV  180 (219)
                      .++||.+|++.-+..+++.+.+.    ++++..++|.. ........ .+..+|+|+|.     . -..++++. +++||
T Consensus       178 ~~~lVF~~s~~~a~~l~~~L~~~----~~~v~~lhg~~-R~~~~~~F~~g~~~vLVaT~-----v-~e~GiDip-v~~VI  245 (440)
T 1yks_A          178 RPTAWFLPSIRAANVMAASLRKA----GKSVVVLNRKT-FEREYPTIKQKKPDFILATD-----I-AEMGANLC-VERVL  245 (440)
T ss_dssp             SCEEEECSCHHHHHHHHHHHHHT----TCCEEECCSSS-CC--------CCCSEEEESS-----S-TTCCTTCC-CSEEE
T ss_pred             CCEEEEeCCHHHHHHHHHHHHHc----CCCEEEecchh-HHHHHhhhcCCCceEEEECC-----h-hheeeccC-ceEEE
Confidence            56999999999999999988775    57777888733 22223333 24679999994     2 24677888 88877

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=87.30  E-value=0.23  Score=41.75  Aligned_cols=54  Identities=22%  Similarity=0.230  Sum_probs=32.0

Q ss_pred             ccCccccCCCCHHHHHHHHHCC---CCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHh
Q 027749           31 AITSFDAMGIKDDLLRGIYQYG---FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        31 ~~~~~~~~~l~~~~~~~l~~~~---~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~   87 (219)
                      +-.+|++.+=-..+.+.+.+.-   +..|.-++..-   +...+.+++.||.|+|||+.+
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            3457888876666666665431   11222222111   123467999999999999443

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=87.28  E-value=0.33  Score=35.30  Aligned_cols=19  Identities=11%  Similarity=0.324  Sum_probs=15.6

Q ss_pred             CCCcEEEEcCCCCchhHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~   87 (219)
                      .|+-+++.||+|+|||...
T Consensus         4 ~g~~i~i~GpsGsGKSTL~   22 (180)
T 1kgd_A            4 MRKTLVLLGAHGVGRRHIK   22 (180)
T ss_dssp             CCCEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4667899999999999544

>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=87.15  E-value=1.2  Score=35.23  Aligned_cols=20  Identities=25%  Similarity=0.474  Sum_probs=15.5

Q ss_pred             CCcEEEEcCCCCchhHHhHH
Q 027749           70 GRDVIAQAQSGTGKTSMIAL   89 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~   89 (219)
                      ++-+++.|++|+|||.....
T Consensus       105 g~vi~lvG~~GsGKTTl~~~  124 (296)
T 2px0_A          105 SKYIVLFGSTGAGKTTTLAK  124 (296)
T ss_dssp             SSEEEEEESTTSSHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHH
Confidence            45688999999999955443

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=87.00  E-value=1.1  Score=35.70  Aligned_cols=19  Identities=32%  Similarity=0.480  Sum_probs=15.8

Q ss_pred             CCCcEEEEcCCCCchhHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~   87 (219)
                      .+.++++.|++|+|||..+
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            4578999999999999443

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=86.93  E-value=0.63  Score=37.58  Aligned_cols=19  Identities=42%  Similarity=0.712  Sum_probs=16.7

Q ss_pred             HhCCCcEEEEcCCCCchhH
Q 027749           67 IIKGRDVIAQAQSGTGKTS   85 (219)
Q Consensus        67 ~~~~~~~lv~~~tG~GKT~   85 (219)
                      +..|..+.+.||+|+|||.
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            4578899999999999994

>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=86.86  E-value=2.7  Score=40.41  Aligned_cols=40  Identities=18%  Similarity=0.182  Sum_probs=29.5

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ++=+.+|+||+---+|..-+..+...++...+++-+|..+
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            3456899999987777766778888888876666565543

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=86.64  E-value=0.37  Score=35.59  Aligned_cols=21  Identities=19%  Similarity=0.164  Sum_probs=16.6

Q ss_pred             hCCCcEEEEcCCCCchhHHhH
Q 027749           68 IKGRDVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        68 ~~~~~~lv~~~tG~GKT~~~~   88 (219)
                      ..++.+++.|++|+|||...-
T Consensus        23 ~~~~~i~l~G~~GsGKsTl~~   43 (199)
T 3vaa_A           23 NAMVRIFLTGYMGAGKTTLGK   43 (199)
T ss_dssp             -CCCEEEEECCTTSCHHHHHH
T ss_pred             CCCCEEEEEcCCCCCHHHHHH
Confidence            356789999999999995543

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=86.62  E-value=0.36  Score=35.78  Aligned_cols=19  Identities=32%  Similarity=0.613  Sum_probs=14.7

Q ss_pred             CCCcEEEEcCCCCchhHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~   87 (219)
                      .|+-+.+.||+|+|||...
T Consensus         3 ~g~~i~lvGpsGaGKSTLl   21 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTLL   21 (198)
T ss_dssp             --CCEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4678999999999999544

>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=86.57  E-value=1  Score=38.72  Aligned_cols=27  Identities=11%  Similarity=0.261  Sum_probs=18.9

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhh
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTV   95 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~   95 (219)
                      .+.+++|.|+||+|||.+.-..+...+
T Consensus       166 ~~pHlLIaG~TGSGKSt~L~~li~sLl  192 (512)
T 2ius_A          166 KMPHLLVAGTTGSGASVGVNAMILSML  192 (512)
T ss_dssp             GSCSEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             cCceEEEECCCCCCHHHHHHHHHHHHH
Confidence            457899999999999955433333333

>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=86.43  E-value=3.6  Score=32.44  Aligned_cols=19  Identities=26%  Similarity=0.230  Sum_probs=14.1

Q ss_pred             CCcEEEEcCCCCchhHHhH
Q 027749           70 GRDVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~   88 (219)
                      ++-+.+.++.|+|||....
T Consensus        98 ~~~i~i~g~~G~GKTT~~~  116 (295)
T 1ls1_A           98 RNLWFLVGLQGSGKTTTAA  116 (295)
T ss_dssp             SEEEEEECCTTTTHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            3456788999999995443

>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=86.07  E-value=2.9  Score=37.87  Aligned_cols=75  Identities=17%  Similarity=0.146  Sum_probs=54.7

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhc-------cccceeEEEEECCcccHHHHHHhc---------CCCeEEEeChHHHHH
Q 027749          101 EVQALILSPTRELATQTEKVILAIG-------DFINIQAHACVGGKSVGEDIRKLE---------HGVHVVSGTPGRVCD  164 (219)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~l~---------~~~~I~v~Tp~~l~~  164 (219)
                      +..+||.+|++.-+..+.+.+.+..       ...++.+..++|+.+..++...+.         +...|+|+|.     
T Consensus       303 ~g~iLVF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~~~eR~~v~~~f~~~~~~~g~~kVlVAT~-----  377 (773)
T 2xau_A          303 AGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNGRPGRKVVISTN-----  377 (773)
T ss_dssp             SCEEEEECSCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECTTCCHHHHGGGGSCCCCCSSSSCCEEEEEECT-----
T ss_pred             CCCEEEECCCHHHHHHHHHHHHHHHHhhcccccCCCeEEEEeCCCCCHHHHHHHHhhcccccCCCCceEEEEeCc-----
Confidence            4579999999999999999887532       224788889999988776644432         2468999994     


Q ss_pred             HHHcCCCCCCCccEEEe
Q 027749          165 MIKRKTLRTRAIKLLVL  181 (219)
Q Consensus       165 ~l~~~~~~~~~l~~lVv  181 (219)
                      .+ ..++++.++.+||-
T Consensus       378 ia-e~GidIp~v~~VId  393 (773)
T 2xau_A          378 IA-ETSLTIDGIVYVVD  393 (773)
T ss_dssp             HH-HHTCCCTTEEEEEE
T ss_pred             HH-HhCcCcCCeEEEEe
Confidence            22 35678888887663

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=86.06  E-value=1.9  Score=36.64  Aligned_cols=96  Identities=16%  Similarity=0.147  Sum_probs=54.5

Q ss_pred             CchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEEC--------CcccHHHH---HHhc
Q 027749           81 TGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVG--------GKSVGEDI---RKLE  149 (219)
Q Consensus        81 ~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~---~~l~  149 (219)
                      ++|. ..+..++..........++||.++++..+..+.+.+........+.+..+.|        +.+..++.   ....
T Consensus       370 ~~k~-~~l~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~  448 (555)
T 3tbk_A          370 NPKL-RDLYLVLQEEYHLKPETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFR  448 (555)
T ss_dssp             CHHH-HHHHHHHHHHHHHCTTCCEEEECSSHHHHHHHHHHHHHCGGGTTCCEEECCC-----------------------
T ss_pred             CHHH-HHHHHHHHHHhccCCCceEEEEeCcHHHHHHHHHHHhhCcCcCceeeeEEEecCCcccccccCHHHHHHHHHHHh
Confidence            4555 3334444444333345679999999999999999998764333344444443        43333332   2222


Q ss_pred             --CCCeEEEeChHHHHHHHHcCCCCCCCccEEEecc
Q 027749          150 --HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDE  183 (219)
Q Consensus       150 --~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE  183 (219)
                        +..+|+|+|.     . -..++++..+++||.=+
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              3578999994     1 24678888888877533

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=86.05  E-value=0.36  Score=35.77  Aligned_cols=21  Identities=24%  Similarity=0.430  Sum_probs=17.2

Q ss_pred             HhCCCcEEEEcCCCCchhHHh
Q 027749           67 IIKGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        67 ~~~~~~~lv~~~tG~GKT~~~   87 (219)
                      +..++-++++||+|+|||...
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            456778999999999999544

>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=86.04  E-value=0.4  Score=36.75  Aligned_cols=52  Identities=15%  Similarity=0.205  Sum_probs=27.4

Q ss_pred             CccccCCCCHHHHHHHHHCC--CCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHh
Q 027749           33 TSFDAMGIKDDLLRGIYQYG--FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        33 ~~~~~~~l~~~~~~~l~~~~--~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~   87 (219)
                      .+|+++.=...+.+.+.+.-  +..|..+...   .+...+.+++.||+|+|||...
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            35666655566666554321  1111111111   1123467999999999999443

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=85.85  E-value=0.37  Score=37.82  Aligned_cols=53  Identities=9%  Similarity=0.135  Sum_probs=30.8

Q ss_pred             cCccccCCCCHHHHHHHHHCCCCCChHHHH-HHHHHH-hCCCcEEEEcCCCCchhHHh
Q 027749           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQ-RAVMPI-IKGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        32 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~-~~~~~~-~~~~~~lv~~~tG~GKT~~~   87 (219)
                      ..+|+++.=...+.+.+.+.-.   .+... +.+..+ ..++.+++.||+|+|||...
T Consensus        17 ~~~~~~i~G~~~~~~~l~~~i~---~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la   71 (297)
T 3b9p_A           17 KVEWTDIAGQDVAKQALQEMVI---LPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLA   71 (297)
T ss_dssp             CCCGGGSCCCHHHHHHHHHHTH---HHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHH
T ss_pred             CCCHHHhCChHHHHHHHHHHHH---hhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHH
Confidence            4568887667777777765310   11000 000011 13578999999999999544

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=85.75  E-value=0.43  Score=37.19  Aligned_cols=20  Identities=20%  Similarity=0.305  Sum_probs=16.4

Q ss_pred             HhCCCcEEEEcCCCCchhHH
Q 027749           67 IIKGRDVIAQAQSGTGKTSM   86 (219)
Q Consensus        67 ~~~~~~~lv~~~tG~GKT~~   86 (219)
                      +..|.-+.+.||+|+|||..
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            45677799999999999944

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=85.43  E-value=0.47  Score=38.56  Aligned_cols=18  Identities=22%  Similarity=0.438  Sum_probs=14.4

Q ss_pred             CcEEEEcCCCCchhHHhH
Q 027749           71 RDVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~   88 (219)
                      +-++|.||||+|||....
T Consensus        41 ~lIvI~GPTgsGKTtLa~   58 (339)
T 3a8t_A           41 KLLVLMGATGTGKSRLSI   58 (339)
T ss_dssp             EEEEEECSTTSSHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            458899999999994443

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=85.40  E-value=0.18  Score=39.60  Aligned_cols=53  Identities=13%  Similarity=0.270  Sum_probs=27.8

Q ss_pred             cCccccCCCCHHHHHHHHHCCCCCChHHH-HHHHHHH--hCCCcEEEEcCCCCchhHHh
Q 027749           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQ-QRAVMPI--IKGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        32 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q-~~~~~~~--~~~~~~lv~~~tG~GKT~~~   87 (219)
                      -.+|++.+-...+.+.+.+.-.   +|+. ..++..+  .-.+.+++.||.|+|||...
T Consensus         6 ~~~~~di~g~~~~~~~l~~~i~---~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLa   61 (274)
T 2x8a_A            6 NVTWADIGALEDIREELTMAIL---APVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLA   61 (274)
T ss_dssp             ------CCHHHHHHHHHHHHHT---HHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHH
T ss_pred             CCCHHHhCCHHHHHHHHHHHHH---HHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHH
Confidence            4578888777777777765311   2221 1233322  12245999999999999443

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=85.36  E-value=0.45  Score=34.41  Aligned_cols=19  Identities=26%  Similarity=0.253  Sum_probs=15.6

Q ss_pred             CCcEEEEcCCCCchhHHhH
Q 027749           70 GRDVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~   88 (219)
                      .+.+++.|++|+|||...-
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            4678999999999995543

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=85.29  E-value=0.38  Score=34.73  Aligned_cols=21  Identities=19%  Similarity=0.338  Sum_probs=16.8

Q ss_pred             hCCCcEEEEcCCCCchhHHhH
Q 027749           68 IKGRDVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        68 ~~~~~~lv~~~tG~GKT~~~~   88 (219)
                      ..++.+++.|+.|+|||...-
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            356789999999999995543

>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=85.07  E-value=2.1  Score=34.85  Aligned_cols=18  Identities=28%  Similarity=0.506  Sum_probs=15.2

Q ss_pred             CCcEEEEcCCCCchhHHh
Q 027749           70 GRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~   87 (219)
                      ..+++++||+|+|||...
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            468999999999999544

>4ag6_A VIRB4 ATPase, type IV secretory pathway VIRB4 components-like P; hydrolase, type IV secretion, conjugation; 2.35A {Thermoanaerobacter pseudethanolicus} PDB: 4ag5_A

Probab=85.02  E-value=1.1  Score=36.73  Aligned_cols=42  Identities=12%  Similarity=0.064  Sum_probs=29.2

Q ss_pred             CccEEEeccchhhhc---cccHHHHHHHHHhCCC-CCeEEEEeecc
Q 027749          175 AIKLLVLDESDEMLS---RGFKDQIYDVYRYLPP-DLQVCCPGSCF  216 (219)
Q Consensus       175 ~l~~lVvDE~h~l~~---~~~~~~~~~i~~~~~~-~~q~i~~SATl  216 (219)
                      .-.++|+||+|.++.   ..+...+..+++..++ +.-+++.|..+
T Consensus       262 ~~~~i~iDEa~~~~~~~~~~~~~~l~~~~~~~Rk~g~~~~~~tQ~~  307 (392)
T 4ag6_A          262 ERTVLVVDEAWMLVDPQTPQAIAFLRDTSKRIRKYNGSLIVISQNV  307 (392)
T ss_dssp             TTCEEEETTGGGGCCTTCTHHHHHHHHHHHHGGGGTCEEEEEESCG
T ss_pred             ccEEEEEecHHHHhCcCchHHHHHHHHHHHHhhhhCeEEEEEcCCH
Confidence            356899999999985   3355667777777655 55566666544

>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=84.94  E-value=0.65  Score=34.54  Aligned_cols=19  Identities=26%  Similarity=0.471  Sum_probs=15.4

Q ss_pred             CCCcEEEEcCCCCchhHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~   87 (219)
                      .|+-+++.||+|+|||...
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            4566889999999999544

>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=84.81  E-value=0.56  Score=38.36  Aligned_cols=18  Identities=22%  Similarity=0.405  Sum_probs=14.8

Q ss_pred             CCCcEEEEcCCCCchhHH
Q 027749           69 KGRDVIAQAQSGTGKTSM   86 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~   86 (219)
                      .+..++|.||||+|||..
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            455789999999999943

>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=84.74  E-value=0.53  Score=33.77  Aligned_cols=18  Identities=28%  Similarity=0.505  Sum_probs=14.7

Q ss_pred             CCcEEEEcCCCCchhHHh
Q 027749           70 GRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~   87 (219)
                      ++-+++.|++|+|||...
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            456899999999999554

>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=84.73  E-value=0.54  Score=34.69  Aligned_cols=17  Identities=35%  Similarity=0.776  Sum_probs=14.3

Q ss_pred             CcEEEEcCCCCchhHHh
Q 027749           71 RDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~   87 (219)
                      +.++++||.|+|||...
T Consensus         2 RpIVi~GPSG~GK~Tl~   18 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLL   18 (186)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            56899999999999543

>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=84.72  E-value=5.7  Score=31.93  Aligned_cols=18  Identities=28%  Similarity=0.364  Sum_probs=14.1

Q ss_pred             CCcEEEEcCCCCchhHHh
Q 027749           70 GRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~   87 (219)
                      +.-+.+.||+|+|||...
T Consensus       129 g~vi~lvG~nGaGKTTll  146 (328)
T 3e70_C          129 PYVIMFVGFNGSGKTTTI  146 (328)
T ss_dssp             SEEEEEECCTTSSHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            345789999999999543

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=84.65  E-value=0.43  Score=38.65  Aligned_cols=18  Identities=50%  Similarity=0.815  Sum_probs=15.0

Q ss_pred             CCcEEEEcCCCCchhHHh
Q 027749           70 GRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~   87 (219)
                      ++.+++.||+|+|||...
T Consensus        70 ~~~vLl~GppGtGKT~la   87 (368)
T 3uk6_A           70 GRAVLIAGQPGTGKTAIA   87 (368)
T ss_dssp             TCEEEEEESTTSSHHHHH
T ss_pred             CCEEEEECCCCCCHHHHH
Confidence            357999999999999544

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=84.45  E-value=0.47  Score=36.44  Aligned_cols=53  Identities=23%  Similarity=0.246  Sum_probs=28.9

Q ss_pred             cCccccCCCCHHHHHHHHHCC--CCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHh
Q 027749           32 ITSFDAMGIKDDLLRGIYQYG--FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        32 ~~~~~~~~l~~~~~~~l~~~~--~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~   87 (219)
                      ..+|+++.-.+.+.+.+.+.-  +..+..++..   .....+.+++.||+|+|||...
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            356888776777766665420  0011100000   0112357999999999999443

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=84.34  E-value=0.9  Score=37.14  Aligned_cols=73  Identities=16%  Similarity=0.142  Sum_probs=45.5

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh---c-CCCeEEEeChHHHHHHHHcCCCCCCCc
Q 027749          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL---E-HGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (219)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l---~-~~~~I~v~Tp~~l~~~l~~~~~~~~~l  176 (219)
                      ..++||.++++..+..+.+.+.+.    ++.+..++|+.+..++...+   . +..+|+|+|.     . -..++++.++
T Consensus       280 ~~~~lvf~~~~~~~~~l~~~l~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~-~~~Gidip~v  349 (414)
T 3eiq_A          280 ITQAVIFINTRRKVDWLTEKMHAR----DFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTD-----L-LARGIDVQQV  349 (414)
T ss_dssp             CSSCEEECSCHHHHHHHHHHHHTT----TCCCEEC---CHHHHHHHHHHHHSCC---CEEECS-----S-CC--CCGGGC
T ss_pred             CCcEEEEeCCHHHHHHHHHHHHhc----CCeEEEecCCCCHHHHHHHHHHHHcCCCcEEEECC-----c-cccCCCccCC
Confidence            346999999999999888877654    57777888887765543333   2 3578999994     1 2356777778


Q ss_pred             cEEEecc
Q 027749          177 KLLVLDE  183 (219)
Q Consensus       177 ~~lVvDE  183 (219)
                      ++||.-+
T Consensus       350 ~~Vi~~~  356 (414)
T 3eiq_A          350 SLVINYD  356 (414)
T ss_dssp             SCEEESS
T ss_pred             CEEEEeC
Confidence            8776533

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=84.24  E-value=0.32  Score=40.90  Aligned_cols=55  Identities=20%  Similarity=0.327  Sum_probs=33.7

Q ss_pred             CccCccccCCCCHHHHHHHHHC---CCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHh
Q 027749           30 EAITSFDAMGIKDDLLRGIYQY---GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        30 ~~~~~~~~~~l~~~~~~~l~~~---~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~   87 (219)
                      .+-.+|++.+=-..+.+.+.+.   -+..|.-++..-+   ...+.+++.||.|+|||+.+
T Consensus       176 ~p~v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi---~~prGvLLyGPPGTGKTlLA  233 (437)
T 4b4t_I          176 SPTESYSDIGGLESQIQEIKESVELPLTHPELYEEMGI---KPPKGVILYGAPGTGKTLLA  233 (437)
T ss_dssp             SCCCCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTC---CCCSEEEEESSTTTTHHHHH
T ss_pred             CCCCcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCCCCceECCCCchHHHHH
Confidence            3446899987566666666543   1223333332222   22467999999999999443

>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=84.21  E-value=1.8  Score=40.96  Aligned_cols=78  Identities=13%  Similarity=0.105  Sum_probs=59.0

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCCc
Q 027749          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (219)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~l  176 (219)
                      +.+++|++++..-+..+.+.+.+...  +.++..++|+.+..++...+    .+..+|+|+|.      +-..++++.++
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 GGQVYYLYNDVENIQKAAERLAELVP--EARIAIGHGQMRERELERVMNDFHHQRFNVLVCTT------IIETGIDIPTA  883 (1151)
T ss_dssp             TCEEEEECCCSSCHHHHHHHHHHHCT--TSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESS------TTGGGSCCTTE
T ss_pred             CCeEEEEECCHHHHHHHHHHHHHhCC--CCeEEEEeCCCCHHHHHHHHHHHHcCCCcEEEECC------cceeeecccCC
Confidence            45799999999999999999987643  46777888887765543222    34689999994      23467899999


Q ss_pred             cEEEeccchh
Q 027749          177 KLLVLDESDE  186 (219)
Q Consensus       177 ~~lVvDE~h~  186 (219)
                      ++||+..++.
T Consensus       884 ~~VIi~~~~~  893 (1151)
T 2eyq_A          884 NTIIIERADH  893 (1151)
T ss_dssp             EEEEETTTTS
T ss_pred             cEEEEeCCCC
Confidence            9999887764

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=84.00  E-value=0.54  Score=34.57  Aligned_cols=20  Identities=30%  Similarity=0.411  Sum_probs=16.2

Q ss_pred             hCCCcEEEEcCCCCchhHHh
Q 027749           68 IKGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        68 ~~~~~~lv~~~tG~GKT~~~   87 (219)
                      ..|.-+.+.||.|+|||...
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            35677899999999999544

>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=83.94  E-value=0.52  Score=33.34  Aligned_cols=16  Identities=19%  Similarity=0.470  Sum_probs=13.2

Q ss_pred             cEEEEcCCCCchhHHh
Q 027749           72 DVIAQAQSGTGKTSMI   87 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~   87 (219)
                      -++++|++|+|||...
T Consensus         3 ~I~l~G~~GsGKsT~a   18 (179)
T 3lw7_A            3 VILITGMPGSGKSEFA   18 (179)
T ss_dssp             EEEEECCTTSCHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4789999999999544

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=83.88  E-value=0.6  Score=33.97  Aligned_cols=19  Identities=47%  Similarity=0.749  Sum_probs=15.8

Q ss_pred             CCCcEEEEcCCCCchhHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~   87 (219)
                      .+..+++.|++|+|||...
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            4567999999999999554

>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=83.85  E-value=3.4  Score=36.63  Aligned_cols=76  Identities=14%  Similarity=0.149  Sum_probs=56.0

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHH---hc-CCCeEEEeChHHHHHHHHcCCCCCCCc
Q 027749          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRK---LE-HGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (219)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---l~-~~~~I~v~Tp~~l~~~l~~~~~~~~~l  176 (219)
                      +.++||.++++..+..+.+.+.+.    ++.+..++|+.+..++...   +. +..+|+|+|.     . ...++++..+
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-----L-LREGLDIPEV  508 (664)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESC-----C-CCTTCCCTTE
T ss_pred             CCEEEEEECCHHHHHHHHHHHHhc----CCCceeecCCCCHHHHHHHHHHhhcCCceEEEccC-----h-hhcCccCCCC
Confidence            457999999999999988888765    5677777777765554333   22 3578999983     1 2467888899


