Psyllid ID: psy14082

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230---
Protein Sequence
MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPKGPQDCLPLHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQVIEVVQDYEKEKRLFSLIRELGKYTLITQESSSTLSEMVL
Secondary Structure (PSIPRED)
cccccccccEEccccEEEEcccccccccccccccccccccccccccEEEEcccHHHHHHHHHHHHHHHHcccEEEEEcccccccccccHHHHHHHHHHHHHHccccccEEEEEcccHHHHHHHHHHHcccccHHHHHccccHHHHHHHHHHccccccHHHHHHHHHHccccccccEEEEEccccccccccccEEEEEcccccHHHHHHHHHHHcccEEEEEcccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHccccEcHHHEEEEEEcHHHHHHcccccHHHHHHHcccccccEEEEcccHHHHHHHHHHHHHHHcccEEEEEEcccccEEEEEEEccccHHHHcHEEEcccccHEEHHHHcHHHHHHHHHHHHccccHHHHHHHcccHHHHHHHHHHccccccHEHHHHHHHHccccccccEEEEccccccHHHHHcccccEEcccccEEEEEEEccccHHHHHHHHHHHHcccccccc
Coil and Loop (DISEMBL)
mlppsesgcqnfskitnyllsppqymlpaavhishqepvkqgdgpialvlAPTRELAQQIQTVAKEFSSALRNICifggtpkgpqdclplhrfvfncqyemaknpaFKVIVFVETKKKVEDITRALRRERHSaicihgdktqqdrDYVLNdfrqgkapilVATDVaargldvedvntvNIGSLQLSANHNISQVIEVVQDYEKEKRLFSLIRELGKYTLITQESSSTLSEMVL
Flexible Loop (DISEMBL)
mlppsesgCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPKGPQDCLPLHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITralrrerhsaicihgdktqqdrDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSlqlsanhnISQVIEVVQDYEKEKRLFSLIRELgkytlitqessstlsemvl
Low Complexity Region (SEG)
MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPKGPQDCLPLHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQVIEVVQDYEKEKRLFSLIRELGKYTLITQESSSTLSEMVL
Disordered region (IsUnstruct)
***********FSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPKGPQDCLPLHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQVIEVVQDYEKEKRLFSLIRELGKYTLIT************
Disordered Region (DISOPRED)
*****ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPKGPQDCLPLHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQVIEVVQDYEKEKRLFSLIRELGKYTLITQESSSTLSEMVL
Disordered Region (DISEMBL)
********CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPKGPQDCLPLHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQVIEVVQDYEKEKRLFSLIRELGKYTLITQE**********
Disordered Region (DISPRO)
MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPKGPQDCLPLHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQVIEVVQDYEKEKRLFSLIRELGKYTLITQESSSTLS***L
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPKGPQDCLPLHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQVIEVVQDYEKEKRLFSLIRELGKYTLITQESSSTLSEMVL
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	233	2.2.26 [Sep-21-2011]
A5A6J2	614	Probable ATP-dependent RN	yes	N/A	0.763	0.289	0.398	6e-27
Q5R4I9	614	Probable ATP-dependent RN	yes	N/A	0.763	0.289	0.393	7e-26
P17844	614	Probable ATP-dependent RN	yes	N/A	0.763	0.289	0.393	7e-26
Q4R6M5	614	Probable ATP-dependent RN	N/A	N/A	0.763	0.289	0.393	8e-26
Q61656	614	Probable ATP-dependent RN	yes	N/A	0.763	0.289	0.393	8e-26
P19109	719	ATP-dependent RNA helicas	yes	N/A	0.763	0.247	0.383	2e-25
Q92841	729	Probable ATP-dependent RN	no	N/A	0.763	0.244	0.378	2e-25
Q501J6	650	Probable ATP-dependent RN	no	N/A	0.763	0.273	0.378	2e-25
P0CQ76	540	ATP-dependent RNA helicas	yes	N/A	0.815	0.351	0.369	9e-22
P0CQ77	540	ATP-dependent RNA helicas	N/A	N/A	0.815	0.351	0.369	9e-22

>sp|A5A6J2|DDX5_PANTR Probable ATP-dependent RNA helicase DDX5 OS=Pan troglodytes GN=DDX5 PE=2 SV=1

 Score =  120 bits (302), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 80/201 (39%), Positives = 114/201 (56%), Gaps = 23/201 (11%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSA--LRNICIFGGTPK 82
           Y+LPA VHI+HQ  +++GDGPI LVLAPTRELAQQ+Q VA E+  A  L++ CI+GG PK
Sbjct: 148 YLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPK 207

Query: 83  GPQDCLPLHRFVFNCQYEMAKNPAFKVIVFVETKKK---------VEDITRALRRERHSA 133
           GPQ    L R V NC       P  ++I F+E  K          +++  R L       
Sbjct: 208 GPQ-IRDLERGVENC----IATPG-RLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQ 261

Query: 134 ICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQ 193
           I    D+ + DR  ++      K    +A D       ++D   +NIG+L+LSANHNI Q
Sbjct: 262 IRKIVDQIRPDRQTLMWSATWPKEVRQLAEDF------LKDYIHINIGALELSANHNILQ 315

Query: 194 VIEVVQDYEKEKRLFSLIREL 214
           +++V  D EK+++L  L+ E+
Sbjct: 316 IVDVCHDVEKDEKLIRLMEEI 336

Involved in the alternative regulation of pre-mRNA splicing; its RNA helicase activity is necessary for increasing tau exon 10 inclusion and occurs in a RBM4-dependent manner. Binds to the tau pre-mRNA in the stem-loop region downstream of exon 10. The rate of ATP hydrolysis is highly stimulated by single-stranded RNA. Involved in transcriptional regulation; the function is independent of the RNA helicase activity. Transcriptional coactivator for estrogen receptor ESR1 and androgen receptor AR. Increases ESR1 AF-1 domain-mediated transactivation and ESR1 AF-1 and AF-2 domains transcriptional synergistic activity. Synergizes with DDX17 and SRA1 RNA to activate MYOD1 transcriptional activity and involved in skeletal muscle differentiation. Transcriptional coactivator for p53/TP53 and involved in p53/TP53 transcriptional response to DNA damage and p53/TP53-dependent apoptosis. Transcriptional coactivator for RUNX2 and involved in regulation of osteoblast differentiation. Acts as transcriptional repressor in a promoter-specicic manner; the function probbaly involves association with histone deacetylases, such as HDAC1.
Pan troglodytes (taxid: 9598)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q5R4I9|DDX5_PONAB Probable ATP-dependent RNA helicase DDX5 OS=Pongo abelii GN=DDX5 PE=2 SV=1

 Score =  117 bits (293), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 79/201 (39%), Positives = 113/201 (56%), Gaps = 23/201 (11%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSA--LRNICIFGGTPK 82
           Y+LPA VHI+HQ  +++GDGPI LVLAPTRELAQQ+Q VA E+  A  L++ CI+GG PK
Sbjct: 148 YLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPK 207

Query: 83  GPQDCLPLHRFVFNCQYEMAKNPAFKVIVFVETKKK---------VEDITRALRRERHSA 133
           GPQ    L R V  C       P  ++I F+E  K          +++  R L       
Sbjct: 208 GPQ-IRDLERGVEIC----IATPG-RLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQ 261

Query: 134 ICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQ 193
           I    D+ + DR  ++      K    +A D       ++D   +NIG+L+LSANHNI Q
Sbjct: 262 IRKIVDQIRPDRQTLMWSATWPKEVRQLAEDF------LKDYIHINIGALELSANHNILQ 315

Query: 194 VIEVVQDYEKEKRLFSLIREL 214
           +++V  D EK+++L  L+ E+
Sbjct: 316 IVDVCHDVEKDEKLIRLMEEI 336

Involved in the alternative regulation of pre-mRNA splicing; its RNA helicase activity is necessary for increasing tau exon 10 inclusion and occurs in a RBM4-dependent manner. Binds to the tau pre-mRNA in the stem-loop region downstream of exon 10. The rate of ATP hydrolysis is highly stimulated by single-stranded RNA. Involved in transcriptional regulation; the function is independent of the RNA helicase activity. Transcriptional coactivator for estrogen receptor ESR1 and androgen receptor AR. Increases ESR1 AF-1 domain-mediated transactivation and ESR1 AF-1 and AF-2 domains transcriptional synergistic activity. Synergizes with DDX17 and SRA1 RNA to activate MYOD1 transcriptional activity and involved in skeletal muscle differentiation. Transcriptional coactivator for p53/TP53 and involved in p53/TP53 transcriptional response to DNA damage and p53/TP53-dependent apoptosis. Transcriptional coactivator for RUNX2 and involved in regulation of osteoblast differentiation. Acts as transcriptional repressor in a promoter-specicic manner; the function probbaly involves association with histone deacetylases, such as HDAC1.

Pongo abelii (taxid: 9601)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|P17844|DDX5_HUMAN Probable ATP-dependent RNA helicase DDX5 OS=Homo sapiens GN=DDX5 PE=1 SV=1

 Score =  117 bits (293), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 79/201 (39%), Positives = 113/201 (56%), Gaps = 23/201 (11%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSA--LRNICIFGGTPK 82
           Y+LPA VHI+HQ  +++GDGPI LVLAPTRELAQQ+Q VA E+  A  L++ CI+GG PK
Sbjct: 148 YLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPK 207

Query: 83  GPQDCLPLHRFVFNCQYEMAKNPAFKVIVFVETKKK---------VEDITRALRRERHSA 133
           GPQ    L R V  C       P  ++I F+E  K          +++  R L       
Sbjct: 208 GPQ-IRDLERGVEIC----IATPG-RLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQ 261

Query: 134 ICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQ 193
           I    D+ + DR  ++      K    +A D       ++D   +NIG+L+LSANHNI Q
Sbjct: 262 IRKIVDQIRPDRQTLMWSATWPKEVRQLAEDF------LKDYIHINIGALELSANHNILQ 315

Query: 194 VIEVVQDYEKEKRLFSLIREL 214
           +++V  D EK+++L  L+ E+
Sbjct: 316 IVDVCHDVEKDEKLIRLMEEI 336

Involved in the alternative regulation of pre-mRNA splicing; its RNA helicase activity is necessary for increasing tau exon 10 inclusion and occurs in a RBM4-dependent manner. Binds to the tau pre-mRNA in the stem-loop region downstream of exon 10. The rate of ATP hydrolysis is highly stimulated by single-stranded RNA. Involved in transcriptional regulation; the function is independent of the RNA helicase activity. Transcriptional coactivator for estrogen receptor ESR1 and androgen receptor AR. Increases ESR1 AF-1 domain-mediated transactivation and ESR1 AF-1 and AF-2 domains transcriptional synergistic activity. Synergizes with DDX17 and SRA1 RNA to activate MYOD1 transcriptional activity and involved in skeletal muscle differentiation. Transcriptional coactivator for p53/TP53 and involved in p53/TP53 transcriptional response to DNA damage and p53/TP53-dependent apoptosis. Transcriptional coactivator for RUNX2 and involved in regulation of osteoblast differentiation. Acts as transcriptional repressor in a promoter-specicic manner; the function probbaly involves association with histone deacetylases, such as HDAC1.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q4R6M5|DDX5_MACFA Probable ATP-dependent RNA helicase DDX5 OS=Macaca fascicularis GN=DDX5 PE=2 SV=1

 Score =  117 bits (293), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 79/201 (39%), Positives = 113/201 (56%), Gaps = 23/201 (11%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSA--LRNICIFGGTPK 82
           Y+LPA VHI+HQ  +++GDGPI LVLAPTRELAQQ+Q VA E+  A  L++ CI+GG PK
Sbjct: 148 YLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPK 207

Query: 83  GPQDCLPLHRFVFNCQYEMAKNPAFKVIVFVETKKK---------VEDITRALRRERHSA 133
           GPQ    L R V  C       P  ++I F+E  K          +++  R L       
Sbjct: 208 GPQ-IRDLERGVEIC----IATPG-RLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQ 261

Query: 134 ICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQ 193
           I    D+ + DR  ++      K    +A D       ++D   +NIG+L+LSANHNI Q
Sbjct: 262 IRKIVDQIRPDRQTLMWSATWPKEVRQLAEDF------LKDYIHINIGALELSANHNILQ 315

Query: 194 VIEVVQDYEKEKRLFSLIREL 214
           +++V  D EK+++L  L+ E+
Sbjct: 316 IVDVCHDVEKDEKLIRLMEEI 336

Involved in the alternative regulation of pre-mRNA splicing; its RNA helicase activity is necessary for increasing tau exon 10 inclusion and occurs in a RBM4-dependent manner. Binds to the tau pre-mRNA in the stem-loop region downstream of exon 10. The rate of ATP hydrolysis is highly stimulated by single-stranded RNA. Involved in transcriptional regulation; the function is independent of the RNA helicase activity. Transcriptional coactivator for estrogen receptor ESR1 and androgen receptor AR. Increases ESR1 AF-1 domain-mediated transactivation and ESR1 AF-1 and AF-2 domains transcriptional synergistic activity. Synergizes with DDX17 and SRA1 RNA to activate MYOD1 transcriptional activity and involved in skeletal muscle differentiation. Transcriptional coactivator for p53/TP53 and involved in p53/TP53 transcriptional response to DNA damage and p53/TP53-dependent apoptosis. Transcriptional coactivator for RUNX2 and involved in regulation of osteoblast differentiation. Acts as transcriptional repressor in a promoter-specicic manner; the function probbaly involves association with histone deacetylases, such as HDAC1.

Macaca fascicularis (taxid: 9541)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q61656|DDX5_MOUSE Probable ATP-dependent RNA helicase DDX5 OS=Mus musculus GN=Ddx5 PE=1 SV=2

 Score =  117 bits (292), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 79/201 (39%), Positives = 113/201 (56%), Gaps = 23/201 (11%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSA--LRNICIFGGTPK 82
           Y+LPA VHI+HQ  +++GDGPI LVLAPTRELAQQ+Q VA E+  A  L++ CI+GG PK
Sbjct: 148 YLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPK 207

Query: 83  GPQDCLPLHRFVFNCQYEMAKNPAFKVIVFVETKKK---------VEDITRALRRERHSA 133
           GPQ    L R V  C       P  ++I F+E  K          +++  R L       
Sbjct: 208 GPQ-IRDLERGVEIC----IATPG-RLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQ 261

Query: 134 ICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQ 193
           I    D+ + DR  ++      K    +A D       ++D   +NIG+L+LSANHNI Q
Sbjct: 262 IRKIVDQIRPDRQTLMWSATWPKEVRQLAEDF------LKDYIHINIGALELSANHNILQ 315

Query: 194 VIEVVQDYEKEKRLFSLIREL 214
           +++V  D EK+++L  L+ E+
Sbjct: 316 IVDVCHDVEKDEKLIRLMEEI 336

Involved in the alternative regulation of pre-mRNA splicing; its RNA helicase activity is necessary for increasing tau exon 10 inclusion and occurs in a RBM4-dependent manner. Binds to the tau pre-mRNA in the stem-loop region downstream of exon 10. The rate of ATP hydrolysis is highly stimulated by single-stranded RNA. Involved in transcriptional regulation; the function is independent of the RNA helicase activity. Transcriptional coactivator for estrogen receptor ESR1 and androgen receptor AR. Increases ESR1 AF-1 domain-mediated transactivation and ESR1 AF-1 and AF-2 domains transcriptional synergistic activity. Synergizes with DDX17 and SRA1 RNA to activate MYOD1 transcriptional activity and involved in skeletal muscle differentiation. Transcriptional coactivator for p53/TP53 and involved in p53/TP53 transcriptional response to DNA damage and p53/TP53-dependent apoptosis. Transcriptional coactivator for RUNX2 and involved in regulation of osteoblast differentiation. Acts as transcriptional repressor in a promoter-specicic manner; the function probbaly involves association with histone deacetylases, such as HDAC1.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|P19109|DDX17_DROME ATP-dependent RNA helicase p62 OS=Drosophila melanogaster GN=Rm62 PE=1 SV=3

 Score =  115 bits (289), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 77/201 (38%), Positives = 113/201 (56%), Gaps = 23/201 (11%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGGTPK 82
           Y+LPA VHI++Q+P+++GDGPIALVLAPTRELAQQIQ VA EF  SS +RN C+FGG PK
Sbjct: 335 YILPAIVHINNQQPLQRGDGPIALVLAPTRELAQQIQQVATEFGSSSYVRNTCVFGGAPK 394

Query: 83  GPQDCLPLHRFVFNCQYEMAKNPAFKVIVFVETKKK---------VEDITRALRRERHSA 133
           G Q    +      C+  +A  P  ++I F+              +++  R L       
Sbjct: 395 GGQ----MRDLQRGCEIVIA-TPG-RLIDFLSAGSTNLKRCTYLVLDEADRMLDMGFEPQ 448

Query: 134 ICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQ 193
           I     + + DR  ++      K    +A D     +       +NIGSL+LSANHNI Q
Sbjct: 449 IRKIVSQIRPDRQTLMWSATWPKEVKQLAEDFLGNYIQ------INIGSLELSANHNIRQ 502

Query: 194 VIEVVQDYEKEKRLFSLIREL 214
           V++V  ++ KE++L +L+ ++
Sbjct: 503 VVDVCDEFSKEEKLKTLLSDI 523

Involved in RNA interference (RNAi); double-stranded RNA induces potent and specific gene silencing. RNAi is mediated by the RNA-induced silencing complex (RISC), a sequence-specific, multicomponent nuclease that destroys messenger RNAs homologous to the silencing trigger.

Drosophila melanogaster (taxid: 7227)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q92841|DDX17_HUMAN Probable ATP-dependent RNA helicase DDX17 OS=Homo sapiens GN=DDX17 PE=1 SV=2

 Score =  115 bits (289), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 76/201 (37%), Positives = 112/201 (55%), Gaps = 23/201 (11%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS--SALRNICIFGGTPK 82
           Y+LPA VHI+HQ  +++GDGPI LVLAPTRELAQQ+Q VA ++   S L++ CI+GG PK
Sbjct: 225 YLLPAIVHINHQPYLERGDGPICLVLAPTRELAQQVQQVADDYGKCSRLKSTCIYGGAPK 284

Query: 83  GPQDCLPLHRFVFNCQYEMAKNPAFKVIVFVETKKK---------VEDITRALRRERHSA 133
           GPQ    L R V  C       P  ++I F+E+ K          +++  R L       
Sbjct: 285 GPQ-IRDLERGVEIC----IATPG-RLIDFLESGKTNLRRCTYLVLDEADRMLDMGFEPQ 338

Query: 134 ICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQ 193
           I    D+ + DR  ++      K    +A D       + D   +N+G+L+LSANHNI Q
Sbjct: 339 IRKIVDQIRPDRQTLMWSATWPKEVRQLAEDF------LRDYTQINVGNLELSANHNILQ 392

Query: 194 VIEVVQDYEKEKRLFSLIREL 214
           +++V  + EK+ +L  L+ E+
Sbjct: 393 IVDVCMESEKDHKLIQLMEEI 413

RNA-dependent ATPase activity. Involved in transcriptional regulation. Transcriptional coactivator for estrogen receptor ESR1. Increases ESR1 AF-1 domain-mediated transactivation. Synergizes with DDX5 and SRA1 RNA to activate MYOD1 transcriptional activity and probably involved in skeletal muscle differentiation.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q501J6|DDX17_MOUSE Probable ATP-dependent RNA helicase DDX17 OS=Mus musculus GN=Ddx17 PE=2 SV=1

 Score =  115 bits (289), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 76/201 (37%), Positives = 112/201 (55%), Gaps = 23/201 (11%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS--SALRNICIFGGTPK 82
           Y+LPA VHI+HQ  +++GDGPI LVLAPTRELAQQ+Q VA ++   S L++ CI+GG PK
Sbjct: 146 YLLPAIVHINHQPYLERGDGPICLVLAPTRELAQQVQQVADDYGKCSRLKSTCIYGGAPK 205

Query: 83  GPQDCLPLHRFVFNCQYEMAKNPAFKVIVFVETKKK---------VEDITRALRRERHSA 133
           GPQ    L R V  C       P  ++I F+E+ K          +++  R L       
Sbjct: 206 GPQ-IRDLERGVEIC----IATPG-RLIDFLESGKTNLRRCTYLVLDEADRMLDMGFEPQ 259

Query: 134 ICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQ 193
           I    D+ + DR  ++      K    +A D       + D   +N+G+L+LSANHNI Q
Sbjct: 260 IRKIVDQIRPDRQTLMWSATWPKEVRQLAEDF------LRDYTQINVGNLELSANHNILQ 313

Query: 194 VIEVVQDYEKEKRLFSLIREL 214
           +++V  + EK+ +L  L+ E+
Sbjct: 314 IVDVCMESEKDHKLIQLMEEI 334

RNA-dependent ATPase activity. Involved in transcriptional regulation. Transcriptional coactivator for estrogen receptor ESR1. Increases ESR1 AF-1 domain-mediated transactivation (By similarity). Synergizes with DDX5 and SRA1 RNA to activate MYOD1 transcriptional activity and probably involved in skeletal muscle differentiation.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|P0CQ76|DBP2_CRYNJ ATP-dependent RNA helicase DBP2-A OS=Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC MYA-565) GN=DBP2 PE=3 SV=1

 Score =  103 bits (257), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 78/211 (36%), Positives = 112/211 (53%), Gaps = 21/211 (9%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGGTPK 82
           + LPA VHI+ Q  +  GDGPI L+LAPTRELA QIQT A +F  SS +RN  I+GG PK
Sbjct: 164 FCLPAMVHINAQPLLAPGDGPIVLILAPTRELAVQIQTEATKFGQSSRIRNTAIYGGAPK 223

Query: 83  GPQDCLPLHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQ 142
           GPQ    L R V  C       P  ++I  +ET K        L  +    +   G + Q
Sbjct: 224 GPQ-IRDLQRGVEIC----VATPG-RLIDMLETGKTNLKRVTYLVMDEADRMLDMGFEPQ 277

Query: 143 QDRDYVLNDFRQGKAPILVAT----DVAARGLD-VEDVNTVNIGSLQLSANHNISQVIEV 197
             +  +++  R  +  +L +     +V    +D + D   VNIGSL L+ANHN++Q +EV
Sbjct: 278 IRK--IVSQIRPDRQTLLFSATWPKEVQRLAMDFLHDFIQVNIGSLDLTANHNVAQHVEV 335

Query: 198 VQDYEKEKRLFSLIRELGKYTLITQESSSTL 228
             D++K  +L S + +      I+QE+   L
Sbjct: 336 CTDFDKRSKLLSHLEK------ISQENGKVL 360

ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.

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

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|P0CQ77|DBP2_CRYNB ATP-dependent RNA helicase DBP2-A OS=Cryptococcus neoformans var. neoformans serotype D (strain B-3501A) GN=DBP2 PE=3 SV=1

 Score =  103 bits (257), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 78/211 (36%), Positives = 112/211 (53%), Gaps = 21/211 (9%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGGTPK 82
           + LPA VHI+ Q  +  GDGPI L+LAPTRELA QIQT A +F  SS +RN  I+GG PK
Sbjct: 164 FCLPAMVHINAQPLLAPGDGPIVLILAPTRELAVQIQTEATKFGQSSRIRNTAIYGGAPK 223

Query: 83  GPQDCLPLHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQ 142
           GPQ    L R V  C       P  ++I  +ET K        L  +    +   G + Q
Sbjct: 224 GPQ-IRDLQRGVEIC----VATPG-RLIDMLETGKTNLKRVTYLVMDEADRMLDMGFEPQ 277

Query: 143 QDRDYVLNDFRQGKAPILVAT----DVAARGLD-VEDVNTVNIGSLQLSANHNISQVIEV 197
             +  +++  R  +  +L +     +V    +D + D   VNIGSL L+ANHN++Q +EV
Sbjct: 278 IRK--IVSQIRPDRQTLLFSATWPKEVQRLAMDFLHDFIQVNIGSLDLTANHNVAQHVEV 335

Query: 198 VQDYEKEKRLFSLIRELGKYTLITQESSSTL 228
             D++K  +L S + +      I+QE+   L
Sbjct: 336 CTDFDKRSKLLSHLEK------ISQENGKVL 360

ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.

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

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	233
328697410	718	PREDICTED: probable ATP-dependent RNA he	0.763	0.247	0.447	2e-31
389585395	465	helicase [Plasmodium cynomolgi strain B]	0.811	0.406	0.357	2e-30
380014980	728	PREDICTED: probable ATP-dependent RNA he	0.772	0.247	0.418	1e-28
328780921	726	PREDICTED: probable ATP-dependent RNA he	0.772	0.247	0.418	1e-28
307183175	705	Probable ATP-dependent RNA helicase DDX1	0.768	0.253	0.425	2e-28
332025289	706	Putative ATP-dependent RNA helicase DDX1	0.768	0.253	0.420	3e-28
307202009	724	Probable ATP-dependent RNA helicase DDX1	0.768	0.247	0.420	5e-28
383862185	713	PREDICTED: probable ATP-dependent RNA he	0.772	0.252	0.418	6e-28
340717724	713	PREDICTED: probable ATP-dependent RNA he	0.772	0.252	0.413	2e-27
350418218	712	PREDICTED: probable ATP-dependent RNA he	0.772	0.252	0.413	2e-27

>gi|328697410|ref|XP_001948642.2| PREDICTED: probable ATP-dependent RNA helicase DDX5-like [Acyrthosiphon pisum]

 Score =  141 bits (355), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 89/199 (44%), Positives = 123/199 (61%), Gaps = 21/199 (10%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPKGP 84
           YMLPAAVHIS+QEP+++GDGPIALVLAPTRELAQQIQ+VAK FSS++RN CIFGGTPKGP
Sbjct: 161 YMLPAAVHISNQEPLQRGDGPIALVLAPTRELAQQIQSVAKMFSSSIRNTCIFGGTPKGP 220

Query: 85  QDCLPLHRFVFNCQYEMAKNPAFKVIVFVETK----KKV-----EDITRALRRERHSAIC 135
           Q     H      +  +A  P  ++I F+E      K+V     ++  R L       I 
Sbjct: 221 Q----AHDLQNGVEIVIAT-PG-RLIDFLERGSTNLKRVTYLVLDEADRMLDMGFEPQIR 274

Query: 136 IHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQVI 195
              ++ + DR  ++      K    +A D       + D   +N+GSL+L+ANHNI Q+I
Sbjct: 275 KIIEQIRPDRQVLMWSATWPKEVQALAADF------LVDYIQINVGSLELAANHNIQQLI 328

Query: 196 EVVQDYEKEKRLFSLIREL 214
           EV +D+EK+ +LF L+ ++
Sbjct: 329 EVCEDHEKDYKLFDLLMKI 347

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|389585395|dbj|GAB68126.1| helicase [Plasmodium cynomolgi strain B]

 Score =  138 bits (347), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 90/252 (35%), Positives = 123/252 (48%), Gaps = 63/252 (25%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS--SALRNICIFGGTPK 82
           ++LPA VHI  Q  +K GDGP+ LV+APTRELA+QI+    +FS  S +RN C +GG PK
Sbjct: 167 FILPAFVHILAQPSLKYGDGPVVLVMAPTRELAEQIRQECIKFSIESKIRNTCAYGGVPK 226

Query: 83  G------------------------PQDCLPLHRFVF-------------NCQYEMAKNP 105
                                     Q+   L R  +             + ++E   N 
Sbjct: 227 SGQIYALKQGVHILIACPGRLIDLLEQNVTNLMRVTYLVLDEADKIAPCTSREHEKIANL 286

Query: 106 AF----------KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQG 155
                       ++IVFVETKK  + IT+ALR +   A+CIHGDK Q +R +VLNDF+ G
Sbjct: 287 KLLLQRIFRDNDRIIVFVETKKNADFITKALRLDGVPALCIHGDKKQDERRWVLNDFKTG 346

Query: 156 KAPILVATDVAARGLDVEDVNTV--------------NIGSLQLSANHNISQVIEVVQDY 201
           K+PIL+ATDVA+RGLD++DV  V               IG    +  H  S        Y
Sbjct: 347 KSPILIATDVASRGLDIKDVKYVINFDFPNQIEDYVHRIGRTGRAGAHGASFTFLTSDKY 406

Query: 202 EKEKRLFSLIRE 213
              + L  ++RE
Sbjct: 407 RLARDLVKILRE 418

Source: Plasmodium cynomolgi strain B

Species: Plasmodium cynomolgi

Genus: Plasmodium

Order: Haemosporida

Class: Aconoidasida

Phylum: Apicomplexa

Superkingdom: Eukaryota

>gi|380014980|ref|XP_003691490.1| PREDICTED: probable ATP-dependent RNA helicase DDX17-like [Apis florea]

 Score =  132 bits (331), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 85/203 (41%), Positives = 119/203 (58%), Gaps = 23/203 (11%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGGTPK 82
           Y+LPA VHI+HQ  + +GDGPI L+LAPTRELAQQIQ+VA++F  SS +RN CIFGG+PK
Sbjct: 162 YILPATVHINHQPRLSRGDGPIVLILAPTRELAQQIQSVARDFGSSSCIRNTCIFGGSPK 221

Query: 83  GPQDCLPLHRFVFNCQYEMAKNPAFKVIVFVE---------TKKKVEDITRALRRERHSA 133
           GPQ    L R V  C       P  ++I F+E         T   +++  R L       
Sbjct: 222 GPQ-ARDLERGVEIC----IATPG-RLIDFLEKGTTNLRRCTYLVLDEADRMLDMGFEPQ 275

Query: 134 ICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQ 193
           I    ++ + DR  ++      K    +A D       + D   +NIGSL L+ANHNI Q
Sbjct: 276 IRKIIEQIRPDRQVLMWSATWPKEVQALAEDF------LSDYIQINIGSLTLAANHNIRQ 329

Query: 194 VIEVVQDYEKEKRLFSLIRELGK 216
           ++E+ Q++EKE +L +L+RE+GK
Sbjct: 330 IVEICQEHEKEMKLSNLLREIGK 352

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328780921|ref|XP_394723.3| PREDICTED: probable ATP-dependent RNA helicase DDX17-like [Apis mellifera]

 Score =  132 bits (331), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 85/203 (41%), Positives = 119/203 (58%), Gaps = 23/203 (11%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGGTPK 82
           Y+LPA VHI+HQ  + +GDGPI L+LAPTRELAQQIQ+VA++F  SS +RN CIFGG+PK
Sbjct: 160 YILPATVHINHQPRLSRGDGPIVLILAPTRELAQQIQSVARDFGSSSCIRNTCIFGGSPK 219

Query: 83  GPQDCLPLHRFVFNCQYEMAKNPAFKVIVFVE---------TKKKVEDITRALRRERHSA 133
           GPQ    L R V  C       P  ++I F+E         T   +++  R L       
Sbjct: 220 GPQ-ARDLERGVEIC----IATPG-RLIDFLEKGTTNLRRCTYLVLDEADRMLDMGFEPQ 273

Query: 134 ICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQ 193
           I    ++ + DR  ++      K    +A D       + D   +NIGSL L+ANHNI Q
Sbjct: 274 IRKIIEQIRPDRQVLMWSATWPKEVQALAEDF------LSDYIQINIGSLTLAANHNIRQ 327

Query: 194 VIEVVQDYEKEKRLFSLIRELGK 216
           ++E+ Q++EKE +L +L+RE+GK
Sbjct: 328 IVEICQEHEKEMKLSNLLREIGK 350

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307183175|gb|EFN70084.1| Probable ATP-dependent RNA helicase DDX17 [Camponotus floridanus]

 Score =  131 bits (329), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 86/202 (42%), Positives = 117/202 (57%), Gaps = 23/202 (11%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGGTPK 82
           Y+LPA VHI+HQ  + +GDGPI L+LAPTRELAQQIQTVA++F  SS +RN CIFGG+PK
Sbjct: 163 YILPATVHINHQPRLNRGDGPIVLILAPTRELAQQIQTVARDFGSSSCIRNTCIFGGSPK 222

Query: 83  GPQDCLPLHRFVFNCQYEMAKNPAFKVIVFVE---------TKKKVEDITRALRRERHSA 133
           GPQ    L R V  C       P  ++I F+E         T   +++  R L       
Sbjct: 223 GPQ-ARDLERGVEIC----IATPG-RLIDFLEKGTTNLRRCTYLVLDEADRMLDMGFEPQ 276

Query: 134 ICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQ 193
           I    ++ + DR  ++      K    +A D       + D   +NIGSL L+ANHNI Q
Sbjct: 277 IRKIIEQIRPDRQVLMWSATWPKEVQALAEDF------LTDYIQINIGSLSLAANHNIRQ 330

Query: 194 VIEVVQDYEKEKRLFSLIRELG 215
           +IE+ Q++EKE +L  L+RE+G
Sbjct: 331 IIEICQEHEKEYKLSQLLREIG 352

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332025289|gb|EGI65460.1| Putative ATP-dependent RNA helicase DDX17 [Acromyrmex echinatior]

 Score =  130 bits (328), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 85/202 (42%), Positives = 117/202 (57%), Gaps = 23/202 (11%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGGTPK 82
           Y+LPA VHI+HQ  + +GDGPI L+LAPTRELAQQIQTVA++F  SS +RN CIFGG+PK
Sbjct: 161 YILPATVHINHQPRLSRGDGPIVLILAPTRELAQQIQTVARDFGSSSCIRNTCIFGGSPK 220

Query: 83  GPQDCLPLHRFVFNCQYEMAKNPAFKVIVFVE---------TKKKVEDITRALRRERHSA 133
           GPQ    L R V  C       P  ++I F+E         T   +++  R L       
Sbjct: 221 GPQ-ARDLERGVEIC----IATPG-RLIDFLEKGTTNLRRCTYLVLDEADRMLDMGFEPQ 274

Query: 134 ICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQ 193
           I    ++ + DR  ++      K    +A D       + D   +NIGSL L+ANHNI Q
Sbjct: 275 IRKIIEQIRPDRQVLMWSATWPKEVQALAEDF------LSDYIQINIGSLTLAANHNIRQ 328

Query: 194 VIEVVQDYEKEKRLFSLIRELG 215
           ++E+ Q++EKE +L  L+RE+G
Sbjct: 329 IVEICQEHEKEMKLSQLLREIG 350

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307202009|gb|EFN81574.1| Probable ATP-dependent RNA helicase DDX17 [Harpegnathos saltator]

 Score =  130 bits (327), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 85/202 (42%), Positives = 117/202 (57%), Gaps = 23/202 (11%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGGTPK 82
           Y+LPA VHI+HQ  + +GDGPI L+LAPTRELAQQIQTVA++F  SS +RN CIFGG+PK
Sbjct: 162 YILPATVHINHQPRLSRGDGPIVLILAPTRELAQQIQTVARDFGSSSCIRNTCIFGGSPK 221

Query: 83  GPQDCLPLHRFVFNCQYEMAKNPAFKVIVFVE---------TKKKVEDITRALRRERHSA 133
           GPQ    L R V  C       P  ++I F+E         T   +++  R L       
Sbjct: 222 GPQ-ARDLERGVEIC----IATPG-RLIDFLEKGTTNLRRCTYLVLDEADRMLDMGFEPQ 275

Query: 134 ICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQ 193
           I    ++ + DR  ++      K    +A D       + D   +NIGSL L+ANHNI Q
Sbjct: 276 IRKIIEQIRPDRQVLMWSATWPKEVQALAEDF------LTDYIQINIGSLTLAANHNIRQ 329

Query: 194 VIEVVQDYEKEKRLFSLIRELG 215
           ++E+ Q++EKE +L  L+RE+G
Sbjct: 330 IVEICQEHEKETKLSQLLREIG 351

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383862185|ref|XP_003706564.1| PREDICTED: probable ATP-dependent RNA helicase DDX17-like [Megachile rotundata]

 Score =  130 bits (326), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 85/203 (41%), Positives = 118/203 (58%), Gaps = 23/203 (11%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGGTPK 82
           Y+LPA VHI++Q  + +GDGPI L+LAPTRELAQQIQ+VA++F  SS +RN CIFGG+PK
Sbjct: 160 YILPATVHINNQPRLSRGDGPIVLILAPTRELAQQIQSVARDFGSSSCIRNTCIFGGSPK 219

Query: 83  GPQDCLPLHRFVFNCQYEMAKNPAFKVIVFVE---------TKKKVEDITRALRRERHSA 133
           GPQ    L R V  C       P  ++I F+E         T   +++  R L       
Sbjct: 220 GPQ-ARDLERGVEIC----IATPG-RLIDFLEKGTTNLRRCTYLVLDEADRMLDMGFEPQ 273

Query: 134 ICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQ 193
           I    ++ + DR  ++      K    +A D       + D   +NIGSL L+ANHNI Q
Sbjct: 274 IRKIIEQIRPDRQVLMWSATWPKEVQALAEDF------LSDYIQINIGSLTLAANHNIRQ 327

Query: 194 VIEVVQDYEKEKRLFSLIRELGK 216
           +IE+ Q++EKE +L  L+RE+GK
Sbjct: 328 IIEICQEHEKETKLSGLLREIGK 350

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340717724|ref|XP_003397328.1| PREDICTED: probable ATP-dependent RNA helicase DDX17-like [Bombus terrestris]

 Score =  128 bits (321), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 84/203 (41%), Positives = 118/203 (58%), Gaps = 23/203 (11%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGGTPK 82
           Y+LPA VHI++Q  + +G+GPI L+LAPTRELAQQIQ+VA++F  SS +RN CIFGG+PK
Sbjct: 161 YILPATVHINNQPRLNRGEGPIVLILAPTRELAQQIQSVARDFGSSSCIRNTCIFGGSPK 220

Query: 83  GPQDCLPLHRFVFNCQYEMAKNPAFKVIVFVE---------TKKKVEDITRALRRERHSA 133
           GPQ    L R V  C       P  ++I F+E         T   +++  R L       
Sbjct: 221 GPQ-ARDLERGVEIC----IATPG-RLIDFLEKGTTNLRRCTYLVLDEADRMLDMGFEPQ 274

Query: 134 ICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQ 193
           I    ++ + DR  ++      K    +A D       + D   +NIGSL L+ANHNI Q
Sbjct: 275 IRKIIEQIRPDRQVLMWSATWPKEVQALAEDF------LSDYIQINIGSLTLAANHNIRQ 328

Query: 194 VIEVVQDYEKEKRLFSLIRELGK 216
           +IE+ Q++EKE +L  L+RE+GK
Sbjct: 329 IIEICQEHEKETKLSGLLREIGK 351

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350418218|ref|XP_003491789.1| PREDICTED: probable ATP-dependent RNA helicase DDX17-like [Bombus impatiens]

 Score =  128 bits (321), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 84/203 (41%), Positives = 118/203 (58%), Gaps = 23/203 (11%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGGTPK 82
           Y+LPA VHI++Q  + +G+GPI L+LAPTRELAQQIQ+VA++F  SS +RN CIFGG+PK
Sbjct: 159 YILPATVHINNQPRLNRGEGPIVLILAPTRELAQQIQSVARDFGSSSCIRNTCIFGGSPK 218

Query: 83  GPQDCLPLHRFVFNCQYEMAKNPAFKVIVFVE---------TKKKVEDITRALRRERHSA 133
           GPQ    L R V  C       P  ++I F+E         T   +++  R L       
Sbjct: 219 GPQ-ARDLERGVEIC----IATPG-RLIDFLEKGTTNLRRCTYLVLDEADRMLDMGFEPQ 272

Query: 134 ICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQ 193
           I    ++ + DR  ++      K    +A D       + D   +NIGSL L+ANHNI Q
Sbjct: 273 IRKIIEQIRPDRQVLMWSATWPKEVQALAEDF------LSDYIQINIGSLTLAANHNIRQ 326

Query: 194 VIEVVQDYEKEKRLFSLIRELGK 216
           +IE+ Q++EKE +L  L+RE+GK
Sbjct: 327 IIEICQEHEKETKLSGLLREIGK 349

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	233
TAIR|locus:2035741	501	RH20 "RNA helicase 20" [Arabid	0.304	0.141	0.577	6.2e-35
WB|WBGene00010260	561	F58E10.3 [Caenorhabditis elega	0.304	0.126	0.591	6.5e-35
ASPGD|ASPL0000006660	563	AN5931 [Emericella nidulans (t	0.339	0.140	0.518	1.7e-34
GENEDB_PFALCIPARUM|PF14_0437	527	PF14_0437 "helicase, truncated	0.304	0.134	0.577	2.1e-33
UNIPROTKB|Q8IL13	527	PF14_0437 "Helicase, putative"	0.304	0.134	0.577	2.1e-33
UNIPROTKB|E9PT29	651	Ddx17 "Protein Ddx17" [Rattus	0.373	0.133	0.568	1.2e-28
TAIR|locus:2084178	619	DRH1 "DEAD box RNA helicase 1"	0.326	0.122	0.545	7.9e-28
TAIR|locus:2222617	712	AT5G14610 [Arabidopsis thalian	0.326	0.106	0.519	1.2e-26
TAIR|locus:2081061	1088	AT3G06480 [Arabidopsis thalian	0.300	0.064	0.535	2.6e-26
UNIPROTKB|A5A6J2	614	DDX5 "Probable ATP-dependent R	0.781	0.296	0.411	2.7e-26

TAIR|locus:2035741 RH20 "RNA helicase 20" [Arabidopsis thaliana (taxid:3702)]

 Score = 218 (81.8 bits), Expect = 6.2e-35, Sum P(2) = 6.2e-35
 Identities = 41/71 (57%), Positives = 57/71 (80%)

Query:   108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
             +++VF++TKK  + ITR LR +   A+ IHGDK+Q +RD+VL++FR GK+PI+ ATDVAA
Sbjct:   346 RILVFLDTKKGCDQITRQLRMDGWPALSIHGDKSQAERDWVLSEFRSGKSPIMTATDVAA 405

Query:   168 RGLDVEDVNTV 178
             RGLDV+DV  V
Sbjct:   406 RGLDVKDVKYV 416

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

GO:0005829 "cytosol" evidence=IDA

WB|WBGene00010260 F58E10.3 [Caenorhabditis elegans (taxid:6239)]

 Score = 238 (88.8 bits), Expect = 6.5e-35, Sum P(2) = 6.5e-35
 Identities = 42/71 (59%), Positives = 58/71 (81%)

Query:   108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
             K I+FVETK+K +++TRA+RR+    +CIHGDK Q +RD+VL +F+ GK PI++ATDVAA
Sbjct:   378 KTIIFVETKRKADELTRAMRRDGWPTLCIHGDKNQGERDWVLQEFKAGKTPIMLATDVAA 437

Query:   168 RGLDVEDVNTV 178
             RGLDV+D+  V
Sbjct:   438 RGLDVDDIKFV 448

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0004386 "helicase activity" evidence=IEA

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

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

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

ASPGD|ASPL0000006660 AN5931 [Emericella nidulans (taxid:162425)]

 Score = 217 (81.4 bits), Expect = 1.7e-34, Sum P(2) = 1.7e-34
 Identities = 41/79 (51%), Positives = 60/79 (75%)

Query:   100 EMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPI 159
             ++ +N   K +VF  TK+  ++ITR LR++   A+ IHGDK QQ+RD+VLN+F+ GK+PI
Sbjct:   381 KIMENRGNKCLVFTGTKRIADEITRFLRQDGWPALSIHGDKQQQERDWVLNEFKTGKSPI 440

Query:   160 LVATDVAARGLDVEDVNTV 178
             +VATDVA+RG+DV D+  V
Sbjct:   441 MVATDVASRGIDVRDITHV 459

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0005730 "nucleolus" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

GENEDB_PFALCIPARUM|PF14_0437 PF14_0437 "helicase, truncated, putative" [Plasmodium falciparum (taxid:5833)]

 Score = 225 (84.3 bits), Expect = 2.1e-33, Sum P(2) = 2.1e-33
 Identities = 41/71 (57%), Positives = 59/71 (83%)

Query:   108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
             ++IVFVETKK  + IT+ALR +   A+CIHGDK Q++R +VLN+F+ GK+PI++ATDVA+
Sbjct:   362 RIIVFVETKKNADFITKALRLDGMPALCIHGDKKQEERRWVLNEFKTGKSPIMIATDVAS 421

Query:   168 RGLDVEDVNTV 178
             RGLD+++V  V
Sbjct:   422 RGLDIKNVKYV 432

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q8IL13 PF14_0437 "Helicase, putative" [Plasmodium falciparum 3D7 (taxid:36329)]

 Score = 225 (84.3 bits), Expect = 2.1e-33, Sum P(2) = 2.1e-33
 Identities = 41/71 (57%), Positives = 59/71 (83%)

Query:   108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
             ++IVFVETKK  + IT+ALR +   A+CIHGDK Q++R +VLN+F+ GK+PI++ATDVA+
Sbjct:   362 RIIVFVETKKNADFITKALRLDGMPALCIHGDKKQEERRWVLNEFKTGKSPIMIATDVAS 421

Query:   168 RGLDVEDVNTV 178
             RGLD+++V  V
Sbjct:   422 RGLDIKNVKYV 432

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|E9PT29 Ddx17 "Protein Ddx17" [Rattus norvegicus (taxid:10116)]

 Score = 258 (95.9 bits), Expect = 1.2e-28, Sum P(2) = 1.2e-28
 Identities = 50/88 (56%), Positives = 68/88 (77%)

Query:    91 HRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLN 150
             H+ +   +  MA+    K I+FVETK++ +D+TR +RR+   A+CIHGDK+Q +RD+VLN
Sbjct:   324 HKLIQLMEEIMAEKEN-KTIIFVETKRRCDDLTRRMRRDGWPAMCIHGDKSQPERDWVLN 382

Query:   151 DFRQGKAPILVATDVAARGLDVEDVNTV 178
             +FR GKAPIL+ATDVA+RGLDVEDV  V
Sbjct:   383 EFRSGKAPILIATDVASRGLDVEDVKFV 410

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

TAIR|locus:2084178 DRH1 "DEAD box RNA helicase 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 215 (80.7 bits), Expect = 7.9e-28, Sum P(2) = 7.9e-28
 Identities = 42/77 (54%), Positives = 55/77 (71%)

Query:   102 AKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILV 161
             ++ P  KVI+F  TK+  + +TR L R+   A  IHGDK+Q +RD VLN FR G+ P+LV
Sbjct:   399 SQEPGSKVIIFCSTKRMCDQLTRNLTRQ-FGAAAIHGDKSQPERDNVLNQFRSGRTPVLV 457

Query:   162 ATDVAARGLDVEDVNTV 178
             ATDVAARGLDV+D+  V
Sbjct:   458 ATDVAARGLDVKDIRAV 474

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0016887 "ATPase activity" evidence=IDA

TAIR|locus:2222617 AT5G14610 [Arabidopsis thaliana (taxid:3702)]

 Score = 205 (77.2 bits), Expect = 1.2e-26, Sum P(2) = 1.2e-26
 Identities = 40/77 (51%), Positives = 53/77 (68%)

Query:   102 AKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILV 161
             ++ P  K+I+F  TK+  + + R L R    A  IHGDK+Q +RD VLN FR G+ P+LV
Sbjct:   470 SQEPGSKIIIFCSTKRMCDQLARNLTRT-FGAAAIHGDKSQAERDDVLNQFRSGRTPVLV 528

Query:   162 ATDVAARGLDVEDVNTV 178
             ATDVAARGLDV+D+  V
Sbjct:   529 ATDVAARGLDVKDIRVV 545

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

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

GO:0009664 "plant-type cell wall organization" evidence=RCA

GO:0042545 "cell wall modification" evidence=RCA

TAIR|locus:2081061 AT3G06480 [Arabidopsis thaliana (taxid:3702)]

 Score = 200 (75.5 bits), Expect = 2.6e-26, Sum P(2) = 2.6e-26
 Identities = 38/71 (53%), Positives = 53/71 (74%)

Query:   108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
             KVI+F  TK+  + + R++ R    A+ IHGDKTQ +RD+VLN FR GK+ +L+ATDVAA
Sbjct:   682 KVIIFCSTKRLCDHLARSVGRH-FGAVVIHGDKTQGERDWVLNQFRSGKSCVLIATDVAA 740

Query:   168 RGLDVEDVNTV 178
             RGLD++D+  V
Sbjct:   741 RGLDIKDIRVV 751

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

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

GO:0005773 "vacuole" evidence=IDA

GO:0006635 "fatty acid beta-oxidation" evidence=RCA

GO:0016558 "protein import into peroxisome matrix" evidence=RCA

UNIPROTKB|A5A6J2 DDX5 "Probable ATP-dependent RNA helicase DDX5" [Pan troglodytes (taxid:9598)]

 Score = 304 (112.1 bits), Expect = 2.7e-26, P = 2.7e-26
 Identities = 81/197 (41%), Positives = 119/197 (60%)

Query:    25 YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSA--LRNICIFGGTPK 82
             Y+LPA VHI+HQ  +++GDGPI LVLAPTRELAQQ+Q VA E+  A  L++ CI+GG PK
Sbjct:   148 YLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPK 207

Query:    83 GPQDCLPLHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQ 142
             GPQ    L R V NC   +A  P  ++I F+E  K     T  L  +    +   G + Q
Sbjct:   208 GPQ-IRDLERGVENC---IA-TPG-RLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQ 261

Query:   143 QDRDYVLNDFRQGKAPIL-VAT---DVAARGLD-VEDVNTVNIGSLQLSANHNISQVIEV 197
               +  +++  R  +  ++  AT   +V     D ++D   +NIG+L+LSANHNI Q+++V
Sbjct:   262 IRK--IVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIGALELSANHNILQIVDV 319

Query:   198 VQDYEKEKRLFSLIREL 214
               D EK+++L  L+ E+
Sbjct:   320 CHDVEKDEKLIRLMEEI 336

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISS

GO:0000381 "regulation of alternative mRNA splicing, via spliceosome" evidence=ISS

GO:0003713 "transcription coactivator activity" evidence=ISS

GO:0003724 "RNA helicase activity" evidence=ISS

GO:0005730 "nucleolus" evidence=ISS

GO:0030331 "estrogen receptor binding" evidence=ISS

GO:0043517 "positive regulation of DNA damage response, signal transduction by p53 class mediator" evidence=ISS

GO:0045667 "regulation of osteoblast differentiation" evidence=ISS

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

GO:0050681 "androgen receptor binding" evidence=ISS

GO:0060765 "regulation of androgen receptor signaling pathway" evidence=ISS

GO:0072332 "intrinsic apoptotic signaling pathway by p53 class mediator" evidence=ISS

GO:2001014 "regulation of skeletal muscle cell differentiation" evidence=ISS

---

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 EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4	LOW CONFIDENCE prediction!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	233
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	4e-28
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	2e-23
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	3e-23
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	4e-19
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	1e-18
smart00490	82	smart00490, HELICc, helicase superfamily c-termina	1e-17
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	2e-17
cd00268	203	cd00268, DEADc, DEAD-box helicases	1e-14
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	3e-13
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	4e-13
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	1e-12
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	6e-12
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	7e-12
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	4e-11
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	4e-10
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	8e-10
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	1e-08
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	5e-07
PRK13766	773	PRK13766, PRK13766, Hef nuclease; Provisional	9e-07
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	2e-06
COG1061	442	COG1061, SSL2, DNA or RNA helicases of superfamily	3e-06
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	4e-06
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	5e-06
COG1111	542	COG1111, MPH1, ERCC4-like helicases [DNA replicati	5e-06
COG0514	590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	2e-05
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	3e-05
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	4e-05
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	2e-04
TIGR01389	591	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	3e-04
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	7e-04
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	0.001
COG4098	441	COG4098, comFA, Superfamily II DNA/RNA helicase re	0.004

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

 Score =  111 bits (278), Expect = 4e-28
 Identities = 40/75 (53%), Positives = 58/75 (77%)

Query: 104 NPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVAT 163
               K+++FVETKK  + +T+ LR +   A+CIHGDK Q++R +VLN+F+ GK+PI++AT
Sbjct: 375 RDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIAT 434

Query: 164 DVAARGLDVEDVNTV 178
           DVA+RGLDV+DV  V
Sbjct: 435 DVASRGLDVKDVKYV 449

Length = 545

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

 Score = 97.6 bits (243), Expect = 2e-23
 Identities = 35/77 (45%), Positives = 49/77 (63%)

Query: 102 AKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILV 161
                 +VIVFV TK+ VE++  +LR+       +HGD  Q++RD  L  F+ G+  +LV
Sbjct: 269 KDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLV 328

Query: 162 ATDVAARGLDVEDVNTV 178
           ATDVAARGLD+ DV+ V
Sbjct: 329 ATDVAARGLDIPDVSHV 345

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 = 90.8 bits (226), Expect = 3e-23
 Identities = 30/71 (42%), Positives = 50/71 (70%)

Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           KV++F  +KK ++++   LR+       +HGD +Q++R+ VL DFR+G+  +LVATDV A
Sbjct: 30  KVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIA 89

Query: 168 RGLDVEDVNTV 178
           RG+D+ +V+ V
Sbjct: 90  RGIDLPNVSVV 100

Length = 131

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

 Score = 84.9 bits (211), Expect = 4e-19
 Identities = 32/69 (46%), Positives = 45/69 (65%)

Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
           +VF  TKK+ +++  AL  +  SA+ +HGD  Q+DRD VL  F      +LVATDVAARG
Sbjct: 246 VVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARG 305

Query: 170 LDVEDVNTV 178
           LD++ +  V
Sbjct: 306 LDIKALEAV 314

Length = 460

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

 Score = 83.7 bits (207), Expect = 1e-18
 Identities = 34/63 (53%), Positives = 44/63 (69%), Gaps = 2/63 (3%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGGTPK 82
           ++LPA VHI+ Q  ++ GDGPI LVLAPTRELA+QI+    +F  SS +RN   +GG PK
Sbjct: 184 FLLPAIVHINAQPLLRYGDGPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPK 243

Query: 83  GPQ 85
             Q
Sbjct: 244 RGQ 246

Length = 545

>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain

 Score = 74.2 bits (183), Expect = 1e-17
 Identities = 23/59 (38%), Positives = 36/59 (61%)

Query: 120 EDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTV 178
           E++   L+        +HG  +Q++R+ +L+ F  GK  +LVATDVA RGLD+  V+ V
Sbjct: 1   EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLV 59

Length = 82

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

 Score = 74.1 bits (183), Expect = 2e-17
 Identities = 26/53 (49%), Positives = 37/53 (69%)

Query: 126 LRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTV 178
           LR+       +HG  +Q++R+ +L DFR GK+ +LVATDVA RG+D+ DVN V
Sbjct: 3   LRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLV 55

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

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

 Score = 69.4 bits (171), Expect = 1e-14
 Identities = 25/63 (39%), Positives = 37/63 (58%), Gaps = 5/63 (7%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSA--LRNICIFGGTPK 82
           +++P    +   +P  + DGP AL+LAPTRELA QI  VA++      L+ + I+GGT  
Sbjct: 53  FLIPI---LEKLDPSPKKDGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSI 109

Query: 83  GPQ 85
             Q
Sbjct: 110 DKQ 112

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

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

 Score = 67.9 bits (166), Expect = 3e-13
 Identities = 26/69 (37%), Positives = 46/69 (66%)

Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
           I++  T++KV+ +T+ +     +  C+HGD  Q+DRD ++ +FR G   +L+ TD+ ARG
Sbjct: 271 IIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARG 330

Query: 170 LDVEDVNTV 178
           +DV+ V+ V
Sbjct: 331 IDVQQVSLV 339

Length = 401

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

 Score = 67.3 bits (165), Expect = 4e-13
 Identities = 26/71 (36%), Positives = 44/71 (61%)

Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           + IVFV T+++V ++   LR+   +   + G+  Q  R+  +     G+  +LVATDVAA
Sbjct: 247 RSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAA 306

Query: 168 RGLDVEDVNTV 178
           RG+D++DV+ V
Sbjct: 307 RGIDIDDVSHV 317

Length = 434

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

 Score = 66.5 bits (162), Expect = 1e-12
 Identities = 32/78 (41%), Positives = 49/78 (62%)

Query: 101 MAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPIL 160
           ++++   + +VFV TK  VE + R L R  +    + GD  Q+ R+ +LN F++G+  IL
Sbjct: 252 LSRSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEIL 311

Query: 161 VATDVAARGLDVEDVNTV 178
           VATDVAARGL ++ V  V
Sbjct: 312 VATDVAARGLHIDGVKYV 329

Length = 572

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

 Score = 63.8 bits (156), Expect = 6e-12
 Identities = 29/71 (40%), Positives = 40/71 (56%)

Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           + I+F  TK + E+I   L  + H    + GD  Q+ R  +L +F +G   ILVATDVAA
Sbjct: 257 RAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAA 316

Query: 168 RGLDVEDVNTV 178
           RGL +  V  V
Sbjct: 317 RGLHIPAVTHV 327

Length = 423

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

 Score = 63.7 bits (155), Expect = 7e-12
 Identities = 29/71 (40%), Positives = 43/71 (60%)

Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           +V+VF  TK     +   L ++   +  IHG+K+Q  R   L DF+ G   +LVATD+AA
Sbjct: 247 QVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAA 306

Query: 168 RGLDVEDVNTV 178
           RGLD+E++  V
Sbjct: 307 RGLDIEELPHV 317

Length = 456

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

 Score = 61.8 bits (150), Expect = 4e-11
 Identities = 33/90 (36%), Positives = 48/90 (53%), Gaps = 10/90 (11%)

Query: 99  YEMAKNPAF----------KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYV 148
           + M KN A             I+FV TK    ++  AL R  +++  ++GD  Q  R+  
Sbjct: 228 WGMRKNEALVRFLEAEDFDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQT 287

Query: 149 LNDFRQGKAPILVATDVAARGLDVEDVNTV 178
           L   + G+  IL+ATDVAARGLDVE ++ V
Sbjct: 288 LERLKDGRLDILIATDVAARGLDVERISLV 317

Length = 629

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

 Score = 58.6 bits (142), Expect = 4e-10
 Identities = 20/64 (31%), Positives = 28/64 (43%), Gaps = 6/64 (9%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNI---CIFGGTP 81
           ++LP    I      K      AL+LAPTRELA QI    ++    L  +    ++GG  
Sbjct: 83  FLLPLLQKILKSVERKY---VSALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVS 139

Query: 82  KGPQ 85
              Q
Sbjct: 140 IRKQ 143

Length = 513

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

 Score = 58.0 bits (140), Expect = 8e-10
 Identities = 29/78 (37%), Positives = 45/78 (57%)

Query: 101 MAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPIL 160
           + +NP  +V+VF   K +V  I   L ++  +A  + GD  Q  R   L  FR+GK  +L
Sbjct: 330 VTQNPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVL 389

Query: 161 VATDVAARGLDVEDVNTV 178
           VATDVA RG+ ++ ++ V
Sbjct: 390 VATDVAGRGIHIDGISHV 407

Length = 475

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

 Score = 52.6 bits (127), Expect = 1e-08
 Identities = 23/63 (36%), Positives = 31/63 (49%), Gaps = 7/63 (11%)

Query: 25 YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSA--LRNICIFGGTPK 82
          ++LP    +  ++   Q     ALVLAPTRELA+QI    K+      LR   + GGT  
Sbjct: 31 FLLPILQALLPKKGGPQ-----ALVLAPTRELAEQIYEELKKLFKILGLRVALLTGGTSL 85

Query: 83 GPQ 85
            Q
Sbjct: 86 KEQ 88

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

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

 Score = 49.4 bits (118), Expect = 5e-07
 Identities = 21/50 (42%), Positives = 33/50 (66%)

Query: 167 ARGLDVEDVNTVNIGSLQLSANHNISQVIEVVQDYEKEKRLFSLIRELGK 216
           AR L  E+   VN+GSL L+A HNI Q + VV+++EK  +L  L++ + +
Sbjct: 326 ARDLCKEEPVHVNVGSLDLTACHNIKQEVFVVEEHEKRGKLKMLLQRIMR 375

Length = 545

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

 Score = 48.7 bits (117), Expect = 9e-07
 Identities = 29/87 (33%), Positives = 48/87 (55%), Gaps = 8/87 (9%)

Query: 100 EMAKNPAFKVIVFVETKKKVEDITRALRRERHSAI------CIHGDK--TQQDRDYVLND 151
           ++ KNP  ++IVF + +   E I   L +E   A+         GDK  +Q+++  +L+ 
Sbjct: 359 QLGKNPDSRIIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQKEQIEILDK 418

Query: 152 FRQGKAPILVATDVAARGLDVEDVNTV 178
           FR G+  +LV+T VA  GLD+  V+ V
Sbjct: 419 FRAGEFNVLVSTSVAEEGLDIPSVDLV 445

Length = 773

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

 Score = 47.5 bits (113), Expect = 2e-06
 Identities = 25/64 (39%), Positives = 38/64 (59%), Gaps = 3/64 (4%)

Query: 25  YMLPAAVHISHQEPVKQGDGPI-ALVLAPTRELAQQIQTVAKEFSSAL--RNICIFGGTP 81
           + LP   H+  ++P  +G  P+ AL+L PTRELA QI    +++S  L  R++ +FGG  
Sbjct: 55  FTLPLLQHLITRQPHAKGRRPVRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVS 114

Query: 82  KGPQ 85
             PQ
Sbjct: 115 INPQ 118

Length = 456

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

 Score = 47.0 bits (112), Expect = 3e-06
 Identities = 16/71 (22%), Positives = 32/71 (45%), Gaps = 1/71 (1%)

Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           K ++F    +   +I +           I G+  +++R+ +L  FR G   +LV   V  
Sbjct: 285 KTLIFASDVEHAYEIAKLFLAP-GIVEAITGETPKEEREAILERFRTGGIKVLVTVKVLD 343

Query: 168 RGLDVEDVNTV 178
            G+D+ D + +
Sbjct: 344 EGVDIPDADVL 354

Length = 442

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

 Score = 45.9 bits (109), Expect = 4e-06
 Identities = 23/64 (35%), Positives = 32/64 (50%), Gaps = 8/64 (12%)

Query: 24 QYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGGTP 81
            +LPA   +      K+G G   LVL PTRELA+Q     K+   S  L+ + ++GG  
Sbjct: 40 AALLPALEAL------KRGKGGRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDS 93

Query: 82 KGPQ 85
          K  Q
Sbjct: 94 KREQ 97

Length = 201

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

 Score = 44.6 bits (106), Expect = 5e-06
 Identities = 21/72 (29%), Positives = 27/72 (37%), Gaps = 7/72 (9%)

Query: 24 QYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIF-GGTPK 82
            +LP    +          G   LVLAPTRELA Q+    KE       +    GGT  
Sbjct: 16 AALLPILELL------DSLKGGQVLVLAPTRELANQVAERLKELFGEGIKVGYLIGGTSI 69

Query: 83 GPQDCLPLHRFV 94
            Q+ L   +  
Sbjct: 70 KQQEKLLSGKTD 81

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

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

 Score = 46.2 bits (110), Expect = 5e-06
 Identities = 28/85 (32%), Positives = 46/85 (54%), Gaps = 9/85 (10%)

Query: 103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICI-------HGDK--TQQDRDYVLNDFR 153
           KN   +VIVF E +   E+I   L++    A           GDK  +Q+++  +++ FR
Sbjct: 363 KNGDSRVIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQKEIIDQFR 422

Query: 154 QGKAPILVATDVAARGLDVEDVNTV 178
           +G+  +LVAT V   GLD+ +V+ V
Sbjct: 423 KGEYNVLVATSVGEEGLDIPEVDLV 447

Length = 542

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

 Score = 44.6 bits (106), Expect = 2e-05
 Identities = 22/69 (31%), Positives = 37/69 (53%)

Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
           I++  T+KKVE++   LR+   SA   H   + ++R+ V   F   +  ++VAT+    G
Sbjct: 234 IIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMG 293

Query: 170 LDVEDVNTV 178
           +D  DV  V
Sbjct: 294 IDKPDVRFV 302

Length = 590

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

 Score = 44.0 bits (104), Expect = 3e-05
 Identities = 29/122 (23%), Positives = 52/122 (42%), Gaps = 42/122 (34%)

Query: 101 MAKNPAF--------------KVIVFVETKKKVEDITRALRRERH--------------- 131
           +AK+                 ++ ++VETK+K + +   L+ ++H               
Sbjct: 321 LAKDIILISIGNPNRPNKAVKQLAIWVETKQKKQKLFDILKSKQHFKPPAVVFVSSRLGA 380

Query: 132 -------------SAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTV 178
                         A+ IHG+K+ ++R  V+  F  G+ P++VAT V  RG+D+  V  V
Sbjct: 381 DLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQV 440

Query: 179 NI 180
            I
Sbjct: 441 II 442

Length = 518

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

 Score = 43.6 bits (104), Expect = 4e-05
 Identities = 23/45 (51%), Positives = 26/45 (57%), Gaps = 9/45 (20%)

Query: 47  ALVLAPTRELAQQIQTVAKE---FSSALRNICIF---GGTPKGPQ 85
           ALVL PTRELA Q   VAKE    +  + NI +    GG P GPQ
Sbjct: 75  ALVLCPTRELADQ---VAKEIRRLARFIPNIKVLTLCGGVPMGPQ 116

Length = 460

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

 Score = 41.5 bits (98), Expect = 2e-04
 Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 3/63 (4%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALR-NIC-IFGGTPK 82
           ++LPA  H+    P ++   P  L+L PTRELA Q+   A+E +     +I  I GG   
Sbjct: 55  FLLPALQHLL-DFPRRKSGPPRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAY 113

Query: 83  GPQ 85
              
Sbjct: 114 MNH 116

Length = 434

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

 Score = 41.2 bits (97), Expect = 3e-04
 Identities = 19/69 (27%), Positives = 34/69 (49%)

Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
           I++  ++KKVE++   L  +  SA+  H   + + R     DF      ++VAT+    G
Sbjct: 228 IIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMG 287

Query: 170 LDVEDVNTV 178
           +D  +V  V
Sbjct: 288 IDKPNVRFV 296

The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ [DNA metabolism, DNA replication, recombination, and repair]. Length = 591

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

 Score = 39.8 bits (93), Expect = 7e-04
 Identities = 20/36 (55%), Positives = 22/36 (61%), Gaps = 2/36 (5%)

Query: 47  ALVLAPTRELAQQIQTVAKEFSSALRNIC--IFGGT 80
           AL+LAPTRELAQQIQ V       L+  C    GGT
Sbjct: 99  ALILAPTRELAQQIQKVVLALGDYLKVRCHACVGGT 134

Length = 401

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

 Score = 39.2 bits (92), Expect = 0.001
 Identities = 23/58 (39%), Positives = 33/58 (56%), Gaps = 5/58 (8%)

Query: 27  LPAAVH--ISHQEPV-KQGDGPIALVLAPTRELAQQIQTVAKEFSSA--LRNICIFGG 79
           L A  H  +SH  P  ++ + P AL++APTRELA QI   A+  + A  L+    +GG
Sbjct: 63  LTATFHYLLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGG 120

Length = 423

>gnl|CDD|226583 COG4098, comFA, Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]

 Score = 37.4 bits (87), Expect = 0.004
 Identities = 19/85 (22%), Positives = 39/85 (45%), Gaps = 4/85 (4%)

Query: 100 EMAKNPAFKVIVFVETKKKVEDITRALRRERH--SAICIHGDKTQQDRDYVLNDFRQGKA 157
           E  +     V++F    + +E +  AL+++    +   +H     Q R   +  FR GK 
Sbjct: 299 EKQRKTGRPVLIFFPEIETMEQVAAALKKKLPKETIASVHS--EDQHRKEKVEAFRDGKI 356

Query: 158 PILVATDVAARGLDVEDVNTVNIGS 182
            +L+ T +  RG+   +V+   +G+
Sbjct: 357 TLLITTTILERGVTFPNVDVFVLGA 381

Length = 441

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	233
KOG0330|consensus	476		100.0
KOG0331|consensus	519		100.0
KOG0340|consensus	442		100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
KOG0328|consensus	400		100.0
KOG0338|consensus	691		100.0
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0342|consensus	543		100.0
KOG0333|consensus	673		100.0
PTZ00110	545	helicase; Provisional	100.0
KOG0345|consensus	567		100.0
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	100.0
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	100.0
KOG0326|consensus	459		100.0
KOG0335|consensus	482		100.0
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	100.0
KOG0343|consensus	758		100.0
KOG0348|consensus	708		100.0
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	100.0
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	100.0
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0336|consensus	629		100.0
KOG0347|consensus	731		100.0
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	100.0
KOG0341|consensus	610		100.0
KOG0334|consensus	997		100.0
KOG0346|consensus	569		100.0
KOG0339|consensus	731		100.0
PTZ00424	401	helicase 45; Provisional	100.0
KOG0332|consensus	477		100.0
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	100.0
KOG0350|consensus	620		100.0
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	100.0
KOG0327|consensus	397		100.0
KOG0344|consensus	593		100.0
KOG4284|consensus	980		100.0
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	100.0
PRK13767	876	ATP-dependent helicase; Provisional	99.97
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.97
KOG0337|consensus	529		99.97
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.97
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.96
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.96
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.96
PRK10689	1147	transcription-repair coupling factor; Provisional	99.96
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.96
PRK09401	1176	reverse gyrase; Reviewed	99.95
PRK02362	737	ski2-like helicase; Provisional	99.95
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.95
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.95
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.94
PHA02558	501	uvsW UvsW helicase; Provisional	99.94
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.94
PRK00254	720	ski2-like helicase; Provisional	99.94
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.94
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.94
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.93
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.93
PHA02653	675	RNA helicase NPH-II; Provisional	99.93
PRK01172	674	ski2-like helicase; Provisional	99.93
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.93
PRK14701	1638	reverse gyrase; Provisional	99.92
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.92
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.92
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.92
PRK13766	773	Hef nuclease; Provisional	99.91
KOG0349|consensus	725		99.91
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.9
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.9
KOG0329|consensus	387		99.89
KOG0354|consensus	746		99.88
COG1204	766	Superfamily II helicase [General function predicti	99.86
COG1205	851	Distinct helicase family with a unique C-terminal	99.86
COG1202	830	Superfamily II helicase, archaea-specific [General	99.85
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.84
KOG0351|consensus	941		99.84
PRK05580	679	primosome assembly protein PriA; Validated	99.84
KOG0352|consensus	641		99.83
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.82
PRK04914	956	ATP-dependent helicase HepA; Validated	99.82
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.81
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.81
KOG0353|consensus	695		99.79
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.78
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.77
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.75
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	99.75
KOG0952|consensus	1230		99.75
PRK09694	878	helicase Cas3; Provisional	99.74
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.72
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.71
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.7
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.66
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	99.66
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	99.63
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.61
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	99.59
KOG0951|consensus	1674		99.58
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.56
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	99.55
PRK05298	652	excinuclease ABC subunit B; Provisional	99.5
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.45
COG1198	730	PriA Primosomal protein N' (replication factor Y)	99.42
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.42
smart00490	82	HELICc helicase superfamily c-terminal domain.	99.4
KOG0385|consensus	971		99.4
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.38
COG4096	875	HsdR Type I site-specific restriction-modification	99.38
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.36
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.36
KOG0387|consensus	923		99.35
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	99.34
KOG0953|consensus	700		99.3
KOG0948|consensus	1041		99.24
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.12
KOG0384|consensus	1373		99.11
KOG0392|consensus	1549		99.1
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.08
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	99.06
KOG1123|consensus	776		99.05
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.03
KOG0389|consensus	941		99.01
PRK12326	764	preprotein translocase subunit SecA; Reviewed	99.01
KOG0947|consensus	1248		98.98
KOG0390|consensus	776		98.97
KOG1002|consensus	791		98.92
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	98.91
KOG0950|consensus	1008		98.9
CHL00122	870	secA preprotein translocase subunit SecA; Validate	98.89
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	98.79
KOG4150|consensus	1034		98.76
COG4889	1518	Predicted helicase [General function prediction on	98.72
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	98.66
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	98.59
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	98.53
KOG1000|consensus	689		98.52
KOG0386|consensus	1157		98.51
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	98.49
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	98.49
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	98.49
smart00487	201	DEXDc DEAD-like helicases superfamily.	98.47
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	98.46
KOG0922|consensus	674		98.38
KOG0391|consensus	1958		98.37
PRK14873	665	primosome assembly protein PriA; Provisional	98.36
KOG0949|consensus	1330		98.34
KOG4439|consensus	901		98.31
KOG0924|consensus	1042		98.27
KOG0951|consensus	1674		98.23
KOG0920|consensus	924		98.21
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	98.21
KOG0926|consensus	1172		98.2
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	98.16
PF13245	76	AAA_19: Part of AAA domain	98.15
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	98.01
KOG0923|consensus	902		97.97
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	97.9
PF13307	167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	97.72
KOG0388|consensus	1185		97.68
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	97.62
KOG1015|consensus	1567		97.51
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	97.44
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	97.39
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	97.18
KOG0331|consensus	519		97.11
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	97.06
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	97.04
KOG1803|consensus	649		97.03
KOG2340|consensus	698		96.97
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	96.97
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	96.94
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	96.92
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	96.84
TIGR00376	637	DNA helicase, putative. The gene product may repre	96.79
PRK05580	679	primosome assembly protein PriA; Validated	96.75
PRK15483	986	type III restriction-modification system StyLTI en	96.72
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	96.6
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	96.58
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	96.56
TIGR00595	505	priA primosomal protein N'. All proteins in this f	96.51
smart00492	141	HELICc3 helicase superfamily c-terminal domain.	96.42
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	96.33
KOG1802|consensus	935		96.28
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	96.21
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	96.13
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	96.11
smart00491	142	HELICc2 helicase superfamily c-terminal domain.	96.07
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	96.02
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	96.01
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	96.01
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	95.96
KOG0339|consensus	731		95.94
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	95.94
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	95.94
PRK10689	1147	transcription-repair coupling factor; Provisional	95.93
KOG0335|consensus	482		95.7
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	95.65
PRK13897	606	type IV secretion system component VirD4; Provisio	95.65
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	95.51
COG1198	730	PriA Primosomal protein N' (replication factor Y)	95.45
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	95.42
PRK14701	1638	reverse gyrase; Provisional	95.38
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	95.35
COG0610	962	Type I site-specific restriction-modification syst	95.24
PRK13851	344	type IV secretion system protein VirB11; Provision	95.24
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	95.22
COG3973	747	Superfamily I DNA and RNA helicases [General funct	95.22
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	95.16
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	95.13
PRK13850	670	type IV secretion system protein VirD4; Provisiona	95.09
KOG0952|consensus	1230		95.05
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	95.04
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	95.01
PRK13833	323	conjugal transfer protein TrbB; Provisional	95.0
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	94.91
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	94.88
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	94.79
PRK13822	641	conjugal transfer coupling protein TraG; Provision	94.72
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	94.65
cd01127	410	TrwB Bacterial conjugation protein TrwB, ATP bindi	94.65
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	94.62
PRK11054	684	helD DNA helicase IV; Provisional	94.6
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	94.6
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	94.6
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	94.55
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	94.5
TIGR02767	623	TraG-Ti Ti-type conjugative transfer system protie	94.33
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	94.24
KOG0333|consensus	673		94.21
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	94.2
PRK05298	652	excinuclease ABC subunit B; Provisional	94.2
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	94.14
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	94.13
COG1484	254	DnaC DNA replication protein [DNA replication, rec	94.12
PRK13876	663	conjugal transfer coupling protein TraG; Provision	94.06
KOG0925|consensus	699		94.05
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	94.02
smart00382	148	AAA ATPases associated with a variety of cellular	93.99
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	93.94
PRK13880	636	conjugal transfer coupling protein TraG; Provision	93.88
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	93.85
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	93.83
cd01132	274	F1_ATPase_alpha F1 ATP synthase alpha, central dom	93.82
PRK04328	249	hypothetical protein; Provisional	93.63
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	93.59
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	93.38
PRK06921	266	hypothetical protein; Provisional	93.33
PRK08533	230	flagellar accessory protein FlaH; Reviewed	93.27
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	93.23
PF12846	304	AAA_10: AAA-like domain	93.18
PRK06526	254	transposase; Provisional	93.07
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	93.05
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	92.98
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	92.98
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	92.88
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	92.77
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	92.75
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	92.71
PRK08181	269	transposase; Validated	92.7
TIGR03743	634	SXT_TraD conjugative coupling factor TraD, SXT/TOL	92.63
PRK05973	237	replicative DNA helicase; Provisional	92.6
CHL00181	287	cbbX CbbX; Provisional	92.58
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	92.55
KOG0347|consensus	731		92.51
PRK12377	248	putative replication protein; Provisional	92.45
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	92.38
COG3587	985	Restriction endonuclease [Defense mechanisms]	92.37
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	92.37
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	92.35
KOG0744|consensus	423		92.21
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	92.2
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	92.18
KOG1016|consensus	1387		92.14
cd01134	369	V_A-ATPase_A V/A-type ATP synthase catalytic subun	92.14
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	92.13
PF01935	229	DUF87: Domain of unknown function DUF87; InterPro:	92.13
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	92.07
PRK10875	615	recD exonuclease V subunit alpha; Provisional	92.01
PRK09183	259	transposase/IS protein; Provisional	91.96
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	91.91
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	91.89
PRK08727	233	hypothetical protein; Validated	91.76
TIGR03754	643	conj_TOL_TraD conjugative coupling factor TraD, TO	91.75
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	91.75
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	91.72
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	91.58
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	91.48
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	91.36
PTZ00185	574	ATPase alpha subunit; Provisional	91.29
PRK07952	244	DNA replication protein DnaC; Validated	91.28
cd01394	218	radB RadB. The archaeal protein radB shares simila	91.27
PRK10536	262	hypothetical protein; Provisional	91.21
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	91.19
KOG0701|consensus	1606		91.15
KOG0338|consensus	691		91.11
PRK13764	602	ATPase; Provisional	91.06
TIGR02759	566	TraD_Ftype type IV conjugative transfer system cou	91.06
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	91.03
COG1074	1139	RecB ATP-dependent exoDNAse (exonuclease V) beta s	90.94
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	90.89
PF00006	215	ATP-synt_ab: ATP synthase alpha/beta family, nucle	90.78
PRK13700	732	conjugal transfer protein TraD; Provisional	90.75
PRK06835	329	DNA replication protein DnaC; Validated	90.6
PF13555	62	AAA_29: P-loop containing region of AAA domain	90.58
COG0593	408	DnaA ATPase involved in DNA replication initiation	90.5
PRK09281	502	F0F1 ATP synthase subunit alpha; Validated	90.48
PTZ00110	545	helicase; Provisional	90.46
KOG0330|consensus	476		90.46
KOG0334|consensus	997		90.4
cd00983	325	recA RecA is a bacterial enzyme which has roles in	90.39
PRK09280	463	F0F1 ATP synthase subunit beta; Validated	90.31
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	90.3
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	90.3
TIGR02237	209	recomb_radB DNA repair and recombination protein R	90.18
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	89.99
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	89.85
PRK10436	462	hypothetical protein; Provisional	89.84
PRK08116	268	hypothetical protein; Validated	89.83
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	89.79
PRK12597	461	F0F1 ATP synthase subunit beta; Provisional	89.7
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	89.67
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	89.61
TIGR03324	497	alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit a	89.56
PRK11823	446	DNA repair protein RadA; Provisional	89.52
PRK09376	416	rho transcription termination factor Rho; Provisio	89.49
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	89.46
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	89.43
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	89.35
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	89.34
PRK04296	190	thymidine kinase; Provisional	89.31
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	89.31
PF05872	502	DUF853: Bacterial protein of unknown function (DUF	89.31
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	89.21
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	89.2
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	89.2
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	89.15
KOG1533|consensus	290		89.09
CHL00059	485	atpA ATP synthase CF1 alpha subunit	89.05
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	88.99
COG4185	187	Uncharacterized protein conserved in bacteria [Fun	88.95
PRK09401	1176	reverse gyrase; Reviewed	88.91
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	88.91
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	88.91
PRK06067	234	flagellar accessory protein FlaH; Validated	88.87
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	88.85
PRK00149	450	dnaA chromosomal replication initiation protein; R	88.84
TIGR02784	1141	addA_alphas double-strand break repair helicase Ad	88.83
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	88.82
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	88.81
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	88.75
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	88.47
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	88.47
cd01128	249	rho_factor Transcription termination factor rho is	88.39
PRK14087	450	dnaA chromosomal replication initiation protein; P	88.36
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	88.34
PF05729	166	NACHT: NACHT domain	88.32
KOG1807|consensus	1025		88.07
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	87.94
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	87.87
KOG1942|consensus	456		87.74
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	87.71
TIGR03305	449	alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit	87.68
PF07088	484	GvpD: GvpD gas vesicle protein; InterPro: IPR00978	87.56
KOG1132|consensus	945		87.55
cd01524	90	RHOD_Pyr_redox Member of the Rhodanese Homology Do	87.49
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	87.47
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	87.43
PRK08972	444	fliI flagellum-specific ATP synthase; Validated	87.32
PRK05642	234	DNA replication initiation factor; Validated	87.27
PTZ00301	210	uridine kinase; Provisional	87.26
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	87.2
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	87.2
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	87.08
PRK14088	440	dnaA chromosomal replication initiation protein; P	87.03
KOG1133|consensus	821		86.96
PRK06893	229	DNA replication initiation factor; Validated	86.94
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	86.92
TIGR01039	461	atpD ATP synthase, F1 beta subunit. The sequences	86.87
PRK08084	235	DNA replication initiation factor; Provisional	86.86
PRK08939	306	primosomal protein DnaI; Reviewed	86.73
PF04364	137	DNA_pol3_chi: DNA polymerase III chi subunit, HolC	86.64
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	86.56
PF00004	132	AAA: ATPase family associated with various cellula	86.52
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	86.49
TIGR02533	486	type_II_gspE general secretory pathway protein E.	86.39
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	86.38
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	86.34
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	86.3
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	86.23
PF09439	181	SRPRB: Signal recognition particle receptor beta s	86.16
PRK13766	773	Hef nuclease; Provisional	86.11
TIGR00962	501	atpA proton translocating ATP synthase, F1 alpha s	86.02
PRK14974	336	cell division protein FtsY; Provisional	86.0
PRK13343	502	F0F1 ATP synthase subunit alpha; Provisional	85.63
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	85.62
KOG0735|consensus	952		85.54
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	85.52
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	85.42
PRK12678	672	transcription termination factor Rho; Provisional	85.41
PRK09302	509	circadian clock protein KaiC; Reviewed	85.36
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	85.36
PRK09302	509	circadian clock protein KaiC; Reviewed	85.32
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	85.24
COG1125	309	OpuBA ABC-type proline/glycine betaine transport s	85.12
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	85.1
cd01523	100	RHOD_Lact_B Member of the Rhodanese Homology Domai	84.86
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	84.85
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	84.81
KOG1131|consensus	755		84.79
PRK12608	380	transcription termination factor Rho; Provisional	84.76
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	84.73
PRK06936	439	type III secretion system ATPase; Provisional	84.46
PRK09354	349	recA recombinase A; Provisional	84.35
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	84.29
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	84.24
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	84.19
KOG1806|consensus	1320		84.19
PRK08903	227	DnaA regulatory inactivator Hda; Validated	84.17
TIGR03498	418	FliI_clade3 flagellar protein export ATPase FliI.	84.0
cd01136	326	ATPase_flagellum-secretory_path_III Flagellum-spec	83.98
KOG0348|consensus	708		83.89
KOG0745|consensus	564		83.86
TIGR00665	434	DnaB replicative DNA helicase. This model describe	83.86
smart00115	241	CASc Caspase, interleukin-1 beta converting enzyme	83.86
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	83.8
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	83.77
TIGR02746	797	TraC-F-type type-IV secretion system protein TraC.	83.56
PRK05728	142	DNA polymerase III subunit chi; Validated	83.52
PRK07004	460	replicative DNA helicase; Provisional	83.5
KOG0741|consensus	744		83.44
KOG0329|consensus	387		83.26
PRK05748	448	replicative DNA helicase; Provisional	82.8
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	82.74
COG4604	252	CeuD ABC-type enterochelin transport system, ATPas	82.66
PRK13889	988	conjugal transfer relaxase TraA; Provisional	82.62
PRK14729	300	miaA tRNA delta(2)-isopentenylpyrophosphate transf	82.52
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	82.51
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	82.46
KOG0743|consensus	457		82.39
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	82.38
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	82.28
KOG1133|consensus	821		82.25
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	82.13
KOG0991|consensus	333		82.11
PRK14530	215	adenylate kinase; Provisional	82.09
TIGR03496	411	FliI_clade1 flagellar protein export ATPase FliI.	82.09
KOG0391|consensus	1958		82.08
COG5008	375	PilU Tfp pilus assembly protein, ATPase PilU [Cell	81.99
PRK00411	394	cdc6 cell division control protein 6; Reviewed	81.81
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	81.76
COG3451	796	VirB4 Type IV secretory pathway, VirB4 components	81.71
TIGR00064	272	ftsY signal recognition particle-docking protein F	81.7
TIGR01043	578	ATP_syn_A_arch ATP synthase archaeal, A subunit. A	81.67
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	81.58
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	81.54
TIGR03744	893	traC_PFL_4706 conjugative transfer ATPase, PFL_470	81.54
cd03115	173	SRP The signal recognition particle (SRP) mediates	81.51
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	81.46
PRK07960	455	fliI flagellum-specific ATP synthase; Validated	81.38
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	81.36
PF03237	384	Terminase_6: Terminase-like family; InterPro: IPR0	81.31
PRK08506	472	replicative DNA helicase; Provisional	81.3
PRK14086	617	dnaA chromosomal replication initiation protein; P	81.27
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	81.27
PRK04192	586	V-type ATP synthase subunit A; Provisional	81.24
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	81.21
PRK05595	444	replicative DNA helicase; Provisional	81.18
KOG0060|consensus	659		81.15
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	81.15
KOG1015|consensus	1567		81.04
TIGR02236	310	recomb_radA DNA repair and recombination protein R	81.0
KOG1001|consensus	674		80.74
smart00450	100	RHOD Rhodanese Homology Domain. An alpha beta fold	80.63
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	80.53
COG3972	660	Superfamily I DNA and RNA helicases [General funct	80.5
KOG0326|consensus	459		80.37
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	80.35
PRK06904	472	replicative DNA helicase; Validated	80.26
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	80.22
KOG0345|consensus	567		80.2
PRK12422	445	chromosomal replication initiation protein; Provis	80.19

>KOG0330|consensus

Probab=100.00  E-value=1e-48  Score=321.41  Aligned_cols=220  Identities=28%  Similarity=0.324  Sum_probs=193.6

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~g   78 (233)
                      |||.++.|+|+|+.|+||||||.+|++|++++++++     ...+++|||+||||||.|+.+.++.+  +.++++.++.|
T Consensus        91 aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~~-----p~~~~~lVLtPtRELA~QI~e~fe~Lg~~iglr~~~lvG  165 (476)
T KOG0330|consen   91 AIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQE-----PKLFFALVLTPTRELAQQIAEQFEALGSGIGLRVAVLVG  165 (476)
T ss_pred             hcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHcC-----CCCceEEEecCcHHHHHHHHHHHHHhccccCeEEEEEec
Confidence            799999999999999999999999999999999986     34589999999999999999999999  56889999999


Q ss_pred             CCCC---------CCeeEEe----------------ccc-----------------------------------------
Q psy14082         79 GTPK---------GPQDCLP----------------LHR-----------------------------------------   92 (233)
Q Consensus        79 g~~~---------~~~~lv~----------------l~r-----------------------------------------   92 (233)
                      |.+.         +++++||                +++                                         
T Consensus       166 G~~m~~q~~~L~kkPhilVaTPGrL~dhl~~Tkgf~le~lk~LVlDEADrlLd~dF~~~ld~ILk~ip~erqt~LfsATM  245 (476)
T KOG0330|consen  166 GMDMMLQANQLSKKPHILVATPGRLWDHLENTKGFSLEQLKFLVLDEADRLLDMDFEEELDYILKVIPRERQTFLFSATM  245 (476)
T ss_pred             CchHHHHHHHhhcCCCEEEeCcHHHHHHHHhccCccHHHhHHHhhchHHhhhhhhhHHHHHHHHHhcCccceEEEEEeec
Confidence            9765         7888888                000                                         


Q ss_pred             -------------------------hhhhchH----------------HHhcCCCCeEEEEecchhHHHHHHHHHhhCCC
Q psy14082         93 -------------------------FVFNCQY----------------EMAKNPAFKVIVFVETKKKVEDITRALRRERH  131 (233)
Q Consensus        93 -------------------------~~~~~~~----------------~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~  131 (233)
                                               .++-+.+                ++....+..+||||++...+++++-.|...|+
T Consensus       246 t~kv~kL~rasl~~p~~v~~s~ky~tv~~lkQ~ylfv~~k~K~~yLV~ll~e~~g~s~iVF~~t~~tt~~la~~L~~lg~  325 (476)
T KOG0330|consen  246 TKKVRKLQRASLDNPVKVAVSSKYQTVDHLKQTYLFVPGKDKDTYLVYLLNELAGNSVIVFCNTCNTTRFLALLLRNLGF  325 (476)
T ss_pred             chhhHHHHhhccCCCeEEeccchhcchHHhhhheEeccccccchhHHHHHHhhcCCcEEEEEeccchHHHHHHHHHhcCc
Confidence                                     0000000                44566778999999999999999999999999


Q ss_pred             eeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc------------ceeeEEee
Q psy14082        132 SAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI------------SQVIEVVQ  199 (233)
Q Consensus       132 ~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i------------~~~~~~~~  199 (233)
                      .+..+||+|++..|...++.|++|...||||||+++||+|+|.||+|||||+|.+..+||            |.++++++
T Consensus       326 ~a~~LhGqmsq~~Rlg~l~~Fk~~~r~iLv~TDVaSRGLDip~Vd~VVNyDiP~~skDYIHRvGRtaRaGrsG~~ItlVt  405 (476)
T KOG0330|consen  326 QAIPLHGQMSQSKRLGALNKFKAGARSILVCTDVASRGLDIPHVDVVVNYDIPTHSKDYIHRVGRTARAGRSGKAITLVT  405 (476)
T ss_pred             ceecccchhhHHHHHHHHHHHhccCCcEEEecchhcccCCCCCceEEEecCCCCcHHHHHHHcccccccCCCcceEEEEe
Confidence            999999999999999999999999999999999999999999999999999999999999            46778999


Q ss_pred             cchHHHHHHHHHHhhcCcccccccchhh
Q psy14082        200 DYEKEKRLFSLIRELGKYTLITQESSST  227 (233)
Q Consensus       200 ~~~~~~~~~~~i~~~~~~~~~~~~~~~~  227 (233)
                      +++  ..++..||...+..++..+...+
T Consensus       406 qyD--ve~~qrIE~~~gkkl~~~~~~~~  431 (476)
T KOG0330|consen  406 QYD--VELVQRIEHALGKKLPEYKVDKN  431 (476)
T ss_pred             hhh--hHHHHHHHHHHhcCCCccCcchH
Confidence            877  88999999988888877666554

>KOG0331|consensus

Probab=100.00  E-value=7.1e-48  Score=332.72  Aligned_cols=192  Identities=45%  Similarity=0.722  Sum_probs=169.4

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhc-cCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh--cCCcEEEEE
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISH-QEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS--SALRNICIF   77 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~-~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~--~~~~~~~~~   77 (233)
                      +||.++.|+|++++|.||||||++|++|++.++.. +....+.++|++|||+||||||.|+.+.+.++.  ..+++.|++
T Consensus       121 ~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLVL~PTRELA~QV~~~~~~~~~~~~~~~~cvy  200 (519)
T KOG0331|consen  121 GWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVLAPTRELAVQVQAEAREFGKSLRLRSTCVY  200 (519)
T ss_pred             ccceeccCCceEEEeccCCcchhhhhhHHHHHHHhccccccCCCCCeEEEEcCcHHHHHHHHHHHHHHcCCCCccEEEEe
Confidence            58999999999999999999999999999999997 555566779999999999999999999999994  456699999


Q ss_pred             cCCCCCCee---------EEe---------------ccc-----------------------------------------
Q psy14082         78 GGTPKGPQD---------CLP---------------LHR-----------------------------------------   92 (233)
Q Consensus        78 gg~~~~~~~---------lv~---------------l~r-----------------------------------------   92 (233)
                      ||.++.+|+         +||               |+|                                         
T Consensus       201 GG~~~~~Q~~~l~~gvdiviaTPGRl~d~le~g~~~l~~v~ylVLDEADrMldmGFe~qI~~Il~~i~~~~rQtlm~saT  280 (519)
T KOG0331|consen  201 GGAPKGPQLRDLERGVDVVIATPGRLIDLLEEGSLNLSRVTYLVLDEADRMLDMGFEPQIRKILSQIPRPDRQTLMFSAT  280 (519)
T ss_pred             CCCCccHHHHHHhcCCcEEEeCChHHHHHHHcCCccccceeEEEeccHHhhhccccHHHHHHHHHhcCCCcccEEEEeee
Confidence            999997776         666               111                                         


Q ss_pred             -----------------------------------hhhhchH------------HHhcCCCCeEEEEecchhHHHHHHHH
Q psy14082         93 -----------------------------------FVFNCQY------------EMAKNPAFKVIVFVETKKKVEDITRA  125 (233)
Q Consensus        93 -----------------------------------~~~~~~~------------~~~~~~~~k~iIf~~~~~~~~~l~~~  125 (233)
                                                         ++..|..            ......+.|+||||+|++.|+.++..
T Consensus       281 wp~~v~~lA~~fl~~~~~i~ig~~~~~~a~~~i~qive~~~~~~K~~~l~~lL~~~~~~~~~KvIIFc~tkr~~~~l~~~  360 (519)
T KOG0331|consen  281 WPKEVRQLAEDFLNNPIQINVGNKKELKANHNIRQIVEVCDETAKLRKLGKLLEDISSDSEGKVIIFCETKRTCDELARN  360 (519)
T ss_pred             ccHHHHHHHHHHhcCceEEEecchhhhhhhcchhhhhhhcCHHHHHHHHHHHHHHHhccCCCcEEEEecchhhHHHHHHH
Confidence                                               2222211            11245778999999999999999999


Q ss_pred             HhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCcccccc
Q psy14082        126 LRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNIS  192 (233)
Q Consensus       126 L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i~  192 (233)
                      |+..++++..+||+.++.+|..+++.|++|...||||||+++||||+|+|++|||||+|.+.+.|||
T Consensus       361 l~~~~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATdVAaRGLDi~dV~lVInydfP~~vEdYVH  427 (519)
T KOG0331|consen  361 LRRKGWPAVAIHGDKSQSERDWVLKGFREGKSPVLVATDVAARGLDVPDVDLVINYDFPNNVEDYVH  427 (519)
T ss_pred             HHhcCcceeeecccccHHHHHHHHHhcccCCcceEEEcccccccCCCccccEEEeCCCCCCHHHHHh
Confidence            9999999999999999999999999999999999999999999999999999999999999998883

>KOG0340|consensus

Probab=100.00  E-value=3.4e-43  Score=285.92  Aligned_cols=221  Identities=26%  Similarity=0.337  Sum_probs=190.8

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~g   78 (233)
                      .||.++.|+|+|.+|.||||||++|++|+++++-+.     ..|.-+||+.||||||.|+.++|..+  ..++++..++|
T Consensus        37 cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLsed-----P~giFalvlTPTrELA~QiaEQF~alGk~l~lK~~vivG  111 (442)
T KOG0340|consen   37 CIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSED-----PYGIFALVLTPTRELALQIAEQFIALGKLLNLKVSVIVG  111 (442)
T ss_pred             hhHHHhcccccccccccCCCcchhhhHHHHHhhccC-----CCcceEEEecchHHHHHHHHHHHHHhcccccceEEEEEc
Confidence            389999999999999999999999999999999765     46889999999999999999999999  55789999999


Q ss_pred             CCCC---------CCeeEEe-------------------ccc--------------------------------------
Q psy14082         79 GTPK---------GPQDCLP-------------------LHR--------------------------------------   92 (233)
Q Consensus        79 g~~~---------~~~~lv~-------------------l~r--------------------------------------   92 (233)
                      |.+.         +++++|+                   ++|                                      
T Consensus       112 G~d~i~qa~~L~~rPHvVvatPGRlad~l~sn~~~~~~~~~rlkflVlDEADrvL~~~f~d~L~~i~e~lP~~RQtLlfS  191 (442)
T KOG0340|consen  112 GTDMIMQAAILSDRPHVVVATPGRLADHLSSNLGVCSWIFQRLKFLVLDEADRVLAGCFPDILEGIEECLPKPRQTLLFS  191 (442)
T ss_pred             cHHHhhhhhhcccCCCeEecCccccccccccCCccchhhhhceeeEEecchhhhhccchhhHHhhhhccCCCccceEEEE
Confidence            9664         6667777                   111                                      


Q ss_pred             --------------------------------------------------hhhhchHHHhcCCCCeEEEEecchhHHHHH
Q psy14082         93 --------------------------------------------------FVFNCQYEMAKNPAFKVIVFVETKKKVEDI  122 (233)
Q Consensus        93 --------------------------------------------------~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l  122 (233)
                                                                        ++..+. .+......-++||+++...++.+
T Consensus       192 ATitd~i~ql~~~~i~k~~a~~~e~~~~vstvetL~q~yI~~~~~vkdaYLv~~Lr-~~~~~~~~simIFvnttr~cQ~l  270 (442)
T KOG0340|consen  192 ATITDTIKQLFGCPITKSIAFELEVIDGVSTVETLYQGYILVSIDVKDAYLVHLLR-DFENKENGSIMIFVNTTRECQLL  270 (442)
T ss_pred             eehhhHHHHhhcCCcccccceEEeccCCCCchhhhhhheeecchhhhHHHHHHHHh-hhhhccCceEEEEeehhHHHHHH
Confidence                                                              111111 12222567899999999999999


Q ss_pred             HHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc-----------
Q psy14082        123 TRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI-----------  191 (233)
Q Consensus       123 ~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i-----------  191 (233)
                      +..|+.+++.+..+||.|++++|...+.+|+++..+||+|||+++||+|+|.|++|||||+|.++..||           
T Consensus       271 ~~~l~~le~r~~~lHs~m~Q~eR~~aLsrFrs~~~~iliaTDVAsRGLDIP~V~LVvN~diPr~P~~yiHRvGRtARAGR  350 (442)
T KOG0340|consen  271 SMTLKNLEVRVVSLHSQMPQKERLAALSRFRSNAARILIATDVASRGLDIPTVELVVNHDIPRDPKDYIHRVGRTARAGR  350 (442)
T ss_pred             HHHHhhhceeeeehhhcchHHHHHHHHHHHhhcCccEEEEechhhcCCCCCceeEEEecCCCCCHHHHHHhhcchhcccC
Confidence            999999999999999999999999999999999999999999999999999999999999999999888           


Q ss_pred             -ceeeEEeecchHHHHHHHHHHhhcCcccccccchhhHh
Q psy14082        192 -SQVIEVVQDYEKEKRLFSLIRELGKYTLITQESSSTLS  229 (233)
Q Consensus       192 -~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~  229 (233)
                       |.+++++++.+  .+++..||+..+.++.+.+....-.
T Consensus       351 ~G~aiSivt~rD--v~l~~aiE~~igkKl~e~~~~~~~~  387 (442)
T KOG0340|consen  351 KGMAISIVTQRD--VELLQAIEEEIGKKLTEYNKVQRTV  387 (442)
T ss_pred             CcceEEEechhh--HHHHHHHHHHHhcccccccccchhh
Confidence             56778999766  8899999998888887777655443

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

Probab=100.00  E-value=3.1e-42  Score=306.08  Aligned_cols=214  Identities=30%  Similarity=0.410  Sum_probs=176.6

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hc-CCcEEEEE
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SS-ALRNICIF   77 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~-~~~~~~~~   77 (233)
                      |||.++.|+|++++|+||||||++|++|+++++....  . .....+|||+||||||.|+++.+..+  +. ++++.+++
T Consensus        59 ~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~--~-~~~~~aLil~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~  135 (513)
T COG0513          59 AIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSV--E-RKYVSALILAPTRELAVQIAEELRKLGKNLGGLRVAVVY  135 (513)
T ss_pred             HHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhccc--c-cCCCceEEECCCHHHHHHHHHHHHHHHhhcCCccEEEEE
Confidence            6899999999999999999999999999999987420  1 11112999999999999999999999  44 78999999


Q ss_pred             cCCCC---------CCeeEEe--------ccc------------------------------------------------
Q psy14082         78 GGTPK---------GPQDCLP--------LHR------------------------------------------------   92 (233)
Q Consensus        78 gg~~~---------~~~~lv~--------l~r------------------------------------------------   92 (233)
                      ||.+.         .++++||        +.+                                                
T Consensus       136 GG~~~~~q~~~l~~~~~ivVaTPGRllD~i~~~~l~l~~v~~lVlDEADrmLd~Gf~~~i~~I~~~~p~~~qtllfSAT~  215 (513)
T COG0513         136 GGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEADRMLDMGFIDDIEKILKALPPDRQTLLFSATM  215 (513)
T ss_pred             CCCCHHHHHHHHhcCCCEEEECccHHHHHHHcCCcchhhcCEEEeccHhhhhcCCCHHHHHHHHHhCCcccEEEEEecCC
Confidence            99876         3667888        000                                                


Q ss_pred             --------------------------------------------hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhh
Q psy14082         93 --------------------------------------------FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRR  128 (233)
Q Consensus        93 --------------------------------------------~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~  128 (233)
                                                                  -...+..++......++||||+|+..++.++..|..
T Consensus       216 ~~~i~~l~~~~l~~p~~i~v~~~~~~~~~~~i~q~~~~v~~~~~k~~~L~~ll~~~~~~~~IVF~~tk~~~~~l~~~l~~  295 (513)
T COG0513         216 PDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLELLLKLLKDEDEGRVIVFVRTKRLVEELAESLRK  295 (513)
T ss_pred             CHHHHHHHHHHccCCcEEEEccccccccccCceEEEEEeCCHHHHHHHHHHHHhcCCCCeEEEEeCcHHHHHHHHHHHHH
Confidence                                                        001111134444566899999999999999999999


Q ss_pred             CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc------------ceeeE
Q psy14082        129 ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI------------SQVIE  196 (233)
Q Consensus       129 ~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i------------~~~~~  196 (233)
                      .|+++..+||+|++++|..+++.|++|+.+||||||+++||||+|+|++|||||+|.+++.|+            |.+++
T Consensus       296 ~g~~~~~lhG~l~q~~R~~~l~~F~~g~~~vLVaTDvaaRGiDi~~v~~VinyD~p~~~e~yvHRiGRTgRaG~~G~ai~  375 (513)
T COG0513         296 RGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAIS  375 (513)
T ss_pred             CCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEEechhhccCCccccceeEEccCCCCHHHheeccCccccCCCCCeEEE
Confidence            999999999999999999999999999999999999999999999999999999999999777            56777


Q ss_pred             EeecchHHHHHHHHHHhhcCcc
Q psy14082        197 VVQDYEKEKRLFSLIRELGKYT  218 (233)
Q Consensus       197 ~~~~~~~~~~~~~~i~~~~~~~  218 (233)
                      |+.+. .+...+..+++.....
T Consensus       376 fv~~~-~e~~~l~~ie~~~~~~  396 (513)
T COG0513         376 FVTEE-EEVKKLKRIEKRLERK  396 (513)
T ss_pred             EeCcH-HHHHHHHHHHHHHhcc
Confidence            88863 2466667777655433

>KOG0328|consensus

Probab=100.00  E-value=5.6e-42  Score=271.67  Aligned_cols=221  Identities=26%  Similarity=0.359  Sum_probs=181.0

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~g   78 (233)
                      |||+++.|+|||+||.+|+|||.+|.+.+++.+.-.     .+..++|||+|||||+.|+.+.+..+  ..++.++.++|
T Consensus        57 Ai~~IlkGrdViaQaqSGTGKTa~~si~vlq~~d~~-----~r~tQ~lilsPTRELa~Qi~~vi~alg~~mnvq~hacig  131 (400)
T KOG0328|consen   57 AIPQILKGRDVIAQAQSGTGKTATFSISVLQSLDIS-----VRETQALILSPTRELAVQIQKVILALGDYMNVQCHACIG  131 (400)
T ss_pred             hhhhhhcccceEEEecCCCCceEEEEeeeeeecccc-----cceeeEEEecChHHHHHHHHHHHHHhcccccceEEEEec
Confidence            799999999999999999999999999999877654     45688999999999999999999999  56889999999


Q ss_pred             CCCCCCee---------EEe--------ccc-------------------------------------------------
Q psy14082         79 GTPKGPQD---------CLP--------LHR-------------------------------------------------   92 (233)
Q Consensus        79 g~~~~~~~---------lv~--------l~r-------------------------------------------------   92 (233)
                      |.+..+++         +.|        ++|                                                 
T Consensus       132 g~n~gedikkld~G~hvVsGtPGrv~dmikr~~L~tr~vkmlVLDEaDemL~kgfk~Qiydiyr~lp~~~Qvv~~SATlp  211 (400)
T KOG0328|consen  132 GKNLGEDIKKLDYGQHVVSGTPGRVLDMIKRRSLRTRAVKMLVLDEADEMLNKGFKEQIYDIYRYLPPGAQVVLVSATLP  211 (400)
T ss_pred             CCccchhhhhhcccceEeeCCCchHHHHHHhccccccceeEEEeccHHHHHHhhHHHHHHHHHHhCCCCceEEEEeccCc
Confidence            98854433         333        111                                                 


Q ss_pred             --------------------------------hhhhchH---------HHhcCCCCeEEEEecchhHHHHHHHHHhhCCC
Q psy14082         93 --------------------------------FVFNCQY---------EMAKNPAFKVIVFVETKKKVEDITRALRRERH  131 (233)
Q Consensus        93 --------------------------------~~~~~~~---------~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~  131 (233)
                                                      ++.+-.+         +...-.-.+.+|||||+..++++.+.|++.++
T Consensus       212 ~eilemt~kfmtdpvrilvkrdeltlEgIKqf~v~ve~EewKfdtLcdLYd~LtItQavIFcnTk~kVdwLtekm~~~nf  291 (400)
T KOG0328|consen  212 HEILEMTEKFMTDPVRILVKRDELTLEGIKQFFVAVEKEEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANF  291 (400)
T ss_pred             HHHHHHHHHhcCCceeEEEecCCCchhhhhhheeeechhhhhHhHHHHHhhhhehheEEEEecccchhhHHHHHHHhhCc
Confidence                                            1111000         22333456899999999999999999999999


Q ss_pred             eeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc------------ceeeEEee
Q psy14082        132 SAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI------------SQVIEVVQ  199 (233)
Q Consensus       132 ~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i------------~~~~~~~~  199 (233)
                      .+..+||+|++++|.+++++|++|+.++|++||+-+||+|+|.|++|||||+|.+.+.||            |-++.|+.
T Consensus       292 tVssmHGDm~qkERd~im~dFRsg~SrvLitTDVwaRGiDv~qVslviNYDLP~nre~YIHRIGRSGRFGRkGvainFVk  371 (400)
T KOG0328|consen  292 TVSSMHGDMEQKERDKIMNDFRSGKSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAINFVK  371 (400)
T ss_pred             eeeeccCCcchhHHHHHHHHhhcCCceEEEEechhhccCCcceeEEEEecCCCccHHHHhhhhccccccCCcceEEEEec
Confidence            999999999999999999999999999999999999999999999999999999998666            35566777


Q ss_pred             cchHHHHHHHHHHhhcCcccccccchhhHhh
Q psy14082        200 DYEKEKRLFSLIRELGKYTLITQESSSTLSE  230 (233)
Q Consensus       200 ~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~  230 (233)
                      +.  +.+.+..++++.+..+  .+.|-+..+
T Consensus       372 ~~--d~~~lrdieq~yst~i--~emp~nvad  398 (400)
T KOG0328|consen  372 SD--DLRILRDIEQYYSTQI--DEMPMNVAD  398 (400)
T ss_pred             HH--HHHHHHHHHHHHhhhc--ccccchhhh
Confidence            54  4888888888775533  344444433

>KOG0338|consensus

Probab=100.00  E-value=5.2e-42  Score=290.07  Aligned_cols=210  Identities=26%  Similarity=0.330  Sum_probs=182.8

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~g   78 (233)
                      .||..+-|+|+.++|.||||||+||++|++++++..+..  -..-|+|||||||||+.|+|+..+++  |.++.+++.+|
T Consensus       211 ~IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~--~~~TRVLVL~PTRELaiQv~sV~~qlaqFt~I~~~L~vG  288 (691)
T KOG0338|consen  211 TIPVALLGKDICACAATGSGKTAAFALPILERLLYRPKK--VAATRVLVLVPTRELAIQVHSVTKQLAQFTDITVGLAVG  288 (691)
T ss_pred             cccHHhhcchhhheecccCCchhhhHHHHHHHHhcCccc--CcceeEEEEeccHHHHHHHHHHHHHHHhhccceeeeeec
Confidence            389999999999999999999999999999999986432  34678999999999999999999999  88999999999


Q ss_pred             CCCC---------CCeeEEe--------ccc-------------------------------hhhhchH-----------
Q psy14082         79 GTPK---------GPQDCLP--------LHR-------------------------------FVFNCQY-----------   99 (233)
Q Consensus        79 g~~~---------~~~~lv~--------l~r-------------------------------~~~~~~~-----------   99 (233)
                      |.+-         .|+|+||        |+.                               ++.+|.+           
T Consensus       289 GL~lk~QE~~LRs~PDIVIATPGRlIDHlrNs~sf~ldsiEVLvlDEADRMLeegFademnEii~lcpk~RQTmLFSATM  368 (691)
T KOG0338|consen  289 GLDLKAQEAVLRSRPDIVIATPGRLIDHLRNSPSFNLDSIEVLVLDEADRMLEEGFADEMNEIIRLCPKNRQTMLFSATM  368 (691)
T ss_pred             CccHHHHHHHHhhCCCEEEecchhHHHHhccCCCccccceeEEEechHHHHHHHHHHHHHHHHHHhccccccceeehhhh
Confidence            9875         5677888        111                               2222222           


