Citrus Sinensis ID: 028124

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210---
Protein Sequence
MAIDGVESPCPPCQSPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL
Secondary Structure (PSIPRED)
cccccccccccccccccccccccEEEEEccccccHHHHHHHHHHHHHHcccccccEEEEEcccHHHHHHHHHHHcccccEEEEccccccHHHHHHHHHHHHccccccccccccccccccccccccccEEEEEEccccHHHHccccccccccEEEEEcccccccccEEEcccccccccEEEEEEEccHHHHHHHHHHHHccccccccccHHHcc
Secondary Structure Prediction (SSPRO)
cccHHcccccEEEEEHEEHccccEEEEEEcHHHHHHHHHHHHHHHcEEcccccccEEEEEccHHHHHHHHHHHHHccccEEEEccccccHHHHHHHHHHHHccccEEccEEEccccccccccccccccEEEEEccccHHHHHccccEEEEEEEEEccccccccHEEEEccccccccEEEEEEccHHHHHHHHHHHHHHcccHccccccHHHHc
Coil and Loop (DISEMBL)
maidgvespcppcqspshfsqprhFYVAVDRLQFKMETLVELLHLVVagrrpglpmivccssrdELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKvteqsgdesetgkdehkshmIVVTDAclpllssgesaiSARVLINyelptkkeTYIRRMTTCLAadgsviniVVGGEVVTLRSMEESLGLIvaevpiniseil
Flexible Loop (DISEMBL)
MAIDGVESPCPPCQSPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKwnqkvteqsgdesetgkdehkshMIVVTDACLPLLSSGESAISARVLINyelptkkeTYIRRMTTclaadgsviniVVGGEVVTLRSMEeslglivaevpiniseil
Low Complexity Region (SEG)
MAIDGVESPCPPCQSPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL
Disordered region (IsUnstruct)
**********************RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKW**********************MIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINI****
Disordered Region (DISOPRED)
***********************HFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVT************EHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL
Disordered Region (DISEMBL)
******************FSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWN******************KSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL
Disordered Region (DISPRO)
**IDGVESPCPPCQSPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE*************KSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINI****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAIDGVESPCPPCQSPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	213	2.2.26 [Sep-21-2011]
O02494	405	Eukaryotic initiation fac	yes	no	0.741	0.390	0.269	1e-14
Q2HFP1	397	ATP-dependent RNA helicas	N/A	no	0.741	0.397	0.253	1e-12
Q7RV88	397	ATP-dependent RNA helicas	N/A	no	0.741	0.397	0.248	2e-12
A4QVP2	396	ATP-dependent RNA helicas	N/A	no	0.741	0.398	0.248	3e-12
Q5U526	415	Eukaryotic initiation fac	N/A	no	0.741	0.380	0.238	3e-12
Q0CXD0	396	ATP-dependent RNA helicas	N/A	no	0.741	0.398	0.243	3e-12
Q2UPY3	421	ATP-dependent RNA helicas	yes	no	0.741	0.375	0.243	3e-12
A1CJT5	398	ATP-dependent RNA helicas	N/A	no	0.741	0.396	0.243	4e-12
Q5ZM36	412	Eukaryotic initiation fac	yes	no	0.741	0.383	0.238	5e-12
Q7ZVA6	406	Eukaryotic initiation fac	yes	no	0.741	0.389	0.238	5e-12

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

 Score = 80.1 bits (196), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 52/193 (26%), Positives = 93/193 (48%), Gaps = 35/193 (18%)

Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           R FYV V++ ++KM+TL++L   +       +  I+ C++R  +D +   +    D + S
Sbjct: 245 RQFYVGVEKDEWKMDTLIDLYETLTI-----VQAIIYCNTRRRVDQLTKQMRE-RDFTCS 298

Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
           S+H D+ + +R +I+ +FR  +                       S +++ TD    LL+
Sbjct: 299 SMHGDMDQKDREVIMRQFRSGS-----------------------SRVLITTD----LLA 331

Query: 143 SGESAISARVLINYELPTKKETYIRRM--TTCLAADGSVINIVVGGEVVTLRSMEESLGL 200
            G       ++INY+LP   ETYI R+  +      G  IN V   ++V LR +E     
Sbjct: 332 RGIDVQQVSLVINYDLPVSPETYIHRIGRSGRFGKKGVSINFVTDDDIVCLRDIERHYNT 391

Query: 201 IVAEVPINISEIL 213
            + E+P+ I++IL
Sbjct: 392 QIEEMPMGITDIL 404

ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon.
Cryptosporidium parvum (taxid: 5807)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q2HFP1|IF4A_CHAGB ATP-dependent RNA helicase eIF4A OS=Chaetomium globosum (strain ATCC 6205 / CBS 148.51 / DSM 1962 / NBRC 6347 / NRRL 1970) GN=TIF1 PE=3 SV=1

 Score = 72.8 bits (177), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 95/193 (49%), Gaps = 35/193 (18%)

Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           + FY+AV++  +K++TL +L   V   +      ++ C++R ++D +   +    D + S
Sbjct: 238 KQFYIAVEKEDWKLDTLSDLYETVTITQ-----AVIFCNTRRKVDWLTDKL-QARDFTVS 291

Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
           ++H D+ +T+R LI++EFR             SG           S +++ TD    LL+
Sbjct: 292 AMHGDMDQTQRDLIMKEFR-------------SG----------SSRVLIATD----LLA 324

Query: 143 SGESAISARVLINYELPTKKETYIRRMTTCLAADGS--VINIVVGGEVVTLRSMEESLGL 200
            G       ++INY+LP  +E YI R+            IN V   +V  +R +E+    
Sbjct: 325 RGIDVQQVSLVINYDLPANRENYIHRIGRGGRFGRKGVAINFVTADDVRMMREIEQFYST 384

Query: 201 IVAEVPINISEIL 213
            + E+P+N+++++
Sbjct: 385 QIEEMPMNVADLI 397

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.

Chaetomium globosum (strain ATCC 6205 / CBS 148.51 / DSM 1962 / NBRC 6347 / NRRL 1970) (taxid: 306901)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q7RV88|IF4A_NEUCR ATP-dependent RNA helicase eIF4A OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=tif-1 PE=3 SV=2

 Score = 72.0 bits (175), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 48/193 (24%), Positives = 96/193 (49%), Gaps = 35/193 (18%)

Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           + FY+AV++ ++K++TL +L   V   +      ++ C++R ++D +   ++   D + S
Sbjct: 238 KQFYIAVEKEEWKLDTLSDLYETVTITQ-----AVIFCNTRRKVDWLTDKLTA-RDFTVS 291

Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
           ++H D+ + +R LI++EFR             SG           S +++ TD    LL+
Sbjct: 292 AMHGDMDQAQRDLIMKEFR-------------SG----------SSRVLIATD----LLA 324

Query: 143 SGESAISARVLINYELPTKKETYIRRMTTCLAADGS--VINIVVGGEVVTLRSMEESLGL 200
            G       ++INY+LP  +E YI R+            IN V   +V  +R +E+    
Sbjct: 325 RGIDVQQVSLVINYDLPANRENYIHRIGRGGRFGRKGVAINFVTADDVRMMREIEQFYST 384

Query: 201 IVAEVPINISEIL 213
            + E+P+N+++++
Sbjct: 385 QIEEMPMNVADLI 397

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.

Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (taxid: 367110)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A4QVP2|IF4A_MAGO7 ATP-dependent RNA helicase eIF4A OS=Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) GN=TIF1 PE=3 SV=1

 Score = 72.0 bits (175), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 48/193 (24%), Positives = 96/193 (49%), Gaps = 35/193 (18%)

Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           + FY+AV++ ++K++TL +L   V   +      ++ C++R ++D +   ++   D + S
Sbjct: 237 KQFYIAVEKEEWKLDTLSDLYETVTITQ-----AVIFCNTRRKVDWLTDKLTA-RDFTVS 290

Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
           ++H D+ + +R LI++EFR             SG           S +++ TD    LL+
Sbjct: 291 AMHGDMDQAQRDLIMKEFR-------------SG----------SSRVLIATD----LLA 323

Query: 143 SGESAISARVLINYELPTKKETYIRRMTTCLAADGS--VINIVVGGEVVTLRSMEESLGL 200
            G       ++INY+LP  +E YI R+            IN V   +V  +R +E+    
Sbjct: 324 RGIDVQQVSLVINYDLPANRENYIHRIGRGGRFGRKGVAINFVTADDVRMMREIEQFYST 383

Query: 201 IVAEVPINISEIL 213
            + E+P+N+++++
Sbjct: 384 QIEEMPMNVADLI 396

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.

Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) (taxid: 242507)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

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

 Score = 71.6 bits (174), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 46/193 (23%), Positives = 94/193 (48%), Gaps = 35/193 (18%)

Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           + F+VAV+R ++K +TL +L   +   +      ++ C+++ ++D +   +   A+ + S
Sbjct: 256 KQFFVAVEREEWKFDTLCDLYDTLTITQ-----AVIFCNTKRKVDWLTEKMRE-ANFTVS 309

Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
           S+H D+ + ER  I++EFR  A                       S +++ TD    + +
Sbjct: 310 SMHGDMPQKERESIMKEFRSGA-----------------------SRVLISTD----VWA 342

Query: 143 SGESAISARVLINYELPTKKETYIRRM--TTCLAADGSVINIVVGGEVVTLRSMEESLGL 200
            G       ++INY+LP  +E YI R+  +      G  IN V   ++  LR +E+    
Sbjct: 343 RGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGGKGVAINFVKNDDIRILRDIEQYYST 402

Query: 201 IVAEVPINISEIL 213
            + E+P+N+++++
Sbjct: 403 QIDEMPMNVADLI 415

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

Xenopus laevis (taxid: 8355)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q0CXD0|IF4A_ASPTN ATP-dependent RNA helicase eIF4A OS=Aspergillus terreus (strain NIH 2624 / FGSC A1156) GN=tif1 PE=3 SV=2

 Score = 71.6 bits (174), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 47/193 (24%), Positives = 97/193 (50%), Gaps = 35/193 (18%)

Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           + FY+AV++ ++K++TL +L   V   +      ++ C++R ++D +   ++   D + S
Sbjct: 237 KQFYIAVEKEEWKLDTLSDLYETVTITQ-----AVIFCNTRRKVDWLTDKLTA-RDFTVS 290

Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
           ++H D+ +++R +I++EFR             SG           S +++ TD    LL+
Sbjct: 291 AMHGDMEQSQRDIIMKEFR-------------SG----------SSRVLIATD----LLA 323

Query: 143 SGESAISARVLINYELPTKKETYIRRMTTCLAADGS--VINIVVGGEVVTLRSMEESLGL 200
            G       ++INY+LP  +E YI R+            IN V   +V  +R +E+    
Sbjct: 324 RGIDVQQVSLVINYDLPANRENYIHRIGRGGRFGRKGVAINFVTADDVRMMREIEQFYST 383

Query: 201 IVAEVPINISEIL 213
            + E+P+N+++++
Sbjct: 384 QIEEMPMNVADLI 396

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.

Aspergillus terreus (strain NIH 2624 / FGSC A1156) (taxid: 341663)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q2UPY3|IF4A_ASPOR ATP-dependent RNA helicase eIF4A OS=Aspergillus oryzae (strain ATCC 42149 / RIB 40) GN=tif1 PE=3 SV=1

 Score = 71.6 bits (174), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 47/193 (24%), Positives = 97/193 (50%), Gaps = 35/193 (18%)

Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           + FY+AV++ ++K++TL +L   V   +      ++ C++R ++D +   ++   D + S
Sbjct: 262 KQFYIAVEKEEWKLDTLSDLYETVTITQ-----AVIFCNTRRKVDWLTDKLTA-RDFTVS 315

Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
           ++H D+ +++R +I++EFR             SG           S +++ TD    LL+
Sbjct: 316 AMHGDMEQSQRDVIMKEFR-------------SG----------SSRVLIATD----LLA 348

Query: 143 SGESAISARVLINYELPTKKETYIRRMTTCLAADGS--VINIVVGGEVVTLRSMEESLGL 200
            G       ++INY+LP  +E YI R+            IN V   +V  +R +E+    
Sbjct: 349 RGIDVQQVSLVINYDLPANRENYIHRIGRGGRFGRKGVAINFVTADDVRMMREIEQFYST 408

Query: 201 IVAEVPINISEIL 213
            + E+P+N+++++
Sbjct: 409 QIEEMPMNVADLI 421

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.

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

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A1CJT5|IF4A_ASPCL ATP-dependent RNA helicase eIF4A OS=Aspergillus clavatus (strain ATCC 1007 / CBS 513.65 / DSM 816 / NCTC 3887 / NRRL 1) GN=tif1 PE=3 SV=1

 Score = 71.6 bits (174), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 47/193 (24%), Positives = 97/193 (50%), Gaps = 35/193 (18%)

Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           + FY+AV++ ++K++TL +L   V   +      ++ C++R ++D +   ++   D + S
Sbjct: 239 KQFYIAVEKEEWKLDTLSDLYETVTITQ-----AVIFCNTRRKVDWLTDKLTA-RDFTVS 292

Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
           ++H D+ +++R +I++EFR             SG           S +++ TD    LL+
Sbjct: 293 AMHGDMEQSQRDVIMKEFR-------------SG----------SSRVLIATD----LLA 325

Query: 143 SGESAISARVLINYELPTKKETYIRRMTTCLAADGS--VINIVVGGEVVTLRSMEESLGL 200
            G       ++INY+LP  +E YI R+            IN V   +V  +R +E+    
Sbjct: 326 RGIDVQQVSLVINYDLPANRENYIHRIGRGGRFGRKGVAINFVTADDVRMMREIEQFYST 385

Query: 201 IVAEVPINISEIL 213
            + E+P+N+++++
Sbjct: 386 QIEEMPMNVADLI 398

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.

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

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

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

 Score = 71.2 bits (173), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 46/193 (23%), Positives = 93/193 (48%), Gaps = 35/193 (18%)

Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           + F+VAV+R ++K +TL +L   +   +      ++ C+++ ++D +   +   A+ + S
Sbjct: 253 KQFFVAVEREEWKFDTLCDLYDTLTITQ-----AVIFCNTKRKVDWLTEKMRE-ANFTVS 306

Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
           S+H D+ + ER  I++EFR  A                       S +++ TD    + +
Sbjct: 307 SMHGDMPQKERESIMKEFRSGA-----------------------SRVLISTD----VWA 339

Query: 143 SGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLRSMEESLGL 200
            G       ++INY+LP  +E YI R+         G  IN V   ++  LR +E+    
Sbjct: 340 RGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYST 399

Query: 201 IVAEVPINISEIL 213
            + E+P+N+++++
Sbjct: 400 QIDEMPMNVADLI 412

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

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

 Score = 71.2 bits (173), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 46/193 (23%), Positives = 94/193 (48%), Gaps = 35/193 (18%)

Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           + F+VAV+R ++K +TL +L   +   +      ++ C+++ ++D +   +   A+ + S
Sbjct: 247 KQFFVAVEREEWKFDTLCDLYDTLTITQ-----AVIFCNTKRKVDWLTEKMRE-ANFTVS 300

Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
           S+H D+ + ER  I++EFR  A                       S +++ TD    + +
Sbjct: 301 SMHGDMPQKERESIMKEFRSGA-----------------------SRVLISTD----VWA 333

Query: 143 SGESAISARVLINYELPTKKETYIRRM--TTCLAADGSVINIVVGGEVVTLRSMEESLGL 200
            G       ++INY+LP  +E YI R+  +      G  IN V   ++  LR +E+    
Sbjct: 334 RGLDVSQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYST 393

Query: 201 IVAEVPINISEIL 213
            + E+P+N+++++
Sbjct: 394 QIDEMPMNVADLI 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. Binds spliced mRNA in sequence-independent manner, 20-24 nucleotides upstream of mRNA exon-exon junctions.

Danio rerio (taxid: 7955)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	213
255565156	207	conserved hypothetical protein [Ricinus	0.882	0.908	0.764	9e-78
449448328	211	PREDICTED: ATP-dependent RNA helicase eI	0.990	1.0	0.718	1e-74
225438690	210	PREDICTED: eukaryotic initiation factor	0.985	1.0	0.718	2e-74
449448326	233	PREDICTED: ATP-dependent RNA helicase eI	0.990	0.905	0.704	1e-73
449448332	208	PREDICTED: ATP-dependent RNA helicase eI	0.967	0.990	0.711	3e-72
18419954	212	uncharacterized protein [Arabidopsis tha	0.981	0.985	0.654	3e-68
297798174	212	hypothetical protein ARALYDRAFT_912642 [	0.981	0.985	0.649	2e-67
334187233	258	uncharacterized protein [Arabidopsis tha	0.962	0.794	0.642	3e-66
356496882	209	PREDICTED: eukaryotic initiation factor	0.976	0.995	0.593	4e-64
224094352	231	predicted protein [Populus trichocarpa]	0.887	0.818	0.629	1e-62

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

 Score =  295 bits (755), Expect = 9e-78,   Method: Compositional matrix adjust.
 Identities = 146/191 (76%), Positives = 165/191 (86%), Gaps = 3/191 (1%)

Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           RHFYVAVDRL FKMETLVELL   VAGRR GLPM+VCCSSRDELDAVCS VSNL  ISF+
Sbjct: 20  RHFYVAVDRLHFKMETLVELLG--VAGRRSGLPMVVCCSSRDELDAVCSVVSNLPYISFA 77

Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
           SL+SDLAE ERT +LE+FR   M+WNQ +T QSG++ E  K E KSHMIVVTD CLPLL+
Sbjct: 78  SLYSDLAEAERTSVLEKFRQVTMRWNQNITAQSGNKDEIEK-EDKSHMIVVTDTCLPLLA 136

Query: 143 SGESAISARVLINYELPTKKETYIRRMTTCLAADGSVINIVVGGEVVTLRSMEESLGLIV 202
           SGES ISARVLINYELPTKKETY RRM++CLAADG VIN+VVGGEVVTL+++EES  L++
Sbjct: 137 SGESPISARVLINYELPTKKETYARRMSSCLAADGIVINMVVGGEVVTLKNIEESSSLVI 196

Query: 203 AEVPINISEIL 213
           AE+PINISEIL
Sbjct: 197 AEMPINISEIL 207

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  285 bits (728), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 153/213 (71%), Positives = 178/213 (83%), Gaps = 2/213 (0%)

Query: 1   MAIDGVESPCPPCQSPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCC 60
           MAID  E+  PP  S SHFSQ RHFYVAVDRLQFKMETLV LL   VAGRRP LPM+VCC
Sbjct: 1   MAIDPFEAFSPPSHSSSHFSQQRHFYVAVDRLQFKMETLVGLLD--VAGRRPSLPMVVCC 58

Query: 61  SSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESE 120
           SSRDELD+VCSAVSNL  IS +SL+SDLAE +R+LILE+FR T  +W+QK +  S ++ E
Sbjct: 59  SSRDELDSVCSAVSNLHYISLASLYSDLAEADRSLILEKFRQTTSRWSQKFSSLSEEKCE 118

Query: 121 TGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSVI 180
             K   KSHMIVVTDACLPLL+SGES +SA VLINYE+PTKKETY+RRMTTC A+DG +I
Sbjct: 119 AEKVGEKSHMIVVTDACLPLLASGESPLSAHVLINYEIPTKKETYMRRMTTCSASDGILI 178

Query: 181 NIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 213
           N+VVGGEVVTL+S+EES GL++AE+PINISEIL
Sbjct: 179 NMVVGGEVVTLKSIEESSGLVIAEMPINISEIL 211

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  284 bits (727), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 153/213 (71%), Positives = 171/213 (80%), Gaps = 3/213 (1%)

Query: 1   MAIDGVESPCPPCQSPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCC 60
           M ID  E+  P   SPSH SQ RHFYVAVDR QFKMETLV+LL L  A  RP LP+ VCC
Sbjct: 1   MGIDAAEASSPLSPSPSHSSQQRHFYVAVDRPQFKMETLVDLLEL--ASHRPCLPIAVCC 58

Query: 61  SSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESE 120
           SSRDELDAVCSAVSNL  IS +SL+SDLAE ER LILE FR   M++ Q V  QSG++ E
Sbjct: 59  SSRDELDAVCSAVSNLPFISLASLYSDLAEAERALILENFRQATMRY-QNVIAQSGEDKE 117

Query: 121 TGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSVI 180
             K E KSHM+VVTDACLP L+SGES+ISARVLINYELPTKKETY+RRM TCL ADG VI
Sbjct: 118 IKKGEDKSHMVVVTDACLPFLASGESSISARVLINYELPTKKETYMRRMATCLGADGIVI 177

Query: 181 NIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 213
           N+VVGGEVVTL+SMEES GL VAE+P++ISEIL
Sbjct: 178 NMVVGGEVVTLKSMEESSGLTVAEMPMHISEIL 210

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  281 bits (719), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 150/213 (70%), Positives = 177/213 (83%), Gaps = 2/213 (0%)

Query: 1   MAIDGVESPCPPCQSPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCC 60
           MAID  E+  PP  S SHFSQ RHFYVAVDRLQFKMETLV LL   VAGRRP LPM+VCC
Sbjct: 1   MAIDPFEAFSPPSHSSSHFSQQRHFYVAVDRLQFKMETLVGLLD--VAGRRPSLPMVVCC 58

Query: 61  SSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESE 120
           SSRDELD+VCSAVSNL  IS +SL+SDLAE +R+LILE+FR T  +W+QK +  S ++ E
Sbjct: 59  SSRDELDSVCSAVSNLHYISLASLYSDLAEADRSLILEKFRQTTSRWSQKFSSLSEEKCE 118

Query: 121 TGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSVI 180
             K   KSHMIVVTDACLPLL+SGES +SA VLINYE+PTKKETY+RRMTTC A+DG +I
Sbjct: 119 AEKVGEKSHMIVVTDACLPLLASGESPLSAHVLINYEIPTKKETYMRRMTTCSASDGILI 178

Query: 181 NIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 213
           N+VVGGEVVTL+S+EES GL++AE+PIN+S +L
Sbjct: 179 NMVVGGEVVTLKSIEESSGLVIAEMPINVSILL 211

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  276 bits (707), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 148/208 (71%), Positives = 173/208 (83%), Gaps = 2/208 (0%)

Query: 1   MAIDGVESPCPPCQSPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCC 60
           MAID  E+  PP  S SHFSQ RHFYVAVDRLQFKMETLV LL   VAGRRP LPM+VCC
Sbjct: 1   MAIDPFEAFSPPSHSSSHFSQQRHFYVAVDRLQFKMETLVGLLD--VAGRRPSLPMVVCC 58

Query: 61  SSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESE 120
           SSRDELD+VCSAVSNL  IS +SL+SDLAE +R+LILE+FR T  +W+QK +  S ++ E
Sbjct: 59  SSRDELDSVCSAVSNLHYISLASLYSDLAEADRSLILEKFRQTTSRWSQKFSSLSEEKCE 118

Query: 121 TGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSVI 180
             K   KSHMIVVTDACLPLL+SGES +SA VLINYE+PTKKETY+RRMTTC A+DG +I
Sbjct: 119 AEKVGEKSHMIVVTDACLPLLASGESPLSAHVLINYEIPTKKETYMRRMTTCSASDGILI 178

Query: 181 NIVVGGEVVTLRSMEESLGLIVAEVPIN 208
           N+VVGGEVVTL+S+EES GL++AE+PIN
Sbjct: 179 NMVVGGEVVTLKSIEESSGLVIAEMPIN 206

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  263 bits (673), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 140/214 (65%), Positives = 175/214 (81%), Gaps = 5/214 (2%)

Query: 3   IDGVESPCPPCQSPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSS 62
           +D +E+P  P QSPS  SQ  HFY+AVDR QFKMET+VELL   V GRRP LP++VCCSS
Sbjct: 1   MDSMEAPSLPFQSPSRSSQQLHFYLAVDRPQFKMETVVELLG--VLGRRPWLPIVVCCSS 58

Query: 63  RDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQK---VTEQSGDES 119
           RDELDAVCS++S L  IS ++L+SDLA+ ER +++E+FR   + WNQ+   V E+  +ES
Sbjct: 59  RDELDAVCSSLSTLPYISLAALYSDLADRERAMVIEKFRQATINWNQQLNSVVEEGLEES 118

Query: 120 ETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSV 179
           E GK+E  SH++VVTD CLPLLSSGES++SARVLINYELPTKKETY RR+TTCLA+ G V
Sbjct: 119 ENGKEEKTSHLVVVTDVCLPLLSSGESSLSARVLINYELPTKKETYTRRITTCLASGGIV 178

Query: 180 INIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 213
           IN+VVGGEV TL+S+EES G+++AE+PINISEIL
Sbjct: 179 INMVVGGEVTTLKSLEESSGILIAEMPINISEIL 212

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  260 bits (665), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 139/214 (64%), Positives = 175/214 (81%), Gaps = 5/214 (2%)

Query: 3   IDGVESPCPPCQSPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSS 62
           +D +E+P PP QSPS  SQ  HFY+AVDR QFKMET+VELL   V GRRP LP++VCCSS
Sbjct: 1   MDSMEAPSPPFQSPSRSSQQLHFYLAVDRPQFKMETVVELLG--VLGRRPWLPIVVCCSS 58

Query: 63  RDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESE-- 120
           RDELDAVCS++S L  IS ++L+SDLA+ ERT+++E+FR   + WNQ++     +  E  
Sbjct: 59  RDELDAVCSSLSTLPYISLAALYSDLADRERTMVIEKFRQATINWNQQLNSVVEEVLEES 118

Query: 121 -TGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSV 179
            T K+E+KSH++VVTD CLPLLSSGES++SARVLINYELPTKKETY RR+TTCLA+ G +
Sbjct: 119 ETRKEENKSHLVVVTDVCLPLLSSGESSLSARVLINYELPTKKETYTRRITTCLASGGII 178

Query: 180 INIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 213
           IN+VVGGEV TL+S+EES G+I+AE+PINISEIL
Sbjct: 179 INMVVGGEVTTLKSLEESSGIIIAEMPINISEIL 212

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  257 bits (656), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 135/210 (64%), Positives = 171/210 (81%), Gaps = 5/210 (2%)

Query: 3   IDGVESPCPPCQSPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSS 62
           +D +E+P  P QSPS  SQ  HFY+AVDR QFKMET+VELL   V GRRP LP++VCCSS
Sbjct: 1   MDSMEAPSLPFQSPSRSSQQLHFYLAVDRPQFKMETVVELLG--VLGRRPWLPIVVCCSS 58

Query: 63  RDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQK---VTEQSGDES 119
           RDELDAVCS++S L  IS ++L+SDLA+ ER +++E+FR   + WNQ+   V E+  +ES
Sbjct: 59  RDELDAVCSSLSTLPYISLAALYSDLADRERAMVIEKFRQATINWNQQLNSVVEEGLEES 118

Query: 120 ETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSV 179
           E GK+E  SH++VVTD CLPLLSSGES++SARVLINYELPTKKETY RR+TTCLA+ G V
Sbjct: 119 ENGKEEKTSHLVVVTDVCLPLLSSGESSLSARVLINYELPTKKETYTRRITTCLASGGIV 178

Query: 180 INIVVGGEVVTLRSMEESLGLIVAEVPINI 209
           IN+VVGGEV TL+S+EES G+++AE+PIN+
Sbjct: 179 INMVVGGEVTTLKSLEESSGILIAEMPINV 208

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356496882|ref|XP_003517294.1| PREDICTED: eukaryotic initiation factor 4A-like [Glycine max]

 Score =  249 bits (637), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 127/214 (59%), Positives = 165/214 (77%), Gaps = 6/214 (2%)

Query: 1   MAIDGVESPCPPCQS-PSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVC 59
           MAID V +  PP QS PS  S  RHFY+AVDRL FKM+T++EL+ LV   RRP LP++VC
Sbjct: 1   MAIDSVYTSSPPFQSGPSGHS--RHFYLAVDRLHFKMQTVIELVDLV--ARRPCLPIVVC 56

Query: 60  CSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDES 119
           CS+RD+LD++CS++S L  +S S+L+SDL E ER+ ILE+FR    +WNQ     + +E 
Sbjct: 57  CSTRDDLDSLCSSLSTLPFLSSSALYSDLGEDERSFILEKFRQVTARWNQTNHGGAPNED 116

Query: 120 ETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSV 179
           E GKDE +SHMI+VTDACLPLL+SGE  ++A +LINYELP KKETY RR+ TCL ADG V
Sbjct: 117 EIGKDE-RSHMIIVTDACLPLLASGEFPLNAHLLINYELPAKKETYGRRLATCLTADGIV 175

Query: 180 INIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 213
           IN+VVGGEVVTL+S+EES  +++ E+P+ I +IL
Sbjct: 176 INMVVGGEVVTLKSIEESSNIVMQEMPMQILDIL 209

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  244 bits (624), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 131/208 (62%), Positives = 160/208 (76%), Gaps = 19/208 (9%)

Query: 19  FSQP--RHFYVAV-DRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSN 75
           FSQP  RHFYV V DRL FKM+TLV LL   VA RRP LP++VCC+SRD+LDAVCSAVSN
Sbjct: 9   FSQPPPRHFYVTVVDRLHFKMDTLVHLLG--VAARRPALPIVVCCTSRDQLDAVCSAVSN 66

Query: 76  LADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVT----EQSGDESETG--------- 122
           L  IS +SL+SDLAE++R +ILEEFR   ++W+Q V        G   ETG         
Sbjct: 67  LPFISLASLYSDLAESDRNVILEEFRKATVRWSQIVNAGQSAGGGSGGETGNNNDESNTN 126

Query: 123 KDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSVINI 182
            ++ KSHMIVVTDACLPLL+ GE+ +SARVLINYELP+ KETY+RRM TCLAADG VIN+
Sbjct: 127 NNKTKSHMIVVTDACLPLLALGEAPVSARVLINYELPS-KETYLRRMATCLAADGIVINV 185

Query: 183 VVGGEVVTLRSMEESLGLIVAEVPINIS 210
           VVGGEV+TL+++EES  L++AE+PIN+S
Sbjct: 186 VVGGEVITLKNIEESSSLVIAEMPINVS 213

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	213
UNIPROTKB|A4QVP2	396	TIF1 "ATP-dependent RNA helica	0.342	0.184	0.278	2.8e-11
ASPGD|ASPL0000037981	398	AN2932 [Emericella nidulans (t	0.384	0.206	0.284	4.6e-11
ZFIN|ZDB-GENE-031030-2	406	eif4a1a "eukaryotic translatio	0.384	0.201	0.306	1.6e-10
ZFIN|ZDB-GENE-040120-6	429	eif4a1b "eukaryotic translatio	0.384	0.191	0.318	2.3e-10
UNIPROTKB|I3LLD5	401	I3LLD5 "Uncharacterized protei	0.384	0.204	0.306	2.5e-10
UNIPROTKB|Q3SZ54	406	EIF4A1 "Eukaryotic initiation	0.384	0.201	0.306	2.6e-10
UNIPROTKB|F1P895	406	EIF4A1 "Uncharacterized protei	0.384	0.201	0.306	2.6e-10
UNIPROTKB|J9NY67	406	EIF4A1 "Uncharacterized protei	0.384	0.201	0.306	2.6e-10
UNIPROTKB|P60842	406	EIF4A1 "Eukaryotic initiation	0.384	0.201	0.306	2.6e-10
UNIPROTKB|A6M928	406	EIF4A1 "Uncharacterized protei	0.384	0.201	0.306	2.6e-10

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

 Score = 109 (43.4 bits), Expect = 2.8e-11, Sum P(2) = 2.8e-11
 Identities = 22/79 (27%), Positives = 49/79 (62%)

Query:    23 RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
             + FY+AV++ ++K++TL +L   V   +      ++ C++R ++D +   ++   D + S
Sbjct:   237 KQFYIAVEKEEWKLDTLSDLYETVTITQA-----VIFCNTRRKVDWLTDKLT-ARDFTVS 290

Query:    83 SLHSDLAETERTLILEEFR 101
             ++H D+ + +R LI++EFR
Sbjct:   291 AMHGDMDQAQRDLIMKEFR 309

GO:0005575 "cellular_component" evidence=ND

GO:0043581 "mycelium development" evidence=IEP

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

 Score = 109 (43.4 bits), Expect = 4.6e-11, Sum P(2) = 4.6e-11
 Identities = 25/88 (28%), Positives = 46/88 (52%)

Query:   128 SHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVG 185
             S +++ TD    LL+ G       ++INY+LP  +E YI R+         G  IN V  
Sbjct:   315 SRVLIATD----LLARGIDVQQVSLVINYDLPANRENYIHRIGRGGRFGRKGVAINFVTA 370

Query:   186 GEVVTLRSMEESLGLIVAEVPINISEIL 213
              +V  +R +E+     + E+P+N+++++
Sbjct:   371 DDVRMMREIEQFYSTQIEEMPMNVADLI 398

GO:0008150 "biological_process" evidence=ND

GO:0005829 "cytosol" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

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

 Score = 114 (45.2 bits), Expect = 1.6e-10, Sum P(2) = 1.6e-10
 Identities = 27/88 (30%), Positives = 47/88 (53%)

Query:   128 SHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVG 185
             S +++ TD    LL+ G       ++INY+LPT +E YI R+         G  IN++  
Sbjct:   323 SRVLITTD----LLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMITE 378

Query:   186 GEVVTLRSMEESLGLIVAEVPINISEIL 213
              +  TLR +E      V E+P+N+++++
Sbjct:   379 DDKRTLRDIETFYNTTVEEMPMNVADLI 406

GO:0004386 "helicase activity" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

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

GO:0006413 "translational initiation" evidence=IEA

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

 Score = 115 (45.5 bits), Expect = 2.3e-10, Sum P(2) = 2.3e-10
 Identities = 28/88 (31%), Positives = 47/88 (53%)

Query:   128 SHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVG 185
             S +++ TD    LL+ G       ++INY+LPT +E YI R+         G  IN+V  
Sbjct:   346 SRVLITTD----LLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTE 401

Query:   186 GEVVTLRSMEESLGLIVAEVPINISEIL 213
              +  TLR +E      V E+P+N+++++
Sbjct:   402 DDKRTLRDIETFYNTTVEEMPMNVADLI 429

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

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

GO:0006413 "translational initiation" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

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

 Score = 113 (44.8 bits), Expect = 2.5e-10, Sum P(2) = 2.5e-10
 Identities = 27/88 (30%), Positives = 47/88 (53%)

Query:   128 SHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVG 185
             S +++ TD    LL+ G       ++INY+LPT +E YI R+         G  IN+V  
Sbjct:   318 SRVLITTD----LLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTE 373

Query:   186 GEVVTLRSMEESLGLIVAEVPINISEIL 213
              +  TLR +E      + E+P+N+++++
Sbjct:   374 EDKRTLRDIETFYNTSIEEMPLNVADLI 401

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

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

 Score = 113 (44.8 bits), Expect = 2.6e-10, Sum P(2) = 2.6e-10
 Identities = 27/88 (30%), Positives = 47/88 (53%)

Query:   128 SHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVG 185
             S +++ TD    LL+ G       ++INY+LPT +E YI R+         G  IN+V  
Sbjct:   323 SRVLITTD----LLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTE 378

Query:   186 GEVVTLRSMEESLGLIVAEVPINISEIL 213
              +  TLR +E      + E+P+N+++++
Sbjct:   379 EDKRTLRDIETFYNTSIEEMPLNVADLI 406

GO:0005524 "ATP binding" evidence=IEA

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

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

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

 Score = 113 (44.8 bits), Expect = 2.6e-10, Sum P(2) = 2.6e-10
 Identities = 27/88 (30%), Positives = 47/88 (53%)

Query:   128 SHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVG 185
             S +++ TD    LL+ G       ++INY+LPT +E YI R+         G  IN+V  
Sbjct:   323 SRVLITTD----LLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTE 378

Query:   186 GEVVTLRSMEESLGLIVAEVPINISEIL 213
              +  TLR +E      + E+P+N+++++
Sbjct:   379 EDKRTLRDIETFYNTSIEEMPLNVADLI 406

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

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

 Score = 113 (44.8 bits), Expect = 2.6e-10, Sum P(2) = 2.6e-10
 Identities = 27/88 (30%), Positives = 47/88 (53%)

Query:   128 SHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVG 185
             S +++ TD    LL+ G       ++INY+LPT +E YI R+         G  IN+V  
Sbjct:   323 SRVLITTD----LLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTE 378

Query:   186 GEVVTLRSMEESLGLIVAEVPINISEIL 213
              +  TLR +E      + E+P+N+++++
Sbjct:   379 EDKRTLRDIETFYNTSIEEMPLNVADLI 406

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

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

 Score = 113 (44.8 bits), Expect = 2.6e-10, Sum P(2) = 2.6e-10
 Identities = 27/88 (30%), Positives = 47/88 (53%)

Query:   128 SHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVG 185
             S +++ TD    LL+ G       ++INY+LPT +E YI R+         G  IN+V  
Sbjct:   323 SRVLITTD----LLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTE 378

Query:   186 GEVVTLRSMEESLGLIVAEVPINISEIL 213
              +  TLR +E      + E+P+N+++++
Sbjct:   379 EDKRTLRDIETFYNTSIEEMPLNVADLI 406

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

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

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003729 "mRNA binding" evidence=TAS

GO:0004386 "helicase activity" evidence=TAS

GO:0000339 "RNA cap binding" evidence=TAS

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

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

GO:0005515 "protein binding" evidence=IPI

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

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

GO:0005829 "cytosol" evidence=TAS

GO:0006412 "translation" evidence=TAS

GO:0006413 "translational initiation" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

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

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

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

 Score = 113 (44.8 bits), Expect = 2.6e-10, Sum P(2) = 2.6e-10
 Identities = 27/88 (30%), Positives = 47/88 (53%)

Query:   128 SHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVG 185
             S +++ TD    LL+ G       ++INY+LPT +E YI R+         G  IN+V  
Sbjct:   323 SRVLITTD----LLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTE 378

Query:   186 GEVVTLRSMEESLGLIVAEVPINISEIL 213
              +  TLR +E      + E+P+N+++++
Sbjct:   379 EDKRTLRDIETFYNTSIEEMPLNVADLI 406

GO:0005524 "ATP binding" evidence=IEA

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

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00019480001 SubName- Full=Chromosome chr7 scaffold_20, whole genome shotgun sequence; (198 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	213
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	3e-19
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	6e-07
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	6e-05
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	0.001

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

 Score = 84.5 bits (209), Expect = 3e-19
 Identities = 49/193 (25%), Positives = 89/193 (46%), Gaps = 35/193 (18%)

Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           R FYVAV++ ++K +TL +L   +   +      I+ C++R ++D +   +    D + S
Sbjct: 242 RQFYVAVEKEEWKFDTLCDLYETLTITQ-----AIIYCNTRRKVDYLTKKMHE-RDFTVS 295

Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
            +H D+ + +R LI+ EFR             SG           + +++ TD    LL+
Sbjct: 296 CMHGDMDQKDRDLIMREFR-------------SG----------STRVLITTD----LLA 328

Query: 143 SGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLRSMEESLGL 200
            G       ++INY+LP   E YI R+         G  IN V   ++  L+ +E     
Sbjct: 329 RGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIEQLKEIERHYNT 388

Query: 201 IVAEVPINISEIL 213
            + E+P+ +++ L
Sbjct: 389 QIEEMPMEVADYL 401

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 = 48.6 bits (116), Expect = 6e-07
 Identities = 34/145 (23%), Positives = 60/145 (41%), Gaps = 33/145 (22%)

Query: 24  HFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSS 83
            FY+ V+  + K+E L++LL     GR     +IV   ++  ++ +  ++        ++
Sbjct: 249 QFYLEVESEEEKLELLLKLLKDEDEGR-----VIVFVRTKRLVEELAESLRKR-GFKVAA 302

Query: 84  LHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSS 143
           LH DL + ER   LE+F+              G+             +V TD    + + 
Sbjct: 303 LHGDLPQEERDRALEKFK-------------DGELRV----------LVATD----VAAR 335

Query: 144 GESAISARVLINYELPTKKETYIRR 168
           G        +INY+LP   E Y+ R
Sbjct: 336 GLDIPDVSHVINYDLPLDPEDYVHR 360

Length = 513

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

 Score = 41.1 bits (97), Expect = 6e-05
 Identities = 34/149 (22%), Positives = 66/149 (44%), Gaps = 33/149 (22%)

Query: 21  QPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADIS 80
             + + + V+    K+E L+ELL   +     G  +++ C S+  LD +   +     I 
Sbjct: 1   PIKQYVLPVE--DEKLEALLELLKEHLK---KGGKVLIFCPSKKMLDELAELLRKP-GIK 54

Query: 81  FSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPL 140
            ++LH D ++ ER  +L++FR                       E +  ++V TD     
Sbjct: 55  VAALHGDGSQEEREEVLKDFR-----------------------EGEIVVLVATDV---- 87

Query: 141 LSSGESAISARVLINYELPTKKETYIRRM 169
           ++ G    +  V+INY+LP    +Y++R+
Sbjct: 88  IARGIDLPNVSVVINYDLPWSPSSYLQRI 116

Length = 131

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

 Score = 36.3 bits (85), Expect = 0.001
 Identities = 25/98 (25%), Positives = 37/98 (37%), Gaps = 33/98 (33%)

Query: 75  NLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVT 134
               I  + LH  L++ ER  ILE+FR                         KS ++V T
Sbjct: 4   RKPGIKVARLHGGLSQEEREEILEDFR-----------------------NGKSKVLVAT 40

Query: 135 DACLPLLSSGESAI---SARVLINYELPTKKETYIRRM 169
           D            I      ++INY+LP    +YI+R+
Sbjct: 41  DV-------AGRGIDLPDVNLVINYDLPWNPASYIQRI 71

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	213
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	100.0
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.97
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	99.97
KOG0326	459	consensus ATP-dependent RNA helicase [RNA processi	99.97
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	99.97
KOG0340	442	consensus ATP-dependent RNA helicase [RNA processi	99.96
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.96
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	99.96
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.95
PTZ00110	545	helicase; Provisional	99.95
KOG0327	397	consensus Translation initiation factor 4F, helica	99.95
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.95
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.95
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.95
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.95
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.94
PTZ00424	401	helicase 45; Provisional	99.94
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.94
KOG0342	543	consensus ATP-dependent RNA helicase pitchoune [RN	99.93
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	99.93
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	99.93
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	99.93
KOG0343	758	consensus RNA Helicase [RNA processing and modific	99.93
KOG0346	569	consensus RNA helicase [RNA processing and modific	99.92
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	99.91
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.91
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.9
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	99.9
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.9
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.89
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	99.89
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	99.89
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	99.89
KOG0350	620	consensus DEAD-box ATP-dependent RNA helicase [RNA	99.89
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.88
KOG0334	997	consensus RNA helicase [RNA processing and modific	99.86
KOG4284	980	consensus DEAD box protein [Transcription]	99.86
KOG0347	731	consensus RNA helicase [RNA processing and modific	99.86
PRK04914	956	ATP-dependent helicase HepA; Validated	99.86
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.85
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.84
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.83
PRK05298	652	excinuclease ABC subunit B; Provisional	99.82
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.82
PRK13767	876	ATP-dependent helicase; Provisional	99.81
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.81
PRK13766	773	Hef nuclease; Provisional	99.79
KOG0337	529	consensus ATP-dependent RNA helicase [RNA processi	99.79
PRK10689	1147	transcription-repair coupling factor; Provisional	99.79
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.79
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.78
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	99.78
PHA02653	675	RNA helicase NPH-II; Provisional	99.78
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.78
KOG0349	725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	99.78
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.77
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.75
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.75
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.74
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.73
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.72
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	99.71
KOG0351	941	consensus ATP-dependent DNA helicase [Replication,	99.7
PRK02362	737	ski2-like helicase; Provisional	99.7
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.69
KOG0354	746	consensus DEAD-box like helicase [General function	99.69
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.66
PHA02558	501	uvsW UvsW helicase; Provisional	99.66
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.66
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.66
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.64
PRK09401	1176	reverse gyrase; Reviewed	99.64
PRK00254	720	ski2-like helicase; Provisional	99.62
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.6
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	99.6
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.59
smart00490	82	HELICc helicase superfamily c-terminal domain.	99.59
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	99.55
PRK14701	1638	reverse gyrase; Provisional	99.54
PRK01172	674	ski2-like helicase; Provisional	99.54
COG1202	830	Superfamily II helicase, archaea-specific [General	99.53
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	99.52
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.48
KOG0352	641	consensus ATP-dependent DNA helicase [Replication,	99.48
PRK09694	878	helicase Cas3; Provisional	99.43
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.39
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.35
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.32
KOG0353	695	consensus ATP-dependent DNA helicase [General func	99.3
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	99.29
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.18
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.15
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.13
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.12
COG1205	851	Distinct helicase family with a unique C-terminal	99.09
PRK05580	679	primosome assembly protein PriA; Validated	99.09
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.08
KOG4150	1034	consensus Predicted ATP-dependent RNA helicase [RN	99.04
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.01
KOG0391	1958	consensus SNF2 family DNA-dependent ATPase [Genera	98.78
COG1204	766	Superfamily II helicase [General function predicti	98.76
KOG0385	971	consensus Chromatin remodeling complex WSTF-ISWI,	98.68
KOG0384	1373	consensus Chromodomain-helicase DNA-binding protei	98.67
KOG0950	1008	consensus DNA polymerase theta/eta, DEAD-box super	98.65
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	98.64
KOG0390	776	consensus DNA repair protein, SNF2 family [Replica	98.62
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	98.6
KOG1000	689	consensus Chromatin remodeling protein HARP/SMARCA	98.52
KOG0389	941	consensus SNF2 family DNA-dependent ATPase [Chroma	98.51
KOG0953	700	consensus Mitochondrial RNA helicase SUV3, DEAD-bo	98.46
KOG1002	791	consensus Nucleotide excision repair protein RAD16	98.43
KOG0922	674	consensus DEAH-box RNA helicase [RNA processing an	98.41
KOG0387	923	consensus Transcription-coupled repair protein CSB	98.41
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	98.41
KOG0947	1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	98.4
KOG0392	1549	consensus SNF2 family DNA-dependent ATPase domain-	98.36
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	98.32
KOG0388	1185	consensus SNF2 family DNA-dependent ATPase [Replic	98.25
KOG0920	924	consensus ATP-dependent RNA helicase A [RNA proces	98.2
KOG0923	902	consensus mRNA splicing factor ATP-dependent RNA h	98.15
KOG0948	1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	98.12
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	98.11
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	98.03
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	97.97
KOG1123	776	consensus RNA polymerase II transcription initiati	97.95
COG4096	875	HsdR Type I site-specific restriction-modification	97.88
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	97.86
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	97.83
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	97.82
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	97.81
PRK12326	764	preprotein translocase subunit SecA; Reviewed	97.77
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	97.74
KOG0386	1157	consensus Chromatin remodeling complex SWI/SNF, co	97.62
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	97.6
PF13307	167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	97.45
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	97.41
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	97.35
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	97.25
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	97.23
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	97.17
KOG0926	1172	consensus DEAH-box RNA helicase [RNA processing an	97.1
KOG4439	901	consensus RNA polymerase II transcription terminat	97.02
COG4889	1518	Predicted helicase [General function prediction on	96.99
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	96.98
KOG1015	1567	consensus Transcription regulator XNP/ATRX, DEAD-b	96.96
COG1198	730	PriA Primosomal protein N' (replication factor Y)	96.94
CHL00122	870	secA preprotein translocase subunit SecA; Validate	96.71
KOG0949	1330	consensus Predicted helicase, DEAD-box superfamily	96.65
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	96.49
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	96.29
PRK05580	679	primosome assembly protein PriA; Validated	96.27
KOG0925	699	consensus mRNA splicing factor ATP-dependent RNA h	96.2
PRK14873	665	primosome assembly protein PriA; Provisional	96.17
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	96.09
TIGR00595	505	priA primosomal protein N'. All proteins in this f	96.0
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	95.98
PF13871	278	Helicase_C_4: Helicase_C-like	95.55
COG1198	730	PriA Primosomal protein N' (replication factor Y)	95.38
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	95.34
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	95.29
KOG0701	1606	consensus dsRNA-specific nuclease Dicer and relate	94.96
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	94.39
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	94.28
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	93.97
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	93.86
smart00492	141	HELICc3 helicase superfamily c-terminal domain.	93.49
PRK10689	1147	transcription-repair coupling factor; Provisional	93.28
KOG1016	1387	consensus Predicted DNA helicase, DEAD-box superfa	93.23
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	92.87
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	91.62
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	91.29
PF10593	239	Z1: Z1 domain; InterPro: IPR018310 This entry repr	91.02
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	90.88
PRK14701	1638	reverse gyrase; Provisional	90.81
KOG2340	698	consensus Uncharacterized conserved protein [Funct	90.35
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	89.89
KOG0347	731	consensus RNA helicase [RNA processing and modific	89.13
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	89.12
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	89.0
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	88.9
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	88.72
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	87.49
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	86.77
cd01524	90	RHOD_Pyr_redox Member of the Rhodanese Homology Do	86.43
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	86.18
smart00491	142	HELICc2 helicase superfamily c-terminal domain.	86.14
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	85.84
cd00158	89	RHOD Rhodanese Homology Domain (RHOD); an alpha be	85.75
KOG1513	1300	consensus Nuclear helicase MOP-3/SNO (DEAD-box sup	85.08
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	84.95
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	84.94
KOG1001	674	consensus Helicase-like transcription factor HLTF/	84.11
cd01449	118	TST_Repeat_2 Thiosulfate sulfurtransferase (TST),	83.95
cd01444	96	GlpE_ST GlpE sulfurtransferase (ST) and homologs a	83.67
cd01529	96	4RHOD_Repeats Member of the Rhodanese Homology Dom	83.39
smart00450	100	RHOD Rhodanese Homology Domain. An alpha beta fold	83.37
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	82.43
cd01523	100	RHOD_Lact_B Member of the Rhodanese Homology Domai	82.02
PTZ00110	545	helicase; Provisional	81.56
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	81.25
cd01519	106	RHOD_HSP67B2 Member of the Rhodanese Homology Doma	80.9
cd01527	99	RHOD_YgaP Member of the Rhodanese Homology Domain	80.28
PRK09401	1176	reverse gyrase; Reviewed	80.09

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

Probab=100.00  E-value=1.1e-36  Score=259.57  Aligned_cols=164  Identities=26%  Similarity=0.558  Sum_probs=154.6

Q ss_pred             CCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHH
Q 028124           17 SHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI   96 (213)
Q Consensus        17 ~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~   96 (213)
                      -+..+|+|||+.++.+++|++.|++|...++.     .+++|||||+..++||.+.++... +.+.++||+|+++||.++
T Consensus       235 ltlEgIKqf~v~ve~EewKfdtLcdLYd~LtI-----tQavIFcnTk~kVdwLtekm~~~n-ftVssmHGDm~qkERd~i  308 (400)
T KOG0328|consen  235 LTLEGIKQFFVAVEKEEWKFDTLCDLYDTLTI-----TQAVIFCNTKRKVDWLTEKMREAN-FTVSSMHGDMEQKERDKI  308 (400)
T ss_pred             CchhhhhhheeeechhhhhHhHHHHHhhhheh-----heEEEEecccchhhHHHHHHHhhC-ceeeeccCCcchhHHHHH
Confidence            34567999999999999999999999998544     799999999999999999998875 899999999999999999


Q ss_pred             HHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cC
Q 028124           97 LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LA  174 (213)
Q Consensus        97 l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~  174 (213)
                      +.+||+|.                       .++||+||+    .+||+|+|.|++|||||+|.+.+.||||+||.  .|
T Consensus       309 m~dFRsg~-----------------------SrvLitTDV----waRGiDv~qVslviNYDLP~nre~YIHRIGRSGRFG  361 (400)
T KOG0328|consen  309 MNDFRSGK-----------------------SRVLITTDV----WARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFG  361 (400)
T ss_pred             HHHhhcCC-----------------------ceEEEEech----hhccCCcceeEEEEecCCCccHHHHhhhhccccccC
Confidence            99999984                       999999999    99999999999999999999999999999995  68


Q ss_pred             CCCeEEEEEeCchhHHHHHHHHHhcccccccCccccccC
Q 028124          175 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL  213 (213)
Q Consensus       175 ~~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~~~~~~  213 (213)
                      +.|++|+|+..+|...++.+|++++..+.++|+++.+++
T Consensus       362 RkGvainFVk~~d~~~lrdieq~yst~i~emp~nvad~i  400 (400)
T KOG0328|consen  362 RKGVAINFVKSDDLRILRDIEQYYSTQIDEMPMNVADLI  400 (400)
T ss_pred             CcceEEEEecHHHHHHHHHHHHHHhhhcccccchhhhcC
Confidence            999999999999999999999999999999999988764

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

Probab=100.00  E-value=9.3e-33  Score=243.49  Aligned_cols=160  Identities=25%  Similarity=0.397  Sum_probs=149.7

Q ss_pred             CCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHH
Q 028124           17 SHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI   96 (213)
Q Consensus        17 ~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~   96 (213)
                      .+-++++|+|.+++... |...|..+|+.     ..+..+||||+++.++.+++-.|+..| +.+..+||+|++..|...
T Consensus       270 ~tv~~lkQ~ylfv~~k~-K~~yLV~ll~e-----~~g~s~iVF~~t~~tt~~la~~L~~lg-~~a~~LhGqmsq~~Rlg~  342 (476)
T KOG0330|consen  270 QTVDHLKQTYLFVPGKD-KDTYLVYLLNE-----LAGNSVIVFCNTCNTTRFLALLLRNLG-FQAIPLHGQMSQSKRLGA  342 (476)
T ss_pred             cchHHhhhheEeccccc-cchhHHHHHHh-----hcCCcEEEEEeccchHHHHHHHHHhcC-cceecccchhhHHHHHHH
Confidence            45578999999999987 99999999998     455899999999999999999999998 899999999999999999


Q ss_pred             HHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cC
Q 028124           97 LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LA  174 (213)
Q Consensus        97 l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~  174 (213)
                      +++|++|.                       .+||||||+    ++||+|+|.|++|||||+|.+..+||||+||+  .|
T Consensus       343 l~~Fk~~~-----------------------r~iLv~TDV----aSRGLDip~Vd~VVNyDiP~~skDYIHRvGRtaRaG  395 (476)
T KOG0330|consen  343 LNKFKAGA-----------------------RSILVCTDV----ASRGLDIPHVDVVVNYDIPTHSKDYIHRVGRTARAG  395 (476)
T ss_pred             HHHHhccC-----------------------CcEEEecch----hcccCCCCCceEEEecCCCCcHHHHHHHcccccccC
Confidence            99999985                       999999999    99999999999999999999999999999995  78


Q ss_pred             CCCeEEEEEeCchhHHHHHHHHHhcccccccCcccc
Q 028124          175 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINIS  210 (213)
Q Consensus       175 ~~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~~~  210 (213)
                      ++|.+|+||+..|.+.+++||..++.++.+.+++-.
T Consensus       396 rsG~~ItlVtqyDve~~qrIE~~~gkkl~~~~~~~~  431 (476)
T KOG0330|consen  396 RSGKAITLVTQYDVELVQRIEHALGKKLPEYKVDKN  431 (476)
T ss_pred             CCcceEEEEehhhhHHHHHHHHHHhcCCCccCcchH
Confidence            999999999999999999999999999988666543

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

Probab=99.97  E-value=1.3e-30  Score=242.99  Aligned_cols=153  Identities=25%  Similarity=0.430  Sum_probs=142.3

Q ss_pred             CCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHH
Q 028124           18 HFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLIL   97 (213)
Q Consensus        18 ~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l   97 (213)
                      +...|.|+|+.++..+.|+..|..+++.     ....++||||+|+..++.|+..|...| +++..+||+|++++|.+++
T Consensus       243 ~~~~i~q~~~~v~~~~~k~~~L~~ll~~-----~~~~~~IVF~~tk~~~~~l~~~l~~~g-~~~~~lhG~l~q~~R~~~l  316 (513)
T COG0513         243 TLKKIKQFYLEVESEEEKLELLLKLLKD-----EDEGRVIVFVRTKRLVEELAESLRKRG-FKVAALHGDLPQEERDRAL  316 (513)
T ss_pred             cccCceEEEEEeCCHHHHHHHHHHHHhc-----CCCCeEEEEeCcHHHHHHHHHHHHHCC-CeEEEecCCCCHHHHHHHH
Confidence            6789999999999866699999999987     344589999999999999999999998 8999999999999999999


Q ss_pred             HHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCC
Q 028124           98 EEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAA  175 (213)
Q Consensus        98 ~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~  175 (213)
                      ++|++|.                       .++|||||+    ++||||++++++|||||+|.++++|+||+||+  +|+
T Consensus       317 ~~F~~g~-----------------------~~vLVaTDv----aaRGiDi~~v~~VinyD~p~~~e~yvHRiGRTgRaG~  369 (513)
T COG0513         317 EKFKDGE-----------------------LRVLVATDV----AARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGR  369 (513)
T ss_pred             HHHHcCC-----------------------CCEEEEech----hhccCCccccceeEEccCCCCHHHheeccCccccCCC
Confidence            9999985                       999999999    99999999999999999999999999999996  678


Q ss_pred             CCeEEEEEeCc-hhHHHHHHHHHhccccc
Q 028124          176 DGSVINIVVGG-EVVTLRSMEESLGLIVA  203 (213)
Q Consensus       176 ~g~~i~~~~~~-e~~~~~~le~~l~~~~~  203 (213)
                      .|.+++|+.+. |...+..+++.++..+.
T Consensus       370 ~G~ai~fv~~~~e~~~l~~ie~~~~~~~~  398 (513)
T COG0513         370 KGVAISFVTEEEEVKKLKRIEKRLERKLP  398 (513)
T ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhcccc
Confidence            99999999976 99999999999877754

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

Probab=99.97  E-value=5.3e-31  Score=242.24  Aligned_cols=162  Identities=21%  Similarity=0.352  Sum_probs=145.6

Q ss_pred             CCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHH
Q 028124           17 SHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI   96 (213)
Q Consensus        17 ~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~   96 (213)
                      ....+|.|....++... |...|.++|..+..  .++.|+||||+|+.+|++|+..|+..+ +.+..+||+.++.+|..+
T Consensus       308 ~a~~~i~qive~~~~~~-K~~~l~~lL~~~~~--~~~~KvIIFc~tkr~~~~l~~~l~~~~-~~a~~iHGd~sQ~eR~~~  383 (519)
T KOG0331|consen  308 KANHNIRQIVEVCDETA-KLRKLGKLLEDISS--DSEGKVIIFCETKRTCDELARNLRRKG-WPAVAIHGDKSQSERDWV  383 (519)
T ss_pred             hhhcchhhhhhhcCHHH-HHHHHHHHHHHHhc--cCCCcEEEEecchhhHHHHHHHHHhcC-cceeeecccccHHHHHHH
Confidence            55678999999999555 99999999988542  567899999999999999999999987 899999999999999999


Q ss_pred             HHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhcccc--C
Q 028124           97 LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--A  174 (213)
Q Consensus        97 l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~--~  174 (213)
                      |+.||+|.                       ..+|||||+    ++||||+++|++|||||+|.+.++|+||+||+|  +
T Consensus       384 L~~FreG~-----------------------~~vLVATdV----AaRGLDi~dV~lVInydfP~~vEdYVHRiGRTGRa~  436 (519)
T KOG0331|consen  384 LKGFREGK-----------------------SPVLVATDV----AARGLDVPDVDLVINYDFPNNVEDYVHRIGRTGRAG  436 (519)
T ss_pred             HHhcccCC-----------------------cceEEEccc----ccccCCCccccEEEeCCCCCCHHHHHhhcCccccCC
Confidence            99999995                       999999999    999999999999999999999999999999974  5


Q ss_pred             CCCeEEEEEeCchhHHHHHHHHHhcccccccCccc
Q 028124          175 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINI  209 (213)
Q Consensus       175 ~~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~~  209 (213)
                      +.|.+++|++..+......+.+.+.-..+.+|-.+
T Consensus       437 ~~G~A~tfft~~~~~~a~~l~~~l~e~~q~v~~~l  471 (519)
T KOG0331|consen  437 KKGTAITFFTSDNAKLARELIKVLREAGQTVPPDL  471 (519)
T ss_pred             CCceEEEEEeHHHHHHHHHHHHHHHHccCCCChHH
Confidence            78999999999999998888888866666665444

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

Probab=99.97  E-value=4.1e-31  Score=228.74  Aligned_cols=161  Identities=24%  Similarity=0.446  Sum_probs=150.8

Q ss_pred             CCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHH
Q 028124           17 SHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI   96 (213)
Q Consensus        17 ~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~   96 (213)
                      -+..++.|||.++...+ |+.-|..|+..+     .-.++|||||+..++|.||..+...| +.+.++|+.|.++.|..+
T Consensus       292 Ltl~GvtQyYafV~e~q-KvhCLntLfskL-----qINQsIIFCNS~~rVELLAkKITelG-yscyyiHakM~Q~hRNrV  364 (459)
T KOG0326|consen  292 LTLKGVTQYYAFVEERQ-KVHCLNTLFSKL-----QINQSIIFCNSTNRVELLAKKITELG-YSCYYIHAKMAQEHRNRV  364 (459)
T ss_pred             hhhcchhhheeeechhh-hhhhHHHHHHHh-----cccceEEEeccchHhHHHHHHHHhcc-chhhHHHHHHHHhhhhhh
Confidence            45578999999999987 999999988874     34799999999999999999999998 899999999999999999


Q ss_pred             HHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cC
Q 028124           97 LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LA  174 (213)
Q Consensus        97 l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~  174 (213)
                      +.+||+|.                       ++.|||||.    +.||+|++.+++|||||+|++.++|+||+||.  .|
T Consensus       365 FHdFr~G~-----------------------crnLVctDL----~TRGIDiqavNvVINFDfpk~aEtYLHRIGRsGRFG  417 (459)
T KOG0326|consen  365 FHDFRNGK-----------------------CRNLVCTDL----FTRGIDIQAVNVVINFDFPKNAETYLHRIGRSGRFG  417 (459)
T ss_pred             hhhhhccc-----------------------cceeeehhh----hhcccccceeeEEEecCCCCCHHHHHHHccCCccCC
Confidence            99999994                       999999999    99999999999999999999999999999996  58


Q ss_pred             CCCeEEEEEeCchhHHHHHHHHHhcccccccCccccc
Q 028124          175 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISE  211 (213)
Q Consensus       175 ~~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~~~~  211 (213)
                      ..|.+|++++.+|...+..+|+.+|.++.++|..++.
T Consensus       418 hlGlAInLityedrf~L~~IE~eLGtEI~pip~~iDk  454 (459)
T KOG0326|consen  418 HLGLAINLITYEDRFNLYRIEQELGTEIKPIPSNIDK  454 (459)
T ss_pred             CcceEEEEEehhhhhhHHHHHHHhccccccCCCcCCc
Confidence            8899999999999999999999999999999987754

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

Probab=99.97  E-value=1.3e-29  Score=230.24  Aligned_cols=146  Identities=19%  Similarity=0.366  Sum_probs=135.3

Q ss_pred             CCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHH
Q 028124           20 SQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEE   99 (213)
Q Consensus        20 ~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~   99 (213)
                      +-++|.++.++.++ |+..|.++|+.     ....++|||+|+++.|++||+.|.+.| +++..|||+-++++|.-+|+.
T Consensus       490 ~rveQ~v~m~~ed~-k~kkL~eil~~-----~~~ppiIIFvN~kk~~d~lAk~LeK~g-~~~~tlHg~k~qeQRe~aL~~  562 (673)
T KOG0333|consen  490 PRVEQKVEMVSEDE-KRKKLIEILES-----NFDPPIIIFVNTKKGADALAKILEKAG-YKVTTLHGGKSQEQRENALAD  562 (673)
T ss_pred             cchheEEEEecchH-HHHHHHHHHHh-----CCCCCEEEEEechhhHHHHHHHHhhcc-ceEEEeeCCccHHHHHHHHHH
Confidence            45899999999988 89999999988     356899999999999999999999998 899999999999999999999


Q ss_pred             HhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCCCC
Q 028124          100 FRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADG  177 (213)
Q Consensus       100 Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~~g  177 (213)
                      ||.|.                       .+||||||+    ++||+|+|+|++|||||++.++++|+|||||+  +|+.|
T Consensus       563 fr~~t-----------------------~dIlVaTDv----AgRGIDIpnVSlVinydmaksieDYtHRIGRTgRAGk~G  615 (673)
T KOG0333|consen  563 FREGT-----------------------GDILVATDV----AGRGIDIPNVSLVINYDMAKSIEDYTHRIGRTGRAGKSG  615 (673)
T ss_pred             HHhcC-----------------------CCEEEEecc----cccCCCCCccceeeecchhhhHHHHHHHhccccccccCc
Confidence            99985                       999999999    99999999999999999999999999999996  68899


Q ss_pred             eEEEEEeCchhHHHHHHHHHhc
Q 028124          178 SVINIVVGGEVVTLRSMEESLG  199 (213)
Q Consensus       178 ~~i~~~~~~e~~~~~~le~~l~  199 (213)
                      .+|+|+++.|-..+..|.+.+-
T Consensus       616 taiSflt~~dt~v~ydLkq~l~  637 (673)
T KOG0333|consen  616 TAISFLTPADTAVFYDLKQALR  637 (673)
T ss_pred             eeEEEeccchhHHHHHHHHHHH
Confidence            9999999998777777766553

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

Probab=99.96  E-value=1.6e-29  Score=221.04  Aligned_cols=162  Identities=25%  Similarity=0.357  Sum_probs=150.3

Q ss_pred             CCCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHH
Q 028124           16 PSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTL   95 (213)
Q Consensus        16 ~~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~   95 (213)
                      .++.+.+.|-|+.++... |-..|..+|..+..  .....++||+|+..+|+.|+..|+..+ +.+..+|+.|++.+|..
T Consensus       220 vstvetL~q~yI~~~~~v-kdaYLv~~Lr~~~~--~~~~simIFvnttr~cQ~l~~~l~~le-~r~~~lHs~m~Q~eR~~  295 (442)
T KOG0340|consen  220 VSTVETLYQGYILVSIDV-KDAYLVHLLRDFEN--KENGSIMIFVNTTRECQLLSMTLKNLE-VRVVSLHSQMPQKERLA  295 (442)
T ss_pred             CCchhhhhhheeecchhh-hHHHHHHHHhhhhh--ccCceEEEEeehhHHHHHHHHHHhhhc-eeeeehhhcchHHHHHH
Confidence            466788999999999987 99999999987433  246889999999999999999999997 89999999999999999


Q ss_pred             HHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--c
Q 028124           96 ILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--L  173 (213)
Q Consensus        96 ~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~  173 (213)
                      .|.+||++.                       .++|||||+    ++||+|+|.|++|||||+|+++.+||||+||+  +
T Consensus       296 aLsrFrs~~-----------------------~~iliaTDV----AsRGLDIP~V~LVvN~diPr~P~~yiHRvGRtARA  348 (442)
T KOG0340|consen  296 ALSRFRSNA-----------------------ARILIATDV----ASRGLDIPTVELVVNHDIPRDPKDYIHRVGRTARA  348 (442)
T ss_pred             HHHHHhhcC-----------------------ccEEEEech----hhcCCCCCceeEEEecCCCCCHHHHHHhhcchhcc
Confidence            999999985                       999999999    99999999999999999999999999999995  8


Q ss_pred             CCCCeEEEEEeCchhHHHHHHHHHhcccccccCcc
Q 028124          174 AADGSVINIVVGGEVVTLRSMEESLGLIVAEVPIN  208 (213)
Q Consensus       174 ~~~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~  208 (213)
                      |+.|.+|+|++..|.+.+..+|+.+|.++.|.+..
T Consensus       349 GR~G~aiSivt~rDv~l~~aiE~~igkKl~e~~~~  383 (442)
T KOG0340|consen  349 GRKGMAISIVTQRDVELLQAIEEEIGKKLTEYNKV  383 (442)
T ss_pred             cCCcceEEEechhhHHHHHHHHHHHhccccccccc
Confidence            99999999999999999999999999999988754

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.96  E-value=4.5e-29  Score=227.14  Aligned_cols=161  Identities=19%  Similarity=0.270  Sum_probs=144.4

Q ss_pred             CCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHH
Q 028124           18 HFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLIL   97 (213)
Q Consensus        18 ~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l   97 (213)
                      ....+++.+......+ |...|..+++.     ....++||||+++..|+.++..|...+ +.+..+||+|++++|..++
T Consensus       226 ~~~~i~~~~~~~~~~~-k~~~l~~ll~~-----~~~~~~lVF~~t~~~~~~l~~~L~~~g-~~v~~lhg~~~~~~R~~~l  298 (423)
T PRK04837        226 TGHRIKEELFYPSNEE-KMRLLQTLIEE-----EWPDRAIIFANTKHRCEEIWGHLAADG-HRVGLLTGDVAQKKRLRIL  298 (423)
T ss_pred             CCCceeEEEEeCCHHH-HHHHHHHHHHh-----cCCCeEEEEECCHHHHHHHHHHHHhCC-CcEEEecCCCChhHHHHHH
Confidence            3456777777666554 99999998876     356799999999999999999999887 8999999999999999999


Q ss_pred             HHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCC
Q 028124           98 EEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAA  175 (213)
Q Consensus        98 ~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~  175 (213)
                      ++|++|+                       +++|||||+    ++||+|+|++++|||||+|.+.++|+||+||+  .|+
T Consensus       299 ~~F~~g~-----------------------~~vLVaTdv----~~rGiDip~v~~VI~~d~P~s~~~yiqR~GR~gR~G~  351 (423)
T PRK04837        299 EEFTRGD-----------------------LDILVATDV----AARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGA  351 (423)
T ss_pred             HHHHcCC-----------------------CcEEEEech----hhcCCCccccCEEEEeCCCCchhheEeccccccCCCC
Confidence            9999985                       999999999    99999999999999999999999999999996  577


Q ss_pred             CCeEEEEEeCchhHHHHHHHHHhcccccccCcccccc
Q 028124          176 DGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEI  212 (213)
Q Consensus       176 ~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~~~~~  212 (213)
                      .|.+|+|+.+++...+..+++.++..+++.+++..++
T Consensus       352 ~G~ai~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~  388 (423)
T PRK04837        352 SGHSISLACEEYALNLPAIETYIGHSIPVSKYDSDAL  388 (423)
T ss_pred             CeeEEEEeCHHHHHHHHHHHHHhCCCCCCccCChhhh
Confidence            8999999999999999999999999988777766554

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

Probab=99.96  E-value=7.4e-29  Score=218.00  Aligned_cols=157  Identities=22%  Similarity=0.384  Sum_probs=143.1

Q ss_pred             CCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHH
Q 028124           17 SHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI   96 (213)
Q Consensus        17 ~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~   96 (213)
                      -+.++|+|+|+.|+..++|+++|.++...+     .-++.||||.|+++|.+|+..|+..| ..+..+||+|.-.+|..+
T Consensus       299 l~L~~IkQlyv~C~~~~~K~~~l~~lyg~~-----tigqsiIFc~tk~ta~~l~~~m~~~G-h~V~~l~G~l~~~~R~~i  372 (477)
T KOG0332|consen  299 LALDNIKQLYVLCACRDDKYQALVNLYGLL-----TIGQSIIFCHTKATAMWLYEEMRAEG-HQVSLLHGDLTVEQRAAI  372 (477)
T ss_pred             ccccchhhheeeccchhhHHHHHHHHHhhh-----hhhheEEEEeehhhHHHHHHHHHhcC-ceeEEeeccchhHHHHHH
Confidence            456889999999999999999999988774     34799999999999999999999998 699999999999999999


Q ss_pred             HHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCC------ChHHHHHhhc
Q 028124           97 LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPT------KKETYIRRMT  170 (213)
Q Consensus        97 l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~------~~~~yi~R~G  170 (213)
                      +.+||.|                       +.++||+|++    .+||+|++.|++|||||+|-      +.++|+||+|
T Consensus       373 i~~Fr~g-----------------------~~kVLitTnV----~ARGiDv~qVs~VvNydlP~~~~~~pD~etYlHRiG  425 (477)
T KOG0332|consen  373 IDRFREG-----------------------KEKVLITTNV----CARGIDVAQVSVVVNYDLPVKYTGEPDYETYLHRIG  425 (477)
T ss_pred             HHHHhcC-----------------------cceEEEEech----hhcccccceEEEEEecCCccccCCCCCHHHHHHHhc
Confidence            9999998                       4999999999    89999999999999999996      6899999999


Q ss_pred             cc--cCCCCeEEEEEeCc-hhHHHHHHHHHhcccccccC
Q 028124          171 TC--LAADGSVINIVVGG-EVVTLRSMEESLGLIVAEVP  206 (213)
Q Consensus       171 R~--~~~~g~~i~~~~~~-e~~~~~~le~~l~~~~~~~~  206 (213)
                      |+  .|+.|.+|+|+..+ ....+..|+++++..+..+.
T Consensus       426 RtGRFGkkG~a~n~v~~~~s~~~mn~iq~~F~~~i~~~~  464 (477)
T KOG0332|consen  426 RTGRFGKKGLAINLVDDKDSMNIMNKIQKHFNMKIKRLD  464 (477)
T ss_pred             ccccccccceEEEeecccCcHHHHHHHHHHHhhcceecC
Confidence            97  58999999999754 67888999999987776543

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.95  E-value=1.4e-27  Score=219.47  Aligned_cols=155  Identities=23%  Similarity=0.373  Sum_probs=141.6

Q ss_pred             CCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHH
Q 028124           19 FSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILE   98 (213)
Q Consensus        19 ~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~   98 (213)
                      ...+.|+|+.++..+ |++.|..++..     ....++||||+++..++.+++.|...+ +.+..+||+|++.+|..+++
T Consensus       214 ~~~i~~~~~~~~~~~-k~~~l~~ll~~-----~~~~~~lVF~~t~~~~~~l~~~L~~~~-~~v~~~hg~~~~~eR~~~l~  286 (460)
T PRK11776        214 LPAIEQRFYEVSPDE-RLPALQRLLLH-----HQPESCVVFCNTKKECQEVADALNAQG-FSALALHGDLEQRDRDQVLV  286 (460)
T ss_pred             CCCeeEEEEEeCcHH-HHHHHHHHHHh-----cCCCceEEEECCHHHHHHHHHHHHhCC-CcEEEEeCCCCHHHHHHHHH
Confidence            456899999998877 99999999976     345789999999999999999999987 89999999999999999999


Q ss_pred             HHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCCC
Q 028124           99 EFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAAD  176 (213)
Q Consensus        99 ~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~~  176 (213)
                      +|++|+                       .++||||++    ++||+|+|++++|||||+|.+.++|+||+||+  .|+.
T Consensus       287 ~F~~g~-----------------------~~vLVaTdv----~~rGiDi~~v~~VI~~d~p~~~~~yiqR~GRtGR~g~~  339 (460)
T PRK11776        287 RFANRS-----------------------CSVLVATDV----AARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSK  339 (460)
T ss_pred             HHHcCC-----------------------CcEEEEecc----cccccchhcCCeEEEecCCCCHhHhhhhcccccCCCCc
Confidence            999985                       999999999    99999999999999999999999999999997  5677


Q ss_pred             CeEEEEEeCchhHHHHHHHHHhcccccccCc
Q 028124          177 GSVINIVVGGEVVTLRSMEESLGLIVAEVPI  207 (213)
Q Consensus       177 g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~  207 (213)
                      |.+++|+.+.|...+..+++.++..+...++
T Consensus       340 G~ai~l~~~~e~~~~~~i~~~~~~~~~~~~l  370 (460)
T PRK11776        340 GLALSLVAPEEMQRANAIEDYLGRKLNWEPL  370 (460)
T ss_pred             ceEEEEEchhHHHHHHHHHHHhCCCCceecC
Confidence            9999999999999999999999887765443

>PTZ00110 helicase; Provisional

Probab=99.95  E-value=1.6e-27  Score=223.85  Aligned_cols=163  Identities=20%  Similarity=0.318  Sum_probs=145.6

Q ss_pred             CCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHH
Q 028124           17 SHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI   96 (213)
Q Consensus        17 ~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~   96 (213)
                      ....+++|.+..+...+ |...|.++++.+..   ...++||||+++++|+.|+..|...+ +.+..+||++++++|..+
T Consensus       345 ~~~~~i~q~~~~~~~~~-k~~~L~~ll~~~~~---~~~k~LIF~~t~~~a~~l~~~L~~~g-~~~~~ihg~~~~~eR~~i  419 (545)
T PTZ00110        345 TACHNIKQEVFVVEEHE-KRGKLKMLLQRIMR---DGDKILIFVETKKGADFLTKELRLDG-WPALCIHGDKKQEERTWV  419 (545)
T ss_pred             ccCCCeeEEEEEEechh-HHHHHHHHHHHhcc---cCCeEEEEecChHHHHHHHHHHHHcC-CcEEEEECCCcHHHHHHH
Confidence            34467888888887765 99999999987432   56899999999999999999999887 799999999999999999


Q ss_pred             HHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cC
Q 028124           97 LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LA  174 (213)
Q Consensus        97 l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~  174 (213)
                      +++|++|.                       .++|||||+    ++||+|++++++|||||+|.++++|+||+||+  .|
T Consensus       420 l~~F~~G~-----------------------~~ILVaTdv----~~rGIDi~~v~~VI~~d~P~s~~~yvqRiGRtGR~G  472 (545)
T PTZ00110        420 LNEFKTGK-----------------------SPIMIATDV----ASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAG  472 (545)
T ss_pred             HHHHhcCC-----------------------CcEEEEcch----hhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCC
Confidence            99999985                       999999999    99999999999999999999999999999997  56


Q ss_pred             CCCeEEEEEeCchhHHHHHHHHHhcccccccCccccc
Q 028124          175 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISE  211 (213)
Q Consensus       175 ~~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~~~~  211 (213)
                      +.|.+++|+++.+......+.+.+....+++|-.+.+
T Consensus       473 ~~G~ai~~~~~~~~~~~~~l~~~l~~~~q~vp~~l~~  509 (545)
T PTZ00110        473 AKGASYTFLTPDKYRLARDLVKVLREAKQPVPPELEK  509 (545)
T ss_pred             CCceEEEEECcchHHHHHHHHHHHHHccCCCCHHHHH
Confidence            7899999999999999999999988888888865544

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

Probab=99.95  E-value=7.8e-28  Score=211.88  Aligned_cols=161  Identities=27%  Similarity=0.564  Sum_probs=152.7

Q ss_pred             CCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHH
Q 028124           17 SHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI   96 (213)
Q Consensus        17 ~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~   96 (213)
                      -+...++|+|+.+..++ |+..|+++.+.       ..+.+|||||+..++.+..+|...+ ..+..+||+|.+.+|..+
T Consensus       235 ltl~gikq~~i~v~k~~-k~~~l~dl~~~-------~~q~~if~nt~r~v~~l~~~L~~~~-~~~s~~~~d~~q~~R~~~  305 (397)
T KOG0327|consen  235 LTLEGIKQFYINVEKEE-KLDTLCDLYRR-------VTQAVIFCNTRRKVDNLTDKLRAHG-FTVSAIHGDMEQNERDTL  305 (397)
T ss_pred             hhhhheeeeeeeccccc-cccHHHHHHHh-------hhcceEEecchhhHHHHHHHHhhCC-ceEEEeecccchhhhhHH
Confidence            44678999999999998 99999999985       3689999999999999999998887 899999999999999999


Q ss_pred             HHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cC
Q 028124           97 LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LA  174 (213)
Q Consensus        97 l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~  174 (213)
                      +++|++|+                       +++||+|+.    ++||+|+.+++.|||||+|...++|+||+||+  .|
T Consensus       306 ~~ef~~gs-----------------------srvlIttdl----~argidv~~~slvinydlP~~~~~yihR~gr~gr~g  358 (397)
T KOG0327|consen  306 MREFRSGS-----------------------SRVLITTDL----LARGIDVQQVSLVVNYDLPARKENYIHRIGRAGRFG  358 (397)
T ss_pred             HHHhhcCC-----------------------ceEEeeccc----cccccchhhcceeeeeccccchhhhhhhcccccccC
Confidence            99999996                       999999999    99999999999999999999999999999996  68


Q ss_pred             CCCeEEEEEeCchhHHHHHHHHHhcccccccCccccccC
Q 028124          175 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL  213 (213)
Q Consensus       175 ~~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~~~~~~  213 (213)
                      ++|.++++++..+...++++|++++..++|+|.++.+++
T Consensus       359 rkg~~in~v~~~d~~~lk~ie~~y~~~i~e~p~~~~~l~  397 (397)
T KOG0327|consen  359 RKGVAINFVTEEDVRDLKDIEKFYNTPIEELPSNFADLL  397 (397)
T ss_pred             CCceeeeeehHhhHHHHHhHHHhcCCcceecccchhhcC
Confidence            999999999999999999999999999999999998875

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.95  E-value=6.2e-27  Score=213.52  Aligned_cols=155  Identities=18%  Similarity=0.321  Sum_probs=140.8

Q ss_pred             CCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHH
Q 028124           17 SHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI   96 (213)
Q Consensus        17 ~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~   96 (213)
                      ....++.|+|..++..+.|.+.|..+++.     ....++||||+++.+++.++..|...+ +.+..+||+|++.+|..+
T Consensus       214 ~~~~~i~~~~~~~~~~~~k~~~l~~l~~~-----~~~~~~lVF~~s~~~~~~l~~~L~~~~-~~~~~l~g~~~~~~R~~~  287 (434)
T PRK11192        214 RERKKIHQWYYRADDLEHKTALLCHLLKQ-----PEVTRSIVFVRTRERVHELAGWLRKAG-INCCYLEGEMVQAKRNEA  287 (434)
T ss_pred             ccccCceEEEEEeCCHHHHHHHHHHHHhc-----CCCCeEEEEeCChHHHHHHHHHHHhCC-CCEEEecCCCCHHHHHHH
Confidence            44567899999888777799999998875     456799999999999999999999887 899999999999999999


Q ss_pred             HHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cC
Q 028124           97 LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LA  174 (213)
Q Consensus        97 l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~  174 (213)
                      +++|++|+                       +++|||||+    ++||+|+|++++|||||+|.+.+.|+||+||+  .|
T Consensus       288 l~~f~~G~-----------------------~~vLVaTd~----~~~GiDip~v~~VI~~d~p~s~~~yiqr~GR~gR~g  340 (434)
T PRK11192        288 IKRLTDGR-----------------------VNVLVATDV----AARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAG  340 (434)
T ss_pred             HHHHhCCC-----------------------CcEEEEccc----cccCccCCCCCEEEEECCCCCHHHHhhcccccccCC
Confidence            99999985                       999999999    99999999999999999999999999999997  56


Q ss_pred             CCCeEEEEEeCchhHHHHHHHHHhcccccc
Q 028124          175 ADGSVINIVVGGEVVTLRSMEESLGLIVAE  204 (213)
Q Consensus       175 ~~g~~i~~~~~~e~~~~~~le~~l~~~~~~  204 (213)
                      +.|.+++|+...|...+.++++++...+.+
T Consensus       341 ~~g~ai~l~~~~d~~~~~~i~~~~~~~~~~  370 (434)
T PRK11192        341 RKGTAISLVEAHDHLLLGKIERYIEEPLKA  370 (434)
T ss_pred             CCceEEEEecHHHHHHHHHHHHHHhccccc
Confidence            779999999999999999999988776644

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.95  E-value=5.1e-27  Score=215.91  Aligned_cols=154  Identities=22%  Similarity=0.320  Sum_probs=139.1

Q ss_pred             CCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHH
Q 028124           18 HFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLIL   97 (213)
Q Consensus        18 ~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l   97 (213)
                      ...++.+++..++... |.+.|..++..     ....++||||+++..++.+++.|...+ +.+..+||+|++.+|.+++
T Consensus       216 ~~~~i~~~~~~~~~~~-k~~~l~~l~~~-----~~~~~~lVF~~t~~~~~~l~~~L~~~g-~~~~~lhg~~~~~~R~~~l  288 (456)
T PRK10590        216 ASEQVTQHVHFVDKKR-KRELLSQMIGK-----GNWQQVLVFTRTKHGANHLAEQLNKDG-IRSAAIHGNKSQGARTRAL  288 (456)
T ss_pred             cccceeEEEEEcCHHH-HHHHHHHHHHc-----CCCCcEEEEcCcHHHHHHHHHHHHHCC-CCEEEEECCCCHHHHHHHH
Confidence            3456888888877665 88888887765     456799999999999999999999887 8999999999999999999


Q ss_pred             HHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCC
Q 028124           98 EEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAA  175 (213)
Q Consensus        98 ~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~  175 (213)
                      ++|++|.                       +++|||||+    ++||+|+|++++|||||+|.++++|+||+||+  .|.
T Consensus       289 ~~F~~g~-----------------------~~iLVaTdv----~~rGiDip~v~~VI~~~~P~~~~~yvqR~GRaGR~g~  341 (456)
T PRK10590        289 ADFKSGD-----------------------IRVLVATDI----AARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAA  341 (456)
T ss_pred             HHHHcCC-----------------------CcEEEEccH----HhcCCCcccCCEEEEeCCCCCHHHhhhhccccccCCC
Confidence            9999985                       999999999    99999999999999999999999999999997  467


Q ss_pred             CCeEEEEEeCchhHHHHHHHHHhccccccc
Q 028124          176 DGSVINIVVGGEVVTLRSMEESLGLIVAEV  205 (213)
Q Consensus       176 ~g~~i~~~~~~e~~~~~~le~~l~~~~~~~  205 (213)
                      .|.+++|+...|...++.+++.++.+++..
T Consensus       342 ~G~ai~l~~~~d~~~~~~ie~~l~~~~~~~  371 (456)
T PRK10590        342 TGEALSLVCVDEHKLLRDIEKLLKKEIPRI  371 (456)
T ss_pred             CeeEEEEecHHHHHHHHHHHHHhcCCCccc
Confidence            799999999999999999999998887543

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.95  E-value=5.9e-27  Score=221.07  Aligned_cols=157  Identities=19%  Similarity=0.321  Sum_probs=140.6

Q ss_pred             CCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHH
Q 028124           18 HFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLIL   97 (213)
Q Consensus        18 ~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l   97 (213)
                      ....++|.++.....+ |+..|..++..     ....++|||||+++.++.|++.|...+ +.+..+||+|++.+|..++
T Consensus       228 ~~~~i~q~~~~~~~~~-k~~~L~~ll~~-----~~~~k~LVF~nt~~~ae~l~~~L~~~g-~~v~~lhg~l~~~eR~~il  300 (572)
T PRK04537        228 TAARVRQRIYFPADEE-KQTLLLGLLSR-----SEGARTMVFVNTKAFVERVARTLERHG-YRVGVLSGDVPQKKRESLL  300 (572)
T ss_pred             cccceeEEEEecCHHH-HHHHHHHHHhc-----ccCCcEEEEeCCHHHHHHHHHHHHHcC-CCEEEEeCCCCHHHHHHHH
Confidence            4456788887766655 99998888876     456899999999999999999999987 8999999999999999999


Q ss_pred             HHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCC
Q 028124           98 EEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAA  175 (213)
Q Consensus        98 ~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~  175 (213)
                      ++|++|+                       .+||||||+    ++||+|++++++|||||+|.+.++|+||+||+  .|+
T Consensus       301 ~~Fr~G~-----------------------~~VLVaTdv----~arGIDip~V~~VInyd~P~s~~~yvqRiGRaGR~G~  353 (572)
T PRK04537        301 NRFQKGQ-----------------------LEILVATDV----AARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGE  353 (572)
T ss_pred             HHHHcCC-----------------------CeEEEEehh----hhcCCCccCCCEEEEcCCCCCHHHHhhhhcccccCCC
Confidence            9999985                       999999999    99999999999999999999999999999997  567


Q ss_pred             CCeEEEEEeCchhHHHHHHHHHhcccccccCcc
Q 028124          176 DGSVINIVVGGEVVTLRSMEESLGLIVAEVPIN  208 (213)
Q Consensus       176 ~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~  208 (213)
                      .|.+|+|+.+.+...+..+++.++.++...+++
T Consensus       354 ~G~ai~~~~~~~~~~l~~i~~~~~~~~~~~~~~  386 (572)
T PRK04537        354 EGDAISFACERYAMSLPDIEAYIEQKIPVEPVT  386 (572)
T ss_pred             CceEEEEecHHHHHHHHHHHHHHcCCCCccccC
Confidence            899999999999999999999998887655443

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.95  E-value=8.7e-27  Score=221.84  Aligned_cols=160  Identities=21%  Similarity=0.325  Sum_probs=145.6

Q ss_pred             CCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHH
Q 028124           17 SHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI   96 (213)
Q Consensus        17 ~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~   96 (213)
                      .....+.|.|+.+...+ |.+.|..+|..     ....++||||+|+..++.|++.|...+ +.+..+||+|++.+|.++
T Consensus       215 ~~~~~i~q~~~~v~~~~-k~~~L~~~L~~-----~~~~~~IVF~~tk~~a~~l~~~L~~~g-~~~~~lhgd~~q~~R~~i  287 (629)
T PRK11634        215 TTRPDISQSYWTVWGMR-KNEALVRFLEA-----EDFDAAIIFVRTKNATLEVAEALERNG-YNSAALNGDMNQALREQT  287 (629)
T ss_pred             ccCCceEEEEEEechhh-HHHHHHHHHHh-----cCCCCEEEEeccHHHHHHHHHHHHhCC-CCEEEeeCCCCHHHHHHH
Confidence            34567889998888766 99999999876     345799999999999999999999987 899999999999999999


Q ss_pred             HHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cC
Q 028124           97 LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LA  174 (213)
Q Consensus        97 l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~  174 (213)
                      +++|++|.                       +++|||||+    ++||+|+|++++|||||+|.++++|+||+||+  .|
T Consensus       288 l~~Fr~G~-----------------------~~ILVATdv----~arGIDip~V~~VI~~d~P~~~e~yvqRiGRtGRaG  340 (629)
T PRK11634        288 LERLKDGR-----------------------LDILIATDV----AARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAG  340 (629)
T ss_pred             HHHHhCCC-----------------------CCEEEEcch----HhcCCCcccCCEEEEeCCCCCHHHHHHHhccccCCC
Confidence            99999985                       999999999    99999999999999999999999999999997  56


Q ss_pred             CCCeEEEEEeCchhHHHHHHHHHhcccccccCcccc
Q 028124          175 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINIS  210 (213)
Q Consensus       175 ~~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~~~  210 (213)
                      +.|.+++|+.+.|...++.+++.++..+++++++-.
T Consensus       341 r~G~ai~~v~~~e~~~l~~ie~~~~~~i~~~~~p~~  376 (629)
T PRK11634        341 RAGRALLFVENRERRLLRNIERTMKLTIPEVELPNA  376 (629)
T ss_pred             CcceEEEEechHHHHHHHHHHHHhCCCcceecCCcH
Confidence            789999999999999999999999999988776644

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.94  E-value=3.1e-26  Score=211.54  Aligned_cols=151  Identities=23%  Similarity=0.336  Sum_probs=136.9

Q ss_pred             CCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHH
Q 028124           19 FSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILE   98 (213)
Q Consensus        19 ~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~   98 (213)
                      ..++.+++..+...+ |...|.+++..     ....++||||+++++++.+++.|...+ +.+..+||++++++|.++++
T Consensus       307 ~~~~~~~~~~~~~~~-k~~~l~~ll~~-----~~~~~~IVF~~s~~~~~~l~~~L~~~~-~~~~~~~g~~~~~~R~~~~~  379 (475)
T PRK01297        307 SDTVEQHVYAVAGSD-KYKLLYNLVTQ-----NPWERVMVFANRKDEVRRIEERLVKDG-INAAQLSGDVPQHKRIKTLE  379 (475)
T ss_pred             CCcccEEEEEecchh-HHHHHHHHHHh-----cCCCeEEEEeCCHHHHHHHHHHHHHcC-CCEEEEECCCCHHHHHHHHH
Confidence            345777777777665 99999888876     456799999999999999999999887 89999999999999999999


Q ss_pred             HHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCCC
Q 028124           99 EFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAAD  176 (213)
Q Consensus        99 ~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~~  176 (213)
                      +|++|+                       +++||||++    +++|+|++++++|||||+|.+..+|+||+||+  .|+.
T Consensus       380 ~Fr~G~-----------------------~~vLvaT~~----l~~GIDi~~v~~VI~~~~P~s~~~y~Qr~GRaGR~g~~  432 (475)
T PRK01297        380 GFREGK-----------------------IRVLVATDV----AGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGAS  432 (475)
T ss_pred             HHhCCC-----------------------CcEEEEccc----cccCCcccCCCEEEEeCCCCCHHHHHHhhCccCCCCCC
Confidence            999985                       999999999    99999999999999999999999999999997  4667


Q ss_pred             CeEEEEEeCchhHHHHHHHHHhccccc
Q 028124          177 GSVINIVVGGEVVTLRSMEESLGLIVA  203 (213)
Q Consensus       177 g~~i~~~~~~e~~~~~~le~~l~~~~~  203 (213)
                      |.+++|+..+|...+..+++.++.++.
T Consensus       433 g~~i~~~~~~d~~~~~~~~~~~~~~~~  459 (475)
T PRK01297        433 GVSISFAGEDDAFQLPEIEELLGRKIS  459 (475)
T ss_pred             ceEEEEecHHHHHHHHHHHHHhCCCCc
Confidence            999999999999999999999998874

>PTZ00424 helicase 45; Provisional

Probab=99.94  E-value=2.2e-26  Score=206.97  Aligned_cols=163  Identities=28%  Similarity=0.567  Sum_probs=147.7

Q ss_pred             CCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHH
Q 028124           18 HFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLIL   97 (213)
Q Consensus        18 ~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l   97 (213)
                      ...+++++|+.++....+...+.++++.     ....++||||+++..++.+++.|...+ +.+..+||+|++++|..++
T Consensus       237 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~-----~~~~~~ivF~~t~~~~~~l~~~l~~~~-~~~~~~h~~~~~~~R~~i~  310 (401)
T PTZ00424        237 TLEGIRQFYVAVEKEEWKFDTLCDLYET-----LTITQAIIYCNTRRKVDYLTKKMHERD-FTVSCMHGDMDQKDRDLIM  310 (401)
T ss_pred             ccCCceEEEEecChHHHHHHHHHHHHHh-----cCCCeEEEEecCcHHHHHHHHHHHHCC-CcEEEEeCCCCHHHHHHHH
Confidence            4567889998888777788888888776     345789999999999999999999886 7999999999999999999


Q ss_pred             HHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCC
Q 028124           98 EEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAA  175 (213)
Q Consensus        98 ~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~  175 (213)
                      ++|++|.                       +++||||++    +++|+|+|++++||+||+|.+..+|+||+||+  .|+
T Consensus       311 ~~f~~g~-----------------------~~vLvaT~~----l~~GiDip~v~~VI~~~~p~s~~~y~qr~GRagR~g~  363 (401)
T PTZ00424        311 REFRSGS-----------------------TRVLITTDL----LARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGR  363 (401)
T ss_pred             HHHHcCC-----------------------CCEEEEccc----ccCCcCcccCCEEEEECCCCCHHHEeecccccccCCC
Confidence            9999985                       999999999    99999999999999999999999999999997  467


Q ss_pred             CCeEEEEEeCchhHHHHHHHHHhcccccccCccccccC
Q 028124          176 DGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL  213 (213)
Q Consensus       176 ~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~~~~~~  213 (213)
                      .|.|+.|+++.+...+..+++.++..+++.++..-+.|
T Consensus       364 ~G~~i~l~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~  401 (401)
T PTZ00424        364 KGVAINFVTPDDIEQLKEIERHYNTQIEEMPMEVADYL  401 (401)
T ss_pred             CceEEEEEcHHHHHHHHHHHHHHCCcccccCcchhhcC
Confidence            89999999999999999999999999999988776543

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

Probab=99.94  E-value=4.6e-26  Score=212.78  Aligned_cols=161  Identities=20%  Similarity=0.307  Sum_probs=139.5

Q ss_pred             CCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHH
Q 028124           19 FSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILE   98 (213)
Q Consensus        19 ~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~   98 (213)
                      ...++|.+..+...+ |...|.+++....   ....++||||+++..++.+++.|....++.+..+||+|++.+|..+++
T Consensus       337 ~~~v~q~~~~~~~~~-k~~~l~~~l~~~~---~~~~~~iVFv~s~~~a~~l~~~L~~~~g~~~~~~Hg~~~~~eR~~il~  412 (518)
T PLN00206        337 NKAVKQLAIWVETKQ-KKQKLFDILKSKQ---HFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMK  412 (518)
T ss_pred             CcceeEEEEeccchh-HHHHHHHHHHhhc---ccCCCEEEEcCCchhHHHHHHHHhhccCcceEEeeCCCCHHHHHHHHH
Confidence            345788888887766 8888888887521   234689999999999999999997642389999999999999999999


Q ss_pred             HHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCCC
Q 028124           99 EFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAAD  176 (213)
Q Consensus        99 ~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~~  176 (213)
                      +|++|+                       .++||||++    ++||+|+|++++|||||+|.+.++|+||+||+  .|..
T Consensus       413 ~Fr~G~-----------------------~~ILVaTdv----l~rGiDip~v~~VI~~d~P~s~~~yihRiGRaGR~g~~  465 (518)
T PLN00206        413 SFLVGE-----------------------VPVIVATGV----LGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEK  465 (518)
T ss_pred             HHHCCC-----------------------CCEEEEecH----hhccCCcccCCEEEEeCCCCCHHHHHHhccccccCCCC
Confidence            999985                       999999999    99999999999999999999999999999997  4578


Q ss_pred             CeEEEEEeCchhHHHHHHHHHhcccccccCcccc
Q 028124          177 GSVINIVVGGEVVTLRSMEESLGLIVAEVPINIS  210 (213)
Q Consensus       177 g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~~~  210 (213)
                      |.+++|++.++...+..+.+.+...-.++|-.+.
T Consensus       466 G~ai~f~~~~~~~~~~~l~~~l~~~~~~vp~~l~  499 (518)
T PLN00206        466 GTAIVFVNEEDRNLFPELVALLKSSGAAIPRELA  499 (518)
T ss_pred             eEEEEEEchhHHHHHHHHHHHHHHcCCCCCHHHH
Confidence            9999999999999999999888877777775543

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

Probab=99.93  E-value=7.9e-26  Score=204.26  Aligned_cols=167  Identities=17%  Similarity=0.216  Sum_probs=147.9

Q ss_pred             CCCCCCCCCCCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCC
Q 028124            8 SPCPPCQSPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSD   87 (213)
Q Consensus         8 ~~~~~~~~~~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~   87 (213)
                      -.|.....+.+...+.|-|+.++.+. ++-.|..+|++.    ....++||||.|+..+..+++.|.... +.+..+||+
T Consensus       290 v~~~d~~~~~The~l~Qgyvv~~~~~-~f~ll~~~LKk~----~~~~KiiVF~sT~~~vk~~~~lL~~~d-lpv~eiHgk  363 (543)
T KOG0342|consen  290 VNVDDGGERETHERLEQGYVVAPSDS-RFSLLYTFLKKN----IKRYKIIVFFSTCMSVKFHAELLNYID-LPVLEIHGK  363 (543)
T ss_pred             eecCCCCCcchhhcccceEEeccccc-hHHHHHHHHHHh----cCCceEEEEechhhHHHHHHHHHhhcC-CchhhhhcC
Confidence            34555667888899999999999887 799999999883    334899999999999999999999875 899999999


Q ss_pred             CCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHH
Q 028124           88 LAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIR  167 (213)
Q Consensus        88 ~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~  167 (213)
                      +++..|..+..+|++.+                       .-||||||+    ++||+|+|+|++||.||+|.++++|||
T Consensus       364 ~~Q~kRT~~~~~F~kae-----------------------sgIL~cTDV----aARGlD~P~V~~VvQ~~~P~d~~~YIH  416 (543)
T KOG0342|consen  364 QKQNKRTSTFFEFCKAE-----------------------SGILVCTDV----AARGLDIPDVDWVVQYDPPSDPEQYIH  416 (543)
T ss_pred             CcccccchHHHHHhhcc-----------------------cceEEecch----hhccCCCCCceEEEEeCCCCCHHHHHH
Confidence            99999999999999975                       889999999    999999999999999999999999999


Q ss_pred             hhccc--cCCCCeEEEEEeCchhHHHHHHHHHhcccccccCcccc
Q 028124          168 RMTTC--LAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINIS  210 (213)
Q Consensus       168 R~GR~--~~~~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~~~  210 (213)
                      |+||+  .|..|.++.|..+.|...++.+.   ...+.+.+++..
T Consensus       417 RvGRTaR~gk~G~alL~l~p~El~Flr~LK---~lpl~~~e~~~~  458 (543)
T KOG0342|consen  417 RVGRTAREGKEGKALLLLAPWELGFLRYLK---KLPLEEFEFPPL  458 (543)
T ss_pred             HhccccccCCCceEEEEeChhHHHHHHHHh---hCCCcccCCCCC
Confidence            99997  46679999999999999999998   455666665543

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

Probab=99.93  E-value=6.9e-26  Score=203.86  Aligned_cols=170  Identities=16%  Similarity=0.254  Sum_probs=146.0

Q ss_pred             CCCCCCCCCCCCCC----CCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc-C
Q 028124            3 IDGVESPCPPCQSP----SHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL-A   77 (213)
Q Consensus         3 ~~~~~~~~~~~~~~----~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~-~   77 (213)
                      .-|+++|.+++...    .+|+.+..+|..|...+ |+..|.++|..     ...+++|||.+|+..+++....|... +
T Consensus       207 raGLRNpv~V~V~~k~~~~tPS~L~~~Y~v~~a~e-K~~~lv~~L~~-----~~~kK~iVFF~TCasVeYf~~~~~~~l~  280 (567)
T KOG0345|consen  207 RAGLRNPVRVSVKEKSKSATPSSLALEYLVCEADE-KLSQLVHLLNN-----NKDKKCIVFFPTCASVEYFGKLFSRLLK  280 (567)
T ss_pred             HhhccCceeeeecccccccCchhhcceeeEecHHH-HHHHHHHHHhc-----cccccEEEEecCcchHHHHHHHHHHHhC
Confidence            34778877765522    37888999999999988 99999999987     56789999999999999999999875 5


Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEec
Q 028124           78 DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYE  157 (213)
Q Consensus        78 ~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd  157 (213)
                      .+.+..+||.|++..|.++++.|+..                       +..+|+|||+    ++||+|+|++++||+||
T Consensus       281 ~~~i~~iHGK~~q~~R~k~~~~F~~~-----------------------~~~vl~~TDV----aARGlDip~iD~VvQ~D  333 (567)
T KOG0345|consen  281 KREIFSIHGKMSQKARAKVLEAFRKL-----------------------SNGVLFCTDV----AARGLDIPGIDLVVQFD  333 (567)
T ss_pred             CCcEEEecchhcchhHHHHHHHHHhc-----------------------cCceEEeehh----hhccCCCCCceEEEecC
Confidence            58899999999999999999999995                       3779999999    99999999999999999


Q ss_pred             CCCChHHHHHhhccc--cCCCCeEEEEEeCchhHHHHHHHHHhccccccc
Q 028124          158 LPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLRSMEESLGLIVAEV  205 (213)
Q Consensus       158 ~P~~~~~yi~R~GR~--~~~~g~~i~~~~~~e~~~~~~le~~l~~~~~~~  205 (213)
                      +|.+++.|+||+||+  .|+.|.+|.|+.+.|..+..-|.-.-...++++
T Consensus       334 pP~~~~~FvHR~GRTaR~gr~G~Aivfl~p~E~aYveFl~i~~~v~le~~  383 (567)
T KOG0345|consen  334 PPKDPSSFVHRCGRTARAGREGNAIVFLNPREEAYVEFLRIKGKVELERI  383 (567)
T ss_pred             CCCChhHHHhhcchhhhccCccceEEEecccHHHHHHHHHhcCccchhhh
Confidence            999999999999996  688999999999988777666654433444443

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

Probab=99.93  E-value=1.3e-25  Score=199.88  Aligned_cols=159  Identities=21%  Similarity=0.275  Sum_probs=141.4

Q ss_pred             CCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHH
Q 028124           18 HFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLIL   97 (213)
Q Consensus        18 ~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l   97 (213)
                      .-.+++|.+ .+..+..|++....+++.    ..+..++||||..+..|+.|..-|.-.| +.+-.|||+-.+.+|...+
T Consensus       435 a~~sVkQ~i-~v~~d~~k~~~~~~f~~~----ms~ndKvIiFv~~K~~AD~LSSd~~l~g-i~~q~lHG~r~Q~DrE~al  508 (629)
T KOG0336|consen  435 AVKSVKQNI-IVTTDSEKLEIVQFFVAN----MSSNDKVIIFVSRKVMADHLSSDFCLKG-ISSQSLHGNREQSDREMAL  508 (629)
T ss_pred             eeeeeeeeE-EecccHHHHHHHHHHHHh----cCCCceEEEEEechhhhhhccchhhhcc-cchhhccCChhhhhHHHHH
Confidence            345788988 455555599888888777    5678999999999999999999998777 8999999999999999999


Q ss_pred             HHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCC
Q 028124           98 EEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAA  175 (213)
Q Consensus        98 ~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~  175 (213)
                      +.|++|+                       ++|||+||+    ++||+|++++.+|+|||||.+++.|+||+||+  +|+
T Consensus       509 ~~~ksG~-----------------------vrILvaTDl----aSRGlDv~DiTHV~NyDFP~nIeeYVHRvGrtGRaGr  561 (629)
T KOG0336|consen  509 EDFKSGE-----------------------VRILVATDL----ASRGLDVPDITHVYNYDFPRNIEEYVHRVGRTGRAGR  561 (629)
T ss_pred             HhhhcCc-----------------------eEEEEEech----hhcCCCchhcceeeccCCCccHHHHHHHhcccccCCC
Confidence            9999996                       999999999    99999999999999999999999999999996  688


Q ss_pred             CCeEEEEEeCchhHHHHHHHHHhcccccccCccc
Q 028124          176 DGSVINIVVGGEVVTLRSMEESLGLIVAEVPINI  209 (213)
Q Consensus       176 ~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~~  209 (213)
                      .|.+++|++.+|-....+|-+.|...-+++|-.+
T Consensus       562 ~G~sis~lt~~D~~~a~eLI~ILe~aeQevPdeL  595 (629)
T KOG0336|consen  562 TGTSISFLTRNDWSMAEELIQILERAEQEVPDEL  595 (629)
T ss_pred             CcceEEEEehhhHHHHHHHHHHHHHhhhhCcHHH
Confidence            8999999999999999988888877777777544

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

Probab=99.93  E-value=3.9e-25  Score=201.13  Aligned_cols=163  Identities=20%  Similarity=0.303  Sum_probs=142.9

Q ss_pred             CCCCCCceEEEEEecCcchHHHHHHHHHHHhhc----CCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHH
Q 028124           16 PSHFSQPRHFYVAVDRLQFKMETLVELLHLVVA----GRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAET   91 (213)
Q Consensus        16 ~~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~----~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~   91 (213)
                      -.+..++.|....|.+.+ |...|.++|....+    +.....+++|||.+++.|+.|+..|...+ +.+..+||+-++.
T Consensus       297 g~~~~ni~q~i~~V~~~~-kr~~Lldll~~~~~~~~~~~~~~e~tlvFvEt~~~~d~l~~~l~~~~-~~~~sIhg~~tq~  374 (482)
T KOG0335|consen  297 GSTSENITQKILFVNEME-KRSKLLDLLNKDDGPPSDGEPKWEKTLVFVETKRGADELAAFLSSNG-YPAKSIHGDRTQI  374 (482)
T ss_pred             ccccccceeEeeeecchh-hHHHHHHHhhcccCCcccCCcccceEEEEeeccchhhHHHHHHhcCC-CCceeecchhhhh
Confidence            356788999999999887 99999999975332    12223589999999999999999999987 8999999999999


Q ss_pred             HHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhcc
Q 028124           92 ERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTT  171 (213)
Q Consensus        92 ~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR  171 (213)
                      +|.+.++.|+.|.                       ..+||||++    ++||+|+++|++|||||+|.+.++|+|||||
T Consensus       375 er~~al~~Fr~g~-----------------------~pvlVaT~V----aaRGlDi~~V~hVInyDmP~d~d~YvHRIGR  427 (482)
T KOG0335|consen  375 EREQALNDFRNGK-----------------------APVLVATNV----AARGLDIPNVKHVINYDMPADIDDYVHRIGR  427 (482)
T ss_pred             HHHHHHHHhhcCC-----------------------cceEEEehh----hhcCCCCCCCceeEEeecCcchhhHHHhccc
Confidence            9999999999984                       999999999    9999999999999999999999999999999