Q ss_pred             cEEEeccchh
Q 027749          177 KLLVLDESDE  186 (219)
Q Consensus       177 ~~lVvDE~h~  186 (219)
                      +++|+=+++.
T Consensus       509 ~lVI~~d~d~  518 (664)
T 1c4o_A          509 SLVAILDADK  518 (664)
T ss_dssp             EEEEETTTTS
T ss_pred             CEEEEeCCcc
Confidence            9988877754

>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=83.80  E-value=1.6  Score=38.09  Aligned_cols=41  Identities=15%  Similarity=0.314  Sum_probs=25.6

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhhccC-CCceeEEEEcCC
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTS-SREVQALILSPT  110 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~~~~-~~~~~~lil~P~  110 (219)
                      ..+++|.|.||+|||.+.-..++..+... ....+.+++=|.
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            46899999999999955444444444332 334455555454

>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=83.79  E-value=0.37  Score=35.07  Aligned_cols=21  Identities=19%  Similarity=0.466  Sum_probs=16.5

Q ss_pred             HhCCCcEEEEcCCCCchhHHh
Q 027749           67 IIKGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        67 ~~~~~~~lv~~~tG~GKT~~~   87 (219)
                      +..|.-+++.||.|+|||...
T Consensus         6 i~~g~~i~l~G~~GsGKSTl~   26 (191)
T 1zp6_A            6 DLGGNILLLSGHPGSGKSTIA   26 (191)
T ss_dssp             CCTTEEEEEEECTTSCHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHH
Confidence            345667899999999999543

>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=83.59  E-value=0.75  Score=37.03  Aligned_cols=16  Identities=25%  Similarity=0.181  Sum_probs=13.1

Q ss_pred             cEEEEcCCCCchhHHh
Q 027749           72 DVIAQAQSGTGKTSMI   87 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~   87 (219)
                      -++|.||||+|||...
T Consensus         5 ~i~i~GptgsGKt~la   20 (322)
T 3exa_A            5 LVAIVGPTAVGKTKTS   20 (322)
T ss_dssp             EEEEECCTTSCHHHHH
T ss_pred             EEEEECCCcCCHHHHH
Confidence            4688999999999444

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=83.57  E-value=0.42  Score=36.68  Aligned_cols=54  Identities=11%  Similarity=0.078  Sum_probs=30.4

Q ss_pred             ccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHh--CCCcEEEEcCCCCchhHHh
Q 027749           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII--KGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        31 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~--~~~~~lv~~~tG~GKT~~~   87 (219)
                      +-.+|+++.-.+.....++.....  . -....+..+.  -.+.+++.||+|+|||...
T Consensus        11 ~~~~~~~i~g~~~~~~~l~~l~~~--~-~~~~~~~~~~~~~~~g~ll~G~~G~GKTtl~   66 (254)
T 1ixz_A           11 PKVTFKDVAGAEEAKEELKEIVEF--L-KNPSRFHEMGARIPKGVLLVGPPGVGKTHLA   66 (254)
T ss_dssp             CSCCGGGCCSCHHHHHHHHHHHHH--H-HCHHHHHHTTCCCCSEEEEECCTTSSHHHHH
T ss_pred             CCCCHHHhCCcHHHHHHHHHHHHH--H-HCHHHHHHcCCCCCCeEEEECCCCCCHHHHH
Confidence            446788877666666666543110  0 0112232221  1245999999999999433

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=83.54  E-value=0.54  Score=37.71  Aligned_cols=50  Identities=12%  Similarity=0.152  Sum_probs=30.9

Q ss_pred             cCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHh-----CCCcEEEEcCCCCchhHHh
Q 027749           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII-----KGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        32 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~-----~~~~~lv~~~tG~GKT~~~   87 (219)
                      -.+|+++.=...+.+.+.+.-.   +|.+   .|.+.     ..+.+++.||+|+|||...
T Consensus         8 ~~~~~di~G~~~~k~~l~~~v~---~p~~---~~~~~~~~~~~~~~iLL~GppGtGKT~la   62 (322)
T 1xwi_A            8 NVKWSDVAGLEGAKEALKEAVI---LPIK---FPHLFTGKRTPWRGILLFGPPGTGKSYLA   62 (322)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHHH---HHHH---CGGGSCTTCCCCSEEEEESSSSSCHHHHH
T ss_pred             CCCHHHhcCHHHHHHHHHHHHH---HHHh---CHHHHhCCCCCCceEEEECCCCccHHHHH
Confidence            3578888777777777764310   1111   11221     2367999999999999443

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=83.43  E-value=1.2  Score=33.63  Aligned_cols=51  Identities=20%  Similarity=0.329  Sum_probs=27.9

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA  123 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~  123 (219)
                      |.-+++.|++|+|||...+--+.+.+.....  .++|+.-. .-..++...+..
T Consensus        30 G~l~~i~G~pG~GKT~l~l~~~~~~~~~~~~--~v~~~s~E-~~~~~~~~~~~~   80 (251)
T 2zts_A           30 GTTVLLTGGTGTGKTTFAAQFIYKGAEEYGE--PGVFVTLE-ERARDLRREMAS   80 (251)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHHHHHHCC--CEEEEESS-SCHHHHHHHHHT
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHhcCC--Cceeeccc-CCHHHHHHHHHH
Confidence            4568999999999994433323333333222  25665433 334455555543

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=83.14  E-value=0.7  Score=32.92  Aligned_cols=18  Identities=22%  Similarity=0.447  Sum_probs=14.9

Q ss_pred             CCcEEEEcCCCCchhHHh
Q 027749           70 GRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~   87 (219)
                      +..+.+.|+.|+|||...
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            467899999999999543

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=83.09  E-value=0.69  Score=38.00  Aligned_cols=20  Identities=20%  Similarity=0.305  Sum_probs=16.1

Q ss_pred             HhCCCcEEEEcCCCCchhHH
Q 027749           67 IIKGRDVIAQAQSGTGKTSM   86 (219)
Q Consensus        67 ~~~~~~~lv~~~tG~GKT~~   86 (219)
                      +..|..+++.||||+|||..
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            34566799999999999944

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=83.02  E-value=10  Score=32.02  Aligned_cols=74  Identities=8%  Similarity=0.005  Sum_probs=48.6

Q ss_pred             eEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCCccE
Q 027749          103 QALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAIKL  178 (219)
Q Consensus       103 ~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~  178 (219)
                      ..++++....-+..+.+.+.+.    +.++..+.|+.+..++...+    .+..+|+|+|+..+.     .++++.++.+
T Consensus       349 ~~~ivf~~~~~~~~l~~~L~~~----~~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv~T~~~~~-----~GiDip~v~~  419 (510)
T 2oca_A          349 NAFVMFKHVSHGKAIFDLIKNE----YDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFS-----TGISVKNLHH  419 (510)
T ss_dssp             EEEEEESSHHHHHHHHHHHHTT----CSSEEEESSSTTHHHHHHHHHHHHHCCSCEEEEEHHHHH-----HSCCCCSEEE
T ss_pred             CeEEEEecHHHHHHHHHHHHHc----CCCeEEEECCCCHHHHHHHHHHHhCCCCCEEEEEcChhh-----cccccccCcE
Confidence            3455555566666666666543    34777788877755443222    346789999964333     5678999999


Q ss_pred             EEeccch
Q 027749          179 LVLDESD  185 (219)
Q Consensus       179 lVvDE~h  185 (219)
                      ||+....
T Consensus       420 vi~~~~~  426 (510)
T 2oca_A          420 VVLAHGV  426 (510)
T ss_dssp             EEESSCC
T ss_pred             EEEeCCC
Confidence            9998887

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=82.99  E-value=0.68  Score=33.99  Aligned_cols=19  Identities=47%  Similarity=0.623  Sum_probs=15.6

Q ss_pred             CCCcEEEEcCCCCchhHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~   87 (219)
                      .|.-+.+.||+|+|||...
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            5667889999999999544

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=82.94  E-value=0.73  Score=34.64  Aligned_cols=20  Identities=25%  Similarity=0.315  Sum_probs=16.1

Q ss_pred             hCCCcEEEEcCCCCchhHHh
Q 027749           68 IKGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        68 ~~~~~~lv~~~tG~GKT~~~   87 (219)
                      ..|+-+.+.||+|+|||...
T Consensus        21 ~~G~~~~lvGpsGsGKSTLl   40 (218)
T 1z6g_A           21 NNIYPLVICGPSGVGKGTLI   40 (218)
T ss_dssp             -CCCCEEEECSTTSSHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHH
Confidence            46778999999999999443

>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=82.94  E-value=5  Score=38.65  Aligned_cols=40  Identities=18%  Similarity=0.155  Sum_probs=27.8

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ++-+.+|+||+---+|..-+..+...++.+.++.-+|+.+
T Consensus       571 ~~~~IliLDE~tSaLD~~te~~i~~~l~~~~~~~T~iiia  610 (1321)
T 4f4c_A          571 RNPKILLLDEATSALDAESEGIVQQALDKAAKGRTTIIIA  610 (1321)
T ss_dssp             TCCSEEEEESTTTTSCTTTHHHHHHHHHHHHTTSEEEEEC
T ss_pred             cCCCEEEEecccccCCHHHHHHHHHHHHHHhCCCEEEEEc
Confidence            5667899999987777765667777776655555455443

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=82.93  E-value=0.53  Score=37.19  Aligned_cols=17  Identities=18%  Similarity=0.010  Sum_probs=13.9

Q ss_pred             CcEEEEcCCCCchhHHh
Q 027749           71 RDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~   87 (219)
                      +.+++.||+|+|||...
T Consensus        37 ~~lLl~GppGtGKT~la   53 (293)
T 3t15_A           37 LILGIWGGKGQGKSFQC   53 (293)
T ss_dssp             SEEEEEECTTSCHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            46889999999999443

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=82.81  E-value=0.59  Score=36.10  Aligned_cols=17  Identities=24%  Similarity=0.219  Sum_probs=13.6

Q ss_pred             cEEEEcCCCCchhHHhH
Q 027749           72 DVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~   88 (219)
                      -+++.||+|+|||....
T Consensus         3 li~I~G~~GSGKSTla~   19 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMAI   19 (253)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             EEEEECCCCcCHHHHHH
Confidence            36899999999995543

>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=82.77  E-value=0.94  Score=33.73  Aligned_cols=19  Identities=16%  Similarity=0.396  Sum_probs=16.0

Q ss_pred             CCCcEEEEcCCCCchhHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~   87 (219)
                      .|+-+++.||+|+|||...
T Consensus        18 ~g~~ivl~GPSGaGKsTL~   36 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIK   36 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECcCCCCHHHHH
Confidence            5778899999999999543

>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=82.73  E-value=0.75  Score=34.48  Aligned_cols=19  Identities=32%  Similarity=0.494  Sum_probs=15.2

Q ss_pred             CCCcEEEEcCCCCchhHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~   87 (219)
                      .++-+++.||||+|||...
T Consensus        33 ~g~~ilI~GpsGsGKStLA   51 (205)
T 2qmh_A           33 YGLGVLITGDSGVGKSETA   51 (205)
T ss_dssp             TTEEEEEECCCTTTTHHHH
T ss_pred             CCEEEEEECCCCCCHHHHH
Confidence            4566899999999999443

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=82.71  E-value=3.4  Score=36.75  Aligned_cols=68  Identities=6%  Similarity=0.011  Sum_probs=47.8

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhc-CCCeEEEeChHHHHHHHHcCCCCCCCccEE
Q 027749          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLL  179 (219)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~l  179 (219)
                      +.++||.+|++.-++.+++.+.+.    ++++..++|. .......... ...+|+|+|.     . -..++++. +++|
T Consensus       410 ~~~~lVF~~s~~~~e~la~~L~~~----g~~v~~lHg~-eR~~v~~~F~~g~~~VLVaTd-----v-~e~GIDip-v~~V  477 (673)
T 2wv9_A          410 AGKTVWFVASVKMSNEIAQCLQRA----GKRVIQLNRK-SYDTEYPKCKNGDWDFVITTD-----I-SEMGANFG-ASRV  477 (673)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHTT----TCCEEEECSS-SHHHHGGGGGTCCCSEEEECG-----G-GGTTCCCC-CSEE
T ss_pred             CCCEEEEECCHHHHHHHHHHHHhC----CCeEEEeChH-HHHHHHHHHHCCCceEEEECc-----h-hhcceeeC-CcEE
Confidence            356999999999999888888764    6778888874 2222222332 4678999994     2 24667888 8876


Q ss_pred             E
Q 027749          180 V  180 (219)
Q Consensus       180 V  180 (219)
                      |
T Consensus       478 I  478 (673)
T 2wv9_A          478 I  478 (673)
T ss_dssp             E
T ss_pred             E
Confidence            6

>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=82.37  E-value=0.71  Score=37.57  Aligned_cols=18  Identities=22%  Similarity=0.427  Sum_probs=14.9

Q ss_pred             CCcEEEEcCCCCchhHHh
Q 027749           70 GRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~   87 (219)
                      .+.+++.||+|+|||..+
T Consensus        84 ~~~iLL~GppGtGKT~la  101 (355)
T 2qp9_X           84 TSGILLYGPPGTGKSYLA  101 (355)
T ss_dssp             CCCEEEECSTTSCHHHHH
T ss_pred             CceEEEECCCCCcHHHHH
Confidence            357999999999999544

>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=82.26  E-value=0.68  Score=37.19  Aligned_cols=16  Identities=19%  Similarity=0.434  Sum_probs=13.1

Q ss_pred             cEEEEcCCCCchhHHh
Q 027749           72 DVIAQAQSGTGKTSMI   87 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~   87 (219)
                      -++|.||||+|||...
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            3788999999999444

>3ice_A Transcription termination factor RHO; transcription, ATPase, hexamer, helicase, RNA, RECA, OB fold ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A

Probab=82.09  E-value=2.6  Score=35.09  Aligned_cols=33  Identities=18%  Similarity=0.281  Sum_probs=24.8

Q ss_pred             CChHHHHHHHHHHh---CCCcEEEEcCCCCchhHHh
Q 027749           55 KPSAIQQRAVMPII---KGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~---~~~~~lv~~~tG~GKT~~~   87 (219)
                      .|-..-.+++..+.   .|..+.+.+|+|+|||...
T Consensus       156 ~~~~tGiraID~~~pi~rGQr~~IvG~sG~GKTtLl  191 (422)
T 3ice_A          156 STEDLTARVLDLASPIGRGQRGLIVAPPKAGKTMLL  191 (422)
T ss_dssp             CTTHHHHHHHHHHSCCBTTCEEEEECCSSSSHHHHH
T ss_pred             CcccccceeeeeeeeecCCcEEEEecCCCCChhHHH
Confidence            35555566776654   7889999999999999544

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=81.88  E-value=2.4  Score=37.45  Aligned_cols=91  Identities=13%  Similarity=0.141  Sum_probs=48.5

Q ss_pred             HHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEEC--------CcccHHHHH---Hhc--CCCeE
Q 027749           88 ALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVG--------GKSVGEDIR---KLE--HGVHV  154 (219)
Q Consensus        88 ~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~---~l~--~~~~I  154 (219)
                      +..++........+.++||.++++..+..+.+.+........+++..++|        +.+..++..   ...  +..+|
T Consensus       385 L~~ll~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F~~~g~~~v  464 (696)
T 2ykg_A          385 LCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNI  464 (696)
T ss_dssp             HHHHHHHHHTTCTTCCEEEECSCHHHHHHHHHHHHHCTTCCSCCEEC-----------------------------CCSC
T ss_pred             HHHHHHHHhccCCCCcEEEEeCcHHHHHHHHHHHHhCCCccccceeEEEccCCCccccCCCHHHHHHHHHHHHhcCCccE
Confidence            33344433323345679999999999999999998764333356665544        444333322   222  35789


Q ss_pred             EEeChHHHHHHHHcCCCCCCCccEEEeccc
Q 027749          155 VSGTPGRVCDMIKRKTLRTRAIKLLVLDES  184 (219)
Q Consensus       155 ~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~  184 (219)
                      +|+|.      +-..++++.++++||.=+.
T Consensus       465 LVaT~------v~~~GiDip~v~~VI~~d~  488 (696)
T 2ykg_A          465 LIATS------VADEGIDIAQCNLVILYEY  488 (696)
T ss_dssp             SEEEE------SSCCC---CCCSEEEEESC
T ss_pred             EEEec------hhhcCCcCccCCEEEEeCC
Confidence            99993      1246788888888776444

>3nwn_A Kinesin-like protein KIF9; motor domain, ADP, structural genomics, structural consortium, SGC, contractIle protein; HET: ADP; 2.00A {Homo sapiens}

Probab=81.87  E-value=1.2  Score=36.51  Aligned_cols=24  Identities=29%  Similarity=0.555  Sum_probs=17.6

Q ss_pred             HHHHhCCCc--EEEEcCCCCchhHHh
Q 027749           64 VMPIIKGRD--VIAQAQSGTGKTSMI   87 (219)
Q Consensus        64 ~~~~~~~~~--~lv~~~tG~GKT~~~   87 (219)
                      +..+++|.|  ++.-|+||+|||...
T Consensus        97 v~~~l~G~N~tifAYGQTGSGKTyTM  122 (359)
T 3nwn_A           97 VSQALDGYNGTIMCYGQTGAGKTYTM  122 (359)
T ss_dssp             HHHHHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HHHHhCCCCEEEEEeCCCCCCccEEe
Confidence            344567876  667799999999544

>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=81.67  E-value=0.7  Score=38.99  Aligned_cols=19  Identities=42%  Similarity=0.699  Sum_probs=15.6

Q ss_pred             CCcEEEEcCCCCchhHHhH
Q 027749           70 GRDVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~   88 (219)
                      ++++++.||+|+|||..+.
T Consensus        63 ~~~iLl~GppGtGKT~la~   81 (456)
T 2c9o_A           63 GRAVLLAGPPGTGKTALAL   81 (456)
T ss_dssp             TCEEEEECCTTSSHHHHHH
T ss_pred             CCeEEEECCCcCCHHHHHH
Confidence            4689999999999995543

>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=81.63  E-value=0.94  Score=33.52  Aligned_cols=21  Identities=19%  Similarity=0.159  Sum_probs=16.2

Q ss_pred             CCCcEEEEcCCCCchhHHhHH
Q 027749           69 KGRDVIAQAQSGTGKTSMIAL   89 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~   89 (219)
                      .|.-+++.|++|+|||.....
T Consensus        19 ~G~~~~i~G~~GsGKTtl~~~   39 (220)
T 2cvh_A           19 PGVLTQVYGPYASGKTTLALQ   39 (220)
T ss_dssp             TTSEEEEECSTTSSHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHH
Confidence            456689999999999954433

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=81.58  E-value=1.1  Score=35.13  Aligned_cols=17  Identities=24%  Similarity=0.421  Sum_probs=14.3

Q ss_pred             CcEEEEcCCCCchhHHh
Q 027749           71 RDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~   87 (219)
                      ..+++.||+|+|||..+
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            36999999999999544

>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=81.44  E-value=0.83  Score=34.53  Aligned_cols=21  Identities=43%  Similarity=0.646  Sum_probs=16.2

Q ss_pred             HhCCCcEEEEcCCCCchhHHh
Q 027749           67 IIKGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        67 ~~~~~~~lv~~~tG~GKT~~~   87 (219)
                      +..|.-+++.||.|+|||...
T Consensus        13 ~~~G~ii~l~GpsGsGKSTLl   33 (219)
T 1s96_A           13 MAQGTLYIVSAPSGAGKSSLI   33 (219)
T ss_dssp             --CCCEEEEECCTTSCHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHH
Confidence            456778999999999999543

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=81.31  E-value=0.82  Score=32.99  Aligned_cols=18  Identities=22%  Similarity=0.377  Sum_probs=14.9

Q ss_pred             CCcEEEEcCCCCchhHHh
Q 027749           70 GRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~   87 (219)
                      +..+++.|+.|+|||...
T Consensus         3 ~~~I~i~G~~GsGKsT~~   20 (192)
T 1kht_A            3 NKVVVVTGVPGVGSTTSS   20 (192)
T ss_dssp             CCEEEEECCTTSCHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            456899999999999543

>3b5x_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; 5.50A {Vibrio cholerae}

Probab=81.25  E-value=6.1  Score=34.32  Aligned_cols=40  Identities=23%  Similarity=0.238  Sum_probs=28.3

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      .+-+++++||.-.-+|......+...++.+.++.-+|+.|
T Consensus       497 ~~p~illlDEpts~LD~~~~~~i~~~l~~~~~~~tvi~it  536 (582)
T 3b5x_A          497 RDAPVLILDEATSALDTESERAIQAALDELQKNKTVLVIA  536 (582)
T ss_pred             cCCCEEEEECccccCCHHHHHHHHHHHHHHcCCCEEEEEe
Confidence            5557999999988788766777777777765444444443

>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=81.10  E-value=0.8  Score=37.24  Aligned_cols=18  Identities=28%  Similarity=0.396  Sum_probs=15.2

Q ss_pred             CCcEEEEcCCCCchhHHh
Q 027749           70 GRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~   87 (219)
                      .+.+++.||+|+|||..+
T Consensus       117 ~~~vLl~GppGtGKT~la  134 (357)
T 3d8b_A          117 PKGILLFGPPGTGKTLIG  134 (357)
T ss_dssp             CSEEEEESSTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            467999999999999544

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=81.10  E-value=0.87  Score=33.51  Aligned_cols=19  Identities=37%  Similarity=0.594  Sum_probs=15.7

Q ss_pred             CCCcEEEEcCCCCchhHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~   87 (219)
                      .|.-+++.|+.|+|||...
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            4667899999999999544

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=81.00  E-value=0.72  Score=33.16  Aligned_cols=20  Identities=25%  Similarity=0.338  Sum_probs=15.8

Q ss_pred             CCCcEEEEcCCCCchhHHhH
Q 027749           69 KGRDVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~   88 (219)
                      .|.-+.+.||.|+|||..+-
T Consensus         8 ~gei~~l~G~nGsGKSTl~~   27 (171)
T 4gp7_A            8 ELSLVVLIGSSGSGKSTFAK   27 (171)
T ss_dssp             SSEEEEEECCTTSCHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHH
Confidence            45668899999999995544

>1bg2_A Kinesin; motor protein, ATPase, microtubule associated; HET: ADP; 1.80A {Homo sapiens} SCOP: c.37.1.9 PDB: 2p4n_K* 1mkj_A* 2kin_A* 3kin_A*

Probab=80.95  E-value=1.4  Score=35.45  Aligned_cols=24  Identities=29%  Similarity=0.567  Sum_probs=17.6

Q ss_pred             HHHHhCCCc--EEEEcCCCCchhHHh
Q 027749           64 VMPIIKGRD--VIAQAQSGTGKTSMI   87 (219)
Q Consensus        64 ~~~~~~~~~--~lv~~~tG~GKT~~~   87 (219)
                      +..++.|.|  ++.-|+||+|||...
T Consensus        70 v~~~l~G~n~tifAYGqTGSGKTyTm   95 (325)
T 1bg2_A           70 VKDVLEGYNGTIFAYGQTSSGKTHTM   95 (325)
T ss_dssp             HHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHhCCCeEEEEEECCCCCCCceEe
Confidence            344567876  667899999999544

>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=80.84  E-value=0.8  Score=32.43  Aligned_cols=17  Identities=18%  Similarity=0.122  Sum_probs=13.7

Q ss_pred             cEEEEcCCCCchhHHhH
Q 027749           72 DVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~   88 (219)
                      .+++.|+.|+|||...-
T Consensus         3 ~i~l~G~~GsGKsT~~~   19 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAA   19 (173)
T ss_dssp             EEEEECSSSSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47899999999995543

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=80.74  E-value=0.81  Score=32.66  Aligned_cols=16  Identities=19%  Similarity=0.385  Sum_probs=13.3

Q ss_pred             cEEEEcCCCCchhHHh
Q 027749           72 DVIAQAQSGTGKTSMI   87 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~   87 (219)
                      -+++.|+.|+|||...
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            4789999999999544

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=80.63  E-value=0.62  Score=36.30  Aligned_cols=54  Identities=11%  Similarity=0.088  Sum_probs=31.4