Q ss_pred             ---------------------------------------------------HHhcCCCCeEEEEecchhHHHHHHHHHhh
Q psy14082        100 ---------------------------------------------------EMAKNPAFKVIVFVETKKKVEDITRALRR  128 (233)
Q Consensus       100 ---------------------------------------------------~~~~~~~~k~iIf~~~~~~~~~l~~~L~~  128 (233)
                                                                         ++.+....+++||+.|++.++.+.-.|--
T Consensus       369 teeVkdL~slSL~kPvrifvd~~~~~a~~LtQEFiRIR~~re~dRea~l~~l~~rtf~~~~ivFv~tKk~AHRl~IllGL  448 (691)
T KOG0338|consen  369 TEEVKDLASLSLNKPVRIFVDPNKDTAPKLTQEFIRIRPKREGDREAMLASLITRTFQDRTIVFVRTKKQAHRLRILLGL  448 (691)
T ss_pred             HHHHHHHHHhhcCCCeEEEeCCccccchhhhHHHheeccccccccHHHHHHHHHHhcccceEEEEehHHHHHHHHHHHHH
Confidence                                                               33445678899999999999999999999


Q ss_pred             CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc------------ceeeE
Q psy14082        129 ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI------------SQVIE  196 (233)
Q Consensus       129 ~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i------------~~~~~  196 (233)
                      +|+++.-+||.+++.+|.+.++.|+++++++|||||+++||+|+++|..||||++|.+.++|+            |++++
T Consensus       449 lgl~agElHGsLtQ~QRlesL~kFk~~eidvLiaTDvAsRGLDI~gV~tVINy~mP~t~e~Y~HRVGRTARAGRaGrsVt  528 (691)
T KOG0338|consen  449 LGLKAGELHGSLTQEQRLESLEKFKKEEIDVLIATDVASRGLDIEGVQTVINYAMPKTIEHYLHRVGRTARAGRAGRSVT  528 (691)
T ss_pred             hhchhhhhcccccHHHHHHHHHHHHhccCCEEEEechhhccCCccceeEEEeccCchhHHHHHHHhhhhhhcccCcceEE
Confidence            999999999999999999999999999999999999999999999999999999999999999            68888


Q ss_pred             EeecchHHHHHHHHHHhh
Q psy14082        197 VVQDYEKEKRLFSLIREL  214 (233)
Q Consensus       197 ~~~~~~~~~~~~~~i~~~  214 (233)
                      |+.+.+  +++++.+-+.
T Consensus       529 lvgE~d--RkllK~iik~  544 (691)
T KOG0338|consen  529 LVGESD--RKLLKEIIKS  544 (691)
T ss_pred             Eecccc--HHHHHHHHhh
Confidence            999655  7777777654

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=5.7e-41  Score=293.20  Aligned_cols=219  Identities=25%  Similarity=0.273  Sum_probs=180.0

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCC--CCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEE
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPV--KQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICI   76 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~--~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~   76 (233)
                      |||.++.|+|++++||||||||++|++|++++++..+..  ....++++|||+||||||.|+++.+..+  ..++++..+
T Consensus        38 aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~~~~lil~PtreLa~Qi~~~~~~l~~~~~~~v~~~  117 (423)
T PRK04837         38 ALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQATGLKLGLA  117 (423)
T ss_pred             HHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhcccccccccCCceEEEECCcHHHHHHHHHHHHHHhccCCceEEEE
Confidence            589999999999999999999999999999999865321  1234689999999999999999999998  457889999


Q ss_pred             EcCCCC---------CCeeEEe---------------ccc----------------------------------------
Q psy14082         77 FGGTPK---------GPQDCLP---------------LHR----------------------------------------   92 (233)
Q Consensus        77 ~gg~~~---------~~~~lv~---------------l~r----------------------------------------   92 (233)
                      +||.+.         ..+++|+               +.+                                        
T Consensus       118 ~gg~~~~~~~~~l~~~~~IlV~TP~~l~~~l~~~~~~l~~v~~lViDEad~l~~~~f~~~i~~i~~~~~~~~~~~~~l~S  197 (423)
T PRK04837        118 YGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEADRMFDLGFIKDIRWLFRRMPPANQRLNMLFS  197 (423)
T ss_pred             ECCCCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccccEEEEecHHHHhhcccHHHHHHHHHhCCCccceeEEEEe
Confidence            998653         3467777               000                                        


Q ss_pred             --------------------------------------------hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhh
Q psy14082         93 --------------------------------------------FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRR  128 (233)
Q Consensus        93 --------------------------------------------~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~  128 (233)
                                                                  ....+...+......++||||++++.++.++..|..
T Consensus       198 AT~~~~~~~~~~~~~~~p~~i~v~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lVF~~t~~~~~~l~~~L~~  277 (423)
T PRK04837        198 ATLSYRVRELAFEHMNNPEYVEVEPEQKTGHRIKEELFYPSNEEKMRLLQTLIEEEWPDRAIIFANTKHRCEEIWGHLAA  277 (423)
T ss_pred             ccCCHHHHHHHHHHCCCCEEEEEcCCCcCCCceeEEEEeCCHHHHHHHHHHHHHhcCCCeEEEEECCHHHHHHHHHHHHh
Confidence                                                        000001123344568999999999999999999999


Q ss_pred             CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc------------ceeeE
Q psy14082        129 ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI------------SQVIE  196 (233)
Q Consensus       129 ~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i------------~~~~~  196 (233)
                      .|+++..+||+|++++|..++++|++|++++|||||+++||+|+|++++|||||+|.+.+.|+            |.++.
T Consensus       278 ~g~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLVaTdv~~rGiDip~v~~VI~~d~P~s~~~yiqR~GR~gR~G~~G~ai~  357 (423)
T PRK04837        278 DGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSIS  357 (423)
T ss_pred             CCCcEEEecCCCChhHHHHHHHHHHcCCCcEEEEechhhcCCCccccCEEEEeCCCCchhheEeccccccCCCCCeeEEE
Confidence            999999999999999999999999999999999999999999999999999999999999887            34566


Q ss_pred             EeecchHHHHHHHHHHhhcCccccc
Q psy14082        197 VVQDYEKEKRLFSLIRELGKYTLIT  221 (233)
Q Consensus       197 ~~~~~~~~~~~~~~i~~~~~~~~~~  221 (233)
                      |+.+++  ...+..+++..+..++.
T Consensus       358 ~~~~~~--~~~~~~i~~~~~~~~~~  380 (423)
T PRK04837        358 LACEEY--ALNLPAIETYIGHSIPV  380 (423)
T ss_pred             EeCHHH--HHHHHHHHHHhCCCCCC
Confidence            787644  66677777766655543

>KOG0342|consensus

Probab=100.00  E-value=7.3e-41  Score=282.06  Aligned_cols=220  Identities=26%  Similarity=0.306  Sum_probs=184.1

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hc-CCcEEEEE
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SS-ALRNICIF   77 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~-~~~~~~~~   77 (233)
                      .||+++.|+|+++.|.||||||+||++|+++.+...+... +++..++|+|||||||.|++.+.+++  +. .+.+..++
T Consensus       112 ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~~-r~~~~vlIi~PTRELA~Q~~~eak~Ll~~h~~~~v~~vi  190 (543)
T KOG0342|consen  112 TIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFKP-RNGTGVLIICPTRELAMQIFAEAKELLKYHESITVGIVI  190 (543)
T ss_pred             hcCccCCCccceeeeccCCCceeeehhHHHHHHHhcccCC-CCCeeEEEecccHHHHHHHHHHHHHHHhhCCCcceEEEe
Confidence            4899999999999999999999999999999999875444 37889999999999999999999999  44 88999999


Q ss_pred             cCCCC---------CCeeEEe--------c-------------------------------cc-----------------
Q psy14082         78 GGTPK---------GPQDCLP--------L-------------------------------HR-----------------   92 (233)
Q Consensus        78 gg~~~---------~~~~lv~--------l-------------------------------~r-----------------   92 (233)
                      ||.+.         ..+++||        |                               .+                 
T Consensus       191 GG~~~~~e~~kl~k~~niliATPGRLlDHlqNt~~f~~r~~k~lvlDEADrlLd~GF~~di~~Ii~~lpk~rqt~LFSAT  270 (543)
T KOG0342|consen  191 GGNNFSVEADKLVKGCNILIATPGRLLDHLQNTSGFLFRNLKCLVLDEADRLLDIGFEEDVEQIIKILPKQRQTLLFSAT  270 (543)
T ss_pred             CCccchHHHHHhhccccEEEeCCchHHhHhhcCCcchhhccceeEeecchhhhhcccHHHHHHHHHhccccceeeEeeCC
Confidence            99775         4566787        0                               00                 


Q ss_pred             ------------------hhhhc---------------------------hHHHhcCCC-CeEEEEecchhHHHHHHHHH
Q psy14082         93 ------------------FVFNC---------------------------QYEMAKNPA-FKVIVFVETKKKVEDITRAL  126 (233)
Q Consensus        93 ------------------~~~~~---------------------------~~~~~~~~~-~k~iIf~~~~~~~~~l~~~L  126 (233)
                                        +++..                           -..+.++.. .|+||||+|...+..+++.|
T Consensus       271 ~~~kV~~l~~~~L~~d~~~v~~~d~~~~~The~l~Qgyvv~~~~~~f~ll~~~LKk~~~~~KiiVF~sT~~~vk~~~~lL  350 (543)
T KOG0342|consen  271 QPSKVKDLARGALKRDPVFVNVDDGGERETHERLEQGYVVAPSDSRFSLLYTFLKKNIKRYKIIVFFSTCMSVKFHAELL  350 (543)
T ss_pred             CcHHHHHHHHHhhcCCceEeecCCCCCcchhhcccceEEeccccchHHHHHHHHHHhcCCceEEEEechhhHHHHHHHHH
Confidence                              00000                           003344444 89999999999999999999


Q ss_pred             hhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCcccccc------------ee
Q psy14082        127 RRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNIS------------QV  194 (233)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i~------------~~  194 (233)
                      ....++|..+||++++..|..+..+|++.+..||||||+.+||+|+|+|+|||+||+|.++++|||            .+
T Consensus       351 ~~~dlpv~eiHgk~~Q~kRT~~~~~F~kaesgIL~cTDVaARGlD~P~V~~VvQ~~~P~d~~~YIHRvGRTaR~gk~G~a  430 (543)
T KOG0342|consen  351 NYIDLPVLEIHGKQKQNKRTSTFFEFCKAESGILVCTDVAARGLDIPDVDWVVQYDPPSDPEQYIHRVGRTAREGKEGKA  430 (543)
T ss_pred             hhcCCchhhhhcCCcccccchHHHHHhhcccceEEecchhhccCCCCCceEEEEeCCCCCHHHHHHHhccccccCCCceE
Confidence            999999999999999999999999999999999999999999999999999999999999999994            44


Q ss_pred             eEEeecchHHHHHHHHHHhhcCccccccc
Q psy14082        195 IEVVQDYEKEKRLFSLIRELGKYTLITQE  223 (233)
Q Consensus       195 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~  223 (233)
                      +.++.+  ++..++..+++.--.++++.+
T Consensus       431 lL~l~p--~El~Flr~LK~lpl~~~e~~~  457 (543)
T KOG0342|consen  431 LLLLAP--WELGFLRYLKKLPLEEFEFPP  457 (543)
T ss_pred             EEEeCh--hHHHHHHHHhhCCCcccCCCC
Confidence            556664  458899999875544444444

>KOG0333|consensus

Probab=100.00  E-value=1.2e-40  Score=282.54  Aligned_cols=202  Identities=29%  Similarity=0.432  Sum_probs=174.9

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCC----CCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEE
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPV----KQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNI   74 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~----~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~   74 (233)
                      |||..+..+|+|..|.||||||++|++|++..+...++.    +...||+++||+|||||++|+.+.-.+|  ..++++.
T Consensus       275 aipl~lQ~rD~igvaETgsGktaaf~ipLl~~IsslP~~~~~en~~~gpyaiilaptReLaqqIeeEt~kf~~~lg~r~v  354 (673)
T KOG0333|consen  275 AIPLGLQNRDPIGVAETGSGKTAAFLIPLLIWISSLPPMARLENNIEGPYAIILAPTRELAQQIEEETNKFGKPLGIRTV  354 (673)
T ss_pred             hccchhccCCeeeEEeccCCccccchhhHHHHHHcCCCcchhhhcccCceeeeechHHHHHHHHHHHHHHhcccccceEE
Confidence            789999999999999999999999999999999877543    2356999999999999999999999999  5568999


Q ss_pred             EEEcCCCCCCe---------eEEe--------ccc---------------------------------------------
Q psy14082         75 CIFGGTPKGPQ---------DCLP--------LHR---------------------------------------------   92 (233)
Q Consensus        75 ~~~gg~~~~~~---------~lv~--------l~r---------------------------------------------   92 (233)
                      .++||.+..+|         ++||        |.+                                             
T Consensus       355 svigg~s~EEq~fqls~gceiviatPgrLid~Lenr~lvl~qctyvvldeadrmiDmgfE~dv~~iL~~mPssn~k~~td  434 (673)
T KOG0333|consen  355 SVIGGLSFEEQGFQLSMGCEIVIATPGRLIDSLENRYLVLNQCTYVVLDEADRMIDMGFEPDVQKILEQMPSSNAKPDTD  434 (673)
T ss_pred             EEecccchhhhhhhhhccceeeecCchHHHHHHHHHHHHhccCceEeccchhhhhcccccHHHHHHHHhCCccccCCCcc
Confidence            99999876544         4666        000                                             


Q ss_pred             ---------------------------------------------------------------------hhhhchHHHhc
Q psy14082         93 ---------------------------------------------------------------------FVFNCQYEMAK  103 (233)
Q Consensus        93 ---------------------------------------------------------------------~~~~~~~~~~~  103 (233)
                                                                                           -.+-+.+.+.+
T Consensus       435 e~~~~~~~~~~~~~~k~yrqT~mftatm~p~verlar~ylr~pv~vtig~~gk~~~rveQ~v~m~~ed~k~kkL~eil~~  514 (673)
T KOG0333|consen  435 EKEGEERVRKNFSSSKKYRQTVMFTATMPPAVERLARSYLRRPVVVTIGSAGKPTPRVEQKVEMVSEDEKRKKLIEILES  514 (673)
T ss_pred             chhhHHHHHhhcccccceeEEEEEecCCChHHHHHHHHHhhCCeEEEeccCCCCccchheEEEEecchHHHHHHHHHHHh
Confidence                                                                                 01111114556


Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecC
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSL  183 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~  183 (233)
                      +...++|||+|+++.++.+++.|.+.|+++..+||+.++++|+.+++.|++|..+||||||+++||+|+|+|.+||||||
T Consensus       515 ~~~ppiIIFvN~kk~~d~lAk~LeK~g~~~~tlHg~k~qeQRe~aL~~fr~~t~dIlVaTDvAgRGIDIpnVSlVinydm  594 (673)
T KOG0333|consen  515 NFDPPIIIFVNTKKGADALAKILEKAGYKVTTLHGGKSQEQRENALADFREGTGDILVATDVAGRGIDIPNVSLVINYDM  594 (673)
T ss_pred             CCCCCEEEEEechhhHHHHHHHHhhccceEEEeeCCccHHHHHHHHHHHHhcCCCEEEEecccccCCCCCccceeeecch
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCccccc------------ceeeEEeecch
Q psy14082        184 QLSANHNI------------SQVIEVVQDYE  202 (233)
Q Consensus       184 P~~~~~~i------------~~~~~~~~~~~  202 (233)
                      ++|++.|+            |.+++|+++.+
T Consensus       595 aksieDYtHRIGRTgRAGk~GtaiSflt~~d  625 (673)
T KOG0333|consen  595 AKSIEDYTHRIGRTGRAGKSGTAISFLTPAD  625 (673)
T ss_pred             hhhHHHHHHHhccccccccCceeEEEeccch
Confidence            99998666            57788999755

>PTZ00110 helicase; Provisional

Probab=100.00  E-value=2e-40  Score=296.76  Aligned_cols=202  Identities=40%  Similarity=0.616  Sum_probs=168.7

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~g   78 (233)
                      |||.+++|+|++++||||||||++|++|++.+++.++......++++|||+||||||.|+++.+++|  ..++++.+++|
T Consensus       160 aip~~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~~~~~gp~~LIL~PTreLa~Qi~~~~~~~~~~~~i~~~~~~g  239 (545)
T PTZ00110        160 GWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYG  239 (545)
T ss_pred             HHHHHhcCCCEEEEeCCCChHHHHHHHHHHHHHHhcccccCCCCcEEEEECChHHHHHHHHHHHHHHhcccCccEEEEeC
Confidence            5899999999999999999999999999999988764444456899999999999999999999999  44678899999


Q ss_pred             CCCC---------CCeeEEe---------------ccc-----------------------h------------------
Q psy14082         79 GTPK---------GPQDCLP---------------LHR-----------------------F------------------   93 (233)
Q Consensus        79 g~~~---------~~~~lv~---------------l~r-----------------------~------------------   93 (233)
                      |.+.         ..+++|+               ++|                       +                  
T Consensus       240 g~~~~~q~~~l~~~~~IlVaTPgrL~d~l~~~~~~l~~v~~lViDEAd~mld~gf~~~i~~il~~~~~~~q~l~~SAT~p  319 (545)
T PTZ00110        240 GVPKRGQIYALRRGVEILIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLDMGFEPQIRKIVSQIRPDRQTLMWSATWP  319 (545)
T ss_pred             CCCHHHHHHHHHcCCCEEEECHHHHHHHHHcCCCChhhCcEEEeehHHhhhhcchHHHHHHHHHhCCCCCeEEEEEeCCC
Confidence            9765         2456776               000                       0                  


Q ss_pred             ----------h------------------------hhc---------hHHHhc--CCCCeEEEEecchhHHHHHHHHHhh
Q psy14082         94 ----------V------------------------FNC---------QYEMAK--NPAFKVIVFVETKKKVEDITRALRR  128 (233)
Q Consensus        94 ----------~------------------------~~~---------~~~~~~--~~~~k~iIf~~~~~~~~~l~~~L~~  128 (233)
                                .                        ..+         .+.+..  ....++||||++++.++.++..|..
T Consensus       320 ~~v~~l~~~l~~~~~v~i~vg~~~l~~~~~i~q~~~~~~~~~k~~~L~~ll~~~~~~~~k~LIF~~t~~~a~~l~~~L~~  399 (545)
T PTZ00110        320 KEVQSLARDLCKEEPVHVNVGSLDLTACHNIKQEVFVVEEHEKRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRL  399 (545)
T ss_pred             HHHHHHHHHHhccCCEEEEECCCccccCCCeeEEEEEEechhHHHHHHHHHHHhcccCCeEEEEecChHHHHHHHHHHHH
Confidence                      0                        000         001111  1567999999999999999999999


Q ss_pred             CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc------------ceeeE
Q psy14082        129 ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI------------SQVIE  196 (233)
Q Consensus       129 ~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i------------~~~~~  196 (233)
                      .++.+..+||+|++++|..++++|++|+.+||||||+++||+|+|++++|||||+|.+.+.|+            |.++.
T Consensus       400 ~g~~~~~ihg~~~~~eR~~il~~F~~G~~~ILVaTdv~~rGIDi~~v~~VI~~d~P~s~~~yvqRiGRtGR~G~~G~ai~  479 (545)
T PTZ00110        400 DGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYT  479 (545)
T ss_pred             cCCcEEEEECCCcHHHHHHHHHHHhcCCCcEEEEcchhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEE
Confidence            999999999999999999999999999999999999999999999999999999999998776            35566


Q ss_pred             Eeecch
Q psy14082        197 VVQDYE  202 (233)
Q Consensus       197 ~~~~~~  202 (233)
                      |+++.+
T Consensus       480 ~~~~~~  485 (545)
T PTZ00110        480 FLTPDK  485 (545)
T ss_pred             EECcch
Confidence            777644

>KOG0345|consensus

Probab=100.00  E-value=3.1e-39  Score=270.91  Aligned_cols=192  Identities=28%  Similarity=0.331  Sum_probs=164.5

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh---hcCCcEEEEE
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF---SSALRNICIF   77 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~---~~~~~~~~~~   77 (233)
                      +||.+++++||.+.|+||||||+||++|+++.+.......+.....+|||+|||||+.||++.+..|   ..++++.+++
T Consensus        36 tIPlll~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vgalIIsPTRELa~QI~~V~~~F~~~l~~l~~~l~v  115 (567)
T KOG0345|consen   36 TIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGALIISPTRELARQIREVAQPFLEHLPNLNCELLV  115 (567)
T ss_pred             hhHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCccceeEEEecCcHHHHHHHHHHHHHHHHhhhccceEEEe
Confidence            5899999999999999999999999999999997654444444678999999999999999999999   5789999999


Q ss_pred             cCCCC----------CCeeEEe--------ccc-----------------------------------------------
Q psy14082         78 GGTPK----------GPQDCLP--------LHR-----------------------------------------------   92 (233)
Q Consensus        78 gg~~~----------~~~~lv~--------l~r-----------------------------------------------   92 (233)
                      ||.+.          .++++||        ++|                                               
T Consensus       116 GG~~v~~Di~~fkee~~nIlVgTPGRL~di~~~~~~~l~~rsLe~LVLDEADrLldmgFe~~~n~ILs~LPKQRRTGLFS  195 (567)
T KOG0345|consen  116 GGRSVEEDIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRSLEILVLDEADRLLDMGFEASVNTILSFLPKQRRTGLFS  195 (567)
T ss_pred             cCccHHHHHHHHHHhCCcEEEeCchhHHHHHhchhhhccccccceEEecchHhHhcccHHHHHHHHHHhccccccccccc
Confidence            99665          4566888        111                                               


Q ss_pred             ----------------------------------------------hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHH
Q psy14082         93 ----------------------------------------------FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRAL  126 (233)
Q Consensus        93 ----------------------------------------------~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L  126 (233)
                                                                    -...+-+.+......|+|||++|...++.....+
T Consensus       196 ATq~~~v~dL~raGLRNpv~V~V~~k~~~~tPS~L~~~Y~v~~a~eK~~~lv~~L~~~~~kK~iVFF~TCasVeYf~~~~  275 (567)
T KOG0345|consen  196 ATQTQEVEDLARAGLRNPVRVSVKEKSKSATPSSLALEYLVCEADEKLSQLVHLLNNNKDKKCIVFFPTCASVEYFGKLF  275 (567)
T ss_pred             chhhHHHHHHHHhhccCceeeeecccccccCchhhcceeeEecHHHHHHHHHHHHhccccccEEEEecCcchHHHHHHHH
Confidence                                                          1111112556678899999999999999999998


Q ss_pred             hhC--CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCcccccc
Q psy14082        127 RRE--RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNIS  192 (233)
Q Consensus       127 ~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i~  192 (233)
                      ...  +.....+||.|+++.|..++.+|++....+|+|||+++||+|+|++|+||+||+|.+++.++|
T Consensus       276 ~~~l~~~~i~~iHGK~~q~~R~k~~~~F~~~~~~vl~~TDVaARGlDip~iD~VvQ~DpP~~~~~FvH  343 (567)
T KOG0345|consen  276 SRLLKKREIFSIHGKMSQKARAKVLEAFRKLSNGVLFCTDVAARGLDIPGIDLVVQFDPPKDPSSFVH  343 (567)
T ss_pred             HHHhCCCcEEEecchhcchhHHHHHHHHHhccCceEEeehhhhccCCCCCceEEEecCCCCChhHHHh
Confidence            765  678899999999999999999999988889999999999999999999999999999986663

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=3.2e-39  Score=290.17  Aligned_cols=218  Identities=27%  Similarity=0.355  Sum_probs=177.6

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCC--CCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEE
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPV--KQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICI   76 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~--~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~   76 (233)
                      +||.++.|+|++++||||||||++|++|++++++..+..  ....++++|||+||+||+.|+++.+..+  ..++++..+
T Consensus        39 ~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~raLIl~PTreLa~Qi~~~~~~l~~~~~i~v~~l  118 (572)
T PRK04537         39 TLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKFGADLGLRFALV  118 (572)
T ss_pred             HHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCceEEEEeCcHHHHHHHHHHHHHHhccCCceEEEE
Confidence            589999999999999999999999999999999764321  1123689999999999999999999999  446789999


Q ss_pred             EcCCCC---------CCeeEEe--------ccc-----------------------------------------------
Q psy14082         77 FGGTPK---------GPQDCLP--------LHR-----------------------------------------------   92 (233)
Q Consensus        77 ~gg~~~---------~~~~lv~--------l~r-----------------------------------------------   92 (233)
                      +||.+.         ..+++|+        +.+                                               
T Consensus       119 ~Gg~~~~~q~~~l~~~~dIiV~TP~rL~~~l~~~~~~~l~~v~~lViDEAh~lld~gf~~~i~~il~~lp~~~~~q~ll~  198 (572)
T PRK04537        119 YGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFDLGFIKDIRFLLRRMPERGTRQTLLF  198 (572)
T ss_pred             ECCCCHHHHHHHHhCCCCEEEECHHHHHHHHHhccccchhheeeeEecCHHHHhhcchHHHHHHHHHhcccccCceEEEE
Confidence            999765         2456777        000                                               


Q ss_pred             ---------------------------------------------hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHh
Q psy14082         93 ---------------------------------------------FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALR  127 (233)
Q Consensus        93 ---------------------------------------------~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~  127 (233)
                                                                   .+..+..++....+.++||||++++.++.+++.|.
T Consensus       199 SATl~~~v~~l~~~~l~~p~~i~v~~~~~~~~~i~q~~~~~~~~~k~~~L~~ll~~~~~~k~LVF~nt~~~ae~l~~~L~  278 (572)
T PRK04537        199 SATLSHRVLELAYEHMNEPEKLVVETETITAARVRQRIYFPADEEKQTLLLGLLSRSEGARTMVFVNTKAFVERVARTLE  278 (572)
T ss_pred             eCCccHHHHHHHHHHhcCCcEEEeccccccccceeEEEEecCHHHHHHHHHHHHhcccCCcEEEEeCCHHHHHHHHHHHH
Confidence                                                         00000013344567899999999999999999999


Q ss_pred             hCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc------------ceee
Q psy14082        128 RERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI------------SQVI  195 (233)
Q Consensus       128 ~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i------------~~~~  195 (233)
                      +.++.+..+||+|++.+|..+++.|++|+.+||||||++++|+|+|++++|||||+|.+.+.|+            |.++
T Consensus       279 ~~g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaTdv~arGIDip~V~~VInyd~P~s~~~yvqRiGRaGR~G~~G~ai  358 (572)
T PRK04537        279 RHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAI  358 (572)
T ss_pred             HcCCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEehhhhcCCCccCCCEEEEcCCCCCHHHHhhhhcccccCCCCceEE
Confidence            9999999999999999999999999999999999999999999999999999999999998777            3455


Q ss_pred             EEeecchHHHHHHHHHHhhcCcccc
Q psy14082        196 EVVQDYEKEKRLFSLIRELGKYTLI  220 (233)
Q Consensus       196 ~~~~~~~~~~~~~~~i~~~~~~~~~  220 (233)
                      .|+.+.+  ...+..+++..+.+++
T Consensus       359 ~~~~~~~--~~~l~~i~~~~~~~~~  381 (572)
T PRK04537        359 SFACERY--AMSLPDIEAYIEQKIP  381 (572)
T ss_pred             EEecHHH--HHHHHHHHHHHcCCCC
Confidence            5777543  5567777776555443

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=100.00  E-value=4.1e-39  Score=283.69  Aligned_cols=217  Identities=28%  Similarity=0.400  Sum_probs=177.6

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCC-CCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEE
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPV-KQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIF   77 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~-~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~   77 (233)
                      |||.++.|+|++++||||||||++|++|+++.+...... .....+++|||+||||||.|+++.++.+  ..++++..++
T Consensus        31 ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~~~~~aLil~PtreLa~Qi~~~~~~~~~~~~~~~~~~~  110 (456)
T PRK10590         31 AIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALILTPTRELAAQIGENVRDYSKYLNIRSLVVF  110 (456)
T ss_pred             HHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhcccccccCCCceEEEEeCcHHHHHHHHHHHHHHhccCCCEEEEEE
Confidence            578899999999999999999999999999998764321 1234568999999999999999999998  4567888899


Q ss_pred             cCCCC---------CCeeEEe---------------ccc-----------------------------------------
Q psy14082         78 GGTPK---------GPQDCLP---------------LHR-----------------------------------------   92 (233)
Q Consensus        78 gg~~~---------~~~~lv~---------------l~r-----------------------------------------   92 (233)
                      ||.+.         ..+++|+               +++                                         
T Consensus       111 gg~~~~~~~~~l~~~~~IiV~TP~rL~~~~~~~~~~l~~v~~lViDEah~ll~~~~~~~i~~il~~l~~~~q~l~~SAT~  190 (456)
T PRK10590        111 GGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRMLDMGFIHDIRRVLAKLPAKRQNLLFSATF  190 (456)
T ss_pred             CCcCHHHHHHHHcCCCcEEEEChHHHHHHHHcCCcccccceEEEeecHHHHhccccHHHHHHHHHhCCccCeEEEEeCCC
Confidence            98764         3456777               000                                         


Q ss_pred             -----------------------------------------hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCC
Q psy14082         93 -----------------------------------------FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERH  131 (233)
Q Consensus        93 -----------------------------------------~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~  131 (233)
                                                               ...++...+......++||||++++.++.+++.|.+.++
T Consensus       191 ~~~~~~l~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~l~~~~~~~~~lVF~~t~~~~~~l~~~L~~~g~  270 (456)
T PRK10590        191 SDDIKALAEKLLHNPLEIEVARRNTASEQVTQHVHFVDKKRKRELLSQMIGKGNWQQVLVFTRTKHGANHLAEQLNKDGI  270 (456)
T ss_pred             cHHHHHHHHHHcCCCeEEEEecccccccceeEEEEEcCHHHHHHHHHHHHHcCCCCcEEEEcCcHHHHHHHHHHHHHCCC
Confidence                                                     000011123344567999999999999999999999999


Q ss_pred             eeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc------------ceeeEEee
Q psy14082        132 SAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI------------SQVIEVVQ  199 (233)
Q Consensus       132 ~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i------------~~~~~~~~  199 (233)
                      .+..+||+|++.+|..++++|++|+.+||||||++++|+|+|++++|||||+|.+...|+            |.++.++.
T Consensus       271 ~~~~lhg~~~~~~R~~~l~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yvqR~GRaGR~g~~G~ai~l~~  350 (456)
T PRK10590        271 RSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLVC  350 (456)
T ss_pred             CEEEEECCCCHHHHHHHHHHHHcCCCcEEEEccHHhcCCCcccCCEEEEeCCCCCHHHhhhhccccccCCCCeeEEEEec
Confidence            999999999999999999999999999999999999999999999999999999998777            35566777


Q ss_pred             cchHHHHHHHHHHhhcCccc
Q psy14082        200 DYEKEKRLFSLIRELGKYTL  219 (233)
Q Consensus       200 ~~~~~~~~~~~i~~~~~~~~  219 (233)
                      ..+  ..+++.+++..+.++
T Consensus       351 ~~d--~~~~~~ie~~l~~~~  368 (456)
T PRK10590        351 VDE--HKLLRDIEKLLKKEI  368 (456)
T ss_pred             HHH--HHHHHHHHHHhcCCC
Confidence            544  777888888665554

>KOG0326|consensus

Probab=100.00  E-value=2.5e-40  Score=266.29  Aligned_cols=212  Identities=25%  Similarity=0.310  Sum_probs=179.4

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~g   78 (233)
                      +||.++.|+|+++-|..|+|||.+|.+|+++++...     +...+++|++||||||.|+.+.++++  ..++++...+|
T Consensus       115 sIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~~-----~~~IQ~~ilVPtrelALQtSqvc~~lskh~~i~vmvttG  189 (459)
T KOG0326|consen  115 SIPIALTGRDILARAKNGTGKTAAYCIPVLEKIDPK-----KNVIQAIILVPTRELALQTSQVCKELSKHLGIKVMVTTG  189 (459)
T ss_pred             ccceeecchhhhhhccCCCCCccceechhhhhcCcc-----ccceeEEEEeecchhhHHHHHHHHHHhcccCeEEEEecC
Confidence            689999999999999999999999999999999865     56889999999999999999999999  45788999999


Q ss_pred             CCCCCCee---------EEe-ccc--------------------------------------------------------
Q psy14082         79 GTPKGPQD---------CLP-LHR--------------------------------------------------------   92 (233)
Q Consensus        79 g~~~~~~~---------lv~-l~r--------------------------------------------------------   92 (233)
                      |++.+.++         +|| -.|                                                        
T Consensus       190 GT~lrDDI~Rl~~~VH~~vgTPGRIlDL~~KgVa~ls~c~~lV~DEADKlLs~~F~~~~e~li~~lP~~rQillySATFP  269 (459)
T KOG0326|consen  190 GTSLRDDIMRLNQTVHLVVGTPGRILDLAKKGVADLSDCVILVMDEADKLLSVDFQPIVEKLISFLPKERQILLYSATFP  269 (459)
T ss_pred             CcccccceeeecCceEEEEcCChhHHHHHhcccccchhceEEEechhhhhhchhhhhHHHHHHHhCCccceeeEEecccc
Confidence            99987666         555 011                                                        


Q ss_pred             ---------------------------------------hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCCee
Q psy14082         93 ---------------------------------------FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSA  133 (233)
Q Consensus        93 ---------------------------------------~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~  133 (233)
                                                             .+.....++.+-.-.+.|||||+.+.++.+++.+.+.|++|
T Consensus       270 ~tVk~Fm~~~l~kPy~INLM~eLtl~GvtQyYafV~e~qKvhCLntLfskLqINQsIIFCNS~~rVELLAkKITelGysc  349 (459)
T KOG0326|consen  270 LTVKGFMDRHLKKPYEINLMEELTLKGVTQYYAFVEERQKVHCLNTLFSKLQINQSIIFCNSTNRVELLAKKITELGYSC  349 (459)
T ss_pred             hhHHHHHHHhccCcceeehhhhhhhcchhhheeeechhhhhhhHHHHHHHhcccceEEEeccchHhHHHHHHHHhccchh
Confidence                                                   11111115666677899999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc------------ceeeEEeecc
Q psy14082        134 ICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI------------SQVIEVVQDY  201 (233)
Q Consensus       134 ~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i------------~~~~~~~~~~  201 (233)
                      .++|+.|-+++|..++.+|++|.++.|||||.+.||+|+++|++|||||+|.+++.|.            |-++.+++-.
T Consensus       350 yyiHakM~Q~hRNrVFHdFr~G~crnLVctDL~TRGIDiqavNvVINFDfpk~aEtYLHRIGRsGRFGhlGlAInLitye  429 (459)
T KOG0326|consen  350 YYIHAKMAQEHRNRVFHDFRNGKCRNLVCTDLFTRGIDIQAVNVVINFDFPKNAETYLHRIGRSGRFGHLGLAINLITYE  429 (459)
T ss_pred             hHHHHHHHHhhhhhhhhhhhccccceeeehhhhhcccccceeeEEEecCCCCCHHHHHHHccCCccCCCcceEEEEEehh
Confidence            9999999999999999999999999999999999999999999999999999998555            3455666643


Q ss_pred             hHHHHHHHHHHhhcCccc
Q psy14082        202 EKEKRLFSLIRELGKYTL  219 (233)
Q Consensus       202 ~~~~~~~~~i~~~~~~~~  219 (233)
                      +  +.-+..||+..+.++
T Consensus       430 d--rf~L~~IE~eLGtEI  445 (459)
T KOG0326|consen  430 D--RFNLYRIEQELGTEI  445 (459)
T ss_pred             h--hhhHHHHHHHhcccc
Confidence            3  555666776555444

>KOG0335|consensus

Probab=100.00  E-value=4.2e-39  Score=274.39  Aligned_cols=215  Identities=31%  Similarity=0.463  Sum_probs=173.7

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCC-----CCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcE
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQ-----GDGPIALVLAPTRELAQQIQTVAKEF--SSALRN   73 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~-----~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~   73 (233)
                      +||.+..|+|++++|+||||||.+|++|++.+++......+     ...|++|||+||||||.|+|++.+++  ...+++
T Consensus       104 sip~i~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~~~~~~~~~~~~P~~lIlapTReL~~Qi~nea~k~~~~s~~~~  183 (482)
T KOG0335|consen  104 SIPIISGGRDLMACAQTGSGKTAAFLIPIISYLLDEGPEDRGESGGGVYPRALILAPTRELVDQIYNEARKFSYLSGMKS  183 (482)
T ss_pred             ccceeecCCceEEEccCCCcchHHHHHHHHHHHHhcCcccCcccCCCCCCceEEEeCcHHHhhHHHHHHHhhccccccee
Confidence            68999999999999999999999999999999997643211     13699999999999999999999999  557899


Q ss_pred             EEEEcCCCCC---------CeeEEe---------------------------------------ccc-------------
Q psy14082         74 ICIFGGTPKG---------PQDCLP---------------------------------------LHR-------------   92 (233)
Q Consensus        74 ~~~~gg~~~~---------~~~lv~---------------------------------------l~r-------------   92 (233)
                      ...|||.+..         .+++|+                                       +++             
T Consensus       184 ~~~ygg~~~~~q~~~~~~gcdIlvaTpGrL~d~~e~g~i~l~~~k~~vLDEADrMlD~mgF~p~Ir~iv~~~~~~~~~~~  263 (482)
T KOG0335|consen  184 VVVYGGTDLGAQLRFIKRGCDILVATPGRLKDLIERGKISLDNCKFLVLDEADRMLDEMGFEPQIRKIVEQLGMPPKNNR  263 (482)
T ss_pred             eeeeCCcchhhhhhhhccCccEEEecCchhhhhhhcceeehhhCcEEEecchHHhhhhccccccHHHHhcccCCCCccce
Confidence            9999996653         334666                                       000             


Q ss_pred             ---------------------------------------------------hhhhchHHHhcC----CC-----CeEEEE
Q psy14082         93 ---------------------------------------------------FVFNCQYEMAKN----PA-----FKVIVF  112 (233)
Q Consensus        93 ---------------------------------------------------~~~~~~~~~~~~----~~-----~k~iIf  112 (233)
                                                                         ..+.+.+++...    ..     .+++||
T Consensus       264 qt~mFSAtfp~~iq~l~~~fl~~~yi~laV~rvg~~~~ni~q~i~~V~~~~kr~~Lldll~~~~~~~~~~~~~~e~tlvF  343 (482)
T KOG0335|consen  264 QTLLFSATFPKEIQRLAADFLKDNYIFLAVGRVGSTSENITQKILFVNEMEKRSKLLDLLNKDDGPPSDGEPKWEKTLVF  343 (482)
T ss_pred             eEEEEeccCChhhhhhHHHHhhccceEEEEeeeccccccceeEeeeecchhhHHHHHHHhhcccCCcccCCcccceEEEE
Confidence                                                               000000022111    12     389999


Q ss_pred             ecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc-
Q psy14082        113 VETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI-  191 (233)
Q Consensus       113 ~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i-  191 (233)
                      |+|++.+..++..|...++++..+||+-++.+|.+.++.|++|...+||||++++||+|+|+|++|||||+|.+.++|+ 
T Consensus       344 vEt~~~~d~l~~~l~~~~~~~~sIhg~~tq~er~~al~~Fr~g~~pvlVaT~VaaRGlDi~~V~hVInyDmP~d~d~YvH  423 (482)
T KOG0335|consen  344 VETKRGADELAAFLSSNGYPAKSIHGDRTQIEREQALNDFRNGKAPVLVATNVAARGLDIPNVKHVINYDMPADIDDYVH  423 (482)
T ss_pred             eeccchhhHHHHHHhcCCCCceeecchhhhhHHHHHHHHhhcCCcceEEEehhhhcCCCCCCCceeEEeecCcchhhHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999998777 


Q ss_pred             -----------ceeeEEeecch--HHHHHHHHHHhhc
Q psy14082        192 -----------SQVIEVVQDYE--KEKRLFSLIRELG  215 (233)
Q Consensus       192 -----------~~~~~~~~~~~--~~~~~~~~i~~~~  215 (233)
                                 |+++.|+.+..  --+.+.+.+.+.+
T Consensus       424 RIGRTGR~Gn~G~atsf~n~~~~~i~~~L~~~l~ea~  460 (482)
T KOG0335|consen  424 RIGRTGRVGNGGRATSFFNEKNQNIAKALVEILTEAN  460 (482)
T ss_pred             hccccccCCCCceeEEEeccccchhHHHHHHHHHHhc
Confidence                       46667887333  3344555555544

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=100.00  E-value=1.2e-38  Score=281.27  Aligned_cols=213  Identities=27%  Similarity=0.355  Sum_probs=175.5

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh---cCCcEEEEE
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS---SALRNICIF   77 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~---~~~~~~~~~   77 (233)
                      |||.++.|+|++++||||||||++|++|+++++...     ..++++|||+||||||.|+++.++.+.   .++++..++
T Consensus        34 ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~-----~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~v~~~~  108 (460)
T PRK11776         34 SLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVK-----RFRVQALVLCPTRELADQVAKEIRRLARFIPNIKVLTLC  108 (460)
T ss_pred             HHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhhc-----cCCceEEEEeCCHHHHHHHHHHHHHHHhhCCCcEEEEEE
Confidence            578899999999999999999999999999998643     346789999999999999999999883   478899999


Q ss_pred             cCCCC---------CCeeEEe--------ccc------------------------------------------------
Q psy14082         78 GGTPK---------GPQDCLP--------LHR------------------------------------------------   92 (233)
Q Consensus        78 gg~~~---------~~~~lv~--------l~r------------------------------------------------   92 (233)
                      ||.+.         ..+++|+        +.+                                                
T Consensus       109 Gg~~~~~~~~~l~~~~~IvV~Tp~rl~~~l~~~~~~l~~l~~lViDEad~~l~~g~~~~l~~i~~~~~~~~q~ll~SAT~  188 (460)
T PRK11776        109 GGVPMGPQIDSLEHGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMGFQDAIDAIIRQAPARRQTLLFSATY  188 (460)
T ss_pred             CCCChHHHHHHhcCCCCEEEEChHHHHHHHHcCCccHHHCCEEEEECHHHHhCcCcHHHHHHHHHhCCcccEEEEEEecC
Confidence            99765         3456666        000                                                


Q ss_pred             ----------------------------------------hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCCe
Q psy14082         93 ----------------------------------------FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHS  132 (233)
Q Consensus        93 ----------------------------------------~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~  132 (233)
                                                              ....+...+......++||||++++.++.+++.|.+.++.
T Consensus       189 ~~~~~~l~~~~~~~~~~i~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lVF~~t~~~~~~l~~~L~~~~~~  268 (460)
T PRK11776        189 PEGIAAISQRFQRDPVEVKVESTHDLPAIEQRFYEVSPDERLPALQRLLLHHQPESCVVFCNTKKECQEVADALNAQGFS  268 (460)
T ss_pred             cHHHHHHHHHhcCCCEEEEECcCCCCCCeeEEEEEeCcHHHHHHHHHHHHhcCCCceEEEECCHHHHHHHHHHHHhCCCc
Confidence                                                    0000111334456678999999999999999999999999


Q ss_pred             eEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc------------ceeeEEeec
Q psy14082        133 AICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI------------SQVIEVVQD  200 (233)
Q Consensus       133 ~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i------------~~~~~~~~~  200 (233)
                      +..+||+|++.+|..+++.|++|+.++|||||+++||+|+|++++|||||+|.+.+.|+            |.++.++.+
T Consensus       269 v~~~hg~~~~~eR~~~l~~F~~g~~~vLVaTdv~~rGiDi~~v~~VI~~d~p~~~~~yiqR~GRtGR~g~~G~ai~l~~~  348 (460)
T PRK11776        269 ALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAP  348 (460)
T ss_pred             EEEEeCCCCHHHHHHHHHHHHcCCCcEEEEecccccccchhcCCeEEEecCCCCHhHhhhhcccccCCCCcceEEEEEch
Confidence            99999999999999999999999999999999999999999999999999999998777            345557765


Q ss_pred             chHHHHHHHHHHhhcCcccc
Q psy14082        201 YEKEKRLFSLIRELGKYTLI  220 (233)
Q Consensus       201 ~~~~~~~~~~i~~~~~~~~~  220 (233)
                      .+  ...++.+++..+..++
T Consensus       349 ~e--~~~~~~i~~~~~~~~~  366 (460)
T PRK11776        349 EE--MQRANAIEDYLGRKLN  366 (460)
T ss_pred             hH--HHHHHHHHHHhCCCCc
Confidence            44  6667777776555443

>KOG0343|consensus

Probab=100.00  E-value=8.3e-40  Score=278.96  Aligned_cols=195  Identities=25%  Similarity=0.248  Sum_probs=169.4

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~g   78 (233)
                      +||.++.|+|+++.|.||||||+||++|++++|...++ .+..|.-||||+||||||.|+++.+.+.  +..+++.+++|
T Consensus        99 ~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~kW-s~~DGlGalIISPTRELA~QtFevL~kvgk~h~fSaGLiiG  177 (758)
T KOG0343|consen   99 TIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLKW-SPTDGLGALIISPTRELALQTFEVLNKVGKHHDFSAGLIIG  177 (758)
T ss_pred             hcchhccCcccccccccCCCceeeehHHHHHHHHHcCC-CCCCCceeEEecchHHHHHHHHHHHHHHhhccccccceeec
Confidence            58999999999999999999999999999999998744 3456899999999999999999999999  67899999999


Q ss_pred             CCCC--------CCeeEEe-----cc----------------------c-------------------------------
Q psy14082         79 GTPK--------GPQDCLP-----LH----------------------R-------------------------------   92 (233)
Q Consensus        79 g~~~--------~~~~lv~-----l~----------------------r-------------------------------   92 (233)
                      |.+.        +-.|+|+     |.                      |                               
T Consensus       178 G~~~k~E~eRi~~mNILVCTPGRLLQHmde~~~f~t~~lQmLvLDEADR~LDMGFk~tL~~Ii~~lP~~RQTLLFSATqt  257 (758)
T KOG0343|consen  178 GKDVKFELERISQMNILVCTPGRLLQHMDENPNFSTSNLQMLVLDEADRMLDMGFKKTLNAIIENLPKKRQTLLFSATQT  257 (758)
T ss_pred             CchhHHHHHhhhcCCeEEechHHHHHHhhhcCCCCCCcceEEEeccHHHHHHHhHHHHHHHHHHhCChhheeeeeecccc
Confidence            9775        2334666     00                      0                               


Q ss_pred             ------------------------------------------hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhC-
Q psy14082         93 ------------------------------------------FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRE-  129 (233)
Q Consensus        93 ------------------------------------------~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~-  129 (233)
                                                                -++++-..+..+...+.|||+.|.+.+..++..+.++ 
T Consensus       258 ~svkdLaRLsL~dP~~vsvhe~a~~atP~~L~Q~y~~v~l~~Ki~~L~sFI~shlk~K~iVF~SscKqvkf~~e~F~rlr  337 (758)
T KOG0343|consen  258 KSVKDLARLSLKDPVYVSVHENAVAATPSNLQQSYVIVPLEDKIDMLWSFIKSHLKKKSIVFLSSCKQVKFLYEAFCRLR  337 (758)
T ss_pred             hhHHHHHHhhcCCCcEEEEeccccccChhhhhheEEEEehhhHHHHHHHHHHhccccceEEEEehhhHHHHHHHHHHhcC
Confidence                                                      1111111457788899999999999999999999876 


Q ss_pred             -CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCcccccceeeE
Q psy14082        130 -RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQVIE  196 (233)
Q Consensus       130 -~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i~~~~~  196 (233)
                       |++...+||.|++..|.+++.+|.....-||+|||+++||+|+|.|||||+||-|.+.+.||||+++
T Consensus       338 pg~~l~~L~G~~~Q~~R~ev~~~F~~~~~~vLF~TDv~aRGLDFpaVdwViQ~DCPedv~tYIHRvGR  405 (758)
T KOG0343|consen  338 PGIPLLALHGTMSQKKRIEVYKKFVRKRAVVLFCTDVAARGLDFPAVDWVIQVDCPEDVDTYIHRVGR  405 (758)
T ss_pred             CCCceeeeccchhHHHHHHHHHHHHHhcceEEEeehhhhccCCCcccceEEEecCchhHHHHHHHhhh
Confidence             7899999999999999999999999999999999999999999999999999999999999965554

>KOG0348|consensus

Probab=100.00  E-value=2.3e-38  Score=269.24  Aligned_cols=215  Identities=23%  Similarity=0.311  Sum_probs=174.8

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccC-CCCCCCCceEEEEcCcHHHHHHHHHHHHHh---hcCCcEEEE
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQE-PVKQGDGPIALVLAPTRELAQQIQTVAKEF---SSALRNICI   76 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~-~~~~~~~~~~lil~PtreL~~Q~~~~~~~~---~~~~~~~~~   76 (233)
                      |||.++.|+|+++-|+||||||++|++|+++.+...+ +..+..|+.|||||||||||.|+|+.++++   +.=+-.+.+
T Consensus       167 ~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~G~~ALVivPTREL~~Q~y~~~qKLl~~~hWIVPg~l  246 (708)
T KOG0348|consen  167 AIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRSDGPYALVIVPTRELALQIYETVQKLLKPFHWIVPGVL  246 (708)
T ss_pred             chhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCccccccCCceEEEEechHHHHHHHHHHHHHHhcCceEEeecee
Confidence            6999999999999999999999999999999999764 345578999999999999999999999999   334456788


Q ss_pred             EcCCCCC---------CeeEEe----------------ccc---------------------------------------
Q psy14082         77 FGGTPKG---------PQDCLP----------------LHR---------------------------------------   92 (233)
Q Consensus        77 ~gg~~~~---------~~~lv~----------------l~r---------------------------------------   92 (233)
                      .||.+++         -.|+||                +.|                                       
T Consensus       247 mGGEkkKSEKARLRKGiNILIgTPGRLvDHLknT~~i~~s~LRwlVlDEaDrlleLGfekdit~Il~~v~~~~~~e~~~~  326 (708)
T KOG0348|consen  247 MGGEKKKSEKARLRKGINILIGTPGRLVDHLKNTKSIKFSRLRWLVLDEADRLLELGFEKDITQILKAVHSIQNAECKDP  326 (708)
T ss_pred             ecccccccHHHHHhcCceEEEcCchHHHHHHhccchheeeeeeEEEecchhHHHhccchhhHHHHHHHHhhccchhcccc
Confidence            8887652         234777                000                                       


Q ss_pred             --------------------------------------------------------------------------------
Q psy14082         93 --------------------------------------------------------------------------------   92 (233)
Q Consensus        93 --------------------------------------------------------------------------------   92 (233)
                                                                                                      
T Consensus       327 ~lp~q~q~mLlSATLtd~V~rLa~~sLkDpv~I~ld~s~~~~~p~~~a~~ev~~~~~~~~l~~~~iPeqL~qry~vVPpK  406 (708)
T KOG0348|consen  327 KLPHQLQNMLLSATLTDGVNRLADLSLKDPVYISLDKSHSQLNPKDKAVQEVDDGPAGDKLDSFAIPEQLLQRYTVVPPK  406 (708)
T ss_pred             cccHHHHhHhhhhhhHHHHHHHhhccccCceeeeccchhhhcCcchhhhhhcCCcccccccccccCcHHhhhceEecCCc
Confidence                                                                                            


Q ss_pred             -----hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhC----------------------CCeeEEEeCCCCHHHH
Q psy14082         93 -----FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRE----------------------RHSAICIHGDKTQQDR  145 (233)
Q Consensus        93 -----~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~----------------------~~~~~~~~~~~~~~~r  145 (233)
                           +..++.+.+......|+|||+.+.+.++.-+..|.+.                      +.+..-+||+|++++|
T Consensus       407 LRLV~Laa~L~~~~k~~~~qk~iVF~S~~d~VeFHy~lf~~~l~~~~e~~s~~~~s~g~~~l~~~~k~~rLHGsm~QeeR  486 (708)
T KOG0348|consen  407 LRLVALAALLLNKVKFEEKQKMIVFFSCSDSVEFHYSLFSEALLSHLEGSSGAPDSEGLPPLFMDLKFYRLHGSMEQEER  486 (708)
T ss_pred             hhHHHHHHHHHHHhhhhhhceeEEEEechhHHHHHHHHHHhhhhcccccccCCcccCCChhhhhcceEEEecCchhHHHH
Confidence                 1111111344556679999999999999888887631                      3467889999999999


Q ss_pred             HHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc------------ceeeEEeecchHHHHHHHHHHh
Q psy14082        146 DYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI------------SQVIEVVQDYEKEKRLFSLIRE  213 (233)
Q Consensus       146 ~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i------------~~~~~~~~~~~~~~~~~~~i~~  213 (233)
                      ..+++.|+...--||.|||+++||+|+|+|++||+||.|.++++|+            |.++.|..+.|  ...++.++.
T Consensus       487 ts~f~~Fs~~~~~VLLcTDVAaRGLDlP~V~~vVQYd~P~s~adylHRvGRTARaG~kG~alLfL~P~E--aey~~~l~~  564 (708)
T KOG0348|consen  487 TSVFQEFSHSRRAVLLCTDVAARGLDLPHVGLVVQYDPPFSTADYLHRVGRTARAGEKGEALLFLLPSE--AEYVNYLKK  564 (708)
T ss_pred             HHHHHhhccccceEEEehhhhhccCCCCCcCeEEEeCCCCCHHHHHHHhhhhhhccCCCceEEEecccH--HHHHHHHHh
Confidence            9999999999888999999999999999999999999999999888            56677888766  447777776


Q ss_pred             hcCc
Q psy14082        214 LGKY  217 (233)
Q Consensus       214 ~~~~  217 (233)
                      ....
T Consensus       565 ~~~~  568 (708)
T KOG0348|consen  565 HHIM  568 (708)
T ss_pred             hcch
Confidence            5433

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=100.00  E-value=2.2e-38  Score=286.60  Aligned_cols=216  Identities=28%  Similarity=0.401  Sum_probs=179.9

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh---hcCCcEEEEE
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF---SSALRNICIF   77 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~---~~~~~~~~~~   77 (233)
                      +||.++.|+|++++||||||||++|++|+++.+...     ..++++|||+||+|||.|+++.+..+   ..++++..++
T Consensus        36 ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~-----~~~~~~LIL~PTreLa~Qv~~~l~~~~~~~~~i~v~~~~  110 (629)
T PRK11634         36 CIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPE-----LKAPQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALY  110 (629)
T ss_pred             HHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhc-----cCCCeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEE
Confidence            478899999999999999999999999999988653     35689999999999999999999988   3478899999


Q ss_pred             cCCCC---------CCeeEEe--------ccc------------------------------------------------
Q psy14082         78 GGTPK---------GPQDCLP--------LHR------------------------------------------------   92 (233)
Q Consensus        78 gg~~~---------~~~~lv~--------l~r------------------------------------------------   92 (233)
                      ||.++         ..+++|+        +.+                                                
T Consensus       111 gG~~~~~q~~~l~~~~~IVVgTPgrl~d~l~r~~l~l~~l~~lVlDEAd~ml~~gf~~di~~Il~~lp~~~q~llfSAT~  190 (629)
T PRK11634        111 GGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMGFIEDVETIMAQIPEGHQTALFSATM  190 (629)
T ss_pred             CCcCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcchhhceEEEeccHHHHhhcccHHHHHHHHHhCCCCCeEEEEEccC
Confidence            99764         3567777        000                                                


