Citrus Sinensis ID: 029910

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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-----
Protein Sequence
MSVSFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL
Secondary Structure (PSIPRED)
ccccEEHHHHHHHHHHHHHHcccccccEEEEEccHHcHHHHHHHHHcccccEEEcccccccHHHHHHHHHHHHHcHHccccccccccccccccccccccEEEEEEccccccccccccccccccEEEEEcccccccccEEEcccccccccEEEEEEEccHHHHHHHHHHHHccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccHHHHHHHHHHHHHHcccccccEEEEEccHHHHHHHHHHHHHcccEEEEcccccccHHHHHHHHHHHHHcccHHHHHHcccccccccccccccccEEEEEEccHHHHHHccccccEEEEEEEEcccccHHHHHHHHHHHHccccEEEEEEcccHHHHHHHHHHHccccHHHccccHHHHc
Coil and Loop (DISEMBL)
MSVSFTFQETLVELLHLVVagrrpglpmivccssrdELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKvteqsgdesetgkdehkshmIVVTDAclpllssgesaiSARVLINyelptkkeTYIRRMTTCLAadgsviniVVGGEVVTLRSMEESLGLIvaevpiniseil
Flexible Loop (DISEMBL)
MSVSFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKwnqkvteqsgdesetgkdehkshMIVVTDACLPLLSSGESAISARVLINyelptkkeTYIRRMTTclaadgsviniVVGGEVVTLRSMEeslglivaevpiniseil
Low Complexity Region (SEG)
MSVSFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL
Disordered region (IsUnstruct)
****FTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKW**********************MIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINI****
Disordered Region (DISOPRED)
**VSFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE*********KDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL
Disordered Region (DISEMBL)
MSVSFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWN******************KSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL
Disordered Region (DISPRO)
***SFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE************HKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINI****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSVSFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL
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	185	2.2.26 [Sep-21-2011]
O02494	405	Eukaryotic initiation fac	yes	no	0.697	0.318	0.276	3e-10
Q10055	394	ATP-dependent RNA helicas	yes	no	0.697	0.327	0.232	2e-09
Q6C347	397	ATP-dependent RNA helicas	yes	no	0.697	0.324	0.226	4e-09
Q5A9Z6	399	ATP-dependent RNA helicas	N/A	no	0.697	0.323	0.226	5e-09
Q5U526	415	Eukaryotic initiation fac	N/A	no	0.697	0.310	0.232	5e-09
Q4WEB4	398	ATP-dependent RNA helicas	yes	no	0.697	0.324	0.238	5e-09
A1C595	399	ATP-dependent RNA helicas	N/A	no	0.697	0.323	0.238	6e-09
A1D071	399	ATP-dependent RNA helicas	N/A	no	0.697	0.323	0.238	6e-09
Q5AUL4	399	ATP-dependent RNA helicas	yes	no	0.697	0.323	0.238	6e-09
Q2UAK1	398	ATP-dependent RNA helicas	yes	no	0.697	0.324	0.238	6e-09

>sp|O02494|IF4A_CRYPV Eukaryotic initiation factor 4A OS=Cryptosporidium parvum GN=EIF4-A PE=2 SV=1

 Score = 64.7 bits (156), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 44/159 (27%), Positives = 75/159 (47%), Gaps = 30/159 (18%)

Query: 29  IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 88
           I+ C++R  +D +   +    D + SS+H D+ + +R +I+ +FR             SG
Sbjct: 274 IIYCNTRRRVDQLTKQMRE-RDFTCSSMHGDMDQKDREVIMRQFR-------------SG 319

Query: 89  DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRM--TTCLA 146
                      S +++ TD    LL+ G       ++INY+LP   ETYI R+  +    
Sbjct: 320 ----------SSRVLITTD----LLARGIDVQQVSLVINYDLPVSPETYIHRIGRSGRFG 365

Query: 147 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
             G  IN V   ++V LR +E      + E+P+ I++IL
Sbjct: 366 KKGVSINFVTDDDIVCLRDIERHYNTQIEEMPMGITDIL 404

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.
Cryptosporidium parvum (taxid: 5807)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q10055|FAL1_SCHPO ATP-dependent RNA helicase fal1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=tif412 PE=1 SV=1

 Score = 62.0 bits (149), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 37/159 (23%), Positives = 75/159 (47%), Gaps = 30/159 (18%)

Query: 29  IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 88
           ++ C+SR ++D +   +   A+ + +S+H ++ + ER  I+++FR               
Sbjct: 264 VIFCNSRRKVDWLTEKMRE-ANFTVTSMHGEMPQKERDAIMQDFR--------------- 307

Query: 89  DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LA 146
                   +  S +++ TD    + + G       ++INY+LP  +E YI R+       
Sbjct: 308 --------QGNSRVLICTD----IWARGIDVQQVSLVINYDLPANRENYIHRIGRSGRFG 355

Query: 147 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
             G  IN V   +V  LR +E+    ++ E+P+NI +++
Sbjct: 356 RKGVAINFVTNEDVRILRDIEQYYSTVIDEMPMNIGDMV 394

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.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q6C347|FAL1_YARLI ATP-dependent RNA helicase FAL1 OS=Yarrowia lipolytica (strain CLIB 122 / E 150) GN=FAL1 PE=3 SV=1

 Score = 60.8 bits (146), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 36/159 (22%), Positives = 76/159 (47%), Gaps = 30/159 (18%)

Query: 29  IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 88
           ++ C+++ ++D +   + +  + +  S+H D+A+ +R  I+ EFR             SG
Sbjct: 267 VIFCNTKKKVDWLTQQMKD-NNFTVCSMHGDMAQKDRDSIMNEFR-------------SG 312

Query: 89  DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LA 146
                     +S +++ TD    + + G       ++INY+LP  +E YI R+       
Sbjct: 313 ----------RSRVLISTD----VWARGIDVQQVSLVINYDLPPNRENYIHRIGRSGRFG 358

Query: 147 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
             G  IN     ++ TLR +E+     + E+P+N+++++
Sbjct: 359 RKGVAINFATNDDITTLRDIEQYYSTQIDEMPVNVTDMM 397

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.

Yarrowia lipolytica (strain CLIB 122 / E 150) (taxid: 284591)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5A9Z6|FAL1_CANAL ATP-dependent RNA helicase FAL1 OS=Candida albicans (strain SC5314 / ATCC MYA-2876) GN=FAL1 PE=3 SV=1

 Score = 60.8 bits (146), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 36/159 (22%), Positives = 76/159 (47%), Gaps = 30/159 (18%)

Query: 29  IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 88
           ++ C+++ +++ +   +    + +  ++H D+ + ER  I+ +FR               
Sbjct: 269 VIFCNTKLKVNWLADQMKK-QNFTVVAMHGDMKQDERDSIMNDFRRG------------- 314

Query: 89  DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRM--TTCLA 146
                      S +++ TD    + + G       ++INY+LPT KE YI R+  +    
Sbjct: 315 ----------NSRVLISTD----VWARGIDVQQVSLVINYDLPTDKENYIHRIGRSGRFG 360

Query: 147 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
             G+ IN++   +VVTL+  E+     + E+P+NI++I+
Sbjct: 361 RKGTAINLITKDDVVTLKEFEKYYSTKIKEMPMNINDIM 399

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.

Candida albicans (strain SC5314 / ATCC MYA-2876) (taxid: 237561)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5U526|I4A3A_XENLA Eukaryotic initiation factor 4A-III-A OS=Xenopus laevis GN=eif4a3-a PE=2 SV=1

 Score = 60.8 bits (146), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 37/159 (23%), Positives = 75/159 (47%), Gaps = 30/159 (18%)

Query: 29  IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 88
           ++ C+++ ++D +   +   A+ + SS+H D+ + ER  I++EFR  A            
Sbjct: 285 VIFCNTKRKVDWLTEKMRE-ANFTVSSMHGDMPQKERESIMKEFRSGA------------ 331

Query: 89  DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LA 146
                      S +++ TD    + + G       ++INY+LP  +E YI R+       
Sbjct: 332 -----------SRVLISTD----VWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYG 376

Query: 147 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
             G  IN V   ++  LR +E+     + E+P+N+++++
Sbjct: 377 GKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI 415

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. When overexpressed, induces epidermis in dissociated cells that would otherwise adopt a neural fate, a process that requires an active BMP signaling pathway. Binds spliced mRNA in sequence-independent manner, 20-24 nucleotides upstream of mRNA exon-exon junctions.

Xenopus laevis (taxid: 8355)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q4WEB4|FAL1_ASPFU ATP-dependent RNA helicase fal1 OS=Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) GN=fal1 PE=3 SV=2

 Score = 60.8 bits (146), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 38/159 (23%), Positives = 75/159 (47%), Gaps = 30/159 (18%)

Query: 29  IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 88
           ++ C++R ++D +   +   A+ + SS+H ++ + ER  I+++FR               
Sbjct: 267 VIFCNTRRKVDWLTDKMRE-ANFTVSSMHGEMPQKERDSIMQDFR--------------- 310

Query: 89  DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LA 146
                   +  S +++ TD    + + G       ++INY+LPT +E YI R+       
Sbjct: 311 --------QGNSRVLISTD----VWARGIDVQQVSLVINYDLPTNRENYIHRIGRSGRFG 358

Query: 147 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
             G  IN V   +V  LR +E      + E+P+N++++L
Sbjct: 359 RKGVAINFVTSDDVRILRDIELYYSTQIDEMPMNVADLL 397

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.

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

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A1C595|FAL1_ASPCL ATP-dependent RNA helicase fal1 OS=Aspergillus clavatus (strain ATCC 1007 / CBS 513.65 / DSM 816 / NCTC 3887 / NRRL 1) GN=fal1 PE=3 SV=1

 Score = 60.5 bits (145), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 38/159 (23%), Positives = 75/159 (47%), Gaps = 30/159 (18%)

Query: 29  IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 88
           ++ C++R ++D +   +   A+ + SS+H ++ + ER  I+++FR               
Sbjct: 268 VIFCNTRRKVDWLTDKMRE-ANFTVSSMHGEMPQKERDSIMQDFR--------------- 311

Query: 89  DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LA 146
                   +  S +++ TD    + + G       ++INY+LPT +E YI R+       
Sbjct: 312 --------QGNSRVLISTD----VWARGIDVQQVSLVINYDLPTNRENYIHRIGRSGRFG 359

Query: 147 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
             G  IN V   +V  LR +E      + E+P+N++++L
Sbjct: 360 RKGVAINFVTSDDVRILRDIELYYSTQIDEMPMNVADLL 398

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.

Aspergillus clavatus (strain ATCC 1007 / CBS 513.65 / DSM 816 / NCTC 3887 / NRRL 1) (taxid: 344612)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A1D071|FAL1_NEOFI ATP-dependent RNA helicase fal1 OS=Neosartorya fischeri (strain ATCC 1020 / DSM 3700 / FGSC A1164 / NRRL 181) GN=fal1 PE=3 SV=1

 Score = 60.5 bits (145), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 38/159 (23%), Positives = 76/159 (47%), Gaps = 30/159 (18%)

Query: 29  IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 88
           ++ C++R ++D +   +   A+ + SS+H ++ + ER  I+++FR               
Sbjct: 268 VIFCNTRRKVDWLTDKMRE-ANFTVSSMHGEMPQKERDSIMQDFR--------------- 311

Query: 89  DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRM--TTCLA 146
                   +  S +++ TD    + + G       ++INY+LPT +E YI R+  +    
Sbjct: 312 --------QGNSRVLISTD----VWARGIDVQQVSLVINYDLPTNRENYIHRIGRSGRFG 359

Query: 147 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
             G  IN V   +V  LR +E      + E+P+N++++L
Sbjct: 360 RKGVAINFVTSDDVRILRDIELYYSTQIDEMPMNVADLL 398

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.

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

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5AUL4|FAL1_EMENI ATP-dependent RNA helicase fal1 OS=Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) GN=fal1 PE=3 SV=1

 Score = 60.5 bits (145), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 38/159 (23%), Positives = 76/159 (47%), Gaps = 30/159 (18%)

Query: 29  IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 88
           ++ C++R ++D +   +   A+ + SS+H ++ + ER  I+++FR               
Sbjct: 268 VIFCNTRRKVDWLTDKMRE-ANFTVSSMHGEMPQKERDSIMQDFR--------------- 311

Query: 89  DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRM--TTCLA 146
                   +  S +++ TD    + + G       ++INY+LPT +E YI R+  +    
Sbjct: 312 --------QGNSRVLISTD----VWARGIDVQQVSLVINYDLPTNRENYIHRIGRSGRFG 359

Query: 147 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
             G  IN V   +V  LR +E      + E+P+N++++L
Sbjct: 360 RKGVAINFVTSDDVRILRDIELYYSTQIDEMPMNVADLL 398

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.

Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (taxid: 227321)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q2UAK1|FAL1_ASPOR ATP-dependent RNA helicase fal1 OS=Aspergillus oryzae (strain ATCC 42149 / RIB 40) GN=fal1 PE=3 SV=1

 Score = 60.5 bits (145), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 38/159 (23%), Positives = 76/159 (47%), Gaps = 30/159 (18%)

Query: 29  IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 88
           ++ C++R ++D +   +   A+ + SS+H ++ + ER  I+++FR               
Sbjct: 267 VIFCNTRRKVDWLTDKMRE-ANFTVSSMHGEMPQKERDSIMQDFR--------------- 310

Query: 89  DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRM--TTCLA 146
                   +  S +++ TD    + + G       ++INY+LPT +E YI R+  +    
Sbjct: 311 --------QGNSRVLISTD----VWARGIDVQQVSLVINYDLPTNRENYIHRIGRSGRFG 358

Query: 147 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
             G  IN V   +V  LR +E      + E+P+N++++L
Sbjct: 359 RKGVAINFVTSDDVRILRDIELYYSTQIDEMPMNVADLL 397

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.

Aspergillus oryzae (strain ATCC 42149 / RIB 40) (taxid: 510516)

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	185
255565156	207	conserved hypothetical protein [Ricinus	0.940	0.840	0.751	2e-69
225438690	210	PREDICTED: eukaryotic initiation factor	0.940	0.828	0.728	4e-65
449448328	211	PREDICTED: ATP-dependent RNA helicase eI	0.945	0.829	0.711	5e-65
449448326	233	PREDICTED: ATP-dependent RNA helicase eI	0.945	0.751	0.694	7e-64
449448332	208	PREDICTED: ATP-dependent RNA helicase eI	0.918	0.817	0.703	1e-62
18419954	212	uncharacterized protein [Arabidopsis tha	0.945	0.825	0.661	2e-55
224094352	231	predicted protein [Populus trichocarpa]	0.924	0.740	0.614	4e-55
4006874	225	putative protein [Arabidopsis thaliana]	0.924	0.76	0.647	1e-53
334187233	258	uncharacterized protein [Arabidopsis tha	0.924	0.662	0.647	2e-53
297798174	212	hypothetical protein ARALYDRAFT_912642 [	0.945	0.825	0.65	2e-53

>gi|255565156|ref|XP_002523570.1| conserved hypothetical protein [Ricinus communis] gi|223537132|gb|EEF38765.1| conserved hypothetical protein [Ricinus communis]

 Score =  266 bits (681), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 133/177 (75%), Positives = 152/177 (85%), Gaps = 3/177 (1%)

Query: 9   ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI 68
           ETLVELL   VAGRR GLPM+VCCSSRDELDAVCS VSNL  ISF+SL+SDLAE ERT +
Sbjct: 34  ETLVELLG--VAGRRSGLPMVVCCSSRDELDAVCSVVSNLPYISFASLYSDLAEAERTSV 91

Query: 69  LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINY 128
           LE+FR   M+WNQ +T QSG++ E  K E KSHMIVVTD CLPLL+SGES ISARVLINY
Sbjct: 92  LEKFRQVTMRWNQNITAQSGNKDEIEK-EDKSHMIVVTDTCLPLLASGESPISARVLINY 150

Query: 129 ELPTKKETYIRRMTTCLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
           ELPTKKETY RRM++CLAADG VIN+VVGGEVVTL+++EES  L++AE+PINISEIL
Sbjct: 151 ELPTKKETYARRMSSCLAADGIVINMVVGGEVVTLKNIEESSSLVIAEMPINISEIL 207

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225438690|ref|XP_002277554.1| PREDICTED: eukaryotic initiation factor 4A [Vitis vinifera] gi|296082429|emb|CBI21434.3| unnamed protein product [Vitis vinifera]

 Score =  252 bits (644), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 129/177 (72%), Positives = 146/177 (82%), Gaps = 3/177 (1%)

Query: 9   ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI 68
           ETLV+LL L  A  RP LP+ VCCSSRDELDAVCSAVSNL  IS +SL+SDLAE ER LI
Sbjct: 37  ETLVDLLEL--ASHRPCLPIAVCCSSRDELDAVCSAVSNLPFISLASLYSDLAEAERALI 94

Query: 69  LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINY 128
           LE FR   M++ Q V  QSG++ E  K E KSHM+VVTDACLP L+SGES+ISARVLINY
Sbjct: 95  LENFRQATMRY-QNVIAQSGEDKEIKKGEDKSHMVVVTDACLPFLASGESSISARVLINY 153

Query: 129 ELPTKKETYIRRMTTCLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
           ELPTKKETY+RRM TCL ADG VIN+VVGGEVVTL+SMEES GL VAE+P++ISEIL
Sbjct: 154 ELPTKKETYMRRMATCLGADGIVINMVVGGEVVTLKSMEESSGLTVAEMPMHISEIL 210

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449448328|ref|XP_004141918.1| PREDICTED: ATP-dependent RNA helicase eIF4A-like isoform 2 [Cucumis sativus] gi|449448330|ref|XP_004141919.1| PREDICTED: ATP-dependent RNA helicase eIF4A-like isoform 3 [Cucumis sativus] gi|449530829|ref|XP_004172394.1| PREDICTED: ATP-dependent RNA helicase eIF4A-like isoform 2 [Cucumis sativus]

 Score =  252 bits (644), Expect = 5e-65,   Method: Compositional matrix adjust.
 Identities = 126/177 (71%), Positives = 150/177 (84%), Gaps = 2/177 (1%)

Query: 9   ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI 68
           ETLV LL   VAGRRP LPM+VCCSSRDELD+VCSAVSNL  IS +SL+SDLAE +R+LI
Sbjct: 37  ETLVGLLD--VAGRRPSLPMVVCCSSRDELDSVCSAVSNLHYISLASLYSDLAEADRSLI 94

Query: 69  LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINY 128
           LE+FR T  +W+QK +  S ++ E  K   KSHMIVVTDACLPLL+SGES +SA VLINY
Sbjct: 95  LEKFRQTTSRWSQKFSSLSEEKCEAEKVGEKSHMIVVTDACLPLLASGESPLSAHVLINY 154

Query: 129 ELPTKKETYIRRMTTCLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
           E+PTKKETY+RRMTTC A+DG +IN+VVGGEVVTL+S+EES GL++AE+PINISEIL
Sbjct: 155 EIPTKKETYMRRMTTCSASDGILINMVVGGEVVTLKSIEESSGLVIAEMPINISEIL 211

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449448326|ref|XP_004141917.1| PREDICTED: ATP-dependent RNA helicase eIF4A-like isoform 1 [Cucumis sativus] gi|449530827|ref|XP_004172393.1| PREDICTED: ATP-dependent RNA helicase eIF4A-like isoform 1 [Cucumis sativus]

 Score =  248 bits (633), Expect = 7e-64,   Method: Compositional matrix adjust.
 Identities = 123/177 (69%), Positives = 149/177 (84%), Gaps = 2/177 (1%)

Query: 9   ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI 68
           ETLV LL   VAGRRP LPM+VCCSSRDELD+VCSAVSNL  IS +SL+SDLAE +R+LI
Sbjct: 37  ETLVGLLD--VAGRRPSLPMVVCCSSRDELDSVCSAVSNLHYISLASLYSDLAEADRSLI 94

Query: 69  LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINY 128
           LE+FR T  +W+QK +  S ++ E  K   KSHMIVVTDACLPLL+SGES +SA VLINY
Sbjct: 95  LEKFRQTTSRWSQKFSSLSEEKCEAEKVGEKSHMIVVTDACLPLLASGESPLSAHVLINY 154

Query: 129 ELPTKKETYIRRMTTCLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
           E+PTKKETY+RRMTTC A+DG +IN+VVGGEVVTL+S+EES GL++AE+PIN+S +L
Sbjct: 155 EIPTKKETYMRRMTTCSASDGILINMVVGGEVVTLKSIEESSGLVIAEMPINVSILL 211

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449448332|ref|XP_004141920.1| PREDICTED: ATP-dependent RNA helicase eIF4A-like isoform 4 [Cucumis sativus] gi|449530831|ref|XP_004172395.1| PREDICTED: ATP-dependent RNA helicase eIF4A-like isoform 3 [Cucumis sativus]

 Score =  244 bits (623), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 121/172 (70%), Positives = 145/172 (84%), Gaps = 2/172 (1%)

Query: 9   ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI 68
           ETLV LL   VAGRRP LPM+VCCSSRDELD+VCSAVSNL  IS +SL+SDLAE +R+LI
Sbjct: 37  ETLVGLLD--VAGRRPSLPMVVCCSSRDELDSVCSAVSNLHYISLASLYSDLAEADRSLI 94

Query: 69  LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINY 128
           LE+FR T  +W+QK +  S ++ E  K   KSHMIVVTDACLPLL+SGES +SA VLINY
Sbjct: 95  LEKFRQTTSRWSQKFSSLSEEKCEAEKVGEKSHMIVVTDACLPLLASGESPLSAHVLINY 154

Query: 129 ELPTKKETYIRRMTTCLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPIN 180
           E+PTKKETY+RRMTTC A+DG +IN+VVGGEVVTL+S+EES GL++AE+PIN
Sbjct: 155 EIPTKKETYMRRMTTCSASDGILINMVVGGEVVTLKSIEESSGLVIAEMPIN 206

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18419954|ref|NP_568013.1| uncharacterized protein [Arabidopsis thaliana] gi|11762152|gb|AAG40354.1|AF325002_1 AT4g37020 [Arabidopsis thaliana] gi|110736928|dbj|BAF00421.1| hypothetical protein [Arabidopsis thaliana] gi|332661336|gb|AEE86736.1| uncharacterized protein [Arabidopsis thaliana]

 Score =  220 bits (561), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 119/180 (66%), Positives = 150/180 (83%), Gaps = 5/180 (2%)

Query: 9   ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI 68
           ET+VELL   V GRRP LP++VCCSSRDELDAVCS++S L  IS ++L+SDLA+ ER ++
Sbjct: 35  ETVVELLG--VLGRRPWLPIVVCCSSRDELDAVCSSLSTLPYISLAALYSDLADRERAMV 92

Query: 69  LEEFRHTAMKWNQK---VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVL 125
           +E+FR   + WNQ+   V E+  +ESE GK+E  SH++VVTD CLPLLSSGES++SARVL
Sbjct: 93  IEKFRQATINWNQQLNSVVEEGLEESENGKEEKTSHLVVVTDVCLPLLSSGESSLSARVL 152

Query: 126 INYELPTKKETYIRRMTTCLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
           INYELPTKKETY RR+TTCLA+ G VIN+VVGGEV TL+S+EES G+++AE+PINISEIL
Sbjct: 153 INYELPTKKETYTRRITTCLASGGIVINMVVGGEVTTLKSLEESSGILIAEMPINISEIL 212

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224094352|ref|XP_002310146.1| predicted protein [Populus trichocarpa] gi|222853049|gb|EEE90596.1| predicted protein [Populus trichocarpa]

 Score =  219 bits (558), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 115/187 (61%), Positives = 144/187 (77%), Gaps = 16/187 (8%)

Query: 9   ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI 68
           +TLV LL   VA RRP LP++VCC+SRD+LDAVCSAVSNL  IS +SL+SDLAE++R +I
Sbjct: 30  DTLVHLLG--VAARRPALPIVVCCTSRDQLDAVCSAVSNLPFISLASLYSDLAESDRNVI 87

Query: 69  LEEFRHTAMKWNQKVT----EQSGDESETG---------KDEHKSHMIVVTDACLPLLSS 115
           LEEFR   ++W+Q V        G   ETG          ++ KSHMIVVTDACLPLL+ 
Sbjct: 88  LEEFRKATVRWSQIVNAGQSAGGGSGGETGNNNDESNTNNNKTKSHMIVVTDACLPLLAL 147

Query: 116 GESAISARVLINYELPTKKETYIRRMTTCLAADGSVINIVVGGEVVTLRSMEESLGLIVA 175
           GE+ +SARVLINYELP+ KETY+RRM TCLAADG VIN+VVGGEV+TL+++EES  L++A
Sbjct: 148 GEAPVSARVLINYELPS-KETYLRRMATCLAADGIVINVVVGGEVITLKNIEESSSLVIA 206

Query: 176 EVPINIS 182
           E+PIN+S
Sbjct: 207 EMPINVS 213

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|4006874|emb|CAB16792.1| putative protein [Arabidopsis thaliana] gi|7270651|emb|CAB80368.1| putative protein [Arabidopsis thaliana]

 Score =  214 bits (545), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 114/176 (64%), Positives = 146/176 (82%), Gaps = 5/176 (2%)

Query: 9   ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI 68
           ET+VELL   V GRRP LP++VCCSSRDELDAVCS++S L  IS ++L+SDLA+ ER ++
Sbjct: 2   ETVVELLG--VLGRRPWLPIVVCCSSRDELDAVCSSLSTLPYISLAALYSDLADRERAMV 59

Query: 69  LEEFRHTAMKWNQK---VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVL 125
           +E+FR   + WNQ+   V E+  +ESE GK+E  SH++VVTD CLPLLSSGES++SARVL
Sbjct: 60  IEKFRQATINWNQQLNSVVEEGLEESENGKEEKTSHLVVVTDVCLPLLSSGESSLSARVL 119

Query: 126 INYELPTKKETYIRRMTTCLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINI 181
           INYELPTKKETY RR+TTCLA+ G VIN+VVGGEV TL+S+EES G+++AE+PIN+
Sbjct: 120 INYELPTKKETYTRRITTCLASGGIVINMVVGGEVTTLKSLEESSGILIAEMPINV 175

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334187233|ref|NP_001190941.1| uncharacterized protein [Arabidopsis thaliana] gi|332661337|gb|AEE86737.1| uncharacterized protein [Arabidopsis thaliana]

 Score =  214 bits (544), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 114/176 (64%), Positives = 146/176 (82%), Gaps = 5/176 (2%)

Query: 9   ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI 68
           ET+VELL   V GRRP LP++VCCSSRDELDAVCS++S L  IS ++L+SDLA+ ER ++
Sbjct: 35  ETVVELLG--VLGRRPWLPIVVCCSSRDELDAVCSSLSTLPYISLAALYSDLADRERAMV 92

Query: 69  LEEFRHTAMKWNQK---VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVL 125
           +E+FR   + WNQ+   V E+  +ESE GK+E  SH++VVTD CLPLLSSGES++SARVL
Sbjct: 93  IEKFRQATINWNQQLNSVVEEGLEESENGKEEKTSHLVVVTDVCLPLLSSGESSLSARVL 152

Query: 126 INYELPTKKETYIRRMTTCLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINI 181
           INYELPTKKETY RR+TTCLA+ G VIN+VVGGEV TL+S+EES G+++AE+PIN+
Sbjct: 153 INYELPTKKETYTRRITTCLASGGIVINMVVGGEVTTLKSLEESSGILIAEMPINV 208

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297798174|ref|XP_002866971.1| hypothetical protein ARALYDRAFT_912642 [Arabidopsis lyrata subsp. lyrata] gi|297312807|gb|EFH43230.1| hypothetical protein ARALYDRAFT_912642 [Arabidopsis lyrata subsp. lyrata]

 Score =  214 bits (544), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 117/180 (65%), Positives = 149/180 (82%), Gaps = 5/180 (2%)

Query: 9   ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI 68
           ET+VELL   V GRRP LP++VCCSSRDELDAVCS++S L  IS ++L+SDLA+ ERT++
Sbjct: 35  ETVVELLG--VLGRRPWLPIVVCCSSRDELDAVCSSLSTLPYISLAALYSDLADRERTMV 92

Query: 69  LEEFRHTAMKWNQKVTEQSGDESE---TGKDEHKSHMIVVTDACLPLLSSGESAISARVL 125
           +E+FR   + WNQ++     +  E   T K+E+KSH++VVTD CLPLLSSGES++SARVL
Sbjct: 93  IEKFRQATINWNQQLNSVVEEVLEESETRKEENKSHLVVVTDVCLPLLSSGESSLSARVL 152

Query: 126 INYELPTKKETYIRRMTTCLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
           INYELPTKKETY RR+TTCLA+ G +IN+VVGGEV TL+S+EES G+I+AE+PINISEIL
Sbjct: 153 INYELPTKKETYTRRITTCLASGGIIINMVVGGEVTTLKSLEESSGIIIAEMPINISEIL 212

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	185
UNIPROTKB|A4QVP2	396	TIF1 "ATP-dependent RNA helica	0.443	0.207	0.284	3e-08
ZFIN|ZDB-GENE-031030-2	406	eif4a1a "eukaryotic translatio	0.443	0.201	0.306	4.2e-08
ASPGD|ASPL0000037981	398	AN2932 [Emericella nidulans (t	0.443	0.206	0.284	5e-08
ZFIN|ZDB-GENE-040120-6	429	eif4a1b "eukaryotic translatio	0.443	0.191	0.318	5.9e-08
UNIPROTKB|I3LLD5	401	I3LLD5 "Uncharacterized protei	0.443	0.204	0.306	1.4e-07
UNIPROTKB|Q3SZ54	406	EIF4A1 "Eukaryotic initiation	0.443	0.201	0.306	1.5e-07
UNIPROTKB|F1P895	406	EIF4A1 "Uncharacterized protei	0.443	0.201	0.306	1.5e-07
UNIPROTKB|J9NY67	406	EIF4A1 "Uncharacterized protei	0.443	0.201	0.306	1.5e-07
UNIPROTKB|P60842	406	EIF4A1 "Eukaryotic initiation	0.443	0.201	0.306	1.5e-07
UNIPROTKB|A6M928	406	EIF4A1 "Uncharacterized protei	0.443	0.201	0.306	1.5e-07

UNIPROTKB|A4QVP2 TIF1 "ATP-dependent RNA helicase eIF4A" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 109 (43.4 bits), Expect = 3.0e-08, Sum P(2) = 3.0e-08
 Identities = 25/88 (28%), Positives = 46/88 (52%)

Query:   100 SHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVG 157
             S +++ TD    LL+ G       ++INY+LP  +E YI R+         G  IN V  
Sbjct:   313 SRVLIATD----LLARGIDVQQVSLVINYDLPANRENYIHRIGRGGRFGRKGVAINFVTA 368

Query:   158 GEVVTLRSMEESLGLIVAEVPINISEIL 185
              +V  +R +E+     + E+P+N+++++
Sbjct:   369 DDVRMMREIEQFYSTQIEEMPMNVADLI 396

GO:0005575 "cellular_component" evidence=ND

GO:0043581 "mycelium development" evidence=IEP

ZFIN|ZDB-GENE-031030-2 eif4a1a "eukaryotic translation initiation factor 4A, isoform 1A" [Danio rerio (taxid:7955)]

 Score = 114 (45.2 bits), Expect = 4.2e-08, Sum P(2) = 4.2e-08
 Identities = 27/88 (30%), Positives = 47/88 (53%)

Query:   100 SHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVG 157
             S +++ TD    LL+ G       ++INY+LPT +E YI R+         G  IN++  
Sbjct:   323 SRVLITTD----LLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMITE 378

Query:   158 GEVVTLRSMEESLGLIVAEVPINISEIL 185
              +  TLR +E      V E+P+N+++++
Sbjct:   379 DDKRTLRDIETFYNTTVEEMPMNVADLI 406

GO:0004386 "helicase activity" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

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

GO:0006413 "translational initiation" evidence=IEA

ASPGD|ASPL0000037981 AN2932 [Emericella nidulans (taxid:162425)]

 Score = 109 (43.4 bits), Expect = 5.0e-08, Sum P(2) = 5.0e-08
 Identities = 25/88 (28%), Positives = 46/88 (52%)

Query:   100 SHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVG 157
             S +++ TD    LL+ G       ++INY+LP  +E YI R+         G  IN V  
Sbjct:   315 SRVLIATD----LLARGIDVQQVSLVINYDLPANRENYIHRIGRGGRFGRKGVAINFVTA 370

Query:   158 GEVVTLRSMEESLGLIVAEVPINISEIL 185
              +V  +R +E+     + E+P+N+++++
Sbjct:   371 DDVRMMREIEQFYSTQIEEMPMNVADLI 398

GO:0008150 "biological_process" evidence=ND

GO:0005829 "cytosol" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

ZFIN|ZDB-GENE-040120-6 eif4a1b "eukaryotic translation initiation factor 4A, isoform 1B" [Danio rerio (taxid:7955)]

 Score = 115 (45.5 bits), Expect = 5.9e-08, Sum P(2) = 5.9e-08
 Identities = 28/88 (31%), Positives = 47/88 (53%)

Query:   100 SHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVG 157
             S +++ TD    LL+ G       ++INY+LPT +E YI R+         G  IN+V  
Sbjct:   346 SRVLITTD----LLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTE 401

Query:   158 GEVVTLRSMEESLGLIVAEVPINISEIL 185
              +  TLR +E      V E+P+N+++++
Sbjct:   402 DDKRTLRDIETFYNTTVEEMPMNVADLI 429

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

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

GO:0006413 "translational initiation" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|I3LLD5 I3LLD5 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 113 (44.8 bits), Expect = 1.4e-07, Sum P(2) = 1.4e-07
 Identities = 27/88 (30%), Positives = 47/88 (53%)

Query:   100 SHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVG 157
             S +++ TD    LL+ G       ++INY+LPT +E YI R+         G  IN+V  
Sbjct:   318 SRVLITTD----LLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTE 373

Query:   158 GEVVTLRSMEESLGLIVAEVPINISEIL 185
              +  TLR +E      + E+P+N+++++
Sbjct:   374 EDKRTLRDIETFYNTSIEEMPLNVADLI 401

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q3SZ54 EIF4A1 "Eukaryotic initiation factor 4A-I" [Bos taurus (taxid:9913)]

 Score = 113 (44.8 bits), Expect = 1.5e-07, Sum P(2) = 1.5e-07
 Identities = 27/88 (30%), Positives = 47/88 (53%)

Query:   100 SHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVG 157
             S +++ TD    LL+ G       ++INY+LPT +E YI R+         G  IN+V  
Sbjct:   323 SRVLITTD----LLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTE 378

Query:   158 GEVVTLRSMEESLGLIVAEVPINISEIL 185
              +  TLR +E      + E+P+N+++++
Sbjct:   379 EDKRTLRDIETFYNTSIEEMPLNVADLI 406

GO:0005524 "ATP binding" evidence=IEA

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

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

UNIPROTKB|F1P895 EIF4A1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 113 (44.8 bits), Expect = 1.5e-07, Sum P(2) = 1.5e-07
 Identities = 27/88 (30%), Positives = 47/88 (53%)

Query:   100 SHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVG 157
             S +++ TD    LL+ G       ++INY+LPT +E YI R+         G  IN+V  
Sbjct:   323 SRVLITTD----LLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTE 378

Query:   158 GEVVTLRSMEESLGLIVAEVPINISEIL 185
              +  TLR +E      + E+P+N+++++
Sbjct:   379 EDKRTLRDIETFYNTSIEEMPLNVADLI 406

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|J9NY67 EIF4A1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 113 (44.8 bits), Expect = 1.5e-07, Sum P(2) = 1.5e-07
 Identities = 27/88 (30%), Positives = 47/88 (53%)

Query:   100 SHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVG 157
             S +++ TD    LL+ G       ++INY+LPT +E YI R+         G  IN+V  
Sbjct:   323 SRVLITTD----LLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTE 378

Query:   158 GEVVTLRSMEESLGLIVAEVPINISEIL 185
              +  TLR +E      + E+P+N+++++
Sbjct:   379 EDKRTLRDIETFYNTSIEEMPLNVADLI 406

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|P60842 EIF4A1 "Eukaryotic initiation factor 4A-I" [Homo sapiens (taxid:9606)]

 Score = 113 (44.8 bits), Expect = 1.5e-07, Sum P(2) = 1.5e-07
 Identities = 27/88 (30%), Positives = 47/88 (53%)

Query:   100 SHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVG 157
             S +++ TD    LL+ G       ++INY+LPT +E YI R+         G  IN+V  
Sbjct:   323 SRVLITTD----LLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTE 378

Query:   158 GEVVTLRSMEESLGLIVAEVPINISEIL 185
              +  TLR +E      + E+P+N+++++
Sbjct:   379 EDKRTLRDIETFYNTSIEEMPLNVADLI 406

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

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

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003729 "mRNA binding" evidence=TAS

GO:0004386 "helicase activity" evidence=TAS

GO:0000339 "RNA cap binding" evidence=TAS

GO:0008135 "translation factor activity, nucleic acid binding" evidence=TAS

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

GO:0005515 "protein binding" evidence=IPI

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:0006412 "translation" evidence=TAS

GO:0006413 "translational initiation" 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

GO:0044267 "cellular protein metabolic process" evidence=TAS

UNIPROTKB|A6M928 EIF4A1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 113 (44.8 bits), Expect = 1.5e-07, Sum P(2) = 1.5e-07
 Identities = 27/88 (30%), Positives = 47/88 (53%)

Query:   100 SHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVG 157
             S +++ TD    LL+ G       ++INY+LPT +E YI R+         G  IN+V  
Sbjct:   323 SRVLITTD----LLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTE 378

Query:   158 GEVVTLRSMEESLGLIVAEVPINISEIL 185
              +  TLR +E      + E+P+N+++++
Sbjct:   379 EDKRTLRDIETFYNTSIEEMPLNVADLI 406

GO:0005524 "ATP binding" evidence=IEA

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

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	185
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	4e-13
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	0.002
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	0.002
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	0.004

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

 Score = 66.0 bits (161), Expect = 4e-13
 Identities = 39/159 (24%), Positives = 71/159 (44%), Gaps = 30/159 (18%)

Query: 29  IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 88
           I+ C++R ++D +   +    D + S +H D+ + +R LI+ EFR             SG
Sbjct: 271 IIYCNTRRKVDYLTKKMHE-RDFTVSCMHGDMDQKDRDLIMREFR-------------SG 316

Query: 89  DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LA 146
                      + +++ TD    LL+ G       ++INY+LP   E YI R+       
Sbjct: 317 ----------STRVLITTD----LLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFG 362

Query: 147 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
             G  IN V   ++  L+ +E      + E+P+ +++ L
Sbjct: 363 RKGVAINFVTPDDIEQLKEIERHYNTQIEEMPMEVADYL 401

Length = 401

>gnl|CDD|201125 pfam00271, Helicase_C, Helicase conserved C-terminal domain

 Score = 35.6 bits (83), Expect = 0.002
 Identities = 25/95 (26%), Positives = 37/95 (38%), Gaps = 27/95 (28%)

Query: 47  NLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVT 106
               I  + LH  L++ ER  ILE+FR                         KS ++V T
Sbjct: 4   RKPGIKVARLHGGLSQEEREEILEDFR-----------------------NGKSKVLVAT 40

Query: 107 DACLPLLSSGESAISARVLINYELPTKKETYIRRM 141
           D        G       ++INY+LP    +YI+R+
Sbjct: 41  DV----AGRGIDLPDVNLVINYDLPWNPASYIQRI 71

The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. Length = 78

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

 Score = 37.5 bits (87), Expect = 0.002
 Identities = 30/132 (22%), Positives = 52/132 (39%), Gaps = 33/132 (25%)

Query: 9   ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI 68
           E L++LL     GR     +IV   ++  ++ +  ++        ++LH DL + ER   
Sbjct: 262 ELLLKLLKDEDEGR-----VIVFVRTKRLVEELAESLRKR-GFKVAALHGDLPQEERDRA 315

Query: 69  LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINY 128
           LE+F+              G+             +V TD    + + G        +INY
Sbjct: 316 LEKFK-------------DGELRV----------LVATD----VAARGLDIPDVSHVINY 348

Query: 129 ELPTKKETYIRR 140
           +LP   E Y+ R
Sbjct: 349 DLPLDPEDYVHR 360

Length = 513

>gnl|CDD|238034 cd00079, HELICc, Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process

 Score = 35.7 bits (83), Expect = 0.004
 Identities = 32/133 (24%), Positives = 59/133 (44%), Gaps = 31/133 (23%)

Query: 9   ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI 68
           E L+ELL   +     G  +++ C S+  LD +   +     I  ++LH D ++ ER  +
Sbjct: 15  EALLELLKEHLK---KGGKVLIFCPSKKMLDELAELLRKP-GIKVAALHGDGSQEEREEV 70

Query: 69  LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINY 128
           L++FR                       E +  ++V TD     ++ G    +  V+INY
Sbjct: 71  LKDFR-----------------------EGEIVVLVATDV----IARGIDLPNVSVVINY 103

Query: 129 ELPTKKETYIRRM 141
           +LP    +Y++R+
Sbjct: 104 DLPWSPSSYLQRI 116

Length = 131

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	185
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	100.0
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	99.97
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	99.97
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.96
KOG0326	459	consensus ATP-dependent RNA helicase [RNA processi	99.96
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.96
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	99.96
KOG0340	442	consensus ATP-dependent RNA helicase [RNA processi	99.96
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.95
PTZ00110	545	helicase; Provisional	99.94
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.94
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.94
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	99.94
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.94
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.94
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.93
PTZ00424	401	helicase 45; Provisional	99.93
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.93
KOG0327	397	consensus Translation initiation factor 4F, helica	99.93
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	99.92
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	99.92
KOG0342	543	consensus ATP-dependent RNA helicase pitchoune [RN	99.91
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.91
KOG0343	758	consensus RNA Helicase [RNA processing and modific	99.9
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	99.9
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	99.89
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.89
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.89
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	99.89
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	99.89
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.89
KOG0347	731	consensus RNA helicase [RNA processing and modific	99.87
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	99.87
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.87
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	99.87
PRK04914	956	ATP-dependent helicase HepA; Validated	99.85
KOG0350	620	consensus DEAD-box ATP-dependent RNA helicase [RNA	99.85
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.85
KOG0346	569	consensus RNA helicase [RNA processing and modific	99.85
KOG4284	980	consensus DEAD box protein [Transcription]	99.84
PRK05298	652	excinuclease ABC subunit B; Provisional	99.83
PRK13767	876	ATP-dependent helicase; Provisional	99.83
KOG0334	997	consensus RNA helicase [RNA processing and modific	99.83
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.82
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.82
PRK13766	773	Hef nuclease; Provisional	99.8
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.8
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.79
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.78
KOG0337	529	consensus ATP-dependent RNA helicase [RNA processi	99.76
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.76
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	99.76
PHA02653	675	RNA helicase NPH-II; Provisional	99.75
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	99.75
KOG0349	725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	99.75
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.75
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.74
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.73
KOG0354	746	consensus DEAD-box like helicase [General function	99.73
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.73
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.72
PRK02362	737	ski2-like helicase; Provisional	99.72
PRK10689	1147	transcription-repair coupling factor; Provisional	99.71
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.7
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.7
KOG0351	941	consensus ATP-dependent DNA helicase [Replication,	99.69
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.68
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.66
PRK00254	720	ski2-like helicase; Provisional	99.66
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.66
PHA02558	501	uvsW UvsW helicase; Provisional	99.66
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.63
smart00490	82	HELICc helicase superfamily c-terminal domain.	99.62
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.62
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	99.61
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.61
PRK01172	674	ski2-like helicase; Provisional	99.6
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.56
PRK09401	1176	reverse gyrase; Reviewed	99.54
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	99.49
PRK09694	878	helicase Cas3; Provisional	99.44
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	99.42
KOG0352	641	consensus ATP-dependent DNA helicase [Replication,	99.41
PRK14701	1638	reverse gyrase; Provisional	99.4
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.39
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	99.38
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.38
COG1202	830	Superfamily II helicase, archaea-specific [General	99.36
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.3
KOG0353	695	consensus ATP-dependent DNA helicase [General func	99.28
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.24
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.21
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.16
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.15
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.14
PRK05580	679	primosome assembly protein PriA; Validated	99.13
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.09
COG1204	766	Superfamily II helicase [General function predicti	98.97
COG1205	851	Distinct helicase family with a unique C-terminal	98.91
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	98.81
KOG4150	1034	consensus Predicted ATP-dependent RNA helicase [RN	98.76
KOG0950	1008	consensus DNA polymerase theta/eta, DEAD-box super	98.72
KOG0947	1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	98.66
KOG0384	1373	consensus Chromodomain-helicase DNA-binding protei	98.66
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	98.59
KOG0953	700	consensus Mitochondrial RNA helicase SUV3, DEAD-bo	98.52
KOG0390	776	consensus DNA repair protein, SNF2 family [Replica	98.51
KOG0391	1958	consensus SNF2 family DNA-dependent ATPase [Genera	98.46
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	98.42
KOG0385	971	consensus Chromatin remodeling complex WSTF-ISWI,	98.39
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	98.37
KOG0387	923	consensus Transcription-coupled repair protein CSB	98.36
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	98.34
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	98.32
KOG1000	689	consensus Chromatin remodeling protein HARP/SMARCA	98.31
KOG0948	1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	98.24
PRK12326	764	preprotein translocase subunit SecA; Reviewed	98.22
KOG0392	1549	consensus SNF2 family DNA-dependent ATPase domain-	98.22
KOG0920	924	consensus ATP-dependent RNA helicase A [RNA proces	98.21
KOG0389	941	consensus SNF2 family DNA-dependent ATPase [Chroma	98.17
KOG0922	674	consensus DEAH-box RNA helicase [RNA processing an	98.17
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	98.11
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	98.05
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	98.03
KOG0388	1185	consensus SNF2 family DNA-dependent ATPase [Replic	98.0
COG4096	875	HsdR Type I site-specific restriction-modification	97.95
KOG1002	791	consensus Nucleotide excision repair protein RAD16	97.91
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	97.9
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	97.77
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	97.75
KOG0923	902	consensus mRNA splicing factor ATP-dependent RNA h	97.72
KOG1123	776	consensus RNA polymerase II transcription initiati	97.72
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	97.71
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	97.65
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	97.6
PF13307	167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	97.57
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	97.57
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	97.43
KOG0949	1330	consensus Predicted helicase, DEAD-box superfamily	97.28
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	97.19
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	97.18
COG4889	1518	Predicted helicase [General function prediction on	97.16
CHL00122	870	secA preprotein translocase subunit SecA; Validate	97.16
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	97.01
KOG4439	901	consensus RNA polymerase II transcription terminat	96.92
COG1198	730	PriA Primosomal protein N' (replication factor Y)	96.86
KOG0386	1157	consensus Chromatin remodeling complex SWI/SNF, co	96.76
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	96.59
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	96.55
KOG1015	1567	consensus Transcription regulator XNP/ATRX, DEAD-b	96.32
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	96.25
KOG0926	1172	consensus DEAH-box RNA helicase [RNA processing an	96.16
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	96.06
PRK05580	679	primosome assembly protein PriA; Validated	96.03
TIGR00595	505	priA primosomal protein N'. All proteins in this f	95.77
PF13871	278	Helicase_C_4: Helicase_C-like	95.77
PRK14873	665	primosome assembly protein PriA; Provisional	95.76
KOG0925	699	consensus mRNA splicing factor ATP-dependent RNA h	95.65
KOG0701	1606	consensus dsRNA-specific nuclease Dicer and relate	95.54
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	95.38
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	95.33
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	95.14
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	95.07
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	94.87
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	94.66
PRK10689	1147	transcription-repair coupling factor; Provisional	94.28
smart00492	141	HELICc3 helicase superfamily c-terminal domain.	94.24
COG1198	730	PriA Primosomal protein N' (replication factor Y)	93.87
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	93.74
KOG2340	698	consensus Uncharacterized conserved protein [Funct	93.45
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	93.44
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	93.43
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	93.4
PRK14701	1638	reverse gyrase; Provisional	93.27
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	92.85
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	92.22
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	91.23
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	91.02
KOG1016	1387	consensus Predicted DNA helicase, DEAD-box superfa	90.05
cd01524	90	RHOD_Pyr_redox Member of the Rhodanese Homology Do	89.72
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	89.67
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	89.43
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	89.39
KOG0347	731	consensus RNA helicase [RNA processing and modific	89.26
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	89.01
cd00158	89	RHOD Rhodanese Homology Domain (RHOD); an alpha be	88.97
KOG1001	674	consensus Helicase-like transcription factor HLTF/	88.94
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	88.72
cd01449	118	TST_Repeat_2 Thiosulfate sulfurtransferase (TST),	88.63
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	88.56
smart00491	142	HELICc2 helicase superfamily c-terminal domain.	88.44
cd01528	101	RHOD_2 Member of the Rhodanese Homology Domain sup	88.42
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	88.41
cd01518	101	RHOD_YceA Member of the Rhodanese Homology Domain	88.34
cd01448	122	TST_Repeat_1 Thiosulfate sulfurtransferase (TST),	87.68
smart00450	100	RHOD Rhodanese Homology Domain. An alpha beta fold	87.14
cd01529	96	4RHOD_Repeats Member of the Rhodanese Homology Dom	87.1
cd01523	100	RHOD_Lact_B Member of the Rhodanese Homology Domai	86.46
cd01519	106	RHOD_HSP67B2 Member of the Rhodanese Homology Doma	86.24
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	86.03
cd01444	96	GlpE_ST GlpE sulfurtransferase (ST) and homologs a	85.88
KOG1513	1300	consensus Nuclear helicase MOP-3/SNO (DEAD-box sup	85.61
PF10593	239	Z1: Z1 domain; InterPro: IPR018310 This entry repr	85.11
cd01532	92	4RHOD_Repeat_1 Member of the Rhodanese Homology Do	84.87
cd01520	128	RHOD_YbbB Member of the Rhodanese Homology Domain	84.17
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	84.06
cd01527	99	RHOD_YgaP Member of the Rhodanese Homology Domain	83.94
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	83.75
cd01533	109	4RHOD_Repeat_2 Member of the Rhodanese Homology Do	82.67
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	82.63
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	82.36
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	82.17
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	81.89
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	81.61
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	81.26
cd01447	103	Polysulfide_ST Polysulfide-sulfurtransferase - Rho	81.17
PTZ00110	545	helicase; Provisional	81.04
cd01445	138	TST_Repeats Thiosulfate sulfurtransferases (TST) c	80.97
cd01525	105	RHOD_Kc Member of the Rhodanese Homology Domain su	80.96
cd01534	95	4RHOD_Repeat_3 Member of the Rhodanese Homology Do	80.64
cd01526	122	RHOD_ThiF Member of the Rhodanese Homology Domain	80.41
cd01522	117	RHOD_1 Member of the Rhodanese Homology Domain sup	80.15

>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=2e-34  Score=240.84  Aligned_cols=150  Identities=25%  Similarity=0.485  Sum_probs=135.4

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ   86 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~   86 (185)
                      +.+++.+-|..|.. ...-.++||||||++.+++|.+.+++.. +.+.++||+|++++|.+++.+||+|           
T Consensus       249 ~EewKfdtLcdLYd-~LtItQavIFcnTk~kVdwLtekm~~~n-ftVssmHGDm~qkERd~im~dFRsg-----------  315 (400)
T KOG0328|consen  249 KEEWKFDTLCDLYD-TLTITQAVIFCNTKRKVDWLTEKMREAN-FTVSSMHGDMEQKERDKIMNDFRSG-----------  315 (400)
T ss_pred             hhhhhHhHHHHHhh-hhehheEEEEecccchhhHHHHHHHhhC-ceeeeccCCcchhHHHHHHHHhhcC-----------
Confidence            34444444444333 3444899999999999999999999987 7999999999999999999999999           


Q ss_pred             CCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHHHHH
Q 029910           87 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLR  164 (185)
Q Consensus        87 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~~~  164 (185)
                                  +.++||+||+    .+||+|+|.|++|||||+|.+.+.|+||+||.  .|+.|++|+||...|...++
T Consensus       316 ------------~SrvLitTDV----waRGiDv~qVslviNYDLP~nre~YIHRIGRSGRFGRkGvainFVk~~d~~~lr  379 (400)
T KOG0328|consen  316 ------------KSRVLITTDV----WARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAINFVKSDDLRILR  379 (400)
T ss_pred             ------------CceEEEEech----hhccCCcceeEEEEecCCCccHHHHhhhhccccccCCcceEEEEecHHHHHHHH
Confidence                        7999999999    99999999999999999999999999999995  68999999999999999999


Q ss_pred             HHHHHhCCccccccCCccccC
Q 029910          165 SMEESLGLIVAEVPINISEIL  185 (185)
Q Consensus       165 ~l~~~~~~~~~~~~~~~~~~l  185 (185)
                      ++|+.+...+.++|+++.+++
T Consensus       380 dieq~yst~i~emp~nvad~i  400 (400)
T KOG0328|consen  380 DIEQYYSTQIDEMPMNVADLI  400 (400)
T ss_pred             HHHHHHhhhcccccchhhhcC
Confidence            999999999999999998874

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

Probab=99.97  E-value=1.7e-30  Score=233.26  Aligned_cols=147  Identities=22%  Similarity=0.361  Sum_probs=131.6

Q ss_pred             cchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccc
Q 029910            6 TFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE   85 (185)
Q Consensus         6 ~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~   85 (185)
                      .|.+++.++|..+.  ...+.|+||||+|++.|+.|...|+..+ +.+..+||++++.+|..+|+.|++|          
T Consensus       324 ~K~~~l~~lL~~~~--~~~~~KvIIFc~tkr~~~~l~~~l~~~~-~~a~~iHGd~sQ~eR~~~L~~FreG----------  390 (519)
T KOG0331|consen  324 AKLRKLGKLLEDIS--SDSEGKVIIFCETKRTCDELARNLRRKG-WPAVAIHGDKSQSERDWVLKGFREG----------  390 (519)
T ss_pred             HHHHHHHHHHHHHh--ccCCCcEEEEecchhhHHHHHHHHHhcC-cceeeecccccHHHHHHHHHhcccC----------
Confidence            36677888888744  4566899999999999999999999988 8999999999999999999999999          


Q ss_pred             cCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCchHHHH
Q 029910           86 QSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGGEVVTL  163 (185)
Q Consensus        86 ~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e~~~~  163 (185)
                                   ...||||||+    ++||+|+|+|++|||||+|.++++|+||+||++  +..|.+++|++..+....
T Consensus       391 -------------~~~vLVATdV----AaRGLDi~dV~lVInydfP~~vEdYVHRiGRTGRa~~~G~A~tfft~~~~~~a  453 (519)
T KOG0331|consen  391 -------------KSPVLVATDV----AARGLDVPDVDLVINYDFPNNVEDYVHRIGRTGRAGKKGTAITFFTSDNAKLA  453 (519)
T ss_pred             -------------CcceEEEccc----ccccCCCccccEEEeCCCCCCHHHHHhhcCccccCCCCceEEEEEeHHHHHHH
Confidence                         7999999999    999999999999999999999999999999984  578999999999999888


Q ss_pred             HHHHHHhCCccccccCCcc
Q 029910          164 RSMEESLGLIVAEVPINIS  182 (185)
Q Consensus       164 ~~l~~~~~~~~~~~~~~~~  182 (185)
                      ..+.+.+...-+++|..+.
T Consensus       454 ~~l~~~l~e~~q~v~~~l~  472 (519)
T KOG0331|consen  454 RELIKVLREAGQTVPPDLL  472 (519)
T ss_pred             HHHHHHHHHccCCCChHHH
Confidence            8888887766666665543

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

Probab=99.97  E-value=1.5e-30  Score=224.72  Aligned_cols=141  Identities=26%  Similarity=0.422  Sum_probs=129.3

Q ss_pred             hHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccC
Q 029910            8 QETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQS   87 (185)
Q Consensus         8 ~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~   87 (185)
                      ...|+.|++.     ..+.++||||+++.++++++-.|++.| +.+..|||+|++..|...+++|+.+            
T Consensus       288 ~~yLV~ll~e-----~~g~s~iVF~~t~~tt~~la~~L~~lg-~~a~~LhGqmsq~~Rlg~l~~Fk~~------------  349 (476)
T KOG0330|consen  288 DTYLVYLLNE-----LAGNSVIVFCNTCNTTRFLALLLRNLG-FQAIPLHGQMSQSKRLGALNKFKAG------------  349 (476)
T ss_pred             chhHHHHHHh-----hcCCcEEEEEeccchHHHHHHHHHhcC-cceecccchhhHHHHHHHHHHHhcc------------
Confidence            3445555554     445999999999999999999999999 8999999999999999999999999            


Q ss_pred             CCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHHHHHH
Q 029910           88 GDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLRS  165 (185)
Q Consensus        88 ~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~~~~  165 (185)
                                 ...||||||+    ++||+|+|.|++|||||+|.+..+||||+||+  +|++|.+|++|+.+|++.+++
T Consensus       350 -----------~r~iLv~TDV----aSRGLDip~Vd~VVNyDiP~~skDYIHRvGRtaRaGrsG~~ItlVtqyDve~~qr  414 (476)
T KOG0330|consen  350 -----------ARSILVCTDV----ASRGLDIPHVDVVVNYDIPTHSKDYIHRVGRTARAGRSGKAITLVTQYDVELVQR  414 (476)
T ss_pred             -----------CCcEEEecch----hcccCCCCCceEEEecCCCCcHHHHHHHcccccccCCCcceEEEEehhhhHHHHH
Confidence                       6999999999    99999999999999999999999999999995  689999999999999999999


Q ss_pred             HHHHhCCccccccCCc
Q 029910          166 MEESLGLIVAEVPINI  181 (185)
Q Consensus       166 l~~~~~~~~~~~~~~~  181 (185)
                      ||..++.++.+.+.+-
T Consensus       415 IE~~~gkkl~~~~~~~  430 (476)
T KOG0330|consen  415 IEHALGKKLPEYKVDK  430 (476)
T ss_pred             HHHHHhcCCCccCcch
Confidence            9999999998766543

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

Probab=99.96  E-value=8.9e-29  Score=224.76  Aligned_cols=143  Identities=24%  Similarity=0.375  Sum_probs=129.2

Q ss_pred             EecchHH-HHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccc
Q 029910            4 SFTFQET-LVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQK   82 (185)
Q Consensus         4 ~~~~~~~-l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~   82 (185)
                      ++++.+. ++++|..++. .....++||||+|+..++.|+..|...| +++..+||+|++++|.+++++|++|       
T Consensus       252 ~~v~~~~~k~~~L~~ll~-~~~~~~~IVF~~tk~~~~~l~~~l~~~g-~~~~~lhG~l~q~~R~~~l~~F~~g-------  322 (513)
T COG0513         252 LEVESEEEKLELLLKLLK-DEDEGRVIVFVRTKRLVEELAESLRKRG-FKVAALHGDLPQEERDRALEKFKDG-------  322 (513)
T ss_pred             EEeCCHHHHHHHHHHHHh-cCCCCeEEEEeCcHHHHHHHHHHHHHCC-CeEEEecCCCCHHHHHHHHHHHHcC-------
Confidence            3344333 7888888777 5555689999999999999999999999 8999999999999999999999999       


Q ss_pred             ccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCc-h
Q 029910           83 VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGG-E  159 (185)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~-e  159 (185)
                                      ..+||||||+    ++||+|+|++++|||||+|.++++|+||+||+  +|+.|.+|+|+++. |
T Consensus       323 ----------------~~~vLVaTDv----aaRGiDi~~v~~VinyD~p~~~e~yvHRiGRTgRaG~~G~ai~fv~~~~e  382 (513)
T COG0513         323 ----------------ELRVLVATDV----AARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEE  382 (513)
T ss_pred             ----------------CCCEEEEech----hhccCCccccceeEEccCCCCHHHheeccCccccCCCCCeEEEEeCcHHH
Confidence                            7999999999    99999999999999999999999999999997  67889999999986 8


Q ss_pred             HHHHHHHHHHhCCccc
Q 029910          160 VVTLRSMEESLGLIVA  175 (185)
Q Consensus       160 ~~~~~~l~~~~~~~~~  175 (185)
                      ...+..+++.++..++
T Consensus       383 ~~~l~~ie~~~~~~~~  398 (513)
T COG0513         383 VKKLKRIEKRLERKLP  398 (513)
T ss_pred             HHHHHHHHHHHhcccc
Confidence            9999999999877654

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

Probab=99.96  E-value=3.1e-29  Score=212.69  Aligned_cols=151  Identities=24%  Similarity=0.453  Sum_probs=141.8

Q ss_pred             EecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccc
Q 029910            4 SFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKV   83 (185)
Q Consensus         4 ~~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~   83 (185)
                      .|++..-++.-|++|++ +.+-.++|||||+..+++.|++.+.+.| +++.++|+.|.++.|..++.+|++|        
T Consensus       302 afV~e~qKvhCLntLfs-kLqINQsIIFCNS~~rVELLAkKITelG-yscyyiHakM~Q~hRNrVFHdFr~G--------  371 (459)
T KOG0326|consen  302 AFVEERQKVHCLNTLFS-KLQINQSIIFCNSTNRVELLAKKITELG-YSCYYIHAKMAQEHRNRVFHDFRNG--------  371 (459)
T ss_pred             eeechhhhhhhHHHHHH-HhcccceEEEeccchHhHHHHHHHHhcc-chhhHHHHHHHHhhhhhhhhhhhcc--------
Confidence            35677778888888887 7778999999999999999999999999 8999999999999999999999999        


Q ss_pred             cccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHH
Q 029910           84 TEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVV  161 (185)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~  161 (185)
                                     .++.|||||.    +.||+|++.+++|||||+|++.++|+||+||.  .|..|.+|++++-+|..
T Consensus       372 ---------------~crnLVctDL----~TRGIDiqavNvVINFDfpk~aEtYLHRIGRsGRFGhlGlAInLityedrf  432 (459)
T KOG0326|consen  372 ---------------KCRNLVCTDL----FTRGIDIQAVNVVINFDFPKNAETYLHRIGRSGRFGHLGLAINLITYEDRF  432 (459)
T ss_pred             ---------------ccceeeehhh----hhcccccceeeEEEecCCCCCHHHHHHHccCCccCCCcceEEEEEehhhhh
Confidence                           7999999999    99999999999999999999999999999996  57789999999999999


Q ss_pred             HHHHHHHHhCCccccccCCccc
Q 029910          162 TLRSMEESLGLIVAEVPINISE  183 (185)
Q Consensus       162 ~~~~l~~~~~~~~~~~~~~~~~  183 (185)
                      .+.++|+.+|.+++++|..+..
T Consensus       433 ~L~~IE~eLGtEI~pip~~iDk  454 (459)
T KOG0326|consen  433 NLYRIEQELGTEIKPIPSNIDK  454 (459)
T ss_pred             hHHHHHHHhccccccCCCcCCc
Confidence            9999999999999999988754

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.96  E-value=2.1e-28  Score=216.79  Aligned_cols=152  Identities=20%  Similarity=0.321  Sum_probs=135.3

Q ss_pred             EecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccc
Q 029910            4 SFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKV   83 (185)
Q Consensus         4 ~~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~   83 (185)
                      .|...+.+..+|..++. .....++||||++++.|+.++..|...| +.+..+||+|++++|.+++++|++|        
T Consensus       235 ~~~~~~~k~~~l~~ll~-~~~~~~~lVF~~t~~~~~~l~~~L~~~g-~~v~~lhg~~~~~~R~~~l~~F~~g--------  304 (423)
T PRK04837        235 FYPSNEEKMRLLQTLIE-EEWPDRAIIFANTKHRCEEIWGHLAADG-HRVGLLTGDVAQKKRLRILEEFTRG--------  304 (423)
T ss_pred             EeCCHHHHHHHHHHHHH-hcCCCeEEEEECCHHHHHHHHHHHHhCC-CcEEEecCCCChhHHHHHHHHHHcC--------
Confidence            44455666667776666 4556899999999999999999999988 8999999999999999999999999        


Q ss_pred             cccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHH
Q 029910           84 TEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVV  161 (185)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~  161 (185)
                                     .+++|||||+    ++||+|+|++++|||||+|.++++|+||+||+  .|+.|.+|+|+++.+..
T Consensus       305 ---------------~~~vLVaTdv----~~rGiDip~v~~VI~~d~P~s~~~yiqR~GR~gR~G~~G~ai~~~~~~~~~  365 (423)
T PRK04837        305 ---------------DLDILVATDV----AARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISLACEEYAL  365 (423)
T ss_pred             ---------------CCcEEEEech----hhcCCCccccCEEEEeCCCCchhheEeccccccCCCCCeeEEEEeCHHHHH
Confidence                           6999999999    99999999999999999999999999999997  56779999999999999


Q ss_pred             HHHHHHHHhCCccccccCCcccc
Q 029910          162 TLRSMEESLGLIVAEVPINISEI  184 (185)
Q Consensus       162 ~~~~l~~~~~~~~~~~~~~~~~~  184 (185)
                      .+..+++.++..+++.+.+..++
T Consensus       366 ~~~~i~~~~~~~~~~~~~~~~~~  388 (423)
T PRK04837        366 NLPAIETYIGHSIPVSKYDSDAL  388 (423)
T ss_pred             HHHHHHHHhCCCCCCccCChhhh
Confidence            99999999999887776665543

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

Probab=99.96  E-value=3.3e-28  Score=216.36  Aligned_cols=139  Identities=18%  Similarity=0.362  Sum_probs=121.3

Q ss_pred             eEecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccc
Q 029910            3 VSFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQK   82 (185)
Q Consensus         3 v~~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~   82 (185)
                      |++...+...+-|..+++ .....|+|||+|+++.|+.|++.|...| +++..|||+.++++|.-+++.|+.+       
T Consensus       496 v~m~~ed~k~kkL~eil~-~~~~ppiIIFvN~kk~~d~lAk~LeK~g-~~~~tlHg~k~qeQRe~aL~~fr~~-------  566 (673)
T KOG0333|consen  496 VEMVSEDEKRKKLIEILE-SNFDPPIIIFVNTKKGADALAKILEKAG-YKVTTLHGGKSQEQRENALADFREG-------  566 (673)
T ss_pred             EEEecchHHHHHHHHHHH-hCCCCCEEEEEechhhHHHHHHHHhhcc-ceEEEeeCCccHHHHHHHHHHHHhc-------
Confidence            444544444555555565 4466899999999999999999999999 8999999999999999999999999       


Q ss_pred             ccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchH
Q 029910           83 VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEV  160 (185)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~  160 (185)
                                      ..+||||||+    ++||+|+|+|.+|||||++.+.++|+|||||+  +|+.|.+|+|+++.|-
T Consensus       567 ----------------t~dIlVaTDv----AgRGIDIpnVSlVinydmaksieDYtHRIGRTgRAGk~GtaiSflt~~dt  626 (673)
T KOG0333|consen  567 ----------------TGDILVATDV----AGRGIDIPNVSLVINYDMAKSIEDYTHRIGRTGRAGKSGTAISFLTPADT  626 (673)
T ss_pred             ----------------CCCEEEEecc----cccCCCCCccceeeecchhhhHHHHHHHhccccccccCceeEEEeccchh
Confidence                            6999999999    99999999999999999999999999999997  6788999999999887


Q ss_pred             HHHHHHHHHh
Q 029910          161 VTLRSMEESL  170 (185)
Q Consensus       161 ~~~~~l~~~~  170 (185)
                      ..|.+|.+.+
T Consensus       627 ~v~ydLkq~l  636 (673)
T KOG0333|consen  627 AVFYDLKQAL  636 (673)
T ss_pred             HHHHHHHHHH
Confidence            7666665553

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

Probab=99.96  E-value=3.4e-28  Score=208.23  Aligned_cols=144  Identities=24%  Similarity=0.399  Sum_probs=131.4

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ   86 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~   86 (185)
                      +..-+..+|.. .+ ......++||+|+..+|+.|+..|...+ +.+..+|+.|++.+|...+.+|+++           
T Consensus       238 kdaYLv~~Lr~-~~-~~~~~simIFvnttr~cQ~l~~~l~~le-~r~~~lHs~m~Q~eR~~aLsrFrs~-----------  303 (442)
T KOG0340|consen  238 KDAYLVHLLRD-FE-NKENGSIMIFVNTTRECQLLSMTLKNLE-VRVVSLHSQMPQKERLAALSRFRSN-----------  303 (442)
T ss_pred             hHHHHHHHHhh-hh-hccCceEEEEeehhHHHHHHHHHHhhhc-eeeeehhhcchHHHHHHHHHHHhhc-----------
Confidence            44556666666 33 2256899999999999999999999998 9999999999999999999999999           


Q ss_pred             CCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHHHHH
Q 029910           87 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLR  164 (185)
Q Consensus        87 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~~~  164 (185)
                                  ..++|||||+    ++||+|+|.|++|||||+|.+|.+|+||+||+  +|+.|.+|+||+..|++.+.
T Consensus       304 ------------~~~iliaTDV----AsRGLDIP~V~LVvN~diPr~P~~yiHRvGRtARAGR~G~aiSivt~rDv~l~~  367 (442)
T KOG0340|consen  304 ------------AARILIATDV----ASRGLDIPTVELVVNHDIPRDPKDYIHRVGRTARAGRKGMAISIVTQRDVELLQ  367 (442)
T ss_pred             ------------CccEEEEech----hhcCCCCCceeEEEecCCCCCHHHHHHhhcchhcccCCcceEEEechhhHHHHH
Confidence                        7999999999    99999999999999999999999999999995  78999999999999999999


Q ss_pred             HHHHHhCCccccccCC
Q 029910          165 SMEESLGLIVAEVPIN  180 (185)
Q Consensus       165 ~l~~~~~~~~~~~~~~  180 (185)
                      .+|+.+|.++.+.+..
T Consensus       368 aiE~~igkKl~e~~~~  383 (442)
T KOG0340|consen  368 AIEEEIGKKLTEYNKV  383 (442)
T ss_pred             HHHHHHhccccccccc
Confidence            9999999999987643

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.95  E-value=1.5e-26  Score=207.12  Aligned_cols=145  Identities=22%  Similarity=0.345  Sum_probs=130.9

Q ss_pred             EecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccc
Q 029910            4 SFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKV   83 (185)
Q Consensus         4 ~~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~   83 (185)
                      .+...+...+++..++. .....++||||++++.++.+++.|...+ +.+..+||+|++.+|.+++++|++|        
T Consensus       225 ~~~~~~~k~~~l~~l~~-~~~~~~~lVF~~t~~~~~~l~~~L~~~g-~~~~~lhg~~~~~~R~~~l~~F~~g--------  294 (456)
T PRK10590        225 HFVDKKRKRELLSQMIG-KGNWQQVLVFTRTKHGANHLAEQLNKDG-IRSAAIHGNKSQGARTRALADFKSG--------  294 (456)
T ss_pred             EEcCHHHHHHHHHHHHH-cCCCCcEEEEcCcHHHHHHHHHHHHHCC-CCEEEEECCCCHHHHHHHHHHHHcC--------
Confidence            34455566777887666 5667899999999999999999999988 8999999999999999999999999        


Q ss_pred             cccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCchHH
Q 029910           84 TEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGGEVV  161 (185)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e~~  161 (185)
                                     .++||||||+    ++||+|+|++++|||||+|.++++|+||+||++  +..|.+++|+...|..
T Consensus       295 ---------------~~~iLVaTdv----~~rGiDip~v~~VI~~~~P~~~~~yvqR~GRaGR~g~~G~ai~l~~~~d~~  355 (456)
T PRK10590        295 ---------------DIRVLVATDI----AARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEHK  355 (456)
T ss_pred             ---------------CCcEEEEccH----HhcCCCcccCCEEEEeCCCCCHHHhhhhccccccCCCCeeEEEEecHHHHH
Confidence                           7999999999    999999999999999999999999999999974  5679999999999999


Q ss_pred             HHHHHHHHhCCccccc
Q 029910          162 TLRSMEESLGLIVAEV  177 (185)
Q Consensus       162 ~~~~l~~~~~~~~~~~  177 (185)
                      .++.+++.++..+++.
T Consensus       356 ~~~~ie~~l~~~~~~~  371 (456)
T PRK10590        356 LLRDIEKLLKKEIPRI  371 (456)
T ss_pred             HHHHHHHHhcCCCccc
Confidence            9999999988887543

>PTZ00110 helicase; Provisional

Probab=99.94  E-value=7.9e-27  Score=213.33  Aligned_cols=132  Identities=21%  Similarity=0.362  Sum_probs=123.3

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEE
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMI  103 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iL  103 (185)
                      .+.++||||+++++|+.|++.|...+ +.+..+||++++++|.+++++|++|                       ..+||
T Consensus       376 ~~~k~LIF~~t~~~a~~l~~~L~~~g-~~~~~ihg~~~~~eR~~il~~F~~G-----------------------~~~IL  431 (545)
T PTZ00110        376 DGDKILIFVETKKGADFLTKELRLDG-WPALCIHGDKKQEERTWVLNEFKTG-----------------------KSPIM  431 (545)
T ss_pred             cCCeEEEEecChHHHHHHHHHHHHcC-CcEEEEECCCcHHHHHHHHHHHhcC-----------------------CCcEE
Confidence            56899999999999999999999887 8999999999999999999999999                       69999


Q ss_pred             EEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHHHHHHHHHHhCCccccccCCc
Q 029910          104 VVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINI  181 (185)
Q Consensus       104 V~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~~~~l~~~~~~~~~~~~~~~  181 (185)
                      ||||+    ++||+|+|++++|||||+|.++++|+||+||+  .|+.|.+++|+++.+......+.+.+....+++|..+
T Consensus       432 VaTdv----~~rGIDi~~v~~VI~~d~P~s~~~yvqRiGRtGR~G~~G~ai~~~~~~~~~~~~~l~~~l~~~~q~vp~~l  507 (545)
T PTZ00110        432 IATDV----ASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYRLARDLVKVLREAKQPVPPEL  507 (545)
T ss_pred             EEcch----hhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEECcchHHHHHHHHHHHHHccCCCCHHH
Confidence            99999    99999999999999999999999999999997  5677999999999999999999999888888888766


Q ss_pred             cc
Q 029910          182 SE  183 (185)
Q Consensus       182 ~~  183 (185)
                      .+
T Consensus       508 ~~  509 (545)
T PTZ00110        508 EK  509 (545)
T ss_pred             HH
Confidence            54

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.94  E-value=2.6e-26  Score=205.35  Aligned_cols=143  Identities=22%  Similarity=0.368  Sum_probs=127.4

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ   86 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~   86 (185)
                      ..+.+.+.+..++. .....++||||++++.++.+++.|...+ +.+..+||+|++.+|.+++++|++|           
T Consensus       225 ~~~~k~~~l~~ll~-~~~~~~~lVF~~t~~~~~~l~~~L~~~~-~~v~~~hg~~~~~eR~~~l~~F~~g-----------  291 (460)
T PRK11776        225 SPDERLPALQRLLL-HHQPESCVVFCNTKKECQEVADALNAQG-FSALALHGDLEQRDRDQVLVRFANR-----------  291 (460)
T ss_pred             CcHHHHHHHHHHHH-hcCCCceEEEECCHHHHHHHHHHHHhCC-CcEEEEeCCCCHHHHHHHHHHHHcC-----------
Confidence            33445556665555 4556899999999999999999999998 8999999999999999999999999           


Q ss_pred             CCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHHHHH
Q 029910           87 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLR  164 (185)
Q Consensus        87 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~~~  164 (185)
                                  ..++|||||+    ++||+|+|++++|||||+|.++++|+||+||+  .|+.|.+++|+.+.|...+.
T Consensus       292 ------------~~~vLVaTdv----~~rGiDi~~v~~VI~~d~p~~~~~yiqR~GRtGR~g~~G~ai~l~~~~e~~~~~  355 (460)
T PRK11776        292 ------------SCSVLVATDV----AARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQRAN  355 (460)
T ss_pred             ------------CCcEEEEecc----cccccchhcCCeEEEecCCCCHhHhhhhcccccCCCCcceEEEEEchhHHHHHH
Confidence                        6999999999    99999999999999999999999999999997  45679999999999999999


Q ss_pred             HHHHHhCCcccccc
Q 029910          165 SMEESLGLIVAEVP  178 (185)
Q Consensus       165 ~l~~~~~~~~~~~~  178 (185)
                      .+++.++..++..+
T Consensus       356 ~i~~~~~~~~~~~~  369 (460)
T PRK11776        356 AIEDYLGRKLNWEP  369 (460)
T ss_pred             HHHHHhCCCCceec
Confidence            99999988776543

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.94  E-value=3.4e-26  Score=210.21  Aligned_cols=145  Identities=20%  Similarity=0.362  Sum_probs=128.6

Q ss_pred             cchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccc
Q 029910            6 TFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE   85 (185)
Q Consensus         6 ~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~   85 (185)
                      ...+.+..++..++. ...+.++||||+|++.++.|++.|...+ +.+..+||+|++.+|.+++++|+++          
T Consensus       239 ~~~~~k~~~L~~ll~-~~~~~k~LVF~nt~~~ae~l~~~L~~~g-~~v~~lhg~l~~~eR~~il~~Fr~G----------  306 (572)
T PRK04537        239 PADEEKQTLLLGLLS-RSEGARTMVFVNTKAFVERVARTLERHG-YRVGVLSGDVPQKKRESLLNRFQKG----------  306 (572)
T ss_pred             cCHHHHHHHHHHHHh-cccCCcEEEEeCCHHHHHHHHHHHHHcC-CCEEEEeCCCCHHHHHHHHHHHHcC----------
Confidence            344445555555555 5567899999999999999999999998 8999999999999999999999999          


Q ss_pred             cCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHHHH
Q 029910           86 QSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTL  163 (185)
Q Consensus        86 ~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~~  163 (185)
                                   ..+||||||+    ++||+|+|++++|||||+|.++++|+||+||+  .|..|.+|+|+...+...+
T Consensus       307 -------------~~~VLVaTdv----~arGIDip~V~~VInyd~P~s~~~yvqRiGRaGR~G~~G~ai~~~~~~~~~~l  369 (572)
T PRK04537        307 -------------QLEILVATDV----AARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFACERYAMSL  369 (572)
T ss_pred             -------------CCeEEEEehh----hhcCCCccCCCEEEEcCCCCCHHHHhhhhcccccCCCCceEEEEecHHHHHHH
Confidence                         7999999999    99999999999999999999999999999997  4577999999999999999


Q ss_pred             HHHHHHhCCccccccC
Q 029910          164 RSMEESLGLIVAEVPI  179 (185)
Q Consensus       164 ~~l~~~~~~~~~~~~~  179 (185)
                      ..+++.++.++...+.
T Consensus       370 ~~i~~~~~~~~~~~~~  385 (572)
T PRK04537        370 PDIEAYIEQKIPVEPV  385 (572)
T ss_pred             HHHHHHHcCCCCcccc
Confidence            9999999888765443

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

Probab=99.94  E-value=4.8e-26  Score=196.12  Aligned_cols=129  Identities=21%  Similarity=0.387  Sum_probs=118.3

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeE
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHM  102 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  102 (185)
                      ..-.+.||||.|+++|.+|+..|+..| ..+..|||+|...+|..++++||.|                       ..++
T Consensus       328 ~tigqsiIFc~tk~ta~~l~~~m~~~G-h~V~~l~G~l~~~~R~~ii~~Fr~g-----------------------~~kV  383 (477)
T KOG0332|consen  328 LTIGQSIIFCHTKATAMWLYEEMRAEG-HQVSLLHGDLTVEQRAAIIDRFREG-----------------------KEKV  383 (477)
T ss_pred             hhhhheEEEEeehhhHHHHHHHHHhcC-ceeEEeeccchhHHHHHHHHHHhcC-----------------------cceE
Confidence            344899999999999999999999999 6999999999999999999999999                       7999


Q ss_pred             EEEecCCCCcccCcCCCCCCcEEEEcCCCC------CHHHHHHHHhhh--cCCCCEEEEEeeC-chHHHHHHHHHHhCCc
Q 029910          103 IVVTDACLPLLSSGESAISARVLINYELPT------KKETYIRRMTTC--LAADGSVINIVVG-GEVVTLRSMEESLGLI  173 (185)
Q Consensus       103 LV~Td~~~~~~~~G~d~~~v~~VI~~d~P~------~~~~yiqR~GR~--~~~~g~~i~~v~~-~e~~~~~~l~~~~~~~  173 (185)
                      ||+|++    ++||+|++.|++|||||+|.      +.++|+||+||+  .|+.|.+|+|+.. ...+.+..++++.+.+
T Consensus       384 LitTnV----~ARGiDv~qVs~VvNydlP~~~~~~pD~etYlHRiGRtGRFGkkG~a~n~v~~~~s~~~mn~iq~~F~~~  459 (477)
T KOG0332|consen  384 LITTNV----CARGIDVAQVSVVVNYDLPVKYTGEPDYETYLHRIGRTGRFGKKGLAINLVDDKDSMNIMNKIQKHFNMK  459 (477)
T ss_pred             EEEech----hhcccccceEEEEEecCCccccCCCCCHHHHHHHhcccccccccceEEEeecccCcHHHHHHHHHHHhhc
Confidence            999999    99999999999999999995      789999999997  5788999999975 5678888999999887


Q ss_pred             cccccC
Q 029910          174 VAEVPI  179 (185)
Q Consensus       174 ~~~~~~  179 (185)
                      +.++..
T Consensus       460 i~~~~~  465 (477)
T KOG0332|consen  460 IKRLDP  465 (477)
T ss_pred             ceecCC
Confidence            776654

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.94  E-value=1.5e-25  Score=198.93  Aligned_cols=140  Identities=17%  Similarity=0.312  Sum_probs=127.5

Q ss_pred             hHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccC
Q 029910            8 QETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQS   87 (185)
Q Consensus         8 ~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~   87 (185)
                      .+.+.+++..++. .....++||||+++++++.++..|...+ +.+..+||+|++.+|..++++|++|            
T Consensus       229 ~~~k~~~l~~l~~-~~~~~~~lVF~~s~~~~~~l~~~L~~~~-~~~~~l~g~~~~~~R~~~l~~f~~G------------  294 (434)
T PRK11192        229 LEHKTALLCHLLK-QPEVTRSIVFVRTRERVHELAGWLRKAG-INCCYLEGEMVQAKRNEAIKRLTDG------------  294 (434)
T ss_pred             HHHHHHHHHHHHh-cCCCCeEEEEeCChHHHHHHHHHHHhCC-CCEEEecCCCCHHHHHHHHHHHhCC------------
Confidence            4667788888776 5567899999999999999999999987 8999999999999999999999999            


Q ss_pred             CCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHHHHHH
Q 029910           88 GDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLRS  165 (185)
Q Consensus        88 ~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~~~~  165 (185)
                                 ..+||||||+    +++|+|+|++++|||||+|.+.+.|+||+||+  .|..|.+++++...|...+..
T Consensus       295 -----------~~~vLVaTd~----~~~GiDip~v~~VI~~d~p~s~~~yiqr~GR~gR~g~~g~ai~l~~~~d~~~~~~  359 (434)
T PRK11192        295 -----------RVNVLVATDV----AARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLVEAHDHLLLGK  359 (434)
T ss_pred             -----------CCcEEEEccc----cccCccCCCCCEEEEECCCCCHHHHhhcccccccCCCCceEEEEecHHHHHHHHH
Confidence                       7999999999    99999999999999999999999999999997  456799999999999999999


Q ss_pred             HHHHhCCcccc
Q 029910          166 MEESLGLIVAE  176 (185)
Q Consensus       166 l~~~~~~~~~~  176 (185)
                      +++.+...+.+
T Consensus       360 i~~~~~~~~~~  370 (434)
T PRK11192        360 IERYIEEPLKA  370 (434)
T ss_pred             HHHHHhccccc
Confidence            99887766543

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.94  E-value=1.7e-25  Score=201.03  Aligned_cols=139  Identities=24%  Similarity=0.361  Sum_probs=126.0

Q ss_pred             hHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccC
Q 029910            8 QETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQS   87 (185)
Q Consensus         8 ~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~   87 (185)
                      ......++..++. .....++||||+++++++.+++.|...+ +.+..+||+++.++|.+++++|++|            
T Consensus       319 ~~~k~~~l~~ll~-~~~~~~~IVF~~s~~~~~~l~~~L~~~~-~~~~~~~g~~~~~~R~~~~~~Fr~G------------  384 (475)
T PRK01297        319 GSDKYKLLYNLVT-QNPWERVMVFANRKDEVRRIEERLVKDG-INAAQLSGDVPQHKRIKTLEGFREG------------  384 (475)
T ss_pred             chhHHHHHHHHHH-hcCCCeEEEEeCCHHHHHHHHHHHHHcC-CCEEEEECCCCHHHHHHHHHHHhCC------------
Confidence            3445566666665 5566899999999999999999999888 8999999999999999999999999            


Q ss_pred             CCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCchHHHHHH
Q 029910           88 GDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGGEVVTLRS  165 (185)
Q Consensus        88 ~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e~~~~~~  165 (185)
                                 .+++||||++    +++|+|+|++++||+||+|.++.+|+||+||++  |+.|.+++|+..+|...+..
T Consensus       385 -----------~~~vLvaT~~----l~~GIDi~~v~~VI~~~~P~s~~~y~Qr~GRaGR~g~~g~~i~~~~~~d~~~~~~  449 (475)
T PRK01297        385 -----------KIRVLVATDV----AGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGEDDAFQLPE  449 (475)
T ss_pred             -----------CCcEEEEccc----cccCCcccCCCEEEEeCCCCCHHHHHHhhCccCCCCCCceEEEEecHHHHHHHHH
Confidence                       7999999999    999999999999999999999999999999974  56799999999999999999


Q ss_pred             HHHHhCCccc
Q 029910          166 MEESLGLIVA  175 (185)
Q Consensus       166 l~~~~~~~~~  175 (185)
                      +++.++.++.
T Consensus       450 ~~~~~~~~~~  459 (475)
T PRK01297        450 IEELLGRKIS  459 (475)
T ss_pred             HHHHhCCCCc
Confidence            9999998874

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

Probab=99.93  E-value=9.8e-26  Score=204.97  Aligned_cols=132  Identities=21%  Similarity=0.331  Sum_probs=120.0

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEE
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIV  104 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV  104 (185)
                      ..++||||+++..++.+++.|....++.+..+||+|++.+|..++++|++|                       ..+|||
T Consensus       367 ~~~~iVFv~s~~~a~~l~~~L~~~~g~~~~~~Hg~~~~~eR~~il~~Fr~G-----------------------~~~ILV  423 (518)
T PLN00206        367 KPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVG-----------------------EVPVIV  423 (518)
T ss_pred             CCCEEEEcCCchhHHHHHHHHhhccCcceEEeeCCCCHHHHHHHHHHHHCC-----------------------CCCEEE
Confidence            468999999999999999999864338999999999999999999999999                       799999


Q ss_pred             EecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCchHHHHHHHHHHhCCccccccCCcc
Q 029910          105 VTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINIS  182 (185)
Q Consensus       105 ~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e~~~~~~l~~~~~~~~~~~~~~~~  182 (185)
                      |||+    ++||+|+|++++|||||+|.++++|+||+||+|  |..|.+++|++.++...+..+.+.+....+++|.++.
T Consensus       424 aTdv----l~rGiDip~v~~VI~~d~P~s~~~yihRiGRaGR~g~~G~ai~f~~~~~~~~~~~l~~~l~~~~~~vp~~l~  499 (518)
T PLN00206        424 ATGV----LGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEEDRNLFPELVALLKSSGAAIPRELA  499 (518)
T ss_pred             EecH----hhccCCcccCCEEEEeCCCCCHHHHHHhccccccCCCCeEEEEEEchhHHHHHHHHHHHHHHcCCCCCHHHH
Confidence            9999    999999999999999999999999999999974  5679999999999998999998888877777776654


Q ss_pred             c
Q 029910          183 E  183 (185)
Q Consensus       183 ~  183 (185)
                      +
T Consensus       500 ~  500 (518)
T PLN00206        500 N  500 (518)
T ss_pred             h
Confidence            3

>PTZ00424 helicase 45; Provisional

Probab=99.93  E-value=1.3e-25  Score=196.43  Aligned_cols=148  Identities=25%  Similarity=0.479  Sum_probs=132.4

Q ss_pred             HHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCC
Q 029910            9 ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG   88 (185)
Q Consensus         9 ~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~   88 (185)
                      +...+.+..+.. .....++||||++++.++.+++.|...+ +.+..+||+|++++|..++++|++|             
T Consensus       252 ~~~~~~l~~~~~-~~~~~~~ivF~~t~~~~~~l~~~l~~~~-~~~~~~h~~~~~~~R~~i~~~f~~g-------------  316 (401)
T PTZ00424        252 EWKFDTLCDLYE-TLTITQAIIYCNTRRKVDYLTKKMHERD-FTVSCMHGDMDQKDRDLIMREFRSG-------------  316 (401)
T ss_pred             HHHHHHHHHHHH-hcCCCeEEEEecCcHHHHHHHHHHHHCC-CcEEEEeCCCCHHHHHHHHHHHHcC-------------
Confidence            334444544444 4455799999999999999999999887 8999999999999999999999999             


Q ss_pred             CCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCchHHHHHHH
Q 029910           89 DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGGEVVTLRSM  166 (185)
Q Consensus        89 ~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e~~~~~~l  166 (185)
                                .+++||||++    +++|+|+|++++||+||+|.+..+|+||+||++  |..|.|+.|+++.+...+..+
T Consensus       317 ----------~~~vLvaT~~----l~~GiDip~v~~VI~~~~p~s~~~y~qr~GRagR~g~~G~~i~l~~~~~~~~~~~~  382 (401)
T PTZ00424        317 ----------STRVLITTDL----LARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIEQLKEI  382 (401)
T ss_pred             ----------CCCEEEEccc----ccCCcCcccCCEEEEECCCCCHHHEeecccccccCCCCceEEEEEcHHHHHHHHHH
Confidence                      7999999999    999999999999999999999999999999974  567999999999999999999


Q ss_pred             HHHhCCccccccCCccccC
Q 029910          167 EESLGLIVAEVPINISEIL  185 (185)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~l  185 (185)
                      ++.++..+++.++...+.|
T Consensus       383 e~~~~~~~~~~~~~~~~~~  401 (401)
T PTZ00424        383 ERHYNTQIEEMPMEVADYL  401 (401)
T ss_pred             HHHHCCcccccCcchhhcC
Confidence            9999999999998877653

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.93  E-value=1.6e-25  Score=207.68  Aligned_cols=142  Identities=20%  Similarity=0.328  Sum_probs=127.1

Q ss_pred             HHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCC
Q 029910           12 VELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDES   91 (185)
Q Consensus        12 ~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~   91 (185)
                      .+.|..++. .....++||||+|+..++.|++.|...+ +.+..+||+|++.+|.+++++|++|                
T Consensus       233 ~~~L~~~L~-~~~~~~~IVF~~tk~~a~~l~~~L~~~g-~~~~~lhgd~~q~~R~~il~~Fr~G----------------  294 (629)
T PRK11634        233 NEALVRFLE-AEDFDAAIIFVRTKNATLEVAEALERNG-YNSAALNGDMNQALREQTLERLKDG----------------  294 (629)
T ss_pred             HHHHHHHHH-hcCCCCEEEEeccHHHHHHHHHHHHhCC-CCEEEeeCCCCHHHHHHHHHHHhCC----------------
Confidence            333443344 3445799999999999999999999998 8999999999999999999999999                


Q ss_pred             CCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHHHHHHHHHH
Q 029910           92 ETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLRSMEES  169 (185)
Q Consensus        92 ~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~~~~l~~~  169 (185)
                             +.+||||||+    +++|+|+|++++|||||+|.++++|+||+||+  .|+.|.+++|+.+.+...++.+++.
T Consensus       295 -------~~~ILVATdv----~arGIDip~V~~VI~~d~P~~~e~yvqRiGRtGRaGr~G~ai~~v~~~e~~~l~~ie~~  363 (629)
T PRK11634        295 -------RLDILIATDV----AARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVENRERRLLRNIERT  363 (629)
T ss_pred             -------CCCEEEEcch----HhcCCCcccCCEEEEeCCCCCHHHHHHHhccccCCCCcceEEEEechHHHHHHHHHHHH
Confidence                   7999999999    99999999999999999999999999999997  4667999999999999999999999


Q ss_pred             hCCccccccCCcc
Q 029910          170 LGLIVAEVPINIS  182 (185)
Q Consensus       170 ~~~~~~~~~~~~~  182 (185)
                      ++..+++++++-.
T Consensus       364 ~~~~i~~~~~p~~  376 (629)
T PRK11634        364 MKLTIPEVELPNA  376 (629)
T ss_pred             hCCCcceecCCcH
Confidence            9999988766544

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

Probab=99.93  E-value=8e-26  Score=194.87  Aligned_cols=144  Identities=27%  Similarity=0.547  Sum_probs=133.5

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ   86 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~   86 (185)
                      |.+.++++.+       .-.+.+||||+++.+..+..+|...+ ..+..+||+|.+.+|..++.+|+.|           
T Consensus       252 k~~~l~dl~~-------~~~q~~if~nt~r~v~~l~~~L~~~~-~~~s~~~~d~~q~~R~~~~~ef~~g-----------  312 (397)
T KOG0327|consen  252 KLDTLCDLYR-------RVTQAVIFCNTRRKVDNLTDKLRAHG-FTVSAIHGDMEQNERDTLMREFRSG-----------  312 (397)
T ss_pred             cccHHHHHHH-------hhhcceEEecchhhHHHHHHHHhhCC-ceEEEeecccchhhhhHHHHHhhcC-----------
Confidence            3445555555       23799999999999999999998888 8999999999999999999999999           


Q ss_pred             CCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHHHHH
Q 029910           87 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLR  164 (185)
Q Consensus        87 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~~~  164 (185)
                                  .+++||+||.    ++||+|+.++++|||||+|.+.++|+||+||+  .|++|.+|+|++..++..++
T Consensus       313 ------------ssrvlIttdl----~argidv~~~slvinydlP~~~~~yihR~gr~gr~grkg~~in~v~~~d~~~lk  376 (397)
T KOG0327|consen  313 ------------SSRVLITTDL----LARGIDVQQVSLVVNYDLPARKENYIHRIGRAGRFGRKGVAINFVTEEDVRDLK  376 (397)
T ss_pred             ------------CceEEeeccc----cccccchhhcceeeeeccccchhhhhhhcccccccCCCceeeeeehHhhHHHHH
Confidence                        6999999999    99999999999999999999999999999997  68999999999999999999


Q ss_pred             HHHHHhCCccccccCCccccC
Q 029910          165 SMEESLGLIVAEVPINISEIL  185 (185)
Q Consensus       165 ~l~~~~~~~~~~~~~~~~~~l  185 (185)
                      +++++++..++++|.++.+++
T Consensus       377 ~ie~~y~~~i~e~p~~~~~l~  397 (397)
T KOG0327|consen  377 DIEKFYNTPIEELPSNFADLL  397 (397)
T ss_pred             hHHHhcCCcceecccchhhcC
Confidence            999999999999999998875

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

Probab=99.92  E-value=5.6e-25  Score=195.51  Aligned_cols=151  Identities=22%  Similarity=0.319  Sum_probs=132.4

Q ss_pred             ecchHHHHHHHHHHHcc-------CCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccc
Q 029910            5 FTFQETLVELLHLVVAG-------RRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAM   77 (185)
Q Consensus         5 ~~~~~~l~~ll~~l~~~-------~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~   77 (185)
                      +.+.++..+|++.|...       ...+++++|||+|++.|+.|+.+|...+ +++..+||+-++.+|.+.+..|+.|  
T Consensus       310 V~~~~kr~~Lldll~~~~~~~~~~~~~~e~tlvFvEt~~~~d~l~~~l~~~~-~~~~sIhg~~tq~er~~al~~Fr~g--  386 (482)
T KOG0335|consen  310 VNEMEKRSKLLDLLNKDDGPPSDGEPKWEKTLVFVETKRGADELAAFLSSNG-YPAKSIHGDRTQIEREQALNDFRNG--  386 (482)
T ss_pred             ecchhhHHHHHHHhhcccCCcccCCcccceEEEEeeccchhhHHHHHHhcCC-CCceeecchhhhhHHHHHHHHhhcC--
Confidence            33455555666554421       2223589999999999999999999998 8999999999999999999999999  


Q ss_pred             cccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEe
Q 029910           78 KWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIV  155 (185)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v  155 (185)
                                           +.++||||++    ++||+|+|+|++|||||+|.+.++|+|||||+  .|+.|.+++|+
T Consensus       387 ---------------------~~pvlVaT~V----aaRGlDi~~V~hVInyDmP~d~d~YvHRIGRTGR~Gn~G~atsf~  441 (482)
T KOG0335|consen  387 ---------------------KAPVLVATNV----AARGLDIPNVKHVINYDMPADIDDYVHRIGRTGRVGNGGRATSFF  441 (482)
T ss_pred             ---------------------CcceEEEehh----hhcCCCCCCCceeEEeecCcchhhHHHhccccccCCCCceeEEEe
Confidence                                 7999999999    99999999999999999999999999999997  67889999999


Q ss_pred             eCchHHHHHHHHHHhCCccccccCCccc
Q 029910          156 VGGEVVTLRSMEESLGLIVAEVPINISE  183 (185)
Q Consensus       156 ~~~e~~~~~~l~~~~~~~~~~~~~~~~~  183 (185)
                      ...+....+.+.+.+.-.-+++|..+.+
T Consensus       442 n~~~~~i~~~L~~~l~ea~q~vP~wl~~  469 (482)
T KOG0335|consen  442 NEKNQNIAKALVEILTEANQEVPQWLSE  469 (482)
T ss_pred             ccccchhHHHHHHHHHHhcccCcHHHHh
Confidence            9988888899999988888888887765

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

Probab=99.92  E-value=3.1e-25  Score=193.37  Aligned_cols=147  Identities=22%  Similarity=0.344  Sum_probs=134.9

Q ss_pred             hHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccC
Q 029910            8 QETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQS   87 (185)
Q Consensus         8 ~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~   87 (185)
                      ...++++...+++...+..|+||||..+..|+.|+.-|.-.| +.+-.|||+-++.+|...++.|++|            
T Consensus       448 d~~k~~~~~~f~~~ms~ndKvIiFv~~K~~AD~LSSd~~l~g-i~~q~lHG~r~Q~DrE~al~~~ksG------------  514 (629)
T KOG0336|consen  448 DSEKLEIVQFFVANMSSNDKVIIFVSRKVMADHLSSDFCLKG-ISSQSLHGNREQSDREMALEDFKSG------------  514 (629)
T ss_pred             cHHHHHHHHHHHHhcCCCceEEEEEechhhhhhccchhhhcc-cchhhccCChhhhhHHHHHHhhhcC------------
Confidence            445568888888878899999999999999999999998888 9999999999999999999999999            


Q ss_pred             CCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHHHHHH
Q 029910           88 GDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLRS  165 (185)
Q Consensus        88 ~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~~~~  165 (185)
                                 .++|||+||+    ++||+|+|++.+|+|||+|.+++.|+||+||+  +|+.|.+|+|++.+|-.+...
T Consensus       515 -----------~vrILvaTDl----aSRGlDv~DiTHV~NyDFP~nIeeYVHRvGrtGRaGr~G~sis~lt~~D~~~a~e  579 (629)
T KOG0336|consen  515 -----------EVRILVATDL----ASRGLDVPDITHVYNYDFPRNIEEYVHRVGRTGRAGRTGTSISFLTRNDWSMAEE  579 (629)
T ss_pred             -----------ceEEEEEech----hhcCCCchhcceeeccCCCccHHHHHHHhcccccCCCCcceEEEEehhhHHHHHH
Confidence                       6999999999    99999999999999999999999999999996  678899999999999999988


Q ss_pred             HHHHhCCccccccCCcc
Q 029910          166 MEESLGLIVAEVPINIS  182 (185)
Q Consensus       166 l~~~~~~~~~~~~~~~~  182 (185)
                      +-+.+...-+++|.++.
T Consensus       580 LI~ILe~aeQevPdeL~  596 (629)
T KOG0336|consen  580 LIQILERAEQEVPDELV  596 (629)
T ss_pred             HHHHHHHhhhhCcHHHH
Confidence            88888888788876654

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

Probab=99.91  E-value=4.8e-24  Score=188.54  Aligned_cols=135  Identities=20%  Similarity=0.292  Sum_probs=117.5

Q ss_pred             HHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCC
Q 029910           14 LLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESET   93 (185)
Q Consensus        14 ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~   93 (185)
                      ++-.+++......++||||+|+..+.+.++.|.... +.+..+||++++..|..+..+|++.                  
T Consensus       319 ll~~~LKk~~~~~KiiVF~sT~~~vk~~~~lL~~~d-lpv~eiHgk~~Q~kRT~~~~~F~ka------------------  379 (543)
T KOG0342|consen  319 LLYTFLKKNIKRYKIIVFFSTCMSVKFHAELLNYID-LPVLEIHGKQKQNKRTSTFFEFCKA------------------  379 (543)
T ss_pred             HHHHHHHHhcCCceEEEEechhhHHHHHHHHHhhcC-CchhhhhcCCcccccchHHHHHhhc------------------
Confidence            333334424445999999999999999999999776 8999999999999999999999998                  


Q ss_pred             CCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCchHHHHHHHHHHhC
Q 029910           94 GKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGGEVVTLRSMEESLG  171 (185)
Q Consensus        94 ~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e~~~~~~l~~~~~  171 (185)
                           ..-||||||+    ++||+|+|+|++||+||+|.++++||||+||++  |..|.++.+..+.|..+++.+.   .
T Consensus       380 -----esgIL~cTDV----aARGlD~P~V~~VvQ~~~P~d~~~YIHRvGRTaR~gk~G~alL~l~p~El~Flr~LK---~  447 (543)
T KOG0342|consen  380 -----ESGILVCTDV----AARGLDIPDVDWVVQYDPPSDPEQYIHRVGRTAREGKEGKALLLLAPWELGFLRYLK---K  447 (543)
T ss_pred             -----ccceEEecch----hhccCCCCCceEEEEeCCCCCHHHHHHHhccccccCCCceEEEEeChhHHHHHHHHh---h
Confidence                 6889999999    999999999999999999999999999999975  4558999999999999999998   3


Q ss_pred             CccccccC
Q 029910          172 LIVAEVPI  179 (185)
Q Consensus       172 ~~~~~~~~  179 (185)
                      ..+.+.+.
T Consensus       448 lpl~~~e~  455 (543)
T KOG0342|consen  448 LPLEEFEF  455 (543)
T ss_pred             CCCcccCC
Confidence            44444443

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.91  E-value=2.1e-23  Score=187.60  Aligned_cols=129  Identities=22%  Similarity=0.360  Sum_probs=113.2

Q ss_pred             HHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCC
Q 029910           11 LVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDE   90 (185)
Q Consensus        11 l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~   90 (185)
                      +.+++..+.. ..+++++||||++++.++.++..|...| +.+..+||+|++++|.+++++|++|               
T Consensus       213 ~~~l~~~l~~-~~~~~~~IIF~~s~~~~e~la~~L~~~g-~~~~~~H~~l~~~eR~~i~~~F~~g---------------  275 (470)
T TIGR00614       213 LEDLLRFIRK-EFKGKSGIIYCPSRKKSEQVTASLQNLG-IAAGAYHAGLEISARDDVHHKFQRD---------------  275 (470)
T ss_pred             HHHHHHHHHH-hcCCCceEEEECcHHHHHHHHHHHHhcC-CCeeEeeCCCCHHHHHHHHHHHHcC---------------
Confidence            3344444332 4556778999999999999999999998 8999999999999999999999999               


Q ss_pred             CCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHHHHHHHHH
Q 029910           91 SETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLRSMEE  168 (185)
Q Consensus        91 ~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~~~~l~~  168 (185)
                              ..++||||++    +++|+|+|+|++||||++|.+++.|+||+||+  .|.+|.|+.|+.+.|...++.+..
T Consensus       276 --------~~~vLVaT~~----~~~GID~p~V~~VI~~~~P~s~~~y~Qr~GRaGR~G~~~~~~~~~~~~d~~~~~~~~~  343 (470)
T TIGR00614       276 --------EIQVVVATVA----FGMGINKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECHLFYAPADINRLRRLLM  343 (470)
T ss_pred             --------CCcEEEEech----hhccCCcccceEEEEeCCCCCHHHHHhhhcCcCCCCCCceEEEEechhHHHHHHHHHh
Confidence                    7999999999    99999999999999999999999999999997  456789999999888876666543

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

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=99.90  E-value=2.5e-23  Score=186.35  Aligned_cols=148  Identities=18%  Similarity=0.305  Sum_probs=126.2

Q ss_pred             EecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcC-CCceEEEEecCCCHHHHHHHHHHHhccccccccc
Q 029910            4 SFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL-ADISFSSLHSDLAETERTLILEEFRHTAMKWNQK   82 (185)
Q Consensus         4 ~~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~-~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~   82 (185)
                      +.+..+.++++|-.++. .....+.|||++|++++.++++.+... +++....|||.|++..|..++.+|-+.       
T Consensus       293 ~~v~l~~Ki~~L~sFI~-shlk~K~iVF~SscKqvkf~~e~F~rlrpg~~l~~L~G~~~Q~~R~ev~~~F~~~-------  364 (758)
T KOG0343|consen  293 VIVPLEDKIDMLWSFIK-SHLKKKSIVFLSSCKQVKFLYEAFCRLRPGIPLLALHGTMSQKKRIEVYKKFVRK-------  364 (758)
T ss_pred             EEEehhhHHHHHHHHHH-hccccceEEEEehhhHHHHHHHHHHhcCCCCceeeeccchhHHHHHHHHHHHHHh-------
Confidence            34466777888877666 677799999999999999999999765 449999999999999999999999997       


Q ss_pred             ccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCch-
Q 029910           83 VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGGE-  159 (185)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e-  159 (185)
                                      .--||+|||+    ++||+|||.|+|||+||.|.++++|+||+||++  ...|.++.++++.+ 
T Consensus       365 ----------------~~~vLF~TDv----~aRGLDFpaVdwViQ~DCPedv~tYIHRvGRtAR~~~~G~sll~L~psEe  424 (758)
T KOG0343|consen  365 ----------------RAVVLFCTDV----AARGLDFPAVDWVIQVDCPEDVDTYIHRVGRTARYKERGESLLMLTPSEE  424 (758)
T ss_pred             ----------------cceEEEeehh----hhccCCCcccceEEEecCchhHHHHHHHhhhhhcccCCCceEEEEcchhH
Confidence                            6779999999    999999999999999999999999999999975  45699999999887 


Q ss_pred             HHHHHHHHHHhCCccccccCC
Q 029910          160 VVTLRSMEESLGLIVAEVPIN  180 (185)
Q Consensus       160 ~~~~~~l~~~~~~~~~~~~~~  180 (185)
                      ..++..+++.. +.+.++..+
T Consensus       425 E~~l~~Lq~k~-I~i~~i~i~  444 (758)
T KOG0343|consen  425 EAMLKKLQKKK-IPIKEIKID  444 (758)
T ss_pred             HHHHHHHHHcC-CCHHhhccC
Confidence            56667776654 555555444

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

Probab=99.90  E-value=8.7e-24  Score=183.38  Aligned_cols=144  Identities=21%  Similarity=0.351  Sum_probs=122.4

Q ss_pred             ecc-hHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccc
Q 029910            5 FTF-QETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKV   83 (185)
Q Consensus         5 ~~~-~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~   83 (185)
                      |++ ..++.-||+-|.+   ...|++|||..+..++.+.++|.-.| +.+..+||+.++++|...++.||.|        
T Consensus       403 yVkqEaKiVylLeCLQK---T~PpVLIFaEkK~DVD~IhEYLLlKG-VEavaIHGGKDQedR~~ai~afr~g--------  470 (610)
T KOG0341|consen  403 YVKQEAKIVYLLECLQK---TSPPVLIFAEKKADVDDIHEYLLLKG-VEAVAIHGGKDQEDRHYAIEAFRAG--------  470 (610)
T ss_pred             HHHhhhhhhhHHHHhcc---CCCceEEEeccccChHHHHHHHHHcc-ceeEEeecCcchhHHHHHHHHHhcC--------
Confidence            454 3455667777533   44799999999999999999999998 9999999999999999999999999        


Q ss_pred             cccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCc-hH
Q 029910           84 TEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGG-EV  160 (185)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~-e~  160 (185)
                                     +.++||+||+    ++.|+|+|++.+|||||+|..++.|+||+||++  |+.|.+.+|++.+ +.
T Consensus       471 ---------------kKDVLVATDV----ASKGLDFp~iqHVINyDMP~eIENYVHRIGRTGRsg~~GiATTfINK~~~e  531 (610)
T KOG0341|consen  471 ---------------KKDVLVATDV----ASKGLDFPDIQHVINYDMPEEIENYVHRIGRTGRSGKTGIATTFINKNQEE  531 (610)
T ss_pred             ---------------CCceEEEecc----hhccCCCccchhhccCCChHHHHHHHHHhcccCCCCCcceeeeeecccchH
Confidence                           7999999999    999999999999999999999999999999974  5679999999875 56


Q ss_pred             HHHHHHHHHhCCccccccC
Q 029910          161 VTLRSMEESLGLIVAEVPI  179 (185)
Q Consensus       161 ~~~~~l~~~~~~~~~~~~~  179 (185)
                      ..+..+...+--.-+++|.
T Consensus       532 svLlDLK~LL~EakQ~vP~  550 (610)
T KOG0341|consen  532 SVLLDLKHLLQEAKQEVPP  550 (610)
T ss_pred             HHHHHHHHHHHHhhccCCH
Confidence            6666666665544444443

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

Probab=99.89  E-value=9.9e-23  Score=179.67  Aligned_cols=143  Identities=14%  Similarity=0.234  Sum_probs=118.0

Q ss_pred             HHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcC-CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCC
Q 029910           10 TLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL-ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG   88 (185)
Q Consensus        10 ~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~-~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~   88 (185)
                      .+...+-+++. ....+++|||.+|+..+++....|... +...+..+||.|++.+|.++++.|+..             
T Consensus       241 eK~~~lv~~L~-~~~~kK~iVFF~TCasVeYf~~~~~~~l~~~~i~~iHGK~~q~~R~k~~~~F~~~-------------  306 (567)
T KOG0345|consen  241 EKLSQLVHLLN-NNKDKKCIVFFPTCASVEYFGKLFSRLLKKREIFSIHGKMSQKARAKVLEAFRKL-------------  306 (567)
T ss_pred             HHHHHHHHHHh-ccccccEEEEecCcchHHHHHHHHHHHhCCCcEEEecchhcchhHHHHHHHHHhc-------------
Confidence            33333333455 466699999999999999999999876 568999999999999999999999996             


Q ss_pred             CCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHHHHHHH
Q 029910           89 DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLRSM  166 (185)
Q Consensus        89 ~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~~~~l  166 (185)
                                +..+|+|||+    ++||+|+|++++||+||+|.+++.|+||+||+  .|+.|.+|.|+.+.|..+..-+
T Consensus       307 ----------~~~vl~~TDV----aARGlDip~iD~VvQ~DpP~~~~~FvHR~GRTaR~gr~G~Aivfl~p~E~aYveFl  372 (567)
T KOG0345|consen  307 ----------SNGVLFCTDV----AARGLDIPGIDLVVQFDPPKDPSSFVHRCGRTARAGREGNAIVFLNPREEAYVEFL  372 (567)
T ss_pred             ----------cCceEEeehh----hhccCCCCCceEEEecCCCCChhHHHhhcchhhhccCccceEEEecccHHHHHHHH
Confidence                      6889999999    99999999999999999999999999999997  6788999999999776655444


Q ss_pred             HHHhCCccccccCC
Q 029910          167 EESLGLIVAEVPIN  180 (185)
Q Consensus       167 ~~~~~~~~~~~~~~  180 (185)
                      .-.-...++++..+
T Consensus       373 ~i~~~v~le~~~~e  386 (567)
T KOG0345|consen  373 RIKGKVELERIDTE  386 (567)
T ss_pred             HhcCccchhhhccc
Confidence            43333445544433

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.89  E-value=1.5e-22  Score=187.27  Aligned_cols=118  Identities=19%  Similarity=0.335  Sum_probs=107.9

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCcee
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSH  101 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (185)
                      ...+.++||||+|++.++.++..|...| +.+..+||+|++++|.+++++|+.+                       ..+
T Consensus       233 ~~~~~~~IIFc~tr~~~e~la~~L~~~g-~~v~~~Ha~l~~~~R~~i~~~F~~g-----------------------~~~  288 (607)
T PRK11057        233 EQRGKSGIIYCNSRAKVEDTAARLQSRG-ISAAAYHAGLDNDVRADVQEAFQRD-----------------------DLQ  288 (607)
T ss_pred             hcCCCCEEEEECcHHHHHHHHHHHHhCC-CCEEEecCCCCHHHHHHHHHHHHCC-----------------------CCC
Confidence            3456899999999999999999999998 8999999999999999999999999                       799


Q ss_pred             EEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCchHHHHHHHH
Q 029910          102 MIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGGEVVTLRSME  167 (185)
Q Consensus       102 iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e~~~~~~l~  167 (185)
                      |||||++    +++|+|+|+|++|||||+|.+.++|+||+||++  |.+|.|++|+++.|...++.+.
T Consensus       289 VLVaT~a----~~~GIDip~V~~VI~~d~P~s~~~y~Qr~GRaGR~G~~~~~ill~~~~d~~~~~~~~  352 (607)
T PRK11057        289 IVVATVA----FGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCL  352 (607)
T ss_pred             EEEEech----hhccCCCCCcCEEEEeCCCCCHHHHHHHhhhccCCCCCceEEEEeCHHHHHHHHHHH
Confidence            9999999    999999999999999999999999999999974  4568999999988876655443

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

Probab=99.89  E-value=1.2e-22  Score=195.29  Aligned_cols=119  Identities=16%  Similarity=0.236  Sum_probs=108.6

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCcee
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSH  101 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (185)
                      .....+.||||++++.++.++..|...| +.+..+||+|++++|..++++|+.|                       .++
T Consensus       677 ~~~~esgIIYC~SRke~E~LAe~L~~~G-ika~~YHAGLs~eeR~~vqe~F~~G-----------------------ei~  732 (1195)
T PLN03137        677 NHFDECGIIYCLSRMDCEKVAERLQEFG-HKAAFYHGSMDPAQRAFVQKQWSKD-----------------------EIN  732 (1195)
T ss_pred             cccCCCceeEeCchhHHHHHHHHHHHCC-CCeeeeeCCCCHHHHHHHHHHHhcC-----------------------CCc
Confidence            4445789999999999999999999998 8999999999999999999999999                       799


Q ss_pred             EEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCchHHHHHHHHH
Q 029910          102 MIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGGEVVTLRSMEE  168 (185)
Q Consensus       102 iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e~~~~~~l~~  168 (185)
                      |||||++    +++|+|+|+|++|||||+|.+++.|+||+||+|  |.+|.||+|+...|...++.+..
T Consensus       733 VLVATdA----FGMGIDkPDVR~VIHydlPkSiEsYyQriGRAGRDG~~g~cILlys~~D~~~~~~lI~  797 (1195)
T PLN03137        733 IICATVA----FGMGINKPDVRFVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLYYSYSDYIRVKHMIS  797 (1195)
T ss_pred             EEEEech----hhcCCCccCCcEEEEcCCCCCHHHHHhhhcccCCCCCCceEEEEecHHHHHHHHHHHh
Confidence            9999999    999999999999999999999999999999974  56799999998877766665543

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

Probab=99.89  E-value=1e-22  Score=183.01  Aligned_cols=146  Identities=21%  Similarity=0.366  Sum_probs=126.4

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ   86 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~   86 (185)
                      +...++-.+..++. ..-..|.+||+.+.++|.+|.+.|....++.+.++||+.++.+|...+++||.|           
T Consensus       370 se~~K~lA~rq~v~-~g~~PP~lIfVQs~eRak~L~~~L~~~~~i~v~vIh~e~~~~qrde~~~~FR~g-----------  437 (593)
T KOG0344|consen  370 SEKGKLLALRQLVA-SGFKPPVLIFVQSKERAKQLFEELEIYDNINVDVIHGERSQKQRDETMERFRIG-----------  437 (593)
T ss_pred             cchhHHHHHHHHHh-ccCCCCeEEEEecHHHHHHHHHHhhhccCcceeeEecccchhHHHHHHHHHhcc-----------
Confidence            34444444455455 445689999999999999999999655559999999999999999999999999           


Q ss_pred             CCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHHHHH
Q 029910           87 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLR  164 (185)
Q Consensus        87 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~~~  164 (185)
                                  .+.+|||||+    ++||+|+.++++|||||+|.+..+|+||+||+  +|++|.+|+|++..+...++
T Consensus       438 ------------~IwvLicTdl----l~RGiDf~gvn~VInyD~p~s~~syihrIGRtgRag~~g~Aitfytd~d~~~ir  501 (593)
T KOG0344|consen  438 ------------KIWVLICTDL----LARGIDFKGVNLVINYDFPQSDLSYIHRIGRTGRAGRSGKAITFYTDQDMPRIR  501 (593)
T ss_pred             ------------CeeEEEehhh----hhccccccCcceEEecCCCchhHHHHHHhhccCCCCCCcceEEEeccccchhhh
Confidence                        7999999999    99999999999999999999999999999996  67889999999999999999


Q ss_pred             HHHHHhCCccccccCC
Q 029910          165 SMEESLGLIVAEVPIN  180 (185)
Q Consensus       165 ~l~~~~~~~~~~~~~~  180 (185)
                      .+.+.+....-++|..
T Consensus       502 ~iae~~~~sG~evpe~  517 (593)
T KOG0344|consen  502 SIAEVMEQSGCEVPEK  517 (593)
T ss_pred             hHHHHHHHcCCcchHH
Confidence            8888776655555543

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

Probab=99.89  E-value=5.4e-23  Score=182.93  Aligned_cols=120  Identities=22%  Similarity=0.348  Sum_probs=112.0

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCcee
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSH  101 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (185)
                      +....++|||+.|+++|..+.-.|--.| +++.-+||.+++++|...++.|+..                       .++
T Consensus       423 rtf~~~~ivFv~tKk~AHRl~IllGLlg-l~agElHGsLtQ~QRlesL~kFk~~-----------------------eid  478 (691)
T KOG0338|consen  423 RTFQDRTIVFVRTKKQAHRLRILLGLLG-LKAGELHGSLTQEQRLESLEKFKKE-----------------------EID  478 (691)
T ss_pred             HhcccceEEEEehHHHHHHHHHHHHHhh-chhhhhcccccHHHHHHHHHHHHhc-----------------------cCC
Confidence            4445899999999999999988887777 8999999999999999999999999                       699


Q ss_pred             EEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHHHHHHHHHH
Q 029910          102 MIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLRSMEES  169 (185)
Q Consensus       102 iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~~~~l~~~  169 (185)
                      +|||||+    ++||+|++.|..||||++|.+.+.|+||+||+  +|+.|.+++|+...|...++.+-+.
T Consensus       479 vLiaTDv----AsRGLDI~gV~tVINy~mP~t~e~Y~HRVGRTARAGRaGrsVtlvgE~dRkllK~iik~  544 (691)
T KOG0338|consen  479 VLIATDV----ASRGLDIEGVQTVINYAMPKTIEHYLHRVGRTARAGRAGRSVTLVGESDRKLLKEIIKS  544 (691)
T ss_pred             EEEEech----hhccCCccceeEEEeccCchhHHHHHHHhhhhhhcccCcceEEEeccccHHHHHHHHhh
Confidence            9999999    99999999999999999999999999999996  7899999999999999988877665

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

Probab=99.89  E-value=1.6e-22  Score=190.78  Aligned_cols=140  Identities=14%  Similarity=0.147  Sum_probs=119.5

Q ss_pred             HHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcC--------CCceEEEEecCCCHHHHHHHHHHHhcccccccc
Q 029910           10 TLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL--------ADISFSSLHSDLAETERTLILEEFRHTAMKWNQ   81 (185)
Q Consensus        10 ~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~--------~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~   81 (185)
                      ...+++..++.   .+.++||||+|++.++.++..|+..        + ..+..+||++++++|.+++++|++|      
T Consensus       259 ~~~~~l~~l~~---~~~~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~-~~v~~~hgg~~~~eR~~ie~~f~~G------  328 (742)
T TIGR03817       259 EAADLLADLVA---EGARTLTFVRSRRGAELVAAIARRLLGEVDPDLA-ERVAAYRAGYLPEDRRELERALRDG------  328 (742)
T ss_pred             HHHHHHHHHHH---CCCCEEEEcCCHHHHHHHHHHHHHHHHhhccccc-cchhheecCCCHHHHHHHHHHHHcC------
Confidence            34566666555   2479999999999999999988753        3 5788999999999999999999999      


Q ss_pred             cccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEee--C
Q 029910           82 KVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVV--G  157 (185)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~--~  157 (185)
                                       ++++|||||+    +++|+|+|++++|||||+|.+.++|+||+||+|  |+.|.+++++.  +
T Consensus       329 -----------------~i~vLVaTd~----lerGIDI~~vd~VI~~~~P~s~~~y~qRiGRaGR~G~~g~ai~v~~~~~  387 (742)
T TIGR03817       329 -----------------ELLGVATTNA----LELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRGQGALVVLVARDDP  387 (742)
T ss_pred             -----------------CceEEEECch----HhccCCcccccEEEEeCCCCCHHHHHHhccccCCCCCCcEEEEEeCCCh
Confidence                             7999999999    999999999999999999999999999999985  45689998886  3


Q ss_pred             chHHHHHHHHHHhCCccccccCC
Q 029910          158 GEVVTLRSMEESLGLIVAEVPIN  180 (185)
Q Consensus       158 ~e~~~~~~l~~~~~~~~~~~~~~  180 (185)
                      .|...+...++.++..+++...+
T Consensus       388 ~d~~~~~~~~~~~~~~~e~~~~~  410 (742)
T TIGR03817       388 LDTYLVHHPEALFDRPVEATVFD  410 (742)
T ss_pred             HHHHHHhCHHHHhcCCCccceeC
Confidence            46677788888888887765443

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.