Q ss_pred             ccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHh--CCCcEEEEcCCCCchhHHh
Q 027749           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII--KGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        31 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~--~~~~~lv~~~tG~GKT~~~   87 (219)
                      +-.+|+++.-.+.+.+.+......  .. ....+..+.  -.+.+++.||+|+|||...
T Consensus        35 ~~~~~~~i~g~~~~~~~l~~l~~~--~~-~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~   90 (278)
T 1iy2_A           35 PKVTFKDVAGAEEAKEELKEIVEF--LK-NPSRFHEMGARIPKGVLLVGPPGVGKTHLA   90 (278)
T ss_dssp             CCCCGGGSSSCHHHHHHHHHHHHH--HH-CHHHHHHTTCCCCCEEEEECCTTSSHHHHH
T ss_pred             CCCCHHHhCChHHHHHHHHHHHHH--HH-CHHHHHHcCCCCCCeEEEECCCcChHHHHH
Confidence            456788887777777666543110  00 012222221  1245999999999999443

>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=80.59  E-value=4.8  Score=33.73  Aligned_cols=67  Identities=9%  Similarity=0.009  Sum_probs=47.0

Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh-cCCCeEEEeChHHHHHHHHcCCCCCCCccEEE
Q 027749          102 VQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL-EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLV  180 (219)
Q Consensus       102 ~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l-~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lV  180 (219)
                      .++||.+|++.-++++.+.+.+.    ++.+..+++.... ...... .+..+|+|+|.     . -..++++.. ++||
T Consensus       189 ~~~lVF~~s~~~a~~l~~~L~~~----g~~~~~lh~~~~~-~~~~~f~~g~~~vLVaT~-----v-~~~GiDip~-~~VI  256 (451)
T 2jlq_A          189 GKTVWFVPSIKAGNDIANCLRKS----GKRVIQLSRKTFD-TEYPKTKLTDWDFVVTTD-----I-SEMGANFRA-GRVI  256 (451)
T ss_dssp             SCEEEECSSHHHHHHHHHHHHTT----TCCEEEECTTTHH-HHGGGGGSSCCSEEEECG-----G-GGSSCCCCC-SEEE
T ss_pred             CCEEEEcCCHHHHHHHHHHHHHc----CCeEEECCHHHHH-HHHHhhccCCceEEEECC-----H-HHhCcCCCC-CEEE
Confidence            36999999999999988888664    5677777765442 222233 34679999994     2 346778888 7665

>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=80.49  E-value=0.76  Score=32.86  Aligned_cols=18  Identities=22%  Similarity=0.329  Sum_probs=14.8

Q ss_pred             CCcEEEEcCCCCchhHHh
Q 027749           70 GRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~   87 (219)
                      +..+++.|+.|+|||...
T Consensus         8 g~~i~l~G~~GsGKSTl~   25 (175)
T 1knq_A            8 HHIYVLMGVSGSGKSAVA   25 (175)
T ss_dssp             SEEEEEECSTTSCHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHH
Confidence            456889999999999554

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=80.44  E-value=0.43  Score=36.84  Aligned_cols=18  Identities=33%  Similarity=0.495  Sum_probs=14.8

Q ss_pred             CCcEEEEcCCCCchhHHh
Q 027749           70 GRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~   87 (219)
                      .+.+++.||+|+|||...
T Consensus        44 ~~~vll~G~~GtGKT~la   61 (268)
T 2r62_A           44 PKGVLLVGPPGTGKTLLA   61 (268)
T ss_dssp             CSCCCCBCSSCSSHHHHH
T ss_pred             CceEEEECCCCCcHHHHH
Confidence            456999999999999544

>1np6_A Molybdopterin-guanine dinucleotide biosynthesis protein B; mixed alpha-beta fold, elongated beta-sheet, walker A motif, P-loop structural motif; 1.90A {Escherichia coli} SCOP: c.37.1.10 PDB: 1p9n_A

Probab=80.32  E-value=2.5  Score=30.62  Aligned_cols=37  Identities=19%  Similarity=0.097  Sum_probs=21.9

Q ss_pred             cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcC
Q 027749           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P  109 (219)
                      -+++.|+.|+||| .++-.++..+........++-.-|
T Consensus         8 ~i~i~G~sGsGKT-Tl~~~l~~~l~~~g~~v~~i~~~~   44 (174)
T 1np6_A            8 LLAFAAWSGTGKT-TLLKKLIPALCARGIRPGLIKHTH   44 (174)
T ss_dssp             EEEEECCTTSCHH-HHHHHHHHHHHHTTCCEEEEEECC
T ss_pred             EEEEEeCCCCCHH-HHHHHHHHhccccCCceeEEeeCC
Confidence            4789999999999 344444444443333344444444

>3dc4_A Kinesin-like protein NOD; catalytic domain, ATPase, microtubule, ADP, nucleotide-binding protein, ATP-binding, coiled coil, motor protein; HET: ADP; 1.90A {Drosophila melanogaster} PDB: 3dcb_A* 3dco_N* 3pxn_A*

Probab=80.27  E-value=1.3  Score=36.00  Aligned_cols=23  Identities=30%  Similarity=0.514  Sum_probs=17.0

Q ss_pred             HHHhCCCc--EEEEcCCCCchhHHh
Q 027749           65 MPIIKGRD--VIAQAQSGTGKTSMI   87 (219)
Q Consensus        65 ~~~~~~~~--~lv~~~tG~GKT~~~   87 (219)
                      ..++.|.|  ++..|+||+|||...
T Consensus        88 ~~~l~G~N~tifAYGQTGSGKTyTM  112 (344)
T 3dc4_A           88 DKLLEGFQCTALAYGQTGTGKSYSM  112 (344)
T ss_dssp             HHHHHTCCEEEEEESSTTSSHHHHH
T ss_pred             hHhhCCCceEEEEecCCCCCCCeEE
Confidence            34467776  567799999999554

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=80.11  E-value=1.2  Score=36.19  Aligned_cols=16  Identities=19%  Similarity=0.360  Sum_probs=13.4

Q ss_pred             cEEEEcCCCCchhHHh
Q 027749           72 DVIAQAQSGTGKTSMI   87 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~   87 (219)
                      -++|.||||+|||...
T Consensus         9 lI~I~GptgSGKTtla   24 (340)
T 3d3q_A            9 LIVIVGPTASGKTELS   24 (340)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             eEEEECCCcCcHHHHH
Confidence            4789999999999544

---

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	219
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	2e-44
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	5e-39
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	6e-38
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	7e-38
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	7e-31
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	5e-30
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	1e-29
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	3e-27
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	8e-22
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	2e-17
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	3e-17
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	1e-16
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	4e-14
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	3e-10

>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 =  146 bits (368), Expect = 2e-44
 Identities = 131/195 (67%), Positives = 165/195 (84%)

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 YDVYRYLPPDLQVCC 211
           YDVYRYLPP  QV  
Sbjct: 181 YDVYRYLPPATQVVL 195

>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 =  131 bits (331), Expect = 5e-39
 Identities = 97/182 (53%), Positives = 131/182 (71%), Gaps = 1/182 (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 CC 211
             
Sbjct: 186 VL 187

>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 =  129 bits (324), Expect = 6e-38
 Identities = 101/183 (55%), Positives = 138/183 (75%), Gaps = 1/183 (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 HG-VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ 208
               H++ GTPGRV DM+ R+ L  + IK+ VLDE+DEMLSRGFKDQIYD+++ L  + Q
Sbjct: 129 MEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQ 188

Query: 209 VCC 211
           V  
Sbjct: 189 VVL 191

>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 =  128 bits (323), Expect = 7e-38
 Identities = 58/179 (32%), Positives = 103/179 (57%), Gaps = 3/179 (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 HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCC 211
           ++V GTPGR+ D I R TL  + +K  +LDE+DEML+ GF   +  +      D ++  
Sbjct: 123 NIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRILL 181

>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 =  110 bits (276), Expect = 7e-31
 Identities = 60/180 (33%), Positives = 108/180 (60%), Gaps = 1/180 (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 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCC 211
           VHVV  TPGR+ D+IK+   +   ++++VLDE+D++LS+ F   + D+   LP + Q+  
Sbjct: 123 VHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILL 182

>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 =  108 bits (270), Expect = 5e-30
 Identities = 60/180 (33%), Positives = 96/180 (53%), Gaps = 3/180 (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

>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 =  108 bits (270), Expect = 1e-29
 Identities = 53/195 (27%), Positives = 94/195 (48%), Gaps = 13/195 (6%)

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----PPDLQVCC 211
                    + Q   
Sbjct: 198 EESNMPSGINRQTLM 212

>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 =  100 bits (250), Expect = 3e-27
 Identities = 73/178 (41%), Positives = 108/178 (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 VVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCC 211
           ++ GTPGRV D+  RK        L ++DE+D+MLSR FK  I  +  +LPP  Q   
Sbjct: 122 ILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSLL 179

>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 = 87.0 bits (214), Expect = 8e-22
 Identities = 51/183 (27%), Positives = 85/183 (46%), Gaps = 4/183 (2%)

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 VCC 211
           +  
Sbjct: 181 MLV 183

>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 = 75.0 bits (183), Expect = 2e-17
 Identities = 28/174 (16%), Positives = 62/174 (35%), Gaps = 10/174 (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---IYDVYRYLPPDLQV 209
             +   +I+ +    +A+  LV+DE   + S         +    R +   L+V
Sbjct: 122 SEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTKMRRMNKALRV 175

>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 = 75.3 bits (184), Expect = 3e-17
 Identities = 26/196 (13%), Positives = 55/196 (28%), Gaps = 25/196 (12%)

Query: 31  AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALT 90
           ++  F    +  +     ++    +P AIQ+     I++     A A +G GKTS     
Sbjct: 20  SLCLFPEDFLLKEF-VEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAM 78

Query: 91  VCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGE------D 144
                       +  ++ PT  L  Q  + I    +   +     +G            +
Sbjct: 79  SLFLALKGK---RCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKEN 135

Query: 145 IRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-----------GFK 193
             +      +V  T   +    +           + +D+ D +L             GF 
Sbjct: 136 FMQNLRNFKIVITTTQFLSKHYR----ELGHFDFIFVDDVDAILKASKNVDKLLHLLGFH 191

Query: 194 DQIYDVYRYLPPDLQV 209
             +            +
Sbjct: 192 YDLKTKSWVGEARGCL 207

>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 = 73.5 bits (179), Expect = 1e-16
 Identities = 24/185 (12%), Positives = 58/185 (31%), Gaps = 11/185 (5%)

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 LQVCC 211
           L    
Sbjct: 175 LPFMA 179

>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 = 67.6 bits (164), Expect = 4e-14
 Identities = 27/143 (18%), Positives = 47/143 (32%), Gaps = 14/143 (9%)

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 SRGFKDQIYDVYRYLPPDLQVCC 211
                 + Y   R    +     
Sbjct: 114 PASIAARGYISTRVEMGEAAGIF 136

>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 = 55.6 bits (132), Expect = 3e-10
 Identities = 28/164 (17%), Positives = 59/164 (35%), Gaps = 4/164 (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 RKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCC 211
              +    + L+V DE+   +       I   Y+    +  V  
Sbjct: 118 AGRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIG 161

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	219
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
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	100.0
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	100.0
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	100.0
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	100.0
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.97
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.96
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.96
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.95
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.87
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.85
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.84
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.83
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.81
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.8
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	99.72
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.39
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.22
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	98.96
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	98.9
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	98.76
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	98.15
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	97.95
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	97.88
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	97.6
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	97.5
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	97.49
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	97.45
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	97.41
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.39
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	97.31
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	96.86
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	96.69
d2qy9a2	211	GTPase domain of the signal recognition particle r	96.61
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	96.55
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	96.3
d1okkd2	207	GTPase domain of the signal recognition particle r	96.24
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.19
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	96.16
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.06
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	96.03
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	96.01
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	95.79
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	95.75
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	95.58
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	95.51
d1j8yf2	211	GTPase domain of the signal sequence recognition p	95.49
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	95.47
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	95.12
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	95.02
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	94.92
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	94.77
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	94.73
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	94.69
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	94.66
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	94.58
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	94.41
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	94.02
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	93.86
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	93.62
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	93.29
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	92.74
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	92.65
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	92.55
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	91.92
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	91.9
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	91.74
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	91.4
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	91.22
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	91.1
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	90.95
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	90.88
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	89.84
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	89.67
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	89.64
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	89.55
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	89.06
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	89.02
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	88.87
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	88.55
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	88.45
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	88.21
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	88.2
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	87.99
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	87.33
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	86.74
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	86.72
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	86.55
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	86.5
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	86.5
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	86.13
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	86.04
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	85.91
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	85.52
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	85.44
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	85.31
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	85.31
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	85.1
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	85.03
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	84.97
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	84.66
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	84.57
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	84.57
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	84.46
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	84.19
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	84.06
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	83.13
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	83.04
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	82.86
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	82.21
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	82.19
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	82.09
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	81.83
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	81.71
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	80.86
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	80.86
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	80.55
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	80.54

>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=1e-47  Score=297.99  Aligned_cols=199  Identities=65%  Similarity=1.054  Sum_probs=188.5

Q ss_pred             cceeeccCCCCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCC
Q 027749           20 KMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS   99 (219)
Q Consensus        20 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~   99 (219)
                      ..+++.++..+...+|+++++++.++++|.++||..|+|+|..+||.+++|+|+++.||||+|||++|++|+++.+....
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            34555566677778999999999999999999999999999999999999999999999999999999999999998888


Q ss_pred             CceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEE
Q 027749          100 REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLL  179 (219)
Q Consensus       100 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~l  179 (219)
                      ..++++|++||++|+.|+++.+.++.+..++++..++|+.+...+...+..+++|+|+||++|.+++.++...+++++++
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             EeccchhhhccccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          180 VLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       180 VvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      |+||||.|++.+|...+..+++.+|+++|+++||||+|.
T Consensus       164 VlDEaD~ll~~~f~~~i~~I~~~l~~~~Q~ilfSAT~~~  202 (222)
T d2j0sa1         164 VLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPH  202 (222)
T ss_dssp             EEETHHHHTSTTTHHHHHHHHTTSCTTCEEEEEESCCCH
T ss_pred             eecchhHhhhcCcHHHHHHHHHhCCCCCEEEEEEEeCCH
Confidence            999999999999999999999999999999999999985

>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=1.7e-45  Score=282.96  Aligned_cols=187  Identities=33%  Similarity=0.616  Sum_probs=176.5

Q ss_pred             cCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCH
Q 027749           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (219)
Q Consensus        32 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~  111 (219)
                      ..+|++++++++++++|.+.||..|+|+|+++||.+++|+|+++++|||+|||++|++|+++.+.....+++++|++|++
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            47899999999999999999999999999999999999999999999999999999999999999888899999999999


Q ss_pred             HHHHHHHHHHHHhcccc-ceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhcc
Q 027749          112 ELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (219)
Q Consensus       112 ~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~  190 (219)
                      +++.|+++.+..+.... +..+....|+.....+...+..+++|+|+||+++.+++..+...+++++++|+||||.|++.
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            99999999998887654 46777778888888888888899999999999999999999999999999999999999999


Q ss_pred             ccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          191 GFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       191 ~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      +|...+..+++.+|+++|+++||||+|.
T Consensus       162 ~f~~~i~~I~~~~~~~~Q~~l~SAT~~~  189 (206)
T d1veca_         162 DFVQIMEDIILTLPKNRQILLYSATFPL  189 (206)
T ss_dssp             TTHHHHHHHHHHSCTTCEEEEEESCCCH
T ss_pred             chHHHHHHHHHhCCCCCEEEEEEecCCH
Confidence            9999999999999999999999999985

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=5.2e-45  Score=282.23  Aligned_cols=191  Identities=53%  Similarity=0.878  Sum_probs=176.4

Q ss_pred             CCCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEE
Q 027749           28 GVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALIL  107 (219)
Q Consensus        28 ~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil  107 (219)
                      .++++.+|+++++++.++++|.++||..|+++|..+||.++.|+|++++||||+|||++|++|+++.+.....+++++|+
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             cCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh-cCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchh
Q 027749          108 SPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL-EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDE  186 (219)
Q Consensus       108 ~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l-~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~  186 (219)
                      +||++|+.|+++.+..+....+.....+.++.....+.... .++++|+|+||+++.+++.++...+++++++|+||||.
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            99999999999999999999999888888777665554333 45789999999999999999889999999999999999


Q ss_pred             hhccccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          187 MLSRGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       187 l~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      |++.+|...+..+++.++++.|+++||||+|.
T Consensus       167 ll~~~f~~~~~~Il~~~~~~~Q~il~SAT~~~  198 (218)
T d2g9na1         167 MLSRGFKDQIYDIFQKLNSNTQVVLLSATMPS  198 (218)
T ss_dssp             HHHTTCHHHHHHHHHHSCTTCEEEEEESCCCH
T ss_pred             hhcCchHHHHHHHHHhCCCCCeEEEEEecCCH
Confidence            99999999999999999999999999999985

>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=3.4e-44  Score=275.79  Aligned_cols=187  Identities=32%  Similarity=0.548  Sum_probs=173.5

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHH
Q 027749           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (219)
Q Consensus        33 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  112 (219)
                      ++|+++++++++++++.++||..|+|+|.++||.+++|+|++++||||+|||++|++|+++.+.....+++++|++|+++
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            47999999999999999999999999999999999999999999999999999999999999988888899999999999


Q ss_pred             HHHHHHHHHHHhccccc-eeEEEEECCcccHHHHHHh-cCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhcc
Q 027749          113 LATQTEKVILAIGDFIN-IQAHACVGGKSVGEDIRKL-EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (219)
Q Consensus       113 l~~q~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~l-~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~  190 (219)
                      |+.|+.+.+..+....+ ++...+.|+.+...+...+ ..+++|+|+||+++.+++.++.+++++++++|+||||.|++.
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            99999999999987754 5677778888877776666 467999999999999999998899999999999999999985


Q ss_pred             -ccHHHHHHHHHhCCCCCeEEEEeecccCC
Q 027749          191 -GFKDQIYDVYRYLPPDLQVCCPGSCFLFD  219 (219)
Q Consensus       191 -~~~~~~~~i~~~~~~~~q~i~~SATl~~~  219 (219)
                       +|...+..+++.+++++|+++||||+|.+
T Consensus       161 ~~~~~~i~~I~~~~~~~~Q~il~SAT~~~~  190 (207)
T d1t6na_         161 LDMRRDVQEIFRMTPHEKQVMMFSATLSKE  190 (207)
T ss_dssp             HHHHHHHHHHHHTSCSSSEEEEEESCCCTT
T ss_pred             CCcHHHHHHHHHhCCCCCEEEEEeeeCCHH
Confidence             89999999999999999999999999864

>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=2.3e-44  Score=277.52  Aligned_cols=190  Identities=51%  Similarity=0.839  Sum_probs=172.0

Q ss_pred             CCCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEE
Q 027749           28 GVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALIL  107 (219)
Q Consensus        28 ~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil  107 (219)
                      -++++.+|++++++++++++|.++||..|+|+|.++||.+++|+|+++++|||+|||++|++|+++.+.....+++++|+
T Consensus         5 ~~~~~~sF~~l~l~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~~~~~~~lil   84 (212)
T d1qdea_           5 YDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALML   84 (212)
T ss_dssp             CCCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEE
T ss_pred             CcccccChhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhhccCCCcceEEE
Confidence            46778999999999999999999999999999999999999999999999999999999999999999988889999999


Q ss_pred             cCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhh
Q 027749          108 SPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (219)
Q Consensus       108 ~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l  187 (219)
                      +|+++++.|+...+..+............++....++...+ ++++|+|+||+++.+++..+.+.+++++++|+||||.|
T Consensus        85 ~pt~el~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~IvI~TP~~l~~~~~~~~~~l~~l~~lVlDEad~l  163 (212)
T d1qdea_          85 APTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGL-RDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEM  163 (212)
T ss_dssp             CSSHHHHHHHHHHHHHHTTTSCCCEEEECC----------C-TTCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHH
T ss_pred             cccHHHhhhhhhhhcccccccccceeeEeeccchhHHHHHh-cCCcEEEECCCccccccccCceecCcceEEeehhhhhh
Confidence            99999999999999999988888888888887777665554 47899999999999999999999999999999999999


Q ss_pred             hccccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          188 LSRGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       188 ~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      ++.+|...+..+++.+++++|+++||||+|.
T Consensus       164 ld~~f~~~v~~I~~~~~~~~Q~vl~SAT~~~  194 (212)
T d1qdea_         164 LSSGFKEQIYQIFTLLPPTTQVVLLSATMPN  194 (212)
T ss_dssp             HHTTCHHHHHHHHHHSCTTCEEEEEESSCCH
T ss_pred             cccchHHHHHHHHHhCCCCCeEEEEEeeCCH
Confidence            9999999999999999999999999999975

>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=1.1e-42  Score=267.28  Aligned_cols=186  Identities=40%  Similarity=0.670  Sum_probs=179.7

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHH
Q 027749           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (219)
Q Consensus        33 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  112 (219)
                      .+|+++++++.++++|.+.||..|+|+|..+||.+++|+|+++.+|||+|||++|++|+++.+.....++++++++|+.+
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             HHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhcccc
Q 027749          113 LATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF  192 (219)
Q Consensus       113 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~  192 (219)
                      ++.+....+..+....++++....|+.........+..+++|+|+||++|.++++.+.+.+++++++|+||||.|++.+|
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            99999999999999999999999999999988888889999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          193 KDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       193 ~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      ...+..+++.+++++|+++||||+|.
T Consensus       161 ~~~v~~I~~~l~~~~Q~il~SATl~~  186 (206)
T d1s2ma1         161 KTIIEQILSFLPPTHQSLLFSATFPL  186 (206)
T ss_dssp             HHHHHHHHTTSCSSCEEEEEESCCCH
T ss_pred             HHHHHHHHHhCCCCCEEEEEEEeCCH
Confidence            99999999999999999999999985

>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=1.3e-42  Score=267.13  Aligned_cols=184  Identities=32%  Similarity=0.556  Sum_probs=171.2

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCC-cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCH
Q 027749           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGR-DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (219)
Q Consensus        33 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~-~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~  111 (219)
                      .+|+++++++.++++|.++||..|+|+|.++||.+++|+ |+++++|||+|||++|.+|+++..... .+++++|++|++
T Consensus         4 msf~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~~-~~~~~lil~pt~   82 (208)
T d1hv8a1           4 MNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNEN-NGIEAIILTPTR   82 (208)
T ss_dssp             CCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSS-SSCCEEEECSCH
T ss_pred             cCHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeecccccccccc-cCcceEEEeecc
Confidence            489999999999999999999999999999999999875 999999999999999999999876554 568999999999


Q ss_pred             HHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccc
Q 027749          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG  191 (219)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~  191 (219)
                      +|+.|+.+.+.++....+.++....|+.+...+...+ ++++|+|+||++|.++++++.+++++++++|+||||+|++.+
T Consensus        83 ~l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l-~~~~IlV~TP~~l~~~l~~~~~~~~~l~~lViDEad~l~~~~  161 (208)
T d1hv8a1          83 ELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKAL-KNANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMG  161 (208)
T ss_dssp             HHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHH-HTCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHTTT
T ss_pred             ccchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhc-CCCCEEEEChHHHHHHHHcCCCCcccCcEEEEEChHHhhcCC
Confidence            9999999999999999899999999998887776655 579999999999999999999999999999999999999999


Q ss_pred             cHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          192 FKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       192 ~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      +...+..+++.+++++|++++|||+|+
T Consensus       162 ~~~~i~~I~~~~~~~~Q~i~~SAT~~~  188 (208)
T d1hv8a1         162 FIKDVEKILNACNKDKRILLFSATMPR  188 (208)
T ss_dssp             THHHHHHHHHTSCSSCEEEEECSSCCH
T ss_pred             ChHHHHHHHHhCCCCCeEEEEEccCCH
Confidence            999999999999999999999999985

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=100.00  E-value=3.6e-43  Score=275.35  Aligned_cols=192  Identities=28%  Similarity=0.450  Sum_probs=178.2

