Psyllid ID: psy6712

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210
Protein Sequence
MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRSLHSYPARY
Secondary Structure (PSIPRED)
cccEEEEEEccccHHHHHHHHcccccEEEcccHHHHHHHHccEEEEccEEEEEEEHHHHHcccHHHHcHHccEEEccccHHHHHHHHHHHHcccEEEEccccccHHHHHHHHHHHcccccEEEEEEEccccccccccEEEEEEEcccccccccEEEcccccccccccEEEEEEcHHHHHHHHHHHHHHcccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccEEEEEEccccHHHHHHHHHcccEEEEEcHHHHHHHHcccccccccccEEEEccHHHHHccccHHHHHHHHHccccccEEEEEEccccHcccEEEEEcccccHHHHHHHHHHHHcccccEEEEEHHHHcccccccEEEEEEEcccccHHHHEEEEcccccccccEEEEEEcccccHHHHHHHHHHHHHHHHcccccHHHHHHcccccc
Coil and Loop (DISEMBL)
mnvqchaciggtnlsedlrkldygqhvvsgtpgrVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVyrylppatqvdWLTEKMREAnftvssmhgdmpqkerDGIMKEFRSGTSRVLITTDvwargidvQQVSLVINydlpnnrelyIHRIgrsgrfgrkgvAISFVKSDDIRILRDIEQYYSTqidempmngkrslhsypary
Flexible Loop (DISEMBL)
mnvqchacIGGTNLSEDLRKLDYGqhvvsgtpgrvfdmirRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVDWLTEKMREANFtvssmhgdmpqkERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHrigrsgrfgrkgvaisfvksddirilRDIEQYystqidempmngkrslhsypary
Low Complexity Region (SEG)
MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRSLHSYPARY
Disordered region (IsUnstruct)
***QCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVDWLTEKMR***************************GTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQI******************
Disordered Region (DISOPRED)
MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRSLHSYP***
Disordered Region (DISEMBL)
MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRSLHSYPARY
Disordered Region (DISPRO)
MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRSLHSYPA**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRSLHSYPARY
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	210	2.2.26 [Sep-21-2011]
P41380	391	Eukaryotic initiation fac	N/A	N/A	0.561	0.301	0.915	2e-60
Q4R3Q1	411	Eukaryotic initiation fac	N/A	N/A	0.561	0.287	0.906	2e-60
P38919	411	Eukaryotic initiation fac	yes	N/A	0.561	0.287	0.906	2e-60
Q3B8Q2	411	Eukaryotic initiation fac	yes	N/A	0.561	0.287	0.906	2e-60
A6M931	411	Eukaryotic initiation fac	yes	N/A	0.561	0.287	0.906	2e-60
Q2NL22	411	Eukaryotic initiation fac	yes	N/A	0.561	0.287	0.906	2e-60
Q91VC3	411	Eukaryotic initiation fac	yes	N/A	0.561	0.287	0.906	2e-60
Q7ZVA6	406	Eukaryotic initiation fac	yes	N/A	0.561	0.290	0.906	2e-60
O42226	414	Eukaryotic initiation fac	N/A	N/A	0.561	0.285	0.906	3e-60
Q5ZM36	412	Eukaryotic initiation fac	yes	N/A	0.561	0.286	0.906	4e-60

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

 Score =  232 bits (591), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 108/118 (91%), Positives = 113/118 (95%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +VDWLT KMRE NFTVSSMHGDMPQKERD IM EFR GT+RVLITTDVWARG+DVQQVSL
Sbjct: 269 KVDWLTSKMRENNFTVSSMHGDMPQKERDAIMAEFRGGTTRVLITTDVWARGLDVQQVSL 328

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           VINYDLPNNRELYIHRIGRSGRFGRKGVAI+FVKSDDI+ILRDIEQYYSTQIDEMPMN
Sbjct: 329 VINYDLPNNRELYIHRIGRSGRFGRKGVAINFVKSDDIKILRDIEQYYSTQIDEMPMN 386

ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon.
Nicotiana plumbaginifolia (taxid: 4092)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q4R3Q1|IF4A3_MACFA Eukaryotic initiation factor 4A-III OS=Macaca fascicularis GN=EIF4A3 PE=2 SV=3

 Score =  231 bits (590), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 107/118 (90%), Positives = 115/118 (97%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +VDWLTEKMREANFTVSSMHGDMPQKER+ IMKEFRSG SRVLI+TDVWARG+DV QVSL
Sbjct: 289 KVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSL 348

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           +INYDLPNNRELYIHRIGRSGR+GRKGVAI+FVK+DDIRILRDIEQYYSTQIDEMPMN
Sbjct: 349 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN 406

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

Macaca fascicularis (taxid: 9541)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

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

 Score =  231 bits (590), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 107/118 (90%), Positives = 115/118 (97%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +VDWLTEKMREANFTVSSMHGDMPQKER+ IMKEFRSG SRVLI+TDVWARG+DV QVSL
Sbjct: 289 KVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSL 348

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           +INYDLPNNRELYIHRIGRSGR+GRKGVAI+FVK+DDIRILRDIEQYYSTQIDEMPMN
Sbjct: 349 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN 406

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

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

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

 Score =  231 bits (590), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 107/118 (90%), Positives = 115/118 (97%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +VDWLTEKMREANFTVSSMHGDMPQKER+ IMKEFRSG SRVLI+TDVWARG+DV QVSL
Sbjct: 289 KVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSL 348

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           +INYDLPNNRELYIHRIGRSGR+GRKGVAI+FVK+DDIRILRDIEQYYSTQIDEMPMN
Sbjct: 349 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN 406

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

Rattus norvegicus (taxid: 10116)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

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

 Score =  231 bits (590), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 107/118 (90%), Positives = 115/118 (97%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +VDWLTEKMREANFTVSSMHGDMPQKER+ IMKEFRSG SRVLI+TDVWARG+DV QVSL
Sbjct: 289 KVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSL 348

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           +INYDLPNNRELYIHRIGRSGR+GRKGVAI+FVK+DDIRILRDIEQYYSTQIDEMPMN
Sbjct: 349 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN 406

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

Sus scrofa (taxid: 9823)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

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

 Score =  231 bits (590), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 107/118 (90%), Positives = 115/118 (97%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +VDWLTEKMREANFTVSSMHGDMPQKER+ IMKEFRSG SRVLI+TDVWARG+DV QVSL
Sbjct: 289 KVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSL 348

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           +INYDLPNNRELYIHRIGRSGR+GRKGVAI+FVK+DDIRILRDIEQYYSTQIDEMPMN
Sbjct: 349 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN 406

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

Bos taurus (taxid: 9913)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

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

 Score =  231 bits (590), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 107/118 (90%), Positives = 115/118 (97%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +VDWLTEKMREANFTVSSMHGDMPQKER+ IMKEFRSG SRVLI+TDVWARG+DV QVSL
Sbjct: 289 KVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSL 348

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           +INYDLPNNRELYIHRIGRSGR+GRKGVAI+FVK+DDIRILRDIEQYYSTQIDEMPMN
Sbjct: 349 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN 406

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

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

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

 Score =  231 bits (590), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 107/118 (90%), Positives = 115/118 (97%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +VDWLTEKMREANFTVSSMHGDMPQKER+ IMKEFRSG SRVLI+TDVWARG+DV QVSL
Sbjct: 284 KVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVSQVSL 343

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           +INYDLPNNRELYIHRIGRSGR+GRKGVAI+FVK+DDIRILRDIEQYYSTQIDEMPMN
Sbjct: 344 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN 401

ATP-dependent RNA helicase. Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Constitutes at least part of the platform anchoring other EJC proteins to spliced mRNAs. Binds spliced mRNA in sequence-independent manner, 20-24 nucleotides upstream of mRNA exon-exon junctions.

Danio rerio (taxid: 7955)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|O42226|I4A3B_XENLA Eukaryotic initiation factor 4A-III-B OS=Xenopus laevis GN=eif4a3-b PE=2 SV=1

 Score =  231 bits (589), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 107/118 (90%), Positives = 115/118 (97%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +VDWLTEKMREANFTVSSMHGDMPQKER+ IMKEFRSG SRVLI+TDVWARG+DV QVSL
Sbjct: 292 KVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSL 351

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           +INYDLPNNRELYIHRIGRSGR+GRKGVAI+FVK+DDIRILRDIEQYYSTQIDEMPMN
Sbjct: 352 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN 409

ATP-dependent RNA helicase. Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Constitutes at least part of the platform anchoring other EJC proteins to spliced mRNAs. Binds spliced mRNA in sequence-independent manner, 20-24 nucleotides upstream of mRNA exon-exon junctions (By similarity). When overexpressed, induces epidermis in dissociated cells that would otherwise adopt a neural fate, a process that requires an active BMP signaling pathway.

Xenopus laevis (taxid: 8355)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5ZM36|IF4A3_CHICK Eukaryotic initiation factor 4A-III OS=Gallus gallus GN=EIF4A3 PE=2 SV=1

 Score =  231 bits (588), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 107/118 (90%), Positives = 115/118 (97%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +VDWLTEKMREANFTVSSMHGDMPQKER+ IMKEFRSG SRVLI+TDVWARG+DV QVSL
Sbjct: 290 KVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSL 349

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           +INYDLPNNRELYIHRIGRSGR+GRKGVAI+FVK+DDIRILRDIEQYYSTQIDEMPMN
Sbjct: 350 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN 407

ATP-dependent RNA helicase. Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Constitutes at least part of the platform anchoring other EJC proteins to spliced mRNAs. Binds spliced mRNA in sequence-independent manner, 20-24 nucleotides upstream of mRNA exon-exon junctions.

Gallus gallus (taxid: 9031)

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	210
194216574	375	PREDICTED: eukaryotic initiation factor	0.942	0.528	0.764	1e-101
432111715	324	Eukaryotic initiation factor 4A-III [Myo	0.919	0.595	0.762	3e-82
428174639	382	hypothetical protein GUITHDRAFT_153197 [	0.942	0.518	0.609	7e-79
432096348	322	Eukaryotic initiation factor 4A-III [Myo	0.814	0.531	0.743	4e-77
357154181	323	PREDICTED: LOW QUALITY PROTEIN: DEAD-box	0.933	0.606	0.671	5e-74
405950923	1228	Eukaryotic initiation factor 4A-III [Cra	0.585	0.100	0.926	2e-62
170071047	222	DEAD box ATP-dependent RNA helicase [Cul	0.561	0.531	0.966	3e-61
291242437	398	PREDICTED: eukaryotic translation initia	0.561	0.296	0.957	4e-61
196014693	401	DEAD box ATP-dependent RNA helicase [Tri	0.561	0.294	0.957	5e-61
125775187	399	GA20384 [Drosophila pseudoobscura pseudo	0.561	0.295	0.957	5e-61

>gi|194216574|ref|XP_001490317.2| PREDICTED: eukaryotic initiation factor 4A-III [Equus caballus]

 Score =  372 bits (954), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 182/238 (76%), Positives = 192/238 (80%), Gaps = 40/238 (16%)

Query: 1   MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEM 60
           MNVQCHACIGGTN+ ED+RKLDYGQHVV+GTPGRVFDMIRRR LRTR IKMLVLDEADEM
Sbjct: 133 MNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEM 192

Query: 61  LNKGFKEQIYDVYRYLPPATQV-------------------------------------- 82
           LNKGFKEQIYDVYRYLPPATQV                                      
Sbjct: 193 LNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRFYYIHPLFD 252

Query: 83  --DWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
             DWLTEKMREANFTVSSMHGDMPQKER+ IMKEFRSG SRVLI+TDVWARG+DV QVSL
Sbjct: 253 PVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSL 312

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           +INYDLPNNRELYIHRIGRSGR+GRKGVAI+FVK+DDIRILRDIEQYYSTQIDEMPMN
Sbjct: 313 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN 370

Source: Equus caballus

Species: Equus caballus

Genus: Equus

Family: Equidae

Order: Perissodactyla

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|432111715|gb|ELK34777.1| Eukaryotic initiation factor 4A-III [Myotis davidii]

 Score =  310 bits (794), Expect = 3e-82,   Method: Compositional matrix adjust.
 Identities = 151/198 (76%), Positives = 170/198 (85%), Gaps = 5/198 (2%)

Query: 1   MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEM 60
           M VQCHACIGGT++ ED+RKL  GQHVV+ TPGRVF+MIRRR LRTR I+MLVLDEADEM
Sbjct: 127 MKVQCHACIGGTHVGEDIRKLVRGQHVVACTPGRVFEMIRRRSLRTRAIQMLVLDEADEM 186

Query: 61  LNKGFKEQIYDVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTS 120
           LN+GFKEQIYDVYRYLPPATQV      + +         GD+PQKE + IMKEFRSGTS
Sbjct: 187 LNQGFKEQIYDVYRYLPPATQV-----VLPQRYAAPRDPPGDLPQKEPESIMKEFRSGTS 241

Query: 121 RVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRI 180
           RVLI+TDVWARG+DV QVS VI+YDLPNNRELYIHRIGRSGR+GRKGVAI+FVK DDIRI
Sbjct: 242 RVLISTDVWARGLDVPQVSRVISYDLPNNRELYIHRIGRSGRYGRKGVAINFVKDDDIRI 301

Query: 181 LRDIEQYYSTQIDEMPMN 198
           LRD+EQYYSTQI+EMPM+
Sbjct: 302 LRDMEQYYSTQINEMPMD 319

Source: Myotis davidii

Species: Myotis davidii

Genus: Myotis

Family: Vespertilionidae

Order: Chiroptera

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|428174639|gb|EKX43533.1| hypothetical protein GUITHDRAFT_153197 [Guillardia theta CCMP2712]

 Score =  298 bits (764), Expect = 7e-79,   Method: Compositional matrix adjust.
 Identities = 156/256 (60%), Positives = 173/256 (67%), Gaps = 58/256 (22%)

Query: 1   MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEAD-- 58
           M +Q HACIGG ++ ED+RKLDYG H+VSGTPGRVFDMIRRR LRTRNIK LVLDEAD  
Sbjct: 122 MQIQAHACIGGKSVGEDIRKLDYGVHIVSGTPGRVFDMIRRRNLRTRNIKTLVLDEADEM 181

Query: 59  ----------------------------------EMLNKGFKEQIYDVYR---------- 74
                                             E+  +G K+    V R          
Sbjct: 182 LNQGFKEQIYDVYRYLPPQIQFMTDPVRILVKRDELTLEGIKQFFVAVEREEWKFDTLCD 241

Query: 75  ------------YLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRV 122
                       +     +VDWLT+KMREANFTVSSMHGDMPQ +RD IM EFR G+SRV
Sbjct: 242 LYDTLTITQAVIFCNTKRKVDWLTDKMREANFTVSSMHGDMPQNDRDAIMGEFRGGSSRV 301

Query: 123 LITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILR 182
           LITTDVWARG+DV QVSLVINYDLPNNRELYIHRIGRSGR+GRKGVAI+FVK+DDIRILR
Sbjct: 302 LITTDVWARGLDVSQVSLVINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKADDIRILR 361

Query: 183 DIEQYYSTQIDEMPMN 198
           DIEQYYSTQIDEMPMN
Sbjct: 362 DIEQYYSTQIDEMPMN 377

Source: Guillardia theta CCMP2712

Species: Guillardia theta

Genus: Guillardia

Family: Geminigeraceae

Order: Pyrenomonadales

Class: Cryptophyta

Superkingdom: Eukaryota

>gi|432096348|gb|ELK27104.1| Eukaryotic initiation factor 4A-III [Myotis davidii]

 Score =  293 bits (749), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 142/191 (74%), Positives = 159/191 (83%), Gaps = 20/191 (10%)

Query: 1   MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEM 60
           MNVQCHACIGGTN+ ED+RKLDYGQHVV+G PGRVFD IRRR LRTR IKML+LDEADEM
Sbjct: 133 MNVQCHACIGGTNVGEDIRKLDYGQHVVAGMPGRVFDTIRRRSLRTRAIKMLILDEADEM 192

Query: 61  LNKGFKEQIYDVYRYLPPATQV----------------DWLTEKMR---EANFTVSSMHG 101
           LNKGFKEQIYDVYRYLPPATQV                 ++T+ +R   + NFTVSSMHG
Sbjct: 193 LNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPLRILGKPNFTVSSMHG 252

Query: 102 DMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSG 161
           DMPQKER+ IM EFRSG SRVLI+T+VWARG+DV+QVSL+INYDLPNNRELYIHRIGRSG
Sbjct: 253 DMPQKERESIM-EFRSGASRVLISTNVWARGLDVRQVSLIINYDLPNNRELYIHRIGRSG 311

Query: 162 RFGRKGVAISF 172
           R+GRKGVA + 
Sbjct: 312 RYGRKGVASTL 322

Source: Myotis davidii

Species: Myotis davidii

Genus: Myotis

Family: Vespertilionidae

Order: Chiroptera

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|357154181|ref|XP_003576698.1| PREDICTED: LOW QUALITY PROTEIN: DEAD-box ATP-dependent RNA helicase 34-like [Brachypodium distachyon]

 Score =  282 bits (722), Expect = 5e-74,   Method: Compositional matrix adjust.
 Identities = 133/198 (67%), Positives = 161/198 (81%), Gaps = 2/198 (1%)

Query: 1   MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEM 60
           M+++ HAC+GG ++ ED+RKL++G HVVSGTPGRV D+I RR LRTR IK+LVLDEAD+M
Sbjct: 123 MSIRVHACVGGNSVGEDIRKLEHGVHVVSGTPGRVCDLINRRTLRTRAIKLLVLDEADDM 182

Query: 61  LNKGFKEQIYDVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTS 120
           L +GFK QIYD+YRYLPP  Q   ++  M      V+S    M   ER+ IM +FRSG +
Sbjct: 183 LERGFKSQIYDIYRYLPPDLQGVLISATMPAEILEVTSKF--MTDPERNAIMADFRSGAT 240

Query: 121 RVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRI 180
           RVLITTD+WARG+DVQQVSLVINYDLP++RELYIHR+GRSGRFGRKGVAI+FV+  DI I
Sbjct: 241 RVLITTDIWARGLDVQQVSLVINYDLPSDRELYIHRMGRSGRFGRKGVAINFVREIDITI 300

Query: 181 LRDIEQYYSTQIDEMPMN 198
           LRDIEQ+YS QIDEMPMN
Sbjct: 301 LRDIEQFYSAQIDEMPMN 318

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|405950923|gb|EKC18878.1| Eukaryotic initiation factor 4A-III [Crassostrea gigas]

 Score =  244 bits (622), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 114/123 (92%), Positives = 119/123 (96%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +VDWLTEKMREANFTVSSMHGDM QKER+ IMKEFRSG SRVLITTDVWARGIDVQQVSL
Sbjct: 276 KVDWLTEKMREANFTVSSMHGDMVQKEREAIMKEFRSGASRVLITTDVWARGIDVQQVSL 335

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGK 200
           VINYDLPNNRELYIHRIGRSGRFGRKGVAI+FVKSDDIRILRDIEQYY+TQIDEMPMNG 
Sbjct: 336 VINYDLPNNRELYIHRIGRSGRFGRKGVAINFVKSDDIRILRDIEQYYATQIDEMPMNGL 395

Query: 201 RSL 203
           RS+
Sbjct: 396 RSI 398

Source: Crassostrea gigas

Species: Crassostrea gigas

Genus: Crassostrea

Family: Ostreidae

Order: Ostreoida

Class: Bivalvia

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|170071047|ref|XP_001869798.1| DEAD box ATP-dependent RNA helicase [Culex quinquefasciatus] gi|167866996|gb|EDS30379.1| DEAD box ATP-dependent RNA helicase [Culex quinquefasciatus]

 Score =  240 bits (612), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 114/118 (96%), Positives = 116/118 (98%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +VDWLTEKMREANFTVSSMHGDMPQKERD IMKEFRSG SRVLITTDVWARGIDVQQVSL
Sbjct: 100 KVDWLTEKMREANFTVSSMHGDMPQKERDEIMKEFRSGQSRVLITTDVWARGIDVQQVSL 159

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           VINYDLPNNRELYIHRIGRSGRFGRKGVAI+FVKSDDIRILRDIEQYYSTQIDEMPMN
Sbjct: 160 VINYDLPNNRELYIHRIGRSGRFGRKGVAINFVKSDDIRILRDIEQYYSTQIDEMPMN 217

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|291242437|ref|XP_002741112.1| PREDICTED: eukaryotic translation initiation factor 4A-like [Saccoglossus kowalevskii]

 Score =  239 bits (611), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 113/118 (95%), Positives = 116/118 (98%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +VDWLTEKMREANFTVSSMHGDMPQKERD IMKEFRSG SRVLITTDVWARGIDVQQVSL
Sbjct: 276 KVDWLTEKMREANFTVSSMHGDMPQKERDAIMKEFRSGASRVLITTDVWARGIDVQQVSL 335

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           VINYDLPNNRELYIHRIGRSGR+GRKGVAI+FVKSDDIRILRDIEQYYSTQIDEMPMN
Sbjct: 336 VINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKSDDIRILRDIEQYYSTQIDEMPMN 393

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|196014693|ref|XP_002117205.1| DEAD box ATP-dependent RNA helicase [Trichoplax adhaerens] gi|190580170|gb|EDV20255.1| DEAD box ATP-dependent RNA helicase [Trichoplax adhaerens]

 Score =  239 bits (610), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 113/118 (95%), Positives = 116/118 (98%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +VDWLTEKMREANFTVSSMHGDMPQKERD IMKEFRSG SRVLITTDVWARGIDVQQVSL
Sbjct: 279 KVDWLTEKMREANFTVSSMHGDMPQKERDAIMKEFRSGASRVLITTDVWARGIDVQQVSL 338

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           VINYDLPNNRELYIHRIGRSGR+GRKGVAI+FVKSDDIRILRDIEQYYSTQIDEMPMN
Sbjct: 339 VINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKSDDIRILRDIEQYYSTQIDEMPMN 396

Source: Trichoplax adhaerens

Species: Trichoplax adhaerens

Genus: Trichoplax

Phylum: Placozoa

Superkingdom: Eukaryota

>gi|125775187|ref|XP_001358845.1| GA20384 [Drosophila pseudoobscura pseudoobscura] gi|195144826|ref|XP_002013397.1| GL23429 [Drosophila persimilis] gi|54638586|gb|EAL27988.1| GA20384 [Drosophila pseudoobscura pseudoobscura] gi|194102340|gb|EDW24383.1| GL23429 [Drosophila persimilis]

 Score =  239 bits (610), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 113/118 (95%), Positives = 116/118 (98%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +VDWLTEKMREANFTVSSMHGDMPQKERD IMKEFR+G SRVLITTDVWARGIDVQQVSL
Sbjct: 277 KVDWLTEKMREANFTVSSMHGDMPQKERDEIMKEFRAGQSRVLITTDVWARGIDVQQVSL 336

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           VINYDLPNNRELYIHRIGRSGRFGRKGVAI+FVKSDDIRILRDIEQYYSTQIDEMPMN
Sbjct: 337 VINYDLPNNRELYIHRIGRSGRFGRKGVAINFVKSDDIRILRDIEQYYSTQIDEMPMN 394

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	210
FB|FBgn0037573	399	eIF4AIII "eIF4AIII" [Drosophil	0.561	0.295	0.949	6.8e-98
ZFIN|ZDB-GENE-040426-915	406	eif4a3 "eukaryotic translation	0.561	0.290	0.906	3.3e-96
UNIPROTKB|Q5ZM36	412	EIF4A3 "Eukaryotic initiation	0.561	0.286	0.906	4.2e-96
UNIPROTKB|Q2NL22	411	EIF4A3 "Eukaryotic initiation	0.561	0.287	0.906	4.2e-96
UNIPROTKB|E2RDZ4	411	EIF4A3 "Uncharacterized protei	0.561	0.287	0.906	4.2e-96
UNIPROTKB|P38919	411	EIF4A3 "Eukaryotic initiation	0.561	0.287	0.906	4.2e-96
UNIPROTKB|A6M931	411	EIF4A3 "Eukaryotic initiation	0.561	0.287	0.906	4.2e-96
UNIPROTKB|F1RZ83	411	EIF4A3 "Eukaryotic initiation	0.561	0.287	0.906	4.2e-96
RGD|1591139	411	Eif4a3 "eukaryotic translation	0.561	0.287	0.906	4.2e-96
WB|WBGene00018007	399	F33D11.10 [Caenorhabditis eleg	0.561	0.295	0.872	1.8e-93

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

 Score = 583 (210.3 bits), Expect = 6.8e-98, Sum P(2) = 6.8e-98
 Identities = 112/118 (94%), Positives = 116/118 (98%)

Query:    81 QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
             +VDWLTEKMREANFTVSSMHGDMPQKERD IMKEFR+G SRVLITTDVWARGIDVQQVSL
Sbjct:   277 KVDWLTEKMREANFTVSSMHGDMPQKERDEIMKEFRAGQSRVLITTDVWARGIDVQQVSL 336

Query:   141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
             VINYDLPNNRELYIHRIGRSGRFGRKGVAI+FVKSDDIRILRDIEQYYSTQIDEMP+N
Sbjct:   337 VINYDLPNNRELYIHRIGRSGRFGRKGVAINFVKSDDIRILRDIEQYYSTQIDEMPVN 394

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

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

GO:0006413 "translational initiation" evidence=ISS

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

GO:0005524 "ATP binding" evidence=IEA

GO:0045495 "pole plasm" evidence=IDA

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

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0071011 "precatalytic spliceosome" evidence=IDA

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

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

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

GO:0008380 "RNA splicing" evidence=IMP

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

 Score = 571 (206.1 bits), Expect = 3.3e-96, Sum P(2) = 3.3e-96
 Identities = 107/118 (90%), Positives = 115/118 (97%)

Query:    81 QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
             +VDWLTEKMREANFTVSSMHGDMPQKER+ IMKEFRSG SRVLI+TDVWARG+DV QVSL
Sbjct:   284 KVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVSQVSL 343

Query:   141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
             +INYDLPNNRELYIHRIGRSGR+GRKGVAI+FVK+DDIRILRDIEQYYSTQIDEMPMN
Sbjct:   344 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN 401

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0004386 "helicase activity" evidence=IEA

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

GO:0005737 "cytoplasm" evidence=IEA

GO:0006810 "transport" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0051028 "mRNA transport" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006417 "regulation of translation" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

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

 Score = 570 (205.7 bits), Expect = 4.2e-96, Sum P(2) = 4.2e-96
 Identities = 107/118 (90%), Positives = 115/118 (97%)

Query:    81 QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
             +VDWLTEKMREANFTVSSMHGDMPQKER+ IMKEFRSG SRVLI+TDVWARG+DV QVSL
Sbjct:   290 KVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSL 349

Query:   141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
             +INYDLPNNRELYIHRIGRSGR+GRKGVAI+FVK+DDIRILRDIEQYYSTQIDEMPMN
Sbjct:   350 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN 407

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

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0006417 "regulation of translation" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0051028 "mRNA transport" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

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

 Score = 570 (205.7 bits), Expect = 4.2e-96, Sum P(2) = 4.2e-96
 Identities = 107/118 (90%), Positives = 115/118 (97%)

Query:    81 QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
             +VDWLTEKMREANFTVSSMHGDMPQKER+ IMKEFRSG SRVLI+TDVWARG+DV QVSL
Sbjct:   289 KVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSL 348

Query:   141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
             +INYDLPNNRELYIHRIGRSGR+GRKGVAI+FVK+DDIRILRDIEQYYSTQIDEMPMN
Sbjct:   349 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN 406

GO:0016607 "nuclear speck" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

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

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

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

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

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

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

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

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

GO:0051028 "mRNA transport" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

 Score = 570 (205.7 bits), Expect = 4.2e-96, Sum P(2) = 4.2e-96
 Identities = 107/118 (90%), Positives = 115/118 (97%)

Query:    81 QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
             +VDWLTEKMREANFTVSSMHGDMPQKER+ IMKEFRSG SRVLI+TDVWARG+DV QVSL
Sbjct:   289 KVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSL 348

Query:   141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
             +INYDLPNNRELYIHRIGRSGR+GRKGVAI+FVK+DDIRILRDIEQYYSTQIDEMPMN
Sbjct:   349 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN 406

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

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

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

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

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

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

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

GO:0005737 "cytoplasm" evidence=IEA

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

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

GO:0005524 "ATP binding" evidence=IEA

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

 Score = 570 (205.7 bits), Expect = 4.2e-96, Sum P(2) = 4.2e-96
 Identities = 107/118 (90%), Positives = 115/118 (97%)

Query:    81 QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
             +VDWLTEKMREANFTVSSMHGDMPQKER+ IMKEFRSG SRVLI+TDVWARG+DV QVSL
Sbjct:   289 KVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSL 348

Query:   141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
             +INYDLPNNRELYIHRIGRSGR+GRKGVAI+FVK+DDIRILRDIEQYYSTQIDEMPMN
Sbjct:   349 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN 406

GO:0006364 "rRNA processing" evidence=IEA

GO:0051028 "mRNA transport" evidence=IEA

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

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

GO:0016607 "nuclear speck" evidence=IEA

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

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

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

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

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

GO:0005515 "protein binding" evidence=IPI

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

GO:0005524 "ATP binding" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

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

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

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

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

GO:0005829 "cytosol" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

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

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

 Score = 570 (205.7 bits), Expect = 4.2e-96, Sum P(2) = 4.2e-96
 Identities = 107/118 (90%), Positives = 115/118 (97%)

Query:    81 QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
             +VDWLTEKMREANFTVSSMHGDMPQKER+ IMKEFRSG SRVLI+TDVWARG+DV QVSL
Sbjct:   289 KVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSL 348

Query:   141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
             +INYDLPNNRELYIHRIGRSGR+GRKGVAI+FVK+DDIRILRDIEQYYSTQIDEMPMN
Sbjct:   349 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN 406

GO:0016607 "nuclear speck" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0051028 "mRNA transport" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006417 "regulation of translation" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

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

UNIPROTKB|F1RZ83 EIF4A3 "Eukaryotic initiation factor 4A-III" [Sus scrofa (taxid:9823)]

 Score = 570 (205.7 bits), Expect = 4.2e-96, Sum P(2) = 4.2e-96
 Identities = 107/118 (90%), Positives = 115/118 (97%)

Query:    81 QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
             +VDWLTEKMREANFTVSSMHGDMPQKER+ IMKEFRSG SRVLI+TDVWARG+DV QVSL
Sbjct:   289 KVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSL 348

Query:   141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
             +INYDLPNNRELYIHRIGRSGR+GRKGVAI+FVK+DDIRILRDIEQYYSTQIDEMPMN
Sbjct:   349 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN 406

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

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

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

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

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

GO:0005737 "cytoplasm" evidence=IEA

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

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

GO:0005524 "ATP binding" evidence=IEA

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

 Score = 570 (205.7 bits), Expect = 4.2e-96, Sum P(2) = 4.2e-96
 Identities = 107/118 (90%), Positives = 115/118 (97%)

Query:    81 QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
             +VDWLTEKMREANFTVSSMHGDMPQKER+ IMKEFRSG SRVLI+TDVWARG+DV QVSL
Sbjct:   289 KVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSL 348

Query:   141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
             +INYDLPNNRELYIHRIGRSGR+GRKGVAI+FVK+DDIRILRDIEQYYSTQIDEMPMN
Sbjct:   349 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN 406

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

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

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

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

GO:0008380 "RNA splicing" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

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

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

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

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

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

GO:0051028 "mRNA transport" evidence=IEA

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

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

 Score = 555 (200.4 bits), Expect = 1.8e-93, Sum P(2) = 1.8e-93
 Identities = 103/118 (87%), Positives = 114/118 (96%)

Query:    81 QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
             +VDWLT+KM+EANFTVSSMHGDM QK+RD +MKEFR+GT+RVLI+TDVWARG+DV QVSL
Sbjct:   277 KVDWLTDKMKEANFTVSSMHGDMEQKDRDEVMKEFRAGTTRVLISTDVWARGLDVPQVSL 336

Query:   141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
             VINYDLPNNRELYIHRIGRSGRFGRKGVAI+FVK DD+RILRDIEQYYSTQIDEMPMN
Sbjct:   337 VINYDLPNNRELYIHRIGRSGRFGRKGVAINFVKQDDVRILRDIEQYYSTQIDEMPMN 394

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0004386 "helicase activity" evidence=IEA

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

GO:0009790 "embryo development" evidence=IMP

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

GO:0000003 "reproduction" evidence=IMP

GO:0051301 "cell division" evidence=IMP

GO:0000910 "cytokinesis" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

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

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P0CQ72	FAL1_CRYNJ	3, ., 6, ., 4, ., 1, 3	0.8728	0.5619	0.2979	yes	N/A
Q4IAA0	FAL1_GIBZE	3, ., 6, ., 4, ., 1, 3	0.6153	0.8	0.4189	yes	N/A
Q2NL22	IF4A3_BOVIN	3, ., 6, ., 4, ., 1, 3	0.9067	0.5619	0.2871	yes	N/A
Q5VNM3	RH2_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.8898	0.5619	0.2920	yes	N/A
B5FZY7	IF4A3_TAEGU	3, ., 6, ., 4, ., 1, 3	0.9067	0.5619	0.2878	yes	N/A
Q55D61	IF4A_DICDI	3, ., 6, ., 4, ., 1, 3	0.6021	0.8190	0.4246	yes	N/A
O42226	I4A3B_XENLA	3, ., 6, ., 4, ., 1, 3	0.9067	0.5619	0.2850	N/A	N/A
A3GFV3	FAL1_PICST	3, ., 6, ., 4, ., 1, 3	0.7288	0.5619	0.2957	yes	N/A
P41380	IF4A3_NICPL	3, ., 6, ., 4, ., 1, 3	0.9152	0.5619	0.3017	N/A	N/A
A6M931	IF4A3_PIG	3, ., 6, ., 4, ., 1, 3	0.9067	0.5619	0.2871	yes	N/A
Q6BT27	FAL1_DEBHA	3, ., 6, ., 4, ., 1, 3	0.6612	0.5761	0.3032	yes	N/A
Q2UAK1	FAL1_ASPOR	3, ., 6, ., 4, ., 1, 3	0.8728	0.5619	0.2964	yes	N/A
B5DG42	IF4A3_SALSA	3, ., 6, ., 4, ., 1, 3	0.9067	0.5619	0.2906	N/A	N/A
Q91VC3	IF4A3_MOUSE	3, ., 6, ., 4, ., 1, 3	0.9067	0.5619	0.2871	yes	N/A
A5AAE5	FAL1_ASPNC	3, ., 6, ., 4, ., 1, 3	0.8728	0.5619	0.2957	yes	N/A
Q7ZVA6	IF4A3_DANRE	3, ., 6, ., 4, ., 1, 3	0.9067	0.5619	0.2906	yes	N/A
O02494	IF4A_CRYPV	3, ., 6, ., 4, ., 1, 3	0.7413	0.5523	0.2864	yes	N/A
Q12099	FAL1_YEAST	3, ., 6, ., 4, ., 1, 3	0.6694	0.5333	0.2807	yes	N/A
P38919	IF4A3_HUMAN	3, ., 6, ., 4, ., 1, 3	0.9067	0.5619	0.2871	yes	N/A
Q5ZM36	IF4A3_CHICK	3, ., 6, ., 4, ., 1, 3	0.9067	0.5619	0.2864	yes	N/A
B7ZTW1	IF4A3_XENTR	3, ., 6, ., 4, ., 1, 3	0.9067	0.5619	0.2843	yes	N/A
Q4R3Q1	IF4A3_MACFA	3, ., 6, ., 4, ., 1, 3	0.9067	0.5619	0.2871	N/A	N/A
Q6C347	FAL1_YARLI	3, ., 6, ., 4, ., 1, 3	0.5794	0.8	0.4231	yes	N/A
Q10I26	RH34_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.8898	0.5619	0.2920	yes	N/A
Q94A52	RH2_ARATH	3, ., 6, ., 4, ., 1, 3	0.9152	0.5619	0.2892	yes	N/A
Q3B8Q2	IF4A3_RAT	3, ., 6, ., 4, ., 1, 3	0.9067	0.5619	0.2871	yes	N/A
Q10055	FAL1_SCHPO	3, ., 6, ., 4, ., 1, 3	0.6	0.8	0.4263	yes	N/A
Q5AUL4	FAL1_EMENI	3, ., 6, ., 4, ., 1, 3	0.8728	0.5619	0.2957	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4.13	0.914
3rd Layer	3.6.4	0.921

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	210
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	7e-67
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	2e-41
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	3e-38
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	2e-36
cd00268	203	cd00268, DEADc, DEAD-box helicases	3e-36
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	7e-36
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	7e-34
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	3e-32
smart00490	82	smart00490, HELICc, helicase superfamily c-termina	3e-31
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	5e-29
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	3e-26
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	2e-25
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	8e-25
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	8e-25
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	4e-23
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	6e-22
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	4e-20
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	5e-20
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	5e-16
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	5e-16
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	1e-15
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	1e-12
COG0514	590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	2e-11
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	1e-10
COG1111	542	COG1111, MPH1, ERCC4-like helicases [DNA replicati	8e-10
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	1e-09
TIGR01389	591	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	1e-09
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	2e-09
TIGR00643	630	TIGR00643, recG, ATP-dependent DNA helicase RecG	1e-08
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	3e-08
TIGR00614	470	TIGR00614, recQ_fam, ATP-dependent DNA helicase, R	5e-08
COG1205	851	COG1205, COG1205, Distinct helicase family with a	9e-08
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	1e-06
PLN03137	1195	PLN03137, PLN03137, ATP-dependent DNA helicase; Q4	2e-06
COG1200	677	COG1200, RecG, RecG-like helicase [DNA replication	3e-06
PRK13766	773	PRK13766, PRK13766, Hef nuclease; Provisional	4e-06
PRK11057	607	PRK11057, PRK11057, ATP-dependent DNA helicase Rec	4e-06
COG1061	442	COG1061, SSL2, DNA or RNA helicases of superfamily	5e-06
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	3e-05
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	4e-05
PRK10917	681	PRK10917, PRK10917, ATP-dependent DNA helicase Rec	8e-05
COG0553	866	COG0553, HepA, Superfamily II DNA/RNA helicases, S	3e-04
COG0556	663	COG0556, UvrB, Helicase subunit of the DNA excisio	6e-04
PRK09751	1490	PRK09751, PRK09751, putative ATP-dependent helicas	0.002
TIGR00580	926	TIGR00580, mfd, transcription-repair coupling fact	0.002
TIGR00595	505	TIGR00595, priA, primosomal protein N'	0.003
TIGR00631	655	TIGR00631, uvrb, excinuclease ABC, B subunit	0.004

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

 Score =  210 bits (536), Expect = 7e-67
 Identities = 87/117 (74%), Positives = 104/117 (88%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +VD+LT+KM E +FTVS MHGDM QK+RD IM+EFRSG++RVLITTD+ ARGIDVQQVSL
Sbjct: 279 KVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSL 338

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPM 197
           VINYDLP + E YIHRIGRSGRFGRKGVAI+FV  DDI  L++IE++Y+TQI+EMPM
Sbjct: 339 VINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIEQLKEIERHYNTQIEEMPM 395

Length = 401

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

 Score =  146 bits (370), Expect = 2e-41
 Identities = 57/114 (50%), Positives = 83/114 (72%), Gaps = 1/114 (0%)

Query: 82  VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLV 141
           V+ L E +R+  F V+++HGD+PQ+ERD  +++F+ G  RVL+ TDV ARG+D+  VS V
Sbjct: 286 VEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHV 345

Query: 142 INYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSD-DIRILRDIEQYYSTQIDE 194
           INYDLP + E Y+HRIGR+GR GRKGVAISFV  + +++ L+ IE+    ++  
Sbjct: 346 INYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVKKLKRIEKRLERKLPS 399

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 =  128 bits (324), Expect = 3e-38
 Identities = 56/134 (41%), Positives = 81/134 (60%), Gaps = 4/134 (2%)

Query: 39  IRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVDWLTEKMREANFTVSS 98
           I++ VL   + K+  L E    L K   ++   V  + P    +D L E +R+    V++
Sbjct: 2   IKQYVLPVEDEKLEALLE----LLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAA 57

Query: 99  MHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIG 158
           +HGD  Q+ER+ ++K+FR G   VL+ TDV ARGID+  VS+VINYDLP +   Y+ RIG
Sbjct: 58  LHGDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIG 117

Query: 159 RSGRFGRKGVAISF 172
           R+GR G+KG AI  
Sbjct: 118 RAGRAGQKGTAILL 131

Length = 131

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

 Score =  131 bits (332), Expect = 2e-36
 Identities = 47/103 (45%), Positives = 66/103 (64%)

Query: 85  LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINY 144
           L   +R+A      + G+M Q +R+  +K    G   VL+ TDV ARGID+  VS VIN+
Sbjct: 261 LAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINF 320

Query: 145 DLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQY 187
           D+P + + Y+HRIGR+GR GRKG AIS V++ D  +L  IE+Y
Sbjct: 321 DMPRSADTYLHRIGRTGRAGRKGTAISLVEAHDHLLLGKIERY 363

Length = 434

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

 Score =  125 bits (317), Expect = 3e-36
 Identities = 34/82 (41%), Positives = 51/82 (62%)

Query: 1   MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEM 60
            N++     GGT++ + +RKL  G H+V  TPGR+ D++ R  L    +K LVLDEAD M
Sbjct: 96  TNLKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRM 155

Query: 61  LNKGFKEQIYDVYRYLPPATQV 82
           L+ GF++QI ++ + LP   Q 
Sbjct: 156 LDMGFEDQIREILKLLPKDRQT 177

A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region. Length = 203

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

 Score =  130 bits (329), Expect = 7e-36
 Identities = 42/127 (33%), Positives = 77/127 (60%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +   + + +    F+  ++HGD+ Q++RD ++  F + +  VL+ TDV ARG+D++ +  
Sbjct: 254 ECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEA 313

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGK 200
           VINY+L  + E+++HRIGR+GR G KG+A+S V  ++++    IE Y   +++  P+   
Sbjct: 314 VINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQRANAIEDYLGRKLNWEPLPSL 373

Query: 201 RSLHSYP 207
             L   P
Sbjct: 374 SPLSGVP 380

Length = 460

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

 Score =  124 bits (312), Expect = 7e-34
 Identities = 49/89 (55%), Positives = 67/89 (75%)

Query: 1   MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEM 60
           + V+CHAC+GGT + +D+ KL  G H+V GTPGRV+DMI +R LR  ++K+ +LDEADEM
Sbjct: 123 LKVRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEM 182

Query: 61  LNKGFKEQIYDVYRYLPPATQVDWLTEKM 89
           L++GFK QIYDV++ LPP  QV   +  M
Sbjct: 183 LSRGFKGQIYDVFKKLPPDVQVALFSATM 211

Length = 401

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

 Score =  111 bits (280), Expect = 3e-32
 Identities = 40/78 (51%), Positives = 57/78 (73%)

Query: 87  EKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDL 146
           + +R+    V+ +HG + Q+ER+ I+++FR+G S+VL+ TDV  RGID+  V+LVINYDL
Sbjct: 1   KLLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDL 60

Query: 147 PNNRELYIHRIGRSGRFG 164
           P N   YI RIGR+GR G
Sbjct: 61  PWNPASYIQRIGRAGRAG 78

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|197757 smart00490, HELICc, helicase superfamily c-terminal domain

 Score =  109 bits (274), Expect = 3e-31
 Identities = 37/82 (45%), Positives = 54/82 (65%)

Query: 83  DWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVI 142
           + L E ++E    V+ +HG + Q+ER+ I+ +F +G  +VL+ TDV  RG+D+  V LVI
Sbjct: 1   EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60

Query: 143 NYDLPNNRELYIHRIGRSGRFG 164
            YDLP +   YI RIGR+GR G
Sbjct: 61  IYDLPWSPASYIQRIGRAGRAG 82

Length = 82

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

 Score =  112 bits (282), Expect = 5e-29
 Identities = 46/102 (45%), Positives = 70/102 (68%)

Query: 83  DWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVI 142
           D+LT+++R   +    +HGD  Q+ER  ++ EF++G S ++I TDV +RG+DV+ V  VI
Sbjct: 391 DFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVI 450

Query: 143 NYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDI 184
           N+D PN  E Y+HRIGR+GR G KG + +F+  D  R+ RD+
Sbjct: 451 NFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYRLARDL 492

Length = 545

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

 Score =  103 bits (260), Expect = 3e-26
 Identities = 41/92 (44%), Positives = 56/92 (60%)

Query: 101 GDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRS 160
           GD+ QK+R  I++EF  G   +L+ TDV ARG+ +  V+ V NYDLP++ E Y+HRIGR+
Sbjct: 287 GDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRT 346

Query: 161 GRFGRKGVAISFVKSDDIRILRDIEQYYSTQI 192
           GR G  G +IS    +    L  IE Y    I
Sbjct: 347 GRAGASGHSISLACEEYALNLPAIETYIGHSI 378

Length = 423

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

 Score =  102 bits (255), Expect = 2e-25
 Identities = 45/115 (39%), Positives = 74/115 (64%)

Query: 85  LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINY 144
           L E++ +     +++HG+  Q  R   + +F+SG  RVL+ TD+ ARG+D++++  V+NY
Sbjct: 261 LAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHVVNY 320

Query: 145 DLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNG 199
           +LPN  E Y+HRIGR+GR    G A+S V  D+ ++LRDIE+    +I  + + G
Sbjct: 321 ELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEHKLLRDIEKLLKKEIPRIAIPG 375

Length = 456

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

 Score =  100 bits (250), Expect = 8e-25
 Identities = 48/117 (41%), Positives = 71/117 (60%), Gaps = 1/117 (0%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +V  + E++ +     + + GD+PQ +R   ++ FR G  RVL+ TDV  RGI +  +S 
Sbjct: 347 EVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISH 406

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQID-EMP 196
           VIN+ LP + + Y+HRIGR+GR G  GV+ISF   DD   L +IE+    +I  EMP
Sbjct: 407 VINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGEDDAFQLPEIEELLGRKISCEMP 463

Length = 475

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

 Score =  101 bits (252), Expect = 8e-25
 Identities = 51/128 (39%), Positives = 82/128 (64%), Gaps = 5/128 (3%)

Query: 87  EKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDL 146
           E +    +  ++++GDM Q  R+  ++  + G   +LI TDV ARG+DV+++SLV+NYD+
Sbjct: 263 EALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDI 322

Query: 147 PNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN-----GKR 201
           P + E Y+HRIGR+GR GR G A+ FV++ + R+LR+IE+     I E+ +      GKR
Sbjct: 323 PMDSESYVHRIGRTGRAGRAGRALLFVENRERRLLRNIERTMKLTIPEVELPNAELLGKR 382

Query: 202 SLHSYPAR 209
            L  + A+
Sbjct: 383 RLEKFAAK 390

Length = 629

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

 Score = 95.6 bits (238), Expect = 4e-23
 Identities = 29/81 (35%), Positives = 45/81 (55%)

Query: 2   NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEML 61
            ++     GG ++ + +  L  G  +V  TPGR+ D+I+R  L    ++ LVLDEAD ML
Sbjct: 128 GLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEADRML 187

Query: 62  NKGFKEQIYDVYRYLPPATQV 82
           + GF + I  + + LPP  Q 
Sbjct: 188 DMGFIDDIEKILKALPPDRQT 208

Length = 513

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

 Score = 92.7 bits (230), Expect = 6e-22
 Identities = 45/116 (38%), Positives = 66/116 (56%)

Query: 82  VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLV 141
           V+ +   +    + V  + GD+PQK+R+ ++  F+ G   +L+ TDV ARG+ +  V  V
Sbjct: 270 VERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYV 329

Query: 142 INYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPM 197
            NYDLP + E Y+HRIGR+ R G +G AISF        L DIE Y   +I   P+
Sbjct: 330 YNYDLPFDAEDYVHRIGRTARLGEEGDAISFACERYAMSLPDIEAYIEQKIPVEPV 385

Length = 572

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

 Score = 82.7 bits (205), Expect = 4e-20
 Identities = 33/84 (39%), Positives = 54/84 (64%), Gaps = 2/84 (2%)

Query: 1   MNVQCHACIGGTNLSEDLRKLDYGQ-HVVSGTPGRVFDMIRRRVLRT-RNIKMLVLDEAD 58
           + ++     GGT+L E  RKL  G+  ++ GTPGR+ D++RR  L+  +N+K+LVLDEA 
Sbjct: 72  LGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKLKLLKNLKLLVLDEAH 131

Query: 59  EMLNKGFKEQIYDVYRYLPPATQV 82
            +L+ GF + + ++   LPP  Q+
Sbjct: 132 RLLDMGFGDDLEEILSRLPPDRQI 155

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

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

 Score = 86.8 bits (215), Expect = 5e-20
 Identities = 45/136 (33%), Positives = 69/136 (50%), Gaps = 12/136 (8%)

Query: 63  KGFKEQIYDVY----RYLPPAT-------QVDWLTEKMREAN-FTVSSMHGDMPQKERDG 110
           K  K++++D+      + PPA          D L   +         S+HG+   KER  
Sbjct: 350 KQKKQKLFDILKSKQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERRE 409

Query: 111 IMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAI 170
           +MK F  G   V++ T V  RG+D+ +V  VI +D+PN  + YIH+IGR+ R G KG AI
Sbjct: 410 VMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAI 469

Query: 171 SFVKSDDIRILRDIEQ 186
            FV  +D  +  ++  
Sbjct: 470 VFVNEEDRNLFPELVA 485

Length = 518

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

 Score = 71.6 bits (176), Expect = 5e-16
 Identities = 27/81 (33%), Positives = 43/81 (53%)

Query: 2   NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEML 61
            ++    IGGT++ +  + L     +V GTPGR+ D + R  L  + + +L+LDEA  +L
Sbjct: 57  GIKVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLL 116

Query: 62  NKGFKEQIYDVYRYLPPATQV 82
           N+GF      +   LP   QV
Sbjct: 117 NQGFGLLGLKILLKLPKDRQV 137

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

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

 Score = 72.5 bits (178), Expect = 5e-16
 Identities = 26/83 (31%), Positives = 48/83 (57%), Gaps = 1/83 (1%)

Query: 1   MNVQCHACIGGTNLSEDLRKLDYGQ-HVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADE 59
           + ++     GG +  E LRKL+ G+  ++  TPGR+ D++    L   N+ +++LDEA  
Sbjct: 81  LGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHR 140

Query: 60  MLNKGFKEQIYDVYRYLPPATQV 82
           +L+ GF +Q+  + + LP   Q+
Sbjct: 141 LLDGGFGDQLEKLLKLLPKNVQL 163

Length = 201

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

 Score = 74.5 bits (184), Expect = 1e-15
 Identities = 28/72 (38%), Positives = 42/72 (58%)

Query: 10  GGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQI 69
           GG  +   +  L++G H++ GTPGR+ D +R+  L    +  LVLDEAD ML+ GF++ I
Sbjct: 109 GGVPMGPQIDSLEHGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMGFQDAI 168

Query: 70  YDVYRYLPPATQ 81
             + R  P   Q
Sbjct: 169 DAIIRQAPARRQ 180

Length = 460

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

 Score = 65.3 bits (159), Expect = 1e-12
 Identities = 38/107 (35%), Positives = 50/107 (46%)

Query: 2   NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEML 61
            V   A  GG      LR L  G  +V GTPGR+ D ++R  L    +  LVLDEADEML
Sbjct: 103 GVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEML 162

Query: 62  NKGFKEQIYDVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKER 108
             GF E +  +   +P   Q    +  M EA   ++      PQ+ R
Sbjct: 163 RMGFIEDVETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEPQEVR 209

Length = 629

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

 Score = 61.9 bits (151), Expect = 2e-11
 Identities = 33/102 (32%), Positives = 54/102 (52%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +V+ L E +R+   +  + H  +  +ER+ + + F +   +V++ T+ +  GID   V  
Sbjct: 242 KVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRF 301

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILR 182
           VI+YDLP + E Y    GR+GR G    AI     +DIR  R
Sbjct: 302 VIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSPEDIRWQR 343

Length = 590

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

 Score = 59.8 bits (145), Expect = 1e-10
 Identities = 23/69 (33%), Positives = 44/69 (63%)

Query: 9   IGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQ 68
           +GG  + + L ++  G  ++ GTPGR+ D++ +  +   N+ +LVLDE D ML +GF++Q
Sbjct: 231 VGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDNVSVLVLDEVDCMLERGFRDQ 290

Query: 69  IYDVYRYLP 77
           +  +++ L 
Sbjct: 291 VMQIFQALS 299

Length = 518

>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication, recombination, and repair]

 Score = 57.4 bits (139), Expect = 8e-10
 Identities = 39/105 (37%), Positives = 53/105 (50%), Gaps = 9/105 (8%)

Query: 103 MPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNREL-YIHRIGRSG 161
           M QKE+  I+ +FR G   VL+ T V   G+D+ +V LVI Y+ P   E+  I R GR+G
Sbjct: 409 MSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYE-PVPSEIRSIQRKGRTG 467

Query: 162 RFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRSLHSY 206
           R  RKG  +  V        RD   YYS++  E  M    S+   
Sbjct: 468 R-KRKGRVVVLVTEGT----RDEAYYYSSRRKEQKM--IESIRGL 505

Length = 542

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

 Score = 56.9 bits (138), Expect = 1e-09
 Identities = 26/72 (36%), Positives = 43/72 (59%)

Query: 10  GGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQI 69
           GG    + L+ L+ G  ++ GT GR+ D  ++  +    I+++VLDEAD M + GF + I
Sbjct: 119 GGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEADRMFDLGFIKDI 178

Query: 70  YDVYRYLPPATQ 81
             ++R +PPA Q
Sbjct: 179 RWLFRRMPPANQ 190

Length = 423

>gnl|CDD|130456 TIGR01389, recQ, ATP-dependent DNA helicase RecQ

 Score = 56.6 bits (137), Expect = 1e-09
 Identities = 34/107 (31%), Positives = 53/107 (49%), Gaps = 1/107 (0%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +V+ L E++     +  + H  +  K R    ++F     +V++ T+ +  GID   V  
Sbjct: 236 KVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRF 295

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRD-IEQ 186
           VI+YD+P N E Y    GR+GR G    AI      DI +L+  IEQ
Sbjct: 296 VIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSPADIALLKRRIEQ 342

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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 591

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

 Score = 56.0 bits (135), Expect = 2e-09
 Identities = 27/72 (37%), Positives = 41/72 (56%)

Query: 10  GGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQI 69
           GG +++  + KL  G  V+  TPGR+ D+  +  ++   +++LVLDEAD ML+ GF   I
Sbjct: 111 GGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRMLDMGFIHDI 170

Query: 70  YDVYRYLPPATQ 81
             V   LP   Q
Sbjct: 171 RRVLAKLPAKRQ 182

Length = 456

>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG

 Score = 53.9 bits (130), Expect = 1e-08
 Identities = 32/131 (24%), Positives = 49/131 (37%), Gaps = 23/131 (17%)

Query: 54  LDEADEMLNKGFKE--QIYDVY------RYLPPATQVD-WLTEKMREANFTVSSMHGDMP 104
            D   E + +   +  Q Y VY        L        +   K     + V  +HG M 
Sbjct: 434 KDIVYEFIEEEIAKGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMK 493

Query: 105 QKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRS---- 160
             E++ +M+EFR G   +L+ T V   G+DV   ++++  D          R G S    
Sbjct: 494 SDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIED--------AERFGLSQLHQ 545

Query: 161 --GRFGRKGVA 169
             GR GR    
Sbjct: 546 LRGRVGRGDHQ 556

[DNA metabolism, DNA replication, recombination, and repair]. Length = 630

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

 Score = 52.6 bits (126), Expect = 3e-08
 Identities = 28/94 (29%), Positives = 50/94 (53%), Gaps = 6/94 (6%)

Query: 9   IGGTNLSEDLRKLDYGQH--VVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFK 66
           +GG +  + L++L+  +   ++  TPGR+ D  +R  +    ++++VLDEAD ML+ GF 
Sbjct: 197 VGGMDFDKQLKQLE-ARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLDEADRMLDMGFI 255

Query: 67  EQIYDVYRYLPPATQVDWLTEKMREANFTVSSMH 100
            Q+  + R  P   +   L   +  A FT   M+
Sbjct: 256 PQVRQIIRQTPRKEERQTL---LFSATFTDDVMN 286

Length = 475

>gnl|CDD|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family

 Score = 51.7 bits (124), Expect = 5e-08
 Identities = 33/132 (25%), Positives = 58/132 (43%), Gaps = 2/132 (1%)

Query: 53  VLDEADEMLNKGFKEQIYDVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIM 112
           +L++    + K FK +   +Y   P   + + +T  ++       + H  +    RD + 
Sbjct: 212 ILEDLLRFIRKEFKGKSGIIY--CPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVH 269

Query: 113 KEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISF 172
            +F+    +V++ T  +  GI+   V  VI+Y LP + E Y    GR+GR G       F
Sbjct: 270 HKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECHLF 329

Query: 173 VKSDDIRILRDI 184
               DI  LR +
Sbjct: 330 YAPADINRLRRL 341

All proteins in this family for which functions are known are 3'-5' DNA-DNA helicases. These proteins are used for recombination, recombinational repair, and possibly maintenance of chromosome stability. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 470

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

 Score = 51.3 bits (123), Expect = 9e-08
 Identities = 31/110 (28%), Positives = 49/110 (44%), Gaps = 11/110 (10%)

Query: 96  VSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNREL-YI 154
           VS+    + ++ER  I  EF+ G    +I T+    GID+  +  VI Y  P    L + 
Sbjct: 341 VSTYRAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGYPGVSVLSFR 400

Query: 155 HRIGRSGRFGRKGVAISFVKSDDIRILRD--IEQYYSTQIDEMPMNGKRS 202
            R GR+GR  R   ++  V      +LR   ++ YY    +E+   G   
Sbjct: 401 QRAGRAGR--RGQESLVLV------VLRSDPLDSYYLRHPEELLETGFGP 442

Length = 851

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

 Score = 48.2 bits (115), Expect = 1e-06
 Identities = 23/65 (35%), Positives = 32/65 (49%), Gaps = 1/65 (1%)

Query: 6   HACI-GGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKG 64
           +    GG      +  L  G  ++   PGR+ D +   V   R +  LVLDEAD ML+ G
Sbjct: 234 NTVAYGGVPKRGQIYALRRGVEILIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLDMG 293

Query: 65  FKEQI 69
           F+ QI
Sbjct: 294 FEPQI 298

Length = 545

>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like; Provisional

 Score = 47.2 bits (112), Expect = 2e-06
 Identities = 31/114 (27%), Positives = 54/114 (47%), Gaps = 4/114 (3%)

Query: 85  LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINY 144
           + E+++E     +  HG M   +R  + K++      ++  T  +  GI+   V  VI++
Sbjct: 696 VAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHH 755

Query: 145 DLPNNRELYIHRIGRSGRFG-RKGVAISFVKSDDIRILRDIEQYYSTQIDEMPM 197
            LP + E Y    GR+GR G R    + +  SD IR+   I Q     +++ PM
Sbjct: 756 SLPKSIEGYHQECGRAGRDGQRSSCVLYYSYSDYIRVKHMISQ---GGVEQSPM 806

Length = 1195

>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination, and repair / Transcription]

 Score = 46.8 bits (112), Expect = 3e-06
 Identities = 21/84 (25%), Positives = 36/84 (42%), Gaps = 14/84 (16%)

Query: 92  ANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRE 151
               V  +HG M   E+D +M+ F+ G   +L+ T V   G+DV   ++++  +      
Sbjct: 506 PELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVDVPNATVMVIEN------ 559

Query: 152 LYIHRIGRS------GRFGRKGVA 169
               R G +      GR GR  + 
Sbjct: 560 --AERFGLAQLHQLRGRVGRGDLQ 581

Length = 677

>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional

 Score = 46.4 bits (111), Expect = 4e-06
 Identities = 36/103 (34%), Positives = 53/103 (51%), Gaps = 9/103 (8%)

Query: 103 MPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNREL-YIHRIGRSG 161
           M QKE+  I+ +FR+G   VL++T V   G+D+  V LVI Y+ P   E+  I R GR+G
Sbjct: 407 MSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYE-PVPSEIRSIQRKGRTG 465

Query: 162 RFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRSLH 204
           R   +G  +  +        RD   Y+S++  E  M  K  L 
Sbjct: 466 R-QEEGRVVVLIAKGT----RDEAYYWSSRRKEKKM--KEELK 501

Length = 773

>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional

 Score = 46.2 bits (110), Expect = 4e-06
 Identities = 24/103 (23%), Positives = 49/103 (47%)

Query: 80  TQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVS 139
            +V+    +++    + ++ H  +    R  + + F+    ++++ T  +  GI+   V 
Sbjct: 247 AKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVR 306

Query: 140 LVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILR 182
            V+++D+P N E Y    GR+GR G    A+ F    D+  LR
Sbjct: 307 FVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLR 349

Length = 607

>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]

 Score = 45.9 bits (109), Expect = 5e-06
 Identities = 26/108 (24%), Positives = 51/108 (47%), Gaps = 3/108 (2%)

Query: 96  VSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIH 155
           V ++ G+ P++ER+ I++ FR+G  +VL+T  V   G+D+    ++I      +R L+I 
Sbjct: 309 VEAITGETPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLIILRPTGSRRLFIQ 368

Query: 156 RIGRSGR-FGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRS 202
           R+GR  R    K   ++   S         E+  + +     +    +
Sbjct: 369 RLGRGLRPAEGKEDTLALDYSLVPD--DLGEEDIARRRRLFLIRKGYT 414

Length = 442

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

 Score = 43.8 bits (104), Expect = 3e-05
 Identities = 21/60 (35%), Positives = 29/60 (48%)

Query: 10  GGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQI 69
           GG             Q +V  TPGR+   I+      R ++ L+LDEAD ML+ GF + I
Sbjct: 109 GGVAYMNHAEVFSENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRMLDMGFAQDI 168

Length = 434

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

 Score = 43.4 bits (102), Expect = 4e-05
 Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 1/69 (1%)

Query: 10  GGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRR-RVLRTRNIKMLVLDEADEMLNKGFKEQ 68
           GG +  +    L  G  V+  TPGR+ D +++ +V+     ++ VLDEAD M + GF + 
Sbjct: 120 GGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFDLGFIKD 179

Query: 69  IYDVYRYLP 77
           I  + R +P
Sbjct: 180 IRFLLRRMP 188

Length = 572

>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional

 Score = 42.4 bits (101), Expect = 8e-05
 Identities = 14/37 (37%), Positives = 22/37 (59%)

Query: 99  MHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDV 135
           +HG M   E+D +M  F++G   +L+ T V   G+DV
Sbjct: 511 LHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDV 547

Length = 681

>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]

 Score = 40.9 bits (95), Expect = 3e-04
 Identities = 27/135 (20%), Positives = 56/135 (41%), Gaps = 7/135 (5%)

Query: 36  FDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQ--IYDVYRYLPPATQVDWLTEKMREAN 93
           FD +++ +++    K+  LDE   +L     E+   + V  +      +D L + ++   
Sbjct: 679 FDYLKKPLIQLSKGKLQALDE---LLLDKLLEEGHYHKVLIFSQFTPVLDLLEDYLKALG 735

Query: 94  FTVSSMHGDMPQKERDGIMKEFRSGTSR--VLITTDVWARGIDVQQVSLVINYDLPNNRE 151
                + G  P K R  ++  F +       L++      G+++     VI +D   N  
Sbjct: 736 IKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLKAGGLGLNLTGADTVILFDPWWNPA 795

Query: 152 LYIHRIGRSGRFGRK 166
           + +  I R+ R G+K
Sbjct: 796 VELQAIDRAHRIGQK 810

Length = 866

>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]

 Score = 39.9 bits (94), Expect = 6e-04
 Identities = 29/84 (34%), Positives = 44/84 (52%), Gaps = 7/84 (8%)

Query: 85  LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINY 144
           LTE ++E    V  +H D+   ER  I+++ R G   VL+  ++   G+D+ +VSLV   
Sbjct: 462 LTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAIL 521

Query: 145 D------LPNNRELYIHRIGRSGR 162
           D      L + R L I  IGR+ R
Sbjct: 522 DADKEGFLRSERSL-IQTIGRAAR 544

Length = 663

>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr; Provisional

 Score = 38.8 bits (90), Expect = 0.002
 Identities = 22/68 (32%), Positives = 34/68 (50%)

Query: 94  FTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELY 153
           F   S HG + +++R    +  +SG  R ++ T     GID+  V LVI    P +    
Sbjct: 302 FIARSHHGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASG 361

Query: 154 IHRIGRSG 161
           + RIGR+G
Sbjct: 362 LQRIGRAG 369

Length = 1490

>gnl|CDD|233032 TIGR00580, mfd, transcription-repair coupling factor (mfd)

 Score = 38.5 bits (90), Expect = 0.002
 Identities = 25/72 (34%), Positives = 36/72 (50%), Gaps = 3/72 (4%)

Query: 100 HGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVI--NYDLPNNRELYIHRI 157
           HG M + E + +M EF  G  +VL+ T +   GID+   + +I    D     +LY  R 
Sbjct: 693 HGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLR- 751

Query: 158 GRSGRFGRKGVA 169
           GR GR  +K  A
Sbjct: 752 GRVGRSKKKAYA 763

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 transcribed 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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 926

>gnl|CDD|233040 TIGR00595, priA, primosomal protein N'

 Score = 37.7 bits (88), Expect = 0.003
 Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 12/78 (15%)

Query: 105 QKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL--VINYD----LPNNR------EL 152
           +   + ++ +F +G + +LI T + A+G     V+L  V++ D     P+ R      +L
Sbjct: 298 KGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQL 357

Query: 153 YIHRIGRSGRFGRKGVAI 170
                GR+GR    G  I
Sbjct: 358 LTQVAGRAGRAEDPGQVI 375

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) [DNA metabolism, DNA replication, recombination, and repair]. Length = 505

>gnl|CDD|233063 TIGR00631, uvrb, excinuclease ABC, B subunit

 Score = 37.3 bits (87), Expect = 0.004
 Identities = 27/84 (32%), Positives = 44/84 (52%), Gaps = 7/84 (8%)

Query: 85  LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINY 144
           LT+ ++E    V  +H ++   ER  I+++ R G   VL+  ++   G+D+ +VSLV   
Sbjct: 458 LTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAIL 517

Query: 145 D------LPNNRELYIHRIGRSGR 162
           D      L + R L I  IGR+ R
Sbjct: 518 DADKEGFLRSERSL-IQTIGRAAR 540

All proteins in this family for wich functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 655

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	210
KOG0328|consensus	400		100.0
KOG0330|consensus	476		100.0
KOG0331|consensus	519		100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
KOG0326|consensus	459		100.0
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0333|consensus	673		100.0
PTZ00110	545	helicase; Provisional	100.0
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	100.0
KOG0342|consensus	543		100.0
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	100.0
KOG0336|consensus	629		100.0
KOG0341|consensus	610		100.0
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	100.0
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	100.0
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	100.0
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0338|consensus	691		100.0
KOG0335|consensus	482		100.0
KOG0340|consensus	442		100.0
KOG0345|consensus	567		100.0
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	100.0
PTZ00424	401	helicase 45; Provisional	100.0
KOG0339|consensus	731		100.0
KOG0343|consensus	758		100.0
KOG0348|consensus	708		100.0
KOG0347|consensus	731		100.0
KOG0327|consensus	397		100.0
KOG4284|consensus	980		100.0
KOG0350|consensus	620		100.0
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	100.0
KOG0332|consensus	477		99.98
KOG0334|consensus	997		99.97
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.97
KOG0346|consensus	569		99.97
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.97
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.97
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.97
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.97
KOG0337|consensus	529		99.96
KOG0344|consensus	593		99.96
KOG0329|consensus	387		99.96
PRK13767	876	ATP-dependent helicase; Provisional	99.96
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.96
KOG0349|consensus	725		99.95
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.94
PRK02362	737	ski2-like helicase; Provisional	99.94
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.94
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.94
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.93
PRK10689	1147	transcription-repair coupling factor; Provisional	99.93
PRK00254	720	ski2-like helicase; Provisional	99.93
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.92
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.92
PRK01172	674	ski2-like helicase; Provisional	99.91
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.91
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.9
KOG0351|consensus	941		99.9
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.89
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.89
PHA02653	675	RNA helicase NPH-II; Provisional	99.88
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.88
PHA02558	501	uvsW UvsW helicase; Provisional	99.88
PRK13766	773	Hef nuclease; Provisional	99.87
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.86
KOG0352|consensus	641		99.86
PRK14701	1638	reverse gyrase; Provisional	99.85
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	99.85
COG1204	766	Superfamily II helicase [General function predicti	99.85
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.85
PRK09401	1176	reverse gyrase; Reviewed	99.85
COG1202	830	Superfamily II helicase, archaea-specific [General	99.85
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.84
KOG0354|consensus	746		99.84
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.84
PRK05580	679	primosome assembly protein PriA; Validated	99.83
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.82
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.8
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.79
PRK04914	956	ATP-dependent helicase HepA; Validated	99.78
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.77
smart00490	82	HELICc helicase superfamily c-terminal domain.	99.76
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.76
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.75
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.75
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	99.74
KOG0353|consensus	695		99.74
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.73
COG1205	851	Distinct helicase family with a unique C-terminal	99.73
PRK05298	652	excinuclease ABC subunit B; Provisional	99.73
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.72
KOG0952|consensus	1230		99.69
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	99.65
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.63
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.61
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.61
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.57
KOG0951|consensus	1674		99.56
KOG0953|consensus	700		99.53
KOG0385|consensus	971		99.52
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.49
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	99.48
PRK09694	878	helicase Cas3; Provisional	99.48
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	99.47
KOG0947|consensus	1248		99.47
KOG0950|consensus	1008		99.47
KOG0948|consensus	1041		99.4
COG1198	730	PriA Primosomal protein N' (replication factor Y)	99.36
KOG0384|consensus	1373		99.35
KOG0949|consensus	1330		99.35
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	99.35
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.32
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.31
KOG0922|consensus	674		99.28
KOG4150|consensus	1034		99.25
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	99.21
KOG0923|consensus	902		99.13
KOG0387|consensus	923		99.09
KOG0920|consensus	924		99.09
PRK12326	764	preprotein translocase subunit SecA; Reviewed	99.06
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.03
KOG0389|consensus	941		99.01
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.0
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	99.0
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	98.97
KOG0924|consensus	1042		98.95
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	98.94
KOG0390|consensus	776		98.84
KOG1123|consensus	776		98.83
COG4889	1518	Predicted helicase [General function prediction on	98.73
KOG1002|consensus	791		98.7
KOG0386|consensus	1157		98.68
KOG0392|consensus	1549		98.67
KOG0926|consensus	1172		98.66
CHL00122	870	secA preprotein translocase subunit SecA; Validate	98.65
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	98.62
COG4096	875	HsdR Type I site-specific restriction-modification	98.54
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	98.53
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	98.44
KOG1000|consensus	689		98.34
KOG0925|consensus	699		98.33
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	98.29
KOG0951|consensus	1674		98.29
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	98.26
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	98.17
KOG0388|consensus	1185		98.08
smart00487	201	DEXDc DEAD-like helicases superfamily.	97.91
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	97.84
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	97.72
PF13871	278	Helicase_C_4: Helicase_C-like	97.68
PF13307	167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	97.65
smart00491	142	HELICc2 helicase superfamily c-terminal domain.	97.64
KOG0391|consensus	1958		97.64
smart00492	141	HELICc3 helicase superfamily c-terminal domain.	97.62
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	97.49
KOG2340|consensus	698		97.49
PRK14873	665	primosome assembly protein PriA; Provisional	97.49
KOG4439|consensus	901		97.47
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	97.43
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	97.29
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	97.28
KOG1015|consensus	1567		97.2
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	97.0
KOG0921|consensus	1282		96.96
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	96.88
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	96.18
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	96.14
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	96.13
KOG0701|consensus	1606		96.07
PF10593	239	Z1: Z1 domain; InterPro: IPR018310 This entry repr	95.54
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	95.25
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	95.19
KOG1513|consensus	1300		94.99
KOG3089|consensus	271		94.55
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	94.44
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	94.35
PRK09401	1176	reverse gyrase; Reviewed	94.14
KOG1016|consensus	1387		93.54
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	93.35
KOG1001|consensus	674		93.17
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	93.13
PRK05580	679	primosome assembly protein PriA; Validated	92.73
TIGR00595	505	priA primosomal protein N'. All proteins in this f	92.01
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	91.98
PF06733	174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	91.78
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	91.71
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	91.42
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	91.14
PRK14873	665	primosome assembly protein PriA; Provisional	90.47
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	89.91
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	89.91
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	88.83
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	88.61
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	87.79
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	87.47
KOG1133|consensus	821		87.26
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	86.64
KOG0339|consensus	731		85.72
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	84.69
COG3587	985	Restriction endonuclease [Defense mechanisms]	84.52
PRK10689	1147	transcription-repair coupling factor; Provisional	83.68
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	83.52
COG1198	730	PriA Primosomal protein N' (replication factor Y)	82.82
PF05872	502	DUF853: Bacterial protein of unknown function (DUF	82.71
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	82.56
KOG0391|consensus	1958		81.17
smart00490	82	HELICc helicase superfamily c-terminal domain.	80.5
KOG0952|consensus	1230		80.06

>KOG0328|consensus

Probab=100.00  E-value=9.2e-45  Score=274.50  Aligned_cols=201  Identities=89%  Similarity=1.383  Sum_probs=196.1

Q ss_pred             CCceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCch
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPAT   80 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~   80 (210)
                      |||+|+.++||.+..+.++.+.-|.+++.||||++.+++.++.+..+.++++|+||||.|++.+|.+++..++.++|+..
T Consensus       122 mnvq~hacigg~n~gedikkld~G~hvVsGtPGrv~dmikr~~L~tr~vkmlVLDEaDemL~kgfk~Qiydiyr~lp~~~  201 (400)
T KOG0328|consen  122 MNVQCHACIGGKNLGEDIKKLDYGQHVVSGTPGRVLDMIKRRSLRTRAVKMLVLDEADEMLNKGFKEQIYDIYRYLPPGA  201 (400)
T ss_pred             ccceEEEEecCCccchhhhhhcccceEeeCCCchHHHHHHhccccccceeEEEeccHHHHHHhhHHHHHHHHHHhCCCCc
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999888


Q ss_pred             h----------------------------------------------------------------------------HHH
Q psy6712          81 Q----------------------------------------------------------------------------VDW   84 (210)
Q Consensus        81 ~----------------------------------------------------------------------------~~~   84 (210)
                      |                                                                            ++|
T Consensus       202 Qvv~~SATlp~eilemt~kfmtdpvrilvkrdeltlEgIKqf~v~ve~EewKfdtLcdLYd~LtItQavIFcnTk~kVdw  281 (400)
T KOG0328|consen  202 QVVLVSATLPHEILEMTEKFMTDPVRILVKRDELTLEGIKQFFVAVEKEEWKFDTLCDLYDTLTITQAVIFCNTKRKVDW  281 (400)
T ss_pred             eEEEEeccCcHHHHHHHHHhcCCceeEEEecCCCchhhhhhheeeechhhhhHhHHHHHhhhhehheEEEEecccchhhH
Confidence            8                                                                            899


Q ss_pred             HHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCC
Q psy6712          85 LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFG  164 (210)
Q Consensus        85 l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g  164 (210)
                      |.+.+++.++.+..+||+|++++|.+++..|+.|+.++|++|+..++|+|+|.+++|||||+|.+...|+||+||.||.|
T Consensus       282 Ltekm~~~nftVssmHGDm~qkERd~im~dFRsg~SrvLitTDVwaRGiDv~qVslviNYDLP~nre~YIHRIGRSGRFG  361 (400)
T KOG0328|consen  282 LTEKMREANFTVSSMHGDMEQKERDKIMNDFRSGKSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFG  361 (400)
T ss_pred             HHHHHHhhCceeeeccCCcchhHHHHHHHHhhcCCceEEEEechhhccCCcceeEEEEecCCCccHHHHhhhhccccccC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CceeEEEEeccCcHHHHHHHHHHhcCccccccCCccc
Q psy6712         165 RKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKR  201 (210)
Q Consensus       165 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  201 (210)
                      +.|.++-|+..++...++.++++++..+.++|++.-.
T Consensus       362 RkGvainFVk~~d~~~lrdieq~yst~i~emp~nvad  398 (400)
T KOG0328|consen  362 RKGVAINFVKSDDLRILRDIEQYYSTQIDEMPMNVAD  398 (400)
T ss_pred             CcceEEEEecHHHHHHHHHHHHHHhhhcccccchhhh
Confidence            9999999999999999999999999999999998654

>KOG0330|consensus

Probab=100.00  E-value=2.7e-44  Score=281.89  Aligned_cols=199  Identities=32%  Similarity=0.646  Sum_probs=190.6

Q ss_pred             CCceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHh-cCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCc
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRR-RVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPA   79 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~-~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~   79 (210)
                      +|++|+++.||.++..|...+.+.|||||+|||+|++++.+ +.+++.+++++|+||||++++..|.+.+++|+..+|..
T Consensus       156 iglr~~~lvGG~~m~~q~~~L~kkPhilVaTPGrL~dhl~~Tkgf~le~lk~LVlDEADrlLd~dF~~~ld~ILk~ip~e  235 (476)
T KOG0330|consen  156 IGLRVAVLVGGMDMMLQANQLSKKPHILVATPGRLWDHLENTKGFSLEQLKFLVLDEADRLLDMDFEEELDYILKVIPRE  235 (476)
T ss_pred             cCeEEEEEecCchHHHHHHHhhcCCCEEEeCcHHHHHHHHhccCccHHHhHHHhhchHHhhhhhhhHHHHHHHHHhcCcc
Confidence            58999999999999999999999999999999999999995 78999999999999999999999999999999999987


Q ss_pred             hh---------------------------------------------------------------------------HHH
Q psy6712          80 TQ---------------------------------------------------------------------------VDW   84 (210)
Q Consensus        80 ~~---------------------------------------------------------------------------~~~   84 (210)
                      ++                                                                           +.+
T Consensus       236 rqt~LfsATMt~kv~kL~rasl~~p~~v~~s~ky~tv~~lkQ~ylfv~~k~K~~yLV~ll~e~~g~s~iVF~~t~~tt~~  315 (476)
T KOG0330|consen  236 RQTFLFSATMTKKVRKLQRASLDNPVKVAVSSKYQTVDHLKQTYLFVPGKDKDTYLVYLLNELAGNSVIVFCNTCNTTRF  315 (476)
T ss_pred             ceEEEEEeecchhhHHHHhhccCCCeEEeccchhcchHHhhhheEeccccccchhHHHHHHhhcCCcEEEEEeccchHHH
Confidence            77                                                                           788


Q ss_pred             HHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCC
Q psy6712          85 LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFG  164 (210)
Q Consensus        85 l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g  164 (210)
                      ++-.|+..|+.+..+||.|++..|...++.|++|..+|||||+++++|+|+|.+++|||||+|.+..+|+||+||++|.|
T Consensus       316 la~~L~~lg~~a~~LhGqmsq~~Rlg~l~~Fk~~~r~iLv~TDVaSRGLDip~Vd~VVNyDiP~~skDYIHRvGRtaRaG  395 (476)
T KOG0330|consen  316 LALLLRNLGFQAIPLHGQMSQSKRLGALNKFKAGARSILVCTDVASRGLDIPHVDVVVNYDIPTHSKDYIHRVGRTARAG  395 (476)
T ss_pred             HHHHHHhcCcceecccchhhHHHHHHHHHHHhccCCcEEEecchhcccCCCCCceEEEecCCCCcHHHHHHHcccccccC
Confidence            88889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CceeEEEEeccCcHHHHHHHHHHhcCccccccCCc
Q psy6712         165 RKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNG  199 (210)
Q Consensus       165 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  199 (210)
                      ++|.++.+++.-|.+.++++|..++..+++.+.+-
T Consensus       396 rsG~~ItlVtqyDve~~qrIE~~~gkkl~~~~~~~  430 (476)
T KOG0330|consen  396 RSGKAITLVTQYDVELVQRIEHALGKKLPEYKVDK  430 (476)
T ss_pred             CCcceEEEEehhhhHHHHHHHHHHhcCCCccCcch
Confidence            99999999999999999999999999998865554

>KOG0331|consensus

Probab=100.00  E-value=9.9e-44  Score=292.85  Aligned_cols=201  Identities=41%  Similarity=0.686  Sum_probs=190.8

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhC-CCch
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYL-PPAT   80 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~-~~~~   80 (210)
                      ++++.+++||.+...|...+.++++|+||||||+.+++..+.++++++.++|+||||+|++.+|.+++..|+..+ ++.+
T Consensus       193 ~~~~~cvyGG~~~~~Q~~~l~~gvdiviaTPGRl~d~le~g~~~l~~v~ylVLDEADrMldmGFe~qI~~Il~~i~~~~r  272 (519)
T KOG0331|consen  193 RLRSTCVYGGAPKGPQLRDLERGVDVVIATPGRLIDLLEEGSLNLSRVTYLVLDEADRMLDMGFEPQIRKILSQIPRPDR  272 (519)
T ss_pred             CccEEEEeCCCCccHHHHHHhcCCcEEEeCChHHHHHHHcCCccccceeEEEeccHHhhhccccHHHHHHHHHhcCCCcc
Confidence            578999999999999999999999999999999999999999999999999999999999999999999999999 4444


Q ss_pred             h-------------------------------------------------------------------------------
Q psy6712          81 Q-------------------------------------------------------------------------------   81 (210)
Q Consensus        81 ~-------------------------------------------------------------------------------   81 (210)
                      |                                                                               
T Consensus       273 Qtlm~saTwp~~v~~lA~~fl~~~~~i~ig~~~~~~a~~~i~qive~~~~~~K~~~l~~lL~~~~~~~~~KvIIFc~tkr  352 (519)
T KOG0331|consen  273 QTLMFSATWPKEVRQLAEDFLNNPIQINVGNKKELKANHNIRQIVEVCDETAKLRKLGKLLEDISSDSEGKVIIFCETKR  352 (519)
T ss_pred             cEEEEeeeccHHHHHHHHHHhcCceEEEecchhhhhhhcchhhhhhhcCHHHHHHHHHHHHHHHhccCCCcEEEEecchh
Confidence            5                                                                               


Q ss_pred             -HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhh
Q psy6712          82 -VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRS  160 (210)
Q Consensus        82 -~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~  160 (210)
                       ++.|+..|+..++++..+||+.++.+|..+++.|++|++.|||||+.+++|+|+|+|++|||||+|.+.++|+||+||+
T Consensus       353 ~~~~l~~~l~~~~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATdVAaRGLDi~dV~lVInydfP~~vEdYVHRiGRT  432 (519)
T KOG0331|consen  353 TCDELARNLRRKGWPAVAIHGDKSQSERDWVLKGFREGKSPVLVATDVAARGLDVPDVDLVINYDFPNNVEDYVHRIGRT  432 (519)
T ss_pred             hHHHHHHHHHhcCcceeeecccccHHHHHHHHHhcccCCcceEEEcccccccCCCccccEEEeCCCCCCHHHHHhhcCcc
Confidence             8889999988899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCceeEEEEeccCcHHHHHHHHHHhcCccccccCCcccc
Q psy6712         161 GRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRS  202 (210)
Q Consensus       161 gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  202 (210)
                      ||.|+.|.++.|+...+......+.+.+....+.+|..+...
T Consensus       433 GRa~~~G~A~tfft~~~~~~a~~l~~~l~e~~q~v~~~l~~~  474 (519)
T KOG0331|consen  433 GRAGKKGTAITFFTSDNAKLARELIKVLREAGQTVPPDLLEY  474 (519)
T ss_pred             ccCCCCceEEEEEeHHHHHHHHHHHHHHHHccCCCChHHHHH
Confidence            999999999999999999999999999988888887766544

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

Probab=100.00  E-value=2.7e-41  Score=286.19  Aligned_cols=192  Identities=45%  Similarity=0.804  Sum_probs=183.9

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchh
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ   81 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~   81 (210)
                      +++++.++||.+...|...+..++|||||||||+++++.++.++++.++++|+||||+|++.||.+++..|+..++...|
T Consensus       128 ~~~~~~i~GG~~~~~q~~~l~~~~~ivVaTPGRllD~i~~~~l~l~~v~~lVlDEADrmLd~Gf~~~i~~I~~~~p~~~q  207 (513)
T COG0513         128 GLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEADRMLDMGFIDDIEKILKALPPDRQ  207 (513)
T ss_pred             CccEEEEECCCCHHHHHHHHhcCCCEEEECccHHHHHHHcCCcchhhcCEEEeccHhhhhcCCCHHHHHHHHHhCCcccE
Confidence            57899999999999999999989999999999999999999999999999999999999999999999999999998666


Q ss_pred             ------------------------------------------------------------------------------HH
Q psy6712          82 ------------------------------------------------------------------------------VD   83 (210)
Q Consensus        82 ------------------------------------------------------------------------------~~   83 (210)
                                                                                                    ++
T Consensus       208 tllfSAT~~~~i~~l~~~~l~~p~~i~v~~~~~~~~~~~i~q~~~~v~~~~~k~~~L~~ll~~~~~~~~IVF~~tk~~~~  287 (513)
T COG0513         208 TLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLELLLKLLKDEDEGRVIVFVRTKRLVE  287 (513)
T ss_pred             EEEEecCCCHHHHHHHHHHccCCcEEEEccccccccccCceEEEEEeCCHHHHHHHHHHHHhcCCCCeEEEEeCcHHHHH
Confidence                                                                                          78


Q ss_pred             HHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCC
Q psy6712          84 WLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRF  163 (210)
Q Consensus        84 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~  163 (210)
                      .+++.|...|+++..+||+|++++|.++++.|++|+.+|||||+++++|+|+|++++|||||+|.+...|+||+||+||.
T Consensus       288 ~l~~~l~~~g~~~~~lhG~l~q~~R~~~l~~F~~g~~~vLVaTDvaaRGiDi~~v~~VinyD~p~~~e~yvHRiGRTgRa  367 (513)
T COG0513         288 ELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRA  367 (513)
T ss_pred             HHHHHHHHCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEEechhhccCCccccceeEEccCCCCHHHheeccCccccC
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCceeEEEEeccC-cHHHHHHHHHHhcCccc
Q psy6712         164 GRKGVAISFVKSD-DIRILRDIEQYYSTQID  193 (210)
Q Consensus       164 g~~g~~~~~~~~~-~~~~~~~~~~~~~~~~~  193 (210)
                      |..|.++.|+.+. |...+..+++.+...++
T Consensus       368 G~~G~ai~fv~~~~e~~~l~~ie~~~~~~~~  398 (513)
T COG0513         368 GRKGVAISFVTEEEEVKKLKRIEKRLERKLP  398 (513)
T ss_pred             CCCCeEEEEeCcHHHHHHHHHHHHHHhcccc
Confidence            9999999999986 88999999999877644

>KOG0326|consensus

Probab=100.00  E-value=1.9e-41  Score=260.45  Aligned_cols=203  Identities=39%  Similarity=0.716  Sum_probs=197.2

Q ss_pred             CCceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCch
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPAT   80 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~   80 (210)
                      +|++|...+||++.+..+-++.+.+|++|+||||++++...+...++++..+|+||||.|++..|.+.+..++.++|+.+
T Consensus       180 ~~i~vmvttGGT~lrDDI~Rl~~~VH~~vgTPGRIlDL~~KgVa~ls~c~~lV~DEADKlLs~~F~~~~e~li~~lP~~r  259 (459)
T KOG0326|consen  180 LGIKVMVTTGGTSLRDDIMRLNQTVHLVVGTPGRILDLAKKGVADLSDCVILVMDEADKLLSVDFQPIVEKLISFLPKER  259 (459)
T ss_pred             cCeEEEEecCCcccccceeeecCceEEEEcCChhHHHHHhcccccchhceEEEechhhhhhchhhhhHHHHHHHhCCccc
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             h--------------------------------------------------------------------------HHHHH
Q psy6712          81 Q--------------------------------------------------------------------------VDWLT   86 (210)
Q Consensus        81 ~--------------------------------------------------------------------------~~~l~   86 (210)
                      |                                                                          ++.++
T Consensus       260 QillySATFP~tVk~Fm~~~l~kPy~INLM~eLtl~GvtQyYafV~e~qKvhCLntLfskLqINQsIIFCNS~~rVELLA  339 (459)
T KOG0326|consen  260 QILLYSATFPLTVKGFMDRHLKKPYEINLMEELTLKGVTQYYAFVEERQKVHCLNTLFSKLQINQSIIFCNSTNRVELLA  339 (459)
T ss_pred             eeeEEecccchhHHHHHHHhccCcceeehhhhhhhcchhhheeeechhhhhhhHHHHHHHhcccceEEEeccchHhHHHH
Confidence            8                                                                          89999


Q ss_pred             HHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCCc
Q psy6712          87 EKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRK  166 (210)
Q Consensus        87 ~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~~  166 (210)
                      +.+.+.|+.+.++|+.|-++.|..++-.|++|.++.||||+.+.+|+|++++++|||||+|.+.++|+||+||+||.|.-
T Consensus       340 kKITelGyscyyiHakM~Q~hRNrVFHdFr~G~crnLVctDL~TRGIDiqavNvVINFDfpk~aEtYLHRIGRsGRFGhl  419 (459)
T KOG0326|consen  340 KKITELGYSCYYIHAKMAQEHRNRVFHDFRNGKCRNLVCTDLFTRGIDIQAVNVVINFDFPKNAETYLHRIGRSGRFGHL  419 (459)
T ss_pred             HHHHhccchhhHHHHHHHHhhhhhhhhhhhccccceeeehhhhhcccccceeeEEEecCCCCCHHHHHHHccCCccCCCc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCcHHHHHHHHHHhcCccccccCCccccC
Q psy6712         167 GVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRSL  203 (210)
Q Consensus       167 g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  203 (210)
                      |.++.+++-+|...+..+|+.++.++..+|....+.+
T Consensus       420 GlAInLityedrf~L~~IE~eLGtEI~pip~~iDk~l  456 (459)
T KOG0326|consen  420 GLAINLITYEDRFNLYRIEQELGTEIKPIPSNIDKSL  456 (459)
T ss_pred             ceEEEEEehhhhhhHHHHHHHhccccccCCCcCCccc
Confidence            9999999999999999999999999999998877655

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=2.6e-40  Score=275.92  Aligned_cols=204  Identities=34%  Similarity=0.567  Sum_probs=188.9

Q ss_pred             CCceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCch
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPAT   80 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~   80 (210)
                      +|+++..++||.+...+...+.+++||+|+||+++.+++.++.+++++++++|+||||++++.++...+..++..++...
T Consensus       110 ~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~TP~~l~~~l~~~~~~l~~v~~lViDEad~l~~~~f~~~i~~i~~~~~~~~  189 (423)
T PRK04837        110 TGLKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEADRMFDLGFIKDIRWLFRRMPPAN  189 (423)
T ss_pred             CCceEEEEECCCCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccccEEEEecHHHHhhcccHHHHHHHHHhCCCcc
Confidence            37889999999999999999988999999999999999999999999999999999999999999988888887766422


Q ss_pred             h-----------------------------------------------------------------------------HH
Q psy6712          81 Q-----------------------------------------------------------------------------VD   83 (210)
Q Consensus        81 ~-----------------------------------------------------------------------------~~   83 (210)
                      +                                                                             ++
T Consensus       190 ~~~~~l~SAT~~~~~~~~~~~~~~~p~~i~v~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lVF~~t~~~~~  269 (423)
T PRK04837        190 QRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTGHRIKEELFYPSNEEKMRLLQTLIEEEWPDRAIIFANTKHRCE  269 (423)
T ss_pred             ceeEEEEeccCCHHHHHHHHHHCCCCEEEEEcCCCcCCCceeEEEEeCCHHHHHHHHHHHHHhcCCCeEEEEECCHHHHH
Confidence            1                                                                             77


Q ss_pred             HHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCC
Q psy6712          84 WLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRF  163 (210)
Q Consensus        84 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~  163 (210)
                      .+.+.|.+.++++..+||+|++++|..++++|++|++++||||+++++|+|+|++++||+||+|.+..+|+||+||+||.
T Consensus       270 ~l~~~L~~~g~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLVaTdv~~rGiDip~v~~VI~~d~P~s~~~yiqR~GR~gR~  349 (423)
T PRK04837        270 EIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRA  349 (423)
T ss_pred             HHHHHHHhCCCcEEEecCCCChhHHHHHHHHHHcCCCcEEEEechhhcCCCccccCEEEEeCCCCchhheEeccccccCC
Confidence            88889988999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCceeEEEEeccCcHHHHHHHHHHhcCccccccCCccccCC
Q psy6712         164 GRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRSLH  204 (210)
Q Consensus       164 g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  204 (210)
                      |+.|.+++|+.+.+...+..+++++...++..+.+...++.
T Consensus       350 G~~G~ai~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~  390 (423)
T PRK04837        350 GASGHSISLACEEYALNLPAIETYIGHSIPVSKYDSDALLT  390 (423)
T ss_pred             CCCeeEEEEeCHHHHHHHHHHHHHhCCCCCCccCChhhhhh
Confidence            99999999999999999999999999998888777776663

>KOG0333|consensus

Probab=100.00  E-value=6.3e-40  Score=265.63  Aligned_cols=189  Identities=37%  Similarity=0.678  Sum_probs=179.7

Q ss_pred             CCceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCch
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPAT   80 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~   80 (210)
                      +|++++.++||.+.++|--.+..+|+|+|+||++|.+.|.+..+-++++.++|+||||+|+|.+|.+++..++...|...
T Consensus       349 lg~r~vsvigg~s~EEq~fqls~gceiviatPgrLid~Lenr~lvl~qctyvvldeadrmiDmgfE~dv~~iL~~mPssn  428 (673)
T KOG0333|consen  349 LGIRTVSVIGGLSFEEQGFQLSMGCEIVIATPGRLIDSLENRYLVLNQCTYVVLDEADRMIDMGFEPDVQKILEQMPSSN  428 (673)
T ss_pred             ccceEEEEecccchhhhhhhhhccceeeecCchHHHHHHHHHHHHhccCceEeccchhhhhcccccHHHHHHHHhCCccc
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999887543


Q ss_pred             h-------------------------------------------------------------------------------
Q psy6712          81 Q-------------------------------------------------------------------------------   81 (210)
Q Consensus        81 ~-------------------------------------------------------------------------------   81 (210)
                      .                                                                               
T Consensus       429 ~k~~tde~~~~~~~~~~~~~~k~yrqT~mftatm~p~verlar~ylr~pv~vtig~~gk~~~rveQ~v~m~~ed~k~kkL  508 (673)
T KOG0333|consen  429 AKPDTDEKEGEERVRKNFSSSKKYRQTVMFTATMPPAVERLARSYLRRPVVVTIGSAGKPTPRVEQKVEMVSEDEKRKKL  508 (673)
T ss_pred             cCCCccchhhHHHHHhhcccccceeEEEEEecCCChHHHHHHHHHhhCCeEEEeccCCCCccchheEEEEecchHHHHHH
Confidence            3                                                                               


Q ss_pred             ---------------------HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcE
Q psy6712          82 ---------------------VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL  140 (210)
Q Consensus        82 ---------------------~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~  140 (210)
                                           ++++++.|.+.++++..+||+-++++|..+++.|++|..+|||||+++++|+|+|+|.+
T Consensus       509 ~eil~~~~~ppiIIFvN~kk~~d~lAk~LeK~g~~~~tlHg~k~qeQRe~aL~~fr~~t~dIlVaTDvAgRGIDIpnVSl  588 (673)
T KOG0333|consen  509 IEILESNFDPPIIIFVNTKKGADALAKILEKAGYKVTTLHGGKSQEQRENALADFREGTGDILVATDVAGRGIDIPNVSL  588 (673)
T ss_pred             HHHHHhCCCCCEEEEEechhhHHHHHHHHhhccceEEEeeCCccHHHHHHHHHHHHhcCCCEEEEecccccCCCCCccce
Confidence                                 89999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecCCCChhHHHHhhhhhcCCCCceeEEEEeccCcHHHHHHHHHHhc
Q psy6712         141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYS  189 (210)
Q Consensus       141 vi~~~~p~s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~  189 (210)
                      |||||++.+..+|+||+||+||.|+.|.+++|+++.+...+..+.+.+.
T Consensus       589 VinydmaksieDYtHRIGRTgRAGk~GtaiSflt~~dt~v~ydLkq~l~  637 (673)
T KOG0333|consen  589 VINYDMAKSIEDYTHRIGRTGRAGKSGTAISFLTPADTAVFYDLKQALR  637 (673)
T ss_pred             eeecchhhhHHHHHHHhccccccccCceeEEEeccchhHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999887777776654

>PTZ00110 helicase; Provisional

Probab=100.00  E-value=4.7e-39  Score=274.66  Aligned_cols=201  Identities=36%  Similarity=0.647  Sum_probs=186.0

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchh
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ   81 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~   81 (210)
                      ++++..++||.+...|...+.++++|+|+||++|.+++.++..++++++++|+||||+|++++|...+..++..++...|
T Consensus       231 ~i~~~~~~gg~~~~~q~~~l~~~~~IlVaTPgrL~d~l~~~~~~l~~v~~lViDEAd~mld~gf~~~i~~il~~~~~~~q  310 (545)
T PTZ00110        231 KIRNTVAYGGVPKRGQIYALRRGVEILIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLDMGFEPQIRKIVSQIRPDRQ  310 (545)
T ss_pred             CccEEEEeCCCCHHHHHHHHHcCCCEEEECHHHHHHHHHcCCCChhhCcEEEeehHHhhhhcchHHHHHHHHHhCCCCCe
Confidence            57889999999999999999999999999999999999999899999999999999999999998888888765544333


Q ss_pred             -------------------------------------------------------------------------------H
Q psy6712          82 -------------------------------------------------------------------------------V   82 (210)
Q Consensus        82 -------------------------------------------------------------------------------~   82 (210)
                                                                                                     +
T Consensus       311 ~l~~SAT~p~~v~~l~~~l~~~~~v~i~vg~~~l~~~~~i~q~~~~~~~~~k~~~L~~ll~~~~~~~~k~LIF~~t~~~a  390 (545)
T PTZ00110        311 TLMWSATWPKEVQSLARDLCKEEPVHVNVGSLDLTACHNIKQEVFVVEEHEKRGKLKMLLQRIMRDGDKILIFVETKKGA  390 (545)
T ss_pred             EEEEEeCCCHHHHHHHHHHhccCCEEEEECCCccccCCCeeEEEEEEechhHHHHHHHHHHHhcccCCeEEEEecChHHH
Confidence                                                                                           7


Q ss_pred             HHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcC
Q psy6712          83 DWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGR  162 (210)
Q Consensus        83 ~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR  162 (210)
                      +.+++.|+..++.+..+||+|++++|..++++|++|+.+|||||+++++|+|+|++++||+||+|.+..+|+||+||+||
T Consensus       391 ~~l~~~L~~~g~~~~~ihg~~~~~eR~~il~~F~~G~~~ILVaTdv~~rGIDi~~v~~VI~~d~P~s~~~yvqRiGRtGR  470 (545)
T PTZ00110        391 DFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGR  470 (545)
T ss_pred             HHHHHHHHHcCCcEEEEECCCcHHHHHHHHHHHhcCCCcEEEEcchhhcCCCcccCCEEEEeCCCCCHHHHHHHhccccc
Confidence            88888888889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCceeEEEEeccCcHHHHHHHHHHhcCccccccCCcccc
Q psy6712         163 FGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRS  202 (210)
Q Consensus       163 ~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  202 (210)
                      .|+.|.+++|+++.+...++.+.+.+....+++|..+.++
T Consensus       471 ~G~~G~ai~~~~~~~~~~~~~l~~~l~~~~q~vp~~l~~~  510 (545)
T PTZ00110        471 AGAKGASYTFLTPDKYRLARDLVKVLREAKQPVPPELEKL  510 (545)
T ss_pred             CCCCceEEEEECcchHHHHHHHHHHHHHccCCCCHHHHHH
Confidence            9999999999999999999999999999999888666544

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=100.00  E-value=1.8e-38  Score=267.45  Aligned_cols=197  Identities=35%  Similarity=0.686  Sum_probs=184.4

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchh
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ   81 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~   81 (210)
                      ++++..++||.+.+.|...+..+++|+|+||+++.+++.++.+.+++++++|+||||+|++.++...+..++..++...|
T Consensus       101 ~~~v~~~~Gg~~~~~~~~~l~~~~~IvV~Tp~rl~~~l~~~~~~l~~l~~lViDEad~~l~~g~~~~l~~i~~~~~~~~q  180 (460)
T PRK11776        101 NIKVLTLCGGVPMGPQIDSLEHGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMGFQDAIDAIIRQAPARRQ  180 (460)
T ss_pred             CcEEEEEECCCChHHHHHHhcCCCCEEEEChHHHHHHHHcCCccHHHCCEEEEECHHHHhCcCcHHHHHHHHHhCCcccE
Confidence            57899999999999999999999999999999999999999999999999999999999999999998888887765544


Q ss_pred             --------------------------------------------------------------------------HHHHHH
Q psy6712          82 --------------------------------------------------------------------------VDWLTE   87 (210)
Q Consensus        82 --------------------------------------------------------------------------~~~l~~   87 (210)
                                                                                                ++.+++
T Consensus       181 ~ll~SAT~~~~~~~l~~~~~~~~~~i~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lVF~~t~~~~~~l~~  260 (460)
T PRK11776        181 TLLFSATYPEGIAAISQRFQRDPVEVKVESTHDLPAIEQRFYEVSPDERLPALQRLLLHHQPESCVVFCNTKKECQEVAD  260 (460)
T ss_pred             EEEEEecCcHHHHHHHHHhcCCCEEEEECcCCCCCCeeEEEEEeCcHHHHHHHHHHHHhcCCCceEEEECCHHHHHHHHH
Confidence                                                                                      788899


Q ss_pred             HHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCCce
Q psy6712          88 KMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKG  167 (210)
Q Consensus        88 ~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~~g  167 (210)
                      .|.+.++.+..+||+|++.+|..++++|++|+.++||||+++++|+|+|++++||+||+|.+...|+||+||+||.|+.|
T Consensus       261 ~L~~~~~~v~~~hg~~~~~eR~~~l~~F~~g~~~vLVaTdv~~rGiDi~~v~~VI~~d~p~~~~~yiqR~GRtGR~g~~G  340 (460)
T PRK11776        261 ALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKG  340 (460)
T ss_pred             HHHhCCCcEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEecccccccchhcCCeEEEecCCCCHhHhhhhcccccCCCCcc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEeccCcHHHHHHHHHHhcCccccccCC
Q psy6712         168 VAISFVKSDDIRILRDIEQYYSTQIDEMPMN  198 (210)
Q Consensus       168 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  198 (210)
                      .+++|+.+.+...++.+++.++..+...+++
T Consensus       341 ~ai~l~~~~e~~~~~~i~~~~~~~~~~~~l~  371 (460)
T PRK11776        341 LALSLVAPEEMQRANAIEDYLGRKLNWEPLP  371 (460)
T ss_pred             eEEEEEchhHHHHHHHHHHHhCCCCceecCC
Confidence            9999999999999999999998877765543

>KOG0342|consensus

Probab=100.00  E-value=3.6e-39  Score=259.45  Aligned_cols=195  Identities=34%  Similarity=0.599  Sum_probs=180.0

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHh-cCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCch
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRR-RVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPAT   80 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~-~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~   80 (210)
                      ++.|..++||.+.......+..+++|+|+|||||.+++++ +.+-.++++++|+||||++++.+|.+++..|+..+|..+
T Consensus       183 ~~~v~~viGG~~~~~e~~kl~k~~niliATPGRLlDHlqNt~~f~~r~~k~lvlDEADrlLd~GF~~di~~Ii~~lpk~r  262 (543)
T KOG0342|consen  183 SITVGIVIGGNNFSVEADKLVKGCNILIATPGRLLDHLQNTSGFLFRNLKCLVLDEADRLLDIGFEEDVEQIIKILPKQR  262 (543)
T ss_pred             CcceEEEeCCccchHHHHHhhccccEEEeCCchHHhHhhcCCcchhhccceeEeecchhhhhcccHHHHHHHHHhccccc
Confidence            5779999999999999999988999999999999999999 345567889999999999999999999999999999887


Q ss_pred             h-------------------------------------------------------------------------------
Q psy6712          81 Q-------------------------------------------------------------------------------   81 (210)
Q Consensus        81 ~-------------------------------------------------------------------------------   81 (210)
                      |                                                                               
T Consensus       263 qt~LFSAT~~~kV~~l~~~~L~~d~~~v~~~d~~~~~The~l~Qgyvv~~~~~~f~ll~~~LKk~~~~~KiiVF~sT~~~  342 (543)
T KOG0342|consen  263 QTLLFSATQPSKVKDLARGALKRDPVFVNVDDGGERETHERLEQGYVVAPSDSRFSLLYTFLKKNIKRYKIIVFFSTCMS  342 (543)
T ss_pred             eeeEeeCCCcHHHHHHHHHhhcCCceEeecCCCCCcchhhcccceEEeccccchHHHHHHHHHHhcCCceEEEEechhhH
Confidence            7                                                                               


Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhc
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSG  161 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~g  161 (210)
                      +.++++.|....++|.-+||++++..|..+...|++.+..|||||+.++||+|+|+|++||+||+|.++.+|+||+||+|
T Consensus       343 vk~~~~lL~~~dlpv~eiHgk~~Q~kRT~~~~~F~kaesgIL~cTDVaARGlD~P~V~~VvQ~~~P~d~~~YIHRvGRTa  422 (543)
T KOG0342|consen  343 VKFHAELLNYIDLPVLEIHGKQKQNKRTSTFFEFCKAESGILVCTDVAARGLDIPDVDWVVQYDPPSDPEQYIHRVGRTA  422 (543)
T ss_pred             HHHHHHHHhhcCCchhhhhcCCcccccchHHHHHhhcccceEEecchhhccCCCCCceEEEEeCCCCCHHHHHHHhcccc
Confidence            78888888888999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCceeEEEEeccCcHHHHHHHHHHhcCccccccCCc
Q psy6712         162 RFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNG  199 (210)
Q Consensus       162 R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  199 (210)
                      |.|..|.+++++.+.|..+++.++   ..++.+.+.+.
T Consensus       423 R~gk~G~alL~l~p~El~Flr~LK---~lpl~~~e~~~  457 (543)
T KOG0342|consen  423 REGKEGKALLLLAPWELGFLRYLK---KLPLEEFEFPP  457 (543)
T ss_pred             ccCCCceEEEEeChhHHHHHHHHh---hCCCcccCCCC
Confidence            999999999999999999999998   44555544443

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=100.00  E-value=2.8e-38  Score=265.68  Aligned_cols=196  Identities=37%  Similarity=0.676  Sum_probs=181.3

Q ss_pred             CCceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCch
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPAT   80 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~   80 (210)
                      +++++..++||.+.+.++..+..+++|+|+||++|.+++..+.+++++++++|+||||+++++++...+..++..++...
T Consensus       102 ~~~~~~~~~gg~~~~~~~~~l~~~~~IiV~TP~rL~~~~~~~~~~l~~v~~lViDEah~ll~~~~~~~i~~il~~l~~~~  181 (456)
T PRK10590        102 LNIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRMLDMGFIHDIRRVLAKLPAKR  181 (456)
T ss_pred             CCCEEEEEECCcCHHHHHHHHcCCCcEEEEChHHHHHHHHcCCcccccceEEEeecHHHHhccccHHHHHHHHHhCCccC
Confidence            36788999999999999999999999999999999999998888999999999999999999998877777777665544


Q ss_pred             h---------------------------------------------------------------------------HHHH
Q psy6712          81 Q---------------------------------------------------------------------------VDWL   85 (210)
Q Consensus        81 ~---------------------------------------------------------------------------~~~l   85 (210)
                      |                                                                           ++.+
T Consensus       182 q~l~~SAT~~~~~~~l~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~l~~~~~~~~~lVF~~t~~~~~~l  261 (456)
T PRK10590        182 QNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQHVHFVDKKRKRELLSQMIGKGNWQQVLVFTRTKHGANHL  261 (456)
T ss_pred             eEEEEeCCCcHHHHHHHHHHcCCCeEEEEecccccccceeEEEEEcCHHHHHHHHHHHHHcCCCCcEEEEcCcHHHHHHH
Confidence            4                                                                           7888


Q ss_pred             HHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCC
Q psy6712          86 TEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGR  165 (210)
Q Consensus        86 ~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~  165 (210)
                      ++.|...++.+..+||+|++.+|.+++++|++|+++|||||+++++|+|+|++++||+|++|.+..+|+||+||+||.|.
T Consensus       262 ~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yvqR~GRaGR~g~  341 (456)
T PRK10590        262 AEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAA  341 (456)
T ss_pred             HHHHHHCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEccHHhcCCCcccCCEEEEeCCCCCHHHhhhhccccccCCC
Confidence            89999899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceeEEEEeccCcHHHHHHHHHHhcCcccccc
Q psy6712         166 KGVAISFVKSDDIRILRDIEQYYSTQIDEMP  196 (210)
Q Consensus       166 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  196 (210)
                      .|.+++|+...+...++.+++.+..+++...
T Consensus       342 ~G~ai~l~~~~d~~~~~~ie~~l~~~~~~~~  372 (456)
T PRK10590        342 TGEALSLVCVDEHKLLRDIEKLLKKEIPRIA  372 (456)
T ss_pred             CeeEEEEecHHHHHHHHHHHHHhcCCCcccc
Confidence            9999999999999999999999988875543

>KOG0336|consensus

Probab=100.00  E-value=1.5e-39  Score=257.11  Aligned_cols=203  Identities=35%  Similarity=0.610  Sum_probs=189.9

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchh
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ   81 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~   81 (210)
                      |.+..+++||.+..+|+..++.+.+|+++||++|.++.-.+.++++.+-++|+||||+|++.+|.+++.+|+--+.+.+|
T Consensus       321 g~ksvc~ygggnR~eqie~lkrgveiiiatPgrlndL~~~n~i~l~siTYlVlDEADrMLDMgFEpqIrkilldiRPDRq  400 (629)
T KOG0336|consen  321 GLKSVCVYGGGNRNEQIEDLKRGVEIIIATPGRLNDLQMDNVINLASITYLVLDEADRMLDMGFEPQIRKILLDIRPDRQ  400 (629)
T ss_pred             CcceEEEecCCCchhHHHHHhcCceEEeeCCchHhhhhhcCeeeeeeeEEEEecchhhhhcccccHHHHHHhhhcCCcce
Confidence            67889999999999999999999999999999999999999999999999999999999999999999999987777766


Q ss_pred             -----------------------------------------------------------------------------HHH
Q psy6712          82 -----------------------------------------------------------------------------VDW   84 (210)
Q Consensus        82 -----------------------------------------------------------------------------~~~   84 (210)
                                                                                                   ++.
T Consensus       401 tvmTSATWP~~VrrLa~sY~Kep~~v~vGsLdL~a~~sVkQ~i~v~~d~~k~~~~~~f~~~ms~ndKvIiFv~~K~~AD~  480 (629)
T KOG0336|consen  401 TVMTSATWPEGVRRLAQSYLKEPMIVYVGSLDLVAVKSVKQNIIVTTDSEKLEIVQFFVANMSSNDKVIIFVSRKVMADH  480 (629)
T ss_pred             eeeecccCchHHHHHHHHhhhCceEEEecccceeeeeeeeeeEEecccHHHHHHHHHHHHhcCCCceEEEEEechhhhhh
Confidence                                                                                         555


Q ss_pred             HHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCC
Q psy6712          85 LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFG  164 (210)
Q Consensus        85 l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g  164 (210)
                      |+..|--.|+.+-.+||+-++.+|+..++.|+.|+.+|||+|+.+++|+|+|+++||+|||+|.++..|.||+||+||.|
T Consensus       481 LSSd~~l~gi~~q~lHG~r~Q~DrE~al~~~ksG~vrILvaTDlaSRGlDv~DiTHV~NyDFP~nIeeYVHRvGrtGRaG  560 (629)
T KOG0336|consen  481 LSSDFCLKGISSQSLHGNREQSDREMALEDFKSGEVRILVATDLASRGLDVPDITHVYNYDFPRNIEEYVHRVGRTGRAG  560 (629)
T ss_pred             ccchhhhcccchhhccCChhhhhHHHHHHhhhcCceEEEEEechhhcCCCchhcceeeccCCCccHHHHHHHhcccccCC
Confidence            66666667899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CceeEEEEeccCcHHHHHHHHHHhcCccccccCCccccCC
Q psy6712         165 RKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRSLH  204 (210)
Q Consensus       165 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  204 (210)
                      +.|..+.|+.-.+..++.++-+.+...-+++|.++.+...
T Consensus       561 r~G~sis~lt~~D~~~a~eLI~ILe~aeQevPdeL~~mAe  600 (629)
T KOG0336|consen  561 RTGTSISFLTRNDWSMAEELIQILERAEQEVPDELVRMAE  600 (629)
T ss_pred             CCcceEEEEehhhHHHHHHHHHHHHHhhhhCcHHHHHHHH
Confidence            9999999999999999999999999999999887765443

>KOG0341|consensus

Probab=100.00  E-value=1.8e-39  Score=255.26  Aligned_cols=202  Identities=33%  Similarity=0.629  Sum_probs=189.9

Q ss_pred             ceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchh-
Q psy6712           3 VQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ-   81 (210)
Q Consensus         3 i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~-   81 (210)
                      +++.+++||.+..+|....+.|+||+|+|||||.++|..+.+++.-++++.+||||+|++.||.+++..++.++...+| 
T Consensus       281 lRs~LciGG~~v~eql~~v~~GvHivVATPGRL~DmL~KK~~sLd~CRyL~lDEADRmiDmGFEddir~iF~~FK~QRQT  360 (610)
T KOG0341|consen  281 LRSLLCIGGVPVREQLDVVRRGVHIVVATPGRLMDMLAKKIMSLDACRYLTLDEADRMIDMGFEDDIRTIFSFFKGQRQT  360 (610)
T ss_pred             hhhhhhhcCccHHHHHHHHhcCeeEEEcCcchHHHHHHHhhccHHHHHHhhhhhHHHHhhccchhhHHHHHHHHhhhhhe
Confidence            5788999999999999999999999999999999999999999999999999999999999999999999999988877 


Q ss_pred             -------------------------------------------------------------------------HHHHHHH
Q psy6712          82 -------------------------------------------------------------------------VDWLTEK   88 (210)
Q Consensus        82 -------------------------------------------------------------------------~~~l~~~   88 (210)
                                                                                               ++.+.++
T Consensus       361 LLFSATMP~KIQ~FAkSALVKPvtvNVGRAGAAsldViQevEyVkqEaKiVylLeCLQKT~PpVLIFaEkK~DVD~IhEY  440 (610)
T KOG0341|consen  361 LLFSATMPKKIQNFAKSALVKPVTVNVGRAGAASLDVIQEVEYVKQEAKIVYLLECLQKTSPPVLIFAEKKADVDDIHEY  440 (610)
T ss_pred             eeeeccccHHHHHHHHhhcccceEEecccccccchhHHHHHHHHHhhhhhhhHHHHhccCCCceEEEeccccChHHHHHH
Confidence                                                                                     7788899


Q ss_pred             HHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCCcee
Q psy6712          89 MREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGV  168 (210)
Q Consensus        89 l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~~g~  168 (210)
                      |--+|..+..+||+-.+++|...+++|+.|+-++||+|+.++.|+|+|++.+|||||+|..+.+|.||+||+||.|+.|.
T Consensus       441 LLlKGVEavaIHGGKDQedR~~ai~afr~gkKDVLVATDVASKGLDFp~iqHVINyDMP~eIENYVHRIGRTGRsg~~Gi  520 (610)
T KOG0341|consen  441 LLLKGVEAVAIHGGKDQEDRHYAIEAFRAGKKDVLVATDVASKGLDFPDIQHVINYDMPEEIENYVHRIGRTGRSGKTGI  520 (610)
T ss_pred             HHHccceeEEeecCcchhHHHHHHHHHhcCCCceEEEecchhccCCCccchhhccCCChHHHHHHHHHhcccCCCCCcce
Confidence            98899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEecc-CcHHHHHHHHHHhcCccccccCCccccCC
Q psy6712         169 AISFVKS-DDIRILRDIEQYYSTQIDEMPMNGKRSLH  204 (210)
Q Consensus       169 ~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  204 (210)
                      +..|++. .+...+-.++..+....+++|..+..+..
T Consensus       521 ATTfINK~~~esvLlDLK~LL~EakQ~vP~~L~~L~~  557 (610)
T KOG0341|consen  521 ATTFINKNQEESVLLDLKHLLQEAKQEVPPVLAELAG  557 (610)
T ss_pred             eeeeecccchHHHHHHHHHHHHHhhccCCHHHHHhCC
Confidence            9999987 46677888888888888888877665543

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

Probab=100.00  E-value=5.8e-38  Score=266.96  Aligned_cols=200  Identities=32%  Similarity=0.616  Sum_probs=180.5

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchh
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ   81 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~   81 (210)
                      +++++.++||.....|...+..+++|+|+||++|.+++.++.+.+++++++|+||||+|++++|.+.+..++..++....
T Consensus       224 ~~~~~~~~gG~~~~~q~~~l~~~~~IiV~TPgrL~~~l~~~~~~l~~v~~lViDEad~ml~~gf~~~i~~i~~~l~~~q~  303 (518)
T PLN00206        224 PFKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDNVSVLVLDEVDCMLERGFRDQVMQIFQALSQPQV  303 (518)
T ss_pred             CceEEEEECCcchHHHHHHhcCCCCEEEECHHHHHHHHHcCCccchheeEEEeecHHHHhhcchHHHHHHHHHhCCCCcE
Confidence            57889999999999999999999999999999999999999999999999999999999999998888777665432111


Q ss_pred             ----------------------------------------------------------------------------HHHH
Q psy6712          82 ----------------------------------------------------------------------------VDWL   85 (210)
Q Consensus        82 ----------------------------------------------------------------------------~~~l   85 (210)
                                                                                                  ++.+
T Consensus       304 l~~SATl~~~v~~l~~~~~~~~~~i~~~~~~~~~~~v~q~~~~~~~~~k~~~l~~~l~~~~~~~~~~iVFv~s~~~a~~l  383 (518)
T PLN00206        304 LLFSATVSPEVEKFASSLAKDIILISIGNPNRPNKAVKQLAIWVETKQKKQKLFDILKSKQHFKPPAVVFVSSRLGADLL  383 (518)
T ss_pred             EEEEeeCCHHHHHHHHHhCCCCEEEEeCCCCCCCcceeEEEEeccchhHHHHHHHHHHhhcccCCCEEEEcCCchhHHHH
Confidence                                                                                        5667


Q ss_pred             HHHHHh-cCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCC
Q psy6712          86 TEKMRE-ANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFG  164 (210)
Q Consensus        86 ~~~l~~-~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g  164 (210)
                      ++.|.. .++.+..+||+|+..+|..++++|++|+.+|||||+++++|+|+|++++||+||+|.+..+|+||+||+||.|
T Consensus       384 ~~~L~~~~g~~~~~~Hg~~~~~eR~~il~~Fr~G~~~ILVaTdvl~rGiDip~v~~VI~~d~P~s~~~yihRiGRaGR~g  463 (518)
T PLN00206        384 ANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMG  463 (518)
T ss_pred             HHHHhhccCcceEEeeCCCCHHHHHHHHHHHHCCCCCEEEEecHhhccCCcccCCEEEEeCCCCCHHHHHHhccccccCC
Confidence            777754 5889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CceeEEEEeccCcHHHHHHHHHHhcCccccccCCccc
Q psy6712         165 RKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKR  201 (210)
Q Consensus       165 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  201 (210)
                      ..|.+++|+.+.+...+..+.+.+....+.+|.++.+
T Consensus       464 ~~G~ai~f~~~~~~~~~~~l~~~l~~~~~~vp~~l~~  500 (518)
T PLN00206        464 EKGTAIVFVNEEDRNLFPELVALLKSSGAAIPRELAN  500 (518)
T ss_pred             CCeEEEEEEchhHHHHHHHHHHHHHHcCCCCCHHHHh
Confidence            9999999999999999999999999888887776544

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=100.00  E-value=9.9e-38  Score=269.24  Aligned_cols=199  Identities=39%  Similarity=0.673  Sum_probs=186.1

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchh
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ   81 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~   81 (210)
                      ++++..++||.+.+.+...+..+++|+|+||+++.+++.++.+++++++++|+||||+|++.++.+.+..++..++...|
T Consensus       103 ~i~v~~~~gG~~~~~q~~~l~~~~~IVVgTPgrl~d~l~r~~l~l~~l~~lVlDEAd~ml~~gf~~di~~Il~~lp~~~q  182 (629)
T PRK11634        103 GVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMGFIEDVETIMAQIPEGHQ  182 (629)
T ss_pred             CceEEEEECCcCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcchhhceEEEeccHHHHhhcccHHHHHHHHHhCCCCCe
Confidence            67899999999999999999999999999999999999999999999999999999999999999999888877765544


Q ss_pred             ---------------------------------------------------------------------------HHHHH
Q psy6712          82 ---------------------------------------------------------------------------VDWLT   86 (210)
Q Consensus        82 ---------------------------------------------------------------------------~~~l~   86 (210)
                                                                                                 ++.++
T Consensus       183 ~llfSAT~p~~i~~i~~~~l~~~~~i~i~~~~~~~~~i~q~~~~v~~~~k~~~L~~~L~~~~~~~~IVF~~tk~~a~~l~  262 (629)
T PRK11634        183 TALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVWGMRKNEALVRFLEAEDFDAAIIFVRTKNATLEVA  262 (629)
T ss_pred             EEEEEccCChhHHHHHHHHcCCCeEEEccCccccCCceEEEEEEechhhHHHHHHHHHHhcCCCCEEEEeccHHHHHHHH
Confidence                                                                                       77888