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=99.87  E-value=2e-22  Score=180.54  Aligned_cols=122  Identities=23%  Similarity=0.355  Sum_probs=114.6

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEE
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMI  103 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iL  103 (185)
                      -+.++|||||+.+.+..|+-.|...+ |....||..|.+.+|.+.+++|++.                       ...+|
T Consensus       462 yPGrTlVF~NsId~vKRLt~~L~~L~-i~p~~LHA~M~QKqRLknLEkF~~~-----------------------~~~VL  517 (731)
T KOG0347|consen  462 YPGRTLVFCNSIDCVKRLTVLLNNLD-IPPLPLHASMIQKQRLKNLEKFKQS-----------------------PSGVL  517 (731)
T ss_pred             cCCceEEEechHHHHHHHHHHHhhcC-CCCchhhHHHHHHHHHHhHHHHhcC-----------------------CCeEE
Confidence            35899999999999999999999998 9999999999999999999999998                       68899


Q ss_pred             EEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHHHHHHHHHHhCCc
Q 029910          104 VVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLRSMEESLGLI  173 (185)
Q Consensus       104 V~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~~~~l~~~~~~~  173 (185)
                      ||||+    ++||+|+|.|.+||+|.+|.+.+-|+||.||+  +++.|+.+.++.+.+...+..+.+.+...
T Consensus       518 iaTDV----AARGLDIp~V~HVIHYqVPrtseiYVHRSGRTARA~~~Gvsvml~~P~e~~~~~KL~ktL~k~  585 (731)
T KOG0347|consen  518 IATDV----AARGLDIPGVQHVIHYQVPRTSEIYVHRSGRTARANSEGVSVMLCGPQEVGPLKKLCKTLKKK  585 (731)
T ss_pred             Eeehh----hhccCCCCCcceEEEeecCCccceeEecccccccccCCCeEEEEeChHHhHHHHHHHHHHhhc
Confidence            99999    99999999999999999999999999999996  56779999999999999999888887644

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

Probab=99.87  E-value=9.3e-22  Score=175.08  Aligned_cols=155  Identities=18%  Similarity=0.285  Sum_probs=139.9

Q ss_pred             CeeEecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccc
Q 029910            1 MSVSFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWN   80 (185)
Q Consensus         1 ~~v~~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~   80 (185)
                      ++|+.....++-.|+++|.+ .....++|||+..+..++.++..|.-.+ +++..+||+|.+.+|.+++.+|+++     
T Consensus       445 V~V~~s~~~Kl~wl~~~L~~-f~S~gkvlifVTKk~~~e~i~a~Lklk~-~~v~llhgdkdqa~rn~~ls~fKkk-----  517 (731)
T KOG0339|consen  445 VSVCPSEEKKLNWLLRHLVE-FSSEGKVLIFVTKKADAEEIAANLKLKG-FNVSLLHGDKDQAERNEVLSKFKKK-----  517 (731)
T ss_pred             eeeccCcHHHHHHHHHHhhh-hccCCcEEEEEeccCCHHHHHHHhcccc-ceeeeecCchhhHHHHHHHHHHhhc-----
Confidence            45677778888889999777 6777899999999999999999999998 8999999999999999999999998     


Q ss_pred             ccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCc
Q 029910           81 QKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGG  158 (185)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~  158 (185)
                                        ..+|||+||+    ++||+|+|++..|||||+-.++++|.||+||+  .|..|+++++|+..
T Consensus       518 ------------------~~~VlvatDv----aargldI~~ikTVvnyD~ardIdththrigrtgRag~kGvayTlvTeK  575 (731)
T KOG0339|consen  518 ------------------RKPVLVATDV----AARGLDIPSIKTVVNYDFARDIDTHTHRIGRTGRAGEKGVAYTLVTEK  575 (731)
T ss_pred             ------------------CCceEEEeeH----hhcCCCccccceeecccccchhHHHHHHhhhcccccccceeeEEechh
Confidence                              7999999999    99999999999999999999999999999996  56679999999999


Q ss_pred             hHHHHHHHHHHhCCccccccCCcccc
Q 029910          159 EVVTLRSMEESLGLIVAEVPINISEI  184 (185)
Q Consensus       159 e~~~~~~l~~~~~~~~~~~~~~~~~~  184 (185)
                      |..+.-.|.+.+...-+.+|.++.+|
T Consensus       576 Da~fAG~LVnnLe~agQnVP~~l~dl  601 (731)
T KOG0339|consen  576 DAEFAGHLVNNLEGAGQNVPDELMDL  601 (731)
T ss_pred             hHHHhhHHHHHHhhccccCChHHHHH
Confidence            99988888888777777777766543

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.87  E-value=2.9e-21  Score=178.00  Aligned_cols=115  Identities=21%  Similarity=0.333  Sum_probs=105.6

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEE
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMI  103 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iL  103 (185)
                      .+.++||||+|++.++.+++.|...| +.+..+||+|+.++|..++++|+.|                       ..++|
T Consensus       223 ~~~~~IIf~~sr~~~e~la~~L~~~g-~~~~~~H~~l~~~~R~~i~~~F~~g-----------------------~~~vl  278 (591)
T TIGR01389       223 RGQSGIIYASSRKKVEELAERLESQG-ISALAYHAGLSNKVRAENQEDFLYD-----------------------DVKVM  278 (591)
T ss_pred             CCCCEEEEECcHHHHHHHHHHHHhCC-CCEEEEECCCCHHHHHHHHHHHHcC-----------------------CCcEE
Confidence            36899999999999999999999988 8999999999999999999999999                       69999


Q ss_pred             EEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCchHHHHHHH
Q 029910          104 VVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGGEVVTLRSM  166 (185)
Q Consensus       104 V~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e~~~~~~l  166 (185)
                      |||++    +++|+|+|++++||+||+|.+.+.|+||+||++  |.+|.|+.++.+.|...++.+
T Consensus       279 VaT~a----~~~GID~p~v~~VI~~~~p~s~~~y~Q~~GRaGR~G~~~~~il~~~~~d~~~~~~~  339 (591)
T TIGR01389       279 VATNA----FGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSPADIALLKRR  339 (591)
T ss_pred             EEech----hhccCcCCCCCEEEEcCCCCCHHHHhhhhccccCCCCCceEEEecCHHHHHHHHHH
Confidence            99999    999999999999999999999999999999985  566899999888776655544

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.

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

Probab=99.87  E-value=2e-21  Score=173.76  Aligned_cols=134  Identities=22%  Similarity=0.361  Sum_probs=113.4

Q ss_pred             HHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcC---------------------CCceEEEEecCCCHHHHHHHH
Q 029910           11 LVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL---------------------ADISFSSLHSDLAETERTLIL   69 (185)
Q Consensus        11 l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~---------------------~~~~~~~l~g~~~~~~R~~~l   69 (185)
                      |..+|....+ .....++|||.+|++.+++=+..|+..                     -..++.-|||+|++++|..++
T Consensus       412 Laa~L~~~~k-~~~~qk~iVF~S~~d~VeFHy~lf~~~l~~~~e~~s~~~~s~g~~~l~~~~k~~rLHGsm~QeeRts~f  490 (708)
T KOG0348|consen  412 LAALLLNKVK-FEEKQKMIVFFSCSDSVEFHYSLFSEALLSHLEGSSGAPDSEGLPPLFMDLKFYRLHGSMEQEERTSVF  490 (708)
T ss_pred             HHHHHHHHhh-hhhhceeEEEEechhHHHHHHHHHHhhhhcccccccCCcccCCChhhhhcceEEEecCchhHHHHHHHH
Confidence            3444554444 445579999999999999877766431                     126789999999999999999


Q ss_pred             HHHhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCC
Q 029910           70 EEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAA  147 (185)
Q Consensus        70 ~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~  147 (185)
                      +.|++.                       ...||+|||+    ++||+|+|+|.+||+||.|.++++|+||+||+  .|.
T Consensus       491 ~~Fs~~-----------------------~~~VLLcTDV----AaRGLDlP~V~~vVQYd~P~s~adylHRvGRTARaG~  543 (708)
T KOG0348|consen  491 QEFSHS-----------------------RRAVLLCTDV----AARGLDLPHVGLVVQYDPPFSTADYLHRVGRTARAGE  543 (708)
T ss_pred             Hhhccc-----------------------cceEEEehhh----hhccCCCCCcCeEEEeCCCCCHHHHHHHhhhhhhccC
Confidence            999998                       5679999999    99999999999999999999999999999996  788


Q ss_pred             CCEEEEEeeCchHHHHHHHHHHhCC
Q 029910          148 DGSVINIVVGGEVVTLRSMEESLGL  172 (185)
Q Consensus       148 ~g~~i~~v~~~e~~~~~~l~~~~~~  172 (185)
                      .|.++.|..+.|.+++..++.....
T Consensus       544 kG~alLfL~P~Eaey~~~l~~~~~~  568 (708)
T KOG0348|consen  544 KGEALLFLLPSEAEYVNYLKKHHIM  568 (708)
T ss_pred             CCceEEEecccHHHHHHHHHhhcch
Confidence            8999999999999988777776443

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.85  E-value=8.9e-21  Score=181.93  Aligned_cols=118  Identities=16%  Similarity=0.203  Sum_probs=100.1

Q ss_pred             HHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHh-cCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCC
Q 029910           11 LVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVS-NLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGD   89 (185)
Q Consensus        11 l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~-~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~   89 (185)
                      +.+.|..++. ...+.|+||||+++.++..|.+.|+ ..| +.+..+||+|+..+|.++++.|++++             
T Consensus       480 Ki~~L~~~L~-~~~~~KvLVF~~~~~t~~~L~~~L~~~~G-i~~~~ihG~~s~~eR~~~~~~F~~~~-------------  544 (956)
T PRK04914        480 RVEWLIDFLK-SHRSEKVLVICAKAATALQLEQALREREG-IRAAVFHEGMSIIERDRAAAYFADEE-------------  544 (956)
T ss_pred             HHHHHHHHHH-hcCCCeEEEEeCcHHHHHHHHHHHhhccC-eeEEEEECCCCHHHHHHHHHHHhcCC-------------
Confidence            4444444444 3446899999999999999999995 456 89999999999999999999999851             


Q ss_pred             CCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEe
Q 029910           90 ESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIV  155 (185)
Q Consensus        90 ~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v  155 (185)
                              +..++||||++    +++|+|++.+++|||||+|||++.|.||+||+  .|+.+.+..++
T Consensus       545 --------~~~~VLIsTdv----gseGlNlq~a~~VInfDlP~nP~~~eQRIGR~~RiGQ~~~V~i~~  600 (956)
T PRK04914        545 --------DGAQVLLCSEI----GSEGRNFQFASHLVLFDLPFNPDLLEQRIGRLDRIGQKHDIQIHV  600 (956)
T ss_pred             --------CCccEEEechh----hccCCCcccccEEEEecCCCCHHHHHHHhcccccCCCCceEEEEE
Confidence                    15899999999    99999999999999999999999999999996  56667655544

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

Probab=99.85  E-value=4.5e-21  Score=170.24  Aligned_cols=124  Identities=19%  Similarity=0.307  Sum_probs=112.7

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHh-cC--CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCC
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVS-NL--ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEH   98 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~-~~--~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (185)
                      ...+.++|+|+++.+++..|++.|. ..  .+.++..++|.++...|.+.++.|+.|                       
T Consensus       426 ~~k~~r~lcf~~S~~sa~Rl~~~L~v~~~~~~~~~s~~t~~l~~k~r~k~l~~f~~g-----------------------  482 (620)
T KOG0350|consen  426 SNKLNRTLCFVNSVSSANRLAHVLKVEFCSDNFKVSEFTGQLNGKRRYKMLEKFAKG-----------------------  482 (620)
T ss_pred             HhhcceEEEEecchHHHHHHHHHHHHHhccccchhhhhhhhhhHHHHHHHHHHHhcC-----------------------
Confidence            5667999999999999999999997 22  237888899999999999999999999                       


Q ss_pred             ceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHHHHHHHHHHhCC
Q 029910           99 KSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLRSMEESLGL  172 (185)
Q Consensus        99 ~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~~~~l~~~~~~  172 (185)
                      .+++|||+|+    ++||+|+.+++.|||||+|.+..+|+||+||+  +|+.|.|++++.+.+...|.++-+..+.
T Consensus       483 ~i~vLIcSD~----laRGiDv~~v~~VINYd~P~~~ktyVHR~GRTARAgq~G~a~tll~~~~~r~F~klL~~~~~  554 (620)
T KOG0350|consen  483 DINVLICSDA----LARGIDVNDVDNVINYDPPASDKTYVHRAGRTARAGQDGYAITLLDKHEKRLFSKLLKKTNL  554 (620)
T ss_pred             CceEEEehhh----hhcCCcccccceEeecCCCchhhHHHHhhcccccccCCceEEEeeccccchHHHHHHHHhcc
Confidence            7999999999    99999999999999999999999999999996  7888999999999998888887776544

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

Probab=99.85  E-value=1.4e-20  Score=167.36  Aligned_cols=127  Identities=20%  Similarity=0.286  Sum_probs=112.2

Q ss_pred             eEecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEE--EEe-------cCCCHHHHHHHHHHHh
Q 029910            3 VSFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS--SLH-------SDLAETERTLILEEFR   73 (185)
Q Consensus         3 v~~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~--~l~-------g~~~~~~R~~~l~~F~   73 (185)
                      |-..|++.+.++++..++ ...+.++|||++.+++|+.+...|...+ +.+.  ++-       .||++.++.+++++|+
T Consensus       345 v~HPKl~~l~eilke~~~-k~~~~RvIVFT~yRdTae~i~~~L~~~~-~~~~~rFiGQa~r~~~~GMsQkeQ~eiI~~Fr  422 (542)
T COG1111         345 VEHPKLEKLREILKEQLE-KNGDSRVIVFTEYRDTAEEIVNFLKKIG-IKARVRFIGQASREGDKGMSQKEQKEIIDQFR  422 (542)
T ss_pred             CCCccHHHHHHHHHHHHh-cCCCceEEEEehhHhHHHHHHHHHHhcC-CcceeEEeeccccccccccCHHHHHHHHHHHh
Confidence            445689999999998776 5666999999999999999999999887 5553  222       4699999999999999


Q ss_pred             cccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhcC-CCCEEE
Q 029910           74 HTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLA-ADGSVI  152 (185)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~~-~~g~~i  152 (185)
                      +|                       ..++||||++    .++|+|+|++|+||.||+-.|+..++||+||+|+ ++|.++
T Consensus       423 ~G-----------------------e~nVLVaTSV----gEEGLDIp~vDlVifYEpvpSeIR~IQR~GRTGR~r~Grv~  475 (542)
T COG1111         423 KG-----------------------EYNVLVATSV----GEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGRKRKGRVV  475 (542)
T ss_pred             cC-----------------------CceEEEEccc----ccccCCCCcccEEEEecCCcHHHHHHHhhCccccCCCCeEE
Confidence            99                       6999999999    9999999999999999999999999999999965 568998


Q ss_pred             EEeeCc
Q 029910          153 NIVVGG  158 (185)
Q Consensus       153 ~~v~~~  158 (185)
                      .+++.+
T Consensus       476 vLvt~g  481 (542)
T COG1111         476 VLVTEG  481 (542)
T ss_pred             EEEecC
Confidence            888776

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=99.85  E-value=4.1e-21  Score=168.55  Aligned_cols=141  Identities=19%  Similarity=0.255  Sum_probs=115.4

Q ss_pred             ecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccc
Q 029910            5 FTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVT   84 (185)
Q Consensus         5 ~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~   84 (185)
                      ..++++++-++.. ++-+.=.++.|||+||-+.+-.|.-.|...| ++...|+|.||...|..++++|..|         
T Consensus       249 cse~DKflllyal-lKL~LI~gKsliFVNtIdr~YrLkLfLeqFG-iksciLNseLP~NSR~Hii~QFNkG---------  317 (569)
T KOG0346|consen  249 CSEEDKFLLLYAL-LKLRLIRGKSLIFVNTIDRCYRLKLFLEQFG-IKSCILNSELPANSRCHIIEQFNKG---------  317 (569)
T ss_pred             eccchhHHHHHHH-HHHHHhcCceEEEEechhhhHHHHHHHHHhC-cHhhhhcccccccchhhHHHHhhCc---------
Confidence            3455665554443 3223334899999999999999999999998 9999999999999999999999999         


Q ss_pred             ccCCCCCCCCCCCCceeEEEEecCC-------C------------------------CcccCcCCCCCCcEEEEcCCCCC
Q 029910           85 EQSGDESETGKDEHKSHMIVVTDAC-------L------------------------PLLSSGESAISARVLINYELPTK  133 (185)
Q Consensus        85 ~~~~~~~~~~~~~~~~~iLV~Td~~-------~------------------------~~~~~G~d~~~v~~VI~~d~P~~  133 (185)
                                    ..+++||||..       .                        --++||+|+..|..|||||+|.+
T Consensus       318 --------------~YdivIAtD~s~~~~~~eee~kgk~~e~~~kndkkskkK~D~E~GVsRGIDF~~V~~VlNFD~P~t  383 (569)
T KOG0346|consen  318 --------------LYDIVIATDDSADGDKLEEEVKGKSDEKNPKNDKKSKKKLDKESGVSRGIDFHHVSNVLNFDFPET  383 (569)
T ss_pred             --------------ceeEEEEccCccchhhhhccccccccccCCCCccccccccCchhchhccccchheeeeeecCCCCc
Confidence                          57777777710       0                        00369999999999999999999


Q ss_pred             HHHHHHHHhhh--cCCCCEEEEEeeCchHHHHHHHHHHh
Q 029910          134 KETYIRRMTTC--LAADGSVINIVVGGEVVTLRSMEESL  170 (185)
Q Consensus       134 ~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~~~~l~~~~  170 (185)
                      +..|+||+||+  ++++|.+++||.+.+......+|...
T Consensus       384 ~~sYIHRvGRTaRg~n~GtalSfv~P~e~~g~~~le~~~  422 (569)
T KOG0346|consen  384 VTSYIHRVGRTARGNNKGTALSFVSPKEEFGKESLESIL  422 (569)
T ss_pred             hHHHHHhccccccCCCCCceEEEecchHHhhhhHHHHHH
Confidence            99999999996  78899999999998887666666553

>KOG4284 consensus DEAD box protein [Transcription]

Probab=99.84  E-value=7.1e-21  Score=173.22  Aligned_cols=131  Identities=17%  Similarity=0.352  Sum_probs=119.0

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ   86 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~   86 (185)
                      .++.++..|..+++ +.+..++||||+....|+-++..|++.| +.+.++.|.|++.+|..+++++|+.           
T Consensus       255 emrlklq~L~~vf~-~ipy~QAlVF~~~~sra~~~a~~L~ssG-~d~~~ISgaM~Q~~Rl~a~~~lr~f-----------  321 (980)
T KOG4284|consen  255 EMRLKLQKLTHVFK-SIPYVQALVFCDQISRAEPIATHLKSSG-LDVTFISGAMSQKDRLLAVDQLRAF-----------  321 (980)
T ss_pred             HHHHHHHHHHHHHh-hCchHHHHhhhhhhhhhhHHHHHhhccC-CCeEEeccccchhHHHHHHHHhhhc-----------
Confidence            45667788888777 8899999999999999999999999999 8999999999999999999999999           


Q ss_pred             CCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchH-HHH
Q 029910           87 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEV-VTL  163 (185)
Q Consensus        87 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~-~~~  163 (185)
                                  ..+|||+||+    .+||+|.+.|++|||.|.|.+-++|.|||||+  .|..|.+++|+..+.. ..|
T Consensus       322 ------------~~rILVsTDL----taRGIDa~~vNLVVNiD~p~d~eTY~HRIGRAgRFG~~G~aVT~~~~~~e~~~f  385 (980)
T KOG4284|consen  322 ------------RVRILVSTDL----TARGIDADNVNLVVNIDAPADEETYFHRIGRAGRFGAHGAAVTLLEDERELKGF  385 (980)
T ss_pred             ------------eEEEEEecch----hhccCCccccceEEecCCCcchHHHHHHhhhcccccccceeEEEeccchhhhhh
Confidence                        7999999999    99999999999999999999999999999997  5778999999976543 555


Q ss_pred             HHH
Q 029910          164 RSM  166 (185)
Q Consensus       164 ~~l  166 (185)
                      ..+
T Consensus       386 ~~m  388 (980)
T KOG4284|consen  386 TAM  388 (980)
T ss_pred             HHH
Confidence            444

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=99.83  E-value=6.8e-20  Score=170.88  Aligned_cols=143  Identities=17%  Similarity=0.217  Sum_probs=123.4

Q ss_pred             HHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCC
Q 029910           11 LVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDE   90 (185)
Q Consensus        11 l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~   90 (185)
                      +..++..|......+.++||||+|+..++.|++.|...| +.+..+||+++..+|.+++++|+.|               
T Consensus       432 ~~~L~~~L~~~~~~g~~viIf~~t~~~ae~L~~~L~~~g-i~~~~~h~~~~~~~R~~~l~~f~~g---------------  495 (652)
T PRK05298        432 VDDLLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELG-IKVRYLHSDIDTLERVEIIRDLRLG---------------  495 (652)
T ss_pred             HHHHHHHHHHHHhCCCEEEEEeCCHHHHHHHHHHHhhcc-eeEEEEECCCCHHHHHHHHHHHHcC---------------
Confidence            334455544334567899999999999999999999998 8999999999999999999999999               


Q ss_pred             CCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCC-----CCCHHHHHHHHhhhcC-CCCEEEEEeeC-------
Q 029910           91 SETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYEL-----PTKKETYIRRMTTCLA-ADGSVINIVVG-------  157 (185)
Q Consensus        91 ~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~-----P~~~~~yiqR~GR~~~-~~g~~i~~v~~-------  157 (185)
                              ...++|||++    +++|+|+|++++||++|.     |.+..+|+||+||+++ ..|.+++|++.       
T Consensus       496 --------~i~vlV~t~~----L~rGfdlp~v~lVii~d~eifG~~~~~~~yiqr~GR~gR~~~G~~i~~~~~~~~~~~~  563 (652)
T PRK05298        496 --------EFDVLVGINL----LREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDSMQK  563 (652)
T ss_pred             --------CceEEEEeCH----HhCCccccCCcEEEEeCCcccccCCCHHHHHHHhccccCCCCCEEEEEecCCCHHHHH
Confidence                    7999999999    999999999999999985     8899999999999754 46999999984       


Q ss_pred             --chHHHHHHHHHHhCCccccccCCc
Q 029910          158 --GEVVTLRSMEESLGLIVAEVPINI  181 (185)
Q Consensus       158 --~e~~~~~~l~~~~~~~~~~~~~~~  181 (185)
                        .+...+++++..++.+...+|-++
T Consensus       564 ~~~~~~~~~~i~~~~~~~~~~~~~~~  589 (652)
T PRK05298        564 AIDETERRREIQIAYNEEHGITPKTI  589 (652)
T ss_pred             HHHHHHHHHHHHHHhhhccCCCChhH
Confidence              467777888888888887777554

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.83  E-value=1.1e-19  Score=174.29  Aligned_cols=138  Identities=14%  Similarity=0.150  Sum_probs=105.7

Q ss_pred             HHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCC-----CceEEEEecCCCHHHHHHHHHHHhcccccccccccc
Q 029910           11 LVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLA-----DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE   85 (185)
Q Consensus        11 l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~-----~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~   85 (185)
                      +.+.+..++.   .++++||||||++.|+.++..|....     ...+..+||+|++++|..++++|++|          
T Consensus       273 l~~~L~~~i~---~~~~~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls~~~R~~ve~~fk~G----------  339 (876)
T PRK13767        273 LYETLHELIK---EHRTTLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEVEEKLKRG----------  339 (876)
T ss_pred             HHHHHHHHHh---cCCCEEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCCHHHHHHHHHHHHcC----------
Confidence            3444444333   35799999999999999999998631     25799999999999999999999999          


Q ss_pred             cCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhcCCC---CEEEEEee-CchH-
Q 029910           86 QSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAAD---GSVINIVV-GGEV-  160 (185)
Q Consensus        86 ~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~~~~---g~~i~~v~-~~e~-  160 (185)
                                   ..++||||+.    +++|+|+|++++||+|+.|.++.+|+||+||+|++.   +.++.+.. ..+. 
T Consensus       340 -------------~i~vLVaTs~----Le~GIDip~Vd~VI~~~~P~sv~~ylQRiGRaGR~~g~~~~g~ii~~~~~~l~  402 (876)
T PRK13767        340 -------------ELKVVVSSTS----LELGIDIGYIDLVVLLGSPKSVSRLLQRIGRAGHRLGEVSKGRIIVVDRDDLV  402 (876)
T ss_pred             -------------CCeEEEECCh----HHhcCCCCCCcEEEEeCCCCCHHHHHHhcccCCCCCCCCCcEEEEEcCchhHH
Confidence                         6999999999    999999999999999999999999999999986543   23333333 3332 


Q ss_pred             HHHHHHHHHhCCcccccc
Q 029910          161 VTLRSMEESLGLIVAEVP  178 (185)
Q Consensus       161 ~~~~~l~~~~~~~~~~~~  178 (185)
                      +...-++......++++.
T Consensus       403 e~~~~~~~~~~~~ie~~~  420 (876)
T PRK13767        403 ECAVLLKKAREGKIDRVH  420 (876)
T ss_pred             HHHHHHHHHHhCCCCCCC
Confidence            222233444555555543

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=99.83  E-value=2.8e-20  Score=175.83  Aligned_cols=144  Identities=19%  Similarity=0.374  Sum_probs=125.2

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ   86 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~   86 (185)
                      +.+++..|+..|-. .....++||||..+..|+.+.+.|.+.| +.+..|||+.++.+|..++++|+++           
T Consensus       596 e~eKf~kL~eLl~e-~~e~~~tiiFv~~qe~~d~l~~~L~~ag-~~~~slHGgv~q~dR~sti~dfK~~-----------  662 (997)
T KOG0334|consen  596 ENEKFLKLLELLGE-RYEDGKTIIFVDKQEKADALLRDLQKAG-YNCDSLHGGVDQHDRSSTIEDFKNG-----------  662 (997)
T ss_pred             chHHHHHHHHHHHH-HhhcCCEEEEEcCchHHHHHHHHHHhcC-cchhhhcCCCchHHHHhHHHHHhcc-----------
Confidence            55566666665433 4446899999999999999999999888 7888899999999999999999999           


Q ss_pred             CCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHHHHH
Q 029910           87 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLR  164 (185)
Q Consensus        87 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~~~  164 (185)
                                  .+.+||+|++    ++||+|+.+..+|||||+|...++|+||+||+  +|+.|.|++|+.+.+....-
T Consensus       663 ------------~~~LLvaTsv----varGLdv~~l~Lvvnyd~pnh~edyvhR~gRTgragrkg~AvtFi~p~q~~~a~  726 (997)
T KOG0334|consen  663 ------------VVNLLVATSV----VARGLDVKELILVVNYDFPNHYEDYVHRVGRTGRAGRKGAAVTFITPDQLKYAG  726 (997)
T ss_pred             ------------CceEEEehhh----hhcccccccceEEEEcccchhHHHHHHHhcccccCCccceeEEEeChHHhhhHH
Confidence                        7999999999    99999999999999999999999999999997  67889999999998888878


Q ss_pred             HHHHHhCCccccccC
Q 029910          165 SMEESLGLIVAEVPI  179 (185)
Q Consensus       165 ~l~~~~~~~~~~~~~  179 (185)
                      .|.+.+...-.++|-
T Consensus       727 dl~~al~~~~~~~P~  741 (997)
T KOG0334|consen  727 DLCKALELSKQPVPK  741 (997)
T ss_pred             HHHHHHHhccCCCch
Confidence            887777554445553

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.82  E-value=1.9e-19  Score=167.71  Aligned_cols=131  Identities=16%  Similarity=0.219  Sum_probs=113.7

Q ss_pred             HHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCC
Q 029910           11 LVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDE   90 (185)
Q Consensus        11 l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~   90 (185)
                      +..|++.|......+.++||||+|++.++.|++.|...| +.+..+||+++..+|.+++++|+.|               
T Consensus       428 i~~Ll~eI~~~~~~g~~vLIf~~tk~~ae~L~~~L~~~g-i~~~~lh~~~~~~eR~~~l~~fr~G---------------  491 (655)
T TIGR00631       428 VDDLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELG-IKVRYLHSEIDTLERVEIIRDLRLG---------------  491 (655)
T ss_pred             HHHHHHHHHHHHcCCCEEEEEECCHHHHHHHHHHHhhhc-cceeeeeCCCCHHHHHHHHHHHhcC---------------
Confidence            334555544434567899999999999999999999998 8999999999999999999999999               


Q ss_pred             CCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcC-----CCCCHHHHHHHHhhhcC-CCCEEEEEeeCchHHHHH
Q 029910           91 SETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYE-----LPTKKETYIRRMTTCLA-ADGSVINIVVGGEVVTLR  164 (185)
Q Consensus        91 ~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d-----~P~~~~~yiqR~GR~~~-~~g~~i~~v~~~e~~~~~  164 (185)
                              .+++||||+.    +++|+|+|++++||++|     .|.+..+|+||+||+++ ..|.++++++..+..+..
T Consensus       492 --------~i~VLV~t~~----L~rGfDiP~v~lVvi~DadifG~p~~~~~~iqriGRagR~~~G~vi~~~~~~~~~~~~  559 (655)
T TIGR00631       492 --------EFDVLVGINL----LREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVIMYADKITDSMQK  559 (655)
T ss_pred             --------CceEEEEcCh----hcCCeeeCCCcEEEEeCcccccCCCCHHHHHHHhcCCCCCCCCEEEEEEcCCCHHHHH
Confidence                    7999999999    99999999999999999     89999999999999865 458999999887665555


Q ss_pred             HHHHH
Q 029910          165 SMEES  169 (185)
Q Consensus       165 ~l~~~  169 (185)
                      .+++.
T Consensus       560 ai~~~  564 (655)
T TIGR00631       560 AIEET  564 (655)
T ss_pred             HHHHH
Confidence            55544

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

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

Probab=99.82  E-value=1.9e-19  Score=164.62  Aligned_cols=120  Identities=20%  Similarity=0.322  Sum_probs=109.6

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCcee
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSH  101 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (185)
                      .......||||.|++.++.++++|...| +++..+|++|+.++|..+-++|..+                       +.+
T Consensus       227 ~~~~~~GIIYc~sRk~~E~ia~~L~~~g-~~a~~YHaGl~~~eR~~~q~~f~~~-----------------------~~~  282 (590)
T COG0514         227 PQLSKSGIIYCLTRKKVEELAEWLRKNG-ISAGAYHAGLSNEERERVQQAFLND-----------------------EIK  282 (590)
T ss_pred             cccCCCeEEEEeeHHhHHHHHHHHHHCC-CceEEecCCCCHHHHHHHHHHHhcC-----------------------CCc
Confidence            4455779999999999999999999998 8999999999999999999999999                       799


Q ss_pred             EEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCchHHHHHHHHHH
Q 029910          102 MIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGGEVVTLRSMEES  169 (185)
Q Consensus       102 iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e~~~~~~l~~~  169 (185)
                      |+|||.+    +.+|+|-|+|++|||||+|.|+++|.|-+||+|  |.+..|+.++.+.|....+.+.+.
T Consensus       283 iiVAT~A----FGMGIdKpdVRfViH~~lP~s~EsYyQE~GRAGRDG~~a~aill~~~~D~~~~~~~i~~  348 (590)
T COG0514         283 VMVATNA----FGMGIDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSPEDIRWQRYLIEQ  348 (590)
T ss_pred             EEEEecc----ccCccCCCCceEEEEecCCCCHHHHHHHHhhccCCCCcceEEEeeccccHHHHHHHHHh
Confidence            9999999    999999999999999999999999999999984  677899999999887766555443

>PRK13766 Hef nuclease; Provisional

Probab=99.80  E-value=8.4e-19  Score=165.80  Aligned_cols=123  Identities=21%  Similarity=0.309  Sum_probs=109.2

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecC--------CCHHHHHHHHHHHhccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSD--------LAETERTLILEEFRHTAMK   78 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~--------~~~~~R~~~l~~F~~~~~~   78 (185)
                      |.+.+.++|+.+.. ..++.++||||+++++|+.|.+.|...+ +.+..+||.        |++.+|.+++++|+.+   
T Consensus       348 K~~~L~~il~~~~~-~~~~~kvlIF~~~~~t~~~L~~~L~~~~-~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~g---  422 (773)
T PRK13766        348 KLEKLREIVKEQLG-KNPDSRIIVFTQYRDTAEKIVDLLEKEG-IKAVRFVGQASKDGDKGMSQKEQIEILDKFRAG---  422 (773)
T ss_pred             HHHHHHHHHHHHHh-cCCCCeEEEEeCcHHHHHHHHHHHHhCC-CceEEEEccccccccCCCCHHHHHHHHHHHHcC---
Confidence            56667777777554 4677999999999999999999998887 789999986        9999999999999998   


Q ss_pred             ccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhcC-CCCEEEEEeeC
Q 029910           79 WNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLA-ADGSVINIVVG  157 (185)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~~-~~g~~i~~v~~  157 (185)
                                          ..++||+|++    +++|+|+|++++||+||+|+++..|+||+||+++ .+|.++.++..
T Consensus       423 --------------------~~~vLvaT~~----~~eGldi~~~~~VI~yd~~~s~~r~iQR~GR~gR~~~~~v~~l~~~  478 (773)
T PRK13766        423 --------------------EFNVLVSTSV----AEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRTGRQEEGRVVVLIAK  478 (773)
T ss_pred             --------------------CCCEEEECCh----hhcCCCcccCCEEEEeCCCCCHHHHHHHhcccCcCCCCEEEEEEeC
Confidence                                6999999999    9999999999999999999999999999999855 34888888876


Q ss_pred             c
Q 029910          158 G  158 (185)
Q Consensus       158 ~  158 (185)
                      +
T Consensus       479 ~  479 (773)
T PRK13766        479 G  479 (773)
T ss_pred             C
Confidence            4

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.80  E-value=5.5e-19  Score=174.86  Aligned_cols=130  Identities=13%  Similarity=0.126  Sum_probs=103.8

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcCC--------------------------------CceEEEEecCCCHHHHHHHHHH
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNLA--------------------------------DISFSSLHSDLAETERTLILEE   71 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~~--------------------------------~~~~~~l~g~~~~~~R~~~l~~   71 (185)
                      .+.++||||||++.|+.++..|++..                                ...+..+||+|++++|..+.+.
T Consensus       243 ~~~stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~HHGsLSkeeR~~IE~~  322 (1490)
T PRK09751        243 RHRSTIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVDAAHFESTSGATSNRVQSSDVFIARSHHGSVSKEQRAITEQA  322 (1490)
T ss_pred             cCCCEEEECCCHHHHHHHHHHHHHhhhhhccccccccchhhhhhhccccchhccccccceeeeeccccCCHHHHHHHHHH
Confidence            35899999999999999999997531                                0125789999999999999999


Q ss_pred             HhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhcCCC-CE
Q 029910           72 FRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAAD-GS  150 (185)
Q Consensus        72 F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~~~~-g~  150 (185)
                      |++|                       .+++||||+.    +++|+|++++++||||+.|.++.+|+||+||++++. |.
T Consensus       323 fK~G-----------------------~LrvLVATss----LELGIDIg~VDlVIq~gsP~sVas~LQRiGRAGR~~gg~  375 (1490)
T PRK09751        323 LKSG-----------------------ELRCVVATSS----LELGIDMGAVDLVIQVATPLSVASGLQRIGRAGHQVGGV  375 (1490)
T ss_pred             HHhC-----------------------CceEEEeCcH----HHccCCcccCCEEEEeCCCCCHHHHHHHhCCCCCCCCCc
Confidence            9999                       7999999999    999999999999999999999999999999997654 33


Q ss_pred             EEEEeeCchHHH-H---HHHHHHhCCccccccCC
Q 029910          151 VINIVVGGEVVT-L---RSMEESLGLIVAEVPIN  180 (185)
Q Consensus       151 ~i~~v~~~e~~~-~---~~l~~~~~~~~~~~~~~  180 (185)
                      +..++.+.+... +   --++..+...++++..+
T Consensus       376 s~gli~p~~r~dlle~~~~ve~~l~g~iE~~~~p  409 (1490)
T PRK09751        376 SKGLFFPRTRRDLVDSAVIVECMFAGRLENLTPP  409 (1490)
T ss_pred             cEEEEEeCcHHHHHhhHHHHHHHhcCCCCccCCC
Confidence            333333323222 2   23677777777775544

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.79  E-value=1.5e-18  Score=160.74  Aligned_cols=125  Identities=13%  Similarity=0.099  Sum_probs=99.5

Q ss_pred             cchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccc
Q 029910            6 TFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE   85 (185)
Q Consensus         6 ~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~   85 (185)
                      ++.++...|.+.+......+.++||||+|+..++.++..|...| +++..+||+++.  |...+..|+.+          
T Consensus       454 t~~~K~~aL~~~i~~~~~~~~pvLIft~t~~~se~L~~~L~~~g-i~~~~Lhg~~~~--rE~~ii~~ag~----------  520 (656)
T PRK12898        454 TAAAKWAAVAARVRELHAQGRPVLVGTRSVAASERLSALLREAG-LPHQVLNAKQDA--EEAAIVARAGQ----------  520 (656)
T ss_pred             CHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCC-CCEEEeeCCcHH--HHHHHHHHcCC----------
Confidence            33444444444432222346889999999999999999999998 899999998664  44555566655          


Q ss_pred             cCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCC---CCc-----EEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEe
Q 029910           86 QSGDESETGKDEHKSHMIVVTDACLPLLSSGESAI---SAR-----VLINYELPTKKETYIRRMTTC--LAADGSVINIV  155 (185)
Q Consensus        86 ~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~---~v~-----~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v  155 (185)
                                   +..|+||||+    ++||+|++   +|.     +|||||+|.+...|+||+||+  .|.+|.+++|+
T Consensus       521 -------------~g~VlVATdm----AgRGtDI~l~~~V~~~GGLhVI~~d~P~s~r~y~hr~GRTGRqG~~G~s~~~i  583 (656)
T PRK12898        521 -------------RGRITVATNM----AGRGTDIKLEPGVAARGGLHVILTERHDSARIDRQLAGRCGRQGDPGSYEAIL  583 (656)
T ss_pred             -------------CCcEEEEccc----hhcccCcCCccchhhcCCCEEEEcCCCCCHHHHHHhcccccCCCCCeEEEEEe
Confidence                         4679999999    99999999   666     999999999999999999997  46779999999


Q ss_pred             eCchH
Q 029910          156 VGGEV  160 (185)
Q Consensus       156 ~~~e~  160 (185)
                      +..|.
T Consensus       584 s~eD~  588 (656)
T PRK12898        584 SLEDD  588 (656)
T ss_pred             chhHH
Confidence            87553

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.78  E-value=1.8e-18  Score=163.19  Aligned_cols=125  Identities=15%  Similarity=0.181  Sum_probs=104.7

Q ss_pred             cchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccc
Q 029910            6 TFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE   85 (185)
Q Consensus         6 ~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~   85 (185)
                      +..++...+++.+......+.|+||||+|++.++.++..|...| +.+..+||++++.++..+...++.           
T Consensus       409 ~~~~K~~al~~~i~~~~~~~~pvLIf~~t~~~se~l~~~L~~~g-i~~~~L~~~~~~~e~~~i~~ag~~-----------  476 (790)
T PRK09200        409 TLDEKYKAVIEEVKERHETGRPVLIGTGSIEQSETFSKLLDEAG-IPHNLLNAKNAAKEAQIIAEAGQK-----------  476 (790)
T ss_pred             CHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCC-CCEEEecCCccHHHHHHHHHcCCC-----------
Confidence            34444444555543323567999999999999999999999998 899999999999888877777655           


Q ss_pred             cCCCCCCCCCCCCceeEEEEecCCCCcccCcCCC---CCCc-----EEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEe
Q 029910           86 QSGDESETGKDEHKSHMIVVTDACLPLLSSGESA---ISAR-----VLINYELPTKKETYIRRMTTC--LAADGSVINIV  155 (185)
Q Consensus        86 ~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~---~~v~-----~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v  155 (185)
                                    .+|+||||+    ++||+|+   |+|.     +|||||+|.+...|+||+||+  .|.+|.+++|+
T Consensus       477 --------------g~VlIATdm----AgRG~DI~l~~~V~~~GGL~VI~~d~p~s~r~y~qr~GRtGR~G~~G~s~~~i  538 (790)
T PRK09200        477 --------------GAVTVATNM----AGRGTDIKLGEGVHELGGLAVIGTERMESRRVDLQLRGRSGRQGDPGSSQFFI  538 (790)
T ss_pred             --------------CeEEEEccc----hhcCcCCCcccccccccCcEEEeccCCCCHHHHHHhhccccCCCCCeeEEEEE
Confidence                          369999999    9999999   7998     999999999999999999997  46779999999


Q ss_pred             eCchH
Q 029910          156 VGGEV  160 (185)
Q Consensus       156 ~~~e~  160 (185)
                      +..|.
T Consensus       539 s~eD~  543 (790)
T PRK09200        539 SLEDD  543 (790)
T ss_pred             cchHH
Confidence            87543

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

Probab=99.76  E-value=7.3e-19  Score=153.75  Aligned_cols=144  Identities=19%  Similarity=0.261  Sum_probs=127.2

Q ss_pred             ecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccc
Q 029910            5 FTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVT   84 (185)
Q Consensus         5 ~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~   84 (185)
                      +...+.+...|-.++.+....+++||||.|+.+++++...|...| +.+..++|.|+++.|...+.+|+.+         
T Consensus       241 ~~~~a~K~aaLl~il~~~~~~~~t~vf~~tk~hve~~~~ll~~~g-~~~s~iysslD~~aRk~~~~~F~~~---------  310 (529)
T KOG0337|consen  241 RVRKAEKEAALLSILGGRIKDKQTIVFVATKHHVEYVRGLLRDFG-GEGSDIYSSLDQEARKINGRDFRGR---------  310 (529)
T ss_pred             eeccHHHHHHHHHHHhccccccceeEEecccchHHHHHHHHHhcC-CCccccccccChHhhhhccccccCC---------
Confidence            344444444444445546667899999999999999999999998 7999999999999999999999998         


Q ss_pred             ccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHHH
Q 029910           85 EQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVT  162 (185)
Q Consensus        85 ~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~  162 (185)
                                    +..+||+||+    ++||+|+|-.+.|||||+|.+..-|+||+||.  +|+.|.++++|.+.+..+
T Consensus       311 --------------k~~~lvvTdv----aaRG~diplldnvinyd~p~~~klFvhRVgr~aragrtg~aYs~V~~~~~~y  372 (529)
T KOG0337|consen  311 --------------KTSILVVTDV----AARGLDIPLLDNVINYDFPPDDKLFVHRVGRVARAGRTGRAYSLVASTDDPY  372 (529)
T ss_pred             --------------ccceEEEehh----hhccCCCccccccccccCCCCCceEEEEecchhhccccceEEEEEecccchh
Confidence                          7999999999    99999999999999999999999999999996  689999999999999999


Q ss_pred             HHHHHHHhCCcccc
Q 029910          163 LRSMEESLGLIVAE  176 (185)
Q Consensus       163 ~~~l~~~~~~~~~~  176 (185)
                      +.++..+++..+..
T Consensus       373 l~DL~lflgr~~~~  386 (529)
T KOG0337|consen  373 LLDLQLFLGRPLIF  386 (529)
T ss_pred             hhhhhhhcCCceee
Confidence            99999999876543

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.76  E-value=3.3e-18  Score=164.35  Aligned_cols=130  Identities=12%  Similarity=0.157  Sum_probs=109.6

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcC-CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeE
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNL-ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHM  102 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~-~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  102 (185)
                      .+.+++||||++++++.+++.|... +++++..+||+|++.+|.+++++|++|                       +.+|
T Consensus       659 ~g~qv~if~n~i~~~e~l~~~L~~~~p~~~v~~lHG~m~~~eRe~im~~F~~G-----------------------k~~I  715 (926)
T TIGR00580       659 RGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKG-----------------------EFQV  715 (926)
T ss_pred             cCCeEEEEECCcHHHHHHHHHHHHhCCCCeEEEecCCCCHHHHHHHHHHHHcC-----------------------CCCE
Confidence            3589999999999999999999875 347999999999999999999999999                       7999


Q ss_pred             EEEecCCCCcccCcCCCCCCcEEEEcCCCC-CHHHHHHHHhhh--cCCCCEEEEEeeC------chHHHHHHHHHHh---
Q 029910          103 IVVTDACLPLLSSGESAISARVLINYELPT-KKETYIRRMTTC--LAADGSVINIVVG------GEVVTLRSMEESL---  170 (185)
Q Consensus       103 LV~Td~~~~~~~~G~d~~~v~~VI~~d~P~-~~~~yiqR~GR~--~~~~g~~i~~v~~------~e~~~~~~l~~~~---  170 (185)
                      ||||++    +++|+|+|++++||+++.|. +...|.||+||+  ++..|.|++++..      .....++.+++..   
T Consensus       716 LVaT~i----ie~GIDIp~v~~VIi~~a~~~gls~l~Qr~GRvGR~g~~g~aill~~~~~~l~~~~~~RL~~~~~~~~~g  791 (926)
T TIGR00580       716 LVCTTI----IETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQKALTEDAQKRLEAIQEFSELG  791 (926)
T ss_pred             EEECCh----hhcccccccCCEEEEecCCCCCHHHHHHHhcCCCCCCCCeEEEEEECCcccCCHHHHHHHHHHHHhhcch
Confidence            999999    99999999999999999976 678999999997  4566999999854      3456666776653   


Q ss_pred             -CCccccccCC
Q 029910          171 -GLIVAEVPIN  180 (185)
Q Consensus       171 -~~~~~~~~~~  180 (185)
                       |..+++.++.
T Consensus       792 ~gf~ia~~Dl~  802 (926)
T TIGR00580       792 AGFKIALHDLE  802 (926)
T ss_pred             hhHHHHHHHHH
Confidence             5555544443

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.

>cd00079 HELICc Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process

Probab=99.76  E-value=2.2e-17  Score=121.71  Aligned_cols=102  Identities=27%  Similarity=0.509  Sum_probs=93.4

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEE
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMI  103 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iL  103 (185)
                      ++.++||||++.+.++.+++.|...+ ..+..+||+++..+|..+++.|+.+                       ...+|
T Consensus        27 ~~~~~lvf~~~~~~~~~~~~~l~~~~-~~~~~~~~~~~~~~~~~~~~~f~~~-----------------------~~~il   82 (131)
T cd00079          27 KGGKVLIFCPSKKMLDELAELLRKPG-IKVAALHGDGSQEEREEVLKDFREG-----------------------EIVVL   82 (131)
T ss_pred             CCCcEEEEeCcHHHHHHHHHHHHhcC-CcEEEEECCCCHHHHHHHHHHHHcC-----------------------CCcEE
Confidence            57899999999999999999998876 7899999999999999999999998                       68999


Q ss_pred             EEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEE
Q 029910          104 VVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVIN  153 (185)
Q Consensus       104 V~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~  153 (185)
                      ++|..    +++|+|+|.+++||.+++|++...|.|++||++  ++.|.++.
T Consensus        83 i~t~~----~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~  130 (131)
T cd00079          83 VATDV----IARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAIL  130 (131)
T ss_pred             EEcCh----hhcCcChhhCCEEEEeCCCCCHHHheecccccccCCCCceEEe
Confidence            99999    999999999999999999999999999999974  44565543

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.75  E-value=1e-17  Score=156.39  Aligned_cols=115  Identities=16%  Similarity=0.172  Sum_probs=97.7

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcCC-CceEEEEecCCCHHHHHHHHHHH-hcccccccccccccCCCCCCCCCCCCcee
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNLA-DISFSSLHSDLAETERTLILEEF-RHTAMKWNQKVTEQSGDESETGKDEHKSH  101 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~~-~~~~~~l~g~~~~~~R~~~l~~F-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (185)
                      .+.++||||+++..++.+++.|.... ++.+..+||+|++.  .+.+++| ++|                       +.+
T Consensus       394 ~~g~iLVFlpg~~ei~~l~~~L~~~~~~~~v~~LHG~Lsq~--eq~l~~ff~~g-----------------------k~k  448 (675)
T PHA02653        394 KGSSGIVFVASVSQCEEYKKYLEKRLPIYDFYIIHGKVPNI--DEILEKVYSSK-----------------------NPS  448 (675)
T ss_pred             cCCcEEEEECcHHHHHHHHHHHHhhcCCceEEeccCCcCHH--HHHHHHHhccC-----------------------cee
Confidence            45789999999999999999998761 38999999999975  5677887 566                       799


Q ss_pred             EEEEecCCCCcccCcCCCCCCcEEEEcC---CCC---------CHHHHHHHHhhhcC-CCCEEEEEeeCchHHHHHHHH
Q 029910          102 MIVVTDACLPLLSSGESAISARVLINYE---LPT---------KKETYIRRMTTCLA-ADGSVINIVVGGEVVTLRSME  167 (185)
Q Consensus       102 iLV~Td~~~~~~~~G~d~~~v~~VI~~d---~P~---------~~~~yiqR~GR~~~-~~g~~i~~v~~~e~~~~~~l~  167 (185)
                      ||||||+    ++||+|+|+|++||+++   .|.         |.++|+||+||+|+ ++|.|+.|++..+...+.++.
T Consensus       449 ILVATdI----AERGIDIp~V~~VID~G~~k~p~~~~g~~~~iSkasa~QRaGRAGR~~~G~c~rLyt~~~~~pI~ri~  523 (675)
T PHA02653        449 IIISTPY----LESSVTIRNATHVYDTGRVYVPEPFGGKEMFISKSMRTQRKGRVGRVSPGTYVYFYDLDLLKPIKRID  523 (675)
T ss_pred             EEeccCh----hhccccccCeeEEEECCCccCCCcccCcccccCHHHHHHhccCcCCCCCCeEEEEECHHHhHHHHHHh
Confidence            9999999    99999999999999998   665         88999999999865 569999999876654444443

>PF00271 Helicase_C: Helicase conserved C-terminal domain; InterPro: IPR001650 The domain, which defines this group of proteins is found in a wide variety of helicases and helicase related proteins

Probab=99.75  E-value=5e-18  Score=116.46  Aligned_cols=76  Identities=26%  Similarity=0.421  Sum_probs=71.4

Q ss_pred             HHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCc
Q 029910           44 AVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISAR  123 (185)
Q Consensus        44 ~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~  123 (185)
                      .|+..+ +.+..+||+++..+|.+++++|+++                       ..++||+|++    +++|+|+|+++
T Consensus         2 ~L~~~~-~~~~~i~~~~~~~~r~~~~~~f~~~-----------------------~~~vli~t~~----~~~Gid~~~~~   53 (78)
T PF00271_consen    2 FLEKKG-IKVAIIHGDMSQKERQEILKKFNSG-----------------------EIRVLIATDI----LGEGIDLPDAS   53 (78)
T ss_dssp             HHHHTT-SSEEEESTTSHHHHHHHHHHHHHTT-----------------------SSSEEEESCG----GTTSSTSTTES
T ss_pred             ChHHCC-CcEEEEECCCCHHHHHHHHHHhhcc-----------------------CceEEEeecc----ccccccccccc
Confidence            567777 8999999999999999999999999                       5799999999    99999999999


Q ss_pred             EEEEcCCCCCHHHHHHHHhhhcCC
Q 029910          124 VLINYELPTKKETYIRRMTTCLAA  147 (185)
Q Consensus       124 ~VI~~d~P~~~~~yiqR~GR~~~~  147 (185)
                      +||+|++|+++..|.|++||+++.
T Consensus        54 ~vi~~~~~~~~~~~~Q~~GR~~R~   77 (78)
T PF00271_consen   54 HVIFYDPPWSPEEYIQRIGRAGRI   77 (78)
T ss_dssp             EEEESSSESSHHHHHHHHTTSSTT
T ss_pred             cccccccCCCHHHHHHHhhcCCCC
Confidence            999999999999999999998654

It may be that this is not an autonomously folding unit, but an integral part of the helicase. The eukaryotic translation initiation factor 4A (eIF4A) is a member of the DEA(D/H)-box RNA helicase family This is a diverse group of proteins that couples an ATPase activity to RNA binding and unwinding. The structure of the carboxyl-terminal domain of eIF4A has been determined to 1.75 A resolution; it has a parallel alpha-beta topology that superimposes, with minor variations, on the structures and conserved motifs of the equivalent domain in other, distantly related helicases [].; GO: 0003676 nucleic acid binding, 0004386 helicase activity, 0005524 ATP binding; PDB: 2Z83_A 2JGN_C 2I4I_A 2BMF_A 2BHR_B 1WP9_E 2WAX_C 2WAY_C 3JUX_A 3DIN_B ....

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

Probab=99.75  E-value=1e-17  Score=147.53  Aligned_cols=133  Identities=23%  Similarity=0.370  Sum_probs=116.3

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcCC--CceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCc
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNLA--DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHK   99 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~~--~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (185)
                      +....++||||.|+..|+.|-+.+...|  .+++.++||+..+.+|.+.++.|+++                       .
T Consensus       502 ~h~mdkaiifcrtk~dcDnLer~~~qkgg~~~scvclhgDrkP~Erk~nle~Fkk~-----------------------d  558 (725)
T KOG0349|consen  502 RHAMDKAIIFCRTKQDCDNLERMMNQKGGKHYSCVCLHGDRKPDERKANLESFKKF-----------------------D  558 (725)
T ss_pred             hhccCceEEEEeccccchHHHHHHHHcCCccceeEEEecCCChhHHHHHHHhhhhc-----------------------C
Confidence            3455899999999999999999998875  37899999999999999999999999                       7


Q ss_pred             eeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeC--------------------
Q 029910          100 SHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVG--------------------  157 (185)
Q Consensus       100 ~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~--------------------  157 (185)
                      .+.|||||+    ++||+|+..+.++||..+|.+...|+||+||.+  -+-|.+|++|..                    
T Consensus       559 vkflictdv----aargldi~g~p~~invtlpd~k~nyvhrigrvgraermglaislvat~~ekvwyh~c~srgr~c~nt  634 (725)
T KOG0349|consen  559 VKFLICTDV----AARGLDITGLPFMINVTLPDDKTNYVHRIGRVGRAERMGLAISLVATVPEKVWYHWCKSRGRSCNNT  634 (725)
T ss_pred             eEEEEEehh----hhccccccCCceEEEEecCcccchhhhhhhccchhhhcceeEEEeeccchheeehhhhccCCcccCC
Confidence            999999999    999999999999999999999999999999964  355777776521                    


Q ss_pred             ------------chHHHHHHHHHHhCCccccccCCc
Q 029910          158 ------------GEVVTLRSMEESLGLIVAEVPINI  181 (185)
Q Consensus       158 ------------~e~~~~~~l~~~~~~~~~~~~~~~  181 (185)
                                  +|.+.+..+|+.+++.++.++..+
T Consensus       635 ~l~e~~gc~iwyne~~llaeve~hln~ti~qv~~~~  670 (725)
T KOG0349|consen  635 NLTEVRGCCIWYNEPNLLAEVEDHLNITIQQVDKTM  670 (725)
T ss_pred             ccccccceEEEeCchhHHHHHHHhhcceeeeeCCCC
Confidence                        466788899999999988776544

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.75  E-value=1.8e-17  Score=155.32  Aligned_cols=131  Identities=15%  Similarity=0.232  Sum_probs=104.4

Q ss_pred             CCCCcEEEEcCCh--------hhHHHHHHHHhcC-CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCC
Q 029910           23 RPGLPMIVCCSSR--------DELDAVCSAVSNL-ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESET   93 (185)
Q Consensus        23 ~~~~~~IIF~~~~--------~~~~~l~~~L~~~-~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~   93 (185)
                      ..+.+++|||+..        ..++.+++.|... +.+.+..+||+|+.++|.+++++|++|                  
T Consensus       469 ~~g~q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g------------------  530 (681)
T PRK10917        469 AKGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAG------------------  530 (681)
T ss_pred             HcCCcEEEEEcccccccchhHHHHHHHHHHHHHHCCCCcEEEEeCCCCHHHHHHHHHHHHcC------------------
Confidence            4568999999853        4566777777755 227899999999999999999999999                  


Q ss_pred             CCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCC-CHHHHHHHHhhhc--CCCCEEEEEee-C---chHHHHHHH
Q 029910           94 GKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPT-KKETYIRRMTTCL--AADGSVINIVV-G---GEVVTLRSM  166 (185)
Q Consensus        94 ~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~-~~~~yiqR~GR~~--~~~g~~i~~v~-~---~e~~~~~~l  166 (185)
                           +.+|||||++    +++|+|+|++++||+|+.|. ....|.||+||+|  +..|.|+.++. +   .....+..+
T Consensus       531 -----~~~ILVaT~v----ie~GiDip~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~ill~~~~~~~~~~~rl~~~  601 (681)
T PRK10917        531 -----EIDILVATTV----IEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDPLSETARERLKIM  601 (681)
T ss_pred             -----CCCEEEECcc----eeeCcccCCCcEEEEeCCCCCCHHHHHHHhhcccCCCCceEEEEEECCCCChhHHHHHHHH
Confidence                 6999999999    99999999999999999998 4677888999974  56799999995 3   244556666


Q ss_pred             HHH-hCCccccccCC
Q 029910          167 EES-LGLIVAEVPIN  180 (185)
Q Consensus       167 ~~~-~~~~~~~~~~~  180 (185)
                      ++. .|..+++.++.
T Consensus       602 ~~~~dgf~iae~dl~  616 (681)
T PRK10917        602 RETNDGFVIAEKDLE  616 (681)
T ss_pred             HHhcchHHHHHHhHh
Confidence            552 45555555443

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.74  E-value=1.5e-17  Score=158.25  Aligned_cols=109  Identities=12%  Similarity=0.158  Sum_probs=97.7

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcC--CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeE
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNL--ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHM  102 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~--~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  102 (185)
                      ..++||||+++..++.+++.|...  .++.+..+||+|++++|.++++.|++|                       ..+|
T Consensus       209 ~g~iLVFlpg~~eI~~l~~~L~~~~~~~~~v~pLHg~L~~~eq~~~~~~~~~G-----------------------~rkV  265 (819)
T TIGR01970       209 TGSILVFLPGQAEIRRVQEQLAERLDSDVLICPLYGELSLAAQDRAIKPDPQG-----------------------RRKV  265 (819)
T ss_pred             CCcEEEEECCHHHHHHHHHHHHhhcCCCcEEEEecCCCCHHHHHHHHhhcccC-----------------------CeEE
Confidence            478999999999999999999863  238999999999999999999999999                       7999


Q ss_pred             EEEecCCCCcccCcCCCCCCcEEEEcCCCCC------------------HHHHHHHHhhhcC-CCCEEEEEeeCchH
Q 029910          103 IVVTDACLPLLSSGESAISARVLINYELPTK------------------KETYIRRMTTCLA-ADGSVINIVVGGEV  160 (185)
Q Consensus       103 LV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~------------------~~~yiqR~GR~~~-~~g~~i~~v~~~e~  160 (185)
                      |||||+    +++|+|+|+|++|||+++|+.                  .++|+||+||+|+ .+|.|+.+++..+.
T Consensus       266 lVATnI----AErgItIp~V~~VID~Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRAGR~~~G~cyrL~t~~~~  338 (819)
T TIGR01970       266 VLATNI----AETSLTIEGIRVVIDSGLARVARFDPKTGITRLETVRISQASATQRAGRAGRLEPGVCYRLWSEEQH  338 (819)
T ss_pred             EEecch----HhhcccccCceEEEEcCcccccccccccCCceeeEEEECHHHHHhhhhhcCCCCCCEEEEeCCHHHH
Confidence            999999    999999999999999999863                  3569999999876 67999999987544

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.

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.73  E-value=4.2e-17  Score=151.68  Aligned_cols=129  Identities=16%  Similarity=0.213  Sum_probs=101.3

Q ss_pred             CCCCcEEEEcCCh--------hhHHHHHHHHhcC-CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCC
Q 029910           23 RPGLPMIVCCSSR--------DELDAVCSAVSNL-ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESET   93 (185)
Q Consensus        23 ~~~~~~IIF~~~~--------~~~~~l~~~L~~~-~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~   93 (185)
                      ..+.+++|||+..        ..++.+++.|... +++.+..+||+|+..+|.+++++|++|                  
T Consensus       446 ~~g~q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g------------------  507 (630)
T TIGR00643       446 AKGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREG------------------  507 (630)
T ss_pred             HhCCcEEEEEccccccccchHHHHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHHHHHHHHcC------------------
Confidence            3568999999875        4566777777653 347899999999999999999999999                  


Q ss_pred             CCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCC-CHHHHHHHHhhhc--CCCCEEEEEe-eCch---HHHHHHH
Q 029910           94 GKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPT-KKETYIRRMTTCL--AADGSVINIV-VGGE---VVTLRSM  166 (185)
Q Consensus        94 ~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~-~~~~yiqR~GR~~--~~~g~~i~~v-~~~e---~~~~~~l  166 (185)
                           +.+|||||++    +++|+|+|++++||+|+.|. +...|.||+||+|  +..|.|+.++ .+..   ...++.+
T Consensus       508 -----~~~ILVaT~v----ie~GvDiP~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~il~~~~~~~~~~~~rl~~~  578 (630)
T TIGR00643       508 -----EVDILVATTV----IEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKNPKSESAKKRLRVM  578 (630)
T ss_pred             -----CCCEEEECce----eecCcccCCCcEEEEeCCCcCCHHHHHHHhhhcccCCCCcEEEEEECCCCCHHHHHHHHHH
Confidence                 7999999999    99999999999999999997 5778888999974  5679999998 3322   2334444


Q ss_pred             HHH-hCCcccccc
Q 029910          167 EES-LGLIVAEVP  178 (185)
Q Consensus       167 ~~~-~~~~~~~~~  178 (185)
                      ++. -|..+++.+
T Consensus       579 ~~~~dgf~iae~d  591 (630)
T TIGR00643       579 ADTLDGFVIAEED  591 (630)
T ss_pred             HhhcccHHHHHHH
Confidence            432 344444443

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

Probab=99.73  E-value=7.3e-17  Score=149.92  Aligned_cols=130  Identities=19%  Similarity=0.291  Sum_probs=108.7

Q ss_pred             cchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcC--CCceEEEEec--------CCCHHHHHHHHHHHhcc
Q 029910            6 TFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL--ADISFSSLHS--------DLAETERTLILEEFRHT   75 (185)
Q Consensus         6 ~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~--~~~~~~~l~g--------~~~~~~R~~~l~~F~~~   75 (185)
                      .+.+++.+.+..... ..+..++||||.+|..|..|..+|...  .++++..+-|        +|++.++.+++++|+.|
T Consensus       395 pkle~l~~~l~e~f~-~~~dsR~IIFve~R~sa~~l~~~l~~~~~~~ir~~~fiGq~~s~~~~gmtqk~Q~evl~~Fr~G  473 (746)
T KOG0354|consen  395 PKLEKLVEILVEQFE-QNPDSRTIIFVETRESALALKKWLLQLHELGIKAEIFIGQGKSTQSTGMTQKEQKEVLDKFRDG  473 (746)
T ss_pred             hhHHHHHHHHHHHhh-cCCCccEEEEEehHHHHHHHHHHHHhhhhcccccceeeeccccccccccCHHHHHHHHHHHhCC
Confidence            356677777766556 788899999999999999999999832  1145555554        69999999999999999


Q ss_pred             cccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhcCCCCEEEEEe
Q 029910           76 AMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSVINIV  155 (185)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~~~~g~~i~~v  155 (185)
                                             .+++||||++    +++|+|+++|++||.||.-.|+...+||+||+..+.|.++.+.
T Consensus       474 -----------------------~~NvLVATSV----~EEGLDI~ec~lVIcYd~~snpIrmIQrrGRgRa~ns~~vll~  526 (746)
T KOG0354|consen  474 -----------------------EINVLVATSV----AEEGLDIGECNLVICYDYSSNPIRMVQRRGRGRARNSKCVLLT  526 (746)
T ss_pred             -----------------------CccEEEEecc----hhccCCcccccEEEEecCCccHHHHHHHhccccccCCeEEEEE
Confidence                                   6999999999    9999999999999999999999999999999555668888888


Q ss_pred             eCchHHHH
Q 029910          156 VGGEVVTL  163 (185)
Q Consensus       156 ~~~e~~~~  163 (185)
                      ++.+...+
T Consensus       527 t~~~~~~~  534 (746)
T KOG0354|consen  527 TGSEVIEF  534 (746)
T ss_pred             cchhHHHH
Confidence            76554444

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.73  E-value=7.1e-17  Score=139.62  Aligned_cols=94  Identities=21%  Similarity=0.300  Sum_probs=82.9

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCCC-ceEEEEecCCCHHHHHHH----HHHHhcccccccccccccCCCCCCCCCCC
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLAD-ISFSSLHSDLAETERTLI----LEEFRHTAMKWNQKVTEQSGDESETGKDE   97 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~-~~~~~l~g~~~~~~R~~~----l~~F~~~~~~~~~~~~~~~~~~~~~~~~~   97 (185)
                      ..+.++||||+|+++++.+++.|...+. ..+..+||++++.+|.+.    +++|+++                      
T Consensus       220 ~~~~~~lVf~~t~~~~~~~~~~L~~~~~~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~----------------------  277 (358)
T TIGR01587       220 KKGGKIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKN----------------------  277 (358)
T ss_pred             hCCCeEEEEECCHHHHHHHHHHHHhhcCCCeEEEEECCCCHHHHHHHHHHHHHHhcCC----------------------
Confidence            3468999999999999999999987651 369999999999999764    8899998                      


Q ss_pred             CceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhcC
Q 029910           98 HKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLA  146 (185)
Q Consensus        98 ~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~~  146 (185)
                       ..++||||++    +++|+|++ +++||+++.|  +++|+||+||+++
T Consensus       278 -~~~ilvaT~~----~~~GiDi~-~~~vi~~~~~--~~~~iqr~GR~gR  318 (358)
T TIGR01587       278 -EKFVIVATQV----IEASLDIS-ADVMITELAP--IDSLIQRLGRLHR  318 (358)
T ss_pred             -CCeEEEECcc----hhceeccC-CCEEEEcCCC--HHHHHHHhccccC
Confidence             6999999999    99999995 8999999877  7899999999744

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.

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.72  E-value=5.5e-17  Score=152.30  Aligned_cols=127  Identities=17%  Similarity=0.141  Sum_probs=105.0

Q ss_pred             eEecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccc
Q 029910            3 VSFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQK   82 (185)
Q Consensus         3 v~~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~   82 (185)
                      |+.+..++...+++.+......+.|+||||+|++.++.++..|...| +++..+||++++.+|..+.+.|+.        
T Consensus       402 i~~~~~~K~~ai~~~i~~~~~~~~pvLIft~s~~~se~ls~~L~~~g-i~~~~L~a~~~~~E~~ii~~ag~~--------  472 (762)
T TIGR03714       402 IYATLPEKLMATLEDVKEYHETGQPVLLITGSVEMSEIYSELLLREG-IPHNLLNAQNAAKEAQIIAEAGQK--------  472 (762)
T ss_pred             EEECHHHHHHHHHHHHHHHhhCCCCEEEEECcHHHHHHHHHHHHHCC-CCEEEecCCChHHHHHHHHHcCCC--------
Confidence            34445555555555544323567999999999999999999999998 999999999999888777665555        


Q ss_pred             ccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCC---------CCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEE
Q 029910           83 VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAI---------SARVLINYELPTKKETYIRRMTTC--LAADGSV  151 (185)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~---------~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~  151 (185)
                                       ..|+||||+    ++||+|++         ++.+|++|++|....+ +||+||+  .|.+|.+
T Consensus       473 -----------------g~VlIATdm----AgRGtDI~l~~~v~~~GGL~vIit~~~ps~rid-~qr~GRtGRqG~~G~s  530 (762)
T TIGR03714       473 -----------------GAVTVATSM----AGRGTDIKLGKGVAELGGLAVIGTERMENSRVD-LQLRGRSGRQGDPGSS  530 (762)
T ss_pred             -----------------CeEEEEccc----cccccCCCCCccccccCCeEEEEecCCCCcHHH-HHhhhcccCCCCceeE
Confidence                             469999999    99999999         9999999999998877 9999997  4677999


Q ss_pred             EEEeeCchH
Q 029910          152 INIVVGGEV  160 (185)
Q Consensus       152 i~~v~~~e~  160 (185)
                      ++|++..|.
T Consensus       531 ~~~is~eD~  539 (762)
T TIGR03714       531 QFFVSLEDD  539 (762)
T ss_pred             EEEEccchh
Confidence            999987554

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.

>PRK02362 ski2-like helicase; Provisional

Probab=99.72  E-value=8.1e-17  Score=152.01  Aligned_cols=127  Identities=19%  Similarity=0.209  Sum_probs=101.4

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcCCC-----------------------------------ceEEEEecCCCHHHHHHH
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNLAD-----------------------------------ISFSSLHSDLAETERTLI   68 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~~~-----------------------------------~~~~~l~g~~~~~~R~~~   68 (185)
                      .+.++||||++++.|+.++..|.....                                   ..++++|++|++.+|..+
T Consensus       242 ~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~L~~~l~~gva~hHagl~~~eR~~v  321 (737)
T PRK02362        242 EGGQCLVFVSSRRNAEGFAKRAASALKKTLTAAERAELAELAEEIREVSDTETSKDLADCVAKGAAFHHAGLSREHRELV  321 (737)
T ss_pred             cCCCeEEEEeCHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhccCccccHHHHHHHHhCEEeecCCCCHHHHHHH
Confidence            458999999999999998888764310                                   247899999999999999


Q ss_pred             HHHHhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEE----cC-----CCCCHHHHHH
Q 029910           69 LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLIN----YE-----LPTKKETYIR  139 (185)
Q Consensus        69 l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~----~d-----~P~~~~~yiq  139 (185)
                      .+.|++|                       .+++||||+.    +++|+|+|.+++||+    ||     .|.+..+|.|
T Consensus       322 e~~Fr~G-----------------------~i~VLvaT~t----la~GvnlPa~~VVI~~~~~yd~~~g~~~~s~~~y~Q  374 (737)
T PRK02362        322 EDAFRDR-----------------------LIKVISSTPT----LAAGLNLPARRVIIRDYRRYDGGAGMQPIPVLEYHQ  374 (737)
T ss_pred             HHHHHcC-----------------------CCeEEEechh----hhhhcCCCceEEEEecceeecCCCCceeCCHHHHHH
Confidence            9999999                       7999999999    999999999999998    87     6899999999


Q ss_pred             HHhhhcCC----CCEEEEEeeCchHHHHHHHHHHhCCcccccc
Q 029910          140 RMTTCLAA----DGSVINIVVGGEVVTLRSMEESLGLIVAEVP  178 (185)
Q Consensus       140 R~GR~~~~----~g~~i~~v~~~e~~~~~~l~~~~~~~~~~~~  178 (185)
                      |+||+|+.    .|.++.++...+. .-+.+++++....+++.
T Consensus       375 m~GRAGR~g~d~~G~~ii~~~~~~~-~~~~~~~~l~~~~~~i~  416 (737)
T PRK02362        375 MAGRAGRPGLDPYGEAVLLAKSYDE-LDELFERYIWADPEDVR  416 (737)
T ss_pred             HhhcCCCCCCCCCceEEEEecCchh-HHHHHHHHHhCCCCcee
Confidence            99998653    3889998876432 11223444444444443

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.71  E-value=4.5e-17  Score=159.40  Aligned_cols=140  Identities=12%  Similarity=0.155  Sum_probs=108.0

Q ss_pred             HHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcC-CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCC
Q 029910           11 LVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL-ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGD   89 (185)
Q Consensus        11 l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~-~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~   89 (185)
                      +..++..+..    +.+++||||+++.++.+++.|... ++..+..+||+|++.+|.+++.+|++|              
T Consensus       799 k~~il~el~r----~gqv~vf~n~i~~ie~la~~L~~~~p~~~v~~lHG~m~q~eRe~im~~Fr~G--------------  860 (1147)
T PRK10689        799 REAILREILR----GGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQ--------------  860 (1147)
T ss_pred             HHHHHHHHhc----CCeEEEEECCHHHHHHHHHHHHHhCCCCcEEEEeCCCCHHHHHHHHHHHHhc--------------
Confidence            3445555433    478999999999999999999876 237899999999999999999999999              


Q ss_pred             CCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCC-CCHHHHHHHHhhhc--CCCCEEEEEeeCc------hH
Q 029910           90 ESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELP-TKKETYIRRMTTCL--AADGSVINIVVGG------EV  160 (185)
Q Consensus        90 ~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P-~~~~~yiqR~GR~~--~~~g~~i~~v~~~------e~  160 (185)
                               +.+|||||++    +++|+|+|++++||..+.. .+...|+||+||+|  +..|.|+.++...      ..
T Consensus       861 ---------k~~VLVaTdI----ierGIDIP~v~~VIi~~ad~fglaq~~Qr~GRvGR~g~~g~a~ll~~~~~~~~~~~~  927 (1147)
T PRK10689        861 ---------RFNVLVCTTI----IETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQ  927 (1147)
T ss_pred             ---------CCCEEEECch----hhcccccccCCEEEEecCCCCCHHHHHHHhhccCCCCCceEEEEEeCCCcccCHHHH
Confidence                     7999999999    9999999999999944332 24567999999975  4568999887442      34


Q ss_pred             HHHHHHHHHh----CCccccccCCc
Q 029910          161 VTLRSMEESL----GLIVAEVPINI  181 (185)
Q Consensus       161 ~~~~~l~~~~----~~~~~~~~~~~  181 (185)
                      ..++.+++..    |..++..++.+
T Consensus       928 ~rl~~~~~~~~lg~gf~~a~~dl~~  952 (1147)
T PRK10689        928 KRLEAIASLEDLGAGFALATHDLEI  952 (1147)
T ss_pred             HHHHHHHHhcCCcchHHHHHHHHHh
Confidence            5556666552    45555544443

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.70  E-value=5.3e-17  Score=154.52  Aligned_cols=109  Identities=10%  Similarity=0.163  Sum_probs=97.2

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcC--CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeE
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNL--ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHM  102 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~--~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  102 (185)
                      ..++||||+++..++.+++.|...  .++.+..+||+|+.++|.++++.|++|                       ..+|
T Consensus       212 ~g~iLVFlpg~~ei~~l~~~L~~~~~~~~~v~~Lhg~l~~~eq~~~~~~~~~G-----------------------~rkV  268 (812)
T PRK11664        212 SGSLLLFLPGVGEIQRVQEQLASRVASDVLLCPLYGALSLAEQQKAILPAPAG-----------------------RRKV  268 (812)
T ss_pred             CCCEEEEcCCHHHHHHHHHHHHHhccCCceEEEeeCCCCHHHHHHHhccccCC-----------------------CeEE
Confidence            589999999999999999999862  238899999999999999999999998                       7999


Q ss_pred             EEEecCCCCcccCcCCCCCCcEEEEcCCCCC------------------HHHHHHHHhhhcC-CCCEEEEEeeCchH
Q 029910          103 IVVTDACLPLLSSGESAISARVLINYELPTK------------------KETYIRRMTTCLA-ADGSVINIVVGGEV  160 (185)
Q Consensus       103 LV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~------------------~~~yiqR~GR~~~-~~g~~i~~v~~~e~  160 (185)
                      +||||+    +++|+|+|+|++|||+++|+.                  .++|+||+||+|+ .+|.|+.+++..+.
T Consensus       269 lvATnI----AErsLtIp~V~~VID~Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRaGR~~~G~cyrL~t~~~~  341 (812)
T PRK11664        269 VLATNI----AETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRISQASMTQRAGRAGRLEPGICLHLYSKEQA  341 (812)
T ss_pred             EEecch----HHhcccccCceEEEECCCcccccccccCCcceeEEEeechhhhhhhccccCCCCCcEEEEecCHHHH
Confidence            999999    999999999999999887753                  3689999999865 57999999987544

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.70  E-value=2.1e-16  Score=147.83  Aligned_cols=128  Identities=14%  Similarity=0.104  Sum_probs=111.1

Q ss_pred             eEecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccc
Q 029910            3 VSFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQK   82 (185)
Q Consensus         3 v~~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~   82 (185)
                      |+-++.++...+++.+......+.|+||||++...++.++..|...| +++..+|++  ..+|...+..|+.+       
T Consensus       383 i~~t~~~k~~ai~~~i~~~~~~grpvLV~t~si~~se~ls~~L~~~g-i~~~~Lna~--q~~rEa~ii~~ag~-------  452 (745)
T TIGR00963       383 VYKTEEEKWKAVVDEIKERHAKGQPVLVGTTSVEKSELLSNLLKERG-IPHNVLNAK--NHEREAEIIAQAGR-------  452 (745)
T ss_pred             EEcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcC-CCeEEeeCC--hHHHHHHHHHhcCC-------
Confidence            34445566666666654445678999999999999999999999998 899999998  88999999999988       


Q ss_pred             ccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCC-------CcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEE
Q 029910           83 VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAIS-------ARVLINYELPTKKETYIRRMTTCL--AADGSVIN  153 (185)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~-------v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~  153 (185)
                                      +..|+|||++    ++||+|++.       .-+||++++|.|...|.||.||+|  |.+|.+.+
T Consensus       453 ----------------~g~VtIATnm----AgRGtDI~l~~V~~~GGl~VI~t~~p~s~ri~~q~~GRtGRqG~~G~s~~  512 (745)
T TIGR00963       453 ----------------KGAVTIATNM----AGRGTDIKLEEVKELGGLYVIGTERHESRRIDNQLRGRSGRQGDPGSSRF  512 (745)
T ss_pred             ----------------CceEEEEecc----ccCCcCCCccchhhcCCcEEEecCCCCcHHHHHHHhccccCCCCCcceEE
Confidence                            7999999999    999999999       559999999999999999999974  67799999


Q ss_pred             EeeCchH
Q 029910          154 IVVGGEV  160 (185)
Q Consensus       154 ~v~~~e~  160 (185)
                      |++..|.
T Consensus       513 ~ls~eD~  519 (745)
T TIGR00963       513 FLSLEDN  519 (745)
T ss_pred             EEeccHH
Confidence            9987654

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.

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

Probab=99.69  E-value=1.9e-16  Score=151.64  Aligned_cols=140  Identities=25%  Similarity=0.328  Sum_probs=122.4

Q ss_pred             eeEecc-hHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccc
Q 029910            2 SVSFTF-QETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWN   80 (185)
Q Consensus         2 ~v~~~~-~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~   80 (185)
                      +|...+ .+...+++..+.. ..+....||||.++..|+.++..|.+.+ +++..+|++|++.+|..+-++|..+     
T Consensus       462 eV~~k~~~~~~~~~~~~~~~-~~~~~s~IIYC~sr~~ce~vs~~L~~~~-~~a~~YHAGl~~~~R~~Vq~~w~~~-----  534 (941)
T KOG0351|consen  462 EVSPKTDKDALLDILEESKL-RHPDQSGIIYCLSRKECEQVSAVLRSLG-KSAAFYHAGLPPKERETVQKAWMSD-----  534 (941)
T ss_pred             EEEeccCccchHHHHHHhhh-cCCCCCeEEEeCCcchHHHHHHHHHHhc-hhhHhhhcCCCHHHHHHHHHHHhcC-----
Confidence            344444 4555666666333 7888999999999999999999999998 8999999999999999999999999     


Q ss_pred             ccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCc
Q 029910           81 QKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGG  158 (185)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~  158 (185)
                                        +++|++||-+    +++|+|.|||+.||+|.+|.+.+.|.|-+||+|  |....|+.|+...
T Consensus       535 ------------------~~~VivATVA----FGMGIdK~DVR~ViH~~lPks~E~YYQE~GRAGRDG~~s~C~l~y~~~  592 (941)
T KOG0351|consen  535 ------------------KIRVIVATVA----FGMGIDKPDVRFVIHYSLPKSFEGYYQEAGRAGRDGLPSSCVLLYGYA  592 (941)
T ss_pred             ------------------CCeEEEEEee----ccCCCCCCceeEEEECCCchhHHHHHHhccccCcCCCcceeEEecchh
Confidence                              6999999999    999999999999999999999999999999984  5678999999988


Q ss_pred             hHHHHHHHHHHh
Q 029910          159 EVVTLRSMEESL  170 (185)
Q Consensus       159 e~~~~~~l~~~~  170 (185)
                      +...++.+....
T Consensus       593 D~~~l~~ll~s~  604 (941)
T KOG0351|consen  593 DISELRRLLTSG  604 (941)
T ss_pred             HHHHHHHHHHcc
Confidence            887777665543

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

Probab=99.68  E-value=3.5e-16  Score=148.22  Aligned_cols=112  Identities=20%  Similarity=0.269  Sum_probs=86.9

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHH-----HHHHHHhcccccccccccccCCCCCCCCCCC
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERT-----LILEEFRHTAMKWNQKVTEQSGDESETGKDE   97 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~-----~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~   97 (185)
                      ..+.++||||||++.|+.+++.|...+ +  ..+||+|++.+|.     +++++|++...         .+.+   +...
T Consensus       270 e~g~~vLVF~NTv~~Aq~L~~~L~~~g-~--~lLHG~m~q~dR~~~~~~~il~~Fk~~~~---------~g~~---~~~~  334 (844)
T TIGR02621       270 DSGGAILVFCRTVKHVRKVFAKLPKEK-F--ELLTGTLRGAERDDLVKKEIFNRFLPQML---------SGSR---ARPQ  334 (844)
T ss_pred             hCCCcEEEEECCHHHHHHHHHHHHhcC-C--eEeeCCCCHHHHhhHHHHHHHHHHhcccc---------cccc---cccc
Confidence            346899999999999999999999887 4  8999999999999     78999987210         0000   0001


Q ss_pred             CceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhcC--C-CCEEEEEee
Q 029910           98 HKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLA--A-DGSVINIVV  156 (185)
Q Consensus        98 ~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~~--~-~g~~i~~v~  156 (185)
                      ...++||||++    +++|+|++. ++||++..|  .++|+||+||+++  . .+..++++.
T Consensus       335 ~g~~ILVATdV----aerGLDId~-d~VI~d~aP--~esyIQRiGRtgR~G~~~~~~i~vv~  389 (844)
T TIGR02621       335 QGTVYLVCTSA----GEVGVNISA-DHLVCDLAP--FESMQQRFGRVNRFGELQACQIAVVH  389 (844)
T ss_pred             ccceEEeccch----hhhcccCCc-ceEEECCCC--HHHHHHHhcccCCCCCCCCceEEEEe
Confidence            13679999999    999999986 899998877  6999999999743  3 345566663

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.

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.66  E-value=1.2e-15  Score=143.02  Aligned_cols=108  Identities=18%  Similarity=0.180  Sum_probs=92.3

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEE
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMI  103 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iL  103 (185)
                      .+.++||||++.+.++.++..|   +   +..+||+++..+|.+++++|+++.                      ..++|
T Consensus       495 ~g~kiLVF~~~~~~l~~~a~~L---~---~~~I~G~ts~~ER~~il~~Fr~~~----------------------~i~vL  546 (732)
T TIGR00603       495 RGDKIIVFSDNVFALKEYAIKL---G---KPFIYGPTSQQERMQILQNFQHNP----------------------KVNTI  546 (732)
T ss_pred             cCCeEEEEeCCHHHHHHHHHHc---C---CceEECCCCHHHHHHHHHHHHhCC----------------------CccEE
Confidence            6789999999999999999988   2   356999999999999999999763                      68999


Q ss_pred             EEecCCCCcccCcCCCCCCcEEEEcCCC-CCHHHHHHHHhhhcC--CCC-------EEEEEeeCchHHHH
Q 029910          104 VVTDACLPLLSSGESAISARVLINYELP-TKKETYIRRMTTCLA--ADG-------SVINIVVGGEVVTL  163 (185)
Q Consensus       104 V~Td~~~~~~~~G~d~~~v~~VI~~d~P-~~~~~yiqR~GR~~~--~~g-------~~i~~v~~~e~~~~  163 (185)
                      |+|++    +.+|+|+|++++||+++.| .|...|+||+||.++  .+|       ..+++|+.++.+..
T Consensus       547 v~SkV----gdeGIDlP~a~vvI~~s~~~gS~~q~iQRlGRilR~~~~~~~~~~~A~fY~lVs~dT~E~~  612 (732)
T TIGR00603       547 FLSKV----GDTSIDLPEANVLIQISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDTQEMY  612 (732)
T ss_pred             EEecc----cccccCCCCCCEEEEeCCCCCCHHHHHHHhcccccCCCCCccccccceEEEEecCCchHHH
Confidence            99999    9999999999999999998 499999999999643  223       34889988755443

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).

>PRK00254 ski2-like helicase; Provisional

Probab=99.66  E-value=1.1e-15  Score=144.14  Aligned_cols=108  Identities=22%  Similarity=0.242  Sum_probs=91.4

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcC---------------------------------CCceEEEEecCCCHHHHHHHHH
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNL---------------------------------ADISFSSLHSDLAETERTLILE   70 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~---------------------------------~~~~~~~l~g~~~~~~R~~~l~   70 (185)
                      .++++||||+|++.|+.++..|...                                 . ..+.++|++|++++|..+.+
T Consensus       237 ~~~~vLVF~~sr~~~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~-~gv~~hHagl~~~eR~~ve~  315 (720)
T PRK00254        237 KGKGALVFVNTRRSAEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLKKALR-GGVAFHHAGLGRTERVLIED  315 (720)
T ss_pred             hCCCEEEEEcChHHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHhcCCCcHHHHHHHh-hCEEEeCCCCCHHHHHHHHH
Confidence            3589999999999998877666321                                 1 24899999999999999999


Q ss_pred             HHhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEE-------cCCCC-CHHHHHHHHh
Q 029910           71 EFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLIN-------YELPT-KKETYIRRMT  142 (185)
Q Consensus        71 ~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~-------~d~P~-~~~~yiqR~G  142 (185)
                      .|++|                       .+++||||+.    +++|+|+|.+++||.       |+.|. +..+|.||+|
T Consensus       316 ~F~~G-----------------------~i~VLvaT~t----La~Gvnipa~~vVI~~~~~~~~~~~~~~~~~~~~Qm~G  368 (720)
T PRK00254        316 AFREG-----------------------LIKVITATPT----LSAGINLPAFRVIIRDTKRYSNFGWEDIPVLEIQQMMG  368 (720)
T ss_pred             HHHCC-----------------------CCeEEEeCcH----HhhhcCCCceEEEECCceEcCCCCceeCCHHHHHHhhh
Confidence            99999                       7999999999    999999999999993       66655 5779999999


Q ss_pred             hhcCC----CCEEEEEeeCch
Q 029910          143 TCLAA----DGSVINIVVGGE  159 (185)
Q Consensus       143 R~~~~----~g~~i~~v~~~e  159 (185)
                      |+|+.    .|.++.++...+
T Consensus       369 RAGR~~~d~~G~~ii~~~~~~  389 (720)
T PRK00254        369 RAGRPKYDEVGEAIIVATTEE  389 (720)
T ss_pred             ccCCCCcCCCceEEEEecCcc
Confidence            98763    489999987655

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.66  E-value=9.2e-16  Score=144.54  Aligned_cols=128  Identities=11%  Similarity=0.119  Sum_probs=107.8

Q ss_pred             eEecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccc
Q 029910            3 VSFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQK   82 (185)
Q Consensus         3 v~~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~   82 (185)
                      |+.++.++...+.+.+......+.|+||||+|+..++.|++.|...| +++..+|+++...++..+.+.++.|       
T Consensus       418 i~~t~~~K~~al~~~i~~~~~~g~pvLI~t~si~~se~ls~~L~~~g-i~~~~Lna~~~~~Ea~ii~~ag~~g-------  489 (796)
T PRK12906        418 LYPTLDSKFNAVVKEIKERHAKGQPVLVGTVAIESSERLSHLLDEAG-IPHAVLNAKNHAKEAEIIMNAGQRG-------  489 (796)
T ss_pred             EEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHCC-CCeeEecCCcHHHHHHHHHhcCCCc-------
Confidence            34445555555666554434578999999999999999999999998 8999999999988888888777776       


Q ss_pred             ccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCC---CCc-----EEEEcCCCCCHHHHHHHHhhhc--CCCCEEE
Q 029910           83 VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAI---SAR-----VLINYELPTKKETYIRRMTTCL--AADGSVI  152 (185)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~---~v~-----~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i  152 (185)
                                        .|+|||++    ++||+|++   +|.     +||+++.|.+...|.|+.||+|  |.+|.++
T Consensus       490 ------------------~VtIATnm----AGRGtDI~l~~~V~~~GGLhVI~te~pes~ri~~Ql~GRtGRqG~~G~s~  547 (796)
T PRK12906        490 ------------------AVTIATNM----AGRGTDIKLGPGVKELGGLAVIGTERHESRRIDNQLRGRSGRQGDPGSSR  547 (796)
T ss_pred             ------------------eEEEEecc----ccCCCCCCCCcchhhhCCcEEEeeecCCcHHHHHHHhhhhccCCCCcceE
Confidence                              39999999    99999994   899     9999999999999999999974  6779999


Q ss_pred             EEeeCchH
Q 029910          153 NIVVGGEV  160 (185)
Q Consensus       153 ~~v~~~e~  160 (185)
                      .|++..|.
T Consensus       548 ~~~sleD~  555 (796)
T PRK12906        548 FYLSLEDD  555 (796)
T ss_pred             EEEeccch
Confidence            99987643

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.66  E-value=1.3e-15  Score=138.27  Aligned_cols=95  Identities=13%  Similarity=0.102  Sum_probs=88.0

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEE
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMI  103 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iL  103 (185)
                      .+.+++|||++.++++.|++.|...+ +++..+||+++..+|.++++.|+.+                       ...+|
T Consensus       343 ~~~~~lV~~~~~~h~~~L~~~L~~~g-~~v~~i~G~~~~~eR~~i~~~~~~~-----------------------~~~vL  398 (501)
T PHA02558        343 KGENTFVMFKYVEHGKPLYEMLKKVY-DKVYYVSGEVDTEDRNEMKKIAEGG-----------------------KGIII  398 (501)
T ss_pred             cCCCEEEEEEEHHHHHHHHHHHHHcC-CCEEEEeCCCCHHHHHHHHHHHhCC-----------------------CCeEE
Confidence            45788888889999999999999988 8999999999999999999999988                       67899


Q ss_pred             EEe-cCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhcC
Q 029910          104 VVT-DACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLA  146 (185)
Q Consensus       104 V~T-d~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~~  146 (185)
                      ||| ++    +++|+|+|++++||++++|.+...|+||+||+++
T Consensus       399 vaT~~~----l~eG~Dip~ld~vIl~~p~~s~~~~~QriGR~~R  438 (501)
T PHA02558        399 VASYGV----FSTGISIKNLHHVIFAHPSKSKIIVLQSIGRVLR  438 (501)
T ss_pred             EEEcce----eccccccccccEEEEecCCcchhhhhhhhhcccc
Confidence            998 89    9999999999999999999999999999999744

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.63  E-value=2.1e-15  Score=131.61  Aligned_cols=87  Identities=13%  Similarity=0.173  Sum_probs=75.1

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCC-CceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCcee
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLA-DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSH  101 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~-~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (185)
                      .++.++||||||++.++.++..|+..+ ++.+..+||.+++.+|.+.      +                       +.+
T Consensus       270 ~~~~k~LIf~nt~~~~~~l~~~L~~~~~~~~~~~l~g~~~~~~R~~~------~-----------------------~~~  320 (357)
T TIGR03158       270 LPGERGAIILDSLDEVNRLSDLLQQQGLGDDIGRITGFAPKKDRERA------M-----------------------QFD  320 (357)
T ss_pred             cCCCeEEEEECCHHHHHHHHHHHhhhCCCceEEeeecCCCHHHHHHh------c-----------------------cCC
Confidence            456899999999999999999998764 2578899999999998653      2                       478


Q ss_pred             EEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc
Q 029910          102 MIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL  145 (185)
Q Consensus       102 iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~  145 (185)
                      +|||||+    ++||+|++.+ +|| ++ |.+.++|+||+||+|
T Consensus       321 iLVaTdv----~~rGiDi~~~-~vi-~~-p~~~~~yiqR~GR~g  357 (357)
T TIGR03158       321 ILLGTST----VDVGVDFKRD-WLI-FS-ARDAAAFWQRLGRLG  357 (357)
T ss_pred             EEEEecH----HhcccCCCCc-eEE-EC-CCCHHHHhhhcccCC
Confidence            9999999    9999999987 566 56 999999999999974

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.