Q ss_pred             CCCCccCccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccC--------
Q 027749           27 EGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS--------   98 (219)
Q Consensus        27 ~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~--------   98 (219)
                      ..++++.+|+++++++++.++|.+.||..|+|+|..+||.+++|+|+++++|||+|||++|++|+++.+...        
T Consensus        15 ~~~~~~~~F~~l~l~~~l~~~L~~~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~~~   94 (238)
T d1wrba1          15 SATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYS   94 (238)
T ss_dssp             SCCSCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------
T ss_pred             CCCCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeHHHHHHHHHhccccccccc
Confidence            446778999999999999999999999999999999999999999999999999999999999999987432        


Q ss_pred             -CCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCcc
Q 027749           99 -SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIK  177 (219)
Q Consensus        99 -~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~  177 (219)
                       ..+++++|++|+++|+.|+.+.+..+....++++..+.|+.....+......+++|+|+||++|.+++..+...+++++
T Consensus        95 ~~~~~~alil~pt~el~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ivV~TP~~l~~~~~~~~~~l~~v~  174 (238)
T d1wrba1          95 KTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCK  174 (238)
T ss_dssp             CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCTTCC
T ss_pred             CCCCceEEEeccchhhhcchheeeeecccCCCcEEEEEeccchhhHHHhhcccCCceeecCHHHHHhHHccCceeccccc
Confidence             3468899999999999999999999999999999999999998888888889999999999999999999999999999


Q ss_pred             EEEeccchhhhccccHHHHHHHHHhCCC----CCeEEEEeecccC
Q 027749          178 LLVLDESDEMLSRGFKDQIYDVYRYLPP----DLQVCCPGSCFLF  218 (219)
Q Consensus       178 ~lVvDE~h~l~~~~~~~~~~~i~~~~~~----~~q~i~~SATl~~  218 (219)
                      ++|+||+|.|++.+|...+..+++.++.    ++|++++|||+|.
T Consensus       175 ~lViDEaD~ll~~~f~~~i~~Il~~~~~~~~~~~Q~il~SAT~~~  219 (238)
T d1wrba1         175 YIVLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPK  219 (238)
T ss_dssp             EEEEETHHHHHHTTCHHHHHHHHHSSCCCCGGGCEEEEEESSCCH
T ss_pred             eeeeehhhhhhhhccHHHHHHHHHHhcCCCCCCCEEEEEeeeCCH
Confidence            9999999999999999999999997642    6799999999975

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=100.00  E-value=1.5e-40  Score=255.75  Aligned_cols=187  Identities=34%  Similarity=0.523  Sum_probs=169.8

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHH
Q 027749           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (219)
Q Consensus        33 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  112 (219)
                      ++|++++++++++++|++.||..|+|+|+++||.+++|+|+++++|||||||++|++|+++........+..++++|+..
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             HHHHHHHHHHHhcccc----ceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhh
Q 027749          113 LATQTEKVILAIGDFI----NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (219)
Q Consensus       113 l~~q~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~  188 (219)
                      ++.+....+.......    ...+....++.+...+......+++|+|+||+++..++.+....+++++++|+||||.++
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            9999998887664443    355666667776666666667789999999999999999988889999999999999999


Q ss_pred             ccccHHHHHHHHHhCCCCCeEEEEeecccCC
Q 027749          189 SRGFKDQIYDVYRYLPPDLQVCCPGSCFLFD  219 (219)
Q Consensus       189 ~~~~~~~~~~i~~~~~~~~q~i~~SATl~~~  219 (219)
                      +++|...+..+++.+++++|++++|||+|++
T Consensus       161 ~~~f~~~v~~I~~~~~~~~Q~il~SATl~~~  191 (209)
T d1q0ua_         161 DMGFITDVDQIAARMPKDLQMLVFSATIPEK  191 (209)
T ss_dssp             HTTCHHHHHHHHHTSCTTCEEEEEESCCCGG
T ss_pred             ccccHHHHHHHHHHCCCCCEEEEEEccCCHH
Confidence            9999999999999999999999999999864

>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=1e-30  Score=199.51  Aligned_cols=172  Identities=16%  Similarity=0.182  Sum_probs=137.6

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHH
Q 027749           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (219)
Q Consensus        40 l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~  119 (219)
                      +++.+...|++.|+..|+|+|.++++.+.+|+++++++|||+|||.++.++++..+...   .++|+++|+++|+.|+.+
T Consensus        10 ~~~~~~~~l~~~g~~~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~~~---~~vl~l~P~~~L~~q~~~   86 (202)
T d2p6ra3          10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKG---GKSLYVVPLRALAGEKYE   86 (202)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHTT---CCEEEEESSHHHHHHHHH
T ss_pred             hhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhhcc---CcceeecccHHHHHHHHH
Confidence            67888999999999999999999999999999999999999999999999888877543   469999999999999999


Q ss_pred             HHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHH--
Q 027749          120 VILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIY--  197 (219)
Q Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~--  197 (219)
                      .++++... ...+....++.....   .....++|+++||..+..++.+....+..+++||+||+|.+.++.+...+.  
T Consensus        87 ~~~~~~~~-~~~v~~~~~~~~~~~---~~~~~~~ii~~~~~~~~~~~~~~~~~~~~~~~ii~DE~h~~~~~~r~~~~~~~  162 (202)
T d2p6ra3          87 SFKKWEKI-GLRIGISTGDYESRD---EHLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEIL  162 (202)
T ss_dssp             HHTTTTTT-TCCEEEECSSCBCCS---SCSTTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCTTTHHHHHHH
T ss_pred             HHHHHhhc-cccceeeccCccccc---ccccccceeeeccHHHHHHHhccchhhhhhhhccccHHHHhcccccchHHHHH
Confidence            99887654 344444444443321   223468999999999999998888788899999999999998776544433  


Q ss_pred             -HHHHhCCCCCeEEEEeecccC
Q 027749          198 -DVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       198 -~i~~~~~~~~q~i~~SATl~~  218 (219)
                       ..++..++++|++++|||+|.
T Consensus       163 l~~i~~~~~~~~~l~lSATl~n  184 (202)
T d2p6ra3         163 VTKMRRMNKALRVIGLSATAPN  184 (202)
T ss_dssp             HHHHHHHCTTCEEEEEECCCTT
T ss_pred             HHHHHhcCCCCcEEEEcCCCCc
Confidence             334445678999999999974

>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=7.2e-30  Score=199.32  Aligned_cols=165  Identities=15%  Similarity=0.114  Sum_probs=124.7

Q ss_pred             HHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 027749           45 LRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (219)
Q Consensus        45 ~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~  124 (219)
                      ..++.+.++.+|+++|+.+++.++.|+|+++++|||+|||++++++++.....   +.+++|++|+++|+.|+++.++++
T Consensus        33 ~~~~~~~~~~~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~~---~~rvliv~Pt~~La~Q~~~~l~~~  109 (237)
T d1gkub1          33 FVEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALK---GKRCYVIFPTSLLVIQAAETIRKY  109 (237)
T ss_dssp             HHHHHHTTTCSCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHTT---SCCEEEEESCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhccCCCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHHh---cCeEEEEeccHHHHHHHHHHHHHH
Confidence            34555668889999999999999999999999999999999999988876654   356999999999999999999998


Q ss_pred             ccccceeE----EEEECCcccHHHHHHh--cCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHH
Q 027749          125 GDFINIQA----HACVGGKSVGEDIRKL--EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYD  198 (219)
Q Consensus       125 ~~~~~~~~----~~~~~~~~~~~~~~~l--~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~  198 (219)
                      .+..++.+    ....+......+...+  ..+++|+|+||+.+.+    ....++++++|||||+|.+++.+..  +..
T Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Ilv~Tp~~l~~----~~~~~~~~~~vVvDE~d~~l~~~~~--~~~  183 (237)
T d1gkub1         110 AEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSK----HYRELGHFDFIFVDDVDAILKASKN--VDK  183 (237)
T ss_dssp             HTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHH----CSTTSCCCSEEEESCHHHHHTSTHH--HHH
T ss_pred             HHHcCCceEEEEeeeecccchhhhhhhhccccccceeccChHHHHH----hhhhcCCCCEEEEEChhhhhhcccc--hhH
Confidence            77665433    2333444433333222  3468999999987654    3345678999999999999876422  222


Q ss_pred             HHHh-------------CCCCCeEEEEeecccC
Q 027749          199 VYRY-------------LPPDLQVCCPGSCFLF  218 (219)
Q Consensus       199 i~~~-------------~~~~~q~i~~SATl~~  218 (219)
                      ++..             .+...|++++|||++.
T Consensus       184 ~~~~~g~~~~~~~~~~~~~~~~~~i~~SAT~~~  216 (237)
T d1gkub1         184 LLHLLGFHYDLKTKSWVGEARGCLMVSTATAKK  216 (237)
T ss_dssp             HHHHTTEEEETTTTEEEECCSSEEEECCCCSCC
T ss_pred             HHHhcCChHHHHHHHhhCCCCCeEEEEeCCCCc
Confidence            2222             2457789999999975

>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=99.96  E-value=5e-31  Score=201.75  Aligned_cols=179  Identities=13%  Similarity=0.122  Sum_probs=134.3

Q ss_pred             CccccCCCCHHHHHHHHHC-CCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCH
Q 027749           33 TSFDAMGIKDDLLRGIYQY-GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (219)
Q Consensus        33 ~~~~~~~l~~~~~~~l~~~-~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~  111 (219)
                      ...+.++|++.+.+.|++. |+..++|+|.++++.+++|+|+++++|||+|||++|.+|++..      ..++++++|++
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            3567888999999999865 9999999999999999999999999999999999999998764      34699999999


Q ss_pred             HHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccc
Q 027749          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG  191 (219)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~  191 (219)
                      +|++|+.+.++.+............+...............+|+++||..+............+++++|+||+|.+.+++
T Consensus        76 ~L~~q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~t~~~~~~~~~~~~~~~~~v~~lviDEaH~~~~~~  155 (206)
T d1oywa2          76 SLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWG  155 (206)
T ss_dssp             HHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGGGGCTTS
T ss_pred             hhhhhHHHHHHhhcccccccccccccccchhHHHHHhcCCceEEEEechhhhchhhcccchhheeeeeeeeeeeeeeccc
Confidence            99999999998875432211111111111112222234568899999988865444444567789999999999998875


Q ss_pred             c--HH---HHHHHHHhCCCCCeEEEEeecccC
Q 027749          192 F--KD---QIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       192 ~--~~---~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      +  ..   .+..+.+.+ +++|+++||||+|+
T Consensus       156 ~~~~~~~~~~~~l~~~~-~~~~ii~lSATl~~  186 (206)
T d1oywa2         156 HDFRPEYAALGQLRQRF-PTLPFMALTATADD  186 (206)
T ss_dssp             SCCCHHHHGGGGHHHHC-TTSCEEEEESCCCH
T ss_pred             cchHHHHHHHHHHHHhC-CCCceEEEEeCCCH
Confidence            2  22   233444555 46899999999985

>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=3.6e-27  Score=179.02  Aligned_cols=161  Identities=17%  Similarity=0.136  Sum_probs=129.8

Q ss_pred             CCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEE
Q 027749           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAH  133 (219)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~  133 (219)
                      -.|+++|.+++..+. ++|+++++|||+|||+++++++...+...  +.+++|++|+++|+.|+++.+.++....+..+.
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            379999999998876 56899999999999999888777666544  346999999999999999999999887778877


Q ss_pred             EEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       134 ~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ...++...... .....+++++++||+.+...+.+....++++++||+||||++........+...+....++++++++|
T Consensus        85 ~~~~~~~~~~~-~~~~~~~~i~i~t~~~~~~~~~~~~~~~~~~~~vIiDE~H~~~~~~~~~~~~~~~~~~~~~~~~l~~S  163 (200)
T d1wp9a1          85 ALTGEKSPEER-SKAWARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLT  163 (200)
T ss_dssp             EECSCSCHHHH-HHHHHHCSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTTCHHHHHHHHHHHHCSSCCEEEEE
T ss_pred             eeecccchhHH-HHhhhcccccccccchhHHHHhhhhhhccccceEEEEehhhhhcchhHHHHHHHHHhcCCCCcEEEEE
Confidence            76666555444 33334578999999999999988888889999999999999876654444554544445678999999


Q ss_pred             ecccC
Q 027749          214 SCFLF  218 (219)
Q Consensus       214 ATl~~  218 (219)
                      ||.+.
T Consensus       164 ATp~~  168 (200)
T d1wp9a1         164 ASPGS  168 (200)
T ss_dssp             SCSCS
T ss_pred             ecCCC
Confidence            99754

>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=99.87  E-value=4.5e-21  Score=147.42  Aligned_cols=168  Identities=15%  Similarity=0.173  Sum_probs=130.1

Q ss_pred             CCCCHHHHHHHHHCCCCCChHHHHHHHHHHh----CC--CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCH
Q 027749           38 MGIKDDLLRGIYQYGFEKPSAIQQRAVMPII----KG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (219)
Q Consensus        38 ~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~----~~--~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~  111 (219)
                      +..+....+.+.+.-...+++-|..++..+.    ++  .+.+++|.||||||.+|+..+...+..   +.++++++|+.
T Consensus        38 ~~~~~~~~~~~~~~lP~~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~---g~qv~~l~Pt~  114 (233)
T d2eyqa3          38 FKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDN---HKQVAVLVPTT  114 (233)
T ss_dssp             CCCCHHHHHHHHHTCCSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTT---TCEEEEECSSH
T ss_pred             CCCCHHHHHhhhhccccccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHc---CCceEEEccHH
Confidence            3456777777766555589999999998764    33  378999999999999999988777754   45699999999


Q ss_pred             HHHHHHHHHHHHhccccceeEEEEECCcccHHHHH---Hh-cCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhh
Q 027749          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIR---KL-EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (219)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~l-~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l  187 (219)
                      .|+.|.++.++++....++++..+.|..+..++..   .+ .+..+|+|+|-     .+-...+.++++++|||||-|+.
T Consensus       115 ~La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGth-----s~l~~~~~f~~LgLiIiDEeH~f  189 (233)
T d2eyqa3         115 LLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTH-----KLLQSDVKFKDLGLLIVDEEHRF  189 (233)
T ss_dssp             HHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECT-----HHHHSCCCCSSEEEEEEESGGGS
T ss_pred             HhHHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCCCCCEEEeeh-----hhhccCCccccccceeeechhhh
Confidence            99999999999999988999999998888665433   33 34689999993     33346677899999999999973


Q ss_pred             hccccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          188 LSRGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       188 ~~~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                         ++..  +..++....++.++++|||..|
T Consensus       190 ---g~kQ--~~~l~~~~~~~~~l~~SATPip  215 (233)
T d2eyqa3         190 ---GVRH--KERIKAMRANVDILTLTATPIP  215 (233)
T ss_dssp             ---CHHH--HHHHHHHHTTSEEEEEESSCCC
T ss_pred             ---hhHH--HHHHHhhCCCCCEEEEecchhH
Confidence               3222  2333444457889999999876

>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=99.85  E-value=5.9e-21  Score=149.35  Aligned_cols=164  Identities=19%  Similarity=0.233  Sum_probs=122.9

Q ss_pred             CHHHHHHHH-HCCCCCChHHHHHHHHHHhC----C--CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHH
Q 027749           41 KDDLLRGIY-QYGFEKPSAIQQRAVMPIIK----G--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (219)
Q Consensus        41 ~~~~~~~l~-~~~~~~~~~~Q~~~~~~~~~----~--~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l  113 (219)
                      ...+.+.+. ...| .+|..|++++..+..    +  .+.+++|.||||||.+|+..++..+...   .++++++||..|
T Consensus        69 ~~~l~~~f~~~LPF-eLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~g---~q~~~m~Pt~~L  144 (264)
T d1gm5a3          69 EGKLAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAG---FQTAFMVPTSIL  144 (264)
T ss_dssp             CTHHHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHT---SCEEEECSCHHH
T ss_pred             ChHHHHHHHhhccc-cCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhcc---cceeEEeehHhh
Confidence            344444444 4445 799999999988752    3  4789999999999999999888877664   359999999999


Q ss_pred             HHHHHHHHHHhccccceeEEEEECCcccHHHHHH---h-cCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhc
Q 027749          114 ATQTEKVILAIGDFINIQAHACVGGKSVGEDIRK---L-EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (219)
Q Consensus       114 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---l-~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~  189 (219)
                      +.|.++.+.++....++.+..+.|+.+..++...   + .+.++|+|||-.     +-+..+.++++++|||||-|+..-
T Consensus       145 a~Qh~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThs-----l~~~~~~f~~LglviiDEqH~fgv  219 (264)
T d1gm5a3         145 AIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHA-----LIQEDVHFKNLGLVIIDEQHRFGV  219 (264)
T ss_dssp             HHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTT-----HHHHCCCCSCCCEEEEESCCCC--
T ss_pred             hHHHHHHHHHhhhhccccceeeccccchHHHHHHHHHHHCCCCCEEEeehH-----HhcCCCCccccceeeeccccccch
Confidence            9999999999999989999999988876554333   3 347899999942     223455678999999999997432


Q ss_pred             cccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          190 RGFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       190 ~~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      .     -+..+..-..++.++++|||..+
T Consensus       220 ~-----Qr~~l~~~~~~~~~l~~SATPip  243 (264)
T d1gm5a3         220 K-----QREALMNKGKMVDTLVMSATPIP  243 (264)
T ss_dssp             --------CCCCSSSSCCCEEEEESSCCC
T ss_pred             h-----hHHHHHHhCcCCCEEEEECCCCH
Confidence            1     12222233346889999999765

>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=99.84  E-value=4e-21  Score=152.81  Aligned_cols=152  Identities=20%  Similarity=0.170  Sum_probs=113.0

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEE
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (219)
                      .|+++|++++..++..++.++.+|||+|||+.....+.......  ..++||++|+.+|+.|+.+.+.++.......+..
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            79999999999999888999999999999977655433332322  3469999999999999999999987665555555


Q ss_pred             EECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEee
Q 027749          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGS  214 (219)
Q Consensus       135 ~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SA  214 (219)
                      ..++.....   ......+|+|+|++++...   ....++++++||+||||++.    ...+..++..+.+..-.++|||
T Consensus       191 ~~~g~~~~~---~~~~~~~i~i~t~qs~~~~---~~~~~~~f~~VIvDEaH~~~----a~~~~~il~~~~~~~~rlGlTa  260 (282)
T d1rifa_         191 IGGGASKDD---KYKNDAPVVVGTWQTVVKQ---PKEWFSQFGMMMNDECHLAT----GKSISSIISGLNNCMFKFGLSG  260 (282)
T ss_dssp             CSTTCSSTT---CCCTTCSEEEECHHHHTTS---CGGGGGGEEEEEEETGGGCC----HHHHHHHTTTCTTCCEEEEECS
T ss_pred             ecceecccc---cccccceEEEEeeehhhhh---cccccCCCCEEEEECCCCCC----chhHHHHHHhccCCCeEEEEEe
Confidence            555544322   1224578999999876543   22346789999999999865    3456677777755445799999


Q ss_pred             cccC
Q 027749          215 CFLF  218 (219)
Q Consensus       215 Tl~~  218 (219)
                      |++.
T Consensus       261 T~~~  264 (282)
T d1rifa_         261 SLRD  264 (282)
T ss_dssp             SCCT
T ss_pred             ecCC
Confidence            9864

>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=99.83  E-value=4.1e-21  Score=153.87  Aligned_cols=136  Identities=17%  Similarity=0.096  Sum_probs=96.0

Q ss_pred             HhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHH
Q 027749           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIR  146 (219)
Q Consensus        67 ~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  146 (219)
                      +.+++++++.+|||+|||++|+++++......  +.++||++|+++|+.|+++.+..+....  .....         ..
T Consensus         6 ~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~--~~~~lvi~Ptr~La~q~~~~l~~~~~~~--~~~~~---------~~   72 (305)
T d2bmfa2           6 FRKKRLTIMDLHPGAGKTKRYLPAIVREAIKR--GLRTLILAPTRVVAAEMEEALRGLPIRY--QTPAI---------RA   72 (305)
T ss_dssp             SSTTCEEEECCCTTSSTTTTHHHHHHHHHHHH--TCCEEEEESSHHHHHHHHHHTTTSCCBC--CC--------------
T ss_pred             hhcCCcEEEEECCCCCHHHHHHHHHHHHHHhc--CCEEEEEccHHHHHHHHHHHHhcCCcce--eeeEE---------ee
Confidence            45788999999999999999988888766554  4579999999999999999886653221  11110         01


Q ss_pred             HhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhcccc--HHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          147 KLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF--KDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       147 ~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~--~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      .......|+++|++.|..... ....+.+++++|+||+|++..+++  ...+..+..  ....+++++|||.|.
T Consensus        73 ~~~~~~~i~~~t~~~l~~~~~-~~~~~~~~~~vViDE~H~~~~~~~~~~~~l~~~~~--~~~~~~v~~SAT~~~  143 (305)
T d2bmfa2          73 EHTGREIVDLMCHATFTMRLL-SPIRVPNYNLIIMDEAHFTDPASIAARGYISTRVE--MGEAAGIFMTATPPG  143 (305)
T ss_dssp             ---CCCSEEEEEHHHHHHHHT-SSSCCCCCSEEEEESTTCCSHHHHHHHHHHHHHHH--HTSCEEEEECSSCTT
T ss_pred             cccCccccccCCcHHHHHHHh-cCccccceeEEEeeeeeecchhhHHHHHHHHHhhc--cccceEEEeecCCCc
Confidence            122356799999998877655 444578899999999998876542  222222222  346899999999875

>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=99.81  E-value=3e-20  Score=131.94  Aligned_cols=136  Identities=11%  Similarity=0.115  Sum_probs=91.2

Q ss_pred             HhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHH
Q 027749           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIR  146 (219)
Q Consensus        67 ~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  146 (219)
                      +.+|+++++++|||+|||.+++..++......  +.++++++|++.+++|..+.+...    ...+....+....     
T Consensus         4 l~~~~~~il~~~tGsGKT~~~~~~~~~~~~~~--~~~vli~~p~~~l~~q~~~~~~~~----~~~~~~~~~~~~~-----   72 (140)
T d1yksa1           4 LKKGMTTVLDFHPGAGKTRRFLPQILAECARR--RLRTLVLAPTRVVLSEMKEAFHGL----DVKFHTQAFSAHG-----   72 (140)
T ss_dssp             TSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTTTS----CEEEESSCCCCCC-----
T ss_pred             HHcCCcEEEEcCCCCChhHHHHHHHHHHhhhc--CceeeeeecchhHHHHHHHHhhhh----hhhhccccccccc-----
Confidence            34688999999999999988877777666554  456999999999999988876433    2222211111111     


Q ss_pred             HhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHH-HHHHHHHhCCCCCeEEEEeeccc
Q 027749          147 KLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKD-QIYDVYRYLPPDLQVCCPGSCFL  217 (219)
Q Consensus       147 ~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~-~~~~i~~~~~~~~q~i~~SATl~  217 (219)
                        ..+..+.+.|...+.... .....+.++++||+||||.+...++.. .+...+.. .++.++++||||.|
T Consensus        73 --~~~~~~~~~~~~~l~~~~-~~~~~~~~~~lvIiDEaH~~~~~~~~~~~~~~~~~~-~~~~~~l~lTATPp  140 (140)
T d1yksa1          73 --SGREVIDAMCHATLTYRM-LEPTRVVNWEVIIMDEAHFLDPASIAARGWAAHRAR-ANESATILMTATPP  140 (140)
T ss_dssp             --CSSCCEEEEEHHHHHHHH-TSSSCCCCCSEEEETTTTCCSHHHHHHHHHHHHHHH-TTSCEEEEECSSCT
T ss_pred             --ccccchhhhhHHHHHHHH-hccccccceeEEEEccccccChhhHHHHHHHHHHhh-CCCCCEEEEEcCCC
Confidence              123567777777766643 344567899999999999875443221 12222222 35789999999987

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.80  E-value=4.2e-19  Score=134.88  Aligned_cols=136  Identities=15%  Similarity=0.131  Sum_probs=100.0

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEE
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (219)
                      .++++|++++..+.++++.++.+|||+|||++++..+ ..+     +.++||++|+.+|+.|+.+.+..+...   .+..
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            6899999999999998899999999999998765543 332     235999999999999999999877543   2222


Q ss_pred             EECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEee
Q 027749          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGS  214 (219)
Q Consensus       135 ~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SA  214 (219)
                      ..|...         ...+|+++|.+.+.......   .+++++||+||||++....    +..+++.++ ....++|||
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            222221         34579999998877654431   3568899999999976443    345555553 345789999