Q ss_pred             HHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCCc
Q psy6712          87 EKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRK  166 (210)
Q Consensus        87 ~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~~  166 (210)
                      +.|...++.+..+||+|++.+|.+++++|++|+++|||||+++++|+|+|++++||+||+|.+...|+||+||+||.|+.
T Consensus       263 ~~L~~~g~~~~~lhgd~~q~~R~~il~~Fr~G~~~ILVATdv~arGIDip~V~~VI~~d~P~~~e~yvqRiGRtGRaGr~  342 (629)
T PRK11634        263 EALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRA  342 (629)
T ss_pred             HHHHhCCCCEEEeeCCCCHHHHHHHHHHHhCCCCCEEEEcchHhcCCCcccCCEEEEeCCCCCHHHHHHHhccccCCCCc
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCcHHHHHHHHHHhcCccccccCCcc
Q psy6712         167 GVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGK  200 (210)
Q Consensus       167 g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  200 (210)
                      |.+++|+.+.+...++.+++.++..+++++.+..
T Consensus       343 G~ai~~v~~~e~~~l~~ie~~~~~~i~~~~~p~~  376 (629)
T PRK11634        343 GRALLFVENRERRLLRNIERTMKLTIPEVELPNA  376 (629)
T ss_pred             ceEEEEechHHHHHHHHHHHHhCCCcceecCCcH
Confidence            9999999999999999999999999888765543

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=100.00  E-value=1.8e-37  Score=259.75  Aligned_cols=194  Identities=36%  Similarity=0.599  Sum_probs=177.8

Q ss_pred             CCceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCch
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPAT   80 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~   80 (210)
                      +++++..++||.....+...+.++++|||+||++|.+++..+.+++++++++|+||||+|+++++...+..+...++...
T Consensus       100 ~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~Tp~rl~~~~~~~~~~~~~v~~lViDEah~~l~~~~~~~~~~i~~~~~~~~  179 (434)
T PRK11192        100 THLDIATITGGVAYMNHAEVFSENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRMLDMGFAQDIETIAAETRWRK  179 (434)
T ss_pred             CCcEEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCcCcccCCEEEEECHHHHhCCCcHHHHHHHHHhCcccc
Confidence            36889999999999999888888999999999999999999999999999999999999999888877766655443322


Q ss_pred             h-----------------------------------------------------------------------------HH
Q psy6712          81 Q-----------------------------------------------------------------------------VD   83 (210)
Q Consensus        81 ~-----------------------------------------------------------------------------~~   83 (210)
                      |                                                                             ++
T Consensus       180 q~~~~SAT~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~~lVF~~s~~~~~  259 (434)
T PRK11192        180 QTLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRERKKIHQWYYRADDLEHKTALLCHLLKQPEVTRSIVFVRTRERVH  259 (434)
T ss_pred             EEEEEEeecCHHHHHHHHHHHccCCEEEEecCCcccccCceEEEEEeCCHHHHHHHHHHHHhcCCCCeEEEEeCChHHHH
Confidence            2                                                                             78


Q ss_pred             HHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCC
Q psy6712          84 WLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRF  163 (210)
Q Consensus        84 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~  163 (210)
                      .+++.|.+.++.+..+||+|++.+|..+++.|++|+++|||||+++++|+|+|++++||+||+|.+...|+||+||+||.
T Consensus       260 ~l~~~L~~~~~~~~~l~g~~~~~~R~~~l~~f~~G~~~vLVaTd~~~~GiDip~v~~VI~~d~p~s~~~yiqr~GR~gR~  339 (434)
T PRK11192        260 ELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRA  339 (434)
T ss_pred             HHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHhCCCCcEEEEccccccCccCCCCCEEEEECCCCCHHHHhhcccccccC
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCceeEEEEeccCcHHHHHHHHHHhcCcccc
Q psy6712         164 GRKGVAISFVKSDDIRILRDIEQYYSTQIDE  194 (210)
Q Consensus       164 g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~  194 (210)
                      |..|.+++++...|...+.++++++...+..
T Consensus       340 g~~g~ai~l~~~~d~~~~~~i~~~~~~~~~~  370 (434)
T PRK11192        340 GRKGTAISLVEAHDHLLLGKIERYIEEPLKA  370 (434)
T ss_pred             CCCceEEEEecHHHHHHHHHHHHHHhccccc
Confidence            9999999999999999999999988877654

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=1.3e-37  Score=266.84  Aligned_cols=199  Identities=35%  Similarity=0.628  Sum_probs=181.9

Q ss_pred             CCceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhc-CccCCCccEEEechhhHHhccchHHHHHHHHhhCCC-
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRR-VLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPP-   78 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~-~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~-   78 (210)
                      +++++..++||.+.+.+...+.+++||||+||++|++++.+. .+.++.++++||||||.|++.++...+..++..++. 
T Consensus       111 ~~i~v~~l~Gg~~~~~q~~~l~~~~dIiV~TP~rL~~~l~~~~~~~l~~v~~lViDEAh~lld~gf~~~i~~il~~lp~~  190 (572)
T PRK04537        111 LGLRFALVYGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFDLGFIKDIRFLLRRMPER  190 (572)
T ss_pred             CCceEEEEECCCCHHHHHHHHhCCCCEEEECHHHHHHHHHhccccchhheeeeEecCHHHHhhcchHHHHHHHHHhcccc
Confidence            368899999999999999989889999999999999988775 578899999999999999999999888888877664 


Q ss_pred             -chh---------------------------------------------------------------------------H
Q psy6712          79 -ATQ---------------------------------------------------------------------------V   82 (210)
Q Consensus        79 -~~~---------------------------------------------------------------------------~   82 (210)
                       ..|                                                                           +
T Consensus       191 ~~~q~ll~SATl~~~v~~l~~~~l~~p~~i~v~~~~~~~~~i~q~~~~~~~~~k~~~L~~ll~~~~~~k~LVF~nt~~~a  270 (572)
T PRK04537        191 GTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAARVRQRIYFPADEEKQTLLLGLLSRSEGARTMVFVNTKAFV  270 (572)
T ss_pred             cCceEEEEeCCccHHHHHHHHHHhcCCcEEEeccccccccceeEEEEecCHHHHHHHHHHHHhcccCCcEEEEeCCHHHH
Confidence             222                                                                           7


Q ss_pred             HHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcC
Q psy6712          83 DWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGR  162 (210)
Q Consensus        83 ~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR  162 (210)
                      +.+++.|...++.+..+||+|++.+|.+++++|++|+++|||||+++++|+|+|++++||+||+|.+..+|+||+||+||
T Consensus       271 e~l~~~L~~~g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaTdv~arGIDip~V~~VInyd~P~s~~~yvqRiGRaGR  350 (572)
T PRK04537        271 ERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTAR  350 (572)
T ss_pred             HHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEehhhhcCCCccCCCEEEEcCCCCCHHHHhhhhccccc
Confidence            88889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCceeEEEEeccCcHHHHHHHHHHhcCccccccCCc
Q psy6712         163 FGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNG  199 (210)
Q Consensus       163 ~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  199 (210)
                      .|..|.+++|+.+.+...+..+++.+..+++..+...
T Consensus       351 ~G~~G~ai~~~~~~~~~~l~~i~~~~~~~~~~~~~~~  387 (572)
T PRK04537        351 LGEEGDAISFACERYAMSLPDIEAYIEQKIPVEPVTA  387 (572)
T ss_pred             CCCCceEEEEecHHHHHHHHHHHHHHcCCCCccccCh
Confidence            9999999999999999999999999988876655544

>KOG0338|consensus

Probab=100.00  E-value=2.7e-38  Score=255.58  Aligned_cols=186  Identities=33%  Similarity=0.602  Sum_probs=171.0

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhc-CccCCCccEEEechhhHHhccchHHHHHHHHhhCCCch
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRR-VLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPAT   80 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~-~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~   80 (210)
                      +|.|.+++||.+.+.|...|+..|||+|+||||+.+++.+. .++++++-.+|+||||+|++.+|.++++.|+..|++.+
T Consensus       280 ~I~~~L~vGGL~lk~QE~~LRs~PDIVIATPGRlIDHlrNs~sf~ldsiEVLvlDEADRMLeegFademnEii~lcpk~R  359 (691)
T KOG0338|consen  280 DITVGLAVGGLDLKAQEAVLRSRPDIVIATPGRLIDHLRNSPSFNLDSIEVLVLDEADRMLEEGFADEMNEIIRLCPKNR  359 (691)
T ss_pred             cceeeeeecCccHHHHHHHHhhCCCEEEecchhHHHHhccCCCccccceeEEEechHHHHHHHHHHHHHHHHHHhccccc
Confidence            58899999999999999999999999999999999999984 68999999999999999999999999999999999999


Q ss_pred             h------------------------------------------------------------------------------H
Q psy6712          81 Q------------------------------------------------------------------------------V   82 (210)
Q Consensus        81 ~------------------------------------------------------------------------------~   82 (210)
                      |                                                                              +
T Consensus       360 QTmLFSATMteeVkdL~slSL~kPvrifvd~~~~~a~~LtQEFiRIR~~re~dRea~l~~l~~rtf~~~~ivFv~tKk~A  439 (691)
T KOG0338|consen  360 QTMLFSATMTEEVKDLASLSLNKPVRIFVDPNKDTAPKLTQEFIRIRPKREGDREAMLASLITRTFQDRTIVFVRTKKQA  439 (691)
T ss_pred             cceeehhhhHHHHHHHHHhhcCCCeEEEeCCccccchhhhHHHheeccccccccHHHHHHHHHHhcccceEEEEehHHHH
Confidence            9                                                                              1


Q ss_pred             HHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcC
Q psy6712          83 DWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGR  162 (210)
Q Consensus        83 ~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR  162 (210)
                      ..+.=.|--.|+++.-+||.+++.+|.+.++.|+.+++++||||+.+++|+|++.+..||||++|.+...|+||+||++|
T Consensus       440 HRl~IllGLlgl~agElHGsLtQ~QRlesL~kFk~~eidvLiaTDvAsRGLDI~gV~tVINy~mP~t~e~Y~HRVGRTAR  519 (691)
T KOG0338|consen  440 HRLRILLGLLGLKAGELHGSLTQEQRLESLEKFKKEEIDVLIATDVASRGLDIEGVQTVINYAMPKTIEHYLHRVGRTAR  519 (691)
T ss_pred             HHHHHHHHHhhchhhhhcccccHHHHHHHHHHHHhccCCEEEEechhhccCCccceeEEEeccCchhHHHHHHHhhhhhh
Confidence            11111111137899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCceeEEEEeccCcHHHHHHHHHH
Q psy6712         163 FGRKGVAISFVKSDDIRILRDIEQY  187 (210)
Q Consensus       163 ~g~~g~~~~~~~~~~~~~~~~~~~~  187 (210)
                      .|+.|.++.|+...+.+.++.+-+.
T Consensus       520 AGRaGrsVtlvgE~dRkllK~iik~  544 (691)
T KOG0338|consen  520 AGRAGRSVTLVGESDRKLLKEIIKS  544 (691)
T ss_pred             cccCcceEEEeccccHHHHHHHHhh
Confidence            9999999999999999998887765

>KOG0335|consensus

Probab=100.00  E-value=2.1e-38  Score=257.75  Aligned_cols=200  Identities=37%  Similarity=0.611  Sum_probs=187.7

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhc-cchHHHHHHHHhhCCCc-
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLN-KGFKEQIYDVYRYLPPA-   79 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~-~~~~~~~~~i~~~~~~~-   79 (210)
                      ++++..+|||.+...|...+..+|||+|+|||+|.+++..+++.+++++++|+||||+|+| .+|.+++.+|+...... 
T Consensus       180 ~~~~~~~ygg~~~~~q~~~~~~gcdIlvaTpGrL~d~~e~g~i~l~~~k~~vLDEADrMlD~mgF~p~Ir~iv~~~~~~~  259 (482)
T KOG0335|consen  180 GMKSVVVYGGTDLGAQLRFIKRGCDILVATPGRLKDLIERGKISLDNCKFLVLDEADRMLDEMGFEPQIRKIVEQLGMPP  259 (482)
T ss_pred             cceeeeeeCCcchhhhhhhhccCccEEEecCchhhhhhhcceeehhhCcEEEecchHHhhhhccccccHHHHhcccCCCC
Confidence            5788999999999999999999999999999999999999999999999999999999999 89999999998766432 


Q ss_pred             ---hh---------------------------------------------------------------------------
Q psy6712          80 ---TQ---------------------------------------------------------------------------   81 (210)
Q Consensus        80 ---~~---------------------------------------------------------------------------   81 (210)
                         +|                                                                           
T Consensus       260 ~~~~qt~mFSAtfp~~iq~l~~~fl~~~yi~laV~rvg~~~~ni~q~i~~V~~~~kr~~Lldll~~~~~~~~~~~~~~e~  339 (482)
T KOG0335|consen  260 KNNRQTLLFSATFPKEIQRLAADFLKDNYIFLAVGRVGSTSENITQKILFVNEMEKRSKLLDLLNKDDGPPSDGEPKWEK  339 (482)
T ss_pred             ccceeEEEEeccCChhhhhhHHHHhhccceEEEEeeeccccccceeEeeeecchhhHHHHHHHhhcccCCcccCCcccce
Confidence               22                                                                           


Q ss_pred             ----------HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChh
Q psy6712          82 ----------VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRE  151 (210)
Q Consensus        82 ----------~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~  151 (210)
                                +..+...|...++++..+||.-++.+|.+.++.|+.|++++||||+++++|+|+|+|++||+||+|.+..
T Consensus       340 tlvFvEt~~~~d~l~~~l~~~~~~~~sIhg~~tq~er~~al~~Fr~g~~pvlVaT~VaaRGlDi~~V~hVInyDmP~d~d  419 (482)
T KOG0335|consen  340 TLVFVETKRGADELAAFLSSNGYPAKSIHGDRTQIEREQALNDFRNGKAPVLVATNVAARGLDIPNVKHVINYDMPADID  419 (482)
T ss_pred             EEEEeeccchhhHHHHHHhcCCCCceeecchhhhhHHHHHHHHhhcCCcceEEEehhhhcCCCCCCCceeEEeecCcchh
Confidence                      8889999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhhhhcCCCCceeEEEEeccCcHHHHHHHHHHhcCccccccCCccc
Q psy6712         152 LYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKR  201 (210)
Q Consensus       152 ~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  201 (210)
                      +|+||+||+||.|..|.+..|++..+....+.+.+.+...-+++|.=+..
T Consensus       420 ~YvHRIGRTGR~Gn~G~atsf~n~~~~~i~~~L~~~l~ea~q~vP~wl~~  469 (482)
T KOG0335|consen  420 DYVHRIGRTGRVGNGGRATSFFNEKNQNIAKALVEILTEANQEVPQWLSE  469 (482)
T ss_pred             hHHHhccccccCCCCceeEEEeccccchhHHHHHHHHHHhcccCcHHHHh
Confidence            99999999999999999999999999999999999999998888866554

>KOG0340|consensus

Probab=100.00  E-value=4.2e-38  Score=244.67  Aligned_cols=201  Identities=37%  Similarity=0.606  Sum_probs=189.5

Q ss_pred             CCceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhc----CccCCCccEEEechhhHHhccchHHHHHHHHhhC
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRR----VLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYL   76 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~----~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~   76 (210)
                      ++++|.+++||.++-.|...|...+|++|+|||++.+++.++    ...+++++++|+||||.+++..|.+.+..+..-+
T Consensus       102 l~lK~~vivGG~d~i~qa~~L~~rPHvVvatPGRlad~l~sn~~~~~~~~~rlkflVlDEADrvL~~~f~d~L~~i~e~l  181 (442)
T KOG0340|consen  102 LNLKVSVIVGGTDMIMQAAILSDRPHVVVATPGRLADHLSSNLGVCSWIFQRLKFLVLDEADRVLAGCFPDILEGIEECL  181 (442)
T ss_pred             ccceEEEEEccHHHhhhhhhcccCCCeEecCccccccccccCCccchhhhhceeeEEecchhhhhccchhhHHhhhhccC
Confidence            588999999999999999999999999999999999998875    3457899999999999999999999999999988


Q ss_pred             CCchh---------------------------------------------------------------------------
Q psy6712          77 PPATQ---------------------------------------------------------------------------   81 (210)
Q Consensus        77 ~~~~~---------------------------------------------------------------------------   81 (210)
                      |..+|                                                                           
T Consensus       182 P~~RQtLlfSATitd~i~ql~~~~i~k~~a~~~e~~~~vstvetL~q~yI~~~~~vkdaYLv~~Lr~~~~~~~~simIFv  261 (442)
T KOG0340|consen  182 PKPRQTLLFSATITDTIKQLFGCPITKSIAFELEVIDGVSTVETLYQGYILVSIDVKDAYLVHLLRDFENKENGSIMIFV  261 (442)
T ss_pred             CCccceEEEEeehhhHHHHhhcCCcccccceEEeccCCCCchhhhhhheeecchhhhHHHHHHHHhhhhhccCceEEEEe
Confidence            88777                                                                           


Q ss_pred             -----HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHh
Q psy6712          82 -----VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHR  156 (210)
Q Consensus        82 -----~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~  156 (210)
                           ++.++..|+..++.+..+|+.|++.+|...+.+|+.+..+|||||+.+++|+|+|.|++|||||.|.++.+|+||
T Consensus       262 nttr~cQ~l~~~l~~le~r~~~lHs~m~Q~eR~~aLsrFrs~~~~iliaTDVAsRGLDIP~V~LVvN~diPr~P~~yiHR  341 (442)
T KOG0340|consen  262 NTTRECQLLSMTLKNLEVRVVSLHSQMPQKERLAALSRFRSNAARILIATDVASRGLDIPTVELVVNHDIPRDPKDYIHR  341 (442)
T ss_pred             ehhHHHHHHHHHHhhhceeeeehhhcchHHHHHHHHHHHhhcCccEEEEechhhcCCCCCceeEEEecCCCCCHHHHHHh
Confidence                 788888999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhcCCCCceeEEEEeccCcHHHHHHHHHHhcCccccccCCccc
Q psy6712         157 IGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKR  201 (210)
Q Consensus       157 ~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  201 (210)
                      +||++|.|+.|.+++++...|.+.+..+|+-.+..+.+.+.....
T Consensus       342 vGRtARAGR~G~aiSivt~rDv~l~~aiE~~igkKl~e~~~~~~~  386 (442)
T KOG0340|consen  342 VGRTARAGRKGMAISIVTQRDVELLQAIEEEIGKKLTEYNKVQRT  386 (442)
T ss_pred             hcchhcccCCcceEEEechhhHHHHHHHHHHHhcccccccccchh
Confidence            999999999999999999999999999999999999988766543

>KOG0345|consensus

Probab=100.00  E-value=1.4e-37  Score=249.16  Aligned_cols=183  Identities=34%  Similarity=0.698  Sum_probs=163.1

Q ss_pred             CceEEEEEcCcchHHHHHHhcC-CCcEEEEChHHHHHHHHhcC--ccCCCccEEEechhhHHhccchHHHHHHHHhhCCC
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDY-GQHVVSGTPGRVFDMIRRRV--LRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPP   78 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~-~~~Ili~Tp~~l~~~l~~~~--~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~   78 (210)
                      +++|.+++||.+.++..+.+.+ +++|+|||||||.+++++..  ++++++.++|+||||++++.||...++.|+.++|+
T Consensus       108 ~l~~~l~vGG~~v~~Di~~fkee~~nIlVgTPGRL~di~~~~~~~l~~rsLe~LVLDEADrLldmgFe~~~n~ILs~LPK  187 (567)
T KOG0345|consen  108 NLNCELLVGGRSVEEDIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRSLEILVLDEADRLLDMGFEASVNTILSFLPK  187 (567)
T ss_pred             ccceEEEecCccHHHHHHHHHHhCCcEEEeCchhHHHHHhchhhhccccccceEEecchHhHhcccHHHHHHHHHHhccc
Confidence            5789999999999999999975 79999999999999999954  45569999999999999999999999999999998


Q ss_pred             chh-----------------------------------------------------------------------------
Q psy6712          79 ATQ-----------------------------------------------------------------------------   81 (210)
Q Consensus        79 ~~~-----------------------------------------------------------------------------   81 (210)
                      .+.                                                                             
T Consensus       188 QRRTGLFSATq~~~v~dL~raGLRNpv~V~V~~k~~~~tPS~L~~~Y~v~~a~eK~~~lv~~L~~~~~kK~iVFF~TCas  267 (567)
T KOG0345|consen  188 QRRTGLFSATQTQEVEDLARAGLRNPVRVSVKEKSKSATPSSLALEYLVCEADEKLSQLVHLLNNNKDKKCIVFFPTCAS  267 (567)
T ss_pred             ccccccccchhhHHHHHHHHhhccCceeeeecccccccCchhhcceeeEecHHHHHHHHHHHHhccccccEEEEecCcch
Confidence            766                                                                             


Q ss_pred             HHHHHHHHHh--cCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhh
Q psy6712          82 VDWLTEKMRE--ANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGR  159 (210)
Q Consensus        82 ~~~l~~~l~~--~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR  159 (210)
                      ++.....|..  ...++..+||.|++..|..++++|+.....+|+||+++++|+|+|++++||+||+|.+++.|.||+||
T Consensus       268 VeYf~~~~~~~l~~~~i~~iHGK~~q~~R~k~~~~F~~~~~~vl~~TDVaARGlDip~iD~VvQ~DpP~~~~~FvHR~GR  347 (567)
T KOG0345|consen  268 VEYFGKLFSRLLKKREIFSIHGKMSQKARAKVLEAFRKLSNGVLFCTDVAARGLDIPGIDLVVQFDPPKDPSSFVHRCGR  347 (567)
T ss_pred             HHHHHHHHHHHhCCCcEEEecchhcchhHHHHHHHHHhccCceEEeehhhhccCCCCCceEEEecCCCCChhHHHhhcch
Confidence            3444444432  36789999999999999999999999888999999999999999999999999999999999999999


Q ss_pred             hcCCCCceeEEEEeccCcHHHHHHH
Q psy6712         160 SGRFGRKGVAISFVKSDDIRILRDI  184 (210)
Q Consensus       160 ~gR~g~~g~~~~~~~~~~~~~~~~~  184 (210)
                      +||.|+.|.+++|+.+.+.....-+
T Consensus       348 TaR~gr~G~Aivfl~p~E~aYveFl  372 (567)
T KOG0345|consen  348 TARAGREGNAIVFLNPREEAYVEFL  372 (567)
T ss_pred             hhhccCccceEEEecccHHHHHHHH
Confidence            9999999999999999665554433

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=3.3e-36  Score=254.44  Aligned_cols=206  Identities=35%  Similarity=0.618  Sum_probs=183.0

Q ss_pred             CCceEEEEEcCcchHHHHHHhcC-CCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCc
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLDY-GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPA   79 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~~-~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~   79 (210)
                      +|+++..++||.+...+.+.+.. .++|||+||++|++++.++...+++++++||||+|.+.+.++...+..++..++..
T Consensus       189 ~~~~v~~~~gg~~~~~~~~~~~~~~~~Iiv~TP~~Ll~~~~~~~~~l~~l~~lViDEah~l~~~~~~~~l~~i~~~~~~~  268 (475)
T PRK01297        189 TGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLDEADRMLDMGFIPQVRQIIRQTPRK  268 (475)
T ss_pred             CCCEEEEEEccCChHHHHHHHhCCCCCEEEECHHHHHHHHHcCCcccccCceEEechHHHHHhcccHHHHHHHHHhCCCC
Confidence            36889999999998888888754 68999999999999998888899999999999999999988888887777665431


Q ss_pred             --hh---------------------------------------------------------------------------H
Q psy6712          80 --TQ---------------------------------------------------------------------------V   82 (210)
Q Consensus        80 --~~---------------------------------------------------------------------------~   82 (210)
                        .+                                                                           +
T Consensus       269 ~~~q~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~ll~~~~~~~~IVF~~s~~~~  348 (475)
T PRK01297        269 EERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTVEQHVYAVAGSDKYKLLYNLVTQNPWERVMVFANRKDEV  348 (475)
T ss_pred             CCceEEEEEeecCHHHHHHHHHhccCCEEEEeccCcCCCCcccEEEEEecchhHHHHHHHHHHhcCCCeEEEEeCCHHHH
Confidence              11                                                                           7


Q ss_pred             HHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcC
Q psy6712          83 DWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGR  162 (210)
Q Consensus        83 ~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR  162 (210)
                      +.+++.|...++.+..+||+|+.++|.++++.|++|++++||||+++++|+|+|++++||+|++|.+..+|+||+||+||
T Consensus       349 ~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~Fr~G~~~vLvaT~~l~~GIDi~~v~~VI~~~~P~s~~~y~Qr~GRaGR  428 (475)
T PRK01297        349 RRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGR  428 (475)
T ss_pred             HHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHhCCCCcEEEEccccccCCcccCCCEEEEeCCCCCHHHHHHhhCccCC
Confidence            88888998889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCceeEEEEeccCcHHHHHHHHHHhcCccccccCCccccCCCCC
Q psy6712         163 FGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRSLHSYP  207 (210)
Q Consensus       163 ~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  207 (210)
                      .|+.|.+++|+.+.|...+..+++.++.++. +.++..+++...|
T Consensus       429 ~g~~g~~i~~~~~~d~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~  472 (475)
T PRK01297        429 AGASGVSISFAGEDDAFQLPEIEELLGRKIS-CEMPPAELLKPVP  472 (475)
T ss_pred             CCCCceEEEEecHHHHHHHHHHHHHhCCCCc-ccCCcHHHhhhhh
Confidence            9999999999999999999999999988873 4555555555444

>PTZ00424 helicase 45; Provisional

Probab=100.00  E-value=3e-36  Score=250.06  Aligned_cols=200  Identities=67%  Similarity=1.101  Sum_probs=181.3

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchh
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ   81 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~   81 (210)
                      ++++..+.||.....++..+.++++|+|+||+++.+++.++...+++++++|+||+|++.+.++...+..++..++...+
T Consensus       124 ~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~l~~i~lvViDEah~~~~~~~~~~~~~i~~~~~~~~~  203 (401)
T PTZ00424        124 KVRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSRGFKGQIYDVFKKLPPDVQ  203 (401)
T ss_pred             CceEEEEECCcCHHHHHHHHcCCCCEEEECcHHHHHHHHhCCcccccccEEEEecHHHHHhcchHHHHHHHHhhCCCCcE
Confidence            56788899999988888888889999999999999999988888999999999999999988877666666655443322


Q ss_pred             ----------------------------------------------------------------------------HHHH
Q psy6712          82 ----------------------------------------------------------------------------VDWL   85 (210)
Q Consensus        82 ----------------------------------------------------------------------------~~~l   85 (210)
                                                                                                  ++.+
T Consensus       204 ~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ivF~~t~~~~~~l  283 (401)
T PTZ00424        204 VALFSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKEEWKFDTLCDLYETLTITQAIIYCNTRRKVDYL  283 (401)
T ss_pred             EEEEEecCCHHHHHHHHHHcCCCEEEEeCCCCcccCCceEEEEecChHHHHHHHHHHHHHhcCCCeEEEEecCcHHHHHH
Confidence                                                                                        7788


Q ss_pred             HHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCC
Q psy6712          86 TEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGR  165 (210)
Q Consensus        86 ~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~  165 (210)
                      ++.|.+.++.+..+||+|+.++|..++++|++|++++||||+.+++|+|+|++++||++|+|.+...|+||+||+||.|.
T Consensus       284 ~~~l~~~~~~~~~~h~~~~~~~R~~i~~~f~~g~~~vLvaT~~l~~GiDip~v~~VI~~~~p~s~~~y~qr~GRagR~g~  363 (401)
T PTZ00424        284 TKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGR  363 (401)
T ss_pred             HHHHHHCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEcccccCCcCcccCCEEEEECCCCCHHHEeecccccccCCC
Confidence            88898889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceeEEEEeccCcHHHHHHHHHHhcCccccccCCccc
Q psy6712         166 KGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKR  201 (210)
Q Consensus       166 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  201 (210)
                      .|.|+.++.+.+...++.+++.+...+++.++....
T Consensus       364 ~G~~i~l~~~~~~~~~~~~e~~~~~~~~~~~~~~~~  399 (401)
T PTZ00424        364 KGVAINFVTPDDIEQLKEIERHYNTQIEEMPMEVAD  399 (401)
T ss_pred             CceEEEEEcHHHHHHHHHHHHHHCCcccccCcchhh
Confidence            999999999999999999999999999988776544

>KOG0339|consensus

Probab=100.00  E-value=3.3e-36  Score=243.47  Aligned_cols=203  Identities=32%  Similarity=0.544  Sum_probs=193.1

Q ss_pred             CCceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCch
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPAT   80 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~   80 (210)
                      .||+++++|||.+..+|.+.|..+++|+||||+||.+++..+..+++++.++||||+++|++.||..++..|...+.+.+
T Consensus       323 ygl~~v~~ygGgsk~eQ~k~Lk~g~EivVaTPgRlid~VkmKatn~~rvS~LV~DEadrmfdmGfe~qVrSI~~hirpdr  402 (731)
T KOG0339|consen  323 YGLRVVAVYGGGSKWEQSKELKEGAEIVVATPGRLIDMVKMKATNLSRVSYLVLDEADRMFDMGFEPQVRSIKQHIRPDR  402 (731)
T ss_pred             ccceEEEeecCCcHHHHHHhhhcCCeEEEechHHHHHHHHhhcccceeeeEEEEechhhhhccccHHHHHHHHhhcCCcc
Confidence            38999999999999999999999999999999999999999999999999999999999999999999999999888887


Q ss_pred             h-----------------------------------------------------------------------------HH
Q psy6712          81 Q-----------------------------------------------------------------------------VD   83 (210)
Q Consensus        81 ~-----------------------------------------------------------------------------~~   83 (210)
                      |                                                                             ++
T Consensus       403 QtllFsaTf~~kIe~lard~L~dpVrvVqg~vgean~dITQ~V~V~~s~~~Kl~wl~~~L~~f~S~gkvlifVTKk~~~e  482 (731)
T KOG0339|consen  403 QTLLFSATFKKKIEKLARDILSDPVRVVQGEVGEANEDITQTVSVCPSEEKKLNWLLRHLVEFSSEGKVLIFVTKKADAE  482 (731)
T ss_pred             eEEEeeccchHHHHHHHHHHhcCCeeEEEeehhccccchhheeeeccCcHHHHHHHHHHhhhhccCCcEEEEEeccCCHH
Confidence            7                                                                             77


Q ss_pred             HHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCC
Q psy6712          84 WLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRF  163 (210)
Q Consensus        84 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~  163 (210)
                      .++..|.-+++++..+||+|.+.+|.+++..|+.+...|||+|+...+|+|+|++..||+||+-.++..|.||+||+||.
T Consensus       483 ~i~a~Lklk~~~v~llhgdkdqa~rn~~ls~fKkk~~~VlvatDvaargldI~~ikTVvnyD~ardIdththrigrtgRa  562 (731)
T KOG0339|consen  483 EIAANLKLKGFNVSLLHGDKDQAERNEVLSKFKKKRKPVLVATDVAARGLDIPSIKTVVNYDFARDIDTHTHRIGRTGRA  562 (731)
T ss_pred             HHHHHhccccceeeeecCchhhHHHHHHHHHHhhcCCceEEEeeHhhcCCCccccceeecccccchhHHHHHHhhhcccc
Confidence            78888888899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCceeEEEEeccCcHHHHHHHHHHhcCccccccCCccccC
Q psy6712         164 GRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRSL  203 (210)
Q Consensus       164 g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  203 (210)
                      |..|.++.++.+.+..+.-.+-+.+....+.+|.+.-.+.
T Consensus       563 g~kGvayTlvTeKDa~fAG~LVnnLe~agQnVP~~l~dla  602 (731)
T KOG0339|consen  563 GEKGVAYTLVTEKDAEFAGHLVNNLEGAGQNVPDELMDLA  602 (731)
T ss_pred             cccceeeEEechhhHHHhhHHHHHHhhccccCChHHHHHH
Confidence            9999999999999999999999999998888887765543

>KOG0343|consensus

Probab=100.00  E-value=4.9e-36  Score=244.47  Aligned_cols=196  Identities=32%  Similarity=0.574  Sum_probs=174.6

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhc-CccCCCccEEEechhhHHhccchHHHHHHHHhhCCCch
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRR-VLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPAT   80 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~-~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~   80 (210)
                      +.++.+++||.+.+....++ ++.||||||||||+.++... .++.+++.++|+||||+|++.||...++.|+.++|..+
T Consensus       169 ~fSaGLiiGG~~~k~E~eRi-~~mNILVCTPGRLLQHmde~~~f~t~~lQmLvLDEADR~LDMGFk~tL~~Ii~~lP~~R  247 (758)
T KOG0343|consen  169 DFSAGLIIGGKDVKFELERI-SQMNILVCTPGRLLQHMDENPNFSTSNLQMLVLDEADRMLDMGFKKTLNAIIENLPKKR  247 (758)
T ss_pred             ccccceeecCchhHHHHHhh-hcCCeEEechHHHHHHhhhcCCCCCCcceEEEeccHHHHHHHhHHHHHHHHHHhCChhh
Confidence            45788999999988777665 57899999999999999874 67889999999999999999999999999999999988


Q ss_pred             h-----------------------------------------------------------------------------HH
Q psy6712          81 Q-----------------------------------------------------------------------------VD   83 (210)
Q Consensus        81 ~-----------------------------------------------------------------------------~~   83 (210)
                      |                                                                             +.
T Consensus       248 QTLLFSATqt~svkdLaRLsL~dP~~vsvhe~a~~atP~~L~Q~y~~v~l~~Ki~~L~sFI~shlk~K~iVF~SscKqvk  327 (758)
T KOG0343|consen  248 QTLLFSATQTKSVKDLARLSLKDPVYVSVHENAVAATPSNLQQSYVIVPLEDKIDMLWSFIKSHLKKKSIVFLSSCKQVK  327 (758)
T ss_pred             eeeeeecccchhHHHHHHhhcCCCcEEEEeccccccChhhhhheEEEEehhhHHHHHHHHHHhccccceEEEEehhhHHH
Confidence            8                                                                             77


Q ss_pred             HHHHHHHh--cCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhc
Q psy6712          84 WLTEKMRE--ANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSG  161 (210)
Q Consensus        84 ~l~~~l~~--~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~g  161 (210)
                      ++++.+..  -|++...+||.|++..|.++++.|...+.-||+||+++++|+|+|.|++||++|+|.++.+|+||+||++
T Consensus       328 f~~e~F~rlrpg~~l~~L~G~~~Q~~R~ev~~~F~~~~~~vLF~TDv~aRGLDFpaVdwViQ~DCPedv~tYIHRvGRtA  407 (758)
T KOG0343|consen  328 FLYEAFCRLRPGIPLLALHGTMSQKKRIEVYKKFVRKRAVVLFCTDVAARGLDFPAVDWVIQVDCPEDVDTYIHRVGRTA  407 (758)
T ss_pred             HHHHHHHhcCCCCceeeeccchhHHHHHHHHHHHHHhcceEEEeehhhhccCCCcccceEEEecCchhHHHHHHHhhhhh
Confidence            77887755  3889999999999999999999999988899999999999999999999999999999999999999999


Q ss_pred             CCCCceeEEEEeccCc-HHHHHHHHHHhcCccccccCCc
Q psy6712         162 RFGRKGVAISFVKSDD-IRILRDIEQYYSTQIDEMPMNG  199 (210)
Q Consensus       162 R~g~~g~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~  199 (210)
                      |.+..|.+++++.+.+ ..++..+++.- +.+.++....
T Consensus       408 R~~~~G~sll~L~psEeE~~l~~Lq~k~-I~i~~i~i~~  445 (758)
T KOG0343|consen  408 RYKERGESLLMLTPSEEEAMLKKLQKKK-IPIKEIKIDP  445 (758)
T ss_pred             cccCCCceEEEEcchhHHHHHHHHHHcC-CCHHhhccCH
Confidence            9999999999999988 56677776654 5555554443

>KOG0348|consensus

Probab=100.00  E-value=2.2e-35  Score=239.82  Aligned_cols=187  Identities=32%  Similarity=0.576  Sum_probs=164.6

Q ss_pred             eEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHh-cCccCCCccEEEechhhHHhccchHHHHHHHHhhCCC----
Q psy6712           4 QCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRR-RVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPP----   78 (210)
Q Consensus         4 ~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~-~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~----   78 (210)
                      --..+.||.+.+....+|++|++|||+|||||.+++.+ +.+.++.++++|+||+|++++.||..++..|++.+..    
T Consensus       242 VPg~lmGGEkkKSEKARLRKGiNILIgTPGRLvDHLknT~~i~~s~LRwlVlDEaDrlleLGfekdit~Il~~v~~~~~~  321 (708)
T KOG0348|consen  242 VPGVLMGGEKKKSEKARLRKGINILIGTPGRLVDHLKNTKSIKFSRLRWLVLDEADRLLELGFEKDITQILKAVHSIQNA  321 (708)
T ss_pred             eeceeecccccccHHHHHhcCceEEEcCchHHHHHHhccchheeeeeeEEEecchhHHHhccchhhHHHHHHHHhhccch
Confidence            34578999999999999999999999999999999998 6788999999999999999999999999999987732    


Q ss_pred             ch---------h--------------------------------------------------------------------
Q psy6712          79 AT---------Q--------------------------------------------------------------------   81 (210)
Q Consensus        79 ~~---------~--------------------------------------------------------------------   81 (210)
                      .+         |                                                                    
T Consensus       322 e~~~~~lp~q~q~mLlSATLtd~V~rLa~~sLkDpv~I~ld~s~~~~~p~~~a~~ev~~~~~~~~l~~~~iPeqL~qry~  401 (708)
T KOG0348|consen  322 ECKDPKLPHQLQNMLLSATLTDGVNRLADLSLKDPVYISLDKSHSQLNPKDKAVQEVDDGPAGDKLDSFAIPEQLLQRYT  401 (708)
T ss_pred             hcccccccHHHHhHhhhhhhHHHHHHHhhccccCceeeeccchhhhcCcchhhhhhcCCcccccccccccCcHHhhhceE
Confidence            11         1                                                                    


Q ss_pred             ------------------------------------HHHHHHHHHhc----------------------CceEEEecCCC
Q psy6712          82 ------------------------------------VDWLTEKMREA----------------------NFTVSSMHGDM  103 (210)
Q Consensus        82 ------------------------------------~~~l~~~l~~~----------------------~~~~~~~~~~~  103 (210)
                                                          +++-.+.|.+.                      +.+..-+||+|
T Consensus       402 vVPpKLRLV~Laa~L~~~~k~~~~qk~iVF~S~~d~VeFHy~lf~~~l~~~~e~~s~~~~s~g~~~l~~~~k~~rLHGsm  481 (708)
T KOG0348|consen  402 VVPPKLRLVALAALLLNKVKFEEKQKMIVFFSCSDSVEFHYSLFSEALLSHLEGSSGAPDSEGLPPLFMDLKFYRLHGSM  481 (708)
T ss_pred             ecCCchhHHHHHHHHHHHhhhhhhceeEEEEechhHHHHHHHHHHhhhhcccccccCCcccCCChhhhhcceEEEecCch
Confidence                                                44444444331                      35788899999


Q ss_pred             CHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCCceeEEEEeccCcHHHHHH
Q psy6712         104 PQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRD  183 (210)
Q Consensus       104 ~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~  183 (210)
                      ++++|..++..|......||+||+.+++|+|+|+|.+||+||+|.+..+|+||+||++|.|..|.+++|+.+.|.+.+..
T Consensus       482 ~QeeRts~f~~Fs~~~~~VLLcTDVAaRGLDlP~V~~vVQYd~P~s~adylHRvGRTARaG~kG~alLfL~P~Eaey~~~  561 (708)
T KOG0348|consen  482 EQEERTSVFQEFSHSRRAVLLCTDVAARGLDLPHVGLVVQYDPPFSTADYLHRVGRTARAGEKGEALLFLLPSEAEYVNY  561 (708)
T ss_pred             hHHHHHHHHHhhccccceEEEehhhhhccCCCCCcCeEEEeCCCCCHHHHHHHhhhhhhccCCCceEEEecccHHHHHHH
Confidence            99999999999999888899999999999999999999999999999999999999999999999999999999998887


Q ss_pred             HHHHhcC
Q psy6712         184 IEQYYST  190 (210)
Q Consensus       184 ~~~~~~~  190 (210)
                      ++++...
T Consensus       562 l~~~~~~  568 (708)
T KOG0348|consen  562 LKKHHIM  568 (708)
T ss_pred             HHhhcch
Confidence            7765443

>KOG0347|consensus

Probab=100.00  E-value=1.5e-35  Score=241.46  Aligned_cols=192  Identities=31%  Similarity=0.534  Sum_probs=177.6

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCc---cCCCccEEEechhhHHhccchHHHHHHHHhhCCC
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVL---RTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPP   78 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~---~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~   78 (210)
                      ||+++.++||...+.|.+.|...+||+|+|||||+.++..+..   ++++++++|+||+|+|++.|+-+++..++..+..
T Consensus       291 ~i~v~si~GGLavqKQqRlL~~~p~IVVATPGRlweli~e~n~~l~~~k~vkcLVlDEaDRmvekghF~Els~lL~~L~e  370 (731)
T KOG0347|consen  291 QIRVASITGGLAVQKQQRLLNQRPDIVVATPGRLWELIEEDNTHLGNFKKVKCLVLDEADRMVEKGHFEELSKLLKHLNE  370 (731)
T ss_pred             CeEEEEeechhHHHHHHHHHhcCCCEEEecchHHHHHHHhhhhhhhhhhhceEEEEccHHHHhhhccHHHHHHHHHHhhh
Confidence            7999999999999999999999999999999999999988654   6789999999999999999999999999887762


Q ss_pred             c-----hh------------------------------------------------------------------------
Q psy6712          79 A-----TQ------------------------------------------------------------------------   81 (210)
Q Consensus        79 ~-----~~------------------------------------------------------------------------   81 (210)
                      .     +|                                                                        
T Consensus       371 ~~~~~qrQTlVFSATlt~~~~~~~~~~~k~~~k~~~~~~kiq~Lmk~ig~~~kpkiiD~t~q~~ta~~l~Es~I~C~~~e  450 (731)
T KOG0347|consen  371 EQKNRQRQTLVFSATLTLVLQQPLSSSRKKKDKEDELNAKIQHLMKKIGFRGKPKIIDLTPQSATASTLTESLIECPPLE  450 (731)
T ss_pred             hhcccccceEEEEEEeehhhcChhHHhhhccchhhhhhHHHHHHHHHhCccCCCeeEecCcchhHHHHHHHHhhcCCccc
Confidence            1     11                                                                        


Q ss_pred             -------------------------HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCC
Q psy6712          82 -------------------------VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQ  136 (210)
Q Consensus        82 -------------------------~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~  136 (210)
                                               +..|.-+|...+++...+|+.|.+.+|.+.+++|++....+||||+.+++|+|+|
T Consensus       451 KD~ylyYfl~ryPGrTlVF~NsId~vKRLt~~L~~L~i~p~~LHA~M~QKqRLknLEkF~~~~~~VLiaTDVAARGLDIp  530 (731)
T KOG0347|consen  451 KDLYLYYFLTRYPGRTLVFCNSIDCVKRLTVLLNNLDIPPLPLHASMIQKQRLKNLEKFKQSPSGVLIATDVAARGLDIP  530 (731)
T ss_pred             cceeEEEEEeecCCceEEEechHHHHHHHHHHHhhcCCCCchhhHHHHHHHHHHhHHHHhcCCCeEEEeehhhhccCCCC
Confidence                                     7778888888999999999999999999999999999999999999999999999


Q ss_pred             CCcEEEEecCCCChhHHHHhhhhhcCCCCceeEEEEeccCcHHHHHHHHHHhcCccc
Q psy6712         137 QVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQID  193 (210)
Q Consensus       137 ~~~~vi~~~~p~s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~  193 (210)
                      .++|||||.+|.+..-|+||.||++|.+..|..++++.+.+...+.++.+.++..-+
T Consensus       531 ~V~HVIHYqVPrtseiYVHRSGRTARA~~~Gvsvml~~P~e~~~~~KL~ktL~k~~d  587 (731)
T KOG0347|consen  531 GVQHVIHYQVPRTSEIYVHRSGRTARANSEGVSVMLCGPQEVGPLKKLCKTLKKKED  587 (731)
T ss_pred             CcceEEEeecCCccceeEecccccccccCCCeEEEEeChHHhHHHHHHHHHHhhccC
Confidence            999999999999999999999999999999999999999999999999988866543

>KOG0327|consensus

Probab=100.00  E-value=1.2e-34  Score=227.49  Aligned_cols=202  Identities=63%  Similarity=1.021  Sum_probs=190.2

Q ss_pred             CCceEEEEEcCcchHHHHHHhc-CCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCc
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLD-YGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPA   79 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~-~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~   79 (210)
                      ++++|+.+.||.+...+-..+. ..++|+++|||++.+.+..+.+..+.++++|+||+|.|+..++.+++..++..+|..
T Consensus       121 ~~~~v~~~igg~~~~~~~~~i~~~~~hivvGTpgrV~dml~~~~l~~~~iKmfvlDEaDEmLs~gfkdqI~~if~~lp~~  200 (397)
T KOG0327|consen  121 MDVSVHACIGGTNVRREDQALLKDKPHIVVGTPGRVFDMLNRGSLSTDGIKMFVLDEADEMLSRGFKDQIYDIFQELPSD  200 (397)
T ss_pred             cceeeeeecCcccchhhhhhhhccCceeecCCchhHHHhhccccccccceeEEeecchHhhhccchHHHHHHHHHHcCcc
Confidence            5789999999999886665554 479999999999999999998888999999999999999999999999999999887


Q ss_pred             hh-------------------------------------------------------------------------HHHHH
Q psy6712          80 TQ-------------------------------------------------------------------------VDWLT   86 (210)
Q Consensus        80 ~~-------------------------------------------------------------------------~~~l~   86 (210)
                      .|                                                                         +.++.
T Consensus       201 vQv~l~SAT~p~~vl~vt~~f~~~pv~i~vkk~~ltl~gikq~~i~v~k~~k~~~l~dl~~~~~q~~if~nt~r~v~~l~  280 (397)
T KOG0327|consen  201 VQVVLLSATMPSDVLEVTKKFMREPVRILVKKDELTLEGIKQFYINVEKEEKLDTLCDLYRRVTQAVIFCNTRRKVDNLT  280 (397)
T ss_pred             hhheeecccCcHHHHHHHHHhccCceEEEecchhhhhhheeeeeeeccccccccHHHHHHHhhhcceEEecchhhHHHHH
Confidence            77                                                                         67788


Q ss_pred             HHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCCc
Q psy6712          87 EKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRK  166 (210)
Q Consensus        87 ~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~~  166 (210)
                      .+|...+..+..+|+.|.+.+|..++..|+.|..++||+|+..++|+|+.+++.|++|++|....+|+||+||+||.|++
T Consensus       281 ~~L~~~~~~~s~~~~d~~q~~R~~~~~ef~~gssrvlIttdl~argidv~~~slvinydlP~~~~~yihR~gr~gr~grk  360 (397)
T KOG0327|consen  281 DKLRAHGFTVSAIHGDMEQNERDTLMREFRSGSSRVLITTDLLARGIDVQQVSLVVNYDLPARKENYIHRIGRAGRFGRK  360 (397)
T ss_pred             HHHhhCCceEEEeecccchhhhhHHHHHhhcCCceEEeeccccccccchhhcceeeeeccccchhhhhhhcccccccCCC
Confidence            88888999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCcHHHHHHHHHHhcCccccccCCcccc
Q psy6712         167 GVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRS  202 (210)
Q Consensus       167 g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  202 (210)
                      |.++.++.+.+...++++++++...++++|.+...+
T Consensus       361 g~~in~v~~~d~~~lk~ie~~y~~~i~e~p~~~~~l  396 (397)
T KOG0327|consen  361 GVAINFVTEEDVRDLKDIEKFYNTPIEELPSNFADL  396 (397)
T ss_pred             ceeeeeehHhhHHHHHhHHHhcCCcceecccchhhc
Confidence            999999999999999999999999999999987664

>KOG4284|consensus

Probab=100.00  E-value=3.2e-33  Score=231.61  Aligned_cols=182  Identities=33%  Similarity=0.637  Sum_probs=169.4

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhc-cchHHHHHHHHhhCCCch
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLN-KGFKEQIYDVYRYLPPAT   80 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~-~~~~~~~~~i~~~~~~~~   80 (210)
                      |.+|..++||+.......+++ .++|+||||||+..++..+.++.++++++|+||||.|.+ ..|.+++..|+..+|..+
T Consensus       122 g~~csvfIGGT~~~~d~~rlk-~~rIvIGtPGRi~qL~el~~~n~s~vrlfVLDEADkL~~t~sfq~~In~ii~slP~~r  200 (980)
T KOG4284|consen  122 GARCSVFIGGTAHKLDLIRLK-QTRIVIGTPGRIAQLVELGAMNMSHVRLFVLDEADKLMDTESFQDDINIIINSLPQIR  200 (980)
T ss_pred             CcceEEEecCchhhhhhhhhh-hceEEecCchHHHHHHHhcCCCccceeEEEeccHHhhhchhhHHHHHHHHHHhcchhh
Confidence            678999999999998887774 678999999999999999999999999999999999998 689999999999999998


Q ss_pred             h-------------------------------------------------------------------------------
Q psy6712          81 Q-------------------------------------------------------------------------------   81 (210)
Q Consensus        81 ~-------------------------------------------------------------------------------   81 (210)
                      |                                                                               
T Consensus       201 Qv~a~SATYp~nLdn~Lsk~mrdp~lVr~n~~d~~L~GikQyv~~~~s~nnsveemrlklq~L~~vf~~ipy~QAlVF~~  280 (980)
T KOG4284|consen  201 QVAAFSATYPRNLDNLLSKFMRDPALVRFNADDVQLFGIKQYVVAKCSPNNSVEEMRLKLQKLTHVFKSIPYVQALVFCD  280 (980)
T ss_pred             eeeEEeccCchhHHHHHHHHhcccceeecccCCceeechhheeeeccCCcchHHHHHHHHHHHHHHHhhCchHHHHhhhh
Confidence            8                                                                               


Q ss_pred             ----HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhh
Q psy6712          82 ----VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRI  157 (210)
Q Consensus        82 ----~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~  157 (210)
                          ++.++.+|...|+.+.++.|.|++.+|..+++.++.-..+|||+|+..++|+|-+++++|||.|+|.+...|.||+
T Consensus       281 ~~sra~~~a~~L~ssG~d~~~ISgaM~Q~~Rl~a~~~lr~f~~rILVsTDLtaRGIDa~~vNLVVNiD~p~d~eTY~HRI  360 (980)
T KOG4284|consen  281 QISRAEPIATHLKSSGLDVTFISGAMSQKDRLLAVDQLRAFRVRILVSTDLTARGIDADNVNLVVNIDAPADEETYFHRI  360 (980)
T ss_pred             hhhhhhHHHHHhhccCCCeEEeccccchhHHHHHHHHhhhceEEEEEecchhhccCCccccceEEecCCCcchHHHHHHh
Confidence                7888899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhcCCCCceeEEEEeccCcH-HHHHHH
Q psy6712         158 GRSGRFGRKGVAISFVKSDDI-RILRDI  184 (210)
Q Consensus       158 GR~gR~g~~g~~~~~~~~~~~-~~~~~~  184 (210)
                      |||||.|..|.++.|+...+. ..+..+
T Consensus       361 GRAgRFG~~G~aVT~~~~~~e~~~f~~m  388 (980)
T KOG4284|consen  361 GRAGRFGAHGAAVTLLEDERELKGFTAM  388 (980)
T ss_pred             hhcccccccceeEEEeccchhhhhhHHH
Confidence            999999999999999987654 444444

>KOG0350|consensus

Probab=100.00  E-value=2.8e-32  Score=220.21  Aligned_cols=188  Identities=30%  Similarity=0.566  Sum_probs=161.7

Q ss_pred             CceEEEEEcCcchHHHHHHhcC-CC----cEEEEChHHHHHHHHh-cCccCCCccEEEechhhHHhccchHHHHHHHHhh
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDY-GQ----HVVSGTPGRVFDMIRR-RVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRY   75 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~-~~----~Ili~Tp~~l~~~l~~-~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~   75 (210)
                      |+.|..+.|-.+.+.....|.+ .+    ||||+|||||.+++.+ +.+++++++++||||||+|++..|..++..+...
T Consensus       243 gL~V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPGRLVDHl~~~k~f~Lk~LrfLVIDEADRll~qsfQ~Wl~~v~~~  322 (620)
T KOG0350|consen  243 GLAVCSLSGQNSLEDEARQLASDPPECRIDILVATPGRLVDHLNNTKSFDLKHLRFLVIDEADRLLDQSFQEWLDTVMSL  322 (620)
T ss_pred             ceEEEecccccchHHHHHHHhcCCCccccceEEcCchHHHHhccCCCCcchhhceEEEechHHHHHHHHHHHHHHHHHHH
Confidence            6678888999998888888865 33    9999999999999995 7899999999999999999998888877777665


Q ss_pred             CCCchh--------------------------------------------------------------------------
Q psy6712          76 LPPATQ--------------------------------------------------------------------------   81 (210)
Q Consensus        76 ~~~~~~--------------------------------------------------------------------------   81 (210)
                      +...+.                                                                          
T Consensus       323 ~~~~k~~~~~~nii~~~~~~~pt~~~e~~t~~~~~~~~l~kL~~satLsqdP~Kl~~l~l~~Prl~~v~~~~~~ryslp~  402 (620)
T KOG0350|consen  323 CKTMKRVACLDNIIRQRQAPQPTVLSELLTKLGKLYPPLWKLVFSATLSQDPSKLKDLTLHIPRLFHVSKPLIGRYSLPS  402 (620)
T ss_pred             hCCchhhcChhhhhhhcccCCchhhHHHHhhcCCcCchhHhhhcchhhhcChHHHhhhhcCCCceEEeecccceeeecCh
Confidence            543311                                                                          


Q ss_pred             ---------------------------------------HHHHHH----HHHhcCceEEEecCCCCHhHHHHHHHHHhcC
Q psy6712          82 ---------------------------------------VDWLTE----KMREANFTVSSMHGDMPQKERDGIMKEFRSG  118 (210)
Q Consensus        82 ---------------------------------------~~~l~~----~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g  118 (210)
                                                             +..++.    .+...+.++..+.|.++...|.+.+++|+.|
T Consensus       403 ~l~~~~vv~~~~~kpl~~~~lI~~~k~~r~lcf~~S~~sa~Rl~~~L~v~~~~~~~~~s~~t~~l~~k~r~k~l~~f~~g  482 (620)
T KOG0350|consen  403 SLSHRLVVTEPKFKPLAVYALITSNKLNRTLCFVNSVSSANRLAHVLKVEFCSDNFKVSEFTGQLNGKRRYKMLEKFAKG  482 (620)
T ss_pred             hhhhceeecccccchHhHHHHHHHhhcceEEEEecchHHHHHHHHHHHHHhccccchhhhhhhhhhHHHHHHHHHHHhcC
Confidence                                                   333333    3445678888899999999999999999999


Q ss_pred             CCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCCceeEEEEeccCcHHHHHHHHHHhc
Q psy6712         119 TSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYS  189 (210)
Q Consensus       119 ~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~  189 (210)
                      ++.+||||++++||+|+-+++.||+||+|.+...|+||+||++|.|+.|.|+.++...+...+.++-+...
T Consensus       483 ~i~vLIcSD~laRGiDv~~v~~VINYd~P~~~ktyVHR~GRTARAgq~G~a~tll~~~~~r~F~klL~~~~  553 (620)
T KOG0350|consen  483 DINVLICSDALARGIDVNDVDNVINYDPPASDKTYVHRAGRTARAGQDGYAITLLDKHEKRLFSKLLKKTN  553 (620)
T ss_pred             CceEEEehhhhhcCCcccccceEeecCCCchhhHHHHhhcccccccCCceEEEeeccccchHHHHHHHHhc
Confidence            99999999999999999999999999999999999999999999999999999999988887776665443

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

Probab=100.00  E-value=1.5e-31  Score=236.67  Aligned_cols=184  Identities=22%  Similarity=0.356  Sum_probs=148.5

Q ss_pred             CCceEEEEEcCcchHHHHHHhc------CCCcEEEEChHHHHH--HHHhc--Cc-cCCCccEEEechhhHHhccc--hHH
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLD------YGQHVVSGTPGRVFD--MIRRR--VL-RTRNIKMLVLDEADEMLNKG--FKE   67 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~------~~~~Ili~Tp~~l~~--~l~~~--~~-~~~~~~~lviDE~~~l~~~~--~~~   67 (210)
                      .||+++.++||.+..++...+.      ..++||++||+++..  .+.+.  .+ ....+.+|||||||++.+||  |.+
T Consensus       523 ~GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTPERL~~~d~ll~~L~~L~~~~~LslIVIDEAHcVSqWGhDFRp  602 (1195)
T PLN03137        523 ANIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTPEKVAKSDSLLRHLENLNSRGLLARFVIDEAHCVSQWGHDFRP  602 (1195)
T ss_pred             CCCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEChHHhhcchHHHHHHHhhhhccccceeccCcchhhhhcccchHH
Confidence            4789999999999887765553      357999999999853  22221  11 23458899999999999987  444


Q ss_pred             HHHHH---HhhCC-------------------------------------------------------------------
Q psy6712          68 QIYDV---YRYLP-------------------------------------------------------------------   77 (210)
Q Consensus        68 ~~~~i---~~~~~-------------------------------------------------------------------   77 (210)
                      ....+   ...++                                                                   
T Consensus       603 dYr~L~~Lr~~fp~vPilALTATAT~~V~eDI~~~L~l~~~~vfr~Sf~RpNL~y~Vv~k~kk~le~L~~~I~~~~~~es  682 (1195)
T PLN03137        603 DYQGLGILKQKFPNIPVLALTATATASVKEDVVQALGLVNCVVFRQSFNRPNLWYSVVPKTKKCLEDIDKFIKENHFDEC  682 (1195)
T ss_pred             HHHHHHHHHHhCCCCCeEEEEecCCHHHHHHHHHHcCCCCcEEeecccCccceEEEEeccchhHHHHHHHHHHhcccCCC
Confidence            33221   11111                                                                   


Q ss_pred             ------CchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChh
Q psy6712          78 ------PATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRE  151 (210)
Q Consensus        78 ------~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~  151 (210)
                            ...+++.+++.|...|+.+..+||+|++++|..+.++|..|+++|||||+++++|+|+|++++||||++|.++.
T Consensus       683 gIIYC~SRke~E~LAe~L~~~Gika~~YHAGLs~eeR~~vqe~F~~Gei~VLVATdAFGMGIDkPDVR~VIHydlPkSiE  762 (1195)
T PLN03137        683 GIIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIE  762 (1195)
T ss_pred             ceeEeCchhHHHHHHHHHHHCCCCeeeeeCCCCHHHHHHHHHHHhcCCCcEEEEechhhcCCCccCCcEEEEcCCCCCHH
Confidence                  11117888999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhhhhcCCCCceeEEEEeccCcHHHHHHH
Q psy6712         152 LYIHRIGRSGRFGRKGVAISFVKSDDIRILRDI  184 (210)
Q Consensus       152 ~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~  184 (210)
                      .|+||+|||||.|..|.|++|++..|...++.+
T Consensus       763 sYyQriGRAGRDG~~g~cILlys~~D~~~~~~l  795 (1195)
T PLN03137        763 GYHQECGRAGRDGQRSSCVLYYSYSDYIRVKHM  795 (1195)
T ss_pred             HHHhhhcccCCCCCCceEEEEecHHHHHHHHHH
Confidence            999999999999999999999987666554444

>KOG0332|consensus

Probab=99.98  E-value=7.2e-32  Score=211.22  Aligned_cols=173  Identities=45%  Similarity=0.831  Sum_probs=157.8

Q ss_pred             CcEEEEChHHHHHHHHh-cCccCCCccEEEechhhHHhc-cchHHHHHHHHhhCCCchh---------------------
Q psy6712          25 QHVVSGTPGRVFDMIRR-RVLRTRNIKMLVLDEADEMLN-KGFKEQIYDVYRYLPPATQ---------------------   81 (210)
Q Consensus        25 ~~Ili~Tp~~l~~~l~~-~~~~~~~~~~lviDE~~~l~~-~~~~~~~~~i~~~~~~~~~---------------------   81 (210)
                      .+|+|+|||.+.+++.. +.+++..++.+|+||||.|++ .||.+.-..|...+|+..|                     
T Consensus       208 eqIviGTPGtv~Dlm~klk~id~~kikvfVlDEAD~Mi~tqG~~D~S~rI~~~lP~~~QllLFSATf~e~V~~Fa~kivp  287 (477)
T KOG0332|consen  208 EQIVIGTPGTVLDLMLKLKCIDLEKIKVFVLDEADVMIDTQGFQDQSIRIMRSLPRNQQLLLFSATFVEKVAAFALKIVP  287 (477)
T ss_pred             hheeeCCCccHHHHHHHHHhhChhhceEEEecchhhhhhcccccccchhhhhhcCCcceEEeeechhHHHHHHHHHHhcC
Confidence            48999999999999888 889999999999999999997 5788777788888776666                     


Q ss_pred             -------------------------------------------------------HHHHHHHHHhcCceEEEecCCCCHh
Q psy6712          82 -------------------------------------------------------VDWLTEKMREANFTVSSMHGDMPQK  106 (210)
Q Consensus        82 -------------------------------------------------------~~~l~~~l~~~~~~~~~~~~~~~~~  106 (210)
                                                                             +.++++.+.+.|..+..+||+|..+
T Consensus       288 n~n~i~Lk~eel~L~~IkQlyv~C~~~~~K~~~l~~lyg~~tigqsiIFc~tk~ta~~l~~~m~~~Gh~V~~l~G~l~~~  367 (477)
T KOG0332|consen  288 NANVIILKREELALDNIKQLYVLCACRDDKYQALVNLYGLLTIGQSIIFCHTKATAMWLYEEMRAEGHQVSLLHGDLTVE  367 (477)
T ss_pred             CCceeeeehhhccccchhhheeeccchhhHHHHHHHHHhhhhhhheEEEEeehhhHHHHHHHHHhcCceeEEeeccchhH
Confidence                                                                   8999999999999999999999999


Q ss_pred             HHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCC------CChhHHHHhhhhhcCCCCceeEEEEeccC-cHH
Q psy6712         107 ERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLP------NNRELYIHRIGRSGRFGRKGVAISFVKSD-DIR  179 (210)
Q Consensus       107 ~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p------~s~~~~~q~~GR~gR~g~~g~~~~~~~~~-~~~  179 (210)
                      +|..+++.|+.|+.++||+|+.++||+|.+.+++|||||+|      .+...|+||+||+||.|+.|.++.+++.. ...
T Consensus       368 ~R~~ii~~Fr~g~~kVLitTnV~ARGiDv~qVs~VvNydlP~~~~~~pD~etYlHRiGRtGRFGkkG~a~n~v~~~~s~~  447 (477)
T KOG0332|consen  368 QRAAIIDRFREGKEKVLITTNVCARGIDVAQVSVVVNYDLPVKYTGEPDYETYLHRIGRTGRFGKKGLAINLVDDKDSMN  447 (477)
T ss_pred             HHHHHHHHHhcCcceEEEEechhhcccccceEEEEEecCCccccCCCCCHHHHHHHhcccccccccceEEEeecccCcHH
Confidence            99999999999999999999999999999999999999999      57999999999999999999999999875 557


Q ss_pred             HHHHHHHHhcCccccccC
Q psy6712         180 ILRDIEQYYSTQIDEMPM  197 (210)
Q Consensus       180 ~~~~~~~~~~~~~~~~~~  197 (210)
                      .+.+++++++.....+..
T Consensus       448 ~mn~iq~~F~~~i~~~~~  465 (477)
T KOG0332|consen  448 IMNKIQKHFNMKIKRLDP  465 (477)
T ss_pred             HHHHHHHHHhhcceecCC
Confidence            788999999877766543

>KOG0334|consensus

Probab=99.97  E-value=1.2e-31  Score=232.26  Aligned_cols=202  Identities=35%  Similarity=0.656  Sum_probs=184.9

Q ss_pred             CCceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCcc---CCCccEEEechhhHHhccchHHHHHHHHhhCC
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLR---TRNIKMLVLDEADEMLNKGFKEQIYDVYRYLP   77 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~---~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~   77 (210)
                      +|+++++++||....+|+..+++++.|+|||||++.+++..+.-.   +..+-++|+||||+|++.+|.+++..|++.++
T Consensus       465 l~ir~v~vygg~~~~~qiaelkRg~eIvV~tpGRmiD~l~~n~grvtnlrR~t~lv~deaDrmfdmgfePq~~~Ii~nlr  544 (997)
T KOG0334|consen  465 LGIRVVCVYGGSGISQQIAELKRGAEIVVCTPGRMIDILCANSGRVTNLRRVTYLVLDEADRMFDMGFEPQITRILQNLR  544 (997)
T ss_pred             cCceEEEecCCccHHHHHHHHhcCCceEEeccchhhhhHhhcCCccccccccceeeechhhhhheeccCcccchHHhhcc
Confidence            589999999999999999999999999999999999988775444   44555999999999999999999999999998


Q ss_pred             Cchh----------------------------------------------------------------------------
Q psy6712          78 PATQ----------------------------------------------------------------------------   81 (210)
Q Consensus        78 ~~~~----------------------------------------------------------------------------   81 (210)
                      +.+|                                                                            
T Consensus       545 pdrQtvlfSatfpr~m~~la~~vl~~Pveiiv~~~svV~k~V~q~v~V~~~e~eKf~kL~eLl~e~~e~~~tiiFv~~qe  624 (997)
T KOG0334|consen  545 PDRQTVLFSATFPRSMEALARKVLKKPVEIIVGGRSVVCKEVTQVVRVCAIENEKFLKLLELLGERYEDGKTIIFVDKQE  624 (997)
T ss_pred             hhhhhhhhhhhhhHHHHHHHHHhhcCCeeEEEccceeEeccceEEEEEecCchHHHHHHHHHHHHHhhcCCEEEEEcCch
Confidence            8887                                                                            


Q ss_pred             -HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhh
Q psy6712          82 -VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRS  160 (210)
Q Consensus        82 -~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~  160 (210)
                       +..+.+.|.+.++++..+||+.++.+|..+++.|+++.+.+||+|+.+++|+|+.+..+|||||+|....+|.||+||+
T Consensus       625 ~~d~l~~~L~~ag~~~~slHGgv~q~dR~sti~dfK~~~~~LLvaTsvvarGLdv~~l~Lvvnyd~pnh~edyvhR~gRT  704 (997)
T KOG0334|consen  625 KADALLRDLQKAGYNCDSLHGGVDQHDRSSTIEDFKNGVVNLLVATSVVARGLDVKELILVVNYDFPNHYEDYVHRVGRT  704 (997)
T ss_pred             HHHHHHHHHHhcCcchhhhcCCCchHHHHhHHHHHhccCceEEEehhhhhcccccccceEEEEcccchhHHHHHHHhccc
Confidence             8888899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCceeEEEEeccCcHHHHHHHHHHhcCccccccCCcccc
Q psy6712         161 GRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRS  202 (210)
Q Consensus       161 gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  202 (210)
                      ||.|+.|.+++|+.+.+....-.+.+.+...-...|..++.+
T Consensus       705 gragrkg~AvtFi~p~q~~~a~dl~~al~~~~~~~P~~l~~l  746 (997)
T KOG0334|consen  705 GRAGRKGAAVTFITPDQLKYAGDLCKALELSKQPVPKLLQAL  746 (997)
T ss_pred             ccCCccceeEEEeChHHhhhHHHHHHHHHhccCCCchHHHHH
Confidence            999999999999999888888899999877766666554443

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.97  E-value=9.6e-31  Score=220.73  Aligned_cols=184  Identities=21%  Similarity=0.345  Sum_probs=146.0

Q ss_pred             CCceEEEEEcCcchHHHHH---HhcC-CCcEEEEChHHHHHHH-HhcCc-cCCCccEEEechhhHHhccc--hHHHHHHH
Q psy6712           1 MNVQCHACIGGTNLSEDLR---KLDY-GQHVVSGTPGRVFDMI-RRRVL-RTRNIKMLVLDEADEMLNKG--FKEQIYDV   72 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~---~l~~-~~~Ili~Tp~~l~~~l-~~~~~-~~~~~~~lviDE~~~l~~~~--~~~~~~~i   72 (210)
                      +|+++..+.|+.+.+++..   .+.. .++|+++||+++.... ....+ ...+++++||||||++.+|+  |.+....+
T Consensus        74 ~gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TPe~l~~~~~~~~~l~~~~~i~~iViDEaH~i~~~g~~fr~~~~~l  153 (470)
T TIGR00614        74 SGIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKCSASNRLLQTLEERKGITLIAVDEAHCISQWGHDFRPDYKAL  153 (470)
T ss_pred             cCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHcCchhHHHHHHhcCCcCEEEEeCCcccCccccccHHHHHHH
Confidence            4788888888877664432   3333 5899999999875422 11122 56789999999999998875  33322211


Q ss_pred             ---HhhCC------------------------------------------------------------------------
Q psy6712          73 ---YRYLP------------------------------------------------------------------------   77 (210)
Q Consensus        73 ---~~~~~------------------------------------------------------------------------   77 (210)
                         ...++                                                                        
T Consensus       154 ~~l~~~~~~~~~l~lTAT~~~~~~~di~~~l~l~~~~~~~~s~~r~nl~~~v~~~~~~~~~~l~~~l~~~~~~~~~IIF~  233 (470)
T TIGR00614       154 GSLKQKFPNVPIMALTATASPSVREDILRQLNLKNPQIFCTSFDRPNLYYEVRRKTPKILEDLLRFIRKEFKGKSGIIYC  233 (470)
T ss_pred             HHHHHHcCCCceEEEecCCCHHHHHHHHHHcCCCCCcEEeCCCCCCCcEEEEEeCCccHHHHHHHHHHHhcCCCceEEEE
Confidence               11111                                                                        


Q ss_pred             -CchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHh
Q psy6712          78 -PATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHR  156 (210)
Q Consensus        78 -~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~  156 (210)
                       ....++.+++.|++.++.+..+||+|++++|.+++++|++|+++|||||+++++|+|+|++++||++++|.+...|+||
T Consensus       234 ~s~~~~e~la~~L~~~g~~~~~~H~~l~~~eR~~i~~~F~~g~~~vLVaT~~~~~GID~p~V~~VI~~~~P~s~~~y~Qr  313 (470)
T TIGR00614       234 PSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQE  313 (470)
T ss_pred             CcHHHHHHHHHHHHhcCCCeeEeeCCCCHHHHHHHHHHHHcCCCcEEEEechhhccCCcccceEEEEeCCCCCHHHHHhh
Confidence             1111788889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhcCCCCceeEEEEeccCcHHHHHHH
Q psy6712         157 IGRSGRFGRKGVAISFVKSDDIRILRDI  184 (210)
Q Consensus       157 ~GR~gR~g~~g~~~~~~~~~~~~~~~~~  184 (210)
                      +||+||.|..|.|++++++.+...++.+
T Consensus       314 ~GRaGR~G~~~~~~~~~~~~d~~~~~~~  341 (470)
T TIGR00614       314 SGRAGRDGLPSECHLFYAPADINRLRRL  341 (470)
T ss_pred             hcCcCCCCCCceEEEEechhHHHHHHHH
Confidence            9999999999999999998776655544

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

>KOG0346|consensus

Probab=99.97  E-value=5.6e-31  Score=210.01  Aligned_cols=188  Identities=27%  Similarity=0.405  Sum_probs=165.4

Q ss_pred             eEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcC-ccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchh-
Q psy6712           4 QCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRV-LRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ-   81 (210)
Q Consensus         4 ~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~-~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~-   81 (210)
                      +++-++...+...+...|...|||+|+||++++.++..+. ..+..+.++|+||||.++..||.+++.++...+|+..| 
T Consensus       125 r~~nl~s~~sdsv~~~~L~d~pdIvV~TP~~ll~~~~~~~~~~~~~l~~LVvDEADLllsfGYeedlk~l~~~LPr~~Q~  204 (569)
T KOG0346|consen  125 RAINLASSMSDSVNSVALMDLPDIVVATPAKLLRHLAAGVLEYLDSLSFLVVDEADLLLSFGYEEDLKKLRSHLPRIYQC  204 (569)
T ss_pred             hhhhhhcccchHHHHHHHccCCCeEEeChHHHHHHHhhccchhhhheeeEEechhhhhhhcccHHHHHHHHHhCCchhhh
Confidence            4444555666666667788899999999999999999987 67889999999999999999999999999999999888 


Q ss_pred             ----------------------------------------------------------------------------HHHH
Q psy6712          82 ----------------------------------------------------------------------------VDWL   85 (210)
Q Consensus        82 ----------------------------------------------------------------------------~~~l   85 (210)
                                                                                                  +-.+
T Consensus       205 ~LmSATl~dDv~~LKkL~l~nPviLkl~e~el~~~dqL~Qy~v~cse~DKflllyallKL~LI~gKsliFVNtIdr~YrL  284 (569)
T KOG0346|consen  205 FLMSATLSDDVQALKKLFLHNPVILKLTEGELPNPDQLTQYQVKCSEEDKFLLLYALLKLRLIRGKSLIFVNTIDRCYRL  284 (569)
T ss_pred             eeehhhhhhHHHHHHHHhccCCeEEEeccccCCCcccceEEEEEeccchhHHHHHHHHHHHHhcCceEEEEechhhhHHH
Confidence                                                                                        4444


Q ss_pred             HHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEec-----------------------------------Ccc
Q psy6712          86 TEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTD-----------------------------------VWA  130 (210)
Q Consensus        86 ~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~-----------------------------------~~~  130 (210)
                      --.|+.-|++.+.++|+||...|..++++|+.|-++++|||+                                   -++
T Consensus       285 kLfLeqFGiksciLNseLP~NSR~Hii~QFNkG~YdivIAtD~s~~~~~~eee~kgk~~e~~~kndkkskkK~D~E~GVs  364 (569)
T KOG0346|consen  285 KLFLEQFGIKSCILNSELPANSRCHIIEQFNKGLYDIVIATDDSADGDKLEEEVKGKSDEKNPKNDKKSKKKLDKESGVS  364 (569)
T ss_pred             HHHHHHhCcHhhhhcccccccchhhHHHHhhCcceeEEEEccCccchhhhhccccccccccCCCCccccccccCchhchh
Confidence            555666799999999999999999999999999999999998                                   245


Q ss_pred             ccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCCceeEEEEeccCcHHHHHHHHHHhcCc
Q psy6712         131 RGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQ  191 (210)
Q Consensus       131 ~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~  191 (210)
                      +|+|+.+|.+|+|||+|.++..|+||+||++|.++.|.+++|+.+.+..-...++..+...
T Consensus       365 RGIDF~~V~~VlNFD~P~t~~sYIHRvGRTaRg~n~GtalSfv~P~e~~g~~~le~~~~d~  425 (569)
T KOG0346|consen  365 RGIDFHHVSNVLNFDFPETVTSYIHRVGRTARGNNKGTALSFVSPKEEFGKESLESILKDE  425 (569)
T ss_pred             ccccchheeeeeecCCCCchHHHHHhccccccCCCCCceEEEecchHHhhhhHHHHHHhhH
Confidence            8999999999999999999999999999999999999999999999888667777666554

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

Probab=99.97  E-value=3e-30  Score=226.68  Aligned_cols=195  Identities=17%  Similarity=0.264  Sum_probs=150.2

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhc----CccCCCccEEEechhhHHhccchHHHHHHHHh---
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRR----VLRTRNIKMLVLDEADEMLNKGFKEQIYDVYR---   74 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~----~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~---   74 (210)
                      ++++..+.|+.+. ++.+.+.++++|+|+||+++...+...    ...+++++++|+||+|.+.+ .|...+..++.   
T Consensus       108 ~i~v~~~~Gdt~~-~~r~~i~~~~~IivtTPd~L~~~~L~~~~~~~~~l~~l~~vViDEah~~~g-~fg~~~~~il~rL~  185 (742)
T TIGR03817       108 GVRPATYDGDTPT-EERRWAREHARYVLTNPDMLHRGILPSHARWARFLRRLRYVVIDECHSYRG-VFGSHVALVLRRLR  185 (742)
T ss_pred             CeEEEEEeCCCCH-HHHHHHhcCCCEEEEChHHHHHhhccchhHHHHHHhcCCEEEEeChhhccC-ccHHHHHHHHHHHH
Confidence            5788888888774 455677788999999999987543321    12378999999999999854 12222111110   


Q ss_pred             --------------------------------------------------------------------------------
Q psy6712          75 --------------------------------------------------------------------------------   74 (210)
Q Consensus        75 --------------------------------------------------------------------------------   74 (210)
                                                                                                      
T Consensus       186 ri~~~~g~~~q~i~~SATi~n~~~~~~~l~g~~~~~i~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~l~  265 (742)
T TIGR03817       186 RLCARYGASPVFVLASATTADPAAAASRLIGAPVVAVTEDGSPRGARTVALWEPPLTELTGENGAPVRRSASAEAADLLA  265 (742)
T ss_pred             HHHHhcCCCCEEEEEecCCCCHHHHHHHHcCCCeEEECCCCCCcCceEEEEecCCccccccccccccccchHHHHHHHHH
Confidence                                                                                            


Q ss_pred             -----------hCCCchhHHHHHHHHHhc--------CceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCC
Q psy6712          75 -----------YLPPATQVDWLTEKMREA--------NFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDV  135 (210)
Q Consensus        75 -----------~~~~~~~~~~l~~~l~~~--------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~  135 (210)
                                 |++....++.+++.+++.        +.++..+||+|++++|++++++|++|++++||||+++++|+|+
T Consensus       266 ~l~~~~~~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~hgg~~~~eR~~ie~~f~~G~i~vLVaTd~lerGIDI  345 (742)
T TIGR03817       266 DLVAEGARTLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYLPEDRRELERALRDGELLGVATTNALELGVDI  345 (742)
T ss_pred             HHHHCCCCEEEEcCCHHHHHHHHHHHHHHHHhhccccccchhheecCCCHHHHHHHHHHHHcCCceEEEECchHhccCCc
Confidence                       111111155566655442        5678899999999999999999999999999999999999999


Q ss_pred             CCCcEEEEecCCCChhHHHHhhhhhcCCCCceeEEEEec--cCcHHHHHHHHHHhcCccccccCC
Q psy6712         136 QQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVK--SDDIRILRDIEQYYSTQIDEMPMN  198 (210)
Q Consensus       136 ~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~~g~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~  198 (210)
                      |++++||++++|.+..+|+||+||+||.|+.|.++++..  +.|...+...++.++..++....+
T Consensus       346 ~~vd~VI~~~~P~s~~~y~qRiGRaGR~G~~g~ai~v~~~~~~d~~~~~~~~~~~~~~~e~~~~~  410 (742)
T TIGR03817       346 SGLDAVVIAGFPGTRASLWQQAGRAGRRGQGALVVLVARDDPLDTYLVHHPEALFDRPVEATVFD  410 (742)
T ss_pred             ccccEEEEeCCCCCHHHHHHhccccCCCCCCcEEEEEeCCChHHHHHHhCHHHHhcCCCccceeC
Confidence            999999999999999999999999999999999999986  346667777788888877665443

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.

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.97  E-value=1.2e-29  Score=219.49  Aligned_cols=183  Identities=20%  Similarity=0.323  Sum_probs=145.8

Q ss_pred             CCceEEEEEcCcchHHHHHH---hc-CCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccc--hHHHH---HH
Q psy6712           1 MNVQCHACIGGTNLSEDLRK---LD-YGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKG--FKEQI---YD   71 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~---l~-~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~--~~~~~---~~   71 (210)
                      +|+.+..+.++.+.+++...   +. ...+++++||+++........+...+++++|+||||++.+|+  |.+..   ..
T Consensus        88 ~gi~~~~~~s~~~~~~~~~~~~~~~~g~~~il~~tPe~l~~~~~~~~l~~~~l~~iVIDEaH~i~~~G~~fr~~y~~L~~  167 (607)
T PRK11057         88 NGVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMDNFLEHLAHWNPALLAVDEAHCISQWGHDFRPEYAALGQ  167 (607)
T ss_pred             cCCcEEEEcCCCCHHHHHHHHHHHhCCCCcEEEEChHHhcChHHHHHHhhCCCCEEEEeCccccccccCcccHHHHHHHH
Confidence            36788888888877665432   33 357999999999874222223445678999999999998875  33222   11


Q ss_pred             HHhhCCC-----------------------------------------------------------------------ch
Q psy6712          72 VYRYLPP-----------------------------------------------------------------------AT   80 (210)
Q Consensus        72 i~~~~~~-----------------------------------------------------------------------~~   80 (210)
                      +...++.                                                                       ..
T Consensus       168 l~~~~p~~~~v~lTAT~~~~~~~di~~~l~l~~~~~~~~~~~r~nl~~~v~~~~~~~~~l~~~l~~~~~~~~IIFc~tr~  247 (607)
T PRK11057        168 LRQRFPTLPFMALTATADDTTRQDIVRLLGLNDPLIQISSFDRPNIRYTLVEKFKPLDQLMRYVQEQRGKSGIIYCNSRA  247 (607)
T ss_pred             HHHhCCCCcEEEEecCCChhHHHHHHHHhCCCCeEEEECCCCCCcceeeeeeccchHHHHHHHHHhcCCCCEEEEECcHH
Confidence            1111111                                                                       11


Q ss_pred             hHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhh
Q psy6712          81 QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRS  160 (210)
Q Consensus        81 ~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~  160 (210)
                      .++.+++.|++.++++..+|++|++++|.++++.|++|+++|||||+++++|+|+|++++||+||+|.|..+|+||+|||
T Consensus       248 ~~e~la~~L~~~g~~v~~~Ha~l~~~~R~~i~~~F~~g~~~VLVaT~a~~~GIDip~V~~VI~~d~P~s~~~y~Qr~GRa  327 (607)
T PRK11057        248 KVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRA  327 (607)
T ss_pred             HHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHHCCCCCEEEEechhhccCCCCCcCEEEEeCCCCCHHHHHHHhhhc
Confidence            18889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCceeEEEEeccCcHHHHHH
Q psy6712         161 GRFGRKGVAISFVKSDDIRILRD  183 (210)
Q Consensus       161 gR~g~~g~~~~~~~~~~~~~~~~  183 (210)
                      ||.|..|.|++|+++.+...++.
T Consensus       328 GR~G~~~~~ill~~~~d~~~~~~  350 (607)
T PRK11057        328 GRDGLPAEAMLFYDPADMAWLRR  350 (607)
T ss_pred             cCCCCCceEEEEeCHHHHHHHHH
Confidence            99999999999999877655443

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.97  E-value=1e-29  Score=220.02  Aligned_cols=182  Identities=24%  Similarity=0.358  Sum_probs=148.2

Q ss_pred             CCceEEEEEcCcchHHHHHH---hc-CCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccc--hHHHHHHH--
Q psy6712           1 MNVQCHACIGGTNLSEDLRK---LD-YGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKG--FKEQIYDV--   72 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~---l~-~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~--~~~~~~~i--   72 (210)
                      +|+++..++|+.+.+++...   +. ..++|+++||+++........+...+++++|+||||++.+|+  |.+....+  
T Consensus        76 ~gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe~l~~~~~~~~l~~~~l~~iViDEaH~i~~~g~~frp~y~~l~~  155 (591)
T TIGR01389        76 AGVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQDYFLNMLQRIPIALVAVDEAHCVSQWGHDFRPEYQRLGS  155 (591)
T ss_pred             cCCcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChhHhcChHHHHHHhcCCCCEEEEeCCcccccccCccHHHHHHHHH
Confidence            47889999999887765432   33 467999999999875444444566789999999999998875  33333222  


Q ss_pred             -HhhCCCc-----------------------------------------------------------------------h
Q psy6712          73 -YRYLPPA-----------------------------------------------------------------------T   80 (210)
Q Consensus        73 -~~~~~~~-----------------------------------------------------------------------~   80 (210)
                       ...++..                                                                       .
T Consensus       156 l~~~~~~~~vi~lTAT~~~~~~~~i~~~l~~~~~~~~~~~~~r~nl~~~v~~~~~~~~~l~~~l~~~~~~~~IIf~~sr~  235 (591)
T TIGR01389       156 LAERFPQVPRIALTATADAETRQDIRELLRLADANEFITSFDRPNLRFSVVKKNNKQKFLLDYLKKHRGQSGIIYASSRK  235 (591)
T ss_pred             HHHhCCCCCEEEEEeCCCHHHHHHHHHHcCCCCCCeEecCCCCCCcEEEEEeCCCHHHHHHHHHHhcCCCCEEEEECcHH
Confidence             1111110                                                                       0


Q ss_pred             hHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhh
Q psy6712          81 QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRS  160 (210)
Q Consensus        81 ~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~  160 (210)
                      .++.+++.|...++++..+|++|+.++|..+.+.|.+|++++||||+++++|+|+|++++||+|++|.|...|.|++||+
T Consensus       236 ~~e~la~~L~~~g~~~~~~H~~l~~~~R~~i~~~F~~g~~~vlVaT~a~~~GID~p~v~~VI~~~~p~s~~~y~Q~~GRa  315 (591)
T TIGR01389       236 KVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRA  315 (591)
T ss_pred             HHHHHHHHHHhCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEechhhccCcCCCCCEEEEcCCCCCHHHHhhhhccc
Confidence            18889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCceeEEEEeccCcHHHHH
Q psy6712         161 GRFGRKGVAISFVKSDDIRILR  182 (210)
Q Consensus       161 gR~g~~g~~~~~~~~~~~~~~~  182 (210)
                      ||.|..+.|++++++.+...++
T Consensus       316 GR~G~~~~~il~~~~~d~~~~~  337 (591)
T TIGR01389       316 GRDGLPAEAILLYSPADIALLK  337 (591)
T ss_pred             cCCCCCceEEEecCHHHHHHHH
Confidence            9999999999999877655443

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.

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

Probab=99.97  E-value=3.4e-29  Score=210.35  Aligned_cols=186  Identities=25%  Similarity=0.404  Sum_probs=153.0

Q ss_pred             CCceEEEEEcCcchHHHHHHh---cC-CCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccc--hHHHHHHHHh
Q psy6712           1 MNVQCHACIGGTNLSEDLRKL---DY-GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKG--FKEQIYDVYR   74 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l---~~-~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~--~~~~~~~i~~   74 (210)
                      .||+++.+++..+.++....+   .. ..++|.-+|+++..---...+.-..+.+++|||||++.+||  |+++...+-.
T Consensus        80 ~Gi~A~~lnS~l~~~e~~~v~~~l~~g~~klLyisPErl~~~~f~~~L~~~~i~l~vIDEAHCiSqWGhdFRP~Y~~lg~  159 (590)
T COG0514          80 AGIRAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERLMSPRFLELLKRLPISLVAIDEAHCISQWGHDFRPDYRRLGR  159 (590)
T ss_pred             cCceeehhhcccCHHHHHHHHHHHhcCceeEEEECchhhcChHHHHHHHhCCCceEEechHHHHhhcCCccCHhHHHHHH
Confidence            478999999998877655333   33 47999999999776433333345678899999999999997  5544433322


Q ss_pred             h---CC-------------------------------------------------------------------------C
Q psy6712          75 Y---LP-------------------------------------------------------------------------P   78 (210)
Q Consensus        75 ~---~~-------------------------------------------------------------------------~   78 (210)
                      .   ++                                                                         .
T Consensus       160 l~~~~~~~p~~AlTATA~~~v~~DI~~~L~l~~~~~~~~sfdRpNi~~~v~~~~~~~~q~~fi~~~~~~~~~~GIIYc~s  239 (590)
T COG0514         160 LRAGLPNPPVLALTATATPRVRDDIREQLGLQDANIFRGSFDRPNLALKVVEKGEPSDQLAFLATVLPQLSKSGIIYCLT  239 (590)
T ss_pred             HHhhCCCCCEEEEeCCCChHHHHHHHHHhcCCCcceEEecCCCchhhhhhhhcccHHHHHHHHHhhccccCCCeEEEEee
Confidence            1   11                                                                         1


Q ss_pred             chhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhh
Q psy6712          79 ATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIG  158 (210)
Q Consensus        79 ~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~G  158 (210)
                      .+.++.++++|...|+++..+|++|+.++|..+.++|..++.+|+|||.++++|+|-|++.+|||||+|.|+.+|.|.+|
T Consensus       240 Rk~~E~ia~~L~~~g~~a~~YHaGl~~~eR~~~q~~f~~~~~~iiVAT~AFGMGIdKpdVRfViH~~lP~s~EsYyQE~G  319 (590)
T COG0514         240 RKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPGSIESYYQETG  319 (590)
T ss_pred             HHhHHHHHHHHHHCCCceEEecCCCCHHHHHHHHHHHhcCCCcEEEEeccccCccCCCCceEEEEecCCCCHHHHHHHHh
Confidence            11189999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhcCCCCceeEEEEeccCcHHHHHHHHH
Q psy6712         159 RSGRFGRKGVAISFVKSDDIRILRDIEQ  186 (210)
Q Consensus       159 R~gR~g~~g~~~~~~~~~~~~~~~~~~~  186 (210)
                      ||||+|..+.|++|+++.|....+.+.+
T Consensus       320 RAGRDG~~a~aill~~~~D~~~~~~~i~  347 (590)
T COG0514         320 RAGRDGLPAEAILLYSPEDIRWQRYLIE  347 (590)
T ss_pred             hccCCCCcceEEEeeccccHHHHHHHHH
Confidence            9999999999999999988765554443

>KOG0337|consensus

Probab=99.96  E-value=2.9e-30  Score=204.96  Aligned_cols=193  Identities=30%  Similarity=0.530  Sum_probs=182.4

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchh
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ   81 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~   81 (210)
                      +.++++++||.+..+|+..+.+++|||++||+++..+...-.+.++.+.++|+||+|.+++.||.+++.+++..++...|
T Consensus       118 ~lr~s~~~ggD~~eeqf~~l~~npDii~ATpgr~~h~~vem~l~l~sveyVVfdEadrlfemgfqeql~e~l~rl~~~~Q  197 (529)
T KOG0337|consen  118 KLRQSLLVGGDSIEEQFILLNENPDIIIATPGRLLHLGVEMTLTLSSVEYVVFDEADRLFEMGFQEQLHEILSRLPESRQ  197 (529)
T ss_pred             chhhhhhcccchHHHHHHHhccCCCEEEecCceeeeeehheeccccceeeeeehhhhHHHhhhhHHHHHHHHHhCCCcce
Confidence            56789999999999999999999999999999999887776788999999999999999999999999999999988777


Q ss_pred             ----------------------------------------------------------------------------HHHH
Q psy6712          82 ----------------------------------------------------------------------------VDWL   85 (210)
Q Consensus        82 ----------------------------------------------------------------------------~~~l   85 (210)
                                                                                                  ++.+
T Consensus       198 TllfSatlp~~lv~fakaGl~~p~lVRldvetkise~lk~~f~~~~~a~K~aaLl~il~~~~~~~~t~vf~~tk~hve~~  277 (529)
T KOG0337|consen  198 TLLFSATLPRDLVDFAKAGLVPPVLVRLDVETKISELLKVRFFRVRKAEKEAALLSILGGRIKDKQTIVFVATKHHVEYV  277 (529)
T ss_pred             EEEEeccCchhhHHHHHccCCCCceEEeehhhhcchhhhhheeeeccHHHHHHHHHHHhccccccceeEEecccchHHHH
Confidence                                                                                        8889


Q ss_pred             HHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCC
Q psy6712          86 TEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGR  165 (210)
Q Consensus        86 ~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~  165 (210)
                      .+.|+..|+.+..++|.|++..|......|+.++..++|.|+.+++|+|+|-.+.||+||+|.+..-|.||+||+.|.|+
T Consensus       278 ~~ll~~~g~~~s~iysslD~~aRk~~~~~F~~~k~~~lvvTdvaaRG~diplldnvinyd~p~~~klFvhRVgr~aragr  357 (529)
T KOG0337|consen  278 RGLLRDFGGEGSDIYSSLDQEARKINGRDFRGRKTSILVVTDVAARGLDIPLLDNVINYDFPPDDKLFVHRVGRVARAGR  357 (529)
T ss_pred             HHHHHhcCCCccccccccChHhhhhccccccCCccceEEEehhhhccCCCccccccccccCCCCCceEEEEecchhhccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceeEEEEeccCcHHHHHHHHHHhcCcccc
Q psy6712         166 KGVAISFVKSDDIRILRDIEQYYSTQIDE  194 (210)
Q Consensus       166 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~  194 (210)
                      .|.++.++.+.+...+-.+..+++.++.-
T Consensus       358 tg~aYs~V~~~~~~yl~DL~lflgr~~~~  386 (529)
T KOG0337|consen  358 TGRAYSLVASTDDPYLLDLQLFLGRPLIF  386 (529)
T ss_pred             cceEEEEEecccchhhhhhhhhcCCceee
Confidence            99999999999999999999888876654

>KOG0344|consensus

Probab=99.96  E-value=4.8e-29  Score=205.07  Aligned_cols=175  Identities=38%  Similarity=0.591  Sum_probs=156.8

Q ss_pred             cCCCcEEEEChHHHHHHHHhcC--ccCCCccEEEechhhHHhcc-chHHHHHHHHhhCCCchh-----------------
Q psy6712          22 DYGQHVVSGTPGRVFDMIRRRV--LRTRNIKMLVLDEADEMLNK-GFKEQIYDVYRYLPPATQ-----------------   81 (210)
Q Consensus        22 ~~~~~Ili~Tp~~l~~~l~~~~--~~~~~~~~lviDE~~~l~~~-~~~~~~~~i~~~~~~~~~-----------------   81 (210)
                      ...++|+++||-++..++..+.  ++++.+.++|+||+|.+++. .|..++..|+..+....-                 
T Consensus       260 ~~k~dili~TP~ri~~~~~~~~~~idl~~V~~lV~dEaD~lfe~~~f~~Qla~I~sac~s~~i~~a~FSat~~~~VEE~~  339 (593)
T KOG0344|consen  260 DEKYDILISTPMRIVGLLGLGKLNIDLSKVEWLVVDEADLLFEPEFFVEQLADIYSACQSPDIRVALFSATISVYVEEWA  339 (593)
T ss_pred             HHHHHHHhcCHHHHHHHhcCCCccchhheeeeEeechHHhhhChhhHHHHHHHHHHHhcCcchhhhhhhccccHHHHHHH
Confidence            3467999999999999998876  78999999999999999998 888888888876643221                 


Q ss_pred             ------------------------------------------------------------HHHHHHHH-HhcCceEEEec
Q psy6712          82 ------------------------------------------------------------VDWLTEKM-REANFTVSSMH  100 (210)
Q Consensus        82 ------------------------------------------------------------~~~l~~~l-~~~~~~~~~~~  100 (210)
                                                                                  +..|.+.| .-.++++.++|
T Consensus       340 ~~i~~~~~~vivg~~~sa~~~V~QelvF~gse~~K~lA~rq~v~~g~~PP~lIfVQs~eRak~L~~~L~~~~~i~v~vIh  419 (593)
T KOG0344|consen  340 ELIKSDLKRVIVGLRNSANETVDQELVFCGSEKGKLLALRQLVASGFKPPVLIFVQSKERAKQLFEELEIYDNINVDVIH  419 (593)
T ss_pred             HHhhccceeEEEecchhHhhhhhhhheeeecchhHHHHHHHHHhccCCCCeEEEEecHHHHHHHHHHhhhccCcceeeEe
Confidence                                                                        77788888 56789999999


Q ss_pred             CCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCCceeEEEEeccCcHHH
Q psy6712         101 GDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRI  180 (210)
Q Consensus       101 ~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~~~  180 (210)
                      |+.++.+|.+++++|+.|++++|+||+.+++|+|+.+++.||+||+|.+..+|+||+||+||.|+.|.++.|+...+...
T Consensus       420 ~e~~~~qrde~~~~FR~g~IwvLicTdll~RGiDf~gvn~VInyD~p~s~~syihrIGRtgRag~~g~Aitfytd~d~~~  499 (593)
T KOG0344|consen  420 GERSQKQRDETMERFRIGKIWVLICTDLLARGIDFKGVNLVINYDFPQSDLSYIHRIGRTGRAGRSGKAITFYTDQDMPR  499 (593)
T ss_pred             cccchhHHHHHHHHHhccCeeEEEehhhhhccccccCcceEEecCCCchhHHHHHHhhccCCCCCCcceEEEeccccchh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcCcccccc
Q psy6712         181 LRDIEQYYSTQIDEMP  196 (210)
Q Consensus       181 ~~~~~~~~~~~~~~~~  196 (210)
                      ++-+.+.+..+.-++|
T Consensus       500 ir~iae~~~~sG~evp  515 (593)
T KOG0344|consen  500 IRSIAEVMEQSGCEVP  515 (593)
T ss_pred             hhhHHHHHHHcCCcch
Confidence            8888877766555554

>KOG0329|consensus

Probab=99.96  E-value=1.3e-28  Score=184.77  Aligned_cols=193  Identities=35%  Similarity=0.703  Sum_probs=152.5

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhc-cchHHHHHHHHhhCCCch
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLN-KGFKEQIYDVYRYLPPAT   80 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~-~~~~~~~~~i~~~~~~~~   80 (210)
                      +++|++++||.+.+.....+++-|+|+|+||||++.+.+++.+++++++++|+||||.|++ ..+.+++.+|+..+|..+
T Consensus       139 ~vkvaVFfGG~~Ikkdee~lk~~PhivVgTPGrilALvr~k~l~lk~vkhFvlDEcdkmle~lDMrRDvQEifr~tp~~K  218 (387)
T KOG0329|consen  139 SVKVSVFFGGLFIKKDEELLKNCPHIVVGTPGRILALVRNRSLNLKNVKHFVLDECDKMLEQLDMRRDVQEIFRMTPHEK  218 (387)
T ss_pred             CceEEEEEcceeccccHHHHhCCCeEEEcCcHHHHHHHHhccCchhhcceeehhhHHHHHHHHHHHHHHHHHhhcCcccc
Confidence            5789999999999999999999999999999999999999999999999999999999996 478999999999999888


Q ss_pred             hH-----------HHHHHHHHhcCceE-------EEecCCC----CHhHHHHHHH-----------------------HH
Q psy6712          81 QV-----------DWLTEKMREANFTV-------SSMHGDM----PQKERDGIMK-----------------------EF  115 (210)
Q Consensus        81 ~~-----------~~l~~~l~~~~~~~-------~~~~~~~----~~~~r~~~~~-----------------------~f  115 (210)
                      |+           .-++..+.+....+       ..+||-.    ..++.++..+                       .|
T Consensus       219 QvmmfsatlskeiRpvC~kFmQdPmEi~vDdE~KLtLHGLqQ~YvkLke~eKNrkl~dLLd~LeFNQVvIFvKsv~Rl~f  298 (387)
T KOG0329|consen  219 QVMMFSATLSKEIRPVCHKFMQDPMEIFVDDEAKLTLHGLQQYYVKLKENEKNRKLNDLLDVLEFNQVVIFVKSVQRLSF  298 (387)
T ss_pred             eeeeeeeecchhhHHHHHhhhcCchhhhccchhhhhhhhHHHHHHhhhhhhhhhhhhhhhhhhhhcceeEeeehhhhhhh
Confidence            82           22222222211111       1122210    0000000000                       02


Q ss_pred             hcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCCceeEEEEeccC-cHHHHHHHHHHhcCcccc
Q psy6712         116 RSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSD-DIRILRDIEQYYSTQIDE  194 (210)
Q Consensus       116 ~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~~g~~~~~~~~~-~~~~~~~~~~~~~~~~~~  194 (210)
                         .-+ +|+|+.+++|+|+..+++++|||+|.+.++|+||.|||||.|..|.++.|++.. +...+......+...+.+
T Consensus       299 ---~kr-~vat~lfgrgmdiervNi~~NYdmp~~~DtYlHrv~rAgrfGtkglaitfvs~e~da~iLn~vqdRf~v~i~e  374 (387)
T KOG0329|consen  299 ---QKR-LVATDLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNPVQDRFEVNIKE  374 (387)
T ss_pred             ---hhh-hHHhhhhccccCcccceeeeccCCCCCchHHHHHhhhhhccccccceeehhcchhhHHHhchhhHhhhccHhh
Confidence               113 899999999999999999999999999999999999999999999999999874 667788888889999999


Q ss_pred             ccCC
Q psy6712         195 MPMN  198 (210)
Q Consensus       195 ~~~~  198 (210)
                      +|.+
T Consensus       375 Lpde  378 (387)
T KOG0329|consen  375 LPDE  378 (387)
T ss_pred             cCcc
Confidence            8877

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.96  E-value=1.1e-27  Score=214.04  Aligned_cols=173  Identities=16%  Similarity=0.288  Sum_probs=137.0

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCc--cCCCccEEEechhhHHhccchHHH----HHHHHh-
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVL--RTRNIKMLVLDEADEMLNKGFKEQ----IYDVYR-   74 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~--~~~~~~~lviDE~~~l~~~~~~~~----~~~i~~-   74 (210)
                      +++++.++|+.+..++.+.+.+.++|+|+||+++..++.+...  .+++++++|+||+|.+.+......    +..+.. 
T Consensus       124 ~i~v~v~~Gdt~~~~r~~~l~~~p~IlVtTPE~L~~ll~~~~~~~~l~~l~~VVIDE~H~l~~~~RG~~l~~~L~rL~~l  203 (876)
T PRK13767        124 EIRVAIRTGDTSSYEKQKMLKKPPHILITTPESLAILLNSPKFREKLRTVKWVIVDEIHSLAENKRGVHLSLSLERLEEL  203 (876)
T ss_pred             CeeEEEEcCCCCHHHHHHHHhCCCCEEEecHHHHHHHhcChhHHHHHhcCCEEEEechhhhccCccHHHHHHHHHHHHHh
Confidence            5789999999999988888888999999999999887766543  578999999999999985432111    111110 


Q ss_pred             --------------------------------------------------------------------------------
Q psy6712          75 --------------------------------------------------------------------------------   74 (210)
Q Consensus        75 --------------------------------------------------------------------------------   74 (210)
                                                                                                      
T Consensus       204 ~~~~~q~IglSATl~~~~~va~~L~~~~~~~~~r~~~iv~~~~~k~~~i~v~~p~~~l~~~~~~~~~~~l~~~L~~~i~~  283 (876)
T PRK13767        204 AGGEFVRIGLSATIEPLEEVAKFLVGYEDDGEPRDCEIVDARFVKPFDIKVISPVDDLIHTPAEEISEALYETLHELIKE  283 (876)
T ss_pred             cCCCCeEEEEecccCCHHHHHHHhcCccccCCCCceEEEccCCCccceEEEeccCccccccccchhHHHHHHHHHHHHhc
Confidence                                                                                            


Q ss_pred             ------hCCCchhHHHHHHHHHh------cCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEE
Q psy6712          75 ------YLPPATQVDWLTEKMRE------ANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVI  142 (210)
Q Consensus        75 ------~~~~~~~~~~l~~~l~~------~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi  142 (210)
                            |++...+++.+++.|.+      .+..+.++||+|++++|..++++|++|++++||||+.+++|+|+|++++||
T Consensus       284 ~~~~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls~~~R~~ve~~fk~G~i~vLVaTs~Le~GIDip~Vd~VI  363 (876)
T PRK13767        284 HRTTLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEVEEKLKRGELKVVVSSTSLELGIDIGYIDLVV  363 (876)
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCCHHHHHHHHHHHHcCCCeEEEECChHHhcCCCCCCcEEE
Confidence                  00111116666666655      246799999999999999999999999999999999999999999999999


Q ss_pred             EecCCCChhHHHHhhhhhcCCC-CceeEEEEec
Q psy6712         143 NYDLPNNRELYIHRIGRSGRFG-RKGVAISFVK  174 (210)
Q Consensus       143 ~~~~p~s~~~~~q~~GR~gR~g-~~g~~~~~~~  174 (210)
                      +++.|.+..+|+||+||+||.+ ..+.+.++..
T Consensus       364 ~~~~P~sv~~ylQRiGRaGR~~g~~~~g~ii~~  396 (876)
T PRK13767        364 LLGSPKSVSRLLQRIGRAGHRLGEVSKGRIIVV  396 (876)
T ss_pred             EeCCCCCHHHHHHhcccCCCCCCCCCcEEEEEc
Confidence            9999999999999999999874 3344444443

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.96  E-value=2.3e-27  Score=216.88  Aligned_cols=194  Identities=21%  Similarity=0.336  Sum_probs=147.0

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhc-CccCCCccEEEechhhHHhcc--c--hHHHHHHHH---
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRR-VLRTRNIKMLVLDEADEMLNK--G--FKEQIYDVY---   73 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~-~~~~~~~~~lviDE~~~l~~~--~--~~~~~~~i~---   73 (210)
                      +++|..++|+++.+++.+.+++.+||||+||++|..++.++ ...++++++||+||+|.+.+.  |  +...+..+.   
T Consensus        77 ~i~V~vrtGDt~~~eR~rll~~ppdILVTTPEsL~~LLtsk~r~~L~~Vr~VIVDE~H~L~g~kRG~~Lel~LeRL~~l~  156 (1490)
T PRK09751         77 NLRVGIRTGDTPAQERSKLTRNPPDILITTPESLYLMLTSRARETLRGVETVIIDEVHAVAGSKRGAHLALSLERLDALL  156 (1490)
T ss_pred             ceEEEEEECCCCHHHHHHHhcCCCCEEEecHHHHHHHHhhhhhhhhccCCEEEEecHHHhcccccccHHHHHHHHHHHhC
Confidence            68999999999999988888889999999999999887764 346899999999999999854  2  111111111   


Q ss_pred             --------------------------------------------------------------------------------
Q psy6712          74 --------------------------------------------------------------------------------   73 (210)
Q Consensus        74 --------------------------------------------------------------------------------   73 (210)
                                                                                                      
T Consensus       157 ~~~~QrIgLSATI~n~eevA~~L~g~~pv~Iv~~~~~r~~~l~v~vp~~d~~~~~~~~~~~~~~~~~~r~~~i~~~v~~~  236 (1490)
T PRK09751        157 HTSAQRIGLSATVRSASDVAAFLGGDRPVTVVNPPAMRHPQIRIVVPVANMDDVSSVASGTGEDSHAGREGSIWPYIETG  236 (1490)
T ss_pred             CCCCeEEEEEeeCCCHHHHHHHhcCCCCEEEECCCCCcccceEEEEecCchhhccccccccccccchhhhhhhhHHHHHH
Confidence                                                                                            


Q ss_pred             ------------hhCCCchhHHHHHHHHHhcC---------------------------------ceEEEecCCCCHhHH
Q psy6712          74 ------------RYLPPATQVDWLTEKMREAN---------------------------------FTVSSMHGDMPQKER  108 (210)
Q Consensus        74 ------------~~~~~~~~~~~l~~~l~~~~---------------------------------~~~~~~~~~~~~~~r  108 (210)
                                  .|++....++.++..|.+..                                 ..+..+||+|++++|
T Consensus       237 il~~i~~~~stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~HHGsLSkeeR  316 (1490)
T PRK09751        237 ILDEVLRHRSTIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVDAAHFESTSGATSNRVQSSDVFIARSHHGSVSKEQR  316 (1490)
T ss_pred             HHHHHhcCCCEEEECCCHHHHHHHHHHHHHhhhhhccccccccchhhhhhhccccchhccccccceeeeeccccCCHHHH
Confidence                        12222222566666664421                                 125789999999999


Q ss_pred             HHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCC-CCceeEEEEeccCcHHH---HHHH
Q psy6712         109 DGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRF-GRKGVAISFVKSDDIRI---LRDI  184 (210)
Q Consensus       109 ~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~-g~~g~~~~~~~~~~~~~---~~~~  184 (210)
                      ..++++|++|++++||||+.+++|+|++++++||+++.|.++.+|+||+||+||. |..+.++++.... .+.   ...+
T Consensus       317 ~~IE~~fK~G~LrvLVATssLELGIDIg~VDlVIq~gsP~sVas~LQRiGRAGR~~gg~s~gli~p~~r-~dlle~~~~v  395 (1490)
T PRK09751        317 AITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGRAGHQVGGVSKGLFFPRTR-RDLVDSAVIV  395 (1490)
T ss_pred             HHHHHHHHhCCceEEEeCcHHHccCCcccCCEEEEeCCCCCHHHHHHHhCCCCCCCCCccEEEEEeCcH-HHHHhhHHHH
Confidence            9999999999999999999999999999999999999999999999999999997 3345555444332 222   2235


Q ss_pred             HHHhcCcccccc
Q psy6712         185 EQYYSTQIDEMP  196 (210)
Q Consensus       185 ~~~~~~~~~~~~  196 (210)
                      +.+++..++.+.
T Consensus       396 e~~l~g~iE~~~  407 (1490)
T PRK09751        396 ECMFAGRLENLT  407 (1490)
T ss_pred             HHHhcCCCCccC
Confidence            667776666643

>KOG0349|consensus

Probab=99.95  E-value=4e-27  Score=188.25  Aligned_cols=204  Identities=32%  Similarity=0.592  Sum_probs=180.5

Q ss_pred             ceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchh-
Q psy6712           3 VQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ-   81 (210)
Q Consensus         3 i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~-   81 (210)
                      ++..+++||...+.|.+.+.++.||+|+||+|+.+.+..+.+.+.+++++++||++.++..++.+.+..+...+|.... 
T Consensus       318 ~r~lLmiggv~~r~Q~~ql~~g~~ivvGtpgRl~~~is~g~~~lt~crFlvlDead~lL~qgy~d~I~r~h~qip~~tsd  397 (725)
T KOG0349|consen  318 VRSLLMIGGVLKRTQCKQLKDGTHIVVGTPGRLLQPISKGLVTLTHCRFLVLDEADLLLGQGYDDKIYRFHGQIPHMTSD  397 (725)
T ss_pred             hhhhhhhhhHHhHHHHHHhhcCceeeecCchhhhhhhhccceeeeeeEEEEecchhhhhhcccHHHHHHHhccchhhhcC
Confidence            3566889999999999999999999999999999999999999999999999999999999999988888777665443 


Q ss_pred             --------------------------------------------------------------------------------
Q psy6712          82 --------------------------------------------------------------------------------   81 (210)
Q Consensus        82 --------------------------------------------------------------------------------   81 (210)
                                                                                                      
T Consensus       398 g~rlq~~vCsatlh~feVkk~~ervmhfptwVdLkgeD~vpetvHhvv~lv~p~~d~sw~~lr~~i~td~vh~kdn~~pg  477 (725)
T KOG0349|consen  398 GFRLQSPVCSATLHIFEVKKVGERVMHFPTWVDLKGEDLVPETVHHVVKLVCPSVDGSWCDLRQFIETDKVHTKDNLLPG  477 (725)
T ss_pred             CcccccceeeeEEeEEEeeehhhhhccCceeEecccccccchhhccceeecCCccCccHHHHhhhhccCCcccccccccc
Confidence                                                                                            


Q ss_pred             ----------------------------------------HHHHHHHHHhc---CceEEEecCCCCHhHHHHHHHHHhcC
Q psy6712          82 ----------------------------------------VDWLTEKMREA---NFTVSSMHGDMPQKERDGIMKEFRSG  118 (210)
Q Consensus        82 ----------------------------------------~~~l~~~l~~~---~~~~~~~~~~~~~~~r~~~~~~f~~g  118 (210)
                                                              ++.|.+.+.++   ++.+.++||+..+++|++.+++|+.+
T Consensus       478 ~~Spe~~s~a~kilkgEy~v~ai~~h~mdkaiifcrtk~dcDnLer~~~qkgg~~~scvclhgDrkP~Erk~nle~Fkk~  557 (725)
T KOG0349|consen  478 QVSPENPSSATKILKGEYGVVAIRRHAMDKAIIFCRTKQDCDNLERMMNQKGGKHYSCVCLHGDRKPDERKANLESFKKF  557 (725)
T ss_pred             cCCCCChhhhhHHhcCchhhhhhhhhccCceEEEEeccccchHHHHHHHHcCCccceeEEEecCCChhHHHHHHHhhhhc
Confidence                                                    67888888775   47999999999999999999999999


Q ss_pred             CCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCCceeEEEEecc-----------------------
Q psy6712         119 TSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKS-----------------------  175 (210)
Q Consensus       119 ~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~~g~~~~~~~~-----------------------  175 (210)
                      +.+.||||+.+++|+|+..+.++|+.-+|.+...|.||+||+||..+-|.+++++..                       
T Consensus       558 dvkflictdvaargldi~g~p~~invtlpd~k~nyvhrigrvgraermglaislvat~~ekvwyh~c~srgr~c~nt~l~  637 (725)
T KOG0349|consen  558 DVKFLICTDVAARGLDITGLPFMINVTLPDDKTNYVHRIGRVGRAERMGLAISLVATVPEKVWYHWCKSRGRSCNNTNLT  637 (725)
T ss_pred             CeEEEEEehhhhccccccCCceEEEEecCcccchhhhhhhccchhhhcceeEEEeeccchheeehhhhccCCcccCCccc
Confidence            999999999999999999999999999999999999999999998777777777631                       


Q ss_pred             ---------CcHHHHHHHHHHhcCccccccCCccccCCCC
Q psy6712         176 ---------DDIRILRDIEQYYSTQIDEMPMNGKRSLHSY  206 (210)
Q Consensus       176 ---------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  206 (210)
                               .+...+.++|.++++.++++...+.-..+-|
T Consensus       638 e~~gc~iwyne~~llaeve~hln~ti~qv~~~~~vpv~~f  677 (725)
T KOG0349|consen  638 EVRGCCIWYNEPNLLAEVEDHLNITIQQVDKTMDVPVNDF  677 (725)
T ss_pred             cccceEEEeCchhHHHHHHHhhcceeeeeCCCCCCccccc
Confidence                     3567888999999999999887766544443

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.94  E-value=1.5e-25  Score=196.17  Aligned_cols=170  Identities=20%  Similarity=0.310  Sum_probs=129.7

Q ss_pred             CCceEEEEEcCcchH---HHHHHhcC-CCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchH----------
Q psy6712           1 MNVQCHACIGGTNLS---EDLRKLDY-GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFK----------   66 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~---~~~~~l~~-~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~----------   66 (210)
                      +|+++..++||.+..   +++..+.+ .++|+||||+.+.+     .+.+++++++|+||+|++......          
T Consensus       337 ~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~-----~v~~~~l~lvVIDE~Hrfg~~qr~~l~~~~~~~~  411 (681)
T PRK10917        337 LGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQD-----DVEFHNLGLVIIDEQHRFGVEQRLALREKGENPH  411 (681)
T ss_pred             cCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcc-----cchhcccceEEEechhhhhHHHHHHHHhcCCCCC
Confidence            478999999999854   34455655 48999999987643     356789999999999986321100          


Q ss_pred             ----------HHH-------------------------------------HHHHh----------hCCC--------chh
Q psy6712          67 ----------EQI-------------------------------------YDVYR----------YLPP--------ATQ   81 (210)
Q Consensus        67 ----------~~~-------------------------------------~~i~~----------~~~~--------~~~   81 (210)
                                ..+                                     ..+..          +++.        ...
T Consensus       412 iL~~SATp~prtl~~~~~g~~~~s~i~~~p~~r~~i~~~~~~~~~~~~~~~~i~~~~~~g~q~~v~~~~ie~s~~l~~~~  491 (681)
T PRK10917        412 VLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIPDSRRDEVYERIREEIAKGRQAYVVCPLIEESEKLDLQS  491 (681)
T ss_pred             EEEEeCCCCHHHHHHHHcCCCceEEEecCCCCCCCcEEEEeCcccHHHHHHHHHHHHHcCCcEEEEEcccccccchhHHH
Confidence                      000                                     00000          0000        000


Q ss_pred             HHHHHHHHHhc--CceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCC-ChhHHHHhhh
Q psy6712          82 VDWLTEKMREA--NFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPN-NRELYIHRIG  158 (210)
Q Consensus        82 ~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~-s~~~~~q~~G  158 (210)
                      ++.+++.|.+.  +.++..+||+|+.++|.+++++|++|+.+|||||+++++|+|+|++++||++++|. ..+.+.|++|
T Consensus       492 ~~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~GiDip~v~~VIi~~~~r~gls~lhQ~~G  571 (681)
T PRK10917        492 AEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPNATVMVIENAERFGLAQLHQLRG  571 (681)
T ss_pred             HHHHHHHHHHHCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECcceeeCcccCCCcEEEEeCCCCCCHHHHHHHhh
Confidence            33455566544  46899999999999999999999999999999999999999999999999999997 5788889999


Q ss_pred             hhcCCCCceeEEEEecc
Q psy6712         159 RSGRFGRKGVAISFVKS  175 (210)
Q Consensus       159 R~gR~g~~g~~~~~~~~  175 (210)
                      |+||.|..|.|++++..
T Consensus       572 RvGR~g~~g~~ill~~~  588 (681)
T PRK10917        572 RVGRGAAQSYCVLLYKD  588 (681)
T ss_pred             cccCCCCceEEEEEECC
Confidence            99999999999999953

>PRK02362 ski2-like helicase; Provisional

Probab=99.94  E-value=7.4e-26  Score=200.15  Aligned_cols=173  Identities=20%  Similarity=0.285  Sum_probs=134.1

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhC---CC
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYL---PP   78 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~---~~   78 (210)
                      |++|..++|+.+.+.+   ....++|+|+||+++..+++++...+++++++|+||+|.+.+.++...+..++..+   ..
T Consensus        94 g~~v~~~tGd~~~~~~---~l~~~~IiV~Tpek~~~llr~~~~~l~~v~lvViDE~H~l~d~~rg~~le~il~rl~~~~~  170 (737)
T PRK02362         94 GVRVGISTGDYDSRDE---WLGDNDIIVATSEKVDSLLRNGAPWLDDITCVVVDEVHLIDSANRGPTLEVTLAKLRRLNP  170 (737)
T ss_pred             CCEEEEEeCCcCcccc---ccCCCCEEEECHHHHHHHHhcChhhhhhcCEEEEECccccCCCcchHHHHHHHHHHHhcCC
Confidence            7899999999876542   23468999999999999988766668899999999999987654443332222111   00


Q ss_pred             --------------------------------------------------------------------------------
Q psy6712          79 --------------------------------------------------------------------------------   78 (210)
Q Consensus        79 --------------------------------------------------------------------------------   78 (210)
                                                                                                      
T Consensus       171 ~~qii~lSATl~n~~~la~wl~~~~~~~~~rpv~l~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LVF~  250 (737)
T PRK02362        171 DLQVVALSATIGNADELADWLDAELVDSEWRPIDLREGVFYGGAIHFDDSQREVEVPSKDDTLNLVLDTLEEGGQCLVFV  250 (737)
T ss_pred             CCcEEEEcccCCCHHHHHHHhCCCcccCCCCCCCCeeeEecCCeeccccccccCCCccchHHHHHHHHHHHcCCCeEEEE
Confidence                                                                                            


Q ss_pred             --chhHHHHHHHHHhc------------------------------------CceEEEecCCCCHhHHHHHHHHHhcCCC
Q psy6712          79 --ATQVDWLTEKMREA------------------------------------NFTVSSMHGDMPQKERDGIMKEFRSGTS  120 (210)
Q Consensus        79 --~~~~~~l~~~l~~~------------------------------------~~~~~~~~~~~~~~~r~~~~~~f~~g~~  120 (210)
                        ..+++.+++.|...                                    ...+.++|++|++.+|..+++.|++|.+
T Consensus       251 ~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~L~~~l~~gva~hHagl~~~eR~~ve~~Fr~G~i  330 (737)
T PRK02362        251 SSRRNAEGFAKRAASALKKTLTAAERAELAELAEEIREVSDTETSKDLADCVAKGAAFHHAGLSREHRELVEDAFRDRLI  330 (737)
T ss_pred             eCHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhccCccccHHHHHHHHhCEEeecCCCCHHHHHHHHHHHHcCCC
Confidence              00033333333211                                    1368899999999999999999999999


Q ss_pred             cEEEEecCccccCCCCCCcEEEE----ec-----CCCChhHHHHhhhhhcCCCCc--eeEEEEeccCc
Q psy6712         121 RVLITTDVWARGIDVQQVSLVIN----YD-----LPNNRELYIHRIGRSGRFGRK--GVAISFVKSDD  177 (210)
Q Consensus       121 ~ilv~T~~~~~g~d~~~~~~vi~----~~-----~p~s~~~~~q~~GR~gR~g~~--g~~~~~~~~~~  177 (210)
                      ++||||+.+++|+|+|..++||.    ||     .|.+..+|.||+|||||.|.+  |.+++++.+.+
T Consensus       331 ~VLvaT~tla~GvnlPa~~VVI~~~~~yd~~~g~~~~s~~~y~Qm~GRAGR~g~d~~G~~ii~~~~~~  398 (737)
T PRK02362        331 KVISSTPTLAAGLNLPARRVIIRDYRRYDGGAGMQPIPVLEYHQMAGRAGRPGLDPYGEAVLLAKSYD  398 (737)
T ss_pred             eEEEechhhhhhcCCCceEEEEecceeecCCCCceeCCHHHHHHHhhcCCCCCCCCCceEEEEecCch
Confidence            99999999999999999999997    66     588999999999999999874  89999987653

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.94  E-value=2.3e-25  Score=198.44  Aligned_cols=169  Identities=21%  Similarity=0.311  Sum_probs=131.8

Q ss_pred             CceEEEEEcCcchHHH---HHHhcC-CCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHH-----
Q psy6712           2 NVQCHACIGGTNLSED---LRKLDY-GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDV-----   72 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~---~~~l~~-~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i-----   72 (210)
                      ++++..++|+.+.+++   ...+.. .+|||||||..    + .+.+.+++++++|+||+|++.... .+.+..+     
T Consensus       528 ~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~l----l-~~~v~f~~L~llVIDEahrfgv~~-~~~L~~~~~~~~  601 (926)
T TIGR00580       528 PVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKL----L-QKDVKFKDLGLLIIDEEQRFGVKQ-KEKLKELRTSVD  601 (926)
T ss_pred             CcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHH----h-hCCCCcccCCEEEeecccccchhH-HHHHHhcCCCCC
Confidence            6788999998875544   344545 58999999942    2 456788999999999999863211 1111000     


Q ss_pred             ----------------------------------------------------H----------hhCCCchhHHHHHHHHH
Q psy6712          73 ----------------------------------------------------Y----------RYLPPATQVDWLTEKMR   90 (210)
Q Consensus        73 ----------------------------------------------------~----------~~~~~~~~~~~l~~~l~   90 (210)
                                                                          .          .+++....++.+++.|+
T Consensus       602 vL~~SATpiprtl~~~l~g~~d~s~I~~~p~~R~~V~t~v~~~~~~~i~~~i~~el~~g~qv~if~n~i~~~e~l~~~L~  681 (926)
T TIGR00580       602 VLTLSATPIPRTLHMSMSGIRDLSIIATPPEDRLPVRTFVMEYDPELVREAIRRELLRGGQVFYVHNRIESIEKLATQLR  681 (926)
T ss_pred             EEEEecCCCHHHHHHHHhcCCCcEEEecCCCCccceEEEEEecCHHHHHHHHHHHHHcCCeEEEEECCcHHHHHHHHHHH
Confidence                                                                0          01111111667777787


Q ss_pred             hc--CceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCC-ChhHHHHhhhhhcCCCCce
Q psy6712          91 EA--NFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPN-NRELYIHRIGRSGRFGRKG  167 (210)
Q Consensus        91 ~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~-s~~~~~q~~GR~gR~g~~g  167 (210)
                      +.  +.++..+||+|++.+|.+++++|++|+.+|||||+++++|+|+|++++||++++|. +..+|.||+||+||.|+.|
T Consensus       682 ~~~p~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~iie~GIDIp~v~~VIi~~a~~~gls~l~Qr~GRvGR~g~~g  761 (926)
T TIGR00580       682 ELVPEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKA  761 (926)
T ss_pred             HhCCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECChhhcccccccCCEEEEecCCCCCHHHHHHHhcCCCCCCCCe
Confidence            63  78999999999999999999999999999999999999999999999999999875 6789999999999999999


Q ss_pred             eEEEEeccC
Q psy6712         168 VAISFVKSD  176 (210)
Q Consensus       168 ~~~~~~~~~  176 (210)
                      .|++++.+.
T Consensus       762 ~aill~~~~  770 (926)
T TIGR00580       762 YAYLLYPHQ  770 (926)
T ss_pred             EEEEEECCc
Confidence            999999653

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.