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=99.62  E-value=2.7e-15  Score=101.85  Aligned_cols=80  Identities=30%  Similarity=0.479  Sum_probs=73.5

Q ss_pred             HHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCC
Q 029910           40 AVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESA  119 (185)
Q Consensus        40 ~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~  119 (185)
                      .+.+.|...+ +.+..+||++++.+|..+++.|+.+                       ...+||+|++    +++|+|+
T Consensus         2 ~l~~~l~~~~-~~~~~~~~~~~~~~r~~~~~~f~~~-----------------------~~~vli~t~~----~~~Gi~~   53 (82)
T smart00490        2 ELAELLKELG-IKVARLHGGLSQEEREEILEKFNNG-----------------------KIKVLVATDV----AERGLDL   53 (82)
T ss_pred             HHHHHHHHCC-CeEEEEECCCCHHHHHHHHHHHHcC-----------------------CCeEEEECCh----hhCCcCh
Confidence            4667777776 8999999999999999999999998                       5799999999    9999999


Q ss_pred             CCCcEEEEcCCCCCHHHHHHHHhhhcCC
Q 029910          120 ISARVLINYELPTKKETYIRRMTTCLAA  147 (185)
Q Consensus       120 ~~v~~VI~~d~P~~~~~yiqR~GR~~~~  147 (185)
                      |.++.||.+++|++...|.|++||+++.
T Consensus        54 ~~~~~vi~~~~~~~~~~~~Q~~gR~~R~   81 (82)
T smart00490       54 PGVDLVIIYDLPWSPASYIQRIGRAGRA   81 (82)
T ss_pred             hcCCEEEEeCCCCCHHHHHHhhcccccC
Confidence            9999999999999999999999997553

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

Probab=99.62  E-value=9.3e-15  Score=138.08  Aligned_cols=117  Identities=15%  Similarity=0.186  Sum_probs=99.9

Q ss_pred             HHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCC
Q 029910           11 LVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDE   90 (185)
Q Consensus        11 l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~   90 (185)
                      ..+.+..+.+   ..+.++||+||+.+++.++..|+..+...+..+||+++.++|..+.++|++|               
T Consensus       242 ~~~~i~~~v~---~~~ttLIF~NTR~~aE~l~~~L~~~~~~~i~~HHgSlSre~R~~vE~~lk~G---------------  303 (814)
T COG1201         242 LYERIAELVK---KHRTTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEG---------------  303 (814)
T ss_pred             HHHHHHHHHh---hcCcEEEEEeChHHHHHHHHHHHHhcCCceeeecccccHHHHHHHHHHHhcC---------------
Confidence            3444444343   3369999999999999999999988657899999999999999999999999               


Q ss_pred             CCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc---CCCCEEEEEeeC
Q 029910           91 SETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL---AADGSVINIVVG  157 (185)
Q Consensus        91 ~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~---~~~g~~i~~v~~  157 (185)
                              ..+++|||.-    ++-|+|+.+++.||+|..|.++...+||+||++   +..+.++.+...
T Consensus       304 --------~lravV~TSS----LELGIDiG~vdlVIq~~SP~sV~r~lQRiGRsgHr~~~~Skg~ii~~~  361 (814)
T COG1201         304 --------ELKAVVATSS----LELGIDIGDIDLVIQLGSPKSVNRFLQRIGRAGHRLGEVSKGIIIAED  361 (814)
T ss_pred             --------CceEEEEccc----hhhccccCCceEEEEeCCcHHHHHHhHhccccccccCCcccEEEEecC
Confidence                    6999999999    999999999999999999999999999999974   333455555544

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=99.61  E-value=4.9e-15  Score=141.31  Aligned_cols=129  Identities=14%  Similarity=0.141  Sum_probs=108.3

Q ss_pred             eEecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccc
Q 029910            3 VSFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQK   82 (185)
Q Consensus         3 v~~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~   82 (185)
                      ||.+..++...+++.+......+.|+||||+|++.++.|++.|...+ +.+..||+  .+.+|...+..|+.+       
T Consensus       576 vy~t~~eK~~Ali~~I~~~~~~grpVLIft~Sve~sE~Ls~~L~~~g-I~h~vLna--kq~~REa~Iia~AG~-------  645 (1025)
T PRK12900        576 VYKTRREKYNAIVLKVEELQKKGQPVLVGTASVEVSETLSRMLRAKR-IAHNVLNA--KQHDREAEIVAEAGQ-------  645 (1025)
T ss_pred             EecCHHHHHHHHHHHHHHHhhCCCCEEEEeCcHHHHHHHHHHHHHcC-CCceeecC--CHHHhHHHHHHhcCC-------
Confidence            44455555555666543334567999999999999999999999998 99999997  588999999999998       


Q ss_pred             ccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCC---CCc-----EEEEcCCCCCHHHHHHHHhhh--cCCCCEEE
Q 029910           83 VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAI---SAR-----VLINYELPTKKETYIRRMTTC--LAADGSVI  152 (185)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~---~v~-----~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i  152 (185)
                                      +..|+|||++    ++||+|++   .|.     +||+++.|.+...|.||.||+  .|.+|.++
T Consensus       646 ----------------~g~VtIATNM----AGRGtDIkl~~~V~~vGGL~VIgterhes~Rid~Ql~GRtGRqGdpGsS~  705 (1025)
T PRK12900        646 ----------------KGAVTIATNM----AGRGTDIKLGEGVRELGGLFILGSERHESRRIDRQLRGRAGRQGDPGESV  705 (1025)
T ss_pred             ----------------CCeEEEeccC----cCCCCCcCCccchhhhCCceeeCCCCCchHHHHHHHhhhhhcCCCCcceE
Confidence                            7999999999    99999999   554     349999999999999999997  46779999


Q ss_pred             EEeeCchHH
Q 029910          153 NIVVGGEVV  161 (185)
Q Consensus       153 ~~v~~~e~~  161 (185)
                      +|++..|.-
T Consensus       706 ffvSleD~L  714 (1025)
T PRK12900        706 FYVSLEDEL  714 (1025)
T ss_pred             EEechhHHH
Confidence            999876543

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.61  E-value=3.8e-15  Score=146.04  Aligned_cols=109  Identities=15%  Similarity=0.289  Sum_probs=93.2

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCC--CceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCce
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLA--DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKS  100 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~--~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~  100 (185)
                      ....++||||+++..++.+++.|...+  ...+..+||+|++.+|.++++.  .+                       ..
T Consensus       284 ~~~GdILVFLpg~~EIe~lae~L~~~~~~~~~VlpLhg~Ls~~eQ~~Vf~~--~g-----------------------~r  338 (1294)
T PRK11131        284 EGPGDILIFMSGEREIRDTADALNKLNLRHTEILPLYARLSNSEQNRVFQS--HS-----------------------GR  338 (1294)
T ss_pred             CCCCCEEEEcCCHHHHHHHHHHHHhcCCCcceEeecccCCCHHHHHHHhcc--cC-----------------------Ce
Confidence            345789999999999999999998765  2347899999999999999875  34                       58


Q ss_pred             eEEEEecCCCCcccCcCCCCCCcEEEEcC---------------CC---CCHHHHHHHHhhhcC-CCCEEEEEeeCchH
Q 029910          101 HMIVVTDACLPLLSSGESAISARVLINYE---------------LP---TKKETYIRRMTTCLA-ADGSVINIVVGGEV  160 (185)
Q Consensus       101 ~iLV~Td~~~~~~~~G~d~~~v~~VI~~d---------------~P---~~~~~yiqR~GR~~~-~~g~~i~~v~~~e~  160 (185)
                      +|+|||++    +++|+|+|+|++|||++               +|   .|.++|.||+||+|+ .+|.|+.+++..+.
T Consensus       339 kIIVATNI----AEtSITIpgI~yVID~Gl~k~~~Yd~~~~~~~Lp~~~iSkasa~QRaGRAGR~~~G~c~rLyte~d~  413 (1294)
T PRK11131        339 RIVLATNV----AETSLTVPGIKYVIDPGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRVSEGICIRLYSEDDF  413 (1294)
T ss_pred             eEEEeccH----HhhccccCcceEEEECCCccccccccccCcccCCeeecCHhhHhhhccccCCCCCcEEEEeCCHHHH
Confidence            99999999    99999999999999985               44   456899999999866 56999999987554

>PRK01172 ski2-like helicase; Provisional

Probab=99.60  E-value=8.4e-15  Score=137.05  Aligned_cols=120  Identities=18%  Similarity=0.170  Sum_probs=92.9

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcCC----C--------------------ceEEEEecCCCHHHHHHHHHHHhcccccc
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNLA----D--------------------ISFSSLHSDLAETERTLILEEFRHTAMKW   79 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~~----~--------------------~~~~~l~g~~~~~~R~~~l~~F~~~~~~~   79 (185)
                      .++++||||++++.++.++..|....    .                    ..+.++||+|++++|..+.+.|++|    
T Consensus       235 ~~~~vLVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~~hagl~~~eR~~ve~~f~~g----  310 (674)
T PRK01172        235 DGGQVLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQRRFIEEMFRNR----  310 (674)
T ss_pred             CCCcEEEEeccHHHHHHHHHHHHHhhhhcccccccccccccccHHHHHHHhcCEEEecCCCCHHHHHHHHHHHHcC----
Confidence            46899999999999999998886431    0                    1378899999999999999999999    


Q ss_pred             cccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCC---------CCCHHHHHHHHhhhcCC---
Q 029910           80 NQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYEL---------PTKKETYIRRMTTCLAA---  147 (185)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~---------P~~~~~yiqR~GR~~~~---  147 (185)
                                         .+++||||++    +++|+|+|+..+|| +|.         |.++.+|.||+||+|+.   
T Consensus       311 -------------------~i~VLvaT~~----la~Gvnipa~~VII-~~~~~~~~~~~~~~s~~~~~Qm~GRAGR~g~d  366 (674)
T PRK01172        311 -------------------YIKVIVATPT----LAAGVNLPARLVIV-RDITRYGNGGIRYLSNMEIKQMIGRAGRPGYD  366 (674)
T ss_pred             -------------------CCeEEEecch----hhccCCCcceEEEE-cCceEeCCCCceeCCHHHHHHHhhcCCCCCCC
Confidence                               7999999999    99999999865544 443         56889999999998654   


Q ss_pred             -CCEEEEEeeCchHHHHHHHHHHhCCc
Q 029910          148 -DGSVINIVVGGEVVTLRSMEESLGLI  173 (185)
Q Consensus       148 -~g~~i~~v~~~e~~~~~~l~~~~~~~  173 (185)
                       .|.++.++...+  .+..+++++...
T Consensus       367 ~~g~~~i~~~~~~--~~~~~~~~l~~~  391 (674)
T PRK01172        367 QYGIGYIYAASPA--SYDAAKKYLSGE  391 (674)
T ss_pred             CcceEEEEecCcc--cHHHHHHHHcCC
Confidence             477777765433  123344555333

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.56  E-value=2.5e-14  Score=140.49  Aligned_cols=119  Identities=10%  Similarity=0.183  Sum_probs=96.7

Q ss_pred             HHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCC--CceEEEEecCCCHHHHHHHHHHHhcccccccccccccCC
Q 029910           11 LVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLA--DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG   88 (185)
Q Consensus        11 l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~--~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~   88 (185)
                      +.+++..+..  .....+|||++++..++.+++.|...+  .+.+..+||+|+.++|.++++   .+.            
T Consensus       267 i~~~I~~l~~--~~~GdILVFLpg~~EI~~l~~~L~~~~~~~~~VlpLhg~Ls~~eQ~~vf~---~~~------------  329 (1283)
T TIGR01967       267 ILDAVDELFA--EGPGDILIFLPGEREIRDAAEILRKRNLRHTEILPLYARLSNKEQQRVFQ---PHS------------  329 (1283)
T ss_pred             HHHHHHHHHh--hCCCCEEEeCCCHHHHHHHHHHHHhcCCCCcEEEeccCCCCHHHHHHHhC---CCC------------
Confidence            3445555443  244799999999999999999998653  367899999999999998854   331            


Q ss_pred             CCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCC------------------CHHHHHHHHhhhcC-CCC
Q 029910           89 DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPT------------------KKETYIRRMTTCLA-ADG  149 (185)
Q Consensus        89 ~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~------------------~~~~yiqR~GR~~~-~~g  149 (185)
                                ..+|+|||++    +++|+|+|+|++||++++++                  |.++|.||+||+|+ .+|
T Consensus       330 ----------~rkIVLATNI----AEtSLTIpgV~yVIDsGl~r~~~yd~~~~~~~L~~~~ISkasa~QRaGRAGR~~~G  395 (1283)
T TIGR01967       330 ----------GRRIVLATNV----AETSLTVPGIHYVIDTGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRVAPG  395 (1283)
T ss_pred             ----------CceEEEeccH----HHhccccCCeeEEEeCCCccccccccccCccccCCccCCHHHHHHHhhhhCCCCCc
Confidence                      3789999999    99999999999999998543                  66899999999865 469


Q ss_pred             EEEEEeeCchH
Q 029910          150 SVINIVVGGEV  160 (185)
Q Consensus       150 ~~i~~v~~~e~  160 (185)
                      .|+.+++..+.
T Consensus       396 ~cyRLyte~~~  406 (1283)
T TIGR01967       396 ICIRLYSEEDF  406 (1283)
T ss_pred             eEEEecCHHHH
Confidence            99999986544

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.

>PRK09401 reverse gyrase; Reviewed

Probab=99.54  E-value=1.4e-14  Score=142.37  Aligned_cols=87  Identities=16%  Similarity=0.148  Sum_probs=79.7

Q ss_pred             CcEEEEcCChhh---HHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeE
Q 029910           26 LPMIVCCSSRDE---LDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHM  102 (185)
Q Consensus        26 ~~~IIF~~~~~~---~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  102 (185)
                      .++||||++++.   ++.+++.|...| +++..+||+|     .+.+++|++|                       +.++
T Consensus       329 ~~~LIFv~t~~~~~~ae~l~~~L~~~g-i~v~~~hg~l-----~~~l~~F~~G-----------------------~~~V  379 (1176)
T PRK09401        329 DGGLIFVPSDKGKEYAEELAEYLEDLG-INAELAISGF-----ERKFEKFEEG-----------------------EVDV  379 (1176)
T ss_pred             CCEEEEEecccChHHHHHHHHHHHHCC-CcEEEEeCcH-----HHHHHHHHCC-----------------------CCCE
Confidence            589999999888   999999999998 8999999999     2346999999                       7999


Q ss_pred             EEE----ecCCCCcccCcCCCCC-CcEEEEcCCCC------CHHHHHHHHhhhc
Q 029910          103 IVV----TDACLPLLSSGESAIS-ARVLINYELPT------KKETYIRRMTTCL  145 (185)
Q Consensus       103 LV~----Td~~~~~~~~G~d~~~-v~~VI~~d~P~------~~~~yiqR~GR~~  145 (185)
                      ||+    ||+    ++||+|+|+ +++|||||+|.      ..+.|.||+||..
T Consensus       380 LVatas~tdv----~aRGIDiP~~IryVI~y~vP~~~~~~~~~~~~~~~~~r~~  429 (1176)
T PRK09401        380 LVGVASYYGV----LVRGIDLPERIRYAIFYGVPKFKFSLEEELAPPFLLLRLL  429 (1176)
T ss_pred             EEEecCCCCc----eeecCCCCcceeEEEEeCCCCEEEeccccccCHHHHHHHH
Confidence            999    689    999999999 89999999998      7789999999974

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=99.49  E-value=6.8e-13  Score=128.63  Aligned_cols=135  Identities=13%  Similarity=0.158  Sum_probs=107.8

Q ss_pred             hHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccC
Q 029910            8 QETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQS   87 (185)
Q Consensus         8 ~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~   87 (185)
                      +..+..||..+   ...+.++||||......+.|...|...+ +....++|+++..+|.+++++|....           
T Consensus       473 l~lLdkLL~~L---k~~g~KVLIFSQft~~LdiLed~L~~~g-~~y~rIdGsts~~eRq~~Id~Fn~~~-----------  537 (1033)
T PLN03142        473 MVLLDKLLPKL---KERDSRVLIFSQMTRLLDILEDYLMYRG-YQYCRIDGNTGGEDRDASIDAFNKPG-----------  537 (1033)
T ss_pred             HHHHHHHHHHH---HhcCCeEEeehhHHHHHHHHHHHHHHcC-CcEEEECCCCCHHHHHHHHHHhcccc-----------
Confidence            34444555553   3357899999999999999999999888 89999999999999999999998652           


Q ss_pred             CCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCC--CEEEEEeeCc--hHH
Q 029910           88 GDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAAD--GSVINIVVGG--EVV  161 (185)
Q Consensus        88 ~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~--g~~i~~v~~~--e~~  161 (185)
                               +...-+|++|.+    .+.|+|++.+++||+||+||||..+.|++||+  .|+.  -.++.+++.+  |..
T Consensus       538 ---------s~~~VfLLSTrA----GGlGINLt~Ad~VIiyD~dWNP~~d~QAidRaHRIGQkk~V~VyRLIt~gTIEEk  604 (1033)
T PLN03142        538 ---------SEKFVFLLSTRA----GGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEK  604 (1033)
T ss_pred             ---------CCceEEEEeccc----cccCCchhhCCEEEEeCCCCChHHHHHHHHHhhhcCCCceEEEEEEEeCCcHHHH
Confidence                     113457899999    99999999999999999999999999999996  4554  3567778776  445


Q ss_pred             HHHHHHHHh
Q 029910          162 TLRSMEESL  170 (185)
Q Consensus       162 ~~~~l~~~~  170 (185)
                      .+....+.+
T Consensus       605 Ilera~~Kl  613 (1033)
T PLN03142        605 VIERAYKKL  613 (1033)
T ss_pred             HHHHHHHHH
Confidence            555544443

>PRK09694 helicase Cas3; Provisional

Probab=99.44  E-value=7.4e-13  Score=126.90  Aligned_cols=105  Identities=16%  Similarity=0.341  Sum_probs=83.6

Q ss_pred             HHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCC--CceEEEEecCCCHHHHH----HHHHHH-hccccccccccccc
Q 029910           14 LLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLA--DISFSSLHSDLAETERT----LILEEF-RHTAMKWNQKVTEQ   86 (185)
Q Consensus        14 ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~--~~~~~~l~g~~~~~~R~----~~l~~F-~~~~~~~~~~~~~~   86 (185)
                      +++.+......+++++|||||++.|..+++.|+..+  ...+..+||.++..+|.    ++++.| +++.          
T Consensus       549 ~l~~i~~~~~~g~~vLVf~NTV~~Aq~ly~~L~~~~~~~~~v~llHsrf~~~dR~~~E~~vl~~fgk~g~----------  618 (878)
T PRK09694        549 LLQRMIAAANAGAQVCLICNLVDDAQKLYQRLKELNNTQVDIDLFHARFTLNDRREKEQRVIENFGKNGK----------  618 (878)
T ss_pred             HHHHHHHHHhcCCEEEEEECCHHHHHHHHHHHHhhCCCCceEEEEeCCCCHHHHHHHHHHHHHHHHhcCC----------
Confidence            444433323456899999999999999999998653  25799999999999994    577788 4441          


Q ss_pred             CCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc
Q 029910           87 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL  145 (185)
Q Consensus        87 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~  145 (185)
                                .....|||+|++    +++|+|+ +++++|....|  .+.|+||+||++
T Consensus       619 ----------r~~~~ILVaTQV----iE~GLDI-d~DvlItdlaP--idsLiQRaGR~~  660 (878)
T PRK09694        619 ----------RNQGRILVATQV----VEQSLDL-DFDWLITQLCP--VDLLFQRLGRLH  660 (878)
T ss_pred             ----------cCCCeEEEECcc----hhheeec-CCCeEEECCCC--HHHHHHHHhccC
Confidence                      002579999999    9999999 68999998888  789999999973

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

Probab=99.42  E-value=1.5e-13  Score=114.63  Aligned_cols=75  Identities=23%  Similarity=0.515  Sum_probs=68.2

Q ss_pred             EEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeC-chHHHHHHHHHHhCCccccccC
Q 029910          103 IVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVG-GEVVTLRSMEESLGLIVAEVPI  179 (185)
Q Consensus       103 LV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~-~e~~~~~~l~~~~~~~~~~~~~  179 (185)
                      +|+|++    +.||+|+..++.|+|||+|.+.++|+||.||+  .|.+|.+|+|++. ++...+..++......+.++|.
T Consensus       302 ~vat~l----fgrgmdiervNi~~NYdmp~~~DtYlHrv~rAgrfGtkglaitfvs~e~da~iLn~vqdRf~v~i~eLpd  377 (387)
T KOG0329|consen  302 LVATDL----FGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNPVQDRFEVNIKELPD  377 (387)
T ss_pred             hHHhhh----hccccCcccceeeeccCCCCCchHHHHHhhhhhccccccceeehhcchhhHHHhchhhHhhhccHhhcCc
Confidence            899999    99999999999999999999999999999997  5788999999975 5778888999988888888886


Q ss_pred             Cc
Q 029910          180 NI  181 (185)
Q Consensus       180 ~~  181 (185)
                      .+
T Consensus       378 ei  379 (387)
T KOG0329|consen  378 EI  379 (387)
T ss_pred             cc
Confidence            54

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

Probab=99.41  E-value=8.1e-13  Score=116.59  Aligned_cols=110  Identities=18%  Similarity=0.202  Sum_probs=99.9

Q ss_pred             CcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEEE
Q 029910           26 LPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVV  105 (185)
Q Consensus        26 ~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~  105 (185)
                      .-.||||.|++.|++++-.|+..| +.+..+|.++...+|.++-+.|-++                       +..|+++
T Consensus       256 GCGIVYCRTR~~cEq~AI~l~~~G-i~A~AYHAGLK~~ERTeVQe~WM~~-----------------------~~PvI~A  311 (641)
T KOG0352|consen  256 GCGIVYCRTRNECEQVAIMLEIAG-IPAMAYHAGLKKKERTEVQEKWMNN-----------------------EIPVIAA  311 (641)
T ss_pred             cceEEEeccHHHHHHHHHHhhhcC-cchHHHhcccccchhHHHHHHHhcC-----------------------CCCEEEE
Confidence            567999999999999999999998 9999999999999999999999999                       7999999


Q ss_pred             ecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCchHHHH
Q 029910          106 TDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGGEVVTL  163 (185)
Q Consensus       106 Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e~~~~  163 (185)
                      |.-    +.+|+|-|+|+.||++|+|.|+..|.|-.||+|  |.++.|=..+..+|...+
T Consensus       312 T~S----FGMGVDKp~VRFViHW~~~qn~AgYYQESGRAGRDGk~SyCRLYYsR~D~~~i  367 (641)
T KOG0352|consen  312 TVS----FGMGVDKPDVRFVIHWSPSQNLAGYYQESGRAGRDGKRSYCRLYYSRQDKNAL  367 (641)
T ss_pred             Eec----cccccCCcceeEEEecCchhhhHHHHHhccccccCCCccceeeeecccchHHH
Confidence            999    999999999999999999999999999999974  455777777766665544

>PRK14701 reverse gyrase; Provisional

Probab=99.40  E-value=6.7e-13  Score=133.56  Aligned_cols=84  Identities=8%  Similarity=0.120  Sum_probs=76.3

Q ss_pred             CCcEEEEcCChhh---HHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCcee
Q 029910           25 GLPMIVCCSSRDE---LDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSH  101 (185)
Q Consensus        25 ~~~~IIF~~~~~~---~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (185)
                      +.+.||||++++.   |+.+++.|...| +++..+||+     |.+++++|++|                       +.+
T Consensus       330 g~~gIVF~~t~~~~e~ae~la~~L~~~G-i~a~~~h~~-----R~~~l~~F~~G-----------------------~~~  380 (1638)
T PRK14701        330 GKGGLIFVPIDEGAEKAEEIEKYLLEDG-FKIELVSAK-----NKKGFDLFEEG-----------------------EID  380 (1638)
T ss_pred             CCCeEEEEeccccchHHHHHHHHHHHCC-CeEEEecch-----HHHHHHHHHcC-----------------------CCC
Confidence            4689999999876   589999999998 899999995     88999999999                       799


Q ss_pred             EEEEec----CCCCcccCcCCCCC-CcEEEEcCCCC---CHHHHHHHH
Q 029910          102 MIVVTD----ACLPLLSSGESAIS-ARVLINYELPT---KKETYIRRM  141 (185)
Q Consensus       102 iLV~Td----~~~~~~~~G~d~~~-v~~VI~~d~P~---~~~~yiqR~  141 (185)
                      +||+|+    +    ++||+|+|+ |++|||||+|.   +.+.|.|..
T Consensus       381 VLVaT~s~~gv----aaRGIDiP~~Vryvi~~~~Pk~~~~~e~~~~~~  424 (1638)
T PRK14701        381 YLIGVATYYGT----LVRGLDLPERIRFAVFYGVPKFRFRVDLEDPTI  424 (1638)
T ss_pred             EEEEecCCCCe----eEecCccCCccCEEEEeCCCCCCcchhhcccch
Confidence            999994    7    899999999 99999999999   888777765

>TIGR01054 rgy reverse gyrase

Probab=99.39  E-value=1.6e-12  Score=127.99  Aligned_cols=75  Identities=15%  Similarity=0.192  Sum_probs=70.2

Q ss_pred             CcEEEEcCCh---hhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeE
Q 029910           26 LPMIVCCSSR---DELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHM  102 (185)
Q Consensus        26 ~~~IIF~~~~---~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  102 (185)
                      .++||||+++   +.|+.|+..|...| +++..+||+++.    +++++|++|                       +.++
T Consensus       327 ~~~IVFv~t~~~~~~a~~l~~~L~~~g-~~a~~lhg~~~~----~~l~~Fr~G-----------------------~~~v  378 (1171)
T TIGR01054       327 TGGIVYVSIDYGKEKAEEIAEFLENHG-VKAVAYHATKPK----EDYEKFAEG-----------------------EIDV  378 (1171)
T ss_pred             CCEEEEEeccccHHHHHHHHHHHHhCC-ceEEEEeCCCCH----HHHHHHHcC-----------------------CCCE
Confidence            6899999999   99999999999998 899999999973    789999999                       7999


Q ss_pred             EEEe----cCCCCcccCcCCCCC-CcEEEEcCCCC
Q 029910          103 IVVT----DACLPLLSSGESAIS-ARVLINYELPT  132 (185)
Q Consensus       103 LV~T----d~~~~~~~~G~d~~~-v~~VI~~d~P~  132 (185)
                      ||+|    |+    ++||+|+|+ |++|||||+|.
T Consensus       379 LVata~~tdv----~aRGIDip~~V~~vI~~~~P~  409 (1171)
T TIGR01054       379 LIGVASYYGT----LVRGLDLPERVRYAVFLGVPK  409 (1171)
T ss_pred             EEEeccccCc----ccccCCCCccccEEEEECCCC
Confidence            9994    89    999999999 89999999997

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.

>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]

Probab=99.38  E-value=5.7e-12  Score=113.65  Aligned_cols=121  Identities=17%  Similarity=0.201  Sum_probs=105.5

Q ss_pred             HHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCC
Q 029910           12 VELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDES   91 (185)
Q Consensus        12 ~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~   91 (185)
                      -+|+..+......+.+++|-+=|++.|+.|.++|...| +++.++|++...-+|.+++++.|.|                
T Consensus       433 dDL~~EI~~r~~~~eRvLVTtLTKkmAEdLT~Yl~e~g-ikv~YlHSdidTlER~eIirdLR~G----------------  495 (663)
T COG0556         433 DDLLSEIRKRVAKNERVLVTTLTKKMAEDLTEYLKELG-IKVRYLHSDIDTLERVEIIRDLRLG----------------  495 (663)
T ss_pred             HHHHHHHHHHHhcCCeEEEEeehHHHHHHHHHHHHhcC-ceEEeeeccchHHHHHHHHHHHhcC----------------
Confidence            45555544434456999999999999999999999999 9999999999999999999999999                


Q ss_pred             CCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcC-----CCCCHHHHHHHHhhhcCC-CCEEEEEeeCchH
Q 029910           92 ETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYE-----LPTKKETYIRRMTTCLAA-DGSVINIVVGGEV  160 (185)
Q Consensus        92 ~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d-----~P~~~~~yiqR~GR~~~~-~g~~i~~v~~~e~  160 (185)
                             ..++||.-..    +-+|+|+|.|.+|..+|     +.+|-.+.+|-|||++++ .|.+|.....-..
T Consensus       496 -------~~DvLVGINL----LREGLDiPEVsLVAIlDADKeGFLRse~SLIQtIGRAARN~~GkvIlYAD~iT~  559 (663)
T COG0556         496 -------EFDVLVGINL----LREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITD  559 (663)
T ss_pred             -------CccEEEeehh----hhccCCCcceeEEEEeecCccccccccchHHHHHHHHhhccCCeEEEEchhhhH
Confidence                   6999999999    99999999999999887     567999999999998765 5999988765333

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

Probab=99.38  E-value=1.1e-11  Score=111.16  Aligned_cols=94  Identities=21%  Similarity=0.305  Sum_probs=89.0

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEE
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMI  103 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iL  103 (185)
                      .+.+++|||.++.++..++..+...+ + +..++|+.+..+|.+++++|+.|                       ..++|
T Consensus       282 ~~~~~lif~~~~~~a~~i~~~~~~~~-~-~~~it~~t~~~eR~~il~~fr~g-----------------------~~~~l  336 (442)
T COG1061         282 RGDKTLIFASDVEHAYEIAKLFLAPG-I-VEAITGETPKEEREAILERFRTG-----------------------GIKVL  336 (442)
T ss_pred             CCCcEEEEeccHHHHHHHHHHhcCCC-c-eEEEECCCCHHHHHHHHHHHHcC-----------------------CCCEE
Confidence            56899999999999999999998887 5 89999999999999999999999                       69999


Q ss_pred             EEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhcC
Q 029910          104 VVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLA  146 (185)
Q Consensus       104 V~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~~  146 (185)
                      |++.+    +.+|+|+|+++++|......|...|+||+||..+
T Consensus       337 v~~~v----l~EGvDiP~~~~~i~~~~t~S~~~~~Q~lGR~LR  375 (442)
T COG1061         337 VTVKV----LDEGVDIPDADVLIILRPTGSRRLFIQRLGRGLR  375 (442)
T ss_pred             EEeee----ccceecCCCCcEEEEeCCCCcHHHHHHHhhhhcc
Confidence            99999    9999999999999999999999999999999643

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

Probab=99.36  E-value=2.7e-12  Score=116.65  Aligned_cols=123  Identities=17%  Similarity=0.215  Sum_probs=100.8

Q ss_pred             hHHHHHHHHHHHcc-------CCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccc
Q 029910            8 QETLVELLHLVVAG-------RRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWN   80 (185)
Q Consensus         8 ~~~l~~ll~~l~~~-------~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~   80 (185)
                      ...+.+++..|.+.       ..-..|+|||+++++.|..|+..|..+| +++..+|++++..+|..+-.+|..+     
T Consensus       416 e~eK~~ii~~L~k~E~~~~sskg~rGQtIVFT~SRrr~h~lA~~L~~kG-~~a~pYHaGL~y~eRk~vE~~F~~q-----  489 (830)
T COG1202         416 ESEKWDIIARLVKREFSTESSKGYRGQTIVFTYSRRRCHELADALTGKG-LKAAPYHAGLPYKERKSVERAFAAQ-----  489 (830)
T ss_pred             chHHHHHHHHHHHHHHhhhhccCcCCceEEEecchhhHHHHHHHhhcCC-cccccccCCCcHHHHHHHHHHHhcC-----
Confidence            44556666665431       2234899999999999999999999998 9999999999999999999999999     


Q ss_pred             ccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEE---cCCCC-CHHHHHHHHhhhcCC----CCEEE
Q 029910           81 QKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLIN---YELPT-KKETYIRRMTTCLAA----DGSVI  152 (185)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~---~d~P~-~~~~yiqR~GR~~~~----~g~~i  152 (185)
                                        .+.++|+|-+    ++-|+|||.-.+|+-   ...-| ++.+|.|++||+|+.    .|+++
T Consensus       490 ------------------~l~~VVTTAA----L~AGVDFPASQVIFEsLaMG~~WLs~~EF~QM~GRAGRp~yHdrGkVy  547 (830)
T COG1202         490 ------------------ELAAVVTTAA----LAAGVDFPASQVIFESLAMGIEWLSVREFQQMLGRAGRPDYHDRGKVY  547 (830)
T ss_pred             ------------------CcceEeehhh----hhcCCCCchHHHHHHHHHcccccCCHHHHHHHhcccCCCCcccCceEE
Confidence                              6999999999    999999997655431   12223 899999999998764    48999


Q ss_pred             EEeeCc
Q 029910          153 NIVVGG  158 (185)
Q Consensus       153 ~~v~~~  158 (185)
                      .++.++
T Consensus       548 llvepg  553 (830)
T COG1202         548 LLVEPG  553 (830)
T ss_pred             EEecCC
Confidence            998664

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

Probab=99.30  E-value=9.8e-11  Score=101.12  Aligned_cols=127  Identities=19%  Similarity=0.315  Sum_probs=101.0

Q ss_pred             HHHHHHHccCCCCCcEEEEcCChhhHHHHHHHH-hcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCC
Q 029910           13 ELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAV-SNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDES   91 (185)
Q Consensus        13 ~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L-~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~   91 (185)
                      .|+..|-+.+..+.|++||+++....+.++..| ...+....+++|+.  ...|.+.+++||+|                
T Consensus       293 kl~~~lekq~~~~~P~liF~p~I~~~eq~a~~lk~~~~~~~i~~Vhs~--d~~R~EkV~~fR~G----------------  354 (441)
T COG4098         293 KLKRWLEKQRKTGRPVLIFFPEIETMEQVAAALKKKLPKETIASVHSE--DQHRKEKVEAFRDG----------------  354 (441)
T ss_pred             HHHHHHHHHHhcCCcEEEEecchHHHHHHHHHHHhhCCccceeeeecc--CccHHHHHHHHHcC----------------
Confidence            344444444667899999999999999999999 55676677899976  67899999999999                


Q ss_pred             CCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEE-EcCCC-CCHHHHHHHHhhhcCC----CCEEEEEeeCchHHHHHH
Q 029910           92 ETGKDEHKSHMIVVTDACLPLLSSGESAISARVLI-NYELP-TKKETYIRRMTTCLAA----DGSVINIVVGGEVVTLRS  165 (185)
Q Consensus        92 ~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI-~~d~P-~~~~~yiqR~GR~~~~----~g~~i~~v~~~e~~~~~~  165 (185)
                             ..++||+|.+    ++||+.+|+|++.| ..+-+ -+.++.+|-+||.|++    .|.++.|-.+....+.+.
T Consensus       355 -------~~~lLiTTTI----LERGVTfp~vdV~Vlgaeh~vfTesaLVQIaGRvGRs~~~PtGdv~FFH~G~skaM~~A  423 (441)
T COG4098         355 -------KITLLITTTI----LERGVTFPNVDVFVLGAEHRVFTESALVQIAGRVGRSLERPTGDVLFFHYGKSKAMKQA  423 (441)
T ss_pred             -------ceEEEEEeeh----hhcccccccceEEEecCCcccccHHHHHHHhhhccCCCcCCCCcEEEEeccchHHHHHH
Confidence                   7999999999    99999999999855 44332 4788999999997654    388888887766666544


Q ss_pred             HHH
Q 029910          166 MEE  168 (185)
Q Consensus       166 l~~  168 (185)
                      ..+
T Consensus       424 ~ke  426 (441)
T COG4098         424 RKE  426 (441)
T ss_pred             HHH
Confidence            433

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

Probab=99.28  E-value=1.5e-11  Score=107.62  Aligned_cols=102  Identities=23%  Similarity=0.352  Sum_probs=92.8

Q ss_pred             HHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCC
Q 029910           10 TLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGD   89 (185)
Q Consensus        10 ~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~   89 (185)
                      ...+=+..+++++-.++..||||=++..++.++..|.+.| +.+..+|..|.+.+|...-+.|-.|              
T Consensus       302 d~~edi~k~i~~~f~gqsgiiyc~sq~d~ekva~alkn~g-i~a~~yha~lep~dks~~hq~w~a~--------------  366 (695)
T KOG0353|consen  302 DCIEDIAKLIKGDFAGQSGIIYCFSQKDCEKVAKALKNHG-IHAGAYHANLEPEDKSGAHQGWIAG--------------  366 (695)
T ss_pred             HHHHHHHHHhccccCCCcceEEEeccccHHHHHHHHHhcC-ccccccccccCcccccccccccccc--------------
Confidence            3333333446668889999999999999999999999999 9999999999999999999999998              


Q ss_pred             CCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHH
Q 029910           90 ESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIR  139 (185)
Q Consensus        90 ~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiq  139 (185)
                               +++++|+|-+    +..|+|-|+|+.||+-.+|.+.+.|.|
T Consensus       367 ---------eiqvivatva----fgmgidkpdvrfvihhsl~ksienyyq  403 (695)
T KOG0353|consen  367 ---------EIQVIVATVA----FGMGIDKPDVRFVIHHSLPKSIENYYQ  403 (695)
T ss_pred             ---------ceEEEEEEee----ecccCCCCCeeEEEecccchhHHHHHH
Confidence                     6999999999    999999999999999999999999999

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

Probab=99.24  E-value=8.3e-11  Score=108.72  Aligned_cols=148  Identities=14%  Similarity=0.220  Sum_probs=112.7

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCCh--------hhHHHHHHHHhcC-CCceEEEEecCCCHHHHHHHHHHHhcccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSR--------DELDAVCSAVSNL-ADISFSSLHSDLAETERTLILEEFRHTAM   77 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~--------~~~~~l~~~L~~~-~~~~~~~l~g~~~~~~R~~~l~~F~~~~~   77 (185)
                      +.+.+-++++.+.+.-..+.|+.+-|+-.        ..|..+++.|+.. ++.++..+||.|+..++.+++++|+++  
T Consensus       455 ~~~~~~~v~e~i~~ei~~GrQaY~VcPLIeESE~l~l~~a~~~~~~L~~~~~~~~vgL~HGrm~~~eKd~vM~~Fk~~--  532 (677)
T COG1200         455 PHERRPEVYERIREEIAKGRQAYVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEG--  532 (677)
T ss_pred             ccccHHHHHHHHHHHHHcCCEEEEEeccccccccchhhhHHHHHHHHHHHcccceeEEEecCCChHHHHHHHHHHHcC--
Confidence            34455555555444344678999999743        3566777777743 457899999999999999999999999  


Q ss_pred             cccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHH-hhh--cCCCCEEEEE
Q 029910           78 KWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRM-TTC--LAADGSVINI  154 (185)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~-GR~--~~~~g~~i~~  154 (185)
                                           +.+|||||.+    .+-|+|+|+++++|.+|.-+---+-+|+. ||.  ++..+.|+.+
T Consensus       533 ---------------------e~~ILVaTTV----IEVGVdVPnATvMVIe~AERFGLaQLHQLRGRVGRG~~qSyC~Ll  587 (677)
T COG1200         533 ---------------------EIDILVATTV----IEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGDLQSYCVLL  587 (677)
T ss_pred             ---------------------CCcEEEEeeE----EEecccCCCCeEEEEechhhhhHHHHHHhccccCCCCcceEEEEE
Confidence                                 6999999999    99999999999999999777666667775 884  5566899998


Q ss_pred             eeCch----HHHHHHHHHH-hCCccccccCCc
Q 029910          155 VVGGE----VVTLRSMEES-LGLIVAEVPINI  181 (185)
Q Consensus       155 v~~~e----~~~~~~l~~~-~~~~~~~~~~~~  181 (185)
                      ..+..    ...++-+.+. -|+.++|.++.+
T Consensus       588 ~~~~~~~~a~~RL~im~~t~DGF~IAE~DLkl  619 (677)
T COG1200         588 YKPPLSEVAKQRLKIMRETTDGFVIAEEDLKL  619 (677)
T ss_pred             eCCCCChhHHHHHHHHHhcCCcceehhhhHhc
Confidence            86644    3556666555 667777766554

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

Probab=99.21  E-value=1.6e-10  Score=113.61  Aligned_cols=94  Identities=11%  Similarity=0.173  Sum_probs=79.4

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcC-----CC---ceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCC
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNL-----AD---ISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKD   96 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~-----~~---~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~   96 (185)
                      ..|+||||.++++|+.+.+.|...     ++   ..+..+||+.+  ++.+++++|+++.                    
T Consensus       698 ~~KtiIF~~s~~HA~~i~~~L~~~f~~~~~~~~~~~v~~itg~~~--~~~~li~~Fk~~~--------------------  755 (1123)
T PRK11448        698 EGKTLIFAATDAHADMVVRLLKEAFKKKYGQVEDDAVIKITGSID--KPDQLIRRFKNER--------------------  755 (1123)
T ss_pred             CCcEEEEEcCHHHHHHHHHHHHHHHHhhcCCcCccceEEEeCCcc--chHHHHHHHhCCC--------------------
Confidence            479999999999999998887642     11   24567899875  5678999999872                    


Q ss_pred             CCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhcC
Q 029910           97 EHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLA  146 (185)
Q Consensus        97 ~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~~  146 (185)
                        ..+|+|++|+    +..|+|+|.+.+||.+++|.|...|+|++||+.+
T Consensus       756 --~p~IlVsvdm----L~TG~DvP~v~~vVf~rpvkS~~lf~QmIGRgtR  799 (1123)
T PRK11448        756 --LPNIVVTVDL----LTTGIDVPSICNLVFLRRVRSRILYEQMLGRATR  799 (1123)
T ss_pred             --CCeEEEEecc----cccCCCcccccEEEEecCCCCHHHHHHHHhhhcc
Confidence              2369999999    9999999999999999999999999999999643

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.16  E-value=5.2e-10  Score=106.40  Aligned_cols=127  Identities=13%  Similarity=0.095  Sum_probs=103.8

Q ss_pred             eEecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccc
Q 029910            3 VSFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQK   82 (185)
Q Consensus         3 v~~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~   82 (185)
                      |+.+..++...+.+.+......+.|+||||+|+..++.|++.|...| +++..||+.  +.+|...+..|+.+       
T Consensus       408 i~~t~~~K~~aI~~~I~~~~~~grpVLIft~Si~~se~Ls~~L~~~g-i~~~vLnak--q~eREa~Iia~Ag~-------  477 (830)
T PRK12904        408 IYKTEKEKFDAVVEDIKERHKKGQPVLVGTVSIEKSELLSKLLKKAG-IPHNVLNAK--NHEREAEIIAQAGR-------  477 (830)
T ss_pred             EEECHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCC-CceEeccCc--hHHHHHHHHHhcCC-------
Confidence            44455555555555543323567999999999999999999999998 999999996  78999999999998       


Q ss_pred             ccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCC--------------------------------------cE
Q 029910           83 VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISA--------------------------------------RV  124 (185)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v--------------------------------------~~  124 (185)
                                      +.+|+|||++    ++||+|++--                                      =+
T Consensus       478 ----------------~g~VtIATNm----AGRGtDI~LgGn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~GGLh  537 (830)
T PRK12904        478 ----------------PGAVTIATNM----AGRGTDIKLGGNPEMLAAALLEEETEEQIAKIKAEWQEEHEEVLEAGGLH  537 (830)
T ss_pred             ----------------CceEEEeccc----ccCCcCccCCCchhhhhhhhhhhhhhHHHHHHHHHHhhhhhhHHHcCCCE
Confidence                            7999999999    9999999864                                      16


Q ss_pred             EEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCch
Q 029910          125 LINYELPTKKETYIRRMTTCL--AADGSVINIVVGGE  159 (185)
Q Consensus       125 VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e  159 (185)
                      ||--..|.|..-=-|-.||+|  |.+|.+-.|++-.|
T Consensus       538 VigTerhesrRid~QlrGRagRQGdpGss~f~lSleD  574 (830)
T PRK12904        538 VIGTERHESRRIDNQLRGRSGRQGDPGSSRFYLSLED  574 (830)
T ss_pred             EEecccCchHHHHHHhhcccccCCCCCceeEEEEcCc
Confidence            888888998877778889975  45688888887654

>TIGR00595 priA primosomal protein N'

Probab=99.15  E-value=4.4e-10  Score=102.52  Aligned_cols=89  Identities=15%  Similarity=0.255  Sum_probs=72.1

Q ss_pred             HHHHHHHHhcC-CCceEEEEecCCCHHHH--HHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCccc
Q 029910           38 LDAVCSAVSNL-ADISFSSLHSDLAETER--TLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS  114 (185)
Q Consensus        38 ~~~l~~~L~~~-~~~~~~~l~g~~~~~~R--~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~  114 (185)
                      .+.+.+.|... ++.++..+|++++..++  .+++++|++|                       +.+|||+|++    ++
T Consensus       271 te~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~l~~f~~g-----------------------~~~ILVgT~~----i~  323 (505)
T TIGR00595       271 TEQVEEELAKLFPGARIARIDSDTTSRKGAHEALLNQFANG-----------------------KADILIGTQM----IA  323 (505)
T ss_pred             HHHHHHHHHhhCCCCcEEEEecccccCccHHHHHHHHHhcC-----------------------CCCEEEeCcc----cc
Confidence            57777887765 34789999999987766  8999999999                       6999999999    99


Q ss_pred             CcCCCCCCcEE--EEcCC----CC------CHHHHHHHHhhhcC--CCCEEEE
Q 029910          115 SGESAISARVL--INYEL----PT------KKETYIRRMTTCLA--ADGSVIN  153 (185)
Q Consensus       115 ~G~d~~~v~~V--I~~d~----P~------~~~~yiqR~GR~~~--~~g~~i~  153 (185)
                      +|+|+|+|++|  +|+|.    |.      ....|+|++||+++  ..|.++.
T Consensus       324 kG~d~~~v~lV~vl~aD~~l~~pd~ra~E~~~~ll~q~~GRagR~~~~g~vii  376 (505)
T TIGR00595       324 KGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVAGRAGRAEDPGQVII  376 (505)
T ss_pred             cCCCCCcccEEEEEcCcccccCcccchHHHHHHHHHHHHhccCCCCCCCEEEE
Confidence            99999999987  47775    42      24678999999754  5577663

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).

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.14  E-value=5.3e-10  Score=106.73  Aligned_cols=127  Identities=15%  Similarity=0.116  Sum_probs=105.4

Q ss_pred             eEecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccc
Q 029910            3 VSFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQK   82 (185)
Q Consensus         3 v~~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~   82 (185)
                      |+-+..++...+++.+......+.|+||||+|++.++.|+..|...| +++..||+.+.+.+|..+.+.|+.|       
T Consensus       422 v~~t~~~k~~av~~~i~~~~~~g~PVLVgt~Sie~sE~ls~~L~~~g-i~h~vLnak~~q~Ea~iia~Ag~~G-------  493 (896)
T PRK13104        422 VYLTQADKFQAIIEDVRECGVRKQPVLVGTVSIEASEFLSQLLKKEN-IKHQVLNAKFHEKEAQIIAEAGRPG-------  493 (896)
T ss_pred             EEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHcC-CCeEeecCCCChHHHHHHHhCCCCC-------
Confidence            55666777777777765556788999999999999999999999998 9999999999999999999999997       


Q ss_pred             ccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCC--------------------------------------cE
Q 029910           83 VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISA--------------------------------------RV  124 (185)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v--------------------------------------~~  124 (185)
                                      .  |+|||++    ++||+|+.--                                      =+
T Consensus       494 ----------------~--VtIATNm----AGRGtDI~Lggn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~  551 (896)
T PRK13104        494 ----------------A--VTIATNM----AGRGTDIVLGGSLAADLANLPADASEQEKEAVKKEWQKRHDEVIAAGGLR  551 (896)
T ss_pred             ----------------c--EEEeccC----ccCCcceecCCchhhhhhccccchhhHHHHHHHHHhhhhhhHHHHcCCCE
Confidence                            3  9999999    9999998732                                      16


Q ss_pred             EEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCch
Q 029910          125 LINYELPTKKETYIRRMTTCL--AADGSVINIVVGGE  159 (185)
Q Consensus       125 VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e  159 (185)
                      ||--..|.|..-=-|=.||+|  |.+|.+-.|++-.|
T Consensus       552 VIgTerhesrRID~QLrGRaGRQGDPGss~f~lSleD  588 (896)
T PRK13104        552 IIGSERHESRRIDNQLRGRAGRQGDPGSSRFYLSLED  588 (896)
T ss_pred             EEeeccCchHHHHHHhccccccCCCCCceEEEEEcCc
Confidence            787788877665666678875  45688888887644

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.13  E-value=5.7e-10  Score=105.01  Aligned_cols=93  Identities=11%  Similarity=0.145  Sum_probs=74.1

Q ss_pred             hHHHHHHHHhcC-CCceEEEEecCCC--HHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcc
Q 029910           37 ELDAVCSAVSNL-ADISFSSLHSDLA--ETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLL  113 (185)
Q Consensus        37 ~~~~l~~~L~~~-~~~~~~~l~g~~~--~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~  113 (185)
                      .++.+.+.|... ++.++..+|+++.  ..++.+++++|++|                       +.+|||+|++    +
T Consensus       438 G~e~~~e~l~~~fp~~~v~~~~~d~~~~~~~~~~~l~~f~~g-----------------------~~~ILVgT~~----i  490 (679)
T PRK05580        438 GTERLEEELAELFPEARILRIDRDTTRRKGALEQLLAQFARG-----------------------EADILIGTQM----L  490 (679)
T ss_pred             cHHHHHHHHHHhCCCCcEEEEeccccccchhHHHHHHHHhcC-----------------------CCCEEEEChh----h
Confidence            456777777765 3478999999986  46789999999999                       6999999999    9


Q ss_pred             cCcCCCCCCcEEE--EcCCCCC----------HHHHHHHHhhhc--CCCCEEEEEee
Q 029910          114 SSGESAISARVLI--NYELPTK----------KETYIRRMTTCL--AADGSVINIVV  156 (185)
Q Consensus       114 ~~G~d~~~v~~VI--~~d~P~~----------~~~yiqR~GR~~--~~~g~~i~~v~  156 (185)
                      ++|+|+|++++|+  ++|.+-+          ...|.|++||++  +..|.++....
T Consensus       491 akG~d~p~v~lV~il~aD~~l~~pdfra~Er~~~~l~q~~GRagR~~~~g~viiqT~  547 (679)
T PRK05580        491 AKGHDFPNVTLVGVLDADLGLFSPDFRASERTFQLLTQVAGRAGRAEKPGEVLIQTY  547 (679)
T ss_pred             ccCCCCCCcCEEEEEcCchhccCCccchHHHHHHHHHHHHhhccCCCCCCEEEEEeC
Confidence            9999999999985  5565533          367999999975  45677775543

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.09  E-value=9.3e-10  Score=105.01  Aligned_cols=128  Identities=14%  Similarity=0.153  Sum_probs=107.2

Q ss_pred             eEecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccc
Q 029910            3 VSFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQK   82 (185)
Q Consensus         3 v~~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~   82 (185)
                      ||.++.++...+++.+......+.|+||||+|...++.++..|...+ +.+..||+++++.++..+.+.|+.|       
T Consensus       427 iy~t~~~K~~Aii~ei~~~~~~GrpVLV~t~sv~~se~ls~~L~~~g-i~~~vLnak~~~~Ea~ii~~Ag~~G-------  498 (908)
T PRK13107        427 VYLTADEKYQAIIKDIKDCRERGQPVLVGTVSIEQSELLARLMVKEK-IPHEVLNAKFHEREAEIVAQAGRTG-------  498 (908)
T ss_pred             EEeCHHHHHHHHHHHHHHHHHcCCCEEEEeCcHHHHHHHHHHHHHCC-CCeEeccCcccHHHHHHHHhCCCCC-------
Confidence            56677777777887766556778999999999999999999999998 9999999999999999999999998       


Q ss_pred             ccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCC-------------------------------------cEE
Q 029910           83 VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISA-------------------------------------RVL  125 (185)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v-------------------------------------~~V  125 (185)
                                      .  |+|||++    ++||+|+.--                                     =+|
T Consensus       499 ----------------~--VtIATnm----AGRGTDIkLggn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~V  556 (908)
T PRK13107        499 ----------------A--VTIATNM----AGRGTDIVLGGNWNMEIEALENPTAEQKAKIKADWQIRHDEVVAAGGLHI  556 (908)
T ss_pred             ----------------c--EEEecCC----cCCCcceecCCchHHhhhhhcchhhHHHHHHHHHHHhhHHHHHHcCCCEE
Confidence                            4  9999999    9999998732                                     268


Q ss_pred             EEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCchH
Q 029910          126 INYELPTKKETYIRRMTTCL--AADGSVINIVVGGEV  160 (185)
Q Consensus       126 I~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e~  160 (185)
                      |--..|.|..-=-|=.||+|  |.+|.+-.|++-.|.
T Consensus       557 IgTerheSrRID~QLrGRaGRQGDPGss~f~lSlED~  593 (908)
T PRK13107        557 LGTERHESRRIDNQLRGRAGRQGDAGSSRFYLSMEDS  593 (908)
T ss_pred             EecccCchHHHHhhhhcccccCCCCCceeEEEEeCcH
Confidence            88888887666666678875  456888888876543

>COG1204 Superfamily II helicase [General function prediction only]

Probab=98.97  E-value=2.6e-09  Score=101.63  Aligned_cols=109  Identities=19%  Similarity=0.263  Sum_probs=90.1

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcC------------------CC------------------ceEEEEecCCCHHHH
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNL------------------AD------------------ISFSSLHSDLAETER   65 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~------------------~~------------------~~~~~l~g~~~~~~R   65 (185)
                      -..+.+++|||++++.+...++.|+..                  ..                  .-++++|++++.++|
T Consensus       250 ~~~~~qvLvFv~sR~~a~~~A~~l~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~l~e~v~~GvafHhAGL~~~~R  329 (766)
T COG1204         250 LAEGGQVLVFVHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGVAFHHAGLPREDR  329 (766)
T ss_pred             HhcCCeEEEEEecCchHHHHHHHHHHHHhhcCChhhhhhccccccccccccccccchHHHHHHHHhCccccccCCCHHHH
Confidence            345689999999999999999988830                  00                  126789999999999


Q ss_pred             HHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEE----EcC-----CCCCHHH
Q 029910           66 TLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLI----NYE-----LPTKKET  136 (185)
Q Consensus        66 ~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI----~~d-----~P~~~~~  136 (185)
                      .-+-+.|+.|                       .++||+||+.    ++.|+|.|.-.+||    -||     .+-++-+
T Consensus       330 ~~vE~~Fr~g-----------------------~ikVlv~TpT----LA~GVNLPA~~VIIk~~~~y~~~~g~~~i~~~d  382 (766)
T COG1204         330 QLVEDAFRKG-----------------------KIKVLVSTPT----LAAGVNLPARTVIIKDTRRYDPKGGIVDIPVLD  382 (766)
T ss_pred             HHHHHHHhcC-----------------------CceEEEechH----HhhhcCCcceEEEEeeeEEEcCCCCeEECchhh
Confidence            9999999999                       7999999999    99999999887777    467     5678999


Q ss_pred             HHHHHhhhcCCC----CEEEEEeeC
Q 029910          137 YIRRMTTCLAAD----GSVINIVVG  157 (185)
Q Consensus       137 yiqR~GR~~~~~----g~~i~~v~~  157 (185)
                      |+|.+||+|+..    |.++.+.+.
T Consensus       383 v~QM~GRAGRPg~d~~G~~~i~~~~  407 (766)
T COG1204         383 VLQMAGRAGRPGYDDYGEAIILATS  407 (766)
T ss_pred             HhhccCcCCCCCcCCCCcEEEEecC
Confidence            999999986543    666666643

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

Probab=98.91  E-value=3.1e-09  Score=102.13  Aligned_cols=121  Identities=22%  Similarity=0.238  Sum_probs=98.0

Q ss_pred             CCCcEEEEcCChhhHHHHH----HHHhcCC---CceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCC
Q 029910           24 PGLPMIVCCSSRDELDAVC----SAVSNLA---DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKD   96 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~----~~L~~~~---~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~   96 (185)
                      ++.++|+|+.+++.++.+.    ..+...+   ...+...++++..++|.++...|++|                     
T Consensus       305 ~~~~tL~F~~sr~~~e~~~~~~~~~~~~~~~~l~~~v~~~~~~~~~~er~~ie~~~~~g---------------------  363 (851)
T COG1205         305 NGIQTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEG---------------------  363 (851)
T ss_pred             cCceEEEEEehhhhhhhhhhchhHHHhhcchhhhhheeeccccCCHHHHHHHHHHHhcC---------------------
Confidence            5689999999999999886    3333222   24688889999999999999999999                     


Q ss_pred             CCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCC-CHHHHHHHHhhhcCCCCEEEEEeeC----chHHHHHHHHHHhC
Q 029910           97 EHKSHMIVVTDACLPLLSSGESAISARVLINYELPT-KKETYIRRMTTCLAADGSVINIVVG----GEVVTLRSMEESLG  171 (185)
Q Consensus        97 ~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~-~~~~yiqR~GR~~~~~g~~i~~v~~----~e~~~~~~l~~~~~  171 (185)
                        ....+++|.+    +.-|+|+.+++.||++..|. +..++.||.||++++...++.++..    -+..+...-+....
T Consensus       364 --~~~~~~st~A----lelgidiG~ldavi~~g~P~~s~~~~~Q~~GRaGR~~~~~l~~~v~~~~~~d~yy~~~p~~~~~  437 (851)
T COG1205         364 --ELLGVIATNA----LELGIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGRRGQESLVLVVLRSDPLDSYYLRHPEELLE  437 (851)
T ss_pred             --CccEEecchh----hhhceeehhhhhHhhcCCCCchHHHHHHhhhhccCCCCCceEEEEeCCCccchhhhhCcHhhhh
Confidence              7999999999    99999999999999999999 8999999999998777544444422    34455555555554

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

Probab=98.81  E-value=5.9e-08  Score=94.42  Aligned_cols=120  Identities=10%  Similarity=0.107  Sum_probs=97.3

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcC-CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCcee
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNL-ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSH  101 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~-~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (185)
                      ..+.|+---+|..++.+.++..|+.. +..++++.||.|++.+-.+++.+|.+|                       ..+
T Consensus       801 ~RgGQvfYv~NrV~~Ie~~~~~L~~LVPEarI~vaHGQM~e~eLE~vM~~F~~g-----------------------~~d  857 (1139)
T COG1197         801 LRGGQVFYVHNRVESIEKKAERLRELVPEARIAVAHGQMRERELEEVMLDFYNG-----------------------EYD  857 (1139)
T ss_pred             hcCCEEEEEecchhhHHHHHHHHHHhCCceEEEEeecCCCHHHHHHHHHHHHcC-----------------------CCC
Confidence            34688888889999999999999876 557899999999999999999999999                       799


Q ss_pred             EEEEecCCCCcccCcCCCCCCcEEEEcCCCC-CHHHHHHHHhhhcCCC--CEEEEEeeCc------hHHHHHHHHHH
Q 029910          102 MIVVTDACLPLLSSGESAISARVLINYELPT-KKETYIRRMTTCLAAD--GSVINIVVGG------EVVTLRSMEES  169 (185)
Q Consensus       102 iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~-~~~~yiqR~GR~~~~~--g~~i~~v~~~------e~~~~~~l~~~  169 (185)
                      |||||.+    .+-|+|+|.++.+|.-+.-. -.+...|--||.|++.  +.|+.++.+.      -...++.++++
T Consensus       858 VLv~TTI----IEtGIDIPnANTiIIe~AD~fGLsQLyQLRGRVGRS~~~AYAYfl~p~~k~lT~~A~kRL~aI~~~  930 (1139)
T COG1197         858 VLVCTTI----IETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSNKQAYAYFLYPPQKALTEDAEKRLEAIASF  930 (1139)
T ss_pred             EEEEeee----eecCcCCCCCceEEEeccccccHHHHHHhccccCCccceEEEEEeecCccccCHHHHHHHHHHHhh
Confidence            9999999    99999999999988765443 3566667679876554  7888888642      23445555543

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

Probab=98.76  E-value=2.5e-08  Score=91.27  Aligned_cols=132  Identities=15%  Similarity=0.167  Sum_probs=100.7

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcC----CC---ceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCC
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNL----AD---ISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKD   96 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~----~~---~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~   96 (185)
                      .+-++|-||..++.|+.+....++.    +-   -.+..+.|+-+.++|.++..+.-.|                     
T Consensus       524 ~~~R~IAFC~~R~~CEL~~~~~R~I~~ET~~~LV~~i~SYRGGY~A~DRRKIE~~~F~G---------------------  582 (1034)
T KOG4150|consen  524 HGLRCIAFCPSRKLCELVLCLTREILAETAPHLVEAITSYRGGYIAEDRRKIESDLFGG---------------------  582 (1034)
T ss_pred             cCCcEEEeccHHHHHHHHHHHHHHHHHHhhHHHHHHHHhhcCccchhhHHHHHHHhhCC---------------------
Confidence            5689999999999999776554432    20   1245667889999999999998888                     


Q ss_pred             CCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhcCCC--CEEEEEe--eCchHHHHHHHHHHhCC
Q 029910           97 EHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAAD--GSVINIV--VGGEVVTLRSMEESLGL  172 (185)
Q Consensus        97 ~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~~~~--g~~i~~v--~~~e~~~~~~l~~~~~~  172 (185)
                        ...-+|+|.+    ++-|+|+...+.|+...+|.+...+.|+.||+|++.  +.++.++  .+-|..++..-+...+.
T Consensus       583 --~L~giIaTNA----LELGIDIG~LDAVl~~GFP~S~aNl~QQ~GRAGRRNk~SLavyva~~~PVDQ~Y~~HP~~l~~~  656 (1034)
T KOG4150|consen  583 --KLCGIIATNA----LELGIDIGHLDAVLHLGFPGSIANLWQQAGRAGRRNKPSLAVYVAFLGPVDQYYMSHPDKLFGS  656 (1034)
T ss_pred             --eeeEEEecch----hhhccccccceeEEEccCchhHHHHHHHhccccccCCCceEEEEEeccchhhHhhcCcHHHhCC
Confidence              7999999999    999999999999999999999999999999997665  3333333  34456666666666555


Q ss_pred             ccccccCCcc
Q 029910          173 IVAEVPINIS  182 (185)
Q Consensus       173 ~~~~~~~~~~  182 (185)
                      .-.++-+++.
T Consensus       657 pN~EL~LD~~  666 (1034)
T KOG4150|consen  657 PNEELHLDSQ  666 (1034)
T ss_pred             CcceeEEecc
Confidence            5555544443

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

Probab=98.72  E-value=8.6e-08  Score=91.42  Aligned_cols=115  Identities=23%  Similarity=0.343  Sum_probs=94.7

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcC--------------------------------------CCceEEEEecCCCHHHH
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNL--------------------------------------ADISFSSLHSDLAETER   65 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~--------------------------------------~~~~~~~l~g~~~~~~R   65 (185)
                      .+.++||||++++.|+.++..+...                                      + .-++++|.+++.++|
T Consensus       459 e~~~~lvfc~sk~~ce~~a~~~~~~vpk~~~~e~~~~~~~~~s~s~~lr~~~~~ld~Vl~~ti~-~GvAyHhaGLT~eER  537 (1008)
T KOG0950|consen  459 EGSSVLVFCPSKKNCENVASLIAKKVPKHIKSEKRLGLWELLSISNLLRRIPGILDPVLAKTIP-YGVAYHHAGLTSEER  537 (1008)
T ss_pred             cCCeEEEEcCcccchHHHHHHHHHHhhHhhhhhhhhhHHHHHHHHhHhhcCCcccchHHheecc-ccceecccccccchH
Confidence            3567999999999998777444220                                      2 347899999999999


Q ss_pred             HHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCC----CCCHHHHHHHH
Q 029910           66 TLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYEL----PTKKETYIRRM  141 (185)
Q Consensus        66 ~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~----P~~~~~yiqR~  141 (185)
                      .-+-..|+.|                       -..++.||+.    ++-|++.|..+++|-.-.    +-+.-+|.|++
T Consensus       538 ~~iE~afr~g-----------------------~i~vl~aTST----laaGVNLPArRVIiraP~~g~~~l~~~~YkQM~  590 (1008)
T KOG0950|consen  538 EIIEAAFREG-----------------------NIFVLVATST----LAAGVNLPARRVIIRAPYVGREFLTRLEYKQMV  590 (1008)
T ss_pred             HHHHHHHHhc-----------------------CeEEEEecch----hhccCcCCcceeEEeCCccccchhhhhhHHhhh
Confidence            9999999999                       6999999999    999999999999997643    34788999999


Q ss_pred             hhhcC----CCCEEEEEeeCchHHHHHHH
Q 029910          142 TTCLA----ADGSVINIVVGGEVVTLRSM  166 (185)
Q Consensus       142 GR~~~----~~g~~i~~v~~~e~~~~~~l  166 (185)
                      ||+++    ..|.+|.++.+.|...+..+
T Consensus       591 GRAGR~gidT~GdsiLI~k~~e~~~~~~l  619 (1008)
T KOG0950|consen  591 GRAGRTGIDTLGDSILIIKSSEKKRVREL  619 (1008)
T ss_pred             hhhhhcccccCcceEEEeeccchhHHHHH
Confidence            99754    45899999999888666544

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

Probab=98.66  E-value=1.7e-07  Score=89.56  Aligned_cols=120  Identities=17%  Similarity=0.230  Sum_probs=93.7

Q ss_pred             HHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCC--------------------------------------C
Q 029910            9 ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLA--------------------------------------D   50 (185)
Q Consensus         9 ~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~--------------------------------------~   50 (185)
                      ...++++..|..  .+-.|+||||=+++.|++-+..|.+..                                      .
T Consensus       553 ~~~l~lin~L~k--~~lLP~VvFvFSkkrCde~a~~L~~~nL~~~~EKseV~lfl~k~~~rLk~~DR~LPQvl~m~~ll~  630 (1248)
T KOG0947|consen  553 PTWLDLINHLRK--KNLLPVVVFVFSKKRCDEYADYLTNLNLTDSKEKSEVHLFLSKAVARLKGEDRNLPQVLSMRSLLL  630 (1248)
T ss_pred             chHHHHHHHHhh--cccCceEEEEEccccHHHHHHHHhccCcccchhHHHHHHHHHHHHHhcChhhccchHHHHHHHHHh
Confidence            457888888544  345899999999999999999887620                                      0


Q ss_pred             ceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCC
Q 029910           51 ISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYEL  130 (185)
Q Consensus        51 ~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~  130 (185)
                      --++++||++=+--+.-+-.-|.+|                       -+++|+||+.    ++.|++.|.-.+|+. .+
T Consensus       631 RGiaVHH~GlLPivKE~VE~LFqrG-----------------------lVKVLFATET----FAMGVNMPARtvVF~-Sl  682 (1248)
T KOG0947|consen  631 RGIAVHHGGLLPIVKEVVELLFQRG-----------------------LVKVLFATET----FAMGVNMPARTVVFS-SL  682 (1248)
T ss_pred             hcchhhcccchHHHHHHHHHHHhcC-----------------------ceEEEeehhh----hhhhcCCCceeEEee-eh
Confidence            1267888998888888888889999                       7999999999    999999997665553 33


Q ss_pred             CC---------CHHHHHHHHhhhcCCC----CEEEEEeeCc
Q 029910          131 PT---------KKETYIRRMTTCLAAD----GSVINIVVGG  158 (185)
Q Consensus       131 P~---------~~~~yiqR~GR~~~~~----g~~i~~v~~~  158 (185)
                      -+         .+-.|.|++||+|+++    |.+|.++...
T Consensus       683 ~KhDG~efR~L~PGEytQMAGRAGRRGlD~tGTVii~~~~~  723 (1248)
T KOG0947|consen  683 RKHDGNEFRELLPGEYTQMAGRAGRRGLDETGTVIIMCKDS  723 (1248)
T ss_pred             hhccCcceeecCChhHHhhhccccccccCcCceEEEEecCC
Confidence            22         5789999999987655    8888777543

>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]

Probab=98.66  E-value=3.9e-07  Score=88.78  Aligned_cols=126  Identities=14%  Similarity=0.184  Sum_probs=108.9

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCcee
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSH  101 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (185)
                      +..+.+++||..-+...+-|+++|..++ +..--|.|.+.-+-|++.++.|....                    +....
T Consensus       696 k~~GHrVLIFSQMVRmLDIL~eYL~~r~-ypfQRLDGsvrgelRq~AIDhFnap~--------------------SddFv  754 (1373)
T KOG0384|consen  696 KEGGHRVLIFSQMVRMLDILAEYLSLRG-YPFQRLDGSVRGELRQQAIDHFNAPD--------------------SDDFV  754 (1373)
T ss_pred             hcCCceEEEhHHHHHHHHHHHHHHHHcC-CcceeccCCcchHHHHHHHHhccCCC--------------------CCceE
Confidence            4567999999999999999999999998 79999999999999999999999873                    23677


Q ss_pred             EEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCC--EEEEEeeCc--hHHHHHHHHHHhCC
Q 029910          102 MIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADG--SVINIVVGG--EVVTLRSMEESLGL  172 (185)
Q Consensus       102 iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g--~~i~~v~~~--e~~~~~~l~~~~~~  172 (185)
                      .|++|-+    .+-||++..++.||.||--|||..=+|-+.||  -|+..  .++-||+.+  |.+++++-...++.
T Consensus       755 FLLSTRA----GGLGINLatADTVIIFDSDWNPQNDLQAqARaHRIGQkk~VnVYRLVTk~TvEeEilERAk~KmvL  827 (1373)
T KOG0384|consen  755 FLLSTRA----GGLGINLATADTVIIFDSDWNPQNDLQAQARAHRIGQKKHVNVYRLVTKNTVEEEILERAKLKMVL  827 (1373)
T ss_pred             EEEeccc----CcccccccccceEEEeCCCCCcchHHHHHHHHHhhcccceEEEEEEecCCchHHHHHHHHHHHhhh
Confidence            9999999    99999999999999999999999999999997  45553  567788875  66777666666553

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=98.59  E-value=4e-07  Score=86.56  Aligned_cols=111  Identities=15%  Similarity=0.185  Sum_probs=87.4

Q ss_pred             ccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCc
Q 029910           20 AGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHK   99 (185)
Q Consensus        20 ~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (185)
                      .....+++++|-|||+..|..++..|+..+. ++..+|+.+....|.+.+++.+.-.   .                ...
T Consensus       435 ~~~~~~~kvlvI~NTV~~Aie~Y~~Lk~~~~-~v~LlHSRf~~~dR~~ke~~l~~~~---~----------------~~~  494 (733)
T COG1203         435 EEVKEGKKVLVIVNTVDRAIELYEKLKEKGP-KVLLLHSRFTLKDREEKERELKKLF---K----------------QNE  494 (733)
T ss_pred             hhhccCCcEEEEEecHHHHHHHHHHHHhcCC-CEEEEecccchhhHHHHHHHHHHHH---h----------------ccC
Confidence            3366789999999999999999999999984 8999999999999999988765310   0                015


Q ss_pred             eeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhcC----CCCEEEEEeeC
Q 029910          100 SHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLA----ADGSVINIVVG  157 (185)
Q Consensus       100 ~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~~----~~g~~i~~v~~  157 (185)
                      ..|+|+|.+    .+-|+|+. .+++|-  =+..+++.+||+||+.|    .+|.++.+...
T Consensus       495 ~~IvVaTQV----IEagvDid-fd~mIT--e~aPidSLIQR~GRv~R~g~~~~~~~~v~~~~  549 (733)
T COG1203         495 GFIVVATQV----IEAGVDID-FDVLIT--ELAPIDSLIQRAGRVNRHGKKENGKIYVYNDE  549 (733)
T ss_pred             CeEEEEeeE----EEEEeccc-cCeeee--cCCCHHHHHHHHHHHhhcccccCCceeEeecc
Confidence            789999999    99999975 666654  35668999999999733    34566665543

>KOG0953 consensus Mitochondrial RNA helicase SUV3, DEAD-box superfamily [RNA processing and modification]

Probab=98.52  E-value=1e-06  Score=80.40  Aligned_cols=126  Identities=14%  Similarity=0.115  Sum_probs=91.4

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEE
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIV  104 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV  104 (185)
                      ..-|||.. +++..-.+...+...|+.++++++|++|++.|.+--..|...+                     ...+|||
T Consensus       357 ~GDCvV~F-Skk~I~~~k~kIE~~g~~k~aVIYGsLPPeTr~aQA~~FNd~~---------------------~e~dvlV  414 (700)
T KOG0953|consen  357 PGDCVVAF-SKKDIFTVKKKIEKAGNHKCAVIYGSLPPETRLAQAALFNDPS---------------------NECDVLV  414 (700)
T ss_pred             CCCeEEEe-ehhhHHHHHHHHHHhcCcceEEEecCCCCchhHHHHHHhCCCC---------------------CccceEE
Confidence            35566655 5677888999999888667999999999999999999999853                     2699999


Q ss_pred             EecCCCCcccCcCCCCCCcEEEEcCC---------CCCHHHHHHHHhhhcCCCC-EEEEEeeCchHHHHHHHHHHhCCcc
Q 029910          105 VTDACLPLLSSGESAISARVLINYEL---------PTKKETYIRRMTTCLAADG-SVINIVVGGEVVTLRSMEESLGLIV  174 (185)
Q Consensus       105 ~Td~~~~~~~~G~d~~~v~~VI~~d~---------P~~~~~yiqR~GR~~~~~g-~~i~~v~~~e~~~~~~l~~~~~~~~  174 (185)
                      |||+    .++|+++. ++-||.|++         |-+...-.|-+||+|+.++ ...=+++.-..+.+..+.+.+....
T Consensus       415 AsDA----IGMGLNL~-IrRiiF~sl~Kysg~e~~~it~sqikQIAGRAGRf~s~~~~G~vTtl~~eDL~~L~~~l~~p~  489 (700)
T KOG0953|consen  415 ASDA----IGMGLNLN-IRRIIFYSLIKYSGRETEDITVSQIKQIAGRAGRFGSKYPQGEVTTLHSEDLKLLKRILKRPV  489 (700)
T ss_pred             eecc----cccccccc-eeEEEEeecccCCcccceeccHHHHHHHhhcccccccCCcCceEEEeeHhhHHHHHHHHhCCc
Confidence            9999    99999986 566676664         3467888898899865431 2222233334455566666666555


Q ss_pred             ccc
Q 029910          175 AEV  177 (185)
Q Consensus       175 ~~~  177 (185)
                      +++
T Consensus       490 epi  492 (700)
T KOG0953|consen  490 EPI  492 (700)
T ss_pred             hHH
Confidence            543

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

Probab=98.51  E-value=2.5e-06  Score=80.88  Aligned_cols=115  Identities=13%  Similarity=0.137  Sum_probs=88.4

Q ss_pred             CcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCcee-EEE
Q 029910           26 LPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSH-MIV  104 (185)
Q Consensus        26 ~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-iLV  104 (185)
                      .++++-.|.+.+.+.+....+-.| ..+..|||+|+..+|.++++.|....+                     ... .|.
T Consensus       596 ~~~v~Isny~~tldl~e~~~~~~g-~~~~rLdG~~~~~qRq~~vd~FN~p~~---------------------~~~vfLl  653 (776)
T KOG0390|consen  596 VKSVLISNYTQTLDLFEQLCRWRG-YEVLRLDGKTSIKQRQKLVDTFNDPES---------------------PSFVFLL  653 (776)
T ss_pred             eEEEEeccHHHHHHHHHHHHhhcC-ceEEEEcCCCchHHHHHHHHhccCCCC---------------------CceEEEE
Confidence            444444566666666666666666 899999999999999999999998741                     224 456


Q ss_pred             EecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCC--CEEEEEeeCc--hHHHHHHH
Q 029910          105 VTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAAD--GSVINIVVGG--EVVTLRSM  166 (185)
Q Consensus       105 ~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~--g~~i~~v~~~--e~~~~~~l  166 (185)
                      +|-+    .+.|+++-+++-||.||++|||+.=.|-|+|+  -|+.  ..++-+++.+  |...+++-
T Consensus       654 SsKA----gg~GinLiGAsRlil~D~dWNPa~d~QAmaR~~RdGQKk~v~iYrLlatGtiEEk~~qrq  717 (776)
T KOG0390|consen  654 SSKA----GGEGLNLIGASRLILFDPDWNPAVDQQAMARAWRDGQKKPVYIYRLLATGTIEEKIYQRQ  717 (776)
T ss_pred             eccc----ccCceeecccceEEEeCCCCCchhHHHHHHHhccCCCcceEEEEEeecCCCchHHHHHHH
Confidence            6777    89999999999999999999999999999996  4555  4566677665  44555443

>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]

Probab=98.46  E-value=2.1e-06  Score=83.66  Aligned_cols=123  Identities=15%  Similarity=0.187  Sum_probs=98.6

Q ss_pred             ecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccc
Q 029910            5 FTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVT   84 (185)
Q Consensus         5 ~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~   84 (185)
                      ..|.++|.-||..|..   .+.+++||+.--+..+-|-..|+.+| +.-.-|.|..+-++|+..+++|..+.        
T Consensus      1259 cGKLQtLAiLLqQLk~---eghRvLIfTQMtkmLDVLeqFLnyHg-ylY~RLDg~t~vEqRQaLmerFNaD~-------- 1326 (1958)
T KOG0391|consen 1259 CGKLQTLAILLQQLKS---EGHRVLIFTQMTKMLDVLEQFLNYHG-YLYVRLDGNTSVEQRQALMERFNADR-------- 1326 (1958)
T ss_pred             cchHHHHHHHHHHHHh---cCceEEehhHHHHHHHHHHHHHhhcc-eEEEEecCCccHHHHHHHHHHhcCCC--------
Confidence            3578899999998644   57999999999999999999999888 78888999999999999999999873        


Q ss_pred             ccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCH------HHHHHHHhhhcCCCCEEEEEeeCc
Q 029910           85 EQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKK------ETYIRRMTTCLAADGSVINIVVGG  158 (185)
Q Consensus        85 ~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~------~~yiqR~GR~~~~~g~~i~~v~~~  158 (185)
                                   .-...+++|--    ..-|+|+.++|.||.||--||+      .+.-||||++  +.-..+-|++.+
T Consensus      1327 -------------RIfcfILSTrS----ggvGiNLtgADTVvFYDsDwNPtMDaQAQDrChRIGqt--RDVHIYRLISe~ 1387 (1958)
T KOG0391|consen 1327 -------------RIFCFILSTRS----GGVGINLTGADTVVFYDSDWNPTMDAQAQDRCHRIGQT--RDVHIYRLISER 1387 (1958)
T ss_pred             -------------ceEEEEEeccC----CccccccccCceEEEecCCCCchhhhHHHHHHHhhcCc--cceEEEEeeccc
Confidence                         22445677887    8899999999999999999986      4556666655  223345566554

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

Probab=98.42  E-value=1.2e-06  Score=84.00  Aligned_cols=110  Identities=15%  Similarity=0.212  Sum_probs=92.3

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhc--C-CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCc
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSN--L-ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHK   99 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~--~-~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (185)
                      ...+-++||.+-.+..+..++.|..  . ....+..|||.++..++.++++.--.+                       +
T Consensus       257 ~~~GdILvFLpG~~EI~~~~~~L~~~~l~~~~~i~PLy~~L~~~eQ~rvF~p~~~~-----------------------~  313 (845)
T COG1643         257 EGSGSILVFLPGQREIERTAEWLEKAELGDDLEILPLYGALSAEEQVRVFEPAPGG-----------------------K  313 (845)
T ss_pred             CCCCCEEEECCcHHHHHHHHHHHHhccccCCcEEeeccccCCHHHHHhhcCCCCCC-----------------------c
Confidence            3468999999999999999999987  2 247899999999999999976655554                       4


Q ss_pred             eeEEEEecCCCCcccCcCCCCCCcEEEEcCC------------------CCCHHHHHHHHhhhcCC-CCEEEEEeeCch
Q 029910          100 SHMIVVTDACLPLLSSGESAISARVLINYEL------------------PTKKETYIRRMTTCLAA-DGSVINIVVGGE  159 (185)
Q Consensus       100 ~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~------------------P~~~~~yiqR~GR~~~~-~g~~i~~v~~~e  159 (185)
                      .+|+++|++    ++-++.+|+|++||.-.+                  |-|-++-.||.||||+. +|.|+-+++..+
T Consensus       314 RKVVlATNI----AETSLTI~gIr~VIDsG~ak~~~y~~~~g~~~L~~~~ISqAsA~QRaGRAGR~~pGicyRLyse~~  388 (845)
T COG1643         314 RKVVLATNI----AETSLTIPGIRYVIDSGLAKEKRYDPRTGLTRLETEPISKASADQRAGRAGRTGPGICYRLYSEED  388 (845)
T ss_pred             ceEEEEccc----cccceeeCCeEEEecCCcccccccccccCceeeeEEEechhhhhhhccccccCCCceEEEecCHHH
Confidence            669999999    999999999999995432                  44778999999999874 599999998643

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

Probab=98.39  E-value=8.1e-06  Score=76.93  Aligned_cols=126  Identities=17%  Similarity=0.179  Sum_probs=103.4

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ   86 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~   86 (185)
                      |+..|-.||..|.   ..+.+++||..-....+-|-.+..-++ +...-+.|.++.++|...++.|....          
T Consensus       472 Km~vLDkLL~~Lk---~~GhRVLIFSQmt~mLDILeDyc~~R~-y~ycRiDGSt~~eeR~~aI~~fn~~~----------  537 (971)
T KOG0385|consen  472 KMLVLDKLLPKLK---EQGHRVLIFSQMTRMLDILEDYCMLRG-YEYCRLDGSTSHEEREDAIEAFNAPP----------  537 (971)
T ss_pred             ceehHHHHHHHHH---hCCCeEEEeHHHHHHHHHHHHHHHhcC-ceeEeecCCCCcHHHHHHHHhcCCCC----------
Confidence            4455666676653   367999999988888888888888887 79999999999999999999998873          


Q ss_pred             CCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCC--CEEEEEeeCchH
Q 029910           87 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAAD--GSVINIVVGGEV  160 (185)
Q Consensus        87 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~--g~~i~~v~~~e~  160 (185)
                                +...=.|++|-+    .+-|+++..+++||.||--|||..=+|-+-||  -|+.  -.++.+++.+.+
T Consensus       538 ----------s~~FiFlLSTRA----GGLGINL~aADtVIlyDSDWNPQ~DLQAmDRaHRIGQ~K~V~V~RLitentV  601 (971)
T KOG0385|consen  538 ----------SEKFIFLLSTRA----GGLGINLTAADTVILYDSDWNPQVDLQAMDRAHRIGQKKPVVVYRLITENTV  601 (971)
T ss_pred             ----------cceEEEEEeccc----cccccccccccEEEEecCCCCchhhhHHHHHHHhhCCcCceEEEEEeccchH
Confidence                      113447899999    99999999999999999999999999998887  3444  467788887644

>COG0553 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]

Probab=98.37  E-value=9e-06  Score=77.24  Aligned_cols=124  Identities=15%  Similarity=0.222  Sum_probs=100.9

Q ss_pred             chHHHHHHH-HHHHccCCCCC--cEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccc
Q 029910            7 FQETLVELL-HLVVAGRRPGL--PMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKV   83 (185)
Q Consensus         7 ~~~~l~~ll-~~l~~~~~~~~--~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~   83 (185)
                      |...+.+++ ..+..   .+.  +++||++.....+-+...|...+ +....++|+++..+|...+++|..++       
T Consensus       693 k~~~l~~ll~~~~~~---~~~~~kvlifsq~t~~l~il~~~l~~~~-~~~~~ldG~~~~~~r~~~i~~f~~~~-------  761 (866)
T COG0553         693 KLQALDELLLDKLLE---EGHYHKVLIFSQFTPVLDLLEDYLKALG-IKYVRLDGSTPAKRRQELIDRFNADE-------  761 (866)
T ss_pred             HHHHHHHHHHHHHHh---hcccccEEEEeCcHHHHHHHHHHHHhcC-CcEEEEeCCCChhhHHHHHHHhhcCC-------
Confidence            455566666 44332   345  99999999999999999999998 78999999999999999999999963       


Q ss_pred             cccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCC--CEEEEEeeCch
Q 029910           84 TEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAAD--GSVINIVVGGE  159 (185)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~--g~~i~~v~~~e  159 (185)
                                    ...-.++++.+    .+-|+++..++.||.||..|++....|.+.|+  .|+.  -.++.+++.+.
T Consensus       762 --------------~~~v~lls~ka----gg~glnLt~a~~vi~~d~~wnp~~~~Qa~dRa~RigQ~~~v~v~r~i~~~t  823 (866)
T COG0553         762 --------------EEKVFLLSLKA----GGLGLNLTGADTVILFDPWWNPAVELQAIDRAHRIGQKRPVKVYRLITRGT  823 (866)
T ss_pred             --------------CCceEEEEecc----cccceeecccceEEEeccccChHHHHHHHHHHHHhcCcceeEEEEeecCCc
Confidence                          12445667778    99999999999999999999999999999996  3444  35677777664

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

Probab=98.36  E-value=6.3e-06  Score=77.77  Aligned_cols=124  Identities=15%  Similarity=0.208  Sum_probs=100.6

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhc-CCCceEEEEecCCCHHHHHHHHHHHhcccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSN-LADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE   85 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~-~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~   85 (185)
                      |++.+..||..   ...++.++++|..++...+.|-..|.. .+ ++.+-+.|..+...|..++++|..++         
T Consensus       531 Km~vl~~ll~~---W~kqg~rvllFsqs~~mLdilE~fL~~~~~-ysylRmDGtT~~~~R~~lVd~Fne~~---------  597 (923)
T KOG0387|consen  531 KMKVLAKLLKD---WKKQGDRVLLFSQSRQMLDILESFLRRAKG-YSYLRMDGTTPAALRQKLVDRFNEDE---------  597 (923)
T ss_pred             hHHHHHHHHHH---HhhCCCEEEEehhHHHHHHHHHHHHHhcCC-ceEEEecCCCccchhhHHHHhhcCCC---------
Confidence            45555666654   245668999999999999999999984 55 89999999999999999999999885         


Q ss_pred             cCCCCCCCCCCCCcee-EEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCC-CCE-EEEEeeCchH
Q 029910           86 QSGDESETGKDEHKSH-MIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAA-DGS-VINIVVGGEV  160 (185)
Q Consensus        86 ~~~~~~~~~~~~~~~~-iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~-~g~-~i~~v~~~e~  160 (185)
                                   ... .|++|-+    ..-|+++..++-||.||+-|||.+=.|-.-|+  .|+ +.+ ++-+++++.+
T Consensus       598 -------------s~~VFLLTTrv----GGLGlNLTgAnRVIIfDPdWNPStD~QAreRawRiGQkkdV~VYRL~t~gTI  660 (923)
T KOG0387|consen  598 -------------SIFVFLLTTRV----GGLGLNLTGANRVIIFDPDWNPSTDNQARERAWRIGQKKDVVVYRLMTAGTI  660 (923)
T ss_pred             -------------ceEEEEEEecc----cccccccccCceEEEECCCCCCccchHHHHHHHhhcCccceEEEEEecCCcH
Confidence                         555 5678888    99999999999999999999999999987775  444 444 4556777643

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

Probab=98.34  E-value=3.7e-06  Score=82.46  Aligned_cols=121  Identities=19%  Similarity=0.224  Sum_probs=93.1

Q ss_pred             HHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcC-------------------------------------CCceEEEEe
Q 029910           15 LHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL-------------------------------------ADISFSSLH   57 (185)
Q Consensus        15 l~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~-------------------------------------~~~~~~~l~   57 (185)
                      ++++++ .....|+|||+.+|+.+...|++++..                                     + .-++.+|
T Consensus       537 yeKVm~-~agk~qVLVFVHsRkET~ktA~aIRd~~le~dtls~fmre~s~s~eilrtea~~~kn~dLkdLLp-ygfaIHh  614 (1674)
T KOG0951|consen  537 YEKVLE-HAGKNQVLVFVHSRKETAKTARAIRDKALEEDTLSRFMREDSASREILRTEAGQAKNPDLKDLLP-YGFAIHH  614 (1674)
T ss_pred             HHHHHH-hCCCCcEEEEEEechHHHHHHHHHHHHHhhhhHHHHHHhcccchhhhhhhhhhcccChhHHHHhh-ccceeec
Confidence            345555 233389999999998888877777620                                     2 4578999


Q ss_pred             cCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEE----EcCC---
Q 029910           58 SDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLI----NYEL---  130 (185)
Q Consensus        58 g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI----~~d~---  130 (185)
                      .+|+..+|...-+-|+.|                       .+++||+|-.    ++.|+++|.=.++|    -||+   
T Consensus       615 AGl~R~dR~~~EdLf~~g-----------------------~iqvlvstat----lawgvnlpahtViikgtqvy~pekg  667 (1674)
T KOG0951|consen  615 AGLNRKDRELVEDLFADG-----------------------HIQVLVSTAT----LAWGVNLPAHTVIIKGTQVYDPEKG  667 (1674)
T ss_pred             cCCCcchHHHHHHHHhcC-----------------------ceeEEEeehh----hhhhcCCCcceEEecCccccCcccC
Confidence            999999999999999999                       7999999999    99999999877777    4665   


Q ss_pred             ---CCCHHHHHHHHhhhcCCC----CEEEEEeeCchHHHHH
Q 029910          131 ---PTKKETYIRRMTTCLAAD----GSVINIVVGGEVVTLR  164 (185)
Q Consensus       131 ---P~~~~~yiqR~GR~~~~~----g~~i~~v~~~e~~~~~  164 (185)
                         +-++.+-.|+.||+++..    |..|..-...+...+.
T Consensus       668 ~w~elsp~dv~qmlgragrp~~D~~gegiiit~~se~qyyl  708 (1674)
T KOG0951|consen  668 RWTELSPLDVMQMLGRAGRPQYDTCGEGIIITDHSELQYYL  708 (1674)
T ss_pred             ccccCCHHHHHHHHhhcCCCccCcCCceeeccCchHhhhhH
Confidence               347999999999986543    5555554444544443

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=98.32  E-value=6.6e-06  Score=78.81  Aligned_cols=127  Identities=9%  Similarity=0.109  Sum_probs=98.4

Q ss_pred             eEecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccc
Q 029910            3 VSFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQK   82 (185)
Q Consensus         3 v~~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~   82 (185)
                      |+-+..++...+++.+......++|+||.|.+...++.|++.|...| +...+|+..-... =.+++.  ..|.      
T Consensus       404 iy~t~~~K~~Aii~ei~~~~~~gqPVLVgT~SIe~SE~ls~~L~~~g-i~h~vLNAk~~e~-EA~IIa--~AG~------  473 (925)
T PRK12903        404 IFGTKHAKWKAVVKEVKRVHKKGQPILIGTAQVEDSETLHELLLEAN-IPHTVLNAKQNAR-EAEIIA--KAGQ------  473 (925)
T ss_pred             EEEcHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCC-CCceeecccchhh-HHHHHH--hCCC------
Confidence            45566777777888766545678999999999999999999999998 8999999863322 222333  3342      


Q ss_pred             ccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCc--------EEEEcCCCCCHHHHHHHHhhhc--CCCCEEE
Q 029910           83 VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISAR--------VLINYELPTKKETYIRRMTTCL--AADGSVI  152 (185)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~--------~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i  152 (185)
                                      ...|.|||.+    ++||.|+.--.        +||....|.|..-=-|-.||+|  |.+|.+-
T Consensus       474 ----------------~GaVTIATNM----AGRGTDI~Lg~~V~~~GGLhVIgTerheSrRIDnQLrGRaGRQGDpGss~  533 (925)
T PRK12903        474 ----------------KGAITIATNM----AGRGTDIKLSKEVLELGGLYVLGTDKAESRRIDNQLRGRSGRQGDVGESR  533 (925)
T ss_pred             ----------------CCeEEEeccc----ccCCcCccCchhHHHcCCcEEEecccCchHHHHHHHhcccccCCCCCcce
Confidence                            5779999999    99999998554        8999999998777778889975  4568887


Q ss_pred             EEeeCch
Q 029910          153 NIVVGGE  159 (185)
Q Consensus       153 ~~v~~~e  159 (185)
                      .|++-.|
T Consensus       534 f~lSLeD  540 (925)
T PRK12903        534 FFISLDD  540 (925)
T ss_pred             EEEecch
Confidence            7776544

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

Probab=98.31  E-value=3.3e-06  Score=76.40  Aligned_cols=124  Identities=15%  Similarity=0.197  Sum_probs=94.0

Q ss_pred             cCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCce
Q 029910           21 GRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKS  100 (185)
Q Consensus        21 ~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~  100 (185)
                      ...++.|++|||.-....+.+...+..++ +..+-+.|..+..+|....++|...+                      ..
T Consensus       488 ~d~~~~KflVFaHH~~vLd~Iq~~~~~r~-vg~IRIDGst~s~~R~ll~qsFQ~se----------------------ev  544 (689)
T KOG1000|consen  488 PDAPPRKFLVFAHHQIVLDTIQVEVNKRK-VGSIRIDGSTPSHRRTLLCQSFQTSE----------------------EV  544 (689)
T ss_pred             ccCCCceEEEEehhHHHHHHHHHHHHHcC-CCeEEecCCCCchhHHHHHHHhcccc----------------------ce
Confidence            36677999999999999999999999997 89999999999999999999999874                      44


Q ss_pred             eE-EEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhh---hcCCCCE-EEEEeeCc--hHHHHHHHHHHhC
Q 029910          101 HM-IVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTT---CLAADGS-VINIVVGG--EVVTLRSMEESLG  171 (185)
Q Consensus       101 ~i-LV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR---~~~~~g~-~i~~v~~~--e~~~~~~l~~~~~  171 (185)
                      +| +++-.+    ++.|+++..++.||..++|||+.-.+|-=-|   .|..+++ ++.||..+  |...+..+.++++
T Consensus       545 ~VAvlsItA----~gvGLt~tAa~~VVFaEL~wnPgvLlQAEDRaHRiGQkssV~v~ylvAKgT~Ddy~Wp~l~~KL~  618 (689)
T KOG1000|consen  545 RVAVLSITA----AGVGLTLTAASVVVFAELHWNPGVLLQAEDRAHRIGQKSSVFVQYLVAKGTADDYMWPMLQQKLD  618 (689)
T ss_pred             EEEEEEEee----cccceeeeccceEEEEEecCCCceEEechhhhhhccccceeeEEEEEecCchHHHHHHHHHHHHH
Confidence            42 334455    7999999999999999999997555442222   2233333 45556554  5566666666543

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

Probab=98.24  E-value=1.9e-06  Score=81.00  Aligned_cols=119  Identities=20%  Similarity=0.269  Sum_probs=88.8

Q ss_pred             HHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCC--------------------------------------c
Q 029910           10 TLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLAD--------------------------------------I   51 (185)
Q Consensus        10 ~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~--------------------------------------~   51 (185)
                      .+..+.+.+..  .+..|+|||+=+++.|+.++..++...+                                      -
T Consensus       370 ~i~kiVkmi~~--~~~~PVIvFSFSkkeCE~~Alqm~kldfN~deEk~~V~~iF~nAi~~LseeDr~LPqie~iLPLL~R  447 (1041)
T KOG0948|consen  370 DIYKIVKMIME--RNYLPVIVFSFSKKECEAYALQMSKLDFNTDEEKELVETIFNNAIDQLSEEDRELPQIENILPLLRR  447 (1041)
T ss_pred             cHHHHHHHHHh--hcCCceEEEEecHhHHHHHHHhhccCcCCChhHHHHHHHHHHHHHHhcChhhccchHHHHHHHHHHh
Confidence            34556665444  5668999999999999999988865310                                      1


Q ss_pred             eEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEE----
Q 029910           52 SFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLIN----  127 (185)
Q Consensus        52 ~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~----  127 (185)
                      -+..+|+++=+-=+..+-=-|..|                       -+++|.||+.    ++.|++.|.-.+|+-    
T Consensus       448 GIGIHHsGLLPIlKE~IEILFqEG-----------------------LvKvLFATET----FsiGLNMPAkTVvFT~~rK  500 (1041)
T KOG0948|consen  448 GIGIHHSGLLPILKEVIEILFQEG-----------------------LVKVLFATET----FSIGLNMPAKTVVFTAVRK  500 (1041)
T ss_pred             ccccccccchHHHHHHHHHHHhcc-----------------------HHHHHHhhhh----hhhccCCcceeEEEeeccc
Confidence            145677777776666666678888                       7999999999    999999998776662    


Q ss_pred             cC---CCC-CHHHHHHHHhhhcCCC----CEEEEEeeC
Q 029910          128 YE---LPT-KKETYIRRMTTCLAAD----GSVINIVVG  157 (185)
Q Consensus       128 ~d---~P~-~~~~yiqR~GR~~~~~----g~~i~~v~~  157 (185)
                      ||   +-| +.-.|+|+.||+|+++    |.||.+++.
T Consensus       501 fDG~~fRwissGEYIQMSGRAGRRG~DdrGivIlmiDe  538 (1041)
T KOG0948|consen  501 FDGKKFRWISSGEYIQMSGRAGRRGIDDRGIVILMIDE  538 (1041)
T ss_pred             cCCcceeeecccceEEecccccccCCCCCceEEEEecC
Confidence            22   222 5678999999986654    999999865

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=98.22  E-value=2.1e-05  Score=74.34  Aligned_cols=127  Identities=14%  Similarity=0.088  Sum_probs=99.3

Q ss_pred             eEecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccc
Q 029910            3 VSFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQK   82 (185)
Q Consensus         3 v~~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~   82 (185)
                      |+-++.++...+++.+......++|+||.|.+...++.|+..|...| ++...|+..-.. .-.+++.+=-.        
T Consensus       405 iy~t~~~k~~Aii~ei~~~~~~GrPVLVgt~sI~~SE~ls~~L~~~g-I~h~vLNAk~~~-~EA~IIa~AG~--------  474 (764)
T PRK12326        405 VYATAAEKNDAIVEHIAEVHETGQPVLVGTHDVAESEELAERLRAAG-VPAVVLNAKNDA-EEARIIAEAGK--------  474 (764)
T ss_pred             eEeCHHHHHHHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHhCC-CcceeeccCchH-hHHHHHHhcCC--------
Confidence            55667777777888766656788999999999999999999999998 999999986433 22444443222        


Q ss_pred             ccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCC---------------cEEEEcCCCCCHHHHHHHHhhhc--
Q 029910           83 VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISA---------------RVLINYELPTKKETYIRRMTTCL--  145 (185)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v---------------~~VI~~d~P~~~~~yiqR~GR~~--  145 (185)
                                      ...|-|||.+    ++||.|+.--               =+||--..|.|..-=-|=.||++  
T Consensus       475 ----------------~gaVTIATNM----AGRGTDIkLg~~~~~~~~~V~~~GGLhVIgTerheSrRID~QLrGRaGRQ  534 (764)
T PRK12326        475 ----------------YGAVTVSTQM----AGRGTDIRLGGSDEADRDRVAELGGLHVIGTGRHRSERLDNQLRGRAGRQ  534 (764)
T ss_pred             ----------------CCcEEEEecC----CCCccCeecCCCcccchHHHHHcCCcEEEeccCCchHHHHHHHhcccccC
Confidence                            4779999999    9999998733               27999999999877778889975  


Q ss_pred             CCCCEEEEEeeCch
Q 029910          146 AADGSVINIVVGGE  159 (185)
Q Consensus       146 ~~~g~~i~~v~~~e  159 (185)
                      |.+|.+-.|++-.|
T Consensus       535 GDpGss~f~lSleD  548 (764)
T PRK12326        535 GDPGSSVFFVSLED  548 (764)
T ss_pred             CCCCceeEEEEcch
Confidence            55688888887544

>KOG0392 consensus SNF2 family DNA-dependent ATPase domain-containing protein [Transcription]

Probab=98.22  E-value=8.2e-06  Score=79.91  Aligned_cols=109  Identities=15%  Similarity=0.256  Sum_probs=89.9

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcC--CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCcee
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNL--ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSH  101 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~--~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (185)
                      .+.+++|||.-+...+.+-+-|.+.  +.+.-..|.|..++.+|.+++++|.++.                      .++
T Consensus      1339 sqHRiLIFcQlK~mlDlVekDL~k~~mpsVtymRLDGSVpp~~R~kiV~~FN~Dp----------------------tID 1396 (1549)
T KOG0392|consen 1339 SQHRILIFCQLKSMLDLVEKDLFKKYMPSVTYMRLDGSVPPGDRQKIVERFNEDP----------------------TID 1396 (1549)
T ss_pred             ccceeEEeeeHHHHHHHHHHHHhhhhcCceeEEEecCCCCcHHHHHHHHHhcCCC----------------------cee
Confidence            4689999999999999999888654  3233447889999999999999999984                      688


Q ss_pred             EE-EEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCE--EEEEeeCc
Q 029910          102 MI-VVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGS--VINIVVGG  158 (185)
Q Consensus       102 iL-V~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~--~i~~v~~~  158 (185)
                      +| ++|-+    .+-|+++.+++.||.++--|||-.=+|-|-|+  .|++.+  ++-+++.+
T Consensus      1397 vLlLTThV----GGLGLNLTGADTVVFvEHDWNPMrDLQAMDRAHRIGQKrvVNVyRlItrG 1454 (1549)
T KOG0392|consen 1397 VLLLTTHV----GGLGLNLTGADTVVFVEHDWNPMRDLQAMDRAHRIGQKRVVNVYRLITRG 1454 (1549)
T ss_pred             EEEEeeec----cccccccCCCceEEEEecCCCchhhHHHHHHHHhhcCceeeeeeeehhcc
Confidence            65 67888    99999999999999999999999999999997  455542  45556655

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

Probab=98.21  E-value=4.4e-06  Score=80.53  Aligned_cols=125  Identities=12%  Similarity=0.156  Sum_probs=101.9

Q ss_pred             hHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcC------CCceEEEEecCCCHHHHHHHHHHHhcccccccc
Q 029910            8 QETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL------ADISFSSLHSDLAETERTLILEEFRHTAMKWNQ   81 (185)
Q Consensus         8 ~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~------~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~   81 (185)
                      .+-+.+++..+.. ....+.+|||-+.......+.+.|...      .++.+..+|+.|+..+++.++..--.|      
T Consensus       397 ~~Li~~li~~I~~-~~~~GaILVFLPG~~eI~~~~~~L~~~~~f~~~~~~~ilplHs~~~s~eQ~~VF~~pp~g------  469 (924)
T KOG0920|consen  397 YDLIEDLIEYIDE-REFEGAILVFLPGWEEILQLKELLEVNLPFADSLKFAILPLHSSIPSEEQQAVFKRPPKG------  469 (924)
T ss_pred             HHHHHHHHHhccc-CCCCceEEEEcCCHHHHHHHHHHhhhccccccccceEEEeccccCChHHHHHhcCCCCCC------
Confidence            4556667777666 566799999999999999999999642      136789999999999999998777777      


Q ss_pred             cccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEE--------cCCCC----------CHHHHHHHHhh
Q 029910           82 KVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLIN--------YELPT----------KKETYIRRMTT  143 (185)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~--------~d~P~----------~~~~yiqR~GR  143 (185)
                                       ..+|+++|.+    ++-.+.++||-+||.        ||+-.          +...-.||.||
T Consensus       470 -----------------~RKIIlaTNI----AETSITIdDVvyVIDsG~~Ke~~yD~~~~~s~l~~~wvSkAna~QR~GR  528 (924)
T KOG0920|consen  470 -----------------TRKIILATNI----AETSITIDDVVYVIDSGLVKEKSYDPERKVSCLLLSWVSKANAKQRRGR  528 (924)
T ss_pred             -----------------cchhhhhhhh----HhhcccccCeEEEEecCeeeeeeecccCCcchhheeeccccchHHhccc
Confidence                             6899999999    999999999999994        55433          45667899999


Q ss_pred             hcC-CCCEEEEEeeCchH
Q 029910          144 CLA-ADGSVINIVVGGEV  160 (185)
Q Consensus       144 ~~~-~~g~~i~~v~~~e~  160 (185)
                      +|+ .+|.|+.+++....
T Consensus       529 AGRv~~G~cy~L~~~~~~  546 (924)
T KOG0920|consen  529 AGRVRPGICYHLYTRSRY  546 (924)
T ss_pred             ccCccCCeeEEeechhhh
Confidence            976 67999999987433

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

Probab=98.17  E-value=2.8e-05  Score=73.55  Aligned_cols=122  Identities=16%  Similarity=0.218  Sum_probs=97.4

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ   86 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~   86 (185)
                      |.+.|..||..+.   ..+.+++||..--...+-|-..|...+ ++..-|.|...-..|+.++++|...+          
T Consensus       762 K~r~L~~LLp~~k---~~G~RVLiFSQFTqmLDILE~~L~~l~-~~ylRLDGsTqV~~RQ~lId~Fn~d~----------  827 (941)
T KOG0389|consen  762 KCRKLKELLPKIK---KKGDRVLIFSQFTQMLDILEVVLDTLG-YKYLRLDGSTQVNDRQDLIDEFNTDK----------  827 (941)
T ss_pred             hHhHHHHHHHHHh---hcCCEEEEeeHHHHHHHHHHHHHHhcC-ceEEeecCCccchHHHHHHHhhccCC----------
Confidence            5567777777753   456999999988888888888898888 89999999999999999999999885          


Q ss_pred             CCCCCCCCCCCCcee-EEEEecCCCCcccCcCCCCCCcEEEEcCCCCCH------HHHHHHHhhhcCCCCEEEEEeeCch
Q 029910           87 SGDESETGKDEHKSH-MIVVTDACLPLLSSGESAISARVLINYELPTKK------ETYIRRMTTCLAADGSVINIVVGGE  159 (185)
Q Consensus        87 ~~~~~~~~~~~~~~~-iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~------~~yiqR~GR~~~~~g~~i~~v~~~e  159 (185)
                                  .+. .|++|-+    .+-|+++..+++||.||+--||      ++--||+|-+  ++-.++-+++.+.
T Consensus       828 ------------difVFLLSTKA----GG~GINLt~An~VIihD~dFNP~dD~QAEDRcHRvGQt--kpVtV~rLItk~T  889 (941)
T KOG0389|consen  828 ------------DIFVFLLSTKA----GGFGINLTCANTVIIHDIDFNPYDDKQAEDRCHRVGQT--KPVTVYRLITKST  889 (941)
T ss_pred             ------------ceEEEEEeecc----CcceecccccceEEEeecCCCCcccchhHHHHHhhCCc--ceeEEEEEEecCc
Confidence                        444 5788999    9999999999999999986554      5555555422  3356777888764


Q ss_pred             H
Q 029910          160 V  160 (185)
Q Consensus       160 ~  160 (185)
                      +
T Consensus       890 I  890 (941)
T KOG0389|consen  890 I  890 (941)
T ss_pred             H
Confidence            4

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

Probab=98.17  E-value=4.5e-06  Score=77.41  Aligned_cols=112  Identities=15%  Similarity=0.231  Sum_probs=92.6

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcCC----C---ceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCC
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNLA----D---ISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETG   94 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~~----~---~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~   94 (185)
                      ..+..-++||-..++..+.+++.|.+..    .   ..+..+||.++.+++.++++.--.|                   
T Consensus       255 ~E~~GDILvFLtGqeEIe~~~~~l~e~~~~~~~~~~~~~lply~aL~~e~Q~rvF~p~p~g-------------------  315 (674)
T KOG0922|consen  255 TEPPGDILVFLTGQEEIEAACELLRERAKSLPEDCPELILPLYGALPSEEQSRVFDPAPPG-------------------  315 (674)
T ss_pred             cCCCCCEEEEeCCHHHHHHHHHHHHHHhhhccccCcceeeeecccCCHHHhhccccCCCCC-------------------
Confidence            3556799999999999999999997651    0   1357899999999999887766666                   


Q ss_pred             CCCCceeEEEEecCCCCcccCcCCCCCCcEEEEc--------CC----------CCCHHHHHHHHhhhcCC-CCEEEEEe
Q 029910           95 KDEHKSHMIVVTDACLPLLSSGESAISARVLINY--------EL----------PTKKETYIRRMTTCLAA-DGSVINIV  155 (185)
Q Consensus        95 ~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~--------d~----------P~~~~~yiqR~GR~~~~-~g~~i~~v  155 (185)
                          ..+++++|.+    ++-.+.++++.+||.-        ++          |-|.+.-.||.||+|+. +|.|+-++
T Consensus       316 ----~RKvIlsTNI----AETSlTI~GI~YVVDsG~vK~~~y~p~~g~~~L~v~~ISkasA~QRaGRAGRt~pGkcyRLY  387 (674)
T KOG0922|consen  316 ----KRKVILSTNI----AETSLTIDGIRYVVDSGFVKQKKYNPRTGLDSLIVVPISKASANQRAGRAGRTGPGKCYRLY  387 (674)
T ss_pred             ----cceEEEEcce----eeeeEEecceEEEEcCCceEEEeeccccCccceeEEechHHHHhhhcccCCCCCCceEEEee
Confidence                6899999999    9999999999999954        32          56889999999999874 59999998


Q ss_pred             eCchH
Q 029910          156 VGGEV  160 (185)
Q Consensus       156 ~~~e~  160 (185)
                      +..+.
T Consensus       388 te~~~  392 (674)
T KOG0922|consen  388 TESAY  392 (674)
T ss_pred             eHHHH
Confidence            86544

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

Probab=98.11  E-value=3.2e-05  Score=74.96  Aligned_cols=116  Identities=17%  Similarity=0.240  Sum_probs=89.7

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcC----C-----------C-------ceEEEEecCCCHHHHHHHHHHHhcccccccc
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNL----A-----------D-------ISFSSLHSDLAETERTLILEEFRHTAMKWNQ   81 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~----~-----------~-------~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~   81 (185)
                      .+.+++|||.++..+...++.|.+.    |           .       .-...+|.+|...+|.-.-..|..|      
T Consensus       348 ~g~qVlvFvhsR~~Ti~tA~~l~~~a~~~g~~~~f~~~~~~k~l~elf~~g~~iHhAGm~r~DR~l~E~~F~~G------  421 (1230)
T KOG0952|consen  348 EGHQVLVFVHSRNETIRTAKKLRERAETNGEKDLFLPSPRNKQLKELFQQGMGIHHAGMLRSDRQLVEKEFKEG------  421 (1230)
T ss_pred             cCCeEEEEEecChHHHHHHHHHHHHHHhcCcccccCCChhhHHHHHHHHhhhhhcccccchhhHHHHHHHHhcC------
Confidence            4699999999999888888888553    1           0       2367788999999999999999999      


Q ss_pred             cccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEE----EcCCCC------CHHHHHHHHhhhcC----C
Q 029910           82 KVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLI----NYELPT------KKETYIRRMTTCLA----A  147 (185)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI----~~d~P~------~~~~yiqR~GR~~~----~  147 (185)
                                       .+++|+||..    ++-|+++|+=-++|    .||.-.      ..-+-+|-.||+|+    +
T Consensus       422 -----------------~i~vL~cTaT----LAwGVNLPA~aViIKGT~~ydsskg~f~dlgilDVlQifGRAGRPqFd~  480 (1230)
T KOG0952|consen  422 -----------------HIKVLCCTAT----LAWGVNLPAYAVIIKGTQVYDSSKGSFVDLGILDVLQIFGRAGRPQFDS  480 (1230)
T ss_pred             -----------------CceEEEecce----eeeccCCcceEEEecCCcccccccCceeeehHHHHHHHHhccCCCCCCC
Confidence                             7999999999    99999999755555    345433      45678888888765    4


Q ss_pred             CCEEEEEeeCchHHHHHHH
Q 029910          148 DGSVINIVVGGEVVTLRSM  166 (185)
Q Consensus       148 ~g~~i~~v~~~e~~~~~~l  166 (185)
                      .|.+|.+.+.+-...+.++
T Consensus       481 ~G~giIiTt~dkl~~Y~sL  499 (1230)
T KOG0952|consen  481 SGEGIIITTRDKLDHYESL  499 (1230)
T ss_pred             CceEEEEecccHHHHHHHH
Confidence            5888887776655555443

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

Probab=98.05  E-value=1.8e-05  Score=76.55  Aligned_cols=90  Identities=17%  Similarity=0.239  Sum_probs=65.8

Q ss_pred             HHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcC---CCceEEEEecCCCHHHHHHHHHHHhccccccccccccc
Q 029910           10 TLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL---ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ   86 (185)
Q Consensus        10 ~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~---~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~   86 (185)
                      .+.+.+..+.. . ...+++||+++.+.++.++..|...   .++.  .+..+.. ..|.+++++|+.+           
T Consensus       661 ~ia~~i~~l~~-~-~~g~~LVlftS~~~l~~v~~~L~~~~~~~~~~--~l~q~~~-~~r~~ll~~F~~~-----------  724 (850)
T TIGR01407       661 EIASYIIEITA-I-TSPKILVLFTSYEMLHMVYDMLNELPEFEGYE--VLAQGIN-GSRAKIKKRFNNG-----------  724 (850)
T ss_pred             HHHHHHHHHHH-h-cCCCEEEEeCCHHHHHHHHHHHhhhccccCce--EEecCCC-ccHHHHHHHHHhC-----------
Confidence            44555555444 2 3469999999999999999999752   1133  2333333 5789999999998           


Q ss_pred             CCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcE--EEEcCCC
Q 029910           87 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARV--LINYELP  131 (185)
Q Consensus        87 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~--VI~~d~P  131 (185)
                                  +..+|++|+.    +.+|+|+|+..+  ||...+|
T Consensus       725 ------------~~~iLlgt~s----f~EGVD~~g~~l~~viI~~LP  755 (850)
T TIGR01407       725 ------------EKAILLGTSS----FWEGVDFPGNGLVCLVIPRLP  755 (850)
T ss_pred             ------------CCeEEEEcce----eecccccCCCceEEEEEeCCC
Confidence                        6889999999    999999999885  4544444

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.