Q ss_pred             ---h--------------------------------------hhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCC
Q psy14082         93 ---F--------------------------------------VFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERH  131 (233)
Q Consensus        93 ---~--------------------------------------~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~  131 (233)
                         +                                      ...+...+......++||||+|+..++.++..|.+.|+
T Consensus       191 p~~i~~i~~~~l~~~~~i~i~~~~~~~~~i~q~~~~v~~~~k~~~L~~~L~~~~~~~~IVF~~tk~~a~~l~~~L~~~g~  270 (629)
T PRK11634        191 PEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVWGMRKNEALVRFLEAEDFDAAIIFVRTKNATLEVAEALERNGY  270 (629)
T ss_pred             ChhHHHHHHHHcCCCeEEEccCccccCCceEEEEEEechhhHHHHHHHHHHhcCCCCEEEEeccHHHHHHHHHHHHhCCC
Confidence               0                                      00000123334557899999999999999999999999


Q ss_pred             eeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc------------ceeeEEee
Q psy14082        132 SAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI------------SQVIEVVQ  199 (233)
Q Consensus       132 ~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i------------~~~~~~~~  199 (233)
                      .+..+||+|++.+|..++++|++|+.+||||||++++|+|+|++++|||||+|.+.+.|+            |.++.|+.
T Consensus       271 ~~~~lhgd~~q~~R~~il~~Fr~G~~~ILVATdv~arGIDip~V~~VI~~d~P~~~e~yvqRiGRtGRaGr~G~ai~~v~  350 (629)
T PRK11634        271 NSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVE  350 (629)
T ss_pred             CEEEeeCCCCHHHHHHHHHHHhCCCCCEEEEcchHhcCCCcccCCEEEEeCCCCCHHHHHHHhccccCCCCcceEEEEec
Confidence            999999999999999999999999999999999999999999999999999999998777            45667887


Q ss_pred             cchHHHHHHHHHHhhcCccccccc
Q psy14082        200 DYEKEKRLFSLIRELGKYTLITQE  223 (233)
Q Consensus       200 ~~~~~~~~~~~i~~~~~~~~~~~~  223 (233)
                      +.+  ...++.+++..+..++..+
T Consensus       351 ~~e--~~~l~~ie~~~~~~i~~~~  372 (629)
T PRK11634        351 NRE--RRLLRNIERTMKLTIPEVE  372 (629)
T ss_pred             hHH--HHHHHHHHHHhCCCcceec
Confidence            544  6788888887666654443

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=100.00  E-value=3.6e-38  Score=276.46  Aligned_cols=213  Identities=26%  Similarity=0.376  Sum_probs=174.2

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~g   78 (233)
                      |||.++.|+|++++||||||||++|++|++++++..+ .....++++||++||+|||.|+++.+..+  ..++++..++|
T Consensus        31 ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~-~~~~~~~~~lil~Pt~eLa~Q~~~~~~~l~~~~~~~v~~~~g  109 (434)
T PRK11192         31 AIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFP-RRKSGPPRILILTPTRELAMQVADQARELAKHTHLDIATITG  109 (434)
T ss_pred             HHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhcc-ccCCCCceEEEECCcHHHHHHHHHHHHHHHccCCcEEEEEEC
Confidence            5788999999999999999999999999999997542 12234679999999999999999999998  45788999999


Q ss_pred             CCCC---------CCeeEEe---------------ccc------------------------------------------
Q psy14082         79 GTPK---------GPQDCLP---------------LHR------------------------------------------   92 (233)
Q Consensus        79 g~~~---------~~~~lv~---------------l~r------------------------------------------   92 (233)
                      |.+.         +.+++|+               +++                                          
T Consensus       110 g~~~~~~~~~l~~~~~IlV~Tp~rl~~~~~~~~~~~~~v~~lViDEah~~l~~~~~~~~~~i~~~~~~~~q~~~~SAT~~  189 (434)
T PRK11192        110 GVAYMNHAEVFSENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRMLDMGFAQDIETIAAETRWRKQTLLFSATLE  189 (434)
T ss_pred             CCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCcCcccCCEEEEECHHHHhCCCcHHHHHHHHHhCccccEEEEEEeecC
Confidence            8754         3456777               000                                          


Q ss_pred             ------------------------------------------hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCC
Q psy14082         93 ------------------------------------------FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRER  130 (233)
Q Consensus        93 ------------------------------------------~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~  130 (233)
                                                                ...++...+......++||||+++++++.++..|.+.+
T Consensus       190 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~~lVF~~s~~~~~~l~~~L~~~~  269 (434)
T PRK11192        190 GDAVQDFAERLLNDPVEVEAEPSRRERKKIHQWYYRADDLEHKTALLCHLLKQPEVTRSIVFVRTRERVHELAGWLRKAG  269 (434)
T ss_pred             HHHHHHHHHHHccCCEEEEecCCcccccCceEEEEEeCCHHHHHHHHHHHHhcCCCCeEEEEeCChHHHHHHHHHHHhCC
Confidence                                                      00111113334467899999999999999999999999


Q ss_pred             CeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc---c---------eeeEEe
Q psy14082        131 HSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI---S---------QVIEVV  198 (233)
Q Consensus       131 ~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i---~---------~~~~~~  198 (233)
                      +.+..+||+|++.+|..+++.|++|+.+||||||++++|+|+|++++|||||+|.+.+.|+   |         .++.++
T Consensus       270 ~~~~~l~g~~~~~~R~~~l~~f~~G~~~vLVaTd~~~~GiDip~v~~VI~~d~p~s~~~yiqr~GR~gR~g~~g~ai~l~  349 (434)
T PRK11192        270 INCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLV  349 (434)
T ss_pred             CCEEEecCCCCHHHHHHHHHHHhCCCCcEEEEccccccCccCCCCCEEEEECCCCCHHHHhhcccccccCCCCceEEEEe
Confidence            9999999999999999999999999999999999999999999999999999999988666   3         345567


Q ss_pred             ecchHHHHHHHHHHhhcC
Q psy14082        199 QDYEKEKRLFSLIRELGK  216 (233)
Q Consensus       199 ~~~~~~~~~~~~i~~~~~  216 (233)
                      +.++  ...+..++++..
T Consensus       350 ~~~d--~~~~~~i~~~~~  365 (434)
T PRK11192        350 EAHD--HLLLGKIERYIE  365 (434)
T ss_pred             cHHH--HHHHHHHHHHHh
Confidence            6544  666667766443

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=1.8e-37  Score=274.78  Aligned_cols=218  Identities=24%  Similarity=0.307  Sum_probs=178.3

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCC--CCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEE
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQ--GDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICI   76 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~--~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~   76 (233)
                      |||.++.|+|+++.|+||||||++|++|+++.+...+....  .+++++|||+||+||+.|+++.++.+  ..++++..+
T Consensus       117 ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~~aLil~PtreLa~Q~~~~~~~l~~~~~~~v~~~  196 (475)
T PRK01297        117 VLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRALIIAPTRELVVQIAKDAAALTKYTGLNVMTF  196 (475)
T ss_pred             HHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCceEEEEeCcHHHHHHHHHHHHHhhccCCCEEEEE
Confidence            57889999999999999999999999999999986532111  23689999999999999999999998  456788899


Q ss_pred             EcCCCC----------CCeeEEe--------------------------------------ccch---------------
Q psy14082         77 FGGTPK----------GPQDCLP--------------------------------------LHRF---------------   93 (233)
Q Consensus        77 ~gg~~~----------~~~~lv~--------------------------------------l~r~---------------   93 (233)
                      +||.+.          ..+++|+                                      ++++               
T Consensus       197 ~gg~~~~~~~~~~~~~~~~Iiv~TP~~Ll~~~~~~~~~l~~l~~lViDEah~l~~~~~~~~l~~i~~~~~~~~~~q~i~~  276 (475)
T PRK01297        197 VGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLDEADRMLDMGFIPQVRQIIRQTPRKEERQTLLF  276 (475)
T ss_pred             EccCChHHHHHHHhCCCCCEEEECHHHHHHHHHcCCcccccCceEEechHHHHHhcccHHHHHHHHHhCCCCCCceEEEE
Confidence            998643          3456777                                      0000               


Q ss_pred             ----------------------------------------------hhhchHHHhcCCCCeEEEEecchhHHHHHHHHHh
Q psy14082         94 ----------------------------------------------VFNCQYEMAKNPAFKVIVFVETKKKVEDITRALR  127 (233)
Q Consensus        94 ----------------------------------------------~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~  127 (233)
                                                                    ...+.+.+......++||||++++.++.+++.|.
T Consensus       277 SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~ll~~~~~~~~IVF~~s~~~~~~l~~~L~  356 (475)
T PRK01297        277 SATFTDDVMNLAKQWTTDPAIVEIEPENVASDTVEQHVYAVAGSDKYKLLYNLVTQNPWERVMVFANRKDEVRRIEERLV  356 (475)
T ss_pred             EeecCHHHHHHHHHhccCCEEEEeccCcCCCCcccEEEEEecchhHHHHHHHHHHhcCCCeEEEEeCCHHHHHHHHHHHH
Confidence                                                          0001112334455799999999999999999999


Q ss_pred             hCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc------------ceee
Q psy14082        128 RERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI------------SQVI  195 (233)
Q Consensus       128 ~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i------------~~~~  195 (233)
                      +.++.+..+||++++++|.++++.|++|+.++|||||++++|+|+|++++||+||+|.|...|+            |.++
T Consensus       357 ~~~~~~~~~~g~~~~~~R~~~~~~Fr~G~~~vLvaT~~l~~GIDi~~v~~VI~~~~P~s~~~y~Qr~GRaGR~g~~g~~i  436 (475)
T PRK01297        357 KDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSI  436 (475)
T ss_pred             HcCCCEEEEECCCCHHHHHHHHHHHhCCCCcEEEEccccccCCcccCCCEEEEeCCCCCHHHHHHhhCccCCCCCCceEE
Confidence            9999999999999999999999999999999999999999999999999999999999998777            3456


Q ss_pred             EEeecchHHHHHHHHHHhhcCcccc
Q psy14082        196 EVVQDYEKEKRLFSLIRELGKYTLI  220 (233)
Q Consensus       196 ~~~~~~~~~~~~~~~i~~~~~~~~~  220 (233)
                      .|+++.  +...+..+++..+.++.
T Consensus       437 ~~~~~~--d~~~~~~~~~~~~~~~~  459 (475)
T PRK01297        437 SFAGED--DAFQLPEIEELLGRKIS  459 (475)
T ss_pred             EEecHH--HHHHHHHHHHHhCCCCc
Confidence            677754  36678888887766653

>KOG0336|consensus

Probab=100.00  E-value=1.8e-38  Score=262.82  Aligned_cols=226  Identities=28%  Similarity=0.450  Sum_probs=186.4

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCC-CCCCCCceEEEEcCcHHHHHHHHHHHHHh-hcCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEP-VKQGDGPIALVLAPTRELAQQIQTVAKEF-SSALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~-~~~~~~~~~lil~PtreL~~Q~~~~~~~~-~~~~~~~~~~g   78 (233)
                      |+|.++.|.|+|+.|+||+|||++|++|-+-++..++. ..+..++.+|++.|||||+.|+.-.+.++ +.+++..|++|
T Consensus       250 aWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr~~p~~lvl~ptreLalqie~e~~kysyng~ksvc~yg  329 (629)
T KOG0336|consen  250 AWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQRNGPGVLVLTPTRELALQIEGEVKKYSYNGLKSVCVYG  329 (629)
T ss_pred             ccceeecCcceEEEEecCCCcCHHHhccceeeeeccchhhhccCCCceEEEeccHHHHHHHHhHHhHhhhcCcceEEEec
Confidence            79999999999999999999999999999999987643 33467999999999999999999999999 88999999999


Q ss_pred             CCCCCCee---------EEe--------------------------------------ccc-------------------
Q psy14082         79 GTPKGPQD---------CLP--------------------------------------LHR-------------------   92 (233)
Q Consensus        79 g~~~~~~~---------lv~--------------------------------------l~r-------------------   92 (233)
                      |.+...|+         +++                                      +++                   
T Consensus       330 ggnR~eqie~lkrgveiiiatPgrlndL~~~n~i~l~siTYlVlDEADrMLDMgFEpqIrkilldiRPDRqtvmTSATWP  409 (629)
T KOG0336|consen  330 GGNRNEQIEDLKRGVEIIIATPGRLNDLQMDNVINLASITYLVLDEADRMLDMGFEPQIRKILLDIRPDRQTVMTSATWP  409 (629)
T ss_pred             CCCchhHHHHHhcCceEEeeCCchHhhhhhcCeeeeeeeEEEEecchhhhhcccccHHHHHHhhhcCCcceeeeecccCc
Confidence            98886655         444                                      000                   


Q ss_pred             -----------------------------------------hhhhchHHH-hcCCCCeEEEEecchhHHHHHHHHHhhCC
Q psy14082         93 -----------------------------------------FVFNCQYEM-AKNPAFKVIVFVETKKKVEDITRALRRER  130 (233)
Q Consensus        93 -----------------------------------------~~~~~~~~~-~~~~~~k~iIf~~~~~~~~~l~~~L~~~~  130 (233)
                                                               .....+... ......|+||||.++..++.+...|.-.|
T Consensus       410 ~~VrrLa~sY~Kep~~v~vGsLdL~a~~sVkQ~i~v~~d~~k~~~~~~f~~~ms~ndKvIiFv~~K~~AD~LSSd~~l~g  489 (629)
T KOG0336|consen  410 EGVRRLAQSYLKEPMIVYVGSLDLVAVKSVKQNIIVTTDSEKLEIVQFFVANMSSNDKVIIFVSRKVMADHLSSDFCLKG  489 (629)
T ss_pred             hHHHHHHHHhhhCceEEEecccceeeeeeeeeeEEecccHHHHHHHHHHHHhcCCCceEEEEEechhhhhhccchhhhcc
Confidence                                                     111111122 44577899999999999999999999999


Q ss_pred             CeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc------------ceeeEEe
Q psy14082        131 HSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI------------SQVIEVV  198 (233)
Q Consensus       131 ~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i------------~~~~~~~  198 (233)
                      +++..+||+-++.+|+..++.|++|+.+|||+||+++||+|++++.||+|||+|.+.++|+            |.+++|+
T Consensus       490 i~~q~lHG~r~Q~DrE~al~~~ksG~vrILvaTDlaSRGlDv~DiTHV~NyDFP~nIeeYVHRvGrtGRaGr~G~sis~l  569 (629)
T KOG0336|consen  490 ISSQSLHGNREQSDREMALEDFKSGEVRILVATDLASRGLDVPDITHVYNYDFPRNIEEYVHRVGRTGRAGRTGTSISFL  569 (629)
T ss_pred             cchhhccCChhhhhHHHHHHhhhcCceEEEEEechhhcCCCchhcceeeccCCCccHHHHHHHhcccccCCCCcceEEEE
Confidence            9999999999999999999999999999999999999999999999999999999999887            3455677


Q ss_pred             ecch--HHHHHHHHHHhhcCcccccccchhhHhhhc
Q psy14082        199 QDYE--KEKRLFSLIRELGKYTLITQESSSTLSEMV  232 (233)
Q Consensus       199 ~~~~--~~~~~~~~i~~~~~~~~~~~~~~~~~~~l~  232 (233)
                      ...+  --+.+.+++++.      .++.|..|..||
T Consensus       570 t~~D~~~a~eLI~ILe~a------eQevPdeL~~mA  599 (629)
T KOG0336|consen  570 TRNDWSMAEELIQILERA------EQEVPDELVRMA  599 (629)
T ss_pred             ehhhHHHHHHHHHHHHHh------hhhCcHHHHHHH
Confidence            6544  223444555544      467777776665

>KOG0347|consensus

Probab=100.00  E-value=2.5e-38  Score=269.74  Aligned_cols=202  Identities=24%  Similarity=0.300  Sum_probs=170.4

Q ss_pred             CCCCCCCC-CceeEecCCCCCchHHhHHHHHHhhhccCCC--------CCCCCceEEEEcCcHHHHHHHHHHHHHh--hc
Q psy14082          1 MLPPSESG-CQNFSKITNYLLSPPQYMLPAAVHISHQEPV--------KQGDGPIALVLAPTRELAQQIQTVAKEF--SS   69 (233)
Q Consensus         1 aip~~~~g-~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~--------~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~   69 (233)
                      .||.+.+| .|+++.|.||||||+||.||+++++.+....        .+...+.+||++||||||.|+.+.+...  ++
T Consensus       211 ~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e~~~~~~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t  290 (731)
T KOG0347|consen  211 VLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLESSDDSQELSNTSAKYVKPIALVVTPTRELAHQVKQHLKAIAEKT  290 (731)
T ss_pred             cccHhhccchhcccccccCCCceeeecchhhhhhhhccchHhhhhhHHhccCcceeEEecChHHHHHHHHHHHHHhcccc
Confidence            37999999 8999999999999999999999977764221        1122345999999999999999999999  78


Q ss_pred             CCcEEEEEcCCC---------CCCeeEEe-----------------------------------------ccc-------
Q psy14082         70 ALRNICIFGGTP---------KGPQDCLP-----------------------------------------LHR-------   92 (233)
Q Consensus        70 ~~~~~~~~gg~~---------~~~~~lv~-----------------------------------------l~r-------   92 (233)
                      ++++..++||..         ..++|+||                                         |+.       
T Consensus       291 ~i~v~si~GGLavqKQqRlL~~~p~IVVATPGRlweli~e~n~~l~~~k~vkcLVlDEaDRmvekghF~Els~lL~~L~e  370 (731)
T KOG0347|consen  291 QIRVASITGGLAVQKQQRLLNQRPDIVVATPGRLWELIEEDNTHLGNFKKVKCLVLDEADRMVEKGHFEELSKLLKHLNE  370 (731)
T ss_pred             CeEEEEeechhHHHHHHHHHhcCCCEEEecchHHHHHHHhhhhhhhhhhhceEEEEccHHHHhhhccHHHHHHHHHHhhh
Confidence            999999999954         37888888                                         000       


Q ss_pred             -------------------------------------------------------hhhhchH------------------
Q psy14082         93 -------------------------------------------------------FVFNCQY------------------   99 (233)
Q Consensus        93 -------------------------------------------------------~~~~~~~------------------   99 (233)
                                                                             ++++-.+                  
T Consensus       371 ~~~~~qrQTlVFSATlt~~~~~~~~~~~k~~~k~~~~~~kiq~Lmk~ig~~~kpkiiD~t~q~~ta~~l~Es~I~C~~~e  450 (731)
T KOG0347|consen  371 EQKNRQRQTLVFSATLTLVLQQPLSSSRKKKDKEDELNAKIQHLMKKIGFRGKPKIIDLTPQSATASTLTESLIECPPLE  450 (731)
T ss_pred             hhcccccceEEEEEEeehhhcChhHHhhhccchhhhhhHHHHHHHHHhCccCCCeeEecCcchhHHHHHHHHhhcCCccc
Confidence                                                                   1111111                  


Q ss_pred             ------HHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCC
Q psy14082        100 ------EMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVE  173 (233)
Q Consensus       100 ------~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~  173 (233)
                            ++.....+++|||||+.+.+..++-.|...++....+|+.|.+++|...+++|++....+|+|||+++||+|+|
T Consensus       451 KD~ylyYfl~ryPGrTlVF~NsId~vKRLt~~L~~L~i~p~~LHA~M~QKqRLknLEkF~~~~~~VLiaTDVAARGLDIp  530 (731)
T KOG0347|consen  451 KDLYLYYFLTRYPGRTLVFCNSIDCVKRLTVLLNNLDIPPLPLHASMIQKQRLKNLEKFKQSPSGVLIATDVAARGLDIP  530 (731)
T ss_pred             cceeEEEEEeecCCceEEEechHHHHHHHHHHHhhcCCCCchhhHHHHHHHHHHhHHHHhcCCCeEEEeehhhhccCCCC
Confidence                  44556788999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CccEEEEecCCCCcccccc------------eeeEEeecch
Q psy14082        174 DVNTVNIGSLQLSANHNIS------------QVIEVVQDYE  202 (233)
Q Consensus       174 ~v~~VI~~d~P~~~~~~i~------------~~~~~~~~~~  202 (233)
                      +|+|||||.+|.+.+-|||            -.+.++.+.+
T Consensus       531 ~V~HVIHYqVPrtseiYVHRSGRTARA~~~Gvsvml~~P~e  571 (731)
T KOG0347|consen  531 GVQHVIHYQVPRTSEIYVHRSGRTARANSEGVSVMLCGPQE  571 (731)
T ss_pred             CcceEEEeecCCccceeEecccccccccCCCeEEEEeChHH
Confidence            9999999999999999994            4555777644

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

Probab=100.00  E-value=1.5e-37  Score=277.14  Aligned_cols=202  Identities=23%  Similarity=0.363  Sum_probs=163.2

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCC--CCCCCCceEEEEcCcHHHHHHHHHHHHHhh--cCCcEEEE
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEP--VKQGDGPIALVLAPTRELAQQIQTVAKEFS--SALRNICI   76 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~--~~~~~~~~~lil~PtreL~~Q~~~~~~~~~--~~~~~~~~   76 (233)
                      |||.++.|+|++++||||||||++|++|++.+++....  .....++++|||+||||||.|+++.++.+.  .++++.++
T Consensus       151 aip~il~g~dviv~ApTGSGKTlayllPil~~l~~~~~~~~~~~~~~~aLIL~PTreLa~Qi~~~~~~l~~~~~~~~~~~  230 (518)
T PLN00206        151 AIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALV  230 (518)
T ss_pred             HHHHHhcCCCEEEEecCCCCccHHHHHHHHHHHHhhccccccccCCceEEEEeCCHHHHHHHHHHHHHHhCCCCceEEEE
Confidence            57889999999999999999999999999999875421  122468999999999999999999999983  45678888


Q ss_pred             EcCCCC---------CCeeEEe---------------ccc----------------------------------------
Q psy14082         77 FGGTPK---------GPQDCLP---------------LHR----------------------------------------   92 (233)
Q Consensus        77 ~gg~~~---------~~~~lv~---------------l~r----------------------------------------   92 (233)
                      +||...         ..+++|+               +++                                        
T Consensus       231 ~gG~~~~~q~~~l~~~~~IiV~TPgrL~~~l~~~~~~l~~v~~lViDEad~ml~~gf~~~i~~i~~~l~~~q~l~~SATl  310 (518)
T PLN00206        231 VGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDNVSVLVLDEVDCMLERGFRDQVMQIFQALSQPQVLLFSATV  310 (518)
T ss_pred             ECCcchHHHHHHhcCCCCEEEECHHHHHHHHHcCCccchheeEEEeecHHHHhhcchHHHHHHHHHhCCCCcEEEEEeeC
Confidence            888654         2456666               000                                        


Q ss_pred             --------------------------------hhhhch---------HHHh--cCCCCeEEEEecchhHHHHHHHHHhh-
Q psy14082         93 --------------------------------FVFNCQ---------YEMA--KNPAFKVIVFVETKKKVEDITRALRR-  128 (233)
Q Consensus        93 --------------------------------~~~~~~---------~~~~--~~~~~k~iIf~~~~~~~~~l~~~L~~-  128 (233)
                                                      ++..+.         +.+.  .....++||||+++..++.++..|.. 
T Consensus       311 ~~~v~~l~~~~~~~~~~i~~~~~~~~~~~v~q~~~~~~~~~k~~~l~~~l~~~~~~~~~~iVFv~s~~~a~~l~~~L~~~  390 (518)
T PLN00206        311 SPEVEKFASSLAKDIILISIGNPNRPNKAVKQLAIWVETKQKKQKLFDILKSKQHFKPPAVVFVSSRLGADLLANAITVV  390 (518)
T ss_pred             CHHHHHHHHHhCCCCEEEEeCCCCCCCcceeEEEEeccchhHHHHHHHHHHhhcccCCCEEEEcCCchhHHHHHHHHhhc
Confidence                                            000000         0111  12346899999999999999999975 


Q ss_pred             CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc------------ceeeE
Q psy14082        129 ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI------------SQVIE  196 (233)
Q Consensus       129 ~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i------------~~~~~  196 (233)
                      .++.+..+||+|++++|..++++|++|+.+|||||++++||+|+|++++|||||+|.+..+|+            |.++.
T Consensus       391 ~g~~~~~~Hg~~~~~eR~~il~~Fr~G~~~ILVaTdvl~rGiDip~v~~VI~~d~P~s~~~yihRiGRaGR~g~~G~ai~  470 (518)
T PLN00206        391 TGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIV  470 (518)
T ss_pred             cCcceEEeeCCCCHHHHHHHHHHHHCCCCCEEEEecHhhccCCcccCCEEEEeCCCCCHHHHHHhccccccCCCCeEEEE
Confidence            689999999999999999999999999999999999999999999999999999999998777            35566


Q ss_pred             Eeecch
Q psy14082        197 VVQDYE  202 (233)
Q Consensus       197 ~~~~~~  202 (233)
                      |+++.+
T Consensus       471 f~~~~~  476 (518)
T PLN00206        471 FVNEED  476 (518)
T ss_pred             EEchhH
Confidence            776533

>KOG0341|consensus

Probab=100.00  E-value=1.6e-38  Score=261.68  Aligned_cols=190  Identities=32%  Similarity=0.465  Sum_probs=164.7

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCC---CCCCCCceEEEEcCcHHHHHHHHHHHHHh--------hcC
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEP---VKQGDGPIALVLAPTRELAQQIQTVAKEF--------SSA   70 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~---~~~~~~~~~lil~PtreL~~Q~~~~~~~~--------~~~   70 (233)
                      ||.+++|+|.|.+|-||||||++|++|++...++++.   -.++.||..||+||+||||.|+++.+..+        ++.
T Consensus       201 lPvvLsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~lPf~~~EGP~gLiicPSRELArQt~~iie~~~~~L~e~g~P~  280 (610)
T KOG0341|consen  201 LPVVLSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMMLPFARGEGPYGLIICPSRELARQTHDIIEQYVAALQEAGYPE  280 (610)
T ss_pred             cceEeecCceeeEEeecCCceEEEeHHHHHHHHHHHhcCccccCCCCeeEEEcCcHHHHHHHHHHHHHHHHHHHhcCChh
Confidence            7999999999999999999999999999998887643   33477999999999999999999999998        567


Q ss_pred             CcEEEEEcCCCCCCee---------EEe-ccc------------------------------------------------
Q psy14082         71 LRNICIFGGTPKGPQD---------CLP-LHR------------------------------------------------   92 (233)
Q Consensus        71 ~~~~~~~gg~~~~~~~---------lv~-l~r------------------------------------------------   92 (233)
                      +++.+++||.+.+.|.         +|+ -.|                                                
T Consensus       281 lRs~LciGG~~v~eql~~v~~GvHivVATPGRL~DmL~KK~~sLd~CRyL~lDEADRmiDmGFEddir~iF~~FK~QRQT  360 (610)
T KOG0341|consen  281 LRSLLCIGGVPVREQLDVVRRGVHIVVATPGRLMDMLAKKIMSLDACRYLTLDEADRMIDMGFEDDIRTIFSFFKGQRQT  360 (610)
T ss_pred             hhhhhhhcCccHHHHHHHHhcCeeEEEcCcchHHHHHHHhhccHHHHHHhhhhhHHHHhhccchhhHHHHHHHHhhhhhe
Confidence            8999999998875554         565 000                                                


Q ss_pred             ---------------------------------hhhhchH--------------HHhcCCCCeEEEEecchhHHHHHHHH
Q psy14082         93 ---------------------------------FVFNCQY--------------EMAKNPAFKVIVFVETKKKVEDITRA  125 (233)
Q Consensus        93 ---------------------------------~~~~~~~--------------~~~~~~~~k~iIf~~~~~~~~~l~~~  125 (233)
                                                       -++++++              .+......+++|||..+..++.+.++
T Consensus       361 LLFSATMP~KIQ~FAkSALVKPvtvNVGRAGAAsldViQevEyVkqEaKiVylLeCLQKT~PpVLIFaEkK~DVD~IhEY  440 (610)
T KOG0341|consen  361 LLFSATMPKKIQNFAKSALVKPVTVNVGRAGAASLDVIQEVEYVKQEAKIVYLLECLQKTSPPVLIFAEKKADVDDIHEY  440 (610)
T ss_pred             eeeeccccHHHHHHHHhhcccceEEecccccccchhHHHHHHHHHhhhhhhhHHHHhccCCCceEEEeccccChHHHHHH
Confidence                                             0011100              23455678999999999999999999


Q ss_pred             HhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc
Q psy14082        126 LRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI  191 (233)
Q Consensus       126 L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i  191 (233)
                      |--.|..++.+||+.++++|...++.|+.|+.++||+||+++.|+|+|++.||||||+|...+.|+
T Consensus       441 LLlKGVEavaIHGGKDQedR~~ai~afr~gkKDVLVATDVASKGLDFp~iqHVINyDMP~eIENYV  506 (610)
T KOG0341|consen  441 LLLKGVEAVAIHGGKDQEDRHYAIEAFRAGKKDVLVATDVASKGLDFPDIQHVINYDMPEEIENYV  506 (610)
T ss_pred             HHHccceeEEeecCcchhHHHHHHHHHhcCCCceEEEecchhccCCCccchhhccCCChHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999998666

>KOG0334|consensus

Probab=100.00  E-value=6.4e-37  Score=277.56  Aligned_cols=227  Identities=30%  Similarity=0.469  Sum_probs=189.5

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~g   78 (233)
                      |||.+++|+|||++|.||||||++|++|++.+++.+++.....||.+||++|||||+.|+++.++.|  ..++++.+.+|
T Consensus       395 AiP~ImsGrdvIgvakTgSGKT~af~LPmirhi~dQr~~~~gdGPi~li~aPtrela~QI~r~~~kf~k~l~ir~v~vyg  474 (997)
T KOG0334|consen  395 AIPAIMSGRDVIGVAKTGSGKTLAFLLPMIRHIKDQRPLEEGDGPIALILAPTRELAMQIHREVRKFLKLLGIRVVCVYG  474 (997)
T ss_pred             hcchhccCcceEEeeccCCccchhhhcchhhhhhcCCChhhCCCceEEEEcCCHHHHHHHHHHHHHHHhhcCceEEEecC
Confidence            8999999999999999999999999999999999988777788999999999999999999999999  66889999999


Q ss_pred             CCCCCCee---------EEe------------------ccc---------------------------------------
Q psy14082         79 GTPKGPQD---------CLP------------------LHR---------------------------------------   92 (233)
Q Consensus        79 g~~~~~~~---------lv~------------------l~r---------------------------------------   92 (233)
                      |.+...|+         +|+                  |+|                                       
T Consensus       475 g~~~~~qiaelkRg~eIvV~tpGRmiD~l~~n~grvtnlrR~t~lv~deaDrmfdmgfePq~~~Ii~nlrpdrQtvlfSa  554 (997)
T KOG0334|consen  475 GSGISQQIAELKRGAEIVVCTPGRMIDILCANSGRVTNLRRVTYLVLDEADRMFDMGFEPQITRILQNLRPDRQTVLFSA  554 (997)
T ss_pred             CccHHHHHHHHhcCCceEEeccchhhhhHhhcCCccccccccceeeechhhhhheeccCcccchHHhhcchhhhhhhhhh
Confidence            98886655         555                  222                                       


Q ss_pred             ----------------------------------hhhhch-----------HHHhcCCCCeEEEEecchhHHHHHHHHHh
Q psy14082         93 ----------------------------------FVFNCQ-----------YEMAKNPAFKVIVFVETKKKVEDITRALR  127 (233)
Q Consensus        93 ----------------------------------~~~~~~-----------~~~~~~~~~k~iIf~~~~~~~~~l~~~L~  127 (233)
                                                        .+.+|.           -+-......++||||.....++.+...|.
T Consensus       555 tfpr~m~~la~~vl~~Pveiiv~~~svV~k~V~q~v~V~~~e~eKf~kL~eLl~e~~e~~~tiiFv~~qe~~d~l~~~L~  634 (997)
T KOG0334|consen  555 TFPRSMEALARKVLKKPVEIIVGGRSVVCKEVTQVVRVCAIENEKFLKLLELLGERYEDGKTIIFVDKQEKADALLRDLQ  634 (997)
T ss_pred             hhhHHHHHHHHHhhcCCeeEEEccceeEeccceEEEEEecCchHHHHHHHHHHHHHhhcCCEEEEEcCchHHHHHHHHHH
Confidence                                              111111           01123347899999999999999999999


Q ss_pred             hCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc------------ceee
Q psy14082        128 RERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI------------SQVI  195 (233)
Q Consensus       128 ~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i------------~~~~  195 (233)
                      +.|+.|..+||+.++.+|..++++|+++..++||+|++++||+|++++.+|||||+|...++|+            |.++
T Consensus       635 ~ag~~~~slHGgv~q~dR~sti~dfK~~~~~LLvaTsvvarGLdv~~l~Lvvnyd~pnh~edyvhR~gRTgragrkg~Av  714 (997)
T KOG0334|consen  635 KAGYNCDSLHGGVDQHDRSSTIEDFKNGVVNLLVATSVVARGLDVKELILVVNYDFPNHYEDYVHRVGRTGRAGRKGAAV  714 (997)
T ss_pred             hcCcchhhhcCCCchHHHHhHHHHHhccCceEEEehhhhhcccccccceEEEEcccchhHHHHHHHhcccccCCccceeE
Confidence            9999999999999999999999999999999999999999999999999999999999999888            5778


Q ss_pred             EEeecchHHHHHHHHHHhhcCcccccccchhhHhhh
Q psy14082        196 EVVQDYEKEKRLFSLIRELGKYTLITQESSSTLSEM  231 (233)
Q Consensus       196 ~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~l  231 (233)
                      +|+.+ ++......+.+.+   .+..++.|+.+..|
T Consensus       715 tFi~p-~q~~~a~dl~~al---~~~~~~~P~~l~~l  746 (997)
T KOG0334|consen  715 TFITP-DQLKYAGDLCKAL---ELSKQPVPKLLQAL  746 (997)
T ss_pred             EEeCh-HHhhhHHHHHHHH---HhccCCCchHHHHH
Confidence            89987 4444444444444   22334444555443

>KOG0346|consensus

Probab=100.00  E-value=3.2e-37  Score=257.07  Aligned_cols=202  Identities=22%  Similarity=0.315  Sum_probs=165.7

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCC-CCCCCceEEEEcCcHHHHHHHHHHHHHh----hcCCcEEE
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPV-KQGDGPIALVLAPTRELAQQIQTVAKEF----SSALRNIC   75 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~-~~~~~~~~lil~PtreL~~Q~~~~~~~~----~~~~~~~~   75 (233)
                      |||.++.|+|+++.|.||||||+||++|+++.++..+.. ....++.++||+||||||+|+++.+.++    ...+++.-
T Consensus        49 aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~sa~iLvPTkEL~qQvy~viekL~~~c~k~lr~~n  128 (569)
T KOG0346|consen   49 AIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSAVILVPTKELAQQVYKVIEKLVEYCSKDLRAIN  128 (569)
T ss_pred             ccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhhhcccccccceeEEEechHHHHHHHHHHHHHHHHHHHHhhhhhh
Confidence            799999999999999999999999999999999986543 4467999999999999999999999999    23445444


Q ss_pred             EEcCCC---------CCCeeEEe----------------------------------------------ccc--------
Q psy14082         76 IFGGTP---------KGPQDCLP----------------------------------------------LHR--------   92 (233)
Q Consensus        76 ~~gg~~---------~~~~~lv~----------------------------------------------l~r--------   92 (233)
                      +....+         ..++++|+                                              |.|        
T Consensus       129 l~s~~sdsv~~~~L~d~pdIvV~TP~~ll~~~~~~~~~~~~~l~~LVvDEADLllsfGYeedlk~l~~~LPr~~Q~~LmS  208 (569)
T KOG0346|consen  129 LASSMSDSVNSVALMDLPDIVVATPAKLLRHLAAGVLEYLDSLSFLVVDEADLLLSFGYEEDLKKLRSHLPRIYQCFLMS  208 (569)
T ss_pred             hhcccchHHHHHHHccCCCeEEeChHHHHHHHhhccchhhhheeeEEechhhhhhhcccHHHHHHHHHhCCchhhheeeh
Confidence            443322         25667777                                              111        


Q ss_pred             ------------------------------------hhhhchH----------HHhcCCCCeEEEEecchhHHHHHHHHH
Q psy14082         93 ------------------------------------FVFNCQY----------EMAKNPAFKVIVFVETKKKVEDITRAL  126 (233)
Q Consensus        93 ------------------------------------~~~~~~~----------~~~~~~~~k~iIf~~~~~~~~~l~~~L  126 (233)
                                                          +.-.|.+          +-.+--.+|+|||+||.+.+..+.-.|
T Consensus       209 ATl~dDv~~LKkL~l~nPviLkl~e~el~~~dqL~Qy~v~cse~DKflllyallKL~LI~gKsliFVNtIdr~YrLkLfL  288 (569)
T KOG0346|consen  209 ATLSDDVQALKKLFLHNPVILKLTEGELPNPDQLTQYQVKCSEEDKFLLLYALLKLRLIRGKSLIFVNTIDRCYRLKLFL  288 (569)
T ss_pred             hhhhhHHHHHHHHhccCCeEEEeccccCCCcccceEEEEEeccchhHHHHHHHHHHHHhcCceEEEEechhhhHHHHHHH
Confidence                                                1111111          112335689999999999999999999


Q ss_pred             hhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----------------------------------cCcCCcC
Q psy14082        127 RRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----------------------------------VAARGLD  171 (233)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----------------------------------~~~~Gld  171 (233)
                      +..|++..++.|.||...|..++++|+.|-++++||||                                   -.+||+|
T Consensus       289 eqFGiksciLNseLP~NSR~Hii~QFNkG~YdivIAtD~s~~~~~~eee~kgk~~e~~~kndkkskkK~D~E~GVsRGID  368 (569)
T KOG0346|consen  289 EQFGIKSCILNSELPANSRCHIIEQFNKGLYDIVIATDDSADGDKLEEEVKGKSDEKNPKNDKKSKKKLDKESGVSRGID  368 (569)
T ss_pred             HHhCcHhhhhcccccccchhhHHHHhhCcceeEEEEccCccchhhhhccccccccccCCCCccccccccCchhchhcccc
Confidence            99999999999999999999999999999999999996                                   2459999


Q ss_pred             CCCccEEEEecCCCCccccc------------ceeeEEeecch
Q psy14082        172 VEDVNTVNIGSLQLSANHNI------------SQVIEVVQDYE  202 (233)
Q Consensus       172 i~~v~~VI~~d~P~~~~~~i------------~~~~~~~~~~~  202 (233)
                      +.+|.+|+|||+|.++..||            |.+++|+.+.+
T Consensus       369 F~~V~~VlNFD~P~t~~sYIHRvGRTaRg~n~GtalSfv~P~e  411 (569)
T KOG0346|consen  369 FHHVSNVLNFDFPETVTSYIHRVGRTARGNNKGTALSFVSPKE  411 (569)
T ss_pred             chheeeeeecCCCCchHHHHHhccccccCCCCCceEEEecchH
Confidence            99999999999999999888            45667887655

>KOG0339|consensus

Probab=100.00  E-value=4.1e-36  Score=254.32  Aligned_cols=226  Identities=32%  Similarity=0.480  Sum_probs=187.7

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~g   78 (233)
                      |+|..++|+|++.+|-||||||.||+.|++.+++.++..++..+|.+||+|||||||.|++.++++|  .-++++.+++|
T Consensus       253 alptalsgrdvigIAktgSgktaAfi~pm~~himdq~eL~~g~gPi~vilvPTrela~Qi~~eaKkf~K~ygl~~v~~yg  332 (731)
T KOG0339|consen  253 ALPTALSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPELKPGEGPIGVILVPTRELASQIFSEAKKFGKAYGLRVVAVYG  332 (731)
T ss_pred             ccccccccccchheeeccCcchhHHHHHHHHHhcchhhhcCCCCCeEEEEeccHHHHHHHHHHHHHhhhhccceEEEeec
Confidence            6899999999999999999999999999999999998888899999999999999999999999999  44789999999


Q ss_pred             CCCCCC---------eeEEe---------------ccc------------------------------------------
Q psy14082         79 GTPKGP---------QDCLP---------------LHR------------------------------------------   92 (233)
Q Consensus        79 g~~~~~---------~~lv~---------------l~r------------------------------------------   92 (233)
                      |.+..+         .++|+               +.|                                          
T Consensus       333 Ggsk~eQ~k~Lk~g~EivVaTPgRlid~VkmKatn~~rvS~LV~DEadrmfdmGfe~qVrSI~~hirpdrQtllFsaTf~  412 (731)
T KOG0339|consen  333 GGSKWEQSKELKEGAEIVVATPGRLIDMVKMKATNLSRVSYLVLDEADRMFDMGFEPQVRSIKQHIRPDRQTLLFSATFK  412 (731)
T ss_pred             CCcHHHHHHhhhcCCeEEEechHHHHHHHHhhcccceeeeEEEEechhhhhccccHHHHHHHHhhcCCcceEEEeeccch
Confidence            987644         34776               111                                          


Q ss_pred             -------------------------------hhh-----------hchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCC
Q psy14082         93 -------------------------------FVF-----------NCQYEMAKNPAFKVIVFVETKKKVEDITRALRRER  130 (233)
Q Consensus        93 -------------------------------~~~-----------~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~  130 (233)
                                                     .+.           +.+++......+++|+|+..+..++.++..|+-.+
T Consensus       413 ~kIe~lard~L~dpVrvVqg~vgean~dITQ~V~V~~s~~~Kl~wl~~~L~~f~S~gkvlifVTKk~~~e~i~a~Lklk~  492 (731)
T KOG0339|consen  413 KKIEKLARDILSDPVRVVQGEVGEANEDITQTVSVCPSEEKKLNWLLRHLVEFSSEGKVLIFVTKKADAEEIAANLKLKG  492 (731)
T ss_pred             HHHHHHHHHHhcCCeeEEEeehhccccchhheeeeccCcHHHHHHHHHHhhhhccCCcEEEEEeccCCHHHHHHHhcccc
Confidence                                           111           11113344466899999999999999999999999


Q ss_pred             CeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCcc---ccc---------ceeeEEe
Q psy14082        131 HSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSAN---HNI---------SQVIEVV  198 (233)
Q Consensus       131 ~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~---~~i---------~~~~~~~  198 (233)
                      +++..+||+|.+.+|.+++.+|+.+..+|||+||+..||+|++++..|||||+-.+.+   |+|         |.+.+++
T Consensus       493 ~~v~llhgdkdqa~rn~~ls~fKkk~~~VlvatDvaargldI~~ikTVvnyD~ardIdththrigrtgRag~kGvayTlv  572 (731)
T KOG0339|consen  493 FNVSLLHGDKDQAERNEVLSKFKKKRKPVLVATDVAARGLDIPSIKTVVNYDFARDIDTHTHRIGRTGRAGEKGVAYTLV  572 (731)
T ss_pred             ceeeeecCchhhHHHHHHHHHHhhcCCceEEEeeHhhcCCCccccceeecccccchhHHHHHHhhhcccccccceeeEEe
Confidence            9999999999999999999999999999999999999999999999999999999987   455         4566678


Q ss_pred             ecchHH--HHHHHHHHhhcCcccccccchhhHhhhc
Q psy14082        199 QDYEKE--KRLFSLIRELGKYTLITQESSSTLSEMV  232 (233)
Q Consensus       199 ~~~~~~--~~~~~~i~~~~~~~~~~~~~~~~~~~l~  232 (233)
                      ++.+..  ..+++.|+--      -+..|..+-+||
T Consensus       573 TeKDa~fAG~LVnnLe~a------gQnVP~~l~dla  602 (731)
T KOG0339|consen  573 TEKDAEFAGHLVNNLEGA------GQNVPDELMDLA  602 (731)
T ss_pred             chhhHHHhhHHHHHHhhc------cccCChHHHHHH
Confidence            764422  2333333332      366777777665

>PTZ00424 helicase 45; Provisional

Probab=100.00  E-value=3.9e-35  Score=254.83  Aligned_cols=214  Identities=26%  Similarity=0.356  Sum_probs=172.5

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh--cCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS--SALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~--~~~~~~~~~g   78 (233)
                      |||.+++|+|++++||||||||++|++|+++.+...     ..+.++|||+||+||+.|+.+.+..+.  .++.+..+.|
T Consensus        58 ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~-----~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g  132 (401)
T PTZ00424         58 GIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYD-----LNACQALILAPTRELAQQIQKVVLALGDYLKVRCHACVG  132 (401)
T ss_pred             HHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCC-----CCCceEEEECCCHHHHHHHHHHHHHHhhhcCceEEEEEC
Confidence            578889999999999999999999999999888543     346789999999999999999999983  4566777777


Q ss_pred             CCCC---------CCeeEEe---------------ccc------------------------------------------
Q psy14082         79 GTPK---------GPQDCLP---------------LHR------------------------------------------   92 (233)
Q Consensus        79 g~~~---------~~~~lv~---------------l~r------------------------------------------   92 (233)
                      +...         ..+++|+               +++                                          
T Consensus       133 ~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~l~~i~lvViDEah~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~  212 (401)
T PTZ00424        133 GTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSRGFKGQIYDVFKKLPPDVQVALFSATMP  212 (401)
T ss_pred             CcCHHHHHHHHcCCCCEEEECcHHHHHHHHhCCcccccccEEEEecHHHHHhcchHHHHHHHHhhCCCCcEEEEEEecCC
Confidence            7532         2356666               000                                          


Q ss_pred             -----------------------------------------hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCC
Q psy14082         93 -----------------------------------------FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERH  131 (233)
Q Consensus        93 -----------------------------------------~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~  131 (233)
                                                               ....+.+.+......++||||+++++++.++..|.+.++
T Consensus       213 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ivF~~t~~~~~~l~~~l~~~~~  292 (401)
T PTZ00424        213 NEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKEEWKFDTLCDLYETLTITQAIIYCNTRRKVDYLTKKMHERDF  292 (401)
T ss_pred             HHHHHHHHHHcCCCEEEEeCCCCcccCCceEEEEecChHHHHHHHHHHHHHhcCCCeEEEEecCcHHHHHHHHHHHHCCC
Confidence                                                     000000122334567899999999999999999999999


Q ss_pred             eeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc------------ceeeEEee
Q psy14082        132 SAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI------------SQVIEVVQ  199 (233)
Q Consensus       132 ~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i------------~~~~~~~~  199 (233)
                      .+..+||+|++++|..+++.|++|+.+|||||+.+++|+|+|++++||+||+|.+...|+            |.++.+++
T Consensus       293 ~~~~~h~~~~~~~R~~i~~~f~~g~~~vLvaT~~l~~GiDip~v~~VI~~~~p~s~~~y~qr~GRagR~g~~G~~i~l~~  372 (401)
T PTZ00424        293 TVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVT  372 (401)
T ss_pred             cEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEcccccCCcCcccCCEEEEECCCCCHHHEeecccccccCCCCceEEEEEc
Confidence            999999999999999999999999999999999999999999999999999999987666            34466777


Q ss_pred             cchHHHHHHHHHHhhcCccccc
Q psy14082        200 DYEKEKRLFSLIRELGKYTLIT  221 (233)
Q Consensus       200 ~~~~~~~~~~~i~~~~~~~~~~  221 (233)
                      +++  ...+..+++.....++.
T Consensus       373 ~~~--~~~~~~~e~~~~~~~~~  392 (401)
T PTZ00424        373 PDD--IEQLKEIERHYNTQIEE  392 (401)
T ss_pred             HHH--HHHHHHHHHHHCCcccc
Confidence            544  66778888877665554

>KOG0332|consensus

Probab=100.00  E-value=1.7e-35  Score=242.42  Aligned_cols=223  Identities=25%  Similarity=0.324  Sum_probs=177.5

Q ss_pred             CCCCCCC--CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEE
Q psy14082          1 MLPPSES--GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICI   76 (233)
Q Consensus         1 aip~~~~--g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~   76 (233)
                      |+|.++.  .++.|+||.+|||||+||++.++.++...     ...|+++-|+||||||.|+.+.+.+.  +.+++....
T Consensus       120 aLPlll~~Pp~nlIaQsqsGtGKTaaFvL~MLsrvd~~-----~~~PQ~iCLaPtrELA~Q~~eVv~eMGKf~~ita~ya  194 (477)
T KOG0332|consen  120 ALPLLLAEPPQNLIAQSQSGTGKTAAFVLTMLSRVDPD-----VVVPQCICLAPTRELAPQTGEVVEEMGKFTELTASYA  194 (477)
T ss_pred             hcchhhcCCchhhhhhhcCCCchhHHHHHHHHHhcCcc-----ccCCCceeeCchHHHHHHHHHHHHHhcCceeeeEEEE
Confidence            6787766  78999999999999999999999999765     56889999999999999999999999  556677666


Q ss_pred             EcCC------CCCCeeEEe-------------------------------------------------------------
Q psy14082         77 FGGT------PKGPQDCLP-------------------------------------------------------------   89 (233)
Q Consensus        77 ~gg~------~~~~~~lv~-------------------------------------------------------------   89 (233)
                      +-|.      ...+||+||                                                             
T Consensus       195 ir~sk~~rG~~i~eqIviGTPGtv~Dlm~klk~id~~kikvfVlDEAD~Mi~tqG~~D~S~rI~~~lP~~~QllLFSATf  274 (477)
T KOG0332|consen  195 IRGSKAKRGNKLTEQIVIGTPGTVLDLMLKLKCIDLEKIKVFVLDEADVMIDTQGFQDQSIRIMRSLPRNQQLLLFSATF  274 (477)
T ss_pred             ecCcccccCCcchhheeeCCCccHHHHHHHHHhhChhhceEEEecchhhhhhcccccccchhhhhhcCCcceEEeeechh
Confidence            6654      335677777                                                             


Q ss_pred             -------------------ccc----------hhhhchH----------HHhcCCCCeEEEEecchhHHHHHHHHHhhCC
Q psy14082         90 -------------------LHR----------FVFNCQY----------EMAKNPAFKVIVFVETKKKVEDITRALRRER  130 (233)
Q Consensus        90 -------------------l~r----------~~~~~~~----------~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~  130 (233)
                                         |+|          +.-.|..          +.....-+++||||.|++++.+++..|...|
T Consensus       275 ~e~V~~Fa~kivpn~n~i~Lk~eel~L~~IkQlyv~C~~~~~K~~~l~~lyg~~tigqsiIFc~tk~ta~~l~~~m~~~G  354 (477)
T KOG0332|consen  275 VEKVAAFALKIVPNANVIILKREELALDNIKQLYVLCACRDDKYQALVNLYGLLTIGQSIIFCHTKATAMWLYEEMRAEG  354 (477)
T ss_pred             HHHHHHHHHHhcCCCceeeeehhhccccchhhheeeccchhhHHHHHHHHHhhhhhhheEEEEeehhhHHHHHHHHHhcC
Confidence                               000          1111111          2333355789999999999999999999999


Q ss_pred             CeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCcc---------cccceeeE-----
Q psy14082        131 HSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSAN---------HNISQVIE-----  196 (233)
Q Consensus       131 ~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~---------~~i~~~~~-----  196 (233)
                      +.+..+||+|...+|..++++|+.|..++||+|++++||+|++.|++|||||+|....         |||||.++     
T Consensus       355 h~V~~l~G~l~~~~R~~ii~~Fr~g~~kVLitTnV~ARGiDv~qVs~VvNydlP~~~~~~pD~etYlHRiGRtGRFGkkG  434 (477)
T KOG0332|consen  355 HQVSLLHGDLTVEQRAAIIDRFREGKEKVLITTNVCARGIDVAQVSVVVNYDLPVKYTGEPDYETYLHRIGRTGRFGKKG  434 (477)
T ss_pred             ceeEEeeccchhHHHHHHHHHHhcCcceEEEEechhhcccccceEEEEEecCCccccCCCCCHHHHHHHhcccccccccc
Confidence            9999999999999999999999999999999999999999999999999999997653         66654444     


Q ss_pred             ----EeecchHHHHHHHHHHhhcCcccccccchhhHhh
Q psy14082        197 ----VVQDYEKEKRLFSLIRELGKYTLITQESSSTLSE  230 (233)
Q Consensus       197 ----~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~  230 (233)
                          ++.+ ++...+++.|+++.+..+..... .++++
T Consensus       435 ~a~n~v~~-~~s~~~mn~iq~~F~~~i~~~~~-~d~~E  470 (477)
T KOG0332|consen  435 LAINLVDD-KDSMNIMNKIQKHFNMKIKRLDP-DDLDE  470 (477)
T ss_pred             eEEEeecc-cCcHHHHHHHHHHHhhcceecCC-ccHHH
Confidence                4544 46678888888877555443333 44433

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

Probab=100.00  E-value=1.1e-34  Score=267.18  Aligned_cols=213  Identities=19%  Similarity=0.221  Sum_probs=167.1

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh-cCCcEEEEEcC
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS-SALRNICIFGG   79 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~-~~~~~~~~~gg   79 (233)
                      |||.++.|+|+++.+|||||||++|++|+++++...      +++++|||+|||||+.|+++.++.+. .++++..+.|+
T Consensus        44 ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~~------~~~~aL~l~PtraLa~q~~~~l~~l~~~~i~v~~~~Gd  117 (742)
T TIGR03817        44 AAELAHAGRHVVVATGTASGKSLAYQLPVLSALADD------PRATALYLAPTKALAADQLRAVRELTLRGVRPATYDGD  117 (742)
T ss_pred             HHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhhC------CCcEEEEEcChHHHHHHHHHHHHHhccCCeEEEEEeCC
Confidence            578899999999999999999999999999999753      46799999999999999999999983 46788888888


Q ss_pred             CCC--------CCeeEEe---------------------------------------------ccchhhhch--------
Q psy14082         80 TPK--------GPQDCLP---------------------------------------------LHRFVFNCQ--------   98 (233)
Q Consensus        80 ~~~--------~~~~lv~---------------------------------------------l~r~~~~~~--------   98 (233)
                      .+.        +++++|+                                             ++|+..++.        
T Consensus       118 t~~~~r~~i~~~~~IivtTPd~L~~~~L~~~~~~~~~l~~l~~vViDEah~~~g~fg~~~~~il~rL~ri~~~~g~~~q~  197 (742)
T TIGR03817       118 TPTEERRWAREHARYVLTNPDMLHRGILPSHARWARFLRRLRYVVIDECHSYRGVFGSHVALVLRRLRRLCARYGASPVF  197 (742)
T ss_pred             CCHHHHHHHhcCCCEEEEChHHHHHhhccchhHHHHHHhcCCEEEEeChhhccCccHHHHHHHHHHHHHHHHhcCCCCEE
Confidence            653        3455666                                             000000000        


Q ss_pred             -------------------------------------------------------------H---HH--hcCCCCeEEEE
Q psy14082         99 -------------------------------------------------------------Y---EM--AKNPAFKVIVF  112 (233)
Q Consensus        99 -------------------------------------------------------------~---~~--~~~~~~k~iIf  112 (233)
                                                                                   +   .+  .-..+.++|||
T Consensus       198 i~~SATi~n~~~~~~~l~g~~~~~i~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~l~~l~~~~~~~IVF  277 (742)
T TIGR03817       198 VLASATTADPAAAASRLIGAPVVAVTEDGSPRGARTVALWEPPLTELTGENGAPVRRSASAEAADLLADLVAEGARTLTF  277 (742)
T ss_pred             EEEecCCCCHHHHHHHHcCCCeEEECCCCCCcCceEEEEecCCccccccccccccccchHHHHHHHHHHHHHCCCCEEEE
Confidence                                                                         0   00  00135799999


Q ss_pred             ecchhHHHHHHHHHhhC--------CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCC
Q psy14082        113 VETKKKVEDITRALRRE--------RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQ  184 (233)
Q Consensus       113 ~~~~~~~~~l~~~L~~~--------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P  184 (233)
                      |+|++.++.++..|++.        +.++..+||++++++|.+++++|++|+.++|||||++++|+|+|++++|||||+|
T Consensus       278 ~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~hgg~~~~eR~~ie~~f~~G~i~vLVaTd~lerGIDI~~vd~VI~~~~P  357 (742)
T TIGR03817       278 VRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYLPEDRRELERALRDGELLGVATTNALELGVDISGLDAVVIAGFP  357 (742)
T ss_pred             cCCHHHHHHHHHHHHHHHHhhccccccchhheecCCCHHHHHHHHHHHHcCCceEEEECchHhccCCcccccEEEEeCCC
Confidence            99999999999998753        5678899999999999999999999999999999999999999999999999999


Q ss_pred             CCccccc---c---------eeeEEeecchHHHHHHHHHHhhcCccc
Q psy14082        185 LSANHNI---S---------QVIEVVQDYEKEKRLFSLIRELGKYTL  219 (233)
Q Consensus       185 ~~~~~~i---~---------~~~~~~~~~~~~~~~~~~i~~~~~~~~  219 (233)
                      .+...|+   |         .++.+.++...+..++..+++..+..+
T Consensus       358 ~s~~~y~qRiGRaGR~G~~g~ai~v~~~~~~d~~~~~~~~~~~~~~~  404 (742)
T TIGR03817       358 GTRASLWQQAGRAGRRGQGALVVLVARDDPLDTYLVHHPEALFDRPV  404 (742)
T ss_pred             CCHHHHHHhccccCCCCCCcEEEEEeCCChHHHHHHhCHHHHhcCCC
Confidence            9998666   2         334455544444556666665544443

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.