Q ss_pred             cc
Q 027749          215 CF  216 (219)
Q Consensus       215 Tl  216 (219)
                      |+
T Consensus       204 Tl  205 (206)
T d2fz4a1         204 TF  205 (206)
T ss_dssp             SC
T ss_pred             CC
Confidence            97

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=99.72  E-value=1.6e-17  Score=117.68  Aligned_cols=126  Identities=13%  Similarity=0.103  Sum_probs=85.3

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcC
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH  150 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  150 (219)
                      +..++.+|||+|||+.+...+.    .  .+.+++|++|++.|++|+.+.+.+.....   .....++....       .
T Consensus         9 ~~~ll~apTGsGKT~~~~~~~~----~--~~~~vli~~P~~~l~~q~~~~~~~~~~~~---~~~~~~~~~~~-------~   72 (136)
T d1a1va1           9 QVAHLHAPTGSGKSTKVPAAYA----A--QGYKVLVLNPSVAATLGFGAYMSKAHGVD---PNIRTGVRTIT-------T   72 (136)
T ss_dssp             EEEEEECCTTSCTTTHHHHHHH----T--TTCCEEEEESCHHHHHHHHHHHHHHHSCC---CEEECSSCEEC-------C
T ss_pred             CEEEEEeCCCCCHHHHHHHHHH----H--cCCcEEEEcChHHHHHHHHHHHHHHhhcc---ccccccccccc-------c
Confidence            5679999999999965533322    1  24569999999999999999998765332   22223222221       2


Q ss_pred             CCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCC--CCCeEEEEeecc
Q 027749          151 GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP--PDLQVCCPGSCF  216 (219)
Q Consensus       151 ~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~--~~~q~i~~SATl  216 (219)
                      ...+.++|.+.+...   ....++++++||+||+|.+... ....+..+++.+.  ++..++++|||-
T Consensus        73 ~~~~~~~~~~~~~~~---~~~~~~~~~~vIiDE~H~~~~~-~~~~~~~~l~~~~~~~~~~~l~~TATP  136 (136)
T d1a1va1          73 GSPITYSTYGKFLAD---GGCSGGAYDIIICDECHSTDAT-SILGIGTVLDQAETAGARLVVLATATP  136 (136)
T ss_dssp             CCSEEEEEHHHHHHT---TGGGGCCCSEEEEETTTCCSHH-HHHHHHHHHHHTTTTTCSEEEEEESSC
T ss_pred             ccceEEEeeeeeccc---cchhhhcCCEEEEecccccCHH-HHHHHHHHHHHHHHCCCCcEEEEeCCC
Confidence            356888888765433   3345788999999999975432 2344556666654  356799999993

>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=99.39  E-value=9.3e-12  Score=98.81  Aligned_cols=155  Identities=14%  Similarity=0.091  Sum_probs=97.4

Q ss_pred             CChHHHHHHHHHHh---------CCCcEEEEcCCCCchhHHhHHHHHhhhccC----CCceeEEEEcCCHHHHHHHHHHH
Q 027749           55 KPSAIQQRAVMPII---------KGRDVIAQAQSGTGKTSMIALTVCQTVDTS----SREVQALILSPTRELATQTEKVI  121 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~---------~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~----~~~~~~lil~P~~~l~~q~~~~~  121 (219)
                      .+.|+|.+++.-+.         .+...|+.-.+|.|||+..+..+...+...    .....+|||+|.. +..|+.+++
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            57899999987542         345689999999999975543332322222    1224599999965 889999999


Q ss_pred             HHhccccceeEEEEECCcccHHHHH--H-hc-----CCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccH
Q 027749          122 LAIGDFINIQAHACVGGKSVGEDIR--K-LE-----HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFK  193 (219)
Q Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~~~~--~-l~-----~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~  193 (219)
                      .++... ...+....++........  . ..     ...+++++|.+.+.....  .+.-.+.++||+||+|++-+.+  
T Consensus       134 ~k~~~~-~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i~sy~~~~~~~~--~l~~~~~~~vI~DEaH~ikn~~--  208 (298)
T d1z3ix2         134 GKWLGG-RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAE--VLHKGKVGLVICDEGHRLKNSD--  208 (298)
T ss_dssp             HHHHGG-GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTT--TTTTSCCCEEEETTGGGCCTTC--
T ss_pred             HhhcCC-ceeEEEEeCchHHHHHHHHHHhhhccCccccceEEEEeecccccchh--cccccceeeeeccccccccccc--
Confidence            988754 344444555443322211  1 11     135789999877665432  2223356789999999987654  


Q ss_pred             HHHHHHHHhCCCCCeEEEEeecc
Q 027749          194 DQIYDVYRYLPPDLQVCCPGSCF  216 (219)
Q Consensus       194 ~~~~~i~~~~~~~~q~i~~SATl  216 (219)
                      ......+..+ +....+++|||.
T Consensus       209 s~~~~a~~~l-~~~~rllLTGTP  230 (298)
T d1z3ix2         209 NQTYLALNSM-NAQRRVLISGTP  230 (298)
T ss_dssp             HHHHHHHHHH-CCSEEEEECSSC
T ss_pred             chhhhhhhcc-ccceeeeecchH
Confidence            2222233333 345679999996

>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=99.22  E-value=3.1e-11  Score=92.18  Aligned_cols=148  Identities=11%  Similarity=0.099  Sum_probs=94.1

Q ss_pred             CChHHHHHHHHHHh----CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccce
Q 027749           55 KPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~----~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  130 (219)
                      .+.|+|.+++..+.    .+...++.-++|.|||...+.. +..+.......+++||+| ..+..++.+++.++....  
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i~~-~~~~~~~~~~~~~LIv~p-~~l~~~W~~e~~~~~~~~--   87 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAV-FSDAKKENELTPSLVICP-LSVLKNWEEELSKFAPHL--   87 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHH-HHHHHHTTCCSSEEEEEC-STTHHHHHHHHHHHCTTS--
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHHHh-hhhhhhcccccccceecc-hhhhhHHHHHHHhhcccc--
Confidence            57899999986542    4556899999999999776544 444433333446899999 567788999998886543  


Q ss_pred             eEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEE
Q 027749          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVC  210 (219)
Q Consensus       131 ~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i  210 (219)
                      .+....+......     ..+.+|+++|.+.+...-.-   .--..++||+||+|.+-+..  .........+. ....+
T Consensus        88 ~~~~~~~~~~~~~-----~~~~~vvi~~~~~~~~~~~l---~~~~~~~vI~DEah~~k~~~--s~~~~~~~~l~-a~~r~  156 (230)
T d1z63a1          88 RFAVFHEDRSKIK-----LEDYDIILTTYAVLLRDTRL---KEVEWKYIVIDEAQNIKNPQ--TKIFKAVKELK-SKYRI  156 (230)
T ss_dssp             CEEECSSSTTSCC-----GGGSSEEEEEHHHHTTCHHH---HTCCEEEEEEETGGGGSCTT--SHHHHHHHTSC-EEEEE
T ss_pred             cceeeccccchhh-----ccCcCEEEeeHHHHHhHHHH---hcccceEEEEEhhhcccccc--hhhhhhhhhhc-cceEE
Confidence            2222221111111     12468999998776542221   11245789999999987654  22223334443 34578


Q ss_pred             EEeeccc
Q 027749          211 CPGSCFL  217 (219)
Q Consensus       211 ~~SATl~  217 (219)
                      ++|||.-
T Consensus       157 ~LTgTPi  163 (230)
T d1z63a1         157 ALTGTPI  163 (230)
T ss_dssp             EECSSCS
T ss_pred             EEecchH
Confidence            9999963

>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=98.96  E-value=9.9e-09  Score=78.53  Aligned_cols=127  Identities=20%  Similarity=0.257  Sum_probs=99.4

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEE
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  134 (219)
                      .|++.|...--.+.+|  -+.+..||-|||++..+|++-.....++   +=|++.+.-||..=.+.+..+....|+++.+
T Consensus        80 RhyDVQLiGgi~L~~G--~iaem~TGEGKTL~a~l~a~l~al~g~~---vhvvTvNdyLA~RDae~m~~iy~~lGlsvg~  154 (273)
T d1tf5a3          80 FPFKVQLMGGVALHDG--NIAEMKTGEGKTLTSTLPVYLNALTGKG---VHVVTVNEYLASRDAEQMGKIFEFLGLTVGL  154 (273)
T ss_dssp             CCCHHHHHHHHHHHTT--SEEECCTTSCHHHHHHHHHHHHHTTSSC---EEEEESSHHHHHHHHHHHHHHHHHTTCCEEE
T ss_pred             EEehhHHHHHHHHHhh--hheeecCCCcchhHHHHHHHHHHhcCCC---ceEEecCccccchhhhHHhHHHHHcCCCccc
Confidence            7888887766666666  5889999999999999988887776543   7888899999998888889998999999998


Q ss_pred             EECCcccHHHHHHhcCCCeEEEeChHHHHH-HHHcCC------CCCCCccEEEeccchhhh
Q 027749          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCD-MIKRKT------LRTRAIKLLVLDESDEML  188 (219)
Q Consensus       135 ~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~-~l~~~~------~~~~~l~~lVvDE~h~l~  188 (219)
                      ...+.+..++...  ..|+|+.+|...|-. .++.+-      ...+.+.+.||||+|.++
T Consensus       155 ~~~~~~~~~r~~~--Y~~di~Ygt~~e~~fDyLrd~~~~~~~~~~~r~~~~aIvDEvDsil  213 (273)
T d1tf5a3         155 NLNSMSKDEKREA--YAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSIL  213 (273)
T ss_dssp             CCTTSCHHHHHHH--HHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHH
T ss_pred             cccccCHHHHHHH--hhCCceecchhhhhhhhcchhhhcChhhhccCCCCEEEEEcchhhh
Confidence            8777666554433  378999999988864 444321      223568899999999876

>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=98.76  E-value=2.8e-08  Score=80.25  Aligned_cols=140  Identities=16%  Similarity=0.156  Sum_probs=86.4

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHH--HHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeE
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIAL--TVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQA  132 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~--~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  132 (219)
                      ....+|+.|+..++.++-++|.||.|+|||....-  ..+.... ...+.++++++||..-+..+.+.+...........
T Consensus       148 ~~~~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i~~~l~~l~~~~-~~~~~~I~l~ApTgkAA~~L~e~~~~~~~~~~~~~  226 (359)
T d1w36d1         148 DEINWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMA-DGERCRIRLAAPTGKAAARLTESLGKALRQLPLTD  226 (359)
T ss_dssp             TSCCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTC-SSCCCCEEEEBSSHHHHHHHHHHHTHHHHHSSCCS
T ss_pred             ccccHHHHHHHHHHcCCeEEEEcCCCCCceehHHHHHHHHHHHH-hccCCeEEEecCcHHHHHHHHHHHHHHHhhcCchh
Confidence            45678999999999999999999999999965422  2222222 23456799999999999988887754432221110


Q ss_pred             EEEECCcccHHHHHHhcCCCeEEEeChHHHHH------HHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCC
Q 027749          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCD------MIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPD  206 (219)
Q Consensus       133 ~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~------~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~  206 (219)
                      .... .             ...-..|..++..      .+.....+...+++|||||+-++.    ...+..++..++++
T Consensus       227 ~~~~-~-------------~~~~~~t~~~ll~~~~~~~~~~~~~~~~l~~d~lIIDEaSmv~----~~l~~~ll~~~~~~  288 (359)
T d1w36d1         227 EQKK-R-------------IPEDASTLHRLLGAQPGSQRLRHHAGNPLHLDVLVVDEASMID----LPMMSRLIDALPDH  288 (359)
T ss_dssp             CCCC-S-------------CSCCCBTTTSCC-----------CTTSCCSCSEEEECSGGGCB----HHHHHHHHHTCCTT
T ss_pred             hhhh-h-------------hhhhhhHHHHHHhhhhcchHHHHhhhcccccceeeehhhhccC----HHHHHHHHHHhcCC
Confidence            0000 0             0000111111111      112233345568899999998643    45677888889988


Q ss_pred             CeEEEEe
Q 027749          207 LQVCCPG  213 (219)
Q Consensus       207 ~q~i~~S  213 (219)
                      .++|++.
T Consensus       289 ~~lILvG  295 (359)
T d1w36d1         289 ARVIFLG  295 (359)
T ss_dssp             CEEEEEE
T ss_pred             CEEEEEC
Confidence            9998875

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=98.15  E-value=2.6e-06  Score=66.32  Aligned_cols=70  Identities=17%  Similarity=0.135  Sum_probs=52.1

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhcc-CCCceeEEEEcCCHHHHHHHHHHHHHhcc
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT-SSREVQALILSPTRELATQTEKVILAIGD  126 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~l~~q~~~~~~~~~~  126 (219)
                      +++|-|++++..  ...+++|.|+.|||||.+.+--+.+.+.. .....+++++++|+.+++.+.+.+.+...
T Consensus         1 ~L~~eQ~~av~~--~~~~~lI~g~aGTGKTt~l~~rv~~ll~~~~~~~~~ILvlt~tn~a~~~i~~~~~~~~~   71 (306)
T d1uaaa1           1 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLG   71 (306)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHSC
T ss_pred             CcCHHHHHHHhC--CCCCEEEEeeCCccHHHHHHHHHHHHHHhcCCChhHEEEEeCcHHHHHHHHHHHHHhcC
Confidence            468899999965  34579999999999997665444333332 22334699999999999999988877643

>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=97.95  E-value=1.3e-05  Score=62.70  Aligned_cols=69  Identities=17%  Similarity=0.194  Sum_probs=52.4

Q ss_pred             CChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCC-CceeEEEEcCCHHHHHHHHHHHHHhc
Q 027749           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-REVQALILSPTRELATQTEKVILAIG  125 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~-~~~~~lil~P~~~l~~q~~~~~~~~~  125 (219)
                      .+++-|++++...  +.+++|.|+.|||||.+.+--+.+.+.... ..-+++++++++..+..+...+....
T Consensus        11 ~L~~eQ~~~v~~~--~g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~lt~t~~aa~~~~~~~~~~~   80 (318)
T d1pjra1          11 HLNKEQQEAVRTT--EGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLL   80 (318)
T ss_dssp             TSCHHHHHHHHCC--SSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHhCC--CCCEEEEecCCccHHHHHHHHHHHHHHcCCCCHHHeEeEeccHHHHHHHHHHHHhhc
Confidence            4788999999753  457999999999999776554444443332 23469999999999999999886653

>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=97.88  E-value=1.9e-05  Score=58.28  Aligned_cols=41  Identities=5%  Similarity=0.081  Sum_probs=29.3

Q ss_pred             CCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEee
Q 027749          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGS  214 (219)
Q Consensus       173 ~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SA  214 (219)
                      ....+++|+||+|.|.... ...+.++++..+++..+|+.+-
T Consensus       106 ~~~~kviIide~d~l~~~a-~n~Llk~lEep~~~~~fIl~t~  146 (207)
T d1a5ta2         106 LGGAKVVWVTDAALLTDAA-ANALLKTLEEPPAETWFFLATR  146 (207)
T ss_dssp             TSSCEEEEESCGGGBCHHH-HHHHHHHHTSCCTTEEEEEEES
T ss_pred             cCccceEEechhhhhhhhh-hHHHHHHHHhhcccceeeeeec
Confidence            3467899999999987543 5667777777776666666543

>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=97.50  E-value=0.00098  Score=49.05  Aligned_cols=44  Identities=20%  Similarity=0.457  Sum_probs=29.5

Q ss_pred             CCCCCCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          169 KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       169 ~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ........+++|+||+|.+.... ...+..+++..++.+.+++.+
T Consensus        93 ~~~~~~~~kiiiiDe~d~~~~~~-~~~Ll~~le~~~~~~~~~~~~  136 (227)
T d1sxjc2          93 RQIFSKGFKLIILDEADAMTNAA-QNALRRVIERYTKNTRFCVLA  136 (227)
T ss_dssp             CCSSSCSCEEEEETTGGGSCHHH-HHHHHHHHHHTTTTEEEEEEE
T ss_pred             ccccCCCeEEEEEeccccchhhH-HHHHHHHhhhcccceeecccc
Confidence            33445566799999999877553 556667777766665555544

>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=97.49  E-value=0.0013  Score=49.03  Aligned_cols=39  Identities=10%  Similarity=0.179  Sum_probs=26.6

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ...+++|+||+|.|.... ...+...++..+.++.+|+.+
T Consensus       114 ~~~kviiIde~d~l~~~~-q~~Llk~lE~~~~~~~~il~t  152 (239)
T d1njfa_         114 GRFKVYLIDEVHMLSRHS-FNALLKTLEEPPEHVKFLLAT  152 (239)
T ss_dssp             SSSEEEEEETGGGSCHHH-HHHHHHHHHSCCTTEEEEEEE
T ss_pred             CCCEEEEEECcccCCHHH-HHHHHHHHhcCCCCeEEEEEc
Confidence            356799999999976433 455667777666666666554

>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=97.45  E-value=0.00031  Score=52.56  Aligned_cols=51  Identities=14%  Similarity=0.205  Sum_probs=33.6

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHHHHHhhhc
Q 027749           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVD   96 (219)
Q Consensus        33 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~   96 (219)
                      .+|+++-.+..+.+.|..+--..            ....++++.||.|+|||..+ ..+++.+.
T Consensus         8 ~~~~diig~~~~~~~L~~~~~~~------------~~~~~lll~Gp~G~GKTt~~-~~la~~l~   58 (252)
T d1sxje2           8 KSLNALSHNEELTNFLKSLSDQP------------RDLPHLLLYGPNGTGKKTRC-MALLESIF   58 (252)
T ss_dssp             CSGGGCCSCHHHHHHHHTTTTCT------------TCCCCEEEECSTTSSHHHHH-HTHHHHHS
T ss_pred             CCHHHccCcHHHHHHHHHHHHcC------------CCCCeEEEECCCCCCHHHHH-HHHHHhhc
Confidence            56888888888888887542110            11236899999999999544 34445443

>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=97.41  E-value=0.00098  Score=48.42  Aligned_cols=42  Identities=7%  Similarity=0.112  Sum_probs=31.6

Q ss_pred             CCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEeec
Q 027749          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSC  215 (219)
Q Consensus       173 ~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SAT  215 (219)
                      ....+++|+||||.|.... ...+.+.++.-|++..+++.|..
T Consensus        77 ~~~~KviIId~ad~l~~~a-qNaLLK~LEEPp~~t~fiLit~~  118 (198)
T d2gnoa2          77 LYTRKYVIVHDCERMTQQA-ANAFLKALEEPPEYAVIVLNTRR  118 (198)
T ss_dssp             SSSSEEEEETTGGGBCHHH-HHHTHHHHHSCCTTEEEEEEESC
T ss_pred             cCCCEEEEEeCccccchhh-hhHHHHHHhCCCCCceeeeccCC
Confidence            3567899999999987553 66778888887777777776543

>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=97.39  E-value=0.00051  Score=50.58  Aligned_cols=45  Identities=13%  Similarity=0.118  Sum_probs=28.7

Q ss_pred             CCccEEEeccchhhhcc-ccHHHHHHHHHhCCCCCeEEEEeecccC
Q 027749          174 RAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPPDLQVCCPGSCFLF  218 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~-~~~~~~~~i~~~~~~~~q~i~~SATl~~  218 (219)
                      ...++|++|++|.+... .....+..++..+......+++|+..+|
T Consensus        96 ~~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p  141 (213)
T d1l8qa2          96 KSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHP  141 (213)
T ss_dssp             HTCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCG
T ss_pred             hhccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcc
Confidence            35779999999988653 3455566676665433334555655554

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.31  E-value=0.0006  Score=50.27  Aligned_cols=43  Identities=14%  Similarity=0.207  Sum_probs=29.7

Q ss_pred             CCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEeecc
Q 027749          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPGSCF  216 (219)
Q Consensus       173 ~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~SATl  216 (219)
                      ...-+++|+||+|.+.... ...+...++..+..+.+++.+...
T Consensus        99 ~~~~kviiiDe~d~~~~~~-~~~ll~~~e~~~~~~~~i~~~~~~  141 (224)
T d1sxjb2          99 PGKHKIVILDEADSMTAGA-QQALRRTMELYSNSTRFAFACNQS  141 (224)
T ss_dssp             TTCCEEEEEESGGGSCHHH-HHTTHHHHHHTTTTEEEEEEESCG
T ss_pred             CcceEEEEEecccccchhH-HHHHhhhccccccceeeeeccCch
Confidence            3456799999999987653 455666667766676776665543

>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=96.86  E-value=0.0093  Score=43.65  Aligned_cols=40  Identities=13%  Similarity=0.305  Sum_probs=25.5

Q ss_pred             CCCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       173 ~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ...-.++++||+|.+.... ...+..++...+.++.+++.+
T Consensus       107 ~~~~~iilide~d~~~~~~-~~~ll~~l~~~~~~~~~i~~~  146 (231)
T d1iqpa2         107 GASFKIIFLDEADALTQDA-QQALRRTMEMFSSNVRFILSC  146 (231)
T ss_dssp             GCSCEEEEEETGGGSCHHH-HHHHHHHHHHTTTTEEEEEEE
T ss_pred             CCCceEEeehhhhhcchhH-HHHHhhhcccCCcceEEEecc
Confidence            3456789999999877543 445556666655555555443

>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=96.69  E-value=0.0018  Score=52.31  Aligned_cols=67  Identities=24%  Similarity=0.350  Sum_probs=48.3

Q ss_pred             CChHHHHHHHHHHh----CC-CcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccc
Q 027749           55 KPSAIQQRAVMPII----KG-RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDF  127 (219)
Q Consensus        55 ~~~~~Q~~~~~~~~----~~-~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (219)
                      .|...|=+++..+.    +| ++.++.|-||||||+... .++....     ..+|||+|+..+|.|+++.+..+...
T Consensus        11 ~p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~~iA-~l~~~~~-----rp~LVVt~n~~~A~qL~~dL~~~l~~   82 (413)
T d1t5la1          11 EPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTIS-NVIAQVN-----KPTLVIAHNKTLAGQLYSELKEFFPH   82 (413)
T ss_dssp             CCCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHHHHH-HHHHHHT-----CCEEEECSSHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHHHHH-HHHHHhC-----CCEEEEeCCHHHHHHHHHHHHHHcCC
Confidence            56667766665544    34 568899999999994432 2333321     23899999999999999999988654

>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=96.61  E-value=0.0097  Score=43.36  Aligned_cols=85  Identities=20%  Similarity=0.238  Sum_probs=44.7

Q ss_pred             EEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----
Q 027749           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----  148 (219)
Q Consensus        73 ~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----  148 (219)
                      ++++||||+|||....=-+ ..+...+ ..-+||-+-+.-.+  -.+.++.+.+..++.+.....+..........    
T Consensus        12 i~lvGptGvGKTTTiAKLA-~~~~~~g-~kV~lit~Dt~R~g--A~eQL~~~a~~l~v~~~~~~~~~d~~~~l~~~~~~a   87 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTIGKLA-RQFEQQG-KSVMLAAGDTFRAA--AVEQLQVWGQRNNIPVIAQHTGADSASVIFDAIQAA   87 (211)
T ss_dssp             EEEECCTTSCHHHHHHHHH-HHHHTTT-CCEEEECCCTTCHH--HHHHHHHHHHHTTCCEECCSTTCCHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH-HHHHHCC-CcEEEEeccccccc--chhhhhhhhhhcCCcccccccCCCHHHHHHHHHHHH
Confidence            5579999999996654433 3333332 23355555553332  13444445555567766555544433322211    


Q ss_pred             -cCCCe-EEEeChHH
Q 027749          149 -EHGVH-VVSGTPGR  161 (219)
Q Consensus       149 -~~~~~-I~v~Tp~~  161 (219)
                       .++++ |+|=|+++
T Consensus        88 ~~~~~d~ilIDTaGr  102 (211)
T d2qy9a2          88 KARNIDVLIADTAGR  102 (211)
T ss_dssp             HHTTCSEEEECCCCC
T ss_pred             HHcCCCEEEeccCCC
Confidence             23444 56778774

>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=96.55  E-value=0.0049  Score=46.14  Aligned_cols=53  Identities=15%  Similarity=0.257  Sum_probs=30.6