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

Probab=98.03  E-value=8e-05  Score=70.33  Aligned_cols=105  Identities=14%  Similarity=0.096  Sum_probs=77.2

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcCC----CceEEEEecCCCHH---------------------HHHHHHHHHhcccccc
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNLA----DISFSSLHSDLAET---------------------ERTLILEEFRHTAMKW   79 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~~----~~~~~~l~g~~~~~---------------------~R~~~l~~F~~~~~~~   79 (185)
                      +.+++|||.++..|..+.+.|....    ...+..++++.+..                     ...+++++|+...   
T Consensus       514 ~~kamvv~~sr~~a~~~~~~l~~~~~~~~~~~~vv~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Fk~~~---  590 (667)
T TIGR00348       514 KFKAMVVAISRYACVEEKNALDEELNEKFEASAIVMTGKESDDAEIRDYNKHIRTKFDKSDGFEIYYKDLERFKKEE---  590 (667)
T ss_pred             cCceeEEEecHHHHHHHHHHHHhhcccccCCeeEEecCCccchhHHHHHHHHhccccccchhhhHHHHHHHHhcCCC---
Confidence            5899999999999999998886541    13566677665443                     1235677776532   


Q ss_pred             cccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhcC------CCCEEEE
Q 029910           80 NQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLA------ADGSVIN  153 (185)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~~------~~g~~i~  153 (185)
                                         ..+|||++|+    +.-|+|.|.+++++..-+-.+ ..++|.+||+.+      ..|.++-
T Consensus       591 -------------------~~~ilIVvdm----llTGFDaP~l~tLyldKplk~-h~LlQai~R~nR~~~~~K~~g~IvD  646 (667)
T TIGR00348       591 -------------------NPKLLIVVDM----LLTGFDAPILNTLYLDKPLKY-HGLLQAIARTNRIDGKDKTFGLIVD  646 (667)
T ss_pred             -------------------CceEEEEEcc----cccccCCCccceEEEeccccc-cHHHHHHHHhccccCCCCCCEEEEE
Confidence                               6899999999    999999999999988775555 468999999744      1255555


Q ss_pred             Eee
Q 029910          154 IVV  156 (185)
Q Consensus       154 ~v~  156 (185)
                      |+.
T Consensus       647 y~g  649 (667)
T TIGR00348       647 YRG  649 (667)
T ss_pred             CcC
Confidence            554

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

>KOG0388 consensus SNF2 family DNA-dependent ATPase [Replication, recombination and repair]

Probab=98.00  E-value=5e-05  Score=71.46  Aligned_cols=123  Identities=15%  Similarity=0.180  Sum_probs=103.1

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ   86 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~   86 (185)
                      |..+|.+||..|.+   .+.++++|..-.+..+.+-.+|..++ +.-+-|.|.....+|..++++|...+          
T Consensus      1029 KL~~LDeLL~kLka---egHRvL~yfQMTkM~dl~EdYl~yr~-Y~ylRLDGSsk~~dRrd~vrDwQ~sd---------- 1094 (1185)
T KOG0388|consen 1029 KLVVLDELLPKLKA---EGHRVLMYFQMTKMIDLIEDYLVYRG-YTYLRLDGSSKASDRRDVVRDWQASD---------- 1094 (1185)
T ss_pred             ceeeHHHHHHHhhc---CCceEEehhHHHHHHHHHHHHHHhhc-cceEEecCcchhhHHHHHHhhccCCc----------
Confidence            45667778877533   56899999999999999999999888 79999999999999999999999974          


Q ss_pred             CCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCC--CEEEEEeeCch
Q 029910           87 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAAD--GSVINIVVGGE  159 (185)
Q Consensus        87 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~--g~~i~~v~~~e  159 (185)
                                  ..-.|++|-+    .+-|+++..++.||.||--|+|..=.|-|-|+  .|+.  -.++-+++.+.
T Consensus      1095 ------------iFvFLLSTRA----GGLGINLTAADTViFYdSDWNPT~D~QAMDRAHRLGQTrdvtvyrl~~rgT 1155 (1185)
T KOG0388|consen 1095 ------------IFVFLLSTRA----GGLGINLTAADTVIFYDSDWNPTADQQAMDRAHRLGQTRDVTVYRLITRGT 1155 (1185)
T ss_pred             ------------eEEEEEeccc----CcccccccccceEEEecCCCCcchhhHHHHHHHhccCccceeeeeeccccc
Confidence                        5667899999    99999999999999999999999888988886  4544  34555666543

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

Probab=97.95  E-value=6.6e-05  Score=71.42  Aligned_cols=111  Identities=14%  Similarity=0.118  Sum_probs=83.0

Q ss_pred             chHHHHHHHHHHHcc---CCCCCcEEEEcCChhhHHHHHHHHhcC----CCceEEEEecCCCHHHHHHHHHHHhcccccc
Q 029910            7 FQETLVELLHLVVAG---RRPGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEEFRHTAMKW   79 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~---~~~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~   79 (185)
                      ..+.....+...+..   .....|+||||.+.++|+++...|.+.    ++--+..++|+-  ++-++.++.|...+   
T Consensus       405 ~~~~V~r~~~~~l~~~~~g~~~~KTIvFa~n~dHAe~i~~~~~~~ype~~~~~a~~IT~d~--~~~q~~Id~f~~ke---  479 (875)
T COG4096         405 RTETVARELTEYLKRGATGDEIGKTIVFAKNHDHAERIREALVNEYPEYNGRYAMKITGDA--EQAQALIDNFIDKE---  479 (875)
T ss_pred             hHHHHHHHHHHHhccccCCCccCceEEEeeCcHHHHHHHHHHHHhCccccCceEEEEeccc--hhhHHHHHHHHhcC---
Confidence            345555555544442   223589999999999999999999764    223466777763  33344577776642   


Q ss_pred             cccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh
Q 029910           80 NQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC  144 (185)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~  144 (185)
                                        +--+|-|+.|+    +.-|+|+|.|-.+|.+..-.|...|.|++||+
T Consensus       480 ------------------~~P~Iaitvdl----L~TGiDvpev~nlVF~r~VrSktkF~QMvGRG  522 (875)
T COG4096         480 ------------------KYPRIAITVDL----LTTGVDVPEVVNLVFDRKVRSKTKFKQMVGRG  522 (875)
T ss_pred             ------------------CCCceEEehhh----hhcCCCchheeeeeehhhhhhHHHHHHHhcCc
Confidence                              24568888899    99999999999999999999999999999994

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]

Probab=97.91  E-value=0.00011  Score=66.85  Aligned_cols=126  Identities=15%  Similarity=0.090  Sum_probs=99.1

Q ss_pred             cchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccc
Q 029910            6 TFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE   85 (185)
Q Consensus         6 ~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~   85 (185)
                      +|.+.|.+-|..|.+ +...-|.|||..-....+.+...|...| +.+.-|-|+|++..|...++.|++.-         
T Consensus       620 TKIEAL~EEl~~l~~-rd~t~KsIVFSQFTSmLDLi~~rL~kaG-fscVkL~GsMs~~ardatik~F~nd~---------  688 (791)
T KOG1002|consen  620 TKIEALVEELYFLRE-RDRTAKSIVFSQFTSMLDLIEWRLGKAG-FSCVKLVGSMSPAARDATIKYFKNDI---------  688 (791)
T ss_pred             hHHHHHHHHHHHHHH-cccchhhhhHHHHHHHHHHHHHHhhccC-ceEEEeccCCChHHHHHHHHHhccCC---------
Confidence            566777777776556 7777899999998888889989999998 89999999999999999999999973         


Q ss_pred             cCCCCCCCCCCCCceeEEEE-ecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh---c-CCCCEEEEEeeCch
Q 029910           86 QSGDESETGKDEHKSHMIVV-TDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC---L-AADGSVINIVVGGE  159 (185)
Q Consensus        86 ~~~~~~~~~~~~~~~~iLV~-Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~---~-~~~g~~i~~v~~~e  159 (185)
                                   .+++++. -.+    .+-.+++..++.|+..|+-||+.--.|-.-|.   | -++-.++.|+-.+.
T Consensus       689 -------------~c~vfLvSLkA----GGVALNLteASqVFmmDPWWNpaVe~Qa~DRiHRIGQ~rPvkvvrf~iEns  750 (791)
T KOG1002|consen  689 -------------DCRVFLVSLKA----GGVALNLTEASQVFMMDPWWNPAVEWQAQDRIHRIGQYRPVKVVRFCIENS  750 (791)
T ss_pred             -------------CeEEEEEEecc----CceEeeechhceeEeecccccHHHHhhhhhhHHhhcCccceeEEEeehhcc
Confidence                         6776655 455    66778999999999999999886555533331   1 24557788886553

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=97.90  E-value=0.00015  Score=70.38  Aligned_cols=128  Identities=13%  Similarity=0.126  Sum_probs=98.1

Q ss_pred             eEecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccc
Q 029910            3 VSFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQK   82 (185)
Q Consensus         3 v~~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~   82 (185)
                      |+.+..++...+++.+......+.|++|-|.+....+.|+..|...| +....|+..-...| .+++.+  .|.      
T Consensus       546 iy~t~~~k~~ai~~ei~~~~~~grPvLigt~si~~se~ls~~L~~~g-i~h~vLNak~~~~E-a~iia~--AG~------  615 (970)
T PRK12899        546 FYMTEREKYHAIVAEIASIHRKGNPILIGTESVEVSEKLSRILRQNR-IEHTVLNAKNHAQE-AEIIAG--AGK------  615 (970)
T ss_pred             EecCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHcC-CcceecccchhhhH-HHHHHh--cCC------
Confidence            44555667777777766656778999999999999999999999998 89999988633222 233332  231      


Q ss_pred             ccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCc--------EEEEcCCCCCHHHHHHHHhhhc--CCCCEEE
Q 029910           83 VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISAR--------VLINYELPTKKETYIRRMTTCL--AADGSVI  152 (185)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~--------~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i  152 (185)
                                      ...|.|||.+    ++||.|+.--.        +||.-..|.|..--.|-.||+|  |.+|.+.
T Consensus       616 ----------------~g~VTIATNm----AGRGTDIkl~~~v~~~GGLhVIgTer~es~Rid~Ql~GRagRQGdpGss~  675 (970)
T PRK12899        616 ----------------LGAVTVATNM----AGRGTDIKLDEEAVAVGGLYVIGTSRHQSRRIDRQLRGRCARLGDPGAAK  675 (970)
T ss_pred             ----------------CCcEEEeecc----ccCCcccccCchHHhcCCcEEEeeccCchHHHHHHHhcccccCCCCCcee
Confidence                            4779999999    99999986432        7889899999988889899985  5569988


Q ss_pred             EEeeCchH
Q 029910          153 NIVVGGEV  160 (185)
Q Consensus       153 ~~v~~~e~  160 (185)
                      .|++-.|.
T Consensus       676 f~lSlEDd  683 (970)
T PRK12899        676 FFLSFEDR  683 (970)
T ss_pred             EEEEcchH
Confidence            88876543

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=97.77  E-value=0.0002  Score=69.92  Aligned_cols=127  Identities=16%  Similarity=0.123  Sum_probs=98.4

Q ss_pred             eEecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccc
Q 029910            3 VSFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQK   82 (185)
Q Consensus         3 v~~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~   82 (185)
                      ||-++.++...+++.+......++|+||=|.+.+..+.|++.|...| +...+|+......|- +++.+=  |.      
T Consensus       606 vy~t~~eK~~Aii~ei~~~~~~GrPVLVGT~SVe~SE~lS~~L~~~g-I~H~VLNAK~h~~EA-eIVA~A--G~------  675 (1112)
T PRK12901        606 VYKTKREKYNAVIEEITELSEAGRPVLVGTTSVEISELLSRMLKMRK-IPHNVLNAKLHQKEA-EIVAEA--GQ------  675 (1112)
T ss_pred             EecCHHHHHHHHHHHHHHHHHCCCCEEEEeCcHHHHHHHHHHHHHcC-CcHHHhhccchhhHH-HHHHhc--CC------
Confidence            45567777777888777656788999999999999999999999998 888888876443332 333332  21      


Q ss_pred             ccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCC--------CCcEEEEcCCCCCHHHHHHHHhhhcC--CCCEEE
Q 029910           83 VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAI--------SARVLINYELPTKKETYIRRMTTCLA--ADGSVI  152 (185)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~--------~v~~VI~~d~P~~~~~yiqR~GR~~~--~~g~~i  152 (185)
                                      ...|-|||.+    ++||.|+.        +==+||--..|.|..---|-.||+|+  .+|.+-
T Consensus       676 ----------------~GaVTIATNM----AGRGTDIkLg~~V~e~GGL~VIgTerheSrRID~QLrGRaGRQGDPGsS~  735 (1112)
T PRK12901        676 ----------------PGTVTIATNM----AGRGTDIKLSPEVKAAGGLAIIGTERHESRRVDRQLRGRAGRQGDPGSSQ  735 (1112)
T ss_pred             ----------------CCcEEEeccC----cCCCcCcccchhhHHcCCCEEEEccCCCcHHHHHHHhcccccCCCCCcce
Confidence                            4679999999    99999987        23478999999998888888899864  568888


Q ss_pred             EEeeCch
Q 029910          153 NIVVGGE  159 (185)
Q Consensus       153 ~~v~~~e  159 (185)
                      .|++-.|
T Consensus       736 f~lSLED  742 (1112)
T PRK12901        736 FYVSLED  742 (1112)
T ss_pred             EEEEccc
Confidence            8887644

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

Probab=97.75  E-value=0.00015  Score=70.84  Aligned_cols=117  Identities=20%  Similarity=0.223  Sum_probs=88.5

Q ss_pred             HHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCC---------------------------Cce------------
Q 029910           12 VELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLA---------------------------DIS------------   52 (185)
Q Consensus        12 ~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~---------------------------~~~------------   52 (185)
                      .++++.+.  ..+..|+|+||=+++.|+..+..+....                           ++.            
T Consensus       368 ~~iv~~l~--~~~~lP~I~F~FSr~~Ce~~a~~~~~ldl~~~~~~e~~i~~ii~~~i~~L~~ed~~lp~~~~~~~~~L~R  445 (1041)
T COG4581         368 PEIVNKLD--KDNLLPAIVFSFSRRGCEEAAQILSTLDLVLTEEKERAIREIIDHAIGDLAEEDRELPLQILEISALLLR  445 (1041)
T ss_pred             hHHHhhhh--hhcCCceEEEEEchhhHHHHHHHhcccccccCCcHHHHHHHHHHHHHhhcChhhhcCcccHHHHHHHHhh
Confidence            34455433  2456899999999999999888876310                           011            


Q ss_pred             -EEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCC-
Q 029910           53 -FSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYEL-  130 (185)
Q Consensus        53 -~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~-  130 (185)
                       .+++|++|=+..|..+-..|..|                       -++++++|+.    ++.|++.|.-.+|+ +.+ 
T Consensus       446 GiavHH~GlLP~~K~~vE~Lfq~G-----------------------LvkvvFaTeT----~s~GiNmPartvv~-~~l~  497 (1041)
T COG4581         446 GIAVHHAGLLPAIKELVEELFQEG-----------------------LVKVVFATET----FAIGINMPARTVVF-TSLS  497 (1041)
T ss_pred             hhhhhccccchHHHHHHHHHHhcc-----------------------ceeEEeehhh----hhhhcCCcccceee-eeeE
Confidence             34788999999999999999999                       7999999999    99999999765554 332 


Q ss_pred             --------CCCHHHHHHHHhhhcCCC----CEEEEEeeCc
Q 029910          131 --------PTKKETYIRRMTTCLAAD----GSVINIVVGG  158 (185)
Q Consensus       131 --------P~~~~~yiqR~GR~~~~~----g~~i~~v~~~  158 (185)
                              +-++..|.|..||+|+++    |.+|+...+.
T Consensus       498 K~dG~~~r~L~~gEy~QmsGRAGRRGlD~~G~vI~~~~~~  537 (1041)
T COG4581         498 KFDGNGHRWLSPGEYTQMSGRAGRRGLDVLGTVIVIEPPF  537 (1041)
T ss_pred             EecCCceeecChhHHHHhhhhhccccccccceEEEecCCC
Confidence                    337899999999886654    8888876553

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

Probab=97.72  E-value=0.00016  Score=67.69  Aligned_cols=129  Identities=12%  Similarity=0.182  Sum_probs=96.3

Q ss_pred             eeEecc---hHHHHHHHHHHHc--cCCCCCcEEEEcCChhhHHHHHHHHhcC----C----CceEEEEecCCCHHHHHHH
Q 029910            2 SVSFTF---QETLVELLHLVVA--GRRPGLPMIVCCSSRDELDAVCSAVSNL----A----DISFSSLHSDLAETERTLI   68 (185)
Q Consensus         2 ~v~~~~---~~~l~~ll~~l~~--~~~~~~~~IIF~~~~~~~~~l~~~L~~~----~----~~~~~~l~g~~~~~~R~~~   68 (185)
                      .++|++   .+-+-..+..++.  -..+..-+|||-.-.+..+...+.|...    |    .+-+..+|+.+|.+.+.++
T Consensus       445 di~Yt~~PEAdYldAai~tVlqIH~tqp~GDILVFltGQeEIEt~~e~l~~~~~~LGski~eliv~PiYaNLPselQakI  524 (902)
T KOG0923|consen  445 DIFYTKAPEADYLDAAIVTVLQIHLTQPLGDILVFLTGQEEIETVKENLKERCRRLGSKIRELIVLPIYANLPSELQAKI  524 (902)
T ss_pred             eeecccCCchhHHHHHHhhheeeEeccCCccEEEEeccHHHHHHHHHHHHHHHHHhccccceEEEeeccccCChHHHHhh
Confidence            445553   2333334444432  2455688999998888777666655432    2    3678999999999999999


Q ss_pred             HHHHhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCC------------------
Q 029910           69 LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYEL------------------  130 (185)
Q Consensus        69 l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~------------------  130 (185)
                      ++.--.|                       ..++++||++    ++-.+.++++.+||.-.+                  
T Consensus       525 FePtP~g-----------------------aRKVVLATNI----AETSlTIdgI~yViDpGf~K~nsynprtGmesL~v~  577 (902)
T KOG0923|consen  525 FEPTPPG-----------------------ARKVVLATNI----AETSLTIDGIKYVIDPGFVKQNSYNPRTGMESLLVT  577 (902)
T ss_pred             cCCCCCC-----------------------ceeEEEeecc----hhhceeecCeEEEecCccccccCcCCCcCceeEEEe
Confidence            8776666                       5889999999    999999999999994332                  


Q ss_pred             CCCHHHHHHHHhhhcCC-CCEEEEEeeC
Q 029910          131 PTKKETYIRRMTTCLAA-DGSVINIVVG  157 (185)
Q Consensus       131 P~~~~~yiqR~GR~~~~-~g~~i~~v~~  157 (185)
                      |-|..+-.||+||+|+. +|.|.-+++.
T Consensus       578 piSKAsA~QRaGRAGRtgPGKCfRLYt~  605 (902)
T KOG0923|consen  578 PISKASANQRAGRAGRTGPGKCFRLYTA  605 (902)
T ss_pred             eechhhhhhhccccCCCCCCceEEeech
Confidence            55778899999999875 5999999875

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

Probab=97.72  E-value=0.0006  Score=62.30  Aligned_cols=110  Identities=17%  Similarity=0.180  Sum_probs=84.2

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCcee
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSH  101 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (185)
                      ...+.|+|||..++-.....+-.|   +   --+++|..++.+|.++++.|+...                      .++
T Consensus       540 E~RgDKiIVFsDnvfALk~YAikl---~---KpfIYG~Tsq~ERm~ILqnFq~n~----------------------~vN  591 (776)
T KOG1123|consen  540 ERRGDKIIVFSDNVFALKEYAIKL---G---KPFIYGPTSQNERMKILQNFQTNP----------------------KVN  591 (776)
T ss_pred             HhcCCeEEEEeccHHHHHHHHHHc---C---CceEECCCchhHHHHHHHhcccCC----------------------ccc
Confidence            446799999988776655555544   3   246889999999999999999874                      788


Q ss_pred             EEEEecCCCCcccCcCCCCCCcEEEEcCCCC-CHHHHHHHHhhhc----CC----CCEEEEEeeCchHHHH
Q 029910          102 MIVVTDACLPLLSSGESAISARVLINYELPT-KKETYIRRMTTCL----AA----DGSVINIVVGGEVVTL  163 (185)
Q Consensus       102 iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~-~~~~yiqR~GR~~----~~----~g~~i~~v~~~e~~~~  163 (185)
                      -+...-+    ..-.+|+|.++++|+..-.. |-..=.||.||..    ++    ....+++|+.+..+++
T Consensus       592 TIFlSKV----gDtSiDLPEAnvLIQISSH~GSRRQEAQRLGRILRAKk~~de~fnafFYSLVS~DTqEM~  658 (776)
T KOG1123|consen  592 TIFLSKV----GDTSIDLPEANVLIQISSHGGSRRQEAQRLGRILRAKKRNDEEFNAFFYSLVSKDTQEMY  658 (776)
T ss_pred             eEEEeec----cCccccCCcccEEEEEcccccchHHHHHHHHHHHHHhhcCccccceeeeeeeecchHHHH
Confidence            8888888    88899999999999988764 5667789999942    11    1367778887765555

>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=97.71  E-value=0.0013  Score=59.42  Aligned_cols=128  Identities=13%  Similarity=0.127  Sum_probs=101.1

Q ss_pred             HHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCC
Q 029910           14 LLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESET   93 (185)
Q Consensus        14 ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~   93 (185)
                      +|-.+.. ......++||+++--.--.|.+.|+..+ +....+|-..+..+-..+-..|.+|                  
T Consensus       290 iLP~l~~-~~~~~~~LIfIPSYfDfVRlRN~lk~~~-~sF~~i~EYts~~~isRAR~~F~~G------------------  349 (442)
T PF06862_consen  290 ILPQLKR-DSKMSGTLIFIPSYFDFVRLRNYLKKEN-ISFVQISEYTSNSDISRARSQFFHG------------------  349 (442)
T ss_pred             HHHHhhh-ccCCCcEEEEecchhhhHHHHHHHHhcC-CeEEEecccCCHHHHHHHHHHHHcC------------------
Confidence            3444332 4456899999999999999999999776 8999999999999999999999999                  


Q ss_pred             CCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhcCC--------CCEEEEEeeCchHHHHHH
Q 029910           94 GKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAA--------DGSVINIVVGGEVVTLRS  165 (185)
Q Consensus        94 ~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~~~--------~g~~i~~v~~~e~~~~~~  165 (185)
                           ..++|+.|+-.  ..-+=..+-+++.||.|.+|..+.=|..-+.--..+        ...|..+++..|.-.++.
T Consensus       350 -----~~~iLL~TER~--HFfrRy~irGi~~viFY~~P~~p~fY~El~n~~~~~~~~~~~~~~~~~~~lysk~D~~~LEr  422 (442)
T PF06862_consen  350 -----RKPILLYTERF--HFFRRYRIRGIRHVIFYGPPENPQFYSELLNMLDESSGGEVDAADATVTVLYSKYDALRLER  422 (442)
T ss_pred             -----CceEEEEEhHH--hhhhhceecCCcEEEEECCCCChhHHHHHHhhhcccccccccccCceEEEEecHhHHHHHHH
Confidence                 79999999861  023455677899999999999999998887543222        357888888888876665


Q ss_pred             HHH
Q 029910          166 MEE  168 (185)
Q Consensus       166 l~~  168 (185)
                      +-.
T Consensus       423 IVG  425 (442)
T PF06862_consen  423 IVG  425 (442)
T ss_pred             HhC
Confidence            543

; GO: 0005634 nucleus

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=97.65  E-value=0.00035  Score=67.38  Aligned_cols=42  Identities=12%  Similarity=0.131  Sum_probs=32.8

Q ss_pred             cchHHHHHHHHHHHcc------CCCCCcEEEEcCChhhHHHHHHHHhc
Q 029910            6 TFQETLVELLHLVVAG------RRPGLPMIVCCSSRDELDAVCSAVSN   47 (185)
Q Consensus         6 ~~~~~l~~ll~~l~~~------~~~~~~~IIF~~~~~~~~~l~~~L~~   47 (185)
                      .|-+.|.++|+.+...      ..+..++||||+.+++|.+|.+.|..
T Consensus       270 PKw~~L~eiL~eI~~~~~~~~~~~~~~~iLI~~~d~~T~~qL~~~L~~  317 (814)
T TIGR00596       270 PKWEVLTDVLKEISHEMRMTNRLQGPGKVLIMCSDNRTCLQLRDYLTT  317 (814)
T ss_pred             CCHHHHHHHHHHHHhHHhhhcccCCCCcEEEEEcchHHHHHHHHHHHh
Confidence            3566778888776552      14557899999999999999999965

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

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

Probab=97.60  E-value=0.00031  Score=68.35  Aligned_cols=90  Identities=19%  Similarity=0.319  Sum_probs=72.3

Q ss_pred             hHHHHHHHHHHHccCCCCCcEEEEcCC---hhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccc
Q 029910            8 QETLVELLHLVVAGRRPGLPMIVCCSS---RDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVT   84 (185)
Q Consensus         8 ~~~l~~ll~~l~~~~~~~~~~IIF~~~---~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~   84 (185)
                      .++..++++. +     +.-.|||++.   ++-+++|++.|++.| +++..+|..     ..+.++.|..|         
T Consensus       324 ~e~~~elvk~-l-----G~GgLIfV~~d~G~e~aeel~e~Lr~~G-i~a~~~~a~-----~~~~le~F~~G---------  382 (1187)
T COG1110         324 LEKVVELVKK-L-----GDGGLIFVPIDYGREKAEELAEYLRSHG-INAELIHAE-----KEEALEDFEEG---------  382 (1187)
T ss_pred             HHHHHHHHHH-h-----CCCeEEEEEcHHhHHHHHHHHHHHHhcC-ceEEEeecc-----chhhhhhhccC---------
Confidence            3455566665 2     2578999999   899999999999999 899999973     37789999999         


Q ss_pred             ccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCC-CcEEEEcCCCC
Q 029910           85 EQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAIS-ARVLINYELPT  132 (185)
Q Consensus        85 ~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~-v~~VI~~d~P~  132 (185)
                                    ++++||....+---+.||+|+|. ++++|.|..|+
T Consensus       383 --------------eidvLVGvAsyYG~lVRGlDLP~rirYaIF~GvPk  417 (1187)
T COG1110         383 --------------EVDVLVGVASYYGVLVRGLDLPHRIRYAVFYGVPK  417 (1187)
T ss_pred             --------------ceeEEEEecccccceeecCCchhheeEEEEecCCc
Confidence                          69999886432222799999997 56899999994

>PF13307 Helicase_C_2: Helicase C-terminal domain; PDB: 4A15_A 2VSF_A 3CRV_A 3CRW_1 2VL7_A

Probab=97.57  E-value=0.001  Score=52.02  Aligned_cols=77  Identities=21%  Similarity=0.282  Sum_probs=56.7

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcCC---CceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCcee
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNLA---DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSH  101 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~~---~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (185)
                      +..++||+++.+..+.+...+...+   ++. ....   +..++.+.+++|+.+                       ...
T Consensus         9 ~g~~lv~f~Sy~~l~~~~~~~~~~~~~~~~~-v~~q---~~~~~~~~l~~~~~~-----------------------~~~   61 (167)
T PF13307_consen    9 PGGVLVFFPSYRRLEKVYERLKERLEEKGIP-VFVQ---GSKSRDELLEEFKRG-----------------------EGA   61 (167)
T ss_dssp             SSEEEEEESSHHHHHHHHTT-TSS-E-ETSC-EEES---TCCHHHHHHHHHCCS-----------------------SSE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhhcccccce-eeec---CcchHHHHHHHHHhc-----------------------cCe
Confidence            3899999999999999999998764   122 2222   367888999999998                       577


Q ss_pred             EEEEec--CCCCcccCcCCCCC--CcEEEEcCCCC
Q 029910          102 MIVVTD--ACLPLLSSGESAIS--ARVLINYELPT  132 (185)
Q Consensus       102 iLV~Td--~~~~~~~~G~d~~~--v~~VI~~d~P~  132 (185)
                      +|+++.  .    +++|+|+++  ++.||...+|-
T Consensus        62 il~~v~~g~----~~EGiD~~~~~~r~vii~glPf   92 (167)
T PF13307_consen   62 ILLAVAGGS----FSEGIDFPGDLLRAVIIVGLPF   92 (167)
T ss_dssp             EEEEETTSC----CGSSS--ECESEEEEEEES---
T ss_pred             EEEEEeccc----EEEeecCCCchhheeeecCCCC
Confidence            999997  7    899999997  66788888773

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=97.57  E-value=0.00053  Score=66.33  Aligned_cols=127  Identities=12%  Similarity=0.118  Sum_probs=95.9

Q ss_pred             eEecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccc
Q 029910            3 VSFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQK   82 (185)
Q Consensus         3 v~~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~   82 (185)
                      ||-++.++...+++.+......+.|+||-|.|.+..+.|++.|...+ +..-+|+..-. +.-.+++.  ..|.      
T Consensus       427 vy~t~~eK~~Ai~~ei~~~~~~GrPVLVGT~SVe~SE~ls~~L~~~g-i~h~VLNAk~~-~~EA~IIa--~AG~------  496 (913)
T PRK13103        427 VYLTAEEKYAAIITDIKECMALGRPVLVGTATIETSEHMSNLLKKEG-IEHKVLNAKYH-EKEAEIIA--QAGR------  496 (913)
T ss_pred             EEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCCHHHHHHHHHHHHHcC-CcHHHhccccc-hhHHHHHH--cCCC------
Confidence            56667777777887766656788999999999999999999999998 88888887633 22233433  2332      


Q ss_pred             ccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCC--------------------------------C-----cEE
Q 029910           83 VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAIS--------------------------------A-----RVL  125 (185)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~--------------------------------v-----~~V  125 (185)
                                      ...|-|||.+    ++||.|+.-                                |     =+|
T Consensus       497 ----------------~GaVTIATNM----AGRGTDIkLg~n~~~~~~~~~~~~~~~~~~~~~~~~~~~e~V~e~GGLhV  556 (913)
T PRK13103        497 ----------------PGALTIATNM----AGRGTDILLGGNWEVEVAALENPTPEQIAQIKADWQKRHQQVIEAGGLHV  556 (913)
T ss_pred             ----------------CCcEEEeccC----CCCCCCEecCCchHHHHHhhhhhhHHHHHHHHHHHHhHHHHHHHcCCCEE
Confidence                            5779999999    999999951                                1     268


Q ss_pred             EEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCch
Q 029910          126 INYELPTKKETYIRRMTTCL--AADGSVINIVVGGE  159 (185)
Q Consensus       126 I~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e  159 (185)
                      |--..|.|..-=-|=.||+|  |.+|.+-.|++-.|
T Consensus       557 IgTerheSrRID~QLrGRaGRQGDPGsS~f~lSlED  592 (913)
T PRK13103        557 IASERHESRRIDNQLRGRAGRQGDPGSSRFYLSLED  592 (913)
T ss_pred             EeeccCchHHHHHHhccccccCCCCCceEEEEEcCc
Confidence            88888888766667678875  45688888887644

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

Probab=97.43  E-value=0.00026  Score=66.52  Aligned_cols=107  Identities=13%  Similarity=0.226  Sum_probs=85.1

Q ss_pred             CCCcEEEEcCChhhHH----HHHHHHhcC---C--CceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCC
Q 029910           24 PGLPMIVCCSSRDELD----AVCSAVSNL---A--DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETG   94 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~----~l~~~L~~~---~--~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~   94 (185)
                      ...-++||...++..+    .+.+.|...   +  .+.++.+++.++..-+.++++.--.+                   
T Consensus       562 ~~GdilIfmtGqediE~t~~~i~~~l~ql~~~~~~~L~vlpiYSQLp~dlQ~kiFq~a~~~-------------------  622 (1042)
T KOG0924|consen  562 PPGDILIFMTGQEDIECTCDIIKEKLEQLDSAPTTDLAVLPIYSQLPADLQAKIFQKAEGG-------------------  622 (1042)
T ss_pred             CCCCEEEecCCCcchhHHHHHHHHHHHhhhcCCCCceEEEeehhhCchhhhhhhcccCCCC-------------------
Confidence            4477999998766555    444444332   2  48899999999999999887776666                   


Q ss_pred             CCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcC------------------CCCCHHHHHHHHhhhcCC-CCEEEEEe
Q 029910           95 KDEHKSHMIVVTDACLPLLSSGESAISARVLINYE------------------LPTKKETYIRRMTTCLAA-DGSVINIV  155 (185)
Q Consensus        95 ~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d------------------~P~~~~~yiqR~GR~~~~-~g~~i~~v  155 (185)
                          -.+++|+|.+    ++-.+.+|++.+||...                  .|-|-..--||.||+|+. +|.|+-++
T Consensus       623 ----vRK~IvATNI----AETSLTi~gI~yVID~Gy~K~kvyn~~~G~D~L~~~pIS~AnA~QRaGRAGRt~pG~cYRlY  694 (1042)
T KOG0924|consen  623 ----VRKCIVATNI----AETSLTIPGIRYVIDTGYCKLKVYNPRIGMDALQIVPISQANADQRAGRAGRTGPGTCYRLY  694 (1042)
T ss_pred             ----ceeEEEeccc----hhhceeecceEEEEecCceeeeecccccccceeEEEechhccchhhccccCCCCCcceeeeh
Confidence                6889999999    99999999999999654                  366778889999999774 59999988


Q ss_pred             eC
Q 029910          156 VG  157 (185)
Q Consensus       156 ~~  157 (185)
                      +.
T Consensus       695 Te  696 (1042)
T KOG0924|consen  695 TE  696 (1042)
T ss_pred             hh
Confidence            76

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

Probab=97.28  E-value=0.00061  Score=66.13  Aligned_cols=78  Identities=19%  Similarity=0.235  Sum_probs=64.7

Q ss_pred             EEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcC-CC
Q 029910           53 FSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYE-LP  131 (185)
Q Consensus        53 ~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d-~P  131 (185)
                      ..++|++|+..+|..+.--||.|                       ...+|++|..    ++-|++.|--.+|+--| +-
T Consensus       965 iG~HHaglNr~yR~~VEvLFR~g-----------------------~L~VlfaT~T----LsLGiNMPCrTVvF~gDsLQ 1017 (1330)
T KOG0949|consen  965 IGVHHAGLNRKYRSLVEVLFRQG-----------------------HLQVLFATET----LSLGINMPCRTVVFAGDSLQ 1017 (1330)
T ss_pred             ccccccccchHHHHHHHHHhhcC-----------------------ceEEEEEeee----hhcccCCCceeEEEeccccc
Confidence            57889999999999999999999                       7999999999    99999999766666555 44


Q ss_pred             CCHHHHHHHHhhhcCCC----CEEEEEeeC
Q 029910          132 TKKETYIRRMTTCLAAD----GSVINIVVG  157 (185)
Q Consensus       132 ~~~~~yiqR~GR~~~~~----g~~i~~v~~  157 (185)
                      -++-.|-|.+||+|+++    |-++.+-.+
T Consensus      1018 L~plny~QmaGRAGRRGFD~lGnV~FmgiP 1047 (1330)
T KOG0949|consen 1018 LDPLNYKQMAGRAGRRGFDTLGNVVFMGIP 1047 (1330)
T ss_pred             cCchhHHhhhccccccccccccceEEEeCc
Confidence            57899999999987765    666655443

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

Probab=97.19  E-value=0.0056  Score=60.05  Aligned_cols=93  Identities=14%  Similarity=0.230  Sum_probs=65.1

Q ss_pred             HHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCce-EEEEecCCCHHHHHHHHHHHhcccccccccccccCC
Q 029910           10 TLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADIS-FSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG   88 (185)
Q Consensus        10 ~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~-~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~   88 (185)
                      .+.+.+..+..  ....+++||+++.+..+.++..|....... ...+.-+++...|.+++++|+.+             
T Consensus       739 ~la~~i~~l~~--~~~g~~LVLFtSy~~l~~v~~~l~~~~~~~~~~ll~Qg~~~~~r~~l~~~F~~~-------------  803 (928)
T PRK08074        739 EVAAYIAKIAK--ATKGRMLVLFTSYEMLKKTYYNLKNEEELEGYVLLAQGVSSGSRARLTKQFQQF-------------  803 (928)
T ss_pred             HHHHHHHHHHH--hCCCCEEEEECCHHHHHHHHHHHhhcccccCceEEecCCCCCCHHHHHHHHHhc-------------
Confidence            44444444333  234689999999999999999997543111 22232244446788999999987             


Q ss_pred             CCCCCCCCCCceeEEEEecCCCCcccCcCCCCCC--cEEEEcCCC
Q 029910           89 DESETGKDEHKSHMIVVTDACLPLLSSGESAISA--RVLINYELP  131 (185)
Q Consensus        89 ~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v--~~VI~~d~P  131 (185)
                                ...||++|..    +.+|+|+|+-  ++||...+|
T Consensus       804 ----------~~~iLlG~~s----FwEGVD~pg~~l~~viI~kLP  834 (928)
T PRK08074        804 ----------DKAILLGTSS----FWEGIDIPGDELSCLVIVRLP  834 (928)
T ss_pred             ----------CCeEEEecCc----ccCccccCCCceEEEEEecCC
Confidence                      4679999999    9999999986  567765544

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

Probab=97.18  E-value=0.0046  Score=57.98  Aligned_cols=90  Identities=19%  Similarity=0.262  Sum_probs=64.0

Q ss_pred             HHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCC
Q 029910           11 LVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDE   90 (185)
Q Consensus        11 l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~   90 (185)
                      +...+..++. ..+ .+++||+++.+.++.+.+.+...........+|.   ..+...+++|+...              
T Consensus       467 ~~~~i~~~~~-~~~-~~~lvlF~Sy~~l~~~~~~~~~~~~~~~v~~q~~---~~~~~~l~~f~~~~--------------  527 (654)
T COG1199         467 LAAYLREILK-ASP-GGVLVLFPSYEYLKRVAERLKDERSTLPVLTQGE---DEREELLEKFKASG--------------  527 (654)
T ss_pred             HHHHHHHHHh-hcC-CCEEEEeccHHHHHHHHHHHhhcCccceeeecCC---CcHHHHHHHHHHhc--------------
Confidence            3444444444 333 4999999999999999999987651123444444   55558899999872              


Q ss_pred             CCCCCCCCceeEEEEecCCCCcccCcCCCCCC--cEEEEcCCC
Q 029910           91 SETGKDEHKSHMIVVTDACLPLLSSGESAISA--RVLINYELP  131 (185)
Q Consensus        91 ~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v--~~VI~~d~P  131 (185)
                              ..-++|+|.-    +++|+|+|+=  +.||...+|
T Consensus       528 --------~~~~lv~~gs----f~EGVD~~g~~l~~vvI~~lP  558 (654)
T COG1199         528 --------EGLILVGGGS----FWEGVDFPGDALRLVVIVGLP  558 (654)
T ss_pred             --------CCeEEEeecc----ccCcccCCCCCeeEEEEEecC
Confidence                    2279999999    9999999987  456666555

>COG4889 Predicted helicase [General function prediction only]

Probab=97.16  E-value=0.00049  Score=66.38  Aligned_cols=108  Identities=12%  Similarity=0.131  Sum_probs=76.5

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhc-----------C-CCceEEE--EecCCCHHHHHHHHHHHhcccccccccccccCCC
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSN-----------L-ADISFSS--LHSDLAETERTLILEEFRHTAMKWNQKVTEQSGD   89 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~-----------~-~~~~~~~--l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~   89 (185)
                      +.+++|-||.+.++...++..+..           . .++++.+  +.|.|+-.+|.+.++--...+             
T Consensus       459 p~~RAIaF~k~I~tSK~i~~sFe~Vve~Y~~Elk~d~~nL~iSi~HvDGtmNal~R~~l~~l~~~~~-------------  525 (1518)
T COG4889         459 PMQRAIAFAKDIKTSKQIAESFETVVEAYDEELKKDFKNLKISIDHVDGTMNALERLDLLELKNTFE-------------  525 (1518)
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhcCCCceEEeecccccccHHHHHHHHhccCCCC-------------
Confidence            346788899888887777765532           1 2244444  448899999944433211111             


Q ss_pred             CCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh-----cCCCCEEEEEe
Q 029910           90 ESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC-----LAADGSVINIV  155 (185)
Q Consensus        90 ~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~-----~~~~g~~i~~v  155 (185)
                             +..++||--.-.    +++|+|+|..+.||.||+-.+..+.+|-+||.     +...|..|.-+
T Consensus       526 -------~neckIlSNaRc----LSEGVDVPaLDsViFf~pr~smVDIVQaVGRVMRKa~gK~yGYIILPI  585 (1518)
T COG4889         526 -------PNECKILSNARC----LSEGVDVPALDSVIFFDPRSSMVDIVQAVGRVMRKAKGKKYGYIILPI  585 (1518)
T ss_pred             -------cchheeeccchh----hhcCCCccccceEEEecCchhHHHHHHHHHHHHHhCcCCccceEEEEe
Confidence                   115777766666    99999999999999999999999999999995     23347777765

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=97.16  E-value=0.007  Score=58.55  Aligned_cols=89  Identities=9%  Similarity=0.166  Sum_probs=68.7

Q ss_pred             eEecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCC-CHHHHHHHHHHHhcccccccc
Q 029910            3 VSFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDL-AETERTLILEEFRHTAMKWNQ   81 (185)
Q Consensus         3 v~~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~-~~~~R~~~l~~F~~~~~~~~~   81 (185)
                      |+-+..++...+++.+......++|++|-|.+....+.|+..|...| ++..+|+..- ..+.=.+++.+  .|.     
T Consensus       402 v~~t~~~K~~AI~~ei~~~~~~grPVLIgT~SIe~SE~ls~~L~~~g-i~h~vLNAk~~~~~~EA~IIA~--AG~-----  473 (870)
T CHL00122        402 IYKDELSKWRAIADECLQMHQTGRPILIGTTTIEKSELLSQLLKEYR-LPHQLLNAKPENVRRESEIVAQ--AGR-----  473 (870)
T ss_pred             EEeCHHHHHHHHHHHHHHHHhcCCCEEEeeCCHHHHHHHHHHHHHcC-CccceeeCCCccchhHHHHHHh--cCC-----
Confidence            44556667777777766656788999999999999999999999998 9999999862 22333345554  332     


Q ss_pred             cccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCC
Q 029910           82 KVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAI  120 (185)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~  120 (185)
                                       +..|-|||.+    ++||.|+.
T Consensus       474 -----------------~G~VTIATNM----AGRGTDI~  491 (870)
T CHL00122        474 -----------------KGSITIATNM----AGRGTDII  491 (870)
T ss_pred             -----------------CCcEEEeccc----cCCCcCee
Confidence                             5779999999    99998864

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

Probab=97.01  E-value=0.013  Score=56.76  Aligned_cols=88  Identities=15%  Similarity=0.204  Sum_probs=61.3

Q ss_pred             HHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCC
Q 029910           10 TLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGD   89 (185)
Q Consensus        10 ~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~   89 (185)
                      .+.+.+..+.   ..+++++|++++.+..+.++..|.... ..+ ..-|.-.  .|.+++++|+++              
T Consensus       635 ~~~~~i~~~~---~~~g~~LVLFtS~~~l~~v~~~l~~~~-~~~-l~Qg~~~--~~~~l~~~F~~~--------------  693 (820)
T PRK07246        635 EIAKRLEELK---QLQQPILVLFNSKKHLLAVSDLLDQWQ-VSH-LAQEKNG--TAYNIKKRFDRG--------------  693 (820)
T ss_pred             HHHHHHHHHH---hcCCCEEEEECcHHHHHHHHHHHhhcC-CcE-EEeCCCc--cHHHHHHHHHcC--------------
Confidence            3444444433   245799999999999999999997654 444 4444322  256689999987              


Q ss_pred             CCCCCCCCCceeEEEEecCCCCcccCcCCCCC--CcEEEEcCCC
Q 029910           90 ESETGKDEHKSHMIVVTDACLPLLSSGESAIS--ARVLINYELP  131 (185)
Q Consensus        90 ~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~--v~~VI~~d~P  131 (185)
                               ...||++|+.    +.+|+|+|+  ...||..-+|
T Consensus       694 ---------~~~vLlG~~s----FwEGVD~p~~~~~~viI~kLP  724 (820)
T PRK07246        694 ---------EQQILLGLGS----FWEGVDFVQADRMIEVITRLP  724 (820)
T ss_pred             ---------CCeEEEecch----hhCCCCCCCCCeEEEEEecCC
Confidence                     5779999999    999999974  4445544443

>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=96.92  E-value=0.03  Score=53.11  Aligned_cols=124  Identities=15%  Similarity=0.201  Sum_probs=91.5

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ   86 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~   86 (185)
                      |....++.++.++  .....++||-..-.....-+...|...| .....+||.....+|+.+++.|....          
T Consensus       730 Ki~~~l~~le~i~--~~skeK~viVSQwtsvLniv~~hi~~~g-~~y~si~Gqv~vK~Rq~iv~~FN~~k----------  796 (901)
T KOG4439|consen  730 KIAMVLEILETIL--TSSKEKVVIVSQWTSVLNIVRKHIQKGG-HIYTSITGQVLVKDRQEIVDEFNQEK----------  796 (901)
T ss_pred             HHHHHHHHHHHHh--hcccceeeehhHHHHHHHHHHHHHhhCC-eeeeeecCccchhHHHHHHHHHHhcc----------
Confidence            5566677777752  3444677777666666677788888888 79999999999999999999998752          


Q ss_pred             CCCCCCCCCCCCceeEE-EEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCC-CEEE-EEeeCc
Q 029910           87 SGDESETGKDEHKSHMI-VVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAAD-GSVI-NIVVGG  158 (185)
Q Consensus        87 ~~~~~~~~~~~~~~~iL-V~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~-g~~i-~~v~~~  158 (185)
                                 +..+++ +.=.+    .+-|+++...+++|..|+.||+.-=-|-+-|.  .|+. -+.| -|+..+
T Consensus       797 -----------~~~rVmLlSLtA----GGVGLNL~GaNHlilvDlHWNPaLEqQAcDRIYR~GQkK~V~IhR~~~~g  858 (901)
T KOG4439|consen  797 -----------GGARVMLLSLTA----GGVGLNLIGANHLILVDLHWNPALEQQACDRIYRMGQKKDVFIHRLMCKG  858 (901)
T ss_pred             -----------CCceEEEEEEcc----CcceeeecccceEEEEecccCHHHHHHHHHHHHHhcccCceEEEEEEecC
Confidence                       124444 44455    78899999999999999999998777777773  4444 3433 355554

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

Probab=96.86  E-value=0.011  Score=56.42  Aligned_cols=98  Identities=10%  Similarity=0.181  Sum_probs=65.0

Q ss_pred             cEEEEcCChhhHHHHHHHHhcC-CCceEEEEecCCCHHH--HHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEE
Q 029910           27 PMIVCCSSRDELDAVCSAVSNL-ADISFSSLHSDLAETE--RTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMI  103 (185)
Q Consensus        27 ~~IIF~~~~~~~~~l~~~L~~~-~~~~~~~l~g~~~~~~--R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iL  103 (185)
                      ..|+++-  ..++++.+.|... ++.+++.+.++.....  =...+.+|..|                       +.+||
T Consensus       484 ~~L~~~G--~GterieeeL~~~FP~~rv~r~d~Dtt~~k~~~~~~l~~~~~g-----------------------e~dIL  538 (730)
T COG1198         484 EHLRAVG--PGTERIEEELKRLFPGARIIRIDSDTTRRKGALEDLLDQFANG-----------------------EADIL  538 (730)
T ss_pred             CeeEEec--ccHHHHHHHHHHHCCCCcEEEEccccccchhhHHHHHHHHhCC-----------------------CCCee
Confidence            3455552  2344555555443 3467888888865544  45689999999                       69999


Q ss_pred             EEecCCCCcccCcCCCCCCcEEEE--cCC----C--CCH----HHHHHHHhhhcC--CCCEEEE
Q 029910          104 VVTDACLPLLSSGESAISARVLIN--YEL----P--TKK----ETYIRRMTTCLA--ADGSVIN  153 (185)
Q Consensus       104 V~Td~~~~~~~~G~d~~~v~~VI~--~d~----P--~~~----~~yiqR~GR~~~--~~g~~i~  153 (185)
                      |.|.+    ++.|.|+|++.+|.-  .|.    |  +..    .-+.|=+||+++  .+|.++.
T Consensus       539 iGTQm----iaKG~~fp~vtLVgvl~aD~~L~~~DfRA~Er~fqll~QvaGRAgR~~~~G~VvI  598 (730)
T COG1198         539 IGTQM----IAKGHDFPNVTLVGVLDADTGLGSPDFRASERTFQLLMQVAGRAGRAGKPGEVVI  598 (730)
T ss_pred             ecchh----hhcCCCcccceEEEEEechhhhcCCCcchHHHHHHHHHHHHhhhccCCCCCeEEE
Confidence            99999    999999999998654  332    2  233    445555688755  4454443

>KOG0386 consensus Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics; Transcription]

Probab=96.76  E-value=0.015  Score=56.85  Aligned_cols=109  Identities=15%  Similarity=0.126  Sum_probs=89.7

Q ss_pred             hHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccC
Q 029910            8 QETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQS   87 (185)
Q Consensus         8 ~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~   87 (185)
                      .+-+..+|-+|   ...+.+++.||.-..-.+-+-.+|.-.+ ++-.-+.|....++|-..++.|..+.+          
T Consensus       712 fELLDRiLPKL---katgHRVLlF~qMTrlmdimEdyL~~~~-~kYlRLDG~TK~~eRg~ll~~FN~Pds----------  777 (1157)
T KOG0386|consen  712 FELLDRILPKL---KATGHRVLLFSQMTRLMDILEDYLQIRE-YKYLRLDGQTKVEERGDLLEIFNAPDS----------  777 (1157)
T ss_pred             HHHHHhhhHHH---HhcCcchhhHHHHHHHHHHHHHHHhhhh-hheeeecCCcchhhHHHHHHHhcCCCC----------
Confidence            33444444443   3467999999988888888888887777 789999999999999999999998731          


Q ss_pred             CCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh
Q 029910           88 GDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC  144 (185)
Q Consensus        88 ~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~  144 (185)
                                .-...|..|.+    ...|++++-++.||.||.-|++-...|+--|+
T Consensus       778 ----------~yf~Fllstra----gglglNlQtadtviifdsdwnp~~d~qaqdra  820 (1157)
T KOG0386|consen  778 ----------PYFIFLLSTRA----GGLGLNLQTADTVIIFDSDWNPHQDLQAQDRA  820 (1157)
T ss_pred             ----------ceeeeeeeecc----cccccchhhcceEEEecCCCCchhHHHHHHHH
Confidence                      23557889999    99999999999999999999999888888775

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=96.59  E-value=0.011  Score=56.01  Aligned_cols=80  Identities=19%  Similarity=0.227  Sum_probs=67.4

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcC----CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCC
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEH   98 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (185)
                      ..+.+++|-++|+.-|.+.++.+...    + +++..+||+++..+|.+.++...+|                       
T Consensus       308 ~~g~q~lilaPT~~LA~Q~~~~l~~l~~~~~-i~v~ll~G~~~~~~r~~~~~~l~~g-----------------------  363 (681)
T PRK10917        308 EAGYQAALMAPTEILAEQHYENLKKLLEPLG-IRVALLTGSLKGKERREILEAIASG-----------------------  363 (681)
T ss_pred             HcCCeEEEEeccHHHHHHHHHHHHHHHhhcC-cEEEEEcCCCCHHHHHHHHHHHhCC-----------------------
Confidence            34679999999999999888777643    5 8999999999999999999999998                       


Q ss_pred             ceeEEEEecCCCCcccCcCCCCCCcEEEEcC
Q 029910           99 KSHMIVVTDACLPLLSSGESAISARVLINYE  129 (185)
Q Consensus        99 ~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d  129 (185)
                      ..+|+|+|..   ++...+.+.++.+||.=+
T Consensus       364 ~~~IvVgT~~---ll~~~v~~~~l~lvVIDE  391 (681)
T PRK10917        364 EADIVIGTHA---LIQDDVEFHNLGLVIIDE  391 (681)
T ss_pred             CCCEEEchHH---HhcccchhcccceEEEec
Confidence            6999999986   256677888999888533

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=96.55  E-value=0.0095  Score=57.85  Aligned_cols=90  Identities=14%  Similarity=0.163  Sum_probs=70.0

Q ss_pred             eEecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecC-CCHHHHHHHHHHHhcccccccc
Q 029910            3 VSFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSD-LAETERTLILEEFRHTAMKWNQ   81 (185)
Q Consensus         3 v~~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~-~~~~~R~~~l~~F~~~~~~~~~   81 (185)
                      |+-++.++...+++.+......+.|++|-|.+.+..+.|++.|...| +...+|+.. ...+.=.+++.+  .|.     
T Consensus       417 vy~t~~~K~~Ai~~ei~~~~~~GrPVLIgT~SVe~SE~ls~~L~~~g-i~h~vLNAk~~~~~~EA~IIa~--AG~-----  488 (939)
T PRK12902        417 VYKTEIAKWRAVANETAEMHKQGRPVLVGTTSVEKSELLSALLQEQG-IPHNLLNAKPENVEREAEIVAQ--AGR-----  488 (939)
T ss_pred             EEcCHHHHHHHHHHHHHHHHhCCCCEEEeeCCHHHHHHHHHHHHHcC-CchheeeCCCcchHhHHHHHHh--cCC-----
Confidence            45556677777777766656688999999999999999999999998 899999986 333344445554  332     


Q ss_pred             cccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCC
Q 029910           82 KVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAIS  121 (185)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~  121 (185)
                                       ...|-|||.+    ++||.|+.-
T Consensus       489 -----------------~GaVTIATNM----AGRGTDIkL  507 (939)
T PRK12902        489 -----------------KGAVTIATNM----AGRGTDIIL  507 (939)
T ss_pred             -----------------CCcEEEeccC----CCCCcCEee
Confidence                             5779999999    999998753

>KOG1015 consensus Transcription regulator XNP/ATRX, DEAD-box superfamily [Transcription]

Probab=96.32  E-value=0.02  Score=56.07  Aligned_cols=121  Identities=16%  Similarity=0.186  Sum_probs=90.7

Q ss_pred             HHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcC---C------------------CceEEEEecCCCHHHHHHHH
Q 029910           11 LVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL---A------------------DISFSSLHSDLAETERTLIL   69 (185)
Q Consensus        11 l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~---~------------------~~~~~~l~g~~~~~~R~~~l   69 (185)
                      |+++|..   -..-+.+++||..+-.+.+.+-..|+..   |                  +..-.-|.|.....+|.+..
T Consensus      1131 LleIL~m---ceeIGDKlLVFSQSL~SLdLIe~fLe~v~r~gk~~~d~~~~~~~eGkW~~GkDyyriDGst~s~~R~k~~ 1207 (1567)
T KOG1015|consen 1131 LLEILRM---CEEIGDKLLVFSQSLISLDLIEDFLELVSREGKEDKDKPLIYKGEGKWLRGKDYYRLDGSTTSQSRKKWA 1207 (1567)
T ss_pred             HHHHHHH---HHHhcceeEEeecccchhHHHHHHHHhhcccCccccccccccccccceecCCceEEecCcccHHHHHHHH
Confidence            4455543   1345689999999998888888777531   1                  14556778889999999999


Q ss_pred             HHHhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCC
Q 029910           70 EEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAA  147 (185)
Q Consensus        70 ~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~  147 (185)
                      ++|...+-+                   .-.-.||+|-+    .+-|+++-.++-||.||..|||..=+|-+=|.  .|+
T Consensus      1208 ~~FNdp~Nl-------------------RaRl~LISTRA----GsLGiNLvAANRVIIfDasWNPSyDtQSIFRvyRfGQ 1264 (1567)
T KOG1015|consen 1208 EEFNDPTNL-------------------RARLFLISTRA----GSLGINLVAANRVIIFDASWNPSYDTQSIFRVYRFGQ 1264 (1567)
T ss_pred             HHhcCcccc-------------------eeEEEEEeecc----CccccceeecceEEEEecccCCccchHHHHHHHhhcC
Confidence            999987411                   01337899999    99999999999999999999999999988774  444


Q ss_pred             C--CEEEEEeeC
Q 029910          148 D--GSVINIVVG  157 (185)
Q Consensus       148 ~--g~~i~~v~~  157 (185)
                      .  -+++-|+..
T Consensus      1265 tKPvyiYRfiAq 1276 (1567)
T KOG1015|consen 1265 TKPVYIYRFIAQ 1276 (1567)
T ss_pred             cCceeehhhhhc
Confidence            3  445555544

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=96.25  E-value=0.04  Score=52.57  Aligned_cols=93  Identities=16%  Similarity=0.239  Sum_probs=63.1

Q ss_pred             HHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCC
Q 029910            9 ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG   88 (185)
Q Consensus         9 ~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~   88 (185)
                      +.+.+.+..+..   ....++||+++.+..+.++..|..... .-+..+|.   ..|.+++++|++.-            
T Consensus       521 ~~~~~~i~~l~~---~~gg~LVlFtSy~~l~~v~~~l~~~~~-~~ll~Q~~---~~~~~ll~~f~~~~------------  581 (697)
T PRK11747        521 AEMAEFLPELLE---KHKGSLVLFASRRQMQKVADLLPRDLR-LMLLVQGD---QPRQRLLEKHKKRV------------  581 (697)
T ss_pred             HHHHHHHHHHHh---cCCCEEEEeCcHHHHHHHHHHHHHhcC-CcEEEeCC---chHHHHHHHHHHHh------------
Confidence            344555555444   334589999999999999999875421 33555664   35778888887520            


Q ss_pred             CCCCCCCCCCceeEEEEecCCCCcccCcCCCCC--CcEEEEcCCC
Q 029910           89 DESETGKDEHKSHMIVVTDACLPLLSSGESAIS--ARVLINYELP  131 (185)
Q Consensus        89 ~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~--v~~VI~~d~P  131 (185)
                             ..+...||++|..    +.+|+|+|+  .++||..-+|
T Consensus       582 -------~~~~~~VL~g~~s----f~EGVD~pGd~l~~vII~kLP  615 (697)
T PRK11747        582 -------DEGEGSVLFGLQS----FAEGLDLPGDYLTQVIITKIP  615 (697)
T ss_pred             -------ccCCCeEEEEecc----ccccccCCCCceEEEEEEcCC
Confidence                   0003569999999    999999997  5678766655

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

Probab=96.16  E-value=0.0027  Score=60.83  Aligned_cols=80  Identities=13%  Similarity=0.151  Sum_probs=61.3

Q ss_pred             ceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEc--
Q 029910           51 ISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINY--  128 (185)
Q Consensus        51 ~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~--  128 (185)
                      ..++.|++=++.+++.++++.--.|                       ..-++|+|.+    ++-.+.+|++.+||..  
T Consensus       605 LyvLPLYSLLs~~~Q~RVF~~~p~g-----------------------~RLcVVaTNV----AETSLTIPgIkYVVD~Gr  657 (1172)
T KOG0926|consen  605 LYVLPLYSLLSTEKQMRVFDEVPKG-----------------------ERLCVVATNV----AETSLTIPGIKYVVDCGR  657 (1172)
T ss_pred             eEEeehhhhcCHHHhhhhccCCCCC-----------------------ceEEEEeccc----hhcccccCCeeEEEeccc
Confidence            3466667777888887777766666                       4668999999    9999999999999954  


Q ss_pred             ------CCCC----------CHHHHHHHHhhhcCC-CCEEEEEeeC
Q 029910          129 ------ELPT----------KKETYIRRMTTCLAA-DGSVINIVVG  157 (185)
Q Consensus       129 ------d~P~----------~~~~yiqR~GR~~~~-~g~~i~~v~~  157 (185)
                            |--.          |..+--||+||+|+. +|.|+-++++
T Consensus       658 ~K~R~Yd~~TGV~~FeV~wiSkASadQRAGRAGRtgpGHcYRLYSS  703 (1172)
T KOG0926|consen  658 VKERLYDSKTGVSSFEVDWISKASADQRAGRAGRTGPGHCYRLYSS  703 (1172)
T ss_pred             hhhhccccccCceeEEEEeeeccccchhccccCCCCCCceeehhhh
Confidence                  4322          445567999999875 4999988865

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=96.06  E-value=0.03  Score=52.68  Aligned_cols=80  Identities=20%  Similarity=0.247  Sum_probs=66.9

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcC----CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCC
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEH   98 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (185)
                      ..+.+++|-++|+.-|.+.++.++..    | +++..+||+++..+|...++...+|                       
T Consensus       282 ~~g~qvlilaPT~~LA~Q~~~~~~~l~~~~g-i~v~lltg~~~~~~r~~~~~~i~~g-----------------------  337 (630)
T TIGR00643       282 EAGYQVALMAPTEILAEQHYNSLRNLLAPLG-IEVALLTGSLKGKRRKELLETIASG-----------------------  337 (630)
T ss_pred             HcCCcEEEECCHHHHHHHHHHHHHHHhcccC-cEEEEEecCCCHHHHHHHHHHHhCC-----------------------
Confidence            34679999999999999888777643    4 8999999999999999999999998                       


Q ss_pred             ceeEEEEecCCCCcccCcCCCCCCcEEEEcC
Q 029910           99 KSHMIVVTDACLPLLSSGESAISARVLINYE  129 (185)
Q Consensus        99 ~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d  129 (185)
                      ..+|+|+|..   ++...+++.++.+||.=+
T Consensus       338 ~~~IiVgT~~---ll~~~~~~~~l~lvVIDE  365 (630)
T TIGR00643       338 QIHLVVGTHA---LIQEKVEFKRLALVIIDE  365 (630)
T ss_pred             CCCEEEecHH---HHhccccccccceEEEec
Confidence            6899999987   356677888888877533

>PRK05580 primosome assembly protein PriA; Validated

Probab=96.03  E-value=0.051  Score=51.66  Aligned_cols=77  Identities=13%  Similarity=0.073  Sum_probs=63.8

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEE
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIV  104 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV  104 (185)
                      +.++||.+++++-+.++.+.|++.-+..+..+||+++..+|.+.+.+...+                       ..+|+|
T Consensus       190 g~~vLvLvPt~~L~~Q~~~~l~~~fg~~v~~~~s~~s~~~r~~~~~~~~~g-----------------------~~~IVV  246 (679)
T PRK05580        190 GKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRG-----------------------EAKVVI  246 (679)
T ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhCCCEEEEECCCCHHHHHHHHHHHHcC-----------------------CCCEEE
Confidence            579999999999999999999875227899999999999999999999988                       689999


Q ss_pred             EecCCCCcccCcCCCCCCcEEEEcC
Q 029910          105 VTDACLPLLSSGESAISARVLINYE  129 (185)
Q Consensus       105 ~Td~~~~~~~~G~d~~~v~~VI~~d  129 (185)
                      +|..    .. -..+.++.+||.-+
T Consensus       247 gTrs----al-~~p~~~l~liVvDE  266 (679)
T PRK05580        247 GARS----AL-FLPFKNLGLIIVDE  266 (679)
T ss_pred             eccH----Hh-cccccCCCEEEEEC
Confidence            9975    21 24567778877655

>TIGR00595 priA primosomal protein N'

Probab=95.77  E-value=0.066  Score=49.22  Aligned_cols=90  Identities=14%  Similarity=0.126  Sum_probs=68.8

Q ss_pred             HHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCC
Q 029910            9 ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG   88 (185)
Q Consensus         9 ~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~   88 (185)
                      +..+.++...+.   .++++||-+++..-+.++.+.|+..-+..+..+||+++..+|.+.+.+.++|             
T Consensus        12 ~v~l~~i~~~l~---~g~~vLvlvP~i~L~~Q~~~~l~~~f~~~v~vlhs~~~~~er~~~~~~~~~g-------------   75 (505)
T TIGR00595        12 EVYLQAIEKVLA---LGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNG-------------   75 (505)
T ss_pred             HHHHHHHHHHHH---cCCeEEEEeCcHHHHHHHHHHHHHHhCCcEEEEECCCCHHHHHHHHHHHHcC-------------
Confidence            344455554443   3578999999999999999999865336899999999999999999988888             


Q ss_pred             CCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcC
Q 029910           89 DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYE  129 (185)
Q Consensus        89 ~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d  129 (185)
                                ..+|+|+|..    +. -..+.+..+||.-+
T Consensus        76 ----------~~~IVVGTrs----al-f~p~~~l~lIIVDE  101 (505)
T TIGR00595        76 ----------EILVVIGTRS----AL-FLPFKNLGLIIVDE  101 (505)
T ss_pred             ----------CCCEEECChH----HH-cCcccCCCEEEEEC
Confidence                      6889999975    21 23467778877544

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).

>PF13871 Helicase_C_4: Helicase_C-like

Probab=95.77  E-value=0.076  Score=45.31  Aligned_cols=67  Identities=22%  Similarity=0.299  Sum_probs=48.1

Q ss_pred             ceeEEEEecCCCCcccCcCCCCC--------CcEEEEcCCCCCHHHHHHHHhhhcCCC---CEEEEEeeC---chHHHHH
Q 029910           99 KSHMIVVTDACLPLLSSGESAIS--------ARVLINYELPTKKETYIRRMTTCLAAD---GSVINIVVG---GEVVTLR  164 (185)
Q Consensus        99 ~~~iLV~Td~~~~~~~~G~d~~~--------v~~VI~~d~P~~~~~yiqR~GR~~~~~---g~~i~~v~~---~e~~~~~  164 (185)
                      ..+|+|.+++    .+-|+.++.        -++-|-.++||+.+..+|..||+.++.   ...+.++..   +|.....
T Consensus        61 ~k~v~iis~A----gstGiSlHAd~~~~nqr~Rv~i~le~pwsad~aiQ~~GR~hRsnQ~~~P~y~~l~t~~~gE~Rfas  136 (278)
T PF13871_consen   61 EKDVAIISDA----GSTGISLHADRRVKNQRRRVHITLELPWSADKAIQQFGRTHRSNQVSAPEYRFLVTDLPGERRFAS  136 (278)
T ss_pred             CceEEEEecc----cccccchhccccCCCCCceEEEEeeCCCCHHHHHHHhccccccccccCCEEEEeecCCHHHHHHHH
Confidence            6899999999    999987764        357788999999999999999974433   333444433   4555555


Q ss_pred             HHHHH
Q 029910          165 SMEES  169 (185)
Q Consensus       165 ~l~~~  169 (185)
                      .+.+.
T Consensus       137 ~va~r  141 (278)
T PF13871_consen  137 TVARR  141 (278)
T ss_pred             HHHHH
Confidence            54444

>PRK14873 primosome assembly protein PriA; Provisional

Probab=95.76  E-value=0.093  Score=49.87  Aligned_cols=93  Identities=12%  Similarity=0.131  Sum_probs=74.5

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCC-ceEEEEecCCCHHHHHHHHHHHhcccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLAD-ISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE   85 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~-~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~   85 (185)
                      |-+..+++++..+.   .++++||-++....+..+.+.|+..-+ ..+..+|++++..+|.+.+.+.++|          
T Consensus       173 KTevyl~~i~~~l~---~Gk~vLvLvPEi~lt~q~~~rl~~~f~~~~v~~lhS~l~~~~R~~~w~~~~~G----------  239 (665)
T PRK14873        173 WARRLAAAAAATLR---AGRGALVVVPDQRDVDRLEAALRALLGAGDVAVLSAGLGPADRYRRWLAVLRG----------  239 (665)
T ss_pred             HHHHHHHHHHHHHH---cCCeEEEEecchhhHHHHHHHHHHHcCCCcEEEECCCCCHHHHHHHHHHHhCC----------
Confidence            45566677776555   468999999999999999999987632 5799999999999999999999999          


Q ss_pred             cCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCC
Q 029910           86 QSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYEL  130 (185)
Q Consensus        86 ~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~  130 (185)
                                   ..+|+|.|-.     +--.=+++..+||..|-
T Consensus       240 -------------~~~IViGtRS-----AvFaP~~~LgLIIvdEE  266 (665)
T PRK14873        240 -------------QARVVVGTRS-----AVFAPVEDLGLVAIWDD  266 (665)
T ss_pred             -------------CCcEEEEcce-----eEEeccCCCCEEEEEcC
Confidence                         6999999975     34445567778887664

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

Probab=95.65  E-value=0.077  Score=48.72  Aligned_cols=108  Identities=14%  Similarity=0.214  Sum_probs=80.2

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcC--------CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCC
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNL--------ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGK   95 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~--------~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~   95 (185)
                      ...-++||....+..+..++.+...        |.+++..||    +.++..+   |+..               ++...
T Consensus       252 e~GDilvFLtgeeeIe~aC~~i~re~~~L~~~~g~l~v~PLy----P~~qq~i---Fep~---------------p~~~~  309 (699)
T KOG0925|consen  252 EPGDILVFLTGEEEIEDACRKISREVDNLGPQVGPLKVVPLY----PAQQQRI---FEPA---------------PEKRN  309 (699)
T ss_pred             CCCCEEEEecCHHHHHHHHHHHHHHHHhhccccCCceEEecC----chhhccc---cCCC---------------CcccC
Confidence            3578999999998888888777632        457888888    4444433   2222               13334


Q ss_pred             CCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCC------------------CCCHHHHHHHHhhhcC-CCCEEEEEee
Q 029910           96 DEHKSHMIVVTDACLPLLSSGESAISARVLINYEL------------------PTKKETYIRRMTTCLA-ADGSVINIVV  156 (185)
Q Consensus        96 ~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~------------------P~~~~~yiqR~GR~~~-~~g~~i~~v~  156 (185)
                      +....+++|+|.+    ++-.+.++++.+||.-.+                  |-|..+--||.||+++ ++|.|.-+++
T Consensus       310 ~~~~RkvVvstni----aetsltidgiv~VIDpGf~kqkVYNPRIRvesllv~PISkasA~qR~gragrt~pGkcfrLYt  385 (699)
T KOG0925|consen  310 GAYGRKVVVSTNI----AETSLTIDGIVFVIDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRTRPGKCFRLYT  385 (699)
T ss_pred             CCccceEEEEecc----hheeeeeccEEEEecCchhhhcccCcceeeeeeeeccchHhHHHHHhhhccCCCCCceEEeec
Confidence            5567889999999    999999999999996432                  6688889999999866 5699988886


Q ss_pred             C
Q 029910          157 G  157 (185)
Q Consensus       157 ~  157 (185)
                      .
T Consensus       386 e  386 (699)
T KOG0925|consen  386 E  386 (699)
T ss_pred             H
Confidence            5

>KOG0701 consensus dsRNA-specific nuclease Dicer and related ribonucleases [RNA processing and modification]

Probab=95.54  E-value=0.0072  Score=61.70  Aligned_cols=92  Identities=13%  Similarity=0.234  Sum_probs=75.0

Q ss_pred             CcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCC-----------CHHHHHHHHHHHhcccccccccccccCCCCCCCC
Q 029910           26 LPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDL-----------AETERTLILEEFRHTAMKWNQKVTEQSGDESETG   94 (185)
Q Consensus        26 ~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~-----------~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~   94 (185)
                      --.|+||+.+.++..+.+.++...-.....+.|.+           ..-.+.+++..|+..                   
T Consensus       293 l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~k~~~~~~~~~~~~vl~~~~~~-------------------  353 (1606)
T KOG0701|consen  293 LSGIIFVDQRYTAYVLLELLREIFSNDPLFVTGASGANLWKSFKNELELRQAEVLRRFHFH-------------------  353 (1606)
T ss_pred             hhheeecccchHHHHHHHHHHHhhccCcceeeccccCccchhhHHHHHhhhHHHHHHHhhh-------------------
Confidence            56799999999999888888765322333455543           123356688889888                   


Q ss_pred             CCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh
Q 029910           95 KDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC  144 (185)
Q Consensus        95 ~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~  144 (185)
                          ..++|++|.+    +.+|+|++.++.|+.++.|..-..|+|+.||+
T Consensus       354 ----~ln~L~~~~~----~~e~~d~~~~~~~~~~~~~~~~~~~vq~~~r~  395 (1606)
T KOG0701|consen  354 ----ELNLLIATSV----LEEGVDVPKCNLVVLFDAPTYYRSYVQKKGRA  395 (1606)
T ss_pred             ----hhhHHHHHHH----HHhhcchhhhhhheeccCcchHHHHHHhhccc
Confidence                6999999999    99999999999999999999999999999996

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=95.38  E-value=0.075  Score=52.29  Aligned_cols=79  Identities=18%  Similarity=0.142  Sum_probs=66.8

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcC----CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCc
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHK   99 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (185)
                      .+.+++|.++|+.-|.+.++.+...    + +++..++|..+..++.++++.++.|                       .
T Consensus       499 ~g~qvlvLvPT~~LA~Q~~~~f~~~~~~~~-i~v~~Lsg~~~~~e~~~~~~~l~~g-----------------------~  554 (926)
T TIGR00580       499 DGKQVAVLVPTTLLAQQHFETFKERFANFP-VTIELLSRFRSAKEQNEILKELASG-----------------------K  554 (926)
T ss_pred             hCCeEEEEeCcHHHHHHHHHHHHHHhccCC-cEEEEEeccccHHHHHHHHHHHHcC-----------------------C
Confidence            3589999999999999988877653    4 7889999999999999999999998                       6


Q ss_pred             eeEEEEecCCCCcccCcCCCCCCcEEEEcC
Q 029910          100 SHMIVVTDACLPLLSSGESAISARVLINYE  129 (185)
Q Consensus       100 ~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d  129 (185)
                      .+|+|+|..   ++.+.+.+.++.+||-=+
T Consensus       555 ~dIVIGTp~---ll~~~v~f~~L~llVIDE  581 (926)
T TIGR00580       555 IDILIGTHK---LLQKDVKFKDLGLLIIDE  581 (926)
T ss_pred             ceEEEchHH---HhhCCCCcccCCEEEeec
Confidence            999999985   367778889999887643

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.

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=95.33  E-value=0.18  Score=48.13  Aligned_cols=97  Identities=18%  Similarity=0.204  Sum_probs=65.0

Q ss_pred             HHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCC------ceEEEEecCCCHHHHHHHHHHHhcccccccccc
Q 029910           10 TLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLAD------ISFSSLHSDLAETERTLILEEFRHTAMKWNQKV   83 (185)
Q Consensus        10 ~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~------~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~   83 (185)
                      .+.+++..+.+ . .+..++||.++....+.+.+.+...+.      .+.+..-+. ...++.+++++|+..-       
T Consensus       509 ~l~~~i~~~~~-~-~pgg~lvfFpSy~~l~~v~~~~~~~~~~~~i~~~k~i~~E~~-~~~~~~~~l~~f~~~~-------  578 (705)
T TIGR00604       509 NLGELLVEFSK-I-IPDGIVVFFPSYSYLENIVSTWKEMGILENIEKKKLIFVETK-DAQETSDALERYKQAV-------  578 (705)
T ss_pred             HHHHHHHHHhh-c-CCCcEEEEccCHHHHHHHHHHHHhcCHHHHHhcCCCEEEeCC-CcchHHHHHHHHHHHH-------
Confidence            34445545444 2 347899999999999999988875431      122333222 2267889999997630       


Q ss_pred             cccCCCCCCCCCCCCceeEEEEe--cCCCCcccCcCCCCC--CcEEEEcCCCC
Q 029910           84 TEQSGDESETGKDEHKSHMIVVT--DACLPLLSSGESAIS--ARVLINYELPT  132 (185)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~iLV~T--d~~~~~~~~G~d~~~--v~~VI~~d~P~  132 (185)
                                  ..+...||+++  ..    +++|+|+++  .+.||...+|-
T Consensus       579 ------------~~~~gavL~av~gGk----~sEGIDf~~~~~r~ViivGlPf  615 (705)
T TIGR00604       579 ------------SEGRGAVLLSVAGGK----VSEGIDFCDDLGRAVIMVGIPY  615 (705)
T ss_pred             ------------hcCCceEEEEecCCc----ccCccccCCCCCcEEEEEccCC
Confidence                        00034589988  77    899999998  57888888775

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).

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

Probab=95.14  E-value=0.17  Score=47.83  Aligned_cols=93  Identities=10%  Similarity=-0.012  Sum_probs=63.7

Q ss_pred             HHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCC
Q 029910           11 LVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDE   90 (185)
Q Consensus        11 l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~   90 (185)
                      +.+.+..++. ... .+++|-+.+.+.++.+++.|...- -..+.+.|+.+  .+.+.+++|+..-              
T Consensus       458 ~~~~~~~~~~-~~~-G~~lvLfTS~~~~~~~~~~l~~~l-~~~~l~qg~~~--~~~~l~~~f~~~~--------------  518 (636)
T TIGR03117       458 VSLSTAAILR-KAQ-GGTLVLTTAFSHISAIGQLVELGI-PAEIVIQSEKN--RLASAEQQFLALY--------------  518 (636)
T ss_pred             HHHHHHHHHH-HcC-CCEEEEechHHHHHHHHHHHHhhc-CCCEEEeCCCc--cHHHHHHHHHHhh--------------
Confidence            4455555444 333 577777778899999999997643 13456666543  4567899999730              


Q ss_pred             CCCCCCCCceeEEEEecCCCCcccCcCCC----------CCCcEEEEcCCC
Q 029910           91 SETGKDEHKSHMIVVTDACLPLLSSGESA----------ISARVLINYELP  131 (185)
Q Consensus        91 ~~~~~~~~~~~iLV~Td~~~~~~~~G~d~----------~~v~~VI~~d~P  131 (185)
                           .++...||++|+-    +-+|+|+          ..++.||...+|
T Consensus       519 -----~~~~~~vL~gt~s----fweGvDv~~~~~~p~~G~~Ls~ViI~kLP  560 (636)
T TIGR03117       519 -----ANGIQPVLIAAGG----AWTGIDLTHKPVSPDKDNLLTDLIITCAP  560 (636)
T ss_pred             -----cCCCCcEEEeCCc----cccccccCCccCCCCCCCcccEEEEEeCC
Confidence                 0013679999999    9999999          347788877776

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.

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

Probab=95.07  E-value=0.14  Score=48.42  Aligned_cols=92  Identities=21%  Similarity=0.245  Sum_probs=75.6

Q ss_pred             hHHHHHHHHHHHccCCCCCcEEEEcCChhhHH----HHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccc
Q 029910            8 QETLVELLHLVVAGRRPGLPMIVCCSSRDELD----AVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKV   83 (185)
Q Consensus         8 ~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~----~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~   83 (185)
                      ..++..++..+.. -..+.|+..-++|---|+    .+.++|...| +.+..+.|.+...+|.+++++..+|        
T Consensus       295 GKTvVA~laml~a-i~~G~Q~ALMAPTEILA~QH~~~~~~~l~~~~-i~V~lLtG~~kgk~r~~~l~~l~~G--------  364 (677)
T COG1200         295 GKTVVALLAMLAA-IEAGYQAALMAPTEILAEQHYESLRKWLEPLG-IRVALLTGSLKGKARKEILEQLASG--------  364 (677)
T ss_pred             CHHHHHHHHHHHH-HHcCCeeEEeccHHHHHHHHHHHHHHHhhhcC-CeEEEeecccchhHHHHHHHHHhCC--------
Confidence            3466666666444 667899999999965554    5556666667 9999999999999999999999999        


Q ss_pred             cccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEE
Q 029910           84 TEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLIN  127 (185)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~  127 (185)
                                     .++++|.|-+   |+...+++.+.-+||-
T Consensus       365 ---------------~~~ivVGTHA---LiQd~V~F~~LgLVIi  390 (677)
T COG1200         365 ---------------EIDIVVGTHA---LIQDKVEFHNLGLVII  390 (677)
T ss_pred             ---------------CCCEEEEcch---hhhcceeecceeEEEE
Confidence                           6999999998   5788999999988876

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

Probab=94.87  E-value=0.17  Score=46.49  Aligned_cols=91  Identities=14%  Similarity=0.229  Sum_probs=63.7

Q ss_pred             HHHHHHHHHHc-cCCCCCcEEEEcCChhhHHHHHHHHhcCC----CceEEEEecCCCHHHHHHHHHHHhccccccccccc
Q 029910           10 TLVELLHLVVA-GRRPGLPMIVCCSSRDELDAVCSAVSNLA----DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVT   84 (185)
Q Consensus        10 ~l~~ll~~l~~-~~~~~~~~IIF~~~~~~~~~l~~~L~~~~----~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~   84 (185)
                      -++-+|+.+.. ......++||.++|++-|.++++.+...+    .+.+..+.|+++...+.+.+++   +         
T Consensus        83 f~lP~l~~l~~~~~~~~~~aLil~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~~---~---------  150 (513)
T COG0513          83 FLLPLLQKILKSVERKYVSALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKR---G---------  150 (513)
T ss_pred             HHHHHHHHHhcccccCCCceEEECCCHHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHhc---C---------
Confidence            34556666442 12222239999999999999998886542    3678999999998888755544   5         


Q ss_pred             ccCCCCCCCCCCCCceeEEEEecCCC-CcccCc-CCCCCCcEEEE
Q 029910           85 EQSGDESETGKDEHKSHMIVVTDACL-PLLSSG-ESAISARVLIN  127 (185)
Q Consensus        85 ~~~~~~~~~~~~~~~~~iLV~Td~~~-~~~~~G-~d~~~v~~VI~  127 (185)
                                     .+|+|+|+.++ -++.++ +++..+.++|.
T Consensus       151 ---------------~~ivVaTPGRllD~i~~~~l~l~~v~~lVl  180 (513)
T COG0513         151 ---------------VDIVVATPGRLLDLIKRGKLDLSGVETLVL  180 (513)
T ss_pred             ---------------CCEEEECccHHHHHHHcCCcchhhcCEEEe
Confidence                           78999998631 113455 88888988774

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=94.66  E-value=0.081  Score=51.15  Aligned_cols=91  Identities=13%  Similarity=0.141  Sum_probs=70.1

Q ss_pred             eEecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccc
Q 029910            3 VSFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQK   82 (185)
Q Consensus         3 v~~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~   82 (185)
                      |+.+..++....+..+......++|+||-+.+.+..+.+++.|...| +...+|...-.  +|..-+-.+.-.       
T Consensus       407 vy~t~~~K~~Aiv~~I~~~~~~gqPvLvgT~sie~SE~ls~~L~~~~-i~h~VLNAk~h--~~EA~Iia~AG~-------  476 (822)
T COG0653         407 VYKTEEEKFKAIVEDIKERHEKGQPVLVGTVSIEKSELLSKLLRKAG-IPHNVLNAKNH--AREAEIIAQAGQ-------  476 (822)
T ss_pred             cccchHHHHHHHHHHHHHHHhcCCCEEEcCcceecchhHHHHHHhcC-CCceeeccccH--HHHHHHHhhcCC-------
Confidence            56677888888888877767889999999999999999999999998 89888887644  333322222221       


Q ss_pred             ccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCc
Q 029910           83 VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISAR  123 (185)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~  123 (185)
                                      ...+-|+|.+    ++||.|+.--.
T Consensus       477 ----------------~gaVTiATNM----AGRGTDIkLg~  497 (822)
T COG0653         477 ----------------PGAVTIATNM----AGRGTDIKLGG  497 (822)
T ss_pred             ----------------CCcccccccc----ccCCcccccCC
Confidence                            3557899999    99999986433

>PRK10689 transcription-repair coupling factor; Provisional

Probab=94.28  E-value=0.22  Score=50.16  Aligned_cols=77  Identities=18%  Similarity=0.104  Sum_probs=64.5

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcC----CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCc
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHK   99 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (185)
                      .+.+++|-|+|+.-|.+.++.+...    + +.+..++|..+..++.++++..+.+                       .
T Consensus       648 ~g~qvlvLvPT~eLA~Q~~~~f~~~~~~~~-v~i~~l~g~~s~~e~~~il~~l~~g-----------------------~  703 (1147)
T PRK10689        648 NHKQVAVLVPTTLLAQQHYDNFRDRFANWP-VRIEMLSRFRSAKEQTQILAEAAEG-----------------------K  703 (1147)
T ss_pred             cCCeEEEEeCcHHHHHHHHHHHHHhhccCC-ceEEEEECCCCHHHHHHHHHHHHhC-----------------------C
Confidence            4689999999999999998887653    3 6888999999999999999999988                       6


Q ss_pred             eeEEEEecCCCCcccCcCCCCCCcEEEE
Q 029910          100 SHMIVVTDACLPLLSSGESAISARVLIN  127 (185)
Q Consensus       100 ~~iLV~Td~~~~~~~~G~d~~~v~~VI~  127 (185)
                      .+|+|+|..   ++...+.+.++.++|-
T Consensus       704 ~dIVVgTp~---lL~~~v~~~~L~lLVI  728 (1147)
T PRK10689        704 IDILIGTHK---LLQSDVKWKDLGLLIV  728 (1147)
T ss_pred             CCEEEECHH---HHhCCCCHhhCCEEEE
Confidence            899999974   2566677888888774

>smart00492 HELICc3 helicase superfamily c-terminal domain

Probab=94.24  E-value=0.25  Score=37.77  Aligned_cols=48  Identities=21%  Similarity=0.288  Sum_probs=37.0

Q ss_pred             CCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCC--cEEEEcCCCC
Q 029910           59 DLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISA--RVLINYELPT  132 (185)
Q Consensus        59 ~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v--~~VI~~d~P~  132 (185)
                      +.+..+..+++++|+...                      ...||+++.-    +++|+|+|+-  +.||...+|.
T Consensus        30 ~~~~~~~~~~l~~f~~~~----------------------~~~iL~~~~~----~~EGiD~~g~~~r~vii~glPf   79 (141)
T smart00492       30 GEDGKETGKLLEKYVEAC----------------------ENAILLATAR----FSEGVDFPGDYLRAVIIDGLPF   79 (141)
T ss_pred             CCChhHHHHHHHHHHHcC----------------------CCEEEEEccc----eecceecCCCCeeEEEEEecCC
Confidence            344556788999999862                      2369999988    9999999985  5788777763

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

Probab=93.87  E-value=0.29  Score=46.99  Aligned_cols=92  Identities=17%  Similarity=0.146  Sum_probs=73.9

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ   86 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~   86 (185)
                      |-|..++++...++   .++++||-++.......+...|..+-+.++..+|+++++.+|.+...+.++|           
T Consensus       230 KTEvYl~~i~~~L~---~GkqvLvLVPEI~Ltpq~~~rf~~rFg~~v~vlHS~Ls~~er~~~W~~~~~G-----------  295 (730)
T COG1198         230 KTEVYLEAIAKVLA---QGKQVLVLVPEIALTPQLLARFKARFGAKVAVLHSGLSPGERYRVWRRARRG-----------  295 (730)
T ss_pred             HHHHHHHHHHHHHH---cCCEEEEEeccccchHHHHHHHHHHhCCChhhhcccCChHHHHHHHHHHhcC-----------
Confidence            45667777877665   5699999999999888888888876448999999999999999999999999           


Q ss_pred             CCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcC
Q 029910           87 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYE  129 (185)
Q Consensus        87 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d  129 (185)
                                  ..+|+|.|--     +--.=+++.-+||-.+
T Consensus       296 ------------~~~vVIGtRS-----AlF~Pf~~LGLIIvDE  321 (730)
T COG1198         296 ------------EARVVIGTRS-----ALFLPFKNLGLIIVDE  321 (730)
T ss_pred             ------------CceEEEEech-----hhcCchhhccEEEEec
Confidence                        6999999974     3334456666666543

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=93.74  E-value=0.26  Score=48.97  Aligned_cols=107  Identities=11%  Similarity=0.088  Sum_probs=66.3

Q ss_pred             EEEcCChhhHHHHHHHHhcCC-----CceEEEEecCCCHHHHHHHHHHH---h---cccccccccccccCCCCCCCCCCC
Q 029910           29 IVCCSSRDELDAVCSAVSNLA-----DISFSSLHSDLAETERTLILEEF---R---HTAMKWNQKVTEQSGDESETGKDE   97 (185)
Q Consensus        29 IIF~~~~~~~~~l~~~L~~~~-----~~~~~~l~g~~~~~~R~~~l~~F---~---~~~~~~~~~~~~~~~~~~~~~~~~   97 (185)
                      +|=.++.+.+-.++..|....     .+...++|+..+...|..+.++.   -   .++..|.-.+..+....   +.-.
T Consensus       760 liR~anI~p~V~~A~~L~~~~~~~~~~i~~~~yHSr~~l~~Rs~~E~~Ld~~L~R~~~~~~~~~~~i~~~l~~---~~~~  836 (1110)
T TIGR02562       760 LIRVANIDPLIRLAQFLYALLAEEKYQIHLCCYHAQDPLLLRSYIERRLDQLLTRHKPEQLFQDDEIIDLMQN---SPAL  836 (1110)
T ss_pred             EEEEcCchHHHHHHHHHHhhccccCCceeEEEecccChHHHHHHHHHHHHHHhcccChhhhhchHHHHHHHhc---cccc
Confidence            455567777777777775441     25688899999888888766553   1   11111211111111100   0011


Q ss_pred             CceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc
Q 029910           98 HKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL  145 (185)
Q Consensus        98 ~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~  145 (185)
                      +...|+|+|.+    .+-|+|+ +.+++|  .-|.+....+||+||+.
T Consensus       837 ~~~~i~v~Tqv----~E~g~D~-dfd~~~--~~~~~~~sliQ~aGR~~  877 (1110)
T TIGR02562       837 NHLFIVLATPV----EEVGRDH-DYDWAI--ADPSSMRSIIQLAGRVN  877 (1110)
T ss_pred             CCCeEEEEeee----EEEEecc-cCCeee--eccCcHHHHHHHhhccc
Confidence            24679999999    9999995 355554  34778999999999973

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.

>KOG2340 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.45  E-value=0.54  Score=43.70  Aligned_cols=116  Identities=11%  Similarity=0.114  Sum_probs=85.8

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEE
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIV  104 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV  104 (185)
                      ..-++||.++--.-..+.+.++..+ +....+|--.+...-..+-+-|.+|                       ...+|+
T Consensus       552 ~s~~LiyIPSYfDFVRvRNy~K~e~-i~F~~i~EYssk~~vsRAR~lF~qg-----------------------r~~vlL  607 (698)
T KOG2340|consen  552 ESGILIYIPSYFDFVRVRNYMKKEE-ISFVMINEYSSKSKVSRARELFFQG-----------------------RKSVLL  607 (698)
T ss_pred             cCceEEEecchhhHHHHHHHhhhhh-cchHHHhhhhhHhhhhHHHHHHHhc-----------------------CceEEE
Confidence            4678999999988889999998887 7888888666666666666779998                       688999


Q ss_pred             EecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHH---HHHhhhcCCC------CEEEEEeeCchHHHHHHH
Q 029910          105 VTDACLPLLSSGESAISARVLINYELPTKKETYI---RRMTTCLAAD------GSVINIVVGGEVVTLRSM  166 (185)
Q Consensus       105 ~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yi---qR~GR~~~~~------g~~i~~v~~~e~~~~~~l  166 (185)
                      -|+-+ - .-|-.++.+|.-||.|.+|.+|.=|.   ..++|+..++      -.|..+++..|.-.+..+
T Consensus       608 yTER~-h-ffrR~~ikGVk~vVfYqpP~~P~FYsEiinm~~k~~~~gn~d~d~~t~~ilytKyD~i~Le~i  676 (698)
T KOG2340|consen  608 YTERA-H-FFRRYHIKGVKNVVFYQPPNNPHFYSEIINMSDKTTSQGNTDLDIFTVRILYTKYDRIRLENI  676 (698)
T ss_pred             Eehhh-h-hhhhheecceeeEEEecCCCCcHHHHHHHhhhhhhhccCCccccceEEEEEeechhhHHHHHh
Confidence            99860 0 24677999999999999999987664   4557752222      355566677776555444

>cd00268 DEADc DEAD-box helicases

Probab=93.44  E-value=0.66  Score=36.40  Aligned_cols=91  Identities=14%  Similarity=0.197  Sum_probs=59.4

Q ss_pred             HHHHHHHHHccC--CCCCcEEEEcCChhhHHHHHHHHhcC---CCceEEEEecCCCHHHHHHHHHHHhcccccccccccc
Q 029910           11 LVELLHLVVAGR--RPGLPMIVCCSSRDELDAVCSAVSNL---ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE   85 (185)
Q Consensus        11 l~~ll~~l~~~~--~~~~~~IIF~~~~~~~~~l~~~L~~~---~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~   85 (185)
                      +..++..+.. .  ..+.++||.|+++.-+.+..+.++..   .++.+..++|+.+..++...++    .          
T Consensus        54 ~~~~l~~~~~-~~~~~~~~viii~p~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~----------  118 (203)
T cd00268          54 LIPILEKLDP-SPKKDGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLK----R----------  118 (203)
T ss_pred             HHHHHHHHHh-hcccCCceEEEEcCCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhc----C----------
Confidence            4445565444 3  45678999999999988877766543   2378899999988776654332    2          


Q ss_pred             cCCCCCCCCCCCCceeEEEEecCCCC--cccCcCCCCCCcEEEEcC
Q 029910           86 QSGDESETGKDEHKSHMIVVTDACLP--LLSSGESAISARVLINYE  129 (185)
Q Consensus        86 ~~~~~~~~~~~~~~~~iLV~Td~~~~--~~~~G~d~~~v~~VI~~d  129 (185)
                                   ..+++|+|.-.+-  +...-.++++++++|.=+
T Consensus       119 -------------~~~iiv~T~~~l~~~l~~~~~~~~~l~~lIvDE  151 (203)
T cd00268         119 -------------GPHIVVATPGRLLDLLERGKLDLSKVKYLVLDE  151 (203)
T ss_pred             -------------CCCEEEEChHHHHHHHHcCCCChhhCCEEEEeC
Confidence                         4789999952100  012335677888877543

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.