Q ss_pred             c--cCCCCeEEEEEeCchhHHHHHHHHHhcccccccCc
Q 028124          172 C--LAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPI  207 (213)
Q Consensus       172 ~--~~~~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~  207 (213)
                      +  +|+.|.+++|+...+....+.|.+.+.-.-+++|-
T Consensus       428 TGR~Gn~G~atsf~n~~~~~i~~~L~~~l~ea~q~vP~  465 (482)
T KOG0335|consen  428 TGRVGNGGRATSFFNEKNQNIAKALVEILTEANQEVPQ  465 (482)
T ss_pred             cccCCCCceeEEEeccccchhHHHHHHHHHHhcccCcH
Confidence            7  68889999999988888888888877655555553

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=99.93  E-value=4.4e-25  Score=201.87  Aligned_cols=161  Identities=19%  Similarity=0.296  Sum_probs=141.7

Q ss_pred             CCCCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc-CCceEEEecCCCCHHHH
Q 028124           15 SPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL-ADISFSSLHSDLAETER   93 (213)
Q Consensus        15 ~~~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~-~~~~~~~lhg~~~~~~R   93 (213)
                      ..++|++++|+|+.++-.+ |+..|.-+++.     ....+.|||+.|++.+..+++.+.+. +++.+..|||.|++..|
T Consensus       281 ~~atP~~L~Q~y~~v~l~~-Ki~~L~sFI~s-----hlk~K~iVF~SscKqvkf~~e~F~rlrpg~~l~~L~G~~~Q~~R  354 (758)
T KOG0343|consen  281 VAATPSNLQQSYVIVPLED-KIDMLWSFIKS-----HLKKKSIVFLSSCKQVKFLYEAFCRLRPGIPLLALHGTMSQKKR  354 (758)
T ss_pred             cccChhhhhheEEEEehhh-HHHHHHHHHHh-----ccccceEEEEehhhHHHHHHHHHHhcCCCCceeeeccchhHHHH
Confidence            3678999999999999887 99999999988     45689999999999999999999865 45899999999999999


Q ss_pred             HHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhcccc
Q 028124           94 TLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL  173 (213)
Q Consensus        94 ~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~  173 (213)
                      ..++.+|-..                       +.-+|+|||+    ++||+|||.|+|||.||.|.++++||||+||++
T Consensus       355 ~ev~~~F~~~-----------------------~~~vLF~TDv----~aRGLDFpaVdwViQ~DCPedv~tYIHRvGRtA  407 (758)
T KOG0343|consen  355 IEVYKKFVRK-----------------------RAVVLFCTDV----AARGLDFPAVDWVIQVDCPEDVDTYIHRVGRTA  407 (758)
T ss_pred             HHHHHHHHHh-----------------------cceEEEeehh----hhccCCCcccceEEEecCchhHHHHHHHhhhhh
Confidence            9999999886                       4779999999    999999999999999999999999999999974


Q ss_pred             --CCCCeEEEEEeCch-hHHHHHHHHHhcccccccCccc
Q 028124          174 --AADGSVINIVVGGE-VVTLRSMEESLGLIVAEVPINI  209 (213)
Q Consensus       174 --~~~g~~i~~~~~~e-~~~~~~le~~l~~~~~~~~~~~  209 (213)
                        ...|.++.++++.+ ..++..|++.. +.+.++-++.
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              55699999999887 67777777754 5565555443

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=99.92  E-value=5.7e-25  Score=196.81  Aligned_cols=173  Identities=18%  Similarity=0.213  Sum_probs=139.5

Q ss_pred             CCCCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHH
Q 028124           15 SPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERT   94 (213)
Q Consensus        15 ~~~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~   94 (213)
                      ..+.++++.||++.|... +|+..+..+++.    +.-.++.|||+||.+.|.+|.-.|...| ++...++|.||..-|.
T Consensus       235 el~~~dqL~Qy~v~cse~-DKflllyallKL----~LI~gKsliFVNtIdr~YrLkLfLeqFG-iksciLNseLP~NSR~  308 (569)
T KOG0346|consen  235 ELPNPDQLTQYQVKCSEE-DKFLLLYALLKL----RLIRGKSLIFVNTIDRCYRLKLFLEQFG-IKSCILNSELPANSRC  308 (569)
T ss_pred             cCCCcccceEEEEEeccc-hhHHHHHHHHHH----HHhcCceEEEEechhhhHHHHHHHHHhC-cHhhhhcccccccchh
Confidence            345788999999999955 499999999986    2235799999999999999999999998 9999999999999999


Q ss_pred             HHHHHHhccccccccccc--c------------cCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCC
Q 028124           95 LILEEFRHTAMKWNQKVT--E------------QSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPT  160 (213)
Q Consensus        95 ~~l~~Fr~g~~~~~~~~~--~------------~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~  160 (213)
                      .++++|..|.++..-.+-  +            ..+++.++++.+++  -+-.-.-    ++||+||..|.+|||||+|.
T Consensus       309 Hii~QFNkG~YdivIAtD~s~~~~~~eee~kgk~~e~~~kndkkskk--K~D~E~G----VsRGIDF~~V~~VlNFD~P~  382 (569)
T KOG0346|consen  309 HIIEQFNKGLYDIVIATDDSADGDKLEEEVKGKSDEKNPKNDKKSKK--KLDKESG----VSRGIDFHHVSNVLNFDFPE  382 (569)
T ss_pred             hHHHHhhCcceeEEEEccCccchhhhhccccccccccCCCCcccccc--ccCchhc----hhccccchheeeeeecCCCC
Confidence            999999999866544311  1            11122234442332  3444445    79999999999999999999


Q ss_pred             ChHHHHHhhccc--cCCCCeEEEEEeCchhHHHHHHHHHhc
Q 028124          161 KKETYIRRMTTC--LAADGSVINIVVGGEVVTLRSMEESLG  199 (213)
Q Consensus       161 ~~~~yi~R~GR~--~~~~g~~i~~~~~~e~~~~~~le~~l~  199 (213)
                      +...||||+||+  |+++|.+++||.+.+..-...+|..+.
T Consensus       383 t~~sYIHRvGRTaRg~n~GtalSfv~P~e~~g~~~le~~~~  423 (569)
T KOG0346|consen  383 TVTSYIHRVGRTARGNNKGTALSFVSPKEEFGKESLESILK  423 (569)
T ss_pred             chHHHHHhccccccCCCCCceEEEecchHHhhhhHHHHHHh
Confidence            999999999995  788999999999988876677776654

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

Probab=99.91  E-value=2.1e-24  Score=195.96  Aligned_cols=159  Identities=19%  Similarity=0.307  Sum_probs=138.8

Q ss_pred             CCCCCCCCCCC--CCCCCceEEEEEec--CcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceE
Q 028124            6 VESPCPPCQSP--SHFSQPRHFYVAVD--RLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISF   81 (213)
Q Consensus         6 ~~~~~~~~~~~--~~~~~i~~~~~~~~--~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~   81 (213)
                      ++-|..+..-+  .+...++|.|+.+.  .+.++-..|..|+..++     ..++|||+.|++.|+++.-.|--.| +++
T Consensus       380 L~kPvrifvd~~~~~a~~LtQEFiRIR~~re~dRea~l~~l~~rtf-----~~~~ivFv~tKk~AHRl~IllGLlg-l~a  453 (691)
T KOG0338|consen  380 LNKPVRIFVDPNKDTAPKLTQEFIRIRPKREGDREAMLASLITRTF-----QDRTIVFVRTKKQAHRLRILLGLLG-LKA  453 (691)
T ss_pred             cCCCeEEEeCCccccchhhhHHHheeccccccccHHHHHHHHHHhc-----ccceEEEEehHHHHHHHHHHHHHhh-chh
Confidence            45555555544  34567899998765  34458888889988743     5899999999999999987777777 899


Q ss_pred             EEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCC
Q 028124           82 SSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTK  161 (213)
Q Consensus        82 ~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~  161 (213)
                      .-+||.+++++|...|++|+.++                       +++|||||+    ++||+|++.|.+||||++|.+
T Consensus       454 gElHGsLtQ~QRlesL~kFk~~e-----------------------idvLiaTDv----AsRGLDI~gV~tVINy~mP~t  506 (691)
T KOG0338|consen  454 GELHGSLTQEQRLESLEKFKKEE-----------------------IDVLIATDV----ASRGLDIEGVQTVINYAMPKT  506 (691)
T ss_pred             hhhcccccHHHHHHHHHHHHhcc-----------------------CCEEEEech----hhccCCccceeEEEeccCchh
Confidence            99999999999999999999986                       999999999    999999999999999999999


Q ss_pred             hHHHHHhhccc--cCCCCeEEEEEeCchhHHHHHHHHH
Q 028124          162 KETYIRRMTTC--LAADGSVINIVVGGEVVTLRSMEES  197 (213)
Q Consensus       162 ~~~yi~R~GR~--~~~~g~~i~~~~~~e~~~~~~le~~  197 (213)
                      .+.|+||+||+  +|+.|.+++|+...|...++.+-+.
T Consensus       507 ~e~Y~HRVGRTARAGRaGrsVtlvgE~dRkllK~iik~  544 (691)
T KOG0338|consen  507 IEHYLHRVGRTARAGRAGRSVTLVGESDRKLLKEIIKS  544 (691)
T ss_pred             HHHHHHHhhhhhhcccCcceEEEeccccHHHHHHHHhh
Confidence            99999999995  8999999999999999999988776

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.91  E-value=2.9e-23  Score=191.80  Aligned_cols=129  Identities=22%  Similarity=0.357  Sum_probs=114.7

Q ss_pred             HHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccccccccc
Q 028124           35 KMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ  114 (213)
Q Consensus        35 K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~  114 (213)
                      +++.+.+++..    ..+++++||||++++.++.++..|...| +.+..+||+|++++|..++++|++|.          
T Consensus       212 ~~~~l~~~l~~----~~~~~~~IIF~~s~~~~e~la~~L~~~g-~~~~~~H~~l~~~eR~~i~~~F~~g~----------  276 (470)
T TIGR00614       212 ILEDLLRFIRK----EFKGKSGIIYCPSRKKSEQVTASLQNLG-IAAGAYHAGLEISARDDVHHKFQRDE----------  276 (470)
T ss_pred             HHHHHHHHHHH----hcCCCceEEEECcHHHHHHHHHHHHhcC-CCeeEeeCCCCHHHHHHHHHHHHcCC----------
Confidence            55666666653    2456778999999999999999999987 89999999999999999999999985          


Q ss_pred             CCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCCCCeEEEEEeCchhHHHH
Q 028124          115 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLR  192 (213)
Q Consensus       115 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~~g~~i~~~~~~e~~~~~  192 (213)
                                   +++||||++    +++|+|+|++++||||++|.+.+.|+||+||+  .|..|.|+.|+.+.|...++
T Consensus       277 -------------~~vLVaT~~----~~~GID~p~V~~VI~~~~P~s~~~y~Qr~GRaGR~G~~~~~~~~~~~~d~~~~~  339 (470)
T TIGR00614       277 -------------IQVVVATVA----FGMGINKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECHLFYAPADINRLR  339 (470)
T ss_pred             -------------CcEEEEech----hhccCCcccceEEEEeCCCCCHHHHHhhhcCcCCCCCCceEEEEechhHHHHHH
Confidence                         999999999    99999999999999999999999999999997  56779999999988877666


Q ss_pred             HHH
Q 028124          193 SME  195 (213)
Q Consensus       193 ~le  195 (213)
                      .+.
T Consensus       340 ~~~  342 (470)
T TIGR00614       340 RLL  342 (470)
T ss_pred             HHH
Confidence            654

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

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

Probab=99.90  E-value=4.8e-23  Score=202.86  Aligned_cols=145  Identities=15%  Similarity=0.225  Sum_probs=120.5

Q ss_pred             CCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHH
Q 028124           17 SHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI   96 (213)
Q Consensus        17 ~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~   96 (213)
                      ..++++  +|..++.....+..|.+++..    .....+.||||++++.|+.++..|...| +.+..+||+|++++|..+
T Consensus       650 f~RpNL--~y~Vv~k~kk~le~L~~~I~~----~~~~esgIIYC~SRke~E~LAe~L~~~G-ika~~YHAGLs~eeR~~v  722 (1195)
T PLN03137        650 FNRPNL--WYSVVPKTKKCLEDIDKFIKE----NHFDECGIIYCLSRMDCEKVAERLQEFG-HKAAFYHGSMDPAQRAFV  722 (1195)
T ss_pred             cCccce--EEEEeccchhHHHHHHHHHHh----cccCCCceeEeCchhHHHHHHHHHHHCC-CCeeeeeCCCCHHHHHHH
Confidence            344454  344444433234556666654    2345689999999999999999999988 899999999999999999


Q ss_pred             HHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cC
Q 028124           97 LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LA  174 (213)
Q Consensus        97 l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~  174 (213)
                      +++|+.|+                       ++|||||++    +++|||+|+|++|||||+|.+++.|+||+||+  .|
T Consensus       723 qe~F~~Ge-----------------------i~VLVATdA----FGMGIDkPDVR~VIHydlPkSiEsYyQriGRAGRDG  775 (1195)
T PLN03137        723 QKQWSKDE-----------------------INIICATVA----FGMGINKPDVRFVIHHSLPKSIEGYHQECGRAGRDG  775 (1195)
T ss_pred             HHHHhcCC-----------------------CcEEEEech----hhcCCCccCCcEEEEcCCCCCHHHHHhhhcccCCCC
Confidence            99999985                       999999999    99999999999999999999999999999997  46


Q ss_pred             CCCeEEEEEeCchhHHHHHHH
Q 028124          175 ADGSVINIVVGGEVVTLRSME  195 (213)
Q Consensus       175 ~~g~~i~~~~~~e~~~~~~le  195 (213)
                      ..|.|+.|+...|...++.+.
T Consensus       776 ~~g~cILlys~~D~~~~~~lI  796 (1195)
T PLN03137        776 QRSSCVLYYSYSDYIRVKHMI  796 (1195)
T ss_pred             CCceEEEEecHHHHHHHHHHH
Confidence            779999999887776666554

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

Probab=99.90  E-value=2.4e-23  Score=191.41  Aligned_cols=157  Identities=20%  Similarity=0.313  Sum_probs=139.9

Q ss_pred             CCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHH
Q 028124           18 HFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLIL   97 (213)
Q Consensus        18 ~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l   97 (213)
                      ....|.|..+++....-|+-.+++++...     -..+++||+.+.++|..|++.|....++.+.++||+.++.+|...+
T Consensus       357 a~~~V~QelvF~gse~~K~lA~rq~v~~g-----~~PP~lIfVQs~eRak~L~~~L~~~~~i~v~vIh~e~~~~qrde~~  431 (593)
T KOG0344|consen  357 ANETVDQELVFCGSEKGKLLALRQLVASG-----FKPPVLIFVQSKERAKQLFEELEIYDNINVDVIHGERSQKQRDETM  431 (593)
T ss_pred             HhhhhhhhheeeecchhHHHHHHHHHhcc-----CCCCeEEEEecHHHHHHHHHHhhhccCcceeeEecccchhHHHHHH
Confidence            35678999999998888999999999883     3479999999999999999999544459999999999999999999


Q ss_pred             HHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCC
Q 028124           98 EEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAA  175 (213)
Q Consensus        98 ~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~  175 (213)
                      ++||.|+                       +.+||||++    ++||+|+.++++|||||+|.+.-+|+||+||+  +|+
T Consensus       432 ~~FR~g~-----------------------IwvLicTdl----l~RGiDf~gvn~VInyD~p~s~~syihrIGRtgRag~  484 (593)
T KOG0344|consen  432 ERFRIGK-----------------------IWVLICTDL----LARGIDFKGVNLVINYDFPQSDLSYIHRIGRTGRAGR  484 (593)
T ss_pred             HHHhccC-----------------------eeEEEehhh----hhccccccCcceEEecCCCchhHHHHHHhhccCCCCC
Confidence            9999995                       999999999    99999999999999999999999999999995  788


Q ss_pred             CCeEEEEEeCchhHHHHHHHHHhcccccccC
Q 028124          176 DGSVINIVVGGEVVTLRSMEESLGLIVAEVP  206 (213)
Q Consensus       176 ~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~  206 (213)
                      .|.+|+|++..+...++.+.+.+...--++|
T Consensus       485 ~g~Aitfytd~d~~~ir~iae~~~~sG~evp  515 (593)
T KOG0344|consen  485 SGKAITFYTDQDMPRIRSIAEVMEQSGCEVP  515 (593)
T ss_pred             CcceEEEeccccchhhhhHHHHHHHcCCcch
Confidence            9999999999998888888777654444444

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.90  E-value=1e-22  Score=193.47  Aligned_cols=127  Identities=18%  Similarity=0.345  Sum_probs=113.6

Q ss_pred             HHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccccccccc
Q 028124           35 KMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ  114 (213)
Q Consensus        35 K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~  114 (213)
                      +...|..++..     ..+.++||||+|+++|+.++..|...+ +.+..+||+|++++|.+++++|+.|.          
T Consensus       223 ~~~~l~~~l~~-----~~~~~~IIFc~tr~~~e~la~~L~~~g-~~v~~~Ha~l~~~~R~~i~~~F~~g~----------  286 (607)
T PRK11057        223 PLDQLMRYVQE-----QRGKSGIIYCNSRAKVEDTAARLQSRG-ISAAAYHAGLDNDVRADVQEAFQRDD----------  286 (607)
T ss_pred             hHHHHHHHHHh-----cCCCCEEEEECcHHHHHHHHHHHHhCC-CCEEEecCCCCHHHHHHHHHHHHCCC----------
Confidence            55666666654     456899999999999999999999987 89999999999999999999999985          


Q ss_pred             CCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCCCCeEEEEEeCchhHHHH
Q 028124          115 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLR  192 (213)
Q Consensus       115 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~~g~~i~~~~~~e~~~~~  192 (213)
                                   +++||||++    +++|+|+|+|++|||||+|.+.++|+||+||+  .|.+|.|+.|+.+.|...++
T Consensus       287 -------------~~VLVaT~a----~~~GIDip~V~~VI~~d~P~s~~~y~Qr~GRaGR~G~~~~~ill~~~~d~~~~~  349 (607)
T PRK11057        287 -------------LQIVVATVA----FGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLR  349 (607)
T ss_pred             -------------CCEEEEech----hhccCCCCCcCEEEEeCCCCCHHHHHHHhhhccCCCCCceEEEEeCHHHHHHHH
Confidence                         999999999    99999999999999999999999999999997  45678999999988876655


Q ss_pred             HH
Q 028124          193 SM  194 (213)
Q Consensus       193 ~l  194 (213)
                      .+
T Consensus       350 ~~  351 (607)
T PRK11057        350 RC  351 (607)
T ss_pred             HH
Confidence            44

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

Probab=99.89  E-value=7.3e-23  Score=198.22  Aligned_cols=140  Identities=13%  Similarity=0.132  Sum_probs=120.1

Q ss_pred             HHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc--------CCceEEEecCCCCHHHHHHHHHHHhccccc
Q 028124           35 KMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL--------ADISFSSLHSDLAETERTLILEEFRHTAMK  106 (213)
Q Consensus        35 K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~--------~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~  106 (213)
                      +.+.|.++++.       +.++||||||++.|+.++..|+..        + ..+..+||++++++|.+++++|++|.  
T Consensus       260 ~~~~l~~l~~~-------~~~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~-~~v~~~hgg~~~~eR~~ie~~f~~G~--  329 (742)
T TIGR03817       260 AADLLADLVAE-------GARTLTFVRSRRGAELVAAIARRLLGEVDPDLA-ERVAAYRAGYLPEDRRELERALRDGE--  329 (742)
T ss_pred             HHHHHHHHHHC-------CCCEEEEcCCHHHHHHHHHHHHHHHHhhccccc-cchhheecCCCHHHHHHHHHHHHcCC--
Confidence            55555555543       579999999999999999998753        3 57889999999999999999999985  


Q ss_pred             ccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhcccc--CCCCeEEEEEe
Q 028124          107 WNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVV  184 (213)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~--~~~g~~i~~~~  184 (213)
                                           +++|||||+    ++||+|++++++|||||+|.+.++|+||+||+|  |+.|.+++++.
T Consensus       330 ---------------------i~vLVaTd~----lerGIDI~~vd~VI~~~~P~s~~~y~qRiGRaGR~G~~g~ai~v~~  384 (742)
T TIGR03817       330 ---------------------LLGVATTNA----LELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRGQGALVVLVAR  384 (742)
T ss_pred             ---------------------ceEEEECch----HhccCCcccccEEEEeCCCCCHHHHHHhccccCCCCCCcEEEEEeC
Confidence                                 999999999    999999999999999999999999999999974  56799999886


Q ss_pred             --CchhHHHHHHHHHhcccccccCccc
Q 028124          185 --GGEVVTLRSMEESLGLIVAEVPINI  209 (213)
Q Consensus       185 --~~e~~~~~~le~~l~~~~~~~~~~~  209 (213)
                        +.|...+..+++.++..+++..++.
T Consensus       385 ~~~~d~~~~~~~~~~~~~~~e~~~~~~  411 (742)
T TIGR03817       385 DDPLDTYLVHHPEALFDRPVEATVFDP  411 (742)
T ss_pred             CChHHHHHHhCHHHHhcCCCccceeCC
Confidence              4577788888989888877655443

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.

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

Probab=99.89  E-value=4.8e-23  Score=187.14  Aligned_cols=163  Identities=15%  Similarity=0.223  Sum_probs=147.5

Q ss_pred             CCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHH
Q 028124           18 HFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLIL   97 (213)
Q Consensus        18 ~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l   97 (213)
                      ...+|.|.+..+++...|+.+|..-|..    ....+++|||+..+..++.++..|+-.+ +.+..+||+|.+.+|.++|
T Consensus       437 an~dITQ~V~V~~s~~~Kl~wl~~~L~~----f~S~gkvlifVTKk~~~e~i~a~Lklk~-~~v~llhgdkdqa~rn~~l  511 (731)
T KOG0339|consen  437 ANEDITQTVSVCPSEEKKLNWLLRHLVE----FSSEGKVLIFVTKKADAEEIAANLKLKG-FNVSLLHGDKDQAERNEVL  511 (731)
T ss_pred             cccchhheeeeccCcHHHHHHHHHHhhh----hccCCcEEEEEeccCCHHHHHHHhcccc-ceeeeecCchhhHHHHHHH
Confidence            4467999999999999999999888766    2457899999999999999999999887 8999999999999999999


Q ss_pred             HHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCC
Q 028124           98 EEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAA  175 (213)
Q Consensus        98 ~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~  175 (213)
                      .+|+.+.                       ..|||+||+    ++||+|++++..|||||+.+++++|.||+||+  .|.
T Consensus       512 s~fKkk~-----------------------~~VlvatDv----aargldI~~ikTVvnyD~ardIdththrigrtgRag~  564 (731)
T KOG0339|consen  512 SKFKKKR-----------------------KPVLVATDV----AARGLDIPSIKTVVNYDFARDIDTHTHRIGRTGRAGE  564 (731)
T ss_pred             HHHhhcC-----------------------CceEEEeeH----hhcCCCccccceeecccccchhHHHHHHhhhcccccc
Confidence            9999984                       999999999    99999999999999999999999999999996  567


Q ss_pred             CCeEEEEEeCchhHHHHHHHHHhcccccccCcccccc
Q 028124          176 DGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEI  212 (213)
Q Consensus       176 ~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~~~~~  212 (213)
                      .|++++++++.|......|.+.|.---+.+|-.+.+|
T Consensus       565 kGvayTlvTeKDa~fAG~LVnnLe~agQnVP~~l~dl  601 (731)
T KOG0339|consen  565 KGVAYTLVTEKDAEFAGHLVNNLEGAGQNVPDELMDL  601 (731)
T ss_pred             cceeeEEechhhHHHhhHHHHHHhhccccCChHHHHH
Confidence            7999999999999999999998877777777666543

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

Probab=99.89  E-value=9.8e-23  Score=185.98  Aligned_cols=157  Identities=22%  Similarity=0.305  Sum_probs=135.9

Q ss_pred             CCCCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc---------------C--
Q 028124           15 SPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL---------------A--   77 (213)
Q Consensus        15 ~~~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~---------------~--   77 (213)
                      +...|+++.|.|..|+..- ++-.|..+|..... ....+++|||+.+.+.++.-+..|...               |  
T Consensus       389 ~~~iPeqL~qry~vVPpKL-RLV~Laa~L~~~~k-~~~~qk~iVF~S~~d~VeFHy~lf~~~l~~~~e~~s~~~~s~g~~  466 (708)
T KOG0348|consen  389 SFAIPEQLLQRYTVVPPKL-RLVALAALLLNKVK-FEEKQKMIVFFSCSDSVEFHYSLFSEALLSHLEGSSGAPDSEGLP  466 (708)
T ss_pred             cccCcHHhhhceEecCCch-hHHHHHHHHHHHhh-hhhhceeEEEEechhHHHHHHHHHHhhhhcccccccCCcccCCCh
Confidence            3577899999999999876 88888888876554 344579999999999999887777532               0  


Q ss_pred             ----CceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEE
Q 028124           78 ----DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVL  153 (213)
Q Consensus        78 ----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~V  153 (213)
                          +.++.-|||+|++++|..+++.|+...                       ..||+|||+    ++||+|+|+|++|
T Consensus       467 ~l~~~~k~~rLHGsm~QeeRts~f~~Fs~~~-----------------------~~VLLcTDV----AaRGLDlP~V~~v  519 (708)
T KOG0348|consen  467 PLFMDLKFYRLHGSMEQEERTSVFQEFSHSR-----------------------RAVLLCTDV----AARGLDLPHVGLV  519 (708)
T ss_pred             hhhhcceEEEecCchhHHHHHHHHHhhcccc-----------------------ceEEEehhh----hhccCCCCCcCeE
Confidence                256889999999999999999999964                       669999999    9999999999999


Q ss_pred             EEecCCCChHHHHHhhccc--cCCCCeEEEEEeCchhHHHHHHHHHhcc
Q 028124          154 INYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLRSMEESLGL  200 (213)
Q Consensus       154 I~yd~P~~~~~yi~R~GR~--~~~~g~~i~~~~~~e~~~~~~le~~l~~  200 (213)
                      |.||.|.++++|+||+||+  .|..|.++.|..+.|.++++.++.....
T Consensus       520 VQYd~P~s~adylHRvGRTARaG~kG~alLfL~P~Eaey~~~l~~~~~~  568 (708)
T KOG0348|consen  520 VQYDPPFSTADYLHRVGRTARAGEKGEALLFLLPSEAEYVNYLKKHHIM  568 (708)
T ss_pred             EEeCCCCCHHHHHHHhhhhhhccCCCceEEEecccHHHHHHHHHhhcch
Confidence            9999999999999999995  7889999999999999988888876544

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

Probab=99.89  E-value=7.7e-24  Score=187.55  Aligned_cols=143  Identities=20%  Similarity=0.323  Sum_probs=125.4

Q ss_pred             CceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHH
Q 028124           21 QPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEF  100 (213)
Q Consensus        21 ~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~F  100 (213)
                      ++.|.+.++..+. |+--|.+.|..      ...+++|||..+..++.+.++|.-.| +.++.+||+-++++|...++.|
T Consensus       396 dViQevEyVkqEa-KiVylLeCLQK------T~PpVLIFaEkK~DVD~IhEYLLlKG-VEavaIHGGKDQedR~~ai~af  467 (610)
T KOG0341|consen  396 DVIQEVEYVKQEA-KIVYLLECLQK------TSPPVLIFAEKKADVDDIHEYLLLKG-VEAVAIHGGKDQEDRHYAIEAF  467 (610)
T ss_pred             hHHHHHHHHHhhh-hhhhHHHHhcc------CCCceEEEeccccChHHHHHHHHHcc-ceeEEeecCcchhHHHHHHHHH
Confidence            4566666777766 88888888876      45799999999999999999999888 9999999999999999999999


Q ss_pred             hcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCCCCe
Q 028124          101 RHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGS  178 (213)
Q Consensus       101 r~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~~g~  178 (213)
                      |.|                       +.++||+||+    ++.|+|||++.+|||||+|..++.|+||+||+  .|+.|.
T Consensus       468 r~g-----------------------kKDVLVATDV----ASKGLDFp~iqHVINyDMP~eIENYVHRIGRTGRsg~~Gi  520 (610)
T KOG0341|consen  468 RAG-----------------------KKDVLVATDV----ASKGLDFPDIQHVINYDMPEEIENYVHRIGRTGRSGKTGI  520 (610)
T ss_pred             hcC-----------------------CCceEEEecc----hhccCCCccchhhccCCChHHHHHHHHHhcccCCCCCcce
Confidence            998                       4999999999    99999999999999999999999999999997  577799


Q ss_pred             EEEEEeCc-hhHHHHHHHHHh
Q 028124          179 VINIVVGG-EVVTLRSMEESL  198 (213)
Q Consensus       179 ~i~~~~~~-e~~~~~~le~~l  198 (213)
                      +.+|++.. +...+-.+..++
T Consensus       521 ATTfINK~~~esvLlDLK~LL  541 (610)
T KOG0341|consen  521 ATTFINKNQEESVLLDLKHLL  541 (610)
T ss_pred             eeeeecccchHHHHHHHHHHH
Confidence            99999876 444555555554

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

Probab=99.89  E-value=6.8e-23  Score=185.75  Aligned_cols=152  Identities=19%  Similarity=0.250  Sum_probs=136.0

Q ss_pred             CCCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHh-cc--CCceEEEecCCCCHHH
Q 028124           16 PSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVS-NL--ADISFSSLHSDLAETE   92 (213)
Q Consensus        16 ~~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~-~~--~~~~~~~lhg~~~~~~   92 (213)
                      .+.+..+.|.++.++... |.-.+..+++.     .+..++|+|+++.+.+.+++..|+ ..  .++++..+.|.++.+.
T Consensus       398 yslp~~l~~~~vv~~~~~-kpl~~~~lI~~-----~k~~r~lcf~~S~~sa~Rl~~~L~v~~~~~~~~~s~~t~~l~~k~  471 (620)
T KOG0350|consen  398 YSLPSSLSHRLVVTEPKF-KPLAVYALITS-----NKLNRTLCFVNSVSSANRLAHVLKVEFCSDNFKVSEFTGQLNGKR  471 (620)
T ss_pred             eecChhhhhceeeccccc-chHhHHHHHHH-----hhcceEEEEecchHHHHHHHHHHHHHhccccchhhhhhhhhhHHH
Confidence            356678899999888876 88888999987     578999999999999999999998 22  3467888999999999


Q ss_pred             HHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc
Q 028124           93 RTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC  172 (213)
Q Consensus        93 R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~  172 (213)
                      |.+.+++|+.|.                       +++|||+|+    ++||+|+.+++.|||||+|.+..+|+||+||+
T Consensus       472 r~k~l~~f~~g~-----------------------i~vLIcSD~----laRGiDv~~v~~VINYd~P~~~ktyVHR~GRT  524 (620)
T KOG0350|consen  472 RYKMLEKFAKGD-----------------------INVLICSDA----LARGIDVNDVDNVINYDPPASDKTYVHRAGRT  524 (620)
T ss_pred             HHHHHHHHhcCC-----------------------ceEEEehhh----hhcCCcccccceEeecCCCchhhHHHHhhccc
Confidence            999999999985                       999999999    99999999999999999999999999999995


Q ss_pred             --cCCCCeEEEEEeCchhHHHHHHHHHhcc
Q 028124          173 --LAADGSVINIVVGGEVVTLRSMEESLGL  200 (213)
Q Consensus       173 --~~~~g~~i~~~~~~e~~~~~~le~~l~~  200 (213)
                        +|+.|.|++++...+...|-++-+..+.
T Consensus       525 ARAgq~G~a~tll~~~~~r~F~klL~~~~~  554 (620)
T KOG0350|consen  525 ARAGQDGYAITLLDKHEKRLFSKLLKKTNL  554 (620)
T ss_pred             ccccCCceEEEeeccccchHHHHHHHHhcc
Confidence              7899999999999998888888776654

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.88  E-value=1.4e-21  Score=185.03  Aligned_cols=128  Identities=21%  Similarity=0.323  Sum_probs=114.6

Q ss_pred             hHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccc
Q 028124           34 FKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE  113 (213)
Q Consensus        34 ~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~  113 (213)
                      .+.+.+.+++..     ..+.++||||+|++.++.+++.|...+ +.+..+||+|+.++|..++++|++|.         
T Consensus       210 ~~~~~l~~~l~~-----~~~~~~IIf~~sr~~~e~la~~L~~~g-~~~~~~H~~l~~~~R~~i~~~F~~g~---------  274 (591)
T TIGR01389       210 NKQKFLLDYLKK-----HRGQSGIIYASSRKKVEELAERLESQG-ISALAYHAGLSNKVRAENQEDFLYDD---------  274 (591)
T ss_pred             CHHHHHHHHHHh-----cCCCCEEEEECcHHHHHHHHHHHHhCC-CCEEEEECCCCHHHHHHHHHHHHcCC---------
Confidence            377888888776     346799999999999999999999887 89999999999999999999999985         


Q ss_pred             cCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhcccc--CCCCeEEEEEeCchhHHH
Q 028124          114 QSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGGEVVTL  191 (213)
Q Consensus       114 ~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~--~~~g~~i~~~~~~e~~~~  191 (213)
                                    +++||||++    +++|+|+|++++|||||+|.+.+.|+||+||+|  |..|.|+.++.+.|...+
T Consensus       275 --------------~~vlVaT~a----~~~GID~p~v~~VI~~~~p~s~~~y~Q~~GRaGR~G~~~~~il~~~~~d~~~~  336 (591)
T TIGR01389       275 --------------VKVMVATNA----FGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSPADIALL  336 (591)
T ss_pred             --------------CcEEEEech----hhccCcCCCCCEEEEcCCCCCHHHHhhhhccccCCCCCceEEEecCHHHHHHH
Confidence                          999999999    999999999999999999999999999999974  667899999888776555


Q ss_pred             HHH
Q 028124          192 RSM  194 (213)
Q Consensus       192 ~~l  194 (213)
                      +.+
T Consensus       337 ~~~  339 (591)
T TIGR01389       337 KRR  339 (591)
T ss_pred             HHH
Confidence            544

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.

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=99.86  E-value=1.9e-21  Score=188.12  Aligned_cols=156  Identities=19%  Similarity=0.324  Sum_probs=140.8

Q ss_pred             CCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHH
Q 028124           20 SQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEE   99 (213)
Q Consensus        20 ~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~   99 (213)
                      ..+.|.+..++.++.|+..|.+||..    .....++||||.++..|+.+.+.|.+.| +.+..+||+.++.+|..+++.
T Consensus       584 k~V~q~v~V~~~e~eKf~kL~eLl~e----~~e~~~tiiFv~~qe~~d~l~~~L~~ag-~~~~slHGgv~q~dR~sti~d  658 (997)
T KOG0334|consen  584 KEVTQVVRVCAIENEKFLKLLELLGE----RYEDGKTIIFVDKQEKADALLRDLQKAG-YNCDSLHGGVDQHDRSSTIED  658 (997)
T ss_pred             ccceEEEEEecCchHHHHHHHHHHHH----HhhcCCEEEEEcCchHHHHHHHHHHhcC-cchhhhcCCCchHHHHhHHHH
Confidence            56889999999666799999999987    3457899999999999999999999887 888889999999999999999


Q ss_pred             HhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCCCC
Q 028124          100 FRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADG  177 (213)
Q Consensus       100 Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~~g  177 (213)
                      |+++.                       +.+||+|++    ++||+|+.+..+|||||+|...++|+||+||+  .|+.|
T Consensus       659 fK~~~-----------------------~~LLvaTsv----varGLdv~~l~Lvvnyd~pnh~edyvhR~gRTgragrkg  711 (997)
T KOG0334|consen  659 FKNGV-----------------------VNLLVATSV----VARGLDVKELILVVNYDFPNHYEDYVHRVGRTGRAGRKG  711 (997)
T ss_pred             HhccC-----------------------ceEEEehhh----hhcccccccceEEEEcccchhHHHHHHHhcccccCCccc
Confidence            99985                       999999999    99999999999999999999999999999996  68889


Q ss_pred             eEEEEEeCchhHHHHHHHHHhcccccccCc
Q 028124          178 SVINIVVGGEVVTLRSMEESLGLIVAEVPI  207 (213)
Q Consensus       178 ~~i~~~~~~e~~~~~~le~~l~~~~~~~~~  207 (213)
                      .|++|+.+.+......|.+.+...=.++|-
T Consensus       712 ~AvtFi~p~q~~~a~dl~~al~~~~~~~P~  741 (997)
T KOG0334|consen  712 AAVTFITPDQLKYAGDLCKALELSKQPVPK  741 (997)
T ss_pred             eeEEEeChHHhhhHHHHHHHHHhccCCCch
Confidence            999999998888888888888555555553

>KOG4284 consensus DEAD box protein [Transcription]

Probab=99.86  E-value=1.7e-21  Score=181.04  Aligned_cols=145  Identities=17%  Similarity=0.365  Sum_probs=127.1

Q ss_pred             CCceEEEEEecCc-------chHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHH
Q 028124           20 SQPRHFYVAVDRL-------QFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETE   92 (213)
Q Consensus        20 ~~i~~~~~~~~~~-------~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~   92 (213)
                      -+|+|||+.+...       ..|++.|..+++.     .+..+.||||+....|+-++..|+..| +.+.++.|.|++.+
T Consensus       237 ~GikQyv~~~~s~nnsveemrlklq~L~~vf~~-----ipy~QAlVF~~~~sra~~~a~~L~ssG-~d~~~ISgaM~Q~~  310 (980)
T KOG4284|consen  237 FGIKQYVVAKCSPNNSVEEMRLKLQKLTHVFKS-----IPYVQALVFCDQISRAEPIATHLKSSG-LDVTFISGAMSQKD  310 (980)
T ss_pred             echhheeeeccCCcchHHHHHHHHHHHHHHHhh-----CchHHHHhhhhhhhhhhHHHHHhhccC-CCeEEeccccchhH
Confidence            4699999887754       2377777777776     677999999999999999999999998 89999999999999


Q ss_pred             HHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc
Q 028124           93 RTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC  172 (213)
Q Consensus        93 R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~  172 (213)
                      |..+++++|+..                       .+|||+||+    .+||+|-++|++|||.|.|.+-++|.|||||+
T Consensus       311 Rl~a~~~lr~f~-----------------------~rILVsTDL----taRGIDa~~vNLVVNiD~p~d~eTY~HRIGRA  363 (980)
T KOG4284|consen  311 RLLAVDQLRAFR-----------------------VRILVSTDL----TARGIDADNVNLVVNIDAPADEETYFHRIGRA  363 (980)
T ss_pred             HHHHHHHhhhce-----------------------EEEEEecch----hhccCCccccceEEecCCCcchHHHHHHhhhc
Confidence            999999999984                       999999999    99999999999999999999999999999997


Q ss_pred             --cCCCCeEEEEEeCc-hhHHHHHHHHH
Q 028124          173 --LAADGSVINIVVGG-EVVTLRSMEES  197 (213)
Q Consensus       173 --~~~~g~~i~~~~~~-e~~~~~~le~~  197 (213)
                        .|..|.+++|+..+ +..-++.|...
T Consensus       364 gRFG~~G~aVT~~~~~~e~~~f~~m~~r  391 (980)
T KOG4284|consen  364 GRFGAHGAAVTLLEDERELKGFTAMAYR  391 (980)
T ss_pred             ccccccceeEEEeccchhhhhhHHHHHH
Confidence              58889999999765 43555555333

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=99.86  E-value=6.2e-22  Score=181.25  Aligned_cols=150  Identities=22%  Similarity=0.294  Sum_probs=126.2

Q ss_pred             CCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHH
Q 028124           17 SHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI   96 (213)
Q Consensus        17 ~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~   96 (213)
                      .+...+....+.|+-.+ |---|..+|-.      -.+++|||||+.+.+.+|+-.|...+ +....||..|.+..|.+.
T Consensus       434 ~ta~~l~Es~I~C~~~e-KD~ylyYfl~r------yPGrTlVF~NsId~vKRLt~~L~~L~-i~p~~LHA~M~QKqRLkn  505 (731)
T KOG0347|consen  434 ATASTLTESLIECPPLE-KDLYLYYFLTR------YPGRTLVFCNSIDCVKRLTVLLNNLD-IPPLPLHASMIQKQRLKN  505 (731)
T ss_pred             hHHHHHHHHhhcCCccc-cceeEEEEEee------cCCceEEEechHHHHHHHHHHHhhcC-CCCchhhHHHHHHHHHHh
Confidence            33444555555555444 43333334432      35799999999999999999999997 999999999999999999


Q ss_pred             HHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cC
Q 028124           97 LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LA  174 (213)
Q Consensus        97 l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~  174 (213)
                      |++|+..                       +..+|||||+    ++||+|+|.|.+||||..|++.+-|+||.||+  ++
T Consensus       506 LEkF~~~-----------------------~~~VLiaTDV----AARGLDIp~V~HVIHYqVPrtseiYVHRSGRTARA~  558 (731)
T KOG0347|consen  506 LEKFKQS-----------------------PSGVLIATDV----AARGLDIPGVQHVIHYQVPRTSEIYVHRSGRTARAN  558 (731)
T ss_pred             HHHHhcC-----------------------CCeEEEeehh----hhccCCCCCcceEEEeecCCccceeEeccccccccc
Confidence            9999997                       4889999999    99999999999999999999999999999996  67


Q ss_pred             CCCeEEEEEeCchhHHHHHHHHHhccc
Q 028124          175 ADGSVINIVVGGEVVTLRSMEESLGLI  201 (213)
Q Consensus       175 ~~g~~i~~~~~~e~~~~~~le~~l~~~  201 (213)
                      +.|+.+.+|.+.+...+.+|.+.|...
T Consensus       559 ~~Gvsvml~~P~e~~~~~KL~ktL~k~  585 (731)
T KOG0347|consen  559 SEGVSVMLCGPQEVGPLKKLCKTLKKK  585 (731)
T ss_pred             CCCeEEEEeChHHhHHHHHHHHHHhhc
Confidence            789999999999999999998887643

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.86  E-value=7.1e-21  Score=187.31  Aligned_cols=121  Identities=16%  Similarity=0.228  Sum_probs=106.6

Q ss_pred             chHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHh-ccCCceEEEecCCCCHHHHHHHHHHHhcccccccccc
Q 028124           33 QFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVS-NLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKV  111 (213)
Q Consensus        33 ~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~-~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~  111 (213)
                      +.|++.|.++|+.     ....|+||||+++.+++.|++.|+ ..| +.+..+||+|++.+|.+++++|++++       
T Consensus       478 d~Ki~~L~~~L~~-----~~~~KvLVF~~~~~t~~~L~~~L~~~~G-i~~~~ihG~~s~~eR~~~~~~F~~~~-------  544 (956)
T PRK04914        478 DPRVEWLIDFLKS-----HRSEKVLVICAKAATALQLEQALREREG-IRAAVFHEGMSIIERDRAAAYFADEE-------  544 (956)
T ss_pred             CHHHHHHHHHHHh-----cCCCeEEEEeCcHHHHHHHHHHHhhccC-eeEEEEECCCCHHHHHHHHHHHhcCC-------
Confidence            4599999999987     346899999999999999999995 456 89999999999999999999999852       


Q ss_pred             cccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCCCCeEEEEEe
Q 028124          112 TEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVV  184 (213)
Q Consensus       112 ~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~~g~~i~~~~  184 (213)
                                    +..++||||++    +++|+|++.+++|||||+||+++.|.||+||+  .|+.+.+..++.
T Consensus       545 --------------~~~~VLIsTdv----gseGlNlq~a~~VInfDlP~nP~~~eQRIGR~~RiGQ~~~V~i~~~  601 (956)
T PRK04914        545 --------------DGAQVLLCSEI----GSEGRNFQFASHLVLFDLPFNPDLLEQRIGRLDRIGQKHDIQIHVP  601 (956)
T ss_pred             --------------CCccEEEechh----hccCCCcccccEEEEecCCCCHHHHHHHhcccccCCCCceEEEEEc
Confidence                          24899999999    99999999999999999999999999999996  567776555553

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

Probab=99.85  E-value=5.6e-21  Score=178.80  Aligned_cols=150  Identities=18%  Similarity=0.247  Sum_probs=126.0

Q ss_pred             CCCCCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHH
Q 028124           14 QSPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETER   93 (213)
Q Consensus        14 ~~~~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R   93 (213)
                      .....++||.-..+...+...++.++.+.+      ....+..||||.|++.++.++++|...| +.+..+|++|+.++|
T Consensus       197 ~~sfdRpNi~~~v~~~~~~~~q~~fi~~~~------~~~~~~GIIYc~sRk~~E~ia~~L~~~g-~~a~~YHaGl~~~eR  269 (590)
T COG0514         197 RGSFDRPNLALKVVEKGEPSDQLAFLATVL------PQLSKSGIIYCLTRKKVEELAEWLRKNG-ISAGAYHAGLSNEER  269 (590)
T ss_pred             EecCCCchhhhhhhhcccHHHHHHHHHhhc------cccCCCeEEEEeeHHhHHHHHHHHHHCC-CceEEecCCCCHHHH
Confidence            345667777766666554444555444411      2456789999999999999999999997 899999999999999


Q ss_pred             HHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc-
Q 028124           94 TLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC-  172 (213)
Q Consensus        94 ~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~-  172 (213)
                      ..+-++|.+++                       ++++|||.+    +++|||-|||++|||||+|.|+++|+|-+||+ 
T Consensus       270 ~~~q~~f~~~~-----------------------~~iiVAT~A----FGMGIdKpdVRfViH~~lP~s~EsYyQE~GRAG  322 (590)
T COG0514         270 ERVQQAFLNDE-----------------------IKVMVATNA----FGMGIDKPDVRFVIHYDLPGSIESYYQETGRAG  322 (590)
T ss_pred             HHHHHHHhcCC-----------------------CcEEEEecc----ccCccCCCCceEEEEecCCCCHHHHHHHHhhcc
Confidence            99999999985                       999999999    99999999999999999999999999999997 


Q ss_pred             -cCCCCeEEEEEeCchhHHHHHHHHH
Q 028124          173 -LAADGSVINIVVGGEVVTLRSMEES  197 (213)
Q Consensus       173 -~~~~g~~i~~~~~~e~~~~~~le~~  197 (213)
                       .|.+..|+.|+.++|....+.+.+.
T Consensus       323 RDG~~a~aill~~~~D~~~~~~~i~~  348 (590)
T COG0514         323 RDGLPAEAILLYSPEDIRWQRYLIEQ  348 (590)
T ss_pred             CCCCcceEEEeeccccHHHHHHHHHh
Confidence             5777999999999987766665443

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

Probab=99.84  E-value=6.2e-20  Score=167.05  Aligned_cols=128  Identities=20%  Similarity=0.283  Sum_probs=112.2

Q ss_pred             cCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEE-Eec--------CCCCHHHHHHHHHHH
Q 028124           30 DRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS-SLH--------SDLAETERTLILEEF  100 (213)
Q Consensus        30 ~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~-~lh--------g~~~~~~R~~~l~~F  100 (213)
                      .-++.|++.+.+++++.+. ...+.++|||++.+++|+.+.+.|.+.+ ..+. .+-        .||+++++.+++++|
T Consensus       344 ~v~HPKl~~l~eilke~~~-k~~~~RvIVFT~yRdTae~i~~~L~~~~-~~~~~rFiGQa~r~~~~GMsQkeQ~eiI~~F  421 (542)
T COG1111         344 GVEHPKLEKLREILKEQLE-KNGDSRVIVFTEYRDTAEEIVNFLKKIG-IKARVRFIGQASREGDKGMSQKEQKEIIDQF  421 (542)
T ss_pred             cCCCccHHHHHHHHHHHHh-cCCCceEEEEehhHhHHHHHHHHHHhcC-CcceeEEeeccccccccccCHHHHHHHHHHH
Confidence            3346699999999988665 4567899999999999999999999886 4442 222        469999999999999


Q ss_pred             hcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccccCC-CCeE
Q 028124          101 RHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAA-DGSV  179 (213)
Q Consensus       101 r~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~~~-~g~~  179 (213)
                      ++|+                       .++||||++    .++|+|+|+++.||.|++-.|...++||.||+|++ .|.+
T Consensus       422 r~Ge-----------------------~nVLVaTSV----gEEGLDIp~vDlVifYEpvpSeIR~IQR~GRTGR~r~Grv  474 (542)
T COG1111         422 RKGE-----------------------YNVLVATSV----GEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGRKRKGRV  474 (542)
T ss_pred             hcCC-----------------------ceEEEEccc----ccccCCCCcccEEEEecCCcHHHHHHHhhCccccCCCCeE
Confidence            9997                       999999999    99999999999999999999999999999999755 5999


Q ss_pred             EEEEeCc
Q 028124          180 INIVVGG  186 (213)
Q Consensus       180 i~~~~~~  186 (213)
                      +.+++.+
T Consensus       475 ~vLvt~g  481 (542)
T COG1111         475 VVLVTEG  481 (542)
T ss_pred             EEEEecC
Confidence            9999876

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.83  E-value=4.6e-20  Score=181.70  Aligned_cols=169  Identities=12%  Similarity=0.134  Sum_probs=127.8

Q ss_pred             CCCCCCCCCCCCCCCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc-CCceEE
Q 028124            4 DGVESPCPPCQSPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL-ADISFS   82 (213)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~-~~~~~~   82 (213)
                      -++..++.+...|..+..+++++......    .....+++.+    ..+++++||||++++++.+++.|++. +++++.
T Consensus       619 ~g~~d~s~I~~~p~~R~~V~t~v~~~~~~----~i~~~i~~el----~~g~qv~if~n~i~~~e~l~~~L~~~~p~~~v~  690 (926)
T TIGR00580       619 SGIRDLSIIATPPEDRLPVRTFVMEYDPE----LVREAIRREL----LRGGQVFYVHNRIESIEKLATQLRELVPEARIA  690 (926)
T ss_pred             hcCCCcEEEecCCCCccceEEEEEecCHH----HHHHHHHHHH----HcCCeEEEEECCcHHHHHHHHHHHHhCCCCeEE
Confidence            34555555555555556677776543221    1111222332    23579999999999999999999875 447999


Q ss_pred             EecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCC-C
Q 028124           83 SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPT-K  161 (213)
Q Consensus        83 ~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~-~  161 (213)
                      .+||+|++++|.+++++|++|+                       .++||||++    +++|+|+|++++||+++.|. .
T Consensus       691 ~lHG~m~~~eRe~im~~F~~Gk-----------------------~~ILVaT~i----ie~GIDIp~v~~VIi~~a~~~g  743 (926)
T TIGR00580       691 IAHGQMTENELEEVMLEFYKGE-----------------------FQVLVCTTI----IETGIDIPNANTIIIERADKFG  743 (926)
T ss_pred             EecCCCCHHHHHHHHHHHHcCC-----------------------CCEEEECCh----hhcccccccCCEEEEecCCCCC
Confidence            9999999999999999999985                       999999999    99999999999999999986 6


Q ss_pred             hHHHHHhhccc--cCCCCeEEEEEeC------chhHHHHHHHHHh----cccccccCc
Q 028124          162 KETYIRRMTTC--LAADGSVINIVVG------GEVVTLRSMEESL----GLIVAEVPI  207 (213)
Q Consensus       162 ~~~yi~R~GR~--~~~~g~~i~~~~~------~e~~~~~~le~~l----~~~~~~~~~  207 (213)
                      ..+|.||+||+  +++.|.||.++..      .....++.++++.    |+.+++..+
T Consensus       744 ls~l~Qr~GRvGR~g~~g~aill~~~~~~l~~~~~~RL~~~~~~~~~g~gf~ia~~Dl  801 (926)
T TIGR00580       744 LAQLYQLRGRVGRSKKKAYAYLLYPHQKALTEDAQKRLEAIQEFSELGAGFKIALHDL  801 (926)
T ss_pred             HHHHHHHhcCCCCCCCCeEEEEEECCcccCCHHHHHHHHHHHHhhcchhhHHHHHHHH
Confidence            78999999996  5677999999854      3456667777664    555554443

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.

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=99.82  E-value=2.8e-19  Score=171.22  Aligned_cols=145  Identities=17%  Similarity=0.217  Sum_probs=126.6

Q ss_pred             hHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccc
Q 028124           34 FKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE  113 (213)
Q Consensus        34 ~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~  113 (213)
                      .++..|.+.|....   ..+.++||||+++..++.|++.|...| +.+..+||++++.+|.+++++|+.|.         
T Consensus       430 ~q~~~L~~~L~~~~---~~g~~viIf~~t~~~ae~L~~~L~~~g-i~~~~~h~~~~~~~R~~~l~~f~~g~---------  496 (652)
T PRK05298        430 GQVDDLLSEIRKRV---AKGERVLVTTLTKRMAEDLTDYLKELG-IKVRYLHSDIDTLERVEIIRDLRLGE---------  496 (652)
T ss_pred             ccHHHHHHHHHHHH---hCCCEEEEEeCCHHHHHHHHHHHhhcc-eeEEEEECCCCHHHHHHHHHHHHcCC---------
Confidence            36667777665532   357899999999999999999999987 89999999999999999999999985         


Q ss_pred             cCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecC-----CCChHHHHHhhccccC-CCCeEEEEEeC--
Q 028124          114 QSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYEL-----PTKKETYIRRMTTCLA-ADGSVINIVVG--  185 (213)
Q Consensus       114 ~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~-----P~~~~~yi~R~GR~~~-~~g~~i~~~~~--  185 (213)
                                    ..+||||+.    +++|+|+|++++||++|.     |.+..+|+||+||+|+ ..|.|++|+..  
T Consensus       497 --------------i~vlV~t~~----L~rGfdlp~v~lVii~d~eifG~~~~~~~yiqr~GR~gR~~~G~~i~~~~~~~  558 (652)
T PRK05298        497 --------------FDVLVGINL----LREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKIT  558 (652)
T ss_pred             --------------ceEEEEeCH----HhCCccccCCcEEEEeCCcccccCCCHHHHHHHhccccCCCCCEEEEEecCCC
Confidence                          999999999    999999999999999984     8899999999999754 46999999984  


Q ss_pred             -------chhHHHHHHHHHhcccccccCccc
Q 028124          186 -------GEVVTLRSMEESLGLIVAEVPINI  209 (213)
Q Consensus       186 -------~e~~~~~~le~~l~~~~~~~~~~~  209 (213)
                             .+...+++++..++.+...+|.++
T Consensus       559 ~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~  589 (652)
T PRK05298        559 DSMQKAIDETERRREIQIAYNEEHGITPKTI  589 (652)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhccCCCChhH
Confidence                   577888889999998888887654

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.82  E-value=1.3e-19  Score=172.00  Aligned_cols=134  Identities=13%  Similarity=0.095  Sum_probs=111.6

Q ss_pred             CceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHH
Q 028124           21 QPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEF  100 (213)
Q Consensus        21 ~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~F  100 (213)
                      ...+.+++++..+ |+..|.++++...   ..+.++||||+|+..++.++..|...| +.+..+||++++.+  ..+..|
T Consensus       445 ~~~~~~v~~t~~~-K~~aL~~~i~~~~---~~~~pvLIft~t~~~se~L~~~L~~~g-i~~~~Lhg~~~~rE--~~ii~~  517 (656)
T PRK12898        445 RHLPDEVFLTAAA-KWAAVAARVRELH---AQGRPVLVGTRSVAASERLSALLREAG-LPHQVLNAKQDAEE--AAIVAR  517 (656)
T ss_pred             eecCCEEEeCHHH-HHHHHHHHHHHHH---hcCCCEEEEeCcHHHHHHHHHHHHHCC-CCEEEeeCCcHHHH--HHHHHH
Confidence            3556677777655 9999999997732   245789999999999999999999987 89999999875444  445555


Q ss_pred             hcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCC---CCC-----EEEEecCCCChHHHHHhhccc
Q 028124          101 RHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAI---SAR-----VLINYELPTKKETYIRRMTTC  172 (213)
Q Consensus       101 r~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~---~v~-----~VI~yd~P~~~~~yi~R~GR~  172 (213)
                      +.+                       +..|+||||+    ++||+|++   +|.     +|||||+|.+...|+||+||+
T Consensus       518 ag~-----------------------~g~VlVATdm----AgRGtDI~l~~~V~~~GGLhVI~~d~P~s~r~y~hr~GRT  570 (656)
T PRK12898        518 AGQ-----------------------RGRITVATNM----AGRGTDIKLEPGVAARGGLHVILTERHDSARIDRQLAGRC  570 (656)
T ss_pred             cCC-----------------------CCcEEEEccc----hhcccCcCCccchhhcCCCEEEEcCCCCCHHHHHHhcccc
Confidence            554                       2669999999    99999999   676     999999999999999999997


Q ss_pred             --cCCCCeEEEEEeCchh
Q 028124          173 --LAADGSVINIVVGGEV  188 (213)
Q Consensus       173 --~~~~g~~i~~~~~~e~  188 (213)
                        .|.+|.+++|++.+|.
T Consensus       571 GRqG~~G~s~~~is~eD~  588 (656)
T PRK12898        571 GRQGDPGSYEAILSLEDD  588 (656)
T ss_pred             cCCCCCeEEEEEechhHH
Confidence              5778999999997654

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.81  E-value=3e-19  Score=175.92  Aligned_cols=97  Identities=12%  Similarity=0.169  Sum_probs=89.0

Q ss_pred             CCCcEEEEeCchHHHHHHHHHHhcc-C----CceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCC
Q 028124           52 PGLPMIVCCSSRDELDAVCSAVSNL-A----DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEH  126 (213)
Q Consensus        52 ~~~~~IIF~~~~~~~~~l~~~L~~~-~----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~  126 (213)
                      ..+++||||||++.|+.++..|+.. +    ...+..+||+|++++|..++++|++|.                      
T Consensus       283 ~~~~~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls~~~R~~ve~~fk~G~----------------------  340 (876)
T PRK13767        283 EHRTTLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEVEEKLKRGE----------------------  340 (876)
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCCHHHHHHHHHHHHcCC----------------------
Confidence            3578999999999999999999863 1    257899999999999999999999985                      


Q ss_pred             ceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccccCC
Q 028124          127 KSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAA  175 (213)
Q Consensus       127 ~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~~~  175 (213)
                       +++||||++    +++|+|++++++||+|+.|.+..+|+||+||+|++
T Consensus       341 -i~vLVaTs~----Le~GIDip~Vd~VI~~~~P~sv~~ylQRiGRaGR~  384 (876)
T PRK13767        341 -LKVVVSSTS----LELGIDIGYIDLVVLLGSPKSVSRLLQRIGRAGHR  384 (876)
T ss_pred             -CeEEEECCh----HHhcCCCCCCcEEEEeCCCCCHHHHHHhcccCCCC
Confidence             999999999    99999999999999999999999999999998644

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.81  E-value=7.5e-19  Score=168.06  Aligned_cols=134  Identities=16%  Similarity=0.218  Sum_probs=115.6

Q ss_pred             chHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccccccc
Q 028124           33 QFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVT  112 (213)
Q Consensus        33 ~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~  112 (213)
                      ..+++.|.+.++...   ..+.++||||+|+..++.|++.|...| +.+..+||++++.+|.+++++|+.|.        
T Consensus       425 ~~qi~~Ll~eI~~~~---~~g~~vLIf~~tk~~ae~L~~~L~~~g-i~~~~lh~~~~~~eR~~~l~~fr~G~--------  492 (655)
T TIGR00631       425 DGQVDDLLSEIRQRV---ARNERVLVTTLTKKMAEDLTDYLKELG-IKVRYLHSEIDTLERVEIIRDLRLGE--------  492 (655)
T ss_pred             cchHHHHHHHHHHHH---cCCCEEEEEECCHHHHHHHHHHHhhhc-cceeeeeCCCCHHHHHHHHHHHhcCC--------
Confidence            336777777665532   357899999999999999999999987 89999999999999999999999985        


Q ss_pred             ccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEec-----CCCChHHHHHhhccccCC-CCeEEEEEeCc
Q 028124          113 EQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYE-----LPTKKETYIRRMTTCLAA-DGSVINIVVGG  186 (213)
Q Consensus       113 ~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd-----~P~~~~~yi~R~GR~~~~-~g~~i~~~~~~  186 (213)
                                     +.+||||+.    +++|+|+|++++||++|     +|.+..+|+||+||+++. .|.|+.++...
T Consensus       493 ---------------i~VLV~t~~----L~rGfDiP~v~lVvi~DadifG~p~~~~~~iqriGRagR~~~G~vi~~~~~~  553 (655)
T TIGR00631       493 ---------------FDVLVGINL----LREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVIMYADKI  553 (655)
T ss_pred             ---------------ceEEEEcCh----hcCCeeeCCCcEEEEeCcccccCCCCHHHHHHHhcCCCCCCCCEEEEEEcCC
Confidence                           999999999    99999999999999999     899999999999998544 69999999876


Q ss_pred             hhHHHHHHHHH
Q 028124          187 EVVTLRSMEES  197 (213)
Q Consensus       187 e~~~~~~le~~  197 (213)
                      +..+...+++.
T Consensus       554 ~~~~~~ai~~~  564 (655)
T TIGR00631       554 TDSMQKAIEET  564 (655)
T ss_pred             CHHHHHHHHHH
Confidence            65555555443

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

>PRK13766 Hef nuclease; Provisional

Probab=99.79  E-value=1.8e-18  Score=168.29  Aligned_cols=127  Identities=21%  Similarity=0.304  Sum_probs=112.5

Q ss_pred             CcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCC--------CCHHHHHHHHHHHhc
Q 028124           31 RLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSD--------LAETERTLILEEFRH  102 (213)
Q Consensus        31 ~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~--------~~~~~R~~~l~~Fr~  102 (213)
                      ....|++.|.++|+.... ..++.++||||+++++|+.|++.|...+ +.+..+||.        |++.+|..++++|+.
T Consensus       344 ~~~pK~~~L~~il~~~~~-~~~~~kvlIF~~~~~t~~~L~~~L~~~~-~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~  421 (773)
T PRK13766        344 IEHPKLEKLREIVKEQLG-KNPDSRIIVFTQYRDTAEKIVDLLEKEG-IKAVRFVGQASKDGDKGMSQKEQIEILDKFRA  421 (773)
T ss_pred             cCChHHHHHHHHHHHHHh-cCCCCeEEEEeCcHHHHHHHHHHHHhCC-CceEEEEccccccccCCCCHHHHHHHHHHHHc
Confidence            345699999999987543 3567899999999999999999998876 788889886        999999999999999


Q ss_pred             ccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccccCC-CCeEEE
Q 028124          103 TAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAA-DGSVIN  181 (213)
Q Consensus       103 g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~~~-~g~~i~  181 (213)
                      |+                       .++||+|++    +++|+|+|++++||+||+|++...|+||+||+++. .|.++.
T Consensus       422 g~-----------------------~~vLvaT~~----~~eGldi~~~~~VI~yd~~~s~~r~iQR~GR~gR~~~~~v~~  474 (773)
T PRK13766        422 GE-----------------------FNVLVSTSV----AEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRTGRQEEGRVVV  474 (773)
T ss_pred             CC-----------------------CCEEEECCh----hhcCCCcccCCEEEEeCCCCCHHHHHHHhcccCcCCCCEEEE
Confidence            85                       999999999    99999999999999999999999999999998653 588888


Q ss_pred             EEeCc
Q 028124          182 IVVGG  186 (213)
Q Consensus       182 ~~~~~  186 (213)
                      ++..+
T Consensus       475 l~~~~  479 (773)
T PRK13766        475 LIAKG  479 (773)
T ss_pred             EEeCC
Confidence            88754

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

Probab=99.79  E-value=1.7e-19  Score=161.09  Aligned_cols=155  Identities=19%  Similarity=0.252  Sum_probs=141.4

Q ss_pred             CCCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHH
Q 028124           16 PSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTL   95 (213)
Q Consensus        16 ~~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~   95 (213)
                      ....+.+++.+..+...+ |...|..++...    ...++++|||.|+..++.+...|...| +.+..++|.|+++.|..
T Consensus       229 tkise~lk~~f~~~~~a~-K~aaLl~il~~~----~~~~~t~vf~~tk~hve~~~~ll~~~g-~~~s~iysslD~~aRk~  302 (529)
T KOG0337|consen  229 TKISELLKVRFFRVRKAE-KEAALLSILGGR----IKDKQTIVFVATKHHVEYVRGLLRDFG-GEGSDIYSSLDQEARKI  302 (529)
T ss_pred             hhcchhhhhheeeeccHH-HHHHHHHHHhcc----ccccceeEEecccchHHHHHHHHHhcC-CCccccccccChHhhhh
Confidence            344567888999999887 999999999872    346799999999999999999999987 79999999999999999


Q ss_pred             HHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--c
Q 028124           96 ILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--L  173 (213)
Q Consensus        96 ~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~  173 (213)
                      .+++|+.+                       +..+||.||+    ++||+|+|-.+.|||||+|.+...|.||+||.  .
T Consensus       303 ~~~~F~~~-----------------------k~~~lvvTdv----aaRG~diplldnvinyd~p~~~klFvhRVgr~ara  355 (529)
T KOG0337|consen  303 NGRDFRGR-----------------------KTSILVVTDV----AARGLDIPLLDNVINYDFPPDDKLFVHRVGRVARA  355 (529)
T ss_pred             ccccccCC-----------------------ccceEEEehh----hhccCCCccccccccccCCCCCceEEEEecchhhc
Confidence            99999997                       5899999999    99999999999999999999999999999995  6


Q ss_pred             CCCCeEEEEEeCchhHHHHHHHHHhccccc
Q 028124          174 AADGSVINIVVGGEVVTLRSMEESLGLIVA  203 (213)
Q Consensus       174 ~~~g~~i~~~~~~e~~~~~~le~~l~~~~~  203 (213)
                      |+.|.+|+||.+.+..++-.|..++|..+.
T Consensus       356 grtg~aYs~V~~~~~~yl~DL~lflgr~~~  385 (529)
T KOG0337|consen  356 GRTGRAYSLVASTDDPYLLDLQLFLGRPLI  385 (529)
T ss_pred             cccceEEEEEecccchhhhhhhhhcCCcee
Confidence            899999999999999999999999987654

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.79  E-value=7.4e-19  Score=176.37  Aligned_cols=170  Identities=12%  Similarity=0.164  Sum_probs=123.4

Q ss_pred             CCCCCCCCCCCCCCCCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc-CCceE
Q 028124            3 IDGVESPCPPCQSPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL-ADISF   81 (213)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~-~~~~~   81 (213)
                      ..++..|..+...|..+..+++++........|..    ++..+.    .+++++||||++..++.+++.|.+. ++..+
T Consensus       767 ~~gl~d~~~I~~~p~~r~~v~~~~~~~~~~~~k~~----il~el~----r~gqv~vf~n~i~~ie~la~~L~~~~p~~~v  838 (1147)
T PRK10689        767 MSGMRDLSIIATPPARRLAVKTFVREYDSLVVREA----ILREIL----RGGQVYYLYNDVENIQKAAERLAELVPEARI  838 (1147)
T ss_pred             HhhCCCcEEEecCCCCCCCceEEEEecCcHHHHHH----HHHHHh----cCCeEEEEECCHHHHHHHHHHHHHhCCCCcE
Confidence            34555666555555555667777765443222333    333321    2479999999999999999999876 34789


Q ss_pred             EEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCC-C
Q 028124           82 SSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELP-T  160 (213)
Q Consensus        82 ~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P-~  160 (213)
                      ..+||+|++++|.+++++|++|.                       .++||||++    ++||+|+|++++||.++.. .
T Consensus       839 ~~lHG~m~q~eRe~im~~Fr~Gk-----------------------~~VLVaTdI----ierGIDIP~v~~VIi~~ad~f  891 (1147)
T PRK10689        839 AIGHGQMRERELERVMNDFHHQR-----------------------FNVLVCTTI----IETGIDIPTANTIIIERADHF  891 (1147)
T ss_pred             EEEeCCCCHHHHHHHHHHHHhcC-----------------------CCEEEECch----hhcccccccCCEEEEecCCCC
Confidence            99999999999999999999985                       999999999    9999999999999954432 2


Q ss_pred             ChHHHHHhhccc--cCCCCeEEEEEeCc------hhHHHHHHHHHh----cccccccCc
Q 028124          161 KKETYIRRMTTC--LAADGSVINIVVGG------EVVTLRSMEESL----GLIVAEVPI  207 (213)
Q Consensus       161 ~~~~yi~R~GR~--~~~~g~~i~~~~~~------e~~~~~~le~~l----~~~~~~~~~  207 (213)
                      +...|+||+||+  .++.|.|+.+....      ....+..++++.    |+.+++..+
T Consensus       892 glaq~~Qr~GRvGR~g~~g~a~ll~~~~~~~~~~~~~rl~~~~~~~~lg~gf~~a~~dl  950 (1147)
T PRK10689        892 GLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALATHDL  950 (1147)
T ss_pred             CHHHHHHHhhccCCCCCceEEEEEeCCCcccCHHHHHHHHHHHHhcCCcchHHHHHHHH
Confidence            456799999997  45679999887532      344555565543    344444433

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.79  E-value=1.6e-18  Score=167.63  Aligned_cols=127  Identities=15%  Similarity=0.155  Sum_probs=110.6

Q ss_pred             EecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccc
Q 028124           28 AVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKW  107 (213)
Q Consensus        28 ~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~  107 (213)
                      ++.. ..|+..|.+.+....   ..+.++||||+|+..++.++..|.+.+ +.+..+||++++.++..+...++.     
T Consensus       407 ~~~~-~~K~~al~~~i~~~~---~~~~pvLIf~~t~~~se~l~~~L~~~g-i~~~~L~~~~~~~e~~~i~~ag~~-----  476 (790)
T PRK09200        407 FVTL-DEKYKAVIEEVKERH---ETGRPVLIGTGSIEQSETFSKLLDEAG-IPHNLLNAKNAAKEAQIIAEAGQK-----  476 (790)
T ss_pred             EcCH-HHHHHHHHHHHHHHH---hcCCCEEEEeCcHHHHHHHHHHHHHCC-CCEEEecCCccHHHHHHHHHcCCC-----
Confidence            3444 449999999887631   357899999999999999999999987 899999999999888877777665     


Q ss_pred             cccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCC---CCCC-----EEEEecCCCChHHHHHhhccc--cCCCC
Q 028124          108 NQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESA---ISAR-----VLINYELPTKKETYIRRMTTC--LAADG  177 (213)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~---~~v~-----~VI~yd~P~~~~~yi~R~GR~--~~~~g  177 (213)
                                          .+|+||||+    ++||+|+   ++|.     +|||||+|.+...|+||+||+  .|.+|
T Consensus       477 --------------------g~VlIATdm----AgRG~DI~l~~~V~~~GGL~VI~~d~p~s~r~y~qr~GRtGR~G~~G  532 (790)
T PRK09200        477 --------------------GAVTVATNM----AGRGTDIKLGEGVHELGGLAVIGTERMESRRVDLQLRGRSGRQGDPG  532 (790)
T ss_pred             --------------------CeEEEEccc----hhcCcCCCcccccccccCcEEEeccCCCCHHHHHHhhccccCCCCCe
Confidence                                469999999    9999999   7998     999999999999999999997  57789


Q ss_pred             eEEEEEeCchh
Q 028124          178 SVINIVVGGEV  188 (213)
Q Consensus       178 ~~i~~~~~~e~  188 (213)
                      .+++|++.+|.
T Consensus       533 ~s~~~is~eD~  543 (790)
T PRK09200        533 SSQFFISLEDD  543 (790)
T ss_pred             eEEEEEcchHH
Confidence            99999987654

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.78  E-value=1.9e-18  Score=168.68  Aligned_cols=139  Identities=12%  Similarity=0.145  Sum_probs=111.4

Q ss_pred             CCceEEEEEecCcchHH-HHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc--CCceEEEecCCCCHHHHHHH
Q 028124           20 SQPRHFYVAVDRLQFKM-ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL--ADISFSSLHSDLAETERTLI   96 (213)
Q Consensus        20 ~~i~~~~~~~~~~~~K~-~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~--~~~~~~~lhg~~~~~~R~~~   96 (213)
                      ..++++|..+...+ ++ ..+...+..+..  ...+++||||+++.+++.+++.|.+.  .++.+..+||+|++++|..+
T Consensus       178 ~pVe~~y~~~~~~~-~~~~~v~~~l~~~l~--~~~g~iLVFlpg~~eI~~l~~~L~~~~~~~~~v~pLHg~L~~~eq~~~  254 (819)
T TIGR01970       178 FPVEIRYLPLRGDQ-RLEDAVSRAVEHALA--SETGSILVFLPGQAEIRRVQEQLAERLDSDVLICPLYGELSLAAQDRA  254 (819)
T ss_pred             eeeeeEEeecchhh-hHHHHHHHHHHHHHH--hcCCcEEEEECCHHHHHHHHHHHHhhcCCCcEEEEecCCCCHHHHHHH
Confidence            35888888776554 33 222222222221  13578999999999999999999863  24889999999999999999


Q ss_pred             HHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCC---------------
Q 028124           97 LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTK---------------  161 (213)
Q Consensus        97 l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~---------------  161 (213)
                      ++.|++|.                       .+||||||+    +++|+|+++|++|||+++|+.               
T Consensus       255 ~~~~~~G~-----------------------rkVlVATnI----AErgItIp~V~~VID~Gl~r~~~yd~~~g~~~L~~~  307 (819)
T TIGR01970       255 IKPDPQGR-----------------------RKVVLATNI----AETSLTIEGIRVVIDSGLARVARFDPKTGITRLETV  307 (819)
T ss_pred             HhhcccCC-----------------------eEEEEecch----HhhcccccCceEEEEcCcccccccccccCCceeeEE
Confidence            99999984                       999999999    999999999999999999863               


Q ss_pred             ---hHHHHHhhccccC-CCCeEEEEEeCchh
Q 028124          162 ---KETYIRRMTTCLA-ADGSVINIVVGGEV  188 (213)
Q Consensus       162 ---~~~yi~R~GR~~~-~~g~~i~~~~~~e~  188 (213)
                         .++|+||+||+|+ ++|.||.+++..+.
T Consensus       308 ~iSkasa~QR~GRAGR~~~G~cyrL~t~~~~  338 (819)
T TIGR01970       308 RISQASATQRAGRAGRLEPGVCYRLWSEEQH  338 (819)
T ss_pred             EECHHHHHhhhhhcCCCCCCEEEEeCCHHHH
Confidence               3468999999875 57999999987654

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.

>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=99.78  E-value=6.6e-18  Score=127.83  Aligned_cols=127  Identities=28%  Similarity=0.512  Sum_probs=109.7

Q ss_pred             ceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHh
Q 028124           22 PRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFR  101 (213)
Q Consensus        22 i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr  101 (213)
                      |+++|...++  .|...+.+++....   ....++||||++...++.+++.|...+ ..+..+||++++.+|..++++|+
T Consensus         2 i~~~~~~~~~--~k~~~i~~~i~~~~---~~~~~~lvf~~~~~~~~~~~~~l~~~~-~~~~~~~~~~~~~~~~~~~~~f~   75 (131)
T cd00079           2 IKQYVLPVED--EKLEALLELLKEHL---KKGGKVLIFCPSKKMLDELAELLRKPG-IKVAALHGDGSQEEREEVLKDFR   75 (131)
T ss_pred             cEEEEEECCH--HHHHHHHHHHHhcc---cCCCcEEEEeCcHHHHHHHHHHHHhcC-CcEEEEECCCCHHHHHHHHHHHH
Confidence            5666665443  59999999987732   257899999999999999999998865 78999999999999999999999


Q ss_pred             cccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCCCCeE
Q 028124          102 HTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSV  179 (213)
Q Consensus       102 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~~g~~  179 (213)
                      .+.                       ..+|++|.+    +++|+|+|.+++||.+++|++...|+|++||+  .|+.|.+
T Consensus        76 ~~~-----------------------~~ili~t~~----~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~  128 (131)
T cd00079          76 EGE-----------------------IVVLVATDV----IARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTA  128 (131)
T ss_pred             cCC-----------------------CcEEEEcCh----hhcCcChhhCCEEEEeCCCCCHHHheecccccccCCCCceE
Confidence            984                       899999999    99999999999999999999999999999996  4445665


Q ss_pred             EE
Q 028124          180 IN  181 (213)
Q Consensus       180 i~  181 (213)
                      +.
T Consensus       129 ~~  130 (131)
T cd00079         129 IL  130 (131)
T ss_pred             Ee
Confidence            54

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.78  E-value=3.5e-18  Score=163.63  Aligned_cols=146  Identities=15%  Similarity=0.147  Sum_probs=111.0

Q ss_pred             CCCCceEEEEEecC---------cchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc-CCceEEEecCC
Q 028124           18 HFSQPRHFYVAVDR---------LQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL-ADISFSSLHSD   87 (213)
Q Consensus        18 ~~~~i~~~~~~~~~---------~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~-~~~~~~~lhg~   87 (213)
                      +...|+|+|+....         ...|...+..+.+. .  ...++++||||+++.+++.+++.|.+. +++.+..+||+
T Consensus       354 t~~pV~~~yi~~~~~~~~~~~y~~~~k~~~l~~L~~~-~--~~~~g~iLVFlpg~~ei~~l~~~L~~~~~~~~v~~LHG~  430 (675)
T PHA02653        354 TLFPISEVYVKNKYNPKNKRAYIEEEKKNIVTALKKY-T--PPKGSSGIVFVASVSQCEEYKKYLEKRLPIYDFYIIHGK  430 (675)
T ss_pred             cCCCeEEEEeecCcccccchhhhHHHHHHHHHHHHHh-h--cccCCcEEEEECcHHHHHHHHHHHHhhcCCceEEeccCC
Confidence            34678888875431         11233333333222 1  123568999999999999999999876 23899999999


Q ss_pred             CCHHHHHHHHHHH-hcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEec---CCC---
Q 028124           88 LAETERTLILEEF-RHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYE---LPT---  160 (213)
Q Consensus        88 ~~~~~R~~~l~~F-r~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd---~P~---  160 (213)
                      |++.  .+.+++| ++|                       +.++|||||+    ++||+|+++|++||+++   .|.   
T Consensus       431 Lsq~--eq~l~~ff~~g-----------------------k~kILVATdI----AERGIDIp~V~~VID~G~~k~p~~~~  481 (675)
T PHA02653        431 VPNI--DEILEKVYSSK-----------------------NPSIIISTPY----LESSVTIRNATHVYDTGRVYVPEPFG  481 (675)
T ss_pred             cCHH--HHHHHHHhccC-----------------------ceeEEeccCh----hhccccccCeeEEEECCCccCCCccc
Confidence            9974  5677887 566                       4999999999    99999999999999999   676   


Q ss_pred             ------ChHHHHHhhccccC-CCCeEEEEEeCchhHHHHHHH
Q 028124          161 ------KKETYIRRMTTCLA-ADGSVINIVVGGEVVTLRSME  195 (213)
Q Consensus       161 ------~~~~yi~R~GR~~~-~~g~~i~~~~~~e~~~~~~le  195 (213)
                            |.++|+||+||+|+ ++|.|+.|+++.+...+.+++
T Consensus       482 g~~~~iSkasa~QRaGRAGR~~~G~c~rLyt~~~~~pI~ri~  523 (675)
T PHA02653        482 GKEMFISKSMRTQRKGRVGRVSPGTYVYFYDLDLLKPIKRID  523 (675)
T ss_pred             CcccccCHHHHHHhccCcCCCCCCeEEEEECHHHhHHHHHHh
Confidence                  88999999999865 469999999987654444444

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.78  E-value=2.8e-18  Score=174.32  Aligned_cols=129  Identities=14%  Similarity=0.132  Sum_probs=102.7

Q ss_pred             CCCcEEEEeCchHHHHHHHHHHhccC--------------------------------CceEEEecCCCCHHHHHHHHHH
Q 028124           52 PGLPMIVCCSSRDELDAVCSAVSNLA--------------------------------DISFSSLHSDLAETERTLILEE   99 (213)
Q Consensus        52 ~~~~~IIF~~~~~~~~~l~~~L~~~~--------------------------------~~~~~~lhg~~~~~~R~~~l~~   99 (213)
                      ...++||||||+..|+.++..|++..                                .+.+..+||+|++++|..+.++
T Consensus       243 ~~~stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~HHGsLSkeeR~~IE~~  322 (1490)
T PRK09751        243 RHRSTIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVDAAHFESTSGATSNRVQSSDVFIARSHHGSVSKEQRAITEQA  322 (1490)
T ss_pred             cCCCEEEECCCHHHHHHHHHHHHHhhhhhccccccccchhhhhhhccccchhccccccceeeeeccccCCHHHHHHHHHH
Confidence            35799999999999999999997531                                0125689999999999999999


Q ss_pred             HhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccccCCC-Ce
Q 028124          100 FRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAAD-GS  178 (213)
Q Consensus       100 Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~~~~-g~  178 (213)
                      |++|.                       +++||||+.    +++|||++++++||||+.|.+..+|+||+||+|++. |.
T Consensus       323 fK~G~-----------------------LrvLVATss----LELGIDIg~VDlVIq~gsP~sVas~LQRiGRAGR~~gg~  375 (1490)
T PRK09751        323 LKSGE-----------------------LRCVVATSS----LELGIDMGAVDLVIQVATPLSVASGLQRIGRAGHQVGGV  375 (1490)
T ss_pred             HHhCC-----------------------ceEEEeCcH----HHccCCcccCCEEEEeCCCCCHHHHHHHhCCCCCCCCCc
Confidence            99995                       999999999    999999999999999999999999999999987654 33


Q ss_pred             EEEEEeCchhHHH----HHHHHHhcccccccCc
Q 028124          179 VINIVVGGEVVTL----RSMEESLGLIVAEVPI  207 (213)
Q Consensus       179 ~i~~~~~~e~~~~----~~le~~l~~~~~~~~~  207 (213)
                      +..++.+.+...+    --++..+...++++..
T Consensus       376 s~gli~p~~r~dlle~~~~ve~~l~g~iE~~~~  408 (1490)
T PRK09751        376 SKGLFFPRTRRDLVDSAVIVECMFAGRLENLTP  408 (1490)
T ss_pred             cEEEEEeCcHHHHHhhHHHHHHHhcCCCCccCC
Confidence            3333333222222    2367777777776544

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

Probab=99.78  E-value=1.5e-18  Score=155.83  Aligned_cols=132  Identities=23%  Similarity=0.365  Sum_probs=117.3

Q ss_pred             CCCCcEEEEeCchHHHHHHHHHHhccC--CceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCce
Q 028124           51 RPGLPMIVCCSSRDELDAVCSAVSNLA--DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKS  128 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~~L~~~~--~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~  128 (213)
                      ....++||||.|+..|+.|-+++..+|  +++++++||+..+.||.+.++.|+.+.                       .
T Consensus       503 h~mdkaiifcrtk~dcDnLer~~~qkgg~~~scvclhgDrkP~Erk~nle~Fkk~d-----------------------v  559 (725)
T KOG0349|consen  503 HAMDKAIIFCRTKQDCDNLERMMNQKGGKHYSCVCLHGDRKPDERKANLESFKKFD-----------------------V  559 (725)
T ss_pred             hccCceEEEEeccccchHHHHHHHHcCCccceeEEEecCCChhHHHHHHHhhhhcC-----------------------e
Confidence            467899999999999999999998774  378999999999999999999999986                       9


Q ss_pred             eEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccccCC--CCeEEEEEeC---------------------
Q 028124          129 HMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAA--DGSVINIVVG---------------------  185 (213)
Q Consensus       129 ~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~~~--~g~~i~~~~~---------------------  185 (213)
                      +.|||||+    ++||+|+..+.++||.-+|.+...|+||+||.|+.  -|.+|+++..                     
T Consensus       560 kflictdv----aargldi~g~p~~invtlpd~k~nyvhrigrvgraermglaislvat~~ekvwyh~c~srgr~c~nt~  635 (725)
T KOG0349|consen  560 KFLICTDV----AARGLDITGLPFMINVTLPDDKTNYVHRIGRVGRAERMGLAISLVATVPEKVWYHWCKSRGRSCNNTN  635 (725)
T ss_pred             EEEEEehh----hhccccccCCceEEEEecCcccchhhhhhhccchhhhcceeEEEeeccchheeehhhhccCCcccCCc
Confidence            99999999    99999999999999999999999999999997544  4888888742                     


Q ss_pred             -----------chhHHHHHHHHHhcccccccCccc
Q 028124          186 -----------GEVVTLRSMEESLGLIVAEVPINI  209 (213)
Q Consensus       186 -----------~e~~~~~~le~~l~~~~~~~~~~~  209 (213)
                                 +|...+.++|.++++.++.+..++
T Consensus       636 l~e~~gc~iwyne~~llaeve~hln~ti~qv~~~~  670 (725)
T KOG0349|consen  636 LTEVRGCCIWYNEPNLLAEVEDHLNITIQQVDKTM  670 (725)
T ss_pred             cccccceEEEeCchhHHHHHHHhhcceeeeeCCCC
Confidence                       355788899999999988776554

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.77  E-value=4.8e-18  Score=163.53  Aligned_cols=130  Identities=15%  Similarity=0.225  Sum_probs=104.0

Q ss_pred             CCCcEEEEeCch--------HHHHHHHHHHhcc-CCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCC
Q 028124           52 PGLPMIVCCSSR--------DELDAVCSAVSNL-ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETG  122 (213)
Q Consensus        52 ~~~~~IIF~~~~--------~~~~~l~~~L~~~-~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~  122 (213)
                      .+.+++|||+..        ..++.+++.|.+. +++.+..+||+|++++|.+++++|++|+                  
T Consensus       470 ~g~q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~------------------  531 (681)
T PRK10917        470 KGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGE------------------  531 (681)
T ss_pred             cCCcEEEEEcccccccchhHHHHHHHHHHHHHHCCCCcEEEEeCCCCHHHHHHHHHHHHcCC------------------
Confidence            578999999953        4567778888764 2378999999999999999999999985                  


Q ss_pred             CCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCC-hHHHHHhhccc--cCCCCeEEEEEe-C---chhHHHHHHH
Q 028124          123 KDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTK-KETYIRRMTTC--LAADGSVINIVV-G---GEVVTLRSME  195 (213)
Q Consensus       123 ~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~-~~~yi~R~GR~--~~~~g~~i~~~~-~---~e~~~~~~le  195 (213)
                           .++||||++    +++|+|+|++++||+|+.|+. .+.|.||+||+  +|..|.|+.++. +   .....+..++
T Consensus       532 -----~~ILVaT~v----ie~GiDip~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~ill~~~~~~~~~~~rl~~~~  602 (681)
T PRK10917        532 -----IDILVATTV----IEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDPLSETARERLKIMR  602 (681)
T ss_pred             -----CCEEEECcc----eeeCcccCCCcEEEEeCCCCCCHHHHHHHhhcccCCCCceEEEEEECCCCChhHHHHHHHHH
Confidence                 999999999    999999999999999999984 67788899996  566799999995 3   2344555565


Q ss_pred             H-HhcccccccCcc
Q 028124          196 E-SLGLIVAEVPIN  208 (213)
Q Consensus       196 ~-~l~~~~~~~~~~  208 (213)
                      + .-|+.+++..+.
T Consensus       603 ~~~dgf~iae~dl~  616 (681)
T PRK10917        603 ETNDGFVIAEKDLE  616 (681)
T ss_pred             HhcchHHHHHHhHh
Confidence            4 235555554443

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.75  E-value=6.8e-18  Score=164.83  Aligned_cols=138  Identities=9%  Similarity=0.149  Sum_probs=111.6

Q ss_pred             CceEEEEEecCcchHHH-HHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc--CCceEEEecCCCCHHHHHHHH
Q 028124           21 QPRHFYVAVDRLQFKME-TLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL--ADISFSSLHSDLAETERTLIL   97 (213)
Q Consensus        21 ~i~~~~~~~~~~~~K~~-~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~--~~~~~~~lhg~~~~~~R~~~l   97 (213)
                      .++++|..++..+ ++. .+...+..+..  ...+++||||+++.+++.+++.|...  .++.+..+||+|++++|.+++
T Consensus       182 pV~~~y~~~~~~~-~~~~~v~~~l~~~l~--~~~g~iLVFlpg~~ei~~l~~~L~~~~~~~~~v~~Lhg~l~~~eq~~~~  258 (812)
T PRK11664        182 PVERRYQPLPAHQ-RFDEAVARATAELLR--QESGSLLLFLPGVGEIQRVQEQLASRVASDVLLCPLYGALSLAEQQKAI  258 (812)
T ss_pred             cceEEeccCchhh-hHHHHHHHHHHHHHH--hCCCCEEEEcCCHHHHHHHHHHHHHhccCCceEEEeeCCCCHHHHHHHh
Confidence            5888888776655 443 22223332222  23579999999999999999999862  237899999999999999999


Q ss_pred             HHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCC----------------
Q 028124           98 EEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTK----------------  161 (213)
Q Consensus        98 ~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~----------------  161 (213)
                      +.|++|.                       .+||||||+    +++|+|+++|++|||+++|+.                
T Consensus       259 ~~~~~G~-----------------------rkVlvATnI----AErsLtIp~V~~VID~Gl~r~~~yd~~~g~~~L~~~~  311 (812)
T PRK11664        259 LPAPAGR-----------------------RKVVLATNI----AETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQR  311 (812)
T ss_pred             ccccCCC-----------------------eEEEEecch----HHhcccccCceEEEECCCcccccccccCCcceeEEEe
Confidence            9999984                       999999999    999999999999999888763                


Q ss_pred             --hHHHHHhhccccC-CCCeEEEEEeCchh
Q 028124          162 --KETYIRRMTTCLA-ADGSVINIVVGGEV  188 (213)
Q Consensus       162 --~~~yi~R~GR~~~-~~g~~i~~~~~~e~  188 (213)
                        .++|+||+||+|+ .+|.||.++++.+.
T Consensus       312 iSkasa~QR~GRaGR~~~G~cyrL~t~~~~  341 (812)
T PRK11664        312 ISQASMTQRAGRAGRLEPGICLHLYSKEQA  341 (812)
T ss_pred             echhhhhhhccccCCCCCcEEEEecCHHHH
Confidence              3589999999865 57999999997544

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.75  E-value=1.9e-17  Score=158.20  Aligned_cols=105  Identities=14%  Similarity=0.189  Sum_probs=92.4

Q ss_pred             CCCcEEEEeCch--------HHHHHHHHHHhcc-CCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCC
Q 028124           52 PGLPMIVCCSSR--------DELDAVCSAVSNL-ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETG  122 (213)
Q Consensus        52 ~~~~~IIF~~~~--------~~~~~l~~~L~~~-~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~  122 (213)
                      .+.+++|||+..        ..++.+++.|... +++.+..+||+|++++|..++++|++|+                  
T Consensus       447 ~g~q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~------------------  508 (630)
T TIGR00643       447 KGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGE------------------  508 (630)
T ss_pred             hCCcEEEEEccccccccchHHHHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHHHHHHHHcCC------------------
Confidence            468999999875        4577788888753 4478999999999999999999999985                  


Q ss_pred             CCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCC-ChHHHHHhhccc--cCCCCeEEEEE
Q 028124          123 KDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPT-KKETYIRRMTTC--LAADGSVINIV  183 (213)
Q Consensus       123 ~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~-~~~~yi~R~GR~--~~~~g~~i~~~  183 (213)
                           .++||||++    +++|+|+|++++||+|+.|+ ..+.|.||+||+  +|+.|.|+.+.
T Consensus       509 -----~~ILVaT~v----ie~GvDiP~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~il~~  563 (630)
T TIGR00643       509 -----VDILVATTV----IEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVY  563 (630)
T ss_pred             -----CCEEEECce----eecCcccCCCcEEEEeCCCcCCHHHHHHHhhhcccCCCCcEEEEEE
Confidence                 999999999    99999999999999999997 567788899996  56779999998

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.74  E-value=5.4e-17  Score=144.29  Aligned_cols=117  Identities=21%  Similarity=0.318  Sum_probs=96.5

Q ss_pred             hHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccC-CceEEEecCCCCHHHHHH----HHHHHhccccccc
Q 028124           34 FKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLA-DISFSSLHSDLAETERTL----ILEEFRHTAMKWN  108 (213)
Q Consensus        34 ~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~-~~~~~~lhg~~~~~~R~~----~l~~Fr~g~~~~~  108 (213)
                      .|.+.+.++++.+    ..+.++|||||+++.|+.+++.|++.+ ...+..+||++++.+|.+    ++++|+++.    
T Consensus       207 ~~~~~l~~l~~~~----~~~~~~lVf~~t~~~~~~~~~~L~~~~~~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~~----  278 (358)
T TIGR01587       207 GEISSLERLLEFI----KKGGKIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNE----  278 (358)
T ss_pred             cCHHHHHHHHHHh----hCCCeEEEEECCHHHHHHHHHHHHhhcCCCeEEEEECCCCHHHHHHHHHHHHHHhcCCC----
Confidence            4777888887652    346899999999999999999998764 136999999999999976    488999974    


Q ss_pred             ccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccccC--C-C---CeEEEE
Q 028124          109 QKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLA--A-D---GSVINI  182 (213)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~~--~-~---g~~i~~  182 (213)
                                         .++||||++    +++|+|++ +++||+++.|  +++|+||+||+++  + .   |.++.+
T Consensus       279 -------------------~~ilvaT~~----~~~GiDi~-~~~vi~~~~~--~~~~iqr~GR~gR~g~~~~~~~~~~v~  332 (358)
T TIGR01587       279 -------------------KFVIVATQV----IEASLDIS-ADVMITELAP--IDSLIQRLGRLHRYGRKNGENFEVYII  332 (358)
T ss_pred             -------------------CeEEEECcc----hhceeccC-CCEEEEcCCC--HHHHHHHhccccCCCCCCCCCCeEEEE
Confidence                               899999999    99999995 8999999887  7899999999743  2 2   366666


Q ss_pred             Ee
Q 028124          183 VV  184 (213)
Q Consensus       183 ~~  184 (213)
                      ..
T Consensus       333 ~~  334 (358)
T TIGR01587       333 TI  334 (358)
T ss_pred             ee
Confidence            54

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

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.73  E-value=3.7e-17  Score=157.26  Aligned_cols=127  Identities=14%  Similarity=0.113  Sum_probs=109.3

Q ss_pred             EEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccc
Q 028124           27 VAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMK  106 (213)
Q Consensus        27 ~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~  106 (213)
                      ++....+ |+..+.+.+....   ..+.++||||+|++.++.++..|.+.| +.+..+||++.+.++..+.+.|+.    
T Consensus       402 i~~~~~~-K~~ai~~~i~~~~---~~~~pvLIft~s~~~se~ls~~L~~~g-i~~~~L~a~~~~~E~~ii~~ag~~----  472 (762)
T TIGR03714       402 IYATLPE-KLMATLEDVKEYH---ETGQPVLLITGSVEMSEIYSELLLREG-IPHNLLNAQNAAKEAQIIAEAGQK----  472 (762)
T ss_pred             EEECHHH-HHHHHHHHHHHHh---hCCCCEEEEECcHHHHHHHHHHHHHCC-CCEEEecCCChHHHHHHHHHcCCC----
Confidence            4455544 9999999887632   357899999999999999999999987 899999999999888777766665    


Q ss_pred             ccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCC---------CCCEEEEecCCCChHHHHHhhccc--cCC
Q 028124          107 WNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAI---------SARVLINYELPTKKETYIRRMTTC--LAA  175 (213)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~---------~v~~VI~yd~P~~~~~yi~R~GR~--~~~  175 (213)
                                           ..|+||||+    ++||+|++         ++.+|++|++|....+ +||+||+  .|.
T Consensus       473 ---------------------g~VlIATdm----AgRGtDI~l~~~v~~~GGL~vIit~~~ps~rid-~qr~GRtGRqG~  526 (762)
T TIGR03714       473 ---------------------GAVTVATSM----AGRGTDIKLGKGVAELGGLAVIGTERMENSRVD-LQLRGRSGRQGD  526 (762)
T ss_pred             ---------------------CeEEEEccc----cccccCCCCCccccccCCeEEEEecCCCCcHHH-HHhhhcccCCCC
Confidence                                 459999999    99999999         9999999999998777 9999997  577


Q ss_pred             CCeEEEEEeCchh
Q 028124          176 DGSVINIVVGGEV  188 (213)
Q Consensus       176 ~g~~i~~~~~~e~  188 (213)
                      +|.+++|++.+|.
T Consensus       527 ~G~s~~~is~eD~  539 (762)
T TIGR03714       527 PGSSQFFVSLEDD  539 (762)
T ss_pred             ceeEEEEEccchh
Confidence            8999999987654

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.

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

Probab=99.72  E-value=6.4e-17  Score=157.00  Aligned_cols=140  Identities=19%  Similarity=0.246  Sum_probs=100.3

Q ss_pred             CCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHH-----
Q 028124           20 SQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERT-----   94 (213)
Q Consensus        20 ~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~-----   94 (213)
                      .++.|+ +.++... |+..+...+..+..  ..++++||||||++.|+.+++.|.+.+ +  ..+||+|++.+|.     
T Consensus       243 ~ki~q~-v~v~~e~-Kl~~lv~~L~~ll~--e~g~~vLVF~NTv~~Aq~L~~~L~~~g-~--~lLHG~m~q~dR~~~~~~  315 (844)
T TIGR02621       243 KKIVKL-VPPSDEK-FLSTMVKELNLLMK--DSGGAILVFCRTVKHVRKVFAKLPKEK-F--ELLTGTLRGAERDDLVKK  315 (844)
T ss_pred             cceEEE-EecChHH-HHHHHHHHHHHHHh--hCCCcEEEEECCHHHHHHHHHHHHhcC-C--eEeeCCCCHHHHhhHHHH
Confidence            455664 3444433 66555554433222  356799999999999999999999876 4  8999999999999     


Q ss_pred             HHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhcccc-
Q 028124           95 LILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL-  173 (213)
Q Consensus        95 ~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~-  173 (213)
                      +++++|+++..         +|+  +... .++..+||||++    ++||+|++. ++|||+..|  .++|+||+||++ 
T Consensus       316 ~il~~Fk~~~~---------~g~--~~~~-~~g~~ILVATdV----aerGLDId~-d~VI~d~aP--~esyIQRiGRtgR  376 (844)
T TIGR02621       316 EIFNRFLPQML---------SGS--RARP-QQGTVYLVCTSA----GEVGVNISA-DHLVCDLAP--FESMQQRFGRVNR  376 (844)
T ss_pred             HHHHHHhcccc---------ccc--cccc-cccceEEeccch----hhhcccCCc-ceEEECCCC--HHHHHHHhcccCC
Confidence            88999987210         000  0000 112689999999    999999986 899998887  699999999973 


Q ss_pred             -CC-CCeEEEEEeC
Q 028124          174 -AA-DGSVINIVVG  185 (213)
Q Consensus       174 -~~-~g~~i~~~~~  185 (213)
                       |+ .+..++++..
T Consensus       377 ~G~~~~~~i~vv~~  390 (844)
T TIGR02621       377 FGELQACQIAVVHL  390 (844)
T ss_pred             CCCCCCceEEEEee
Confidence             33 3555676643

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.

>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=99.71  E-value=2.5e-17  Score=115.70  Aligned_cols=75  Identities=27%  Similarity=0.425  Sum_probs=70.4

Q ss_pred             HHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCC
Q 028124           72 AVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISAR  151 (213)
Q Consensus        72 ~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~  151 (213)
                      .|...+ +.+..+||++++.+|..++++|+++.                       ..+||||++    +++|+|+|+++
T Consensus         2 ~L~~~~-~~~~~i~~~~~~~~r~~~~~~f~~~~-----------------------~~vli~t~~----~~~Gid~~~~~   53 (78)
T PF00271_consen    2 FLEKKG-IKVAIIHGDMSQKERQEILKKFNSGE-----------------------IRVLIATDI----LGEGIDLPDAS   53 (78)
T ss_dssp             HHHHTT-SSEEEESTTSHHHHHHHHHHHHHTTS-----------------------SSEEEESCG----GTTSSTSTTES
T ss_pred             ChHHCC-CcEEEEECCCCHHHHHHHHHHhhccC-----------------------ceEEEeecc----ccccccccccc
Confidence            566666 89999999999999999999999985                       799999999    99999999999


Q ss_pred             EEEEecCCCChHHHHHhhccccC
Q 028124          152 VLINYELPTKKETYIRRMTTCLA  174 (213)
Q Consensus       152 ~VI~yd~P~~~~~yi~R~GR~~~  174 (213)
                      +||+|++|++...|+|++||+++
T Consensus        54 ~vi~~~~~~~~~~~~Q~~GR~~R   76 (78)
T PF00271_consen   54 HVIFYDPPWSPEEYIQRIGRAGR   76 (78)
T ss_dssp             EEEESSSESSHHHHHHHHTTSST
T ss_pred             cccccccCCCHHHHHHHhhcCCC
Confidence            99999999999999999999865

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 ....

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

Probab=99.70  E-value=1.7e-16  Score=155.81  Aligned_cols=157  Identities=20%  Similarity=0.240  Sum_probs=128.1

Q ss_pred             CCCCCCCCCCCCCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEec
Q 028124            6 VESPCPPCQSPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLH   85 (213)
Q Consensus         6 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lh   85 (213)
                      +.. |....+...++++...+.. +...+..-.+...++.    ..+.+..||||.++.+|+.++..|.+.+ +++..+|
T Consensus       444 l~~-~~~~~~sfnR~NL~yeV~~-k~~~~~~~~~~~~~~~----~~~~~s~IIYC~sr~~ce~vs~~L~~~~-~~a~~YH  516 (941)
T KOG0351|consen  444 LRN-PELFKSSFNRPNLKYEVSP-KTDKDALLDILEESKL----RHPDQSGIIYCLSRKECEQVSAVLRSLG-KSAAFYH  516 (941)
T ss_pred             CCC-cceecccCCCCCceEEEEe-ccCccchHHHHHHhhh----cCCCCCeEEEeCCcchHHHHHHHHHHhc-hhhHhhh
Confidence            444 3345566777776554433 2212233344444444    5678999999999999999999999998 8999999


Q ss_pred             CCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHH
Q 028124           86 SDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETY  165 (213)
Q Consensus        86 g~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~y  165 (213)
                      ++|++.+|..+.++|..++                       ++|+|||=+    ++.|||.+||+.||||.+|.+.+.|
T Consensus       517 AGl~~~~R~~Vq~~w~~~~-----------------------~~VivATVA----FGMGIdK~DVR~ViH~~lPks~E~Y  569 (941)
T KOG0351|consen  517 AGLPPKERETVQKAWMSDK-----------------------IRVIVATVA----FGMGIDKPDVRFVIHYSLPKSFEGY  569 (941)
T ss_pred             cCCCHHHHHHHHHHHhcCC-----------------------CeEEEEEee----ccCCCCCCceeEEEECCCchhHHHH
Confidence            9999999999999999984                       999999999    9999999999999999999999999


Q ss_pred             HHhhcccc--CCCCeEEEEEeCchhHHHHHHHH
Q 028124          166 IRRMTTCL--AADGSVINIVVGGEVVTLRSMEE  196 (213)
Q Consensus       166 i~R~GR~~--~~~g~~i~~~~~~e~~~~~~le~  196 (213)
                      .|-+||+|  |....|+.|+...|...++.+-.
T Consensus       570 YQE~GRAGRDG~~s~C~l~y~~~D~~~l~~ll~  602 (941)
T KOG0351|consen  570 YQEAGRAGRDGLPSSCVLLYGYADISELRRLLT  602 (941)
T ss_pred             HHhccccCcCCCcceeEEecchhHHHHHHHHHH
Confidence            99999974  66789999999888777766644

>PRK02362 ski2-like helicase; Provisional

Probab=99.70  E-value=1.7e-16  Score=154.11  Aligned_cols=108  Identities=20%  Similarity=0.264  Sum_probs=94.2

Q ss_pred             CCCcEEEEeCchHHHHHHHHHHhccCC-----------------------------------ceEEEecCCCCHHHHHHH
Q 028124           52 PGLPMIVCCSSRDELDAVCSAVSNLAD-----------------------------------ISFSSLHSDLAETERTLI   96 (213)
Q Consensus        52 ~~~~~IIF~~~~~~~~~l~~~L~~~~~-----------------------------------~~~~~lhg~~~~~~R~~~   96 (213)
                      .++++||||++++.|+.++..|.....                                   ..+..+||+|++.+|..+
T Consensus       242 ~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~L~~~l~~gva~hHagl~~~eR~~v  321 (737)
T PRK02362        242 EGGQCLVFVSSRRNAEGFAKRAASALKKTLTAAERAELAELAEEIREVSDTETSKDLADCVAKGAAFHHAGLSREHRELV  321 (737)
T ss_pred             cCCCeEEEEeCHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhccCccccHHHHHHHHhCEEeecCCCCHHHHHHH
Confidence            467999999999999999888864310                                   247889999999999999


Q ss_pred             HHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEE----ec-----CCCChHHHHH
Q 028124           97 LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLIN----YE-----LPTKKETYIR  167 (213)
Q Consensus        97 l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~----yd-----~P~~~~~yi~  167 (213)
                      .+.|++|.                       +++||||+.    +++|+|+|.+++||+    ||     .|.+..+|.|
T Consensus       322 e~~Fr~G~-----------------------i~VLvaT~t----la~GvnlPa~~VVI~~~~~yd~~~g~~~~s~~~y~Q  374 (737)
T PRK02362        322 EDAFRDRL-----------------------IKVISSTPT----LAAGLNLPARRVIIRDYRRYDGGAGMQPIPVLEYHQ  374 (737)
T ss_pred             HHHHHcCC-----------------------CeEEEechh----hhhhcCCCceEEEEecceeecCCCCceeCCHHHHHH
Confidence            99999985                       999999999    999999999999998    87     6889999999


Q ss_pred             hhccccCC----CCeEEEEEeCc
Q 028124          168 RMTTCLAA----DGSVINIVVGG  186 (213)
Q Consensus       168 R~GR~~~~----~g~~i~~~~~~  186 (213)
                      |+||+|+.    .|.++.++...
T Consensus       375 m~GRAGR~g~d~~G~~ii~~~~~  397 (737)
T PRK02362        375 MAGRAGRPGLDPYGEAVLLAKSY  397 (737)
T ss_pred             HhhcCCCCCCCCCceEEEEecCc
Confidence            99998643    38999998764

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.69  E-value=7.6e-16  Score=147.66  Aligned_cols=127  Identities=13%  Similarity=0.112  Sum_probs=111.3

Q ss_pred             CcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccccc
Q 028124           31 RLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQK  110 (213)
Q Consensus        31 ~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~  110 (213)
                      ....|+..+.+.+....   ..+.|+||||+|+..++.++..|.+.| +....+|++  +.+|...+..|+.+       
T Consensus       386 t~~~k~~ai~~~i~~~~---~~grpvLV~t~si~~se~ls~~L~~~g-i~~~~Lna~--q~~rEa~ii~~ag~-------  452 (745)
T TIGR00963       386 TEEEKWKAVVDEIKERH---AKGQPVLVGTTSVEKSELLSNLLKERG-IPHNVLNAK--NHEREAEIIAQAGR-------  452 (745)
T ss_pred             CHHHHHHHHHHHHHHHH---hcCCCEEEEeCcHHHHHHHHHHHHHcC-CCeEEeeCC--hHHHHHHHHHhcCC-------
Confidence            34459988888775532   468999999999999999999999998 899999998  78999999999987       


Q ss_pred             ccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCC-------CCEEEEecCCCChHHHHHhhccc--cCCCCeEEE
Q 028124          111 VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAIS-------ARVLINYELPTKKETYIRRMTTC--LAADGSVIN  181 (213)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~-------v~~VI~yd~P~~~~~yi~R~GR~--~~~~g~~i~  181 (213)
                                      +..|+|||++    ++||+|++.       .-+||+++.|.+...|.||.||+  .|.+|.+..
T Consensus       453 ----------------~g~VtIATnm----AgRGtDI~l~~V~~~GGl~VI~t~~p~s~ri~~q~~GRtGRqG~~G~s~~  512 (745)
T TIGR00963       453 ----------------KGAVTIATNM----AGRGTDIKLEEVKELGGLYVIGTERHESRRIDNQLRGRSGRQGDPGSSRF  512 (745)
T ss_pred             ----------------CceEEEEecc----ccCCcCCCccchhhcCCcEEEecCCCCcHHHHHHHhccccCCCCCcceEE
Confidence                            4999999999    999999998       55999999999999999999997  577899999


Q ss_pred             EEeCchhHH
Q 028124          182 IVVGGEVVT  190 (213)
Q Consensus       182 ~~~~~e~~~  190 (213)
                      |++.+|.-.
T Consensus       513 ~ls~eD~l~  521 (745)
T TIGR00963       513 FLSLEDNLM  521 (745)
T ss_pred             EEeccHHHH
Confidence            999876533

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

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

Probab=99.69  E-value=3.8e-16  Score=148.66  Aligned_cols=132  Identities=20%  Similarity=0.296  Sum_probs=109.8

Q ss_pred             cCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc--CCceEEEecC--------CCCHHHHHHHHHH
Q 028124           30 DRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL--ADISFSSLHS--------DLAETERTLILEE   99 (213)
Q Consensus        30 ~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~--~~~~~~~lhg--------~~~~~~R~~~l~~   99 (213)
                      +.++.|++.|.+.|.+... ..+..++||||.++..|+.|..+|...  ..++...+-|        +|++.++.+++++
T Consensus       391 ~~~npkle~l~~~l~e~f~-~~~dsR~IIFve~R~sa~~l~~~l~~~~~~~ir~~~fiGq~~s~~~~gmtqk~Q~evl~~  469 (746)
T KOG0354|consen  391 PKENPKLEKLVEILVEQFE-QNPDSRTIIFVETRESALALKKWLLQLHELGIKAEIFIGQGKSTQSTGMTQKEQKEVLDK  469 (746)
T ss_pred             CccChhHHHHHHHHHHHhh-cCCCccEEEEEehHHHHHHHHHHHHhhhhcccccceeeeccccccccccCHHHHHHHHHH
Confidence            3456799999999977555 577899999999999999999999732  1144444433        6999999999999


Q ss_pred             HhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccccCCCCeE
Q 028124          100 FRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSV  179 (213)
Q Consensus       100 Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~~~~g~~  179 (213)
                      |+.|+                       +++||||++    +++|+|+++|+.||-||.-.++...+||+||+-.+.|.+
T Consensus       470 Fr~G~-----------------------~NvLVATSV----~EEGLDI~ec~lVIcYd~~snpIrmIQrrGRgRa~ns~~  522 (746)
T KOG0354|consen  470 FRDGE-----------------------INVLVATSV----AEEGLDIGECNLVICYDYSSNPIRMVQRRGRGRARNSKC  522 (746)
T ss_pred             HhCCC-----------------------ccEEEEecc----hhccCCcccccEEEEecCCccHHHHHHHhccccccCCeE
Confidence            99996                       999999999    999999999999999999999999999999943455888


Q ss_pred             EEEEeCchhH
Q 028124          180 INIVVGGEVV  189 (213)
Q Consensus       180 i~~~~~~e~~  189 (213)
                      +.+.+..+..
T Consensus       523 vll~t~~~~~  532 (746)
T KOG0354|consen  523 VLLTTGSEVI  532 (746)
T ss_pred             EEEEcchhHH
Confidence            8888754433

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.66  E-value=8.7e-16  Score=137.60  Aligned_cols=116  Identities=16%  Similarity=0.193  Sum_probs=89.4

Q ss_pred             CCceEEEEEecCcchHHHHHHHHHHHhhcC--CCCCCcEEEEeCchHHHHHHHHHHhccC-CceEEEecCCCCHHHHHHH
Q 028124           20 SQPRHFYVAVDRLQFKMETLVELLHLVVAG--RRPGLPMIVCCSSRDELDAVCSAVSNLA-DISFSSLHSDLAETERTLI   96 (213)
Q Consensus        20 ~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~--~~~~~~~IIF~~~~~~~~~l~~~L~~~~-~~~~~~lhg~~~~~~R~~~   96 (213)
                      +.+.+.+.. .. ..|.+.+..+++.+...  ..++.++||||||++.+++++..|+..+ ++.+..+||.+++.+|.+.
T Consensus       239 ~~i~~~~~~-~~-~~~~~~l~~l~~~i~~~~~~~~~~k~LIf~nt~~~~~~l~~~L~~~~~~~~~~~l~g~~~~~~R~~~  316 (357)
T TIGR03158       239 PPVELELIP-AP-DFKEEELSELAEEVIERFRQLPGERGAIILDSLDEVNRLSDLLQQQGLGDDIGRITGFAPKKDRERA  316 (357)
T ss_pred             cceEEEEEe-CC-chhHHHHHHHHHHHHHHHhccCCCeEEEEECCHHHHHHHHHHHhhhCCCceEEeeecCCCHHHHHHh
Confidence            357776655 33 34777666665543210  1356799999999999999999998754 2578899999999988643


Q ss_pred             HHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhcccc
Q 028124           97 LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL  173 (213)
Q Consensus        97 l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~  173 (213)
                            +                       +.++||||++    ++||+|++.+ +|| ++ |.+.++|+||+||+|
T Consensus       317 ------~-----------------------~~~iLVaTdv----~~rGiDi~~~-~vi-~~-p~~~~~yiqR~GR~g  357 (357)
T TIGR03158       317 ------M-----------------------QFDILLGTST----VDVGVDFKRD-WLI-FS-ARDAAAFWQRLGRLG  357 (357)
T ss_pred             ------c-----------------------cCCEEEEecH----HhcccCCCCc-eEE-EC-CCCHHHHhhhcccCC
Confidence                  2                       2789999999    9999999986 666 56 899999999999974

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.