>KOG0350|consensus

Probab=100.00  E-value=4.6e-34  Score=241.38  Aligned_cols=208  Identities=20%  Similarity=0.256  Sum_probs=168.8

Q ss_pred             CCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEcCC
Q psy14082          3 PPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGGT   80 (233)
Q Consensus         3 p~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~gg~   80 (233)
                      |+-.+++|+.+.||||||||++|++|+++.+...+    -+..||||++|||+|+.|+++.|.++  ..++.++.+.|..
T Consensus       178 p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R~----v~~LRavVivPtr~L~~QV~~~f~~~~~~tgL~V~~~sgq~  253 (620)
T KOG0350|consen  178 PPPSRPRDICVNAPTGSGKTLAYVIPIVQLLSSRP----VKRLRAVVIVPTRELALQVYDTFKRLNSGTGLAVCSLSGQN  253 (620)
T ss_pred             CCCCCCCceEEecCCCCCceeeehhHHHHHHccCC----ccceEEEEEeeHHHHHHHHHHHHHHhccCCceEEEeccccc
Confidence            66778999999999999999999999999887642    34689999999999999999999999  5677878888774


Q ss_pred             CC--------------CCeeEEe----------------ccc--------------------------------------
Q psy14082         81 PK--------------GPQDCLP----------------LHR--------------------------------------   92 (233)
Q Consensus        81 ~~--------------~~~~lv~----------------l~r--------------------------------------   92 (233)
                      +.              +-+++|+                |+.                                      
T Consensus       254 sl~~E~~qL~~~~~~~~~DIlVaTPGRLVDHl~~~k~f~Lk~LrfLVIDEADRll~qsfQ~Wl~~v~~~~~~~k~~~~~~  333 (620)
T KOG0350|consen  254 SLEDEARQLASDPPECRIDILVATPGRLVDHLNNTKSFDLKHLRFLVIDEADRLLDQSFQEWLDTVMSLCKTMKRVACLD  333 (620)
T ss_pred             chHHHHHHHhcCCCccccceEEcCchHHHHhccCCCCcchhhceEEEechHHHHHHHHHHHHHHHHHHHhCCchhhcChh
Confidence            43              1255676                000                                      


Q ss_pred             ---------------------------------------------------------------hhhhc------------
Q psy14082         93 ---------------------------------------------------------------FVFNC------------   97 (233)
Q Consensus        93 ---------------------------------------------------------------~~~~~------------   97 (233)
                                                                                     .+.++            
T Consensus       334 nii~~~~~~~pt~~~e~~t~~~~~~~~l~kL~~satLsqdP~Kl~~l~l~~Prl~~v~~~~~~ryslp~~l~~~~vv~~~  413 (620)
T KOG0350|consen  334 NIIRQRQAPQPTVLSELLTKLGKLYPPLWKLVFSATLSQDPSKLKDLTLHIPRLFHVSKPLIGRYSLPSSLSHRLVVTEP  413 (620)
T ss_pred             hhhhhcccCCchhhHHHHhhcCCcCchhHhhhcchhhhcChHHHhhhhcCCCceEEeecccceeeecChhhhhceeeccc
Confidence                                                                           00000            


Q ss_pred             -------hHHHhcCCCCeEEEEecchhHHHHHHHHHh----hCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccC
Q psy14082         98 -------QYEMAKNPAFKVIVFVETKKKVEDITRALR----RERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVA  166 (233)
Q Consensus        98 -------~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~----~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~  166 (233)
                             -.++...+..++|+|+++...+..++..|.    ..+.++..++|+++.+.|.+.+++|+.|++++|||+|++
T Consensus       414 ~~kpl~~~~lI~~~k~~r~lcf~~S~~sa~Rl~~~L~v~~~~~~~~~s~~t~~l~~k~r~k~l~~f~~g~i~vLIcSD~l  493 (620)
T KOG0350|consen  414 KFKPLAVYALITSNKLNRTLCFVNSVSSANRLAHVLKVEFCSDNFKVSEFTGQLNGKRRYKMLEKFAKGDINVLICSDAL  493 (620)
T ss_pred             ccchHhHHHHHHHhhcceEEEEecchHHHHHHHHHHHHHhccccchhhhhhhhhhHHHHHHHHHHHhcCCceEEEehhhh
Confidence                   004566788999999999999999998887    345677789999999999999999999999999999999


Q ss_pred             cCCcCCCCccEEEEecCCCCccccc------------ceeeEEeecchHHHHHHHHHHhhc
Q psy14082        167 ARGLDVEDVNTVNIGSLQLSANHNI------------SQVIEVVQDYEKEKRLFSLIRELG  215 (233)
Q Consensus       167 ~~Gldi~~v~~VI~~d~P~~~~~~i------------~~~~~~~~~~~~~~~~~~~i~~~~  215 (233)
                      +||+|+.+++.|||||+|.+...||            |.++.++++++ ...|.+++++..
T Consensus       494 aRGiDv~~v~~VINYd~P~~~ktyVHR~GRTARAgq~G~a~tll~~~~-~r~F~klL~~~~  553 (620)
T KOG0350|consen  494 ARGIDVNDVDNVINYDPPASDKTYVHRAGRTARAGQDGYAITLLDKHE-KRLFSKLLKKTN  553 (620)
T ss_pred             hcCCcccccceEeecCCCchhhHHHHhhcccccccCCceEEEeecccc-chHHHHHHHHhc
Confidence            9999999999999999999999888            45566777654 456667776643

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=100.00  E-value=5.9e-33  Score=245.38  Aligned_cols=178  Identities=21%  Similarity=0.178  Sum_probs=145.2

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCC
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGT   80 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~   80 (233)
                      |||.+++|+|+++++|||||||++|++|++.           .+..+||++||+||+.|+.+.+..+  ++.+..+.|+.
T Consensus        19 ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~-----------~~~~~lVi~P~~~L~~dq~~~l~~~--gi~~~~l~~~~   85 (470)
T TIGR00614        19 VINAVLLGRDCFVVMPTGGGKSLCYQLPALC-----------SDGITLVISPLISLMEDQVLQLKAS--GIPATFLNSSQ   85 (470)
T ss_pred             HHHHHHcCCCEEEEcCCCCcHhHHHHHHHHH-----------cCCcEEEEecHHHHHHHHHHHHHHc--CCcEEEEeCCC
Confidence            5788899999999999999999999999984           1346999999999999999988876  56666666654


Q ss_pred             CCC-------------CeeEEe--------------c--------------c--------------c-------------
Q psy14082         81 PKG-------------PQDCLP--------------L--------------H--------------R-------------   92 (233)
Q Consensus        81 ~~~-------------~~~lv~--------------l--------------~--------------r-------------   92 (233)
                      ..+             .+++++              +              +              +             
T Consensus        86 ~~~~~~~i~~~~~~~~~~il~~TPe~l~~~~~~~~~l~~~~~i~~iViDEaH~i~~~g~~fr~~~~~l~~l~~~~~~~~~  165 (470)
T TIGR00614        86 SKEQQKNVLTDLKDGKIKLLYVTPEKCSASNRLLQTLEERKGITLIAVDEAHCISQWGHDFRPDYKALGSLKQKFPNVPI  165 (470)
T ss_pred             CHHHHHHHHHHHhcCCCCEEEECHHHHcCchhHHHHHHhcCCcCEEEEeCCcccCccccccHHHHHHHHHHHHHcCCCce
Confidence            321             223322              0              0              0             


Q ss_pred             ----------------------------------------------hhhhchHHHh-cCCCCeEEEEecchhHHHHHHHH
Q psy14082         93 ----------------------------------------------FVFNCQYEMA-KNPAFKVIVFVETKKKVEDITRA  125 (233)
Q Consensus        93 ----------------------------------------------~~~~~~~~~~-~~~~~k~iIf~~~~~~~~~l~~~  125 (233)
                                                                    ....+.+.+. ...+.++||||++++.++.++..
T Consensus       166 l~lTAT~~~~~~~di~~~l~l~~~~~~~~s~~r~nl~~~v~~~~~~~~~~l~~~l~~~~~~~~~IIF~~s~~~~e~la~~  245 (470)
T TIGR00614       166 MALTATASPSVREDILRQLNLKNPQIFCTSFDRPNLYYEVRRKTPKILEDLLRFIRKEFKGKSGIIYCPSRKKSEQVTAS  245 (470)
T ss_pred             EEEecCCCHHHHHHHHHHcCCCCCcEEeCCCCCCCcEEEEEeCCccHHHHHHHHHHHhcCCCceEEEECcHHHHHHHHHH
Confidence                                                          0000011222 34556679999999999999999


Q ss_pred             HhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc
Q psy14082        126 LRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI  191 (233)
Q Consensus       126 L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i  191 (233)
                      |.+.|+.+..+||+|++++|..++++|++|+.+|||||+++++|+|+|+|++|||||+|.|.+.|+
T Consensus       246 L~~~g~~~~~~H~~l~~~eR~~i~~~F~~g~~~vLVaT~~~~~GID~p~V~~VI~~~~P~s~~~y~  311 (470)
T TIGR00614       246 LQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYY  311 (470)
T ss_pred             HHhcCCCeeEeeCCCCHHHHHHHHHHHHcCCCcEEEEechhhccCCcccceEEEEeCCCCCHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999998777

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

>KOG0327|consensus

Probab=100.00  E-value=4e-33  Score=229.49  Aligned_cols=219  Identities=27%  Similarity=0.413  Sum_probs=181.0

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~g   78 (233)
                      ||+|...|.|+++++++|+|||.+|.+++++++...     ....+|++++|||||+.|+++....+  ..+.+++.++|
T Consensus        56 aI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~-----~ke~qalilaPtreLa~qi~~v~~~lg~~~~~~v~~~ig  130 (397)
T KOG0327|consen   56 AILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMS-----VKETQALILAPTRELAQQIQKVVRALGDHMDVSVHACIG  130 (397)
T ss_pred             cccccccCCceeEeeeccccchhhhHHHHHhhcCcc-----hHHHHHHHhcchHHHHHHHHHHHHhhhcccceeeeeecC
Confidence            799999999999999999999999999999998643     45678999999999999999999988  55778998999


Q ss_pred             CCCCC----------CeeEEe--------ccc------------------------------------------------
Q psy14082         79 GTPKG----------PQDCLP--------LHR------------------------------------------------   92 (233)
Q Consensus        79 g~~~~----------~~~lv~--------l~r------------------------------------------------   92 (233)
                      |.+..          +.+++|        +.+                                                
T Consensus       131 g~~~~~~~~~i~~~~~hivvGTpgrV~dml~~~~l~~~~iKmfvlDEaDEmLs~gfkdqI~~if~~lp~~vQv~l~SAT~  210 (397)
T KOG0327|consen  131 GTNVRREDQALLKDKPHIVVGTPGRVFDMLNRGSLSTDGIKMFVLDEADEMLSRGFKDQIYDIFQELPSDVQVVLLSATM  210 (397)
T ss_pred             cccchhhhhhhhccCceeecCCchhHHHhhccccccccceeEEeecchHhhhccchHHHHHHHHHHcCcchhheeecccC
Confidence            87652          344555        100                                                


Q ss_pred             ---------------------------------hhhhchH-------HHhcCCCCeEEEEecchhHHHHHHHHHhhCCCe
Q psy14082         93 ---------------------------------FVFNCQY-------EMAKNPAFKVIVFVETKKKVEDITRALRRERHS  132 (233)
Q Consensus        93 ---------------------------------~~~~~~~-------~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~  132 (233)
                                                       ++.+.++       .+.. ...+.++|||++..+..+...|..++..
T Consensus       211 p~~vl~vt~~f~~~pv~i~vkk~~ltl~gikq~~i~v~k~~k~~~l~dl~~-~~~q~~if~nt~r~v~~l~~~L~~~~~~  289 (397)
T KOG0327|consen  211 PSDVLEVTKKFMREPVRILVKKDELTLEGIKQFYINVEKEEKLDTLCDLYR-RVTQAVIFCNTRRKVDNLTDKLRAHGFT  289 (397)
T ss_pred             cHHHHHHHHHhccCceEEEecchhhhhhheeeeeeeccccccccHHHHHHH-hhhcceEEecchhhHHHHHHHHhhCCce
Confidence                                             0000000       1222 5678999999999999999999999999


Q ss_pred             eEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc------------ceeeEEeec
Q psy14082        133 AICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI------------SQVIEVVQD  200 (233)
Q Consensus       133 ~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i------------~~~~~~~~~  200 (233)
                      +.++||+|.+.+|..+++.|+.|..++||+|+.++||+|+..++.|||||+|.+.++|+            |.++.++.+
T Consensus       290 ~s~~~~d~~q~~R~~~~~ef~~gssrvlIttdl~argidv~~~slvinydlP~~~~~yihR~gr~gr~grkg~~in~v~~  369 (397)
T KOG0327|consen  290 VSAIHGDMEQNERDTLMREFRSGSSRVLITTDLLARGIDVQQVSLVVNYDLPARKENYIHRIGRAGRFGRKGVAINFVTE  369 (397)
T ss_pred             EEEeecccchhhhhHHHHHhhcCCceEEeeccccccccchhhcceeeeeccccchhhhhhhcccccccCCCceeeeeehH
Confidence            99999999999999999999999999999999999999999999999999999999888            467778886


Q ss_pred             chHHHHHHHHHHhhcCcccccccchhhHh
Q psy14082        201 YEKEKRLFSLIRELGKYTLITQESSSTLS  229 (233)
Q Consensus       201 ~~~~~~~~~~i~~~~~~~~~~~~~~~~~~  229 (233)
                      ++  .+.++.++++.+-.++  |.|.+..
T Consensus       370 ~d--~~~lk~ie~~y~~~i~--e~p~~~~  394 (397)
T KOG0327|consen  370 ED--VRDLKDIEKFYNTPIE--ELPSNFA  394 (397)
T ss_pred             hh--HHHHHhHHHhcCCcce--ecccchh
Confidence            55  8888888887766554  4444433

>KOG0344|consensus

Probab=100.00  E-value=6.9e-33  Score=238.46  Aligned_cols=202  Identities=25%  Similarity=0.301  Sum_probs=162.6

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh----cCCcEEEE
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS----SALRNICI   76 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~----~~~~~~~~   76 (233)
                      |||..+.++|+++++|||||||++|.+|+++++......+...|-+++|+.|||||+.|+|..+.++.    .+.+.+.+
T Consensus       166 aipvfl~~r~~lAcapTGsgKtlaf~~Pil~~L~~~~~~~~~~gl~a~Il~ptreLa~Qi~re~~k~~~~~~t~~~a~~~  245 (593)
T KOG0344|consen  166 AIPVFLEKRDVLACAPTGSGKTLAFNLPILQHLKDLSQEKHKVGLRALILSPTRELAAQIYREMRKYSIDEGTSLRAAQF  245 (593)
T ss_pred             hhhhhhcccceEEeccCCCcchhhhhhHHHHHHHHhhcccCccceEEEEecchHHHHHHHHHHHHhcCCCCCCchhhhhc
Confidence            68999999999999999999999999999999987644444678999999999999999999999993    22333333


Q ss_pred             EcCCCCC----------CeeEEe-----------------------------------------ccchhhh---------
Q psy14082         77 FGGTPKG----------PQDCLP-----------------------------------------LHRFVFN---------   96 (233)
Q Consensus        77 ~gg~~~~----------~~~lv~-----------------------------------------l~r~~~~---------   96 (233)
                      .......          .+++|+                                         +.+++..         
T Consensus       246 ~~~~~~~qk~a~~~~~k~dili~TP~ri~~~~~~~~~~idl~~V~~lV~dEaD~lfe~~~f~~Qla~I~sac~s~~i~~a  325 (593)
T KOG0344|consen  246 SKPAYPSQKPAFLSDEKYDILISTPMRIVGLLGLGKLNIDLSKVEWLVVDEADLLFEPEFFVEQLADIYSACQSPDIRVA  325 (593)
T ss_pred             ccccchhhccchhHHHHHHHHhcCHHHHHHHhcCCCccchhheeeeEeechHHhhhChhhHHHHHHHHHHHhcCcchhhh
Confidence            3321110          011111                                         0001111         


Q ss_pred             ----------------------------------------------------chHHHhcCCCCeEEEEecchhHHHHHHH
Q psy14082         97 ----------------------------------------------------CQYEMAKNPAFKVIVFVETKKKVEDITR  124 (233)
Q Consensus        97 ----------------------------------------------------~~~~~~~~~~~k~iIf~~~~~~~~~l~~  124 (233)
                                                                          +.+.+...-..+++||+.+.+++.++..
T Consensus       326 ~FSat~~~~VEE~~~~i~~~~~~vivg~~~sa~~~V~QelvF~gse~~K~lA~rq~v~~g~~PP~lIfVQs~eRak~L~~  405 (593)
T KOG0344|consen  326 LFSATISVYVEEWAELIKSDLKRVIVGLRNSANETVDQELVFCGSEKGKLLALRQLVASGFKPPVLIFVQSKERAKQLFE  405 (593)
T ss_pred             hhhccccHHHHHHHHHhhccceeEEEecchhHhhhhhhhheeeecchhHHHHHHHHHhccCCCCeEEEEecHHHHHHHHH
Confidence                                                                1125566678899999999999999999


Q ss_pred             HH-hhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc------------
Q psy14082        125 AL-RRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI------------  191 (233)
Q Consensus       125 ~L-~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i------------  191 (233)
                      .| .-.++.+.++||..++.+|.+.+++|+.|++++|+||++++||+|+.++++|||||+|.+...||            
T Consensus       406 ~L~~~~~i~v~vIh~e~~~~qrde~~~~FR~g~IwvLicTdll~RGiDf~gvn~VInyD~p~s~~syihrIGRtgRag~~  485 (593)
T KOG0344|consen  406 ELEIYDNINVDVIHGERSQKQRDETMERFRIGKIWVLICTDLLARGIDFKGVNLVINYDFPQSDLSYIHRIGRTGRAGRS  485 (593)
T ss_pred             HhhhccCcceeeEecccchhHHHHHHHHHhccCeeEEEehhhhhccccccCcceEEecCCCchhHHHHHHhhccCCCCCC
Confidence            99 66789999999999999999999999999999999999999999999999999999999988777            


Q ss_pred             ceeeEEeecch
Q psy14082        192 SQVIEVVQDYE  202 (233)
Q Consensus       192 ~~~~~~~~~~~  202 (233)
                      |+++.|+++.+
T Consensus       486 g~Aitfytd~d  496 (593)
T KOG0344|consen  486 GKAITFYTDQD  496 (593)
T ss_pred             cceEEEecccc
Confidence            57788888744

>KOG4284|consensus

Probab=100.00  E-value=2.3e-33  Score=243.34  Aligned_cols=191  Identities=21%  Similarity=0.285  Sum_probs=166.9

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh---hcCCcEEEEE
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF---SSALRNICIF   77 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~---~~~~~~~~~~   77 (233)
                      |||.+.++-|.|++|.+|+|||++|.+.+++.+..+     ...++++|++||||+|.|+++.+.++   +.+++|+.++
T Consensus        55 AIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~~-----~~~~q~~Iv~PTREiaVQI~~tv~~v~~sf~g~~csvfI  129 (980)
T KOG4284|consen   55 AIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDSR-----SSHIQKVIVTPTREIAVQIKETVRKVAPSFTGARCSVFI  129 (980)
T ss_pred             hhhhhhcccceEEEecCCCCceEEEEeeeehhcCcc-----cCcceeEEEecchhhhhHHHHHHHHhcccccCcceEEEe
Confidence            799999999999999999999999999999888765     66889999999999999999999999   6789999999


Q ss_pred             cCCCC--------CCeeEEe------------------------------------------------------------
Q psy14082         78 GGTPK--------GPQDCLP------------------------------------------------------------   89 (233)
Q Consensus        78 gg~~~--------~~~~lv~------------------------------------------------------------   89 (233)
                      ||++-        +..++||                                                            
T Consensus       130 GGT~~~~d~~rlk~~rIvIGtPGRi~qL~el~~~n~s~vrlfVLDEADkL~~t~sfq~~In~ii~slP~~rQv~a~SATY  209 (980)
T KOG4284|consen  130 GGTAHKLDLIRLKQTRIVIGTPGRIAQLVELGAMNMSHVRLFVLDEADKLMDTESFQDDINIIINSLPQIRQVAAFSATY  209 (980)
T ss_pred             cCchhhhhhhhhhhceEEecCchHHHHHHHhcCCCccceeEEEeccHHhhhchhhHHHHHHHHHHhcchhheeeEEeccC
Confidence            99765        3445777                                                            


Q ss_pred             -----------------------------ccc-----------------hhhhchHHHhcCCCCeEEEEecchhHHHHHH
Q psy14082         90 -----------------------------LHR-----------------FVFNCQYEMAKNPAFKVIVFVETKKKVEDIT  123 (233)
Q Consensus        90 -----------------------------l~r-----------------~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~  123 (233)
                                                   +++                 ....+.+.+..-+..++||||+....|+.++
T Consensus       210 p~nLdn~Lsk~mrdp~lVr~n~~d~~L~GikQyv~~~~s~nnsveemrlklq~L~~vf~~ipy~QAlVF~~~~sra~~~a  289 (980)
T KOG4284|consen  210 PRNLDNLLSKFMRDPALVRFNADDVQLFGIKQYVVAKCSPNNSVEEMRLKLQKLTHVFKSIPYVQALVFCDQISRAEPIA  289 (980)
T ss_pred             chhHHHHHHHHhcccceeecccCCceeechhheeeeccCCcchHHHHHHHHHHHHHHHhhCchHHHHhhhhhhhhhhHHH
Confidence                                         000                 1111222566678889999999999999999


Q ss_pred             HHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCcc---cccceeeE
Q psy14082        124 RALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSAN---HNISQVIE  196 (233)
Q Consensus       124 ~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~---~~i~~~~~  196 (233)
                      ..|...|+.|.++.|.|++.+|..++..++.-..+|||+||..+||+|-++|++|||.|.|.+..   |+|||+++
T Consensus       290 ~~L~ssG~d~~~ISgaM~Q~~Rl~a~~~lr~f~~rILVsTDLtaRGIDa~~vNLVVNiD~p~d~eTY~HRIGRAgR  365 (980)
T KOG4284|consen  290 THLKSSGLDVTFISGAMSQKDRLLAVDQLRAFRVRILVSTDLTARGIDADNVNLVVNIDAPADEETYFHRIGRAGR  365 (980)
T ss_pred             HHhhccCCCeEEeccccchhHHHHHHHHhhhceEEEEEecchhhccCCccccceEEecCCCcchHHHHHHhhhccc
Confidence            99999999999999999999999999999999999999999999999999999999999999987   55654444

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

Probab=100.00  E-value=9.5e-32  Score=249.27  Aligned_cols=178  Identities=19%  Similarity=0.183  Sum_probs=143.6

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCC
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGT   80 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~   80 (233)
                      |||.++.|+|+++++|||+|||++|++|++..           +..+|||+|+++|+.+....+...  ++++..+.|+.
T Consensus       468 aI~aiL~GrDVLVimPTGSGKSLcYQLPAL~~-----------~GiTLVISPLiSLmqDQV~~L~~~--GI~Aa~L~s~~  534 (1195)
T PLN03137        468 IINATMSGYDVFVLMPTGGGKSLTYQLPALIC-----------PGITLVISPLVSLIQDQIMNLLQA--NIPAASLSAGM  534 (1195)
T ss_pred             HHHHHHcCCCEEEEcCCCccHHHHHHHHHHHc-----------CCcEEEEeCHHHHHHHHHHHHHhC--CCeEEEEECCC
Confidence            57889999999999999999999999999852           346999999999998554444443  67777777775


Q ss_pred             CC---------------CCeeEEe----c-------------------cc------------------------------
Q psy14082         81 PK---------------GPQDCLP----L-------------------HR------------------------------   92 (233)
Q Consensus        81 ~~---------------~~~~lv~----l-------------------~r------------------------------   92 (233)
                      +.               ..+++++    +                   .+                              
T Consensus       535 s~~eq~~ilr~l~s~~g~~~ILyvTPERL~~~d~ll~~L~~L~~~~~LslIVIDEAHcVSqWGhDFRpdYr~L~~Lr~~f  614 (1195)
T PLN03137        535 EWAEQLEILQELSSEYSKYKLLYVTPEKVAKSDSLLRHLENLNSRGLLARFVIDEAHCVSQWGHDFRPDYQGLGILKQKF  614 (1195)
T ss_pred             CHHHHHHHHHHHHhcCCCCCEEEEChHHhhcchHHHHHHHhhhhccccceeccCcchhhhhcccchHHHHHHHHHHHHhC
Confidence            42               1233333    0                   00                              


Q ss_pred             ---------------------------------------------------hhhhchHHHh-cCCCCeEEEEecchhHHH
Q psy14082         93 ---------------------------------------------------FVFNCQYEMA-KNPAFKVIVFVETKKKVE  120 (233)
Q Consensus        93 ---------------------------------------------------~~~~~~~~~~-~~~~~k~iIf~~~~~~~~  120 (233)
                                                                         ....+.+++. .....+.||||++++.++
T Consensus       615 p~vPilALTATAT~~V~eDI~~~L~l~~~~vfr~Sf~RpNL~y~Vv~k~kk~le~L~~~I~~~~~~esgIIYC~SRke~E  694 (1195)
T PLN03137        615 PNIPVLALTATATASVKEDVVQALGLVNCVVFRQSFNRPNLWYSVVPKTKKCLEDIDKFIKENHFDECGIIYCLSRMDCE  694 (1195)
T ss_pred             CCCCeEEEEecCCHHHHHHHHHHcCCCCcEEeecccCccceEEEEeccchhHHHHHHHHHHhcccCCCceeEeCchhHHH
Confidence                                                               0000111222 223567899999999999


Q ss_pred             HHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc
Q psy14082        121 DITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI  191 (233)
Q Consensus       121 ~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i  191 (233)
                      .++..|.+.|+++..+||+|++++|..++++|+.|+++|||||+++++|||+|+|++|||||+|.+.+.|+
T Consensus       695 ~LAe~L~~~Gika~~YHAGLs~eeR~~vqe~F~~Gei~VLVATdAFGMGIDkPDVR~VIHydlPkSiEsYy  765 (1195)
T PLN03137        695 KVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYH  765 (1195)
T ss_pred             HHHHHHHHCCCCeeeeeCCCCHHHHHHHHHHHhcCCCcEEEEechhhcCCCccCCcEEEEcCCCCCHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999777

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.97  E-value=1.3e-31  Score=251.01  Aligned_cols=191  Identities=16%  Similarity=0.168  Sum_probs=152.0

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCC-CCCCCceEEEEcCcHHHHHHHHHHHHHh-------h----
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPV-KQGDGPIALVLAPTRELAQQIQTVAKEF-------S----   68 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~-~~~~~~~~lil~PtreL~~Q~~~~~~~~-------~----   68 (233)
                      |||.++.|+|++++||||||||++|.+|+++++...... ...+++++||++|||+|+.|+++.+...       .    
T Consensus        40 Ai~~il~g~nvli~APTGSGKTlaa~Lpil~~l~~~~~~~~~~~~~~~LyIsPtraLa~di~~~L~~~l~~i~~~~~~~g  119 (876)
T PRK13767         40 AIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYVSPLRALNNDIHRNLEEPLTEIREIAKERG  119 (876)
T ss_pred             HHHHHHcCCCEEEECCCCCcHHHHHHHHHHHHHHhhccccCCCCCeEEEEEcCHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            578889999999999999999999999999998854221 1245789999999999999999876632       1    


Q ss_pred             ---cCCcEEEEEcCCCC---------CCeeEEe--------------------------------------------ccc
Q psy14082         69 ---SALRNICIFGGTPK---------GPQDCLP--------------------------------------------LHR   92 (233)
Q Consensus        69 ---~~~~~~~~~gg~~~---------~~~~lv~--------------------------------------------l~r   92 (233)
                         +++++...+|+.+.         .++++|+                                            +.|
T Consensus       120 ~~~~~i~v~v~~Gdt~~~~r~~~l~~~p~IlVtTPE~L~~ll~~~~~~~~l~~l~~VVIDE~H~l~~~~RG~~l~~~L~r  199 (876)
T PRK13767        120 EELPEIRVAIRTGDTSSYEKQKMLKKPPHILITTPESLAILLNSPKFREKLRTVKWVIVDEIHSLAENKRGVHLSLSLER  199 (876)
T ss_pred             CCcCCeeEEEEcCCCCHHHHHHHHhCCCCEEEecHHHHHHHhcChhHHHHHhcCCEEEEechhhhccCccHHHHHHHHHH
Confidence               25678889998653         3456666                                            000


Q ss_pred             hhhhc----------------------------------------------------h-----------------HHH--
Q psy14082         93 FVFNC----------------------------------------------------Q-----------------YEM--  101 (233)
Q Consensus        93 ~~~~~----------------------------------------------------~-----------------~~~--  101 (233)
                      +..++                                                    .                 +.+  
T Consensus       200 L~~l~~~~~q~IglSATl~~~~~va~~L~~~~~~~~~r~~~iv~~~~~k~~~i~v~~p~~~l~~~~~~~~~~~l~~~L~~  279 (876)
T PRK13767        200 LEELAGGEFVRIGLSATIEPLEEVAKFLVGYEDDGEPRDCEIVDARFVKPFDIKVISPVDDLIHTPAEEISEALYETLHE  279 (876)
T ss_pred             HHHhcCCCCeEEEEecccCCHHHHHHHhcCccccCCCCceEEEccCCCccceEEEeccCccccccccchhHHHHHHHHHH
Confidence            00000                                                    0                 000  


Q ss_pred             hcCCCCeEEEEecchhHHHHHHHHHhhC------CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCc
Q psy14082        102 AKNPAFKVIVFVETKKKVEDITRALRRE------RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDV  175 (233)
Q Consensus       102 ~~~~~~k~iIf~~~~~~~~~l~~~L~~~------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v  175 (233)
                      .-...+++||||||++.++.++..|.+.      +..+..+||+|++++|..++++|++|+.++||||+.+++|+|+|++
T Consensus       280 ~i~~~~~~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls~~~R~~ve~~fk~G~i~vLVaTs~Le~GIDip~V  359 (876)
T PRK13767        280 LIKEHRTTLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEVEEKLKRGELKVVVSSTSLELGIDIGYI  359 (876)
T ss_pred             HHhcCCCEEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCCHHHHHHHHHHHHcCCCeEEEECChHHhcCCCCCC
Confidence            0123578999999999999999999873      4678999999999999999999999999999999999999999999


Q ss_pred             cEEEEecCCCCccccc
Q psy14082        176 NTVNIGSLQLSANHNI  191 (233)
Q Consensus       176 ~~VI~~d~P~~~~~~i  191 (233)
                      ++||+||.|.+...|+
T Consensus       360 d~VI~~~~P~sv~~yl  375 (876)
T PRK13767        360 DLVVLLGSPKSVSRLL  375 (876)
T ss_pred             cEEEEeCCCCCHHHHH
Confidence            9999999999988555

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.97  E-value=5.1e-31  Score=239.09  Aligned_cols=178  Identities=17%  Similarity=0.159  Sum_probs=144.3

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCC
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGT   80 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~   80 (233)
                      |||.++.|+|+++.+|||+|||++|++|++.+           +..+||++|+++|+.|+.+.++.+  ++...++.++.
T Consensus        33 ai~~il~g~dvlv~apTGsGKTl~y~lpal~~-----------~g~tlVisPl~sL~~dqv~~l~~~--gi~~~~~~s~~   99 (607)
T PRK11057         33 IIDAVLSGRDCLVVMPTGGGKSLCYQIPALVL-----------DGLTLVVSPLISLMKDQVDQLLAN--GVAAACLNSTQ   99 (607)
T ss_pred             HHHHHHcCCCEEEEcCCCchHHHHHHHHHHHc-----------CCCEEEEecHHHHHHHHHHHHHHc--CCcEEEEcCCC
Confidence            46778999999999999999999999999842           236899999999999999988876  45555555543


Q ss_pred             CCC-------------CeeEEe-----------------------------c-----------cc---------------
Q psy14082         81 PKG-------------PQDCLP-----------------------------L-----------HR---------------   92 (233)
Q Consensus        81 ~~~-------------~~~lv~-----------------------------l-----------~r---------------   92 (233)
                      +..             .++++.                             +           ++               
T Consensus       100 ~~~~~~~~~~~~~~g~~~il~~tPe~l~~~~~~~~l~~~~l~~iVIDEaH~i~~~G~~fr~~y~~L~~l~~~~p~~~~v~  179 (607)
T PRK11057        100 TREQQLEVMAGCRTGQIKLLYIAPERLMMDNFLEHLAHWNPALLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTLPFMA  179 (607)
T ss_pred             CHHHHHHHHHHHhCCCCcEEEEChHHhcChHHHHHHhhCCCCEEEEeCccccccccCcccHHHHHHHHHHHhCCCCcEEE
Confidence            221             111111                             0           00               


Q ss_pred             ------------h-------------------------------hhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhC
Q psy14082         93 ------------F-------------------------------VFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRE  129 (233)
Q Consensus        93 ------------~-------------------------------~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~  129 (233)
                                  +                               ...+...+....+.++||||+|+++++.++..|.+.
T Consensus       180 lTAT~~~~~~~di~~~l~l~~~~~~~~~~~r~nl~~~v~~~~~~~~~l~~~l~~~~~~~~IIFc~tr~~~e~la~~L~~~  259 (607)
T PRK11057        180 LTATADDTTRQDIVRLLGLNDPLIQISSFDRPNIRYTLVEKFKPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSR  259 (607)
T ss_pred             EecCCChhHHHHHHHHhCCCCeEEEECCCCCCcceeeeeeccchHHHHHHHHHhcCCCCEEEEECcHHHHHHHHHHHHhC
Confidence                        0                               000011234456789999999999999999999999


Q ss_pred             CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc
Q psy14082        130 RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI  191 (233)
Q Consensus       130 ~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i  191 (233)
                      |+++..+||+|++++|.++++.|+.|+.+|||||+++++|+|+|+|++|||||+|.|.+.|+
T Consensus       260 g~~v~~~Ha~l~~~~R~~i~~~F~~g~~~VLVaT~a~~~GIDip~V~~VI~~d~P~s~~~y~  321 (607)
T PRK11057        260 GISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYY  321 (607)
T ss_pred             CCCEEEecCCCCHHHHHHHHHHHHCCCCCEEEEechhhccCCCCCcCEEEEeCCCCCHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999998777

>KOG0337|consensus

Probab=99.97  E-value=6.3e-31  Score=218.53  Aligned_cols=216  Identities=27%  Similarity=0.331  Sum_probs=172.8

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~g   78 (233)
                      .||.++.|+|+...|-||||||+||++|+++++....    ..|.++||++|||||+.|+.+..+.+  +.++++++++|
T Consensus        51 TipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s----~~g~RalilsptreLa~qtlkvvkdlgrgt~lr~s~~~g  126 (529)
T KOG0337|consen   51 TIPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHS----QTGLRALILSPTRELALQTLKVVKDLGRGTKLRQSLLVG  126 (529)
T ss_pred             cccceeeccccceeeecCCcchhhHHHHHHHHHhhcc----ccccceeeccCcHHHHHHHHHHHHHhccccchhhhhhcc
Confidence            4899999999999999999999999999999997642    45789999999999999999999999  67889999999


Q ss_pred             CCCC---------CCeeEEe------------------------------------------ccc---------------
Q psy14082         79 GTPK---------GPQDCLP------------------------------------------LHR---------------   92 (233)
Q Consensus        79 g~~~---------~~~~lv~------------------------------------------l~r---------------   92 (233)
                      |-+.         ++++++|                                          +.|               
T Consensus       127 gD~~eeqf~~l~~npDii~ATpgr~~h~~vem~l~l~sveyVVfdEadrlfemgfqeql~e~l~rl~~~~QTllfSatlp  206 (529)
T KOG0337|consen  127 GDSIEEQFILLNENPDIIIATPGRLLHLGVEMTLTLSSVEYVVFDEADRLFEMGFQEQLHEILSRLPESRQTLLFSATLP  206 (529)
T ss_pred             cchHHHHHHHhccCCCEEEecCceeeeeehheeccccceeeeeehhhhHHHhhhhHHHHHHHHHhCCCcceEEEEeccCc
Confidence            8554         5666776                                          000               


Q ss_pred             --hhhhchH-------------------------------------HHhcC--CCCeEEEEecchhHHHHHHHHHhhCCC
Q psy14082         93 --FVFNCQY-------------------------------------EMAKN--PAFKVIVFVETKKKVEDITRALRRERH  131 (233)
Q Consensus        93 --~~~~~~~-------------------------------------~~~~~--~~~k~iIf~~~~~~~~~l~~~L~~~~~  131 (233)
                        +++..+.                                     .+..+  ...++++|+.|..+++.+...|...|+
T Consensus       207 ~~lv~fakaGl~~p~lVRldvetkise~lk~~f~~~~~a~K~aaLl~il~~~~~~~~t~vf~~tk~hve~~~~ll~~~g~  286 (529)
T KOG0337|consen  207 RDLVDFAKAGLVPPVLVRLDVETKISELLKVRFFRVRKAEKEAALLSILGGRIKDKQTIVFVATKHHVEYVRGLLRDFGG  286 (529)
T ss_pred             hhhHHHHHccCCCCceEEeehhhhcchhhhhheeeeccHHHHHHHHHHHhccccccceeEEecccchHHHHHHHHHhcCC
Confidence              0000000                                     11122  345899999999999999999999999


Q ss_pred             eeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCcc---ccc---------ceeeEEee
Q psy14082        132 SAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSAN---HNI---------SQVIEVVQ  199 (233)
Q Consensus       132 ~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~---~~i---------~~~~~~~~  199 (233)
                      .+..++|.|++..|...+++|+.+...+||.||+++||+|+|-.+-|||||+|.+..   |++         |++.+++.
T Consensus       287 ~~s~iysslD~~aRk~~~~~F~~~k~~~lvvTdvaaRG~diplldnvinyd~p~~~klFvhRVgr~aragrtg~aYs~V~  366 (529)
T KOG0337|consen  287 EGSDIYSSLDQEARKINGRDFRGRKTSILVVTDVAARGLDIPLLDNVINYDFPPDDKLFVHRVGRVARAGRTGRAYSLVA  366 (529)
T ss_pred             CccccccccChHhhhhccccccCCccceEEEehhhhccCCCccccccccccCCCCCceEEEEecchhhccccceEEEEEe
Confidence            999999999999999999999999999999999999999999999999999998876   333         56777787


Q ss_pred             cchHHHHHHHHHHhhcCcccccc
Q psy14082        200 DYEKEKRLFSLIRELGKYTLITQ  222 (233)
Q Consensus       200 ~~~~~~~~~~~i~~~~~~~~~~~  222 (233)
                      +.+ ...++ .|....+..+.+.
T Consensus       367 ~~~-~~yl~-DL~lflgr~~~~~  387 (529)
T KOG0337|consen  367 STD-DPYLL-DLQLFLGRPLIFA  387 (529)
T ss_pred             ccc-chhhh-hhhhhcCCceeec
Confidence            643 23333 3333344444433

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.97  E-value=3.7e-30  Score=233.49  Aligned_cols=178  Identities=16%  Similarity=0.144  Sum_probs=146.2

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCC
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGT   80 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~   80 (233)
                      |||.++.|+|+++.+|||+|||++|++|++..           +..++|++|+++|+.|..+.++.+  ++.+..+.++.
T Consensus        21 ~i~~il~g~dvlv~~PTG~GKTl~y~lpal~~-----------~g~~lVisPl~sL~~dq~~~l~~~--gi~~~~~~s~~   87 (591)
T TIGR01389        21 IISHVLDGRDVLVVMPTGGGKSLCYQVPALLL-----------KGLTVVISPLISLMKDQVDQLRAA--GVAAAYLNSTL   87 (591)
T ss_pred             HHHHHHcCCCEEEEcCCCccHhHHHHHHHHHc-----------CCcEEEEcCCHHHHHHHHHHHHHc--CCcEEEEeCCC
Confidence            46788999999999999999999999999841           235899999999999999999887  56677676664


Q ss_pred             CCC-------------CeeEEe-----------------------------c-----------cc---------------
Q psy14082         81 PKG-------------PQDCLP-----------------------------L-----------HR---------------   92 (233)
Q Consensus        81 ~~~-------------~~~lv~-----------------------------l-----------~r---------------   92 (233)
                      +.+             .++++.                             +           .+               
T Consensus        88 ~~~~~~~~~~~l~~~~~~il~~tpe~l~~~~~~~~l~~~~l~~iViDEaH~i~~~g~~frp~y~~l~~l~~~~~~~~vi~  167 (591)
T TIGR01389        88 SAKEQQDIEKALVNGELKLLYVAPERLEQDYFLNMLQRIPIALVAVDEAHCVSQWGHDFRPEYQRLGSLAERFPQVPRIA  167 (591)
T ss_pred             CHHHHHHHHHHHhCCCCCEEEEChhHhcChHHHHHHhcCCCCEEEEeCCcccccccCccHHHHHHHHHHHHhCCCCCEEE
Confidence            321             122222                             0           00               


Q ss_pred             -------------------------------------------hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhC
Q psy14082         93 -------------------------------------------FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRE  129 (233)
Q Consensus        93 -------------------------------------------~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~  129 (233)
                                                                 ....+.+.+....+.++||||++++.++.+++.|...
T Consensus       168 lTAT~~~~~~~~i~~~l~~~~~~~~~~~~~r~nl~~~v~~~~~~~~~l~~~l~~~~~~~~IIf~~sr~~~e~la~~L~~~  247 (591)
T TIGR01389       168 LTATADAETRQDIRELLRLADANEFITSFDRPNLRFSVVKKNNKQKFLLDYLKKHRGQSGIIYASSRKKVEELAERLESQ  247 (591)
T ss_pred             EEeCCCHHHHHHHHHHcCCCCCCeEecCCCCCCcEEEEEeCCCHHHHHHHHHHhcCCCCEEEEECcHHHHHHHHHHHHhC
Confidence                                                       0011111344445789999999999999999999999


Q ss_pred             CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc
Q psy14082        130 RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI  191 (233)
Q Consensus       130 ~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i  191 (233)
                      |+++..+||+|+.++|..+++.|.+|+.+|||||+++++|+|+|++++|||||+|.|.+.|+
T Consensus       248 g~~~~~~H~~l~~~~R~~i~~~F~~g~~~vlVaT~a~~~GID~p~v~~VI~~~~p~s~~~y~  309 (591)
T TIGR01389       248 GISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLESYY  309 (591)
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEechhhccCcCCCCCEEEEcCCCCCHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999998776

The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ.

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.96  E-value=7e-29  Score=227.50  Aligned_cols=168  Identities=20%  Similarity=0.194  Sum_probs=138.9

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhc--CCcEEEEEcCCCC----
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSS--ALRNICIFGGTPK----   82 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~--~~~~~~~~gg~~~----   82 (233)
                      .+.+++++||||||++|++|++..+.        ++.+++|++||++||.|+++.++++..  ++++.+++|+.+.    
T Consensus       283 ~~~Ll~~~TGSGKT~va~~~il~~~~--------~g~q~lilaPT~~LA~Q~~~~l~~l~~~~~i~v~ll~G~~~~~~r~  354 (681)
T PRK10917        283 MNRLLQGDVGSGKTVVAALAALAAIE--------AGYQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERR  354 (681)
T ss_pred             ceEEEECCCCCcHHHHHHHHHHHHHH--------cCCeEEEEeccHHHHHHHHHHHHHHHhhcCcEEEEEcCCCCHHHHH
Confidence            47999999999999999999998873        477899999999999999999999843  5899999999762    


Q ss_pred             ---------CCeeEEe----c------cc---------------------------------------------------
Q psy14082         83 ---------GPQDCLP----L------HR---------------------------------------------------   92 (233)
Q Consensus        83 ---------~~~~lv~----l------~r---------------------------------------------------   92 (233)
                               +.+++||    +      ++                                                   
T Consensus       355 ~~~~~l~~g~~~IvVgT~~ll~~~v~~~~l~lvVIDE~Hrfg~~qr~~l~~~~~~~~iL~~SATp~prtl~~~~~g~~~~  434 (681)
T PRK10917        355 EILEAIASGEADIVIGTHALIQDDVEFHNLGLVIIDEQHRFGVEQRLALREKGENPHVLVMTATPIPRTLAMTAYGDLDV  434 (681)
T ss_pred             HHHHHHhCCCCCEEEchHHHhcccchhcccceEEEechhhhhHHHHHHHHhcCCCCCEEEEeCCCCHHHHHHHHcCCCce
Confidence                     3566777    0      00                                                   


Q ss_pred             -------------------------hhhhchHHHhcCCCCeEEEEecch--------hHHHHHHHHHhhC--CCeeEEEe
Q psy14082         93 -------------------------FVFNCQYEMAKNPAFKVIVFVETK--------KKVEDITRALRRE--RHSAICIH  137 (233)
Q Consensus        93 -------------------------~~~~~~~~~~~~~~~k~iIf~~~~--------~~~~~l~~~L~~~--~~~~~~~~  137 (233)
                                               ++..+.+  ....+.+++|||+..        ..++.+++.|.+.  ++++..+|
T Consensus       435 s~i~~~p~~r~~i~~~~~~~~~~~~~~~~i~~--~~~~g~q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~~~~~v~~lH  512 (681)
T PRK10917        435 SVIDELPPGRKPITTVVIPDSRRDEVYERIRE--EIAKGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLH  512 (681)
T ss_pred             EEEecCCCCCCCcEEEEeCcccHHHHHHHHHH--HHHcCCcEEEEEcccccccchhHHHHHHHHHHHHHHCCCCcEEEEe
Confidence                                     0011111  114678999999954        4566778888765  47899999


Q ss_pred             CCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCC
Q psy14082        138 GDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLS  186 (233)
Q Consensus       138 ~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~  186 (233)
                      |+|++++|..++++|++|+.+|||||+++++|+|+|++++||+||.|..
T Consensus       513 G~m~~~eR~~i~~~F~~g~~~ILVaT~vie~GiDip~v~~VIi~~~~r~  561 (681)
T PRK10917        513 GRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPNATVMVIENAERF  561 (681)
T ss_pred             CCCCHHHHHHHHHHHHcCCCCEEEECcceeeCcccCCCcEEEEeCCCCC
Confidence            9999999999999999999999999999999999999999999999974

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

Probab=99.96  E-value=9.9e-29  Score=224.63  Aligned_cols=195  Identities=20%  Similarity=0.208  Sum_probs=162.6

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~g   78 (233)
                      |||.+.+|++++++||||||||+|..+|+++.+....+.+...+..+|+++|.|+|...+...++.+  ..++.+..-+|
T Consensus        30 a~~~i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIsPLkALn~Di~~rL~~~~~~~G~~v~vRhG  109 (814)
T COG1201          30 AIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLKALNNDIRRRLEEPLRELGIEVAVRHG  109 (814)
T ss_pred             HHHHHhCCCceEEEcCCCCChHHHHHHHHHHHHHhccCCCCCCceEEEEeCcHHHHHHHHHHHHHHHHHHcCCccceecC
Confidence            6889999999999999999999999999999999874344456899999999999999999999998  56788899999


Q ss_pred             CCCC---------CCeeEEe--------------------------------------------ccchhhhch-------
Q psy14082         79 GTPK---------GPQDCLP--------------------------------------------LHRFVFNCQ-------   98 (233)
Q Consensus        79 g~~~---------~~~~lv~--------------------------------------------l~r~~~~~~-------   98 (233)
                      +++.         -++|+|.                                            |.|+..++.       
T Consensus       110 DT~~~er~r~~~~PPdILiTTPEsL~lll~~~~~r~~l~~vr~VIVDEiHel~~sKRG~~Lsl~LeRL~~l~~~~qRIGL  189 (814)
T COG1201         110 DTPQSEKQKMLKNPPHILITTPESLAILLNSPKFRELLRDVRYVIVDEIHALAESKRGVQLALSLERLRELAGDFQRIGL  189 (814)
T ss_pred             CCChHHhhhccCCCCcEEEeChhHHHHHhcCHHHHHHhcCCcEEEeehhhhhhccccchhhhhhHHHHHhhCcccEEEee
Confidence            8765         3445555                                            111100000       


Q ss_pred             -------------------------------------------------------H-HHhcCCCCeEEEEecchhHHHHH
Q psy14082         99 -------------------------------------------------------Y-EMAKNPAFKVIVFVETKKKVEDI  122 (233)
Q Consensus        99 -------------------------------------------------------~-~~~~~~~~k~iIf~~~~~~~~~l  122 (233)
                                                                             . .........++||+||+..++.+
T Consensus       190 SATV~~~~~varfL~g~~~~~~Iv~~~~~k~~~i~v~~p~~~~~~~~~~~~~~~~~i~~~v~~~~ttLIF~NTR~~aE~l  269 (814)
T COG1201         190 SATVGPPEEVAKFLVGFGDPCEIVDVSAAKKLEIKVISPVEDLIYDEELWAALYERIAELVKKHRTTLIFTNTRSGAERL  269 (814)
T ss_pred             hhccCCHHHHHHHhcCCCCceEEEEcccCCcceEEEEecCCccccccchhHHHHHHHHHHHhhcCcEEEEEeChHHHHHH
Confidence                                                                   0 11222444899999999999999


Q ss_pred             HHHHhhCC-CeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCcc---cccceee
Q psy14082        123 TRALRRER-HSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSAN---HNISQVI  195 (233)
Q Consensus       123 ~~~L~~~~-~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~---~~i~~~~  195 (233)
                      +..|++.+ ..+..+||+++.+.|..+.++|++|+.+.+|||+.++-|||+.++|.||+|+.|.+.+   |+|||++
T Consensus       270 ~~~L~~~~~~~i~~HHgSlSre~R~~vE~~lk~G~lravV~TSSLELGIDiG~vdlVIq~~SP~sV~r~lQRiGRsg  346 (814)
T COG1201         270 AFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSLELGIDIGDIDLVIQLGSPKSVNRFLQRIGRAG  346 (814)
T ss_pred             HHHHHHhcCCceeeecccccHHHHHHHHHHHhcCCceEEEEccchhhccccCCceEEEEeCCcHHHHHHhHhccccc
Confidence            99999887 8899999999999999999999999999999999999999999999999999999987   6665443

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.96  E-value=1.3e-28  Score=229.81  Aligned_cols=170  Identities=19%  Similarity=0.144  Sum_probs=141.1

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhc--CCcEEEEEcCCCC---
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSS--ALRNICIFGGTPK---   82 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~--~~~~~~~~gg~~~---   82 (233)
                      +.|.+++|+||||||++|++|++..+.        .+.+++||+||++||.|+++.+++++.  ++++..++|+.+.   
T Consensus       472 ~~d~Ll~adTGsGKT~val~a~l~al~--------~g~qvlvLvPT~~LA~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~  543 (926)
T TIGR00580       472 PMDRLVCGDVGFGKTEVAMRAAFKAVL--------DGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQ  543 (926)
T ss_pred             cCCEEEECCCCccHHHHHHHHHHHHHH--------hCCeEEEEeCcHHHHHHHHHHHHHHhccCCcEEEEEeccccHHHH
Confidence            479999999999999999999998874        357899999999999999999999843  5677888887542   


Q ss_pred             ----------CCeeEEeccc------------------------------------------------------------
Q psy14082         83 ----------GPQDCLPLHR------------------------------------------------------------   92 (233)
Q Consensus        83 ----------~~~~lv~l~r------------------------------------------------------------   92 (233)
                                +.+++||-.+                                                            
T Consensus       544 ~~~~~~l~~g~~dIVIGTp~ll~~~v~f~~L~llVIDEahrfgv~~~~~L~~~~~~~~vL~~SATpiprtl~~~l~g~~d  623 (926)
T TIGR00580       544 NEILKELASGKIDILIGTHKLLQKDVKFKDLGLLIIDEEQRFGVKQKEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRD  623 (926)
T ss_pred             HHHHHHHHcCCceEEEchHHHhhCCCCcccCCEEEeecccccchhHHHHHHhcCCCCCEEEEecCCCHHHHHHHHhcCCC
Confidence                      3567777000                                                            


Q ss_pred             -----------------hhh----hchHH--HhcCCCCeEEEEecchhHHHHHHHHHhhC--CCeeEEEeCCCCHHHHHH
Q psy14082         93 -----------------FVF----NCQYE--MAKNPAFKVIVFVETKKKVEDITRALRRE--RHSAICIHGDKTQQDRDY  147 (233)
Q Consensus        93 -----------------~~~----~~~~~--~~~~~~~k~iIf~~~~~~~~~l~~~L~~~--~~~~~~~~~~~~~~~r~~  147 (233)
                                       +..    .+.+.  .....++++++||+++++++.+++.|++.  ++++..+||+|++++|..
T Consensus       624 ~s~I~~~p~~R~~V~t~v~~~~~~~i~~~i~~el~~g~qv~if~n~i~~~e~l~~~L~~~~p~~~v~~lHG~m~~~eRe~  703 (926)
T TIGR00580       624 LSIIATPPEDRLPVRTFVMEYDPELVREAIRRELLRGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEE  703 (926)
T ss_pred             cEEEecCCCCccceEEEEEecCHHHHHHHHHHHHHcCCeEEEEECCcHHHHHHHHHHHHhCCCCeEEEecCCCCHHHHHH
Confidence                             000    00000  11235689999999999999999999885  789999999999999999


Q ss_pred             HHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCC
Q psy14082        148 VLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQL  185 (233)
Q Consensus       148 ~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~  185 (233)
                      ++++|++|+.+|||||+++++|+|+|++++||++|.|.
T Consensus       704 im~~F~~Gk~~ILVaT~iie~GIDIp~v~~VIi~~a~~  741 (926)
T TIGR00580       704 VMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADK  741 (926)
T ss_pred             HHHHHHcCCCCEEEECChhhcccccccCCEEEEecCCC
Confidence            99999999999999999999999999999999999875

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.