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

Probab=93.43  E-value=0.33  Score=48.02  Aligned_cols=72  Identities=17%  Similarity=0.252  Sum_probs=55.6

Q ss_pred             HHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCC----CceEEE-EecCCCHHHHHHHHHHHhcccccccccccccC
Q 029910           13 ELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLA----DISFSS-LHSDLAETERTLILEEFRHTAMKWNQKVTEQS   87 (185)
Q Consensus        13 ~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~----~~~~~~-l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~   87 (185)
                      -++-.+.. ...++++++-++|.--+.+.++.|...+    ...+.+ +|+.|+.+++.+++++|.+|            
T Consensus       114 g~~~sl~~-a~kgkr~yii~PT~~Lv~Q~~~kl~~~~e~~~~~~~~~~yh~~l~~~ekee~le~i~~g------------  180 (1187)
T COG1110         114 GLLMSLYL-AKKGKRVYIIVPTTTLVRQVYERLKKFAEDAGSLDVLVVYHSALPTKEKEEALERIESG------------  180 (1187)
T ss_pred             HHHHHHHH-HhcCCeEEEEecCHHHHHHHHHHHHHHHhhcCCcceeeeeccccchHHHHHHHHHHhcC------------
Confidence            34444343 3455899999999998888888886642    122222 99999999999999999999            


Q ss_pred             CCCCCCCCCCCceeEEEEecC
Q 029910           88 GDESETGKDEHKSHMIVVTDA  108 (185)
Q Consensus        88 ~~~~~~~~~~~~~~iLV~Td~  108 (185)
                                 ..+|||+|..
T Consensus       181 -----------dfdIlitTs~  190 (1187)
T COG1110         181 -----------DFDILITTSQ  190 (1187)
T ss_pred             -----------CccEEEEeHH
Confidence                       7999999987

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

Probab=93.40  E-value=0.93  Score=44.00  Aligned_cols=87  Identities=14%  Similarity=0.184  Sum_probs=65.6

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEE
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMI  103 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iL  103 (185)
                      .++++-|||+|...++.+++.....+ .++..++++.+..+    ++.|.                         ..+++
T Consensus       281 ~gknIcvfsSt~~~~~~v~~~~~~~~-~~Vl~l~s~~~~~d----v~~W~-------------------------~~~Vv  330 (824)
T PF02399_consen  281 AGKNICVFSSTVSFAEIVARFCARFT-KKVLVLNSTDKLED----VESWK-------------------------KYDVV  330 (824)
T ss_pred             CCCcEEEEeChHHHHHHHHHHHHhcC-CeEEEEcCCCCccc----ccccc-------------------------ceeEE
Confidence            45888899999999999999998887 68999988766662    23343                         48899


Q ss_pred             EEecCCCCcccCcCCCCCC--cEEEEc--CCC--CCHHHHHHHHhhh
Q 029910          104 VVTDACLPLLSSGESAISA--RVLINY--ELP--TKKETYIRRMTTC  144 (185)
Q Consensus       104 V~Td~~~~~~~~G~d~~~v--~~VI~~--d~P--~~~~~yiqR~GR~  144 (185)
                      +-|++    +.-|+++.+.  +-|.-|  ...  .+..+..|.+||.
T Consensus       331 iYT~~----itvG~Sf~~~HF~~~f~yvk~~~~gpd~~s~~Q~lgRv  373 (824)
T PF02399_consen  331 IYTPV----ITVGLSFEEKHFDSMFAYVKPMSYGPDMVSVYQMLGRV  373 (824)
T ss_pred             EEece----EEEEeccchhhceEEEEEecCCCCCCcHHHHHHHHHHH
Confidence            99999    9999988754  335545  222  3456788999994

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

>PRK14701 reverse gyrase; Provisional

Probab=93.27  E-value=0.42  Score=49.81  Aligned_cols=63  Identities=16%  Similarity=0.263  Sum_probs=54.3

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcCC-----CceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCC
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNLA-----DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEH   98 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~~-----~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (185)
                      ++.++||.++|+.-+.++...|...+     ++.+..+||+++..++.+.++.+++|                       
T Consensus       121 ~g~~aLVl~PTreLa~Qi~~~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g-----------------------  177 (1638)
T PRK14701        121 KGKKCYIILPTTLLVKQTVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENG-----------------------  177 (1638)
T ss_pred             cCCeEEEEECHHHHHHHHHHHHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcC-----------------------
Confidence            45799999999999999998887631     26789999999999999999999988                       


Q ss_pred             ceeEEEEecCC
Q 029910           99 KSHMIVVTDAC  109 (185)
Q Consensus        99 ~~~iLV~Td~~  109 (185)
                      ..+|||+|+..
T Consensus       178 ~~dILV~TPgr  188 (1638)
T PRK14701        178 DFDILVTTAQF  188 (1638)
T ss_pred             CCCEEEECCch
Confidence            68899999874

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=92.85  E-value=0.4  Score=43.07  Aligned_cols=90  Identities=23%  Similarity=0.285  Sum_probs=60.7

Q ss_pred             HHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcC----CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccC
Q 029910           12 VELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQS   87 (185)
Q Consensus        12 ~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~   87 (185)
                      +-++..+.. .....++||.|+|++-|.++++.++..    .++.+..++|+.+...+.+.++   .             
T Consensus        60 lpil~~l~~-~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~---~-------------  122 (460)
T PRK11776         60 LGLLQKLDV-KRFRVQALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLE---H-------------  122 (460)
T ss_pred             HHHHHHhhh-ccCCceEEEEeCCHHHHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhc---C-------------
Confidence            345555332 333457999999999999988877643    2378999999998877654443   3             


Q ss_pred             CCCCCCCCCCCceeEEEEecCCCC-ccc-CcCCCCCCcEEEEcC
Q 029910           88 GDESETGKDEHKSHMIVVTDACLP-LLS-SGESAISARVLINYE  129 (185)
Q Consensus        88 ~~~~~~~~~~~~~~iLV~Td~~~~-~~~-~G~d~~~v~~VI~~d  129 (185)
                                 ..+|+|+|+-++- ++. ..+++.++++||.=+
T Consensus       123 -----------~~~IvV~Tp~rl~~~l~~~~~~l~~l~~lViDE  155 (460)
T PRK11776        123 -----------GAHIIVGTPGRILDHLRKGTLDLDALNTLVLDE  155 (460)
T ss_pred             -----------CCCEEEEChHHHHHHHHcCCccHHHCCEEEEEC
Confidence                       3789999964211 022 456788888887533

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=92.22  E-value=0.67  Score=43.82  Aligned_cols=88  Identities=17%  Similarity=0.157  Sum_probs=57.9

Q ss_pred             HHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcC----CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccC
Q 029910           12 VELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQS   87 (185)
Q Consensus        12 ~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~   87 (185)
                      +.+++.+.. .....++||.|+|++-|.++++.+...    .++.+..+||+.+...+...+   +.+            
T Consensus        62 lpll~~l~~-~~~~~~~LIL~PTreLa~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l---~~~------------  125 (629)
T PRK11634         62 LPLLHNLDP-ELKAPQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRAL---RQG------------  125 (629)
T ss_pred             HHHHHHhhh-ccCCCeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHh---cCC------------
Confidence            334555333 334568999999999999988776543    237899999998876665433   343            


Q ss_pred             CCCCCCCCCCCceeEEEEecCCCC-ccc-CcCCCCCCcEEEE
Q 029910           88 GDESETGKDEHKSHMIVVTDACLP-LLS-SGESAISARVLIN  127 (185)
Q Consensus        88 ~~~~~~~~~~~~~~iLV~Td~~~~-~~~-~G~d~~~v~~VI~  127 (185)
                                  .+|+|+|+.++- ++. ..+++.++.+||.
T Consensus       126 ------------~~IVVgTPgrl~d~l~r~~l~l~~l~~lVl  155 (629)
T PRK11634        126 ------------PQIVVGTPGRLLDHLKRGTLDLSKLSGLVL  155 (629)
T ss_pred             ------------CCEEEECHHHHHHHHHcCCcchhhceEEEe
Confidence                        679999953210 022 3467788887774

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=91.23  E-value=10  Score=33.71  Aligned_cols=78  Identities=13%  Similarity=0.191  Sum_probs=54.2

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcC---CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCcee
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNL---ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSH  101 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~---~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (185)
                      ..++||.++|++-+.++.+.+...   .++.+..++|+.+...+...+   ..                        ..+
T Consensus        73 ~~~~lil~Pt~eLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l---~~------------------------~~~  125 (434)
T PRK11192         73 PPRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVF---SE------------------------NQD  125 (434)
T ss_pred             CceEEEECCcHHHHHHHHHHHHHHHccCCcEEEEEECCCCHHHHHHHh---cC------------------------CCC
Confidence            468999999999988877665432   238899999999887765443   22                        378


Q ss_pred             EEEEecCCC--CcccCcCCCCCCcEEEEcC
Q 029910          102 MIVVTDACL--PLLSSGESAISARVLINYE  129 (185)
Q Consensus       102 iLV~Td~~~--~~~~~G~d~~~v~~VI~~d  129 (185)
                      |+|+|+-++  -+....+++.++++||.=+
T Consensus       126 IlV~Tp~rl~~~~~~~~~~~~~v~~lViDE  155 (434)
T PRK11192        126 IVVATPGRLLQYIKEENFDCRAVETLILDE  155 (434)
T ss_pred             EEEEChHHHHHHHHcCCcCcccCCEEEEEC
Confidence            999997310  0023566788888887533

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=91.02  E-value=0.85  Score=41.28  Aligned_cols=72  Identities=14%  Similarity=0.163  Sum_probs=58.5

Q ss_pred             HHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCC
Q 029910            9 ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG   88 (185)
Q Consensus         9 ~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~   88 (185)
                      .++.-++-.+..    ...+||.+++++-+......|...| +.+..++++.+..++..++.+...+             
T Consensus        39 KTl~y~lp~l~~----~~~~lVi~P~~~L~~dq~~~l~~~g-i~~~~l~~~~~~~~~~~i~~~~~~~-------------  100 (470)
T TIGR00614        39 KSLCYQLPALCS----DGITLVISPLISLMEDQVLQLKASG-IPATFLNSSQSKEQQKNVLTDLKDG-------------  100 (470)
T ss_pred             HhHHHHHHHHHc----CCcEEEEecHHHHHHHHHHHHHHcC-CcEEEEeCCCCHHHHHHHHHHHhcC-------------
Confidence            344444544332    3689999999999998889998888 8999999999999999999999887             


Q ss_pred             CCCCCCCCCCceeEEEEecC
Q 029910           89 DESETGKDEHKSHMIVVTDA  108 (185)
Q Consensus        89 ~~~~~~~~~~~~~iLV~Td~  108 (185)
                                ..+++++|+-
T Consensus       101 ----------~~~il~~TPe  110 (470)
T TIGR00614       101 ----------KIKLLYVTPE  110 (470)
T ss_pred             ----------CCCEEEECHH
Confidence                      6888988875

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

>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [General function prediction only]

Probab=90.05  E-value=1.3  Score=43.10  Aligned_cols=113  Identities=15%  Similarity=0.160  Sum_probs=85.4

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcCC-----------------CceEEEEecCCCHHHHHHHHHHHhccccccccccc
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNLA-----------------DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVT   84 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~~-----------------~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~   84 (185)
                      ..-+.++|||..+-.+.+.+-+.|....                 +..-.-+.|..+..+|.+.+.+|.....       
T Consensus       716 ~~~g~kil~fSq~l~~Ld~ieeil~krq~pc~~gdnG~~aqkW~~n~sy~rldG~t~a~~rekLinqfN~e~~-------  788 (1387)
T KOG1016|consen  716 TQIGEKILIFSQNLTALDMIEEILKKRQIPCKDGDNGCPAQKWEKNRSYLRLDGTTSAADREKLINQFNSEPG-------  788 (1387)
T ss_pred             cccCceEEEeecchhHHHHHHHHHhcccccCCCCCCCCchhhhhhccceecccCCcccchHHHHHHhccCCCC-------
Confidence            3446899999998888888888886641                 1334467788999999999999988631       


Q ss_pred             ccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCC--CCEEEEEeeCc
Q 029910           85 EQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAA--DGSVINIVVGG  158 (185)
Q Consensus        85 ~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~--~g~~i~~v~~~  158 (185)
                                   ...-+|++|-+    ..-|+++-.++-+|.||.-|++..=.|-+-|.  .|+  +..++-+|..+
T Consensus       789 -------------lsWlfllstra----g~lGinLIsanr~~ifda~wnpchdaqavcRvyrYGQ~KpcfvYRlVmD~  849 (1387)
T KOG1016|consen  789 -------------LSWLFLLSTRA----GSLGINLISANRCIIFDACWNPCHDAQAVCRVYRYGQQKPCFVYRLVMDN  849 (1387)
T ss_pred             -------------ceeeeeehhcc----ccccceeeccceEEEEEeecCccccchhhhhhhhhcCcCceeEEeehhhh
Confidence                         12457788999    89999999999999999999998777766553  343  36677777654

>cd01524 RHOD_Pyr_redox Member of the Rhodanese Homology Domain superfamily

Probab=89.72  E-value=0.66  Score=31.89  Aligned_cols=38  Identities=11%  Similarity=0.061  Sum_probs=32.5

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      .+.+++|+||++-..+...+..|+..|. .+..+.|+++
T Consensus        49 ~~~~~vvl~c~~g~~a~~~a~~L~~~G~-~v~~l~GG~~   86 (90)
T cd01524          49 PKDKEIIVYCAVGLRGYIAARILTQNGF-KVKNLDGGYK   86 (90)
T ss_pred             CCCCcEEEEcCCChhHHHHHHHHHHCCC-CEEEecCCHH
Confidence            4458999999987788888999999995 8999999875

Included in this CD are the Lactococcus lactis NADH oxidase, Bacillus cereus NADH dehydrogenase, and Bacteroides thetaiotaomicron pyridine nucleotide-disulphide oxidoreductase, and similar rhodanese-like domains found C-terminal of the pyridine nucleotide-disulphide oxidoreductase (Pyr-redox) domain and the Pyr-redox dimerization domain.

>TIGR01054 rgy reverse gyrase

Probab=89.67  E-value=0.82  Score=46.29  Aligned_cols=62  Identities=18%  Similarity=0.272  Sum_probs=50.9

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcCC---Cce---EEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCC
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNLA---DIS---FSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEH   98 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~~---~~~---~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (185)
                      +.+++|.++|+.-|.++++.+....   ++.   +..+||+++..+|...+++++++                       
T Consensus       121 g~~vLIL~PTreLa~Qi~~~l~~l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~-----------------------  177 (1171)
T TIGR01054       121 GKRCYIILPTTLLVIQVAEKISSLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENG-----------------------  177 (1171)
T ss_pred             CCeEEEEeCHHHHHHHHHHHHHHHHHhcCCceeeeeeecCCCCHHHHHHHHHHHhcC-----------------------
Confidence            5899999999999999988887542   133   34689999999999999999987                       


Q ss_pred             ceeEEEEecCC
Q 029910           99 KSHMIVVTDAC  109 (185)
Q Consensus        99 ~~~iLV~Td~~  109 (185)
                      ..+|+|+|+.+
T Consensus       178 ~~dIlV~Tp~r  188 (1171)
T TIGR01054       178 DFDILITTTMF  188 (1171)
T ss_pred             CCCEEEECHHH
Confidence            58899999874

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.

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

Probab=89.43  E-value=2.2  Score=38.32  Aligned_cols=90  Identities=14%  Similarity=0.165  Sum_probs=63.8

Q ss_pred             HHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCC---CceEEEEecCCCHHHHHHHHHHHhcccccccccccc
Q 029910            9 ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLA---DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE   85 (185)
Q Consensus         9 ~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~---~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~   85 (185)
                      ...+-+++.|+. ....-.++|.++|++-|.++++.+...|   ++.+..+-|+++...+  .+..+++           
T Consensus       114 afaLPIl~~LL~-~p~~~~~lVLtPtRELA~QI~e~fe~Lg~~iglr~~~lvGG~~m~~q--~~~L~kk-----------  179 (476)
T KOG0330|consen  114 AFALPILQRLLQ-EPKLFFALVLTPTRELAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQ--ANQLSKK-----------  179 (476)
T ss_pred             hhHHHHHHHHHc-CCCCceEEEecCcHHHHHHHHHHHHHhccccCeEEEEEecCchHHHH--HHHhhcC-----------
Confidence            345678888887 5556889999999999999999887652   3899999999876544  4555655           


Q ss_pred             cCCCCCCCCCCCCceeEEEEecCCCC--cc-cCcCCCCCCcEEE
Q 029910           86 QSGDESETGKDEHKSHMIVVTDACLP--LL-SSGESAISARVLI  126 (185)
Q Consensus        86 ~~~~~~~~~~~~~~~~iLV~Td~~~~--~~-~~G~d~~~v~~VI  126 (185)
                                    .+|||||+-++-  |- ..|+.+..+.+.|
T Consensus       180 --------------PhilVaTPGrL~dhl~~Tkgf~le~lk~LV  209 (476)
T KOG0330|consen  180 --------------PHILVATPGRLWDHLENTKGFSLEQLKFLV  209 (476)
T ss_pred             --------------CCEEEeCcHHHHHHHHhccCccHHHhHHHh
Confidence                          457999986310  00 3566666655544

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=89.39  E-value=2.8  Score=39.05  Aligned_cols=91  Identities=11%  Similarity=0.079  Sum_probs=65.4

Q ss_pred             HHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCC
Q 029910            9 ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG   88 (185)
Q Consensus         9 ~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~   88 (185)
                      .+++-++-.+..    ...+||.+++..-+..-...|...| +.+..+|++++..++..+++....+             
T Consensus        41 KTl~y~lpal~~----~g~~lVisPl~sL~~dq~~~l~~~g-i~~~~~~s~~~~~~~~~~~~~l~~~-------------  102 (591)
T TIGR01389        41 KSLCYQVPALLL----KGLTVVISPLISLMKDQVDQLRAAG-VAAAYLNSTLSAKEQQDIEKALVNG-------------  102 (591)
T ss_pred             HhHHHHHHHHHc----CCcEEEEcCCHHHHHHHHHHHHHcC-CcEEEEeCCCCHHHHHHHHHHHhCC-------------
Confidence            344444544332    3578999999999998888998888 8999999999999999999999888             


Q ss_pred             CCCCCCCCCCceeEEEEecCCC--CcccCcCCCCCCcEEEE
Q 029910           89 DESETGKDEHKSHMIVVTDACL--PLLSSGESAISARVLIN  127 (185)
Q Consensus        89 ~~~~~~~~~~~~~iLV~Td~~~--~~~~~G~d~~~v~~VI~  127 (185)
                                ..+++++|+-.+  +...+-+....+.+||.
T Consensus       103 ----------~~~il~~tpe~l~~~~~~~~l~~~~l~~iVi  133 (591)
T TIGR01389       103 ----------ELKLLYVAPERLEQDYFLNMLQRIPIALVAV  133 (591)
T ss_pred             ----------CCCEEEEChhHhcChHHHHHHhcCCCCEEEE
Confidence                      688888886521  00112233445666664

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.

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=89.26  E-value=0.95  Score=42.33  Aligned_cols=44  Identities=18%  Similarity=0.312  Sum_probs=39.1

Q ss_pred             EEEEcCChhhHHHHHHHHhcC---CCceEEEEecCCCHHHHHHHHHH
Q 029910           28 MIVCCSSRDELDAVCSAVSNL---ADISFSSLHSDLAETERTLILEE   71 (185)
Q Consensus        28 ~IIF~~~~~~~~~l~~~L~~~---~~~~~~~l~g~~~~~~R~~~l~~   71 (185)
                      .+||++||+-|-++...|...   .++.++.+.|+|+...++.++.+
T Consensus       266 ~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQqRlL~~  312 (731)
T KOG0347|consen  266 ALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQRLLNQ  312 (731)
T ss_pred             eEEecChHHHHHHHHHHHHHhccccCeEEEEeechhHHHHHHHHHhc
Confidence            999999999999999888543   34999999999999999999887

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=89.01  E-value=3  Score=37.04  Aligned_cols=77  Identities=6%  Similarity=0.042  Sum_probs=52.5

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcC---CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCcee
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNL---ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSH  101 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~---~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (185)
                      +.++||.++|++-|.++.+.+...   -++++..++|+.+...+...   +..+                        .+
T Consensus        83 ~~~~lil~PtreLa~Qi~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~---l~~~------------------------~~  135 (423)
T PRK04837         83 QPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKV---LESG------------------------VD  135 (423)
T ss_pred             CceEEEECCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHH---hcCC------------------------CC
Confidence            468999999999999887655432   23889999999876665443   3333                        68


Q ss_pred             EEEEecCCCC-cc-cCcCCCCCCcEEEEc
Q 029910          102 MIVVTDACLP-LL-SSGESAISARVLINY  128 (185)
Q Consensus       102 iLV~Td~~~~-~~-~~G~d~~~v~~VI~~  128 (185)
                      |+|+|+-++- ++ ...+++..+.++|.=
T Consensus       136 IlV~TP~~l~~~l~~~~~~l~~v~~lViD  164 (423)
T PRK04837        136 ILIGTTGRLIDYAKQNHINLGAIQVVVLD  164 (423)
T ss_pred             EEEECHHHHHHHHHcCCcccccccEEEEe
Confidence            9999974210 01 245678888887753

>cd00158 RHOD Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein

Probab=88.97  E-value=0.86  Score=30.36  Aligned_cols=40  Identities=13%  Similarity=0.254  Sum_probs=34.3

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      ..+..++|++|++...+...+..|...|+..+..+.|++.
T Consensus        47 ~~~~~~vv~~c~~~~~a~~~~~~l~~~G~~~v~~l~gG~~   86 (89)
T cd00158          47 LDKDKPIVVYCRSGNRSARAAKLLRKAGGTNVYNLEGGML   86 (89)
T ss_pred             cCCCCeEEEEeCCCchHHHHHHHHHHhCcccEEEecCChh
Confidence            4567999999999889999999999998677888888864

The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins.

>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=88.94  E-value=0.16  Score=48.33  Aligned_cols=92  Identities=11%  Similarity=0.052  Sum_probs=79.6

Q ss_pred             CcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEE-E
Q 029910           26 LPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMI-V  104 (185)
Q Consensus        26 ~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iL-V  104 (185)
                      .++|||+.-..-++-+...|...+ +....+.|.|+...|.+.+..|..+.                      ..++| +
T Consensus       540 ~kiiifsq~~~~l~l~~~~l~~~~-~~~~~~~g~~~~~~r~~s~~~~~~~~----------------------~~~vll~  596 (674)
T KOG1001|consen  540 PKIVIFSQLIWGLALVCLRLFFKG-FVFLRYDGEMLMKIRTKSFTDFPCDP----------------------LVTALLM  596 (674)
T ss_pred             CceeeehhHHHHHHHhhhhhhhcc-cccchhhhhhHHHHHHhhhcccccCc----------------------cHHHHHH
Confidence            499999999999998888888777 78899999999999999999999662                      45544 5


Q ss_pred             EecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh
Q 029910          105 VTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC  144 (185)
Q Consensus       105 ~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~  144 (185)
                      +.-+    ..-|+++..+.+|+-.|+-|++..--|-+-|+
T Consensus       597 Slka----g~~glnlt~a~~v~~~d~~wnp~~eeQaidR~  632 (674)
T KOG1001|consen  597 SLKA----GKVGLNLTAASHVLLMDPWWNPAVEEQAIDRA  632 (674)
T ss_pred             HHHH----hhhhhchhhhhHHHhhchhcChHHHHHHHHHH
Confidence            5666    88999999999999999999999888888776

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=88.72  E-value=3.1  Score=37.44  Aligned_cols=75  Identities=11%  Similarity=0.148  Sum_probs=52.7

Q ss_pred             CcEEEEcCChhhHHHHHHHHhcC---CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeE
Q 029910           26 LPMIVCCSSRDELDAVCSAVSNL---ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHM  102 (185)
Q Consensus        26 ~~~IIF~~~~~~~~~l~~~L~~~---~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  102 (185)
                      .++||.|+|++-|.++.+.+...   ..+.+..++|+.+...+..   .++.                        ..+|
T Consensus        76 ~~aLil~PtreLa~Qi~~~~~~~~~~~~~~~~~~~gg~~~~~~~~---~l~~------------------------~~~I  128 (456)
T PRK10590         76 VRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMM---KLRG------------------------GVDV  128 (456)
T ss_pred             ceEEEEeCcHHHHHHHHHHHHHHhccCCCEEEEEECCcCHHHHHH---HHcC------------------------CCcE
Confidence            47999999999999888877643   1278889999988766543   2333                        4789


Q ss_pred             EEEecCCCC--cccCcCCCCCCcEEEE
Q 029910          103 IVVTDACLP--LLSSGESAISARVLIN  127 (185)
Q Consensus       103 LV~Td~~~~--~~~~G~d~~~v~~VI~  127 (185)
                      +|+|+-++-  +....+++..+++||.
T Consensus       129 iV~TP~rL~~~~~~~~~~l~~v~~lVi  155 (456)
T PRK10590        129 LVATPGRLLDLEHQNAVKLDQVEILVL  155 (456)
T ss_pred             EEEChHHHHHHHHcCCcccccceEEEe
Confidence            999963210  0244567888888775

>cd01449 TST_Repeat_2 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain

Probab=88.63  E-value=1.4  Score=31.62  Aligned_cols=38  Identities=21%  Similarity=0.228  Sum_probs=31.3

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCC
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDL   60 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~   60 (185)
                      .+.+++|+||++-..+...+..|...|+-.+..+.|++
T Consensus        76 ~~~~~iv~yc~~g~~s~~~~~~l~~~G~~~v~~l~GG~  113 (118)
T cd01449          76 TPDKPVIVYCGSGVTACVLLLALELLGYKNVRLYDGSW  113 (118)
T ss_pred             CCCCCEEEECCcHHHHHHHHHHHHHcCCCCeeeeCChH
Confidence            46789999999988888899999998843577888875

TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue.

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=88.56  E-value=2  Score=40.07  Aligned_cols=76  Identities=9%  Similarity=0.148  Sum_probs=52.5

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcCC---CceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCcee
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNLA---DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSH  101 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~~---~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (185)
                      ..++||.|+|++-+.++.+.+...+   ++.+..++|+.+...+...+.   .                        ..+
T Consensus        84 ~~raLIl~PTreLa~Qi~~~~~~l~~~~~i~v~~l~Gg~~~~~q~~~l~---~------------------------~~d  136 (572)
T PRK04537         84 DPRALILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQRELLQ---Q------------------------GVD  136 (572)
T ss_pred             CceEEEEeCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHHh---C------------------------CCC
Confidence            3689999999999998887765431   278999999998877655442   2                        378


Q ss_pred             EEEEecCCC-CcccC--cCCCCCCcEEEE
Q 029910          102 MIVVTDACL-PLLSS--GESAISARVLIN  127 (185)
Q Consensus       102 iLV~Td~~~-~~~~~--G~d~~~v~~VI~  127 (185)
                      |+|+|+-.+ .++.+  .+++..+++||.
T Consensus       137 IiV~TP~rL~~~l~~~~~~~l~~v~~lVi  165 (572)
T PRK04537        137 VIIATPGRLIDYVKQHKVVSLHACEICVL  165 (572)
T ss_pred             EEEECHHHHHHHHHhccccchhheeeeEe
Confidence            999996310 00222  356777777664

>smart00491 HELICc2 helicase superfamily c-terminal domain

Probab=88.44  E-value=1.8  Score=32.95  Aligned_cols=46  Identities=17%  Similarity=0.294  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEEEe--cCCCCcccCcCCCCC--CcEEEEcCCCC
Q 029910           63 TERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVT--DACLPLLSSGESAIS--ARVLINYELPT  132 (185)
Q Consensus        63 ~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~T--d~~~~~~~~G~d~~~--v~~VI~~d~P~  132 (185)
                      .+..+++++|+...                 +.+   ..||+++  ..    +++|+|+|+  ++.||...+|-
T Consensus        31 ~~~~~~l~~f~~~~-----------------~~~---g~iL~~v~~G~----~~EGiD~~g~~~r~vii~glPf   80 (142)
T smart00491       31 GETEELLEKYSAAC-----------------EAR---GALLLAVARGK----VSEGIDFPDDLGRAVIIVGIPF   80 (142)
T ss_pred             chHHHHHHHHHHhc-----------------CCC---CEEEEEEeCCe----eecceecCCCccEEEEEEecCC
Confidence            35578899999862                 000   2467665  34    699999998  46788877773

>cd01528 RHOD_2 Member of the Rhodanese Homology Domain superfamily, subgroup 2

Probab=88.42  E-value=1.6  Score=30.57  Aligned_cols=53  Identities=11%  Similarity=0.105  Sum_probs=37.8

Q ss_pred             HHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCH
Q 029910            9 ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAE   62 (185)
Q Consensus         9 ~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~   62 (185)
                      +.+.+.+..+.. ..+.+++++||++-..+...+..|...|.-.+..+.|++..
T Consensus        43 ~~~~~~~~~~~~-~~~~~~vv~~c~~g~rs~~~~~~l~~~G~~~v~~l~GG~~~   95 (101)
T cd01528          43 SEIPERSKELDS-DNPDKDIVVLCHHGGRSMQVAQWLLRQGFENVYNLQGGIDA   95 (101)
T ss_pred             HHHHHHHHHhcc-cCCCCeEEEEeCCCchHHHHHHHHHHcCCccEEEecCCHHH
Confidence            334444444322 23468999999998888888999988885468889998654

Subgroup 2 includes uncharacterized putative rhodanese-related domains.

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

Probab=88.41  E-value=6.4  Score=40.39  Aligned_cols=115  Identities=13%  Similarity=0.225  Sum_probs=73.8

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcC--C-------------------CceEEEEecCCCHHHHHHHHHHHhccccccc
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNL--A-------------------DISFSSLHSDLAETERTLILEEFRHTAMKWN   80 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~--~-------------------~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~   80 (185)
                      ..+.++.+||+++++.|..++-.|-..  +                   .++...=|-+++.....-+-.-|..|     
T Consensus      1356 a~~~k~~~vf~p~rk~~~~~a~~~~~~s~~~~~~~l~~~~e~~~~~l~e~l~~gvg~e~~s~~d~~iv~~l~e~g----- 1430 (1674)
T KOG0951|consen 1356 AGNRKPAIVFLPTRKHARLVAVDLVTFSHADEPDYLLSELEECDETLRESLKHGVGHEGLSSNDQEIVQQLFEAG----- 1430 (1674)
T ss_pred             hcCCCCeEEEeccchhhhhhhhccchhhccCcHHHHHHHHhcchHhhhhcccccccccccCcchHHHHHHHHhcC-----
Confidence            456799999999999999887655321  0                   01112225666666666555666666     


Q ss_pred             ccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEE-----EcC------CCCCHHHHHHHHhhhcCCCC
Q 029910           81 QKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLI-----NYE------LPTKKETYIRRMTTCLAADG  149 (185)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI-----~~d------~P~~~~~yiqR~GR~~~~~g  149 (185)
                                        .+.++|...-|     .|+-.. .+.||     .||      .+.......|.+|++.| .|
T Consensus      1431 ------------------~i~v~v~s~~~-----~~~~~~-~~lVvvmgt~~ydg~e~~~~~y~i~~ll~m~G~a~~-~~ 1485 (1674)
T KOG0951|consen 1431 ------------------AIQVCVMSRDC-----YGTKLK-AHLVVVMGTQYYDGKEHSYEDYPIAELLQMVGLASG-AG 1485 (1674)
T ss_pred             ------------------cEEEEEEEccc-----cccccc-ceEEEEecceeecccccccccCchhHHHHHhhhhcC-Cc
Confidence                              68888876432     122222 23344     233      35568999999999977 78


Q ss_pred             EEEEEeeCchHHHHHHH
Q 029910          150 SVINIVVGGEVVTLRSM  166 (185)
Q Consensus       150 ~~i~~v~~~e~~~~~~l  166 (185)
                      .|+.++......+++++
T Consensus      1486 k~vi~~~~~~k~yykkf 1502 (1674)
T KOG0951|consen 1486 KCVIMCHTPKKEYYKKF 1502 (1674)
T ss_pred             cEEEEecCchHHHHHHh
Confidence            88888877766666543

>cd01518 RHOD_YceA Member of the Rhodanese Homology Domain superfamily

Probab=88.34  E-value=1.2  Score=31.22  Aligned_cols=39  Identities=8%  Similarity=0.139  Sum_probs=30.8

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      .+.+++||||.+-..+...+..|...|+-.+..|.|++.
T Consensus        59 ~~~~~ivvyC~~G~rs~~a~~~L~~~G~~~v~~l~GG~~   97 (101)
T cd01518          59 LKGKKVLMYCTGGIRCEKASAYLKERGFKNVYQLKGGIL   97 (101)
T ss_pred             cCCCEEEEECCCchhHHHHHHHHHHhCCcceeeechhHH
Confidence            456899999998777778888898888435888888864

This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins.

>cd01448 TST_Repeat_1 Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain

Probab=87.68  E-value=1.5  Score=31.65  Aligned_cols=52  Identities=13%  Similarity=0.052  Sum_probs=37.4

Q ss_pred             HHHHHHHHHHHccCCCCCcEEEEcCC-hhhHHHHHHHHhcCCCceEEEEecCCCH
Q 029910            9 ETLVELLHLVVAGRRPGLPMIVCCSS-RDELDAVCSAVSNLADISFSSLHSDLAE   62 (185)
Q Consensus         9 ~~l~~ll~~l~~~~~~~~~~IIF~~~-~~~~~~l~~~L~~~~~~~~~~l~g~~~~   62 (185)
                      +.+.+.+.. .. ..+.+++|+||++ -..+...+..|...|.-.+..+.|++..
T Consensus        65 ~~~~~~~~~-~~-~~~~~~vv~~c~~g~~~a~~~~~~l~~~G~~~v~~l~GG~~~  117 (122)
T cd01448          65 EEFAELLGS-LG-ISNDDTVVVYDDGGGFFAARAWWTLRYFGHENVRVLDGGLQA  117 (122)
T ss_pred             HHHHHHHHH-cC-CCCCCEEEEECCCCCccHHHHHHHHHHcCCCCEEEecCCHHH
Confidence            444455544 22 4567899999998 4778888888988885558888888743

TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but it is believed to be involved in protein interaction.

>smart00450 RHOD Rhodanese Homology Domain

Probab=87.14  E-value=1.1  Score=30.13  Aligned_cols=41  Identities=17%  Similarity=0.197  Sum_probs=34.2

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCH
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAE   62 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~   62 (185)
                      ..+..++||||.+...+..++..|...|.-.+..|.|++..
T Consensus        53 ~~~~~~iv~~c~~g~~a~~~~~~l~~~G~~~v~~l~GG~~~   93 (100)
T smart00450       53 LDKDKPVVVYCRSGNRSAKAAWLLRELGFKNVYLLDGGYKE   93 (100)
T ss_pred             CCCCCeEEEEeCCCcHHHHHHHHHHHcCCCceEEecCCHHH
Confidence            55678999999998999999999999985448889998643

An alpha beta fold found duplicated in the Rhodanese protein. The the Cysteine containing enzymatically active version of the domain is also found in the CDC25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and stress proteins such as Senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions with a loss of the cysteine are also seen in Dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases. These are likely to play a role in protein interactions.

>cd01529 4RHOD_Repeats Member of the Rhodanese Homology Domain superfamily

Probab=87.10  E-value=1.4  Score=30.58  Aligned_cols=40  Identities=8%  Similarity=0.071  Sum_probs=32.9

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      ..+.+++|+||++...+...+..|...|.-++..+.|++.
T Consensus        53 ~~~~~~ivv~c~~g~~s~~~~~~l~~~G~~~v~~l~GG~~   92 (96)
T cd01529          53 PGRATRYVLTCDGSLLARFAAQELLALGGKPVALLDGGTS   92 (96)
T ss_pred             CCCCCCEEEEeCChHHHHHHHHHHHHcCCCCEEEeCCCHH
Confidence            3566899999999888888899998888446888888863

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. Only the second and most of the fourth repeats contain the putative catalytic Cys residue. This CD aligns the 1st , 2nd, 3rd, and 4th repeats.

>cd01523 RHOD_Lact_B Member of the Rhodanese Homology Domain superfamily

Probab=86.46  E-value=1.1  Score=31.20  Aligned_cols=39  Identities=10%  Similarity=0.166  Sum_probs=32.6

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCH
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAE   62 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~   62 (185)
                      .+.+++||+|.+-..+...+..|...| +.+..|.|++..
T Consensus        59 ~~~~~ivv~C~~G~rs~~aa~~L~~~G-~~~~~l~GG~~~   97 (100)
T cd01523          59 PDDQEVTVICAKEGSSQFVAELLAERG-YDVDYLAGGMKA   97 (100)
T ss_pred             CCCCeEEEEcCCCCcHHHHHHHHHHcC-ceeEEeCCcHHh
Confidence            456899999998888899999999998 678889898743

This CD includes predicted proteins with rhodanese-like domains found N-terminal of the metallo-beta-lactamase domain.

>cd01519 RHOD_HSP67B2 Member of the Rhodanese Homology Domain superfamily

Probab=86.24  E-value=1.3  Score=30.94  Aligned_cols=39  Identities=10%  Similarity=0.111  Sum_probs=31.8

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      .+.+++|+||++-..+...+..|...|+-.+..+.|++.
T Consensus        64 ~~~~~ivv~c~~g~~s~~~~~~l~~~G~~~v~~~~Gg~~  102 (106)
T cd01519          64 SKDKELIFYCKAGVRSKAAAELARSLGYENVGNYPGSWL  102 (106)
T ss_pred             CCCCeEEEECCCcHHHHHHHHHHHHcCCccceecCCcHH
Confidence            346899999999888889999999998445777888764

This CD includes the heat shock protein 67B2 of Drosophila melanogaster and other similar proteins, many of which are uncharacterized.

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

Probab=86.03  E-value=4.1  Score=41.08  Aligned_cols=79  Identities=16%  Similarity=0.136  Sum_probs=67.1

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHH----hcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCC
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAV----SNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDE   97 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L----~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~   97 (185)
                      -..++|+.|.|+|---|++=++.+    ...+ +++..|..=.+..+..++++..++|                      
T Consensus       640 V~~GKQVAvLVPTTlLA~QHy~tFkeRF~~fP-V~I~~LSRF~s~kE~~~il~~la~G----------------------  696 (1139)
T COG1197         640 VMDGKQVAVLVPTTLLAQQHYETFKERFAGFP-VRIEVLSRFRSAKEQKEILKGLAEG----------------------  696 (1139)
T ss_pred             hcCCCeEEEEcccHHhHHHHHHHHHHHhcCCC-eeEEEecccCCHHHHHHHHHHHhcC----------------------
Confidence            445799999999977666555555    4457 8999999999999999999999999                      


Q ss_pred             CceeEEEEecCCCCcccCcCCCCCCcEEEE
Q 029910           98 HKSHMIVVTDACLPLLSSGESAISARVLIN  127 (185)
Q Consensus        98 ~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~  127 (185)
                       +++|+|.|-.   |++.++-+.+.-++|.
T Consensus       697 -~vDIvIGTHr---LL~kdv~FkdLGLlII  722 (1139)
T COG1197         697 -KVDIVIGTHR---LLSKDVKFKDLGLLII  722 (1139)
T ss_pred             -CccEEEechH---hhCCCcEEecCCeEEE
Confidence             7999999976   5889999999998874

>cd01444 GlpE_ST GlpE sulfurtransferase (ST) and homologs are members of the Rhodanese Homology Domain superfamily

Probab=85.88  E-value=2  Score=29.40  Aligned_cols=39  Identities=15%  Similarity=0.258  Sum_probs=32.8

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      .+.+++||+|++-..+...+..|...|+-.+..+.|++.
T Consensus        54 ~~~~~ivv~c~~g~~s~~a~~~l~~~G~~~v~~l~gG~~   92 (96)
T cd01444          54 DRDRPVVVYCYHGNSSAQLAQALREAGFTDVRSLAGGFE   92 (96)
T ss_pred             CCCCCEEEEeCCCChHHHHHHHHHHcCCceEEEcCCCHH
Confidence            456899999999999999999999998556888888753

Unlike other rhodanese sulfurtransferases, GlpE is a single domain protein but indications are that it functions as a dimer. The active site contains a catalytically active cysteine.

>KOG1513 consensus Nuclear helicase MOP-3/SNO (DEAD-box superfamily) [Transcription; Signal transduction mechanisms]

Probab=85.61  E-value=1.4  Score=43.06  Aligned_cols=63  Identities=22%  Similarity=0.259  Sum_probs=44.0

Q ss_pred             ceeEEEEecCCCCcccCcCCCCCCcEE--------EEcCCCCCHHHHHHHHhhhcCCC---CEEEEEe-e--CchHHHHH
Q 029910           99 KSHMIVVTDACLPLLSSGESAISARVL--------INYELPTKKETYIRRMTTCLAAD---GSVINIV-V--GGEVVTLR  164 (185)
Q Consensus        99 ~~~iLV~Td~~~~~~~~G~d~~~v~~V--------I~~d~P~~~~~yiqR~GR~~~~~---g~~i~~v-~--~~e~~~~~  164 (185)
                      ...|-|..++    ++.|+.++.=+-|        |-+++||+.+.-||+.||+.++.   +--+.|+ +  .+|..+..
T Consensus       857 eK~vAIISEA----aSSGiSLQsDrRv~NqRRRvHiTLELPWSADrAIQQFGRTHRSNQVsaPEYvFlIseLAGErRFAS  932 (1300)
T KOG1513|consen  857 EKLVAIISEA----ASSGISLQSDRRVQNQRRRVHITLELPWSADRAIQQFGRTHRSNQVSAPEYVFLISELAGERRFAS  932 (1300)
T ss_pred             cceeeeeehh----hccCceeecchhhhhhhheEEEEEECCcchhHHHHHhcccccccccCCCeEEEEehhhccchHHHH
Confidence            4667778888    9999988765444        55789999999999999986554   3334444 2  24554443


Q ss_pred             H
Q 029910          165 S  165 (185)
Q Consensus       165 ~  165 (185)
                      .
T Consensus       933 ~  933 (1300)
T KOG1513|consen  933 I  933 (1300)
T ss_pred             H
Confidence            3

>PF10593 Z1: Z1 domain; InterPro: IPR018310 This entry represents the Z1 domain of unknown function that is found in a group of putative endonucleases

Probab=85.11  E-value=6.2  Score=32.82  Aligned_cols=45  Identities=16%  Similarity=0.050  Sum_probs=36.2

Q ss_pred             eeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh-cCCCC
Q 029910          100 SHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC-LAADG  149 (185)
Q Consensus       100 ~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~-~~~~g  149 (185)
                      ..|+|.=+.    ++||+.+++..+.....-|.+.+++.|| ||= |-++|
T Consensus       136 ~~I~VGGn~----LsRGlTleGL~vsYf~R~s~~~DTL~Qm-gRwFGYR~g  181 (239)
T PF10593_consen  136 NVIAVGGNK----LSRGLTLEGLTVSYFLRNSKQYDTLMQM-GRWFGYRPG  181 (239)
T ss_pred             eEEEECCcc----ccCceeECCcEEEEecCCCchHHHHHHH-hhcccCCcc
Confidence            778999999    9999999999998888888877777665 574 44444

This domain is found associated with a helicase domain of superfamily type II [].

>cd01532 4RHOD_Repeat_1 Member of the Rhodanese Homology Domain superfamily, repeat 1

Probab=84.87  E-value=1.6  Score=30.24  Aligned_cols=38  Identities=18%  Similarity=0.234  Sum_probs=30.1

Q ss_pred             CCCcEEEEcCC--hhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910           24 PGLPMIVCCSS--RDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus        24 ~~~~~IIF~~~--~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      +.+++||||.+  +..+...+..|...|+-++..+.|++.
T Consensus        49 ~~~~ivl~c~~G~~~~s~~aa~~L~~~G~~~v~~l~GG~~   88 (92)
T cd01532          49 RDTPIVVYGEGGGEDLAPRAARRLSELGYTDVALLEGGLQ   88 (92)
T ss_pred             CCCeEEEEeCCCCchHHHHHHHHHHHcCccCEEEccCCHH
Confidence            36799999998  455778888888888557888988874

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 1st repeat which does not contain the putative catalytic Cys residue.

>cd01520 RHOD_YbbB Member of the Rhodanese Homology Domain superfamily

Probab=84.17  E-value=2.8  Score=30.90  Aligned_cols=40  Identities=10%  Similarity=0.207  Sum_probs=31.7

Q ss_pred             CCCCCcEEEEcC-ChhhHHHHHHHHhcCCCceEEEEecCCCH
Q 029910           22 RRPGLPMIVCCS-SRDELDAVCSAVSNLADISFSSLHSDLAE   62 (185)
Q Consensus        22 ~~~~~~~IIF~~-~~~~~~~l~~~L~~~~~~~~~~l~g~~~~   62 (185)
                      -.+.+++||||+ +-..+...+..|+..| +.+..|.|+++.
T Consensus        83 i~~~~~vvvyC~~~G~rs~~a~~~L~~~G-~~v~~L~GG~~a  123 (128)
T cd01520          83 LERDPKLLIYCARGGMRSQSLAWLLESLG-IDVPLLEGGYKA  123 (128)
T ss_pred             cCCCCeEEEEeCCCCccHHHHHHHHHHcC-CceeEeCCcHHH
Confidence            456689999996 4566777888888888 589999999754

This CD includes several putative ATP /GTP binding proteins including E. coli YbbB.

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

Probab=84.06  E-value=3.1  Score=38.79  Aligned_cols=74  Identities=12%  Similarity=0.144  Sum_probs=52.4

Q ss_pred             CCcEEEEcCChhhHHHHHHHHh----cCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCce
Q 029910           25 GLPMIVCCSSRDELDAVCSAVS----NLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKS  100 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~----~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~  100 (185)
                      +.=.+|.|+|++-|.++...-+    .+| +.+.++||+++..++.+-|+   .|                        .
T Consensus       296 gPi~vilvPTrela~Qi~~eaKkf~K~yg-l~~v~~ygGgsk~eQ~k~Lk---~g------------------------~  347 (731)
T KOG0339|consen  296 GPIGVILVPTRELASQIFSEAKKFGKAYG-LRVVAVYGGGSKWEQSKELK---EG------------------------A  347 (731)
T ss_pred             CCeEEEEeccHHHHHHHHHHHHHhhhhcc-ceEEEeecCCcHHHHHHhhh---cC------------------------C
Confidence            3446778899998887765544    345 89999999999999987776   44                        6


Q ss_pred             eEEEEecCCCC--cccCcCCCCCCcEEE
Q 029910          101 HMIVVTDACLP--LLSSGESAISARVLI  126 (185)
Q Consensus       101 ~iLV~Td~~~~--~~~~G~d~~~v~~VI  126 (185)
                      .++|||+-++=  +--.+.|+..+.++|
T Consensus       348 EivVaTPgRlid~VkmKatn~~rvS~LV  375 (731)
T KOG0339|consen  348 EIVVATPGRLIDMVKMKATNLSRVSYLV  375 (731)
T ss_pred             eEEEechHHHHHHHHhhcccceeeeEEE
Confidence            78999975310  002466777777655

>cd01527 RHOD_YgaP Member of the Rhodanese Homology Domain superfamily

Probab=83.94  E-value=2.1  Score=29.71  Aligned_cols=39  Identities=13%  Similarity=0.105  Sum_probs=31.8

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      ...++++++|++-..+...+..|...|+-.+..+.|++.
T Consensus        52 ~~~~~iv~~c~~g~~s~~~~~~L~~~g~~~v~~l~gG~~   90 (99)
T cd01527          52 VGANAIIFHCRSGMRTQQNAERLAAISAGEAYVLEGGLD   90 (99)
T ss_pred             CCCCcEEEEeCCCchHHHHHHHHHHcCCccEEEeeCCHH
Confidence            456899999999888888999998887546888999863

This CD includes Escherichia coli YgaP, and similar uncharacterized putative rhodanese-related sulfurtransferases.

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

Probab=83.75  E-value=8.8  Score=35.90  Aligned_cols=88  Identities=17%  Similarity=0.189  Sum_probs=63.3

Q ss_pred             HHHHHHHHHc--cCCCCCcEEEEcCChhhHHHHHHHHhc---CCCceEEEEecCCCHHHHHHHHHHHhcccccccccccc
Q 029910           11 LVELLHLVVA--GRRPGLPMIVCCSSRDELDAVCSAVSN---LADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE   85 (185)
Q Consensus        11 l~~ll~~l~~--~~~~~~~~IIF~~~~~~~~~l~~~L~~---~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~   85 (185)
                      .+-+|+.|+.  ...+-.++||.|+|++-+-++......   .-.|.+...-|+++...+.+.++   +.          
T Consensus       236 ~lPiLERLlYrPk~~~~TRVLVL~PTRELaiQv~sV~~qlaqFt~I~~~L~vGGL~lk~QE~~LR---s~----------  302 (691)
T KOG0338|consen  236 ALPILERLLYRPKKVAATRVLVLVPTRELAIQVHSVTKQLAQFTDITVGLAVGGLDLKAQEAVLR---SR----------  302 (691)
T ss_pred             HHHHHHHHhcCcccCcceeEEEEeccHHHHHHHHHHHHHHHhhccceeeeeecCccHHHHHHHHh---hC----------
Confidence            4556666554  133458999999999988776655543   33488888889999999987764   33          


Q ss_pred             cCCCCCCCCCCCCceeEEEEecCCCCcc------cCcCCCCCCcEEEEc
Q 029910           86 QSGDESETGKDEHKSHMIVVTDACLPLL------SSGESAISARVLINY  128 (185)
Q Consensus        86 ~~~~~~~~~~~~~~~~iLV~Td~~~~~~------~~G~d~~~v~~VI~~  128 (185)
                                    -+|+|||+-+   +      +-++++.++.++|.=
T Consensus       303 --------------PDIVIATPGR---lIDHlrNs~sf~ldsiEVLvlD  334 (691)
T KOG0338|consen  303 --------------PDIVIATPGR---LIDHLRNSPSFNLDSIEVLVLD  334 (691)
T ss_pred             --------------CCEEEecchh---HHHHhccCCCccccceeEEEec
Confidence                          6799999863   2      457788888877753

>cd01533 4RHOD_Repeat_2 Member of the Rhodanese Homology Domain superfamily, repeat 2

Probab=82.67  E-value=4.4  Score=28.72  Aligned_cols=39  Identities=18%  Similarity=0.284  Sum_probs=30.9

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcCCCce-EEEEecCCCH
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNLADIS-FSSLHSDLAE   62 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~-~~~l~g~~~~   62 (185)
                      +.++++|||.+-..+...+..|...|+-. +..+.|+++.
T Consensus        65 ~~~~ivv~C~~G~rs~~a~~~L~~~G~~~~v~~l~gG~~~  104 (109)
T cd01533          65 PRTPIVVNCAGRTRSIIGAQSLINAGLPNPVAALRNGTQG  104 (109)
T ss_pred             CCCeEEEECCCCchHHHHHHHHHHCCCCcceeEecCCHHH
Confidence            45799999998877777888898888324 7889999744

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 2nd repeat which does contain the putative catalytic Cys residue.

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

Probab=82.63  E-value=5  Score=40.70  Aligned_cols=59  Identities=19%  Similarity=0.161  Sum_probs=50.3

Q ss_pred             CcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhc--ccccccccccccCCCCCCCCCCCCceeEE
Q 029910           26 LPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRH--TAMKWNQKVTEQSGDESETGKDEHKSHMI  103 (185)
Q Consensus        26 ~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~iL  103 (185)
                      ..+||.+++++-+..-...|...+ +.+..++++++..++.++++++..  +                       ..++|
T Consensus       501 GiTLVISPLiSLmqDQV~~L~~~G-I~Aa~L~s~~s~~eq~~ilr~l~s~~g-----------------------~~~IL  556 (1195)
T PLN03137        501 GITLVISPLVSLIQDQIMNLLQAN-IPAASLSAGMEWAEQLEILQELSSEYS-----------------------KYKLL  556 (1195)
T ss_pred             CcEEEEeCHHHHHHHHHHHHHhCC-CeEEEEECCCCHHHHHHHHHHHHhcCC-----------------------CCCEE
Confidence            679999999999876566666677 899999999999999999999876  5                       58899


Q ss_pred             EEecC
Q 029910          104 VVTDA  108 (185)
Q Consensus       104 V~Td~  108 (185)
                      ++|+-
T Consensus       557 yvTPE  561 (1195)
T PLN03137        557 YVTPE  561 (1195)
T ss_pred             EEChH
Confidence            99975

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=82.36  E-value=8.3  Score=34.82  Aligned_cols=77  Identities=8%  Similarity=0.132  Sum_probs=52.3

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcC---CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCcee
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNL---ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSH  101 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~---~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (185)
                      ..++||.++|++-+.++.+.++..   .++.+..++|+.+...+.   +++...                       ..+
T Consensus       162 ~~~aLil~PtreLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~---~~~~~~-----------------------~~~  215 (475)
T PRK01297        162 EPRALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQL---KQLEAR-----------------------FCD  215 (475)
T ss_pred             CceEEEEeCcHHHHHHHHHHHHHhhccCCCEEEEEEccCChHHHH---HHHhCC-----------------------CCC
Confidence            368999999999999888877643   137889999998766554   344444                       478


Q ss_pred             EEEEecCCC-Cccc-CcCCCCCCcEEEE
Q 029910          102 MIVVTDACL-PLLS-SGESAISARVLIN  127 (185)
Q Consensus       102 iLV~Td~~~-~~~~-~G~d~~~v~~VI~  127 (185)
                      |+|+|+-.+ ++.. ..+.+..+++||.
T Consensus       216 Iiv~TP~~Ll~~~~~~~~~l~~l~~lVi  243 (475)
T PRK01297        216 ILVATPGRLLDFNQRGEVHLDMVEVMVL  243 (475)
T ss_pred             EEEECHHHHHHHHHcCCcccccCceEEe
Confidence            999997421 1112 2456677777765

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=82.17  E-value=5.3  Score=37.51  Aligned_cols=49  Identities=8%  Similarity=0.055  Sum_probs=44.6

Q ss_pred             CcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcc
Q 029910           26 LPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHT   75 (185)
Q Consensus        26 ~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~   75 (185)
                      ..+||.+++++-+......|...| +.+..+++..+..++..+++..+.+
T Consensus        66 g~tlVisPl~sL~~dqv~~l~~~g-i~~~~~~s~~~~~~~~~~~~~~~~g  114 (607)
T PRK11057         66 GLTLVVSPLISLMKDQVDQLLANG-VAAACLNSTQTREQQLEVMAGCRTG  114 (607)
T ss_pred             CCEEEEecHHHHHHHHHHHHHHcC-CcEEEEcCCCCHHHHHHHHHHHhCC
Confidence            578999999999999899998888 8999999999999999999988887

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

Probab=81.89  E-value=13  Score=27.60  Aligned_cols=77  Identities=9%  Similarity=0.167  Sum_probs=51.6

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcCC---CceEEEEecCCCHH-HHHHHHHHHhcccccccccccccCCCCCCCCCCCCc
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNLA---DISFSSLHSDLAET-ERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHK   99 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~~---~~~~~~l~g~~~~~-~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (185)
                      ...++|+.|+++..++.....+....   ++++..++++.+.. +....+    .+                       .
T Consensus        43 ~~~~~lii~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~-----------------------~   95 (169)
T PF00270_consen   43 KDARVLIIVPTRALAEQQFERLRKFFSNTNVRVVLLHGGQSISEDQREVL----SN-----------------------Q   95 (169)
T ss_dssp             SSSEEEEEESSHHHHHHHHHHHHHHTTTTTSSEEEESTTSCHHHHHHHHH----HT-----------------------T
T ss_pred             CCceEEEEeecccccccccccccccccccccccccccccccccccccccc----cc-----------------------c
Confidence            44699999999999998888876552   26889999998855 333333    33                       4


Q ss_pred             eeEEEEecCCCCc-c-cCcCCCCCCcEEEE
Q 029910          100 SHMIVVTDACLPL-L-SSGESAISARVLIN  127 (185)
Q Consensus       100 ~~iLV~Td~~~~~-~-~~G~d~~~v~~VI~  127 (185)
                      .+|+|+|..++-- . ....++..+++||.
T Consensus        96 ~~ilv~T~~~l~~~~~~~~~~~~~~~~iVi  125 (169)
T PF00270_consen   96 ADILVTTPEQLLDLISNGKINISRLSLIVI  125 (169)
T ss_dssp             SSEEEEEHHHHHHHHHTTSSTGTTESEEEE
T ss_pred             ccccccCcchhhccccccccccccceeecc
Confidence            8899999752100 1 12346677777775

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=81.61  E-value=6.6  Score=37.93  Aligned_cols=53  Identities=15%  Similarity=0.218  Sum_probs=40.1

Q ss_pred             HHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCC--CceEEEEecCCCHHHHH
Q 029910           12 VELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLA--DISFSSLHSDLAETERT   66 (185)
Q Consensus        12 ~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~--~~~~~~l~g~~~~~~R~   66 (185)
                      +-+|+.+..  .+..++|+.++|++-+.+..+.|...+  ++.+..++|+.+..+|.
T Consensus        70 LPiL~~l~~--~~~~~aL~l~PtraLa~q~~~~l~~l~~~~i~v~~~~Gdt~~~~r~  124 (742)
T TIGR03817        70 LPVLSALAD--DPRATALYLAPTKALAADQLRAVRELTLRGVRPATYDGDTPTEERR  124 (742)
T ss_pred             HHHHHHHhh--CCCcEEEEEcChHHHHHHHHHHHHHhccCCeEEEEEeCCCCHHHHH
Confidence            445555443  345789999999999999998887652  37889999999987764

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.

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

Probab=81.26  E-value=4.7  Score=37.39  Aligned_cols=96  Identities=10%  Similarity=0.142  Sum_probs=65.6

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcCC---CceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCC
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNLA---DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEH   98 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~~---~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (185)
                      +..+..+||-++||+-|.++...+...+   .++..+++|+.+...+.   ++.++|                       
T Consensus       162 ~~~~P~vLVL~PTRELA~QV~~~~~~~~~~~~~~~~cvyGG~~~~~Q~---~~l~~g-----------------------  215 (519)
T KOG0331|consen  162 RGDGPIVLVLAPTRELAVQVQAEAREFGKSLRLRSTCVYGGAPKGPQL---RDLERG-----------------------  215 (519)
T ss_pred             CCCCCeEEEEcCcHHHHHHHHHHHHHHcCCCCccEEEEeCCCCccHHH---HHHhcC-----------------------
Confidence            3345779999999999999998886652   26799999999888875   445565                       


Q ss_pred             ceeEEEEecCCCC-cccC-cCCCCCCcEEEEc--------CCCCCHHHHHHHHhhh
Q 029910           99 KSHMIVVTDACLP-LLSS-GESAISARVLINY--------ELPTKKETYIRRMTTC  144 (185)
Q Consensus        99 ~~~iLV~Td~~~~-~~~~-G~d~~~v~~VI~~--------d~P~~~~~yiqR~GR~  144 (185)
                       +.|+|+|+-++- ++.+ -+|+..+.++|-=        ++-.++...++++.|.
T Consensus       216 -vdiviaTPGRl~d~le~g~~~l~~v~ylVLDEADrMldmGFe~qI~~Il~~i~~~  270 (519)
T KOG0331|consen  216 -VDVVIATPGRLIDLLEEGSLNLSRVTYLVLDEADRMLDMGFEPQIRKILSQIPRP  270 (519)
T ss_pred             -CcEEEeCChHHHHHHHcCCccccceeEEEeccHHhhhccccHHHHHHHHHhcCCC
Confidence             889999986311 1233 4577788887731        2333455555565554

>cd01447 Polysulfide_ST Polysulfide-sulfurtransferase - Rhodanese Homology Domain

Probab=81.17  E-value=1.5  Score=30.35  Aligned_cols=40  Identities=8%  Similarity=0.184  Sum_probs=31.4

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCH
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAE   62 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~   62 (185)
                      .+.++++|||.+-..+...+..|...|.-.+..+.|++..
T Consensus        59 ~~~~~ivv~c~~g~~s~~~~~~l~~~G~~~v~~l~Gg~~~   98 (103)
T cd01447          59 AEDKPFVFYCASGWRSALAGKTLQDMGLKPVYNIEGGFKD   98 (103)
T ss_pred             CCCCeEEEEcCCCCcHHHHHHHHHHcChHHhEeecCcHHH
Confidence            4568999999987778888899988884347888887643

This domain is believed to serve as a polysulfide binding and transferase domain in anaerobic gram-negative bacteria, functioning in oxidative phosphorylation with polysulfide-sulfur as a terminal electron acceptor. The active site contains the same conserved cysteine that is the catalytic residue in other Rhodanese Homology Domain proteins.

>PTZ00110 helicase; Provisional

Probab=81.04  E-value=6.2  Score=36.60  Aligned_cols=76  Identities=12%  Similarity=0.190  Sum_probs=52.1

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcCC---CceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCcee
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNLA---DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSH  101 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~~---~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (185)
                      +..+||.|+|++-|.++.+.+...+   .+.+..++|+.+...+..   ..+.+                        .+
T Consensus       203 gp~~LIL~PTreLa~Qi~~~~~~~~~~~~i~~~~~~gg~~~~~q~~---~l~~~------------------------~~  255 (545)
T PTZ00110        203 GPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQIY---ALRRG------------------------VE  255 (545)
T ss_pred             CcEEEEECChHHHHHHHHHHHHHHhcccCccEEEEeCCCCHHHHHH---HHHcC------------------------CC
Confidence            4579999999999998888776542   367888999887665543   33444                        78


Q ss_pred             EEEEecCCC-CcccC-cCCCCCCcEEEE
Q 029910          102 MIVVTDACL-PLLSS-GESAISARVLIN  127 (185)
Q Consensus       102 iLV~Td~~~-~~~~~-G~d~~~v~~VI~  127 (185)
                      |+|+|+-++ -++.+ -.++..+++||.
T Consensus       256 IlVaTPgrL~d~l~~~~~~l~~v~~lVi  283 (545)
T PTZ00110        256 ILIACPGRLIDFLESNVTNLRRVTYLVL  283 (545)
T ss_pred             EEEECHHHHHHHHHcCCCChhhCcEEEe
Confidence            999996310 00333 356777887764

>cd01445 TST_Repeats Thiosulfate sulfurtransferases (TST) contain 2 copies of the Rhodanese Homology Domain

Probab=80.97  E-value=5.1  Score=30.21  Aligned_cols=51  Identities=6%  Similarity=-0.049  Sum_probs=35.7

Q ss_pred             HHHHHHHHHHHccCCCCCcEEEEcCC---hhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910            9 ETLVELLHLVVAGRRPGLPMIVCCSS---RDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus         9 ~~l~~ll~~l~~~~~~~~~~IIF~~~---~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      +.+..++.. .. -.+..++||||.+   -..+..++-.|...|.-.+..+.|+++
T Consensus        81 ~~~~~~~~~-~G-I~~~~~vVvY~~~~~~g~~A~r~~~~l~~~G~~~v~ildGG~~  134 (138)
T cd01445          81 AEFAAMFEA-KG-IDLDKHLIATDGDDLGGFTACHIALAARLCGHPDVAILDGGFF  134 (138)
T ss_pred             HHHHHHHHH-cC-CCCCCeEEEECCCCCcchHHHHHHHHHHHcCCCCeEEeCCCHH
Confidence            355556655 23 4566899999986   455667777788888656888988854

Only the second repeat contains the catalytically active Cys residue. The role of the 1st repeat is uncertain, but believed to be involved in protein interaction. This CD aligns the 1st and 2nd repeats.

>cd01525 RHOD_Kc Member of the Rhodanese Homology Domain superfamily

Probab=80.96  E-value=2.4  Score=29.60  Aligned_cols=37  Identities=8%  Similarity=0.107  Sum_probs=30.8

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      .++++++|.+...+...+..|...|+-.+..+.|+++
T Consensus        65 ~~~vv~~c~~g~~s~~~a~~L~~~G~~~v~~l~GG~~  101 (105)
T cd01525          65 GKIIVIVSHSHKHAALFAAFLVKCGVPRVCILDGGIN  101 (105)
T ss_pred             CCeEEEEeCCCccHHHHHHHHHHcCCCCEEEEeCcHH
Confidence            5789999998888888888999988545888999864

Included in this CD are the rhodanese-like domains found C-terminal of the serine/threonine protein kinases catalytic (S_TKc) domain and the Tre-2, BUB2p, Cdc16p (TBC) domain. The putative active site Cys residue is not present in this CD.

>cd01534 4RHOD_Repeat_3 Member of the Rhodanese Homology Domain superfamily, repeat 3

Probab=80.64  E-value=2.7  Score=29.03  Aligned_cols=37  Identities=16%  Similarity=0.196  Sum_probs=30.1

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      ..+++|+||.+-..+...+..|...| +.+..+.|++.
T Consensus        55 ~~~~iv~~c~~G~rs~~aa~~L~~~G-~~v~~l~GG~~   91 (95)
T cd01534          55 RGARIVLADDDGVRADMTASWLAQMG-WEVYVLEGGLA   91 (95)
T ss_pred             CCCeEEEECCCCChHHHHHHHHHHcC-CEEEEecCcHH
Confidence            35789999998777888888998888 56777888863

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 3rd repeat which does not contain the putative catalytic Cys residue.

>cd01526 RHOD_ThiF Member of the Rhodanese Homology Domain superfamily

Probab=80.41  E-value=2.7  Score=30.58  Aligned_cols=40  Identities=13%  Similarity=0.227  Sum_probs=33.1

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCCC-ceEEEEecCCCH
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLAD-ISFSSLHSDLAE   62 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~-~~~~~l~g~~~~   62 (185)
                      ...+++++||++-..+...+..|...|+ -.+..+.|++..
T Consensus        70 ~~~~~ivv~C~~G~rs~~aa~~L~~~G~~~~v~~l~GG~~~  110 (122)
T cd01526          70 DKDSPIYVVCRRGNDSQTAVRKLKELGLERFVRDIIGGLKA  110 (122)
T ss_pred             CCCCcEEEECCCCCcHHHHHHHHHHcCCccceeeecchHHH
Confidence            4568999999998888899999999984 368999998743

This CD includes several putative molybdopterin synthase sulfurylases including the molybdenum cofactor biosynthetic protein (CnxF) of Aspergillus nidulans and the molybdenum cofactor synthesis protein 3 (MOCS3) of Homo sapiens. These rhodanese-like domains are found C-terminal of the ThiF and MoeZ_MoeB domains.

>cd01522 RHOD_1 Member of the Rhodanese Homology Domain superfamily, subgroup 1

Probab=80.15  E-value=4.9  Score=29.13  Aligned_cols=40  Identities=13%  Similarity=0.176  Sum_probs=32.2

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCH
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAE   62 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~   62 (185)
                      .+.+++|+||.+-..+...+..|...|+-++..+.|++..
T Consensus        62 ~~~~~ivv~C~~G~rs~~aa~~L~~~G~~~v~~l~gG~~~  101 (117)
T cd01522          62 GKDRPVLLLCRSGNRSIAAAEAAAQAGFTNVYNVLEGFEG  101 (117)
T ss_pred             CCCCeEEEEcCCCccHHHHHHHHHHCCCCeEEECcCceec
Confidence            4568999999998888899999999985567778887643

This CD includes the putative rhodanese-related sulfurtransferases of several uncharacterized proteins.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	185
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		6e-10
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		7e-10
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		7e-10
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		7e-10
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		7e-10
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		7e-10
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		7e-08
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		7e-08
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		1e-07
1fuk_A	165	Crystal Structure Of The Carboxy Terminal Domain Of		2e-07
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		7e-07
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		9e-07
2wax_A	193	Structure Of The Human Ddx6 C-Terminal Domain In Co		3e-06

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score = 60.1 bits (144), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 37/159 (23%), Positives = 75/159 (47%), Gaps = 30/159 (18%)
Query: 29  IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 88
           ++ C+++ ++D +   +   A+ + SS+H D+ + ER  I++EFR  A            
Sbjct: 259 VIFCNTKRKVDWLTEKMRE-ANFTVSSMHGDMPQKERESIMKEFRSGA------------ 305
Query: 89  DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LA 146
                      S +++ TD    + + G       ++INY+LP  +E YI R+       
Sbjct: 306 -----------SRVLISTD----VWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYG 350
Query: 147 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
             G  IN V   ++  LR +E+     + E+P+N+++++
Sbjct: 351 RKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI 389

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 60.1 bits (144), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 36/159 (22%), Positives = 76/159 (47%), Gaps = 30/159 (18%)
Query: 29  IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 88
           ++ C+++ ++D +   +   A+ + SS+H D+ + ER  I++EFR  A            
Sbjct: 244 VIFCNTKRKVDWLTEKMRE-ANFTVSSMHGDMPQKERESIMKEFRSGA------------ 290
Query: 89  DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRM--TTCLA 146
                      S +++ TD    + + G       ++INY+LP  +E YI R+  +    
Sbjct: 291 -----------SRVLISTD----VWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYG 335
Query: 147 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
             G  +N V   ++  LR +E+     + E+P+N+++++
Sbjct: 336 RKGVAVNFVKNDDIRVLRDIEQYYSTQIDEMPMNVADLI 374

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score = 60.1 bits (144), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 37/159 (23%), Positives = 76/159 (47%), Gaps = 30/159 (18%)
Query: 29  IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 88
           ++ C+++ ++D +   +   A+ + SS+H D+ + ER  I++EFR  A            
Sbjct: 280 VIFCNTKRKVDWLTEKMRE-ANFTVSSMHGDMPQKERESIMKEFRSGA------------ 326
Query: 89  DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRM--TTCLA 146
                      S +++ TD    + + G       ++INY+LP  +E YI R+  +    
Sbjct: 327 -----------SRVLISTD----VWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYG 371
Query: 147 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
             G  IN V   ++  LR +E+     + E+P+N+++++
Sbjct: 372 RKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI 410

>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 = 60.1 bits (144), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 37/159 (23%), Positives = 76/159 (47%), Gaps = 30/159 (18%)
Query: 29  IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 88
           ++ C+++ ++D +   +   A+ + SS+H D+ + ER  I++EFR  A            
Sbjct: 281 VIFCNTKRKVDWLTEKMRE-ANFTVSSMHGDMPQKERESIMKEFRSGA------------ 327
Query: 89  DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRM--TTCLA 146
                      S +++ TD    + + G       ++INY+LP  +E YI R+  +    
Sbjct: 328 -----------SRVLISTD----VWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYG 372
Query: 147 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
             G  IN V   ++  LR +E+     + E+P+N+++++
Sbjct: 373 RKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI 411

>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 = 60.1 bits (144), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 37/159 (23%), Positives = 76/159 (47%), Gaps = 30/159 (18%)
Query: 29  IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 88
           ++ C+++ ++D +   +   A+ + SS+H D+ + ER  I++EFR  A            
Sbjct: 281 VIFCNTKRKVDWLTEKMRE-ANFTVSSMHGDMPQKERESIMKEFRSGA------------ 327
Query: 89  DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRM--TTCLA 146
                      S +++ TD    + + G       ++INY+LP  +E YI R+  +    
Sbjct: 328 -----------SRVLISTD----VWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYG 372
Query: 147 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
             G  IN V   ++  LR +E+     + E+P+N+++++
Sbjct: 373 RKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI 411

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 60.1 bits (144), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 36/159 (22%), Positives = 76/159 (47%), Gaps = 30/159 (18%)
Query: 29  IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 88
           ++ C+++ ++D +   +   A+ + SS+H D+ + ER  I++EFR  A            
Sbjct: 244 VIFCNTKRKVDWLTEKMRE-ANFTVSSMHGDMPQKERESIMKEFRSGA------------ 290
Query: 89  DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRM--TTCLA 146
                      S +++ TD    + + G       ++INY+LP  +E YI R+  +    
Sbjct: 291 -----------SRVLISTD----VWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYG 335
Query: 147 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
             G  +N V   ++  LR +E+     + E+P+N+++++
Sbjct: 336 RKGVAVNFVKNDDIRVLRDIEQYYSTQIDEMPMNVADLI 374

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score = 53.5 bits (127), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 40/159 (25%), Positives = 76/159 (47%), Gaps = 30/159 (18%)
Query: 29  IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 88
           ++  ++R ++D +   + +  D + S++H D+ + ER +I+ EFR             SG
Sbjct: 284 VIFINTRRKVDWLTEKM-HARDFTVSAMHGDMDQKERDVIMREFR-------------SG 329
Query: 89  DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAAD 148
                      S +++ TD    LL+ G       ++INY+LPT +E YI R+       
Sbjct: 330 ----------SSRVLITTD----LLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFG 375
Query: 149 GS--VINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
                IN+V   +  TLR +E      + E+P+N+++++
Sbjct: 376 RKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVADLI 414

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score = 53.5 bits (127), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 40/159 (25%), Positives = 76/159 (47%), Gaps = 30/159 (18%)
Query: 29  IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 88
           ++  ++R ++D +   + +  D + S++H D+ + ER +I+ EFR             SG
Sbjct: 258 VIFINTRRKVDWLTEKM-HARDFTVSAMHGDMDQKERDVIMREFR-------------SG 303
Query: 89  DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAAD 148
                      S +++ TD    LL+ G       ++INY+LPT +E YI R+       
Sbjct: 304 ----------SSRVLITTD----LLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFG 349
Query: 149 GS--VINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
                IN+V   +  TLR +E      + E+P+N+++++
Sbjct: 350 RKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVADLI 388

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score = 52.4 bits (124), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 41/159 (25%), Positives = 75/159 (47%), Gaps = 30/159 (18%)
Query: 29  IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 88
           ++ C++R +++ + + + N    + S+++SDL + ER  I++EFR             SG
Sbjct: 264 VIFCNTRRKVEELTTKLRN-DKFTVSAIYSDLPQQERDTIMKEFR-------------SG 309
Query: 89  DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAAD 148
                      S +++ TD    LL+ G       ++INY+LP  KE YI R+       
Sbjct: 310 ----------SSRILISTD----LLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFG 355
Query: 149 GS--VINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
                IN V   +V  +R +E+     + E+P +I+ +L
Sbjct: 356 RKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIATLL 394

>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast Eif4a Length = 165

Iteration: 1
 Score = 51.6 bits (122), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 41/159 (25%), Positives = 75/159 (47%), Gaps = 30/159 (18%)
Query: 29  IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 88
           ++ C++R +++ + + + N    + S+++SDL + ER  I++EFR             SG
Sbjct: 34  VIFCNTRRKVEELTTKLRN-DKFTVSAIYSDLPQQERDTIMKEFR-------------SG 79
Query: 89  DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAAD 148
                      S +++ TD    LL+ G       ++INY+LP  KE YI R+       
Sbjct: 80  ----------SSRILISTD----LLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFG 125
Query: 149 GS--VINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
                IN V   +V  +R +E+     + E+P +I+ +L
Sbjct: 126 RKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIATLL 164

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score = 50.1 bits (118), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 41/159 (25%), Positives = 73/159 (45%), Gaps = 30/159 (18%)
Query: 29  IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 88
           ++ C++R +++ + + + N    + S+++SDL + ER  I +EFR             SG
Sbjct: 263 VIFCNTRRKVEELTTKLRN-DKFTVSAIYSDLPQQERDTIXKEFR-------------SG 308
Query: 89  DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAAD 148
                      S +++ TD    LL+ G       ++INY+LP  KE YI R+       
Sbjct: 309 ----------SSRILISTD----LLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFG 354
Query: 149 GS--VINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
                IN V   +V   R +E+     + E+P +I+ +L
Sbjct: 355 RKGVAINFVTNEDVGAXRELEKFYSTQIEELPSDIATLL 393

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score = 49.7 bits (117), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 38/159 (23%), Positives = 67/159 (42%), Gaps = 30/159 (18%)
Query: 29  IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 88
           I+ C+S + ++ +   +++L    + S H+ + + ER  +  EFR               
Sbjct: 262 IIFCNSTNRVELLAKKITDLGYSCYYS-HARMKQQERNKVFHEFRQ-------------- 306
Query: 89  DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LA 146
                GK        V T  C  LL+ G    +  V+IN++ P   ETY+ R+       
Sbjct: 307 -----GK--------VRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFG 353
Query: 147 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
             G  IN++   +   L  +E+ LG  +A +P  I + L
Sbjct: 354 HLGLAINLINWNDRFNLYKIEQELGTEIAAIPATIDKSL 392

>pdb|2WAX|A Chain A, Structure Of The Human Ddx6 C-Terminal Domain In Complex With An Edc3-Fdf Peptide Length = 193

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 36/159 (22%), Positives = 66/159 (41%), Gaps = 30/159 (18%)
Query: 29  IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 88
           I+ C+S   ++ +   +S L    F  +H+ + +  R  +  +FR+   +          
Sbjct: 48  IIFCNSSQRVELLAKKISQLGYSCFY-IHAKMRQEHRNRVFHDFRNGLCR---------- 96
Query: 89  DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LA 146
                         +V TD    L + G    +  V+IN++ P   ETY+ R+       
Sbjct: 97  -------------NLVCTD----LFTRGIDIQAVNVVINFDFPKLAETYLHRIGRSGRFG 139
Query: 147 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
             G  IN++   +   L+S+EE LG  +  +P NI + L
Sbjct: 140 HLGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNIDKSL 178

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	185
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	2e-10
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	4e-08
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	6e-08
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	8e-08
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	3e-07
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	2e-06
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	8e-06
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	3e-05
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	9e-05
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	2e-04
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	3e-04

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19 Length = 165

 Score = 56.0 bits (136), Expect = 2e-10
 Identities = 42/164 (25%), Positives = 77/164 (46%), Gaps = 40/164 (24%)

Query: 29  IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 88
           ++ C++R +++ + + + N    + S+++SDL + ER  I++EFR             SG
Sbjct: 34  VIFCNTRRKVEELTTKLRND-KFTVSAIYSDLPQQERDTIMKEFR-------------SG 79

Query: 89  DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRM------- 141
                      S +++ TD    LL+ G       ++INY+LP  KE YI R+       
Sbjct: 80  ----------SSRILISTD----LLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFG 125

Query: 142 TTCLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
              +A     IN V   +V  +R +E+     + E+P +I+ +L
Sbjct: 126 RKGVA-----INFVTNEDVGAMRELEKFYSTQIEELPSDIATLL 164

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A* Length = 394

 Score = 51.0 bits (123), Expect = 4e-08
 Identities = 43/162 (26%), Positives = 78/162 (48%), Gaps = 34/162 (20%)

Query: 28  MIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQS 87
            ++ C++R +++ + + + N    + S+++SDL + ER  I++EFR             S
Sbjct: 262 AVIFCNTRRKVEELTTKLRND-KFTVSAIYSDLPQQERDTIMKEFR-------------S 307

Query: 88  GDESETGKDEHKSHMIVVTDACLPLLSSG--ESAISARVLINYELPTKKETYIRRM--TT 143
           G           S +++ TD    LL+ G     +S  ++INY+LP  KE YI R+    
Sbjct: 308 G----------SSRILISTD----LLARGIDVQQVS--LVINYDLPANKENYIHRIGRGG 351

Query: 144 CLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
                G  IN V   +V  +R +E+     + E+P +I+ +L
Sbjct: 352 RFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIATLL 393

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens} Length = 414

 Score = 50.3 bits (121), Expect = 6e-08
 Identities = 42/162 (25%), Positives = 78/162 (48%), Gaps = 34/162 (20%)

Query: 28  MIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQS 87
            ++  ++R ++D +   +    D + S++H D+ + ER +I+ EFR             S
Sbjct: 283 AVIFINTRRKVDWLTEKMHAR-DFTVSAMHGDMDQKERDVIMREFR-------------S 328

Query: 88  GDESETGKDEHKSHMIVVTDACLPLLSSG--ESAISARVLINYELPTKKETYIRRM--TT 143
           G           S +++ TD    LL+ G     +S  ++INY+LPT +E YI R+    
Sbjct: 329 G----------SSRVLITTD----LLARGIDVQQVS--LVINYDLPTNRENYIHRIGRGG 372

Query: 144 CLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
                G  IN+V   +  TLR +E      + E+P+N+++++
Sbjct: 373 RFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVADLI 414

>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 = 49.9 bits (120), Expect = 8e-08
 Identities = 38/162 (23%), Positives = 78/162 (48%), Gaps = 34/162 (20%)

Query: 28  MIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQS 87
            ++ C+++ ++D +   +    + + SS+H D+ + ER  I++EFR             S
Sbjct: 279 AVIFCNTKRKVDWLTEKMREA-NFTVSSMHGDMPQKERESIMKEFR-------------S 324

Query: 88  GDESETGKDEHKSHMIVVTDACLPLLSSG--ESAISARVLINYELPTKKETYIRRM--TT 143
           G           S +++ TD    + + G     +S  ++INY+LP  +E YI R+  + 
Sbjct: 325 G----------ASRVLISTD----VWARGLDVPQVS--LIINYDLPNNRELYIHRIGRSG 368

Query: 144 CLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
                G  IN V   ++  LR +E+     + E+P+N+++++
Sbjct: 369 RYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI 410

>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 = 48.3 bits (116), Expect = 3e-07
 Identities = 34/168 (20%), Positives = 65/168 (38%), Gaps = 46/168 (27%)

Query: 28  MIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQS 87
            I+ C+S + ++ +   +++L   S    H+ + + ER  +  EFR              
Sbjct: 261 AIIFCNSTNRVELLAKKITDL-GYSCYYSHARMKQQERNKVFHEFR-------------- 305

Query: 88  GDESETGKDEHKSHMIVVTDACLPLLSSGESAISAR--------VLINYELPTKKETYIR 139
                    + K   +V +D            +  R        V+IN++ P   ETY+ 
Sbjct: 306 ---------QGKVRTLVCSD------------LLTRGIDIQAVNVVINFDFPKTAETYLH 344

Query: 140 RM--TTCLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
           R+  +      G  IN++   +   L  +E+ LG  +A +P  I + L
Sbjct: 345 RIGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPATIDKSL 392

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis} Length = 163

 Score = 42.9 bits (102), Expect = 8e-06
 Identities = 29/161 (18%), Positives = 60/161 (37%), Gaps = 46/161 (28%)

Query: 28  MIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQS 87
            I+ C +++ ++ +   + +        +H  + + +R  ++ EF+              
Sbjct: 38  CIIFCRTKEHVNQLTDEL-DDLGYPCDKIHGGMIQEDRFDVMNEFK-------------- 82

Query: 88  GDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVL--------INYELPTKKETYIR 139
                      +   +V TD            ++AR +        INY+LP +KE+Y+ 
Sbjct: 83  ---------RGEYRYLVATD------------VAARGIDIENISLVINYDLPLEKESYVH 121

Query: 140 RM--TTCLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVP 178
           R   T      G  I+ V   E   L  +EE +G  + ++ 
Sbjct: 122 RTGRTGRAGNKGKAISFVTAFEKRFLADIEEYIGFEIQKIE 162

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens} Length = 175

 Score = 41.8 bits (99), Expect = 3e-05
 Identities = 31/191 (16%), Positives = 66/191 (34%), Gaps = 57/191 (29%)

Query: 9   ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI 68
           + L  +   +  G+      I+ C +R     +   +        S L  +L   +R  I
Sbjct: 23  QALCNIYGSITIGQ-----AIIFCQTRRNAKWLTVEMIQD-GHQVSLLSGELTVEQRASI 76

Query: 69  LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISAR----- 123
           ++ FR              G          K  +++ T+ C            AR     
Sbjct: 77  IQRFR-------------DG----------KEKVLITTNVC------------ARGIDVK 101

Query: 124 ---VLINYELPTKK------ETYIRRM--TTCLAADGSVINIVVGGEVVTLRSMEESLGL 172
              +++N++LP K+      ETY+ R+  T      G   N++   E+ +L  +++    
Sbjct: 102 QVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDELPSLMKIQDHFNS 161

Query: 173 IVAEVPINISE 183
            + ++     +
Sbjct: 162 SIKQLNAEDMD 172

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19 Length = 172

 Score = 40.3 bits (95), Expect = 9e-05
 Identities = 24/173 (13%), Positives = 56/173 (32%), Gaps = 57/173 (32%)

Query: 29  IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 88
           ++   S     A+   +    +    ++H  + + ER    ++F+               
Sbjct: 35  VIFVKSVQRCIALAQLLVEQ-NFPAIAIHRGMPQEERLSRYQQFK--------------- 78

Query: 89  DESETGKDEHKSHMIVVTDACLPLLSSGESAISAR--------VLINYELPTKKETYIRR 140
                   + +  ++V T+            +  R        +  NY++P   +TY+ R
Sbjct: 79  --------DFQRRILVATN------------LFGRGMDIERVNIAFNYDMPEDSDTYLHR 118

Query: 141 M-------TTCLAADGSVINIVVG-GEVVTLRSMEESLGLIVAEVPINISEIL 185
           +       T  LA     I  V    +   L  +++   + ++E+P  I    
Sbjct: 119 VARAGRFGTKGLA-----ITFVSDENDAKILNDVQDRFEVNISELPDEIDISS 166

>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 = 40.6 bits (95), Expect = 2e-04
 Identities = 26/164 (15%), Positives = 62/164 (37%), Gaps = 47/164 (28%)

Query: 28  MIVCCSSRDELDAVCSAVSNLA--DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE 85
            I+   +      +CS + N    D+     H  + + +RT +++ F+            
Sbjct: 291 AIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFK------------ 338

Query: 86  QSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVL--------INYELPTKKETY 137
                      + +S ++V TD            + AR +        +   +P++   Y
Sbjct: 339 -----------KDESGILVCTD------------VGARGMDFPNVHEVLQIGVPSELANY 375

Query: 138 IRRM-TTCLA-ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPI 179
           I R+  T  +  +GS +  +   E+  +R +E++  +++A+   
Sbjct: 376 IHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQEK 419

>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 = 39.4 bits (92), Expect = 3e-04
 Identities = 26/164 (15%), Positives = 62/164 (37%), Gaps = 47/164 (28%)

Query: 28  MIVCCSSRDELDAVCSAVSNLA--DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE 85
            I+   +      +CS + N    D+     H  + + +RT +++ F+            
Sbjct: 342 AIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFK------------ 389

Query: 86  QSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVL--------INYELPTKKETY 137
                      + +S ++V TD            + AR +        +   +P++   Y
Sbjct: 390 -----------KDESGILVCTD------------VGARGMDFPNVHEVLQIGVPSELANY 426

Query: 138 IRRM-TTCLA-ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPI 179
           I R+  T  +  +GS +  +   E+  +R +E++  +++A+   
Sbjct: 427 IHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQEK 470

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	185
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	99.97
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	99.97
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	99.97
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.97
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	99.96
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.96
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.96
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	99.95
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.94
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	99.9
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.94
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.94
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.94
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.93
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.92
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.92
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.92
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.91
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.91
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.91
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.9
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.89
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.89
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.89
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.88
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.88
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.88
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.87
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.87
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.87
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.86
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.86
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.86
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.85
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.85
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.83
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.83
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.82
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.81
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.81
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.8
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.8
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.79
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.77
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.77
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.77
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.76
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.76
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.76
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.76
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.75
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.75
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.74
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.74
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.74
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.74
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.73
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.72
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.72
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.71
3h1t_A	590	Type I site-specific restriction-modification syst	99.7
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.7
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.69
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.68
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.68
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.67
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.66
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.54
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.53
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.24
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	98.38
3hgt_A	328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	97.67
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	97.37
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	96.43
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	95.85
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	95.49
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	94.63
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	93.69
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	93.13
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	92.59
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	91.76
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	91.65
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	91.32
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	90.44
3bor_A	237	Human initiation factor 4A-II; translation initiat	90.21
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	90.14
3gk5_A	108	Uncharacterized rhodanese-related protein TVG08686	89.64
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	89.31
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	89.3
2jtq_A	85	Phage shock protein E; solution structure rhodanes	89.05
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	89.0
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	88.58
3hix_A	106	ALR3790 protein; rhodanese, rhodanese_3, Q8YQN0, Q	87.45
3foj_A	100	Uncharacterized protein; protein SSP1007, structur	87.44
3eme_A	103	Rhodanese-like domain protein; alpha-beta-alpha sa	86.86
3iwh_A	103	Rhodanese-like domain protein; alpha-beta-alpha sa	86.83
3g5j_A	134	Putative ATP/GTP binding protein; N-terminal domai	86.65
1tq1_A	129	AT5G66040, senescence-associated family protein; C	86.59
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	86.4
2lnd_A	112	De novo designed protein, PFK fold; structural gen	86.2
1wv9_A	94	Rhodanese homolog TT1651; CDC25, phosphatase, sulf	85.98
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	85.62
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	85.37
1gmx_A	108	GLPE protein; transferase, rhodanese, sulfurtransf	85.36
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	85.11
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	84.54
2l82_A	162	Designed protein OR32; structural genomics, northe	83.83
2k0z_A	110	Uncharacterized protein HP1203; A/B domain, struct	83.43
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	83.17
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	82.92
2fsx_A	148	RV0390, COG0607: rhodanese-related sulfurtransfera	82.74
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	82.73
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	82.72
3ilm_A	141	ALR3790 protein; rhodanese-like, NSR437H, NESG, st	82.68
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	82.21
3flh_A	124	Uncharacterized protein LP_1913; alpha-beta protei	82.08
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	81.1
1qxn_A	137	SUD, sulfide dehydrogenase; polysulfide-sulfur tra	80.95
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	80.75
3d1p_A	139	Putative thiosulfate sulfurtransferase YOR285W; at	80.55
3nhv_A	144	BH2092 protein; alpha-beta protein, structural gen	80.09

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=99.97  E-value=7e-30  Score=197.24  Aligned_cols=145  Identities=22%  Similarity=0.411  Sum_probs=129.9

Q ss_pred             ecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccc
Q 029910            5 FTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVT   84 (185)
Q Consensus         5 ~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~   84 (185)
                      ....+.+.+.|..++. ..++.++||||+++++++.+++.|...| +.+..+||+|++.+|.+++++|+++         
T Consensus        16 ~~~~~~K~~~L~~ll~-~~~~~~~lVF~~~~~~~~~l~~~L~~~~-~~~~~~hg~~~~~~r~~~~~~f~~g---------   84 (163)
T 2hjv_A           16 QVREENKFSLLKDVLM-TENPDSCIIFCRTKEHVNQLTDELDDLG-YPCDKIHGGMIQEDRFDVMNEFKRG---------   84 (163)
T ss_dssp             ECCGGGHHHHHHHHHH-HHCCSSEEEECSSHHHHHHHHHHHHHTT-CCEEEECTTSCHHHHHHHHHHHHTT---------
T ss_pred             ECChHHHHHHHHHHHH-hcCCCcEEEEECCHHHHHHHHHHHHHcC-CcEEEEeCCCCHHHHHHHHHHHHcC---------
Confidence            3444555666655555 3456899999999999999999999998 8999999999999999999999999         


Q ss_pred             ccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHHH
Q 029910           85 EQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVT  162 (185)
Q Consensus        85 ~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~  162 (185)
                                    ..++||+|++    +++|+|+|++++||+||+|+++..|+||+||+  .|+.|.+++|+++.+...
T Consensus        85 --------------~~~vlv~T~~----~~~Gld~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~  146 (163)
T 2hjv_A           85 --------------EYRYLVATDV----AARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAFEKRF  146 (163)
T ss_dssp             --------------SCSEEEECGG----GTTTCCCSCCSEEEESSCCSSHHHHHHHTTTSSCTTCCEEEEEEECGGGHHH
T ss_pred             --------------CCeEEEECCh----hhcCCchhcCCEEEEeCCCCCHHHHHHhccccCcCCCCceEEEEecHHHHHH
Confidence                          6999999999    99999999999999999999999999999997  456799999999999999


Q ss_pred             HHHHHHHhCCcccccc
Q 029910          163 LRSMEESLGLIVAEVP  178 (185)
Q Consensus       163 ~~~l~~~~~~~~~~~~  178 (185)
                      ++.+++.++.++++++
T Consensus       147 ~~~i~~~~~~~~~~~~  162 (163)
T 2hjv_A          147 LADIEEYIGFEIQKIE  162 (163)
T ss_dssp             HHHHHHHHTSCCEECC
T ss_pred             HHHHHHHHCCCcCccC
Confidence            9999999999988764

>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=99.97  E-value=1.3e-29  Score=197.83  Aligned_cols=147  Identities=16%  Similarity=0.297  Sum_probs=128.3

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ   86 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~   86 (185)
                      +.+.+.+.|..++. ..++.++||||+++++++.++..|...+ +.+..+||+|++.+|.+++++|++|           
T Consensus        14 ~~~~K~~~L~~ll~-~~~~~~~lVF~~~~~~~~~l~~~L~~~~-~~~~~~hg~~~~~~r~~~~~~f~~g-----------   80 (172)
T 1t5i_A           14 KDNEKNRKLFDLLD-VLEFNQVVIFVKSVQRCIALAQLLVEQN-FPAIAIHRGMPQEERLSRYQQFKDF-----------   80 (172)
T ss_dssp             CGGGHHHHHHHHHH-HSCCSSEEEECSSHHHHHHHHHHHHHTT-CCEEEECTTSCHHHHHHHHHHHHTT-----------
T ss_pred             ChHHHHHHHHHHHH-hCCCCcEEEEECCHHHHHHHHHHHHhcC-CCEEEEECCCCHHHHHHHHHHHHCC-----------
Confidence            44445555555555 4456899999999999999999999988 8999999999999999999999999           


Q ss_pred             CCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCc-hHHHH
Q 029910           87 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGG-EVVTL  163 (185)
Q Consensus        87 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~-e~~~~  163 (185)
                                  ..++||||++    +++|+|+|++++||+||+|+++..|+||+||+  .|+.|.+++|+++. +...+
T Consensus        81 ------------~~~vLvaT~~----~~~Gldi~~~~~Vi~~d~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~  144 (172)
T 1t5i_A           81 ------------QRRILVATNL----FGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKIL  144 (172)
T ss_dssp             ------------SCSEEEESSC----CSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHHHHHHH
T ss_pred             ------------CCcEEEECCc----hhcCcchhhCCEEEEECCCCCHHHHHHHhcccccCCCCcEEEEEEcChhHHHHH
Confidence                        6999999999    99999999999999999999999999999997  56789999999875 67888


Q ss_pred             HHHHHHhCCccccccCCcc
Q 029910          164 RSMEESLGLIVAEVPINIS  182 (185)
Q Consensus       164 ~~l~~~~~~~~~~~~~~~~  182 (185)
                      +.+++.++..++++|.++.
T Consensus       145 ~~l~~~~~~~~~~~~~~~~  163 (172)
T 1t5i_A          145 NDVQDRFEVNISELPDEID  163 (172)
T ss_dssp             HHHHHHHCCCEEECC----
T ss_pred             HHHHHHHhcchhhCChhhc
Confidence            9999999999999987654

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=99.97  E-value=4.3e-30  Score=198.56  Aligned_cols=146  Identities=28%  Similarity=0.480  Sum_probs=131.7

Q ss_pred             HHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCC
Q 029910           11 LVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDE   90 (185)
Q Consensus        11 l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~   90 (185)
                      +.+.|..++. ..++.++||||++++.++.++..|...+ +.+..+||+|++.+|.+++++|+++               
T Consensus        17 K~~~l~~ll~-~~~~~~~lVF~~~~~~~~~l~~~L~~~~-~~~~~~~~~~~~~~r~~~~~~f~~g---------------   79 (165)
T 1fuk_A           17 KYECLTDLYD-SISVTQAVIFCNTRRKVEELTTKLRNDK-FTVSAIYSDLPQQERDTIMKEFRSG---------------   79 (165)
T ss_dssp             HHHHHHHHHH-HTTCSCEEEEESSHHHHHHHHHHHHHTT-CCEEEECTTSCHHHHHHHHHHHHTT---------------
T ss_pred             HHHHHHHHHH-hCCCCCEEEEECCHHHHHHHHHHHHHcC-CCEEEEECCCCHHHHHHHHHHHHcC---------------
Confidence            5555555555 3456899999999999999999999988 8999999999999999999999999               


Q ss_pred             CCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCchHHHHHHHHH
Q 029910           91 SETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGGEVVTLRSMEE  168 (185)
Q Consensus        91 ~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e~~~~~~l~~  168 (185)
                              ..++||||++    +++|+|+|++++||+||+|+++.+|+||+||++  |+.|.+++|+++.+...+..+++
T Consensus        80 --------~~~vlv~T~~----~~~G~d~~~~~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~  147 (165)
T 1fuk_A           80 --------SSRILISTDL----LARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEK  147 (165)
T ss_dssp             --------SCSEEEEEGG----GTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETTTHHHHHHHHH
T ss_pred             --------CCEEEEEcCh----hhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEEcchHHHHHHHHHH
Confidence                    6999999999    999999999999999999999999999999974  56799999999999999999999


Q ss_pred             HhCCccccccCCccccC
Q 029910          169 SLGLIVAEVPINISEIL  185 (185)
Q Consensus       169 ~~~~~~~~~~~~~~~~l  185 (185)
                      .++..++++|.++.+++
T Consensus       148 ~~~~~~~~~~~~~~~~~  164 (165)
T 1fuk_A          148 FYSTQIEELPSDIATLL  164 (165)
T ss_dssp             HSSCCCEECCSCCTTTT
T ss_pred             HHccCccccCccHHhhc
Confidence            99999999999988764

>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=99.97  E-value=3e-29  Score=195.52  Aligned_cols=146  Identities=17%  Similarity=0.315  Sum_probs=131.9

Q ss_pred             HHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCC
Q 029910            9 ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG   88 (185)
Q Consensus         9 ~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~   88 (185)
                      +.+.+.|..++. ..+..++||||+++++++.++..|...+ +.+..+||+|++.+|.+++++|++|             
T Consensus        19 ~~K~~~L~~ll~-~~~~~~~lVF~~~~~~~~~l~~~L~~~~-~~~~~~~g~~~~~~R~~~~~~f~~g-------------   83 (175)
T 2rb4_A           19 KDKYQALCNIYG-SITIGQAIIFCQTRRNAKWLTVEMIQDG-HQVSLLSGELTVEQRASIIQRFRDG-------------   83 (175)
T ss_dssp             HHHHHHHHHHHT-TSCCSEEEEECSCHHHHHHHHHHHHTTT-CCEEEECSSCCHHHHHHHHHHHHTT-------------
T ss_pred             HhHHHHHHHHHH-hCCCCCEEEEECCHHHHHHHHHHHHHcC-CcEEEEeCCCCHHHHHHHHHHHHcC-------------
Confidence            436677776676 5567899999999999999999999998 8999999999999999999999999             


Q ss_pred             CCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCC------CCHHHHHHHHhhh--cCCCCEEEEEeeCchH
Q 029910           89 DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELP------TKKETYIRRMTTC--LAADGSVINIVVGGEV  160 (185)
Q Consensus        89 ~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P------~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~  160 (185)
                                ..++||||++    +++|+|+|++++||+||+|      .+..+|+||+||+  .|+.|.+++|+.+.+.
T Consensus        84 ----------~~~vLvaT~~----~~~Gid~~~~~~Vi~~d~p~~~~~~~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~~  149 (175)
T 2rb4_A           84 ----------KEKVLITTNV----CARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDEL  149 (175)
T ss_dssp             ----------SCSEEEECCS----CCTTTCCTTEEEEEESSCCC--CCSCCHHHHHHHHCBC----CCEEEEEEECGGGH
T ss_pred             ----------CCeEEEEecc----hhcCCCcccCCEEEEeCCCCCccccCCHHHHHHHhcccccCCCCceEEEEEccchH
Confidence                      6999999999    9999999999999999999      8999999999997  4577999999999999


Q ss_pred             HHHHHHHHHhCCccccccCCccc
Q 029910          161 VTLRSMEESLGLIVAEVPINISE  183 (185)
Q Consensus       161 ~~~~~l~~~~~~~~~~~~~~~~~  183 (185)
                      ..+..+++.++..+++++.+-.+
T Consensus       150 ~~~~~i~~~~~~~~~~~~~~~~~  172 (175)
T 2rb4_A          150 PSLMKIQDHFNSSIKQLNAEDMD  172 (175)
T ss_dssp             HHHHHHHHHHTCCCEEECSSCCC
T ss_pred             HHHHHHHHHhcCcccccCCchhc
Confidence            99999999999999998876443

>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=99.96  E-value=8.7e-29  Score=199.27  Aligned_cols=146  Identities=21%  Similarity=0.294  Sum_probs=128.6

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ   86 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~   86 (185)
                      ..+.+++.|..++. ..++.++||||++++.++.+++.|...+ +.+..+||+|++.+|.+++++|++|           
T Consensus        14 ~~~~k~~~l~~ll~-~~~~~~~lVF~~~~~~~~~l~~~L~~~~-~~~~~lhg~~~~~~r~~~~~~f~~g-----------   80 (212)
T 3eaq_A           14 PVRGRLEVLSDLLY-VASPDRAMVFTRTKAETEEIAQGLLRLG-HPAQALHGDLSQGERERVLGAFRQG-----------   80 (212)
T ss_dssp             CTTSHHHHHHHHHH-HHCCSCEEEECSSHHHHHHHHHHHHHHT-CCEEEECSSSCHHHHHHHHHHHHSS-----------
T ss_pred             CHHHHHHHHHHHHH-hCCCCeEEEEeCCHHHHHHHHHHHHHcC-CCEEEEECCCCHHHHHHHHHHHHCC-----------
Confidence            33444555555454 3446899999999999999999999988 8999999999999999999999999           


Q ss_pred             CCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCchHHHHH
Q 029910           87 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGGEVVTLR  164 (185)
Q Consensus        87 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e~~~~~  164 (185)
                                  ..++||||++    +++|+|+|++++|||||+|+++..|+||+||++  |++|.++.|+++.+...++
T Consensus        81 ------------~~~vlvaT~~----~~~Gidi~~v~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~l~~~~~~~~~~  144 (212)
T 3eaq_A           81 ------------EVRVLVATDV----AARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVE  144 (212)
T ss_dssp             ------------SCCEEEECTT----TTCSSSCCCBSEEEESSCCSSHHHHHHHHTTBCCCC--BEEEEEECGGGHHHHH
T ss_pred             ------------CCeEEEecCh----hhcCCCCccCcEEEECCCCcCHHHHHHHhcccCCCCCCCeEEEEEchhHHHHHH
Confidence                        6999999999    999999999999999999999999999999975  4679999999999999999


Q ss_pred             HHHHHhCCccccccCCc
Q 029910          165 SMEESLGLIVAEVPINI  181 (185)
Q Consensus       165 ~l~~~~~~~~~~~~~~~  181 (185)
                      .+++.++..+++++.+.
T Consensus       145 ~i~~~~~~~~~~~~~~~  161 (212)
T 3eaq_A          145 ALERAVGRRFKRVNPPT  161 (212)
T ss_dssp             HHHHHHSSCCEECCCCC
T ss_pred             HHHHHhcCcCeecCCCC
Confidence            99999999998877553

>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=99.96  E-value=2.5e-29  Score=198.73  Aligned_cols=151  Identities=18%  Similarity=0.272  Sum_probs=116.9

Q ss_pred             ecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccc
Q 029910            5 FTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVT   84 (185)
Q Consensus         5 ~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~   84 (185)
                      +.....+.+.|..++....++.++||||++++.++.++..|...| +.+..+||+|++.+|.+++++|++|         
T Consensus        26 ~v~~~~K~~~L~~ll~~~~~~~k~lVF~~~~~~~~~l~~~L~~~g-~~~~~lhg~~~~~~r~~~~~~f~~g---------   95 (185)
T 2jgn_A           26 WVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEG-YACTSIHGDRSQRDREEALHQFRSG---------   95 (185)
T ss_dssp             ECCGGGHHHHHHHHHHHC-CCSCEEEEESCHHHHHHHHHHHHHTT-CCEEEEC--------CHHHHHHHHT---------
T ss_pred             EeCcHHHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHcC-CceEEEeCCCCHHHHHHHHHHHHcC---------
Confidence            334444445454445434467899999999999999999999988 8999999999999999999999999         


Q ss_pred             ccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHHH
Q 029910           85 EQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVT  162 (185)
Q Consensus        85 ~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~  162 (185)
                                    ..++||||++    +++|+|+|++++||+||+|+++.+|+||+||+  .|+.|.+++|+++.+...
T Consensus        96 --------------~~~vLvaT~~----~~~Gldi~~~~~VI~~d~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~  157 (185)
T 2jgn_A           96 --------------KSPILVATAV----AARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINI  157 (185)
T ss_dssp             --------------SSSEEEEEC----------CCCSBSEEEESSCCSSHHHHHHHHTTBCCTTSCEEEEEEECGGGGGG
T ss_pred             --------------CCeEEEEcCh----hhcCCCcccCCEEEEeCCCCCHHHHHHHccccCCCCCCcEEEEEEchhhHHH
Confidence                          6999999999    99999999999999999999999999999997  456799999999999999


Q ss_pred             HHHHHHHhCCccccccCCccc
Q 029910          163 LRSMEESLGLIVAEVPINISE  183 (185)
Q Consensus       163 ~~~l~~~~~~~~~~~~~~~~~  183 (185)
                      ++.+++.++...+++|..+.+
T Consensus       158 ~~~l~~~l~~~~~~~~~~l~~  178 (185)
T 2jgn_A          158 TKDLLDLLVEAKQEVPSWLEN  178 (185)
T ss_dssp             HHHHHHHHHHTTCCCCHHHHH
T ss_pred             HHHHHHHHHhccCCCCHHHHH
Confidence            999999998887887765543

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=99.96  E-value=1.4e-28  Score=195.59  Aligned_cols=150  Identities=20%  Similarity=0.324  Sum_probs=128.2

Q ss_pred             EecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccc
Q 029910            4 SFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKV   83 (185)
Q Consensus         4 ~~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~   83 (185)
                      .+...+.+.+.|..++. . .+.++||||++++.++.++..|...+ +.+..+||+|++.+|.+++++|+++        
T Consensus        35 ~~~~~~~K~~~L~~~l~-~-~~~~~lVF~~~~~~~~~l~~~L~~~g-~~~~~lhg~~~~~~R~~~l~~F~~g--------  103 (191)
T 2p6n_A           35 EYVKEEAKMVYLLECLQ-K-TPPPVLIFAEKKADVDAIHEYLLLKG-VEAVAIHGGKDQEERTKAIEAFREG--------  103 (191)
T ss_dssp             EECCGGGHHHHHHHHHT-T-SCSCEEEECSCHHHHHHHHHHHHHHT-CCEEEECTTSCHHHHHHHHHHHHHT--------
T ss_pred             EEcChHHHHHHHHHHHH-h-CCCCEEEEECCHHHHHHHHHHHHHcC-CcEEEEeCCCCHHHHHHHHHHHhcC--------
Confidence            44555556666665565 2 24689999999999999999999888 8999999999999999999999999        


Q ss_pred             cccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCc-hH
Q 029910           84 TEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGG-EV  160 (185)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~-e~  160 (185)
                                     ..++||||++    +++|+|+|++++||+||+|+++++|+||+||+  .|+.|.+++|+++. +.
T Consensus       104 ---------------~~~vLvaT~~----~~~Gldi~~v~~VI~~d~p~~~~~~~qr~GR~gR~g~~g~~i~l~~~~~~~  164 (191)
T 2p6n_A          104 ---------------KKDVLVATDV----ASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDE  164 (191)
T ss_dssp             ---------------SCSEEEECHH----HHTTCCCCCCSEEEESSCCSSHHHHHHHHTTSCC---CCEEEEEECTTSCH
T ss_pred             ---------------CCEEEEEcCc----hhcCCCcccCCEEEEeCCCCCHHHHHHHhCccccCCCCcEEEEEEcCchhH
Confidence                           6999999999    99999999999999999999999999999997  45679999999875 77


Q ss_pred             HHHHHHHHHhCCccccccCCccc
Q 029910          161 VTLRSMEESLGLIVAEVPINISE  183 (185)
Q Consensus       161 ~~~~~l~~~~~~~~~~~~~~~~~  183 (185)
                      ..++.+++.++....++|..+.+
T Consensus       165 ~~~~~l~~~l~~~~~~~p~~l~~  187 (191)
T 2p6n_A          165 SVLMDLKALLLEAKQKVPPVLQV  187 (191)
T ss_dssp             HHHHHHHHHHHHTTCCCCHHHHS
T ss_pred             HHHHHHHHHHHHccCcCCHHHHh
Confidence            88899999888777777765544

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=99.95  E-value=1.5e-27  Score=202.31  Aligned_cols=147  Identities=18%  Similarity=0.285  Sum_probs=128.9