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.66  E-value=1.1e-15  Score=142.57  Aligned_cols=120  Identities=12%  Similarity=0.105  Sum_probs=100.7

Q ss_pred             hHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccc
Q 028124           34 FKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE  113 (213)
Q Consensus        34 ~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~  113 (213)
                      .|.+.+.+++..+.   ..+.+++|||++.++++.|++.|.+.+ +.+..+||+|+.++|..+++.|+.|.         
T Consensus       328 ~Rn~~I~~~~~~~~---~~~~~~lV~~~~~~h~~~L~~~L~~~g-~~v~~i~G~~~~~eR~~i~~~~~~~~---------  394 (501)
T PHA02558        328 KRNKWIANLALKLA---KKGENTFVMFKYVEHGKPLYEMLKKVY-DKVYYVSGEVDTEDRNEMKKIAEGGK---------  394 (501)
T ss_pred             HHHHHHHHHHHHHH---hcCCCEEEEEEEHHHHHHHHHHHHHcC-CCEEEEeCCCCHHHHHHHHHHHhCCC---------
Confidence            36666676665533   245788888899999999999999987 79999999999999999999999874         


Q ss_pred             cCCCCCcCCCCCCceeEEEEe-CCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccccCCC-----CeEEEEEe
Q 028124          114 QSGDESETGKDEHKSHMIVVT-DACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAAD-----GSVINIVV  184 (213)
Q Consensus       114 ~~~~~~~~~~~~~~~~iLV~T-d~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~~~~-----g~~i~~~~  184 (213)
                                    ..+|||| ++    +++|+|+|++++||++++|.+...|+||+||+++..     ..++.|+.
T Consensus       395 --------------~~vLvaT~~~----l~eG~Dip~ld~vIl~~p~~s~~~~~QriGR~~R~~~~K~~~~i~D~vD  453 (501)
T PHA02558        395 --------------GIIIVASYGV----FSTGISIKNLHHVIFAHPSKSKIIVLQSIGRVLRKHGSKSIATVWDIID  453 (501)
T ss_pred             --------------CeEEEEEcce----eccccccccccEEEEecCCcchhhhhhhhhccccCCCCCceEEEEEeec
Confidence                          7899998 89    999999999999999999999999999999974321     35555664

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.66  E-value=1.4e-15  Score=146.95  Aligned_cols=124  Identities=13%  Similarity=0.141  Sum_probs=109.4

Q ss_pred             cchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccc
Q 028124           32 LQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKV  111 (213)
Q Consensus        32 ~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~  111 (213)
                      ...|+..+.+.+....   ..+.|+||||+|+..++.|+..|.+.+ +....+|+++...++..+.+.++.|        
T Consensus       422 ~~~K~~al~~~i~~~~---~~g~pvLI~t~si~~se~ls~~L~~~g-i~~~~Lna~~~~~Ea~ii~~ag~~g--------  489 (796)
T PRK12906        422 LDSKFNAVVKEIKERH---AKGQPVLVGTVAIESSERLSHLLDEAG-IPHAVLNAKNHAKEAEIIMNAGQRG--------  489 (796)
T ss_pred             HHHHHHHHHHHHHHHH---hCCCCEEEEeCcHHHHHHHHHHHHHCC-CCeeEecCCcHHHHHHHHHhcCCCc--------
Confidence            3459999999886532   468999999999999999999999997 8999999999988888888888775        


Q ss_pred             cccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCC---CCCC-----EEEEecCCCChHHHHHhhccc--cCCCCeEEE
Q 028124          112 TEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESA---ISAR-----VLINYELPTKKETYIRRMTTC--LAADGSVIN  181 (213)
Q Consensus       112 ~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~---~~v~-----~VI~yd~P~~~~~yi~R~GR~--~~~~g~~i~  181 (213)
                                       .|+|||++    ++||+|+   ++|.     +||+++.|.+...|.||.||+  .|.+|.++.
T Consensus       490 -----------------~VtIATnm----AGRGtDI~l~~~V~~~GGLhVI~te~pes~ri~~Ql~GRtGRqG~~G~s~~  548 (796)
T PRK12906        490 -----------------AVTIATNM----AGRGTDIKLGPGVKELGGLAVIGTERHESRRIDNQLRGRSGRQGDPGSSRF  548 (796)
T ss_pred             -----------------eEEEEecc----ccCCCCCCCCcchhhhCCcEEEeeecCCcHHHHHHHhhhhccCCCCcceEE
Confidence                             39999999    9999999   4899     999999999999999999997  577899999


Q ss_pred             EEeCchh
Q 028124          182 IVVGGEV  188 (213)
Q Consensus       182 ~~~~~e~  188 (213)
                      |++.+|.
T Consensus       549 ~~sleD~  555 (796)
T PRK12906        549 YLSLEDD  555 (796)
T ss_pred             EEeccch
Confidence            9987654

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.66  E-value=1.9e-15  Score=145.34  Aligned_cols=120  Identities=18%  Similarity=0.183  Sum_probs=100.0

Q ss_pred             hHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccc
Q 028124           34 FKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE  113 (213)
Q Consensus        34 ~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~  113 (213)
                      .|++.+..+++..   +..+.++||||++...++.++..|.      +..+||++++.+|.+++++|+++.         
T Consensus       480 ~K~~~~~~Li~~h---e~~g~kiLVF~~~~~~l~~~a~~L~------~~~I~G~ts~~ER~~il~~Fr~~~---------  541 (732)
T TIGR00603       480 NKFRACQFLIRFH---EQRGDKIIVFSDNVFALKEYAIKLG------KPFIYGPTSQQERMQILQNFQHNP---------  541 (732)
T ss_pred             HHHHHHHHHHHHH---hhcCCeEEEEeCCHHHHHHHHHHcC------CceEECCCCHHHHHHHHHHHHhCC---------
Confidence            3888888888752   1367899999999999999999882      345899999999999999999752         


Q ss_pred             cCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCC-CChHHHHHhhccccC--CCC-------eEEEEE
Q 028124          114 QSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELP-TKKETYIRRMTTCLA--ADG-------SVINIV  183 (213)
Q Consensus       114 ~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P-~~~~~yi~R~GR~~~--~~g-------~~i~~~  183 (213)
                                   .+++||+|++    +.+|+|+|++++||+++.| .+...|+||+||.++  ..|       ..|+|+
T Consensus       542 -------------~i~vLv~SkV----gdeGIDlP~a~vvI~~s~~~gS~~q~iQRlGRilR~~~~~~~~~~~A~fY~lV  604 (732)
T TIGR00603       542 -------------KVNTIFLSKV----GDTSIDLPEANVLIQISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLV  604 (732)
T ss_pred             -------------CccEEEEecc----cccccCCCCCCEEEEeCCCCCCHHHHHHHhcccccCCCCCccccccceEEEEe
Confidence                         4899999999    9999999999999999998 499999999999632  223       448899


Q ss_pred             eCchh
Q 028124          184 VGGEV  188 (213)
Q Consensus       184 ~~~e~  188 (213)
                      +.+..
T Consensus       605 s~dT~  609 (732)
T TIGR00603       605 SKDTQ  609 (732)
T ss_pred             cCCch
Confidence            87633

All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.64  E-value=2.2e-15  Score=151.48  Aligned_cols=137  Identities=12%  Similarity=0.232  Sum_probs=106.2

Q ss_pred             CceEEEEEecCcc-----hHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccC--CceEEEecCCCCHHHH
Q 028124           21 QPRHFYVAVDRLQ-----FKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLA--DISFSSLHSDLAETER   93 (213)
Q Consensus        21 ~i~~~~~~~~~~~-----~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~--~~~~~~lhg~~~~~~R   93 (213)
                      .+.++|..+....     +++..+.+.+..+..  ...+++||||++..+++.+++.|.+.+  ...+..+||+|++++|
T Consensus       251 pVei~y~p~~~~~~~~~~d~l~~ll~~V~~l~~--~~~GdILVFLpg~~EIe~lae~L~~~~~~~~~VlpLhg~Ls~~eQ  328 (1294)
T PRK11131        251 PVEVRYRPIVEEADDTERDQLQAIFDAVDELGR--EGPGDILIFMSGEREIRDTADALNKLNLRHTEILPLYARLSNSEQ  328 (1294)
T ss_pred             cceEEEeecccccchhhHHHHHHHHHHHHHHhc--CCCCCEEEEcCCHHHHHHHHHHHHhcCCCcceEeecccCCCHHHH
Confidence            4778887764322     234444444333222  356789999999999999999998764  2347889999999999


Q ss_pred             HHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEec---------------C
Q 028124           94 TLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYE---------------L  158 (213)
Q Consensus        94 ~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd---------------~  158 (213)
                      ..+++.  .|                       +.+|||||++    +++|+|+|++++|||++               +
T Consensus       329 ~~Vf~~--~g-----------------------~rkIIVATNI----AEtSITIpgI~yVID~Gl~k~~~Yd~~~~~~~L  379 (1294)
T PRK11131        329 NRVFQS--HS-----------------------GRRIVLATNV----AETSLTVPGIKYVIDPGTARISRYSYRTKVQRL  379 (1294)
T ss_pred             HHHhcc--cC-----------------------CeeEEEeccH----HhhccccCcceEEEECCCccccccccccCcccC
Confidence            998875  33                       3899999999    99999999999999985               4


Q ss_pred             CC---ChHHHHHhhccccC-CCCeEEEEEeCchh
Q 028124          159 PT---KKETYIRRMTTCLA-ADGSVINIVVGGEV  188 (213)
Q Consensus       159 P~---~~~~yi~R~GR~~~-~~g~~i~~~~~~e~  188 (213)
                      |.   |.++|.||+||+|+ .+|.||.+++..+.
T Consensus       380 p~~~iSkasa~QRaGRAGR~~~G~c~rLyte~d~  413 (1294)
T PRK11131        380 PIEPISQASANQRKGRCGRVSEGICIRLYSEDDF  413 (1294)
T ss_pred             CeeecCHhhHhhhccccCCCCCcEEEEeCCHHHH
Confidence            43   55899999999865 46999999997654

>PRK09401 reverse gyrase; Reviewed

Probab=99.64  E-value=1e-15  Score=154.15  Aligned_cols=114  Identities=18%  Similarity=0.209  Sum_probs=99.2

Q ss_pred             CCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHH---HHHHHHHHhccCCceEEEecCCCCHHHHH
Q 028124           18 HFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDE---LDAVCSAVSNLADISFSSLHSDLAETERT   94 (213)
Q Consensus        18 ~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~---~~~l~~~L~~~~~~~~~~lhg~~~~~~R~   94 (213)
                      ...+|.|.|+.++  + |.+.|.++++.+      +.++||||+++..   |+++++.|...| +++..+||+|     .
T Consensus       302 ~~rnI~~~yi~~~--~-k~~~L~~ll~~l------~~~~LIFv~t~~~~~~ae~l~~~L~~~g-i~v~~~hg~l-----~  366 (1176)
T PRK09401        302 YLRNIVDSYIVDE--D-SVEKLVELVKRL------GDGGLIFVPSDKGKEYAEELAEYLEDLG-INAELAISGF-----E  366 (1176)
T ss_pred             ccCCceEEEEEcc--c-HHHHHHHHHHhc------CCCEEEEEecccChHHHHHHHHHHHHCC-CcEEEEeCcH-----H
Confidence            4568999998776  3 888888888762      3589999999888   999999999998 8999999999     2


Q ss_pred             HHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEE----eCCCCCcCcCCCCCCC-CCEEEEecCCC------ChH
Q 028124           95 LILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVV----TDACLPLLSSGESAIS-ARVLINYELPT------KKE  163 (213)
Q Consensus        95 ~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~----Td~~~~~~~rGld~~~-v~~VI~yd~P~------~~~  163 (213)
                      +.+++|++|+                       +++||+    ||+    ++||+|+|+ +++|||||+|.      ..+
T Consensus       367 ~~l~~F~~G~-----------------------~~VLVatas~tdv----~aRGIDiP~~IryVI~y~vP~~~~~~~~~~  419 (1176)
T PRK09401        367 RKFEKFEEGE-----------------------VDVLVGVASYYGV----LVRGIDLPERIRYAIFYGVPKFKFSLEEEL  419 (1176)
T ss_pred             HHHHHHHCCC-----------------------CCEEEEecCCCCc----eeecCCCCcceeEEEEeCCCCEEEeccccc
Confidence            3459999995                       999999    689    999999999 89999999998      678


Q ss_pred             HHHHhhcccc
Q 028124          164 TYIRRMTTCL  173 (213)
Q Consensus       164 ~yi~R~GR~~  173 (213)
                      .|.||+||..
T Consensus       420 ~~~~~~~r~~  429 (1176)
T PRK09401        420 APPFLLLRLL  429 (1176)
T ss_pred             cCHHHHHHHH
Confidence            9999999963

>PRK00254 ski2-like helicase; Provisional

Probab=99.62  E-value=4.5e-15  Score=143.77  Aligned_cols=108  Identities=22%  Similarity=0.244  Sum_probs=91.3

Q ss_pred             CCCcEEEEeCchHHHHHHHHHHhcc---------------------------------CCceEEEecCCCCHHHHHHHHH
Q 028124           52 PGLPMIVCCSSRDELDAVCSAVSNL---------------------------------ADISFSSLHSDLAETERTLILE   98 (213)
Q Consensus        52 ~~~~~IIF~~~~~~~~~l~~~L~~~---------------------------------~~~~~~~lhg~~~~~~R~~~l~   98 (213)
                      .++++||||+|++.|+.++..|...                                 . ..+..+||+|++++|..+.+
T Consensus       237 ~~~~vLVF~~sr~~~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~-~gv~~hHagl~~~eR~~ve~  315 (720)
T PRK00254        237 KGKGALVFVNTRRSAEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLKKALR-GGVAFHHAGLGRTERVLIED  315 (720)
T ss_pred             hCCCEEEEEcChHHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHhcCCCcHHHHHHHh-hCEEEeCCCCCHHHHHHHHH
Confidence            3679999999999999887766421                                 1 24889999999999999999


Q ss_pred             HHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEE-------ecCCC-ChHHHHHhhc
Q 028124           99 EFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLIN-------YELPT-KKETYIRRMT  170 (213)
Q Consensus        99 ~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~-------yd~P~-~~~~yi~R~G  170 (213)
                      .|++|.                       +++||||+.    +++|+|+|.+++||.       |+.|. ...+|.||+|
T Consensus       316 ~F~~G~-----------------------i~VLvaT~t----La~Gvnipa~~vVI~~~~~~~~~~~~~~~~~~~~Qm~G  368 (720)
T PRK00254        316 AFREGL-----------------------IKVITATPT----LSAGINLPAFRVIIRDTKRYSNFGWEDIPVLEIQQMMG  368 (720)
T ss_pred             HHHCCC-----------------------CeEEEeCcH----HhhhcCCCceEEEECCceEcCCCCceeCCHHHHHHhhh
Confidence            999985                       999999999    999999999999994       66555 4679999999


Q ss_pred             cccC----CCCeEEEEEeCch
Q 028124          171 TCLA----ADGSVINIVVGGE  187 (213)
Q Consensus       171 R~~~----~~g~~i~~~~~~e  187 (213)
                      |+|+    ..|.++.++...+
T Consensus       369 RAGR~~~d~~G~~ii~~~~~~  389 (720)
T PRK00254        369 RAGRPKYDEVGEAIIVATTEE  389 (720)
T ss_pred             ccCCCCcCCCceEEEEecCcc
Confidence            9865    3599999997654

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

Probab=99.60  E-value=8.5e-15  Score=141.79  Aligned_cols=94  Identities=14%  Similarity=0.205  Sum_probs=89.3

Q ss_pred             CCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEE
Q 028124           53 GLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIV  132 (213)
Q Consensus        53 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV  132 (213)
                      ...++||+||+.+++.++..|++.+...+...||.++.+.|..+-++|++|+                       .+++|
T Consensus       253 ~~ttLIF~NTR~~aE~l~~~L~~~~~~~i~~HHgSlSre~R~~vE~~lk~G~-----------------------lravV  309 (814)
T COG1201         253 HRTTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGE-----------------------LKAVV  309 (814)
T ss_pred             cCcEEEEEeChHHHHHHHHHHHHhcCCceeeecccccHHHHHHHHHHHhcCC-----------------------ceEEE
Confidence            4689999999999999999999886578999999999999999999999995                       99999


Q ss_pred             EeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhcccc
Q 028124          133 VTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL  173 (213)
Q Consensus       133 ~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~  173 (213)
                      ||..    ++-|||+.+++.||+|.-|.+....+||+||+|
T Consensus       310 ~TSS----LELGIDiG~vdlVIq~~SP~sV~r~lQRiGRsg  346 (814)
T COG1201         310 ATSS----LELGIDIGDIDLVIQLGSPKSVNRFLQRIGRAG  346 (814)
T ss_pred             Eccc----hhhccccCCceEEEEeCCcHHHHHHhHhccccc
Confidence            9999    999999999999999999999999999999974

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=99.60  E-value=9.6e-15  Score=142.69  Aligned_cols=127  Identities=12%  Similarity=0.138  Sum_probs=110.1

Q ss_pred             cCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccc
Q 028124           30 DRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQ  109 (213)
Q Consensus        30 ~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~  109 (213)
                      .....|+..|.+.+....   ..+.++||||+|+..++.|+..|...+ +.+..||+  .+.+|...+..|+.+.     
T Consensus       578 ~t~~eK~~Ali~~I~~~~---~~grpVLIft~Sve~sE~Ls~~L~~~g-I~h~vLna--kq~~REa~Iia~AG~~-----  646 (1025)
T PRK12900        578 KTRREKYNAIVLKVEELQ---KKGQPVLVGTASVEVSETLSRMLRAKR-IAHNVLNA--KQHDREAEIVAEAGQK-----  646 (1025)
T ss_pred             cCHHHHHHHHHHHHHHHh---hCCCCEEEEeCcHHHHHHHHHHHHHcC-CCceeecC--CHHHhHHHHHHhcCCC-----
Confidence            334449999999997632   367999999999999999999999997 89999997  5789999999999984     


Q ss_pred             cccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCC---CCC-----EEEEecCCCChHHHHHhhccc--cCCCCeE
Q 028124          110 KVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAI---SAR-----VLINYELPTKKETYIRRMTTC--LAADGSV  179 (213)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~---~v~-----~VI~yd~P~~~~~yi~R~GR~--~~~~g~~  179 (213)
                                        ..|+|||++    ++||+|++   +|.     +||+++.|.+...|.||.||+  .|.+|.+
T Consensus       647 ------------------g~VtIATNM----AGRGtDIkl~~~V~~vGGL~VIgterhes~Rid~Ql~GRtGRqGdpGsS  704 (1025)
T PRK12900        647 ------------------GAVTIATNM----AGRGTDIKLGEGVRELGGLFILGSERHESRRIDRQLRGRAGRQGDPGES  704 (1025)
T ss_pred             ------------------CeEEEeccC----cCCCCCcCCccchhhhCCceeeCCCCCchHHHHHHHhhhhhcCCCCcce
Confidence                              899999999    99999999   554     349999999999999999997  5778999


Q ss_pred             EEEEeCchhH
Q 028124          180 INIVVGGEVV  189 (213)
Q Consensus       180 i~~~~~~e~~  189 (213)
                      +.|++.+|.-
T Consensus       705 ~ffvSleD~L  714 (1025)
T PRK12900        705 VFYVSLEDEL  714 (1025)
T ss_pred             EEEechhHHH
Confidence            9999986653

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.59  E-value=1e-14  Score=146.88  Aligned_cols=138  Identities=9%  Similarity=0.145  Sum_probs=107.2

Q ss_pred             CceEEEEEecCc-----chHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccC--CceEEEecCCCCHHHH
Q 028124           21 QPRHFYVAVDRL-----QFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLA--DISFSSLHSDLAETER   93 (213)
Q Consensus        21 ~i~~~~~~~~~~-----~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~--~~~~~~lhg~~~~~~R   93 (213)
                      .+..+|......     .++.+.+.+.+..+..  ...+.+|||+++..+++.+++.|.+.+  ++.+..+||+|++++|
T Consensus       244 PVev~Y~~~~~~~~~~~~~~~~~i~~~I~~l~~--~~~GdILVFLpg~~EI~~l~~~L~~~~~~~~~VlpLhg~Ls~~eQ  321 (1283)
T TIGR01967       244 PVEVRYRPLVEEQEDDDLDQLEAILDAVDELFA--EGPGDILIFLPGEREIRDAAEILRKRNLRHTEILPLYARLSNKEQ  321 (1283)
T ss_pred             cceeEEecccccccchhhhHHHHHHHHHHHHHh--hCCCCEEEeCCCHHHHHHHHHHHHhcCCCCcEEEeccCCCCHHHH
Confidence            466666654321     1355666666655433  245799999999999999999998653  3678999999999999


Q ss_pred             HHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCC-------------
Q 028124           94 TLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPT-------------  160 (213)
Q Consensus        94 ~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~-------------  160 (213)
                      .++++.   +.                      ..+|+|||++    +++|+|+|++++||++++++             
T Consensus       322 ~~vf~~---~~----------------------~rkIVLATNI----AEtSLTIpgV~yVIDsGl~r~~~yd~~~~~~~L  372 (1283)
T TIGR01967       322 QRVFQP---HS----------------------GRRIVLATNV----AETSLTVPGIHYVIDTGTARISRYSYRTKVQRL  372 (1283)
T ss_pred             HHHhCC---CC----------------------CceEEEeccH----HHhccccCCeeEEEeCCCccccccccccCcccc
Confidence            988543   31                      3789999999    99999999999999998654             


Q ss_pred             -----ChHHHHHhhccccCC-CCeEEEEEeCchhH
Q 028124          161 -----KKETYIRRMTTCLAA-DGSVINIVVGGEVV  189 (213)
Q Consensus       161 -----~~~~yi~R~GR~~~~-~g~~i~~~~~~e~~  189 (213)
                           |.++|.||+||+|+. +|.||.+++..+..
T Consensus       373 ~~~~ISkasa~QRaGRAGR~~~G~cyRLyte~~~~  407 (1283)
T TIGR01967       373 PIEPISQASANQRKGRCGRVAPGICIRLYSEEDFN  407 (1283)
T ss_pred             CCccCCHHHHHHHhhhhCCCCCceEEEecCHHHHH
Confidence                 558999999998654 69999999876543

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.

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=99.59  E-value=7.9e-15  Score=102.10  Aligned_cols=79  Identities=28%  Similarity=0.460  Sum_probs=73.0

Q ss_pred             HHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCC
Q 028124           68 AVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESA  147 (213)
Q Consensus        68 ~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~  147 (213)
                      .+++.|...+ +.+..+||++++++|..+++.|+.+.                       ..+||+|++    +++|+|+
T Consensus         2 ~l~~~l~~~~-~~~~~~~~~~~~~~r~~~~~~f~~~~-----------------------~~vli~t~~----~~~Gi~~   53 (82)
T smart00490        2 ELAELLKELG-IKVARLHGGLSQEEREEILEKFNNGK-----------------------IKVLVATDV----AERGLDL   53 (82)
T ss_pred             HHHHHHHHCC-CeEEEEECCCCHHHHHHHHHHHHcCC-----------------------CeEEEECCh----hhCCcCh
Confidence            4677787776 79999999999999999999999984                       799999999    9999999


Q ss_pred             CCCCEEEEecCCCChHHHHHhhccccC
Q 028124          148 ISARVLINYELPTKKETYIRRMTTCLA  174 (213)
Q Consensus       148 ~~v~~VI~yd~P~~~~~yi~R~GR~~~  174 (213)
                      +++++||.+++|++...|.|++||+++
T Consensus        54 ~~~~~vi~~~~~~~~~~~~Q~~gR~~R   80 (82)
T smart00490       54 PGVDLVIIYDLPWSPASYIQRIGRAGR   80 (82)
T ss_pred             hcCCEEEEeCCCCCHHHHHHhhccccc
Confidence            999999999999999999999999754

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

Probab=99.55  E-value=1.6e-15  Score=128.94  Aligned_cols=123  Identities=20%  Similarity=0.425  Sum_probs=104.9

Q ss_pred             CCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHH
Q 028124           17 SHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI   96 (213)
Q Consensus        17 ~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~   96 (213)
                      -+..+++|+|+...+.+ |...|.+||..+     .+.+++||+.+..+       |                       
T Consensus       253 LtLHGLqQ~YvkLke~e-KNrkl~dLLd~L-----eFNQVvIFvKsv~R-------l-----------------------  296 (387)
T KOG0329|consen  253 LTLHGLQQYYVKLKENE-KNRKLNDLLDVL-----EFNQVVIFVKSVQR-------L-----------------------  296 (387)
T ss_pred             hhhhhHHHHHHhhhhhh-hhhhhhhhhhhh-----hhcceeEeeehhhh-------h-----------------------
Confidence            34578999999999887 999999999884     45899999987765       1                       


Q ss_pred             HHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cC
Q 028124           97 LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LA  174 (213)
Q Consensus        97 l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~  174 (213)
                       . |.                          .+ +|+|++    ++||+|+..++.|+|||+|.+.++|+||+||+  .|
T Consensus       297 -~-f~--------------------------kr-~vat~l----fgrgmdiervNi~~NYdmp~~~DtYlHrv~rAgrfG  343 (387)
T KOG0329|consen  297 -S-FQ--------------------------KR-LVATDL----FGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG  343 (387)
T ss_pred             -h-hh--------------------------hh-hHHhhh----hccccCcccceeeeccCCCCCchHHHHHhhhhhccc
Confidence             0 31                          33 899999    99999999999999999999999999999997  57


Q ss_pred             CCCeEEEEEeC-chhHHHHHHHHHhcccccccCcc
Q 028124          175 ADGSVINIVVG-GEVVTLRSMEESLGLIVAEVPIN  208 (213)
Q Consensus       175 ~~g~~i~~~~~-~e~~~~~~le~~l~~~~~~~~~~  208 (213)
                      ..|.+|+|+.. ++...+..+...+...+.++|-.
T Consensus       344 tkglaitfvs~e~da~iLn~vqdRf~v~i~eLpde  378 (387)
T KOG0329|consen  344 TKGLAITFVSDENDAKILNPVQDRFEVNIKELPDE  378 (387)
T ss_pred             cccceeehhcchhhHHHhchhhHhhhccHhhcCcc
Confidence            88999999975 57788899999888888888854

>PRK14701 reverse gyrase; Provisional

Probab=99.54  E-value=1.9e-14  Score=148.42  Aligned_cols=112  Identities=13%  Similarity=0.181  Sum_probs=94.7

Q ss_pred             CCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHH---HHHHHHHHhccCCceEEEecCCCCHHHH
Q 028124           17 SHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDE---LDAVCSAVSNLADISFSSLHSDLAETER   93 (213)
Q Consensus        17 ~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~---~~~l~~~L~~~~~~~~~~lhg~~~~~~R   93 (213)
                      .+..++.|.|+.++... | ..|.++++.+      +.+.||||++++.   |+++++.|...| +++..+||+     |
T Consensus       302 ~~lr~i~~~yi~~~~~~-k-~~L~~ll~~~------g~~gIVF~~t~~~~e~ae~la~~L~~~G-i~a~~~h~~-----R  367 (1638)
T PRK14701        302 SALRNIVDVYLNPEKII-K-EHVRELLKKL------GKGGLIFVPIDEGAEKAEEIEKYLLEDG-FKIELVSAK-----N  367 (1638)
T ss_pred             CCCCCcEEEEEECCHHH-H-HHHHHHHHhC------CCCeEEEEeccccchHHHHHHHHHHHCC-CeEEEecch-----H
Confidence            34568999998876554 5 5677777762      4689999999886   589999999998 899999995     8


Q ss_pred             HHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeC----CCCCcCcCCCCCCC-CCEEEEecCCC---ChHHH
Q 028124           94 TLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTD----ACLPLLSSGESAIS-ARVLINYELPT---KKETY  165 (213)
Q Consensus        94 ~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td----~~~~~~~rGld~~~-v~~VI~yd~P~---~~~~y  165 (213)
                      ..++++|++|+                       +++||+|+    +    ++||||+|+ |++|||||+|.   +.+.|
T Consensus       368 ~~~l~~F~~G~-----------------------~~VLVaT~s~~gv----aaRGIDiP~~Vryvi~~~~Pk~~~~~e~~  420 (1638)
T PRK14701        368 KKGFDLFEEGE-----------------------IDYLIGVATYYGT----LVRGLDLPERIRFAVFYGVPKFRFRVDLE  420 (1638)
T ss_pred             HHHHHHHHcCC-----------------------CCEEEEecCCCCe----eEecCccCCccCEEEEeCCCCCCcchhhc
Confidence            89999999995                       99999994    7    899999999 99999999999   88877


Q ss_pred             HHhh
Q 028124          166 IRRM  169 (213)
Q Consensus       166 i~R~  169 (213)
                      .|..
T Consensus       421 ~~~~  424 (1638)
T PRK14701        421 DPTI  424 (1638)
T ss_pred             ccch
Confidence            7765

>PRK01172 ski2-like helicase; Provisional

Probab=99.54  E-value=9.2e-14  Score=133.71  Aligned_cols=107  Identities=19%  Similarity=0.186  Sum_probs=87.2

Q ss_pred             CCCcEEEEeCchHHHHHHHHHHhccC----C--------------------ceEEEecCCCCHHHHHHHHHHHhcccccc
Q 028124           52 PGLPMIVCCSSRDELDAVCSAVSNLA----D--------------------ISFSSLHSDLAETERTLILEEFRHTAMKW  107 (213)
Q Consensus        52 ~~~~~IIF~~~~~~~~~l~~~L~~~~----~--------------------~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~  107 (213)
                      .++++||||++++.++.++..|....    .                    ..+..+||+|++++|..+.+.|++|.   
T Consensus       235 ~~~~vLVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~~hagl~~~eR~~ve~~f~~g~---  311 (674)
T PRK01172        235 DGGQVLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQRRFIEEMFRNRY---  311 (674)
T ss_pred             CCCcEEEEeccHHHHHHHHHHHHHhhhhcccccccccccccccHHHHHHHhcCEEEecCCCCHHHHHHHHHHHHcCC---
Confidence            46899999999999999998886530    0                    13678999999999999999999985   


Q ss_pred             cccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecC---------CCChHHHHHhhccccCC---
Q 028124          108 NQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYEL---------PTKKETYIRRMTTCLAA---  175 (213)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~---------P~~~~~yi~R~GR~~~~---  175 (213)
                                          +++||||++    +++|+|+|+. .||++|.         |-+..+|.||+||+|+.   
T Consensus       312 --------------------i~VLvaT~~----la~Gvnipa~-~VII~~~~~~~~~~~~~~s~~~~~Qm~GRAGR~g~d  366 (674)
T PRK01172        312 --------------------IKVIVATPT----LAAGVNLPAR-LVIVRDITRYGNGGIRYLSNMEIKQMIGRAGRPGYD  366 (674)
T ss_pred             --------------------CeEEEecch----hhccCCCcce-EEEEcCceEeCCCCceeCCHHHHHHHhhcCCCCCCC
Confidence                                999999999    9999999986 4555554         44788999999998653   


Q ss_pred             -CCeEEEEEeCc
Q 028124          176 -DGSVINIVVGG  186 (213)
Q Consensus       176 -~g~~i~~~~~~  186 (213)
                       .|.++.++...
T Consensus       367 ~~g~~~i~~~~~  378 (674)
T PRK01172        367 QYGIGYIYAASP  378 (674)
T ss_pred             CcceEEEEecCc
Confidence             47777776543

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

Probab=99.53  E-value=2.5e-14  Score=132.41  Aligned_cols=140  Identities=16%  Similarity=0.157  Sum_probs=116.5

Q ss_pred             CCCCceEEEEEecCcchHHHHHHHHHHHhhcC---CCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHH
Q 028124           18 HFSQPRHFYVAVDRLQFKMETLVELLHLVVAG---RRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERT   94 (213)
Q Consensus        18 ~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~---~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~   94 (213)
                      .|-.+..+.+.+.++..|++.+..+.+.-...   .--.+|+|||++++..|++|+..|..+| +++..+|++|+..+|.
T Consensus       402 RPVplErHlvf~~~e~eK~~ii~~L~k~E~~~~sskg~rGQtIVFT~SRrr~h~lA~~L~~kG-~~a~pYHaGL~y~eRk  480 (830)
T COG1202         402 RPVPLERHLVFARNESEKWDIIARLVKREFSTESSKGYRGQTIVFTYSRRRCHELADALTGKG-LKAAPYHAGLPYKERK  480 (830)
T ss_pred             CCCChhHeeeeecCchHHHHHHHHHHHHHHhhhhccCcCCceEEEecchhhHHHHHHHhhcCC-cccccccCCCcHHHHH
Confidence            34457778889998888999999999752221   1123899999999999999999999998 9999999999999999


Q ss_pred             HHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEE----ecCCC-ChHHHHHhh
Q 028124           95 LILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLIN----YELPT-KKETYIRRM  169 (213)
Q Consensus        95 ~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~----yd~P~-~~~~yi~R~  169 (213)
                      .+-.+|.+++                       +.++|+|.+    ++-|+|||.-. ||.    ...-| ++..|.|+.
T Consensus       481 ~vE~~F~~q~-----------------------l~~VVTTAA----L~AGVDFPASQ-VIFEsLaMG~~WLs~~EF~QM~  532 (830)
T COG1202         481 SVERAFAAQE-----------------------LAAVVTTAA----LAAGVDFPASQ-VIFESLAMGIEWLSVREFQQML  532 (830)
T ss_pred             HHHHHHhcCC-----------------------cceEeehhh----hhcCCCCchHH-HHHHHHHcccccCCHHHHHHHh
Confidence            9999999986                       999999999    99999999654 443    33445 789999999


Q ss_pred             ccccCC----CCeEEEEEeCc
Q 028124          170 TTCLAA----DGSVINIVVGG  186 (213)
Q Consensus       170 GR~~~~----~g~~i~~~~~~  186 (213)
                      ||+|+.    .|.++.++.++
T Consensus       533 GRAGRp~yHdrGkVyllvepg  553 (830)
T COG1202         533 GRAGRPDYHDRGKVYLLVEPG  553 (830)
T ss_pred             cccCCCCcccCceEEEEecCC
Confidence            998654    39999999764

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=99.52  E-value=2.3e-13  Score=135.24  Aligned_cols=138  Identities=14%  Similarity=0.153  Sum_probs=115.8

Q ss_pred             hHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccc
Q 028124           34 FKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE  113 (213)
Q Consensus        34 ~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~  113 (213)
                      .|+.+|.++|..+.   ..+.++|||+......+.|.+.|...+ +....+||+++..+|..++++|....         
T Consensus       471 gKl~lLdkLL~~Lk---~~g~KVLIFSQft~~LdiLed~L~~~g-~~y~rIdGsts~~eRq~~Id~Fn~~~---------  537 (1033)
T PLN03142        471 GKMVLLDKLLPKLK---ERDSRVLIFSQMTRLLDILEDYLMYRG-YQYCRIDGNTGGEDRDASIDAFNKPG---------  537 (1033)
T ss_pred             hHHHHHHHHHHHHH---hcCCeEEeehhHHHHHHHHHHHHHHcC-CcEEEECCCCCHHHHHHHHHHhcccc---------
Confidence            49999999998754   367899999999999999999999887 79999999999999999999997642         


Q ss_pred             cCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCCC--CeEEEEEeCc--h
Q 028124          114 QSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAAD--GSVINIVVGG--E  187 (213)
Q Consensus       114 ~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~~--g~~i~~~~~~--e  187 (213)
                                 +...-+|++|.+    .+.|+|++.+++||+||+||++..+.|++||+  -|+.  -.++.|++.+  |
T Consensus       538 -----------s~~~VfLLSTrA----GGlGINLt~Ad~VIiyD~dWNP~~d~QAidRaHRIGQkk~V~VyRLIt~gTIE  602 (1033)
T PLN03142        538 -----------SEKFVFLLSTRA----GGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIE  602 (1033)
T ss_pred             -----------CCceEEEEeccc----cccCCchhhCCEEEEeCCCCChHHHHHHHHHhhhcCCCceEEEEEEEeCCcHH
Confidence                       113568999999    99999999999999999999999999999996  3444  4677888876  5


Q ss_pred             hHHHHHHHHHhc
Q 028124          188 VVTLRSMEESLG  199 (213)
Q Consensus       188 ~~~~~~le~~l~  199 (213)
                      ...+....+.++
T Consensus       603 EkIlera~~Kl~  614 (1033)
T PLN03142        603 EKVIERAYKKLA  614 (1033)
T ss_pred             HHHHHHHHHHHH
Confidence            556655555553

>TIGR01054 rgy reverse gyrase

Probab=99.48  E-value=3e-13  Score=136.60  Aligned_cols=103  Identities=17%  Similarity=0.233  Sum_probs=87.5

Q ss_pred             CCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCch---HHHHHHHHHHhccCCceEEEecCCCCHHHHH
Q 028124           18 HFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSR---DELDAVCSAVSNLADISFSSLHSDLAETERT   94 (213)
Q Consensus        18 ~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~---~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~   94 (213)
                      ...+|.|.|+..+.   +...|.++++.+      +.++||||+++   +.|++|++.|.+.| +.+..+||++++    
T Consensus       300 ~~r~I~~~~~~~~~---~~~~L~~ll~~l------~~~~IVFv~t~~~~~~a~~l~~~L~~~g-~~a~~lhg~~~~----  365 (1171)
T TIGR01054       300 TLRNVVDVYVEDED---LKETLLEIVKKL------GTGGIVYVSIDYGKEKAEEIAEFLENHG-VKAVAYHATKPK----  365 (1171)
T ss_pred             cccceEEEEEeccc---HHHHHHHHHHHc------CCCEEEEEeccccHHHHHHHHHHHHhCC-ceEEEEeCCCCH----
Confidence            35678898876543   345677777762      36899999999   99999999999987 899999999973    


Q ss_pred             HHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEe----CCCCCcCcCCCCCCC-CCEEEEecCCCC
Q 028124           95 LILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVT----DACLPLLSSGESAIS-ARVLINYELPTK  161 (213)
Q Consensus        95 ~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~T----d~~~~~~~rGld~~~-v~~VI~yd~P~~  161 (213)
                      +++++|++|+                       +++||+|    |+    ++||+|+|+ +++|||||+|..
T Consensus       366 ~~l~~Fr~G~-----------------------~~vLVata~~tdv----~aRGIDip~~V~~vI~~~~P~~  410 (1171)
T TIGR01054       366 EDYEKFAEGE-----------------------IDVLIGVASYYGT----LVRGLDLPERVRYAVFLGVPKF  410 (1171)
T ss_pred             HHHHHHHcCC-----------------------CCEEEEeccccCc----ccccCCCCccccEEEEECCCCE
Confidence            6899999995                       9999994    89    999999999 899999999974

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.

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

Probab=99.48  E-value=9.5e-14  Score=124.99  Aligned_cols=161  Identities=14%  Similarity=0.130  Sum_probs=123.8

Q ss_pred             CCCCCCCCCCCCCCCCceEEEEEecCcchHHHHHHHHHHHhhcC--------CCCCCcEEEEeCchHHHHHHHHHHhccC
Q 028124            6 VESPCPPCQSPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAG--------RRPGLPMIVCCSSRDELDAVCSAVSNLA   77 (213)
Q Consensus         6 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~--------~~~~~~~IIF~~~~~~~~~l~~~L~~~~   77 (213)
                      +..|..+...|.-+.++=.-..+-..-++-+..|.++-..-.+.        +...+-.||||.|+..|+.++-.|...|
T Consensus       200 L~~PVAiFkTP~FR~NLFYD~~~K~~I~D~~~~LaDF~~~~LG~~~~~~~~~K~~~GCGIVYCRTR~~cEq~AI~l~~~G  279 (641)
T KOG0352|consen  200 LRNPVAIFKTPTFRDNLFYDNHMKSFITDCLTVLADFSSSNLGKHEKASQNKKTFTGCGIVYCRTRNECEQVAIMLEIAG  279 (641)
T ss_pred             hcCcHHhccCcchhhhhhHHHHHHHHhhhHhHhHHHHHHHhcCChhhhhcCCCCcCcceEEEeccHHHHHHHHHHhhhcC
Confidence            34556666666666554211111111223556666655432220        1123678999999999999999999998


Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEec
Q 028124           78 DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYE  157 (213)
Q Consensus        78 ~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd  157 (213)
                       +.+..+|.++...||.++-++|.+++                       +.|+++|..    +++|+|-|+|+.|||+|
T Consensus       280 -i~A~AYHAGLK~~ERTeVQe~WM~~~-----------------------~PvI~AT~S----FGMGVDKp~VRFViHW~  331 (641)
T KOG0352|consen  280 -IPAMAYHAGLKKKERTEVQEKWMNNE-----------------------IPVIAATVS----FGMGVDKPDVRFVIHWS  331 (641)
T ss_pred             -cchHHHhcccccchhHHHHHHHhcCC-----------------------CCEEEEEec----cccccCCcceeEEEecC
Confidence             99999999999999999999999985                       999999999    99999999999999999


Q ss_pred             CCCChHHHHHhhccc--cCCCCeEEEEEeCchhHHHHHH
Q 028124          158 LPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLRSM  194 (213)
Q Consensus       158 ~P~~~~~yi~R~GR~--~~~~g~~i~~~~~~e~~~~~~l  194 (213)
                      +|.+.+.|.|..||+  .|.++.|-.++..+|...+..|
T Consensus       332 ~~qn~AgYYQESGRAGRDGk~SyCRLYYsR~D~~~i~FL  370 (641)
T KOG0352|consen  332 PSQNLAGYYQESGRAGRDGKRSYCRLYYSRQDKNALNFL  370 (641)
T ss_pred             chhhhHHHHHhccccccCCCccceeeeecccchHHHHHH
Confidence            999999999999997  4677889888888776655444

>PRK09694 helicase Cas3; Provisional

Probab=99.43  E-value=1.7e-12  Score=127.55  Aligned_cols=107  Identities=14%  Similarity=0.317  Sum_probs=85.4

Q ss_pred             HHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccC--CceEEEecCCCCHHHH----HHHHHHH-hccccccc
Q 028124           36 METLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLA--DISFSSLHSDLAETER----TLILEEF-RHTAMKWN  108 (213)
Q Consensus        36 ~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~--~~~~~~lhg~~~~~~R----~~~l~~F-r~g~~~~~  108 (213)
                      ...+..+++.+    ..+++++|||||++.|+.+++.|++..  +..+..+||.++..+|    .++++.| +++.    
T Consensus       547 ~~~l~~i~~~~----~~g~~vLVf~NTV~~Aq~ly~~L~~~~~~~~~v~llHsrf~~~dR~~~E~~vl~~fgk~g~----  618 (878)
T PRK09694        547 LTLLQRMIAAA----NAGAQVCLICNLVDDAQKLYQRLKELNNTQVDIDLFHARFTLNDRREKEQRVIENFGKNGK----  618 (878)
T ss_pred             HHHHHHHHHHH----hcCCEEEEEECCHHHHHHHHHHHHhhCCCCceEEEEeCCCCHHHHHHHHHHHHHHHHhcCC----
Confidence            34444455442    357899999999999999999998753  2579999999999999    4577888 4442    


Q ss_pred             ccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhcccc
Q 028124          109 QKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL  173 (213)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~  173 (213)
                                      ..+..|||+|++    +++|+|+ +++++|....|  .+.|+||+||++
T Consensus       619 ----------------r~~~~ILVaTQV----iE~GLDI-d~DvlItdlaP--idsLiQRaGR~~  660 (878)
T PRK09694        619 ----------------RNQGRILVATQV----VEQSLDL-DFDWLITQLCP--VDLLFQRLGRLH  660 (878)
T ss_pred             ----------------cCCCeEEEECcc----hhheeec-CCCeEEECCCC--HHHHHHHHhccC
Confidence                            012579999999    9999999 68999999988  789999999974

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

Probab=99.39  E-value=8.2e-12  Score=118.01  Aligned_cols=165  Identities=13%  Similarity=0.214  Sum_probs=121.2

Q ss_pred             CCCCCCCCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchH--------HHHHHHHHHhcc-CCceE
Q 028124           11 PPCQSPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRD--------ELDAVCSAVSNL-ADISF   81 (213)
Q Consensus        11 ~~~~~~~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~--------~~~~l~~~L~~~-~~~~~   81 (213)
                      .+..-|+.+..|..+.+....   +-+++..+-+++    ..+.|+.|.|+-.+        .|+.+++.|++. ++.++
T Consensus       438 ~IdElP~GRkpI~T~~i~~~~---~~~v~e~i~~ei----~~GrQaY~VcPLIeESE~l~l~~a~~~~~~L~~~~~~~~v  510 (677)
T COG1200         438 IIDELPPGRKPITTVVIPHER---RPEVYERIREEI----AKGRQAYVVCPLIEESEKLELQAAEELYEELKSFLPELKV  510 (677)
T ss_pred             hhccCCCCCCceEEEEecccc---HHHHHHHHHHHH----HcCCEEEEEeccccccccchhhhHHHHHHHHHHHccccee
Confidence            344456666778877765433   444444444443    35889999999443        566778888743 55789


Q ss_pred             EEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCC
Q 028124           82 SSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTK  161 (213)
Q Consensus        82 ~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~  161 (213)
                      ..+||.|+..++.+++++|++|+                       .+|||||.+    .+-|+|+|+++++|.+|.-+-
T Consensus       511 gL~HGrm~~~eKd~vM~~Fk~~e-----------------------~~ILVaTTV----IEVGVdVPnATvMVIe~AERF  563 (677)
T COG1200         511 GLVHGRMKPAEKDAVMEAFKEGE-----------------------IDILVATTV----IEVGVDVPNATVMVIENAERF  563 (677)
T ss_pred             EEEecCCChHHHHHHHHHHHcCC-----------------------CcEEEEeeE----EEecccCCCCeEEEEechhhh
Confidence            99999999999999999999986                       999999999    999999999999999997775


Q ss_pred             hHHHHHhh-ccc--cCCCCeEEEEEeCch----hHHHHHHHHHh-cccccccCccc
Q 028124          162 KETYIRRM-TTC--LAADGSVINIVVGGE----VVTLRSMEESL-GLIVAEVPINI  209 (213)
Q Consensus       162 ~~~yi~R~-GR~--~~~~g~~i~~~~~~e----~~~~~~le~~l-~~~~~~~~~~~  209 (213)
                      -=+-+|+. ||.  |+..+.|+.+..+..    ...++-+.+.. |+.++|..+.+
T Consensus       564 GLaQLHQLRGRVGRG~~qSyC~Ll~~~~~~~~a~~RL~im~~t~DGF~IAE~DLkl  619 (677)
T COG1200         564 GLAQLHQLRGRVGRGDLQSYCVLLYKPPLSEVAKQRLKIMRETTDGFVIAEEDLKL  619 (677)
T ss_pred             hHHHHHHhccccCCCCcceEEEEEeCCCCChhHHHHHHHHHhcCCcceehhhhHhc
Confidence            44445544 884  667799999997654    34455554443 67777765544

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

Probab=99.35  E-value=1.2e-11  Score=122.34  Aligned_cols=150  Identities=14%  Similarity=0.178  Sum_probs=125.2

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc-CCc
Q 028124            1 MAIDGVESPCPPCQSPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL-ADI   79 (213)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~-~~~   79 (213)
                      ||+-|++..+.+..+|..+-.|+.++...+..--|-.+++++.        .++|+..-+|..++.+.++..|+.. ++.
T Consensus       759 Msm~GiRdlSvI~TPP~~R~pV~T~V~~~d~~~ireAI~REl~--------RgGQvfYv~NrV~~Ie~~~~~L~~LVPEa  830 (1139)
T COG1197         759 MSLSGIRDLSVIATPPEDRLPVKTFVSEYDDLLIREAILRELL--------RGGQVFYVHNRVESIEKKAERLRELVPEA  830 (1139)
T ss_pred             HHHhcchhhhhccCCCCCCcceEEEEecCChHHHHHHHHHHHh--------cCCEEEEEecchhhHHHHHHHHHHhCCce
Confidence            8899999999999999999999988876665543333333333        3589999999999999999999876 778


Q ss_pred             eEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCC
Q 028124           80 SFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELP  159 (213)
Q Consensus        80 ~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P  159 (213)
                      ++...||.|+..+-.+++.+|-+|+                       .+|||||.+    .+-|+|+|+++++|..+.-
T Consensus       831 rI~vaHGQM~e~eLE~vM~~F~~g~-----------------------~dVLv~TTI----IEtGIDIPnANTiIIe~AD  883 (1139)
T COG1197         831 RIAVAHGQMRERELEEVMLDFYNGE-----------------------YDVLVCTTI----IETGIDIPNANTIIIERAD  883 (1139)
T ss_pred             EEEEeecCCCHHHHHHHHHHHHcCC-----------------------CCEEEEeee----eecCcCCCCCceEEEeccc
Confidence            9999999999999999999999995                       999999999    9999999999999987655


Q ss_pred             C-ChHHHHHhhccccCC--CCeEEEEEeC
Q 028124          160 T-KKETYIRRMTTCLAA--DGSVINIVVG  185 (213)
Q Consensus       160 ~-~~~~yi~R~GR~~~~--~g~~i~~~~~  185 (213)
                      . -.+...|--||.|++  .+.|+.++.+
T Consensus       884 ~fGLsQLyQLRGRVGRS~~~AYAYfl~p~  912 (1139)
T COG1197         884 KFGLAQLYQLRGRVGRSNKQAYAYFLYPP  912 (1139)
T ss_pred             cccHHHHHHhccccCCccceEEEEEeecC
Confidence            4 466777766886544  5888888864

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

Probab=99.32  E-value=3.5e-11  Score=110.82  Aligned_cols=106  Identities=21%  Similarity=0.276  Sum_probs=95.5

Q ss_pred             hHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccc
Q 028124           34 FKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE  113 (213)
Q Consensus        34 ~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~  113 (213)
                      .|+..+..++...    ..+.+++|||.+..+++.++..+...+ + +..++|+.+..+|.+++++|+.|.         
T Consensus       268 ~~~~~~~~~~~~~----~~~~~~lif~~~~~~a~~i~~~~~~~~-~-~~~it~~t~~~eR~~il~~fr~g~---------  332 (442)
T COG1061         268 RKIAAVRGLLLKH----ARGDKTLIFASDVEHAYEIAKLFLAPG-I-VEAITGETPKEEREAILERFRTGG---------  332 (442)
T ss_pred             HHHHHHHHHHHHh----cCCCcEEEEeccHHHHHHHHHHhcCCC-c-eEEEECCCCHHHHHHHHHHHHcCC---------
Confidence            3666777777651    146799999999999999999998876 5 889999999999999999999984         


Q ss_pred             cCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc
Q 028124          114 QSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC  172 (213)
Q Consensus       114 ~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~  172 (213)
                                    +++||++.+    +.+|+|+|+++++|....+.|...|+||+||.
T Consensus       333 --------------~~~lv~~~v----l~EGvDiP~~~~~i~~~~t~S~~~~~Q~lGR~  373 (442)
T COG1061         333 --------------IKVLVTVKV----LDEGVDIPDADVLIILRPTGSRRLFIQRLGRG  373 (442)
T ss_pred             --------------CCEEEEeee----ccceecCCCCcEEEEeCCCCcHHHHHHHhhhh
Confidence                          999999999    99999999999999999999999999999995

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

Probab=99.30  E-value=1.2e-11  Score=110.27  Aligned_cols=120  Identities=19%  Similarity=0.224  Sum_probs=101.1

Q ss_pred             CCCCCCceEEEEEecC-cchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHH
Q 028124           16 PSHFSQPRHFYVAVDR-LQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERT   94 (213)
Q Consensus        16 ~~~~~~i~~~~~~~~~-~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~   94 (213)
                      ..++++++..+..-+. .++-.+-+.++++.    ...++..||||=+++.|+.++..|++.| +.+..+|..|.+++|.
T Consensus       283 ~fnr~nl~yev~qkp~n~dd~~edi~k~i~~----~f~gqsgiiyc~sq~d~ekva~alkn~g-i~a~~yha~lep~dks  357 (695)
T KOG0353|consen  283 GFNRPNLKYEVRQKPGNEDDCIEDIAKLIKG----DFAGQSGIIYCFSQKDCEKVAKALKNHG-IHAGAYHANLEPEDKS  357 (695)
T ss_pred             ccCCCCceeEeeeCCCChHHHHHHHHHHhcc----ccCCCcceEEEeccccHHHHHHHHHhcC-ccccccccccCccccc
Confidence            3456666655544433 33344445555543    5678999999999999999999999998 9999999999999999


Q ss_pred             HHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHH
Q 028124           95 LILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIR  167 (213)
Q Consensus        95 ~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~  167 (213)
                      .+-+.|-.|+                       ++++|+|-+    ++.|+|-|+|+.|||-.+|.+.+.|.|
T Consensus       358 ~~hq~w~a~e-----------------------iqvivatva----fgmgidkpdvrfvihhsl~ksienyyq  403 (695)
T KOG0353|consen  358 GAHQGWIAGE-----------------------IQVIVATVA----FGMGIDKPDVRFVIHHSLPKSIENYYQ  403 (695)
T ss_pred             cccccccccc-----------------------eEEEEEEee----ecccCCCCCeeEEEecccchhHHHHHH
Confidence            9999999985                       999999999    999999999999999999999999999

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

Probab=99.29  E-value=6e-11  Score=109.48  Aligned_cols=106  Identities=17%  Similarity=0.243  Sum_probs=98.9

Q ss_pred             CCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEE
Q 028124           52 PGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMI  131 (213)
Q Consensus        52 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iL  131 (213)
                      .+.+++|-+=|++.|+.|.++|...| +++..+|+++..-+|.+++++.|.|+                       .++|
T Consensus       445 ~~eRvLVTtLTKkmAEdLT~Yl~e~g-ikv~YlHSdidTlER~eIirdLR~G~-----------------------~DvL  500 (663)
T COG0556         445 KNERVLVTTLTKKMAEDLTEYLKELG-IKVRYLHSDIDTLERVEIIRDLRLGE-----------------------FDVL  500 (663)
T ss_pred             cCCeEEEEeehHHHHHHHHHHHHhcC-ceEEeeeccchHHHHHHHHHHHhcCC-----------------------ccEE
Confidence            56899999999999999999999998 99999999999999999999999996                       9999


Q ss_pred             EEeCCCCCcCcCCCCCCCCCEEEEec-----CCCChHHHHHhhccccCC-CCeEEEEEeC
Q 028124          132 VVTDACLPLLSSGESAISARVLINYE-----LPTKKETYIRRMTTCLAA-DGSVINIVVG  185 (213)
Q Consensus       132 V~Td~~~~~~~rGld~~~v~~VI~yd-----~P~~~~~yi~R~GR~~~~-~g~~i~~~~~  185 (213)
                      |.-++    +.+|+|+|+|+.|..+|     |.+|-.+.||-+||++++ .|.||.+...
T Consensus       501 VGINL----LREGLDiPEVsLVAIlDADKeGFLRse~SLIQtIGRAARN~~GkvIlYAD~  556 (663)
T COG0556         501 VGINL----LREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADK  556 (663)
T ss_pred             Eeehh----hhccCCCcceeEEEEeecCccccccccchHHHHHHHHhhccCCeEEEEchh
Confidence            99999    99999999999999987     677899999999998766 5999988865

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

Probab=99.18  E-value=8.5e-10  Score=97.44  Aligned_cols=114  Identities=18%  Similarity=0.295  Sum_probs=92.3

Q ss_pred             CCCCCcEEEEeCchHHHHHHHHHHh-ccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCce
Q 028124           50 RRPGLPMIVCCSSRDELDAVCSAVS-NLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKS  128 (213)
Q Consensus        50 ~~~~~~~IIF~~~~~~~~~l~~~L~-~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~  128 (213)
                      ...+.+++||+++....+.++..|+ ..+......+|+.  ...|.+.+++||+|.                       +
T Consensus       302 ~~~~~P~liF~p~I~~~eq~a~~lk~~~~~~~i~~Vhs~--d~~R~EkV~~fR~G~-----------------------~  356 (441)
T COG4098         302 RKTGRPVLIFFPEIETMEQVAAALKKKLPKETIASVHSE--DQHRKEKVEAFRDGK-----------------------I  356 (441)
T ss_pred             HhcCCcEEEEecchHHHHHHHHHHHhhCCccceeeeecc--CccHHHHHHHHHcCc-----------------------e
Confidence            4578999999999999999999994 5566677899986  368899999999995                       9


Q ss_pred             eEEEEeCCCCCcCcCCCCCCCCCEEEEecCC--CChHHHHHhhccccCC----CCeEEEEEeCchhHHHH
Q 028124          129 HMIVVTDACLPLLSSGESAISARVLINYELP--TKKETYIRRMTTCLAA----DGSVINIVVGGEVVTLR  192 (213)
Q Consensus       129 ~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P--~~~~~yi~R~GR~~~~----~g~~i~~~~~~e~~~~~  192 (213)
                      ++||+|.+    ++||+.+|+|++.|.=.-.  .+-+..+|-+||.|++    .|.++.|-......+.+
T Consensus       357 ~lLiTTTI----LERGVTfp~vdV~Vlgaeh~vfTesaLVQIaGRvGRs~~~PtGdv~FFH~G~skaM~~  422 (441)
T COG4098         357 TLLITTTI----LERGVTFPNVDVFVLGAEHRVFTESALVQIAGRVGRSLERPTGDVLFFHYGKSKAMKQ  422 (441)
T ss_pred             EEEEEeeh----hhcccccccceEEEecCCcccccHHHHHHHhhhccCCCcCCCCcEEEEeccchHHHHH
Confidence            99999999    9999999999986653323  3678999988987655    38888777655544443

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

Probab=99.15  E-value=2.8e-10  Score=114.74  Aligned_cols=92  Identities=11%  Similarity=0.183  Sum_probs=79.1

Q ss_pred             CCcEEEEeCchHHHHHHHHHHhcc-----CC---ceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCC
Q 028124           53 GLPMIVCCSSRDELDAVCSAVSNL-----AD---ISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKD  124 (213)
Q Consensus        53 ~~~~IIF~~~~~~~~~l~~~L~~~-----~~---~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~  124 (213)
                      ..++||||.++.+|+.+++.|...     ++   ..+..+||+++  ++.+++++|+++.                    
T Consensus       698 ~~KtiIF~~s~~HA~~i~~~L~~~f~~~~~~~~~~~v~~itg~~~--~~~~li~~Fk~~~--------------------  755 (1123)
T PRK11448        698 EGKTLIFAATDAHADMVVRLLKEAFKKKYGQVEDDAVIKITGSID--KPDQLIRRFKNER--------------------  755 (1123)
T ss_pred             CCcEEEEEcCHHHHHHHHHHHHHHHHhhcCCcCccceEEEeCCcc--chHHHHHHHhCCC--------------------
Confidence            479999999999999999887652     11   24567999875  5678999999974                    


Q ss_pred             CCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc
Q 028124          125 EHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC  172 (213)
Q Consensus       125 ~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~  172 (213)
                        ..+|+|++|+    +++|+|+|.+.+||+++++.|...|+|++||+
T Consensus       756 --~p~IlVsvdm----L~TG~DvP~v~~vVf~rpvkS~~lf~QmIGRg  797 (1123)
T PRK11448        756 --LPNIVVTVDL----LTTGIDVPSICNLVFLRRVRSRILYEQMLGRA  797 (1123)
T ss_pred             --CCeEEEEecc----cccCCCcccccEEEEecCCCCHHHHHHHHhhh
Confidence              2379999999    99999999999999999999999999999995

>TIGR00595 priA primosomal protein N'

Probab=99.13  E-value=5.4e-10  Score=104.62  Aligned_cols=90  Identities=13%  Similarity=0.207  Sum_probs=73.1

Q ss_pred             HHHHHHHHhcc-CCceEEEecCCCCHHHH--HHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCc
Q 028124           66 LDAVCSAVSNL-ADISFSSLHSDLAETER--TLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS  142 (213)
Q Consensus        66 ~~~l~~~L~~~-~~~~~~~lhg~~~~~~R--~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~  142 (213)
                      ++++.+.|.+. ++..+..+|++++..++  .+++++|++|+                       .+|||+|++    ++
T Consensus       271 te~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~l~~f~~g~-----------------------~~ILVgT~~----i~  323 (505)
T TIGR00595       271 TEQVEEELAKLFPGARIARIDSDTTSRKGAHEALLNQFANGK-----------------------ADILIGTQM----IA  323 (505)
T ss_pred             HHHHHHHHHhhCCCCcEEEEecccccCccHHHHHHHHHhcCC-----------------------CCEEEeCcc----cc
Confidence            57888888765 45789999999987766  88999999985                       999999999    99


Q ss_pred             CCCCCCCCCEEE--EecC----CC------ChHHHHHhhcccc--CCCCeEEEE
Q 028124          143 SGESAISARVLI--NYEL----PT------KKETYIRRMTTCL--AADGSVINI  182 (213)
Q Consensus       143 rGld~~~v~~VI--~yd~----P~------~~~~yi~R~GR~~--~~~g~~i~~  182 (213)
                      +|+|+|++++|+  |+|.    |.      ....|+|++||+|  +..|.++..
T Consensus       324 kG~d~~~v~lV~vl~aD~~l~~pd~ra~E~~~~ll~q~~GRagR~~~~g~viiq  377 (505)
T TIGR00595       324 KGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVAGRAGRAEDPGQVIIQ  377 (505)
T ss_pred             cCCCCCcccEEEEEcCcccccCcccchHHHHHHHHHHHHhccCCCCCCCEEEEE
Confidence            999999999874  6664    42      2467899999974  456877743

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).

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.12  E-value=1.8e-09  Score=105.40  Aligned_cols=125  Identities=14%  Similarity=0.095  Sum_probs=104.5

Q ss_pred             CcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccccc
Q 028124           31 RLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQK  110 (213)
Q Consensus        31 ~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~  110 (213)
                      ....|+..+.+.+....   ..+.|+||||+|+..++.|+..|...+ +.+..+|+.  +.+|...+..|+.+       
T Consensus       411 t~~~K~~aI~~~I~~~~---~~grpVLIft~Si~~se~Ls~~L~~~g-i~~~vLnak--q~eREa~Iia~Ag~-------  477 (830)
T PRK12904        411 TEKEKFDAVVEDIKERH---KKGQPVLVGTVSIEKSELLSKLLKKAG-IPHNVLNAK--NHEREAEIIAQAGR-------  477 (830)
T ss_pred             CHHHHHHHHHHHHHHHH---hcCCCEEEEeCcHHHHHHHHHHHHHCC-CceEeccCc--hHHHHHHHHHhcCC-------
Confidence            33459999999886532   357899999999999999999999987 899999996  78999999999998       


Q ss_pred             ccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCC--------------------------------------CE
Q 028124          111 VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISA--------------------------------------RV  152 (213)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v--------------------------------------~~  152 (213)
                                      +..|+|||++    ++||+|++--                                      =+
T Consensus       478 ----------------~g~VtIATNm----AGRGtDI~LgGn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~GGLh  537 (830)
T PRK12904        478 ----------------PGAVTIATNM----AGRGTDIKLGGNPEMLAAALLEEETEEQIAKIKAEWQEEHEEVLEAGGLH  537 (830)
T ss_pred             ----------------CceEEEeccc----ccCCcCccCCCchhhhhhhhhhhhhhHHHHHHHHHHhhhhhhHHHcCCCE
Confidence                            4999999999    9999999753                                      16


Q ss_pred             EEEecCCCChHHHHHhhcccc--CCCCeEEEEEeCchh
Q 028124          153 LINYELPTKKETYIRRMTTCL--AADGSVINIVVGGEV  188 (213)
Q Consensus       153 VI~yd~P~~~~~yi~R~GR~~--~~~g~~i~~~~~~e~  188 (213)
                      ||--..|.|..-=-|-.||+|  |.+|.+-.|++-+|.
T Consensus       538 VigTerhesrRid~QlrGRagRQGdpGss~f~lSleD~  575 (830)
T PRK12904        538 VIGTERHESRRIDNQLRGRSGRQGDPGSSRFYLSLEDD  575 (830)
T ss_pred             EEecccCchHHHHHHhhcccccCCCCCceeEEEEcCcH
Confidence            888888888777778779975  667998888876543

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

Probab=99.09  E-value=7.7e-10  Score=109.03  Aligned_cols=160  Identities=23%  Similarity=0.224  Sum_probs=120.2

Q ss_pred             CCCCceEEEEEec---------CcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHH----HHHhccC---CceE
Q 028124           18 HFSQPRHFYVAVD---------RLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVC----SAVSNLA---DISF   81 (213)
Q Consensus        18 ~~~~i~~~~~~~~---------~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~----~~L~~~~---~~~~   81 (213)
                      .+...++++..-+         ..+ +...+..++..+.   ..+.++|+|+.+++.++.+.    +.+...+   ...+
T Consensus       266 ~~~~~~~~~~~~p~~~~~~~~~r~s-~~~~~~~~~~~~~---~~~~~tL~F~~sr~~~e~~~~~~~~~~~~~~~~l~~~v  341 (851)
T COG1205         266 SPRGLRYFVRREPPIRELAESIRRS-ALAELATLAALLV---RNGIQTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAV  341 (851)
T ss_pred             CCCCceEEEEeCCcchhhhhhcccc-hHHHHHHHHHHHH---HcCceEEEEEehhhhhhhhhhchhHHHhhcchhhhhhe
Confidence            3444566665555         223 6777777766543   36889999999999999996    3333322   1357


Q ss_pred             EEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCC-
Q 028124           82 SSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPT-  160 (213)
Q Consensus        82 ~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~-  160 (213)
                      ..+++++..++|.++.+.|++|+                       ..++++|.+    +.-|+|+.+++.||++..|. 
T Consensus       342 ~~~~~~~~~~er~~ie~~~~~g~-----------------------~~~~~st~A----lelgidiG~ldavi~~g~P~~  394 (851)
T COG1205         342 STYRAGLHREERRRIEAEFKEGE-----------------------LLGVIATNA----LELGIDIGSLDAVIAYGYPGV  394 (851)
T ss_pred             eeccccCCHHHHHHHHHHHhcCC-----------------------ccEEecchh----hhhceeehhhhhHhhcCCCCc
Confidence            88899999999999999999995                       999999999    99999999999999999999 


Q ss_pred             ChHHHHHhhccccCCCCeEEEEE--e--CchhHHHHHHHHHhc---ccccccCcc
Q 028124          161 KKETYIRRMTTCLAADGSVINIV--V--GGEVVTLRSMEESLG---LIVAEVPIN  208 (213)
Q Consensus       161 ~~~~yi~R~GR~~~~~g~~i~~~--~--~~e~~~~~~le~~l~---~~~~~~~~~  208 (213)
                      +..++.||.||+|++...++.++  .  +-+..+...-+..++   ...+.+.++
T Consensus       395 s~~~~~Q~~GRaGR~~~~~l~~~v~~~~~~d~yy~~~p~~~~~~~~~~~e~~~~~  449 (851)
T COG1205         395 SVLSFRQRAGRAGRRGQESLVLVVLRSDPLDSYYLRHPEELLETGFGPVESVRVD  449 (851)
T ss_pred             hHHHHHHhhhhccCCCCCceEEEEeCCCccchhhhhCcHhhhhcccCcccccccC
Confidence            89999999999877764444444  2  236666666677666   444444443

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.09  E-value=1.2e-09  Score=105.62  Aligned_cols=93  Identities=11%  Similarity=0.141  Sum_probs=74.9

Q ss_pred             HHHHHHHHHhcc-CCceEEEecCCCC--HHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcC
Q 028124           65 ELDAVCSAVSNL-ADISFSSLHSDLA--ETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLL  141 (213)
Q Consensus        65 ~~~~l~~~L~~~-~~~~~~~lhg~~~--~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~  141 (213)
                      .++++++.|.+. ++..+..+|+++.  ++++.+++++|++|+                       .+|||+|++    +
T Consensus       438 G~e~~~e~l~~~fp~~~v~~~~~d~~~~~~~~~~~l~~f~~g~-----------------------~~ILVgT~~----i  490 (679)
T PRK05580        438 GTERLEEELAELFPEARILRIDRDTTRRKGALEQLLAQFARGE-----------------------ADILIGTQM----L  490 (679)
T ss_pred             cHHHHHHHHHHhCCCCcEEEEeccccccchhHHHHHHHHhcCC-----------------------CCEEEEChh----h
Confidence            566888888765 4578999999986  467899999999985                       999999999    9


Q ss_pred             cCCCCCCCCCEEE--EecCCCC----------hHHHHHhhcccc--CCCCeEEEEEe
Q 028124          142 SSGESAISARVLI--NYELPTK----------KETYIRRMTTCL--AADGSVINIVV  184 (213)
Q Consensus       142 ~rGld~~~v~~VI--~yd~P~~----------~~~yi~R~GR~~--~~~g~~i~~~~  184 (213)
                      ++|+|+|++++|+  ++|.+-+          ...|+|++||+|  +..|.++....
T Consensus       491 akG~d~p~v~lV~il~aD~~l~~pdfra~Er~~~~l~q~~GRagR~~~~g~viiqT~  547 (679)
T PRK05580        491 AKGHDFPNVTLVGVLDADLGLFSPDFRASERTFQLLTQVAGRAGRAEKPGEVLIQTY  547 (679)
T ss_pred             ccCCCCCCcCEEEEEcCchhccCCccchHHHHHHHHHHHHhhccCCCCCCEEEEEeC
Confidence            9999999999985  4554433          367899999974  56688886554

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.08  E-value=2.4e-09  Score=104.91  Aligned_cols=124  Identities=15%  Similarity=0.109  Sum_probs=101.1

Q ss_pred             cchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccc
Q 028124           32 LQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKV  111 (213)
Q Consensus        32 ~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~  111 (213)
                      ...|+.++.+.+...-   ..++|+||||+|+..++.|+..|.+.| +....||+.+.+.+|..+.+.|+.|.       
T Consensus       426 ~~~k~~av~~~i~~~~---~~g~PVLVgt~Sie~sE~ls~~L~~~g-i~h~vLnak~~q~Ea~iia~Ag~~G~-------  494 (896)
T PRK13104        426 QADKFQAIIEDVRECG---VRKQPVLVGTVSIEASEFLSQLLKKEN-IKHQVLNAKFHEKEAQIIAEAGRPGA-------  494 (896)
T ss_pred             HHHHHHHHHHHHHHHH---hCCCCEEEEeCcHHHHHHHHHHHHHcC-CCeEeecCCCChHHHHHHHhCCCCCc-------
Confidence            3449999888886532   478999999999999999999999998 99999999999999999999999972       


Q ss_pred             cccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCC--------------------------------------CEE
Q 028124          112 TEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISA--------------------------------------RVL  153 (213)
Q Consensus       112 ~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v--------------------------------------~~V  153 (213)
                                        |+|||++    ++||+|+.=-                                      =+|
T Consensus       495 ------------------VtIATNm----AGRGtDI~Lggn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~V  552 (896)
T PRK13104        495 ------------------VTIATNM----AGRGTDIVLGGSLAADLANLPADASEQEKEAVKKEWQKRHDEVIAAGGLRI  552 (896)
T ss_pred             ------------------EEEeccC----ccCCcceecCCchhhhhhccccchhhHHHHHHHHHhhhhhhHHHHcCCCEE
Confidence                              9999999    9999998621                                      156


Q ss_pred             EEecCCCChHHHHHhhcccc--CCCCeEEEEEeCchh
Q 028124          154 INYELPTKKETYIRRMTTCL--AADGSVINIVVGGEV  188 (213)
Q Consensus       154 I~yd~P~~~~~yi~R~GR~~--~~~g~~i~~~~~~e~  188 (213)
                      |--.-+.|..-=-|=.||+|  |.+|.+-.|++-+|.
T Consensus       553 IgTerhesrRID~QLrGRaGRQGDPGss~f~lSleD~  589 (896)
T PRK13104        553 IGSERHESRRIDNQLRGRAGRQGDPGSSRFYLSLEDN  589 (896)
T ss_pred             EeeccCchHHHHHHhccccccCCCCCceEEEEEcCcH
Confidence            76666766555556668875  567988888876543

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

Probab=99.04  E-value=1.6e-09  Score=100.95  Aligned_cols=147  Identities=16%  Similarity=0.180  Sum_probs=114.3

Q ss_pred             HHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc----C-C--ceEEEecCCCCHHHHHHHHHHHhcccccc
Q 028124           35 KMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL----A-D--ISFSSLHSDLAETERTLILEEFRHTAMKW  107 (213)
Q Consensus        35 K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~----~-~--~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~  107 (213)
                      |..-...++.++..   .+-++|-||.+++-|+.+....+..    + +  -.+..+.|+-..++|.++-.+.-.|    
T Consensus       510 ~i~E~s~~~~~~i~---~~~R~IAFC~~R~~CEL~~~~~R~I~~ET~~~LV~~i~SYRGGY~A~DRRKIE~~~F~G----  582 (1034)
T KOG4150|consen  510 KVVEVSHLFAEMVQ---HGLRCIAFCPSRKLCELVLCLTREILAETAPHLVEAITSYRGGYIAEDRRKIESDLFGG----  582 (1034)
T ss_pred             HHHHHHHHHHHHHH---cCCcEEEeccHHHHHHHHHHHHHHHHHHhhHHHHHHHHhhcCccchhhHHHHHHHhhCC----
Confidence            55555556655443   5789999999999999887666542    1 1  1256688899999999999998887    


Q ss_pred             cccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccccCCC--CeEEEEE--
Q 028124          108 NQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAAD--GSVINIV--  183 (213)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~~~~--g~~i~~~--  183 (213)
                                         +...+|+|++    ++-|+|+...+.|++..+|.+.+.+.|+.||+|++.  +.++.++  
T Consensus       583 -------------------~L~giIaTNA----LELGIDIG~LDAVl~~GFP~S~aNl~QQ~GRAGRRNk~SLavyva~~  639 (1034)
T KOG4150|consen  583 -------------------KLCGIIATNA----LELGIDIGHLDAVLHLGFPGSIANLWQQAGRAGRRNKPSLAVYVAFL  639 (1034)
T ss_pred             -------------------eeeEEEecch----hhhccccccceeEEEccCchhHHHHHHHhccccccCCCceEEEEEec
Confidence                               4999999999    999999999999999999999999999999997665  3443333  


Q ss_pred             eCchhHHHHHHHHHhcccccccCccccc
Q 028124          184 VGGEVVTLRSMEESLGLIVAEVPINISE  211 (213)
Q Consensus       184 ~~~e~~~~~~le~~l~~~~~~~~~~~~~  211 (213)
                      .+-|..++..-+..++..-.|+-+++.+
T Consensus       640 ~PVDQ~Y~~HP~~l~~~pN~EL~LD~~N  667 (1034)
T KOG4150|consen  640 GPVDQYYMSHPDKLFGSPNEELHLDSQN  667 (1034)
T ss_pred             cchhhHhhcCcHHHhCCCcceeEEeccc
Confidence            3447777777777777777776666554

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.01  E-value=9.8e-09  Score=100.53  Aligned_cols=124  Identities=12%  Similarity=0.132  Sum_probs=102.0

Q ss_pred             cchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccc
Q 028124           32 LQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKV  111 (213)
Q Consensus        32 ~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~  111 (213)
                      ...|+..+.+-+..+.   ..++|+||||+|...++.++..|...+ +....+|+.+++.++..+.+.|+.|        
T Consensus       431 ~~~K~~Aii~ei~~~~---~~GrpVLV~t~sv~~se~ls~~L~~~g-i~~~vLnak~~~~Ea~ii~~Ag~~G--------  498 (908)
T PRK13107        431 ADEKYQAIIKDIKDCR---ERGQPVLVGTVSIEQSELLARLMVKEK-IPHEVLNAKFHEREAEIVAQAGRTG--------  498 (908)
T ss_pred             HHHHHHHHHHHHHHHH---HcCCCEEEEeCcHHHHHHHHHHHHHCC-CCeEeccCcccHHHHHHHHhCCCCC--------
Confidence            3448988888877643   468999999999999999999999987 8999999999999999999999997        


Q ss_pred             cccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCC-------------------------------------CEEE
Q 028124          112 TEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISA-------------------------------------RVLI  154 (213)
Q Consensus       112 ~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v-------------------------------------~~VI  154 (213)
                                      . |+|||++    ++||+|+.=-                                     =+||
T Consensus       499 ----------------~-VtIATnm----AGRGTDIkLggn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VI  557 (908)
T PRK13107        499 ----------------A-VTIATNM----AGRGTDIVLGGNWNMEIEALENPTAEQKAKIKADWQIRHDEVVAAGGLHIL  557 (908)
T ss_pred             ----------------c-EEEecCC----cCCCcceecCCchHHhhhhhcchhhHHHHHHHHHHHhhHHHHHHcCCCEEE
Confidence                            2 9999999    9999998622                                     1677


Q ss_pred             EecCCCChHHHHHhhcccc--CCCCeEEEEEeCchh
Q 028124          155 NYELPTKKETYIRRMTTCL--AADGSVINIVVGGEV  188 (213)
Q Consensus       155 ~yd~P~~~~~yi~R~GR~~--~~~g~~i~~~~~~e~  188 (213)
                      --..|.|..-=-|=.||+|  |.+|.+-.|++-+|.
T Consensus       558 gTerheSrRID~QLrGRaGRQGDPGss~f~lSlED~  593 (908)
T PRK13107        558 GTERHESRRIDNQLRGRAGRQGDAGSSRFYLSMEDS  593 (908)
T ss_pred             ecccCchHHHHhhhhcccccCCCCCceeEEEEeCcH
Confidence            7777776555556668875  567988888876654

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

Probab=98.78  E-value=1.2e-07  Score=94.15  Aligned_cols=121  Identities=16%  Similarity=0.222  Sum_probs=102.5

Q ss_pred             HHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccccccccc
Q 028124           35 KMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ  114 (213)
Q Consensus        35 K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~  114 (213)
                      |++.|.-||.++.   ..+.+++||+.-.+..+-|-..|...| +.-+-|.|...-++|+.++++|....          
T Consensus      1261 KLQtLAiLLqQLk---~eghRvLIfTQMtkmLDVLeqFLnyHg-ylY~RLDg~t~vEqRQaLmerFNaD~---------- 1326 (1958)
T KOG0391|consen 1261 KLQTLAILLQQLK---SEGHRVLIFTQMTKMLDVLEQFLNYHG-YLYVRLDGNTSVEQRQALMERFNADR---------- 1326 (1958)
T ss_pred             hHHHHHHHHHHHH---hcCceEEehhHHHHHHHHHHHHHhhcc-eEEEEecCCccHHHHHHHHHHhcCCC----------
Confidence            8888888887753   478999999999999999999998888 78899999999999999999998873          


Q ss_pred             CCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCCh------HHHHHhhccccCCCCeEEEEEeCc
Q 028124          115 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKK------ETYIRRMTTCLAADGSVINIVVGG  186 (213)
Q Consensus       115 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~------~~yi~R~GR~~~~~g~~i~~~~~~  186 (213)
                                 .-..++++|-.    .+-|+|+.++++||.||--|++      .+..||||+|  ++-.+|-|+.+.
T Consensus      1327 -----------RIfcfILSTrS----ggvGiNLtgADTVvFYDsDwNPtMDaQAQDrChRIGqt--RDVHIYRLISe~ 1387 (1958)
T KOG0391|consen 1327 -----------RIFCFILSTRS----GGVGINLTGADTVVFYDSDWNPTMDAQAQDRCHRIGQT--RDVHIYRLISER 1387 (1958)
T ss_pred             -----------ceEEEEEeccC----CccccccccCceEEEecCCCCchhhhHHHHHHHhhcCc--cceEEEEeeccc
Confidence                       12346677887    8999999999999999998875      6789999997  456777788765

>COG1204 Superfamily II helicase [General function prediction only]

Probab=98.76  E-value=1e-07  Score=93.11  Aligned_cols=107  Identities=20%  Similarity=0.277  Sum_probs=86.8

Q ss_pred             CCCCcEEEEeCchHHHHHHHHHHhcc-----------------CC-------------------ceEEEecCCCCHHHHH
Q 028124           51 RPGLPMIVCCSSRDELDAVCSAVSNL-----------------AD-------------------ISFSSLHSDLAETERT   94 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~~L~~~-----------------~~-------------------~~~~~lhg~~~~~~R~   94 (213)
                      ..+++++|||++++.+...|..|+..                 ..                   .-+...|.+|+.++|.
T Consensus       251 ~~~~qvLvFv~sR~~a~~~A~~l~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~l~e~v~~GvafHhAGL~~~~R~  330 (766)
T COG1204         251 AEGGQVLVFVHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGVAFHHAGLPREDRQ  330 (766)
T ss_pred             hcCCeEEEEEecCchHHHHHHHHHHHHhhcCChhhhhhccccccccccccccccchHHHHHHHHhCccccccCCCHHHHH
Confidence            46789999999999999999999831                 00                   1256788999999999


Q ss_pred             HHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEE----Eec-----CCCChHHH
Q 028124           95 LILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLI----NYE-----LPTKKETY  165 (213)
Q Consensus        95 ~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI----~yd-----~P~~~~~y  165 (213)
                      -+-+.|+.|                       +++||+||+.    ++.|+|+|.-.+||    -||     .+-+.-+|
T Consensus       331 ~vE~~Fr~g-----------------------~ikVlv~TpT----LA~GVNLPA~~VIIk~~~~y~~~~g~~~i~~~dv  383 (766)
T COG1204         331 LVEDAFRKG-----------------------KIKVLVSTPT----LAAGVNLPARTVIIKDTRRYDPKGGIVDIPVLDV  383 (766)
T ss_pred             HHHHHHhcC-----------------------CceEEEechH----HhhhcCCcceEEEEeeeEEEcCCCCeEECchhhH
Confidence            999999998                       5999999999    99999999777766    366     45568999


Q ss_pred             HHhhccccCC----CCeEEEEEe
Q 028124          166 IRRMTTCLAA----DGSVINIVV  184 (213)
Q Consensus       166 i~R~GR~~~~----~g~~i~~~~  184 (213)
                      +|..||+|+-    .|.++.+.+
T Consensus       384 ~QM~GRAGRPg~d~~G~~~i~~~  406 (766)
T COG1204         384 LQMAGRAGRPGYDDYGEAIILAT  406 (766)
T ss_pred             hhccCcCCCCCcCCCCcEEEEec
Confidence            9999997543    366666663

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

Probab=98.68  E-value=3e-07  Score=88.27  Aligned_cols=142  Identities=18%  Similarity=0.167  Sum_probs=114.4

Q ss_pred             ecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccc
Q 028124           29 VDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWN  108 (213)
Q Consensus        29 ~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~  108 (213)
                      +.+.- |+.+|-+||..+.   ..+.+++||..-....+-|..++.-++ +...-+.|.++.++|...++.|....    
T Consensus       467 v~nSG-Km~vLDkLL~~Lk---~~GhRVLIFSQmt~mLDILeDyc~~R~-y~ycRiDGSt~~eeR~~aI~~fn~~~----  537 (971)
T KOG0385|consen  467 VTNSG-KMLVLDKLLPKLK---EQGHRVLIFSQMTRMLDILEDYCMLRG-YEYCRLDGSTSHEEREDAIEAFNAPP----  537 (971)
T ss_pred             HhcCc-ceehHHHHHHHHH---hCCCeEEEeHHHHHHHHHHHHHHHhcC-ceeEeecCCCCcHHHHHHHHhcCCCC----
Confidence            33445 9999999998764   478999999998899999999998887 79999999999999999999998863    


Q ss_pred             ccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc---c-CCCCeEEEEEe
Q 028124          109 QKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC---L-AADGSVINIVV  184 (213)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~---~-~~~g~~i~~~~  184 (213)
                                      +.+.-.|++|.+    .+-||++..+++||.||--|++..=.|-+-||   | -++-.|+.|++
T Consensus       538 ----------------s~~FiFlLSTRA----GGLGINL~aADtVIlyDSDWNPQ~DLQAmDRaHRIGQ~K~V~V~RLit  597 (971)
T KOG0385|consen  538 ----------------SEKFIFLLSTRA----GGLGINLTAADTVILYDSDWNPQVDLQAMDRAHRIGQKKPVVVYRLIT  597 (971)
T ss_pred             ----------------cceEEEEEeccc----cccccccccccEEEEecCCCCchhhhHHHHHHHhhCCcCceEEEEEec
Confidence                            124668999999    99999999999999999999987666655554   2 23468899998


Q ss_pred             Cc--hhHHHHHHHHHhc
Q 028124          185 GG--EVVTLRSMEESLG  199 (213)
Q Consensus       185 ~~--e~~~~~~le~~l~  199 (213)
                      .+  |...+++-+..+.
T Consensus       598 entVEe~IveRA~~KL~  614 (971)
T KOG0385|consen  598 ENTVEEKIVERAAAKLR  614 (971)
T ss_pred             cchHHHHHHHHHHHHhc
Confidence            86  4455555555543

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

Probab=98.67  E-value=1.5e-07  Score=93.79  Aligned_cols=138  Identities=16%  Similarity=0.191  Sum_probs=114.3

Q ss_pred             HHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccccccccc
Q 028124           35 KMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ  114 (213)
Q Consensus        35 K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~  114 (213)
                      |+-+|-+||-.+   +..+.++|||..=....+-|+++|..++ +..--|.|.+.-+-|++.+..|....          
T Consensus       684 KlVLLDKLL~rL---k~~GHrVLIFSQMVRmLDIL~eYL~~r~-ypfQRLDGsvrgelRq~AIDhFnap~----------  749 (1373)
T KOG0384|consen  684 KLVLLDKLLPRL---KEGGHRVLIFSQMVRMLDILAEYLSLRG-YPFQRLDGSVRGELRQQAIDHFNAPD----------  749 (1373)
T ss_pred             cEEeHHHHHHHH---hcCCceEEEhHHHHHHHHHHHHHHHHcC-CcceeccCCcchHHHHHHHHhccCCC----------
Confidence            555666677554   3468999999999999999999999998 79999999999999999999998864          


Q ss_pred             CCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCCC--CeEEEEEeCc--hh
Q 028124          115 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAAD--GSVINIVVGG--EV  188 (213)
Q Consensus       115 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~~--g~~i~~~~~~--e~  188 (213)
                                +...-+|+||-+    .+-||++..+++||.||--|++..=+|-+.||  -|+.  -.+|-||+.+  |.
T Consensus       750 ----------SddFvFLLSTRA----GGLGINLatADTVIIFDSDWNPQNDLQAqARaHRIGQkk~VnVYRLVTk~TvEe  815 (1373)
T KOG0384|consen  750 ----------SDDFVFLLSTRA----GGLGINLATADTVIIFDSDWNPQNDLQAQARAHRIGQKKHVNVYRLVTKNTVEE  815 (1373)
T ss_pred             ----------CCceEEEEeccc----CcccccccccceEEEeCCCCCcchHHHHHHHHHhhcccceEEEEEEecCCchHH
Confidence                      235789999999    99999999999999999999998888877776  2333  5788889876  66


Q ss_pred             HHHHHHHHHhcc
Q 028124          189 VTLRSMEESLGL  200 (213)
Q Consensus       189 ~~~~~le~~l~~  200 (213)
                      +++.+-...++.
T Consensus       816 EilERAk~KmvL  827 (1373)
T KOG0384|consen  816 EILERAKLKMVL  827 (1373)
T ss_pred             HHHHHHHHHhhh
Confidence            777776666653

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

Probab=98.65  E-value=1.5e-07  Score=91.89  Aligned_cols=115  Identities=23%  Similarity=0.335  Sum_probs=94.5

Q ss_pred             CCcEEEEeCchHHHHHHHHHHhcc--------------------------------------CCceEEEecCCCCHHHHH
Q 028124           53 GLPMIVCCSSRDELDAVCSAVSNL--------------------------------------ADISFSSLHSDLAETERT   94 (213)
Q Consensus        53 ~~~~IIF~~~~~~~~~l~~~L~~~--------------------------------------~~~~~~~lhg~~~~~~R~   94 (213)
                      +.++||||++++.|+.+|..+.+.                                      + .-+++.|.+++.++|.
T Consensus       460 ~~~~lvfc~sk~~ce~~a~~~~~~vpk~~~~e~~~~~~~~~s~s~~lr~~~~~ld~Vl~~ti~-~GvAyHhaGLT~eER~  538 (1008)
T KOG0950|consen  460 GSSVLVFCPSKKNCENVASLIAKKVPKHIKSEKRLGLWELLSISNLLRRIPGILDPVLAKTIP-YGVAYHHAGLTSEERE  538 (1008)
T ss_pred             CCeEEEEcCcccchHHHHHHHHHHhhHhhhhhhhhhHHHHHHHHhHhhcCCcccchHHheecc-ccceecccccccchHH
Confidence            467999999999999887555322                                      1 3467889999999999


Q ss_pred             HHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecC----CCChHHHHHhhc
Q 028124           95 LILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYEL----PTKKETYIRRMT  170 (213)
Q Consensus        95 ~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~----P~~~~~yi~R~G  170 (213)
                      .+-..||.|.                       ..+++||+.    ++-|+++|..+++|-+..    +-+.-.|.|++|
T Consensus       539 ~iE~afr~g~-----------------------i~vl~aTST----laaGVNLPArRVIiraP~~g~~~l~~~~YkQM~G  591 (1008)
T KOG0950|consen  539 IIEAAFREGN-----------------------IFVLVATST----LAAGVNLPARRVIIRAPYVGREFLTRLEYKQMVG  591 (1008)
T ss_pred             HHHHHHHhcC-----------------------eEEEEecch----hhccCcCCcceeEEeCCccccchhhhhhHHhhhh
Confidence            9999999996                       999999999    999999999999987532    236789999999


Q ss_pred             cccC----CCCeEEEEEeCchhHHHHHHH
Q 028124          171 TCLA----ADGSVINIVVGGEVVTLRSME  195 (213)
Q Consensus       171 R~~~----~~g~~i~~~~~~e~~~~~~le  195 (213)
                      |+|+    .-|.+|.++...+...+..+-
T Consensus       592 RAGR~gidT~GdsiLI~k~~e~~~~~~lv  620 (1008)
T KOG0950|consen  592 RAGRTGIDTLGDSILIIKSSEKKRVRELV  620 (1008)
T ss_pred             hhhhcccccCcceEEEeeccchhHHHHHH
Confidence            9753    349999999999887776554

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

Probab=98.64  E-value=2.5e-07  Score=90.82  Aligned_cols=145  Identities=12%  Similarity=0.176  Sum_probs=109.2

Q ss_pred             CCCCCCCceEEEEEecCcch-HHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhc--c-CCceEEEecCCCCH
Q 028124           15 SPSHFSQPRHFYVAVDRLQF-KMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSN--L-ADISFSSLHSDLAE   90 (213)
Q Consensus        15 ~~~~~~~i~~~~~~~~~~~~-K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~--~-~~~~~~~lhg~~~~   90 (213)
                      .+...-.++-+|......++ -.+.+...+.....  ...+.++||.+-..+.+..++.|.+  . +++.+..+||.|+.
T Consensus       222 i~GR~fPVei~Y~~~~~~d~~l~~ai~~~v~~~~~--~~~GdILvFLpG~~EI~~~~~~L~~~~l~~~~~i~PLy~~L~~  299 (845)
T COG1643         222 IEGRTYPVEIRYLPEAEADYILLDAIVAAVDIHLR--EGSGSILVFLPGQREIERTAEWLEKAELGDDLEILPLYGALSA  299 (845)
T ss_pred             ecCCccceEEEecCCCCcchhHHHHHHHHHHHhcc--CCCCCEEEECCcHHHHHHHHHHHHhccccCCcEEeeccccCCH
Confidence            33444457777755443443 44555555554333  4578999999999999999999987  3 24789999999999


Q ss_pred             HHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCC-----------
Q 028124           91 TERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELP-----------  159 (213)
Q Consensus        91 ~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P-----------  159 (213)
                      +++.++++---.|                       +.+|+++|++    ++-++.++++++||.-.+-           
T Consensus       300 ~eQ~rvF~p~~~~-----------------------~RKVVlATNI----AETSLTI~gIr~VIDsG~ak~~~y~~~~g~  352 (845)
T COG1643         300 EEQVRVFEPAPGG-----------------------KRKVVLATNI----AETSLTIPGIRYVIDSGLAKEKRYDPRTGL  352 (845)
T ss_pred             HHHHhhcCCCCCC-----------------------cceEEEEccc----cccceeeCCeEEEecCCcccccccccccCc
Confidence            9998876665554                       3669999999    9999999999999974322           


Q ss_pred             -------CChHHHHHhhccccCC-CCeEEEEEeCchh
Q 028124          160 -------TKKETYIRRMTTCLAA-DGSVINIVVGGEV  188 (213)
Q Consensus       160 -------~~~~~yi~R~GR~~~~-~g~~i~~~~~~e~  188 (213)
                             -|-++-.||.||||+- +|.||-+++.++.
T Consensus       353 ~~L~~~~ISqAsA~QRaGRAGR~~pGicyRLyse~~~  389 (845)
T COG1643         353 TRLETEPISKASADQRAGRAGRTGPGICYRLYSEEDF  389 (845)
T ss_pred             eeeeEEEechhhhhhhccccccCCCceEEEecCHHHH
Confidence                   2557889999999865 5999999997544

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

Probab=98.62  E-value=7.7e-07  Score=86.33  Aligned_cols=126  Identities=14%  Similarity=0.135  Sum_probs=98.9

Q ss_pred             hHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccc
Q 028124           34 FKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE  113 (213)
Q Consensus        34 ~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~  113 (213)
                      .|+..|..++....  +....++++-.|.+.+.+.+.+..+-+| +.+..+||.|+..+|+.+++.|....         
T Consensus       578 ~kl~~L~~ll~~~~--ek~~~~~v~Isny~~tldl~e~~~~~~g-~~~~rLdG~~~~~qRq~~vd~FN~p~---------  645 (776)
T KOG0390|consen  578 GKLLVLVFLLEVIR--EKLLVKSVLISNYTQTLDLFEQLCRWRG-YEVLRLDGKTSIKQRQKLVDTFNDPE---------  645 (776)
T ss_pred             hHHHHHHHHHHHHh--hhcceEEEEeccHHHHHHHHHHHHhhcC-ceEEEEcCCCchHHHHHHHHhccCCC---------
Confidence            37788888774422  1334555666677777777777777776 89999999999999999999998864         


Q ss_pred             cCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCCC--CeEEEEEeCc
Q 028124          114 QSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAAD--GSVINIVVGG  186 (213)
Q Consensus       114 ~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~~--g~~i~~~~~~  186 (213)
                                 +...-.|.+|-+    .+.||++-+++-||.||+.|+++.=.|-++|+  .|+.  -.+|-|++.+
T Consensus       646 -----------~~~~vfLlSsKA----gg~GinLiGAsRlil~D~dWNPa~d~QAmaR~~RdGQKk~v~iYrLlatG  707 (776)
T KOG0390|consen  646 -----------SPSFVFLLSSKA----GGEGLNLIGASRLILFDPDWNPAVDQQAMARAWRDGQKKPVYIYRLLATG  707 (776)
T ss_pred             -----------CCceEEEEeccc----ccCceeecccceEEEeCCCCCchhHHHHHHHhccCCCcceEEEEEeecCC
Confidence                       112447778889    79999999999999999999999999999995  5554  5777788765

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=98.60  E-value=2.4e-07  Score=90.50  Aligned_cols=107  Identities=17%  Similarity=0.225  Sum_probs=85.6

Q ss_pred             CCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeE
Q 028124           51 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHM  130 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~i  130 (213)
                      ..+.+++|-|||+..|.+++..|+..+. .+..+||.+...+|.+.+++++.--                   ..+...|
T Consensus       438 ~~~~kvlvI~NTV~~Aie~Y~~Lk~~~~-~v~LlHSRf~~~dR~~ke~~l~~~~-------------------~~~~~~I  497 (733)
T COG1203         438 KEGKKVLVIVNTVDRAIELYEKLKEKGP-KVLLLHSRFTLKDREEKERELKKLF-------------------KQNEGFI  497 (733)
T ss_pred             ccCCcEEEEEecHHHHHHHHHHHHhcCC-CEEEEecccchhhHHHHHHHHHHHH-------------------hccCCeE
Confidence            5689999999999999999999999874 7999999999999999998766410                   0014789


Q ss_pred             EEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhcccc--C--CCCeEEEEEe
Q 028124          131 IVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--A--ADGSVINIVV  184 (213)
Q Consensus       131 LV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~--~--~~g~~i~~~~  184 (213)
                      +|+|.+    .+-|+|+. .+++|-==.|  +++.+||+||+.  |  ..|.++.+..
T Consensus       498 vVaTQV----IEagvDid-fd~mITe~aP--idSLIQR~GRv~R~g~~~~~~~~v~~~  548 (733)
T COG1203         498 VVATQV----IEAGVDID-FDVLITELAP--IDSLIQRAGRVNRHGKKENGKIYVYND  548 (733)
T ss_pred             EEEeeE----EEEEeccc-cCeeeecCCC--HHHHHHHHHHHhhcccccCCceeEeec
Confidence            999999    99999976 7777764444  899999999973  3  2456665554

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

Probab=98.52  E-value=2e-06  Score=79.50  Aligned_cols=136  Identities=17%  Similarity=0.199  Sum_probs=103.6

Q ss_pred             HHHHHHHHHHH-hhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccc
Q 028124           35 KMETLVELLHL-VVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE  113 (213)
Q Consensus        35 K~~~L~~ll~~-~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~  113 (213)
                      |...+++-|.. .+-...+..+++|||......+.+...+.+++ +..+-+.|..+..+|..+.++|+..+         
T Consensus       473 K~~av~eyi~~~~~l~d~~~~KflVFaHH~~vLd~Iq~~~~~r~-vg~IRIDGst~s~~R~ll~qsFQ~se---------  542 (689)
T KOG1000|consen  473 KAAAVCEYILENYFLPDAPPRKFLVFAHHQIVLDTIQVEVNKRK-VGSIRIDGSTPSHRRTLLCQSFQTSE---------  542 (689)
T ss_pred             ccHHHHHHHHhCcccccCCCceEEEEehhHHHHHHHHHHHHHcC-CCeEEecCCCCchhHHHHHHHhcccc---------
Confidence            55555554433 11124678999999999999999999999886 89999999999999999999999864         


Q ss_pred             cCCCCCcCCCCCCcee-EEEEeCCCCCcCcCCCCCCCCCEEEEecCCCCh------HHHHHhhccccCCCCeEEEEEeCc
Q 028124          114 QSGDESETGKDEHKSH-MIVVTDACLPLLSSGESAISARVLINYELPTKK------ETYIRRMTTCLAADGSVINIVVGG  186 (213)
Q Consensus       114 ~~~~~~~~~~~~~~~~-iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~------~~yi~R~GR~~~~~g~~i~~~~~~  186 (213)
                                   ... .+++-.+    ++.|+++..++.||...+||++      ++-+||+|..  +.-.++.||..+
T Consensus       543 -------------ev~VAvlsItA----~gvGLt~tAa~~VVFaEL~wnPgvLlQAEDRaHRiGQk--ssV~v~ylvAKg  603 (689)
T KOG1000|consen  543 -------------EVRVAVLSITA----AGVGLTLTAASVVVFAELHWNPGVLLQAEDRAHRIGQK--SSVFVQYLVAKG  603 (689)
T ss_pred             -------------ceEEEEEEEee----cccceeeeccceEEEEEecCCCceEEechhhhhhcccc--ceeeEEEEEecC
Confidence                         233 3444555    7999999999999999999986      6667777754  223456666654


Q ss_pred             --hhHHHHHHHHHhc
Q 028124          187 --EVVTLRSMEESLG  199 (213)
Q Consensus       187 --e~~~~~~le~~l~  199 (213)
                        |...+..+.+.+.
T Consensus       604 T~Ddy~Wp~l~~KL~  618 (689)
T KOG1000|consen  604 TADDYMWPMLQQKLD  618 (689)
T ss_pred             chHHHHHHHHHHHHH
Confidence              6777777777664

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

Probab=98.51  E-value=3e-06  Score=81.69  Aligned_cols=123  Identities=17%  Similarity=0.203  Sum_probs=106.0

Q ss_pred             hHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccc
Q 028124           34 FKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE  113 (213)
Q Consensus        34 ~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~  113 (213)
                      -|.+.|..||..+.   .++.+++||.......+-|-..|...+ ++..-+.|...-.+|+.++.+|-...         
T Consensus       761 gK~r~L~~LLp~~k---~~G~RVLiFSQFTqmLDILE~~L~~l~-~~ylRLDGsTqV~~RQ~lId~Fn~d~---------  827 (941)
T KOG0389|consen  761 GKCRKLKELLPKIK---KKGDRVLIFSQFTQMLDILEVVLDTLG-YKYLRLDGSTQVNDRQDLIDEFNTDK---------  827 (941)
T ss_pred             hhHhHHHHHHHHHh---hcCCEEEEeeHHHHHHHHHHHHHHhcC-ceEEeecCCccchHHHHHHHhhccCC---------
Confidence            39999999998753   467999999999999999999999987 89999999999999999999998864         


Q ss_pred             cCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCC------hHHHHHhhccccCCCCeEEEEEeCch
Q 028124          114 QSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTK------KETYIRRMTTCLAADGSVINIVVGGE  187 (213)
Q Consensus       114 ~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~------~~~yi~R~GR~~~~~g~~i~~~~~~e  187 (213)
                                  .-.-+|++|-+    .+-||++..+++||.||+-.+      .++..||+|.+  ++-.++.+++.+.
T Consensus       828 ------------difVFLLSTKA----GG~GINLt~An~VIihD~dFNP~dD~QAEDRcHRvGQt--kpVtV~rLItk~T  889 (941)
T KOG0389|consen  828 ------------DIFVFLLSTKA----GGFGINLTCANTVIIHDIDFNPYDDKQAEDRCHRVGQT--KPVTVYRLITKST  889 (941)
T ss_pred             ------------ceEEEEEeecc----CcceecccccceEEEeecCCCCcccchhHHHHHhhCCc--ceeEEEEEEecCc
Confidence                        22347889999    999999999999999997654      58888888875  5678999998763

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

Probab=98.46  E-value=2e-06  Score=80.29  Aligned_cols=122  Identities=16%  Similarity=0.201  Sum_probs=87.2

Q ss_pred             CCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeE
Q 028124           51 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHM  130 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~i  130 (213)
                      .++..++-|  +++..-.+...+.+.++.++.+++|++|++.|.+--..|.+.+                     +..+|
T Consensus       356 k~GDCvV~F--Skk~I~~~k~kIE~~g~~k~aVIYGsLPPeTr~aQA~~FNd~~---------------------~e~dv  412 (700)
T KOG0953|consen  356 KPGDCVVAF--SKKDIFTVKKKIEKAGNHKCAVIYGSLPPETRLAQAALFNDPS---------------------NECDV  412 (700)
T ss_pred             CCCCeEEEe--ehhhHHHHHHHHHHhcCcceEEEecCCCCchhHHHHHHhCCCC---------------------Cccce
Confidence            445444444  6778899999998888777999999999999999999998864                     35999


Q ss_pred             EEEeCCCCCcCcCCCCCCCCCEEEEecCC---------CChHHHHHhhccccCCC-----CeEEEEEeCchhHHHHHHHH
Q 028124          131 IVVTDACLPLLSSGESAISARVLINYELP---------TKKETYIRRMTTCLAAD-----GSVINIVVGGEVVTLRSMEE  196 (213)
Q Consensus       131 LV~Td~~~~~~~rGld~~~v~~VI~yd~P---------~~~~~yi~R~GR~~~~~-----g~~i~~~~~~e~~~~~~le~  196 (213)
                      |||||+    .++|+++. ++-||.|++-         -+...-.|-+||+|+-.     |.+.++-.    +.+..+.+
T Consensus       413 lVAsDA----IGMGLNL~-IrRiiF~sl~Kysg~e~~~it~sqikQIAGRAGRf~s~~~~G~vTtl~~----eDL~~L~~  483 (700)
T KOG0953|consen  413 LVASDA----IGMGLNLN-IRRIIFYSLIKYSGRETEDITVSQIKQIAGRAGRFGSKYPQGEVTTLHS----EDLKLLKR  483 (700)
T ss_pred             EEeecc----cccccccc-eeEEEEeecccCCcccceeccHHHHHHHhhcccccccCCcCceEEEeeH----hhHHHHHH
Confidence            999999    99999976 6777777644         24566678778865432     55555433    33444444