Q ss_pred             cCccccCCCCHHHHHHHHHCC--CCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHh
Q 027749           32 ITSFDAMGIKDDLLRGIYQYG--FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        32 ~~~~~~~~l~~~~~~~l~~~~--~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~   87 (219)
                      -.+|++..-...+.+.+.+.-  +..|..++..-   ....+.+++.||.|+|||...
T Consensus         5 ~~~~~di~G~~~~k~~l~~~i~~l~~~~~~~~~g---~~~~~giLl~GppGtGKT~la   59 (247)
T d1ixza_           5 KVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMG---ARIPKGVLLVGPPGVGKTHLA   59 (247)
T ss_dssp             SCCGGGCCSCHHHHHHHHHHHHHHHCHHHHHHTT---CCCCSEEEEECCTTSSHHHHH
T ss_pred             CCcHHHHccHHHHHHHHHHHHHHHHCHHHHHHcC---CCCCceEEEecCCCCChhHHH
Confidence            367899876777777665420  11111111110   112356999999999999443

>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=96.30  E-value=0.0041  Score=45.30  Aligned_cols=91  Identities=12%  Similarity=0.100  Sum_probs=67.5

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCCc
Q 027749          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (219)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~l  176 (219)
                      +.++.||+|..+-...+.+.+.+...  +.++..++|..+..+.-..+    .+..+|+|+|.     .+ ..+++..+.
T Consensus        31 GgQvy~V~p~I~~~e~~~~~l~~~~p--~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~Tt-----vI-EvGiDvpnA  102 (211)
T d2eyqa5          31 GGQVYYLYNDVENIQKAAERLAELVP--EARIAIGHGQMRERELERVMNDFHHQRFNVLVCTT-----II-ETGIDIPTA  102 (211)
T ss_dssp             TCEEEEECCCSSCHHHHHHHHHHHCT--TSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESS-----TT-GGGSCCTTE
T ss_pred             CCeEEEEEcCccchhhHHHHHHHhCC--ceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEeh-----hh-hhccCCCCC
Confidence            56799999999999999999988765  46788889988876543332    34789999994     22 456789999


Q ss_pred             cEEEeccchhhhccccHHHHHHHHHhC
Q 027749          177 KLLVLDESDEMLSRGFKDQIYDVYRYL  203 (219)
Q Consensus       177 ~~lVvDE~h~l~~~~~~~~~~~i~~~~  203 (219)
                      .++|+.+||++.    ..++.-+....
T Consensus       103 ~~iiI~~a~rfG----LaQLhQLRGRV  125 (211)
T d2eyqa5         103 NTIIIERADHFG----LAQLHQLRGRV  125 (211)
T ss_dssp             EEEEETTTTSSC----HHHHHHHHTTC
T ss_pred             cEEEEecchhcc----cccccccccee
Confidence            999999999743    33444444443

>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=96.24  E-value=0.019  Score=41.61  Aligned_cols=87  Identities=21%  Similarity=0.152  Sum_probs=42.6

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCC-HHHHHHHHHHHHHhccccceeEEEEECCcccHHHHH--
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT-RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIR--  146 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~-~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--  146 (219)
                      ++-++++||||+|||....=-+ .++...+. .-++|-+-+ |.-+.++.+.+   .+..++.+.....+........  
T Consensus         6 ~~vi~lvGptGvGKTTTiaKLA-~~~~~~g~-kV~lit~Dt~R~gA~eQL~~~---a~~l~i~~~~~~~~~d~~~~~~~~   80 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTIAKLG-RYYQNLGK-KVMFCAGDTFRAAGGTQLSEW---GKRLSIPVIQGPEGTDPAALAYDA   80 (207)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHH-HHHHTTTC-CEEEECCCCSSTTHHHHHHHH---HHHHTCCEECCCTTCCHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHH-HHHHHCCC-cEEEEEeccccccchhhHhhc---ccccCceEEeccCCccHHHHHHHH
Confidence            3457889999999996654332 23333333 334555554 44443333333   3333555544443333322221  


Q ss_pred             ----HhcCCCeEEEeChHH
Q 027749          147 ----KLEHGVHVVSGTPGR  161 (219)
Q Consensus       147 ----~l~~~~~I~v~Tp~~  161 (219)
                          .....--|+|=|+++
T Consensus        81 ~~~~~~~~~d~ilIDTaGr   99 (207)
T d1okkd2          81 VQAMKARGYDLLFVDTAGR   99 (207)
T ss_dssp             HHHHHHHTCSEEEECCCCC
T ss_pred             HHHHHHCCCCEEEcCcccc
Confidence                112223366777774

>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=96.19  E-value=0.01  Score=43.18  Aligned_cols=64  Identities=19%  Similarity=0.250  Sum_probs=32.1

Q ss_pred             EEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcC-CHHHHHHHHHHHHHhccccceeEEEEECCccc
Q 027749           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP-TRELATQTEKVILAIGDFINIQAHACVGGKSV  141 (219)
Q Consensus        73 ~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P-~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~  141 (219)
                      ++++||||+|||....--+.+ +..++.+ -+++-+- .|.-+.   +.++.+.+..++.+.........
T Consensus        13 i~lvGp~GvGKTTTiaKLA~~-~~~~g~k-V~lit~Dt~R~gA~---eQL~~~a~~l~v~~~~~~~~~~~   77 (207)
T d1ls1a2          13 WFLVGLQGSGKTTTAAKLALY-YKGKGRR-PLLVAADTQRPAAR---EQLRLLGEKVGVPVLEVMDGESP   77 (207)
T ss_dssp             EEEECCTTTTHHHHHHHHHHH-HHHTTCC-EEEEECCSSCHHHH---HHHHHHHHHHTCCEEECCTTCCH
T ss_pred             EEEECCCCCCHHHHHHHHHHH-HHHCCCc-EEEEecccccchHH---HHHHHHHHhcCCccccccccchh
Confidence            567999999999655433322 2233222 2344343 333333   33333444446666655544443

>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=96.16  E-value=0.0039  Score=45.79  Aligned_cols=39  Identities=18%  Similarity=0.306  Sum_probs=25.3

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      ...+.+|+||+|.+.... ...+..++...+..+.+++.+
T Consensus       107 ~~~~viiiDe~d~l~~~~-~~~l~~~~~~~~~~~~~i~~~  145 (237)
T d1sxjd2         107 PPYKIIILDEADSMTADA-QSALRRTMETYSGVTRFCLIC  145 (237)
T ss_dssp             CSCEEEEETTGGGSCHHH-HHHHHHHHHHTTTTEEEEEEE
T ss_pred             cCceEEEEecccccCHHH-HHHHhhccccccccccccccc
Confidence            345689999999887553 445555666655555555544

>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=96.06  E-value=0.049  Score=39.53  Aligned_cols=84  Identities=17%  Similarity=0.168  Sum_probs=42.8

Q ss_pred             EEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHH-----HHH
Q 027749           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGED-----IRK  147 (219)
Q Consensus        73 ~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~  147 (219)
                      ++++||||+|||....=-+ .++..++. .-++|-+.+.-.+.  .+.++.+.+..++.+.....+.....-     ...
T Consensus        14 i~lvGptGvGKTTTiAKLA-a~~~~~~~-kV~lit~Dt~R~gA--~eQL~~~a~~l~i~~~~~~~~~d~~~~~~~~~~~~   89 (213)
T d1vmaa2          14 IMVVGVNGTGKTTSCGKLA-KMFVDEGK-SVVLAAADTFRAAA--IEQLKIWGERVGATVISHSEGADPAAVAFDAVAHA   89 (213)
T ss_dssp             EEEECCTTSSHHHHHHHHH-HHHHHTTC-CEEEEEECTTCHHH--HHHHHHHHHHHTCEEECCSTTCCHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH-HHHHHCCC-ceEEEeecccccch--hHHHHHHhhhcCccccccCCCCcHHHHHHHHHHHH
Confidence            5679999999996654333 23333333 34666666543332  133444444446665544433332221     111


Q ss_pred             hcCCC-eEEEeChH
Q 027749          148 LEHGV-HVVSGTPG  160 (219)
Q Consensus       148 l~~~~-~I~v~Tp~  160 (219)
                      ..+++ -|+|=|++
T Consensus        90 ~~~~~d~ilIDTaG  103 (213)
T d1vmaa2          90 LARNKDVVIIDTAG  103 (213)
T ss_dssp             HHTTCSEEEEEECC
T ss_pred             HHcCCCEEEEeccc
Confidence            22344 46688886

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=96.03  E-value=0.037  Score=39.13  Aligned_cols=95  Identities=16%  Similarity=0.156  Sum_probs=69.7

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhc----CCCeEEEeChHHHHHHHHcCCCCCCCc
Q 027749          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (219)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~----~~~~I~v~Tp~~l~~~l~~~~~~~~~l  176 (219)
                      +.++||.++++.-++.+...+.+.    ++.+..++|+.+..++...+.    +..+|+|+|.      +..++++..++
T Consensus        31 ~~~~iif~~~~~~~~~~~~~l~~~----g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTd------v~~rGiDip~v  100 (181)
T d1t5la2          31 NERTLVTTLTKKMAEDLTDYLKEA----GIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN------LLREGLDIPEV  100 (181)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHTT----TCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESC------CCSSSCCCTTE
T ss_pred             CCeEEEEeehhhhhHHHHHHHHhC----CcceeEecCCccHHHHHHHHHHHHCCCCCEEEehh------HHHccCCCCCC
Confidence            346999999999998888777654    789999999999877655543    4789999994      23577899999


Q ss_pred             cEEEeccchhhhc-cccHHHHHHHHHhCCC
Q 027749          177 KLLVLDESDEMLS-RGFKDQIYDVYRYLPP  205 (219)
Q Consensus       177 ~~lVvDE~h~l~~-~~~~~~~~~i~~~~~~  205 (219)
                      ++||.-+++.... .++...+.++-+.-..
T Consensus       101 ~~VI~~d~p~~~~~~s~~~yi~R~GRagR~  130 (181)
T d1t5la2         101 SLVAILDADKEGFLRSERSLIQTIGRAARN  130 (181)
T ss_dssp             EEEEETTTTSCSGGGSHHHHHHHHGGGTTS
T ss_pred             CEEEEecCCcccccccHHHHHHHHHhhccc
Confidence            9999888775321 2345556666555443

>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=96.01  E-value=0.0083  Score=46.70  Aligned_cols=64  Identities=22%  Similarity=0.294  Sum_probs=39.3

Q ss_pred             HHHHHCCCCC---ChHHHHHHH-HHHhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHH
Q 027749           46 RGIYQYGFEK---PSAIQQRAV-MPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (219)
Q Consensus        46 ~~l~~~~~~~---~~~~Q~~~~-~~~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l  113 (219)
                      ..|.+.|+..   ..+.+...+ ..+..+++++|+|+|||||| .++-+++..+..   .-+++.+-.+.++
T Consensus       138 ~~l~~~g~~~~~~~~~~~~~~l~~~v~~~~nili~G~tgSGKT-T~l~al~~~i~~---~~rivtiEd~~El  205 (323)
T d1g6oa_         138 SFFEEQGFYNLLDNKEQAISAIKDGIAIGKNVIVCGGTGSGKT-TYIKSIMEFIPK---EERIISIEDTEEI  205 (323)
T ss_dssp             HHHHHTTTTTTCSSHHHHHHHHHHHHHHTCCEEEEESTTSSHH-HHHHHHGGGSCT---TCCEEEEESSCCC
T ss_pred             HHHHHHhhhcccccHHHHHHHHHHHHHhCCCEEEEeeccccch-HHHHHHhhhccc---ccceeeccchhhh
Confidence            3344444432   233333334 34567789999999999999 455566665533   3347777666665

>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=95.79  E-value=0.023  Score=39.35  Aligned_cols=73  Identities=12%  Similarity=0.129  Sum_probs=55.9

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCCc
Q 027749          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (219)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~l  176 (219)
                      ..++||.|.++..++++.+.+...    ++.+..++|+.+..++...+    .....|+|+|.     . ..+++++.++
T Consensus        27 ~~k~iIF~~s~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Td-----v-~~rGiDi~~v   96 (162)
T d1fuka_          27 VTQAVIFCNTRRKVEELTTKLRND----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTD-----L-LARGIDVQQV   96 (162)
T ss_dssp             CSCEEEEESSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEG-----G-GTTTCCCCSC
T ss_pred             CCcEEEEEEEEchHHHHHHHHhhc----CceEEEeccCCchhhHHHHHHHHhhcccceeeccc-----c-ccccccCCCc
Confidence            346999999999999998877654    67888889888877665443    24678999994     2 3577889999


Q ss_pred             cEEEecc
Q 027749          177 KLLVLDE  183 (219)
Q Consensus       177 ~~lVvDE  183 (219)
                      ++||.=+
T Consensus        97 ~~VI~~d  103 (162)
T d1fuka_          97 SLVINYD  103 (162)
T ss_dssp             SEEEESS
T ss_pred             eEEEEec
Confidence            9887655

>d2b8ta1 c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-terminal domain {Ureaplasma urealyticum [TaxId: 2130]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

Probab=95.75  E-value=0.0098  Score=40.36  Aligned_cols=101  Identities=15%  Similarity=0.134  Sum_probs=55.6

Q ss_pred             EEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCC
Q 027749           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGV  152 (219)
Q Consensus        73 ~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  152 (219)
                      .++.||+.+||| +-++-.+++....+  .+++++-|...-         +...  .+  . ...+..         . .
T Consensus         5 ~~i~GpMfsGKT-teLi~~~~~~~~~~--~kv~~ikp~~D~---------R~~~--~i--~-s~~g~~---------~-~   57 (139)
T d2b8ta1           5 EFITGPMFAGKT-AELIRRLHRLEYAD--VKYLVFKPKIDT---------RSIR--NI--Q-SRTGTS---------L-P   57 (139)
T ss_dssp             EEEECSTTSCHH-HHHHHHHHHHHHTT--CCEEEEEECCCG---------GGCS--SC--C-CCCCCS---------S-C
T ss_pred             EEEEccccCHHH-HHHHHHHHHHHHCC--CcEEEEEEcccc---------cccc--eE--E-cccCce---------e-e
Confidence            478899999999 55555556555443  348888886432         0111  01  0 000100         1 2


Q ss_pred             eEEEeChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHHhC
Q 027749          153 HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL  203 (219)
Q Consensus       153 ~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~  203 (219)
                      .+.+.....+...+..... ..+.++|.|||++-+.+  -...+...+...
T Consensus        58 ~~~~~~~~~~~~~~~~~~~-~~~~dvI~IDE~QFf~d--~i~~~~~~~~~~  105 (139)
T d2b8ta1          58 SVEVESAPEILNYIMSNSF-NDETKVIGIDEVQFFDD--RICEVANILAEN  105 (139)
T ss_dssp             CEEESSTHHHHHHHHSTTS-CTTCCEEEECSGGGSCT--HHHHHHHHHHHT
T ss_pred             eEEeccchhhHHHHHhhcc-ccCcCEEEechhhhcch--hHHHHHHHHHhc
Confidence            3455555666666554432 46789999999986432  233444444443

>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=95.58  E-value=0.013  Score=47.36  Aligned_cols=56  Identities=20%  Similarity=0.121  Sum_probs=41.6

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhhccCC---------CceeEEEEcCCHHHHHHHHHHHHHhc
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSS---------REVQALILSPTRELATQTEKVILAIG  125 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~---------~~~~~lil~P~~~l~~q~~~~~~~~~  125 (219)
                      ...++|.|+.|||||.+..--++..+....         ..-.+|+|+=|+.-|.++.+++.+..
T Consensus        16 ~g~~lv~A~AGsGKT~~l~~r~~~ll~~~~~~~~~~~~~~~~~IL~lTFT~kAA~Emk~RI~~~L   80 (485)
T d1w36b1          16 QGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSNI   80 (485)
T ss_dssp             SSCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEcCchHHHHHHHHHHHHHHhhCcccccccCCCCcccEeEeccHHHHHHHHHHHHHHHH
Confidence            357899999999999776665655553321         12359999999999999998886554

>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=95.51  E-value=0.098  Score=36.58  Aligned_cols=94  Identities=13%  Similarity=0.065  Sum_probs=67.8

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCCc
Q 027749          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (219)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~l  176 (219)
                      +.++||.|+++..++.+.+.+.+.    +++...++|+.+..++...+    .+..+|+|+|.      +...+++..++
T Consensus        31 g~r~lvfc~t~~~~~~l~~~L~~~----Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~------v~~~GiDip~V  100 (174)
T d1c4oa2          31 GERTLVTVLTVRMAEELTSFLVEH----GIRARYLHHELDAFKRQALIRDLRLGHYDCLVGIN------LLREGLDIPEV  100 (174)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESC------CCCTTCCCTTE
T ss_pred             CCcEEEEEcchhHHHHHHHHHHhc----CCceEEEecccchHHHHHHHHHHHCCCeEEEEeee------eeeeeccCCCC
Confidence            456999999999999988888765    78999999998877665444    24789999994      23577899999


Q ss_pred             cEEEeccchhhhcc-ccHHHHHHHHHhCC
Q 027749          177 KLLVLDESDEMLSR-GFKDQIYDVYRYLP  204 (219)
Q Consensus       177 ~~lVvDE~h~l~~~-~~~~~~~~i~~~~~  204 (219)
                      .+||+=.++...-. .....+..+=+...
T Consensus       101 ~~Vi~~~~~~~~~~~~~~~~iq~~GR~gR  129 (174)
T d1c4oa2         101 SLVAILDADKEGFLRSERSLIQTIGRAAR  129 (174)
T ss_dssp             EEEEETTTTSCSGGGSHHHHHHHHGGGTT
T ss_pred             cEEEEeccccccccchhHHHHHHhhhhhh
Confidence            99988776643211 22344555544443

>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=95.49  E-value=0.016  Score=42.13  Aligned_cols=62  Identities=15%  Similarity=0.130  Sum_probs=28.1

Q ss_pred             EEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECC
Q 027749           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGG  138 (219)
Q Consensus        73 ~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~  138 (219)
                      ++++||||+|||....=-+ .++...+. .-++|-+-+.-.+.  .+.++.+.+..++.+......
T Consensus        15 i~lvGptGvGKTTTiAKLA-~~~~~~g~-kV~lit~Dt~R~ga--~eQL~~~a~~l~v~~~~~~~~   76 (211)
T d1j8yf2          15 IMLVGVQGTGKATTAGKLA-YFYKKKGF-KVGLVGADVYRPAA--LEQLQQLGQQIGVPVYGEPGE   76 (211)
T ss_dssp             EEEECSCCC----HHHHHH-HHHHHTTC-CEEEEECCCSSHHH--HHHHHHHHHHHTCCEECCTTC
T ss_pred             EEEECCCCCCHHHHHHHHH-HHHHHCCC-ceEEEEeeccccch--hHHHHHhccccCcceeecccc
Confidence            5668999999996644322 23333332 33566665433322  233344444445665544333

>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=95.47  E-value=0.033  Score=38.87  Aligned_cols=75  Identities=11%  Similarity=0.052  Sum_probs=56.9

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCCc
Q 027749          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (219)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~l  176 (219)
                      ..++||.|+++..++.+...+...    ++.+..++|+.+..++...+    ....+|+|+|..      ..+++++..+
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            457999999999999888888765    67888888888866554433    246889999952      3567888899


Q ss_pred             cEEEeccch
Q 027749          177 KLLVLDESD  185 (219)
Q Consensus       177 ~~lVvDE~h  185 (219)
                      .+||.=+..
T Consensus       102 ~~VI~~d~p  110 (171)
T d1s2ma2         102 NVVINFDFP  110 (171)
T ss_dssp             EEEEESSCC
T ss_pred             EEEEecCCc
Confidence            988866554

>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=95.12  E-value=0.013  Score=46.44  Aligned_cols=17  Identities=29%  Similarity=0.558  Sum_probs=15.0

Q ss_pred             CcEEEEcCCCCchhHHh
Q 027749           71 RDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~   87 (219)
                      .++++.||||.|||..+
T Consensus        69 ~niLfiGPTGvGKTElA   85 (364)
T d1um8a_          69 SNILLIGPTGSGKTLMA   85 (364)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             cceeeeCCCCccHHHHH
Confidence            57999999999999655

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=95.02  E-value=0.052  Score=38.93  Aligned_cols=71  Identities=14%  Similarity=0.136  Sum_probs=53.1

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCCc
Q 027749          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (219)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~l  176 (219)
                      +.++||-++|+..++.+...+...    ++.+..++|+.+..++...+    ....+|+|+|.     + ...++++.++
T Consensus        30 ~~~~IIF~~t~~~~~~l~~~l~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd-----~-~~~GiD~p~v   99 (200)
T d1oywa3          30 GKSGIIYCNSRAKVEDTAARLQSK----GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATV-----A-FGMGINKPNV   99 (200)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECT-----T-SCTTTCCTTC
T ss_pred             CCCEEEEEeeehhhHHhhhhhccC----CceeEEecCCCcHHHHHHHHHHHhcccceEEEecc-----h-hhhccCCCCC
Confidence            456999999999999888877654    67788888888766554333    24678999995     2 3567888888


Q ss_pred             cEEEe
Q 027749          177 KLLVL  181 (219)
Q Consensus       177 ~~lVv  181 (219)
                      ++||.
T Consensus       100 ~~VI~  104 (200)
T d1oywa3         100 RFVVH  104 (200)
T ss_dssp             CEEEE
T ss_pred             CEEEE
Confidence            88773

>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=94.92  E-value=0.011  Score=40.90  Aligned_cols=29  Identities=24%  Similarity=0.414  Sum_probs=21.1

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhccCCC
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSR  100 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~  100 (219)
                      |++++.||+|+|||. .+..++..+.....
T Consensus         2 k~v~ItG~~GtGKTt-l~~~i~~~l~~~~~   30 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTT-LIHKASEVLKSSGV   30 (189)
T ss_dssp             CCEEEESCCSSCHHH-HHHHHHHHHHHTTC
T ss_pred             cEEEEECCCCCcHHH-HHHHHHHHHHHCCC
Confidence            689999999999995 44455666655443

>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=94.77  E-value=0.045  Score=38.04  Aligned_cols=73  Identities=11%  Similarity=0.121  Sum_probs=54.0

Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhc----CCCeEEEeChHHHHHHHHcCCCCCCCcc
Q 027749          102 VQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRAIK  177 (219)
Q Consensus       102 ~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~----~~~~I~v~Tp~~l~~~l~~~~~~~~~l~  177 (219)
                      .++||.|+++.-++.+.+.+.+.    ++.+..++|+.+..++...+.    ...+|+|+|..      ...++++..+.
T Consensus        28 ~k~iIF~~~~~~~~~l~~~L~~~----~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T~~------~~~Gid~~~~~   97 (168)
T d1t5ia_          28 NQVVIFVKSVQRCIALAQLLVEQ----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNL------FGRGMDIERVN   97 (168)
T ss_dssp             SSEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSC------CSTTCCGGGCS
T ss_pred             CeEEEEEeeeecchhhhhhhccc----cccccccccccchhhhhhhhhhhccccceeeecccc------ccchhhcccch
Confidence            46999999999998888877654    677888899888776654432    46889999942      24667788888


Q ss_pred             EEEeccc
Q 027749          178 LLVLDES  184 (219)
Q Consensus       178 ~lVvDE~  184 (219)
                      ++|.=+.
T Consensus        98 ~vi~~~~  104 (168)
T d1t5ia_          98 IAFNYDM  104 (168)
T ss_dssp             EEEESSC
T ss_pred             hhhhhhc
Confidence            7776554

>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=94.73  E-value=0.015  Score=44.86  Aligned_cols=18  Identities=22%  Similarity=0.542  Sum_probs=15.6

Q ss_pred             CCcEEEEcCCCCchhHHh
Q 027749           70 GRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~   87 (219)
                      .++++++||||+|||..+
T Consensus        49 ~~~iLl~GPpG~GKT~lA   66 (309)
T d1ofha_          49 PKNILMIGPTGVGKTEIA   66 (309)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            478999999999999554

>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=94.66  E-value=0.034  Score=44.40  Aligned_cols=39  Identities=18%  Similarity=0.327  Sum_probs=25.3