Q ss_pred             cchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccc
Q 029910            6 TFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE   85 (185)
Q Consensus         6 ~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~   85 (185)
                      ...+.+++.|..++. ...+.++||||++++.++.+++.|...+ +.+..+||+|++.+|.++++.|++|          
T Consensus        10 ~~~~~K~~~L~~ll~-~~~~~~~LVF~~t~~~~~~l~~~L~~~g-~~~~~lhg~l~~~~r~~~~~~f~~g----------   77 (300)
T 3i32_A           10 APVRGRLEVLSDLLY-VASPDRAMVFTRTKAETEEIAQGLLRLG-HPAQALHGDMSQGERERVMGAFRQG----------   77 (300)
T ss_dssp             CCSSSHHHHHHHHHH-HHCCSSEEEECSSHHHHHHHHHHHHTTT-CCEEEECSCCCTHHHHHHHHHHHHT----------
T ss_pred             CCHHHHHHHHHHHHH-hcCCCCEEEEECCHHHHHHHHHHHHhCC-CCEEEEeCCCCHHHHHHHHHHhhcC----------
Confidence            344445555555554 3336899999999999999999999988 8999999999999999999999999          


Q ss_pred             cCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCchHHHH
Q 029910           86 QSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGGEVVTL  163 (185)
Q Consensus        86 ~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e~~~~  163 (185)
                                   ..++||||++    +++|+|+|++++|||||+|++.+.|+||+||++  |++|.|+.|+++.+...+
T Consensus        78 -------------~~~vLVaT~v----a~~Gidi~~v~~VI~~d~p~s~~~y~Qr~GRagR~g~~G~~i~l~~~~e~~~~  140 (300)
T 3i32_A           78 -------------EVRVLVATDV----AARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDV  140 (300)
T ss_dssp             -------------SCCEEEECST----TTCSTTCCCCSEEEESSCCSSTTHHHHHHTCCC-----CEEEEEECSSTHHHH
T ss_pred             -------------CceEEEEech----hhcCccccceeEEEEcCCCCCHHHHHHHccCcCcCCCCceEEEEeChHHHHHH
Confidence                         7999999999    999999999999999999999999999999975  467999999999999999


Q ss_pred             HHHHHHhCCccccccCCc
Q 029910          164 RSMEESLGLIVAEVPINI  181 (185)
Q Consensus       164 ~~l~~~~~~~~~~~~~~~  181 (185)
                      +.+++.++..+++++.+.
T Consensus       141 ~~ie~~~~~~~~~~~~~~  158 (300)
T 3i32_A          141 EALERAVGRRFKRVNPPT  158 (300)
T ss_dssp             HHHHHHHTCCCEECCCCC
T ss_pred             HHHHHHhCCcceEeCCCC
Confidence            999999999998877653

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=99.94  E-value=1.3e-26  Score=199.66  Aligned_cols=134  Identities=26%  Similarity=0.547  Sum_probs=127.3

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEE
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMI  103 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iL  103 (185)
                      ...++||||++++.++.+++.|...+ +.+..+||++++.+|.+++++|++|                       ..++|
T Consensus       275 ~~~~~lVf~~~~~~~~~l~~~L~~~~-~~~~~~h~~~~~~~r~~~~~~f~~g-----------------------~~~vl  330 (410)
T 2j0s_A          275 TITQAVIFCNTKRKVDWLTEKMREAN-FTVSSMHGDMPQKERESIMKEFRSG-----------------------ASRVL  330 (410)
T ss_dssp             TSSEEEEECSSHHHHHHHHHHHHHTT-CCCEEECTTSCHHHHHHHHHHHHHT-----------------------SSCEE
T ss_pred             CCCcEEEEEcCHHHHHHHHHHHHhCC-CceEEeeCCCCHHHHHHHHHHHHCC-----------------------CCCEE
Confidence            34699999999999999999999998 8999999999999999999999999                       69999


Q ss_pred             EEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHHHHHHHHHHhCCccccccCCc
Q 029910          104 VVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINI  181 (185)
Q Consensus       104 V~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~~~~l~~~~~~~~~~~~~~~  181 (185)
                      |+|++    +++|+|+|++++||+||+|+++..|+||+||+  .|+.|.+++|++..+...++.++++++..++++|.++
T Consensus       331 v~T~~----~~~Gidi~~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~  406 (410)
T 2j0s_A          331 ISTDV----WARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNV  406 (410)
T ss_dssp             EECGG----GSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGGGHHHHHHHHHHTTCCCEECCSCC
T ss_pred             EECCh----hhCcCCcccCCEEEEECCCCCHHHHHHhcccccCCCCceEEEEEecHHHHHHHHHHHHHhCCCceecccch
Confidence            99999    99999999999999999999999999999997  4678999999999999999999999999999999998


Q ss_pred             cccC
Q 029910          182 SEIL  185 (185)
Q Consensus       182 ~~~l  185 (185)
                      .++|
T Consensus       407 ~~~~  410 (410)
T 2j0s_A          407 ADLI  410 (410)
T ss_dssp             TTTC
T ss_pred             hhcC
Confidence            8765

>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=99.90  E-value=4.3e-29  Score=194.01  Aligned_cols=143  Identities=16%  Similarity=0.296  Sum_probs=128.3

Q ss_pred             HHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCC
Q 029910            9 ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG   88 (185)
Q Consensus         9 ~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~   88 (185)
                      +.+.++|..++. ...+.++||||+++++++.++..|...+ +.+..+||+|++.+|.+++++|++|             
T Consensus        15 ~~k~~~l~~ll~-~~~~~~~iVF~~~~~~~~~l~~~L~~~~-~~~~~~~g~~~~~~r~~~~~~f~~g-------------   79 (170)
T 2yjt_D           15 EHKTALLVHLLK-QPEATRSIVFVRKRERVHELANWLREAG-INNCYLEGEMVQGKRNEAIKRLTEG-------------   79 (170)
Confidence            455666666565 4556899999999999999999999987 8999999999999999999999999             


Q ss_pred             CCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHHHHHHH
Q 029910           89 DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLRSM  166 (185)
Q Consensus        89 ~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~~~~l  166 (185)
                                ..++||||++    +++|+|+|++++||+||+|+++..|+||+||+  .|+.|.+++++...+...++.+
T Consensus        80 ----------~~~vLvaT~~----~~~Gid~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~  145 (170)
T 2yjt_D           80 ----------RVNVLVATDV----AARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHDHLLLGKV  145 (170)
Confidence                      6999999999    99999999999999999999999999999997  4567999999999999999999


Q ss_pred             HHHhCCccccccCC
Q 029910          167 EESLGLIVAEVPIN  180 (185)
Q Consensus       167 ~~~~~~~~~~~~~~  180 (185)
                      ++.++..+++.+++
T Consensus       146 ~~~~~~~~~~~~~~  159 (170)
T 2yjt_D          146 GRYIEEPIKARVID  159 (170)
Confidence            99998888766543

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=99.94  E-value=3.6e-26  Score=200.93  Aligned_cols=131  Identities=19%  Similarity=0.301  Sum_probs=120.2

Q ss_pred             CcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEEE
Q 029910           26 LPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVV  105 (185)
Q Consensus        26 ~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~  105 (185)
                      .++||||++++.++.+++.|...+ +.+..+||++++.+|.+++++|++|                       ..+||||
T Consensus       301 ~~~lVF~~t~~~a~~l~~~L~~~~-~~~~~lhg~~~~~~R~~~l~~F~~g-----------------------~~~vLva  356 (434)
T 2db3_A          301 DGTIVFVETKRGADFLASFLSEKE-FPTTSIHGDRLQSQREQALRDFKNG-----------------------SMKVLIA  356 (434)
T ss_dssp             TTEEEECSSHHHHHHHHHHHHHTT-CCEEEESTTSCHHHHHHHHHHHHTS-----------------------SCSEEEE
T ss_pred             CCEEEEEeCcHHHHHHHHHHHhCC-CCEEEEeCCCCHHHHHHHHHHHHcC-----------------------CCcEEEE
Confidence            359999999999999999999998 8999999999999999999999999                       6999999


Q ss_pred             ecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeC-chHHHHHHHHHHhCCccccccCCcc
Q 029910          106 TDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVG-GEVVTLRSMEESLGLIVAEVPINIS  182 (185)
Q Consensus       106 Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~-~e~~~~~~l~~~~~~~~~~~~~~~~  182 (185)
                      |++    ++||+|+|++++|||||+|.+.++|+||+||+  .|+.|.+++|+++ .+......+.+.+....+++|..+.
T Consensus       357 T~v----~~rGlDi~~v~~VI~~d~p~~~~~y~qriGR~gR~g~~G~a~~~~~~~~~~~~~~~l~~~l~~~~~~vp~~l~  432 (434)
T 2db3_A          357 TSV----ASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAIAADLVKILEGSGQTVPDFLR  432 (434)
T ss_dssp             CGG----GTSSCCCTTCCEEEESSCCSSHHHHHHHHTTSSCTTCCEEEEEEECTTTCGGGHHHHHHHHHHTTCCCCGGGC
T ss_pred             chh----hhCCCCcccCCEEEEECCCCCHHHHHHHhcccccCCCCCEEEEEEeccccHHHHHHHHHHHHHcCCCCCHHHH
Confidence            999    99999999999999999999999999999997  4678999999985 5777888999999888899998876


Q ss_pred             cc
Q 029910          183 EI  184 (185)
Q Consensus       183 ~~  184 (185)
                      ++
T Consensus       433 ~~  434 (434)
T 2db3_A          433 TC  434 (434)
T ss_dssp             --
T ss_pred             hC
Confidence            54

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=99.94  E-value=9.2e-26  Score=193.52  Aligned_cols=148  Identities=24%  Similarity=0.429  Sum_probs=132.9

Q ss_pred             hHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccC
Q 029910            8 QETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQS   87 (185)
Q Consensus         8 ~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~   87 (185)
                      ...+...+..++. .....++||||++++.++.+++.|...+ +.+..+||+++..+|.+++++|+++            
T Consensus       242 ~~~k~~~l~~~~~-~~~~~~~lVf~~~~~~~~~l~~~L~~~~-~~~~~~~~~~~~~~r~~~~~~f~~g------------  307 (400)
T 1s2m_A          242 ERQKLHCLNTLFS-KLQINQAIIFCNSTNRVELLAKKITDLG-YSCYYSHARMKQQERNKVFHEFRQG------------  307 (400)
T ss_dssp             GGGHHHHHHHHHH-HSCCSEEEEECSSHHHHHHHHHHHHHHT-CCEEEECTTSCHHHHHHHHHHHHTT------------
T ss_pred             hhhHHHHHHHHHh-hcCCCcEEEEEecHHHHHHHHHHHHhcC-CCeEEecCCCCHHHHHHHHHHHhcC------------
Confidence            3344455555454 3456899999999999999999999988 8999999999999999999999999            


Q ss_pred             CCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCchHHHHHH
Q 029910           88 GDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGGEVVTLRS  165 (185)
Q Consensus        88 ~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e~~~~~~  165 (185)
                                 ..++||+|++    +++|+|+|++++||+||+|+++..|+||+||++  |+.|.|+.+++..+...++.
T Consensus       308 -----------~~~vLv~T~~----~~~Gidip~~~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~l~~~~~~~~~~~  372 (400)
T 1s2m_A          308 -----------KVRTLVCSDL----LTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYK  372 (400)
T ss_dssp             -----------SSSEEEESSC----SSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGGGHHHHHH
T ss_pred             -----------CCcEEEEcCc----cccCCCccCCCEEEEeCCCCCHHHHHHhcchhcCCCCCceEEEEeccchHHHHHH
Confidence                       6999999999    999999999999999999999999999999974  56799999999999999999


Q ss_pred             HHHHhCCccccccCCcccc
Q 029910          166 MEESLGLIVAEVPINISEI  184 (185)
Q Consensus       166 l~~~~~~~~~~~~~~~~~~  184 (185)
                      +++.++.+++++|.++.+.
T Consensus       373 i~~~~~~~~~~~~~~~~~~  391 (400)
T 1s2m_A          373 IEQELGTEIAAIPATIDKS  391 (400)
T ss_dssp             HHHHHTCCCEECCSSCCGG
T ss_pred             HHHHhCCCccccccccccc
Confidence            9999999999999887764

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=99.94  E-value=2.5e-26  Score=197.32  Aligned_cols=148  Identities=26%  Similarity=0.465  Sum_probs=119.3

Q ss_pred             HHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCC
Q 029910            9 ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG   88 (185)
Q Consensus         9 ~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~   88 (185)
                      +...+.+..++. .....++||||++++.++.+++.|...+ +.+..+||+++..+|.+++++|++|             
T Consensus       265 ~~~~~~l~~~~~-~~~~~~~lvf~~~~~~~~~l~~~l~~~~-~~~~~~h~~~~~~~r~~~~~~f~~g-------------  329 (414)
T 3eiq_A          265 EWKLDTLCDLYE-TLTITQAVIFINTRRKVDWLTEKMHARD-FTVSAMHGDMDQKERDVIMREFRSG-------------  329 (414)
T ss_dssp             TTHHHHHHHHHH-SSCCSSCEEECSCHHHHHHHHHHHHTTT-CCCEEC---CHHHHHHHHHHHHSCC-------------
T ss_pred             HhHHHHHHHHHH-hCCCCcEEEEeCCHHHHHHHHHHHHhcC-CeEEEecCCCCHHHHHHHHHHHHcC-------------
Confidence            334555555555 4566899999999999999999999998 8999999999999999999999999             


Q ss_pred             CCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCchHHHHHHH
Q 029910           89 DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGGEVVTLRSM  166 (185)
Q Consensus        89 ~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e~~~~~~l  166 (185)
                                ..++||||++    +++|+|+|++++||+||+|+++..|+||+||++  |+.|.|+.|+++.+...++.+
T Consensus       330 ----------~~~vlv~T~~----~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~  395 (414)
T 3eiq_A          330 ----------SSRVLITTDL----LARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDI  395 (414)
T ss_dssp             -------------CEEECSS----CC--CCGGGCSCEEESSCCSSTHHHHHHSCCC-------CEEEEECSTHHHHHHHH
T ss_pred             ----------CCcEEEECCc----cccCCCccCCCEEEEeCCCCCHHHhhhhcCcccCCCCCceEEEEEcHHHHHHHHHH
Confidence                      6999999999    999999999999999999999999999999974  567999999999999999999


Q ss_pred             HHHhCCccccccCCccccC
Q 029910          167 EESLGLIVAEVPINISEIL  185 (185)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~l  185 (185)
                      ++.++..++++|.++.++|
T Consensus       396 ~~~~~~~~~~~~~~~~~l~  414 (414)
T 3eiq_A          396 ETFYNTSIEEMPLNVADLI  414 (414)
T ss_dssp             HHHTTCCCEECCC------
T ss_pred             HHHHcCCccccChhhhhcC
Confidence            9999999999999998875

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=99.93  E-value=1.2e-25  Score=193.49  Aligned_cols=149  Identities=18%  Similarity=0.252  Sum_probs=129.2

Q ss_pred             cchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccc
Q 029910            6 TFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE   85 (185)
Q Consensus         6 ~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~   85 (185)
                      ...+...+.+..++.....+.++||||++++.++.+++.|...+ +.+..+||+++..+|.+++++|++|          
T Consensus       257 ~~~~~~~~~l~~~l~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~-~~~~~~h~~~~~~~r~~~~~~f~~g----------  325 (417)
T 2i4i_A          257 VEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEG-YACTSIHGDRSQRDREEALHQFRSG----------  325 (417)
T ss_dssp             CCGGGHHHHHHHHHHTCCTTCEEEEECSSHHHHHHHHHHHHHTT-CCEEEECTTSCHHHHHHHHHHHHHT----------
T ss_pred             eccHhHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHCC-CCeeEecCCCCHHHHHHHHHHHHcC----------
Confidence            33444455555555535567899999999999999999999988 8999999999999999999999999          


Q ss_pred             cCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCchHHHH
Q 029910           86 QSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGGEVVTL  163 (185)
Q Consensus        86 ~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e~~~~  163 (185)
                                   ..++||||++    +++|+|+|++++||+||+|+++..|+||+||++  |+.|.++.|+++.+...+
T Consensus       326 -------------~~~vlvaT~~----~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~  388 (417)
T 2i4i_A          326 -------------KSPILVATAV----AARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINIT  388 (417)
T ss_dssp             -------------SSCEEEECHH----HHTTSCCCCEEEEEESSCCSSHHHHHHHHTTBCC--CCEEEEEEECGGGGGGH
T ss_pred             -------------CCCEEEECCh----hhcCCCcccCCEEEEEcCCCCHHHHHHhcCccccCCCCceEEEEEccccHHHH
Confidence                         6999999999    999999999999999999999999999999974  567999999999999999


Q ss_pred             HHHHHHhCCccccccCCcc
Q 029910          164 RSMEESLGLIVAEVPINIS  182 (185)
Q Consensus       164 ~~l~~~~~~~~~~~~~~~~  182 (185)
                      ..+.+.+.....++|..+.
T Consensus       389 ~~l~~~~~~~~~~~~~~l~  407 (417)
T 2i4i_A          389 KDLLDLLVEAKQEVPSWLE  407 (417)
T ss_dssp             HHHHHHHHHTTCCCCHHHH
T ss_pred             HHHHHHHHHhcCcCCHHHH
Confidence            9999988777777665544

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=99.92  E-value=2.1e-24  Score=183.93  Aligned_cols=142  Identities=16%  Similarity=0.301  Sum_probs=125.8

Q ss_pred             HHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCC
Q 029910           12 VELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDES   91 (185)
Q Consensus        12 ~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~   91 (185)
                      ...+..++. ...+.++||||++++.++.+++.|...+ +.+..+||+++..+|.+++++|+++                
T Consensus       238 ~~~l~~~l~-~~~~~~~lvf~~~~~~~~~l~~~L~~~~-~~~~~~~~~~~~~~r~~~~~~f~~~----------------  299 (391)
T 1xti_A          238 NRKLFDLLD-VLEFNQVVIFVKSVQRCIALAQLLVEQN-FPAIAIHRGMPQEERLSRYQQFKDF----------------  299 (391)
T ss_dssp             HHHHHHHHH-HSCCSEEEEECSCHHHHHHHHHHHHHTT-CCEEEECTTSCHHHHHHHHHHHHTT----------------
T ss_pred             HHHHHHHHH-hcCCCcEEEEeCcHHHHHHHHHHHHhCC-CcEEEEeCCCCHHHHHHHHHHHhcC----------------
Confidence            333333344 3466899999999999999999999998 8999999999999999999999999                


Q ss_pred             CCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCc-hHHHHHHHHH
Q 029910           92 ETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGG-EVVTLRSMEE  168 (185)
Q Consensus        92 ~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~-e~~~~~~l~~  168 (185)
                             ..++||+|++    +++|+|+|++++||+||+|+++..|+||+||++  |+.|.++.++++. +...++.+++
T Consensus       300 -------~~~vlv~T~~----~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~  368 (391)
T 1xti_A          300 -------QRRILVATNL----FGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQD  368 (391)
T ss_dssp             -------CCSEEEESCC----CSSCBCCTTEEEEEESSCCSSHHHHHHHHCBCSSSCCCCEEEEEECSHHHHHHHHHHHH
T ss_pred             -------CCcEEEECCh----hhcCCCcccCCEEEEeCCCCCHHHHHHhcccccCCCCceEEEEEEcccchHHHHHHHHH
Confidence                   6999999999    999999999999999999999999999999974  5779999999876 5677899999


Q ss_pred             HhCCccccccCCcc
Q 029910          169 SLGLIVAEVPINIS  182 (185)
Q Consensus       169 ~~~~~~~~~~~~~~  182 (185)
                      .++..++++|.++.
T Consensus       369 ~~~~~~~~~~~~~~  382 (391)
T 1xti_A          369 RFEVNISELPDEID  382 (391)
T ss_dssp             HTTCCCEECCSCCC
T ss_pred             HhcCChhhCCcccc
Confidence            99999999997643

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=99.92  E-value=1.9e-24  Score=185.18  Aligned_cols=144  Identities=19%  Similarity=0.331  Sum_probs=123.7

Q ss_pred             HHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCC
Q 029910            9 ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG   88 (185)
Q Consensus         9 ~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~   88 (185)
                      +.+...+..++. ...+.++||||++++.++.++..|...+ +.+..+||+|+..+|.+++++|++|             
T Consensus       251 ~~~~~~l~~~~~-~~~~~~~lvf~~~~~~~~~l~~~L~~~~-~~~~~~~~~~~~~~r~~~~~~f~~g-------------  315 (412)
T 3fht_A          251 DEKFQALCNLYG-AITIAQAMIFCHTRKTASWLAAELSKEG-HQVALLSGEMMVEQRAAVIERFREG-------------  315 (412)
T ss_dssp             HHHHHHHHHHHH-HHSSSEEEEECSSHHHHHHHHHHHHHTT-CCCEEECTTSCHHHHHHHHHHHHTT-------------
T ss_pred             HHHHHHHHHHHh-hcCCCCEEEEeCCHHHHHHHHHHHHhCC-CeEEEecCCCCHHHHHHHHHHHHCC-------------
Confidence            344444444444 3445799999999999999999999998 8999999999999999999999999             


Q ss_pred             CCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCC------CHHHHHHHHhhhc--CCCCEEEEEeeCc-h
Q 029910           89 DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPT------KKETYIRRMTTCL--AADGSVINIVVGG-E  159 (185)
Q Consensus        89 ~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~------~~~~yiqR~GR~~--~~~g~~i~~v~~~-e  159 (185)
                                ..++||||++    +++|+|+|++++||+||+|+      +...|+||+||++  |+.|.++.++.+. +
T Consensus       316 ----------~~~vlv~T~~----~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~  381 (412)
T 3fht_A          316 ----------KEKVLVTTNV----CARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHS  381 (412)
T ss_dssp             ----------SCSEEEECGG----GTSSCCCTTEEEEEESSCCBCSSSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHHH
T ss_pred             ----------CCcEEEEcCc----cccCCCccCCCEEEEECCCCCCCCCcchheeecccCcccCCCCCceEEEEEcChhh
Confidence                      6999999999    99999999999999999994      6799999999974  5679999999876 4


Q ss_pred             HHHHHHHHHHhCCccccccCCc
Q 029910          160 VVTLRSMEESLGLIVAEVPINI  181 (185)
Q Consensus       160 ~~~~~~l~~~~~~~~~~~~~~~  181 (185)
                      ...++.+++.++..+++++.+.
T Consensus       382 ~~~~~~i~~~~~~~~~~~~~~~  403 (412)
T 3fht_A          382 MNILNRIQEHFNKKIERLDTDD  403 (412)
T ss_dssp             HHHHHHHHHHHTCCCEEC----
T ss_pred             HHHHHHHHHHHCCccccCCCcc
Confidence            8899999999999999887654

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=99.92  E-value=1e-23  Score=177.46  Aligned_cols=139  Identities=22%  Similarity=0.442  Sum_probs=125.1

Q ss_pred             HHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCC
Q 029910           11 LVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDE   90 (185)
Q Consensus        11 l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~   90 (185)
                      ..+.+..++.  ..+.++||||++++.++.+++.|...+ +.+..+||+++..+|.+++++|+++               
T Consensus       226 ~~~~l~~~l~--~~~~~~lvf~~~~~~~~~l~~~L~~~~-~~~~~~~~~~~~~~r~~~~~~f~~~---------------  287 (367)
T 1hv8_A          226 RFEALCRLLK--NKEFYGLVFCKTKRDTKELASMLRDIG-FKAGAIHGDLSQSQREKVIRLFKQK---------------  287 (367)
T ss_dssp             HHHHHHHHHC--STTCCEEEECSSHHHHHHHHHHHHHTT-CCEEEECSSSCHHHHHHHHHHHHTT---------------
T ss_pred             HHHHHHHHHh--cCCCcEEEEECCHHHHHHHHHHHHhcC-CCeEEeeCCCCHHHHHHHHHHHHcC---------------
Confidence            3344443344  456899999999999999999999998 8999999999999999999999998               


Q ss_pred             CCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCchHHHHHHHHH
Q 029910           91 SETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGGEVVTLRSMEE  168 (185)
Q Consensus        91 ~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e~~~~~~l~~  168 (185)
                              ..++||+|++    +++|+|+|++++||+||+|+++.+|+||+||++  |++|.++.++++.+...++.+++
T Consensus       288 --------~~~vlv~T~~----~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~i~~  355 (367)
T 1hv8_A          288 --------KIRILIATDV----MSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKKLRYIER  355 (367)
T ss_dssp             --------SSSEEEECTT----HHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTTSHHHHHHHHH
T ss_pred             --------CCeEEEECCh----hhcCCCcccCCEEEEecCCCCHHHhhhcccccccCCCccEEEEEEcHHHHHHHHHHHH
Confidence                    6999999999    999999999999999999999999999999974  46799999999999999999999


Q ss_pred             HhCCccccccC
Q 029910          169 SLGLIVAEVPI  179 (185)
Q Consensus       169 ~~~~~~~~~~~  179 (185)
                      .++.++++++.
T Consensus       356 ~~~~~~~~~~~  366 (367)
T 1hv8_A          356 AMKLKIKKLKF  366 (367)
T ss_dssp             HHTCCCCCBC-
T ss_pred             HhCCCCceecc
Confidence            99999988753

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=99.91  E-value=1.1e-23  Score=179.00  Aligned_cols=145  Identities=21%  Similarity=0.390  Sum_probs=128.2

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ   86 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~   86 (185)
                      ......+.+..+.. .....++||||++++.++.+++.|+..+ +.+..+||+++..+|.+++++|++|           
T Consensus       226 ~~~~~~~~l~~~~~-~~~~~~~lvf~~~~~~~~~l~~~l~~~~-~~~~~~~~~~~~~~r~~~~~~f~~g-----------  292 (395)
T 3pey_A          226 NEADKFDVLTELYG-LMTIGSSIIFVATKKTANVLYGKLKSEG-HEVSILHGDLQTQERDRLIDDFREG-----------  292 (395)
T ss_dssp             SHHHHHHHHHHHHT-TTTSSEEEEECSCHHHHHHHHHHHHHTT-CCCEEECTTSCHHHHHHHHHHHHTT-----------
T ss_pred             chHHHHHHHHHHHH-hccCCCEEEEeCCHHHHHHHHHHHHhcC-CcEEEeCCCCCHHHHHHHHHHHHCC-----------
Confidence            44556667777666 5667899999999999999999999998 8999999999999999999999999           


Q ss_pred             CCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCC------CHHHHHHHHhhhc--CCCCEEEEEeeC-
Q 029910           87 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPT------KKETYIRRMTTCL--AADGSVINIVVG-  157 (185)
Q Consensus        87 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~------~~~~yiqR~GR~~--~~~g~~i~~v~~-  157 (185)
                                  ..++||||++    +++|+|+|++++||+||+|+      ++..|+||+||++  |+.|.++.++.. 
T Consensus       293 ------------~~~vlv~T~~----~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~  356 (395)
T 3pey_A          293 ------------RSKVLITTNV----LARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDK  356 (395)
T ss_dssp             ------------SCCEEEECGG----GSSSCCCTTEEEEEESSCCBCTTSSBCHHHHHHHHTTSSCTTCCEEEEEEECSH
T ss_pred             ------------CCCEEEECCh----hhcCCCcccCCEEEEcCCCCCCcCCCCHHHhhHhccccccCCCCceEEEEEech
Confidence                        6999999999    99999999999999999999      9999999999974  567999999986 


Q ss_pred             chHHHHHHHHHHhC-CccccccCC
Q 029910          158 GEVVTLRSMEESLG-LIVAEVPIN  180 (185)
Q Consensus       158 ~e~~~~~~l~~~~~-~~~~~~~~~  180 (185)
                      ++...++.+++.++ ..+.+++.+
T Consensus       357 ~~~~~~~~i~~~~~~~~~~~~~~~  380 (395)
T 3pey_A          357 NSFNILSAIQKYFGDIEMTRVPTD  380 (395)
T ss_dssp             HHHHHHHHHHHHTTSCCCEECCSS
T ss_pred             HHHHHHHHHHHHhCCceeecCChH
Confidence            46678889999888 777777754

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=99.91  E-value=6.3e-24  Score=190.88  Aligned_cols=128  Identities=19%  Similarity=0.386  Sum_probs=118.7

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcC---CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCC
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNL---ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEH   98 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~---~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (185)
                      ...+.++||||++++.++.++..|...   + +.+..+||+|++.+|.+++++|++|                       
T Consensus       336 ~~~~~~~iVF~~s~~~~~~l~~~L~~~~~~~-~~v~~~h~~~~~~~R~~~~~~f~~g-----------------------  391 (563)
T 3i5x_A          336 RDSNYKAIIFAPTVKFTSFLCSILKNEFKKD-LPILEFHGKITQNKRTSLVKRFKKD-----------------------  391 (563)
T ss_dssp             TTTCCEEEEECSCHHHHHHHHHHHHHHHTTT-SCEEEESTTSCHHHHHHHHHHHHHC-----------------------
T ss_pred             cCCCCcEEEEcCcHHHHHHHHHHHHHhccCC-ceEEEecCCCCHHHHHHHHHHHhcC-----------------------
Confidence            466789999999999999999999875   6 7999999999999999999999999                       


Q ss_pred             ceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCchHHHHHHHHHHhCCcccc
Q 029910           99 KSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGGEVVTLRSMEESLGLIVAE  176 (185)
Q Consensus        99 ~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e~~~~~~l~~~~~~~~~~  176 (185)
                      ..+|||||++    +++|+|+|++++||+||+|.++..|+||+||++  |..|.+++|+.+.+...++.+++..+..+++
T Consensus       392 ~~~vLvaT~~----~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~~~~~~l~~~~~~~~~~  467 (563)
T 3i5x_A          392 ESGILVCTDV----GARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAK  467 (563)
T ss_dssp             SSEEEEECGG----GTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGHHHHHHHHHHHCCCCCE
T ss_pred             CCCEEEEcch----hhcCCCcccCCEEEEECCCCchhhhhhhcCccccCCCCceEEEEEchhHHHHHHHHHHHhCCCccc
Confidence            7999999999    999999999999999999999999999999974  5679999999999999999999998877765


Q ss_pred             c
Q 029910          177 V  177 (185)
Q Consensus       177 ~  177 (185)
                      .
T Consensus       468 ~  468 (563)
T 3i5x_A          468 Q  468 (563)
T ss_dssp             E
T ss_pred             c
Confidence            4

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.91  E-value=1.4e-23  Score=190.32  Aligned_cols=128  Identities=19%  Similarity=0.384  Sum_probs=118.5

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcC---CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCC
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNL---ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEH   98 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~---~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (185)
                      ...+.++||||++++.++.+++.|...   + +.+..+||+|++.+|.+++++|+++                       
T Consensus       285 ~~~~~~~iVF~~t~~~~~~l~~~L~~~~~~~-~~v~~~hg~~~~~~R~~~~~~F~~g-----------------------  340 (579)
T 3sqw_A          285 RDSNYKAIIFAPTVKFTSFLCSILKNEFKKD-LPILEFHGKITQNKRTSLVKRFKKD-----------------------  340 (579)
T ss_dssp             TTTCCEEEEECSSHHHHHHHHHHHHHHHTTT-SCEEEESTTSCHHHHHHHHHHHHHC-----------------------
T ss_pred             cCCCCcEEEECCcHHHHHHHHHHHHHhhcCC-CcEEEecCCCCHHHHHHHHHHhhcC-----------------------
Confidence            466789999999999999999999876   5 7999999999999999999999999                       


Q ss_pred             ceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHHHHHHHHHHhCCcccc
Q 029910           99 KSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLRSMEESLGLIVAE  176 (185)
Q Consensus        99 ~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~~~~l~~~~~~~~~~  176 (185)
                      ..+|||||++    +++|+|+|++++||+||+|.+++.|+||+||+  .|..|.|++|+.+.|...++.+++..+..+.+
T Consensus       341 ~~~vLVaT~~----~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~~~~~~l~~~~~~~~~~  416 (579)
T 3sqw_A          341 ESGILVCTDV----GARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAK  416 (579)
T ss_dssp             SSEEEEECGG----GTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGHHHHHHHHHHHCCCCCE
T ss_pred             CCeEEEEcch----hhcCCCcccCCEEEEcCCCCCHHHhhhhccccccCCCCceEEEEEcccHHHHHHHHHHHhCCCccc
Confidence            6999999999    99999999999999999999999999999997  45679999999999999999999998877654


Q ss_pred             c
Q 029910          177 V  177 (185)
Q Consensus       177 ~  177 (185)
                      .
T Consensus       417 ~  417 (579)
T 3sqw_A          417 Q  417 (579)
T ss_dssp             E
T ss_pred             c
Confidence            4

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=99.90  E-value=1.6e-25  Score=190.87  Aligned_cols=145  Identities=28%  Similarity=0.488  Sum_probs=0.0

Q ss_pred             HHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCC
Q 029910           12 VELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDES   91 (185)
Q Consensus        12 ~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~   91 (185)
                      .+.+..++. .....++||||++++.++.+++.|...+ +.+..+||+++..+|.+++++|+++                
T Consensus       247 ~~~l~~~~~-~~~~~~~lVf~~~~~~~~~l~~~L~~~~-~~~~~~~~~~~~~~r~~~~~~f~~~----------------  308 (394)
T 1fuu_A          247 YECLTDLYD-SISVTQAVIFCNTRRKVEELTTKLRNDK-FTVSAIYSDLPQQERDTIMKEFRSG----------------  308 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHh-cCCCCcEEEEECCHHHHHHHHHHHHHcC-CeEEEeeCCCCHHHHHHHHHHHHCC----------------
Confidence            334444343 3455799999999999999999999987 8999999999999999999999998                


Q ss_pred             CCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCchHHHHHHHHHH
Q 029910           92 ETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGGEVVTLRSMEES  169 (185)
Q Consensus        92 ~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e~~~~~~l~~~  169 (185)
                             ..++||||++    +++|+|+|++++||+||+|+++..|+||+||++  |++|.++.++++.+...++.+++.
T Consensus       309 -------~~~vlv~T~~----~~~Gldi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~l~~~  377 (394)
T 1fuu_A          309 -------SSRILISTDL----LARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKF  377 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             -------CCcEEEECCh----hhcCCCcccCCEEEEeCCCCCHHHHHHHcCcccCCCCCceEEEEEchhHHHHHHHHHHH
Confidence                   6999999999    999999999999999999999999999999974  567999999999999999999999


Q ss_pred             hCCccccccCCccccC
Q 029910          170 LGLIVAEVPINISEIL  185 (185)
Q Consensus       170 ~~~~~~~~~~~~~~~l  185 (185)
                      ++..++++|.++.++|
T Consensus       378 ~~~~~~~~~~~~~~~~  393 (394)
T 1fuu_A          378 YSTQIEELPSDIATLL  393 (394)
T ss_dssp             ----------------
T ss_pred             hCCcccccCcchhhhc
Confidence            9999999999887764

>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=99.89  E-value=1.8e-22  Score=184.78  Aligned_cols=125  Identities=21%  Similarity=0.359  Sum_probs=110.9

Q ss_pred             HHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCC
Q 029910           13 ELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESE   92 (185)
Q Consensus        13 ~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~   92 (185)
                      .+++. +....++.++||||++++.++.++..|...| +.+..+||+|+..+|.+++++|+++                 
T Consensus       256 ~l~~~-l~~~~~~~~~IVf~~sr~~~e~la~~L~~~g-~~~~~~h~~l~~~~R~~~~~~F~~g-----------------  316 (591)
T 2v1x_A          256 DIVKL-INGRYKGQSGIIYCFSQKDSEQVTVSLQNLG-IHAGAYHANLEPEDKTTVHRKWSAN-----------------  316 (591)
T ss_dssp             HHHHH-HTTTTTTCEEEEECSSHHHHHHHHHHHHHTT-CCEEEECTTSCHHHHHHHHHHHHTT-----------------
T ss_pred             HHHHH-HHHhccCCCeEEEeCcHHHHHHHHHHHHHCC-CCEEEecCCCCHHHHHHHHHHHHcC-----------------
Confidence            33343 4424567899999999999999999999998 8999999999999999999999999                 


Q ss_pred             CCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCchHHHHHHH
Q 029910           93 TGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGGEVVTLRSM  166 (185)
Q Consensus        93 ~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e~~~~~~l  166 (185)
                            ..+|||||++    +++|+|+|+|++||+||+|.+++.|+||+||++  |.+|.|+.++.+.|...+..+
T Consensus       317 ------~~~VlVAT~a----~~~GID~p~V~~VI~~~~p~s~~~y~Qr~GRaGR~G~~g~~i~l~~~~D~~~~~~~  382 (591)
T 2v1x_A          317 ------EIQVVVATVA----FGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYGFGDIFRISSM  382 (591)
T ss_dssp             ------SSSEEEECTT----SCTTCCCSCEEEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHHH
T ss_pred             ------CCeEEEEech----hhcCCCcccccEEEEeCCCCCHHHHHHHhccCCcCCCCceEEEEEChHHHHHHHHH
Confidence                  6999999999    999999999999999999999999999999985  567899999988777665544

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.89  E-value=4.7e-24  Score=188.89  Aligned_cols=132  Identities=15%  Similarity=0.171  Sum_probs=90.1

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCC---C--------ceEEEEecCCCHHHHHHHHHHHhc-
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLA---D--------ISFSSLHSDLAETERTLILEEFRH-   74 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~---~--------~~~~~l~g~~~~~~R~~~l~~F~~-   74 (185)
                      |.+.+.++|..+.. ..+..++||||+++++++.++..|...+   +        .....+||+|++.+|.+++++|++ 
T Consensus       372 k~~~l~~~l~~~~~-~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~  450 (555)
T 3tbk_A          372 KLRDLYLVLQEEYH-LKPETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFRAS  450 (555)
T ss_dssp             HHHHHHHHHHHHHH-HCTTCCEEEECSSHHHHHHHHHHHHHCGGGTTCCEEECCC-------------------------
T ss_pred             HHHHHHHHHHHHhc-cCCCceEEEEeCcHHHHHHHHHHHhhCcCcCceeeeEEEecCCcccccccCHHHHHHHHHHHhcC
Confidence            55667777776554 4567899999999999999999998763   1        244555669999999999999999 


Q ss_pred             ccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhcCCCCEEEEE
Q 029910           75 TAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSVINI  154 (185)
Q Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~~~~g~~i~~  154 (185)
                      |                       ..+|||||++    +++|+|+|++++||+||+|+|+..|+||+||+..++|.++.|
T Consensus       451 g-----------------------~~~vLvaT~~----~~~GlDlp~v~~VI~~d~p~s~~~~~Qr~GRgR~~~g~~~~l  503 (555)
T 3tbk_A          451 G-----------------------DNNILIATSV----ADEGIDIAECNLVILYEYVGNVIKMIQTRGRGRARDSKCFLL  503 (555)
T ss_dssp             ------------------------CCSEEEECCC----TTCCEETTSCSEEEEESCCSSCCCEECSSCCCTTTSCEEEEE
T ss_pred             C-----------------------CeeEEEEcch----hhcCCccccCCEEEEeCCCCCHHHHHHhcCcCcCCCceEEEE
Confidence            7                       6999999999    999999999999999999999999999999943356899999


Q ss_pred             eeCchHHHHHHH
Q 029910          155 VVGGEVVTLRSM  166 (185)
Q Consensus       155 v~~~e~~~~~~l  166 (185)
                      +++++......+
T Consensus       504 ~~~~~~~~~~~~  515 (555)
T 3tbk_A          504 TSSADVIEKEKA  515 (555)
T ss_dssp             ESCHHHHHHHHH
T ss_pred             EcCCCHHHHHHH
Confidence            988766555444

>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=99.89  E-value=2.5e-22  Score=181.12  Aligned_cols=116  Identities=19%  Similarity=0.341  Sum_probs=107.0

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEE
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMI  103 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iL  103 (185)
                      ++.++||||++++.++.+++.|...| +.+..+||+|+.++|.+++++|+++                       ..+||
T Consensus       235 ~~~~~IVf~~sr~~~e~l~~~L~~~g-~~~~~~h~~l~~~~R~~~~~~f~~g-----------------------~~~vl  290 (523)
T 1oyw_A          235 RGKSGIIYCNSRAKVEDTAARLQSKG-ISAAAYHAGLENNVRADVQEKFQRD-----------------------DLQIV  290 (523)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHHHTT-CCEEEECTTSCHHHHHHHHHHHHTT-----------------------SCSEE
T ss_pred             CCCcEEEEeCCHHHHHHHHHHHHHCC-CCEEEecCCCCHHHHHHHHHHHHcC-----------------------CCeEE
Confidence            56899999999999999999999998 8999999999999999999999999                       69999


Q ss_pred             EEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCchHHHHHHHH
Q 029910          104 VVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGGEVVTLRSME  167 (185)
Q Consensus       104 V~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e~~~~~~l~  167 (185)
                      |||++    +++|+|+|++++||+||+|++++.|+||+||++  |.+|.++.++++.|...++.+.
T Consensus       291 VaT~a----~~~GiD~p~v~~VI~~~~p~s~~~y~Qr~GRaGR~g~~~~~~l~~~~~d~~~~~~~~  352 (523)
T 1oyw_A          291 VATVA----FGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCL  352 (523)
T ss_dssp             EECTT----SCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHHHH
T ss_pred             EEech----hhCCCCccCccEEEEECCCCCHHHHHHHhccccCCCCCceEEEEeCHHHHHHHHHHH
Confidence            99999    999999999999999999999999999999985  5678999999887776655543

>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=99.88  E-value=4.9e-23  Score=182.94  Aligned_cols=125  Identities=15%  Similarity=0.202  Sum_probs=67.3

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcC------------CCceEEEEecCCCHHHHHHHHHHHhc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL------------ADISFSSLHSDLAETERTLILEEFRH   74 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~------------~~~~~~~l~g~~~~~~R~~~l~~F~~   74 (185)
                      |.+.+.++|..... ..++.++||||+++++++.+++.|...            | .....+||+|+..+|.+++++|++
T Consensus       373 K~~~L~~~l~~~~~-~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g-~~~~~~~~~~~~~~R~~~~~~F~~  450 (556)
T 4a2p_A          373 KLEELVCILDDAYR-YNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMG-RGRRDQTTGMTLPSQKGVLDAFKT  450 (556)
T ss_dssp             HHHHHHHHHHHHHH-HCTTCCEEEEESSHHHHHHHHHHHTTCSGGGSCCEEC----------------------------
T ss_pred             HHHHHHHHHHHHhc-CCCCceEEEEEccHHHHHHHHHHHHhCCCcceeeeeEEEc-cCCcccccccCHHHHHHHHHHhcc
Confidence            45556666655443 356789999999999999999999875            3 455566788999999999999999


Q ss_pred             -ccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhcCCCCEEEE
Q 029910           75 -TAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSVIN  153 (185)
Q Consensus        75 -~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~~~~g~~i~  153 (185)
                       |                       ..+|||||++    +++|+|+|++++||+||+|+|+..|+||+||+-..+|.++.
T Consensus       451 ~g-----------------------~~~vLvaT~~----~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GRgR~~~g~~~~  503 (556)
T 4a2p_A          451 SK-----------------------DNRLLIATSV----ADEGIDIVQCNLVVLYEYSGNVTKMIQVRGRGRAAGSKCIL  503 (556)
T ss_dssp             --------------------------CCEEEEEC---------------CEEEEETCCSCHHHHHHC--------CCEEE
T ss_pred             cC-----------------------ceEEEEEcCc----hhcCCCchhCCEEEEeCCCCCHHHHHHhcCCCCCCCceEEE
Confidence             7                       6999999999    99999999999999999999999999999993224589999


Q ss_pred             EeeCchH
Q 029910          154 IVVGGEV  160 (185)
Q Consensus       154 ~v~~~e~  160 (185)
                      |++.++.
T Consensus       504 l~~~~~~  510 (556)
T 4a2p_A          504 VTSKTEV  510 (556)
T ss_dssp             EESCHHH
T ss_pred             EEeCcch
Confidence            9988655

>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=99.88  E-value=8.1e-23  Score=187.74  Aligned_cols=122  Identities=16%  Similarity=0.208  Sum_probs=100.0

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcC------CCceEEEEecC--------CCHHHHHHHHHHH
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL------ADISFSSLHSD--------LAETERTLILEEF   72 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~------~~~~~~~l~g~--------~~~~~R~~~l~~F   72 (185)
                      +.+.+.++|.........+.++||||+++++++.|++.|...      | +.+..+||+        |+..+|.+++++|
T Consensus       382 k~~~L~~~L~~~~~~~~~~~~~IVF~~s~~~~~~l~~~L~~~~~l~~~g-~~~~~lhg~~~~~~~~~~~~~eR~~~~~~F  460 (699)
T 4gl2_A          382 KLTKLRNTIMEQYTRTEESARGIIFTKTRQSAYALSQWITENEKFAEVG-VKAHHLIGAGHSSEFKPMTQNEQKEVISKF  460 (699)
T ss_dssp             CSSCSHHHHHHHHHHSSSCCCEEEECSCHHHHHHHHHHHHSSCSCC------CEECCCSCCCTTCCCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCCCCCcEEEEECcHHHHHHHHHHHHhCccccccC-cceEEEECCCCccCCCCCCHHHHHHHHHHH
Confidence            444556666654442222799999999999999999999987      6 899999999        9999999999999


Q ss_pred             hcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhcCCCCEEE
Q 029910           73 RHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSVI  152 (185)
Q Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~~~~g~~i  152 (185)
                      ++|                       ..+|||||++    +++|+|+|++++||+||+|+|+..|+||+||+ |+.|.++
T Consensus       461 ~~g-----------------------~~~VLVaT~~----~~~GIDip~v~~VI~~d~p~s~~~~~Qr~GRA-rr~g~~~  512 (699)
T 4gl2_A          461 RTG-----------------------KINLLIATTV----AEEGLDIKECNIVIRYGLVTNEIAMVQARGRA-RADESTY  512 (699)
T ss_dssp             CC--------------------------CCSEEECS----CCTTSCCCSCCCCEEESCCCCHHHHHHHHTTS-CSSSCEE
T ss_pred             hcC-----------------------CCcEEEEccc----cccCCccccCCEEEEeCCCCCHHHHHHHcCCC-CCCCceE
Confidence            999                       6999999999    99999999999999999999999999999995 5666666


Q ss_pred             EEeeC
Q 029910          153 NIVVG  157 (185)
Q Consensus       153 ~~v~~  157 (185)
                      .++..
T Consensus       513 ~l~~~  517 (699)
T 4gl2_A          513 VLVAH  517 (699)
T ss_dssp             EEEEE
T ss_pred             EEEEe
Confidence            66644

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens}

Probab=99.88  E-value=2.3e-24  Score=190.46  Aligned_cols=130  Identities=20%  Similarity=0.373  Sum_probs=0.0

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeE
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHM  102 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  102 (185)
                      ....++||||++++.++.++..|...+ +.+..+||+|++.+|.+++++|++|                       ..+|
T Consensus       331 ~~~~~~lvF~~s~~~~~~l~~~L~~~~-~~v~~lh~~~~~~~R~~~~~~f~~g-----------------------~~~i  386 (479)
T 3fmp_B          331 ITIAQAMIFCHTRKTASWLAAELSKEG-HQVALLSGEMMVEQRAAVIERFREG-----------------------KEKV  386 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccCCceEEEeCcHHHHHHHHHHHHhCC-ccEEEecCCCCHHHHHHHHHHHHcC-----------------------CCcE
Confidence            345799999999999999999999987 8999999999999999999999999                       6999


Q ss_pred             EEEecCCCCcccCcCCCCCCcEEEEcCCCC------CHHHHHHHHhhhc--CCCCEEEEEeeCc-hHHHHHHHHHHhCCc
Q 029910          103 IVVTDACLPLLSSGESAISARVLINYELPT------KKETYIRRMTTCL--AADGSVINIVVGG-EVVTLRSMEESLGLI  173 (185)
Q Consensus       103 LV~Td~~~~~~~~G~d~~~v~~VI~~d~P~------~~~~yiqR~GR~~--~~~g~~i~~v~~~-e~~~~~~l~~~~~~~  173 (185)
                      ||||++    +++|+|+|++++||+||+|.      +...|+||+||++  |..|.+++|+.+. +...++.+++.++..
T Consensus       387 Lv~T~~----~~~GlDip~v~~VI~~d~p~~~~~~~s~~~~~Qr~GRagR~g~~G~~i~~~~~~~~~~~~~~i~~~~~~~  462 (479)
T 3fmp_B          387 LVTTNV----CARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKK  462 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             EEEccc----cccCCccccCCEEEEecCCCCCccCCCHHHHHHHhcccccCCCCceEEEEEcCcchHHHHHHHHHHhCCC
Confidence            999999    99999999999999999995      5689999999974  5679999999865 488889999999999


Q ss_pred             cccccCC
Q 029910          174 VAEVPIN  180 (185)
Q Consensus       174 ~~~~~~~  180 (185)
                      +.+++.+
T Consensus       463 ~~~l~~~  469 (479)
T 3fmp_B          463 IERLDTD  469 (479)
T ss_dssp             -------
T ss_pred             ceECCCc
Confidence            9888754

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.87  E-value=9.2e-22  Score=170.41  Aligned_cols=130  Identities=16%  Similarity=0.232  Sum_probs=110.5

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEE-EEecCCCHHHHHHHHHHHhcccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS-SLHSDLAETERTLILEEFRHTAMKWNQKVTE   85 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~-~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~   85 (185)
                      +.+.+.++++. .     +.++||||++++.++.++..|...+ +.+. .+||+    +|.  +++|++|          
T Consensus       240 ~~~~l~~~l~~-~-----~~~~lVF~~~~~~~~~l~~~L~~~~-~~~~~~~h~~----~r~--~~~f~~g----------  296 (414)
T 3oiy_A          240 SKEKLVELLEI-F-----RDGILIFAQTEEEGKELYEYLKRFK-FNVGETWSEF----EKN--FEDFKVG----------  296 (414)
T ss_dssp             CHHHHHHHHHH-H-----CSSEEEEESSHHHHHHHHHHHHHTT-CCEEESSSCH----HHH--HHHHHTT----------
T ss_pred             HHHHHHHHHHH-c-----CCCEEEEECCHHHHHHHHHHHHHcC-CceehhhcCc----chH--HHHHhCC----------
Confidence            45555666655 2     2899999999999999999999998 8898 99985    444  9999999          


Q ss_pred             cCCCCCCCCCCCCceeEEEE----ecCCCCcccCcCCCCC-CcEEEEcCCC--CCHHHHHHHHhhhcC------CCCEEE
Q 029910           86 QSGDESETGKDEHKSHMIVV----TDACLPLLSSGESAIS-ARVLINYELP--TKKETYIRRMTTCLA------ADGSVI  152 (185)
Q Consensus        86 ~~~~~~~~~~~~~~~~iLV~----Td~~~~~~~~G~d~~~-v~~VI~~d~P--~~~~~yiqR~GR~~~------~~g~~i  152 (185)
                                   ..++|||    |++    +++|+|+|+ +++||+||+|  .++.+|+||+||+++      ..|.++
T Consensus       297 -------------~~~vLvat~s~T~~----~~~GiDip~~v~~VI~~~~p~~~~~~~y~qr~GR~gR~g~~~~~~g~~i  359 (414)
T 3oiy_A          297 -------------KINILIGVQAYYGK----LTRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSV  359 (414)
T ss_dssp             -------------SCSEEEEECCTTCC----CCCCCCCTTTCCEEEEESCCTTTCHHHHHHHHGGGCCEETTEECCEEEE
T ss_pred             -------------CCeEEEEecCcCch----hhccCccccccCEEEEECCCCCCCHHHHHHHhCccccCCCCCCcceEEE
Confidence                         7999999    999    999999999 9999999999  999999999999865      479999


Q ss_pred             EEeeCchHHHHHHHHHHhC--Ccccccc
Q 029910          153 NIVVGGEVVTLRSMEESLG--LIVAEVP  178 (185)
Q Consensus       153 ~~v~~~e~~~~~~l~~~~~--~~~~~~~  178 (185)
                      +|+  .+...++.+++.++  ..++..+
T Consensus       360 ~~~--~~~~~~~~l~~~~~~~~~~~~~~  385 (414)
T 3oiy_A          360 IFE--EDEEIFESLKTRLLLIAEEEIIE  385 (414)
T ss_dssp             EEC--CCHHHHHHHHHHHHHHHCCCEEE
T ss_pred             EEE--ccHHHHHHHHHHhcccccccccc
Confidence            999  67888888888887  5554433

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.87  E-value=7.2e-23  Score=187.98  Aligned_cols=144  Identities=14%  Similarity=0.173  Sum_probs=86.4

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCC---ceEEEE--------ecCCCHHHHHHHHHHHhc-
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLAD---ISFSSL--------HSDLAETERTLILEEFRH-   74 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~---~~~~~l--------~g~~~~~~R~~~l~~F~~-   74 (185)
                      +.+.+.+++..... ..++.++||||+++++++.+++.|...+.   +++..+        ||+|+..+|.+++++|++ 
T Consensus       381 k~~~L~~ll~~~~~-~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F~~~  459 (696)
T 2ykg_A          381 KLEDLCFILQEEYH-LNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKAS  459 (696)
T ss_dssp             HHHHHHHHHHHHHT-TCTTCCEEEECSCHHHHHHHHHHHHHCTTCCSCCEEC----------------------------
T ss_pred             HHHHHHHHHHHHhc-cCCCCcEEEEeCcHHHHHHHHHHHHhCCCccccceeEEEccCCCccccCCCHHHHHHHHHHHHhc
Confidence            34445555555333 34668999999999999999999988752   678888        559999999999999998 


Q ss_pred             ccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhcC-CCCEEEE
Q 029910           75 TAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLA-ADGSVIN  153 (185)
Q Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~~-~~g~~i~  153 (185)
                      |                       ..+|||||++    +++|+|+|++++||+||+|++++.|+||+|| |+ ++|.++.
T Consensus       460 g-----------------------~~~vLVaT~v----~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-GR~~~g~~~~  511 (696)
T 2ykg_A          460 G-----------------------DHNILIATSV----ADEGIDIAQCNLVILYEYVGNVIKMIQTRGR-GRARGSKCFL  511 (696)
T ss_dssp             ------------------------CCSCSEEEES----SCCC---CCCSEEEEESCC--CCCC----------CCCEEEE
T ss_pred             C-----------------------CccEEEEech----hhcCCcCccCCEEEEeCCCCCHHHHHHhhcc-CcCCCceEEE
Confidence            8                       6999999999    9999999999999999999999999999999 55 4588998


Q ss_pred             EeeCchHHHHHHH----HHHhCCccccccC
Q 029910          154 IVVGGEVVTLRSM----EESLGLIVAEVPI  179 (185)
Q Consensus       154 ~v~~~e~~~~~~l----~~~~~~~~~~~~~  179 (185)
                      +++.++......+    ++.++..+.+++.
T Consensus       512 l~~~~~~~~~~~~~~~~e~~~~~~~~~~~~  541 (696)
T 2ykg_A          512 LTSNAGVIEKEQINMYKEKMMNDSILRLQT  541 (696)
T ss_dssp             EESCHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             EecCCCHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            8888777555555    5555555555543

>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=99.87  E-value=6.8e-22  Score=170.29  Aligned_cols=126  Identities=20%  Similarity=0.259  Sum_probs=107.2

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEec--------CCCHHHHHHHHHHHhccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHS--------DLAETERTLILEEFRHTAMK   78 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g--------~~~~~~R~~~l~~F~~~~~~   78 (185)
                      |.+.+.+++..+.. ..++.++||||+++++++.+++.|...+ +.+..+||        +|+..+|.+++++|+++   
T Consensus       344 k~~~l~~~l~~~~~-~~~~~k~lVF~~~~~~~~~l~~~L~~~~-~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~~---  418 (494)
T 1wp9_A          344 KMDKLKEIIREQLQ-RKQNSKIIVFTNYRETAKKIVNELVKDG-IKAKRFVGQASKENDRGLSQREQKLILDEFARG---  418 (494)
T ss_dssp             HHHHHHHHHHHHHH-HCTTCCEEEECSCHHHHHHHHHHHHHTT-CCEEEECCSSCC-------CCHHHHHHHHHHHT---
T ss_pred             HHHHHHHHHHHHhc-cCCCCeEEEEEccHHHHHHHHHHHHHcC-CCcEEEeccccccccccCCHHHHHHHHHHHhcC---
Confidence            44555666665443 2567899999999999999999999997 89999999        99999999999999998   


Q ss_pred             ccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhcCC-CCEEEEEeeC
Q 029910           79 WNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAA-DGSVINIVVG  157 (185)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~~~-~g~~i~~v~~  157 (185)
                                          ..++||+|++    +++|+|+|++++||+||+|+++..|+||+||+++. .|.++.+++.
T Consensus       419 --------------------~~~vLv~T~~----~~~Gldl~~~~~Vi~~d~~~~~~~~~Qr~GR~~R~g~g~~~~l~~~  474 (494)
T 1wp9_A          419 --------------------EFNVLVATSV----GEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMPGRVIILMAK  474 (494)
T ss_dssp             --------------------SCSEEEECGG----GGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCCCSEEEEEEET
T ss_pred             --------------------CceEEEECCc----cccCCCchhCCEEEEeCCCCCHHHHHHHHhhccCCCCceEEEEEec
Confidence                                6899999999    99999999999999999999999999999997432 2999999988


Q ss_pred             chHH
Q 029910          158 GEVV  161 (185)
Q Consensus       158 ~e~~  161 (185)
                      ++.+
T Consensus       475 ~t~e  478 (494)
T 1wp9_A          475 GTRD  478 (494)
T ss_dssp             TSHH
T ss_pred             CCHH
Confidence            7543

>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=99.86  E-value=2.6e-21  Score=179.14  Aligned_cols=126  Identities=16%  Similarity=0.190  Sum_probs=109.1

Q ss_pred             HHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCC
Q 029910           11 LVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDE   90 (185)
Q Consensus        11 l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~   90 (185)
                      +..++..|......+.++||||+|+..++.|++.|...| +.+..+||++++.+|.+++++|+.|               
T Consensus       431 ~~~Ll~~l~~~~~~~~~vlVf~~t~~~ae~L~~~L~~~g-i~~~~lh~~~~~~~R~~~l~~f~~g---------------  494 (661)
T 2d7d_A          431 IDDLIGEIQARIERNERVLVTTLTKKMSEDLTDYLKEIG-IKVNYLHSEIKTLERIEIIRDLRLG---------------  494 (661)
T ss_dssp             HHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHHHHHTT-CCEEEECTTCCHHHHHHHHHHHHHT---------------
T ss_pred             HHHHHHHHHHHHhcCCeEEEEECCHHHHHHHHHHHHhcC-CCeEEEeCCCCHHHHHHHHHHHhcC---------------
Confidence            334444443323356899999999999999999999998 8999999999999999999999999               


Q ss_pred             CCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCC-----CCCHHHHHHHHhhhcC-CCCEEEEEeeCchHHHHH
Q 029910           91 SETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYEL-----PTKKETYIRRMTTCLA-ADGSVINIVVGGEVVTLR  164 (185)
Q Consensus        91 ~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~-----P~~~~~yiqR~GR~~~-~~g~~i~~v~~~e~~~~~  164 (185)
                              ..+|||+|++    +++|+|+|++++||+||.     |.+..+|+||+||+++ ..|.+++|+++.+....+
T Consensus       495 --------~~~VLVaT~~----l~~GlDip~v~lVi~~d~d~~G~p~s~~~~iQr~GRagR~~~G~~i~~~~~~~~~~~~  562 (661)
T 2d7d_A          495 --------KYDVLVGINL----LREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAEGRVIMYADKITKSMEI  562 (661)
T ss_dssp             --------SCSEEEESCC----CSTTCCCTTEEEEEETTTTCCTTTTSHHHHHHHHHTTTTSTTCEEEEECSSCCHHHHH
T ss_pred             --------CeEEEEecch----hhCCcccCCCCEEEEeCcccccCCCCHHHHHHHhCcccCCCCCEEEEEEeCCCHHHHH
Confidence                    6999999999    999999999999999997     9999999999999865 569999999886554443

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}

Probab=99.86  E-value=1.1e-21  Score=163.49  Aligned_cols=118  Identities=20%  Similarity=0.341  Sum_probs=104.5

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCcee
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSH  101 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (185)
                      ...+.++||||++++.++.+++.|.     .+..+||+++..+|.+++++|+++                       ..+
T Consensus       217 ~~~~~~~lvf~~~~~~~~~l~~~l~-----~~~~~~~~~~~~~r~~~~~~f~~~-----------------------~~~  268 (337)
T 2z0m_A          217 ENKDKGVIVFVRTRNRVAKLVRLFD-----NAIELRGDLPQSVRNRNIDAFREG-----------------------EYD  268 (337)
T ss_dssp             TCCCSSEEEECSCHHHHHHHHTTCT-----TEEEECTTSCHHHHHHHHHHHHTT-----------------------SCS
T ss_pred             hCCCCcEEEEEcCHHHHHHHHHHhh-----hhhhhcCCCCHHHHHHHHHHHHcC-----------------------CCc
Confidence            4566899999999999999999885     578999999999999999999999                       699


Q ss_pred             EEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHHHHHHHHHHhCC
Q 029910          102 MIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLRSMEESLGL  172 (185)
Q Consensus       102 iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~~~~l~~~~~~  172 (185)
                      +||||++    +++|+|+|++++||+||+|+++..|+||+||+  .|+.|.++.++. .+...++.+++.++.
T Consensus       269 vlv~T~~----~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~gR~g~~g~~~~~~~-~~~~~~~~i~~~~~~  336 (337)
T 2z0m_A          269 MLITTDV----ASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFIL-NEYWLEKEVKKVSQK  336 (337)
T ss_dssp             EEEECHH----HHTTCCCCCBSEEEESSCCSSHHHHHHHHTTBCGGGCCEEEEEEES-SCHHHHHHHC-----
T ss_pred             EEEEcCc----cccCCCccCCCEEEEecCCCCHHHhhHhcCccccCCCCceEEEEEe-CcHHHHHHHHHHhcc
Confidence            9999999    99999999999999999999999999999997  457799999999 888888888887653

>1c4o_A DNA nucleotide excision repair enzyme UVRB; uvrabc, helicase, hypertherm protein, replication; HET: DNA BOG; 1.50A {Thermus thermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1d2m_A*

Probab=99.85  E-value=7.8e-21  Score=176.01  Aligned_cols=127  Identities=14%  Similarity=0.159  Sum_probs=108.8

Q ss_pred             HHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCC
Q 029910           12 VELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDES   91 (185)
Q Consensus        12 ~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~   91 (185)
                      ..++..|......+.++||||+|+..++.|++.|...| +.+..+||++++.+|.+++++|+.|                
T Consensus       426 ~~Ll~~l~~~~~~~~~vlVf~~t~~~ae~L~~~L~~~g-i~~~~lh~~~~~~~R~~~~~~f~~g----------------  488 (664)
T 1c4o_A          426 LDLMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHG-IRARYLHHELDAFKRQALIRDLRLG----------------  488 (664)
T ss_dssp             HHHHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHHTT-CCEEEECTTCCHHHHHHHHHHHHTT----------------
T ss_pred             HHHHHHHHHHHhcCCEEEEEECCHHHHHHHHHHHHhcC-CCceeecCCCCHHHHHHHHHHhhcC----------------
Confidence            33444433222345799999999999999999999998 8999999999999999999999999                


Q ss_pred             CCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCC-----CCCHHHHHHHHhhhcC-CCCEEEEEeeCchHHHHHH
Q 029910           92 ETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYEL-----PTKKETYIRRMTTCLA-ADGSVINIVVGGEVVTLRS  165 (185)
Q Consensus        92 ~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~-----P~~~~~yiqR~GR~~~-~~g~~i~~v~~~e~~~~~~  165 (185)
                             ..+|||+|++    +++|+|+|++++||+||.     |.+..+|+||+||+++ ..|.++++++..+....+.
T Consensus       489 -------~~~VLvaT~~----l~~GlDip~v~lVI~~d~d~~G~p~s~~~~iQr~GRagR~~~G~~i~~~~~~~~~~~~~  557 (664)
T 1c4o_A          489 -------HYDCLVGINL----LREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNARGEVWLYADRVSEAMQRA  557 (664)
T ss_dssp             -------SCSEEEESCC----CCTTCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTTCEEEEECSSCCHHHHHH
T ss_pred             -------CceEEEccCh----hhcCccCCCCCEEEEeCCcccCCCCCHHHHHHHHCccCcCCCCEEEEEEcCCCHHHHHH
Confidence                   6999999999    999999999999999997     9999999999999865 4689999998866544443


Q ss_pred             H
Q 029910          166 M  166 (185)
Q Consensus       166 l  166 (185)
                      +
T Consensus       558 i  558 (664)
T 1c4o_A          558 I  558 (664)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=99.85  E-value=2.6e-21  Score=181.60  Aligned_cols=125  Identities=15%  Similarity=0.202  Sum_probs=72.5

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcC------------CCceEEEEecCCCHHHHHHHHHHHhc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL------------ADISFSSLHSDLAETERTLILEEFRH   74 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~------------~~~~~~~l~g~~~~~~R~~~l~~F~~   74 (185)
                      |.+.+.++|..... ..++.++||||+++++++.|+..|...            | .....+||+|+..+|.+++++|++
T Consensus       614 K~~~L~~lL~~~~~-~~~~~kvLIF~~~~~~~~~L~~~L~~~~~~~~~~~~~l~G-~~~~~~hg~~~~~eR~~~l~~F~~  691 (797)
T 4a2q_A          614 KLEELVCILDDAYR-YNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMG-RGRRDQTTGMTLPSQKGVLDAFKT  691 (797)
T ss_dssp             HHHHHHHHHHHHHH-HCSSCCEEEEESSHHHHHHHHHHHHTCSTTCSCCCEEC---------------------------
T ss_pred             HHHHHHHHHHHHhc-cCCCCeEEEEECcHHHHHHHHHHHHhCcccccccceEEEe-cCCcccCCCCCHHHHHHHHHHhhc
Confidence            45556666655343 356689999999999999999999764            3 456677889999999999999999


Q ss_pred             -ccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhcCCCCEEEE
Q 029910           75 -TAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSVIN  153 (185)
Q Consensus        75 -~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~~~~g~~i~  153 (185)
                       |                       ..++||||++    +++|+|+|+|++||+||+|+|+..|+||+||+-..+|.++.
T Consensus       692 ~g-----------------------~~~vLVaT~~----~~~GIDlp~v~~VI~yd~p~s~~~~iQr~GRGR~~~g~~i~  744 (797)
T 4a2q_A          692 SK-----------------------DNRLLIATSV----ADEGIDIVQCNLVVLYEYSGNVTKMIQVRGRGRAAGSKCIL  744 (797)
T ss_dssp             -------------------------CCSEEEEECC-----------CCCSEEEEESCCSCHHHHHTC-------CCCEEE
T ss_pred             cC-----------------------CceEEEEcCc----hhcCCCchhCCEEEEeCCCCCHHHHHHhcCCCCCCCceEEE
Confidence             7                       6999999999    99999999999999999999999999999993225689999


Q ss_pred             EeeCchH
Q 029910          154 IVVGGEV  160 (185)
Q Consensus       154 ~v~~~e~  160 (185)
                      |++.++.
T Consensus       745 l~~~~~~  751 (797)
T 4a2q_A          745 VTSKTEV  751 (797)
T ss_dssp             EECCHHH
T ss_pred             EEeCCcH
Confidence            9988655

>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=99.83  E-value=6.5e-21  Score=182.19  Aligned_cols=125  Identities=15%  Similarity=0.202  Sum_probs=72.7

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcC------------CCceEEEEecCCCHHHHHHHHHHHhc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL------------ADISFSSLHSDLAETERTLILEEFRH   74 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~------------~~~~~~~l~g~~~~~~R~~~l~~F~~   74 (185)
                      |.+.+.++|..... ..++.++||||+++++++.|+..|...            | .....+||+|+..+|.+++++|++
T Consensus       614 K~~~L~~lL~~~~~-~~~~~rvLIF~~t~~~ae~L~~~L~~~~~l~~ik~~~l~G-~~~~~~hg~m~~~eR~~il~~Fr~  691 (936)
T 4a2w_A          614 KLEELVCILDDAYR-YNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMG-RGRRDQTTGMTLPSQKGVLDAFKT  691 (936)
T ss_dssp             HHHHHHHHHHHTTT-SCTTCCEEEEESSHHHHHHHHHHHHHCSTTSSCCCEEC---------------------------
T ss_pred             HHHHHHHHHHHHhc-cCCCCeEEEEeCCHHHHHHHHHHHhhCccccccceeEEec-CCCcccCCCCCHHHHHHHHHHhhc
Confidence            44455555555333 456799999999999999999999875            3 455667888999999999999999


Q ss_pred             -ccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhcCCCCEEEE
Q 029910           75 -TAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSVIN  153 (185)
Q Consensus        75 -~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~~~~g~~i~  153 (185)
                       |                       ..++||||++    +++|+|+|+|++||+||+|+|+..|+||+||+....|.++.
T Consensus       692 ~g-----------------------~~~VLVaT~~----~~eGIDlp~v~~VI~yD~p~s~~~~iQr~GRGR~~~g~vi~  744 (936)
T 4a2w_A          692 SK-----------------------DNRLLIATSV----ADEGIDIVQCNLVVLYEYSGNVTKMIQVRGRGRAAGSKCIL  744 (936)
T ss_dssp             -------------------------CCSEEEEECC----------CCCCSEEEEESCCSCSHHHHCC-------CCCEEE
T ss_pred             cC-----------------------CeeEEEEeCc----hhcCCcchhCCEEEEeCCCCCHHHHHHhcCCCCCCCCEEEE
Confidence             7                       6999999999    99999999999999999999999999999993224588999


Q ss_pred             EeeCchH
Q 029910          154 IVVGGEV  160 (185)
Q Consensus       154 ~v~~~e~  160 (185)
                      +++.++.
T Consensus       745 Li~~~t~  751 (936)
T 4a2w_A          745 VTSKTEV  751 (936)
T ss_dssp             EESCHHH
T ss_pred             EEeCCCH
Confidence            9987654

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=99.83  E-value=2.8e-20  Score=155.29  Aligned_cols=132  Identities=13%  Similarity=0.107  Sum_probs=100.6

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcC-CCceEEEEecCCCHHHHHHHHHHHhcccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL-ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE   85 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~-~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~   85 (185)
                      |.+.+.+++..+..   .+.++||||+++..++.|...|... | +.+..+||+++..+|.+++++|+++.         
T Consensus        97 K~~~L~~ll~~~~~---~~~kvlIFs~~~~~~~~l~~~L~~~~g-~~~~~l~G~~~~~~R~~~i~~F~~~~---------  163 (271)
T 1z5z_A           97 KMIRTMEIIEEALD---EGDKIAIFTQFVDMGKIIRNIIEKELN-TEVPFLYGELSKKERDDIISKFQNNP---------  163 (271)
T ss_dssp             HHHHHHHHHHHHHH---TTCCEEEEESCHHHHHHHHHHHHHHHC-SCCCEECTTSCHHHHHHHHHHHHHCT---------
T ss_pred             HHHHHHHHHHHHHh---CCCeEEEEeccHHHHHHHHHHHHHhcC-CcEEEEECCCCHHHHHHHHHHhcCCC---------
Confidence            45566666666433   4589999999999999999999875 7 89999999999999999999999983         


Q ss_pred             cCCCCCCCCCCCCcee-EEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCC--CEEEEEeeCc--
Q 029910           86 QSGDESETGKDEHKSH-MIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAAD--GSVINIVVGG--  158 (185)
Q Consensus        86 ~~~~~~~~~~~~~~~~-iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~--g~~i~~v~~~--  158 (185)
                                   ..+ +|++|++    +++|+|++.+++||+||+|||+..|.||+||+  .|+.  ..++.+++.+  
T Consensus       164 -------------~~~v~L~st~~----~g~Glnl~~a~~VI~~d~~wnp~~~~Q~~gR~~R~Gq~~~v~v~~li~~~Ti  226 (271)
T 1z5z_A          164 -------------SVKFIVLSVKA----GGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTL  226 (271)
T ss_dssp             -------------TCCEEEEECCT----TCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEETTSH
T ss_pred             -------------CCCEEEEehhh----hcCCcCcccCCEEEEECCCCChhHHHHHHHhccccCCCCceEEEEEeeCCCH
Confidence                         455 7899999    99999999999999999999999999999997  3444  3567788876  


Q ss_pred             hHHHHHHHHH
Q 029910          159 EVVTLRSMEE  168 (185)
Q Consensus       159 e~~~~~~l~~  168 (185)
                      |...++.++.
T Consensus       227 Ee~i~~~~~~  236 (271)
T 1z5z_A          227 EEKIDQLLAF  236 (271)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            4444444443

>1tf5_A Preprotein translocase SECA subunit; ATPase, helicase, translocation, secretion, protein transport; 2.18A {Bacillus subtilis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1tf2_A 3iqy_A 1m6n_A 1m74_A* 3iqm_A 3jv2_A* 2ibm_A* 3dl8_A 1sx0_A 1sx1_A 1tm6_A

Probab=99.82  E-value=4e-20  Score=173.99  Aligned_cols=106  Identities=13%  Similarity=0.142  Sum_probs=95.2

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEE
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMI  103 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iL  103 (185)
                      .+.|+||||+|++.++.|+..|...| +.+.+|||++.+.+|..+.+.|+.                         .+|+
T Consensus       431 ~~~pvLVft~s~~~se~Ls~~L~~~g-i~~~vLhg~~~~rEr~ii~~ag~~-------------------------g~Vl  484 (844)
T 1tf5_A          431 TGQPVLVGTVAVETSELISKLLKNKG-IPHQVLNAKNHEREAQIIEEAGQK-------------------------GAVT  484 (844)
T ss_dssp             HTCCEEEEESCHHHHHHHHHHHHTTT-CCCEEECSSCHHHHHHHHTTTTST-------------------------TCEE
T ss_pred             cCCcEEEEECCHHHHHHHHHHHHHCC-CCEEEeeCCccHHHHHHHHHcCCC-------------------------CeEE
Confidence            45799999999999999999999998 899999999988888766555554                         3599


Q ss_pred             EEecCCCCcccCcCCCC--------CCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCch
Q 029910          104 VVTDACLPLLSSGESAI--------SARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGE  159 (185)
Q Consensus       104 V~Td~~~~~~~~G~d~~--------~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e  159 (185)
                      ||||+    ++||+|++        ++.+|||||+|.+...|+||+||+  .|.+|.+++|++..|
T Consensus       485 IATdm----AgRG~DI~l~~~V~~~ggl~VIn~d~p~s~r~y~hr~GRTGRqG~~G~s~~~vs~eD  546 (844)
T 1tf5_A          485 IATNM----AGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMED  546 (844)
T ss_dssp             EEETT----SSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTS
T ss_pred             EeCCc----cccCcCccccchhhhcCCcEEEEecCCCCHHHHHhhcCccccCCCCCeEEEEecHHH
Confidence            99999    99999999        788999999999999999999997  578899999998765

>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=99.81  E-value=2.6e-20  Score=164.61  Aligned_cols=114  Identities=13%  Similarity=0.093  Sum_probs=95.0

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEE
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIV  104 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV  104 (185)
                      +.++||||++++.++.+++.|...+ +.+..+||    .+|.+++++|++|                       ..+|||
T Consensus       177 ~~~~lVF~~s~~~a~~l~~~L~~~~-~~v~~lhg----~~R~~~~~~F~~g-----------------------~~~vLV  228 (440)
T 1yks_A          177 KRPTAWFLPSIRAANVMAASLRKAG-KSVVVLNR----KTFEREYPTIKQK-----------------------KPDFIL  228 (440)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTT-CCEEECCS----SSCC--------C-----------------------CCSEEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHcC-CCEEEecc----hhHHHHHhhhcCC-----------------------CceEEE
Confidence            5799999999999999999999987 89999999    4688999999999                       799999


Q ss_pred             EecCCCCcccCcCCCCCCcEEEE-------------------cCCCCCHHHHHHHHhhhcC---CCCEEEEEe---eCch
Q 029910          105 VTDACLPLLSSGESAISARVLIN-------------------YELPTKKETYIRRMTTCLA---ADGSVINIV---VGGE  159 (185)
Q Consensus       105 ~Td~~~~~~~~G~d~~~v~~VI~-------------------~d~P~~~~~yiqR~GR~~~---~~g~~i~~v---~~~e  159 (185)
                      ||++    +++|+|+| +++||+                   ||.|.+.++|+||+||+++   ..|.|++|+   ++.+
T Consensus       229 aT~v----~e~GiDip-v~~VI~~g~~~~pv~~~~~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~g~~~~l~~~~~~~~  303 (440)
T 1yks_A          229 ATDI----AEMGANLC-VERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYSEPTSENN  303 (440)
T ss_dssp             ESSS----TTCCTTCC-CSEEEECCEEEEEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCC
T ss_pred             ECCh----hheeeccC-ceEEEeCCccceeeecccccceeeccccccCHHHHHHhccccCCCCCCCceEEEEeccCChhh
Confidence            9999    99999999 999986                   9999999999999999754   479999996   6778


Q ss_pred             HHHHHHHHHHhC
Q 029910          160 VVTLRSMEESLG  171 (185)
Q Consensus       160 ~~~~~~l~~~~~  171 (185)
                      ...++.++..+.
T Consensus       304 ~~~l~~l~~~~~  315 (440)
T 1yks_A          304 AHHVCWLEASML  315 (440)
T ss_dssp             TTBHHHHHHHHH
T ss_pred             hhhhhhhhHHhc
Confidence            888888887753

>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=99.81  E-value=1.6e-19  Score=173.26  Aligned_cols=122  Identities=13%  Similarity=0.173  Sum_probs=102.2

Q ss_pred             HHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhc-CCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCC
Q 029910           10 TLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSN-LADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG   88 (185)
Q Consensus        10 ~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~-~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~   88 (185)
                      .+...+..++. ..++.++||||+++.+++.++..|.. .| +.+..+||+|+..+|.+++++|++++            
T Consensus       489 ~K~~~L~~ll~-~~~~~k~iVF~~~~~~~~~l~~~L~~~~g-~~~~~lhG~~~~~~R~~~l~~F~~g~------------  554 (968)
T 3dmq_A          489 PRVEWLMGYLT-SHRSQKVLVICAKAATALQLEQVLREREG-IRAAVFHEGMSIIERDRAAAWFAEED------------  554 (968)
T ss_dssp             HHHHHHHHHHH-HTSSSCCCEECSSTHHHHHHHHHHHTTTC-CCEEEECTTSCTTHHHHHHHHHHSTT------------
T ss_pred             HHHHHHHHHHH-hCCCCCEEEEeCcHHHHHHHHHHHHHHcC-CcEEEEeCCCCHHHHHHHHHHHhCCC------------
Confidence            34444444454 35678999999999999999999995 46 89999999999999999999999981            


Q ss_pred             CCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEE--EEEeeCc
Q 029910           89 DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSV--INIVVGG  158 (185)
Q Consensus        89 ~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~--i~~v~~~  158 (185)
                               ...++||||++    +++|+|+|++++||+||+|+++..|.||+||+  .|+.|.+  +.++..+
T Consensus       555 ---------~~~~vLvaT~v----~~~GlDl~~~~~VI~~d~p~~~~~~~Q~~GR~~R~Gq~~~v~v~~~~~~~  615 (968)
T 3dmq_A          555 ---------TGAQVLLCSEI----GSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQIHVPYLEK  615 (968)
T ss_dssp             ---------SSCEEEECSCC----TTCSSCCTTCCEEECSSCCSSHHHHHHHHHTTSCSSSCSCCEEEEEEETT
T ss_pred             ---------CcccEEEecch----hhcCCCcccCcEEEEecCCCCHHHHHHHhhccccCCCCceEEEEEecCCC
Confidence                     12999999999    99999999999999999999999999999997  4555644  4444544

>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=99.80  E-value=1.2e-19  Score=167.03  Aligned_cols=114  Identities=10%  Similarity=-0.003  Sum_probs=102.7

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEE
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIV  104 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV  104 (185)
                      ..++||||++++.++.+++.|...+ +.+..+||+    +|.+++++|++|                       ..+|||
T Consensus       355 ~~~~LVF~~s~~~a~~l~~~L~~~g-~~v~~lhg~----~R~~~l~~F~~g-----------------------~~~VLV  406 (618)
T 2whx_A          355 QGKTVWFVPSIKAGNDIANCLRKSG-KRVIQLSRK----TFDTEYPKTKLT-----------------------DWDFVV  406 (618)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHTT-CCEEEECTT----THHHHTTHHHHS-----------------------CCSEEE
T ss_pred             CCCEEEEECChhHHHHHHHHHHHcC-CcEEEEChH----HHHHHHHhhcCC-----------------------CcEEEE
Confidence            4799999999999999999999998 899999984    788899999999                       799999


Q ss_pred             EecCCCCcccCcCCCCCCcEE--------------------EEcCCCCCHHHHHHHHhhhcCC---CCEEEEEee---Cc
Q 029910          105 VTDACLPLLSSGESAISARVL--------------------INYELPTKKETYIRRMTTCLAA---DGSVINIVV---GG  158 (185)
Q Consensus       105 ~Td~~~~~~~~G~d~~~v~~V--------------------I~~d~P~~~~~yiqR~GR~~~~---~g~~i~~v~---~~  158 (185)
                      |||+    +++|+|+| +++|                    ||||+|.+.++|+||+||+++.   +|.+++|++   +.
T Consensus       407 aTdv----~~rGiDi~-v~~VId~g~~~~P~~~~~~~~~~~i~~d~P~s~~~yiQR~GRaGR~g~~~G~ai~l~~~~~~~  481 (618)
T 2whx_A          407 TTDI----SEMGANFR-AGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDPLKN  481 (618)
T ss_dssp             ECGG----GGTTCCCC-CSEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCC
T ss_pred             ECcH----HHcCcccC-ceEEEECcceecceecccCCCceEEcccccCCHHHHHHhccccCCCCCCCCeEEEEccCCchh
Confidence            9999    99999997 9888                    8889999999999999998543   689999997   77


Q ss_pred             hHHHHHHHHHHhC
Q 029910          159 EVVTLRSMEESLG  171 (185)
Q Consensus       159 e~~~~~~l~~~~~  171 (185)
                      |...++.++..+.
T Consensus       482 d~~~l~~le~~i~  494 (618)
T 2whx_A          482 DEDHAHWTEAKML  494 (618)
T ss_dssp             CTTCHHHHHHHHH
T ss_pred             hHHHHHHHHhHhc
Confidence            8888888888753

>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=99.80  E-value=5.6e-19  Score=164.30  Aligned_cols=126  Identities=13%  Similarity=0.154  Sum_probs=102.6

Q ss_pred             EecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccc
Q 029910            4 SFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKV   83 (185)
Q Consensus         4 ~~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~   83 (185)
                      +.++.++...+++.+......+.|+||||+|++.++.|+..|...| +.+..+||++...++..+.+.|+.+        
T Consensus       453 y~t~~eK~~al~~~I~~~~~~gqpVLVFt~S~e~sE~Ls~~L~~~G-i~~~vLhgkq~~rE~~ii~~ag~~g--------  523 (822)
T 3jux_A          453 FRTQKEKYEKIVEEIEKRYKKGQPVLVGTTSIEKSELLSSMLKKKG-IPHQVLNAKYHEKEAEIVAKAGQKG--------  523 (822)
T ss_dssp             ESSHHHHHHHHHHHHHHHHHHTCCEEEEESSHHHHHHHHHHHHTTT-CCCEEECSCHHHHHHHHHHHHHSTT--------
T ss_pred             EecHHHHHHHHHHHHHHHhhCCCCEEEEECCHHHHHHHHHHHHHCC-CCEEEeeCCchHHHHHHHHhCCCCC--------
Confidence            3344455555555543322356899999999999999999999998 8999999997666666555556554        


Q ss_pred             cccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCC--------CCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEE
Q 029910           84 TEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAI--------SARVLINYELPTKKETYIRRMTTC--LAADGSVIN  153 (185)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~--------~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~  153 (185)
                                       .|+||||+    ++||+|++        +..+||||++|.+...|+||+||+  .|.+|.+++
T Consensus       524 -----------------~VtVATdm----AgRGtDI~lg~~V~~~GglhVInte~Pes~r~y~qriGRTGRqG~~G~a~~  582 (822)
T 3jux_A          524 -----------------MVTIATNM----AGRGTDIKLGPGVAELGGLCIIGTERHESRRIDNQLRGRAGRQGDPGESIF  582 (822)
T ss_dssp             -----------------CEEEEETT----TTTTCCCCCCTTTTTTTSCEEEESSCCSSHHHHHHHHTTSSCSSCCCEEEE
T ss_pred             -----------------eEEEEcch----hhCCcCccCCcchhhcCCCEEEecCCCCCHHHHHHhhCccccCCCCeeEEE
Confidence                             59999999    99999998        667999999999999999999997  567899999


Q ss_pred             EeeCch
Q 029910          154 IVVGGE  159 (185)
Q Consensus       154 ~v~~~e  159 (185)
                      |++..|
T Consensus       583 fvsleD  588 (822)
T 3jux_A          583 FLSLED  588 (822)
T ss_dssp             EEETTS
T ss_pred             EechhH
Confidence            999876

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.79  E-value=5.4e-19  Score=171.54  Aligned_cols=125  Identities=15%  Similarity=0.231  Sum_probs=103.7

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEE-EEecCCCHHHHHHHHHHHhcccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS-SLHSDLAETERTLILEEFRHTAMKWNQKVTE   85 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~-~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~   85 (185)
                      +.+.+.+++.. .     +.++||||++++.++.++..|...| +.+. .+||+     |.+ +++|++|          
T Consensus       297 k~~~L~~ll~~-~-----~~~~LVF~~s~~~a~~l~~~L~~~g-~~~~~~lhg~-----rr~-l~~F~~G----------  353 (1104)
T 4ddu_A          297 SKEKLVELLEI-F-----RDGILIFAQTEEEGKELYEYLKRFK-FNVGETWSEF-----EKN-FEDFKVG----------  353 (1104)
T ss_dssp             CHHHHHHHHHH-H-----CSSEEEEESSSHHHHHHHHHHHHTT-CCEEESSSSH-----HHH-HHHHHHT----------
T ss_pred             HHHHHHHHHHh-c-----CCCEEEEECcHHHHHHHHHHHHhCC-CCeeeEecCc-----HHH-HHHHHCC----------
Confidence            44555566655 2     2899999999999999999999998 8998 99993     555 9999999          


Q ss_pred             cCCCCCCCCCCCCceeEEEE----ecCCCCcccCcCCCCC-CcEEEEcCCCC----------------------------
Q 029910           86 QSGDESETGKDEHKSHMIVV----TDACLPLLSSGESAIS-ARVLINYELPT----------------------------  132 (185)
Q Consensus        86 ~~~~~~~~~~~~~~~~iLV~----Td~~~~~~~~G~d~~~-v~~VI~~d~P~----------------------------  132 (185)
                                   ..++|||    |++    ++||+|+|+ |++|||||+|.                            
T Consensus       354 -------------~~~VLVatas~Tdv----larGIDip~~V~~VI~~d~P~~~~Sle~~~~~~~~~~~l~~l~~~~~~~  416 (1104)
T 4ddu_A          354 -------------KINILIGVQAYYGK----LTRGVDLPERIKYVIFWGTPSMRFSLELDKAPRFVLARVLKEMGLIKAQ  416 (1104)
T ss_dssp             -------------SCSEEEEETTTHHH----HCCSCCCTTTCCEEEEESCCEEEEECSSSSCCHHHHHHHHHHHSSCSSC
T ss_pred             -------------CCCEEEEecCCCCe----eEecCcCCCCCCEEEEECCCCCCCCcccccCHHHHHHHHHHHHHHHHHH
Confidence                         7999999    999    999999999 99999999999                            


Q ss_pred             --------------------------------------------CHHHHHHHHhhhcC--CCC--EEEEEeeCchHHHHH
Q 029910          133 --------------------------------------------KKETYIRRMTTCLA--ADG--SVINIVVGGEVVTLR  164 (185)
Q Consensus       133 --------------------------------------------~~~~yiqR~GR~~~--~~g--~~i~~v~~~e~~~~~  164 (185)
                                                                  ++.+|+||+||+++  .+|  .+++++..+|...+.
T Consensus       417 ~~~~~~~~~e~~~~~l~~~~~~~~i~~~~~~l~~~~~~~~~~~pd~~tYihr~GRtgR~~~gg~~~Glsi~~~~d~~~~~  496 (1104)
T 4ddu_A          417 ENPDVEELRKIAKEHLTQKEFVEKVKEMFRGVVVKDEDLELIIPDVYTYIQASGRSSRILNGVLVKGVSVIFEEDEEIFE  496 (1104)
T ss_dssp             CCCHHHHHHHHHHHCCCHHHHHHHHHHHCCSSEEETTTTEEEEECHHHHHHHHHTTCCEETTEECCEEEEEECCCHHHHH
T ss_pred             HHHHHHHHHHHHHHHhccHHHHHHHhhccceEEecCCeeEEEecChhhhhcccCchhcccCCCcccceEEEEEecHHHHH
Confidence                                                        88999999999865  332  334444447888888


Q ss_pred             HHHHHhC
Q 029910          165 SMEESLG  171 (185)
Q Consensus       165 ~l~~~~~  171 (185)
                      .+++.++
T Consensus       497 ~l~~~~~  503 (1104)
T 4ddu_A          497 SLKTRLL  503 (1104)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            8888775

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.77  E-value=4.5e-18  Score=157.41  Aligned_cols=143  Identities=19%  Similarity=0.209  Sum_probs=109.2

Q ss_pred             HHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCC-----------------------------------ceE
Q 029910            9 ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLAD-----------------------------------ISF   53 (185)
Q Consensus         9 ~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~-----------------------------------~~~   53 (185)
                      +.+.+++..+..   ++.++||||++++.++.++..|.....                                   ..+
T Consensus       239 ~~~~~~~~~~~~---~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~~~v  315 (715)
T 2va8_A          239 DAIIAYTLDSLS---KNGQVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSLISKGV  315 (715)
T ss_dssp             SHHHHHHHHHHT---TTCCEEEECSSHHHHHHHHHHHHHTTTSSCCCHHHHHHHHHHHHTCCSSCHHHHHHHHHHHTTTE
T ss_pred             hHHHHHHHHHHh---cCCCEEEEECCHHHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHhhhccccccHHHHHHHhcCE
Confidence            445555555443   458999999999999999999976421                                   138


Q ss_pred             EEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEE----cC
Q 029910           54 SSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLIN----YE  129 (185)
Q Consensus        54 ~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~----~d  129 (185)
                      ..+||+|+..+|..+++.|++|                       ..+|||||++    +++|+|+|++++||+    ||
T Consensus       316 ~~~h~~l~~~~r~~v~~~f~~g-----------------------~~~vlvaT~~----l~~Gidip~~~~VI~~~~~~d  368 (715)
T 2va8_A          316 AYHHAGLSKALRDLIEEGFRQR-----------------------KIKVIVATPT----LAAGVNLPARTVIIGDIYRFN  368 (715)
T ss_dssp             EEECTTSCHHHHHHHHHHHHTT-----------------------CSCEEEECGG----GGGSSCCCBSEEEECCC----
T ss_pred             EEECCCCCHHHHHHHHHHHHcC-----------------------CCeEEEEChH----HhcccCCCceEEEEeCCeecc
Confidence            9999999999999999999999                       7999999999    999999999999999    99


Q ss_pred             -------CCCCHHHHHHHHhhhcCC----CCEEEEEeeCchHHHHHHHHHHhCCccccccCCcc
Q 029910          130 -------LPTKKETYIRRMTTCLAA----DGSVINIVVGGEVVTLRSMEESLGLIVAEVPINIS  182 (185)
Q Consensus       130 -------~P~~~~~yiqR~GR~~~~----~g~~i~~v~~~e~~~~~~l~~~~~~~~~~~~~~~~  182 (185)
                             .|.+..+|.||+||+|+.    .|.|+.+++..+. ....+++.+....+++..++.
T Consensus       369 ~~~~~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~~-~~~~~~~~l~~~~e~~~s~l~  431 (715)
T 2va8_A          369 KKIAGYYDEIPIMEYKQMSGRAGRPGFDQIGESIVVVRDKED-VDRVFKKYVLSDVEPIESKLG  431 (715)
T ss_dssp             ----------CHHHHHHHHTTBCCTTTCSCEEEEEECSCGGG-HHHHHHHTTSSCCCCCCCSCC
T ss_pred             ccCCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEEeCCchH-HHHHHHHHHcCCCCCceecCC
Confidence                   899999999999998653    5899999877653 112344455555555554443

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.77  E-value=6.7e-19  Score=163.40  Aligned_cols=114  Identities=9%  Similarity=0.029  Sum_probs=101.3

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEE
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMI  103 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iL  103 (185)
                      .+.++||||++++.++.+++.|...+ +.+..+||+    +|.+++++|++|                       ..+||
T Consensus       409 ~~~~~lVF~~s~~~~e~la~~L~~~g-~~v~~lHg~----eR~~v~~~F~~g-----------------------~~~VL  460 (673)
T 2wv9_A          409 YAGKTVWFVASVKMSNEIAQCLQRAG-KRVIQLNRK----SYDTEYPKCKNG-----------------------DWDFV  460 (673)
T ss_dssp             CCSCEEEECSSHHHHHHHHHHHHTTT-CCEEEECSS----SHHHHGGGGGTC-----------------------CCSEE
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHhCC-CeEEEeChH----HHHHHHHHHHCC-----------------------CceEE
Confidence            46899999999999999999999997 899999993    899999999999                       79999


Q ss_pred             EEecCCCCcccCcCCCCCCcEEEE--------------------cCCCCCHHHHHHHHhhhc---CCCCEEEEEe---eC
Q 029910          104 VVTDACLPLLSSGESAISARVLIN--------------------YELPTKKETYIRRMTTCL---AADGSVINIV---VG  157 (185)
Q Consensus       104 V~Td~~~~~~~~G~d~~~v~~VI~--------------------~d~P~~~~~yiqR~GR~~---~~~g~~i~~v---~~  157 (185)
                      |||++    +++|+|+| +++|||                    ||+|.+.++|+||+||++   +..|.|+.|+   ++
T Consensus       461 VaTdv----~e~GIDip-v~~VI~~g~~~~p~vi~da~~r~~ll~d~P~s~~~y~Qr~GRaGR~~g~~G~ai~l~~~~~~  535 (673)
T 2wv9_A          461 ITTDI----SEMGANFG-ASRVIDCRKSVKPTILDEGEGRVILSVPSAITSASAAQRRGRVGRNPSQIGDEYHYGGGTSE  535 (673)
T ss_dssp             EECGG----GGTTCCCC-CSEEEECCEECCEEEECSTTCEEEECCSEECCHHHHHHHHTTSSCCSSCCCEEEEECSCCCC
T ss_pred             EECch----hhcceeeC-CcEEEECCCcccceeeecccccceecccCCCCHHHHHHHhhccCCCCCCCCEEEEEEecCCh
Confidence            99999    99999999 999998                    679999999999999974   4578999996   56


Q ss_pred             chHHHHHHHHHHh
Q 029910          158 GEVVTLRSMEESL  170 (185)
Q Consensus       158 ~e~~~~~~l~~~~  170 (185)
                      .+...++.++..+
T Consensus       536 ~d~~~l~~ie~~~  548 (673)
T 2wv9_A          536 DDTMLAHWTEAKI  548 (673)
T ss_dssp             CCTTBHHHHHHHH
T ss_pred             hHHHHHHHHHHHH
Confidence            7776777777664

>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=99.77  E-value=1.5e-19  Score=160.39  Aligned_cols=101  Identities=9%  Similarity=0.023  Sum_probs=89.6

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEE
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIV  104 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV  104 (185)
                      ..++||||++++.++.+++.|...+ +.+..+||+    +|.+++++|++|                       ..+|||
T Consensus       190 ~~~~LVF~~s~~~~~~l~~~L~~~g-~~v~~lh~~----~R~~~~~~f~~g-----------------------~~~iLV  241 (459)
T 2z83_A          190 AGKTVWFVASVKMGNEIAMCLQRAG-KKVIQLNRK----SYDTEYPKCKNG-----------------------DWDFVI  241 (459)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTT-CCEEEESTT----CCCCCGGGSSSC-----------------------CCSEEE
T ss_pred             CCCEEEEeCChHHHHHHHHHHHhcC-CcEEecCHH----HHHHHHhhccCC-----------------------CceEEE
Confidence            4799999999999999999999998 899999994    788899999998                       799999


Q ss_pred             EecCCCCcccCcCCCCCCcEEEE--------------------cCCCCCHHHHHHHHhhhcCC---CCEEEEEeeCc
Q 029910          105 VTDACLPLLSSGESAISARVLIN--------------------YELPTKKETYIRRMTTCLAA---DGSVINIVVGG  158 (185)
Q Consensus       105 ~Td~~~~~~~~G~d~~~v~~VI~--------------------~d~P~~~~~yiqR~GR~~~~---~g~~i~~v~~~  158 (185)
                      ||++    +++|+|+|+ ++||+                    ||+|.+.++|+||+||+++.   +|.++.|+...
T Consensus       242 aT~v----~~~GiDip~-~~VI~~G~~~~~~~~~~~~~~~~~~~d~p~s~~~~~QR~GRaGR~g~~~G~~~~~~~~~  313 (459)
T 2z83_A          242 TTDI----SEMGANFGA-SRVIDCRKSVKPTILEEGEGRVILGNPSPITSASAAQRRGRVGRNPNQVGDEYHYGGAT  313 (459)
T ss_dssp             ESSC----C---CCCSC-SEEEECCEECCEEEECSSSCEEEECSCEECCHHHHHHHHTTSSCCTTCCCEEEEECSCC
T ss_pred             ECCh----HHhCeecCC-CEEEECCcccccccccccccccccccCCCCCHHHHHHhccccCCCCCCCCeEEEEEccc
Confidence            9999    999999999 99999                    88999999999999998543   78999999764

>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=99.76  E-value=2.6e-18  Score=161.69  Aligned_cols=124  Identities=12%  Similarity=0.141  Sum_probs=103.9

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ   86 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~   86 (185)
                      ..++...+++.+......+.|+||||+|++.++.|+..|...| +++.+|||++.+.++..+.+.|+.|           
T Consensus       423 ~~~K~~al~~~i~~~~~~gqpvLVft~sie~se~Ls~~L~~~g-i~~~vLnak~~~rEa~iia~agr~G-----------  490 (853)
T 2fsf_A          423 EAEKIQAIIEDIKERTAKGQPVLVGTISIEKSELVSNELTKAG-IKHNVLNAKFHANEAAIVAQAGYPA-----------  490 (853)
T ss_dssp             HHHHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHHHTT-CCCEECCTTCHHHHHHHHHTTTSTT-----------
T ss_pred             HHHHHHHHHHHHHHHhcCCCCEEEEECcHHHHHHHHHHHHHCC-CCEEEecCChhHHHHHHHHhcCCCC-----------
Confidence            3344334444432322467899999999999999999999998 8999999999888888888888775           


Q ss_pred             CCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCC-------------------------------------cEEEEcC
Q 029910           87 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISA-------------------------------------RVLINYE  129 (185)
Q Consensus        87 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v-------------------------------------~~VI~~d  129 (185)
                                    .|+||||+    ++||+|++..                                     .+|||||
T Consensus       491 --------------~VtIATnm----AgRGtDI~l~gn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGl~VI~te  552 (853)
T 2fsf_A          491 --------------AVTIATNM----AGRGTDIVLGGSWQAEVAALENPTAEQIEKIKADWQVRHDAVLEAGGLHIIGTE  552 (853)
T ss_dssp             --------------CEEEEESC----CSSCSCCCTTCCHHHHHHHCSSCCSSHHHHHHHHHHHHHHHHHHTTSEEEEESS
T ss_pred             --------------eEEEeccc----ccCCcCccCCCchHhhhhhcccchhHHHHHHHHHhhhhhhHHHhcCCcEEEEcc
Confidence                          49999999    9999999984                                     5999999


Q ss_pred             CCCCHHHHHHHHhhh--cCCCCEEEEEeeCchH
Q 029910          130 LPTKKETYIRRMTTC--LAADGSVINIVVGGEV  160 (185)
Q Consensus       130 ~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~  160 (185)
                      +|.+...|.||+||+  .|.+|.+++|++..|.
T Consensus       553 ~pes~riy~qr~GRTGRqGd~G~s~~fls~eD~  585 (853)
T 2fsf_A          553 RHESRRIDNQLRGRSGRQGDAGSSRFYLSMEDA  585 (853)
T ss_dssp             CCSSHHHHHHHHTTSSGGGCCEEEEEEEETTSG
T ss_pred             CCCCHHHHHhhccccccCCCCeeEEEEecccHH
Confidence            999999999999997  5788999999987663

>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=99.76  E-value=4.1e-18  Score=158.08  Aligned_cols=139  Identities=18%  Similarity=0.155  Sum_probs=111.2

Q ss_pred             HHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCC-----------------C---------------ceEEEEec
Q 029910           11 LVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLA-----------------D---------------ISFSSLHS   58 (185)
Q Consensus        11 l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~-----------------~---------------~~~~~l~g   58 (185)
                      +.+++..+..   ++.++||||++++.++.++..|....                 .               ..+..+||
T Consensus       226 ~~~~~~~~~~---~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~v~~~h~  302 (720)
T 2zj8_A          226 WEELVYDAIR---KKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHHA  302 (720)
T ss_dssp             TTHHHHHHHH---TTCCEEEECSCHHHHHHHHHHHHHHHGGGSCHHHHHHHHHHHHTSCSCHHHHHHHHHHTTTEEEECT
T ss_pred             HHHHHHHHHh---CCCCEEEEecCHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHhcccchHHHHHHHhcCeeeecC
Confidence            3444444333   35899999999999999999987531                 0               13899999


Q ss_pred             CCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEE----cC----C
Q 029910           59 DLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLIN----YE----L  130 (185)
Q Consensus        59 ~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~----~d----~  130 (185)
                      +|+..+|..+++.|++|                       .++|||||++    +++|+|+|++++||+    ||    .
T Consensus       303 ~l~~~~R~~v~~~f~~g-----------------------~~~vlvaT~~----l~~Gvdip~~~~VI~~~~~yd~~g~~  355 (720)
T 2zj8_A          303 GLGRDERVLVEENFRKG-----------------------IIKAVVATPT----LSAGINTPAFRVIIRDIWRYSDFGME  355 (720)
T ss_dssp             TSCHHHHHHHHHHHHTT-----------------------SSCEEEECST----TGGGCCCCBSEEEECCSEECCSSSCE
T ss_pred             CCCHHHHHHHHHHHHCC-----------------------CCeEEEECcH----hhccCCCCceEEEEcCCeeecCCCCc
Confidence            99999999999999999                       7999999999    999999999999999    88    6


Q ss_pred             CCCHHHHHHHHhhhcCC----CCEEEEEeeCchHHHHHHHHHHhCCccccccCCc
Q 029910          131 PTKKETYIRRMTTCLAA----DGSVINIVVGGEVVTLRSMEESLGLIVAEVPINI  181 (185)
Q Consensus       131 P~~~~~yiqR~GR~~~~----~g~~i~~v~~~e~~~~~~l~~~~~~~~~~~~~~~  181 (185)
                      |.+..+|.||+||+++.    .|.|+.+++..+..  ..+++.+....+++...+
T Consensus       356 ~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~~~--~~~~~~~~~~~~~i~s~l  408 (720)
T 2zj8_A          356 RIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSDDPR--EVMNHYIFGKPEKLFSQL  408 (720)
T ss_dssp             ECCHHHHHHHHTTBCCTTTCSEEEEEEECSSSCHH--HHHHHHTTSCCCCCCCCT
T ss_pred             cCCHHHHHHHHhhcCCCCCCCCceEEEEecCccHH--HHHHHHhcCCCCCcEeec
Confidence            99999999999998663    58899999877632  234556665666655443

>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=99.76  E-value=2.5e-18  Score=166.16  Aligned_cols=114  Identities=16%  Similarity=0.179  Sum_probs=98.3

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEE
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIV  104 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV  104 (185)
                      +.++||||++++.|+.+++.|...  +.+..+||++     .+++++|++|                       ..++||
T Consensus       275 ~~~~LVF~~t~~~a~~l~~~L~~~--~~v~~lhg~~-----~~~l~~F~~G-----------------------~~~VLV  324 (1054)
T 1gku_B          275 GTGGIIYARTGEEAEEIYESLKNK--FRIGIVTATK-----KGDYEKFVEG-----------------------EIDHLI  324 (1054)
T ss_dssp             CSCEEEEESSHHHHHHHHHTTTTS--SCEEECTTSS-----SHHHHHHHHT-----------------------SCSEEE
T ss_pred             CCCEEEEEcCHHHHHHHHHHHhhc--cCeeEEeccH-----HHHHHHHHcC-----------------------CCcEEE
Confidence            478999999999999999999877  7999999998     3788999999                       699999


Q ss_pred             E----ecCCCCcccCcCCCCCC-cEEEEcCCC------------------------------------------------
Q 029910          105 V----TDACLPLLSSGESAISA-RVLINYELP------------------------------------------------  131 (185)
Q Consensus       105 ~----Td~~~~~~~~G~d~~~v-~~VI~~d~P------------------------------------------------  131 (185)
                      |    |++    +++|+|+|+| ++||+||+|                                                
T Consensus       325 aTas~Tdv----~~rGIDip~VI~~VI~~~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  400 (1054)
T 1gku_B          325 GTAHYYGT----LVRGLDLPERIRFAVFVGCPSFRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLLPAVERHIDEVREIL  400 (1054)
T ss_dssp             EECC----------CCSCCTTTCCEEEEESCCEEEEECSCGGGSCHHHHHHHHTTTSCHHHHHTTCTTTSSCHHHHHHHH
T ss_pred             EecCCCCe----eEeccccCCcccEEEEeCCCcccccccccccChHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            9    899    9999999996 999999999                                                