Q ss_pred             Hhcccccc
Q 028124          197 SLGLIVAE  204 (213)
Q Consensus       197 ~l~~~~~~  204 (213)
                      .+....++
T Consensus       484 ~l~~p~ep  491 (700)
T KOG0953|consen  484 ILKRPVEP  491 (700)
T ss_pred             HHhCCchH
Confidence            44444443

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

Probab=98.43  E-value=2.7e-06  Score=78.64  Aligned_cols=124  Identities=17%  Similarity=0.166  Sum_probs=103.6

Q ss_pred             chHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccccccc
Q 028124           33 QFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVT  112 (213)
Q Consensus        33 ~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~  112 (213)
                      ..|+++|.+-|..+.. +....+.|||.......+.+...|.+.| +.++.+-|+|++..|...++.|++..        
T Consensus       619 STKIEAL~EEl~~l~~-rd~t~KsIVFSQFTSmLDLi~~rL~kaG-fscVkL~GsMs~~ardatik~F~nd~--------  688 (791)
T KOG1002|consen  619 STKIEALVEELYFLRE-RDRTAKSIVFSQFTSMLDLIEWRLGKAG-FSCVKLVGSMSPAARDATIKYFKNDI--------  688 (791)
T ss_pred             hhHHHHHHHHHHHHHH-cccchhhhhHHHHHHHHHHHHHHhhccC-ceEEEeccCCChHHHHHHHHHhccCC--------
Confidence            3499999998876655 5567899999999999999999999988 89999999999999999999999973        


Q ss_pred             ccCCCCCcCCCCCCcee-EEEEeCCCCCcCcCCCCCCCCCEEEEecCCCCh------HHHHHhhccccCCCCeEEEEEeC
Q 028124          113 EQSGDESETGKDEHKSH-MIVVTDACLPLLSSGESAISARVLINYELPTKK------ETYIRRMTTCLAADGSVINIVVG  185 (213)
Q Consensus       113 ~~~~~~~~~~~~~~~~~-iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~------~~yi~R~GR~~~~~g~~i~~~~~  185 (213)
                                    .++ +|++-.+    .+-.+++..++.|.+.|+=|++      .+.+||+|.+  ++-.++.|+-+
T Consensus       689 --------------~c~vfLvSLkA----GGVALNLteASqVFmmDPWWNpaVe~Qa~DRiHRIGQ~--rPvkvvrf~iE  748 (791)
T KOG1002|consen  689 --------------DCRVFLVSLKA----GGVALNLTEASQVFMMDPWWNPAVEWQAQDRIHRIGQY--RPVKVVRFCIE  748 (791)
T ss_pred             --------------CeEEEEEEecc----CceEeeechhceeEeecccccHHHHhhhhhhHHhhcCc--cceeEEEeehh
Confidence                          355 5666677    7888999999999999987765      5667888765  56678888876


Q ss_pred             c
Q 028124          186 G  186 (213)
Q Consensus       186 ~  186 (213)
                      +
T Consensus       749 n  749 (791)
T KOG1002|consen  749 N  749 (791)
T ss_pred             c
Confidence            5

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

Probab=98.41  E-value=1.9e-06  Score=81.65  Aligned_cols=146  Identities=14%  Similarity=0.248  Sum_probs=111.2

Q ss_pred             CCCCCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc----CC---ceEEEecC
Q 028124           14 QSPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL----AD---ISFSSLHS   86 (213)
Q Consensus        14 ~~~~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~----~~---~~~~~lhg   86 (213)
                      .-+...-.|+.+|..-+..+.--+.+.-.++-...  .+.+-++||-..+++.+.+++.|.+.    +.   .....+||
T Consensus       221 ~i~GR~fPVei~y~~~p~~dYv~a~~~tv~~Ih~~--E~~GDILvFLtGqeEIe~~~~~l~e~~~~~~~~~~~~~lply~  298 (674)
T KOG0922|consen  221 TIPGRTFPVEILYLKEPTADYVDAALITVIQIHLT--EPPGDILVFLTGQEEIEAACELLRERAKSLPEDCPELILPLYG  298 (674)
T ss_pred             eecCCCCceeEEeccCCchhhHHHHHHHHHHHHcc--CCCCCEEEEeCCHHHHHHHHHHHHHHhhhccccCcceeeeecc
Confidence            33444556888888766666455555555443222  56679999999999999999999765    11   13567999


Q ss_pred             CCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEE--------ecC
Q 028124           87 DLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLIN--------YEL  158 (213)
Q Consensus        87 ~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~--------yd~  158 (213)
                      .|+.+++.++++.--.|                       ..+++++|++    ++-.+.++++.+||.        |++
T Consensus       299 aL~~e~Q~rvF~p~p~g-----------------------~RKvIlsTNI----AETSlTI~GI~YVVDsG~vK~~~y~p  351 (674)
T KOG0922|consen  299 ALPSEEQSRVFDPAPPG-----------------------KRKVILSTNI----AETSLTIDGIRYVVDSGFVKQKKYNP  351 (674)
T ss_pred             cCCHHHhhccccCCCCC-----------------------cceEEEEcce----eeeeEEecceEEEEcCCceEEEeecc
Confidence            99999998887766665                       4899999999    999999999999996        332


Q ss_pred             ----------CCChHHHHHhhccccCC-CCeEEEEEeCchh
Q 028124          159 ----------PTKKETYIRRMTTCLAA-DGSVINIVVGGEV  188 (213)
Q Consensus       159 ----------P~~~~~yi~R~GR~~~~-~g~~i~~~~~~e~  188 (213)
                                |-|.+.-.||.||+|+. +|.|+-++++.+.
T Consensus       352 ~~g~~~L~v~~ISkasA~QRaGRAGRt~pGkcyRLYte~~~  392 (674)
T KOG0922|consen  352 RTGLDSLIVVPISKASANQRAGRAGRTGPGKCYRLYTESAY  392 (674)
T ss_pred             ccCccceeEEechHHHHhhhcccCCCCCCceEEEeeeHHHH
Confidence                      44678889999999765 5999999987554

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

Probab=98.41  E-value=5.3e-06  Score=80.03  Aligned_cols=123  Identities=17%  Similarity=0.202  Sum_probs=103.6

Q ss_pred             HHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhc-cCCceEEEecCCCCHHHHHHHHHHHhcccccccccccc
Q 028124           35 KMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSN-LADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE  113 (213)
Q Consensus        35 K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~-~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~  113 (213)
                      |++++..+|+.-.   ..+.+++.|..++...+.|-..|.. .+ +...-+.|..+-..|..++.+|..++         
T Consensus       531 Km~vl~~ll~~W~---kqg~rvllFsqs~~mLdilE~fL~~~~~-ysylRmDGtT~~~~R~~lVd~Fne~~---------  597 (923)
T KOG0387|consen  531 KMKVLAKLLKDWK---KQGDRVLLFSQSRQMLDILESFLRRAKG-YSYLRMDGTTPAALRQKLVDRFNEDE---------  597 (923)
T ss_pred             hHHHHHHHHHHHh---hCCCEEEEehhHHHHHHHHHHHHHhcCC-ceEEEecCCCccchhhHHHHhhcCCC---------
Confidence            9999999997632   3678999999999999999999984 55 89999999999999999999999875         


Q ss_pred             cCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCC-C-CeEEEEEeCc
Q 028124          114 QSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAA-D-GSVINIVVGG  186 (213)
Q Consensus       114 ~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~-~-g~~i~~~~~~  186 (213)
                                  ...-+|++|-+    .+-|+++..++-||.||+-|++.+=.|-.-|+  .|+ . -.+|-|++.+
T Consensus       598 ------------s~~VFLLTTrv----GGLGlNLTgAnRVIIfDPdWNPStD~QAreRawRiGQkkdV~VYRL~t~g  658 (923)
T KOG0387|consen  598 ------------SIFVFLLTTRV----GGLGLNLTGANRVIIFDPDWNPSTDNQARERAWRIGQKKDVVVYRLMTAG  658 (923)
T ss_pred             ------------ceEEEEEEecc----cccccccccCceEEEECCCCCCccchHHHHHHHhhcCccceEEEEEecCC
Confidence                        22347899999    99999999999999999999998888866664  333 3 4666788775

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

Probab=98.41  E-value=7.1e-06  Score=80.26  Aligned_cols=125  Identities=15%  Similarity=0.237  Sum_probs=104.7

Q ss_pred             hHHHHHHHHH-HHhhcCCCCCC--cEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccccc
Q 028124           34 FKMETLVELL-HLVVAGRRPGL--PMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQK  110 (213)
Q Consensus        34 ~K~~~L~~ll-~~~~~~~~~~~--~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~  110 (213)
                      .|+..+.+++ ..+.   ..+.  +++||++.....+.+...|...+ +....++|.++.+.|...+++|.+++      
T Consensus       692 ~k~~~l~~ll~~~~~---~~~~~~kvlifsq~t~~l~il~~~l~~~~-~~~~~ldG~~~~~~r~~~i~~f~~~~------  761 (866)
T COG0553         692 GKLQALDELLLDKLL---EEGHYHKVLIFSQFTPVLDLLEDYLKALG-IKYVRLDGSTPAKRRQELIDRFNADE------  761 (866)
T ss_pred             hHHHHHHHHHHHHHH---hhcccccEEEEeCcHHHHHHHHHHHHhcC-CcEEEEeCCCChhhHHHHHHHhhcCC------
Confidence            4899998888 4432   3455  99999999999999999999987 78999999999999999999999963      


Q ss_pred             ccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCCC--CeEEEEEeCc
Q 028124          111 VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAAD--GSVINIVVGG  186 (213)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~~--g~~i~~~~~~  186 (213)
                                     ...-+++++.+    .+.|+++..+++||+||..|++....|.+.|+  .|+.  -.++.++..+
T Consensus       762 ---------------~~~v~lls~ka----gg~glnLt~a~~vi~~d~~wnp~~~~Qa~dRa~RigQ~~~v~v~r~i~~~  822 (866)
T COG0553         762 ---------------EEKVFLLSLKA----GGLGLNLTGADTVILFDPWWNPAVELQAIDRAHRIGQKRPVKVYRLITRG  822 (866)
T ss_pred             ---------------CCceEEEEecc----cccceeecccceEEEeccccChHHHHHHHHHHHHhcCcceeEEEEeecCC
Confidence                           13557788889    99999999999999999999999998888885  2333  4777788765


Q ss_pred             h
Q 028124          187 E  187 (213)
Q Consensus       187 e  187 (213)
                      .
T Consensus       823 t  823 (866)
T COG0553         823 T  823 (866)
T ss_pred             c
Confidence            3

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

Probab=98.40  E-value=2.4e-06  Score=83.82  Aligned_cols=119  Identities=17%  Similarity=0.246  Sum_probs=89.2

Q ss_pred             HHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccC-----------------------C---------------c
Q 028124           38 TLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLA-----------------------D---------------I   79 (213)
Q Consensus        38 ~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~-----------------------~---------------~   79 (213)
                      ...+++..+..  .+-.|+||||=+++.|++-+++|....                       .               -
T Consensus       554 ~~l~lin~L~k--~~lLP~VvFvFSkkrCde~a~~L~~~nL~~~~EKseV~lfl~k~~~rLk~~DR~LPQvl~m~~ll~R  631 (1248)
T KOG0947|consen  554 TWLDLINHLRK--KNLLPVVVFVFSKKRCDEYADYLTNLNLTDSKEKSEVHLFLSKAVARLKGEDRNLPQVLSMRSLLLR  631 (1248)
T ss_pred             hHHHHHHHHhh--cccCceEEEEEccccHHHHHHHHhccCcccchhHHHHHHHHHHHHHhcChhhccchHHHHHHHHHhh
Confidence            45566655443  567899999999999999999886540                       0               1


Q ss_pred             eEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCC
Q 028124           80 SFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELP  159 (213)
Q Consensus        80 ~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P  159 (213)
                      -+++.||++=+--+.-+-.-|..|-                       +++|+||+.    ++.|++.|.-.+|+ -.+-
T Consensus       632 GiaVHH~GlLPivKE~VE~LFqrGl-----------------------VKVLFATET----FAMGVNMPARtvVF-~Sl~  683 (1248)
T KOG0947|consen  632 GIAVHHGGLLPIVKEVVELLFQRGL-----------------------VKVLFATET----FAMGVNMPARTVVF-SSLR  683 (1248)
T ss_pred             cchhhcccchHHHHHHHHHHHhcCc-----------------------eEEEeehhh----hhhhcCCCceeEEe-eehh
Confidence            1566788877777666777799984                       999999999    99999999655554 3332


Q ss_pred             C---------ChHHHHHhhccccCCC----CeEEEEEeCc
Q 028124          160 T---------KKETYIRRMTTCLAAD----GSVINIVVGG  186 (213)
Q Consensus       160 ~---------~~~~yi~R~GR~~~~~----g~~i~~~~~~  186 (213)
                      .         .+-.|.|.+||+|++.    |.+|.++...
T Consensus       684 KhDG~efR~L~PGEytQMAGRAGRRGlD~tGTVii~~~~~  723 (1248)
T KOG0947|consen  684 KHDGNEFRELLPGEYTQMAGRAGRRGLDETGTVIIMCKDS  723 (1248)
T ss_pred             hccCcceeecCChhHHhhhccccccccCcCceEEEEecCC
Confidence            2         4689999999986554    9999988754

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

Probab=98.36  E-value=9.1e-06  Score=81.44  Aligned_cols=128  Identities=16%  Similarity=0.251  Sum_probs=99.6

Q ss_pred             chHHHHHHHHHHHhhcCC-----------CCCCcEEEEeCchHHHHHHHHHHhcc--CCceEEEecCCCCHHHHHHHHHH
Q 028124           33 QFKMETLVELLHLVVAGR-----------RPGLPMIVCCSSRDELDAVCSAVSNL--ADISFSSLHSDLAETERTLILEE   99 (213)
Q Consensus        33 ~~K~~~L~~ll~~~~~~~-----------~~~~~~IIF~~~~~~~~~l~~~L~~~--~~~~~~~lhg~~~~~~R~~~l~~   99 (213)
                      ..|+.+|.++|.+--.+.           -.+.|++|||.-++.++.+-+-|.+.  +.+.-.-+.|..++.+|.+++++
T Consensus      1309 spKl~AL~qLL~eCGig~~~~~~~g~~s~vsqHRiLIFcQlK~mlDlVekDL~k~~mpsVtymRLDGSVpp~~R~kiV~~ 1388 (1549)
T KOG0392|consen 1309 SPKLSALKQLLSECGIGNNSDSEVGTPSDVSQHRILIFCQLKSMLDLVEKDLFKKYMPSVTYMRLDGSVPPGDRQKIVER 1388 (1549)
T ss_pred             chhHHHHHHHHHHhCCCCCCcccccCcchhccceeEEeeeHHHHHHHHHHHHhhhhcCceeEEEecCCCCcHHHHHHHHH
Confidence            459999999997521111           13589999999999999999988654  43445579999999999999999


Q ss_pred             HhcccccccccccccCCCCCcCCCCCCceeEE-EEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCCC
Q 028124          100 FRHTAMKWNQKVTEQSGDESETGKDEHKSHMI-VVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAAD  176 (213)
Q Consensus       100 Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iL-V~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~~  176 (213)
                      |.++.                      ++++| .+|-+    .+-|+++.++++||.++=-|++..=.|-+-|+  -|+.
T Consensus      1389 FN~Dp----------------------tIDvLlLTThV----GGLGLNLTGADTVVFvEHDWNPMrDLQAMDRAHRIGQK 1442 (1549)
T KOG0392|consen 1389 FNEDP----------------------TIDVLLLTTHV----GGLGLNLTGADTVVFVEHDWNPMRDLQAMDRAHRIGQK 1442 (1549)
T ss_pred             hcCCC----------------------ceeEEEEeeec----cccccccCCCceEEEEecCCCchhhHHHHHHHHhhcCc
Confidence            99984                      68755 56778    99999999999999999999987777777775  3333


Q ss_pred             --CeEEEEEeCc
Q 028124          177 --GSVINIVVGG  186 (213)
Q Consensus       177 --g~~i~~~~~~  186 (213)
                        -.|+-+++.+
T Consensus      1443 rvVNVyRlItrG 1454 (1549)
T KOG0392|consen 1443 RVVNVYRLITRG 1454 (1549)
T ss_pred             eeeeeeeehhcc
Confidence              3455566655

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

Probab=98.32  E-value=8.2e-06  Score=81.98  Aligned_cols=147  Identities=18%  Similarity=0.208  Sum_probs=104.5

Q ss_pred             CCCCceEEEEEecCc--chHHHHHHHHH-HHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc------------------
Q 028124           18 HFSQPRHFYVAVDRL--QFKMETLVELL-HLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL------------------   76 (213)
Q Consensus        18 ~~~~i~~~~~~~~~~--~~K~~~L~~ll-~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~------------------   76 (213)
                      .+-.++|.|+-+...  ..++++..+.. +.+.. .....|+|||+.+++++.+.|.+++..                  
T Consensus       509 RpvPL~qq~Igi~ek~~~~~~qamNe~~yeKVm~-~agk~qVLVFVHsRkET~ktA~aIRd~~le~dtls~fmre~s~s~  587 (1674)
T KOG0951|consen  509 RPVPLKQQYIGITEKKPLKRFQAMNEACYEKVLE-HAGKNQVLVFVHSRKETAKTARAIRDKALEEDTLSRFMREDSASR  587 (1674)
T ss_pred             CcCCccceEeccccCCchHHHHHHHHHHHHHHHH-hCCCCcEEEEEEechHHHHHHHHHHHHHhhhhHHHHHHhcccchh
Confidence            345588888766543  33444443332 22222 133489999999999998888877611                  


Q ss_pred             -------------------CCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCC
Q 028124           77 -------------------ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDAC  137 (213)
Q Consensus        77 -------------------~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~  137 (213)
                                         + +.++..|.||+..+|..+-..|+.|.                       +++||+|.. 
T Consensus       588 eilrtea~~~kn~dLkdLLp-ygfaIHhAGl~R~dR~~~EdLf~~g~-----------------------iqvlvstat-  642 (1674)
T KOG0951|consen  588 EILRTEAGQAKNPDLKDLLP-YGFAIHHAGLNRKDRELVEDLFADGH-----------------------IQVLVSTAT-  642 (1674)
T ss_pred             hhhhhhhhcccChhHHHHhh-ccceeeccCCCcchHHHHHHHHhcCc-----------------------eeEEEeehh-
Confidence                               2 45788999999999999999999985                       999999999 


Q ss_pred             CCcCcCCCCCCCCCEEEE----ecCC------CChHHHHHhhccccCC----CCeEEEEEeCchhHHHHH
Q 028124          138 LPLLSSGESAISARVLIN----YELP------TKKETYIRRMTTCLAA----DGSVINIVVGGEVVTLRS  193 (213)
Q Consensus       138 ~~~~~rGld~~~v~~VI~----yd~P------~~~~~yi~R~GR~~~~----~g~~i~~~~~~e~~~~~~  193 (213)
                         ++.|+++|.=.++|-    ||+-      -++-+-.|+.||+|+.    .|..|..-...+...+..
T Consensus       643 ---lawgvnlpahtViikgtqvy~pekg~w~elsp~dv~qmlgragrp~~D~~gegiiit~~se~qyyls  709 (1674)
T KOG0951|consen  643 ---LAWGVNLPAHTVIIKGTQVYDPEKGRWTELSPLDVMQMLGRAGRPQYDTCGEGIIITDHSELQYYLS  709 (1674)
T ss_pred             ---hhhhcCCCcceEEecCccccCcccCccccCCHHHHHHHHhhcCCCccCcCCceeeccCchHhhhhHH
Confidence               999999997776663    6643      3688999999998644    366665555555554444

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

Probab=98.25  E-value=8e-06  Score=78.27  Aligned_cols=123  Identities=16%  Similarity=0.200  Sum_probs=105.5

Q ss_pred             hHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccc
Q 028124           34 FKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE  113 (213)
Q Consensus        34 ~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~  113 (213)
                      -|+..|-+||..+.   ..+.++++|..-.+..+.+-++|..++ +.-.-+.|.....+|..++.+|+..+         
T Consensus      1028 gKL~~LDeLL~kLk---aegHRvL~yfQMTkM~dl~EdYl~yr~-Y~ylRLDGSsk~~dRrd~vrDwQ~sd--------- 1094 (1185)
T KOG0388|consen 1028 GKLVVLDELLPKLK---AEGHRVLMYFQMTKMIDLIEDYLVYRG-YTYLRLDGSSKASDRRDVVRDWQASD--------- 1094 (1185)
T ss_pred             cceeeHHHHHHHhh---cCCceEEehhHHHHHHHHHHHHHHhhc-cceEEecCcchhhHHHHHHhhccCCc---------
Confidence            38999999998764   368999999999999999999999988 79999999999999999999999964         


Q ss_pred             cCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCC--CCeEEEEEeCc
Q 028124          114 QSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAA--DGSVINIVVGG  186 (213)
Q Consensus       114 ~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~--~g~~i~~~~~~  186 (213)
                                   ..-+|++|.+    .+-||++..++.||.||--|++..=.|-+.|+  .|+  .-.++-+++.+
T Consensus      1095 -------------iFvFLLSTRA----GGLGINLTAADTViFYdSDWNPT~D~QAMDRAHRLGQTrdvtvyrl~~rg 1154 (1185)
T KOG0388|consen 1095 -------------IFVFLLSTRA----GGLGINLTAADTVIFYDSDWNPTADQQAMDRAHRLGQTRDVTVYRLITRG 1154 (1185)
T ss_pred             -------------eEEEEEeccc----CcccccccccceEEEecCCCCcchhhHHHHHHHhccCccceeeeeecccc
Confidence                         5668999999    99999999999999999999987777766664  333  35677777765

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

Probab=98.20  E-value=3.9e-06  Score=82.80  Aligned_cols=125  Identities=12%  Similarity=0.165  Sum_probs=102.4

Q ss_pred             hHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc----C--CceEEEecCCCCHHHHHHHHHHHhcccccc
Q 028124           34 FKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL----A--DISFSSLHSDLAETERTLILEEFRHTAMKW  107 (213)
Q Consensus        34 ~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~----~--~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~  107 (213)
                      -...++.+++..+.. ....+.+|||-+....+..+.+.|...    +  .+.+..+|+.|+..+++.+..+--.|.   
T Consensus       395 id~~Li~~li~~I~~-~~~~GaILVFLPG~~eI~~~~~~L~~~~~f~~~~~~~ilplHs~~~s~eQ~~VF~~pp~g~---  470 (924)
T KOG0920|consen  395 IDYDLIEDLIEYIDE-REFEGAILVFLPGWEEILQLKELLEVNLPFADSLKFAILPLHSSIPSEEQQAVFKRPPKGT---  470 (924)
T ss_pred             ccHHHHHHHHHhccc-CCCCceEEEEcCCHHHHHHHHHHhhhccccccccceEEEeccccCChHHHHHhcCCCCCCc---
Confidence            467788888877655 355789999999999999999999642    1  266889999999999998888887774   


Q ss_pred             cccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEE--------ecCCCCh----------HHHHHhh
Q 028124          108 NQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLIN--------YELPTKK----------ETYIRRM  169 (213)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~--------yd~P~~~----------~~yi~R~  169 (213)
                                          .+|+++|.+    ++-.+.++||-+||.        ||+-.+.          +.-.||.
T Consensus       471 --------------------RKIIlaTNI----AETSITIdDVvyVIDsG~~Ke~~yD~~~~~s~l~~~wvSkAna~QR~  526 (924)
T KOG0920|consen  471 --------------------RKIILATNI----AETSITIDDVVYVIDSGLVKEKSYDPERKVSCLLLSWVSKANAKQRR  526 (924)
T ss_pred             --------------------chhhhhhhh----HhhcccccCeEEEEecCeeeeeeecccCCcchhheeeccccchHHhc
Confidence                                889999999    999999999999996        5655433          4448999


Q ss_pred             ccccC-CCCeEEEEEeCc
Q 028124          170 TTCLA-ADGSVINIVVGG  186 (213)
Q Consensus       170 GR~~~-~~g~~i~~~~~~  186 (213)
                      ||+|+ .+|.||.+++..
T Consensus       527 GRAGRv~~G~cy~L~~~~  544 (924)
T KOG0920|consen  527 GRAGRVRPGICYHLYTRS  544 (924)
T ss_pred             ccccCccCCeeEEeechh
Confidence            99875 469999999864

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

Probab=98.15  E-value=9.2e-06  Score=77.32  Aligned_cols=147  Identities=14%  Similarity=0.227  Sum_probs=114.5

Q ss_pred             CCCCCCCCCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc--------CCceE
Q 028124           10 CPPCQSPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL--------ADISF   81 (213)
Q Consensus        10 ~~~~~~~~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~--------~~~~~   81 (213)
                      +++..-|..+-.+.-+|-..+..+.--+++..+++-.+  ..+.+-+|||-.-.+..+...+.|..+        .++.+
T Consensus       432 apIF~iPGRRyPVdi~Yt~~PEAdYldAai~tVlqIH~--tqp~GDILVFltGQeEIEt~~e~l~~~~~~LGski~eliv  509 (902)
T KOG0923|consen  432 APIFRIPGRRYPVDIFYTKAPEADYLDAAIVTVLQIHL--TQPLGDILVFLTGQEEIETVKENLKERCRRLGSKIRELIV  509 (902)
T ss_pred             CcEEeccCcccceeeecccCCchhHHHHHHhhheeeEe--ccCCccEEEEeccHHHHHHHHHHHHHHHHHhccccceEEE
Confidence            45566677778889999988888755555555554322  256789999999888877766666432        24678


Q ss_pred             EEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecC---
Q 028124           82 SSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYEL---  158 (213)
Q Consensus        82 ~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~---  158 (213)
                      ..+|+.+|.+.+.++++.--.|.                       .++++||++    ++-.+.++++.+||.-.+   
T Consensus       510 ~PiYaNLPselQakIFePtP~ga-----------------------RKVVLATNI----AETSlTIdgI~yViDpGf~K~  562 (902)
T KOG0923|consen  510 LPIYANLPSELQAKIFEPTPPGA-----------------------RKVVLATNI----AETSLTIDGIKYVIDPGFVKQ  562 (902)
T ss_pred             eeccccCChHHHHhhcCCCCCCc-----------------------eeEEEeecc----hhhceeecCeEEEecCccccc
Confidence            89999999999999988877774                       889999999    999999999999996332   


Q ss_pred             ---------------CCChHHHHHhhccccCC-CCeEEEEEeC
Q 028124          159 ---------------PTKKETYIRRMTTCLAA-DGSVINIVVG  185 (213)
Q Consensus       159 ---------------P~~~~~yi~R~GR~~~~-~g~~i~~~~~  185 (213)
                                     |-|.++-.||+||+|+. +|.|+-+++.
T Consensus       563 nsynprtGmesL~v~piSKAsA~QRaGRAGRtgPGKCfRLYt~  605 (902)
T KOG0923|consen  563 NSYNPRTGMESLLVTPISKASANQRAGRAGRTGPGKCFRLYTA  605 (902)
T ss_pred             cCcCCCcCceeEEEeeechhhhhhhccccCCCCCCceEEeech
Confidence                           22567779999999765 5999999985

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

Probab=98.12  E-value=7.3e-06  Score=78.87  Aligned_cols=109  Identities=22%  Similarity=0.241  Sum_probs=81.5

Q ss_pred             CCCCcEEEEeCchHHHHHHHHHHhccCC--------------------------------------ceEEEecCCCCHHH
Q 028124           51 RPGLPMIVCCSSRDELDAVCSAVSNLAD--------------------------------------ISFSSLHSDLAETE   92 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~--------------------------------------~~~~~lhg~~~~~~   92 (213)
                      ++..++|||+=+++.|+.+|..+.+...                                      --+...|+|+-+--
T Consensus       381 ~~~~PVIvFSFSkkeCE~~Alqm~kldfN~deEk~~V~~iF~nAi~~LseeDr~LPqie~iLPLL~RGIGIHHsGLLPIl  460 (1041)
T KOG0948|consen  381 RNYLPVIVFSFSKKECEAYALQMSKLDFNTDEEKELVETIFNNAIDQLSEEDRELPQIENILPLLRRGIGIHHSGLLPIL  460 (1041)
T ss_pred             hcCCceEEEEecHhHHHHHHHhhccCcCCChhHHHHHHHHHHHHHHhcChhhccchHHHHHHHHHHhccccccccchHHH
Confidence            4568999999999999999988876510                                      01455677776666


Q ss_pred             HHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEE----ec---CCC-ChHH
Q 028124           93 RTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLIN----YE---LPT-KKET  164 (213)
Q Consensus        93 R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~----yd---~P~-~~~~  164 (213)
                      +..+---|..|                       -+++|.||+.    ++.|++.|.-++|.-    ||   +-| +.-.
T Consensus       461 KE~IEILFqEG-----------------------LvKvLFATET----FsiGLNMPAkTVvFT~~rKfDG~~fRwissGE  513 (1041)
T KOG0948|consen  461 KEVIEILFQEG-----------------------LVKVLFATET----FSIGLNMPAKTVVFTAVRKFDGKKFRWISSGE  513 (1041)
T ss_pred             HHHHHHHHhcc-----------------------HHHHHHhhhh----hhhccCCcceeEEEeeccccCCcceeeecccc
Confidence            55566668887                       4999999999    999999997666653    22   222 5678


Q ss_pred             HHHhhccccCC----CCeEEEEEeCc
Q 028124          165 YIRRMTTCLAA----DGSVINIVVGG  186 (213)
Q Consensus       165 yi~R~GR~~~~----~g~~i~~~~~~  186 (213)
                      |||..||+|++    .|.||.++...
T Consensus       514 YIQMSGRAGRRG~DdrGivIlmiDek  539 (1041)
T KOG0948|consen  514 YIQMSGRAGRRGIDDRGIVILMIDEK  539 (1041)
T ss_pred             eEEecccccccCCCCCceEEEEecCc
Confidence            99999987655    49999999753

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=98.11  E-value=5.7e-05  Score=74.31  Aligned_cols=128  Identities=10%  Similarity=0.145  Sum_probs=96.5

Q ss_pred             EEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccc
Q 028124           27 VAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMK  106 (213)
Q Consensus        27 ~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~  106 (213)
                      ++.... .|+..+.+-+...-   ..++|+||.|.+....+.|+..|.+.| +....|+..-...| ..++.  +.|.  
T Consensus       404 iy~t~~-~K~~Aii~ei~~~~---~~gqPVLVgT~SIe~SE~ls~~L~~~g-i~h~vLNAk~~e~E-A~IIa--~AG~--  473 (925)
T PRK12903        404 IFGTKH-AKWKAVVKEVKRVH---KKGQPILIGTAQVEDSETLHELLLEAN-IPHTVLNAKQNARE-AEIIA--KAGQ--  473 (925)
T ss_pred             EEEcHH-HHHHHHHHHHHHHH---hcCCCEEEEeCcHHHHHHHHHHHHHCC-CCceeecccchhhH-HHHHH--hCCC--
Confidence            333444 48888888776532   468999999999999999999999987 88888887533222 33443  3442  


Q ss_pred             ccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCC--------EEEEecCCCChHHHHHhhcccc--CCC
Q 028124          107 WNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISAR--------VLINYELPTKKETYIRRMTTCL--AAD  176 (213)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~--------~VI~yd~P~~~~~yi~R~GR~~--~~~  176 (213)
                                          +-.|.|||++    ++||.|+.--.        +||.-..|.|..-=-|-.||+|  |.+
T Consensus       474 --------------------~GaVTIATNM----AGRGTDI~Lg~~V~~~GGLhVIgTerheSrRIDnQLrGRaGRQGDp  529 (925)
T PRK12903        474 --------------------KGAITIATNM----AGRGTDIKLSKEVLELGGLYVLGTDKAESRRIDNQLRGRSGRQGDV  529 (925)
T ss_pred             --------------------CCeEEEeccc----ccCCcCccCchhHHHcCCcEEEecccCchHHHHHHHhcccccCCCC
Confidence                                5779999999    99999997443        8999999988776678889974  667


Q ss_pred             CeEEEEEeCchh
Q 028124          177 GSVINIVVGGEV  188 (213)
Q Consensus       177 g~~i~~~~~~e~  188 (213)
                      |.+-.|++-+|.
T Consensus       530 Gss~f~lSLeD~  541 (925)
T PRK12903        530 GESRFFISLDDQ  541 (925)
T ss_pred             CcceEEEecchH
Confidence            888888876543

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

Probab=98.03  E-value=2.4e-05  Score=77.76  Aligned_cols=91  Identities=16%  Similarity=0.235  Sum_probs=66.0

Q ss_pred             HHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc---CCceEEEecCCCCHHHHHHHHHHHhcccccccccccc
Q 028124           37 ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL---ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE  113 (213)
Q Consensus        37 ~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~---~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~  113 (213)
                      +.+.+.|..+..  ...++++||+++.+.++.++..|...   .++.+  +..+.. ..|.+++++|+.++         
T Consensus       660 ~~ia~~i~~l~~--~~~g~~LVlftS~~~l~~v~~~L~~~~~~~~~~~--l~q~~~-~~r~~ll~~F~~~~---------  725 (850)
T TIGR01407       660 QEIASYIIEITA--ITSPKILVLFTSYEMLHMVYDMLNELPEFEGYEV--LAQGIN-GSRAKIKKRFNNGE---------  725 (850)
T ss_pred             HHHHHHHHHHHH--hcCCCEEEEeCCHHHHHHHHHHHhhhccccCceE--EecCCC-ccHHHHHHHHHhCC---------
Confidence            345555544333  34579999999999999999999752   11333  223333 57899999999974         


Q ss_pred             cCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCC--EEEEecCC
Q 028124          114 QSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISAR--VLINYELP  159 (213)
Q Consensus       114 ~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~--~VI~yd~P  159 (213)
                                    ..+|++|+.    +.+|+|+++..  +||...+|
T Consensus       726 --------------~~iLlgt~s----f~EGVD~~g~~l~~viI~~LP  755 (850)
T TIGR01407       726 --------------KAILLGTSS----FWEGVDFPGNGLVCLVIPRLP  755 (850)
T ss_pred             --------------CeEEEEcce----eecccccCCCceEEEEEeCCC
Confidence                          789999999    99999999877  45655555

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.

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

Probab=97.97  E-value=5.5e-05  Score=75.06  Aligned_cols=113  Identities=17%  Similarity=0.242  Sum_probs=84.3

Q ss_pred             CCCcEEEEeCchHHHHHHHHHHhcc----CC------------------ceEEEecCCCCHHHHHHHHHHHhcccccccc
Q 028124           52 PGLPMIVCCSSRDELDAVCSAVSNL----AD------------------ISFSSLHSDLAETERTLILEEFRHTAMKWNQ  109 (213)
Q Consensus        52 ~~~~~IIF~~~~~~~~~l~~~L~~~----~~------------------~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~  109 (213)
                      .+.+++|||.++..+-..|+.|...    |.                  .-....|.+|...+|.-.-..|..|.     
T Consensus       348 ~g~qVlvFvhsR~~Ti~tA~~l~~~a~~~g~~~~f~~~~~~k~l~elf~~g~~iHhAGm~r~DR~l~E~~F~~G~-----  422 (1230)
T KOG0952|consen  348 EGHQVLVFVHSRNETIRTAKKLRERAETNGEKDLFLPSPRNKQLKELFQQGMGIHHAGMLRSDRQLVEKEFKEGH-----  422 (1230)
T ss_pred             cCCeEEEEEecChHHHHHHHHHHHHHHhcCcccccCCChhhHHHHHHHHhhhhhcccccchhhHHHHHHHHhcCC-----
Confidence            4899999999999999998888654    10                  12456788999999999999999985     


Q ss_pred             cccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEE----ecCCC------ChHHHHHhhcccc----CC
Q 028124          110 KVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLIN----YELPT------KKETYIRRMTTCL----AA  175 (213)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~----yd~P~------~~~~yi~R~GR~~----~~  175 (213)
                                        +++|+||..    ++-|+++|+=-++|-    ||.-.      ..-+-+|-.||+|    .+
T Consensus       423 ------------------i~vL~cTaT----LAwGVNLPA~aViIKGT~~ydsskg~f~dlgilDVlQifGRAGRPqFd~  480 (1230)
T KOG0952|consen  423 ------------------IKVLCCTAT----LAWGVNLPAYAVIIKGTQVYDSSKGSFVDLGILDVLQIFGRAGRPQFDS  480 (1230)
T ss_pred             ------------------ceEEEecce----eeeccCCcceEEEecCCcccccccCceeeehHHHHHHHHhccCCCCCCC
Confidence                              999999999    999999996544442    44333      2456677777764    45


Q ss_pred             CCeEEEEEeCchhHHH
Q 028124          176 DGSVINIVVGGEVVTL  191 (213)
Q Consensus       176 ~g~~i~~~~~~e~~~~  191 (213)
                      .|.+|.+-+.+-...+
T Consensus       481 ~G~giIiTt~dkl~~Y  496 (1230)
T KOG0952|consen  481 SGEGIIITTRDKLDHY  496 (1230)
T ss_pred             CceEEEEecccHHHHH
Confidence            5888877765444433

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

Probab=97.95  E-value=0.00011  Score=68.45  Aligned_cols=131  Identities=16%  Similarity=0.175  Sum_probs=97.4

Q ss_pred             eEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhc
Q 028124           23 RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRH  102 (213)
Q Consensus        23 ~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~  102 (213)
                      +...+++-+.. |++.-.-|++..   +..+.++|||..+.-.....|-.|.+      -.++|..++.||.++|+.|+.
T Consensus       517 kr~lLyvMNP~-KFraCqfLI~~H---E~RgDKiIVFsDnvfALk~YAikl~K------pfIYG~Tsq~ERm~ILqnFq~  586 (776)
T KOG1123|consen  517 KRMLLYVMNPN-KFRACQFLIKFH---ERRGDKIIVFSDNVFALKEYAIKLGK------PFIYGPTSQNERMKILQNFQT  586 (776)
T ss_pred             hhheeeecCcc-hhHHHHHHHHHH---HhcCCeEEEEeccHHHHHHHHHHcCC------ceEECCCchhHHHHHHHhccc
Confidence            34556677777 998876677543   24789999998877666665555522      357899999999999999998


Q ss_pred             ccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCC-ChHHHHHhhccc--c--CC--
Q 028124          103 TAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPT-KKETYIRRMTTC--L--AA--  175 (213)
Q Consensus       103 g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~-~~~~yi~R~GR~--~--~~--  175 (213)
                      ..                      +++-+..+.+    ..-.+|+|+++++|...-.. |...=-||.||.  +  ++  
T Consensus       587 n~----------------------~vNTIFlSKV----gDtSiDLPEAnvLIQISSH~GSRRQEAQRLGRILRAKk~~de  640 (776)
T KOG1123|consen  587 NP----------------------KVNTIFLSKV----GDTSIDLPEANVLIQISSHGGSRRQEAQRLGRILRAKKRNDE  640 (776)
T ss_pred             CC----------------------ccceEEEeec----cCccccCCcccEEEEEcccccchHHHHHHHHHHHHHhhcCcc
Confidence            74                      6888888888    89999999999999987664 455667999994  1  11  


Q ss_pred             --CCeEEEEEeCchhH
Q 028124          176 --DGSVINIVVGGEVV  189 (213)
Q Consensus       176 --~g~~i~~~~~~e~~  189 (213)
                        ....+++|..+..+
T Consensus       641 ~fnafFYSLVS~DTqE  656 (776)
T KOG1123|consen  641 EFNAFFYSLVSKDTQE  656 (776)
T ss_pred             ccceeeeeeeecchHH
Confidence              24777888766433

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

Probab=97.88  E-value=6.9e-05  Score=72.97  Aligned_cols=93  Identities=13%  Similarity=0.154  Sum_probs=76.1

Q ss_pred             CCCcEEEEeCchHHHHHHHHHHhcc-CC---ceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCc
Q 028124           52 PGLPMIVCCSSRDELDAVCSAVSNL-AD---ISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHK  127 (213)
Q Consensus        52 ~~~~~IIF~~~~~~~~~l~~~L~~~-~~---~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~  127 (213)
                      ..+|+||||.+.++|+++...|.+. ++   --+..+.|+-  ++-.+.+..|...+                     .-
T Consensus       425 ~~~KTIvFa~n~dHAe~i~~~~~~~ype~~~~~a~~IT~d~--~~~q~~Id~f~~ke---------------------~~  481 (875)
T COG4096         425 EIGKTIVFAKNHDHAERIREALVNEYPEYNGRYAMKITGDA--EQAQALIDNFIDKE---------------------KY  481 (875)
T ss_pred             ccCceEEEeeCcHHHHHHHHHHHHhCccccCceEEEEeccc--hhhHHHHHHHHhcC---------------------CC
Confidence            3689999999999999999999764 21   3467777764  33455666776643                     24


Q ss_pred             eeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhcc
Q 028124          128 SHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTT  171 (213)
Q Consensus       128 ~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR  171 (213)
                      .+|.|+.|+    +.-|+|+|.|.++|.+..=+|...|.|.+||
T Consensus       482 P~Iaitvdl----L~TGiDvpev~nlVF~r~VrSktkF~QMvGR  521 (875)
T COG4096         482 PRIAITVDL----LTTGVDVPEVVNLVFDRKVRSKTKFKQMVGR  521 (875)
T ss_pred             CceEEehhh----hhcCCCchheeeeeehhhhhhHHHHHHHhcC
Confidence            779999999    9999999999999999999999999999999

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

Probab=97.86  E-value=3.7e-05  Score=73.58  Aligned_cols=142  Identities=11%  Similarity=0.205  Sum_probs=103.7

Q ss_pred             CCCCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHH----HHHHHhcc---C--CceEEEec
Q 028124           15 SPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDA----VCSAVSNL---A--DISFSSLH   85 (213)
Q Consensus        15 ~~~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~----l~~~L~~~---~--~~~~~~lh   85 (213)
                      -|...-.+.-.|...+-++.--.++.+.+.-...  ...+-.+||..-.+..+-    |.+.|...   +  ++.+..++
T Consensus       527 IpGRTyPV~~~~~k~p~eDYVeaavkq~v~Ihl~--~~~GdilIfmtGqediE~t~~~i~~~l~ql~~~~~~~L~vlpiY  604 (1042)
T KOG0924|consen  527 IPGRTYPVEIMYTKTPVEDYVEAAVKQAVQIHLS--GPPGDILIFMTGQEDIECTCDIIKEKLEQLDSAPTTDLAVLPIY  604 (1042)
T ss_pred             ecCCccceEEEeccCchHHHHHHHHhhheEeecc--CCCCCEEEecCCCcchhHHHHHHHHHHHhhhcCCCCceEEEeeh
Confidence            3444445777777777666555555555543222  345789999987665554    44444332   2  47899999


Q ss_pred             CCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEec--------
Q 028124           86 SDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYE--------  157 (213)
Q Consensus        86 g~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd--------  157 (213)
                      +.||..-+.++++.--.|.                       .+++|+|++    ++-.+.++++.+||...        
T Consensus       605 SQLp~dlQ~kiFq~a~~~v-----------------------RK~IvATNI----AETSLTi~gI~yVID~Gy~K~kvyn  657 (1042)
T KOG0924|consen  605 SQLPADLQAKIFQKAEGGV-----------------------RKCIVATNI----AETSLTIPGIRYVIDTGYCKLKVYN  657 (1042)
T ss_pred             hhCchhhhhhhcccCCCCc-----------------------eeEEEeccc----hhhceeecceEEEEecCceeeeecc
Confidence            9999999988877766663                       889999999    99999999999999753        


Q ss_pred             ----------CCCChHHHHHhhccccCC-CCeEEEEEeC
Q 028124          158 ----------LPTKKETYIRRMTTCLAA-DGSVINIVVG  185 (213)
Q Consensus       158 ----------~P~~~~~yi~R~GR~~~~-~g~~i~~~~~  185 (213)
                                .|-|-+.--||.||+|+. +|.|+-+++.
T Consensus       658 ~~~G~D~L~~~pIS~AnA~QRaGRAGRt~pG~cYRlYTe  696 (1042)
T KOG0924|consen  658 PRIGMDALQIVPISQANADQRAGRAGRTGPGTCYRLYTE  696 (1042)
T ss_pred             cccccceeEEEechhccchhhccccCCCCCcceeeehhh
Confidence                      344566778999999765 6999999986

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=97.83  E-value=0.00011  Score=72.61  Aligned_cols=45  Identities=13%  Similarity=0.142  Sum_probs=36.2

Q ss_pred             CcchHHHHHHHHHHHhhcC------CCCCCcEEEEeCchHHHHHHHHHHhc
Q 028124           31 RLQFKMETLVELLHLVVAG------RRPGLPMIVCCSSRDELDAVCSAVSN   75 (213)
Q Consensus        31 ~~~~K~~~L~~ll~~~~~~------~~~~~~~IIF~~~~~~~~~l~~~L~~   75 (213)
                      ++..|++.|.++|+++...      ..+..++||||+..++|..|.+.|..
T Consensus       267 Ee~PKw~~L~eiL~eI~~~~~~~~~~~~~~~iLI~~~d~~T~~qL~~~L~~  317 (814)
T TIGR00596       267 EENPKWEVLTDVLKEISHEMRMTNRLQGPGKVLIMCSDNRTCLQLRDYLTT  317 (814)
T ss_pred             ccCCCHHHHHHHHHHHHhHHhhhcccCCCCcEEEEEcchHHHHHHHHHHHh
Confidence            3567999999999875542      13457899999999999999999965

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

>PF06862 DUF1253: Protein of unknown function (DUF1253); InterPro: IPR010678 This family is defined by a C-terminal region of approximately 500 residues, Digestive organ expansion factor (DEF) is thought to Regulate the p53 pathway to control the expansion growth of digestive organs and is required for the expansion growth of intestine, liver and exocrine pancreas, but not endocrine pancreas [, ]

Probab=97.82  E-value=0.0011  Score=61.32  Aligned_cols=151  Identities=13%  Similarity=0.134  Sum_probs=114.2

Q ss_pred             CCCCceEEEEEecC------cchHHHHHHH-HHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCH
Q 028124           18 HFSQPRHFYVAVDR------LQFKMETLVE-LLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAE   90 (213)
Q Consensus        18 ~~~~i~~~~~~~~~------~~~K~~~L~~-ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~   90 (213)
                      ...+|+|.+..++.      .+.+++.+.+ +|..+.. ......++||+++--.=-.|-+.|++.. +....+|--.+.
T Consensus       259 v~~~v~Q~F~r~~~~s~~~~~d~Rf~yF~~~iLP~l~~-~~~~~~~LIfIPSYfDfVRlRN~lk~~~-~sF~~i~EYts~  336 (442)
T PF06862_consen  259 VVVQVRQVFQRFDCSSPADDPDARFKYFTKKILPQLKR-DSKMSGTLIFIPSYFDFVRLRNYLKKEN-ISFVQISEYTSN  336 (442)
T ss_pred             cccCCceEEEEecCCCcchhhhHHHHHHHHHHHHHhhh-ccCCCcEEEEecchhhhHHHHHHHHhcC-CeEEEecccCCH
Confidence            44578899987553      2456666666 5555442 2466899999999999999999999765 899999999999


Q ss_pred             HHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhc
Q 028124           91 TERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMT  170 (213)
Q Consensus        91 ~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~G  170 (213)
                      .+-.++-..|.+|.                       .++|+.|+-.  -.=|=..+.++..||.|.+|..+.-|..-+.
T Consensus       337 ~~isRAR~~F~~G~-----------------------~~iLL~TER~--HFfrRy~irGi~~viFY~~P~~p~fY~El~n  391 (442)
T PF06862_consen  337 SDISRARSQFFHGR-----------------------KPILLYTERF--HFFRRYRIRGIRHVIFYGPPENPQFYSELLN  391 (442)
T ss_pred             HHHHHHHHHHHcCC-----------------------ceEEEEEhHH--hhhhhceecCCcEEEEECCCCChhHHHHHHh
Confidence            99999999999985                       9999999951  1123345678999999999999988877664


Q ss_pred             cccC--------CCCeEEEEEeCchhHHHHHHH
Q 028124          171 TCLA--------ADGSVINIVVGGEVVTLRSME  195 (213)
Q Consensus       171 R~~~--------~~g~~i~~~~~~e~~~~~~le  195 (213)
                      --..        ....|..+++..|...+..|.
T Consensus       392 ~~~~~~~~~~~~~~~~~~~lysk~D~~~LErIV  424 (442)
T PF06862_consen  392 MLDESSGGEVDAADATVTVLYSKYDALRLERIV  424 (442)
T ss_pred             hhcccccccccccCceEEEEecHhHHHHHHHHh
Confidence            3221        246888888888876555553

; GO: 0005634 nucleus

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

Probab=97.81  E-value=0.00031  Score=68.19  Aligned_cols=106  Identities=14%  Similarity=0.082  Sum_probs=78.4

Q ss_pred             CCcEEEEeCchHHHHHHHHHHhcc-C---CceEEEecCCCCHH---------------------HHHHHHHHHhcccccc
Q 028124           53 GLPMIVCCSSRDELDAVCSAVSNL-A---DISFSSLHSDLAET---------------------ERTLILEEFRHTAMKW  107 (213)
Q Consensus        53 ~~~~IIF~~~~~~~~~l~~~L~~~-~---~~~~~~lhg~~~~~---------------------~R~~~l~~Fr~g~~~~  107 (213)
                      +.+++|||.++..|..+.+.|... +   ....+.+++..+.+                     ...+++++|+..    
T Consensus       514 ~~kamvv~~sr~~a~~~~~~l~~~~~~~~~~~~vv~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Fk~~----  589 (667)
T TIGR00348       514 KFKAMVVAISRYACVEEKNALDEELNEKFEASAIVMTGKESDDAEIRDYNKHIRTKFDKSDGFEIYYKDLERFKKE----  589 (667)
T ss_pred             cCceeEEEecHHHHHHHHHHHHhhcccccCCeeEEecCCccchhHHHHHHHHhccccccchhhhHHHHHHHHhcCC----
Confidence            589999999999999999988654 1   13556677654433                     123566677653    


Q ss_pred             cccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccccC-----C-CCeEEE
Q 028124          108 NQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLA-----A-DGSVIN  181 (213)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~~-----~-~g~~i~  181 (213)
                                        +..++||++|.    +..|+|.|.+++++..-+-.+ ..++|.+||+.+     + .|.++.
T Consensus       590 ------------------~~~~ilIVvdm----llTGFDaP~l~tLyldKplk~-h~LlQai~R~nR~~~~~K~~g~IvD  646 (667)
T TIGR00348       590 ------------------ENPKLLIVVDM----LLTGFDAPILNTLYLDKPLKY-HGLLQAIARTNRIDGKDKTFGLIVD  646 (667)
T ss_pred             ------------------CCceEEEEEcc----cccccCCCccceEEEeccccc-cHHHHHHHHhccccCCCCCCEEEEE
Confidence                              25899999999    999999999999998776665 468999999633     2 267777


Q ss_pred             EEeC
Q 028124          182 IVVG  185 (213)
Q Consensus       182 ~~~~  185 (213)
                      |+..
T Consensus       647 y~g~  650 (667)
T TIGR00348       647 YRGL  650 (667)
T ss_pred             CcCh
Confidence            7653

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

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=97.77  E-value=0.0005  Score=66.80  Aligned_cols=123  Identities=15%  Similarity=0.103  Sum_probs=94.5

Q ss_pred             chHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccccccc
Q 028124           33 QFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVT  112 (213)
Q Consensus        33 ~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~  112 (213)
                      ..|++.+.+-+...-   ..++|+||.|.+....+.|+..|.+.+ +....|+..-...| ..++.+-  |         
T Consensus       410 ~~k~~Aii~ei~~~~---~~GrPVLVgt~sI~~SE~ls~~L~~~g-I~h~vLNAk~~~~E-A~IIa~A--G---------  473 (764)
T PRK12326        410 AEKNDAIVEHIAEVH---ETGQPVLVGTHDVAESEELAERLRAAG-VPAVVLNAKNDAEE-ARIIAEA--G---------  473 (764)
T ss_pred             HHHHHHHHHHHHHHH---HcCCCEEEEeCCHHHHHHHHHHHHhCC-CcceeeccCchHhH-HHHHHhc--C---------
Confidence            448888888776532   478999999999999999999999987 88888887633333 4444432  2         


Q ss_pred             ccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCC---------------CEEEEecCCCChHHHHHhhcccc--CC
Q 028124          113 EQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISA---------------RVLINYELPTKKETYIRRMTTCL--AA  175 (213)
Q Consensus       113 ~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v---------------~~VI~yd~P~~~~~yi~R~GR~~--~~  175 (213)
                                   .+-.|-|||.+    ++||.|+.=-               =+||--..|.|..-=-|=.||+|  |.
T Consensus       474 -------------~~gaVTIATNM----AGRGTDIkLg~~~~~~~~~V~~~GGLhVIgTerheSrRID~QLrGRaGRQGD  536 (764)
T PRK12326        474 -------------KYGAVTVSTQM----AGRGTDIRLGGSDEADRDRVAELGGLHVIGTGRHRSERLDNQLRGRAGRQGD  536 (764)
T ss_pred             -------------CCCcEEEEecC----CCCccCeecCCCcccchHHHHHcCCcEEEeccCCchHHHHHHHhcccccCCC
Confidence                         14679999999    9999998632               27888888988877778779975  66


Q ss_pred             CCeEEEEEeCchh
Q 028124          176 DGSVINIVVGGEV  188 (213)
Q Consensus       176 ~g~~i~~~~~~e~  188 (213)
                      +|.+-.|++-+|.
T Consensus       537 pGss~f~lSleDd  549 (764)
T PRK12326        537 PGSSVFFVSLEDD  549 (764)
T ss_pred             CCceeEEEEcchh
Confidence            7988888876543

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

Probab=97.74  E-value=0.00018  Score=71.46  Aligned_cols=105  Identities=18%  Similarity=0.316  Sum_probs=84.7

Q ss_pred             CCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCc---hHHHHHHHHHHhccCCceEEEecCCCCHHHH
Q 028124           17 SHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSS---RDELDAVCSAVSNLADISFSSLHSDLAETER   93 (213)
Q Consensus        17 ~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~---~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R   93 (213)
                      ....||...|+..   . -.+.+.++++.+      +.-.|||++.   ++.+++|++.|++.| +++..+|+.     .
T Consensus       309 ~~LRNIvD~y~~~---~-~~e~~~elvk~l------G~GgLIfV~~d~G~e~aeel~e~Lr~~G-i~a~~~~a~-----~  372 (1187)
T COG1110         309 EGLRNIVDIYVES---E-SLEKVVELVKKL------GDGGLIFVPIDYGREKAEELAEYLRSHG-INAELIHAE-----K  372 (1187)
T ss_pred             hhhhheeeeeccC---c-cHHHHHHHHHHh------CCCeEEEEEcHHhHHHHHHHHHHHHhcC-ceEEEeecc-----c
Confidence            3446777777665   2 556667777762      3568999999   999999999999998 899999983     3


Q ss_pred             HHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCC-CCEEEEecCCC
Q 028124           94 TLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAIS-ARVLINYELPT  160 (213)
Q Consensus        94 ~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~-v~~VI~yd~P~  160 (213)
                      .+.++.|..|+                       +++||....-+--+.||+|+|+ ++++|.|+.|+
T Consensus       373 ~~~le~F~~Ge-----------------------idvLVGvAsyYG~lVRGlDLP~rirYaIF~GvPk  417 (1187)
T COG1110         373 EEALEDFEEGE-----------------------VDVLVGVASYYGVLVRGLDLPHRIRYAVFYGVPK  417 (1187)
T ss_pred             hhhhhhhccCc-----------------------eeEEEEecccccceeecCCchhheeEEEEecCCc
Confidence            77899999996                       9999987655555899999995 67999999994

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

Probab=97.62  E-value=0.00047  Score=68.38  Aligned_cols=123  Identities=15%  Similarity=0.151  Sum_probs=101.1

Q ss_pred             HHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccccccccc
Q 028124           35 KMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ  114 (213)
Q Consensus        35 K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~  114 (213)
                      |+++|-.+|-.+.   ..+++++.||.-..-.+-+-.+|.-.+ ++-.-+.|....++|-..++.|.....         
T Consensus       711 KfELLDRiLPKLk---atgHRVLlF~qMTrlmdimEdyL~~~~-~kYlRLDG~TK~~eRg~ll~~FN~Pds---------  777 (1157)
T KOG0386|consen  711 KFELLDRILPKLK---ATGHRVLLFSQMTRLMDILEDYLQIRE-YKYLRLDGQTKVEERGDLLEIFNAPDS---------  777 (1157)
T ss_pred             HHHHHHhhhHHHH---hcCcchhhHHHHHHHHHHHHHHHhhhh-hheeeecCCcchhhHHHHHHHhcCCCC---------
Confidence            8999999997764   478999999998888888889998776 799999999999999999999988642         


Q ss_pred             CCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCC--CCeEEEEEeC
Q 028124          115 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAA--DGSVINIVVG  185 (213)
Q Consensus       115 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~--~g~~i~~~~~  185 (213)
                                 .-..+|.+|.+    .+.|++++-++.||.||--|++....|+--|+  -|.  +-.++-+++.
T Consensus       778 -----------~yf~Fllstra----gglglNlQtadtviifdsdwnp~~d~qaqdrahrigq~~evRv~rl~tv  837 (1157)
T KOG0386|consen  778 -----------PYFIFLLSTRA----GGLGLNLQTADTVIIFDSDWNPHQDLQAQDRAHRIGQKKEVRVLRLITV  837 (1157)
T ss_pred             -----------ceeeeeeeecc----cccccchhhcceEEEecCCCCchhHHHHHHHHHHhhchhheeeeeeehh
Confidence                       23668999999    99999999999999999999988777766664  222  3455555544

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=97.60  E-value=0.0015  Score=65.09  Aligned_cols=125  Identities=13%  Similarity=0.122  Sum_probs=95.1

Q ss_pred             CcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccccc
Q 028124           31 RLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQK  110 (213)
Q Consensus        31 ~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~  110 (213)
                      ....|+.++.+-+...-   ..+.|++|-|.+....+.|+..|...| +....++..-...| ..++.+  .|.      
T Consensus       549 t~~~k~~ai~~ei~~~~---~~grPvLigt~si~~se~ls~~L~~~g-i~h~vLNak~~~~E-a~iia~--AG~------  615 (970)
T PRK12899        549 TEREKYHAIVAEIASIH---RKGNPILIGTESVEVSEKLSRILRQNR-IEHTVLNAKNHAQE-AEIIAG--AGK------  615 (970)
T ss_pred             CHHHHHHHHHHHHHHHH---hCCCCEEEEeCcHHHHHHHHHHHHHcC-CcceecccchhhhH-HHHHHh--cCC------
Confidence            33458888888776632   468999999999999999999999987 88888887633222 334433  232      


Q ss_pred             ccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCC--------CEEEEecCCCChHHHHHhhcccc--CCCCeEE
Q 028124          111 VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISA--------RVLINYELPTKKETYIRRMTTCL--AADGSVI  180 (213)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v--------~~VI~yd~P~~~~~yi~R~GR~~--~~~g~~i  180 (213)
                                      +-.|-|||.+    ++||.|+.--        =+||--..|.|..---|-.||+|  |.+|.+.
T Consensus       616 ----------------~g~VTIATNm----AGRGTDIkl~~~v~~~GGLhVIgTer~es~Rid~Ql~GRagRQGdpGss~  675 (970)
T PRK12899        616 ----------------LGAVTVATNM----AGRGTDIKLDEEAVAVGGLYVIGTSRHQSRRIDRQLRGRCARLGDPGAAK  675 (970)
T ss_pred             ----------------CCcEEEeecc----ccCCcccccCchHHhcCCcEEEeeccCchHHHHHHHhcccccCCCCCcee
Confidence                            4679999999    9999998522        17888889998888888889975  6679999


Q ss_pred             EEEeCchh
Q 028124          181 NIVVGGEV  188 (213)
Q Consensus       181 ~~~~~~e~  188 (213)
                      .|++-+|.
T Consensus       676 f~lSlEDd  683 (970)
T PRK12899        676 FFLSFEDR  683 (970)
T ss_pred             EEEEcchH
Confidence            99987654

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

Probab=97.45  E-value=0.00044  Score=55.53  Aligned_cols=78  Identities=21%  Similarity=0.265  Sum_probs=57.0

Q ss_pred             CCCcEEEEeCchHHHHHHHHHHhccC---CceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCce
Q 028124           52 PGLPMIVCCSSRDELDAVCSAVSNLA---DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKS  128 (213)
Q Consensus        52 ~~~~~IIF~~~~~~~~~l~~~L~~~~---~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~  128 (213)
                      ..+.++||+++.+..+.+...++...   ++. +...+   ..++..++++|+.++                       -
T Consensus         8 ~~g~~lv~f~Sy~~l~~~~~~~~~~~~~~~~~-v~~q~---~~~~~~~l~~~~~~~-----------------------~   60 (167)
T PF13307_consen    8 VPGGVLVFFPSYRRLEKVYERLKERLEEKGIP-VFVQG---SKSRDELLEEFKRGE-----------------------G   60 (167)
T ss_dssp             CSSEEEEEESSHHHHHHHHTT-TSS-E-ETSC-EEEST---CCHHHHHHHHHCCSS-----------------------S
T ss_pred             CCCCEEEEeCCHHHHHHHHHHHHhhcccccce-eeecC---cchHHHHHHHHHhcc-----------------------C
Confidence            45799999999999999999998653   122 22332   467889999999974                       7


Q ss_pred             eEEEEeC--CCCCcCcCCCCCCC--CCEEEEecCCC
Q 028124          129 HMIVVTD--ACLPLLSSGESAIS--ARVLINYELPT  160 (213)
Q Consensus       129 ~iLV~Td--~~~~~~~rGld~~~--v~~VI~yd~P~  160 (213)
                      .+|+++.  .    +.+|+|+++  ++.||...+|-
T Consensus        61 ~il~~v~~g~----~~EGiD~~~~~~r~vii~glPf   92 (167)
T PF13307_consen   61 AILLAVAGGS----FSEGIDFPGDLLRAVIIVGLPF   92 (167)
T ss_dssp             EEEEEETTSC----CGSSS--ECESEEEEEEES---
T ss_pred             eEEEEEeccc----EEEeecCCCchhheeeecCCCC
Confidence            7999997  7    899999996  77899888774

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=97.41  E-value=0.0017  Score=65.20  Aligned_cols=123  Identities=15%  Similarity=0.147  Sum_probs=93.8

Q ss_pred             chHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccccccc
Q 028124           33 QFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVT  112 (213)
Q Consensus        33 ~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~  112 (213)
                      ..|+.++.+-+..+.   ..++|+||-|.|....+.|+..|...| +..-+|+......| .+++.+-  |.        
T Consensus       611 ~eK~~Aii~ei~~~~---~~GrPVLVGT~SVe~SE~lS~~L~~~g-I~H~VLNAK~h~~E-AeIVA~A--G~--------  675 (1112)
T PRK12901        611 REKYNAVIEEITELS---EAGRPVLVGTTSVEISELLSRMLKMRK-IPHNVLNAKLHQKE-AEIVAEA--GQ--------  675 (1112)
T ss_pred             HHHHHHHHHHHHHHH---HCCCCEEEEeCcHHHHHHHHHHHHHcC-CcHHHhhccchhhH-HHHHHhc--CC--------
Confidence            348988888876643   478999999999999999999999987 77777776543333 3344432  21        


Q ss_pred             ccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCC--------CCCEEEEecCCCChHHHHHhhcccc--CCCCeEEEE
Q 028124          113 EQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAI--------SARVLINYELPTKKETYIRRMTTCL--AADGSVINI  182 (213)
Q Consensus       113 ~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~--------~v~~VI~yd~P~~~~~yi~R~GR~~--~~~g~~i~~  182 (213)
                                    +-.|-|||.+    ++||.|+.        +==+||--..|.|..---|-.||+|  |.+|.+-.|
T Consensus       676 --------------~GaVTIATNM----AGRGTDIkLg~~V~e~GGL~VIgTerheSrRID~QLrGRaGRQGDPGsS~f~  737 (1112)
T PRK12901        676 --------------PGTVTIATNM----AGRGTDIKLSPEVKAAGGLAIIGTERHESRRVDRQLRGRAGRQGDPGSSQFY  737 (1112)
T ss_pred             --------------CCcEEEeccC----cCCCcCcccchhhHHcCCCEEEEccCCCcHHHHHHHhcccccCCCCCcceEE
Confidence                          4679999999    99999996        2237888888988887788889975  567988888


Q ss_pred             EeCchh
Q 028124          183 VVGGEV  188 (213)
Q Consensus       183 ~~~~e~  188 (213)
                      ++-+|.
T Consensus       738 lSLEDd  743 (1112)
T PRK12901        738 VSLEDN  743 (1112)
T ss_pred             EEcccH
Confidence            876543

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

Probab=97.35  E-value=0.0011  Score=66.74  Aligned_cols=108  Identities=20%  Similarity=0.222  Sum_probs=82.1

Q ss_pred             CCCCcEEEEeCchHHHHHHHHHHhccC---------------------------Cc-------------eEEEecCCCCH
Q 028124           51 RPGLPMIVCCSSRDELDAVCSAVSNLA---------------------------DI-------------SFSSLHSDLAE   90 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~~L~~~~---------------------------~~-------------~~~~lhg~~~~   90 (213)
                      .+..++|+|+=++..|+..+..+....                           ++             -....|++|=+
T Consensus       377 ~~~lP~I~F~FSr~~Ce~~a~~~~~ldl~~~~~~e~~i~~ii~~~i~~L~~ed~~lp~~~~~~~~~L~RGiavHH~GlLP  456 (1041)
T COG4581         377 DNLLPAIVFSFSRRGCEEAAQILSTLDLVLTEEKERAIREIIDHAIGDLAEEDRELPLQILEISALLLRGIAVHHAGLLP  456 (1041)
T ss_pred             hcCCceEEEEEchhhHHHHHHHhcccccccCCcHHHHHHHHHHHHHhhcChhhhcCcccHHHHHHHHhhhhhhhccccch
Confidence            467899999999999999888776320                           01             02367788888


Q ss_pred             HHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecC---------CCC
Q 028124           91 TERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYEL---------PTK  161 (213)
Q Consensus        91 ~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~---------P~~  161 (213)
                      ..|..+-+.|..|-                       ++++++|+.    ++.|++.|.-++|+ +.+         +-+
T Consensus       457 ~~K~~vE~Lfq~GL-----------------------vkvvFaTeT----~s~GiNmPartvv~-~~l~K~dG~~~r~L~  508 (1041)
T COG4581         457 AIKELVEELFQEGL-----------------------VKVVFATET----FAIGINMPARTVVF-TSLSKFDGNGHRWLS  508 (1041)
T ss_pred             HHHHHHHHHHhccc-----------------------eeEEeehhh----hhhhcCCcccceee-eeeEEecCCceeecC
Confidence            88888888999985                       999999999    99999999655544 322         125


Q ss_pred             hHHHHHhhccccCCC----CeEEEEEeCc
Q 028124          162 KETYIRRMTTCLAAD----GSVINIVVGG  186 (213)
Q Consensus       162 ~~~yi~R~GR~~~~~----g~~i~~~~~~  186 (213)
                      +..|.|..||+|++.    |.+|+...+.
T Consensus       509 ~gEy~QmsGRAGRRGlD~~G~vI~~~~~~  537 (1041)
T COG4581         509 PGEYTQMSGRAGRRGLDVLGTVIVIEPPF  537 (1041)
T ss_pred             hhHHHHhhhhhccccccccceEEEecCCC
Confidence            789999888876553    8999887654

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

Probab=97.25  E-value=0.0059  Score=61.48  Aligned_cols=94  Identities=14%  Similarity=0.189  Sum_probs=66.6

Q ss_pred             HHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCc--eEEEecCCCCHHHHHHHHHHHhccccccccccccc
Q 028124           37 ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADI--SFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ  114 (213)
Q Consensus        37 ~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~--~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~  114 (213)
                      +.+.+.|..+..  ...++++||+++.+..+.+++.|......  ...... +++...|.+++++|+.++          
T Consensus       738 ~~la~~i~~l~~--~~~g~~LVLFtSy~~l~~v~~~l~~~~~~~~~~ll~Q-g~~~~~r~~l~~~F~~~~----------  804 (928)
T PRK08074        738 EEVAAYIAKIAK--ATKGRMLVLFTSYEMLKKTYYNLKNEEELEGYVLLAQ-GVSSGSRARLTKQFQQFD----------  804 (928)
T ss_pred             HHHHHHHHHHHH--hCCCCEEEEECCHHHHHHHHHHHhhcccccCceEEec-CCCCCCHHHHHHHHHhcC----------
Confidence            455555544332  34579999999999999999999754210  112223 343356789999999874          


Q ss_pred             CCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCC--CEEEEecCCC
Q 028124          115 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISA--RVLINYELPT  160 (213)
Q Consensus       115 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v--~~VI~yd~P~  160 (213)
                                   -.+|++|..    +.+|+|+|+-  ++||...+|.
T Consensus       805 -------------~~iLlG~~s----FwEGVD~pg~~l~~viI~kLPF  835 (928)
T PRK08074        805 -------------KAILLGTSS----FWEGIDIPGDELSCLVIVRLPF  835 (928)
T ss_pred             -------------CeEEEecCc----ccCccccCCCceEEEEEecCCC
Confidence                         679999998    9999999975  6788766554

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=97.23  E-value=0.0034  Score=62.42  Aligned_cols=123  Identities=12%  Similarity=0.127  Sum_probs=90.5

Q ss_pred             chHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccccccc
Q 028124           33 QFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVT  112 (213)
Q Consensus        33 ~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~  112 (213)
                      ..|+.++.+-+...-   ..++|+||-+.|....+.|+..|+..+ +..-.|+..-...| ..++.  +.|.        
T Consensus       432 ~eK~~Ai~~ei~~~~---~~GrPVLVGT~SVe~SE~ls~~L~~~g-i~h~VLNAk~~~~E-A~IIa--~AG~--------  496 (913)
T PRK13103        432 EEKYAAIITDIKECM---ALGRPVLVGTATIETSEHMSNLLKKEG-IEHKVLNAKYHEKE-AEIIA--QAGR--------  496 (913)
T ss_pred             HHHHHHHHHHHHHHH---hCCCCEEEEeCCHHHHHHHHHHHHHcC-CcHHHhccccchhH-HHHHH--cCCC--------
Confidence            349999888887642   478999999999999999999999987 77777776533222 34444  2332        


Q ss_pred             ccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCC--------------------------------C-----CEEEE
Q 028124          113 EQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAIS--------------------------------A-----RVLIN  155 (213)
Q Consensus       113 ~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~--------------------------------v-----~~VI~  155 (213)
                                    +-.|-|||.+    ++||.|+.=                                |     =+||-
T Consensus       497 --------------~GaVTIATNM----AGRGTDIkLg~n~~~~~~~~~~~~~~~~~~~~~~~~~~~e~V~e~GGLhVIg  558 (913)
T PRK13103        497 --------------PGALTIATNM----AGRGTDILLGGNWEVEVAALENPTPEQIAQIKADWQKRHQQVIEAGGLHVIA  558 (913)
T ss_pred             --------------CCcEEEeccC----CCCCCCEecCCchHHHHHhhhhhhHHHHHHHHHHHHhHHHHHHHcCCCEEEe
Confidence                          4679999999    999999941                                1     16777


Q ss_pred             ecCCCChHHHHHhhcccc--CCCCeEEEEEeCchh
Q 028124          156 YELPTKKETYIRRMTTCL--AADGSVINIVVGGEV  188 (213)
Q Consensus       156 yd~P~~~~~yi~R~GR~~--~~~g~~i~~~~~~e~  188 (213)
                      -..|.|..-=-|=.||+|  |.+|.+-.|++-+|.
T Consensus       559 TerheSrRID~QLrGRaGRQGDPGsS~f~lSlED~  593 (913)
T PRK13103        559 SERHESRRIDNQLRGRAGRQGDPGSSRFYLSLEDS  593 (913)
T ss_pred             eccCchHHHHHHhccccccCCCCCceEEEEEcCcH
Confidence            778877655566668875  567988888876543

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

Probab=97.17  E-value=0.016  Score=57.66  Aligned_cols=90  Identities=16%  Similarity=0.200  Sum_probs=63.8

Q ss_pred             HHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccC
Q 028124           36 METLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQS  115 (213)
Q Consensus        36 ~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~  115 (213)
                      .+.+.+.+..+..   ..++++|+++|.+..+.+++.|.... +.. ...|.-.  .|.+++++|+.++           
T Consensus       633 ~~~~~~~i~~~~~---~~g~~LVLFtS~~~l~~v~~~l~~~~-~~~-l~Qg~~~--~~~~l~~~F~~~~-----------  694 (820)
T PRK07246        633 AEEIAKRLEELKQ---LQQPILVLFNSKKHLLAVSDLLDQWQ-VSH-LAQEKNG--TAYNIKKRFDRGE-----------  694 (820)
T ss_pred             HHHHHHHHHHHHh---cCCCEEEEECcHHHHHHHHHHHhhcC-CcE-EEeCCCc--cHHHHHHHHHcCC-----------
Confidence            3355555544332   46799999999999999999997653 344 4445321  2566899999874           


Q ss_pred             CCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCC--CCCEEEEecCC
Q 028124          116 GDESETGKDEHKSHMIVVTDACLPLLSSGESAI--SARVLINYELP  159 (213)
Q Consensus       116 ~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~--~v~~VI~yd~P  159 (213)
                                  ..||++|..    +.+|+|+|  +...||...+|
T Consensus       695 ------------~~vLlG~~s----FwEGVD~p~~~~~~viI~kLP  724 (820)
T PRK07246        695 ------------QQILLGLGS----FWEGVDFVQADRMIEVITRLP  724 (820)
T ss_pred             ------------CeEEEecch----hhCCCCCCCCCeEEEEEecCC
Confidence                        679999998    99999997  35556655555

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

Probab=97.10  E-value=0.0022  Score=62.74  Aligned_cols=56  Identities=11%  Similarity=0.115  Sum_probs=43.5

Q ss_pred             CceeEEEEeCCCCCcCcCCCCCCCCCEEEEe--------cCCCC----------hHHHHHhhccccCC-CCeEEEEEeC
Q 028124          126 HKSHMIVVTDACLPLLSSGESAISARVLINY--------ELPTK----------KETYIRRMTTCLAA-DGSVINIVVG  185 (213)
Q Consensus       126 ~~~~iLV~Td~~~~~~~rGld~~~v~~VI~y--------d~P~~----------~~~yi~R~GR~~~~-~g~~i~~~~~  185 (213)
                      +..-++|+|++    ++-.+.+|++.+||..        |--..          -++--||+||+|+. +|.||-++..
T Consensus       629 g~RLcVVaTNV----AETSLTIPgIkYVVD~Gr~K~R~Yd~~TGV~~FeV~wiSkASadQRAGRAGRtgpGHcYRLYSS  703 (1172)
T KOG0926|consen  629 GERLCVVATNV----AETSLTIPGIKYVVDCGRVKERLYDSKTGVSSFEVDWISKASADQRAGRAGRTGPGHCYRLYSS  703 (1172)
T ss_pred             CceEEEEeccc----hhcccccCCeeEEEeccchhhhccccccCceeEEEEeeeccccchhccccCCCCCCceeehhhh
Confidence            33558899999    9999999999999964        43222          34447999999876 4999999875

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

Probab=97.02  E-value=0.0084  Score=57.97  Aligned_cols=131  Identities=16%  Similarity=0.208  Sum_probs=97.2

Q ss_pred             ecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccc
Q 028124           29 VDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWN  108 (213)
Q Consensus        29 ~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~  108 (213)
                      ......|+....+.++.+..  ....+++|...-.....-+...|.+.| .....+||....++|+.+++.|....    
T Consensus       724 ~~r~S~Ki~~~l~~le~i~~--~skeK~viVSQwtsvLniv~~hi~~~g-~~y~si~Gqv~vK~Rq~iv~~FN~~k----  796 (901)
T KOG4439|consen  724 PDRPSCKIAMVLEILETILT--SSKEKVVIVSQWTSVLNIVRKHIQKGG-HIYTSITGQVLVKDRQEIVDEFNQEK----  796 (901)
T ss_pred             cccchhHHHHHHHHHHHHhh--cccceeeehhHHHHHHHHHHHHHhhCC-eeeeeecCccchhHHHHHHHHHHhcc----
Confidence            34445689999998887622  456788887777777777888888888 79999999999999999999998742    


Q ss_pred             ccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCCC--CeEEEEEe
Q 028124          109 QKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAAD--GSVINIVV  184 (213)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~~--g~~i~~~~  184 (213)
                                      ++..-.|+.=.+    .+-|+++..++++|..|+.|++.-=-|-+.|.  .|+.  -...-|+.
T Consensus       797 ----------------~~~rVmLlSLtA----GGVGLNL~GaNHlilvDlHWNPaLEqQAcDRIYR~GQkK~V~IhR~~~  856 (901)
T KOG4439|consen  797 ----------------GGARVMLLSLTA----GGVGLNLIGANHLILVDLHWNPALEQQACDRIYRMGQKKDVFIHRLMC  856 (901)
T ss_pred             ----------------CCceEEEEEEcc----CcceeeecccceEEEEecccCHHHHHHHHHHHHHhcccCceEEEEEEe
Confidence                            223445555556    79999999999999999999987766666662  3333  33444555


Q ss_pred             Cc
Q 028124          185 GG  186 (213)
Q Consensus       185 ~~  186 (213)
                      .+
T Consensus       857 ~g  858 (901)
T KOG4439|consen  857 KG  858 (901)
T ss_pred             cC
Confidence            54

>COG4889 Predicted helicase [General function prediction only]

Probab=96.99  E-value=0.00071  Score=66.72  Aligned_cols=108  Identities=12%  Similarity=0.154  Sum_probs=75.6

Q ss_pred             CCcEEEEeCchHHHHHHHHHHhc-----------c-CCceEEE--ecCCCCHHHHHHHHHHHhcccccccccccccCCCC
Q 028124           53 GLPMIVCCSSRDELDAVCSAVSN-----------L-ADISFSS--LHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDE  118 (213)
Q Consensus        53 ~~~~IIF~~~~~~~~~l~~~L~~-----------~-~~~~~~~--lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~  118 (213)
                      .++.|-||.+.++...++..+..           . .++++.+  +.|.|+..+|...+.- .+. ++            
T Consensus       460 ~~RAIaF~k~I~tSK~i~~sFe~Vve~Y~~Elk~d~~nL~iSi~HvDGtmNal~R~~l~~l-~~~-~~------------  525 (1518)
T COG4889         460 MQRAIAFAKDIKTSKQIAESFETVVEAYDEELKKDFKNLKISIDHVDGTMNALERLDLLEL-KNT-FE------------  525 (1518)
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhcCCCceEEeecccccccHHHHHHHHhc-cCC-CC------------
Confidence            47889999998888877665532           1 2345544  5588999998443332 111 00            


Q ss_pred             CcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc-----cCCCCeEEEEEe
Q 028124          119 SETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC-----LAADGSVINIVV  184 (213)
Q Consensus       119 ~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~-----~~~~g~~i~~~~  184 (213)
                            ...++||=-...    +++|+|+|..+.||.||+-.+..+.+|-+||.     +..-|.+|.-+.
T Consensus       526 ------~neckIlSNaRc----LSEGVDVPaLDsViFf~pr~smVDIVQaVGRVMRKa~gK~yGYIILPIa  586 (1518)
T COG4889         526 ------PNECKILSNARC----LSEGVDVPALDSVIFFDPRSSMVDIVQAVGRVMRKAKGKKYGYIILPIA  586 (1518)
T ss_pred             ------cchheeeccchh----hhcCCCccccceEEEecCchhHHHHHHHHHHHHHhCcCCccceEEEEec
Confidence                  123666655554    99999999999999999999999999999995     233488887663

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

Probab=96.98  E-value=0.016  Score=55.86  Aligned_cols=80  Identities=18%  Similarity=0.208  Sum_probs=61.8

Q ss_pred             CCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEE
Q 028124           52 PGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMI  131 (213)
Q Consensus        52 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iL  131 (213)
                      ..++++||+++...++.+++.++..........+|.   ..+..++++|+.+.                      ..-++
T Consensus       478 ~~~~~lvlF~Sy~~l~~~~~~~~~~~~~~~v~~q~~---~~~~~~l~~f~~~~----------------------~~~~l  532 (654)
T COG1199         478 SPGGVLVLFPSYEYLKRVAERLKDERSTLPVLTQGE---DEREELLEKFKASG----------------------EGLIL  532 (654)
T ss_pred             cCCCEEEEeccHHHHHHHHHHHhhcCccceeeecCC---CcHHHHHHHHHHhc----------------------CCeEE
Confidence            445999999999999999999987641134556665   44558999999973                      11799


Q ss_pred             EEeCCCCCcCcCCCCCCCC--CEEEEecCCC
Q 028124          132 VVTDACLPLLSSGESAISA--RVLINYELPT  160 (213)
Q Consensus       132 V~Td~~~~~~~rGld~~~v--~~VI~yd~P~  160 (213)
                      |+|..    +++|+|+++-  +.||...+|.
T Consensus       533 v~~gs----f~EGVD~~g~~l~~vvI~~lPf  559 (654)
T COG1199         533 VGGGS----FWEGVDFPGDALRLVVIVGLPF  559 (654)
T ss_pred             Eeecc----ccCcccCCCCCeeEEEEEecCC
Confidence            99999    9999999866  6788777664

>KOG1015 consensus Transcription regulator XNP/ATRX, DEAD-box superfamily [Transcription]

Probab=96.96  E-value=0.0052  Score=61.20  Aligned_cols=128  Identities=17%  Similarity=0.198  Sum_probs=98.0

Q ss_pred             chHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc---C------------------CceEEEecCCCCHH
Q 028124           33 QFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL---A------------------DISFSSLHSDLAET   91 (213)
Q Consensus        33 ~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~---~------------------~~~~~~lhg~~~~~   91 (213)
                      ..|+-+|.++|+.-   ..-+.++|||..+..+.+.|-.+|...   |                  +..-.-|.|.....
T Consensus      1125 SgKmiLLleIL~mc---eeIGDKlLVFSQSL~SLdLIe~fLe~v~r~gk~~~d~~~~~~~eGkW~~GkDyyriDGst~s~ 1201 (1567)
T KOG1015|consen 1125 SGKMILLLEILRMC---EEIGDKLLVFSQSLISLDLIEDFLELVSREGKEDKDKPLIYKGEGKWLRGKDYYRLDGSTTSQ 1201 (1567)
T ss_pred             CcceehHHHHHHHH---HHhcceeEEeecccchhHHHHHHHHhhcccCccccccccccccccceecCCceEEecCcccHH
Confidence            44999999999652   235799999999999999988888532   1                  13356678888999


Q ss_pred             HHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhcc
Q 028124           92 ERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTT  171 (213)
Q Consensus        92 ~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR  171 (213)
                      .|....++|....                 |.  .-.-.||+|.+    .+-|+++-.++-||.||..|++..=+|-+=|
T Consensus      1202 ~R~k~~~~FNdp~-----------------Nl--RaRl~LISTRA----GsLGiNLvAANRVIIfDasWNPSyDtQSIFR 1258 (1567)
T KOG1015|consen 1202 SRKKWAEEFNDPT-----------------NL--RARLFLISTRA----GSLGINLVAANRVIIFDASWNPSYDTQSIFR 1258 (1567)
T ss_pred             HHHHHHHHhcCcc-----------------cc--eeEEEEEeecc----CccccceeecceEEEEecccCCccchHHHHH
Confidence            9999999998864                 00  01348999999    9999999999999999999999887776666


Q ss_pred             c--cC--CCCeEEEEEeCc
Q 028124          172 C--LA--ADGSVINIVVGG  186 (213)
Q Consensus       172 ~--~~--~~g~~i~~~~~~  186 (213)
                      .  .|  ++-++|-|+..+
T Consensus      1259 vyRfGQtKPvyiYRfiAqG 1277 (1567)
T KOG1015|consen 1259 VYRFGQTKPVYIYRFIAQG 1277 (1567)
T ss_pred             HHhhcCcCceeehhhhhcc
Confidence            3  33  345677777543

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

Probab=96.94  E-value=0.005  Score=60.25  Aligned_cols=92  Identities=11%  Similarity=0.183  Sum_probs=67.4

Q ss_pred             HHHHHHHHHhcc-CCceEEEecCCCCHHH--HHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcC
Q 028124           65 ELDAVCSAVSNL-ADISFSSLHSDLAETE--RTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLL  141 (213)
Q Consensus        65 ~~~~l~~~L~~~-~~~~~~~lhg~~~~~~--R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~  141 (213)
                      -++++.+.|.+. ++.+++.+.+|.....  -...+.+|..|+                       .+|||.|.+    +
T Consensus       492 GterieeeL~~~FP~~rv~r~d~Dtt~~k~~~~~~l~~~~~ge-----------------------~dILiGTQm----i  544 (730)
T COG1198         492 GTERIEEELKRLFPGARIIRIDSDTTRRKGALEDLLDQFANGE-----------------------ADILIGTQM----I  544 (730)
T ss_pred             cHHHHHHHHHHHCCCCcEEEEccccccchhhHHHHHHHHhCCC-----------------------CCeeecchh----h
Confidence            567788888754 6678999999875533  467899999995                       999999999    9


Q ss_pred             cCCCCCCCCCEEEEecC------CC------ChHHHHHhhccccC--CCCeEEEEE
Q 028124          142 SSGESAISARVLINYEL------PT------KKETYIRRMTTCLA--ADGSVINIV  183 (213)
Q Consensus       142 ~rGld~~~v~~VI~yd~------P~------~~~~yi~R~GR~~~--~~g~~i~~~  183 (213)
                      +.|.|+|++..|.-.|.      |.      ....+.|=.||+|+  .+|.++.-.
T Consensus       545 aKG~~fp~vtLVgvl~aD~~L~~~DfRA~Er~fqll~QvaGRAgR~~~~G~VvIQT  600 (730)
T COG1198         545 AKGHDFPNVTLVGVLDADTGLGSPDFRASERTFQLLMQVAGRAGRAGKPGEVVIQT  600 (730)
T ss_pred             hcCCCcccceEEEEEechhhhcCCCcchHHHHHHHHHHHHhhhccCCCCCeEEEEe
Confidence            99999999998665432      21      23445676788754  556555544

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=96.71  E-value=0.013  Score=58.12  Aligned_cols=87  Identities=10%  Similarity=0.200  Sum_probs=65.6

Q ss_pred             cCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCC-CCHHHHHHHHHHHhccccccc
Q 028124           30 DRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSD-LAETERTLILEEFRHTAMKWN  108 (213)
Q Consensus        30 ~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~-~~~~~R~~~l~~Fr~g~~~~~  108 (213)
                      .....|+..+.+-+...   ...++|++|-|.|....+.|+..|...| +...+|+.. .....=..++.+  .|.    
T Consensus       404 ~t~~~K~~AI~~ei~~~---~~~grPVLIgT~SIe~SE~ls~~L~~~g-i~h~vLNAk~~~~~~EA~IIA~--AG~----  473 (870)
T CHL00122        404 KDELSKWRAIADECLQM---HQTGRPILIGTTTIEKSELLSQLLKEYR-LPHQLLNAKPENVRRESEIVAQ--AGR----  473 (870)
T ss_pred             eCHHHHHHHHHHHHHHH---HhcCCCEEEeeCCHHHHHHHHHHHHHcC-CccceeeCCCccchhHHHHHHh--cCC----
Confidence            33444888887766553   2478999999999999999999999997 888888885 222222445554  332    


Q ss_pred             ccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCC
Q 028124          109 QKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAI  148 (213)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~  148 (213)
                                        +-.|-|||.+    ++||.|+.
T Consensus       474 ------------------~G~VTIATNM----AGRGTDI~  491 (870)
T CHL00122        474 ------------------KGSITIATNM----AGRGTDII  491 (870)
T ss_pred             ------------------CCcEEEeccc----cCCCcCee
Confidence                              5779999999    99999984

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

Probab=96.65  E-value=0.0045  Score=61.69  Aligned_cols=77  Identities=19%  Similarity=0.240  Sum_probs=62.3

Q ss_pred             EEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEE-ec-C
Q 028124           81 FSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLIN-YE-L  158 (213)
Q Consensus        81 ~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~-yd-~  158 (213)
                      +...|++|+..+|..+---||.|.                       ..+|++|..    ++-|++.| +++|+. -| +
T Consensus       965 iG~HHaglNr~yR~~VEvLFR~g~-----------------------L~VlfaT~T----LsLGiNMP-CrTVvF~gDsL 1016 (1330)
T KOG0949|consen  965 IGVHHAGLNRKYRSLVEVLFRQGH-----------------------LQVLFATET----LSLGINMP-CRTVVFAGDSL 1016 (1330)
T ss_pred             ccccccccchHHHHHHHHHhhcCc-----------------------eEEEEEeee----hhcccCCC-ceeEEEecccc
Confidence            456889999999999888999995                       999999999    99999999 555554 33 3


Q ss_pred             CCChHHHHHhhccccCCC----CeEEEEEeC
Q 028124          159 PTKKETYIRRMTTCLAAD----GSVINIVVG  185 (213)
Q Consensus       159 P~~~~~yi~R~GR~~~~~----g~~i~~~~~  185 (213)
                      --++-.|-|.+||+|++.    |.|+.+--+
T Consensus      1017 QL~plny~QmaGRAGRRGFD~lGnV~FmgiP 1047 (1330)
T KOG0949|consen 1017 QLDPLNYKQMAGRAGRRGFDTLGNVVFMGIP 1047 (1330)
T ss_pred             ccCchhHHhhhccccccccccccceEEEeCc
Confidence            347889999999987664    777766655

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=96.49  E-value=0.02  Score=57.01  Aligned_cols=86  Identities=14%  Similarity=0.187  Sum_probs=66.2

Q ss_pred             CcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCC-CCHHHHHHHHHHHhcccccccc
Q 028124           31 RLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSD-LAETERTLILEEFRHTAMKWNQ  109 (213)
Q Consensus        31 ~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~-~~~~~R~~~l~~Fr~g~~~~~~  109 (213)
                      ....|+..+.+-+...-   ..++|++|-|.|....+.|+..|...| +...+|+.. ...+.=..++.+  .|.     
T Consensus       420 t~~~K~~Ai~~ei~~~~---~~GrPVLIgT~SVe~SE~ls~~L~~~g-i~h~vLNAk~~~~~~EA~IIa~--AG~-----  488 (939)
T PRK12902        420 TEIAKWRAVANETAEMH---KQGRPVLVGTTSVEKSELLSALLQEQG-IPHNLLNAKPENVEREAEIVAQ--AGR-----  488 (939)
T ss_pred             CHHHHHHHHHHHHHHHH---hCCCCEEEeeCCHHHHHHHHHHHHHcC-CchheeeCCCcchHhHHHHHHh--cCC-----
Confidence            33458988888776532   478999999999999999999999997 888888885 333333455555  332     


Q ss_pred             cccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCC
Q 028124          110 KVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAI  148 (213)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~  148 (213)
                                       +-.|-|||.+    ++||.|+.
T Consensus       489 -----------------~GaVTIATNM----AGRGTDIk  506 (939)
T PRK12902        489 -----------------KGAVTIATNM----AGRGTDII  506 (939)
T ss_pred             -----------------CCcEEEeccC----CCCCcCEe
Confidence                             4679999999    99999984

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

Probab=96.29  E-value=0.084  Score=51.16  Aligned_cols=83  Identities=11%  Similarity=-0.021  Sum_probs=61.7

Q ss_pred             CCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEE
Q 028124           52 PGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMI  131 (213)
Q Consensus        52 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iL  131 (213)
                      ..++++|-+.+...++.+++.|...- -..+.+.|+.+  .+..++++|+...                   ..+.-.||
T Consensus       469 ~~G~~lvLfTS~~~~~~~~~~l~~~l-~~~~l~qg~~~--~~~~l~~~f~~~~-------------------~~~~~~vL  526 (636)
T TIGR03117       469 AQGGTLVLTTAFSHISAIGQLVELGI-PAEIVIQSEKN--RLASAEQQFLALY-------------------ANGIQPVL  526 (636)
T ss_pred             cCCCEEEEechHHHHHHHHHHHHhhc-CCCEEEeCCCc--cHHHHHHHHHHhh-------------------cCCCCcEE
Confidence            55688888889999999999997542 13456667543  5577899999840                   00126799


Q ss_pred             EEeCCCCCcCcCCCCC----------CCCCEEEEecCCC
Q 028124          132 VVTDACLPLLSSGESA----------ISARVLINYELPT  160 (213)
Q Consensus       132 V~Td~~~~~~~rGld~----------~~v~~VI~yd~P~  160 (213)
                      ++|+.    +-+|+|+          ..+++||...+|.
T Consensus       527 ~gt~s----fweGvDv~~~~~~p~~G~~Ls~ViI~kLPF  561 (636)
T TIGR03117       527 IAAGG----AWTGIDLTHKPVSPDKDNLLTDLIITCAPF  561 (636)
T ss_pred             EeCCc----cccccccCCccCCCCCCCcccEEEEEeCCC
Confidence            99999    9999999          3478899887773

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.

>PRK05580 primosome assembly protein PriA; Validated

Probab=96.27  E-value=0.059  Score=52.64  Aligned_cols=102  Identities=15%  Similarity=0.077  Sum_probs=78.7

Q ss_pred             EEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc-CCceEEEecCCCCHHHHHHHHHHHhcc
Q 028124           25 FYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL-ADISFSSLHSDLAETERTLILEEFRHT  103 (213)
Q Consensus        25 ~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~-~~~~~~~lhg~~~~~~R~~~l~~Fr~g  103 (213)
                      ..+..+...-|......++.....   .+.++||.++++.-+..+.+.|++. | ..+..+||+++..+|.+.+.+.+.|
T Consensus       165 ~Ll~~~TGSGKT~v~l~~i~~~l~---~g~~vLvLvPt~~L~~Q~~~~l~~~fg-~~v~~~~s~~s~~~r~~~~~~~~~g  240 (679)
T PRK05580        165 FLLDGVTGSGKTEVYLQAIAEVLA---QGKQALVLVPEIALTPQMLARFRARFG-APVAVLHSGLSDGERLDEWRKAKRG  240 (679)
T ss_pred             EEEECCCCChHHHHHHHHHHHHHH---cCCeEEEEeCcHHHHHHHHHHHHHHhC-CCEEEEECCCCHHHHHHHHHHHHcC
Confidence            444444444488887777655332   3679999999999999999999864 5 6899999999999999999999987


Q ss_pred             cccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecC
Q 028124          104 AMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYEL  158 (213)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~  158 (213)
                      +                       .+|+|+|..    . --+.+.++.+||--+-
T Consensus       241 ~-----------------------~~IVVgTrs----a-l~~p~~~l~liVvDEe  267 (679)
T PRK05580        241 E-----------------------AKVVIGARS----A-LFLPFKNLGLIIVDEE  267 (679)
T ss_pred             C-----------------------CCEEEeccH----H-hcccccCCCEEEEECC
Confidence            4                       899999985    2 2255778888886653

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

Probab=96.20  E-value=0.045  Score=51.30  Aligned_cols=137  Identities=13%  Similarity=0.208  Sum_probs=90.8

Q ss_pred             CceEEEEEecCcchHHHHHHH-HHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc--------CCceEEEecCCCCHH
Q 028124           21 QPRHFYVAVDRLQFKMETLVE-LLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL--------ADISFSSLHSDLAET   91 (213)
Q Consensus        21 ~i~~~~~~~~~~~~K~~~L~~-ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~--------~~~~~~~lhg~~~~~   91 (213)
                      .+.-+|-.-+..+ .++.... .++-...  ...+-+++|....++.+..++.+...        |.+++..+|    +.
T Consensus       223 PvEi~Yt~e~erD-ylEaairtV~qih~~--ee~GDilvFLtgeeeIe~aC~~i~re~~~L~~~~g~l~v~PLy----P~  295 (699)
T KOG0925|consen  223 PVEIFYTPEPERD-YLEAAIRTVLQIHMC--EEPGDILVFLTGEEEIEDACRKISREVDNLGPQVGPLKVVPLY----PA  295 (699)
T ss_pred             ceEEEecCCCChh-HHHHHHHHHHHHHhc--cCCCCEEEEecCHHHHHHHHHHHHHHHHhhccccCCceEEecC----ch
Confidence            3555655544444 4444444 4432222  34678999999999998888888643        447888898    33


Q ss_pred             HHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecC-------------
Q 028124           92 ERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYEL-------------  158 (213)
Q Consensus        92 ~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~-------------  158 (213)
                      ++..+++--..                  +..+.-..+++|+|.+    ++-.+.++.+.+||.-.+             
T Consensus       296 ~qq~iFep~p~------------------~~~~~~~RkvVvstni----aetsltidgiv~VIDpGf~kqkVYNPRIRve  353 (699)
T KOG0925|consen  296 QQQRIFEPAPE------------------KRNGAYGRKVVVSTNI----AETSLTIDGIVFVIDPGFSKQKVYNPRIRVE  353 (699)
T ss_pred             hhccccCCCCc------------------ccCCCccceEEEEecc----hheeeeeccEEEEecCchhhhcccCcceeee
Confidence            43333322111                  1112234789999999    999999999999997443             


Q ss_pred             -----CCChHHHHHhhccccC-CCCeEEEEEeCc
Q 028124          159 -----PTKKETYIRRMTTCLA-ADGSVINIVVGG  186 (213)
Q Consensus       159 -----P~~~~~yi~R~GR~~~-~~g~~i~~~~~~  186 (213)
                           |-|..+-.||.||+|+ ++|.|+-+++++
T Consensus       354 sllv~PISkasA~qR~gragrt~pGkcfrLYte~  387 (699)
T KOG0925|consen  354 SLLVSPISKASAQQRAGRAGRTRPGKCFRLYTEE  387 (699)
T ss_pred             eeeeccchHhHHHHHhhhccCCCCCceEEeecHH
Confidence                 3356777899999865 569999999853

>PRK14873 primosome assembly protein PriA; Provisional

Probab=96.17  E-value=0.051  Score=52.97  Aligned_cols=95  Identities=12%  Similarity=0.079  Sum_probs=79.4

Q ss_pred             hHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc-CCceEEEecCCCCHHHHHHHHHHHhccccccccccc
Q 028124           34 FKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL-ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVT  112 (213)
Q Consensus        34 ~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~-~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~  112 (213)
                      -|.+.+.++++....   .++++||.++....+..+.+.|+.. |...+..+|+++++.+|.+.+.+.++|+        
T Consensus       172 GKTevyl~~i~~~l~---~Gk~vLvLvPEi~lt~q~~~rl~~~f~~~~v~~lhS~l~~~~R~~~w~~~~~G~--------  240 (665)
T PRK14873        172 DWARRLAAAAAATLR---AGRGALVVVPDQRDVDRLEAALRALLGAGDVAVLSAGLGPADRYRRWLAVLRGQ--------  240 (665)
T ss_pred             cHHHHHHHHHHHHHH---cCCeEEEEecchhhHHHHHHHHHHHcCCCcEEEECCCCCHHHHHHHHHHHhCCC--------
Confidence            488888898877543   5789999999999999999999865 3247899999999999999999999985        


Q ss_pred             ccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCC
Q 028124          113 EQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELP  159 (213)
Q Consensus       113 ~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P  159 (213)
                                     .+|+|.|-.     +--.=+++...||-.|-.
T Consensus       241 ---------------~~IViGtRS-----AvFaP~~~LgLIIvdEEh  267 (665)
T PRK14873        241 ---------------ARVVVGTRS-----AVFAPVEDLGLVAIWDDG  267 (665)
T ss_pred             ---------------CcEEEEcce-----eEEeccCCCCEEEEEcCC
Confidence                           899999995     555667788888877643

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=96.09  E-value=0.031  Score=54.48  Aligned_cols=103  Identities=17%  Similarity=0.124  Sum_probs=76.9

Q ss_pred             EEEEecCcchHHHHHH-HHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc----CCceEEEecCCCCHHHHHHHHHH
Q 028124           25 FYVAVDRLQFKMETLV-ELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEE   99 (213)
Q Consensus        25 ~~~~~~~~~~K~~~L~-~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~lhg~~~~~~R~~~l~~   99 (213)
                      ..+..+...=|..+.. .++..+    .++.+++|-++|+.-|...++.++..    + +++..+||+++..+|.+.++.
T Consensus       285 ~Ll~~~TGSGKT~va~~~il~~~----~~g~q~lilaPT~~LA~Q~~~~l~~l~~~~~-i~v~ll~G~~~~~~r~~~~~~  359 (681)
T PRK10917        285 RLLQGDVGSGKTVVAALAALAAI----EAGYQAALMAPTEILAEQHYENLKKLLEPLG-IRVALLTGSLKGKERREILEA  359 (681)
T ss_pred             EEEECCCCCcHHHHHHHHHHHHH----HcCCeEEEEeccHHHHHHHHHHHHHHHhhcC-cEEEEEcCCCCHHHHHHHHHH
Confidence            4444444433554433 233332    34679999999999999888887653    4 789999999999999999999


Q ss_pred             HhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecC
Q 028124          100 FRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYEL  158 (213)
Q Consensus       100 Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~  158 (213)
                      ..+|.                       .+|+|+|..-   +...+.+.++.+||.-..
T Consensus       360 l~~g~-----------------------~~IvVgT~~l---l~~~v~~~~l~lvVIDE~  392 (681)
T PRK10917        360 IASGE-----------------------ADIVIGTHAL---IQDDVEFHNLGLVIIDEQ  392 (681)
T ss_pred             HhCCC-----------------------CCEEEchHHH---hcccchhcccceEEEech
Confidence            99985                       9999999862   556678889998886543

>TIGR00595 priA primosomal protein N'

Probab=96.00  E-value=0.052  Score=51.19  Aligned_cols=92  Identities=15%  Similarity=0.128  Sum_probs=72.2

Q ss_pred             HHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccccccccc
Q 028124           35 KMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ  114 (213)
Q Consensus        35 K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~  114 (213)
                      |..+...++.....   .++++||.+++..-+..+++.|++.-+..+..+||+++..+|.+.+.+.++|+          
T Consensus        10 KT~v~l~~i~~~l~---~g~~vLvlvP~i~L~~Q~~~~l~~~f~~~v~vlhs~~~~~er~~~~~~~~~g~----------   76 (505)
T TIGR00595        10 KTEVYLQAIEKVLA---LGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGE----------   76 (505)
T ss_pred             HHHHHHHHHHHHHH---cCCeEEEEeCcHHHHHHHHHHHHHHhCCcEEEEECCCCHHHHHHHHHHHHcCC----------
Confidence            77777766655332   46799999999999999999998652267899999999999999999988874          


Q ss_pred             CCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEec
Q 028124          115 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYE  157 (213)
Q Consensus       115 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd  157 (213)
                                   .+|+|+|..    + --..+.+..+||.-+
T Consensus        77 -------------~~IVVGTrs----a-lf~p~~~l~lIIVDE  101 (505)
T TIGR00595        77 -------------ILVVIGTRS----A-LFLPFKNLGLIIVDE  101 (505)
T ss_pred             -------------CCEEECChH----H-HcCcccCCCEEEEEC
Confidence                         889999985    2 224577888888654

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).

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=95.98  E-value=0.06  Score=52.70  Aligned_cols=95  Identities=16%  Similarity=0.224  Sum_probs=65.3

Q ss_pred             HHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccC
Q 028124           36 METLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQS  115 (213)
Q Consensus        36 ~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~  115 (213)
                      .+.+.+.+..+..   ..+.++||+++....+.++..|..... .-+..+|.   ..|.+++++|++.-           
T Consensus       520 ~~~~~~~i~~l~~---~~gg~LVlFtSy~~l~~v~~~l~~~~~-~~ll~Q~~---~~~~~ll~~f~~~~-----------  581 (697)
T PRK11747        520 TAEMAEFLPELLE---KHKGSLVLFASRRQMQKVADLLPRDLR-LMLLVQGD---QPRQRLLEKHKKRV-----------  581 (697)
T ss_pred             HHHHHHHHHHHHh---cCCCEEEEeCcHHHHHHHHHHHHHhcC-CcEEEeCC---chHHHHHHHHHHHh-----------
Confidence            4455555555433   344589999999999999999974321 33455664   35678888887520           


Q ss_pred             CCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCC--CCEEEEecCCC
Q 028124          116 GDESETGKDEHKSHMIVVTDACLPLLSSGESAIS--ARVLINYELPT  160 (213)
Q Consensus       116 ~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~--v~~VI~yd~P~  160 (213)
                              ..+...||++|..    +.+|+|+|+  +++||...+|-
T Consensus       582 --------~~~~~~VL~g~~s----f~EGVD~pGd~l~~vII~kLPF  616 (697)
T PRK11747        582 --------DEGEGSVLFGLQS----FAEGLDLPGDYLTQVIITKIPF  616 (697)
T ss_pred             --------ccCCCeEEEEecc----ccccccCCCCceEEEEEEcCCC
Confidence                    0012569999988    999999986  67888876663

>PF13871 Helicase_C_4: Helicase_C-like

Probab=95.55  E-value=0.099  Score=45.68  Aligned_cols=67  Identities=24%  Similarity=0.310  Sum_probs=48.2

Q ss_pred             eeEEEEeCCCCCcCcCCCCCCC--------CCEEEEecCCCChHHHHHhhccccCCC---CeEEEEEe---CchhHHHHH
Q 028124          128 SHMIVVTDACLPLLSSGESAIS--------ARVLINYELPTKKETYIRRMTTCLAAD---GSVINIVV---GGEVVTLRS  193 (213)
Q Consensus       128 ~~iLV~Td~~~~~~~rGld~~~--------v~~VI~yd~P~~~~~yi~R~GR~~~~~---g~~i~~~~---~~e~~~~~~  193 (213)
                      ..|+|.+++    .+.|+.++.        -++-|-.++||+.+..+|..||+.+..   .-.+.++.   ++|......
T Consensus        62 k~v~iis~A----gstGiSlHAd~~~~nqr~Rv~i~le~pwsad~aiQ~~GR~hRsnQ~~~P~y~~l~t~~~gE~Rfas~  137 (278)
T PF13871_consen   62 KDVAIISDA----GSTGISLHADRRVKNQRRRVHITLELPWSADKAIQQFGRTHRSNQVSAPEYRFLVTDLPGERRFAST  137 (278)
T ss_pred             ceEEEEecc----cccccchhccccCCCCCceEEEEeeCCCCHHHHHHHhccccccccccCCEEEEeecCCHHHHHHHHH
Confidence            899999999    999998874        346778899999999999999974332   33344443   246655555


Q ss_pred             HHHHh
Q 028124          194 MEESL  198 (213)
Q Consensus       194 le~~l  198 (213)
                      +.+.+
T Consensus       138 va~rL  142 (278)
T PF13871_consen  138 VARRL  142 (278)
T ss_pred             HHHHH
Confidence            55544

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

Probab=95.38  E-value=0.094  Score=51.53  Aligned_cols=103  Identities=17%  Similarity=0.126  Sum_probs=83.2

Q ss_pred             eEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc-CCceEEEecCCCCHHHHHHHHHHHh
Q 028124           23 RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL-ADISFSSLHSDLAETERTLILEEFR  101 (213)
Q Consensus        23 ~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~-~~~~~~~lhg~~~~~~R~~~l~~Fr  101 (213)
                      ..+++.--..+-|.+++.++++....   .++++||-++.......+.+.|..+ | .++..+|+++++.+|...+.+.+
T Consensus       218 ~~~Ll~GvTGSGKTEvYl~~i~~~L~---~GkqvLvLVPEI~Ltpq~~~rf~~rFg-~~v~vlHS~Ls~~er~~~W~~~~  293 (730)
T COG1198         218 APFLLDGVTGSGKTEVYLEAIAKVLA---QGKQVLVLVPEIALTPQLLARFKARFG-AKVAVLHSGLSPGERYRVWRRAR  293 (730)
T ss_pred             cceeEeCCCCCcHHHHHHHHHHHHHH---cCCEEEEEeccccchHHHHHHHHHHhC-CChhhhcccCChHHHHHHHHHHh
Confidence            34445444445599999999987654   6899999999999999888888765 6 79999999999999999999999


Q ss_pred             cccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEec
Q 028124          102 HTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYE  157 (213)
Q Consensus       102 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd  157 (213)
                      +|+                       .+|+|.|-.     +--.=+++...||-.+
T Consensus       294 ~G~-----------------------~~vVIGtRS-----AlF~Pf~~LGLIIvDE  321 (730)
T COG1198         294 RGE-----------------------ARVVIGTRS-----ALFLPFKNLGLIIVDE  321 (730)
T ss_pred             cCC-----------------------ceEEEEech-----hhcCchhhccEEEEec
Confidence            996                       999999985     4555667777777543

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=95.34  E-value=0.075  Score=51.36  Aligned_cols=103  Identities=17%  Similarity=0.153  Sum_probs=76.0

Q ss_pred             EEEEecCcchHHHHH-HHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc----CCceEEEecCCCCHHHHHHHHHH
Q 028124           25 FYVAVDRLQFKMETL-VELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEE   99 (213)
Q Consensus        25 ~~~~~~~~~~K~~~L-~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~lhg~~~~~~R~~~l~~   99 (213)
                      ..+..+...=|..+. ..++..+    ..+.+++|-++|+.-|..+++.+++.    + +++..+||+++..+|...++.
T Consensus       259 ~Ll~g~TGSGKT~va~l~il~~~----~~g~qvlilaPT~~LA~Q~~~~~~~l~~~~g-i~v~lltg~~~~~~r~~~~~~  333 (630)
T TIGR00643       259 RLLQGDVGSGKTLVAALAMLAAI----EAGYQVALMAPTEILAEQHYNSLRNLLAPLG-IEVALLTGSLKGKRRKELLET  333 (630)
T ss_pred             EEEECCCCCcHHHHHHHHHHHHH----HcCCcEEEECCHHHHHHHHHHHHHHHhcccC-cEEEEEecCCCHHHHHHHHHH
Confidence            344444433355433 3334432    34679999999999999888877653    4 899999999999999999999


Q ss_pred             HhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecC
Q 028124          100 FRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYEL  158 (213)
Q Consensus       100 Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~  158 (213)
                      ..+|+                       .+++|+|..-   +...+.+.++.+||.-+.
T Consensus       334 i~~g~-----------------------~~IiVgT~~l---l~~~~~~~~l~lvVIDEa  366 (630)
T TIGR00643       334 IASGQ-----------------------IHLVVGTHAL---IQEKVEFKRLALVIIDEQ  366 (630)
T ss_pred             HhCCC-----------------------CCEEEecHHH---HhccccccccceEEEech
Confidence            99985                       8999999972   556678888888886443

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=95.29  E-value=0.19  Score=49.15  Aligned_cols=98  Identities=18%  Similarity=0.220  Sum_probs=66.7

Q ss_pred             HHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCC------ceEEEecC-CCCHHHHHHHHHHHhccccccc
Q 028124           36 METLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLAD------ISFSSLHS-DLAETERTLILEEFRHTAMKWN  108 (213)
Q Consensus        36 ~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~------~~~~~lhg-~~~~~~R~~~l~~Fr~g~~~~~  108 (213)
                      .+.+.+.|..+..  ...+.++||+++....+.+++.+...+.      .+.+..-+ ++  .++.+++++|+..-    
T Consensus       507 ~~~l~~~i~~~~~--~~pgg~lvfFpSy~~l~~v~~~~~~~~~~~~i~~~k~i~~E~~~~--~~~~~~l~~f~~~~----  578 (705)
T TIGR00604       507 VRNLGELLVEFSK--IIPDGIVVFFPSYSYLENIVSTWKEMGILENIEKKKLIFVETKDA--QETSDALERYKQAV----  578 (705)
T ss_pred             HHHHHHHHHHHhh--cCCCcEEEEccCHHHHHHHHHHHHhcCHHHHHhcCCCEEEeCCCc--chHHHHHHHHHHHH----
Confidence            4556666655443  3457899999999999999988865420      02233322 22  57889999997631    


Q ss_pred             ccccccCCCCCcCCCCCCceeEEEEe--CCCCCcCcCCCCCCC--CCEEEEecCCC
Q 028124          109 QKVTEQSGDESETGKDEHKSHMIVVT--DACLPLLSSGESAIS--ARVLINYELPT  160 (213)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~iLV~T--d~~~~~~~rGld~~~--v~~VI~yd~P~  160 (213)
                                     ..++-.+|+++  .-    +++|+|+++  ++.||...+|.
T Consensus       579 ---------------~~~~gavL~av~gGk----~sEGIDf~~~~~r~ViivGlPf  615 (705)
T TIGR00604       579 ---------------SEGRGAVLLSVAGGK----VSEGIDFCDDLGRAVIMVGIPY  615 (705)
T ss_pred             ---------------hcCCceEEEEecCCc----ccCccccCCCCCcEEEEEccCC
Confidence                           00124588888  66    899999987  68899998886

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).