Q ss_pred             hHHHHHHHHHHhCCC--cEEEEcCCCCchhHHhHHHHHhhhc
Q 027749           57 SAIQQRAVMPIIKGR--DVIAQAQSGTGKTSMIALTVCQTVD   96 (219)
Q Consensus        57 ~~~Q~~~~~~~~~~~--~~lv~~~tG~GKT~~~~~~~~~~~~   96 (219)
                      .+.|...+..+....  =+++.||||||||... ..++..+.
T Consensus       143 ~~~~~~~l~~l~~~~~GliLvtGpTGSGKSTTl-~~~l~~~~  183 (401)
T d1p9ra_         143 TAHNHDNFRRLIKRPHGIILVTGPTGSGKSTTL-YAGLQELN  183 (401)
T ss_dssp             CHHHHHHHHHHHTSSSEEEEEECSTTSCHHHHH-HHHHHHHC
T ss_pred             cHHHHHHHHHHHhhhhceEEEEcCCCCCccHHH-HHHhhhhc
Confidence            455555666655443  4889999999999544 33455443

>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=94.58  E-value=0.066  Score=37.17  Aligned_cols=96  Identities=14%  Similarity=0.098  Sum_probs=64.7

Q ss_pred             EEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----c
Q 027749           74 IAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----E  149 (219)
Q Consensus        74 lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~  149 (219)
                      .+..+..-.|. .++..++...    ...++||.|+++..++.+.+.+...    ++.+..++|+.+..++...+    .
T Consensus        12 ~v~v~~~~~K~-~~L~~ll~~~----~~~k~iiF~~~~~~~~~~~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~fk~   82 (168)
T d2j0sa2          12 FVAVEREEWKF-DTLCDLYDTL----TITQAVIFCNTKRKVDWLTEKMREA----NFTVSSMHGDMPQKERESIMKEFRS   82 (168)
T ss_dssp             EEEESSTTHHH-HHHHHHHHHH----TSSEEEEECSSHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHH
T ss_pred             EEEecChHHHH-HHHHHHHHhC----CCCceEEEeeeHHHHHHHHHHhhhc----ccchhhhhhhhhHHHHHHHHHHHhc
Confidence            33334444564 3344444332    2357999999999999888877765    56777888888877664444    2


Q ss_pred             CCCeEEEeChHHHHHHHHcCCCCCCCccEEEeccc
Q 027749          150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDES  184 (219)
Q Consensus       150 ~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~  184 (219)
                      ...+|+|+|-     . ..+++++.++++||.=++
T Consensus        83 g~~~iLv~Td-----~-~~rGiDi~~v~~VIn~d~  111 (168)
T d2j0sa2          83 GASRVLISTD-----V-WARGLDVPQVSLIINYDL  111 (168)
T ss_dssp             TSSCEEEECG-----G-GSSSCCCTTEEEEEESSC
T ss_pred             CCccEEeccc-----h-hcccccccCcceEEEecC
Confidence            4679999994     2 357889999998775443

>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=94.41  E-value=0.05  Score=43.53  Aligned_cols=67  Identities=28%  Similarity=0.371  Sum_probs=46.4

Q ss_pred             CChHHHHHHHHH----HhCCCc-EEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccc
Q 027749           55 KPSAIQQRAVMP----IIKGRD-VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDF  127 (219)
Q Consensus        55 ~~~~~Q~~~~~~----~~~~~~-~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  127 (219)
                      .|+.-|-+++..    +.+|.. ..+.|.+|++|++... .++....    . .+|||+|+...|.++++.+..+...
T Consensus         8 ~p~~dqp~aI~~l~~~L~~g~~~~~L~GlsgS~ka~~~A-~l~~~~~----r-p~LvVt~~~~~A~~l~~dL~~~l~~   79 (408)
T d1c4oa1           8 SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMA-KVIEALG----R-PALVLAPNKILAAQLAAEFRELFPE   79 (408)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHH-HHHHHHT----C-CEEEEESSHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEecCCCCHHHHHHH-HHHHHhC----C-CEEEEeCCHHHHHHHHHHHHHhcCc
Confidence            555566555654    445554 6889999999993322 2222221    1 2899999999999999999988654

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=94.02  E-value=0.35  Score=34.81  Aligned_cols=50  Identities=16%  Similarity=0.236  Sum_probs=27.9

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA  123 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~  123 (219)
                      |.-++|.|++|+|||...+-. +..+...  +..++++.-.. -..++.+.+..
T Consensus        26 gsl~li~G~pGsGKT~l~~qi-a~~~~~~--~~~~~~is~e~-~~~~~~~~~~~   75 (242)
T d1tf7a2          26 DSIILATGATGTGKTLLVSRF-VENACAN--KERAILFAYEE-SRAQLLRNAYS   75 (242)
T ss_dssp             SCEEEEEECTTSSHHHHHHHH-HHHHHTT--TCCEEEEESSS-CHHHHHHHHHT
T ss_pred             CeEEEEEeCCCCCHHHHHHHH-HHHHHHh--ccccceeeccC-CHHHHHHHHHH
Confidence            457899999999999544443 3333333  23366665432 23334444433

>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=93.86  E-value=0.089  Score=38.57  Aligned_cols=26  Identities=19%  Similarity=0.245  Sum_probs=18.6

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhcc
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDT   97 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~   97 (219)
                      .++++.||+|+|||... -.+...+..
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            57999999999999443 334555543

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=93.62  E-value=0.17  Score=34.31  Aligned_cols=74  Identities=12%  Similarity=0.223  Sum_probs=52.6

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHh----cCCCeEEEeChHHHHHHHHcCCCCCCCc
Q 027749          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (219)
Q Consensus       101 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l----~~~~~I~v~Tp~~l~~~l~~~~~~~~~l  176 (219)
                      +.++||.++++.-+.++...+.+.    ++.+..+.|+.+..++...+    .....|+|+|.     .+ ..++++..+
T Consensus        28 ~~k~IIF~~s~~~~~~l~~~L~~~----g~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~-----~~-~~Gid~~~v   97 (155)
T d1hv8a2          28 EFYGLVFCKTKRDTKELASMLRDI----GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATD-----VM-SRGIDVNDL   97 (155)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECT-----TH-HHHCCCSCC
T ss_pred             CCCEEEEECchHHHHHHHhhhccc----ccccccccccchhhhhhhhhhhhhcccceeeeehh-----HH-hhhhhhccC
Confidence            346999999999999888888764    67788888887766654443    23678999994     22 245677778


Q ss_pred             cEEEeccc
Q 027749          177 KLLVLDES  184 (219)
Q Consensus       177 ~~lVvDE~  184 (219)
                      ++||.=+.
T Consensus        98 ~~Vi~~d~  105 (155)
T d1hv8a2          98 NCVINYHL  105 (155)
T ss_dssp             SEEEESSC
T ss_pred             cEEEEecC
Confidence            87775433

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=93.29  E-value=0.018  Score=46.76  Aligned_cols=18  Identities=22%  Similarity=0.542  Sum_probs=15.2

Q ss_pred             CCcEEEEcCCCCchhHHh
Q 027749           70 GRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~   87 (219)
                      .+|+|+.||||+|||+.+
T Consensus        49 ksNILliGPTGvGKTlLA   66 (443)
T d1g41a_          49 PKNILMIGPTGVGKTEIA   66 (443)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             cccEEEECCCCCCHHHHH
Confidence            358999999999999544

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.74  E-value=0.1  Score=38.18  Aligned_cols=54  Identities=11%  Similarity=0.027  Sum_probs=31.6

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCChHHH-HHHHHHH-----hCCCcEEEEcCCCCchhHHhH
Q 027749           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQ-QRAVMPI-----IKGRDVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        33 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q-~~~~~~~-----~~~~~~lv~~~tG~GKT~~~~   88 (219)
                      .+|+++-..+...+.|..+-  .-+... ...+...     ...+.+++.||.|+|||.+.-
T Consensus        11 ~~~~dlig~~~~~~~L~~~l--~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~   70 (253)
T d1sxja2          11 TNLQQVCGNKGSVMKLKNWL--ANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAH   70 (253)
T ss_dssp             SSGGGCCSCHHHHHHHHHHH--HTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHH
T ss_pred             CCHHHhcCCHHHHHHHHHHH--HhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHH
Confidence            57899888888888776531  001111 0111111     112469999999999994443

>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=92.65  E-value=0.19  Score=35.75  Aligned_cols=113  Identities=13%  Similarity=0.200  Sum_probs=59.9

Q ss_pred             CcEEEEcCCCCchhHHhHHHHHhhhccCC-----CceeEEEEcCCHHHH------HHHHHHHHHhcccc---ceeEEEEE
Q 027749           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSS-----REVQALILSPTRELA------TQTEKVILAIGDFI---NIQAHACV  136 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~~~~~~~~~~~-----~~~~~lil~P~~~l~------~q~~~~~~~~~~~~---~~~~~~~~  136 (219)
                      .|.+++|+.|.|||... --+.+++....     .+. -++-+....|+      -++.+.++.+....   .-+++++.
T Consensus        44 ~n~lLvG~pGVGKTalv-~~LA~ri~~~~vp~~L~~~-~i~~ld~~~LiAg~~~rG~~E~rl~~il~e~~~~~~~iILfI  121 (195)
T d1jbka_          44 NNPVLIGEPGVGKTAIV-EGLAQRIINGEVPEGLKGR-RVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFI  121 (195)
T ss_dssp             CEEEEECCTTSCHHHHH-HHHHHHHHHTCSCGGGTTC-EEEEECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEE
T ss_pred             CCeEEEecCCcccHHHH-HHHHHHHHhCCCCHHHcCc-eEEEeeHHHHhccCCccHHHHHHHHHHHHHHhcCCCcEEEEc
Confidence            48999999999999443 33334333221     123 45555545544      24444454333221   11233333


Q ss_pred             CC-------------cccHHHHHH-hc-CCCeEE-EeChHHHHHHHHcCCCCCCCccEEEeccch
Q 027749          137 GG-------------KSVGEDIRK-LE-HGVHVV-SGTPGRVCDMIKRKTLRTRAIKLLVLDESD  185 (219)
Q Consensus       137 ~~-------------~~~~~~~~~-l~-~~~~I~-v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h  185 (219)
                      +.             .+...-... +. .+.++| -+||+.+...+....-..+++..|-|+|-+
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            11             111111111 11 234444 577999888877665556778889999875

>d1yksa2 c.37.1.14 (A:325-623) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=92.55  E-value=0.15  Score=38.81  Aligned_cols=68  Identities=6%  Similarity=-0.066  Sum_probs=44.6

Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEE
Q 027749          102 VQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLV  180 (219)
Q Consensus       102 ~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lV  180 (219)
                      .+++|.+|+..-++++.+.+.+.    +..+..++|.....+.........+|+|+|.     .+ ..++.+ ++.+||
T Consensus        37 g~~~~F~~s~~~~~~~a~~L~~~----g~~V~~l~~~~~~~e~~~~~~~~~~~~~~t~-----~~-~~~~~~-~~~~vi  104 (299)
T d1yksa2          37 RPTAWFLPSIRAANVMAASLRKA----GKSVVVLNRKTFEREYPTIKQKKPDFILATD-----IA-EMGANL-CVERVL  104 (299)
T ss_dssp             SCEEEECSCHHHHHHHHHHHHHT----TCCEEECCSSSCC--------CCCSEEEESS-----ST-TCCTTC-CCSEEE
T ss_pred             CCEEEEeCCHHHHHHHHHHHHhc----CCeEEEEcCcCcHhHHhhhhcCCcCEEEEec-----hh-hhceec-CceEEE
Confidence            45999999999999999988765    5677888887776655444455788999994     22 344555 465554

>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=91.92  E-value=0.058  Score=36.20  Aligned_cols=20  Identities=20%  Similarity=0.366  Sum_probs=16.3

Q ss_pred             CCcEEEEcCCCCchhHHhHH
Q 027749           70 GRDVIAQAQSGTGKTSMIAL   89 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~   89 (219)
                      .+++++.||.|+|||...-.
T Consensus         2 ~k~I~l~G~~GsGKSTvak~   21 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIGRQ   21 (169)
T ss_dssp             CCCEEEECCTTSCHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHH
Confidence            46899999999999965544

>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=91.90  E-value=0.059  Score=42.94  Aligned_cols=42  Identities=19%  Similarity=0.353  Sum_probs=25.4

Q ss_pred             hCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHH
Q 027749           68 IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (219)
Q Consensus        68 ~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  112 (219)
                      ...++++|.|+||+|||... ..++..+...+  ..++|+=|..+
T Consensus        48 ~~~~H~~I~G~tGsGKT~~l-~~li~~~~~~g--~~~iiiD~kge   89 (433)
T d1e9ra_          48 AEPRHLLVNGATGTGKSVLL-RELAYTGLLRG--DRMVIVDPNGD   89 (433)
T ss_dssp             GGGGCEEEEECTTSSHHHHH-HHHHHHHHHTT--CEEEEEEETTH
T ss_pred             cccceEEEEeCCCCcHHHHH-HHHHHHHHhCC--CCEEEEeCChh
Confidence            44578999999999999654 33444333322  22444444443

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=91.74  E-value=0.053  Score=39.51  Aligned_cols=49  Identities=18%  Similarity=0.199  Sum_probs=28.3

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHhHH
Q 027749           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIAL   89 (219)
Q Consensus        33 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~~~   89 (219)
                      .+|+++--.+.+.+.|... .      + .....-....++++.||+|+|||..+-+
T Consensus         6 ~~~~divGqe~~~~~l~~~-i------~-~~~~~~~~~~~~L~~GPpGtGKT~lA~~   54 (238)
T d1in4a2           6 KSLDEFIGQENVKKKLSLA-L------E-AAKMRGEVLDHVLLAGPPGLGKTTLAHI   54 (238)
T ss_dssp             SSGGGCCSCHHHHHHHHHH-H------H-HHHHHTCCCCCEEEESSTTSSHHHHHHH
T ss_pred             CcHHHcCChHHHHHHHHHH-H------H-HHHhcCCCCCeEEEECCCCCcHHHHHHH
Confidence            4677776566666665532 0      0 0000001124799999999999965533

>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=91.40  E-value=0.33  Score=36.25  Aligned_cols=35  Identities=14%  Similarity=0.253  Sum_probs=26.0

Q ss_pred             CeEE-EeChHHHHHHHHcCCCCCCCccEEEeccchh
Q 027749          152 VHVV-SGTPGRVCDMIKRKTLRTRAIKLLVLDESDE  186 (219)
Q Consensus       152 ~~I~-v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~  186 (219)
                      .++| -+||+.+...+....-....+..|-|+|-+.
T Consensus       148 i~vIgatT~eey~~~~e~d~al~rrF~~I~V~Eps~  183 (268)
T d1r6bx2         148 IRVIGSTTYQEFSNIFEKDRALARRFQKIDITEPSI  183 (268)
T ss_dssp             CEEEEEECHHHHHCCCCCTTSSGGGEEEEECCCCCH
T ss_pred             CeEEEeCCHHHHHHHHhhcHHHHhhhcccccCCCCH
Confidence            4444 5779888877766665567889999999873

>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=91.22  E-value=0.064  Score=39.10  Aligned_cols=18  Identities=22%  Similarity=0.420  Sum_probs=15.1

Q ss_pred             CcEEEEcCCCCchhHHhH
Q 027749           71 RDVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~   88 (219)
                      .++++.||+|+|||..+-
T Consensus        36 ~~~Ll~GPpG~GKTtla~   53 (239)
T d1ixsb2          36 EHLLLFGPPGLGKTTLAH   53 (239)
T ss_dssp             CCEEEECCTTSCHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHH
Confidence            479999999999995543

>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=91.10  E-value=0.17  Score=33.85  Aligned_cols=65  Identities=18%  Similarity=0.204  Sum_probs=48.1

Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCcccHHHHHHhcCCCeEEEeChHHHHHHHHcCCCCCCCccEEE
Q 027749          102 VQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLV  180 (219)
Q Consensus       102 ~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~I~v~Tp~~l~~~l~~~~~~~~~l~~lV  180 (219)
                      .++||.|+|+.-|+++.+.+.+.    ++.+..++++.+..+.   -....+|+|+|.     .+ ..+++ .++++||
T Consensus        36 ~k~IVFc~t~~~ae~la~~L~~~----G~~~~~~H~~~~~~~~---~~~~~~vlvaTd-----~~-~~GiD-~~v~~Vi  100 (138)
T d1jr6a_          36 GRHLIFCHSKKKCDELAAKLVAL----GINAVAYYRGLDVSVI---PTNGDVVVVATD-----AL-MTGFT-GDFDSVI  100 (138)
T ss_dssp             SCEEEECSCHHHHHHHHHHHHHH----TCEEEEECTTCCSCCC---TTSSCEEEEESS-----SS-CSSSC-CCBSEEE
T ss_pred             CCEEEEeCcHHHHHHHHHHHhcc----ccchhhhhccchhhhh---hhhhcceeehhH-----HH-Hhccc-cccceEE
Confidence            35999999999999999988765    6788888888775432   234689999994     22 34566 6777764

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

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 multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=90.95  E-value=0.23  Score=36.86  Aligned_cols=40  Identities=20%  Similarity=0.203  Sum_probs=29.0

Q ss_pred             CCccEEEeccchhhhccccHHHHHHHHHhCCCCCeEEEEe
Q 027749          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCCPG  213 (219)
Q Consensus       174 ~~l~~lVvDE~h~l~~~~~~~~~~~i~~~~~~~~q~i~~S  213 (219)
                      .+-+++|+||.-.-+|..-...+...++.+.++.-+|+.|
T Consensus       171 ~~p~ililDEpts~LD~~t~~~i~~~l~~l~~~~TvI~it  210 (255)
T d2hyda1         171 NNPPILILDEATSALDLESESIIQEALDVLSKDRTTLIVA  210 (255)
T ss_dssp             HCCSEEEEESTTTTCCHHHHHHHHHHHHHHTTTSEEEEEC
T ss_pred             cCCCEEEEeCccccCCHHHHHHHHHHHHHHhcCCEEEEEe
Confidence            3456899999998888766777777777766655555554

>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=90.88  E-value=0.059  Score=36.84  Aligned_cols=19  Identities=42%  Similarity=0.693  Sum_probs=15.7

Q ss_pred             CCcEEEEcCCCCchhHHhH
Q 027749           70 GRDVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~   88 (219)
                      +.++++.||+|+|||...-
T Consensus         5 ~~~I~i~G~~GsGKTT~~~   23 (174)
T d1y63a_           5 GINILITGTPGTGKTSMAE   23 (174)
T ss_dssp             SCEEEEECSTTSSHHHHHH
T ss_pred             CCEEEEEeCCCCCHHHHHH
Confidence            4679999999999996543

>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=89.84  E-value=0.073  Score=35.57  Aligned_cols=15  Identities=20%  Similarity=0.494  Sum_probs=12.6

Q ss_pred             EEEEcCCCCchhHHh
Q 027749           73 VIAQAQSGTGKTSMI   87 (219)
Q Consensus        73 ~lv~~~tG~GKT~~~   87 (219)
                      ++++|++|+|||...
T Consensus         5 Iii~G~pGsGKTTla   19 (152)
T d1ly1a_           5 ILTIGCPGSGKSTWA   19 (152)
T ss_dssp             EEEECCTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            678999999999543

>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=89.67  E-value=0.076  Score=36.01  Aligned_cols=16  Identities=25%  Similarity=0.360  Sum_probs=13.4

Q ss_pred             cEEEEcCCCCchhHHh
Q 027749           72 DVIAQAQSGTGKTSMI   87 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~   87 (219)
                      -+++.||+|+|||..+
T Consensus         4 lI~i~G~~GsGKTTva   19 (176)
T d2bdta1           4 LYIITGPAGVGKSTTC   19 (176)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4789999999999654

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=89.64  E-value=0.085  Score=35.84  Aligned_cols=18  Identities=22%  Similarity=0.468  Sum_probs=14.6

Q ss_pred             CcEEEEcCCCCchhHHhH
Q 027749           71 RDVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~   88 (219)
                      .++++.||.|+|||...-
T Consensus         5 ~~I~i~G~pGsGKTTia~   22 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGK   22 (173)
T ss_dssp             CCEEEECSTTSSHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            468999999999995443

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=89.55  E-value=0.059  Score=37.03  Aligned_cols=17  Identities=18%  Similarity=0.407  Sum_probs=14.4

Q ss_pred             CcEEEEcCCCCchhHHh
Q 027749           71 RDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~   87 (219)
                      +.+++.||+|+|||...
T Consensus         8 K~I~i~G~~GsGKTTla   24 (192)
T d1lw7a2           8 KTVAILGGESSGKSVLV   24 (192)
T ss_dssp             EEEEEECCTTSHHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            57999999999999443

>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=89.06  E-value=0.082  Score=38.94  Aligned_cols=16  Identities=38%  Similarity=0.563  Sum_probs=13.6

Q ss_pred             cEEEEcCCCCchhHHh
Q 027749           72 DVIAQAQSGTGKTSMI   87 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~   87 (219)
                      .+++.||+|+|||..+
T Consensus        34 ~ilL~GpPGtGKT~la   49 (273)
T d1gvnb_          34 AFLLGGQPGSGKTSLR   49 (273)
T ss_dssp             EEEEECCTTSCTHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            5899999999999543

>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=89.02  E-value=0.072  Score=39.39  Aligned_cols=17  Identities=24%  Similarity=0.421  Sum_probs=14.2

Q ss_pred             CcEEEEcCCCCchhHHh
Q 027749           71 RDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~   87 (219)
                      +.+++.||+|+|||...
T Consensus        41 ~~vLL~GppGtGKT~la   57 (246)
T d1d2na_          41 VSVLLEGPPHSGKTALA   57 (246)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             eEEEEECcCCCCHHHHH
Confidence            36999999999999443

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=88.87  E-value=0.072  Score=36.40  Aligned_cols=19  Identities=21%  Similarity=0.532  Sum_probs=15.1

Q ss_pred             CCCcEEEEcCCCCchhHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~   87 (219)
                      .|+-+++.||+|+|||...
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            4556789999999999543

>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=88.55  E-value=2  Score=33.49  Aligned_cols=34  Identities=15%  Similarity=0.207  Sum_probs=24.2

Q ss_pred             Ce-EEEeChHHHHHHHHcCCCCCCCccEEEeccchh
Q 027749          152 VH-VVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDE  186 (219)
Q Consensus       152 ~~-I~v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~  186 (219)
                      .+ |.-+||+.+.. +....-..+++..|-|+|-+.
T Consensus       152 ~~~I~~tT~~ey~~-~e~d~al~rrF~~v~v~ep~~  186 (387)
T d1qvra2         152 LRLIGATTLDEYRE-IEKDPALERRFQPVYVDEPTV  186 (387)
T ss_dssp             CCEEEEECHHHHHH-HTTCTTTCSCCCCEEECCCCH
T ss_pred             cceeeecCHHHHHH-hcccHHHHHhcccccCCCCcH
Confidence            44 44677998865 555555567889999999773

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=88.45  E-value=0.12  Score=35.34  Aligned_cols=18  Identities=17%  Similarity=0.477  Sum_probs=14.9

Q ss_pred             CcEEEEcCCCCchhHHhH
Q 027749           71 RDVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~   88 (219)
                      +++++.|+.|+|||...-
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            578999999999995543

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=88.21  E-value=0.08  Score=36.14  Aligned_cols=21  Identities=14%  Similarity=0.295  Sum_probs=16.4

Q ss_pred             hCCCcEEEEcCCCCchhHHhH
Q 027749           68 IKGRDVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        68 ~~~~~~lv~~~tG~GKT~~~~   88 (219)
                      .+|.-+.+.|++|+|||...-
T Consensus         4 ~~g~~I~l~G~~GsGKTTia~   24 (183)
T d1m8pa3           4 TQGFTIFLTGYMNSGKDAIAR   24 (183)
T ss_dssp             TCCEEEEEECSTTSSHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHH
Confidence            456667899999999996653

>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=88.20  E-value=0.27  Score=32.54  Aligned_cols=37  Identities=8%  Similarity=0.170  Sum_probs=25.9

Q ss_pred             EEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHH
Q 027749           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (219)
Q Consensus        73 ~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  112 (219)
                      .++.||+.+||| +-++-.++.....+  .+++++-|...
T Consensus         5 ~li~GpMfsGKT-t~Li~~~~~~~~~g--~~v~~ikp~~D   41 (133)
T d1xbta1           5 QVILGPMFSGKS-TELMRRVRRFQIAQ--YKCLVIKYAKD   41 (133)
T ss_dssp             EEEECCTTSCHH-HHHHHHHHHHHTTT--CCEEEEEETTC
T ss_pred             EEEEecccCHHH-HHHHHHHHHHHHcC--CcEEEEecccc
Confidence            578999999999 55555566555443  34888887643