Q ss_pred             -----------------------CCHHHHHHHHhhhcC--CCC--EEEEEeeCchHHHHHHHHHHhCC
Q 029910          132 -----------------------TKKETYIRRMTTCLA--ADG--SVINIVVGGEVVTLRSMEESLGL  172 (185)
Q Consensus       132 -----------------------~~~~~yiqR~GR~~~--~~g--~~i~~v~~~e~~~~~~l~~~~~~  172 (185)
                                             .+..+|+||+||+++  .+|  .+++++...+...+..+++.++.
T Consensus       401 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~yiQr~GRagR~g~~g~~~g~~~~~~~d~~~~~~l~~~l~~  468 (1054)
T 1gku_B          401 KKVMGKERPQAKDVVVREGEVIFPDLRTYIQGSGRTSRLFAGGLTKGASFLLEDDSELLSAFIERAKL  468 (1054)
T ss_dssp             HHHHTTSCCSCSSSEEETTEEEEECHHHHHHHHHTTCCEETTEECCEEEEEECSCHHHHHHHHHHHHT
T ss_pred             HHHhccccccccceeEeecceecCcHHHHhhhhchhhhccCCCCceEEEEEEecCHHHHHHHHHHHhh
Confidence                                   799999999999866  565  48888988899999999988774

>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=99.76  E-value=5.5e-19  Score=166.12  Aligned_cols=111  Identities=12%  Similarity=0.165  Sum_probs=99.4

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhc----------CCCceEEEEecCCCHHHHHHHHHHHh-----cccccccccccccC
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSN----------LADISFSSLHSDLAETERTLILEEFR-----HTAMKWNQKVTEQS   87 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~----------~~~~~~~~l~g~~~~~~R~~~l~~F~-----~~~~~~~~~~~~~~   87 (185)
                      ....++||||++++.++.+++.|..          ..++.+..+||+|++++|.++++.|+     .|            
T Consensus       301 ~~~g~iLVF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~~~eR~~v~~~f~~~~~~~g------------  368 (773)
T 2xau_A          301 EEAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNGRP------------  368 (773)
T ss_dssp             SCSCEEEEECSCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECTTCCHHHHGGGGSCCCCCSSSSC------------
T ss_pred             cCCCCEEEECCCHHHHHHHHHHHHHHHHhhcccccCCCeEEEEeCCCCCHHHHHHHHhhcccccCCCC------------
Confidence            3468999999999999999999974          13388999999999999999999998     76            


Q ss_pred             CCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCC------------------CCCHHHHHHHHhhhcC-CC
Q 029910           88 GDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYEL------------------PTKKETYIRRMTTCLA-AD  148 (185)
Q Consensus        88 ~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~------------------P~~~~~yiqR~GR~~~-~~  148 (185)
                                 ..+|||||++    +++|+|+|++++||++++                  |.+.++|+||+||+|+ .+
T Consensus       369 -----------~~kVlVAT~i----ae~GidIp~v~~VId~g~~k~~~yd~~~g~~~L~~~p~S~~s~~QR~GRaGR~~~  433 (773)
T 2xau_A          369 -----------GRKVVISTNI----AETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRTRP  433 (773)
T ss_dssp             -----------CEEEEEECTH----HHHTCCCTTEEEEEECSEEEEEEEETTTTEEEEEEEECCHHHHHHHHHGGGSSSS
T ss_pred             -----------ceEEEEeCcH----HHhCcCcCCeEEEEeCCCccceeeccccCccccccccCCHHHHHhhccccCCCCC
Confidence                       7999999999    999999999999999888                  8999999999999976 57


Q ss_pred             CEEEEEeeCchH
Q 029910          149 GSVINIVVGGEV  160 (185)
Q Consensus       149 g~~i~~v~~~e~  160 (185)
                      |.|+.+++..+.
T Consensus       434 G~~~~l~~~~~~  445 (773)
T 2xau_A          434 GKCFRLYTEEAF  445 (773)
T ss_dssp             EEEEESSCHHHH
T ss_pred             CEEEEEecHHHh
Confidence            999999976543

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.75  E-value=6.2e-18  Score=162.92  Aligned_cols=128  Identities=17%  Similarity=0.196  Sum_probs=106.1

Q ss_pred             HHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCc--------------------------------------
Q 029910           10 TLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADI--------------------------------------   51 (185)
Q Consensus        10 ~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~--------------------------------------   51 (185)
                      .+..++..+..  ....++||||++++.|+.++..|...+..                                      
T Consensus       330 ~l~~l~~~l~~--~~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~  407 (1010)
T 2xgj_A          330 DIYKIVKMIWK--KKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRR  407 (1010)
T ss_dssp             HHHHHHHHHHH--HTCCSEEEEESSHHHHHHHHHTTTTSCCCCHHHHHHHHHHHHHHHTTSCGGGTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHh--cCCCCEEEEECCHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHHhC
Confidence            34455555433  23469999999999999999999775410                                      


Q ss_pred             eEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEE----
Q 029910           52 SFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLIN----  127 (185)
Q Consensus        52 ~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~----  127 (185)
                      .+..+||+|++.+|..+++.|++|                       .+++||||++    +++|+|+|++++||+    
T Consensus       408 gI~~~Hggl~~~eR~~ve~~F~~G-----------------------~ikVLVAT~~----la~GIDiP~~~vVI~~~~k  460 (1010)
T 2xgj_A          408 GIGIHHSGLLPILKEVIEILFQEG-----------------------FLKVLFATET----FSIGLNMPAKTVVFTSVRK  460 (1010)
T ss_dssp             TEEEESTTSCHHHHHHHHHHHHTT-----------------------CCSEEEEEGG----GGGSTTCCBSEEEESCSEE
T ss_pred             CeeEECCCCCHHHHHHHHHHHhcC-----------------------CCcEEEEehH----hhccCCCCCceEEEeCCcc
Confidence            178899999999999999999999                       7999999999    999999999999999    


Q ss_pred             cCC----CCCHHHHHHHHhhhcCC----CCEEEEEeeCc-hHHHHHHH
Q 029910          128 YEL----PTKKETYIRRMTTCLAA----DGSVINIVVGG-EVVTLRSM  166 (185)
Q Consensus       128 ~d~----P~~~~~yiqR~GR~~~~----~g~~i~~v~~~-e~~~~~~l  166 (185)
                      ||.    |.++.+|+||+||+++.    .|.|+.++++. +...+..+
T Consensus       461 fd~~~~rp~s~~~y~Qr~GRAGR~G~d~~G~vi~l~~~~~e~~~~~~l  508 (1010)
T 2xgj_A          461 WDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGM  508 (1010)
T ss_dssp             ECSSCEEECCHHHHHHHHTTBCCTTTCSSEEEEEEECSCCCHHHHHHH
T ss_pred             cCCcCCccCCHHHHhHhhhhcccCCCCCceEEEEEECCCCCHHHHHHH
Confidence            999    99999999999998654    39999999865 54444444

>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=99.75  E-value=7.8e-18  Score=155.79  Aligned_cols=140  Identities=18%  Similarity=0.218  Sum_probs=110.2

Q ss_pred             HHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCC-----------------------------CceEEEEecCCC
Q 029910           11 LVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLA-----------------------------DISFSSLHSDLA   61 (185)
Q Consensus        11 l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~-----------------------------~~~~~~l~g~~~   61 (185)
                      +.+++..++.   ++.++||||++++.++.++..|....                             ...+..+||+|+
T Consensus       231 ~~~~~~~~~~---~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~i~~~~~~~~~~~l~~~~~~~v~~~h~~l~  307 (702)
T 2p6r_A          231 FEELVEECVA---ENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLL  307 (702)
T ss_dssp             HHHHHHHHHH---TTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSC
T ss_pred             HHHHHHHHHh---cCCCEEEEcCCHHHHHHHHHHHHHHHHhhcChHHHHHHHHhhccccccHHHHHHHhcCeEEecCCCC
Confidence            4455544343   45899999999999999999886420                             024788999999


Q ss_pred             HHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEE----cC---CCCCH
Q 029910           62 ETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLIN----YE---LPTKK  134 (185)
Q Consensus        62 ~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~----~d---~P~~~  134 (185)
                      .++|..+++.|++|                       .++|||||++    +++|+|+|++++||+    ||   .|.+.
T Consensus       308 ~~~R~~v~~~f~~g-----------------------~~~vlvaT~~----l~~Gidip~~~~VI~~~~~yd~~~~~~s~  360 (702)
T 2p6r_A          308 NGQRRVVEDAFRRG-----------------------NIKVVVATPT----LAAGVNLPARRVIVRSLYRFDGYSKRIKV  360 (702)
T ss_dssp             HHHHHHHHHHHHTT-----------------------SCCEEEECST----TTSSSCCCBSEEEECCSEEESSSEEECCH
T ss_pred             HHHHHHHHHHHHCC-----------------------CCeEEEECcH----HhccCCCCceEEEEcCceeeCCCCCcCCH
Confidence            99999999999999                       7999999999    999999999999999    77   79999


Q ss_pred             HHHHHHHhhhcCC----CCEEEEEeeCchHHHHHHHHHHhCCccccccCCcc
Q 029910          135 ETYIRRMTTCLAA----DGSVINIVVGGEVVTLRSMEESLGLIVAEVPINIS  182 (185)
Q Consensus       135 ~~yiqR~GR~~~~----~g~~i~~v~~~e~~~~~~l~~~~~~~~~~~~~~~~  182 (185)
                      .+|.||+||+++.    .|.|+.+++..+..  ..+++.+....+++..++.
T Consensus       361 ~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~~~--~~~~~~l~~~~e~~~s~l~  410 (702)
T 2p6r_A          361 SEYKQMAGRAGRPGMDERGEAIIIVGKRDRE--IAVKRYIFGEPERITSKLG  410 (702)
T ss_dssp             HHHHHHHTTBSCTTTCSCEEEEEECCGGGHH--HHHHTTTSSCCCCCCCCCC
T ss_pred             HHHHHHhhhcCCCCCCCCceEEEEecCccHH--HHHHHHhcCCCCCceeecC
Confidence            9999999998653    58999999877632  2233445555555554443

>1nkt_A Preprotein translocase SECA 1 subunit; preprotein translocation, ATPase, transmembrane transport, helicase-like motor domain; HET: ADP; 2.60A {Mycobacterium tuberculosis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1nl3_A

Probab=99.74  E-value=1.6e-17  Score=156.93  Aligned_cols=124  Identities=14%  Similarity=0.144  Sum_probs=102.8

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ   86 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~   86 (185)
                      ..++...+++.+......++|+||||+|++.++.|+..|...| +++.+|||++.+.++..+.+.|+.|           
T Consensus       442 ~~~K~~al~~~i~~~~~~gqpvLVft~Sie~sE~Ls~~L~~~G-i~~~vLnak~~~rEa~iia~agr~G-----------  509 (922)
T 1nkt_A          442 EEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRR-IPHNVLNAKYHEQEATIIAVAGRRG-----------  509 (922)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTT-CCCEEECSSCHHHHHHHHHTTTSTT-----------
T ss_pred             HHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCC-CCEEEecCChhHHHHHHHHhcCCCC-----------
Confidence            3334334444433312356899999999999999999999998 9999999998888877777777765           


Q ss_pred             CCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCC--------------------------------------------
Q 029910           87 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISA--------------------------------------------  122 (185)
Q Consensus        87 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v--------------------------------------------  122 (185)
                                    .|+||||+    ++||+|++.+                                            
T Consensus       510 --------------~VtIATnm----AgRGtDI~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  571 (922)
T 1nkt_A          510 --------------GVTVATNM----AGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEA  571 (922)
T ss_dssp             --------------CEEEEETT----CSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHH
T ss_pred             --------------eEEEecch----hhcCccccCCCCHHHHHHHHHhhccccccccchhhHHHHHHHHHHHHHHHHHhh
Confidence                          48999999    9999999986                                            


Q ss_pred             --------cEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchH
Q 029910          123 --------RVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEV  160 (185)
Q Consensus       123 --------~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~  160 (185)
                              .+|||||+|.+...|.||+||+  .|.+|.+++|++..|.
T Consensus       572 ~~V~~~GGlhVI~te~pes~riy~qr~GRTGRqGdpG~s~fflSleD~  619 (922)
T 1nkt_A          572 KEVIEAGGLYVLGTERHESRRIDNQLRGRSGRQGDPGESRFYLSLGDE  619 (922)
T ss_dssp             HHHHHTTSEEEEECSCCSSHHHHHHHHHTSSGGGCCEEEEEEEETTSH
T ss_pred             hHHHhcCCcEEEeccCCCCHHHHHHHhcccccCCCCeeEEEEechhHH
Confidence                    4999999999999999999997  5788999999987654

>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=99.74  E-value=5.4e-18  Score=149.92  Aligned_cols=99  Identities=11%  Similarity=0.036  Sum_probs=89.2

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEE
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIV  104 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV  104 (185)
                      ..++||||++++.++.+++.|...+ +.+..+||++.    .+++++|++|                       ..+|||
T Consensus       188 ~~~~lVF~~s~~~a~~l~~~L~~~g-~~~~~lh~~~~----~~~~~~f~~g-----------------------~~~vLV  239 (451)
T 2jlq_A          188 QGKTVWFVPSIKAGNDIANCLRKSG-KRVIQLSRKTF----DTEYPKTKLT-----------------------DWDFVV  239 (451)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHTTT-CCEEEECTTTH----HHHGGGGGSS-----------------------CCSEEE
T ss_pred             CCCEEEEcCCHHHHHHHHHHHHHcC-CeEEECCHHHH----HHHHHhhccC-----------------------CceEEE
Confidence            4699999999999999999999988 89999999754    5789999999                       799999


Q ss_pred             EecCCCCcccCcCCCCCCcEEEEcC--------------------CCCCHHHHHHHHhhhcC--C-CCEEEEEee
Q 029910          105 VTDACLPLLSSGESAISARVLINYE--------------------LPTKKETYIRRMTTCLA--A-DGSVINIVV  156 (185)
Q Consensus       105 ~Td~~~~~~~~G~d~~~v~~VI~~d--------------------~P~~~~~yiqR~GR~~~--~-~g~~i~~v~  156 (185)
                      ||++    +++|+|+|+ ++|||||                    +|.+.++|+||+||+++  . +|.++.|..
T Consensus       240 aT~v----~~~GiDip~-~~VI~~~~~~~~~~d~~~~~~l~~~~~~p~s~~~y~Qr~GRaGR~g~~~g~~~~~~~  309 (451)
T 2jlq_A          240 TTDI----SEMGANFRA-GRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSG  309 (451)
T ss_dssp             ECGG----GGSSCCCCC-SEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECS
T ss_pred             ECCH----HHhCcCCCC-CEEEECCCcccccccccccceeeecccccCCHHHHHHhccccCCCCCCCccEEEEeC
Confidence            9999    999999999 9999999                    99999999999999743  3 678887764

>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=99.74  E-value=1.5e-17  Score=147.39  Aligned_cols=124  Identities=13%  Similarity=0.135  Sum_probs=99.4

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcC-CCceEEEEecCCCHHHHHHHHHHHhcccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL-ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE   85 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~-~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~   85 (185)
                      |...+.+++..+.   ..+.++||||+++.+++.+...|... + +.+..+||+++..+|.+++++|+++.         
T Consensus       326 K~~~l~~~l~~~~---~~~~k~lvF~~~~~~~~~l~~~l~~~~~-~~~~~~~g~~~~~~R~~~~~~F~~~~---------  392 (500)
T 1z63_A          326 KMIRTMEIIEEAL---DEGDKIAIFTQFVDMGKIIRNIIEKELN-TEVPFLYGELSKKERDDIISKFQNNP---------  392 (500)
T ss_dssp             HHHHHHHHHHHHH---TTTCCEEEECSCHHHHHHHHHHHHHHHT-CCCCEEETTSCHHHHHHHHHHHHHCT---------
T ss_pred             hHHHHHHHHHHHH---ccCCcEEEEEehHHHHHHHHHHHHHhhC-CCeEEEECCCCHHHHHHHHHHhcCCC---------
Confidence            3445556665543   35689999999999999999999875 6 78999999999999999999999983         


Q ss_pred             cCCCCCCCCCCCCcee-EEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCC--CEEEEEeeCchH
Q 029910           86 QSGDESETGKDEHKSH-MIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAAD--GSVINIVVGGEV  160 (185)
Q Consensus        86 ~~~~~~~~~~~~~~~~-iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~--g~~i~~v~~~e~  160 (185)
                                   ..+ +|++|++    +++|+|+|.+++||+||+|||+..|.||+||+  .|+.  ..++.++..+..
T Consensus       393 -------------~~~vil~st~~----~~~Glnl~~~~~vi~~d~~~~~~~~~Q~~gR~~R~Gq~~~v~v~~lv~~~ti  455 (500)
T 1z63_A          393 -------------SVKFIVLSVKA----GGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTL  455 (500)
T ss_dssp             -------------TCCCCEEECCC----C-CCCCCTTCSEEEESSCCSCC---CHHHHTTTTTTTTSCEEEEEEEETTSH
T ss_pred             -------------CCCEEEEeccc----ccCCCchhhCCEEEEeCCCCCcchHHHHHHHHHHcCCCCeeEEEEEEeCCCH
Confidence                         344 7999999    99999999999999999999999999999997  3443  345777877643

>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=99.74  E-value=7.7e-18  Score=163.54  Aligned_cols=121  Identities=17%  Similarity=0.205  Sum_probs=99.1

Q ss_pred             hHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCce-----------------------------------
Q 029910            8 QETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADIS-----------------------------------   52 (185)
Q Consensus         8 ~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~-----------------------------------   52 (185)
                      ...+..++..+..  ....++||||++++.|+.++..|...+ +.                                   
T Consensus       426 ~~~l~~li~~l~~--~~~~~vIVF~~sr~~~e~la~~L~~~~-~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~  502 (1108)
T 3l9o_A          426 KGDIYKIVKMIWK--KKYNPVIVFSFSKRDCEELALKMSKLD-FNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPL  502 (1108)
T ss_dssp             HHHHHHHHHHHHH--TTCCCEEEEESCHHHHHHHHHHTCSHH-HHCC----CHHHHGGGSCTHHHHHTTCCHHHHHHTHH
T ss_pred             hhHHHHHHHHHHh--cCCCCEEEEeCcHHHHHHHHHHHHhcc-CCCHHHHHHHHHHHHHHHhhcchhhhhhhhHHHHHHh
Confidence            4455566666444  346799999999999999999986643 22                                   


Q ss_pred             ----EEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEc
Q 029910           53 ----FSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINY  128 (185)
Q Consensus        53 ----~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~  128 (185)
                          +..+||+|++.+|..+++.|++|                       .++|||||++    +++|+|+|++++||++
T Consensus       503 l~~gV~~~Hg~l~~~~R~~v~~~F~~G-----------------------~ikVLVAT~v----la~GIDiP~v~~VI~~  555 (1108)
T 3l9o_A          503 LRRGIGIHHSGLLPILKEVIEILFQEG-----------------------FLKVLFATET----FSIGLNMPAKTVVFTS  555 (1108)
T ss_dssp             HHHTEEEECSCSCHHHHHHHHHHHHHT-----------------------CCCEEEEESC----CCSCCCC--CEEEESC
T ss_pred             hhcCeeeecCCCCHHHHHHHHHHHhCC-----------------------CCeEEEECcH----HhcCCCCCCceEEEec
Confidence                79999999999999999999999                       7999999999    9999999999999988


Q ss_pred             CCC--------CCHHHHHHHHhhhcCC----CCEEEEEeeCc
Q 029910          129 ELP--------TKKETYIRRMTTCLAA----DGSVINIVVGG  158 (185)
Q Consensus       129 d~P--------~~~~~yiqR~GR~~~~----~g~~i~~v~~~  158 (185)
                      +.|        .++..|+||+||+++.    .|.|+.++.+.
T Consensus       556 ~~~~d~~~~r~iS~~eyiQr~GRAGR~G~d~~G~~ill~~~~  597 (1108)
T 3l9o_A          556 VRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEK  597 (1108)
T ss_dssp             SEEESSSCEEECCHHHHHHHHHHSCCSSSCSSEEEEEEECCC
T ss_pred             CcccCccccccCCHHHHHHhhcccCCCCCCCceEEEEEecCC
Confidence            764        3778899999998643    47888888765

>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=99.73  E-value=1.6e-18  Score=160.45  Aligned_cols=118  Identities=19%  Similarity=0.233  Sum_probs=97.7

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEE
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMI  103 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iL  103 (185)
                      .+.++||||++++.++.+++.|+..+ +.+..+||+|++++       |+++                       ..+||
T Consensus       395 ~~~~vLVFv~Tr~~ae~la~~L~~~g-~~v~~lHG~l~q~e-------r~~~-----------------------~~~VL  443 (666)
T 3o8b_A          395 RGGRHLIFCHSKKKCDELAAKLSGLG-INAVAYYRGLDVSV-------IPTI-----------------------GDVVV  443 (666)
T ss_dssp             SSSEEEEECSCHHHHHHHHHHHHTTT-CCEEEECTTSCGGG-------SCSS-----------------------SCEEE
T ss_pred             cCCcEEEEeCCHHHHHHHHHHHHhCC-CcEEEecCCCCHHH-------HHhC-----------------------CCcEE
Confidence            56899999999999999999999998 89999999999875       3444                       46999


Q ss_pred             EEecCCCCcccCcCCCCCCcEEE----------EcC-----------CCCCHHHHHHHHhhhcC-CCCEEEEEeeCchHH
Q 029910          104 VVTDACLPLLSSGESAISARVLI----------NYE-----------LPTKKETYIRRMTTCLA-ADGSVINIVVGGEVV  161 (185)
Q Consensus       104 V~Td~~~~~~~~G~d~~~v~~VI----------~~d-----------~P~~~~~yiqR~GR~~~-~~g~~i~~v~~~e~~  161 (185)
                      ||||+    ++||+|++ +++||          |||           +|.+.++|+||+||+++ .+|. +.|+++.+..
T Consensus       444 VATdV----aerGIDId-V~~VI~~Gl~~~~ViNyDydP~~gl~~~~~P~s~~syiQRiGRtGRg~~G~-i~lvt~~e~~  517 (666)
T 3o8b_A          444 VATDA----LMTGYTGD-FDSVIDCNTCVTQTVDFSLDPTFTIETTTVPQDAVSRSQRRGRTGRGRRGI-YRFVTPGERP  517 (666)
T ss_dssp             EECTT----HHHHCCCC-BSEEEECCEEEEEEEECCCSSSCEEEEEEEECBHHHHHHHHTTBCSSSCEE-EEESCCCCBC
T ss_pred             EECCh----HHccCCCC-CcEEEecCcccccccccccccccccccccCcCCHHHHHHHhccCCCCCCCE-EEEEecchhh
Confidence            99999    99999987 99988          788           99999999999999865 5588 9999876654


Q ss_pred             H--H--HHHHHHhCCcccccc
Q 029910          162 T--L--RSMEESLGLIVAEVP  178 (185)
Q Consensus       162 ~--~--~~l~~~~~~~~~~~~  178 (185)
                      .  +  ..+++..+..+.+..
T Consensus       518 ~~~l~~~~i~~~~~~~~~~~~  538 (666)
T 3o8b_A          518 SGMFDSSVLCECYDAGCAWYE  538 (666)
T ss_dssp             SSBCCHHHHHHHHHHHHHTSC
T ss_pred             cccccHHHHHHHhcCCccccc
Confidence            4  3  566665554444443

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.72  E-value=3.5e-17  Score=151.97  Aligned_cols=119  Identities=16%  Similarity=0.224  Sum_probs=100.0

Q ss_pred             CcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhc--ccccccccccccCCCCCCCCCCCCceeEE
Q 029910           26 LPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRH--TAMKWNQKVTEQSGDESETGKDEHKSHMI  103 (185)
Q Consensus        26 ~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~iL  103 (185)
                      ...||||++++.++.+++.|...+ +.+..+||+|++++|.++++.|++  |                       ..+||
T Consensus       321 ~g~iIf~~s~~~ie~la~~L~~~g-~~v~~lHG~L~~~~R~~~~~~F~~~~g-----------------------~~~VL  376 (677)
T 3rc3_A          321 PGDCIVCFSKNDIYSVSRQIEIRG-LESAVIYGSLPPGTKLAQAKKFNDPND-----------------------PCKIL  376 (677)
T ss_dssp             TTEEEECSSHHHHHHHHHHHHHTT-CCCEEECTTSCHHHHHHHHHHHHCTTS-----------------------SCCEE
T ss_pred             CCCEEEEcCHHHHHHHHHHHHhcC-CCeeeeeccCCHHHHHHHHHHHHccCC-----------------------CeEEE
Confidence            456899999999999999999987 899999999999999999999998  6                       69999


Q ss_pred             EEecCCCCcccCcCCCCCCcEEEEcCC--------------CCCHHHHHHHHhhhcCCC-----CEEEEEeeCchHHHHH
Q 029910          104 VVTDACLPLLSSGESAISARVLINYEL--------------PTKKETYIRRMTTCLAAD-----GSVINIVVGGEVVTLR  164 (185)
Q Consensus       104 V~Td~~~~~~~~G~d~~~v~~VI~~d~--------------P~~~~~yiqR~GR~~~~~-----g~~i~~v~~~e~~~~~  164 (185)
                      |||++    +++|+|+ ++++||++++              |.+..+|+||+||+|+.+     |.|+.+ ...+...++
T Consensus       377 VATdi----~e~GlDi-~v~~VI~~~~~k~~~~~~G~~~~~p~s~~~~~QR~GRAGR~g~~g~~G~v~~l-~~~d~~~~~  450 (677)
T 3rc3_A          377 VATDA----IGMGLNL-SIRRIIFYSLIKPSINEKGERELEPITTSQALQIAGRAGRFSSRFKEGEVTTM-NHEDLSLLK  450 (677)
T ss_dssp             EECGG----GGSSCCC-CBSEEEESCSBC-----------CBCCHHHHHHHHTTBTCTTSSCSSEEEEES-STTHHHHHH
T ss_pred             EeCcH----HHCCcCc-CccEEEECCccccccccCCccccccCCHHHHHHHhcCCCCCCCCCCCEEEEEE-ecchHHHHH
Confidence            99999    9999999 8999999999              889999999999986543     555544 455655555


Q ss_pred             HHHHHhCCcc
Q 029910          165 SMEESLGLIV  174 (185)
Q Consensus       165 ~l~~~~~~~~  174 (185)
                      .+.......+
T Consensus       451 ~~~~~~~~~i  460 (677)
T 3rc3_A          451 EILKRPVDPI  460 (677)
T ss_dssp             HHHHSCCCCC
T ss_pred             HHHhcCcchh
Confidence            5555433333

>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=99.72  E-value=5.8e-18  Score=148.95  Aligned_cols=114  Identities=18%  Similarity=0.278  Sum_probs=96.4

Q ss_pred             HHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCC
Q 029910           12 VELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDES   91 (185)
Q Consensus        12 ~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~   91 (185)
                      .+.+..++. ...+.++||||++++.++.+++.|.      +..+||+++..+|.+++++|++|                
T Consensus       337 ~~~l~~~l~-~~~~~k~lvF~~~~~~~~~l~~~l~------~~~~~g~~~~~~R~~~~~~F~~g----------------  393 (472)
T 2fwr_A          337 IRKLREILE-RHRKDKIIIFTRHNELVYRISKVFL------IPAITHRTSREEREEILEGFRTG----------------  393 (472)
T ss_dssp             HHHHHHHHH-HTSSSCBCCBCSCHHHHHHHHHHTT------CCBCCSSSCSHHHHTHHHHHHHS----------------
T ss_pred             HHHHHHHHH-hCCCCcEEEEECCHHHHHHHHHHhC------cceeeCCCCHHHHHHHHHHHhCC----------------
Confidence            344444444 3557899999999999999999883      45789999999999999999998                


Q ss_pred             CCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhcC--C---CCEEEEEeeCch
Q 029910           92 ETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLA--A---DGSVINIVVGGE  159 (185)
Q Consensus        92 ~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~~--~---~g~~i~~v~~~e  159 (185)
                             ..++||+|++    +++|+|+|++++||+||+|+++..|+||+||+++  +   ...++.+++.+.
T Consensus       394 -------~~~vLv~T~~----~~~Gldlp~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~k~~~~i~~lv~~~t  455 (472)
T 2fwr_A          394 -------RFRAIVSSQV----LDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYELISRGT  455 (472)
T ss_dssp             -------SCSBCBCSSC----CCSSSCSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTTCCEEEEEEEECSC
T ss_pred             -------CCCEEEEcCc----hhcCcccccCcEEEEECCCCCHHHHHHHHhhccCCCCCCceEEEEEEEeCCC
Confidence                   6999999999    9999999999999999999999999999999743  2   235666777653

>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=99.71  E-value=1.2e-16  Score=147.23  Aligned_cols=121  Identities=14%  Similarity=0.170  Sum_probs=102.6

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEE
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMI  103 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iL  103 (185)
                      .+.++||||+++.+++.+...|...| +.+..+||+++..+|.+++++|+++..                    ....+|
T Consensus       415 ~~~k~lIFs~~~~~~~~l~~~l~~~g-~~~~~l~G~~~~~~R~~~i~~F~~~~~--------------------~~~v~L  473 (644)
T 1z3i_X          415 TSDKVVLVSNYTQTLDLFEKLCRNRR-YLYVRLDGTMSIKKRAKIVERFNNPSS--------------------PEFIFM  473 (644)
T ss_dssp             CCCEEEEEESCHHHHHHHHHHHHHHT-CCEEEECSSCCHHHHHHHHHHHHSTTC--------------------CCCEEE
T ss_pred             CCCEEEEEEccHHHHHHHHHHHHHCC-CCEEEEeCCCCHHHHHHHHHHhcCCCC--------------------CcEEEE
Confidence            46899999999999999999999888 899999999999999999999999830                    012489


Q ss_pred             EEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCC--CEEEEEeeCc--hHHHHHHHHHH
Q 029910          104 VVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAAD--GSVINIVVGG--EVVTLRSMEES  169 (185)
Q Consensus       104 V~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~--g~~i~~v~~~--e~~~~~~l~~~  169 (185)
                      ++|++    +++|+|++.+++||+||+|||+..|.|++||+  .|+.  ..++.+++.+  |...++..+.+
T Consensus       474 ~st~a----~g~Glnl~~a~~Vi~~d~~wnp~~~~Qa~gR~~R~Gq~~~v~v~~lv~~~tiEe~i~~~~~~K  541 (644)
T 1z3i_X          474 LSSKA----GGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTGTIEEKILQRQAHK  541 (644)
T ss_dssp             EEGGG----SCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEEEEEETTSHHHHHHHHHHHH
T ss_pred             Eeccc----ccCCcccccCCEEEEECCCCCccHHHHHHHhhhhcCCCCceEEEEEEECCCHHHHHHHHHHHH
Confidence            99999    99999999999999999999999999999997  3443  4677788876  44455555554

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.70  E-value=5.6e-17  Score=146.95  Aligned_cols=97  Identities=13%  Similarity=0.180  Sum_probs=84.3

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcCC-------CceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCC
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNLA-------DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETG   94 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~~-------~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~   94 (185)
                      ..++.++||||+++++|+.++..|...+       .-.+..+||+++. +|.+++++|+++                   
T Consensus       436 ~~~~~k~lVF~~~~~~a~~l~~~L~~~~~~~~~~~~~~~~~i~g~~~~-~r~~~l~~F~~~-------------------  495 (590)
T 3h1t_A          436 TDRFAKTIVFCVDQEHADEMRRALNNLNSDLSRKHPDYVARVTSEEGK-IGKGHLSRFQEL-------------------  495 (590)
T ss_dssp             HCTTSEEEEEESSHHHHHHHHHHHHHHTHHHHTTCTTSEEECSSTTHH-HHHHHHHHHHCT-------------------
T ss_pred             cCCCccEEEEECCHHHHHHHHHHHHHhhhhhhccCCCeEEEEeCCChH-HHHHHHHHHhCC-------------------
Confidence            4566899999999999999999997653       0237889998764 799999999998                   


Q ss_pred             CCCCcee---EEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhcC
Q 029910           95 KDEHKSH---MIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLA  146 (185)
Q Consensus        95 ~~~~~~~---iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~~  146 (185)
                          ..+   |||||++    +++|+|+|++++||+|++|+++..|+||+||+++
T Consensus       496 ----~~~~~~ilvtt~~----l~~GiDip~v~~Vi~~~~~~s~~~~~Q~iGR~~R  542 (590)
T 3h1t_A          496 ----ETSTPVILTTSQL----LTTGVDAPTCKNVVLARVVNSMSEFKQIVGRGTR  542 (590)
T ss_dssp             ----TCCCCCEEEESST----TTTTCCCTTEEEEEEESCCCCHHHHHHHHTTSCC
T ss_pred             ----CCCCCEEEEECCh----hhcCccchheeEEEEEecCCChHHHHHHHhhhcc
Confidence                344   8889999    9999999999999999999999999999999855

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.70  E-value=4.6e-17  Score=144.53  Aligned_cols=104  Identities=12%  Similarity=0.104  Sum_probs=91.0

Q ss_pred             HHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCC
Q 029910           11 LVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDE   90 (185)
Q Consensus        11 l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~   90 (185)
                      +.+++.....  ..+.++||||+ .+.++.+++.|...+ ..+..+||+++..+|.+++++|+++               
T Consensus       336 l~~~l~~~~~--~~~~~~ivf~~-~~~~~~l~~~L~~~~-~~v~~~~g~~~~~~r~~i~~~f~~g---------------  396 (510)
T 2oca_A          336 IAKLAIKLAQ--KDENAFVMFKH-VSHGKAIFDLIKNEY-DKVYYVSGEVDTETRNIMKTLAENG---------------  396 (510)
T ss_dssp             HHHHHHHHHT--TTCEEEEEESS-HHHHHHHHHHHHTTC-SSEEEESSSTTHHHHHHHHHHHHHC---------------
T ss_pred             HHHHHHHHHh--cCCCeEEEEec-HHHHHHHHHHHHHcC-CCeEEEECCCCHHHHHHHHHHHhCC---------------
Confidence            4444444222  34577888887 888999999999987 5999999999999999999999998               


Q ss_pred             CCCCCCCCceeEEEEe-cCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc
Q 029910           91 SETGKDEHKSHMIVVT-DACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL  145 (185)
Q Consensus        91 ~~~~~~~~~~~iLV~T-d~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~  145 (185)
                              ..++|||| ++    +++|+|+|++++||++++|+++..|+||+||++
T Consensus       397 --------~~~vLv~T~~~----~~~GiDip~v~~vi~~~~~~s~~~~~Q~~GR~g  440 (510)
T 2oca_A          397 --------KGIIIVASYGV----FSTGISVKNLHHVVLAHGVKSKIIVLQTIGRVL  440 (510)
T ss_dssp             --------CSCEEEEEHHH----HHHSCCCCSEEEEEESSCCCSCCHHHHHHHHHH
T ss_pred             --------CCCEEEEEcCh----hhcccccccCcEEEEeCCCCCHHHHHHHHhccc
Confidence                    68999999 99    999999999999999999999999999999974

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=99.69  E-value=1.9e-16  Score=148.96  Aligned_cols=138  Identities=16%  Similarity=0.217  Sum_probs=113.5

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ   86 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~   86 (185)
                      |...+.++|..+   ...+.++||||+...+++.|...|...| +.+..+||+++..+|.+++++|+++.          
T Consensus       557 K~~~L~~lL~~~---~~~g~kvLIFsq~~~~ld~L~~~L~~~g-~~~~~i~G~~~~~eR~~~i~~F~~~~----------  622 (800)
T 3mwy_W          557 KMVLLDQLLTRL---KKDGHRVLIFSQMVRMLDILGDYLSIKG-INFQRLDGTVPSAQRRISIDHFNSPD----------  622 (800)
T ss_dssp             HHHHHHHHHHHH---TTTTCCEEEEESCHHHHHHHHHHHHHHT-CCCEEESTTSCHHHHHHHHHTTSSTT----------
T ss_pred             HHHHHHHHHHHH---hhCCCeEEEEechHHHHHHHHHHHHhCC-CCEEEEeCCCCHHHHHHHHHHhhCCC----------
Confidence            344555566553   3456899999999999999999999888 89999999999999999999999873          


Q ss_pred             CCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCC--CEEEEEeeCc--hH
Q 029910           87 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AAD--GSVINIVVGG--EV  160 (185)
Q Consensus        87 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~--g~~i~~v~~~--e~  160 (185)
                                +....+|++|.+    ++.|+|++.+++||+||+|||+..++||+||+.  |+.  ..++.+++.+  |.
T Consensus       623 ----------~~~~v~LlSt~a----gg~GlNL~~a~~VI~~D~~wnp~~~~Qa~gR~~RiGQ~k~V~Vyrlv~~~TiEe  688 (800)
T 3mwy_W          623 ----------SNDFVFLLSTRA----GGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTVEE  688 (800)
T ss_dssp             ----------CSCCCEEEEHHH----HTTTCCCTTCCEEEESSCCSCSHHHHHHHTTTSCSSCCSCEEEEEEEETTSHHH
T ss_pred             ----------CCceEEEEeccc----ccCCCCccccceEEEecCCCChhhHHHHHHHHHhcCCCceEEEEEEecCCCHHH
Confidence                      012359999999    999999999999999999999999999999973  333  4667788876  66


Q ss_pred             HHHHHHHHHhCC
Q 029910          161 VTLRSMEESLGL  172 (185)
Q Consensus       161 ~~~~~l~~~~~~  172 (185)
                      ..++..+++...
T Consensus       689 ~i~~~~~~K~~l  700 (800)
T 3mwy_W          689 EVLERARKKMIL  700 (800)
T ss_dssp             HHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHH
Confidence            677777766543

>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=99.68  E-value=1.3e-16  Score=155.52  Aligned_cols=108  Identities=11%  Similarity=0.130  Sum_probs=98.0

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcC-CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeE
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNL-ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHM  102 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~-~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  102 (185)
                      .+.+++|||+++++++.+++.|... ++..+..+||+|++.+|.+++++|++|                       ..+|
T Consensus       811 ~g~qvlvf~~~v~~~~~l~~~L~~~~p~~~v~~lhg~~~~~eR~~il~~F~~g-----------------------~~~V  867 (1151)
T 2eyq_A          811 RGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQ-----------------------RFNV  867 (1151)
T ss_dssp             TTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTT-----------------------SCCE
T ss_pred             cCCeEEEEECCHHHHHHHHHHHHHhCCCCeEEEEeCCCCHHHHHHHHHHHHcC-----------------------CCcE
Confidence            4689999999999999999999876 237899999999999999999999999                       6999


Q ss_pred             EEEecCCCCcccCcCCCCCCcEEEEcCC-CCCHHHHHHHHhhhc--CCCCEEEEEeeCc
Q 029910          103 IVVTDACLPLLSSGESAISARVLINYEL-PTKKETYIRRMTTCL--AADGSVINIVVGG  158 (185)
Q Consensus       103 LV~Td~~~~~~~~G~d~~~v~~VI~~d~-P~~~~~yiqR~GR~~--~~~g~~i~~v~~~  158 (185)
                      ||||++    +++|+|+|++++||+++. ++++..|.||+||++  ++.|.|+.++.+.
T Consensus       868 LVaT~v----~e~GiDip~v~~VIi~~~~~~~l~~l~Qr~GRvgR~g~~g~~~ll~~~~  922 (1151)
T 2eyq_A          868 LVCTTI----IETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHP  922 (1151)
T ss_dssp             EEESST----TGGGSCCTTEEEEEETTTTSSCHHHHHHHHTTCCBTTBCEEEEEEECCG
T ss_pred             EEECCc----ceeeecccCCcEEEEeCCCCCCHHHHHHHHhccCcCCCceEEEEEECCc
Confidence            999999    999999999999999998 579999999999974  5568999888664

>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=99.68  E-value=2.1e-17  Score=155.54  Aligned_cols=113  Identities=12%  Similarity=0.109  Sum_probs=95.9

Q ss_pred             CCCCCcEEEEcCCh--------hhHHHHHHHHhc-C-CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCC
Q 029910           22 RRPGLPMIVCCSSR--------DELDAVCSAVSN-L-ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDES   91 (185)
Q Consensus        22 ~~~~~~~IIF~~~~--------~~~~~l~~~L~~-~-~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~   91 (185)
                      -..+.+++|||++.        ..++.+++.|.. . +++.+..+||+|+..+|.+++++|++|                
T Consensus       575 l~~g~qvlVf~~~ie~se~l~~~~a~~l~~~L~~~~~~~~~v~~lHG~m~~~eR~~v~~~F~~G----------------  638 (780)
T 1gm5_A          575 VMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEG----------------  638 (780)
T ss_dssp             TTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTT----------------
T ss_pred             HhcCCcEEEEecchhhhhhhhHHHHHHHHHHHHhhhcCCCcEEEEeCCCCHHHHHHHHHHHHCC----------------
Confidence            34568999999965        457888899987 2 237899999999999999999999999                


Q ss_pred             CCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCC-CHHHHHHHHhhhc--CCCCEEEEEeeCchHH
Q 029910           92 ETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPT-KKETYIRRMTTCL--AADGSVINIVVGGEVV  161 (185)
Q Consensus        92 ~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~-~~~~yiqR~GR~~--~~~g~~i~~v~~~e~~  161 (185)
                             ..+|||||++    +++|+|+|++++||+||.|+ +...|.||+||++  +..|.|+.++.+.+..
T Consensus       639 -------~~~ILVaT~v----ie~GIDiP~v~~VIi~d~~r~~l~~l~Qr~GRaGR~g~~g~~ill~~~~~~~  700 (780)
T 1gm5_A          639 -------RYDILVSTTV----IEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDVGEE  700 (780)
T ss_dssp             -------SSSBCCCSSC----CCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCSCCHH
T ss_pred             -------CCeEEEECCC----CCccccCCCCCEEEEeCCCCCCHHHHHHHhcccCcCCCCCEEEEEECCCChH
Confidence                   6999999999    99999999999999999996 6888999999974  5679999998753333

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.67  E-value=1.2e-16  Score=140.67  Aligned_cols=98  Identities=9%  Similarity=0.008  Sum_probs=86.0

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEE
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIV  104 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV  104 (185)
                      +.++||||++++.++.+++.|+..+ +.+..+||+    +|.+++++|++|                       ..+|||
T Consensus       171 ~~~~lVF~~~~~~~~~l~~~L~~~~-~~v~~lhg~----~r~~~~~~f~~g-----------------------~~~vLV  222 (431)
T 2v6i_A          171 DGRTVWFVHSIKQGAEIGTCLQKAG-KKVLYLNRK----TFESEYPKCKSE-----------------------KWDFVI  222 (431)
T ss_dssp             SSCEEEECSSHHHHHHHHHHHHHTT-CCEEEESTT----THHHHTTHHHHS-----------------------CCSEEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHcC-CeEEEeCCc----cHHHHHHhhcCC-----------------------CCeEEE
Confidence            4689999999999999999999987 899999997    678899999999                       799999


Q ss_pred             EecCCCCcccCcCCCCCCcE-----------------EEEcCCCCCHHHHHHHHhhhcCC---CCEEEEEe
Q 029910          105 VTDACLPLLSSGESAISARV-----------------LINYELPTKKETYIRRMTTCLAA---DGSVINIV  155 (185)
Q Consensus       105 ~Td~~~~~~~~G~d~~~v~~-----------------VI~~d~P~~~~~yiqR~GR~~~~---~g~~i~~v  155 (185)
                      ||++    +++|+|+| +..                 ||+++.|.+.++|+||+||+++.   .|.++.+.
T Consensus       223 aT~v----~e~GiDip-~~~VI~~g~~~~~v~d~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~~~~~~~~  288 (431)
T 2v6i_A          223 TTDI----SEMGANFK-ADRVIDPRKTIKPILLDGRVSMQGPIAITPASAAQRRGRIGRNPEKLGDIYAYS  288 (431)
T ss_dssp             ECGG----GGTSCCCC-CSEEEECCEEEEEEEETTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCCEEEEC
T ss_pred             ECch----HHcCcccC-CcEEEecCccccceecccceeecccccCCHHHHHHhhhccCCCCCCCCeEEEEc
Confidence            9999    99999999 544                 68899999999999999998543   34555554

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.66  E-value=3.8e-16  Score=150.36  Aligned_cols=126  Identities=16%  Similarity=0.219  Sum_probs=99.8

Q ss_pred             HHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCc--------------------------------------
Q 029910           10 TLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADI--------------------------------------   51 (185)
Q Consensus        10 ~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~--------------------------------------   51 (185)
                      .+..+++.+..  ....++||||++++.|+.++..|...+ +                                      
T Consensus       323 ~~~~li~~l~~--~~~~~~IVF~~sr~~~e~la~~L~~~~-~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~  399 (997)
T 4a4z_A          323 TWPEIVNYLRK--RELLPMVVFVFSKKRCEEYADWLEGIN-FCNNKEKSQIHMFIEKSITRLKKEDRDLPQILKTRSLLE  399 (997)
T ss_dssp             HHHHHHHHHHH--TTCCSEEEECSCHHHHHHHHHTTTTCC-CCCHHHHHHHHHHHHHHHTTSCHHHHTCHHHHHHHHHHT
T ss_pred             HHHHHHHHHHh--CCCCCEEEEECCHHHHHHHHHHHhcCC-CCCHHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHhh
Confidence            34455555333  345899999999999999999997765 3                                      


Q ss_pred             -eEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCC
Q 029910           52 -SFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYEL  130 (185)
Q Consensus        52 -~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~  130 (185)
                       .+..+||+|++.+|..+++.|++|                       .++|||||++    +++|+|+|++ .||.+++
T Consensus       400 ~gi~~~H~gl~~~~R~~v~~~F~~G-----------------------~~kVLvAT~~----~a~GIDiP~~-~VVi~~~  451 (997)
T 4a4z_A          400 RGIAVHHGGLLPIVKELIEILFSKG-----------------------FIKVLFATET----FAMGLNLPTR-TVIFSSI  451 (997)
T ss_dssp             TTEEEECTTSCHHHHHHHHHHHHTT-----------------------CCSEEEECTH----HHHSCCCCCS-EEEESCS
T ss_pred             cCeeeecCCCCHHHHHHHHHHHHCC-----------------------CCcEEEEchH----hhCCCCCCCc-eEEEecc
Confidence             378999999999999999999999                       7999999999    9999999994 4555555


Q ss_pred             CC---------CHHHHHHHHhhhcC----CCCEEEEEee--CchHHHHHHH
Q 029910          131 PT---------KKETYIRRMTTCLA----ADGSVINIVV--GGEVVTLRSM  166 (185)
Q Consensus       131 P~---------~~~~yiqR~GR~~~----~~g~~i~~v~--~~e~~~~~~l  166 (185)
                      |+         ++.+|+||+||+++    ..|.++.++.  ..+...++.+
T Consensus       452 ~k~dg~~~~~~s~~~y~Qr~GRAGR~G~~~~G~vi~l~~~~~~~~~~~~~~  502 (997)
T 4a4z_A          452 RKHDGNGLRELTPGEFTQMAGRAGRRGLDSTGTVIVMAYNSPLSIATFKEV  502 (997)
T ss_dssp             EEEETTEEEECCHHHHHHHHGGGCCTTTCSSEEEEEECCSSCCCHHHHHHH
T ss_pred             ccccCccCCCCCHHHHhHHhcccccCCCCcceEEEEecCCCcchHHHHHHH
Confidence            54         99999999999866    3477887773  2345555444

>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=99.54  E-value=3.1e-14  Score=143.16  Aligned_cols=118  Identities=18%  Similarity=0.244  Sum_probs=98.3

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcC----C-----------------------------CceEEEEecCCCHHHHHHH
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNL----A-----------------------------DISFSSLHSDLAETERTLI   68 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~----~-----------------------------~~~~~~l~g~~~~~~R~~~   68 (185)
                      ..+.+++||||++++.|+.++..|...    .                             ...++++||+|++.+|..+
T Consensus      1152 ~~~~~~~lVF~~sR~~~~~~A~~L~~~~~~~~~~~~~~~~~~~~l~~~l~~~~d~~L~~~l~~GIa~hHagL~~~~R~~V 1231 (1724)
T 4f92_B         1152 HSPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYLHEGLSPMERRLV 1231 (1724)
T ss_dssp             HCSSSCEEEEESSHHHHHHHHHHHHHHHHHTTCTTTTBCSCHHHHHHHHTTCCCHHHHHHHHTTEEEECTTSCHHHHHHH
T ss_pred             hcCCCCeeeeCCCHHHHHHHHHHHHHHHhhccchhhhhcccHHHHHHHHhhcccHHHHHHHhCCEEEECCCCCHHHHHHH
Confidence            456689999999999999887766321    0                             0237899999999999999


Q ss_pred             HHHHhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEE----c------CCCCCHHHHH
Q 029910           69 LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLIN----Y------ELPTKKETYI  138 (185)
Q Consensus        69 l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~----~------d~P~~~~~yi  138 (185)
                      .+.|++|                       .+++||||+.    +++|+|+|...+||.    |      ..|.++.+|+
T Consensus      1232 E~lF~~G-----------------------~i~VLvaT~t----lA~GVnlPa~~VVI~~~~~~dg~~~~~~~~s~~~~~ 1284 (1724)
T 4f92_B         1232 EQLFSSG-----------------------AIQVVVASRS----LCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVL 1284 (1724)
T ss_dssp             HHHHHHT-----------------------SBCEEEEEGG----GSSSCCCCBSEEEEECSEEEETTTTEEEECCHHHHH
T ss_pred             HHHHHCC-----------------------CCeEEEEChH----HHcCCCCCccEEEEecCccccCcccccCCCCHHHHH
Confidence            9999999                       7999999999    999999999999993    3      3467899999


Q ss_pred             HHHhhhcCC----CCEEEEEeeCchHHHHHHH
Q 029910          139 RRMTTCLAA----DGSVINIVVGGEVVTLRSM  166 (185)
Q Consensus       139 qR~GR~~~~----~g~~i~~v~~~e~~~~~~l  166 (185)
                      ||+||+|+.    .|.|+.++.+.+...++.+
T Consensus      1285 Qm~GRAGR~g~d~~G~avll~~~~~~~~~~~l 1316 (1724)
T 4f92_B         1285 QMVGHANRPLQDDEGRCVIMCQGSKKDFFKKF 1316 (1724)
T ss_dssp             HHHTTBCCTTTCSCEEEEEEEEGGGHHHHHHH
T ss_pred             HhhccccCCCCCCceEEEEEecchHHHHHHHH
Confidence            999998653    4899999998887766554

>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=99.53  E-value=1.5e-14  Score=145.53  Aligned_cols=118  Identities=20%  Similarity=0.276  Sum_probs=98.6

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcC----C--------------------------------CceEEEEecCCCHHHH
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNL----A--------------------------------DISFSSLHSDLAETER   65 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~----~--------------------------------~~~~~~l~g~~~~~~R   65 (185)
                      ...+.++||||++++.|+.++..|...    +                                ...++++||+|++.+|
T Consensus       314 ~~~~~~~LVF~~sR~~~~~~A~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Gva~HHagL~~~~R  393 (1724)
T 4f92_B          314 HAGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHAGMTRVDR  393 (1724)
T ss_dssp             CCSSCCEEEECSSTTTTHHHHHHHHHHHHHTTSTTCCSSCCTTCSSHHHHTTSCCSTHHHHHHTTTTEEEECSSSCTHHH
T ss_pred             HhcCCcEEEECCCHHHHHHHHHHHHHHHhhccchhhhcccchhHHHHHHhhhcccccHHHHHHhhcCEEEEcCCCCHHHH
Confidence            455689999999999998888877531    0                                0237899999999999


Q ss_pred             HHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEE----cCC------CCCHH
Q 029910           66 TLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLIN----YEL------PTKKE  135 (185)
Q Consensus        66 ~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~----~d~------P~~~~  135 (185)
                      ..+.+.|++|                       .+++||||+.    ++.|+|+|..++||.    ||.      |-++.
T Consensus       394 ~~vE~~F~~G-----------------------~i~vlvaTsT----La~GVNlPa~~vVI~~~~~~~~~~~~~~~ls~~  446 (1724)
T 4f92_B          394 TLVEDLFADK-----------------------HIQVLVSTAT----LAWGVNLPAHTVIIKGTQVYSPEKGRWTELGAL  446 (1724)
T ss_dssp             HHHHHHHHTT-----------------------CCCEEEECHH----HHHHSCCCBSEEEEECCEEEETTTTEEEECCHH
T ss_pred             HHHHHHHHCC-----------------------CCeEEEEcch----hHhhCCCCCceEEEeCCEEecCcCCCcccCCHH
Confidence            9999999999                       7999999999    999999999999995    553      56899


Q ss_pred             HHHHHHhhhcCC----CCEEEEEeeCchHHHHHHH
Q 029910          136 TYIRRMTTCLAA----DGSVINIVVGGEVVTLRSM  166 (185)
Q Consensus       136 ~yiqR~GR~~~~----~g~~i~~v~~~e~~~~~~l  166 (185)
                      +|.||+||||+.    .|.++.++...+...+..+
T Consensus       447 ~~~Qm~GRAGR~g~d~~G~~ii~~~~~~~~~~~~l  481 (1724)
T 4f92_B          447 DILQMLGRAGRPQYDTKGEGILITSHGELQYYLSL  481 (1724)
T ss_dssp             HHHHHHTTBSCTTTCSCEEEEEEEESTTCCHHHHH
T ss_pred             HHHHhhhhccCCCCCCccEEEEEecchhHHHHHHH
Confidence            999999998664    4899999988877665554

>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=99.24  E-value=2.7e-11  Score=117.03  Aligned_cols=106  Identities=9%  Similarity=0.131  Sum_probs=84.7

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcCC-----------CceE-EEEecC----------C----------CHH--------
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNLA-----------DISF-SSLHSD----------L----------AET--------   63 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~~-----------~~~~-~~l~g~----------~----------~~~--------   63 (185)
                      .+.++||||+++..|..+++.|...+           .+++ ..+||+          +          ++.        
T Consensus       536 ~g~kamVf~~S~~~A~~~~~~l~~~~~~~~~~~~~~~~~k~avv~s~~~~~~~~~~G~~~~e~~~~~~~~~~~r~~l~~~  615 (1038)
T 2w00_A          536 KGFNAMLAVSSVDAAKAYYATFKRLQEEAANKSATYKPLRIATIFSFAANEEQNAIGEISDETFDTSAMDSSAKEFLDAA  615 (1038)
T ss_dssp             CCCEEEEEESSHHHHHHHHHHHHHHHHHHTTTSSSCCCCCEEEECCCCC------CCCCCCCCSCGGGSCHHHHHHHHHH
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHhhhhhhcccccccccCcEEEEEeCCCccccccccccccccccccccchhHHHHHHHH
Confidence            45689999999999999999997642           1444 455542          2          221        


Q ss_pred             ---------------------HHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCC
Q 029910           64 ---------------------ERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISA  122 (185)
Q Consensus        64 ---------------------~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v  122 (185)
                                           +|..++++|+++                       ..++||+||+    +.+|+|+|.+
T Consensus       616 I~dyn~~f~~~~~~~~~~~~~~R~~i~~~Fk~g-----------------------~i~ILIvvd~----lltGfDiP~l  668 (1038)
T 2w00_A          616 IREYNSHFKTNFSTDSNGFQNYYRDLAQRVKNQ-----------------------DIDLLIVVGM----FLTGFDAPTL  668 (1038)
T ss_dssp             HHHHHHHHTCCCCSSHHHHHHHHHHHHHHHHTT-----------------------SSSEEEESST----TSSSCCCTTE
T ss_pred             HHHHHHHhcccccccchhhhHHHHHHHHHHHcC-----------------------CCeEEEEcch----HHhCcCcccc
Confidence                                 478899999998                       7999999999    9999999999


Q ss_pred             cEEEEcCCCCCHHHHHHHHhhhcC--C----CCEEEEEeeC
Q 029910          123 RVLINYELPTKKETYIRRMTTCLA--A----DGSVINIVVG  157 (185)
Q Consensus       123 ~~VI~~d~P~~~~~yiqR~GR~~~--~----~g~~i~~v~~  157 (185)
                       .++++|.|.+...|+||+||++|  .    .|.++.|+..
T Consensus       669 -~tlylDkpl~~~~liQaIGRtnR~~~~~K~~G~IVdf~~~  708 (1038)
T 2w00_A          669 -NTLFVDKNLRYHGLMQAFSRTNRIYDATKTFGNIVTFRDL  708 (1038)
T ss_dssp             -EEEEEESCCCHHHHHHHHHTTCCCCCTTCCSEEEEESSCC
T ss_pred             -cEEEEccCCCccceeehhhccCcCCCCCCCcEEEEEcccc
Confidence             67899999999999999999733  2    2778887753

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=98.38  E-value=1.4e-06  Score=78.44  Aligned_cols=88  Identities=17%  Similarity=0.154  Sum_probs=56.8

Q ss_pred             HHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCC
Q 029910            9 ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG   88 (185)
Q Consensus         9 ~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~   88 (185)
                      +.+.+.+..+.. . .+..++||++|...++.+++.|...    ....+|..  .+|.+++++|+.+             
T Consensus       370 ~~~~~~l~~~~~-~-~~g~~lvff~S~~~~~~v~~~l~~~----~~~~q~~~--~~~~~~l~~f~~~-------------  428 (540)
T 2vl7_A          370 PIYSILLKRIYE-N-SSKSVLVFFPSYEMLESVRIHLSGI----PVIEENKK--TRHEEVLELMKTG-------------  428 (540)
T ss_dssp             HHHHHHHHHHHH-T-CSSEEEEEESCHHHHHHHHTTCTTS----CEEESTTT--CCHHHHHHHHHTS-------------
T ss_pred             HHHHHHHHHHHH-h-CCCCEEEEeCCHHHHHHHHHHhccC----ceEecCCC--CcHHHHHHHHhcC-------------
Confidence            446666666555 2 3468999999999999999988653    24556654  5788899999886             


Q ss_pred             CCCCCCCCCCceeEEE--EecCCCCcccCcCCCCC----CcEEEEcCCCC
Q 029910           89 DESETGKDEHKSHMIV--VTDACLPLLSSGESAIS----ARVLINYELPT  132 (185)
Q Consensus        89 ~~~~~~~~~~~~~iLV--~Td~~~~~~~~G~d~~~----v~~VI~~d~P~  132 (185)
                                 ..+|+  +|+.    +++|+|+|+    +++||++++|.
T Consensus       429 -----------~~il~~V~~~~----~~EGiD~~~~~~~~~~Vii~~lPf  463 (540)
T 2vl7_A          429 -----------KYLVMLVMRAK----ESEGVEFREKENLFESLVLAGLPY  463 (540)
T ss_dssp             -----------CCEEEEEC-------------------CEEEEEEESCCC
T ss_pred             -----------CeEEEEEecCc----eecceecCCCcccccEEEEECCCC
Confidence                       24666  8899    999999998    89999999983

>3hgt_A HDA1 complex subunit 3; RECA-like domain, SWI2/SNF2 helical domain, chromatin regulator, coiled coil, nucleus, repressor, transcription; 2.20A {Saccharomyces cerevisiae} PDB: 3hgq_A

Probab=97.67  E-value=0.00062  Score=58.04  Aligned_cols=120  Identities=8%  Similarity=0.089  Sum_probs=80.9

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ   86 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~   86 (185)
                      |+..+-.||..+   ...+.+++||++..++.+-+-.++...+ +...-+.|.....+ .+.    .+.           
T Consensus       110 Kf~~L~~LL~~l---~~~~~kVLIfsq~t~~LDilE~~l~~~~-~~y~RlDG~~~~~~-~k~----~~~-----------  169 (328)
T 3hgt_A          110 KFSVLRDLINLV---QEYETETAIVCRPGRTMDLLEALLLGNK-VHIKRYDGHSIKSA-AAA----NDF-----------  169 (328)
T ss_dssp             HHHHHHHHHHHH---TTSCEEEEEEECSTHHHHHHHHHHTTSS-CEEEESSSCCC------------CC-----------
T ss_pred             cHHHHHHHHHHH---HhCCCEEEEEECChhHHHHHHHHHhcCC-CceEeCCCCchhhh-hhc----ccC-----------
Confidence            445555666654   3457899999999999999999999887 79999999854432 211    122           


Q ss_pred             CCCCCCCCCCCCceeEEEEecCCCCcccCcCC-----CCCCcEEEEcCCCCCHHH-HHHHHhhhc------CCCCEEEEE
Q 029910           87 SGDESETGKDEHKSHMIVVTDACLPLLSSGES-----AISARVLINYELPTKKET-YIRRMTTCL------AADGSVINI  154 (185)
Q Consensus        87 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d-----~~~v~~VI~~d~P~~~~~-yiqR~GR~~------~~~g~~i~~  154 (185)
                                  ...+.+.|..    ..-|++     ...++.||-||.-||+.. .+|.+-|+.      ++.-.++-+
T Consensus       170 ------------~~~i~Lltsa----g~~gin~~~~nl~~aD~VI~~DsdwNp~~d~iQa~~r~~R~~~gq~k~v~V~RL  233 (328)
T 3hgt_A          170 ------------SCTVHLFSSE----GINFTKYPIKSKARFDMLICLDTTVDTSQKDIQYLLQYKRERKGLERYAPIVRL  233 (328)
T ss_dssp             ------------SEEEEEEESS----CCCTTTSCCCCCSCCSEEEECSTTCCTTSHHHHHHHCCC---------CCEEEE
T ss_pred             ------------CceEEEEECC----CCCCcCcccccCCCCCEEEEECCCCCCCChHHHHHHHHhhhccCCCCcceEEEE
Confidence                        3444444555    555665     789999999999998876 478766532      234578888


Q ss_pred             eeCchHHH
Q 029910          155 VVGGEVVT  162 (185)
Q Consensus       155 v~~~e~~~  162 (185)
                      ++.+.++.
T Consensus       234 vt~~TiEh  241 (328)
T 3hgt_A          234 VAINSIDH  241 (328)
T ss_dssp             EETTSHHH
T ss_pred             eCCCCHHH
Confidence            88875544

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=97.37  E-value=0.00091  Score=63.95  Aligned_cols=44  Identities=14%  Similarity=0.174  Sum_probs=35.6

Q ss_pred             eEecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHh
Q 029910            3 VSFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVS   46 (185)
Q Consensus         3 v~~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~   46 (185)
                      |+.++.++...+++.+......++|+||+|.|.+.++.|+..|.
T Consensus       421 vy~t~~~K~~AIv~eI~~~~~~GqPVLVgT~SIe~SE~LS~~L~  464 (997)
T 2ipc_A          421 VYRTEKGKFYAVVEEIAEKYERGQPVLVGTISIEKSERLSQMLK  464 (997)
T ss_dssp             EESSHHHHHHHHHHHHHHHHHHTCCEEEECSSHHHHHHHHHHHH
T ss_pred             EEcCHHHHHHHHHHHHHHHHHCCCCEEEEeCCHHHHHHHHHHHh
Confidence            45566777777777766544678999999999999999999998

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=96.43  E-value=0.0066  Score=55.52  Aligned_cols=89  Identities=20%  Similarity=0.210  Sum_probs=58.7

Q ss_pred             HHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCC
Q 029910           10 TLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGD   89 (185)
Q Consensus        10 ~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~   89 (185)
                      .+.+.+..+.. . .+..++||+++....+.+++.|...+ .+   ...+++..+|.+++++|+ +              
T Consensus       435 ~~~~~i~~l~~-~-~~g~~lvlF~Sy~~l~~v~~~l~~~~-~~---~~q~~~~~~~~~ll~~f~-~--------------  493 (620)
T 4a15_A          435 RMATVIEDIIL-K-VKKNTIVYFPSYSLMDRVENRVSFEH-MK---EYRGIDQKELYSMLKKFR-R--------------  493 (620)
T ss_dssp             HHHHHHHHHHH-H-HCSCEEEEESCHHHHHHHTSSCCSCC-EE---CCTTCCSHHHHHHHHHHT-T--------------
T ss_pred             HHHHHHHHHHH-h-CCCCEEEEeCCHHHHHHHHHHHHhcc-hh---ccCCCChhHHHHHHHHhc-c--------------
Confidence            34455555443 2 23679999999999999999887322 22   566677789999999999 6              


Q ss_pred             CCCCCCCCCceeEEEEec--CCCCcccCcCCCCC--CcEEEEcCCCC
Q 029910           90 ESETGKDEHKSHMIVVTD--ACLPLLSSGESAIS--ARVLINYELPT  132 (185)
Q Consensus        90 ~~~~~~~~~~~~iLV~Td--~~~~~~~~G~d~~~--v~~VI~~d~P~  132 (185)
                               ...||+++.  .    +++|+|+|+  .+.||...+|-
T Consensus       494 ---------~~~vL~~v~~gs----f~EGiD~~g~~l~~viI~~lPf  527 (620)
T 4a15_A          494 ---------DHGTIFAVSGGR----LSEGINFPGNELEMIILAGLPF  527 (620)
T ss_dssp             ---------SCCEEEEETTSC----C--------CCCCEEEESSCCC
T ss_pred             ---------CCcEEEEEecCc----eeccccCCCCceEEEEEEcCCC
Confidence                     577999984  7    899999998  44788877763

>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=95.85  E-value=0.022  Score=53.58  Aligned_cols=81  Identities=14%  Similarity=0.083  Sum_probs=67.4

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcC----CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCce
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKS  100 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~  100 (185)
                      +.+++|.++|+.-+.+.++.+...    + +++..+||+++..+|.+.++...+|                       ..
T Consensus       417 g~qvlvlaPtr~La~Q~~~~l~~~~~~~g-i~v~~l~G~~~~~~r~~~~~~l~~g-----------------------~~  472 (780)
T 1gm5_A          417 GFQTAFMVPTSILAIQHYRRTVESFSKFN-IHVALLIGATTPSEKEKIKSGLRNG-----------------------QI  472 (780)
T ss_dssp             TSCEEEECSCHHHHHHHHHHHHHHHTCSS-CCEEECCSSSCHHHHHHHHHHHHSS-----------------------CC
T ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhhhcC-ceEEEEeCCCCHHHHHHHHHHHhcC-----------------------CC
Confidence            579999999999888877776543    5 8999999999999999999999998                       69


Q ss_pred             eEEEEecCCCCcccCcCCCCCCcEEEEcCCCC
Q 029910          101 HMIVVTDACLPLLSSGESAISARVLINYELPT  132 (185)
Q Consensus       101 ~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~  132 (185)
                      +|+|+|..   ++...+++.++.+||.=+...
T Consensus       473 ~IvVgT~~---ll~~~~~~~~l~lVVIDEaHr  501 (780)
T 1gm5_A          473 DVVIGTHA---LIQEDVHFKNLGLVIIDEQHR  501 (780)
T ss_dssp             CEEEECTT---HHHHCCCCSCCCEEEEESCCC
T ss_pred             CEEEECHH---HHhhhhhccCCceEEecccch
Confidence            99999987   356678888999888655443

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=95.49  E-value=0.06  Score=45.63  Aligned_cols=84  Identities=10%  Similarity=0.120  Sum_probs=65.1

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhc---CCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCc
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSN---LADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHK   99 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~---~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (185)
                      ..+.++||.++++.-+.++++.+..   .+ +++..++|+.+..++...++.+..+                       .
T Consensus        62 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~v~~~~g~~~~~~~~~~~~~l~~~-----------------------~  117 (414)
T 3oiy_A           62 RKGKKSALVFPTVTLVKQTLERLQKLADEK-VKIFGFYSSMKKEEKEKFEKSFEED-----------------------D  117 (414)
T ss_dssp             TTTCCEEEEESSHHHHHHHHHHHHHHCCSS-CCEEECCTTSCHHHHHHHHHHHHHT-----------------------C
T ss_pred             cCCCEEEEEECCHHHHHHHHHHHHHHccCC-ceEEEEECCCChhhHHHHHHHhhcC-----------------------C
Confidence            4568999999999999999999887   45 7999999999999999989999887                       5


Q ss_pred             eeEEEEecCCCCcccCcCCCCCCcEEEEcCC
Q 029910          100 SHMIVVTDACLPLLSSGESAISARVLINYEL  130 (185)
Q Consensus       100 ~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~  130 (185)
                      .+|+|+|+-.+--.-+-++...+++||.=+.
T Consensus       118 ~~Iiv~Tp~~l~~~l~~~~~~~~~~iViDEa  148 (414)
T 3oiy_A          118 YHILVFSTQFVSKNREKLSQKRFDFVFVDDV  148 (414)
T ss_dssp             CSEEEEEHHHHHHCHHHHTTCCCSEEEESCH
T ss_pred             CCEEEECHHHHHHHHHHhccccccEEEEeCh
Confidence            8999999762100011245567888776443

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=94.63  E-value=0.15  Score=45.59  Aligned_cols=88  Identities=13%  Similarity=0.115  Sum_probs=59.0

Q ss_pred             HHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCC
Q 029910            9 ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG   88 (185)
Q Consensus         9 ~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~   88 (185)
                      +.+.+.+..+.. . .+..++||+++....+.+++.   .+ ..+..-..+++.   .+.++.|+..             
T Consensus       379 ~~l~~~i~~l~~-~-~~g~~lvlF~Sy~~l~~v~~~---~~-~~v~~q~~~~~~---~~~~~~~~~~-------------  436 (551)
T 3crv_A          379 KRYADYLLKIYF-Q-AKANVLVVFPSYEIMDRVMSR---IS-LPKYVESEDSSV---EDLYSAISAN-------------  436 (551)
T ss_dssp             HHHHHHHHHHHH-H-CSSEEEEEESCHHHHHHHHTT---CC-SSEEECCSSCCH---HHHHHHTTSS-------------
T ss_pred             HHHHHHHHHHHH-h-CCCCEEEEecCHHHHHHHHHh---cC-CcEEEcCCCCCH---HHHHHHHHhc-------------
Confidence            455666666554 2 336899999999999988872   23 333333334553   4567778643             


Q ss_pred             CCCCCCCCCCceeEEEEe--cCCCCcccCcCCCC-----CCcEEEEcCCCC
Q 029910           89 DESETGKDEHKSHMIVVT--DACLPLLSSGESAI-----SARVLINYELPT  132 (185)
Q Consensus        89 ~~~~~~~~~~~~~iLV~T--d~~~~~~~~G~d~~-----~v~~VI~~d~P~  132 (185)
                                ...||+++  ..    +.+|+|+|     ..+.||...+|-
T Consensus       437 ----------~~~vl~~v~gg~----~~EGiD~~d~~g~~l~~viI~~lPf  473 (551)
T 3crv_A          437 ----------NKVLIGSVGKGK----LAEGIELRNNDRSLISDVVIVGIPY  473 (551)
T ss_dssp             ----------SSCEEEEESSCC----SCCSSCCEETTEESEEEEEEESCCC
T ss_pred             ----------CCeEEEEEecce----ecccccccccCCcceeEEEEEcCCC
Confidence                      24689998  57    89999999     467888776653

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=93.69  E-value=0.23  Score=48.41  Aligned_cols=83  Identities=12%  Similarity=0.155  Sum_probs=65.5

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCC--CceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCce
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLA--DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKS  100 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~--~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~  100 (185)
                      ..+.++||.++|+.-|.++++.+...+  ++++..+||+++..+|.+.++.++.+                       ..
T Consensus       119 ~~~~~~Lil~PtreLa~Q~~~~l~~l~~~~i~v~~l~Gg~~~~er~~~~~~l~~g-----------------------~~  175 (1104)
T 4ddu_A          119 RKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEED-----------------------DY  175 (1104)
T ss_dssp             TTTCCEEEEESSHHHHHHHHHHHHTTSCTTSCEEEECTTCCTTHHHHHHHHHHTS-----------------------CC
T ss_pred             hcCCeEEEEechHHHHHHHHHHHHHhhCCCCeEEEEeCCCCHHHHHHHHHHHhCC-----------------------CC
Confidence            456899999999999999999998832  27999999999999999999999998                       68


Q ss_pred             eEEEEecCCC-CcccCcCCCCCCcEEEEcC
Q 029910          101 HMIVVTDACL-PLLSSGESAISARVLINYE  129 (185)
Q Consensus       101 ~iLV~Td~~~-~~~~~G~d~~~v~~VI~~d  129 (185)
                      +|+|+|+-.+ .++.+ ++..++++||.=+
T Consensus       176 ~IlV~Tp~rL~~~l~~-l~~~~l~~lViDE  204 (1104)
T 4ddu_A          176 HILVFSTQFVSKNREK-LSQKRFDFVFVDD  204 (1104)
T ss_dssp             SEEEEEHHHHHHSHHH-HHTSCCSEEEESC
T ss_pred             CEEEECHHHHHHHHHh-hcccCcCEEEEeC
Confidence            9999997521 00111 4567788887644

>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=93.13  E-value=0.59  Score=37.01  Aligned_cols=87  Identities=17%  Similarity=0.247  Sum_probs=58.3

Q ss_pred             HHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcC----CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCC
Q 029910           13 ELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG   88 (185)
Q Consensus        13 ~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~   88 (185)
                      -++..+.. ...+.++||.|+++.-+.++++.+...    + +.+..++|+.+..++...+   ..              
T Consensus       100 ~il~~l~~-~~~~~~~lil~Ptr~L~~q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~---~~--------------  160 (249)
T 3ber_A          100 PILNALLE-TPQRLFALVLTPTRELAFQISEQFEALGSSIG-VQSAVIVGGIDSMSQSLAL---AK--------------  160 (249)
T ss_dssp             HHHHHHHH-SCCSSCEEEECSSHHHHHHHHHHHHHHHGGGT-CCEEEECTTSCHHHHHHHH---HT--------------
T ss_pred             HHHHHHhc-CCCCceEEEEeCCHHHHHHHHHHHHHHhccCC-eeEEEEECCCChHHHHHHh---cC--------------
Confidence            34444444 445578999999999998888777554    5 7899999998876654332   23              


Q ss_pred             CCCCCCCCCCceeEEEEecCCC-Ccc--cCcCCCCCCcEEEEc
Q 029910           89 DESETGKDEHKSHMIVVTDACL-PLL--SSGESAISARVLINY  128 (185)
Q Consensus        89 ~~~~~~~~~~~~~iLV~Td~~~-~~~--~~G~d~~~v~~VI~~  128 (185)
                                ..+|+|+|+-.+ .++  ..++++..+++||.=
T Consensus       161 ----------~~~I~v~Tp~~l~~~l~~~~~~~l~~~~~lViD  193 (249)
T 3ber_A          161 ----------KPHIIIATPGRLIDHLENTKGFNLRALKYLVMD  193 (249)
T ss_dssp             ----------CCSEEEECHHHHHHHHHHSTTCCCTTCCEEEEC
T ss_pred             ----------CCCEEEECHHHHHHHHHcCCCcCccccCEEEEc
Confidence                      378999996410 001  145678888887753

>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=92.59  E-value=0.44  Score=46.53  Aligned_cols=79  Identities=18%  Similarity=0.122  Sum_probs=65.4

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhc----CCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCc
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSN----LADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHK   99 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~----~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (185)
                      .+.+++|.|+|+.-+.+.++.+..    .+ +.+..++|..+..++.+.++....|                       .
T Consensus       651 ~g~~vlvlvPt~~La~Q~~~~~~~~~~~~~-i~v~~l~~~~~~~~~~~~~~~l~~g-----------------------~  706 (1151)
T 2eyq_A          651 NHKQVAVLVPTTLLAQQHYDNFRDRFANWP-VRIEMISRFRSAKEQTQILAEVAEG-----------------------K  706 (1151)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHHSTTTT-CCEEEESTTSCHHHHHHHHHHHHTT-----------------------C
T ss_pred             hCCeEEEEechHHHHHHHHHHHHHHhhcCC-CeEEEEeCCCCHHHHHHHHHHHhcC-----------------------C
Confidence            457999999999999888877763    24 7899999999999999999999998                       6


Q ss_pred             eeEEEEecCCCCcccCcCCCCCCcEEEEcC
Q 029910          100 SHMIVVTDACLPLLSSGESAISARVLINYE  129 (185)
Q Consensus       100 ~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d  129 (185)
                      .+|+|+|..   ++...+.+.++.+||.=+
T Consensus       707 ~dIvV~T~~---ll~~~~~~~~l~lvIiDE  733 (1151)
T 2eyq_A          707 IDILIGTHK---LLQSDVKFKDLGLLIVDE  733 (1151)
T ss_dssp             CSEEEECTH---HHHSCCCCSSEEEEEEES
T ss_pred             CCEEEECHH---HHhCCccccccceEEEec
Confidence            999999965   266678888888877533

>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=91.76  E-value=0.68  Score=35.39  Aligned_cols=80  Identities=13%  Similarity=0.222  Sum_probs=55.4

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcC----CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCc
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHK   99 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (185)
                      ...++||.|+++.-+.++.+.+...    +++++..++|+.+..++.+.   +..+                       .
T Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~---~~~~-----------------------~  134 (220)
T 1t6n_A           81 GQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEV---LKKN-----------------------C  134 (220)
T ss_dssp             TCCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHH---HHHS-----------------------C
T ss_pred             CCEEEEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHH---HhcC-----------------------C
Confidence            3458999999999999888777654    14789999999887766544   3344                       4


Q ss_pred             eeEEEEecCCCC-cc-cCcCCCCCCcEEEEcC
Q 029910          100 SHMIVVTDACLP-LL-SSGESAISARVLINYE  129 (185)
Q Consensus       100 ~~iLV~Td~~~~-~~-~~G~d~~~v~~VI~~d  129 (185)
                      .+|+|+|.-.+- ++ ...+++..+++||.=+
T Consensus       135 ~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDE  166 (220)
T 1t6n_A          135 PHIVVGTPGRILALARNKSLNLKHIKHFILDE  166 (220)
T ss_dssp             CSEEEECHHHHHHHHHTTSSCCTTCCEEEEES
T ss_pred             CCEEEeCHHHHHHHHHhCCCCcccCCEEEEcC
Confidence            689999963100 01 2345778888877533

>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=91.65  E-value=0.44  Score=42.26  Aligned_cols=49  Identities=8%  Similarity=0.072  Sum_probs=45.6

Q ss_pred             CcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcc
Q 029910           26 LPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHT   75 (185)
Q Consensus        26 ~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~   75 (185)
                      .++||.++++.-+......|...| +.+..++++.+..++...+..+..+
T Consensus        66 g~~lvi~P~~aL~~q~~~~l~~~g-i~~~~l~~~~~~~~~~~~~~~~~~~  114 (523)
T 1oyw_A           66 GLTVVVSPLISLMKDQVDQLQANG-VAAACLNSTQTREQQLEVMTGCRTG  114 (523)
T ss_dssp             SEEEEECSCHHHHHHHHHHHHHTT-CCEEEECTTSCHHHHHHHHHHHHHT
T ss_pred             CCEEEECChHHHHHHHHHHHHHcC-CcEEEEeCCCCHHHHHHHHHHHhcC
Confidence            689999999999999999999988 8999999999999999999999888

>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=91.32  E-value=0.59  Score=36.27  Aligned_cols=85  Identities=14%  Similarity=0.173  Sum_probs=57.1

Q ss_pred             HHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCC----CceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCC
Q 029910           14 LLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLA----DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGD   89 (185)
Q Consensus        14 ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~----~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~   89 (185)
                      ++..+.. ...+.++||.|+++.-+.++.+.+...+    ++.+..++|+.+..++.+.+    .               
T Consensus        82 ~l~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~----~---------------  141 (230)
T 2oxc_A           82 ALDSLVL-ENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRL----K---------------  141 (230)
T ss_dssp             HHHHCCT-TSCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHT----T---------------
T ss_pred             HHHHHHh-cCCCceEEEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhc----c---------------
Confidence            3444333 4456799999999999999888886542    37899999998877665432    1               


Q ss_pred             CCCCCCCCCceeEEEEecCCCC-cc-cCcCCCCCCcEEEE
Q 029910           90 ESETGKDEHKSHMIVVTDACLP-LL-SSGESAISARVLIN  127 (185)
Q Consensus        90 ~~~~~~~~~~~~iLV~Td~~~~-~~-~~G~d~~~v~~VI~  127 (185)
                               ..+|+|+|.-.+- ++ ...+++..+++||.
T Consensus       142 ---------~~~Iiv~Tp~~l~~~~~~~~~~~~~~~~lVi  172 (230)
T 2oxc_A          142 ---------KCHIAVGSPGRIKQLIELDYLNPGSIRLFIL  172 (230)
T ss_dssp             ---------SCSEEEECHHHHHHHHHTTSSCGGGCCEEEE
T ss_pred             ---------CCCEEEECHHHHHHHHhcCCcccccCCEEEe
Confidence                     3789999974100 01 23456677777775

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A*

Probab=90.44  E-value=0.52  Score=42.64  Aligned_cols=48  Identities=15%  Similarity=0.159  Sum_probs=43.6

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHh
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFR   73 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~   73 (185)
                      ..++||.++++.-+......|...| +.+..++|+++..++..++..+.
T Consensus        84 ~g~~lVisP~~~L~~q~~~~l~~~g-i~~~~l~~~~~~~~~~~~~~~l~  131 (591)
T 2v1x_A           84 DGFTLVICPLISLMEDQLMVLKQLG-ISATMLNASSSKEHVKWVHAEMV  131 (591)
T ss_dssp             SSEEEEECSCHHHHHHHHHHHHHHT-CCEEECCSSCCHHHHHHHHHHHH
T ss_pred             CCcEEEEeCHHHHHHHHHHHHHhcC-CcEEEEeCCCCHHHHHHHHHHhh
Confidence            3689999999999999999999887 89999999999999999888884

>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=90.21  E-value=0.68  Score=36.13  Aligned_cols=79  Identities=10%  Similarity=0.130  Sum_probs=46.3

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCC---CceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCc
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLA---DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHK   99 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~---~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (185)
                      ..+.++||.|+++.-+.++.+.+...+   .+.+..++|+.+....   .+.+..+                       .
T Consensus        96 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~---~~~l~~~-----------------------~  149 (237)
T 3bor_A           96 FKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNE---MQKLQAE-----------------------A  149 (237)
T ss_dssp             SCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECC----------------C-----------------------C
T ss_pred             CCCceEEEEECcHHHHHHHHHHHHHHhhhcCceEEEEECCCchHHH---HHHHhcC-----------------------C
Confidence            356799999999999998888886542   2678888887654433   2333444                       4


Q ss_pred             eeEEEEecCCC-Cccc-CcCCCCCCcEEEE
Q 029910          100 SHMIVVTDACL-PLLS-SGESAISARVLIN  127 (185)
Q Consensus       100 ~~iLV~Td~~~-~~~~-~G~d~~~v~~VI~  127 (185)
                      .+|+|+|+-.+ .++. ..+++..+++||.
T Consensus       150 ~~Ilv~Tp~~l~~~l~~~~~~~~~~~~lVi  179 (237)
T 3bor_A          150 PHIVVGTPGRVFDMLNRRYLSPKWIKMFVL  179 (237)
T ss_dssp             CSEEEECHHHHHHHHHTTSSCSTTCCEEEE
T ss_pred             CCEEEECHHHHHHHHHhCCcCcccCcEEEE
Confidence            78999994210 0022 3456777888775

>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=90.14  E-value=4.6  Score=30.09  Aligned_cols=79  Identities=8%  Similarity=0.167  Sum_probs=53.3

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcC----CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCC
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDE   97 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~   97 (185)
                      ...+.++||.|+++.-+.++.+.+...    +++.+..++|+.+..+...   .+..                       
T Consensus        68 ~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~---~~~~-----------------------  121 (206)
T 1vec_A           68 KKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIM---RLDD-----------------------  121 (206)
T ss_dssp             TSCSCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHH---HTTS-----------------------
T ss_pred             cCCCeeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHH---hcCC-----------------------
Confidence            345578999999999999888877543    2478999999987765533   2233                       


Q ss_pred             CceeEEEEecCCC-Ccc-cCcCCCCCCcEEEE
Q 029910           98 HKSHMIVVTDACL-PLL-SSGESAISARVLIN  127 (185)
Q Consensus        98 ~~~~iLV~Td~~~-~~~-~~G~d~~~v~~VI~  127 (185)
                       ..+|+|+|.-.+ .++ ....++..+++||.
T Consensus       122 -~~~i~v~T~~~l~~~~~~~~~~~~~~~~lVi  152 (206)
T 1vec_A          122 -TVHVVIATPGRILDLIKKGVAKVDHVQMIVL  152 (206)
T ss_dssp             -CCSEEEECHHHHHHHHHTTCSCCTTCCEEEE
T ss_pred             -CCCEEEeCHHHHHHHHHcCCcCcccCCEEEE
Confidence             478999997310 001 22346777888775

>3gk5_A Uncharacterized rhodanese-related protein TVG0868615; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.40A {Thermoplasma volcanium GSS1}

Probab=89.64  E-value=0.7  Score=31.94  Aligned_cols=39  Identities=13%  Similarity=0.172  Sum_probs=33.9

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      -.+.+++|+||.+-..+...+..|...|+ .+..+.|++.
T Consensus        52 l~~~~~ivvyC~~G~rs~~aa~~L~~~G~-~v~~l~GG~~   90 (108)
T 3gk5_A           52 LERDKKYAVICAHGNRSAAAVEFLSQLGL-NIVDVEGGIQ   90 (108)
T ss_dssp             SCTTSCEEEECSSSHHHHHHHHHHHTTTC-CEEEETTHHH
T ss_pred             CCCCCeEEEEcCCCcHHHHHHHHHHHcCC-CEEEEcCcHH
Confidence            35568999999999999999999999995 9999999843

>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=89.31  E-value=1.5  Score=32.82  Aligned_cols=78  Identities=13%  Similarity=0.068  Sum_probs=54.0

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCC-CceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCcee
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLA-DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSH  101 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~-~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (185)
                      ..+.++||.|+++.-+..+.+.+.... .+.+..++|+.+...+...+   ..                        ..+
T Consensus        70 ~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~------------------------~~~  122 (207)
T 2gxq_A           70 GRKPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEAL---LR------------------------GAD  122 (207)
T ss_dssp             TCCCSEEEECSSHHHHHHHHHHHHHHCTTSCEEEECSSSCSHHHHHHH---HH------------------------CCS
T ss_pred             CCCCcEEEEECCHHHHHHHHHHHHHHhhcceEEEEECCCChHHHHHHh---hC------------------------CCC
Confidence            346789999999999999999887652 36788999988766554333   23                        377


Q ss_pred             EEEEecCCC-Ccc-cCcCCCCCCcEEEE
Q 029910          102 MIVVTDACL-PLL-SSGESAISARVLIN  127 (185)
Q Consensus       102 iLV~Td~~~-~~~-~~G~d~~~v~~VI~  127 (185)
                      |+|+|+-.+ .++ ...+++..+++||.
T Consensus       123 i~v~T~~~l~~~~~~~~~~~~~~~~iVi  150 (207)
T 2gxq_A          123 AVVATPGRALDYLRQGVLDLSRVEVAVL  150 (207)
T ss_dssp             EEEECHHHHHHHHHHTSSCCTTCSEEEE
T ss_pred             EEEECHHHHHHHHHcCCcchhhceEEEE
Confidence            999996310 001 23456778888775

>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=89.30  E-value=1.2  Score=34.63  Aligned_cols=78  Identities=12%  Similarity=0.104  Sum_probs=55.1

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcC----CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCC
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEH   98 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (185)
                      ..+.++||.|+++.-+.++.+.+...    + +.+..++|+.+..++...+   +.+                       
T Consensus       100 ~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~---~~~-----------------------  152 (242)
T 3fe2_A          100 GDGPICLVLAPTRELAQQVQQVAAEYCRACR-LKSTCIYGGAPKGPQIRDL---ERG-----------------------  152 (242)
T ss_dssp             TCCCSEEEECSSHHHHHHHHHHHHHHHHHTT-CCEEEECTTSCHHHHHHHH---HHC-----------------------
T ss_pred             CCCCEEEEEeCcHHHHHHHHHHHHHHHhhcC-ceEEEEECCCChHHHHHHh---cCC-----------------------
Confidence            34678999999999999887776553    5 7899999998887765443   333                       


Q ss_pred             ceeEEEEecCCC-Cccc-CcCCCCCCcEEEEc
Q 029910           99 KSHMIVVTDACL-PLLS-SGESAISARVLINY  128 (185)
Q Consensus        99 ~~~iLV~Td~~~-~~~~-~G~d~~~v~~VI~~  128 (185)
                       .+|+|+|+-++ .++. ...++..+++||.=
T Consensus       153 -~~I~v~Tp~~l~~~l~~~~~~~~~~~~lViD  183 (242)
T 3fe2_A          153 -VEICIATPGRLIDFLECGKTNLRRTTYLVLD  183 (242)
T ss_dssp             -CSEEEECHHHHHHHHHHTSCCCTTCCEEEET
T ss_pred             -CCEEEECHHHHHHHHHcCCCCcccccEEEEe
Confidence             78999996310 0022 34577888887753

>2jtq_A Phage shock protein E; solution structure rhodanese, stress response, transferase; NMR {Escherichia coli} PDB: 2jtr_A 2jts_A

Probab=89.05  E-value=1.6  Score=28.42  Aligned_cols=50  Identities=10%  Similarity=0.120  Sum_probs=35.8

Q ss_pred             HHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910            9 ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus         9 ~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      +.+.+.+..+ . ..+.+++|+||.+-..+...+..|...|+-.+..+ |++.
T Consensus        27 ~~l~~~~~~l-~-~~~~~~ivv~C~~g~rs~~aa~~L~~~G~~~v~~l-GG~~   76 (85)
T 2jtq_A           27 KEVKERIATA-V-PDKNDTVKVYCNAGRQSGQAKEILSEMGYTHVENA-GGLK   76 (85)
T ss_dssp             HHHHHHHHHH-C-CCTTSEEEEEESSSHHHHHHHHHHHHTTCSSEEEE-EETT
T ss_pred             HHHHHHHHHh-C-CCCCCcEEEEcCCCchHHHHHHHHHHcCCCCEEec-cCHH
Confidence            4445555553 1 24568999999998889999999999984456666 7643

>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=89.00  E-value=1.1  Score=34.47  Aligned_cols=78  Identities=14%  Similarity=0.113  Sum_probs=50.5

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcC--CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCcee
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNL--ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSH  101 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~--~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (185)
                      .+.++||.++++.-+.++.+.+...  .++.+..++|+.+..++..   .+..+                        .+
T Consensus        93 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~------------------------~~  145 (228)
T 3iuy_A           93 NGPGMLVLTPTRELALHVEAECSKYSYKGLKSICIYGGRNRNGQIE---DISKG------------------------VD  145 (228)
T ss_dssp             CCCSEEEECSSHHHHHHHHHHHHHHCCTTCCEEEECC------CHH---HHHSC------------------------CS
T ss_pred             CCCcEEEEeCCHHHHHHHHHHHHHhcccCceEEEEECCCChHHHHH---HhcCC------------------------CC
Confidence            5688999999999999998888764  2378999999876655433   33343                        78


Q ss_pred             EEEEecCCCC--cccCcCCCCCCcEEEEc
Q 029910          102 MIVVTDACLP--LLSSGESAISARVLINY  128 (185)
Q Consensus       102 iLV~Td~~~~--~~~~G~d~~~v~~VI~~  128 (185)
                      |+|+|+-++-  +....+++..+++||.=
T Consensus       146 iiv~Tp~~l~~~~~~~~~~~~~~~~lViD  174 (228)
T 3iuy_A          146 IIIATPGRLNDLQMNNSVNLRSITYLVID  174 (228)
T ss_dssp             EEEECHHHHHHHHHTTCCCCTTCCEEEEC
T ss_pred             EEEECHHHHHHHHHcCCcCcccceEEEEE
Confidence            9999963100  01235678888887753

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=88.58  E-value=1.5  Score=36.00  Aligned_cols=80  Identities=11%  Similarity=0.192  Sum_probs=55.4

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcC----CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCC
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDE   97 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~   97 (185)
                      ...+.++||.|+++.-+.++.+.+...    +++.+..++|+.+..++...+   ..+                      
T Consensus        73 ~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~---~~~----------------------  127 (391)
T 1xti_A           73 VTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVL---KKN----------------------  127 (391)
T ss_dssp             CTTCCCEEEECSCHHHHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHHH---HHS----------------------
T ss_pred             cCCCeeEEEECCCHHHHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHHH---hcC----------------------
Confidence            344579999999999999888777653    248899999998877665443   344                      


Q ss_pred             CceeEEEEecCCCC--cccCcCCCCCCcEEEE
Q 029910           98 HKSHMIVVTDACLP--LLSSGESAISARVLIN  127 (185)
Q Consensus        98 ~~~~iLV~Td~~~~--~~~~G~d~~~v~~VI~  127 (185)
                       ..+|+|+|.-.+-  +....+++..+++||.
T Consensus       128 -~~~iiv~T~~~l~~~~~~~~~~~~~~~~vVi  158 (391)
T 1xti_A          128 -CPHIVVGTPGRILALARNKSLNLKHIKHFIL  158 (391)
T ss_dssp             -CCSEEEECHHHHHHHHHTTSSCCTTCSEEEE
T ss_pred             -CCCEEEECHHHHHHHHHcCCccccccCEEEE
Confidence             4689999964100  0123456778888775

>3hix_A ALR3790 protein; rhodanese, rhodanese_3, Q8YQN0, Q8YQN0_anAsp, NSR437I, NESG, structural genomics, PSI-2, protein structure initiative; 1.92A {Anabaena SP} PDB: 3k9r_A

Probab=87.45  E-value=1.4  Score=30.23  Aligned_cols=39  Identities=13%  Similarity=0.112  Sum_probs=32.5

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      .+.+++||||.+-..+...+..|...|+-.+..|.|++.
T Consensus        50 ~~~~~ivvyc~~g~rs~~a~~~L~~~G~~~v~~l~GG~~   88 (106)
T 3hix_A           50 EKSRDIYVYGAGDEQTSQAVNLLRSAGFEHVSELKGGLA   88 (106)
T ss_dssp             CTTSCEEEECSSHHHHHHHHHHHHHTTCSCEEECTTHHH
T ss_pred             CCCCeEEEEECCCChHHHHHHHHHHcCCcCEEEecCCHH
Confidence            455899999999989999999999998445888988843

>3foj_A Uncharacterized protein; protein SSP1007, structural genomics, PSI-2, protein structure initiative; 1.60A {Staphylococcus saprophyticus subsp}

Probab=87.44  E-value=0.62  Score=31.58  Aligned_cols=38  Identities=5%  Similarity=0.093  Sum_probs=33.0

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      .+.+++|+||.+-..+...+..|...|+ ++..+.|++.
T Consensus        54 ~~~~~ivvyC~~g~rs~~a~~~L~~~G~-~v~~l~GG~~   91 (100)
T 3foj_A           54 NDNETYYIICKAGGRSAQVVQYLEQNGV-NAVNVEGGMD   91 (100)
T ss_dssp             CTTSEEEEECSSSHHHHHHHHHHHTTTC-EEEEETTHHH
T ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHCCC-CEEEecccHH
Confidence            4568999999999999999999999995 9999998843

>3iwh_A Rhodanese-like domain protein; alpha-beta-alpha sandwich, structural genomics, C structural genomics of infectious diseases, csgid; 2.00A {Staphylococcus aureus subsp} PDB: 3mzz_A

Probab=86.83  E-value=0.59  Score=32.39  Aligned_cols=37  Identities=8%  Similarity=0.108  Sum_probs=32.0

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCC
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDL   60 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~   60 (185)
                      .+.+++++||.+-..+...+..|...| ++...+.|++
T Consensus        54 ~~~~~ivv~C~~G~rS~~aa~~L~~~G-~~~~~l~GG~   90 (103)
T 3iwh_A           54 NKNEIYYIVCAGGVRSAKVVEYLEANG-IDAVNVEGGM   90 (103)
T ss_dssp             CTTSEEEEECSSSSHHHHHHHHHHTTT-CEEEEETTHH
T ss_pred             cCCCeEEEECCCCHHHHHHHHHHHHcC-CCEEEecChH
Confidence            456899999999888999999999998 6888888874

>3g5j_A Putative ATP/GTP binding protein; N-terminal domain of ATP/GTP binding protein, PSI, MCSG, STR genomics, protein structure initiative; HET: PGE; 1.76A {Clostridium difficile}

Probab=86.65  E-value=0.62  Score=32.77  Aligned_cols=36  Identities=11%  Similarity=0.220  Sum_probs=31.1

Q ss_pred             CcEEEEc-CChhhHHHHHHHHhcCCCceEEEEecCCCH
Q 029910           26 LPMIVCC-SSRDELDAVCSAVSNLADISFSSLHSDLAE   62 (185)
Q Consensus        26 ~~~IIF~-~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~   62 (185)
                      +++|||| .+-..+...+..|...|+ .+..|.|++..
T Consensus        90 ~~ivvyC~~~G~rs~~a~~~L~~~G~-~v~~l~GG~~~  126 (134)
T 3g5j_A           90 DNIVIYCARGGMRSGSIVNLLSSLGV-NVYQLEGGYKA  126 (134)
T ss_dssp             SEEEEECSSSSHHHHHHHHHHHHTTC-CCEEETTHHHH
T ss_pred             CeEEEEECCCChHHHHHHHHHHHcCC-ceEEEeCcHHH
Confidence            7999999 577888899999999995 99999998654

>1tq1_A AT5G66040, senescence-associated family protein; CESG, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana} SCOP: c.46.1.3

Probab=86.59  E-value=0.61  Score=33.29  Aligned_cols=39  Identities=10%  Similarity=0.077  Sum_probs=32.7

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      .+.+++||||.+-..+...+..|...|+-.+..+.|++.
T Consensus        80 ~~~~~ivvyC~~G~rs~~aa~~L~~~G~~~v~~l~GG~~  118 (129)
T 1tq1_A           80 GQSDNIIVGCQSGGRSIKATTDLLHAGFTGVKDIVGGYS  118 (129)
T ss_dssp             CTTSSEEEEESSCSHHHHHHHHHHHHHCCSEEEEECCHH
T ss_pred             CCCCeEEEECCCCcHHHHHHHHHHHcCCCCeEEeCCcHH
Confidence            456899999999888999999999888435888999964

>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=86.40  E-value=1.6  Score=33.31  Aligned_cols=78  Identities=12%  Similarity=0.064  Sum_probs=46.6

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcC---CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCC
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNL---ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEH   98 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~---~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (185)
                      ...+.++||.|+++.-+.++.+.+...   .++.+..++|+.+..++...   +  .                       
T Consensus        79 ~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~--~-----------------------  130 (224)
T 1qde_A           79 SVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEG---L--R-----------------------  130 (224)
T ss_dssp             TCCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC-------------C--T-----------------------
T ss_pred             cCCCceEEEEECCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHhc---C--C-----------------------
Confidence            445679999999999998888877643   13788899998765544321   1  1                       


Q ss_pred             ceeEEEEecCCC--CcccCcCCCCCCcEEEE
Q 029910           99 KSHMIVVTDACL--PLLSSGESAISARVLIN  127 (185)
Q Consensus        99 ~~~iLV~Td~~~--~~~~~G~d~~~v~~VI~  127 (185)
                      ..+|+|+|.-.+  .+.....++..+++||.
T Consensus       131 ~~~iiv~Tp~~l~~~~~~~~~~~~~~~~iVi  161 (224)
T 1qde_A          131 DAQIVVGTPGRVFDNIQRRRFRTDKIKMFIL  161 (224)
T ss_dssp             TCSEEEECHHHHHHHHHTTSSCCTTCCEEEE
T ss_pred             CCCEEEECHHHHHHHHHhCCcchhhCcEEEE
Confidence            367999996410  00134556777888775

>2lnd_A De novo designed protein, PFK fold; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Artificial gene}

Probab=86.20  E-value=6.1  Score=26.83  Aligned_cols=66  Identities=18%  Similarity=0.333  Sum_probs=47.7

Q ss_pred             ecchHHHHHHHHHHHccCCCCCcEEEEcCCh--hhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcc
Q 029910            5 FTFQETLVELLHLVVAGRRPGLPMIVCCSSR--DELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHT   75 (185)
Q Consensus         5 ~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~--~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~   75 (185)
                      .+..+.+.++++.+   .++++|.+||+|..  ..+......-+..| ++-.++.+ .++++-.+-+++|-..
T Consensus        34 atssqdirdiiksm---kdngkplvvfvngasqndvnefqneakkeg-vsydvlks-tdpeeltqrvreflkt  101 (112)
T 2lnd_A           34 ATSSQDIRDIIKSM---KDNGKPLVVFVNGASQNDVNEFQNEAKKEG-VSYDVLKS-TDPEELTQRVREFLKT  101 (112)
T ss_dssp             ECSHHHHHHHHHHH---TTCCSCEEEEECSCCHHHHHHHHHHHHHHT-CEEEEEEC-CCHHHHHHHHHHHHHH
T ss_pred             ccchhhHHHHHHHH---HhcCCeEEEEecCcccccHHHHHHHHHhcC-cchhhhcc-CCHHHHHHHHHHHHHh
Confidence            34567788888885   56789999999854  45556666666667 77777775 4667777777888664

>1wv9_A Rhodanese homolog TT1651; CDC25, phosphatase, sulfurtransferase, structural genomics, NPPSFA; 2.00A {Thermus thermophilus}

Probab=85.98  E-value=0.75  Score=30.80  Aligned_cols=37  Identities=14%  Similarity=0.149  Sum_probs=31.6

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      .+ +++|+||.+-..+...+..|...| +.+..+.|++.
T Consensus        52 ~~-~~ivvyC~~g~rs~~a~~~L~~~G-~~v~~l~GG~~   88 (94)
T 1wv9_A           52 PR-RPLLLVCEKGLLSQVAALYLEAEG-YEAMSLEGGLQ   88 (94)
T ss_dssp             CS-SCEEEECSSSHHHHHHHHHHHHHT-CCEEEETTGGG
T ss_pred             CC-CCEEEEcCCCChHHHHHHHHHHcC-CcEEEEcccHH
Confidence            34 899999999988999999999998 56888888864

>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=85.62  E-value=0.71  Score=37.78  Aligned_cols=86  Identities=6%  Similarity=0.015  Sum_probs=53.0

Q ss_pred             HHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcC----CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCC
Q 029910           13 ELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG   88 (185)
Q Consensus        13 ~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~   88 (185)
                      .++..+.. ...+.++||.|+|+.-|.++...+...    +.+.+..+.|+.+...+.       ..             
T Consensus       151 p~l~~l~~-~~~~~~~lil~PtreLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~-------~~-------------  209 (300)
T 3fmo_B          151 AMLSQVEP-ANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ-------KI-------------  209 (300)
T ss_dssp             HHHHHCCT-TSCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTTC-------CC-------------
T ss_pred             HHHHhhhc-cCCCceEEEEcCcHHHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhhh-------cC-------------
Confidence            44554333 344558999999999998887776543    236777777765432221       11             


Q ss_pred             CCCCCCCCCCceeEEEEecCCC-Ccc-c-CcCCCCCCcEEEEcC
Q 029910           89 DESETGKDEHKSHMIVVTDACL-PLL-S-SGESAISARVLINYE  129 (185)
Q Consensus        89 ~~~~~~~~~~~~~iLV~Td~~~-~~~-~-~G~d~~~v~~VI~~d  129 (185)
                                ..+|+|+|+-++ -++ . ..+++..+.++|.=+
T Consensus       210 ----------~~~IlV~TP~~l~~~l~~~~~~~l~~l~~lVlDE  243 (300)
T 3fmo_B          210 ----------SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDE  243 (300)
T ss_dssp             ----------CCSEEEECHHHHHHHHTTTCCCCGGGCSEEEETT
T ss_pred             ----------CCCEEEECHHHHHHHHHhcCCCChhhceEEEEeC
Confidence                      468999997521 001 1 356788899888633

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=85.37  E-value=2.6  Score=32.46  Aligned_cols=77  Identities=13%  Similarity=0.173  Sum_probs=51.1

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCC---CceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCc
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLA---DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHK   99 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~---~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (185)
                      ..+.++||.|+++.-+.+..+.+...+   ++.+..++|+.+.......+     .                       .
T Consensus        95 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-----~-----------------------~  146 (236)
T 2pl3_A           95 TDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERI-----N-----------------------N  146 (236)
T ss_dssp             GGCCCEEEECSSHHHHHHHHHHHHHHTTTSSCCEEEECCC--CHHHHHHH-----T-----------------------T
T ss_pred             cCCceEEEEeCCHHHHHHHHHHHHHHhCCCCeeEEEEECCCCHHHHHHhC-----C-----------------------C
Confidence            346789999999999998888886542   26889999987766554332     2                       3


Q ss_pred             eeEEEEecCCC-CcccC--cCCCCCCcEEEE
Q 029910          100 SHMIVVTDACL-PLLSS--GESAISARVLIN  127 (185)
Q Consensus       100 ~~iLV~Td~~~-~~~~~--G~d~~~v~~VI~  127 (185)
                      .+|+|+|.-.+ .++.+  .++...+++||.
T Consensus       147 ~~iiv~Tp~~l~~~l~~~~~~~~~~~~~lVi  177 (236)
T 2pl3_A          147 INILVCTPGRLLQHMDETVSFHATDLQMLVL  177 (236)
T ss_dssp             CSEEEECHHHHHHHHHHCSSCCCTTCCEEEE
T ss_pred             CCEEEECHHHHHHHHHhcCCcccccccEEEE
Confidence            78999996411 00112  356777887775

>1gmx_A GLPE protein; transferase, rhodanese, sulfurtransferase, glycerol metabolism; 1.1A {Escherichia coli} SCOP: c.46.1.3 PDB: 1gn0_A

Probab=85.36  E-value=1.5  Score=29.98  Aligned_cols=39  Identities=10%  Similarity=0.130  Sum_probs=32.7

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      .+.+++||||.+-..+...+..|...|+-.+..+.|++.
T Consensus        56 ~~~~~ivvyc~~g~rs~~a~~~L~~~G~~~v~~l~GG~~   94 (108)
T 1gmx_A           56 DFDTPVMVMCYHGNSSKGAAQYLLQQGYDVVYSIDGGFE   94 (108)
T ss_dssp             CTTSCEEEECSSSSHHHHHHHHHHHHTCSSEEEETTHHH
T ss_pred             CCCCCEEEEcCCCchHHHHHHHHHHcCCceEEEecCCHH
Confidence            456899999999888999999999998445888999854

>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=85.11  E-value=0.82  Score=35.59  Aligned_cols=90  Identities=17%  Similarity=0.258  Sum_probs=53.1