>KOG0701 consensus dsRNA-specific nuclease Dicer and related ribonucleases [RNA processing and modification]

Probab=94.96  E-value=0.012  Score=61.57  Aligned_cols=92  Identities=12%  Similarity=0.223  Sum_probs=74.4

Q ss_pred             CcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCH-----------HHHHHHHHHHhcccccccccccccCCCCCcCC
Q 028124           54 LPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAE-----------TERTLILEEFRHTAMKWNQKVTEQSGDESETG  122 (213)
Q Consensus        54 ~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~-----------~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~  122 (213)
                      -..||||+...++..+.+.++...-.....+.|.+.+           ..+.+++..|+...                  
T Consensus       293 l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~k~~~~~~~~~~~~vl~~~~~~~------------------  354 (1606)
T KOG0701|consen  293 LSGIIFVDQRYTAYVLLELLREIFSNDPLFVTGASGANLWKSFKNELELRQAEVLRRFHFHE------------------  354 (1606)
T ss_pred             hhheeecccchHHHHHHHHHHHhhccCcceeeccccCccchhhHHHHHhhhHHHHHHHhhhh------------------
Confidence            4679999999999999888876522233335554321           24566888888864                  


Q ss_pred             CCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc
Q 028124          123 KDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC  172 (213)
Q Consensus       123 ~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~  172 (213)
                           .++|+.|.+    +..|+|++.++.|+.++.|.....|+|+.||+
T Consensus       355 -----ln~L~~~~~----~~e~~d~~~~~~~~~~~~~~~~~~~vq~~~r~  395 (1606)
T KOG0701|consen  355 -----LNLLIATSV----LEEGVDVPKCNLVVLFDAPTYYRSYVQKKGRA  395 (1606)
T ss_pred             -----hhHHHHHHH----HHhhcchhhhhhheeccCcchHHHHHHhhccc
Confidence                 999999999    99999999999999999999999999999995

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

Probab=94.39  E-value=0.19  Score=50.77  Aligned_cols=62  Identities=18%  Similarity=0.295  Sum_probs=52.4

Q ss_pred             CCCCcEEEEeCchHHHHHHHHHHhccC------CceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCC
Q 028124           51 RPGLPMIVCCSSRDELDAVCSAVSNLA------DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKD  124 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~~L~~~~------~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~  124 (213)
                      ..++++++.++|..-+...++.|.+.+      ++.+. +||.|+.+++..++++|.+|.                    
T Consensus       123 ~kgkr~yii~PT~~Lv~Q~~~kl~~~~e~~~~~~~~~~-yh~~l~~~ekee~le~i~~gd--------------------  181 (1187)
T COG1110         123 KKGKRVYIIVPTTTLVRQVYERLKKFAEDAGSLDVLVV-YHSALPTKEKEEALERIESGD--------------------  181 (1187)
T ss_pred             hcCCeEEEEecCHHHHHHHHHHHHHHHhhcCCcceeee-eccccchHHHHHHHHHHhcCC--------------------
Confidence            456899999999999999888887652      12333 999999999999999999996                    


Q ss_pred             CCceeEEEEeCC
Q 028124          125 EHKSHMIVVTDA  136 (213)
Q Consensus       125 ~~~~~iLV~Td~  136 (213)
                         .+|||+|..
T Consensus       182 ---fdIlitTs~  190 (1187)
T COG1110         182 ---FDILITTSQ  190 (1187)
T ss_pred             ---ccEEEEeHH
Confidence               999999986

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=94.28  E-value=0.41  Score=48.48  Aligned_cols=103  Identities=17%  Similarity=0.077  Sum_probs=77.7

Q ss_pred             EEEEecCcchHHHHHHH-HHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc----CCceEEEecCCCCHHHHHHHHHH
Q 028124           25 FYVAVDRLQFKMETLVE-LLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEE   99 (213)
Q Consensus        25 ~~~~~~~~~~K~~~L~~-ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~lhg~~~~~~R~~~l~~   99 (213)
                      .++..+...=|..+... +++.+    ..+.+++|.++|+.-|...++.+++.    + +++..++|..+..++.+++++
T Consensus       475 ~Ll~adTGsGKT~val~a~l~al----~~g~qvlvLvPT~~LA~Q~~~~f~~~~~~~~-i~v~~Lsg~~~~~e~~~~~~~  549 (926)
T TIGR00580       475 RLVCGDVGFGKTEVAMRAAFKAV----LDGKQVAVLVPTTLLAQQHFETFKERFANFP-VTIELLSRFRSAKEQNEILKE  549 (926)
T ss_pred             EEEECCCCccHHHHHHHHHHHHH----HhCCeEEEEeCcHHHHHHHHHHHHHHhccCC-cEEEEEeccccHHHHHHHHHH
Confidence            45555554446654433 33332    23579999999999999998887653    4 688899999999999999999


Q ss_pred             HhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecC
Q 028124          100 FRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYEL  158 (213)
Q Consensus       100 Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~  158 (213)
                      ++.|.                       .+|+|+|..   ++.+.+.+.++.+||--..
T Consensus       550 l~~g~-----------------------~dIVIGTp~---ll~~~v~f~~L~llVIDEa  582 (926)
T TIGR00580       550 LASGK-----------------------IDILIGTHK---LLQKDVKFKDLGLLIIDEE  582 (926)
T ss_pred             HHcCC-----------------------ceEEEchHH---HhhCCCCcccCCEEEeecc
Confidence            99984                       899999985   2667788899999886543

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.

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=93.97  E-value=0.17  Score=51.50  Aligned_cols=107  Identities=11%  Similarity=0.068  Sum_probs=66.6

Q ss_pred             EEEeCchHHHHHHHHHHhcc-----CCceEEEecCCCCHHHHHHHHHHH---hcc---cccccccccccCCCCCcCCCCC
Q 028124           57 IVCCSSRDELDAVCSAVSNL-----ADISFSSLHSDLAETERTLILEEF---RHT---AMKWNQKVTEQSGDESETGKDE  125 (213)
Q Consensus        57 IIF~~~~~~~~~l~~~L~~~-----~~~~~~~lhg~~~~~~R~~~l~~F---r~g---~~~~~~~~~~~~~~~~~~~~~~  125 (213)
                      +|=+++++.+-.+++.|...     ..+...++|+..+...|..+-++.   .+.   +.-|.......-+   .+.+..
T Consensus       760 liR~anI~p~V~~A~~L~~~~~~~~~~i~~~~yHSr~~l~~Rs~~E~~Ld~~L~R~~~~~~~~~~~i~~~l---~~~~~~  836 (1110)
T TIGR02562       760 LIRVANIDPLIRLAQFLYALLAEEKYQIHLCCYHAQDPLLLRSYIERRLDQLLTRHKPEQLFQDDEIIDLM---QNSPAL  836 (1110)
T ss_pred             EEEEcCchHHHHHHHHHHhhccccCCceeEEEecccChHHHHHHHHHHHHHHhcccChhhhhchHHHHHHH---hccccc
Confidence            55567788888888888654     125578899999888776655543   111   1111111111000   011223


Q ss_pred             CceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhcccc
Q 028124          126 HKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL  173 (213)
Q Consensus       126 ~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~  173 (213)
                      +...++|+|.+    .+-|+|+. .+++|-  -|.+.++.+||+||+.
T Consensus       837 ~~~~i~v~Tqv----~E~g~D~d-fd~~~~--~~~~~~sliQ~aGR~~  877 (1110)
T TIGR02562       837 NHLFIVLATPV----EEVGRDHD-YDWAIA--DPSSMRSIIQLAGRVN  877 (1110)
T ss_pred             CCCeEEEEeee----EEEEeccc-CCeeee--ccCcHHHHHHHhhccc
Confidence            45789999999    99999953 555443  4667999999999973

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.

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

Probab=93.86  E-value=0.38  Score=45.42  Aligned_cols=93  Identities=14%  Similarity=0.228  Sum_probs=63.1

Q ss_pred             HHHHHHHHHHhhc-CCCCCCcEEEEeCchHHHHHHHHHHhccC----CceEEEecCCCCHHHHHHHHHHHhccccccccc
Q 028124           36 METLVELLHLVVA-GRRPGLPMIVCCSSRDELDAVCSAVSNLA----DISFSSLHSDLAETERTLILEEFRHTAMKWNQK  110 (213)
Q Consensus        36 ~~~L~~ll~~~~~-~~~~~~~~IIF~~~~~~~~~l~~~L~~~~----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~  110 (213)
                      +.++.-+|+.+.. ......++||.++|+.-|..+++.+...+    .+.+..++|+++...+...+   +.|       
T Consensus        81 ~Af~lP~l~~l~~~~~~~~~~aLil~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l---~~~-------  150 (513)
T COG0513          81 AAFLLPLLQKILKSVERKYVSALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEAL---KRG-------  150 (513)
T ss_pred             HHHHHHHHHHHhcccccCCCceEEECCCHHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHH---hcC-------
Confidence            4445556665431 11222229999999999999998887542    36789999999877766444   445       


Q ss_pred             ccccCCCCCcCCCCCCceeEEEEeCCCC-CcCcCC-CCCCCCCEEEE
Q 028124          111 VTEQSGDESETGKDEHKSHMIVVTDACL-PLLSSG-ESAISARVLIN  155 (213)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~~iLV~Td~~~-~~~~rG-ld~~~v~~VI~  155 (213)
                                       .+|||+|+..+ -.+.+| +++..+.++|.
T Consensus       151 -----------------~~ivVaTPGRllD~i~~~~l~l~~v~~lVl  180 (513)
T COG0513         151 -----------------VDIVVATPGRLLDLIKRGKLDLSGVETLVL  180 (513)
T ss_pred             -----------------CCEEEECccHHHHHHHcCCcchhhcCEEEe
Confidence                             88999998410 013555 78888998885

>smart00492 HELICc3 helicase superfamily c-terminal domain

Probab=93.49  E-value=0.37  Score=37.68  Aligned_cols=47  Identities=21%  Similarity=0.287  Sum_probs=36.5

Q ss_pred             CCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCC--CCEEEEecCCC
Q 028124           88 LAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAIS--ARVLINYELPT  160 (213)
Q Consensus        88 ~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~--v~~VI~yd~P~  160 (213)
                      ....+..+++++|+...                      ...+|+++.-    +++|+|+++  ++.||...+|.
T Consensus        31 ~~~~~~~~~l~~f~~~~----------------------~~~iL~~~~~----~~EGiD~~g~~~r~vii~glPf   79 (141)
T smart00492       31 EDGKETGKLLEKYVEAC----------------------ENAILLATAR----FSEGVDFPGDYLRAVIIDGLPF   79 (141)
T ss_pred             CChhHHHHHHHHHHHcC----------------------CCEEEEEccc----eecceecCCCCeeEEEEEecCC
Confidence            34446788999999852                      2369999988    999999997  46788888774

>PRK10689 transcription-repair coupling factor; Provisional

Probab=93.28  E-value=0.28  Score=50.71  Aligned_cols=103  Identities=19%  Similarity=0.063  Sum_probs=73.8

Q ss_pred             EEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc-C--CceEEEecCCCCHHHHHHHHHHHh
Q 028124           25 FYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL-A--DISFSSLHSDLAETERTLILEEFR  101 (213)
Q Consensus        25 ~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~-~--~~~~~~lhg~~~~~~R~~~l~~Fr  101 (213)
                      ..+..+...=|..+....+-...   ..+.+++|-|+|+.-|..+++.+++. +  .+.+..++|..+..++.+++++.+
T Consensus       624 ~Ll~a~TGsGKT~val~aa~~~~---~~g~qvlvLvPT~eLA~Q~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~  700 (1147)
T PRK10689        624 RLVCGDVGFGKTEVAMRAAFLAV---ENHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAA  700 (1147)
T ss_pred             EEEEcCCCcCHHHHHHHHHHHHH---HcCCeEEEEeCcHHHHHHHHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHH
Confidence            34444444446654332221111   24689999999999999998888753 1  267888999999999999999998


Q ss_pred             cccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEe
Q 028124          102 HTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINY  156 (213)
Q Consensus       102 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~y  156 (213)
                      +|.                       .+|+|+|..   ++...+.+.++.++|--
T Consensus       701 ~g~-----------------------~dIVVgTp~---lL~~~v~~~~L~lLVID  729 (1147)
T PRK10689        701 EGK-----------------------IDILIGTHK---LLQSDVKWKDLGLLIVD  729 (1147)
T ss_pred             hCC-----------------------CCEEEECHH---HHhCCCCHhhCCEEEEe
Confidence            874                       899999975   15556777888887753

>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [General function prediction only]

Probab=93.23  E-value=0.53  Score=46.66  Aligned_cols=122  Identities=15%  Similarity=0.126  Sum_probs=88.8

Q ss_pred             CCCcEEEEeCchHHHHHHHHHHhcc------C-----------CceEEEecCCCCHHHHHHHHHHHhccccccccccccc
Q 028124           52 PGLPMIVCCSSRDELDAVCSAVSNL------A-----------DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ  114 (213)
Q Consensus        52 ~~~~~IIF~~~~~~~~~l~~~L~~~------~-----------~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~  114 (213)
                      .+.+.|||..+..+.+.|-+.|.++      |           +..-.-+.|..+..+|.+++++|....          
T Consensus       718 ~g~kil~fSq~l~~Ld~ieeil~krq~pc~~gdnG~~aqkW~~n~sy~rldG~t~a~~rekLinqfN~e~----------  787 (1387)
T KOG1016|consen  718 IGEKILIFSQNLTALDMIEEILKKRQIPCKDGDNGCPAQKWEKNRSYLRLDGTTSAADREKLINQFNSEP----------  787 (1387)
T ss_pred             cCceEEEeecchhHHHHHHHHHhcccccCCCCCCCCchhhhhhccceecccCCcccchHHHHHHhccCCC----------
Confidence            4678999999999999998888765      1           133456778888899999999997753          


Q ss_pred             CCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhcc---cc-CCCCeEEEEEeCc--hh
Q 028124          115 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTT---CL-AADGSVINIVVGG--EV  188 (213)
Q Consensus       115 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR---~~-~~~g~~i~~~~~~--e~  188 (213)
                                +..--+|++|.+    ..-|+++-.++-+|.||.-|++..=.|-+-|   .| -++..++-++...  |.
T Consensus       788 ----------~lsWlfllstra----g~lGinLIsanr~~ifda~wnpchdaqavcRvyrYGQ~KpcfvYRlVmD~~lEk  853 (1387)
T KOG1016|consen  788 ----------GLSWLFLLSTRA----GSLGINLISANRCIIFDACWNPCHDAQAVCRVYRYGQQKPCFVYRLVMDNSLEK  853 (1387)
T ss_pred             ----------Cceeeeeehhcc----ccccceeeccceEEEEEeecCccccchhhhhhhhhcCcCceeEEeehhhhhhHH
Confidence                      111237788999    9999999999999999999988766664444   23 3457888888764  44


Q ss_pred             HHHHHHHHH
Q 028124          189 VTLRSMEES  197 (213)
Q Consensus       189 ~~~~~le~~  197 (213)
                      ..+.+--..
T Consensus       854 kIydRQIsK  862 (1387)
T KOG1016|consen  854 KIYDRQISK  862 (1387)
T ss_pred             HHHHHHHhh
Confidence            444444333

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

Probab=92.87  E-value=0.98  Score=44.89  Aligned_cols=100  Identities=14%  Similarity=0.185  Sum_probs=72.3

Q ss_pred             HHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccccccccc
Q 028124           35 KMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ  114 (213)
Q Consensus        35 K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~  114 (213)
                      +..++..|+..+    ..++.+-||+.|...++.+++..+..+ .++..++|.-+..+    ++.|.+            
T Consensus       268 ~~tF~~~L~~~L----~~gknIcvfsSt~~~~~~v~~~~~~~~-~~Vl~l~s~~~~~d----v~~W~~------------  326 (824)
T PF02399_consen  268 ETTFFSELLARL----NAGKNICVFSSTVSFAEIVARFCARFT-KKVLVLNSTDKLED----VESWKK------------  326 (824)
T ss_pred             hhhHHHHHHHHH----hCCCcEEEEeChHHHHHHHHHHHHhcC-CeEEEEcCCCCccc----cccccc------------
Confidence            455666666664    347788899999999999999998886 68888888655442    234443            


Q ss_pred             CCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCC--CEEEEe--cCC--CChHHHHHhhccc
Q 028124          115 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISA--RVLINY--ELP--TKKETYIRRMTTC  172 (213)
Q Consensus       115 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v--~~VI~y--d~P--~~~~~yi~R~GR~  172 (213)
                                   .++++-|.+    ..-|+++.+.  +-|.-|  ...  .+..+..|.+||.
T Consensus       327 -------------~~VviYT~~----itvG~Sf~~~HF~~~f~yvk~~~~gpd~~s~~Q~lgRv  373 (824)
T PF02399_consen  327 -------------YDVVIYTPV----ITVGLSFEEKHFDSMFAYVKPMSYGPDMVSVYQMLGRV  373 (824)
T ss_pred             -------------eeEEEEece----EEEEeccchhhceEEEEEecCCCCCCcHHHHHHHHHHH
Confidence                         899999999    9999999754  334444  222  2455688999994

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

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

Probab=91.62  E-value=1  Score=43.76  Aligned_cols=80  Identities=19%  Similarity=0.184  Sum_probs=66.6

Q ss_pred             CCCCcEEEEeCchHHHHHHHH----HHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCC
Q 028124           51 RPGLPMIVCCSSRDELDAVCS----AVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEH  126 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~----~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~  126 (213)
                      ..+.|+..-++|---|+.-+.    +|...+ +.+..+.|.+...+|.+++++..+|+                      
T Consensus       309 ~~G~Q~ALMAPTEILA~QH~~~~~~~l~~~~-i~V~lLtG~~kgk~r~~~l~~l~~G~----------------------  365 (677)
T COG1200         309 EAGYQAALMAPTEILAEQHYESLRKWLEPLG-IRVALLTGSLKGKARKEILEQLASGE----------------------  365 (677)
T ss_pred             HcCCeeEEeccHHHHHHHHHHHHHHHhhhcC-CeEEEeecccchhHHHHHHHHHhCCC----------------------
Confidence            457899999998766665544    444456 89999999999999999999999996                      


Q ss_pred             ceeEEEEeCCCCCcCcCCCCCCCCCEEEEec
Q 028124          127 KSHMIVVTDACLPLLSSGESAISARVLINYE  157 (213)
Q Consensus       127 ~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd  157 (213)
                       ++++|.|-+   +....+++.+.-+||--.
T Consensus       366 -~~ivVGTHA---LiQd~V~F~~LgLVIiDE  392 (677)
T COG1200         366 -IDIVVGTHA---LIQDKVEFHNLGLVIIDE  392 (677)
T ss_pred             -CCEEEEcch---hhhcceeecceeEEEEec
Confidence             999999998   478889999998888644

>cd00268 DEADc DEAD-box helicases

Probab=91.29  E-value=2.9  Score=33.53  Aligned_cols=110  Identities=14%  Similarity=0.147  Sum_probs=67.6

Q ss_pred             eEEEEEecCcchHHHH-HHHHHHHhhcCC-CCCCcEEEEeCchHHHHHHHHHHhcc---CCceEEEecCCCCHHHHHHHH
Q 028124           23 RHFYVAVDRLQFKMET-LVELLHLVVAGR-RPGLPMIVCCSSRDELDAVCSAVSNL---ADISFSSLHSDLAETERTLIL   97 (213)
Q Consensus        23 ~~~~~~~~~~~~K~~~-L~~ll~~~~~~~-~~~~~~IIF~~~~~~~~~l~~~L~~~---~~~~~~~lhg~~~~~~R~~~l   97 (213)
                      ++.++..+...-|... +..++..+.... ..+.++||.|+++.-+...++.+...   .++.+..++|+.+..++...+
T Consensus        37 ~~~li~~~TG~GKT~~~~~~~l~~~~~~~~~~~~~viii~p~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  116 (203)
T cd00268          37 RDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKL  116 (203)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHHHhhcccCCceEEEEcCCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHh
Confidence            3455666555446544 444444433210 34678999999999988887766544   247888999998876654333


Q ss_pred             HHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCc-C-cCCCCCCCCCEEEEecCC
Q 028124           98 EEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPL-L-SSGESAISARVLINYELP  159 (213)
Q Consensus        98 ~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~-~-~rGld~~~v~~VI~yd~P  159 (213)
                         ..                        ...++|+|...+.. + ..-.++.+++++|.-+..
T Consensus       117 ---~~------------------------~~~iiv~T~~~l~~~l~~~~~~~~~l~~lIvDE~h  153 (203)
T cd00268         117 ---KR------------------------GPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEAD  153 (203)
T ss_pred             ---cC------------------------CCCEEEEChHHHHHHHHcCCCChhhCCEEEEeChH
Confidence               22                        27899999531100 1 223567788888765444

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.

>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=91.02  E-value=1.2  Score=37.89  Aligned_cols=55  Identities=11%  Similarity=-0.069  Sum_probs=42.9

Q ss_pred             ceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc-cCCC---CeEEEEEeCc
Q 028124          127 KSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC-LAAD---GSVINIVVGG  186 (213)
Q Consensus       127 ~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~-~~~~---g~~i~~~~~~  186 (213)
                      ...|+|.=+.    ++||+.+.+..+.....-|.+.+++.|+ ||= |=++   ..|=.+.+++
T Consensus       135 ~~~I~VGGn~----LsRGlTleGL~vsYf~R~s~~~DTL~Qm-gRwFGYR~gY~dl~Ri~~~~~  193 (239)
T PF10593_consen  135 LNVIAVGGNK----LSRGLTLEGLTVSYFLRNSKQYDTLMQM-GRWFGYRPGYEDLCRIYMPEE  193 (239)
T ss_pred             ceEEEECCcc----ccCceeECCcEEEEecCCCchHHHHHHH-hhcccCCcccccceEEecCHH
Confidence            4789999999    9999999999999999999999999885 784 4343   3444444443

This domain is found associated with a helicase domain of superfamily type II [].

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=90.88  E-value=1  Score=41.60  Aligned_cols=106  Identities=20%  Similarity=0.189  Sum_probs=68.1

Q ss_pred             EEEEecCcchHHHH-HHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc----CCceEEEecCCCCHHHHHHHHHH
Q 028124           25 FYVAVDRLQFKMET-LVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEE   99 (213)
Q Consensus        25 ~~~~~~~~~~K~~~-L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~lhg~~~~~~R~~~l~~   99 (213)
                      .++..+...=|... +.-++..+.. .....+++|.|+|++-|..+++.++..    .++.+..++|+.+...+...+  
T Consensus        44 vi~~a~TGsGKT~a~~lpil~~l~~-~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l--  120 (460)
T PRK11776         44 VIAQAKTGSGKTAAFGLGLLQKLDV-KRFRVQALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSL--  120 (460)
T ss_pred             EEEECCCCCcHHHHHHHHHHHHhhh-ccCCceEEEEeCCHHHHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHh--
Confidence            45555554446543 3444444322 223457999999999999988877653    247899999999876654333  


Q ss_pred             HhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCc-C-cCCCCCCCCCEEEEecC
Q 028124          100 FRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPL-L-SSGESAISARVLINYEL  158 (213)
Q Consensus       100 Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~-~-~rGld~~~v~~VI~yd~  158 (213)
                       +.+                        .+|+|+|+-.+.. + ...+++.++++||.-+.
T Consensus       121 -~~~------------------------~~IvV~Tp~rl~~~l~~~~~~l~~l~~lViDEa  156 (460)
T PRK11776        121 -EHG------------------------AHIIVGTPGRILDHLRKGTLDLDALNTLVLDEA  156 (460)
T ss_pred             -cCC------------------------CCEEEEChHHHHHHHHcCCccHHHCCEEEEECH
Confidence             343                        7899999642110 2 24578889999886543

>PRK14701 reverse gyrase; Provisional

Probab=90.81  E-value=1.8  Score=46.44  Aligned_cols=63  Identities=16%  Similarity=0.259  Sum_probs=54.0

Q ss_pred             CCCcEEEEeCchHHHHHHHHHHhccC-----CceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCC
Q 028124           52 PGLPMIVCCSSRDELDAVCSAVSNLA-----DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEH  126 (213)
Q Consensus        52 ~~~~~IIF~~~~~~~~~l~~~L~~~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~  126 (213)
                      ++.+++|.++|+.-+..+++.|+..+     ++.+..+||+++..++.+.++++++|.                      
T Consensus       121 ~g~~aLVl~PTreLa~Qi~~~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~----------------------  178 (1638)
T PRK14701        121 KGKKCYIILPTTLLVKQTVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGD----------------------  178 (1638)
T ss_pred             cCCeEEEEECHHHHHHHHHHHHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCC----------------------
Confidence            46789999999999999999887631     267889999999999999999999874                      


Q ss_pred             ceeEEEEeCCC
Q 028124          127 KSHMIVVTDAC  137 (213)
Q Consensus       127 ~~~iLV~Td~~  137 (213)
                       .+|||+|+..
T Consensus       179 -~dILV~TPgr  188 (1638)
T PRK14701        179 -FDILVTTAQF  188 (1638)
T ss_pred             -CCEEEECCch
Confidence             8899999874

>KOG2340 consensus Uncharacterized conserved protein [Function unknown]

Probab=90.35  E-value=1.7  Score=41.38  Aligned_cols=139  Identities=13%  Similarity=0.150  Sum_probs=92.9

Q ss_pred             chHHHHHHHHH-HHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccc
Q 028124           33 QFKMETLVELL-HLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKV  111 (213)
Q Consensus        33 ~~K~~~L~~ll-~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~  111 (213)
                      +.++..+..-+ -.+..  ....-++||.++--.--++-.++++.. +....+|--.++..-..+-+-|..|.       
T Consensus       533 D~RFkyFv~~ImPq~~k--~t~s~~LiyIPSYfDFVRvRNy~K~e~-i~F~~i~EYssk~~vsRAR~lF~qgr-------  602 (698)
T KOG2340|consen  533 DARFKYFVDKIMPQLIK--RTESGILIYIPSYFDFVRVRNYMKKEE-ISFVMINEYSSKSKVSRARELFFQGR-------  602 (698)
T ss_pred             hHHHHHHHHhhchhhcc--cccCceEEEecchhhHHHHHHHhhhhh-cchHHHhhhhhHhhhhHHHHHHHhcC-------
Confidence            34666655533 34322  235678999999999889999998876 67777776555555455566688874       


Q ss_pred             cccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHH---HHhhccc--cCC-C---CeEEEE
Q 028124          112 TEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETY---IRRMTTC--LAA-D---GSVINI  182 (213)
Q Consensus       112 ~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~y---i~R~GR~--~~~-~---g~~i~~  182 (213)
                                      .++|+-|+-.  -.-|-.++.+|..||.|.+|.++.-|   +..++|+  .|+ .   -.|..+
T Consensus       603 ----------------~~vlLyTER~--hffrR~~ikGVk~vVfYqpP~~P~FYsEiinm~~k~~~~gn~d~d~~t~~il  664 (698)
T KOG2340|consen  603 ----------------KSVLLYTERA--HFFRRYHIKGVKNVVFYQPPNNPHFYSEIINMSDKTTSQGNTDLDIFTVRIL  664 (698)
T ss_pred             ----------------ceEEEEehhh--hhhhhheecceeeEEEecCCCCcHHHHHHHhhhhhhhccCCccccceEEEEE
Confidence                            8899998861  13466788999999999999998766   4555674  222 2   355556


Q ss_pred             EeCchhHHHHHHHHHhcccc
Q 028124          183 VVGGEVVTLRSMEESLGLIV  202 (213)
Q Consensus       183 ~~~~e~~~~~~le~~l~~~~  202 (213)
                      ++..|..   .||...|.+.
T Consensus       665 ytKyD~i---~Le~ivGter  681 (698)
T KOG2340|consen  665 YTKYDRI---RLENIVGTER  681 (698)
T ss_pred             eechhhH---HHHHhhhHHH
Confidence            6666654   4555555443

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=89.89  E-value=1.7  Score=42.17  Aligned_cols=104  Identities=14%  Similarity=0.094  Sum_probs=65.0

Q ss_pred             EEEEecCcchHHHHH-HHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc----CCceEEEecCCCCHHHHHHHHHH
Q 028124           25 FYVAVDRLQFKMETL-VELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEE   99 (213)
Q Consensus        25 ~~~~~~~~~~K~~~L-~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~lhg~~~~~~R~~~l~~   99 (213)
                      .++..+...=|..++ .-++..+.. .....++||.|+|+.-|..+++.+...    .++.+..+||+.+.+.+...   
T Consensus        46 vl~~ApTGsGKT~af~lpll~~l~~-~~~~~~~LIL~PTreLa~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~---  121 (629)
T PRK11634         46 VLGMAQTGSGKTAAFSLPLLHNLDP-ELKAPQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRA---  121 (629)
T ss_pred             EEEEcCCCCcHHHHHHHHHHHHhhh-ccCCCeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHH---
Confidence            444444444465543 334444322 234568999999999999888877543    24788999999876655433   


Q ss_pred             HhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCC-cCc-CCCCCCCCCEEEEe
Q 028124          100 FRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLP-LLS-SGESAISARVLINY  156 (213)
Q Consensus       100 Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~-~~~-rGld~~~v~~VI~y  156 (213)
                      ++.+                        .+|+|+|+..+- .+. ..+++.++.+||.-
T Consensus       122 l~~~------------------------~~IVVgTPgrl~d~l~r~~l~l~~l~~lVlD  156 (629)
T PRK11634        122 LRQG------------------------PQIVVGTPGRLLDHLKRGTLDLSKLSGLVLD  156 (629)
T ss_pred             hcCC------------------------CCEEEECHHHHHHHHHcCCcchhhceEEEec
Confidence            3343                        789999963110 023 34678888887753

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=89.13  E-value=0.86  Score=43.55  Aligned_cols=44  Identities=18%  Similarity=0.312  Sum_probs=39.4

Q ss_pred             EEEEeCchHHHHHHHHHHhcc---CCceEEEecCCCCHHHHHHHHHH
Q 028124           56 MIVCCSSRDELDAVCSAVSNL---ADISFSSLHSDLAETERTLILEE   99 (213)
Q Consensus        56 ~IIF~~~~~~~~~l~~~L~~~---~~~~~~~lhg~~~~~~R~~~l~~   99 (213)
                      .+||++|+.-|..+.+.|...   .++++..+.|||+...+++++++
T Consensus       266 ~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQqRlL~~  312 (731)
T KOG0347|consen  266 ALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQRLLNQ  312 (731)
T ss_pred             eEEecChHHHHHHHHHHHHHhccccCeEEEEeechhHHHHHHHHHhc
Confidence            899999999999999998643   44999999999999999999988

>TIGR01054 rgy reverse gyrase

Probab=89.12  E-value=2.9  Score=43.53  Aligned_cols=85  Identities=14%  Similarity=0.162  Sum_probs=59.9

Q ss_pred             EEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccC---Cce---EEEecCCCCHHHHHHHHHH
Q 028124           26 YVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLA---DIS---FSSLHSDLAETERTLILEE   99 (213)
Q Consensus        26 ~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~---~~~---~~~lhg~~~~~~R~~~l~~   99 (213)
                      .+..+...=|..+..-++..+.   ..+.+++|.++|+.-|..+++.++...   ++.   +..+||+++..+|...+++
T Consensus        97 vi~ApTGsGKT~f~l~~~~~l~---~~g~~vLIL~PTreLa~Qi~~~l~~l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~  173 (1171)
T TIGR01054        97 AIIAPTGVGKTTFGLAMSLFLA---KKGKRCYIILPTTLLVIQVAEKISSLAEKAGVGTVNIGAYHSRLPTKEKKEFMER  173 (1171)
T ss_pred             EEECCCCCCHHHHHHHHHHHHH---hcCCeEEEEeCHHHHHHHHHHHHHHHHHhcCCceeeeeeecCCCCHHHHHHHHHH
Confidence            3444444446654433333222   246799999999999999988887642   133   3358999999999999999


Q ss_pred             HhcccccccccccccCCCCCcCCCCCCceeEEEEeCC
Q 028124          100 FRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDA  136 (213)
Q Consensus       100 Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~  136 (213)
                      ++++.                       .+|||+|+.
T Consensus       174 l~~~~-----------------------~dIlV~Tp~  187 (1171)
T TIGR01054       174 IENGD-----------------------FDILITTTM  187 (1171)
T ss_pred             HhcCC-----------------------CCEEEECHH
Confidence            98874                       789999986

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.

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

Probab=89.00  E-value=2.5  Score=43.53  Aligned_cols=78  Identities=15%  Similarity=0.111  Sum_probs=68.3

Q ss_pred             CCCCcEEEEeCchHHHHHHHHHHhcc----CCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCC
Q 028124           51 RPGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEH  126 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~  126 (213)
                      .+++|+.|.|+|.--|+.-++-++.+    | +++..+.+-.+.++...+++..++|.                      
T Consensus       641 ~~GKQVAvLVPTTlLA~QHy~tFkeRF~~fP-V~I~~LSRF~s~kE~~~il~~la~G~----------------------  697 (1139)
T COG1197         641 MDGKQVAVLVPTTLLAQQHYETFKERFAGFP-VRIEVLSRFRSAKEQKEILKGLAEGK----------------------  697 (1139)
T ss_pred             cCCCeEEEEcccHHhHHHHHHHHHHHhcCCC-eeEEEecccCCHHHHHHHHHHHhcCC----------------------
Confidence            46799999999998888777777654    7 89999999999999999999999995                      


Q ss_pred             ceeEEEEeCCCCCcCcCCCCCCCCCEEEE
Q 028124          127 KSHMIVVTDACLPLLSSGESAISARVLIN  155 (213)
Q Consensus       127 ~~~iLV~Td~~~~~~~rGld~~~v~~VI~  155 (213)
                       ++|+|.|-.   +++.++-+.|...+|-
T Consensus       698 -vDIvIGTHr---LL~kdv~FkdLGLlII  722 (1139)
T COG1197         698 -VDIVIGTHR---LLSKDVKFKDLGLLII  722 (1139)
T ss_pred             -ccEEEechH---hhCCCcEEecCCeEEE
Confidence             999999987   4788899999998885

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=88.90  E-value=0.98  Score=44.97  Aligned_cols=109  Identities=15%  Similarity=0.189  Sum_probs=70.2

Q ss_pred             CCCCCCCCCCCCCCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEe
Q 028124            5 GVESPCPPCQSPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSL   84 (213)
Q Consensus         5 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~l   84 (213)
                      +|..-..|+..|..+.+-....  ......|+..+.+-+...   ...++|+||-+.+....+.+.+.|.+.+ +....|
T Consensus       386 ~l~vv~iPTnrp~~R~D~~D~v--y~t~~~K~~Aiv~~I~~~---~~~gqPvLvgT~sie~SE~ls~~L~~~~-i~h~VL  459 (822)
T COG0653         386 GLDVVVIPTNRPIIRLDEPDLV--YKTEEEKFKAIVEDIKER---HEKGQPVLVGTVSIEKSELLSKLLRKAG-IPHNVL  459 (822)
T ss_pred             CCceeeccCCCcccCCCCcccc--ccchHHHHHHHHHHHHHH---HhcCCCEEEcCcceecchhHHHHHHhcC-CCceee
Confidence            3444344444444433322222  223344888888877653   2478999999999999999999999887 777777


Q ss_pred             cCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCC
Q 028124           85 HSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAI  148 (213)
Q Consensus        85 hg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~  148 (213)
                      ...-...+ .++.. + .|.                      +-.+-|+|..    ++||-|+.
T Consensus       460 NAk~h~~E-A~Iia-~-AG~----------------------~gaVTiATNM----AGRGTDIk  494 (822)
T COG0653         460 NAKNHARE-AEIIA-Q-AGQ----------------------PGAVTIATNM----AGRGTDIK  494 (822)
T ss_pred             ccccHHHH-HHHHh-h-cCC----------------------CCcccccccc----ccCCcccc
Confidence            76543333 22222 1 221                      3558899999    99999985

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=88.72  E-value=2.8  Score=38.94  Aligned_cols=60  Identities=12%  Similarity=0.136  Sum_probs=52.9

Q ss_pred             CCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEE
Q 028124           53 GLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIV  132 (213)
Q Consensus        53 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV  132 (213)
                      .+.+||.+++++-+......|...+ +.+..++++.+..++..++.+...+.                       .++++
T Consensus        51 ~~~~lVi~P~~~L~~dq~~~l~~~g-i~~~~l~~~~~~~~~~~i~~~~~~~~-----------------------~~il~  106 (470)
T TIGR00614        51 DGITLVISPLISLMEDQVLQLKASG-IPATFLNSSQSKEQQKNVLTDLKDGK-----------------------IKLLY  106 (470)
T ss_pred             CCcEEEEecHHHHHHHHHHHHHHcC-CcEEEEeCCCCHHHHHHHHHHHhcCC-----------------------CCEEE
Confidence            4689999999999998889998887 89999999999999999999998874                       88888


Q ss_pred             EeCC
Q 028124          133 VTDA  136 (213)
Q Consensus       133 ~Td~  136 (213)
                      +|+-
T Consensus       107 ~TPe  110 (470)
T TIGR00614       107 VTPE  110 (470)
T ss_pred             ECHH
Confidence            8875

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

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=87.49  E-value=13  Score=33.80  Aligned_cols=106  Identities=12%  Similarity=0.147  Sum_probs=65.2

Q ss_pred             EEEEecCcchHHHH-HHHHHHHhhc---CCCCCCcEEEEeCchHHHHHHHHHHhcc---CCceEEEecCCCCHHHHHHHH
Q 028124           25 FYVAVDRLQFKMET-LVELLHLVVA---GRRPGLPMIVCCSSRDELDAVCSAVSNL---ADISFSSLHSDLAETERTLIL   97 (213)
Q Consensus        25 ~~~~~~~~~~K~~~-L~~ll~~~~~---~~~~~~~~IIF~~~~~~~~~l~~~L~~~---~~~~~~~lhg~~~~~~R~~~l   97 (213)
                      .++..+...=|-.. +.-++..+..   ......++||.++|+.-+..+++.+...   .++.+..++|+.+...+...+
T Consensus        41 ~l~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~~lil~Pt~eLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l  120 (434)
T PRK11192         41 VLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVF  120 (434)
T ss_pred             EEEECCCCChHHHHHHHHHHHHHhhccccCCCCceEEEECCcHHHHHHHHHHHHHHHccCCcEEEEEECCCCHHHHHHHh
Confidence            55555554435433 3333333221   0122468999999999988887766543   237899999999877665433


Q ss_pred             HHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCC--cCcCCCCCCCCCEEEEec
Q 028124           98 EEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLP--LLSSGESAISARVLINYE  157 (213)
Q Consensus        98 ~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~--~~~rGld~~~v~~VI~yd  157 (213)
                         ..+                        .+|+|+|+..+-  .....+++.++++||.-+
T Consensus       121 ---~~~------------------------~~IlV~Tp~rl~~~~~~~~~~~~~v~~lViDE  155 (434)
T PRK11192        121 ---SEN------------------------QDIVVATPGRLLQYIKEENFDCRAVETLILDE  155 (434)
T ss_pred             ---cCC------------------------CCEEEEChHHHHHHHHcCCcCcccCCEEEEEC
Confidence               232                        789999973100  023566788899888654

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

Probab=86.77  E-value=1.9  Score=40.96  Aligned_cols=76  Identities=12%  Similarity=0.116  Sum_probs=54.7

Q ss_pred             CCcEEEEeCchHHHHHHHHHHhccC---CceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCcee
Q 028124           53 GLPMIVCCSSRDELDAVCSAVSNLA---DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSH  129 (213)
Q Consensus        53 ~~~~IIF~~~~~~~~~l~~~L~~~~---~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (213)
                      +.=.+|.|+|+.-|..+...-++.+   ++.++++||+++..++.+-|+   .|                        ..
T Consensus       296 gPi~vilvPTrela~Qi~~eaKkf~K~ygl~~v~~ygGgsk~eQ~k~Lk---~g------------------------~E  348 (731)
T KOG0339|consen  296 GPIGVILVPTRELASQIFSEAKKFGKAYGLRVVAVYGGGSKWEQSKELK---EG------------------------AE  348 (731)
T ss_pred             CCeEEEEeccHHHHHHHHHHHHHhhhhccceEEEeecCCcHHHHHHhhh---cC------------------------Ce
Confidence            3446788899999998877766541   389999999999999887766   44                        77


Q ss_pred             EEEEeCCCCCc--CcCCCCCCCCCEEEE
Q 028124          130 MIVVTDACLPL--LSSGESAISARVLIN  155 (213)
Q Consensus       130 iLV~Td~~~~~--~~rGld~~~v~~VI~  155 (213)
                      ++|||+-.|==  --.+.|+..++++|.
T Consensus       349 ivVaTPgRlid~VkmKatn~~rvS~LV~  376 (731)
T KOG0339|consen  349 IVVATPGRLIDMVKMKATNLSRVSYLVL  376 (731)
T ss_pred             EEEechHHHHHHHHhhcccceeeeEEEE
Confidence            89999831000  135677777777664

>cd01524 RHOD_Pyr_redox Member of the Rhodanese Homology Domain superfamily

Probab=86.43  E-value=2.7  Score=29.43  Aligned_cols=38  Identities=11%  Similarity=0.061  Sum_probs=32.4

Q ss_pred             CCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCC
Q 028124           51 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   89 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~   89 (213)
                      .+.+++++||++-..+...+..|+..|. .+..+.|+++
T Consensus        49 ~~~~~vvl~c~~g~~a~~~a~~L~~~G~-~v~~l~GG~~   86 (90)
T cd01524          49 PKDKEIIVYCAVGLRGYIAARILTQNGF-KVKNLDGGYK   86 (90)
T ss_pred             CCCCcEEEEcCCChhHHHHHHHHHHCCC-CEEEecCCHH
Confidence            3567999999988888889999999885 8999999974

Included in this CD are the Lactococcus lactis NADH oxidase, Bacillus cereus NADH dehydrogenase, and Bacteroides thetaiotaomicron pyridine nucleotide-disulphide oxidoreductase, and similar rhodanese-like domains found C-terminal of the pyridine nucleotide-disulphide oxidoreductase (Pyr-redox) domain and the Pyr-redox dimerization domain.

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=86.18  E-value=5  Score=38.41  Aligned_cols=80  Identities=11%  Similarity=0.056  Sum_probs=60.2

Q ss_pred             CCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEE
Q 028124           53 GLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIV  132 (213)
Q Consensus        53 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV  132 (213)
                      .+.++|.+++++-+......|+..| +.+..+|++++..++..+++....+.                       .++|+
T Consensus        53 ~g~~lVisPl~sL~~dq~~~l~~~g-i~~~~~~s~~~~~~~~~~~~~l~~~~-----------------------~~il~  108 (591)
T TIGR01389        53 KGLTVVISPLISLMKDQVDQLRAAG-VAAAYLNSTLSAKEQQDIEKALVNGE-----------------------LKLLY  108 (591)
T ss_pred             CCcEEEEcCCHHHHHHHHHHHHHcC-CcEEEEeCCCCHHHHHHHHHHHhCCC-----------------------CCEEE
Confidence            4678999999999998888998887 89999999999999999999998874                       88888


Q ss_pred             EeCCCCC--cCcCCCCCCCCCEEEEe
Q 028124          133 VTDACLP--LLSSGESAISARVLINY  156 (213)
Q Consensus       133 ~Td~~~~--~~~rGld~~~v~~VI~y  156 (213)
                      +|+-.+-  ...+-+...++++||--
T Consensus       109 ~tpe~l~~~~~~~~l~~~~l~~iViD  134 (591)
T TIGR01389       109 VAPERLEQDYFLNMLQRIPIALVAVD  134 (591)
T ss_pred             EChhHhcChHHHHHHhcCCCCEEEEe
Confidence            8765210  01112334456666643

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.

>smart00491 HELICc2 helicase superfamily c-terminal domain

Probab=86.14  E-value=2.5  Score=33.01  Aligned_cols=47  Identities=17%  Similarity=0.285  Sum_probs=31.2

Q ss_pred             HHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCC--CCEEEEecCCC
Q 028124           92 ERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAIS--ARVLINYELPT  160 (213)
Q Consensus        92 ~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~--v~~VI~yd~P~  160 (213)
                      +..+++++|+...                  ..+  -.+|+++.-  -++++|+|+++  ++.||...+|-
T Consensus        32 ~~~~~l~~f~~~~------------------~~~--g~iL~~v~~--G~~~EGiD~~g~~~r~vii~glPf   80 (142)
T smart00491       32 ETEELLEKYSAAC------------------EAR--GALLLAVAR--GKVSEGIDFPDDLGRAVIIVGIPF   80 (142)
T ss_pred             hHHHHHHHHHHhc------------------CCC--CEEEEEEeC--CeeecceecCCCccEEEEEEecCC
Confidence            4478899999852                  000  146666541  01699999987  57898888774

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

Probab=85.84  E-value=7.9  Score=40.65  Aligned_cols=114  Identities=13%  Similarity=0.219  Sum_probs=75.4

Q ss_pred             CCCCcEEEEeCchHHHHHHHHHHhcc--C-------------------CceEEEecCCCCHHHHHHHHHHHhcccccccc
Q 028124           51 RPGLPMIVCCSSRDELDAVCSAVSNL--A-------------------DISFSSLHSDLAETERTLILEEFRHTAMKWNQ  109 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~~L~~~--~-------------------~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~  109 (213)
                      .+.++.+||+++++.|..++..|-..  +                   .++...=|-+++..+..-+-.-|..|.     
T Consensus      1357 ~~~k~~~vf~p~rk~~~~~a~~~~~~s~~~~~~~l~~~~e~~~~~l~e~l~~gvg~e~~s~~d~~iv~~l~e~g~----- 1431 (1674)
T KOG0951|consen 1357 GNRKPAIVFLPTRKHARLVAVDLVTFSHADEPDYLLSELEECDETLRESLKHGVGHEGLSSNDQEIVQQLFEAGA----- 1431 (1674)
T ss_pred             cCCCCeEEEeccchhhhhhhhccchhhccCcHHHHHHHHhcchHhhhhcccccccccccCcchHHHHHHHHhcCc-----
Confidence            46789999999999998877655322  0                   022222266777777666666677774     


Q ss_pred             cccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEE-----ec------CCCChHHHHHhhccccCCCCe
Q 028124          110 KVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLIN-----YE------LPTKKETYIRRMTTCLAADGS  178 (213)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~-----yd------~P~~~~~yi~R~GR~~~~~g~  178 (213)
                                        +.++|...-|+..     -. .+..||-     ||      .+-......|.+|++.| -|.
T Consensus      1432 ------------------i~v~v~s~~~~~~-----~~-~~~lVvvmgt~~ydg~e~~~~~y~i~~ll~m~G~a~~-~~k 1486 (1674)
T KOG0951|consen 1432 ------------------IQVCVMSRDCYGT-----KL-KAHLVVVMGTQYYDGKEHSYEDYPIAELLQMVGLASG-AGK 1486 (1674)
T ss_pred             ------------------EEEEEEEcccccc-----cc-cceEEEEecceeecccccccccCchhHHHHHhhhhcC-Ccc
Confidence                              8888887666322     11 1333332     33      33458899999999876 788


Q ss_pred             EEEEEeCchhHHHHHH
Q 028124          179 VINIVVGGEVVTLRSM  194 (213)
Q Consensus       179 ~i~~~~~~e~~~~~~l  194 (213)
                      |+.++......+++++
T Consensus      1487 ~vi~~~~~~k~yykkf 1502 (1674)
T KOG0951|consen 1487 CVIMCHTPKKEYYKKF 1502 (1674)
T ss_pred             EEEEecCchHHHHHHh
Confidence            9999887777766654

>cd00158 RHOD Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein

Probab=85.75  E-value=1.7  Score=29.65  Aligned_cols=39  Identities=13%  Similarity=0.279  Sum_probs=33.4

Q ss_pred             CCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCC
Q 028124           51 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   89 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~   89 (213)
                      .+..++|++|+....+...+..|...|+..+..+.|++.
T Consensus        48 ~~~~~vv~~c~~~~~a~~~~~~l~~~G~~~v~~l~gG~~   86 (89)
T cd00158          48 DKDKPIVVYCRSGNRSARAAKLLRKAGGTNVYNLEGGML   86 (89)
T ss_pred             CCCCeEEEEeCCCchHHHHHHHHHHhCcccEEEecCChh
Confidence            467899999999899999999999988667888888864

The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins.

>KOG1513 consensus Nuclear helicase MOP-3/SNO (DEAD-box superfamily) [Transcription; Signal transduction mechanisms]

Probab=85.08  E-value=1.5  Score=43.69  Aligned_cols=44  Identities=25%  Similarity=0.305  Sum_probs=35.9

Q ss_pred             eeEEEEeCCCCCcCcCCCCCCCCCEEE--------EecCCCChHHHHHhhccccCC
Q 028124          128 SHMIVVTDACLPLLSSGESAISARVLI--------NYELPTKKETYIRRMTTCLAA  175 (213)
Q Consensus       128 ~~iLV~Td~~~~~~~rGld~~~v~~VI--------~yd~P~~~~~yi~R~GR~~~~  175 (213)
                      ..|-|.+++    ++.||.++.=+-|+        -..+||+.+.-||+.||+.++
T Consensus       858 K~vAIISEA----aSSGiSLQsDrRv~NqRRRvHiTLELPWSADrAIQQFGRTHRS  909 (1300)
T KOG1513|consen  858 KLVAIISEA----ASSGISLQSDRRVQNQRRRVHITLELPWSADRAIQQFGRTHRS  909 (1300)
T ss_pred             ceeeeeehh----hccCceeecchhhhhhhheEEEEEECCcchhHHHHHhcccccc
Confidence            667777888    99999987655554        478999999999999998544

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=84.95  E-value=2.3  Score=40.82  Aligned_cols=78  Identities=10%  Similarity=0.123  Sum_probs=53.8

Q ss_pred             CCcEEEEeCchHHHHHHHHHHhccC---CceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCcee
Q 028124           53 GLPMIVCCSSRDELDAVCSAVSNLA---DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSH  129 (213)
Q Consensus        53 ~~~~IIF~~~~~~~~~l~~~L~~~~---~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (213)
                      ..++||.++|++-|..+++.+...+   .+.+..+||+.+...+...++   .+                        .+
T Consensus        84 ~~raLIl~PTreLa~Qi~~~~~~l~~~~~i~v~~l~Gg~~~~~q~~~l~---~~------------------------~d  136 (572)
T PRK04537         84 DPRALILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQRELLQ---QG------------------------VD  136 (572)
T ss_pred             CceEEEEeCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHHh---CC------------------------CC
Confidence            3689999999999998888776541   278899999988776654443   22                        78


Q ss_pred             EEEEeCCCCCc-CcC--CCCCCCCCEEEEec
Q 028124          130 MIVVTDACLPL-LSS--GESAISARVLINYE  157 (213)
Q Consensus       130 iLV~Td~~~~~-~~r--Gld~~~v~~VI~yd  157 (213)
                      |||+|.-.|-. +.+  .+++..+++||.-+
T Consensus       137 IiV~TP~rL~~~l~~~~~~~l~~v~~lViDE  167 (572)
T PRK04537        137 VIIATPGRLIDYVKQHKVVSLHACEICVLDE  167 (572)
T ss_pred             EEEECHHHHHHHHHhccccchhheeeeEecC
Confidence            99999631100 222  36677788777543

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

Probab=84.94  E-value=4.4  Score=37.29  Aligned_cols=106  Identities=11%  Similarity=0.130  Sum_probs=67.9

Q ss_pred             HHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccC---CceEEEecCCCCHHHHHHHHHHHhccccccccccc
Q 028124           36 METLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLA---DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVT  112 (213)
Q Consensus        36 ~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~---~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~  112 (213)
                      ...+.-+|..+.. ....-.++|.++|++-|..+++.+...|   ++++..+-|+++  .+.+.+..++.          
T Consensus       113 ~afaLPIl~~LL~-~p~~~~~lVLtPtRELA~QI~e~fe~Lg~~iglr~~~lvGG~~--m~~q~~~L~kk----------  179 (476)
T KOG0330|consen  113 GAFALPILQRLLQ-EPKLFFALVLTPTRELAQQIAEQFEALGSGIGLRVAVLVGGMD--MMLQANQLSKK----------  179 (476)
T ss_pred             hhhHHHHHHHHHc-CCCCceEEEecCcHHHHHHHHHHHHHhccccCeEEEEEecCch--HHHHHHHhhcC----------
Confidence            3444445555544 3445789999999999999988887652   388999999985  44555666666          


Q ss_pred             ccCCCCCcCCCCCCceeEEEEeCCCCCc--C-cCCCCCCCCCE--------EEEecCCCChHHHHHhh
Q 028124          113 EQSGDESETGKDEHKSHMIVVTDACLPL--L-SSGESAISARV--------LINYELPTKKETYIRRM  169 (213)
Q Consensus       113 ~~~~~~~~~~~~~~~~~iLV~Td~~~~~--~-~rGld~~~v~~--------VI~yd~P~~~~~yi~R~  169 (213)
                                     .+|||||+-.|-.  . .+|+.+..+.+        +.+.||-...+.++-++
T Consensus       180 ---------------PhilVaTPGrL~dhl~~Tkgf~le~lk~LVlDEADrlLd~dF~~~ld~ILk~i  232 (476)
T KOG0330|consen  180 ---------------PHILVATPGRLWDHLENTKGFSLEQLKFLVLDEADRLLDMDFEEELDYILKVI  232 (476)
T ss_pred             ---------------CCEEEeCcHHHHHHHHhccCccHHHhHHHhhchHHhhhhhhhHHHHHHHHHhc
Confidence                           6789999852110  0 56666654444        44555554444444433

>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=84.11  E-value=0.23  Score=48.47  Aligned_cols=111  Identities=11%  Similarity=0.069  Sum_probs=87.5

Q ss_pred             cchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccc
Q 028124           32 LQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKV  111 (213)
Q Consensus        32 ~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~  111 (213)
                      ...|+..+..+|..... ... .++|||+.-..-++-+...|...+ +....+.|.|+...|.+.+..|..+.       
T Consensus       520 ~s~ki~~~~~~l~~~~~-s~~-~kiiifsq~~~~l~l~~~~l~~~~-~~~~~~~g~~~~~~r~~s~~~~~~~~-------  589 (674)
T KOG1001|consen  520 ESSKIYAFLKILQAKEM-SEQ-PKIVIFSQLIWGLALVCLRLFFKG-FVFLRYDGEMLMKIRTKSFTDFPCDP-------  589 (674)
T ss_pred             hhhhhHHHHHHHhhccC-CCC-CceeeehhHHHHHHHhhhhhhhcc-cccchhhhhhHHHHHHhhhcccccCc-------
Confidence            44588888888874333 222 499999999999999988888776 78888999999999999999998653       


Q ss_pred             cccCCCCCcCCCCCCcee-EEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhcc
Q 028124          112 TEQSGDESETGKDEHKSH-MIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTT  171 (213)
Q Consensus       112 ~~~~~~~~~~~~~~~~~~-iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR  171 (213)
                                     ... .+++.-+    ..-|+++..+.+|+..|+=|++..--|-+-|
T Consensus       590 ---------------~~~vll~Slka----g~~glnlt~a~~v~~~d~~wnp~~eeQaidR  631 (674)
T KOG1001|consen  590 ---------------LVTALLMSLKA----GKVGLNLTAASHVLLMDPWWNPAVEEQAIDR  631 (674)
T ss_pred             ---------------cHHHHHHHHHH----hhhhhchhhhhHHHhhchhcChHHHHHHHHH
Confidence                           233 4556666    8999999999999999999988666554444

>cd01449 TST_Repeat_2 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain

Probab=83.95  E-value=3.1  Score=30.50  Aligned_cols=50  Identities=22%  Similarity=0.211  Sum_probs=36.1

Q ss_pred             HHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCC
Q 028124           37 ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDL   88 (213)
Q Consensus        37 ~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~   88 (213)
                      +.+..++..+-  ..+.+++|+||++-..+...+..|+..|.-.+..+.|++
T Consensus        64 ~~~~~~~~~~~--~~~~~~iv~yc~~g~~s~~~~~~l~~~G~~~v~~l~GG~  113 (118)
T cd01449          64 EELRALFAALG--ITPDKPVIVYCGSGVTACVLLLALELLGYKNVRLYDGSW  113 (118)
T ss_pred             HHHHHHHHHcC--CCCCCCEEEECCcHHHHHHHHHHHHHcCCCCeeeeCChH
Confidence            34444554421  235789999999988889999999988843577888876

TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue.

>cd01444 GlpE_ST GlpE sulfurtransferase (ST) and homologs are members of the Rhodanese Homology Domain superfamily

Probab=83.67  E-value=4.2  Score=28.46  Aligned_cols=38  Identities=16%  Similarity=0.265  Sum_probs=32.5

Q ss_pred             CCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCC
Q 028124           51 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDL   88 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~   88 (213)
                      .+..+++|+|++-..+...+..|...|.-.+..+.|++
T Consensus        54 ~~~~~ivv~c~~g~~s~~a~~~l~~~G~~~v~~l~gG~   91 (96)
T cd01444          54 DRDRPVVVYCYHGNSSAQLAQALREAGFTDVRSLAGGF   91 (96)
T ss_pred             CCCCCEEEEeCCCChHHHHHHHHHHcCCceEEEcCCCH
Confidence            35789999999999999999999999855677888886

Unlike other rhodanese sulfurtransferases, GlpE is a single domain protein but indications are that it functions as a dimer. The active site contains a catalytically active cysteine.

>cd01529 4RHOD_Repeats Member of the Rhodanese Homology Domain superfamily

Probab=83.39  E-value=2.7  Score=29.83  Aligned_cols=39  Identities=8%  Similarity=0.080  Sum_probs=32.2

Q ss_pred             CCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCC
Q 028124           51 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   89 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~   89 (213)
                      .+..++|+||++-..+...+..|+..|.-++..+.|++.
T Consensus        54 ~~~~~ivv~c~~g~~s~~~~~~l~~~G~~~v~~l~GG~~   92 (96)
T cd01529          54 GRATRYVLTCDGSLLARFAAQELLALGGKPVALLDGGTS   92 (96)
T ss_pred             CCCCCEEEEeCChHHHHHHHHHHHHcCCCCEEEeCCCHH
Confidence            456899999999888889999998888446888888873

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. Only the second and most of the fourth repeats contain the putative catalytic Cys residue. This CD aligns the 1st , 2nd, 3rd, and 4th repeats.

>smart00450 RHOD Rhodanese Homology Domain

Probab=83.37  E-value=2.2  Score=29.38  Aligned_cols=39  Identities=15%  Similarity=0.195  Sum_probs=33.0

Q ss_pred             CCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCC
Q 028124           51 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   89 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~   89 (213)
                      .+..++||||.+...+..++..|...|.-.+..+.|++.
T Consensus        54 ~~~~~iv~~c~~g~~a~~~~~~l~~~G~~~v~~l~GG~~   92 (100)
T smart00450       54 DKDKPVVVYCRSGNRSAKAAWLLRELGFKNVYLLDGGYK   92 (100)
T ss_pred             CCCCeEEEEeCCCcHHHHHHHHHHHcCCCceEEecCCHH
Confidence            567899999999999999999999988444888899873

An alpha beta fold found duplicated in the Rhodanese protein. The the Cysteine containing enzymatically active version of the domain is also found in the CDC25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and stress proteins such as Senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions with a loss of the cysteine are also seen in Dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases. These are likely to play a role in protein interactions.

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=82.43  E-value=5.3  Score=36.38  Aligned_cols=78  Identities=8%  Similarity=0.014  Sum_probs=53.3

Q ss_pred             CCcEEEEeCchHHHHHHHHHHhcc---CCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCcee
Q 028124           53 GLPMIVCCSSRDELDAVCSAVSNL---ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSH  129 (213)
Q Consensus        53 ~~~~IIF~~~~~~~~~l~~~L~~~---~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (213)
                      ..++||.++|++-|..+++.+...   -++.+..++|+.+...+..   .+..+                        .+
T Consensus        83 ~~~~lil~PtreLa~Qi~~~~~~l~~~~~~~v~~~~gg~~~~~~~~---~l~~~------------------------~~  135 (423)
T PRK04837         83 QPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLK---VLESG------------------------VD  135 (423)
T ss_pred             CceEEEECCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHH---HhcCC------------------------CC
Confidence            468999999999999887665432   2378899999877655433   33333                        78


Q ss_pred             EEEEeCCCCCc--CcCCCCCCCCCEEEEec
Q 028124          130 MIVVTDACLPL--LSSGESAISARVLINYE  157 (213)
Q Consensus       130 iLV~Td~~~~~--~~rGld~~~v~~VI~yd  157 (213)
                      |+|+|+..+-.  ....+++.++.++|.-+
T Consensus       136 IlV~TP~~l~~~l~~~~~~l~~v~~lViDE  165 (423)
T PRK04837        136 ILIGTTGRLIDYAKQNHINLGAIQVVVLDE  165 (423)
T ss_pred             EEEECHHHHHHHHHcCCcccccccEEEEec
Confidence            99999842100  13456788888888644

>cd01523 RHOD_Lact_B Member of the Rhodanese Homology Domain superfamily

Probab=82.02  E-value=2.1  Score=30.53  Aligned_cols=37  Identities=11%  Similarity=0.183  Sum_probs=31.9

Q ss_pred             CCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCC
Q 028124           52 PGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   89 (213)
Q Consensus        52 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~   89 (213)
                      +.++++++|.+-..+...+..|...| +.+..+.|++.
T Consensus        60 ~~~~ivv~C~~G~rs~~aa~~L~~~G-~~~~~l~GG~~   96 (100)
T cd01523          60 DDQEVTVICAKEGSSQFVAELLAERG-YDVDYLAGGMK   96 (100)
T ss_pred             CCCeEEEEcCCCCcHHHHHHHHHHcC-ceeEEeCCcHH
Confidence            56799999999888899999999998 67888889874

This CD includes predicted proteins with rhodanese-like domains found N-terminal of the metallo-beta-lactamase domain.

>PTZ00110 helicase; Provisional

Probab=81.56  E-value=8.3  Score=36.72  Aligned_cols=78  Identities=13%  Similarity=0.169  Sum_probs=53.1

Q ss_pred             CCcEEEEeCchHHHHHHHHHHhccC---CceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCcee
Q 028124           53 GLPMIVCCSSRDELDAVCSAVSNLA---DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSH  129 (213)
Q Consensus        53 ~~~~IIF~~~~~~~~~l~~~L~~~~---~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (213)
                      +..+||.++|++-|..+.+.+...+   .+.+..++|+.+.....   ..++.+                        .+
T Consensus       203 gp~~LIL~PTreLa~Qi~~~~~~~~~~~~i~~~~~~gg~~~~~q~---~~l~~~------------------------~~  255 (545)
T PTZ00110        203 GPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQI---YALRRG------------------------VE  255 (545)
T ss_pred             CcEEEEECChHHHHHHHHHHHHHHhcccCccEEEEeCCCCHHHHH---HHHHcC------------------------CC
Confidence            4579999999999999888887652   26788889988765543   334454                        78


Q ss_pred             EEEEeCCCCC-cCcC-CCCCCCCCEEEEec
Q 028124          130 MIVVTDACLP-LLSS-GESAISARVLINYE  157 (213)
Q Consensus       130 iLV~Td~~~~-~~~r-Gld~~~v~~VI~yd  157 (213)
                      |||+|+..+- .+.+ -+++..+++||.-+
T Consensus       256 IlVaTPgrL~d~l~~~~~~l~~v~~lViDE  285 (545)
T PTZ00110        256 ILIACPGRLIDFLESNVTNLRRVTYLVLDE  285 (545)
T ss_pred             EEEECHHHHHHHHHcCCCChhhCcEEEeeh
Confidence            9999962100 0333 35677888877644

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=81.25  E-value=6  Score=36.55  Aligned_cols=77  Identities=12%  Similarity=0.142  Sum_probs=53.8

Q ss_pred             CcEEEEeCchHHHHHHHHHHhcc---CCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeE
Q 028124           54 LPMIVCCSSRDELDAVCSAVSNL---ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHM  130 (213)
Q Consensus        54 ~~~IIF~~~~~~~~~l~~~L~~~---~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~i  130 (213)
                      .++||.|+|+.-|..+.+.+...   -.+.+..++|+.+..++..   .++.                        ..+|
T Consensus        76 ~~aLil~PtreLa~Qi~~~~~~~~~~~~~~~~~~~gg~~~~~~~~---~l~~------------------------~~~I  128 (456)
T PRK10590         76 VRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMM---KLRG------------------------GVDV  128 (456)
T ss_pred             ceEEEEeCcHHHHHHHHHHHHHHhccCCCEEEEEECCcCHHHHHH---HHcC------------------------CCcE
Confidence            37999999999999888877653   1267888999988665432   3333                        2789


Q ss_pred             EEEeCCCCCc--CcCCCCCCCCCEEEEec
Q 028124          131 IVVTDACLPL--LSSGESAISARVLINYE  157 (213)
Q Consensus       131 LV~Td~~~~~--~~rGld~~~v~~VI~yd  157 (213)
                      +|+|+-.+-.  ....+++..+++||.-+
T Consensus       129 iV~TP~rL~~~~~~~~~~l~~v~~lViDE  157 (456)
T PRK10590        129 LVATPGRLLDLEHQNAVKLDQVEILVLDE  157 (456)
T ss_pred             EEEChHHHHHHHHcCCcccccceEEEeec
Confidence            9999732100  24556788898888644

>cd01519 RHOD_HSP67B2 Member of the Rhodanese Homology Domain superfamily

Probab=80.90  E-value=3.2  Score=29.75  Aligned_cols=38  Identities=11%  Similarity=0.115  Sum_probs=31.4

Q ss_pred             CCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCC
Q 028124           52 PGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   89 (213)
Q Consensus        52 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~   89 (213)
                      +.+++|+||++-..+...+..|...|.-.+..+.|++.
T Consensus        65 ~~~~ivv~c~~g~~s~~~~~~l~~~G~~~v~~~~Gg~~  102 (106)
T cd01519          65 KDKELIFYCKAGVRSKAAAELARSLGYENVGNYPGSWL  102 (106)
T ss_pred             CCCeEEEECCCcHHHHHHHHHHHHcCCccceecCCcHH
Confidence            46899999999888899999999888445777888763

This CD includes the heat shock protein 67B2 of Drosophila melanogaster and other similar proteins, many of which are uncharacterized.

>cd01527 RHOD_YgaP Member of the Rhodanese Homology Domain superfamily

Probab=80.28  E-value=3.2  Score=29.46  Aligned_cols=38  Identities=13%  Similarity=0.110  Sum_probs=31.6

Q ss_pred             CCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCC
Q 028124           51 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDL   88 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~   88 (213)
                      .+.++++++|++-..+...+..|.+.|...+..+.|++
T Consensus        52 ~~~~~iv~~c~~g~~s~~~~~~L~~~g~~~v~~l~gG~   89 (99)
T cd01527          52 VGANAIIFHCRSGMRTQQNAERLAAISAGEAYVLEGGL   89 (99)
T ss_pred             CCCCcEEEEeCCCchHHHHHHHHHHcCCccEEEeeCCH
Confidence            45689999999988888999999888744677799986

This CD includes Escherichia coli YgaP, and similar uncharacterized putative rhodanese-related sulfurtransferases.

>PRK09401 reverse gyrase; Reviewed

Probab=80.09  E-value=8.2  Score=40.35  Aligned_cols=106  Identities=14%  Similarity=0.109  Sum_probs=65.8

Q ss_pred             EEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccC---CceEE--EecCCCCHHHHHHHHHH
Q 028124           25 FYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLA---DISFS--SLHSDLAETERTLILEE   99 (213)
Q Consensus        25 ~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~---~~~~~--~lhg~~~~~~R~~~l~~   99 (213)
                      +.+..+...=|..++.-++..+ .  ..+.+++|.++|+.-+..+++.++..+   ++.+.  ..|++++..++.+..+.
T Consensus        98 v~i~ApTGsGKT~f~l~~~~~l-~--~~g~~alIL~PTreLa~Qi~~~l~~l~~~~~~~~~~~~g~~~~~~~ek~~~~~~  174 (1176)
T PRK09401         98 FAIIAPTGVGKTTFGLVMSLYL-A--KKGKKSYIIFPTRLLVEQVVEKLEKFGEKVGCGVKILYYHSSLKKKEKEEFLER  174 (1176)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHH-H--hcCCeEEEEeccHHHHHHHHHHHHHHhhhcCceEEEEEccCCcchhHHHHHHHH
Confidence            3444454444665433322222 1  246899999999999999999987653   13333  34556677888888888


Q ss_pred             HhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEe
Q 028124          100 FRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINY  156 (213)
Q Consensus       100 Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~y  156 (213)
                      +..+.                       .+|+|+|...+...-..+....++++|--
T Consensus       175 l~~~~-----------------------~~IlV~Tp~rL~~~~~~l~~~~~~~lVvD  208 (1176)
T PRK09401        175 LKEGD-----------------------FDILVTTSQFLSKNFDELPKKKFDFVFVD  208 (1176)
T ss_pred             HhcCC-----------------------CCEEEECHHHHHHHHHhccccccCEEEEE
Confidence            88864                       89999997421111123444446666643

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	213
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		4e-13
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		4e-13
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		4e-13
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		4e-13
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		5e-13
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		5e-13
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		8e-12
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		1e-11
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		8e-10
1fuk_A	165	Crystal Structure Of The Carboxy Terminal Domain Of		9e-10
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		3e-09
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		1e-06
2wax_A	193	Structure Of The Human Ddx6 C-Terminal Domain In Co		5e-06

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score = 71.2 bits (173), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 46/193 (23%), Positives = 94/193 (48%), Gaps = 35/193 (18%)
Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           + F+VAV+R ++K +TL +L   +   +      ++ C+++ ++D +   +   A+ + S
Sbjct: 230 KQFFVAVEREEWKFDTLCDLYDTLTITQ-----AVIFCNTKRKVDWLTEKMRE-ANFTVS 283
Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
           S+H D+ + ER  I++EFR  A                       S +++ TD    + +
Sbjct: 284 SMHGDMPQKERESIMKEFRSGA-----------------------SRVLISTD----VWA 316
Query: 143 SGESAISARVLINYELPTKKETYIRRM--TTCLAADGSVINIVVGGEVVTLRSMEESLGL 200
            G       ++INY+LP  +E YI R+  +      G  IN V   ++  LR +E+    
Sbjct: 317 RGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYST 376
Query: 201 IVAEVPINISEIL 213
            + E+P+N+++++
Sbjct: 377 QIDEMPMNVADLI 389

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score = 71.2 bits (173), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 46/193 (23%), Positives = 94/193 (48%), Gaps = 35/193 (18%)
Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           + F+VAV+R ++K +TL +L   +   +      ++ C+++ ++D +   +   A+ + S
Sbjct: 251 KQFFVAVEREEWKFDTLCDLYDTLTITQ-----AVIFCNTKRKVDWLTEKMRE-ANFTVS 304
Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
           S+H D+ + ER  I++EFR  A                       S +++ TD    + +
Sbjct: 305 SMHGDMPQKERESIMKEFRSGA-----------------------SRVLISTD----VWA 337
Query: 143 SGESAISARVLINYELPTKKETYIRRM--TTCLAADGSVINIVVGGEVVTLRSMEESLGL 200
            G       ++INY+LP  +E YI R+  +      G  IN V   ++  LR +E+    
Sbjct: 338 RGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYST 397
Query: 201 IVAEVPINISEIL 213
            + E+P+N+++++
Sbjct: 398 QIDEMPMNVADLI 410

>pdb|2HYI|C Chain C, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 413

Iteration: 1
 Score = 70.9 bits (172), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 46/193 (23%), Positives = 94/193 (48%), Gaps = 35/193 (18%)
Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           + F+VAV+R ++K +TL +L   +   +      ++ C+++ ++D +   +   A+ + S
Sbjct: 252 KQFFVAVEREEWKFDTLCDLYDTLTITQ-----AVIFCNTKRKVDWLTEKMRE-ANFTVS 305
Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
           S+H D+ + ER  I++EFR  A                       S +++ TD    + +
Sbjct: 306 SMHGDMPQKERESIMKEFRSGA-----------------------SRVLISTD----VWA 338
Query: 143 SGESAISARVLINYELPTKKETYIRRM--TTCLAADGSVINIVVGGEVVTLRSMEESLGL 200
            G       ++INY+LP  +E YI R+  +      G  IN V   ++  LR +E+    
Sbjct: 339 RGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYST 398
Query: 201 IVAEVPINISEIL 213
            + E+P+N+++++
Sbjct: 399 QIDEMPMNVADLI 411

>pdb|2XB2|A Chain A, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 411

Iteration: 1
 Score = 70.9 bits (172), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 46/193 (23%), Positives = 93/193 (48%), Gaps = 35/193 (18%)
Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           + F+VAV+R ++K +TL +L   +   +      ++ C+++ ++D +   +   A+ + S
Sbjct: 252 KQFFVAVEREEWKFDTLCDLYDTLTITQ-----AVIFCNTKRKVDWLTEKMRE-ANFTVS 305
Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
           S+H D+ + ER  I++EFR  A                       S +++ TD    + +
Sbjct: 306 SMHGDMPQKERESIMKEFRSGA-----------------------SRVLISTD----VWA 338
Query: 143 SGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLRSMEESLGL 200
            G       ++INY+LP  +E YI R+         G  IN V   ++  LR +E+    
Sbjct: 339 RGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYST 398
Query: 201 IVAEVPINISEIL 213
            + E+P+N+++++
Sbjct: 399 QIDEMPMNVADLI 411

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 70.9 bits (172), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 45/193 (23%), Positives = 94/193 (48%), Gaps = 35/193 (18%)
Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           + F+VAV+R ++K +TL +L   +   +      ++ C+++ ++D +   +   A+ + S
Sbjct: 215 KQFFVAVEREEWKFDTLCDLYDTLTITQ-----AVIFCNTKRKVDWLTEKMRE-ANFTVS 268
Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
           S+H D+ + ER  I++EFR  A                       S +++ TD    + +
Sbjct: 269 SMHGDMPQKERESIMKEFRSGA-----------------------SRVLISTD----VWA 301
Query: 143 SGESAISARVLINYELPTKKETYIRRM--TTCLAADGSVINIVVGGEVVTLRSMEESLGL 200
            G       ++INY+LP  +E YI R+  +      G  +N V   ++  LR +E+    
Sbjct: 302 RGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAVNFVKNDDIRVLRDIEQYYST 361
Query: 201 IVAEVPINISEIL 213
            + E+P+N+++++
Sbjct: 362 QIDEMPMNVADLI 374

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 70.9 bits (172), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 45/193 (23%), Positives = 93/193 (48%), Gaps = 35/193 (18%)
Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           + F+VAV+R ++K +TL +L   +   +      ++ C+++ ++D +   +   A+ + S
Sbjct: 215 KQFFVAVEREEWKFDTLCDLYDTLTITQ-----AVIFCNTKRKVDWLTEKMRE-ANFTVS 268
Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
           S+H D+ + ER  I++EFR  A                       S +++ TD    + +
Sbjct: 269 SMHGDMPQKERESIMKEFRSGA-----------------------SRVLISTD----VWA 301
Query: 143 SGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLRSMEESLGL 200
            G       ++INY+LP  +E YI R+         G  +N V   ++  LR +E+    
Sbjct: 302 RGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAVNFVKNDDIRVLRDIEQYYST 361
Query: 201 IVAEVPINISEIL 213
            + E+P+N+++++
Sbjct: 362 QIDEMPMNVADLI 374

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score = 67.0 bits (162), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 94/193 (48%), Gaps = 35/193 (18%)
Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           R FY+ V+R ++K++TL +L   +   +      ++  ++R ++D +   + +  D + S
Sbjct: 255 RQFYINVEREEWKLDTLCDLYETLTITQ-----AVIFINTRRKVDWLTEKM-HARDFTVS 308
Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
           ++H D+ + ER +I+ EFR             SG           S +++ TD    LL+
Sbjct: 309 AMHGDMDQKERDVIMREFR-------------SG----------SSRVLITTD----LLA 341
Query: 143 SGESAISARVLINYELPTKKETYIRRMTTCLAADGS--VINIVVGGEVVTLRSMEESLGL 200
            G       ++INY+LPT +E YI R+            IN+V   +  TLR +E     
Sbjct: 342 RGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNT 401
Query: 201 IVAEVPINISEIL 213
            + E+P+N+++++
Sbjct: 402 SIEEMPLNVADLI 414

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score = 66.2 bits (160), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 94/193 (48%), Gaps = 35/193 (18%)
Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           R FY+ V+R ++K++TL +L   +   +      ++  ++R ++D +   + +  D + S
Sbjct: 229 RQFYINVEREEWKLDTLCDLYETLTITQ-----AVIFINTRRKVDWLTEKM-HARDFTVS 282
Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
           ++H D+ + ER +I+ EFR             SG           S +++ TD    LL+
Sbjct: 283 AMHGDMDQKERDVIMREFR-------------SG----------SSRVLITTD----LLA 315
Query: 143 SGESAISARVLINYELPTKKETYIRRMTTCLAADGS--VINIVVGGEVVTLRSMEESLGL 200
            G       ++INY+LPT +E YI R+            IN+V   +  TLR +E     
Sbjct: 316 RGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNT 375
Query: 201 IVAEVPINISEIL 213
            + E+P+N+++++
Sbjct: 376 SIEEMPLNVADLI 388

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score = 60.1 bits (144), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 90/193 (46%), Gaps = 35/193 (18%)
Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           + FYV V+  ++K E L +L   +   +      ++ C++R +++ + + + N    + S
Sbjct: 235 KQFYVNVEEEEYKYECLTDLYDSISVTQ-----AVIFCNTRRKVEELTTKLRN-DKFTVS 288
Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
           +++SDL + ER  I++EFR             SG           S +++ TD    LL+
Sbjct: 289 AIYSDLPQQERDTIMKEFR-------------SG----------SSRILISTD----LLA 321
Query: 143 SGESAISARVLINYELPTKKETYIRRMTTCLAADGS--VINIVVGGEVVTLRSMEESLGL 200
            G       ++INY+LP  KE YI R+            IN V   +V  +R +E+    
Sbjct: 322 RGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYST 381
Query: 201 IVAEVPINISEIL 213
            + E+P +I+ +L
Sbjct: 382 QIEELPSDIATLL 394

>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast Eif4a Length = 165

Iteration: 1
 Score = 60.1 bits (144), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 90/193 (46%), Gaps = 35/193 (18%)
Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           + FYV V+  ++K E L +L   +   +      ++ C++R +++ + + + N    + S
Sbjct: 5   KQFYVNVEEEEYKYECLTDLYDSISVTQ-----AVIFCNTRRKVEELTTKLRN-DKFTVS 58
Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
           +++SDL + ER  I++EFR             SG           S +++ TD    LL+
Sbjct: 59  AIYSDLPQQERDTIMKEFR-------------SG----------SSRILISTD----LLA 91
Query: 143 SGESAISARVLINYELPTKKETYIRRMTTCLAADGS--VINIVVGGEVVTLRSMEESLGL 200
            G       ++INY+LP  KE YI R+            IN V   +V  +R +E+    
Sbjct: 92  RGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYST 151
Query: 201 IVAEVPINISEIL 213
            + E+P +I+ +L
Sbjct: 152 QIEELPSDIATLL 164

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score = 58.2 bits (139), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 88/193 (45%), Gaps = 35/193 (18%)
Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           + FYV V+  ++K E L +L   +   +      ++ C++R +++ + + + N    + S
Sbjct: 234 KQFYVNVEEEEYKYECLTDLYDSISVTQ-----AVIFCNTRRKVEELTTKLRN-DKFTVS 287
Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
           +++SDL + ER  I +EFR             SG           S +++ TD    LL+
Sbjct: 288 AIYSDLPQQERDTIXKEFR-------------SG----------SSRILISTD----LLA 320
Query: 143 SGESAISARVLINYELPTKKETYIRRMTTCLAADGS--VINIVVGGEVVTLRSMEESLGL 200
            G       ++INY+LP  KE YI R+            IN V   +V   R +E+    
Sbjct: 321 RGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAXRELEKFYST 380
Query: 201 IVAEVPINISEIL 213
            + E+P +I+ +L
Sbjct: 381 QIEELPSDIATLL 393

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 38/159 (23%), Positives = 67/159 (42%), Gaps = 30/159 (18%)
Query: 57  IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 116
           I+ C+S + ++ +   +++L    + S H+ + + ER  +  EFR               
Sbjct: 262 IIFCNSTNRVELLAKKITDLGYSCYYS-HARMKQQERNKVFHEFRQ-------------- 306
Query: 117 DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LA 174
                GK        V T  C  LL+ G    +  V+IN++ P   ETY+ R+       
Sbjct: 307 -----GK--------VRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFG 353
Query: 175 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 213
             G  IN++   +   L  +E+ LG  +A +P  I + L
Sbjct: 354 HLGLAINLINWNDRFNLYKIEQELGTEIAAIPATIDKSL 392

>pdb|2WAX|A Chain A, Structure Of The Human Ddx6 C-Terminal Domain In Complex With An Edc3-Fdf Peptide Length = 193

Iteration: 1
 Score = 47.4 bits (111), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 36/159 (22%), Positives = 67/159 (42%), Gaps = 30/159 (18%)
Query: 57  IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 116
           I+ C+S   ++ +   +S L    F  +H+ + +  R  +  +FR+   +          
Sbjct: 48  IIFCNSSQRVELLAKKISQLGYSCFY-IHAKMRQEHRNRVFHDFRNGLCR---------- 96
Query: 117 DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRM--TTCLA 174
                         +V TD    L + G    +  V+IN++ P   ETY+ R+  +    
Sbjct: 97  -------------NLVCTD----LFTRGIDIQAVNVVINFDFPKLAETYLHRIGRSGRFG 139
Query: 175 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 213
             G  IN++   +   L+S+EE LG  +  +P NI + L
Sbjct: 140 HLGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNIDKSL 178

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	213
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	8e-16
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	6e-13
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	9e-12
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	2e-11
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	5e-11
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	3e-10
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	3e-09
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	6e-09
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	2e-07
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	5e-07
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	1e-06
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	5e-06
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	7e-06
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	1e-05
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	3e-05
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	2e-04
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	9e-04

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19 Length = 165

 Score = 70.7 bits (174), Expect = 8e-16
 Identities = 50/198 (25%), Positives = 92/198 (46%), Gaps = 45/198 (22%)

Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           + FYV V+  ++K E L +L   +   +      ++ C++R +++ + + + N    + S
Sbjct: 5   KQFYVNVEEEEYKYECLTDLYDSISVTQ-----AVIFCNTRRKVEELTTKLRND-KFTVS 58

Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
           +++SDL + ER  I++EFR             SG           S +++ TD    LL+
Sbjct: 59  AIYSDLPQQERDTIMKEFR-------------SG----------SSRILISTD----LLA 91

Query: 143 SGESAISARVLINYELPTKKETYIRRM-------TTCLAADGSVINIVVGGEVVTLRSME 195
            G       ++INY+LP  KE YI R+          +A     IN V   +V  +R +E
Sbjct: 92  RGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVA-----INFVTNEDVGAMRELE 146

Query: 196 ESLGLIVAEVPINISEIL 213
           +     + E+P +I+ +L
Sbjct: 147 KFYSTQIEELPSDIATLL 164

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A* Length = 394

 Score = 65.6 bits (161), Expect = 6e-13
 Identities = 51/195 (26%), Positives = 93/195 (47%), Gaps = 39/195 (20%)

Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           + FYV V+  ++K E L +L   +   +      ++ C++R +++ + + + N    + S
Sbjct: 234 KQFYVNVEEEEYKYECLTDLYDSISVTQ-----AVIFCNTRRKVEELTTKLRND-KFTVS 287

Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
           +++SDL + ER  I++EFR             SG           S +++ TD    LL+
Sbjct: 288 AIYSDLPQQERDTIMKEFR-------------SG----------SSRILISTD----LLA 320

Query: 143 SG--ESAISARVLINYELPTKKETYIRRM--TTCLAADGSVINIVVGGEVVTLRSMEESL 198
            G     +S  ++INY+LP  KE YI R+         G  IN V   +V  +R +E+  
Sbjct: 321 RGIDVQQVS--LVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFY 378

Query: 199 GLIVAEVPINISEIL 213
              + E+P +I+ +L
Sbjct: 379 STQIEELPSDIATLL 393

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens} Length = 414

 Score = 62.2 bits (152), Expect = 9e-12
 Identities = 51/195 (26%), Positives = 96/195 (49%), Gaps = 39/195 (20%)

Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           R FY+ V+R ++K++TL +L   +   +      ++  ++R ++D +   +    D + S
Sbjct: 255 RQFYINVEREEWKLDTLCDLYETLTITQ-----AVIFINTRRKVDWLTEKMHAR-DFTVS 308

Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
           ++H D+ + ER +I+ EFR             SG           S +++ TD    LL+
Sbjct: 309 AMHGDMDQKERDVIMREFR-------------SG----------SSRVLITTD----LLA 341

Query: 143 SG--ESAISARVLINYELPTKKETYIRRM--TTCLAADGSVINIVVGGEVVTLRSMEESL 198
            G     +S  ++INY+LPT +E YI R+         G  IN+V   +  TLR +E   
Sbjct: 342 RGIDVQQVS--LVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFY 399

Query: 199 GLIVAEVPINISEIL 213
              + E+P+N+++++
Sbjct: 400 NTSIEEMPLNVADLI 414

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A Length = 410

 Score = 61.0 bits (149), Expect = 2e-11
 Identities = 47/195 (24%), Positives = 96/195 (49%), Gaps = 39/195 (20%)

Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           + F+VAV+R ++K +TL +L   +   +      ++ C+++ ++D +   +    + + S
Sbjct: 251 KQFFVAVEREEWKFDTLCDLYDTLTITQ-----AVIFCNTKRKVDWLTEKMREA-NFTVS 304

Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
           S+H D+ + ER  I++EFR             SG           S +++ TD    + +
Sbjct: 305 SMHGDMPQKERESIMKEFR-------------SG----------ASRVLISTD----VWA 337

Query: 143 SG--ESAISARVLINYELPTKKETYIRRM--TTCLAADGSVINIVVGGEVVTLRSMEESL 198
            G     +S  ++INY+LP  +E YI R+  +      G  IN V   ++  LR +E+  
Sbjct: 338 RGLDVPQVS--LIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYY 395

Query: 199 GLIVAEVPINISEIL 213
              + E+P+N+++++
Sbjct: 396 STQIDEMPMNVADLI 410

>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 = 56.1 bits (136), Expect = 3e-10
 Identities = 35/205 (17%), Positives = 73/205 (35%), Gaps = 57/205 (27%)

Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           R +YV  +  + K + L  +   +  G+      I+ C +R     +   +        S
Sbjct: 9   RQYYVLCEHRKDKYQALCNIYGSITIGQ-----AIIFCQTRRNAKWLTVEMIQD-GHQVS 62

Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
            L  +L   +R  I++ FR              G          K  +++ T+ C     
Sbjct: 63  LLSGELTVEQRASIIQRFR-------------DG----------KEKVLITTNVC----- 94

Query: 143 SGESAISAR--------VLINYELPTKK------ETYIRRM--TTCLAADGSVINIVVGG 186
                  AR        +++N++LP K+      ETY+ R+  T      G   N++   
Sbjct: 95  -------ARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVD 147

Query: 187 EVVTLRSMEESLGLIVAEVPINISE 211
           E+ +L  +++     + ++     +
Sbjct: 148 ELPSLMKIQDHFNSSIKQLNAEDMD 172

>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 = 54.9 bits (133), Expect = 3e-09
 Identities = 40/199 (20%), Positives = 76/199 (38%), Gaps = 52/199 (26%)

Query: 25  FYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSL 84
           +Y  V+  Q K+  L  L   +    +     I+ C+S + ++ +   +++L   S    
Sbjct: 236 YYAFVEERQ-KLHCLNTLFSKL----QINQ-AIIFCNSTNRVELLAKKITDL-GYSCYYS 288

Query: 85  HSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSG 144
           H+ + + ER  +  EFR                       + K   +V +D         
Sbjct: 289 HARMKQQERNKVFHEFR-----------------------QGKVRTLVCSD--------- 316

Query: 145 ESAISAR--------VLINYELPTKKETYIRRM--TTCLAADGSVINIVVGGEVVTLRSM 194
              +  R        V+IN++ P   ETY+ R+  +      G  IN++   +   L  +
Sbjct: 317 ---LLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKI 373

Query: 195 EESLGLIVAEVPINISEIL 213
           E+ LG  +A +P  I + L
Sbjct: 374 EQELGTEIAAIPATIDKSL 392

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis} Length = 163

 Score = 52.1 bits (126), Expect = 6e-09
 Identities = 35/194 (18%), Positives = 69/194 (35%), Gaps = 52/194 (26%)

Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
            H  + V     K   L ++L        P    I+ C +++ ++ +   + +       
Sbjct: 11  EHAVIQVREEN-KFSLLKDVLMTE----NPDS-CIIFCRTKEHVNQLTDEL-DDLGYPCD 63

Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
            +H  + + +R  ++ EF+                         +   +V TD       
Sbjct: 64  KIHGGMIQEDRFDVMNEFK-----------------------RGEYRYLVATD------- 93

Query: 143 SGESAISARVL--------INYELPTKKETYIRRM--TTCLAADGSVINIVVGGEVVTLR 192
                ++AR +        INY+LP +KE+Y+ R   T      G  I+ V   E   L 
Sbjct: 94  -----VAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAFEKRFLA 148

Query: 193 SMEESLGLIVAEVP 206
            +EE +G  + ++ 
Sbjct: 149 DIEEYIGFEIQKIE 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 = 48.0 bits (115), Expect = 2e-07
 Identities = 30/207 (14%), Positives = 70/207 (33%), Gaps = 63/207 (30%)

Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           + +YV +   + K   L +LL ++         +++   S     A+   +    +    
Sbjct: 7   QQYYVKLKDNE-KNRKLFDLLDVL----EFNQ-VVIFVKSVQRCIALAQLLVEQ-NFPAI 59

Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
           ++H  + + ER    ++F+                       + +  ++V T+       
Sbjct: 60  AIHRGMPQEERLSRYQQFK-----------------------DFQRRILVATN------- 89

Query: 143 SGESAISAR--------VLINYELPTKKETYIRRM-------TTCLAADGSVINIVVG-G 186
                +  R        +  NY++P   +TY+ R+       T  LA     I  V    
Sbjct: 90  -----LFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLA-----ITFVSDEN 139

Query: 187 EVVTLRSMEESLGLIVAEVPINISEIL 213
           +   L  +++   + ++E+P  I    
Sbjct: 140 DAKILNDVQDRFEVNISELPDEIDISS 166

>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 = 48.3 bits (116), Expect = 5e-07
 Identities = 36/206 (17%), Positives = 70/206 (33%), Gaps = 58/206 (28%)

Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           + +YV       K + L  L   +   +      ++ C +R     + + +S       +
Sbjct: 241 KQYYVLCSSRDEKFQALCNLYGAITIAQ-----AMIFCHTRKTASWLAAELSK-EGHQVA 294

Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
            L  ++   +R  ++E FR              G          K  ++V T+ C     
Sbjct: 295 LLSGEMMVEQRAAVIERFR-------------EG----------KEKVLVTTNVC----- 326

Query: 143 SGESAISAR--------VLINYELPTKK------ETYIRRM--TTCLAADGSVINIVVGG 186
                  AR        V+IN++LP  K      ETY+ R+  T      G  +N+V   
Sbjct: 327 -------ARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSK 379

Query: 187 EVV-TLRSMEESLGLIVAEVPINISE 211
             +  L  ++E     +  +  +  +
Sbjct: 380 HSMNILNRIQEHFNKKIERLDTDDLD 405

>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 = 47.3 bits (113), Expect = 1e-06
 Identities = 35/206 (16%), Positives = 69/206 (33%), Gaps = 58/206 (28%)

Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           + +YV       K + L  L   +   +      ++ C +R     + + +S       +
Sbjct: 308 KQYYVLCSSRDEKFQALCNLYGAITIAQ-----AMIFCHTRKTASWLAAELSK-EGHQVA 361

Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
            L  ++   +R  ++E FR              G          K  ++V T+ C     
Sbjct: 362 LLSGEMMVEQRAAVIERFR-------------EG----------KEKVLVTTNVC----- 393

Query: 143 SGESAISARVL--------INYELPTKK------ETYIRRM--TTCLAADGSVINIVVGG 186
                  AR +        IN++LP  K      ETY+ R+  T      G  +N+V   
Sbjct: 394 -------ARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSK 446

Query: 187 EVV-TLRSMEESLGLIVAEVPINISE 211
             +  L  ++E     +  +  +  +
Sbjct: 447 HSMNILNRIQEHFNKKIERLDTDDLD 472

>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 = 45.2 bits (108), Expect = 5e-06
 Identities = 40/207 (19%), Positives = 74/207 (35%), Gaps = 59/207 (28%)

Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           +  Y+       K + L EL  L+  G       I+  +++   + +   + +      S
Sbjct: 218 KQLYMDCKNEADKFDVLTELYGLMTIGS-----SIIFVATKKTANVLYGKLKS-EGHEVS 271

Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
            LH DL   ER  ++++FR              G          +S +++ T+       
Sbjct: 272 ILHGDLQTQERDRLIDDFR-------------EG----------RSKVLITTNVL----- 303

Query: 143 SGESAISAR--------VLINYELPTKK------ETYIRRM--TTCLAADGSVINIVVGG 186
                  AR        +++NY+LPT         TYI R+  T      G  I+ V   
Sbjct: 304 -------ARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDK 356

Query: 187 EVV-TLRSMEESLGLI-VAEVPINISE 211
                L ++++  G I +  VP +  +
Sbjct: 357 NSFNILSAIQKYFGDIEMTRVPTDDWD 383

>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 = 45.2 bits (107), Expect = 7e-06
 Identities = 30/197 (15%), Positives = 71/197 (36%), Gaps = 47/197 (23%)

Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLA--DIS 80
               V  ++    +   VE +   +  R      I+   +      +CS + N    D+ 
Sbjct: 258 DQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLP 317

Query: 81  FSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPL 140
               H  + + +RT +++ F+                       + +S ++V TD     
Sbjct: 318 ILEFHGKITQNKRTSLVKRFK-----------------------KDESGILVCTD----- 349

Query: 141 LSSGESAISARVL--------INYELPTKKETYIRRM-TTCLA-ADGSVINIVVGGEVVT 190
                  + AR +        +   +P++   YI R+  T  +  +GS +  +   E+  
Sbjct: 350 -------VGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPF 402

Query: 191 LRSMEESLGLIVAEVPI 207
           +R +E++  +++A+   
Sbjct: 403 VRELEDAKNIVIAKQEK 419

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* Length = 563

 Score = 44.4 bits (105), Expect = 1e-05
 Identities = 30/197 (15%), Positives = 71/197 (36%), Gaps = 47/197 (23%)

Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLA--DIS 80
               V  ++    +   VE +   +  R      I+   +      +CS + N    D+ 
Sbjct: 309 DQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLP 368

Query: 81  FSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPL 140
               H  + + +RT +++ F+                       + +S ++V TD     
Sbjct: 369 ILEFHGKITQNKRTSLVKRFK-----------------------KDESGILVCTD----- 400

Query: 141 LSSGESAISARVL--------INYELPTKKETYIRRM-TTCLA-ADGSVINIVVGGEVVT 190
                  + AR +        +   +P++   YI R+  T  +  +GS +  +   E+  
Sbjct: 401 -------VGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPF 453

Query: 191 LRSMEESLGLIVAEVPI 207
           +R +E++  +++A+   
Sbjct: 454 VRELEDAKNIVIAKQEK 470

>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 = 43.0 bits (102), Expect = 3e-05
 Identities = 28/196 (14%), Positives = 68/196 (34%), Gaps = 53/196 (27%)

Query: 25  FYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSL 84
           +YV +   + K   L +LL ++   +     +++   S     A+   +    +    ++
Sbjct: 228 YYVKLKDNE-KNRKLFDLLDVLEFNQ-----VVIFVKSVQRCIALAQLL-VEQNFPAIAI 280

Query: 85  HSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSG 144
           H  + + ER    ++F+                       + +  ++V T+         
Sbjct: 281 HRGMPQEERLSRYQQFK-----------------------DFQRRILVATN--------- 308

Query: 145 ESAISAR--------VLINYELPTKKETYIRRM--TTCLAADGSVINIVVG-GEVVTLRS 193
              +  R        +  NY++P   +TY+ R+         G  I  V    +   L  
Sbjct: 309 ---LFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILND 365

Query: 194 MEESLGLIVAEVPINI 209
           +++   + ++E+P  I
Sbjct: 366 VQDRFEVNISELPDEI 381

>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 = 39.5 bits (93), Expect = 2e-04
 Identities = 34/195 (17%), Positives = 69/195 (35%), Gaps = 51/195 (26%)

Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
             +Y   D L+ K   LV LL    A R      IV    R+ +  + + +   A I+  
Sbjct: 5   HQWYYRADDLEHKTALLVHLLKQPEATR-----SIVFVRKRERVHELANWL-REAGINNC 58

Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
            L  ++ + +R   ++                          E + +++V TD       
Sbjct: 59  YLEGEMVQGKRNEAIKRLT-----------------------EGRVNVLVATD------- 88

Query: 143 SGESAISARVL--------INYELPTKKETYIRRM--TTCLAADGSVINIVVGGEVVTLR 192
                ++AR +         N+++P   +TY+ R+  T      G+ I++V   + + L 
Sbjct: 89  -----VAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHDHLLLG 143

Query: 193 SMEESLGLIVAEVPI 207
            +   +   +    I
Sbjct: 144 KVGRYIEEPIKARVI 158

>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 = 38.0 bits (89), Expect = 9e-04
 Identities = 38/204 (18%), Positives = 70/204 (34%), Gaps = 57/204 (27%)

Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
               V       ++E L +LL++           +V   ++ E + +      L  +   
Sbjct: 7   EEEAVPAPVRG-RLEVLSDLLYV-----ASPDRAMVFTRTKAETEEI---AQGLLRLGHP 57

Query: 83  --SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPL 140
             +LH DL++ ER  +L  FR                       + +  ++V TD     
Sbjct: 58  AQALHGDLSQGERERVLGAFR-----------------------QGEVRVLVATD----- 89

Query: 141 LSSGESAISARVL--------INYELPTKKETYIRRM--TTCLAADGSVINIVVGGEVVT 190
                  ++AR L        ++Y LP + E Y  R   T      G V+ +    E   
Sbjct: 90  -------VAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRD 142

Query: 191 LRSMEESLGLIVAEVPI-NISEIL 213
           + ++E ++G     V      E+L
Sbjct: 143 VEALERAVGRRFKRVNPPTPEEVL 166

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	213
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	100.0
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	100.0
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	100.0
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	100.0
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.97
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.97
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	99.97
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	99.96
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	99.93
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.95
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.95
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.95
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.95
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.94
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.94
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.93
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.93
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.92
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.92
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.92
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.91
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.9
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.89
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.89
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.88
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.88
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.87
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.87
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.87
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.87
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.86
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.85
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.85
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.84
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.84
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.84
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.83
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.82
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.8
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.8
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.8
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.8
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.79
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.78
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.78
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.77
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.76
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.76
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.75
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.74
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.74
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.73
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.73
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.73
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.73
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.72
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.72
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.72
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.71
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.71
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.7
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.69
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.69
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.68
3h1t_A	590	Type I site-specific restriction-modification syst	99.68
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.67
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.66
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.49
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.48
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.18
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	98.28
3hgt_A	328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	97.93
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	97.08
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	96.53
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	95.42
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	94.56
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	94.22
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	91.03
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	90.34
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	89.98
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	89.16
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	88.35
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	88.25
3gk5_A	108	Uncharacterized rhodanese-related protein TVG08686	88.19
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	87.82
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	87.21
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	86.09
2jtq_A	85	Phage shock protein E; solution structure rhodanes	86.07
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	85.25
1gmx_A	108	GLPE protein; transferase, rhodanese, sulfurtransf	84.74
3foj_A	100	Uncharacterized protein; protein SSP1007, structur	84.18
3iwh_A	103	Rhodanese-like domain protein; alpha-beta-alpha sa	83.09
3g5j_A	134	Putative ATP/GTP binding protein; N-terminal domai	82.97
1wv9_A	94	Rhodanese homolog TT1651; CDC25, phosphatase, sulf	82.92
3bor_A	237	Human initiation factor 4A-II; translation initiat	82.83
3eme_A	103	Rhodanese-like domain protein; alpha-beta-alpha sa	82.8
3hix_A	106	ALR3790 protein; rhodanese, rhodanese_3, Q8YQN0, Q	82.09
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	81.8
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	81.5
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	81.24
3flh_A	124	Uncharacterized protein LP_1913; alpha-beta protei	80.93

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=100.00  E-value=2.3e-32  Score=216.96  Aligned_cols=161  Identities=29%  Similarity=0.544  Sum_probs=146.6

Q ss_pred             CCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHH
Q 028124           20 SQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEE   99 (213)
Q Consensus        20 ~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~   99 (213)
                      .+|+|+|+.++..+.|++.|.++++.     .+..++||||+++..++.++..|...+ +.+..+||+|++.+|.+++++
T Consensus         2 ~~i~~~~~~~~~~~~K~~~l~~ll~~-----~~~~~~lVF~~~~~~~~~l~~~L~~~~-~~~~~~~~~~~~~~r~~~~~~   75 (165)
T 1fuk_A            2 EGIKQFYVNVEEEEYKYECLTDLYDS-----ISVTQAVIFCNTRRKVEELTTKLRNDK-FTVSAIYSDLPQQERDTIMKE   75 (165)
T ss_dssp             --CEEEEEEEESGGGHHHHHHHHHHH-----TTCSCEEEEESSHHHHHHHHHHHHHTT-CCEEEECTTSCHHHHHHHHHH
T ss_pred             CCcEEEEEECCcchhHHHHHHHHHHh-----CCCCCEEEEECCHHHHHHHHHHHHHcC-CCEEEEECCCCHHHHHHHHHH
Confidence            47999999999877799999999988     356899999999999999999999887 799999999999999999999


Q ss_pred             HhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCCCC
Q 028124          100 FRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADG  177 (213)
Q Consensus       100 Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~~g  177 (213)
                      |++|.                       .++||||++    +++|+|+|++++||+||+|++..+|+||+||+  .|+.|
T Consensus        76 f~~g~-----------------------~~vlv~T~~----~~~G~d~~~~~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g  128 (165)
T 1fuk_A           76 FRSGS-----------------------SRILISTDL----LARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKG  128 (165)
T ss_dssp             HHTTS-----------------------CSEEEEEGG----GTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----C
T ss_pred             HHcCC-----------------------CEEEEEcCh----hhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCc
Confidence            99985                       899999999    99999999999999999999999999999997  45789


Q ss_pred             eEEEEEeCchhHHHHHHHHHhcccccccCccccccC
Q 028124          178 SVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL  213 (213)
Q Consensus       178 ~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~~~~~~  213 (213)
                      .|++|+++.+...+..+++.++..++++|.++.+++
T Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (165)
T 1fuk_A          129 VAINFVTNEDVGAMRELEKFYSTQIEELPSDIATLL  164 (165)
T ss_dssp             EEEEEEETTTHHHHHHHHHHSSCCCEECCSCCTTTT
T ss_pred             eEEEEEcchHHHHHHHHHHHHccCccccCccHHhhc
Confidence            999999999999999999999999999999887764

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=100.00  E-value=4.5e-32  Score=215.07  Aligned_cols=157  Identities=21%  Similarity=0.385  Sum_probs=144.2

Q ss_pred             CCCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHH
Q 028124           16 PSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTL   95 (213)
Q Consensus        16 ~~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~   95 (213)
                      ...+.+|+|+|+.++..+ |+..|.++++.     ....++||||+++..++.+++.|...+ +.+..+||+|++.+|..
T Consensus         4 ~~~~~~i~~~~~~~~~~~-K~~~L~~ll~~-----~~~~~~lVF~~~~~~~~~l~~~L~~~~-~~~~~~hg~~~~~~r~~   76 (163)
T 2hjv_A            4 GLTTRNIEHAVIQVREEN-KFSLLKDVLMT-----ENPDSCIIFCRTKEHVNQLTDELDDLG-YPCDKIHGGMIQEDRFD   76 (163)
T ss_dssp             --CCCCEEEEEEECCGGG-HHHHHHHHHHH-----HCCSSEEEECSSHHHHHHHHHHHHHTT-CCEEEECTTSCHHHHHH
T ss_pred             ccCcccceEEEEECChHH-HHHHHHHHHHh-----cCCCcEEEEECCHHHHHHHHHHHHHcC-CcEEEEeCCCCHHHHHH
Confidence            345667999999998876 99999999987     356799999999999999999999987 89999999999999999