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.94  E-value=3.8e-25  Score=192.33  Aligned_cols=169  Identities=22%  Similarity=0.396  Sum_probs=128.7

Q ss_pred             CCceEEEEEcCcchHH---HHHHhcC-CCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhc--------cch---
Q psy6712           1 MNVQCHACIGGTNLSE---DLRKLDY-GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLN--------KGF---   65 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~---~~~~l~~-~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~--------~~~---   65 (210)
                      +|++++.++||.+..+   ++..+.+ .++|+|+||+.+.+     .+.+++++++|+||+|++..        .+.   
T Consensus       311 ~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~-----~~~~~~l~lvVIDEaH~fg~~qr~~l~~~~~~~~  385 (630)
T TIGR00643       311 LGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQE-----KVEFKRLALVIIDEQHRFGVEQRKKLREKGQGGF  385 (630)
T ss_pred             cCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhc-----cccccccceEEEechhhccHHHHHHHHHhcccCC
Confidence            3789999999988665   4555554 58999999987643     35678999999999998421        110   


Q ss_pred             H------------HHHH-H--------HHhhCCCc---------------------------------------------
Q psy6712          66 K------------EQIY-D--------VYRYLPPA---------------------------------------------   79 (210)
Q Consensus        66 ~------------~~~~-~--------i~~~~~~~---------------------------------------------   79 (210)
                      .            ..+. .        .+...+..                                             
T Consensus       386 ~~~~l~~SATp~prtl~l~~~~~l~~~~i~~~p~~r~~i~~~~~~~~~~~~~~~~i~~~l~~g~q~~v~~~~i~~s~~~~  465 (630)
T TIGR00643       386 TPHVLVMSATPIPRTLALTVYGDLDTSIIDELPPGRKPITTVLIKHDEKDIVYEFIEEEIAKGRQAYVVYPLIEESEKLD  465 (630)
T ss_pred             CCCEEEEeCCCCcHHHHHHhcCCcceeeeccCCCCCCceEEEEeCcchHHHHHHHHHHHHHhCCcEEEEEccccccccch
Confidence            0            0000 0        00000000                                             


Q ss_pred             -hhHHHHHHHHHh--cCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCC-ChhHHHH
Q psy6712          80 -TQVDWLTEKMRE--ANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPN-NRELYIH  155 (210)
Q Consensus        80 -~~~~~l~~~l~~--~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~-s~~~~~q  155 (210)
                       ..++.+++.|.+  .++++..+||+|+.++|..++++|++|+.+|||||+++++|+|+|++++||++++|. +...|.|
T Consensus       466 ~~~a~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~GvDiP~v~~VIi~~~~r~gls~lhQ  545 (630)
T TIGR00643       466 LKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQ  545 (630)
T ss_pred             HHHHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECceeecCcccCCCcEEEEeCCCcCCHHHHHH
Confidence             003345555554  367899999999999999999999999999999999999999999999999999986 6788889


Q ss_pred             hhhhhcCCCCceeEEEEec
Q psy6712         156 RIGRSGRFGRKGVAISFVK  174 (210)
Q Consensus       156 ~~GR~gR~g~~g~~~~~~~  174 (210)
                      ++||+||.|..|.|++++.
T Consensus       546 ~~GRvGR~g~~g~~il~~~  564 (630)
T TIGR00643       546 LRGRVGRGDHQSYCLLVYK  564 (630)
T ss_pred             HhhhcccCCCCcEEEEEEC
Confidence            9999999999999999993

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

Probab=99.93  E-value=5.7e-25  Score=178.85  Aligned_cols=94  Identities=31%  Similarity=0.497  Sum_probs=85.0

Q ss_pred             HHHHHHHHHhcCceEE--Ee-------cCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhH
Q psy6712          82 VDWLTEKMREANFTVS--SM-------HGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNREL  152 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~--~~-------~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~  152 (210)
                      ++.+.+.|.+.+..+.  ++       ..||++.++.+++++|++|++++||||++.++|+|+|+++.||+|++-+|...
T Consensus       379 ae~i~~~L~~~~~~~~~rFiGQa~r~~~~GMsQkeQ~eiI~~Fr~Ge~nVLVaTSVgEEGLDIp~vDlVifYEpvpSeIR  458 (542)
T COG1111         379 AEEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIR  458 (542)
T ss_pred             HHHHHHHHHhcCCcceeEEeeccccccccccCHHHHHHHHHHHhcCCceEEEEcccccccCCCCcccEEEEecCCcHHHH
Confidence            7778888887777663  22       24699999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhhhcCCCCceeEEEEeccC
Q psy6712         153 YIHRIGRSGRFGRKGVAISFVKSD  176 (210)
Q Consensus       153 ~~q~~GR~gR~g~~g~~~~~~~~~  176 (210)
                      ++||.||+||. +.|.+++++...
T Consensus       459 ~IQR~GRTGR~-r~Grv~vLvt~g  481 (542)
T COG1111         459 SIQRKGRTGRK-RKGRVVVLVTEG  481 (542)
T ss_pred             HHHhhCccccC-CCCeEEEEEecC
Confidence            99999999998 889999999876

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.93  E-value=1.3e-24  Score=197.30  Aligned_cols=168  Identities=19%  Similarity=0.255  Sum_probs=130.0

Q ss_pred             CceEEEEEcCcchHHHHHHh---cC-CCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHH-----
Q psy6712           2 NVQCHACIGGTNLSEDLRKL---DY-GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDV-----   72 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l---~~-~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i-----   72 (210)
                      ++++..++|+.+..++...+   .+ +++|+||||+.+     ++.+.+++++++|+||+|++... ....+..+     
T Consensus       677 ~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL-----~~~v~~~~L~lLVIDEahrfG~~-~~e~lk~l~~~~q  750 (1147)
T PRK10689        677 PVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLL-----QSDVKWKDLGLLIVDEEHRFGVR-HKERIKAMRADVD  750 (1147)
T ss_pred             CceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHH-----hCCCCHhhCCEEEEechhhcchh-HHHHHHhcCCCCc
Confidence            57888999998877766544   33 689999999632     34567889999999999998421 11111000     


Q ss_pred             ----------------------------------------------------Hh----------hCCCchhHHHHHHHHH
Q psy6712          73 ----------------------------------------------------YR----------YLPPATQVDWLTEKMR   90 (210)
Q Consensus        73 ----------------------------------------------------~~----------~~~~~~~~~~l~~~l~   90 (210)
                                                                          +.          +++....++.+++.|.
T Consensus       751 vLl~SATpiprtl~l~~~gl~d~~~I~~~p~~r~~v~~~~~~~~~~~~k~~il~el~r~gqv~vf~n~i~~ie~la~~L~  830 (1147)
T PRK10689        751 ILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSLVVREAILREILRGGQVYYLYNDVENIQKAAERLA  830 (1147)
T ss_pred             EEEEcCCCCHHHHHHHHhhCCCcEEEecCCCCCCCceEEEEecCcHHHHHHHHHHHhcCCeEEEEECCHHHHHHHHHHHH
Confidence                                                                00          0111111566777777


Q ss_pred             hc--CceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCC-CChhHHHHhhhhhcCCCCce
Q psy6712          91 EA--NFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLP-NNRELYIHRIGRSGRFGRKG  167 (210)
Q Consensus        91 ~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p-~s~~~~~q~~GR~gR~g~~g  167 (210)
                      +.  +.++..+||+|++++|.+++.+|++|+++|||||+++++|+|+|++++||..+.+ .+..+|.||+||+||.|..|
T Consensus       831 ~~~p~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaTdIierGIDIP~v~~VIi~~ad~fglaq~~Qr~GRvGR~g~~g  910 (1147)
T PRK10689        831 ELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQA  910 (1147)
T ss_pred             HhCCCCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEECchhhcccccccCCEEEEecCCCCCHHHHHHHhhccCCCCCce
Confidence            65  6789999999999999999999999999999999999999999999999976554 46788999999999999999


Q ss_pred             eEEEEecc
Q psy6712         168 VAISFVKS  175 (210)
Q Consensus       168 ~~~~~~~~  175 (210)
                      .|++++..
T Consensus       911 ~a~ll~~~  918 (1147)
T PRK10689        911 YAWLLTPH  918 (1147)
T ss_pred             EEEEEeCC
Confidence            99999864

>PRK00254 ski2-like helicase; Provisional

Probab=99.93  E-value=7.1e-25  Score=193.50  Aligned_cols=174  Identities=16%  Similarity=0.213  Sum_probs=132.9

Q ss_pred             CCceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCch
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPAT   80 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~   80 (210)
                      +|++|..++|+.+.+.++   ..+++|+|+||+++..++.++...+++++++|+||+|.+.+.++...+..++..+....
T Consensus        94 ~g~~v~~~~Gd~~~~~~~---~~~~~IiV~Tpe~~~~ll~~~~~~l~~l~lvViDE~H~l~~~~rg~~le~il~~l~~~~  170 (720)
T PRK00254         94 LGLRVAMTTGDYDSTDEW---LGKYDIIIATAEKFDSLLRHGSSWIKDVKLVVADEIHLIGSYDRGATLEMILTHMLGRA  170 (720)
T ss_pred             cCCEEEEEeCCCCCchhh---hccCCEEEEcHHHHHHHHhCCchhhhcCCEEEEcCcCccCCccchHHHHHHHHhcCcCC
Confidence            478999999998765432   25689999999999998887766789999999999999876554444433333221111


Q ss_pred             h-------------------------------------------------------------------------------
Q psy6712          81 Q-------------------------------------------------------------------------------   81 (210)
Q Consensus        81 ~-------------------------------------------------------------------------------   81 (210)
                      +                                                                               
T Consensus       171 qiI~lSATl~n~~~la~wl~~~~~~~~~rpv~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~vLVF~~sr~~  250 (720)
T PRK00254        171 QILGLSATVGNAEELAEWLNAELVVSDWRPVKLRKGVFYQGFLFWEDGKIERFPNSWESLVYDAVKKGKGALVFVNTRRS  250 (720)
T ss_pred             cEEEEEccCCCHHHHHHHhCCccccCCCCCCcceeeEecCCeeeccCcchhcchHHHHHHHHHHHHhCCCEEEEEcChHH
Confidence            1                                                                               


Q ss_pred             HHHHHHHHHh---------------------------------cCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecC
Q psy6712          82 VDWLTEKMRE---------------------------------ANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDV  128 (210)
Q Consensus        82 ~~~l~~~l~~---------------------------------~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~  128 (210)
                      ++.++..|..                                 ....+.++|++|++++|..+.+.|++|.+++||||+.
T Consensus       251 ~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~hHagl~~~eR~~ve~~F~~G~i~VLvaT~t  330 (720)
T PRK00254        251 AEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLKKALRGGVAFHHAGLGRTERVLIEDAFREGLIKVITATPT  330 (720)
T ss_pred             HHHHHHHHHHHHHHhcCchhHHHHHHHHHHHhcCCCcHHHHHHHhhCEEEeCCCCCHHHHHHHHHHHHCCCCeEEEeCcH
Confidence            2222222211                                 0235899999999999999999999999999999999


Q ss_pred             ccccCCCCCCcEEEE-------ecCC-CChhHHHHhhhhhcCCC--CceeEEEEeccCc
Q psy6712         129 WARGIDVQQVSLVIN-------YDLP-NNRELYIHRIGRSGRFG--RKGVAISFVKSDD  177 (210)
Q Consensus       129 ~~~g~d~~~~~~vi~-------~~~p-~s~~~~~q~~GR~gR~g--~~g~~~~~~~~~~  177 (210)
                      +++|+|+|.+++||.       ++.| .+..+|.||+|||||.|  ..|.+++++.+.+
T Consensus       331 La~Gvnipa~~vVI~~~~~~~~~~~~~~~~~~~~Qm~GRAGR~~~d~~G~~ii~~~~~~  389 (720)
T PRK00254        331 LSAGINLPAFRVIIRDTKRYSNFGWEDIPVLEIQQMMGRAGRPKYDEVGEAIIVATTEE  389 (720)
T ss_pred             HhhhcCCCceEEEECCceEcCCCCceeCCHHHHHHhhhccCCCCcCCCceEEEEecCcc
Confidence            999999999999994       4443 35779999999999976  4689999987654

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

Probab=99.92  E-value=2.8e-24  Score=186.72  Aligned_cols=175  Identities=18%  Similarity=0.335  Sum_probs=147.4

Q ss_pred             CCceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCc--cCCCccEEEechhhHHhccchHH----HHHHHHh
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVL--RTRNIKMLVLDEADEMLNKGFKE----QIYDVYR   74 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~--~~~~~~~lviDE~~~l~~~~~~~----~~~~i~~   74 (210)
                      +|+.+...+|+++..+..+..++.|||||+||+.|.-++..+++  .+++++++|+||.|.+.++...-    .+..+..
T Consensus       100 ~G~~v~vRhGDT~~~er~r~~~~PPdILiTTPEsL~lll~~~~~r~~l~~vr~VIVDEiHel~~sKRG~~Lsl~LeRL~~  179 (814)
T COG1201         100 LGIEVAVRHGDTPQSEKQKMLKNPPHILITTPESLAILLNSPKFRELLRDVRYVIVDEIHALAESKRGVQLALSLERLRE  179 (814)
T ss_pred             cCCccceecCCCChHHhhhccCCCCcEEEeChhHHHHHhcCHHHHHHhcCCcEEEeehhhhhhccccchhhhhhHHHHHh
Confidence            68899999999999999999999999999999998888877543  58999999999999998653221    1122222


Q ss_pred             hCC-----------------------------------------------------------------------------
Q psy6712          75 YLP-----------------------------------------------------------------------------   77 (210)
Q Consensus        75 ~~~-----------------------------------------------------------------------------   77 (210)
                      +.+                                                                             
T Consensus       180 l~~~~qRIGLSATV~~~~~varfL~g~~~~~~Iv~~~~~k~~~i~v~~p~~~~~~~~~~~~~~~~~i~~~v~~~~ttLIF  259 (814)
T COG1201         180 LAGDFQRIGLSATVGPPEEVAKFLVGFGDPCEIVDVSAAKKLEIKVISPVEDLIYDEELWAALYERIAELVKKHRTTLIF  259 (814)
T ss_pred             hCcccEEEeehhccCCHHHHHHHhcCCCCceEEEEcccCCcceEEEEecCCccccccchhHHHHHHHHHHHhhcCcEEEE
Confidence            221                                                                             


Q ss_pred             --CchhHHHHHHHHHhcC-ceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHH
Q psy6712          78 --PATQVDWLTEKMREAN-FTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYI  154 (210)
Q Consensus        78 --~~~~~~~l~~~l~~~~-~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~  154 (210)
                        ...+++.++..|++.+ ..+..+||.++.++|..+.++|++|+.+.+|||+.++.|+|+.+++.||+++.|.++...+
T Consensus       260 ~NTR~~aE~l~~~L~~~~~~~i~~HHgSlSre~R~~vE~~lk~G~lravV~TSSLELGIDiG~vdlVIq~~SP~sV~r~l  339 (814)
T COG1201         260 TNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSLELGIDIGDIDLVIQLGSPKSVNRFL  339 (814)
T ss_pred             EeChHHHHHHHHHHHHhcCCceeeecccccHHHHHHHHHHHhcCCceEEEEccchhhccccCCceEEEEeCCcHHHHHHh
Confidence              1111888888888776 8999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhhhhcCC-CCceeEEEEecc
Q psy6712         155 HRIGRSGRF-GRKGVAISFVKS  175 (210)
Q Consensus       155 q~~GR~gR~-g~~g~~~~~~~~  175 (210)
                      ||+||+|+. +..++.+++...
T Consensus       340 QRiGRsgHr~~~~Skg~ii~~~  361 (814)
T COG1201         340 QRIGRAGHRLGEVSKGIIIAED  361 (814)
T ss_pred             HhccccccccCCcccEEEEecC
Confidence            999999965 556777777766

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

Probab=99.92  E-value=5.4e-24  Score=185.87  Aligned_cols=161  Identities=25%  Similarity=0.353  Sum_probs=131.5

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCc----------------cCCCccEEEechhhHHhccch
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVL----------------RTRNIKMLVLDEADEMLNKGF   65 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~----------------~~~~~~~lviDE~~~l~~~~~   65 (210)
                      +++|..++||.+.+.|+..++.+++|||||++    ++.++.+                .+++++++|+||||  ++.+|
T Consensus       113 ~l~v~~l~GG~~~~~q~~~l~~~p~IIVgT~D----~i~sr~L~~gYg~~~~~~pi~ag~L~~v~~LVLDEAD--Ld~gF  186 (844)
T TIGR02621       113 PLAISTLRGQFADNDEWMLDPHRPAVIVGTVD----MIGSRLLFSGYGCGFKSRPLHAGFLGQDALIVHDEAH--LEPAF  186 (844)
T ss_pred             CeEEEEEECCCChHHHHHhcCCCCcEEEECHH----HHcCCccccccccccccccchhhhhccceEEEEehhh--hcccc
Confidence            48899999999999999999999999999964    4445444                27889999999999  67889


Q ss_pred             HHHHHHHHhhC--CCc---hh-----------------------------------------------------------
Q psy6712          66 KEQIYDVYRYL--PPA---TQ-----------------------------------------------------------   81 (210)
Q Consensus        66 ~~~~~~i~~~~--~~~---~~-----------------------------------------------------------   81 (210)
                      .+.+..|+..+  +..   .|                                                           
T Consensus       187 ~~~l~~Il~~l~rp~~~rprQtLLFSAT~p~ei~~l~~~~~~~p~~i~V~~~~l~a~ki~q~v~v~~e~Kl~~lv~~L~~  266 (844)
T TIGR02621       187 QELLKQIMNEQQRPPDFLPLRVVELTATSRTDGPDRTTLLSAEDYKHPVLKKRLAAKKIVKLVPPSDEKFLSTMVKELNL  266 (844)
T ss_pred             HHHHHHHHHhcccCcccccceEEEEecCCCccHHHHHHHHccCCceeecccccccccceEEEEecChHHHHHHHHHHHHH
Confidence            99999999864  221   22                                                           


Q ss_pred             ------------------HHHHHHHHHhcCceEEEecCCCCHhHHH-----HHHHHHhc----CC-------CcEEEEec
Q psy6712          82 ------------------VDWLTEKMREANFTVSSMHGDMPQKERD-----GIMKEFRS----GT-------SRVLITTD  127 (210)
Q Consensus        82 ------------------~~~l~~~l~~~~~~~~~~~~~~~~~~r~-----~~~~~f~~----g~-------~~ilv~T~  127 (210)
                                        ++.+++.|++.++  ..+||+|++.+|.     .++++|++    |+       ..+||||+
T Consensus       267 ll~e~g~~vLVF~NTv~~Aq~L~~~L~~~g~--~lLHG~m~q~dR~~~~~~~il~~Fk~~~~~g~~~~~~~g~~ILVATd  344 (844)
T TIGR02621       267 LMKDSGGAILVFCRTVKHVRKVFAKLPKEKF--ELLTGTLRGAERDDLVKKEIFNRFLPQMLSGSRARPQQGTVYLVCTS  344 (844)
T ss_pred             HHhhCCCcEEEEECCHHHHHHHHHHHHhcCC--eEeeCCCCHHHHhhHHHHHHHHHHhccccccccccccccceEEeccc
Confidence                              6667777766665  8999999999999     88999987    44       68999999


Q ss_pred             CccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCCc-eeEEEEe
Q psy6712         128 VWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRK-GVAISFV  173 (210)
Q Consensus       128 ~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~~-g~~~~~~  173 (210)
                      ++++|+|++. ++||++..|  ...|+||+||+||.|.. +..+.++
T Consensus       345 VaerGLDId~-d~VI~d~aP--~esyIQRiGRtgR~G~~~~~~i~vv  388 (844)
T TIGR02621       345 AGEVGVNISA-DHLVCDLAP--FESMQQRFGRVNRFGELQACQIAVV  388 (844)
T ss_pred             hhhhcccCCc-ceEEECCCC--HHHHHHHhcccCCCCCCCCceEEEE
Confidence            9999999986 888887766  68999999999999884 3334444

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.

>PRK01172 ski2-like helicase; Provisional

Probab=99.91  E-value=1.9e-23  Score=183.53  Aligned_cols=183  Identities=19%  Similarity=0.233  Sum_probs=132.5

Q ss_pred             CCceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhh-----
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRY-----   75 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~-----   75 (210)
                      +|++|...+|+.+....   ....+||+|+||+++..++.+....+++++++|+||+|.+.+.++...+..++..     
T Consensus        91 ~g~~v~~~~G~~~~~~~---~~~~~dIiv~Tpek~~~l~~~~~~~l~~v~lvViDEaH~l~d~~rg~~le~ll~~~~~~~  167 (674)
T PRK01172         91 LGMRVKISIGDYDDPPD---FIKRYDVVILTSEKADSLIHHDPYIINDVGLIVADEIHIIGDEDRGPTLETVLSSARYVN  167 (674)
T ss_pred             cCCeEEEEeCCCCCChh---hhccCCEEEECHHHHHHHHhCChhHHhhcCEEEEecchhccCCCccHHHHHHHHHHHhcC
Confidence            37788899998775432   2346799999999999888876666889999999999998765443333322211     


Q ss_pred             ---------------------------------------------------------------------------CCCch
Q psy6712          76 ---------------------------------------------------------------------------LPPAT   80 (210)
Q Consensus        76 ---------------------------------------------------------------------------~~~~~   80 (210)
                                                                                                 ++...
T Consensus       168 ~~~riI~lSATl~n~~~la~wl~~~~~~~~~r~vpl~~~i~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~vLVF~~sr~  247 (674)
T PRK01172        168 PDARILALSATVSNANELAQWLNASLIKSNFRPVPLKLGILYRKRLILDGYERSQVDINSLIKETVNDGGQVLVFVSSRK  247 (674)
T ss_pred             cCCcEEEEeCccCCHHHHHHHhCCCccCCCCCCCCeEEEEEecCeeeecccccccccHHHHHHHHHhCCCcEEEEeccHH
Confidence                                                                                       11111


Q ss_pred             hHHHHHHHHHhc-------------------------CceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCC
Q psy6712          81 QVDWLTEKMREA-------------------------NFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDV  135 (210)
Q Consensus        81 ~~~~l~~~l~~~-------------------------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~  135 (210)
                      +++.+++.|.+.                         ...+.++|++|+.++|..+.+.|++|.++|||||+.+++|+|+
T Consensus       248 ~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~~hagl~~~eR~~ve~~f~~g~i~VLvaT~~la~Gvni  327 (674)
T PRK01172        248 NAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQRRFIEEMFRNRYIKVIVATPTLAAGVNL  327 (674)
T ss_pred             HHHHHHHHHHHhhhhcccccccccccccccHHHHHHHhcCEEEecCCCCHHHHHHHHHHHHcCCCeEEEecchhhccCCC
Confidence            144455444331                         1247889999999999999999999999999999999999999


Q ss_pred             CCCcEEEEecC---------CCChhHHHHhhhhhcCCCC--ceeEEEEeccCcHHHHHHHHHHhc
Q psy6712         136 QQVSLVINYDL---------PNNRELYIHRIGRSGRFGR--KGVAISFVKSDDIRILRDIEQYYS  189 (210)
Q Consensus       136 ~~~~~vi~~~~---------p~s~~~~~q~~GR~gR~g~--~g~~~~~~~~~~~~~~~~~~~~~~  189 (210)
                      |+..+ |+.+.         |.+..+|.||+|||||.|.  .|.+++++.+.+.  ....++++.
T Consensus       328 pa~~V-II~~~~~~~~~~~~~~s~~~~~Qm~GRAGR~g~d~~g~~~i~~~~~~~--~~~~~~~l~  389 (674)
T PRK01172        328 PARLV-IVRDITRYGNGGIRYLSNMEIKQMIGRAGRPGYDQYGIGYIYAASPAS--YDAAKKYLS  389 (674)
T ss_pred             cceEE-EEcCceEeCCCCceeCCHHHHHHHhhcCCCCCCCCcceEEEEecCccc--HHHHHHHHc
Confidence            98654 44443         4688899999999999985  5778888765431  223455553

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.91  E-value=3.8e-23  Score=180.26  Aligned_cols=95  Identities=25%  Similarity=0.356  Sum_probs=87.8

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCC---CCCc-----EEEEecCCCChhHH
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDV---QQVS-----LVINYDLPNNRELY  153 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~---~~~~-----~vi~~~~p~s~~~~  153 (210)
                      ++.+++.|.+.|+++..+||.++.+++..+..+++.|  .|+|||++++||+|+   |++.     +||++++|.+...|
T Consensus       441 se~l~~~L~~~gi~~~~L~~~~~~~e~~~i~~ag~~g--~VlIATdmAgRG~DI~l~~~V~~~GGL~VI~~d~p~s~r~y  518 (790)
T PRK09200        441 SETFSKLLDEAGIPHNLLNAKNAAKEAQIIAEAGQKG--AVTVATNMAGRGTDIKLGEGVHELGGLAVIGTERMESRRVD  518 (790)
T ss_pred             HHHHHHHHHHCCCCEEEecCCccHHHHHHHHHcCCCC--eEEEEccchhcCcCCCcccccccccCcEEEeccCCCCHHHH
Confidence            8889999999999999999999998888888887765  799999999999999   7998     99999999999999


Q ss_pred             HHhhhhhcCCCCceeEEEEeccCcH
Q psy6712         154 IHRIGRSGRFGRKGVAISFVKSDDI  178 (210)
Q Consensus       154 ~q~~GR~gR~g~~g~~~~~~~~~~~  178 (210)
                      .||+||+||.|.+|.++.|++..|.
T Consensus       519 ~qr~GRtGR~G~~G~s~~~is~eD~  543 (790)
T PRK09200        519 LQLRGRSGRQGDPGSSQFFISLEDD  543 (790)
T ss_pred             HHhhccccCCCCCeeEEEEEcchHH
Confidence            9999999999999999999987544

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.90  E-value=4.6e-23  Score=182.02  Aligned_cols=156  Identities=19%  Similarity=0.360  Sum_probs=123.8

Q ss_pred             cCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhH-HhccchH----HHHHH-------------------------
Q psy6712          22 DYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADE-MLNKGFK----EQIYD-------------------------   71 (210)
Q Consensus        22 ~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~-l~~~~~~----~~~~~-------------------------   71 (210)
                      ..+.+|+|+|||++.+.+.+ ...+++++++||||+|. +++.++.    .++..                         
T Consensus        88 s~~t~I~v~T~G~Llr~l~~-d~~L~~v~~VIiDEaHER~L~~Dl~L~ll~~i~~~lr~dlqlIlmSATl~~~~l~~~l~  166 (819)
T TIGR01970        88 SRRTRLEVVTEGILTRMIQD-DPELDGVGALIFDEFHERSLDADLGLALALDVQSSLREDLKILAMSATLDGERLSSLLP  166 (819)
T ss_pred             CCCCcEEEECCcHHHHHHhh-CcccccCCEEEEeccchhhhccchHHHHHHHHHHhcCCCceEEEEeCCCCHHHHHHHcC
Confidence            45679999999999998876 45789999999999995 4543221    11100                         


Q ss_pred             ---------------------------------------------HHhhCCCchhHHHHHHHHHh---cCceEEEecCCC
Q psy6712          72 ---------------------------------------------VYRYLPPATQVDWLTEKMRE---ANFTVSSMHGDM  103 (210)
Q Consensus        72 ---------------------------------------------i~~~~~~~~~~~~l~~~l~~---~~~~~~~~~~~~  103 (210)
                                                                   ++.|++....++.+.+.|.+   .++.+..+||+|
T Consensus       167 ~~~vI~~~gr~~pVe~~y~~~~~~~~~~~~v~~~l~~~l~~~~g~iLVFlpg~~eI~~l~~~L~~~~~~~~~v~pLHg~L  246 (819)
T TIGR01970       167 DAPVVESEGRSFPVEIRYLPLRGDQRLEDAVSRAVEHALASETGSILVFLPGQAEIRRVQEQLAERLDSDVLICPLYGEL  246 (819)
T ss_pred             CCcEEEecCcceeeeeEEeecchhhhHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHhhcCCCcEEEEecCCC
Confidence                                                         11122222226777777766   478999999999


Q ss_pred             CHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCC------------------ChhHHHHhhhhhcCCCC
Q psy6712         104 PQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPN------------------NRELYIHRIGRSGRFGR  165 (210)
Q Consensus       104 ~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~------------------s~~~~~q~~GR~gR~g~  165 (210)
                      +.++|..+++.|++|+.+|+|||+++++|+|+|++++||+++.|.                  |..+|.||+||+||. .
T Consensus       247 ~~~eq~~~~~~~~~G~rkVlVATnIAErgItIp~V~~VID~Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRAGR~-~  325 (819)
T TIGR01970       247 SLAAQDRAIKPDPQGRRKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLETVRISQASATQRAGRAGRL-E  325 (819)
T ss_pred             CHHHHHHHHhhcccCCeEEEEecchHhhcccccCceEEEEcCcccccccccccCCceeeEEEECHHHHHhhhhhcCCC-C
Confidence            999999999999999999999999999999999999999999874                  345689999999999 8


Q ss_pred             ceeEEEEeccCcHH
Q psy6712         166 KGVAISFVKSDDIR  179 (210)
Q Consensus       166 ~g~~~~~~~~~~~~  179 (210)
                      .|.|+.+++..+..
T Consensus       326 ~G~cyrL~t~~~~~  339 (819)
T TIGR01970       326 PGVCYRLWSEEQHQ  339 (819)
T ss_pred             CCEEEEeCCHHHHH
Confidence            99999999876543

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.

>KOG0351|consensus

Probab=99.90  E-value=2.7e-23  Score=183.69  Aligned_cols=184  Identities=24%  Similarity=0.349  Sum_probs=149.4

Q ss_pred             CceEEEEEcCcchHHHH---HHhcC---CCcEEEEChHHHHHH--HHhcCccCCC---ccEEEechhhHHhccc--hHHH
Q psy6712           2 NVQCHACIGGTNLSEDL---RKLDY---GQHVVSGTPGRVFDM--IRRRVLRTRN---IKMLVLDEADEMLNKG--FKEQ   68 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~---~~l~~---~~~Ili~Tp~~l~~~--l~~~~~~~~~---~~~lviDE~~~l~~~~--~~~~   68 (210)
                      +|+..++.|+-...++.   +.+.+   ..+|+.-||+++...  +.+...++..   +..+||||||++.+|+  |++.
T Consensus       328 ~I~a~~L~s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~~~~~~L~~~~~lal~vIDEAHCVSqWgHdFRp~  407 (941)
T KOG0351|consen  328 GIPACFLSSIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLYARGLLALFVIDEAHCVSQWGHDFRPS  407 (941)
T ss_pred             CcceeeccccccHHHHHHHHHHHhCCCCeEEEEEeCHHHhhcccchhhHHHhccCCCeeEEEEecHHHHhhhhcccccHH
Confidence            68888899998876544   44443   469999999987662  3333334555   8899999999999986  3433


Q ss_pred             HHHHH---hhCCCchh----------------------------------------------------------------
Q psy6712          69 IYDVY---RYLPPATQ----------------------------------------------------------------   81 (210)
Q Consensus        69 ~~~i~---~~~~~~~~----------------------------------------------------------------   81 (210)
                      ..++-   ...+..+-                                                                
T Consensus       408 Yk~l~~l~~~~~~vP~iALTATAT~~v~~DIi~~L~l~~~~~~~~sfnR~NL~yeV~~k~~~~~~~~~~~~~~~~~~~~s  487 (941)
T KOG0351|consen  408 YKRLGLLRIRFPGVPFIALTATATERVREDVIRSLGLRNPELFKSSFNRPNLKYEVSPKTDKDALLDILEESKLRHPDQS  487 (941)
T ss_pred             HHHHHHHHhhCCCCCeEEeehhccHHHHHHHHHHhCCCCcceecccCCCCCceEEEEeccCccchHHHHHHhhhcCCCCC
Confidence            32222   11111110                                                                


Q ss_pred             ----------HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChh
Q psy6712          82 ----------VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRE  151 (210)
Q Consensus        82 ----------~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~  151 (210)
                                ++.++..|+..++.+..+|++|+..+|..+-.+|..++++|+|||-++++|+|.|+|..||||.+|.+..
T Consensus       488 ~IIYC~sr~~ce~vs~~L~~~~~~a~~YHAGl~~~~R~~Vq~~w~~~~~~VivATVAFGMGIdK~DVR~ViH~~lPks~E  567 (941)
T KOG0351|consen  488 GIIYCLSRKECEQVSAVLRSLGKSAAFYHAGLPPKERETVQKAWMSDKIRVIVATVAFGMGIDKPDVRFVIHYSLPKSFE  567 (941)
T ss_pred             eEEEeCCcchHHHHHHHHHHhchhhHhhhcCCCHHHHHHHHHHHhcCCCeEEEEEeeccCCCCCCceeEEEECCCchhHH
Confidence                      9999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhhhhcCCCCceeEEEEeccCcHHHHHHHH
Q psy6712         152 LYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIE  185 (210)
Q Consensus       152 ~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~~  185 (210)
                      .|.|.+|||||+|..+.|++|+...+...++.+-
T Consensus       568 ~YYQE~GRAGRDG~~s~C~l~y~~~D~~~l~~ll  601 (941)
T KOG0351|consen  568 GYYQEAGRAGRDGLPSSCVLLYGYADISELRRLL  601 (941)
T ss_pred             HHHHhccccCcCCCcceeEEecchhHHHHHHHHH
Confidence            9999999999999999999999988776655443

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.89  E-value=5.8e-22  Score=170.80  Aligned_cols=97  Identities=23%  Similarity=0.327  Sum_probs=90.5

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCC-------CcEEEEecCCCChhHHH
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQ-------VSLVINYDLPNNRELYI  154 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~-------~~~vi~~~~p~s~~~~~  154 (210)
                      ++.+++.|.+.|+++..+|+.  ..+|+..+.+|..+...|+|||++++||+|++.       .-+||+++.|.|...|.
T Consensus       418 se~ls~~L~~~gi~~~~Lna~--q~~rEa~ii~~ag~~g~VtIATnmAgRGtDI~l~~V~~~GGl~VI~t~~p~s~ri~~  495 (745)
T TIGR00963       418 SELLSNLLKERGIPHNVLNAK--NHEREAEIIAQAGRKGAVTIATNMAGRGTDIKLEEVKELGGLYVIGTERHESRRIDN  495 (745)
T ss_pred             HHHHHHHHHHcCCCeEEeeCC--hHHHHHHHHHhcCCCceEEEEeccccCCcCCCccchhhcCCcEEEecCCCCcHHHHH
Confidence            889999999999999999999  789999999999999999999999999999998       44999999999999999


Q ss_pred             HhhhhhcCCCCceeEEEEeccCcHHH
Q psy6712         155 HRIGRSGRFGRKGVAISFVKSDDIRI  180 (210)
Q Consensus       155 q~~GR~gR~g~~g~~~~~~~~~~~~~  180 (210)
                      |++||+||+|.+|.+.+|++..|.-+
T Consensus       496 q~~GRtGRqG~~G~s~~~ls~eD~l~  521 (745)
T TIGR00963       496 QLRGRSGRQGDPGSSRFFLSLEDNLM  521 (745)
T ss_pred             HHhccccCCCCCcceEEEEeccHHHH
Confidence            99999999999999999999875443

The proteins SecA-F and SecY, not all of which are necessary, comprise the standard prokaryotic protein translocation apparatus. Other, specialized translocation systems also exist but are not as broadly distributed. This model describes SecA, an essential member of the apparatus.

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.89  E-value=3.8e-22  Score=172.81  Aligned_cols=95  Identities=23%  Similarity=0.307  Sum_probs=86.2

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCC---------CCcEEEEecCCCChhH
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQ---------QVSLVINYDLPNNREL  152 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~---------~~~~vi~~~~p~s~~~  152 (210)
                      ++.+++.|.+.|+++..+||.+...++..+..+++.|  .|+|||++++||+|++         .+.+|+++++|....+
T Consensus       437 se~ls~~L~~~gi~~~~L~a~~~~~E~~ii~~ag~~g--~VlIATdmAgRGtDI~l~~~v~~~GGL~vIit~~~ps~rid  514 (762)
T TIGR03714       437 SEIYSELLLREGIPHNLLNAQNAAKEAQIIAEAGQKG--AVTVATSMAGRGTDIKLGKGVAELGGLAVIGTERMENSRVD  514 (762)
T ss_pred             HHHHHHHHHHCCCCEEEecCCChHHHHHHHHHcCCCC--eEEEEccccccccCCCCCccccccCCeEEEEecCCCCcHHH
Confidence            7889999999999999999999998888887777666  7999999999999999         8999999999988777


Q ss_pred             HHHhhhhhcCCCCceeEEEEeccCcHH
Q psy6712         153 YIHRIGRSGRFGRKGVAISFVKSDDIR  179 (210)
Q Consensus       153 ~~q~~GR~gR~g~~g~~~~~~~~~~~~  179 (210)
                       .||+||+||.|.+|.++.|++..|.-
T Consensus       515 -~qr~GRtGRqG~~G~s~~~is~eD~l  540 (762)
T TIGR03714       515 -LQLRGRSGRQGDPGSSQFFVSLEDDL  540 (762)
T ss_pred             -HHhhhcccCCCCceeEEEEEccchhh
Confidence             99999999999999999999876543

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.

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.88  E-value=6.2e-22  Score=171.39  Aligned_cols=173  Identities=16%  Similarity=0.279  Sum_probs=127.4

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccc-----------------
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKG-----------------   64 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~-----------------   64 (210)
                      |.++...+||.+. .+........+|+++|++..       ...+++++++|+||||++...+                 
T Consensus       253 g~~v~v~~Gg~~~-~~~~t~~k~~~Ilv~T~~L~-------l~~L~~v~~VVIDEaHEr~~~~DllL~llk~~~~~~rq~  324 (675)
T PHA02653        253 GSPISLKYGSIPD-ELINTNPKPYGLVFSTHKLT-------LNKLFDYGTVIIDEVHEHDQIGDIIIAVARKHIDKIRSL  324 (675)
T ss_pred             CceEEEEECCcch-HHhhcccCCCCEEEEeCccc-------ccccccCCEEEccccccCccchhHHHHHHHHhhhhcCEE
Confidence            4568889999873 33333334779999997621       1257899999999999975332                 


Q ss_pred             ------hHHHHHHH------------------------------------------------------------HhhCCC
Q psy6712          65 ------FKEQIYDV------------------------------------------------------------YRYLPP   78 (210)
Q Consensus        65 ------~~~~~~~i------------------------------------------------------------~~~~~~   78 (210)
                            +.+++..+                                                            +.|++.
T Consensus       325 ILmSATl~~dv~~l~~~~~~p~~I~I~grt~~pV~~~yi~~~~~~~~~~~y~~~~k~~~l~~L~~~~~~~~g~iLVFlpg  404 (675)
T PHA02653        325 FLMTATLEDDRDRIKEFFPNPAFVHIPGGTLFPISEVYVKNKYNPKNKRAYIEEEKKNIVTALKKYTPPKGSSGIVFVAS  404 (675)
T ss_pred             EEEccCCcHhHHHHHHHhcCCcEEEeCCCcCCCeEEEEeecCcccccchhhhHHHHHHHHHHHHHhhcccCCcEEEEECc
Confidence                  00011111                                                            112222


Q ss_pred             chhHHHHHHHHHhc--CceEEEecCCCCHhHHHHHHHHH-hcCCCcEEEEecCccccCCCCCCcEEEEec---CCC----
Q psy6712          79 ATQVDWLTEKMREA--NFTVSSMHGDMPQKERDGIMKEF-RSGTSRVLITTDVWARGIDVQQVSLVINYD---LPN----  148 (210)
Q Consensus        79 ~~~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f-~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~---~p~----  148 (210)
                      ...++.+.+.|.+.  ++.+..+||+|++.  ++++++| ++|+.+|||||+++++|+|+|++++||+++   .|.    
T Consensus       405 ~~ei~~l~~~L~~~~~~~~v~~LHG~Lsq~--eq~l~~ff~~gk~kILVATdIAERGIDIp~V~~VID~G~~k~p~~~~g  482 (675)
T PHA02653        405 VSQCEEYKKYLEKRLPIYDFYIIHGKVPNI--DEILEKVYSSKNPSIIISTPYLESSVTIRNATHVYDTGRVYVPEPFGG  482 (675)
T ss_pred             HHHHHHHHHHHHhhcCCceEEeccCCcCHH--HHHHHHHhccCceeEEeccChhhccccccCeeEEEECCCccCCCcccC
Confidence            22267777777766  68999999999975  5667787 689999999999999999999999999998   554    


Q ss_pred             -----ChhHHHHhhhhhcCCCCceeEEEEeccCcHHHHHHHH
Q psy6712         149 -----NRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIE  185 (210)
Q Consensus       149 -----s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~~  185 (210)
                           |.++|.||+|||||. ++|.|+.+++..+...+.++.
T Consensus       483 ~~~~iSkasa~QRaGRAGR~-~~G~c~rLyt~~~~~pI~ri~  523 (675)
T PHA02653        483 KEMFISKSMRTQRKGRVGRV-SPGTYVYFYDLDLLKPIKRID  523 (675)
T ss_pred             cccccCHHHHHHhccCcCCC-CCCeEEEEECHHHhHHHHHHh
Confidence                 888999999999999 889999999887655444444

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.88  E-value=3.9e-22  Score=176.39  Aligned_cols=169  Identities=16%  Similarity=0.319  Sum_probs=128.5

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHH-hccc----hHHHH-------
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEM-LNKG----FKEQI-------   69 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l-~~~~----~~~~~-------   69 (210)
                      |..|...++|.+..      ..+.+|+|+|||++.+++.+ ...+++++++||||+|.. ++..    +..++       
T Consensus        77 g~~VGy~vr~~~~~------~~~t~I~v~T~G~Llr~l~~-d~~L~~v~~IIlDEaHER~l~~Dl~L~ll~~i~~~lr~~  149 (812)
T PRK11664         77 GETVGYRMRAESKV------GPNTRLEVVTEGILTRMIQR-DPELSGVGLVILDEFHERSLQADLALALLLDVQQGLRDD  149 (812)
T ss_pred             CceEEEEecCcccc------CCCCcEEEEChhHHHHHHhh-CCCcCcCcEEEEcCCCccccccchHHHHHHHHHHhCCcc
Confidence            34555555554421      23557999999999998875 457899999999999972 2211    10000       


Q ss_pred             ---------------H------------------------------------------------HHHhhCCCchhHHHHH
Q psy6712          70 ---------------Y------------------------------------------------DVYRYLPPATQVDWLT   86 (210)
Q Consensus        70 ---------------~------------------------------------------------~i~~~~~~~~~~~~l~   86 (210)
                                     .                                                .++.|++....++.+.
T Consensus       150 lqlilmSATl~~~~l~~~~~~~~~I~~~gr~~pV~~~y~~~~~~~~~~~~v~~~l~~~l~~~~g~iLVFlpg~~ei~~l~  229 (812)
T PRK11664        150 LKLLIMSATLDNDRLQQLLPDAPVIVSEGRSFPVERRYQPLPAHQRFDEAVARATAELLRQESGSLLLFLPGVGEIQRVQ  229 (812)
T ss_pred             ceEEEEecCCCHHHHHHhcCCCCEEEecCccccceEEeccCchhhhHHHHHHHHHHHHHHhCCCCEEEEcCCHHHHHHHH
Confidence                           0                                                0111223333377778


Q ss_pred             HHHHh---cCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCC---------------
Q psy6712          87 EKMRE---ANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPN---------------  148 (210)
Q Consensus        87 ~~l~~---~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~---------------  148 (210)
                      +.|.+   .++.+..+||+|+.++|..+++.|.+|+.+|+|||+++++|+|+|++++||+++.+.               
T Consensus       230 ~~L~~~~~~~~~v~~Lhg~l~~~eq~~~~~~~~~G~rkVlvATnIAErsLtIp~V~~VID~Gl~r~~~yd~~~g~~~L~~  309 (812)
T PRK11664        230 EQLASRVASDVLLCPLYGALSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVT  309 (812)
T ss_pred             HHHHHhccCCceEEEeeCCCCHHHHHHHhccccCCCeEEEEecchHHhcccccCceEEEECCCcccccccccCCcceeEE
Confidence            88876   578899999999999999999999999999999999999999999999999987664               


Q ss_pred             ---ChhHHHHhhhhhcCCCCceeEEEEeccCcH
Q psy6712         149 ---NRELYIHRIGRSGRFGRKGVAISFVKSDDI  178 (210)
Q Consensus       149 ---s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~  178 (210)
                         |..+|.||.||+||. ..|.|+-+++..+.
T Consensus       310 ~~iSkasa~QR~GRaGR~-~~G~cyrL~t~~~~  341 (812)
T PRK11664        310 QRISQASMTQRAGRAGRL-EPGICLHLYSKEQA  341 (812)
T ss_pred             EeechhhhhhhccccCCC-CCcEEEEecCHHHH
Confidence               346899999999999 69999999987543

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.88  E-value=1.4e-21  Score=166.06  Aligned_cols=86  Identities=19%  Similarity=0.290  Sum_probs=80.2

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEe-cCccccCCCCCCcEEEEecCCCChhHHHHhhhhh
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITT-DVWARGIDVQQVSLVINYDLPNNRELYIHRIGRS  160 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T-~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~  160 (210)
                      ++.+++.|.+.+.++..+||+|+.++|..+++.|++|+..+|||| +.+++|+|+|++++||+++++.|...|+||+||+
T Consensus       357 ~~~L~~~L~~~g~~v~~i~G~~~~~eR~~i~~~~~~~~~~vLvaT~~~l~eG~Dip~ld~vIl~~p~~s~~~~~QriGR~  436 (501)
T PHA02558        357 GKPLYEMLKKVYDKVYYVSGEVDTEDRNEMKKIAEGGKGIIIVASYGVFSTGISIKNLHHVIFAHPSKSKIIVLQSIGRV  436 (501)
T ss_pred             HHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHhCCCCeEEEEEcceeccccccccccEEEEecCCcchhhhhhhhhcc
Confidence            677788888889999999999999999999999999999999998 8999999999999999999999999999999999


Q ss_pred             cCCCCce
Q psy6712         161 GRFGRKG  167 (210)
Q Consensus       161 gR~g~~g  167 (210)
                      +|.+..+
T Consensus       437 ~R~~~~K  443 (501)
T PHA02558        437 LRKHGSK  443 (501)
T ss_pred             ccCCCCC
Confidence            9997643

>PRK13766 Hef nuclease; Provisional

Probab=99.87  E-value=8.8e-21  Score=169.24  Aligned_cols=94  Identities=29%  Similarity=0.484  Sum_probs=83.9

Q ss_pred             HHHHHHHHHhcCceEEEecCC--------CCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHH
Q psy6712          82 VDWLTEKMREANFTVSSMHGD--------MPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELY  153 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~--------~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~  153 (210)
                      ++.+.+.|...++++..+||.        |++.+|..++++|++|+.++||+|+++++|+|+|++++||+||+|++...|
T Consensus       378 ~~~L~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~g~~~vLvaT~~~~eGldi~~~~~VI~yd~~~s~~r~  457 (773)
T PRK13766        378 AEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRS  457 (773)
T ss_pred             HHHHHHHHHhCCCceEEEEccccccccCCCCHHHHHHHHHHHHcCCCCEEEECChhhcCCCcccCCEEEEeCCCCCHHHH
Confidence            566667776778888888886        999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhhhcCCCCceeEEEEeccC
Q psy6712         154 IHRIGRSGRFGRKGVAISFVKSD  176 (210)
Q Consensus       154 ~q~~GR~gR~g~~g~~~~~~~~~  176 (210)
                      +||+||+||.|. |.++.++...
T Consensus       458 iQR~GR~gR~~~-~~v~~l~~~~  479 (773)
T PRK13766        458 IQRKGRTGRQEE-GRVVVLIAKG  479 (773)
T ss_pred             HHHhcccCcCCC-CEEEEEEeCC
Confidence            999999999865 7777777653

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.86  E-value=1.9e-20  Score=160.43  Aligned_cols=95  Identities=20%  Similarity=0.306  Sum_probs=83.8

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCC---CCc-----EEEEecCCCChhHH
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQ---QVS-----LVINYDLPNNRELY  153 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~---~~~-----~vi~~~~p~s~~~~  153 (210)
                      ++.+++.|.+.|+++..+||.++.  ++..+..|..++..|+|||++++||+|++   ++.     +||+++.|.+...|
T Consensus       486 se~L~~~L~~~gi~~~~Lhg~~~~--rE~~ii~~ag~~g~VlVATdmAgRGtDI~l~~~V~~~GGLhVI~~d~P~s~r~y  563 (656)
T PRK12898        486 SERLSALLREAGLPHQVLNAKQDA--EEAAIVARAGQRGRITVATNMAGRGTDIKLEPGVAARGGLHVILTERHDSARID  563 (656)
T ss_pred             HHHHHHHHHHCCCCEEEeeCCcHH--HHHHHHHHcCCCCcEEEEccchhcccCcCCccchhhcCCCEEEEcCCCCCHHHH
Confidence            888999999999999999999754  44555566666678999999999999999   665     99999999999999


Q ss_pred             HHhhhhhcCCCCceeEEEEeccCcH
Q psy6712         154 IHRIGRSGRFGRKGVAISFVKSDDI  178 (210)
Q Consensus       154 ~q~~GR~gR~g~~g~~~~~~~~~~~  178 (210)
                      .||+||+||.|..|.+++|++..|.
T Consensus       564 ~hr~GRTGRqG~~G~s~~~is~eD~  588 (656)
T PRK12898        564 RQLAGRCGRQGDPGSYEAILSLEDD  588 (656)
T ss_pred             HHhcccccCCCCCeEEEEEechhHH
Confidence            9999999999999999999997553

>KOG0352|consensus

Probab=99.86  E-value=7.2e-21  Score=152.28  Aligned_cols=103  Identities=20%  Similarity=0.344  Sum_probs=97.4

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhc
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSG  161 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~g  161 (210)
                      ++.++=.|...|+++..+|+++...+|.++-++|.++++.|+++|..+++|+|-|++.+||++++|.+...|.|..||||
T Consensus       268 cEq~AI~l~~~Gi~A~AYHAGLK~~ERTeVQe~WM~~~~PvI~AT~SFGMGVDKp~VRFViHW~~~qn~AgYYQESGRAG  347 (641)
T KOG0352|consen  268 CEQVAIMLEIAGIPAMAYHAGLKKKERTEVQEKWMNNEIPVIAATVSFGMGVDKPDVRFVIHWSPSQNLAGYYQESGRAG  347 (641)
T ss_pred             HHHHHHHhhhcCcchHHHhcccccchhHHHHHHHhcCCCCEEEEEeccccccCCcceeEEEecCchhhhHHHHHhccccc
Confidence            88888889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCceeEEEEeccCcHHHHHHH
Q psy6712         162 RFGRKGVAISFVKSDDIRILRDI  184 (210)
Q Consensus       162 R~g~~g~~~~~~~~~~~~~~~~~  184 (210)
                      |+|..+.|-++++..|...+..+
T Consensus       348 RDGk~SyCRLYYsR~D~~~i~FL  370 (641)
T KOG0352|consen  348 RDGKRSYCRLYYSRQDKNALNFL  370 (641)
T ss_pred             cCCCccceeeeecccchHHHHHH
Confidence            99999999999998777665543

>PRK14701 reverse gyrase; Provisional

Probab=99.85  E-value=5.9e-21  Score=177.58  Aligned_cols=169  Identities=15%  Similarity=0.224  Sum_probs=131.8

Q ss_pred             CceEEEEEcCcchHHHH---HHhcC-CCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhcc-----------chH
Q psy6712           2 NVQCHACIGGTNLSEDL---RKLDY-GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNK-----------GFK   66 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~---~~l~~-~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~-----------~~~   66 (210)
                      +++++.++||.+.+++.   ..+.+ .++|||+||+++.+.+... .. .+++++|+||||+|+++           +|.
T Consensus       152 ~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPgrL~~~~~~l-~~-~~i~~iVVDEAD~ml~~~knid~~L~llGF~  229 (1638)
T PRK14701        152 DVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQFLARNFPEM-KH-LKFDFIFVDDVDAFLKASKNIDRSLQLLGFY  229 (1638)
T ss_pred             ceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCchhHHhHHHH-hh-CCCCEEEEECceeccccccccchhhhcCCCh
Confidence            57788999999987764   44555 4899999999998876542 22 78999999999999863           666


Q ss_pred             HHHHH----HHh----------------------hCCCchh---------------------------------------
Q psy6712          67 EQIYD----VYR----------------------YLPPATQ---------------------------------------   81 (210)
Q Consensus        67 ~~~~~----i~~----------------------~~~~~~~---------------------------------------   81 (210)
                      +++..    ++.                      .++...+                                       
T Consensus       230 ~e~~~~~~~il~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ll~~SAT~~~r~~~~~l~~~~l~f~v~~~~~~lr~i~~  309 (1638)
T PRK14701        230 EEIIEKAWKIIYLKKQGNIEDAMEKREILNKEIEKIGNKIGCLIVASATGKAKGDRVKLYRELLGFEVGSGRSALRNIVD  309 (1638)
T ss_pred             HHHHHHHHHhhhcccccccchhhhhhhhhhhhhhhcCCCccEEEEEecCCCchhHHHHHhhcCeEEEecCCCCCCCCcEE
Confidence            66643    221                      1111111                                       


Q ss_pred             ------------------------------------HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEE
Q psy6712          82 ------------------------------------VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLIT  125 (210)
Q Consensus        82 ------------------------------------~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~  125 (210)
                                                          ++.+++.|.+.|+++..+|++     |...+++|++|+++||||
T Consensus       310 ~yi~~~~~~k~~L~~ll~~~g~~gIVF~~t~~~~e~ae~la~~L~~~Gi~a~~~h~~-----R~~~l~~F~~G~~~VLVa  384 (1638)
T PRK14701        310 VYLNPEKIIKEHVRELLKKLGKGGLIFVPIDEGAEKAEEIEKYLLEDGFKIELVSAK-----NKKGFDLFEEGEIDYLIG  384 (1638)
T ss_pred             EEEECCHHHHHHHHHHHHhCCCCeEEEEeccccchHHHHHHHHHHHCCCeEEEecch-----HHHHHHHHHcCCCCEEEE
Confidence                                                478999999999999999995     889999999999999999


Q ss_pred             e----cCccccCCCCC-CcEEEEecCCC---ChhHHHHhh-------------hhhcCCCCceeEEEEeccCc
Q psy6712         126 T----DVWARGIDVQQ-VSLVINYDLPN---NRELYIHRI-------------GRSGRFGRKGVAISFVKSDD  177 (210)
Q Consensus       126 T----~~~~~g~d~~~-~~~vi~~~~p~---s~~~~~q~~-------------GR~gR~g~~g~~~~~~~~~~  177 (210)
                      |    +.++||+|+|+ +.+||+||+|.   +...|.|..             ||+||.|..+.+.......+
T Consensus       385 T~s~~gvaaRGIDiP~~Vryvi~~~~Pk~~~~~e~~~~~~~~~~~~~~~~~~~~~a~~~g~~~~~~~~~~~~~  457 (1638)
T PRK14701        385 VATYYGTLVRGLDLPERIRFAVFYGVPKFRFRVDLEDPTIYRILGLLSEILKIEEELKEGIPIEGVLDVFPED  457 (1638)
T ss_pred             ecCCCCeeEecCccCCccCEEEEeCCCCCCcchhhcccchhhhhcchHHHHHhhhhcccCCcchhHHHhHHHH
Confidence            9    48899999998 99999999999   777666655             99999988766654443333

>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=99.85  E-value=3.6e-21  Score=123.63  Aligned_cols=78  Identities=50%  Similarity=0.803  Sum_probs=75.6

Q ss_pred             HHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCC
Q psy6712          87 EKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFG  164 (210)
Q Consensus        87 ~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g  164 (210)
                      +.|++.++++..+||+|+..+|..+++.|+.++..+||||+++++|+|+|++++||++++|++...|.|++||++|.|
T Consensus         1 ~~L~~~~~~~~~i~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gid~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~g   78 (78)
T PF00271_consen    1 KFLEKKGIKVAIIHGDMSQKERQEILKKFNSGEIRVLIATDILGEGIDLPDASHVIFYDPPWSPEEYIQRIGRAGRIG   78 (78)
T ss_dssp             HHHHHTTSSEEEESTTSHHHHHHHHHHHHHTTSSSEEEESCGGTTSSTSTTESEEEESSSESSHHHHHHHHTTSSTTT
T ss_pred             CChHHCCCcEEEEECCCCHHHHHHHHHHhhccCceEEEeeccccccccccccccccccccCCCHHHHHHHhhcCCCCC
Confidence            468889999999999999999999999999999999999999999999999999999999999999999999999986

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 ....

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.85  E-value=3.3e-21  Score=168.96  Aligned_cols=172  Identities=21%  Similarity=0.331  Sum_probs=129.6

Q ss_pred             CCceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCc-
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPA-   79 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~-   79 (210)
                      +|++|...+|+.+...   .-..+++|||+||+++..++++......+++++|+||+|.+.+....+.++.++...... 
T Consensus       102 ~GirV~~~TgD~~~~~---~~l~~~~ViVtT~EK~Dsl~R~~~~~~~~V~lvViDEiH~l~d~~RG~~lE~iv~r~~~~~  178 (766)
T COG1204         102 LGIRVGISTGDYDLDD---ERLARYDVIVTTPEKLDSLTRKRPSWIEEVDLVVIDEIHLLGDRTRGPVLESIVARMRRLN  178 (766)
T ss_pred             cCCEEEEecCCcccch---hhhccCCEEEEchHHhhHhhhcCcchhhcccEEEEeeeeecCCcccCceehhHHHHHHhhC
Confidence            5899999999999764   223478999999999998888877677899999999999888763333333333221111 


Q ss_pred             --hh----------------------------------------------------------------------------
Q psy6712          80 --TQ----------------------------------------------------------------------------   81 (210)
Q Consensus        80 --~~----------------------------------------------------------------------------   81 (210)
                        .+                                                                            
T Consensus       179 ~~~rivgLSATlpN~~evA~wL~a~~~~~~~rp~~l~~~v~~~~~~~~~~~~~k~~~~~~~~~~~~~v~~~~~~~~qvLv  258 (766)
T COG1204         179 ELIRIVGLSATLPNAEEVADWLNAKLVESDWRPVPLRRGVPYVGAFLGADGKKKTWPLLIDNLALELVLESLAEGGQVLV  258 (766)
T ss_pred             cceEEEEEeeecCCHHHHHHHhCCcccccCCCCcccccCCccceEEEEecCccccccccchHHHHHHHHHHHhcCCeEEE
Confidence              01                                                                            


Q ss_pred             -------HHHHHHHHHh-------------------------------------cCceEEEecCCCCHhHHHHHHHHHhc
Q psy6712          82 -------VDWLTEKMRE-------------------------------------ANFTVSSMHGDMPQKERDGIMKEFRS  117 (210)
Q Consensus        82 -------~~~l~~~l~~-------------------------------------~~~~~~~~~~~~~~~~r~~~~~~f~~  117 (210)
                             +...++.++.                                     --..+.++|++++.++|..+.+.|+.
T Consensus       259 Fv~sR~~a~~~A~~l~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~l~e~v~~GvafHhAGL~~~~R~~vE~~Fr~  338 (766)
T COG1204         259 FVHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGVAFHHAGLPREDRQLVEDAFRK  338 (766)
T ss_pred             EEecCchHHHHHHHHHHHHhhcCChhhhhhccccccccccccccccchHHHHHHHHhCccccccCCCHHHHHHHHHHHhc
Confidence                   1111121110                                     02368899999999999999999999


Q ss_pred             CCCcEEEEecCccccCCCCCCcEEE----Eec-----CCCChhHHHHhhhhhcCCCC--ceeEEEEecc
Q psy6712         118 GTSRVLITTDVWARGIDVQQVSLVI----NYD-----LPNNRELYIHRIGRSGRFGR--KGVAISFVKS  175 (210)
Q Consensus       118 g~~~ilv~T~~~~~g~d~~~~~~vi----~~~-----~p~s~~~~~q~~GR~gR~g~--~g~~~~~~~~  175 (210)
                      |+++||+||..+++|+|+|.-..||    .|+     .+.++.+++||+|||||.|-  .|.++++..+
T Consensus       339 g~ikVlv~TpTLA~GVNLPA~~VIIk~~~~y~~~~g~~~i~~~dv~QM~GRAGRPg~d~~G~~~i~~~~  407 (766)
T COG1204         339 GKIKVLVSTPTLAAGVNLPARTVIIKDTRRYDPKGGIVDIPVLDVLQMAGRAGRPGYDDYGEAIILATS  407 (766)
T ss_pred             CCceEEEechHHhhhcCCcceEEEEeeeEEEcCCCCeEECchhhHhhccCcCCCCCcCCCCcEEEEecC
Confidence            9999999999999999999877776    466     56789999999999999986  4667766633

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

Probab=99.85  E-value=4.3e-20  Score=155.94  Aligned_cols=175  Identities=21%  Similarity=0.348  Sum_probs=133.6

Q ss_pred             CCceEEEEEcCcchHH---HHHHhcCC-CcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhc--------cch-H-
Q psy6712           1 MNVQCHACIGGTNLSE---DLRKLDYG-QHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLN--------KGF-K-   66 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~---~~~~l~~~-~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~--------~~~-~-   66 (210)
                      +||+|+.++|.....+   ....+.+| .||+|||    +. |-...+.++++.++|+||-|+..-        .+. . 
T Consensus       338 ~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGT----HA-LiQd~V~F~~LgLVIiDEQHRFGV~QR~~L~~KG~~~P  412 (677)
T COG1200         338 LGIRVALLTGSLKGKARKEILEQLASGEIDIVVGT----HA-LIQDKVEFHNLGLVIIDEQHRFGVHQRLALREKGEQNP  412 (677)
T ss_pred             cCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEc----ch-hhhcceeecceeEEEEeccccccHHHHHHHHHhCCCCC
Confidence            5899999999877444   34555565 8999999    33 444557789999999999998741        121 0 


Q ss_pred             --------------------HHHHHHHhhCCCchh---------------------------------------------
Q psy6712          67 --------------------EQIYDVYRYLPPATQ---------------------------------------------   81 (210)
Q Consensus        67 --------------------~~~~~i~~~~~~~~~---------------------------------------------   81 (210)
                                          +-=-.++..+|+.++                                             
T Consensus       413 h~LvMTATPIPRTLAlt~fgDldvS~IdElP~GRkpI~T~~i~~~~~~~v~e~i~~ei~~GrQaY~VcPLIeESE~l~l~  492 (677)
T COG1200         413 HVLVMTATPIPRTLALTAFGDLDVSIIDELPPGRKPITTVVIPHERRPEVYERIREEIAKGRQAYVVCPLIEESEKLELQ  492 (677)
T ss_pred             cEEEEeCCCchHHHHHHHhccccchhhccCCCCCCceEEEEeccccHHHHHHHHHHHHHcCCEEEEEeccccccccchhh
Confidence                                000122222332222                                             


Q ss_pred             -HHHHHHHHHhc--CceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCC-ChhHHHHhh
Q psy6712          82 -VDWLTEKMREA--NFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPN-NRELYIHRI  157 (210)
Q Consensus        82 -~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~-s~~~~~q~~  157 (210)
                       +..+++.|+..  +.++..+||.|+.+++.+++++|++|+++|||||+.++-|+|+|+++++|..++.+ ..++.=|..
T Consensus       493 ~a~~~~~~L~~~~~~~~vgL~HGrm~~~eKd~vM~~Fk~~e~~ILVaTTVIEVGVdVPnATvMVIe~AERFGLaQLHQLR  572 (677)
T COG1200         493 AAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVDVPNATVMVIENAERFGLAQLHQLR  572 (677)
T ss_pred             hHHHHHHHHHHHcccceeEEEecCCChHHHHHHHHHHHcCCCcEEEEeeEEEecccCCCCeEEEEechhhhhHHHHHHhc
Confidence             55666666532  56799999999999999999999999999999999999999999999999999775 567777888


Q ss_pred             hhhcCCCCceeEEEEeccCcHHH
Q psy6712         158 GRSGRFGRKGVAISFVKSDDIRI  180 (210)
Q Consensus       158 GR~gR~g~~g~~~~~~~~~~~~~  180 (210)
                      ||+||.+..+.|++++.+...+.
T Consensus       573 GRVGRG~~qSyC~Ll~~~~~~~~  595 (677)
T COG1200         573 GRVGRGDLQSYCVLLYKPPLSEV  595 (677)
T ss_pred             cccCCCCcceEEEEEeCCCCChh
Confidence            99999999999999999876333

>PRK09401 reverse gyrase; Reviewed

Probab=99.85  E-value=2.8e-20  Score=169.65  Aligned_cols=154  Identities=18%  Similarity=0.238  Sum_probs=123.4

Q ss_pred             CceEEEEEcCcc-----hHHHHHHhcC-CCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhc-----------cc
Q psy6712           2 NVQCHACIGGTN-----LSEDLRKLDY-GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLN-----------KG   64 (210)
Q Consensus         2 ~i~~~~~~gg~~-----~~~~~~~l~~-~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~-----------~~   64 (210)
                      ++.+..++||.+     .+++...+.+ ++||+|+||++|.+++.  .+..+.++++|+||||+|++           .|
T Consensus       151 ~~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~~~~--~l~~~~~~~lVvDEaD~~L~~~k~id~~l~~lG  228 (1176)
T PRK09401        151 GCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFD--ELPKKKFDFVFVDDVDAVLKSSKNIDKLLYLLG  228 (1176)
T ss_pred             CceEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECHHHHHHHHH--hccccccCEEEEEChHHhhhcccchhhHHHhCC
Confidence            566777887764     2334455554 58999999999999876  45667799999999999986           45


Q ss_pred             hH-HHHHHHHhhCCC------------------------chh--------------------------------------
Q psy6712          65 FK-EQIYDVYRYLPP------------------------ATQ--------------------------------------   81 (210)
Q Consensus        65 ~~-~~~~~i~~~~~~------------------------~~~--------------------------------------   81 (210)
                      |. +++..++..++.                        ..|                                      
T Consensus       229 F~~~~i~~i~~~i~~~~~~~~~~~~i~~l~~~i~~~~~~~~q~ilfSAT~~~~~~~~~l~~~ll~~~v~~~~~~~rnI~~  308 (1176)
T PRK09401        229 FSEEDIEKAMELIRLKRKYEEIYEKIRELEEKIAELKDKKGVLVVSSATGRPRGNRVKLFRELLGFEVGSPVFYLRNIVD  308 (1176)
T ss_pred             CCHHHHHHHHHhcccccccchhhhHHHHHHHhhhhcccCCceEEEEeCCCCccchHHHHhhccceEEecCcccccCCceE
Confidence            63 556666555442                        122                                      


Q ss_pred             -----------------------------------HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEE-
Q psy6712          82 -----------------------------------VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLIT-  125 (210)
Q Consensus        82 -----------------------------------~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~-  125 (210)
                                                         ++.+++.|+..|+++..+||+|     ...+++|++|++++||| 
T Consensus       309 ~yi~~~~k~~~L~~ll~~l~~~~LIFv~t~~~~~~ae~l~~~L~~~gi~v~~~hg~l-----~~~l~~F~~G~~~VLVat  383 (1176)
T PRK09401        309 SYIVDEDSVEKLVELVKRLGDGGLIFVPSDKGKEYAEELAEYLEDLGINAELAISGF-----ERKFEKFEEGEVDVLVGV  383 (1176)
T ss_pred             EEEEcccHHHHHHHHHHhcCCCEEEEEecccChHHHHHHHHHHHHCCCcEEEEeCcH-----HHHHHHHHCCCCCEEEEe
Confidence                                               7889999999999999999999     23459999999999999 


Q ss_pred             ---ecCccccCCCCC-CcEEEEecCCC------ChhHHHHhhhhhcC
Q psy6712         126 ---TDVWARGIDVQQ-VSLVINYDLPN------NRELYIHRIGRSGR  162 (210)
Q Consensus       126 ---T~~~~~g~d~~~-~~~vi~~~~p~------s~~~~~q~~GR~gR  162 (210)
                         |+.++||+|+|+ +.+|||||+|.      ....|.+|.||+..
T Consensus       384 as~tdv~aRGIDiP~~IryVI~y~vP~~~~~~~~~~~~~~~~~r~~~  430 (1176)
T PRK09401        384 ASYYGVLVRGIDLPERIRYAIFYGVPKFKFSLEEELAPPFLLLRLLS  430 (1176)
T ss_pred             cCCCCceeecCCCCcceeEEEEeCCCCEEEeccccccCHHHHHHHHh
Confidence               689999999999 89999999998      67889999999853

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

Probab=99.85  E-value=1.7e-21  Score=160.80  Aligned_cols=177  Identities=18%  Similarity=0.299  Sum_probs=138.4

Q ss_pred             CCceEEEEEcCcchHHHHH----HhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHH---HH
Q psy6712           1 MNVQCHACIGGTNLSEDLR----KLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYD---VY   73 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~----~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~---i~   73 (210)
                      +|++++.-.|-...+....    ......||||||-+-+..+++.+ -++.++..+||||+|.+-+......++-   -+
T Consensus       288 LglkvairVG~srIk~~~~pv~~~t~~dADIIVGTYEGiD~lLRtg-~~lgdiGtVVIDEiHtL~deERG~RLdGLI~RL  366 (830)
T COG1202         288 LGLKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEGIDYLLRTG-KDLGDIGTVVIDEIHTLEDEERGPRLDGLIGRL  366 (830)
T ss_pred             ccceEEEEechhhhcccCCccccCCCCCCcEEEeechhHHHHHHcC-CcccccceEEeeeeeeccchhcccchhhHHHHH
Confidence            5677877777766554321    12236799999999988888887 5789999999999998876332222211   12


Q ss_pred             hhCCCchh------------------------------------------------------------------------
Q psy6712          74 RYLPPATQ------------------------------------------------------------------------   81 (210)
Q Consensus        74 ~~~~~~~~------------------------------------------------------------------------   81 (210)
                      .++-+..|                                                                        
T Consensus       367 r~l~~~AQ~i~LSATVgNp~elA~~l~a~lV~y~~RPVplErHlvf~~~e~eK~~ii~~L~k~E~~~~sskg~rGQtIVF  446 (830)
T COG1202         367 RYLFPGAQFIYLSATVGNPEELAKKLGAKLVLYDERPVPLERHLVFARNESEKWDIIARLVKREFSTESSKGYRGQTIVF  446 (830)
T ss_pred             HHhCCCCeEEEEEeecCChHHHHHHhCCeeEeecCCCCChhHeeeeecCchHHHHHHHHHHHHHHhhhhccCcCCceEEE
Confidence            22222222                                                                        


Q ss_pred             ------HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEE---EecC-CCChh
Q psy6712          82 ------VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVI---NYDL-PNNRE  151 (210)
Q Consensus        82 ------~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi---~~~~-p~s~~  151 (210)
                            +..++..|..+|+++.++|++|+..+|+.+..+|..+++.++|+|.+++.|+|+|..++|+   -++. +-|+.
T Consensus       447 T~SRrr~h~lA~~L~~kG~~a~pYHaGL~y~eRk~vE~~F~~q~l~~VVTTAAL~AGVDFPASQVIFEsLaMG~~WLs~~  526 (830)
T COG1202         447 TYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAAGVDFPASQVIFESLAMGIEWLSVR  526 (830)
T ss_pred             ecchhhHHHHHHHhhcCCcccccccCCCcHHHHHHHHHHHhcCCcceEeehhhhhcCCCCchHHHHHHHHHcccccCCHH
Confidence                  8999999999999999999999999999999999999999999999999999999877664   2333 45899


Q ss_pred             HHHHhhhhhcCCCC--ceeEEEEeccCcH
Q psy6712         152 LYIHRIGRSGRFGR--KGVAISFVKSDDI  178 (210)
Q Consensus       152 ~~~q~~GR~gR~g~--~g~~~~~~~~~~~  178 (210)
                      .|.||+|||||.+-  .|++++++.+...
T Consensus       527 EF~QM~GRAGRp~yHdrGkVyllvepg~~  555 (830)
T COG1202         527 EFQQMLGRAGRPDYHDRGKVYLLVEPGKK  555 (830)
T ss_pred             HHHHHhcccCCCCcccCceEEEEecCChh
Confidence            99999999999975  6999999987543

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.84  E-value=2e-20  Score=169.36  Aligned_cols=153  Identities=20%  Similarity=0.356  Sum_probs=119.7

Q ss_pred             cCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhH-HhccchHHH-HHH----------------------------
Q psy6712          22 DYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADE-MLNKGFKEQ-IYD----------------------------   71 (210)
Q Consensus        22 ~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~-l~~~~~~~~-~~~----------------------------   71 (210)
                      .++++|+++|||+|++.+..... +++++++||||||. +++.++... +..                            
T Consensus       161 s~~t~I~v~TpG~LL~~l~~d~~-Ls~~~~IIIDEAHERsLn~DfLLg~Lk~lL~~rpdlKvILmSATid~e~fs~~F~~  239 (1294)
T PRK11131        161 SDNTMVKLMTDGILLAEIQQDRL-LMQYDTIIIDEAHERSLNIDFILGYLKELLPRRPDLKVIITSATIDPERFSRHFNN  239 (1294)
T ss_pred             CCCCCEEEEChHHHHHHHhcCCc-cccCcEEEecCccccccccchHHHHHHHhhhcCCCceEEEeeCCCCHHHHHHHcCC
Confidence            45789999999999999886544 89999999999994 555443211 111                            


Q ss_pred             -------------------------------------------------HHhhCCCchhHHHHHHHHHhcCc---eEEEe
Q psy6712          72 -------------------------------------------------VYRYLPPATQVDWLTEKMREANF---TVSSM   99 (210)
Q Consensus        72 -------------------------------------------------i~~~~~~~~~~~~l~~~l~~~~~---~~~~~   99 (210)
                                                                       ++.|++....++.+++.|.+.++   .+..+
T Consensus       240 apvI~V~Gr~~pVei~y~p~~~~~~~~~~d~l~~ll~~V~~l~~~~~GdILVFLpg~~EIe~lae~L~~~~~~~~~VlpL  319 (1294)
T PRK11131        240 APIIEVSGRTYPVEVRYRPIVEEADDTERDQLQAIFDAVDELGREGPGDILIFMSGEREIRDTADALNKLNLRHTEILPL  319 (1294)
T ss_pred             CCEEEEcCccccceEEEeecccccchhhHHHHHHHHHHHHHHhcCCCCCEEEEcCCHHHHHHHHHHHHhcCCCcceEeec
Confidence                                                             11123333336777788877665   47789


Q ss_pred             cCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEec---------------CC---CChhHHHHhhhhhc
Q psy6712         100 HGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYD---------------LP---NNRELYIHRIGRSG  161 (210)
Q Consensus       100 ~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~---------------~p---~s~~~~~q~~GR~g  161 (210)
                      ||+|+.++|..+++.  .|..+|+|||+++++|+|+|++++||+++               +|   .|..+|.||.||+|
T Consensus       320 hg~Ls~~eQ~~Vf~~--~g~rkIIVATNIAEtSITIpgI~yVID~Gl~k~~~Yd~~~~~~~Lp~~~iSkasa~QRaGRAG  397 (1294)
T PRK11131        320 YARLSNSEQNRVFQS--HSGRRIVLATNVAETSLTVPGIKYVIDPGTARISRYSYRTKVQRLPIEPISQASANQRKGRCG  397 (1294)
T ss_pred             ccCCCHHHHHHHhcc--cCCeeEEEeccHHhhccccCcceEEEECCCccccccccccCcccCCeeecCHhhHhhhccccC
Confidence            999999999999886  47889999999999999999999999986               23   45689999999999


Q ss_pred             CCCCceeEEEEeccCcH
Q psy6712         162 RFGRKGVAISFVKSDDI  178 (210)
Q Consensus       162 R~g~~g~~~~~~~~~~~  178 (210)
                      |. .+|.|+.++++.+.
T Consensus       398 R~-~~G~c~rLyte~d~  413 (1294)
T PRK11131        398 RV-SEGICIRLYSEDDF  413 (1294)
T ss_pred             CC-CCcEEEEeCCHHHH
Confidence            99 78999999987554

>KOG0354|consensus

Probab=99.84  E-value=6.3e-20  Score=156.91  Aligned_cols=95  Identities=28%  Similarity=0.462  Sum_probs=79.4

Q ss_pred             HHHHHHHHH---hcCceEEEec--------CCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCCh
Q psy6712          82 VDWLTEKMR---EANFTVSSMH--------GDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNR  150 (210)
Q Consensus        82 ~~~l~~~l~---~~~~~~~~~~--------~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~  150 (210)
                      +..+..+|.   ..+++...+-        .+|++.++++++++|+.|++.+||||+++++|+|++.|+.||.||...++
T Consensus       426 a~~l~~~l~~~~~~~ir~~~fiGq~~s~~~~gmtqk~Q~evl~~Fr~G~~NvLVATSV~EEGLDI~ec~lVIcYd~~snp  505 (746)
T KOG0354|consen  426 ALALKKWLLQLHELGIKAEIFIGQGKSTQSTGMTQKEQKEVLDKFRDGEINVLVATSVAEEGLDIGECNLVICYDYSSNP  505 (746)
T ss_pred             HHHHHHHHHhhhhcccccceeeeccccccccccCHHHHHHHHHHHhCCCccEEEEecchhccCCcccccEEEEecCCccH
Confidence            555666654   2334444433        37999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHhhhhhcCCCCceeEEEEeccCcH
Q psy6712         151 ELYIHRIGRSGRFGRKGVAISFVKSDDI  178 (210)
Q Consensus       151 ~~~~q~~GR~gR~g~~g~~~~~~~~~~~  178 (210)
                      ...+||.|| ||. +.|.++++++..+.
T Consensus       506 IrmIQrrGR-gRa-~ns~~vll~t~~~~  531 (746)
T KOG0354|consen  506 IRMVQRRGR-GRA-RNSKCVLLTTGSEV  531 (746)
T ss_pred             HHHHHHhcc-ccc-cCCeEEEEEcchhH
Confidence            999999999 897 67888888875433

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.84  E-value=8.2e-21  Score=155.53  Aligned_cols=92  Identities=21%  Similarity=0.379  Sum_probs=77.6

Q ss_pred             HHHHHHHHHhcCc--eEEEecCCCCHhHHHH----HHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHH
Q psy6712          82 VDWLTEKMREANF--TVSSMHGDMPQKERDG----IMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIH  155 (210)
Q Consensus        82 ~~~l~~~l~~~~~--~~~~~~~~~~~~~r~~----~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q  155 (210)
                      ++.+++.|++.+.  .+..+||+|++.+|.+    +++.|++|+.++||||+++++|+|++ ++++|++..|  ..+|+|
T Consensus       235 ~~~~~~~L~~~~~~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~~~~ilvaT~~~~~GiDi~-~~~vi~~~~~--~~~~iq  311 (358)
T TIGR01587       235 AQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQVIEASLDIS-ADVMITELAP--IDSLIQ  311 (358)
T ss_pred             HHHHHHHHHhhcCCCeEEEEECCCCHHHHHHHHHHHHHHhcCCCCeEEEECcchhceeccC-CCEEEEcCCC--HHHHHH
Confidence            7778888877665  5999999999999976    48899999999999999999999995 7888888665  789999


Q ss_pred             hhhhhcCCCCc----eeEEEEeccC
Q psy6712         156 RIGRSGRFGRK----GVAISFVKSD  176 (210)
Q Consensus       156 ~~GR~gR~g~~----g~~~~~~~~~  176 (210)
                      |+||+||.|+.    |.++++....
T Consensus       312 r~GR~gR~g~~~~~~~~~~v~~~~~  336 (358)
T TIGR01587       312 RLGRLHRYGRKNGENFEVYIITIAP  336 (358)
T ss_pred             HhccccCCCCCCCCCCeEEEEeecC
Confidence            99999999763    3677776643

This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.83  E-value=1.6e-19  Score=157.96  Aligned_cols=123  Identities=21%  Similarity=0.344  Sum_probs=98.8

Q ss_pred             HHHHHHHHHhc--CceEEEecCCCC--HhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCC--CC------
Q psy6712          82 VDWLTEKMREA--NFTVSSMHGDMP--QKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLP--NN------  149 (210)
Q Consensus        82 ~~~l~~~l~~~--~~~~~~~~~~~~--~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p--~s------  149 (210)
                      ++.+.+.|++.  +.++..+|++++  ..++++++++|++|+.+|||+|+++++|+|+|++++|+..|.+  .+      
T Consensus       439 ~e~~~e~l~~~fp~~~v~~~~~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~iakG~d~p~v~lV~il~aD~~l~~pdfra  518 (679)
T PRK05580        439 TERLEEELAELFPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLFSPDFRA  518 (679)
T ss_pred             HHHHHHHHHHhCCCCcEEEEeccccccchhHHHHHHHHhcCCCCEEEEChhhccCCCCCCcCEEEEEcCchhccCCccch
Confidence            67788888775  778999999986  4678999999999999999999999999999999999665543  22      


Q ss_pred             ----hhHHHHhhhhhcCCCCceeEEEEeccCcHHHHHHHH-----HHhcCccccccCCccccCCCCCCCC
Q psy6712         150 ----RELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIE-----QYYSTQIDEMPMNGKRSLHSYPARY  210 (210)
Q Consensus       150 ----~~~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~  210 (210)
                          ...|.|++||+||.+..|.+++.....+...++.+.     .++..++++      +...+||||.
T Consensus       519 ~Er~~~~l~q~~GRagR~~~~g~viiqT~~p~~~~~~~~~~~d~~~f~~~El~~------R~~~~~PPf~  582 (679)
T PRK05580        519 SERTFQLLTQVAGRAGRAEKPGEVLIQTYHPEHPVIQALLAQDYDAFAEQELEE------RRAAGYPPFG  582 (679)
T ss_pred             HHHHHHHHHHHHhhccCCCCCCEEEEEeCCCCCHHHHHHHhCCHHHHHHHHHHH------HHhcCCCCHH
Confidence                367999999999999999999988877766655553     355555555      5566899973

>TIGR00595 priA primosomal protein N'

Probab=99.82  E-value=2.2e-19  Score=152.21  Aligned_cols=123  Identities=21%  Similarity=0.396  Sum_probs=97.6

Q ss_pred             HHHHHHHHHhc--CceEEEecCCCCHhHH--HHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCC---------
Q psy6712          82 VDWLTEKMREA--NFTVSSMHGDMPQKER--DGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPN---------  148 (210)
Q Consensus        82 ~~~l~~~l~~~--~~~~~~~~~~~~~~~r--~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~---------  148 (210)
                      .+.+.+.|++.  +.++..+|++++..++  ++++++|++|+.+|||+|+++++|+|+|++++|+..|.+.         
T Consensus       271 te~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~i~kG~d~~~v~lV~vl~aD~~l~~pd~ra  350 (505)
T TIGR00595       271 TEQVEEELAKLFPGARIARIDSDTTSRKGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRA  350 (505)
T ss_pred             HHHHHHHHHhhCCCCcEEEEecccccCccHHHHHHHHHhcCCCCEEEeCcccccCCCCCcccEEEEEcCcccccCcccch
Confidence            67778888775  7789999999987665  8999999999999999999999999999999986544331         


Q ss_pred             ---ChhHHHHhhhhhcCCCCceeEEEEeccCcHHHHH-----HHHHHhcCccccccCCccccCCCCCCCC
Q psy6712         149 ---NRELYIHRIGRSGRFGRKGVAISFVKSDDIRILR-----DIEQYYSTQIDEMPMNGKRSLHSYPARY  210 (210)
Q Consensus       149 ---s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~  210 (210)
                         ....|.|++||+||.+..|.+++.....+...++     ..+.++..++++      +...+||||.
T Consensus       351 ~E~~~~ll~q~~GRagR~~~~g~viiqt~~p~~~~~~~~~~~d~~~f~~~el~~------R~~~~~PPf~  414 (505)
T TIGR00595       351 AERGFQLLTQVAGRAGRAEDPGQVIIQTYNPNHPAIQAALTGDYEAFYEQELAQ------RRALNYPPFT  414 (505)
T ss_pred             HHHHHHHHHHHHhccCCCCCCCEEEEEeCCCCCHHHHHHHhCCHHHHHHHHHHH------HHHcCCCchh
Confidence               2467899999999998999999777665554443     344566666666      6667899973

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).

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.80  E-value=3.8e-19  Score=161.61  Aligned_cols=170  Identities=19%  Similarity=0.309  Sum_probs=125.5

Q ss_pred             CceEEEEEcC-cchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhH-HhccchHHH-HH--------
Q psy6712           2 NVQCHACIGG-TNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADE-MLNKGFKEQ-IY--------   70 (210)
Q Consensus         2 ~i~~~~~~gg-~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~-l~~~~~~~~-~~--------   70 (210)
                      |.++...+|. ...+.+   ...+..|.++|||.|+..+.... .++.++++||||+|. .++.++... +.        
T Consensus       136 g~~lG~~VGY~vR~~~~---~s~~T~I~~~TdGiLLr~l~~d~-~L~~~~~IIIDEaHERsL~~D~LL~lLk~il~~rpd  211 (1283)
T TIGR01967       136 GTPLGEKVGYKVRFHDQ---VSSNTLVKLMTDGILLAETQQDR-FLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPD  211 (1283)
T ss_pred             CCCcceEEeeEEcCCcc---cCCCceeeeccccHHHHHhhhCc-ccccCcEEEEcCcchhhccchhHHHHHHHHHhhCCC
Confidence            4455555554 333322   23467899999999999887654 478999999999995 544332211 11        


Q ss_pred             ---------------------------------------------------------------------HHHhhCCCchh
Q psy6712          71 ---------------------------------------------------------------------DVYRYLPPATQ   81 (210)
Q Consensus        71 ---------------------------------------------------------------------~i~~~~~~~~~   81 (210)
                                                                                           .++.|++....
T Consensus       212 LKlIlmSATld~~~fa~~F~~apvI~V~Gr~~PVev~Y~~~~~~~~~~~~~~~~~i~~~I~~l~~~~~GdILVFLpg~~E  291 (1283)
T TIGR01967       212 LKIIITSATIDPERFSRHFNNAPIIEVSGRTYPVEVRYRPLVEEQEDDDLDQLEAILDAVDELFAEGPGDILIFLPGERE  291 (1283)
T ss_pred             CeEEEEeCCcCHHHHHHHhcCCCEEEECCCcccceeEEecccccccchhhhHHHHHHHHHHHHHhhCCCCEEEeCCCHHH
Confidence                                                                                 12234444444


Q ss_pred             HHHHHHHHHhcC---ceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCC-----------
Q psy6712          82 VDWLTEKMREAN---FTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLP-----------  147 (210)
Q Consensus        82 ~~~l~~~l~~~~---~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p-----------  147 (210)
                      ++.+++.|.+.+   ..+..+||+|+.++|..+++.+  +..+|+|||++++.|+|+|++.+||+++.+           
T Consensus       292 I~~l~~~L~~~~~~~~~VlpLhg~Ls~~eQ~~vf~~~--~~rkIVLATNIAEtSLTIpgV~yVIDsGl~r~~~yd~~~~~  369 (1283)
T TIGR01967       292 IRDAAEILRKRNLRHTEILPLYARLSNKEQQRVFQPH--SGRRIVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTKV  369 (1283)
T ss_pred             HHHHHHHHHhcCCCCcEEEeccCCCCHHHHHHHhCCC--CCceEEEeccHHHhccccCCeeEEEeCCCccccccccccCc
Confidence            777888887653   5688999999999999886654  246899999999999999999999998843           


Q ss_pred             -------CChhHHHHhhhhhcCCCCceeEEEEeccCcH
Q psy6712         148 -------NNRELYIHRIGRSGRFGRKGVAISFVKSDDI  178 (210)
Q Consensus       148 -------~s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~  178 (210)
                             -|..+|.||.||+||.+ +|.|+.+++..+.
T Consensus       370 ~~L~~~~ISkasa~QRaGRAGR~~-~G~cyRLyte~~~  406 (1283)
T TIGR01967       370 QRLPIEPISQASANQRKGRCGRVA-PGICIRLYSEEDF  406 (1283)
T ss_pred             cccCCccCCHHHHHHHhhhhCCCC-CceEEEecCHHHH
Confidence                   36689999999999996 9999999987544

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.

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

Probab=99.79  E-value=3.2e-18  Score=151.89  Aligned_cols=169  Identities=21%  Similarity=0.335  Sum_probs=127.2

Q ss_pred             CceEEEEEcCcchHHHH---HHhcC-CCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhh--
Q psy6712           2 NVQCHACIGGTNLSEDL---RKLDY-GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRY--   75 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~---~~l~~-~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~--   75 (210)
                      .|+|..+.-=.+.++|.   +.+++ ..||||||     +-|.++.+.++++.++||||=|+..=. ..+.++++...  
T Consensus       671 PV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGT-----HrLL~kdv~FkdLGLlIIDEEqRFGVk-~KEkLK~Lr~~VD  744 (1139)
T COG1197         671 PVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGT-----HRLLSKDVKFKDLGLLIIDEEQRFGVK-HKEKLKELRANVD  744 (1139)
T ss_pred             CeeEEEecccCCHHHHHHHHHHHhcCCccEEEec-----hHhhCCCcEEecCCeEEEechhhcCcc-HHHHHHHHhccCc
Confidence            45566655555555555   44445 47999999     445667889999999999999987522 22222222211  


Q ss_pred             ---------------------------CCC-chh-------------------------------------HHHHHHHHH
Q psy6712          76 ---------------------------LPP-ATQ-------------------------------------VDWLTEKMR   90 (210)
Q Consensus        76 ---------------------------~~~-~~~-------------------------------------~~~l~~~l~   90 (210)
                                                 +|+ .+.                                     .+.+.+.|+
T Consensus       745 vLTLSATPIPRTL~Msm~GiRdlSvI~TPP~~R~pV~T~V~~~d~~~ireAI~REl~RgGQvfYv~NrV~~Ie~~~~~L~  824 (1139)
T COG1197         745 VLTLSATPIPRTLNMSLSGIRDLSVIATPPEDRLPVKTFVSEYDDLLIREAILRELLRGGQVFYVHNRVESIEKKAERLR  824 (1139)
T ss_pred             EEEeeCCCCcchHHHHHhcchhhhhccCCCCCCcceEEEEecCChHHHHHHHHHHHhcCCEEEEEecchhhHHHHHHHHH
Confidence                                       010 000                                     444555554


Q ss_pred             hc--CceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCC-ChhHHHHhhhhhcCCCCce
Q psy6712          91 EA--NFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPN-NRELYIHRIGRSGRFGRKG  167 (210)
Q Consensus        91 ~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~-s~~~~~q~~GR~gR~g~~g  167 (210)
                      +.  ..++.+.||.|+..+-++++.+|.+|+++|||||++++.|+|+|++|.+|..+... ..++..|..||+||.++.+
T Consensus       825 ~LVPEarI~vaHGQM~e~eLE~vM~~F~~g~~dVLv~TTIIEtGIDIPnANTiIIe~AD~fGLsQLyQLRGRVGRS~~~A  904 (1139)
T COG1197         825 ELVPEARIAVAHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSNKQA  904 (1139)
T ss_pred             HhCCceEEEEeecCCCHHHHHHHHHHHHcCCCCEEEEeeeeecCcCCCCCceEEEeccccccHHHHHHhccccCCccceE
Confidence            43  45799999999999999999999999999999999999999999999999887764 6899999999999999999


Q ss_pred             eEEEEeccC
Q psy6712         168 VAISFVKSD  176 (210)
Q Consensus       168 ~~~~~~~~~  176 (210)
                      .|++++.+.
T Consensus       905 YAYfl~p~~  913 (1139)
T COG1197         905 YAYFLYPPQ  913 (1139)
T ss_pred             EEEEeecCc
Confidence            999999863

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.78  E-value=1.1e-18  Score=155.66  Aligned_cols=123  Identities=22%  Similarity=0.302  Sum_probs=105.6

Q ss_pred             hCCCchhHHHHHHHH-HhcCceEEEecCCCCHhHHHHHHHHHhcC--CCcEEEEecCccccCCCCCCcEEEEecCCCChh
Q psy6712          75 YLPPATQVDWLTEKM-REANFTVSSMHGDMPQKERDGIMKEFRSG--TSRVLITTDVWARGIDVQQVSLVINYDLPNNRE  151 (210)
Q Consensus        75 ~~~~~~~~~~l~~~l-~~~~~~~~~~~~~~~~~~r~~~~~~f~~g--~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~  151 (210)
                      |+.....+..+.+.| ...|+++..+||+|+..+|.++++.|+++  ...+||||+++++|+|++.+++||+||+|+++.
T Consensus       499 F~~~~~t~~~L~~~L~~~~Gi~~~~ihG~~s~~eR~~~~~~F~~~~~~~~VLIsTdvgseGlNlq~a~~VInfDlP~nP~  578 (956)
T PRK04914        499 ICAKAATALQLEQALREREGIRAAVFHEGMSIIERDRAAAYFADEEDGAQVLLCSEIGSEGRNFQFASHLVLFDLPFNPD  578 (956)
T ss_pred             EeCcHHHHHHHHHHHhhccCeeEEEEECCCCHHHHHHHHHHHhcCCCCccEEEechhhccCCCcccccEEEEecCCCCHH
Confidence            444445589999999 45699999999999999999999999974  589999999999999999999999999999999


Q ss_pred             HHHHhhhhhcCCCCceeEEEEeccCcHHHHHHHHHHhcCccccccC
Q psy6712         152 LYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPM  197 (210)
Q Consensus       152 ~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  197 (210)
                      .|.||+||++|.|+.+.+.+++...+....+.+.+++...+.-+..
T Consensus       579 ~~eQRIGR~~RiGQ~~~V~i~~~~~~~t~~e~i~~~~~~~l~ife~  624 (956)
T PRK04914        579 LLEQRIGRLDRIGQKHDIQIHVPYLEGTAQERLFRWYHEGLNAFEH  624 (956)
T ss_pred             HHHHHhcccccCCCCceEEEEEccCCCCHHHHHHHHHhhhcCceec
Confidence            9999999999999999888888766655677777777775544433

>TIGR01054 rgy reverse gyrase

Probab=99.77  E-value=1.1e-17  Score=152.91  Aligned_cols=135  Identities=19%  Similarity=0.349  Sum_probs=105.1

Q ss_pred             EEEcCcchHHH---HHHhcC-CCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhc-----------cchHHH-HH
Q psy6712           7 ACIGGTNLSED---LRKLDY-GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLN-----------KGFKEQ-IY   70 (210)
Q Consensus         7 ~~~gg~~~~~~---~~~l~~-~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~-----------~~~~~~-~~   70 (210)
                      .++||.+..++   +..+.+ +++|||+||++|.+.+..  +.. +++++|+||||.|++           .||.++ +.
T Consensus       157 ~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~~~--l~~-~~~~iVvDEaD~~L~~~k~vd~il~llGF~~e~i~  233 (1171)
T TIGR01054       157 AYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDE--LGP-KFDFIFVDDVDALLKASKNVDKLLKLLGFSEELIE  233 (1171)
T ss_pred             eecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHHHH--hcC-CCCEEEEeChHhhhhccccHHHHHHHcCCCHHHHH
Confidence            57899887665   344554 599999999999987765  222 899999999999997           356543 33


Q ss_pred             HHHh----------------------hCCCchh-----------------------------------------------
Q psy6712          71 DVYR----------------------YLPPATQ-----------------------------------------------   81 (210)
Q Consensus        71 ~i~~----------------------~~~~~~~-----------------------------------------------   81 (210)
                      .++.                      .++...+                                               
T Consensus       234 ~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~li~~SAT~~p~~~~~~l~r~ll~~~v~~~~~~~r~I~~~~~~~~~  313 (1171)
T TIGR01054       234 KAWKLIRLRLKLYRALHAKKRLELLEAIPGKKRGCLIVSSATGRPRGKRAKLFRELLGFEVGGGSDTLRNVVDVYVEDED  313 (1171)
T ss_pred             HHHHHhhhccccchHHHHHHHHHHHHhhhhccCcEEEEEeCCCCccccHHHHcccccceEecCccccccceEEEEEeccc
Confidence            3221                      1111100                                               


Q ss_pred             ----------------------------HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEe----cCc
Q psy6712          82 ----------------------------VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITT----DVW  129 (210)
Q Consensus        82 ----------------------------~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T----~~~  129 (210)
                                                  ++.+++.|.+.|+++..+||+|+    +.++++|++|++++||||    +.+
T Consensus       314 ~~~~L~~ll~~l~~~~IVFv~t~~~~~~a~~l~~~L~~~g~~a~~lhg~~~----~~~l~~Fr~G~~~vLVata~~tdv~  389 (1171)
T TIGR01054       314 LKETLLEIVKKLGTGGIVYVSIDYGKEKAEEIAEFLENHGVKAVAYHATKP----KEDYEKFAEGEIDVLIGVASYYGTL  389 (1171)
T ss_pred             HHHHHHHHHHHcCCCEEEEEeccccHHHHHHHHHHHHhCCceEEEEeCCCC----HHHHHHHHcCCCCEEEEeccccCcc
Confidence                                        77888899889999999999997    368999999999999995    899


Q ss_pred             cccCCCCC-CcEEEEecCCC
Q psy6712         130 ARGIDVQQ-VSLVINYDLPN  148 (210)
Q Consensus       130 ~~g~d~~~-~~~vi~~~~p~  148 (210)
                      +||+|+|+ +++||+||+|.
T Consensus       390 aRGIDip~~V~~vI~~~~P~  409 (1171)
T TIGR01054       390 VRGLDLPERVRYAVFLGVPK  409 (1171)
T ss_pred             cccCCCCccccEEEEECCCC
Confidence            99999999 89999999994

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.

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=99.76  E-value=5e-18  Score=109.54  Aligned_cols=81  Identities=46%  Similarity=0.788  Sum_probs=77.4

Q ss_pred             HHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCC
Q psy6712          84 WLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRF  163 (210)
Q Consensus        84 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~  163 (210)
                      .+.+.|+..++.+..+||+|+..+|...++.|+.++..++++|+++++|+|+|++++||.+++|++...|.|++||++|.
T Consensus         2 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gi~~~~~~~vi~~~~~~~~~~~~Q~~gR~~R~   81 (82)
T smart00490        2 ELAELLKELGIKVARLHGGLSQEEREEILEKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRA   81 (82)
T ss_pred             HHHHHHHHCCCeEEEEECCCCHHHHHHHHHHHHcCCCeEEEECChhhCCcChhcCCEEEEeCCCCCHHHHHHhhcccccC
Confidence            46778888899999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             C
Q psy6712         164 G  164 (210)
Q Consensus       164 g  164 (210)
                      |
T Consensus        82 g   82 (82)
T smart00490       82 G   82 (82)
T ss_pred             C
Confidence            5

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.76  E-value=4.1e-17  Score=141.65  Aligned_cols=95  Identities=19%  Similarity=0.279  Sum_probs=79.8

Q ss_pred             eEEEecCCCCHhHHHHHHHHHhcC-CCcEEEEecCccccCCCCCCcEEEEecCC-CChhHHHHhhhhhcCCCCcee----
Q psy6712          95 TVSSMHGDMPQKERDGIMKEFRSG-TSRVLITTDVWARGIDVQQVSLVINYDLP-NNRELYIHRIGRSGRFGRKGV----  168 (210)
Q Consensus        95 ~~~~~~~~~~~~~r~~~~~~f~~g-~~~ilv~T~~~~~g~d~~~~~~vi~~~~p-~s~~~~~q~~GR~gR~g~~g~----  168 (210)
                      .+..+||+++..+|..++++|+.+ ++++||+|+++.+|+|+|+++++|+++.| .|...|+||+||++|.+..|.    
T Consensus       517 ~~~~I~G~ts~~ER~~il~~Fr~~~~i~vLv~SkVgdeGIDlP~a~vvI~~s~~~gS~~q~iQRlGRilR~~~~~~~~~~  596 (732)
T TIGR00603       517 GKPFIYGPTSQQERMQILQNFQHNPKVNTIFLSKVGDTSIDLPEANVLIQISSHYGSRRQEAQRLGRILRAKKGSDAEEY  596 (732)
T ss_pred             CCceEECCCCHHHHHHHHHHHHhCCCccEEEEecccccccCCCCCCEEEEeCCCCCCHHHHHHHhcccccCCCCCccccc
Confidence            356689999999999999999865 88999999999999999999999999987 599999999999999976544    


Q ss_pred             ---EEEEeccC--cHHHHHHHHHHhc
Q psy6712         169 ---AISFVKSD--DIRILRDIEQYYS  189 (210)
Q Consensus       169 ---~~~~~~~~--~~~~~~~~~~~~~  189 (210)
                         .+.+++.+  |+....+..+++.
T Consensus       597 ~A~fY~lVs~dT~E~~~s~~Rq~fl~  622 (732)
T TIGR00603       597 NAFFYSLVSKDTQEMYYSTKRQRFLV  622 (732)
T ss_pred             cceEEEEecCCchHHHHHHHHHHHHH
Confidence               37788765  4455555566654

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).

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.75  E-value=6.3e-17  Score=141.56  Aligned_cols=95  Identities=22%  Similarity=0.327  Sum_probs=85.6

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCC-----------------------
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQV-----------------------  138 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~-----------------------  138 (210)
                      ++.+++.|.+.++++..+|+.  ..+|+..+.+|+.+...|+|||++++||+|++--                       
T Consensus       443 se~Ls~~L~~~gi~~~vLnak--q~eREa~Iia~Ag~~g~VtIATNmAGRGtDI~LgGn~~~~~~~~~~~~~~~~~~~~~  520 (830)
T PRK12904        443 SELLSKLLKKAGIPHNVLNAK--NHEREAEIIAQAGRPGAVTIATNMAGRGTDIKLGGNPEMLAAALLEEETEEQIAKIK  520 (830)
T ss_pred             HHHHHHHHHHCCCceEeccCc--hHHHHHHHHHhcCCCceEEEecccccCCcCccCCCchhhhhhhhhhhhhhHHHHHHH
Confidence            888999999999999999996  7889999999999999999999999999998643                       


Q ss_pred             -------c--------EEEEecCCCChhHHHHhhhhhcCCCCceeEEEEeccCcH
Q psy6712         139 -------S--------LVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDI  178 (210)
Q Consensus       139 -------~--------~vi~~~~p~s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~  178 (210)
                             +        +||-...|.|..---|..||+||+|.+|.+-.|++-+|.
T Consensus       521 ~~~~~~~~~v~~~GGLhVigTerhesrRid~QlrGRagRQGdpGss~f~lSleD~  575 (830)
T PRK12904        521 AEWQEEHEEVLEAGGLHVIGTERHESRRIDNQLRGRSGRQGDPGSSRFYLSLEDD  575 (830)
T ss_pred             HHHhhhhhhHHHcCCCEEEecccCchHHHHHHhhcccccCCCCCceeEEEEcCcH
Confidence                   1        788888899988889999999999999999999987654

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.75  E-value=6.3e-17  Score=141.91  Aligned_cols=95  Identities=23%  Similarity=0.355  Sum_probs=84.1

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCC-----------------------
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQV-----------------------  138 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~-----------------------  138 (210)
                      ++.+++.|.+.|+++..+|+.+...++..+.++|+.|  .|+|||++++||+|+-=-                       
T Consensus       457 sE~ls~~L~~~gi~h~vLnak~~q~Ea~iia~Ag~~G--~VtIATNmAGRGtDI~Lggn~~~~~~~~~~~~~~~~~~~~~  534 (896)
T PRK13104        457 SEFLSQLLKKENIKHQVLNAKFHEKEAQIIAEAGRPG--AVTIATNMAGRGTDIVLGGSLAADLANLPADASEQEKEAVK  534 (896)
T ss_pred             HHHHHHHHHHcCCCeEeecCCCChHHHHHHHhCCCCC--cEEEeccCccCCcceecCCchhhhhhccccchhhHHHHHHH
Confidence            8899999999999999999999999999999999999  499999999999998411                       


Q ss_pred             ----------c-----EEEEecCCCChhHHHHhhhhhcCCCCceeEEEEeccCcH
Q psy6712         139 ----------S-----LVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDI  178 (210)
Q Consensus       139 ----------~-----~vi~~~~p~s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~  178 (210)
                                .     +||-...+.|..-=-|..||+||+|.+|.+-.|++-+|.
T Consensus       535 ~~~~~~~~~V~~~GGL~VIgTerhesrRID~QLrGRaGRQGDPGss~f~lSleD~  589 (896)
T PRK13104        535 KEWQKRHDEVIAAGGLRIIGSERHESRRIDNQLRGRAGRQGDPGSSRFYLSLEDN  589 (896)
T ss_pred             HHhhhhhhHHHHcCCCEEEeeccCchHHHHHHhccccccCCCCCceEEEEEcCcH
Confidence                      0     677777788888778999999999999999999986654

>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=99.74  E-value=8.7e-18  Score=118.00  Aligned_cols=102  Identities=47%  Similarity=0.789  Sum_probs=92.6

Q ss_pred             HHHhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCCh
Q psy6712          71 DVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNR  150 (210)
Q Consensus        71 ~i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~  150 (210)
                      .++.+++....++.+.+.|.+.+.++..+||+++..+|..+.+.|+++...++++|..+++|+|+|.+++||++++|++.
T Consensus        30 ~~lvf~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ili~t~~~~~G~d~~~~~~vi~~~~~~~~  109 (131)
T cd00079          30 KVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSP  109 (131)
T ss_pred             cEEEEeCcHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcChhhcCcChhhCCEEEEeCCCCCH
Confidence            34555566666888889998888999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHhhhhhcCCCCceeEEEE
Q psy6712         151 ELYIHRIGRSGRFGRKGVAISF  172 (210)
Q Consensus       151 ~~~~q~~GR~gR~g~~g~~~~~  172 (210)
                      ..+.|++||++|.|+.|.++++
T Consensus       110 ~~~~Q~~GR~~R~~~~~~~~~~  131 (131)
T cd00079         110 SSYLQRIGRAGRAGQKGTAILL  131 (131)
T ss_pred             HHheecccccccCCCCceEEeC
Confidence            9999999999999988877653

>KOG0353|consensus

Probab=99.74  E-value=1.6e-17  Score=131.70  Aligned_cols=182  Identities=18%  Similarity=0.333  Sum_probs=140.2

Q ss_pred             CCceEEEEEcCcchHHHH---HHhcC---CCcEEEEChHHHHHH---HHh--cCccCCCccEEEechhhHHhccc--hHH
Q psy6712           1 MNVQCHACIGGTNLSEDL---RKLDY---GQHVVSGTPGRVFDM---IRR--RVLRTRNIKMLVLDEADEMLNKG--FKE   67 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~---~~l~~---~~~Ili~Tp~~l~~~---l~~--~~~~~~~~~~lviDE~~~l~~~~--~~~   67 (210)
                      +||....++...+.++..   ..+.+   ....|..||+++...   +..  +.+....++.+.+||+|+..+||  |++
T Consensus       157 lgi~as~lnansske~~k~v~~~i~nkdse~kliyvtpekiaksk~~mnkleka~~~~~~~~iaidevhccsqwghdfr~  236 (695)
T KOG0353|consen  157 LGIDASMLNANSSKEEAKRVEAAITNKDSEFKLIYVTPEKIAKSKKFMNKLEKALEAGFFKLIAIDEVHCCSQWGHDFRP  236 (695)
T ss_pred             hCcchhhccCcccHHHHHHHHHHHcCCCceeEEEEecHHHHHHHHHHHHHHHHHhhcceeEEEeecceeehhhhCcccCc
Confidence            466666677666654432   22222   457999999987652   221  34556778899999999999886  222


Q ss_pred             HHHHH--Hh-hCCCc-----------------------------------------------------------------
Q psy6712          68 QIYDV--YR-YLPPA-----------------------------------------------------------------   79 (210)
Q Consensus        68 ~~~~i--~~-~~~~~-----------------------------------------------------------------   79 (210)
                      +...+  +. .++..                                                                 
T Consensus       237 dy~~l~ilkrqf~~~~iigltatatn~vl~d~k~il~ie~~~tf~a~fnr~nl~yev~qkp~n~dd~~edi~k~i~~~f~  316 (695)
T KOG0353|consen  237 DYKALGILKRQFKGAPIIGLTATATNHVLDDAKDILCIEAAFTFRAGFNRPNLKYEVRQKPGNEDDCIEDIAKLIKGDFA  316 (695)
T ss_pred             chHHHHHHHHhCCCCceeeeehhhhcchhhHHHHHHhHHhhheeecccCCCCceeEeeeCCCChHHHHHHHHHHhccccC
Confidence            21111  10 00000                                                                 


Q ss_pred             -----------hhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCC
Q psy6712          80 -----------TQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPN  148 (210)
Q Consensus        80 -----------~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~  148 (210)
                                 ..++.++..|+..|+.+..+|..|.++++..+-+.|..|++.++|+|-++++|+|-|++.+||+..+|.
T Consensus       317 gqsgiiyc~sq~d~ekva~alkn~gi~a~~yha~lep~dks~~hq~w~a~eiqvivatvafgmgidkpdvrfvihhsl~k  396 (695)
T KOG0353|consen  317 GQSGIIYCFSQKDCEKVAKALKNHGIHAGAYHANLEPEDKSGAHQGWIAGEIQVIVATVAFGMGIDKPDVRFVIHHSLPK  396 (695)
T ss_pred             CCcceEEEeccccHHHHHHHHHhcCccccccccccCccccccccccccccceEEEEEEeeecccCCCCCeeEEEecccch
Confidence                       008999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ChhHHHH-------------------------------------------hhhhhcCCCCceeEEEEeccCcHHHHH
Q psy6712         149 NRELYIH-------------------------------------------RIGRSGRFGRKGVAISFVKSDDIRILR  182 (210)
Q Consensus       149 s~~~~~q-------------------------------------------~~GR~gR~g~~g~~~~~~~~~~~~~~~  182 (210)
                      |...|.|                                           ..||+||.+....|++++.-.+.....
T Consensus       397 sienyyqasarillrmtkqknksdtggstqinilevctnfkiffavfsekesgragrd~~~a~cilyy~~~difk~s  473 (695)
T KOG0353|consen  397 SIENYYQASARILLRMTKQKNKSDTGGSTQINILEVCTNFKIFFAVFSEKESGRAGRDDMKADCILYYGFADIFKIS  473 (695)
T ss_pred             hHHHHHHHHHHHHHHHhhhcccccCCCcceeehhhhhccceeeeeeecchhccccccCCCcccEEEEechHHHHhHH
Confidence            9999999                                           679999999999999999766554443

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.73  E-value=1e-17  Score=145.51  Aligned_cols=114  Identities=25%  Similarity=0.365  Sum_probs=102.0

Q ss_pred             HhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEec-----CC
Q psy6712          73 YRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYD-----LP  147 (210)
Q Consensus        73 ~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~-----~p  147 (210)
                      +.+++....++.+.+.|.+.|+++..+|++++..+|.++++.|+.|+++++|||+.+++|+|+|++++|+++|     .|
T Consensus       446 LIf~~tk~~ae~L~~~L~~~gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t~~L~rGfDiP~v~lVvi~DadifG~p  525 (655)
T TIGR00631       446 LVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFL  525 (655)
T ss_pred             EEEECCHHHHHHHHHHHhhhccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEcChhcCCeeeCCCcEEEEeCcccccCC
Confidence            4466677779999999999999999999999999999999999999999999999999999999999999988     79


Q ss_pred             CChhHHHHhhhhhcCCCCceeEEEEeccCcHHHHHHHHHH
Q psy6712         148 NNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQY  187 (210)
Q Consensus       148 ~s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~  187 (210)
                      .+..+|+||+||+||. ..|.+++++...+..+.+.+++.
T Consensus       526 ~~~~~~iqriGRagR~-~~G~vi~~~~~~~~~~~~ai~~~  564 (655)
T TIGR00631       526 RSERSLIQTIGRAARN-VNGKVIMYADKITDSMQKAIEET  564 (655)
T ss_pred             CCHHHHHHHhcCCCCC-CCCEEEEEEcCCCHHHHHHHHHH
Confidence            9999999999999998 68999999998665555544443

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

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

Probab=99.73  E-value=2.7e-17  Score=146.21  Aligned_cols=188  Identities=24%  Similarity=0.350  Sum_probs=140.1

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhc----CccCCCccEEEechhhHHhc---cchHHHH---HH
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRR----VLRTRNIKMLVLDEADEMLN---KGFKEQI---YD   71 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~----~~~~~~~~~lviDE~~~l~~---~~~~~~~---~~   71 (210)
                      ++.+..+.|+++..+......+.+|||+++|++|..++.+.    ...++++++||+||+|.--.   ....--+   ..
T Consensus       145 ~v~~~~y~Gdt~~~~r~~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDElHtYrGv~GS~vA~llRRL~~  224 (851)
T COG1205         145 KVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYRGVQGSEVALLLRRLLR  224 (851)
T ss_pred             cceeeeecCCCChHHHHHHHhCCCCEEEeCHHHHHHHhccCcchHHHHHhcCcEEEEecceeccccchhHHHHHHHHHHH
Confidence            37788899999988777778889999999999999966653    23567899999999997532   1222222   22


Q ss_pred             HHhhCCCchh----------------------------------------------------------------------
Q psy6712          72 VYRYLPPATQ----------------------------------------------------------------------   81 (210)
Q Consensus        72 i~~~~~~~~~----------------------------------------------------------------------   81 (210)
                      ++...+...|                                                                      
T Consensus       225 ~~~~~~~~~q~i~~SAT~~np~e~~~~l~~~~f~~~v~~~g~~~~~~~~~~~~p~~~~~~~~~r~s~~~~~~~~~~~~~~  304 (851)
T COG1205         225 RLRRYGSPLQIICTSATLANPGEFAEELFGRDFEVPVDEDGSPRGLRYFVRREPPIRELAESIRRSALAELATLAALLVR  304 (851)
T ss_pred             HHhccCCCceEEEEeccccChHHHHHHhcCCcceeeccCCCCCCCceEEEEeCCcchhhhhhcccchHHHHHHHHHHHHH
Confidence            2222222222                                                                      


Q ss_pred             --------------HHHHH----HHHHhcC----ceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCc
Q psy6712          82 --------------VDWLT----EKMREAN----FTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVS  139 (210)
Q Consensus        82 --------------~~~l~----~~l~~~~----~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~  139 (210)
                                    ++.+.    +.+...+    ..+..++++|..++|.++...|+.|+...+++|++++-|+|+.+++
T Consensus       305 ~~~~tL~F~~sr~~~e~~~~~~~~~~~~~~~~l~~~v~~~~~~~~~~er~~ie~~~~~g~~~~~~st~AlelgidiG~ld  384 (851)
T COG1205         305 NGIQTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLD  384 (851)
T ss_pred             cCceEEEEEehhhhhhhhhhchhHHHhhcchhhhhheeeccccCCHHHHHHHHHHHhcCCccEEecchhhhhceeehhhh
Confidence                          23332    2222223    5688899999999999999999999999999999999999999999


Q ss_pred             EEEEecCCC-ChhHHHHhhhhhcCCCCceeEEEEeccC--cHHHHHHHHHHhc
Q psy6712         140 LVINYDLPN-NRELYIHRIGRSGRFGRKGVAISFVKSD--DIRILRDIEQYYS  189 (210)
Q Consensus       140 ~vi~~~~p~-s~~~~~q~~GR~gR~g~~g~~~~~~~~~--~~~~~~~~~~~~~  189 (210)
                      .||.+..|. +..++.||+||+||.++.+..+......  +.......+..+.
T Consensus       385 avi~~g~P~~s~~~~~Q~~GRaGR~~~~~l~~~v~~~~~~d~yy~~~p~~~~~  437 (851)
T COG1205         385 AVIAYGYPGVSVLSFRQRAGRAGRRGQESLVLVVLRSDPLDSYYLRHPEELLE  437 (851)
T ss_pred             hHhhcCCCCchHHHHHHhhhhccCCCCCceEEEEeCCCccchhhhhCcHhhhh
Confidence            999999999 9999999999999999777766666532  4444444444444

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=99.73  E-value=1.1e-17  Score=145.83  Aligned_cols=128  Identities=27%  Similarity=0.381  Sum_probs=113.1

Q ss_pred             HHhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecC-----
Q psy6712          72 VYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDL-----  146 (210)
Q Consensus        72 i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~-----  146 (210)
                      ++.++....+++.+++.|.+.|+++..+||+++..+|.++++.|+.|++.++|||+.+++|+|+|++++||++|.     
T Consensus       449 viIf~~t~~~ae~L~~~L~~~gi~~~~~h~~~~~~~R~~~l~~f~~g~i~vlV~t~~L~rGfdlp~v~lVii~d~eifG~  528 (652)
T PRK05298        449 VLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDIPEVSLVAILDADKEGF  528 (652)
T ss_pred             EEEEeCCHHHHHHHHHHHhhcceeEEEEECCCCHHHHHHHHHHHHcCCceEEEEeCHHhCCccccCCcEEEEeCCccccc
Confidence            344666777799999999999999999999999999999999999999999999999999999999999999874     


Q ss_pred             CCChhHHHHhhhhhcCCCCceeEEEEecc---------CcHHHHHHHHHHhcCccccccCCcc
Q psy6712         147 PNNRELYIHRIGRSGRFGRKGVAISFVKS---------DDIRILRDIEQYYSTQIDEMPMNGK  200 (210)
Q Consensus       147 p~s~~~~~q~~GR~gR~g~~g~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~~~~~~  200 (210)
                      |.+...|+||+||+||. ..|.+++|+..         .+....++++..++.....+|.+..
T Consensus       529 ~~~~~~yiqr~GR~gR~-~~G~~i~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~  590 (652)
T PRK05298        529 LRSERSLIQTIGRAARN-VNGKVILYADKITDSMQKAIDETERRREIQIAYNEEHGITPKTIK  590 (652)
T ss_pred             CCCHHHHHHHhccccCC-CCCEEEEEecCCCHHHHHHHHHHHHHHHHHHHhhhccCCCChhHH
Confidence            78999999999999996 78999999984         4566677778888888877776653

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.72  E-value=1.2e-16  Score=139.39  Aligned_cols=95  Identities=27%  Similarity=0.371  Sum_probs=87.5

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCC---CCc-----EEEEecCCCChhHH
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQ---QVS-----LVINYDLPNNRELY  153 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~---~~~-----~vi~~~~p~s~~~~  153 (210)
                      ++.+++.|.+.++++..+|+++...++..+..+++.|.  |+|||++++||.|++   ++.     +||+++.|.|...|
T Consensus       453 se~ls~~L~~~gi~~~~Lna~~~~~Ea~ii~~ag~~g~--VtIATnmAGRGtDI~l~~~V~~~GGLhVI~te~pes~ri~  530 (796)
T PRK12906        453 SERLSHLLDEAGIPHAVLNAKNHAKEAEIIMNAGQRGA--VTIATNMAGRGTDIKLGPGVKELGGLAVIGTERHESRRID  530 (796)
T ss_pred             HHHHHHHHHHCCCCeeEecCCcHHHHHHHHHhcCCCce--EEEEeccccCCCCCCCCcchhhhCCcEEEeeecCCcHHHH
Confidence            88899999999999999999999888888888887765  999999999999994   888     99999999999999


Q ss_pred             HHhhhhhcCCCCceeEEEEeccCcH
Q psy6712         154 IHRIGRSGRFGRKGVAISFVKSDDI  178 (210)
Q Consensus       154 ~q~~GR~gR~g~~g~~~~~~~~~~~  178 (210)
                      .|+.||+||+|.+|.+..+++.+|.
T Consensus       531 ~Ql~GRtGRqG~~G~s~~~~sleD~  555 (796)
T PRK12906        531 NQLRGRSGRQGDPGSSRFYLSLEDD  555 (796)
T ss_pred             HHHhhhhccCCCCcceEEEEeccch
Confidence            9999999999999999999987653

>KOG0952|consensus

Probab=99.69  E-value=1.4e-16  Score=139.20  Aligned_cols=88  Identities=25%  Similarity=0.374  Sum_probs=71.6

Q ss_pred             eEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEE----EecCC------CChhHHHHhhhhhcCCC
Q psy6712          95 TVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVI----NYDLP------NNRELYIHRIGRSGRFG  164 (210)
Q Consensus        95 ~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi----~~~~p------~s~~~~~q~~GR~gR~g  164 (210)
                      .....|++|..++|..+.+.|..|-+++|+||..+++|+|+|+--.+|    .||..      .+.-+.+|.+|||||..
T Consensus       398 g~~iHhAGm~r~DR~l~E~~F~~G~i~vL~cTaTLAwGVNLPA~aViIKGT~~ydsskg~f~dlgilDVlQifGRAGRPq  477 (1230)
T KOG0952|consen  398 GMGIHHAGMLRSDRQLVEKEFKEGHIKVLCCTATLAWGVNLPAYAVIIKGTQVYDSSKGSFVDLGILDVLQIFGRAGRPQ  477 (1230)
T ss_pred             hhhhcccccchhhHHHHHHHHhcCCceEEEecceeeeccCCcceEEEecCCcccccccCceeeehHHHHHHHHhccCCCC
Confidence            567899999999999999999999999999999999999999855555    24433      35778899999999973


Q ss_pred             --CceeEEEEeccCcHHHHH
Q psy6712         165 --RKGVAISFVKSDDIRILR  182 (210)
Q Consensus       165 --~~g~~~~~~~~~~~~~~~  182 (210)
                        ..|.++++.+.+..+.+.
T Consensus       478 Fd~~G~giIiTt~dkl~~Y~  497 (1230)
T KOG0952|consen  478 FDSSGEGIIITTRDKLDHYE  497 (1230)
T ss_pred             CCCCceEEEEecccHHHHHH
Confidence              468888887765544443

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=99.65  E-value=7.4e-15  Score=132.06  Aligned_cols=94  Identities=21%  Similarity=0.355  Sum_probs=79.6

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCC---CcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhh
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGT---SRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIG  158 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~---~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~G  158 (210)
                      ++.|.+.|...++....++|+++..+|..+++.|+...   .-+|++|.+++.|+|++.+++||+||+||++....|+.|
T Consensus       500 LdiLed~L~~~g~~y~rIdGsts~~eRq~~Id~Fn~~~s~~~VfLLSTrAGGlGINLt~Ad~VIiyD~dWNP~~d~QAid  579 (1033)
T PLN03142        500 LDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVFLLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQD  579 (1033)
T ss_pred             HHHHHHHHHHcCCcEEEECCCCCHHHHHHHHHHhccccCCceEEEEeccccccCCchhhCCEEEEeCCCCChHHHHHHHH
Confidence            34455566667889999999999999999999997643   357899999999999999999999999999999999999


Q ss_pred             hhcCCCCceeE--EEEecc
Q psy6712         159 RSGRFGRKGVA--ISFVKS  175 (210)
Q Consensus       159 R~gR~g~~g~~--~~~~~~  175 (210)
                      |+.|.|+...|  +-|+..
T Consensus       580 RaHRIGQkk~V~VyRLIt~  598 (1033)
T PLN03142        580 RAHRIGQKKEVQVFRFCTE  598 (1033)
T ss_pred             HhhhcCCCceEEEEEEEeC
Confidence            99999996554  344444

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.63  E-value=7e-15  Score=128.99  Aligned_cols=95  Identities=20%  Similarity=0.328  Sum_probs=85.0

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCC-----------------------
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQV-----------------------  138 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~-----------------------  138 (210)
                      .+.+++.|...++++..+|+.++..++..+.++|+.|.  |+|||++++||.|+-=-                       
T Consensus       462 se~ls~~L~~~gi~~~vLnak~~~~Ea~ii~~Ag~~G~--VtIATnmAGRGTDIkLggn~~~~~~~~~~~~~~~~~~~~~  539 (908)
T PRK13107        462 SELLARLMVKEKIPHEVLNAKFHEREAEIVAQAGRTGA--VTIATNMAGRGTDIVLGGNWNMEIEALENPTAEQKAKIKA  539 (908)
T ss_pred             HHHHHHHHHHCCCCeEeccCcccHHHHHHHHhCCCCCc--EEEecCCcCCCcceecCCchHHhhhhhcchhhHHHHHHHH
Confidence            78899999999999999999999999999999999998  99999999999998511                       


Q ss_pred             ---------c-----EEEEecCCCChhHHHHhhhhhcCCCCceeEEEEeccCcH
Q psy6712         139 ---------S-----LVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDI  178 (210)
Q Consensus       139 ---------~-----~vi~~~~p~s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~  178 (210)
                               .     +||-...+.|..-=-|..||+||+|.+|.+..|++-+|.
T Consensus       540 ~~~~~~~~V~~~GGL~VIgTerheSrRID~QLrGRaGRQGDPGss~f~lSlED~  593 (908)
T PRK13107        540 DWQIRHDEVVAAGGLHILGTERHESRRIDNQLRGRAGRQGDAGSSRFYLSMEDS  593 (908)
T ss_pred             HHHhhHHHHHHcCCCEEEecccCchHHHHhhhhcccccCCCCCceeEEEEeCcH
Confidence                     1     778777888888888999999999999999999987654

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.61  E-value=2.2e-14  Score=117.33  Aligned_cols=71  Identities=21%  Similarity=0.441  Sum_probs=59.5

Q ss_pred             HHHHHHHHHhcC--ceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhh
Q psy6712          82 VDWLTEKMREAN--FTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGR  159 (210)
Q Consensus        82 ~~~l~~~l~~~~--~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR  159 (210)
                      ++.+++.|++.+  ..+..+||.+++.+|.+.      ++.++||||+++++|+|+|.. +|| ++ |.+...|+||+||
T Consensus       285 ~~~l~~~L~~~~~~~~~~~l~g~~~~~~R~~~------~~~~iLVaTdv~~rGiDi~~~-~vi-~~-p~~~~~yiqR~GR  355 (357)
T TIGR03158       285 VNRLSDLLQQQGLGDDIGRITGFAPKKDRERA------MQFDILLGTSTVDVGVDFKRD-WLI-FS-ARDAAAFWQRLGR  355 (357)
T ss_pred             HHHHHHHHhhhCCCceEEeeecCCCHHHHHHh------ccCCEEEEecHHhcccCCCCc-eEE-EC-CCCHHHHhhhccc
Confidence            777778887654  578889999999888643      478999999999999999986 555 55 8999999999999


Q ss_pred             hc
Q psy6712         160 SG  161 (210)
Q Consensus       160 ~g  161 (210)
                      +|
T Consensus       356 ~g  357 (357)
T TIGR03158       356 LG  357 (357)
T ss_pred             CC
Confidence            86

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.