Q ss_pred             HHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcC----CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCC
Q 029910           13 ELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG   88 (185)
Q Consensus        13 ~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~   88 (185)
                      .++..+......+.++||.+++++-+.++.+.+...    + +.+..++|+.....+      +...             
T Consensus        86 ~~l~~l~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~-~~~~~~~~~~~~~~~------~~~~-------------  145 (245)
T 3dkp_A           86 PILMQLKQPANKGFRALIISPTRELASQIHRELIKISEGTG-FRIHMIHKAAVAAKK------FGPK-------------  145 (245)
T ss_dssp             HHHHHHCSCCSSSCCEEEECSSHHHHHHHHHHHHHHTTTSC-CCEECCCHHHHHHTT------TSTT-------------
T ss_pred             HHHHHHhhcccCCceEEEEeCCHHHHHHHHHHHHHHhcccC-ceEEEEecCccHHHH------hhhh-------------
Confidence            344443332345668999999999999888888654    4 667777765322111      1110             


Q ss_pred             CCCCCCCCCCceeEEEEecCCCC-cccC---cCCCCCCcEEEEcC
Q 029910           89 DESETGKDEHKSHMIVVTDACLP-LLSS---GESAISARVLINYE  129 (185)
Q Consensus        89 ~~~~~~~~~~~~~iLV~Td~~~~-~~~~---G~d~~~v~~VI~~d  129 (185)
                             .....+|+|+|+-.+- ++.+   .+++.++++||.=+
T Consensus       146 -------~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~~~lViDE  183 (245)
T 3dkp_A          146 -------SSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDE  183 (245)
T ss_dssp             -------SCCCCCEEEECHHHHHHHHHSSSCSCCCTTCCEEEESS
T ss_pred             -------hcCCCCEEEECHHHHHHHHHhCCCCcccccCcEEEEeC
Confidence                   0125789999954110 0112   46888888887633

>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=84.54  E-value=4.3  Score=32.13  Aligned_cols=77  Identities=12%  Similarity=0.145  Sum_probs=53.0

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcCC---CceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCce
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNLA---DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKS  100 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~~---~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~  100 (185)
                      .+.++||.++++.-+.+..+.++...   .+.+..++|+.+...+...   +..+                        .
T Consensus       125 ~~~~~lil~Pt~~La~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~~~~------------------------~  177 (262)
T 3ly5_A          125 NGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQK---LGNG------------------------I  177 (262)
T ss_dssp             GCCCEEEECSSHHHHHHHHHHHHHHTTTCCSCEEEECSSSCHHHHHHH---HHHC------------------------C
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHHhhcCceEEEEECCCCHHHHHHH---hcCC------------------------C
Confidence            46789999999999998888876531   2678889998876665433   3343                        7


Q ss_pred             eEEEEecCCCC-cc--cCcCCCCCCcEEEE
Q 029910          101 HMIVVTDACLP-LL--SSGESAISARVLIN  127 (185)
Q Consensus       101 ~iLV~Td~~~~-~~--~~G~d~~~v~~VI~  127 (185)
                      +|+|+|+-.+- ++  ..++++..+++||.
T Consensus       178 ~Iiv~Tp~~l~~~~~~~~~~~~~~l~~lVi  207 (262)
T 3ly5_A          178 NIIVATPGRLLDHMQNTPGFMYKNLQCLVI  207 (262)
T ss_dssp             SEEEECHHHHHHHHHHCTTCCCTTCCEEEE
T ss_pred             CEEEEcHHHHHHHHHccCCcccccCCEEEE
Confidence            89999952100 01  22467788888775

>2l82_A Designed protein OR32; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, de novo protein; NMR {Artificial gene}

Probab=83.83  E-value=5.2  Score=28.80  Aligned_cols=48  Identities=25%  Similarity=0.319  Sum_probs=43.0

Q ss_pred             cEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcc
Q 029910           27 PMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHT   75 (185)
Q Consensus        27 ~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~   75 (185)
                      -.+||.+...-...+...++..| +.+..++++.....|.+-++.|...
T Consensus         4 ifvvfssdpeilkeivreikrqg-vrvvllysdqdekrrrerleefekq   51 (162)
T 2l82_A            4 IFVVFSSDPEILKEIVREIKRQG-VRVVLLYSDQDEKRRRERLEEFEKQ   51 (162)
T ss_dssp             EEEEEESCHHHHHHHHHHHHHTT-CEEEEEECCSCHHHHHHHHHHHHTT
T ss_pred             EEEEecCCHHHHHHHHHHHHhCC-eEEEEEecCchHHHHHHHHHHHHHc
Confidence            35789888888899999999998 8999999999999999999999775

>2k0z_A Uncharacterized protein HP1203; A/B domain, structural genomics, unknown function, PSI-2, PR structure initiative; NMR {Helicobacter pylori}

Probab=83.43  E-value=1.7  Score=29.94  Aligned_cols=38  Identities=8%  Similarity=0.149  Sum_probs=32.0

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      .+.+++||||.+-..+...+..|...|+-. ..|.|++.
T Consensus        54 ~~~~~ivvyC~~G~rs~~aa~~L~~~G~~~-~~l~GG~~   91 (110)
T 2k0z_A           54 HKDKKVLLHCRAGRRALDAAKSMHELGYTP-YYLEGNVY   91 (110)
T ss_dssp             CSSSCEEEECSSSHHHHHHHHHHHHTTCCC-EEEESCGG
T ss_pred             CCCCEEEEEeCCCchHHHHHHHHHHCCCCE-EEecCCHH
Confidence            456899999999999999999999998444 88889854

>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=83.17  E-value=5.2  Score=31.05  Aligned_cols=76  Identities=9%  Similarity=0.075  Sum_probs=51.7

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcC---CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCcee
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNL---ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSH  101 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~---~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (185)
                      +.++||.|++++-+.++.+.+...   ..+.+..++|+.+..++...   ...                        ..+
T Consensus       100 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~~~------------------------~~~  152 (253)
T 1wrb_A          100 YPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIRE---VQM------------------------GCH  152 (253)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHH---HSS------------------------CCS
T ss_pred             CceEEEEECCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHH---hCC------------------------CCC
Confidence            468999999999999888777543   12678889998876655433   233                        378


Q ss_pred             EEEEecCCCC-cc-cCcCCCCCCcEEEE
Q 029910          102 MIVVTDACLP-LL-SSGESAISARVLIN  127 (185)
Q Consensus       102 iLV~Td~~~~-~~-~~G~d~~~v~~VI~  127 (185)
                      |+|+|.-.+- ++ ...+++..+++||.
T Consensus       153 Ivv~Tp~~l~~~l~~~~~~~~~~~~lVi  180 (253)
T 1wrb_A          153 LLVATPGRLVDFIEKNKISLEFCKYIVL  180 (253)
T ss_dssp             EEEECHHHHHHHHHTTSBCCTTCCEEEE
T ss_pred             EEEECHHHHHHHHHcCCCChhhCCEEEE
Confidence            9999974210 01 22357778888775

>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=82.92  E-value=4.7  Score=32.95  Aligned_cols=48  Identities=15%  Similarity=0.058  Sum_probs=36.6

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcC---CCceEEEEecCCCHHHHHHHH
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNL---ADISFSSLHSDLAETERTLIL   69 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~---~~~~~~~l~g~~~~~~R~~~l   69 (185)
                      ...+.++||.|+++.-+.+..+.+...   .++.+..++|+.+..++...+
T Consensus        86 ~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~  136 (394)
T 1fuu_A           86 SVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGL  136 (394)
T ss_dssp             TCCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECSSCCHHHHHHHH
T ss_pred             cCCCCCEEEEcCCHHHHHHHHHHHHHHhccCCeeEEEEeCCCchHHHHhhc
Confidence            345679999999999998888777542   137899999998877665543

>2fsx_A RV0390, COG0607: rhodanese-related sulfurtransferase; RV0390 BR SAD DATA with FBAR, structural genomics, PSI; 1.80A {Mycobacterium tuberculosis}

Probab=82.74  E-value=1.4  Score=32.08  Aligned_cols=39  Identities=10%  Similarity=0.146  Sum_probs=31.4

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      .+.+++||||.+-..+...+..|...|+-.+..|.|++.
T Consensus        78 ~~~~~ivvyC~~G~rS~~aa~~L~~~G~~~v~~l~GG~~  116 (148)
T 2fsx_A           78 QHERPVIFLCRSGNRSIGAAEVATEAGITPAYNVLDGFE  116 (148)
T ss_dssp             ---CCEEEECSSSSTHHHHHHHHHHTTCCSEEEETTTTT
T ss_pred             CCCCEEEEEcCCChhHHHHHHHHHHcCCcceEEEcCChh
Confidence            456899999999888889999999998446999999874

>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=82.73  E-value=3.6  Score=35.09  Aligned_cols=89  Identities=8%  Similarity=0.118  Sum_probs=58.4

Q ss_pred             HHHHHHHHccC----CCCCcEEEEcCChhhHHHHHHHHhcCC---CceEEEEecCCCHHHHHHHHHHHhccccccccccc
Q 029910           12 VELLHLVVAGR----RPGLPMIVCCSSRDELDAVCSAVSNLA---DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVT   84 (185)
Q Consensus        12 ~~ll~~l~~~~----~~~~~~IIF~~~~~~~~~l~~~L~~~~---~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~   84 (185)
                      +-++..+....    ..+.++||.|+|++-+.++.+.+...+   .+++..++|+.+..++...   ...+         
T Consensus       112 lpil~~l~~~~~~~~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~---l~~~---------  179 (434)
T 2db3_A          112 LPILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNEC---ITRG---------  179 (434)
T ss_dssp             HHHHHHHHHSCCCCCTTCCSEEEECSSHHHHHHHHHHHHHHTTTSSCCCCEECTTSCHHHHHHH---HTTC---------
T ss_pred             HHHHHHHHhcccccccCCccEEEEecCHHHHHHHHHHHHHHhccCCcEEEEEECCCCHHHHHHH---hhcC---------
Confidence            34555544421    235799999999999999988776532   3788899999887765433   3333         


Q ss_pred             ccCCCCCCCCCCCCceeEEEEecCCC-CcccC-cCCCCCCcEEEE
Q 029910           85 EQSGDESETGKDEHKSHMIVVTDACL-PLLSS-GESAISARVLIN  127 (185)
Q Consensus        85 ~~~~~~~~~~~~~~~~~iLV~Td~~~-~~~~~-G~d~~~v~~VI~  127 (185)
                                     .+|+|+|+-++ .++.+ .+++..+++||.
T Consensus       180 ---------------~~Ivv~Tp~~l~~~l~~~~~~l~~~~~lVl  209 (434)
T 2db3_A          180 ---------------CHVVIATPGRLLDFVDRTFITFEDTRFVVL  209 (434)
T ss_dssp             ---------------CSEEEECHHHHHHHHHTTSCCCTTCCEEEE
T ss_pred             ---------------CCEEEEChHHHHHHHHhCCcccccCCeEEE
Confidence                           78999996421 00122 346778888774

>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=82.72  E-value=5.1  Score=33.01  Aligned_cols=80  Identities=15%  Similarity=0.132  Sum_probs=53.0

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCC---CceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCc
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLA---DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHK   99 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~---~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (185)
                      ..+.++||.|+++.-+.+..+.+....   ++.+..++|+.+..+....   .. +                       .
T Consensus        87 ~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~~-~-----------------------~  139 (400)
T 1s2m_A           87 LNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILR---LN-E-----------------------T  139 (400)
T ss_dssp             SCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHH---TT-S-----------------------C
T ss_pred             cCCccEEEEcCCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHHH---hc-C-----------------------C
Confidence            355789999999999988888776531   3788999998876554322   22 2                       4


Q ss_pred             eeEEEEecCCC-Ccc-cCcCCCCCCcEEEEcC
Q 029910          100 SHMIVVTDACL-PLL-SSGESAISARVLINYE  129 (185)
Q Consensus       100 ~~iLV~Td~~~-~~~-~~G~d~~~v~~VI~~d  129 (185)
                      .+|+|+|.-.+ .++ ....++.++++||.=+
T Consensus       140 ~~Ivv~T~~~l~~~~~~~~~~~~~~~~vIiDE  171 (400)
T 1s2m_A          140 VHILVGTPGRVLDLASRKVADLSDCSLFIMDE  171 (400)
T ss_dssp             CSEEEECHHHHHHHHHTTCSCCTTCCEEEEES
T ss_pred             CCEEEEchHHHHHHHHhCCcccccCCEEEEeC
Confidence            78999995310 002 2345677788877533

>3ilm_A ALR3790 protein; rhodanese-like, NSR437H, NESG, structural genomics, protein structure initiative, northeast structural genomics consortium; 2.26A {Nostoc SP} PDB: 2kl3_A

Probab=82.68  E-value=1.6  Score=31.78  Aligned_cols=40  Identities=13%  Similarity=0.091  Sum_probs=33.0

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      -.+.+++||||.+-..+...+..|...|+-.+..|.|++.
T Consensus        53 l~~~~~ivvyC~~g~rs~~aa~~L~~~G~~~v~~l~GG~~   92 (141)
T 3ilm_A           53 LEKSRDIYVYGAGDEQTSQAVNLLRSAGFEHVSELKGGLA   92 (141)
T ss_dssp             SCTTSEEEEECSSHHHHHHHHHHHHHTTCCSEEECTTHHH
T ss_pred             CCCCCeEEEEECCChHHHHHHHHHHHcCCCCEEEecCHHH
Confidence            3456889999999999999999999998545888988843

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=82.21  E-value=2.3  Score=36.61  Aligned_cols=76  Identities=12%  Similarity=0.114  Sum_probs=51.1

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcC----CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCce
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKS  100 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~  100 (185)
                      +.++||.|+++.-+....+.+...    + +.+..++|+.+...+...   +..+                        .
T Consensus        52 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~---~~~~------------------------~  103 (555)
T 3tbk_A           52 KGKVVFFANQIPVYEQQATVFSRYFERLG-YNIASISGATSDSVSVQH---IIED------------------------N  103 (555)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHHHHHTTT-CCEEEECTTTGGGSCHHH---HHHH------------------------C
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHHhccCC-cEEEEEcCCCcchhhHHH---HhcC------------------------C
Confidence            689999999999888877777654    5 899999999876655332   2233                        6


Q ss_pred             eEEEEecCCCC-cccCc-C-CCCCCcEEEEc
Q 029910          101 HMIVVTDACLP-LLSSG-E-SAISARVLINY  128 (185)
Q Consensus       101 ~iLV~Td~~~~-~~~~G-~-d~~~v~~VI~~  128 (185)
                      +|+|+|.-.+- ++.++ + .+..+++||.=
T Consensus       104 ~i~v~T~~~l~~~~~~~~~~~~~~~~~vViD  134 (555)
T 3tbk_A          104 DIIILTPQILVNNLNNGAIPSLSVFTLMIFD  134 (555)
T ss_dssp             SEEEECHHHHHHHHHTSSSCCGGGCSEEEET
T ss_pred             CEEEECHHHHHHHHhcCcccccccCCEEEEE
Confidence            79999864100 01122 3 56667877753

>3flh_A Uncharacterized protein LP_1913; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.00A {Lactobacillus plantarum} PDB: 3fnj_A 3i3u_A

Probab=82.08  E-value=1.5  Score=31.00  Aligned_cols=39  Identities=10%  Similarity=0.012  Sum_probs=32.0

Q ss_pred             CCCCCcEEEEcCChhh--HHHHHHHHhcCCCceEEEEecCCC
Q 029910           22 RRPGLPMIVCCSSRDE--LDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~--~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      -.+.+++||||.+-..  +...+..|...| +++..|.|++.
T Consensus        68 l~~~~~ivvyC~~g~r~~s~~a~~~L~~~G-~~v~~l~GG~~  108 (124)
T 3flh_A           68 LDPAKTYVVYDWTGGTTLGKTALLVLLSAG-FEAYELAGALE  108 (124)
T ss_dssp             SCTTSEEEEECSSSSCSHHHHHHHHHHHHT-CEEEEETTHHH
T ss_pred             CCCCCeEEEEeCCCCchHHHHHHHHHHHcC-CeEEEeCCcHH
Confidence            4456899999998776  788999999998 58888888853

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=81.10  E-value=1.2  Score=34.02  Aligned_cols=79  Identities=10%  Similarity=0.202  Sum_probs=49.3

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcCC-------CceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCC
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNLA-------DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETG   94 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~~-------~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~   94 (185)
                      ...+.++||.|+++.-+.++.+.+....       .+.+..++|+.+..++.+   .+..                    
T Consensus        69 ~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~---~~~~--------------------  125 (219)
T 1q0u_A           69 ERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALE---KLNV--------------------  125 (219)
T ss_dssp             TSCSCCEEEECSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTC---CCSS--------------------
T ss_pred             CcCCceEEEEcCcHHHHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHHHH---HcCC--------------------
Confidence            3346789999999999988887765431       367888888865433211   1111                    


Q ss_pred             CCCCceeEEEEecCCCC-ccc-CcCCCCCCcEEEE
Q 029910           95 KDEHKSHMIVVTDACLP-LLS-SGESAISARVLIN  127 (185)
Q Consensus        95 ~~~~~~~iLV~Td~~~~-~~~-~G~d~~~v~~VI~  127 (185)
                          ..+|+|+|.-.+- ++. ..+++..+++||.
T Consensus       126 ----~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~lVi  156 (219)
T 1q0u_A          126 ----QPHIVIGTPGRINDFIREQALDVHTAHILVV  156 (219)
T ss_dssp             ----CCSEEEECHHHHHHHHHTTCCCGGGCCEEEE
T ss_pred             ----CCCEEEeCHHHHHHHHHcCCCCcCcceEEEE
Confidence                4679999963100 022 2456677787775

>1qxn_A SUD, sulfide dehydrogenase; polysulfide-sulfur transferase, homodimer; NMR {Wolinella succinogenes} SCOP: c.46.1.3

Probab=80.95  E-value=1.3  Score=32.02  Aligned_cols=40  Identities=10%  Similarity=0.210  Sum_probs=33.4

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      -.+.+++||||.+-..+...+..|...|+-.+..|.|++.
T Consensus        79 l~~~~~ivvyC~~G~rS~~aa~~L~~~G~~~v~~l~GG~~  118 (137)
T 1qxn_A           79 LDPEKPVVVFCKTAARAALAGKTLREYGFKTIYNSEGGMD  118 (137)
T ss_dssp             CCTTSCEEEECCSSSCHHHHHHHHHHHTCSCEEEESSCHH
T ss_pred             CCCCCeEEEEcCCCcHHHHHHHHHHHcCCcceEEEcCcHH
Confidence            3456899999999888999999999998446889999953

>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=80.75  E-value=5.3  Score=33.07  Aligned_cols=78  Identities=9%  Similarity=0.094  Sum_probs=52.9

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCC---CceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCc
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLA---DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHK   99 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~---~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (185)
                      ..+.++||.|+++.-+.++.+.+...+   .+.+..++|+.+..++...+   ..+                        
T Consensus       103 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~---~~~------------------------  155 (410)
T 2j0s_A          103 VRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKL---DYG------------------------  155 (410)
T ss_dssp             SCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHH---HHC------------------------
T ss_pred             cCCceEEEEcCcHHHHHHHHHHHHHHhccCCeEEEEEECCCCHHHHHHHh---hcC------------------------
Confidence            456899999999999998888776432   37888999998877665433   333                        


Q ss_pred             eeEEEEecCCC-Cccc-CcCCCCCCcEEEE
Q 029910          100 SHMIVVTDACL-PLLS-SGESAISARVLIN  127 (185)
Q Consensus       100 ~~iLV~Td~~~-~~~~-~G~d~~~v~~VI~  127 (185)
                      .+|+|+|.-.+ .++. ..++...+++||.
T Consensus       156 ~~ivv~Tp~~l~~~l~~~~~~~~~~~~vVi  185 (410)
T 2j0s_A          156 QHVVAGTPGRVFDMIRRRSLRTRAIKMLVL  185 (410)
T ss_dssp             CSEEEECHHHHHHHHHTTSSCCTTCCEEEE
T ss_pred             CCEEEcCHHHHHHHHHhCCccHhheeEEEE
Confidence            67899995210 0022 3456677777774

>3d1p_A Putative thiosulfate sulfurtransferase YOR285W; atomic structure, atomic resolution structure, PSI, MCSG; HET: MSE; 0.98A {Saccharomyces cerevisiae}

Probab=80.55  E-value=1.5  Score=31.45  Aligned_cols=39  Identities=13%  Similarity=0.096  Sum_probs=32.7

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      .+.+++|+||.+-..+...+..|...|+-.+..+.|++.
T Consensus        89 ~~~~~ivvyC~~G~rs~~aa~~L~~~G~~~v~~l~GG~~  127 (139)
T 3d1p_A           89 DSAKELIFYCASGKRGGEAQKVASSHGYSNTSLYPGSMN  127 (139)
T ss_dssp             CTTSEEEEECSSSHHHHHHHHHHHTTTCCSEEECTTHHH
T ss_pred             CCCCeEEEECCCCchHHHHHHHHHHcCCCCeEEeCCcHH
Confidence            456899999999989999999999998445888888853

>3nhv_A BH2092 protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 2.50A {Bacillus halodurans} PDB: 3o3w_A

Probab=80.09  E-value=1.6  Score=31.83  Aligned_cols=38  Identities=11%  Similarity=0.195  Sum_probs=32.0

Q ss_pred             CCCCcEEEEcCCh--hhHHHHHHHHhcCCCceEEEEecCCC
Q 029910           23 RPGLPMIVCCSSR--DELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus        23 ~~~~~~IIF~~~~--~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      .+.+++||||.+-  ..+...+..|...| +++..|.|++.
T Consensus        70 ~~~~~ivvyC~~g~~~rs~~aa~~L~~~G-~~v~~l~GG~~  109 (144)
T 3nhv_A           70 SKEKVIITYCWGPACNGATKAAAKFAQLG-FRVKELIGGIE  109 (144)
T ss_dssp             CTTSEEEEECSCTTCCHHHHHHHHHHHTT-CEEEEEESHHH
T ss_pred             CCCCeEEEEECCCCccHHHHHHHHHHHCC-CeEEEeCCcHH
Confidence            4568999999987  57889999999999 58999999853

---

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	185
d2j0sa2	168	c.37.1.19 (A:244-411) Probable ATP-dependent RNA h	4e-05
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	6e-04
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	0.003

>d2j0sa2 c.37.1.19 (A:244-411) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]} Length = 168

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.9 bits (92), Expect = 4e-05
 Identities = 25/161 (15%), Positives = 54/161 (33%), Gaps = 9/161 (5%)

Query: 29  IVCCSSRDELDAVCSAVSNLADIS--FSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ 86
           +       + D +C     L               +     + E     +        ++
Sbjct: 13  VAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKE 72

Query: 87  SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRM--TTC 144
                +  +      +I            G       ++INY+LP  +E YI R+  +  
Sbjct: 73  RESIMKEFRSGASRVLISTDVWA-----RGLDVPQVSLIINYDLPNNRELYIHRIGRSGR 127

Query: 145 LAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
               G  IN V   ++  LR +E+     + E+P+N+++++
Sbjct: 128 YGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI 168

>d1gkub2 c.37.1.16 (B:251-498) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 248

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 = 37.1 bits (85), Expect = 6e-04
 Identities = 19/178 (10%), Positives = 50/178 (28%), Gaps = 39/178 (21%)

Query: 9   ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI 68
            TL  +L       + G   I+   + +E + +  ++ N            +    +   
Sbjct: 15  STLSSIL------EKLGTGGIIYARTGEEAEEIYESLKN-------KFRIGIVTATKKGD 61

Query: 69  LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSG-ESAISARVLIN 127
            E+F                          +   ++ T      L  G +     R  + 
Sbjct: 62  YEKFVE-----------------------GEIDHLIGTAHYYGTLVRGLDLPERIRFAVF 98

Query: 128 YELPTKKETYIRRMTTCLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 185
              P+ + T        L+     +   +   V  +  +  ++   + EV   + +++
Sbjct: 99  VGCPSFRVTIED--IDSLSPQMVKLLAYLYRNVDEIERLLPAVERHIDEVREILKKVM 154

>d1a1va2 c.37.1.14 (A:326-624) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 299

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]

 Score = 34.9 bits (80), Expect = 0.003
 Identities = 16/139 (11%), Positives = 38/139 (27%), Gaps = 15/139 (10%)

Query: 3   VSFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAE 62
           V+ +    +      +      G   ++ C S+ + D + + +  L  I+  + +  L  
Sbjct: 14  VALSTTGEIPFYGKAIPLEVIKGGRHLIFCHSKKKCDELAAKLVAL-GINAVAYYRGLDV 72

Query: 63  TERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISA 122
           +                +  V   + D   TG       +I         +         
Sbjct: 73  SVIPT------------SGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFSLDPTF- 119

Query: 123 RVLINYELPTKKETYIRRM 141
             +    LP    +  +R 
Sbjct: 120 -TIETTTLPQDAVSRTQRR 137

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	185
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	100.0
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	100.0
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	100.0
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	100.0
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	100.0
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.97
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.96
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.95
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	99.95
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.92
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	99.89
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.82
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	99.81
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.8
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	99.78
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	99.72
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.63
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.62
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	99.59
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.42
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	99.29
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	99.03
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	98.19
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	96.58
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	96.09
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	93.24
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	92.1
d1tq1a_	119	Thiosulfate sulfurtransferase/Senescence-associate	91.18
d1urha2	120	3-mercaptopyruvate sulfurtransferase {Escherichia	90.35
d1gmxa_	108	Sulfurtransferase GlpE {Escherichia coli [TaxId: 5	88.68
d1yt8a4	130	Thiosulfate sulfurtransferase PA2603 {Pseudomonas	87.08
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	86.76
d1qxna_	137	Polysulfide-sulfur transferase (sulfide dehydrogen	84.83
d2eyqa2	117	Transcription-repair coupling factor, TRCF {Escher	84.34
d1e0ca2	136	Sulfurtransferase {Azotobacter vinelandii [TaxId:	83.82
d1yt8a1	136	Thiosulfate sulfurtransferase PA2603 {Pseudomonas	83.37
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	82.74
d1rhsa2	144	Rhodanese {Cow (Bos taurus) [TaxId: 9913]}	80.76
d1yt8a2	101	Thiosulfate sulfurtransferase PA2603 {Pseudomonas	80.67
d1uara2	141	Sulfurtransferase {Thermus thermophilus [TaxId: 27	80.63
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	80.48

>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=100.00  E-value=4.8e-36  Score=231.92  Aligned_cols=150  Identities=28%  Similarity=0.480  Sum_probs=137.5

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ   86 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~   86 (185)
                      +.+.++++|..|++ ..+.+++||||+++.++++++..|...+ +.+..+||+|+..+|.++++.|+.+           
T Consensus        10 ~~e~K~~~L~~ll~-~~~~~k~iIF~~s~~~~~~l~~~L~~~~-~~~~~~~~~~~~~~r~~~l~~f~~~-----------   76 (162)
T d1fuka_          10 EEEYKYECLTDLYD-SISVTQAVIFCNTRRKVEELTTKLRNDK-FTVSAIYSDLPQQERDTIMKEFRSG-----------   76 (162)
T ss_dssp             SGGGHHHHHHHHHH-HTTCSCEEEEESSHHHHHHHHHHHHHTT-CCEEEECTTSCHHHHHHHHHHHHTT-----------
T ss_pred             CcHHHHHHHHHHHH-hCCCCcEEEEEEEEchHHHHHHHHhhcC-ceEEEeccCCchhhHHHHHHHHhhc-----------
Confidence            45667777777776 6677999999999999999999999998 8999999999999999999999999           


Q ss_pred             CCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHHHHH
Q 029910           87 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLR  164 (185)
Q Consensus        87 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~~~  164 (185)
                                  ..++|||||+    ++||+|+|+|++|||||+|++++.|+||+||+  .|+.|.|++|+++.|...++
T Consensus        77 ------------~~~iLv~Tdv----~~rGiDi~~v~~VI~~d~P~~~~~yihR~GR~gR~g~~g~~i~~~~~~d~~~~~  140 (162)
T d1fuka_          77 ------------SSRILISTDL----LARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMR  140 (162)
T ss_dssp             ------------SCSEEEEEGG----GTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETTTHHHHH
T ss_pred             ------------ccceeecccc----ccccccCCCceEEEEeccchhHHHHHhhccccccCCCccEEEEEcCHHHHHHHH
Confidence                        6999999999    99999999999999999999999999999997  57789999999999999999


Q ss_pred             HHHHHhCCccccccCCccccC
Q 029910          165 SMEESLGLIVAEVPINISEIL  185 (185)
Q Consensus       165 ~l~~~~~~~~~~~~~~~~~~l  185 (185)
                      .+++.++..++++|.+++++|
T Consensus       141 ~i~~~~~~~~~~ip~~~~~l~  161 (162)
T d1fuka_         141 ELEKFYSTQIEELPSDIATLL  161 (162)
T ss_dssp             HHHHHSSCCCEECCSCCTTTT
T ss_pred             HHHHHHcCcCCCCChHHHHhh
Confidence            999999999999999999886

>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=100.00  E-value=5e-35  Score=227.46  Aligned_cols=149  Identities=25%  Similarity=0.487  Sum_probs=136.1

Q ss_pred             hHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccC
Q 029910            8 QETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQS   87 (185)
Q Consensus         8 ~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~   87 (185)
                      .+.+++.|..|+. ..+..++||||+++++++.++..|...+ +.+..+||+++..+|.+++++|++|            
T Consensus        18 ~~~K~~~L~~ll~-~~~~~k~iiF~~~~~~~~~~~~~l~~~~-~~~~~~~~~~~~~~r~~~~~~fk~g------------   83 (168)
T d2j0sa2          18 EEWKFDTLCDLYD-TLTITQAVIFCNTKRKVDWLTEKMREAN-FTVSSMHGDMPQKERESIMKEFRSG------------   83 (168)
T ss_dssp             TTHHHHHHHHHHH-HHTSSEEEEECSSHHHHHHHHHHHHHTT-CCCEEECTTSCHHHHHHHHHHHHHT------------
T ss_pred             hHHHHHHHHHHHH-hCCCCceEEEeeeHHHHHHHHHHhhhcc-cchhhhhhhhhHHHHHHHHHHHhcC------------
Confidence            3444555555454 4456899999999999999999999998 8999999999999999999999999            


Q ss_pred             CCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHHHHHH
Q 029910           88 GDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLRS  165 (185)
Q Consensus        88 ~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~~~~  165 (185)
                                 ..++|||||+    ++||+|+|++++|||||+|+++++|+||+||+  .|+.|.+|+|+++.|...++.
T Consensus        84 -----------~~~iLv~Td~----~~rGiDi~~v~~VIn~d~P~~~~~yihR~GR~gR~g~~G~~i~~~~~~d~~~~~~  148 (168)
T d2j0sa2          84 -----------ASRVLISTDV----WARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRD  148 (168)
T ss_dssp             -----------SSCEEEECGG----GSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGGGHHHHHH
T ss_pred             -----------CccEEeccch----hcccccccCcceEEEecCCcCHHHHHhhhccccccCCCcEEEEEECHHHHHHHHH
Confidence                       7999999999    99999999999999999999999999999997  577899999999999999999


Q ss_pred             HHHHhCCccccccCCccccC
Q 029910          166 MEESLGLIVAEVPINISEIL  185 (185)
Q Consensus       166 l~~~~~~~~~~~~~~~~~~l  185 (185)
                      +++.++.+++++|.++.++|
T Consensus       149 i~~~~~~~i~e~p~~~~dii  168 (168)
T d2j0sa2         149 IEQYYSTQIDEMPMNVADLI  168 (168)
T ss_dssp             HHHHTTCCCEECCSCCTTTC
T ss_pred             HHHHHcCcCCCCCcChHHhC
Confidence            99999999999999999986

>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=100.00  E-value=4.6e-34  Score=221.94  Aligned_cols=151  Identities=24%  Similarity=0.441  Sum_probs=137.5

Q ss_pred             ecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccc
Q 029910            5 FTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVT   84 (185)
Q Consensus         5 ~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~   84 (185)
                      +++.+.+.+.|..+++ ..++.++||||+++++++.++..|...| +.+..+||+++.++|.+++++|+.+         
T Consensus        13 ~v~~~~K~~~L~~ll~-~~~~~k~iVF~~~~~~~~~l~~~L~~~g-~~~~~~h~~~~~~~r~~~~~~f~~~---------   81 (171)
T d1s2ma2          13 FVEERQKLHCLNTLFS-KLQINQAIIFCNSTNRVELLAKKITDLG-YSCYYSHARMKQQERNKVFHEFRQG---------   81 (171)
T ss_dssp             ECCGGGHHHHHHHHHH-HSCCSEEEEECSSHHHHHHHHHHHHHHT-CCEEEECTTSCHHHHHHHHHHHHTT---------
T ss_pred             EcCHHHHHHHHHHHHH-hCCCCceEEEEeeeehhhHhHHhhhccc-ccccccccccchhhhhhhhhhcccC---------
Confidence            3455556666666666 4567899999999999999999999998 8999999999999999999999999         


Q ss_pred             ccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHHH
Q 029910           85 EQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVT  162 (185)
Q Consensus        85 ~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~  162 (185)
                                    ..++|||||+    ++||+|+|++++|||||+|+++++|+||+||+  .|+.|.+|+|++++|...
T Consensus        82 --------------~~~ilv~Td~----~~~Gid~~~v~~VI~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~v~~~e~~~  143 (171)
T d1s2ma2          82 --------------KVRTLVCSDL----LTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFN  143 (171)
T ss_dssp             --------------SSSEEEESSC----SSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGGGHHH
T ss_pred             --------------ccccccchhH----hhhccccceeEEEEecCCcchHHHHHHHhhhcccCCCccEEEEEeCHHHHHH
Confidence                          7999999999    99999999999999999999999999999997  457899999999999999


Q ss_pred             HHHHHHHhCCccccccCCcccc
Q 029910          163 LRSMEESLGLIVAEVPINISEI  184 (185)
Q Consensus       163 ~~~l~~~~~~~~~~~~~~~~~~  184 (185)
                      ++.+++.++.+++++|..+.+.
T Consensus       144 ~~~i~~~l~~~~~~~p~~~d~~  165 (171)
T d1s2ma2         144 LYKIEQELGTEIAAIPATIDKS  165 (171)
T ss_dssp             HHHHHHHHTCCCEECCSSCCGG
T ss_pred             HHHHHHHHCCCCCCCCcccchh
Confidence            9999999999999999988764

>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=100.00  E-value=6.7e-32  Score=206.43  Aligned_cols=143  Identities=22%  Similarity=0.418  Sum_probs=129.5

Q ss_pred             ecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccc
Q 029910            5 FTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVT   84 (185)
Q Consensus         5 ~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~   84 (185)
                      .++.+.+++.|..+++ . .+.++||||+++++|+.++..|...| +.+..+||+++..+|..++++|++|         
T Consensus        10 ~v~~~~K~~~L~~ll~-~-~~~k~IIF~~s~~~~~~l~~~L~~~g-~~~~~~~~~~~~~~r~~~~~~f~~~---------   77 (155)
T d1hv8a2          10 EVNENERFEALCRLLK-N-KEFYGLVFCKTKRDTKELASMLRDIG-FKAGAIHGDLSQSQREKVIRLFKQK---------   77 (155)
T ss_dssp             ECCGGGHHHHHHHHHC-S-TTCCEEEECSSHHHHHHHHHHHHHTT-CCEEEECSSSCHHHHHHHHHHHHTT---------
T ss_pred             EeChHHHHHHHHHHHc-c-CCCCEEEEECchHHHHHHHhhhcccc-cccccccccchhhhhhhhhhhhhcc---------
Confidence            3445566666666666 3 34689999999999999999999998 8999999999999999999999999         


Q ss_pred             ccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCchHHH
Q 029910           85 EQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGGEVVT  162 (185)
Q Consensus        85 ~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e~~~  162 (185)
                                    ..++|||||+    +++|+|+|++++|||||+|+|+.+|+||+||++  |+.|.+|+|+++.|...
T Consensus        78 --------------~~~ilv~T~~----~~~Gid~~~v~~Vi~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~d~~~  139 (155)
T d1hv8a2          78 --------------KIRILIATDV----MSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKK  139 (155)
T ss_dssp             --------------SSSEEEECTT----HHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTTSHHH
T ss_pred             --------------cceeeeehhH----HhhhhhhccCcEEEEecCCCCHHHHHHHHHhcCcCCCCceEEEEEchHHHHH
Confidence                          6999999999    999999999999999999999999999999974  57899999999999999


Q ss_pred             HHHHHHHhCCccccc
Q 029910          163 LRSMEESLGLIVAEV  177 (185)
Q Consensus       163 ~~~l~~~~~~~~~~~  177 (185)
                      ++.+++.++.+++++
T Consensus       140 ~~~i~~~~~~~i~~l  154 (155)
T d1hv8a2         140 LRYIERAMKLKIKKL  154 (155)
T ss_dssp             HHHHHHHHTCCCCCB
T ss_pred             HHHHHHHHCCCcccc
Confidence            999999999988875

>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=99.97  E-value=3e-31  Score=205.75  Aligned_cols=146  Identities=16%  Similarity=0.298  Sum_probs=127.8

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ   86 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~   86 (185)
                      ..+.+.+.|..++. .....++||||+++++++.|++.|...| +.+..+||+|++++|.+++++|++|           
T Consensus        10 ~~~~K~~~L~~ll~-~~~~~k~iIF~~~~~~~~~l~~~L~~~~-~~~~~ihg~~~~~~r~~~l~~F~~g-----------   76 (168)
T d1t5ia_          10 KDNEKNRKLFDLLD-VLEFNQVVIFVKSVQRCIALAQLLVEQN-FPAIAIHRGMPQEERLSRYQQFKDF-----------   76 (168)
T ss_dssp             CGGGHHHHHHHHHH-HSCCSSEEEECSSHHHHHHHHHHHHHTT-CCEEEECTTSCHHHHHHHHHHHHTT-----------
T ss_pred             ChHHHHHHHHHHHH-hCCCCeEEEEEeeeecchhhhhhhcccc-ccccccccccchhhhhhhhhhhccc-----------
Confidence            34455555555555 3456899999999999999999999998 8999999999999999999999999           


Q ss_pred             CCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCc-hHHHH
Q 029910           87 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGG-EVVTL  163 (185)
Q Consensus        87 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~-e~~~~  163 (185)
                                  ..++||+|++    +++|+|+|.+++||+||+|+++..|+||+||+  .|+.|.||+|+++. +...+
T Consensus        77 ------------~~~iLv~T~~----~~~Gid~~~~~~vi~~~~p~~~~~yiqr~GR~gR~g~~g~~i~l~~~~~~~~~~  140 (168)
T d1t5ia_          77 ------------QRRILVATNL----FGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKIL  140 (168)
T ss_dssp             ------------SCSEEEESSC----CSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHHHHHHH
T ss_pred             ------------cceeeecccc----ccchhhcccchhhhhhhcccchhhHhhhhhhcccCCCccEEEEEECchHHHHHH
Confidence                        6999999999    99999999999999999999999999999997  56889999999875 67788


Q ss_pred             HHHHHHhCCccccccCCc
Q 029910          164 RSMEESLGLIVAEVPINI  181 (185)
Q Consensus       164 ~~l~~~~~~~~~~~~~~~  181 (185)
                      ..+++.++..++++|.++
T Consensus       141 ~~i~~~~~~~~~elp~~~  158 (168)
T d1t5ia_         141 NDVQDRFEVNISELPDEI  158 (168)
T ss_dssp             HHHHHHHCCCEEECC---
T ss_pred             HHHHHHHcCCcccCCchh
Confidence            899999999999998665

>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=99.96  E-value=3.7e-29  Score=199.23  Aligned_cols=116  Identities=19%  Similarity=0.354  Sum_probs=108.6

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeE
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHM  102 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  102 (185)
                      ..+.++||||+|+..++.|+..|...+ +.+..+||+++..+|.+++++|++|                       +.++
T Consensus        28 ~~~~~~IIF~~t~~~~~~l~~~l~~~~-~~~~~~h~~~~~~~r~~~~~~f~~g-----------------------~~~i   83 (200)
T d1oywa3          28 QRGKSGIIYCNSRAKVEDTAARLQSKG-ISAAAYHAGLENNVRADVQEKFQRD-----------------------DLQI   83 (200)
T ss_dssp             TTTCCEEEECSSHHHHHHHHHHHHHTT-CCEEEECTTSCHHHHHHHHHHHHTT-----------------------SCSE
T ss_pred             cCCCCEEEEEeeehhhHHhhhhhccCC-ceeEEecCCCcHHHHHHHHHHHhcc-----------------------cceE
Confidence            446899999999999999999999998 8999999999999999999999999                       7999


Q ss_pred             EEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCCCEEEEEeeCchHHHHHHH
Q 029910          103 IVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLRSM  166 (185)
Q Consensus       103 LV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~g~~i~~v~~~e~~~~~~l  166 (185)
                      |||||+    ++||+|+|+|++|||||+|+++++|+||+||+  .|.+|.+++|+++.|...++.+
T Consensus        84 lvaTd~----~~~GiD~p~v~~VI~~~~P~~~~~y~qr~GR~gR~g~~g~ai~~~~~~d~~~l~~~  145 (200)
T d1oywa3          84 VVATVA----FGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRC  145 (200)
T ss_dssp             EEECTT----SCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHHH
T ss_pred             EEecch----hhhccCCCCCCEEEECCCccchHHHHHHhhhhhcCCCCceEEEecCHHHHHHHHhh
Confidence            999999    99999999999999999999999999999997  4677999999999888777654

>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=99.95  E-value=7.1e-28  Score=189.23  Aligned_cols=119  Identities=15%  Similarity=0.206  Sum_probs=101.9

Q ss_pred             HHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCC
Q 029910           11 LVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDE   90 (185)
Q Consensus        11 l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~   90 (185)
                      +.+|++.+.+....+.++||||+++.+++.++..|...| +++..+||+|++.+|.+++++|++|               
T Consensus        17 vd~ll~~i~~~~~~~~~~iif~~~~~~~~~~~~~l~~~g-~~~~~~hg~~~~~eR~~~l~~Fr~g---------------   80 (181)
T d1t5la2          17 IDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAG-IKVAYLHSEIKTLERIEIIRDLRLG---------------   80 (181)
T ss_dssp             HHHHHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHTTT-CCEEEECSSCCHHHHHHHHHHHHHT---------------
T ss_pred             HHHHHHHHHHHHhcCCeEEEEeehhhhhHHHHHHHHhCC-cceeEecCCccHHHHHHHHHHHHCC---------------
Confidence            345555544322346799999999999999999999998 8999999999999999999999999               


Q ss_pred             CCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCC-----CHHHHHHHHhhhcCCC-CEEEEEeeC
Q 029910           91 SETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPT-----KKETYIRRMTTCLAAD-GSVINIVVG  157 (185)
Q Consensus        91 ~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~-----~~~~yiqR~GR~~~~~-g~~i~~v~~  157 (185)
                              +.++|||||+    ++||+|+|+|++|||||+|.     +...|+||+||+++.+ |.++.+...
T Consensus        81 --------~~~vLVaTdv----~~rGiDip~v~~VI~~d~p~~~~~~s~~~yi~R~GRagR~g~~~~~~~~~~  141 (181)
T d1t5la2          81 --------KYDVLVGINL----LREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADT  141 (181)
T ss_dssp             --------SCSEEEESCC----CSSSCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTTCEEEEECSS
T ss_pred             --------CCCEEEehhH----HHccCCCCCCCEEEEecCCcccccccHHHHHHHHHhhccccCceeEeecch
Confidence                    7999999999    99999999999999999995     7899999999996654 444444443

>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=99.95  E-value=2.3e-27  Score=185.19  Aligned_cols=130  Identities=14%  Similarity=0.170  Sum_probs=108.7

Q ss_pred             HHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCC
Q 029910           10 TLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGD   89 (185)
Q Consensus        10 ~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~   89 (185)
                      .+.+|++.+.+....+.++||||+++++|+.|+..|...| +++..+||+|++.+|.+++++|++|              
T Consensus        16 qv~dll~~i~~~~~~g~r~lvfc~t~~~~~~l~~~L~~~G-i~a~~~Hg~~~~~eR~~~l~~F~~G--------------   80 (174)
T d1c4oa2          16 QILDLMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHG-IRARYLHHELDAFKRQALIRDLRLG--------------   80 (174)
T ss_dssp             HHHHHHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHHTT-CCEEEECTTCCHHHHHHHHHHHHTT--------------
T ss_pred             CHHHHHHHHHHHHhcCCcEEEEEcchhHHHHHHHHHHhcC-CceEEEecccchHHHHHHHHHHHCC--------------
Confidence            3455666654433467899999999999999999999998 9999999999999999999999999              


Q ss_pred             CCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCC-----CHHHHHHHHhhhcCC-CCEEEEEeeCchHHHH
Q 029910           90 ESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPT-----KKETYIRRMTTCLAA-DGSVINIVVGGEVVTL  163 (185)
Q Consensus        90 ~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~-----~~~~yiqR~GR~~~~-~g~~i~~v~~~e~~~~  163 (185)
                               +.++||+|++    ++||+|+|+|++|||||+|.     +.+.|+||+||+++. .|.++.+....+....
T Consensus        81 ---------~~~vLVaT~v----~~~GiDip~V~~Vi~~~~~~~~~~~~~~~~iq~~GR~gR~~~g~~~~~~~~~~~~~~  147 (174)
T d1c4oa2          81 ---------HYDCLVGINL----LREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNARGEVWLYADRVSEAMQ  147 (174)
T ss_dssp             ---------SCSEEEESCC----CCTTCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTTCEEEEECSSCCHHHH
T ss_pred             ---------CeEEEEeeee----eeeeccCCCCcEEEEeccccccccchhHHHHHHhhhhhhcCCCeeEEeecCCCHHHH
Confidence                     7999999999    99999999999999999765     668999999998654 3777777765444433


Q ss_pred             HHHH
Q 029910          164 RSME  167 (185)
Q Consensus       164 ~~l~  167 (185)
                      +.++
T Consensus       148 ~~i~  151 (174)
T d1c4oa2         148 RAIE  151 (174)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            3333

>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=99.92  E-value=5.8e-25  Score=181.56  Aligned_cols=127  Identities=20%  Similarity=0.258  Sum_probs=109.3

Q ss_pred             cchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEec--------CCCHHHHHHHHHHHhcccc
Q 029910            6 TFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHS--------DLAETERTLILEEFRHTAM   77 (185)
Q Consensus         6 ~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g--------~~~~~~R~~~l~~F~~~~~   77 (185)
                      .|.+.+.++|..++. ..++.++||||+++++++.+++.|...+ +++..+||        +++..+|..++++|++|  
T Consensus       143 pK~~~l~~~l~~~~~-~~~~~k~iiF~~~~~~~~~~~~~L~~~~-~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g--  218 (286)
T d1wp9a2         143 PKMDKLKEIIREQLQ-RKQNSKIIVFTNYRETAKKIVNELVKDG-IKAKRFVGQASKENDRGLSQREQKLILDEFARG--  218 (286)
T ss_dssp             HHHHHHHHHHHHHHH-HCTTCCEEEECSCHHHHHHHHHHHHHTT-CCEEEECCSSCC-------CCHHHHHHHHHHHT--
T ss_pred             cHHHHHHHHHHHHHH-hCCCCcEEEEeCcHHhHHHHHHHHHHcC-CceEEeeccccccccchhchHHHHHHHHHHHcC--
Confidence            356777788877666 5667899999999999999999999987 88888876        57777899999999999  


Q ss_pred             cccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhcC-CCCEEEEEee
Q 029910           78 KWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLA-ADGSVINIVV  156 (185)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~~-~~g~~i~~v~  156 (185)
                                           ++++||||++    +++|+|+|++++||+||+|+|+..|+||+||+++ ..|.++.|++
T Consensus       219 ---------------------~~~vLv~T~~----~~~Gld~~~~~~Vi~~d~~~~~~~~~Qr~GR~gR~~~~~~~~l~~  273 (286)
T d1wp9a2         219 ---------------------EFNVLVATSV----GEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMPGRVIILMA  273 (286)
T ss_dssp             ---------------------SCSEEEECGG----GGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCCCSEEEEEEE
T ss_pred             ---------------------CCcEEEEccc----eeccccCCCCCEEEEeCCCCCHHHHHHHHHhCCCCCCCEEEEEEe
Confidence                                 6999999999    9999999999999999999999999999999754 4588999998


Q ss_pred             CchHH
Q 029910          157 GGEVV  161 (185)
Q Consensus       157 ~~e~~  161 (185)
                      .+..+
T Consensus       274 ~~~~e  278 (286)
T d1wp9a2         274 KGTRD  278 (286)
T ss_dssp             TTSHH
T ss_pred             CCCHH
Confidence            87443

>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=99.89  E-value=1.1e-23  Score=158.54  Aligned_cols=99  Identities=20%  Similarity=0.277  Sum_probs=87.1

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEE
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMI  103 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iL  103 (185)
                      .++++||||+|++.|+.|++.|+..| +.+..+||+|+..+       |+++                       ..++|
T Consensus        34 ~~~k~IVFc~t~~~ae~la~~L~~~G-~~~~~~H~~~~~~~-------~~~~-----------------------~~~vl   82 (138)
T d1jr6a_          34 KGGRHLIFCHSKKKCDELAAKLVALG-INAVAYYRGLDVSV-------IPTN-----------------------GDVVV   82 (138)
T ss_dssp             TTSCEEEECSCHHHHHHHHHHHHHHT-CEEEEECTTCCSCC-------CTTS-----------------------SCEEE
T ss_pred             CCCCEEEEeCcHHHHHHHHHHHhccc-cchhhhhccchhhh-------hhhh-----------------------hccee
Confidence            45799999999999999999999998 89999999998654       5677                       79999


Q ss_pred             EEecCCCCcccCcCCCCCCcEEEEcC----CCCCHHHHHHHHhhhcC-CCCEEEEEeeCch
Q 029910          104 VVTDACLPLLSSGESAISARVLINYE----LPTKKETYIRRMTTCLA-ADGSVINIVVGGE  159 (185)
Q Consensus       104 V~Td~~~~~~~~G~d~~~v~~VI~~d----~P~~~~~yiqR~GR~~~-~~g~~i~~v~~~e  159 (185)
                      ||||+    ++||+| |+++.|||||    +|.++++|+||+||+++ ++| .+.|++++|
T Consensus        83 vaTd~----~~~GiD-~~v~~Vi~~~~~~~~P~~~~~y~qr~GR~gRg~~G-~~~~i~~~e  137 (138)
T d1jr6a_          83 VATDA----LMTGFT-GDFDSVIDCNTSDGKPQDAVSRTQRRGRTGRGKPG-IYRFVAPGE  137 (138)
T ss_dssp             EESSS----SCSSSC-CCBSEEEECSEETTEECCHHHHHHHHTTBCSSSCE-EEEECCSSC
T ss_pred             ehhHH----HHhccc-cccceEEEEEecCCCCCCHHHHHhHhccccCCCCc-EEEEEcCCC
Confidence            99999    999999 9999999865    69999999999999865 556 477887765

>d2p6ra4 c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.82  E-value=3.8e-20  Score=146.48  Aligned_cols=123  Identities=21%  Similarity=0.265  Sum_probs=101.5

Q ss_pred             HHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCC----C-------------------------ceEEEEecC
Q 029910            9 ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLA----D-------------------------ISFSSLHSD   59 (185)
Q Consensus         9 ~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~----~-------------------------~~~~~l~g~   59 (185)
                      ....+++..+++   .+.++||||+|++.|+.++..|....    .                         ..++++||+
T Consensus        27 ~~~~~l~~~~i~---~~~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~  103 (201)
T d2p6ra4          27 VKFEELVEECVA---ENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAG  103 (201)
T ss_dssp             CCHHHHHHHHHH---TTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTT
T ss_pred             hhHHHHHHHHHH---cCCcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHH
Confidence            345667766555   24799999999999998887776420    0                         017889999


Q ss_pred             CCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEE-------cCCCC
Q 029910           60 LAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLIN-------YELPT  132 (185)
Q Consensus        60 ~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~-------~d~P~  132 (185)
                      |++.+|..+.+.|++|                       .+++||||+.    +++|+|+|..++||.       ++.|.
T Consensus       104 l~~~~r~~ie~~f~~g-----------------------~i~vlvaT~~----l~~Gin~p~~~vvi~~~~~~d~~~~~~  156 (201)
T d2p6ra4         104 LLNGQRRVVEDAFRRG-----------------------NIKVVVATPT----LAAGVNLPARRVIVRSLYRFDGYSKRI  156 (201)
T ss_dssp             SCHHHHHHHHHHHHTT-----------------------SCCEEEECST----TTSSSCCCBSEEEECCSEEESSSEEEC
T ss_pred             hhhhhHHHHHHHHhCC-----------------------CceEEEechH----HHhhcCCCCceEEEecceeccCCcCCC
Confidence            9999999999999999                       7999999999    999999999999996       78899


Q ss_pred             CHHHHHHHHhhhcC----CCCEEEEEeeCchHH
Q 029910          133 KKETYIRRMTTCLA----ADGSVINIVVGGEVV  161 (185)
Q Consensus       133 ~~~~yiqR~GR~~~----~~g~~i~~v~~~e~~  161 (185)
                      ++.+|+||+||||+    ..|.++.++.+.+..
T Consensus       157 ~~~~~~q~~GRAGR~g~~~~G~~~l~~~~~~~~  189 (201)
T d2p6ra4         157 KVSEYKQMAGRAGRPGMDERGEAIIIVGKRDRE  189 (201)
T ss_dssp             CHHHHHHHHTTBSCTTTCSCEEEEEECCGGGHH
T ss_pred             CHHHHHHHhcccCCCCCCCeeEEEEEeCCCChH
Confidence            99999999999865    357888887776554

>d1gkub2 c.37.1.16 (B:251-498) 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=99.81  E-value=4.3e-23  Score=167.62  Aligned_cols=105  Identities=11%  Similarity=0.129  Sum_probs=86.4

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEE
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIV  104 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV  104 (185)
                      +.++||||+|+++|+.|+..|+..       +||++++.+|.+++++|++|                       ..++||
T Consensus        25 ~~~~iif~~~~~~~~~l~~~l~~~-------~hg~~~~~~R~~~~~~f~~g-----------------------~~~vLV   74 (248)
T d1gkub2          25 GTGGIIYARTGEEAEEIYESLKNK-------FRIGIVTATKKGDYEKFVEG-----------------------EIDHLI   74 (248)
T ss_dssp             CSCEEEEESSHHHHHHHHHTTTTS-------SCEEECTTSSSHHHHHHHHT-----------------------SCSEEE
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHh-------ccCCCCHHHHHHHHHHHHhC-----------------------CCeEEE
Confidence            368999999999999999999753       79999999999999999999                       699999


Q ss_pred             Ee----cCCCCcccCcCCCCC-CcEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCchHHHHHHHH
Q 029910          105 VT----DACLPLLSSGESAIS-ARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGGEVVTLRSME  167 (185)
Q Consensus       105 ~T----d~~~~~~~~G~d~~~-v~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e~~~~~~l~  167 (185)
                      ||    ++    ++||+|+|+ |++|||||+|+    |.||+||++  +..|.++.++...+...+..+.
T Consensus        75 aT~a~~~v----~~rGlDip~~v~~VI~~d~P~----~~~r~gR~~R~g~~~~~~~~~~~~~~~~~~~l~  136 (248)
T d1gkub2          75 GTAHYYGT----LVRGLDLPERIRFAVFVGCPS----FRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLL  136 (248)
T ss_dssp             EECC----------CCSCCTTTCCEEEEESCCE----EEEECSCGGGSCHHHHHHHHTTTSCHHHHHTTC
T ss_pred             Eeccccch----hhhccCccccccEEEEeCCCc----chhhhhhhhccCcceEeeeeccHhhHHHHHHHH
Confidence            99    88    999999997 99999999996    889999974  4457777777666665554443

>d2fwra1 c.37.1.19 (A:257-456) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.80  E-value=2.7e-20  Score=146.10  Aligned_cols=112  Identities=19%  Similarity=0.276  Sum_probs=93.8

Q ss_pred             HHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCC
Q 029910           13 ELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESE   92 (185)
Q Consensus        13 ~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~   92 (185)
                      +.|..++. ..++.++||||++.+.++.|++.|.      +..+||+++..+|.+++++|++|                 
T Consensus        82 ~~l~~ll~-~~~~~k~lvf~~~~~~~~~l~~~l~------~~~i~g~~~~~~R~~~l~~F~~~-----------------  137 (200)
T d2fwra1          82 RKLREILE-RHRKDKIIIFTRHNELVYRISKVFL------IPAITHRTSREEREEILEGFRTG-----------------  137 (200)
T ss_dssp             HHHHHHHH-HTSSSCBCCBCSCHHHHHHHHHHTT------CCBCCSSSCSHHHHTHHHHHHHS-----------------
T ss_pred             HHHHHHHH-hCCCCcEEEEeCcHHHHHHHHhhcC------cceeeCCCCHHHHHHHHHHhhcC-----------------
Confidence            33444444 3456899999999999999998773      34579999999999999999998                 


Q ss_pred             CCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhhcCC-----CCEEEEEeeCc
Q 029910           93 TGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAA-----DGSVINIVVGG  158 (185)
Q Consensus        93 ~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~~~-----~g~~i~~v~~~  158 (185)
                            ..++||+|++    +++|+|+|.+++||+||+|+|+..|+||+||+++.     ...++.|+..+
T Consensus       138 ------~~~vLv~~~~----~~~Gidl~~~~~vi~~~~~~s~~~~~Q~iGR~~R~~~~k~~~~i~~~v~~~  198 (200)
T d2fwra1         138 ------RFRAIVSSQV----LDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYELISRG  198 (200)
T ss_dssp             ------SCSBCBCSSC----CCSSSCSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTTCCEEEEEEEECS
T ss_pred             ------Ceeeeeecch----hhcccCCCCCCEEEEeCCCCCHHHHHHHHHhcCCCCCCCcEEEEEEEecCC
Confidence                  6899999999    99999999999999999999999999999997432     24566777654

>d1a1va2 c.37.1.14 (A:326-624) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=99.78  E-value=4.9e-20  Score=153.31  Aligned_cols=103  Identities=14%  Similarity=0.093  Sum_probs=86.7

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHH----------HHHHHHHhcccccccccccccCCCCCCCC
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETER----------TLILEEFRHTAMKWNQKVTEQSGDESETG   94 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R----------~~~l~~F~~~~~~~~~~~~~~~~~~~~~~   94 (185)
                      +.++||||++++.|+.|+..|+..| +++..+|++++++.|          ..++++|+.+                   
T Consensus        36 ggk~LVFcnSR~~aE~La~~L~~~G-i~a~~~Hgglsq~~R~~~gd~~i~~~~aLe~f~~G-------------------   95 (299)
T d1a1va2          36 GGRHLIFCHSKKKCDELAAKLVALG-INAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTG-------------------   95 (299)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHTT-CCEEEECTTSCGGGSCSSSSEEEEECTTC---CCC-------------------
T ss_pred             CCCEEEECCcHHHHHHHHHHHHHCC-CCEEEEeCCchHHHHHhccchHHHHHHHHHHHhcC-------------------
Confidence            4799999999999999999999998 899999999999887          4577888888                   


Q ss_pred             CCCCceeEEEEecCCCCcccC---cCCCCCCcEEEEcCCCCCHHHHHHHHhhhcCCCCEEEEEe
Q 029910           95 KDEHKSHMIVVTDACLPLLSS---GESAISARVLINYELPTKKETYIRRMTTCLAADGSVINIV  155 (185)
Q Consensus        95 ~~~~~~~iLV~Td~~~~~~~~---G~d~~~v~~VI~~d~P~~~~~yiqR~GR~~~~~g~~i~~v  155 (185)
                          ..+++|+|++    +++   |+|++.+.+||+||+|.|+++|+||+||+++..+-..+++
T Consensus        96 ----~~dvVVaT~~----~a~g~~giDid~V~~VI~~d~P~SvesyIQRiGRTGRGr~G~~~~l  151 (299)
T d1a1va2          96 ----DFDSVIDCNT----CVTQTVDFSLDPTFTIETTTLPQDAVSRTQRRGRTGRGKPGIYRFV  151 (299)
T ss_dssp             ----CBSEEEECCE----EEEEEEECCCSSSCEEEEEEEECBHHHHHHHHTTBCSSSCEEEEES
T ss_pred             ----CCcEEEEEee----hhccCCCCCCCcceEEEeCCCCCCHHHHHhhccccCCCCCceEEEE
Confidence                7999999999    898   6677777899999999999999999999876433333444

>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=99.72  E-value=1.4e-18  Score=138.35  Aligned_cols=131  Identities=12%  Similarity=0.129  Sum_probs=96.0

Q ss_pred             HHHHHHHHHHHccCCCCCcEEEEcCChhhHH--------HHHHHHhcC--CCceEEEEecCCCHHHHHHHHHHHhccccc
Q 029910            9 ETLVELLHLVVAGRRPGLPMIVCCSSRDELD--------AVCSAVSNL--ADISFSSLHSDLAETERTLILEEFRHTAMK   78 (185)
Q Consensus         9 ~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~--------~l~~~L~~~--~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~   78 (185)
                      +.+.+.++.   .-..+.++-+.|+..+..+        ...+.|...  +++++..+||.|++++|.+++++|++|   
T Consensus        16 ~~v~~~I~~---el~~g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g---   89 (206)
T d1gm5a4          16 NEVYEFVRQ---EVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEG---   89 (206)
T ss_dssp             HHHHHHHHH---HTTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTT---
T ss_pred             HHHHHHHHH---HHHcCCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCC---
Confidence            444444443   2446678888887654333        344444332  347889999999999999999999999   


Q ss_pred             ccccccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHH-HHhhh--cCCCCEEEEEe
Q 029910           79 WNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIR-RMTTC--LAADGSVINIV  155 (185)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiq-R~GR~--~~~~g~~i~~v  155 (185)
                                          +++|||||++    +++|+|+|++++||+++.|....+|+| ..||+  ++..|.|+.++
T Consensus        90 --------------------~~~iLVaTtV----iE~GIDip~a~~iii~~a~~fglsqlhQlrGRvGR~~~~~~~~l~~  145 (206)
T d1gm5a4          90 --------------------RYDILVSTTV----IEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVV  145 (206)
T ss_dssp             --------------------SSSBCCCSSC----CCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCC
T ss_pred             --------------------CEEEEEEehh----hhccccccCCcEEEEEccCCccHHHHHhhhhheeeccccceeEeee
Confidence                                7999999999    999999999999999999986555555 57996  56779999999


Q ss_pred             eCchHHHHHHHHHH
Q 029910          156 VGGEVVTLRSMEES  169 (185)
Q Consensus       156 ~~~e~~~~~~l~~~  169 (185)
                      .+.+....+.++..
T Consensus       146 ~~~~~~~~~rl~~~  159 (206)
T d1gm5a4         146 GDVGEEAMERLRFF  159 (206)
T ss_dssp             CSCCHHHHHHHHHH
T ss_pred             ccccccchhhhhhc
Confidence            87666555555544

>d1z5za1 c.37.1.19 (A:663-906) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.63  E-value=1.2e-15  Score=122.75  Aligned_cols=134  Identities=14%  Similarity=0.125  Sum_probs=98.5

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ   86 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~   86 (185)
                      |.+.+.+++..+..   ++.++||||+.+...+.+...|....++.+..+||+++..+|.+++++|.++.          
T Consensus        70 K~~~l~~~l~~~~~---~g~kviIFs~~~~~~~~l~~~l~~~~~~~~~~i~G~~~~~~R~~~i~~F~~~~----------  136 (244)
T d1z5za1          70 KMIRTMEIIEEALD---EGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNP----------  136 (244)
T ss_dssp             HHHHHHHHHHHHHH---TTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCT----------
T ss_pred             HHHHHHHHHHhhcc---cccceEEEeeceehHHHHHHHHHhhccceEEEEecccchhccchhhhhhhccc----------
Confidence            56667777766443   56899999999999999999887652378899999999999999999999873          


Q ss_pred             CCCCCCCCCCCCceeEEEE-ecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCC--CCEEEEEeeCc--h
Q 029910           87 SGDESETGKDEHKSHMIVV-TDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAA--DGSVINIVVGG--E  159 (185)
Q Consensus        87 ~~~~~~~~~~~~~~~iLV~-Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~--~g~~i~~v~~~--e  159 (185)
                                  ..+++++ |.+    .+.|+|++.++.||+||+|||+..+.|++||+  .|+  +..++.++..+  |
T Consensus       137 ------------~~~vll~~~~~----~g~Glnl~~a~~vi~~~~~wn~~~~~Qa~~R~~R~Gq~~~v~i~~l~~~~Tie  200 (244)
T d1z5za1         137 ------------SVKFIVLSVKA----GGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLE  200 (244)
T ss_dssp             ------------TCCEEEEECCT----TCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEETTSHH
T ss_pred             ------------cchhccccccc----cccccccchhhhhhhcCchhhhHHHhhhcceeeecCCCCceEEEEEeeCCCHH
Confidence                        4666655 467    89999999999999999999999999999996  333  34666777776  4


Q ss_pred             HHHHHHHHHH
Q 029910          160 VVTLRSMEES  169 (185)
Q Consensus       160 ~~~~~~l~~~  169 (185)
                      ...++.++.+
T Consensus       201 e~i~~~~~~K  210 (244)
T d1z5za1         201 EKIDQLLAFK  210 (244)
T ss_dssp             HHHHHHHHHC
T ss_pred             HHHHHHHHHH
Confidence            4445544443

>d1z3ix1 c.37.1.19 (X:390-735) 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=99.62  E-value=3.5e-15  Score=126.60  Aligned_cols=136  Identities=14%  Similarity=0.152  Sum_probs=108.0

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccccccc
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ   86 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~   86 (185)
                      |...+.+++..+..  .++.|+|||++...+.+.|...|...| +....++|+++..+|..++++|+.++          
T Consensus       102 Kl~~L~~ll~~~~~--~~g~KvlIFs~~~~~ld~l~~~l~~~g-~~~~~l~G~~~~~~R~~~i~~F~~~~----------  168 (346)
T d1z3ix1         102 KMLVLDYILAMTRT--TTSDKVVLVSNYTQTLDLFEKLCRNRR-YLYVRLDGTMSIKKRAKIVERFNNPS----------  168 (346)
T ss_dssp             HHHHHHHHHHHHHH--HCCCEEEEEESCHHHHHHHHHHHHHHT-CCEEEECSSCCHHHHHHHHHHHHSTT----------
T ss_pred             HHHHHHHHHHHHHH--hcCCceeEEeehhhhhHHHHHHHhhhh-ccccccccchhHHHHHHHHHhhhccc----------
Confidence            34455556655322  356899999999999999999999998 89999999999999999999999873          


Q ss_pred             CCCCCCCCCCCCce-eEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhhh--cCCC--CEEEEEeeCc--h
Q 029910           87 SGDESETGKDEHKS-HMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAAD--GSVINIVVGG--E  159 (185)
Q Consensus        87 ~~~~~~~~~~~~~~-~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR~--~~~~--g~~i~~v~~~--e  159 (185)
                                 ... -+|++|.+    .+.|+|++.++.||+||++||+..+.|++||+  .|+.  -.++.++..+  |
T Consensus       169 -----------~~~~vlLls~~a----gg~GlnL~~a~~vi~~d~~wnp~~~~Qa~~R~~R~GQ~~~V~v~rli~~~TiE  233 (346)
T d1z3ix1         169 -----------SPEFIFMLSSKA----GGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTGTIE  233 (346)
T ss_dssp             -----------CCCCEEEEEGGG----SCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEEEEEETTSHH
T ss_pred             -----------ccceeeeecchh----hhhccccccceEEEEecCCCccchHhHhhhcccccCCCCceEEEEEEeCCCHH
Confidence                       012 26778888    99999999999999999999999999999996  4444  3566777765  4


Q ss_pred             HHHHHHHHHHh
Q 029910          160 VVTLRSMEESL  170 (185)
Q Consensus       160 ~~~~~~l~~~~  170 (185)
                      ...++....+.
T Consensus       234 e~i~~~~~~K~  244 (346)
T d1z3ix1         234 EKILQRQAHKK  244 (346)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            45555555553

>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=99.59  E-value=9.6e-15  Score=115.98  Aligned_cols=109  Identities=11%  Similarity=0.134  Sum_probs=94.3

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcC-CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCce
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNL-ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKS  100 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~-~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~  100 (185)
                      -..+.|+-+.|+..+..+.+.+.+.+. +++++..+||.|+.+++.+++.+|+++                       +.
T Consensus        28 l~rGgQvy~V~p~I~~~e~~~~~l~~~~p~~~i~~lHGkm~~~eke~im~~F~~g-----------------------~~   84 (211)
T d2eyqa5          28 ILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQ-----------------------RF   84 (211)
T ss_dssp             HTTTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTT-----------------------SC
T ss_pred             HHcCCeEEEEEcCccchhhHHHHHHHhCCceEEEEEEeccCHHHHHHHHHHHHcC-----------------------Cc
Confidence            456799999999999999999888754 558999999999999999999999999                       79


Q ss_pred             eEEEEecCCCCcccCcCCCCCCcEEEEcCCCC-CHHHHHHHHhhh--cCCCCEEEEEeeC
Q 029910          101 HMIVVTDACLPLLSSGESAISARVLINYELPT-KKETYIRRMTTC--LAADGSVINIVVG  157 (185)
Q Consensus       101 ~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~-~~~~yiqR~GR~--~~~~g~~i~~v~~  157 (185)
                      +|||||.+    .+.|+|+|+++++|.++.+. -.+.+-|-.||.  ++..|.|+.+...
T Consensus        85 ~ILv~Ttv----IEvGiDvpnA~~iiI~~a~rfGLaQLhQLRGRVGR~~~~s~c~l~~~~  140 (211)
T d2eyqa5          85 NVLVCTTI----IETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPH  140 (211)
T ss_dssp             CEEEESST----TGGGSCCTTEEEEEETTTTSSCHHHHHHHHTTCCBTTBCEEEEEEECC
T ss_pred             ceEEEehh----hhhccCCCCCcEEEEecchhccccccccccceeeecCccceEEEEecC
Confidence            99999999    99999999999999999987 555555556996  4455899988754

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=99.42  E-value=1.8e-13  Score=111.01  Aligned_cols=101  Identities=14%  Similarity=0.070  Sum_probs=80.6

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEE
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMI  103 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iL  103 (185)
                      ...+++|||++++.++.+++.|...+ ..+..+||++++..+    ..|+++                       ..+++
T Consensus       177 ~~~~~lvf~~~~~~~~~l~~~L~~~~-~~~~~l~~~~~~~~~----~~~~~~-----------------------~~~~l  228 (305)
T d2bmfa2         177 FKGKTVWFVPSIKAGNDIAACLRKNG-KKVIQLSRKTFDSEY----IKTRTN-----------------------DWDFV  228 (305)
T ss_dssp             SCSCEEEECSCHHHHHHHHHHHHHHT-CCCEECCTTCHHHHG----GGGGTS-----------------------CCSEE
T ss_pred             hCCCEEEEeccHHHHHHHHHHHHhCC-CCEEEeCCcChHHHH----hhhhcc-----------------------chhhh
Confidence            45799999999999999999999988 799999999866554    467777                       68999


Q ss_pred             EEecCCCCcccCcCCCCCCcEEE----------EcCC----------CCCHHHHHHHHhhhcC--CCCEEEEEeeC
Q 029910          104 VVTDACLPLLSSGESAISARVLI----------NYEL----------PTKKETYIRRMTTCLA--ADGSVINIVVG  157 (185)
Q Consensus       104 V~Td~~~~~~~~G~d~~~v~~VI----------~~d~----------P~~~~~yiqR~GR~~~--~~g~~i~~v~~  157 (185)
                      |+|++    +++|+|++ ++.||          +||.          |-|..+|+||+||+|+  .++....++..
T Consensus       229 vaT~~----~~~G~~~~-~~~Vi~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~Qr~GR~GR~~~~~~~~~~~~~  299 (305)
T d2bmfa2         229 VTTDI----SEMGANFK-AERVIDPRRCMKPVILTDGEERVILAGPMPVTHSSAAQRRGRVGRNPKNENDQYIYMG  299 (305)
T ss_dssp             EECGG----GGTTCCCC-CSEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCSSSCCCEEEEECS
T ss_pred             hhhHH----HHhcCCCC-ccEEEEcCCceeeeEecCCCCceEEeccccCCHHHHhhhhcCcCcCCCCceEEEEECC
Confidence            99999    99999994 55554          4454          5689999999999854  34555555543

>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=99.29  E-value=4.4e-12  Score=105.34  Aligned_cols=99  Identities=12%  Similarity=0.090  Sum_probs=77.1

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEE
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIV  104 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV  104 (185)
                      .++++|||++...++.+++.|+..| .++..|||.++..++.    +|+++                       ..+++|
T Consensus        36 ~g~~~~F~~s~~~~~~~a~~L~~~g-~~V~~l~~~~~~~e~~----~~~~~-----------------------~~~~~~   87 (299)
T d1yksa2          36 KRPTAWFLPSIRAANVMAASLRKAG-KSVVVLNRKTFEREYP----TIKQK-----------------------KPDFIL   87 (299)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTT-CCEEECCSSSCC------------C-----------------------CCSEEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhcC-CeEEEEcCcCcHhHHh----hhhcC-----------------------CcCEEE
Confidence            4799999999999999999999998 7999999999988865    46677                       689999


Q ss_pred             EecCCCCcccCcCCCCCCcEEEEcCC-------------------CCCHHHHHHHHhhhcCCCC--EEEEEee
Q 029910          105 VTDACLPLLSSGESAISARVLINYEL-------------------PTKKETYIRRMTTCLAADG--SVINIVV  156 (185)
Q Consensus       105 ~Td~~~~~~~~G~d~~~v~~VI~~d~-------------------P~~~~~yiqR~GR~~~~~g--~~i~~v~  156 (185)
                      ||++    ++.|+|+ ++.+||++.+                   |-+..+-.||.||+|+.++  .++.++.
T Consensus        88 ~t~~----~~~~~~~-~~~~vid~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~qr~gr~gr~~~~~~~~~~y~  155 (299)
T d1yksa2          88 ATDI----AEMGANL-CVERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYS  155 (299)
T ss_dssp             ESSS----TTCCTTC-CCSEEEECCEEEEEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEEC
T ss_pred             Eech----hhhceec-CceEEEecCceeceeeecCCCCeeEEeeeecCHHHHHHhcccccccCCCceEEEEeC
Confidence            9999    9999999 5999986543                   3477889999999877653  3444443

>d1tf5a4 c.37.1.19 (A:396-570) 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=99.03  E-value=1.2e-09  Score=83.76  Aligned_cols=127  Identities=13%  Similarity=0.110  Sum_probs=100.1

Q ss_pred             eEecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccc
Q 029910            3 VSFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQK   82 (185)
Q Consensus         3 v~~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~   82 (185)
                      ||.++.++...+++.+......+.|+||+|.|.+.++.++..|+..+ ++..+++.....++ .+++. . .|.      
T Consensus        12 vf~T~~eK~~AIi~eV~~~~~~grPVLIgT~SIe~SE~ls~~L~~~g-i~h~vLnAk~~~~E-a~II~-~-Ag~------   81 (175)
T d1tf5a4          12 IYRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKG-IPHQVLNAKNHERE-AQIIE-E-AGQ------   81 (175)
T ss_dssp             EESSHHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTT-CCCEEECSSCHHHH-HHHHT-T-TTS------
T ss_pred             EEcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcC-CCceeehhhhHHHH-HHHHH-h-ccC------
Confidence            56677778777777765556678999999999999999999999998 89999998753322 23333 2 221      


Q ss_pred             ccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCC--------cEEEEcCCCCCHHHHHHHHhhhc--CCCCEEE
Q 029910           83 VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISA--------RVLINYELPTKKETYIRRMTTCL--AADGSVI  152 (185)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v--------~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i  152 (185)
                                      ...|.|||++    +.||.|+.--        =+||.-..|.+..-..|-.||++  |.+|.+.
T Consensus        82 ----------------~g~VtIATNm----AGRGtDikl~~~v~~~GGLhVI~t~~~~s~Rid~Ql~GR~gRQGdpGs~~  141 (175)
T d1tf5a4          82 ----------------KGAVTIATNM----AGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQ  141 (175)
T ss_dssp             ----------------TTCEEEEETT----SSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEE
T ss_pred             ----------------CCceeehhhH----HHcCCCccchHHHHhCCCcEEEEeccCcchhHHHHHhcchhhhCCCcccE
Confidence                            5679999999    9999987532        27999999999999999999985  5679998


Q ss_pred             EEeeCch
Q 029910          153 NIVVGGE  159 (185)
Q Consensus       153 ~~v~~~e  159 (185)
                      .|++-.|
T Consensus       142 ~~~sleD  148 (175)
T d1tf5a4         142 FYLSMED  148 (175)
T ss_dssp             EEEETTS
T ss_pred             EEEEcCH
Confidence            8887644

>d1nkta4 c.37.1.19 (A:397-615) Translocation ATPase SecA, nucleotide-binding domains {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: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=98.19  E-value=1.5e-05  Score=62.09  Aligned_cols=127  Identities=11%  Similarity=0.129  Sum_probs=97.0

Q ss_pred             eEecchHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhccccccccc
Q 029910            3 VSFTFQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQK   82 (185)
Q Consensus         3 v~~~~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~   82 (185)
                      ||-+..++...+++.+......++|++|.+.|.+..+.|+..|...+ ++..+|+..- .+.=..++.+=-.        
T Consensus        12 Vy~T~~~K~~Avv~ei~~~h~~GqPVLVGT~SVe~SE~lS~lL~~~g-i~h~vLNAK~-herEAeIIAqAG~--------   81 (219)
T d1nkta4          12 IYKTEEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRR-IPHNVLNAKY-HEQEATIIAVAGR--------   81 (219)
T ss_dssp             EESCHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTT-CCCEEECSSC-HHHHHHHHHTTTS--------
T ss_pred             EEcCHHHHHHHHHHHHHHHHhcCCCEEEeeCcHHHHHHHHHHHHHhc-cchhccchhh-HHHHHHHHHhccc--------
Confidence            55677788888888777667788999999999999999999999998 9999999863 3333334443222        


Q ss_pred             ccccCCCCCCCCCCCCceeEEEEecCCCCcccCcCCCCCC----------------------------------------
Q 029910           83 VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISA----------------------------------------  122 (185)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~~G~d~~~v----------------------------------------  122 (185)
                                      ...|-|||.+    +.||.|+.--                                        
T Consensus        82 ----------------~GaVTIATNM----AGRGTDI~LGgn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  141 (219)
T d1nkta4          82 ----------------RGGVTVATNM----AGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEA  141 (219)
T ss_dssp             ----------------TTCEEEEETT----CSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHT
T ss_pred             ----------------CCcEEeeccc----cCCCCceeecCchhhhhHHHhhhcccCcccCHHHHHHHHHHHHHHHHHHH
Confidence                            4779999999    9999999321                                        


Q ss_pred             ------------cEEEEcCCCCCHHHHHHHHhhhc--CCCCEEEEEeeCch
Q 029910          123 ------------RVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGGE  159 (185)
Q Consensus       123 ------------~~VI~~d~P~~~~~yiqR~GR~~--~~~g~~i~~v~~~e  159 (185)
                                  =+||--+-..|-.-=-|=.||++  |-+|.+..|++-.|
T Consensus       142 ~~~~~~V~~~GGL~VIGTErHeSrRIDnQLRGRsGRQGDPGsSrFflSLeD  192 (219)
T d1nkta4         142 SKEAKEVIEAGGLYVLGTERHESRRIDNQLRGRSGRQGDPGESRFYLSLGD  192 (219)
T ss_dssp             THHHHHHHHTTSEEEEECSCCSSHHHHHHHHHTSSGGGCCEEEEEEEETTS
T ss_pred             HHHHHHHHhcCCcEEEeccccccccccccccccccccCCCccceeEEeccH
Confidence                        16888887877666666678875  45689988887654

>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=96.58  E-value=0.0035  Score=49.76  Aligned_cols=91  Identities=13%  Similarity=0.073  Sum_probs=68.6

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHh----cCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCc
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVS----NLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHK   99 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~----~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (185)
                      .+.++++-++|.--+.+....+.    ..| +.+..+||+++..+|.+++.+.++|                       +
T Consensus       131 ~g~q~~~m~Pt~~La~Qh~~~~~~~f~~~~-~~v~~l~~~~~~~~r~~~~~~~~~g-----------------------~  186 (264)
T d1gm5a3         131 AGFQTAFMVPTSILAIQHYRRTVESFSKFN-IHVALLIGATTPSEKEKIKSGLRNG-----------------------Q  186 (264)
T ss_dssp             HTSCEEEECSCHHHHHHHHHHHHHHHTCSS-CCEEECCSSSCHHHHHHHHHHHHSS-----------------------C
T ss_pred             cccceeEEeehHhhhHHHHHHHHHhhhhcc-ccceeeccccchHHHHHHHHHHHCC-----------------------C
Confidence            46899999999887776665554    445 8999999999999999999999999                       6


Q ss_pred             eeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhh
Q 029910          100 SHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTT  143 (185)
Q Consensus       100 ~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR  143 (185)
                      .+|+|.|-.   ++...+.+.+..+||.=+-.+  -.|.||-+-
T Consensus       187 ~~iiIGThs---l~~~~~~f~~LglviiDEqH~--fgv~Qr~~l  225 (264)
T d1gm5a3         187 IDVVIGTHA---LIQEDVHFKNLGLVIIDEQHR--FGVKQREAL  225 (264)
T ss_dssp             CCEEEECTT---HHHHCCCCSCCCEEEEESCCC--C-----CCC
T ss_pred             CCEEEeehH---HhcCCCCccccceeeeccccc--cchhhHHHH
Confidence            999999987   255678888888888655333  367777643

>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=96.09  E-value=0.0093  Score=46.37  Aligned_cols=92  Identities=15%  Similarity=0.060  Sum_probs=74.5

Q ss_pred             CCCCcEEEEcCChhhHHHHHHHHhc----CCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCC
Q 029910           23 RPGLPMIVCCSSRDELDAVCSAVSN----LADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEH   98 (185)
Q Consensus        23 ~~~~~~IIF~~~~~~~~~l~~~L~~----~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (185)
                      ..++++++-+++.--+.+..+.++.    .+ +.+..+||.++..+|.+++....+|                       
T Consensus       102 ~~g~qv~~l~Pt~~La~Q~~~~~~~~~~~~~-~~v~~l~~~~~~~~~~~~~~~~~~g-----------------------  157 (233)
T d2eyqa3         102 DNHKQVAVLVPTTLLAQQHYDNFRDRFANWP-VRIEMISRFRSAKEQTQILAEVAEG-----------------------  157 (233)
T ss_dssp             TTTCEEEEECSSHHHHHHHHHHHHHHSTTTT-CCEEEESTTSCHHHHHHHHHHHHTT-----------------------
T ss_pred             HcCCceEEEccHHHhHHHHHHHHHHHHhhCC-CEEEeccCcccchhHHHHHHHHhCC-----------------------
Confidence            4679999999999999988888875    35 7899999999999999999999999                       


Q ss_pred             ceeEEEEecCCCCcccCcCCCCCCcEEEEcCCCCCHHHHHHHHhh
Q 029910           99 KSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTT  143 (185)
Q Consensus        99 ~~~iLV~Td~~~~~~~~G~d~~~v~~VI~~d~P~~~~~yiqR~GR  143 (185)
                      ..+|+|.|-.   ++...+.+++..+||.=+-.+  -.|.||.+=
T Consensus       158 ~~~iviGths---~l~~~~~f~~LgLiIiDEeH~--fg~kQ~~~l  197 (233)
T d2eyqa3         158 KIDILIGTHK---LLQSDVKFKDLGLLIVDEEHR--FGVRHKERI  197 (233)
T ss_dssp             CCSEEEECTH---HHHSCCCCSSEEEEEEESGGG--SCHHHHHHH
T ss_pred             CCCEEEeehh---hhccCCccccccceeeechhh--hhhHHHHHH
Confidence            7999999986   155578888888877655333  356677643

>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=93.24  E-value=0.15  Score=38.51  Aligned_cols=88  Identities=9%  Similarity=0.085  Sum_probs=61.6

Q ss_pred             HHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcC---CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCC
Q 029910           12 VELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL---ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG   88 (185)
Q Consensus        12 ~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~---~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~   88 (185)
                      +-+++.+.. .....+++|.|+|++-|.++.+.+...   .++++..+.|+.+..+....+   +.+             
T Consensus        73 lPil~~l~~-~~~~~~~lil~PtreLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l---~~~-------------  135 (222)
T d2j0sa1          73 ISVLQCLDI-QVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKL---DYG-------------  135 (222)
T ss_dssp             HHHHHTCCT-TSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHH---HHC-------------
T ss_pred             ccccccccc-cccCceeEEecchHHHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHh---ccC-------------
Confidence            344444333 455678999999999999998777543   237899999998877765554   343             


Q ss_pred             CCCCCCCCCCceeEEEEecCCC--CcccCcCCCCCCcEEEE
Q 029910           89 DESETGKDEHKSHMIVVTDACL--PLLSSGESAISARVLIN  127 (185)
Q Consensus        89 ~~~~~~~~~~~~~iLV~Td~~~--~~~~~G~d~~~v~~VI~  127 (185)
                                 .+|+|+|+-++  -+-...+++.+++++|.
T Consensus       136 -----------~~Ilv~TPgrl~~~~~~~~~~~~~l~~lVl  165 (222)
T d2j0sa1         136 -----------QHVVAGTPGRVFDMIRRRSLRTRAIKMLVL  165 (222)
T ss_dssp             -----------CSEEEECHHHHHHHHHTTSSCCTTCCEEEE
T ss_pred             -----------CeEEeCCCCcHHhcccccccccccceeeee
Confidence                       68999997521  00256778899998874

>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=92.10  E-value=0.26  Score=36.37  Aligned_cols=80  Identities=14%  Similarity=0.197  Sum_probs=57.4

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcC---CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCC
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNL---ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEH   98 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~---~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (185)
                      ...+.++||.|+|++.|..+.+.+...   ....+...+|+.+..++.+.+   + +                       
T Consensus        69 ~~~~~~~lil~pt~~l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l---~-~-----------------------  121 (208)
T d1hv8a1          69 ENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKAL---K-N-----------------------  121 (208)
T ss_dssp             SSSSCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHH---H-T-----------------------
T ss_pred             cccCcceEEEeeccccchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhc---C-C-----------------------
Confidence            556679999999999999887776543   347889999998887766544   2 3                       


Q ss_pred             ceeEEEEecCCC-Ccc-cCcCCCCCCcEEEEcC
Q 029910           99 KSHMIVVTDACL-PLL-SSGESAISARVLINYE  129 (185)
Q Consensus        99 ~~~iLV~Td~~~-~~~-~~G~d~~~v~~VI~~d  129 (185)
                       .+|+|+|+-++ .++ ...+++.++.++|-=+
T Consensus       122 -~~IlV~TP~~l~~~l~~~~~~~~~l~~lViDE  153 (208)
T d1hv8a1         122 -ANIVVGTPGRILDHINRGTLNLKNVKYFILDE  153 (208)
T ss_dssp             -CSEEEECHHHHHHHHHTTCSCTTSCCEEEEET
T ss_pred             -CCEEEEChHHHHHHHHcCCCCcccCcEEEEEC
Confidence             67999996420 012 4566889999887543

>d1tq1a_ c.46.1.3 (A:) Thiosulfate sulfurtransferase/Senescence-associated protein {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Single-domain sulfurtransferase
domain: Thiosulfate sulfurtransferase/Senescence-associated protein
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=91.18  E-value=0.088  Score=35.72  Aligned_cols=40  Identities=10%  Similarity=0.048  Sum_probs=34.3

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      -.+.+++|+||++-..+...+..|...|+-.+..|.|++.
T Consensus        69 ~~~~~~iv~~C~~G~rs~~a~~~L~~~G~~nv~~l~GG~~  108 (119)
T d1tq1a_          69 FGQSDNIIVGCQSGGRSIKATTDLLHAGFTGVKDIVGGYS  108 (119)
T ss_dssp             CCTTSSEEEEESSCSHHHHHHHHHHHHHCCSEEEEECCHH
T ss_pred             cCCCcEEEEEcCCcCcHHHHHHHHHhcccCCeEEecChHH
Confidence            4567899999999999999999999998557999999963

>d1urha2 c.46.1.2 (A:149-268) 3-mercaptopyruvate sulfurtransferase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: 3-mercaptopyruvate sulfurtransferase
species: Escherichia coli [TaxId: 562]

Probab=90.35  E-value=0.24  Score=33.01  Aligned_cols=51  Identities=20%  Similarity=0.206  Sum_probs=38.1

Q ss_pred             HHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910            9 ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus         9 ~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      +.+...+.. . +-...+++|+||++-.++...+..|+..|+-.+..+.|+++
T Consensus        68 ~~~~~~~~~-~-g~~~~~~ii~yC~sG~~A~~~~~~L~~lG~~~v~~y~Gs~~  118 (120)
T d1urha2          68 DELDAIFFG-R-GVSYDKPIIVSCGSGVTAAVVLLALATLDVPNVKLYDGAWS  118 (120)
T ss_dssp             HHHHHHHHT-T-TCCSSSCEEEECCSSSTHHHHHHHHHHTTCSSCEEECCSCC
T ss_pred             HHhhhhhhh-c-ccCccCceEEEccchhHHHHHHHHHHHcCCCCceEcCCChh
Confidence            344444443 2 25567899999999988999999998888556888888875

>d1gmxa_ c.46.1.3 (A:) Sulfurtransferase GlpE {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Single-domain sulfurtransferase
domain: Sulfurtransferase GlpE
species: Escherichia coli [TaxId: 562]

Probab=88.68  E-value=0.31  Score=32.19  Aligned_cols=50  Identities=12%  Similarity=0.157  Sum_probs=38.7

Q ss_pred             hHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910            8 QETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus         8 ~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      .+.+...+..    -.+.+++|+||.+...+...+..|...|+-.+..+.|++.
T Consensus        45 ~~~l~~~~~~----~~~~~~ivv~c~~g~rs~~~a~~L~~~G~~~v~~l~GG~~   94 (108)
T d1gmxa_          45 NDTLGAFMRD----NDFDTPVMVMCYHGNSSKGAAQYLLQQGYDVVYSIDGGFE   94 (108)
T ss_dssp             HHHHHHHHHH----SCTTSCEEEECSSSSHHHHHHHHHHHHTCSSEEEETTHHH
T ss_pred             chhHHHHhhh----ccccCcccccCCCChHHHHHHHHHHHcCCCCEEEEcChHH
Confidence            3444455544    4556899999999999999999999998546888999864

>d1yt8a4 c.46.1.2 (A:243-372) Thiosulfate sulfurtransferase PA2603 {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: Thiosulfate sulfurtransferase PA2603
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=87.08  E-value=0.39  Score=32.86  Aligned_cols=39  Identities=8%  Similarity=0.054  Sum_probs=33.9

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      ..+.+++++||.+...+...+..|...| +.+..|.|++.
T Consensus        77 ~~~~~~ivl~C~~G~rS~~aa~~L~~~G-~~v~~l~GG~~  115 (130)
T d1yt8a4          77 SVRGARLVLVDDDGVRANMSASWLAQMG-WQVAVLDGLSE  115 (130)
T ss_dssp             CSBTCEEEEECSSSSHHHHHHHHHHHTT-CEEEEECSCCG
T ss_pred             CCccceEEeecCCCccHHHHHHHHHHcC-CCeEEEcCchH
Confidence            4556899999999999999999999999 59999998864

>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=86.76  E-value=1.1  Score=32.69  Aligned_cols=90  Identities=11%  Similarity=0.180  Sum_probs=59.9

Q ss_pred             HHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcC----CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccC
Q 029910           12 VELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQS   87 (185)
Q Consensus        12 ~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~   87 (185)
                      +-++..+.. .....+++|.|++++.+..+.+.+...    +.+....++|+.+.......+   .+.            
T Consensus        57 lp~l~~~~~-~~~~~~~lil~PtreL~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l---~~~------------  120 (207)
T d1t6na_          57 LATLQQLEP-VTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVL---KKN------------  120 (207)
T ss_dssp             HHHHHHCCC-CTTCCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHH---HHS------------
T ss_pred             cceeeeecc-cCCCceEEEEeccchhhHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHHH---Hhc------------
Confidence            344444333 455578999999999999888887543    235678888888777654433   233            


Q ss_pred             CCCCCCCCCCCceeEEEEecCCCCc-c-cCcCCCCCCcEEEEc
Q 029910           88 GDESETGKDEHKSHMIVVTDACLPL-L-SSGESAISARVLINY  128 (185)
Q Consensus        88 ~~~~~~~~~~~~~~iLV~Td~~~~~-~-~~G~d~~~v~~VI~~  128 (185)
                                 ..+++|+|+.++-. + ...+++.++.++|--
T Consensus       121 -----------~~~ilI~TP~rl~~~~~~~~~~l~~l~~lVlD  152 (207)
T d1t6na_         121 -----------CPHIVVGTPGRILALARNKSLNLKHIKHFILD  152 (207)
T ss_dssp             -----------CCSEEEECHHHHHHHHHTTSSCCTTCCEEEEE
T ss_pred             -----------CCCEEEeCcchhhhhccCCceeccccceeehh
Confidence                       47899999862111 1 246688899987753

>d1qxna_ c.46.1.3 (A:) Polysulfide-sulfur transferase (sulfide dehydrogenase, Sud) {Wolinella succinogenes [TaxId: 844]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Single-domain sulfurtransferase
domain: Polysulfide-sulfur transferase (sulfide dehydrogenase, Sud)
species: Wolinella succinogenes [TaxId: 844]

Probab=84.83  E-value=0.58  Score=32.34  Aligned_cols=39  Identities=10%  Similarity=0.218  Sum_probs=33.4

Q ss_pred             CCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCC
Q 029910           22 RRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDL   60 (185)
Q Consensus        22 ~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~   60 (185)
                      ..+.+++|+||.+-..+...+..|...|+-.+..+.|++
T Consensus        79 ~~~~~~ivvyC~~G~rs~~aa~~L~~~G~~nV~~l~GG~  117 (137)
T d1qxna_          79 LDPEKPVVVFCKTAARAALAGKTLREYGFKTIYNSEGGM  117 (137)
T ss_dssp             CCTTSCEEEECCSSSCHHHHHHHHHHHTCSCEEEESSCH
T ss_pred             cCcccceeeeecccchHHHHHHHHHHcCCCcEEEecCHH
Confidence            456689999999989999999999999854688899994

>d2eyqa2 c.37.1.19 (A:349-465) 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=84.34  E-value=0.59  Score=31.56  Aligned_cols=65  Identities=12%  Similarity=0.097  Sum_probs=47.5

Q ss_pred             CCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCCCCceeEEE
Q 029910           25 GLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIV  104 (185)
Q Consensus        25 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLV  104 (185)
                      ..++||+|.+...++.|.+.|++.+ +.+..+.+..          +|..+                       .  +.|
T Consensus        34 ~~~Vli~a~s~g~~erl~e~L~~~~-i~~~~~~~~~----------~~~~~-----------------------~--~~i   77 (117)
T d2eyqa2          34 DGPVVFSVESEGRREALGELLARIK-IAPQRIMRLD----------EASDR-----------------------G--RYL   77 (117)
T ss_dssp             CSCCCEEESSHHHHHHHHHHHGGGT-CCCEECSSGG----------GCCTT-----------------------C--CEE
T ss_pred             CCeEEEEECCccHHHHHHHHHHHcC-CCceEecChh----------hhcCc-----------------------e--EEE
Confidence            4689999999999999999999998 7776654421          22222                       2  344


Q ss_pred             EecCCCCcccCcCCCCCCcEEEEcC
Q 029910          105 VTDACLPLLSSGESAISARVLINYE  129 (185)
Q Consensus       105 ~Td~~~~~~~~G~d~~~v~~VI~~d  129 (185)
                      +...    ++.|+-+|+..++|--+
T Consensus        78 ~~~~----l~~GF~~~~~~l~vItE   98 (117)
T d2eyqa2          78 MIGA----AEHGFVDTVRNLALICE   98 (117)
T ss_dssp             EECC----CCSCEEETTTTEEEEEH
T ss_pred             EEec----CccccccCCCCEEEEEc
Confidence            4455    79999999999877643

>d1e0ca2 c.46.1.2 (A:136-271) Sulfurtransferase {Azotobacter vinelandii [TaxId: 354]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: Sulfurtransferase
species: Azotobacter vinelandii [TaxId: 354]

Probab=83.82  E-value=0.37  Score=33.40  Aligned_cols=50  Identities=8%  Similarity=0.118  Sum_probs=37.5

Q ss_pred             HHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCC
Q 029910            9 ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDL   60 (185)
Q Consensus         9 ~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~   60 (185)
                      +.+.++++. .. -.+.+++|+||++-.++...+..|...|+-.+..+.|++
T Consensus        74 ~~l~~~~~~-~g-i~~~~~vV~yC~~G~~a~~~~~~l~~~G~~~v~~ydGg~  123 (136)
T d1e0ca2          74 TDIAGRLEE-LG-ITPDKEIVTHCQTHHRSGLTYLIAKALGYPRVKGYAGSW  123 (136)
T ss_dssp             TTHHHHHHH-TT-CCTTSEEEEECSSSSHHHHHHHHHHHTTCSCEEECSSHH
T ss_pred             HHHhhhhhh-cc-cCCCCceEEeCCChHHHHHHHHHHHHcCCCCcEEecCCH
Confidence            445666665 22 456699999999988888888899888854688888863

>d1yt8a1 c.46.1.2 (A:107-242) Thiosulfate sulfurtransferase PA2603 {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: Thiosulfate sulfurtransferase PA2603
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=83.37  E-value=1.1  Score=30.71  Aligned_cols=51  Identities=18%  Similarity=0.160  Sum_probs=37.9

Q ss_pred             hHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCc-eEEEEecCC
Q 029910            8 QETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADI-SFSSLHSDL   60 (185)
Q Consensus         8 ~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~-~~~~l~g~~   60 (185)
                      ...+...+..+.  ..+..++|+||.+...+...+..|...|+- .+..|.|++
T Consensus        65 ~~~l~~~~~~l~--~~~~~~iV~~C~~g~rs~~aa~~L~~~G~~~~V~~L~GG~  116 (136)
T d1yt8a1          65 GAELVLRVAELA--PDPRTRVIVNCAGRTRSIIGTQSLLNAGIPNPVAALRNGT  116 (136)
T ss_dssp             GGGHHHHHHHHC--CSTTSEEEEECSSSHHHHHHHHHHHHTTCSSCEEEETTHH
T ss_pred             hhHHHHHhhccc--ccccceEEEEcCCCCchHHHHHHHHHcCCCceEEEeCCcH
Confidence            444555566532  234578999999999999999999999843 378899984

>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=82.74  E-value=2  Score=31.56  Aligned_cols=76  Identities=11%  Similarity=0.133  Sum_probs=52.0

Q ss_pred             CCCcEEEEcCChhhHHHHHHHHhcC----C---CceEEEEecCCCHHHHHHHHHHHhcccccccccccccCCCCCCCCCC
Q 029910           24 PGLPMIVCCSSRDELDAVCSAVSNL----A---DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKD   96 (185)
Q Consensus        24 ~~~~~IIF~~~~~~~~~l~~~L~~~----~---~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~   96 (185)
                      +++++||-++++.-+.+..+.+.+.    +   .......+++.+..++.+.++...                       
T Consensus        85 ~~~rvliv~Pt~~La~Q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-----------------------  141 (237)
T d1gkub1          85 KGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLR-----------------------  141 (237)
T ss_dssp             TSCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGG-----------------------
T ss_pred             hcCeEEEEeccHHHHHHHHHHHHHHHHHcCCceEEEEeeeecccchhhhhhhhcccc-----------------------
Confidence            4579999999999999988887642    2   133566677777777776655443                       


Q ss_pred             CCceeEEEEecCCCCcccC-cCCCCCCcEEEE
Q 029910           97 EHKSHMIVVTDACLPLLSS-GESAISARVLIN  127 (185)
Q Consensus        97 ~~~~~iLV~Td~~~~~~~~-G~d~~~v~~VI~  127 (185)
                        ..+|+|+|.-.   +.+ -.+...+++||.
T Consensus       142 --~~~Ilv~Tp~~---l~~~~~~~~~~~~vVv  168 (237)
T d1gkub1         142 --NFKIVITTTQF---LSKHYRELGHFDFIFV  168 (237)
T ss_dssp             --GCSEEEEEHHH---HHHCSTTSCCCSEEEE
T ss_pred             --ccceeccChHH---HHHhhhhcCCCCEEEE
Confidence              36789999641   333 335667888775

>d1rhsa2 c.46.1.2 (A:150-293) Rhodanese {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: Rhodanese
species: Cow (Bos taurus) [TaxId: 9913]

Probab=80.76  E-value=1  Score=31.39  Aligned_cols=53  Identities=11%  Similarity=0.046  Sum_probs=38.3

Q ss_pred             chHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910            7 FQETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus         7 ~~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      ..+.+..++.. .. -.+.+++|+||.+-.++..++-.|...|+-.+..+.|+++
T Consensus        75 ~~~~l~~~~~~-~g-i~~~~~iI~yC~sG~~A~~~~~~l~~lG~~~v~~YdGsw~  127 (144)
T d1rhsa2          75 SPEELRAMFEA-KK-VDLTKPLIATCRKGVTACHIALAAYLCGKPDVAIYDGSWF  127 (144)
T ss_dssp             CHHHHHHHHHH-TT-CCTTSCEEEECSSSSTHHHHHHHHHHTTCCCCEEESSHHH
T ss_pred             CHHHHHHHHHH-cC-CCCCCCEEEEecccchHHHHHHHHHHcCCCCCEEeCCCHH
Confidence            34555666655 22 4566899999998877888888888888546888888743

>d1yt8a2 c.46.1.2 (A:6-106) Thiosulfate sulfurtransferase PA2603 {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: Thiosulfate sulfurtransferase PA2603
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=80.67  E-value=1.8  Score=27.55  Aligned_cols=50  Identities=16%  Similarity=0.157  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcCCCceEEEEecCCC
Q 029910           10 TLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   61 (185)
Q Consensus        10 ~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l~g~~~   61 (185)
                      .+...+..+ . ....++++++|++...+...+..|...|+-.+..+.|++.
T Consensus        45 ~~~~~~~~~-~-~~~~~~vv~~~~~g~~s~~~~~~l~~~G~~nV~~l~GG~~   94 (101)
T d1yt8a2          45 RLELEIHAR-V-PRRDTPITVYDDGEGLAPVAAQRLHDLGYSDVALLDGGLS   94 (101)
T ss_dssp             GHHHHHHHH-S-CCTTSCEEEECSSSSHHHHHHHHHHHTTCSSEEEETTHHH
T ss_pred             chhhhhhhc-c-cccCceeeeccchhhhHHHHHHHHHHcCCCcEEEeCChHH
Confidence            334444442 2 3456899999999999999999999998656888888853

>d1uara2 c.46.1.2 (A:145-285) Sulfurtransferase {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: Sulfurtransferase
species: Thermus thermophilus [TaxId: 274]

Probab=80.63  E-value=1.1  Score=31.11  Aligned_cols=51  Identities=14%  Similarity=0.161  Sum_probs=36.1

Q ss_pred             hHHHHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhc-CCCceEEEEecCC
Q 029910            8 QETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSN-LADISFSSLHSDL   60 (185)
Q Consensus         8 ~~~l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~-~~~~~~~~l~g~~   60 (185)
                      .+.+..++.. . +-.+.+++|+||++-.++...+-.|.. .|+-.+..+.|++
T Consensus        74 ~~~~~~~~~~-~-gi~~d~~vV~yC~~G~~As~~~~~l~~~~G~~~v~~ydGs~  125 (141)
T d1uara2          74 AEELRALYEP-L-GITKDKDIVVYCRIAERSSHSWFVLKYLLGYPHVKNYDGSW  125 (141)
T ss_dssp             HHHHHHHHGG-G-TCCTTSEEEEECSSHHHHHHHHHHHHTTSCCSCEEEESSHH
T ss_pred             HHHHHHHHHH-h-CCCCCCeEEEEecCcchHHHHHHHHHHHcCCCCeeEeCCcH
Confidence            3444445543 2 245668999999998888888888875 6754688888873

>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=80.48  E-value=0.7  Score=34.36  Aligned_cols=90  Identities=13%  Similarity=0.111  Sum_probs=52.1

Q ss_pred             HHHHHHHHHccCCCCCcEEEEcCChhhHHHHHHHHhcC---CCceEEEEecCCCHHHHHHHHHHHhcccccccccccccC
Q 029910           11 LVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL---ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQS   87 (185)
Q Consensus        11 l~~ll~~l~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~---~~~~~~~l~g~~~~~~R~~~l~~F~~~~~~~~~~~~~~~   87 (185)
                      ++-+++.+.. .....++||.|+|++-|.++.+.+...   .......+.++....+..   .+..              
T Consensus        67 llp~l~~i~~-~~~~~~alil~Pt~eL~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~--------------  128 (218)
T d2g9na1          67 AISILQQIEL-DLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEV---QKLQ--------------  128 (218)
T ss_dssp             HHHHHHHCCT-TCCSCCEEEECSSHHHHHHHHHHHHHHHTTTTCCEEEECC--CCCSTT---TSSS--------------
T ss_pred             hhhhhheecc-cccCccEEEEcccchhhhhHHHHHhhhccccceeEEeeecccchhHHH---HHHh--------------
Confidence            3445555433 556788999999999999888776543   225566665543322211   0111              


Q ss_pred             CCCCCCCCCCCceeEEEEecCCCC--cccCcCCCCCCcEEEE
Q 029910           88 GDESETGKDEHKSHMIVVTDACLP--LLSSGESAISARVLIN  127 (185)
Q Consensus        88 ~~~~~~~~~~~~~~iLV~Td~~~~--~~~~G~d~~~v~~VI~  127 (185)
                               ....+|+|+|+.++-  +-.....+..++++|-
T Consensus       129 ---------~~~~~IvV~TP~rl~~~l~~~~~~~~~l~~lVl  161 (218)
T d2g9na1         129 ---------MEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVL  161 (218)
T ss_dssp             ---------SCCCSEEEECHHHHHHHHHTTSSCSTTCCEEEE
T ss_pred             ---------cCCCEEEEeCChhHHHHHhcCCcccccceEEEe
Confidence                     124789999973100  0234567788888774