>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=87.99  E-value=0.25  Score=33.10  Aligned_cols=38  Identities=8%  Similarity=0.094  Sum_probs=26.0

Q ss_pred             cEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCCHH
Q 027749           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  112 (219)
                      =-++.||+.+||| ..++-.+++....+  .+++++-|...
T Consensus         9 l~lI~GpMfSGKT-teLi~~~~~~~~~g--~~vl~i~~~~D   46 (141)
T d1xx6a1           9 VEVIVGPMYSGKS-EELIRRIRRAKIAK--QKIQVFKPEID   46 (141)
T ss_dssp             EEEEECSTTSSHH-HHHHHHHHHHHHTT--CCEEEEEEC--
T ss_pred             EEEEEeccccHHH-HHHHHHHHHhhhcC--CcEEEEEeccc
Confidence            3578999999999 55555566555443  35889988643

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=87.33  E-value=0.72  Score=33.71  Aligned_cols=41  Identities=17%  Similarity=0.204  Sum_probs=25.3

Q ss_pred             HhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcC
Q 027749           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (219)
Q Consensus        67 ~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P  109 (219)
                      ...+..+++.|++|+||+..+  -.++........+.+.+-+.
T Consensus        20 a~~~~pvlI~Ge~GtGK~~~A--~~ih~~s~~~~~~~~~~~~~   60 (247)
T d1ny5a2          20 SCAECPVLITGESGVGKEVVA--RLIHKLSDRSKEPFVALNVA   60 (247)
T ss_dssp             TTCCSCEEEECSTTSSHHHHH--HHHHHHSTTTTSCEEEEETT
T ss_pred             hCCCCCEEEECCCCcCHHHHH--HHHHHhcCCcccccccchhh
Confidence            345678999999999999433  33444444444444444443

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=86.74  E-value=0.73  Score=33.82  Aligned_cols=42  Identities=14%  Similarity=0.124  Sum_probs=25.7

Q ss_pred             HhCCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcCC
Q 027749           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (219)
Q Consensus        67 ~~~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P~  110 (219)
                      +..|.-+++.|++|+|||...+-.+.+.+...  +.+++|+..-
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            34566789999999999944433333333333  2347777654

>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=86.72  E-value=0.17  Score=35.42  Aligned_cols=17  Identities=35%  Similarity=0.776  Sum_probs=14.4

Q ss_pred             CcEEEEcCCCCchhHHh
Q 027749           71 RDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~   87 (219)
                      +.++|+||+|+|||...
T Consensus         2 rpIvl~GpsG~GK~tl~   18 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLL   18 (186)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            57899999999999543

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=86.55  E-value=0.45  Score=37.05  Aligned_cols=43  Identities=14%  Similarity=0.145  Sum_probs=24.9

Q ss_pred             CCCCChHHHHHHHHHHhCC----CcEEEEcCCCCchhHHhHHHHHhhh
Q 027749           52 GFEKPSAIQQRAVMPIIKG----RDVIAQAQSGTGKTSMIALTVCQTV   95 (219)
Q Consensus        52 ~~~~~~~~Q~~~~~~~~~~----~~~lv~~~tG~GKT~~~~~~~~~~~   95 (219)
                      ++......-..++..++.|    +.+++.||+|+|||.. ...++..+
T Consensus       132 ~~~~~~~~i~~~l~~~~~~~~~~~~~~~~g~~~~gk~~~-~~~~~~~~  178 (362)
T d1svma_         132 LLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTL-AAALLELC  178 (362)
T ss_dssp             TSTTHHHHHHHHHHHHHHCCTTCCEEEEECSTTSSHHHH-HHHHHHHH
T ss_pred             cccchHHHHHHHHHHHHhCCCCcCeEEEECCCCCCHHHH-HHHHHHHc
Confidence            3444433333444444433    5799999999999943 33444443

>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=0.16  Score=34.42  Aligned_cols=17  Identities=24%  Similarity=0.405  Sum_probs=13.6

Q ss_pred             EEEEcCCCCchhHHhHH
Q 027749           73 VIAQAQSGTGKTSMIAL   89 (219)
Q Consensus        73 ~lv~~~tG~GKT~~~~~   89 (219)
                      +++.|+.|+|||...-.
T Consensus         9 ivl~G~~GsGKsT~a~~   25 (171)
T d1knqa_           9 YVLMGVSGSGKSAVASE   25 (171)
T ss_dssp             EEEECSTTSCHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            67899999999955443

>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=86.50  E-value=0.38  Score=34.64  Aligned_cols=24  Identities=17%  Similarity=0.101  Sum_probs=17.1

Q ss_pred             CCcEEEEcCCCCchhHHhHHHHHh
Q 027749           70 GRDVIAQAQSGTGKTSMIALTVCQ   93 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~~~~~~~   93 (219)
                      |+-++|.|++|+|||...+-.+.+
T Consensus        36 G~~~li~G~pGsGKT~~~lq~~~~   59 (254)
T d1pzna2          36 QAITEVFGEFGSGKTQLAHTLAVM   59 (254)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHH
Confidence            456899999999999544433333

>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=86.13  E-value=0.43  Score=32.35  Aligned_cols=17  Identities=24%  Similarity=0.392  Sum_probs=13.5

Q ss_pred             CcEEEEcCCCCchhHHh
Q 027749           71 RDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~   87 (219)
                      +-+++.|+.|+|||...
T Consensus         2 kiI~i~G~~GsGKsT~~   18 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSS   18 (190)
T ss_dssp             CEEEEECCTTSCHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            45789999999999433

>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=86.04  E-value=0.2  Score=33.93  Aligned_cols=18  Identities=28%  Similarity=0.505  Sum_probs=14.4

Q ss_pred             CCcEEEEcCCCCchhHHh
Q 027749           70 GRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~   87 (219)
                      .+=+++.|+.|+|||...
T Consensus         3 ~kiI~l~G~~GsGKsTva   20 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIV   20 (178)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            455788999999999554

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=85.91  E-value=0.39  Score=32.16  Aligned_cols=25  Identities=28%  Similarity=0.280  Sum_probs=18.2

Q ss_pred             EEEEcCCCCchhHHhHHHHHhhhccC
Q 027749           73 VIAQAQSGTGKTSMIALTVCQTVDTS   98 (219)
Q Consensus        73 ~lv~~~tG~GKT~~~~~~~~~~~~~~   98 (219)
                      +.|.|+.||||| ..+-.++..+..+
T Consensus         5 i~itG~~GSGKT-TL~~~L~~~l~~~   29 (170)
T d1np6a_           5 LAFAAWSGTGKT-TLLKKLIPALCAR   29 (170)
T ss_dssp             EEEECCTTSCHH-HHHHHHHHHHHHT
T ss_pred             EEEEcCCCCCHH-HHHHHHHHHHHHC
Confidence            678999999999 5555556655554

>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=85.52  E-value=0.19  Score=34.75  Aligned_cols=15  Identities=33%  Similarity=0.543  Sum_probs=12.7

Q ss_pred             cEEEEcCCCCchhHH
Q 027749           72 DVIAQAQSGTGKTSM   86 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~   86 (219)
                      =++++|++|+|||..
T Consensus        16 liil~G~pGsGKST~   30 (172)
T d1yj5a2          16 VVVAVGFPGAGKSTF   30 (172)
T ss_dssp             EEEEECCTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            378999999999954

>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=85.44  E-value=0.27  Score=33.50  Aligned_cols=23  Identities=22%  Similarity=0.538  Sum_probs=16.0

Q ss_pred             cEEEEcCCCCchhHHhHHHHHhhh
Q 027749           72 DVIAQAQSGTGKTSMIALTVCQTV   95 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~~~~~~~~   95 (219)
                      .+++.||+|+|||.. +-.++..+
T Consensus         2 ki~I~G~~G~GKSTL-l~~i~~~l   24 (178)
T d1ye8a1           2 KIIITGEPGVGKTTL-VKKIVERL   24 (178)
T ss_dssp             EEEEECCTTSSHHHH-HHHHHHHH
T ss_pred             EEEEECCCCcHHHHH-HHHHHhcC
Confidence            478999999999943 33344444

>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=85.31  E-value=0.41  Score=34.11  Aligned_cols=19  Identities=21%  Similarity=0.183  Sum_probs=15.2

Q ss_pred             CCCcEEEEcCCCCchhHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~   87 (219)
                      .|+-+++.|++|+|||...
T Consensus        33 ~G~~~li~G~pGsGKT~l~   51 (251)
T d1szpa2          33 TGSITELFGEFRTGKSQLC   51 (251)
T ss_dssp             SSSEEEEEESTTSSHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHH
Confidence            3467999999999999443

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.31  E-value=0.26  Score=34.31  Aligned_cols=25  Identities=20%  Similarity=0.112  Sum_probs=17.7

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQ   93 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~   93 (219)
                      .|.-+++.||+|+|||...+-.+.+
T Consensus        22 ~G~v~~i~G~~GsGKT~l~l~la~~   46 (242)
T d1n0wa_          22 TGSITEMFGEFRTGKTQICHTLAVT   46 (242)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHHH
Confidence            3457899999999999544443333

>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=85.10  E-value=0.2  Score=37.15  Aligned_cols=52  Identities=23%  Similarity=0.277  Sum_probs=29.9

Q ss_pred             CccccCCCCHHHHHHHHHCC--CCCChHHHHHHHHHHhCCCcEEEEcCCCCchhHHh
Q 027749           33 TSFDAMGIKDDLLRGIYQYG--FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        33 ~~~~~~~l~~~~~~~l~~~~--~~~~~~~Q~~~~~~~~~~~~~lv~~~tG~GKT~~~   87 (219)
                      -+|++..-...+.+.+.+.-  +..|..+|..-   ....+.+++.||.|+|||...
T Consensus         9 ~t~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g---~~~~~~iLL~GppGtGKT~la   62 (256)
T d1lv7a_           9 TTFADVAGCDEAKEEVAELVEYLREPSRFQKLG---GKIPKGVLMVGPPGTGKTLLA   62 (256)
T ss_dssp             CCGGGSCSCHHHHHHTHHHHHHHHCGGGC--------CCCCEEEEECCTTSCHHHHH
T ss_pred             CCHHHHhchHHHHHHHHHHHHHHHCHHHHHHcC---CCCCCeEEeeCCCCCCccHHH
Confidence            47888877777776665420  11111111110   112367999999999999543

>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=85.03  E-value=0.23  Score=34.51  Aligned_cols=20  Identities=25%  Similarity=0.410  Sum_probs=15.9

Q ss_pred             CCCcEEEEcCCCCchhHHhH
Q 027749           69 KGRDVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~   88 (219)
                      .|..+++.||+|||||...-
T Consensus         2 ~~~riil~G~pGSGKsT~a~   21 (190)
T d1ak2a1           2 KGVRAVLLGPPGAGKGTQAP   21 (190)
T ss_dssp             CCCEEEEECCTTSSHHHHHH
T ss_pred             CccEEEEECCCCCCHHHHHH
Confidence            35678899999999996543

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=84.97  E-value=0.25  Score=33.79  Aligned_cols=19  Identities=16%  Similarity=0.190  Sum_probs=15.5

Q ss_pred             CcEEEEcCCCCchhHHhHH
Q 027749           71 RDVIAQAQSGTGKTSMIAL   89 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~   89 (219)
                      +.+++.|+.|+|||...-.
T Consensus         3 ~~Iil~G~~GsGKSTia~~   21 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRE   21 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHH
Confidence            5788999999999965544

>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=84.66  E-value=0.24  Score=34.72  Aligned_cols=17  Identities=35%  Similarity=0.737  Sum_probs=14.1

Q ss_pred             CcEEEEcCCCCchhHHh
Q 027749           71 RDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~   87 (219)
                      +.+++.||+|+|||...
T Consensus         1 rpIvl~GPsGsGK~tl~   17 (190)
T d1lvga_           1 RPVVLSGPSGAGKSTLL   17 (190)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            46899999999999543

>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=84.57  E-value=0.17  Score=38.80  Aligned_cols=19  Identities=26%  Similarity=0.400  Sum_probs=15.9

Q ss_pred             CCCcEEEEcCCCCchhHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~   87 (219)
                      .++++++.|+.|+|||..+
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            4578999999999999443

>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=84.57  E-value=0.22  Score=36.87  Aligned_cols=16  Identities=38%  Similarity=0.632  Sum_probs=14.0

Q ss_pred             CcEEEEcCCCCchhHH
Q 027749           71 RDVIAQAQSGTGKTSM   86 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~   86 (219)
                      +.+++.||.|+|||..
T Consensus        39 ~giLL~GppGtGKT~l   54 (258)
T d1e32a2          39 RGILLYGPPGTGKTLI   54 (258)
T ss_dssp             CEEEEECCTTSSHHHH
T ss_pred             ceeEEecCCCCCchHH
Confidence            5799999999999943

>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=84.46  E-value=0.18  Score=37.02  Aligned_cols=15  Identities=27%  Similarity=0.366  Sum_probs=11.8

Q ss_pred             EEEEcCCCCchhHHh
Q 027749           73 VIAQAQSGTGKTSMI   87 (219)
Q Consensus        73 ~lv~~~tG~GKT~~~   87 (219)
                      ++++||+|+|||...
T Consensus        49 l~l~GppGtGKT~l~   63 (287)
T d1w5sa2          49 YGSIGRVGIGKTTLA   63 (287)
T ss_dssp             EECTTCCSSSHHHHH
T ss_pred             EEeECCCCCCHHHHH
Confidence            456799999999444

>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=84.19  E-value=0.48  Score=33.56  Aligned_cols=39  Identities=21%  Similarity=0.265  Sum_probs=23.7

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHHhhhccCCCceeEEEEcC
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~~~~~~~~~~~~~lil~P  109 (219)
                      .|.-+++.|++|+|||...+-.+.+.+.....  .++++..
T Consensus        25 ~G~~~~I~G~~G~GKT~la~~~~~~~~~~~~~--~~~~~s~   63 (242)
T d1tf7a1          25 IGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDE--PGVFVTF   63 (242)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHHCC--CEEEEES
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCC--Ccccccc
Confidence            45678999999999995443333333333222  3666654

>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=84.06  E-value=1.6  Score=32.12  Aligned_cols=98  Identities=17%  Similarity=0.204  Sum_probs=59.0

Q ss_pred             HHHhhhccCCCceeEEEEcCCHHHHHHHHHHHHHhccccceeEEEEECCccc--------HHH---HHHhc-CCCeEEEe
Q 027749           90 TVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSV--------GED---IRKLE-HGVHVVSG  157 (219)
Q Consensus        90 ~~~~~~~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~---~~~l~-~~~~I~v~  157 (219)
                      -++........+.++||.+.++..+..+.+.+.+.    ++.+..+.|....        .++   ..... +.++|+|+
T Consensus       150 ~~l~~~~~~~~~~k~iiF~~~~~~~~~~~~~L~~~----~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~vLv~  225 (286)
T d1wp9a2         150 EIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKD----GIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVA  225 (286)
T ss_dssp             HHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHT----TCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEE
T ss_pred             HHHHHHHHhCCCCcEEEEeCcHHhHHHHHHHHHHc----CCceEEeeccccccccchhchHHHHHHHHHHHcCCCcEEEE
Confidence            33443333344567999999999999888887664    4555555553222        112   12222 36789999


Q ss_pred             ChHHHHHHHHcCCCCCCCccEEEeccchhhhccccHHHHHHHHH
Q 027749          158 TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYR  201 (219)
Q Consensus       158 Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~l~~~~~~~~~~~i~~  201 (219)
                      |-     . ...++++..+++||.=+.+    ++....++++-+
T Consensus       226 T~-----~-~~~Gld~~~~~~Vi~~d~~----~~~~~~~Qr~GR  259 (286)
T d1wp9a2         226 TS-----V-GEEGLDVPEVDLVVFYEPV----PSAIRSIQRRGR  259 (286)
T ss_dssp             CG-----G-GGGGGGSTTCCEEEESSCC----HHHHHHHHHHTT
T ss_pred             cc-----c-eeccccCCCCCEEEEeCCC----CCHHHHHHHHHh
Confidence            94     2 2467889999998864443    233444554433

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=83.13  E-value=0.31  Score=34.70  Aligned_cols=19  Identities=47%  Similarity=0.684  Sum_probs=15.6

Q ss_pred             CCCcEEEEcCCCCchhHHh
Q 027749           69 KGRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~   87 (219)
                      +|+=++++||+|+||+...
T Consensus         1 ~G~livi~GPSG~GK~tl~   19 (205)
T d1s96a_           1 QGTLYIVSAPSGAGKSSLI   19 (205)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            4667899999999999544

>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=83.04  E-value=0.079  Score=38.16  Aligned_cols=82  Identities=13%  Similarity=0.121  Sum_probs=49.5

Q ss_pred             ceeEEEEcCCHHHHHH-----HHHHHHHhccc--cceeEEEEECCcccHHHH---HHh-cCCCeEEEeChHHHHHHHHcC
Q 027749          101 EVQALILSPTRELATQ-----TEKVILAIGDF--INIQAHACVGGKSVGEDI---RKL-EHGVHVVSGTPGRVCDMIKRK  169 (219)
Q Consensus       101 ~~~~lil~P~~~l~~q-----~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~---~~l-~~~~~I~v~Tp~~l~~~l~~~  169 (219)
                      +.++.||+|..+-.+.     ..+....+.+.  .++++..++|..+..+.-   ... .+..+|+|+|.     . -..
T Consensus        29 g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~~~iLVaTt-----V-iE~  102 (206)
T d1gm5a4          29 GGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTT-----V-IEV  102 (206)
T ss_dssp             SCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSS-----C-CCS
T ss_pred             CCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCCEEEEEEeh-----h-hhc
Confidence            4468899998654332     22223333322  256777788887755443   233 34699999994     2 246


Q ss_pred             CCCCCCccEEEeccchhhh
Q 027749          170 TLRTRAIKLLVLDESDEML  188 (219)
Q Consensus       170 ~~~~~~l~~lVvDE~h~l~  188 (219)
                      +++..+..++|+.++++..
T Consensus       103 GIDip~a~~iii~~a~~fg  121 (206)
T d1gm5a4         103 GIDVPRANVMVIENPERFG  121 (206)
T ss_dssp             CSCCTTCCEEEBCSCSSSC
T ss_pred             cccccCCcEEEEEccCCcc
Confidence            7899999999999998643

>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=82.86  E-value=0.52  Score=35.96  Aligned_cols=25  Identities=28%  Similarity=0.534  Sum_probs=18.4

Q ss_pred             HHHHHhCCCc--EEEEcCCCCchhHHh
Q 027749           63 AVMPIIKGRD--VIAQAQSGTGKTSMI   87 (219)
Q Consensus        63 ~~~~~~~~~~--~lv~~~tG~GKT~~~   87 (219)
                      .++.+++|.+  ++..|+||+|||...
T Consensus        67 lv~~~l~G~n~~i~aYGqtgSGKTyT~   93 (323)
T d1bg2a_          67 IVKDVLEGYNGTIFAYGQTSSGKTHTM   93 (323)
T ss_dssp             HHHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHHHcCCCcceeeecccCCCCceec
Confidence            3445678875  678899999999443

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.21  E-value=0.15  Score=35.31  Aligned_cols=19  Identities=32%  Similarity=0.321  Sum_probs=14.4

Q ss_pred             CcEEEEcCCCCchhHHhHH
Q 027749           71 RDVIAQAQSGTGKTSMIAL   89 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~   89 (219)
                      .-++++|++|+|||..+-.
T Consensus        20 ~vI~L~G~pGSGKTTiAk~   38 (195)
T d1x6va3          20 CTVWLTGLSGAGKTTVSMA   38 (195)
T ss_dssp             EEEEEESSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHH
Confidence            3466889999999965543

>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=82.19  E-value=0.35  Score=33.39  Aligned_cols=18  Identities=33%  Similarity=0.637  Sum_probs=14.9

Q ss_pred             CCcEEEEcCCCCchhHHh
Q 027749           70 GRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~   87 (219)
                      |+=+++.||.|+||+...
T Consensus         2 G~iivl~GpsG~GK~tl~   19 (182)
T d1znwa1           2 GRVVVLSGPSAVGKSTVV   19 (182)
T ss_dssp             CCEEEEECSTTSSHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            566899999999999553

>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=82.09  E-value=0.29  Score=36.33  Aligned_cols=17  Identities=29%  Similarity=0.495  Sum_probs=14.5

Q ss_pred             CCcEEEEcCCCCchhHH
Q 027749           70 GRDVIAQAQSGTGKTSM   86 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~   86 (219)
                      .+.+++.||.|+|||..
T Consensus        41 ~~giLL~Gp~GtGKT~l   57 (265)
T d1r7ra3          41 SKGVLFYGPPGCGKTLL   57 (265)
T ss_dssp             CCEEEEBCCTTSSHHHH
T ss_pred             CCeEEEECCCCCcchhH
Confidence            46799999999999943

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=81.83  E-value=0.38  Score=32.61  Aligned_cols=19  Identities=16%  Similarity=0.274  Sum_probs=14.9

Q ss_pred             CcEEEEcCCCCchhHHhHH
Q 027749           71 RDVIAQAQSGTGKTSMIAL   89 (219)
Q Consensus        71 ~~~lv~~~tG~GKT~~~~~   89 (219)
                      .++++.|++|+|||...-.
T Consensus         2 p~IvliG~~G~GKSTig~~   20 (165)
T d2iyva1           2 PKAVLVGLPGSGKSTIGRR   20 (165)
T ss_dssp             CSEEEECSTTSSHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHH
Confidence            3578899999999965443

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.71  E-value=0.37  Score=33.40  Aligned_cols=18  Identities=11%  Similarity=0.368  Sum_probs=14.8

Q ss_pred             CCcEEEEcCCCCchhHHh
Q 027749           70 GRDVIAQAQSGTGKTSMI   87 (219)
Q Consensus        70 ~~~~lv~~~tG~GKT~~~   87 (219)
                      .+-++++||+|+||+...
T Consensus         3 ~k~ivl~Gpsg~GK~tl~   20 (178)
T d1kgda_           3 RKTLVLLGAHGVGRRHIK   20 (178)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             CCcEEEECCCCCCHHHHH
Confidence            356899999999999544

>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=80.86  E-value=0.36  Score=33.15  Aligned_cols=18  Identities=22%  Similarity=0.324  Sum_probs=14.6

Q ss_pred             cEEEEcCCCCchhHHhHH
Q 027749           72 DVIAQAQSGTGKTSMIAL   89 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~~   89 (219)
                      ++++.||.|||||...-.
T Consensus         2 ~I~i~G~pGsGKsT~a~~   19 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVK   19 (181)
T ss_dssp             EEEEECCTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            578999999999965543

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.86  E-value=0.48  Score=34.03  Aligned_cols=24  Identities=21%  Similarity=0.007  Sum_probs=17.3

Q ss_pred             CCCcEEEEcCCCCchhHHhHHHHH
Q 027749           69 KGRDVIAQAQSGTGKTSMIALTVC   92 (219)
Q Consensus        69 ~~~~~lv~~~tG~GKT~~~~~~~~   92 (219)
                      .|.-++|.|++|+|||...+--+.
T Consensus        36 ~G~~~~i~G~~GsGKT~lalq~~~   59 (258)
T d1v5wa_          36 SMAITEAFGEFRTGKTQLSHTLCV   59 (258)
T ss_dssp             SSEEEEEECCTTCTHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            345689999999999955444333

>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=80.55  E-value=0.5  Score=32.21  Aligned_cols=17  Identities=18%  Similarity=0.389  Sum_probs=14.1

Q ss_pred             cEEEEcCCCCchhHHhH
Q 027749           72 DVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~   88 (219)
                      ++++.||.|||||...-
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            47899999999996553

>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=80.54  E-value=0.38  Score=33.35  Aligned_cols=17  Identities=18%  Similarity=0.327  Sum_probs=14.1

Q ss_pred             cEEEEcCCCCchhHHhH
Q 027749           72 DVIAQAQSGTGKTSMIA   88 (219)
Q Consensus        72 ~~lv~~~tG~GKT~~~~   88 (219)
                      .+++.||.|+|||...-
T Consensus         5 ~I~i~GppGsGKsT~a~   21 (189)
T d1zaka1           5 KVMISGAPASGKGTQCE   21 (189)
T ss_dssp             CEEEEESTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            58899999999995543