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.96  E-value=9.6e-29  Score=234.91  Aligned_cols=186  Identities=17%  Similarity=0.116  Sum_probs=145.3

Q ss_pred             CCCCCCCC------CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhc--CCc
Q psy14082          1 MLPPSESG------CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSS--ALR   72 (233)
Q Consensus         1 aip~~~~g------~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~--~~~   72 (233)
                      |||.++.+      .|++++++||+|||.+|+.+++..+.        .+.+++||+||++||.|+++.+++.+.  +++
T Consensus       608 aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~--------~g~qvlvLvPT~eLA~Q~~~~f~~~~~~~~v~  679 (1147)
T PRK10689        608 AINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVE--------NHKQVAVLVPTTLLAQQHYDNFRDRFANWPVR  679 (1147)
T ss_pred             HHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHH--------cCCeEEEEeCcHHHHHHHHHHHHHhhccCCce
Confidence            34555555      89999999999999999988877653        477899999999999999999998643  567


Q ss_pred             EEEEEcCCCC-------------CCeeEEeccc-----------------------------------------------
Q psy14082         73 NICIFGGTPK-------------GPQDCLPLHR-----------------------------------------------   92 (233)
Q Consensus        73 ~~~~~gg~~~-------------~~~~lv~l~r-----------------------------------------------   92 (233)
                      +.++.|+.+.             ..+++||-.+                                               
T Consensus       680 i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL~~~v~~~~L~lLVIDEahrfG~~~~e~lk~l~~~~qvLl~SATpi  759 (1147)
T PRK10689        680 IEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLIVDEEHRFGVRHKERIKAMRADVDILTLTATPI  759 (1147)
T ss_pred             EEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHHhCCCCHhhCCEEEEechhhcchhHHHHHHhcCCCCcEEEEcCCCC
Confidence            7788876443             3466777000                                               


Q ss_pred             -----------------------------hhhh-----c-hH-HHhcCCCCeEEEEecchhHHHHHHHHHhhC--CCeeE
Q psy14082         93 -----------------------------FVFN-----C-QY-EMAKNPAFKVIVFVETKKKVEDITRALRRE--RHSAI  134 (233)
Q Consensus        93 -----------------------------~~~~-----~-~~-~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~--~~~~~  134 (233)
                                                   ++..     . .. ...-..++++++|||+++.++.+++.|.+.  +.++.
T Consensus       760 prtl~l~~~gl~d~~~I~~~p~~r~~v~~~~~~~~~~~~k~~il~el~r~gqv~vf~n~i~~ie~la~~L~~~~p~~~v~  839 (1147)
T PRK10689        760 PRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSLVVREAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIA  839 (1147)
T ss_pred             HHHHHHHHhhCCCcEEEecCCCCCCCceEEEEecCcHHHHHHHHHHHhcCCeEEEEECCHHHHHHHHHHHHHhCCCCcEE
Confidence                                         0000     0 00 111224579999999999999999999887  78899


Q ss_pred             EEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEE-----EecCCCCcccccceee
Q psy14082        135 CIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVN-----IGSLQLSANHNISQVI  195 (233)
Q Consensus       135 ~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI-----~~d~P~~~~~~i~~~~  195 (233)
                      .+||+|++++|.+++++|++|+.+|||||+++++|+|+|++++||     |||+|. .-|++||++
T Consensus       840 ~lHG~m~q~eRe~im~~Fr~Gk~~VLVaTdIierGIDIP~v~~VIi~~ad~fglaq-~~Qr~GRvG  904 (1147)
T PRK10689        840 IGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQ-LHQLRGRVG  904 (1147)
T ss_pred             EEeCCCCHHHHHHHHHHHHhcCCCEEEECchhhcccccccCCEEEEecCCCCCHHH-HHHHhhccC
Confidence            999999999999999999999999999999999999999999999     666653 335555443

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.96  E-value=7.6e-28  Score=230.74  Aligned_cols=179  Identities=20%  Similarity=0.168  Sum_probs=140.3

Q ss_pred             EecCCCCCchHHhHHHHHHhhhccCCC-----CCCCCceEEEEcCcHHHHHHHHHHHHHh--------------hcCCcE
Q psy14082         13 SKITNYLLSPPQYMLPAAVHISHQEPV-----KQGDGPIALVLAPTRELAQQIQTVAKEF--------------SSALRN   73 (233)
Q Consensus        13 ~~a~tGsGKT~~~~lp~l~~l~~~~~~-----~~~~~~~~lil~PtreL~~Q~~~~~~~~--------------~~~~~~   73 (233)
                      ++||||||||++|.+|++++++.....     ...++.++|||+|+|+|+.|+++.++..              ..++++
T Consensus         1 V~APTGSGKTLAA~LpaL~~Ll~~~~~~~~~~~~~~~~raLYISPLKALa~Dv~~~L~~pl~~i~~~~~~~g~~~~~i~V   80 (1490)
T PRK09751          1 VIAPTGSGKTLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKALGTDVQRNLQIPLKGIADERRRRGETEVNLRV   80 (1490)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHhcccccccccccCCCCEEEEEeChHHHHHHHHHHHHHHHHhhhhhhhhcccccCceEE
Confidence            479999999999999999999865311     1134689999999999999999998752              136789


Q ss_pred             EEEEcCCCC---------CCeeEEe-------------------------------------------ccc---------
Q psy14082         74 ICIFGGTPK---------GPQDCLP-------------------------------------------LHR---------   92 (233)
Q Consensus        74 ~~~~gg~~~---------~~~~lv~-------------------------------------------l~r---------   92 (233)
                      ...+|+.+.         .++|+|+                                           +.|         
T Consensus        81 ~vrtGDt~~~eR~rll~~ppdILVTTPEsL~~LLtsk~r~~L~~Vr~VIVDE~H~L~g~kRG~~Lel~LeRL~~l~~~~~  160 (1490)
T PRK09751         81 GIRTGDTPAQERSKLTRNPPDILITTPESLYLMLTSRARETLRGVETVIIDEVHAVAGSKRGAHLALSLERLDALLHTSA  160 (1490)
T ss_pred             EEEECCCCHHHHHHHhcCCCCEEEecHHHHHHHHhhhhhhhhccCCEEEEecHHHhcccccccHHHHHHHHHHHhCCCCC
Confidence            999998664         3567777                                           000         


Q ss_pred             -----------------hh--------------------------hhc-------------------------h-HHH-h
Q psy14082         93 -----------------FV--------------------------FNC-------------------------Q-YEM-A  102 (233)
Q Consensus        93 -----------------~~--------------------------~~~-------------------------~-~~~-~  102 (233)
                                       ++                          +..                         . ..+ .
T Consensus       161 QrIgLSATI~n~eevA~~L~g~~pv~Iv~~~~~r~~~l~v~vp~~d~~~~~~~~~~~~~~~~~~r~~~i~~~v~~~il~~  240 (1490)
T PRK09751        161 QRIGLSATVRSASDVAAFLGGDRPVTVVNPPAMRHPQIRIVVPVANMDDVSSVASGTGEDSHAGREGSIWPYIETGILDE  240 (1490)
T ss_pred             eEEEEEeeCCCHHHHHHHhcCCCCEEEECCCCCcccceEEEEecCchhhccccccccccccchhhhhhhhHHHHHHHHHH
Confidence                             00                          000                         0 000 0


Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhCC---------------------------------CeeEEEeCCCCHHHHHHHH
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRER---------------------------------HSAICIHGDKTQQDRDYVL  149 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~~---------------------------------~~~~~~~~~~~~~~r~~~~  149 (233)
                      .....++||||||++.++.++..|.+..                                 ..+.++||+|++++|..+.
T Consensus       241 i~~~~stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~HHGsLSkeeR~~IE  320 (1490)
T PRK09751        241 VLRHRSTIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVDAAHFESTSGATSNRVQSSDVFIARSHHGSVSKEQRAITE  320 (1490)
T ss_pred             HhcCCCEEEECCCHHHHHHHHHHHHHhhhhhccccccccchhhhhhhccccchhccccccceeeeeccccCCHHHHHHHH
Confidence            1235789999999999999999997531                                 1256789999999999999


Q ss_pred             HHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc
Q psy14082        150 NDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI  191 (233)
Q Consensus       150 ~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i  191 (233)
                      +.|++|+.++||||+.+++|||++++++|||||.|.+...|+
T Consensus       321 ~~fK~G~LrvLVATssLELGIDIg~VDlVIq~gsP~sVas~L  362 (1490)
T PRK09751        321 QALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGL  362 (1490)
T ss_pred             HHHHhCCceEEEeCcHHHccCCcccCCEEEEeCCCCCHHHHH
Confidence            999999999999999999999999999999999999988555

>PRK09401 reverse gyrase; Reviewed

Probab=99.95  E-value=7.3e-28  Score=229.39  Aligned_cols=186  Identities=15%  Similarity=0.166  Sum_probs=142.4

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh--cCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS--SALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~--~~~~~~~~~g   78 (233)
                      ++|.++.|+|++++||||||||+ |++|++..+..       +++++|||+|||||+.|+++.++.+.  .++.+..++|
T Consensus        88 ~i~~il~g~dv~i~ApTGsGKT~-f~l~~~~~l~~-------~g~~alIL~PTreLa~Qi~~~l~~l~~~~~~~~~~~~g  159 (1176)
T PRK09401         88 WAKRLLLGESFAIIAPTGVGKTT-FGLVMSLYLAK-------KGKKSYIIFPTRLLVEQVVEKLEKFGEKVGCGVKILYY  159 (1176)
T ss_pred             HHHHHHCCCcEEEEcCCCCCHHH-HHHHHHHHHHh-------cCCeEEEEeccHHHHHHHHHHHHHHhhhcCceEEEEEc
Confidence            46788999999999999999995 67776665532       37899999999999999999999993  3566777776


Q ss_pred             CCC---------------CCCeeEEe----------------------------cc------c------h--------hh
Q psy14082         79 GTP---------------KGPQDCLP----------------------------LH------R------F--------VF   95 (233)
Q Consensus        79 g~~---------------~~~~~lv~----------------------------l~------r------~--------~~   95 (233)
                      +.+               .+.+++|+                            ++      +      +        ..
T Consensus       160 ~~~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~~~~~l~~~~~~~lVvDEaD~~L~~~k~id~~l~~lGF~~~~i~~i~~  239 (1176)
T PRK09401        160 HSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFDELPKKKFDFVFVDDVDAVLKSSKNIDKLLYLLGFSEEDIEKAME  239 (1176)
T ss_pred             cCCcchhHHHHHHHHHhcCCCCEEEECHHHHHHHHHhccccccCEEEEEChHHhhhcccchhhHHHhCCCCHHHHHHHHH
Confidence            643               13567777                            10      0      0        00


Q ss_pred             hch-------------------------H---------------------------------------------------
Q psy14082         96 NCQ-------------------------Y---------------------------------------------------   99 (233)
Q Consensus        96 ~~~-------------------------~---------------------------------------------------   99 (233)
                      .+.                         .                                                   
T Consensus       240 ~i~~~~~~~~~~~~i~~l~~~i~~~~~~~~q~ilfSAT~~~~~~~~~l~~~ll~~~v~~~~~~~rnI~~~yi~~~~k~~~  319 (1176)
T PRK09401        240 LIRLKRKYEEIYEKIRELEEKIAELKDKKGVLVVSSATGRPRGNRVKLFRELLGFEVGSPVFYLRNIVDSYIVDEDSVEK  319 (1176)
T ss_pred             hcccccccchhhhHHHHHHHhhhhcccCCceEEEEeCCCCccchHHHHhhccceEEecCcccccCCceEEEEEcccHHHH
Confidence            000                         0                                                   


Q ss_pred             --HHhcCCCCeEEEEecchhH---HHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEe----cccCcCCc
Q psy14082        100 --EMAKNPAFKVIVFVETKKK---VEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVA----TDVAARGL  170 (233)
Q Consensus       100 --~~~~~~~~k~iIf~~~~~~---~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~----T~~~~~Gl  170 (233)
                        .+....+.++||||++++.   ++.+++.|.+.|+++..+||+|     ...+++|++|+.+||||    ||+++||+
T Consensus       320 L~~ll~~l~~~~LIFv~t~~~~~~ae~l~~~L~~~gi~v~~~hg~l-----~~~l~~F~~G~~~VLVatas~tdv~aRGI  394 (1176)
T PRK09401        320 LVELVKRLGDGGLIFVPSDKGKEYAEELAEYLEDLGINAELAISGF-----ERKFEKFEEGEVDVLVGVASYYGVLVRGI  394 (1176)
T ss_pred             HHHHHHhcCCCEEEEEecccChHHHHHHHHHHHHCCCcEEEEeCcH-----HHHHHHHHCCCCCEEEEecCCCCceeecC
Confidence              1112234689999999888   9999999999999999999999     23459999999999999    69999999


Q ss_pred             CCCC-ccEEEEecCCC------Ccc---cccceeeEEee
Q psy14082        171 DVED-VNTVNIGSLQL------SAN---HNISQVIEVVQ  199 (233)
Q Consensus       171 di~~-v~~VI~~d~P~------~~~---~~i~~~~~~~~  199 (233)
                      |+|+ +++|||||+|.      ..+   |++++..++..
T Consensus       395 DiP~~IryVI~y~vP~~~~~~~~~~~~~~~~~r~~~~~~  433 (1176)
T PRK09401        395 DLPERIRYAIFYGVPKFKFSLEEELAPPFLLLRLLSLLP  433 (1176)
T ss_pred             CCCcceeEEEEeCCCCEEEeccccccCHHHHHHHHhhcc
Confidence            9999 89999999998      333   45555554444

>PRK02362 ski2-like helicase; Provisional

Probab=99.95  E-value=2.1e-27  Score=220.19  Aligned_cols=182  Identities=16%  Similarity=0.158  Sum_probs=144.5

Q ss_pred             CCC-CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh-cCCcEEEEEcC
Q psy14082          2 LPP-SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS-SALRNICIFGG   79 (233)
Q Consensus         2 ip~-~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~-~~~~~~~~~gg   79 (233)
                      +|. +..|+|++++||||||||++|.+|+++++.        ++.++||++|+++||.|+++.++++. .++++..++|+
T Consensus        32 i~~~~~~g~nvlv~APTGSGKTlia~lail~~l~--------~~~kal~i~P~raLa~q~~~~~~~~~~~g~~v~~~tGd  103 (737)
T PRK02362         32 VEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIA--------RGGKALYIVPLRALASEKFEEFERFEELGVRVGISTGD  103 (737)
T ss_pred             HHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHh--------cCCcEEEEeChHHHHHHHHHHHHHhhcCCCEEEEEeCC
Confidence            444 578999999999999999999999999884        25689999999999999999999873 37889999998


Q ss_pred             CCC------CCeeEEe--------cc----------------------------------c-------------------
Q psy14082         80 TPK------GPQDCLP--------LH----------------------------------R-------------------   92 (233)
Q Consensus        80 ~~~------~~~~lv~--------l~----------------------------------r-------------------   92 (233)
                      .+.      +.+++|+        ++                                  |                   
T Consensus       104 ~~~~~~~l~~~~IiV~Tpek~~~llr~~~~~l~~v~lvViDE~H~l~d~~rg~~le~il~rl~~~~~~~qii~lSATl~n  183 (737)
T PRK02362        104 YDSRDEWLGDNDIIVATSEKVDSLLRNGAPWLDDITCVVVDEVHLIDSANRGPTLEVTLAKLRRLNPDLQVVALSATIGN  183 (737)
T ss_pred             cCccccccCCCCEEEECHHHHHHHHhcChhhhhhcCEEEEECccccCCCcchHHHHHHHHHHHhcCCCCcEEEEcccCCC
Confidence            654      3456666        00                                  0                   


Q ss_pred             ------hhh--------------------------------------hchHHH--hcCCCCeEEEEecchhHHHHHHHHH
Q psy14082         93 ------FVF--------------------------------------NCQYEM--AKNPAFKVIVFVETKKKVEDITRAL  126 (233)
Q Consensus        93 ------~~~--------------------------------------~~~~~~--~~~~~~k~iIf~~~~~~~~~l~~~L  126 (233)
                            ++.                                      .....+  ....++++||||++++.++.++..|
T Consensus       184 ~~~la~wl~~~~~~~~~rpv~l~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LVF~~sr~~~~~~a~~L  263 (737)
T PRK02362        184 ADELADWLDAELVDSEWRPIDLREGVFYGGAIHFDDSQREVEVPSKDDTLNLVLDTLEEGGQCLVFVSSRRNAEGFAKRA  263 (737)
T ss_pred             HHHHHHHhCCCcccCCCCCCCCeeeEecCCeeccccccccCCCccchHHHHHHHHHHHcCCCeEEEEeCHHHHHHHHHHH
Confidence                  000                                      000001  1125679999999999999998888


Q ss_pred             hhCC------------------------------------CeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCc
Q psy14082        127 RRER------------------------------------HSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGL  170 (233)
Q Consensus       127 ~~~~------------------------------------~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gl  170 (233)
                      .+..                                    ..+.++|++|++.+|..+.+.|++|.++|||||+.+++|+
T Consensus       264 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~L~~~l~~gva~hHagl~~~eR~~ve~~Fr~G~i~VLvaT~tla~Gv  343 (737)
T PRK02362        264 ASALKKTLTAAERAELAELAEEIREVSDTETSKDLADCVAKGAAFHHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGL  343 (737)
T ss_pred             HHHhhhcCCHHHHHHHHHHHHHHHhccCccccHHHHHHHHhCEEeecCCCCHHHHHHHHHHHHcCCCeEEEechhhhhhc
Confidence            6431                                    3578899999999999999999999999999999999999


Q ss_pred             CCCCccEEEE----ec-----CCCCccccc
Q psy14082        171 DVEDVNTVNI----GS-----LQLSANHNI  191 (233)
Q Consensus       171 di~~v~~VI~----~d-----~P~~~~~~i  191 (233)
                      |+|++++||+    ||     .|-+..+|.
T Consensus       344 nlPa~~VVI~~~~~yd~~~g~~~~s~~~y~  373 (737)
T PRK02362        344 NLPARRVIIRDYRRYDGGAGMQPIPVLEYH  373 (737)
T ss_pred             CCCceEEEEecceeecCCCCceeCCHHHHH
Confidence            9999999998    77     466665444

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.95  E-value=5.1e-27  Score=213.84  Aligned_cols=170  Identities=18%  Similarity=0.204  Sum_probs=137.1

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhc--CCcEEEEEcCCCC----
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSS--ALRNICIFGGTPK----   82 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~--~~~~~~~~gg~~~----   82 (233)
                      .+.+++++||||||++|++|++..+.        .+.+++|++||++||.|+++.+++++.  ++++.+++|+.+.    
T Consensus       257 ~~~Ll~g~TGSGKT~va~l~il~~~~--------~g~qvlilaPT~~LA~Q~~~~~~~l~~~~gi~v~lltg~~~~~~r~  328 (630)
T TIGR00643       257 MNRLLQGDVGSGKTLVAALAMLAAIE--------AGYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRK  328 (630)
T ss_pred             ccEEEECCCCCcHHHHHHHHHHHHHH--------cCCcEEEECCHHHHHHHHHHHHHHHhcccCcEEEEEecCCCHHHHH
Confidence            35799999999999999999998873        467899999999999999999999844  6899999998653    


Q ss_pred             ---------CCeeEEe----------ccc-------------------h-------------------------------
Q psy14082         83 ---------GPQDCLP----------LHR-------------------F-------------------------------   93 (233)
Q Consensus        83 ---------~~~~lv~----------l~r-------------------~-------------------------------   93 (233)
                               +.+++||          +++                   +                               
T Consensus       329 ~~~~~i~~g~~~IiVgT~~ll~~~~~~~~l~lvVIDEaH~fg~~qr~~l~~~~~~~~~~~~l~~SATp~prtl~l~~~~~  408 (630)
T TIGR00643       329 ELLETIASGQIHLVVGTHALIQEKVEFKRLALVIIDEQHRFGVEQRKKLREKGQGGFTPHVLVMSATPIPRTLALTVYGD  408 (630)
T ss_pred             HHHHHHhCCCCCEEEecHHHHhccccccccceEEEechhhccHHHHHHHHHhcccCCCCCEEEEeCCCCcHHHHHHhcCC
Confidence                     2356666          000                   0                               


Q ss_pred             -----hhhc-----------------hH---HHh--cCCCCeEEEEecch--------hHHHHHHHHHhhC--CCeeEEE
Q psy14082         94 -----VFNC-----------------QY---EMA--KNPAFKVIVFVETK--------KKVEDITRALRRE--RHSAICI  136 (233)
Q Consensus        94 -----~~~~-----------------~~---~~~--~~~~~k~iIf~~~~--------~~~~~l~~~L~~~--~~~~~~~  136 (233)
                           ++..                 ..   .+.  ...+.+++|||+..        ..++.+++.|.+.  ++.+..+
T Consensus       409 l~~~~i~~~p~~r~~i~~~~~~~~~~~~~~~~i~~~l~~g~q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~~~~~~v~~l  488 (630)
T TIGR00643       409 LDTSIIDELPPGRKPITTVLIKHDEKDIVYEFIEEEIAKGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLL  488 (630)
T ss_pred             cceeeeccCCCCCCceEEEEeCcchHHHHHHHHHHHHHhCCcEEEEEccccccccchHHHHHHHHHHHHhhCCCCcEEEE
Confidence                 0000                 00   111  13567899999876        4566777777653  6789999


Q ss_pred             eCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCC
Q psy14082        137 HGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLS  186 (233)
Q Consensus       137 ~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~  186 (233)
                      ||+|++++|..++++|++|+.+|||||+++++|+|+|++++||+||.|..
T Consensus       489 HG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~GvDiP~v~~VIi~~~~r~  538 (630)
T TIGR00643       489 HGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERF  538 (630)
T ss_pred             eCCCCHHHHHHHHHHHHcCCCCEEEECceeecCcccCCCcEEEEeCCCcC
Confidence            99999999999999999999999999999999999999999999999974

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.95  E-value=1.4e-26  Score=207.33  Aligned_cols=96  Identities=18%  Similarity=0.178  Sum_probs=79.5

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCC---Ccc-----
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVE---DVN-----  176 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~---~v~-----  176 (233)
                      .+.++||||+|++.++.++..|.+.|+++..+||++++  |+..+..|+.+...|+||||+++||+|++   +|.     
T Consensus       472 ~~~pvLIft~t~~~se~L~~~L~~~gi~~~~Lhg~~~~--rE~~ii~~ag~~g~VlVATdmAgRGtDI~l~~~V~~~GGL  549 (656)
T PRK12898        472 QGRPVLVGTRSVAASERLSALLREAGLPHQVLNAKQDA--EEAAIVARAGQRGRITVATNMAGRGTDIKLEPGVAARGGL  549 (656)
T ss_pred             cCCCEEEEeCcHHHHHHHHHHHHHCCCCEEEeeCCcHH--HHHHHHHHcCCCCcEEEEccchhcccCcCCccchhhcCCC
Confidence            45789999999999999999999999999999998664  44555566666678999999999999999   676     


Q ss_pred             EEEEecCCCCccccc------------ceeeEEeecch
Q psy14082        177 TVNIGSLQLSANHNI------------SQVIEVVQDYE  202 (233)
Q Consensus       177 ~VI~~d~P~~~~~~i------------~~~~~~~~~~~  202 (233)
                      +|||||+|.|...|+            |.++.+++..+
T Consensus       550 hVI~~d~P~s~r~y~hr~GRTGRqG~~G~s~~~is~eD  587 (656)
T PRK12898        550 HVILTERHDSARIDRQLAGRCGRQGDPGSYEAILSLED  587 (656)
T ss_pred             EEEEcCCCCCHHHHHHhcccccCCCCCeEEEEEechhH
Confidence            999999999986444            34556777544

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

Probab=99.94  E-value=8.1e-26  Score=192.48  Aligned_cols=117  Identities=27%  Similarity=0.369  Sum_probs=95.2

Q ss_pred             hchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeE-EEe--------CCCCHHHHHHHHHHhhCCCCCEEEecccC
Q psy14082         96 NCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAI-CIH--------GDKTQQDRDYVLNDFRQGKAPILVATDVA  166 (233)
Q Consensus        96 ~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~-~~~--------~~~~~~~r~~~~~~f~~g~~~iLv~T~~~  166 (233)
                      ++.+.+.++.+.++|||++.+++++.+.+.|.+.+.++. .+-        .||+++++.+++++|++|++++||||+++
T Consensus       356 ilke~~~k~~~~RvIVFT~yRdTae~i~~~L~~~~~~~~~rFiGQa~r~~~~GMsQkeQ~eiI~~Fr~Ge~nVLVaTSVg  435 (542)
T COG1111         356 ILKEQLEKNGDSRVIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQKEIIDQFRKGEYNVLVATSVG  435 (542)
T ss_pred             HHHHHHhcCCCceEEEEehhHhHHHHHHHHHHhcCCcceeEEeeccccccccccCHHHHHHHHHHHhcCCceEEEEcccc
Confidence            333366777889999999999999999999999987774 333        36999999999999999999999999999


Q ss_pred             cCCcCCCCccEEEEecCCCCccccc-----------ceeeEEeecch-HHHHHHHHHH
Q psy14082        167 ARGLDVEDVNTVNIGSLQLSANHNI-----------SQVIEVVQDYE-KEKRLFSLIR  212 (233)
Q Consensus       167 ~~Gldi~~v~~VI~~d~P~~~~~~i-----------~~~~~~~~~~~-~~~~~~~~i~  212 (233)
                      ++|+|+|++|.||.|++-.|+..+|           |+++-++.+.. ++.+.+..++
T Consensus       436 EEGLDIp~vDlVifYEpvpSeIR~IQR~GRTGR~r~Grv~vLvt~gtrdeayy~~s~r  493 (542)
T COG1111         436 EEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGRKRKGRVVVLVTEGTRDEAYYYSSRR  493 (542)
T ss_pred             cccCCCCcccEEEEecCCcHHHHHHHhhCccccCCCCeEEEEEecCchHHHHHHHHHH
Confidence            9999999999999999988876444           67777776542 3344443333

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.94  E-value=2.8e-26  Score=204.16  Aligned_cols=189  Identities=14%  Similarity=0.148  Sum_probs=143.2

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh--cCCcEEEEEcC
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS--SALRNICIFGG   79 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~--~~~~~~~~~gg   79 (233)
                      ++.++.+.+.++++|||+|||+++.. +...+..      ....++||||||+||+.||.+.++++.  +...+..+.||
T Consensus       123 v~~~l~~~~~il~apTGsGKT~i~~~-l~~~~~~------~~~~~vLilvpt~eL~~Q~~~~l~~~~~~~~~~~~~i~~g  195 (501)
T PHA02558        123 VYEGLKNNRRLLNLPTSAGKSLIQYL-LSRYYLE------NYEGKVLIIVPTTSLVTQMIDDFVDYRLFPREAMHKIYSG  195 (501)
T ss_pred             HHHHHhcCceEEEeCCCCCHHHHHHH-HHHHHHh------cCCCeEEEEECcHHHHHHHHHHHHHhccccccceeEEecC
Confidence            45667788999999999999997543 3322222      224489999999999999999999982  33455566666


Q ss_pred             CCCC--CeeEEe---------------------------------------------------ccc--------------
Q psy14082         80 TPKG--PQDCLP---------------------------------------------------LHR--------------   92 (233)
Q Consensus        80 ~~~~--~~~lv~---------------------------------------------------l~r--------------   92 (233)
                      ....  .+++|+                                                   +.+              
T Consensus       196 ~~~~~~~~I~VaT~qsl~~~~~~~~~~~~~iIvDEaH~~~~~~~~~il~~~~~~~~~lGLTATp~~~~~~~~~~~~~fG~  275 (501)
T PHA02558        196 TAKDTDAPIVVSTWQSAVKQPKEWFDQFGMVIVDECHLFTGKSLTSIITKLDNCKFKFGLTGSLRDGKANILQYVGLFGD  275 (501)
T ss_pred             cccCCCCCEEEeeHHHHhhchhhhccccCEEEEEchhcccchhHHHHHHhhhccceEEEEeccCCCccccHHHHHHhhCC
Confidence            5542  456555                                                   000              


Q ss_pred             ---------hh---------------h--------------------hchH---------H--HhcCCCCeEEEEecchh
Q psy14082         93 ---------FV---------------F--------------------NCQY---------E--MAKNPAFKVIVFVETKK  117 (233)
Q Consensus        93 ---------~~---------------~--------------------~~~~---------~--~~~~~~~k~iIf~~~~~  117 (233)
                               ++               .                    ++..         .  .....+.+++|||++.+
T Consensus       276 i~~~v~~~~li~~g~l~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~l~~~~~Rn~~I~~~~~~~~~~~~~~lV~~~~~~  355 (501)
T PHA02558        276 IFKPVTTSQLMEEGQVTDLKINSIFLRYPDEDRVKLKGEDYQEEIKYITSHTKRNKWIANLALKLAKKGENTFVMFKYVE  355 (501)
T ss_pred             ceEEecHHHHHhCCCcCCceEEEEeccCCHHHhhhhcccchHHHHHHHhccHHHHHHHHHHHHHHHhcCCCEEEEEEEHH
Confidence                     00               0                    0000         0  01124578999999999


Q ss_pred             HHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEec-ccCcCCcCCCCccEEEEecCCCCcc---cccce
Q psy14082        118 KVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVAT-DVAARGLDVEDVNTVNIGSLQLSAN---HNISQ  193 (233)
Q Consensus       118 ~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T-~~~~~Gldi~~v~~VI~~d~P~~~~---~~i~~  193 (233)
                      +++.+++.|.+.+.++..+||+|++++|..+++.|++|+..+|||| +++++|+|+|++++||++++|.|..   ||+||
T Consensus       356 h~~~L~~~L~~~g~~v~~i~G~~~~~eR~~i~~~~~~~~~~vLvaT~~~l~eG~Dip~ld~vIl~~p~~s~~~~~QriGR  435 (501)
T PHA02558        356 HGKPLYEMLKKVYDKVYYVSGEVDTEDRNEMKKIAEGGKGIIIVASYGVFSTGISIKNLHHVIFAHPSKSKIIVLQSIGR  435 (501)
T ss_pred             HHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHhCCCCeEEEEEcceeccccccccccEEEEecCCcchhhhhhhhhc
Confidence            9999999999999999999999999999999999999999999998 8999999999999999999999876   55555


Q ss_pred             eeEE
Q psy14082        194 VIEV  197 (233)
Q Consensus       194 ~~~~  197 (233)
                      +.+.
T Consensus       436 ~~R~  439 (501)
T PHA02558        436 VLRK  439 (501)
T ss_pred             cccC
Confidence            4443

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

Probab=99.94  E-value=9.3e-27  Score=212.82  Aligned_cols=183  Identities=16%  Similarity=0.201  Sum_probs=137.5

Q ss_pred             CCCCCCCCC-ceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEE-EcCcHHHHHHHHHHHHHhhc---------
Q psy14082          1 MLPPSESGC-QNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALV-LAPTRELAQQIQTVAKEFSS---------   69 (233)
Q Consensus         1 aip~~~~g~-d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~li-l~PtreL~~Q~~~~~~~~~~---------   69 (233)
                      +||.++.|+ ++++++|||||||++|+++.+. +...     ...++.|| ++|||||+.|+++.++++..         
T Consensus        23 ~i~~il~G~~~v~~~apTGSGKTaa~aafll~-~~~~-----~~~~~rLv~~vPtReLa~Qi~~~~~~~~k~l~~~~~~~   96 (844)
T TIGR02621        23 LAERFVAGQPPESCSTPTGLGKTSIIAAWLLA-VEIG-----AKVPRRLVYVVNRRTVVDQVTEEAEKIGERLPDVPEVE   96 (844)
T ss_pred             HHHHHHcCCCcceEecCCCCcccHHHHHhhcc-cccc-----ccccceEEEeCchHHHHHHHHHHHHHHHHHhcccchhh
Confidence            467788998 5788899999999987655553 2221     34566666 66999999999999999932         


Q ss_pred             ----------------CCcEEEEEcCCCC---------CCeeEEe---------cc------------------c-----
Q psy14082         70 ----------------ALRNICIFGGTPK---------GPQDCLP---------LH------------------R-----   92 (233)
Q Consensus        70 ----------------~~~~~~~~gg~~~---------~~~~lv~---------l~------------------r-----   92 (233)
                                      ++++..++||.+.         .++++||         |.                  +     
T Consensus        97 ~~~~~~~~~~~~~~~~~l~v~~l~GG~~~~~q~~~l~~~p~IIVgT~D~i~sr~L~~gYg~~~~~~pi~ag~L~~v~~LV  176 (844)
T TIGR02621        97 AALWALCSTRPEKKDRPLAISTLRGQFADNDEWMLDPHRPAVIVGTVDMIGSRLLFSGYGCGFKSRPLHAGFLGQDALIV  176 (844)
T ss_pred             hhhhhhhccccccccCCeEEEEEECCCChHHHHHhcCCCCcEEEECHHHHcCCccccccccccccccchhhhhccceEEE
Confidence                            3788999999776         3455666         10                  0     


Q ss_pred             ----------------hhhhc---h-----H-------------------------------------------------
Q psy14082         93 ----------------FVFNC---Q-----Y-------------------------------------------------   99 (233)
Q Consensus        93 ----------------~~~~~---~-----~-------------------------------------------------   99 (233)
                                      +...+   .     +                                                 
T Consensus       177 LDEADLd~gF~~~l~~Il~~l~rp~~~rprQtLLFSAT~p~ei~~l~~~~~~~p~~i~V~~~~l~a~ki~q~v~v~~e~K  256 (844)
T TIGR02621       177 HDEAHLEPAFQELLKQIMNEQQRPPDFLPLRVVELTATSRTDGPDRTTLLSAEDYKHPVLKKRLAAKKIVKLVPPSDEKF  256 (844)
T ss_pred             EehhhhccccHHHHHHHHHhcccCcccccceEEEEecCCCccHHHHHHHHccCCceeecccccccccceEEEEecChHHH
Confidence                            11100   0     0                                                 


Q ss_pred             ---------HHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHH-----HHHHHhhC----CC-----
Q psy14082        100 ---------EMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRD-----YVLNDFRQ----GK-----  156 (233)
Q Consensus       100 ---------~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~-----~~~~~f~~----g~-----  156 (233)
                               ......+.++||||||++.++.+++.|++.++  ..+||+|++.+|.     .++++|++    |.     
T Consensus       257 l~~lv~~L~~ll~e~g~~vLVF~NTv~~Aq~L~~~L~~~g~--~lLHG~m~q~dR~~~~~~~il~~Fk~~~~~g~~~~~~  334 (844)
T TIGR02621       257 LSTMVKELNLLMKDSGGAILVFCRTVKHVRKVFAKLPKEKF--ELLTGTLRGAERDDLVKKEIFNRFLPQMLSGSRARPQ  334 (844)
T ss_pred             HHHHHHHHHHHHhhCCCcEEEEECCHHHHHHHHHHHHhcCC--eEeeCCCCHHHHhhHHHHHHHHHHhcccccccccccc
Confidence                     01123567899999999999999999998887  8999999999999     78999987    43     


Q ss_pred             --CCEEEecccCcCCcCCCCccEEEEecCCCC-cccccc
Q psy14082        157 --APILVATDVAARGLDVEDVNTVNIGSLQLS-ANHNIS  192 (233)
Q Consensus       157 --~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~-~~~~i~  192 (233)
                        .+|||||+++++|+|++. ++||++..|.+ ..|++|
T Consensus       335 ~g~~ILVATdVaerGLDId~-d~VI~d~aP~esyIQRiG  372 (844)
T TIGR02621       335 QGTVYLVCTSAGEVGVNISA-DHLVCDLAPFESMQQRFG  372 (844)
T ss_pred             ccceEEeccchhhhcccCCc-ceEEECCCCHHHHHHHhc
Confidence              679999999999999986 89999887742 235554

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.

>PRK00254 ski2-like helicase; Provisional

Probab=99.94  E-value=1.8e-26  Score=213.51  Aligned_cols=186  Identities=16%  Similarity=0.148  Sum_probs=143.7

Q ss_pred             CCC-CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh-hcCCcEEEEEcC
Q psy14082          2 LPP-SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF-SSALRNICIFGG   79 (233)
Q Consensus         2 ip~-~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~-~~~~~~~~~~gg   79 (233)
                      +|. +..|+|++++||||||||++|.+|+++++..       .+.++|+|+|+++|+.|+++.+..+ ..++++..++|+
T Consensus        32 i~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~-------~~~~~l~l~P~~aLa~q~~~~~~~~~~~g~~v~~~~Gd  104 (720)
T PRK00254         32 LKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLR-------EGGKAVYLVPLKALAEEKYREFKDWEKLGLRVAMTTGD  104 (720)
T ss_pred             HHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHh-------cCCeEEEEeChHHHHHHHHHHHHHHhhcCCEEEEEeCC
Confidence            443 6789999999999999999999999998864       2568999999999999999999887 347889999998


Q ss_pred             CCC------CCeeEEe--------cc-------c----------------------------------------------
Q psy14082         80 TPK------GPQDCLP--------LH-------R----------------------------------------------   92 (233)
Q Consensus        80 ~~~------~~~~lv~--------l~-------r----------------------------------------------   92 (233)
                      .+.      +.+++|+        ++       +                                              
T Consensus       105 ~~~~~~~~~~~~IiV~Tpe~~~~ll~~~~~~l~~l~lvViDE~H~l~~~~rg~~le~il~~l~~~~qiI~lSATl~n~~~  184 (720)
T PRK00254        105 YDSTDEWLGKYDIIIATAEKFDSLLRHGSSWIKDVKLVVADEIHLIGSYDRGATLEMILTHMLGRAQILGLSATVGNAEE  184 (720)
T ss_pred             CCCchhhhccCCEEEEcHHHHHHHHhCCchhhhcCCEEEEcCcCccCCccchHHHHHHHHhcCcCCcEEEEEccCCCHHH
Confidence            764      2456666        00       0                                              


Q ss_pred             hhh------------------------------------------hchHHHhcCCCCeEEEEecchhHHHHHHHHHhhC-
Q psy14082         93 FVF------------------------------------------NCQYEMAKNPAFKVIVFVETKKKVEDITRALRRE-  129 (233)
Q Consensus        93 ~~~------------------------------------------~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~-  129 (233)
                      +..                                          .+.+.  -..+.++||||+|++.++.++..|.+. 
T Consensus       185 la~wl~~~~~~~~~rpv~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--i~~~~~vLVF~~sr~~~~~~a~~l~~~~  262 (720)
T PRK00254        185 LAEWLNAELVVSDWRPVKLRKGVFYQGFLFWEDGKIERFPNSWESLVYDA--VKKGKGALVFVNTRRSAEKEALELAKKI  262 (720)
T ss_pred             HHHHhCCccccCCCCCCcceeeEecCCeeeccCcchhcchHHHHHHHHHH--HHhCCCEEEEEcChHHHHHHHHHHHHHH
Confidence            000                                          00000  113578999999999999888776421 


Q ss_pred             --------------------------------CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccE
Q psy14082        130 --------------------------------RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNT  177 (233)
Q Consensus       130 --------------------------------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~  177 (233)
                                                      ...+.++|++|++++|..+.+.|++|.++|||||+.+++|+|+|++++
T Consensus       263 ~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~hHagl~~~eR~~ve~~F~~G~i~VLvaT~tLa~Gvnipa~~v  342 (720)
T PRK00254        263 KRFLTKPELRALKELADSLEENPTNEKLKKALRGGVAFHHAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRV  342 (720)
T ss_pred             HHhcCchhHHHHHHHHHHHhcCCCcHHHHHHHhhCEEEeCCCCCHHHHHHHHHHHHCCCCeEEEeCcHHhhhcCCCceEE
Confidence                                            225889999999999999999999999999999999999999999999


Q ss_pred             EEE-------ecCCCCc----ccccceeeE
Q psy14082        178 VNI-------GSLQLSA----NHNISQVIE  196 (233)
Q Consensus       178 VI~-------~d~P~~~----~~~i~~~~~  196 (233)
                      ||.       |+.|.-+    .|++||+++
T Consensus       343 VI~~~~~~~~~~~~~~~~~~~~Qm~GRAGR  372 (720)
T PRK00254        343 IIRDTKRYSNFGWEDIPVLEIQQMMGRAGR  372 (720)
T ss_pred             EECCceEcCCCCceeCCHHHHHHhhhccCC
Confidence            994       5555422    355555544

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.94  E-value=1.2e-25  Score=205.33  Aligned_cols=97  Identities=15%  Similarity=0.187  Sum_probs=85.2

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCC---CCcc----
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDV---EDVN----  176 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi---~~v~----  176 (233)
                      ..+.++||||+|++.++.++..|.+.|+++..+||+++++++..+.++++.|  +|+||||+++||+|+   |+|.    
T Consensus       426 ~~~~pvLIf~~t~~~se~l~~~L~~~gi~~~~L~~~~~~~e~~~i~~ag~~g--~VlIATdmAgRG~DI~l~~~V~~~GG  503 (790)
T PRK09200        426 ETGRPVLIGTGSIEQSETFSKLLDEAGIPHNLLNAKNAAKEAQIIAEAGQKG--AVTVATNMAGRGTDIKLGEGVHELGG  503 (790)
T ss_pred             hcCCCEEEEeCcHHHHHHHHHHHHHCCCCEEEecCCccHHHHHHHHHcCCCC--eEEEEccchhcCcCCCcccccccccC
Confidence            4688999999999999999999999999999999999999888888887766  799999999999999   6998    


Q ss_pred             -EEEEecCCCCccccc------------ceeeEEeecch
Q psy14082        177 -TVNIGSLQLSANHNI------------SQVIEVVQDYE  202 (233)
Q Consensus       177 -~VI~~d~P~~~~~~i------------~~~~~~~~~~~  202 (233)
                       +||+||+|.|...|+            |.++.|++..+
T Consensus       504 L~VI~~d~p~s~r~y~qr~GRtGR~G~~G~s~~~is~eD  542 (790)
T PRK09200        504 LAVIGTERMESRRVDLQLRGRSGRQGDPGSSQFFISLED  542 (790)
T ss_pred             cEEEeccCCCCHHHHHHhhccccCCCCCeeEEEEEcchH
Confidence             999999999987555            34456777644

>TIGR01054 rgy reverse gyrase

Probab=99.94  E-value=3.7e-26  Score=217.98  Aligned_cols=174  Identities=17%  Similarity=0.227  Sum_probs=137.8

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhc--CCcEE---E
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSS--ALRNI---C   75 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~--~~~~~---~   75 (233)
                      ++|.++.|+|++++||||||||+ |++|++..+..       .++++|||+||||||.|+++.++.+..  ++.+.   .
T Consensus        86 ~i~~il~G~d~vi~ApTGsGKT~-f~l~~~~~l~~-------~g~~vLIL~PTreLa~Qi~~~l~~l~~~~~i~~~~i~~  157 (1171)
T TIGR01054        86 WAKRVLRGDSFAIIAPTGVGKTT-FGLAMSLFLAK-------KGKRCYIILPTTLLVIQVAEKISSLAEKAGVGTVNIGA  157 (1171)
T ss_pred             HHHHHhCCCeEEEECCCCCCHHH-HHHHHHHHHHh-------cCCeEEEEeCHHHHHHHHHHHHHHHHHhcCCceeeeee
Confidence            46788999999999999999996 78888776643       368999999999999999999999943  44433   4


Q ss_pred             EEcCCCC-------------CCeeEEe---------------------------cc------c------h----hhh---
Q psy14082         76 IFGGTPK-------------GPQDCLP---------------------------LH------R------F----VFN---   96 (233)
Q Consensus        76 ~~gg~~~-------------~~~~lv~---------------------------l~------r------~----~~~---   96 (233)
                      ++||.+.             +++++|+                           +.      +      +    +..   
T Consensus       158 ~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~~~l~~~~~~iVvDEaD~~L~~~k~vd~il~llGF~~e~i~~il~  237 (1171)
T TIGR01054       158 YHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDELGPKFDFIFVDDVDALLKASKNVDKLLKLLGFSEELIEKAWK  237 (1171)
T ss_pred             ecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHHHHhcCCCCEEEEeChHhhhhccccHHHHHHHcCCCHHHHHHHHH
Confidence            5677543             2566776                           10      0      0    000   


Q ss_pred             -----------------------chH------------------------------------------------------
Q psy14082         97 -----------------------CQY------------------------------------------------------   99 (233)
Q Consensus        97 -----------------------~~~------------------------------------------------------   99 (233)
                                             +..                                                      
T Consensus       238 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~li~~SAT~~p~~~~~~l~r~ll~~~v~~~~~~~r~I~~~~~~~~~~~~~  317 (1171)
T TIGR01054       238 LIRLRLKLYRALHAKKRLELLEAIPGKKRGCLIVSSATGRPRGKRAKLFRELLGFEVGGGSDTLRNVVDVYVEDEDLKET  317 (1171)
T ss_pred             HhhhccccchHHHHHHHHHHHHhhhhccCcEEEEEeCCCCccccHHHHcccccceEecCccccccceEEEEEecccHHHH
Confidence                                   000                                                      


Q ss_pred             --HHhcCCCCeEEEEecch---hHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEe----cccCcCCc
Q psy14082        100 --EMAKNPAFKVIVFVETK---KKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVA----TDVAARGL  170 (233)
Q Consensus       100 --~~~~~~~~k~iIf~~~~---~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~----T~~~~~Gl  170 (233)
                        .+....+.++||||+++   +.++.++..|.+.|+++..+||+|++    .++++|++|+.++|||    ||+++||+
T Consensus       318 L~~ll~~l~~~~IVFv~t~~~~~~a~~l~~~L~~~g~~a~~lhg~~~~----~~l~~Fr~G~~~vLVata~~tdv~aRGI  393 (1171)
T TIGR01054       318 LLEIVKKLGTGGIVYVSIDYGKEKAEEIAEFLENHGVKAVAYHATKPK----EDYEKFAEGEIDVLIGVASYYGTLVRGL  393 (1171)
T ss_pred             HHHHHHHcCCCEEEEEeccccHHHHHHHHHHHHhCCceEEEEeCCCCH----HHHHHHHcCCCCEEEEeccccCcccccC
Confidence              11122346799999999   99999999999999999999999973    6899999999999999    59999999


Q ss_pred             CCCC-ccEEEEecCCCC
Q psy14082        171 DVED-VNTVNIGSLQLS  186 (233)
Q Consensus       171 di~~-v~~VI~~d~P~~  186 (233)
                      |+|+ |++|||||+|..
T Consensus       394 Dip~~V~~vI~~~~P~~  410 (1171)
T TIGR01054       394 DLPERVRYAVFLGVPKF  410 (1171)
T ss_pred             CCCccccEEEEECCCCE
Confidence            9999 899999999976

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.

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

Probab=99.93  E-value=1.3e-25  Score=197.98  Aligned_cols=187  Identities=20%  Similarity=0.234  Sum_probs=149.8

Q ss_pred             CCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCCC
Q psy14082          3 PPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPK   82 (233)
Q Consensus         3 p~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~   82 (233)
                      -.+++|+|+++..|||+||++||.+|.+-.          .| -+||++|...|.....+.++..  ++.+..+.+..+.
T Consensus        27 ~~~l~g~d~lvvmPTGgGKSlCyQiPAll~----------~G-~TLVVSPLiSLM~DQV~~l~~~--Gi~A~~lnS~l~~   93 (590)
T COG0514          27 DALLSGKDTLVVMPTGGGKSLCYQIPALLL----------EG-LTLVVSPLISLMKDQVDQLEAA--GIRAAYLNSTLSR   93 (590)
T ss_pred             HHHHcCCcEEEEccCCCCcchHhhhHHHhc----------CC-CEEEECchHHHHHHHHHHHHHc--CceeehhhcccCH
Confidence            346789999999999999999999999853          23 6899999888888777777766  6888888877554


Q ss_pred             CCee--------------EEe-----------------------------------------------------------
Q psy14082         83 GPQD--------------CLP-----------------------------------------------------------   89 (233)
Q Consensus        83 ~~~~--------------lv~-----------------------------------------------------------   89 (233)
                      ++..              .++                                                           
T Consensus        94 ~e~~~v~~~l~~g~~klLyisPErl~~~~f~~~L~~~~i~l~vIDEAHCiSqWGhdFRP~Y~~lg~l~~~~~~~p~~AlT  173 (590)
T COG0514          94 EERQQVLNQLKSGQLKLLYISPERLMSPRFLELLKRLPISLVAIDEAHCISQWGHDFRPDYRRLGRLRAGLPNPPVLALT  173 (590)
T ss_pred             HHHHHHHHHHhcCceeEEEECchhhcChHHHHHHHhCCCceEEechHHHHhhcCCccCHhHHHHHHHHhhCCCCCEEEEe
Confidence            2211              222                                                           


Q ss_pred             --------------------------ccc---hhhhch------H--HHh---cCCCCeEEEEecchhHHHHHHHHHhhC
Q psy14082         90 --------------------------LHR---FVFNCQ------Y--EMA---KNPAFKVIVFVETKKKVEDITRALRRE  129 (233)
Q Consensus        90 --------------------------l~r---~~~~~~------~--~~~---~~~~~k~iIf~~~~~~~~~l~~~L~~~  129 (233)
                                                ..|   .+.+..      +  .+.   .......||||.|++.++.+++.|.+.
T Consensus       174 ATA~~~v~~DI~~~L~l~~~~~~~~sfdRpNi~~~v~~~~~~~~q~~fi~~~~~~~~~~GIIYc~sRk~~E~ia~~L~~~  253 (590)
T COG0514         174 ATATPRVRDDIREQLGLQDANIFRGSFDRPNLALKVVEKGEPSDQLAFLATVLPQLSKSGIIYCLTRKKVEELAEWLRKN  253 (590)
T ss_pred             CCCChHHHHHHHHHhcCCCcceEEecCCCchhhhhhhhcccHHHHHHHHHhhccccCCCeEEEEeeHHhHHHHHHHHHHC
Confidence                                      000   111110      0  122   445566899999999999999999999


Q ss_pred             CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc---c---------eeeEE
Q psy14082        130 RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI---S---------QVIEV  197 (233)
Q Consensus       130 ~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i---~---------~~~~~  197 (233)
                      |+++..+|+||+.++|..+-++|..++.+|+|||.+++.|||-|+|.+|||||+|.|.+.|.   |         .++.+
T Consensus       254 g~~a~~YHaGl~~~eR~~~q~~f~~~~~~iiVAT~AFGMGIdKpdVRfViH~~lP~s~EsYyQE~GRAGRDG~~a~aill  333 (590)
T COG0514         254 GISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAEAILL  333 (590)
T ss_pred             CCceEEecCCCCHHHHHHHHHHHhcCCCcEEEEeccccCccCCCCceEEEEecCCCCHHHHHHHHhhccCCCCcceEEEe
Confidence            99999999999999999999999999999999999999999999999999999999999888   2         55667


Q ss_pred             eecch
Q psy14082        198 VQDYE  202 (233)
Q Consensus       198 ~~~~~  202 (233)
                      +++.+
T Consensus       334 ~~~~D  338 (590)
T COG0514         334 YSPED  338 (590)
T ss_pred             ecccc
Confidence            77644

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.93  E-value=2.6e-25  Score=190.56  Aligned_cols=91  Identities=16%  Similarity=0.305  Sum_probs=76.8

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCCC--eeEEEeCCCCHHHHHHH----HHHhhCCCCCEEEecccCcCCcCCCCccEE
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRERH--SAICIHGDKTQQDRDYV----LNDFRQGKAPILVATDVAARGLDVEDVNTV  178 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~~--~~~~~~~~~~~~~r~~~----~~~f~~g~~~iLv~T~~~~~Gldi~~v~~V  178 (233)
                      .+.++||||+++++++.+++.|++.+.  .+..+||+|++.+|.+.    ++.|++|..++||||+++++|+|++ +++|
T Consensus       221 ~~~~~lVf~~t~~~~~~~~~~L~~~~~~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~~~~ilvaT~~~~~GiDi~-~~~v  299 (358)
T TIGR01587       221 KGGKIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQVIEASLDIS-ADVM  299 (358)
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHhhcCCCeEEEEECCCCHHHHHHHHHHHHHHhcCCCCeEEEECcchhceeccC-CCEE
Confidence            568999999999999999999988765  58999999999999764    8899999999999999999999995 8999


Q ss_pred             EEecCCCC-cccccceeeE
Q psy14082        179 NIGSLQLS-ANHNISQVIE  196 (233)
Q Consensus       179 I~~d~P~~-~~~~i~~~~~  196 (233)
                      |+++.|.+ ..|++||+++
T Consensus       300 i~~~~~~~~~iqr~GR~gR  318 (358)
T TIGR01587       300 ITELAPIDSLIQRLGRLHR  318 (358)
T ss_pred             EEcCCCHHHHHHHhccccC
Confidence            99887732 1244444444

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.