Q ss_pred             HHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--c
Q 028124           96 ILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--L  173 (213)
Q Consensus        96 ~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~  173 (213)
                      ++++|++|.                       .++||||++    +++|+|+|++++|||||+|+++.+|+||+||+  .
T Consensus        77 ~~~~f~~g~-----------------------~~vlv~T~~----~~~Gld~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~  129 (163)
T 2hjv_A           77 VMNEFKRGE-----------------------YRYLVATDV----AARGIDIENISLVINYDLPLEKESYVHRTGRTGRA  129 (163)
T ss_dssp             HHHHHHTTS-----------------------CSEEEECGG----GTTTCCCSCCSEEEESSCCSSHHHHHHHTTTSSCT
T ss_pred             HHHHHHcCC-----------------------CeEEEECCh----hhcCCchhcCCEEEEeCCCCCHHHHHHhccccCcC
Confidence            999999985                       999999999    99999999999999999999999999999996  5


Q ss_pred             CCCCeEEEEEeCchhHHHHHHHHHhcccccccC
Q 028124          174 AADGSVINIVVGGEVVTLRSMEESLGLIVAEVP  206 (213)
Q Consensus       174 ~~~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~  206 (213)
                      |+.|.+++|+.+.+...++++++.++.++++++
T Consensus       130 g~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~  162 (163)
T 2hjv_A          130 GNKGKAISFVTAFEKRFLADIEEYIGFEIQKIE  162 (163)
T ss_dssp             TCCEEEEEEECGGGHHHHHHHHHHHTSCCEECC
T ss_pred             CCCceEEEEecHHHHHHHHHHHHHHCCCcCccC
Confidence            678999999999999999999999999988765

>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=100.00  E-value=3.7e-32  Score=217.92  Aligned_cols=159  Identities=18%  Similarity=0.360  Sum_probs=142.4

Q ss_pred             CCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHH
Q 028124           18 HFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLIL   97 (213)
Q Consensus        18 ~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l   97 (213)
                      ++.+|+|+|+.++..+ |+..|.++++.     .+..++||||+++++++.+++.|...+ +.+..+||+|++.+|..++
T Consensus         2 ~~~~i~q~~~~~~~~~-K~~~L~~ll~~-----~~~~~~lVF~~~~~~~~~l~~~L~~~~-~~~~~~hg~~~~~~r~~~~   74 (172)
T 1t5i_A            2 SLHGLQQYYVKLKDNE-KNRKLFDLLDV-----LEFNQVVIFVKSVQRCIALAQLLVEQN-FPAIAIHRGMPQEERLSRY   74 (172)
T ss_dssp             ---CCEEEEEECCGGG-HHHHHHHHHHH-----SCCSSEEEECSSHHHHHHHHHHHHHTT-CCEEEECTTSCHHHHHHHH
T ss_pred             ccCCeEEEEEECChHH-HHHHHHHHHHh-----CCCCcEEEEECCHHHHHHHHHHHHhcC-CCEEEEECCCCHHHHHHHH
Confidence            4578999999999876 99999999987     356799999999999999999999987 8999999999999999999


Q ss_pred             HHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCC
Q 028124           98 EEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAA  175 (213)
Q Consensus        98 ~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~  175 (213)
                      ++|++|.                       .++||||++    +++|+|+|++++|||||+|+++..|+||+||+  .|+
T Consensus        75 ~~f~~g~-----------------------~~vLvaT~~----~~~Gldi~~~~~Vi~~d~p~~~~~~~qr~GR~~R~g~  127 (172)
T 1t5i_A           75 QQFKDFQ-----------------------RRILVATNL----FGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGT  127 (172)
T ss_dssp             HHHHTTS-----------------------CSEEEESSC----CSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGC
T ss_pred             HHHHCCC-----------------------CcEEEECCc----hhcCcchhhCCEEEEECCCCCHHHHHHHhcccccCCC
Confidence            9999985                       999999999    99999999999999999999999999999996  567


Q ss_pred             CCeEEEEEeCc-hhHHHHHHHHHhcccccccCcccc
Q 028124          176 DGSVINIVVGG-EVVTLRSMEESLGLIVAEVPINIS  210 (213)
Q Consensus       176 ~g~~i~~~~~~-e~~~~~~le~~l~~~~~~~~~~~~  210 (213)
                      .|.+++|+.+. +...++.+++.++.+++++|..++
T Consensus       128 ~g~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~  163 (172)
T 1t5i_A          128 KGLAITFVSDENDAKILNDVQDRFEVNISELPDEID  163 (172)
T ss_dssp             CCEEEEEECSHHHHHHHHHHHHHHCCCEEECC----
T ss_pred             CcEEEEEEcChhHHHHHHHHHHHHhcchhhCChhhc
Confidence            89999999875 678899999999999999986654

>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=100.00  E-value=5.6e-32  Score=216.65  Aligned_cols=161  Identities=17%  Similarity=0.338  Sum_probs=147.5

Q ss_pred             CCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHH
Q 028124           18 HFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLIL   97 (213)
Q Consensus        18 ~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l   97 (213)
                      ++.+|+|+|+.++..+.|++.|.++++.     .+.+++||||+++.+++.++..|...+ +.+..+||+|++.+|..++
T Consensus         4 ~~~~i~q~~~~~~~~~~K~~~L~~ll~~-----~~~~~~lVF~~~~~~~~~l~~~L~~~~-~~~~~~~g~~~~~~R~~~~   77 (175)
T 2rb4_A            4 TLNNIRQYYVLCEHRKDKYQALCNIYGS-----ITIGQAIIFCQTRRNAKWLTVEMIQDG-HQVSLLSGELTVEQRASII   77 (175)
T ss_dssp             CBCCEEEEEEECSSHHHHHHHHHHHHTT-----SCCSEEEEECSCHHHHHHHHHHHHTTT-CCEEEECSSCCHHHHHHHH
T ss_pred             ccCCceEEEEEcCChHhHHHHHHHHHHh-----CCCCCEEEEECCHHHHHHHHHHHHHcC-CcEEEEeCCCCHHHHHHHH
Confidence            4678999999999877799999999987     356799999999999999999999987 8999999999999999999


Q ss_pred             HHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCC------CChHHHHHhhcc
Q 028124           98 EEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELP------TKKETYIRRMTT  171 (213)
Q Consensus        98 ~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P------~~~~~yi~R~GR  171 (213)
                      ++|++|.                       .++||||++    +++|+|+|++++|||||+|      .+..+|+||+||
T Consensus        78 ~~f~~g~-----------------------~~vLvaT~~----~~~Gid~~~~~~Vi~~d~p~~~~~~~~~~~~~qr~GR  130 (175)
T 2rb4_A           78 QRFRDGK-----------------------EKVLITTNV----CARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGR  130 (175)
T ss_dssp             HHHHTTS-----------------------CSEEEECCS----CCTTTCCTTEEEEEESSCCC--CCSCCHHHHHHHHCB
T ss_pred             HHHHcCC-----------------------CeEEEEecc----hhcCCCcccCCEEEEeCCCCCccccCCHHHHHHHhcc
Confidence            9999985                       999999999    9999999999999999999      899999999999


Q ss_pred             c--cCCCCeEEEEEeCchhHHHHHHHHHhcccccccCccccc
Q 028124          172 C--LAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISE  211 (213)
Q Consensus       172 ~--~~~~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~~~~  211 (213)
                      +  .|+.|.+++|+.+.+...+.++++.++..+++++++-.+
T Consensus       131 ~gR~g~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~  172 (175)
T 2rb4_A          131 TGRFGKKGLAFNMIEVDELPSLMKIQDHFNSSIKQLNAEDMD  172 (175)
T ss_dssp             C----CCEEEEEEECGGGHHHHHHHHHHHTCCCEEECSSCCC
T ss_pred             cccCCCCceEEEEEccchHHHHHHHHHHhcCcccccCCchhc
Confidence            7  467899999999999999999999999999988876543

>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=99.97  E-value=2.5e-31  Score=215.70  Aligned_cols=164  Identities=20%  Similarity=0.268  Sum_probs=133.7

Q ss_pred             CCCCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHH
Q 028124           15 SPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERT   94 (213)
Q Consensus        15 ~~~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~   94 (213)
                      ...++.+|+|+|+.++..+ |+..|.++|+.    ..++.++||||+++..++.++..|...+ +.+..+||+|++.+|.
T Consensus        13 ~~~~~~~i~q~~~~v~~~~-K~~~L~~ll~~----~~~~~k~lVF~~~~~~~~~l~~~L~~~g-~~~~~lhg~~~~~~r~   86 (185)
T 2jgn_A           13 QGSTSENITQKVVWVEESD-KRSFLLDLLNA----TGKDSLTLVFVETKKGADSLEDFLYHEG-YACTSIHGDRSQRDRE   86 (185)
T ss_dssp             ---CCTTEEEEEEECCGGG-HHHHHHHHHHH----C-CCSCEEEEESCHHHHHHHHHHHHHTT-CCEEEEC--------C
T ss_pred             cCCCCCCceEEEEEeCcHH-HHHHHHHHHHh----cCCCCeEEEEECCHHHHHHHHHHHHHcC-CceEEEeCCCCHHHHH
Confidence            3456789999999999876 99999999988    2357899999999999999999999887 8999999999999999


Q ss_pred             HHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--
Q 028124           95 LILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--  172 (213)
Q Consensus        95 ~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--  172 (213)
                      .++++|++|.                       .++||||++    +++|+|+|++++||+||+|+++.+|+||+||+  
T Consensus        87 ~~~~~f~~g~-----------------------~~vLvaT~~----~~~Gldi~~~~~VI~~d~p~s~~~~~Qr~GR~~R  139 (185)
T 2jgn_A           87 EALHQFRSGK-----------------------SPILVATAV----AARGLDISNVKHVINFDLPSDIEEYVHRIGRTGR  139 (185)
T ss_dssp             HHHHHHHHTS-----------------------SSEEEEEC----------CCCSBSEEEESSCCSSHHHHHHHHTTBCC
T ss_pred             HHHHHHHcCC-----------------------CeEEEEcCh----hhcCCCcccCCEEEEeCCCCCHHHHHHHccccCC
Confidence            9999999985                       899999999    99999999999999999999999999999997  


Q ss_pred             cCCCCeEEEEEeCchhHHHHHHHHHhcccccccCccccc
Q 028124          173 LAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISE  211 (213)
Q Consensus       173 ~~~~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~~~~  211 (213)
                      .|+.|.|++|+++.+...++++++.++....++|..+.+
T Consensus       140 ~g~~g~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~l~~  178 (185)
T 2jgn_A          140 VGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLEN  178 (185)
T ss_dssp             TTSCEEEEEEECGGGGGGHHHHHHHHHHTTCCCCHHHHH
T ss_pred             CCCCcEEEEEEchhhHHHHHHHHHHHHhccCCCCHHHHH
Confidence            466899999999999999999999998888888765543

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=99.97  E-value=1.6e-30  Score=212.26  Aligned_cols=160  Identities=21%  Similarity=0.278  Sum_probs=140.9

Q ss_pred             CCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHH
Q 028124           17 SHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI   96 (213)
Q Consensus        17 ~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~   96 (213)
                      .+..+|+|+|+.++..+ |+..|.++|..      ...++||||+++..++.+++.|...+ +.+..+||+|++.+|.++
T Consensus        25 ~~~~~i~q~~~~~~~~~-K~~~L~~~l~~------~~~~~lVF~~~~~~~~~l~~~L~~~g-~~~~~lhg~~~~~~R~~~   96 (191)
T 2p6n_A           25 AASLDVIQEVEYVKEEA-KMVYLLECLQK------TPPPVLIFAEKKADVDAIHEYLLLKG-VEAVAIHGGKDQEERTKA   96 (191)
T ss_dssp             ---CCSEEEEEECCGGG-HHHHHHHHHTT------SCSCEEEECSCHHHHHHHHHHHHHHT-CCEEEECTTSCHHHHHHH
T ss_pred             CCCcCceEEEEEcChHH-HHHHHHHHHHh------CCCCEEEEECCHHHHHHHHHHHHHcC-CcEEEEeCCCCHHHHHHH
Confidence            45678999999998876 99999999876      24689999999999999999999887 899999999999999999


Q ss_pred             HHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cC
Q 028124           97 LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LA  174 (213)
Q Consensus        97 l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~  174 (213)
                      +++|++|+                       .++||||++    +++|+|+|++++|||||+|+++++|+||+||+  .|
T Consensus        97 l~~F~~g~-----------------------~~vLvaT~~----~~~Gldi~~v~~VI~~d~p~~~~~~~qr~GR~gR~g  149 (191)
T 2p6n_A           97 IEAFREGK-----------------------KDVLVATDV----ASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSG  149 (191)
T ss_dssp             HHHHHHTS-----------------------CSEEEECHH----HHTTCCCCCCSEEEESSCCSSHHHHHHHHTTSCC--
T ss_pred             HHHHhcCC-----------------------CEEEEEcCc----hhcCCCcccCCEEEEeCCCCCHHHHHHHhCccccCC
Confidence            99999985                       999999999    99999999999999999999999999999997  46


Q ss_pred             CCCeEEEEEeCc-hhHHHHHHHHHhcccccccCccccc
Q 028124          175 ADGSVINIVVGG-EVVTLRSMEESLGLIVAEVPINISE  211 (213)
Q Consensus       175 ~~g~~i~~~~~~-e~~~~~~le~~l~~~~~~~~~~~~~  211 (213)
                      +.|.+++|+++. +...+..+++.++....++|..+.+
T Consensus       150 ~~g~~i~l~~~~~~~~~~~~l~~~l~~~~~~~p~~l~~  187 (191)
T 2p6n_A          150 NTGIATTFINKACDESVLMDLKALLLEAKQKVPPVLQV  187 (191)
T ss_dssp             -CCEEEEEECTTSCHHHHHHHHHHHHHTTCCCCHHHHS
T ss_pred             CCcEEEEEEcCchhHHHHHHHHHHHHHccCcCCHHHHh
Confidence            789999999876 7788899999998888888765554

>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=99.97  E-value=1.1e-29  Score=209.94  Aligned_cols=155  Identities=21%  Similarity=0.303  Sum_probs=141.4

Q ss_pred             CCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHH
Q 028124           20 SQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEE   99 (213)
Q Consensus        20 ~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~   99 (213)
                      -.+.+.++.++... |++.|.++++.     .+++++||||+++.+++.+++.|...+ +.+..+||+|++.+|..++++
T Consensus         4 i~~~~~~~~~~~~~-k~~~l~~ll~~-----~~~~~~lVF~~~~~~~~~l~~~L~~~~-~~~~~lhg~~~~~~r~~~~~~   76 (212)
T 3eaq_A            4 VTYEEEAVPAPVRG-RLEVLSDLLYV-----ASPDRAMVFTRTKAETEEIAQGLLRLG-HPAQALHGDLSQGERERVLGA   76 (212)
T ss_dssp             CCBCCEEEECCTTS-HHHHHHHHHHH-----HCCSCEEEECSSHHHHHHHHHHHHHHT-CCEEEECSSSCHHHHHHHHHH
T ss_pred             cceeeeEEeCCHHH-HHHHHHHHHHh-----CCCCeEEEEeCCHHHHHHHHHHHHHcC-CCEEEEECCCCHHHHHHHHHH
Confidence            34678888888877 99999999987     356899999999999999999999887 899999999999999999999


Q ss_pred             HhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhcccc--CCCC
Q 028124          100 FRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADG  177 (213)
Q Consensus       100 Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~--~~~g  177 (213)
                      |++|.                       .++||||++    +++|+|+|++++|||||+|++.+.|+||+||+|  |+.|
T Consensus        77 f~~g~-----------------------~~vlvaT~~----~~~Gidi~~v~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g  129 (212)
T 3eaq_A           77 FRQGE-----------------------VRVLVATDV----AARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGG  129 (212)
T ss_dssp             HHSSS-----------------------CCEEEECTT----TTCSSSCCCBSEEEESSCCSSHHHHHHHHTTBCCCC--B
T ss_pred             HHCCC-----------------------CeEEEecCh----hhcCCCCccCcEEEECCCCcCHHHHHHHhcccCCCCCCC
Confidence            99985                       999999999    999999999999999999999999999999974  5679


Q ss_pred             eEEEEEeCchhHHHHHHHHHhcccccccCcc
Q 028124          178 SVINIVVGGEVVTLRSMEESLGLIVAEVPIN  208 (213)
Q Consensus       178 ~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~  208 (213)
                      .|+.|+++.+...++.+++.++..+.+++.+
T Consensus       130 ~~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~  160 (212)
T 3eaq_A          130 RVVLLYGPRERRDVEALERAVGRRFKRVNPP  160 (212)
T ss_dssp             EEEEEECGGGHHHHHHHHHHHSSCCEECCCC
T ss_pred             eEEEEEchhHHHHHHHHHHHhcCcCeecCCC
Confidence            9999999999999999999999988877754

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=99.96  E-value=5.1e-29  Score=216.94  Aligned_cols=154  Identities=19%  Similarity=0.300  Sum_probs=141.6

Q ss_pred             CceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHH
Q 028124           21 QPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEF  100 (213)
Q Consensus        21 ~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~F  100 (213)
                      +++|+|+.++..+ |++.|.++++.     ..++++||||+++.+++.++..|...+ +.+..+||+|++.+|..++++|
T Consensus         2 ~v~~~~i~~~~~~-K~~~L~~ll~~-----~~~~~~LVF~~t~~~~~~l~~~L~~~g-~~~~~lhg~l~~~~r~~~~~~f   74 (300)
T 3i32_A            2 TYEEEAVPAPVRG-RLEVLSDLLYV-----ASPDRAMVFTRTKAETEEIAQGLLRLG-HPAQALHGDMSQGERERVMGAF   74 (300)
T ss_dssp             CSEEEEEECCSSS-HHHHHHHHHHH-----HCCSSEEEECSSHHHHHHHHHHHHTTT-CCEEEECSCCCTHHHHHHHHHH
T ss_pred             ceEEEEEECCHHH-HHHHHHHHHHh-----cCCCCEEEEECCHHHHHHHHHHHHhCC-CCEEEEeCCCCHHHHHHHHHHh
Confidence            4789999999987 99999999987     247899999999999999999999887 8999999999999999999999


Q ss_pred             hcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhcccc--CCCCe
Q 028124          101 RHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AADGS  178 (213)
Q Consensus       101 r~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~--~~~g~  178 (213)
                      ++|.                       .++||||++    +++|+|+|++++|||||+|++.++|+||+||+|  |+.|.
T Consensus        75 ~~g~-----------------------~~vLVaT~v----a~~Gidi~~v~~VI~~d~p~s~~~y~Qr~GRagR~g~~G~  127 (300)
T 3i32_A           75 RQGE-----------------------VRVLVATDV----AARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGR  127 (300)
T ss_dssp             HHTS-----------------------CCEEEECST----TTCSTTCCCCSEEEESSCCSSTTHHHHHHTCCC-----CE
T ss_pred             hcCC-----------------------ceEEEEech----hhcCccccceeEEEEcCCCCCHHHHHHHccCcCcCCCCce
Confidence            9985                       999999999    999999999999999999999999999999974  56799


Q ss_pred             EEEEEeCchhHHHHHHHHHhcccccccCcc
Q 028124          179 VINIVVGGEVVTLRSMEESLGLIVAEVPIN  208 (213)
Q Consensus       179 ~i~~~~~~e~~~~~~le~~l~~~~~~~~~~  208 (213)
                      |+.|+++.+...++.+++.++..+.+++.+
T Consensus       128 ~i~l~~~~e~~~~~~ie~~~~~~~~~~~~~  157 (300)
T 3i32_A          128 VVLLYGPRERRDVEALERAVGRRFKRVNPP  157 (300)
T ss_dssp             EEEEECSSTHHHHHHHHHHHTCCCEECCCC
T ss_pred             EEEEeChHHHHHHHHHHHHhCCcceEeCCC
Confidence            999999999999999999999988877654

>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=99.93  E-value=3.8e-31  Score=211.10  Aligned_cols=157  Identities=18%  Similarity=0.313  Sum_probs=143.1

Q ss_pred             CCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHH
Q 028124           19 FSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILE   98 (213)
Q Consensus        19 ~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~   98 (213)
                      +.+|+|+|+.++..+.|+..|.++++.     ..+.++||||+++..++.+++.|...+ +.+..+||+|++.+|..+++
T Consensus         1 R~~i~~~~~~~~~~~~k~~~l~~ll~~-----~~~~~~iVF~~~~~~~~~l~~~L~~~~-~~~~~~~g~~~~~~r~~~~~   74 (170)
T 2yjt_D            1 RKKIHQWYYRADDLEHKTALLVHLLKQ-----PEATRSIVFVRKRERVHELANWLREAG-INNCYLEGEMVQGKRNEAIK   74 (170)
Confidence            357899999999844599999999976     356799999999999999999999887 89999999999999999999


Q ss_pred             HHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCCC
Q 028124           99 EFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAAD  176 (213)
Q Consensus        99 ~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~~  176 (213)
                      +|++|.                       .++||||++    +++|+|+|++++||+||+|+++.+|+||+||+  .|+.
T Consensus        75 ~f~~g~-----------------------~~vLvaT~~----~~~Gid~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~  127 (170)
T 2yjt_D           75 RLTEGR-----------------------VNVLVATDV----AARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRK  127 (170)
Confidence            999985                       999999999    99999999999999999999999999999996  5678


Q ss_pred             CeEEEEEeCchhHHHHHHHHHhcccccccCcc
Q 028124          177 GSVINIVVGGEVVTLRSMEESLGLIVAEVPIN  208 (213)
Q Consensus       177 g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~  208 (213)
                      |.+++++.+.+...+.++++.++..+.+.+++
T Consensus       128 g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (170)
T 2yjt_D          128 GTAISLVEAHDHLLLGKVGRYIEEPIKARVID  159 (170)
Confidence            99999999999999999999999888776543

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=99.95  E-value=1e-27  Score=212.59  Aligned_cols=164  Identities=27%  Similarity=0.560  Sum_probs=152.0

Q ss_pred             CCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHH
Q 028124           17 SHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI   96 (213)
Q Consensus        17 ~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~   96 (213)
                      ....++.+++..+...+.|...|.++++..     ...++||||++++.++.+++.|...+ +.+..+||++++.+|..+
T Consensus       245 ~~~~~~~~~~~~~~~~~~k~~~l~~~~~~~-----~~~~~lVf~~~~~~~~~l~~~L~~~~-~~~~~~h~~~~~~~r~~~  318 (410)
T 2j0s_A          245 LTLEGIKQFFVAVEREEWKFDTLCDLYDTL-----TITQAVIFCNTKRKVDWLTEKMREAN-FTVSSMHGDMPQKERESI  318 (410)
T ss_dssp             CSCTTEEEEEEEESSTTHHHHHHHHHHHHH-----TSSEEEEECSSHHHHHHHHHHHHHTT-CCCEEECTTSCHHHHHHH
T ss_pred             ccCCCceEEEEEeCcHHhHHHHHHHHHHhc-----CCCcEEEEEcCHHHHHHHHHHHHhCC-CceEEeeCCCCHHHHHHH
Confidence            345678999999998888999999999873     34699999999999999999999987 799999999999999999


Q ss_pred             HHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cC
Q 028124           97 LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LA  174 (213)
Q Consensus        97 l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~  174 (213)
                      +++|++|.                       .++||||++    +++|+|+|++++||+||+|++...|+||+||+  .|
T Consensus       319 ~~~f~~g~-----------------------~~vlv~T~~----~~~Gidi~~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g  371 (410)
T 2j0s_A          319 MKEFRSGA-----------------------SRVLISTDV----WARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYG  371 (410)
T ss_dssp             HHHHHHTS-----------------------SCEEEECGG----GSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGG
T ss_pred             HHHHHCCC-----------------------CCEEEECCh----hhCcCCcccCCEEEEECCCCCHHHHHHhcccccCCC
Confidence            99999985                       899999999    99999999999999999999999999999997  46


Q ss_pred             CCCeEEEEEeCchhHHHHHHHHHhcccccccCccccccC
Q 028124          175 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL  213 (213)
Q Consensus       175 ~~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~~~~~~  213 (213)
                      +.|.|+.|+.+.+...+++++++++.+++++|.+..+++
T Consensus       372 ~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~  410 (410)
T 2j0s_A          372 RKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI  410 (410)
T ss_dssp             CCEEEEEEEEGGGHHHHHHHHHHTTCCCEECCSCCTTTC
T ss_pred             CceEEEEEecHHHHHHHHHHHHHhCCCceecccchhhcC
Confidence            789999999999999999999999999999999988765

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=99.95  E-value=4.2e-27  Score=212.77  Aligned_cols=159  Identities=19%  Similarity=0.303  Sum_probs=142.6

Q ss_pred             CCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHH
Q 028124           18 HFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLIL   97 (213)
Q Consensus        18 ~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l   97 (213)
                      ...++.|.+..+.... |...|.+++..      ...++||||++++.|+.+++.|...+ +.+..+||++++.+|.+++
T Consensus       272 ~~~~i~~~~~~~~~~~-k~~~l~~~l~~------~~~~~lVF~~t~~~a~~l~~~L~~~~-~~~~~lhg~~~~~~R~~~l  343 (434)
T 2db3_A          272 ACSDVKQTIYEVNKYA-KRSKLIEILSE------QADGTIVFVETKRGADFLASFLSEKE-FPTTSIHGDRLQSQREQAL  343 (434)
T ss_dssp             CCTTEEEEEEECCGGG-HHHHHHHHHHH------CCTTEEEECSSHHHHHHHHHHHHHTT-CCEEEESTTSCHHHHHHHH
T ss_pred             cccccceEEEEeCcHH-HHHHHHHHHHh------CCCCEEEEEeCcHHHHHHHHHHHhCC-CCEEEEeCCCCHHHHHHHH
Confidence            4567899998888776 99999999987      22459999999999999999999987 8999999999999999999


Q ss_pred             HHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCC
Q 028124           98 EEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAA  175 (213)
Q Consensus        98 ~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~  175 (213)
                      ++|++|.                       .++||||++    ++||+|+|++++|||||+|++.++|+||+||+  .|+
T Consensus       344 ~~F~~g~-----------------------~~vLvaT~v----~~rGlDi~~v~~VI~~d~p~~~~~y~qriGR~gR~g~  396 (434)
T 2db3_A          344 RDFKNGS-----------------------MKVLIATSV----ASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGN  396 (434)
T ss_dssp             HHHHTSS-----------------------CSEEEECGG----GTSSCCCTTCCEEEESSCCSSHHHHHHHHTTSSCTTC
T ss_pred             HHHHcCC-----------------------CcEEEEchh----hhCCCCcccCCEEEEECCCCCHHHHHHHhcccccCCC
Confidence            9999985                       999999999    99999999999999999999999999999997  567


Q ss_pred             CCeEEEEEeC-chhHHHHHHHHHhcccccccCccccc
Q 028124          176 DGSVINIVVG-GEVVTLRSMEESLGLIVAEVPINISE  211 (213)
Q Consensus       176 ~g~~i~~~~~-~e~~~~~~le~~l~~~~~~~~~~~~~  211 (213)
                      .|.+++|+++ ++......+.+.+....+++|..+.+
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            8999999985 57788899999998888888877654

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=99.95  E-value=2.6e-27  Score=209.43  Aligned_cols=165  Identities=28%  Similarity=0.539  Sum_probs=137.3

Q ss_pred             CCCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHH
Q 028124           16 PSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTL   95 (213)
Q Consensus        16 ~~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~   95 (213)
                      ......+.+++..+...+.|+..+.++++.     ....++||||++++.++.+++.|...+ +.+..+||+|++++|.+
T Consensus       248 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-----~~~~~~lvf~~~~~~~~~l~~~l~~~~-~~~~~~h~~~~~~~r~~  321 (414)
T 3eiq_A          248 ELTLEGIRQFYINVEREEWKLDTLCDLYET-----LTITQAVIFINTRRKVDWLTEKMHARD-FTVSAMHGDMDQKERDV  321 (414)
T ss_dssp             CCCTTSCCEEEEECSSSTTHHHHHHHHHHS-----SCCSSCEEECSCHHHHHHHHHHHHTTT-CCCEEC---CHHHHHHH
T ss_pred             ccCCCCceEEEEEeChHHhHHHHHHHHHHh-----CCCCcEEEEeCCHHHHHHHHHHHHhcC-CeEEEecCCCCHHHHHH
Confidence            345667899999998888899999999987     456799999999999999999999987 89999999999999999


Q ss_pred             HHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--c
Q 028124           96 ILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--L  173 (213)
Q Consensus        96 ~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~  173 (213)
                      ++++|++|.                       .++||||++    +++|+|+|++++||+||+|++...|+||+||+  .
T Consensus       322 ~~~~f~~g~-----------------------~~vlv~T~~----~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~  374 (414)
T 3eiq_A          322 IMREFRSGS-----------------------SRVLITTDL----LARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRF  374 (414)
T ss_dssp             HHHHHSCC--------------------------CEEECSS----CC--CCGGGCSCEEESSCCSSTHHHHHHSCCC---
T ss_pred             HHHHHHcCC-----------------------CcEEEECCc----cccCCCccCCCEEEEeCCCCCHHHhhhhcCcccCC
Confidence            999999985                       899999999    99999999999999999999999999999997  4


Q ss_pred             CCCCeEEEEEeCchhHHHHHHHHHhcccccccCccccccC
Q 028124          174 AADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL  213 (213)
Q Consensus       174 ~~~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~~~~~~  213 (213)
                      |+.|.|+.|+++.+...++.+++.++..++++|.++.++|
T Consensus       375 g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  414 (414)
T 3eiq_A          375 GRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVADLI  414 (414)
T ss_dssp             ----CEEEEECSTHHHHHHHHHHHTTCCCEECCC------
T ss_pred             CCCceEEEEEcHHHHHHHHHHHHHHcCCccccChhhhhcC
Confidence            6679999999999999999999999999999999998875

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=99.95  E-value=2.3e-26  Score=203.06  Aligned_cols=161  Identities=24%  Similarity=0.437  Sum_probs=147.6

Q ss_pred             CCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHH
Q 028124           18 HFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLIL   97 (213)
Q Consensus        18 ~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l   97 (213)
                      ...++.+++..+.... |...+..+++.     ....++||||++++.++.+++.|...+ +.+..+||+|++.+|..++
T Consensus       229 ~~~~~~~~~~~~~~~~-k~~~l~~~~~~-----~~~~~~lVf~~~~~~~~~l~~~L~~~~-~~~~~~~~~~~~~~r~~~~  301 (400)
T 1s2m_A          229 TLKGITQYYAFVEERQ-KLHCLNTLFSK-----LQINQAIIFCNSTNRVELLAKKITDLG-YSCYYSHARMKQQERNKVF  301 (400)
T ss_dssp             BCTTEEEEEEECCGGG-HHHHHHHHHHH-----SCCSEEEEECSSHHHHHHHHHHHHHHT-CCEEEECTTSCHHHHHHHH
T ss_pred             ccCCceeEEEEechhh-HHHHHHHHHhh-----cCCCcEEEEEecHHHHHHHHHHHHhcC-CCeEEecCCCCHHHHHHHH
Confidence            4567888888887765 99999999887     456799999999999999999999887 7999999999999999999


Q ss_pred             HHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCC
Q 028124           98 EEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAA  175 (213)
Q Consensus        98 ~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~  175 (213)
                      ++|++|.                       .++||||++    +++|+|+|++++||+||+|++...|+||+||+  .|+
T Consensus       302 ~~f~~g~-----------------------~~vLv~T~~----~~~Gidip~~~~Vi~~~~p~s~~~~~Qr~GR~gR~g~  354 (400)
T 1s2m_A          302 HEFRQGK-----------------------VRTLVCSDL----LTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGH  354 (400)
T ss_dssp             HHHHTTS-----------------------SSEEEESSC----SSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTC
T ss_pred             HHHhcCC-----------------------CcEEEEcCc----cccCCCccCCCEEEEeCCCCCHHHHHHhcchhcCCCC
Confidence            9999985                       999999999    99999999999999999999999999999997  467


Q ss_pred             CCeEEEEEeCchhHHHHHHHHHhcccccccCcccccc
Q 028124          176 DGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEI  212 (213)
Q Consensus       176 ~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~~~~~  212 (213)
                      .|.|+.|+.++|...++++++.++.+++++|..+.+.
T Consensus       355 ~g~~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~  391 (400)
T 1s2m_A          355 LGLAINLINWNDRFNLYKIEQELGTEIAAIPATIDKS  391 (400)
T ss_dssp             CEEEEEEECGGGHHHHHHHHHHHTCCCEECCSSCCGG
T ss_pred             CceEEEEeccchHHHHHHHHHHhCCCccccccccccc
Confidence            7999999999999999999999999999999887664

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=99.94  E-value=2.6e-25  Score=195.23  Aligned_cols=160  Identities=18%  Similarity=0.353  Sum_probs=144.2

Q ss_pred             CCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHH
Q 028124           17 SHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI   96 (213)
Q Consensus        17 ~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~   96 (213)
                      .....+.+++..+.... |...|.++++.     ....++||||+++++++.+++.|...+ +.+..+||++++++|..+
T Consensus       220 ~~~~~~~~~~~~~~~~~-~~~~l~~~l~~-----~~~~~~lvf~~~~~~~~~l~~~L~~~~-~~~~~~~~~~~~~~r~~~  292 (391)
T 1xti_A          220 LTLHGLQQYYVKLKDNE-KNRKLFDLLDV-----LEFNQVVIFVKSVQRCIALAQLLVEQN-FPAIAIHRGMPQEERLSR  292 (391)
T ss_dssp             CCCTTCEEEEEECCGGG-HHHHHHHHHHH-----SCCSEEEEECSCHHHHHHHHHHHHHTT-CCEEEECTTSCHHHHHHH
T ss_pred             cCcccceEEEEEcCchh-HHHHHHHHHHh-----cCCCcEEEEeCcHHHHHHHHHHHHhCC-CcEEEEeCCCCHHHHHHH
Confidence            34567888888887766 99999999987     466899999999999999999999987 899999999999999999


Q ss_pred             HHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cC
Q 028124           97 LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LA  174 (213)
Q Consensus        97 l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~  174 (213)
                      +++|++|.                       .++||||++    +++|+|+|++++||+||+|++...|+||+||+  .|
T Consensus       293 ~~~f~~~~-----------------------~~vlv~T~~----~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g  345 (391)
T 1xti_A          293 YQQFKDFQ-----------------------RRILVATNL----FGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFG  345 (391)
T ss_dssp             HHHHHTTC-----------------------CSEEEESCC----CSSCBCCTTEEEEEESSCCSSHHHHHHHHCBCSSSC
T ss_pred             HHHHhcCC-----------------------CcEEEECCh----hhcCCCcccCCEEEEeCCCCCHHHHHHhcccccCCC
Confidence            99999985                       899999999    99999999999999999999999999999997  45


Q ss_pred             CCCeEEEEEeCc-hhHHHHHHHHHhcccccccCcccc
Q 028124          175 ADGSVINIVVGG-EVVTLRSMEESLGLIVAEVPINIS  210 (213)
Q Consensus       175 ~~g~~i~~~~~~-e~~~~~~le~~l~~~~~~~~~~~~  210 (213)
                      +.|.|+.++.+. +...++.+++.++..++++|..+.
T Consensus       346 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  382 (391)
T 1xti_A          346 TKGLAITFVSDENDAKILNDVQDRFEVNISELPDEID  382 (391)
T ss_dssp             CCCEEEEEECSHHHHHHHHHHHHHTTCCCEECCSCCC
T ss_pred             CceEEEEEEcccchHHHHHHHHHHhcCChhhCCcccc
Confidence            779999999876 667889999999999999986543

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=99.94  E-value=3.2e-26  Score=202.91  Aligned_cols=162  Identities=20%  Similarity=0.261  Sum_probs=144.1

Q ss_pred             CCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHH
Q 028124           17 SHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI   96 (213)
Q Consensus        17 ~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~   96 (213)
                      ....++.+.+..++..+ |...|.++++.    .....++||||++++.++.+++.|...+ +.+..+||++++++|.++
T Consensus       245 ~~~~~i~~~~~~~~~~~-~~~~l~~~l~~----~~~~~~~lVf~~~~~~~~~l~~~L~~~~-~~~~~~h~~~~~~~r~~~  318 (417)
T 2i4i_A          245 STSENITQKVVWVEESD-KRSFLLDLLNA----TGKDSLTLVFVETKKGADSLEDFLYHEG-YACTSIHGDRSQRDREEA  318 (417)
T ss_dssp             -CCSSEEEEEEECCGGG-HHHHHHHHHHT----CCTTCEEEEECSSHHHHHHHHHHHHHTT-CCEEEECTTSCHHHHHHH
T ss_pred             CCccCceEEEEEeccHh-HHHHHHHHHHh----cCCCCeEEEEECCHHHHHHHHHHHHHCC-CCeeEecCCCCHHHHHHH
Confidence            34567889998888766 99999999987    3457899999999999999999999987 899999999999999999


Q ss_pred             HHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhcccc--C
Q 028124           97 LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--A  174 (213)
Q Consensus        97 l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~--~  174 (213)
                      +++|++|.                       .++||||++    +++|+|+|++++||+||+|++..+|+||+||++  |
T Consensus       319 ~~~f~~g~-----------------------~~vlvaT~~----~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g  371 (417)
T 2i4i_A          319 LHQFRSGK-----------------------SPILVATAV----AARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVG  371 (417)
T ss_dssp             HHHHHHTS-----------------------SCEEEECHH----HHTTSCCCCEEEEEESSCCSSHHHHHHHHTTBCC--
T ss_pred             HHHHHcCC-----------------------CCEEEECCh----hhcCCCcccCCEEEEEcCCCCHHHHHHhcCccccCC
Confidence            99999985                       899999999    999999999999999999999999999999974  6


Q ss_pred             CCCeEEEEEeCchhHHHHHHHHHhcccccccCccccc
Q 028124          175 ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISE  211 (213)
Q Consensus       175 ~~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~~~~  211 (213)
                      +.|.|+.|+++.+...+..+.+.+.....++|..+.+
T Consensus       372 ~~g~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~  408 (417)
T 2i4i_A          372 NLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLEN  408 (417)
T ss_dssp             CCEEEEEEECGGGGGGHHHHHHHHHHTTCCCCHHHHH
T ss_pred             CCceEEEEEccccHHHHHHHHHHHHHhcCcCCHHHHH
Confidence            6799999999999999999999998777777755443

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=99.93  E-value=2.2e-25  Score=196.70  Aligned_cols=160  Identities=19%  Similarity=0.344  Sum_probs=142.0

Q ss_pred             CCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHH
Q 028124           17 SHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI   96 (213)
Q Consensus        17 ~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~   96 (213)
                      .....+.+.+..+.....|...|.+++..     ....++||||++++.++.+++.|...+ +.+..+||+|++++|.++
T Consensus       235 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-----~~~~~~lvf~~~~~~~~~l~~~L~~~~-~~~~~~~~~~~~~~r~~~  308 (412)
T 3fht_A          235 ETLDTIKQYYVLCSSRDEKFQALCNLYGA-----ITIAQAMIFCHTRKTASWLAAELSKEG-HQVALLSGEMMVEQRAAV  308 (412)
T ss_dssp             SSCTTEEEEEEECSSHHHHHHHHHHHHHH-----HSSSEEEEECSSHHHHHHHHHHHHHTT-CCCEEECTTSCHHHHHHH
T ss_pred             ccccCceEEEEEcCChHHHHHHHHHHHhh-----cCCCCEEEEeCCHHHHHHHHHHHHhCC-CeEEEecCCCCHHHHHHH
Confidence            44667899999998888899999999987     345799999999999999999999987 799999999999999999


Q ss_pred             HHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCC------ChHHHHHhhc
Q 028124           97 LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPT------KKETYIRRMT  170 (213)
Q Consensus        97 l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~------~~~~yi~R~G  170 (213)
                      +++|++|.                       .++||||++    +++|+|+|++++||+||+|+      +..+|+||+|
T Consensus       309 ~~~f~~g~-----------------------~~vlv~T~~----~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~G  361 (412)
T 3fht_A          309 IERFREGK-----------------------EKVLVTTNV----CARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIG  361 (412)
T ss_dssp             HHHHHTTS-----------------------CSEEEECGG----GTSSCCCTTEEEEEESSCCBCSSSSBCHHHHHHHHT
T ss_pred             HHHHHCCC-----------------------CcEEEEcCc----cccCCCccCCCEEEEECCCCCCCCCcchheeecccC
Confidence            99999985                       899999999    99999999999999999994      6789999999


Q ss_pred             ccc--CCCCeEEEEEeCc-hhHHHHHHHHHhcccccccCccc
Q 028124          171 TCL--AADGSVINIVVGG-EVVTLRSMEESLGLIVAEVPINI  209 (213)
Q Consensus       171 R~~--~~~g~~i~~~~~~-e~~~~~~le~~l~~~~~~~~~~~  209 (213)
                      |++  |+.|.++.++.+. +...++.+++.++..+.+++.+-
T Consensus       362 R~gR~g~~g~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~  403 (412)
T 3fht_A          362 RTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERLDTDD  403 (412)
T ss_dssp             TSSCTTCCEEEEEEECSHHHHHHHHHHHHHHTCCCEEC----
T ss_pred             cccCCCCCceEEEEEcChhhHHHHHHHHHHHCCccccCCCcc
Confidence            974  6779999999876 58899999999999999887643

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=99.93  E-value=7.3e-25  Score=189.92  Aligned_cols=154  Identities=23%  Similarity=0.452  Sum_probs=140.4

Q ss_pred             CCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHH
Q 028124           19 FSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILE   98 (213)
Q Consensus        19 ~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~   98 (213)
                      ..++.+.+..+...+ |++.|.++++.      ...++||||++++.++.+++.|+..+ +.+..+||+++.++|.++++
T Consensus       211 ~~~~~~~~~~~~~~~-~~~~l~~~l~~------~~~~~lvf~~~~~~~~~l~~~L~~~~-~~~~~~~~~~~~~~r~~~~~  282 (367)
T 1hv8_A          211 NANIEQSYVEVNENE-RFEALCRLLKN------KEFYGLVFCKTKRDTKELASMLRDIG-FKAGAIHGDLSQSQREKVIR  282 (367)
T ss_dssp             SSSSEEEEEECCGGG-HHHHHHHHHCS------TTCCEEEECSSHHHHHHHHHHHHHTT-CCEEEECSSSCHHHHHHHHH
T ss_pred             CCCceEEEEEeChHH-HHHHHHHHHhc------CCCcEEEEECCHHHHHHHHHHHHhcC-CCeEEeeCCCCHHHHHHHHH
Confidence            347888888887766 99888888764      56799999999999999999999987 79999999999999999999


Q ss_pred             HHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCCC
Q 028124           99 EFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAAD  176 (213)
Q Consensus        99 ~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~~  176 (213)
                      +|++|.                       .++||||++    +++|+|+|++++||+|++|++..+|+||+||+  .|+.
T Consensus       283 ~f~~~~-----------------------~~vlv~T~~----~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~  335 (367)
T 1hv8_A          283 LFKQKK-----------------------IRILIATDV----MSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKK  335 (367)
T ss_dssp             HHHTTS-----------------------SSEEEECTT----HHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSC
T ss_pred             HHHcCC-----------------------CeEEEECCh----hhcCCCcccCCEEEEecCCCCHHHhhhcccccccCCCc
Confidence            999984                       999999999    99999999999999999999999999999997  4567


Q ss_pred             CeEEEEEeCchhHHHHHHHHHhcccccccCc
Q 028124          177 GSVINIVVGGEVVTLRSMEESLGLIVAEVPI  207 (213)
Q Consensus       177 g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~  207 (213)
                      |.++.++.+.+...++.+++.++.+++++++
T Consensus       336 g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~  366 (367)
T 1hv8_A          336 GKAISIINRREYKKLRYIERAMKLKIKKLKF  366 (367)
T ss_dssp             CEEEEEECTTSHHHHHHHHHHHTCCCCCBC-
T ss_pred             cEEEEEEcHHHHHHHHHHHHHhCCCCceecc
Confidence            9999999999999999999999999998764

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=99.92  E-value=2e-24  Score=188.96  Aligned_cols=159  Identities=23%  Similarity=0.419  Sum_probs=141.6

Q ss_pred             CCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHH
Q 028124           17 SHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI   96 (213)
Q Consensus        17 ~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~   96 (213)
                      .....+.+.+..+.....|...+.+++..     ....++||||++++.++.+++.|+..+ +.+..+||+|++++|.++
T Consensus       212 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-----~~~~~~lvf~~~~~~~~~l~~~l~~~~-~~~~~~~~~~~~~~r~~~  285 (395)
T 3pey_A          212 VNVDAIKQLYMDCKNEADKFDVLTELYGL-----MTIGSSIIFVATKKTANVLYGKLKSEG-HEVSILHGDLQTQERDRL  285 (395)
T ss_dssp             CSCTTEEEEEEECSSHHHHHHHHHHHHTT-----TTSSEEEEECSCHHHHHHHHHHHHHTT-CCCEEECTTSCHHHHHHH
T ss_pred             cccccccEEEEEcCchHHHHHHHHHHHHh-----ccCCCEEEEeCCHHHHHHHHHHHHhcC-CcEEEeCCCCCHHHHHHH
Confidence            44567889999888877799998888876     456899999999999999999999987 799999999999999999


Q ss_pred             HHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCC------ChHHHHHhhc
Q 028124           97 LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPT------KKETYIRRMT  170 (213)
Q Consensus        97 l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~------~~~~yi~R~G  170 (213)
                      +++|++|.                       .++||||++    +++|+|+|++++||+||+|+      +..+|+||+|
T Consensus       286 ~~~f~~g~-----------------------~~vlv~T~~----~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~G  338 (395)
T 3pey_A          286 IDDFREGR-----------------------SKVLITTNV----LARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIG  338 (395)
T ss_dssp             HHHHHTTS-----------------------CCEEEECGG----GSSSCCCTTEEEEEESSCCBCTTSSBCHHHHHHHHT
T ss_pred             HHHHHCCC-----------------------CCEEEECCh----hhcCCCcccCCEEEEcCCCCCCcCCCCHHHhhHhcc
Confidence            99999985                       899999999    99999999999999999999      9999999999


Q ss_pred             cc--cCCCCeEEEEEeC-chhHHHHHHHHHhc-ccccccCcc
Q 028124          171 TC--LAADGSVINIVVG-GEVVTLRSMEESLG-LIVAEVPIN  208 (213)
Q Consensus       171 R~--~~~~g~~i~~~~~-~e~~~~~~le~~l~-~~~~~~~~~  208 (213)
                      |+  .|+.|.++.++.. ++...++.+++.++ .++.+++.+
T Consensus       339 R~gR~g~~g~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~  380 (395)
T 3pey_A          339 RTGRFGRKGVAISFVHDKNSFNILSAIQKYFGDIEMTRVPTD  380 (395)
T ss_dssp             TSSCTTCCEEEEEEECSHHHHHHHHHHHHHTTSCCCEECCSS
T ss_pred             ccccCCCCceEEEEEechHHHHHHHHHHHHhCCceeecCChH
Confidence            97  4677999999986 46778899999988 777777643

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=99.92  E-value=3.8e-24  Score=197.97  Aligned_cols=161  Identities=17%  Similarity=0.334  Sum_probs=135.9

Q ss_pred             CCCCCCceEEEEEecCcchHHHHHHHHH-HHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc---CCceEEEecCCCCHH
Q 028124           16 PSHFSQPRHFYVAVDRLQFKMETLVELL-HLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL---ADISFSSLHSDLAET   91 (213)
Q Consensus        16 ~~~~~~i~~~~~~~~~~~~K~~~L~~ll-~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~---~~~~~~~lhg~~~~~   91 (213)
                      +.....+.+.+...+....+...+...+ +.+.. ...+.++||||+++..|+.+++.|...   + +.+..+||+|++.
T Consensus       302 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~~iVF~~s~~~~~~l~~~L~~~~~~~-~~v~~~h~~~~~~  379 (563)
T 3i5x_A          302 PEAHERIDQSVVISEKFANSIFAAVEHIKKQIKE-RDSNYKAIIFAPTVKFTSFLCSILKNEFKKD-LPILEFHGKITQN  379 (563)
T ss_dssp             CSSCTTEEEEEEEESSTTHHHHHHHHHHHHHHHH-TTTCCEEEEECSCHHHHHHHHHHHHHHHTTT-SCEEEESTTSCHH
T ss_pred             ccccccCceEEEECchhHhhHHHHHHHHHHHHhh-cCCCCcEEEEcCcHHHHHHHHHHHHHhccCC-ceEEEecCCCCHH
Confidence            4455678888888776554544433333 32221 356789999999999999999999875   5 7999999999999


Q ss_pred             HHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhcc
Q 028124           92 ERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTT  171 (213)
Q Consensus        92 ~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR  171 (213)
                      +|..++++|++|.                       .+|||||++    +++|+|+|++++||+||+|.++++|+||+||
T Consensus       380 ~R~~~~~~f~~g~-----------------------~~vLvaT~~----~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GR  432 (563)
T 3i5x_A          380 KRTSLVKRFKKDE-----------------------SGILVCTDV----GARGMDFPNVHEVLQIGVPSELANYIHRIGR  432 (563)
T ss_dssp             HHHHHHHHHHHCS-----------------------SEEEEECGG----GTSSCCCTTCCEEEEESCCSSTTHHHHHHTT
T ss_pred             HHHHHHHHHhcCC-----------------------CCEEEEcch----hhcCCCcccCCEEEEECCCCchhhhhhhcCc
Confidence            9999999999985                       999999999    9999999999999999999999999999999


Q ss_pred             c--cCCCCeEEEEEeCchhHHHHHHHHHhccccccc
Q 028124          172 C--LAADGSVINIVVGGEVVTLRSMEESLGLIVAEV  205 (213)
Q Consensus       172 ~--~~~~g~~i~~~~~~e~~~~~~le~~l~~~~~~~  205 (213)
                      +  .|+.|.|+.|+.+.|...++.+++..+..+.+.
T Consensus       433 agR~g~~g~~i~~~~~~e~~~~~~l~~~~~~~~~~~  468 (563)
T 3i5x_A          433 TARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQ  468 (563)
T ss_dssp             SSCTTCCEEEEEEEEGGGHHHHHHHHHHHCCCCCEE
T ss_pred             cccCCCCceEEEEEchhHHHHHHHHHHHhCCCcccc
Confidence            7  456799999999999999999999888776543

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.92  E-value=8.5e-24  Score=197.24  Aligned_cols=161  Identities=17%  Similarity=0.334  Sum_probs=135.3

Q ss_pred             CCCCCCceEEEEEecCcchHHHHHHH-HHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc---CCceEEEecCCCCHH
Q 028124           16 PSHFSQPRHFYVAVDRLQFKMETLVE-LLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL---ADISFSSLHSDLAET   91 (213)
Q Consensus        16 ~~~~~~i~~~~~~~~~~~~K~~~L~~-ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~---~~~~~~~lhg~~~~~   91 (213)
                      +.....+.+.+........+...+.+ +.+.+.. .....++||||+++..|+.+++.|...   + +.+..+||+|++.
T Consensus       251 ~~~~~~i~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~~iVF~~t~~~~~~l~~~L~~~~~~~-~~v~~~hg~~~~~  328 (579)
T 3sqw_A          251 PEAHERIDQSVVISEKFANSIFAAVEHIKKQIKE-RDSNYKAIIFAPTVKFTSFLCSILKNEFKKD-LPILEFHGKITQN  328 (579)
T ss_dssp             CSSCTTEEEEEEEESSTTHHHHHHHHHHHHHHHH-TTTCCEEEEECSSHHHHHHHHHHHHHHHTTT-SCEEEESTTSCHH
T ss_pred             cccccccceEEEEecchhhhHHHHHHHHHHHHhh-cCCCCcEEEECCcHHHHHHHHHHHHHhhcCC-CcEEEecCCCCHH
Confidence            44556788888887765434433333 3333221 345789999999999999999999876   5 7999999999999


Q ss_pred             HHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhcc
Q 028124           92 ERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTT  171 (213)
Q Consensus        92 ~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR  171 (213)
                      +|.+++++|+.|+                       .++||||++    +++|+|+|++++||+||+|.+++.|+||+||
T Consensus       329 ~R~~~~~~F~~g~-----------------------~~vLVaT~~----~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GR  381 (579)
T 3sqw_A          329 KRTSLVKRFKKDE-----------------------SGILVCTDV----GARGMDFPNVHEVLQIGVPSELANYIHRIGR  381 (579)
T ss_dssp             HHHHHHHHHHHCS-----------------------SEEEEECGG----GTSSCCCTTCCEEEEESCCSSTTHHHHHHTT
T ss_pred             HHHHHHHHhhcCC-----------------------CeEEEEcch----hhcCCCcccCCEEEEcCCCCCHHHhhhhccc
Confidence            9999999999985                       999999999    9999999999999999999999999999999


Q ss_pred             c--cCCCCeEEEEEeCchhHHHHHHHHHhccccccc
Q 028124          172 C--LAADGSVINIVVGGEVVTLRSMEESLGLIVAEV  205 (213)
Q Consensus       172 ~--~~~~g~~i~~~~~~e~~~~~~le~~l~~~~~~~  205 (213)
                      +  .|+.|.|+.|+.+.|...++.+++..+..+.+.
T Consensus       382 agR~g~~g~~i~~~~~~e~~~~~~l~~~~~~~~~~~  417 (579)
T 3sqw_A          382 TARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQ  417 (579)
T ss_dssp             SSCTTCCEEEEEEEEGGGHHHHHHHHHHHCCCCCEE
T ss_pred             cccCCCCceEEEEEcccHHHHHHHHHHHhCCCcccc
Confidence            7  567899999999999999999999887776543

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=99.91  E-value=1.9e-26  Score=202.39  Aligned_cols=163  Identities=29%  Similarity=0.541  Sum_probs=0.0

Q ss_pred             CCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHH
Q 028124           18 HFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLIL   97 (213)
Q Consensus        18 ~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l   97 (213)
                      ...++.+++..+...+.|...+.++++.     ....++||||++++.++.+++.|...+ +.+..+||+|++.+|..++
T Consensus       229 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~-----~~~~~~lVf~~~~~~~~~l~~~L~~~~-~~~~~~~~~~~~~~r~~~~  302 (394)
T 1fuu_A          229 TLEGIKQFYVNVEEEEYKYECLTDLYDS-----ISVTQAVIFCNTRRKVEELTTKLRNDK-FTVSAIYSDLPQQERDTIM  302 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cCCCceEEEEEcCchhhHHHHHHHHHhc-----CCCCcEEEEECCHHHHHHHHHHHHHcC-CeEEEeeCCCCHHHHHHHH
Confidence            3456788888888777788888888876     345799999999999999999999887 7999999999999999999


Q ss_pred             HHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCC
Q 028124           98 EEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAA  175 (213)
Q Consensus        98 ~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~  175 (213)
                      ++|++|.                       .++||||++    +++|+|+|++++||+||+|++...|+||+||+  .|+
T Consensus       303 ~~f~~~~-----------------------~~vlv~T~~----~~~Gldi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~  355 (394)
T 1fuu_A          303 KEFRSGS-----------------------SRILISTDL----LARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGR  355 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHCCC-----------------------CcEEEECCh----hhcCCCcccCCEEEEeCCCCCHHHHHHHcCcccCCCC
Confidence            9999985                       899999999    99999999999999999999999999999997  457


Q ss_pred             CCeEEEEEeCchhHHHHHHHHHhcccccccCccccccC
Q 028124          176 DGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL  213 (213)
Q Consensus       176 ~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~~~~~~  213 (213)
                      .|.|+.++.+.+...++.++++++.+++++|.++.++|
T Consensus       356 ~g~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~  393 (394)
T 1fuu_A          356 KGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIATLL  393 (394)
T ss_dssp             --------------------------------------
T ss_pred             CceEEEEEchhHHHHHHHHHHHhCCcccccCcchhhhc
Confidence            89999999999999999999999999999998887764

>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=99.90  E-value=1.5e-25  Score=203.87  Aligned_cols=159  Identities=19%  Similarity=0.368  Sum_probs=0.0

Q ss_pred             CCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHH
Q 028124           17 SHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI   96 (213)
Q Consensus        17 ~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~   96 (213)
                      .....+.|.++.+.....|...|..++..     ....++||||+++..++.++..|...+ +.+..+||+|++.+|..+
T Consensus       302 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-----~~~~~~lvF~~s~~~~~~l~~~L~~~~-~~v~~lh~~~~~~~R~~~  375 (479)
T 3fmp_B          302 ETLDTIKQYYVLCSSRDEKFQALCNLYGA-----ITIAQAMIFCHTRKTASWLAAELSKEG-HQVALLSGEMMVEQRAAV  375 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cCcCCceEEEEEeCCHHHHHHHHHHHHhh-----ccCCceEEEeCcHHHHHHHHHHHHhCC-ccEEEecCCCCHHHHHHH
Confidence            34567888898888877799999998876     345799999999999999999999887 799999999999999999


Q ss_pred             HHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCC------ChHHHHHhhc
Q 028124           97 LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPT------KKETYIRRMT  170 (213)
Q Consensus        97 l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~------~~~~yi~R~G  170 (213)
                      +++|++|.                       .++||||++    +++|+|+|++++|||||+|.      +..+|+||+|
T Consensus       376 ~~~f~~g~-----------------------~~iLv~T~~----~~~GlDip~v~~VI~~d~p~~~~~~~s~~~~~Qr~G  428 (479)
T 3fmp_B          376 IERFREGK-----------------------EKVLVTTNV----CARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIG  428 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHcCC-----------------------CcEEEEccc----cccCCccccCCEEEEecCCCCCccCCCHHHHHHHhc
Confidence            99999985                       999999999    99999999999999999995      5689999999


Q ss_pred             cc--cCCCCeEEEEEeCc-hhHHHHHHHHHhcccccccCcc
Q 028124          171 TC--LAADGSVINIVVGG-EVVTLRSMEESLGLIVAEVPIN  208 (213)
Q Consensus       171 R~--~~~~g~~i~~~~~~-e~~~~~~le~~l~~~~~~~~~~  208 (213)
                      |+  .|+.|.|+.|+.+. +...++.+++.++.++.+++.+
T Consensus       429 RagR~g~~G~~i~~~~~~~~~~~~~~i~~~~~~~~~~l~~~  469 (479)
T 3fmp_B          429 RTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERLDTD  469 (479)
T ss_dssp             -----------------------------------------
T ss_pred             ccccCCCCceEEEEEcCcchHHHHHHHHHHhCCCceECCCc
Confidence            97  46789999999865 4888999999999999887754

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A*

Probab=99.89  E-value=1.6e-22  Score=187.39  Aligned_cols=142  Identities=18%  Similarity=0.351  Sum_probs=122.2

Q ss_pred             CCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHH
Q 028124           18 HFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLIL   97 (213)
Q Consensus        18 ~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l   97 (213)
                      .++++.  |...+... +.+.|.++++.     .++.++||||++++.++.+++.|...+ +.+..+||+|++++|..++
T Consensus       209 ~r~~l~--~~v~~~~~-~~~~l~~~l~~-----~~~~~~IVf~~sr~~~e~l~~~L~~~g-~~~~~~h~~l~~~~R~~~~  279 (523)
T 1oyw_A          209 DRPNIR--YMLMEKFK-PLDQLMRYVQE-----QRGKSGIIYCNSRAKVEDTAARLQSKG-ISAAAYHAGLENNVRADVQ  279 (523)
T ss_dssp             CCTTEE--EEEEECSS-HHHHHHHHHHH-----TTTCCEEEECSSHHHHHHHHHHHHHTT-CCEEEECTTSCHHHHHHHH
T ss_pred             CCCceE--EEEEeCCC-HHHHHHHHHHh-----cCCCcEEEEeCCHHHHHHHHHHHHHCC-CCEEEecCCCCHHHHHHHH
Confidence            344554  33334444 88888888876     356899999999999999999999987 8999999999999999999


Q ss_pred             HHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhcccc--CC
Q 028124           98 EEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AA  175 (213)
Q Consensus        98 ~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~--~~  175 (213)
                      ++|++|+                       .++||||++    +++|+|+|++++|||||+|++.+.|+||+||+|  |.
T Consensus       280 ~~f~~g~-----------------------~~vlVaT~a----~~~GiD~p~v~~VI~~~~p~s~~~y~Qr~GRaGR~g~  332 (523)
T 1oyw_A          280 EKFQRDD-----------------------LQIVVATVA----FGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGL  332 (523)
T ss_dssp             HHHHTTS-----------------------CSEEEECTT----SCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSS
T ss_pred             HHHHcCC-----------------------CeEEEEech----hhCCCCccCccEEEEECCCCCHHHHHHHhccccCCCC
Confidence            9999985                       999999999    999999999999999999999999999999974  66


Q ss_pred             CCeEEEEEeCchhHHHHHHH
Q 028124          176 DGSVINIVVGGEVVTLRSME  195 (213)
Q Consensus       176 ~g~~i~~~~~~e~~~~~~le  195 (213)
                      +|.|+.|+.+.|...++.+.
T Consensus       333 ~~~~~l~~~~~d~~~~~~~~  352 (523)
T 1oyw_A          333 PAEAMLFYDPADMAWLRRCL  352 (523)
T ss_dssp             CEEEEEEECHHHHHHHHHHH
T ss_pred             CceEEEEeCHHHHHHHHHHH
Confidence            79999999887776655443

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A*

Probab=99.89  E-value=2e-22  Score=189.56  Aligned_cols=146  Identities=18%  Similarity=0.234  Sum_probs=119.6

Q ss_pred             CCCCCceEEEEEecC-cchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHH
Q 028124           17 SHFSQPRHFYVAVDR-LQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTL   95 (213)
Q Consensus        17 ~~~~~i~~~~~~~~~-~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~   95 (213)
                      ..++++...+..... ...+++.|.++++.    ..++.++||||++++.++.+++.|...| +.+..+||+|++++|.+
T Consensus       234 ~~r~nl~~~v~~~~~~~~~~~~~l~~~l~~----~~~~~~~IVf~~sr~~~e~la~~L~~~g-~~~~~~h~~l~~~~R~~  308 (591)
T 2v1x_A          234 FNRPNLYYEVRQKPSNTEDFIEDIVKLING----RYKGQSGIIYCFSQKDSEQVTVSLQNLG-IHAGAYHANLEPEDKTT  308 (591)
T ss_dssp             CCCTTEEEEEEECCSSHHHHHHHHHHHHTT----TTTTCEEEEECSSHHHHHHHHHHHHHTT-CCEEEECTTSCHHHHHH
T ss_pred             CCCcccEEEEEeCCCcHHHHHHHHHHHHHH----hccCCCeEEEeCcHHHHHHHHHHHHHCC-CCEEEecCCCCHHHHHH
Confidence            344555444333222 12344555555543    2367899999999999999999999987 89999999999999999


Q ss_pred             HHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhcccc--
Q 028124           96 ILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--  173 (213)
Q Consensus        96 ~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~--  173 (213)
                      ++++|++|+                       .+|||||++    +++|+|+|++++|||||+|.+.+.|+||+||+|  
T Consensus       309 ~~~~F~~g~-----------------------~~VlVAT~a----~~~GID~p~V~~VI~~~~p~s~~~y~Qr~GRaGR~  361 (591)
T 2v1x_A          309 VHRKWSANE-----------------------IQVVVATVA----FGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRD  361 (591)
T ss_dssp             HHHHHHTTS-----------------------SSEEEECTT----SCTTCCCSCEEEEEESSCCSSHHHHHHHHTTSCTT
T ss_pred             HHHHHHcCC-----------------------CeEEEEech----hhcCCCcccccEEEEeCCCCCHHHHHHHhccCCcC
Confidence            999999985                       999999999    999999999999999999999999999999974  


Q ss_pred             CCCCeEEEEEeCchhHHHHHH
Q 028124          174 AADGSVINIVVGGEVVTLRSM  194 (213)
Q Consensus       174 ~~~g~~i~~~~~~e~~~~~~l  194 (213)
                      |.+|.|+.|+.+.|...+..+
T Consensus       362 G~~g~~i~l~~~~D~~~~~~~  382 (591)
T 2v1x_A          362 DMKADCILYYGFGDIFRISSM  382 (591)
T ss_dssp             SSCEEEEEEECHHHHHHHHHH
T ss_pred             CCCceEEEEEChHHHHHHHHH
Confidence            667999999988777655544

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.88  E-value=2.3e-22  Score=179.20  Aligned_cols=145  Identities=15%  Similarity=0.198  Sum_probs=122.1

Q ss_pred             CCCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEE-EecCCCCHHHHH
Q 028124           16 PSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS-SLHSDLAETERT   94 (213)
Q Consensus        16 ~~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~-~lhg~~~~~~R~   94 (213)
                      .....++.|.|..+   + |.+.|.++++.      .+.++||||+++..++.++..|...+ +.+. .+||+    +|.
T Consensus       225 ~~~~~~i~~~~~~~---~-~~~~l~~~l~~------~~~~~lVF~~~~~~~~~l~~~L~~~~-~~~~~~~h~~----~r~  289 (414)
T 3oiy_A          225 VSVARNITHVRISS---R-SKEKLVELLEI------FRDGILIFAQTEEEGKELYEYLKRFK-FNVGETWSEF----EKN  289 (414)
T ss_dssp             CCCCCSEEEEEESS---C-CHHHHHHHHHH------HCSSEEEEESSHHHHHHHHHHHHHTT-CCEEESSSCH----HHH
T ss_pred             ccccccchheeecc---C-HHHHHHHHHHH------cCCCEEEEECCHHHHHHHHHHHHHcC-CceehhhcCc----chH
Confidence            34456788888765   2 67778888877      13799999999999999999999987 7888 99995    444


Q ss_pred             HHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEE----eCCCCCcCcCCCCCCC-CCEEEEecCC--CChHHHHH
Q 028124           95 LILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVV----TDACLPLLSSGESAIS-ARVLINYELP--TKKETYIR  167 (213)
Q Consensus        95 ~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~----Td~~~~~~~rGld~~~-v~~VI~yd~P--~~~~~yi~  167 (213)
                        +++|++|+                       .++|||    |++    +++|+|+|+ +++|||||+|  .+..+|+|
T Consensus       290 --~~~f~~g~-----------------------~~vLvat~s~T~~----~~~GiDip~~v~~VI~~~~p~~~~~~~y~q  340 (414)
T 3oiy_A          290 --FEDFKVGK-----------------------INILIGVQAYYGK----LTRGVDLPERIKYVIFWGTPSGPDVYTYIQ  340 (414)
T ss_dssp             --HHHHHTTS-----------------------CSEEEEECCTTCC----CCCCCCCTTTCCEEEEESCCTTTCHHHHHH
T ss_pred             --HHHHhCCC-----------------------CeEEEEecCcCch----hhccCccccccCEEEEECCCCCCCHHHHHH
Confidence              99999985                       999999    999    999999999 9999999999  99999999


Q ss_pred             hhccccC------CCCeEEEEEeCchhHHHHHHHHHhc--ccccccC
Q 028124          168 RMTTCLA------ADGSVINIVVGGEVVTLRSMEESLG--LIVAEVP  206 (213)
Q Consensus       168 R~GR~~~------~~g~~i~~~~~~e~~~~~~le~~l~--~~~~~~~  206 (213)
                      |+||+|+      +.|.++.|+  .+...++.+++.++  .++...+
T Consensus       341 r~GR~gR~g~~~~~~g~~i~~~--~~~~~~~~l~~~~~~~~~~~~~~  385 (414)
T 3oiy_A          341 ASGRSSRILNGVLVKGVSVIFE--EDEEIFESLKTRLLLIAEEEIIE  385 (414)
T ss_dssp             HHGGGCCEETTEECCEEEEEEC--CCHHHHHHHHHHHHHHHCCCEEE
T ss_pred             HhCccccCCCCCCcceEEEEEE--ccHHHHHHHHHHhcccccccccc
Confidence            9999754      579999999  67788889999888  5554433

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.88  E-value=2.3e-23  Score=190.03  Aligned_cols=134  Identities=16%  Similarity=0.199  Sum_probs=92.8

Q ss_pred             chHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccC---Cc--------eEEEecCCCCHHHHHHHHHHHh
Q 028124           33 QFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLA---DI--------SFSSLHSDLAETERTLILEEFR  101 (213)
Q Consensus        33 ~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~---~~--------~~~~lhg~~~~~~R~~~l~~Fr  101 (213)
                      ..|+..|.++|..... ..+..++||||+++++++.+++.|...+   ++        ....+||+|++++|.+++++|+
T Consensus       370 ~~k~~~l~~~l~~~~~-~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~  448 (555)
T 3tbk_A          370 NPKLRDLYLVLQEEYH-LKPETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFR  448 (555)
T ss_dssp             CHHHHHHHHHHHHHHH-HCTTCCEEEECSSHHHHHHHHHHHHHCGGGTTCCEEECCC-----------------------
T ss_pred             CHHHHHHHHHHHHHhc-cCCCceEEEEeCcHHHHHHHHHHHhhCcCcCceeeeEEEecCCcccccccCHHHHHHHHHHHh
Confidence            4599999999977443 2456899999999999999999998753   12        3444556999999999999999


Q ss_pred             c-ccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccccCCCCeEE
Q 028124          102 H-TAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGSVI  180 (213)
Q Consensus       102 ~-g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~~~~g~~i  180 (213)
                      + |.                       +++||||++    +++|+|+|++++|||||+|+++.+|+||+||+..+.|.++
T Consensus       449 ~~g~-----------------------~~vLvaT~~----~~~GlDlp~v~~VI~~d~p~s~~~~~Qr~GRgR~~~g~~~  501 (555)
T 3tbk_A          449 ASGD-----------------------NNILIATSV----ADEGIDIAECNLVILYEYVGNVIKMIQTRGRGRARDSKCF  501 (555)
T ss_dssp             ---C-----------------------CSEEEECCC----TTCCEETTSCSEEEEESCCSSCCCEECSSCCCTTTSCEEE
T ss_pred             cCCC-----------------------eeEEEEcch----hhcCCccccCCEEEEeCCCCCHHHHHHhcCcCcCCCceEE
Confidence            9 74                       899999999    9999999999999999999999999999999323569999


Q ss_pred             EEEeCchhHHHHHH
Q 028124          181 NIVVGGEVVTLRSM  194 (213)
Q Consensus       181 ~~~~~~e~~~~~~l  194 (213)
                      .|+++++......+
T Consensus       502 ~l~~~~~~~~~~~~  515 (555)
T 3tbk_A          502 LLTSSADVIEKEKA  515 (555)
T ss_dssp             EEESCHHHHHHHHH
T ss_pred             EEEcCCCHHHHHHH
Confidence            99998766555544

>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=99.87  E-value=2.5e-22  Score=183.68  Aligned_cols=127  Identities=16%  Similarity=0.218  Sum_probs=71.7

Q ss_pred             chHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc------------CCceEEEecCCCCHHHHHHHHHHH
Q 028124           33 QFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL------------ADISFSSLHSDLAETERTLILEEF  100 (213)
Q Consensus        33 ~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~------------~~~~~~~lhg~~~~~~R~~~l~~F  100 (213)
                      ..|+..|.++|..... ..++.++||||+++++++.+++.|...            | .....+||+|++++|.+++++|
T Consensus       371 ~~K~~~L~~~l~~~~~-~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g-~~~~~~~~~~~~~~R~~~~~~F  448 (556)
T 4a2p_A          371 NPKLEELVCILDDAYR-YNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMG-RGRRDQTTGMTLPSQKGVLDAF  448 (556)
T ss_dssp             CHHHHHHHHHHHHHHH-HCTTCCEEEEESSHHHHHHHHHHHTTCSGGGSCCEEC--------------------------
T ss_pred             ChHHHHHHHHHHHHhc-CCCCceEEEEEccHHHHHHHHHHHHhCCCcceeeeeEEEc-cCCcccccccCHHHHHHHHHHh
Confidence            4599999999976432 145789999999999999999999765            3 3455667889999999999999


Q ss_pred             hc-ccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccccC-CCCe
Q 028124          101 RH-TAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLA-ADGS  178 (213)
Q Consensus       101 r~-g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~~-~~g~  178 (213)
                      ++ |+                       +++||||++    +++|+|+|++++|||||+|+++..|+||+|| |+ +.|.
T Consensus       449 ~~~g~-----------------------~~vLvaT~~----~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-gR~~~g~  500 (556)
T 4a2p_A          449 KTSKD-----------------------NRLLIATSV----ADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRAAGSK  500 (556)
T ss_dssp             ----------------------------CCEEEEEC---------------CEEEEETCCSCHHHHHHC---------CC
T ss_pred             cccCc-----------------------eEEEEEcCc----hhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCCCCce
Confidence            99 74                       999999999    9999999999999999999999999999999 43 4589


Q ss_pred             EEEEEeCchhH
Q 028124          179 VINIVVGGEVV  189 (213)
Q Consensus       179 ~i~~~~~~e~~  189 (213)
                      ++.|++.++..
T Consensus       501 ~~~l~~~~~~~  511 (556)
T 4a2p_A          501 CILVTSKTEVV  511 (556)
T ss_dssp             EEEEESCHHHH
T ss_pred             EEEEEeCcchH
Confidence            99999886553

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.87  E-value=1.1e-22  Score=192.34  Aligned_cols=146  Identities=15%  Similarity=0.188  Sum_probs=91.3

Q ss_pred             cchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCC---ceEEEe--------cCCCCHHHHHHHHHHH
Q 028124           32 LQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLAD---ISFSSL--------HSDLAETERTLILEEF  100 (213)
Q Consensus        32 ~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~---~~~~~l--------hg~~~~~~R~~~l~~F  100 (213)
                      ...|+..|.+++..... ..++.++||||+++++++.|++.|...+.   +.+..+        ||+|++++|.+++++|
T Consensus       378 ~~~k~~~L~~ll~~~~~-~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F  456 (696)
T 2ykg_A          378 ENPKLEDLCFILQEEYH-LNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAF  456 (696)
T ss_dssp             CCHHHHHHHHHHHHHHT-TCTTCCEEEECSCHHHHHHHHHHHHHCTTCCSCCEEC-------------------------
T ss_pred             CCHHHHHHHHHHHHHhc-cCCCCcEEEEeCcHHHHHHHHHHHHhCCCccccceeEEEccCCCccccCCCHHHHHHHHHHH
Confidence            34599999999987432 23568999999999999999999988752   678888        5599999999999999


Q ss_pred             hc-ccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccccCC-CCe
Q 028124          101 RH-TAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAA-DGS  178 (213)
Q Consensus       101 r~-g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~~~-~g~  178 (213)
                      ++ |+                       .++||||++    +++|+|+|++++|||||+|+++++|+||+|| |+. .|.
T Consensus       457 ~~~g~-----------------------~~vLVaT~v----~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-GR~~~g~  508 (696)
T 2ykg_A          457 KASGD-----------------------HNILIATSV----ADEGIDIAQCNLVILYEYVGNVIKMIQTRGR-GRARGSK  508 (696)
T ss_dssp             ----C-----------------------CSCSEEEES----SCCC---CCCSEEEEESCC--CCCC----------CCCE
T ss_pred             HhcCC-----------------------ccEEEEech----hhcCCcCccCCEEEEeCCCCCHHHHHHhhcc-CcCCCce
Confidence            98 85                       999999999    9999999999999999999999999999999 654 588


Q ss_pred             EEEEEeCchhHHHHHH----HHHhcccccccC
Q 028124          179 VINIVVGGEVVTLRSM----EESLGLIVAEVP  206 (213)
Q Consensus       179 ~i~~~~~~e~~~~~~l----e~~l~~~~~~~~  206 (213)
                      ++.++..++......+    |+.++..+.+++
T Consensus       509 ~~~l~~~~~~~~~~~~~~~~e~~~~~~~~~~~  540 (696)
T 2ykg_A          509 CFLLTSNAGVIEKEQINMYKEKMMNDSILRLQ  540 (696)
T ss_dssp             EEEEESCHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             EEEEecCCCHHHHHHHHHHHHHHHHHHHHHhh
Confidence            9999988777555555    556655555544

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}

Probab=99.87  E-value=9.4e-22  Score=168.72  Aligned_cols=141  Identities=21%  Similarity=0.317  Sum_probs=117.2

Q ss_pred             CCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHH
Q 028124           19 FSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILE   98 (213)
Q Consensus        19 ~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~   98 (213)
                      ..++.+.+..+.... +.  ..+.+..     ....++||||++++.++.+++.|.     .+..+||+++..+|.++++
T Consensus       194 ~~~~~~~~~~~~~~~-~~--~~~~~~~-----~~~~~~lvf~~~~~~~~~l~~~l~-----~~~~~~~~~~~~~r~~~~~  260 (337)
T 2z0m_A          194 LANVEHKFVHVKDDW-RS--KVQALRE-----NKDKGVIVFVRTRNRVAKLVRLFD-----NAIELRGDLPQSVRNRNID  260 (337)
T ss_dssp             GGGEEEEEEECSSSS-HH--HHHHHHT-----CCCSSEEEECSCHHHHHHHHTTCT-----TEEEECTTSCHHHHHHHHH
T ss_pred             cCCceEEEEEeChHH-HH--HHHHHHh-----CCCCcEEEEEcCHHHHHHHHHHhh-----hhhhhcCCCCHHHHHHHHH
Confidence            456778887777654 22  2244443     467899999999999999999885     5788999999999999999


Q ss_pred             HHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCCC
Q 028124           99 EFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAAD  176 (213)
Q Consensus        99 ~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~~  176 (213)
                      +|++|+                       .++||||++    +++|+|+|++++||+|++|++...|+||+||+  .|+.
T Consensus       261 ~f~~~~-----------------------~~vlv~T~~----~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~gR~g~~  313 (337)
T 2z0m_A          261 AFREGE-----------------------YDMLITTDV----ASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRK  313 (337)
T ss_dssp             HHHTTS-----------------------CSEEEECHH----HHTTCCCCCBSEEEESSCCSSHHHHHHHHTTBCGGGCC
T ss_pred             HHHcCC-----------------------CcEEEEcCc----cccCCCccCCCEEEEecCCCCHHHhhHhcCccccCCCC
Confidence            999985                       999999999    99999999999999999999999999999997  4678


Q ss_pred             CeEEEEEeCchhHHHHHHHHHhcc
Q 028124          177 GSVINIVVGGEVVTLRSMEESLGL  200 (213)
Q Consensus       177 g~~i~~~~~~e~~~~~~le~~l~~  200 (213)
                      |.++.++. .+...++++++.++.
T Consensus       314 g~~~~~~~-~~~~~~~~i~~~~~~  336 (337)
T 2z0m_A          314 GEAITFIL-NEYWLEKEVKKVSQK  336 (337)
T ss_dssp             EEEEEEES-SCHHHHHHHC-----
T ss_pred             ceEEEEEe-CcHHHHHHHHHHhcc
Confidence            99999999 888888888887654

>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=99.86  E-value=2.8e-22  Score=189.61  Aligned_cols=122  Identities=16%  Similarity=0.232  Sum_probs=100.7

Q ss_pred             hHHHHHHHHHHHhhcCCCC-CCcEEEEeCchHHHHHHHHHHhcc------CCceEEEecCC--------CCHHHHHHHHH
Q 028124           34 FKMETLVELLHLVVAGRRP-GLPMIVCCSSRDELDAVCSAVSNL------ADISFSSLHSD--------LAETERTLILE   98 (213)
Q Consensus        34 ~K~~~L~~ll~~~~~~~~~-~~~~IIF~~~~~~~~~l~~~L~~~------~~~~~~~lhg~--------~~~~~R~~~l~   98 (213)
                      .|+..|.++|..... ..+ +.++||||+++++++.|++.|...      | +.+..+||+        |++.+|.++++
T Consensus       381 ~k~~~L~~~L~~~~~-~~~~~~~~IVF~~s~~~~~~l~~~L~~~~~l~~~g-~~~~~lhg~~~~~~~~~~~~~eR~~~~~  458 (699)
T 4gl2_A          381 EKLTKLRNTIMEQYT-RTEESARGIIFTKTRQSAYALSQWITENEKFAEVG-VKAHHLIGAGHSSEFKPMTQNEQKEVIS  458 (699)
T ss_dssp             -CSSCSHHHHHHHHH-HSSSCCCEEEECSCHHHHHHHHHHHHSSCSCC------CEECCCSCCCTTCCCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHh-cCCCCCcEEEEECcHHHHHHHHHHHHhCccccccC-cceEEEECCCCccCCCCCCHHHHHHHHH
Confidence            366666677655322 123 789999999999999999999876      5 899999999        99999999999


Q ss_pred             HHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccccCCCCe
Q 028124           99 EFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAADGS  178 (213)
Q Consensus        99 ~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~~~~g~  178 (213)
                      +|++|+                       .+|||||++    +++|+|+|++++|||||+|+|+.+|+||+||+ |+.|.
T Consensus       459 ~F~~g~-----------------------~~VLVaT~~----~~~GIDip~v~~VI~~d~p~s~~~~~Qr~GRA-rr~g~  510 (699)
T 4gl2_A          459 KFRTGK-----------------------INLLIATTV----AEEGLDIKECNIVIRYGLVTNEIAMVQARGRA-RADES  510 (699)
T ss_dssp             HHCC--------------------------CCSEEECS----CCTTSCCCSCCCCEEESCCCCHHHHHHHHTTS-CSSSC
T ss_pred             HHhcCC-----------------------CcEEEEccc----cccCCccccCCEEEEeCCCCCHHHHHHHcCCC-CCCCc
Confidence            999985                       999999999    99999999999999999999999999999994 66677


Q ss_pred             EEEEEeC
Q 028124          179 VINIVVG  185 (213)
Q Consensus       179 ~i~~~~~  185 (213)
                      ++.++..
T Consensus       511 ~~~l~~~  517 (699)
T 4gl2_A          511 TYVLVAH  517 (699)
T ss_dssp             EEEEEEE
T ss_pred             eEEEEEe
Confidence            7777754

>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=99.85  E-value=3.3e-21  Score=171.12  Aligned_cols=129  Identities=21%  Similarity=0.265  Sum_probs=111.5

Q ss_pred             CcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecC--------CCCHHHHHHHHHHHhc
Q 028124           31 RLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHS--------DLAETERTLILEEFRH  102 (213)
Q Consensus        31 ~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg--------~~~~~~R~~~l~~Fr~  102 (213)
                      ....|+..|.++|..... ..++.++||||+++..++.+++.|...+ +.+..+||        +|+..+|.+++++|++
T Consensus       340 ~~~~k~~~l~~~l~~~~~-~~~~~k~lVF~~~~~~~~~l~~~L~~~~-~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~  417 (494)
T 1wp9_A          340 LDHPKMDKLKEIIREQLQ-RKQNSKIIVFTNYRETAKKIVNELVKDG-IKAKRFVGQASKENDRGLSQREQKLILDEFAR  417 (494)
T ss_dssp             CSCHHHHHHHHHHHHHHH-HCTTCCEEEECSCHHHHHHHHHHHHHTT-CCEEEECCSSCC-------CCHHHHHHHHHHH
T ss_pred             CCChHHHHHHHHHHHHhc-cCCCCeEEEEEccHHHHHHHHHHHHHcC-CCcEEEeccccccccccCCHHHHHHHHHHHhc
Confidence            344599999999987432 1357899999999999999999999987 89999999        9999999999999999


Q ss_pred             ccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccccCC-CCeEEE
Q 028124          103 TAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAA-DGSVIN  181 (213)
Q Consensus       103 g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~~~-~g~~i~  181 (213)
                      |.                       .++||+|++    +++|+|+|++++||+||+|+++..|+||+||+++. .|.++.
T Consensus       418 ~~-----------------------~~vLv~T~~----~~~Gldl~~~~~Vi~~d~~~~~~~~~Qr~GR~~R~g~g~~~~  470 (494)
T 1wp9_A          418 GE-----------------------FNVLVATSV----GEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMPGRVII  470 (494)
T ss_dssp             TS-----------------------CSEEEECGG----GGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCCCSEEEE
T ss_pred             CC-----------------------ceEEEECCc----cccCCCchhCCEEEEeCCCCCHHHHHHHHhhccCCCCceEEE
Confidence            84                       899999999    99999999999999999999999999999997432 299999


Q ss_pred             EEeCchh
Q 028124          182 IVVGGEV  188 (213)
Q Consensus       182 ~~~~~e~  188 (213)
                      |+.+++.
T Consensus       471 l~~~~t~  477 (494)
T 1wp9_A          471 LMAKGTR  477 (494)
T ss_dssp             EEETTSH
T ss_pred             EEecCCH
Confidence            9998744

>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=99.85  E-value=1.4e-20  Score=179.14  Aligned_cols=144  Identities=15%  Similarity=0.211  Sum_probs=118.2

Q ss_pred             HHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccccccccc
Q 028124           35 KMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ  114 (213)
Q Consensus        35 K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~  114 (213)
                      +...|...|....   ..+.++||||+|+..++.|++.|...| +.+..+||++++.+|.+++++|+.|.          
T Consensus       430 ~~~~Ll~~l~~~~---~~~~~vlVf~~t~~~ae~L~~~L~~~g-i~~~~lh~~~~~~~R~~~l~~f~~g~----------  495 (661)
T 2d7d_A          430 QIDDLIGEIQARI---ERNERVLVTTLTKKMSEDLTDYLKEIG-IKVNYLHSEIKTLERIEIIRDLRLGK----------  495 (661)
T ss_dssp             HHHHHHHHHHHHH---TTTCEEEEECSSHHHHHHHHHHHHHTT-CCEEEECTTCCHHHHHHHHHHHHHTS----------
T ss_pred             hHHHHHHHHHHHH---hcCCeEEEEECCHHHHHHHHHHHHhcC-CCeEEEeCCCCHHHHHHHHHHHhcCC----------
Confidence            5555555554422   246799999999999999999999987 89999999999999999999999985          


Q ss_pred             CCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecC-----CCChHHHHHhhccccC-CCCeEEEEEeCchh
Q 028124          115 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYEL-----PTKKETYIRRMTTCLA-ADGSVINIVVGGEV  188 (213)
Q Consensus       115 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~-----P~~~~~yi~R~GR~~~-~~g~~i~~~~~~e~  188 (213)
                                   .++||+|++    +++|+|+|++++||+||.     |.+.++|+||+||+|+ ..|.|++|+.+.+.
T Consensus       496 -------------~~VLVaT~~----l~~GlDip~v~lVi~~d~d~~G~p~s~~~~iQr~GRagR~~~G~~i~~~~~~~~  558 (661)
T 2d7d_A          496 -------------YDVLVGINL----LREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAEGRVIMYADKITK  558 (661)
T ss_dssp             -------------CSEEEESCC----CSTTCCCTTEEEEEETTTTCCTTTTSHHHHHHHHHTTTTSTTCEEEEECSSCCH
T ss_pred             -------------eEEEEecch----hhCCcccCCCCEEEEeCcccccCCCCHHHHHHHhCcccCCCCCEEEEEEeCCCH
Confidence                         999999999    999999999999999997     9999999999999865 46999999987654


Q ss_pred             HH---------HHHHHHHhcccccccCccc
Q 028124          189 VT---------LRSMEESLGLIVAEVPINI  209 (213)
Q Consensus       189 ~~---------~~~le~~l~~~~~~~~~~~  209 (213)
                      ..         .+.++..++.+....|.++
T Consensus       559 ~~~~~i~~~~~~r~i~~~~~~~~~~~p~~~  588 (661)
T 2d7d_A          559 SMEIAINETKRRREQQERFNEEHGITPKTI  588 (661)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCCCCC
T ss_pred             HHHHHHHHHHHHHHHHHHhhhhcCCCCCch
Confidence            33         3444555555555445443

>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=99.84  E-value=2.8e-20  Score=177.05  Aligned_cols=129  Identities=14%  Similarity=0.141  Sum_probs=110.5

Q ss_pred             HHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccccccccc
Q 028124           35 KMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ  114 (213)
Q Consensus        35 K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~  114 (213)
                      +...|...|....   ..+.++||||+|+..++.|++.|...| +.+..+||+|++.+|.+++++|+.|.          
T Consensus       424 ~~~~Ll~~l~~~~---~~~~~vlVf~~t~~~ae~L~~~L~~~g-i~~~~lh~~~~~~~R~~~~~~f~~g~----------  489 (664)
T 1c4o_A          424 QILDLMEGIRERA---ARGERTLVTVLTVRMAEELTSFLVEHG-IRARYLHHELDAFKRQALIRDLRLGH----------  489 (664)
T ss_dssp             HHHHHHHHHHHHH---HTTCEEEEECSSHHHHHHHHHHHHHTT-CCEEEECTTCCHHHHHHHHHHHHTTS----------
T ss_pred             hHHHHHHHHHHHH---hcCCEEEEEECCHHHHHHHHHHHHhcC-CCceeecCCCCHHHHHHHHHHhhcCC----------
Confidence            5565655554422   246799999999999999999999987 89999999999999999999999985          


Q ss_pred             CCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecC-----CCChHHHHHhhccccCC-CCeEEEEEeCchh
Q 028124          115 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYEL-----PTKKETYIRRMTTCLAA-DGSVINIVVGGEV  188 (213)
Q Consensus       115 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~-----P~~~~~yi~R~GR~~~~-~g~~i~~~~~~e~  188 (213)
                                   .++||+|++    +++|+|+|++++||+||.     |++..+|+||+||+|+. .|.|++++...+.
T Consensus       490 -------------~~VLvaT~~----l~~GlDip~v~lVI~~d~d~~G~p~s~~~~iQr~GRagR~~~G~~i~~~~~~~~  552 (664)
T 1c4o_A          490 -------------YDCLVGINL----LREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNARGEVWLYADRVSE  552 (664)
T ss_dssp             -------------CSEEEESCC----CCTTCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTTCEEEEECSSCCH
T ss_pred             -------------ceEEEccCh----hhcCccCCCCCEEEEeCCcccCCCCCHHHHHHHHCccCcCCCCEEEEEEcCCCH
Confidence                         999999999    999999999999999997     99999999999998643 6999999987655


Q ss_pred             HHHHHH
Q 028124          189 VTLRSM  194 (213)
Q Consensus       189 ~~~~~l  194 (213)
                      ...+.+
T Consensus       553 ~~~~~i  558 (664)
T 1c4o_A          553 AMQRAI  558 (664)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            443333

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=99.84  E-value=2.4e-20  Score=159.79  Aligned_cols=136  Identities=14%  Similarity=0.115  Sum_probs=106.7

Q ss_pred             cchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc-CCceEEEecCCCCHHHHHHHHHHHhccccccccc
Q 028124           32 LQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL-ADISFSSLHSDLAETERTLILEEFRHTAMKWNQK  110 (213)
Q Consensus        32 ~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~-~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~  110 (213)
                      ...|+..|.++|+.+..   .+.++||||++...++.|...|... | +.+..+||++++.+|..++++|+++.      
T Consensus        94 ~s~K~~~L~~ll~~~~~---~~~kvlIFs~~~~~~~~l~~~L~~~~g-~~~~~l~G~~~~~~R~~~i~~F~~~~------  163 (271)
T 1z5z_A           94 RSGKMIRTMEIIEEALD---EGDKIAIFTQFVDMGKIIRNIIEKELN-TEVPFLYGELSKKERDDIISKFQNNP------  163 (271)
T ss_dssp             TCHHHHHHHHHHHHHHH---TTCCEEEEESCHHHHHHHHHHHHHHHC-SCCCEECTTSCHHHHHHHHHHHHHCT------
T ss_pred             cCHHHHHHHHHHHHHHh---CCCeEEEEeccHHHHHHHHHHHHHhcC-CcEEEEECCCCHHHHHHHHHHhcCCC------
Confidence            34599999999987543   5689999999999999999999875 6 78999999999999999999999973      


Q ss_pred             ccccCCCCCcCCCCCCcee-EEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCCC--CeEEEEEeC
Q 028124          111 VTEQSGDESETGKDEHKSH-MIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAAD--GSVINIVVG  185 (213)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~~-iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~~--g~~i~~~~~  185 (213)
                                      ..+ +|++|++    +++|+|++.+++||+||+||++..|.||+||+  .|+.  ..++.|++.
T Consensus       164 ----------------~~~v~L~st~~----~g~Glnl~~a~~VI~~d~~wnp~~~~Q~~gR~~R~Gq~~~v~v~~li~~  223 (271)
T 1z5z_A          164 ----------------SVKFIVLSVKA----GGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISV  223 (271)
T ss_dssp             ----------------TCCEEEEECCT----TCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEET
T ss_pred             ----------------CCCEEEEehhh----hcCCcCcccCCEEEEECCCCChhHHHHHHHhccccCCCCceEEEEEeeC
Confidence                            355 7999999    99999999999999999999999999999996  3444  456888887


Q ss_pred             c--hhHHHHHHHHH
Q 028124          186 G--EVVTLRSMEES  197 (213)
Q Consensus       186 ~--e~~~~~~le~~  197 (213)
                      +  |...+..++..
T Consensus       224 ~TiEe~i~~~~~~K  237 (271)
T 1z5z_A          224 GTLEEKIDQLLAFK  237 (271)
T ss_dssp             TSHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHH
Confidence            6  44555555443

>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=99.84  E-value=1.1e-20  Score=182.50  Aligned_cols=126  Identities=15%  Similarity=0.211  Sum_probs=76.3

Q ss_pred             chHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc------------CCceEEEecCCCCHHHHHHHHHHH
Q 028124           33 QFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL------------ADISFSSLHSDLAETERTLILEEF  100 (213)
Q Consensus        33 ~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~------------~~~~~~~lhg~~~~~~R~~~l~~F  100 (213)
                      ..|+..|.++|..... ..++.++||||+++++++.|++.|...            | .....+||+|++.+|.+++++|
T Consensus       612 ~~K~~~L~~lL~~~~~-~~~~~kvLIF~~~~~~~~~L~~~L~~~~~~~~~~~~~l~G-~~~~~~hg~~~~~eR~~~l~~F  689 (797)
T 4a2q_A          612 NPKLEELVCILDDAYR-YNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMG-RGRRDQTTGMTLPSQKGVLDAF  689 (797)
T ss_dssp             CHHHHHHHHHHHHHHH-HCSSCCEEEEESSHHHHHHHHHHHHTCSTTCSCCCEEC-------------------------
T ss_pred             ChHHHHHHHHHHHHhc-cCCCCeEEEEECcHHHHHHHHHHHHhCcccccccceEEEe-cCCcccCCCCCHHHHHHHHHHh
Confidence            4599999999976332 245689999999999999999999764            3 3556678899999999999999


Q ss_pred             hc-ccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccccC-CCCe
Q 028124          101 RH-TAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLA-ADGS  178 (213)
Q Consensus       101 r~-g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~~-~~g~  178 (213)
                      ++ |.                       +++||||++    +++|+|+|+|++|||||+|+++..|+||+|| |+ +.|.
T Consensus       690 ~~~g~-----------------------~~vLVaT~~----~~~GIDlp~v~~VI~yd~p~s~~~~iQr~GR-GR~~~g~  741 (797)
T 4a2q_A          690 KTSKD-----------------------NRLLIATSV----ADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRAAGSK  741 (797)
T ss_dssp             ----C-----------------------CSEEEEECC-----------CCCSEEEEESCCSCHHHHHTC--------CCC
T ss_pred             hccCC-----------------------ceEEEEcCc----hhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCCCCce
Confidence            99 74                       999999999    9999999999999999999999999999999 43 4599


Q ss_pred             EEEEEeCchh
Q 028124          179 VINIVVGGEV  188 (213)
Q Consensus       179 ~i~~~~~~e~  188 (213)
                      |+.|++.++.
T Consensus       742 ~i~l~~~~~~  751 (797)
T 4a2q_A          742 CILVTSKTEV  751 (797)
T ss_dssp             EEEEECCHHH
T ss_pred             EEEEEeCCcH
Confidence            9999988654

>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=99.83  E-value=1.2e-20  Score=182.19  Aligned_cols=129  Identities=12%  Similarity=0.103  Sum_probs=109.8

Q ss_pred             EEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccc
Q 028124           26 YVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAM  105 (213)
Q Consensus        26 ~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~  105 (213)
                      ++++.. ..|+..|.+++....   ..++++||||+|+..++.|+..|...| +.+..+||++.+.+|..+.+.|+.   
T Consensus       409 ~v~~~~-~~K~~al~~~i~~~~---~~~~pvLVft~s~~~se~Ls~~L~~~g-i~~~vLhg~~~~rEr~ii~~ag~~---  480 (844)
T 1tf5_A          409 LIYRTM-EGKFKAVAEDVAQRY---MTGQPVLVGTVAVETSELISKLLKNKG-IPHQVLNAKNHEREAQIIEEAGQK---  480 (844)
T ss_dssp             EEESSH-HHHHHHHHHHHHHHH---HHTCCEEEEESCHHHHHHHHHHHHTTT-CCCEEECSSCHHHHHHHHTTTTST---
T ss_pred             EEEeCH-HHHHHHHHHHHHHHH---hcCCcEEEEECCHHHHHHHHHHHHHCC-CCEEEeeCCccHHHHHHHHHcCCC---
Confidence            444544 459999999886521   146789999999999999999999998 899999999988888766655655   


Q ss_pred             cccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCC--------CCCEEEEecCCCChHHHHHhhccc--cCC
Q 028124          106 KWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAI--------SARVLINYELPTKKETYIRRMTTC--LAA  175 (213)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~--------~v~~VI~yd~P~~~~~yi~R~GR~--~~~  175 (213)
                                            ..|+||||+    ++||+|++        ++.+|||||+|.+.+.|+||+||+  .|.
T Consensus       481 ----------------------g~VlIATdm----AgRG~DI~l~~~V~~~ggl~VIn~d~p~s~r~y~hr~GRTGRqG~  534 (844)
T 1tf5_A          481 ----------------------GAVTIATNM----AGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGD  534 (844)
T ss_dssp             ----------------------TCEEEEETT----SSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGC
T ss_pred             ----------------------CeEEEeCCc----cccCcCccccchhhhcCCcEEEEecCCCCHHHHHhhcCccccCCC
Confidence                                  459999999    99999999        788999999999999999999997  578


Q ss_pred             CCeEEEEEeCchh
Q 028124          176 DGSVINIVVGGEV  188 (213)
Q Consensus       176 ~g~~i~~~~~~e~  188 (213)
                      +|.+++|++.+|.
T Consensus       535 ~G~s~~~vs~eD~  547 (844)
T 1tf5_A          535 PGITQFYLSMEDE  547 (844)
T ss_dssp             CEEEEEEEETTSS
T ss_pred             CCeEEEEecHHHH
Confidence            8999999997663

>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=99.82  E-value=2.2e-20  Score=183.67  Aligned_cols=126  Identities=15%  Similarity=0.211  Sum_probs=77.6

Q ss_pred             chHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc------------CCceEEEecCCCCHHHHHHHHHHH
Q 028124           33 QFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL------------ADISFSSLHSDLAETERTLILEEF  100 (213)
Q Consensus        33 ~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~------------~~~~~~~lhg~~~~~~R~~~l~~F  100 (213)
                      ..|+..|.++|..... ..++.++||||+++++++.|++.|...            | .....+||+|++.+|.+++++|
T Consensus       612 ~~K~~~L~~lL~~~~~-~~~~~rvLIF~~t~~~ae~L~~~L~~~~~l~~ik~~~l~G-~~~~~~hg~m~~~eR~~il~~F  689 (936)
T 4a2w_A          612 NPKLEELVCILDDAYR-YNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMG-RGRRDQTTGMTLPSQKGVLDAF  689 (936)
T ss_dssp             CHHHHHHHHHHHHTTT-SCTTCCEEEEESSHHHHHHHHHHHHHCSTTSSCCCEEC-------------------------
T ss_pred             CHHHHHHHHHHHHHhc-cCCCCeEEEEeCCHHHHHHHHHHHhhCccccccceeEEec-CCCcccCCCCCHHHHHHHHHHh
Confidence            4599999999987432 245789999999999999999999875            3 3456678999999999999999


Q ss_pred             hc-ccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccccC-CCCe
Q 028124          101 RH-TAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLA-ADGS  178 (213)
Q Consensus       101 r~-g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~~-~~g~  178 (213)
                      ++ |.                       +++||||++    +++|+|+|+|++|||||+|+++..|+||+|| |+ +.|.
T Consensus       690 r~~g~-----------------------~~VLVaT~~----~~eGIDlp~v~~VI~yD~p~s~~~~iQr~GR-GR~~~g~  741 (936)
T 4a2w_A          690 KTSKD-----------------------NRLLIATSV----ADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRAAGSK  741 (936)
T ss_dssp             ----C-----------------------CSEEEEECC----------CCCCSEEEEESCCSCSHHHHCC--------CCC
T ss_pred             hccCC-----------------------eeEEEEeCc----hhcCCcchhCCEEEEeCCCCCHHHHHHhcCC-CCCCCCE
Confidence            99 74                       999999999    9999999999999999999999999999999 43 3589


Q ss_pred             EEEEEeCchh
Q 028124          179 VINIVVGGEV  188 (213)
Q Consensus       179 ~i~~~~~~e~  188 (213)
                      ++.|+..++.
T Consensus       742 vi~Li~~~t~  751 (936)
T 4a2w_A          742 CILVTSKTEV  751 (936)
T ss_dssp             EEEEESCHHH
T ss_pred             EEEEEeCCCH
Confidence            9999987654

>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=99.80  E-value=3e-19  Score=176.17  Aligned_cols=121  Identities=14%  Similarity=0.205  Sum_probs=107.2

Q ss_pred             cchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhc-cCCceEEEecCCCCHHHHHHHHHHHhccccccccc
Q 028124           32 LQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSN-LADISFSSLHSDLAETERTLILEEFRHTAMKWNQK  110 (213)
Q Consensus        32 ~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~-~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~  110 (213)
                      ...|+..|.++++.     .++.++||||+++.+++.++..|.. .| +.+..+||+|++.+|..++++|++|+      
T Consensus       487 ~~~K~~~L~~ll~~-----~~~~k~iVF~~~~~~~~~l~~~L~~~~g-~~~~~lhG~~~~~~R~~~l~~F~~g~------  554 (968)
T 3dmq_A          487 FDPRVEWLMGYLTS-----HRSQKVLVICAKAATALQLEQVLREREG-IRAAVFHEGMSIIERDRAAAWFAEED------  554 (968)
T ss_dssp             TSHHHHHHHHHHHH-----TSSSCCCEECSSTHHHHHHHHHHHTTTC-CCEEEECTTSCTTHHHHHHHHHHSTT------
T ss_pred             ccHHHHHHHHHHHh-----CCCCCEEEEeCcHHHHHHHHHHHHHHcC-CcEEEEeCCCCHHHHHHHHHHHhCCC------
Confidence            34599999999987     4678999999999999999999995 46 89999999999999999999999973      


Q ss_pred             ccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCCCCeEEEEE
Q 028124          111 VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIV  183 (213)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~~g~~i~~~  183 (213)
                                     +.+++||||++    +++|+|+|++++||+||+|+++..|+||+||+  .|+.|.|+.+.
T Consensus       555 ---------------~~~~vLvaT~v----~~~GlDl~~~~~VI~~d~p~~~~~~~Q~~GR~~R~Gq~~~v~v~~  610 (968)
T 3dmq_A          555 ---------------TGAQVLLCSEI----GSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQIHV  610 (968)
T ss_dssp             ---------------SSCEEEECSCC----TTCSSCCTTCCEEECSSCCSSHHHHHHHHHTTSCSSSCSCCEEEE
T ss_pred             ---------------CcccEEEecch----hhcCCCcccCcEEEEecCCCCHHHHHHHhhccccCCCCceEEEEE
Confidence                           24899999999    99999999999999999999999999999996  56666444443

>3jux_A Protein translocase subunit SECA; protein translocation, ATPase, conformational change, peptide binding, ATP-binding, cell inner membrane; HET: ADP; 3.10A {Thermotoga maritima} PDB: 3din_A*

Probab=99.80  E-value=4.6e-19  Score=168.90  Aligned_cols=128  Identities=16%  Similarity=0.169  Sum_probs=107.6

Q ss_pred             EEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccc
Q 028124           27 VAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMK  106 (213)
Q Consensus        27 ~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~  106 (213)
                      ++.. ...|+..+.+.+....   ..++++||||+|+..++.|+..|.+.| +.+..+||+..+.++..+.+.|+.    
T Consensus       452 vy~t-~~eK~~al~~~I~~~~---~~gqpVLVFt~S~e~sE~Ls~~L~~~G-i~~~vLhgkq~~rE~~ii~~ag~~----  522 (822)
T 3jux_A          452 VFRT-QKEKYEKIVEEIEKRY---KKGQPVLVGTTSIEKSELLSSMLKKKG-IPHQVLNAKYHEKEAEIVAKAGQK----  522 (822)
T ss_dssp             EESS-HHHHHHHHHHHHHHHH---HHTCCEEEEESSHHHHHHHHHHHHTTT-CCCEEECSCHHHHHHHHHHHHHST----
T ss_pred             EEec-HHHHHHHHHHHHHHHh---hCCCCEEEEECCHHHHHHHHHHHHHCC-CCEEEeeCCchHHHHHHHHhCCCC----
Confidence            4444 4459999999887632   246899999999999999999999997 899999999766666656666665    


Q ss_pred             ccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCC--------CCCEEEEecCCCChHHHHHhhccc--cCCC
Q 028124          107 WNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAI--------SARVLINYELPTKKETYIRRMTTC--LAAD  176 (213)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~--------~v~~VI~yd~P~~~~~yi~R~GR~--~~~~  176 (213)
                                           ..|+||||+    ++||+|++        +..+||||++|.+...|+||+||+  .|.+
T Consensus       523 ---------------------g~VtVATdm----AgRGtDI~lg~~V~~~GglhVInte~Pes~r~y~qriGRTGRqG~~  577 (822)
T 3jux_A          523 ---------------------GMVTIATNM----AGRGTDIKLGPGVAELGGLCIIGTERHESRRIDNQLRGRAGRQGDP  577 (822)
T ss_dssp             ---------------------TCEEEEETT----TTTTCCCCCCTTTTTTTSCEEEESSCCSSHHHHHHHHTTSSCSSCC
T ss_pred             ---------------------CeEEEEcch----hhCCcCccCCcchhhcCCCEEEecCCCCCHHHHHHhhCccccCCCC
Confidence                                 359999999    99999998        667999999999999999999997  5778


Q ss_pred             CeEEEEEeCchh
Q 028124          177 GSVINIVVGGEV  188 (213)
Q Consensus       177 g~~i~~~~~~e~  188 (213)
                      |.+++|++.+|.
T Consensus       578 G~a~~fvsleD~  589 (822)
T 3jux_A          578 GESIFFLSLEDD  589 (822)
T ss_dssp             CEEEEEEETTSH
T ss_pred             eeEEEEechhHH
Confidence            999999998763

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.80  E-value=1.6e-19  Score=180.13  Aligned_cols=140  Identities=14%  Similarity=0.205  Sum_probs=116.6

Q ss_pred             CCCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEE-EecCCCCHHHHH
Q 028124           16 PSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS-SLHSDLAETERT   94 (213)
Q Consensus        16 ~~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~-~lhg~~~~~~R~   94 (213)
                      .....++.|.|+.+   + |...|.++++..      +.++||||+++..++.++..|...+ +.+. .+||+     |.
T Consensus       282 ~~~~~~i~~~~~~~---~-k~~~L~~ll~~~------~~~~LVF~~s~~~a~~l~~~L~~~g-~~~~~~lhg~-----rr  345 (1104)
T 4ddu_A          282 VSVARNITHVRISS---R-SKEKLVELLEIF------RDGILIFAQTEEEGKELYEYLKRFK-FNVGETWSEF-----EK  345 (1104)
T ss_dssp             CCCCCCEEEEEESC---C-CHHHHHHHHHHH------CSSEEEEESSSHHHHHHHHHHHHTT-CCEEESSSSH-----HH
T ss_pred             CCCcCCceeEEEec---C-HHHHHHHHHHhc------CCCEEEEECcHHHHHHHHHHHHhCC-CCeeeEecCc-----HH
Confidence            44567888988766   2 677778888772      3799999999999999999999987 7898 99992     55


Q ss_pred             HHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEE----eCCCCCcCcCCCCCCC-CCEEEEecCCC---------
Q 028124           95 LILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVV----TDACLPLLSSGESAIS-ARVLINYELPT---------  160 (213)
Q Consensus        95 ~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~----Td~~~~~~~rGld~~~-v~~VI~yd~P~---------  160 (213)
                      + +++|++|+                       .++|||    |++    ++||+|+|+ |++|||||+|.         
T Consensus       346 ~-l~~F~~G~-----------------------~~VLVatas~Tdv----larGIDip~~V~~VI~~d~P~~~~Sle~~~  397 (1104)
T 4ddu_A          346 N-FEDFKVGK-----------------------INILIGVQAYYGK----LTRGVDLPERIKYVIFWGTPSMRFSLELDK  397 (1104)
T ss_dssp             H-HHHHHHTS-----------------------CSEEEEETTTHHH----HCCSCCCTTTCCEEEEESCCEEEEECSSSS
T ss_pred             H-HHHHHCCC-----------------------CCEEEEecCCCCe----eEecCcCCCCCCEEEEECCCCCCCCccccc
Confidence            5 99999985                       999999    999    999999999 99999999999         