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

Probab=99.61  E-value=5.3e-14  Score=110.41  Aligned_cols=99  Identities=20%  Similarity=0.342  Sum_probs=78.6

Q ss_pred             HHHHHHHHHhc--CceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEec--CCCChhHHHHhh
Q psy6712          82 VDWLTEKMREA--NFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYD--LPNNRELYIHRI  157 (210)
Q Consensus        82 ~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~--~p~s~~~~~q~~  157 (210)
                      .+.+++.|+++  ...+..+|+.  .+.|.+..++|++|++++|++|+++++|+.+|++++.+.-.  .-.+-+..+|.+
T Consensus       318 ~eq~a~~lk~~~~~~~i~~Vhs~--d~~R~EkV~~fR~G~~~lLiTTTILERGVTfp~vdV~Vlgaeh~vfTesaLVQIa  395 (441)
T COG4098         318 MEQVAAALKKKLPKETIASVHSE--DQHRKEKVEAFRDGKITLLITTTILERGVTFPNVDVFVLGAEHRVFTESALVQIA  395 (441)
T ss_pred             HHHHHHHHHhhCCccceeeeecc--CccHHHHHHHHHcCceEEEEEeehhhcccccccceEEEecCCcccccHHHHHHHh
Confidence            66677777443  3456788887  56789999999999999999999999999999999887533  225788999999


Q ss_pred             hhhcCCCC--ceeEEEEeccCcHHHHH
Q psy6712         158 GRSGRFGR--KGVAISFVKSDDIRILR  182 (210)
Q Consensus       158 GR~gR~g~--~g~~~~~~~~~~~~~~~  182 (210)
                      ||+||.-.  .|.++.|.......+.+
T Consensus       396 GRvGRs~~~PtGdv~FFH~G~skaM~~  422 (441)
T COG4098         396 GRVGRSLERPTGDVLFFHYGKSKAMKQ  422 (441)
T ss_pred             hhccCCCcCCCCcEEEEeccchHHHHH
Confidence            99999854  68888888776555443

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

Probab=99.57  E-value=6.6e-14  Score=117.42  Aligned_cols=81  Identities=28%  Similarity=0.560  Sum_probs=72.6

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhc
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSG  161 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~g  161 (210)
                      +..++..+...++ +..+.+..+..+|..+++.|+.|++++|+++.++.+|+|+|+++++|...++.|...|+||+||..
T Consensus       296 a~~i~~~~~~~~~-~~~it~~t~~~eR~~il~~fr~g~~~~lv~~~vl~EGvDiP~~~~~i~~~~t~S~~~~~Q~lGR~L  374 (442)
T COG1061         296 AYEIAKLFLAPGI-VEAITGETPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLIILRPTGSRRLFIQRLGRGL  374 (442)
T ss_pred             HHHHHHHhcCCCc-eEEEECCCCHHHHHHHHHHHHcCCCCEEEEeeeccceecCCCCcEEEEeCCCCcHHHHHHHhhhhc
Confidence            4445555544555 779999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CC
Q psy6712         162 RF  163 (210)
Q Consensus       162 R~  163 (210)
                      |.
T Consensus       375 R~  376 (442)
T COG1061         375 RP  376 (442)
T ss_pred             cC
Confidence            94

>KOG0951|consensus

Probab=99.56  E-value=6.6e-15  Score=130.70  Aligned_cols=82  Identities=23%  Similarity=0.380  Sum_probs=70.3

Q ss_pred             ceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEE----EecC------CCChhHHHHhhhhhcCC
Q psy6712          94 FTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVI----NYDL------PNNRELYIHRIGRSGRF  163 (210)
Q Consensus        94 ~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi----~~~~------p~s~~~~~q~~GR~gR~  163 (210)
                      +..+.+|++|+..+|..+.+.|++|.++++|+|-.++||+++|.-+++|    .||+      +.++.+..||.|||||.
T Consensus       608 ygfaIHhAGl~R~dR~~~EdLf~~g~iqvlvstatlawgvnlpahtViikgtqvy~pekg~w~elsp~dv~qmlgragrp  687 (1674)
T KOG0951|consen  608 YGFAIHHAGLNRKDRELVEDLFADGHIQVLVSTATLAWGVNLPAHTVIIKGTQVYDPEKGRWTELSPLDVMQMLGRAGRP  687 (1674)
T ss_pred             ccceeeccCCCcchHHHHHHHHhcCceeEEEeehhhhhhcCCCcceEEecCccccCcccCccccCCHHHHHHHHhhcCCC
Confidence            4788899999999999999999999999999999999999999988888    4664      35799999999999998


Q ss_pred             CC--ceeEEEEecc
Q psy6712         164 GR--KGVAISFVKS  175 (210)
Q Consensus       164 g~--~g~~~~~~~~  175 (210)
                      +-  .|..++....
T Consensus       688 ~~D~~gegiiit~~  701 (1674)
T KOG0951|consen  688 QYDTCGEGIIITDH  701 (1674)
T ss_pred             ccCcCCceeeccCc
Confidence            65  3555555443

>KOG0953|consensus

Probab=99.53  E-value=7.9e-14  Score=115.33  Aligned_cols=107  Identities=20%  Similarity=0.355  Sum_probs=84.5

Q ss_pred             HHHHHHHHHhcCce-EEEecCCCCHhHHHHHHHHHhc--CCCcEEEEecCccccCCCCCCcEEEEecC---------CCC
Q psy6712          82 VDWLTEKMREANFT-VSSMHGDMPQKERDGIMKEFRS--GTSRVLITTDVWARGIDVQQVSLVINYDL---------PNN  149 (210)
Q Consensus        82 ~~~l~~~l~~~~~~-~~~~~~~~~~~~r~~~~~~f~~--g~~~ilv~T~~~~~g~d~~~~~~vi~~~~---------p~s  149 (210)
                      .-.+...+.+.+.. +++++|++|++.|.+....|+.  ++++|||||+++++|+|+ +++.||.++.         |-+
T Consensus       369 I~~~k~kIE~~g~~k~aVIYGsLPPeTr~aQA~~FNd~~~e~dvlVAsDAIGMGLNL-~IrRiiF~sl~Kysg~e~~~it  447 (700)
T KOG0953|consen  369 IFTVKKKIEKAGNHKCAVIYGSLPPETRLAQAALFNDPSNECDVLVASDAIGMGLNL-NIRRIIFYSLIKYSGRETEDIT  447 (700)
T ss_pred             HHHHHHHHHHhcCcceEEEecCCCCchhHHHHHHhCCCCCccceEEeeccccccccc-ceeEEEEeecccCCcccceecc
Confidence            55566777666655 9999999999999999999997  889999999999999999 8888988774         356


Q ss_pred             hhHHHHhhhhhcCCCC---ceeEEEEeccCcHHHHHHHHHHhcCccc
Q psy6712         150 RELYIHRIGRSGRFGR---KGVAISFVKSDDIRILRDIEQYYSTQID  193 (210)
Q Consensus       150 ~~~~~q~~GR~gR~g~---~g~~~~~~~~~~~~~~~~~~~~~~~~~~  193 (210)
                      .++..|.+|||||.|.   .|.+..+.    .+.+..+.+.++.+.+
T Consensus       448 ~sqikQIAGRAGRf~s~~~~G~vTtl~----~eDL~~L~~~l~~p~e  490 (700)
T KOG0953|consen  448 VSQIKQIAGRAGRFGSKYPQGEVTTLH----SEDLKLLKRILKRPVE  490 (700)
T ss_pred             HHHHHHHhhcccccccCCcCceEEEee----HhhHHHHHHHHhCCch
Confidence            8889999999999975   46666655    3344445555554443

>KOG0385|consensus

Probab=99.52  E-value=6.3e-13  Score=113.57  Aligned_cols=91  Identities=21%  Similarity=0.368  Sum_probs=78.1

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCC---CcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhh
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGT---SRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIG  158 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~---~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~G  158 (210)
                      .+.+..+..-+++...-+.|.++.++|...++.|+...   +-.|++|.+.+.|+|+..++.||.||..|+|..=+|...
T Consensus       500 LDILeDyc~~R~y~ycRiDGSt~~eeR~~aI~~fn~~~s~~FiFlLSTRAGGLGINL~aADtVIlyDSDWNPQ~DLQAmD  579 (971)
T KOG0385|consen  500 LDILEDYCMLRGYEYCRLDGSTSHEEREDAIEAFNAPPSEKFIFLLSTRAGGLGINLTAADTVILYDSDWNPQVDLQAMD  579 (971)
T ss_pred             HHHHHHHHHhcCceeEeecCCCCcHHHHHHHHhcCCCCcceEEEEEeccccccccccccccEEEEecCCCCchhhhHHHH
Confidence            44455555556788888999999999999999998755   347899999999999999999999999999999999999


Q ss_pred             hhcCCCCceeEEEE
Q psy6712         159 RSGRFGRKGVAISF  172 (210)
Q Consensus       159 R~gR~g~~g~~~~~  172 (210)
                      ||.|.|+...|.+|
T Consensus       580 RaHRIGQ~K~V~V~  593 (971)
T KOG0385|consen  580 RAHRIGQKKPVVVY  593 (971)
T ss_pred             HHHhhCCcCceEEE
Confidence            99999997655444

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.49  E-value=1.3e-12  Score=115.35  Aligned_cols=95  Identities=21%  Similarity=0.293  Sum_probs=74.7

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCC---Cc-----EEEEecCCCChhHH
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQ---VS-----LVINYDLPNNRELY  153 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~---~~-----~vi~~~~p~s~~~~  153 (210)
                      .+.++..|.+.+++...+++.-...+-.-+.++-+  .-.|.|||++++||.|+.-   +.     +||-...|.|..--
T Consensus       581 se~ls~~L~~~gi~h~vLNak~~~~Ea~iia~AG~--~g~VTIATNmAGRGTDIkl~~~v~~~GGLhVIgTer~es~Rid  658 (970)
T PRK12899        581 SEKLSRILRQNRIEHTVLNAKNHAQEAEIIAGAGK--LGAVTVATNMAGRGTDIKLDEEAVAVGGLYVIGTSRHQSRRID  658 (970)
T ss_pred             HHHHHHHHHHcCCcceecccchhhhHHHHHHhcCC--CCcEEEeeccccCCcccccCchHHhcCCcEEEeeccCchHHHH
Confidence            67888999999999999988744333333333322  2469999999999999842   22     78888899999999


Q ss_pred             HHhhhhhcCCCCceeEEEEeccCcH
Q psy6712         154 IHRIGRSGRFGRKGVAISFVKSDDI  178 (210)
Q Consensus       154 ~q~~GR~gR~g~~g~~~~~~~~~~~  178 (210)
                      -|..||+||+|.+|.+..|++-+|.
T Consensus       659 ~Ql~GRagRQGdpGss~f~lSlEDd  683 (970)
T PRK12899        659 RQLRGRCARLGDPGAAKFFLSFEDR  683 (970)
T ss_pred             HHHhcccccCCCCCceeEEEEcchH
Confidence            9999999999999999999987654

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=99.48  E-value=5.9e-14  Score=123.91  Aligned_cols=106  Identities=20%  Similarity=0.305  Sum_probs=93.7

Q ss_pred             HHhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCC---CCc-----EEEE
Q psy6712          72 VYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQ---QVS-----LVIN  143 (210)
Q Consensus        72 i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~---~~~-----~vi~  143 (210)
                      ++.++.....++.+++.|...++++..+|+  .+.+|+..+.+|..+...|+|||++++||+|++   .|.     +||.
T Consensus       601 VLIft~Sve~sE~Ls~~L~~~gI~h~vLna--kq~~REa~Iia~AG~~g~VtIATNMAGRGtDIkl~~~V~~vGGL~VIg  678 (1025)
T PRK12900        601 VLVGTASVEVSETLSRMLRAKRIAHNVLNA--KQHDREAEIVAEAGQKGAVTIATNMAGRGTDIKLGEGVRELGGLFILG  678 (1025)
T ss_pred             EEEEeCcHHHHHHHHHHHHHcCCCceeecC--CHHHhHHHHHHhcCCCCeEEEeccCcCCCCCcCCccchhhhCCceeeC
Confidence            344566667799999999999999999997  588999999999999999999999999999998   444     4588


Q ss_pred             ecCCCChhHHHHhhhhhcCCCCceeEEEEeccCcHH
Q psy6712         144 YDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIR  179 (210)
Q Consensus       144 ~~~p~s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~~  179 (210)
                      ++.|.|...|.|++||+||+|.+|.+.+|++..|.-
T Consensus       679 terhes~Rid~Ql~GRtGRqGdpGsS~ffvSleD~L  714 (1025)
T PRK12900        679 SERHESRRIDRQLRGRAGRQGDPGESVFYVSLEDEL  714 (1025)
T ss_pred             CCCCchHHHHHHHhhhhhcCCCCcceEEEechhHHH
Confidence            999999999999999999999999999999876543

>PRK09694 helicase Cas3; Provisional

Probab=99.48  E-value=4.9e-13  Score=119.21  Aligned_cols=81  Identities=25%  Similarity=0.524  Sum_probs=68.0

Q ss_pred             HHHHHHHHHhcC---ceEEEecCCCCHhHH----HHHHHHH-hcCC---CcEEEEecCccccCCCCCCcEEEEecCCCCh
Q psy6712          82 VDWLTEKMREAN---FTVSSMHGDMPQKER----DGIMKEF-RSGT---SRVLITTDVWARGIDVQQVSLVINYDLPNNR  150 (210)
Q Consensus        82 ~~~l~~~l~~~~---~~~~~~~~~~~~~~r----~~~~~~f-~~g~---~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~  150 (210)
                      ++.+++.|++.+   .++..+|+.++..+|    +++++.| ++|+   ..|||+|+++++|+|+ +++++|....|  .
T Consensus       573 Aq~ly~~L~~~~~~~~~v~llHsrf~~~dR~~~E~~vl~~fgk~g~r~~~~ILVaTQViE~GLDI-d~DvlItdlaP--i  649 (878)
T PRK09694        573 AQKLYQRLKELNNTQVDIDLFHARFTLNDRREKEQRVIENFGKNGKRNQGRILVATQVVEQSLDL-DFDWLITQLCP--V  649 (878)
T ss_pred             HHHHHHHHHhhCCCCceEEEEeCCCCHHHHHHHHHHHHHHHHhcCCcCCCeEEEECcchhheeec-CCCeEEECCCC--H
Confidence            666777777654   689999999999888    4567788 6666   4799999999999999 68999988777  6


Q ss_pred             hHHHHhhhhhcCCCC
Q psy6712         151 ELYIHRIGRSGRFGR  165 (210)
Q Consensus       151 ~~~~q~~GR~gR~g~  165 (210)
                      +.++||+||++|.+.
T Consensus       650 dsLiQRaGR~~R~~~  664 (878)
T PRK09694        650 DLLFQRLGRLHRHHR  664 (878)
T ss_pred             HHHHHHHhccCCCCC
Confidence            899999999999975

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

Probab=99.47  E-value=8.8e-14  Score=114.76  Aligned_cols=109  Identities=27%  Similarity=0.374  Sum_probs=95.2

Q ss_pred             hCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecC-----CCC
Q psy6712          75 YLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDL-----PNN  149 (210)
Q Consensus        75 ~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~-----p~s  149 (210)
                      .+-..+.++.|.++|.+.|+++.++|++...-+|.+++..++.|.+++||+.+.+.+|+|+|.|.+|-.+|.     ..|
T Consensus       452 TtLTKkmAEdLT~Yl~e~gikv~YlHSdidTlER~eIirdLR~G~~DvLVGINLLREGLDiPEVsLVAIlDADKeGFLRs  531 (663)
T COG0556         452 TTLTKKMAEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRS  531 (663)
T ss_pred             EeehHHHHHHHHHHHHhcCceEEeeeccchHHHHHHHHHHHhcCCccEEEeehhhhccCCCcceeEEEEeecCccccccc
Confidence            333445599999999999999999999999999999999999999999999999999999999999988874     478


Q ss_pred             hhHHHHhhhhhcCCCCceeEEEEeccCcHHHHHHH
Q psy6712         150 RELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDI  184 (210)
Q Consensus       150 ~~~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~  184 (210)
                      -.+.+|-+|||+|. ..|.++++.+.-...+-+.+
T Consensus       532 e~SLIQtIGRAARN-~~GkvIlYAD~iT~sM~~Ai  565 (663)
T COG0556         532 ERSLIQTIGRAARN-VNGKVILYADKITDSMQKAI  565 (663)
T ss_pred             cchHHHHHHHHhhc-cCCeEEEEchhhhHHHHHHH
Confidence            99999999999997 67999999976444443333

>KOG0947|consensus

Probab=99.47  E-value=1.8e-13  Score=119.11  Aligned_cols=81  Identities=25%  Similarity=0.398  Sum_probs=68.4

Q ss_pred             eEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEe----c----CCCChhHHHHhhhhhcCCCC-
Q psy6712          95 TVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINY----D----LPNNRELYIHRIGRSGRFGR-  165 (210)
Q Consensus        95 ~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~----~----~p~s~~~~~q~~GR~gR~g~-  165 (210)
                      .++++||++-+--++-+.--|..|-+++|+||..+++|+|+|.-.+|+..    |    -.-.+..|.||+|||||.|- 
T Consensus       632 GiaVHH~GlLPivKE~VE~LFqrGlVKVLFATETFAMGVNMPARtvVF~Sl~KhDG~efR~L~PGEytQMAGRAGRRGlD  711 (1248)
T KOG0947|consen  632 GIAVHHGGLLPIVKEVVELLFQRGLVKVLFATETFAMGVNMPARTVVFSSLRKHDGNEFRELLPGEYTQMAGRAGRRGLD  711 (1248)
T ss_pred             cchhhcccchHHHHHHHHHHHhcCceEEEeehhhhhhhcCCCceeEEeeehhhccCcceeecCChhHHhhhccccccccC
Confidence            57889999999888888999999999999999999999999987776632    1    12468999999999999987 


Q ss_pred             -ceeEEEEecc
Q psy6712         166 -KGVAISFVKS  175 (210)
Q Consensus       166 -~g~~~~~~~~  175 (210)
                       .|.+++++..
T Consensus       712 ~tGTVii~~~~  722 (1248)
T KOG0947|consen  712 ETGTVIIMCKD  722 (1248)
T ss_pred             cCceEEEEecC
Confidence             5777777754

>KOG0950|consensus

Probab=99.47  E-value=2.9e-13  Score=117.98  Aligned_cols=91  Identities=29%  Similarity=0.449  Sum_probs=80.0

Q ss_pred             ceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEec----CCCChhHHHHhhhhhcCCCC--ce
Q psy6712          94 FTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYD----LPNNRELYIHRIGRSGRFGR--KG  167 (210)
Q Consensus        94 ~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~----~p~s~~~~~q~~GR~gR~g~--~g  167 (210)
                      ..+.++|++++.++|+.+..+|++|-..+++||+.++.|+++|...++|-+.    ...+.-+|.||+|||||+|.  .|
T Consensus       523 ~GvAyHhaGLT~eER~~iE~afr~g~i~vl~aTSTlaaGVNLPArRVIiraP~~g~~~l~~~~YkQM~GRAGR~gidT~G  602 (1008)
T KOG0950|consen  523 YGVAYHHAGLTSEEREIIEAAFREGNIFVLVATSTLAAGVNLPARRVIIRAPYVGREFLTRLEYKQMVGRAGRTGIDTLG  602 (1008)
T ss_pred             ccceecccccccchHHHHHHHHHhcCeEEEEecchhhccCcCCcceeEEeCCccccchhhhhhHHhhhhhhhhcccccCc
Confidence            4788999999999999999999999999999999999999999999888542    34578999999999999987  58


Q ss_pred             eEEEEeccCcHHHHHHH
Q psy6712         168 VAISFVKSDDIRILRDI  184 (210)
Q Consensus       168 ~~~~~~~~~~~~~~~~~  184 (210)
                      .+++.+.+.+.....++
T Consensus       603 dsiLI~k~~e~~~~~~l  619 (1008)
T KOG0950|consen  603 DSILIIKSSEKKRVREL  619 (1008)
T ss_pred             ceEEEeeccchhHHHHH
Confidence            89999999887665533

>KOG0948|consensus

Probab=99.40  E-value=7.3e-14  Score=118.97  Aligned_cols=82  Identities=23%  Similarity=0.412  Sum_probs=69.6

Q ss_pred             eEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEE----ecC----CCChhHHHHhhhhhcCCCC-
Q psy6712          95 TVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVIN----YDL----PNNRELYIHRIGRSGRFGR-  165 (210)
Q Consensus        95 ~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~----~~~----p~s~~~~~q~~GR~gR~g~-  165 (210)
                      .++.+|+++-+--++-+.--|.+|-+++|+||..++.|+|+|.-++|+-    ||-    .-|-..|+||.|||||.|. 
T Consensus       448 GIGIHHsGLLPIlKE~IEILFqEGLvKvLFATETFsiGLNMPAkTVvFT~~rKfDG~~fRwissGEYIQMSGRAGRRG~D  527 (1041)
T KOG0948|consen  448 GIGIHHSGLLPILKEVIEILFQEGLVKVLFATETFSIGLNMPAKTVVFTAVRKFDGKKFRWISSGEYIQMSGRAGRRGID  527 (1041)
T ss_pred             ccccccccchHHHHHHHHHHHhccHHHHHHhhhhhhhccCCcceeEEEeeccccCCcceeeecccceEEecccccccCCC
Confidence            5778999999988888899999999999999999999999999777763    331    2367899999999999997 


Q ss_pred             -ceeEEEEeccC
Q psy6712         166 -KGVAISFVKSD  176 (210)
Q Consensus       166 -~g~~~~~~~~~  176 (210)
                       .|.|+++++..
T Consensus       528 drGivIlmiDek  539 (1041)
T KOG0948|consen  528 DRGIVILMIDEK  539 (1041)
T ss_pred             CCceEEEEecCc
Confidence             47888888753

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

Probab=99.36  E-value=2.4e-12  Score=112.08  Aligned_cols=123  Identities=21%  Similarity=0.418  Sum_probs=96.0

Q ss_pred             HHHHHHHHHhc--CceEEEecCCCCHh--HHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCC----------
Q psy6712          82 VDWLTEKMREA--NFTVSSMHGDMPQK--ERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLP----------  147 (210)
Q Consensus        82 ~~~l~~~l~~~--~~~~~~~~~~~~~~--~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p----------  147 (210)
                      ++.+.+.|+..  +.++..+.++.+..  .-+..++.|.+|+.+|||+|++++.|.|+|+++.|...|.+          
T Consensus       493 terieeeL~~~FP~~rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~~~DfRA  572 (730)
T COG1198         493 TERIEEELKRLFPGARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFRA  572 (730)
T ss_pred             HHHHHHHHHHHCCCCcEEEEccccccchhhHHHHHHHHhCCCCCeeecchhhhcCCCcccceEEEEEechhhhcCCCcch
Confidence            67777777654  56777788776543  35678999999999999999999999999999998765543          


Q ss_pred             --CChhHHHHhhhhhcCCCCceeEEEEeccCcHHHHHHHHH-----HhcCccccccCCccccCCCCCCCC
Q psy6712         148 --NNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQ-----YYSTQIDEMPMNGKRSLHSYPARY  210 (210)
Q Consensus       148 --~s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~  210 (210)
                        .....+.|-.|||||.+.+|.+++-....+...++.+..     +++.++.+      +-...||||+
T Consensus       573 ~Er~fqll~QvaGRAgR~~~~G~VvIQT~~P~hp~i~~~~~~dy~~F~~~El~~------Rk~~~~PPf~  636 (730)
T COG1198         573 SERTFQLLMQVAGRAGRAGKPGEVVIQTYNPDHPAIQALKRGDYEAFYEQELAE------RKELGLPPFS  636 (730)
T ss_pred             HHHHHHHHHHHHhhhccCCCCCeEEEEeCCCCcHHHHHHHhcCHHHHHHHHHHH------HHhcCCCChh
Confidence              235667788999999999999999999888877776654     44444444      5555899985

>KOG0384|consensus

Probab=99.35  E-value=2.4e-11  Score=108.36  Aligned_cols=104  Identities=20%  Similarity=0.306  Sum_probs=89.2

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCC---CcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhh
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGT---SRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIG  158 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~---~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~G  158 (210)
                      .+.|+++|..++++.--+.|.+.-+.|+..++.|+...   +-.|+||.+.+.|||+..++.||+||..|+|..=+|...
T Consensus       712 LDIL~eYL~~r~ypfQRLDGsvrgelRq~AIDhFnap~SddFvFLLSTRAGGLGINLatADTVIIFDSDWNPQNDLQAqA  791 (1373)
T KOG0384|consen  712 LDILAEYLSLRGYPFQRLDGSVRGELRQQAIDHFNAPDSDDFVFLLSTRAGGLGINLATADTVIIFDSDWNPQNDLQAQA  791 (1373)
T ss_pred             HHHHHHHHHHcCCcceeccCCcchHHHHHHHHhccCCCCCceEEEEecccCcccccccccceEEEeCCCCCcchHHHHHH
Confidence            67788999999999999999999999999999998654   458999999999999999999999999999999999999


Q ss_pred             hhcCCCCcee--EEEEeccC--cHHHHHHHH
Q psy6712         159 RSGRFGRKGV--AISFVKSD--DIRILRDIE  185 (210)
Q Consensus       159 R~gR~g~~g~--~~~~~~~~--~~~~~~~~~  185 (210)
                      ||.|.|+...  ++=|++..  |.+.+.+-.
T Consensus       792 RaHRIGQkk~VnVYRLVTk~TvEeEilERAk  822 (1373)
T KOG0384|consen  792 RAHRIGQKKHVNVYRLVTKNTVEEEILERAK  822 (1373)
T ss_pred             HHHhhcccceEEEEEEecCCchHHHHHHHHH
Confidence            9999998654  56666654  444444433

>KOG0949|consensus

Probab=99.35  E-value=7.1e-12  Score=109.64  Aligned_cols=81  Identities=26%  Similarity=0.330  Sum_probs=69.0

Q ss_pred             eEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEec-CCCChhHHHHhhhhhcCCCC--ceeEEE
Q psy6712          95 TVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYD-LPNNRELYIHRIGRSGRFGR--KGVAIS  171 (210)
Q Consensus        95 ~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~-~p~s~~~~~q~~GR~gR~g~--~g~~~~  171 (210)
                      .+.++|++|+...|..+.--|+.|...+|++|..++.|+|+|--++|+--| +.-++-.|-|++|||||.|-  -|.++.
T Consensus       964 GiG~HHaglNr~yR~~VEvLFR~g~L~VlfaT~TLsLGiNMPCrTVvF~gDsLQL~plny~QmaGRAGRRGFD~lGnV~F 1043 (1330)
T KOG0949|consen  964 GIGVHHAGLNRKYRSLVEVLFRQGHLQVLFATETLSLGINMPCRTVVFAGDSLQLDPLNYKQMAGRAGRRGFDTLGNVVF 1043 (1330)
T ss_pred             cccccccccchHHHHHHHHHhhcCceEEEEEeeehhcccCCCceeEEEeccccccCchhHHhhhccccccccccccceEE
Confidence            567899999999999999999999999999999999999998665555444 55789999999999999986  366666


Q ss_pred             Eecc
Q psy6712         172 FVKS  175 (210)
Q Consensus       172 ~~~~  175 (210)
                      +--+
T Consensus      1044 mgiP 1047 (1330)
T KOG0949|consen 1044 MGIP 1047 (1330)
T ss_pred             EeCc
Confidence            5544

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

Probab=99.35  E-value=8.8e-12  Score=110.17  Aligned_cols=152  Identities=19%  Similarity=0.382  Sum_probs=116.0

Q ss_pred             CCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHh-cc----chHHHH-------------------H---------
Q psy6712          24 GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEML-NK----GFKEQI-------------------Y---------   70 (210)
Q Consensus        24 ~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~-~~----~~~~~~-------------------~---------   70 (210)
                      ...|-+.|.|.|++.+.+... ++.++++|+||+|+=. +.    ++..++                   .         
T Consensus       139 ~Trik~mTdGiLlrei~~D~~-Ls~ys~vIiDEaHERSl~tDilLgllk~~~~~rr~DLKiIimSATld~~rfs~~f~~a  217 (845)
T COG1643         139 RTRIKVMTDGILLREIQNDPL-LSGYSVVIIDEAHERSLNTDILLGLLKDLLARRRDDLKLIIMSATLDAERFSAYFGNA  217 (845)
T ss_pred             CceeEEeccHHHHHHHhhCcc-cccCCEEEEcchhhhhHHHHHHHHHHHHHHhhcCCCceEEEEecccCHHHHHHHcCCC
Confidence            446889999999998886554 7999999999999842 11    111110                   0         


Q ss_pred             -------------------------------------------HHHhhCCCchhHHHHHHHHHh----cCceEEEecCCC
Q psy6712          71 -------------------------------------------DVYRYLPPATQVDWLTEKMRE----ANFTVSSMHGDM  103 (210)
Q Consensus        71 -------------------------------------------~i~~~~~~~~~~~~l~~~l~~----~~~~~~~~~~~~  103 (210)
                                                                 .|+.|+|.....+...+.|++    ....+.++||.+
T Consensus       218 pvi~i~GR~fPVei~Y~~~~~~d~~l~~ai~~~v~~~~~~~~GdILvFLpG~~EI~~~~~~L~~~~l~~~~~i~PLy~~L  297 (845)
T COG1643         218 PVIEIEGRTYPVEIRYLPEAEADYILLDAIVAAVDIHLREGSGSILVFLPGQREIERTAEWLEKAELGDDLEILPLYGAL  297 (845)
T ss_pred             CEEEecCCccceEEEecCCCCcchhHHHHHHHHHHHhccCCCCCEEEECCcHHHHHHHHHHHHhccccCCcEEeeccccC
Confidence                                                       111123333336777777776    468899999999


Q ss_pred             CHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecC------------------CCChhHHHHhhhhhcCCCC
Q psy6712         104 PQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDL------------------PNNRELYIHRIGRSGRFGR  165 (210)
Q Consensus       104 ~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~------------------p~s~~~~~q~~GR~gR~g~  165 (210)
                      |.+++..+++.--.|+-+|+++|++++.++.+|++.+||..+.                  |-|..+..||.|||||- .
T Consensus       298 ~~~eQ~rvF~p~~~~~RKVVlATNIAETSLTI~gIr~VIDsG~ak~~~y~~~~g~~~L~~~~ISqAsA~QRaGRAGR~-~  376 (845)
T COG1643         298 SAEEQVRVFEPAPGGKRKVVLATNIAETSLTIPGIRYVIDSGLAKEKRYDPRTGLTRLETEPISKASADQRAGRAGRT-G  376 (845)
T ss_pred             CHHHHHhhcCCCCCCcceEEEEccccccceeeCCeEEEecCCcccccccccccCceeeeEEEechhhhhhhccccccC-C
Confidence            9999999888887787779999999999999999999996442                  35788888999999998 6


Q ss_pred             ceeEEEEeccCc
Q psy6712         166 KGVAISFVKSDD  177 (210)
Q Consensus       166 ~g~~~~~~~~~~  177 (210)
                      +|.|+=+++..+
T Consensus       377 pGicyRLyse~~  388 (845)
T COG1643         377 PGICYRLYSEED  388 (845)
T ss_pred             CceEEEecCHHH
Confidence            899999998743

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

Probab=99.32  E-value=9.3e-12  Score=111.14  Aligned_cols=80  Identities=23%  Similarity=0.387  Sum_probs=68.2

Q ss_pred             EEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEE----ec----CCCChhHHHHhhhhhcCCCCc-
Q psy6712          96 VSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVIN----YD----LPNNRELYIHRIGRSGRFGRK-  166 (210)
Q Consensus        96 ~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~----~~----~p~s~~~~~q~~GR~gR~g~~-  166 (210)
                      ++++|++|-+..+..+...|..|-.+++++|..++.|+|+|.-++|+-    +|    .+-++..|.|+.|||||.|.+ 
T Consensus       447 iavHH~GlLP~~K~~vE~Lfq~GLvkvvFaTeT~s~GiNmPartvv~~~l~K~dG~~~r~L~~gEy~QmsGRAGRRGlD~  526 (1041)
T COG4581         447 IAVHHAGLLPAIKELVEELFQEGLVKVVFATETFAIGINMPARTVVFTSLSKFDGNGHRWLSPGEYTQMSGRAGRRGLDV  526 (1041)
T ss_pred             hhhhccccchHHHHHHHHHHhccceeEEeehhhhhhhcCCcccceeeeeeEEecCCceeecChhHHHHhhhhhccccccc
Confidence            458999999999999999999999999999999999999998777762    33    346899999999999999984 


Q ss_pred             -eeEEEEecc
Q psy6712         167 -GVAISFVKS  175 (210)
Q Consensus       167 -g~~~~~~~~  175 (210)
                       |.+++.-.+
T Consensus       527 ~G~vI~~~~~  536 (1041)
T COG4581         527 LGTVIVIEPP  536 (1041)
T ss_pred             cceEEEecCC
Confidence             666666444

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

Probab=99.31  E-value=6.2e-11  Score=108.64  Aligned_cols=69  Identities=23%  Similarity=0.467  Sum_probs=60.9

Q ss_pred             eEEEecCCCCHhHHHHHHHHHhcCCC-cEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCC
Q psy6712          95 TVSSMHGDMPQKERDGIMKEFRSGTS-RVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGR  165 (210)
Q Consensus        95 ~~~~~~~~~~~~~r~~~~~~f~~g~~-~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~  165 (210)
                      .+..++|+++  ++.+.++.|++++. .|+|+++++.+|+|+|.+.+||+++++.|...|+||+||+.|...
T Consensus       733 ~v~~itg~~~--~~~~li~~Fk~~~~p~IlVsvdmL~TG~DvP~v~~vVf~rpvkS~~lf~QmIGRgtR~~~  802 (1123)
T PRK11448        733 AVIKITGSID--KPDQLIRRFKNERLPNIVVTVDLLTTGIDVPSICNLVFLRRVRSRILYEQMLGRATRLCP  802 (1123)
T ss_pred             ceEEEeCCcc--chHHHHHHHhCCCCCeEEEEecccccCCCcccccEEEEecCCCCHHHHHHHHhhhccCCc
Confidence            3456778775  46779999999887 689999999999999999999999999999999999999999743

>KOG0922|consensus

Probab=99.28  E-value=2.1e-11  Score=103.18  Aligned_cols=96  Identities=18%  Similarity=0.355  Sum_probs=79.2

Q ss_pred             HHHHHHHHHhc----C----ceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEec--------
Q psy6712          82 VDWLTEKMREA----N----FTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYD--------  145 (210)
Q Consensus        82 ~~~l~~~l~~~----~----~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~--------  145 (210)
                      ++.+++.|.+.    .    .-+.++||.+|.+++.++++.--.|..+++++|++++..+.+|.+.+||..+        
T Consensus       271 Ie~~~~~l~e~~~~~~~~~~~~~lply~aL~~e~Q~rvF~p~p~g~RKvIlsTNIAETSlTI~GI~YVVDsG~vK~~~y~  350 (674)
T KOG0922|consen  271 IEAACELLRERAKSLPEDCPELILPLYGALPSEEQSRVFDPAPPGKRKVILSTNIAETSLTIDGIRYVVDSGFVKQKKYN  350 (674)
T ss_pred             HHHHHHHHHHHhhhccccCcceeeeecccCCHHHhhccccCCCCCcceEEEEcceeeeeEEecceEEEEcCCceEEEeec
Confidence            56666666553    1    1357899999999999999998889999999999999999999999999543        


Q ss_pred             C----------CCChhHHHHhhhhhcCCCCceeEEEEeccCcH
Q psy6712         146 L----------PNNRELYIHRIGRSGRFGRKGVAISFVKSDDI  178 (210)
Q Consensus       146 ~----------p~s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~  178 (210)
                      +          |-|..+-.||.|||||. .+|+|+-++...+.
T Consensus       351 p~~g~~~L~v~~ISkasA~QRaGRAGRt-~pGkcyRLYte~~~  392 (674)
T KOG0922|consen  351 PRTGLDSLIVVPISKASANQRAGRAGRT-GPGKCYRLYTESAY  392 (674)
T ss_pred             cccCccceeEEechHHHHhhhcccCCCC-CCceEEEeeeHHHH
Confidence            2          45788888999999998 57999999987554

>KOG4150|consensus

Probab=99.25  E-value=1.2e-10  Score=97.39  Aligned_cols=102  Identities=19%  Similarity=0.348  Sum_probs=81.6

Q ss_pred             EEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCCceeEEEEec-
Q psy6712          96 VSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVK-  174 (210)
Q Consensus        96 ~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~~g~~~~~~~-  174 (210)
                      +..+.|+.+.++|+++....--|+..-+|+|++++.|+|+...+.|++.++|.|...+.|..|||||.++++.++..+. 
T Consensus       560 i~SYRGGY~A~DRRKIE~~~F~G~L~giIaTNALELGIDIG~LDAVl~~GFP~S~aNl~QQ~GRAGRRNk~SLavyva~~  639 (1034)
T KOG4150|consen  560 ITSYRGGYIAEDRRKIESDLFGGKLCGIIATNALELGIDIGHLDAVLHLGFPGSIANLWQQAGRAGRRNKPSLAVYVAFL  639 (1034)
T ss_pred             HHhhcCccchhhHHHHHHHhhCCeeeEEEecchhhhccccccceeEEEccCchhHHHHHHHhccccccCCCceEEEEEec
Confidence            3447789999999999999999999999999999999999999999999999999999999999999988776655554 


Q ss_pred             -cCcHHHHHHHHHHhcCccccccC
Q psy6712         175 -SDDIRILRDIEQYYSTQIDEMPM  197 (210)
Q Consensus       175 -~~~~~~~~~~~~~~~~~~~~~~~  197 (210)
                       +-+...+..-+..+..+-.++.+
T Consensus       640 ~PVDQ~Y~~HP~~l~~~pN~EL~L  663 (1034)
T KOG4150|consen  640 GPVDQYYMSHPDKLFGSPNEELHL  663 (1034)
T ss_pred             cchhhHhhcCcHHHhCCCcceeEE
Confidence             33444444444444444444333

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

Probab=99.21  E-value=5.4e-10  Score=98.70  Aligned_cols=61  Identities=23%  Similarity=0.552  Sum_probs=54.7

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEe----cCccccCCCCC-CcEEEEecCC
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITT----DVWARGIDVQQ-VSLVINYDLP  147 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T----~~~~~g~d~~~-~~~vi~~~~p  147 (210)
                      ++.+++.|++.|+++..+|+.     .++.++.|..|++++||+.    ..+.+|+|+|. +.++|+++.|
T Consensus       351 aeel~e~Lr~~Gi~a~~~~a~-----~~~~le~F~~GeidvLVGvAsyYG~lVRGlDLP~rirYaIF~GvP  416 (1187)
T COG1110         351 AEELAEYLRSHGINAELIHAE-----KEEALEDFEEGEVDVLVGVASYYGVLVRGLDLPHRIRYAVFYGVP  416 (1187)
T ss_pred             HHHHHHHHHhcCceEEEeecc-----chhhhhhhccCceeEEEEecccccceeecCCchhheeEEEEecCC
Confidence            899999999999999999984     3788999999999999887    47889999995 8899998877

>KOG0923|consensus

Probab=99.13  E-value=2.9e-10  Score=96.35  Aligned_cols=82  Identities=18%  Similarity=0.372  Sum_probs=72.6

Q ss_pred             CceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEec------------------CCCChhHHH
Q psy6712          93 NFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYD------------------LPNNRELYI  154 (210)
Q Consensus        93 ~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~------------------~p~s~~~~~  154 (210)
                      .+-+.++|+.+|.+.+.++++.--.|..+|++||++++..+.++++.+||.-+                  .|-|..+-.
T Consensus       506 eliv~PiYaNLPselQakIFePtP~gaRKVVLATNIAETSlTIdgI~yViDpGf~K~nsynprtGmesL~v~piSKAsA~  585 (902)
T KOG0923|consen  506 ELIVLPIYANLPSELQAKIFEPTPPGARKVVLATNIAETSLTIDGIKYVIDPGFVKQNSYNPRTGMESLLVTPISKASAN  585 (902)
T ss_pred             eEEEeeccccCChHHHHhhcCCCCCCceeEEEeecchhhceeecCeEEEecCccccccCcCCCcCceeEEEeeechhhhh
Confidence            46789999999999999999999889999999999999999999999999533                  245778888


Q ss_pred             HhhhhhcCCCCceeEEEEecc
Q psy6712         155 HRIGRSGRFGRKGVAISFVKS  175 (210)
Q Consensus       155 q~~GR~gR~g~~g~~~~~~~~  175 (210)
                      ||+|||||. .+|+|+-+++.
T Consensus       586 QRaGRAGRt-gPGKCfRLYt~  605 (902)
T KOG0923|consen  586 QRAGRAGRT-GPGKCFRLYTA  605 (902)
T ss_pred             hhccccCCC-CCCceEEeech
Confidence            999999998 47999999974

>KOG0387|consensus

Probab=99.09  E-value=2.4e-09  Score=92.43  Aligned_cols=95  Identities=23%  Similarity=0.327  Sum_probs=82.1

Q ss_pred             HHHHHHHHH-hcCceEEEecCCCCHhHHHHHHHHHhcCCCc--EEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhh
Q psy6712          82 VDWLTEKMR-EANFTVSSMHGDMPQKERDGIMKEFRSGTSR--VLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIG  158 (210)
Q Consensus        82 ~~~l~~~l~-~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~--ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~G  158 (210)
                      .+.+...|. .+++...-+.|..+...|...++.|+++..-  .|++|.+.+.|+|+..++-||.|||.|+|+.=.|..-
T Consensus       559 LdilE~fL~~~~~ysylRmDGtT~~~~R~~lVd~Fne~~s~~VFLLTTrvGGLGlNLTgAnRVIIfDPdWNPStD~QAre  638 (923)
T KOG0387|consen  559 LDILESFLRRAKGYSYLRMDGTTPAALRQKLVDRFNEDESIFVFLLTTRVGGLGLNLTGANRVIIFDPDWNPSTDNQARE  638 (923)
T ss_pred             HHHHHHHHHhcCCceEEEecCCCccchhhHHHHhhcCCCceEEEEEEecccccccccccCceEEEECCCCCCccchHHHH
Confidence            566777776 6899999999999999999999999977653  6789999999999999999999999999999999999


Q ss_pred             hhcCCCCceeEE--EEeccC
Q psy6712         159 RSGRFGRKGVAI--SFVKSD  176 (210)
Q Consensus       159 R~gR~g~~g~~~--~~~~~~  176 (210)
                      ||-|.|+...|+  =+++..
T Consensus       639 RawRiGQkkdV~VYRL~t~g  658 (923)
T KOG0387|consen  639 RAWRIGQKKDVVVYRLMTAG  658 (923)
T ss_pred             HHHhhcCccceEEEEEecCC
Confidence            999999965544  445544

>KOG0920|consensus

Probab=99.09  E-value=3.4e-10  Score=100.34  Aligned_cols=106  Identities=24%  Similarity=0.472  Sum_probs=87.5

Q ss_pred             ceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEE--------ecCC----------CChhHHHH
Q psy6712          94 FTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVIN--------YDLP----------NNRELYIH  155 (210)
Q Consensus        94 ~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~--------~~~p----------~s~~~~~q  155 (210)
                      +-+.++|+.|+..+++.++..--.|..+|+++|++++..+.++++-+||.        ||+-          -|...-.|
T Consensus       445 ~~ilplHs~~~s~eQ~~VF~~pp~g~RKIIlaTNIAETSITIdDVvyVIDsG~~Ke~~yD~~~~~s~l~~~wvSkAna~Q  524 (924)
T KOG0920|consen  445 FAILPLHSSIPSEEQQAVFKRPPKGTRKIILATNIAETSITIDDVVYVIDSGLVKEKSYDPERKVSCLLLSWVSKANAKQ  524 (924)
T ss_pred             eEEEeccccCChHHHHHhcCCCCCCcchhhhhhhhHhhcccccCeEEEEecCeeeeeeecccCCcchhheeeccccchHH
Confidence            67889999999999999999999999999999999999999999999995        4433          35666679


Q ss_pred             hhhhhcCCCCceeEEEEeccCcHHHH---HHHHHHhcCccccccCCcc
Q psy6712         156 RIGRSGRFGRKGVAISFVKSDDIRIL---RDIEQYYSTQIDEMPMNGK  200 (210)
Q Consensus       156 ~~GR~gR~g~~g~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~  200 (210)
                      |.|||||. .+|.|+-+++......+   ..+-+.+...++++.+..+
T Consensus       525 R~GRAGRv-~~G~cy~L~~~~~~~~~~~~~q~PEilR~pL~~l~L~iK  571 (924)
T KOG0920|consen  525 RRGRAGRV-RPGICYHLYTRSRYEKLMLAYQLPEILRTPLEELCLHIK  571 (924)
T ss_pred             hcccccCc-cCCeeEEeechhhhhhcccccCChHHHhChHHHhhheee
Confidence            99999998 89999999987544332   3566777777777776665

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=99.06  E-value=5.5e-09  Score=90.65  Aligned_cols=95  Identities=24%  Similarity=0.305  Sum_probs=74.8

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCC----------c-----EEEEecC
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQV----------S-----LVINYDL  146 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~----------~-----~vi~~~~  146 (210)
                      .+.+++.|.+.++++..+++.-...+-..+.++=+  .-.|.|||++++||.|+---          .     +||-...
T Consensus       440 SE~ls~~L~~~gI~h~vLNAk~~~~EA~IIa~AG~--~gaVTIATNMAGRGTDIkLg~~~~~~~~~V~~~GGLhVIgTer  517 (764)
T PRK12326        440 SEELAERLRAAGVPAVVLNAKNDAEEARIIAEAGK--YGAVTVSTQMAGRGTDIRLGGSDEADRDRVAELGGLHVIGTGR  517 (764)
T ss_pred             HHHHHHHHHhCCCcceeeccCchHhHHHHHHhcCC--CCcEEEEecCCCCccCeecCCCcccchHHHHHcCCcEEEeccC
Confidence            78899999999999999998744443333333322  23689999999999998521          1     8888888


Q ss_pred             CCChhHHHHhhhhhcCCCCceeEEEEeccCcH
Q psy6712         147 PNNRELYIHRIGRSGRFGRKGVAISFVKSDDI  178 (210)
Q Consensus       147 p~s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~  178 (210)
                      +.|..---|..||+||+|.+|.+-.|++-+|.
T Consensus       518 heSrRID~QLrGRaGRQGDpGss~f~lSleDd  549 (764)
T PRK12326        518 HRSERLDNQLRGRAGRQGDPGSSVFFVSLEDD  549 (764)
T ss_pred             CchHHHHHHHhcccccCCCCCceeEEEEcchh
Confidence            99999889999999999999999999986653

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.03  E-value=1.3e-09  Score=96.87  Aligned_cols=92  Identities=23%  Similarity=0.380  Sum_probs=76.6

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHh----cCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhh
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFR----SGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRI  157 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~----~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~  157 (210)
                      +..+.+.|++.+.++..+||.++...|.+.++.++    .....|+|+|++++.|+|+ +.+.+|--  +..+++.+||+
T Consensus       453 Aie~Y~~Lk~~~~~v~LlHSRf~~~dR~~ke~~l~~~~~~~~~~IvVaTQVIEagvDi-dfd~mITe--~aPidSLIQR~  529 (733)
T COG1203         453 AIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQVIEAGVDI-DFDVLITE--LAPIDSLIQRA  529 (733)
T ss_pred             HHHHHHHHHhcCCCEEEEecccchhhHHHHHHHHHHHHhccCCeEEEEeeEEEEEecc-ccCeeeec--CCCHHHHHHHH
Confidence            77888888887778999999999999988888554    4677899999999999999 57777653  66788999999


Q ss_pred             hhhcCCC--CceeEEEEeccC
Q psy6712         158 GRSGRFG--RKGVAISFVKSD  176 (210)
Q Consensus       158 GR~gR~g--~~g~~~~~~~~~  176 (210)
                      ||++|.|  ..|.++++....
T Consensus       530 GRv~R~g~~~~~~~~v~~~~~  550 (733)
T COG1203         530 GRVNRHGKKENGKIYVYNDEE  550 (733)
T ss_pred             HHHhhcccccCCceeEeeccc
Confidence            9999999  467777777653

>KOG0389|consensus

Probab=99.01  E-value=9e-09  Score=88.90  Aligned_cols=95  Identities=18%  Similarity=0.258  Sum_probs=79.8

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCC--cEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhh
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTS--RVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGR  159 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~--~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR  159 (210)
                      .+.|...|.-.++...-+.|......|+..++.|...+.  -.|++|.+.+.|+|+..+++||.+|...++-+=.|.-.|
T Consensus       790 LDILE~~L~~l~~~ylRLDGsTqV~~RQ~lId~Fn~d~difVFLLSTKAGG~GINLt~An~VIihD~dFNP~dD~QAEDR  869 (941)
T KOG0389|consen  790 LDILEVVLDTLGYKYLRLDGSTQVNDRQDLIDEFNTDKDIFVFLLSTKAGGFGINLTCANTVIIHDIDFNPYDDKQAEDR  869 (941)
T ss_pred             HHHHHHHHHhcCceEEeecCCccchHHHHHHHhhccCCceEEEEEeeccCcceecccccceEEEeecCCCCcccchhHHH
Confidence            444555555568888889999999999999999987653  367999999999999999999999999999999999999


Q ss_pred             hcCCCCcee--EEEEeccC
Q psy6712         160 SGRFGRKGV--AISFVKSD  176 (210)
Q Consensus       160 ~gR~g~~g~--~~~~~~~~  176 (210)
                      +.|.|+...  ++-+++..
T Consensus       870 cHRvGQtkpVtV~rLItk~  888 (941)
T KOG0389|consen  870 CHRVGQTKPVTVYRLITKS  888 (941)
T ss_pred             HHhhCCcceeEEEEEEecC
Confidence            999998654  45556654

>cd00268 DEADc DEAD-box helicases

Probab=99.00  E-value=8.3e-09  Score=77.89  Aligned_cols=91  Identities=38%  Similarity=0.710  Sum_probs=75.3

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchh
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ   81 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~   81 (210)
                      ++++..++||.+..+....+.++++|+|+||+++.+.+.++...+++++++|+||+|.+.+.++...+..+...++.   
T Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~l~~lIvDE~h~~~~~~~~~~~~~~~~~l~~---  173 (203)
T cd00268          97 NLKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRMLDMGFEDQIREILKLLPK---  173 (203)
T ss_pred             CceEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCCChhhCCEEEEeChHHhhccChHHHHHHHHHhCCc---
Confidence            67889999999988877777778999999999999999988888999999999999999988887777777765432   


Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHh
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQK  106 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~  106 (210)
                                 +..+..+.+.++..
T Consensus       174 -----------~~~~~~~SAT~~~~  187 (203)
T cd00268         174 -----------DRQTLLFSATMPKE  187 (203)
T ss_pred             -----------ccEEEEEeccCCHH
Confidence                       55666677766643

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.

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=99.00  E-value=9.9e-09  Score=90.40  Aligned_cols=94  Identities=28%  Similarity=0.402  Sum_probs=74.2

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcC-CCcEEEEecCccccCCCCCCc--------EEEEecCCCChhH
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSG-TSRVLITTDVWARGIDVQQVS--------LVINYDLPNNREL  152 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~ilv~T~~~~~g~d~~~~~--------~vi~~~~p~s~~~  152 (210)
                      .+.+++.|.+.|+++..+++.-...+-.-+  + +.| .-.|.|||++++||.|+.--.        +||....|.|..-
T Consensus       439 SE~ls~~L~~~gi~h~vLNAk~~e~EA~II--a-~AG~~GaVTIATNMAGRGTDI~Lg~~V~~~GGLhVIgTerheSrRI  515 (925)
T PRK12903        439 SETLHELLLEANIPHTVLNAKQNAREAEII--A-KAGQKGAITIATNMAGRGTDIKLSKEVLELGGLYVLGTDKAESRRI  515 (925)
T ss_pred             HHHHHHHHHHCCCCceeecccchhhHHHHH--H-hCCCCCeEEEecccccCCcCccCchhHHHcCCcEEEecccCchHHH
Confidence            788999999999999999987433333322  2 334 346899999999999985322        8999889999888


Q ss_pred             HHHhhhhhcCCCCceeEEEEeccCcH
Q psy6712         153 YIHRIGRSGRFGRKGVAISFVKSDDI  178 (210)
Q Consensus       153 ~~q~~GR~gR~g~~g~~~~~~~~~~~  178 (210)
                      --|..||+||+|.+|.+-.|++-.|.
T Consensus       516 DnQLrGRaGRQGDpGss~f~lSLeD~  541 (925)
T PRK12903        516 DNQLRGRSGRQGDVGESRFFISLDDQ  541 (925)
T ss_pred             HHHHhcccccCCCCCcceEEEecchH
Confidence            88999999999999999888886543

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=98.97  E-value=5.9e-09  Score=92.41  Aligned_cols=95  Identities=21%  Similarity=0.321  Sum_probs=73.0

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCC-C-----------------------
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQ-Q-----------------------  137 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~-~-----------------------  137 (210)
                      .+.+++.|...++++-.+++.....+-.-+.++-+  .-.|.|||++++||.|+- .                       
T Consensus       462 SE~ls~~L~~~gi~h~VLNAk~~~~EA~IIa~AG~--~GaVTIATNMAGRGTDIkLg~n~~~~~~~~~~~~~~~~~~~~~  539 (913)
T PRK13103        462 SEHMSNLLKKEGIEHKVLNAKYHEKEAEIIAQAGR--PGALTIATNMAGRGTDILLGGNWEVEVAALENPTPEQIAQIKA  539 (913)
T ss_pred             HHHHHHHHHHcCCcHHHhccccchhHHHHHHcCCC--CCcEEEeccCCCCCCCEecCCchHHHHHhhhhhhHHHHHHHHH
Confidence            68889999999998888888744433333333322  336899999999999983 1                       


Q ss_pred             --------Cc-----EEEEecCCCChhHHHHhhhhhcCCCCceeEEEEeccCcH
Q psy6712         138 --------VS-----LVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDI  178 (210)
Q Consensus       138 --------~~-----~vi~~~~p~s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~  178 (210)
                              +.     +||-...+.|..-=-|..||+||+|.+|.+-.|++-+|.
T Consensus       540 ~~~~~~e~V~e~GGLhVIgTerheSrRID~QLrGRaGRQGDPGsS~f~lSlED~  593 (913)
T PRK13103        540 DWQKRHQQVIEAGGLHVIASERHESRRIDNQLRGRAGRQGDPGSSRFYLSLEDS  593 (913)
T ss_pred             HHHhHHHHHHHcCCCEEEeeccCchHHHHHHhccccccCCCCCceEEEEEcCcH
Confidence                    11     778788888888888999999999999999999987543

>KOG0924|consensus

Probab=98.95  E-value=2.9e-09  Score=90.74  Aligned_cols=93  Identities=18%  Similarity=0.391  Sum_probs=78.6

Q ss_pred             HHHHHHHHHh------cCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEec----------
Q psy6712          82 VDWLTEKMRE------ANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYD----------  145 (210)
Q Consensus        82 ~~~l~~~l~~------~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~----------  145 (210)
                      +..+.+.|.+      .++.+..+++.+|..-+.+++..-..|..+++|+|++++..+.+|++.+||..+          
T Consensus       580 ~~~i~~~l~ql~~~~~~~L~vlpiYSQLp~dlQ~kiFq~a~~~vRK~IvATNIAETSLTi~gI~yVID~Gy~K~kvyn~~  659 (1042)
T KOG0924|consen  580 CDIIKEKLEQLDSAPTTDLAVLPIYSQLPADLQAKIFQKAEGGVRKCIVATNIAETSLTIPGIRYVIDTGYCKLKVYNPR  659 (1042)
T ss_pred             HHHHHHHHHhhhcCCCCceEEEeehhhCchhhhhhhcccCCCCceeEEEeccchhhceeecceEEEEecCceeeeecccc
Confidence            4555555544      268999999999999999999988889999999999999999999999999654          


Q ss_pred             --------CCCChhHHHHhhhhhcCCCCceeEEEEecc
Q psy6712         146 --------LPNNRELYIHRIGRSGRFGRKGVAISFVKS  175 (210)
Q Consensus       146 --------~p~s~~~~~q~~GR~gR~g~~g~~~~~~~~  175 (210)
                              .|-|...-.||.|||||. .+|.|+-++..
T Consensus       660 ~G~D~L~~~pIS~AnA~QRaGRAGRt-~pG~cYRlYTe  696 (1042)
T KOG0924|consen  660 IGMDALQIVPISQANADQRAGRAGRT-GPGTCYRLYTE  696 (1042)
T ss_pred             cccceeEEEechhccchhhccccCCC-CCcceeeehhh
Confidence                    356777788999999998 57899988876

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

Probab=98.94  E-value=5e-09  Score=76.57  Aligned_cols=75  Identities=23%  Similarity=0.451  Sum_probs=61.1

Q ss_pred             CceEEEEEcCcchH-HHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhC
Q psy6712           2 NVQCHACIGGTNLS-EDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYL   76 (210)
Q Consensus         2 ~i~~~~~~gg~~~~-~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~   76 (210)
                      ++++..++||.+.. .+...+.++++|+|+||+++.+.+..+..++.+++++|+||+|.+.++.+...+..++..+
T Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~iViDE~h~l~~~~~~~~~~~i~~~~  147 (169)
T PF00270_consen   72 NVRVVLLHGGQSISEDQREVLSNQADILVTTPEQLLDLISNGKINISRLSLIVIDEAHHLSDETFRAMLKSILRRL  147 (169)
T ss_dssp             TSSEEEESTTSCHHHHHHHHHHTTSSEEEEEHHHHHHHHHTTSSTGTTESEEEEETHHHHHHTTHHHHHHHHHHHS
T ss_pred             ccccccccccccccccccccccccccccccCcchhhccccccccccccceeeccCcccccccccHHHHHHHHHHHh
Confidence            56888999999866 4445556789999999999999999876688889999999999999877777666666443

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 ....

>KOG0390|consensus

Probab=98.84  E-value=2.5e-08  Score=87.32  Aligned_cols=91  Identities=20%  Similarity=0.306  Sum_probs=77.9

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCc---EEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhh
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSR---VLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIG  158 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~---ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~G  158 (210)
                      .+.+.+..+.+|..+..++|.|+..+|..+++.|+.....   .|.+|-+.+.|+++-.++.+|.||++|+|+.-.|.++
T Consensus       608 ldl~e~~~~~~g~~~~rLdG~~~~~qRq~~vd~FN~p~~~~~vfLlSsKAgg~GinLiGAsRlil~D~dWNPa~d~QAma  687 (776)
T KOG0390|consen  608 LDLFEQLCRWRGYEVLRLDGKTSIKQRQKLVDTFNDPESPSFVFLLSSKAGGEGLNLIGASRLILFDPDWNPAVDQQAMA  687 (776)
T ss_pred             HHHHHHHHhhcCceEEEEcCCCchHHHHHHHHhccCCCCCceEEEEecccccCceeecccceEEEeCCCCCchhHHHHHH
Confidence            4444555566799999999999999999999999975443   5677789999999999999999999999999999999


Q ss_pred             hhcCCCCceeEEEE
Q psy6712         159 RSGRFGRKGVAISF  172 (210)
Q Consensus       159 R~gR~g~~g~~~~~  172 (210)
                      ||-|.|+.-.|+++
T Consensus       688 R~~RdGQKk~v~iY  701 (776)
T KOG0390|consen  688 RAWRDGQKKPVYIY  701 (776)
T ss_pred             HhccCCCcceEEEE
Confidence            99999997655544

>KOG1123|consensus

Probab=98.83  E-value=5.9e-07  Score=74.65  Aligned_cols=85  Identities=21%  Similarity=0.308  Sum_probs=67.7

Q ss_pred             EecCCCCHhHHHHHHHHHh-cCCCcEEEEecCccccCCCCCCcEEEEecCC-CChhHHHHhhhhhcCCCC------ceeE
Q psy6712          98 SMHGDMPQKERDGIMKEFR-SGTSRVLITTDVWARGIDVQQVSLVINYDLP-NNRELYIHRIGRSGRFGR------KGVA  169 (210)
Q Consensus        98 ~~~~~~~~~~r~~~~~~f~-~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p-~s~~~~~q~~GR~gR~g~------~g~~  169 (210)
                      +++|..++.+|.++++.|+ +.++..++.+-..-..+|+|.++++|+...- .|..+--||.||..|..+      ....
T Consensus       567 fIYG~Tsq~ERm~ILqnFq~n~~vNTIFlSKVgDtSiDLPEAnvLIQISSH~GSRRQEAQRLGRILRAKk~~de~fnafF  646 (776)
T KOG1123|consen  567 FIYGPTSQNERMKILQNFQTNPKVNTIFLSKVGDTSIDLPEANVLIQISSHGGSRRQEAQRLGRILRAKKRNDEEFNAFF  646 (776)
T ss_pred             eEECCCchhHHHHHHHhcccCCccceEEEeeccCccccCCcccEEEEEcccccchHHHHHHHHHHHHHhhcCccccceee
Confidence            4889999999999999998 4567788888888999999999999986543 577888899999888733      3557


Q ss_pred             EEEeccCcHHHHH
Q psy6712         170 ISFVKSDDIRILR  182 (210)
Q Consensus       170 ~~~~~~~~~~~~~  182 (210)
                      +++++.+..+++.
T Consensus       647 YSLVS~DTqEM~Y  659 (776)
T KOG1123|consen  647 YSLVSKDTQEMYY  659 (776)
T ss_pred             eeeeecchHHHHh
Confidence            7777776555443

>COG4889 Predicted helicase [General function prediction only]

Probab=98.73  E-value=4.1e-08  Score=86.06  Aligned_cols=72  Identities=21%  Similarity=0.393  Sum_probs=58.9

Q ss_pred             ceEEEecCCCCHhHHHHHHH---HHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCC
Q psy6712          94 FTVSSMHGDMPQKERDGIMK---EFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGR  165 (210)
Q Consensus        94 ~~~~~~~~~~~~~~r~~~~~---~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~  165 (210)
                      +.+.-+.|.|+-.+|....+   .|...+++||--..++++|+|+|..+-||++++-.+..+.+|.+||+.|...
T Consensus       500 iSi~HvDGtmNal~R~~l~~l~~~~~~neckIlSNaRcLSEGVDVPaLDsViFf~pr~smVDIVQaVGRVMRKa~  574 (1518)
T COG4889         500 ISIDHVDGTMNALERLDLLELKNTFEPNECKILSNARCLSEGVDVPALDSVIFFDPRSSMVDIVQAVGRVMRKAK  574 (1518)
T ss_pred             EEeecccccccHHHHHHHHhccCCCCcchheeeccchhhhcCCCccccceEEEecCchhHHHHHHHHHHHHHhCc
Confidence            34444568899888844333   2345678899999999999999999999999999999999999999999743

>KOG1002|consensus

Probab=98.70  E-value=1.8e-06  Score=71.73  Aligned_cols=94  Identities=20%  Similarity=0.307  Sum_probs=77.4

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcC-CCcEE-EEecCccccCCCCCCcEEEEecCCCChhHHHHhhhh
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSG-TSRVL-ITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGR  159 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~il-v~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR  159 (210)
                      .+.+.-.|.+.|+++.-+.|+|++..|...++.|.+. +++|+ ++-.+.+..+|+..+.+|+.+|+.|++.--+|.-.|
T Consensus       651 LDLi~~rL~kaGfscVkL~GsMs~~ardatik~F~nd~~c~vfLvSLkAGGVALNLteASqVFmmDPWWNpaVe~Qa~DR  730 (791)
T KOG1002|consen  651 LDLIEWRLGKAGFSCVKLVGSMSPAARDATIKYFKNDIDCRVFLVSLKAGGVALNLTEASQVFMMDPWWNPAVEWQAQDR  730 (791)
T ss_pred             HHHHHHHhhccCceEEEeccCCChHHHHHHHHHhccCCCeEEEEEEeccCceEeeechhceeEeecccccHHHHhhhhhh
Confidence            3445555666799999999999999999999999864 45554 555777788999999999999999999999999999


Q ss_pred             hcCCCC--ceeEEEEecc
Q psy6712         160 SGRFGR--KGVAISFVKS  175 (210)
Q Consensus       160 ~gR~g~--~g~~~~~~~~  175 (210)
                      ..|.|+  +=+++-|+-+
T Consensus       731 iHRIGQ~rPvkvvrf~iE  748 (791)
T KOG1002|consen  731 IHRIGQYRPVKVVRFCIE  748 (791)
T ss_pred             HHhhcCccceeEEEeehh
Confidence            999998  4456666654

>KOG0386|consensus

Probab=98.68  E-value=5e-07  Score=80.20  Aligned_cols=93  Identities=20%  Similarity=0.304  Sum_probs=80.3

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCc---EEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhh
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSR---VLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIG  158 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~---ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~G  158 (210)
                      ...+..+|.-.++...-+.|....++|-..++.|+..+..   .|.+|...+.|+|+..++.||.||..|++....|+-.
T Consensus       739 mdimEdyL~~~~~kYlRLDG~TK~~eRg~ll~~FN~Pds~yf~FllstragglglNlQtadtviifdsdwnp~~d~qaqd  818 (1157)
T KOG0386|consen  739 MDILEDYLQIREYKYLRLDGQTKVEERGDLLEIFNAPDSPYFIFLLSTRAGGLGLNLQTADTVIIFDSDWNPHQDLQAQD  818 (1157)
T ss_pred             HHHHHHHHhhhhhheeeecCCcchhhHHHHHHHhcCCCCceeeeeeeecccccccchhhcceEEEecCCCCchhHHHHHH
Confidence            4456666766788889999999999999999999977654   6799999999999999999999999999999999999


Q ss_pred             hhcCCCCceeEEEEec
Q psy6712         159 RSGRFGRKGVAISFVK  174 (210)
Q Consensus       159 R~gR~g~~g~~~~~~~  174 (210)
                      ||.|.|+...+-++..
T Consensus       819 rahrigq~~evRv~rl  834 (1157)
T KOG0386|consen  819 RAHRIGQKKEVRVLRL  834 (1157)
T ss_pred             HHHHhhchhheeeeee
Confidence            9999998665555543

>KOG0392|consensus

Probab=98.67  E-value=4.3e-07  Score=82.04  Aligned_cols=78  Identities=24%  Similarity=0.403  Sum_probs=67.8

Q ss_pred             EecCCCCHhHHHHHHHHHhcC-CCcEE-EEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCCcee--EEEEe
Q psy6712          98 SMHGDMPQKERDGIMKEFRSG-TSRVL-ITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGV--AISFV  173 (210)
Q Consensus        98 ~~~~~~~~~~r~~~~~~f~~g-~~~il-v~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~~g~--~~~~~  173 (210)
                      -+.|..++.+|.++.++|+++ .+++| ++|...+.|+|+..++.||+++=.|++..=+|.+.||.|.|++-.  ++=++
T Consensus      1372 RLDGSVpp~~R~kiV~~FN~DptIDvLlLTThVGGLGLNLTGADTVVFvEHDWNPMrDLQAMDRAHRIGQKrvVNVyRlI 1451 (1549)
T KOG0392|consen 1372 RLDGSVPPGDRQKIVERFNEDPTIDVLLLTTHVGGLGLNLTGADTVVFVEHDWNPMRDLQAMDRAHRIGQKRVVNVYRLI 1451 (1549)
T ss_pred             EecCCCCcHHHHHHHHHhcCCCceeEEEEeeeccccccccCCCceEEEEecCCCchhhHHHHHHHHhhcCceeeeeeeeh
Confidence            578999999999999999998 67765 777899999999999999999999999999999999999998654  34444


Q ss_pred             cc
Q psy6712         174 KS  175 (210)
Q Consensus       174 ~~  175 (210)
                      ..
T Consensus      1452 tr 1453 (1549)
T KOG0392|consen 1452 TR 1453 (1549)
T ss_pred             hc
Confidence            43

>KOG0926|consensus

Probab=98.66  E-value=2.9e-08  Score=86.12  Aligned_cols=82  Identities=16%  Similarity=0.251  Sum_probs=68.5

Q ss_pred             ceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCC------------------CChhHHHH
Q psy6712          94 FTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLP------------------NNRELYIH  155 (210)
Q Consensus        94 ~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p------------------~s~~~~~q  155 (210)
                      .-|..+++-++.+.+..+++.--.|..=++|+|+.++..+.+|++.+||..+..                  -|..+--|
T Consensus       605 LyvLPLYSLLs~~~Q~RVF~~~p~g~RLcVVaTNVAETSLTIPgIkYVVD~Gr~K~R~Yd~~TGV~~FeV~wiSkASadQ  684 (1172)
T KOG0926|consen  605 LYVLPLYSLLSTEKQMRVFDEVPKGERLCVVATNVAETSLTIPGIKYVVDCGRVKERLYDSKTGVSSFEVDWISKASADQ  684 (1172)
T ss_pred             eEEeehhhhcCHHHhhhhccCCCCCceEEEEeccchhcccccCCeeEEEeccchhhhccccccCceeEEEEeeeccccch
Confidence            467788888999999999998888888899999999999999999999965432                  23444559


Q ss_pred             hhhhhcCCCCceeEEEEeccC
Q psy6712         156 RIGRSGRFGRKGVAISFVKSD  176 (210)
Q Consensus       156 ~~GR~gR~g~~g~~~~~~~~~  176 (210)
                      |+|||||. ..|.|+-++++.
T Consensus       685 RAGRAGRt-gpGHcYRLYSSA  704 (1172)
T KOG0926|consen  685 RAGRAGRT-GPGHCYRLYSSA  704 (1172)
T ss_pred             hccccCCC-CCCceeehhhhH
Confidence            99999998 479999999863

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=98.65  E-value=1.1e-06  Score=77.99  Aligned_cols=59  Identities=17%  Similarity=0.260  Sum_probs=41.8

Q ss_pred             CCceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHH-HHHHhcC------ccCCCccEEEechhhHHh
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVF-DMIRRRV------LRTRNIKMLVLDEADEML   61 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~-~~l~~~~------~~~~~~~~lviDE~~~l~   61 (210)
                      +|++|.++.++.+..+..+..  .+||..+|...+- +.|+.+.      .-...+.+.|+||+|.++
T Consensus       144 LGLsvg~i~~~~~~~err~aY--~~DItYgTn~e~gFDyLRDnm~~~~~~~v~r~~~faIVDEvDSiL  209 (870)
T CHL00122        144 LGLTVGLIQEGMSSEERKKNY--LKDITYVTNSELGFDYLRDNMALSLSDVVQRPFNYCIIDEVDSIL  209 (870)
T ss_pred             cCCceeeeCCCCChHHHHHhc--CCCCEecCCccccccchhhccCcChHHhhccccceeeeecchhhe
Confidence            689999999988876544443  6799999995432 3333322      124678899999999985

>PF06862 DUF1253: Protein of unknown function (DUF1253); InterPro: IPR010678 This family is defined by a C-terminal region of approximately 500 residues, Digestive organ expansion factor (DEF) is thought to Regulate the p53 pathway to control the expansion growth of digestive organs and is required for the expansion growth of intestine, liver and exocrine pancreas, but not endocrine pancreas [, ]

Probab=98.62  E-value=4.1e-06  Score=69.77  Aligned_cols=100  Identities=16%  Similarity=0.246  Sum_probs=80.0

Q ss_pred             HHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEec--CccccCCCCCCcEEEEecCCCChhHHHHhhhhhcC
Q psy6712          85 LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTD--VWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGR  162 (210)
Q Consensus        85 l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~--~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR  162 (210)
                      +-.+|++.++....++.-.+..+....-..|..|+.++|+.|.  -.-+-..+.++..||.|.+|..+.=|...++..+.
T Consensus       316 lRN~lk~~~~sF~~i~EYts~~~isRAR~~F~~G~~~iLL~TER~HFfrRy~irGi~~viFY~~P~~p~fY~El~n~~~~  395 (442)
T PF06862_consen  316 LRNYLKKENISFVQISEYTSNSDISRARSQFFHGRKPILLYTERFHFFRRYRIRGIRHVIFYGPPENPQFYSELLNMLDE  395 (442)
T ss_pred             HHHHHHhcCCeEEEecccCCHHHHHHHHHHHHcCCceEEEEEhHHhhhhhceecCCcEEEEECCCCChhHHHHHHhhhcc
Confidence            4455666788899999999999999999999999999999995  23344567789999999999999999998866554


Q ss_pred             CCC------ceeEEEEeccCcHHHHHHH
Q psy6712         163 FGR------KGVAISFVKSDDIRILRDI  184 (210)
Q Consensus       163 ~g~------~g~~~~~~~~~~~~~~~~~  184 (210)
                      ...      ...|.++++.-|...++.+
T Consensus       396 ~~~~~~~~~~~~~~~lysk~D~~~LErI  423 (442)
T PF06862_consen  396 SSGGEVDAADATVTVLYSKYDALRLERI  423 (442)
T ss_pred             cccccccccCceEEEEecHhHHHHHHHH
Confidence            432      4678999988777665544

; GO: 0005634 nucleus

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

Probab=98.54  E-value=6.5e-07  Score=78.33  Aligned_cols=67  Identities=22%  Similarity=0.398  Sum_probs=52.1

Q ss_pred             eEEEecCCCCHhHHHHHHHHHhc-C-CCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCC
Q psy6712          95 TVSSMHGDMPQKERDGIMKEFRS-G-TSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRF  163 (210)
Q Consensus        95 ~~~~~~~~~~~~~r~~~~~~f~~-g-~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~  163 (210)
                      -+..+.++-...  +..++.|.. . .-+|.++.+++..|+|.|.|-.++.+..-.|...|.||+||+-|.
T Consensus       457 ~a~~IT~d~~~~--q~~Id~f~~ke~~P~IaitvdlL~TGiDvpev~nlVF~r~VrSktkF~QMvGRGTRl  525 (875)
T COG4096         457 YAMKITGDAEQA--QALIDNFIDKEKYPRIAITVDLLTTGVDVPEVVNLVFDRKVRSKTKFKQMVGRGTRL  525 (875)
T ss_pred             eEEEEeccchhh--HHHHHHHHhcCCCCceEEehhhhhcCCCchheeeeeehhhhhhHHHHHHHhcCcccc
Confidence            455555554333  334566654 2 336889999999999999999999999999999999999999886

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=98.53  E-value=2.9e-06  Score=75.54  Aligned_cols=59  Identities=17%  Similarity=0.222  Sum_probs=42.8

Q ss_pred             CCceEEEEEcCcchHHHHHHhcCCCcEEEEChHHH-----HHHHHh--cCccCCCccEEEechhhHHh
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRV-----FDMIRR--RVLRTRNIKMLVLDEADEML   61 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l-----~~~l~~--~~~~~~~~~~lviDE~~~l~   61 (210)
                      +|++|.++.++.+..+..  -.-.+||+.+|+..+     .+.+..  +......+.+.|+||+|.++
T Consensus       153 LGLtvg~i~~~~~~~err--~aY~~DItYgTn~e~gFDYLRDnm~~~~~~~vqR~~~faIVDEvDSIL  218 (939)
T PRK12902        153 LGLSVGLIQQDMSPEERK--KNYACDITYATNSELGFDYLRDNMATDISEVVQRPFNYCVIDEVDSIL  218 (939)
T ss_pred             hCCeEEEECCCCChHHHH--HhcCCCeEEecCCcccccchhhhhcccccccccCccceEEEeccccee
Confidence            689999998887665433  334889999999876     444332  22335788899999999985

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

Probab=98.44  E-value=3e-05  Score=68.73  Aligned_cols=54  Identities=17%  Similarity=0.260  Sum_probs=46.2

Q ss_pred             HHHHHHHhc-CCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCC
Q psy6712         109 DGIMKEFRS-GTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRF  163 (210)
Q Consensus       109 ~~~~~~f~~-g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~  163 (210)
                      ...+++|+. +..++||+++++..|+|.|.+++++...+-.+ ..++|.+||+.|.
T Consensus       580 ~~~~~~Fk~~~~~~ilIVvdmllTGFDaP~l~tLyldKplk~-h~LlQai~R~nR~  634 (667)
T TIGR00348       580 YKDLERFKKEENPKLLIVVDMLLTGFDAPILNTLYLDKPLKY-HGLLQAIARTNRI  634 (667)
T ss_pred             HHHHHHhcCCCCceEEEEEcccccccCCCccceEEEeccccc-cHHHHHHHHhccc
Confidence            467888875 67899999999999999999999988776555 4589999999994

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

>KOG1000|consensus

Probab=98.34  E-value=6.9e-06  Score=68.32  Aligned_cols=94  Identities=17%  Similarity=0.308  Sum_probs=77.2

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCC-Cc-EEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhh
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGT-SR-VLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGR  159 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~-~~-ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR  159 (210)
                      .+-+...+.++++...-+.|..+..+|....+.|...+ .. -+++..+++.|+++...+.|++..++|++.-.+|.-.|
T Consensus       505 Ld~Iq~~~~~r~vg~IRIDGst~s~~R~ll~qsFQ~seev~VAvlsItA~gvGLt~tAa~~VVFaEL~wnPgvLlQAEDR  584 (689)
T KOG1000|consen  505 LDTIQVEVNKRKVGSIRIDGSTPSHRRTLLCQSFQTSEEVRVAVLSITAAGVGLTLTAASVVVFAELHWNPGVLLQAEDR  584 (689)
T ss_pred             HHHHHHHHHHcCCCeEEecCCCCchhHHHHHHHhccccceEEEEEEEeecccceeeeccceEEEEEecCCCceEEechhh
Confidence            45566666777888999999999999999999998654 33 34666889999999999999999999999999999999


Q ss_pred             hcCCCCcee--EEEEecc
Q psy6712         160 SGRFGRKGV--AISFVKS  175 (210)
Q Consensus       160 ~gR~g~~g~--~~~~~~~  175 (210)
                      +.|.|+.+.  ++.|+..
T Consensus       585 aHRiGQkssV~v~ylvAK  602 (689)
T KOG1000|consen  585 AHRIGQKSSVFVQYLVAK  602 (689)
T ss_pred             hhhccccceeeEEEEEec
Confidence            999998654  3334443

>KOG0925|consensus

Probab=98.33  E-value=2.6e-06  Score=70.67  Aligned_cols=77  Identities=19%  Similarity=0.404  Sum_probs=57.3

Q ss_pred             ceEEEecCCCCHhHHHHHHHHHh---cC--CCcEEEEecCccccCCCCCCcEEEEecC------------------CCCh
Q psy6712          94 FTVSSMHGDMPQKERDGIMKEFR---SG--TSRVLITTDVWARGIDVQQVSLVINYDL------------------PNNR  150 (210)
Q Consensus        94 ~~~~~~~~~~~~~~r~~~~~~f~---~g--~~~ilv~T~~~~~g~d~~~~~~vi~~~~------------------p~s~  150 (210)
                      +++..+|    +.++..+++..-   +|  ..+++|+|++++..+.++.+.+||.-++                  |-|.
T Consensus       287 l~v~PLy----P~~qq~iFep~p~~~~~~~~RkvVvstniaetsltidgiv~VIDpGf~kqkVYNPRIRvesllv~PISk  362 (699)
T KOG0925|consen  287 LKVVPLY----PAQQQRIFEPAPEKRNGAYGRKVVVSTNIAETSLTIDGIVFVIDPGFSKQKVYNPRIRVESLLVSPISK  362 (699)
T ss_pred             ceEEecC----chhhccccCCCCcccCCCccceEEEEecchheeeeeccEEEEecCchhhhcccCcceeeeeeeeccchH
Confidence            5777787    333333333322   12  2379999999999999999999996442                  5677


Q ss_pred             hHHHHhhhhhcCCCCceeEEEEecc
Q psy6712         151 ELYIHRIGRSGRFGRKGVAISFVKS  175 (210)
Q Consensus       151 ~~~~q~~GR~gR~g~~g~~~~~~~~  175 (210)
                      .+-.||.|||||. ++|+|+.++.+
T Consensus       363 asA~qR~gragrt-~pGkcfrLYte  386 (699)
T KOG0925|consen  363 ASAQQRAGRAGRT-RPGKCFRLYTE  386 (699)
T ss_pred             hHHHHHhhhccCC-CCCceEEeecH
Confidence            8888999999997 78999999975

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=98.29  E-value=1e-06  Score=79.25  Aligned_cols=98  Identities=21%  Similarity=0.340  Sum_probs=77.6

Q ss_pred             chhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCC---CCc-----EEEEecCCCCh
Q psy6712          79 ATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQ---QVS-----LVINYDLPNNR  150 (210)
Q Consensus        79 ~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~---~~~-----~vi~~~~p~s~  150 (210)
                      ....+.+++.|...|+++-++++..-..+-.-+.++=+.  -.|-|||++++||.|+-   .+.     +||-...+.|.
T Consensus       638 Ve~SE~lS~~L~~~gI~H~VLNAK~h~~EAeIVA~AG~~--GaVTIATNMAGRGTDIkLg~~V~e~GGL~VIgTerheSr  715 (1112)
T PRK12901        638 VEISELLSRMLKMRKIPHNVLNAKLHQKEAEIVAEAGQP--GTVTIATNMAGRGTDIKLSPEVKAAGGLAIIGTERHESR  715 (1112)
T ss_pred             HHHHHHHHHHHHHcCCcHHHhhccchhhHHHHHHhcCCC--CcEEEeccCcCCCcCcccchhhHHcCCCEEEEccCCCcH
Confidence            344889999999999999999887554444444444333  36899999999999985   222     78888889999


Q ss_pred             hHHHHhhhhhcCCCCceeEEEEeccCcH
Q psy6712         151 ELYIHRIGRSGRFGRKGVAISFVKSDDI  178 (210)
Q Consensus       151 ~~~~q~~GR~gR~g~~g~~~~~~~~~~~  178 (210)
                      .---|..||+||+|.+|.+-.|++-+|.
T Consensus       716 RID~QLrGRaGRQGDPGsS~f~lSLEDd  743 (1112)
T PRK12901        716 RVDRQLRGRAGRQGDPGSSQFYVSLEDN  743 (1112)
T ss_pred             HHHHHHhcccccCCCCCcceEEEEcccH
Confidence            9999999999999999999999986543

>KOG0951|consensus

Probab=98.29  E-value=3.1e-06  Score=76.94  Aligned_cols=81  Identities=14%  Similarity=0.278  Sum_probs=64.3

Q ss_pred             ecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEE-----ec------CCCChhHHHHhhhhhcCCCCce
Q psy6712          99 MHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVIN-----YD------LPNNRELYIHRIGRSGRFGRKG  167 (210)
Q Consensus        99 ~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~-----~~------~p~s~~~~~q~~GR~gR~g~~g  167 (210)
                      =|.+++.....-+-..|..|.+.++|.+.- .+|..... +.|+.     ||      .+.+....+|+.|+|.|   .|
T Consensus      1411 g~e~~s~~d~~iv~~l~e~g~i~v~v~s~~-~~~~~~~~-~lVvvmgt~~ydg~e~~~~~y~i~~ll~m~G~a~~---~~ 1485 (1674)
T KOG0951|consen 1411 GHEGLSSNDQEIVQQLFEAGAIQVCVMSRD-CYGTKLKA-HLVVVMGTQYYDGKEHSYEDYPIAELLQMVGLASG---AG 1485 (1674)
T ss_pred             cccccCcchHHHHHHHHhcCcEEEEEEEcc-cccccccc-eEEEEecceeecccccccccCchhHHHHHhhhhcC---Cc
Confidence            399999999999999999999999998877 77766633 44442     33      35679999999999988   57


Q ss_pred             eEEEEeccCcHHHHHHH
Q psy6712         168 VAISFVKSDDIRILRDI  184 (210)
Q Consensus       168 ~~~~~~~~~~~~~~~~~  184 (210)
                      .|++++.......++++
T Consensus      1486 k~vi~~~~~~k~yykkf 1502 (1674)
T KOG0951|consen 1486 KCVIMCHTPKKEYYKKF 1502 (1674)
T ss_pred             cEEEEecCchHHHHHHh
Confidence            89999998877766544

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

Probab=98.26  E-value=3.9e-06  Score=76.41  Aligned_cols=106  Identities=18%  Similarity=0.319  Sum_probs=86.6

Q ss_pred             HHHhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcC--CCcEEEEecCccccCCCCCCcEEEEecCCC
Q psy6712          71 DVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSG--TSRVLITTDVWARGIDVQQVSLVINYDLPN  148 (210)
Q Consensus        71 ~i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g--~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~  148 (210)
                      +++.+.+.......+...+...++....++|.++.+.|...++.|.++  ..-.++++.+.+.|+|+..+++||+||++|
T Consensus       713 kvlifsq~t~~l~il~~~l~~~~~~~~~ldG~~~~~~r~~~i~~f~~~~~~~v~lls~kagg~glnLt~a~~vi~~d~~w  792 (866)
T COG0553         713 KVLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLKAGGLGLNLTGADTVILFDPWW  792 (866)
T ss_pred             cEEEEeCcHHHHHHHHHHHHhcCCcEEEEeCCCChhhHHHHHHHhhcCCCCceEEEEecccccceeecccceEEEecccc
Confidence            334444444447778888888888999999999999999999999986  334667778999999999999999999999


Q ss_pred             ChhHHHHhhhhhcCCCCcee--EEEEeccC
Q psy6712         149 NRELYIHRIGRSGRFGRKGV--AISFVKSD  176 (210)
Q Consensus       149 s~~~~~q~~GR~gR~g~~g~--~~~~~~~~  176 (210)
                      ++....|...|+.|.|+...  ++-++...
T Consensus       793 np~~~~Qa~dRa~RigQ~~~v~v~r~i~~~  822 (866)
T COG0553         793 NPAVELQAIDRAHRIGQKRPVKVYRLITRG  822 (866)
T ss_pred             ChHHHHHHHHHHHHhcCcceeEEEEeecCC
Confidence            99999999999999998655  44444443

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=98.17  E-value=1.2e-05  Score=72.86  Aligned_cols=69  Identities=20%  Similarity=0.227  Sum_probs=53.1

Q ss_pred             ceEEEecCCCCHhHHHHHHHHH----------------------hc----CCCcEEEEecCccccCCCCCCcEEEEecCC
Q psy6712          94 FTVSSMHGDMPQKERDGIMKEF----------------------RS----GTSRVLITTDVWARGIDVQQVSLVINYDLP  147 (210)
Q Consensus        94 ~~~~~~~~~~~~~~r~~~~~~f----------------------~~----g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p  147 (210)
                      +...++|+..+...|..+.+..                      .+    +...|+|+|++++.|+|+ +.+.+|-  -|
T Consensus       787 i~~~~yHSr~~l~~Rs~~E~~Ld~~L~R~~~~~~~~~~~i~~~l~~~~~~~~~~i~v~Tqv~E~g~D~-dfd~~~~--~~  863 (1110)
T TIGR02562       787 IHLCCYHAQDPLLLRSYIERRLDQLLTRHKPEQLFQDDEIIDLMQNSPALNHLFIVLATPVEEVGRDH-DYDWAIA--DP  863 (1110)
T ss_pred             eeEEEecccChHHHHHHHHHHHHHHhcccChhhhhchHHHHHHHhcccccCCCeEEEEeeeEEEEecc-cCCeeee--cc
Confidence            5688899998776666555432                      12    356799999999999999 5666554  47


Q ss_pred             CChhHHHHhhhhhcCCCC
Q psy6712         148 NNRELYIHRIGRSGRFGR  165 (210)
Q Consensus       148 ~s~~~~~q~~GR~gR~g~  165 (210)
                      .+..+.+|++||+.|.+.
T Consensus       864 ~~~~sliQ~aGR~~R~~~  881 (1110)
T TIGR02562       864 SSMRSIIQLAGRVNRHRL  881 (1110)
T ss_pred             CcHHHHHHHhhccccccc
Confidence            889999999999999865

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.

>KOG0388|consensus

Probab=98.08  E-value=2.1e-05  Score=68.17  Aligned_cols=87  Identities=18%  Similarity=0.324  Sum_probs=79.3

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCc-EEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhh
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSR-VLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRS  160 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~-ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~  160 (210)
                      .+.+.++|.-+++...-+.|......|+.++..|...++- .|++|.+.+.|+++..++.||+||..|++..=.|...||
T Consensus      1057 ~dl~EdYl~yr~Y~ylRLDGSsk~~dRrd~vrDwQ~sdiFvFLLSTRAGGLGINLTAADTViFYdSDWNPT~D~QAMDRA 1136 (1185)
T KOG0388|consen 1057 IDLIEDYLVYRGYTYLRLDGSSKASDRRDVVRDWQASDIFVFLLSTRAGGLGINLTAADTVIFYDSDWNPTADQQAMDRA 1136 (1185)
T ss_pred             HHHHHHHHHhhccceEEecCcchhhHHHHHHhhccCCceEEEEEecccCcccccccccceEEEecCCCCcchhhHHHHHH
Confidence            6778888888899999999999999999999999976553 679999999999999999999999999999999999999


Q ss_pred             cCCCCcee
Q psy6712         161 GRFGRKGV  168 (210)
Q Consensus       161 gR~g~~g~  168 (210)
                      .|-|+.-.
T Consensus      1137 HRLGQTrd 1144 (1185)
T KOG0388|consen 1137 HRLGQTRD 1144 (1185)
T ss_pred             HhccCccc
Confidence            99998544

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=97.91  E-value=8.3e-05  Score=54.96  Aligned_cols=98  Identities=29%  Similarity=0.581  Sum_probs=66.1

Q ss_pred             EEEEEcCcchHHHHHHhcCCC-cEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchhHH
Q psy6712           5 CHACIGGTNLSEDLRKLDYGQ-HVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVD   83 (210)
Q Consensus         5 ~~~~~gg~~~~~~~~~l~~~~-~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~~~   83 (210)
                      .....++....+.+..+..+. +++++|++.+.+.+.........++++|+||+|.+....+...+..++..+       
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~v~~~t~~~l~~~~~~~~~~~~~~~~iIiDE~h~~~~~~~~~~~~~~~~~~-------  157 (201)
T smart00487       85 VVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDLLELSNVDLVILDEAHRLLDGGFGDQLEKLLKLL-------  157 (201)
T ss_pred             EEEEeCCcchHHHHHHHhcCCCCEEEeChHHHHHHHHcCCcCHhHCCEEEEECHHHHhcCCcHHHHHHHHHhC-------
Confidence            445566666566777777766 999999999999998877778889999999999998654444444444322       


Q ss_pred             HHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhc
Q psy6712          84 WLTEKMREANFTVSSMHGDMPQKERDGIMKEFRS  117 (210)
Q Consensus        84 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~  117 (210)
                             ..+.....+.+..+ .........+..
T Consensus       158 -------~~~~~~v~~saT~~-~~~~~~~~~~~~  183 (201)
T smart00487      158 -------PKNVQLLLLSATPP-EEIENLLELFLN  183 (201)
T ss_pred             -------CccceEEEEecCCc-hhHHHHHHHhcC
Confidence                   22445555555444 444444444443

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=97.84  E-value=9.5e-05  Score=51.40  Aligned_cols=64  Identities=36%  Similarity=0.659  Sum_probs=50.8

Q ss_pred             ceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchH
Q psy6712           3 VQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFK   66 (210)
Q Consensus         3 i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~   66 (210)
                      +++..+.++.....+......+.+|+++|++.+...+..........+++|+||+|.+......
T Consensus        58 ~~~~~~~~~~~~~~~~~~~~~~~~i~i~t~~~~~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~  121 (144)
T cd00046          58 IKVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQGFG  121 (144)
T ss_pred             cEEEEEecCcchhHHHHHhcCCCCEEEECcHHHHHHHHcCCcchhcCCEEEEeCHHHHhhcchH
Confidence            5677888887777666666678999999999998887766555678889999999999865433

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

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

Probab=97.72  E-value=0.00014  Score=66.38  Aligned_cols=96  Identities=18%  Similarity=0.233  Sum_probs=66.3

Q ss_pred             CCchhHHHHHHHHHh----cCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCc--EEEEecCCC--
Q psy6712          77 PPATQVDWLTEKMRE----ANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVS--LVINYDLPN--  148 (210)
Q Consensus        77 ~~~~~~~~l~~~l~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~--~vi~~~~p~--  148 (210)
                      +.....+.+.+.|..    .++.+.  ..+.. ..|.++++.|++++..+|++|+.+++|+|+|+..  +||...+|.  
T Consensus       682 tS~~~l~~v~~~L~~~~~~~~~~~l--~q~~~-~~r~~ll~~F~~~~~~iLlgt~sf~EGVD~~g~~l~~viI~~LPf~~  758 (850)
T TIGR01407       682 TSYEMLHMVYDMLNELPEFEGYEVL--AQGIN-GSRAKIKKRFNNGEKAILLGTSSFWEGVDFPGNGLVCLVIPRLPFAN  758 (850)
T ss_pred             CCHHHHHHHHHHHhhhccccCceEE--ecCCC-ccHHHHHHHHHhCCCeEEEEcceeecccccCCCceEEEEEeCCCCCC
Confidence            344447788888764    344433  33333 5788899999999999999999999999999766  555555441  


Q ss_pred             ----------------------------ChhHHHHhhhhhcCCCCceeEEEEecc
Q psy6712         149 ----------------------------NRELYIHRIGRSGRFGRKGVAISFVKS  175 (210)
Q Consensus       149 ----------------------------s~~~~~q~~GR~gR~g~~g~~~~~~~~  175 (210)
                                                  ....+.|.+||.-|...+.-++++++.
T Consensus       759 p~dp~~~a~~~~~~~~g~~~f~~~~lP~A~~~l~Qa~GRlIRs~~D~G~v~ilD~  813 (850)
T TIGR01407       759 PKHPLTKKYWQKLEQEGKNPFYDYVLPMAIIRLRQALGRLIRRENDRGSIVILDR  813 (850)
T ss_pred             CCCHHHHHHHHHHHHhcCCchHHhhHHHHHHHHHHhhccccccCCceEEEEEEcc
Confidence                                        124455888999998765445555554

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.

>PF13871 Helicase_C_4: Helicase_C-like

Probab=97.68  E-value=0.00016  Score=56.89  Aligned_cols=78  Identities=21%  Similarity=0.348  Sum_probs=59.3

Q ss_pred             HHHHHHhcCCCcEEEEecCccccCCCCC--------CcEEEEecCCCChhHHHHhhhhhcCCCC-ceeEEEEecc---Cc
Q psy6712         110 GIMKEFRSGTSRVLITTDVWARGIDVQQ--------VSLVINYDLPNNRELYIHRIGRSGRFGR-KGVAISFVKS---DD  177 (210)
Q Consensus       110 ~~~~~f~~g~~~ilv~T~~~~~g~d~~~--------~~~vi~~~~p~s~~~~~q~~GR~gR~g~-~g~~~~~~~~---~~  177 (210)
                      ...++|.+|+.+|+|.|++.+.|+.+..        -.+-|...+||+....+|..||+.|.|+ ....+.++.+   .|
T Consensus        52 ~e~~~F~~g~k~v~iis~AgstGiSlHAd~~~~nqr~Rv~i~le~pwsad~aiQ~~GR~hRsnQ~~~P~y~~l~t~~~gE  131 (278)
T PF13871_consen   52 AEKQAFMDGEKDVAIISDAGSTGISLHADRRVKNQRRRVHITLELPWSADKAIQQFGRTHRSNQVSAPEYRFLVTDLPGE  131 (278)
T ss_pred             HHHHHHhCCCceEEEEecccccccchhccccCCCCCceEEEEeeCCCCHHHHHHHhccccccccccCCEEEEeecCCHHH
Confidence            5667999999999999999999998763        2255788899999999999999999998 3444555543   24


Q ss_pred             HHHHHHHHHH
Q psy6712         178 IRILRDIEQY  187 (210)
Q Consensus       178 ~~~~~~~~~~  187 (210)
                      ..+...+.+.
T Consensus       132 ~Rfas~va~r  141 (278)
T PF13871_consen  132 RRFASTVARR  141 (278)
T ss_pred             HHHHHHHHHH
Confidence            4444444443

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

Probab=97.65  E-value=8.9e-05  Score=54.32  Aligned_cols=96  Identities=25%  Similarity=0.374  Sum_probs=58.6

Q ss_pred             CCCchhHHHHHHHHHhcC----ceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEec--CccccCCCCC--CcEEEEecCC
Q psy6712          76 LPPATQVDWLTEKMREAN----FTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTD--VWARGIDVQQ--VSLVINYDLP  147 (210)
Q Consensus        76 ~~~~~~~~~l~~~l~~~~----~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~--~~~~g~d~~~--~~~vi~~~~p  147 (210)
                      ++.....+.+.+.+++..    +.+..-    +..++...++.|+.++-.+|+++.  .+.+|+|+|+  +..||...+|
T Consensus        16 f~Sy~~l~~~~~~~~~~~~~~~~~v~~q----~~~~~~~~l~~~~~~~~~il~~v~~g~~~EGiD~~~~~~r~vii~glP   91 (167)
T PF13307_consen   16 FPSYRRLEKVYERLKERLEEKGIPVFVQ----GSKSRDELLEEFKRGEGAILLAVAGGSFSEGIDFPGDLLRAVIIVGLP   91 (167)
T ss_dssp             ESSHHHHHHHHTT-TSS-E-ETSCEEES----TCCHHHHHHHHHCCSSSEEEEEETTSCCGSSS--ECESEEEEEEES--
T ss_pred             eCCHHHHHHHHHHHHhhcccccceeeec----CcchHHHHHHHHHhccCeEEEEEecccEEEeecCCCchhheeeecCCC
Confidence            334444555555555432    333332    356788999999999999999998  9999999995  7788888877


Q ss_pred             C----C--------------------------hhHHHHhhhhhcCCCCceeEEEEecc
Q psy6712         148 N----N--------------------------RELYIHRIGRSGRFGRKGVAISFVKS  175 (210)
Q Consensus       148 ~----s--------------------------~~~~~q~~GR~gR~g~~g~~~~~~~~  175 (210)
                      .    +                          .....|.+||+-|...+--+++++++
T Consensus        92 fp~~~d~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~Qa~GR~iR~~~D~g~i~llD~  149 (167)
T PF13307_consen   92 FPPPSDPLVQAKREYLDKQGKNPFRDWYLPPAIRKLKQAIGRLIRSEDDYGVIILLDS  149 (167)
T ss_dssp             ---TTCHHHHHHHHHHHHCCTTCHHHHTHHHHHHHHHHHHHCC--STT-EEEEEEESG
T ss_pred             CCCCCCHHHHHHHHHHHHHhccchhhHhhHHHHHHHhhhcCcceeccCCcEEEEEEcC
Confidence            2    1                          11223778999998765555555554

>smart00491 HELICc2 helicase superfamily c-terminal domain

Probab=97.64  E-value=0.00046  Score=49.15  Aligned_cols=42  Identities=19%  Similarity=0.390  Sum_probs=32.6

Q ss_pred             hHHHHHHHHHhcCCC---cEEEEecC--ccccCCCCC--CcEEEEecCC
Q psy6712         106 KERDGIMKEFRSGTS---RVLITTDV--WARGIDVQQ--VSLVINYDLP  147 (210)
Q Consensus       106 ~~r~~~~~~f~~g~~---~ilv~T~~--~~~g~d~~~--~~~vi~~~~p  147 (210)
                      .+..+.++.|++..-   .||+++.-  +++|+|+|+  +..||...+|
T Consensus        31 ~~~~~~l~~f~~~~~~~g~iL~~v~~G~~~EGiD~~g~~~r~vii~glP   79 (142)
T smart00491       31 GETEELLEKYSAACEARGALLLAVARGKVSEGIDFPDDLGRAVIIVGIP   79 (142)
T ss_pred             chHHHHHHHHHHhcCCCCEEEEEEeCCeeecceecCCCccEEEEEEecC
Confidence            344788999987543   58888876  999999996  6788887766

>KOG0391|consensus

Probab=97.64  E-value=0.00096  Score=61.19  Aligned_cols=95  Identities=17%  Similarity=0.293  Sum_probs=76.4

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCC--cEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhh
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTS--RVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGR  159 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~--~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR  159 (210)
                      .+.|...|.-.|+...-+.|..+.++|+..++.|+....  ..+++|...+.|+|+..++.||+||-.|++.-=.|.-.|
T Consensus      1289 LDVLeqFLnyHgylY~RLDg~t~vEqRQaLmerFNaD~RIfcfILSTrSggvGiNLtgADTVvFYDsDwNPtMDaQAQDr 1368 (1958)
T KOG0391|consen 1289 LDVLEQFLNYHGYLYVRLDGNTSVEQRQALMERFNADRRIFCFILSTRSGGVGINLTGADTVVFYDSDWNPTMDAQAQDR 1368 (1958)
T ss_pred             HHHHHHHHhhcceEEEEecCCccHHHHHHHHHHhcCCCceEEEEEeccCCccccccccCceEEEecCCCCchhhhHHHHH
Confidence            566667777778888889999999999999999986542  467899999999999999999999999998777777677


Q ss_pred             hcCCCCc--eeEEEEeccC
Q psy6712         160 SGRFGRK--GVAISFVKSD  176 (210)
Q Consensus       160 ~gR~g~~--g~~~~~~~~~  176 (210)
                      ..|.|+.  =..+-|++..
T Consensus      1369 ChRIGqtRDVHIYRLISe~ 1387 (1958)
T KOG0391|consen 1369 CHRIGQTRDVHIYRLISER 1387 (1958)
T ss_pred             HHhhcCccceEEEEeeccc
Confidence            7777664  3455556553

>smart00492 HELICc3 helicase superfamily c-terminal domain

Probab=97.62  E-value=0.00067  Score=48.23  Aligned_cols=49  Identities=20%  Similarity=0.385  Sum_probs=37.2

Q ss_pred             ecCCCCHhHHHHHHHHHhcCC-CcEEEEecCccccCCCCC--CcEEEEecCC
Q psy6712          99 MHGDMPQKERDGIMKEFRSGT-SRVLITTDVWARGIDVQQ--VSLVINYDLP  147 (210)
Q Consensus        99 ~~~~~~~~~r~~~~~~f~~g~-~~ilv~T~~~~~g~d~~~--~~~vi~~~~p  147 (210)
                      +..+....+...+++.|+... ..||+++.-+.+|+|+|+  +..||...+|
T Consensus        27 ~~e~~~~~~~~~~l~~f~~~~~~~iL~~~~~~~EGiD~~g~~~r~vii~glP   78 (141)
T smart00492       27 LVQGEDGKETGKLLEKYVEACENAILLATARFSEGVDFPGDYLRAVIIDGLP   78 (141)
T ss_pred             EEeCCChhHHHHHHHHHHHcCCCEEEEEccceecceecCCCCeeEEEEEecC
Confidence            333455556788999998754 379999988999999996  5688877766

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=97.49  E-value=0.00073  Score=60.24  Aligned_cols=92  Identities=23%  Similarity=0.333  Sum_probs=62.6

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCc-----------EEEEecCCCCh
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVS-----------LVINYDLPNNR  150 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~-----------~vi~~~~p~s~  150 (210)
                      .+.+++.|.+.+++...++..-...+-..+..+-+.  --+-|+|+++++|-|+.--.           +||-  .-.+-
T Consensus       442 SE~ls~~L~~~~i~h~VLNAk~h~~EA~Iia~AG~~--gaVTiATNMAGRGTDIkLg~~~~~V~~lGGL~VIg--TERhE  517 (822)
T COG0653         442 SELLSKLLRKAGIPHNVLNAKNHAREAEIIAQAGQP--GAVTIATNMAGRGTDIKLGGNPEFVMELGGLHVIG--TERHE  517 (822)
T ss_pred             chhHHHHHHhcCCCceeeccccHHHHHHHHhhcCCC--CccccccccccCCcccccCCCHHHHHHhCCcEEEe--cccch
Confidence            678889999999999888888654444444443332  24779999999999984222           2232  22333


Q ss_pred             hHHH--HhhhhhcCCCCceeEEEEeccCc
Q psy6712         151 ELYI--HRIGRSGRFGRKGVAISFVKSDD  177 (210)
Q Consensus       151 ~~~~--q~~GR~gR~g~~g~~~~~~~~~~  177 (210)
                      +..+  |..||+||+|.+|....|++-.+
T Consensus       518 SRRIDnQLRGRsGRQGDpG~S~F~lSleD  546 (822)
T COG0653         518 SRRIDNQLRGRAGRQGDPGSSRFYLSLED  546 (822)
T ss_pred             hhHHHHHhhcccccCCCcchhhhhhhhHH
Confidence            3333  88899999999888877776543

>KOG2340|consensus

Probab=97.49  E-value=0.0014  Score=55.50  Aligned_cols=92  Identities=18%  Similarity=0.224  Sum_probs=61.9

Q ss_pred             HHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecC--ccccCCCCCCcEEEEecCCCChhHHHHhh---hhhcCC
Q psy6712          89 MREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDV--WARGIDVQQVSLVINYDLPNNRELYIHRI---GRSGRF  163 (210)
Q Consensus        89 l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~--~~~g~d~~~~~~vi~~~~p~s~~~~~q~~---GR~gR~  163 (210)
                      +++..+.-..+|.-.+...-...-+.|..|...+|+-|.=  .-+-.++..+..||.|.+|.++.=|..-+   +|+.-.
T Consensus       572 ~K~e~i~F~~i~EYssk~~vsRAR~lF~qgr~~vlLyTER~hffrR~~ikGVk~vVfYqpP~~P~FYsEiinm~~k~~~~  651 (698)
T KOG2340|consen  572 MKKEEISFVMINEYSSKSKVSRARELFFQGRKSVLLYTERAHFFRRYHIKGVKNVVFYQPPNNPHFYSEIINMSDKTTSQ  651 (698)
T ss_pred             hhhhhcchHHHhhhhhHhhhhHHHHHHHhcCceEEEEehhhhhhhhheecceeeEEEecCCCCcHHHHHHHhhhhhhhcc
Confidence            3333444444555555566667778889999999999963  34567888999999999999987776554   554433


Q ss_pred             CC----ceeEEEEeccCcHHH
Q psy6712         164 GR----KGVAISFVKSDDIRI  180 (210)
Q Consensus       164 g~----~g~~~~~~~~~~~~~  180 (210)
                      |+    ...|.++++.-|.-.
T Consensus       652 gn~d~d~~t~~ilytKyD~i~  672 (698)
T KOG2340|consen  652 GNTDLDIFTVRILYTKYDRIR  672 (698)
T ss_pred             CCccccceEEEEEeechhhHH
Confidence            32    356777777755443

>PRK14873 primosome assembly protein PriA; Provisional

Probab=97.49  E-value=0.00034  Score=61.86  Aligned_cols=112  Identities=10%  Similarity=0.143  Sum_probs=72.1

Q ss_pred             HHHHHHHHHhc--CceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCC------------
Q psy6712          82 VDWLTEKMREA--NFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLP------------  147 (210)
Q Consensus        82 ~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p------------  147 (210)
                      .+.+.+.|.+.  +.++..+.+       ..+++.|. ++.+|||+|+.++.-+. ++++.|+..|..            
T Consensus       440 ter~eeeL~~~FP~~~V~r~d~-------d~~l~~~~-~~~~IlVGTqgaepm~~-g~~~lV~ildaD~~L~~pDfRA~E  510 (665)
T PRK14873        440 ARRTAEELGRAFPGVPVVTSGG-------DQVVDTVD-AGPALVVATPGAEPRVE-GGYGAALLLDAWALLGRQDLRAAE  510 (665)
T ss_pred             HHHHHHHHHHHCCCCCEEEECh-------HHHHHhhc-cCCCEEEECCCCccccc-CCceEEEEEcchhhhcCCCcChHH
Confidence            66677776553  334443332       24788896 59999999993222222 467777765543            


Q ss_pred             CChhHHHHhhhhhcCCCCceeEEEEeccCcHHHHHHHH-----HHhcCccccccCCccccCCCCCCC
Q psy6712         148 NNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIE-----QYYSTQIDEMPMNGKRSLHSYPAR  209 (210)
Q Consensus       148 ~s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~  209 (210)
                      .....+.|-.||+||....|.+++.. ..+...++.+.     .++..++.+      +...+||||
T Consensus       511 r~~qll~qvagragr~~~~G~V~iq~-~p~~~~~~~l~~~d~~~F~~~EL~~------R~~~~~PPf  570 (665)
T PRK14873        511 DTLRRWMAAAALVRPRADGGQVVVVA-ESSLPTVQALIRWDPVGHAERELAE------RAEVGFPPA  570 (665)
T ss_pred             HHHHHHHHHHHhhcCCCCCCEEEEEe-CCCCHHHHHHHhCCHHHHHHHHHHH------HHHcCccCc
Confidence            23556678889999988899999886 44445555443     355555555      666688887

>KOG4439|consensus

Probab=97.47  E-value=0.00091  Score=58.23  Aligned_cols=90  Identities=23%  Similarity=0.344  Sum_probs=75.6

Q ss_pred             HHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhc--CCCcE-EEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhh
Q psy6712          83 DWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRS--GTSRV-LITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGR  159 (210)
Q Consensus        83 ~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~--g~~~i-lv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR  159 (210)
                      ..+...+.+.|.....+||.....+|..+++.|+.  |..++ |++=.+.+-|+|+...+|+|..|+-|++.---|.+.|
T Consensus       760 niv~~hi~~~g~~y~si~Gqv~vK~Rq~iv~~FN~~k~~~rVmLlSLtAGGVGLNL~GaNHlilvDlHWNPaLEqQAcDR  839 (901)
T KOG4439|consen  760 NIVRKHIQKGGHIYTSITGQVLVKDRQEIVDEFNQEKGGARVMLLSLTAGGVGLNLIGANHLILVDLHWNPALEQQACDR  839 (901)
T ss_pred             HHHHHHHhhCCeeeeeecCccchhHHHHHHHHHHhccCCceEEEEEEccCcceeeecccceEEEEecccCHHHHHHHHHH
Confidence            33446667778899999999999999999999974  43454 4666888899999999999999999999999999999


Q ss_pred             hcCCCCceeEEEE
Q psy6712         160 SGRFGRKGVAISF  172 (210)
Q Consensus       160 ~gR~g~~g~~~~~  172 (210)
                      ..|+|+...+++.
T Consensus       840 IYR~GQkK~V~Ih  852 (901)
T KOG4439|consen  840 IYRMGQKKDVFIH  852 (901)
T ss_pred             HHHhcccCceEEE
Confidence            9999997665543

>PF14617 CMS1: U3-containing 90S pre-ribosomal complex subunit

Probab=97.43  E-value=0.00024  Score=55.14  Aligned_cols=46  Identities=33%  Similarity=0.524  Sum_probs=41.3

Q ss_pred             chHHHHHHhcC-CCcEEEEChHHHHHHHHhcCccCCCccEEEechhh
Q psy6712          13 NLSEDLRKLDY-GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEAD   58 (210)
Q Consensus        13 ~~~~~~~~l~~-~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~   58 (210)
                      ..++|+..+.. ..+|.||||+|+..++..+.+.+++++++|+|--|
T Consensus       165 Kl~eqv~~L~~~~~~i~vGTP~Rl~kLle~~~L~l~~l~~ivlD~s~  211 (252)
T PF14617_consen  165 KLEEQVKLLKKTRVHIAVGTPGRLSKLLENGALSLSNLKRIVLDWSY  211 (252)
T ss_pred             cHHHHHHHHHhCCceEEEeChHHHHHHHHcCCCCcccCeEEEEcCCc
Confidence            67788888875 67999999999999999999999999999999754

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

Probab=97.29  E-value=0.0011  Score=61.08  Aligned_cols=98  Identities=14%  Similarity=0.163  Sum_probs=66.1

Q ss_pred             CchhHHHHHHHHHhcCc--eEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCC--CcEEEEecCCC-----
Q psy6712          78 PATQVDWLTEKMREANF--TVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQ--VSLVINYDLPN-----  148 (210)
Q Consensus        78 ~~~~~~~l~~~l~~~~~--~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~--~~~vi~~~~p~-----  148 (210)
                      .....+.+.+.|.....  ....+.-+++...|.+.++.|++++-.||++|..+.+|+|+|+  +.+||...+|.     
T Consensus       761 Sy~~l~~v~~~l~~~~~~~~~~ll~Qg~~~~~r~~l~~~F~~~~~~iLlG~~sFwEGVD~pg~~l~~viI~kLPF~~p~d  840 (928)
T PRK08074        761 SYEMLKKTYYNLKNEEELEGYVLLAQGVSSGSRARLTKQFQQFDKAILLGTSSFWEGIDIPGDELSCLVIVRLPFAPPDQ  840 (928)
T ss_pred             CHHHHHHHHHHHhhcccccCceEEecCCCCCCHHHHHHHHHhcCCeEEEecCcccCccccCCCceEEEEEecCCCCCCCC
Confidence            33446777777764322  1222333444456788999999988899999999999999996  47787766542     


Q ss_pred             -------------------------ChhHHHHhhhhhcCCCCceeEEEEecc
Q psy6712         149 -------------------------NRELYIHRIGRSGRFGRKGVAISFVKS  175 (210)
Q Consensus       149 -------------------------s~~~~~q~~GR~gR~g~~g~~~~~~~~  175 (210)
                                               ....+.|.+||.-|...+--+++++++
T Consensus       841 p~~~a~~~~~~~~g~~~F~~~~lP~A~~~lkQg~GRlIRs~~D~G~v~ilD~  892 (928)
T PRK08074        841 PVMEAKSEWAKEQGENPFQELSLPQAVLRFKQGFGRLIRTETDRGTVFVLDR  892 (928)
T ss_pred             HHHHHHHHHHHHhCCCchhhhhhHHHHHHHHhhhhhhcccCCceEEEEEecC
Confidence                                     133445888999998765334555554

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

Probab=97.28  E-value=0.00091  Score=60.75  Aligned_cols=106  Identities=15%  Similarity=0.158  Sum_probs=67.6

Q ss_pred             hhHHHHHHHHHhcCceEEEecC-CCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCC--CcEEEEecCC---------
Q psy6712          80 TQVDWLTEKMREANFTVSSMHG-DMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQ--VSLVINYDLP---------  147 (210)
Q Consensus        80 ~~~~~l~~~l~~~~~~~~~~~~-~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~--~~~vi~~~~p---------  147 (210)
                      ...+.+++.|......+ ...| +++   +.+.+++|++++..||++|..+.+|+|+|.  ...+|...+|         
T Consensus       658 ~~l~~v~~~l~~~~~~~-l~Qg~~~~---~~~l~~~F~~~~~~vLlG~~sFwEGVD~p~~~~~~viI~kLPF~~P~dP~~  733 (820)
T PRK07246        658 KHLLAVSDLLDQWQVSH-LAQEKNGT---AYNIKKRFDRGEQQILLGLGSFWEGVDFVQADRMIEVITRLPFDNPEDPFV  733 (820)
T ss_pred             HHHHHHHHHHhhcCCcE-EEeCCCcc---HHHHHHHHHcCCCeEEEecchhhCCCCCCCCCeEEEEEecCCCCCCCCHHH
Confidence            33677777776555555 4444 333   456799999988899999999999999973  4555555544         


Q ss_pred             ---------------------CChhHHHHhhhhhcCCCCceeEEEEeccC--cHHHHHHHHHHhc
Q psy6712         148 ---------------------NNRELYIHRIGRSGRFGRKGVAISFVKSD--DIRILRDIEQYYS  189 (210)
Q Consensus       148 ---------------------~s~~~~~q~~GR~gR~g~~g~~~~~~~~~--~~~~~~~~~~~~~  189 (210)
                                           .-...+.|.+||.-|...+--+++++++.  ....-+.+.+.+-
T Consensus       734 ~a~~~~~~~~g~~~F~~~~lP~A~iklkQg~GRLIRs~~D~Gvv~ilD~R~~~k~Yg~~~l~sLP  798 (820)
T PRK07246        734 KKMNQYLLQEGKNPFYDYFLPMTILRLKQAIGRTMRREDQKSAVLILDRRILTKSYGKQILASLA  798 (820)
T ss_pred             HHHHHHHHHhCCCchhheeHHHHHHHHHHHhcccccCCCCcEEEEEECCcccccHHHHHHHHhCC
Confidence                                 12344568889999986543345555543  2233344555444

>KOG1015|consensus

Probab=97.20  E-value=0.0011  Score=59.75  Aligned_cols=81  Identities=23%  Similarity=0.268  Sum_probs=71.5

Q ss_pred             CceEEEecCCCCHhHHHHHHHHHhcCCC----cEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCCcee
Q psy6712          93 NFTVSSMHGDMPQKERDGIMKEFRSGTS----RVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGV  168 (210)
Q Consensus        93 ~~~~~~~~~~~~~~~r~~~~~~f~~g~~----~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~~g~  168 (210)
                      |....-+.|..+..+|....+.|+....    -.||+|.+.+.|+|+-.++.||+||..|+++-=.|.+=|+-|.|+...
T Consensus      1188 GkDyyriDGst~s~~R~k~~~~FNdp~NlRaRl~LISTRAGsLGiNLvAANRVIIfDasWNPSyDtQSIFRvyRfGQtKP 1267 (1567)
T KOG1015|consen 1188 GKDYYRLDGSTTSQSRKKWAEEFNDPTNLRARLFLISTRAGSLGINLVAANRVIIFDASWNPSYDTQSIFRVYRFGQTKP 1267 (1567)
T ss_pred             CCceEEecCcccHHHHHHHHHHhcCcccceeEEEEEeeccCccccceeecceEEEEecccCCccchHHHHHHHhhcCcCc
Confidence            5567778999999999999999986533    378999999999999999999999999999999999999999999777


Q ss_pred             EEEEe
Q psy6712         169 AISFV  173 (210)
Q Consensus       169 ~~~~~  173 (210)
                      |+++-
T Consensus      1268 vyiYR 1272 (1567)
T KOG1015|consen 1268 VYIYR 1272 (1567)
T ss_pred             eeehh
Confidence            76653

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

Probab=97.00  E-value=0.0038  Score=55.52  Aligned_cols=114  Identities=17%  Similarity=0.251  Sum_probs=72.5

Q ss_pred             CCCchhHHHHHHHHHhcCce-EEEecCCCCHhHHHHHHHHHhcCCC-cEEEEecCccccCCCCC--CcEEEEecCC----
Q psy6712          76 LPPATQVDWLTEKMREANFT-VSSMHGDMPQKERDGIMKEFRSGTS-RVLITTDVWARGIDVQQ--VSLVINYDLP----  147 (210)
Q Consensus        76 ~~~~~~~~~l~~~l~~~~~~-~~~~~~~~~~~~r~~~~~~f~~g~~-~ilv~T~~~~~g~d~~~--~~~vi~~~~p----  147 (210)
                      ++.....+.+.+.+...... ....+|..   .+...++.|+.+.- -++|+|..+++|+|+|+  ...||...+|    
T Consensus       486 F~Sy~~l~~~~~~~~~~~~~~~v~~q~~~---~~~~~l~~f~~~~~~~~lv~~gsf~EGVD~~g~~l~~vvI~~lPfp~p  562 (654)
T COG1199         486 FPSYEYLKRVAERLKDERSTLPVLTQGED---EREELLEKFKASGEGLILVGGGSFWEGVDFPGDALRLVVIVGLPFPNP  562 (654)
T ss_pred             eccHHHHHHHHHHHhhcCccceeeecCCC---cHHHHHHHHHHhcCCeEEEeeccccCcccCCCCCeeEEEEEecCCCCC
Confidence            33444477777877765542 33444444   34478888876655 89999999999999986  4677776665    


Q ss_pred             --------------------------CChhHHHHhhhhhcCCCCceeEEEEeccC--cHHHHHHHHHHhcCcc
Q psy6712         148 --------------------------NNRELYIHRIGRSGRFGRKGVAISFVKSD--DIRILRDIEQYYSTQI  192 (210)
Q Consensus       148 --------------------------~s~~~~~q~~GR~gR~g~~g~~~~~~~~~--~~~~~~~~~~~~~~~~  192 (210)
                                                .......|.+||+-|...+.-++++++..  ....-+.+.+++....
T Consensus       563 ~dp~~~~r~~~~~~~g~~~f~~~~l~~A~~~l~QavGRlIR~~~D~G~ivllD~R~~~~~y~~~l~~~l~~~~  635 (654)
T COG1199         563 DDPLLKARLEFLKRLGGDPFEEFYLPPAVIKLRQAVGRLIRSEDDRGVIVLLDKRYATKRYGKLLLDSLPPFP  635 (654)
T ss_pred             CCHHHHHHHHHHHHhcCCCceEeehHHHHHHHHHhhccccccCCCceEEEEecccchhhhHHHHHHHhCCCCc
Confidence                                      23455669999999976554455555442  2223444455554433

>KOG0921|consensus

Probab=96.96  E-value=0.0008  Score=60.08  Aligned_cols=81  Identities=19%  Similarity=0.440  Sum_probs=65.7

Q ss_pred             ceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEec------------------CCCChhHHHH
Q psy6712          94 FTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYD------------------LPNNRELYIH  155 (210)
Q Consensus        94 ~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~------------------~p~s~~~~~q  155 (210)
                      ..+...|+-.+..++.++.+....|..+++++|.+...-+.+-++.+|+..+                  ...+.....|
T Consensus       675 y~ilp~Hsq~~~~eqrkvf~~~p~gv~kii~stniaetsiTidd~v~vid~cka~~~~~~s~nn~~~~Atvw~sktn~eq  754 (1282)
T KOG0921|consen  675 YEILPLHSQLTSQEQRKVFEPVPEGVTKIILSTNIAETSITIDDVVYVIDSCKAKEKLFTSHNNMTHYATVWASKTNLEQ  754 (1282)
T ss_pred             cccccchhhcccHhhhhccCcccccccccccccceeeEeeeecceeEEEeeeeeeeeeeccccceeeeeeecccccchHh
Confidence            4677889999999999999999899999999999998888887767666432                  2256778889


Q ss_pred             hhhhhcCCCCceeEEEEecc
Q psy6712         156 RIGRSGRFGRKGVAISFVKS  175 (210)
Q Consensus       156 ~~GR~gR~g~~g~~~~~~~~  175 (210)
                      |.||+||. +.|.|..+++.
T Consensus       755 r~gr~grv-R~G~~f~lcs~  773 (1282)
T KOG0921|consen  755 RKGRAGRV-RPGFCFHLCSR  773 (1282)
T ss_pred             hcccCcee-cccccccccHH
Confidence            99999998 77888777764

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=96.88  E-value=0.0057  Score=54.80  Aligned_cols=94  Identities=18%  Similarity=0.323  Sum_probs=61.0

Q ss_pred             CchhHHHHHHHHHhc-CceEEEecCCCCHhHHHHHHHHHh----cCCCcEEEEecCccccCCCCC--CcEEEEecCCC--
Q psy6712          78 PATQVDWLTEKMREA-NFTVSSMHGDMPQKERDGIMKEFR----SGTSRVLITTDVWARGIDVQQ--VSLVINYDLPN--  148 (210)
Q Consensus        78 ~~~~~~~l~~~l~~~-~~~~~~~~~~~~~~~r~~~~~~f~----~g~~~ilv~T~~~~~g~d~~~--~~~vi~~~~p~--  148 (210)
                      .....+.+.+.|... +.. ...++..   .+...++.|+    .++..||++|..+.+|+|+|+  +++||...+|.  
T Consensus       543 Sy~~l~~v~~~l~~~~~~~-ll~Q~~~---~~~~ll~~f~~~~~~~~~~VL~g~~sf~EGVD~pGd~l~~vII~kLPF~~  618 (697)
T PRK11747        543 SRRQMQKVADLLPRDLRLM-LLVQGDQ---PRQRLLEKHKKRVDEGEGSVLFGLQSFAEGLDLPGDYLTQVIITKIPFAV  618 (697)
T ss_pred             cHHHHHHHHHHHHHhcCCc-EEEeCCc---hHHHHHHHHHHHhccCCCeEEEEeccccccccCCCCceEEEEEEcCCCCC
Confidence            334467777777543 333 3445543   4566776666    467789999999999999985  78888776552  


Q ss_pred             --C--------------------------hhHHHHhhhhhcCCCCceeEEEEecc
Q psy6712         149 --N--------------------------RELYIHRIGRSGRFGRKGVAISFVKS  175 (210)
Q Consensus       149 --s--------------------------~~~~~q~~GR~gR~g~~g~~~~~~~~  175 (210)
                        +                          ...+.|.+||.-|...+--+++++++
T Consensus       619 p~dp~~~ar~~~~~~~g~~~F~~~~lP~A~~kl~Qg~GRlIRs~~D~G~i~ilD~  673 (697)
T PRK11747        619 PDSPVEATLAEWLKSRGGNPFMEISVPDASFKLIQAVGRLIRSEQDRGRVTILDR  673 (697)
T ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhccccccCCceEEEEEEcc
Confidence              1                          22344778999888654334555544

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=96.18  E-value=0.027  Score=50.71  Aligned_cols=89  Identities=18%  Similarity=0.275  Sum_probs=61.6

Q ss_pred             hHHHHHHHHHhc----CCCcEEEEe--cCccccCCCCC--CcEEEEecCCC-Ch--------------------------
Q psy6712         106 KERDGIMKEFRS----GTSRVLITT--DVWARGIDVQQ--VSLVINYDLPN-NR--------------------------  150 (210)
Q Consensus       106 ~~r~~~~~~f~~----g~~~ilv~T--~~~~~g~d~~~--~~~vi~~~~p~-s~--------------------------  150 (210)
                      .++..+++.|+.    ++-.+|+++  ..+++|+|+++  +..||..++|. ++                          
T Consensus       565 ~~~~~~l~~f~~~~~~~~gavL~av~gGk~sEGIDf~~~~~r~ViivGlPf~~~~~~~~~~~~~~~~~~~~~~~~~~~y~  644 (705)
T TIGR00604       565 QETSDALERYKQAVSEGRGAVLLSVAGGKVSEGIDFCDDLGRAVIMVGIPYEYTESRILLARLEFLRDQYPIRENQDFYE  644 (705)
T ss_pred             chHHHHHHHHHHHHhcCCceEEEEecCCcccCccccCCCCCcEEEEEccCCCCCCCHHHHHHHHHHHhhcCCCccHHHHH
Confidence            577888999964    455699998  88999999996  78899888774 11                          


Q ss_pred             ----hHHHHhhhhhcCCCCceeEEEEeccC--cHHHHHHHHHHhcCcccc
Q psy6712         151 ----ELYIHRIGRSGRFGRKGVAISFVKSD--DIRILRDIEQYYSTQIDE  194 (210)
Q Consensus       151 ----~~~~q~~GR~gR~g~~g~~~~~~~~~--~~~~~~~~~~~~~~~~~~  194 (210)
                          ....|.+||+-|...+--++++++..  +....+.+.+|+...+..
T Consensus       645 ~~a~~~v~QaiGR~IR~~~D~G~iillD~R~~~~~~~~~lp~W~~~~~~~  694 (705)
T TIGR00604       645 FDAMRAVNQAIGRVIRHKDDYGSIVLLDKRYARSNKRKKLPKWIQDTIQS  694 (705)
T ss_pred             HHHHHHHHHHhCccccCcCceEEEEEEehhcCCcchhhhcCHHHHhhccc
Confidence                12338889999986654455565543  223445666777666654

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).