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.93  E-value=2.1e-25  Score=202.18  Aligned_cols=180  Identities=13%  Similarity=0.101  Sum_probs=134.8

Q ss_pred             CCCCCCCCceeEecCCCCCchHH---------hHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh-----
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQ---------YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF-----   67 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~---------~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~-----   67 (233)
                      +|.+..|+|++++|+||||||.+         |++|.+..+....  ....+.+++|++||||||.|+...+.+.     
T Consensus       173 l~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~--~~~~~~~ilvt~PrreLa~qi~~~i~~~vg~~~  250 (675)
T PHA02653        173 FEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKID--PNFIERPIVLSLPRVALVRLHSITLLKSLGFDE  250 (675)
T ss_pred             HHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcc--cccCCcEEEEECcHHHHHHHHHHHHHHHhCccc
Confidence            46778999999999999999987         5556665553211  0134568999999999999999999875     


Q ss_pred             hcCCcEEEEEcCCCC--------CCeeEEe--------cc--------------------------------c-------
Q psy14082         68 SSALRNICIFGGTPK--------GPQDCLP--------LH--------------------------------R-------   92 (233)
Q Consensus        68 ~~~~~~~~~~gg~~~--------~~~~lv~--------l~--------------------------------r-------   92 (233)
                      +.+..+...+||.+.        ..+++++        ++                                +       
T Consensus       251 ~~g~~v~v~~Gg~~~~~~~t~~k~~~Ilv~T~~L~l~~L~~v~~VVIDEaHEr~~~~DllL~llk~~~~~~rq~ILmSAT  330 (675)
T PHA02653        251 IDGSPISLKYGSIPDELINTNPKPYGLVFSTHKLTLNKLFDYGTVIIDEVHEHDQIGDIIIAVARKHIDKIRSLFLMTAT  330 (675)
T ss_pred             cCCceEEEEECCcchHHhhcccCCCCEEEEeCcccccccccCCEEEccccccCccchhHHHHHHHHhhhhcCEEEEEccC
Confidence            235667888888753        1234555        00                                0       


Q ss_pred             -------------------------------hhhh----------ch-------HHHh---cCCCCeEEEEecchhHHHH
Q psy14082         93 -------------------------------FVFN----------CQ-------YEMA---KNPAFKVIVFVETKKKVED  121 (233)
Q Consensus        93 -------------------------------~~~~----------~~-------~~~~---~~~~~k~iIf~~~~~~~~~  121 (233)
                                                     ++..          ..       +.+.   ...++++|||+++++.++.
T Consensus       331 l~~dv~~l~~~~~~p~~I~I~grt~~pV~~~yi~~~~~~~~~~~y~~~~k~~~l~~L~~~~~~~~g~iLVFlpg~~ei~~  410 (675)
T PHA02653        331 LEDDRDRIKEFFPNPAFVHIPGGTLFPISEVYVKNKYNPKNKRAYIEEEKKNIVTALKKYTPPKGSSGIVFVASVSQCEE  410 (675)
T ss_pred             CcHhHHHHHHHhcCCcEEEeCCCcCCCeEEEEeecCcccccchhhhHHHHHHHHHHHHHhhcccCCcEEEEECcHHHHHH
Confidence                                           0000          00       0111   1234689999999999999


Q ss_pred             HHHHHhhC--CCeeEEEeCCCCHHHHHHHHHHh-hCCCCCEEEecccCcCCcCCCCccEEEEec---CCC
Q psy14082        122 ITRALRRE--RHSAICIHGDKTQQDRDYVLNDF-RQGKAPILVATDVAARGLDVEDVNTVNIGS---LQL  185 (233)
Q Consensus       122 l~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f-~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d---~P~  185 (233)
                      +++.|.+.  ++.+..+||+|++.  ++.+++| ++|+.+||||||+++||+|+|+|++||++|   .|.
T Consensus       411 l~~~L~~~~~~~~v~~LHG~Lsq~--eq~l~~ff~~gk~kILVATdIAERGIDIp~V~~VID~G~~k~p~  478 (675)
T PHA02653        411 YKKYLEKRLPIYDFYIIHGKVPNI--DEILEKVYSSKNPSIIISTPYLESSVTIRNATHVYDTGRVYVPE  478 (675)
T ss_pred             HHHHHHhhcCCceEEeccCCcCHH--HHHHHHHhccCceeEEeccChhhccccccCeeEEEECCCccCCC
Confidence            99999887  78999999999975  4667777 789999999999999999999999999999   554

>PRK01172 ski2-like helicase; Provisional

Probab=99.93  E-value=3.5e-25  Score=203.77  Aligned_cols=174  Identities=17%  Similarity=0.192  Sum_probs=136.1

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh-hcCCcEEEEEcCC
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF-SSALRNICIFGGT   80 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~-~~~~~~~~~~gg~   80 (233)
                      ++.+..|++++++||||||||+++.+++++.+..        +.++++++|+++||.|+++.+.++ ..+.++...+|+.
T Consensus        31 i~~l~~~~nvlv~apTGSGKTl~a~lail~~l~~--------~~k~v~i~P~raLa~q~~~~~~~l~~~g~~v~~~~G~~  102 (674)
T PRK01172         31 IEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLA--------GLKSIYIVPLRSLAMEKYEELSRLRSLGMRVKISIGDY  102 (674)
T ss_pred             HHHHhcCCcEEEECCCCchHHHHHHHHHHHHHHh--------CCcEEEEechHHHHHHHHHHHHHHhhcCCeEEEEeCCC
Confidence            4566789999999999999999999999988753        457999999999999999999987 4467888888876


Q ss_pred             CC------CCeeEEe--------ccc------------------------------------------------------
Q psy14082         81 PK------GPQDCLP--------LHR------------------------------------------------------   92 (233)
Q Consensus        81 ~~------~~~~lv~--------l~r------------------------------------------------------   92 (233)
                      +.      ..+++|+        +++                                                      
T Consensus       103 ~~~~~~~~~~dIiv~Tpek~~~l~~~~~~~l~~v~lvViDEaH~l~d~~rg~~le~ll~~~~~~~~~~riI~lSATl~n~  182 (674)
T PRK01172        103 DDPPDFIKRYDVVILTSEKADSLIHHDPYIINDVGLIVADEIHIIGDEDRGPTLETVLSSARYVNPDARILALSATVSNA  182 (674)
T ss_pred             CCChhhhccCCEEEECHHHHHHHHhCChhHHhhcCEEEEecchhccCCCccHHHHHHHHHHHhcCcCCcEEEEeCccCCH
Confidence            53      2345555        000                                                      


Q ss_pred             --hhhh------------------------------------chHHHh--cCCCCeEEEEecchhHHHHHHHHHhhCC--
Q psy14082         93 --FVFN------------------------------------CQYEMA--KNPAFKVIVFVETKKKVEDITRALRRER--  130 (233)
Q Consensus        93 --~~~~------------------------------------~~~~~~--~~~~~k~iIf~~~~~~~~~l~~~L~~~~--  130 (233)
                        +-.+                                    ....+.  ...++++||||++++.++.++..|.+..  
T Consensus       183 ~~la~wl~~~~~~~~~r~vpl~~~i~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~vLVF~~sr~~~~~~a~~L~~~~~~  262 (674)
T PRK01172        183 NELAQWLNASLIKSNFRPVPLKLGILYRKRLILDGYERSQVDINSLIKETVNDGGQVLVFVSSRKNAEDYAEMLIQHFPE  262 (674)
T ss_pred             HHHHHHhCCCccCCCCCCCCeEEEEEecCeeeecccccccccHHHHHHHHHhCCCcEEEEeccHHHHHHHHHHHHHhhhh
Confidence              0000                                    000111  2356799999999999999999886531  


Q ss_pred             -----------------------CeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCC
Q psy14082        131 -----------------------HSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQ  184 (233)
Q Consensus       131 -----------------------~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P  184 (233)
                                             ..+.++||+|++++|..+.+.|++|..+|||||+.+++|+|+|+. .||++|.|
T Consensus       263 ~~~~~~~~~~~~~~~~~L~~~l~~gv~~~hagl~~~eR~~ve~~f~~g~i~VLvaT~~la~Gvnipa~-~VII~~~~  338 (674)
T PRK01172        263 FNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQRRFIEEMFRNRYIKVIVATPTLAAGVNLPAR-LVIVRDIT  338 (674)
T ss_pred             cccccccccccccccHHHHHHHhcCEEEecCCCCHHHHHHHHHHHHcCCCeEEEecchhhccCCCcce-EEEEcCce
Confidence                                   247789999999999999999999999999999999999999986 56666654

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.93  E-value=8.7e-25  Score=202.49  Aligned_cols=172  Identities=13%  Similarity=0.105  Sum_probs=135.9

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh-h--cCCcEEEEEcCCC-
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF-S--SALRNICIFGGTP-   81 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~-~--~~~~~~~~~gg~~-   81 (233)
                      .+++|++++|+||||||.+|.+|+++...        ...+++|++|||++|.|+++.+.+. .  .+..+...+++.+ 
T Consensus        18 ~~~~~vvv~A~TGSGKTt~~pl~lL~~~~--------~~~~ilvlqPrR~aA~qia~rva~~l~~~~g~~VGy~vr~~~~   89 (812)
T PRK11664         18 KTAPQVLLKAPTGAGKSTWLPLQLLQHGG--------INGKIIMLEPRRLAARNVAQRLAEQLGEKPGETVGYRMRAESK   89 (812)
T ss_pred             HhCCCEEEEcCCCCCHHHHHHHHHHHcCC--------cCCeEEEECChHHHHHHHHHHHHHHhCcccCceEEEEecCccc
Confidence            35789999999999999999999997542        2348999999999999999998654 2  2445666666543 


Q ss_pred             --CCCeeEEe--------------ccc-----------------------------------------------------
Q psy14082         82 --KGPQDCLP--------------LHR-----------------------------------------------------   92 (233)
Q Consensus        82 --~~~~~lv~--------------l~r-----------------------------------------------------   92 (233)
                        .+.+++|+              +.+                                                     
T Consensus        90 ~~~~t~I~v~T~G~Llr~l~~d~~L~~v~~IIlDEaHER~l~~Dl~L~ll~~i~~~lr~~lqlilmSATl~~~~l~~~~~  169 (812)
T PRK11664         90 VGPNTRLEVVTEGILTRMIQRDPELSGVGLVILDEFHERSLQADLALALLLDVQQGLRDDLKLLIMSATLDNDRLQQLLP  169 (812)
T ss_pred             cCCCCcEEEEChhHHHHHHhhCCCcCcCcEEEEcCCCccccccchHHHHHHHHHHhCCccceEEEEecCCCHHHHHHhcC
Confidence              23455555              000                                                     


Q ss_pred             -----------------hhh-------------hchHHHhcCCCCeEEEEecchhHHHHHHHHHhh---CCCeeEEEeCC
Q psy14082         93 -----------------FVF-------------NCQYEMAKNPAFKVIVFVETKKKVEDITRALRR---ERHSAICIHGD  139 (233)
Q Consensus        93 -----------------~~~-------------~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~---~~~~~~~~~~~  139 (233)
                                       ++.             .+. .......+++|||+++.+.++.+++.|.+   .++.+..+||+
T Consensus       170 ~~~~I~~~gr~~pV~~~y~~~~~~~~~~~~v~~~l~-~~l~~~~g~iLVFlpg~~ei~~l~~~L~~~~~~~~~v~~Lhg~  248 (812)
T PRK11664        170 DAPVIVSEGRSFPVERRYQPLPAHQRFDEAVARATA-ELLRQESGSLLLFLPGVGEIQRVQEQLASRVASDVLLCPLYGA  248 (812)
T ss_pred             CCCEEEecCccccceEEeccCchhhhHHHHHHHHHH-HHHHhCCCCEEEEcCCHHHHHHHHHHHHHhccCCceEEEeeCC
Confidence                             000             000 11223468899999999999999999987   57889999999


Q ss_pred             CCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCC
Q psy14082        140 KTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLS  186 (233)
Q Consensus       140 ~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~  186 (233)
                      |++++|..+++.|++|+.+|+||||++++|+|+|+|++||++++|..
T Consensus       249 l~~~eq~~~~~~~~~G~rkVlvATnIAErsLtIp~V~~VID~Gl~r~  295 (812)
T PRK11664        249 LSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVVDSGLERV  295 (812)
T ss_pred             CCHHHHHHHhccccCCCeEEEEecchHHhcccccCceEEEECCCccc
Confidence            99999999999999999999999999999999999999999888753

>PRK14701 reverse gyrase; Provisional

Probab=99.92  E-value=5e-25  Score=214.37  Aligned_cols=175  Identities=15%  Similarity=0.125  Sum_probs=137.7

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhc----CCcEEEE
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSS----ALRNICI   76 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~----~~~~~~~   76 (233)
                      +||.++.|+|++++||||||||++++++.+...        .++.++|||+||+||+.|+++.++.+..    ++++..+
T Consensus        87 ~i~~il~G~d~li~APTGsGKTl~~~~~al~~~--------~~g~~aLVl~PTreLa~Qi~~~l~~l~~~~~~~v~v~~~  158 (1638)
T PRK14701         87 WAKRILRGKSFSIVAPTGMGKSTFGAFIALFLA--------LKGKKCYIILPTTLLVKQTVEKIESFCEKANLDVRLVYY  158 (1638)
T ss_pred             HHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHHH--------hcCCeEEEEECHHHHHHHHHHHHHHHHhhcCCceeEEEE
Confidence            468899999999999999999996666555432        2467899999999999999999999832    4567778


Q ss_pred             EcCCCC-------------CCeeEEe----------------------------cc------chhh--------------
Q psy14082         77 FGGTPK-------------GPQDCLP----------------------------LH------RFVF--------------   95 (233)
Q Consensus        77 ~gg~~~-------------~~~~lv~----------------------------l~------r~~~--------------   95 (233)
                      +|+.+.             +.+++|+                            ++      |+++              
T Consensus       159 ~g~~s~~e~~~~~~~l~~g~~dILV~TPgrL~~~~~~l~~~~i~~iVVDEAD~ml~~~knid~~L~llGF~~e~~~~~~~  238 (1638)
T PRK14701        159 HSNLRKKEKEEFLERIENGDFDILVTTAQFLARNFPEMKHLKFDFIFVDDVDAFLKASKNIDRSLQLLGFYEEIIEKAWK  238 (1638)
T ss_pred             eCCCCHHHHHHHHHHHhcCCCCEEEECCchhHHhHHHHhhCCCCEEEEECceeccccccccchhhhcCCChHHHHHHHHH
Confidence            888653             2456666                            10      0000              


Q ss_pred             hc-------------------------hH---------------------------------------------------
Q psy14082         96 NC-------------------------QY---------------------------------------------------   99 (233)
Q Consensus        96 ~~-------------------------~~---------------------------------------------------   99 (233)
                      ++                         ..                                                   
T Consensus       239 il~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ll~~SAT~~~r~~~~~l~~~~l~f~v~~~~~~lr~i~~~yi~~~~~~  318 (1638)
T PRK14701        239 IIYLKKQGNIEDAMEKREILNKEIEKIGNKIGCLIVASATGKAKGDRVKLYRELLGFEVGSGRSALRNIVDVYLNPEKII  318 (1638)
T ss_pred             hhhcccccccchhhhhhhhhhhhhhhcCCCccEEEEEecCCCchhHHHHHhhcCeEEEecCCCCCCCCcEEEEEECCHHH
Confidence            00                         00                                                   


Q ss_pred             -----HHhcCCCCeEEEEecchhH---HHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEec----ccCc
Q psy14082        100 -----EMAKNPAFKVIVFVETKKK---VEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVAT----DVAA  167 (233)
Q Consensus       100 -----~~~~~~~~k~iIf~~~~~~---~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T----~~~~  167 (233)
                           .+....+.++||||++++.   ++.+++.|.+.|+++..+||+     |...+++|++|+.+|||||    ++++
T Consensus       319 k~~L~~ll~~~g~~gIVF~~t~~~~e~ae~la~~L~~~Gi~a~~~h~~-----R~~~l~~F~~G~~~VLVaT~s~~gvaa  393 (1638)
T PRK14701        319 KEHVRELLKKLGKGGLIFVPIDEGAEKAEEIEKYLLEDGFKIELVSAK-----NKKGFDLFEEGEIDYLIGVATYYGTLV  393 (1638)
T ss_pred             HHHHHHHHHhCCCCeEEEEeccccchHHHHHHHHHHHCCCeEEEecch-----HHHHHHHHHcCCCCEEEEecCCCCeeE
Confidence                 1112235689999999886   489999999999999999995     8899999999999999999    5899


Q ss_pred             CCcCCCC-ccEEEEecCCC---Ccc
Q psy14082        168 RGLDVED-VNTVNIGSLQL---SAN  188 (233)
Q Consensus       168 ~Gldi~~-v~~VI~~d~P~---~~~  188 (233)
                      ||||+|+ |.+|||||+|.   +.+
T Consensus       394 RGIDiP~~Vryvi~~~~Pk~~~~~e  418 (1638)
T PRK14701        394 RGLDLPERIRFAVFYGVPKFRFRVD  418 (1638)
T ss_pred             ecCccCCccCEEEEeCCCCCCcchh
Confidence            9999999 99999999999   665

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.92  E-value=2.6e-24  Score=199.07  Aligned_cols=172  Identities=14%  Similarity=0.123  Sum_probs=134.6

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh-hc--CCcEEEEEcCCC-
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF-SS--ALRNICIFGGTP-   81 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~-~~--~~~~~~~~gg~~-   81 (233)
                      ..+++++++|+||||||.+|.+|+++...        .+.+++|+.|||++|.|+++.+.+. ..  +..+...+++.+ 
T Consensus        15 ~~~~~vIi~a~TGSGKTT~vpl~lL~~~~--------~~~~ilvlqPrR~aA~qiA~rva~~~~~~~g~~VGy~vr~~~~   86 (819)
T TIGR01970        15 AAHPQVVLEAPPGAGKSTAVPLALLDAPG--------IGGKIIMLEPRRLAARSAAQRLASQLGEAVGQTVGYRVRGENK   86 (819)
T ss_pred             HcCCcEEEECCCCCCHHHHHHHHHHHhhc--------cCCeEEEEeCcHHHHHHHHHHHHHHhCCCcCcEEEEEEccccc
Confidence            35789999999999999999999998762        2458999999999999999998654 22  234444444322 


Q ss_pred             --CCCeeEEe-------------------------cc-c-----------------------------------------
Q psy14082         82 --KGPQDCLP-------------------------LH-R-----------------------------------------   92 (233)
Q Consensus        82 --~~~~~lv~-------------------------l~-r-----------------------------------------   92 (233)
                        .+.+++++                         .+ |                                         
T Consensus        87 ~s~~t~I~v~T~G~Llr~l~~d~~L~~v~~VIiDEaHER~L~~Dl~L~ll~~i~~~lr~dlqlIlmSATl~~~~l~~~l~  166 (819)
T TIGR01970        87 VSRRTRLEVVTEGILTRMIQDDPELDGVGALIFDEFHERSLDADLGLALALDVQSSLREDLKILAMSATLDGERLSSLLP  166 (819)
T ss_pred             cCCCCcEEEECCcHHHHHHhhCcccccCCEEEEeccchhhhccchHHHHHHHHHHhcCCCceEEEEeCCCCHHHHHHHcC
Confidence              23455444                         00 0                                         


Q ss_pred             -----------------hh-------------hhchHHHhcCCCCeEEEEecchhHHHHHHHHHhh---CCCeeEEEeCC
Q psy14082         93 -----------------FV-------------FNCQYEMAKNPAFKVIVFVETKKKVEDITRALRR---ERHSAICIHGD  139 (233)
Q Consensus        93 -----------------~~-------------~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~---~~~~~~~~~~~  139 (233)
                                       +.             ..+... .....+++|||+++.+.++.+++.|.+   .++.+..+||+
T Consensus       167 ~~~vI~~~gr~~pVe~~y~~~~~~~~~~~~v~~~l~~~-l~~~~g~iLVFlpg~~eI~~l~~~L~~~~~~~~~v~pLHg~  245 (819)
T TIGR01970       167 DAPVVESEGRSFPVEIRYLPLRGDQRLEDAVSRAVEHA-LASETGSILVFLPGQAEIRRVQEQLAERLDSDVLICPLYGE  245 (819)
T ss_pred             CCcEEEecCcceeeeeEEeecchhhhHHHHHHHHHHHH-HHhcCCcEEEEECCHHHHHHHHHHHHhhcCCCcEEEEecCC
Confidence                             00             000001 123457899999999999999999987   47899999999


Q ss_pred             CCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCC
Q psy14082        140 KTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLS  186 (233)
Q Consensus       140 ~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~  186 (233)
                      |++++|..+++.|++|+.+|+||||++++|+|+|+|++||++|+|..
T Consensus       246 L~~~eq~~~~~~~~~G~rkVlVATnIAErgItIp~V~~VID~Gl~r~  292 (819)
T TIGR01970       246 LSLAAQDRAIKPDPQGRRKVVLATNIAETSLTIEGIRVVIDSGLARV  292 (819)
T ss_pred             CCHHHHHHHHhhcccCCeEEEEecchHhhcccccCceEEEEcCcccc
Confidence            99999999999999999999999999999999999999999999864

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.

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.92  E-value=2.1e-24  Score=195.65  Aligned_cols=98  Identities=15%  Similarity=0.182  Sum_probs=84.7

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCC---------C
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVE---------D  174 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~---------~  174 (233)
                      ..+.++||||+|++.++.+...|.+.|+++..+||+++++++..+.++++.|  .|+||||+++||+|++         +
T Consensus       422 ~~~~pvLIft~s~~~se~ls~~L~~~gi~~~~L~a~~~~~E~~ii~~ag~~g--~VlIATdmAgRGtDI~l~~~v~~~GG  499 (762)
T TIGR03714       422 ETGQPVLLITGSVEMSEIYSELLLREGIPHNLLNAQNAAKEAQIIAEAGQKG--AVTVATSMAGRGTDIKLGKGVAELGG  499 (762)
T ss_pred             hCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCCChHHHHHHHHHcCCCC--eEEEEccccccccCCCCCccccccCC
Confidence            5678999999999999999999999999999999999999988887777666  7999999999999999         9


Q ss_pred             ccEEEEecCCCCcc--cccc---------eeeEEeecchH
Q psy14082        175 VNTVNIGSLQLSAN--HNIS---------QVIEVVQDYEK  203 (233)
Q Consensus       175 v~~VI~~d~P~~~~--~~i~---------~~~~~~~~~~~  203 (233)
                      +.+|++|++|++..  |++|         .+..|++..++
T Consensus       500 L~vIit~~~ps~rid~qr~GRtGRqG~~G~s~~~is~eD~  539 (762)
T TIGR03714       500 LAVIGTERMENSRVDLQLRGRSGRQGDPGSSQFFVSLEDD  539 (762)
T ss_pred             eEEEEecCCCCcHHHHHhhhcccCCCCceeEEEEEccchh
Confidence            99999999998754  5553         44567776553

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.

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.92  E-value=2.4e-23  Score=187.94  Aligned_cols=87  Identities=17%  Similarity=0.132  Sum_probs=80.7

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCC-------c
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVED-------V  175 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~-------v  175 (233)
                      ...+.++||||+++..++.++..|.+.|+++..+|++  +.+|+..+.+|+.+...|+||||+++||+|++.       .
T Consensus       402 ~~~grpvLV~t~si~~se~ls~~L~~~gi~~~~Lna~--q~~rEa~ii~~ag~~g~VtIATnmAgRGtDI~l~~V~~~GG  479 (745)
T TIGR00963       402 HAKGQPVLVGTTSVEKSELLSNLLKERGIPHNVLNAK--NHEREAEIIAQAGRKGAVTIATNMAGRGTDIKLEEVKELGG  479 (745)
T ss_pred             HhcCCCEEEEeCcHHHHHHHHHHHHHcCCCeEEeeCC--hHHHHHHHHHhcCCCceEEEEeccccCCcCCCccchhhcCC
Confidence            4578999999999999999999999999999999998  889999999999999999999999999999998       5


Q ss_pred             cEEEEecCCCCccccc
Q psy14082        176 NTVNIGSLQLSANHNI  191 (233)
Q Consensus       176 ~~VI~~d~P~~~~~~i  191 (233)
                      .+||++++|.|...|.
T Consensus       480 l~VI~t~~p~s~ri~~  495 (745)
T TIGR00963       480 LYVIGTERHESRRIDN  495 (745)
T ss_pred             cEEEecCCCCcHHHHH
Confidence            5999999999987333

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.

>PRK13766 Hef nuclease; Provisional

Probab=99.91  E-value=2.7e-23  Score=194.19  Aligned_cols=88  Identities=32%  Similarity=0.470  Sum_probs=82.9

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCC--------CCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCc
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRERHSAICIHGD--------KTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDV  175 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~--------~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v  175 (233)
                      ..+.++||||+++++++.+.+.|...++.+..+||.        |++.+|..++++|++|+.++||+|+++++|+|+|++
T Consensus       363 ~~~~kvlIF~~~~~t~~~L~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~g~~~vLvaT~~~~eGldi~~~  442 (773)
T PRK13766        363 NPDSRIIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSV  442 (773)
T ss_pred             CCCCeEEEEeCcHHHHHHHHHHHHhCCCceEEEEccccccccCCCCHHHHHHHHHHHHcCCCCEEEECChhhcCCCcccC
Confidence            466899999999999999999999999999999886        999999999999999999999999999999999999


Q ss_pred             cEEEEecCCCCccccc
Q psy14082        176 NTVNIGSLQLSANHNI  191 (233)
Q Consensus       176 ~~VI~~d~P~~~~~~i  191 (233)
                      ++||+||+|++...|+
T Consensus       443 ~~VI~yd~~~s~~r~i  458 (773)
T PRK13766        443 DLVIFYEPVPSEIRSI  458 (773)
T ss_pred             CEEEEeCCCCCHHHHH
Confidence            9999999999987555

>KOG0349|consensus

Probab=99.91  E-value=1.6e-24  Score=181.44  Aligned_cols=93  Identities=27%  Similarity=0.501  Sum_probs=85.4

Q ss_pred             HHhcCCCCeEEEEecchhHHHHHHHHHhhCC---CeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCcc
Q psy14082        100 EMAKNPAFKVIVFVETKKKVEDITRALRRER---HSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVN  176 (233)
Q Consensus       100 ~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~---~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~  176 (233)
                      ...+....++||||.|+..++.+...+.+.|   ++|+++||+.-+++|.+.++.|+.++.+.|||||+++||+|+..+.
T Consensus       499 ai~~h~mdkaiifcrtk~dcDnLer~~~qkgg~~~scvclhgDrkP~Erk~nle~Fkk~dvkflictdvaargldi~g~p  578 (725)
T KOG0349|consen  499 AIRRHAMDKAIIFCRTKQDCDNLERMMNQKGGKHYSCVCLHGDRKPDERKANLESFKKFDVKFLICTDVAARGLDITGLP  578 (725)
T ss_pred             hhhhhccCceEEEEeccccchHHHHHHHHcCCccceeEEEecCCChhHHHHHHHhhhhcCeEEEEEehhhhccccccCCc
Confidence            3456677899999999999999999998765   6999999999999999999999999999999999999999999999


Q ss_pred             EEEEecCCCCcccccc
Q psy14082        177 TVNIGSLQLSANHNIS  192 (233)
Q Consensus       177 ~VI~~d~P~~~~~~i~  192 (233)
                      .+||.-+|.+...|+|
T Consensus       579 ~~invtlpd~k~nyvh  594 (725)
T KOG0349|consen  579 FMINVTLPDDKTNYVH  594 (725)
T ss_pred             eEEEEecCcccchhhh
Confidence            9999999998876663

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.90  E-value=5.2e-23  Score=175.97  Aligned_cols=84  Identities=17%  Similarity=0.180  Sum_probs=72.1

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCC--CeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEec
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRER--HSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGS  182 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~--~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d  182 (233)
                      .+.++||||+|++.++.++..|++.+  +.+..+||.+++.+|.+.      ++.++|||||+++||+|++.+ +|| ++
T Consensus       271 ~~~k~LIf~nt~~~~~~l~~~L~~~~~~~~~~~l~g~~~~~~R~~~------~~~~iLVaTdv~~rGiDi~~~-~vi-~~  342 (357)
T TIGR03158       271 PGERGAIILDSLDEVNRLSDLLQQQGLGDDIGRITGFAPKKDRERA------MQFDILLGTSTVDVGVDFKRD-WLI-FS  342 (357)
T ss_pred             CCCeEEEEECCHHHHHHHHHHHhhhCCCceEEeeecCCCHHHHHHh------ccCCEEEEecHHhcccCCCCc-eEE-EC
Confidence            45799999999999999999998864  578889999999998754      478999999999999999986 566 56


Q ss_pred             CCCCcccccceeeEE
Q psy14082        183 LQLSANHNISQVIEV  197 (233)
Q Consensus       183 ~P~~~~~~i~~~~~~  197 (233)
                       |.+.+.|+||+++.
T Consensus       343 -p~~~~~yiqR~GR~  356 (357)
T TIGR03158       343 -ARDAAAFWQRLGRL  356 (357)
T ss_pred             -CCCHHHHhhhcccC
Confidence             88898888877653

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.

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.90  E-value=2.3e-22  Score=182.35  Aligned_cols=91  Identities=20%  Similarity=0.297  Sum_probs=78.7

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCC-CCCEEEecccCcCCcCCCCccEEEEecC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQG-KAPILVATDVAARGLDVEDVNTVNIGSL  183 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~iLv~T~~~~~Gldi~~v~~VI~~d~  183 (233)
                      .+.++||||++...++.++..|     .+.++||++++.+|..++++|+.| .+++||+|+++++|+|+|++++||+++.
T Consensus       495 ~g~kiLVF~~~~~~l~~~a~~L-----~~~~I~G~ts~~ER~~il~~Fr~~~~i~vLv~SkVgdeGIDlP~a~vvI~~s~  569 (732)
T TIGR00603       495 RGDKIIVFSDNVFALKEYAIKL-----GKPFIYGPTSQQERMQILQNFQHNPKVNTIFLSKVGDTSIDLPEANVLIQISS  569 (732)
T ss_pred             cCCeEEEEeCCHHHHHHHHHHc-----CCceEECCCCHHHHHHHHHHHHhCCCccEEEEecccccccCCCCCCEEEEeCC
Confidence            6789999999999999998887     356799999999999999999875 7899999999999999999999999999


Q ss_pred             CC-CcccccceeeEEeec
Q psy14082        184 QL-SANHNISQVIEVVQD  200 (233)
Q Consensus       184 P~-~~~~~i~~~~~~~~~  200 (233)
                      |. |..+|++|.++..+.
T Consensus       570 ~~gS~~q~iQRlGRilR~  587 (732)
T TIGR00603       570 HYGSRRQEAQRLGRILRA  587 (732)
T ss_pred             CCCCHHHHHHHhcccccC
Confidence            84 787777554444443

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).

>KOG0329|consensus

Probab=99.89  E-value=3.4e-23  Score=162.99  Aligned_cols=207  Identities=23%  Similarity=0.304  Sum_probs=138.6

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh---hcCCcEEEEE
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF---SSALRNICIF   77 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~---~~~~~~~~~~   77 (233)
                      .||...-|-|++++|.+|.|||+.|+++-++.+...     .+...+|++|+|||||.|+.+.+.+|   .++++++.++
T Consensus        72 cipqailgmdvlcqaksgmgktavfvl~tlqqiepv-----~g~vsvlvmchtrelafqi~~ey~rfskymP~vkvaVFf  146 (387)
T KOG0329|consen   72 CIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPV-----DGQVSVLVMCHTRELAFQISKEYERFSKYMPSVKVSVFF  146 (387)
T ss_pred             hhhHHhhcchhheecccCCCceeeeehhhhhhcCCC-----CCeEEEEEEeccHHHHHHHHHHHHHHHhhCCCceEEEEE
Confidence            489999999999999999999999999999988654     55788999999999999999999988   5789999999


Q ss_pred             cCCCC---------CCeeEEe-------ccc------------hhhhchH-------------HHhc-CCCCeEEEEecc
Q psy14082         78 GGTPK---------GPQDCLP-------LHR------------FVFNCQY-------------EMAK-NPAFKVIVFVET  115 (233)
Q Consensus        78 gg~~~---------~~~~lv~-------l~r------------~~~~~~~-------------~~~~-~~~~k~iIf~~~  115 (233)
                      ||.++         .+.++||       |-|            +++.|.+             .+.. -..++++.|..|
T Consensus       147 GG~~Ikkdee~lk~~PhivVgTPGrilALvr~k~l~lk~vkhFvlDEcdkmle~lDMrRDvQEifr~tp~~KQvmmfsat  226 (387)
T KOG0329|consen  147 GGLFIKKDEELLKNCPHIVVGTPGRILALVRNRSLNLKNVKHFVLDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSAT  226 (387)
T ss_pred             cceeccccHHHHhCCCeEEEcCcHHHHHHHHhccCchhhcceeehhhHHHHHHHHHHHHHHHHHhhcCcccceeeeeeee
Confidence            99876         3456777       111            3444443             2222 245677777766


Q ss_pred             h-hHHHHHHHHHhhCCCee-------EEEeCC------CCHHHHHHH----HHH--hhC------------CCCCEEEec
Q psy14082        116 K-KKVEDITRALRRERHSA-------ICIHGD------KTQQDRDYV----LND--FRQ------------GKAPILVAT  163 (233)
Q Consensus       116 ~-~~~~~l~~~L~~~~~~~-------~~~~~~------~~~~~r~~~----~~~--f~~------------g~~~iLv~T  163 (233)
                      - +...-+...+.+....+       ..+||-      +...++...    ++.  |+.            -+.+ +|+|
T Consensus       227 lskeiRpvC~kFmQdPmEi~vDdE~KLtLHGLqQ~YvkLke~eKNrkl~dLLd~LeFNQVvIFvKsv~Rl~f~kr-~vat  305 (387)
T KOG0329|consen  227 LSKEIRPVCHKFMQDPMEIFVDDEAKLTLHGLQQYYVKLKENEKNRKLNDLLDVLEFNQVVIFVKSVQRLSFQKR-LVAT  305 (387)
T ss_pred             cchhhHHHHHhhhcCchhhhccchhhhhhhhHHHHHHhhhhhhhhhhhhhhhhhhhhcceeEeeehhhhhhhhhh-hHHh
Confidence            3 33444444443321111       123331      111111111    110  000            0234 8999


Q ss_pred             ccCcCCcCCCCccEEEEecCCCCccccc------------ceeeEEeecchHHHHHHHHHHh
Q psy14082        164 DVAARGLDVEDVNTVNIGSLQLSANHNI------------SQVIEVVQDYEKEKRLFSLIRE  213 (233)
Q Consensus       164 ~~~~~Gldi~~v~~VI~~d~P~~~~~~i------------~~~~~~~~~~~~~~~~~~~i~~  213 (233)
                      ++.+||+|+..++.++|||+|.+.+.|.            |-++.|++..++..-+...-++
T Consensus       306 ~lfgrgmdiervNi~~NYdmp~~~DtYlHrv~rAgrfGtkglaitfvs~e~da~iLn~vqdR  367 (387)
T KOG0329|consen  306 DLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNPVQDR  367 (387)
T ss_pred             hhhccccCcccceeeeccCCCCCchHHHHHhhhhhccccccceeehhcchhhHHHhchhhHh
Confidence            9999999999999999999999999777            4566677764444333333333

>KOG0354|consensus

Probab=99.88  E-value=6.4e-22  Score=177.04  Aligned_cols=101  Identities=29%  Similarity=0.413  Sum_probs=85.4

Q ss_pred             HHhcCCCCeEEEEecchhHHHHHHHHHhh---CCCeeEEEeC--------CCCHHHHHHHHHHhhCCCCCEEEecccCcC
Q psy14082        100 EMAKNPAFKVIVFVETKKKVEDITRALRR---ERHSAICIHG--------DKTQQDRDYVLNDFRQGKAPILVATDVAAR  168 (233)
Q Consensus       100 ~~~~~~~~k~iIf~~~~~~~~~l~~~L~~---~~~~~~~~~~--------~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~  168 (233)
                      .+...+..++||||++|+.++.+...|.+   .++++..+-|        +|+++++.+++++|++|++++||||+++++
T Consensus       407 ~f~~~~dsR~IIFve~R~sa~~l~~~l~~~~~~~ir~~~fiGq~~s~~~~gmtqk~Q~evl~~Fr~G~~NvLVATSV~EE  486 (746)
T KOG0354|consen  407 QFEQNPDSRTIIFVETRESALALKKWLLQLHELGIKAEIFIGQGKSTQSTGMTQKEQKEVLDKFRDGEINVLVATSVAEE  486 (746)
T ss_pred             HhhcCCCccEEEEEehHHHHHHHHHHHHhhhhcccccceeeeccccccccccCHHHHHHHHHHHhCCCccEEEEecchhc
Confidence            44567889999999999999999999973   3455555544        699999999999999999999999999999


Q ss_pred             CcCCCCccEEEEecCCCCccccc----------ceeeEEeec
Q psy14082        169 GLDVEDVNTVNIGSLQLSANHNI----------SQVIEVVQD  200 (233)
Q Consensus       169 Gldi~~v~~VI~~d~P~~~~~~i----------~~~~~~~~~  200 (233)
                      |+|++++++||.||.-+|+...|          |+++.+.+.
T Consensus       487 GLDI~ec~lVIcYd~~snpIrmIQrrGRgRa~ns~~vll~t~  528 (746)
T KOG0354|consen  487 GLDIGECNLVICYDYSSNPIRMVQRRGRGRARNSKCVLLTTG  528 (746)
T ss_pred             cCCcccccEEEEecCCccHHHHHHHhccccccCCeEEEEEcc
Confidence            99999999999999999986444          456666653

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.86  E-value=9.6e-21  Score=174.06  Aligned_cols=170  Identities=17%  Similarity=0.135  Sum_probs=138.3

Q ss_pred             CCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh-hcCCcEEEEEcCCCC
Q psy14082          4 PSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF-SSALRNICIFGGTPK   82 (233)
Q Consensus         4 ~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~-~~~~~~~~~~gg~~~   82 (233)
                      .+..|.|+++++|||||||+...+.+++.+.+.       +.+++++||+|+||.|.++.+.++ .-++++...+|+.+.
T Consensus        43 ~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~-------~~k~vYivPlkALa~Ek~~~~~~~~~~GirV~~~TgD~~~  115 (766)
T COG1204          43 GLLSDENVLISAPTGSGKTLIALLAILSTLLEG-------GGKVVYIVPLKALAEEKYEEFSRLEELGIRVGISTGDYDL  115 (766)
T ss_pred             cccCCCcEEEEcCCCCchHHHHHHHHHHHHHhc-------CCcEEEEeChHHHHHHHHHHhhhHHhcCCEEEEecCCccc
Confidence            345689999999999999999999999999753       568999999999999999999976 568999999999883


Q ss_pred             ------CCeeEEe--------ccc--------------------------------------------------------
Q psy14082         83 ------GPQDCLP--------LHR--------------------------------------------------------   92 (233)
Q Consensus        83 ------~~~~lv~--------l~r--------------------------------------------------------   92 (233)
                            +.+++|+        +++                                                        
T Consensus       116 ~~~~l~~~~ViVtT~EK~Dsl~R~~~~~~~~V~lvViDEiH~l~d~~RG~~lE~iv~r~~~~~~~~rivgLSATlpN~~e  195 (766)
T COG1204         116 DDERLARYDVIVTTPEKLDSLTRKRPSWIEEVDLVVIDEIHLLGDRTRGPVLESIVARMRRLNELIRIVGLSATLPNAEE  195 (766)
T ss_pred             chhhhccCCEEEEchHHhhHhhhcCcchhhcccEEEEeeeeecCCcccCceehhHHHHHHhhCcceEEEEEeeecCCHHH
Confidence                  4556776        000                                                        


Q ss_pred             -----------------------------------h-------hhhchH--HHhcCCCCeEEEEecchhHHHHHHHHHhh
Q psy14082         93 -----------------------------------F-------VFNCQY--EMAKNPAFKVIVFVETKKKVEDITRALRR  128 (233)
Q Consensus        93 -----------------------------------~-------~~~~~~--~~~~~~~~k~iIf~~~~~~~~~l~~~L~~  128 (233)
                                                         .       -..+.+  ......+++++|||++++.+...++.+.+
T Consensus       196 vA~wL~a~~~~~~~rp~~l~~~v~~~~~~~~~~~~~k~~~~~~~~~~~~~v~~~~~~~~qvLvFv~sR~~a~~~A~~l~~  275 (766)
T COG1204         196 VADWLNAKLVESDWRPVPLRRGVPYVGAFLGADGKKKTWPLLIDNLALELVLESLAEGGQVLVFVHSRKEAEKTAKKLRI  275 (766)
T ss_pred             HHHHhCCcccccCCCCcccccCCccceEEEEecCccccccccchHHHHHHHHHHHhcCCeEEEEEecCchHHHHHHHHHH
Confidence                                               0       000000  22445788999999999999999999983


Q ss_pred             C---------------------C----------------CeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcC
Q psy14082        129 E---------------------R----------------HSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLD  171 (233)
Q Consensus       129 ~---------------------~----------------~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gld  171 (233)
                      .                     +                ..+.++|++++.++|..+.+.|+.|.++||+||+.++.|+|
T Consensus       276 ~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~l~e~v~~GvafHhAGL~~~~R~~vE~~Fr~g~ikVlv~TpTLA~GVN  355 (766)
T COG1204         276 KMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGVAFHHAGLPREDRQLVEDAFRKGKIKVLVSTPTLAAGVN  355 (766)
T ss_pred             HHhhcCChhhhhhccccccccccccccccchHHHHHHHHhCccccccCCCHHHHHHHHHHHhcCCceEEEechHHhhhcC
Confidence            0                     0                14578899999999999999999999999999999999999


Q ss_pred             CCCccEEEE
Q psy14082        172 VEDVNTVNI  180 (233)
Q Consensus       172 i~~v~~VI~  180 (233)
                      +|.-..||-
T Consensus       356 LPA~~VIIk  364 (766)
T COG1204         356 LPARTVIIK  364 (766)
T ss_pred             CcceEEEEe
Confidence            998776663

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

Probab=99.86  E-value=1.4e-21  Score=181.77  Aligned_cols=183  Identities=20%  Similarity=0.252  Sum_probs=149.1

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh---hc-CCcEEEEEcCC
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF---SS-ALRNICIFGGT   80 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~---~~-~~~~~~~~gg~   80 (233)
                      +.+|+|+++.++||||||.+|++|+++++++.+      ..++|+|-||++||+...+.++++   .+ ++.+....|+.
T Consensus        82 ~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~------~a~AL~lYPtnALa~DQ~~rl~~~~~~~~~~v~~~~y~Gdt  155 (851)
T COG1205          82 IREGRNVVVTTGTGSGKTESFLLPILDHLLRDP------SARALLLYPTNALANDQAERLRELISDLPGKVTFGRYTGDT  155 (851)
T ss_pred             HHCCCCEEEECCCCCchhHHHHHHHHHHHhhCc------CccEEEEechhhhHhhHHHHHHHHHHhCCCcceeeeecCCC
Confidence            467999999999999999999999999999853      448999999999999999999999   22 57888889987


Q ss_pred             CC---------CCeeEEe---------------------------------------------ccchhhhchH-------
Q psy14082         81 PK---------GPQDCLP---------------------------------------------LHRFVFNCQY-------   99 (233)
Q Consensus        81 ~~---------~~~~lv~---------------------------------------------l~r~~~~~~~-------   99 (233)
                      +.         .++|++.                                             ++|+.+.++.       
T Consensus       156 ~~~~r~~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDElHtYrGv~GS~vA~llRRL~~~~~~~~~~~q~  235 (851)
T COG1205         156 PPEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYRGVQGSEVALLLRRLLRRLRRYGSPLQI  235 (851)
T ss_pred             ChHHHHHHHhCCCCEEEeCHHHHHHHhccCcchHHHHHhcCcEEEEecceeccccchhHHHHHHHHHHHHHhccCCCceE
Confidence            65         3444555                                             2332222210       


Q ss_pred             ----------------------------------------------------------------HHhcCCCCeEEEEecc
Q psy14082        100 ----------------------------------------------------------------EMAKNPAFKVIVFVET  115 (233)
Q Consensus       100 ----------------------------------------------------------------~~~~~~~~k~iIf~~~  115 (233)
                                                                                      ...-..+-++|+|+.+
T Consensus       236 i~~SAT~~np~e~~~~l~~~~f~~~v~~~g~~~~~~~~~~~~p~~~~~~~~~r~s~~~~~~~~~~~~~~~~~~tL~F~~s  315 (851)
T COG1205         236 ICTSATLANPGEFAEELFGRDFEVPVDEDGSPRGLRYFVRREPPIRELAESIRRSALAELATLAALLVRNGIQTLVFFRS  315 (851)
T ss_pred             EEEeccccChHHHHHHhcCCcceeeccCCCCCCCceEEEEeCCcchhhhhhcccchHHHHHHHHHHHHHcCceEEEEEeh
Confidence                                                                            1123377899999999


Q ss_pred             hhHHHHHH----HHHhhCC----CeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCC-C
Q psy14082        116 KKKVEDIT----RALRRER----HSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQL-S  186 (233)
Q Consensus       116 ~~~~~~l~----~~L~~~~----~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~-~  186 (233)
                      ++.++.+.    ..+...+    ..+..++++|...+|..+...|+.|+..++++|+.+.-|+|+.+++.||.++.|. +
T Consensus       316 r~~~e~~~~~~~~~~~~~~~~l~~~v~~~~~~~~~~er~~ie~~~~~g~~~~~~st~AlelgidiG~ldavi~~g~P~~s  395 (851)
T COG1205         316 RKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGYPGVS  395 (851)
T ss_pred             hhhhhhhhhchhHHHhhcchhhhhheeeccccCCHHHHHHHHHHHhcCCccEEecchhhhhceeehhhhhHhhcCCCCch
Confidence            99999997    4444445    5678899999999999999999999999999999999999999999999999999 7


Q ss_pred             cccccce
Q psy14082        187 ANHNISQ  193 (233)
Q Consensus       187 ~~~~i~~  193 (233)
                      ...++++
T Consensus       396 ~~~~~Q~  402 (851)
T COG1205         396 VLSFRQR  402 (851)
T ss_pred             HHHHHHh
Confidence            6655533

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

Probab=99.85  E-value=3.9e-21  Score=166.00  Aligned_cols=167  Identities=20%  Similarity=0.145  Sum_probs=139.6

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhc--CCcEEEEEcC---
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSS--ALRNICIFGG---   79 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~--~~~~~~~~gg---   79 (233)
                      ++.|.|.++.++|+||||+.--++-+.+++.       .|.+-|+|||..+||+|-|+.|+.-+.  ++++++-+|-   
T Consensus       229 LLeG~nllVVSaTasGKTLIgElAGi~~~l~-------~g~KmlfLvPLVALANQKy~dF~~rYs~LglkvairVG~srI  301 (830)
T COG1202         229 LLEGENLLVVSATASGKTLIGELAGIPRLLS-------GGKKMLFLVPLVALANQKYEDFKERYSKLGLKVAIRVGMSRI  301 (830)
T ss_pred             cccCCceEEEeccCCCcchHHHhhCcHHHHh-------CCCeEEEEehhHHhhcchHHHHHHHhhcccceEEEEechhhh
Confidence            5789999999999999999999999988874       477899999999999999999998743  5566666654   


Q ss_pred             ----------CCCCCeeEEe-----------------------------------------ccc----------------
Q psy14082         80 ----------TPKGPQDCLP-----------------------------------------LHR----------------   92 (233)
Q Consensus        80 ----------~~~~~~~lv~-----------------------------------------l~r----------------   92 (233)
                                .+.+.+|+||                                         +.|                
T Consensus       302 k~~~~pv~~~t~~dADIIVGTYEGiD~lLRtg~~lgdiGtVVIDEiHtL~deERG~RLdGLI~RLr~l~~~AQ~i~LSAT  381 (830)
T COG1202         302 KTREEPVVVDTSPDADIIVGTYEGIDYLLRTGKDLGDIGTVVIDEIHTLEDEERGPRLDGLIGRLRYLFPGAQFIYLSAT  381 (830)
T ss_pred             cccCCccccCCCCCCcEEEeechhHHHHHHcCCcccccceEEeeeeeeccchhcccchhhHHHHHHHhCCCCeEEEEEee
Confidence                      3335667888                                         111                


Q ss_pred             -----------------------------------------hhhhchH----HHhcCCCCeEEEEecchhHHHHHHHHHh
Q psy14082         93 -----------------------------------------FVFNCQY----EMAKNPAFKVIVFVETKKKVEDITRALR  127 (233)
Q Consensus        93 -----------------------------------------~~~~~~~----~~~~~~~~k~iIf~~~~~~~~~l~~~L~  127 (233)
                                                               +..+++.    .......+++|||+++++.|+.++..|.
T Consensus       382 VgNp~elA~~l~a~lV~y~~RPVplErHlvf~~~e~eK~~ii~~L~k~E~~~~sskg~rGQtIVFT~SRrr~h~lA~~L~  461 (830)
T COG1202         382 VGNPEELAKKLGAKLVLYDERPVPLERHLVFARNESEKWDIIARLVKREFSTESSKGYRGQTIVFTYSRRRCHELADALT  461 (830)
T ss_pred             cCChHHHHHHhCCeeEeecCCCCChhHeeeeecCchHHHHHHHHHHHHHHhhhhccCcCCceEEEecchhhHHHHHHHhh
Confidence                                                     2222222    2345567899999999999999999999


Q ss_pred             hCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEE
Q psy14082        128 RERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTV  178 (233)
Q Consensus       128 ~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~V  178 (233)
                      ..|+++..+|++++..+|..+...|.+++..++|+|-+++-|+|+|.-.+|
T Consensus       462 ~kG~~a~pYHaGL~y~eRk~vE~~F~~q~l~~VVTTAAL~AGVDFPASQVI  512 (830)
T COG1202         462 GKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAAGVDFPASQVI  512 (830)
T ss_pred             cCCcccccccCCCcHHHHHHHHHHHhcCCcceEeehhhhhcCCCCchHHHH
Confidence            999999999999999999999999999999999999999999999987755

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

Probab=99.84  E-value=7.1e-20  Score=160.52  Aligned_cols=95  Identities=20%  Similarity=0.306  Sum_probs=88.9

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQ  184 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P  184 (233)
                      .+.+++||+.+..+++.++..+...+. +..+++..+..+|..++++|+.|++++||++.++.+|+|+|+++++|...++
T Consensus       282 ~~~~~lif~~~~~~a~~i~~~~~~~~~-~~~it~~t~~~eR~~il~~fr~g~~~~lv~~~vl~EGvDiP~~~~~i~~~~t  360 (442)
T COG1061         282 RGDKTLIFASDVEHAYEIAKLFLAPGI-VEAITGETPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLIILRPT  360 (442)
T ss_pred             CCCcEEEEeccHHHHHHHHHHhcCCCc-eEEEECCCCHHHHHHHHHHHHcCCCCEEEEeeeccceecCCCCcEEEEeCCC
Confidence            578999999999999999999988887 8899999999999999999999999999999999999999999999999999


Q ss_pred             CCcccccceeeEEeec
Q psy14082        185 LSANHNISQVIEVVQD  200 (233)
Q Consensus       185 ~~~~~~i~~~~~~~~~  200 (233)
                      .|...|+++.++..+.
T Consensus       361 ~S~~~~~Q~lGR~LR~  376 (442)
T COG1061         361 GSRRLFIQRLGRGLRP  376 (442)
T ss_pred             CcHHHHHHHhhhhccC
Confidence            9999888777777764

>KOG0351|consensus

Probab=99.84  E-value=2.7e-21  Score=179.40  Aligned_cols=196  Identities=19%  Similarity=0.184  Sum_probs=151.5

Q ss_pred             CCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh-hcCCcEEEEEcCCCC
Q psy14082          4 PSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF-SSALRNICIFGGTPK   82 (233)
Q Consensus         4 ~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~-~~~~~~~~~~gg~~~   82 (233)
                      .++.|+|+++.+|||.||++||.+|++-           .+...|+|.|...|.+.   +..++ ..++....+.++...
T Consensus       275 ~~l~Gkd~fvlmpTG~GKSLCYQlPA~l-----------~~gitvVISPL~SLm~D---Qv~~L~~~~I~a~~L~s~q~~  340 (941)
T KOG0351|consen  275 ATLSGKDCFVLMPTGGGKSLCYQLPALL-----------LGGVTVVISPLISLMQD---QVTHLSKKGIPACFLSSIQTA  340 (941)
T ss_pred             HHHcCCceEEEeecCCceeeEeeccccc-----------cCCceEEeccHHHHHHH---HHHhhhhcCcceeeccccccH
Confidence            4688999999999999999999999873           24488999997777655   44444 447888888877544


Q ss_pred             CC-------------ee---EEe--------------------------------------------------ccc----
Q psy14082         83 GP-------------QD---CLP--------------------------------------------------LHR----   92 (233)
Q Consensus        83 ~~-------------~~---lv~--------------------------------------------------l~r----   92 (233)
                      ..             .+   .|.                                                  +++    
T Consensus       341 ~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~~~~~~L~~~~~lal~vIDEAHCVSqWgHdFRp~Yk~l~~l~~~~~~  420 (941)
T KOG0351|consen  341 AERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLYARGLLALFVIDEAHCVSQWGHDFRPSYKRLGLLRIRFPG  420 (941)
T ss_pred             HHHHHHHHHHhCCCCeEEEEEeCHHHhhcccchhhHHHhccCCCeeEEEEecHHHHhhhhcccccHHHHHHHHHHhhCCC
Confidence            11             11   111                                                  000    


Q ss_pred             ---------------------------------------------------hhhhchHHHhcCCCCeEEEEecchhHHHH
Q psy14082         93 ---------------------------------------------------FVFNCQYEMAKNPAFKVIVFVETKKKVED  121 (233)
Q Consensus        93 ---------------------------------------------------~~~~~~~~~~~~~~~k~iIf~~~~~~~~~  121 (233)
                                                                         ........-...+....||||.++..++.
T Consensus       421 vP~iALTATAT~~v~~DIi~~L~l~~~~~~~~sfnR~NL~yeV~~k~~~~~~~~~~~~~~~~~~~~s~IIYC~sr~~ce~  500 (941)
T KOG0351|consen  421 VPFIALTATATERVREDVIRSLGLRNPELFKSSFNRPNLKYEVSPKTDKDALLDILEESKLRHPDQSGIIYCLSRKECEQ  500 (941)
T ss_pred             CCeEEeehhccHHHHHHHHHHhCCCCcceecccCCCCCceEEEEeccCccchHHHHHHhhhcCCCCCeEEEeCCcchHHH
Confidence                                                               11111112345577889999999999999


Q ss_pred             HHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc---c------
Q psy14082        122 ITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI---S------  192 (233)
Q Consensus       122 l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i---~------  192 (233)
                      ++..|++.|+++..+|+||+..+|..+-++|..++++|+|||=+++.|+|.|+|..||||.+|.|.+.|.   |      
T Consensus       501 vs~~L~~~~~~a~~YHAGl~~~~R~~Vq~~w~~~~~~VivATVAFGMGIdK~DVR~ViH~~lPks~E~YYQE~GRAGRDG  580 (941)
T KOG0351|consen  501 VSAVLRSLGKSAAFYHAGLPPKERETVQKAWMSDKIRVIVATVAFGMGIDKPDVRFVIHYSLPKSFEGYYQEAGRAGRDG  580 (941)
T ss_pred             HHHHHHHhchhhHhhhcCCCHHHHHHHHHHHhcCCCeEEEEEeeccCCCCCCceeEEEECCCchhHHHHHHhccccCcCC
Confidence            9999999999999999999999999999999999999999999999999999999999999999999887   3      