Q ss_pred             ---------------------------------------------------------------ChHHHHHhhccccC--C
Q 028124          161 ---------------------------------------------------------------KKETYIRRMTTCLA--A  175 (213)
Q Consensus       161 ---------------------------------------------------------------~~~~yi~R~GR~~~--~  175 (213)
                                                                                     +..+|+||+||+|+  .
T Consensus       398 ~~~~~~~~l~~l~~~~~~~~~~~~~~~~e~~~~~l~~~~~~~~i~~~~~~l~~~~~~~~~~~pd~~tYihr~GRtgR~~~  477 (1104)
T 4ddu_A          398 APRFVLARVLKEMGLIKAQENPDVEELRKIAKEHLTQKEFVEKVKEMFRGVVVKDEDLELIIPDVYTYIQASGRSSRILN  477 (1104)
T ss_dssp             CCHHHHHHHHHHHSSCSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHCCSSEEETTTTEEEEECHHHHHHHHHTTCCEET
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHhhccceEEecCCeeEEEecChhhhhcccCchhcccC
Confidence                                                                           78899999999754  3


Q ss_pred             CC--eEEEEEeCchhHHHHHHHHHhc
Q 028124          176 DG--SVINIVVGGEVVTLRSMEESLG  199 (213)
Q Consensus       176 ~g--~~i~~~~~~e~~~~~~le~~l~  199 (213)
                      .|  ..++++..+|...++.|++.++
T Consensus       478 gg~~~Glsi~~~~d~~~~~~l~~~~~  503 (1104)
T 4ddu_A          478 GVLVKGVSVIFEEDEEIFESLKTRLL  503 (1104)
T ss_dssp             TEECCEEEEEECCCHHHHHHHHHHHH
T ss_pred             CCcccceEEEEEecHHHHHHHHHHHh
Confidence            32  3455555578888899988875

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A*

Probab=99.80  E-value=6e-20  Score=166.74  Aligned_cols=114  Identities=12%  Similarity=0.083  Sum_probs=95.0

Q ss_pred             CCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEE
Q 028124           53 GLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIV  132 (213)
Q Consensus        53 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV  132 (213)
                      +.++||||++++.++.+++.|+..+ +.+..+||    ++|.+++++|++|+                       .++||
T Consensus       177 ~~~~lVF~~s~~~a~~l~~~L~~~~-~~v~~lhg----~~R~~~~~~F~~g~-----------------------~~vLV  228 (440)
T 1yks_A          177 KRPTAWFLPSIRAANVMAASLRKAG-KSVVVLNR----KTFEREYPTIKQKK-----------------------PDFIL  228 (440)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTT-CCEEECCS----SSCC--------CC-----------------------CSEEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHcC-CCEEEecc----hhHHHHHhhhcCCC-----------------------ceEEE
Confidence            5799999999999999999999987 89999999    46889999999985                       99999


Q ss_pred             EeCCCCCcCcCCCCCCCCCEEEE-------------------ecCCCChHHHHHhhcccc---CCCCeEEEEE---eCch
Q 028124          133 VTDACLPLLSSGESAISARVLIN-------------------YELPTKKETYIRRMTTCL---AADGSVINIV---VGGE  187 (213)
Q Consensus       133 ~Td~~~~~~~rGld~~~v~~VI~-------------------yd~P~~~~~yi~R~GR~~---~~~g~~i~~~---~~~e  187 (213)
                      ||++    +++|+|+| +++|||                   |+.|.+.++|+||+||+|   ++.|.|+.|+   ++.+
T Consensus       229 aT~v----~e~GiDip-v~~VI~~g~~~~pv~~~~~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~g~~~~l~~~~~~~~  303 (440)
T 1yks_A          229 ATDI----AEMGANLC-VERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYSEPTSENN  303 (440)
T ss_dssp             ESSS----TTCCTTCC-CSEEEECCEEEEEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCC
T ss_pred             ECCh----hheeeccC-ceEEEeCCccceeeecccccceeeccccccCHHHHHHhccccCCCCCCCceEEEEeccCChhh
Confidence            9999    99999999 999996                   999999999999999974   4579999996   6778


Q ss_pred             hHHHHHHHHHhc
Q 028124          188 VVTLRSMEESLG  199 (213)
Q Consensus       188 ~~~~~~le~~l~  199 (213)
                      ...+..++..+.
T Consensus       304 ~~~l~~l~~~~~  315 (440)
T 1yks_A          304 AHHVCWLEASML  315 (440)
T ss_dssp             TTBHHHHHHHHH
T ss_pred             hhhhhhhhHHhc
Confidence            888888888753

>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=99.79  E-value=3.1e-19  Score=168.68  Aligned_cols=115  Identities=10%  Similarity=0.006  Sum_probs=103.1

Q ss_pred             CCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEE
Q 028124           53 GLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIV  132 (213)
Q Consensus        53 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV  132 (213)
                      ..++||||++++.++.+++.|+..+ +.+..+||+    +|.+++++|++|.                       .++||
T Consensus       355 ~~~~LVF~~s~~~a~~l~~~L~~~g-~~v~~lhg~----~R~~~l~~F~~g~-----------------------~~VLV  406 (618)
T 2whx_A          355 QGKTVWFVPSIKAGNDIANCLRKSG-KRVIQLSRK----TFDTEYPKTKLTD-----------------------WDFVV  406 (618)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHTT-CCEEEECTT----THHHHTTHHHHSC-----------------------CSEEE
T ss_pred             CCCEEEEECChhHHHHHHHHHHHcC-CcEEEEChH----HHHHHHHhhcCCC-----------------------cEEEE
Confidence            5799999999999999999999987 899999984    7888999999985                       99999


Q ss_pred             EeCCCCCcCcCCCCCCCCCEE--------------------EEecCCCChHHHHHhhccccC---CCCeEEEEEe---Cc
Q 028124          133 VTDACLPLLSSGESAISARVL--------------------INYELPTKKETYIRRMTTCLA---ADGSVINIVV---GG  186 (213)
Q Consensus       133 ~Td~~~~~~~rGld~~~v~~V--------------------I~yd~P~~~~~yi~R~GR~~~---~~g~~i~~~~---~~  186 (213)
                      |||+    +++|+|++ +++|                    ||||+|.+.++|+||+||+|+   ..|.+++|+.   +.
T Consensus       407 aTdv----~~rGiDi~-v~~VId~g~~~~P~~~~~~~~~~~i~~d~P~s~~~yiQR~GRaGR~g~~~G~ai~l~~~~~~~  481 (618)
T 2whx_A          407 TTDI----SEMGANFR-AGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDPLKN  481 (618)
T ss_dssp             ECGG----GGTTCCCC-CSEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCC
T ss_pred             ECcH----HHcCcccC-ceEEEECcceecceecccCCCceEEcccccCCHHHHHHhccccCCCCCCCCeEEEEccCCchh
Confidence            9999    99999997 9988                    889999999999999999753   3789999997   77


Q ss_pred             hhHHHHHHHHHhcc
Q 028124          187 EVVTLRSMEESLGL  200 (213)
Q Consensus       187 e~~~~~~le~~l~~  200 (213)
                      |...+..+++.+..
T Consensus       482 d~~~l~~le~~i~l  495 (618)
T 2whx_A          482 DEDHAHWTEAKMLL  495 (618)
T ss_dssp             CTTCHHHHHHHHHH
T ss_pred             hHHHHHHHHhHhcc
Confidence            88888888887633

>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=99.78  E-value=6.1e-19  Score=175.28  Aligned_cols=140  Identities=16%  Similarity=0.161  Sum_probs=115.5

Q ss_pred             CCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHH
Q 028124           17 SHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLI   96 (213)
Q Consensus        17 ~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~   96 (213)
                      ....++.|.++   . ..|...|.++++.      .+.++||||++++.|+.+++.|+..  +.+..+||++     .++
T Consensus       249 ~~~~~i~~~~~---~-~~k~~~L~~ll~~------~~~~~LVF~~t~~~a~~l~~~L~~~--~~v~~lhg~~-----~~~  311 (1054)
T 1gku_B          249 ITVRNVEDVAV---N-DESISTLSSILEK------LGTGGIIYARTGEEAEEIYESLKNK--FRIGIVTATK-----KGD  311 (1054)
T ss_dssp             ECCCCEEEEEE---S-CCCTTTTHHHHTT------SCSCEEEEESSHHHHHHHHHTTTTS--SCEEECTTSS-----SHH
T ss_pred             cCcCCceEEEe---c-hhHHHHHHHHHhh------cCCCEEEEEcCHHHHHHHHHHHhhc--cCeeEEeccH-----HHH
Confidence            34467888877   2 3377888888876      2578999999999999999999877  7999999998     378


Q ss_pred             HHHHhcccccccccccccCCCCCcCCCCCCceeEEEE----eCCCCCcCcCCCCCCCC-CEEEEecCC------------
Q 028124           97 LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVV----TDACLPLLSSGESAISA-RVLINYELP------------  159 (213)
Q Consensus        97 l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~----Td~~~~~~~rGld~~~v-~~VI~yd~P------------  159 (213)
                      +++|++|.                       .++|||    |++    ++||+|+|+| ++|||||+|            
T Consensus       312 l~~F~~G~-----------------------~~VLVaTas~Tdv----~~rGIDip~VI~~VI~~~~P~~~~~~~~~~~~  364 (1054)
T 1gku_B          312 YEKFVEGE-----------------------IDHLIGTAHYYGT----LVRGLDLPERIRFAVFVGCPSFRVTIEDIDSL  364 (1054)
T ss_dssp             HHHHHHTS-----------------------CSEEEEECC----------CCSCCTTTCCEEEEESCCEEEEECSCGGGS
T ss_pred             HHHHHcCC-----------------------CcEEEEecCCCCe----eEeccccCCcccEEEEeCCCcccccccccccC
Confidence            89999985                       999999    899    9999999996 999999999            


Q ss_pred             -----------------------------------------------------------CChHHHHHhhccccC--CCC-
Q 028124          160 -----------------------------------------------------------TKKETYIRRMTTCLA--ADG-  177 (213)
Q Consensus       160 -----------------------------------------------------------~~~~~yi~R~GR~~~--~~g-  177 (213)
                                                                                 .+..+|+||+||+++  ..| 
T Consensus       365 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~yiQr~GRagR~g~~g~  444 (1054)
T 1gku_B          365 SPQMVKLLAYLYRNVDEIERLLPAVERHIDEVREILKKVMGKERPQAKDVVVREGEVIFPDLRTYIQGSGRTSRLFAGGL  444 (1054)
T ss_dssp             CHHHHHHHHTTTSCHHHHHTTCTTTSSCHHHHHHHHHHHHTTSCCSCSSSEEETTEEEEECHHHHHHHHHTTCCEETTEE
T ss_pred             hHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHhccccccccceeEeecceecCcHHHHhhhhchhhhccCCCC
Confidence                                                                       789999999999865  565 


Q ss_pred             -eEEEEEeCchhHHHHHHHHHhcc
Q 028124          178 -SVINIVVGGEVVTLRSMEESLGL  200 (213)
Q Consensus       178 -~~i~~~~~~e~~~~~~le~~l~~  200 (213)
                       .+++++...+...+..+++.++.
T Consensus       445 ~~g~~~~~~~d~~~~~~l~~~l~~  468 (1054)
T 1gku_B          445 TKGASFLLEDDSELLSAFIERAKL  468 (1054)
T ss_dssp             CCEEEEEECSCHHHHHHHHHHHHT
T ss_pred             ceEEEEEEecCHHHHHHHHHHHhh
Confidence             48999988899999999998875

>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=99.78  E-value=1.3e-18  Score=167.85  Aligned_cols=129  Identities=13%  Similarity=0.157  Sum_probs=111.9

Q ss_pred             EEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccc
Q 028124           26 YVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAM  105 (213)
Q Consensus        26 ~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~  105 (213)
                      ++++.. ..|+..|.+++....   ..++++||||+|+..++.|+..|++.| +.+..+||++.+.++..+.+.|+.|  
T Consensus       418 ~v~~~~-~~K~~al~~~i~~~~---~~gqpvLVft~sie~se~Ls~~L~~~g-i~~~vLnak~~~rEa~iia~agr~G--  490 (853)
T 2fsf_A          418 LVYMTE-AEKIQAIIEDIKERT---AKGQPVLVGTISIEKSELVSNELTKAG-IKHNVLNAKFHANEAAIVAQAGYPA--  490 (853)
T ss_dssp             EEESSH-HHHHHHHHHHHHHHH---TTTCCEEEEESSHHHHHHHHHHHHHTT-CCCEECCTTCHHHHHHHHHTTTSTT--
T ss_pred             EEEeCH-HHHHHHHHHHHHHHh---cCCCCEEEEECcHHHHHHHHHHHHHCC-CCEEEecCChhHHHHHHHHhcCCCC--
Confidence            345554 459999999886532   357899999999999999999999998 8999999999888888888888875  


Q ss_pred             cccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCC-----------------------------------
Q 028124          106 KWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISA-----------------------------------  150 (213)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v-----------------------------------  150 (213)
                                             .|+||||+    ++||+|++..                                   
T Consensus       491 -----------------------~VtIATnm----AgRGtDI~l~gn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~  543 (853)
T 2fsf_A          491 -----------------------AVTIATNM----AGRGTDIVLGGSWQAEVAALENPTAEQIEKIKADWQVRHDAVLEA  543 (853)
T ss_dssp             -----------------------CEEEEESC----CSSCSCCCTTCCHHHHHHHCSSCCSSHHHHHHHHHHHHHHHHHHT
T ss_pred             -----------------------eEEEeccc----ccCCcCccCCCchHhhhhhcccchhHHHHHHHHHhhhhhhHHHhc
Confidence                                   49999999    9999999974                                   


Q ss_pred             --CEEEEecCCCChHHHHHhhccc--cCCCCeEEEEEeCchh
Q 028124          151 --RVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEV  188 (213)
Q Consensus       151 --~~VI~yd~P~~~~~yi~R~GR~--~~~~g~~i~~~~~~e~  188 (213)
                        .+||||++|.+...|.||+||+  .|.+|.+++|++.+|.
T Consensus       544 GGl~VI~te~pes~riy~qr~GRTGRqGd~G~s~~fls~eD~  585 (853)
T 2fsf_A          544 GGLHIIGTERHESRRIDNQLRGRSGRQGDAGSSRFYLSMEDA  585 (853)
T ss_dssp             TSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTSG
T ss_pred             CCcEEEEccCCCCHHHHHhhccccccCCCCeeEEEEecccHH
Confidence              5999999999999999999997  5788999999997764

>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=99.77  E-value=3e-19  Score=172.61  Aligned_cols=140  Identities=11%  Similarity=0.159  Sum_probs=113.1

Q ss_pred             CCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhc----------cCCceEEEecCCCC
Q 028124           20 SQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSN----------LADISFSSLHSDLA   89 (213)
Q Consensus        20 ~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~----------~~~~~~~~lhg~~~   89 (213)
                      ..+.++|...+..+.....+..+++....  ...+++||||+++..++.+++.|..          .+++.+..+||+|+
T Consensus       272 ~pv~~~~~~~~~~~~~~~~l~~l~~~~~~--~~~g~iLVF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~  349 (773)
T 2xau_A          272 YPVELYYTPEFQRDYLDSAIRTVLQIHAT--EEAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLP  349 (773)
T ss_dssp             CCEEEECCSSCCSCHHHHHHHHHHHHHHH--SCSCEEEEECSCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECTTCC
T ss_pred             cceEEEEecCCchhHHHHHHHHHHHHHHh--cCCCCEEEECCCHHHHHHHHHHHHHHHHhhcccccCCCeEEEEeCCCCC
Confidence            45778777666655222333333332211  3568999999999999999999974          13478999999999


Q ss_pred             HHHHHHHHHHHh-----cccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecC------
Q 028124           90 ETERTLILEEFR-----HTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYEL------  158 (213)
Q Consensus        90 ~~~R~~~l~~Fr-----~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~------  158 (213)
                      +++|.++++.|+     .|                       ..+|||||++    +++|+|+|++++||+|++      
T Consensus       350 ~~eR~~v~~~f~~~~~~~g-----------------------~~kVlVAT~i----ae~GidIp~v~~VId~g~~k~~~y  402 (773)
T 2xau_A          350 PHQQQRIFEPAPESHNGRP-----------------------GRKVVISTNI----AETSLTIDGIVYVVDPGFSKQKVY  402 (773)
T ss_dssp             HHHHGGGGSCCCCCSSSSC-----------------------CEEEEEECTH----HHHTCCCTTEEEEEECSEEEEEEE
T ss_pred             HHHHHHHHhhcccccCCCC-----------------------ceEEEEeCcH----HHhCcCcCCeEEEEeCCCccceee
Confidence            999999999999     66                       4999999999    999999999999999887      


Q ss_pred             ------------CCChHHHHHhhccccC-CCCeEEEEEeCchh
Q 028124          159 ------------PTKKETYIRRMTTCLA-ADGSVINIVVGGEV  188 (213)
Q Consensus       159 ------------P~~~~~yi~R~GR~~~-~~g~~i~~~~~~e~  188 (213)
                                  |.+.++|+||+||+|+ .+|.|+.|+++.+.
T Consensus       403 d~~~g~~~L~~~p~S~~s~~QR~GRaGR~~~G~~~~l~~~~~~  445 (773)
T 2xau_A          403 NPRIRVESLLVSPISKASAQQRAGRAGRTRPGKCFRLYTEEAF  445 (773)
T ss_dssp             ETTTTEEEEEEEECCHHHHHHHHHGGGSSSSEEEEESSCHHHH
T ss_pred             ccccCccccccccCCHHHHHhhccccCCCCCCEEEEEecHHHh
Confidence                        8899999999999876 57999999986544

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.76  E-value=9.5e-19  Score=166.84  Aligned_cols=115  Identities=9%  Similarity=0.014  Sum_probs=102.1

Q ss_pred             CCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEE
Q 028124           52 PGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMI  131 (213)
Q Consensus        52 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iL  131 (213)
                      .+.++||||++++.++.+++.|+..+ +.+..+||+    +|.+++++|++|+                       .+||
T Consensus       409 ~~~~~lVF~~s~~~~e~la~~L~~~g-~~v~~lHg~----eR~~v~~~F~~g~-----------------------~~VL  460 (673)
T 2wv9_A          409 YAGKTVWFVASVKMSNEIAQCLQRAG-KRVIQLNRK----SYDTEYPKCKNGD-----------------------WDFV  460 (673)
T ss_dssp             CCSCEEEECSSHHHHHHHHHHHHTTT-CCEEEECSS----SHHHHGGGGGTCC-----------------------CSEE
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHhCC-CeEEEeChH----HHHHHHHHHHCCC-----------------------ceEE
Confidence            46799999999999999999999987 899999994    7899999999985                       9999


Q ss_pred             EEeCCCCCcCcCCCCCCCCCEEEE--------------------ecCCCChHHHHHhhcccc---CCCCeEEEEE---eC
Q 028124          132 VVTDACLPLLSSGESAISARVLIN--------------------YELPTKKETYIRRMTTCL---AADGSVINIV---VG  185 (213)
Q Consensus       132 V~Td~~~~~~~rGld~~~v~~VI~--------------------yd~P~~~~~yi~R~GR~~---~~~g~~i~~~---~~  185 (213)
                      |||++    +++|+|+| +++|||                    ||+|.+.++|+||+||+|   ++.|.|+.|+   .+
T Consensus       461 VaTdv----~e~GIDip-v~~VI~~g~~~~p~vi~da~~r~~ll~d~P~s~~~y~Qr~GRaGR~~g~~G~ai~l~~~~~~  535 (673)
T 2wv9_A          461 ITTDI----SEMGANFG-ASRVIDCRKSVKPTILDEGEGRVILSVPSAITSASAAQRRGRVGRNPSQIGDEYHYGGGTSE  535 (673)
T ss_dssp             EECGG----GGTTCCCC-CSEEEECCEECCEEEECSTTCEEEECCSEECCHHHHHHHHTTSSCCSSCCCEEEEECSCCCC
T ss_pred             EECch----hhcceeeC-CcEEEECCCcccceeeecccccceecccCCCCHHHHHHHhhccCCCCCCCCEEEEEEecCCh
Confidence            99999    99999999 999998                    679999999999999974   4579999996   56


Q ss_pred             chhHHHHHHHHHhc
Q 028124          186 GEVVTLRSMEESLG  199 (213)
Q Consensus       186 ~e~~~~~~le~~l~  199 (213)
                      .+...+..++..+.
T Consensus       536 ~d~~~l~~ie~~~~  549 (673)
T 2wv9_A          536 DDTMLAHWTEAKIL  549 (673)
T ss_dssp             CCTTBHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHh
Confidence            77777777777653

>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=99.76  E-value=7.3e-18  Score=163.17  Aligned_cols=129  Identities=14%  Similarity=0.132  Sum_probs=110.6

Q ss_pred             EEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccc
Q 028124           26 YVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAM  105 (213)
Q Consensus        26 ~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~  105 (213)
                      ++++.. ..|+..|.+.+....   ..++++||||+|+..++.|+..|.+.| +.+..|||++.+.++..+.+.|+.|  
T Consensus       437 ~v~~t~-~~K~~al~~~i~~~~---~~gqpvLVft~Sie~sE~Ls~~L~~~G-i~~~vLnak~~~rEa~iia~agr~G--  509 (922)
T 1nkt_A          437 LIYKTE-EAKYIAVVDDVAERY---AKGQPVLIGTTSVERSEYLSRQFTKRR-IPHNVLNAKYHEQEATIIAVAGRRG--  509 (922)
T ss_dssp             EEESCH-HHHHHHHHHHHHHHH---HTTCCEEEEESCHHHHHHHHHHHHHTT-CCCEEECSSCHHHHHHHHHTTTSTT--
T ss_pred             EEEeCH-HHHHHHHHHHHHHHH---hcCCcEEEEECCHHHHHHHHHHHHHCC-CCEEEecCChhHHHHHHHHhcCCCC--
Confidence            345544 459999999886532   246799999999999999999999998 8999999998888877777778774  


Q ss_pred             cccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCC-----------------------------------
Q 028124          106 KWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISA-----------------------------------  150 (213)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v-----------------------------------  150 (213)
                                             .|+||||+    ++||+|++.+                                   
T Consensus       510 -----------------------~VtIATnm----AgRGtDI~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  562 (922)
T 1nkt_A          510 -----------------------GVTVATNM----AGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPI  562 (922)
T ss_dssp             -----------------------CEEEEETT----CSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHH
T ss_pred             -----------------------eEEEecch----hhcCccccCCCCHHHHHHHHHhhccccccccchhhHHHHHHHHHH
Confidence                                   48999999    9999999975                                   


Q ss_pred             -----------------CEEEEecCCCChHHHHHhhccc--cCCCCeEEEEEeCchh
Q 028124          151 -----------------RVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEV  188 (213)
Q Consensus       151 -----------------~~VI~yd~P~~~~~yi~R~GR~--~~~~g~~i~~~~~~e~  188 (213)
                                       .+||||+.|.+...|.||+||+  .|.+|.+++|++.+|.
T Consensus       563 ~~~~~~~~~~~V~~~GGlhVI~te~pes~riy~qr~GRTGRqGdpG~s~fflSleD~  619 (922)
T 1nkt_A          563 VKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQLRGRSGRQGDPGESRFYLSLGDE  619 (922)
T ss_dssp             HHHHTTHHHHHHHHTTSEEEEECSCCSSHHHHHHHHHTSSGGGCCEEEEEEEETTSH
T ss_pred             HHHHHHHhhhHHHhcCCcEEEeccCCCCHHHHHHHhcccccCCCCeeEEEEechhHH
Confidence                             4999999999999999999997  5788999999997765

>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=99.75  E-value=4.7e-19  Score=161.58  Aligned_cols=101  Identities=9%  Similarity=0.020  Sum_probs=89.2

Q ss_pred             CCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEE
Q 028124           53 GLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIV  132 (213)
Q Consensus        53 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV  132 (213)
                      .+++||||++++.++.+++.|+..+ +.+..+||+    +|.+++++|++|.                       .+|||
T Consensus       190 ~~~~LVF~~s~~~~~~l~~~L~~~g-~~v~~lh~~----~R~~~~~~f~~g~-----------------------~~iLV  241 (459)
T 2z83_A          190 AGKTVWFVASVKMGNEIAMCLQRAG-KKVIQLNRK----SYDTEYPKCKNGD-----------------------WDFVI  241 (459)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTT-CCEEEESTT----CCCCCGGGSSSCC-----------------------CSEEE
T ss_pred             CCCEEEEeCChHHHHHHHHHHHhcC-CcEEecCHH----HHHHHHhhccCCC-----------------------ceEEE
Confidence            5799999999999999999999987 899999995    6788999999985                       99999


Q ss_pred             EeCCCCCcCcCCCCCCCCCEEEE--------------------ecCCCChHHHHHhhccccC--C-CCeEEEEEeCc
Q 028124          133 VTDACLPLLSSGESAISARVLIN--------------------YELPTKKETYIRRMTTCLA--A-DGSVINIVVGG  186 (213)
Q Consensus       133 ~Td~~~~~~~rGld~~~v~~VI~--------------------yd~P~~~~~yi~R~GR~~~--~-~g~~i~~~~~~  186 (213)
                      ||++    +++|+|+|+ ++|||                    ||+|.+.++|+||+||+|+  . +|.++.|+...
T Consensus       242 aT~v----~~~GiDip~-~~VI~~G~~~~~~~~~~~~~~~~~~~d~p~s~~~~~QR~GRaGR~g~~~G~~~~~~~~~  313 (459)
T 2z83_A          242 TTDI----SEMGANFGA-SRVIDCRKSVKPTILEEGEGRVILGNPSPITSASAAQRRGRVGRNPNQVGDEYHYGGAT  313 (459)
T ss_dssp             ESSC----C---CCCSC-SEEEECCEECCEEEECSSSCEEEECSCEECCHHHHHHHHTTSSCCTTCCCEEEEECSCC
T ss_pred             ECCh----HHhCeecCC-CEEEECCcccccccccccccccccccCCCCCHHHHHHhccccCCCCCCCCeEEEEEccc
Confidence            9999    999999999 99999                    8899999999999999753  3 79999999764

>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex, hydrolase/DNA complex complex; 3.00A {Sulfolobus solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A

Probab=99.74  E-value=9.8e-18  Score=152.83  Aligned_cols=124  Identities=15%  Similarity=0.149  Sum_probs=103.9

Q ss_pred             chHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc-CCceEEEecCCCCHHHHHHHHHHHhcccccccccc
Q 028124           33 QFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL-ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKV  111 (213)
Q Consensus        33 ~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~-~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~  111 (213)
                      ..|+..+.++++....   .+.++||||+++..++.+...|... + +.+..+||+++..+|.+++++|+++.       
T Consensus       324 s~K~~~l~~~l~~~~~---~~~k~lvF~~~~~~~~~l~~~l~~~~~-~~~~~~~g~~~~~~R~~~~~~F~~~~-------  392 (500)
T 1z63_A          324 SGKMIRTMEIIEEALD---EGDKIAIFTQFVDMGKIIRNIIEKELN-TEVPFLYGELSKKERDDIISKFQNNP-------  392 (500)
T ss_dssp             CHHHHHHHHHHHHHHT---TTCCEEEECSCHHHHHHHHHHHHHHHT-CCCCEEETTSCHHHHHHHHHHHHHCT-------
T ss_pred             chhHHHHHHHHHHHHc---cCCcEEEEEehHHHHHHHHHHHHHhhC-CCeEEEECCCCHHHHHHHHHHhcCCC-------
Confidence            4599999999987543   5789999999999999999999875 6 78999999999999999999999973       


Q ss_pred             cccCCCCCcCCCCCCcee-EEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCCC--CeEEEEEeCc
Q 028124          112 TEQSGDESETGKDEHKSH-MIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAAD--GSVINIVVGG  186 (213)
Q Consensus       112 ~~~~~~~~~~~~~~~~~~-iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~~--g~~i~~~~~~  186 (213)
                                     ..+ +|++|++    +++|+|++.+++||+||+||++..|.||+||+  .|+.  ..++.++..+
T Consensus       393 ---------------~~~vil~st~~----~~~Glnl~~~~~vi~~d~~~~~~~~~Q~~gR~~R~Gq~~~v~v~~lv~~~  453 (500)
T 1z63_A          393 ---------------SVKFIVLSVKA----GGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVG  453 (500)
T ss_dssp             ---------------TCCCCEEECCC----C-CCCCCTTCSEEEESSCCSCC---CHHHHTTTTTTTTSCEEEEEEEETT
T ss_pred             ---------------CCCEEEEeccc----ccCCCchhhCCEEEEeCCCCCcchHHHHHHHHHHcCCCCeeEEEEEEeCC
Confidence                           244 8999999    99999999999999999999999999999996  3333  4567788776

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.74  E-value=2.2e-17  Score=157.29  Aligned_cols=139  Identities=19%  Similarity=0.197  Sum_probs=105.3

Q ss_pred             HHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCC-----------------------------------c
Q 028124           35 KMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLAD-----------------------------------I   79 (213)
Q Consensus        35 K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~-----------------------------------~   79 (213)
                      +...+.++++       .++++||||++++.++.++..|.....                                   .
T Consensus       241 ~~~~~~~~~~-------~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~~  313 (715)
T 2va8_A          241 IIAYTLDSLS-------KNGQVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSLISK  313 (715)
T ss_dssp             HHHHHHHHHT-------TTCCEEEECSSHHHHHHHHHHHHHTTTSSCCCHHHHHHHHHHHHTCCSSCHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHh-------cCCCEEEEECCHHHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHhhhccccccHHHHHHHhc
Confidence            5555544443       468999999999999999999975410                                   1


Q ss_pred             eEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEE----
Q 028124           80 SFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLIN----  155 (213)
Q Consensus        80 ~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~----  155 (213)
                      .+..+||+|++++|..+++.|++|.                       +++||||++    +++|+|+|++++||+    
T Consensus       314 ~v~~~h~~l~~~~r~~v~~~f~~g~-----------------------~~vlvaT~~----l~~Gidip~~~~VI~~~~~  366 (715)
T 2va8_A          314 GVAYHHAGLSKALRDLIEEGFRQRK-----------------------IKVIVATPT----LAAGVNLPARTVIIGDIYR  366 (715)
T ss_dssp             TEEEECTTSCHHHHHHHHHHHHTTC-----------------------SCEEEECGG----GGGSSCCCBSEEEECCC--
T ss_pred             CEEEECCCCCHHHHHHHHHHHHcCC-----------------------CeEEEEChH----HhcccCCCceEEEEeCCee
Confidence            3889999999999999999999985                       999999999    999999999999999    


Q ss_pred             ec-------CCCChHHHHHhhccccCC----CCeEEEEEeCchhHHHHHHHHHhcccccccCcc
Q 028124          156 YE-------LPTKKETYIRRMTTCLAA----DGSVINIVVGGEVVTLRSMEESLGLIVAEVPIN  208 (213)
Q Consensus       156 yd-------~P~~~~~yi~R~GR~~~~----~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~  208 (213)
                      ||       .|.+..+|.||+||+|+.    .|.|+.+++..+. ....+++++....+++..+
T Consensus       367 ~d~~~~~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~~-~~~~~~~~l~~~~e~~~s~  429 (715)
T 2va8_A          367 FNKKIAGYYDEIPIMEYKQMSGRAGRPGFDQIGESIVVVRDKED-VDRVFKKYVLSDVEPIESK  429 (715)
T ss_dssp             ------------CHHHHHHHHTTBCCTTTCSCEEEEEECSCGGG-HHHHHHHTTSSCCCCCCCS
T ss_pred             ccccCCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEEeCCchH-HHHHHHHHHcCCCCCceec
Confidence            99       899999999999998652    5899999987653 1123344554444444333

>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=99.73  E-value=1.4e-17  Score=159.02  Aligned_cols=138  Identities=17%  Similarity=0.146  Sum_probs=111.2

Q ss_pred             HHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccC-----------------C---------------ceEE
Q 028124           35 KMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLA-----------------D---------------ISFS   82 (213)
Q Consensus        35 K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~-----------------~---------------~~~~   82 (213)
                      +...+.++++.       ++++||||++++.++.++..|....                 .               ..+.
T Consensus       226 ~~~~~~~~~~~-------~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~v~  298 (720)
T 2zj8_A          226 WEELVYDAIRK-------KKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVA  298 (720)
T ss_dssp             TTHHHHHHHHT-------TCCEEEECSCHHHHHHHHHHHHHHHGGGSCHHHHHHHHHHHHTSCSCHHHHHHHHHHTTTEE
T ss_pred             HHHHHHHHHhC-------CCCEEEEecCHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHhcccchHHHHHHHhcCee
Confidence            55666665543       5899999999999999999987531                 0               1388


Q ss_pred             EecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEE----ec-
Q 028124           83 SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLIN----YE-  157 (213)
Q Consensus        83 ~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~----yd-  157 (213)
                      .+||+|++++|..+++.|++|.                       +++||||++    +++|+|+|++++||+    || 
T Consensus       299 ~~h~~l~~~~R~~v~~~f~~g~-----------------------~~vlvaT~~----l~~Gvdip~~~~VI~~~~~yd~  351 (720)
T 2zj8_A          299 FHHAGLGRDERVLVEENFRKGI-----------------------IKAVVATPT----LSAGINTPAFRVIIRDIWRYSD  351 (720)
T ss_dssp             EECTTSCHHHHHHHHHHHHTTS-----------------------SCEEEECST----TGGGCCCCBSEEEECCSEECCS
T ss_pred             eecCCCCHHHHHHHHHHHHCCC-----------------------CeEEEECcH----hhccCCCCceEEEEcCCeeecC
Confidence            9999999999999999999985                       999999999    999999999999999    88 


Q ss_pred             ---CCCChHHHHHhhccccC----CCCeEEEEEeCchhHHHHHHHHHhcccccccCcc
Q 028124          158 ---LPTKKETYIRRMTTCLA----ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPIN  208 (213)
Q Consensus       158 ---~P~~~~~yi~R~GR~~~----~~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~  208 (213)
                         .|.+..+|+||+||+|+    ..|.|+.+++..+..  ..+++++....+++...
T Consensus       352 ~g~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~~~--~~~~~~~~~~~~~i~s~  407 (720)
T 2zj8_A          352 FGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSDDPR--EVMNHYIFGKPEKLFSQ  407 (720)
T ss_dssp             SSCEECCHHHHHHHHTTBCCTTTCSEEEEEEECSSSCHH--HHHHHHTTSCCCCCCCC
T ss_pred             CCCccCCHHHHHHHHhhcCCCCCCCCceEEEEecCccHH--HHHHHHhcCCCCCcEee
Confidence               68999999999999865    358999999877622  23445665555555433

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.73  E-value=1.8e-17  Score=164.15  Aligned_cols=116  Identities=19%  Similarity=0.181  Sum_probs=100.2

Q ss_pred             CCCcEEEEeCchHHHHHHHHHHhccCC--------------------------------------ceEEEecCCCCHHHH
Q 028124           52 PGLPMIVCCSSRDELDAVCSAVSNLAD--------------------------------------ISFSSLHSDLAETER   93 (213)
Q Consensus        52 ~~~~~IIF~~~~~~~~~l~~~L~~~~~--------------------------------------~~~~~lhg~~~~~~R   93 (213)
                      ...++||||+++..|+.++..|...+.                                      ..+..+||+|++.+|
T Consensus       342 ~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gI~~~Hggl~~~eR  421 (1010)
T 2xgj_A          342 KYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILK  421 (1010)
T ss_dssp             TCCSEEEEESSHHHHHHHHHTTTTSCCCCHHHHHHHHHHHHHHHTTSCGGGTTCHHHHHHHHHHHHTEEEESTTSCHHHH
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHHhCCeeEECCCCCHHHH
Confidence            456999999999999999999976431                                      017889999999999


Q ss_pred             HHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEE----ecC----CCChHHH
Q 028124           94 TLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLIN----YEL----PTKKETY  165 (213)
Q Consensus        94 ~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~----yd~----P~~~~~y  165 (213)
                      ..+++.|++|.                       +++||||++    +++|+|+|++++||+    ||.    |.++..|
T Consensus       422 ~~ve~~F~~G~-----------------------ikVLVAT~~----la~GIDiP~~~vVI~~~~kfd~~~~rp~s~~~y  474 (1010)
T 2xgj_A          422 EVIEILFQEGF-----------------------LKVLFATET----FSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEY  474 (1010)
T ss_dssp             HHHHHHHHTTC-----------------------CSEEEEEGG----GGGSTTCCBSEEEESCSEEECSSCEEECCHHHH
T ss_pred             HHHHHHHhcCC-----------------------CcEEEEehH----hhccCCCCCceEEEeCCcccCCcCCccCCHHHH
Confidence            99999999985                       999999999    999999999999999    999    8999999


Q ss_pred             HHhhccccCC----CCeEEEEEeCc-hhHHHHHH
Q 028124          166 IRRMTTCLAA----DGSVINIVVGG-EVVTLRSM  194 (213)
Q Consensus       166 i~R~GR~~~~----~g~~i~~~~~~-e~~~~~~l  194 (213)
                      +||+||+|+.    .|.||.++.+. +...+.++
T Consensus       475 ~Qr~GRAGR~G~d~~G~vi~l~~~~~e~~~~~~l  508 (1010)
T 2xgj_A          475 IQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGM  508 (1010)
T ss_dssp             HHHHTTBCCTTTCSSEEEEEEECSCCCHHHHHHH
T ss_pred             hHhhhhcccCCCCCceEEEEEECCCCCHHHHHHH
Confidence            9999998644    49999999865 44444444

>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=99.73  E-value=4.7e-18  Score=153.93  Aligned_cols=116  Identities=20%  Similarity=0.276  Sum_probs=102.0

Q ss_pred             chHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccccccc
Q 028124           33 QFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVT  112 (213)
Q Consensus        33 ~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~  112 (213)
                      ..|...|.++++.     ..+.++||||++++.++.+++.|.      +..+||+++..+|.+++++|++|+        
T Consensus       334 ~~k~~~l~~~l~~-----~~~~k~lvF~~~~~~~~~l~~~l~------~~~~~g~~~~~~R~~~~~~F~~g~--------  394 (472)
T 2fwr_A          334 KNKIRKLREILER-----HRKDKIIIFTRHNELVYRISKVFL------IPAITHRTSREEREEILEGFRTGR--------  394 (472)
T ss_dssp             SHHHHHHHHHHHH-----TSSSCBCCBCSCHHHHHHHHHHTT------CCBCCSSSCSHHHHTHHHHHHHSS--------
T ss_pred             hHHHHHHHHHHHh-----CCCCcEEEEECCHHHHHHHHHHhC------cceeeCCCCHHHHHHHHHHHhCCC--------
Confidence            3488999999987     457899999999999999999983      446899999999999999999985        


Q ss_pred             ccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhcccc--C---CCCeEEEEEeCc
Q 028124          113 EQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--A---ADGSVINIVVGG  186 (213)
Q Consensus       113 ~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~--~---~~g~~i~~~~~~  186 (213)
                                     .++||+|++    +++|+|+|++++||+||.|+++..|+||+||++  |   +...++.++..+
T Consensus       395 ---------------~~vLv~T~~----~~~Gldlp~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~k~~~~i~~lv~~~  454 (472)
T 2fwr_A          395 ---------------FRAIVSSQV----LDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYELISRG  454 (472)
T ss_dssp             ---------------CSBCBCSSC----CCSSSCSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTTCCEEEEEEEECS
T ss_pred             ---------------CCEEEEcCc----hhcCcccccCcEEEEECCCCCHHHHHHHHhhccCCCCCCceEEEEEEEeCC
Confidence                           999999999    999999999999999999999999999999973  2   234677788764

>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=99.73  E-value=1.1e-17  Score=167.45  Aligned_cols=147  Identities=12%  Similarity=0.135  Sum_probs=115.9

Q ss_pred             CCCCCCCCCCCCCCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc-CCceEEE
Q 028124            5 GVESPCPPCQSPSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL-ADISFSS   83 (213)
Q Consensus         5 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~-~~~~~~~   83 (213)
                      ++..+..+...+..+..+++++....    +......+++.+    ..+.+++||||++++++.+++.|+.. +++.+..
T Consensus       772 ~~~~~~~i~~~~~~r~~i~~~~~~~~----~~~i~~~il~~l----~~g~qvlvf~~~v~~~~~l~~~L~~~~p~~~v~~  843 (1151)
T 2eyq_A          772 GMRDLSIIATPPARRLAVKTFVREYD----SMVVREAILREI----LRGGQVYYLYNDVENIQKAAERLAELVPEARIAI  843 (1151)
T ss_dssp             TTSEEEECCCCCCBCBCEEEEEEECC----HHHHHHHHHHHH----TTTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEE
T ss_pred             cCCCceEEecCCCCccccEEEEecCC----HHHHHHHHHHHH----hcCCeEEEEECCHHHHHHHHHHHHHhCCCCeEEE
Confidence            33333334444445555666655433    333444455542    34689999999999999999999876 3378999


Q ss_pred             ecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecC-CCCh
Q 028124           84 LHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYEL-PTKK  162 (213)
Q Consensus        84 lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~-P~~~  162 (213)
                      +||+|++.+|.+++++|++|.                       .++||||++    +++|+|+|++++||+++. ++++
T Consensus       844 lhg~~~~~eR~~il~~F~~g~-----------------------~~VLVaT~v----~e~GiDip~v~~VIi~~~~~~~l  896 (1151)
T 2eyq_A          844 GHGQMRERELERVMNDFHHQR-----------------------FNVLVCTTI----IETGIDIPTANTIIIERADHFGL  896 (1151)
T ss_dssp             CCSSCCHHHHHHHHHHHHTTS-----------------------CCEEEESST----TGGGSCCTTEEEEEETTTTSSCH
T ss_pred             EeCCCCHHHHHHHHHHHHcCC-----------------------CcEEEECCc----ceeeecccCCcEEEEeCCCCCCH
Confidence            999999999999999999985                       999999999    999999999999999998 5799


Q ss_pred             HHHHHhhccc--cCCCCeEEEEEeCc
Q 028124          163 ETYIRRMTTC--LAADGSVINIVVGG  186 (213)
Q Consensus       163 ~~yi~R~GR~--~~~~g~~i~~~~~~  186 (213)
                      ..|+||+||+  .|+.|.|+.++.+.
T Consensus       897 ~~l~Qr~GRvgR~g~~g~~~ll~~~~  922 (1151)
T 2eyq_A          897 AQLHQLRGRVGRSHHQAYAWLLTPHP  922 (1151)
T ss_dssp             HHHHHHHTTCCBTTBCEEEEEEECCG
T ss_pred             HHHHHHHhccCcCCCceEEEEEECCc
Confidence            9999999997  45679999988764

>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=99.72  E-value=7.1e-17  Score=152.92  Aligned_cols=139  Identities=15%  Similarity=0.159  Sum_probs=115.9

Q ss_pred             chHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccccccc
Q 028124           33 QFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVT  112 (213)
Q Consensus        33 ~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~  112 (213)
                      ..|+..|..+++.+..  ..+.++||||++...++.+...|...+ +.+..+||+++..+|.+++++|+++.        
T Consensus       398 s~K~~~l~~ll~~~~~--~~~~k~lIFs~~~~~~~~l~~~l~~~g-~~~~~l~G~~~~~~R~~~i~~F~~~~--------  466 (644)
T 1z3i_X          398 SGKMLVLDYILAMTRT--TTSDKVVLVSNYTQTLDLFEKLCRNRR-YLYVRLDGTMSIKKRAKIVERFNNPS--------  466 (644)
T ss_dssp             SHHHHHHHHHHHHHHH--HCCCEEEEEESCHHHHHHHHHHHHHHT-CCEEEECSSCCHHHHHHHHHHHHSTT--------
T ss_pred             ChHHHHHHHHHHHHhh--cCCCEEEEEEccHHHHHHHHHHHHHCC-CCEEEEeCCCCHHHHHHHHHHhcCCC--------
Confidence            4589999888876432  346899999999999999999999887 89999999999999999999999974        


Q ss_pred             ccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCC--CCeEEEEEeCc--
Q 028124          113 EQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAA--DGSVINIVVGG--  186 (213)
Q Consensus       113 ~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~--~g~~i~~~~~~--  186 (213)
                                  .....+|++|++    +++|+|++.+++||+||+||++..|.||+||+  .|+  ...++.|+..+  
T Consensus       467 ------------~~~~v~L~st~a----~g~Glnl~~a~~Vi~~d~~wnp~~~~Qa~gR~~R~Gq~~~v~v~~lv~~~ti  530 (644)
T 1z3i_X          467 ------------SPEFIFMLSSKA----GGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTGTI  530 (644)
T ss_dssp             ------------CCCCEEEEEGGG----SCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEEEEEETTSH
T ss_pred             ------------CCcEEEEEeccc----ccCCcccccCCEEEEECCCCCccHHHHHHHhhhhcCCCCceEEEEEEECCCH
Confidence                        001358999999    99999999999999999999999999999996  343  35778888876  


Q ss_pred             hhHHHHHHHHHh
Q 028124          187 EVVTLRSMEESL  198 (213)
Q Consensus       187 e~~~~~~le~~l  198 (213)
                      |...+...+.+.
T Consensus       531 Ee~i~~~~~~K~  542 (644)
T 1z3i_X          531 EEKILQRQAHKK  542 (644)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            555566655554

>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=99.72  E-value=2.5e-17  Score=156.87  Aligned_cols=137  Identities=17%  Similarity=0.176  Sum_probs=107.9

Q ss_pred             HHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc--C---------------------------CceEEEec
Q 028124           35 KMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL--A---------------------------DISFSSLH   85 (213)
Q Consensus        35 K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~--~---------------------------~~~~~~lh   85 (213)
                      +.+.+.+.++       +++++||||++++.++.++..|...  .                           ...+..+|
T Consensus       231 ~~~~~~~~~~-------~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~i~~~~~~~~~~~l~~~~~~~v~~~h  303 (702)
T 2p6r_A          231 FEELVEECVA-------ENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHH  303 (702)
T ss_dssp             HHHHHHHHHH-------TTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEEC
T ss_pred             HHHHHHHHHh-------cCCCEEEEcCCHHHHHHHHHHHHHHHHhhcChHHHHHHHHhhccccccHHHHHHHhcCeEEec
Confidence            4555555543       3689999999999999999998742  0                           02477899


Q ss_pred             CCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEE----ec---C
Q 028124           86 SDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLIN----YE---L  158 (213)
Q Consensus        86 g~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~----yd---~  158 (213)
                      |+|++++|..+++.|++|.                       +++||||++    +++|+|+|++++||+    ||   .
T Consensus       304 ~~l~~~~R~~v~~~f~~g~-----------------------~~vlvaT~~----l~~Gidip~~~~VI~~~~~yd~~~~  356 (702)
T 2p6r_A          304 AGLLNGQRRVVEDAFRRGN-----------------------IKVVVATPT----LAAGVNLPARRVIVRSLYRFDGYSK  356 (702)
T ss_dssp             TTSCHHHHHHHHHHHHTTS-----------------------CCEEEECST----TTSSSCCCBSEEEECCSEEESSSEE
T ss_pred             CCCCHHHHHHHHHHHHCCC-----------------------CeEEEECcH----HhccCCCCceEEEEcCceeeCCCCC
Confidence            9999999999999999985                       999999999    999999999999999    77   7


Q ss_pred             CCChHHHHHhhccccC----CCCeEEEEEeCchhHHHHHHHHHhcccccccCc
Q 028124          159 PTKKETYIRRMTTCLA----ADGSVINIVVGGEVVTLRSMEESLGLIVAEVPI  207 (213)
Q Consensus       159 P~~~~~yi~R~GR~~~----~~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~  207 (213)
                      |.+..+|.||+||+|+    ..|.|+.+++..+..  ..+++++....+++..
T Consensus       357 ~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~~~--~~~~~~l~~~~e~~~s  407 (702)
T 2p6r_A          357 RIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDRE--IAVKRYIFGEPERITS  407 (702)
T ss_dssp             ECCHHHHHHHHTTBSCTTTCSCEEEEEECCGGGHH--HHHHTTTSSCCCCCCC
T ss_pred             cCCHHHHHHHhhhcCCCCCCCCceEEEEecCccHH--HHHHHHhcCCCCCcee
Confidence            8999999999999864    368999999887632  2233444444444433

>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=99.72  E-value=2.3e-17  Score=164.65  Aligned_cols=116  Identities=19%  Similarity=0.192  Sum_probs=94.4

Q ss_pred             CCCCcEEEEeCchHHHHHHHHHHhccCCce---------------------------------------EEEecCCCCHH
Q 028124           51 RPGLPMIVCCSSRDELDAVCSAVSNLADIS---------------------------------------FSSLHSDLAET   91 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~---------------------------------------~~~lhg~~~~~   91 (213)
                      ....++||||+++..|+.++..|...+ +.                                       +..+||+|++.
T Consensus       439 ~~~~~vIVF~~sr~~~e~la~~L~~~~-~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gV~~~Hg~l~~~  517 (1108)
T 3l9o_A          439 KKYNPVIVFSFSKRDCEELALKMSKLD-FNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPI  517 (1108)
T ss_dssp             TTCCCEEEEESCHHHHHHHHHHTCSHH-HHCC----CHHHHGGGSCTHHHHHTTCCHHHHHHTHHHHHTEEEECSCSCHH
T ss_pred             cCCCCEEEEeCcHHHHHHHHHHHHhcc-CCCHHHHHHHHHHHHHHHhhcchhhhhhhhHHHHHHhhhcCeeeecCCCCHH
Confidence            456799999999999999999986532 11                                       78999999999


Q ss_pred             HHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCC--------ChH
Q 028124           92 ERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPT--------KKE  163 (213)
Q Consensus        92 ~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~--------~~~  163 (213)
                      +|..+++.|++|.                       ++|||||++    +++|+|+|++++||+|+.|+        ++.
T Consensus       518 ~R~~v~~~F~~G~-----------------------ikVLVAT~v----la~GIDiP~v~~VI~~~~~~d~~~~r~iS~~  570 (1108)
T 3l9o_A          518 LKEVIEILFQEGF-----------------------LKVLFATET----FSIGLNMPAKTVVFTSVRKWDGQQFRWVSGG  570 (1108)
T ss_dssp             HHHHHHHHHHHTC-----------------------CCEEEEESC----CCSCCCC--CEEEESCSEEESSSCEEECCHH
T ss_pred             HHHHHHHHHhCCC-----------------------CeEEEECcH----HhcCCCCCCceEEEecCcccCccccccCCHH
Confidence            9999999999985                       999999999    99999999999999877644        667


Q ss_pred             HHHHhhccccC----CCCeEEEEEeCc-hhHHHHHH
Q 028124          164 TYIRRMTTCLA----ADGSVINIVVGG-EVVTLRSM  194 (213)
Q Consensus       164 ~yi~R~GR~~~----~~g~~i~~~~~~-e~~~~~~l  194 (213)
                      .|+||+||+|+    ..|.|+.++.+. +...+..+
T Consensus       571 eyiQr~GRAGR~G~d~~G~~ill~~~~~~~~~~~~l  606 (1108)
T 3l9o_A          571 EYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGM  606 (1108)
T ss_dssp             HHHHHHHHSCCSSSCSSEEEEEEECCCCCHHHHHHH
T ss_pred             HHHHhhcccCCCCCCCceEEEEEecCCcCHHHHHHH
Confidence            89999999753    358888888765 33333333

>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=99.71  E-value=1.4e-17  Score=151.33  Aligned_cols=99  Identities=11%  Similarity=0.037  Sum_probs=89.1

Q ss_pred             CCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEE
Q 028124           53 GLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIV  132 (213)
Q Consensus        53 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV  132 (213)
                      .+++||||++++.++.+++.|+..+ +.+..+||++.    .+++++|++|+                       .++||
T Consensus       188 ~~~~lVF~~s~~~a~~l~~~L~~~g-~~~~~lh~~~~----~~~~~~f~~g~-----------------------~~vLV  239 (451)
T 2jlq_A          188 QGKTVWFVPSIKAGNDIANCLRKSG-KRVIQLSRKTF----DTEYPKTKLTD-----------------------WDFVV  239 (451)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHTTT-CCEEEECTTTH----HHHGGGGGSSC-----------------------CSEEE
T ss_pred             CCCEEEEcCCHHHHHHHHHHHHHcC-CeEEECCHHHH----HHHHHhhccCC-----------------------ceEEE
Confidence            5699999999999999999999987 89999999753    57899999985                       99999


Q ss_pred             EeCCCCCcCcCCCCCCCCCEEEEec--------------------CCCChHHHHHhhcccc--CC-CCeEEEEEe
Q 028124          133 VTDACLPLLSSGESAISARVLINYE--------------------LPTKKETYIRRMTTCL--AA-DGSVINIVV  184 (213)
Q Consensus       133 ~Td~~~~~~~rGld~~~v~~VI~yd--------------------~P~~~~~yi~R~GR~~--~~-~g~~i~~~~  184 (213)
                      ||++    +++|+|+|+ ++|||||                    .|.+.++|+||+||+|  |+ .|.++.|..
T Consensus       240 aT~v----~~~GiDip~-~~VI~~~~~~~~~~d~~~~~~l~~~~~~p~s~~~y~Qr~GRaGR~g~~~g~~~~~~~  309 (451)
T 2jlq_A          240 TTDI----SEMGANFRA-GRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSG  309 (451)
T ss_dssp             ECGG----GGSSCCCCC-SEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECS
T ss_pred             ECCH----HHhCcCCCC-CEEEECCCcccccccccccceeeecccccCCHHHHHHhccccCCCCCCCccEEEEeC
Confidence            9999    999999999 9999999                    9999999999999974  44 678888864

>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=99.71  E-value=5.5e-18  Score=161.03  Aligned_cols=120  Identities=19%  Similarity=0.241  Sum_probs=100.0

Q ss_pred             CCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEE
Q 028124           52 PGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMI  131 (213)
Q Consensus        52 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iL  131 (213)
                      ..+++||||++++.++.+++.|+..+ +.+..+||+|++++       |+++                       ..++|
T Consensus       395 ~~~~vLVFv~Tr~~ae~la~~L~~~g-~~v~~lHG~l~q~e-------r~~~-----------------------~~~VL  443 (666)
T 3o8b_A          395 RGGRHLIFCHSKKKCDELAAKLSGLG-INAVAYYRGLDVSV-------IPTI-----------------------GDVVV  443 (666)
T ss_dssp             SSSEEEEECSCHHHHHHHHHHHHTTT-CCEEEECTTSCGGG-------SCSS-----------------------SCEEE
T ss_pred             cCCcEEEEeCCHHHHHHHHHHHHhCC-CcEEEecCCCCHHH-------HHhC-----------------------CCcEE
Confidence            56899999999999999999999987 89999999999875       3444                       26999


Q ss_pred             EEeCCCCCcCcCCCCCCCCCEEE----------Eec-----------CCCChHHHHHhhcccc-CCCCeEEEEEeCchhH
Q 028124          132 VVTDACLPLLSSGESAISARVLI----------NYE-----------LPTKKETYIRRMTTCL-AADGSVINIVVGGEVV  189 (213)
Q Consensus       132 V~Td~~~~~~~rGld~~~v~~VI----------~yd-----------~P~~~~~yi~R~GR~~-~~~g~~i~~~~~~e~~  189 (213)
                      ||||+    ++||+|++ +++||          |||           +|.+.++|+||+||+| ++.|. +.|+++.+..
T Consensus       444 VATdV----aerGIDId-V~~VI~~Gl~~~~ViNyDydP~~gl~~~~~P~s~~syiQRiGRtGRg~~G~-i~lvt~~e~~  517 (666)
T 3o8b_A          444 VATDA----LMTGYTGD-FDSVIDCNTCVTQTVDFSLDPTFTIETTTVPQDAVSRSQRRGRTGRGRRGI-YRFVTPGERP  517 (666)
T ss_dssp             EECTT----HHHHCCCC-BSEEEECCEEEEEEEECCCSSSCEEEEEEEECBHHHHHHHHTTBCSSSCEE-EEESCCCCBC
T ss_pred             EECCh----HHccCCCC-CcEEEecCcccccccccccccccccccccCcCCHHHHHHHhccCCCCCCCE-EEEEecchhh
Confidence            99999    99999986 99988          788           9999999999999976 45588 9999877655


Q ss_pred             H--H--HHHHHHhcccccccCcc
Q 028124          190 T--L--RSMEESLGLIVAEVPIN  208 (213)
Q Consensus       190 ~--~--~~le~~l~~~~~~~~~~  208 (213)
                      .  +  ..+++..+..+.+..++
T Consensus       518 ~~~l~~~~i~~~~~~~~~~~~l~  540 (666)
T 3o8b_A          518 SGMFDSSVLCECYDAGCAWYELT  540 (666)
T ss_dssp             SSBCCHHHHHHHHHHHHHTSCCC
T ss_pred             cccccHHHHHHHhcCCcccccCC
Confidence            4  3  67777776666655544

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.70  E-value=1.2e-16  Score=152.50  Aligned_cols=117  Identities=16%  Similarity=0.248  Sum_probs=97.3

Q ss_pred             CcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEE
Q 028124           54 LPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVV  133 (213)
Q Consensus        54 ~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~  133 (213)
                      ...||||++++.++.+++.|...+ +.+..+||+|++++|.++++.|++++                     ++.+||||
T Consensus       321 ~g~iIf~~s~~~ie~la~~L~~~g-~~v~~lHG~L~~~~R~~~~~~F~~~~---------------------g~~~VLVA  378 (677)
T 3rc3_A          321 PGDCIVCFSKNDIYSVSRQIEIRG-LESAVIYGSLPPGTKLAQAKKFNDPN---------------------DPCKILVA  378 (677)
T ss_dssp             TTEEEECSSHHHHHHHHHHHHHTT-CCCEEECTTSCHHHHHHHHHHHHCTT---------------------SSCCEEEE
T ss_pred             CCCEEEEcCHHHHHHHHHHHHhcC-CCeeeeeccCCHHHHHHHHHHHHccC---------------------CCeEEEEe
Confidence            455899999999999999999887 89999999999999999999999822                     24999999


Q ss_pred             eCCCCCcCcCCCCCCCCCEEEEecC--------------CCChHHHHHhhccccCCC-----CeEEEEEeCchhHHHHHH
Q 028124          134 TDACLPLLSSGESAISARVLINYEL--------------PTKKETYIRRMTTCLAAD-----GSVINIVVGGEVVTLRSM  194 (213)
Q Consensus       134 Td~~~~~~~rGld~~~v~~VI~yd~--------------P~~~~~yi~R~GR~~~~~-----g~~i~~~~~~e~~~~~~l  194 (213)
                      |++    +++|+|+ ++++||+|++              |.+.++|+||+||+|+..     |.|+.+ ...+...+.++
T Consensus       379 Tdi----~e~GlDi-~v~~VI~~~~~k~~~~~~G~~~~~p~s~~~~~QR~GRAGR~g~~g~~G~v~~l-~~~d~~~~~~~  452 (677)
T 3rc3_A          379 TDA----IGMGLNL-SIRRIIFYSLIKPSINEKGERELEPITTSQALQIAGRAGRFSSRFKEGEVTTM-NHEDLSLLKEI  452 (677)
T ss_dssp             CGG----GGSSCCC-CBSEEEESCSBC-----------CBCCHHHHHHHHTTBTCTTSSCSSEEEEES-STTHHHHHHHH
T ss_pred             CcH----HHCCcCc-CccEEEECCccccccccCCccccccCCHHHHHHHhcCCCCCCCCCCCEEEEEE-ecchHHHHHHH
Confidence            999    9999999 9999999999              889999999999975433     555555 44455555555


Q ss_pred             HHHh
Q 028124          195 EESL  198 (213)
Q Consensus       195 e~~l  198 (213)
                      ....
T Consensus       453 ~~~~  456 (677)
T 3rc3_A          453 LKRP  456 (677)
T ss_dssp             HHSC
T ss_pred             HhcC
Confidence            4433

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=99.69  E-value=1.5e-16  Score=153.88  Aligned_cols=140  Identities=17%  Similarity=0.219  Sum_probs=120.2

Q ss_pred             chHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccccccc
Q 028124           33 QFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVT  112 (213)
Q Consensus        33 ~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~  112 (213)
                      ..|+..|.++|..+.   ..+.++||||+....++.|...|...| +.+..+||+++..+|.+++++|+++.        
T Consensus       555 s~K~~~L~~lL~~~~---~~g~kvLIFsq~~~~ld~L~~~L~~~g-~~~~~i~G~~~~~eR~~~i~~F~~~~--------  622 (800)
T 3mwy_W          555 SGKMVLLDQLLTRLK---KDGHRVLIFSQMVRMLDILGDYLSIKG-INFQRLDGTVPSAQRRISIDHFNSPD--------  622 (800)
T ss_dssp             CHHHHHHHHHHHHHT---TTTCCEEEEESCHHHHHHHHHHHHHHT-CCCEEESTTSCHHHHHHHHHTTSSTT--------
T ss_pred             ChHHHHHHHHHHHHh---hCCCeEEEEechHHHHHHHHHHHHhCC-CCEEEEeCCCCHHHHHHHHHHhhCCC--------
Confidence            349999999998853   367899999999999999999999887 89999999999999999999999864        


Q ss_pred             ccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhcccc--CC--CCeEEEEEeCc--
Q 028124          113 EQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL--AA--DGSVINIVVGG--  186 (213)
Q Consensus       113 ~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~--~~--~g~~i~~~~~~--  186 (213)
                                  ++...+|++|.+    ++.|+|++.+++||+||+||++..++||+||+.  |+  ...++.|++.+  
T Consensus       623 ------------~~~~v~LlSt~a----gg~GlNL~~a~~VI~~D~~wnp~~~~Qa~gR~~RiGQ~k~V~Vyrlv~~~Ti  686 (800)
T 3mwy_W          623 ------------SNDFVFLLSTRA----GGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTV  686 (800)
T ss_dssp             ------------CSCCCEEEEHHH----HTTTCCCTTCCEEEESSCCSCSHHHHHHHTTTSCSSCCSCEEEEEEEETTSH
T ss_pred             ------------CCceEEEEeccc----ccCCCCccccceEEEecCCCChhhHHHHHHHHHhcCCCceEEEEEEecCCCH
Confidence                        112469999999    999999999999999999999999999999963  33  36778888876  


Q ss_pred             hhHHHHHHHHHhcc
Q 028124          187 EVVTLRSMEESLGL  200 (213)
Q Consensus       187 e~~~~~~le~~l~~  200 (213)
                      |...++..++.+..
T Consensus       687 Ee~i~~~~~~K~~l  700 (800)
T 3mwy_W          687 EEEVLERARKKMIL  700 (800)
T ss_dssp             HHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHHHH
Confidence            66777777776643

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.69  E-value=7.3e-17  Score=147.39  Aligned_cols=108  Identities=10%  Similarity=0.084  Sum_probs=94.3

Q ss_pred             HHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccccccccc
Q 028124           35 KMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ  114 (213)
Q Consensus        35 K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~  114 (213)
                      |.+.+.+++.....  ..+.++||||+ ...++.+++.|...+ ..+..+||+|++.+|.+++++|++|+          
T Consensus       332 ~~~~l~~~l~~~~~--~~~~~~ivf~~-~~~~~~l~~~L~~~~-~~v~~~~g~~~~~~r~~i~~~f~~g~----------  397 (510)
T 2oca_A          332 RNKWIAKLAIKLAQ--KDENAFVMFKH-VSHGKAIFDLIKNEY-DKVYYVSGEVDTETRNIMKTLAENGK----------  397 (510)
T ss_dssp             HHHHHHHHHHHHHT--TTCEEEEEESS-HHHHHHHHHHHHTTC-SSEEEESSSTTHHHHHHHHHHHHHCC----------
T ss_pred             HHHHHHHHHHHHHh--cCCCeEEEEec-HHHHHHHHHHHHHcC-CCeEEEECCCCHHHHHHHHHHHhCCC----------
Confidence            55667777766432  34567777777 888999999999887 59999999999999999999999985          


Q ss_pred             CCCCCcCCCCCCceeEEEEe-CCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhcccc
Q 028124          115 SGDESETGKDEHKSHMIVVT-DACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL  173 (213)
Q Consensus       115 ~~~~~~~~~~~~~~~iLV~T-d~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~  173 (213)
                                   .++|||| ++    +++|+|+|++++||++++|+++..|+||+||++
T Consensus       398 -------------~~vLv~T~~~----~~~GiDip~v~~vi~~~~~~s~~~~~Q~~GR~g  440 (510)
T 2oca_A          398 -------------GIIIVASYGV----FSTGISVKNLHHVVLAHGVKSKIIVLQTIGRVL  440 (510)
T ss_dssp             -------------SCEEEEEHHH----HHHSCCCCSEEEEEESSCCCSCCHHHHHHHHHH
T ss_pred             -------------CCEEEEEcCh----hhcccccccCcEEEEeCCCCCHHHHHHHHhccc
Confidence                         8999999 99    999999999999999999999999999999963

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.68  E-value=1.3e-16  Score=157.74  Aligned_cols=135  Identities=16%  Similarity=0.203  Sum_probs=106.4

Q ss_pred             EEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCc-------------------------
Q 028124           25 FYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADI-------------------------   79 (213)
Q Consensus        25 ~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~-------------------------   79 (213)
                      ++...... .++..|.+.+..     ....++||||++++.|+.++..|...+ +                         
T Consensus       314 ~~~~~~~~-~~~~~li~~l~~-----~~~~~~IVF~~sr~~~e~la~~L~~~~-~~~~~e~~~i~~~~~~~~~~l~~~d~  386 (997)
T 4a4z_A          314 FTQDGPSK-KTWPEIVNYLRK-----RELLPMVVFVFSKKRCEEYADWLEGIN-FCNNKEKSQIHMFIEKSITRLKKEDR  386 (997)
T ss_dssp             ---CCCCT-THHHHHHHHHHH-----TTCCSEEEECSCHHHHHHHHHTTTTCC-CCCHHHHHHHHHHHHHHHTTSCHHHH
T ss_pred             ccccccch-hHHHHHHHHHHh-----CCCCCEEEEECCHHHHHHHHHHHhcCC-CCCHHHHHHHHHHHHHHHHhcchhhh
Confidence            33333443 478888888876     456899999999999999999997654 3                         


Q ss_pred             --------------eEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCC
Q 028124           80 --------------SFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGE  145 (213)
Q Consensus        80 --------------~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGl  145 (213)
                                    .+..+||+|++.+|..+++.|+.|.                       ++|||||++    +++|+
T Consensus       387 ~l~~~~~l~~~l~~gi~~~H~gl~~~~R~~v~~~F~~G~-----------------------~kVLvAT~~----~a~GI  439 (997)
T 4a4z_A          387 DLPQILKTRSLLERGIAVHHGGLLPIVKELIEILFSKGF-----------------------IKVLFATET----FAMGL  439 (997)
T ss_dssp             TCHHHHHHHHHHTTTEEEECTTSCHHHHHHHHHHHHTTC-----------------------CSEEEECTH----HHHSC
T ss_pred             cchhHHHHHHHhhcCeeeecCCCCHHHHHHHHHHHHCCC-----------------------CcEEEEchH----hhCCC
Confidence                          3789999999999999999999985                       999999999    99999


Q ss_pred             CCCCCCEEEEecCCC---------ChHHHHHhhccccC----CCCeEEEEEe--CchhHHHHHH
Q 028124          146 SAISARVLINYELPT---------KKETYIRRMTTCLA----ADGSVINIVV--GGEVVTLRSM  194 (213)
Q Consensus       146 d~~~v~~VI~yd~P~---------~~~~yi~R~GR~~~----~~g~~i~~~~--~~e~~~~~~l  194 (213)
                      |+|+ ..||++++|.         +...|+||+||+|+    ..|.||.++.  ..+...++.+
T Consensus       440 DiP~-~~VVi~~~~k~dg~~~~~~s~~~y~Qr~GRAGR~G~~~~G~vi~l~~~~~~~~~~~~~~  502 (997)
T 4a4z_A          440 NLPT-RTVIFSSIRKHDGNGLRELTPGEFTQMAGRAGRRGLDSTGTVIVMAYNSPLSIATFKEV  502 (997)
T ss_dssp             CCCC-SEEEESCSEEEETTEEEECCHHHHHHHHGGGCCTTTCSSEEEEEECCSSCCCHHHHHHH
T ss_pred             CCCC-ceEEEeccccccCccCCCCCHHHHhHHhcccccCCCCcceEEEEecCCCcchHHHHHHH
Confidence            9999 5566555555         99999999999865    3578888873  2344455444

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.68  E-value=1.8e-16  Score=147.77  Aligned_cols=99  Identities=13%  Similarity=0.161  Sum_probs=83.8

Q ss_pred             CCCCcEEEEeCchHHHHHHHHHHhccC-------CceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCC
Q 028124           51 RPGLPMIVCCSSRDELDAVCSAVSNLA-------DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGK  123 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~~L~~~~-------~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~  123 (213)
                      ....++||||+++++|+.+++.|...+       .-.+..+||++++ +|.+++++|++++.                  
T Consensus       437 ~~~~k~lVF~~~~~~a~~l~~~L~~~~~~~~~~~~~~~~~i~g~~~~-~r~~~l~~F~~~~~------------------  497 (590)
T 3h1t_A          437 DRFAKTIVFCVDQEHADEMRRALNNLNSDLSRKHPDYVARVTSEEGK-IGKGHLSRFQELET------------------  497 (590)
T ss_dssp             CTTSEEEEEESSHHHHHHHHHHHHHHTHHHHTTCTTSEEECSSTTHH-HHHHHHHHHHCTTC------------------
T ss_pred             CCCccEEEEECCHHHHHHHHHHHHHhhhhhhccCCCeEEEEeCCChH-HHHHHHHHHhCCCC------------------
Confidence            456899999999999999999997652       0137889999864 79999999999740                  


Q ss_pred             CCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccccC
Q 028124          124 DEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLA  174 (213)
Q Consensus       124 ~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~~  174 (213)
                        +...+||||++    +++|+|+|++++||+|++|++...|+||+||+++
T Consensus       498 --~~~~ilvtt~~----l~~GiDip~v~~Vi~~~~~~s~~~~~Q~iGR~~R  542 (590)
T 3h1t_A          498 --STPVILTTSQL----LTTGVDAPTCKNVVLARVVNSMSEFKQIVGRGTR  542 (590)
T ss_dssp             --CCCCEEEESST----TTTTCCCTTEEEEEEESCCCCHHHHHHHHTTSCC
T ss_pred             --CCCEEEEECCh----hhcCccchheeEEEEEecCCChHHHHHHHhhhcc
Confidence              01238999999    9999999999999999999999999999999744

>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=99.67  E-value=1.8e-17  Score=160.19  Aligned_cols=122  Identities=11%  Similarity=0.132  Sum_probs=99.6

Q ss_pred             HHHHHHHHHHHhhcCCCCCCcEEEEeCch--------HHHHHHHHHHhc-c-CCceEEEecCCCCHHHHHHHHHHHhccc
Q 028124           35 KMETLVELLHLVVAGRRPGLPMIVCCSSR--------DELDAVCSAVSN-L-ADISFSSLHSDLAETERTLILEEFRHTA  104 (213)
Q Consensus        35 K~~~L~~ll~~~~~~~~~~~~~IIF~~~~--------~~~~~l~~~L~~-~-~~~~~~~lhg~~~~~~R~~~l~~Fr~g~  104 (213)
                      +...+.+.+...   ...+.+++|||++.        ..++.+++.|.. . +++.+..+||+|++++|..++++|++|+
T Consensus       563 ~~~~l~~~i~~~---l~~g~qvlVf~~~ie~se~l~~~~a~~l~~~L~~~~~~~~~v~~lHG~m~~~eR~~v~~~F~~G~  639 (780)
T 1gm5_A          563 RVNEVYEFVRQE---VMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGR  639 (780)
T ss_dssp             THHHHHHHHHHH---TTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTS
T ss_pred             hHHHHHHHHHHH---HhcCCcEEEEecchhhhhhhhHHHHHHHHHHHHhhhcCCCcEEEEeCCCCHHHHHHHHHHHHCCC
Confidence            334444555432   23578999999965        457889999987 2 2378999999999999999999999985


Q ss_pred             ccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCC-ChHHHHHhhccc--cCCCCeEEE
Q 028124          105 MKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPT-KKETYIRRMTTC--LAADGSVIN  181 (213)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~-~~~~yi~R~GR~--~~~~g~~i~  181 (213)
                                             .+|||||++    +++|+|+|++++||+||.|+ +.+.|.||+||+  +|+.|.|+.
T Consensus       640 -----------------------~~ILVaT~v----ie~GIDiP~v~~VIi~d~~r~~l~~l~Qr~GRaGR~g~~g~~il  692 (780)
T 1gm5_A          640 -----------------------YDILVSTTV----IEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFL  692 (780)
T ss_dssp             -----------------------SSBCCCSSC----CCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEEC
T ss_pred             -----------------------CeEEEECCC----CCccccCCCCCEEEEeCCCCCCHHHHHHHhcccCcCCCCCEEEE
Confidence                                   999999999    99999999999999999997 688899999997  467799999


Q ss_pred             EEeCc
Q 028124          182 IVVGG  186 (213)
Q Consensus       182 ~~~~~  186 (213)
                      ++.+.
T Consensus       693 l~~~~  697 (780)
T 1gm5_A          693 VVGDV  697 (780)
T ss_dssp             CCCSC
T ss_pred             EECCC
Confidence            98743

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.66  E-value=2.6e-16  Score=142.33  Aligned_cols=98  Identities=8%  Similarity=-0.004  Sum_probs=85.8

Q ss_pred             CCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEE
Q 028124           53 GLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIV  132 (213)
Q Consensus        53 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV  132 (213)
                      .+++||||++++.++.+++.|+..+ +.+..+||+    +|.+++++|++|+                       .++||
T Consensus       171 ~~~~lVF~~~~~~~~~l~~~L~~~~-~~v~~lhg~----~r~~~~~~f~~g~-----------------------~~vLV  222 (431)
T 2v6i_A          171 DGRTVWFVHSIKQGAEIGTCLQKAG-KKVLYLNRK----TFESEYPKCKSEK-----------------------WDFVI  222 (431)
T ss_dssp             SSCEEEECSSHHHHHHHHHHHHHTT-CCEEEESTT----THHHHTTHHHHSC-----------------------CSEEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHcC-CeEEEeCCc----cHHHHHHhhcCCC-----------------------CeEEE
Confidence            5689999999999999999999886 899999997    5788999999985                       99999


Q ss_pred             EeCCCCCcCcCCCCCCCCCE-----------------EEEecCCCChHHHHHhhccccCC---CCeEEEEE
Q 028124          133 VTDACLPLLSSGESAISARV-----------------LINYELPTKKETYIRRMTTCLAA---DGSVINIV  183 (213)
Q Consensus       133 ~Td~~~~~~~rGld~~~v~~-----------------VI~yd~P~~~~~yi~R~GR~~~~---~g~~i~~~  183 (213)
                      ||++    +++|+|+| +.+                 ||+|+.|.+.++|+||+||+|+.   .|.++.+.
T Consensus       223 aT~v----~e~GiDip-~~~VI~~g~~~~~v~d~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~~~~~~~~  288 (431)
T 2v6i_A          223 TTDI----SEMGANFK-ADRVIDPRKTIKPILLDGRVSMQGPIAITPASAAQRRGRIGRNPEKLGDIYAYS  288 (431)
T ss_dssp             ECGG----GGTSCCCC-CSEEEECCEEEEEEEETTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCCEEEEC
T ss_pred             ECch----HHcCcccC-CcEEEecCccccceecccceeecccccCCHHHHHHhhhccCCCCCCCCeEEEEc
Confidence            9999    99999999 544                 68999999999999999997543   35556555

>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=99.49  E-value=1.2e-13  Score=142.87  Aligned_cols=148  Identities=18%  Similarity=0.254  Sum_probs=111.5

Q ss_pred             CCceEEEEEecCcc--hHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc----C----------------
Q 028124           20 SQPRHFYVAVDRLQ--FKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL----A----------------   77 (213)
Q Consensus        20 ~~i~~~~~~~~~~~--~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~----~----------------   77 (213)
                      -.+++.++.+....  .+.+.+.+.+..........+++||||+|++.|+.+|..|...    +                
T Consensus       282 vpL~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~LVF~~sR~~~~~~A~~l~~~~~~~~~~~~~~~~~~~~~~~~  361 (1724)
T 4f92_B          282 VPLEQTYVGITEKKAIKRFQIMNEIVYEKIMEHAGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVL  361 (1724)
T ss_dssp             SCEEEECCEECCCCHHHHHHHHHHHHHHHHTTCCSSCCEEEECSSTTTTHHHHHHHHHHHHHTTSTTCCSSCCTTCSSHH
T ss_pred             CccEEEEeccCCcchhhhhHHHHHHHHHHHHHHhcCCcEEEECCCHHHHHHHHHHHHHHHhhccchhhhcccchhHHHHH
Confidence            34677766665442  2333444443322222345679999999999999988887532    0                


Q ss_pred             ----------------CceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcC
Q 028124           78 ----------------DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLL  141 (213)
Q Consensus        78 ----------------~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~  141 (213)
                                      ...+..+||+|++++|..+.+.|++|.                       +++||||+.    +
T Consensus       362 ~~~~~~~~~~~l~~~l~~Gva~HHagL~~~~R~~vE~~F~~G~-----------------------i~vlvaTsT----L  414 (1724)
T 4f92_B          362 RTEAEQCKNLELKDLLPYGFAIHHAGMTRVDRTLVEDLFADKH-----------------------IQVLVSTAT----L  414 (1724)
T ss_dssp             HHTTSCCSTHHHHHHTTTTEEEECSSSCTHHHHHHHHHHHTTC-----------------------CCEEEECHH----H
T ss_pred             HhhhcccccHHHHHHhhcCEEEEcCCCCHHHHHHHHHHHHCCC-----------------------CeEEEEcch----h
Confidence                            013788999999999999999999985                       999999999    9


Q ss_pred             cCCCCCCCCCEEEE----ecC------CCChHHHHHhhccccCC----CCeEEEEEeCchhHHHHHH
Q 028124          142 SSGESAISARVLIN----YEL------PTKKETYIRRMTTCLAA----DGSVINIVVGGEVVTLRSM  194 (213)
Q Consensus       142 ~rGld~~~v~~VI~----yd~------P~~~~~yi~R~GR~~~~----~g~~i~~~~~~e~~~~~~l  194 (213)
                      +.|+|+|..++||.    ||.      |-++.+|.||+||+|+.    .|.+|.++...+...+..+
T Consensus       415 a~GVNlPa~~vVI~~~~~~~~~~~~~~~ls~~~~~Qm~GRAGR~g~d~~G~~ii~~~~~~~~~~~~l  481 (1724)
T 4f92_B          415 AWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQYDTKGEGILITSHGELQYYLSL  481 (1724)
T ss_dssp             HHHSCCCBSEEEEECCEEEETTTTEEEECCHHHHHHHHTTBSCTTTCSCEEEEEEEESTTCCHHHHH
T ss_pred             HhhCCCCCceEEEeCCEEecCcCCCcccCCHHHHHHhhhhccCCCCCCccEEEEEecchhHHHHHHH
Confidence            99999999999996    654      45899999999998653    5899999988877666554

>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=99.48  E-value=1.7e-13  Score=141.73  Aligned_cols=117  Identities=19%  Similarity=0.252  Sum_probs=97.6

Q ss_pred             CCCCcEEEEeCchHHHHHHHHHHhcc----C-----------------------------CceEEEecCCCCHHHHHHHH
Q 028124           51 RPGLPMIVCCSSRDELDAVCSAVSNL----A-----------------------------DISFSSLHSDLAETERTLIL   97 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~~L~~~----~-----------------------------~~~~~~lhg~~~~~~R~~~l   97 (213)
                      .+.+++||||++++.|+.++..|...    .                             ...+..+||+|++.+|..+.
T Consensus      1153 ~~~~~~lVF~~sR~~~~~~A~~L~~~~~~~~~~~~~~~~~~~~l~~~l~~~~d~~L~~~l~~GIa~hHagL~~~~R~~VE 1232 (1724)
T 4f92_B         1153 SPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYLHEGLSPMERRLVE 1232 (1724)
T ss_dssp             CSSSCEEEEESSHHHHHHHHHHHHHHHHHTTCTTTTBCSCHHHHHHHHTTCCCHHHHHHHHTTEEEECTTSCHHHHHHHH
T ss_pred             cCCCCeeeeCCCHHHHHHHHHHHHHHHhhccchhhhhcccHHHHHHHHhhcccHHHHHHHhCCEEEECCCCCHHHHHHHH
Confidence            46789999999999999888776431    0                             02378899999999999999


Q ss_pred             HHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEE----e------cCCCChHHHHH
Q 028124           98 EEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLIN----Y------ELPTKKETYIR  167 (213)
Q Consensus        98 ~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~----y------d~P~~~~~yi~  167 (213)
                      +.|++|.                       +++||||+.    +++|+|+|...+||.    |      ..|.+..+|.|
T Consensus      1233 ~lF~~G~-----------------------i~VLvaT~t----lA~GVnlPa~~VVI~~~~~~dg~~~~~~~~s~~~~~Q 1285 (1724)
T 4f92_B         1233 QLFSSGA-----------------------IQVVVASRS----LCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQ 1285 (1724)
T ss_dssp             HHHHHTS-----------------------BCEEEEEGG----GSSSCCCCBSEEEEECSEEEETTTTEEEECCHHHHHH
T ss_pred             HHHHCCC-----------------------CeEEEEChH----HHcCCCCCccEEEEecCccccCcccccCCCCHHHHHH
Confidence            9999985                       999999999    999999999999993    3      34678999999


Q ss_pred             hhccccCC----CCeEEEEEeCchhHHHHHH
Q 028124          168 RMTTCLAA----DGSVINIVVGGEVVTLRSM  194 (213)
Q Consensus       168 R~GR~~~~----~g~~i~~~~~~e~~~~~~l  194 (213)
                      |+||+|+.    .|.|+.++.+.+...++++
T Consensus      1286 m~GRAGR~g~d~~G~avll~~~~~~~~~~~l 1316 (1724)
T 4f92_B         1286 MVGHANRPLQDDEGRCVIMCQGSKKDFFKKF 1316 (1724)
T ss_dssp             HHTTBCCTTTCSCEEEEEEEEGGGHHHHHHH
T ss_pred             hhccccCCCCCCceEEEEEecchHHHHHHHH
Confidence            99998643    5999999998877666554

>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=99.18  E-value=1.2e-10  Score=115.75  Aligned_cols=106  Identities=9%  Similarity=0.128  Sum_probs=85.0

Q ss_pred             CCCcEEEEeCchHHHHHHHHHHhccC-----------CceE-EEecCC----------C----------CHH--------
Q 028124           52 PGLPMIVCCSSRDELDAVCSAVSNLA-----------DISF-SSLHSD----------L----------AET--------   91 (213)
Q Consensus        52 ~~~~~IIF~~~~~~~~~l~~~L~~~~-----------~~~~-~~lhg~----------~----------~~~--------   91 (213)
                      .+.++||||+++..|..+++.|...+           .+++ +.+||+          +          ++.        
T Consensus       536 ~g~kamVf~~S~~~A~~~~~~l~~~~~~~~~~~~~~~~~k~avv~s~~~~~~~~~~G~~~~e~~~~~~~~~~~r~~l~~~  615 (1038)
T 2w00_A          536 KGFNAMLAVSSVDAAKAYYATFKRLQEEAANKSATYKPLRIATIFSFAANEEQNAIGEISDETFDTSAMDSSAKEFLDAA  615 (1038)
T ss_dssp             CCCEEEEEESSHHHHHHHHHHHHHHHHHHTTTSSSCCCCCEEEECCCCC------CCCCCCCCSCGGGSCHHHHHHHHHH
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHhhhhhhcccccccccCcEEEEEeCCCccccccccccccccccccccchhHHHHHHHH
Confidence            34689999999999999999997642           1344 556653          2          221        


Q ss_pred             ---------------------HHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCC
Q 028124           92 ---------------------ERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISA  150 (213)
Q Consensus        92 ---------------------~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v  150 (213)
                                           +|..++++|++|.                       +++||+||+    +.+|+|+|.+
T Consensus       616 I~dyn~~f~~~~~~~~~~~~~~R~~i~~~Fk~g~-----------------------i~ILIvvd~----lltGfDiP~l  668 (1038)
T 2w00_A          616 IREYNSHFKTNFSTDSNGFQNYYRDLAQRVKNQD-----------------------IDLLIVVGM----FLTGFDAPTL  668 (1038)
T ss_dssp             HHHHHHHHTCCCCSSHHHHHHHHHHHHHHHHTTS-----------------------SSEEEESST----TSSSCCCTTE
T ss_pred             HHHHHHHhcccccccchhhhHHHHHHHHHHHcCC-----------------------CeEEEEcch----HHhCcCcccc
Confidence                                 4788999999985                       999999999    9999999999


Q ss_pred             CEEEEecCCCChHHHHHhhccccC--C----CCeEEEEEeC
Q 028124          151 RVLINYELPTKKETYIRRMTTCLA--A----DGSVINIVVG  185 (213)
Q Consensus       151 ~~VI~yd~P~~~~~yi~R~GR~~~--~----~g~~i~~~~~  185 (213)
                       .++++|.|.+...|+||+||+++  .    .|.++.|+..
T Consensus       669 -~tlylDkpl~~~~liQaIGRtnR~~~~~K~~G~IVdf~~~  708 (1038)
T 2w00_A          669 -NTLFVDKNLRYHGLMQAFSRTNRIYDATKTFGNIVTFRDL  708 (1038)
T ss_dssp             -EEEEEESCCCHHHHHHHHHTTCCCCCTTCCSEEEEESSCC
T ss_pred             -cEEEEccCCCccceeehhhccCcCCCCCCCcEEEEEcccc
Confidence             78899999999999999999632  1    2788888864

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=98.28  E-value=2.4e-06  Score=79.14  Aligned_cols=88  Identities=17%  Similarity=0.154  Sum_probs=55.9

Q ss_pred             HHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCC
Q 028124           37 ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG  116 (213)
Q Consensus        37 ~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~  116 (213)
                      +.+.+.|..+..  ...+.++||++|...++.+++.|...    .+..+|..  .+|.+++++|+.+             
T Consensus       370 ~~~~~~l~~~~~--~~~g~~lvff~S~~~~~~v~~~l~~~----~~~~q~~~--~~~~~~l~~f~~~-------------  428 (540)
T 2vl7_A          370 PIYSILLKRIYE--NSSKSVLVFFPSYEMLESVRIHLSGI----PVIEENKK--TRHEEVLELMKTG-------------  428 (540)
T ss_dssp             HHHHHHHHHHHH--TCSSEEEEEESCHHHHHHHHTTCTTS----CEEESTTT--CCHHHHHHHHHTS-------------
T ss_pred             HHHHHHHHHHHH--hCCCCEEEEeCCHHHHHHHHHHhccC----ceEecCCC--CcHHHHHHHHhcC-------------
Confidence            445555554433  34578999999999999999988653    24556654  4688999999885             


Q ss_pred             CCCcCCCCCCceeEEE--EeCCCCCcCcCCCCCCC----CCEEEEecCCC
Q 028124          117 DESETGKDEHKSHMIV--VTDACLPLLSSGESAIS----ARVLINYELPT  160 (213)
Q Consensus       117 ~~~~~~~~~~~~~iLV--~Td~~~~~~~rGld~~~----v~~VI~yd~P~  160 (213)
                                 ..+|+  +|+.    +++|+|+++    +++||++++|.
T Consensus       429 -----------~~il~~V~~~~----~~EGiD~~~~~~~~~~Vii~~lPf  463 (540)
T 2vl7_A          429 -----------KYLVMLVMRAK----ESEGVEFREKENLFESLVLAGLPY  463 (540)
T ss_dssp             -----------CCEEEEEC-------------------CEEEEEEESCCC
T ss_pred             -----------CeEEEEEecCc----eecceecCCCcccccEEEEECCCC
Confidence                       34555  8899    999999997    89999999995

>3hgt_A HDA1 complex subunit 3; RECA-like domain, SWI2/SNF2 helical domain, chromatin regulator, coiled coil, nucleus, repressor, transcription; 2.20A {Saccharomyces cerevisiae} PDB: 3hgq_A

Probab=97.93  E-value=0.00017  Score=63.04  Aligned_cols=119  Identities=10%  Similarity=0.122  Sum_probs=84.1

Q ss_pred             hHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccc
Q 028124           34 FKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTE  113 (213)
Q Consensus        34 ~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~  113 (213)
                      -|+.+|.++|..+.   ..+.+++||++..++.+.+-.+|..++ +...-+.|.....+ .+.    .+.          
T Consensus       109 GKf~~L~~LL~~l~---~~~~kVLIfsq~t~~LDilE~~l~~~~-~~y~RlDG~~~~~~-~k~----~~~----------  169 (328)
T 3hgt_A          109 GKFSVLRDLINLVQ---EYETETAIVCRPGRTMDLLEALLLGNK-VHIKRYDGHSIKSA-AAA----NDF----------  169 (328)
T ss_dssp             HHHHHHHHHHHHHT---TSCEEEEEEECSTHHHHHHHHHHTTSS-CEEEESSSCCC------------CC----------
T ss_pred             ccHHHHHHHHHHHH---hCCCEEEEEECChhHHHHHHHHHhcCC-CceEeCCCCchhhh-hhc----ccC----------
Confidence            49999999998863   467899999999999999999999887 79999999854432 111    121          


Q ss_pred             cCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCC-----CCCCCEEEEecCCCChHH-HHHhhccc------cCCCCeEEE
Q 028124          114 QSGDESETGKDEHKSHMIVVTDACLPLLSSGES-----AISARVLINYELPTKKET-YIRRMTTC------LAADGSVIN  181 (213)
Q Consensus       114 ~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld-----~~~v~~VI~yd~P~~~~~-yi~R~GR~------~~~~g~~i~  181 (213)
                                   ...+.+.|.+    ..-|++     ...++.||-||.-|++.. .+|.+-|+      -++.-.+|-
T Consensus       170 -------------~~~i~Lltsa----g~~gin~~~~nl~~aD~VI~~DsdwNp~~d~iQa~~r~~R~~~gq~k~v~V~R  232 (328)
T 3hgt_A          170 -------------SCTVHLFSSE----GINFTKYPIKSKARFDMLICLDTTVDTSQKDIQYLLQYKRERKGLERYAPIVR  232 (328)
T ss_dssp             -------------SEEEEEEESS----CCCTTTSCCCCCSCCSEEEECSTTCCTTSHHHHHHHCCC---------CCEEE
T ss_pred             -------------CceEEEEECC----CCCCcCcccccCCCCCEEEEECCCCCCCChHHHHHHHHhhhccCCCCcceEEE
Confidence                         2444444555    566675     789999999999998876 46655442      145678899


Q ss_pred             EEeCchh
Q 028124          182 IVVGGEV  188 (213)
Q Consensus       182 ~~~~~e~  188 (213)
                      +++.+.+
T Consensus       233 Lvt~~Ti  239 (328)
T 3hgt_A          233 LVAINSI  239 (328)
T ss_dssp             EEETTSH
T ss_pred             EeCCCCH
Confidence            9987644

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=97.08  E-value=0.0074  Score=59.19  Aligned_cols=44  Identities=16%  Similarity=0.151  Sum_probs=35.2

Q ss_pred             EecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHh
Q 028124           28 AVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVS   74 (213)
Q Consensus        28 ~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~   74 (213)
                      .+.....|+..+.+-+....   ..++|+||+|.|....+.|++.|+
T Consensus       421 vy~t~~~K~~AIv~eI~~~~---~~GqPVLVgT~SIe~SE~LS~~L~  464 (997)
T 2ipc_A          421 VYRTEKGKFYAVVEEIAEKY---ERGQPVLVGTISIEKSERLSQMLK  464 (997)
T ss_dssp             EESSHHHHHHHHHHHHHHHH---HHTCCEEEECSSHHHHHHHHHHHH
T ss_pred             EEcCHHHHHHHHHHHHHHHH---HCCCCEEEEeCCHHHHHHHHHHHh
Confidence            34555669998887776532   357999999999999999999998

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=96.53  E-value=0.0041  Score=58.46  Aligned_cols=77  Identities=23%  Similarity=0.190  Sum_probs=54.2

Q ss_pred             CCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEE
Q 028124           52 PGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMI  131 (213)
Q Consensus        52 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iL  131 (213)
                      ..+.++||+++....+.+++.|+..+ .+   ...+++..+|.+++++|+ +.                       -.+|
T Consensus       447 ~~g~~lvlF~Sy~~l~~v~~~l~~~~-~~---~~q~~~~~~~~~ll~~f~-~~-----------------------~~vL  498 (620)
T 4a15_A          447 VKKNTIVYFPSYSLMDRVENRVSFEH-MK---EYRGIDQKELYSMLKKFR-RD-----------------------HGTI  498 (620)
T ss_dssp             HCSCEEEEESCHHHHHHHTSSCCSCC-EE---CCTTCCSHHHHHHHHHHT-TS-----------------------CCEE
T ss_pred             CCCCEEEEeCCHHHHHHHHHHHHhcc-hh---ccCCCChhHHHHHHHHhc-cC-----------------------CcEE
Confidence            35679999999999999999887322 22   556677778999999999 53                       6799


Q ss_pred             EEeC--CCCCcCcCCCCCCC--CCEEEEecCCC
Q 028124          132 VVTD--ACLPLLSSGESAIS--ARVLINYELPT  160 (213)
Q Consensus       132 V~Td--~~~~~~~rGld~~~--v~~VI~yd~P~  160 (213)
                      +++.  .    +.+|+|+++  .+.||...+|.
T Consensus       499 ~~v~~gs----f~EGiD~~g~~l~~viI~~lPf  527 (620)
T 4a15_A          499 FAVSGGR----LSEGINFPGNELEMIILAGLPF  527 (620)
T ss_dssp             EEETTSC----C--------CCCCEEEESSCCC
T ss_pred             EEEecCc----eeccccCCCCceEEEEEEcCCC
Confidence            9985  6    899999985  66899888774

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19

Probab=95.42  E-value=0.064  Score=51.79  Aligned_cols=82  Identities=12%  Similarity=0.054  Sum_probs=68.7

Q ss_pred             CCCcEEEEeCchHHHHHHHHHHhcc----CCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCc
Q 028124           52 PGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHK  127 (213)
Q Consensus        52 ~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~  127 (213)
                      .+.+++|.++|+.-+...++.+...    + +++..+||+++..+|...++++.+|+                       
T Consensus       416 ~g~qvlvlaPtr~La~Q~~~~l~~~~~~~g-i~v~~l~G~~~~~~r~~~~~~l~~g~-----------------------  471 (780)
T 1gm5_A          416 AGFQTAFMVPTSILAIQHYRRTVESFSKFN-IHVALLIGATTPSEKEKIKSGLRNGQ-----------------------  471 (780)
T ss_dssp             HTSCEEEECSCHHHHHHHHHHHHHHHTCSS-CCEEECCSSSCHHHHHHHHHHHHSSC-----------------------
T ss_pred             cCCeEEEEeCcHHHHHHHHHHHHHHhhhcC-ceEEEEeCCCCHHHHHHHHHHHhcCC-----------------------
Confidence            3579999999999888888777643    4 89999999999999999999999985                       


Q ss_pred             eeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCC
Q 028124          128 SHMIVVTDACLPLLSSGESAISARVLINYELPT  160 (213)
Q Consensus       128 ~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~  160 (213)
                      .+|+|+|...   +...+.+.++++||--+...
T Consensus       472 ~~IvVgT~~l---l~~~~~~~~l~lVVIDEaHr  501 (780)
T 1gm5_A          472 IDVVIGTHAL---IQEDVHFKNLGLVIIDEQHR  501 (780)
T ss_dssp             CCEEEECTTH---HHHCCCCSCCCEEEEESCCC
T ss_pred             CCEEEECHHH---HhhhhhccCCceEEecccch
Confidence            8999999872   56677888999988766554

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=94.56  E-value=0.19  Score=46.16  Aligned_cols=89  Identities=12%  Similarity=0.106  Sum_probs=60.5

Q ss_pred             HHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccC
Q 028124           36 METLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQS  115 (213)
Q Consensus        36 ~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~  115 (213)
                      .+.+.+.+..+..  ...+.++||+++....+.+++.   .+ ..+..-..+++.   .++++.|+...           
T Consensus       378 ~~~l~~~i~~l~~--~~~g~~lvlF~Sy~~l~~v~~~---~~-~~v~~q~~~~~~---~~~~~~~~~~~-----------  437 (551)
T 3crv_A          378 WKRYADYLLKIYF--QAKANVLVVFPSYEIMDRVMSR---IS-LPKYVESEDSSV---EDLYSAISANN-----------  437 (551)
T ss_dssp             HHHHHHHHHHHHH--HCSSEEEEEESCHHHHHHHHTT---CC-SSEEECCSSCCH---HHHHHHTTSSS-----------
T ss_pred             HHHHHHHHHHHHH--hCCCCEEEEecCHHHHHHHHHh---cC-CcEEEcCCCCCH---HHHHHHHHhcC-----------
Confidence            4555555554433  2456899999999999999873   23 344443345553   45778886431           


Q ss_pred             CCCCcCCCCCCceeEEEEe--CCCCCcCcCCCCCC-----CCCEEEEecCCC
Q 028124          116 GDESETGKDEHKSHMIVVT--DACLPLLSSGESAI-----SARVLINYELPT  160 (213)
Q Consensus       116 ~~~~~~~~~~~~~~iLV~T--d~~~~~~~rGld~~-----~v~~VI~yd~P~  160 (213)
                                  -.+|+++  ..    +.+|+|++     .++.||...+|.
T Consensus       438 ------------~~vl~~v~gg~----~~EGiD~~d~~g~~l~~viI~~lPf  473 (551)
T 3crv_A          438 ------------KVLIGSVGKGK----LAEGIELRNNDRSLISDVVIVGIPY  473 (551)
T ss_dssp             ------------SCEEEEESSCC----SCCSSCCEETTEESEEEEEEESCCC
T ss_pred             ------------CeEEEEEecce----ecccccccccCCcceeEEEEEcCCC
Confidence                        4689998  46    89999999     478899877664

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=94.22  E-value=0.13  Score=44.72  Aligned_cols=85  Identities=12%  Similarity=0.155  Sum_probs=65.8

Q ss_pred             CCCCcEEEEeCchHHHHHHHHHHhccC--CceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCce
Q 028124           51 RPGLPMIVCCSSRDELDAVCSAVSNLA--DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKS  128 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~~L~~~~--~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~  128 (213)
                      ..+.++||.++++.-+..+++.++..+  ++++..+||+.+..+|...++.+..+.                       .
T Consensus        62 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~l~~~~-----------------------~  118 (414)
T 3oiy_A           62 RKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDD-----------------------Y  118 (414)
T ss_dssp             TTTCCEEEEESSHHHHHHHHHHHHHHCCSSCCEEECCTTSCHHHHHHHHHHHHHTC-----------------------C
T ss_pred             cCCCEEEEEECCHHHHHHHHHHHHHHccCCceEEEEECCCChhhHHHHHHHhhcCC-----------------------C
Confidence            356899999999999999999998741  379999999999999988889998874                       8


Q ss_pred             eEEEEeCCCCCcCcCCCCCCCCCEEEEecC
Q 028124          129 HMIVVTDACLPLLSSGESAISARVLINYEL  158 (213)
Q Consensus       129 ~iLV~Td~~~~~~~rGld~~~v~~VI~yd~  158 (213)
                      +|+|+|+..+-..-+-++..++++||.-+.
T Consensus       119 ~Iiv~Tp~~l~~~l~~~~~~~~~~iViDEa  148 (414)
T 3oiy_A          119 HILVFSTQFVSKNREKLSQKRFDFVFVDDV  148 (414)
T ss_dssp             SEEEEEHHHHHHCHHHHTTCCCSEEEESCH
T ss_pred             CEEEECHHHHHHHHHHhccccccEEEEeCh
Confidence            899999862110111255668888887554

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=91.03  E-value=0.95  Score=45.27  Aligned_cols=108  Identities=11%  Similarity=0.083  Sum_probs=75.3

Q ss_pred             EEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccC--CceEEEecCCCCHHHHHHHHHHHhc
Q 028124           25 FYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLA--DISFSSLHSDLAETERTLILEEFRH  102 (213)
Q Consensus        25 ~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~--~~~~~~lhg~~~~~~R~~~l~~Fr~  102 (213)
                      ..+..+...=|-.+..-.+....   ..+.++||.++++.-|..+++.++..+  ++.+..+||+++..+|...++.++.
T Consensus        96 vlv~ApTGSGKTl~~l~~il~~~---~~~~~~Lil~PtreLa~Q~~~~l~~l~~~~i~v~~l~Gg~~~~er~~~~~~l~~  172 (1104)
T 4ddu_A           96 FTMVAPTGVGKTTFGMMTALWLA---RKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEE  172 (1104)
T ss_dssp             EEECCSTTCCHHHHHHHHHHHHH---TTTCCEEEEESSHHHHHHHHHHHHTTSCTTSCEEEECTTCCTTHHHHHHHHHHT
T ss_pred             EEEEeCCCCcHHHHHHHHHHHHH---hcCCeEEEEechHHHHHHHHHHHHHhhCCCCeEEEEeCCCCHHHHHHHHHHHhC
Confidence            34444443336554433332222   356899999999999999999998832  2789999999999899999999998


Q ss_pred             ccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecC
Q 028124          103 TAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYEL  158 (213)
Q Consensus       103 g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~  158 (213)
                      +.                       .+|+|+|+-.+-..-.-+++.++++||.-+.
T Consensus       173 g~-----------------------~~IlV~Tp~rL~~~l~~l~~~~l~~lViDEa  205 (1104)
T 4ddu_A          173 DD-----------------------YHILVFSTQFVSKNREKLSQKRFDFVFVDDV  205 (1104)
T ss_dssp             SC-----------------------CSEEEEEHHHHHHSHHHHHTSCCSEEEESCH
T ss_pred             CC-----------------------CCEEEECHHHHHHHHHhhcccCcCEEEEeCC
Confidence            74                       8999999852100011145678888887554

>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=90.34  E-value=1.9  Score=34.85  Aligned_cols=104  Identities=14%  Similarity=0.164  Sum_probs=64.8

Q ss_pred             EEEEecCcchHHHH-HHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc----CCceEEEecCCCCHHHHHHHHHH
Q 028124           25 FYVAVDRLQFKMET-LVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEE   99 (213)
Q Consensus        25 ~~~~~~~~~~K~~~-L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~lhg~~~~~~R~~~l~~   99 (213)
                      .++..+...=|-.. +.-++..+.. .....++||.++++.-+..+++.++..    + +.+..++|+.+..++...   
T Consensus        83 ~lv~a~TGsGKT~~~~~~il~~l~~-~~~~~~~lil~Ptr~L~~q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~---  157 (249)
T 3ber_A           83 IIGLAETGSGKTGAFALPILNALLE-TPQRLFALVLTPTRELAFQISEQFEALGSSIG-VQSAVIVGGIDSMSQSLA---  157 (249)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHHH-SCCSSCEEEECSSHHHHHHHHHHHHHHHGGGT-CCEEEECTTSCHHHHHHH---
T ss_pred             EEEEcCCCCCchhHhHHHHHHHHhc-CCCCceEEEEeCCHHHHHHHHHHHHHHhccCC-eeEEEEECCCChHHHHHH---
Confidence            44444444335543 3334443322 234568999999999999888777654    4 788999999876554332   


Q ss_pred             HhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCc-C--cCCCCCCCCCEEEEec
Q 028124          100 FRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPL-L--SSGESAISARVLINYE  157 (213)
Q Consensus       100 Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~-~--~rGld~~~v~~VI~yd  157 (213)
                      ...+                        .+|+|+|...+-. +  ..++++..+++||.-+
T Consensus       158 ~~~~------------------------~~I~v~Tp~~l~~~l~~~~~~~l~~~~~lViDE  194 (249)
T 3ber_A          158 LAKK------------------------PHIIIATPGRLIDHLENTKGFNLRALKYLVMDE  194 (249)
T ss_dssp             HHTC------------------------CSEEEECHHHHHHHHHHSTTCCCTTCCEEEECS
T ss_pred             hcCC------------------------CCEEEECHHHHHHHHHcCCCcCccccCEEEEcC
Confidence            2332                        7899999641100 1  2456788888888644

>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=89.98  E-value=1.8  Score=43.51  Aligned_cols=80  Identities=16%  Similarity=0.087  Sum_probs=66.1

Q ss_pred             CCCcEEEEeCchHHHHHHHHHHhcc----CCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCc
Q 028124           52 PGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHK  127 (213)
Q Consensus        52 ~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~  127 (213)
                      .+.+++|.|+|+.-+...++.+...    + +.+..++|..+..++...++.+..|.                       
T Consensus       651 ~g~~vlvlvPt~~La~Q~~~~~~~~~~~~~-i~v~~l~~~~~~~~~~~~~~~l~~g~-----------------------  706 (1151)
T 2eyq_A          651 NHKQVAVLVPTTLLAQQHYDNFRDRFANWP-VRIEMISRFRSAKEQTQILAEVAEGK-----------------------  706 (1151)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHHSTTTT-CCEEEESTTSCHHHHHHHHHHHHTTC-----------------------
T ss_pred             hCCeEEEEechHHHHHHHHHHHHHHhhcCC-CeEEEEeCCCCHHHHHHHHHHHhcCC-----------------------
Confidence            4679999999999998888887643    4 78999999999999999999999984                       


Q ss_pred             eeEEEEeCCCCCcCcCCCCCCCCCEEEEecC
Q 028124          128 SHMIVVTDACLPLLSSGESAISARVLINYEL  158 (213)
Q Consensus       128 ~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~  158 (213)
                      .+|+|+|..   ++...+.+.++++||--..
T Consensus       707 ~dIvV~T~~---ll~~~~~~~~l~lvIiDEa  734 (1151)
T 2eyq_A          707 IDILIGTHK---LLQSDVKFKDLGLLIVDEE  734 (1151)
T ss_dssp             CSEEEECTH---HHHSCCCCSSEEEEEEESG
T ss_pred             CCEEEECHH---HHhCCccccccceEEEech
Confidence            899999975   2566688888888886543

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A*

Probab=89.16  E-value=0.9  Score=41.36  Aligned_cols=51  Identities=8%  Similarity=0.071  Sum_probs=46.3

Q ss_pred             CCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccc
Q 028124           53 GLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTA  104 (213)
Q Consensus        53 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~  104 (213)
                      .+++||.++++.-+....+.|...+ +.+..+||+.+..++...++.++.+.
T Consensus        65 ~g~~lvi~P~~aL~~q~~~~l~~~g-i~~~~l~~~~~~~~~~~~~~~~~~~~  115 (523)
T 1oyw_A           65 NGLTVVVSPLISLMKDQVDQLQANG-VAAACLNSTQTREQQLEVMTGCRTGQ  115 (523)
T ss_dssp             SSEEEEECSCHHHHHHHHHHHHHTT-CCEEEECTTSCHHHHHHHHHHHHHTC
T ss_pred             CCCEEEECChHHHHHHHHHHHHHcC-CcEEEEeCCCCHHHHHHHHHHHhcCC
Confidence            3689999999999999999999887 89999999999999999999998874

>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=88.35  E-value=1.9  Score=33.16  Aligned_cols=106  Identities=11%  Similarity=0.015  Sum_probs=66.0

Q ss_pred             EEEEecCcchHHHH-HHHHHHHhhcC--CCCCCcEEEEeCchHHHHHHHHHHhcc-CCceEEEecCCCCHHHHHHHHHHH
Q 028124           25 FYVAVDRLQFKMET-LVELLHLVVAG--RRPGLPMIVCCSSRDELDAVCSAVSNL-ADISFSSLHSDLAETERTLILEEF  100 (213)
Q Consensus        25 ~~~~~~~~~~K~~~-L~~ll~~~~~~--~~~~~~~IIF~~~~~~~~~l~~~L~~~-~~~~~~~lhg~~~~~~R~~~l~~F  100 (213)
                      ..+..+...=|--. +.-++..+...  ...+.+++|.|+++.-+..+++.+... +.+.+..++|+.+...+...+   
T Consensus        41 ~li~~~TGsGKT~~~~~~~~~~l~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---  117 (207)
T 2gxq_A           41 LIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEAL---  117 (207)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHCCCCCCTTCCCSEEEECSSHHHHHHHHHHHHHHCTTSCEEEECSSSCSHHHHHHH---
T ss_pred             EEEECCCCChHHHHHHHHHHHHHhhccccCCCCcEEEEECCHHHHHHHHHHHHHHhhcceEEEEECCCChHHHHHHh---
Confidence            44555554446654 44444443210  124678999999999999999999865 236788899987755443322   