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

Probab=96.14  E-value=0.059  Score=48.39  Aligned_cols=88  Identities=10%  Similarity=0.159  Sum_probs=53.6

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCC--cEEEEe--cCC--CChhHHHH
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQV--SLVINY--DLP--NNRELYIH  155 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~--~~vi~~--~~p--~s~~~~~q  155 (210)
                      ++.+++..+....++..+++.-+..+.    +.|  +++++++-|+.+.-|+++...  +-+.-|  ...  .+..+..|
T Consensus       295 ~~~v~~~~~~~~~~Vl~l~s~~~~~dv----~~W--~~~~VviYT~~itvG~Sf~~~HF~~~f~yvk~~~~gpd~~s~~Q  368 (824)
T PF02399_consen  295 AEIVARFCARFTKKVLVLNSTDKLEDV----ESW--KKYDVVIYTPVITVGLSFEEKHFDSMFAYVKPMSYGPDMVSVYQ  368 (824)
T ss_pred             HHHHHHHHHhcCCeEEEEcCCCCcccc----ccc--cceeEEEEeceEEEEeccchhhceEEEEEecCCCCCCcHHHHHH
Confidence            344444444445566666665544422    122  467999999999999988532  333333  222  34556799


Q ss_pred             hhhhhcCCCCceeEEEEeccC
Q psy6712         156 RIGRSGRFGRKGVAISFVKSD  176 (210)
Q Consensus       156 ~~GR~gR~g~~g~~~~~~~~~  176 (210)
                      ++||+-.. .....+++++..
T Consensus       369 ~lgRvR~l-~~~ei~v~~d~~  388 (824)
T PF02399_consen  369 MLGRVRSL-LDNEIYVYIDAS  388 (824)
T ss_pred             HHHHHHhh-ccCeEEEEEecc
Confidence            99998443 566777777654

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

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

Probab=96.13  E-value=0.024  Score=50.03  Aligned_cols=95  Identities=15%  Similarity=0.135  Sum_probs=62.9

Q ss_pred             chhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhc----CCCcEEEEecCccccCCC--------C--CCcEEEEe
Q psy6712          79 ATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRS----GTSRVLITTDVWARGIDV--------Q--QVSLVINY  144 (210)
Q Consensus        79 ~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~----g~~~ilv~T~~~~~g~d~--------~--~~~~vi~~  144 (210)
                      ....+.+++.|+..--....+.|+.+  .+...+++|++    |.-.||++|..+.+|+|+        |  .+++||+.
T Consensus       480 ~~~~~~~~~~l~~~l~~~~l~qg~~~--~~~~l~~~f~~~~~~~~~~vL~gt~sfweGvDv~~~~~~p~~G~~Ls~ViI~  557 (636)
T TIGR03117       480 FSHISAIGQLVELGIPAEIVIQSEKN--RLASAEQQFLALYANGIQPVLIAAGGAWTGIDLTHKPVSPDKDNLLTDLIIT  557 (636)
T ss_pred             HHHHHHHHHHHHhhcCCCEEEeCCCc--cHHHHHHHHHHhhcCCCCcEEEeCCccccccccCCccCCCCCCCcccEEEEE
Confidence            34477777777654323445556543  34567888886    468999999999999999        2  48888876


Q ss_pred             cCCC-------------------------ChhHHHHhhhhhcCCCCc--eeEEEEecc
Q psy6712         145 DLPN-------------------------NRELYIHRIGRSGRFGRK--GVAISFVKS  175 (210)
Q Consensus       145 ~~p~-------------------------s~~~~~q~~GR~gR~g~~--g~~~~~~~~  175 (210)
                      .+|.                         ....+.|-+||.-|...+  --++.++++
T Consensus       558 kLPF~~~dp~a~~~~~~~~g~~~f~~~p~a~i~lkQg~GRLIR~~~D~~~G~i~ilD~  615 (636)
T TIGR03117       558 CAPFGLNRSLSMLKRIRKTSVRPWEIINESLMMLRQGLGRLVRHPDMPQNRRIHMLDG  615 (636)
T ss_pred             eCCCCcCChHHHHHHHHhcCCChHhhhHHHHHHHHHhcCceeecCCCcCceEEEEEeC
Confidence            6551                         133455788888888654  334444444

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.

>KOG0701|consensus

Probab=96.07  E-value=0.004  Score=59.37  Aligned_cols=58  Identities=26%  Similarity=0.496  Sum_probs=53.3

Q ss_pred             hHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCC
Q psy6712         106 KERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRF  163 (210)
Q Consensus       106 ~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~  163 (210)
                      ..+.+++..|...++.+|++|.++.+|+|++.++.++.++.|.....|+|..||+-+.
T Consensus       341 ~~~~~vl~~~~~~~ln~L~~~~~~~e~~d~~~~~~~~~~~~~~~~~~~vq~~~r~~~~  398 (1606)
T KOG0701|consen  341 LRQAEVLRRFHFHELNLLIATSVLEEGVDVPKCNLVVLFDAPTYYRSYVQKKGRARAA  398 (1606)
T ss_pred             hhhHHHHHHHhhhhhhHHHHHHHHHhhcchhhhhhheeccCcchHHHHHHhhcccccc
Confidence            3467889999999999999999999999999999999999999999999999998554

>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=95.54  E-value=0.12  Score=40.18  Aligned_cols=89  Identities=9%  Similarity=0.191  Sum_probs=66.8

Q ss_pred             HHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCC----CcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhh
Q psy6712          83 DWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGT----SRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIG  158 (210)
Q Consensus        83 ~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~----~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~G  158 (210)
                      ..+.+.+.. ++.+..++++.+...     -.|.++.    ..|+|+-+.++||+.+++..+.....-+...+++.||.=
T Consensus       101 ~~l~~~~~~-~~~v~~vNS~~~~~~-----ldy~~~~~~~~~~I~VGGn~LsRGlTleGL~vsYf~R~s~~~DTL~QmgR  174 (239)
T PF10593_consen  101 PELPKAISD-GIEVVVVNSGSSDDS-----LDYDDGENLGLNVIAVGGNKLSRGLTLEGLTVSYFLRNSKQYDTLMQMGR  174 (239)
T ss_pred             HHHHHHHhc-CceEEEEeCCCcccc-----ccccccccCCceEEEECCccccCceeECCcEEEEecCCCchHHHHHHHhh
Confidence            444444444 799999998766544     3344443    789999999999999999999999888888888888864


Q ss_pred             hhc-CCCCceeEEEEeccCc
Q psy6712         159 RSG-RFGRKGVAISFVKSDD  177 (210)
Q Consensus       159 R~g-R~g~~g~~~~~~~~~~  177 (210)
                      ..| |.|-...|=++..+.-
T Consensus       175 wFGYR~gY~dl~Ri~~~~~l  194 (239)
T PF10593_consen  175 WFGYRPGYEDLCRIYMPEEL  194 (239)
T ss_pred             cccCCcccccceEEecCHHH
Confidence            455 6666778888887643

This domain is found associated with a helicase domain of superfamily type II [].

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=95.25  E-value=0.062  Score=48.88  Aligned_cols=55  Identities=16%  Similarity=0.177  Sum_probs=44.0

Q ss_pred             HhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHh
Q psy6712          20 KLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYR   74 (210)
Q Consensus        20 ~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~   74 (210)
                      .+.....|+++||..+..=+..+.+++.++..+|+||||++.+......+-.++.
T Consensus         3 ~ly~~ggi~~~T~rIl~~DlL~~ri~~~~itgiiv~~Ahr~~~~~~eaFI~rlyr   57 (814)
T TIGR00596         3 KVYLEGGIFSITSRILVVDLLTGIIPPELITGILVLRADRIIESSQEAFILRLYR   57 (814)
T ss_pred             hHhhcCCEEEEechhhHhHHhcCCCCHHHccEEEEeecccccccccHHHHHHHHH
Confidence            3445667999999998888888999999999999999999987655544444443

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

>PF07517 SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011115 SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane

Probab=95.19  E-value=0.08  Score=41.71  Aligned_cols=59  Identities=17%  Similarity=0.238  Sum_probs=40.8

Q ss_pred             CCceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHH-HHHhcC----c--cCCCccEEEechhhHHh
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFD-MIRRRV----L--RTRNIKMLVLDEADEML   61 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~-~l~~~~----~--~~~~~~~lviDE~~~l~   61 (210)
                      +|++|..++++.+.++..+..  .+||+.+|...+-- .|+...    .  -...+.++|+||+|.++
T Consensus       145 LGlsv~~~~~~~~~~~r~~~Y--~~dI~Y~t~~~~~fD~Lrd~~~~~~~~~~~r~~~~~ivDEvDs~L  210 (266)
T PF07517_consen  145 LGLSVGIITSDMSSEERREAY--AADIVYGTNSEFGFDYLRDNLALSKNEQVQRGFDFAIVDEVDSIL  210 (266)
T ss_dssp             TT--EEEEETTTEHHHHHHHH--HSSEEEEEHHHHHHHHHHHTT-SSGGG--SSSSSEEEECTHHHHT
T ss_pred             hhhccccCccccCHHHHHHHH--hCcccccccchhhHHHHHHHHhhccchhccCCCCEEEEeccceEE
Confidence            689999999998865433333  56799999977653 444421    1  24688999999999986

SecA protein achieves this translocation, in association with SecY protein, in an ATP-dependent manner [,]. This domain represents the N-terminal ATP-dependent helicase domain, which is related to the IPR0011545 from INTERPRO.; GO: 0005524 ATP binding, 0017038 protein import, 0016020 membrane; PDB: 1NL3_B 1NKT_B 3DIN_B 3JUX_A 2FSG_B 2VDA_A 2FSH_A 2FSF_A 2FSI_A 3BXZ_A ....

>KOG1513|consensus

Probab=94.99  E-value=0.046  Score=48.86  Aligned_cols=75  Identities=24%  Similarity=0.357  Sum_probs=55.6

Q ss_pred             HHHHhcCCCcEEEEecCccccCCCCCCcEE--------EEecCCCChhHHHHhhhhhcCCCC-ceeEEEEecc---CcHH
Q psy6712         112 MKEFRSGTSRVLITTDVWARGIDVQQVSLV--------INYDLPNNRELYIHRIGRSGRFGR-KGVAISFVKS---DDIR  179 (210)
Q Consensus       112 ~~~f~~g~~~ilv~T~~~~~g~d~~~~~~v--------i~~~~p~s~~~~~q~~GR~gR~g~-~g~~~~~~~~---~~~~  179 (210)
                      -++|..|+-.|-|.+.+++-|+-++.-..|        |-..+|||.+.-+|.+||+.|.++ .+.-++|+-+   .|..
T Consensus       850 KqrFM~GeK~vAIISEAaSSGiSLQsDrRv~NqRRRvHiTLELPWSADrAIQQFGRTHRSNQVsaPEYvFlIseLAGErR  929 (1300)
T KOG1513|consen  850 KQRFMDGEKLVAIISEAASSGISLQSDRRVQNQRRRVHITLELPWSADRAIQQFGRTHRSNQVSAPEYVFLISELAGERR  929 (1300)
T ss_pred             HhhhccccceeeeeehhhccCceeecchhhhhhhheEEEEEECCcchhHHHHHhcccccccccCCCeEEEEehhhccchH
Confidence            357889999999999999999998765544        457899999999999999999977 3444444432   3555


Q ss_pred             HHHHHHH
Q psy6712         180 ILRDIEQ  186 (210)
Q Consensus       180 ~~~~~~~  186 (210)
                      +..-+.+
T Consensus       930 FAS~VAK  936 (1300)
T KOG1513|consen  930 FASIVAK  936 (1300)
T ss_pred             HHHHHHH
Confidence            5444333

>KOG3089|consensus

Probab=94.55  E-value=0.063  Score=40.55  Aligned_cols=43  Identities=23%  Similarity=0.464  Sum_probs=35.3

Q ss_pred             hHHHHHHhcC-CCcEEEEChHHHHHHHHhcCccCCCccEEEech
Q psy6712          14 LSEDLRKLDY-GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDE   56 (210)
Q Consensus        14 ~~~~~~~l~~-~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE   56 (210)
                      .++|.+.+.+ ..++-||||+|+..+...+.++++.+.++|+|=
T Consensus       185 ~~~~~k~~k~~~v~~gIgTp~Ri~~lv~~~~f~~~~lk~iIlD~  228 (271)
T KOG3089|consen  185 VQAQVKLLKKRVVHLGIGTPGRIKELVKQGGFNLSPLKFIILDW  228 (271)
T ss_pred             HHHHHHHHhhcceeEeecCcHHHHHHHHhcCCCCCcceeEEeec
Confidence            3445555554 468889999999999999999999999999884

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=94.44  E-value=0.13  Score=46.12  Aligned_cols=60  Identities=23%  Similarity=0.398  Sum_probs=48.4

Q ss_pred             HHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCcc-ccCCCCCCcEEEE
Q psy6712          84 WLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWA-RGIDVQQVSLVIN  143 (210)
Q Consensus        84 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~-~g~d~~~~~~vi~  143 (210)
                      .+.+.+...++++..++|+++..++.++++...+|+.+|+|+|.... ..+.+.++.+||.
T Consensus       329 ~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~v~~~~l~lvVI  389 (681)
T PRK10917        329 NLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVII  389 (681)
T ss_pred             HHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcccchhcccceEEE
Confidence            34444555579999999999999999999999999999999997543 3466778887774

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

Probab=94.35  E-value=0.16  Score=44.76  Aligned_cols=61  Identities=20%  Similarity=0.390  Sum_probs=51.5

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccc-cCCCCCCcEEE
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWAR-GIDVQQVSLVI  142 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~-g~d~~~~~~vi  142 (210)
                      ...+.++|...|+.+..+.|.+...+|++++++..+|+++++|+|.++-. .+++.+.-+||
T Consensus       328 ~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALiQd~V~F~~LgLVI  389 (677)
T COG1200         328 YESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQDKVEFHNLGLVI  389 (677)
T ss_pred             HHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhhhcceeecceeEEE
Confidence            55667778878999999999999999999999999999999999987643 56666666665

>PRK09401 reverse gyrase; Reviewed

Probab=94.14  E-value=0.36  Score=45.97  Aligned_cols=50  Identities=14%  Similarity=0.355  Sum_probs=35.4

Q ss_pred             CCceEEEEEcCcchHHHHHHhcC-CCcEEEEChHHHHHHHHhcCccCCC-ccEEEe
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLDY-GQHVVSGTPGRVFDMIRRRVLRTRN-IKMLVL   54 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~~-~~~Ili~Tp~~l~~~l~~~~~~~~~-~~~lvi   54 (210)
                      .|++|..++|+.  +.....+.+ ..+|||||..- -+++. ..+++.+ ++++|+
T Consensus       354 ~gi~v~~~hg~l--~~~l~~F~~G~~~VLVatas~-tdv~a-RGIDiP~~IryVI~  405 (1176)
T PRK09401        354 LGINAELAISGF--ERKFEKFEEGEVDVLVGVASY-YGVLV-RGIDLPERIRYAIF  405 (1176)
T ss_pred             CCCcEEEEeCcH--HHHHHHHHCCCCCEEEEecCC-CCcee-ecCCCCcceeEEEE
Confidence            478999999999  455688876 47999997421 12233 3467777 788886

>KOG1016|consensus

Probab=93.54  E-value=0.18  Score=45.22  Aligned_cols=80  Identities=18%  Similarity=0.257  Sum_probs=66.9

Q ss_pred             eEEEecCCCCHhHHHHHHHHHhcCC---CcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCCceeEEE
Q psy6712          95 TVSSMHGDMPQKERDGIMKEFRSGT---SRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAIS  171 (210)
Q Consensus        95 ~~~~~~~~~~~~~r~~~~~~f~~g~---~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~~g~~~~  171 (210)
                      .-.-+.|..+..+|++.+.+|+..-   .-++++|.....|+++-..+.++.||.-|++.--.|.+-|+-|-|+...|++
T Consensus       763 sy~rldG~t~a~~rekLinqfN~e~~lsWlfllstrag~lGinLIsanr~~ifda~wnpchdaqavcRvyrYGQ~Kpcfv  842 (1387)
T KOG1016|consen  763 SYLRLDGTTSAADREKLINQFNSEPGLSWLFLLSTRAGSLGINLISANRCIIFDACWNPCHDAQAVCRVYRYGQQKPCFV  842 (1387)
T ss_pred             ceecccCCcccchHHHHHHhccCCCCceeeeeehhccccccceeeccceEEEEEeecCccccchhhhhhhhhcCcCceeE
Confidence            3445778888999999999997532   2367889999999999999999999999999999999999999999777766


Q ss_pred             Eec
Q psy6712         172 FVK  174 (210)
Q Consensus       172 ~~~  174 (210)
                      +--
T Consensus       843 YRl  845 (1387)
T KOG1016|consen  843 YRL  845 (1387)
T ss_pred             Eee
Confidence            653

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=93.35  E-value=0.26  Score=43.83  Aligned_cols=58  Identities=17%  Similarity=0.370  Sum_probs=46.5

Q ss_pred             HHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccc-cCCCCCCcEEEE
Q psy6712          86 TEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWAR-GIDVQQVSLVIN  143 (210)
Q Consensus        86 ~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~-g~d~~~~~~vi~  143 (210)
                      .+.+...++++..++|+++..++...++...+|+.+|+|+|...-. .+.+.++.+||.
T Consensus       305 ~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~~~~~~~l~lvVI  363 (630)
T TIGR00643       305 RNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVII  363 (630)
T ss_pred             HHHhcccCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhccccccccceEEE
Confidence            3344445899999999999999999999999999999999975443 456677777763

>KOG1001|consensus

Probab=93.17  E-value=0.012  Score=52.29  Aligned_cols=89  Identities=18%  Similarity=0.195  Sum_probs=72.4

Q ss_pred             HHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCC-c-EEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhh
Q psy6712          83 DWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTS-R-VLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRS  160 (210)
Q Consensus        83 ~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~-~-ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~  160 (210)
                      ..+.-.|...++....+.|.|+...|.+.+..|..+.. . .+++..+...|+++..+.+|+..|+.|++..--|.+-|+
T Consensus       553 ~l~~~~l~~~~~~~~~~~g~~~~~~r~~s~~~~~~~~~~~vll~Slkag~~glnlt~a~~v~~~d~~wnp~~eeQaidR~  632 (674)
T KOG1001|consen  553 ALVCLRLFFKGFVFLRYDGEMLMKIRTKSFTDFPCDPLVTALLMSLKAGKVGLNLTAASHVLLMDPWWNPAVEEQAIDRA  632 (674)
T ss_pred             HHhhhhhhhcccccchhhhhhHHHHHHhhhcccccCccHHHHHHHHHHhhhhhchhhhhHHHhhchhcChHHHHHHHHHH
Confidence            33444444567788889999999999999999985433 3 446778889999999999999999999999999999999


Q ss_pred             cCCCCceeEEE
Q psy6712         161 GRFGRKGVAIS  171 (210)
Q Consensus       161 gR~g~~g~~~~  171 (210)
                      .|.|+...+.+
T Consensus       633 hrigq~k~v~v  643 (674)
T KOG1001|consen  633 HRIGQTKPVKV  643 (674)
T ss_pred             HHhcccceeee
Confidence            99998655443

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

Probab=93.13  E-value=0.17  Score=46.61  Aligned_cols=77  Identities=22%  Similarity=0.458  Sum_probs=49.1

Q ss_pred             HHHHHHHHHh----cC-ceEEE-ecCCCCHhHHHHHHHHHhcCCCcEEEEecCcc-ccCC-CC--CCcEEEEecC-----
Q psy6712          82 VDWLTEKMRE----AN-FTVSS-MHGDMPQKERDGIMKEFRSGTSRVLITTDVWA-RGID-VQ--QVSLVINYDL-----  146 (210)
Q Consensus        82 ~~~l~~~l~~----~~-~~~~~-~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~-~g~d-~~--~~~~vi~~~~-----  146 (210)
                      +.+..+.|..    .+ ..+.. +|+.|+.+++++.+++|.+|+++|||+|+.+- ...+ +.  ..++|+.=|.     
T Consensus       138 v~Q~~~kl~~~~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~FL~k~~e~L~~~kFdfifVDDVDA~Lk  217 (1187)
T COG1110         138 VRQVYERLKKFAEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLSKRFEELSKLKFDFIFVDDVDAILK  217 (1187)
T ss_pred             HHHHHHHHHHHHhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHHHHhhHHHhcccCCCEEEEccHHHHHh
Confidence            4444444433    23 44444 99999999999999999999999999997542 2222 22  3556654442     


Q ss_pred             -CCChhHHHHhhh
Q psy6712         147 -PNNRELYIHRIG  158 (210)
Q Consensus       147 -p~s~~~~~q~~G  158 (210)
                       ..|++..+...|
T Consensus       218 askNvDriL~LlG  230 (1187)
T COG1110         218 ASKNVDRLLRLLG  230 (1187)
T ss_pred             ccccHHHHHHHcC
Confidence             245555554444

>PRK05580 primosome assembly protein PriA; Validated

Probab=92.73  E-value=0.5  Score=42.46  Aligned_cols=63  Identities=16%  Similarity=0.259  Sum_probs=49.0

Q ss_pred             HHHHHHHHHh-cCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEec
Q psy6712          82 VDWLTEKMRE-ANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYD  145 (210)
Q Consensus        82 ~~~l~~~l~~-~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~  145 (210)
                      +..+.+.|++ .+..+..+||+++..+|.+.+.+...|+.+|+|+|..... ..+.++.+||.-+
T Consensus       203 ~~Q~~~~l~~~fg~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~-~p~~~l~liVvDE  266 (679)
T PRK05580        203 TPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALF-LPFKNLGLIIVDE  266 (679)
T ss_pred             HHHHHHHHHHHhCCCEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHhc-ccccCCCEEEEEC
Confidence            5666666654 3678999999999999999999999999999999974432 4566777777543

>TIGR00595 priA primosomal protein N'

Probab=92.01  E-value=0.56  Score=40.62  Aligned_cols=61  Identities=15%  Similarity=0.239  Sum_probs=45.8

Q ss_pred             HHHHHHHHHh-cCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEE
Q psy6712          82 VDWLTEKMRE-ANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVIN  143 (210)
Q Consensus        82 ~~~l~~~l~~-~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~  143 (210)
                      +..+.+.|++ .+..+..+||+++..+|.+.+.+..+|+.+|+|+|..... ..+.++.+||.
T Consensus        38 ~~Q~~~~l~~~f~~~v~vlhs~~~~~er~~~~~~~~~g~~~IVVGTrsalf-~p~~~l~lIIV   99 (505)
T TIGR00595        38 TPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVVIGTRSALF-LPFKNLGLIIV   99 (505)
T ss_pred             HHHHHHHHHHHhCCcEEEEECCCCHHHHHHHHHHHHcCCCCEEECChHHHc-CcccCCCEEEE
Confidence            3444444433 2567899999999999999999999999999999975432 34667777774

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).

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

Probab=91.98  E-value=0.26  Score=43.69  Aligned_cols=41  Identities=15%  Similarity=0.017  Sum_probs=31.1

Q ss_pred             cCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhc
Q psy6712          22 DYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLN   62 (210)
Q Consensus        22 ~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~   62 (210)
                      ...+||+|++..-+...+..+.--+....++||||||++.+
T Consensus       180 a~~AdivItNHalL~~~~~~~~~iLP~~~~lIiDEAH~L~d  220 (636)
T TIGR03117       180 ARRCRILFCTHAMLGLAFRDKWGLLPQPDILIVDEAHLFEQ  220 (636)
T ss_pred             cccCCEEEECHHHHHHHhhhhcCCCCCCCEEEEeCCcchHH
Confidence            35789999999877765544322356689999999999964

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.

>PF06733 DEAD_2: DEAD_2; InterPro: IPR010614 This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin

Probab=91.78  E-value=0.15  Score=37.33  Aligned_cols=45  Identities=22%  Similarity=0.296  Sum_probs=28.5

Q ss_pred             HHhcCCCcEEEEChHHHHHHHHhcCcc--CCCccEEEechhhHHhcc
Q psy6712          19 RKLDYGQHVVSGTPGRVFDMIRRRVLR--TRNIKMLVLDEADEMLNK   63 (210)
Q Consensus        19 ~~l~~~~~Ili~Tp~~l~~~l~~~~~~--~~~~~~lviDE~~~l~~~   63 (210)
                      +......||+|++-.-+++-...+.+.  ..+-..+||||||.+.+.
T Consensus       114 r~~~~~adivi~~y~yl~~~~~~~~~~~~~~~~~ivI~DEAHNL~~~  160 (174)
T PF06733_consen  114 RELAKNADIVICNYNYLFDPSIRKSLFGIDLKDNIVIFDEAHNLEDA  160 (174)
T ss_dssp             HHCGGG-SEEEEETHHHHSHHHHHHHCT--CCCEEEEETTGGGCGGG
T ss_pred             HHhcccCCEEEeCHHHHhhHHHHhhhccccccCcEEEEecccchHHH
Confidence            455567899999977666543333221  134468999999998753

RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast [].; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 3CRV_A 3CRW_1 2VL7_A 4A15_A 2VSF_A.

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=91.71  E-value=0.71  Score=42.24  Aligned_cols=49  Identities=16%  Similarity=0.029  Sum_probs=37.4

Q ss_pred             EEecCccccCCCCC----------------------C----------cEEEEecCCCChhHHHH--hhhhhcCCCCceeE
Q psy6712         124 ITTDVWARGIDVQQ----------------------V----------SLVINYDLPNNRELYIH--RIGRSGRFGRKGVA  169 (210)
Q Consensus       124 v~T~~~~~g~d~~~----------------------~----------~~vi~~~~p~s~~~~~q--~~GR~gR~g~~g~~  169 (210)
                      ++|.....|+|+|.                      +          ++||.|++..+...-+|  |.||.||   .+.+
T Consensus       431 ~~~~~~~e~~d~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~L~e~~P~~VImYEP~~sfIR~IEvyra~r~~r---~~rV  507 (814)
T TIGR00596       431 FEIIDEENDIDIYSGAEFDNLPQHITHFLWGERDEYVLRCSLEELMPRYVIMYEPDISFIRQLEVYKASRPLR---PLRV  507 (814)
T ss_pred             ccccccccccccchhhccccccceeeeecccccchhhHHHHHhhhCCCEEEEECCChHHHHHHHHHHccCCCC---CcEE
Confidence            66777778999887                      4          89999998888888888  5555555   4677


Q ss_pred             EEEecc
Q psy6712         170 ISFVKS  175 (210)
Q Consensus       170 ~~~~~~  175 (210)
                      ++++-.
T Consensus       508 yfL~y~  513 (814)
T TIGR00596       508 YFLYYG  513 (814)
T ss_pred             EEEEEC
Confidence            777754

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

>PF00176 SNF2_N: SNF2 family N-terminal domain; InterPro: IPR000330 This domain is found in proteins involved in a variety of processes including transcription regulation (e

Probab=91.42  E-value=0.21  Score=39.55  Aligned_cols=59  Identities=14%  Similarity=0.068  Sum_probs=33.9

Q ss_pred             ceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHh---cCccCCCccEEEechhhHHh
Q psy6712           3 VQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRR---RVLRTRNIKMLVLDEADEML   61 (210)
Q Consensus         3 i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~---~~~~~~~~~~lviDE~~~l~   61 (210)
                      .++..+.|+..............+++|+|.+.+......   ..+.-.+.+.+|+||+|.+-
T Consensus        86 ~~v~~~~~~~~~~~~~~~~~~~~~vvi~ty~~~~~~~~~~~~~~l~~~~~~~vIvDEaH~~k  147 (299)
T PF00176_consen   86 LRVIIYDGDSERRRLSKNQLPKYDVVITTYETLRKARKKKDKEDLKQIKWDRVIVDEAHRLK  147 (299)
T ss_dssp             S-EEEESSSCHHHHTTSSSCCCSSEEEEEHHHHH--TSTHTTHHHHTSEEEEEEETTGGGGT
T ss_pred             ccccccccccccccccccccccceeeeccccccccccccccccccccccceeEEEecccccc
Confidence            345555555523333333345679999999887710000   11112348899999999984

g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1) [, ]. SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilises energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors. Proteins that contain this domain appear to be distantly related to the DEAX box helicases IPR001410 from INTERPRO, however no helicase activity has ever been demonstrated for these proteins. ; GO: 0003677 DNA binding, 0005524 ATP binding; PDB: 1Z63_B 1Z3I_X 3DMQ_A 3MWY_W.

>PF04851 ResIII: Type III restriction enzyme, res subunit; InterPro: IPR006935 This entry represents a domain found in the N terminus of several proteins, including helicases, the R subunit (HsdR) of type I restriction endonucleases (3

Probab=91.14  E-value=0.28  Score=35.68  Aligned_cols=43  Identities=14%  Similarity=0.252  Sum_probs=30.6

Q ss_pred             cCCCcEEEEChHHHHHHHHhcC-----------ccCCCccEEEechhhHHhccc
Q psy6712          22 DYGQHVVSGTPGRVFDMIRRRV-----------LRTRNIKMLVLDEADEMLNKG   64 (210)
Q Consensus        22 ~~~~~Ili~Tp~~l~~~l~~~~-----------~~~~~~~~lviDE~~~l~~~~   64 (210)
                      ....++++.|...+........           ......+++|+||||+.....
T Consensus       109 ~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~vI~DEaH~~~~~~  162 (184)
T PF04851_consen  109 NNDKDIILTTYQSLQSDIKEEKKIDESARRSYKLLKNKFDLVIIDEAHHYPSDS  162 (184)
T ss_dssp             BSS-SEEEEEHHHHHHHHHH---------GCHHGGGGSESEEEEETGGCTHHHH
T ss_pred             cccccchhhHHHHHHhhcccccccccchhhhhhhccccCCEEEEehhhhcCCHH
Confidence            3467899999999888765421           233467899999999887544

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

>PRK14873 primosome assembly protein PriA; Provisional

Probab=90.47  E-value=1.5  Score=39.42  Aligned_cols=62  Identities=21%  Similarity=0.235  Sum_probs=47.7

Q ss_pred             HHHHHHHHHhc-C-ceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEe
Q psy6712          82 VDWLTEKMREA-N-FTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINY  144 (210)
Q Consensus        82 ~~~l~~~l~~~-~-~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~  144 (210)
                      +..+.+.|++. + ..+..+|+++++.+|.+.+.+..+|+.+|+|+|..+.. .-+++..+||..
T Consensus       201 t~q~~~rl~~~f~~~~v~~lhS~l~~~~R~~~w~~~~~G~~~IViGtRSAvF-aP~~~LgLIIvd  264 (665)
T PRK14873        201 VDRLEAALRALLGAGDVAVLSAGLGPADRYRRWLAVLRGQARVVVGTRSAVF-APVEDLGLVAIW  264 (665)
T ss_pred             HHHHHHHHHHHcCCCcEEEECCCCCHHHHHHHHHHHhCCCCcEEEEcceeEE-eccCCCCEEEEE
Confidence            56666666543 3 57999999999999999999999999999999976533 344566677654

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=89.91  E-value=0.35  Score=38.68  Aligned_cols=44  Identities=23%  Similarity=0.156  Sum_probs=30.2

Q ss_pred             HHHhcCCCcEEEEChHHHHHHHHhcC--ccCCCccEEEechhhHHhc
Q psy6712          18 LRKLDYGQHVVSGTPGRVFDMIRRRV--LRTRNIKMLVLDEADEMLN   62 (210)
Q Consensus        18 ~~~l~~~~~Ili~Tp~~l~~~l~~~~--~~~~~~~~lviDE~~~l~~   62 (210)
                      .+.....+||||++-.-+++-..++.  ..+ .-..+||||||.+.+
T Consensus       205 ~r~~~~~Adivi~ny~yll~~~~r~~~~~~l-~~~~lIiDEAHnL~d  250 (289)
T smart00489      205 SRKAIEFANVVVLPYQYLLDPKIRQALSIEL-KDSIVIFDEAHNLDN  250 (289)
T ss_pred             HHHHhhcCCEEEECHHHHhcHHHHHHhcccc-cccEEEEeCccChHH
Confidence            34445678999999877665443322  233 467999999999975

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=89.91  E-value=0.35  Score=38.68  Aligned_cols=44  Identities=23%  Similarity=0.156  Sum_probs=30.2

Q ss_pred             HHHhcCCCcEEEEChHHHHHHHHhcC--ccCCCccEEEechhhHHhc
Q psy6712          18 LRKLDYGQHVVSGTPGRVFDMIRRRV--LRTRNIKMLVLDEADEMLN   62 (210)
Q Consensus        18 ~~~l~~~~~Ili~Tp~~l~~~l~~~~--~~~~~~~~lviDE~~~l~~   62 (210)
                      .+.....+||||++-.-+++-..++.  ..+ .-..+||||||.+.+
T Consensus       205 ~r~~~~~Adivi~ny~yll~~~~r~~~~~~l-~~~~lIiDEAHnL~d  250 (289)
T smart00488      205 SRKAIEFANVVVLPYQYLLDPKIRQALSIEL-KDSIVIFDEAHNLDN  250 (289)
T ss_pred             HHHHhhcCCEEEECHHHHhcHHHHHHhcccc-cccEEEEeCccChHH
Confidence            34445678999999877665443322  233 467999999999975

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=88.83  E-value=1.3  Score=41.37  Aligned_cols=62  Identities=23%  Similarity=0.320  Sum_probs=48.1

Q ss_pred             HHHHHHHHH----hcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCc-cccCCCCCCcEEEE
Q psy6712          82 VDWLTEKMR----EANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVW-ARGIDVQQVSLVIN  143 (210)
Q Consensus        82 ~~~l~~~l~----~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~-~~g~d~~~~~~vi~  143 (210)
                      +.+..+.++    ..++++..+++..+..++.++++.++.|+.+|+|+|..+ ...+.+.++.++|.
T Consensus       513 A~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~ll~~~v~f~~L~llVI  579 (926)
T TIGR00580       513 AQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLLQKDVKFKDLGLLII  579 (926)
T ss_pred             HHHHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHHhhCCCCcccCCEEEe
Confidence            444444443    346788999999999999999999999999999999743 34567778888774

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.

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

Probab=88.61  E-value=0.71  Score=42.66  Aligned_cols=46  Identities=11%  Similarity=0.111  Sum_probs=30.6

Q ss_pred             HHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhc
Q psy6712          17 DLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLN   62 (210)
Q Consensus        17 ~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~   62 (210)
                      ..+.....+||||+.=.-+...+.....-+...+++||||||++.+
T Consensus       409 ~ar~~a~~AdivItNHa~L~~~~~~~~~ilp~~~~lIiDEAH~L~d  454 (850)
T TIGR01407       409 RAQKNAEQAQILITNHAYLITRLVDNPELFPSFRDLIIDEAHHLPD  454 (850)
T ss_pred             HHHHHHhcCCEEEecHHHHHHHhhcccccCCCCCEEEEECcchHHH
Confidence            3344456889999986655554433222234557999999999975

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.

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

Probab=87.79  E-value=1.3  Score=36.36  Aligned_cols=17  Identities=18%  Similarity=0.460  Sum_probs=15.1

Q ss_pred             CCCccEEEechhhHHhc
Q psy6712          46 TRNIKMLVLDEADEMLN   62 (210)
Q Consensus        46 ~~~~~~lviDE~~~l~~   62 (210)
                      ....+++|+||||++.+
T Consensus        81 ~~~~DviivDEAqrl~~   97 (352)
T PF09848_consen   81 KNKYDVIIVDEAQRLRT   97 (352)
T ss_pred             CCcCCEEEEehhHhhhh
Confidence            46789999999999987

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

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

Probab=87.47  E-value=0.95  Score=32.25  Aligned_cols=33  Identities=12%  Similarity=0.127  Sum_probs=20.9

Q ss_pred             EEEEChHHHHHHHHhcCccCCCccEEEechhhHH
Q psy6712          27 VVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEM   60 (210)
Q Consensus        27 Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l   60 (210)
                      |=+.|-..+...+.+ .....+.+++|+||+|..
T Consensus        75 i~vMc~at~~~~~~~-p~~~~~yd~II~DEcH~~  107 (148)
T PF07652_consen   75 IDVMCHATYGHFLLN-PCRLKNYDVIIMDECHFT  107 (148)
T ss_dssp             EEEEEHHHHHHHHHT-SSCTTS-SEEEECTTT--
T ss_pred             ccccccHHHHHHhcC-cccccCccEEEEeccccC
Confidence            445555555555555 445689999999999975

The domain is related to the DEAD/DEAH box helicase domain which is found in a large family of ATPases.; GO: 0005524 ATP binding, 0008026 ATP-dependent helicase activity, 0019079 viral genome replication; PDB: 2QEQ_A 2V6J_A 2V6I_A 8OHM_A 4A92_B 1JR6_A 1HEI_A 1ONB_A 1A1V_A 1YMF_A ....

>KOG1133|consensus

Probab=87.26  E-value=4.3  Score=36.32  Aligned_cols=83  Identities=19%  Similarity=0.387  Sum_probs=53.2

Q ss_pred             HHHHHHHHh----cCCCcEEEEe--cCccccCCCCC--CcEEEEecCCCC------------------------hhHH--
Q psy6712         108 RDGIMKEFR----SGTSRVLITT--DVWARGIDVQQ--VSLVINYDLPNN------------------------RELY--  153 (210)
Q Consensus       108 r~~~~~~f~----~g~~~ilv~T--~~~~~g~d~~~--~~~vi~~~~p~s------------------------~~~~--  153 (210)
                      -..+++.|.    .|.-.+|++.  ..+++|+|+.+  +..|+..++|..                        ..-|  
T Consensus       672 ~~dvl~~Ya~a~~~g~GaiLlaVVGGKlSEGINF~D~LgRaVvvVGlPyPN~~s~EL~er~k~l~~k~~~~gagke~yEn  751 (821)
T KOG1133|consen  672 VEDVLEGYAEAAERGRGAILLAVVGGKLSEGINFSDDLGRAVVVVGLPYPNIQSVELQERMKHLDGKLPTPGAGKELYEN  751 (821)
T ss_pred             HHHHHHHHHHHhhcCCCeEEEEEeccccccccccccccccEEEEeecCCCCCCCHHHHHHHHHhhhccCCCCchHHHHHH
Confidence            345555554    4554566444  68899999986  778888887721                        1111  


Q ss_pred             ------HHhhhhhcCCCCceeEEEEeccCcH-HHHHHHHHHhcC
Q psy6712         154 ------IHRIGRSGRFGRKGVAISFVKSDDI-RILRDIEQYYST  190 (210)
Q Consensus       154 ------~q~~GR~gR~g~~g~~~~~~~~~~~-~~~~~~~~~~~~  190 (210)
                            =|.+|||-|.-++=.++.+++..-. ...+++.+|+..
T Consensus       752 lCMkAVNQsIGRAIRH~~DYA~i~LlD~RY~~p~~RKLp~WI~~  795 (821)
T KOG1133|consen  752 LCMKAVNQSIGRAIRHRKDYASIYLLDKRYARPLSRKLPKWIRK  795 (821)
T ss_pred             HHHHHHHHHHHHHHhhhccceeEEEehhhhcCchhhhccHHHHh
Confidence                  1788999998776667777765433 455577777743

>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=86.64  E-value=1.3  Score=27.31  Aligned_cols=51  Identities=12%  Similarity=0.106  Sum_probs=37.9

Q ss_pred             CCceEEEEEcCcchHHHHHHhc---C-CCcEEEEChHHHHHHHHhcCccCCCccEEEechh
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLD---Y-GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEA   57 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~---~-~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~   57 (210)
                      .|+++..++|+.+.++....+.   . ..+|||+|.      .....+++..++++|+-+.
T Consensus         6 ~~~~~~~i~~~~~~~~r~~~~~~f~~~~~~vli~t~------~~~~Gid~~~~~~vi~~~~   60 (78)
T PF00271_consen    6 KGIKVAIIHGDMSQKERQEILKKFNSGEIRVLIATD------ILGEGIDLPDASHVIFYDP   60 (78)
T ss_dssp             TTSSEEEESTTSHHHHHHHHHHHHHTTSSSEEEESC------GGTTSSTSTTESEEEESSS
T ss_pred             CCCcEEEEECCCCHHHHHHHHHHhhccCceEEEeec------ccccccccccccccccccc
Confidence            3789999999998777665543   3 569999993      2334578888998887655

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 ....

>KOG0339|consensus

Probab=85.72  E-value=6.5  Score=34.03  Aligned_cols=58  Identities=16%  Similarity=0.227  Sum_probs=43.3

Q ss_pred             HHHHHHHH-HhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEec------CccccCCCCCCcEEEE
Q psy6712          82 VDWLTEKM-REANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTD------VWARGIDVQQVSLVIN  143 (210)
Q Consensus        82 ~~~l~~~l-~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~------~~~~g~d~~~~~~vi~  143 (210)
                      +...++.| +..|+++.++||++|..++..-++    ....++|||.      .-..++|+..+++++.
T Consensus       312 i~~eaKkf~K~ygl~~v~~ygGgsk~eQ~k~Lk----~g~EivVaTPgRlid~VkmKatn~~rvS~LV~  376 (731)
T KOG0339|consen  312 IFSEAKKFGKAYGLRVVAVYGGGSKWEQSKELK----EGAEIVVATPGRLIDMVKMKATNLSRVSYLVL  376 (731)
T ss_pred             HHHHHHHhhhhccceEEEeecCCcHHHHHHhhh----cCCeEEEechHHHHHHHHhhcccceeeeEEEE
Confidence            45556666 667999999999999988775555    3568999996      2234778888887763

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

Probab=84.69  E-value=5.2  Score=37.88  Aligned_cols=62  Identities=18%  Similarity=0.302  Sum_probs=50.4

Q ss_pred             HHHHHHHHHh----cCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEec-CccccCCCCCCcEEEE
Q psy6712          82 VDWLTEKMRE----ANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTD-VWARGIDVQQVSLVIN  143 (210)
Q Consensus        82 ~~~l~~~l~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~-~~~~g~d~~~~~~vi~  143 (210)
                      +++..+.|++    ..+++..+..-.+.+++.++++..++|+++|+|+|. .+..++-+-+.-++|.
T Consensus       656 A~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTHrLL~kdv~FkdLGLlII  722 (1139)
T COG1197         656 AQQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHRLLSKDVKFKDLGLLII  722 (1139)
T ss_pred             HHHHHHHHHHHhcCCCeeEEEecccCCHHHHHHHHHHHhcCCccEEEechHhhCCCcEEecCCeEEE
Confidence            5555555544    467888899999999999999999999999999996 5566777778887774

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=84.52  E-value=2.1  Score=39.12  Aligned_cols=71  Identities=11%  Similarity=0.188  Sum_probs=56.2

Q ss_pred             CCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCC--Cc-----------eeEEEEeccCcHHHHHHHH
Q psy6712         119 TSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFG--RK-----------GVAISFVKSDDIRILRDIE  185 (210)
Q Consensus       119 ~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g--~~-----------g~~~~~~~~~~~~~~~~~~  185 (210)
                      -.+.+.+-.++-+|.|-|+|=.++-.....|..+=.|.+||..|..  ..           ..-.++++..+..+++.+.
T Consensus       483 plRFIFS~waLrEGWDNPNVFtIckL~~S~SeiSK~QeVGRGLRLaVNe~G~RV~~~~~~~n~L~vlv~~sek~Fv~~Lq  562 (985)
T COG3587         483 PLRFIFSKWALREGWDNPNVFTICKLRSSGSEISKLQEVGRGLRLAVNENGERVTKDFDFPNELTVLVNESEKDFVKALQ  562 (985)
T ss_pred             cceeeeehhHHhhcCCCCCeeEEEEecCCCcchHHHHHhccceeeeeccccceecccccccceEEEEecccHHHHHHHHH
Confidence            3578899999999999999999999998999999999999998862  11           2234566777888887776


Q ss_pred             HHhc
Q psy6712         186 QYYS  189 (210)
Q Consensus       186 ~~~~  189 (210)
                      +-+.
T Consensus       563 kEI~  566 (985)
T COG3587         563 KEIN  566 (985)
T ss_pred             HHHH
Confidence            5443

>PRK10689 transcription-repair coupling factor; Provisional

Probab=83.68  E-value=3.3  Score=39.63  Aligned_cols=62  Identities=18%  Similarity=0.230  Sum_probs=46.7

Q ss_pred             HHHHHHHHHh----cCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCc-cccCCCCCCcEEEE
Q psy6712          82 VDWLTEKMRE----ANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVW-ARGIDVQQVSLVIN  143 (210)
Q Consensus        82 ~~~l~~~l~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~-~~g~d~~~~~~vi~  143 (210)
                      +..+.+.+.+    .++++..+++..+..++.++++...+|..+|+|+|..+ ...+.+.++.++|.
T Consensus       662 A~Q~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL~~~v~~~~L~lLVI  728 (1147)
T PRK10689        662 AQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLIV  728 (1147)
T ss_pred             HHHHHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHHhCCCCHhhCCEEEE
Confidence            4545444443    35788899999999999999999999999999999643 33456667777764

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

Probab=83.52  E-value=1.2  Score=33.56  Aligned_cols=39  Identities=15%  Similarity=0.173  Sum_probs=23.3

Q ss_pred             HhcCCCcEEEEChHHHHHHHHhcCccCC--CccEEEechhhHHhc
Q psy6712          20 KLDYGQHVVSGTPGRVFDMIRRRVLRTR--NIKMLVLDEADEMLN   62 (210)
Q Consensus        20 ~l~~~~~Ili~Tp~~l~~~l~~~~~~~~--~~~~lviDE~~~l~~   62 (210)
                      .+.+.++|+++|+.....    ..+...  .++++|||||-.+.+
T Consensus       166 ~~l~~~~vi~~T~~~~~~----~~~~~~~~~~d~vIvDEAsq~~e  206 (236)
T PF13086_consen  166 FILKEADVIFTTLSSAAS----PFLSNFKEKFDVVIVDEASQITE  206 (236)
T ss_dssp             HHHHT-SEEEEETCGGG-----CCGTT-----SEEEETTGGGS-H
T ss_pred             hhcccccccccccccchh----hHhhhhcccCCEEEEeCCCCcch
Confidence            344578999999986522    222212  789999999987653

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

Probab=82.82  E-value=1.9  Score=38.94  Aligned_cols=49  Identities=24%  Similarity=0.383  Sum_probs=40.2

Q ss_pred             CceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEE
Q psy6712          93 NFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVI  142 (210)
Q Consensus        93 ~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi  142 (210)
                      |.++..+|+++++.+|.+.+.+.++|+.+|+|+|..+.- .-+++.-+||
T Consensus       270 g~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSAlF-~Pf~~LGLII  318 (730)
T COG1198         270 GAKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSALF-LPFKNLGLII  318 (730)
T ss_pred             CCChhhhcccCChHHHHHHHHHHhcCCceEEEEechhhc-CchhhccEEE
Confidence            689999999999999999999999999999999975422 2344555555

>PF05872 DUF853: Bacterial protein of unknown function (DUF853); InterPro: IPR008571 Members of this family have a P-loop containing nucleotide triphosphate hydrolases fold

Probab=82.71  E-value=2.6  Score=35.83  Aligned_cols=46  Identities=17%  Similarity=0.230  Sum_probs=29.7

Q ss_pred             CCCccE-EEechhhHHhccchHHHHHHHHhhCCCchhHHHHHHHHHhcCceEEEecC
Q psy6712          46 TRNIKM-LVLDEADEMLNKGFKEQIYDVYRYLPPATQVDWLTEKMREANFTVSSMHG  101 (210)
Q Consensus        46 ~~~~~~-lviDE~~~l~~~~~~~~~~~i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~  101 (210)
                      +.+=++ ++|||||.+++.....-+++          ++.+.+..+++|+.+.++.-
T Consensus       252 ~dkPklVfFfDEAHLLF~da~kall~~----------ieqvvrLIRSKGVGv~fvTQ  298 (502)
T PF05872_consen  252 LDKPKLVFFFDEAHLLFNDAPKALLDK----------IEQVVRLIRSKGVGVYFVTQ  298 (502)
T ss_pred             CCCceEEEEEechhhhhcCCCHHHHHH----------HHHHHHHhhccCceEEEEeC
Confidence            444454 66999999997654332222          46666777777777777554

This family is restricted to bacterial proteins, none of which have currently been characterised.

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

Probab=82.56  E-value=2.1  Score=40.10  Aligned_cols=44  Identities=9%  Similarity=0.070  Sum_probs=29.6

Q ss_pred             HHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhc
Q psy6712          19 RKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLN   62 (210)
Q Consensus        19 ~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~   62 (210)
                      +.-.+..||||+-=.-+...+..+.--+...+++||||||++.+
T Consensus       426 r~~a~~AdivItNHalLl~dl~~~~~ilp~~~~lViDEAH~l~d  469 (928)
T PRK08074        426 KNRAKFADLVITNHALLLTDLTSEEPLLPSYEHIIIDEAHHFEE  469 (928)
T ss_pred             HHHHhcCCEEEECHHHHHHHHhhhcccCCCCCeEEEECCchHHH
Confidence            33346789999976555444422222346679999999999974

>KOG0391|consensus

Probab=81.17  E-value=3.1  Score=39.62  Aligned_cols=60  Identities=22%  Similarity=0.228  Sum_probs=41.4

Q ss_pred             CceEEEEEcCcchHHHHHHhcCC---CcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhcc
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYG---QHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNK   63 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~---~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~   63 (210)
                      |.++..++|........+.-+..   +||.|++-..+..-+..  +.-+..+|+|+||||.+-++
T Consensus       690 glKILTYyGs~kErkeKRqgW~kPnaFHVCItSYklv~qd~~A--FkrkrWqyLvLDEaqnIKnf  752 (1958)
T KOG0391|consen  690 GLKILTYYGSHKERKEKRQGWAKPNAFHVCITSYKLVFQDLTA--FKRKRWQYLVLDEAQNIKNF  752 (1958)
T ss_pred             cceEeeecCCHHHHHHHhhcccCCCeeEEeehhhHHHHhHHHH--HHhhccceeehhhhhhhcch
Confidence            57888899988776666665543   48888876654442221  23356789999999999654

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=80.50  E-value=6.9  Score=23.73  Aligned_cols=50  Identities=16%  Similarity=0.247  Sum_probs=33.7

Q ss_pred             CceEEEEEcCcchHHHHHHhc---C-CCcEEEEChHHHHHHHHhcCccCCCccEEEechh
Q psy6712           2 NVQCHACIGGTNLSEDLRKLD---Y-GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEA   57 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~---~-~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~   57 (210)
                      ++++..++|+.+..++...+.   + ...|+++|.     .+ ...+++..++.+|+-+.
T Consensus        11 ~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~-----~~-~~Gi~~~~~~~vi~~~~   64 (82)
T smart00490       11 GIKVARLHGGLSQEEREEILEKFNNGKIKVLVATD-----VA-ERGLDLPGVDLVIIYDL   64 (82)
T ss_pred             CCeEEEEECCCCHHHHHHHHHHHHcCCCeEEEECC-----hh-hCCcChhcCCEEEEeCC
Confidence            577899999888776554433   3 458888884     22 23456777888876655

>KOG0952|consensus

Probab=80.06  E-value=0.84  Score=42.37  Aligned_cols=59  Identities=15%  Similarity=0.206  Sum_probs=43.6

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHh--cCccCCCccEEEechhhHHhcc
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRR--RVLRTRNIKMLVLDEADEMLNK   63 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~--~~~~~~~~~~lviDE~~~l~~~   63 (210)
                      |+++.-+.|....+  .+. ...++++|+||+++....++  .+-.++++..+|+||.|++.+.
T Consensus      1001 g~k~ie~tgd~~pd--~~~-v~~~~~~ittpek~dgi~Rsw~~r~~v~~v~~iv~de~hllg~~ 1061 (1230)
T KOG0952|consen 1001 GIKVIELTGDVTPD--VKA-VREADIVITTPEKWDGISRSWQTRKYVQSVSLIVLDEIHLLGED 1061 (1230)
T ss_pred             CceeEeccCccCCC--hhh-eecCceEEcccccccCccccccchhhhccccceeecccccccCC
Confidence            56677777776665  222 23679999999998887773  4455789999999999988753

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	210
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		2e-61
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		2e-61
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		2e-61
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		3e-61
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		9e-61
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		9e-61
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		3e-40
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		4e-40
1fuk_A	165	Crystal Structure Of The Carboxy Terminal Domain Of		1e-35
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		2e-35
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		3e-34
2hjv_A	163	Structure Of The Second Domain (Residues 207-368) O		3e-26
2wax_A	193	Structure Of The Human Ddx6 C-Terminal Domain In Co		2e-25
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		2e-25
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		2e-25
2kbf_A	187	Solution Structure Of Carboxyl-Terminal Domain Of D		4e-25
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		5e-25
1qva_A	223	Yeast Initiation Factor 4a N-Terminal Domain Length		7e-25
1qde_A	224	Crystal Structure Of The Atpase Domain Of Translati		9e-25
3gfp_A	189	Structure Of The C-Terminal Domain Of The Dead-Box		1e-24
3peu_A	188	S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To		1e-24
2rb4_A	175	Crystal Structure Of The Helicase Domain Of Human D		1e-23
3bor_A	237	Crystal Structure Of The Deadc Domain Of Human Tran		1e-23
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		4e-23
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		4e-23
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		4e-23
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		4e-23
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		7e-23
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		7e-23
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		7e-23
1t5i_A	172	Crystal Structure Of The C-Terminal Domain Of Uap56		1e-22
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		1e-22
2g9n_A	221	Structure Of The Dead Domain Of Human Eukaryotic In		2e-22
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		2e-21
2jgn_A	185	Ddx3 Helicase Domain Length = 185		3e-21
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		4e-21
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		3e-19
2yjt_D	170	Crystal Structure Of E. Coli Dead-Box Protein Srmb		2e-18
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		7e-17
2p6n_A	191	Human Dead-box Rna Helicase Ddx41, Helicase Domain		3e-16
4db4_A	256	Mss116p Dead-Box Helicase Domain 2 Bound To A Chima		6e-14
4db2_C	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		6e-14
4db2_A	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		6e-14
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		8e-14
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		9e-14
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		1e-13
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		5e-13
3i32_A	300	Dimeric Structure Of A Hera Helicase Fragment Inclu		8e-13
3eaq_A	212	Novel Dimerization Motif In The Dead Box Rna Helica		3e-12
2oxc_A	230	Human Dead-Box Rna Helicase Ddx20, Dead Domain In C		6e-12
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		8e-10
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		8e-10
2kbe_A	226	Solution Structure Of Amino-Terminal Domain Of Dbp5		2e-09
1q0u_A	219	Crystal Structure Of The Bstdead N-Terminal Domain		7e-09
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		1e-08
3ly5_A	262	Ddx18 Dead-Domain Length = 262		4e-08
1t6n_A	220	Crystal Structure Of The N-Terminal Domain Of Human		5e-07
1oyy_A	523	Structure Of The Recq Catalytic Core Bound To Atp-G		1e-06
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		2e-06
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		2e-06
1oyw_A	523	Structure Of The Recq Catalytic Core Length = 523		3e-06
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		1e-05
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		3e-05
4gl2_A	699	Structural Basis For Dsrna Duplex Backbone Recognit		4e-05
1gm5_A	780	Structure Of Recg Bound To Three-Way Dna Junction L		4e-05
1d9z_A	657	Crystal Structure Of The Dna Repair Protein Uvrb In		5e-05
1d9x_A	658	Crystal Structure Of The Dna Repair Protein Uvrb Le		5e-05
2fdc_A	658	Structural Basis Of Dna Damage Recognition And Proc		6e-05
1t5l_A	658	Crystal Structure Of The Dna Repair Protein Uvrb Po		6e-05
3uwx_B	683	Crystal Structure Of Uvra-Uvrb Complex Length = 683		6e-05
1wp9_A	494	Crystal Structure Of Pyrococcus Furiosus Hef Helica		9e-05
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		4e-04
3fmo_B	300	Crystal Structure Of The Nucleoporin Nup214 In Comp		4e-04
3v4r_A	667	Crystal Structure Of A Uvrb Dimer-Dna Complex Lengt		5e-04
2d7d_A	661	Structural Insights Into The Cryptic Dna Dependent		5e-04
3fhc_B	235	Crystal Structure Of Human Dbp5 In Complex With Nup		6e-04

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score =  231 bits (590), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 107/118 (90%), Positives = 115/118 (97%)
Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +VDWLTEKMREANFTVSSMHGDMPQKER+ IMKEFRSG SRVLI+TDVWARG+DV QVSL
Sbjct: 288 KVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSL 347
Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           +INYDLPNNRELYIHRIGRSGR+GRKGVAI+FVK+DDIRILRDIEQYYSTQIDEMPMN
Sbjct: 348 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN 405

>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 =  231 bits (590), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 107/118 (90%), Positives = 115/118 (97%)
Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +VDWLTEKMREANFTVSSMHGDMPQKER+ IMKEFRSG SRVLI+TDVWARG+DV QVSL
Sbjct: 289 KVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSL 348
Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           +INYDLPNNRELYIHRIGRSGR+GRKGVAI+FVK+DDIRILRDIEQYYSTQIDEMPMN
Sbjct: 349 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN 406

>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 =  231 bits (590), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 107/118 (90%), Positives = 115/118 (97%)
Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +VDWLTEKMREANFTVSSMHGDMPQKER+ IMKEFRSG SRVLI+TDVWARG+DV QVSL
Sbjct: 289 KVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSL 348
Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           +INYDLPNNRELYIHRIGRSGR+GRKGVAI+FVK+DDIRILRDIEQYYSTQIDEMPMN
Sbjct: 349 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN 406

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score =  231 bits (588), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 107/118 (90%), Positives = 115/118 (97%)
Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +VDWLTEKMREANFTVSSMHGDMPQKER+ IMKEFRSG SRVLI+TDVWARG+DV QVSL
Sbjct: 267 KVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSL 326
Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           +INYDLPNNRELYIHRIGRSGR+GRKGVAI+FVK+DDIRILRDIEQYYSTQIDEMPMN
Sbjct: 327 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN 384

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score =  229 bits (584), Expect = 9e-61,   Method: Compositional matrix adjust.
 Identities = 105/118 (88%), Positives = 115/118 (97%)
Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +VDWLTEKMREANFTVSSMHGDMPQKER+ IMKEFRSG SRVLI+TDVWARG+DV QVSL
Sbjct: 252 KVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSL 311
Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           +INYDLPNNRELYIHRIGRSGR+GRKGVA++FVK+DDIR+LRDIEQYYSTQIDEMPMN
Sbjct: 312 IINYDLPNNRELYIHRIGRSGRYGRKGVAVNFVKNDDIRVLRDIEQYYSTQIDEMPMN 369

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score =  229 bits (584), Expect = 9e-61,   Method: Compositional matrix adjust.
 Identities = 105/118 (88%), Positives = 115/118 (97%)
Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +VDWLTEKMREANFTVSSMHGDMPQKER+ IMKEFRSG SRVLI+TDVWARG+DV QVSL
Sbjct: 252 KVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSL 311
Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           +INYDLPNNRELYIHRIGRSGR+GRKGVA++FVK+DDIR+LRDIEQYYSTQIDEMPMN
Sbjct: 312 IINYDLPNNRELYIHRIGRSGRYGRKGVAVNFVKNDDIRVLRDIEQYYSTQIDEMPMN 369

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score =  161 bits (407), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 90/118 (76%), Positives = 102/118 (86%)
Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +VDWLTEKM   +FTVS+MHGDM QKERD IM+EFRSG+SRVLITTD+ ARGIDVQQVSL
Sbjct: 266 KVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSL 325
Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           VINYDLP NRE YIHRIGR GRFGRKGVAI+ V  +D R LRDIE +Y+T I+EMP+N
Sbjct: 326 VINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLN 383

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score =  160 bits (406), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 90/118 (76%), Positives = 102/118 (86%)
Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +VDWLTEKM   +FTVS+MHGDM QKERD IM+EFRSG+SRVLITTD+ ARGIDVQQVSL
Sbjct: 292 KVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSL 351
Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           VINYDLP NRE YIHRIGR GRFGRKGVAI+ V  +D R LRDIE +Y+T I+EMP+N
Sbjct: 352 VINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLN 409

>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast Eif4a Length = 165

Iteration: 1
 Score =  145 bits (367), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 78/116 (67%), Positives = 102/116 (87%)
Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +V+ LT K+R   FTVS+++ D+PQ+ERD IMKEFRSG+SR+LI+TD+ ARGIDVQQVSL
Sbjct: 42  KVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSL 101
Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMP 196
           VINYDLP N+E YIHRIGR GRFGRKGVAI+FV ++D+  +R++E++YSTQI+E+P
Sbjct: 102 VINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELP 157

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score =  145 bits (365), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 78/116 (67%), Positives = 102/116 (87%)
Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +V+ LT K+R   FTVS+++ D+PQ+ERD IMKEFRSG+SR+LI+TD+ ARGIDVQQVSL
Sbjct: 272 KVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSL 331
Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMP 196
           VINYDLP N+E YIHRIGR GRFGRKGVAI+FV ++D+  +R++E++YSTQI+E+P
Sbjct: 332 VINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELP 387

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score =  141 bits (355), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 77/116 (66%), Positives = 100/116 (86%)
Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +V+ LT K+R   FTVS+++ D+PQ+ERD I KEFRSG+SR+LI+TD+ ARGIDVQQVSL
Sbjct: 271 KVEELTTKLRNDKFTVSAIYSDLPQQERDTIXKEFRSGSSRILISTDLLARGIDVQQVSL 330
Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMP 196
           VINYDLP N+E YIHRIGR GRFGRKGVAI+FV ++D+   R++E++YSTQI+E+P
Sbjct: 331 VINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAXRELEKFYSTQIEELP 386

>pdb|2HJV|A Chain A, Structure Of The Second Domain (Residues 207-368) Of The Bacillus Subtilis Yxin Protein Length = 163

Iteration: 1
 Score =  114 bits (286), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 54/115 (46%), Positives = 78/115 (67%)
Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
            V+ LT+++ +  +    +HG M Q++R  +M EF+ G  R L+ TDV ARGID++ +SL
Sbjct: 47  HVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISL 106
Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEM 195
           VINYDLP  +E Y+HR GR+GR G KG AISFV + + R L DIE+Y   +I ++
Sbjct: 107 VINYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAFEKRFLADIEEYIGFEIQKI 161

>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 =  112 bits (280), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 54/132 (40%), Positives = 84/132 (63%), Gaps = 2/132 (1%)
Query: 79  ATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQV 138
           + +V+ L +K+ +  ++   +H  M Q+ R+ +  +FR+G  R L+ TD++ RGID+Q V
Sbjct: 54  SQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAV 113
Query: 139 SLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           ++VIN+D P   E Y+HRIGRSGRFG  G+AI+ +  DD   L+ IE+   T+I  +P N
Sbjct: 114 NVVINFDFPKLAETYLHRIGRSGRFGHLGLAINLITYDDRFNLKSIEEQLGTEIKPIPSN 173
Query: 199 GKRSLHSYPARY 210
             +SL  Y A Y
Sbjct: 174 IDKSL--YVAEY 183

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score =  112 bits (280), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 56/108 (51%), Positives = 75/108 (69%), Gaps = 7/108 (6%)
Query: 88  KMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLP 147
           K++     VS +HGD+  +ERD ++ +FR G S+VLITT+V ARGID+  VS+V+NYDLP
Sbjct: 262 KLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLP 321
Query: 148 N------NRELYIHRIGRSGRFGRKGVAISFVK-SDDIRILRDIEQYY 188
                  +   YIHRIGR+GRFGRKGVAISFV   +   IL  I++Y+
Sbjct: 322 TLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYF 369

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score =  112 bits (279), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 56/108 (51%), Positives = 75/108 (69%), Gaps = 7/108 (6%)
Query: 88  KMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLP 147
           K++     VS +HGD+  +ERD ++ +FR G S+VLITT+V ARGID+  VS+V+NYDLP
Sbjct: 262 KLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLP 321
Query: 148 N------NRELYIHRIGRSGRFGRKGVAISFVK-SDDIRILRDIEQYY 188
                  +   YIHRIGR+GRFGRKGVAISFV   +   IL  I++Y+
Sbjct: 322 TLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYF 369

>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p Length = 187

Iteration: 1
 Score =  110 bits (276), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 57/121 (47%), Positives = 79/121 (65%), Gaps = 7/121 (5%)
Query: 75  YLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGID 134
           ++      + L  K++     VS +HGD+  +ERD ++ +FR G S+VLITT+V ARGID
Sbjct: 41  FVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGID 100
Query: 135 VQQVSLVINYDLPN------NRELYIHRIGRSGRFGRKGVAISFVK-SDDIRILRDIEQY 187
           +  VS+V+NYDLP       +   YIHRIGR+GRFGRKGVAISFV   +   IL  I++Y
Sbjct: 101 IPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKY 160
Query: 188 Y 188
           +
Sbjct: 161 F 161

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score =  110 bits (276), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 57/145 (39%), Positives = 84/145 (57%), Gaps = 1/145 (0%)
Query: 61  LNKGF-KEQIYDVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGT 119
           LN  F K QI     +     +V+ L +K+ +  ++    H  M Q+ER+ +  EFR G 
Sbjct: 249 LNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGK 308
Query: 120 SRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIR 179
            R L+ +D+  RGID+Q V++VIN+D P   E Y+HRIGRSGRFG  G+AI+ +  +D  
Sbjct: 309 VRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRF 368
Query: 180 ILRDIEQYYSTQIDEMPMNGKRSLH 204
            L  IEQ   T+I  +P    +SL+
Sbjct: 369 NLYKIEQELGTEIAAIPATIDKSLY 393

>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain Length = 223

Iteration: 1
 Score =  110 bits (274), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 53/89 (59%), Positives = 63/89 (70%), Gaps = 1/89 (1%)
Query: 1   MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEM 60
           M+++ HACIGGT+  ED   L   Q VV GTPGRVFD I+RR  RT  IKM +LDEADEM
Sbjct: 116 MDIKVHACIGGTSFVEDAEGLRDAQIVV-GTPGRVFDNIQRRRFRTDKIKMFILDEADEM 174
Query: 61  LNKGFKEQIYDVYRYLPPATQVDWLTEKM 89
           L+ GFKEQIY ++  LPP TQV  L+  M
Sbjct: 175 LSSGFKEQIYQIFTLLPPTTQVVLLSATM 203

>pdb|1QDE|A Chain A, Crystal Structure Of The Atpase Domain Of Translation Initiation Factor 4a From Saccharomyces Cerevisiae-The Prototype Of The Dead Box Protein Family Length = 224

Iteration: 1
 Score =  109 bits (273), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 53/89 (59%), Positives = 63/89 (70%), Gaps = 1/89 (1%)
Query: 1   MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEM 60
           M+++ HACIGGT+  ED   L   Q VV GTPGRVFD I+RR  RT  IKM +LDEADEM
Sbjct: 109 MDIKVHACIGGTSFVEDAEGLRDAQIVV-GTPGRVFDNIQRRRFRTDKIKMFILDEADEM 167
Query: 61  LNKGFKEQIYDVYRYLPPATQVDWLTEKM 89
           L+ GFKEQIY ++  LPP TQV  L+  M
Sbjct: 168 LSSGFKEQIYQIFTLLPPTTQVVLLSATM 196

>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein Dbp5 Length = 189

Iteration: 1
 Score =  109 bits (273), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 57/121 (47%), Positives = 78/121 (64%), Gaps = 7/121 (5%)
Query: 75  YLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGID 134
           ++      + L  K++     VS +HGD+  +ERD ++ +FR G S+VLITT+V ARGID
Sbjct: 43  FVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGID 102
Query: 135 VQQVSLVINYDLPN------NRELYIHRIGRSGRFGRKGVAISFV-KSDDIRILRDIEQY 187
           +  VS V+NYDLP       +   YIHRIGR+GRFGRKGVAISFV   +   IL  I++Y
Sbjct: 103 IPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKY 162
Query: 188 Y 188
           +
Sbjct: 163 F 163

>pdb|3PEU|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1 H337r And Ip6 Length = 188

Iteration: 1
 Score =  109 bits (272), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 57/121 (47%), Positives = 78/121 (64%), Gaps = 7/121 (5%)
Query: 75  YLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGID 134
           ++      + L  K++     VS +HGD+  +ERD ++ +FR G S+VLITT+V ARGID
Sbjct: 42  FVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGID 101
Query: 135 VQQVSLVINYDLPN------NRELYIHRIGRSGRFGRKGVAISFV-KSDDIRILRDIEQY 187
           +  VS V+NYDLP       +   YIHRIGR+GRFGRKGVAISFV   +   IL  I++Y
Sbjct: 102 IPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKY 161
Query: 188 Y 188
           +
Sbjct: 162 F 162

>pdb|2RB4|A Chain A, Crystal Structure Of The Helicase Domain Of Human Ddx25 Rna Helicase Length = 175

Iteration: 1
 Score =  106 bits (264), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 49/118 (41%), Positives = 82/118 (69%), Gaps = 6/118 (5%)
Query: 84  WLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVIN 143
           WLT +M +    VS + G++  ++R  I++ FR G  +VLITT+V ARGIDV+QV++V+N
Sbjct: 49  WLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVN 108
Query: 144 YDLPNNR------ELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEM 195
           +DLP  +      E Y+HRIGR+GRFG+KG+A + ++ D++  L  I+ ++++ I ++
Sbjct: 109 FDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDELPSLMKIQDHFNSSIKQL 166

>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation Initiation Factor 4a-2 Length = 237

Iteration: 1
 Score =  105 bits (263), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 49/90 (54%), Positives = 65/90 (72%), Gaps = 1/90 (1%)
Query: 1   MNVQCHACIGGTNLSEDLRKLDY-GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADE 59
           M   CHACIGGTN+  +++KL     H+V GTPGRVFDM+ RR L  + IKM VLDEADE
Sbjct: 125 MGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADE 184
Query: 60  MLNKGFKEQIYDVYRYLPPATQVDWLTEKM 89
           ML++GFK+QIY++++ L  + QV  L+  M
Sbjct: 185 MLSRGFKDQIYEIFQKLNTSIQVVLLSATM 214

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score =  104 bits (259), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 48/119 (40%), Positives = 83/119 (69%), Gaps = 7/119 (5%)
Query: 84  WLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVIN 143
           WL  ++ +    V+ + G+M  ++R  +++ FR G  +VL+TT+V ARGIDV+QVS+VIN
Sbjct: 348 WLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVIN 407
Query: 144 YDLPNNR------ELYIHRIGRSGRFGRKGVAISFVKSD-DIRILRDIEQYYSTQIDEM 195
           +DLP ++      E Y+HRIGR+GRFG++G+A++ V S   + IL  I+++++ +I+ +
Sbjct: 408 FDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERL 466

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score =  104 bits (259), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 48/119 (40%), Positives = 83/119 (69%), Gaps = 7/119 (5%)
Query: 84  WLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVIN 143
           WL  ++ +    V+ + G+M  ++R  +++ FR G  +VL+TT+V ARGIDV+QVS+VIN
Sbjct: 297 WLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVIN 356
Query: 144 YDLPNNR------ELYIHRIGRSGRFGRKGVAISFVKSD-DIRILRDIEQYYSTQIDEM 195
           +DLP ++      E Y+HRIGR+GRFG++G+A++ V S   + IL  I+++++ +I+ +
Sbjct: 357 FDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERL 415

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score =  104 bits (259), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 48/119 (40%), Positives = 83/119 (69%), Gaps = 7/119 (5%)
Query: 84  WLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVIN 143
           WL  ++ +    V+ + G+M  ++R  +++ FR G  +VL+TT+V ARGIDV+QVS+VIN
Sbjct: 318 WLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVIN 377
Query: 144 YDLPNNR------ELYIHRIGRSGRFGRKGVAISFVKSD-DIRILRDIEQYYSTQIDEM 195
           +DLP ++      E Y+HRIGR+GRFG++G+A++ V S   + IL  I+++++ +I+ +
Sbjct: 378 FDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERL 436

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score =  104 bits (259), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 48/119 (40%), Positives = 83/119 (69%), Gaps = 7/119 (5%)
Query: 84  WLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVIN 143
           WL  ++ +    V+ + G+M  ++R  +++ FR G  +VL+TT+V ARGIDV+QVS+VIN
Sbjct: 281 WLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVIN 340
Query: 144 YDLPNNR------ELYIHRIGRSGRFGRKGVAISFVKSD-DIRILRDIEQYYSTQIDEM 195
           +DLP ++      E Y+HRIGR+GRFG++G+A++ V S   + IL  I+++++ +I+ +
Sbjct: 341 FDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERL 399

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score =  103 bits (257), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 43/113 (38%), Positives = 76/113 (67%), Gaps = 1/113 (0%)
Query: 85  LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINY 144
           L + + E NF   ++H  MPQ+ER    ++F+    R+L+ T+++ RG+D+++V++  NY
Sbjct: 266 LAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNY 325
Query: 145 DLPNNRELYIHRIGRSGRFGRKGVAISFVK-SDDIRILRDIEQYYSTQIDEMP 196
           D+P + + Y+HR+ R+GRFG KG+AI+FV   +D +IL D++  +   I E+P
Sbjct: 326 DMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELP 378

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score =  103 bits (257), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 43/113 (38%), Positives = 76/113 (67%), Gaps = 1/113 (0%)
Query: 85  LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINY 144
           L + + E NF   ++H  MPQ+ER    ++F+    R+L+ T+++ RG+D+++V++  NY
Sbjct: 266 LAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNY 325
Query: 145 DLPNNRELYIHRIGRSGRFGRKGVAISFVK-SDDIRILRDIEQYYSTQIDEMP 196
           D+P + + Y+HR+ R+GRFG KG+AI+FV   +D +IL D++  +   I E+P
Sbjct: 326 DMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELP 378

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score =  103 bits (257), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 43/113 (38%), Positives = 76/113 (67%), Gaps = 1/113 (0%)
Query: 85  LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINY 144
           L + + E NF   ++H  MPQ+ER    ++F+    R+L+ T+++ RG+D+++V++  NY
Sbjct: 265 LAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNY 324
Query: 145 DLPNNRELYIHRIGRSGRFGRKGVAISFVK-SDDIRILRDIEQYYSTQIDEMP 196
           D+P + + Y+HR+ R+GRFG KG+AI+FV   +D +IL D++  +   I E+P
Sbjct: 325 DMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELP 377

>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56 Length = 172

Iteration: 1
 Score =  103 bits (256), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 43/113 (38%), Positives = 76/113 (67%), Gaps = 1/113 (0%)
Query: 85  LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINY 144
           L + + E NF   ++H  MPQ+ER    ++F+    R+L+ T+++ RG+D+++V++  NY
Sbjct: 47  LAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNY 106
Query: 145 DLPNNRELYIHRIGRSGRFGRKGVAISFVK-SDDIRILRDIEQYYSTQIDEMP 196
           D+P + + Y+HR+ R+GRFG KG+AI+FV   +D +IL D++  +   I E+P
Sbjct: 107 DMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELP 159

>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic Initiation Factor 4a, Eif4a Length = 221

Iteration: 1
 Score =  101 bits (252), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 47/90 (52%), Positives = 61/90 (67%), Gaps = 1/90 (1%)
Query: 1   MNVQCHACIGGTNLSEDLRKLDY-GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADE 59
           M   CHACIGGTN+  +++ L     H++ GTPGRVFDM+ RR L    I M VLDEADE
Sbjct: 110 MGASCHACIGGTNVRAEVQXLQMEAPHIIVGTPGRVFDMLNRRYLSPXYIXMFVLDEADE 169
Query: 60  MLNKGFKEQIYDVYRYLPPATQVDWLTEKM 89
           ML++GF +QIYD+++ L   TQV  L+  M
Sbjct: 170 MLSRGFXDQIYDIFQXLNSNTQVVLLSATM 199

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score = 98.6 bits (244), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 46/102 (45%), Positives = 67/102 (65%)
Query: 85  LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINY 144
           L   +R+  F   ++HGD+ Q +R+ +++ F+    R+LI TDV +RGIDV  ++ VINY
Sbjct: 254 LASXLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVXSRGIDVNDLNCVINY 313
Query: 145 DLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQ 186
            LP N E Y HRIGR+GR G+KG AIS +   + + LR IE+
Sbjct: 314 HLPQNPESYXHRIGRTGRAGKKGKAISIINRREYKKLRYIER 355

>pdb|2JGN|A Chain A, Ddx3 Helicase Domain Length = 185

Iteration: 1
 Score = 98.2 bits (243), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 53/153 (34%), Positives = 88/153 (57%), Gaps = 8/153 (5%)
Query: 50  KMLVLDEAD------EMLNKGFKEQIYDVYRYLPPATQVDWLTEKMREANFTVSSMHGDM 103
           K++ ++E+D      ++LN   K+ +  V+  +      D L + +    +  +S+HGD 
Sbjct: 23  KVVWVEESDKRSFLLDLLNATGKDSLTLVF--VETKKGADSLEDFLYHEGYACTSIHGDR 80
Query: 104 PQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRF 163
            Q++R+  + +FRSG S +L+ T V ARG+D+  V  VIN+DLP++ E Y+HRIGR+GR 
Sbjct: 81  SQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRV 140
Query: 164 GRKGVAISFVKSDDIRILRDIEQYYSTQIDEMP 196
           G  G+A SF    +I I +D+         E+P
Sbjct: 141 GNLGLATSFFNERNINITKDLLDLLVEAKQEVP 173

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score = 97.8 bits (242), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 57/170 (33%), Positives = 95/170 (55%), Gaps = 10/170 (5%)
Query: 35  VFDMIRRRVLRTRNI--KMLVLDEAD------EMLNKGFKEQIYDVYRYLPPATQVDWLT 86
           +F  + R    + NI  K++ ++E+D      ++LN   K+ +  V+  +      D L 
Sbjct: 236 IFLAVGRVGSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVF--VETKKGADSLE 293
Query: 87  EKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDL 146
           + +    +  +S+HGD  Q++R+  + +FRSG S +L+ T V ARG+D+  V  VIN+DL
Sbjct: 294 DFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDL 353
Query: 147 PNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMP 196
           P++ E Y+HRIGR+GR G  G+A SF    +I I +D+         E+P
Sbjct: 354 PSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVP 403

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score = 91.3 bits (225), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 42/108 (38%), Positives = 69/108 (63%), Gaps = 8/108 (7%)
Query: 82  VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLV 141
            D+L   + E  F  +S+HGD  Q +R+  +++F++G+ +VLI T V +RG+D++ +  V
Sbjct: 313 ADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHV 372
Query: 142 INYDLPNNRELYIHRIGRSGRFGRKGVAISF--------VKSDDIRIL 181
           INYD+P+  + Y+HRIGR+GR G  G A SF        + +D ++IL
Sbjct: 373 INYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAIAADLVKIL 420

>pdb|2YJT|D Chain D, Crystal Structure Of E. Coli Dead-Box Protein Srmb Bound To Regulator Of Ribonuclease Activity A (Rraa) Length = 170

Iteration: 1
 Score = 89.0 bits (219), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 46/112 (41%), Positives = 66/112 (58%)
Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +V  L   +REA      + G+M Q +R+  +K    G   VL+ TDV ARGID+  VS 
Sbjct: 42  RVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSH 101
Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQI 192
           V N+D+P + + Y+HRIGR+ R GRKG AIS V++ D  +L  + +Y    I
Sbjct: 102 VFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHDHLLLGKVGRYIEEPI 153

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 83.6 bits (205), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 39/75 (52%), Positives = 52/75 (69%)
Query: 99  MHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIG 158
           + GD+PQ  R+  +  FR G   +LITTDV +RG+D+  V  VIN+D P +   YIHRIG
Sbjct: 246 LRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIG 305
Query: 159 RSGRFGRKGVAISFV 173
           R+GR GRKG AI+F+
Sbjct: 306 RTGRMGRKGEAITFI 320

>pdb|2P6N|A Chain A, Human Dead-box Rna Helicase Ddx41, Helicase Domain Length = 191

Iteration: 1
 Score = 81.6 bits (200), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 40/105 (38%), Positives = 62/105 (59%), Gaps = 1/105 (0%)
Query: 82  VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLV 141
           VD + E +        ++HG   Q+ER   ++ FR G   VL+ TDV ++G+D   +  V
Sbjct: 67  VDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHV 126
Query: 142 INYDLPNNRELYIHRIGRSGRFGRKGVAISFV-KSDDIRILRDIE 185
           INYD+P   E Y+HRIGR+G  G  G+A +F+ K+ D  +L D++
Sbjct: 127 INYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDESVLMDLK 171

>pdb|4DB4|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric Rna-Dna Duplex Length = 256

Iteration: 1
 Score = 73.9 bits (180), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 40/134 (29%), Positives = 71/134 (52%), Gaps = 5/134 (3%)
Query: 57  ADEMLNKGFKEQ--IYDVYRYLPPATQVDWLTEKMR---EANFTVSSMHGDMPQKERDGI 111
           A E + K  KE+   Y    + P      +L   ++   + +  +   HG + Q +R  +
Sbjct: 19  AVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSL 78
Query: 112 MKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAIS 171
           +K F+   S +L+ TDV ARG+D   V  V+   +P+    YIHRIGR+ R G++G ++ 
Sbjct: 79  VKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVL 138
Query: 172 FVKSDDIRILRDIE 185
           F+  D++  +R++E
Sbjct: 139 FICKDELPFVRELE 152

>pdb|4DB2|C Chain C, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex Length = 257

Iteration: 1
 Score = 73.9 bits (180), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 40/134 (29%), Positives = 71/134 (52%), Gaps = 5/134 (3%)
Query: 57  ADEMLNKGFKEQ--IYDVYRYLPPATQVDWLTEKMR---EANFTVSSMHGDMPQKERDGI 111
           A E + K  KE+   Y    + P      +L   ++   + +  +   HG + Q +R  +
Sbjct: 19  AVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSL 78
Query: 112 MKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAIS 171
           +K F+   S +L+ TDV ARG+D   V  V+   +P+    YIHRIGR+ R G++G ++ 
Sbjct: 79  VKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVL 138
Query: 172 FVKSDDIRILRDIE 185
           F+  D++  +R++E
Sbjct: 139 FICKDELPFVRELE 152

>pdb|4DB2|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex Length = 257

Iteration: 1
 Score = 73.9 bits (180), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 40/134 (29%), Positives = 71/134 (52%), Gaps = 5/134 (3%)
Query: 57  ADEMLNKGFKEQ--IYDVYRYLPPATQVDWLTEKMR---EANFTVSSMHGDMPQKERDGI 111
           A E + K  KE+   Y    + P      +L   ++   + +  +   HG + Q +R  +
Sbjct: 19  AVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSL 78
Query: 112 MKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAIS 171
           +K F+   S +L+ TDV ARG+D   V  V+   +P+    YIHRIGR+ R G++G ++ 
Sbjct: 79  VKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVL 138
Query: 172 FVKSDDIRILRDIE 185
           F+  D++  +R++E
Sbjct: 139 FICKDELPFVRELE 152

>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion) Bound To Ssrna And Amp-Pnp Length = 512

Iteration: 1
 Score = 73.6 bits (179), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 40/134 (29%), Positives = 71/134 (52%), Gaps = 5/134 (3%)
Query: 57  ADEMLNKGFKEQ--IYDVYRYLPPATQVDWLTEKMR---EANFTVSSMHGDMPQKERDGI 111
           A E + K  KE+   Y    + P      +L   ++   + +  +   HG + Q +R  +
Sbjct: 274 AVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSL 333
Query: 112 MKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAIS 171
           +K F+   S +L+ TDV ARG+D   V  V+   +P+    YIHRIGR+ R G++G ++ 
Sbjct: 334 VKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVL 393
Query: 172 FVKSDDIRILRDIE 185
           F+  D++  +R++E
Sbjct: 394 FICKDELPFVRELE 407

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 73.2 bits (178), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 40/134 (29%), Positives = 71/134 (52%), Gaps = 5/134 (3%)
Query: 57  ADEMLNKGFKEQ--IYDVYRYLPPATQVDWLTEKMR---EANFTVSSMHGDMPQKERDGI 111
           A E + K  KE+   Y    + P      +L   ++   + +  +   HG + Q +R  +
Sbjct: 325 AVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSL 384
Query: 112 MKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAIS 171
           +K F+   S +L+ TDV ARG+D   V  V+   +P+    YIHRIGR+ R G++G ++ 
Sbjct: 385 VKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVL 444
Query: 172 FVKSDDIRILRDIE 185
           F+  D++  +R++E
Sbjct: 445 FICKDELPFVRELE 458

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score = 72.8 bits (177), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 40/134 (29%), Positives = 71/134 (52%), Gaps = 5/134 (3%)
Query: 57  ADEMLNKGFKEQ--IYDVYRYLPPATQVDWLTEKMR---EANFTVSSMHGDMPQKERDGI 111
           A E + K  KE+   Y    + P      +L   ++   + +  +   HG + Q +R  +
Sbjct: 274 AVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSL 333
Query: 112 MKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAIS 171
           +K F+   S +L+ TDV ARG+D   V  V+   +P+    YIHRIGR+ R G++G ++ 
Sbjct: 334 VKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVL 393
Query: 172 FVKSDDIRILRDIE 185
           F+  D++  +R++E
Sbjct: 394 FICKDELPFVRELE 407

>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A Human Dead-Box Protein Length = 206

Iteration: 1
 Score = 70.9 bits (172), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 32/76 (42%), Positives = 52/76 (68%)
Query: 7   ACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFK 66
           A  GGTNL +D+ +LD   HVV  TPGR+ D+I++ V +  +++M+VLDEAD++L++ F 
Sbjct: 105 ATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFV 164
Query: 67  EQIYDVYRYLPPATQV 82
           + + D+   LP   Q+
Sbjct: 165 QIMEDIILTLPKNRQI 180

>pdb|3I32|A Chain A, Dimeric Structure Of A Hera Helicase Fragment Including The C-Terminal Reca Domain, The Dimerization Domain, And The Rna Binding Domain Length = 300

Iteration: 1
 Score = 70.1 bits (170), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 30/60 (50%), Positives = 41/60 (68%)
Query: 96  VSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIH 155
             ++HGDM Q ER+ +M  FR G  RVL+ TDV ARG+D+ QV LV++Y +P+  E Y H
Sbjct: 55  AQALHGDMSQGERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRMPDRAEAYQH 114

>pdb|3EAQ|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase Hera Form 2, Complete Dimer, Symmetric Length = 212

Iteration: 1
 Score = 68.2 bits (165), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 29/60 (48%), Positives = 41/60 (68%)
Query: 96  VSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIH 155
             ++HGD+ Q ER+ ++  FR G  RVL+ TDV ARG+D+ QV LV++Y LP+  E Y H
Sbjct: 58  AQALHGDLSQGERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRLPDRAEAYQH 117

>pdb|2OXC|A Chain A, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex With Adp Length = 230

Iteration: 1
 Score = 67.4 bits (163), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 38/106 (35%), Positives = 60/106 (56%), Gaps = 14/106 (13%)
Query: 2   NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEML 61
            ++CH  IGGT LS+D  +L    H+  G+PGR+  +I    L   +I++ +LDEAD++L
Sbjct: 121 GLECHVFIGGTPLSQDKTRLKKC-HIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLL 179
Query: 62  NKG-FKEQIYDVYRYLPPATQV------------DWLTEKMREANF 94
            +G F+EQI  +Y  LP + Q+            + LT+ MR+  F
Sbjct: 180 EEGSFQEQINWIYSSLPASKQMLAVSATYPEFLANALTKYMRDPTF 225

>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score = 60.1 bits (144), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 30/80 (37%), Positives = 45/80 (56%)
Query: 2   NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEML 61
           +++  A  GGT   +    L  G   V  TPGR  D +R+ VL    +++ VLDEADEML
Sbjct: 98  HLKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEML 157
Query: 62  NKGFKEQIYDVYRYLPPATQ 81
           + GF+E++  +    PP+ Q
Sbjct: 158 SMGFEEEVEALLSATPPSRQ 177

>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score = 60.1 bits (144), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 30/80 (37%), Positives = 45/80 (56%)
Query: 2   NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEML 61
           +++  A  GGT   +    L  G   V  TPGR  D +R+ VL    +++ VLDEADEML
Sbjct: 98  HLKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEML 157
Query: 62  NKGFKEQIYDVYRYLPPATQ 81
           + GF+E++  +    PP+ Q
Sbjct: 158 SMGFEEEVEALLSATPPSRQ 177

>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p Length = 226

Iteration: 1
 Score = 58.9 bits (141), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 28/68 (41%), Positives = 44/68 (64%), Gaps = 1/68 (1%)
Query: 26  HVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLN-KGFKEQIYDVYRYLPPATQVDW 84
            V+ GTPG V D++RR++++ + IK+ VLDEAD ML+ +G  +Q   V R+LP  TQ+  
Sbjct: 140 QVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLVL 199
Query: 85  LTEKMREA 92
            +    +A
Sbjct: 200 FSATFADA 207

>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain Length = 219

Iteration: 1
 Score = 57.0 bits (136), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 27/57 (47%), Positives = 36/57 (63%)
Query: 9   IGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGF 65
           IGGT+  + L KL+   H+V GTPGR+ D IR + L      +LV+DEAD  L+ GF
Sbjct: 111 IGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLXLDXGF 167

>pdb|1WRB|A Chain A, Crystal Structure Of The N-Terminal Reca-Like Domain Of Djvlgb, A Pranarian Vasa-Like Rna Helicase Length = 253

Iteration: 1
 Score = 56.6 bits (135), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 41/71 (57%), Gaps = 2/71 (2%)
Query: 1   MNVQCHACI--GGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEAD 58
           +N    +C+  GG +    +R++  G H++  TPGR+ D I +  +     K +VLDEAD
Sbjct: 125 LNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEAD 184
Query: 59  EMLNKGFKEQI 69
            ML+ GF+ QI
Sbjct: 185 RMLDMGFEPQI 195

>pdb|3LY5|A Chain A, Ddx18 Dead-Domain Length = 262

Iteration: 1
 Score = 54.7 bits (130), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 25/70 (35%), Positives = 46/70 (65%), Gaps = 1/70 (1%)
Query: 9   IGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRV-LRTRNIKMLVLDEADEMLNKGFKE 67
           +GG+N S + +KL  G +++  TPGR+ D ++       +N++ LV+DEAD +L+ GF+E
Sbjct: 161 MGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEE 220
Query: 68  QIYDVYRYLP 77
           ++  + + LP
Sbjct: 221 ELKQIIKLLP 230

>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56 Length = 220

Iteration: 1
 Score = 50.8 bits (120), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 27/83 (32%), Positives = 45/83 (54%), Gaps = 2/83 (2%)
Query: 2   NVQCHACIGGTNLSEDLRKLDYG-QHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEM 60
           NV+     GG ++ +D   L     H+V GTPGR+  + R + L  ++IK  +LDE D+M
Sbjct: 111 NVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKM 170
Query: 61  LNK-GFKEQIYDVYRYLPPATQV 82
           L +   +  + +++R  P   QV
Sbjct: 171 LEQLDMRRDVQEIFRMTPHEKQV 193

>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S Length = 523

Iteration: 1
 Score = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/108 (23%), Positives = 51/108 (47%)
Query: 75  YLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGID 134
           Y     +V+    +++    + ++ H  +    R  + ++F+    ++++ T  +  GI+
Sbjct: 242 YCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGIN 301
Query: 135 VQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILR 182
              V  V+++D+P N E Y    GR+GR G    A+ F    D+  LR
Sbjct: 302 KPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLR 349

>pdb|4A4D|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human Dead-Box Rna Helicase Ddx5 (P68) Length = 253

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 29/85 (34%), Positives = 38/85 (44%), Gaps = 7/85 (8%)
Query: 5   CHAC-------IGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEA 57
           C AC        GG      +R L+ G  +   TPGR+ D +       R    LVLDEA
Sbjct: 140 CRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEA 199
Query: 58  DEMLNKGFKEQIYDVYRYLPPATQV 82
           D ML+ GF+ QI  +   + P  Q 
Sbjct: 200 DRMLDMGFEPQIRKIVDQIRPDRQT 224

>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I In Complex With Adp Length = 242

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 38/84 (45%), Gaps = 7/84 (8%)
Query: 5   CHAC-------IGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEA 57
           C AC        GG      +R L+ G  +   TPGR+ D +       R    LVLDEA
Sbjct: 126 CRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEA 185
Query: 58  DEMLNKGFKEQIYDVYRYLPPATQ 81
           D ML+ GF+ QI  +   + P  Q
Sbjct: 186 DRMLDMGFEPQIRKIVDQIRPDRQ 209

>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core Length = 523

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 25/108 (23%), Positives = 49/108 (45%)
Query: 75  YLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGID 134
           Y     +V+    +++    + ++ H  +    R  + ++F+    ++++ T  +  GI+
Sbjct: 242 YCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGXGIN 301
Query: 135 VQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILR 182
              V  V+++D+P N E Y    GR+GR G    A  F    D   LR
Sbjct: 302 KPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAXLFYDPADXAWLR 349

>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In Complex With Amp Length = 249

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 1/78 (1%)
Query: 1   MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRR-RVLRTRNIKMLVLDEADE 59
           + VQ    +GG +       L    H++  TPGR+ D +   +    R +K LV+DEAD 
Sbjct: 138 IGVQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADR 197
Query: 60  MLNKGFKEQIYDVYRYLP 77
           +LN  F+ ++  + + +P
Sbjct: 198 ILNMDFETEVDKILKVIP 215

>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain Length = 228

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/63 (38%), Positives = 37/63 (58%), Gaps = 1/63 (1%)
Query: 8   CI-GGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFK 66
           CI GG N +  +  +  G  ++  TPGR+ D+     +  R+I  LV+DEAD+ML+  F+
Sbjct: 126 CIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKMLDMEFE 185
Query: 67  EQI 69
            QI
Sbjct: 186 PQI 188

>pdb|4GL2|A Chain A, Structural Basis For Dsrna Duplex Backbone Recognition By Mda5 Length = 699

Iteration: 1
 Score = 44.7 bits (104), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 25/87 (28%), Positives = 42/87 (48%), Gaps = 10/87 (11%)
Query: 84  WLTEKMREANFTVSSMH----------GDMPQKERDGIMKEFRSGTSRVLITTDVWARGI 133
           W+TE  + A   V + H            M Q E+  ++ +FR+G   +LI T V   G+
Sbjct: 419 WITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGKINLLIATTVAEEGL 478
Query: 134 DVQQVSLVINYDLPNNRELYIHRIGRS 160
           D+++ ++VI Y L  N    +   GR+
Sbjct: 479 DIKECNIVIRYGLVTNEIAMVQARGRA 505

>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction Length = 780

Iteration: 1
 Score = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 39/147 (26%), Positives = 74/147 (50%), Gaps = 19/147 (12%)
Query: 35  VFDMIRRRVLRTRNIKML--VLDEADEMLNKGFKEQIYDVYRYLPPATQVDWLTEKMREA 92
           V++ +R+ V+R     ++  +++E+D++  K   E    +Y YL           K    
Sbjct: 567 VYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVE----MYEYL----------SKEVFP 612
Query: 93  NFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNREL 152
            F +  MHG + Q+E+D +M EF  G   +L++T V   GIDV + ++++  +       
Sbjct: 613 EFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLA 672
Query: 153 YIHRI-GRSGRFGRKGVAISFVKSDDI 178
            +H++ GR GR G++  A  F+   D+
Sbjct: 673 QLHQLRGRVGRGGQE--AYCFLVVGDV 697

>pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb In Complex With Atp Length = 657

Iteration: 1
 Score = 44.3 bits (103), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 39/133 (29%), Positives = 66/133 (49%), Gaps = 15/133 (11%)
Query: 85  LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINY 144
           LT+ ++EA   V+ +H ++   ER  I+++ R G   VL+  ++   G+D+ +VSLV   
Sbjct: 460 LTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAIL 519
Query: 145 D------LPNNRELYIHRIGRSGRFGRKGV---AISFVKSDDIRIL-----RDIEQYYST 190
           D      L + R L I  IGR+ R     V   A +  KS +I I      R I++ Y+ 
Sbjct: 520 DADKEGFLRSERSL-IQTIGRAARNANGHVIMYADTITKSMEIAIQETKRRRAIQEEYNR 578
Query: 191 QIDEMPMNGKRSL 203
           +   +P   K+ +
Sbjct: 579 KHGIVPRTVKKEI 591

>pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb Length = 658

Iteration: 1
 Score = 44.3 bits (103), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 39/133 (29%), Positives = 66/133 (49%), Gaps = 15/133 (11%)
Query: 85  LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINY 144
           LT+ ++EA   V+ +H ++   ER  I+++ R G   VL+  ++   G+D+ +VSLV   
Sbjct: 461 LTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAIL 520
Query: 145 D------LPNNRELYIHRIGRSGRFGRKGV---AISFVKSDDIRIL-----RDIEQYYST 190
           D      L + R L I  IGR+ R     V   A +  KS +I I      R I++ Y+ 
Sbjct: 521 DADKEGFLRSERSL-IQTIGRAARNANGHVIMYADTITKSMEIAIQETKRRRAIQEEYNR 579
Query: 191 QIDEMPMNGKRSL 203
           +   +P   K+ +
Sbjct: 580 KHGIVPRTVKKEI 592

>pdb|2FDC|A Chain A, Structural Basis Of Dna Damage Recognition And Processing By Uvrb: Crystal Structure Of A UvrbDNA COMPLEX Length = 658

Iteration: 1
 Score = 44.3 bits (103), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 39/133 (29%), Positives = 66/133 (49%), Gaps = 15/133 (11%)
Query: 85  LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINY 144
           LT+ ++EA   V+ +H ++   ER  I+++ R G   VL+  ++   G+D+ +VSLV   
Sbjct: 461 LTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAIL 520
Query: 145 D------LPNNRELYIHRIGRSGRFGRKGV---AISFVKSDDIRIL-----RDIEQYYST 190
           D      L + R L I  IGR+ R     V   A +  KS +I I      R I++ Y+ 
Sbjct: 521 DADKEGFLRSERSL-IQTIGRAARNANGHVIMYADTITKSMEIAIQETKRRRAIQEEYNR 579
Query: 191 QIDEMPMNGKRSL 203
           +   +P   K+ +
Sbjct: 580 KHGIVPRTVKKEI 592

>pdb|1T5L|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb Point Mutant Y96a Revealing A Novel Fold For Domain 2 Length = 658

Iteration: 1
 Score = 43.9 bits (102), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 39/133 (29%), Positives = 66/133 (49%), Gaps = 15/133 (11%)
Query: 85  LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINY 144
           LT+ ++EA   V+ +H ++   ER  I+++ R G   VL+  ++   G+D+ +VSLV   
Sbjct: 461 LTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAIL 520
Query: 145 D------LPNNRELYIHRIGRSGRFGRKGV---AISFVKSDDIRIL-----RDIEQYYST 190
           D      L + R L I  IGR+ R     V   A +  KS +I I      R I++ Y+ 
Sbjct: 521 DADKEGFLRSERSL-IQTIGRAARNANGHVIMYADTITKSMEIAIQETKRRRAIQEEYNR 579
Query: 191 QIDEMPMNGKRSL 203
           +   +P   K+ +
Sbjct: 580 KHGIVPRTVKKEI 592

>pdb|3UWX|B Chain B, Crystal Structure Of Uvra-Uvrb Complex Length = 683

Iteration: 1
 Score = 43.9 bits (102), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 39/133 (29%), Positives = 66/133 (49%), Gaps = 15/133 (11%)
Query: 85  LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINY 144
           LT+ ++EA   V+ +H ++   ER  I+++ R G   VL+  ++   G+D+ +VSLV   
Sbjct: 486 LTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAIL 545
Query: 145 D------LPNNRELYIHRIGRSGRFGRKGV---AISFVKSDDIRIL-----RDIEQYYST 190
           D      L + R L I  IGR+ R     V   A +  KS +I I      R I++ Y+ 
Sbjct: 546 DADKEGFLRSERSL-IQTIGRAARNANGHVIMYADTITKSMEIAIQETKRRRAIQEEYNR 604
Query: 191 QIDEMPMNGKRSL 203
           +   +P   K+ +
Sbjct: 605 KHGIVPRTVKKEI 617

>pdb|1WP9|A Chain A, Crystal Structure Of Pyrococcus Furiosus Hef Helicase Domain Length = 494

Iteration: 1
 Score = 43.5 bits (101), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 44/168 (26%), Positives = 73/168 (43%), Gaps = 24/168 (14%)
Query: 34  RVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYD---VYRYLPPATQVDWLTEKMR 90
           ++ ++IR ++ R +N K++V     E   K   E + D     R++  A++ +       
Sbjct: 347 KLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKEN------- 399
Query: 91  EANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNR 150
                       + Q+E+  I+ EF  G   VL+ T V   G+DV +V LV+ Y+   + 
Sbjct: 400 ---------DRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSA 450
Query: 151 ELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
              I R GR+GR     V I   K       RD   Y+S++  E  M 
Sbjct: 451 IRSIQRRGRTGRHMPGRVIILMAKGT-----RDEAYYWSSRQKEKIMQ 493

>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex With Adp Length = 236

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 41/74 (55%), Gaps = 2/74 (2%)
Query: 9   IGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRV-LRTRNIKMLVLDEADEMLNKGFKE 67
           IGG +L  +  +++   +++  TPGR+   +   V     +++MLVLDEAD +L+ GF +
Sbjct: 132 IGGKDLKHEAERIN-NINILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMGFAD 190
Query: 68  QIYDVYRYLPPATQ 81
            +  V   LP   Q
Sbjct: 191 TMNAVIENLPKKRQ 204

>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 300

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 25/64 (39%), Positives = 37/64 (57%), Gaps = 6/64 (9%)
Query: 20  KLDYGQ----HVVSGTPGRVFDMIRR-RVLRTRNIKMLVLDEADEML-NKGFKEQIYDVY 73
           KL+ GQ     +V GTPG V D   + + +  + IK+ VLDEAD M+  +G ++Q   + 
Sbjct: 202 KLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQ 261
Query: 74  RYLP 77
           R LP
Sbjct: 262 RMLP 265

>pdb|3V4R|A Chain A, Crystal Structure Of A Uvrb Dimer-Dna Complex Length = 667

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 7/84 (8%)
Query: 85  LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINY 144
           LT+ ++E    V+ +H ++   ER  I+++ R G   VL+  ++   G+D+ +VSLV   
Sbjct: 467 LTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAIL 526
Query: 145 D------LPNNRELYIHRIGRSGR 162
           D      L + R L I  IGR+ R
Sbjct: 527 DADKEGFLRSERSL-IQTIGRAAR 549

>pdb|2D7D|A Chain A, Structural Insights Into The Cryptic Dna Dependent Atp-Ase Activity Of Uvrb Length = 661

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 7/84 (8%)
Query: 85  LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINY 144
           LT+ ++E    V+ +H ++   ER  I+++ R G   VL+  ++   G+D+ +VSLV   
Sbjct: 461 LTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAIL 520
Query: 145 D------LPNNRELYIHRIGRSGR 162
           D      L + R L I  IGR+ R
Sbjct: 521 DADKEGFLRSERSL-IQTIGRAAR 543

>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214 Length = 235

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 25/64 (39%), Positives = 37/64 (57%), Gaps = 6/64 (9%)
Query: 20  KLDYGQ----HVVSGTPGRVFDMIRR-RVLRTRNIKMLVLDEADEML-NKGFKEQIYDVY 73
           KL+ GQ     +V GTPG V D   + + +  + IK+ VLDEAD M+  +G ++Q   + 
Sbjct: 135 KLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQ 194
Query: 74  RYLP 77
           R LP
Sbjct: 195 RMLP 198

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	210
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	9e-81
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	5e-45
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	1e-80
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	7e-44
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	1e-80
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	1e-80
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	2e-46
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	3e-80
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	4e-41
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	7e-78
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	5e-45
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	1e-77
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	2e-76
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	5e-75
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	9e-75
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	2e-36
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	9e-74
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	8e-36
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	3e-73
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	4e-39
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	2e-71
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	9e-36
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	2e-50
3bor_A	237	Human initiation factor 4A-II; translation initiat	6e-49
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	3e-48
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	1e-47
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	8e-21
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	1e-47
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	9e-46
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	3e-43
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	4e-18
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	7e-43
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	2e-42
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	7e-17
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	3e-42
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	3e-42
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	3e-19
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	2e-41
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	3e-41
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	4e-19
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	5e-41
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	3e-17
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	4e-40
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	4e-38
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	2e-37
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	7e-26
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	4e-10
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	5e-24
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	3e-21
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	1e-19
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	6e-18
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	1e-17
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	4e-17
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	2e-16
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	5e-16
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	8e-15
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	5e-13
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	3e-12
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	3e-11
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	4e-11
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	5e-11
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	5e-11
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	3e-10
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	1e-07
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	4e-07
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	7e-06
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	1e-05
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	3e-05
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	5e-05
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	2e-04
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	7e-04

>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 =  245 bits (628), Expect = 9e-81
 Identities = 90/117 (76%), Positives = 101/117 (86%)

Query: 82  VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLV 141
           VDWLTEKM   +FTVS+MHGDM QKERD IM+EFRSG+SRVLITTD+ ARGIDVQQVSLV
Sbjct: 293 VDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLV 352

Query: 142 INYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           INYDLP NRE YIHRIGR GRFGRKGVAI+ V  +D R LRDIE +Y+T I+EMP+N
Sbjct: 353 INYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLN 409

>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 =  153 bits (389), Expect = 5e-45
 Identities = 48/83 (57%), Positives = 62/83 (74%), Gaps = 1/83 (1%)

Query: 1   MNVQCHACIGGTNLSEDLRKLDY-GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADE 59
           M   CHACIGGTN+  +++KL     H++ GTPGRVFDM+ RR L  + IKM VLDEADE
Sbjct: 135 MGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADE 194

Query: 60  MLNKGFKEQIYDVYRYLPPATQV 82
           ML++GFK+QIYD+++ L   TQV
Sbjct: 195 MLSRGFKDQIYDIFQKLNSNTQV 217

>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 =  244 bits (626), Expect = 1e-80
 Identities = 78/117 (66%), Positives = 102/117 (87%)

Query: 82  VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLV 141
           V+ LT K+R   FTVS+++ D+PQ+ERD IMKEFRSG+SR+LI+TD+ ARGIDVQQVSLV
Sbjct: 272 VEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLV 331

Query: 142 INYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           INYDLP N+E YIHRIGR GRFGRKGVAI+FV ++D+  +R++E++YSTQI+E+P +
Sbjct: 332 INYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSD 388

>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 =  149 bits (380), Expect = 7e-44
 Identities = 49/82 (59%), Positives = 59/82 (71%), Gaps = 1/82 (1%)

Query: 1   MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEM 60
           M+++ HACIGGT+  ED   L     +V GTPGRVFD I+RR  RT  IKM +LDEADEM
Sbjct: 116 MDIKVHACIGGTSFVEDAEGLRDA-QIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEM 174

Query: 61  LNKGFKEQIYDVYRYLPPATQV 82
           L+ GFKEQIY ++  LPP TQV
Sbjct: 175 LSSGFKEQIYQIFTLLPPTTQV 196

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19 Length = 165

 Score =  236 bits (605), Expect = 1e-80
 Identities = 78/117 (66%), Positives = 102/117 (87%)

Query: 82  VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLV 141
           V+ LT K+R   FTVS+++ D+PQ+ERD IMKEFRSG+SR+LI+TD+ ARGIDVQQVSLV
Sbjct: 43  VEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLV 102

Query: 142 INYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           INYDLP N+E YIHRIGR GRFGRKGVAI+FV ++D+  +R++E++YSTQI+E+P +
Sbjct: 103 INYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSD 159

>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 =  245 bits (627), Expect = 1e-80
 Identities = 107/117 (91%), Positives = 114/117 (97%)

Query: 82  VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLV 141
           VDWLTEKMREANFTVSSMHGDMPQKER+ IMKEFRSG SRVLI+TDVWARG+DV QVSL+
Sbjct: 289 VDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLI 348

Query: 142 INYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           INYDLPNNRELYIHRIGRSGR+GRKGVAI+FVK+DDIRILRDIEQYYSTQIDEMPMN
Sbjct: 349 INYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN 405

>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 =  157 bits (399), Expect = 2e-46
 Identities = 76/82 (92%), Positives = 79/82 (96%)

Query: 1   MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEM 60
           MNVQCHACIGGTN+ ED+RKLDYGQHVV+GTPGRVFDMIRRR LRTR IKMLVLDEADEM
Sbjct: 132 MNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEM 191

Query: 61  LNKGFKEQIYDVYRYLPPATQV 82
           LNKGFKEQIYDVYRYLPPATQV
Sbjct: 192 LNKGFKEQIYDVYRYLPPATQV 213

>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 =  237 bits (608), Expect = 7e-78
 Identities = 51/125 (40%), Positives = 76/125 (60%)

Query: 82  VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLV 141
           V+ L +K+ +  ++    H  M Q+ER+ +  EFR G  R L+ +D+  RGID+Q V++V
Sbjct: 271 VELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVV 330

Query: 142 INYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKR 201
           IN+D P   E Y+HRIGRSGRFG  G+AI+ +  +D   L  IEQ   T+I  +P    +
Sbjct: 331 INFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPATIDK 390

Query: 202 SLHSY 206
           SL+  
Sbjct: 391 SLYVA 395

>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 =  153 bits (388), Expect = 5e-45
 Identities = 31/82 (37%), Positives = 49/82 (59%)

Query: 1   MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEM 60
             + C    GGTNL +D+ +L+   H++ GTPGRV D+  R+V    +  + ++DEAD+M
Sbjct: 116 CGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKM 175

Query: 61  LNKGFKEQIYDVYRYLPPATQV 82
           L++ FK  I  +  +LPP  Q 
Sbjct: 176 LSRDFKTIIEQILSFLPPTHQS 197

>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 =  229 bits (586), Expect = 1e-77
 Identities = 49/123 (39%), Positives = 82/123 (66%), Gaps = 6/123 (4%)

Query: 82  VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLV 141
             WLT +M +    VS + G++  ++R  I++ FR G  +VLITT+V ARGIDV+QV++V
Sbjct: 47  AKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIV 106

Query: 142 INYDLPNNR------ELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEM 195
           +N+DLP  +      E Y+HRIGR+GRFG+KG+A + ++ D++  L  I+ ++++ I ++
Sbjct: 107 VNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDELPSLMKIQDHFNSSIKQL 166

Query: 196 PMN 198
              
Sbjct: 167 NAE 169

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis} Length = 163

 Score =  225 bits (577), Expect = 2e-76
 Identities = 54/115 (46%), Positives = 78/115 (67%)

Query: 82  VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLV 141
           V+ LT+++ +  +    +HG M Q++R  +M EF+ G  R L+ TDV ARGID++ +SLV
Sbjct: 48  VNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLV 107

Query: 142 INYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMP 196
           INYDLP  +E Y+HR GR+GR G KG AISFV + + R L DIE+Y   +I ++ 
Sbjct: 108 INYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAFEKRFLADIEEYIGFEIQKIE 162

>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 =  222 bits (569), Expect = 5e-75
 Identities = 44/125 (35%), Positives = 79/125 (63%), Gaps = 1/125 (0%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +   L + + E NF   ++H  MPQ+ER    ++F+    R+L+ T+++ RG+D+++V++
Sbjct: 43  RCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNI 102

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSD-DIRILRDIEQYYSTQIDEMPMNG 199
             NYD+P + + Y+HR+ R+GRFG KG+AI+FV  + D +IL D++  +   I E+P   
Sbjct: 103 AFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI 162

Query: 200 KRSLH 204
             S +
Sbjct: 163 DISSY 167

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B Length = 412

 Score =  230 bits (588), Expect = 9e-75
 Identities = 48/124 (38%), Positives = 84/124 (67%), Gaps = 7/124 (5%)

Query: 82  VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLV 141
             WL  ++ +    V+ + G+M  ++R  +++ FR G  +VL+TT+V ARGIDV+QVS+V
Sbjct: 279 ASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVV 338

Query: 142 INYDLPNNR------ELYIHRIGRSGRFGRKGVAISFVKS-DDIRILRDIEQYYSTQIDE 194
           IN+DLP ++      E Y+HRIGR+GRFG++G+A++ V S   + IL  I+++++ +I+ 
Sbjct: 339 INFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIER 398

Query: 195 MPMN 198
           +  +
Sbjct: 399 LDTD 402

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B Length = 412

 Score =  130 bits (330), Expect = 2e-36
 Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 5/83 (6%)