Q ss_pred             hcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCc-C-cCCCCCCCCCEEEEec
Q 028124          101 RHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPL-L-SSGESAISARVLINYE  157 (213)
Q Consensus       101 r~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~-~-~rGld~~~v~~VI~yd  157 (213)
                      ..+                        .+++|+|...+-. + ...+++.++++||.-+
T Consensus       118 ~~~------------------------~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDE  152 (207)
T 2gxq_A          118 LRG------------------------ADAVVATPGRALDYLRQGVLDLSRVEVAVLDE  152 (207)
T ss_dssp             HHC------------------------CSEEEECHHHHHHHHHHTSSCCTTCSEEEEES
T ss_pred             hCC------------------------CCEEEECHHHHHHHHHcCCcchhhceEEEEEC
Confidence            233                        7899999731000 1 2345677888888644

>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=88.25  E-value=1  Score=41.80  Aligned_cols=48  Identities=15%  Similarity=0.159  Sum_probs=43.7

Q ss_pred             CCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHh
Q 028124           53 GLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFR  101 (213)
Q Consensus        53 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr  101 (213)
                      .+++||.++++.-+....+.|...| +.+..++|+++..++..++..+.
T Consensus        84 ~g~~lVisP~~~L~~q~~~~l~~~g-i~~~~l~~~~~~~~~~~~~~~l~  131 (591)
T 2v1x_A           84 DGFTLVICPLISLMEDQLMVLKQLG-ISATMLNASSSKEHVKWVHAEMV  131 (591)
T ss_dssp             SSEEEEECSCHHHHHHHHHHHHHHT-CCEEECCSSCCHHHHHHHHHHHH
T ss_pred             CCcEEEEeCHHHHHHHHHHHHHhcC-CcEEEEeCCCCHHHHHHHHHHhh
Confidence            4689999999999999999999887 89999999999999998888884

>3gk5_A Uncharacterized rhodanese-related protein TVG0868615; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.40A {Thermoplasma volcanium GSS1}

Probab=88.19  E-value=0.83  Score=32.35  Aligned_cols=37  Identities=14%  Similarity=0.203  Sum_probs=33.2

Q ss_pred             CCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCC
Q 028124           51 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDL   88 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~   88 (213)
                      .+.+++++||.+-..+...+..|...|. .+..+.|++
T Consensus        53 ~~~~~ivvyC~~G~rs~~aa~~L~~~G~-~v~~l~GG~   89 (108)
T 3gk5_A           53 ERDKKYAVICAHGNRSAAAVEFLSQLGL-NIVDVEGGI   89 (108)
T ss_dssp             CTTSCEEEECSSSHHHHHHHHHHHTTTC-CEEEETTHH
T ss_pred             CCCCeEEEEcCCCcHHHHHHHHHHHcCC-CEEEEcCcH
Confidence            4568999999999999999999999995 999999986

>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=87.82  E-value=6.6  Score=30.47  Aligned_cols=107  Identities=11%  Similarity=0.136  Sum_probs=66.1

Q ss_pred             EEEEecCcchHHHHHH-HHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc----CCceEEEecCCCCHHHHHHHHHH
Q 028124           25 FYVAVDRLQFKMETLV-ELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEE   99 (213)
Q Consensus        25 ~~~~~~~~~~K~~~L~-~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~lhg~~~~~~R~~~l~~   99 (213)
                      ..+..+...=|-.... -++..+.. .....++||.|+++.-+..+++.+++.    +++.+..++|+.+..++...   
T Consensus        54 ~li~~~TGsGKT~~~~~~~~~~~~~-~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~---  129 (220)
T 1t6n_A           54 VLCQAKSGMGKTAVFVLATLQQLEP-VTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEV---  129 (220)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHCCC-CTTCCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHH---
T ss_pred             EEEECCCCCchhhhhhHHHHHhhhc-cCCCEEEEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHH---
Confidence            4444444433554333 33333211 223458999999999999988887664    24789999999887665433   


Q ss_pred             HhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCc--CcCCCCCCCCCEEEEecC
Q 028124          100 FRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPL--LSSGESAISARVLINYEL  158 (213)
Q Consensus       100 Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~--~~rGld~~~v~~VI~yd~  158 (213)
                      +..+                       ..+++|+|...+-.  ....+++.++++||.-+.
T Consensus       130 ~~~~-----------------------~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDEa  167 (220)
T 1t6n_A          130 LKKN-----------------------CPHIVVGTPGRILALARNKSLNLKHIKHFILDEC  167 (220)
T ss_dssp             HHHS-----------------------CCSEEEECHHHHHHHHHTTSSCCTTCCEEEEESH
T ss_pred             HhcC-----------------------CCCEEEeCHHHHHHHHHhCCCCcccCCEEEEcCH
Confidence            3443                       26899999741100  123457788888886543

>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=87.21  E-value=2.2  Score=34.12  Aligned_cols=106  Identities=11%  Similarity=0.069  Sum_probs=65.6

Q ss_pred             EEEEecCcchHHHH-HHHHHHHhhc----CCCCCCcEEEEeCchHHHHHHHHHHhcc---CCceEEEecCCCCHHHHHHH
Q 028124           25 FYVAVDRLQFKMET-LVELLHLVVA----GRRPGLPMIVCCSSRDELDAVCSAVSNL---ADISFSSLHSDLAETERTLI   96 (213)
Q Consensus        25 ~~~~~~~~~~K~~~-L~~ll~~~~~----~~~~~~~~IIF~~~~~~~~~l~~~L~~~---~~~~~~~lhg~~~~~~R~~~   96 (213)
                      .++..+...=|-.. +.-++..+..    ....+.++||.|+++.-+..+++.+...   .++.+..++|+.+..++...
T Consensus        69 ~l~~apTGsGKT~~~~l~~l~~l~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~  148 (242)
T 3fe2_A           69 MVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRD  148 (242)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHHTSCCCCTTCCCSEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHH
T ss_pred             EEEECCCcCHHHHHHHHHHHHHHHhccccccCCCCEEEEEeCcHHHHHHHHHHHHHHHhhcCceEEEEECCCChHHHHHH
Confidence            44444544335443 3334443321    0134678999999999999887777653   13789999999887765443


Q ss_pred             HHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCC-cC-cCCCCCCCCCEEEEec
Q 028124           97 LEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLP-LL-SSGESAISARVLINYE  157 (213)
Q Consensus        97 l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~-~~-~rGld~~~v~~VI~yd  157 (213)
                         ++.+                        .+|+|+|.-.+- .+ ...+++.++++||--+
T Consensus       149 ---~~~~------------------------~~I~v~Tp~~l~~~l~~~~~~~~~~~~lViDE  184 (242)
T 3fe2_A          149 ---LERG------------------------VEICIATPGRLIDFLECGKTNLRRTTYLVLDE  184 (242)
T ss_dssp             ---HHHC------------------------CSEEEECHHHHHHHHHHTSCCCTTCCEEEETT
T ss_pred             ---hcCC------------------------CCEEEECHHHHHHHHHcCCCCcccccEEEEeC
Confidence               3343                        789999973100 01 2345778888888643

>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=86.09  E-value=5.5  Score=31.39  Aligned_cols=104  Identities=13%  Similarity=0.084  Sum_probs=66.2

Q ss_pred             EEEEecCcchHHHH-HHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccC----CceEEEecCCCCHHHHHHHHHH
Q 028124           25 FYVAVDRLQFKMET-LVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLA----DISFSSLHSDLAETERTLILEE   99 (213)
Q Consensus        25 ~~~~~~~~~~K~~~-L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~----~~~~~~lhg~~~~~~R~~~l~~   99 (213)
                      ..+..+...=|-.. +.-++..+.. ...+.++||.|+++.-+..+++.+...+    ++.+..++|+.+..++...+  
T Consensus        64 ~l~~a~TGsGKT~~~~l~~l~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~--  140 (230)
T 2oxc_A           64 LIVQAKSGTGKTCVFSTIALDSLVL-ENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRL--  140 (230)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHCCT-TSCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHT--
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHh-cCCCceEEEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhc--
Confidence            44555544446544 3444454322 2346799999999999999988887642    47889999998876654332  


Q ss_pred             HhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCc--CcCCCCCCCCCEEEEec
Q 028124          100 FRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPL--LSSGESAISARVLINYE  157 (213)
Q Consensus       100 Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~--~~rGld~~~v~~VI~yd  157 (213)
                       .                         ..+|+|+|.-.+-.  ....+++.++++||.-+
T Consensus       141 -~-------------------------~~~Iiv~Tp~~l~~~~~~~~~~~~~~~~lViDE  174 (230)
T 2oxc_A          141 -K-------------------------KCHIAVGSPGRIKQLIELDYLNPGSIRLFILDE  174 (230)
T ss_dssp             -T-------------------------SCSEEEECHHHHHHHHHTTSSCGGGCCEEEESS
T ss_pred             -c-------------------------CCCEEEECHHHHHHHHhcCCcccccCCEEEeCC
Confidence             2                         27899999842100  02345677788877643

>2jtq_A Phage shock protein E; solution structure rhodanese, stress response, transferase; NMR {Escherichia coli} PDB: 2jtr_A 2jts_A

Probab=86.07  E-value=2.2  Score=28.47  Aligned_cols=38  Identities=11%  Similarity=0.135  Sum_probs=30.3

Q ss_pred             CCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCC
Q 028124           51 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   89 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~   89 (213)
                      .+.+++++||.+-..+...+..|...|.-.+..+ |++.
T Consensus        39 ~~~~~ivv~C~~g~rs~~aa~~L~~~G~~~v~~l-GG~~   76 (85)
T 2jtq_A           39 DKNDTVKVYCNAGRQSGQAKEILSEMGYTHVENA-GGLK   76 (85)
T ss_dssp             CTTSEEEEEESSSHHHHHHHHHHHHTTCSSEEEE-EETT
T ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHcCCCCEEec-cCHH
Confidence            4568999999999999999999999884346666 7753

>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=85.25  E-value=2  Score=33.85  Aligned_cols=79  Identities=16%  Similarity=0.143  Sum_probs=51.7

Q ss_pred             CCCcEEEEeCchHHHHHHHHHHhcc--CCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCcee
Q 028124           52 PGLPMIVCCSSRDELDAVCSAVSNL--ADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSH  129 (213)
Q Consensus        52 ~~~~~IIF~~~~~~~~~l~~~L~~~--~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (213)
                      .+.++||.++++.-+..+++.+...  .++.+..++|+.+..++.   +.+..+                        .+
T Consensus        93 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~------------------------~~  145 (228)
T 3iuy_A           93 NGPGMLVLTPTRELALHVEAECSKYSYKGLKSICIYGGRNRNGQI---EDISKG------------------------VD  145 (228)
T ss_dssp             CCCSEEEECSSHHHHHHHHHHHHHHCCTTCCEEEECC------CH---HHHHSC------------------------CS
T ss_pred             CCCcEEEEeCCHHHHHHHHHHHHHhcccCceEEEEECCCChHHHH---HHhcCC------------------------CC
Confidence            5678999999999999999888764  237888999987654433   334443                        78


Q ss_pred             EEEEeCCCCCc--CcCCCCCCCCCEEEEec
Q 028124          130 MIVVTDACLPL--LSSGESAISARVLINYE  157 (213)
Q Consensus       130 iLV~Td~~~~~--~~rGld~~~v~~VI~yd  157 (213)
                      |+|+|.-.+-.  ....+++.++++||--+
T Consensus       146 iiv~Tp~~l~~~~~~~~~~~~~~~~lViDE  175 (228)
T 3iuy_A          146 IIIATPGRLNDLQMNNSVNLRSITYLVIDE  175 (228)
T ss_dssp             EEEECHHHHHHHHHTTCCCCTTCCEEEECC
T ss_pred             EEEECHHHHHHHHHcCCcCcccceEEEEEC
Confidence            99999631100  23356788888888644

>1gmx_A GLPE protein; transferase, rhodanese, sulfurtransferase, glycerol metabolism; 1.1A {Escherichia coli} SCOP: c.46.1.3 PDB: 1gn0_A

Probab=84.74  E-value=1.6  Score=30.58  Aligned_cols=39  Identities=10%  Similarity=0.130  Sum_probs=32.8

Q ss_pred             CCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCC
Q 028124           51 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   89 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~   89 (213)
                      .+.+++++||.+-..+...+..|...|.-.+..+.|++.
T Consensus        56 ~~~~~ivvyc~~g~rs~~a~~~L~~~G~~~v~~l~GG~~   94 (108)
T 1gmx_A           56 DFDTPVMVMCYHGNSSKGAAQYLLQQGYDVVYSIDGGFE   94 (108)
T ss_dssp             CTTSCEEEECSSSSHHHHHHHHHHHHTCSSEEEETTHHH
T ss_pred             CCCCCEEEEcCCCchHHHHHHHHHHcCCceEEEecCCHH
Confidence            456899999999889999999999988435888999863

>3foj_A Uncharacterized protein; protein SSP1007, structural genomics, PSI-2, protein structure initiative; 1.60A {Staphylococcus saprophyticus subsp}

Probab=84.18  E-value=1.1  Score=30.97  Aligned_cols=37  Identities=5%  Similarity=0.099  Sum_probs=32.8

Q ss_pred             CCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCC
Q 028124           51 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDL   88 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~   88 (213)
                      .+.+++++||.+-..+...+..|+..|. .+..+.|++
T Consensus        54 ~~~~~ivvyC~~g~rs~~a~~~L~~~G~-~v~~l~GG~   90 (100)
T 3foj_A           54 NDNETYYIICKAGGRSAQVVQYLEQNGV-NAVNVEGGM   90 (100)
T ss_dssp             CTTSEEEEECSSSHHHHHHHHHHHTTTC-EEEEETTHH
T ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHCCC-CEEEecccH
Confidence            3568999999999999999999999995 999999985

>3iwh_A Rhodanese-like domain protein; alpha-beta-alpha sandwich, structural genomics, C structural genomics of infectious diseases, csgid; 2.00A {Staphylococcus aureus subsp} PDB: 3mzz_A

Probab=83.09  E-value=1.1  Score=31.72  Aligned_cols=37  Identities=8%  Similarity=0.108  Sum_probs=32.3

Q ss_pred             CCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCC
Q 028124           51 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDL   88 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~   88 (213)
                      .+.+++++||.+-.++...+..|...| +....+.|++
T Consensus        54 ~~~~~ivv~C~~G~rS~~aa~~L~~~G-~~~~~l~GG~   90 (103)
T 3iwh_A           54 NKNEIYYIVCAGGVRSAKVVEYLEANG-IDAVNVEGGM   90 (103)
T ss_dssp             CTTSEEEEECSSSSHHHHHHHHHHTTT-CEEEEETTHH
T ss_pred             cCCCeEEEECCCCHHHHHHHHHHHHcC-CCEEEecChH
Confidence            456899999999999999999999998 6888888885

>3g5j_A Putative ATP/GTP binding protein; N-terminal domain of ATP/GTP binding protein, PSI, MCSG, STR genomics, protein structure initiative; HET: PGE; 1.76A {Clostridium difficile}

Probab=82.97  E-value=1.2  Score=32.07  Aligned_cols=35  Identities=11%  Similarity=0.226  Sum_probs=30.7

Q ss_pred             CcEEEEe-CchHHHHHHHHHHhccCCceEEEecCCCC
Q 028124           54 LPMIVCC-SSRDELDAVCSAVSNLADISFSSLHSDLA   89 (213)
Q Consensus        54 ~~~IIF~-~~~~~~~~l~~~L~~~~~~~~~~lhg~~~   89 (213)
                      +++|+|| .+-..+...+..|+..|. .+..+.|++.
T Consensus        90 ~~ivvyC~~~G~rs~~a~~~L~~~G~-~v~~l~GG~~  125 (134)
T 3g5j_A           90 DNIVIYCARGGMRSGSIVNLLSSLGV-NVYQLEGGYK  125 (134)
T ss_dssp             SEEEEECSSSSHHHHHHHHHHHHTTC-CCEEETTHHH
T ss_pred             CeEEEEECCCChHHHHHHHHHHHcCC-ceEEEeCcHH
Confidence            7999999 577888899999999995 9999999874

>1wv9_A Rhodanese homolog TT1651; CDC25, phosphatase, sulfurtransferase, structural genomics, NPPSFA; 2.00A {Thermus thermophilus}

Probab=82.92  E-value=1.4  Score=30.09  Aligned_cols=35  Identities=14%  Similarity=0.174  Sum_probs=30.9

Q ss_pred             CcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCC
Q 028124           54 LPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   89 (213)
Q Consensus        54 ~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~   89 (213)
                      +++++||.+-..+...+..|...| +.+..+.|++.
T Consensus        54 ~~ivvyC~~g~rs~~a~~~L~~~G-~~v~~l~GG~~   88 (94)
T 1wv9_A           54 RPLLLVCEKGLLSQVAALYLEAEG-YEAMSLEGGLQ   88 (94)
T ss_dssp             SCEEEECSSSHHHHHHHHHHHHHT-CCEEEETTGGG
T ss_pred             CCEEEEcCCCChHHHHHHHHHHcC-CcEEEEcccHH
Confidence            899999999999999999999998 56888889864

>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=82.83  E-value=16  Score=28.83  Aligned_cols=106  Identities=11%  Similarity=0.102  Sum_probs=57.3

Q ss_pred             EEEEecCcchHHHH-HHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccC---CceEEEecCCCCHHHHHHHHHHH
Q 028124           25 FYVAVDRLQFKMET-LVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLA---DISFSSLHSDLAETERTLILEEF  100 (213)
Q Consensus        25 ~~~~~~~~~~K~~~-L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~---~~~~~~lhg~~~~~~R~~~l~~F  100 (213)
                      .++..+...=|-.. +.-++..+.. .....++||.++++.-+..+++.++..+   .+.+..++|+.+....   .+.+
T Consensus        70 ~li~apTGsGKT~~~~l~~l~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~---~~~l  145 (237)
T 3bor_A           70 VIAQAQSGTGKTATFAISILQQLEI-EFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNE---MQKL  145 (237)
T ss_dssp             EEECCCSSHHHHHHHHHHHHHHCCT-TSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECC--------------
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHh-cCCCceEEEEECcHHHHHHHHHHHHHHhhhcCceEEEEECCCchHHH---HHHH
Confidence            34444444435543 3334444221 2346799999999999999988887642   2677888887654332   2334


Q ss_pred             hcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCC-cCc-CCCCCCCCCEEEEec
Q 028124          101 RHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLP-LLS-SGESAISARVLINYE  157 (213)
Q Consensus       101 r~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~-~~~-rGld~~~v~~VI~yd  157 (213)
                      +.+                       ..+++|+|.-.+- .+. ..+++..+++||.-+
T Consensus       146 ~~~-----------------------~~~Ilv~Tp~~l~~~l~~~~~~~~~~~~lViDE  181 (237)
T 3bor_A          146 QAE-----------------------APHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDE  181 (237)
T ss_dssp             --C-----------------------CCSEEEECHHHHHHHHHTTSSCSTTCCEEEEES
T ss_pred             hcC-----------------------CCCEEEECHHHHHHHHHhCCcCcccCcEEEECC
Confidence            443                       2789999942100 022 345677888888643

>3hix_A ALR3790 protein; rhodanese, rhodanese_3, Q8YQN0, Q8YQN0_anAsp, NSR437I, NESG, structural genomics, PSI-2, protein structure initiative; 1.92A {Anabaena SP} PDB: 3k9r_A

Probab=82.09  E-value=1.5  Score=30.81  Aligned_cols=38  Identities=11%  Similarity=0.093  Sum_probs=32.2

Q ss_pred             CCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCC
Q 028124           51 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDL   88 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~   88 (213)
                      .+..++|+||.+-..+...+..|...|.-.+..+.|++
T Consensus        50 ~~~~~ivvyc~~g~rs~~a~~~L~~~G~~~v~~l~GG~   87 (106)
T 3hix_A           50 EKSRDIYVYGAGDEQTSQAVNLLRSAGFEHVSELKGGL   87 (106)
T ss_dssp             CTTSCEEEECSSHHHHHHHHHHHHHTTCSCEEECTTHH
T ss_pred             CCCCeEEEEECCCChHHHHHHHHHHcCCcCEEEecCCH
Confidence            35678999999999999999999999843588899985

>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=81.80  E-value=15  Score=27.89  Aligned_cols=105  Identities=10%  Similarity=0.121  Sum_probs=64.2

Q ss_pred             EEEEecCcchHHHH-HHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc----CCceEEEecCCCCHHHHHHHHHH
Q 028124           25 FYVAVDRLQFKMET-LVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEE   99 (213)
Q Consensus        25 ~~~~~~~~~~K~~~-L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~lhg~~~~~~R~~~l~~   99 (213)
                      ..+..+...=|-.. +.-++..+.. ...+.++||.|+++.-+..+++.+...    +++.+..++|+.+..+..   ..
T Consensus        43 ~lv~apTGsGKT~~~~~~~~~~~~~-~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~---~~  118 (206)
T 1vec_A           43 ILARAKNGTGKSGAYLIPLLERLDL-KKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDI---MR  118 (206)
T ss_dssp             EEEECCSSSTTHHHHHHHHHHHCCT-TSCSCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHH---HH
T ss_pred             EEEECCCCCchHHHHHHHHHHHhcc-cCCCeeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHH---Hh
Confidence            44555544335543 3334444221 234568999999999999888887654    247889999998765543   22


Q ss_pred             HhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCC-cC-cCCCCCCCCCEEEEec
Q 028124          100 FRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLP-LL-SSGESAISARVLINYE  157 (213)
Q Consensus       100 Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~-~~-~rGld~~~v~~VI~yd  157 (213)
                      +..                        ..+|+|+|...+- .+ ....++.++++||.-+
T Consensus       119 ~~~------------------------~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDE  154 (206)
T 1vec_A          119 LDD------------------------TVHVVIATPGRILDLIKKGVAKVDHVQMIVLDE  154 (206)
T ss_dssp             TTS------------------------CCSEEEECHHHHHHHHHTTCSCCTTCCEEEEET
T ss_pred             cCC------------------------CCCEEEeCHHHHHHHHHcCCcCcccCCEEEEEC
Confidence            333                        2789999973100 01 2234677888887643

>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=81.50  E-value=15  Score=30.72  Aligned_cols=106  Identities=10%  Similarity=0.137  Sum_probs=66.0

Q ss_pred             EEEEecCcchHHHHH-HHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc----CCceEEEecCCCCHHHHHHHHHH
Q 028124           25 FYVAVDRLQFKMETL-VELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEE   99 (213)
Q Consensus        25 ~~~~~~~~~~K~~~L-~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~lhg~~~~~~R~~~l~~   99 (213)
                      ..+..+...=|--.. .-++..+.. .....++||.|+++.-+..+++.+...    +++.+..++|+.+..++...   
T Consensus        48 ~lv~a~TGsGKT~~~~~~~~~~l~~-~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---  123 (391)
T 1xti_A           48 VLCQAKSGMGKTAVFVLATLQQLEP-VTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEV---  123 (391)
T ss_dssp             EEEECSSCSSHHHHHHHHHHHHCCC-CTTCCCEEEECSCHHHHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHH---
T ss_pred             EEEECCCCCcHHHHHHHHHHHhhcc-cCCCeeEEEECCCHHHHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHH---
Confidence            445555444355443 333333211 234569999999999999888877654    24789999999887665443   


Q ss_pred             HhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCc--CcCCCCCCCCCEEEEec
Q 028124          100 FRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPL--LSSGESAISARVLINYE  157 (213)
Q Consensus       100 Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~--~~rGld~~~v~~VI~yd  157 (213)
                      +..+                       ..+|+|+|.-.+-.  ....+++.++++||.-+
T Consensus       124 ~~~~-----------------------~~~iiv~T~~~l~~~~~~~~~~~~~~~~vViDE  160 (391)
T 1xti_A          124 LKKN-----------------------CPHIVVGTPGRILALARNKSLNLKHIKHFILDE  160 (391)
T ss_dssp             HHHS-----------------------CCSEEEECHHHHHHHHHTTSSCCTTCSEEEECS
T ss_pred             HhcC-----------------------CCCEEEECHHHHHHHHHcCCccccccCEEEEeC
Confidence            3343                       26899999741100  12345677888888644

>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=81.24  E-value=5.2  Score=32.48  Aligned_cols=79  Identities=13%  Similarity=0.164  Sum_probs=54.1

Q ss_pred             CCCcEEEEeCchHHHHHHHHHHhccC---CceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCce
Q 028124           52 PGLPMIVCCSSRDELDAVCSAVSNLA---DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKS  128 (213)
Q Consensus        52 ~~~~~IIF~~~~~~~~~l~~~L~~~~---~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~  128 (213)
                      .+.++||.++++.-+..+++.++...   ...+..++|+.+.....   +.+..+                        .
T Consensus       125 ~~~~~lil~Pt~~La~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~---~~~~~~------------------------~  177 (262)
T 3ly5_A          125 NGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEA---QKLGNG------------------------I  177 (262)
T ss_dssp             GCCCEEEECSSHHHHHHHHHHHHHHTTTCCSCEEEECSSSCHHHHH---HHHHHC------------------------C
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHHhhcCceEEEEECCCCHHHHH---HHhcCC------------------------C
Confidence            46789999999999999988887641   26788899987765543   334443                        7


Q ss_pred             eEEEEeCCCCCc-C--cCCCCCCCCCEEEEec
Q 028124          129 HMIVVTDACLPL-L--SSGESAISARVLINYE  157 (213)
Q Consensus       129 ~iLV~Td~~~~~-~--~rGld~~~v~~VI~yd  157 (213)
                      +|+|+|+-.+-. +  ..++++.++++||--+
T Consensus       178 ~Iiv~Tp~~l~~~~~~~~~~~~~~l~~lViDE  209 (262)
T 3ly5_A          178 NIIVATPGRLLDHMQNTPGFMYKNLQCLVIDE  209 (262)
T ss_dssp             SEEEECHHHHHHHHHHCTTCCCTTCCEEEECS
T ss_pred             CEEEEcHHHHHHHHHccCCcccccCCEEEEcC
Confidence            899999521000 1  2346788888888643

>3flh_A Uncharacterized protein LP_1913; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.00A {Lactobacillus plantarum} PDB: 3fnj_A 3i3u_A

Probab=80.93  E-value=1.6  Score=31.58  Aligned_cols=37  Identities=11%  Similarity=0.032  Sum_probs=31.5

Q ss_pred             CCCCcEEEEeCchHH--HHHHHHHHhccCCceEEEecCCC
Q 028124           51 RPGLPMIVCCSSRDE--LDAVCSAVSNLADISFSSLHSDL   88 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~--~~~l~~~L~~~~~~~~~~lhg~~   88 (213)
                      .+.+++|+||.+-..  +...+..|+..| +.+..+.|++
T Consensus        69 ~~~~~ivvyC~~g~r~~s~~a~~~L~~~G-~~v~~l~GG~  107 (124)
T 3flh_A           69 DPAKTYVVYDWTGGTTLGKTALLVLLSAG-FEAYELAGAL  107 (124)
T ss_dssp             CTTSEEEEECSSSSCSHHHHHHHHHHHHT-CEEEEETTHH
T ss_pred             CCCCeEEEEeCCCCchHHHHHHHHHHHcC-CeEEEeCCcH
Confidence            456899999998877  889999999998 6888889986

---

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	213
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	2e-12
d2j0sa2	168	c.37.1.19 (A:244-411) Probable ATP-dependent RNA h	1e-09
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	2e-05
d2rb4a1	168	c.37.1.19 (A:307-474) ATP-dependent RNA helicase D	2e-05

>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 = 60.3 bits (145), Expect = 2e-12
 Identities = 46/193 (23%), Positives = 85/193 (44%), Gaps = 35/193 (18%)

Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           + FYV V+  ++K E L +L              ++ C++R +++ + + + N    + S
Sbjct: 2   KQFYVNVEEEEYKYECLTDLYD-----SISVTQAVIFCNTRRKVEELTTKLRND-KFTVS 55

Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
           +++SDL + ER  I++EFR                          S +++ TD      +
Sbjct: 56  AIYSDLPQQERDTIMKEFRS-----------------------GSSRILISTDLL----A 88

Query: 143 SGESAISARVLINYELPTKKETYIRRMTTC--LAADGSVINIVVGGEVVTLRSMEESLGL 200
            G       ++INY+LP  KE YI R+         G  IN V   +V  +R +E+    
Sbjct: 89  RGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYST 148

Query: 201 IVAEVPINISEIL 213
            + E+P +I+ +L
Sbjct: 149 QIEELPSDIATLL 161

>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 = 53.0 bits (126), Expect = 1e-09
 Identities = 32/193 (16%), Positives = 71/193 (36%), Gaps = 35/193 (18%)

Query: 23  RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
           + F+VAV+R ++K +TL +L              ++ C+++ +                 
Sbjct: 9   KQFFVAVEREEWKFDTLCDLYD-----TLTITQAVIFCNTKRK----------------- 46

Query: 83  SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
                  +     + E     +        ++     +  +      +I           
Sbjct: 47  ------VDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWA----- 95

Query: 143 SGESAISARVLINYELPTKKETYIRRM--TTCLAADGSVINIVVGGEVVTLRSMEESLGL 200
            G       ++INY+LP  +E YI R+  +      G  IN V   ++  LR +E+    
Sbjct: 96  RGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYST 155

Query: 201 IVAEVPINISEIL 213
            + E+P+N+++++
Sbjct: 156 QIDEMPMNVADLI 168

>d1gkub2 c.37.1.16 (B:251-498) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 248

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score = 41.7 bits (97), Expect = 2e-05
 Identities = 19/180 (10%), Positives = 51/180 (28%), Gaps = 39/180 (21%)

Query: 35  KMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERT 94
            + TL  +L       + G   I+   + +E + +  ++ N            +    + 
Sbjct: 13  SISTLSSIL------EKLGTGGIIYARTGEEAEEIYESLKN-------KFRIGIVTATKK 59

Query: 95  LILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSG-ESAISARVL 153
              E+F                          +   ++ T      L  G +     R  
Sbjct: 60  GDYEKFVE-----------------------GEIDHLIGTAHYYGTLVRGLDLPERIRFA 96

Query: 154 INYELPTKKETYIRRMTTCLAADGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL 213
           +    P+ + T        L+     +   +   V  +  +  ++   + EV   + +++
Sbjct: 97  VFVGCPSFRVTIED--IDSLSPQMVKLLAYLYRNVDEIERLLPAVERHIDEVREILKKVM 154

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	213
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	100.0
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	100.0
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	100.0
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	100.0
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	100.0
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	100.0
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.97
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.95
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	99.94
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.9
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	99.89
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	99.84
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.82
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.79
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	99.79
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	99.74
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	99.7
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.64
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.64
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.4
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	99.31
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	98.9
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	97.53
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	96.87
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	96.3
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	92.46
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	91.65
d1tq1a_	119	Thiosulfate sulfurtransferase/Senescence-associate	88.03
d2eyqa2	117	Transcription-repair coupling factor, TRCF {Escher	87.91
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	87.82
d1gmxa_	108	Sulfurtransferase GlpE {Escherichia coli [TaxId: 5	87.56
d1yt8a4	130	Thiosulfate sulfurtransferase PA2603 {Pseudomonas	84.77
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	83.68
d1urha2	120	3-mercaptopyruvate sulfurtransferase {Escherichia	83.56

>d2j0sa2 c.37.1.19 (A:244-411) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.4e-38  Score=253.93  Aligned_cols=163  Identities=28%  Similarity=0.568  Sum_probs=154.5

Q ss_pred             CCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHH
Q 028124           18 HFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLIL   97 (213)
Q Consensus        18 ~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l   97 (213)
                      +..+|+|+|+.++++++|++.|.++++..     +..++||||+++.+++.++..|...+ +.+..+||++++++|..++
T Consensus         4 tl~~i~q~~v~v~~~~~K~~~L~~ll~~~-----~~~k~iiF~~~~~~~~~~~~~l~~~~-~~~~~~~~~~~~~~r~~~~   77 (168)
T d2j0sa2           4 TLEGIKQFFVAVEREEWKFDTLCDLYDTL-----TITQAVIFCNTKRKVDWLTEKMREAN-FTVSSMHGDMPQKERESIM   77 (168)
T ss_dssp             SCTTEEEEEEEESSTTHHHHHHHHHHHHH-----TSSEEEEECSSHHHHHHHHHHHHHTT-CCCEEECTTSCHHHHHHHH
T ss_pred             CCCCcEEEEEEecChHHHHHHHHHHHHhC-----CCCceEEEeeeHHHHHHHHHHhhhcc-cchhhhhhhhhHHHHHHHH
Confidence            56899999999999888999999999873     45799999999999999999999987 8999999999999999999


Q ss_pred             HHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCC
Q 028124           98 EEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAA  175 (213)
Q Consensus        98 ~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~  175 (213)
                      ++|++|+                       .++|||||+    ++||+|+|++++|||||+|++.++|+||+||+  +|+
T Consensus        78 ~~fk~g~-----------------------~~iLv~Td~----~~rGiDi~~v~~VIn~d~P~~~~~yihR~GR~gR~g~  130 (168)
T d2j0sa2          78 KEFRSGA-----------------------SRVLISTDV----WARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGR  130 (168)
T ss_dssp             HHHHHTS-----------------------SCEEEECGG----GSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGC
T ss_pred             HHHhcCC-----------------------ccEEeccch----hcccccccCcceEEEecCCcCHHHHHhhhccccccCC
Confidence            9999985                       999999999    99999999999999999999999999999996  677


Q ss_pred             CCeEEEEEeCchhHHHHHHHHHhcccccccCccccccC
Q 028124          176 DGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEIL  213 (213)
Q Consensus       176 ~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~~~~~~  213 (213)
                      .|.+|+|+.+.|...++.+++.++.+++++|+++.|||
T Consensus       131 ~G~~i~~~~~~d~~~~~~i~~~~~~~i~e~p~~~~dii  168 (168)
T d2j0sa2         131 KGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI  168 (168)
T ss_dssp             CEEEEEEEEGGGHHHHHHHHHHTTCCCEECCSCCTTTC
T ss_pred             CcEEEEEECHHHHHHHHHHHHHHcCcCCCCCcChHHhC
Confidence            89999999999999999999999999999999999986

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=2.1e-38  Score=251.45  Aligned_cols=159  Identities=30%  Similarity=0.552  Sum_probs=148.3

Q ss_pred             ceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHh
Q 028124           22 PRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFR  101 (213)
Q Consensus        22 i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr  101 (213)
                      |+|+|+.+++.+.|++.|.++++.     .+..++||||+++.+++++++.|...+ +.+..+||+|++++|..+++.|+
T Consensus         1 I~q~~~~v~~~e~K~~~L~~ll~~-----~~~~k~iIF~~s~~~~~~l~~~L~~~~-~~~~~~~~~~~~~~r~~~l~~f~   74 (162)
T d1fuka_           1 IKQFYVNVEEEEYKYECLTDLYDS-----ISVTQAVIFCNTRRKVEELTTKLRNDK-FTVSAIYSDLPQQERDTIMKEFR   74 (162)
T ss_dssp             CEEEEEEEESGGGHHHHHHHHHHH-----TTCSCEEEEESSHHHHHHHHHHHHHTT-CCEEEECTTSCHHHHHHHHHHHH
T ss_pred             CEEEEEEeCCcHHHHHHHHHHHHh-----CCCCcEEEEEEEEchHHHHHHHHhhcC-ceEEEeccCCchhhHHHHHHHHh
Confidence            689999999888899999999988     456899999999999999999999987 89999999999999999999999


Q ss_pred             cccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCCCCeE
Q 028124          102 HTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGSV  179 (213)
Q Consensus       102 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~~g~~  179 (213)
                      .|+                       .++|||||+    ++||+|+++|++|||||+|++++.|+||+||+  .|+.|.|
T Consensus        75 ~~~-----------------------~~iLv~Tdv----~~rGiDi~~v~~VI~~d~P~~~~~yihR~GR~gR~g~~g~~  127 (162)
T d1fuka_          75 SGS-----------------------SRILISTDL----LARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVA  127 (162)
T ss_dssp             TTS-----------------------CSEEEEEGG----GTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEE
T ss_pred             hcc-----------------------cceeecccc----ccccccCCCceEEEEeccchhHHHHHhhccccccCCCccEE
Confidence            985                       999999999    99999999999999999999999999999997  6778999


Q ss_pred             EEEEeCchhHHHHHHHHHhcccccccCccccccC
Q 028124          180 INIVVGGEVVTLRSMEESLGLIVAEVPINISEIL  213 (213)
Q Consensus       180 i~~~~~~e~~~~~~le~~l~~~~~~~~~~~~~~~  213 (213)
                      ++|++++|...++.+++.++.+++++|.+++++|
T Consensus       128 i~~~~~~d~~~~~~i~~~~~~~~~~ip~~~~~l~  161 (162)
T d1fuka_         128 INFVTNEDVGAMRELEKFYSTQIEELPSDIATLL  161 (162)
T ss_dssp             EEEEETTTHHHHHHHHHHSSCCCEECCSCCTTTT
T ss_pred             EEEcCHHHHHHHHHHHHHHcCcCCCCChHHHHhh
Confidence            9999999999999999999999999999999886

>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=3.3e-37  Score=246.05  Aligned_cols=161  Identities=24%  Similarity=0.437  Sum_probs=151.4

Q ss_pred             CCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHH
Q 028124           18 HFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLIL   97 (213)
Q Consensus        18 ~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l   97 (213)
                      +..+|+|+|+.+++.+ |+..|.++|+.     .+..++||||+++++++.++..|...| +.+..+||+|++++|.+++
T Consensus         3 tl~~i~q~yi~v~~~~-K~~~L~~ll~~-----~~~~k~iVF~~~~~~~~~l~~~L~~~g-~~~~~~h~~~~~~~r~~~~   75 (171)
T d1s2ma2           3 TLKGITQYYAFVEERQ-KLHCLNTLFSK-----LQINQAIIFCNSTNRVELLAKKITDLG-YSCYYSHARMKQQERNKVF   75 (171)
T ss_dssp             BCTTEEEEEEECCGGG-HHHHHHHHHHH-----SCCSEEEEECSSHHHHHHHHHHHHHHT-CCEEEECTTSCHHHHHHHH
T ss_pred             CccceEEEEEEcCHHH-HHHHHHHHHHh-----CCCCceEEEEeeeehhhHhHHhhhccc-ccccccccccchhhhhhhh
Confidence            4678999999999865 99999999988     466899999999999999999999998 8999999999999999999


Q ss_pred             HHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCC
Q 028124           98 EEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAA  175 (213)
Q Consensus        98 ~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~  175 (213)
                      ++|+.|.                       .++|||||+    ++||+|+|++++|||||+|+++++|+||+||+  .|+
T Consensus        76 ~~f~~~~-----------------------~~ilv~Td~----~~~Gid~~~v~~VI~~d~p~~~~~y~qr~GR~gR~g~  128 (171)
T d1s2ma2          76 HEFRQGK-----------------------VRTLVCSDL----LTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGH  128 (171)
T ss_dssp             HHHHTTS-----------------------SSEEEESSC----SSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTC
T ss_pred             hhcccCc-----------------------cccccchhH----hhhccccceeEEEEecCCcchHHHHHHHhhhcccCCC
Confidence            9999985                       999999999    99999999999999999999999999999997  567


Q ss_pred             CCeEEEEEeCchhHHHHHHHHHhcccccccCcccccc
Q 028124          176 DGSVINIVVGGEVVTLRSMEESLGLIVAEVPINISEI  212 (213)
Q Consensus       176 ~g~~i~~~~~~e~~~~~~le~~l~~~~~~~~~~~~~~  212 (213)
                      .|.||+|+++.|...++.+++.++.++.++|..+++.
T Consensus       129 ~g~~i~~v~~~e~~~~~~i~~~l~~~~~~~p~~~d~~  165 (171)
T d1s2ma2         129 LGLAINLINWNDRFNLYKIEQELGTEIAAIPATIDKS  165 (171)
T ss_dssp             CEEEEEEECGGGHHHHHHHHHHHTCCCEECCSSCCGG
T ss_pred             ccEEEEEeCHHHHHHHHHHHHHHCCCCCCCCcccchh
Confidence            8999999999999999999999999999999988764

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=100.00  E-value=3.3e-35  Score=230.77  Aligned_cols=151  Identities=23%  Similarity=0.467  Sum_probs=141.4

Q ss_pred             CCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHH
Q 028124           20 SQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEE   99 (213)
Q Consensus        20 ~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~   99 (213)
                      ++|+|+|+.++.++ |++.|.++|+.      ...++||||+++++|+.+++.|+..+ +.+..+||++++.+|..++++
T Consensus         2 ~nI~~~~i~v~~~~-K~~~L~~ll~~------~~~k~IIF~~s~~~~~~l~~~L~~~g-~~~~~~~~~~~~~~r~~~~~~   73 (155)
T d1hv8a2           2 ANIEQSYVEVNENE-RFEALCRLLKN------KEFYGLVFCKTKRDTKELASMLRDIG-FKAGAIHGDLSQSQREKVIRL   73 (155)
T ss_dssp             SSSEEEEEECCGGG-HHHHHHHHHCS------TTCCEEEECSSHHHHHHHHHHHHHTT-CCEEEECSSSCHHHHHHHHHH
T ss_pred             CCeEEEEEEeChHH-HHHHHHHHHcc------CCCCEEEEECchHHHHHHHhhhcccc-cccccccccchhhhhhhhhhh
Confidence            58999999998865 99999999876      34689999999999999999999987 899999999999999999999


Q ss_pred             HhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCCCC
Q 028124          100 FRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADG  177 (213)
Q Consensus       100 Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~~g  177 (213)
                      |++|+                       .++|||||+    +++|+|+|++++|||||+|+++.+|+||+||+  .|+.|
T Consensus        74 f~~~~-----------------------~~ilv~T~~----~~~Gid~~~v~~Vi~~d~p~~~~~y~qr~GR~gR~g~~g  126 (155)
T d1hv8a2          74 FKQKK-----------------------IRILIATDV----MSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKG  126 (155)
T ss_dssp             HHTTS-----------------------SSEEEECTT----HHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCC
T ss_pred             hhccc-----------------------ceeeeehhH----HhhhhhhccCcEEEEecCCCCHHHHHHHHHhcCcCCCCc
Confidence            99985                       899999999    99999999999999999999999999999997  46789


Q ss_pred             eEEEEEeCchhHHHHHHHHHhccccccc
Q 028124          178 SVINIVVGGEVVTLRSMEESLGLIVAEV  205 (213)
Q Consensus       178 ~~i~~~~~~e~~~~~~le~~l~~~~~~~  205 (213)
                      .+|+|+.+.|...++.+++.++.+++++
T Consensus       127 ~~i~~~~~~d~~~~~~i~~~~~~~i~~l  154 (155)
T d1hv8a2         127 KAISIINRREYKKLRYIERAMKLKIKKL  154 (155)
T ss_dssp             EEEEEECTTSHHHHHHHHHHHTCCCCCB
T ss_pred             eEEEEEchHHHHHHHHHHHHHCCCcccc
Confidence            9999999999999999999999998876

>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=100.00  E-value=5.6e-34  Score=226.90  Aligned_cols=155  Identities=18%  Similarity=0.365  Sum_probs=141.6

Q ss_pred             CceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHH
Q 028124           21 QPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEF  100 (213)
Q Consensus        21 ~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~F  100 (213)
                      +|+|+|+.+.+++ |++.|.++|+.     ....++||||+++++++.|++.|.+.+ +.+..+||+|++++|.+++++|
T Consensus         1 ~l~q~~v~~~~~~-K~~~L~~ll~~-----~~~~k~iIF~~~~~~~~~l~~~L~~~~-~~~~~ihg~~~~~~r~~~l~~F   73 (168)
T d1t5ia_           1 GLQQYYVKLKDNE-KNRKLFDLLDV-----LEFNQVVIFVKSVQRCIALAQLLVEQN-FPAIAIHRGMPQEERLSRYQQF   73 (168)
T ss_dssp             CCEEEEEECCGGG-HHHHHHHHHHH-----SCCSSEEEECSSHHHHHHHHHHHHHTT-CCEEEECTTSCHHHHHHHHHHH
T ss_pred             CcEEEEEEeChHH-HHHHHHHHHHh-----CCCCeEEEEEeeeecchhhhhhhcccc-ccccccccccchhhhhhhhhhh
Confidence            5899999999866 99999999988     356799999999999999999999987 8999999999999999999999


Q ss_pred             hcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCCCCe
Q 028124          101 RHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAADGS  178 (213)
Q Consensus       101 r~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~~g~  178 (213)
                      ++|+                       .++||||++    +++|+|+|++++|||||+|+++..|+||+||+  +|+.|.
T Consensus        74 ~~g~-----------------------~~iLv~T~~----~~~Gid~~~~~~vi~~~~p~~~~~yiqr~GR~gR~g~~g~  126 (168)
T d1t5ia_          74 KDFQ-----------------------RRILVATNL----FGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGL  126 (168)
T ss_dssp             HTTS-----------------------CSEEEESSC----CSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCE
T ss_pred             cccc-----------------------ceeeecccc----ccchhhcccchhhhhhhcccchhhHhhhhhhcccCCCccE
Confidence            9985                       999999999    99999999999999999999999999999996  578899


Q ss_pred             EEEEEeCc-hhHHHHHHHHHhcccccccCccc
Q 028124          179 VINIVVGG-EVVTLRSMEESLGLIVAEVPINI  209 (213)
Q Consensus       179 ~i~~~~~~-e~~~~~~le~~l~~~~~~~~~~~  209 (213)
                      ||+|+++. +...+..+++.++..+.++|..+
T Consensus       127 ~i~l~~~~~~~~~~~~i~~~~~~~~~elp~~~  158 (168)
T d1t5ia_         127 AITFVSDENDAKILNDVQDRFEVNISELPDEI  158 (168)
T ss_dssp             EEEEECSHHHHHHHHHHHHHHCCCEEECC---
T ss_pred             EEEEECchHHHHHHHHHHHHHcCCcccCCchh
Confidence            99999875 67788999999999999988554

>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=99.97  E-value=1.8e-30  Score=212.18  Aligned_cols=141  Identities=18%  Similarity=0.361  Sum_probs=126.7

Q ss_pred             CCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHH
Q 028124           18 HFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLIL   97 (213)
Q Consensus        18 ~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l   97 (213)
                      .++||.  |..++..+ |++.|.++|+.     ..+.++||||+|+..++.|+..|...+ +.+..+||++++++|.+++
T Consensus         3 ~RpNi~--y~v~~~~~-k~~~L~~~l~~-----~~~~~~IIF~~t~~~~~~l~~~l~~~~-~~~~~~h~~~~~~~r~~~~   73 (200)
T d1oywa3           3 DRPNIR--YMLMEKFK-PLDQLMRYVQE-----QRGKSGIIYCNSRAKVEDTAARLQSKG-ISAAAYHAGLENNVRADVQ   73 (200)
T ss_dssp             CCTTEE--EEEEECSS-HHHHHHHHHHH-----TTTCCEEEECSSHHHHHHHHHHHHHTT-CCEEEECTTSCHHHHHHHH
T ss_pred             CCCCcE--EEEEcCCc-HHHHHHHHHHh-----cCCCCEEEEEeeehhhHHhhhhhccCC-ceeEEecCCCcHHHHHHHH
Confidence            567774  44455555 99999999987     456799999999999999999999987 8999999999999999999


Q ss_pred             HHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCC
Q 028124           98 EEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAA  175 (213)
Q Consensus        98 ~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~  175 (213)
                      ++|++|+                       .++|||||+    ++||+|+|+|++|||||+|+++++|+||+||+  .|+
T Consensus        74 ~~f~~g~-----------------------~~ilvaTd~----~~~GiD~p~v~~VI~~~~P~~~~~y~qr~GR~gR~g~  126 (200)
T d1oywa3          74 EKFQRDD-----------------------LQIVVATVA----FGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGL  126 (200)
T ss_dssp             HHHHTTS-----------------------CSEEEECTT----SCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSS
T ss_pred             HHHhccc-----------------------ceEEEecch----hhhccCCCCCCEEEECCCccchHHHHHHhhhhhcCCC
Confidence            9999985                       999999999    99999999999999999999999999999997  577


Q ss_pred             CCeEEEEEeCchhHHHHHH
Q 028124          176 DGSVINIVVGGEVVTLRSM  194 (213)
Q Consensus       176 ~g~~i~~~~~~e~~~~~~l  194 (213)
                      .|.+++|+++.|...++++
T Consensus       127 ~g~ai~~~~~~d~~~l~~~  145 (200)
T d1oywa3         127 PAEAMLFYDPADMAWLRRC  145 (200)
T ss_dssp             CEEEEEEECHHHHHHHHHH
T ss_pred             CceEEEecCHHHHHHHHhh
Confidence            8999999999888777654

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=99.95  E-value=7.4e-27  Score=187.90  Aligned_cols=105  Identities=15%  Similarity=0.213  Sum_probs=95.1

Q ss_pred             CCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEE
Q 028124           52 PGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMI  131 (213)
Q Consensus        52 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iL  131 (213)
                      .+.++||||+++..++.++..|...| +.+..+||+|++++|.+++++|++|+                       .++|
T Consensus        30 ~~~~~iif~~~~~~~~~~~~~l~~~g-~~~~~~hg~~~~~eR~~~l~~Fr~g~-----------------------~~vL   85 (181)
T d1t5la2          30 RNERTLVTTLTKKMAEDLTDYLKEAG-IKVAYLHSEIKTLERIEIIRDLRLGK-----------------------YDVL   85 (181)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHTTT-CCEEEECSSCCHHHHHHHHHHHHHTS-----------------------CSEE
T ss_pred             cCCeEEEEeehhhhhHHHHHHHHhCC-cceeEecCCccHHHHHHHHHHHHCCC-----------------------CCEE
Confidence            46799999999999999999999998 89999999999999999999999995                       9999


Q ss_pred             EEeCCCCCcCcCCCCCCCCCEEEEecCCC-----ChHHHHHhhccccCCC-CeEEEEEe
Q 028124          132 VVTDACLPLLSSGESAISARVLINYELPT-----KKETYIRRMTTCLAAD-GSVINIVV  184 (213)
Q Consensus       132 V~Td~~~~~~~rGld~~~v~~VI~yd~P~-----~~~~yi~R~GR~~~~~-g~~i~~~~  184 (213)
                      ||||+    ++||+|+|+|++|||||+|.     +..+|+||+||+|+.. |.++.+..
T Consensus        86 VaTdv----~~rGiDip~v~~VI~~d~p~~~~~~s~~~yi~R~GRagR~g~~~~~~~~~  140 (181)
T d1t5la2          86 VGINL----LREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIMYAD  140 (181)
T ss_dssp             EESCC----CSSSCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTTCEEEEECS
T ss_pred             EehhH----HHccCCCCCCCEEEEecCCcccccccHHHHHHHHHhhccccCceeEeecc
Confidence            99999    99999999999999999995     6899999999986554 44444444

>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=99.94  E-value=2.5e-26  Score=183.56  Aligned_cols=115  Identities=14%  Similarity=0.152  Sum_probs=100.4

Q ss_pred             CCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEE
Q 028124           52 PGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMI  131 (213)
Q Consensus        52 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iL  131 (213)
                      .+.++||||++++.|+.|+..|...| +.+..+||+|++.+|.+++++|++|+                       +++|
T Consensus        30 ~g~r~lvfc~t~~~~~~l~~~L~~~G-i~a~~~Hg~~~~~eR~~~l~~F~~G~-----------------------~~vL   85 (174)
T d1c4oa2          30 RGERTLVTVLTVRMAEELTSFLVEHG-IRARYLHHELDAFKRQALIRDLRLGH-----------------------YDCL   85 (174)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHTT-CCEEEECTTCCHHHHHHHHHHHHTTS-----------------------CSEE
T ss_pred             cCCcEEEEEcchhHHHHHHHHHHhcC-CceEEEecccchHHHHHHHHHHHCCC-----------------------eEEE
Confidence            57899999999999999999999998 99999999999999999999999995                       9999


Q ss_pred             EEeCCCCCcCcCCCCCCCCCEEEEecCCC-----ChHHHHHhhccccCC-CCeEEEEEeCchhHHHHHH
Q 028124          132 VVTDACLPLLSSGESAISARVLINYELPT-----KKETYIRRMTTCLAA-DGSVINIVVGGEVVTLRSM  194 (213)
Q Consensus       132 V~Td~~~~~~~rGld~~~v~~VI~yd~P~-----~~~~yi~R~GR~~~~-~g~~i~~~~~~e~~~~~~l  194 (213)
                      |+|++    ++||+|+|+|++|||||+|.     +.+.|+||+||+++. .|.++.+.......+.+.+
T Consensus        86 VaT~v----~~~GiDip~V~~Vi~~~~~~~~~~~~~~~~iq~~GR~gR~~~g~~~~~~~~~~~~~~~~i  150 (174)
T d1c4oa2          86 VGINL----LREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNARGEVWLYADRVSEAMQRAI  150 (174)
T ss_dssp             EESCC----CCTTCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTTCEEEEECSSCCHHHHHHH
T ss_pred             Eeeee----eeeeccCCCCcEEEEeccccccccchhHHHHHHhhhhhhcCCCeeEEeecCCCHHHHHHH
Confidence            99999    99999999999999999765     568899999998644 3777777765443333333

>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=99.90  E-value=2.6e-24  Score=182.46  Aligned_cols=127  Identities=21%  Similarity=0.286  Sum_probs=109.1

Q ss_pred             chHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecC--------CCCHHHHHHHHHHHhccc
Q 028124           33 QFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHS--------DLAETERTLILEEFRHTA  104 (213)
Q Consensus        33 ~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg--------~~~~~~R~~~l~~Fr~g~  104 (213)
                      +.|++.|.++|..+.. ..+..++||||+++++++.+++.|...+ +.+..+||        +++..+|..++++|++|+
T Consensus       142 ~pK~~~l~~~l~~~~~-~~~~~k~iiF~~~~~~~~~~~~~L~~~~-~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~  219 (286)
T d1wp9a2         142 HPKMDKLKEIIREQLQ-RKQNSKIIVFTNYRETAKKIVNELVKDG-IKAKRFVGQASKENDRGLSQREQKLILDEFARGE  219 (286)
T ss_dssp             CHHHHHHHHHHHHHHH-HCTTCCEEEECSCHHHHHHHHHHHHHTT-CCEEEECCSSCC-------CCHHHHHHHHHHHTS
T ss_pred             CcHHHHHHHHHHHHHH-hCCCCcEEEEeCcHHhHHHHHHHHHHcC-CceEEeeccccccccchhchHHHHHHHHHHHcCC
Confidence            4588998888876543 3567899999999999999999999887 78888876        466678999999999985


Q ss_pred             ccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccccC-CCCeEEEEE
Q 028124          105 MKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLA-ADGSVINIV  183 (213)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~~-~~g~~i~~~  183 (213)
                                             +++||||++    +++|+|+|+|++|||||+|+++..|+||+||+++ ++|.++.|+
T Consensus       220 -----------------------~~vLv~T~~----~~~Gld~~~~~~Vi~~d~~~~~~~~~Qr~GR~gR~~~~~~~~l~  272 (286)
T d1wp9a2         220 -----------------------FNVLVATSV----GEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMPGRVIILM  272 (286)
T ss_dssp             -----------------------CSEEEECGG----GGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCCCSEEEEEE
T ss_pred             -----------------------CcEEEEccc----eeccccCCCCCEEEEeCCCCCHHHHHHHHHhCCCCCCCEEEEEE
Confidence                                   999999999    9999999999999999999999999999999753 468999999


Q ss_pred             eCchh
Q 028124          184 VGGEV  188 (213)
Q Consensus       184 ~~~e~  188 (213)
                      +++..
T Consensus       273 ~~~~~  277 (286)
T d1wp9a2         273 AKGTR  277 (286)
T ss_dssp             ETTSH
T ss_pred             eCCCH
Confidence            87643

>d1jr6a_ c.37.1.14 (A:) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=99.89  E-value=2e-24  Score=166.48  Aligned_cols=125  Identities=17%  Similarity=0.189  Sum_probs=98.4

Q ss_pred             CCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHH
Q 028124           20 SQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEE   99 (213)
Q Consensus        20 ~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~   99 (213)
                      ++|++.++..+... ++....-.|+.     ..++++||||+|+++|+.|++.|+..| +.+..+||+|+++       +
T Consensus         8 p~I~~~~~~~~~~~-~~~~~~i~l~~-----~~~~k~IVFc~t~~~ae~la~~L~~~G-~~~~~~H~~~~~~-------~   73 (138)
T d1jr6a_           8 PNIEEVALSTTGEI-PFYGKAIPLEV-----IKGGRHLIFCHSKKKCDELAAKLVALG-INAVAYYRGLDVS-------V   73 (138)
T ss_dssp             TTEEEEECCBCSSE-ECSSCEECHHH-----HTTSCEEEECSCHHHHHHHHHHHHHHT-CEEEEECTTCCSC-------C
T ss_pred             CCeEEEEeccCChh-HHHHhhChHhh-----cCCCCEEEEeCcHHHHHHHHHHHhccc-cchhhhhccchhh-------h
Confidence            46888876655433 21111111333     245799999999999999999999998 8999999999854       4


Q ss_pred             HhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEec----CCCChHHHHHhhccccC-
Q 028124          100 FRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYE----LPTKKETYIRRMTTCLA-  174 (213)
Q Consensus       100 Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd----~P~~~~~yi~R~GR~~~-  174 (213)
                      |+++                       +.++|||||+    ++||+| ++++.|||||    +|.+.++|+||+||+|+ 
T Consensus        74 ~~~~-----------------------~~~vlvaTd~----~~~GiD-~~v~~Vi~~~~~~~~P~~~~~y~qr~GR~gRg  125 (138)
T d1jr6a_          74 IPTN-----------------------GDVVVVATDA----LMTGFT-GDFDSVIDCNTSDGKPQDAVSRTQRRGRTGRG  125 (138)
T ss_dssp             CTTS-----------------------SCEEEEESSS----SCSSSC-CCBSEEEECSEETTEECCHHHHHHHHTTBCSS
T ss_pred             hhhh-----------------------hcceeehhHH----HHhccc-cccceEEEEEecCCCCCCHHHHHhHhccccCC
Confidence            6676                       4999999999    999999 9999999965    69999999999999864 


Q ss_pred             CCCeEEEEEeCch
Q 028124          175 ADGSVINIVVGGE  187 (213)
Q Consensus       175 ~~g~~i~~~~~~e  187 (213)
                      ++| ++.|+.++|
T Consensus       126 ~~G-~~~~i~~~e  137 (138)
T d1jr6a_         126 KPG-IYRFVAPGE  137 (138)
T ss_dssp             SCE-EEEECCSSC
T ss_pred             CCc-EEEEEcCCC
Confidence            556 577888765

>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=99.84  E-value=1.2e-23  Score=175.55  Aligned_cols=126  Identities=13%  Similarity=0.157  Sum_probs=100.3

Q ss_pred             CceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHH
Q 028124           21 QPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEF  100 (213)
Q Consensus        21 ~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~F  100 (213)
                      +|...|.   ++ +|+..|.++|+.+      +.++||||+|+++|+.|+..|+..       +||+|++.+|.+++++|
T Consensus         3 ~v~d~~~---~~-~~~~~l~~~l~~~------~~~~iif~~~~~~~~~l~~~l~~~-------~hg~~~~~~R~~~~~~f   65 (248)
T d1gkub2           3 NVEDVAV---ND-ESISTLSSILEKL------GTGGIIYARTGEEAEEIYESLKNK-------FRIGIVTATKKGDYEKF   65 (248)
T ss_dssp             CEEEEEE---SC-CCTTTTHHHHTTS------CSCEEEEESSHHHHHHHHHTTTTS-------SCEEECTTSSSHHHHHH
T ss_pred             CEEEEec---Cc-hHHHHHHHHHHHh------CCCEEEEECCHHHHHHHHHHHHHh-------ccCCCCHHHHHHHHHHH
Confidence            4555553   34 4999999999862      368999999999999999999642       79999999999999999


Q ss_pred             hcccccccccccccCCCCCcCCCCCCceeEEEEe----CCCCCcCcCCCCCCC-CCEEEEecCCCChHHHHHhhccc--c
Q 028124          101 RHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVT----DACLPLLSSGESAIS-ARVLINYELPTKKETYIRRMTTC--L  173 (213)
Q Consensus       101 r~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~T----d~~~~~~~rGld~~~-v~~VI~yd~P~~~~~yi~R~GR~--~  173 (213)
                      ++|+                       +++||||    ++    ++||+|+|+ |++|||||+|+    |.||+||+  .
T Consensus        66 ~~g~-----------------------~~vLVaT~a~~~v----~~rGlDip~~v~~VI~~d~P~----~~~r~gR~~R~  114 (248)
T d1gkub2          66 VEGE-----------------------IDHLIGTAHYYGT----LVRGLDLPERIRFAVFVGCPS----FRVTIEDIDSL  114 (248)
T ss_dssp             HHTS-----------------------CSEEEEECC----------CCSCCTTTCCEEEEESCCE----EEEECSCGGGS
T ss_pred             HhCC-----------------------CeEEEEeccccch----hhhccCccccccEEEEeCCCc----chhhhhhhhcc
Confidence            9986                       9999999    78    999999997 99999999995    88999997  4


Q ss_pred             CCCCeEEEEEeCchhHHHHHH
Q 028124          174 AADGSVINIVVGGEVVTLRSM  194 (213)
Q Consensus       174 ~~~g~~i~~~~~~e~~~~~~l  194 (213)
                      |+.|.++.++...+......+
T Consensus       115 g~~~~~~~~~~~~~~~~~~~l  135 (248)
T d1gkub2         115 SPQMVKLLAYLYRNVDEIERL  135 (248)
T ss_dssp             CHHHHHHHHTTTSCHHHHHTT
T ss_pred             CcceEeeeeccHhhHHHHHHH
Confidence            556777777766555444433

>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=99.82  E-value=8.5e-21  Score=152.99  Aligned_cols=116  Identities=20%  Similarity=0.273  Sum_probs=100.9

Q ss_pred             chHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccccccc
Q 028124           33 QFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVT  112 (213)
Q Consensus        33 ~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~  112 (213)
                      ..|++.|.++++.     .++.++||||++...++.|++.|.      +..+||+++..+|..++++|++|+        
T Consensus        78 ~~K~~~l~~ll~~-----~~~~k~lvf~~~~~~~~~l~~~l~------~~~i~g~~~~~~R~~~l~~F~~~~--------  138 (200)
T d2fwra1          78 KNKIRKLREILER-----HRKDKIIIFTRHNELVYRISKVFL------IPAITHRTSREEREEILEGFRTGR--------  138 (200)
T ss_dssp             SHHHHHHHHHHHH-----TSSSCBCCBCSCHHHHHHHHHHTT------CCBCCSSSCSHHHHTHHHHHHHSS--------
T ss_pred             HHHHHHHHHHHHh-----CCCCcEEEEeCcHHHHHHHHhhcC------cceeeCCCCHHHHHHHHHHhhcCC--------
Confidence            3599999999987     456899999999999999988873      234799999999999999999985        


Q ss_pred             ccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccccCC-----CCeEEEEEeCc
Q 028124          113 EQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLAA-----DGSVINIVVGG  186 (213)
Q Consensus       113 ~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~~~~-----~g~~i~~~~~~  186 (213)
                                     .++||+|++    +++|+|+|.+++||+||+|+++..|+||+||+++.     ...++.|+..+
T Consensus       139 ---------------~~vLv~~~~----~~~Gidl~~~~~vi~~~~~~s~~~~~Q~iGR~~R~~~~k~~~~i~~~v~~~  198 (200)
T d2fwra1         139 ---------------FRAIVSSQV----LDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYELISRG  198 (200)
T ss_dssp             ---------------CSBCBCSSC----CCSSSCSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTTCCEEEEEEEECS
T ss_pred             ---------------eeeeeecch----hhcccCCCCCCEEEEeCCCCCHHHHHHHHHhcCCCCCCCcEEEEEEEecCC
Confidence                           889999999    99999999999999999999999999999996322     35677787654

>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=1.7e-19  Score=146.42  Aligned_cols=110  Identities=20%  Similarity=0.261  Sum_probs=94.1

Q ss_pred             CCcEEEEeCchHHHHHHHHHHhccC----C-------------------------ceEEEecCCCCHHHHHHHHHHHhcc
Q 028124           53 GLPMIVCCSSRDELDAVCSAVSNLA----D-------------------------ISFSSLHSDLAETERTLILEEFRHT  103 (213)
Q Consensus        53 ~~~~IIF~~~~~~~~~l~~~L~~~~----~-------------------------~~~~~lhg~~~~~~R~~~l~~Fr~g  103 (213)
                      +.++||||+|++.|+.+|..|....    .                         ..+..+||+|++++|..+.+.|++|
T Consensus        40 ~~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~~~r~~ie~~f~~g  119 (201)
T d2p6ra4          40 NGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRG  119 (201)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHHHHHHHHHHHHTT
T ss_pred             CCcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhhhhHHHHHHHHhCC
Confidence            5799999999999998888886520    0                         0167899999999999999999998


Q ss_pred             cccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEE-------ecCCCChHHHHHhhccccC--
Q 028124          104 AMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLIN-------YELPTKKETYIRRMTTCLA--  174 (213)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~-------yd~P~~~~~yi~R~GR~~~--  174 (213)
                      .                       +++||||+.    +++|+|+|..++||+       ++.|.+..+|+||+||+|+  
T Consensus       120 ~-----------------------i~vlvaT~~----l~~Gin~p~~~vvi~~~~~~d~~~~~~~~~~~~q~~GRAGR~g  172 (201)
T d2p6ra4         120 N-----------------------IKVVVATPT----LAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPG  172 (201)
T ss_dssp             S-----------------------CCEEEECST----TTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTT
T ss_pred             C-----------------------ceEEEechH----HHhhcCCCCceEEEecceeccCCcCCCCHHHHHHHhcccCCCC
Confidence            5                       999999999    999999999999996       7888999999999999864  


Q ss_pred             --CCCeEEEEEeCchhH
Q 028124          175 --ADGSVINIVVGGEVV  189 (213)
Q Consensus       175 --~~g~~i~~~~~~e~~  189 (213)
                        ..|.++.++.+.+..
T Consensus       173 ~~~~G~~~l~~~~~~~~  189 (201)
T d2p6ra4         173 MDERGEAIIIVGKRDRE  189 (201)
T ss_dssp             TCSCEEEEEECCGGGHH
T ss_pred             CCCeeEEEEEeCCCChH
Confidence              358888888776543

>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=99.79  E-value=8.8e-21  Score=161.59  Aligned_cols=104  Identities=13%  Similarity=0.090  Sum_probs=87.5

Q ss_pred             CCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHH----------HHHHHHHhcccccccccccccCCCCCcCC
Q 028124           53 GLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETER----------TLILEEFRHTAMKWNQKVTEQSGDESETG  122 (213)
Q Consensus        53 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R----------~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~  122 (213)
                      +.++||||+|+++|+.|+..|++.| +++..+||+++++.|          ...+++|+.|+                  
T Consensus        36 ggk~LVFcnSR~~aE~La~~L~~~G-i~a~~~Hgglsq~~R~~~gd~~i~~~~aLe~f~~G~------------------   96 (299)
T d1a1va2          36 GGRHLIFCHSKKKCDELAAKLVALG-INAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGD------------------   96 (299)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHTT-CCEEEECTTSCGGGSCSSSSEEEEECTTC---CCCC------------------
T ss_pred             CCCEEEECCcHHHHHHHHHHHHHCC-CCEEEEeCCchHHHHHhccchHHHHHHHHHHHhcCC------------------
Confidence            4799999999999999999999998 899999999998876          45778888874                  


Q ss_pred             CCCCceeEEEEeCCCCCcCcC---CCCCCCCCEEEEecCCCChHHHHHhhccccCCCCeEEEEEe
Q 028124          123 KDEHKSHMIVVTDACLPLLSS---GESAISARVLINYELPTKKETYIRRMTTCLAADGSVINIVV  184 (213)
Q Consensus       123 ~~~~~~~iLV~Td~~~~~~~r---Gld~~~v~~VI~yd~P~~~~~yi~R~GR~~~~~g~~i~~~~  184 (213)
                           .+++|+|++    +++   |+|++.+.+|||||+|.|.++|+||+||+|+..+-.++++.
T Consensus        97 -----~dvVVaT~~----~a~g~~giDid~V~~VI~~d~P~SvesyIQRiGRTGRGr~G~~~~l~  152 (299)
T d1a1va2          97 -----FDSVIDCNT----CVTQTVDFSLDPTFTIETTTLPQDAVSRTQRRGRTGRGKPGIYRFVA  152 (299)
T ss_dssp             -----BSEEEECCE----EEEEEEECCCSSSCEEEEEEEECBHHHHHHHHTTBCSSSCEEEEESC
T ss_pred             -----CcEEEEEee----hhccCCCCCCCcceEEEeCCCCCCHHHHHhhccccCCCCCceEEEEe
Confidence                 999999999    998   66777788999999999999999999998765444555553

>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=99.74  E-value=2.7e-19  Score=145.96  Aligned_cols=133  Identities=12%  Similarity=0.124  Sum_probs=99.0

Q ss_pred             HHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHH--------HHHHHHhcc--CCceEEEecCCCCHHHHHHHHHHHhccc
Q 028124           35 KMETLVELLHLVVAGRRPGLPMIVCCSSRDELD--------AVCSAVSNL--ADISFSSLHSDLAETERTLILEEFRHTA  104 (213)
Q Consensus        35 K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~--------~l~~~L~~~--~~~~~~~lhg~~~~~~R~~~l~~Fr~g~  104 (213)
                      |.+.+.+.++.-   -..+.++.+.|+..+..+        ..++.|.+.  +++++..+||.|++++|.+++++|++|+
T Consensus        14 ~~~~v~~~I~~e---l~~g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~   90 (206)
T d1gm5a4          14 RVNEVYEFVRQE---VMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGR   90 (206)
T ss_dssp             THHHHHHHHHHH---TTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTS
T ss_pred             cHHHHHHHHHHH---HHcCCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCC
Confidence            555566666442   246789999998665443        344555432  4578899999999999999999999985


Q ss_pred             ccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCC-hHHHHHhhccc--cCCCCeEEE
Q 028124          105 MKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTK-KETYIRRMTTC--LAADGSVIN  181 (213)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~-~~~yi~R~GR~--~~~~g~~i~  181 (213)
                                             ++|||||++    .++|+|+|+|++||+|+.|.. .+.|.|..||+  +++.|.|+.
T Consensus        91 -----------------------~~iLVaTtV----iE~GIDip~a~~iii~~a~~fglsqlhQlrGRvGR~~~~~~~~l  143 (206)
T d1gm5a4          91 -----------------------YDILVSTTV----IEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFL  143 (206)
T ss_dssp             -----------------------SSBCCCSSC----CCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEEC
T ss_pred             -----------------------EEEEEEehh----hhccccccCCcEEEEEccCCccHHHHHhhhhheeeccccceeEe
Confidence                                   999999999    999999999999999999985 55555557995  677899999


Q ss_pred             EEeCchhHHHHHHHHH
Q 028124          182 IVVGGEVVTLRSMEES  197 (213)
Q Consensus       182 ~~~~~e~~~~~~le~~  197 (213)
                      ++.+.+....++++..
T Consensus       144 ~~~~~~~~~~~rl~~~  159 (206)
T d1gm5a4         144 VVGDVGEEAMERLRFF  159 (206)
T ss_dssp             CCCSCCHHHHHHHHHH
T ss_pred             eeccccccchhhhhhc
Confidence            9987655555555443

>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=99.70  E-value=1.2e-16  Score=130.08  Aligned_cols=135  Identities=12%  Similarity=0.139  Sum_probs=108.8

Q ss_pred             CCCCCCceEEEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc-CCceEEEecCCCCHHHHH
Q 028124           16 PSHFSQPRHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL-ADISFSSLHSDLAETERT   94 (213)
Q Consensus        16 ~~~~~~i~~~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~-~~~~~~~lhg~~~~~~R~   94 (213)
                      |..+..|+.++..  . + +..+...+.+++    ..+.|+.+.||..+..+.+++.+++. +++++..+||.|+++++.
T Consensus         2 P~gR~pI~T~v~~--~-~-~~~i~~~I~~El----~rGgQvy~V~p~I~~~e~~~~~l~~~~p~~~i~~lHGkm~~~eke   73 (211)
T d2eyqa5           2 PARRLAVKTFVRE--Y-D-SMVVREAILREI----LRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELE   73 (211)
T ss_dssp             CCBCBCEEEEEEE--C-C-HHHHHHHHHHHH----TTTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHH
T ss_pred             cccCcCeEEEEeC--C-C-HHHHHHHHHHHH----HcCCeEEEEEcCccchhhHHHHHHHhCCceEEEEEEeccCHHHHH
Confidence            5556667775432  2 2 333433444453    46899999999999999999999764 668999999999999999


Q ss_pred             HHHHHHhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCC-ChHHHHHhhccc-
Q 028124           95 LILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPT-KKETYIRRMTTC-  172 (213)
Q Consensus        95 ~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~-~~~~yi~R~GR~-  172 (213)
                      +++.+|++|+                       ++|||||.+    .+.|+|+|+++++|.++.++ -.+.+.|--||. 
T Consensus        74 ~im~~F~~g~-----------------------~~ILv~Ttv----IEvGiDvpnA~~iiI~~a~rfGLaQLhQLRGRVG  126 (211)
T d2eyqa5          74 RVMNDFHHQR-----------------------FNVLVCTTI----IETGIDIPTANTIIIERADHFGLAQLHQLRGRVG  126 (211)
T ss_dssp             HHHHHHHTTS-----------------------CCEEEESST----TGGGSCCTTEEEEEETTTTSSCHHHHHHHHTTCC
T ss_pred             HHHHHHHcCC-----------------------cceEEEehh----hhhccCCCCCcEEEEecchhccccccccccceee
Confidence            9999999985                       999999999    99999999999999999997 566666666995 


Q ss_pred             -cCCCCeEEEEEeC
Q 028124          173 -LAADGSVINIVVG  185 (213)
Q Consensus       173 -~~~~g~~i~~~~~  185 (213)
                       ++..|.|+.+...
T Consensus       127 R~~~~s~c~l~~~~  140 (211)
T d2eyqa5         127 RSHHQAYAWLLTPH  140 (211)
T ss_dssp             BTTBCEEEEEEECC
T ss_pred             ecCccceEEEEecC
Confidence             5667999998864

>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=99.64  E-value=1.7e-15  Score=131.90  Aligned_cols=140  Identities=15%  Similarity=0.160  Sum_probs=114.8

Q ss_pred             chHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccccccc
Q 028124           33 QFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVT  112 (213)
Q Consensus        33 ~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~  112 (213)
                      ..|+..|.++|+....  .++.|+|||++...+.+.|...|...| +....++|+++..+|..++++|+++.        
T Consensus       100 S~Kl~~L~~ll~~~~~--~~g~KvlIFs~~~~~ld~l~~~l~~~g-~~~~~l~G~~~~~~R~~~i~~F~~~~--------  168 (346)
T d1z3ix1         100 SGKMLVLDYILAMTRT--TTSDKVVLVSNYTQTLDLFEKLCRNRR-YLYVRLDGTMSIKKRAKIVERFNNPS--------  168 (346)
T ss_dssp             SHHHHHHHHHHHHHHH--HCCCEEEEEESCHHHHHHHHHHHHHHT-CCEEEECSSCCHHHHHHHHHHHHSTT--------
T ss_pred             CHHHHHHHHHHHHHHH--hcCCceeEEeehhhhhHHHHHHHhhhh-ccccccccchhHHHHHHHHHhhhccc--------
Confidence            3499999999976432  357899999999999999999999987 89999999999999999999999874        


Q ss_pred             ccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cCCC--CeEEEEEeCc--
Q 028124          113 EQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LAAD--GSVINIVVGG--  186 (213)
Q Consensus       113 ~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~~~--g~~i~~~~~~--  186 (213)
                                  .+..-+|++|.+    .+.|+|++.++.||+||++|++..+.|++||+  -|+.  -.++.|+..+  
T Consensus       169 ------------~~~~vlLls~~a----gg~GlnL~~a~~vi~~d~~wnp~~~~Qa~~R~~R~GQ~~~V~v~rli~~~Ti  232 (346)
T d1z3ix1         169 ------------SPEFIFMLSSKA----GGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTGTI  232 (346)
T ss_dssp             ------------CCCCEEEEEGGG----SCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEEEEEETTSH
T ss_pred             ------------ccceeeeecchh----hhhccccccceEEEEecCCCccchHhHhhhcccccCCCCceEEEEEEeCCCH
Confidence                        011237778888    99999999999999999999999999999996  3443  4667777776  


Q ss_pred             hhHHHHHHHHHhc
Q 028124          187 EVVTLRSMEESLG  199 (213)
Q Consensus       187 e~~~~~~le~~l~  199 (213)
                      |...++.+.....
T Consensus       233 Ee~i~~~~~~K~~  245 (346)
T d1z3ix1         233 EEKILQRQAHKKA  245 (346)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            5556666655543

>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=99.64  E-value=1.1e-15  Score=126.20  Aligned_cols=136  Identities=15%  Similarity=0.139  Sum_probs=102.8

Q ss_pred             chHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccccccc
Q 028124           33 QFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVT  112 (213)
Q Consensus        33 ~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~  112 (213)
                      ..|+..|.+++.....   ++.++||||+.....+.+...|....++.+..+||+++..+|..++++|.++.        
T Consensus        68 S~K~~~l~~~l~~~~~---~g~kviIFs~~~~~~~~l~~~l~~~~~~~~~~i~G~~~~~~R~~~i~~F~~~~--------  136 (244)
T d1z5za1          68 SGKMIRTMEIIEEALD---EGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNP--------  136 (244)
T ss_dssp             CHHHHHHHHHHHHHHH---TTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCT--------
T ss_pred             hhHHHHHHHHHHhhcc---cccceEEEeeceehHHHHHHHHHhhccceEEEEecccchhccchhhhhhhccc--------
Confidence            3499999999987533   57899999999999999999997652278888999999999999999999863        


Q ss_pred             ccCCCCCcCCCCCCceeEEEE-eCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc--cC--CCCeEEEEEeCc-
Q 028124          113 EQSGDESETGKDEHKSHMIVV-TDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC--LA--ADGSVINIVVGG-  186 (213)
Q Consensus       113 ~~~~~~~~~~~~~~~~~iLV~-Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~--~~--~~g~~i~~~~~~-  186 (213)
                                    ...+|++ |.+    .+.|+|++.+++||+||+||++..+.|++||+  .|  ++-.++.|+..+ 
T Consensus       137 --------------~~~vll~~~~~----~g~Glnl~~a~~vi~~~~~wn~~~~~Qa~~R~~R~Gq~~~v~i~~l~~~~T  198 (244)
T d1z5za1         137 --------------SVKFIVLSVKA----GGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGT  198 (244)
T ss_dssp             --------------TCCEEEEECCT----TCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEETTS
T ss_pred             --------------cchhccccccc----cccccccchhhhhhhcCchhhhHHHhhhcceeeecCCCCceEEEEEeeCCC
Confidence                          3566655 567    89999999999999999999999999999995  33  335777788776 


Q ss_pred             -hhHHHHHHHHH
Q 028124          187 -EVVTLRSMEES  197 (213)
Q Consensus       187 -e~~~~~~le~~  197 (213)
                       |...+..++..
T Consensus       199 iee~i~~~~~~K  210 (244)
T d1z5za1         199 LEEKIDQLLAFK  210 (244)
T ss_dssp             HHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHH
Confidence             44455555443

>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=99.40  E-value=3.3e-13  Score=112.59  Aligned_cols=101  Identities=14%  Similarity=0.078  Sum_probs=80.5

Q ss_pred             CCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEE
Q 028124           52 PGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMI  131 (213)
Q Consensus        52 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iL  131 (213)
                      ...+++|||++++.++.+++.|.+.+ +.+..+||++++..+    ..|+++.                       .+++
T Consensus       177 ~~~~~lvf~~~~~~~~~l~~~L~~~~-~~~~~l~~~~~~~~~----~~~~~~~-----------------------~~~l  228 (305)
T d2bmfa2         177 FKGKTVWFVPSIKAGNDIAACLRKNG-KKVIQLSRKTFDSEY----IKTRTND-----------------------WDFV  228 (305)
T ss_dssp             SCSCEEEECSCHHHHHHHHHHHHHHT-CCCEECCTTCHHHHG----GGGGTSC-----------------------CSEE
T ss_pred             hCCCEEEEeccHHHHHHHHHHHHhCC-CCEEEeCCcChHHHH----hhhhccc-----------------------hhhh
Confidence            46799999999999999999999987 799999999866554    4677764                       8999


Q ss_pred             EEeCCCCCcCcCCCCCCCCCEEE----------EecC----------CCChHHHHHhhcccc--CCCCeEEEEEeC
Q 028124          132 VVTDACLPLLSSGESAISARVLI----------NYEL----------PTKKETYIRRMTTCL--AADGSVINIVVG  185 (213)
Q Consensus       132 V~Td~~~~~~~rGld~~~v~~VI----------~yd~----------P~~~~~yi~R~GR~~--~~~g~~i~~~~~  185 (213)
                      |+|++    +++|+|+ +++.||          +||.          |-|.++|+||+||+|  ++.+....++..
T Consensus       229 vaT~~----~~~G~~~-~~~~Vi~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~Qr~GR~GR~~~~~~~~~~~~~  299 (305)
T d2bmfa2         229 VTTDI----SEMGANF-KAERVIDPRRCMKPVILTDGEERVILAGPMPVTHSSAAQRRGRVGRNPKNENDQYIYMG  299 (305)
T ss_dssp             EECGG----GGTTCCC-CCSEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCSSSCCCEEEEECS
T ss_pred             hhhHH----HHhcCCC-CccEEEEcCCceeeeEecCCCCceEEeccccCCHHHHhhhhcCcCcCCCCceEEEEECC
Confidence            99999    9999999 455554          4444          457899999999975  444666666543

>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=1.6e-12  Score=110.77  Aligned_cols=99  Identities=11%  Similarity=0.082  Sum_probs=76.0

Q ss_pred             CCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCCCCceeEEE
Q 028124           53 GLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIV  132 (213)
Q Consensus        53 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV  132 (213)
                      .++++|||++..+++.++..|++.| .++..+||.++..++.    +|++++                       .++||
T Consensus        36 ~g~~~~F~~s~~~~~~~a~~L~~~g-~~V~~l~~~~~~~e~~----~~~~~~-----------------------~~~~~   87 (299)
T d1yksa2          36 KRPTAWFLPSIRAANVMAASLRKAG-KSVVVLNRKTFEREYP----TIKQKK-----------------------PDFIL   87 (299)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTT-CCEEECCSSSCC------------CC-----------------------CSEEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhcC-CeEEEEcCcCcHhHHh----hhhcCC-----------------------cCEEE
Confidence            5799999999999999999999998 7999999999877754    577764                       89999


Q ss_pred             EeCCCCCcCcCCCCCCCCCEEEEecCC-------------------CChHHHHHhhccccCCCC--eEEEEEe
Q 028124          133 VTDACLPLLSSGESAISARVLINYELP-------------------TKKETYIRRMTTCLAADG--SVINIVV  184 (213)
Q Consensus       133 ~Td~~~~~~~rGld~~~v~~VI~yd~P-------------------~~~~~yi~R~GR~~~~~g--~~i~~~~  184 (213)
                      ||++    ++.|+|+ ++.+||++.++                   -+.++-.||.||+|+..+  .++.++.
T Consensus        88 ~t~~----~~~~~~~-~~~~vid~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~qr~gr~gr~~~~~~~~~~y~  155 (299)
T d1yksa2          88 ATDI----AEMGANL-CVERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYS  155 (299)
T ss_dssp             ESSS----TTCCTTC-CCSEEEECCEEEEEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEEC
T ss_pred             Eech----hhhceec-CceEEEecCceeceeeecCCCCeeEEeeeecCHHHHHHhcccccccCCCceEEEEeC
Confidence            9999    9999999 69999965532                   356888999999876543  3444443

>d1tf5a4 c.37.1.19 (A:396-570) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=98.90  E-value=1.3e-08  Score=79.77  Aligned_cols=124  Identities=14%  Similarity=0.147  Sum_probs=97.4

Q ss_pred             CcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccccc
Q 028124           31 RLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQK  110 (213)
Q Consensus        31 ~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~  110 (213)
                      ..+.|+.++.+.++...   ..++|+||+|.|....+.++..|+..+ +....++.....++ .+++.  ..|       
T Consensus        15 T~~eK~~AIi~eV~~~~---~~grPVLIgT~SIe~SE~ls~~L~~~g-i~h~vLnAk~~~~E-a~II~--~Ag-------   80 (175)
T d1tf5a4          15 TMEGKFKAVAEDVAQRY---MTGQPVLVGTVAVETSELISKLLKNKG-IPHQVLNAKNHERE-AQIIE--EAG-------   80 (175)
T ss_dssp             SHHHHHHHHHHHHHHHH---HHTCCEEEEESCHHHHHHHHHHHHTTT-CCCEEECSSCHHHH-HHHHT--TTT-------
T ss_pred             CHHHHHHHHHHHHHHHH---hcCCCEEEEeCcHHHHHHHHHHHHHcC-CCceeehhhhHHHH-HHHHH--hcc-------
Confidence            44459999988886643   367999999999999999999999987 89999998754333 33443  222       


Q ss_pred             ccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCC---CC-----EEEEecCCCChHHHHHhhcccc--CCCCeEE
Q 028124          111 VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAIS---AR-----VLINYELPTKKETYIRRMTTCL--AADGSVI  180 (213)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~---v~-----~VI~yd~P~~~~~yi~R~GR~~--~~~g~~i  180 (213)
                                     .+-.|.|+|++    ++||.|+.-   |.     +||.-..|.+..-..|-.||++  |.+|...
T Consensus        81 ---------------~~g~VtIATNm----AGRGtDikl~~~v~~~GGLhVI~t~~~~s~Rid~Ql~GR~gRQGdpGs~~  141 (175)
T d1tf5a4          81 ---------------QKGAVTIATNM----AGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQ  141 (175)
T ss_dssp             ---------------STTCEEEEETT----SSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEE
T ss_pred             ---------------CCCceeehhhH----HHcCCCccchHHHHhCCCcEEEEeccCcchhHHHHHhcchhhhCCCcccE
Confidence                           24679999999    999999842   22     7999999999999999999975  6679998


Q ss_pred             EEEeCch
Q 028124          181 NIVVGGE  187 (213)
Q Consensus       181 ~~~~~~e  187 (213)
                      .|++-+|
T Consensus       142 ~~~sleD  148 (175)
T d1tf5a4         142 FYLSMED  148 (175)
T ss_dssp             EEEETTS
T ss_pred             EEEEcCH
Confidence            8887654

>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=97.53  E-value=0.0014  Score=51.82  Aligned_cols=125  Identities=11%  Similarity=0.106  Sum_probs=93.1

Q ss_pred             CcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccccc
Q 028124           31 RLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQK  110 (213)
Q Consensus        31 ~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~  110 (213)
                      ....|+.++.+-++...   ..++|+||.+.|....+.|+..|.+.+ +...+|+..-. +.=..++.+--.        
T Consensus        15 T~~~K~~Avv~ei~~~h---~~GqPVLVGT~SVe~SE~lS~lL~~~g-i~h~vLNAK~h-erEAeIIAqAG~--------   81 (219)
T d1nkta4          15 TEEAKYIAVVDDVAERY---AKGQPVLIGTTSVERSEYLSRQFTKRR-IPHNVLNAKYH-EQEATIIAVAGR--------   81 (219)
T ss_dssp             CHHHHHHHHHHHHHHHH---HTTCCEEEEESCHHHHHHHHHHHHHTT-CCCEEECSSCH-HHHHHHHHTTTS--------
T ss_pred             CHHHHHHHHHHHHHHHH---hcCCCEEEeeCcHHHHHHHHHHHHHhc-cchhccchhhH-HHHHHHHHhccc--------
Confidence            34459999999887653   378999999999999999999999997 89999998643 322445544322        


Q ss_pred             ccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCC-----------------------------------------
Q 028124          111 VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAIS-----------------------------------------  149 (213)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~-----------------------------------------  149 (213)
                                      +-.|-|+|++    ++||.|+.=                                         
T Consensus        82 ----------------~GaVTIATNM----AGRGTDI~LGgn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  141 (219)
T d1nkta4          82 ----------------RGGVTVATNM----AGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEA  141 (219)
T ss_dssp             ----------------TTCEEEEETT----CSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHT
T ss_pred             ----------------CCcEEeeccc----cCCCCceeecCchhhhhHHHhhhcccCcccCHHHHHHHHHHHHHHHHHHH
Confidence                            4679999999    999999932                                         


Q ss_pred             ------C-----CEEEEecCCCChHHHHHhhcccc--CCCCeEEEEEeCchh
Q 028124          150 ------A-----RVLINYELPTKKETYIRRMTTCL--AADGSVINIVVGGEV  188 (213)
Q Consensus       150 ------v-----~~VI~yd~P~~~~~yi~R~GR~~--~~~g~~i~~~~~~e~  188 (213)
                            |     =+||--.-..|..-=-|=-||+|  |.+|....|++-+|.
T Consensus       142 ~~~~~~V~~~GGL~VIGTErHeSrRIDnQLRGRsGRQGDPGsSrFflSLeDd  193 (219)
T d1nkta4         142 SKEAKEVIEAGGLYVLGTERHESRRIDNQLRGRSGRQGDPGESRFYLSLGDE  193 (219)
T ss_dssp             THHHHHHHHTTSEEEEECSCCSSHHHHHHHHHTSSGGGCCEEEEEEEETTSH
T ss_pred             HHHHHHHHhcCCcEEEeccccccccccccccccccccCCCccceeEEeccHH
Confidence                  1     16777777766555556568875  557988888876543

>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=96.87  E-value=0.0027  Score=51.74  Aligned_cols=106  Identities=12%  Similarity=0.005  Sum_probs=77.8

Q ss_pred             HHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc----CCceEEEecCCCCHHHHHHHHHHHhccccccccc
Q 028124           35 KMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEEFRHTAMKWNQK  110 (213)
Q Consensus        35 K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~  110 (213)
                      |..+....+....   ..+.++++-++|..-+...++.+++.    | +.+..+||+++..+|.+++++.++|+      
T Consensus       117 KT~Va~~a~~~~~---~~g~q~~~m~Pt~~La~Qh~~~~~~~f~~~~-~~v~~l~~~~~~~~r~~~~~~~~~g~------  186 (264)
T d1gm5a3         117 KTVVAQLAILDNY---EAGFQTAFMVPTSILAIQHYRRTVESFSKFN-IHVALLIGATTPSEKEKIKSGLRNGQ------  186 (264)
T ss_dssp             HHHHHHHHHHHHH---HHTSCEEEECSCHHHHHHHHHHHHHHHTCSS-CCEEECCSSSCHHHHHHHHHHHHSSC------
T ss_pred             ccHHHHHHHHHHH---hcccceeEEeehHhhhHHHHHHHHHhhhhcc-ccceeeccccchHHHHHHHHHHHCCC------
Confidence            6555555443322   25789999999998888877666543    4 78999999999999999999999985      


Q ss_pred             ccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhccc
Q 028124          111 VTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTC  172 (213)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~GR~  172 (213)
                                       ++|+|.|-+   ++...+.+.+..+||.-.-.+  -.|-||-+-.
T Consensus       187 -----------------~~iiIGThs---l~~~~~~f~~LglviiDEqH~--fgv~Qr~~l~  226 (264)
T d1gm5a3         187 -----------------IDVVIGTHA---LIQEDVHFKNLGLVIIDEQHR--FGVKQREALM  226 (264)
T ss_dssp             -----------------CCEEEECTT---HHHHCCCCSCCCEEEEESCCC--C-----CCCC
T ss_pred             -----------------CCEEEeehH---HhcCCCCccccceeeeccccc--cchhhHHHHH
Confidence                             999999998   245578888999988876443  4677876543

>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=96.30  E-value=0.021  Score=45.38  Aligned_cols=114  Identities=17%  Similarity=0.035  Sum_probs=87.4

Q ss_pred             EEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc----CCceEEEecCCCCHHHHHHHHHHH
Q 028124           25 FYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEEF  100 (213)
Q Consensus        25 ~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~lhg~~~~~~R~~~l~~F  100 (213)
                      .++.-+-..=|..+....+....   ..+.++++-+++..-+...++.++++    + +.+..+||.++..+|..+++.+
T Consensus        79 ~LL~GdvGsGKT~V~~~a~~~~~---~~g~qv~~l~Pt~~La~Q~~~~~~~~~~~~~-~~v~~l~~~~~~~~~~~~~~~~  154 (233)
T d2eyqa3          79 RLVCGDVGFGKTEVAMRAAFLAV---DNHKQVAVLVPTTLLAQQHYDNFRDRFANWP-VRIEMISRFRSAKEQTQILAEV  154 (233)
T ss_dssp             EEEECCCCTTTHHHHHHHHHHHH---TTTCEEEEECSSHHHHHHHHHHHHHHSTTTT-CCEEEESTTSCHHHHHHHHHHH
T ss_pred             eEEEcCCCCCcHHHHHHHHHHHH---HcCCceEEEccHHHhHHHHHHHHHHHHhhCC-CEEEeccCcccchhHHHHHHHH
Confidence            34443333337777777665433   46899999999999999998888753    5 7899999999999999999999


Q ss_pred             hcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEecCCCChHHHHHhhc
Q 028124          101 RHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMT  170 (213)
Q Consensus       101 r~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~yd~P~~~~~yi~R~G  170 (213)
                      .+|+                       .+++|.|-+   ++...+.+.+..+||--+-.+  -.|-||.+
T Consensus       155 ~~g~-----------------------~~iviGths---~l~~~~~f~~LgLiIiDEeH~--fg~kQ~~~  196 (233)
T d2eyqa3         155 AEGK-----------------------IDILIGTHK---LLQSDVKFKDLGLLIVDEEHR--FGVRHKER  196 (233)
T ss_dssp             HTTC-----------------------CSEEEECTH---HHHSCCCCSSEEEEEEESGGG--SCHHHHHH
T ss_pred             hCCC-----------------------CCEEEeehh---hhccCCccccccceeeechhh--hhhHHHHH
Confidence            9985                       999999996   144578888999888766443  35566654

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=92.46  E-value=0.93  Score=34.01  Aligned_cols=104  Identities=13%  Similarity=0.133  Sum_probs=67.1

Q ss_pred             EEEEecCcchHHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc---CCceEEEecCCCCHHHHHHHHHHHh
Q 028124           25 FYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL---ADISFSSLHSDLAETERTLILEEFR  101 (213)
Q Consensus        25 ~~~~~~~~~~K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~---~~~~~~~lhg~~~~~~R~~~l~~Fr  101 (213)
                      .++..+...=|.-...-.+-.... ...+.+++|.|+|++-|..+.+.+...   .+..+...+|+.+..++.+.+   +
T Consensus        45 ~iv~a~TGsGKT~~~~l~~~~~~~-~~~~~~~lil~pt~~l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l---~  120 (208)
T d1hv8a1          45 IVAQARTGSGKTASFAIPLIELVN-ENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKAL---K  120 (208)
T ss_dssp             EEEECCSSSSHHHHHHHHHHHHSC-SSSSCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHH---H
T ss_pred             eeeechhcccccceeecccccccc-cccCcceEEEeeccccchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhc---C
Confidence            344444444354443333322122 356679999999999999987777653   346888999998877665433   3


Q ss_pred             cccccccccccccCCCCCcCCCCCCceeEEEEeCCCCC-cC-cCCCCCCCCCEEEEec
Q 028124          102 HTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLP-LL-SSGESAISARVLINYE  157 (213)
Q Consensus       102 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~-~~-~rGld~~~v~~VI~yd  157 (213)
                      +                         .+|+|+|+.++- .+ ...+++.++.++|--+
T Consensus       121 ~-------------------------~~IlV~TP~~l~~~l~~~~~~~~~l~~lViDE  153 (208)
T d1hv8a1         121 N-------------------------ANIVVGTPGRILDHINRGTLNLKNVKYFILDE  153 (208)
T ss_dssp             T-------------------------CSEEEECHHHHHHHHHTTCSCTTSCCEEEEET
T ss_pred             C-------------------------CCEEEEChHHHHHHHHcCCCCcccCcEEEEEC
Confidence            3                         779999964210 02 4567899999988754

>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=91.65  E-value=0.49  Score=36.41  Aligned_cols=104  Identities=9%  Similarity=0.019  Sum_probs=68.1

Q ss_pred             EEEEecCcchH-HHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc---CCceEEEecCCCCHHHHHHHHHHH
Q 028124           25 FYVAVDRLQFK-METLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL---ADISFSSLHSDLAETERTLILEEF  100 (213)
Q Consensus        25 ~~~~~~~~~~K-~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~---~~~~~~~lhg~~~~~~R~~~l~~F  100 (213)
                      ..+..+...=| +..+.-++..+.. .....+++|.|+|++-|..+++.+...   .++++..+.|+.+..+....+   
T Consensus        57 vi~~a~TGSGKTlayllPil~~l~~-~~~~~~~lil~PtreLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l---  132 (222)
T d2j0sa1          57 VIAQSQSGTGKTATFSISVLQCLDI-QVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKL---  132 (222)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHTCCT-TSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHH---
T ss_pred             eEEEcCcchhhhhhhcccccccccc-cccCceeEEecchHHHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHh---
Confidence            44444443323 3444445554322 345678999999999999998877654   237888999998776654443   


Q ss_pred             hcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCC--cCcCCCCCCCCCEEEEe
Q 028124          101 RHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLP--LLSSGESAISARVLINY  156 (213)
Q Consensus       101 r~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~--~~~rGld~~~v~~VI~y  156 (213)
                      +.+                        .+|+|+|+-++-  .....+++.++.++|--
T Consensus       133 ~~~------------------------~~Ilv~TPgrl~~~~~~~~~~~~~l~~lVlD  166 (222)
T d2j0sa1         133 DYG------------------------QHVVAGTPGRVFDMIRRRSLRTRAIKMLVLD  166 (222)
T ss_dssp             HHC------------------------CSEEEECHHHHHHHHHTTSSCCTTCCEEEEE
T ss_pred             ccC------------------------CeEEeCCCCcHHhcccccccccccceeeeec
Confidence            444                        789999975210  02677888999998863

>d1tq1a_ c.46.1.3 (A:) Thiosulfate sulfurtransferase/Senescence-associated protein {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Single-domain sulfurtransferase
domain: Thiosulfate sulfurtransferase/Senescence-associated protein
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=88.03  E-value=0.23  Score=34.33  Aligned_cols=38  Identities=11%  Similarity=0.069  Sum_probs=33.2

Q ss_pred             CCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCC
Q 028124           51 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDL   88 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~   88 (213)
                      .+..++|+||++-.++...+..|...|+-.+..+.|++
T Consensus        70 ~~~~~iv~~C~~G~rs~~a~~~L~~~G~~nv~~l~GG~  107 (119)
T d1tq1a_          70 GQSDNIIVGCQSGGRSIKATTDLLHAGFTGVKDIVGGY  107 (119)
T ss_dssp             CTTSSEEEEESSCSHHHHHHHHHHHHHCCSEEEEECCH
T ss_pred             CCCcEEEEEcCCcCcHHHHHHHHHhcccCCeEEecChH
Confidence            45789999999999999999999999854688899997

>d2eyqa2 c.37.1.19 (A:349-465) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=87.91  E-value=0.24  Score=34.50  Aligned_cols=76  Identities=12%  Similarity=0.110  Sum_probs=53.1

Q ss_pred             HHHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhccccccccccccc
Q 028124           35 KMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ  114 (213)
Q Consensus        35 K~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~  114 (213)
                      -++.|...++.      ...++||.|.+...++.|.+.|+..+ +.+..+.+.-          +|..+           
T Consensus        22 p~~~L~~~i~~------~~~~Vli~a~s~g~~erl~e~L~~~~-i~~~~~~~~~----------~~~~~-----------   73 (117)
T d2eyqa2          22 PLDALRKFLET------FDGPVVFSVESEGRREALGELLARIK-IAPQRIMRLD----------EASDR-----------   73 (117)
T ss_dssp             TTHHHHHHHTT------CCSCCCEEESSHHHHHHHHHHHGGGT-CCCEECSSGG----------GCCTT-----------
T ss_pred             HHHHHHHHHHh------CCCeEEEEECCccHHHHHHHHHHHcC-CCceEecChh----------hhcCc-----------
Confidence            45556666544      35689999999999999999999987 7765555431          12222           


Q ss_pred             CCCCCcCCCCCCceeEEEEeCCCCCcCcCCCCCCCCCEEEEe
Q 028124          115 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINY  156 (213)
Q Consensus       115 ~~~~~~~~~~~~~~~iLV~Td~~~~~~~rGld~~~v~~VI~y  156 (213)
                                    .+.|+...    +..|.-+++..++|--
T Consensus        74 --------------~~~i~~~~----l~~GF~~~~~~l~vIt   97 (117)
T d2eyqa2          74 --------------GRYLMIGA----AEHGFVDTVRNLALIC   97 (117)
T ss_dssp             --------------CCEEEECC----CCSCEEETTTTEEEEE
T ss_pred             --------------eEEEEEec----CccccccCCCCEEEEE
Confidence                          23444455    7999999999988864

>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=87.82  E-value=2.2  Score=31.84  Aligned_cols=106  Identities=10%  Similarity=0.123  Sum_probs=66.7

Q ss_pred             EEEEecCcchH-HHHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhcc----CCceEEEecCCCCHHHHHHHHHH
Q 028124           25 FYVAVDRLQFK-METLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNL----ADISFSSLHSDLAETERTLILEE   99 (213)
Q Consensus        25 ~~~~~~~~~~K-~~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~----~~~~~~~lhg~~~~~~R~~~l~~   99 (213)
                      ..+..+...=| +..+.-++..+.. .....+++|.|+++.-+..+.+.+...    +.+....++|+.+.......   
T Consensus        41 vl~~A~TGsGKTla~~lp~l~~~~~-~~~~~~~lil~PtreL~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---  116 (207)
T d1t6na_          41 VLCQAKSGMGKTAVFVLATLQQLEP-VTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEV---  116 (207)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHCCC-CTTCCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHH---
T ss_pred             eEEEeccccccccccccceeeeecc-cCCCceEEEEeccchhhHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHH---
Confidence            44444443324 3344445555322 345678999999999999888887654    33567888888876654332   


Q ss_pred             HhcccccccccccccCCCCCcCCCCCCceeEEEEeCCCCCc--CcCCCCCCCCCEEEEec
Q 028124          100 FRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPL--LSSGESAISARVLINYE  157 (213)
Q Consensus       100 Fr~g~~~~~~~~~~~~~~~~~~~~~~~~~~iLV~Td~~~~~--~~rGld~~~v~~VI~yd  157 (213)
                      +...                       ..++||+|+.++-.  -...+++.++.++|--+
T Consensus       117 l~~~-----------------------~~~ilI~TP~rl~~~~~~~~~~l~~l~~lVlDE  153 (207)
T d1t6na_         117 LKKN-----------------------CPHIVVGTPGRILALARNKSLNLKHIKHFILDE  153 (207)
T ss_dssp             HHHS-----------------------CCSEEEECHHHHHHHHHTTSSCCTTCCEEEEES
T ss_pred             HHhc-----------------------CCCEEEeCcchhhhhccCCceeccccceeehhh
Confidence            2222                       27899999852111  13567889999888644

>d1gmxa_ c.46.1.3 (A:) Sulfurtransferase GlpE {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Single-domain sulfurtransferase
domain: Sulfurtransferase GlpE
species: Escherichia coli [TaxId: 562]

Probab=87.56  E-value=0.44  Score=32.19  Aligned_cols=49  Identities=12%  Similarity=0.156  Sum_probs=38.7

Q ss_pred             HHHHHHHHHhhcCCCCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCC
Q 028124           37 ETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   89 (213)
Q Consensus        37 ~~L~~ll~~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~   89 (213)
                      ..|...+..    ..+.+++|+||.+-..+...+..|...|+-.+..+.|++.
T Consensus        46 ~~l~~~~~~----~~~~~~ivv~c~~g~rs~~~a~~L~~~G~~~v~~l~GG~~   94 (108)
T d1gmxa_          46 DTLGAFMRD----NDFDTPVMVMCYHGNSSKGAAQYLLQQGYDVVYSIDGGFE   94 (108)
T ss_dssp             HHHHHHHHH----SCTTSCEEEECSSSSHHHHHHHHHHHHTCSSEEEETTHHH
T ss_pred             hhHHHHhhh----ccccCcccccCCCChHHHHHHHHHHHcCCCCEEEEcChHH
Confidence            445555655    2467899999999999999999999998446888999863

>d1yt8a4 c.46.1.2 (A:243-372) Thiosulfate sulfurtransferase PA2603 {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: Thiosulfate sulfurtransferase PA2603
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=84.77  E-value=0.59  Score=32.65  Aligned_cols=38  Identities=8%  Similarity=0.057  Sum_probs=33.7

Q ss_pred             CCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCC
Q 028124           51 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   89 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~   89 (213)
                      .+.+++++||.+-..+...+..|++.| +.+..+.|++.
T Consensus        78 ~~~~~ivl~C~~G~rS~~aa~~L~~~G-~~v~~l~GG~~  115 (130)
T d1yt8a4          78 VRGARLVLVDDDGVRANMSASWLAQMG-WQVAVLDGLSE  115 (130)
T ss_dssp             SBTCEEEEECSSSSHHHHHHHHHHHTT-CEEEEECSCCG
T ss_pred             CccceEEeecCCCccHHHHHHHHHHcC-CCeEEEcCchH
Confidence            467899999999999999999999998 69999999873

>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=83.68  E-value=1.1  Score=33.87  Aligned_cols=77  Identities=10%  Similarity=0.132  Sum_probs=54.1

Q ss_pred             CCCcEEEEeCchHHHHHHHHHHhcc----C---CceEEEecCCCCHHHHHHHHHHHhcccccccccccccCCCCCcCCCC
Q 028124           52 PGLPMIVCCSSRDELDAVCSAVSNL----A---DISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKD  124 (213)
Q Consensus        52 ~~~~~IIF~~~~~~~~~l~~~L~~~----~---~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~~~~~~~~~~~~~~~~~~~  124 (213)
                      ++.++||.++++.-++.+++.+++.    +   ......++++.+..++.+.++....                      
T Consensus        85 ~~~rvliv~Pt~~La~Q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~----------------------  142 (237)
T d1gkub1          85 KGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRN----------------------  142 (237)
T ss_dssp             TSCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGG----------------------
T ss_pred             hcCeEEEEeccHHHHHHHHHHHHHHHHHcCCceEEEEeeeecccchhhhhhhhccccc----------------------
Confidence            5679999999999999998888653    1   1335667788877777766655544                      


Q ss_pred             CCceeEEEEeCCCCCcCcCC-CCCCCCCEEEEe
Q 028124          125 EHKSHMIVVTDACLPLLSSG-ESAISARVLINY  156 (213)
Q Consensus       125 ~~~~~iLV~Td~~~~~~~rG-ld~~~v~~VI~y  156 (213)
                         .+|+|+|...   +.+. .++.++++||.-
T Consensus       143 ---~~Ilv~Tp~~---l~~~~~~~~~~~~vVvD  169 (237)
T d1gkub1         143 ---FKIVITTTQF---LSKHYRELGHFDFIFVD  169 (237)
T ss_dssp             ---CSEEEEEHHH---HHHCSTTSCCCSEEEES
T ss_pred             ---cceeccChHH---HHHhhhhcCCCCEEEEE
Confidence               6799999641   3332 355678888763

>d1urha2 c.46.1.2 (A:149-268) 3-mercaptopyruvate sulfurtransferase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: 3-mercaptopyruvate sulfurtransferase
species: Escherichia coli [TaxId: 562]

Probab=83.56  E-value=1.1  Score=30.24  Aligned_cols=39  Identities=21%  Similarity=0.213  Sum_probs=32.8

Q ss_pred             CCCCcEEEEeCchHHHHHHHHHHhccCCceEEEecCCCC
Q 028124           51 RPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLA   89 (213)
Q Consensus        51 ~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~lhg~~~   89 (213)
                      ....++|+||++-.++...+..|...|+-.+..+.|++.
T Consensus        80 ~~~~~ii~yC~sG~~A~~~~~~L~~lG~~~v~~y~Gs~~  118 (120)
T d1urha2          80 SYDKPIIVSCGSGVTAAVVLLALATLDVPNVKLYDGAWS  118 (120)
T ss_dssp             CSSSCEEEECCSSSTHHHHHHHHHHTTCSSCEEECCSCC
T ss_pred             CccCceEEEccchhHHHHHHHHHHHcCCCCceEcCCChh
Confidence            567899999999999999999998888546888888875