Query: 2   NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRR-RVLRTRNIKMLVLDEADEM 60
            ++    + G  L    +     + +V GTPG V D   + + +  + IK+ VLDEAD M
Sbjct: 124 ELKLAYAVRGNKLERGQKI---SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVM 180

Query: 61  L-NKGFKEQIYDVYRYLPPATQV 82
           +  +G ++Q   + R LP   Q+
Sbjct: 181 IATQGHQDQSIRIQRMLPRNCQM 203

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens} Length = 479

 Score =  229 bits (586), Expect = 9e-74
 Identities = 48/124 (38%), Positives = 84/124 (67%), Gaps = 7/124 (5%)

Query: 82  VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLV 141
             WL  ++ +    V+ + G+M  ++R  +++ FR G  +VL+TT+V ARGIDV+QVS+V
Sbjct: 346 ASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVV 405

Query: 142 INYDLPNNR------ELYIHRIGRSGRFGRKGVAISFVKS-DDIRILRDIEQYYSTQIDE 194
           IN+DLP ++      E Y+HRIGR+GRFG++G+A++ V S   + IL  I+++++ +I+ 
Sbjct: 406 INFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIER 465

Query: 195 MPMN 198
           +  +
Sbjct: 466 LDTD 469

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens} Length = 479

 Score =  130 bits (328), Expect = 8e-36
 Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 5/83 (6%)

Query: 2   NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRR-RVLRTRNIKMLVLDEADEM 60
            ++    + G  L    +     + +V GTPG V D   + + +  + IK+ VLDEAD M
Sbjct: 191 ELKLAYAVRGNKLERGQKI---SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVM 247

Query: 61  L-NKGFKEQIYDVYRYLPPATQV 82
           +  +G ++Q   + R LP   Q+
Sbjct: 248 IATQGHQDQSIRIQRMLPRNCQM 270

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A Length = 391

 Score =  225 bits (577), Expect = 3e-73
 Identities = 43/118 (36%), Positives = 76/118 (64%), Gaps = 1/118 (0%)

Query: 82  VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLV 141
              L + + E NF   ++H  MPQ+ER    ++F+    R+L+ T+++ RG+D+++V++ 
Sbjct: 263 CIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIA 322

Query: 142 INYDLPNNRELYIHRIGRSGRFGRKGVAISFVKS-DDIRILRDIEQYYSTQIDEMPMN 198
            NYD+P + + Y+HR+ R+GRFG KG+AI+FV   +D +IL D++  +   I E+P  
Sbjct: 323 FNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDE 380

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A Length = 391

 Score =  137 bits (347), Expect = 4e-39
 Identities = 27/83 (32%), Positives = 45/83 (54%), Gaps = 2/83 (2%)

Query: 2   NVQCHACIGGTNLSEDLRKLDYG-QHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEM 60
           NV+     GG ++ +D   L     H+V GTPGR+  + R + L  ++IK  +LDE D+M
Sbjct: 105 NVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKM 164

Query: 61  LNK-GFKEQIYDVYRYLPPATQV 82
           L +   +  + +++R  P   QV
Sbjct: 165 LEQLDMRRDVQEIFRMTPHEKQV 187

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A* Length = 395

 Score =  220 bits (564), Expect = 2e-71
 Identities = 58/125 (46%), Positives = 82/125 (65%), Gaps = 8/125 (6%)

Query: 82  VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLV 141
            + L  K++     VS +HGD+  +ERD ++ +FR G S+VLITT+V ARGID+  VS+V
Sbjct: 256 ANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMV 315

Query: 142 INYDLPN------NRELYIHRIGRSGRFGRKGVAISFVKS-DDIRILRDIEQYY-STQID 193
           +NYDLP       +   YIHRIGR+GRFGRKGVAISFV   +   IL  I++Y+   ++ 
Sbjct: 316 VNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYFGDIEMT 375

Query: 194 EMPMN 198
            +P +
Sbjct: 376 RVPTD 380

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A* Length = 395

 Score =  128 bits (324), Expect = 9e-36
 Identities = 27/83 (32%), Positives = 45/83 (54%), Gaps = 5/83 (6%)

Query: 1   MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEM 60
             +     +  +      +       V+ GTPG V D++RR++++ + IK+ VLDEAD M
Sbjct: 102 TKITSQLIVPDSFE----KNKQINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNM 157

Query: 61  LNK-GFKEQIYDVYRYLPPATQV 82
           L++ G  +Q   V R+LP  TQ+
Sbjct: 158 LDQQGLGDQCIRVKRFLPKDTQL 180

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli} Length = 170

 Score =  160 bits (406), Expect = 2e-50
 Identities = 48/127 (37%), Positives = 70/127 (55%)

Query: 82  VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLV 141
           V  L   +REA      + G+M Q +R+  +K    G   VL+ TDV ARGID+  VS V
Sbjct: 43  VHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHV 102

Query: 142 INYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKR 201
            N+D+P + + Y+HRIGR+ R GRKG AIS V++ D  +L  + +Y    I    ++  R
Sbjct: 103 FNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHDHLLLGKVGRYIEEPIKARVIDELR 162

Query: 202 SLHSYPA 208
                P+
Sbjct: 163 PKTRAPS 169

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A* Length = 237

 Score =  158 bits (403), Expect = 6e-49
 Identities = 47/83 (56%), Positives = 62/83 (74%), Gaps = 1/83 (1%)

Query: 1   MNVQCHACIGGTNLSEDLRKLDY-GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADE 59
           M   CHACIGGTN+  +++KL     H+V GTPGRVFDM+ RR L  + IKM VLDEADE
Sbjct: 125 MGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADE 184

Query: 60  MLNKGFKEQIYDVYRYLPPATQV 82
           ML++GFK+QIY++++ L  + QV
Sbjct: 185 MLSRGFKDQIYEIFQKLNTSIQV 207

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A Length = 224

 Score =  156 bits (397), Expect = 3e-48
 Identities = 49/82 (59%), Positives = 59/82 (71%), Gaps = 1/82 (1%)

Query: 1   MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEM 60
           M+++ HACIGGT+  ED   L     +V GTPGRVFD I+RR  RT  IKM +LDEADEM
Sbjct: 109 MDIKVHACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEM 167

Query: 61  LNKGFKEQIYDVYRYLPPATQV 82
           L+ GFKEQIY ++  LPP TQV
Sbjct: 168 LSSGFKEQIYQIFTLLPPTTQV 189

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19 Length = 367

 Score =  159 bits (404), Expect = 1e-47
 Identities = 47/117 (40%), Positives = 72/117 (61%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
               L   +R+  F   ++HGD+ Q +R+ +++ F+    R+LI TDV +RGIDV  ++ 
Sbjct: 250 DTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNC 309

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPM 197
           VINY LP N E Y+HRIGR+GR G+KG AIS +   + + LR IE+    +I ++  
Sbjct: 310 VINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKKLRYIERAMKLKIKKLKF 366

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19 Length = 367

 Score = 87.6 bits (218), Expect = 8e-21
 Identities = 26/73 (35%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 10  GGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQI 69
           GG  +   ++ L    ++V GTPGR+ D I R  L  +N+K  +LDEADEMLN GF + +
Sbjct: 110 GGKAIYPQIKALK-NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKDV 168

Query: 70  YDVYRYLPPATQV 82
             +        ++
Sbjct: 169 EKILNACNKDKRI 181

>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer, ATP-binding, helicase, hydrolase, nucleotide-binding; 2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A Length = 212

 Score =  154 bits (392), Expect = 1e-47
 Identities = 39/118 (33%), Positives = 64/118 (54%)

Query: 80  TQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVS 139
            + + + + +        ++HGD+ Q ER+ ++  FR G  RVL+ TDV ARG+D+ QV 
Sbjct: 42  AETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAARGLDIPQVD 101

Query: 140 LVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPM 197
           LV++Y LP+  E Y HR GR+GR GR G  +      + R +  +E+    +   +  
Sbjct: 102 LVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVGRRFKRVNP 159

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus} Length = 300

 Score =  152 bits (386), Expect = 9e-46
 Identities = 40/117 (34%), Positives = 64/117 (54%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           + + + + +        ++HGDM Q ER+ +M  FR G  RVL+ TDV ARG+D+ QV L
Sbjct: 40  ETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAARGLDIPQVDL 99

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPM 197
           V++Y +P+  E Y HR GR+GR GR G  +      + R +  +E+    +   +  
Sbjct: 100 VVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVGRRFKRVNP 156

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii} Length = 337

 Score =  146 bits (372), Expect = 3e-43
 Identities = 42/106 (39%), Positives = 63/106 (59%), Gaps = 5/106 (4%)

Query: 82  VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLV 141
           V  L      A      + GD+PQ  R+  +  FR G   +LITTDV +RG+D+  V  V
Sbjct: 233 VAKLVRLFDNA----IELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKV 288

Query: 142 INYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQY 187
           IN+D P +   YIHRIGR+GR GRKG AI+F+  ++  + +++++ 
Sbjct: 289 INFDAPQDLRTYIHRIGRTGRMGRKGEAITFI-LNEYWLEKEVKKV 333

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii} Length = 337

 Score = 79.9 bits (198), Expect = 4e-18
 Identities = 17/73 (23%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 10  GGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQI 69
           GG      + ++     +V  TPGR+ D+  + V+   + +++++DEAD M   GF + I
Sbjct: 92  GGMPYKAQINRVR-NADIVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDI 150

Query: 70  YDVYRYLPPATQV 82
             +          
Sbjct: 151 KIILAQTSNRKIT 163

>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} Length = 185

 Score =  141 bits (358), Expect = 7e-43
 Identities = 44/103 (42%), Positives = 66/103 (64%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
             D L + +    +  +S+HGD  Q++R+  + +FRSG S +L+ T V ARG+D+  V  
Sbjct: 58  GADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKH 117

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRD 183
           VIN+DLP++ E Y+HRIGR+GR G  G+A SF    +I I +D
Sbjct: 118 VINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKD 160

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  146 bits (371), Expect = 2e-42
 Identities = 44/104 (42%), Positives = 67/104 (64%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
             D L + +    +  +S+HGD  Q++R+  + +FRSG S +L+ T V ARG+D+  V  
Sbjct: 288 GADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKH 347

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDI 184
           VIN+DLP++ E Y+HRIGR+GR G  G+A SF    +I I +D+
Sbjct: 348 VINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDL 391

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score = 77.2 bits (191), Expect = 7e-17
 Identities = 27/62 (43%), Positives = 39/62 (62%)

Query: 8   CIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKE 67
             GG ++ + +R L+ G H++  TPGR+ DM+ R  +     K LVLDEAD ML+ GF+ 
Sbjct: 135 VYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGFEP 194

Query: 68  QI 69
           QI
Sbjct: 195 QI 196

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A* Length = 230

 Score =  141 bits (357), Expect = 3e-42
 Identities = 33/82 (40%), Positives = 52/82 (63%), Gaps = 2/82 (2%)

Query: 2   NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEML 61
            ++CH  IGGT LS+D  +L    H+  G+PGR+  +I    L   +I++ +LDEAD++L
Sbjct: 121 GLECHVFIGGTPLSQDKTRLKKC-HIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLL 179

Query: 62  NKG-FKEQIYDVYRYLPPATQV 82
            +G F+EQI  +Y  LP + Q+
Sbjct: 180 EEGSFQEQINWIYSSLPASKQM 201

>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 =  148 bits (375), Expect = 3e-42
 Identities = 34/119 (28%), Positives = 62/119 (52%), Gaps = 3/119 (2%)

Query: 81  QVDWLTEKMREAN---FTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQ 137
              +L   ++        +   HG + Q +R  ++K F+   S +L+ TDV ARG+D   
Sbjct: 351 FTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPN 410

Query: 138 VSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMP 196
           V  V+   +P+    YIHRIGR+ R G++G ++ F+  D++  +R++E   +  I +  
Sbjct: 411 VHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQE 469

>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 = 84.1 bits (208), Expect = 3e-19
 Identities = 22/80 (27%), Positives = 41/80 (51%), Gaps = 2/80 (2%)

Query: 1   MNVQCHACIGGTNLSEDLRKLD-YGQHVVSGTPGRVFDMIRRRVLR-TRNIKMLVLDEAD 58
               C + +GGT+    + K++    ++V  TPGR+ D++ +   +  R +   VLDEAD
Sbjct: 177 KKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEAD 236

Query: 59  EMLNKGFKEQIYDVYRYLPP 78
            +L  GF++ +  +   L  
Sbjct: 237 RLLEIGFRDDLETISGILNE 256

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens} Length = 191

 Score =  137 bits (348), Expect = 2e-41
 Identities = 40/104 (38%), Positives = 60/104 (57%), Gaps = 1/104 (0%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
            VD + E +        ++HG   Q+ER   ++ FR G   VL+ TDV ++G+D   +  
Sbjct: 66  DVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQH 125

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFV-KSDDIRILRD 183
           VINYD+P   E Y+HRIGR+G  G  G+A +F+ K+ D  +L D
Sbjct: 126 VINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDESVLMD 169

>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 =  146 bits (369), Expect = 3e-41
 Identities = 34/119 (28%), Positives = 62/119 (52%), Gaps = 3/119 (2%)

Query: 81  QVDWLTEKMREAN---FTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQ 137
              +L   ++        +   HG + Q +R  ++K F+   S +L+ TDV ARG+D   
Sbjct: 300 FTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPN 359

Query: 138 VSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMP 196
           V  V+   +P+    YIHRIGR+ R G++G ++ F+  D++  +R++E   +  I +  
Sbjct: 360 VHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQE 418

>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 = 84.1 bits (208), Expect = 4e-19
 Identities = 22/79 (27%), Positives = 41/79 (51%), Gaps = 2/79 (2%)

Query: 1   MNVQCHACIGGTNLSEDLRKLD-YGQHVVSGTPGRVFDMIRRRVLR-TRNIKMLVLDEAD 58
               C + +GGT+    + K++    ++V  TPGR+ D++ +   +  R +   VLDEAD
Sbjct: 126 KKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEAD 185

Query: 59  EMLNKGFKEQIYDVYRYLP 77
            +L  GF++ +  +   L 
Sbjct: 186 RLLEIGFRDDLETISGILN 204

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster} Length = 434

 Score =  143 bits (362), Expect = 5e-41
 Identities = 42/105 (40%), Positives = 67/105 (63%), Gaps = 1/105 (0%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
             D+L   + E  F  +S+HGD  Q +R+  +++F++G+ +VLI T V +RG+D++ +  
Sbjct: 312 GADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKH 371

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSD-DIRILRDI 184
           VINYD+P+  + Y+HRIGR+GR G  G A SF   + D  I  D+
Sbjct: 372 VINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAIAADL 416

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster} Length = 434

 Score = 78.0 bits (193), Expect = 3e-17
 Identities = 24/68 (35%), Positives = 36/68 (52%)

Query: 2   NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEML 61
            ++     GGT+       +  G HVV  TPGR+ D + R  +   + + +VLDEAD ML
Sbjct: 157 YLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTFITFEDTRFVVLDEADRML 216

Query: 62  NKGFKEQI 69
           + GF E +
Sbjct: 217 DMGFSEDM 224

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19 Length = 206

 Score =  135 bits (342), Expect = 4e-40
 Identities = 32/81 (39%), Positives = 53/81 (65%)

Query: 2   NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEML 61
             +  A  GGTNL +D+ +LD   HVV  TPGR+ D+I++ V +  +++M+VLDEAD++L
Sbjct: 100 GAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLL 159

Query: 62  NKGFKEQIYDVYRYLPPATQV 82
           ++ F + + D+   LP   Q+
Sbjct: 160 SQDFVQIMEDIILTLPKNRQI 180

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens} Length = 300

 Score =  132 bits (335), Expect = 4e-38
 Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 5/83 (6%)

Query: 2   NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRR-RVLRTRNIKMLVLDEADEM 60
            ++    + G  L    +     + +V GTPG V D   + + +  + IK+ VLDEAD M
Sbjct: 191 ELKLAYAVRGNKLERGQKI---SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVM 247

Query: 61  L-NKGFKEQIYDVYRYLPPATQV 82
           +  +G ++Q   + R LP   Q+
Sbjct: 248 IATQGHQDQSIRIQRMLPRNCQM 270

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19 Length = 220

 Score =  128 bits (324), Expect = 2e-37
 Identities = 27/83 (32%), Positives = 44/83 (53%), Gaps = 2/83 (2%)

Query: 2   NVQCHACIGGTNLSEDLRKLDYG-QHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEM 60
           NV+     GG ++ +D   L     H+V GTPGR+  + R + L  ++IK  +LDE D+M
Sbjct: 111 NVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKM 170

Query: 61  L-NKGFKEQIYDVYRYLPPATQV 82
           L     +  + +++R  P   QV
Sbjct: 171 LEQLDMRRDVQEIFRMTPHEKQV 193

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score =  102 bits (255), Expect = 7e-26
 Identities = 24/125 (19%), Positives = 50/125 (40%), Gaps = 14/125 (11%)

Query: 82  VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVW----ARGIDV-Q 136
              L E ++   F V     +  +       ++F+ G   +LI    +     RG+D+ +
Sbjct: 265 GKELYEYLKRFKFNVGETWSEFEK-----NFEDFKVGKINILIGVQAYYGKLTRGVDLPE 319

Query: 137 QVSLVINYDLPNNREL--YIHRIGRSGRFGRKGV--AISFVKSDDIRILRDIEQYYSTQI 192
           ++  VI +  P+  ++  YI   GRS R     +   +S +  +D  I   ++       
Sbjct: 320 RIKYVIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSVIFEEDEEIFESLKTRLLLIA 379

Query: 193 DEMPM 197
           +E  +
Sbjct: 380 EEEII 384

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score = 57.4 bits (139), Expect = 4e-10
 Identities = 18/169 (10%), Positives = 44/169 (26%), Gaps = 27/169 (15%)

Query: 9   IGGTNLSEDLRKLD----YGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKG 64
                  E  +          H++  +   V     R  L  +    + +D+ D +L   
Sbjct: 98  YSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSK--NREKLSQKRFDFVFVDDVDAVLKAS 155

Query: 65  FKEQIYDVYRYLPPATQ-----------VDWLTEKMREANFTVSSMHGDMPQKERDGIMK 113
                  +   +P               +    + ++     VSS     P+  R  + +
Sbjct: 156 RNIDTLLMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAK-PRGIRPLLFR 214

Query: 114 EFRSGT-SRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSG 161
           +  + T  R++          ++  V   I+          +       
Sbjct: 215 DLLNFTVGRLVSVAR------NITHV--RISSRSKEKLVELLEIFRDGI 255

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score = 93.8 bits (234), Expect = 5e-24
 Identities = 30/81 (37%), Positives = 44/81 (54%)

Query: 2   NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEML 61
            +     IGGT+  + L KL+   H+V GTPGR+ D IR + L      +LV+DEAD ML
Sbjct: 104 MIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLML 163

Query: 62  NKGFKEQIYDVYRYLPPATQV 82
           + GF   +  +   +P   Q+
Sbjct: 164 DMGFITDVDQIAARMPKDLQM 184

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A Length = 207

 Score = 86.1 bits (214), Expect = 3e-21
 Identities = 29/74 (39%), Positives = 41/74 (55%)

Query: 9   IGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQ 68
            GGT   +    L  G   V  TPGR  D +R+ VL    +++ VLDEADEML+ GF+E+
Sbjct: 105 YGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEE 164

Query: 69  IYDVYRYLPPATQV 82
           +  +    PP+ Q 
Sbjct: 165 VEALLSATPPSRQT 178

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19 Length = 494

 Score = 85.6 bits (211), Expect = 1e-19
 Identities = 35/145 (24%), Positives = 57/145 (39%), Gaps = 18/145 (12%)

Query: 62  NKGFKEQIYDVYRYLPPATQVDWLTEKMREANFTVSSMHGD--------MPQKERDGIMK 113
            +  K  ++  YR          +  ++ +         G         + Q+E+  I+ 
Sbjct: 359 KQNSKIIVFTNYRET-----AKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILD 413

Query: 114 EFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFV 173
           EF  G   VL+ T V   G+DV +V LV+ Y+   +    I R GR+GR    G  I  +
Sbjct: 414 EFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGR-HMPGRVIILM 472

Query: 174 KSDDIRILRDIEQYYSTQIDEMPMN 198
                   RD   Y+S++  E  M 
Sbjct: 473 AKGT----RDEAYYWSSRQKEKIMQ 493

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} Length = 242

 Score = 78.0 bits (193), Expect = 6e-18
 Identities = 26/81 (32%), Positives = 37/81 (45%)

Query: 1   MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEM 60
             ++     GG      +R L+ G  +   TPGR+ D +       R    LVLDEAD M
Sbjct: 129 CRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRM 188

Query: 61  LNKGFKEQIYDVYRYLPPATQ 81
           L+ GF+ QI  +   + P  Q
Sbjct: 189 LDMGFEPQIRKIVDQIRPDRQ 209

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19 Length = 253

 Score = 77.2 bits (191), Expect = 1e-17
 Identities = 24/65 (36%), Positives = 37/65 (56%), Gaps = 1/65 (1%)

Query: 6   HACI-GGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKG 64
              + GG +    +R++  G H++  TPGR+ D I +  +     K +VLDEAD ML+ G
Sbjct: 131 SCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMG 190

Query: 65  FKEQI 69
           F+ QI
Sbjct: 191 FEPQI 195

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens} Length = 249

 Score = 76.2 bits (188), Expect = 4e-17
 Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 1/82 (1%)

Query: 1   MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRR-RVLRTRNIKMLVLDEADE 59
           + VQ    +GG +       L    H++  TPGR+ D +   +    R +K LV+DEAD 
Sbjct: 138 IGVQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADR 197

Query: 60  MLNKGFKEQIYDVYRYLPPATQ 81
           +LN  F+ ++  + + +P   +
Sbjct: 198 ILNMDFETEVDKILKVIPRDRK 219

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens} Length = 228

 Score = 74.1 bits (183), Expect = 2e-16
 Identities = 24/80 (30%), Positives = 41/80 (51%)

Query: 2   NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEML 61
            ++     GG N +  +  +  G  ++  TPGR+ D+     +  R+I  LV+DEAD+ML
Sbjct: 121 GLKSICIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKML 180

Query: 62  NKGFKEQIYDVYRYLPPATQ 81
           +  F+ QI  +   + P  Q
Sbjct: 181 DMEFEPQIRKILLDVRPDRQ 200

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens} Length = 236

 Score = 72.7 bits (179), Expect = 5e-16
 Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 2/82 (2%)

Query: 1   MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFD-MIRRRVLRTRNIKMLVLDEADE 59
            +      IGG +L  +  +++   +++  TPGR+   M         +++MLVLDEAD 
Sbjct: 124 HDFSAGLIIGGKDLKHEAERIN-NINILVCTPGRLLQHMDETVSFHATDLQMLVLDEADR 182

Query: 60  MLNKGFKEQIYDVYRYLPPATQ 81
           +L+ GF + +  V   LP   Q
Sbjct: 183 ILDMGFADTMNAVIENLPKKRQ 204

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens} Length = 262

 Score = 70.0 bits (172), Expect = 8e-15
 Identities = 28/90 (31%), Positives = 49/90 (54%), Gaps = 9/90 (10%)

Query: 1   MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRR-RVLRTRNIKMLVLDEADE 59
                   +GG+N S + +KL  G +++  TPGR+ D ++       +N++ LV+DEAD 
Sbjct: 153 HVHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADR 212

Query: 60  MLNKGFKEQIYDVYRYLPP--------ATQ 81
           +L+ GF+E++  + + LP         ATQ
Sbjct: 213 ILDVGFEEELKQIIKLLPTRRQTMLFSATQ 242

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens} Length = 245

 Score = 64.9 bits (159), Expect = 5e-13
 Identities = 13/83 (15%), Positives = 35/83 (42%), Gaps = 6/83 (7%)

Query: 2   NVQCHACIGGTNLSEDL-RKLDYGQHVVSGTPGRVFDMIRRRVLRT--RNIKMLVLDEAD 58
             + H        ++    K      ++  TP R+  ++++        +++ LV+DE+D
Sbjct: 126 GFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESD 185

Query: 59  EMLNK---GFKEQIYDVYRYLPP 78
           ++      GF++Q+  ++     
Sbjct: 186 KLFEDGKTGFRDQLASIFLACTS 208

>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription factor, RNA polymerase recycling, activator, ATP-binding, DNA-binding; 3.20A {Escherichia coli K12} Length = 968

 Score = 63.9 bits (155), Expect = 3e-12
 Identities = 25/88 (28%), Positives = 41/88 (46%), Gaps = 3/88 (3%)

Query: 82  VDWLTEKMREA-NFTVSSMHGDMPQKERDGIMKEFRSGTS--RVLITTDVWARGIDVQQV 138
              L + +RE      +  H  M   ERD     F    +  +VL+ +++ + G + Q  
Sbjct: 516 ALQLEQVLREREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEIGSEGRNFQFA 575

Query: 139 SLVINYDLPNNRELYIHRIGRSGRFGRK 166
           S ++ +DLP N +L   RIGR  R G+ 
Sbjct: 576 SHMVMFDLPFNPDLLEQRIGRLDRIGQA 603

>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.70A {Anas platyrhynchos} Length = 936

 Score = 61.1 bits (147), Expect = 3e-11
 Identities = 32/146 (21%), Positives = 49/146 (33%), Gaps = 17/146 (11%)

Query: 62  NKGFKEQIYDVYRYLPPATQVDWLTEKMREANFTVSSMHG--------DMPQKERDGIMK 113
           N   +  ++   R L  A     + E           + G         M    + G++ 
Sbjct: 629 NPQTRTLLFAKTRALVSAL-KKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLD 687

Query: 114 EFRSGTS-RVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISF 172
            F++    R+LI T V   GID+ Q +LV+ Y+   N    I   GR GR       I  
Sbjct: 688 AFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GR-AAGSKCILV 745

Query: 173 VKSDDIRILRDIEQYYSTQIDEMPMN 198
                      +E     +  E  MN
Sbjct: 746 TSKT-----EVVENEKCNRYKEEMMN 766

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 60.8 bits (146), Expect = 4e-11
 Identities = 29/126 (23%), Positives = 43/126 (34%), Gaps = 16/126 (12%)

Query: 82  VDWLTEKMREANFTVSSMHG--------DMPQKERDGIMKEFR-SGTSRVLITTDVWARG 132
            +W+    + +      + G         M    +  I+  F+ SG   +LI T V   G
Sbjct: 415 KNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEG 474

Query: 133 IDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQI 192
           ID+ Q +LVI Y+   N    I   GR     R         +        IE+      
Sbjct: 475 IDIAQCNLVILYEYVGNVIKMIQTRGRGRA--RGSKCFLLTSNAG-----VIEKEQINMY 527

Query: 193 DEMPMN 198
            E  MN
Sbjct: 528 KEKMMN 533

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos} Length = 797

 Score = 60.4 bits (145), Expect = 5e-11
 Identities = 32/146 (21%), Positives = 49/146 (33%), Gaps = 17/146 (11%)

Query: 62  NKGFKEQIYDVYRYLPPATQVDWLTEKMREANFTVSSMHG--------DMPQKERDGIMK 113
           N   +  ++   R L  A     + E           + G         M    + G++ 
Sbjct: 629 NPQTRTLLFAKTRALVSAL-KKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLD 687

Query: 114 EFRSGTS-RVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISF 172
            F++    R+LI T V   GID+ Q +LV+ Y+   N    I   GR GR       I  
Sbjct: 688 AFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GR-AAGSKCILV 745

Query: 173 VKSDDIRILRDIEQYYSTQIDEMPMN 198
                      +E     +  E  MN
Sbjct: 746 TSKT-----EVVENEKCNRYKEEMMN 766

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A* Length = 556

 Score = 60.3 bits (145), Expect = 5e-11
 Identities = 34/198 (17%), Positives = 55/198 (27%), Gaps = 22/198 (11%)

Query: 10  GGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQI 69
             T L + L      +        +       ++     I         +     F +  
Sbjct: 341 PYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTR 400

Query: 70  YDVYRYLPPATQVDWLTEKMREANFTVSSMHG--------DMPQKERDGIMKEFRSGTS- 120
             V            + E           + G         M    + G++  F++    
Sbjct: 401 ALVSAL------KKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDN 454

Query: 121 RVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRI 180
           R+LI T V   GID+ Q +LV+ Y+   N    I   GR GR       I          
Sbjct: 455 RLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GR-AAGSKCILVTSKT---- 508

Query: 181 LRDIEQYYSTQIDEMPMN 198
              +E     +  E  MN
Sbjct: 509 -EVVENEKCNRYKEEMMN 525

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 58.0 bits (139), Expect = 3e-10
 Identities = 34/126 (26%), Positives = 49/126 (38%), Gaps = 16/126 (12%)

Query: 82  VDWLTEKMREANFTVSSMHG--------DMPQKERDGIMKEFR-SGTSRVLITTDVWARG 132
             W+ E    +      + G         M    +  +++ FR SG + +LI T V   G
Sbjct: 406 KKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFRASGDNNILIATSVADEG 465

Query: 133 IDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQI 192
           ID+ + +LVI Y+   N    I   GR GR  R         S D      IE+  +  I
Sbjct: 466 IDIAECNLVILYEYVGNVIKMIQTRGR-GR-ARDSKCFLLTSSAD-----VIEKEKANMI 518

Query: 193 DEMPMN 198
            E  MN
Sbjct: 519 KEKIMN 524

>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* Length = 523

 Score = 50.2 bits (121), Expect = 1e-07
 Identities = 25/107 (23%), Positives = 53/107 (49%), Gaps = 1/107 (0%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +V+    +++    + ++ H  +    R  + ++F+    ++++ T  +  GI+   V  
Sbjct: 248 KVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRF 307

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRD-IEQ 186
           V+++D+P N E Y    GR+GR G    A+ F    D+  LR  +E+
Sbjct: 308 VVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLEE 354

>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* Length = 591

 Score = 48.8 bits (117), Expect = 4e-07
 Identities = 20/101 (19%), Positives = 46/101 (45%)

Query: 82  VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLV 141
            + +T  ++       + H ++  +++  + +++ +   +V++ T  +  GID   V  V
Sbjct: 280 SEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFV 339

Query: 142 INYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILR 182
           I++ +  + E Y    GR+GR   K   I +    DI  + 
Sbjct: 340 IHHSMSKSMENYYQESGRAGRDDMKADCILYYGFGDIFRIS 380

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A* Length = 720

 Score = 45.2 bits (107), Expect = 7e-06
 Identities = 29/146 (19%), Positives = 54/146 (36%), Gaps = 15/146 (10%)

Query: 45  RTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVDWLTEKMREANFTVSSMHGDMP 104
           +   + + +  +   +L K     + ++   L      + L + +R     V+  H  + 
Sbjct: 249 KAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIR---GGVAFHHAGLG 305

Query: 105 QKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVI-----NYDLPNNRELYIHRI-- 157
           + ER  + + FR G  + ++ T   + GI+      VI      Y       + I  +  
Sbjct: 306 RDERVLVEENFRKGIIKAVVATPTLSAGINT-PAFRVIIRDIWRYSDFGMERIPIIEVHQ 364

Query: 158 --GRSGRFG--RKGVAISFVKSDDIR 179
             GR+GR      G  I    SDD R
Sbjct: 365 MLGRAGRPKYDEVGEGIIVSTSDDPR 390

>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* Length = 472

 Score = 44.0 bits (104), Expect = 1e-05
 Identities = 18/66 (27%), Positives = 36/66 (54%)

Query: 94  FTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELY 153
           F + ++     ++ER+ I++ FR+G  R ++++ V   GIDV   ++ +      +   Y
Sbjct: 369 FLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREY 428

Query: 154 IHRIGR 159
           I R+GR
Sbjct: 429 IQRLGR 434

>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 Length = 780

 Score = 43.0 bits (102), Expect = 3e-05
 Identities = 18/43 (41%), Positives = 26/43 (60%)

Query: 93  NFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDV 135
            F +  MHG + Q+E+D +M EF  G   +L++T V   GIDV
Sbjct: 613 EFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDV 655

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4a92_A* 1cu1_A 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A 8ohm_A 2f55_A 1jr6_A 1onb_A Length = 666

 Score = 42.7 bits (100), Expect = 5e-05
 Identities = 15/108 (13%), Positives = 31/108 (28%), Gaps = 27/108 (25%)

Query: 75  YLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARG-- 132
           +     + D L  K+        + +  +        +    +    V++ TD    G  
Sbjct: 402 FCHSKKKCDELAAKLSGLGINAVAYYRGLD-------VSVIPTIGDVVVVATDALMTGYT 454

Query: 133 IDV-------QQVSLVINYDLPNNREL-----------YIHRIGRSGR 162
            D          V+  +++ L     +              R GR+GR
Sbjct: 455 GDFDSVIDCNTCVTQTVDFSLDPTFTIETTTVPQDAVSRSQRRGRTGR 502

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4} Length = 510

 Score = 40.3 bits (93), Expect = 2e-04
 Identities = 13/82 (15%), Positives = 37/82 (45%), Gaps = 1/82 (1%)

Query: 82  VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITT-DVWARGIDVQQVSL 140
              + + ++     V  + G++  + R+ +     +G   +++ +  V++ GI V+ +  
Sbjct: 360 GKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFSTGISVKNLHH 419

Query: 141 VINYDLPNNRELYIHRIGRSGR 162
           V+      ++ + +  IGR  R
Sbjct: 420 VVLAHGVKSKIIVLQTIGRVLR 441

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A Length = 677

 Score = 39.1 bits (90), Expect = 7e-04
 Identities = 26/165 (15%), Positives = 59/165 (35%), Gaps = 21/165 (12%)

Query: 45  RTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVDWLTEKMREANFTVSSMHGDMP 104
             R   + VLD A E L+          +        +  ++ ++       + ++G +P
Sbjct: 300 YKRLTPISVLDHALESLDNLRPGDCIVCFS----KNDIYSVSRQIEIRGLESAVIYGSLP 355

Query: 105 QKERDGIMKEFRSGTSRV--LITTDVWARGIDVQQVSLVIN----YDLPNNRELYIHRI- 157
              +    K+F         L+ TD    G+++    ++        +    E  +  I 
Sbjct: 356 PGTKLAQAKKFNDPNDPCKILVATDAIGMGLNLSIRRIIFYSLIKPSINEKGERELEPIT 415

Query: 158 --------GRSGRFGRKGVA--ISFVKSDDIRILRDIEQYYSTQI 192
                   GR+GRF  +     ++ +  +D+ +L++I +     I
Sbjct: 416 TSQALQIAGRAGRFSSRFKEGEVTTMNHEDLSLLKEILKRPVDPI 460

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	210
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	100.0
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	100.0
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	100.0
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	100.0
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	100.0
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	100.0
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	100.0
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	100.0
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	100.0
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	100.0
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	100.0
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	100.0
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	100.0
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.97
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.97
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.97
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.97
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.97
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.95
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.95
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.95
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	99.95
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.95
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	99.95
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.94
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.94
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	99.94
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.94
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	99.94
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.94
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.94
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.94
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.94
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.94
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.93
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.93
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.93
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.93
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.93
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.93
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	99.93
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.93
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.92
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.92
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	99.86
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.92
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.91
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.91
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.91
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.9
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.9
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.89
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.89
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.88
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.87
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.87
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.87
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.87
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.86
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.86
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.86
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.84
3h1t_A	590	Type I site-specific restriction-modification syst	99.83
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.8
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.79
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.78
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.76
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.74
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.72
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.6
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.48
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.39
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.32
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.29
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.28
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.26
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.25
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.23
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.23
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.21
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.2
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.14
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.14
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.11
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.04
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	98.9
3b6e_A	216	Interferon-induced helicase C domain-containing P;	98.61
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	98.19
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	97.67
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	97.41
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	96.96
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	96.56
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	96.51
3hgt_A	328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	96.22
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	94.88
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	94.17
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	93.47
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	92.16
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	84.88

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=100.00  E-value=3.4e-38  Score=262.98  Aligned_cols=200  Identities=35%  Similarity=0.627  Sum_probs=183.7

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCC--Cc
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLP--PA   79 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~--~~   79 (210)
                      ++++..++||.+...+...+..+++|+|+||++|.+++.++.+.+++++++|+||||+|++.++...+..++..+.  ..
T Consensus       157 ~~~~~~~~gg~~~~~~~~~l~~~~~Ivv~Tp~~l~~~l~~~~~~l~~~~~lVlDEah~~~~~gf~~~~~~i~~~~~~~~~  236 (434)
T 2db3_A          157 YLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTFITFEDTRFVVLDEADRMLDMGFSEDMRRIMTHVTMRPE  236 (434)
T ss_dssp             SCCCCEECTTSCHHHHHHHHTTCCSEEEECHHHHHHHHHTTSCCCTTCCEEEEETHHHHTSTTTHHHHHHHHHCTTSCSS
T ss_pred             CcEEEEEECCCCHHHHHHHhhcCCCEEEEChHHHHHHHHhCCcccccCCeEEEccHhhhhccCcHHHHHHHHHhcCCCCC
Confidence            5788899999999999999999999999999999999999989999999999999999999999999988887642  22


Q ss_pred             hh--------------------------------------------------------------------------HHHH
Q psy6712          80 TQ--------------------------------------------------------------------------VDWL   85 (210)
Q Consensus        80 ~~--------------------------------------------------------------------------~~~l   85 (210)
                      .+                                                                          ++.+
T Consensus       237 ~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~~~~lVF~~t~~~a~~l  316 (434)
T 2db3_A          237 HQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTIYEVNKYAKRSKLIEILSEQADGTIVFVETKRGADFL  316 (434)
T ss_dssp             CEEEEEESCCCHHHHHHHHTTCSSCEEEEESSTTCCCTTEEEEEEECCGGGHHHHHHHHHHHCCTTEEEECSSHHHHHHH
T ss_pred             ceEEEEeccCCHHHHHHHHHhccCCEEEEeccccccccccceEEEEeCcHHHHHHHHHHHHhCCCCEEEEEeCcHHHHHH
Confidence            22                                                                          8889


Q ss_pred             HHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCC
Q psy6712          86 TEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGR  165 (210)
Q Consensus        86 ~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~  165 (210)
                      ++.|.+.++++..+||+|++.+|.+++++|++|+.+|||||+++++|+|+|++++||+||+|.+..+|+||+||+||.|+
T Consensus       317 ~~~L~~~~~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~v~~rGlDi~~v~~VI~~d~p~~~~~y~qriGR~gR~g~  396 (434)
T 2db3_A          317 ASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGN  396 (434)
T ss_dssp             HHHHHHTTCCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECGGGTSSCCCTTCCEEEESSCCSSHHHHHHHHTTSSCTTC
T ss_pred             HHHHHhCCCCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEchhhhCCCCcccCCEEEEECCCCCHHHHHHHhcccccCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceeEEEEecc-CcHHHHHHHHHHhcCccccccCCccc
Q psy6712         166 KGVAISFVKS-DDIRILRDIEQYYSTQIDEMPMNGKR  201 (210)
Q Consensus       166 ~g~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~  201 (210)
                      .|.+++|+.+ .+......+.+.+....+++|..+.+
T Consensus       397 ~G~a~~~~~~~~~~~~~~~l~~~l~~~~~~vp~~l~~  433 (434)
T 2db3_A          397 NGRATSFFDPEKDRAIAADLVKILEGSGQTVPDFLRT  433 (434)
T ss_dssp             CEEEEEEECTTTCGGGHHHHHHHHHHTTCCCCGGGC-
T ss_pred             CCEEEEEEeccccHHHHHHHHHHHHHcCCCCCHHHHh
Confidence            9999999995 57788889999999998888876543

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=100.00  E-value=4.8e-37  Score=253.75  Aligned_cols=201  Identities=90%  Similarity=1.400  Sum_probs=188.5

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchh
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ   81 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~   81 (210)
                      ++++..++||.+..++...+..+++|+|+||+++.+++.++.+.+.+++++|+||||.+.+.++...+..++..++...+
T Consensus       133 ~~~~~~~~g~~~~~~~~~~~~~~~~ivv~Tp~~l~~~l~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~i~~~~~~~~~  212 (410)
T 2j0s_A          133 NVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ  212 (410)
T ss_dssp             TCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHTSTTTHHHHHHHHTTSCTTCE
T ss_pred             CeEEEEEECCCCHHHHHHHhhcCCCEEEcCHHHHHHHHHhCCccHhheeEEEEccHHHHHhhhhHHHHHHHHHhCccCce
Confidence            67889999999999999888889999999999999999998888999999999999999999998888888877665444


Q ss_pred             ----------------------------------------------------------------------------HHHH
Q psy6712          82 ----------------------------------------------------------------------------VDWL   85 (210)
Q Consensus        82 ----------------------------------------------------------------------------~~~l   85 (210)
                                                                                                  ++.+
T Consensus       213 ~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lVf~~~~~~~~~l  292 (410)
T 2j0s_A          213 VVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWL  292 (410)
T ss_dssp             EEEEESCCCHHHHTTGGGTCSSCEEECCCGGGCSCTTEEEEEEEESSTTHHHHHHHHHHHHHTSSEEEEECSSHHHHHHH
T ss_pred             EEEEEcCCCHHHHHHHHHHcCCCEEEEecCccccCCCceEEEEEeCcHHhHHHHHHHHHHhcCCCcEEEEEcCHHHHHHH
Confidence                                                                                        7889


Q ss_pred             HHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCC
Q psy6712          86 TEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGR  165 (210)
Q Consensus        86 ~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~  165 (210)
                      ++.|.+.++.+..+||+|+..+|..+++.|++|+.++||||+++++|+|+|++++||++|+|++...|+||+||+||.|+
T Consensus       293 ~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~  372 (410)
T 2j0s_A          293 TEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGR  372 (410)
T ss_dssp             HHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGC
T ss_pred             HHHHHhCCCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECChhhCcCCcccCCEEEEECCCCCHHHHHHhcccccCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceeEEEEeccCcHHHHHHHHHHhcCccccccCCcccc
Q psy6712         166 KGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRS  202 (210)
Q Consensus       166 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  202 (210)
                      .|.+++|+.+.+...++.++++++.+++++|.+..++
T Consensus       373 ~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~  409 (410)
T 2j0s_A          373 KGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADL  409 (410)
T ss_dssp             CEEEEEEEEGGGHHHHHHHHHHTTCCCEECCSCCTTT
T ss_pred             ceEEEEEecHHHHHHHHHHHHHhCCCceecccchhhc
Confidence            9999999999999999999999999999999887654

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=100.00  E-value=2.9e-35  Score=242.25  Aligned_cols=202  Identities=41%  Similarity=0.748  Sum_probs=186.6

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchh
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ   81 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~   81 (210)
                      ++++..++||.+...+...+..+++|+|+||+++.+.+.++...+++++++|+||||++.+.++...+..++..++...+
T Consensus       117 ~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~~~~~~~~~~i~~~~~~~~~  196 (400)
T 1s2m_A          117 GISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQ  196 (400)
T ss_dssp             TCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEESHHHHSSHHHHHHHHHHHTTSCSSCE
T ss_pred             CceEEEEeCCcchHHHHHHhcCCCCEEEEchHHHHHHHHhCCcccccCCEEEEeCchHhhhhchHHHHHHHHHhCCcCce
Confidence            67899999999998888888889999999999999999888888999999999999999988887777777766554333


Q ss_pred             --------------------------------------------------------------------------HHHHHH
Q psy6712          82 --------------------------------------------------------------------------VDWLTE   87 (210)
Q Consensus        82 --------------------------------------------------------------------------~~~l~~   87 (210)
                                                                                                ++.+++
T Consensus       197 ~i~lSAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lVf~~~~~~~~~l~~  276 (400)
T 1s2m_A          197 SLLFSATFPLTVKEFMVKHLHKPYEINLMEELTLKGITQYYAFVEERQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAK  276 (400)
T ss_dssp             EEEEESCCCHHHHHHHHHHCSSCEEESCCSSCBCTTEEEEEEECCGGGHHHHHHHHHHHSCCSEEEEECSSHHHHHHHHH
T ss_pred             EEEEEecCCHHHHHHHHHHcCCCeEEEeccccccCCceeEEEEechhhHHHHHHHHHhhcCCCcEEEEEecHHHHHHHHH
Confidence                                                                                      788889


Q ss_pred             HHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCCce
Q psy6712          88 KMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKG  167 (210)
Q Consensus        88 ~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~~g  167 (210)
                      .|.+.++.+..+||+|+..+|.++++.|++|+.++||||+++++|+|+|++++||++++|++...|+||+||+||.|+.|
T Consensus       277 ~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~~~~~Gidip~~~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g  356 (400)
T 1s2m_A          277 KITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLG  356 (400)
T ss_dssp             HHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCE
T ss_pred             HHHhcCCCeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCccccCCCccCCCEEEEeCCCCCHHHHHHhcchhcCCCCCc
Confidence            99988999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEeccCcHHHHHHHHHHhcCccccccCCccccC
Q psy6712         168 VAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRSL  203 (210)
Q Consensus       168 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  203 (210)
                      .|++++++.+...++++++.++.+++++|....+.+
T Consensus       357 ~~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~  392 (400)
T 1s2m_A          357 LAINLINWNDRFNLYKIEQELGTEIAAIPATIDKSL  392 (400)
T ss_dssp             EEEEEECGGGHHHHHHHHHHHTCCCEECCSSCCGGG
T ss_pred             eEEEEeccchHHHHHHHHHHhCCCcccccccccccc
Confidence            999999999999999999999999999998887766

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=100.00  E-value=3.1e-36  Score=248.82  Aligned_cols=201  Identities=68%  Similarity=1.100  Sum_probs=168.6

Q ss_pred             CceEEEEEcCcchHHHHHHhc-CCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCch
Q psy6712           2 NVQCHACIGGTNLSEDLRKLD-YGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPAT   80 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~-~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~   80 (210)
                      ++.+..++||.+...+...+. .+++|+|+||+++.+.+.++.+.+++++++|+||||++.++++...+..++..++...
T Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~~~~~~~~~~  215 (414)
T 3eiq_A          136 GASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNT  215 (414)
T ss_dssp             CCCEEECCCCTTHHHHHHHHTTTCCSEEEECHHHHHHHHHHTSSCSTTCCEEEECSHHHHHHTTTHHHHHHHHTTSCTTC
T ss_pred             CceEEEEECCcchHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccCcEEEEECHHHhhccCcHHHHHHHHHhCCCCC
Confidence            577889999999988888876 6789999999999999999888899999999999999999898888888877665444


Q ss_pred             h----------------------------------------------------------------------------HHH
Q psy6712          81 Q----------------------------------------------------------------------------VDW   84 (210)
Q Consensus        81 ~----------------------------------------------------------------------------~~~   84 (210)
                      +                                                                            ++.
T Consensus       216 ~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvf~~~~~~~~~  295 (414)
T 3eiq_A          216 QVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFINTRRKVDW  295 (414)
T ss_dssp             EEEEECSCCCHHHHHHHTTTCSSCEEECCCCCCCCTTSCCEEEEECSSSTTHHHHHHHHHHSSCCSSCEEECSCHHHHHH
T ss_pred             eEEEEEEecCHHHHHHHHHHcCCCEEEEecCCccCCCCceEEEEEeChHHhHHHHHHHHHHhCCCCcEEEEeCCHHHHHH
Confidence            3                                                                            788


Q ss_pred             HHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCC
Q psy6712          85 LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFG  164 (210)
Q Consensus        85 l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g  164 (210)
                      +++.|.+.++.+..+||+|+..+|.++++.|++|+.++||||+++++|+|+|++++||++++|.+...|+||+||+||.|
T Consensus       296 l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g  375 (414)
T 3eiq_A          296 LTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFG  375 (414)
T ss_dssp             HHHHHHTTTCCCEEC---CHHHHHHHHHHHHSCC---CEEECSSCC--CCGGGCSCEEESSCCSSTHHHHHHSCCC----
T ss_pred             HHHHHHhcCCeEEEecCCCCHHHHHHHHHHHHcCCCcEEEECCccccCCCccCCCEEEEeCCCCCHHHhhhhcCcccCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CceeEEEEeccCcHHHHHHHHHHhcCccccccCCcccc
Q psy6712         165 RKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRS  202 (210)
Q Consensus       165 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  202 (210)
                      +.|.+++++.+.+...++.++++++..++++|.+..++
T Consensus       376 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  413 (414)
T 3eiq_A          376 RKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVADL  413 (414)
T ss_dssp             ---CEEEEECSTHHHHHHHHHHHTTCCCEECCC-----
T ss_pred             CCceEEEEEcHHHHHHHHHHHHHHcCCccccChhhhhc
Confidence            99999999999999999999999999999999887765

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=100.00  E-value=8.2e-36  Score=246.63  Aligned_cols=201  Identities=38%  Similarity=0.655  Sum_probs=180.9

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhC--CC-
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYL--PP-   78 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~--~~-   78 (210)
                      ++++..++||.+..++...+..+++|+|+||+++.+++..+.+.+++++++|+||||.+.++++...+..++...  +. 
T Consensus       129 ~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~i~~~~~~~~~  208 (417)
T 2i4i_A          129 RVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDTMPPK  208 (417)
T ss_dssp             SCCEEEECSSSCHHHHHHHHTTCCSEEEECHHHHHHHHHTTSBCCTTCCEEEESSHHHHHHTTCHHHHHHHHTSSSCCCB
T ss_pred             CceEEEEECCCCHHHHHHHhhCCCCEEEEChHHHHHHHHcCCcChhhCcEEEEEChhHhhccCcHHHHHHHHHhccCCCc
Confidence            678999999999999999998899999999999999999988889999999999999999998888888887632  21 


Q ss_pred             -chh----------------------------------------------------------------------------
Q psy6712          79 -ATQ----------------------------------------------------------------------------   81 (210)
Q Consensus        79 -~~~----------------------------------------------------------------------------   81 (210)
                       ..+                                                                            
T Consensus       209 ~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~l~~~l~~~~~~~~~lVf~~~~~~  288 (417)
T 2i4i_A          209 GVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKG  288 (417)
T ss_dssp             TTBEEEEEESCCCHHHHHHHHHHCSSCEEEEEC----CCSSEEEEEEECCGGGHHHHHHHHHHTCCTTCEEEEECSSHHH
T ss_pred             CCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEeCCCCCCccCceEEEEEeccHhHHHHHHHHHHhcCCCCeEEEEECCHHH
Confidence             111                                                                            


Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhc
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSG  161 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~g  161 (210)
                      ++.+++.|.+.++.+..+||+|+.++|.++++.|++|+.++||||+++++|+|+|++++||+||+|.+...|+||+||+|
T Consensus       289 ~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlvaT~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~g  368 (417)
T 2i4i_A          289 ADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTG  368 (417)
T ss_dssp             HHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTSSCEEEECHHHHTTSCCCCEEEEEESSCCSSHHHHHHHHTTBC
T ss_pred             HHHHHHHHHHCCCCeeEecCCCCHHHHHHHHHHHHcCCCCEEEECChhhcCCCcccCCEEEEEcCCCCHHHHHHhcCccc
Confidence            88899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCceeEEEEeccCcHHHHHHHHHHhcCccccccCCcccc
Q psy6712         162 RFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRS  202 (210)
Q Consensus       162 R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  202 (210)
                      |.|+.|.+++|+.+.+...++.+.+.+.....++|.....+
T Consensus       369 R~g~~g~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~  409 (417)
T 2i4i_A          369 RVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENM  409 (417)
T ss_dssp             C--CCEEEEEEECGGGGGGHHHHHHHHHHTTCCCCHHHHHH
T ss_pred             cCCCCceEEEEEccccHHHHHHHHHHHHHhcCcCCHHHHHH
Confidence            99999999999999999999999999988777777655443

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=100.00  E-value=1.1e-33  Score=229.79  Aligned_cols=195  Identities=38%  Similarity=0.689  Sum_probs=177.8

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchh
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ   81 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~   81 (210)
                      ++++..++||.....+...+. +++|+|+||+++.+.+..+...+.+++++|+||||.+.+.++...+..++..++...+
T Consensus       102 ~~~v~~~~~~~~~~~~~~~~~-~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~~~~~~~~~~~~~~~~  180 (367)
T 1hv8_A          102 NLKIAKIYGGKAIYPQIKALK-NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKDKR  180 (367)
T ss_dssp             CCCEEEECTTSCHHHHHHHHH-TCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHTTTTHHHHHHHHHTSCSSCE
T ss_pred             CceEEEEECCcchHHHHhhcC-CCCEEEecHHHHHHHHHcCCcccccCCEEEEeCchHhhhhchHHHHHHHHHhCCCCce
Confidence            567889999999887777665 7899999999999999988888999999999999999988888777777765543333


Q ss_pred             ----------------------------------------------------------------------HHHHHHHHHh
Q psy6712          82 ----------------------------------------------------------------------VDWLTEKMRE   91 (210)
Q Consensus        82 ----------------------------------------------------------------------~~~l~~~l~~   91 (210)
                                                                                            ++.+++.|++
T Consensus       181 ~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~lvf~~~~~~~~~l~~~L~~  260 (367)
T 1hv8_A          181 ILLFSATMPREILNLAKKYMGDYSFIKAKINANIEQSYVEVNENERFEALCRLLKNKEFYGLVFCKTKRDTKELASMLRD  260 (367)
T ss_dssp             EEEECSSCCHHHHHHHHHHCCSEEEEECCSSSSSEEEEEECCGGGHHHHHHHHHCSTTCCEEEECSSHHHHHHHHHHHHH
T ss_pred             EEEEeeccCHHHHHHHHHHcCCCeEEEecCCCCceEEEEEeChHHHHHHHHHHHhcCCCcEEEEECCHHHHHHHHHHHHh
Confidence                                                                                  7888999999


Q ss_pred             cCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCCceeEEE
Q psy6712          92 ANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAIS  171 (210)
Q Consensus        92 ~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~~g~~~~  171 (210)
                      .++.+..+||+|+..+|.++++.|++|+.++||||+++++|+|+|++++||++++|++..+|.||+||+||.|+.|.+++
T Consensus       261 ~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~  340 (367)
T 1hv8_A          261 IGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAIS  340 (367)
T ss_dssp             TTCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEE
T ss_pred             cCCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECChhhcCCCcccCCEEEEecCCCCHHHhhhcccccccCCCccEEEE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeccCcHHHHHHHHHHhcCccccccC
Q psy6712         172 FVKSDDIRILRDIEQYYSTQIDEMPM  197 (210)
Q Consensus       172 ~~~~~~~~~~~~~~~~~~~~~~~~~~  197 (210)
                      ++.+.+...++.+++.++.++++++.
T Consensus       341 ~~~~~~~~~~~~i~~~~~~~~~~~~~  366 (367)
T 1hv8_A          341 IINRREYKKLRYIERAMKLKIKKLKF  366 (367)
T ss_dssp             EECTTSHHHHHHHHHHHTCCCCCBC-
T ss_pred             EEcHHHHHHHHHHHHHhCCCCceecc
Confidence            99999999999999999999988764

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=100.00  E-value=9.1e-34  Score=232.43  Aligned_cols=199  Identities=35%  Similarity=0.701  Sum_probs=178.0

Q ss_pred             CceEEEEEcCcchHHHHHHhcC-CCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhc-cchHHHHHHHHhhCCCc
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDY-GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLN-KGFKEQIYDVYRYLPPA   79 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~-~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~-~~~~~~~~~i~~~~~~~   79 (210)
                      ++++..++||.+.+.+...+.. .++|+|+||+++..++.++...+++++++|+||||.+.+ .++...+..++...+..
T Consensus       105 ~~~~~~~~g~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~vViDEaH~~~~~~~~~~~~~~~~~~~~~~  184 (391)
T 1xti_A          105 NVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHE  184 (391)
T ss_dssp             TCCEEEECTTSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCSEEEECSHHHHTSSHHHHHHHHHHHHTSCSS
T ss_pred             CeEEEEEeCCCCHHHHHHHHhcCCCCEEEECHHHHHHHHHcCCccccccCEEEEeCHHHHhhccchHHHHHHHHhhCCCC
Confidence            6789999999998888777765 479999999999999998888899999999999999987 36667777776655433


Q ss_pred             hh----------------------------------------------------------------------------HH
Q psy6712          80 TQ----------------------------------------------------------------------------VD   83 (210)
Q Consensus        80 ~~----------------------------------------------------------------------------~~   83 (210)
                      .+                                                                            ++
T Consensus       185 ~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~lvf~~~~~~~~  264 (391)
T 1xti_A          185 KQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCI  264 (391)
T ss_dssp             SEEEEEESSCCSTHHHHHHHHCSSCEEEECCCCCCCCCTTCEEEEEECCGGGHHHHHHHHHHHSCCSEEEEECSCHHHHH
T ss_pred             ceEEEEEeeCCHHHHHHHHHHcCCCeEEEecCccccCcccceEEEEEcCchhHHHHHHHHHHhcCCCcEEEEeCcHHHHH
Confidence            33                                                                            78


Q ss_pred             HHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCC
Q psy6712          84 WLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRF  163 (210)
Q Consensus        84 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~  163 (210)
                      .+++.|.+.++.+..+||+|+.++|.+++++|++|+.++||||+++++|+|+|++++||++++|++...|+||+||+||.
T Consensus       265 ~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~  344 (391)
T 1xti_A          265 ALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRF  344 (391)
T ss_dssp             HHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESCCCSSCBCCTTEEEEEESSCCSSHHHHHHHHCBCSSS
T ss_pred             HHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHhcccccCC
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCceeEEEEeccC-cHHHHHHHHHHhcCccccccCCcc
Q psy6712         164 GRKGVAISFVKSD-DIRILRDIEQYYSTQIDEMPMNGK  200 (210)
Q Consensus       164 g~~g~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~  200 (210)
                      |+.|.+++++.+. +...++.+++.++..++++|....
T Consensus       345 g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  382 (391)
T 1xti_A          345 GTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEID  382 (391)
T ss_dssp             CCCCEEEEEECSHHHHHHHHHHHHHTTCCCEECCSCCC
T ss_pred             CCceEEEEEEcccchHHHHHHHHHHhcCChhhCCcccc
Confidence            9999999999876 557789999999999999987643

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=100.00  E-value=6.2e-34  Score=244.15  Aligned_cols=193  Identities=29%  Similarity=0.575  Sum_probs=170.4

Q ss_pred             ceEEEEEcCcchHHHHHHhc-CCCcEEEEChHHHHHHHHhc-CccCCCccEEEechhhHHhccchHHHHHHHHhhCCC--
Q psy6712           3 VQCHACIGGTNLSEDLRKLD-YGQHVVSGTPGRVFDMIRRR-VLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPP--   78 (210)
Q Consensus         3 i~~~~~~gg~~~~~~~~~l~-~~~~Ili~Tp~~l~~~l~~~-~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~--   78 (210)
                      +.+..++||.+...++..+. .+++|+|+||+++.+++.+. ...+++++++|+||||++.++++.+.+..++..++.  
T Consensus       179 ~~~~~~~g~~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~l~~~~f~~~~~~i~~~l~~~~  258 (563)
T 3i5x_A          179 YACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKN  258 (563)
T ss_dssp             SCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTCCEEEEETHHHHTSTTTHHHHHHHHHHHHHHC
T ss_pred             eeEEEEECCcCHHHHHHHHhcCCCCEEEECcHHHHHHHHhccccccccceEEEEeCHHHHhccchHHHHHHHHHhhhhcc
Confidence            56888999999988888874 48999999999999988775 446789999999999999999988888777654321  


Q ss_pred             -----chh------------------------------------------------------------------------
Q psy6712          79 -----ATQ------------------------------------------------------------------------   81 (210)
Q Consensus        79 -----~~~------------------------------------------------------------------------   81 (210)
                           ..+                                                                        
T Consensus       259 ~~~~~~~~~l~~SAT~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  338 (563)
T 3i5x_A          259 SKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDS  338 (563)
T ss_dssp             SSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEESSTTHHHHHHHHHHHHHHHHTTT
T ss_pred             ccCccCceEEEEEccCCHHHHHHHHHhcCCCceEEEeccCCCCccccccCceEEEECchhHhhHHHHHHHHHHHHhhcCC
Confidence                 111                                                                        


Q ss_pred             -------------HHHHHHHHHhc---CceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEec
Q psy6712          82 -------------VDWLTEKMREA---NFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYD  145 (210)
Q Consensus        82 -------------~~~l~~~l~~~---~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~  145 (210)
                                   ++.+++.|.+.   ++.+..+||+|++.+|..+++.|++|+.+|||||+++++|+|+|++++||++|
T Consensus       339 ~~~~iVF~~s~~~~~~l~~~L~~~~~~~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLvaT~~~~~GiDip~v~~VI~~~  418 (563)
T 3i5x_A          339 NYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIG  418 (563)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGGGTSSCCCTTCCEEEEES
T ss_pred             CCcEEEEcCcHHHHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcCCCCEEEEcchhhcCCCcccCCEEEEEC
Confidence                         67788888775   89999999999999999999999999999999999999999999999999999


Q ss_pred             CCCChhHHHHhhhhhcCCCCceeEEEEeccCcHHHHHHHHHHhcCccccc
Q psy6712         146 LPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEM  195 (210)
Q Consensus       146 ~p~s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~  195 (210)
                      +|.++..|+||+||+||.|+.|.+++++.+.+...++.+++.....+...
T Consensus       419 ~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~~~~~~l~~~~~~~~~~~  468 (563)
T 3i5x_A          419 VPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQ  468 (563)
T ss_dssp             CCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGHHHHHHHHHHHCCCCCEE
T ss_pred             CCCchhhhhhhcCccccCCCCceEEEEEchhHHHHHHHHHHHhCCCcccc
Confidence            99999999999999999999999999999999999999999887766544

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=100.00  E-value=1e-33  Score=243.61  Aligned_cols=193  Identities=29%  Similarity=0.572  Sum_probs=171.4

Q ss_pred             ceEEEEEcCcchHHHHHHhcC-CCcEEEEChHHHHHHHHhc-CccCCCccEEEechhhHHhccchHHHHHHHHhhCCC--
Q psy6712           3 VQCHACIGGTNLSEDLRKLDY-GQHVVSGTPGRVFDMIRRR-VLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPP--   78 (210)
Q Consensus         3 i~~~~~~gg~~~~~~~~~l~~-~~~Ili~Tp~~l~~~l~~~-~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~--   78 (210)
                      +.+..++||.....+...+.. +++|+|+||+++.+++.+. ...++.++++|+||||++.+++|.+.+..++..++.  
T Consensus       128 ~~~~~~~gg~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~l~~~gf~~~~~~i~~~l~~~~  207 (579)
T 3sqw_A          128 YACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKN  207 (579)
T ss_dssp             SCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTCCEEEEETHHHHTSTTTHHHHHHHHHHHHHHC
T ss_pred             eEEEEEECCccHHHHHHHHhcCCCCEEEECHHHHHHHHHhccccccccCCEEEEEChHHhhcCCCHHHHHHHHHHhhhhh
Confidence            568889999999988888854 8999999999999988775 456789999999999999999998888777655421  


Q ss_pred             -----chh------------------------------------------------------------------------
Q psy6712          79 -----ATQ------------------------------------------------------------------------   81 (210)
Q Consensus        79 -----~~~------------------------------------------------------------------------   81 (210)
                           ..+                                                                        
T Consensus       208 ~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  287 (579)
T 3sqw_A          208 SKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDS  287 (579)
T ss_dssp             SSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEESSTTHHHHHHHHHHHHHHHHTTT
T ss_pred             cccccCceEEEEeccCChHHHHHHHHHcCCCceEEEeecCccccccccccceEEEEecchhhhHHHHHHHHHHHHhhcCC
Confidence                 111                                                                        


Q ss_pred             -------------HHHHHHHHHhc---CceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEec
Q psy6712          82 -------------VDWLTEKMREA---NFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYD  145 (210)
Q Consensus        82 -------------~~~l~~~l~~~---~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~  145 (210)
                                   ++.+++.|.+.   ++.+..+||+|++.+|.+++++|++|+.+|||||+++++|+|+|++++||+++
T Consensus       288 ~~~~iVF~~t~~~~~~l~~~L~~~~~~~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVaT~~~~~GiDip~v~~VI~~~  367 (579)
T 3sqw_A          288 NYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIG  367 (579)
T ss_dssp             CCEEEEECSSHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGGGTSSCCCTTCCEEEEES
T ss_pred             CCcEEEECCcHHHHHHHHHHHHHhhcCCCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEEcchhhcCCCcccCCEEEEcC
Confidence                         67788888776   89999999999999999999999999999999999999999999999999999


Q ss_pred             CCCChhHHHHhhhhhcCCCCceeEEEEeccCcHHHHHHHHHHhcCccccc
Q psy6712         146 LPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEM  195 (210)
Q Consensus       146 ~p~s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~  195 (210)
                      +|.++..|+||+||+||.|+.|.+++++.+.+...++.+++.....+...
T Consensus       368 ~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~~~~~~l~~~~~~~~~~~  417 (579)
T 3sqw_A          368 VPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQ  417 (579)
T ss_dssp             CCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGHHHHHHHHHHHCCCCCEE
T ss_pred             CCCCHHHhhhhccccccCCCCceEEEEEcccHHHHHHHHHHHhCCCcccc
Confidence            99999999999999999999999999999999999999999887766543

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=100.00  E-value=3.3e-35  Score=241.12  Aligned_cols=201  Identities=63%  Similarity=1.040  Sum_probs=66.0

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchh
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ   81 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~   81 (210)
                      ++++..++||.+..++...+. +++|+|+||+++.+.+.++...+.+++++|+||||.+.++++...+..++..++...+
T Consensus       117 ~~~~~~~~g~~~~~~~~~~~~-~~~i~v~T~~~l~~~~~~~~~~~~~~~~vIiDEah~~~~~~~~~~~~~~~~~~~~~~~  195 (394)
T 1fuu_A          117 DIKVHACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQ  195 (394)
T ss_dssp             CCCEEEECSSCCHHHHHHHHH-HCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHTTCHHHHHHHHHHSCTTCE
T ss_pred             CeeEEEEeCCCchHHHHhhcC-CCCEEEECHHHHHHHHHhCCcchhhCcEEEEEChHHhhCCCcHHHHHHHHHhCCCCce
Confidence            678999999999887776665 6899999999999999988888899999999999999988888777777665544333


Q ss_pred             ----------------------------------------------------------------------------HHHH
Q psy6712          82 ----------------------------------------------------------------------------VDWL   85 (210)
Q Consensus        82 ----------------------------------------------------------------------------~~~l   85 (210)
                                                                                                  ++.+
T Consensus       196 ~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lVf~~~~~~~~~l  275 (394)
T 1fuu_A          196 VVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEEL  275 (394)
T ss_dssp             EEEECSSCCHHHHHHHHHHCCSCEEEEECC--------------------------------------------------
T ss_pred             EEEEEEecCHHHHHHHHHhcCCCeEEEecCccccCCCceEEEEEcCchhhHHHHHHHHHhcCCCCcEEEEECCHHHHHHH
Confidence                                                                                        6777


Q ss_pred             HHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCC
Q psy6712          86 TEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGR  165 (210)
Q Consensus        86 ~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~  165 (210)
                      ++.|++.++.+..+||+|+..+|.++++.|++|+.++||||+++++|+|+|++++||++++|++...|+||+||+||.|+
T Consensus       276 ~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gldi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~  355 (394)
T 1fuu_A          276 TTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGR  355 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHcCCeEEEeeCCCCHHHHHHHHHHHHCCCCcEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHHcCcccCCCC
Confidence            88888888999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceeEEEEeccCcHHHHHHHHHHhcCccccccCCccccC
Q psy6712         166 KGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRSL  203 (210)
Q Consensus       166 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  203 (210)
                      .|.+++++.+.+...++.++++++..++.+|....+++
T Consensus       356 ~g~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~  393 (394)
T 1fuu_A          356 KGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIATLL  393 (394)
T ss_dssp             --------------------------------------
T ss_pred             CceEEEEEchhHHHHHHHHHHHhCCcccccCcchhhhc
Confidence            99999999999999999999999999999998877655

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=100.00  E-value=2.1e-32  Score=225.66  Aligned_cols=199  Identities=36%  Similarity=0.718  Sum_probs=164.5

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHh-cCccCCCccEEEechhhHHhc-cchHHHHHHHHhhCCCc
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRR-RVLRTRNIKMLVLDEADEMLN-KGFKEQIYDVYRYLPPA   79 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~-~~~~~~~~~~lviDE~~~l~~-~~~~~~~~~i~~~~~~~   79 (210)
                      ++++....||.....   ....+++|+|+||+++.+++.+ +.+.+++++++|+||||.+.+ .++...+..+...++..
T Consensus       124 ~~~~~~~~~~~~~~~---~~~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~~~~~~~~~~  200 (412)
T 3fht_A          124 ELKLAYAVRGNKLER---GQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRN  200 (412)
T ss_dssp             TCCEEEECTTCCCCT---TCCCCCSEEEECHHHHHHHHTTSCSSCGGGCCEEEEETHHHHHSTTTTHHHHHHHHHTSCTT
T ss_pred             cceEEEeecCcchhh---hhcCCCCEEEECchHHHHHHHhcCCcChhhCcEEEEeCHHHHhhcCCcHHHHHHHHhhCCCC
Confidence            355666677665432   1234679999999999998866 667789999999999999986 56766666666655544


Q ss_pred             hh----------------------------------------------------------------------------HH
Q psy6712          80 TQ----------------------------------------------------------------------------VD   83 (210)
Q Consensus        80 ~~----------------------------------------------------------------------------~~   83 (210)
                      .+                                                                            ++
T Consensus       201 ~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvf~~~~~~~~  280 (412)
T 3fht_A          201 CQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTAS  280 (412)
T ss_dssp             CEEEEEESCCCHHHHHHHHHHSSSCEEECCCGGGSSCTTEEEEEEECSSHHHHHHHHHHHHHHHSSSEEEEECSSHHHHH
T ss_pred             ceEEEEEeecCHHHHHHHHHhcCCCeEEeeccccccccCceEEEEEcCChHHHHHHHHHHHhhcCCCCEEEEeCCHHHHH
Confidence            33                                                                            88


Q ss_pred             HHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCC------CChhHHHHhh
Q psy6712          84 WLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLP------NNRELYIHRI  157 (210)
Q Consensus        84 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p------~s~~~~~q~~  157 (210)
                      .+++.|.+.++.+..+||+|+..+|.++++.|++|+.++||||+++++|+|+|++++||++|+|      .+...|+||+
T Consensus       281 ~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~  360 (412)
T 3fht_A          281 WLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRI  360 (412)
T ss_dssp             HHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECGGGTSSCCCTTEEEEEESSCCBCSSSSBCHHHHHHHH
T ss_pred             HHHHHHHhCCCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcCccccCCCccCCCEEEEECCCCCCCCCcchheeeccc
Confidence            8999999999999999999999999999999999999999999999999999999999999999      4678999999


Q ss_pred             hhhcCCCCceeEEEEeccCc-HHHHHHHHHHhcCccccccCCccccC
Q psy6712         158 GRSGRFGRKGVAISFVKSDD-IRILRDIEQYYSTQIDEMPMNGKRSL  203 (210)
Q Consensus       158 GR~gR~g~~g~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~  203 (210)
                      ||+||.|+.|.+++++.+.+ ...++.+++.++..+.+++.+..+.+
T Consensus       361 GR~gR~g~~g~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~  407 (412)
T 3fht_A          361 GRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERLDTDDLDEI  407 (412)
T ss_dssp             TTSSCTTCCEEEEEEECSHHHHHHHHHHHHHHTCCCEEC--------
T ss_pred             CcccCCCCCceEEEEEcChhhHHHHHHHHHHHCCccccCCCccHHHH
Confidence            99999999999999998764 78899999999999999887654433

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}

Probab=100.00  E-value=2.8e-32  Score=219.15  Aligned_cols=183  Identities=32%  Similarity=0.593  Sum_probs=156.9

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchh
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ   81 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~   81 (210)
                      ++++..++||.+...+...+. +++|+|+||+++.+.+..+.+.+.+++++|+||||.+.++++...+..++...+...+
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~-~~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~~~~~~~~~~~  162 (337)
T 2z0m_A           84 DTKVAEVYGGMPYKAQINRVR-NADIVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKI  162 (337)
T ss_dssp             CCCEEEECTTSCHHHHHHHHT-TCSEEEECHHHHHHHHHTTSCCGGGCSEEEEESHHHHHHTTCHHHHHHHHHHCTTCSE
T ss_pred             CCcEEEEECCcchHHHHhhcC-CCCEEEECHHHHHHHHHcCCcchhhCcEEEEEChHHhhccccHHHHHHHHhhCCcccE
Confidence            578899999999888777765 4899999999999999888888899999999999999998888888777765544333


Q ss_pred             ----------------------------------------------------------------------HHHHHHHHHh
Q psy6712          82 ----------------------------------------------------------------------VDWLTEKMRE   91 (210)
Q Consensus        82 ----------------------------------------------------------------------~~~l~~~l~~   91 (210)
                                                                                            ++.+++.|. 
T Consensus       163 ~~~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lvf~~~~~~~~~l~~~l~-  241 (337)
T 2z0m_A          163 TGLFSATIPEEIRKVVKDFITNYEEIEACIGLANVEHKFVHVKDDWRSKVQALRENKDKGVIVFVRTRNRVAKLVRLFD-  241 (337)
T ss_dssp             EEEEESCCCHHHHHHHHHHSCSCEEEECSGGGGGEEEEEEECSSSSHHHHHHHHTCCCSSEEEECSCHHHHHHHHTTCT-
T ss_pred             EEEEeCcCCHHHHHHHHHhcCCceeeecccccCCceEEEEEeChHHHHHHHHHHhCCCCcEEEEEcCHHHHHHHHHHhh-
Confidence                                                                                  344444443 


Q ss_pred             cCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCCceeEEE
Q psy6712          92 ANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAIS  171 (210)
Q Consensus        92 ~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~~g~~~~  171 (210)
                         ++..+||+|+..+|.+++++|++|+.++||||+++++|+|+|++++||++++|++...|+||+||+||.|+.|.+++
T Consensus       242 ---~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~gR~g~~g~~~~  318 (337)
T 2z0m_A          242 ---NAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAIT  318 (337)
T ss_dssp             ---TEEEECTTSCHHHHHHHHHHHHTTSCSEEEECHHHHTTCCCCCBSEEEESSCCSSHHHHHHHHTTBCGGGCCEEEEE
T ss_pred             ---hhhhhcCCCCHHHHHHHHHHHHcCCCcEEEEcCccccCCCccCCCEEEEecCCCCHHHhhHhcCccccCCCCceEEE
Confidence               68889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeccCcHHHHHHHHHHhcC
Q psy6712         172 FVKSDDIRILRDIEQYYST  190 (210)
Q Consensus       172 ~~~~~~~~~~~~~~~~~~~  190 (210)
                      ++. .+...++.+++.++.
T Consensus       319 ~~~-~~~~~~~~i~~~~~~  336 (337)
T 2z0m_A          319 FIL-NEYWLEKEVKKVSQK  336 (337)
T ss_dssp             EES-SCHHHHHHHC-----
T ss_pred             EEe-CcHHHHHHHHHHhcc
Confidence            999 888888888877653

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=100.00  E-value=9.5e-32  Score=220.28  Aligned_cols=192  Identities=44%  Similarity=0.811  Sum_probs=163.9

Q ss_pred             ceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhc-cchHHHHHHHHhhCCCchh
Q psy6712           3 VQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLN-KGFKEQIYDVYRYLPPATQ   81 (210)
Q Consensus         3 i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~-~~~~~~~~~i~~~~~~~~~   81 (210)
                      +.+..++|+....    ....+++|+|+||+++.+.+.++...+++++++|+||||.+.+ .++...+..+...++...+
T Consensus       104 ~~~~~~~~~~~~~----~~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~~~~~~~~~~~~~~~~~  179 (395)
T 3pey_A          104 ITSQLIVPDSFEK----NKQINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQ  179 (395)
T ss_dssp             CCEEEESTTSSCT----TSCBCCSEEEECHHHHHHHHHTTCBCCTTCCEEEEETHHHHHHSTTHHHHHHHHHHTSCTTCE
T ss_pred             eeEEEEecCchhh----hccCCCCEEEEcHHHHHHHHHcCCcccccCCEEEEEChhhhcCccccHHHHHHHHHhCCCCcE
Confidence            4455555554332    1123689999999999999998888899999999999999987 5777777777666554433


Q ss_pred             ----------------------------------------------------------------------------HHHH
Q psy6712          82 ----------------------------------------------------------------------------VDWL   85 (210)
Q Consensus        82 ----------------------------------------------------------------------------~~~l   85 (210)
                                                                                                  ++.+
T Consensus       180 ~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvf~~~~~~~~~l  259 (395)
T 3pey_A          180 LVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELYGLMTIGSSIIFVATKKTANVL  259 (395)
T ss_dssp             EEEEESCCCHHHHHHHHHHSCSCEEECCCGGGCSCTTEEEEEEECSSHHHHHHHHHHHHTTTTSSEEEEECSCHHHHHHH
T ss_pred             EEEEEecCCHHHHHHHHHhCCCCeEEEccccccccccccEEEEEcCchHHHHHHHHHHHHhccCCCEEEEeCCHHHHHHH
Confidence                                                                                        8889


Q ss_pred             HHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCC------ChhHHHHhhhh
Q psy6712          86 TEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPN------NRELYIHRIGR  159 (210)
Q Consensus        86 ~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~------s~~~~~q~~GR  159 (210)
                      ++.|++.++.+..+||+|+..+|.++++.|++|+.++||||+++++|+|+|++++||++|+|+      +...|+||+||
T Consensus       260 ~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR  339 (395)
T 3pey_A          260 YGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGR  339 (395)
T ss_dssp             HHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECGGGSSSCCCTTEEEEEESSCCBCTTSSBCHHHHHHHHTT
T ss_pred             HHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECChhhcCCCcccCCEEEEcCCCCCCcCCCCHHHhhHhccc
Confidence            999999999999999999999999999999999999999999999999999999999999999      99999999999


Q ss_pred             hcCCCCceeEEEEeccC-cHHHHHHHHHHhc-CccccccCC
Q psy6712         160 SGRFGRKGVAISFVKSD-DIRILRDIEQYYS-TQIDEMPMN  198 (210)
Q Consensus       160 ~gR~g~~g~~~~~~~~~-~~~~~~~~~~~~~-~~~~~~~~~  198 (210)
                      +||.|+.|.+++++.+. +...++.+++.++ ..+..++.+
T Consensus       340 ~gR~g~~g~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~  380 (395)
T 3pey_A          340 TGRFGRKGVAISFVHDKNSFNILSAIQKYFGDIEMTRVPTD  380 (395)
T ss_dssp             SSCTTCCEEEEEEECSHHHHHHHHHHHHHTTSCCCEECCSS
T ss_pred             cccCCCCceEEEEEechHHHHHHHHHHHHhCCceeecCChH
Confidence            99999999999999864 5567888888887 777766654

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.97  E-value=7.1e-31  Score=217.35  Aligned_cols=188  Identities=20%  Similarity=0.317  Sum_probs=155.6

Q ss_pred             CCceEEEEEcCcch---HHHHHHhcCC-CcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhc-----------cch
Q psy6712           1 MNVQCHACIGGTNL---SEDLRKLDYG-QHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLN-----------KGF   65 (210)
Q Consensus         1 ~~i~~~~~~gg~~~---~~~~~~l~~~-~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~-----------~~~   65 (210)
                      .|+++..++||.+.   ..++..+..+ ++|+|+||+++.+++..  +.+++++++|+||||++.+           .++
T Consensus        90 ~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~--~~~~~~~~iViDEaH~~~~~~~~~d~~l~~~~~  167 (414)
T 3oiy_A           90 EKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK--LSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGI  167 (414)
T ss_dssp             SSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHH--HTTCCCSEEEESCHHHHHHCHHHHHHHHHHTTC
T ss_pred             CCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHH--hccccccEEEEeChHhhhhccchhhhHHhhcCC
Confidence            37899999999998   6677777766 99999999999887765  6678999999999987654           455


Q ss_pred             HHH-HHHHHhhCC-----------Cchh----------------------------------------------------
Q psy6712          66 KEQ-IYDVYRYLP-----------PATQ----------------------------------------------------   81 (210)
Q Consensus        66 ~~~-~~~i~~~~~-----------~~~~----------------------------------------------------   81 (210)
                      .+. +..++..++           ...+                                                    
T Consensus       168 ~~~~~~~i~~~~~~~~~~~~l~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~l~~~  247 (414)
T 3oiy_A          168 PEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLNFTVGRLVSVARNITHVRISSRSKEKLVEL  247 (414)
T ss_dssp             CHHHHHHHHHHHHHTCCCCCCTTCCCCEEEESSCCSSCCSSTTHHHHHHHSCCSSCCCCCCCSEEEEEESSCCHHHHHHH
T ss_pred             cHHHHHHHHHhcccchhhhhcccCCCceEEEEecCCCcchhHHHHHHHhhccCcCccccccccchheeeccCHHHHHHHH
Confidence            555 566665432           2112                                                    


Q ss_pred             -----------------HHHHHHHHHhcCceEE-EecCCCCHhHHHHHHHHHhcCCCcEEEE----ecCccccCCCCC-C
Q psy6712          82 -----------------VDWLTEKMREANFTVS-SMHGDMPQKERDGIMKEFRSGTSRVLIT----TDVWARGIDVQQ-V  138 (210)
Q Consensus        82 -----------------~~~l~~~l~~~~~~~~-~~~~~~~~~~r~~~~~~f~~g~~~ilv~----T~~~~~g~d~~~-~  138 (210)
                                       ++.+++.|.+.++.+. .+||.    +| + ++.|++|+.++|||    |+++++|+|+|+ +
T Consensus       248 l~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~h~~----~r-~-~~~f~~g~~~vLvat~s~T~~~~~GiDip~~v  321 (414)
T 3oiy_A          248 LEIFRDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF----EK-N-FEDFKVGKINILIGVQAYYGKLTRGVDLPERI  321 (414)
T ss_dssp             HHHHCSSEEEEESSHHHHHHHHHHHHHTTCCEEESSSCH----HH-H-HHHHHTTSCSEEEEECCTTCCCCCCCCCTTTC
T ss_pred             HHHcCCCEEEEECCHHHHHHHHHHHHHcCCceehhhcCc----ch-H-HHHHhCCCCeEEEEecCcCchhhccCcccccc
Confidence                             7889999999999998 99985    33 3 99999999999999    999999999999 9


Q ss_pred             cEEEEecCC--CChhHHHHhhhhhcCCC----CceeEEEEeccCcHHHHHHHHHHhc--CccccccCC
Q psy6712         139 SLVINYDLP--NNRELYIHRIGRSGRFG----RKGVAISFVKSDDIRILRDIEQYYS--TQIDEMPMN  198 (210)
Q Consensus       139 ~~vi~~~~p--~s~~~~~q~~GR~gR~g----~~g~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~  198 (210)
                      ++||+||+|  .+...|+||+||+||.|    ..|.+++++  .+...++.+++.++  .+++..+.+
T Consensus       322 ~~VI~~~~p~~~~~~~y~qr~GR~gR~g~~~~~~g~~i~~~--~~~~~~~~l~~~~~~~~~~~~~~~~  387 (414)
T 3oiy_A          322 KYVIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSVIFE--EDEEIFESLKTRLLLIAEEEIIEEA  387 (414)
T ss_dssp             CEEEEESCCTTTCHHHHHHHHGGGCCEETTEECCEEEEEEC--CCHHHHHHHHHHHHHHHCCCEEEGG
T ss_pred             CEEEEECCCCCCCHHHHHHHhCccccCCCCCCcceEEEEEE--ccHHHHHHHHHHhcccccccccccc
Confidence            999999999  99999999999999997    479999999  67788888888888  555554443

>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=99.97  E-value=1.9e-32  Score=230.83  Aligned_cols=194  Identities=37%  Similarity=0.731  Sum_probs=54.8

Q ss_pred             ceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHh-cCccCCCccEEEechhhHHhc-cchHHHHHHHHhhCCCch
Q psy6712           3 VQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRR-RVLRTRNIKMLVLDEADEMLN-KGFKEQIYDVYRYLPPAT   80 (210)
Q Consensus         3 i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~-~~~~~~~~~~lviDE~~~l~~-~~~~~~~~~i~~~~~~~~   80 (210)
                      +.+....||.....   ....+++|+|+||+++.+++.+ +.+.+++++++|+||+|.+.+ .++......+...++...
T Consensus       192 ~~~~~~~~~~~~~~---~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~~i~~~~~~~~  268 (479)
T 3fmp_B          192 LKLAYAVRGNKLER---GQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNC  268 (479)
T ss_dssp             CCEEEESTTCCCCT---TCCCCCSEEEECHHHHHHHHTTSCCCCGGGCCEEEECCHHHHHTSTTHHHHHHHHHTTSCTTS
T ss_pred             ceEEEEeCCccccc---cccCCCCEEEECchHHHHHHHhcCCcCcccCCEEEEECHHHHhhcCCcHHHHHHHHhhCCccc
Confidence            45566666655431   1234679999999999999866 567789999999999999987 566666666666555443


Q ss_pred             h----------------------------------------------------------------------------HHH
Q psy6712          81 Q----------------------------------------------------------------------------VDW   84 (210)
Q Consensus        81 ~----------------------------------------------------------------------------~~~   84 (210)
                      +                                                                            ++.
T Consensus       269 ~~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvF~~s~~~~~~  348 (479)
T 3fmp_B          269 QMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASW  348 (479)
T ss_dssp             EEEEEESCCCHHHHHHHHHHSSSEEEEEEC--------------------------------------------------
T ss_pred             eEEEEeCCCCHHHHHHHHHHcCCCeEEeccccccCcCCceEEEEEeCCHHHHHHHHHHHHhhccCCceEEEeCcHHHHHH
Confidence            3                                                                            777


Q ss_pred             HHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCC------ChhHHHHhhh
Q psy6712          85 LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPN------NRELYIHRIG  158 (210)
Q Consensus        85 l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~------s~~~~~q~~G  158 (210)
                      +++.|...+..+..+||+|+..+|..+++.|++|+.+|||||+++++|+|+|++++||+||+|.      +...|+||+|
T Consensus       349 l~~~L~~~~~~v~~lh~~~~~~~R~~~~~~f~~g~~~iLv~T~~~~~GlDip~v~~VI~~d~p~~~~~~~s~~~~~Qr~G  428 (479)
T 3fmp_B          349 LAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIG  428 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHhCCccEEEecCCCCHHHHHHHHHHHHcCCCcEEEEccccccCCccccCCEEEEecCCCCCccCCCHHHHHHHhc
Confidence            8888888899999999999999999999999999999999999999999999999999999994      6789999999


Q ss_pred             hhcCCCCceeEEEEeccCc-HHHHHHHHHHhcCccccccCCc
Q psy6712         159 RSGRFGRKGVAISFVKSDD-IRILRDIEQYYSTQIDEMPMNG  199 (210)
Q Consensus       159 R~gR~g~~g~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~  199 (210)
                      |+||.|+.|.+++|+.+.+ ...++.+++.++..+.+++.+.
T Consensus       429 RagR~g~~G~~i~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~  470 (479)
T 3fmp_B          429 RTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERLDTDD  470 (479)
T ss_dssp             ------------------------------------------
T ss_pred             ccccCCCCceEEEEEcCcchHHHHHHHHHHhCCCceECCCcc
Confidence            9999999999999998764 7788899999998888877554

>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=99.97  E-value=1.5e-30  Score=221.25  Aligned_cols=183  Identities=20%  Similarity=0.309  Sum_probs=146.6

Q ss_pred             CCceEEEEEcCcchHHHH---HHh-cCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccc--hHHHHHH---
Q psy6712           1 MNVQCHACIGGTNLSEDL---RKL-DYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKG--FKEQIYD---   71 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~---~~l-~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~--~~~~~~~---   71 (210)
                      +|+++..++|+.+..++.   ..+ ...++|+++||+++........+...+++++|+||||++.+++  +.+....   
T Consensus        88 ~gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~~~~~~l~~~~~~~vViDEaH~i~~~g~~fr~~~~~l~~  167 (523)
T 1oyw_A           88 NGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQ  167 (523)
T ss_dssp             TTCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGGGGCTTSSCCCHHHHGGGG
T ss_pred             cCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhChHHHHHHhhCCCCEEEEeCccccCcCCCccHHHHHHHHH
Confidence            478889999998766544   233 3468999999999864322233445789999999999998765  3222211   


Q ss_pred             HHhhC-----------------------------------------------------------------------CCch
Q psy6712          72 VYRYL-----------------------------------------------------------------------PPAT   80 (210)
Q Consensus        72 i~~~~-----------------------------------------------------------------------~~~~   80 (210)
                      +....                                                                       +...
T Consensus       168 l~~~~~~~~~i~lSAT~~~~~~~~i~~~l~~~~~~~~~~~~~r~~l~~~v~~~~~~~~~l~~~l~~~~~~~~IVf~~sr~  247 (523)
T 1oyw_A          168 LRQRFPTLPFMALTATADDTTRQDIVRLLGLNDPLIQISSFDRPNIRYMLMEKFKPLDQLMRYVQEQRGKSGIIYCNSRA  247 (523)
T ss_dssp             HHHHCTTSCEEEEESCCCHHHHHHHHHHHTCCSCEEEECCCCCTTEEEEEEECSSHHHHHHHHHHHTTTCCEEEECSSHH
T ss_pred             HHHhCCCCCEEEEeCCCCHHHHHHHHHHhCCCCCeEEeCCCCCCceEEEEEeCCCHHHHHHHHHHhcCCCcEEEEeCCHH
Confidence            11111                                                                       1111


Q ss_pred             hHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhh
Q psy6712          81 QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRS  160 (210)
Q Consensus        81 ~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~  160 (210)
                      .++.+++.|.+.++.+..+||+|+.++|.+++++|++|+.+|||||+++++|+|+|++++||++++|.|...|.||+||+
T Consensus       248 ~~e~l~~~L~~~g~~~~~~h~~l~~~~R~~~~~~f~~g~~~vlVaT~a~~~GiD~p~v~~VI~~~~p~s~~~y~Qr~GRa  327 (523)
T 1oyw_A          248 KVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRA  327 (523)
T ss_dssp             HHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSCTTTCCTTCCEEEESSCCSSHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhCCCCccCccEEEEECCCCCHHHHHHHhccc
Confidence            18899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCceeEEEEeccCcHHHHHH
Q psy6712         161 GRFGRKGVAISFVKSDDIRILRD  183 (210)
Q Consensus       161 gR~g~~g~~~~~~~~~~~~~~~~  183 (210)
                      ||.|..|.+++++++.+...++.
T Consensus       328 GR~g~~~~~~l~~~~~d~~~~~~  350 (523)
T 1oyw_A          328 GRDGLPAEAMLFYDPADMAWLRR  350 (523)
T ss_dssp             CTTSSCEEEEEEECHHHHHHHHH
T ss_pred             cCCCCCceEEEEeCHHHHHHHHH
Confidence            99999999999998876655443

>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=99.97  E-value=2.2e-30  Score=222.74  Aligned_cols=182  Identities=16%  Similarity=0.296  Sum_probs=146.2

Q ss_pred             CceEEEEEcCcchHHHHHH---h---cCCCcEEEEChHHHHH---HHH--hcCccCCCccEEEechhhHHhccc--hHHH
Q psy6712           2 NVQCHACIGGTNLSEDLRK---L---DYGQHVVSGTPGRVFD---MIR--RRVLRTRNIKMLVLDEADEMLNKG--FKEQ   68 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~---l---~~~~~Ili~Tp~~l~~---~l~--~~~~~~~~~~~lviDE~~~l~~~~--~~~~   68 (210)
                      |+++..++|+.+..++...   +   ..+++|+++||+++..   ++.  .+...+.++.++|+||||++.+++  |.+.
T Consensus       108 gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L~~~~~~~~~l~~~~~~~~i~~iViDEAH~is~~g~dfr~~  187 (591)
T 2v1x_A          108 GISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEKAYEARRFTRIAVDEVHCCSQWGHDFRPD  187 (591)
T ss_dssp             TCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHHHHHSCHHHHHHHHHHHHTTCEEEEEEETGGGGSTTCTTCCGG
T ss_pred             CCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChhHhhccHHHHHHHHhhhhccCCcEEEEECcccccccccccHHH
Confidence            6889999999887665432   2   3478999999998742   221  134457889999999999998765  3221


Q ss_pred             HH------------------------------------------------------------------HHHh--------
Q psy6712          69 IY------------------------------------------------------------------DVYR--------   74 (210)
Q Consensus        69 ~~------------------------------------------------------------------~i~~--------   74 (210)
                      +.                                                                  .++.        
T Consensus       188 ~~~l~~l~~~~~~~~ii~lSAT~~~~v~~~i~~~l~~~~~~~~~~~~~r~nl~~~v~~~~~~~~~~~~~l~~~l~~~~~~  267 (591)
T 2v1x_A          188 YKALGILKRQFPNASLIGLTATATNHVLTDAQKILCIEKCFTFTASFNRPNLYYEVRQKPSNTEDFIEDIVKLINGRYKG  267 (591)
T ss_dssp             GGGGGHHHHHCTTSEEEEEESSCCHHHHHHHHHHTTCCSCEEEECCCCCTTEEEEEEECCSSHHHHHHHHHHHHTTTTTT
T ss_pred             HHHHHHHHHhCCCCcEEEEecCCCHHHHHHHHHHhCCCCcEEEecCCCCcccEEEEEeCCCcHHHHHHHHHHHHHHhccC
Confidence            11                                                                  1111        


Q ss_pred             -----hCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCC
Q psy6712          75 -----YLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNN  149 (210)
Q Consensus        75 -----~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s  149 (210)
                           |++....++.+++.|.+.++.+..+||+|+.++|.+++++|++|+.+|||||+++++|+|+|++++||+|++|.|
T Consensus       268 ~~~IVf~~sr~~~e~la~~L~~~g~~~~~~h~~l~~~~R~~~~~~F~~g~~~VlVAT~a~~~GID~p~V~~VI~~~~p~s  347 (591)
T 2v1x_A          268 QSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKS  347 (591)
T ss_dssp             CEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEECTTSCTTCCCSCEEEEEESSCCSS
T ss_pred             CCeEEEeCcHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhcCCCcccccEEEEeCCCCC
Confidence                 111112288899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHhhhhhcCCCCceeEEEEeccCcHHHHHH
Q psy6712         150 RELYIHRIGRSGRFGRKGVAISFVKSDDIRILRD  183 (210)
Q Consensus       150 ~~~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~  183 (210)
                      ...|+||+||+||.|..|.|++++++.|...++.
T Consensus       348 ~~~y~Qr~GRaGR~G~~g~~i~l~~~~D~~~~~~  381 (591)
T 2v1x_A          348 MENYYQESGRAGRDDMKADCILYYGFGDIFRISS  381 (591)
T ss_dssp             HHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHhccCCcCCCCceEEEEEChHHHHHHHH
Confidence            9999999999999999999999998876655443

>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=99.95  E-value=4.5e-29  Score=213.07  Aligned_cols=84  Identities=26%  Similarity=0.413  Sum_probs=35.7

Q ss_pred             CceEEEecCCCCHhHHHHHHHHHhc-CCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCCceeEEE
Q psy6712          93 NFTVSSMHGDMPQKERDGIMKEFRS-GTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAIS  171 (210)
Q Consensus        93 ~~~~~~~~~~~~~~~r~~~~~~f~~-g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~~g~~~~  171 (210)
                      |.....+||+|+.++|.+++++|++ |+++|||||+++++|+|+|++++||+||+|+|+..|+||+|| ||. +.|.++.
T Consensus       426 g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-gR~-~~g~~~~  503 (556)
T 4a2p_A          426 GRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCIL  503 (556)
T ss_dssp             ----------------------------CCEEEEEC-----------CEEEEETCCSCHHHHHHC----------CCEEE
T ss_pred             ccCCcccccccCHHHHHHHHHHhcccCceEEEEEcCchhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCceEEE
Confidence            3444556778999999999999999 999999999999999999999999999999999999999999 998 8899999


Q ss_pred             EeccCcH
Q psy6712         172 FVKSDDI  178 (210)
Q Consensus       172 ~~~~~~~  178 (210)
                      ++...+.
T Consensus       504 l~~~~~~  510 (556)
T 4a2p_A          504 VTSKTEV  510 (556)
T ss_dssp             EESCHHH
T ss_pred             EEeCcch
Confidence            9987644

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.95  E-value=1.2e-28  Score=216.07  Aligned_cols=113  Identities=26%  Similarity=0.367  Sum_probs=64.1

Q ss_pred             HHHHHHHHHhcC----ceEEEe--------cCCCCHhHHHHHHHHHhc-CCCcEEEEecCccccCCCCCCcEEEEecCCC
Q psy6712          82 VDWLTEKMREAN----FTVSSM--------HGDMPQKERDGIMKEFRS-GTSRVLITTDVWARGIDVQQVSLVINYDLPN  148 (210)
Q Consensus        82 ~~~l~~~l~~~~----~~~~~~--------~~~~~~~~r~~~~~~f~~-g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~  148 (210)
                      ++.+++.|.+.+    +++..+        |++|+.++|.+++++|++ |+.+|||||+++++|+|+|++++||+||+|+
T Consensus       411 ~~~l~~~L~~~~~~~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F~~~g~~~vLVaT~v~~~GiDip~v~~VI~~d~p~  490 (696)
T 2ykg_A          411 VDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVG  490 (696)
T ss_dssp             HHHHHHHHHHCTTCCSCCEEC-----------------------------CCSCSEEEESSCCC---CCCSEEEEESCC-
T ss_pred             HHHHHHHHHhCCCccccceeEEEccCCCccccCCCHHHHHHHHHHHHhcCCccEEEEechhhcCCcCccCCEEEEeCCCC
Confidence            778888888877    888888        559999999999999998 9999999999999999999999999999999


Q ss_pred             ChhHHHHhhhhhcCCCCceeEEEEeccCcHHHHHHH----HHHhcCcccccc
Q psy6712         149 NRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDI----EQYYSTQIDEMP  196 (210)
Q Consensus       149 s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~  196 (210)
                      ++.+|+||+|| ||. +.|.++.++...+......+    ++.+...+++++
T Consensus       491 s~~~~~Qr~GR-GR~-~~g~~~~l~~~~~~~~~~~~~~~~e~~~~~~~~~~~  540 (696)
T 2ykg_A          491 NVIKMIQTRGR-GRA-RGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQ  540 (696)
T ss_dssp             -CCCC-----------CCCEEEEEESCHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CHHHHHHhhcc-CcC-CCceEEEEecCCCHHHHHHHHHHHHHHHHHHHHHhh
Confidence            99999999999 998 78999999987766444444    445555444443

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.95  E-value=3.9e-29  Score=213.18  Aligned_cols=88  Identities=27%  Similarity=0.404  Sum_probs=58.3

Q ss_pred             eEEEecCCCCHhHHHHHHHHHhc-CCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCCceeEEEEe
Q psy6712          95 TVSSMHGDMPQKERDGIMKEFRS-GTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFV  173 (210)
Q Consensus        95 ~~~~~~~~~~~~~r~~~~~~f~~-g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~~g~~~~~~  173 (210)
                      ....+||+|+.++|.+++++|++ |+++|||||+++++|+|+|++++||+||+|+|+..|+||+|| ||. +.|.++.|+
T Consensus       427 ~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~~~~GlDlp~v~~VI~~d~p~s~~~~~Qr~GR-gR~-~~g~~~~l~  504 (555)
T 3tbk_A          427 GRTNRATGMTLPAQKCVLEAFRASGDNNILIATSVADEGIDIAECNLVILYEYVGNVIKMIQTRGR-GRA-RDSKCFLLT  504 (555)
T ss_dssp             -------------------------CCSEEEECCCTTCCEETTSCSEEEEESCCSSCCCEECSSCC-CTT-TSCEEEEEE
T ss_pred             CCcccccccCHHHHHHHHHHHhcCCCeeEEEEcchhhcCCccccCCEEEEeCCCCCHHHHHHhcCc-CcC-CCceEEEEE
Confidence            33445569999999999999999 999999999999999999999999999999999999999999 898 889999999


Q ss_pred             ccCcHHHHHHH
Q psy6712         174 KSDDIRILRDI  184 (210)
Q Consensus       174 ~~~~~~~~~~~  184 (210)
                      .+.+......+
T Consensus       505 ~~~~~~~~~~~  515 (555)
T 3tbk_A          505 SSADVIEKEKA  515 (555)
T ss_dssp             SCHHHHHHHHH
T ss_pred             cCCCHHHHHHH
Confidence            88765544444

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=99.95  E-value=3.7e-27  Score=171.87  Aligned_cols=132  Identities=60%  Similarity=0.962  Sum_probs=119.0

Q ss_pred             HHhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChh
Q psy6712          72 VYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRE  151 (210)
Q Consensus        72 i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~  151 (210)
                      ++.|++....++.+++.|.+.++.+..+||+|+..+|.++++.|++|+.++||||+++++|+|+|++++||+||+|+++.
T Consensus        33 ~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~G~d~~~~~~Vi~~~~p~~~~  112 (165)
T 1fuk_A           33 AVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKE  112 (165)
T ss_dssp             EEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGGGTTTCCCCSCSEEEESSCCSSGG
T ss_pred             EEEEECCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEEcChhhcCCCcccCCEEEEeCCCCCHH
Confidence            34456666779999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhhhhcCCCCceeEEEEeccCcHHHHHHHHHHhcCccccccCCccccC
Q psy6712         152 LYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRSL  203 (210)
Q Consensus       152 ~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  203 (210)
                      .|.||+||+||.|+.|.+++++.+.+...+..+++.++..++++|.....++
T Consensus       113 ~~~qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (165)
T 1fuk_A          113 NYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIATLL  164 (165)
T ss_dssp             GGGGSSCSCC-----CEEEEEEETTTHHHHHHHHHHSSCCCEECCSCCTTTT
T ss_pred             HHHHHhcccccCCCCceEEEEEcchHHHHHHHHHHHHccCccccCccHHhhc
Confidence            9999999999999999999999999999999999999999999998876654

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.95  E-value=4.7e-27  Score=213.64  Aligned_cols=179  Identities=20%  Similarity=0.319  Sum_probs=148.6

Q ss_pred             CCceEEEEEcCcch---HHHHHHhcCC-CcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHh----------c-cch
Q psy6712           1 MNVQCHACIGGTNL---SEDLRKLDYG-QHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEML----------N-KGF   65 (210)
Q Consensus         1 ~~i~~~~~~gg~~~---~~~~~~l~~~-~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~----------~-~~~   65 (210)
                      .|++++.++||.+.   +.++..+.++ ++|+|+||++|.+++..  +.+++++++|+||||++.          + +++
T Consensus       147 ~~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~--l~~~~l~~lViDEaH~l~~~~r~~Dr~L~~~gf  224 (1104)
T 4ddu_A          147 EKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK--LSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGI  224 (1104)
T ss_dssp             TTSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHH--HHTSCCSEEEESCHHHHTTSSHHHHHHHHTSSC
T ss_pred             CCCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHh--hcccCcCEEEEeCCCccccccccchhhhHhcCC
Confidence            36899999999998   7788888776 99999999999888775  677899999999997654          4 666


Q ss_pred             HHH-HHHHHhhCC-----------Cchh----------------------------------------------------
Q psy6712          66 KEQ-IYDVYRYLP-----------PATQ----------------------------------------------------   81 (210)
Q Consensus        66 ~~~-~~~i~~~~~-----------~~~~----------------------------------------------------   81 (210)
                      ... +..++..++           ...+                                                    
T Consensus       225 ~~~~i~~il~~l~~~~~~~~~~~~~~~q~ll~SAT~~p~~~~~~~~~~~l~i~v~~~~~~~~~i~~~~~~~~k~~~L~~l  304 (1104)
T 4ddu_A          225 PEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLNFTVGRLVSVARNITHVRISSRSKEKLVEL  304 (1104)
T ss_dssp             CHHHHHHHHHHHHHTSCCCCCSSCCCCEEEEECBSSCCCSSTTHHHHHHTCCCCCBCCCCCCCEEEEEESCCCHHHHHHH
T ss_pred             CHHHHHHHHHhcccchhhhhhccCCCceEEEEcCCCCcHHHHHHHhhcceeEEeccCCCCcCCceeEEEecCHHHHHHHH
Confidence            666 677776543           2222                                                    


Q ss_pred             -----------------HHHHHHHHHhcCceEE-EecCCCCHhHHHHHHHHHhcCCCcEEEE----ecCccccCCCCC-C
Q psy6712          82 -----------------VDWLTEKMREANFTVS-SMHGDMPQKERDGIMKEFRSGTSRVLIT----TDVWARGIDVQQ-V  138 (210)
Q Consensus        82 -----------------~~~l~~~l~~~~~~~~-~~~~~~~~~~r~~~~~~f~~g~~~ilv~----T~~~~~g~d~~~-~  138 (210)
                                       ++.+++.|...++++. .+||.     |++ +++|++|+.++|||    |+++++|+|+|+ +
T Consensus       305 l~~~~~~~LVF~~s~~~a~~l~~~L~~~g~~~~~~lhg~-----rr~-l~~F~~G~~~VLVatas~TdvlarGIDip~~V  378 (1104)
T 4ddu_A          305 LEIFRDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF-----EKN-FEDFKVGKINILIGVQAYYGKLTRGVDLPERI  378 (1104)
T ss_dssp             HHHHCSSEEEEESSSHHHHHHHHHHHHTTCCEEESSSSH-----HHH-HHHHHHTSCSEEEEETTTHHHHCCSCCCTTTC
T ss_pred             HHhcCCCEEEEECcHHHHHHHHHHHHhCCCCeeeEecCc-----HHH-HHHHHCCCCCEEEEecCCCCeeEecCcCCCCC
Confidence                             8889999999999998 99992     555 99999999999999    999999999999 9


Q ss_pred             cEEEEecCCC----------------------------------------------------------------------
Q psy6712         139 SLVINYDLPN----------------------------------------------------------------------  148 (210)
Q Consensus       139 ~~vi~~~~p~----------------------------------------------------------------------  148 (210)
                      ++||+||+|.                                                                      
T Consensus       379 ~~VI~~d~P~~~~Sle~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~e~~~~~l~~~~~~~~i~~~~~~l~~~~~~~~~~  458 (1104)
T 4ddu_A          379 KYVIFWGTPSMRFSLELDKAPRFVLARVLKEMGLIKAQENPDVEELRKIAKEHLTQKEFVEKVKEMFRGVVVKDEDLELI  458 (1104)
T ss_dssp             CEEEEESCCEEEEECSSSSCCHHHHHHHHHHHSSCSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHCCSSEEETTTTEEE
T ss_pred             CEEEEECCCCCCCCcccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHhhccceEEecCCeeEEE
Confidence            9999999998                                                                      


Q ss_pred             --ChhHHHHhhhhhcCCCCc----eeEEEEeccCcHHHHHHHHHHhc
Q psy6712         149 --NRELYIHRIGRSGRFGRK----GVAISFVKSDDIRILRDIEQYYS  189 (210)
Q Consensus       149 --s~~~~~q~~GR~gR~g~~----g~~~~~~~~~~~~~~~~~~~~~~  189 (210)
                        +..+|+||+||+||.|..    |.+++++  +|...++.+++.++
T Consensus       459 ~pd~~tYihr~GRtgR~~~gg~~~Glsi~~~--~d~~~~~~l~~~~~  503 (1104)
T 4ddu_A          459 IPDVYTYIQASGRSSRILNGVLVKGVSVIFE--EDEEIFESLKTRLL  503 (1104)
T ss_dssp             EECHHHHHHHHHTTCCEETTEECCEEEEEEC--CCHHHHHHHHHHHH
T ss_pred             ecChhhhhcccCchhcccCCCcccceEEEEE--ecHHHHHHHHHHHh
Confidence              778999999999997643    4455555  77788888887765

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=99.95  E-value=1e-26  Score=169.17  Aligned_cols=126  Identities=43%  Similarity=0.739  Sum_probs=118.9

Q ss_pred             HHHhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCCh
Q psy6712          71 DVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNR  150 (210)
Q Consensus        71 ~i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~  150 (210)
                      +++.|++....++.+++.|.+.++.+..+||+|++.+|..++++|++|+.++||+|+++++|+|+|++++||+||+|+++
T Consensus        37 ~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gld~~~~~~Vi~~~~p~~~  116 (163)
T 2hjv_A           37 SCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEK  116 (163)
T ss_dssp             SEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECGGGTTTCCCSCCSEEEESSCCSSH
T ss_pred             cEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEECChhhcCCchhcCCEEEEeCCCCCH
Confidence            34557777788999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHhhhhhcCCCCceeEEEEeccCcHHHHHHHHHHhcCcccccc
Q psy6712         151 ELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMP  196 (210)
Q Consensus       151 ~~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  196 (210)
                      ..|+||+||+||.|+.|.+++|+.+.+...++++++.++.++++++
T Consensus       117 ~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~  162 (163)
T 2hjv_A          117 ESYVHRTGRTGRAGNKGKAISFVTAFEKRFLADIEEYIGFEIQKIE  162 (163)
T ss_dssp             HHHHHHTTTSSCTTCCEEEEEEECGGGHHHHHHHHHHHTSCCEECC
T ss_pred             HHHHHhccccCcCCCCceEEEEecHHHHHHHHHHHHHHCCCcCccC
Confidence            9999999999999999999999999999999999999998887754

>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=99.94  E-value=1.3e-26  Score=204.06  Aligned_cols=190  Identities=16%  Similarity=0.229  Sum_probs=147.5

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCc--
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPA--   79 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~--   79 (210)
                      |++|..++|+.+.+..   ...+++|+|+||+++..++.+....+++++++|+||+|.+.+..+...+..++..++..  
T Consensus        95 g~~v~~~~G~~~~~~~---~~~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~~r~~~~~~ll~~l~~~~~  171 (720)
T 2zj8_A           95 GLRVAMATGDYDSKDE---WLGKYDIIIATAEKFDSLLRHGSSWIKDVKILVADEIHLIGSRDRGATLEVILAHMLGKAQ  171 (720)
T ss_dssp             TCCEEEECSCSSCCCG---GGGGCSEEEECHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCTTTHHHHHHHHHHHBTTBE
T ss_pred             CCEEEEecCCCCcccc---ccCCCCEEEECHHHHHHHHHcChhhhhcCCEEEEECCcccCCCcccHHHHHHHHHhhcCCe
Confidence            7889999998776532   23478999999999999888876668899999999999988766555555544332110  


Q ss_pred             ----------------------------------------------------------------------------hhHH
Q psy6712          80 ----------------------------------------------------------------------------TQVD   83 (210)
Q Consensus        80 ----------------------------------------------------------------------------~~~~   83 (210)
                                                                                                  ..++
T Consensus       172 ii~lSATl~n~~~~~~~l~~~~~~~~~rp~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LVF~~sr~~~~  251 (720)
T 2zj8_A          172 IIGLSATIGNPEELAEWLNAELIVSDWRPVKLRRGVFYQGFVTWEDGSIDRFSSWEELVYDAIRKKKGALIFVNMRRKAE  251 (720)
T ss_dssp             EEEEECCCSCHHHHHHHTTEEEEECCCCSSEEEEEEEETTEEEETTSCEEECSSTTHHHHHHHHTTCCEEEECSCHHHHH
T ss_pred             EEEEcCCcCCHHHHHHHhCCcccCCCCCCCcceEEEEeCCeeeccccchhhhhHHHHHHHHHHhCCCCEEEEecCHHHHH
Confidence                                                                                        0045


Q ss_pred             HHHHHHHhc---------------------------------CceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCcc
Q psy6712          84 WLTEKMREA---------------------------------NFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWA  130 (210)
Q Consensus        84 ~l~~~l~~~---------------------------------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~  130 (210)
                      .+++.|.+.                                 ...+.++||+|+.++|..+++.|++|+++|||||++++
T Consensus       252 ~~a~~L~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~v~~~h~~l~~~~R~~v~~~f~~g~~~vlvaT~~l~  331 (720)
T 2zj8_A          252 RVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHHAGLGRDERVLVEENFRKGIIKAVVATPTLS  331 (720)
T ss_dssp             HHHHHHHHHHGGGSCHHHHHHHHHHHHTSCSCHHHHHHHHHHTTTEEEECTTSCHHHHHHHHHHHHTTSSCEEEECSTTG
T ss_pred             HHHHHHHHHHHHhcChhhHHHHHHHHHHHhcccchHHHHHHHhcCeeeecCCCCHHHHHHHHHHHHCCCCeEEEECcHhh
Confidence            555555432                                 12489999999999999999999999999999999999


Q ss_pred             ccCCCCCCcEEEE----ec----CCCChhHHHHhhhhhcCCC--CceeEEEEeccCcHHHHHHHHHHhcCcccccc
Q psy6712         131 RGIDVQQVSLVIN----YD----LPNNRELYIHRIGRSGRFG--RKGVAISFVKSDDIRILRDIEQYYSTQIDEMP  196 (210)
Q Consensus       131 ~g~d~~~~~~vi~----~~----~p~s~~~~~q~~GR~gR~g--~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  196 (210)
                      +|+|+|++++||+    ||    .|.+..+|.||+|||||.|  ..|.|++++.+.+..  ..+++++....+.+.
T Consensus       332 ~Gvdip~~~~VI~~~~~yd~~g~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~~~--~~~~~~~~~~~~~i~  405 (720)
T 2zj8_A          332 AGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSDDPR--EVMNHYIFGKPEKLF  405 (720)
T ss_dssp             GGCCCCBSEEEECCSEECCSSSCEECCHHHHHHHHTTBCCTTTCSEEEEEEECSSSCHH--HHHHHHTTSCCCCCC
T ss_pred             ccCCCCceEEEEcCCeeecCCCCccCCHHHHHHHHhhcCCCCCCCCceEEEEecCccHH--HHHHHHhcCCCCCcE
Confidence            9999999999998    76    6899999999999999998  478999999887732  234455554444443

>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=99.94  E-value=2e-26  Score=169.51  Aligned_cols=131  Identities=37%  Similarity=0.733  Sum_probs=118.5

Q ss_pred             HHHhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCC---
Q psy6712          71 DVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLP---  147 (210)
Q Consensus        71 ~i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p---  147 (210)
                      +++.|++....++.+++.|.+.++.+..+||+|++.+|..++++|++|+.++||||+++++|+|+|++++||+||+|   
T Consensus        36 ~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~~~~~Gid~~~~~~Vi~~d~p~~~  115 (175)
T 2rb4_A           36 QAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQ  115 (175)
T ss_dssp             EEEEECSCHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECCSCCTTTCCTTEEEEEESSCCC--
T ss_pred             CEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEecchhcCCCcccCCEEEEeCCCCCc
Confidence            34556777777999999999999999999999999999999999999999999999999999999999999999999   


Q ss_pred             ---CChhHHHHhhhhhcCCCCceeEEEEeccCcHHHHHHHHHHhcCccccccCCccc
Q psy6712         148 ---NNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKR  201 (210)
Q Consensus       148 ---~s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  201 (210)
                         .+..+|+||+||+||.|+.|.+++++.+.+...+.++++.++..+++++....+
T Consensus       116 ~~~~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~  172 (175)
T 2rb4_A          116 GEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDELPSLMKIQDHFNSSIKQLNAEDMD  172 (175)
T ss_dssp             CCSCCHHHHHHHHCBC----CCEEEEEEECGGGHHHHHHHHHHHTCCCEEECSSCCC
T ss_pred             cccCCHHHHHHHhcccccCCCCceEEEEEccchHHHHHHHHHHhcCcccccCCchhc
Confidence               899999999999999999999999999999999999999999999998876543

>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=99.94  E-value=1.4e-26  Score=169.95  Aligned_cols=131  Identities=34%  Similarity=0.693  Sum_probs=118.3

Q ss_pred             HHHhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCCh
Q psy6712          71 DVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNR  150 (210)
Q Consensus        71 ~i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~  150 (210)
                      +++.|++....++.+++.|...++++..+||+|++.+|..+++.|++|+.++||||+++++|+|+|++++||+||+|+++
T Consensus        33 ~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldi~~~~~Vi~~d~p~~~  112 (172)
T 1t5i_A           33 QVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDS  112 (172)
T ss_dssp             SEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSCCSTTCCGGGCSEEEESSCCSSH
T ss_pred             cEEEEECCHHHHHHHHHHHHhcCCCEEEEECCCCHHHHHHHHHHHHCCCCcEEEECCchhcCcchhhCCEEEEECCCCCH
Confidence            34556777777999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHhhhhhcCCCCceeEEEEeccC-cHHHHHHHHHHhcCccccccCCccc
Q psy6712         151 ELYIHRIGRSGRFGRKGVAISFVKSD-DIRILRDIEQYYSTQIDEMPMNGKR  201 (210)
Q Consensus       151 ~~~~q~~GR~gR~g~~g~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~  201 (210)
                      ..|+||+||+||.|+.|.+++|+.+. +...++.+++.++..++++|.....
T Consensus       113 ~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~  164 (172)
T 1t5i_A          113 DTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEIDI  164 (172)
T ss_dssp             HHHHHHHHHHTGGGCCCEEEEEECSHHHHHHHHHHHHHHCCCEEECC-----
T ss_pred             HHHHHHhcccccCCCCcEEEEEEcChhHHHHHHHHHHHHhcchhhCChhhch
Confidence            99999999999999999999999875 5678999999999999999877544

>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=99.94  E-value=4e-26  Score=190.84  Aligned_cols=97  Identities=27%  Similarity=0.415  Sum_probs=88.2

Q ss_pred             HHHHHHHHHhcCceEEEecC--------CCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHH
Q psy6712          82 VDWLTEKMREANFTVSSMHG--------DMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELY  153 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~--------~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~  153 (210)
                      ++.+.+.|.+.++++..+||        +|+..+|.+++++|++|+.++||||+++++|+|+|++++||++|+|+++..|
T Consensus       374 ~~~l~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~~~~~vLv~T~~~~~Gldl~~~~~Vi~~d~~~~~~~~  453 (494)
T 1wp9_A          374 AKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRS  453 (494)
T ss_dssp             HHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECGGGGGGGGSTTCCEEEESSCCHHHHHH
T ss_pred             HHHHHHHHHHcCCCcEEEeccccccccccCCHHHHHHHHHHHhcCCceEEEECCccccCCCchhCCEEEEeCCCCCHHHH
Confidence            67788888888999999999        9999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhhhcCCCCceeEEEEeccCcHH
Q psy6712         154 IHRIGRSGRFGRKGVAISFVKSDDIR  179 (210)
Q Consensus       154 ~q~~GR~gR~g~~g~~~~~~~~~~~~  179 (210)
                      .||+||+||.|. |.++.++.+.+.+
T Consensus       454 ~Qr~GR~~R~g~-g~~~~l~~~~t~e  478 (494)
T 1wp9_A          454 IQRRGRTGRHMP-GRVIILMAKGTRD  478 (494)
T ss_dssp             HHHHTTSCSCCC-SEEEEEEETTSHH
T ss_pred             HHHHhhccCCCC-ceEEEEEecCCHH
Confidence            999999999998 9999999887543

>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=99.94  E-value=2.6e-26  Score=173.88  Aligned_cols=129  Identities=30%  Similarity=0.549  Sum_probs=119.5

Q ss_pred             HHHhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCCh
Q psy6712          71 DVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNR  150 (210)
Q Consensus        71 ~i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~  150 (210)
                      .++.|++....++.+++.|.+.++.+..+||+|++.+|..++++|++|+.++||||+++++|+|+|++++||+||+|++.
T Consensus        33 ~~lVF~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~~~~~Gidi~~v~~Vi~~~~p~~~  112 (212)
T 3eaq_A           33 RAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRLPDRA  112 (212)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECTTTTCSSSCCCBSEEEESSCCSSH
T ss_pred             eEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecChhhcCCCCccCcEEEECCCCcCH
Confidence            45667778888999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHhhhhhcCCCCceeEEEEeccCcHHHHHHHHHHhcCccccccCCc
Q psy6712         151 ELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNG  199 (210)
Q Consensus       151 ~~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  199 (210)
                      ..|.||+||+||.|+.|.+++++++.+...++.+++.++..+..++.+.
T Consensus       113 ~~~~qr~GR~gR~g~~g~~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~  161 (212)
T 3eaq_A          113 EAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVGRRFKRVNPPT  161 (212)
T ss_dssp             HHHHHHHTTBCCCC--BEEEEEECGGGHHHHHHHHHHHSSCCEECCCCC
T ss_pred             HHHHHHhcccCCCCCCCeEEEEEchhHHHHHHHHHHHhcCcCeecCCCC
Confidence            9999999999999999999999999999999999999999888876543

>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=99.94  E-value=4e-27  Score=209.24  Aligned_cols=84  Identities=26%  Similarity=0.413  Sum_probs=41.5

Q ss_pred             CceEEEecCCCCHhHHHHHHHHHhc-CCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCCceeEEE
Q psy6712          93 NFTVSSMHGDMPQKERDGIMKEFRS-GTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAIS  171 (210)
Q Consensus        93 ~~~~~~~~~~~~~~~r~~~~~~f~~-g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~~g~~~~  171 (210)
                      |.....+||+|+..+|.+++++|++ |++++||||+++++|+|+|++++||+||+|+|+..|+||+|| ||. +.|.++.
T Consensus       667 G~~~~~~hg~~~~~eR~~~l~~F~~~g~~~vLVaT~~~~~GIDlp~v~~VI~yd~p~s~~~~iQr~GR-GR~-~~g~~i~  744 (797)
T 4a2q_A          667 GRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCIL  744 (797)
T ss_dssp             ---------------------------CCSEEEEECC-------CCCSEEEEESCCSCHHHHHTC---------CCCEEE
T ss_pred             ecCCcccCCCCCHHHHHHHHHHhhccCCceEEEEcCchhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCceEEE
Confidence            4455667888999999999999999 999999999999999999999999999999999999999999 998 8899999


Q ss_pred             EeccCcH
Q psy6712         172 FVKSDDI  178 (210)
Q Consensus       172 ~~~~~~~  178 (210)
                      ++...+.
T Consensus       745 l~~~~~~  751 (797)
T 4a2q_A          745 VTSKTEV  751 (797)
T ss_dssp             EECCHHH
T ss_pred             EEeCCcH
Confidence            9987544

>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=99.94  E-value=4.6e-26  Score=198.53  Aligned_cols=94  Identities=20%  Similarity=0.335  Sum_probs=85.2

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCC--------CCcEEEEecCCCChhHH
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQ--------QVSLVINYDLPNNRELY  153 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~--------~~~~vi~~~~p~s~~~~  153 (210)
                      ++.+++.|...|+++..+||++...++..+..+|+.|  .|+|||++++||+|++        +..+||+|+.|.|...|
T Consensus       445 se~Ls~~L~~~gi~~~vLhg~~~~rEr~ii~~ag~~g--~VlIATdmAgRG~DI~l~~~V~~~ggl~VIn~d~p~s~r~y  522 (844)
T 1tf5_A          445 SELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKG--AVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRID  522 (844)
T ss_dssp             HHHHHHHHHTTTCCCEEECSSCHHHHHHHHTTTTSTT--CEEEEETTSSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHH
T ss_pred             HHHHHHHHHHCCCCEEEeeCCccHHHHHHHHHcCCCC--eEEEeCCccccCcCccccchhhhcCCcEEEEecCCCCHHHH
Confidence            7888888888999999999999888887666666654  7999999999999999        78899999999999999


Q ss_pred             HHhhhhhcCCCCceeEEEEeccCc
Q psy6712         154 IHRIGRSGRFGRKGVAISFVKSDD  177 (210)
Q Consensus       154 ~q~~GR~gR~g~~g~~~~~~~~~~  177 (210)
                      .||+||+||.|.+|.+++|++..|
T Consensus       523 ~hr~GRTGRqG~~G~s~~~vs~eD  546 (844)
T 1tf5_A          523 NQLRGRSGRQGDPGITQFYLSMED  546 (844)
T ss_dssp             HHHHTTSSGGGCCEEEEEEEETTS
T ss_pred             HhhcCccccCCCCCeEEEEecHHH
Confidence            999999999999999999998765

>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea, helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16 c.37.1.16 e.10.1.1 PDB: 1gl9_B*

Probab=99.94  E-value=2.5e-26  Score=208.53  Aligned_cols=174  Identities=18%  Similarity=0.288  Sum_probs=139.5

Q ss_pred             eEEEEEcCcchHHH---HHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCC---
Q psy6712           4 QCHACIGGTNLSED---LRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLP---   77 (210)
Q Consensus         4 ~~~~~~gg~~~~~~---~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~---   77 (210)
                      ++..++||.+...+   ...+.+ ++|+|+||++|.+++.+    +++++++|+||||+++++  ...+..++..+.   
T Consensus       133 ~v~~~~Gg~~~~~~~~~~~~l~~-~~IlV~TP~~L~~~l~~----L~~l~~lViDEah~~l~~--~~~~~~i~~~lgf~~  205 (1054)
T 1gku_B          133 LIGYYHGRIPKREKENFMQNLRN-FKIVITTTQFLSKHYRE----LGHFDFIFVDDVDAILKA--SKNVDKLLHLLGFHY  205 (1054)
T ss_dssp             SEEECCSSCCSHHHHHHHHSGGG-CSEEEEEHHHHHHCSTT----SCCCSEEEESCHHHHHTS--THHHHHHHHHTTEEE
T ss_pred             eEEEEeCCCChhhHHHHHhhccC-CCEEEEcHHHHHHHHHH----hccCCEEEEeChhhhhhc--cccHHHHHHHhCcch
Confidence            89999999987764   455556 99999999999987765    679999999999999872  233333332221   


Q ss_pred             ------------------------------------------------------------------------------Cc
Q psy6712          78 ------------------------------------------------------------------------------PA   79 (210)
Q Consensus        78 ------------------------------------------------------------------------------~~   79 (210)
                                                                                                    ..
T Consensus       206 ~~~~~~~~~~~q~~l~SAT~t~~~~~~~~~~~~~~~i~v~~~~~~~~~i~~~~~~~~k~~~L~~ll~~~~~~~LVF~~t~  285 (1054)
T 1gku_B          206 DLKTKSWVGEARGCLMVSTATAKKGKKAELFRQLLNFDIGSSRITVRNVEDVAVNDESISTLSSILEKLGTGGIIYARTG  285 (1054)
T ss_dssp             ETTTTEEEECCSSEEEECCCCSCCCTTHHHHHHHHCCCCSCCEECCCCEEEEEESCCCTTTTHHHHTTSCSCEEEEESSH
T ss_pred             hhhhhhcccCCceEEEEecCCCchhHHHHHhhcceEEEccCcccCcCCceEEEechhHHHHHHHHHhhcCCCEEEEEcCH
Confidence                                                                                          11


Q ss_pred             hhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEE----ecCccccCCCCCC-cEEEEecCC-------
Q psy6712          80 TQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLIT----TDVWARGIDVQQV-SLVINYDLP-------  147 (210)
Q Consensus        80 ~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~----T~~~~~g~d~~~~-~~vi~~~~p-------  147 (210)
                      ..++.+++.|.+. +++..+||+|     .++++.|++|+.+||||    |+++++|+|+|+| ++||++|+|       
T Consensus       286 ~~a~~l~~~L~~~-~~v~~lhg~~-----~~~l~~F~~G~~~VLVaTas~Tdv~~rGIDip~VI~~VI~~~~P~~~~~~~  359 (1054)
T 1gku_B          286 EEAEEIYESLKNK-FRIGIVTATK-----KGDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCPSFRVTIE  359 (1054)
T ss_dssp             HHHHHHHHTTTTS-SCEEECTTSS-----SHHHHHHHHTSCSEEEEECC------CCSCCTTTCCEEEEESCCEEEEECS
T ss_pred             HHHHHHHHHHhhc-cCeeEEeccH-----HHHHHHHHcCCCcEEEEecCCCCeeEeccccCCcccEEEEeCCCccccccc
Confidence            1188899999887 9999999998     37889999999999999    8999999999996 999999999       


Q ss_pred             ----------------------------------------------------------------CChhHHHHhhhhhcCC
Q psy6712         148 ----------------------------------------------------------------NNRELYIHRIGRSGRF  163 (210)
Q Consensus       148 ----------------------------------------------------------------~s~~~~~q~~GR~gR~  163 (210)
                                                                                      .+..+|+||+||+||.
T Consensus       360 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~yiQr~GRagR~  439 (1054)
T 1gku_B          360 DIDSLSPQMVKLLAYLYRNVDEIERLLPAVERHIDEVREILKKVMGKERPQAKDVVVREGEVIFPDLRTYIQGSGRTSRL  439 (1054)
T ss_dssp             CGGGSCHHHHHHHHTTTSCHHHHHTTCTTTSSCHHHHHHHHHHHHTTSCCSCSSSEEETTEEEEECHHHHHHHHHTTCCE
T ss_pred             ccccChHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHhccccccccceeEeecceecCcHHHHhhhhchhhhc
Confidence                                                                            7899999999999998


Q ss_pred             CCce--eEEEEeccCcHHHHHHHHHHhcC
Q psy6712         164 GRKG--VAISFVKSDDIRILRDIEQYYST  190 (210)
Q Consensus       164 g~~g--~~~~~~~~~~~~~~~~~~~~~~~  190 (210)
                      |..|  .+++++...+...++.+++.++.
T Consensus       440 g~~g~~~g~~~~~~~d~~~~~~l~~~l~~  468 (1054)
T 1gku_B          440 FAGGLTKGASFLLEDDSELLSAFIERAKL  468 (1054)
T ss_dssp             ETTEECCEEEEEECSCHHHHHHHHHHHHT
T ss_pred             cCCCCceEEEEEEecCHHHHHHHHHHHhh
Confidence            7765  48888888888899999988875

>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=99.94  E-value=4.8e-26  Score=199.87  Aligned_cols=174  Identities=18%  Similarity=0.257  Sum_probs=138.6

Q ss_pred             CCceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhC----
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYL----   76 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~----   76 (210)
                      +|+++..++|+....+.   ...+++|+|+||+++..++.+....+++++++|+||+|.+.++++...+..++..+    
T Consensus        94 ~g~~v~~~~G~~~~~~~---~~~~~~Iiv~Tpe~l~~~l~~~~~~l~~~~~vIiDE~H~l~~~~r~~~~~~ll~~l~~~~  170 (702)
T 2p6r_A           94 IGLRIGISTGDYESRDE---HLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTKMRRMN  170 (702)
T ss_dssp             TTCCEEEECSSCBCCSS---CSTTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCTTTHHHHHHHHHHHHHHC
T ss_pred             cCCEEEEEeCCCCcchh---hccCCCEEEECHHHHHHHHHcChhHHhhcCEEEEeeeeecCCCCcccHHHHHHHHHHhcC
Confidence            37889999999776532   22478999999999999988876668899999999999988755544443333211    


Q ss_pred             -------------------------------------------------------------------------------C
Q psy6712          77 -------------------------------------------------------------------------------P   77 (210)
Q Consensus        77 -------------------------------------------------------------------------------~   77 (210)
                                                                                                     +
T Consensus       171 ~~~~ii~lSATl~n~~~~~~~l~~~~~~~~~r~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LVF~~  250 (702)
T 2p6r_A          171 KALRVIGLSATAPNVTEIAEWLDADYYVSDWRPVPLVEGVLCEGTLELFDGAFSTSRRVKFEELVEECVAENGGVLVFES  250 (702)
T ss_dssp             TTCEEEEEECCCTTHHHHHHHTTCEEEECCCCSSCEEEEEECSSEEEEEETTEEEEEECCHHHHHHHHHHTTCCEEEECS
T ss_pred             cCceEEEECCCcCCHHHHHHHhCCCcccCCCCCccceEEEeeCCeeeccCcchhhhhhhhHHHHHHHHHhcCCCEEEEcC
Confidence                                                                                           1


Q ss_pred             CchhHHHHHHHHHhc------------------------------CceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEec
Q psy6712          78 PATQVDWLTEKMREA------------------------------NFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTD  127 (210)
Q Consensus        78 ~~~~~~~l~~~l~~~------------------------------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~  127 (210)
                      ....++.+++.|.+.                              +..+.++||+|+.++|..+++.|++|+.+|||||+
T Consensus       251 s~~~~~~~a~~L~~~~~~~~~~~~~~~~i~~~~~~~~~~~l~~~~~~~v~~~h~~l~~~~R~~v~~~f~~g~~~vlvaT~  330 (702)
T 2p6r_A          251 TRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATP  330 (702)
T ss_dssp             SHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHHHHHHHHHHHHTTSCCEEEECS
T ss_pred             CHHHHHHHHHHHHHHHHhhcChHHHHHHHHhhccccccHHHHHHHhcCeEEecCCCCHHHHHHHHHHHHCCCCeEEEECc
Confidence            111144455544331                              13588899999999999999999999999999999


Q ss_pred             CccccCCCCCCcEEEE----ec---CCCChhHHHHhhhhhcCCCC--ceeEEEEeccCc
Q psy6712         128 VWARGIDVQQVSLVIN----YD---LPNNRELYIHRIGRSGRFGR--KGVAISFVKSDD  177 (210)
Q Consensus       128 ~~~~g~d~~~~~~vi~----~~---~p~s~~~~~q~~GR~gR~g~--~g~~~~~~~~~~  177 (210)
                      ++++|+|+|++++||+    ||   .|.+..+|.||+|||||.|.  .|.|+.++.+.+
T Consensus       331 ~l~~Gidip~~~~VI~~~~~yd~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~  389 (702)
T 2p6r_A          331 TLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRD  389 (702)
T ss_dssp             TTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCGGG
T ss_pred             HHhccCCCCceEEEEcCceeeCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEEecCcc
Confidence            9999999999999998    66   78999999999999999984  789999998876

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.94  E-value=5.2e-26  Score=200.01  Aligned_cols=173  Identities=18%  Similarity=0.215  Sum_probs=134.7

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhC-----
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYL-----   76 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~-----   76 (210)
                      |++|..++|+......  .+ .+++|+|+||+++..++.+....+++++++|+||+|.+.+..+...+..++..+     
T Consensus       102 g~~v~~~~G~~~~~~~--~~-~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~~~~~~l~~i~~~~~~~~i  178 (715)
T 2va8_A          102 GFKVAMTSGDYDTDDA--WL-KNYDIIITTYEKLDSLWRHRPEWLNEVNYFVLDELHYLNDPERGPVVESVTIRAKRRNL  178 (715)
T ss_dssp             TCCEEECCSCSSSCCG--GG-GGCSEEEECHHHHHHHHHHCCGGGGGEEEEEECSGGGGGCTTTHHHHHHHHHHHHTSEE
T ss_pred             CCEEEEEeCCCCCchh--hc-CCCCEEEEcHHHHHHHHhCChhHhhccCEEEEechhhcCCcccchHHHHHHHhcccCcE
Confidence            6789999998776543  22 378999999999999988876668999999999999987655544443332111     


Q ss_pred             --------------------------------------------------------------------------------
Q psy6712          77 --------------------------------------------------------------------------------   76 (210)
Q Consensus        77 --------------------------------------------------------------------------------   76 (210)
                                                                                                      
T Consensus       179 i~lSATl~n~~~~~~~l~~~~~~~~~r~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LVF  258 (715)
T 2va8_A          179 LALSATISNYKQIAKWLGAEPVATNWRPVPLIEGVIYPERKKKEYNVIFKDNTTKKVHGDDAIIAYTLDSLSKNGQVLVF  258 (715)
T ss_dssp             EEEESCCTTHHHHHHHHTCEEEECCCCSSCEEEEEEEECSSTTEEEEEETTSCEEEEESSSHHHHHHHHHHTTTCCEEEE
T ss_pred             EEEcCCCCCHHHHHHHhCCCccCCCCCCCCceEEEEecCCcccceeeecCcchhhhcccchHHHHHHHHHHhcCCCEEEE
Confidence                                                                                            


Q ss_pred             -CCchhHHHHHHHHHhcC------------------------------------ceEEEecCCCCHhHHHHHHHHHhcCC
Q psy6712          77 -PPATQVDWLTEKMREAN------------------------------------FTVSSMHGDMPQKERDGIMKEFRSGT  119 (210)
Q Consensus        77 -~~~~~~~~l~~~l~~~~------------------------------------~~~~~~~~~~~~~~r~~~~~~f~~g~  119 (210)
                       +....++.+++.|.+..                                    ..+.++||+|+.++|..+++.|++|+
T Consensus       259 ~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~~~v~~~h~~l~~~~r~~v~~~f~~g~  338 (715)
T 2va8_A          259 RNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSLISKGVAYHHAGLSKALRDLIEEGFRQRK  338 (715)
T ss_dssp             CSSHHHHHHHHHHHHHTTTSSCCCHHHHHHHHHHHHTCCSSCHHHHHHHHHHHTTTEEEECTTSCHHHHHHHHHHHHTTC
T ss_pred             ECCHHHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHhhhccccccHHHHHHHhcCEEEECCCCCHHHHHHHHHHHHcCC
Confidence             00111555666665431                                    24899999999999999999999999


Q ss_pred             CcEEEEecCccccCCCCCCcEEEE----ec-------CCCChhHHHHhhhhhcCCCC--ceeEEEEeccCc
Q psy6712         120 SRVLITTDVWARGIDVQQVSLVIN----YD-------LPNNRELYIHRIGRSGRFGR--KGVAISFVKSDD  177 (210)
Q Consensus       120 ~~ilv~T~~~~~g~d~~~~~~vi~----~~-------~p~s~~~~~q~~GR~gR~g~--~g~~~~~~~~~~  177 (210)
                      .+|||||+++++|+|+|++++||+    ||       .|.|..+|.||+|||||.|.  .|.|+.++.+.+
T Consensus       339 ~~vlvaT~~l~~Gidip~~~~VI~~~~~~d~~~~~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~  409 (715)
T 2va8_A          339 IKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQMSGRAGRPGFDQIGESIVVVRDKE  409 (715)
T ss_dssp             SCEEEECGGGGGSSCCCBSEEEECCC--------------CHHHHHHHHTTBCCTTTCSCEEEEEECSCGG
T ss_pred             CeEEEEChHHhcccCCCceEEEEeCCeeccccCCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEEeCCch
Confidence            999999999999999999999999    99       89999999999999999984  799999998765

>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=99.93  E-value=2.9e-26  Score=201.04  Aligned_cols=92  Identities=25%  Similarity=0.410  Sum_probs=75.6

Q ss_pred             HHHHHHHHHhc------CceEEEecCC--------CCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCC
Q psy6712          82 VDWLTEKMREA------NFTVSSMHGD--------MPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLP  147 (210)
Q Consensus        82 ~~~l~~~l~~~------~~~~~~~~~~--------~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p  147 (210)
                      ++.+++.|.+.      |+++..+||+        |+..+|.+++++|++|+.+|||||+++++|+|+|++++||+||+|
T Consensus       413 ~~~l~~~L~~~~~l~~~g~~~~~lhg~~~~~~~~~~~~~eR~~~~~~F~~g~~~VLVaT~~~~~GIDip~v~~VI~~d~p  492 (699)
T 4gl2_A          413 AYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGKINLLIATTVAEEGLDIKECNIVIRYGLV  492 (699)
T ss_dssp             HHHHHHHHHSSCSCC-----CEECCCSCCCTTCCCCCHHHHHHHHHHHCC---CCSEEECSCCTTSCCCSCCCCEEESCC
T ss_pred             HHHHHHHHHhCccccccCcceEEEECCCCccCCCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCccccCCEEEEeCCC
Confidence            56677777766      8999999999        999999999999999999999999999999999999999999999


Q ss_pred             CChhHHHHhhhhhcCCCCceeEEEEecc
Q psy6712         148 NNRELYIHRIGRSGRFGRKGVAISFVKS  175 (210)
Q Consensus       148 ~s~~~~~q~~GR~gR~g~~g~~~~~~~~  175 (210)
                      +|+..|+||+|||||.|  +.++++...
T Consensus       493 ~s~~~~~Qr~GRArr~g--~~~~l~~~~  518 (699)
T 4gl2_A          493 TNEIAMVQARGRARADE--STYVLVAHS  518 (699)
T ss_dssp             CCHHHHHHHHTTSCSSS--CEEEEEEES
T ss_pred             CCHHHHHHHcCCCCCCC--ceEEEEEeC
Confidence            99999999999987654  444444443

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=99.93  E-value=4.2e-26  Score=170.00  Aligned_cols=130  Identities=32%  Similarity=0.544  Sum_probs=117.0

Q ss_pred             HHhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChh
Q psy6712          72 VYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRE  151 (210)
Q Consensus        72 i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~  151 (210)
                      ++.|++....++.+++.|...++.+..+||+|++.+|..+++.|++|+.++||||+++++|+|+|++++||+||+|+++.
T Consensus        57 ~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~~~~~Gldi~~v~~VI~~d~p~~~~  136 (191)
T 2p6n_A           57 VLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIE  136 (191)
T ss_dssp             EEEECSCHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHHTSCSEEEECHHHHTTCCCCCCSEEEESSCCSSHH
T ss_pred             EEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEcCchhcCCCcccCCEEEEeCCCCCHH
Confidence            45577777789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhhhhcCCCCceeEEEEeccC-cHHHHHHHHHHhcCccccccCCccc
Q psy6712         152 LYIHRIGRSGRFGRKGVAISFVKSD-DIRILRDIEQYYSTQIDEMPMNGKR  201 (210)
Q Consensus       152 ~~~q~~GR~gR~g~~g~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~  201 (210)
                      .|+||+||+||.|+.|.+++|+.+. +...++.+++.+....+++|..+.+
T Consensus       137 ~~~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~~l~~~l~~~~~~~p~~l~~  187 (191)
T 2p6n_A          137 NYVHRIGRTGCSGNTGIATTFINKACDESVLMDLKALLLEAKQKVPPVLQV  187 (191)
T ss_dssp             HHHHHHTTSCC---CCEEEEEECTTSCHHHHHHHHHHHHHTTCCCCHHHHS
T ss_pred             HHHHHhCccccCCCCcEEEEEEcCchhHHHHHHHHHHHHHccCcCCHHHHh
Confidence            9999999999999999999999976 7888999999998888887765443

>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=99.93  E-value=6.1e-26  Score=206.40  Aligned_cols=97  Identities=21%  Similarity=0.314  Sum_probs=78.6

Q ss_pred             EEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCC--------CChhHHHHhhhhhcCCC--C
Q psy6712          96 VSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLP--------NNRELYIHRIGRSGRFG--R  165 (210)
Q Consensus        96 ~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p--------~s~~~~~q~~GR~gR~g--~  165 (210)
                      +..+||+|++.+|..+++.|++|.++|||||+++++|+|+|++++||+++.|        .++.+|+||+|||||.|  .
T Consensus       507 V~~~Hg~l~~~~R~~v~~~F~~G~ikVLVAT~vla~GIDiP~v~~VI~~~~~~d~~~~r~iS~~eyiQr~GRAGR~G~d~  586 (1108)
T 3l9o_A          507 IGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDD  586 (1108)
T ss_dssp             EEEECSCSCHHHHHHHHHHHHHTCCCEEEEESCCCSCCCC--CEEEESCSEEESSSCEEECCHHHHHHHHHHSCCSSSCS
T ss_pred             eeeecCCCCHHHHHHHHHHHhCCCCeEEEECcHHhcCCCCCCceEEEecCcccCccccccCCHHHHHHhhcccCCCCCCC
Confidence            7899999999999999999999999999999999999999999999977653        47778999999999999  5


Q ss_pred             ceeEEEEeccCcHHHHHHHHHHhcCcccc
Q psy6712         166 KGVAISFVKSDDIRILRDIEQYYSTQIDE  194 (210)
Q Consensus       166 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~  194 (210)
                      .|.|++++.+....  ..+.+++......
T Consensus       587 ~G~~ill~~~~~~~--~~~~~l~~~~~~~  613 (1108)
T 3l9o_A          587 RGIVIMMIDEKMEP--QVAKGMVKGQADR  613 (1108)
T ss_dssp             SEEEEEEECCCCCH--HHHHHHHHCCCCC
T ss_pred             ceEEEEEecCCcCH--HHHHHHhcCCCcc
Confidence            78999998775322  2334444444433

>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=99.93  E-value=5.1e-26  Score=168.77  Aligned_cols=130  Identities=35%  Similarity=0.634  Sum_probs=105.9

Q ss_pred             HHhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChh
Q psy6712          72 VYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRE  151 (210)
Q Consensus        72 i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~  151 (210)
                      ++.|++....++.+++.|...++.+..+||+|+..+|..+++.|++|+.++||||+++++|+|+|++++||+||+|+++.
T Consensus        49 ~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldi~~~~~VI~~d~p~s~~  128 (185)
T 2jgn_A           49 TLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIE  128 (185)
T ss_dssp             EEEEESCHHHHHHHHHHHHHTTCCEEEEC--------CHHHHHHHHTSSSEEEEEC------CCCSBSEEEESSCCSSHH
T ss_pred             EEEEECCHHHHHHHHHHHHHcCCceEEEeCCCCHHHHHHHHHHHHcCCCeEEEEcChhhcCCCcccCCEEEEeCCCCCHH
Confidence            34455566679999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhhhhcCCCCceeEEEEeccCcHHHHHHHHHHhcCccccccCCccc
Q psy6712         152 LYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKR  201 (210)
Q Consensus       152 ~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  201 (210)
                      .|+||+||+||.|+.|.+++|+.+.+...++++++.+....+++|..+..
T Consensus       129 ~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~l~~  178 (185)
T 2jgn_A          129 EYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLEN  178 (185)
T ss_dssp             HHHHHHTTBCCTTSCEEEEEEECGGGGGGHHHHHHHHHHTTCCCCHHHHH
T ss_pred             HHHHHccccCCCCCCcEEEEEEchhhHHHHHHHHHHHHhccCCCCHHHHH
Confidence            99999999999999999999999999999999999998888887765443

>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=99.93  E-value=2e-26  Score=207.33  Aligned_cols=84  Identities=26%  Similarity=0.413  Sum_probs=41.9

Q ss_pred             CceEEEecCCCCHhHHHHHHHHHhc-CCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCCceeEEE
Q psy6712          93 NFTVSSMHGDMPQKERDGIMKEFRS-GTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAIS  171 (210)
Q Consensus        93 ~~~~~~~~~~~~~~~r~~~~~~f~~-g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~~g~~~~  171 (210)
                      |.....+||+|+..+|.+++++|++ |++++||||+++++|+|+|++++||+||+|+|+..|+||+|| ||. ..|.++.
T Consensus       667 G~~~~~~hg~m~~~eR~~il~~Fr~~g~~~VLVaT~~~~eGIDlp~v~~VI~yD~p~s~~~~iQr~GR-GR~-~~g~vi~  744 (936)
T 4a2w_A          667 GRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCIL  744 (936)
T ss_dssp             ---------------------------CCSEEEEECC------CCCCSEEEEESCCSCSHHHHCC---------CCCEEE
T ss_pred             cCCCcccCCCCCHHHHHHHHHHhhccCCeeEEEEeCchhcCCcchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCCEEEE
Confidence            4455566889999999999999999 999999999999999999999999999999999999999999 998 7889999


Q ss_pred             EeccCcH
Q psy6712         172 FVKSDDI  178 (210)
Q Consensus       172 ~~~~~~~  178 (210)
                      ++...+.
T Consensus       745 Li~~~t~  751 (936)
T 4a2w_A          745 VTSKTEV  751 (936)
T ss_dssp             EESCHHH
T ss_pred             EEeCCCH
Confidence            9877543

>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=99.93  E-value=1.2e-25  Score=197.79  Aligned_cols=179  Identities=23%  Similarity=0.323  Sum_probs=135.6

Q ss_pred             CCceEEEEEcCcchHHH---HHHhcC-CCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccc------------
Q psy6712           1 MNVQCHACIGGTNLSED---LRKLDY-GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKG------------   64 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~---~~~l~~-~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~------------   64 (210)
                      +|++++.++||.+..+.   +..+.+ .++|+|+||+.+.+     .+.+++++++|+||+|++....            
T Consensus       444 ~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~-----~~~~~~l~lVVIDEaHr~g~~qr~~l~~~~~~~~  518 (780)
T 1gm5_A          444 FNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE-----DVHFKNLGLVIIDEQHRFGVKQREALMNKGKMVD  518 (780)
T ss_dssp             SSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH-----CCCCSCCCEEEEESCCCC-----CCCCSSSSCCC
T ss_pred             cCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhh-----hhhccCCceEEecccchhhHHHHHHHHHhCCCCC
Confidence            37899999999886653   455555 48999999987643     4678999999999999963110            


Q ss_pred             --------h------------------------------------HHH-HHHHHh----------hCCCc--------hh
Q psy6712          65 --------F------------------------------------KEQ-IYDVYR----------YLPPA--------TQ   81 (210)
Q Consensus        65 --------~------------------------------------~~~-~~~i~~----------~~~~~--------~~   81 (210)
                              .                                    ... +..+..          +++..        ..
T Consensus       519 vL~mSATp~p~tl~~~~~g~~~~s~i~~~p~~r~~i~~~~~~~~~~~~l~~~i~~~l~~g~qvlVf~~~ie~se~l~~~~  598 (780)
T 1gm5_A          519 TLVMSATPIPRSMALAFYGDLDVTVIDEMPPGRKEVQTMLVPMDRVNEVYEFVRQEVMRGGQAFIVYPLIEESDKLNVKS  598 (780)
T ss_dssp             EEEEESSCCCHHHHHHHTCCSSCEEECCCCSSCCCCEECCCCSSTHHHHHHHHHHHTTTSCCBCCBCCCC--------CH
T ss_pred             EEEEeCCCCHHHHHHHHhCCcceeeeeccCCCCcceEEEEeccchHHHHHHHHHHHHhcCCcEEEEecchhhhhhhhHHH
Confidence                    0                                    000 111111          11111        12


Q ss_pred             HHHHHHHHHh---cCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCC-ChhHHHHhh
Q psy6712          82 VDWLTEKMRE---ANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPN-NRELYIHRI  157 (210)
Q Consensus        82 ~~~l~~~l~~---~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~-s~~~~~q~~  157 (210)
                      ++.+++.|.+   .++.+..+||+|+.++|..++++|++|+.+|||||+++++|+|+|++++||++++|. +...|.||+
T Consensus       599 a~~l~~~L~~~~~~~~~v~~lHG~m~~~eR~~v~~~F~~G~~~ILVaT~vie~GIDiP~v~~VIi~d~~r~~l~~l~Qr~  678 (780)
T 1gm5_A          599 AVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLR  678 (780)
T ss_dssp             HHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHH
T ss_pred             HHHHHHHHHhhhcCCCcEEEEeCCCCHHHHHHHHHHHHCCCCeEEEECCCCCccccCCCCCEEEEeCCCCCCHHHHHHHh
Confidence            5677788877   478899999999999999999999999999999999999999999999999999996 788999999


Q ss_pred             hhhcCCCCceeEEEEeccCcHHHHHHH
Q psy6712         158 GRSGRFGRKGVAISFVKSDDIRILRDI  184 (210)
Q Consensus       158 GR~gR~g~~g~~~~~~~~~~~~~~~~~  184 (210)
                      ||+||.|..|.|++++.+.+....+.+
T Consensus       679 GRaGR~g~~g~~ill~~~~~~~~~~rl  705 (780)
T 1gm5_A          679 GRVGRGGQEAYCFLVVGDVGEEAMERL  705 (780)
T ss_dssp             HTSCCSSTTCEEECCCCSCCHHHHHHH
T ss_pred             cccCcCCCCCEEEEEECCCChHHHHHH
Confidence            999999999999999985444433333

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=99.93  E-value=3.9e-25  Score=175.24  Aligned_cols=128  Identities=31%  Similarity=0.561  Sum_probs=116.3

Q ss_pred             HHHhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCCh
Q psy6712          71 DVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNR  150 (210)
Q Consensus        71 ~i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~  150 (210)
                      .++.|++....++.+++.|.+.++.+..+||+|++.+|..+++.|++|+.+|||||+++++|+|+|++++||+||+|++.
T Consensus        30 ~~LVF~~t~~~~~~l~~~L~~~g~~~~~lhg~l~~~~r~~~~~~f~~g~~~vLVaT~va~~Gidi~~v~~VI~~d~p~s~  109 (300)
T 3i32_A           30 RAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRMPDRA  109 (300)
T ss_dssp             SEEEECSSHHHHHHHHHHHHTTTCCEEEECSCCCTHHHHHHHHHHHHTSCCEEEECSTTTCSTTCCCCSEEEESSCCSST
T ss_pred             CEEEEECCHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhcCCceEEEEechhhcCccccceeEEEEcCCCCCH
Confidence            45667778888999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHhhhhhcCCCCceeEEEEeccCcHHHHHHHHHHhcCccccccCC
Q psy6712         151 ELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN  198 (210)
Q Consensus       151 ~~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  198 (210)
                      ..|.||+||+||.|+.|.|++|+++.+...++.+++.++..+..++.+
T Consensus       110 ~~y~Qr~GRagR~g~~G~~i~l~~~~e~~~~~~ie~~~~~~~~~~~~~  157 (300)
T 3i32_A          110 EAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVGRRFKRVNPP  157 (300)
T ss_dssp             THHHHHHTCCC-----CEEEEEECSSTHHHHHHHHHHHTCCCEECCCC
T ss_pred             HHHHHHccCcCcCCCCceEEEEeChHHHHHHHHHHHHhCCcceEeCCC
Confidence            999999999999999999999999999999999999999988877654

>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=99.93  E-value=3.4e-25  Score=192.80  Aligned_cols=95  Identities=19%  Similarity=0.279  Sum_probs=87.8

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCC-----------------------
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQV-----------------------  138 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~-----------------------  138 (210)
                      ++.+++.|...|+++..+||++...++..+..+|+.|  .|+|||++++||+|++..                       
T Consensus       454 se~Ls~~L~~~gi~~~vLnak~~~rEa~iia~agr~G--~VtIATnmAgRGtDI~l~gn~~~~~~~~~~~~~~~~~~~~~  531 (853)
T 2fsf_A          454 SELVSNELTKAGIKHNVLNAKFHANEAAIVAQAGYPA--AVTIATNMAGRGTDIVLGGSWQAEVAALENPTAEQIEKIKA  531 (853)
T ss_dssp             HHHHHHHHHHTTCCCEECCTTCHHHHHHHHHTTTSTT--CEEEEESCCSSCSCCCTTCCHHHHHHHCSSCCSSHHHHHHH
T ss_pred             HHHHHHHHHHCCCCEEEecCChhHHHHHHHHhcCCCC--eEEEecccccCCcCccCCCchHhhhhhcccchhHHHHHHHH
Confidence            7889999999999999999999888888888889887  699999999999999874                       


Q ss_pred             --------------cEEEEecCCCChhHHHHhhhhhcCCCCceeEEEEeccCcH
Q psy6712         139 --------------SLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDI  178 (210)
Q Consensus       139 --------------~~vi~~~~p~s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~  178 (210)
                                    .+||+++.|.|...|.||+||+||.|.+|.+++|++..|.
T Consensus       532 ~~~~~~~~V~~~GGl~VI~te~pes~riy~qr~GRTGRqGd~G~s~~fls~eD~  585 (853)
T 2fsf_A          532 DWQVRHDAVLEAGGLHIIGTERHESRRIDNQLRGRSGRQGDAGSSRFYLSMEDA  585 (853)
T ss_dssp             HHHHHHHHHHHTTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTSG
T ss_pred             HhhhhhhHHHhcCCcEEEEccCCCCHHHHHhhccccccCCCCeeEEEEecccHH
Confidence                          5999999999999999999999999999999999987663

>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=99.92  E-value=2e-24  Score=188.40  Aligned_cols=96  Identities=21%  Similarity=0.292  Sum_probs=87.2

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCC-----------------------
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQV-----------------------  138 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~-----------------------  138 (210)
                      ++.|++.|.+.|+++..+||++...++..+..+|+.|  .|+|||++++||+|++..                       
T Consensus       473 sE~Ls~~L~~~Gi~~~vLnak~~~rEa~iia~agr~G--~VtIATnmAgRGtDI~l~~~~~~~~~~~~~~~~~~~~~~~~  550 (922)
T 1nkt_A          473 SEYLSRQFTKRRIPHNVLNAKYHEQEATIIAVAGRRG--GVTVATNMAGRGTDIVLGGNVDFLTDQRLRERGLDPVETPE  550 (922)
T ss_dssp             HHHHHHHHHHTTCCCEEECSSCHHHHHHHHHTTTSTT--CEEEEETTCSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHH
T ss_pred             HHHHHHHHHHCCCCEEEecCChhHHHHHHHHhcCCCC--eEEEecchhhcCccccCCCCHHHHHHHHHhhccccccccch
Confidence            7888999999999999999998888877777888877  699999999999999975                       


Q ss_pred             -----------------------------cEEEEecCCCChhHHHHhhhhhcCCCCceeEEEEeccCcHH
Q psy6712         139 -----------------------------SLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIR  179 (210)
Q Consensus       139 -----------------------------~~vi~~~~p~s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~~  179 (210)
                                                   .+||+++.|.|...|.||+||+||+|.+|.+.+|++..|.-
T Consensus       551 ~~~~~~~~~~~~~~~~~~~~~~~V~~~GGlhVI~te~pes~riy~qr~GRTGRqGdpG~s~fflSleD~l  620 (922)
T 1nkt_A          551 EYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQLRGRSGRQGDPGESRFYLSLGDEL  620 (922)
T ss_dssp             HHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHHHHHHHTSSGGGCCEEEEEEEETTSHH
T ss_pred             hhHHHHHHHHHHHHHHHHHhhhHHHhcCCcEEEeccCCCCHHHHHHHhcccccCCCCeeEEEEechhHHH
Confidence                                         49999999999999999999999999999999999887653

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4b71_A* 4b73_A* 4b74_A* 4b76_A* 4b75_A* 4a92_A* 1cu1_A 4b6e_A* 4b6f_A* 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A ...

Probab=99.92  E-value=2.5e-25  Score=191.70  Aligned_cols=173  Identities=18%  Similarity=0.229  Sum_probs=136.0

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchh
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ   81 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~   81 (210)
                      +.++...+|+..       +..+++|+|+||++|   +.++.+.+++++++|+|||| +++.++...+..++..++...+
T Consensus       282 g~~vg~~vG~~~-------~~~~~~IlV~TPGrL---l~~~~l~l~~l~~lVlDEAH-~l~~~~~~~l~~Il~~l~~~~~  350 (666)
T 3o8b_A          282 GIDPNIRTGVRT-------ITTGAPVTYSTYGKF---LADGGCSGGAYDIIICDECH-STDSTTILGIGTVLDQAETAGA  350 (666)
T ss_dssp             SCCCEEECSSCE-------ECCCCSEEEEEHHHH---HHTTSCCTTSCSEEEETTTT-CCSHHHHHHHHHHHHHTTTTTC
T ss_pred             CCCeeEEECcEe-------ccCCCCEEEECcHHH---HhCCCcccCcccEEEEccch-hcCccHHHHHHHHHHhhhhcCC
Confidence            344555666654       356789999999996   56777888999999999996 5566777777777765543222


Q ss_pred             ----------------------------------------------------------HHHHHHHHHhcCceEEEecCCC
Q psy6712          82 ----------------------------------------------------------VDWLTEKMREANFTVSSMHGDM  103 (210)
Q Consensus        82 ----------------------------------------------------------~~~l~~~l~~~~~~~~~~~~~~  103 (210)
                                                                                ++.+++.|++.++++..+||+|
T Consensus       351 ~llil~SAT~~~~i~~~~p~i~~v~~~~~~~i~~~~~~~~l~~~~~~~vLVFv~Tr~~ae~la~~L~~~g~~v~~lHG~l  430 (666)
T 3o8b_A          351 RLVVLATATPPGSVTVPHPNIEEVALSNTGEIPFYGKAIPIEAIRGGRHLIFCHSKKKCDELAAKLSGLGINAVAYYRGL  430 (666)
T ss_dssp             SEEEEEESSCTTCCCCCCTTEEEEECBSCSSEEETTEEECGGGSSSSEEEEECSCHHHHHHHHHHHHTTTCCEEEECTTS
T ss_pred             ceEEEECCCCCcccccCCcceEEEeecccchhHHHHhhhhhhhccCCcEEEEeCCHHHHHHHHHHHHhCCCcEEEecCCC
Confidence                                                                      8999999999999999999999


Q ss_pred             CHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEE----------Eec-----------CCCChhHHHHhhhhhcC
Q psy6712         104 PQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVI----------NYD-----------LPNNRELYIHRIGRSGR  162 (210)
Q Consensus       104 ~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi----------~~~-----------~p~s~~~~~q~~GR~gR  162 (210)
                      ++++       |+++..+|||||+++++|+|+| +++||          |||           .|.+..+|+||+||+||
T Consensus       431 ~q~e-------r~~~~~~VLVATdVaerGIDId-V~~VI~~Gl~~~~ViNyDydP~~gl~~~~~P~s~~syiQRiGRtGR  502 (666)
T 3o8b_A          431 DVSV-------IPTIGDVVVVATDALMTGYTGD-FDSVIDCNTCVTQTVDFSLDPTFTIETTTVPQDAVSRSQRRGRTGR  502 (666)
T ss_dssp             CGGG-------SCSSSCEEEEECTTHHHHCCCC-BSEEEECCEEEEEEEECCCSSSCEEEEEEEECBHHHHHHHHTTBCS
T ss_pred             CHHH-------HHhCCCcEEEECChHHccCCCC-CcEEEecCcccccccccccccccccccccCcCCHHHHHHHhccCCC
Confidence            9875       4556679999999999999997 99988          677           89999999999999999


Q ss_pred             CCCceeEEEEeccCcHHH--H--HHHHHHhcCccccc
Q psy6712         163 FGRKGVAISFVKSDDIRI--L--RDIEQYYSTQIDEM  195 (210)
Q Consensus       163 ~g~~g~~~~~~~~~~~~~--~--~~~~~~~~~~~~~~  195 (210)
                       |+.|. +.|+.+.+...  +  ..+++..+..+.+.
T Consensus       503 -g~~G~-i~lvt~~e~~~~~l~~~~i~~~~~~~~~~~  537 (666)
T 3o8b_A          503 -GRRGI-YRFVTPGERPSGMFDSSVLCECYDAGCAWY  537 (666)
T ss_dssp             -SSCEE-EEESCCCCBCSSBCCHHHHHHHHHHHHHTS
T ss_pred             -CCCCE-EEEEecchhhcccccHHHHHHHhcCCcccc
Confidence             89999 89998765543  3  45555554444443

>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=99.86  E-value=6.5e-27  Score=171.39  Aligned_cols=129  Identities=36%  Similarity=0.595  Sum_probs=122.1

Q ss_pred             HHHHhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCC
Q psy6712          70 YDVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNN  149 (210)
Q Consensus        70 ~~i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s  149 (210)
                      .+++.|++....++.+++.|...++.+..+||+|++.+|..+++.|++|+.++||||+++++|+|+|++++||+||+|++
T Consensus        31 ~~~iVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gid~~~~~~Vi~~~~p~~  110 (170)
T 2yjt_D           31 TRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPRS  110 (170)
Confidence            46788898889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHhhhhhcCCCCceeEEEEeccCcHHHHHHHHHHhcCccccccCC
Q psy6712         150 RELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN  198 (210)
Q Consensus       150 ~~~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  198 (210)
                      +..|+||+||+||.|+.|.+++++.+.+...++++++.++..+++.+.+
T Consensus       111 ~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (170)
T 2yjt_D          111 GDTYLHRIGRTARAGRKGTAISLVEAHDHLLLGKVGRYIEEPIKARVID  159 (170)
Confidence            9999999999999999999999999999999999999999888876554

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.92  E-value=4.4e-24  Score=192.77  Aligned_cols=88  Identities=22%  Similarity=0.403  Sum_probs=80.5

Q ss_pred             EEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEE----ecC----CCChhHHHHhhhhhcCCCC--
Q psy6712          96 VSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVIN----YDL----PNNRELYIHRIGRSGRFGR--  165 (210)
Q Consensus        96 ~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~----~~~----p~s~~~~~q~~GR~gR~g~--  165 (210)
                      +..+||+|++.+|..+++.|++|.+++||||+++++|+|+|++++||+    ||.    |.++.+|.||+|||||.|.  
T Consensus       409 I~~~Hggl~~~eR~~ve~~F~~G~ikVLVAT~~la~GIDiP~~~vVI~~~~kfd~~~~rp~s~~~y~Qr~GRAGR~G~d~  488 (1010)
T 2xgj_A          409 IGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDD  488 (1010)
T ss_dssp             EEEESTTSCHHHHHHHHHHHHTTCCSEEEEEGGGGGSTTCCBSEEEESCSEEECSSCEEECCHHHHHHHHTTBCCTTTCS
T ss_pred             eeEECCCCCHHHHHHHHHHHhcCCCcEEEEehHhhccCCCCCceEEEeCCcccCCcCCccCCHHHHhHhhhhcccCCCCC
Confidence            788999999999999999999999999999999999999999999999    998    8999999999999999997  


Q ss_pred             ceeEEEEeccC-cHHHHHH
Q psy6712         166 KGVAISFVKSD-DIRILRD  183 (210)
Q Consensus       166 ~g~~~~~~~~~-~~~~~~~  183 (210)
                      .|.|++++.+. +...+.+
T Consensus       489 ~G~vi~l~~~~~e~~~~~~  507 (1010)
T 2xgj_A          489 RGIVIMMIDEKMEPQVAKG  507 (1010)
T ss_dssp             SEEEEEEECSCCCHHHHHH
T ss_pred             ceEEEEEECCCCCHHHHHH
Confidence            59999999865 4444433

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.91  E-value=7.9e-24  Score=183.73  Aligned_cols=174  Identities=18%  Similarity=0.301  Sum_probs=135.7

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCC-ch
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPP-AT   80 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~-~~   80 (210)
                      |++|..++||.+..  ...-....+++++|++.+.        ..+.++++|+||+|++.+.++...+..++..++. ..
T Consensus       203 g~~v~lltG~~~~i--v~TpGr~~~il~~T~e~~~--------l~~~v~lvVIDEaH~l~d~~~g~~~~~~l~~l~~~~i  272 (677)
T 3rc3_A          203 GVPCDLVTGEERVT--VQPNGKQASHVSCTVEMCS--------VTTPYEVAVIDEIQMIRDPARGWAWTRALLGLCAEEV  272 (677)
T ss_dssp             TCCEEEECSSCEEC--CSTTCCCCSEEEEEGGGCC--------SSSCEEEEEECSGGGGGCTTTHHHHHHHHHHCCEEEE
T ss_pred             CCcEEEEECCeeEE--ecCCCcccceeEecHhHhh--------hcccCCEEEEecceecCCccchHHHHHHHHccCccce
Confidence            67888899987661  0000113678888886543        2467799999999999887777666666655441 11


Q ss_pred             h-----------------------------------------------------------HHHHHHHHHhcCceEEEecC
Q psy6712          81 Q-----------------------------------------------------------VDWLTEKMREANFTVSSMHG  101 (210)
Q Consensus        81 ~-----------------------------------------------------------~~~l~~~l~~~~~~~~~~~~  101 (210)
                      +                                                           ++.+++.|.+.++.+..+||
T Consensus       273 ~il~~SAT~~~i~~l~~~~~~~~~v~~~~r~~~l~~~~~~l~~l~~~~~g~iIf~~s~~~ie~la~~L~~~g~~v~~lHG  352 (677)
T 3rc3_A          273 HLCGEPAAIDLVMELMYTTGEEVEVRDYKRLTPISVLDHALESLDNLRPGDCIVCFSKNDIYSVSRQIEIRGLESAVIYG  352 (677)
T ss_dssp             EEEECGGGHHHHHHHHHHHTCCEEEEECCCSSCEEECSSCCCSGGGCCTTEEEECSSHHHHHHHHHHHHHTTCCCEEECT
T ss_pred             EEEeccchHHHHHHHHHhcCCceEEEEeeecchHHHHHHHHHHHHhcCCCCEEEEcCHHHHHHHHHHHHhcCCCeeeeec
Confidence            1                                                           88899999999999999999


Q ss_pred             CCCHhHHHHHHHHHhc--CCCcEEEEecCccccCCCCCCcEEEEecC--------------CCChhHHHHhhhhhcCCCC
Q psy6712         102 DMPQKERDGIMKEFRS--GTSRVLITTDVWARGIDVQQVSLVINYDL--------------PNNRELYIHRIGRSGRFGR  165 (210)
Q Consensus       102 ~~~~~~r~~~~~~f~~--g~~~ilv~T~~~~~g~d~~~~~~vi~~~~--------------p~s~~~~~q~~GR~gR~g~  165 (210)
                      +|++++|.++++.|++  |+.+|||||+++++|+|+ ++++||++++              |.+..+|.||+|||||.|.
T Consensus       353 ~L~~~~R~~~~~~F~~~~g~~~VLVATdi~e~GlDi-~v~~VI~~~~~k~~~~~~G~~~~~p~s~~~~~QR~GRAGR~g~  431 (677)
T 3rc3_A          353 SLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNL-SIRRIIFYSLIKPSINEKGERELEPITTSQALQIAGRAGRFSS  431 (677)
T ss_dssp             TSCHHHHHHHHHHHHCTTSSCCEEEECGGGGSSCCC-CBSEEEESCSBC-----------CBCCHHHHHHHHTTBTCTTS
T ss_pred             cCCHHHHHHHHHHHHccCCCeEEEEeCcHHHCCcCc-CccEEEECCccccccccCCccccccCCHHHHHHHhcCCCCCCC
Confidence            9999999999999999  889999999999999999 9999999998              7899999999999999986


Q ss_pred             c---eeEEEEeccCcHHHHHHHHHH
Q psy6712         166 K---GVAISFVKSDDIRILRDIEQY  187 (210)
Q Consensus       166 ~---g~~~~~~~~~~~~~~~~~~~~  187 (210)
                      .   |.|+.+. +.+...++++.+.
T Consensus       432 ~g~~G~v~~l~-~~d~~~~~~~~~~  455 (677)
T 3rc3_A          432 RFKEGEVTTMN-HEDLSLLKEILKR  455 (677)
T ss_dssp             SCSSEEEEESS-TTHHHHHHHHHHS
T ss_pred             CCCCEEEEEEe-cchHHHHHHHHhc
Confidence            4   5555554 4444444444443

>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=99.91  E-value=1e-23  Score=192.76  Aligned_cols=169  Identities=18%  Similarity=0.247  Sum_probs=134.5

Q ss_pred             CceEEEEEcCcchHHH---HHHhcC-CCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHH----
Q psy6712           2 NVQCHACIGGTNLSED---LRKLDY-GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVY----   73 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~---~~~l~~-~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~----   73 (210)
                      ++++..++|+.+..++   +..+.. .++|+|+||+.+     ++.+.+++++++|+||+|++... ....+..+.    
T Consensus       680 ~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll-----~~~~~~~~l~lvIiDEaH~~g~~-~~~~l~~l~~~~~  753 (1151)
T 2eyq_A          680 PVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLL-----QSDVKFKDLGLLIVDEEHRFGVR-HKERIKAMRANVD  753 (1151)
T ss_dssp             TCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHH-----HSCCCCSSEEEEEEESGGGSCHH-HHHHHHHHHTTSE
T ss_pred             CCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHH-----hCCccccccceEEEechHhcChH-HHHHHHHhcCCCC
Confidence            5788888887665543   445555 489999999754     34567899999999999996321 111111111    


Q ss_pred             ---------------------------------------------------------------hhCCCchhHHHHHHHHH
Q psy6712          74 ---------------------------------------------------------------RYLPPATQVDWLTEKMR   90 (210)
Q Consensus        74 ---------------------------------------------------------------~~~~~~~~~~~l~~~l~   90 (210)
                                                                                     .+++....++.+++.|+
T Consensus       754 vl~lSATp~p~~l~~~~~~~~~~~~i~~~~~~r~~i~~~~~~~~~~~i~~~il~~l~~g~qvlvf~~~v~~~~~l~~~L~  833 (1151)
T 2eyq_A          754 ILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSMVVREAILREILRGGQVYYLYNDVENIQKAAERLA  833 (1151)
T ss_dssp             EEEEESSCCCHHHHHHHTTTSEEEECCCCCCBCBCEEEEEEECCHHHHHHHHHHHHTTTCEEEEECCCSSCHHHHHHHHH
T ss_pred             EEEEcCCCChhhHHHHHhcCCCceEEecCCCCccccEEEEecCCHHHHHHHHHHHHhcCCeEEEEECCHHHHHHHHHHHH
Confidence                                                                           01222222788888888


Q ss_pred             hc--CceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecC-CCChhHHHHhhhhhcCCCCce
Q psy6712          91 EA--NFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDL-PNNRELYIHRIGRSGRFGRKG  167 (210)
Q Consensus        91 ~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~-p~s~~~~~q~~GR~gR~g~~g  167 (210)
                      +.  +.++..+||+|+..+|.+++++|++|+++|||||+++++|+|+|++++||+++. +++..+|.||+||+||.|+.|
T Consensus       834 ~~~p~~~v~~lhg~~~~~eR~~il~~F~~g~~~VLVaT~v~e~GiDip~v~~VIi~~~~~~~l~~l~Qr~GRvgR~g~~g  913 (1151)
T 2eyq_A          834 ELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQA  913 (1151)
T ss_dssp             HHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSCCTTEEEEEETTTTSSCHHHHHHHHTTCCBTTBCE
T ss_pred             HhCCCCeEEEEeCCCCHHHHHHHHHHHHcCCCcEEEECCcceeeecccCCcEEEEeCCCCCCHHHHHHHHhccCcCCCce
Confidence            76  789999999999999999999999999999999999999999999999999988 579999999999999999999


Q ss_pred             eEEEEeccC
Q psy6712         168 VAISFVKSD  176 (210)
Q Consensus       168 ~~~~~~~~~  176 (210)
                      .|++++.+.
T Consensus       914 ~~~ll~~~~  922 (1151)
T 2eyq_A          914 YAWLLTPHP  922 (1151)
T ss_dssp             EEEEEECCG
T ss_pred             EEEEEECCc
Confidence            999998764

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.91  E-value=2.9e-24  Score=182.11  Aligned_cols=92  Identities=14%  Similarity=0.203  Sum_probs=84.3

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEe-cCccccCCCCCCcEEEEecCCCChhHHHHhhhhh
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITT-DVWARGIDVQQVSLVINYDLPNNRELYIHRIGRS  160 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T-~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~  160 (210)
                      ++.+.+.|.+.+.++..+||+|+..+|.++++.|++|+.++|||| +++++|+|+|++++||++++|+++..|.|++||+
T Consensus       360 ~~~l~~~L~~~~~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv~T~~~~~~GiDip~v~~vi~~~~~~s~~~~~Q~~GR~  439 (510)
T 2oca_A          360 GKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFSTGISVKNLHHVVLAHGVKSKIIVLQTIGRV  439 (510)
T ss_dssp             HHHHHHHHHTTCSSEEEESSSTTHHHHHHHHHHHHHCCSCEEEEEHHHHHHSCCCCSEEEEEESSCCCSCCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCeEEEECCCCHHHHHHHHHHHhCCCCCEEEEEcChhhcccccccCcEEEEeCCCCCHHHHHHHHhcc
Confidence            666888888887899999999999999999999999999999999 9999999999999999999999999999999999


Q ss_pred             cCCCCceeEEEEe
Q psy6712         161 GRFGRKGVAISFV  173 (210)
Q Consensus       161 gR~g~~g~~~~~~  173 (210)
                      ||.|..+.++.++
T Consensus       440 gR~g~~~~~v~i~  452 (510)
T 2oca_A          440 LRKHGSKTIATVW  452 (510)
T ss_dssp             HTTTCCCCCCEEE
T ss_pred             cccCCCCceEEEE
Confidence            9999876444443

>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=99.90  E-value=6.8e-24  Score=199.21  Aligned_cols=90  Identities=17%  Similarity=0.285  Sum_probs=80.6

Q ss_pred             eEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEE----e------cCCCChhHHHHhhhhhcCCC
Q psy6712          95 TVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVIN----Y------DLPNNRELYIHRIGRSGRFG  164 (210)
Q Consensus        95 ~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~----~------~~p~s~~~~~q~~GR~gR~g  164 (210)
                      .++++|++|++.+|..+.+.|++|.+++||||+.+++|+|+|...+||.    |      ..|.++.+|.||+|||||.|
T Consensus      1215 GIa~hHagL~~~~R~~VE~lF~~G~i~VLvaT~tlA~GVnlPa~~VVI~~~~~~dg~~~~~~~~s~~~~~Qm~GRAGR~g 1294 (1724)
T 4f92_B         1215 GVGYLHEGLSPMERRLVEQLFSSGAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPL 1294 (1724)
T ss_dssp             TEEEECTTSCHHHHHHHHHHHHHTSBCEEEEEGGGSSSCCCCBSEEEEECSEEEETTTTEEEECCHHHHHHHHTTBCCTT
T ss_pred             CEEEECCCCCHHHHHHHHHHHHCCCCeEEEEChHHHcCCCCCccEEEEecCccccCcccccCCCCHHHHHHhhccccCCC
Confidence            5899999999999999999999999999999999999999999999983    3      34678999999999999998


Q ss_pred             C--ceeEEEEeccCcHHHHHHH
Q psy6712         165 R--KGVAISFVKSDDIRILRDI  184 (210)
Q Consensus       165 ~--~g~~~~~~~~~~~~~~~~~  184 (210)
                      .  .|.+++++.+.+...++++
T Consensus      1295 ~d~~G~avll~~~~~~~~~~~l 1316 (1724)
T 4f92_B         1295 QDDEGRCVIMCQGSKKDFFKKF 1316 (1724)
T ss_dssp             TCSCEEEEEEEEGGGHHHHHHH
T ss_pred             CCCceEEEEEecchHHHHHHHH
Confidence            7  6999999998887665543

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A*

Probab=99.90  E-value=6.5e-25  Score=183.04  Aligned_cols=110  Identities=17%  Similarity=0.207  Sum_probs=89.0

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEE------------------
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVIN------------------  143 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~------------------  143 (210)
                      ++.+++.|++.++++..+||    ++|.+++++|++|+.+|||||+++++|+|+| +++||+                  
T Consensus       190 a~~l~~~L~~~~~~v~~lhg----~~R~~~~~~F~~g~~~vLVaT~v~e~GiDip-v~~VI~~g~~~~pv~~~~~~~~vi  264 (440)
T 1yks_A          190 ANVMAASLRKAGKSVVVLNR----KTFEREYPTIKQKKPDFILATDIAEMGANLC-VERVLDCRTAFKPVLVDEGRKVAI  264 (440)
T ss_dssp             HHHHHHHHHHTTCCEEECCS----SSCC--------CCCSEEEESSSTTCCTTCC-CSEEEECCEEEEEEEETTTTEEEE
T ss_pred             HHHHHHHHHHcCCCEEEecc----hhHHHHHhhhcCCCceEEEECChhheeeccC-ceEEEeCCccceeeecccccceee
Confidence            89999999999999999999    4688999999999999999999999999999 999986                  


Q ss_pred             -ecCCCChhHHHHhhhhhcCC-CCceeEEEEe---ccCcHHHHHHHHHHhcCcccccc
Q psy6712         144 -YDLPNNRELYIHRIGRSGRF-GRKGVAISFV---KSDDIRILRDIEQYYSTQIDEMP  196 (210)
Q Consensus       144 -~~~p~s~~~~~q~~GR~gR~-g~~g~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~  196 (210)
                       ++.|.+..+|.||+||+||. |..|.|++++   ++.+...++.+++.+.....+++
T Consensus       265 ~~~~p~~~~~~~Qr~GR~GR~g~~~g~~~~l~~~~~~~~~~~l~~l~~~~~~~~~~l~  322 (440)
T 1yks_A          265 KGPLRISASSAAQRRGRIGRNPNRDGDSYYYSEPTSENNAHHVCWLEASMLLDNMEVR  322 (440)
T ss_dssp             EEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTTBHHHHHHHHHHTTSCCG
T ss_pred             ccccccCHHHHHHhccccCCCCCCCceEEEEeccCChhhhhhhhhhhHHhcccccccc
Confidence             89999999999999999998 6799999996   56777778888877644444443

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.89  E-value=7.8e-23  Score=184.59  Aligned_cols=89  Identities=21%  Similarity=0.365  Sum_probs=73.6

Q ss_pred             eEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCC---------CChhHHHHhhhhhcCCC-
Q psy6712          95 TVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLP---------NNRELYIHRIGRSGRFG-  164 (210)
Q Consensus        95 ~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p---------~s~~~~~q~~GR~gR~g-  164 (210)
                      .+..+||+|++.+|..+++.|++|+++|||||+++++|+|+|++.+ |+++.|         .+..+|+||+|||||.| 
T Consensus       401 gi~~~H~gl~~~~R~~v~~~F~~G~~kVLvAT~~~a~GIDiP~~~V-Vi~~~~k~dg~~~~~~s~~~y~Qr~GRAGR~G~  479 (997)
T 4a4z_A          401 GIAVHHGGLLPIVKELIEILFSKGFIKVLFATETFAMGLNLPTRTV-IFSSIRKHDGNGLRELTPGEFTQMAGRAGRRGL  479 (997)
T ss_dssp             TEEEECTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCCSEE-EESCSEEEETTEEEECCHHHHHHHHGGGCCTTT
T ss_pred             CeeeecCCCCHHHHHHHHHHHHCCCCcEEEEchHhhCCCCCCCceE-EEeccccccCccCCCCCHHHHhHHhcccccCCC
Confidence            4789999999999999999999999999999999999999999554 444444         49999999999999998 


Q ss_pred             -CceeEEEEec--cCcHHHHHHH
Q psy6712         165 -RKGVAISFVK--SDDIRILRDI  184 (210)
Q Consensus       165 -~~g~~~~~~~--~~~~~~~~~~  184 (210)
                       ..|.|++++.  ..+...++.+
T Consensus       480 ~~~G~vi~l~~~~~~~~~~~~~~  502 (997)
T 4a4z_A          480 DSTGTVIVMAYNSPLSIATFKEV  502 (997)
T ss_dssp             CSSEEEEEECCSSCCCHHHHHHH
T ss_pred             CcceEEEEecCCCcchHHHHHHH
Confidence             4688888883  2344444433

>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=99.89  E-value=3.8e-23  Score=194.21  Aligned_cols=90  Identities=20%  Similarity=0.325  Sum_probs=79.6

Q ss_pred             eEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEE----ecC------CCChhHHHHhhhhhcCCC
Q psy6712          95 TVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVIN----YDL------PNNRELYIHRIGRSGRFG  164 (210)
Q Consensus        95 ~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~----~~~------p~s~~~~~q~~GR~gR~g  164 (210)
                      .++++||+|+.++|..+.+.|++|.+++||||+.+++|+|+|..++||.    |++      |.++.+|.||+|||||.|
T Consensus       380 Gva~HHagL~~~~R~~vE~~F~~G~i~vlvaTsTLa~GVNlPa~~vVI~~~~~~~~~~~~~~~ls~~~~~Qm~GRAGR~g  459 (1724)
T 4f92_B          380 GFAIHHAGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQ  459 (1724)
T ss_dssp             TEEEECSSSCTHHHHHHHHHHHTTCCCEEEECHHHHHHSCCCBSEEEEECCEEEETTTTEEEECCHHHHHHHHTTBSCTT
T ss_pred             CEEEEcCCCCHHHHHHHHHHHHCCCCeEEEEcchhHhhCCCCCceEEEeCCEEecCcCCCcccCCHHHHHHhhhhccCCC
Confidence            5889999999999999999999999999999999999999999999985    553      568999999999999987


Q ss_pred             C--ceeEEEEeccCcHHHHHHH
Q psy6712         165 R--KGVAISFVKSDDIRILRDI  184 (210)
Q Consensus       165 ~--~g~~~~~~~~~~~~~~~~~  184 (210)
                      .  .|.+++++...+...+..+
T Consensus       460 ~d~~G~~ii~~~~~~~~~~~~l  481 (1724)
T 4f92_B          460 YDTKGEGILITSHGELQYYLSL  481 (1724)
T ss_dssp             TCSCEEEEEEEESTTCCHHHHH
T ss_pred             CCCccEEEEEecchhHHHHHHH
Confidence            5  6999999988776554443

>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=99.88  E-value=1.7e-22  Score=174.38  Aligned_cols=158  Identities=15%  Similarity=0.074  Sum_probs=125.7

Q ss_pred             cEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCC----------------------------
Q psy6712          26 HVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLP----------------------------   77 (210)
Q Consensus        26 ~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~----------------------------   77 (210)
                      .+-+.|.+.+...+... ..+++++++|+||||++ +.++...+..+...++                            
T Consensus       256 ~i~~~t~~~l~~~l~~~-~~l~~~~~iViDEah~~-~~~~~~~~~~i~~~l~~~~~q~il~SAT~~~~~~~~~~~~~~~~  333 (618)
T 2whx_A          256 IVDLMCHATFTTRLLSS-TRVPNYNLIVMDEAHFT-DPCSVAARGYISTRVEMGEAAAIFMTATPPGSTDPFPQSNSPIE  333 (618)
T ss_dssp             CEEEEEHHHHHHHHHHC-SSCCCCSEEEEESTTCC-SHHHHHHHHHHHHHHHHTSCEEEEECSSCTTCCCSSCCCSSCEE
T ss_pred             eEEEEChHHHHHHHhcc-ccccCCeEEEEECCCCC-CccHHHHHHHHHHHhcccCccEEEEECCCchhhhhhhccCCcee
Confidence            34455656555544433 34789999999999998 5555555554444321                            


Q ss_pred             ------------------------------CchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEec
Q psy6712          78 ------------------------------PATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTD  127 (210)
Q Consensus        78 ------------------------------~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~  127 (210)
                                                    ....++.+++.|++.++++..+||+    +|.++++.|++|+.+|||||+
T Consensus       334 ~v~~~~~~~~~~~ll~~l~~~~~~~LVF~~s~~~a~~l~~~L~~~g~~v~~lhg~----~R~~~l~~F~~g~~~VLVaTd  409 (618)
T 2whx_A          334 DIEREIPERSWNTGFDWITDYQGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRK----TFDTEYPKTKLTDWDFVVTTD  409 (618)
T ss_dssp             EEECCCCSSCCSSSCHHHHHCCSCEEEECSSHHHHHHHHHHHHHTTCCEEEECTT----THHHHTTHHHHSCCSEEEECG
T ss_pred             eecccCCHHHHHHHHHHHHhCCCCEEEEECChhHHHHHHHHHHHcCCcEEEEChH----HHHHHHHhhcCCCcEEEEECc
Confidence                                          1111899999999999999999985    788899999999999999999


Q ss_pred             CccccCCCCCCcEE--------------------EEecCCCChhHHHHhhhhhcCCCC-ceeEEEEec---cCcHHHHHH
Q psy6712         128 VWARGIDVQQVSLV--------------------INYDLPNNRELYIHRIGRSGRFGR-KGVAISFVK---SDDIRILRD  183 (210)
Q Consensus       128 ~~~~g~d~~~~~~v--------------------i~~~~p~s~~~~~q~~GR~gR~g~-~g~~~~~~~---~~~~~~~~~  183 (210)
                      ++++|+|+| +++|                    |++++|.+..+|+||+||+||.|. .|.+++|+.   +.+...++.
T Consensus       410 v~~rGiDi~-v~~VId~g~~~~P~~~~~~~~~~~i~~d~P~s~~~yiQR~GRaGR~g~~~G~ai~l~~~~~~~d~~~l~~  488 (618)
T 2whx_A          410 ISEMGANFR-AGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDPLKNDEDHAHW  488 (618)
T ss_dssp             GGGTTCCCC-CSEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTTCHHH
T ss_pred             HHHcCcccC-ceEEEECcceecceecccCCCceEEcccccCCHHHHHHhccccCCCCCCCCeEEEEccCCchhhHHHHHH
Confidence            999999997 8888                    788889999999999999999965 899999997   777778888


Q ss_pred             HHHHhcC
Q psy6712         184 IEQYYST  190 (210)
Q Consensus       184 ~~~~~~~  190 (210)
                      +++.+..
T Consensus       489 le~~i~l  495 (618)
T 2whx_A          489 TEAKMLL  495 (618)
T ss_dssp             HHHHHHH
T ss_pred             HHhHhcc
Confidence            8887644

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A

Probab=99.87  E-value=4.4e-22  Score=166.47  Aligned_cols=145  Identities=17%  Similarity=0.140  Sum_probs=116.5

Q ss_pred             CCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHH-------------------------------
Q psy6712          24 GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDV-------------------------------   72 (210)
Q Consensus        24 ~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i-------------------------------   72 (210)
                      +..|.++|++.+...+.+. ..+++++++|+||||++ +..+......+                               
T Consensus        87 ~~~i~~~t~~~l~~~l~~~-~~l~~~~~iViDEah~~-~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~  164 (451)
T 2jlq_A           87 REIVDLMCHATFTTRLLSS-TRVPNYNLIVMDEAHFT-DPCSVAARGYISTRVEMGEAAAIFMTATPPGSTDPFPQSNSP  164 (451)
T ss_dssp             SCCEEEEEHHHHHHHHHHC-SCCCCCSEEEEETTTCC-SHHHHHHHHHHHHHHHTTSCEEEEECSSCTTCCCSSCCCSSC
T ss_pred             CceEEEEChHHHHHHhhCc-ccccCCCEEEEeCCccC-CcchHHHHHHHHHhhcCCCceEEEEccCCCccchhhhcCCCc
Confidence            4468899999988877654 55789999999999976 22211111111                               


Q ss_pred             ---------------------------HhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEE
Q psy6712          73 ---------------------------YRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLIT  125 (210)
Q Consensus        73 ---------------------------~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~  125 (210)
                                                 +.|++....++.+++.|++.++.+..+|+++.    .++++.|++|+.+||||
T Consensus       165 ~~~~~~~~p~~~~~~~~~~l~~~~~~~lVF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~----~~~~~~f~~g~~~vLVa  240 (451)
T 2jlq_A          165 IEDIEREIPERSWNTGFDWITDYQGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRKTF----DTEYPKTKLTDWDFVVT  240 (451)
T ss_dssp             EEEEECCCCSSCCSSSCHHHHHCCSCEEEECSSHHHHHHHHHHHHTTTCCEEEECTTTH----HHHGGGGGSSCCSEEEE
T ss_pred             eEecCccCCchhhHHHHHHHHhCCCCEEEEcCCHHHHHHHHHHHHHcCCeEEECCHHHH----HHHHHhhccCCceEEEE
Confidence                                       11222222289999999999999999999864    57899999999999999


Q ss_pred             ecCccccCCCCCCcEEEEec--------------------CCCChhHHHHhhhhhcCCCC-ceeEEEEecc
Q psy6712         126 TDVWARGIDVQQVSLVINYD--------------------LPNNRELYIHRIGRSGRFGR-KGVAISFVKS  175 (210)
Q Consensus       126 T~~~~~g~d~~~~~~vi~~~--------------------~p~s~~~~~q~~GR~gR~g~-~g~~~~~~~~  175 (210)
                      |+++++|+|+|+ ++||+||                    .|.+..+|+||+||+||.|. .|.++++...
T Consensus       241 T~v~~~GiDip~-~~VI~~~~~~~~~~d~~~~~~l~~~~~~p~s~~~y~Qr~GRaGR~g~~~g~~~~~~~~  310 (451)
T 2jlq_A          241 TDISEMGANFRA-GRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGD  310 (451)
T ss_dssp             CGGGGSSCCCCC-SEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSC
T ss_pred             CCHHHhCcCCCC-CEEEECCCcccccccccccceeeecccccCCHHHHHHhccccCCCCCCCccEEEEeCC
Confidence            999999999999 9999998                    99999999999999999998 7888888754

>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=99.87  E-value=1.4e-22  Score=178.81  Aligned_cols=154  Identities=18%  Similarity=0.303  Sum_probs=122.8

Q ss_pred             CCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhH-Hhccc-hHHHHHHHHh--------------------------
Q psy6712          23 YGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADE-MLNKG-FKEQIYDVYR--------------------------   74 (210)
Q Consensus        23 ~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~-l~~~~-~~~~~~~i~~--------------------------   74 (210)
                      .+.+|+++|||++.+.+... ..+.+++++|+||+|. .++.. ....+..+..                          
T Consensus       184 ~~~~I~v~T~G~l~r~l~~~-~~l~~~~~lIlDEah~R~ld~d~~~~~l~~l~~~~~~~~iIl~SAT~~~~~l~~~~~~~  262 (773)
T 2xau_A          184 NKTILKYMTDGMLLREAMED-HDLSRYSCIILDEAHERTLATDILMGLLKQVVKRRPDLKIIIMSATLDAEKFQRYFNDA  262 (773)
T ss_dssp             TTCSEEEEEHHHHHHHHHHS-TTCTTEEEEEECSGGGCCHHHHHHHHHHHHHHHHCTTCEEEEEESCSCCHHHHHHTTSC
T ss_pred             CCCCEEEECHHHHHHHHhhC-ccccCCCEEEecCccccccchHHHHHHHHHHHHhCCCceEEEEeccccHHHHHHHhcCC
Confidence            36789999999999877664 4589999999999996 44321 1111111111                          


Q ss_pred             ----------------------------------------------hCCCchhHHHHHHHHHh-----------cCceEE
Q psy6712          75 ----------------------------------------------YLPPATQVDWLTEKMRE-----------ANFTVS   97 (210)
Q Consensus        75 ----------------------------------------------~~~~~~~~~~l~~~l~~-----------~~~~~~   97 (210)
                                                                    |++....++.+++.|.+           .++.+.
T Consensus       263 ~vi~v~gr~~pv~~~~~~~~~~~~~~~~l~~l~~~~~~~~~g~iLVF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~~v~  342 (773)
T 2xau_A          263 PLLAVPGRTYPVELYYTPEFQRDYLDSAIRTVLQIHATEEAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVY  342 (773)
T ss_dssp             CEEECCCCCCCEEEECCSSCCSCHHHHHHHHHHHHHHHSCSCEEEEECSCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEE
T ss_pred             CcccccCcccceEEEEecCCchhHHHHHHHHHHHHHHhcCCCCEEEECCCHHHHHHHHHHHHHHHHhhcccccCCCeEEE
Confidence                                                          12222226677777764           578999


Q ss_pred             EecCCCCHhHHHHHHHHHh-----cCCCcEEEEecCccccCCCCCCcEEEEecC------------------CCChhHHH
Q psy6712          98 SMHGDMPQKERDGIMKEFR-----SGTSRVLITTDVWARGIDVQQVSLVINYDL------------------PNNRELYI  154 (210)
Q Consensus        98 ~~~~~~~~~~r~~~~~~f~-----~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~------------------p~s~~~~~  154 (210)
                      .+||+|+.++|..+++.|.     +|+.+|||||+++++|+|+|++++||++++                  |.|..+|.
T Consensus       343 ~lhg~l~~~eR~~v~~~f~~~~~~~g~~kVlVAT~iae~GidIp~v~~VId~g~~k~~~yd~~~g~~~L~~~p~S~~s~~  422 (773)
T 2xau_A          343 PLYGSLPPHQQQRIFEPAPESHNGRPGRKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQ  422 (773)
T ss_dssp             EECTTCCHHHHGGGGSCCCCCSSSSCCEEEEEECTHHHHTCCCTTEEEEEECSEEEEEEEETTTTEEEEEEEECCHHHHH
T ss_pred             EeCCCCCHHHHHHHHhhcccccCCCCceEEEEeCcHHHhCcCcCCeEEEEeCCCccceeeccccCccccccccCCHHHHH
Confidence            9999999999999999999     999999999999999999999999999877                  88999999


Q ss_pred             HhhhhhcCCCCceeEEEEeccCcH
Q psy6712         155 HRIGRSGRFGRKGVAISFVKSDDI  178 (210)
Q Consensus       155 q~~GR~gR~g~~g~~~~~~~~~~~  178 (210)
                      ||+|||||. ..|.|+.++++.+.
T Consensus       423 QR~GRaGR~-~~G~~~~l~~~~~~  445 (773)
T 2xau_A          423 QRAGRAGRT-RPGKCFRLYTEEAF  445 (773)
T ss_dssp             HHHHGGGSS-SSEEEEESSCHHHH
T ss_pred             hhccccCCC-CCCEEEEEecHHHh
Confidence            999999999 88999999976543

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.87  E-value=2.8e-23  Score=180.55  Aligned_cols=102  Identities=21%  Similarity=0.211  Sum_probs=91.7

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEE------------------
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVIN------------------  143 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~------------------  143 (210)
                      ++.+++.|++.++++..+||+    +|.++++.|++|+.+|||||+++++|+|+| +++||+                  
T Consensus       423 ~e~la~~L~~~g~~v~~lHg~----eR~~v~~~F~~g~~~VLVaTdv~e~GIDip-v~~VI~~g~~~~p~vi~da~~r~~  497 (673)
T 2wv9_A          423 SNEIAQCLQRAGKRVIQLNRK----SYDTEYPKCKNGDWDFVITTDISEMGANFG-ASRVIDCRKSVKPTILDEGEGRVI  497 (673)
T ss_dssp             HHHHHHHHHTTTCCEEEECSS----SHHHHGGGGGTCCCSEEEECGGGGTTCCCC-CSEEEECCEECCEEEECSTTCEEE
T ss_pred             HHHHHHHHHhCCCeEEEeChH----HHHHHHHHHHCCCceEEEECchhhcceeeC-CcEEEECCCcccceeeecccccce
Confidence            899999999999999999994    789999999999999999999999999999 999998                  


Q ss_pred             --ecCCCChhHHHHhhhhhcCC-CCceeEEEEe---ccCcHHHHHHHHHHh
Q psy6712         144 --YDLPNNRELYIHRIGRSGRF-GRKGVAISFV---KSDDIRILRDIEQYY  188 (210)
Q Consensus       144 --~~~p~s~~~~~q~~GR~gR~-g~~g~~~~~~---~~~~~~~~~~~~~~~  188 (210)
                        |++|.+..+|.||+||+||. |+.|.|++|+   .+.+...++.++..+
T Consensus       498 ll~d~P~s~~~y~Qr~GRaGR~~g~~G~ai~l~~~~~~~d~~~l~~ie~~~  548 (673)
T 2wv9_A          498 LSVPSAITSASAAQRRGRVGRNPSQIGDEYHYGGGTSEDDTMLAHWTEAKI  548 (673)
T ss_dssp             ECCSEECCHHHHHHHHTTSSCCSSCCCEEEEECSCCCCCCTTBHHHHHHHH
T ss_pred             ecccCCCCHHHHHHHhhccCCCCCCCCEEEEEEecCChhHHHHHHHHHHHH
Confidence              67899999999999999999 7899999996   466666666666655

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A

Probab=99.87  E-value=6.3e-23  Score=171.90  Aligned_cols=145  Identities=19%  Similarity=0.205  Sum_probs=112.1

Q ss_pred             cEEEEChHHHHHHHHhcCccCCCccEEEechhhH-----HhccchHHHHHH-----------------------------
Q psy6712          26 HVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADE-----MLNKGFKEQIYD-----------------------------   71 (210)
Q Consensus        26 ~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~-----l~~~~~~~~~~~-----------------------------   71 (210)
                      -+.+.|.+.+...+.+. ..+++++++|+||||.     ++..++......                             
T Consensus        91 ~i~~~~~~~l~~~l~~~-~~l~~~~~iViDEaH~~~~~~~~~~~~~~~~~~~~~~~~il~SAT~~~~~~~~~~~~~pi~~  169 (459)
T 2z83_A           91 IVDVMCHATLTHRLMSP-NRVPNYNLFVMDEAHFTDPASIAARGYIATKVELGEAAAIFMTATPPGTTDPFPDSNAPIHD  169 (459)
T ss_dssp             SEEEEEHHHHHHHHHSC-C-CCCCSEEEESSTTCCSHHHHHHHHHHHHHHHTTSCEEEEECSSCTTCCCSSCCCSSCEEE
T ss_pred             EEEEEchHHHHHHhhcc-ccccCCcEEEEECCccCCchhhHHHHHHHHHhccCCccEEEEEcCCCcchhhhccCCCCeEE
Confidence            35566766665544433 4578999999999998     555554433221                             


Q ss_pred             -----------------------HHhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecC
Q psy6712          72 -----------------------VYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDV  128 (210)
Q Consensus        72 -----------------------i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~  128 (210)
                                             ++.|++....++.+++.|+..++.+..+|++    +|.+++++|++|+.+|||||++
T Consensus       170 ~~~~~~~~~~~~~~~~l~~~~~~~LVF~~s~~~~~~l~~~L~~~g~~v~~lh~~----~R~~~~~~f~~g~~~iLVaT~v  245 (459)
T 2z83_A          170 LQDEIPDRAWSSGYEWITEYAGKTVWFVASVKMGNEIAMCLQRAGKKVIQLNRK----SYDTEYPKCKNGDWDFVITTDI  245 (459)
T ss_dssp             EECCCCSSCCSSCCHHHHHCCSCEEEECSCHHHHHHHHHHHHHTTCCEEEESTT----CCCCCGGGSSSCCCSEEEESSC
T ss_pred             ecccCCcchhHHHHHHHHhcCCCEEEEeCChHHHHHHHHHHHhcCCcEEecCHH----HHHHHHhhccCCCceEEEECCh
Confidence                                   1112222222899999999999999999995    6778899999999999999999


Q ss_pred             ccccCCCCCCcEEEE--------------------ecCCCChhHHHHhhhhhcCCCC-ceeEEEEeccC
Q psy6712         129 WARGIDVQQVSLVIN--------------------YDLPNNRELYIHRIGRSGRFGR-KGVAISFVKSD  176 (210)
Q Consensus       129 ~~~g~d~~~~~~vi~--------------------~~~p~s~~~~~q~~GR~gR~g~-~g~~~~~~~~~  176 (210)
                      +++|+|+|+ ++||+                    |++|.+..+|+||+||+||.|. .|.+++|+.+.
T Consensus       246 ~~~GiDip~-~~VI~~G~~~~~~~~~~~~~~~~~~~d~p~s~~~~~QR~GRaGR~g~~~G~~~~~~~~~  313 (459)
T 2z83_A          246 SEMGANFGA-SRVIDCRKSVKPTILEEGEGRVILGNPSPITSASAAQRRGRVGRNPNQVGDEYHYGGAT  313 (459)
T ss_dssp             C---CCCSC-SEEEECCEECCEEEECSSSCEEEECSCEECCHHHHHHHHTTSSCCTTCCCEEEEECSCC
T ss_pred             HHhCeecCC-CEEEECCcccccccccccccccccccCCCCCHHHHHHhccccCCCCCCCCeEEEEEccc
Confidence            999999999 99999                    7799999999999999999997 89999999874

>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=1.1e-21  Score=170.62  Aligned_cols=119  Identities=23%  Similarity=0.363  Sum_probs=102.6

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecC-----CCChhHHHHh
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDL-----PNNRELYIHR  156 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~-----p~s~~~~~q~  156 (210)
                      ++.+++.|.+.|+++..+||+|++.+|.+++++|++|+++|||||+.+++|+|+|++++||++|.     |.+..+|+||
T Consensus       458 ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~~l~~GlDip~v~lVi~~d~d~~G~p~s~~~~iQr  537 (661)
T 2d7d_A          458 SEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQT  537 (661)
T ss_dssp             HHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESCCCSTTCCCTTEEEEEETTTTCCTTTTSHHHHHHH
T ss_pred             HHHHHHHHHhcCCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecchhhCCcccCCCCEEEEeCcccccCCCCHHHHHHH
Confidence            88899999999999999999999999999999999999999999999999999999999999997     9999999999


Q ss_pred             hhhhcCCCCceeEEEEeccCcHHHHHH---------HHHHhcCccccccCCccc
Q psy6712         157 IGRSGRFGRKGVAISFVKSDDIRILRD---------IEQYYSTQIDEMPMNGKR  201 (210)
Q Consensus       157 ~GR~gR~g~~g~~~~~~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~~  201 (210)
                      +||+||. ..|.+++++++.+..+.+.         +++.++......|.+..+
T Consensus       538 ~GRagR~-~~G~~i~~~~~~~~~~~~~i~~~~~~r~i~~~~~~~~~~~p~~~~~  590 (661)
T 2d7d_A          538 IGRAARN-AEGRVIMYADKITKSMEIAINETKRRREQQERFNEEHGITPKTINK  590 (661)
T ss_dssp             HHTTTTS-TTCEEEEECSSCCHHHHHHHHHHHHHHHHHHHHHHHHTCCCCCCCC
T ss_pred             hCcccCC-CCCEEEEEEeCCCHHHHHHHHHHHHHHHHHHHhhhhcCCCCCchhh
Confidence            9999998 7899999998876554443         334455555555554444

>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=99.86  E-value=1.1e-21  Score=164.85  Aligned_cols=82  Identities=23%  Similarity=0.432  Sum_probs=73.7

Q ss_pred             eEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCCc-e--eEEE
Q psy6712          95 TVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRK-G--VAIS  171 (210)
Q Consensus        95 ~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~~-g--~~~~  171 (210)
                      .+..+||+++..+|.+++++|++|+.++||+|+++++|+|+|++++||++++|+++..|.||+||+||.|.. +  .++.
T Consensus       370 ~~~~~~g~~~~~~R~~~~~~F~~g~~~vLv~T~~~~~Gldlp~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~k~~~~i~~  449 (472)
T 2fwr_A          370 LIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYE  449 (472)
T ss_dssp             TCCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSSCSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTTCCEEEEE
T ss_pred             CcceeeCCCCHHHHHHHHHHHhCCCCCEEEEcCchhcCcccccCcEEEEECCCCCHHHHHHHHhhccCCCCCCceEEEEE
Confidence            366799999999999999999999999999999999999999999999999999999999999999999854 3  4445


Q ss_pred             EeccC
Q psy6712         172 FVKSD  176 (210)
Q Consensus       172 ~~~~~  176 (210)
                      ++...
T Consensus       450 lv~~~  454 (472)
T 2fwr_A          450 LISRG  454 (472)
T ss_dssp             EEECS
T ss_pred             EEeCC
Confidence            66543

>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=99.86  E-value=4.3e-21  Score=167.05  Aligned_cols=103  Identities=23%  Similarity=0.380  Sum_probs=94.4

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecC-----CCChhHHHHh
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDL-----PNNRELYIHR  156 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~-----p~s~~~~~q~  156 (210)
                      ++.+++.|.+.++++..+||+|++.+|.+++++|+.|+++|||||+.+++|+|+|++++||++|.     |.+..+|+||
T Consensus       452 ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~~l~~GlDip~v~lVI~~d~d~~G~p~s~~~~iQr  531 (664)
T 1c4o_A          452 AEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQT  531 (664)
T ss_dssp             HHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEEEEEETTTTSCSGGGSHHHHHHH
T ss_pred             HHHHHHHHHhcCCCceeecCCCCHHHHHHHHHHhhcCCceEEEccChhhcCccCCCCCEEEEeCCcccCCCCCHHHHHHH
Confidence            78899999999999999999999999999999999999999999999999999999999999997     8999999999


Q ss_pred             hhhhcCCCCceeEEEEeccCcHHHHHHHH
Q psy6712         157 IGRSGRFGRKGVAISFVKSDDIRILRDIE  185 (210)
Q Consensus       157 ~GR~gR~g~~g~~~~~~~~~~~~~~~~~~  185 (210)
                      +||+||. ..|.+++++++.+....+.++
T Consensus       532 ~GRagR~-~~G~~i~~~~~~~~~~~~~i~  559 (664)
T 1c4o_A          532 IGRAARN-ARGEVWLYADRVSEAMQRAIE  559 (664)
T ss_dssp             HGGGTTS-TTCEEEEECSSCCHHHHHHHH
T ss_pred             HCccCcC-CCCEEEEEEcCCCHHHHHHHH
Confidence            9999998 479999999887665444433

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.84  E-value=3.9e-20  Score=153.82  Aligned_cols=143  Identities=15%  Similarity=0.088  Sum_probs=109.4

Q ss_pred             CcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhh-----------------------------
Q psy6712          25 QHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRY-----------------------------   75 (210)
Q Consensus        25 ~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~-----------------------------   75 (210)
                      .-+.+.|.+.+...+.. ...+++++++|+||+|++ +.++......+...                             
T Consensus        71 ~~~~~~~~~~l~~~l~~-~~~~~~l~~vViDEaH~~-~~~~~~~~~~l~~~~~~~~~~~l~~SAT~~~~~~~~~~~~~~i  148 (431)
T 2v6i_A           71 EIVDFMCHSTFTMKLLQ-GVRVPNYNLYIMDEAHFL-DPASVAARGYIETRVSMGDAGAIFMTATPPGTTEAFPPSNSPI  148 (431)
T ss_dssp             CSEEEEEHHHHHHHHHH-TCCCCCCSEEEEESTTCC-SHHHHHHHHHHHHHHHTTSCEEEEEESSCTTCCCSSCCCSSCC
T ss_pred             ceEEEEchHHHHHHHhc-CccccCCCEEEEeCCccC-CccHHHHHHHHHHHhhCCCCcEEEEeCCCCcchhhhcCCCCce
Confidence            34566788877665555 556899999999999997 32222222222211                             


Q ss_pred             -----------------------------CCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEe
Q psy6712          76 -----------------------------LPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITT  126 (210)
Q Consensus        76 -----------------------------~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T  126 (210)
                                                   ++....++.+++.|++.++++..+||+    +|.+++++|++|+.+|||||
T Consensus       149 ~~~~~~~~~~~~~~~~~~l~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~v~~lhg~----~r~~~~~~f~~g~~~vLVaT  224 (431)
T 2v6i_A          149 IDEETRIPDKAWNSGYEWITEFDGRTVWFVHSIKQGAEIGTCLQKAGKKVLYLNRK----TFESEYPKCKSEKWDFVITT  224 (431)
T ss_dssp             EEEECCCCSSCCSSCCHHHHSCSSCEEEECSSHHHHHHHHHHHHHTTCCEEEESTT----THHHHTTHHHHSCCSEEEEC
T ss_pred             eeccccCCHHHHHHHHHHHHcCCCCEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCc----cHHHHHHhhcCCCCeEEEEC
Confidence                                         111111889999999999999999997    57889999999999999999


Q ss_pred             cCccccCCCCCCcE-----------------EEEecCCCChhHHHHhhhhhcCCCC-ceeEEEEec
Q psy6712         127 DVWARGIDVQQVSL-----------------VINYDLPNNRELYIHRIGRSGRFGR-KGVAISFVK  174 (210)
Q Consensus       127 ~~~~~g~d~~~~~~-----------------vi~~~~p~s~~~~~q~~GR~gR~g~-~g~~~~~~~  174 (210)
                      +++++|+|+| +.+                 +|+++.|.+..+|.||+||+||.|. .+.++++..
T Consensus       225 ~v~e~GiDip-~~~VI~~g~~~~~v~d~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~~~~~~~~~  289 (431)
T 2v6i_A          225 DISEMGANFK-ADRVIDPRKTIKPILLDGRVSMQGPIAITPASAAQRRGRIGRNPEKLGDIYAYSG  289 (431)
T ss_dssp             GGGGTSCCCC-CSEEEECCEEEEEEEETTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCCEEEECS
T ss_pred             chHHcCcccC-CcEEEecCccccceecccceeecccccCCHHHHHHhhhccCCCCCCCCeEEEEcC
Confidence            9999999999 554                 6788999999999999999999985 555666653

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.83  E-value=2e-20  Score=161.26  Aligned_cols=83  Identities=17%  Similarity=0.278  Sum_probs=71.7

Q ss_pred             HHHHHHHHHhcCc--------eEEEecCCCCHhHHHHHHHHHhcCCCc---EEEEecCccccCCCCCCcEEEEecCCCCh
Q psy6712          82 VDWLTEKMREANF--------TVSSMHGDMPQKERDGIMKEFRSGTSR---VLITTDVWARGIDVQQVSLVINYDLPNNR  150 (210)
Q Consensus        82 ~~~l~~~l~~~~~--------~~~~~~~~~~~~~r~~~~~~f~~g~~~---ilv~T~~~~~g~d~~~~~~vi~~~~p~s~  150 (210)
                      ++.+++.|.+.+.        .+..+||.++. +|++++++|++|+.+   |+|||+++++|+|+|++++||++++|+|.
T Consensus       452 a~~l~~~L~~~~~~~~~~~~~~~~~i~g~~~~-~r~~~l~~F~~~~~~~~~ilvtt~~l~~GiDip~v~~Vi~~~~~~s~  530 (590)
T 3h1t_A          452 ADEMRRALNNLNSDLSRKHPDYVARVTSEEGK-IGKGHLSRFQELETSTPVILTTSQLLTTGVDAPTCKNVVLARVVNSM  530 (590)
T ss_dssp             HHHHHHHHHHHTHHHHTTCTTSEEECSSTTHH-HHHHHHHHHHCTTCCCCCEEEESSTTTTTCCCTTEEEEEEESCCCCH
T ss_pred             HHHHHHHHHHhhhhhhccCCCeEEEEeCCChH-HHHHHHHHHhCCCCCCCEEEEECChhhcCccchheeEEEEEecCCCh
Confidence            6666666655433        27788999864 799999999998876   88999999999999999999999999999


Q ss_pred             hHHHHhhhhhcCCCC
Q psy6712         151 ELYIHRIGRSGRFGR  165 (210)
Q Consensus       151 ~~~~q~~GR~gR~g~  165 (210)
                      ..|.||+||+||.+.
T Consensus       531 ~~~~Q~iGR~~R~~~  545 (590)
T 3h1t_A          531 SEFKQIVGRGTRLRE  545 (590)
T ss_dssp             HHHHHHHTTSCCCBG
T ss_pred             HHHHHHHhhhcccCc
Confidence            999999999999875

>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex, hydrolase/DNA complex complex; 3.00A {Sulfolobus solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A

Probab=99.80  E-value=2.2e-19  Score=151.75  Aligned_cols=95  Identities=19%  Similarity=0.319  Sum_probs=77.8

Q ss_pred             HHHHHHHHHhc-CceEEEecCCCCHhHHHHHHHHHhcC-CCc-EEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhh
Q psy6712          82 VDWLTEKMREA-NFTVSSMHGDMPQKERDGIMKEFRSG-TSR-VLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIG  158 (210)
Q Consensus        82 ~~~l~~~l~~~-~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~-ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~G  158 (210)
                      ++.+.+.|... ++.+..+||+|+..+|.+++++|+++ +.+ +|++|+++++|+|+|.+++||++|+|+++..|.|++|
T Consensus       354 ~~~l~~~l~~~~~~~~~~~~g~~~~~~R~~~~~~F~~~~~~~vil~st~~~~~Glnl~~~~~vi~~d~~~~~~~~~Q~~g  433 (500)
T 1z63_A          354 GKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATD  433 (500)
T ss_dssp             HHHHHHHHHHHHTCCCCEEETTSCHHHHHHHHHHHHHCTTCCCCEEECCCC-CCCCCTTCSEEEESSCCSCC---CHHHH
T ss_pred             HHHHHHHHHHhhCCCeEEEECCCCHHHHHHHHHHhcCCCCCCEEEEecccccCCCchhhCCEEEEeCCCCCcchHHHHHH
Confidence            45555666554 88899999999999999999999998 555 7899999999999999999999999999999999999


Q ss_pred             hhcCCCCceeE--EEEeccC
Q psy6712         159 RSGRFGRKGVA--ISFVKSD  176 (210)
Q Consensus       159 R~gR~g~~g~~--~~~~~~~  176 (210)
                      |++|.|+.+.+  +.++...
T Consensus       434 R~~R~Gq~~~v~v~~lv~~~  453 (500)
T 1z63_A          434 RVYRIGQTRNVIVHKLISVG  453 (500)
T ss_dssp             TTTTTTTTSCEEEEEEEETT
T ss_pred             HHHHcCCCCeeEEEEEEeCC
Confidence            99999986554  5555554

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=99.79  E-value=1.6e-18  Score=154.02  Aligned_cols=107  Identities=21%  Similarity=0.343  Sum_probs=90.2

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCc---EEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhh
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSR---VLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIG  158 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~---ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~G  158 (210)
                      ++.+.+.|...++++..+||+++..+|..++++|++++..   +|++|.+++.|+|++.+++||+||+||++..+.|++|
T Consensus       585 ld~L~~~L~~~g~~~~~i~G~~~~~eR~~~i~~F~~~~~~~~v~LlSt~agg~GlNL~~a~~VI~~D~~wnp~~~~Qa~g  664 (800)
T 3mwy_W          585 LDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRAGGLGINLMTADTVVIFDSDWNPQADLQAMA  664 (800)
T ss_dssp             HHHHHHHHHHHTCCCEEESTTSCHHHHHHHHHTTSSTTCSCCCEEEEHHHHTTTCCCTTCCEEEESSCCSCSHHHHHHHT
T ss_pred             HHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhCCCCCceEEEEecccccCCCCccccceEEEecCCCChhhHHHHHH
Confidence            6667777777899999999999999999999999986654   8999999999999999999999999999999999999


Q ss_pred             hhcCCCCcee--EEEEeccC--cHHHHHHHHHHh
Q psy6712         159 RSGRFGRKGV--AISFVKSD--DIRILRDIEQYY  188 (210)
Q Consensus       159 R~gR~g~~g~--~~~~~~~~--~~~~~~~~~~~~  188 (210)
                      |++|.|+...  ++-|+...  |...++..++.+
T Consensus       665 R~~RiGQ~k~V~Vyrlv~~~TiEe~i~~~~~~K~  698 (800)
T 3mwy_W          665 RAHRIGQKNHVMVYRLVSKDTVEEEVLERARKKM  698 (800)
T ss_dssp             TTSCSSCCSCEEEEEEEETTSHHHHHHHHHHHHT
T ss_pred             HHHhcCCCceEEEEEEecCCCHHHHHHHHHHHHH
Confidence            9999998544  45566554  455555554443

>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=99.78  E-value=9.6e-18  Score=144.20  Aligned_cols=95  Identities=23%  Similarity=0.348  Sum_probs=84.5

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCC--------CCcEEEEecCCCChhHH
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQ--------QVSLVINYDLPNNRELY  153 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~--------~~~~vi~~~~p~s~~~~  153 (210)
                      ++.+++.|.+.|+++..+||++...++..+..+++.|  .|+|||++++||+|++        +..+||+++.|.+...|
T Consensus       487 sE~Ls~~L~~~Gi~~~vLhgkq~~rE~~ii~~ag~~g--~VtVATdmAgRGtDI~lg~~V~~~GglhVInte~Pes~r~y  564 (822)
T 3jux_A          487 SELLSSMLKKKGIPHQVLNAKYHEKEAEIVAKAGQKG--MVTIATNMAGRGTDIKLGPGVAELGGLCIIGTERHESRRID  564 (822)
T ss_dssp             HHHHHHHHHTTTCCCEEECSCHHHHHHHHHHHHHSTT--CEEEEETTTTTTCCCCCCTTTTTTTSCEEEESSCCSSHHHH
T ss_pred             HHHHHHHHHHCCCCEEEeeCCchHHHHHHHHhCCCCC--eEEEEcchhhCCcCccCCcchhhcCCCEEEecCCCCCHHHH
Confidence            8889999999999999999996666666566666655  6999999999999997        55699999999999999


Q ss_pred             HHhhhhhcCCCCceeEEEEeccCcH
Q psy6712         154 IHRIGRSGRFGRKGVAISFVKSDDI  178 (210)
Q Consensus       154 ~q~~GR~gR~g~~g~~~~~~~~~~~  178 (210)
                      .||+||+||.|.+|.+++|++..|.
T Consensus       565 ~qriGRTGRqG~~G~a~~fvsleD~  589 (822)
T 3jux_A          565 NQLRGRAGRQGDPGESIFFLSLEDD  589 (822)
T ss_dssp             HHHHTTSSCSSCCCEEEEEEETTSH
T ss_pred             HHhhCccccCCCCeeEEEEechhHH
Confidence            9999999999999999999998763

>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=99.76  E-value=2.1e-17  Score=143.63  Aligned_cols=103  Identities=17%  Similarity=0.294  Sum_probs=86.1

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCc---EEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhh
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSR---VLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIG  158 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~---ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~G  158 (210)
                      ++.+.+.|...++.+..+||+|+..+|.+++++|++++..   +|++|.++++|+|++.+++||+||+||++..+.|++|
T Consensus       429 ~~~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~v~L~st~a~g~Glnl~~a~~Vi~~d~~wnp~~~~Qa~g  508 (644)
T 1z3i_X          429 LDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLVMFDPDWNPANDEQAMA  508 (644)
T ss_dssp             HHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGGGSCTTCCCTTEEEEEECSCCSSHHHHHHHHT
T ss_pred             HHHHHHHHHHCCCCEEEEeCCCCHHHHHHHHHHhcCCCCCcEEEEEecccccCCcccccCCEEEEECCCCCccHHHHHHH
Confidence            4555666666788999999999999999999999998764   8999999999999999999999999999999999999


Q ss_pred             hhcCCCCcee--EEEEeccC--cHHHHHHH
Q psy6712         159 RSGRFGRKGV--AISFVKSD--DIRILRDI  184 (210)
Q Consensus       159 R~gR~g~~g~--~~~~~~~~--~~~~~~~~  184 (210)
                      |++|.|+...  ++-++...  |...++..
T Consensus       509 R~~R~Gq~~~v~v~~lv~~~tiEe~i~~~~  538 (644)
T 1z3i_X          509 RVWRDGQKKTCYIYRLLSTGTIEEKILQRQ  538 (644)
T ss_dssp             TSSSTTCCSCEEEEEEEETTSHHHHHHHHH
T ss_pred             hhhhcCCCCceEEEEEEECCCHHHHHHHHH
Confidence            9999998654  45556554  33344433

>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=99.74  E-value=7.1e-18  Score=152.31  Aligned_cols=114  Identities=25%  Similarity=0.326  Sum_probs=96.8

Q ss_pred             hCCCchhHHHHHHHHHh-cCceEEEecCCCCHhHHHHHHHHHhcCC--CcEEEEecCccccCCCCCCcEEEEecCCCChh
Q psy6712          75 YLPPATQVDWLTEKMRE-ANFTVSSMHGDMPQKERDGIMKEFRSGT--SRVLITTDVWARGIDVQQVSLVINYDLPNNRE  151 (210)
Q Consensus        75 ~~~~~~~~~~l~~~l~~-~~~~~~~~~~~~~~~~r~~~~~~f~~g~--~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~  151 (210)
                      |+.....++.+.+.|.+ .|+++..+||+|+..+|..+++.|++|+  +++||||+++++|+|+|++++||+||+|+++.
T Consensus       509 F~~~~~~~~~l~~~L~~~~g~~~~~lhG~~~~~~R~~~l~~F~~g~~~~~vLvaT~v~~~GlDl~~~~~VI~~d~p~~~~  588 (968)
T 3dmq_A          509 ICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEIGSEGRNFQFASHMVMFDLPFNPD  588 (968)
T ss_dssp             ECSSTHHHHHHHHHHHTTTCCCEEEECTTSCTTHHHHHHHHHHSTTSSCEEEECSCCTTCSSCCTTCCEEECSSCCSSHH
T ss_pred             EeCcHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhCCCCcccEEEecchhhcCCCcccCcEEEEecCCCCHH
Confidence            34444558999999985 5999999999999999999999999998  99999999999999999999999999999999


Q ss_pred             HHHHhhhhhcCCCCceeEEEEeccCcHHHHHHHHHHh
Q psy6712         152 LYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYY  188 (210)
Q Consensus       152 ~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~  188 (210)
                      .|.|++||+||.|+.+.++++....+....+.+.+.+
T Consensus       589 ~~~Q~~GR~~R~Gq~~~v~v~~~~~~~t~ee~i~~~~  625 (968)
T 3dmq_A          589 LLEQRIGRLDRIGQAHDIQIHVPYLEKTAQSVLVRWY  625 (968)
T ss_dssp             HHHHHHHTTSCSSSCSCCEEEEEEETTSHHHHHHHHH
T ss_pred             HHHHHhhccccCCCCceEEEEEecCCChHHHHHHHHH
Confidence            9999999999999988766665433333334455555

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=99.72  E-value=3.3e-18  Score=133.78  Aligned_cols=102  Identities=18%  Similarity=0.293  Sum_probs=76.0

Q ss_pred             hCCCchhHHHHHHHHHhc-CceEEEecCCCCHhHHHHHHHHHhcC-CCc-EEEEecCccccCCCCCCcEEEEecCCCChh
Q psy6712          75 YLPPATQVDWLTEKMREA-NFTVSSMHGDMPQKERDGIMKEFRSG-TSR-VLITTDVWARGIDVQQVSLVINYDLPNNRE  151 (210)
Q Consensus        75 ~~~~~~~~~~l~~~l~~~-~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~-ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~  151 (210)
                      |+.....++.+.+.|... |+.+..+||+++..+|..++++|+++ +.+ +|++|+++++|+|++.+++||+||+||++.
T Consensus       118 Fs~~~~~~~~l~~~L~~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~v~L~st~~~g~Glnl~~a~~VI~~d~~wnp~  197 (271)
T 1z5z_A          118 FTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIHFDRWWNPA  197 (271)
T ss_dssp             EESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEECCTTCCCCCCTTCSEEEECSCCSCTT
T ss_pred             EeccHHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHhcCCCCCCEEEEehhhhcCCcCcccCCEEEEECCCCChh
Confidence            333444488899999875 99999999999999999999999998 677 789999999999999999999999999999


Q ss_pred             HHHHhhhhhcCCCCcee--EEEEeccC
Q psy6712         152 LYIHRIGRSGRFGRKGV--AISFVKSD  176 (210)
Q Consensus       152 ~~~q~~GR~gR~g~~g~--~~~~~~~~  176 (210)
                      .|.|++||++|.|+.+.  ++.++...
T Consensus       198 ~~~Q~~gR~~R~Gq~~~v~v~~li~~~  224 (271)
T 1z5z_A          198 VEDQATDRVYRIGQTRNVIVHKLISVG  224 (271)
T ss_dssp             TC--------------CCEEEEEEETT
T ss_pred             HHHHHHHhccccCCCCceEEEEEeeCC
Confidence            99999999999998655  45566554

>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=99.60  E-value=3.6e-14  Score=128.25  Aligned_cols=68  Identities=13%  Similarity=0.198  Sum_probs=60.9

Q ss_pred             HHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhhhhcCCCCc----eeEEEEecc
Q psy6712         107 ERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRK----GVAISFVKS  175 (210)
Q Consensus       107 ~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~GR~gR~g~~----g~~~~~~~~  175 (210)
                      .|..++++|++|++++||+|+++.+|+|.|.+ .++++|.|.+...|+|++||++|.+..    |.++.|+..
T Consensus       637 ~R~~i~~~Fk~g~i~ILIvvd~lltGfDiP~l-~tlylDkpl~~~~liQaIGRtnR~~~~~K~~G~IVdf~~~  708 (1038)
T 2w00_A          637 YYRDLAQRVKNQDIDLLIVVGMFLTGFDAPTL-NTLFVDKNLRYHGLMQAFSRTNRIYDATKTFGNIVTFRDL  708 (1038)
T ss_dssp             HHHHHHHHHHTTSSSEEEESSTTSSSCCCTTE-EEEEEESCCCHHHHHHHHHTTCCCCCTTCCSEEEEESSCC
T ss_pred             HHHHHHHHHHcCCCeEEEEcchHHhCcCcccc-cEEEEccCCCccceeehhhccCcCCCCCCCcEEEEEcccc
Confidence            37889999999999999999999999999999 678899999999999999999998753    777777753

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.48  E-value=1.3e-12  Score=114.65  Aligned_cols=59  Identities=24%  Similarity=0.387  Sum_probs=49.4

Q ss_pred             CCceEEEEEcCcchHHHHHHhcCCCcEEEEChHHH-HHHHHhcC------ccCC---CccEEEechhhHHh
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRV-FDMIRRRV------LRTR---NIKMLVLDEADEML   61 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l-~~~l~~~~------~~~~---~~~~lviDE~~~l~   61 (210)
                      +|++|.+++||.+.+.  +....++||+||||+++ .++++.+.      +.++   .+.++|+||+|.|+
T Consensus       147 lGLsv~~i~Gg~~~~~--r~~ay~~DIvyGTpgrlgfDyLrd~m~~~~~~l~~r~d~~l~~lIIDEaDsmL  215 (997)
T 2ipc_A          147 LGLSVGVIQHASTPAE--RRKAYLADVTYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAIIDEVDSIL  215 (997)
T ss_dssp             TTCCEEECCTTCCHHH--HHHHHTSSEEEEEHHHHHHHHHHHTSCSSTTTCCSCSSSSSCEEEETTHHHHT
T ss_pred             cCCeEEEEeCCCCHHH--HHHHcCCCEEEECchhhhhHHHHHhhhcchhhcccccCCCcceEEEechHHHH
Confidence            5899999999988543  33344799999999999 88888764      5677   89999999999997

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=99.39  E-value=1.1e-12  Score=100.71  Aligned_cols=99  Identities=28%  Similarity=0.509  Sum_probs=84.6

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchh
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ   81 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~   81 (210)
                      ++++..++||.+...+...+.++++|+|+||+++.+++.++...+++++++|+||||++.++++...+..++..++.   
T Consensus       130 ~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~i~~~~~~---  206 (242)
T 3fe2_A          130 RLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRP---  206 (242)
T ss_dssp             TCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHHTSCCCTTCCEEEETTHHHHHHTTCHHHHHHHHTTSCS---
T ss_pred             CceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCCcccccEEEEeCHHHHhhhCcHHHHHHHHHhCCc---
Confidence            67899999999999999999899999999999999999998889999999999999999999999999999877643   


Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHH
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEF  115 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f  115 (210)
                                 +..+..+.+.++..-+. ..+.|
T Consensus       207 -----------~~q~~~~SAT~~~~~~~-~~~~~  228 (242)
T 3fe2_A          207 -----------DRQTLMWSATWPKEVRQ-LAEDF  228 (242)
T ss_dssp             -----------SCEEEEEESCCCHHHHH-HHHHH
T ss_pred             -----------cceEEEEEeecCHHHHH-HHHHH
Confidence                       34677788888776544 33444

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=99.32  E-value=3.7e-12  Score=96.75  Aligned_cols=96  Identities=26%  Similarity=0.426  Sum_probs=76.6

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchh
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ   81 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~   81 (210)
                      ++++..++||.+...+...+.++++|+|+||+++.+++..+...+++++++|+||||++.++++...+..++..++.   
T Consensus       121 ~~~~~~~~~~~~~~~~~~~~~~~~~iiv~Tp~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~i~~~~~~---  197 (228)
T 3iuy_A          121 GLKSICIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKMLDMEFEPQIRKILLDVRP---  197 (228)
T ss_dssp             TCCEEEECC------CHHHHHSCCSEEEECHHHHHHHHHTTCCCCTTCCEEEECCHHHHHHTTCHHHHHHHHHHSCS---
T ss_pred             CceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCcCcccceEEEEECHHHHhccchHHHHHHHHHhCCc---
Confidence            67889999999999999999999999999999999999988888999999999999999999999998888866542   


Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHH
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGI  111 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~  111 (210)
                                 +..+..+.+.++..-+...
T Consensus       198 -----------~~~~l~~SAT~~~~~~~~~  216 (228)
T 3iuy_A          198 -----------DRQTVMTSATWPDTVRQLA  216 (228)
T ss_dssp             -----------SCEEEEEESCCCHHHHHHH
T ss_pred             -----------CCeEEEEEeeCCHHHHHHH
Confidence                       3467778888877655433

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=99.29  E-value=5.8e-11  Score=88.53  Aligned_cols=99  Identities=34%  Similarity=0.596  Sum_probs=81.4

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchh
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ   81 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~   81 (210)
                      ++++..++||.+..++...+.++++|+|+||+++.+.+.++...+++++++|+||||++.+.++...+..++..++.   
T Consensus       100 ~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~~~~~l~~i~~~~~~---  176 (206)
T 1vec_A          100 GAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPK---  176 (206)
T ss_dssp             SCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEETHHHHTSTTTHHHHHHHHHHSCT---
T ss_pred             CceEEEEeCCccHHHHHHhcCCCCCEEEeCHHHHHHHHHcCCcCcccCCEEEEEChHHhHhhCcHHHHHHHHHhCCc---
Confidence            57889999999999888888889999999999999999988888999999999999999998888888777765542   


Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHH
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEF  115 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f  115 (210)
                                 +..+..+.+.++...+. .++.|
T Consensus       177 -----------~~~~l~~SAT~~~~~~~-~~~~~  198 (206)
T 1vec_A          177 -----------NRQILLYSATFPLSVQK-FMNSH  198 (206)
T ss_dssp             -----------TCEEEEEESCCCHHHHH-HHHHH
T ss_pred             -----------cceEEEEEeeCCHHHHH-HHHHH
Confidence                       35677787877765433 44444

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=99.28  E-value=1.1e-11  Score=96.21  Aligned_cols=96  Identities=28%  Similarity=0.486  Sum_probs=80.2

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhc-CccCCCccEEEechhhHHhccchHHHHHHHHhhCCCch
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRR-VLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPAT   80 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~-~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~   80 (210)
                      ++++..++||.....+...+..+++|+|+||+++.+++... .+.+++++++|+||||++.++++...+..++..++.  
T Consensus       154 ~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~~~~~~~~~~~~l~~lViDEah~l~~~~~~~~l~~i~~~~~~--  231 (262)
T 3ly5_A          154 VHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPT--  231 (262)
T ss_dssp             CSCEEEECSSSCHHHHHHHHHHCCSEEEECHHHHHHHHHHCTTCCCTTCCEEEECSHHHHHHTTCHHHHHHHHHHSCS--
T ss_pred             CceEEEEECCCCHHHHHHHhcCCCCEEEEcHHHHHHHHHccCCcccccCCEEEEcChHHHhhhhHHHHHHHHHHhCCC--
Confidence            57789999999999999888889999999999999988775 477899999999999999999999998888877653  


Q ss_pred             hHHHHHHHHHhcCceEEEecCCCCHhHHHHH
Q psy6712          81 QVDWLTEKMREANFTVSSMHGDMPQKERDGI  111 (210)
Q Consensus        81 ~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~  111 (210)
                                  ...+..+.+.++.+-+...
T Consensus       232 ------------~~q~l~~SAT~~~~v~~~~  250 (262)
T 3ly5_A          232 ------------RRQTMLFSATQTRKVEDLA  250 (262)
T ss_dssp             ------------SSEEEEECSSCCHHHHHHH
T ss_pred             ------------CCeEEEEEecCCHHHHHHH
Confidence                        3467777777776655433

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=99.26  E-value=1.9e-11  Score=94.25  Aligned_cols=100  Identities=25%  Similarity=0.446  Sum_probs=82.5

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHh-cCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCch
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRR-RVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPAT   80 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~-~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~   80 (210)
                      ++++..++||.+...+...+.++++|+|+||+++.+.+.+ +.+.+++++++|+||||++.+.++...+..++..++.  
T Consensus       139 ~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~l~~~~~lViDEah~l~~~~~~~~l~~i~~~~~~--  216 (249)
T 3ber_A          139 GVQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRILNMDFETEVDKILKVIPR--  216 (249)
T ss_dssp             TCCEEEECTTSCHHHHHHHHHTCCSEEEECHHHHHHHHHHSTTCCCTTCCEEEECSHHHHHHTTCHHHHHHHHHSSCS--
T ss_pred             CeeEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCcCccccCEEEEcChhhhhccChHHHHHHHHHhCCC--
Confidence            6789999999999888888889999999999999998887 5678899999999999999999999998888876642  


Q ss_pred             hHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHh
Q psy6712          81 QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFR  116 (210)
Q Consensus        81 ~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~  116 (210)
                                  +..+..+.+.++..-+. ..+.|.
T Consensus       217 ------------~~~~l~~SAT~~~~v~~-~~~~~l  239 (249)
T 3ber_A          217 ------------DRKTFLFSATMTKKVQK-LQRAAL  239 (249)
T ss_dssp             ------------SSEEEEEESSCCHHHHH-HHHHHC
T ss_pred             ------------CCeEEEEeccCCHHHHH-HHHHHC
Confidence                        34677788888765444 444443

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19

Probab=99.25  E-value=2.3e-11  Score=93.78  Aligned_cols=104  Identities=26%  Similarity=0.463  Sum_probs=83.7

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchh
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ   81 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~   81 (210)
                      ++++..++||.+...+...+..+++|+|+||+++.+++.++.+.+++++++|+||||++.++++...+..++..+.... 
T Consensus       128 ~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~i~~~~~~~~-  206 (253)
T 1wrb_A          128 PLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEESNMPS-  206 (253)
T ss_dssp             SCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCTTCCEEEEETHHHHHHTTCHHHHHHHHHSSCCCC-
T ss_pred             CceEEEEECCCCHHHHHHHhCCCCCEEEECHHHHHHHHHcCCCChhhCCEEEEeCHHHHHhCchHHHHHHHHhhccCCC-
Confidence            5778999999999999999988999999999999999999888899999999999999999999999888887432111 


Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHh
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFR  116 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~  116 (210)
                               ..+..+..+.+.++.+-+ +..+.|.
T Consensus       207 ---------~~~~q~l~~SAT~~~~~~-~~~~~~l  231 (253)
T 1wrb_A          207 ---------GINRQTLMFSATFPKEIQ-KLAADFL  231 (253)
T ss_dssp             ---------GGGCEEEEEESSCCHHHH-HHHHHHC
T ss_pred             ---------CCCcEEEEEEEeCCHHHH-HHHHHHc
Confidence                     124567778888776543 3444443

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=99.23  E-value=7.8e-11  Score=90.03  Aligned_cols=101  Identities=49%  Similarity=0.895  Sum_probs=70.9

Q ss_pred             CceEEEEEcCcchHHHHHHhcCC-CcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCch
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYG-QHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPAT   80 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~-~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~   80 (210)
                      ++++..++||.+...+...+..+ ++|+|+||+++.+.+.++...+++++++|+||||++.++++...+..++..++   
T Consensus       126 ~~~~~~~~g~~~~~~~~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~~~~~~~~~l~~i~~~~~---  202 (237)
T 3bor_A          126 GATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLN---  202 (237)
T ss_dssp             TCCEEEECC-------------CCCSEEEECHHHHHHHHHTTSSCSTTCCEEEEESHHHHHHTTCHHHHHHHHHHSC---
T ss_pred             CceEEEEECCCchHHHHHHHhcCCCCEEEECHHHHHHHHHhCCcCcccCcEEEECCchHhhccCcHHHHHHHHHhCC---
Confidence            57788999999988888888765 89999999999999998888899999999999999999888888877775543   


Q ss_pred             hHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhc
Q psy6712          81 QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRS  117 (210)
Q Consensus        81 ~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~  117 (210)
                                 .+..+..+.+.++..-+. ..+.|..
T Consensus       203 -----------~~~~~i~~SAT~~~~~~~-~~~~~l~  227 (237)
T 3bor_A          203 -----------TSIQVVLLSATMPTDVLE-VTKKFMR  227 (237)
T ss_dssp             -----------TTCEEEEECSSCCHHHHH-HHHHHCS
T ss_pred             -----------CCCeEEEEEEecCHHHHH-HHHHHCC
Confidence                       245778888888765444 4445543

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.23  E-value=1.2e-11  Score=93.36  Aligned_cols=100  Identities=32%  Similarity=0.594  Sum_probs=81.2

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchh
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ   81 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~   81 (210)
                      ++++..++||.+...+...+..+++|+|+||+++.+.+.++...+++++++|+||||++.++++...+..++..++    
T Consensus       104 ~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~~~~~~~~~l~~i~~~~~----  179 (219)
T 1q0u_A          104 MIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMGFITDVDQIAARMP----  179 (219)
T ss_dssp             CCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGCCEEEECSHHHHHHTTCHHHHHHHHHTSC----
T ss_pred             ceEEEEEeCCCCHHHHHHHcCCCCCEEEeCHHHHHHHHHcCCCCcCcceEEEEcCchHHhhhChHHHHHHHHHhCC----
Confidence            5788999999998887777777899999999999999998888899999999999999999898888888776653    


Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHh
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFR  116 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~  116 (210)
                                .+..+..+.+.++.+-+. ..+.|.
T Consensus       180 ----------~~~~~l~~SAT~~~~~~~-~~~~~~  203 (219)
T 1q0u_A          180 ----------KDLQMLVFSATIPEKLKP-FLKKYM  203 (219)
T ss_dssp             ----------TTCEEEEEESCCCGGGHH-HHHHHC
T ss_pred             ----------cccEEEEEecCCCHHHHH-HHHHHc
Confidence                      245677788887765443 444443

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=99.21  E-value=3.9e-11  Score=91.28  Aligned_cols=90  Identities=37%  Similarity=0.682  Sum_probs=74.5

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccc-hHHHHHHHHhhCCCch
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKG-FKEQIYDVYRYLPPAT   80 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~-~~~~~~~i~~~~~~~~   80 (210)
                      ++++..++||.+..++...+ ++++|+|+||+++.+++..+.+.+++++++|+||||++.+++ +...+..++..++.  
T Consensus       121 ~~~~~~~~g~~~~~~~~~~~-~~~~Iiv~Tp~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~~i~~~~~~--  197 (230)
T 2oxc_A          121 GLECHVFIGGTPLSQDKTRL-KKCHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPA--  197 (230)
T ss_dssp             TCCEEEECTTSCHHHHHHHT-TSCSEEEECHHHHHHHHHTTSSCGGGCCEEEESSHHHHHSTTSSHHHHHHHHHHSCS--
T ss_pred             CceEEEEeCCCCHHHHHHhc-cCCCEEEECHHHHHHHHhcCCcccccCCEEEeCCchHhhcCcchHHHHHHHHHhCCC--
Confidence            67899999999887776665 478999999999999999888888999999999999999887 88888888766542  


Q ss_pred             hHHHHHHHHHhcCceEEEecCCCCHh
Q psy6712          81 QVDWLTEKMREANFTVSSMHGDMPQK  106 (210)
Q Consensus        81 ~~~~l~~~l~~~~~~~~~~~~~~~~~  106 (210)
                                  +..+..+.+.++.+
T Consensus       198 ------------~~~~l~lSAT~~~~  211 (230)
T 2oxc_A          198 ------------SKQMLAVSATYPEF  211 (230)
T ss_dssp             ------------SCEEEEEESCCCHH
T ss_pred             ------------CCeEEEEEeccCHH
Confidence                        34577777777655

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=99.20  E-value=4.9e-11  Score=88.97  Aligned_cols=99  Identities=29%  Similarity=0.484  Sum_probs=80.2

Q ss_pred             ceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchhH
Q psy6712           3 VQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQV   82 (210)
Q Consensus         3 i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~~   82 (210)
                      +++..++||.+...+...+.++++|+|+||+++.+.+.++...+++++++|+||||++.+.++...+..++..++     
T Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~i~~~~~-----  173 (207)
T 2gxq_A           99 LKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATP-----  173 (207)
T ss_dssp             SCEEEECSSSCSHHHHHHHHHCCSEEEECHHHHHHHHHHTSSCCTTCSEEEEESHHHHHHTTCHHHHHHHHHTSC-----
T ss_pred             ceEEEEECCCChHHHHHHhhCCCCEEEECHHHHHHHHHcCCcchhhceEEEEEChhHhhccchHHHHHHHHHhCC-----
Confidence            578889999998888888888999999999999999999888999999999999999999888888888775543     


Q ss_pred             HHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHh
Q psy6712          83 DWLTEKMREANFTVSSMHGDMPQKERDGIMKEFR  116 (210)
Q Consensus        83 ~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~  116 (210)
                               .+..+..+.+.++..- .+..+.|.
T Consensus       174 ---------~~~~~i~~SAT~~~~~-~~~~~~~~  197 (207)
T 2gxq_A          174 ---------PSRQTLLFSATLPSWA-KRLAERYM  197 (207)
T ss_dssp             ---------TTSEEEEECSSCCHHH-HHHHHHHC
T ss_pred             ---------ccCeEEEEEEecCHHH-HHHHHHHc
Confidence                     2346777777776543 33445553

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=99.14  E-value=1e-10  Score=88.38  Aligned_cols=99  Identities=48%  Similarity=0.839  Sum_probs=70.9

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchh
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ   81 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~   81 (210)
                      ++++..++||.+..++...+.+ ++|+|+||+++.+.+.++...+++++++|+||||++.++++...+..++..++    
T Consensus       110 ~~~~~~~~g~~~~~~~~~~~~~-~~iiv~Tp~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~~~~~l~~i~~~~~----  184 (224)
T 1qde_A          110 DIKVHACIGGTSFVEDAEGLRD-AQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLP----  184 (224)
T ss_dssp             CCCEEEECC----------CTT-CSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHTTCHHHHHHHHHHSC----
T ss_pred             CceEEEEeCCcchHHHHhcCCC-CCEEEECHHHHHHHHHhCCcchhhCcEEEEcChhHHhhhhhHHHHHHHHHhCC----
Confidence            6788999999988877776654 89999999999999999888899999999999999999888888777775543    


Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHh
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFR  116 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~  116 (210)
                                .+..+..+.+.++..-+ +..+.|.
T Consensus       185 ----------~~~~~i~lSAT~~~~~~-~~~~~~~  208 (224)
T 1qde_A          185 ----------PTTQVVLLSATMPNDVL-EVTTKFM  208 (224)
T ss_dssp             ----------TTCEEEEEESSCCHHHH-HHHHHHC
T ss_pred             ----------ccCeEEEEEeecCHHHH-HHHHHHC
Confidence                      23467778888776543 3445554

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=99.14  E-value=1.8e-10  Score=87.73  Aligned_cols=93  Identities=25%  Similarity=0.489  Sum_probs=73.7

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhc-CccCCCccEEEechhhHHhccchHHHHHHHHhhCCCch
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRR-VLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPAT   80 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~-~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~   80 (210)
                      ++++..++||.+...+...+ .+++|+|+||+++.+.+... ...+++++++|+||||++.++++...+..++..++.  
T Consensus       125 ~~~~~~~~g~~~~~~~~~~~-~~~~iiv~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~i~~~~~~--  201 (236)
T 2pl3_A          125 DFSAGLIIGGKDLKHEAERI-NNINILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMGFADTMNAVIENLPK--  201 (236)
T ss_dssp             SCCEEEECCC--CHHHHHHH-TTCSEEEECHHHHHHHHHHCSSCCCTTCCEEEETTHHHHHHTTTHHHHHHHHHTSCT--
T ss_pred             CeeEEEEECCCCHHHHHHhC-CCCCEEEECHHHHHHHHHhcCCcccccccEEEEeChHHHhcCCcHHHHHHHHHhCCC--
Confidence            57889999999888777666 57899999999999988775 577889999999999999999998888888876642  


Q ss_pred             hHHHHHHHHHhcCceEEEecCCCCHhHHH
Q psy6712          81 QVDWLTEKMREANFTVSSMHGDMPQKERD  109 (210)
Q Consensus        81 ~~~~l~~~l~~~~~~~~~~~~~~~~~~r~  109 (210)
                                  +..+..+.+.++..-+.
T Consensus       202 ------------~~~~l~~SAT~~~~~~~  218 (236)
T 2pl3_A          202 ------------KRQTLLFSATQTKSVKD  218 (236)
T ss_dssp             ------------TSEEEEEESSCCHHHHH
T ss_pred             ------------CCeEEEEEeeCCHHHHH
Confidence                        34677788887765443

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=99.11  E-value=2.3e-10  Score=86.28  Aligned_cols=93  Identities=29%  Similarity=0.569  Sum_probs=74.1

Q ss_pred             CceEEEEEcCcchHHHHHHhcC-CCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhc-cchHHHHHHHHhhCCCc
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDY-GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLN-KGFKEQIYDVYRYLPPA   79 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~-~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~-~~~~~~~~~i~~~~~~~   79 (210)
                      ++++..++||.+...+...+.+ .++|+|+||+++.+++.++.+.+++++++|+||||++.+ .++...+..++..++  
T Consensus       111 ~~~v~~~~g~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~~i~~~~~--  188 (220)
T 1t6n_A          111 NVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTP--  188 (220)
T ss_dssp             TCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEESHHHHHSSHHHHHHHHHHHHTSC--
T ss_pred             CceEEEEeCCCChHHHHHHHhcCCCCEEEeCHHHHHHHHHhCCCCcccCCEEEEcCHHHHhcccCcHHHHHHHHHhCC--
Confidence            6789999999998888877765 579999999999999998888899999999999999987 466666666665443  


Q ss_pred             hhHHHHHHHHHhcCceEEEecCCCCHhHH
Q psy6712          80 TQVDWLTEKMREANFTVSSMHGDMPQKER  108 (210)
Q Consensus        80 ~~~~~l~~~l~~~~~~~~~~~~~~~~~~r  108 (210)
                                  .+..+..+.+.++..-+
T Consensus       189 ------------~~~~~i~~SAT~~~~~~  205 (220)
T 1t6n_A          189 ------------HEKQVMMFSATLSKEIR  205 (220)
T ss_dssp             ------------SSSEEEEEESCCCTTTH
T ss_pred             ------------CcCeEEEEEeecCHHHH
Confidence                        23467777777766533

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=99.04  E-value=1.6e-10  Score=91.49  Aligned_cols=91  Identities=26%  Similarity=0.485  Sum_probs=71.6

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHh-cCccCCCccEEEechhhHHhc-cchHHHHHHHHhhCCCc
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRR-RVLRTRNIKMLVLDEADEMLN-KGFKEQIYDVYRYLPPA   79 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~-~~~~~~~~~~lviDE~~~l~~-~~~~~~~~~i~~~~~~~   79 (210)
                      ++++..++||.+...+   ...+++|+|+||+++.+++.+ +.+++++++++|+||||+|++ .++...+..++..++. 
T Consensus       191 ~~~~~~~~~~~~~~~~---~~~~~~IlV~TP~~l~~~l~~~~~~~l~~l~~lVlDEad~l~~~~~~~~~~~~i~~~~~~-  266 (300)
T 3fmo_B          191 ELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPR-  266 (300)
T ss_dssp             TCCEEEESTTCCCCTT---CCCCCSEEEECHHHHHHHHTTTCCCCGGGCSEEEETTHHHHHHSTTHHHHHHHHHTTSCT-
T ss_pred             CcEEEEEeCCccHhhh---hcCCCCEEEECHHHHHHHHHhcCCCChhhceEEEEeCHHHHhhccCcHHHHHHHHHhCCC-
Confidence            4678888888775432   245789999999999999976 667899999999999999998 6888888888877653 


Q ss_pred             hhHHHHHHHHHhcCceEEEecCCCCHhHHH
Q psy6712          80 TQVDWLTEKMREANFTVSSMHGDMPQKERD  109 (210)
Q Consensus        80 ~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~  109 (210)
                                   +..+..+.+.++..-+.
T Consensus       267 -------------~~q~i~~SAT~~~~v~~  283 (300)
T 3fmo_B          267 -------------NCQMLLFSATFEDSVWK  283 (300)
T ss_dssp             -------------TCEEEEEESCCCHHHHH
T ss_pred             -------------CCEEEEEeccCCHHHHH
Confidence                         34677777777765444

>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=98.90  E-value=2.3e-09  Score=82.08  Aligned_cols=101  Identities=14%  Similarity=0.254  Sum_probs=70.4

Q ss_pred             CceEEEEEcCcchHHHHH-HhcCCCcEEEEChHHHHHHHHhc--CccCCCccEEEechhhHHhcc---chHHHHHHHHhh
Q psy6712           2 NVQCHACIGGTNLSEDLR-KLDYGQHVVSGTPGRVFDMIRRR--VLRTRNIKMLVLDEADEMLNK---GFKEQIYDVYRY   75 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~-~l~~~~~Ili~Tp~~l~~~l~~~--~~~~~~~~~lviDE~~~l~~~---~~~~~~~~i~~~   75 (210)
                      ++++..++||.....+.. ....+++|+|+||+++.+++.+.  .+.+++++++|+||||++.++   ++...+..++..
T Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~~~~i~~~  205 (245)
T 3dkp_A          126 GFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFLA  205 (245)
T ss_dssp             CCCEECCCHHHHHHTTTSTTSCCCCCEEEECHHHHHHHHHSSSCSCCCTTCCEEEESSHHHHHHHC--CHHHHHHHHHHH
T ss_pred             CceEEEEecCccHHHHhhhhhcCCCCEEEECHHHHHHHHHhCCCCcccccCcEEEEeChHHhcccccccHHHHHHHHHHh
Confidence            456666666655443332 22457899999999999999876  578899999999999999984   666666666543


Q ss_pred             CCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHh
Q psy6712          76 LPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFR  116 (210)
Q Consensus        76 ~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~  116 (210)
                      +             ...+..+..+.+.++.+-+. ..+.+.
T Consensus       206 ~-------------~~~~~~~~~~SAT~~~~v~~-~~~~~l  232 (245)
T 3dkp_A          206 C-------------TSHKVRRAMFSATFAYDVEQ-WCKLNL  232 (245)
T ss_dssp             C-------------CCTTCEEEEEESSCCHHHHH-HHHHHS
T ss_pred             c-------------CCCCcEEEEEeccCCHHHHH-HHHHhC
Confidence            3             22356778888888765444 444443

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}

Probab=98.61  E-value=1.2e-08  Score=76.14  Aligned_cols=68  Identities=10%  Similarity=0.147  Sum_probs=44.2

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcC------ccCCCccEEEechhhHHhccchHHHH
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRV------LRTRNIKMLVLDEADEMLNKGFKEQI   69 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~------~~~~~~~~lviDE~~~l~~~~~~~~~   69 (210)
                      ++++..++|+.+...+...+..+++|+|+||+++...+....      ..+.+++++|+||||++.+.++...+
T Consensus       110 ~~~v~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~~~~  183 (216)
T 3b6e_A          110 WYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNI  183 (216)
T ss_dssp             TSCEEECCC---CCCCHHHHHHHCSEEEEEHHHHHHHHHC-------CCCGGGCSEEEETTC-------CHHHH
T ss_pred             CceEEEEeCCcccchhHHhhccCCCEEEECHHHHHHHHhccCcccccccchhcccEEEEECchhhccCCcHHHH
Confidence            457778888877666666666678999999999999887743      56789999999999999866544443

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=98.19  E-value=1.4e-06  Score=66.25  Aligned_cols=67  Identities=18%  Similarity=0.245  Sum_probs=47.5

Q ss_pred             CCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHH-hccchH-HHHHHHHhhCCCchhHHHHHHHHHhcCceEEEec
Q psy6712          23 YGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEM-LNKGFK-EQIYDVYRYLPPATQVDWLTEKMREANFTVSSMH  100 (210)
Q Consensus        23 ~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l-~~~~~~-~~~~~i~~~~~~~~~~~~l~~~l~~~~~~~~~~~  100 (210)
                      .+++|+|+||+++.+++..   .+++++++|+||||.+ ++.++. ..+..++...               .+..+..+.
T Consensus       154 ~~~~Ivv~Tpg~l~~~l~~---~l~~~~~lVlDEah~~~~~~~~~~~~l~~i~~~~---------------~~~~~il~S  215 (235)
T 3llm_A          154 PHASIMFCTVGVLLRKLEA---GIRGISHVIVDEIHERDINTDFLLVVLRDVVQAY---------------PEVRIVLMS  215 (235)
T ss_dssp             SSSEEEEEEHHHHHHHHHH---CCTTCCEEEECCTTSCCHHHHHHHHHHHHHHHHC---------------TTSEEEEEE
T ss_pred             CCCeEEEECHHHHHHHHHh---hhcCCcEEEEECCccCCcchHHHHHHHHHHHhhC---------------CCCeEEEEe
Confidence            3578999999999999876   4899999999999985 555544 2333333221               245677777


Q ss_pred             CCCCHhH
Q psy6712         101 GDMPQKE  107 (210)
Q Consensus       101 ~~~~~~~  107 (210)
                      +.++.+.
T Consensus       216 AT~~~~~  222 (235)
T 3llm_A          216 ATIDTSM  222 (235)
T ss_dssp             CSSCCHH
T ss_pred             cCCCHHH
Confidence            7777654

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=97.67  E-value=4.5e-05  Score=64.91  Aligned_cols=92  Identities=12%  Similarity=0.179  Sum_probs=51.1

Q ss_pred             CchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEE--EecCccccCCCCC----CcEEEEecCCCC-h
Q psy6712          78 PATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLI--TTDVWARGIDVQQ----VSLVINYDLPNN-R  150 (210)
Q Consensus        78 ~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv--~T~~~~~g~d~~~----~~~vi~~~~p~s-~  150 (210)
                      .....+.+.+.++.  .. ...++..  .++.+.++.|+++. .+++  +|..+++|+|+|+    +++||++++|.. +
T Consensus       393 S~~~~~~v~~~l~~--~~-~~~q~~~--~~~~~~l~~f~~~~-~il~~V~~~~~~EGiD~~~~~~~~~~Vii~~lPf~~~  466 (540)
T 2vl7_A          393 SYEMLESVRIHLSG--IP-VIEENKK--TRHEEVLELMKTGK-YLVMLVMRAKESEGVEFREKENLFESLVLAGLPYPNV  466 (540)
T ss_dssp             CHHHHHHHHTTCTT--SC-EEESTTT--CCHHHHHHHHHTSC-CEEEEEC---------------CEEEEEEESCCCCCT
T ss_pred             CHHHHHHHHHHhcc--Cc-eEecCCC--CcHHHHHHHHhcCC-eEEEEEecCceecceecCCCcccccEEEEECCCCCCC
Confidence            33446666666643  23 3445443  46888999998864 6776  8899999999997    889999998832 1


Q ss_pred             -----------------------------hHHHHhhhhhcCCCCceeEEEEecc
Q psy6712         151 -----------------------------ELYIHRIGRSGRFGRKGVAISFVKS  175 (210)
Q Consensus       151 -----------------------------~~~~q~~GR~gR~g~~g~~~~~~~~  175 (210)
                                                   ....|.+||+-|...+--+++++++
T Consensus       467 ~d~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~Q~~GR~iR~~~D~g~v~llD~  520 (540)
T 2vl7_A          467 SDDMVRKRIERLSKLTGKDEDSIIHDLTAIVIKQTIGRAFRDPNDYVKIYLCDS  520 (540)
T ss_dssp             TSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHCCSTTCCCEEEEESG
T ss_pred             CCHHHHHHHHHHHHhhCCChhHHHHHHHHHHHHHHhCCcccCCCccEEEEEEcc
Confidence                                         2345889999998554334445543

>1rif_A DAR protein, DNA helicase UVSW; bacteriophage, RECG, SF2, DNA binding protein; HET: DNA; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.23

Probab=97.41  E-value=4.4e-05  Score=59.40  Aligned_cols=53  Identities=21%  Similarity=0.161  Sum_probs=36.7

Q ss_pred             eEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhc
Q psy6712           4 QCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLN   62 (210)
Q Consensus         4 ~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~   62 (210)
                      .+..++||.+...   ....+.+|+|+||+.+..   .....+++++++|+||||++.+
T Consensus       187 ~~~~~~~~~~~~~---~~~~~~~I~v~T~~~l~~---~~~~~~~~~~~vIiDEaH~~~~  239 (282)
T 1rif_A          187 MIKKIGGGASKDD---KYKNDAPVVVGTWQTVVK---QPKEWFSQFGMMMNDECHLATG  239 (282)
T ss_dssp             GEEECSTTCSSTT---CCCTTCSEEEECHHHHTT---SCGGGGGGEEEEEEETGGGCCH
T ss_pred             eEEEEeCCCcchh---hhccCCcEEEEchHHHHh---hHHHHHhhCCEEEEECCccCCc
Confidence            4556666654432   223568999999987543   2334567889999999999874

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=96.96  E-value=0.00052  Score=52.03  Aligned_cols=39  Identities=10%  Similarity=0.205  Sum_probs=29.8

Q ss_pred             CCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccch
Q psy6712          24 GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGF   65 (210)
Q Consensus        24 ~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~   65 (210)
                      ..+|+|+||+.+......   ....++++|+||+|.+.+..+
T Consensus       171 ~~~i~v~T~~~l~~~~~~---~~~~~~llIiDEaH~l~~~~~  209 (237)
T 2fz4_A          171 LKPLTVSTYDSAYVNAEK---LGNRFMLLIFDEVHHLPAESY  209 (237)
T ss_dssp             CCSEEEEEHHHHHHTHHH---HTTTCSEEEEECSSCCCTTTH
T ss_pred             cCCEEEEeHHHHHhhHHH---hcccCCEEEEECCccCCChHH
Confidence            568999999987765542   124689999999999976554

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=96.56  E-value=0.0019  Score=54.96  Aligned_cols=44  Identities=23%  Similarity=0.153  Sum_probs=34.5

Q ss_pred             HHhcCCCcEEEEChHHHHHHHHhcCccC-CCccEEEechhhHHhc
Q psy6712          19 RKLDYGQHVVSGTPGRVFDMIRRRVLRT-RNIKMLVLDEADEMLN   62 (210)
Q Consensus        19 ~~l~~~~~Ili~Tp~~l~~~l~~~~~~~-~~~~~lviDE~~~l~~   62 (210)
                      +....++||||+|+..+.+...+..+.+ .....+||||||.|.+
T Consensus       143 r~~~~~adIVV~~~~~l~~~~~~~~~~~~~~~~~vIiDEAHnl~d  187 (551)
T 3crv_A          143 LNSLYKADVIALTYPYFFIDRYREFIDIDLREYMIVIDEAHNLDK  187 (551)
T ss_dssp             HHHGGGCSEEEEETHHHHCHHHHTTSCCCSTTEEEEETTGGGGGG
T ss_pred             HhhhhcCCEEEeCchHhcCHHHHHhcCCCcCCeEEEEecccchHH
Confidence            3445688999999999998765554443 4677899999999987

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=96.51  E-value=0.0033  Score=54.39  Aligned_cols=95  Identities=19%  Similarity=0.234  Sum_probs=56.2

Q ss_pred             CCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEec--CccccCCCCC--CcEEEEecCCCC---
Q psy6712          77 PPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTD--VWARGIDVQQ--VSLVINYDLPNN---  149 (210)
Q Consensus        77 ~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~--~~~~g~d~~~--~~~vi~~~~p~s---  149 (210)
                      +.....+.+.+.++  ..... ...+|+..++.+.++.|+ ++-.||+++.  .+++|+|+|+  ...||...+|..   
T Consensus       456 ~Sy~~l~~v~~~l~--~~~~~-~~q~~~~~~~~~ll~~f~-~~~~vL~~v~~gsf~EGiD~~g~~l~~viI~~lPfp~~~  531 (620)
T 4a15_A          456 PSYSLMDRVENRVS--FEHMK-EYRGIDQKELYSMLKKFR-RDHGTIFAVSGGRLSEGINFPGNELEMIILAGLPFPRPD  531 (620)
T ss_dssp             SCHHHHHHHTSSCC--SCCEE-CCTTCCSHHHHHHHHHHT-TSCCEEEEETTSCC--------CCCCEEEESSCCCCCCC
T ss_pred             CCHHHHHHHHHHHH--hcchh-ccCCCChhHHHHHHHHhc-cCCcEEEEEecCceeccccCCCCceEEEEEEcCCCCCCC
Confidence            33343555555554  22222 455566778999999999 8888999984  9999999985  778998877621   


Q ss_pred             ----------------h----------hHHHHhhhhhcCCCCceeEEEEecc
Q psy6712         150 ----------------R----------ELYIHRIGRSGRFGRKGVAISFVKS  175 (210)
Q Consensus       150 ----------------~----------~~~~q~~GR~gR~g~~g~~~~~~~~  175 (210)
                                      .          ....|.+||+-|...+--+++++++
T Consensus       532 p~~~ar~~~~~~~~g~~~~~~y~~pa~~~l~Qa~GRlIR~~~D~G~v~llD~  583 (620)
T 4a15_A          532 AINRSLFDYYERKYGKGWEYSVVYPTAIKIRQEIGRLIRSAEDTGACVILDK  583 (620)
T ss_dssp             HHHHHHHHHHHHHHSCHHHHHTHHHHHHHHHHHHHTTCCSTTCCEEEEEECG
T ss_pred             HHHHHHHHHHHHhhCCCchHHhHHHHHHHHHHHhCccccCCCceEEEEEEcc
Confidence                            1          1224888999998654344444433

>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=96.22  E-value=0.043  Score=43.40  Aligned_cols=90  Identities=11%  Similarity=0.072  Sum_probs=61.5

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCC-----CCCCcEEEEecCCCChhHH-HH
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGID-----VQQVSLVINYDLPNNRELY-IH  155 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d-----~~~~~~vi~~~~p~s~~~~-~q  155 (210)
                      .+.+..++..++++..-+.|.....+++ .    .+....+.+.|+..+.|++     +..++.||.||..|++..= +|
T Consensus       138 LDilE~~l~~~~~~y~RlDG~~~~~~~k-~----~~~~~~i~Lltsag~~gin~~~~nl~~aD~VI~~DsdwNp~~d~iQ  212 (328)
T 3hgt_A          138 MDLLEALLLGNKVHIKRYDGHSIKSAAA-A----NDFSCTVHLFSSEGINFTKYPIKSKARFDMLICLDTTVDTSQKDIQ  212 (328)
T ss_dssp             HHHHHHHHTTSSCEEEESSSCCC------------CCSEEEEEEESSCCCTTTSCCCCCSCCSEEEECSTTCCTTSHHHH
T ss_pred             HHHHHHHHhcCCCceEeCCCCchhhhhh-c----ccCCceEEEEECCCCCCcCcccccCCCCCEEEEECCCCCCCChHHH
Confidence            7888888888999999999985443222 1    2345566666777777775     6789999999999998874 89


Q ss_pred             hhhhhcCCC----CceeEEEEeccC
Q psy6712         156 RIGRSGRFG----RKGVAISFVKSD  176 (210)
Q Consensus       156 ~~GR~gR~g----~~g~~~~~~~~~  176 (210)
                      .+-|+.|.|    +.-.++-++...
T Consensus       213 a~~r~~R~~~gq~k~v~V~RLvt~~  237 (328)
T 3hgt_A          213 YLLQYKRERKGLERYAPIVRLVAIN  237 (328)
T ss_dssp             HHHCCC---------CCEEEEEETT
T ss_pred             HHHHHhhhccCCCCcceEEEEeCCC
Confidence            888888873    244577777654

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=94.88  E-value=0.0066  Score=51.56  Aligned_cols=40  Identities=23%  Similarity=0.213  Sum_probs=30.3

Q ss_pred             cCCCcEEEEChHHHHHHHHhcCcc-------CCCccEEEechhhHHh
Q psy6712          22 DYGQHVVSGTPGRVFDMIRRRVLR-------TRNIKMLVLDEADEML   61 (210)
Q Consensus        22 ~~~~~Ili~Tp~~l~~~l~~~~~~-------~~~~~~lviDE~~~l~   61 (210)
                      ..++||+|+|+..+.+....+.+.       +.....+||||||.+.
T Consensus       142 ~~~adiVV~n~~~l~~~~~~~~~~~~~~~~~~~~~~~vIiDEAHnl~  188 (540)
T 2vl7_A          142 LKDKDVIAMTYPYLFQKPIRNSVFCNKDDCLKLEDYLIVIDEAHNLL  188 (540)
T ss_dssp             GGGCSEEEEETHHHHSHHHHHHHSCSSTTSCCGGGEEEEETTGGGGG
T ss_pred             hhcCCEEEEChHHhcCHHHHHhhCcccccccCcCCCEEEEEccccHH
Confidence            456799999999988755443322       3567899999999994

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=94.17  E-value=0.27  Score=41.71  Aligned_cols=81  Identities=14%  Similarity=0.165  Sum_probs=52.5

Q ss_pred             cCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEe--cCccccCCCC-----CCcEEEEecCCCC---------------
Q psy6712          92 ANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITT--DVWARGIDVQ-----QVSLVINYDLPNN---------------  149 (210)
Q Consensus        92 ~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T--~~~~~g~d~~-----~~~~vi~~~~p~s---------------  149 (210)
                      .+.++..-..+++.   .+..+.|+...-.||+++  ..+.+|+|+|     .+..||...+|..               
T Consensus       413 ~~~~v~~q~~~~~~---~~~~~~~~~~~~~vl~~v~gg~~~EGiD~~d~~g~~l~~viI~~lPfp~~dp~~~ar~~~~~~  489 (551)
T 3crv_A          413 ISLPKYVESEDSSV---EDLYSAISANNKVLIGSVGKGKLAEGIELRNNDRSLISDVVIVGIPYPPPDDYLKILAQRVSL  489 (551)
T ss_dssp             CCSSEEECCSSCCH---HHHHHHTTSSSSCEEEEESSCCSCCSSCCEETTEESEEEEEEESCCCCCCSHHHHHHHHHTTC
T ss_pred             cCCcEEEcCCCCCH---HHHHHHHHhcCCeEEEEEecceecccccccccCCcceeEEEEEcCCCCCCCHHHHHHHHHHHH
Confidence            35555554445554   456777754444799998  6999999999     4778888776521               


Q ss_pred             -----h----------hHHHHhhhhhcCCCCceeEEEEecc
Q psy6712         150 -----R----------ELYIHRIGRSGRFGRKGVAISFVKS  175 (210)
Q Consensus       150 -----~----------~~~~q~~GR~gR~g~~g~~~~~~~~  175 (210)
                           .          ....|.+||+-|...+--+++++++
T Consensus       490 ~~g~~~~~~~y~~pa~~~l~Qa~GRlIR~~~D~G~v~llD~  530 (551)
T 3crv_A          490 KMNRENEEFLFKIPALVTIKQAIGRAIRDVNDKCNVWLLDK  530 (551)
T ss_dssp             CSSTTTHHHHTHHHHHHHHHHHHHTTCCSTTCEEEEEEESG
T ss_pred             hhCCchhHHHHHHHHHHHHHHHhccCccCCCccEEEEEeeh
Confidence                 1          1123788999898665445555544

>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=93.47  E-value=0.0091  Score=54.29  Aligned_cols=40  Identities=20%  Similarity=0.188  Sum_probs=28.4

Q ss_pred             CCcEEEEChHHHHHHHHh-cCccCCCccEEEechhhHHhcc
Q psy6712          24 GQHVVSGTPGRVFDMIRR-RVLRTRNIKMLVLDEADEMLNK   63 (210)
Q Consensus        24 ~~~Ili~Tp~~l~~~l~~-~~~~~~~~~~lviDE~~~l~~~   63 (210)
                      ..+|+|+|++.+...... ..+...+++++|+||||++.+.
T Consensus       248 ~~dIvI~T~~~L~~~~~~~~~l~~~~~dlVIvDEAH~~kn~  288 (968)
T 3dmq_A          248 TEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLVWS  288 (968)
T ss_dssp             TCSEEEECHHHHHTSTTTTHHHHTSCCCEEEECCSSCCCCB
T ss_pred             cCCEEEEcHHHHhhCHHHHHHhhhcCCCEEEehhhHhhcCC
Confidence            569999999876532111 2234567899999999999753

>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=92.16  E-value=0.32  Score=43.19  Aligned_cols=58  Identities=24%  Similarity=0.379  Sum_probs=46.6

Q ss_pred             HHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCcc-ccCCCCCCcEEEE
Q psy6712          86 TEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWA-RGIDVQQVSLVIN  143 (210)
Q Consensus        86 ~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~-~g~d~~~~~~vi~  143 (210)
                      .+.+...++++..+||+++..++...++.+.+|+.+|+|+|...- ..+.+.++.+||.
T Consensus       438 ~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~~~~~~l~lVVI  496 (780)
T 1gm5_A          438 VESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLVII  496 (780)
T ss_dssp             HHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCSCCCEEEE
T ss_pred             HHHhhhcCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhhhhhccCCceEEe
Confidence            334444589999999999999999999999999999999997443 3466778887774

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=84.88  E-value=1.7  Score=35.00  Aligned_cols=62  Identities=13%  Similarity=0.303  Sum_probs=46.0

Q ss_pred             HHHHHHHHHh---cCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCcc----ccCCCCCCcEEEE
Q psy6712          82 VDWLTEKMRE---ANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWA----RGIDVQQVSLVIN  143 (210)
Q Consensus        82 ~~~l~~~l~~---~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~----~g~d~~~~~~vi~  143 (210)
                      +....+.++.   .++++..++|+.+..++...++.+..++.+|+|+|.-..    .-++..++++||.
T Consensus        77 ~~q~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~iVi  145 (414)
T 3oiy_A           77 VKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFDFVFV  145 (414)
T ss_dssp             HHHHHHHHHHHCCSSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHHHTTCCCSEEEE
T ss_pred             HHHHHHHHHHHccCCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHHhccccccEEEE
Confidence            3444444444   588999999999999999999999999999999996322    1245557787775

---

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	210
d2j0sa2	168	c.37.1.19 (A:244-411) Probable ATP-dependent RNA h	1e-26
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	2e-26
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	2e-26
d1wp9a2	286	c.37.1.19 (A:201-486) putative ATP-dependent RNA h	4e-23
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	5e-20
d1hv8a2	155	c.37.1.19 (A:211-365) Putative DEAD box RNA helica	9e-20
d2rb4a1	168	c.37.1.19 (A:307-474) ATP-dependent RNA helicase D	9e-20
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	1e-19
d1s2ma2	171	c.37.1.19 (A:252-422) Putative ATP-dependent RNA h	8e-19
d1t5la2	181	c.37.1.19 (A:415-595) Nucleotide excision repair e	2e-16
d2fwra1	200	c.37.1.19 (A:257-456) DNA repair protein RAD25 {Ar	2e-15
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	3e-12
d1c4oa2	174	c.37.1.19 (A:410-583) Nucleotide excision repair e	1e-11
d1jr6a_	138	c.37.1.14 (A:) HCV helicase domain {Human hepatiti	1e-11
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	4e-11
d1oywa3	200	c.37.1.19 (A:207-406) RecQ helicase domain {Escher	9e-11
d1t5ia_	168	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	1e-10
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	8e-09
d2eyqa5	211	c.37.1.19 (A:779-989) Transcription-repair couplin	5e-08
d2p6ra4	201	c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglob	7e-08
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	2e-07
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	2e-06
d1z3ix1	346	c.37.1.19 (X:390-735) Rad54-like, Rad54L {Zebra fi	8e-06
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	1e-05
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	1e-04
d1tf5a4	175	c.37.1.19 (A:396-570) Translocation ATPase SecA, n	2e-04
d1yksa2	299	c.37.1.14 (A:325-623) YFV helicase domain {Yellow	4e-04

>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 = 98.5 bits (244), Expect = 1e-26
 Identities = 107/118 (90%), Positives = 115/118 (97%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +VDWLTEKMREANFTVSSMHGDMPQKER+ IMKEFRSG SRVLI+TDVWARG+DV QVSL
Sbjct: 46  KVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSL 105

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           +INYDLPNNRELYIHRIGRSGR+GRKGVAI+FVK+DDIRILRDIEQYYSTQIDEMPMN
Sbjct: 106 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN 163

>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 =  101 bits (252), Expect = 2e-26
 Identities = 14/102 (13%), Positives = 29/102 (28%), Gaps = 14/102 (13%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKER----------DGIMKEFRSGTSRVLITTDVWA 130
           + D L  K+        + +  +                  +    +G    +I  +   
Sbjct: 48  KCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCV 107

Query: 131 RG---IDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVA 169
                  +     +    LP +      R GR+GR G+ G+ 
Sbjct: 108 TQTVDFSLDPTFTIETTTLPQDAVSRTQRRGRTGR-GKPGIY 148

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 162

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 97.3 bits (241), Expect = 2e-26
 Identities = 77/116 (66%), Positives = 101/116 (87%)

Query: 83  DWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVI 142
           + LT K+R   FTVS+++ D+PQ+ERD IMKEFRSG+SR+LI+TD+ ARGIDVQQVSLVI
Sbjct: 41  EELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVI 100

Query: 143 NYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN 198
           NYDLP N+E YIHRIGR GRFGRKGVAI+FV ++D+  +R++E++YSTQI+E+P +
Sbjct: 101 NYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSD 156

>d1wp9a2 c.37.1.19 (A:201-486) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 286

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 91.9 bits (227), Expect = 4e-23
 Identities = 35/150 (23%), Positives = 59/150 (39%), Gaps = 15/150 (10%)

Query: 50  KMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVDWLTEKMREANFTVSSMHGD------- 102
           KM  L E      +  ++Q   +  +         +  ++ +         G        
Sbjct: 144 KMDKLKEIIREQLQ--RKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDR 201

Query: 103 -MPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSG 161
            + Q+E+  I+ EF  G   VL+ T V   G+DV +V LV+ Y+   +    I R GR+G
Sbjct: 202 GLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTG 261

Query: 162 RFGRKGVAISFVKSDDIRILRDIEQYYSTQ 191
           R    G  I  +        RD   Y+S++
Sbjct: 262 R-HMPGRVIILMAKGT----RDEAYYWSSR 286

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 208

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 82.0 bits (202), Expect = 5e-20
 Identities = 27/82 (32%), Positives = 43/82 (52%), Gaps = 1/82 (1%)

Query: 1   MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEM 60
            N++     GG  +   ++ L    ++V GTPGR+ D I R  L  +N+K  +LDEADEM
Sbjct: 99  KNLKIAKIYGGKAIYPQIKALK-NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEM 157

Query: 61  LNKGFKEQIYDVYRYLPPATQV 82
           LN GF + +  +        ++
Sbjct: 158 LNMGFIKDVEKILNACNKDKRI 179

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 155

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 80.0 bits (196), Expect = 9e-20
 Identities = 47/115 (40%), Positives = 72/115 (62%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
               L   +R+  F   ++HGD+ Q +R+ +++ F+    R+LI TDV +RGIDV  ++ 
Sbjct: 40  DTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNC 99

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEM 195
           VINY LP N E Y+HRIGR+GR G+KG AIS +   + + LR IE+    +I ++
Sbjct: 100 VINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKKLRYIERAMKLKIKKL 154

>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 = 81.7 bits (201), Expect = 1e-19
 Identities = 16/119 (13%), Positives = 38/119 (31%), Gaps = 15/119 (12%)

Query: 82  VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITT----DVWARGIDVQQ 137
            + + E ++            +    + G  ++F  G    LI T        RG+D+ +
Sbjct: 38  AEEIYESLKNK------FRIGIVTATKKGDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPE 91

Query: 138 -VSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEM 195
            +   +    P+    +   I        + V +      ++  +  +       IDE+
Sbjct: 92  RIRFAVFVGCPS----FRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLLPAVERHIDEV 146

>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 171

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 77.8 bits (190), Expect = 8e-19
 Identities = 50/121 (41%), Positives = 74/121 (61%)

Query: 84  WLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVIN 143
            L +K+ +  ++    H  M Q+ER+ +  EFR G  R L+ +D+  RGID+Q V++VIN
Sbjct: 47  LLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVIN 106

Query: 144 YDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRSL 203
           +D P   E Y+HRIGRSGRFG  G+AI+ +  +D   L  IEQ   T+I  +P    +SL
Sbjct: 107 FDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPATIDKSL 166

Query: 204 H 204
           +
Sbjct: 167 Y 167

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]} Length = 181

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]

 Score = 71.4 bits (174), Expect = 2e-16
 Identities = 34/164 (20%), Positives = 67/164 (40%), Gaps = 18/164 (10%)

Query: 53  VLDEADEMLNKGFKEQIYDVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIM 112
           ++ E  E + +  +                + LT+ ++EA   V+ +H ++   ER  I+
Sbjct: 20  LIGEIRERVERNER-----TLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEII 74

Query: 113 KEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNREL-----YIHRIGRSGRFGRKG 167
           ++ R G   VL+  ++   G+D+ +VSLV   D      L      I  IGR+ R     
Sbjct: 75  RDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGH 134

Query: 168 VAISFVKS--------DDIRILRDIEQYYSTQIDEMPMNGKRSL 203
           V +              + +  R I++ Y+ +   +P   K+ +
Sbjct: 135 VIMYADTITKSMEIAIQETKRRRAIQEEYNRKHGIVPRTVKKEI 178

>d2fwra1 c.37.1.19 (A:257-456) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 69.5 bits (169), Expect = 2e-15
 Identities = 19/86 (22%), Positives = 38/86 (44%)

Query: 88  KMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLP 147
                 F + ++     ++ER+ I++ FR+G  R ++++ V   GIDV   ++ +     
Sbjct: 107 YRISKVFLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGS 166

Query: 148 NNRELYIHRIGRSGRFGRKGVAISFV 173
            +   YI R+GR  R  +        
Sbjct: 167 GSAREYIQRLGRILRPSKGKKEAVLY 192

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]} Length = 305

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

 Score = 62.2 bits (150), Expect = 3e-12
 Identities = 20/168 (11%), Positives = 45/168 (26%), Gaps = 23/168 (13%)

Query: 29  SGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVDWLTEK 88
           + TP    D   +      + +  + + +    ++   +       ++P     + +   
Sbjct: 138 TATPPGSRDPFPQSNAPIMDEEREIPERSWNSGHEWVTDFKGKTVWFVPSIKAGNDIAAC 197

Query: 89  MREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDV---------QQVS 139
           +R+    V  +       E               ++TTD+   G +          + + 
Sbjct: 198 LRKNGKKVIQLSRKTFDSEYIKTRTNDW----DFVVTTDISEMGANFKAERVIDPRRCMK 253

Query: 140 LVINYDLPNNREL----------YIHRIGRSGRFGRKGVAISFVKSDD 177
            VI  D      L             R GR GR  +          + 
Sbjct: 254 PVILTDGEERVILAGPMPVTHSSAAQRRGRVGRNPKNENDQYIYMGEP 301

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]} Length = 174

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]

 Score = 58.9 bits (142), Expect = 1e-11
 Identities = 27/138 (19%), Positives = 55/138 (39%), Gaps = 9/138 (6%)

Query: 53  VLDEADEMLNKGFKEQIYDVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIM 112
           +++   E   +G +         +      + LT  + E       +H ++   +R  ++
Sbjct: 20  LMEGIRERAARGER-----TLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALI 74

Query: 113 KEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHR--IGRSGRFGRKGVAI 170
           ++ R G    L+  ++   G+D+ +VSLV   D      L   R  I   GR  R     
Sbjct: 75  RDLRLGHYDCLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNARGE 134

Query: 171 SFVKSDDI--RILRDIEQ 186
            ++ +D +   + R IE+
Sbjct: 135 VWLYADRVSEAMQRAIEE 152

>d1jr6a_ c.37.1.14 (A:) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 138

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 = 57.8 bits (139), Expect = 1e-11
 Identities = 18/100 (18%), Positives = 33/100 (33%), Gaps = 12/100 (12%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVS- 139
           + D L  K+        + +  +        +    +    V++ TD    G      S 
Sbjct: 47  KCDELAAKLVALGINAVAYYRGLD-------VSVIPTNGDVVVVATDALMTGFTGDFDSV 99

Query: 140 --LVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDD 177
                +   P +      R GR+GR G+ G+   FV   +
Sbjct: 100 IDCNTSDGKPQDAVSRTQRRGRTGR-GKPGI-YRFVAPGE 137

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]} Length = 222

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.9 bits (139), Expect = 4e-11
 Identities = 76/82 (92%), Positives = 79/82 (96%)

Query: 1   MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEM 60
           MNVQCHACIGGTN+ ED+RKLDYGQHVV+GTPGRVFDMIRRR LRTR IKMLVLDEADEM
Sbjct: 112 MNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEM 171

Query: 61  LNKGFKEQIYDVYRYLPPATQV 82
           LNKGFKEQIYDVYRYLPPATQV
Sbjct: 172 LNKGFKEQIYDVYRYLPPATQV 193

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

 Score = 57.0 bits (136), Expect = 9e-11
 Identities = 25/120 (20%), Positives = 53/120 (44%)

Query: 81  QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
           +V+    +++    + ++ H  +    R  + ++F+    ++++ T  +  GI+   V  
Sbjct: 42  KVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRF 101

Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGK 200
           V+++D+P N E Y    GR+GR G    A+ F    D+  LR   +       +     K
Sbjct: 102 VVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLEEKPQGQLQDIERHK 161

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]} Length = 168

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (133), Expect = 1e-10
 Identities = 44/122 (36%), Positives = 78/122 (63%), Gaps = 1/122 (0%)

Query: 84  WLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVIN 143
            L + + E NF   ++H  MPQ+ER    ++F+    R+L+ T+++ RG+D+++V++  N
Sbjct: 42  ALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFN 101

Query: 144 YDLPNNRELYIHRIGRSGRFGRKGVAISFV-KSDDIRILRDIEQYYSTQIDEMPMNGKRS 202
           YD+P + + Y+HR+ R+GRFG KG+AI+FV   +D +IL D++  +   I E+P     S
Sbjct: 102 YDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEIDIS 161

Query: 203 LH 204
            +
Sbjct: 162 SY 163

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 212

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 51.4 bits (122), Expect = 8e-09
 Identities = 39/82 (47%), Positives = 47/82 (57%)

Query: 1   MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEM 60
                     G     +  +      +V GTPGRVFD I+RR  RT  IKM +LDEADEM
Sbjct: 104 HMDIKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEM 163

Query: 61  LNKGFKEQIYDVYRYLPPATQV 82
           L+ GFKEQIY ++  LPP TQV
Sbjct: 164 LSSGFKEQIYQIFTLLPPTTQV 185

>d2eyqa5 c.37.1.19 (A:779-989) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]} Length = 211

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]

 Score = 48.9 bits (116), Expect = 5e-08
 Identities = 28/129 (21%), Positives = 50/129 (38%), Gaps = 6/129 (4%)

Query: 50  KMLVLDEADEMLNKGFKEQIYDVY-RYLPPATQVDWLTEKMREANFTVSSMHGDMPQKER 108
            M+V +     + +G   Q+Y +Y          + L E + EA   ++  HG M ++E 
Sbjct: 17  SMVVREAILREILRG--GQVYYLYNDVENIQKAAERLAELVPEAR--IAIGHGQMREREL 72

Query: 109 DGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPN-NRELYIHRIGRSGRFGRKG 167
           + +M +F      VL+ T +   GID+   + +I     +          GR GR   + 
Sbjct: 73  ERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQA 132

Query: 168 VAISFVKSD 176
            A       
Sbjct: 133 YAWLLTPHP 141

>d2p6ra4 c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]} Length = 201

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 48.8 bits (115), Expect = 7e-08
 Identities = 23/107 (21%), Positives = 43/107 (40%), Gaps = 11/107 (10%)

Query: 96  VSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVI-------NYDLPN 148
            +  H  +   +R  +   FR G  +V++ T   A G+++    +++        Y    
Sbjct: 97  AAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRI 156

Query: 149 NRELYIHRIGRSGRFGR--KGVAISFVKSDDIRILRDIEQYYSTQID 193
               Y    GR+GR G   +G AI  V   D  I   +++Y   + +
Sbjct: 157 KVSEYKQMAGRAGRPGMDERGEAIIIVGKRDREIA--VKRYIFGEPE 201

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]} Length = 218

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.5 bits (112), Expect = 2e-07
 Identities = 36/58 (62%), Positives = 46/58 (79%)

Query: 25  QHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQV 82
            H++ GTPGRVFDM+ RR L  + IKM VLDEADEML++GFK+QIYD+++ L   TQV
Sbjct: 132 PHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQV 189

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.2 bits (103), Expect = 2e-06
 Identities = 32/82 (39%), Positives = 53/82 (64%)

Query: 1   MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEM 60
              +  A  GGTNL +D+ +LD   HVV  TPGR+ D+I++ V +  +++M+VLDEAD++
Sbjct: 99  GGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKL 158

Query: 61  LNKGFKEQIYDVYRYLPPATQV 82
           L++ F + + D+   LP   Q+
Sbjct: 159 LSQDFVQIMEDIILTLPKNRQI 180

>d1z3ix1 c.37.1.19 (X:390-735) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]} Length = 346

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]

 Score = 43.4 bits (101), Expect = 8e-06
 Identities = 26/134 (19%), Positives = 54/134 (40%), Gaps = 6/134 (4%)

Query: 36  FDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVDWLTEKMREANFT 95
            +   + V    + KMLVLD    M      +++  V  Y      +D   +  R   + 
Sbjct: 88  QNYSTKAVEPQLSGKMLVLDYILAMTRTTTSDKVVLVSNY---TQTLDLFEKLCRNRRYL 144

Query: 96  VSSMHGDMPQKERDGIMKEFRSGTS---RVLITTDVWARGIDVQQVSLVINYDLPNNREL 152
              + G M  K+R  I++ F + +S     ++++     G+++   + ++ +D   N   
Sbjct: 145 YVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLVMFDPDWNPAN 204

Query: 153 YIHRIGRSGRFGRK 166
               + R  R G+K
Sbjct: 205 DEQAMARVWRDGQK 218

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]} Length = 207

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.6 bits (99), Expect = 1e-05
 Identities = 25/80 (31%), Positives = 41/80 (51%), Gaps = 2/80 (2%)

Query: 5   CHACIGGTNLSEDLRKLD-YGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEML-N 62
                GG ++ +D   L     H+V GTPGR+  + R + L  ++IK  +LDE D+ML  
Sbjct: 101 VAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQ 160

Query: 63  KGFKEQIYDVYRYLPPATQV 82
              +  + +++R  P   QV
Sbjct: 161 LDMRRDVQEIFRMTPHEKQV 180

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 237

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score = 39.5 bits (91), Expect = 1e-04
 Identities = 12/95 (12%), Positives = 24/95 (25%), Gaps = 25/95 (26%)

Query: 26  HVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNK-----------GFKEQIYDVYR 74
            +V  T   +    R       +   + +D+ D +L             GF   +     
Sbjct: 144 KIVITTTQFLSKHYRE----LGHFDFIFVDDVDAILKASKNVDKLLHLLGFHYDLKTKSW 199

Query: 75  YLPPATQVDWLTEKMREA----------NFTVSSM 99
                  +   T   ++           NF + S 
Sbjct: 200 VGEARGCLMVSTATAKKGKKAELFRQLLNFDIGSS 234

>d1tf5a4 c.37.1.19 (A:396-570) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]} Length = 175

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]

 Score = 38.3 bits (89), Expect = 2e-04
 Identities = 26/153 (16%), Positives = 55/153 (35%), Gaps = 20/153 (13%)

Query: 38  MIRR----RVLRTRNIKML-VLDEADEMLNKGFKEQIYDVYRYLPPATQVDWLTEKMREA 92
           ++R      + RT   K   V ++  +    G    +  V          + +++ ++  
Sbjct: 3   VVRDDRPDLIYRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAV-----ETSELISKLLKNK 57

Query: 93  NFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYD------- 145
                 ++    ++E   I +  + G   V I T++  RG D++    V           
Sbjct: 58  GIPHQVLNAKNHEREAQIIEEAGQKGA--VTIATNMAGRGTDIKLGEGVKELGGLAVVGT 115

Query: 146 -LPNNRELYIHRIGRSGRFGRKGVAISFVKSDD 177
               +R +     GRSGR G  G+   ++  +D
Sbjct: 116 ERHESRRIDNQLRGRSGRQGDPGITQFYLSMED 148

>d1yksa2 c.37.1.14 (A:325-623) YFV helicase domain {Yellow fever virus [TaxId: 11089]} 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: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

 Score = 38.0 bits (88), Expect = 4e-04
 Identities = 25/176 (14%), Positives = 50/176 (28%), Gaps = 29/176 (16%)

Query: 49  IKMLVLDEADEMLNKGFK---EQIYDVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQ 105
           I+ +  D   E  N G             +LP     + +   +R+A  +V  ++    +
Sbjct: 13  IEDVQTDIPSEPWNTGHDWILADKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFE 72

Query: 106 KERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELY------------ 153
           +E        +      ++ TD+   G ++  V  V++        L             
Sbjct: 73  RE----YPTIKQKKPDFILATDIAEMGANL-CVERVLDCRTAFKPVLVDEGRKVAIKGPL 127

Query: 154 -------IHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQI--DEMPMNGK 200
                    R GR GR   +     +              +    +  D M + G 
Sbjct: 128 RISASSAAQRRGRIGRNPNRDGDSYYYSEPTSENNAHHVCWLEASMLLDNMEVRGG 183

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	210
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	99.97
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	99.96
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.96
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	99.96
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	99.96
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.95
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.94
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	99.92
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.92
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	99.84
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	99.84
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.82
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.79
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.76
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	99.76
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.72
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	99.7
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	99.68
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	99.58
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.53
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	99.53
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.49
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.44
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	99.42
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.42
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	99.4
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.34
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	99.33
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	99.31
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.29
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	99.15
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	98.47
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	98.14
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	97.93
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	97.7
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	97.37
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	96.95
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	96.77
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	96.68
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	95.98
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	95.14
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	94.5
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	93.99
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	93.81
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	93.81
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	91.33
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	87.2
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	85.51
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	85.08
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	84.51

>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=99.97  E-value=1.6e-30  Score=187.06  Aligned_cols=133  Identities=59%  Similarity=0.958  Sum_probs=121.4

Q ss_pred             HHhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChh
Q psy6712          72 VYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRE  151 (210)
Q Consensus        72 i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~  151 (210)
                      .+.|+.....++.+++.|...++.+..+||+|+..+|..+++.|+.|+.++||||+++++|+|+|++++||+||+|+++.
T Consensus        30 ~iIF~~s~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Tdv~~rGiDi~~v~~VI~~d~P~~~~  109 (162)
T d1fuka_          30 AVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKE  109 (162)
T ss_dssp             EEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGGGTTTCCCCSCSEEEESSCCSSGG
T ss_pred             EEEEEEEEchHHHHHHHHhhcCceEEEeccCCchhhHHHHHHHHhhcccceeeccccccccccCCCceEEEEeccchhHH
Confidence            34466677779999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhhhhcCCCCceeEEEEeccCcHHHHHHHHHHhcCccccccCCccccCC
Q psy6712         152 LYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRSLH  204 (210)
Q Consensus       152 ~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  204 (210)
                      .|+||+||+||.|+.|.+++++++.|...++.+++.++..++++|.++.++++
T Consensus       110 ~yihR~GR~gR~g~~g~~i~~~~~~d~~~~~~i~~~~~~~~~~ip~~~~~l~~  162 (162)
T d1fuka_         110 NYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIATLLN  162 (162)
T ss_dssp             GGGGSSCSCC-----CEEEEEEETTTHHHHHHHHHHSSCCCEECCSCCTTTTC
T ss_pred             HHHhhccccccCCCccEEEEEcCHHHHHHHHHHHHHHcCcCCCCChHHHHhhC
Confidence            99999999999999999999999999999999999999999999999988764

>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=99.96  E-value=7.4e-30  Score=184.57  Aligned_cols=132  Identities=81%  Similarity=1.245  Sum_probs=124.3

Q ss_pred             HHHhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCCh
Q psy6712          71 DVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNR  150 (210)
Q Consensus        71 ~i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~  150 (210)
                      +++.|+.....++.+++.|...++++..+||+|+.++|..+++.|++|+.++||||+++++|+|+|++++||+||+|+++
T Consensus        36 k~iiF~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~fk~g~~~iLv~Td~~~rGiDi~~v~~VIn~d~P~~~  115 (168)
T d2j0sa2          36 QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNR  115 (168)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGGSSSCCCTTEEEEEESSCCSSH
T ss_pred             ceEEEeeeHHHHHHHHHHhhhcccchhhhhhhhhHHHHHHHHHHHhcCCccEEeccchhcccccccCcceEEEecCCcCH
Confidence            34456777777999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHhhhhhcCCCCceeEEEEeccCcHHHHHHHHHHhcCccccccCCcccc
Q psy6712         151 ELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRS  202 (210)
Q Consensus       151 ~~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  202 (210)
                      ..|+||+||+||.|+.|.+++|+.+.|...++.+++.++..++++|.+..+.
T Consensus       116 ~~yihR~GR~gR~g~~G~~i~~~~~~d~~~~~~i~~~~~~~i~e~p~~~~di  167 (168)
T d2j0sa2         116 ELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADL  167 (168)
T ss_dssp             HHHHHHHTTSSGGGCCEEEEEEEEGGGHHHHHHHHHHTTCCCEECCSCCTTT
T ss_pred             HHHHhhhccccccCCCcEEEEEECHHHHHHHHHHHHHHcCcCCCCCcChHHh
Confidence            9999999999999999999999999999999999999999999999876654

>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=99.96  E-value=2.3e-29  Score=182.71  Aligned_cols=133  Identities=38%  Similarity=0.678  Sum_probs=126.3

Q ss_pred             HHHhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCCh
Q psy6712          71 DVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNR  150 (210)
Q Consensus        71 ~i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~  150 (210)
                      +++.|++....++.+++.|...++.+..+||+|+.++|.+++..|++|+.++||||+++++|+|+|++++||+||+|+++
T Consensus        34 k~iVF~~~~~~~~~l~~~L~~~g~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~Td~~~~Gid~~~v~~VI~~d~p~~~  113 (171)
T d1s2ma2          34 QAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTA  113 (171)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCSSSSCCCTTEEEEEESSCCSSH
T ss_pred             ceEEEEeeeehhhHhHHhhhcccccccccccccchhhhhhhhhhcccCccccccchhHhhhccccceeEEEEecCCcchH
Confidence            34557777777999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHhhhhhcCCCCceeEEEEeccCcHHHHHHHHHHhcCccccccCCccccC
Q psy6712         151 ELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRSL  203 (210)
Q Consensus       151 ~~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  203 (210)
                      ..|+||+||+||.|+.|.++.|+.+.+...++++++.++.+++++|....+.+
T Consensus       114 ~~y~qr~GR~gR~g~~g~~i~~v~~~e~~~~~~i~~~l~~~~~~~p~~~d~~~  166 (171)
T d1s2ma2         114 ETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPATIDKSL  166 (171)
T ss_dssp             HHHHHHHCBSSCTTCCEEEEEEECGGGHHHHHHHHHHHTCCCEECCSSCCGGG
T ss_pred             HHHHHHhhhcccCCCccEEEEEeCHHHHHHHHHHHHHHCCCCCCCCcccchhh
Confidence            99999999999999999999999999999999999999999999999888755

>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=99.96  E-value=1.1e-28  Score=176.32  Aligned_cols=123  Identities=38%  Similarity=0.695  Sum_probs=117.5

Q ss_pred             HhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhH
Q psy6712          73 YRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNREL  152 (210)
Q Consensus        73 ~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~  152 (210)
                      +.|++....++.+++.|++.++.+..+|++++..+|..++++|+.|+.++||||+++++|+|+|++++||+||+|+|+..
T Consensus        32 IIF~~s~~~~~~l~~~L~~~g~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~~~~~Gid~~~v~~Vi~~d~p~~~~~  111 (155)
T d1hv8a2          32 LVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPES  111 (155)
T ss_dssp             EEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTHHHHCCCSCCSEEEESSCCSCHHH
T ss_pred             EEEECchHHHHHHHhhhcccccccccccccchhhhhhhhhhhhhcccceeeeehhHHhhhhhhccCcEEEEecCCCCHHH
Confidence            45677777799999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhhhcCCCCceeEEEEeccCcHHHHHHHHHHhcCccccc
Q psy6712         153 YIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEM  195 (210)
Q Consensus       153 ~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~  195 (210)
                      |+||+||+||.|+.|.+++++++.|...++.+++.++.+++++
T Consensus       112 y~qr~GR~gR~g~~g~~i~~~~~~d~~~~~~i~~~~~~~i~~l  154 (155)
T d1hv8a2         112 YMHRIGRTGRAGKKGKAISIINRREYKKLRYIERAMKLKIKKL  154 (155)
T ss_dssp             HHHHSTTTCCSSSCCEEEEEECTTSHHHHHHHHHHHTCCCCCB
T ss_pred             HHHHHHhcCcCCCCceEEEEEchHHHHHHHHHHHHHCCCcccc
Confidence            9999999999999999999999999999999999999988775

>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=99.95  E-value=9e-28  Score=173.62  Aligned_cols=128  Identities=34%  Similarity=0.711  Sum_probs=117.0

Q ss_pred             HHhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChh
Q psy6712          72 VYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRE  151 (210)
Q Consensus        72 i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~  151 (210)
                      ++.|++....++.+.+.|.+.++++..+||+|+.++|.+++++|++|+.++||||+++++|+|+|.+++||+||+|+++.
T Consensus        30 ~iIF~~~~~~~~~l~~~L~~~~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T~~~~~Gid~~~~~~vi~~~~p~~~~  109 (168)
T d1t5ia_          30 VVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSD  109 (168)
T ss_dssp             EEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSCCSTTCCGGGCSEEEESSCCSSHH
T ss_pred             EEEEEeeeecchhhhhhhccccccccccccccchhhhhhhhhhhccccceeeeccccccchhhcccchhhhhhhcccchh
Confidence            44567777779999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhhhhcCCCCceeEEEEeccC-cHHHHHHHHHHhcCccccccCCc
Q psy6712         152 LYIHRIGRSGRFGRKGVAISFVKSD-DIRILRDIEQYYSTQIDEMPMNG  199 (210)
Q Consensus       152 ~~~q~~GR~gR~g~~g~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~  199 (210)
                      .|+||+||+||.|+.|.++.|+++. +...+..+++.++..+.++|.+.
T Consensus       110 ~yiqr~GR~gR~g~~g~~i~l~~~~~~~~~~~~i~~~~~~~~~elp~~~  158 (168)
T d1t5ia_         110 TYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI  158 (168)
T ss_dssp             HHHHHHHHHTGGGCCCEEEEEECSHHHHHHHHHHHHHHCCCEEECC---
T ss_pred             hHhhhhhhcccCCCccEEEEEECchHHHHHHHHHHHHHcCCcccCCchh
Confidence            9999999999999999999999875 56778899999999999988665

>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=99.94  E-value=6.7e-27  Score=173.24  Aligned_cols=113  Identities=22%  Similarity=0.437  Sum_probs=106.0

Q ss_pred             HHhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChh
Q psy6712          72 VYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRE  151 (210)
Q Consensus        72 i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~  151 (210)
                      .+.|++....++.+++.|...++.+..+||+|+.++|.++++.|++|+.++||||+++++|+|+|++++||+||+|.++.
T Consensus        33 ~IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd~~~~GiD~p~v~~VI~~~~P~~~~  112 (200)
T d1oywa3          33 GIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIE  112 (200)
T ss_dssp             EEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSCTTTCCTTCCEEEESSCCSSHH
T ss_pred             EEEEEeeehhhHHhhhhhccCCceeEEecCCCcHHHHHHHHHHHhcccceEEEecchhhhccCCCCCCEEEECCCccchH
Confidence            35577777889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhhhhcCCCCceeEEEEeccCcHHHHHHH
Q psy6712         152 LYIHRIGRSGRFGRKGVAISFVKSDDIRILRDI  184 (210)
Q Consensus       152 ~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~  184 (210)
                      +|+||+||+||.|..|.+++|+.+.|...++++
T Consensus       113 ~y~qr~GR~gR~g~~g~ai~~~~~~d~~~l~~~  145 (200)
T d1oywa3         113 SYYQETGRAGRDGLPAEAMLFYDPADMAWLRRC  145 (200)
T ss_dssp             HHHHHHTTSCTTSSCEEEEEEECHHHHHHHHHH
T ss_pred             HHHHHhhhhhcCCCCceEEEecCHHHHHHHHhh
Confidence            999999999999999999999998877766543

>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=99.92  E-value=1.1e-25  Score=161.74  Aligned_cols=115  Identities=22%  Similarity=0.344  Sum_probs=101.5

Q ss_pred             HHHhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCC--
Q psy6712          71 DVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPN--  148 (210)
Q Consensus        71 ~i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~--  148 (210)
                      ..+.|++....++.+++.|.+.|+++..+||+|+..+|.+++++|++|++++||+|+++++|+|+|++++||+||+|.  
T Consensus        33 r~lvfc~t~~~~~~l~~~L~~~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~v~~~GiDip~V~~Vi~~~~~~~~  112 (174)
T d1c4oa2          33 RTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDADKEG  112 (174)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEEEEEETTTTSCS
T ss_pred             cEEEEEcchhHHHHHHHHHHhcCCceEEEecccchHHHHHHHHHHHCCCeEEEEeeeeeeeeccCCCCcEEEEecccccc
Confidence            456789999999999999999999999999999999999999999999999999999999999999999999999775  


Q ss_pred             ---ChhHHHHhhhhhcCCCCceeEEEEeccCcHHHHHHHHH
Q psy6712         149 ---NRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQ  186 (210)
Q Consensus       149 ---s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~  186 (210)
                         +..+|+||+||+||.|. |.++++.........+.+++
T Consensus       113 ~~~~~~~~iq~~GR~gR~~~-g~~~~~~~~~~~~~~~~i~e  152 (174)
T d1c4oa2         113 FLRSERSLIQTIGRAARNAR-GEVWLYADRVSEAMQRAIEE  152 (174)
T ss_dssp             GGGSHHHHHHHHGGGTTSTT-CEEEEECSSCCHHHHHHHHH
T ss_pred             ccchhHHHHHHhhhhhhcCC-CeeEEeecCCCHHHHHHHHH
Confidence               55889999999999865 77777777655555544444

>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=99.92  E-value=5.3e-25  Score=160.11  Aligned_cols=104  Identities=25%  Similarity=0.392  Sum_probs=93.5

Q ss_pred             HHHhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCC--
Q psy6712          71 DVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPN--  148 (210)
Q Consensus        71 ~i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~--  148 (210)
                      ..+.|++....++.+++.|+..|+++..+||+|++.+|.+++++|++|++++||||+++++|+|+|++++||+||+|.  
T Consensus        33 ~~iif~~~~~~~~~~~~~l~~~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTdv~~rGiDip~v~~VI~~d~p~~~  112 (181)
T d1t5la2          33 RTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEG  112 (181)
T ss_dssp             EEEEECSSHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESCCCSSSCCCTTEEEEEETTTTSCS
T ss_pred             eEEEEeehhhhhHHHHHHHHhCCcceeEecCCccHHHHHHHHHHHHCCCCCEEEehhHHHccCCCCCCCEEEEecCCccc
Confidence            355678888889999999999999999999999999999999999999999999999999999999999999999995  


Q ss_pred             ---ChhHHHHhhhhhcCCCCceeEEEEecc
Q psy6712         149 ---NRELYIHRIGRSGRFGRKGVAISFVKS  175 (210)
Q Consensus       149 ---s~~~~~q~~GR~gR~g~~g~~~~~~~~  175 (210)
                         +...|+||+||+||.|.. .++.+...
T Consensus       113 ~~~s~~~yi~R~GRagR~g~~-~~~~~~~~  141 (181)
T d1t5la2         113 FLRSERSLIQTIGRAARNANG-HVIMYADT  141 (181)
T ss_dssp             GGGSHHHHHHHHGGGTTSTTC-EEEEECSS
T ss_pred             ccccHHHHHHHHHhhccccCc-eeEeecch
Confidence               688999999999999764 44444443

>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=99.84  E-value=1.4e-21  Score=135.73  Aligned_cols=97  Identities=20%  Similarity=0.331  Sum_probs=87.4

Q ss_pred             HHHhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEec----C
Q psy6712          71 DVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYD----L  146 (210)
Q Consensus        71 ~i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~----~  146 (210)
                      +.+.|++....++.+++.|.+.|+++..+|++|+.++       |++|+.++||||+++++|+| |++++||+++    +
T Consensus        37 k~IVFc~t~~~ae~la~~L~~~G~~~~~~H~~~~~~~-------~~~~~~~vlvaTd~~~~GiD-~~v~~Vi~~~~~~~~  108 (138)
T d1jr6a_          37 RHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSV-------IPTNGDVVVVATDALMTGFT-GDFDSVIDCNTSDGK  108 (138)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHHTCEEEEECTTCCSCC-------CTTSSCEEEEESSSSCSSSC-CCBSEEEECSEETTE
T ss_pred             CEEEEeCcHHHHHHHHHHHhccccchhhhhccchhhh-------hhhhhcceeehhHHHHhccc-cccceEEEEEecCCC
Confidence            4577999999999999999999999999999998654       67899999999999999999 9999999855    6


Q ss_pred             CCChhHHHHhhhhhcCCCCceeEEEEeccCc
Q psy6712         147 PNNRELYIHRIGRSGRFGRKGVAISFVKSDD  177 (210)
Q Consensus       147 p~s~~~~~q~~GR~gR~g~~g~~~~~~~~~~  177 (210)
                      |.+...|+||+||+|| |+.|. +.|+.+.|
T Consensus       109 P~~~~~y~qr~GR~gR-g~~G~-~~~i~~~e  137 (138)
T d1jr6a_         109 PQDAVSRTQRRGRTGR-GKPGI-YRFVAPGE  137 (138)
T ss_dssp             ECCHHHHHHHHTTBCS-SSCEE-EEECCSSC
T ss_pred             CCCHHHHHhHhccccC-CCCcE-EEEEcCCC
Confidence            9999999999999999 89995 77887765

>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=99.84  E-value=1.4e-21  Score=144.16  Aligned_cols=94  Identities=26%  Similarity=0.402  Sum_probs=83.5

Q ss_pred             CceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCC-ChhHHHHhhhhhcCCCCceeEEE
Q psy6712          93 NFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPN-NRELYIHRIGRSGRFGRKGVAIS  171 (210)
Q Consensus        93 ~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~-s~~~~~q~~GR~gR~g~~g~~~~  171 (210)
                      +.++..+||.|+++++++++.+|++|+++|||||++++.|+|+|+++++|++++|. ..+++-|..||+||.|..|.|++
T Consensus        64 ~~~v~~lHG~m~~~eke~~m~~F~~g~~~iLVaTtViE~GIDip~a~~iii~~a~~fglsqlhQlrGRvGR~~~~~~~~l  143 (206)
T d1gm5a4          64 EFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFL  143 (206)
T ss_dssp             --CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEEC
T ss_pred             CCeEEEEeecccHHHHHHHHHHHHCCCEEEEEEehhhhccccccCCcEEEEEccCCccHHHHHhhhhheeeccccceeEe
Confidence            56789999999999999999999999999999999999999999999999999997 67777788999999999999999


Q ss_pred             EeccCcHHHHHHHHH
Q psy6712         172 FVKSDDIRILRDIEQ  186 (210)
Q Consensus       172 ~~~~~~~~~~~~~~~  186 (210)
                      ++.+......+.++.
T Consensus       144 ~~~~~~~~~~~rl~~  158 (206)
T d1gm5a4         144 VVGDVGEEAMERLRF  158 (206)
T ss_dssp             CCCSCCHHHHHHHHH
T ss_pred             eeccccccchhhhhh
Confidence            998766655555543

>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=99.82  E-value=1.6e-20  Score=146.27  Aligned_cols=104  Identities=25%  Similarity=0.391  Sum_probs=89.6

Q ss_pred             hCCCchhHHHHHHHHHhcCceEEEecC--------CCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecC
Q psy6712          75 YLPPATQVDWLTEKMREANFTVSSMHG--------DMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDL  146 (210)
Q Consensus        75 ~~~~~~~~~~l~~~l~~~~~~~~~~~~--------~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~  146 (210)
                      |+.....++.+++.|.+.++++..++|        +|+..+|..+++.|++|++++||||+++++|+|+|+|++||+||+
T Consensus       167 F~~~~~~~~~~~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~vLv~T~~~~~Gld~~~~~~Vi~~d~  246 (286)
T d1wp9a2         167 FTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEP  246 (286)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECGGGGGGGGSTTCCEEEESSC
T ss_pred             EeCcHHhHHHHHHHHHHcCCceEEeeccccccccchhchHHHHHHHHHHHcCCCcEEEEccceeccccCCCCCEEEEeCC
Confidence            344444589999999999999998876        567778999999999999999999999999999999999999999


Q ss_pred             CCChhHHHHhhhhhcCCCCceeEEEEeccCcHH
Q psy6712         147 PNNRELYIHRIGRSGRFGRKGVAISFVKSDDIR  179 (210)
Q Consensus       147 p~s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~~  179 (210)
                      |+++..|+||+||+||. ..|.++.|+.+...+
T Consensus       247 ~~~~~~~~Qr~GR~gR~-~~~~~~~l~~~~~~e  278 (286)
T d1wp9a2         247 VPSAIRSIQRRGRTGRH-MPGRVIILMAKGTRD  278 (286)
T ss_dssp             CHHHHHHHHHHTTSCSC-CCSEEEEEEETTSHH
T ss_pred             CCCHHHHHHHHHhCCCC-CCCEEEEEEeCCCHH
Confidence            99999999999999996 568888888876543

>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=99.79  E-value=1.3e-19  Score=133.96  Aligned_cols=95  Identities=25%  Similarity=0.377  Sum_probs=82.2

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEE-------ecCCCChhHHH
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVIN-------YDLPNNRELYI  154 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~-------~~~p~s~~~~~  154 (210)
                      ...|.+.+.   ..++++|++|++++|..+.+.|++|.+++||||+.+++|+|+|..++||.       ++.|.+..+|+
T Consensus        86 ~~~L~~~l~---~GIa~hh~~l~~~~r~~ie~~f~~g~i~vlvaT~~l~~Gin~p~~~vvi~~~~~~d~~~~~~~~~~~~  162 (201)
T d2p6ra4          86 SRKLAECVR---KGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYK  162 (201)
T ss_dssp             HHHHHHHHH---TTCCEECTTSCHHHHHHHHHHHHTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHH
T ss_pred             hHHHHHHHh---ccHHHHHHHhhhhhHHHHHHHHhCCCceEEEechHHHhhcCCCCceEEEecceeccCCcCCCCHHHHH
Confidence            344555553   24789999999999999999999999999999999999999999999996       66788999999


Q ss_pred             HhhhhhcCCCC--ceeEEEEeccCcHH
Q psy6712         155 HRIGRSGRFGR--KGVAISFVKSDDIR  179 (210)
Q Consensus       155 q~~GR~gR~g~--~g~~~~~~~~~~~~  179 (210)
                      ||+|||||.|.  .|.+++++.+.+.+
T Consensus       163 q~~GRAGR~g~~~~G~~~l~~~~~~~~  189 (201)
T d2p6ra4         163 QMAGRAGRPGMDERGEAIIIVGKRDRE  189 (201)
T ss_dssp             HHHTTBSCTTTCSCEEEEEECCGGGHH
T ss_pred             HHhcccCCCCCCCeeEEEEEeCCCChH
Confidence            99999999985  68899888776644

>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=99.76  E-value=1.3e-18  Score=136.05  Aligned_cols=146  Identities=17%  Similarity=0.163  Sum_probs=108.0

Q ss_pred             CCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchH--HHHHHHHh---------------------------
Q psy6712          24 GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFK--EQIYDVYR---------------------------   74 (210)
Q Consensus        24 ~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~--~~~~~i~~---------------------------   74 (210)
                      ...|+++||+.+..... ....+++++++|+||+|.+..+++.  ..+..+..                           
T Consensus        77 ~~~i~~~t~~~l~~~~~-~~~~~~~~~~vViDE~H~~~~~~~~~~~~l~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~  155 (305)
T d2bmfa2          77 REIVDLMCHATFTMRLL-SPIRVPNYNLIIMDEAHFTDPASIAARGYISTRVEMGEAAGIFMTATPPGSRDPFPQSNAPI  155 (305)
T ss_dssp             CCSEEEEEHHHHHHHHT-SSSCCCCCSEEEEESTTCCSHHHHHHHHHHHHHHHHTSCEEEEECSSCTTCCCSSCCCSSCE
T ss_pred             ccccccCCcHHHHHHHh-cCccccceeEEEeeeeeecchhhHHHHHHHHHhhccccceEEEeecCCCcceeeecccCCcc
Confidence            45789999998776554 4456789999999999988755422  11111111                           


Q ss_pred             ----------------------------hCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEe
Q psy6712          75 ----------------------------YLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITT  126 (210)
Q Consensus        75 ----------------------------~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T  126 (210)
                                                  |++...+++.+++.|++.++.+..+||+++...    ...|++|+.+++|+|
T Consensus       156 ~~~~~~~~~~~~~~~~~~~~~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~l~~~~~~~~----~~~~~~~~~~~lvaT  231 (305)
T d2bmfa2         156 MDEEREIPERSWNSGHEWVTDFKGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSRKTFDSE----YIKTRTNDWDFVVTT  231 (305)
T ss_dssp             EEEECCCCCSCCSSCCHHHHSSCSCEEEECSCHHHHHHHHHHHHHHTCCCEECCTTCHHHH----GGGGGTSCCSEEEEC
T ss_pred             eEEEEeccHHHHHHHHHHHHhhCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeCCcChHHH----Hhhhhccchhhhhhh
Confidence                                        122222289999999999999999999986544    347889999999999


Q ss_pred             cCccccCCCCCCcEEE----------Eec----------CCCChhHHHHhhhhhcCCCCceeEEEEecc
Q psy6712         127 DVWARGIDVQQVSLVI----------NYD----------LPNNRELYIHRIGRSGRFGRKGVAISFVKS  175 (210)
Q Consensus       127 ~~~~~g~d~~~~~~vi----------~~~----------~p~s~~~~~q~~GR~gR~g~~g~~~~~~~~  175 (210)
                      +++++|+|+ +++.||          ++|          .|.|..+|+||+||+||.|+.+....++..
T Consensus       232 ~~~~~G~~~-~~~~Vi~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~Qr~GR~GR~~~~~~~~~~~~~  299 (305)
T d2bmfa2         232 DISEMGANF-KAERVIDPRRCMKPVILTDGEERVILAGPMPVTHSSAAQRRGRVGRNPKNENDQYIYMG  299 (305)
T ss_dssp             GGGGTTCCC-CCSEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCSSSCCCEEEEECS
T ss_pred             HHHHhcCCC-CccEEEEcCCceeeeEecCCCCceEEeccccCCHHHHhhhhcCcCcCCCCceEEEEECC
Confidence            999999999 455554          233          356889999999999999987776666654

>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=99.76  E-value=7.4e-18  Score=123.30  Aligned_cols=95  Identities=21%  Similarity=0.316  Sum_probs=83.5

Q ss_pred             HHHHHHHHHh--cCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCC-ChhHHHHhhh
Q psy6712          82 VDWLTEKMRE--ANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPN-NRELYIHRIG  158 (210)
Q Consensus        82 ~~~l~~~l~~--~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~-s~~~~~q~~G  158 (210)
                      .+.+.+.+.+  .+.++..+||.|+.+++.+++.+|.+|+++|||||++++.|+|+|+++++|..+.+. ..+++-|..|
T Consensus        44 ~e~~~~~l~~~~p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~TtvIEvGiDvpnA~~iiI~~a~rfGLaQLhQLRG  123 (211)
T d2eyqa5          44 IQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRG  123 (211)
T ss_dssp             HHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSCCTTEEEEEETTTTSSCHHHHHHHHT
T ss_pred             hhhHHHHHHHhCCceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEehhhhhccCCCCCcEEEEecchhccccccccccc
Confidence            3333444433  367899999999999999999999999999999999999999999999999999885 7889999999


Q ss_pred             hhcCCCCceeEEEEeccC
Q psy6712         159 RSGRFGRKGVAISFVKSD  176 (210)
Q Consensus       159 R~gR~g~~g~~~~~~~~~  176 (210)
                      |+||.+..+.|++++.+.
T Consensus       124 RVGR~~~~s~c~l~~~~~  141 (211)
T d2eyqa5         124 RVGRSHHQAYAWLLTPHP  141 (211)
T ss_dssp             TCCBTTBCEEEEEEECCG
T ss_pred             eeeecCccceEEEEecCC
Confidence            999999999999999653

>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=99.72  E-value=2.2e-18  Score=127.28  Aligned_cols=93  Identities=22%  Similarity=0.391  Sum_probs=79.0

Q ss_pred             CchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecCCCChhHHHHhh
Q psy6712          78 PATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRI  157 (210)
Q Consensus        78 ~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~  157 (210)
                      ....++.+++.|     .+..+||+++..+|..++++|++|+.++||+|+++++|+|+|.+++||++++|+|+..|+||+
T Consensus       102 ~~~~~~~l~~~l-----~~~~i~g~~~~~~R~~~l~~F~~~~~~vLv~~~~~~~Gidl~~~~~vi~~~~~~s~~~~~Q~i  176 (200)
T d2fwra1         102 HNELVYRISKVF-----LIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRL  176 (200)
T ss_dssp             CHHHHHHHHHHT-----TCCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSSCSCCBSEEEEECCSSCCHHHHHHH
T ss_pred             cHHHHHHHHhhc-----CcceeeCCCCHHHHHHHHHHhhcCCeeeeeecchhhcccCCCCCCEEEEeCCCCCHHHHHHHH
Confidence            333366666665     455689999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhcCCCCc---eeEEEEecc
Q psy6712         158 GRSGRFGRK---GVAISFVKS  175 (210)
Q Consensus       158 GR~gR~g~~---g~~~~~~~~  175 (210)
                      ||++|.|+.   ..++-|+..
T Consensus       177 GR~~R~~~~k~~~~i~~~v~~  197 (200)
T d2fwra1         177 GRILRPSKGKKEAVLYELISR  197 (200)
T ss_dssp             HHSBCCCTTTCCEEEEEEEEC
T ss_pred             HhcCCCCCCCcEEEEEEEecC
Confidence            999999863   334445543

>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=99.70  E-value=2.4e-20  Score=142.47  Aligned_cols=103  Identities=14%  Similarity=0.234  Sum_probs=84.8

Q ss_pred             HhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEe----cCccccCCCCC-CcEEEEecCC
Q psy6712          73 YRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITT----DVWARGIDVQQ-VSLVINYDLP  147 (210)
Q Consensus        73 ~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T----~~~~~g~d~~~-~~~vi~~~~p  147 (210)
                      +.|++....++.+++.|+..      +||+|++.+|.+++++|++|++++||||    +.+++|+|+|+ +++|||||+|
T Consensus        29 iif~~~~~~~~~l~~~l~~~------~hg~~~~~~R~~~~~~f~~g~~~vLVaT~a~~~v~~rGlDip~~v~~VI~~d~P  102 (248)
T d1gkub2          29 IIYARTGEEAEEIYESLKNK------FRIGIVTATKKGDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCP  102 (248)
T ss_dssp             EEEESSHHHHHHHHHTTTTS------SCEEECTTSSSHHHHHHHHTSCSEEEEECC------CCSCCTTTCCEEEEESCC
T ss_pred             EEEECCHHHHHHHHHHHHHh------ccCCCCHHHHHHHHHHHHhCCCeEEEEeccccchhhhccCccccccEEEEeCCC
Confidence            44566666688888888652      8999999999999999999999999999    67899999996 9999999999


Q ss_pred             CChhHHHHhhhhhcCCCCceeEEEEeccCcHHHHHHHH
Q psy6712         148 NNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIE  185 (210)
Q Consensus       148 ~s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~~~~~~~~  185 (210)
                      +    |.||+||+||.|..|.+++++...+......+.
T Consensus       103 ~----~~~r~gR~~R~g~~~~~~~~~~~~~~~~~~~l~  136 (248)
T d1gkub2         103 S----FRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLL  136 (248)
T ss_dssp             E----EEEECSCGGGSCHHHHHHHHTTTSCHHHHHTTC
T ss_pred             c----chhhhhhhhccCcceEeeeeccHhhHHHHHHHH
Confidence            5    889999999999998888888776666554443

>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=99.68  E-value=7.9e-18  Score=128.57  Aligned_cols=102  Identities=14%  Similarity=0.166  Sum_probs=89.1

Q ss_pred             HHHhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHH----------HHHHHHHhcCCCcEEEEecCccc---cCCCCC
Q psy6712          71 DVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKER----------DGIMKEFRSGTSRVLITTDVWAR---GIDVQQ  137 (210)
Q Consensus        71 ~i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r----------~~~~~~f~~g~~~ilv~T~~~~~---g~d~~~  137 (210)
                      +.+.|++...+++.+++.|++.|+++..+|++|+.+.|          ...++.|..|+.+++|+|+...+   |+|++.
T Consensus        38 k~LVFcnSR~~aE~La~~L~~~Gi~a~~~Hgglsq~~R~~~gd~~i~~~~aLe~f~~G~~dvVVaT~~~a~g~~giDid~  117 (299)
T d1a1va2          38 RHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFSLDP  117 (299)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCGGGSCSSSSEEEEECTTC---CCCCBSEEEECCEEEEEEEECCCSS
T ss_pred             CEEEECCcHHHHHHHHHHHHHCCCCEEEEeCCchHHHHHhccchHHHHHHHHHHHhcCCCcEEEEEeehhccCCCCCCCc
Confidence            56789999999999999999999999999999998876          56788999999999999999888   677888


Q ss_pred             CcEEEEecCCCChhHHHHhhhhhcCCCCceeEEEEe
Q psy6712         138 VSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFV  173 (210)
Q Consensus       138 ~~~vi~~~~p~s~~~~~q~~GR~gR~g~~g~~~~~~  173 (210)
                      +.+||++++|.|+.+|+||+||+|| |++|....+.
T Consensus       118 V~~VI~~d~P~SvesyIQRiGRTGR-Gr~G~~~~l~  152 (299)
T d1a1va2         118 TFTIETTTLPQDAVSRTQRRGRTGR-GKPGIYRFVA  152 (299)
T ss_dssp             SCEEEEEEEECBHHHHHHHHTTBCS-SSCEEEEESC
T ss_pred             ceEEEeCCCCCCHHHHHhhccccCC-CCCceEEEEe
Confidence            8899999999999999999999999 8888765444

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=2.4e-15  Score=112.28  Aligned_cols=80  Identities=93%  Similarity=1.475  Sum_probs=75.0

Q ss_pred             CCceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCch
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPAT   80 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~   80 (210)
                      +++++..++||.+..++...+..++||+|+||+++.+++..+.+++++++++|+||||.|++.++.+.+..++..++..+
T Consensus       112 ~~i~~~~~~g~~~~~~~~~~l~~~~~Ilv~TPgrl~~~~~~~~~~~~~l~~lVlDEaD~ll~~~f~~~i~~I~~~l~~~~  191 (222)
T d2j0sa1         112 MNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPAT  191 (222)
T ss_dssp             TTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHTSTTTHHHHHHHHTTSCTTC
T ss_pred             cceeEEEEeecccchhhHHHhccCCeEEeCCCCcHHhcccccccccccceeeeecchhHhhhcCcHHHHHHHHHhCCCCC
Confidence            46889999999999999999999999999999999999999999999999999999999999999999999999887544

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.53  E-value=1.2e-14  Score=107.43  Aligned_cols=100  Identities=32%  Similarity=0.652  Sum_probs=85.1

Q ss_pred             CCceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCch
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPAT   80 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~   80 (210)
                      .++++..++|+.+...+...+.+++||||+||+++.+++..+.+++++++++|+||||.|++.+|.+.+..++..+++.+
T Consensus        96 ~~~~~~~~~g~~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~lV~DEaD~l~~~~f~~~v~~I~~~l~~~~  175 (206)
T d1s2ma1          96 CGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTH  175 (206)
T ss_dssp             TTCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEESHHHHSSHHHHHHHHHHHTTSCSSC
T ss_pred             cCeeEEeecCccchhhHHHHhcccceEEEECCcccccccccceeecccceEEEeechhhhhhhhhHHHHHHHHHhCCCCC
Confidence            36889999999999999999999999999999999999999999999999999999999999999999999999887543


Q ss_pred             hHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHH
Q psy6712          81 QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEF  115 (210)
Q Consensus        81 ~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f  115 (210)
                                    ....+.+.++.+-.. ..+.|
T Consensus       176 --------------Q~il~SATl~~~v~~-~~~~~  195 (206)
T d1s2ma1         176 --------------QSLLFSATFPLTVKE-FMVKH  195 (206)
T ss_dssp             --------------EEEEEESCCCHHHHH-HHHHH
T ss_pred             --------------EEEEEEEeCCHHHHH-HHHHH
Confidence                          455666666654333 44444

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=3.1e-14  Score=105.11  Aligned_cols=99  Identities=33%  Similarity=0.587  Sum_probs=82.9

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchh
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ   81 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~   81 (210)
                      ++.+....||.....+...+..++||+|+||+++.+++..+.+++++++++|+||||.|++.+|.+.+..++..+++.. 
T Consensus       100 ~~~~~~~~g~~~~~~~~~~l~~~~~ivv~TPgrl~~~~~~~~~~~~~l~~lVlDEaD~ll~~~f~~~i~~I~~~~~~~~-  178 (206)
T d1veca_         100 GAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNR-  178 (206)
T ss_dssp             SCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEETHHHHTSTTTHHHHHHHHHHSCTTC-
T ss_pred             CcccccccCCccHHHHHHHHHhccCeEEeCCccccccccchhccccccceEEEeccccccccchHHHHHHHHHhCCCCC-
Confidence            4567888999999999999999999999999999999999999999999999999999999999999999998887543 


Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHH
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEF  115 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f  115 (210)
                                   ...++.+.++.+-+ +..+.|
T Consensus       179 -------------Q~~l~SAT~~~~v~-~l~~~~  198 (206)
T d1veca_         179 -------------QILLYSATFPLSVQ-KFMNSH  198 (206)
T ss_dssp             -------------EEEEEESCCCHHHH-HHHHHH
T ss_pred             -------------EEEEEEecCCHHHH-HHHHHH
Confidence                         45566666665433 334444

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.49  E-value=5.7e-14  Score=103.83  Aligned_cols=99  Identities=30%  Similarity=0.539  Sum_probs=81.1

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchh
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ   81 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~   81 (210)
                      ++++..++|+.+..++.+.+ +++||+|+||+++.+++.++.+++++++++|+||||.|++.++.+.+..++..+++.  
T Consensus       100 ~~~v~~~~g~~~~~~~~~~l-~~~~IlV~TP~~l~~~l~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~I~~~~~~~--  176 (208)
T d1hv8a1         100 NLKIAKIYGGKAIYPQIKAL-KNANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKD--  176 (208)
T ss_dssp             CCCEEEECTTSCHHHHHHHH-HTCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHTTTTHHHHHHHHHTSCSS--
T ss_pred             CeEEEEeeCCCChHHHHHhc-CCCCEEEEChHHHHHHHHcCCCCcccCcEEEEEChHHhhcCCChHHHHHHHHhCCCC--
Confidence            57889999999998888776 479999999999999999999999999999999999999999999999999877643  


Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHh
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFR  116 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~  116 (210)
                                  .....+.+.++.+-. +..+.|.
T Consensus       177 ------------~Q~i~~SAT~~~~v~-~~~~~~l  198 (208)
T d1hv8a1         177 ------------KRILLFSATMPREIL-NLAKKYM  198 (208)
T ss_dssp             ------------CEEEEECSSCCHHHH-HHHHHHC
T ss_pred             ------------CeEEEEEccCCHHHH-HHHHHHC
Confidence                        345566666665433 4455554

>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=99.44  E-value=3.3e-13  Score=106.83  Aligned_cols=103  Identities=17%  Similarity=0.298  Sum_probs=87.1

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCc---EEEEecCccccCCCCCCcEEEEecCCCChhHHHHhhh
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSR---VLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIG  158 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~---ilv~T~~~~~g~d~~~~~~vi~~~~p~s~~~~~q~~G  158 (210)
                      .+.+.+.|...++....++|.++..+|..+++.|+++...   +|++|.+++.|+|++.+++||+||++|++..+.|++|
T Consensus       131 ld~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~vlLls~~agg~GlnL~~a~~vi~~d~~wnp~~~~Qa~~  210 (346)
T d1z3ix1         131 LDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLVMFDPDWNPANDEQAMA  210 (346)
T ss_dssp             HHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGGGSCTTCCCTTEEEEEECSCCSSHHHHHHHHT
T ss_pred             hHHHHHHHhhhhccccccccchhHHHHHHHHHhhhcccccceeeeecchhhhhccccccceEEEEecCCCccchHhHhhh
Confidence            7788899999999999999999999999999999987653   6788899999999999999999999999999999999


Q ss_pred             hhcCCCCceeE--EEEeccC--cHHHHHHH
Q psy6712         159 RSGRFGRKGVA--ISFVKSD--DIRILRDI  184 (210)
Q Consensus       159 R~gR~g~~g~~--~~~~~~~--~~~~~~~~  184 (210)
                      |+.|.|+...|  +-++...  |...++..
T Consensus       211 R~~R~GQ~~~V~v~rli~~~TiEe~i~~~~  240 (346)
T d1z3ix1         211 RVWRDGQKKTCYIYRLLSTGTIEEKILQRQ  240 (346)
T ss_dssp             TSSSTTCCSCEEEEEEEETTSHHHHHHHHH
T ss_pred             cccccCCCCceEEEEEEeCCCHHHHHHHHH
Confidence            99999986544  3444443  33444443

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=99.42  E-value=1.4e-12  Score=98.20  Aligned_cols=106  Identities=25%  Similarity=0.444  Sum_probs=87.4

Q ss_pred             CCceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCch
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPAT   80 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~   80 (210)
                      +++++..++|+.....+......++||+|+||++|.+++..+...+++++++|+||||.|++.+|.+++..++..+....
T Consensus       125 ~~~~~~~~~g~~~~~~~~~~~~~~~~ivV~TP~~l~~~~~~~~~~l~~v~~lViDEaD~ll~~~f~~~i~~Il~~~~~~~  204 (238)
T d1wrba1         125 TPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEESNMPS  204 (238)
T ss_dssp             SSCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCTTCCEEEEETHHHHHHTTCHHHHHHHHHSSCCCC
T ss_pred             CCcEEEEEeccchhhHHHhhcccCCceeecCHHHHHhHHccCceeccccceeeeehhhhhhhhccHHHHHHHHHHhcCCC
Confidence            36889999999999999999999999999999999999999999999999999999999999999999999987654321


Q ss_pred             hHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhc
Q psy6712          81 QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRS  117 (210)
Q Consensus        81 ~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~  117 (210)
                                .......++.+.|+.+- .+..+.|-.
T Consensus       205 ----------~~~~Q~il~SAT~~~~v-~~l~~~~~~  230 (238)
T d1wrba1         205 ----------GINRQTLMFSATFPKEI-QKLAADFLY  230 (238)
T ss_dssp             ----------GGGCEEEEEESSCCHHH-HHHHHHHCS
T ss_pred             ----------CCCCEEEEEeeeCCHHH-HHHHHHHCC
Confidence                      12235667777776543 556666654

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.42  E-value=2.9e-13  Score=99.85  Aligned_cols=77  Identities=31%  Similarity=0.653  Sum_probs=68.7

Q ss_pred             ceEEEEEcCcchHHHHHHhc-CCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhcc-chHHHHHHHHhhCCCc
Q psy6712           3 VQCHACIGGTNLSEDLRKLD-YGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNK-GFKEQIYDVYRYLPPA   79 (210)
Q Consensus         3 i~~~~~~gg~~~~~~~~~l~-~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~-~~~~~~~~i~~~~~~~   79 (210)
                      ++++.++||.+.+.+...+. .++||+|+||+++.+++.++.+++++++++|+||||.|++. ++.+.+..++..++..
T Consensus        99 ~~~~~~~g~~~~~~~~~~l~~~~~~ilI~TP~rl~~~~~~~~~~l~~l~~lVlDEaD~ll~~~~~~~~i~~I~~~~~~~  177 (207)
T d1t6na_          99 VKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHE  177 (207)
T ss_dssp             CCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEESHHHHHSSHHHHHHHHHHHHTSCSS
T ss_pred             ceeEEEeccccHHHHHHHHHhcCCCEEEeCcchhhhhccCCceeccccceeehhhhhhhhhcCCcHHHHHHHHHhCCCC
Confidence            56888999999998888774 57999999999999999999999999999999999999984 8999999999887654

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.40  E-value=4.8e-13  Score=99.03  Aligned_cols=99  Identities=51%  Similarity=0.883  Sum_probs=72.2

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchh
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ   81 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~   81 (210)
                      ++++..+.|+.+..++...++ ++||+|+||+++..++..+.+++++++++|+||||.|++.++.+.+..++..++..+ 
T Consensus       106 ~~~~~~~~~~~~~~~~~~~~~-~~~IvI~TP~~l~~~~~~~~~~l~~l~~lVlDEad~lld~~f~~~v~~I~~~~~~~~-  183 (212)
T d1qdea_         106 DIKVHACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTT-  183 (212)
T ss_dssp             CCCEEEECC----------CT-TCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHTTCHHHHHHHHHHSCTTC-
T ss_pred             ccceeeEeeccchhHHHHHhc-CCcEEEECCCccccccccCceecCcceEEeehhhhhhcccchHHHHHHHHHhCCCCC-
Confidence            467788888888887777664 789999999999999999999999999999999999999999999999998876543 


Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHh
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFR  116 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~  116 (210)
                                   ....+.+.++.. -.+..+.|.
T Consensus       184 -------------Q~vl~SAT~~~~-v~~l~~~~l  204 (212)
T d1qdea_         184 -------------QVVLLSATMPND-VLEVTTKFM  204 (212)
T ss_dssp             -------------EEEEEESSCCHH-HHHHHHHHC
T ss_pred             -------------eEEEEEeeCCHH-HHHHHHHHC
Confidence                         455666667654 333445553

>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=99.34  E-value=4.4e-13  Score=101.32  Aligned_cols=102  Identities=18%  Similarity=0.270  Sum_probs=69.1

Q ss_pred             hCCCchhHHHHHHHHHh-cCceEEEecCCCCHhHHHHHHHHHhcCC-CcEEEE-ecCccccCCCCCCcEEEEecCCCChh
Q psy6712          75 YLPPATQVDWLTEKMRE-ANFTVSSMHGDMPQKERDGIMKEFRSGT-SRVLIT-TDVWARGIDVQQVSLVINYDLPNNRE  151 (210)
Q Consensus        75 ~~~~~~~~~~l~~~l~~-~~~~~~~~~~~~~~~~r~~~~~~f~~g~-~~ilv~-T~~~~~g~d~~~~~~vi~~~~p~s~~  151 (210)
                      |+......+.+.+.+.. .+..+..+||+++..+|..+++.|.++. ..++++ |.+.+.|+|++.+++||++++||++.
T Consensus        91 Fs~~~~~~~~l~~~l~~~~~~~~~~i~G~~~~~~R~~~i~~F~~~~~~~vll~~~~~~g~Glnl~~a~~vi~~~~~wn~~  170 (244)
T d1z5za1          91 FTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIHFDRWWNPA  170 (244)
T ss_dssp             EESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEECCTTCCCCCCTTCSEEEECSCCSCTT
T ss_pred             EeeceehHHHHHHHHHhhccceEEEEecccchhccchhhhhhhccccchhccccccccccccccchhhhhhhcCchhhhH
Confidence            33333336667777754 4888999999999999999999998764 566655 57889999999999999999999999


Q ss_pred             HHHHhhhhhcCCCCcee--EEEEeccC
Q psy6712         152 LYIHRIGRSGRFGRKGV--AISFVKSD  176 (210)
Q Consensus       152 ~~~q~~GR~gR~g~~g~--~~~~~~~~  176 (210)
                      .+.|+.||+.|.|+...  ++-++...
T Consensus       171 ~~~Qa~~R~~R~Gq~~~v~i~~l~~~~  197 (244)
T d1z5za1         171 VEDQATDRVYRIGQTRNVIVHKLISVG  197 (244)
T ss_dssp             TC--------------CCEEEEEEETT
T ss_pred             HHhhhcceeeecCCCCceEEEEEeeCC
Confidence            99999999999998543  44455544

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.33  E-value=1.1e-12  Score=97.47  Aligned_cols=101  Identities=49%  Similarity=0.872  Sum_probs=77.6

Q ss_pred             CceEEEEEcCcchHHHHHHhc-CCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCch
Q psy6712           2 NVQCHACIGGTNLSEDLRKLD-YGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPAT   80 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~-~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~   80 (210)
                      ++++..+.||....++..... ++++|+|+||+++.+++.++...+++++++|+||||.|++.+|.+.+..++..++.. 
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~IvV~TP~rl~~~l~~~~~~~~~l~~lVlDEaD~ll~~~f~~~~~~Il~~~~~~-  186 (218)
T d2g9na1         108 GASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSN-  186 (218)
T ss_dssp             TCCEEEECC--CCCSTTTSSSSCCCSEEEECHHHHHHHHHTTSSCSTTCCEEEEESHHHHHHTTCHHHHHHHHHHSCTT-
T ss_pred             ceeEEeeecccchhHHHHHHhcCCCEEEEeCChhHHHHHhcCCcccccceEEEeeecchhhcCchHHHHHHHHHhCCCC-
Confidence            456777788777666554443 578999999999999999999999999999999999999999999999999888643 


Q ss_pred             hHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhc
Q psy6712          81 QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRS  117 (210)
Q Consensus        81 ~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~  117 (210)
                                   .....+.+.++.+ -.+..+.|-.
T Consensus       187 -------------~Q~il~SAT~~~~-v~~~~~~~l~  209 (218)
T d2g9na1         187 -------------TQVVLLSATMPSD-VLEVTKKFMR  209 (218)
T ss_dssp             -------------CEEEEEESCCCHH-HHHHHHHHCS
T ss_pred             -------------CeEEEEEecCCHH-HHHHHHHHCC
Confidence                         3556666777664 3334455543

>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=99.31  E-value=3.8e-12  Score=98.26  Aligned_cols=99  Identities=16%  Similarity=0.240  Sum_probs=76.9

Q ss_pred             HHHhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCCCcEEEEecC----
Q psy6712          71 DVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDL----  146 (210)
Q Consensus        71 ~i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~~~~vi~~~~----  146 (210)
                      +++.|++....++.+++.|++.|.++..+||.++..++.    +|++++.+++|||++++.|+++ ++.+||+++.    
T Consensus        38 ~~~~F~~s~~~~~~~a~~L~~~g~~V~~l~~~~~~~e~~----~~~~~~~~~~~~t~~~~~~~~~-~~~~vid~g~~~~~  112 (299)
T d1yksa2          38 PTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYP----TIKQKKPDFILATDIAEMGANL-CVERVLDCRTAFKP  112 (299)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHTTCCEEECCSSSCC------------CCCSEEEESSSTTCCTTC-CCSEEEECCEEEEE
T ss_pred             CEEEEeCCHHHHHHHHHHHHhcCCeEEEEcCcCcHhHHh----hhhcCCcCEEEEechhhhceec-CceEEEecCceece
Confidence            456688888999999999999999999999999887755    5778999999999999999999 5999986543    


Q ss_pred             ---------------CCChhHHHHhhhhhcCCCCceeEEEEec
Q psy6712         147 ---------------PNNRELYIHRIGRSGRFGRKGVAISFVK  174 (210)
Q Consensus       147 ---------------p~s~~~~~q~~GR~gR~g~~g~~~~~~~  174 (210)
                                     |.|.++-.||.||+||.+....++.++.
T Consensus       113 ~~~~~~~~~~~~~~~~~~~~~~~qr~gr~gr~~~~~~~~~~y~  155 (299)
T d1yksa2         113 VLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYS  155 (299)
T ss_dssp             EEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEEC
T ss_pred             eeecCCCCeeEEeeeecCHHHHHHhcccccccCCCceEEEEeC
Confidence                           2477888999999999865544444443

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=99.29  E-value=2.6e-12  Score=94.64  Aligned_cols=99  Identities=32%  Similarity=0.598  Sum_probs=81.4

Q ss_pred             ceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchhH
Q psy6712           3 VQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQV   82 (210)
Q Consensus         3 i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~~   82 (210)
                      ..+..+.|+.+...+......+++|+|+||+++..++.++...+++++++|+||||.++++++.+.+..++..+++.   
T Consensus       102 ~~~~~~~~~~~~~~~~~~~~~~~~Ilv~TP~~l~~~~~~~~~~~~~l~~lViDEad~ll~~~f~~~v~~I~~~~~~~---  178 (209)
T d1q0ua_         102 IVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMGFITDVDQIAARMPKD---  178 (209)
T ss_dssp             CCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGCCEEEECSHHHHHHTTCHHHHHHHHHTSCTT---
T ss_pred             ccccccccchhhHHHHHHhccCceEEEecCchhhhhhhhhccccccceEEEEeecccccccccHHHHHHHHHHCCCC---
Confidence            45667788888887777788899999999999999999999999999999999999999999999999999887643   


Q ss_pred             HHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHh
Q psy6712          83 DWLTEKMREANFTVSSMHGDMPQKERDGIMKEFR  116 (210)
Q Consensus        83 ~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~  116 (210)
                                 .....+.+.++.+-++ ..+.|-
T Consensus       179 -----------~Q~il~SATl~~~v~~-l~~~~l  200 (209)
T d1q0ua_         179 -----------LQMLVFSATIPEKLKP-FLKKYM  200 (209)
T ss_dssp             -----------CEEEEEESCCCGGGHH-HHHHHC
T ss_pred             -----------CEEEEEEccCCHHHHH-HHHHHC
Confidence                       3566777777665443 555554

>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=99.15  E-value=1.9e-11  Score=86.25  Aligned_cols=106  Identities=19%  Similarity=0.289  Sum_probs=84.5

Q ss_pred             HHHHhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCC---Cc-----EE
Q psy6712          70 YDVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQ---VS-----LV  141 (210)
Q Consensus        70 ~~i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~---~~-----~v  141 (210)
                      ..++..+......+.+++.|.+.++++.++++....++-.-+.++  ...-.|.|+|+++++|.|+.-   +.     +|
T Consensus        35 rPVLIgT~SIe~SE~ls~~L~~~gi~h~vLnAk~~~~Ea~II~~A--g~~g~VtIATNmAGRGtDikl~~~v~~~GGLhV  112 (175)
T d1tf5a4          35 QPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEA--GQKGAVTIATNMAGRGTDIKLGEGVKELGGLAV  112 (175)
T ss_dssp             CCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHHHHTTT--TSTTCEEEEETTSSTTCCCCCCTTSGGGTSEEE
T ss_pred             CCEEEEeCcHHHHHHHHHHHHHcCCCceeehhhhHHHHHHHHHhc--cCCCceeehhhHHHcCCCccchHHHHhCCCcEE
Confidence            345556667777999999999999999999998654444333333  233479999999999999842   22     89


Q ss_pred             EEecCCCChhHHHHhhhhhcCCCCceeEEEEeccCc
Q psy6712         142 INYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDD  177 (210)
Q Consensus       142 i~~~~p~s~~~~~q~~GR~gR~g~~g~~~~~~~~~~  177 (210)
                      |....|.|..-..|..||+||+|.+|.+.+|++-+|
T Consensus       113 I~t~~~~s~Rid~Ql~GR~gRQGdpGs~~~~~sleD  148 (175)
T d1tf5a4         113 VGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMED  148 (175)
T ss_dssp             EESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTS
T ss_pred             EEeccCcchhHHHHHhcchhhhCCCcccEEEEEcCH
Confidence            999999999999999999999999999999997654

>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=98.47  E-value=6.2e-08  Score=69.46  Aligned_cols=106  Identities=19%  Similarity=0.245  Sum_probs=77.9

Q ss_pred             HHHhhCCCchhHHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccccCCCCC-------------
Q psy6712          71 DVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQ-------------  137 (210)
Q Consensus        71 ~i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~g~d~~~-------------  137 (210)
                      -++.-+......+.+++.|.+.++++.++++.--.++-.-+.++=  ..-.|-|+|+++++|.|+-=             
T Consensus        36 PVLVGT~SVe~SE~lS~lL~~~gi~h~vLNAK~herEAeIIAqAG--~~GaVTIATNMAGRGTDI~LGgn~~~~~~~~~~  113 (219)
T d1nkta4          36 PVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQEATIIAVAG--RRGGVTVATNMAGRGTDIVLGGNVDFLTDQRLR  113 (219)
T ss_dssp             CEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHHHHHHHHTTT--STTCEEEEETTCSTTCCCCTTCCHHHHHHHHHH
T ss_pred             CEEEeeCcHHHHHHHHHHHHHhccchhccchhhHHHHHHHHHhcc--cCCcEEeeccccCCCCceeecCchhhhhHHHhh
Confidence            334445566668999999999999999999984333333222222  23368999999999999821             


Q ss_pred             ----------------------------------C-----cEEEEecCCCChhHHHHhhhhhcCCCCceeEEEEeccCcH
Q psy6712         138 ----------------------------------V-----SLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDI  178 (210)
Q Consensus       138 ----------------------------------~-----~~vi~~~~p~s~~~~~q~~GR~gR~g~~g~~~~~~~~~~~  178 (210)
                                                        |     =+||-.....|..-=-|..||+||+|.+|.+.+|++-+|.
T Consensus       114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIGTErHeSrRIDnQLRGRsGRQGDPGsSrFflSLeDd  193 (219)
T d1nkta4         114 ERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQLRGRSGRQGDPGESRFYLSLGDE  193 (219)
T ss_dssp             HTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHHHHHHHTSSGGGCCEEEEEEEETTSH
T ss_pred             hcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcEEEeccccccccccccccccccccCCCccceeEEeccHH
Confidence                                              0     0677766667777777999999999999999999987654

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=98.14  E-value=1e-05  Score=57.76  Aligned_cols=62  Identities=18%  Similarity=0.185  Sum_probs=48.4

Q ss_pred             CceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccc
Q psy6712           2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKG   64 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~   64 (210)
                      +.++....++....... ......+|+++||+.+...+....+.+++++++|+||||.+....
T Consensus        80 ~~~v~~~~~~~~~~~~~-~~~~~~~i~i~t~~~~~~~~~~~~~~~~~~~~vIiDE~H~~~~~~  141 (200)
T d1wp9a1          80 PEKIVALTGEKSPEERS-KAWARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNY  141 (200)
T ss_dssp             GGGEEEECSCSCHHHHH-HHHHHCSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTTC
T ss_pred             ccceeeeecccchhHHH-HhhhcccccccccchhHHHHhhhhhhccccceEEEEehhhhhcch
Confidence            45667777776665433 333456899999999999999888889999999999999887544

>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=97.93  E-value=5.6e-06  Score=61.05  Aligned_cols=55  Identities=13%  Similarity=0.091  Sum_probs=38.3

Q ss_pred             EEEEcCcchHHHHHHh--cCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccc
Q psy6712           6 HACIGGTNLSEDLRKL--DYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKG   64 (210)
Q Consensus         6 ~~~~gg~~~~~~~~~l--~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~   64 (210)
                      ....++.....+...+  ..+++|+|+||+++.+    ....+++++++|+||+|.+++.+
T Consensus       122 ~~~~~~~~~~~~~~~l~~~~~~~Ilv~Tp~~l~~----~~~~~~~~~~vVvDE~d~~l~~~  178 (237)
T d1gkub1         122 GYYHGRIPKREKENFMQNLRNFKIVITTTQFLSK----HYRELGHFDFIFVDDVDAILKAS  178 (237)
T ss_dssp             EECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHH----CSTTSCCCSEEEESCHHHHHTST
T ss_pred             eeeecccchhhhhhhhccccccceeccChHHHHH----hhhhcCCCCEEEEEChhhhhhcc
Confidence            3444555444444433  3468999999998654    33457889999999999998754

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=97.70  E-value=2.4e-05  Score=56.09  Aligned_cols=89  Identities=13%  Similarity=0.154  Sum_probs=59.2

Q ss_pred             ceEEEEEcCcchHHHHHHhcCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchhH
Q psy6712           3 VQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQV   82 (210)
Q Consensus         3 i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~~   82 (210)
                      .++....|+....   ......++|+++||..+...+.++...+.+++++|+||+|.+.+.........++..+      
T Consensus        96 ~~v~~~~~~~~~~---~~~~~~~~ii~~~~~~~~~~~~~~~~~~~~~~~ii~DE~h~~~~~~r~~~~~~~l~~i------  166 (202)
T d2p6ra3          96 LRIGISTGDYESR---DEHLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTKM------  166 (202)
T ss_dssp             CCEEEECSSCBCC---SSCSTTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCTTTHHHHHHHHHHH------
T ss_pred             ccceeeccCcccc---cccccccceeeeccHHHHHHHhccchhhhhhhhccccHHHHhcccccchHHHHHHHHH------
Confidence            3455555655443   2223468999999999999998888888899999999999998766544443333211      


Q ss_pred             HHHHHHHHhcCceEEEecCCCCH
Q psy6712          83 DWLTEKMREANFTVSSMHGDMPQ  105 (210)
Q Consensus        83 ~~l~~~l~~~~~~~~~~~~~~~~  105 (210)
                         .+ + ..+.+...+.+.++.
T Consensus       167 ---~~-~-~~~~~~l~lSATl~n  184 (202)
T d2p6ra3         167 ---RR-M-NKALRVIGLSATAPN  184 (202)
T ss_dssp             ---HH-H-CTTCEEEEEECCCTT
T ss_pred             ---Hh-c-CCCCcEEEEcCCCCc
Confidence               11 1 124567777777654

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=97.37  E-value=5.9e-05  Score=54.07  Aligned_cols=85  Identities=14%  Similarity=0.111  Sum_probs=57.1

Q ss_pred             cCCCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhccchHHHHHHHHhhCCCchhHHHHHHHHHhcCceEEEecC
Q psy6712          22 DYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVDWLTEKMREANFTVSSMHG  101 (210)
Q Consensus        22 ~~~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~~~~~~~~~i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~  101 (210)
                      ....+|+++||+++...........++++++|+||+|.+.+++........        ....+...+  .+.++..+.+
T Consensus       113 ~~~~~i~~~t~~~~~~~~~~~~~~~~~v~~lviDEaH~~~~~~~~~~~~~~--------~~~~l~~~~--~~~~ii~lSA  182 (206)
T d1oywa2         113 TGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWGHDFRPEYA--------ALGQLRQRF--PTLPFMALTA  182 (206)
T ss_dssp             HTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGGGGCTTSSCCCHHHH--------GGGGHHHHC--TTSCEEEEES
T ss_pred             cCCceEEEEechhhhchhhcccchhheeeeeeeeeeeeeeccccchHHHHH--------HHHHHHHhC--CCCceEEEEe
Confidence            346899999999877655555566788999999999999876532111100        011122223  2467888999


Q ss_pred             CCCHhHHHHHHHHHh
Q psy6712         102 DMPQKERDGIMKEFR  116 (210)
Q Consensus       102 ~~~~~~r~~~~~~f~  116 (210)
                      .++++.++.+.+.+.
T Consensus       183 Tl~~~v~~di~~~L~  197 (206)
T d1oywa2         183 TADDTTRQDIVRLLG  197 (206)
T ss_dssp             CCCHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHcC
Confidence            999887777777763

>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=96.95  E-value=0.0012  Score=49.05  Aligned_cols=74  Identities=22%  Similarity=0.276  Sum_probs=53.7

Q ss_pred             HHHHHHHHHhcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccc-cCCCCCCcEEEEecCCCChhHHHHhh
Q psy6712          82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWAR-GIDVQQVSLVINYDLPNNRELYIHRI  157 (210)
Q Consensus        82 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~-g~d~~~~~~vi~~~~p~s~~~~~q~~  157 (210)
                      .+.+.+.+...++.+..+||+++..+|.+++.+.++|+.+|+|+|..+-. .+.+.+..+||.=.  ..--.|.||-
T Consensus       149 ~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~~~~~f~~LglviiDE--qH~fgv~Qr~  223 (264)
T d1gm5a3         149 YRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLVIIDE--QHRFGVKQRE  223 (264)
T ss_dssp             HHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCSCCCEEEEES--CCCC-----C
T ss_pred             HHHHHHhhhhccccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhcCCCCccccceeeecc--ccccchhhHH
Confidence            34455666666899999999999999999999999999999999987655 57777888777532  2223445554

>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=96.77  E-value=0.00036  Score=51.93  Aligned_cols=56  Identities=27%  Similarity=0.358  Sum_probs=41.3

Q ss_pred             CCceEEEEEcCcchHH---HHHHhcC-CCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHh
Q psy6712           1 MNVQCHACIGGTNLSE---DLRKLDY-GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEML   61 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~---~~~~l~~-~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~   61 (210)
                      +|++++.++|+.+..+   .+..+.+ .++|+|||=    .++. ..+.++++.++|+||-|+..
T Consensus       159 ~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGTh----sl~~-~~~~f~~LglviiDEqH~fg  218 (264)
T d1gm5a3         159 FNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTH----ALIQ-EDVHFKNLGLVIIDEQHRFG  218 (264)
T ss_dssp             SSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECT----THHH-HCCCCSCCCEEEEESCCCC-
T ss_pred             ccccceeeccccchHHHHHHHHHHHCCCCCEEEeeh----HHhc-CCCCccccceeeeccccccc
Confidence            4789999999987554   3455545 589999994    3333 45667899999999999764

>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=96.68  E-value=0.001  Score=48.43  Aligned_cols=55  Identities=15%  Similarity=0.228  Sum_probs=41.3

Q ss_pred             CCceEEEEEcCcchHHH---HHHhcC-CCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHH
Q psy6712           1 MNVQCHACIGGTNLSED---LRKLDY-GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEM   60 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~---~~~l~~-~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l   60 (210)
                      ++++++.++|+.+..+.   +..+.+ ..+|+|||=     .+....+.++++.++|+||-|+.
T Consensus       131 ~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGth-----s~l~~~~~f~~LgLiIiDEeH~f  189 (233)
T d2eyqa3         131 WPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTH-----KLLQSDVKFKDLGLLIVDEEHRF  189 (233)
T ss_dssp             TTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECT-----HHHHSCCCCSSEEEEEEESGGGS
T ss_pred             CCCEEEeccCcccchhHHHHHHHHhCCCCCEEEeeh-----hhhccCCccccccceeeechhhh
Confidence            46889999999886554   345555 479999993     23335567899999999999964

>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=95.98  E-value=0.0067  Score=43.97  Aligned_cols=62  Identities=18%  Similarity=0.250  Sum_probs=50.7

Q ss_pred             HHHHHHHHH----hcCceEEEecCCCCHhHHHHHHHHHhcCCCcEEEEecCccc-cCCCCCCcEEEE
Q psy6712          82 VDWLTEKMR----EANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWAR-GIDVQQVSLVIN  143 (210)
Q Consensus        82 ~~~l~~~l~----~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~-g~d~~~~~~vi~  143 (210)
                      +....+.++    ..+.++..+|+.++..+|.+++..+.+|+.+|+|+|..+.. .+.+++..+||.
T Consensus       117 a~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~~~~~f~~LgLiIi  183 (233)
T d2eyqa3         117 AQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLIV  183 (233)
T ss_dssp             HHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCSSEEEEEE
T ss_pred             HHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhccCCccccccceee
Confidence            555555554    45789999999999999999999999999999999986654 577778777765

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=95.14  E-value=0.036  Score=35.68  Aligned_cols=38  Identities=13%  Similarity=0.088  Sum_probs=26.6

Q ss_pred             CcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhcc
Q psy6712          25 QHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNK   63 (210)
Q Consensus        25 ~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~   63 (210)
                      ..+.+.|...+.... .....+.+++++|+||||.+...
T Consensus        76 ~~~~~~~~~~l~~~~-~~~~~~~~~~lvIiDEaH~~~~~  113 (140)
T d1yksa1          76 EVIDAMCHATLTYRM-LEPTRVVNWEVIIMDEAHFLDPA  113 (140)
T ss_dssp             CCEEEEEHHHHHHHH-TSSSCCCCCSEEEETTTTCCSHH
T ss_pred             cchhhhhHHHHHHHH-hccccccceeEEEEccccccChh
Confidence            356677776655543 34456789999999999987433

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=94.50  E-value=0.024  Score=36.91  Aligned_cols=34  Identities=12%  Similarity=0.139  Sum_probs=24.4

Q ss_pred             CcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHh
Q psy6712          25 QHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEML   61 (210)
Q Consensus        25 ~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~   61 (210)
                      ..++++|.+.+..   .....+++++++|+||+|.+-
T Consensus        74 ~~~~~~~~~~~~~---~~~~~~~~~~~vIiDE~H~~~  107 (136)
T d1a1va1          74 SPITYSTYGKFLA---DGGCSGGAYDIIICDECHSTD  107 (136)
T ss_dssp             CSEEEEEHHHHHH---TTGGGGCCCSEEEEETTTCCS
T ss_pred             cceEEEeeeeecc---ccchhhhcCCEEEEecccccC
Confidence            3577888775433   233457899999999999763

>d1tf5a3 c.37.1.19 (A:1-226,A:349-395) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=93.99  E-value=0.054  Score=39.69  Aligned_cols=59  Identities=19%  Similarity=0.376  Sum_probs=43.6

Q ss_pred             CCceEEEEEcCcchHHHHHHhcCCCcEEEEChHHH-HHHHHhcC------ccCCCccEEEechhhHHh
Q psy6712           1 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRV-FDMIRRRV------LRTRNIKMLVLDEADEML   61 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~Tp~~l-~~~l~~~~------~~~~~~~~lviDE~~~l~   61 (210)
                      +|++|.++..+.+..+.....  .+||+.+|...+ .+.|+.+.      ...+.+.+.|+||+|.++
T Consensus       148 lGlsvg~~~~~~~~~~r~~~Y--~~di~Ygt~~e~~fDyLrd~~~~~~~~~~~r~~~~aIvDEvDsil  213 (273)
T d1tf5a3         148 LGLTVGLNLNSMSKDEKREAY--AADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSIL  213 (273)
T ss_dssp             TTCCEEECCTTSCHHHHHHHH--HSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHH
T ss_pred             cCCCccccccccCHHHHHHHh--hCCceecchhhhhhhhcchhhhcChhhhccCCCCEEEEEcchhhh
Confidence            689999998887776554444  789999999664 34555432      235678999999999986

>d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: DNA helicase UvsW
domain: DNA helicase UvsW
species: Bacteriophage T4 [TaxId: 10665]

Probab=93.81  E-value=0.0074  Score=45.03  Aligned_cols=35  Identities=23%  Similarity=0.115  Sum_probs=25.5

Q ss_pred             CCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHh
Q psy6712          24 GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEML   61 (210)
Q Consensus        24 ~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~   61 (210)
                      ..+|+++|+..+...   ....+++++++|+||||+..
T Consensus       204 ~~~i~i~t~qs~~~~---~~~~~~~f~~VIvDEaH~~~  238 (282)
T d1rifa_         204 DAPVVVGTWQTVVKQ---PKEWFSQFGMMMNDECHLAT  238 (282)
T ss_dssp             TCSEEEECHHHHTTS---CGGGGGGEEEEEEETGGGCC
T ss_pred             cceEEEEeeehhhhh---cccccCCCCEEEEECCCCCC
Confidence            457999998764432   23345789999999999764

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=91.33  E-value=0.063  Score=37.63  Aligned_cols=35  Identities=11%  Similarity=0.207  Sum_probs=25.4

Q ss_pred             CcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhc
Q psy6712          25 QHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLN   62 (210)
Q Consensus        25 ~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~   62 (210)
                      .+|+++|...+......   ...+++++|+||||++..
T Consensus       149 ~~i~i~t~~~~~~~~~~---~~~~~~lvIiDEaH~~~a  183 (206)
T d2fz4a1         149 KPLTVSTYDSAYVNAEK---LGNRFMLLIFDEVHHLPA  183 (206)
T ss_dssp             CSEEEEEHHHHHHTHHH---HTTTCSEEEEECSSCCCT
T ss_pred             cccccceehhhhhhhHh---hCCcCCEEEEECCeeCCc
Confidence            46899998876654332   235788999999998753

>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=87.20  E-value=0.24  Score=33.92  Aligned_cols=53  Identities=13%  Similarity=0.197  Sum_probs=40.2

Q ss_pred             CCceEEEEEcCcchHHHHHHh---cC-CCcEEEEChHHHHHHHHhcCccCCCccEEEechhhH
Q psy6712           1 MNVQCHACIGGTNLSEDLRKL---DY-GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADE   59 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~~~l---~~-~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~   59 (210)
                      .|+++..++|+.+..+....+   ++ ..+|||||.     + ....+++.+++++|.-++..
T Consensus        54 ~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTd-----v-~~rGiDip~v~~VI~~d~p~  110 (181)
T d1t5la2          54 AGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN-----L-LREGLDIPEVSLVAILDADK  110 (181)
T ss_dssp             TTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESC-----C-CSSSCCCTTEEEEEETTTTS
T ss_pred             CCcceeEecCCccHHHHHHHHHHHHCCCCCEEEehh-----H-HHccCCCCCCCEEEEecCCc
Confidence            488999999999977655444   44 689999994     2 33457899999999777653

>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=85.51  E-value=0.23  Score=34.93  Aligned_cols=54  Identities=15%  Similarity=0.132  Sum_probs=40.8

Q ss_pred             CceEEEEEcCcchHHHHHH---hcC-CCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHh
Q psy6712           2 NVQCHACIGGTNLSEDLRK---LDY-GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEML   61 (210)
Q Consensus         2 ~i~~~~~~gg~~~~~~~~~---l~~-~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~   61 (210)
                      ++++..++|-.+.++..+.   +.+ ..+|||||.     .+. -.+++.+..++||.+|+++.
T Consensus        57 ~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~Tt-----vIE-vGiDvpnA~~iiI~~a~rfG  114 (211)
T d2eyqa5          57 EARIAIGHGQMRERELERVMNDFHHQRFNVLVCTT-----IIE-TGIDIPTANTIIIERADHFG  114 (211)
T ss_dssp             TSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESS-----TTG-GGSCCTTEEEEEETTTTSSC
T ss_pred             ceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEeh-----hhh-hccCCCCCcEEEEecchhcc
Confidence            4678899999887765544   444 589999995     233 34788999999999999763

>d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=85.08  E-value=0.65  Score=34.05  Aligned_cols=38  Identities=13%  Similarity=0.132  Sum_probs=25.5

Q ss_pred             CCcEEEEChHHHHHHHHhcCccCCCccEEEechhhHHhcc
Q psy6712          24 GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNK   63 (210)
Q Consensus        24 ~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~l~~~   63 (210)
                      ..+++++|.+.+....  ..+.-.+.+++|+||+|.+-+.
T Consensus       170 ~~~v~i~sy~~~~~~~--~~l~~~~~~~vI~DEaH~ikn~  207 (298)
T d1z3ix2         170 PTPILIISYETFRLHA--EVLHKGKVGLVICDEGHRLKNS  207 (298)
T ss_dssp             SCCEEEEEHHHHHHHT--TTTTTSCCCEEEETTGGGCCTT
T ss_pred             cceEEEEeecccccch--hcccccceeeeecccccccccc
Confidence            3478999887655432  2233346779999999988643

>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=84.51  E-value=0.39  Score=32.63  Aligned_cols=53  Identities=13%  Similarity=0.179  Sum_probs=39.6

Q ss_pred             CCceEEEEEcCcchHHHH---HHhcC-CCcEEEEChHHHHHHHHhcCccCCCccEEEechhhH
Q psy6712           1 MNVQCHACIGGTNLSEDL---RKLDY-GQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADE   59 (210)
Q Consensus         1 ~~i~~~~~~gg~~~~~~~---~~l~~-~~~Ili~Tp~~l~~~l~~~~~~~~~~~~lviDE~~~   59 (210)
                      .|+++..++|+.+..+-.   ..+.+ ..+|||+|.      +....+++.+++++|+=.++.
T Consensus        54 ~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~------v~~~GiDip~V~~Vi~~~~~~  110 (174)
T d1c4oa2          54 HGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGIN------LLREGLDIPEVSLVAILDADK  110 (174)
T ss_dssp             TTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESC------CCCTTCCCTTEEEEEETTTTS
T ss_pred             cCCceEEEecccchHHHHHHHHHHHCCCeEEEEeee------eeeeeccCCCCcEEEEecccc
Confidence            489999999999866544   44444 589999994      334457899999999866654