Q ss_pred             ---eeeEEeecchHHHHHHHHHHhh
Q psy14082        193 ---QVIEVVQDYEKEKRLFSLIREL  214 (233)
Q Consensus       193 ---~~~~~~~~~~~~~~~~~~i~~~  214 (233)
                         .++.|++. .+..++..++..-
T Consensus       581 ~~s~C~l~y~~-~D~~~l~~ll~s~  604 (941)
T KOG0351|consen  581 LPSSCVLLYGY-ADISELRRLLTSG  604 (941)
T ss_pred             CcceeEEecch-hHHHHHHHHHHcc
Confidence               44445554 3555555555553

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.84  E-value=1.3e-19  Score=166.10  Aligned_cols=170  Identities=19%  Similarity=0.218  Sum_probs=129.9

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCCC-----
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPK-----   82 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~-----   82 (233)
                      +++.++.++||||||.+|+.++.+.+.        .+.++|||+||++|+.|+++.+++.+ +.++..++|+.+.     
T Consensus       162 ~~~~Ll~~~TGSGKT~v~l~~i~~~l~--------~g~~vLvLvPt~~L~~Q~~~~l~~~f-g~~v~~~~s~~s~~~r~~  232 (679)
T PRK05580        162 FSPFLLDGVTGSGKTEVYLQAIAEVLA--------QGKQALVLVPEIALTPQMLARFRARF-GAPVAVLHSGLSDGERLD  232 (679)
T ss_pred             CCcEEEECCCCChHHHHHHHHHHHHHH--------cCCeEEEEeCcHHHHHHHHHHHHHHh-CCCEEEEECCCCHHHHHH
Confidence            478999999999999999988777663        36689999999999999999999864 5688888888653     


Q ss_pred             --------CCeeEEe--------ccc------------------------------------------------------
Q psy14082         83 --------GPQDCLP--------LHR------------------------------------------------------   92 (233)
Q Consensus        83 --------~~~~lv~--------l~r------------------------------------------------------   92 (233)
                              +.+++||        +++                                                      
T Consensus       233 ~~~~~~~g~~~IVVgTrsal~~p~~~l~liVvDEeh~~s~~~~~~p~y~~r~va~~ra~~~~~~~il~SATps~~s~~~~  312 (679)
T PRK05580        233 EWRKAKRGEAKVVIGARSALFLPFKNLGLIIVDEEHDSSYKQQEGPRYHARDLAVVRAKLENIPVVLGSATPSLESLANA  312 (679)
T ss_pred             HHHHHHcCCCCEEEeccHHhcccccCCCEEEEECCCccccccCcCCCCcHHHHHHHHhhccCCCEEEEcCCCCHHHHHHH
Confidence                    3456776        000                                                      


Q ss_pred             -----------------------hhhhch-----------H----HH--hcCCCCeEEEEecch----------------
Q psy14082         93 -----------------------FVFNCQ-----------Y----EM--AKNPAFKVIVFVETK----------------  116 (233)
Q Consensus        93 -----------------------~~~~~~-----------~----~~--~~~~~~k~iIf~~~~----------------  116 (233)
                                             ++++-.           .    .+  ....+.++|+|+|++                
T Consensus       313 ~~g~~~~~~l~~r~~~~~~p~v~~id~~~~~~~~~~~~ls~~l~~~i~~~l~~g~qvll~~nrrGy~~~~~C~~Cg~~~~  392 (679)
T PRK05580        313 QQGRYRLLRLTKRAGGARLPEVEIIDMRELLRGENGSFLSPPLLEAIKQRLERGEQVLLFLNRRGYAPFLLCRDCGWVAE  392 (679)
T ss_pred             hccceeEEEeccccccCCCCeEEEEechhhhhhcccCCCCHHHHHHHHHHHHcCCeEEEEEcCCCCCCceEhhhCcCccC
Confidence                                   111100           0    00  112456899998863                


Q ss_pred             --------------------------------------------hHHHHHHHHHhhC--CCeeEEEeCCCC--HHHHHHH
Q psy14082        117 --------------------------------------------KKVEDITRALRRE--RHSAICIHGDKT--QQDRDYV  148 (233)
Q Consensus       117 --------------------------------------------~~~~~l~~~L~~~--~~~~~~~~~~~~--~~~r~~~  148 (233)
                                                                  ..++.+++.|++.  +.++..+|++++  +++++++
T Consensus       393 C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~l~~~g~G~e~~~e~l~~~fp~~~v~~~~~d~~~~~~~~~~~  472 (679)
T PRK05580        393 CPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGSTDLVPVGPGTERLEEELAELFPEARILRIDRDTTRRKGALEQL  472 (679)
T ss_pred             CCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCCeeEEeeccHHHHHHHHHHhCCCCcEEEEeccccccchhHHHH
Confidence                                                        2457788888776  778999999986  4678999


Q ss_pred             HHHhhCCCCCEEEecccCcCCcCCCCccEEEEe--cCCCC
Q psy14082        149 LNDFRQGKAPILVATDVAARGLDVEDVNTVNIG--SLQLS  186 (233)
Q Consensus       149 ~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~--d~P~~  186 (233)
                      +++|++|+.+|||+|+++++|+|+|+|++|+.+  |.+.+
T Consensus       473 l~~f~~g~~~ILVgT~~iakG~d~p~v~lV~il~aD~~l~  512 (679)
T PRK05580        473 LAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLF  512 (679)
T ss_pred             HHHHhcCCCCEEEEChhhccCCCCCCcCEEEEEcCchhcc
Confidence            999999999999999999999999999999655  54443

>KOG0352|consensus

Probab=99.83  E-value=1.3e-20  Score=157.86  Aligned_cols=85  Identities=21%  Similarity=0.212  Sum_probs=82.2

Q ss_pred             CeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCC
Q psy14082        107 FKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLS  186 (233)
Q Consensus       107 ~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~  186 (233)
                      +-.||||.|++.++.++-.|...|+.+..+|.|+-..+|.++-++|-+++..|+++|..++.|+|-|+|..|||||+|.|
T Consensus       256 GCGIVYCRTR~~cEq~AI~l~~~Gi~A~AYHAGLK~~ERTeVQe~WM~~~~PvI~AT~SFGMGVDKp~VRFViHW~~~qn  335 (641)
T KOG0352|consen  256 GCGIVYCRTRNECEQVAIMLEIAGIPAMAYHAGLKKKERTEVQEKWMNNEIPVIAATVSFGMGVDKPDVRFVIHWSPSQN  335 (641)
T ss_pred             cceEEEeccHHHHHHHHHHhhhcCcchHHHhcccccchhHHHHHHHhcCCCCEEEEEeccccccCCcceeEEEecCchhh
Confidence            45699999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q psy14082        187 ANHNI  191 (233)
Q Consensus       187 ~~~~i  191 (233)
                      ...|-
T Consensus       336 ~AgYY  340 (641)
T KOG0352|consen  336 LAGYY  340 (641)
T ss_pred             hHHHH
Confidence            98777

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.82  E-value=3e-19  Score=163.77  Aligned_cols=70  Identities=19%  Similarity=0.262  Sum_probs=66.4

Q ss_pred             hcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCC
Q psy14082        102 AKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVE  173 (233)
Q Consensus       102 ~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~  173 (233)
                      ....+.++||||+|++.++.++..|.+.|+++..+|+.+.++++..+.++|+.|  .|+||||+++||+|+.
T Consensus       440 ~~~~g~PVLVgt~Sie~sE~ls~~L~~~gi~h~vLnak~~q~Ea~iia~Ag~~G--~VtIATNmAGRGtDI~  509 (896)
T PRK13104        440 CGVRKQPVLVGTVSIEASEFLSQLLKKENIKHQVLNAKFHEKEAQIIAEAGRPG--AVTIATNMAGRGTDIV  509 (896)
T ss_pred             HHhCCCCEEEEeCcHHHHHHHHHHHHHcCCCeEeecCCCChHHHHHHHhCCCCC--cEEEeccCccCCccee
Confidence            456889999999999999999999999999999999999999999999999999  4999999999999985

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.82  E-value=6e-19  Score=164.98  Aligned_cols=87  Identities=18%  Similarity=0.262  Sum_probs=80.8

Q ss_pred             CCCCeEEEEecchhHHHHHHHHH-hhCCCeeEEEeCCCCHHHHHHHHHHhhCC--CCCEEEecccCcCCcCCCCccEEEE
Q psy14082        104 NPAFKVIVFVETKKKVEDITRAL-RRERHSAICIHGDKTQQDRDYVLNDFRQG--KAPILVATDVAARGLDVEDVNTVNI  180 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L-~~~~~~~~~~~~~~~~~~r~~~~~~f~~g--~~~iLv~T~~~~~Gldi~~v~~VI~  180 (233)
                      ....|+||||+++..+..+.+.| ...|+++..+||+|++.+|.++++.|+++  ..+|||||+++++|+|++.+++|||
T Consensus       491 ~~~~KvLVF~~~~~t~~~L~~~L~~~~Gi~~~~ihG~~s~~eR~~~~~~F~~~~~~~~VLIsTdvgseGlNlq~a~~VIn  570 (956)
T PRK04914        491 HRSEKVLVICAKAATALQLEQALREREGIRAAVFHEGMSIIERDRAAAYFADEEDGAQVLLCSEIGSEGRNFQFASHLVL  570 (956)
T ss_pred             cCCCeEEEEeCcHHHHHHHHHHHhhccCeeEEEEECCCCHHHHHHHHHHHhcCCCCccEEEechhhccCCCcccccEEEE
Confidence            45789999999999999999999 46799999999999999999999999984  5999999999999999999999999


Q ss_pred             ecCCCCcccc
Q psy14082        181 GSLQLSANHN  190 (233)
Q Consensus       181 ~d~P~~~~~~  190 (233)
                      ||+|+++..|
T Consensus       571 fDlP~nP~~~  580 (956)
T PRK04914        571 FDLPFNPDLL  580 (956)
T ss_pred             ecCCCCHHHH
Confidence            9999999733

>TIGR00595 priA primosomal protein N'

Probab=99.81  E-value=1.3e-18  Score=154.51  Aligned_cols=65  Identities=28%  Similarity=0.399  Sum_probs=57.3

Q ss_pred             HHHHHHHHhhC--CCeeEEEeCCCCHHHH--HHHHHHhhCCCCCEEEecccCcCCcCCCCccEEE--EecC
Q psy14082        119 VEDITRALRRE--RHSAICIHGDKTQQDR--DYVLNDFRQGKAPILVATDVAARGLDVEDVNTVN--IGSL  183 (233)
Q Consensus       119 ~~~l~~~L~~~--~~~~~~~~~~~~~~~r--~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI--~~d~  183 (233)
                      ++.+.+.|++.  +.++..+|++++...+  .+++++|++|+.+|||+|+++++|+|+|+|++|+  ++|.
T Consensus       271 te~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~i~kG~d~~~v~lV~vl~aD~  341 (505)
T TIGR00595       271 TEQVEEELAKLFPGARIARIDSDTTSRKGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADS  341 (505)
T ss_pred             HHHHHHHHHhhCCCCcEEEEecccccCccHHHHHHHHHhcCCCCEEEeCcccccCCCCCcccEEEEEcCcc
Confidence            58888888876  6789999999987766  8999999999999999999999999999999985  5554

All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

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

Probab=99.81  E-value=6.9e-19  Score=155.79  Aligned_cols=162  Identities=20%  Similarity=0.217  Sum_probs=132.3

Q ss_pred             eEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh--cCCcEEEEEcCCCC-------
Q psy14082         12 FSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS--SALRNICIFGGTPK-------   82 (233)
Q Consensus        12 i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~--~~~~~~~~~gg~~~-------   82 (233)
                      ++|+--|||||++.+++++..+        ..|.++..++||--||.|.++.+.+++  .++++..++|....       
T Consensus       287 LlQGDVGSGKTvVA~laml~ai--------~~G~Q~ALMAPTEILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l  358 (677)
T COG1200         287 LLQGDVGSGKTVVALLAMLAAI--------EAGYQAALMAPTEILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEIL  358 (677)
T ss_pred             HhccCcCCCHHHHHHHHHHHHH--------HcCCeeEEeccHHHHHHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHH
Confidence            5688899999999999999888        458899999999999999999999993  37899999998654       


Q ss_pred             ------CCeeEEe--------------------------------------------------ccc--------------
Q psy14082         83 ------GPQDCLP--------------------------------------------------LHR--------------   92 (233)
Q Consensus        83 ------~~~~lv~--------------------------------------------------l~r--------------   92 (233)
                            +.+++||                                                  +.|              
T Consensus       359 ~~l~~G~~~ivVGTHALiQd~V~F~~LgLVIiDEQHRFGV~QR~~L~~KG~~~Ph~LvMTATPIPRTLAlt~fgDldvS~  438 (677)
T COG1200         359 EQLASGEIDIVVGTHALIQDKVEFHNLGLVIIDEQHRFGVHQRLALREKGEQNPHVLVMTATPIPRTLALTAFGDLDVSI  438 (677)
T ss_pred             HHHhCCCCCEEEEcchhhhcceeecceeEEEEeccccccHHHHHHHHHhCCCCCcEEEEeCCCchHHHHHHHhccccchh
Confidence                  3344777                                                  111              


Q ss_pred             -----------------------hhhhchHHHhcCCCCeEEEEecchhHH--------HHHHHHHhhC--CCeeEEEeCC
Q psy14082         93 -----------------------FVFNCQYEMAKNPAFKVIVFVETKKKV--------EDITRALRRE--RHSAICIHGD  139 (233)
Q Consensus        93 -----------------------~~~~~~~~~~~~~~~k~iIf~~~~~~~--------~~l~~~L~~~--~~~~~~~~~~  139 (233)
                                             ++..+.+.+  .+++++.+.|+-.+..        +.+++.|+..  +.++..+||.
T Consensus       439 IdElP~GRkpI~T~~i~~~~~~~v~e~i~~ei--~~GrQaY~VcPLIeESE~l~l~~a~~~~~~L~~~~~~~~vgL~HGr  516 (677)
T COG1200         439 IDELPPGRKPITTVVIPHERRPEVYERIREEI--AKGRQAYVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGR  516 (677)
T ss_pred             hccCCCCCCceEEEEeccccHHHHHHHHHHHH--HcCCEEEEEeccccccccchhhhHHHHHHHHHHHcccceeEEEecC
Confidence                                   233332233  3889999999877544        4666666643  4679999999


Q ss_pred             CCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecC
Q psy14082        140 KTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSL  183 (233)
Q Consensus       140 ~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~  183 (233)
                      |+.+++++++++|++|+.+|||||.+.+-|+|+|+.+++|++|.
T Consensus       517 m~~~eKd~vM~~Fk~~e~~ILVaTTVIEVGVdVPnATvMVIe~A  560 (677)
T COG1200         517 MKPAEKDAVMEAFKEGEIDILVATTVIEVGVDVPNATVMVIENA  560 (677)
T ss_pred             CChHHHHHHHHHHHcCCCcEEEEeeEEEecccCCCCeEEEEech
Confidence            99999999999999999999999999999999999999998884

>KOG0353|consensus

Probab=99.79  E-value=1.1e-19  Score=150.56  Aligned_cols=178  Identities=20%  Similarity=0.221  Sum_probs=141.4

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCC
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGT   80 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~   80 (233)
                      ||...++|.|+++..|||.||++||.+|.+.           ...-+|++||...|.....-+++.+  ++....+...+
T Consensus       102 ain~~ma~ed~~lil~tgggkslcyqlpal~-----------adg~alvi~plislmedqil~lkql--gi~as~lnans  168 (695)
T KOG0353|consen  102 AINATMAGEDAFLILPTGGGKSLCYQLPALC-----------ADGFALVICPLISLMEDQILQLKQL--GIDASMLNANS  168 (695)
T ss_pred             HhhhhhccCceEEEEeCCCccchhhhhhHHh-----------cCCceEeechhHHHHHHHHHHHHHh--CcchhhccCcc
Confidence            4667789999999999999999999999985           2446899999988888777777776  55555555443


Q ss_pred             CC-------------CCee---EEe--------------------------------------------------ccc--
Q psy14082         81 PK-------------GPQD---CLP--------------------------------------------------LHR--   92 (233)
Q Consensus        81 ~~-------------~~~~---lv~--------------------------------------------------l~r--   92 (233)
                      ++             +...   .|.                                                  |+|  
T Consensus       169 ske~~k~v~~~i~nkdse~kliyvtpekiaksk~~mnkleka~~~~~~~~iaidevhccsqwghdfr~dy~~l~ilkrqf  248 (695)
T KOG0353|consen  169 SKEEAKRVEAAITNKDSEFKLIYVTPEKIAKSKKFMNKLEKALEAGFFKLIAIDEVHCCSQWGHDFRPDYKALGILKRQF  248 (695)
T ss_pred             cHHHHHHHHHHHcCCCceeEEEEecHHHHHHHHHHHHHHHHHhhcceeEEEeecceeehhhhCcccCcchHHHHHHHHhC
Confidence            33             1111   111                                                  111  


Q ss_pred             ------------------------------------------------------hhhhchHHH-hcCCCCeEEEEecchh
Q psy14082         93 ------------------------------------------------------FVFNCQYEM-AKNPAFKVIVFVETKK  117 (233)
Q Consensus        93 ------------------------------------------------------~~~~~~~~~-~~~~~~k~iIf~~~~~  117 (233)
                                                                            .+.-+.+.. ....+...||||-+++
T Consensus       249 ~~~~iigltatatn~vl~d~k~il~ie~~~tf~a~fnr~nl~yev~qkp~n~dd~~edi~k~i~~~f~gqsgiiyc~sq~  328 (695)
T KOG0353|consen  249 KGAPIIGLTATATNHVLDDAKDILCIEAAFTFRAGFNRPNLKYEVRQKPGNEDDCIEDIAKLIKGDFAGQSGIIYCFSQK  328 (695)
T ss_pred             CCCceeeeehhhhcchhhHHHHHHhHHhhheeecccCCCCceeEeeeCCCChHHHHHHHHHHhccccCCCcceEEEeccc
Confidence                                                                  111111122 2335566799999999


Q ss_pred             HHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc
Q psy14082        118 KVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI  191 (233)
Q Consensus       118 ~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i  191 (233)
                      .++.++..|+.+|+.+..+|..|.+.+|..+-+.|..|+++++|+|-.++.|+|-|+|..|||-.+|.|.+.|-
T Consensus       329 d~ekva~alkn~gi~a~~yha~lep~dks~~hq~w~a~eiqvivatvafgmgidkpdvrfvihhsl~ksienyy  402 (695)
T KOG0353|consen  329 DCEKVAKALKNHGIHAGAYHANLEPEDKSGAHQGWIAGEIQVIVATVAFGMGIDKPDVRFVIHHSLPKSIENYY  402 (695)
T ss_pred             cHHHHHHHHHhcCccccccccccCccccccccccccccceEEEEEEeeecccCCCCCeeEEEecccchhHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999998776

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.78  E-value=5.8e-18  Score=155.06  Aligned_cols=69  Identities=17%  Similarity=0.245  Sum_probs=65.3

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCC
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVED  174 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~  174 (233)
                      ..+.++||||+|+..++.++..|.+.|+++..+|+.  +.+|+..+.+|+.+...|+||||+++||+|++-
T Consensus       428 ~~grpVLIft~Si~~se~Ls~~L~~~gi~~~vLnak--q~eREa~Iia~Ag~~g~VtIATNmAGRGtDI~L  496 (830)
T PRK12904        428 KKGQPVLVGTVSIEKSELLSKLLKKAGIPHNVLNAK--NHEREAEIIAQAGRPGAVTIATNMAGRGTDIKL  496 (830)
T ss_pred             hcCCCEEEEeCcHHHHHHHHHHHHHCCCceEeccCc--hHHHHHHHHHhcCCCceEEEecccccCCcCccC
Confidence            577899999999999999999999999999999996  789999999999999999999999999999864

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

Probab=99.77  E-value=2.9e-17  Score=134.52  Aligned_cols=161  Identities=15%  Similarity=0.237  Sum_probs=132.7

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCCC--CC
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPK--GP   84 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~--~~   84 (233)
                      ...|.++.|-||+|||.+ +.+.++..+.       .|.++.|-+|..+.|..++.++++-+.+..+.+++|+++.  +.
T Consensus       115 ~k~~~lv~AV~GaGKTEM-if~~i~~al~-------~G~~vciASPRvDVclEl~~Rlk~aF~~~~I~~Lyg~S~~~fr~  186 (441)
T COG4098         115 QKEDTLVWAVTGAGKTEM-IFQGIEQALN-------QGGRVCIASPRVDVCLELYPRLKQAFSNCDIDLLYGDSDSYFRA  186 (441)
T ss_pred             hcCcEEEEEecCCCchhh-hHHHHHHHHh-------cCCeEEEecCcccchHHHHHHHHHhhccCCeeeEecCCchhccc
Confidence            467899999999999988 7777777764       4889999999999999999999999999999999999875  45


Q ss_pred             eeEEe----ccc--------------------------------------------------------------------
Q psy14082         85 QDCLP----LHR--------------------------------------------------------------------   92 (233)
Q Consensus        85 ~~lv~----l~r--------------------------------------------------------------------   92 (233)
                      +++|+    |-|                                                                    
T Consensus       187 plvVaTtHQLlrFk~aFD~liIDEVDAFP~~~d~~L~~Av~~ark~~g~~IylTATp~k~l~r~~~~g~~~~~klp~RfH  266 (441)
T COG4098         187 PLVVATTHQLLRFKQAFDLLIIDEVDAFPFSDDQSLQYAVKKARKKEGATIYLTATPTKKLERKILKGNLRILKLPARFH  266 (441)
T ss_pred             cEEEEehHHHHHHHhhccEEEEeccccccccCCHHHHHHHHHhhcccCceEEEecCChHHHHHHhhhCCeeEeecchhhc
Confidence            66676    000                                                                    


Q ss_pred             ---------------------------hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhC-C-CeeEEEeCCCCHH
Q psy14082         93 ---------------------------FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRE-R-HSAICIHGDKTQQ  143 (233)
Q Consensus        93 ---------------------------~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~-~-~~~~~~~~~~~~~  143 (233)
                                                 ++.+++  .....+.+++||+++....+.++..|++. . ..+..+|+.  ..
T Consensus       267 ~~pLpvPkf~w~~~~~k~l~r~kl~~kl~~~le--kq~~~~~P~liF~p~I~~~eq~a~~lk~~~~~~~i~~Vhs~--d~  342 (441)
T COG4098         267 GKPLPVPKFVWIGNWNKKLQRNKLPLKLKRWLE--KQRKTGRPVLIFFPEIETMEQVAAALKKKLPKETIASVHSE--DQ  342 (441)
T ss_pred             CCCCCCCceEEeccHHHHhhhccCCHHHHHHHH--HHHhcCCcEEEEecchHHHHHHHHHHHhhCCccceeeeecc--Cc
Confidence                                       111111  13446789999999999999999999544 3 455788886  56


Q ss_pred             HHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEE
Q psy14082        144 DRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVN  179 (233)
Q Consensus       144 ~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI  179 (233)
                      .|.+.+++|++|+..+|++|.+++||+.+|+||+.+
T Consensus       343 ~R~EkV~~fR~G~~~lLiTTTILERGVTfp~vdV~V  378 (441)
T COG4098         343 HRKEKVEAFRDGKITLLITTTILERGVTFPNVDVFV  378 (441)
T ss_pred             cHHHHHHHHHcCceEEEEEeehhhcccccccceEEE
Confidence            789999999999999999999999999999999876

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.75  E-value=5.6e-17  Score=148.04  Aligned_cols=87  Identities=17%  Similarity=0.232  Sum_probs=78.4

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCC---Ccc---
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVE---DVN---  176 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~---~v~---  176 (233)
                      ...+.++||||+|+..++.++..|.+.|+++..+|+++..+++..+.++++.|.  |+|||++++||.|++   +|.   
T Consensus       437 ~~~g~pvLI~t~si~~se~ls~~L~~~gi~~~~Lna~~~~~Ea~ii~~ag~~g~--VtIATnmAGRGtDI~l~~~V~~~G  514 (796)
T PRK12906        437 HAKGQPVLVGTVAIESSERLSHLLDEAGIPHAVLNAKNHAKEAEIIMNAGQRGA--VTIATNMAGRGTDIKLGPGVKELG  514 (796)
T ss_pred             HhCCCCEEEEeCcHHHHHHHHHHHHHCCCCeeEecCCcHHHHHHHHHhcCCCce--EEEEeccccCCCCCCCCcchhhhC
Confidence            457899999999999999999999999999999999999888888888777775  999999999999994   899   


Q ss_pred             --EEEEecCCCCccccc
Q psy14082        177 --TVNIGSLQLSANHNI  191 (233)
Q Consensus       177 --~VI~~d~P~~~~~~i  191 (233)
                        +||++++|.|..-|.
T Consensus       515 GLhVI~te~pes~ri~~  531 (796)
T PRK12906        515 GLAVIGTERHESRRIDN  531 (796)
T ss_pred             CcEEEeeecCCcHHHHH
Confidence              999999999987443

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

Probab=99.75  E-value=1.9e-16  Score=136.24  Aligned_cols=109  Identities=27%  Similarity=0.320  Sum_probs=91.5

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEec
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGS  182 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d  182 (233)
                      ...+.+++|-+-|++.++.+.++|.+.|+++..+|++...-+|.+++++++.|+++|||.-+.+-+|+|+|.|.+|-.+|
T Consensus       443 ~~~~eRvLVTtLTKkmAEdLT~Yl~e~gikv~YlHSdidTlER~eIirdLR~G~~DvLVGINLLREGLDiPEVsLVAIlD  522 (663)
T COG0556         443 VAKNERVLVTTLTKKMAEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILD  522 (663)
T ss_pred             HhcCCeEEEEeehHHHHHHHHHHHHhcCceEEeeeccchHHHHHHHHHHHhcCCccEEEeehhhhccCCCcceeEEEEee
Confidence            44668999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             C-----CCCcc---ccc--------ceeeEEeecchHHHHHHHHHHh
Q psy14082        183 L-----QLSAN---HNI--------SQVIEVVQDYEKEKRLFSLIRE  213 (233)
Q Consensus       183 ~-----P~~~~---~~i--------~~~~~~~~~~~~~~~~~~~i~~  213 (233)
                      -     ..|..   +-|        |+++.....  -...+-+.|++
T Consensus       523 ADKeGFLRse~SLIQtIGRAARN~~GkvIlYAD~--iT~sM~~Ai~E  567 (663)
T COG0556         523 ADKEGFLRSERSLIQTIGRAARNVNGKVILYADK--ITDSMQKAIDE  567 (663)
T ss_pred             cCccccccccchHHHHHHHHhhccCCeEEEEchh--hhHHHHHHHHH
Confidence            4     33433   333        566666653  33555555544

>KOG0952|consensus

Probab=99.75  E-value=3.7e-17  Score=149.35  Aligned_cols=178  Identities=18%  Similarity=0.147  Sum_probs=137.2

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccC--CCCCCCCceEEEEcCcHHHHHHHHHHHHHhhc--CCcEEEEEcCCC
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQE--PVKQGDGPIALVLAPTRELAQQIQTVAKEFSS--ALRNICIFGGTP   81 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~--~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~--~~~~~~~~gg~~   81 (233)
                      -+.-+.+++||||||||..|++.+++.+-++.  ......+-++++++|+++||..+.+.|.+-+.  ++++.-++|+..
T Consensus       124 ~SneNMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKALa~Em~~~~~kkl~~~gi~v~ELTGD~q  203 (1230)
T KOG0952|consen  124 KSNENMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAAEMVDKFSKKLAPLGISVRELTGDTQ  203 (1230)
T ss_pred             cCCCCEEEECCCCCCchHHHHHHHHHHHHhhccccccccCCceEEEEechHHHHHHHHHHHhhhcccccceEEEecCcch
Confidence            45678999999999999999999998887532  12225678999999999999999999988744  899999999965


Q ss_pred             C------CCeeEEe------------------------------------------------------------------
Q psy14082         82 K------GPQDCLP------------------------------------------------------------------   89 (233)
Q Consensus        82 ~------~~~~lv~------------------------------------------------------------------   89 (233)
                      -      +.|++|.                                                                  
T Consensus       204 l~~tei~~tqiiVTTPEKwDvvTRk~~~d~~l~~~V~LviIDEVHlLhd~RGpvlEtiVaRtlr~vessqs~IRivgLSA  283 (1230)
T KOG0952|consen  204 LTKTEIADTQIIVTTPEKWDVVTRKSVGDSALFSLVRLVIIDEVHLLHDDRGPVLETIVARTLRLVESSQSMIRIVGLSA  283 (1230)
T ss_pred             hhHHHHHhcCEEEecccceeeeeeeeccchhhhhheeeEEeeeehhhcCcccchHHHHHHHHHHHHHhhhhheEEEEeec
Confidence            3      4555555                                                                  


Q ss_pred             -ccchhhhch----------------------------------------------H--HHhcCCCCeEEEEecchhHHH
Q psy14082         90 -LHRFVFNCQ----------------------------------------------Y--EMAKNPAFKVIVFVETKKKVE  120 (233)
Q Consensus        90 -l~r~~~~~~----------------------------------------------~--~~~~~~~~k~iIf~~~~~~~~  120 (233)
                       |..+.|+..                                              +  .-.-..+.+++|||.+++.+.
T Consensus       284 TlPN~eDvA~fL~vn~~~glfsFd~~yRPvpL~~~~iG~k~~~~~~~~~~~d~~~~~kv~e~~~~g~qVlvFvhsR~~Ti  363 (1230)
T KOG0952|consen  284 TLPNYEDVARFLRVNPYAGLFSFDQRYRPVPLTQGFIGIKGKKNRQQKKNIDEVCYDKVVEFLQEGHQVLVFVHSRNETI  363 (1230)
T ss_pred             cCCCHHHHHHHhcCCCccceeeecccccccceeeeEEeeecccchhhhhhHHHHHHHHHHHHHHcCCeEEEEEecChHHH
Confidence             000111100                                              0  112347889999999999999


Q ss_pred             HHHHHHhhC----C-------------------CeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccE
Q psy14082        121 DITRALRRE----R-------------------HSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNT  177 (233)
Q Consensus       121 ~l~~~L~~~----~-------------------~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~  177 (233)
                      ..++.|.+.    |                   ....+.|+||..++|....+.|+.|.+++|+||..++.|.|+|+-- 
T Consensus       364 ~tA~~l~~~a~~~g~~~~f~~~~~~k~l~elf~~g~~iHhAGm~r~DR~l~E~~F~~G~i~vL~cTaTLAwGVNLPA~a-  442 (1230)
T KOG0952|consen  364 RTAKKLRERAETNGEKDLFLPSPRNKQLKELFQQGMGIHHAGMLRSDRQLVEKEFKEGHIKVLCCTATLAWGVNLPAYA-  442 (1230)
T ss_pred             HHHHHHHHHHHhcCcccccCCChhhHHHHHHHHhhhhhcccccchhhHHHHHHHHhcCCceEEEecceeeeccCCcceE-
Confidence            999998743    1                   2356789999999999999999999999999999999999998765 


Q ss_pred             EEEecCC
Q psy14082        178 VNIGSLQ  184 (233)
Q Consensus       178 VI~~d~P  184 (233)
                      ||..+-+
T Consensus       443 ViIKGT~  449 (1230)
T KOG0952|consen  443 VIIKGTQ  449 (1230)
T ss_pred             EEecCCc
Confidence            4444433

>PRK09694 helicase Cas3; Provisional

Probab=99.74  E-value=7.3e-17  Score=150.16  Aligned_cols=91  Identities=21%  Similarity=0.304  Sum_probs=74.5

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCC---CeeEEEeCCCCHHHH----HHHHHHh-hCCC---CCEEEecccCcCCcCCC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRER---HSAICIHGDKTQQDR----DYVLNDF-RQGK---APILVATDVAARGLDVE  173 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~---~~~~~~~~~~~~~~r----~~~~~~f-~~g~---~~iLv~T~~~~~Gldi~  173 (233)
                      .+++++|||||++.++.+++.|++.+   .++..+||+++..+|    .++++.| ++|+   ..|||+|+++++|+|+ 
T Consensus       559 ~g~~vLVf~NTV~~Aq~ly~~L~~~~~~~~~v~llHsrf~~~dR~~~E~~vl~~fgk~g~r~~~~ILVaTQViE~GLDI-  637 (878)
T PRK09694        559 AGAQVCLICNLVDDAQKLYQRLKELNNTQVDIDLFHARFTLNDRREKEQRVIENFGKNGKRNQGRILVATQVVEQSLDL-  637 (878)
T ss_pred             cCCEEEEEECCHHHHHHHHHHHHhhCCCCceEEEEeCCCCHHHHHHHHHHHHHHHHhcCCcCCCeEEEECcchhheeec-
Confidence            56789999999999999999998765   689999999999999    4577888 6665   4699999999999999 


Q ss_pred             CccEEEEecCCCCc-ccccceeeE
Q psy14082        174 DVNTVNIGSLQLSA-NHNISQVIE  196 (233)
Q Consensus       174 ~v~~VI~~d~P~~~-~~~i~~~~~  196 (233)
                      ++|++|....|.+. -|++||+.+
T Consensus       638 d~DvlItdlaPidsLiQRaGR~~R  661 (878)
T PRK09694        638 DFDWLITQLCPVDLLFQRLGRLHR  661 (878)
T ss_pred             CCCeEEECCCCHHHHHHHHhccCC
Confidence            68999998888432 244444333

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.72  E-value=1.4e-16  Score=146.10  Aligned_cols=69  Identities=20%  Similarity=0.311  Sum_probs=65.9

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCC
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVE  173 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~  173 (233)
                      ...+.++||||+|...++.++..|.+.|+++..+|+.+++.++..+.++|+.|.  |+||||+++||.|+.
T Consensus       446 ~~~GrpVLV~t~sv~~se~ls~~L~~~gi~~~vLnak~~~~Ea~ii~~Ag~~G~--VtIATnmAGRGTDIk  514 (908)
T PRK13107        446 RERGQPVLVGTVSIEQSELLARLMVKEKIPHEVLNAKFHEREAEIVAQAGRTGA--VTIATNMAGRGTDIV  514 (908)
T ss_pred             HHcCCCEEEEeCcHHHHHHHHHHHHHCCCCeEeccCcccHHHHHHHHhCCCCCc--EEEecCCcCCCccee
Confidence            457899999999999999999999999999999999999999999999999997  999999999999985

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

Probab=99.71  E-value=2.4e-16  Score=150.40  Aligned_cols=93  Identities=18%  Similarity=0.297  Sum_probs=77.9

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhC------C---CeeEEEeCCCCHHHHHHHHHHhhCCCC-CEEEecccCcCCcCCCC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRE------R---HSAICIHGDKTQQDRDYVLNDFRQGKA-PILVATDVAARGLDVED  174 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~------~---~~~~~~~~~~~~~~r~~~~~~f~~g~~-~iLv~T~~~~~Gldi~~  174 (233)
                      ..+|+||||.++++++.+.+.|.+.      +   ..+..+||+++  ++.+++++|+++.. +|+|+++++++|+|+|.
T Consensus       697 ~~~KtiIF~~s~~HA~~i~~~L~~~f~~~~~~~~~~~v~~itg~~~--~~~~li~~Fk~~~~p~IlVsvdmL~TG~DvP~  774 (1123)
T PRK11448        697 GEGKTLIFAATDAHADMVVRLLKEAFKKKYGQVEDDAVIKITGSID--KPDQLIRRFKNERLPNIVVTVDLLTTGIDVPS  774 (1123)
T ss_pred             CCCcEEEEEcCHHHHHHHHHHHHHHHHhhcCCcCccceEEEeCCcc--chHHHHHHHhCCCCCeEEEEecccccCCCccc
Confidence            3479999999999999999887653      2   24567899876  46789999999887 58999999999999999


Q ss_pred             ccEEEEecCCCCccc---ccceeeEEee
Q psy14082        175 VNTVNIGSLQLSANH---NISQVIEVVQ  199 (233)
Q Consensus       175 v~~VI~~d~P~~~~~---~i~~~~~~~~  199 (233)
                      +++||.+++|.|...   .|||+.+.+.
T Consensus       775 v~~vVf~rpvkS~~lf~QmIGRgtR~~~  802 (1123)
T PRK11448        775 ICNLVFLRRVRSRILYEQMLGRATRLCP  802 (1123)
T ss_pred             ccEEEEecCCCCHHHHHHHHhhhccCCc
Confidence            999999999999874   4577777665

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.70  E-value=1.6e-16  Score=151.31  Aligned_cols=77  Identities=17%  Similarity=0.283  Sum_probs=69.9

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCCCe---eEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEE
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRERHS---AICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNI  180 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~~~---~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~  180 (233)
                      ...+++|||+++...++.+++.|.+.++.   +..+||+|++++|..+++.  .|..+|+||||++++|+|+|+|++||+
T Consensus       284 ~~~GdILVFLpg~~EIe~lae~L~~~~~~~~~VlpLhg~Ls~~eQ~~Vf~~--~g~rkIIVATNIAEtSITIpgI~yVID  361 (1294)
T PRK11131        284 EGPGDILIFMSGEREIRDTADALNKLNLRHTEILPLYARLSNSEQNRVFQS--HSGRRIVLATNVAETSLTVPGIKYVID  361 (1294)
T ss_pred             CCCCCEEEEcCCHHHHHHHHHHHHhcCCCcceEeecccCCCHHHHHHHhcc--cCCeeEEEeccHHhhccccCcceEEEE
Confidence            45678999999999999999999987764   6789999999999999886  477899999999999999999999999


Q ss_pred             ec
Q psy14082        181 GS  182 (233)
Q Consensus       181 ~d  182 (233)
                      +|
T Consensus       362 ~G  363 (1294)
T PRK11131        362 PG  363 (1294)
T ss_pred             CC
Confidence            86

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

Probab=99.66  E-value=5.8e-15  Score=137.70  Aligned_cols=167  Identities=22%  Similarity=0.185  Sum_probs=134.0

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcC--CcEEEEEcCCCC---
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSA--LRNICIFGGTPK---   82 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~--~~~~~~~gg~~~---   82 (233)
                      .-|=++|+--|-|||-+.+=+++-.++        .|.++.+||||--||+|.|++|++-+.+  +++..+.-=.+.   
T Consensus       615 pMDRLiCGDVGFGKTEVAmRAAFkAV~--------~GKQVAvLVPTTlLA~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~  686 (1139)
T COG1197         615 PMDRLICGDVGFGKTEVAMRAAFKAVM--------DGKQVAVLVPTTLLAQQHYETFKERFAGFPVRIEVLSRFRSAKEQ  686 (1139)
T ss_pred             cchheeecCcCCcHHHHHHHHHHHHhc--------CCCeEEEEcccHHhHHHHHHHHHHHhcCCCeeEEEecccCCHHHH
Confidence            457789999999999998888887775        4789999999999999999999997554  455555443322   


Q ss_pred             ----------CCeeEEeccc------------------------------------------------------------
Q psy14082         83 ----------GPQDCLPLHR------------------------------------------------------------   92 (233)
Q Consensus        83 ----------~~~~lv~l~r------------------------------------------------------------   92 (233)
                                +-+|+||-+|                                                            
T Consensus       687 ~~il~~la~G~vDIvIGTHrLL~kdv~FkdLGLlIIDEEqRFGVk~KEkLK~Lr~~VDvLTLSATPIPRTL~Msm~GiRd  766 (1139)
T COG1197         687 KEILKGLAEGKVDIVIGTHRLLSKDVKFKDLGLLIIDEEQRFGVKHKEKLKELRANVDVLTLSATPIPRTLNMSLSGIRD  766 (1139)
T ss_pred             HHHHHHHhcCCccEEEechHhhCCCcEEecCCeEEEechhhcCccHHHHHHHHhccCcEEEeeCCCCcchHHHHHhcchh
Confidence                      3445777222                                                            


Q ss_pred             ----------------hhhh-----chH-H-HhcCCCCeEEEEecchhHHHHHHHHHhhC--CCeeEEEeCCCCHHHHHH
Q psy14082         93 ----------------FVFN-----CQY-E-MAKNPAFKVIVFVETKKKVEDITRALRRE--RHSAICIHGDKTQQDRDY  147 (233)
Q Consensus        93 ----------------~~~~-----~~~-~-~~~~~~~k~iIf~~~~~~~~~l~~~L~~~--~~~~~~~~~~~~~~~r~~  147 (233)
                                      ++..     +++ . -....++++.-..|..++.+.++..|+++  ..++.+.||.|+..+-++
T Consensus       767 lSvI~TPP~~R~pV~T~V~~~d~~~ireAI~REl~RgGQvfYv~NrV~~Ie~~~~~L~~LVPEarI~vaHGQM~e~eLE~  846 (1139)
T COG1197         767 LSVIATPPEDRLPVKTFVSEYDDLLIREAILRELLRGGQVFYVHNRVESIEKKAERLRELVPEARIAVAHGQMRERELEE  846 (1139)
T ss_pred             hhhccCCCCCCcceEEEEecCChHHHHHHHHHHHhcCCEEEEEecchhhHHHHHHHHHHhCCceEEEEeecCCCHHHHHH
Confidence                            0000     000 1 12347889999999999999999999987  568899999999999999


Q ss_pred             HHHHhhCCCCCEEEecccCcCCcCCCCccEEEEec
Q psy14082        148 VLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGS  182 (233)
Q Consensus       148 ~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d  182 (233)
                      ++.+|.+|+++|||||.+.+.|+|+|+++.+|.-+
T Consensus       847 vM~~F~~g~~dVLv~TTIIEtGIDIPnANTiIIe~  881 (1139)
T COG1197         847 VMLDFYNGEYDVLVCTTIIETGIDIPNANTIIIER  881 (1139)
T ss_pred             HHHHHHcCCCCEEEEeeeeecCcCCCCCceEEEec
Confidence            99999999999999999999999999999999765

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=99.66  E-value=1.3e-14  Score=136.77  Aligned_cols=108  Identities=18%  Similarity=0.298  Sum_probs=92.8

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCC---CCEEEecccCcCCcCCCCccEEEEe
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGK---APILVATDVAARGLDVEDVNTVNIG  181 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~---~~iLv~T~~~~~Gldi~~v~~VI~~  181 (233)
                      .+.|+|||+......+.+.+.|...++....++|+++..+|..+++.|+...   .-+|++|.+++.|+|+..+++||+|
T Consensus       486 ~g~KVLIFSQft~~LdiLed~L~~~g~~y~rIdGsts~~eRq~~Id~Fn~~~s~~~VfLLSTrAGGlGINLt~Ad~VIiy  565 (1033)
T PLN03142        486 RDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVFLLSTRAGGLGINLATADIVILY  565 (1033)
T ss_pred             cCCeEEeehhHHHHHHHHHHHHHHcCCcEEEECCCCCHHHHHHHHHHhccccCCceEEEEeccccccCCchhhCCEEEEe
Confidence            5679999999999999999999999999999999999999999999998643   3478999999999999999999999


Q ss_pred             cCCCCcc---------cccc-----eeeEEeecchHHHHHHHHHH
Q psy14082        182 SLQLSAN---------HNIS-----QVIEVVQDYEKEKRLFSLIR  212 (233)
Q Consensus       182 d~P~~~~---------~~i~-----~~~~~~~~~~~~~~~~~~i~  212 (233)
                      |+|+++.         ||||     .+.+++...--++++++...
T Consensus       566 D~dWNP~~d~QAidRaHRIGQkk~V~VyRLIt~gTIEEkIlera~  610 (1033)
T PLN03142        566 DSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAY  610 (1033)
T ss_pred             CCCCChHHHHHHHHHhhhcCCCceEEEEEEEeCCcHHHHHHHHHH
Confidence            9999986         6666     56677776655566665443

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

Probab=99.63  E-value=9.4e-15  Score=133.83  Aligned_cols=79  Identities=27%  Similarity=0.418  Sum_probs=69.9

Q ss_pred             cCCCCeEEEEecc---hhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEec----ccCcCCcCCCC-
Q psy14082        103 KNPAFKVIVFVET---KKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVAT----DVAARGLDVED-  174 (233)
Q Consensus       103 ~~~~~k~iIf~~~---~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T----~~~~~Gldi~~-  174 (233)
                      +.-+.-.|||++.   ++.++++++.|+++|+++..+|+.     ..+.++.|..|+.++||+.    ..+.||+|+|. 
T Consensus       332 k~lG~GgLIfV~~d~G~e~aeel~e~Lr~~Gi~a~~~~a~-----~~~~le~F~~GeidvLVGvAsyYG~lVRGlDLP~r  406 (1187)
T COG1110         332 KKLGDGGLIFVPIDYGREKAEELAEYLRSHGINAELIHAE-----KEEALEDFEEGEVDVLVGVASYYGVLVRGLDLPHR  406 (1187)
T ss_pred             HHhCCCeEEEEEcHHhHHHHHHHHHHHHhcCceEEEeecc-----chhhhhhhccCceeEEEEecccccceeecCCchhh
Confidence            3455578999999   999999999999999999999994     4789999999999999885    68999999996 


Q ss_pred             ccEEEEecCCCC
Q psy14082        175 VNTVNIGSLQLS  186 (233)
Q Consensus       175 v~~VI~~d~P~~  186 (233)
                      +.++|.|+.|+-
T Consensus       407 irYaIF~GvPk~  418 (1187)
T COG1110         407 IRYAVFYGVPKF  418 (1187)
T ss_pred             eeEEEEecCCce
Confidence            789999999943

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.61  E-value=8.5e-15  Score=139.99  Aligned_cols=79  Identities=16%  Similarity=0.276  Sum_probs=69.6

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCC---CeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEe
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRER---HSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIG  181 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~---~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~  181 (233)
                      ..+.+|||+++...++.+++.|.+.+   ..+..+||+|++++|..+++.+  +..+|++|||++++|+|+|+|++||++
T Consensus       278 ~~GdILVFLpg~~EI~~l~~~L~~~~~~~~~VlpLhg~Ls~~eQ~~vf~~~--~~rkIVLATNIAEtSLTIpgV~yVIDs  355 (1283)
T TIGR01967       278 GPGDILIFLPGEREIRDAAEILRKRNLRHTEILPLYARLSNKEQQRVFQPH--SGRRIVLATNVAETSLTVPGIHYVIDT  355 (1283)
T ss_pred             CCCCEEEeCCCHHHHHHHHHHHHhcCCCCcEEEeccCCCCHHHHHHHhCCC--CCceEEEeccHHHhccccCCeeEEEeC
Confidence            45789999999999999999998764   4578899999999999986654  246899999999999999999999999


Q ss_pred             cCCC
Q psy14082        182 SLQL  185 (233)
Q Consensus       182 d~P~  185 (233)
                      |++.
T Consensus       356 Gl~r  359 (1283)
T TIGR01967       356 GTAR  359 (1283)
T ss_pred             CCcc
Confidence            9664

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.

>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=99.59  E-value=9.7e-16  Score=102.62  Aligned_cols=73  Identities=27%  Similarity=0.469  Sum_probs=67.3

Q ss_pred             HHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCcccccceeeE
Q psy14082        124 RALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQVIE  196 (233)
Q Consensus       124 ~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i~~~~~  196 (233)
                      +.|++.++++..+||+++.++|..+++.|++++.++||||+.+++|+|+|++++||+||+|+|...|+++.++
T Consensus         1 ~~L~~~~~~~~~i~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gid~~~~~~vi~~~~~~~~~~~~Q~~GR   73 (78)
T PF00271_consen    1 KFLEKKGIKVAIIHGDMSQKERQEILKKFNSGEIRVLIATDILGEGIDLPDASHVIFYDPPWSPEEYIQRIGR   73 (78)
T ss_dssp             HHHHHTTSSEEEESTTSHHHHHHHHHHHHHTTSSSEEEESCGGTTSSTSTTESEEEESSSESSHHHHHHHHTT
T ss_pred             CChHHCCCcEEEEECCCCHHHHHHHHHHhhccCceEEEeeccccccccccccccccccccCCCHHHHHHHhhc
Confidence            3678889999999999999999999999999999999999999999999999999999999999877754443

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 ....

>KOG0951|consensus

Probab=99.58  E-value=6.5e-14  Score=130.24  Aligned_cols=173  Identities=16%  Similarity=0.166  Sum_probs=135.1

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCC---CCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEcCCCC
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEP---VKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGGTPK   82 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~---~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~gg~~~   82 (233)
                      .-+++++||||+|||-..++-+++.+-.+..   ...-...++++++|.+.|++.+...|.+.  .-++++.-++|+...
T Consensus       325 ~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAPmKaLvqE~VgsfSkRla~~GI~V~ElTgD~~l  404 (1674)
T KOG0951|consen  325 DENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAPMKALVQEMVGSFSKRLAPLGITVLELTGDSQL  404 (1674)
T ss_pred             cCcEEEeccCCCCchHHHHHHHHHHHhcccccccceecccceEEEEeeHHHHHHHHHHHHHhhccccCcEEEEecccccc
Confidence            4568999999999999999999998876532   11123468999999999999999988776  558899999998552


Q ss_pred             ------CCeeEEe-------ccc---------------------------------------------------------
Q psy14082         83 ------GPQDCLP-------LHR---------------------------------------------------------   92 (233)
Q Consensus        83 ------~~~~lv~-------l~r---------------------------------------------------------   92 (233)
                            ..|++|+       +.|                                                         
T Consensus       405 ~~~qieeTqVIV~TPEK~DiITRk~gdraY~qlvrLlIIDEIHLLhDdRGpvLESIVaRt~r~ses~~e~~RlVGLSATL  484 (1674)
T KOG0951|consen  405 GKEQIEETQVIVTTPEKWDIITRKSGDRAYEQLVRLLIIDEIHLLHDDRGPVLESIVARTFRRSESTEEGSRLVGLSATL  484 (1674)
T ss_pred             hhhhhhcceeEEeccchhhhhhcccCchhHHHHHHHHhhhhhhhcccccchHHHHHHHHHHHHhhhcccCceeeeecccC
Confidence                  4455666       000                                                         


Q ss_pred             -----------------------------------------------hhhhchH-HHhcCCCCeEEEEecchhHHHHHHH
Q psy14082         93 -----------------------------------------------FVFNCQY-EMAKNPAFKVIVFVETKKKVEDITR  124 (233)
Q Consensus        93 -----------------------------------------------~~~~~~~-~~~~~~~~k~iIf~~~~~~~~~l~~  124 (233)
                                                                     +-+.|-+ .+......++|||+.+|+.+...+.
T Consensus       485 PNy~DV~~Fl~v~~~glf~fd~syRpvPL~qq~Igi~ek~~~~~~qamNe~~yeKVm~~agk~qVLVFVHsRkET~ktA~  564 (1674)
T KOG0951|consen  485 PNYEDVASFLRVDPEGLFYFDSSYRPVPLKQQYIGITEKKPLKRFQAMNEACYEKVLEHAGKNQVLVFVHSRKETAKTAR  564 (1674)
T ss_pred             CchhhhHHHhccCcccccccCcccCcCCccceEeccccCCchHHHHHHHHHHHHHHHHhCCCCcEEEEEEechHHHHHHH
Confidence                                                           1112211 3444556899999999999988888


Q ss_pred             HHhh-------------------------------------CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCc
Q psy14082        125 ALRR-------------------------------------ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA  167 (233)
Q Consensus       125 ~L~~-------------------------------------~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~  167 (233)
                      .++.                                     ..+...+.|+||+..+|..+.+.|++|++++||+|-.++
T Consensus       565 aIRd~~le~dtls~fmre~s~s~eilrtea~~~kn~dLkdLLpygfaIHhAGl~R~dR~~~EdLf~~g~iqvlvstatla  644 (1674)
T KOG0951|consen  565 AIRDKALEEDTLSRFMREDSASREILRTEAGQAKNPDLKDLLPYGFAIHHAGLNRKDRELVEDLFADGHIQVLVSTATLA  644 (1674)
T ss_pred             HHHHHHhhhhHHHHHHhcccchhhhhhhhhhcccChhHHHHhhccceeeccCCCcchHHHHHHHHhcCceeEEEeehhhh
Confidence            8872                                     023678899999999999999999999999999999999


Q ss_pred             CCcCCCCccEEEE
Q psy14082        168 RGLDVEDVNTVNI  180 (233)
Q Consensus       168 ~Gldi~~v~~VI~  180 (233)
                      +|+|+|.-.++|-
T Consensus       645 wgvnlpahtViik  657 (1674)
T KOG0951|consen  645 WGVNLPAHTVIIK  657 (1674)
T ss_pred             hhcCCCcceEEec
Confidence            9999999887763

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.56  E-value=3.1e-14  Score=129.85  Aligned_cols=107  Identities=26%  Similarity=0.327  Sum_probs=93.4

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEec--
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGS--  182 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d--  182 (233)
                      .+.+++|||++++.++.+++.|.+.|+.+..+||++++.+|.++++.|+.|++++||||+.+++|+|+|++++|+++|  
T Consensus       441 ~g~~vLIf~~tk~~ae~L~~~L~~~gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t~~L~rGfDiP~v~lVvi~Dad  520 (655)
T TIGR00631       441 RNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDAD  520 (655)
T ss_pred             CCCEEEEEECCHHHHHHHHHHHhhhccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEcChhcCCeeeCCCcEEEEeCcc
Confidence            567899999999999999999999999999999999999999999999999999999999999999999999999999  


Q ss_pred             ---CCCCccccc-----------ceeeEEeecchHHHHHHHHHHh
Q psy14082        183 ---LQLSANHNI-----------SQVIEVVQDYEKEKRLFSLIRE  213 (233)
Q Consensus       183 ---~P~~~~~~i-----------~~~~~~~~~~~~~~~~~~~i~~  213 (233)
                         +|.+...||           |+++.+++...  ..+.+.|++
T Consensus       521 ifG~p~~~~~~iqriGRagR~~~G~vi~~~~~~~--~~~~~ai~~  563 (655)
T TIGR00631       521 KEGFLRSERSLIQTIGRAARNVNGKVIMYADKIT--DSMQKAIEE  563 (655)
T ss_pred             cccCCCCHHHHHHHhcCCCCCCCCEEEEEEcCCC--HHHHHHHHH
Confidence               898887666           45566766433  444444444

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

>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=99.55  E-value=3.6e-14  Score=103.83  Aligned_cols=96  Identities=33%  Similarity=0.535  Sum_probs=88.3

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQ  184 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P  184 (233)
                      .+.++||||++.+.++.+++.|.+.+..+..+||+++..+|..++++|+++...+|++|+.+++|+|+|.+++||.+++|
T Consensus        27 ~~~~~lvf~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ili~t~~~~~G~d~~~~~~vi~~~~~  106 (131)
T cd00079          27 KGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLP  106 (131)
T ss_pred             CCCcEEEEeCcHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcChhhcCcChhhCCEEEEeCCC
Confidence            47899999999999999999999988999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcccccceeeEEeec
Q psy14082        185 LSANHNISQVIEVVQD  200 (233)
Q Consensus       185 ~~~~~~i~~~~~~~~~  200 (233)
                      ++...+++..++..+.
T Consensus       107 ~~~~~~~Q~~GR~~R~  122 (131)
T cd00079         107 WSPSSYLQRIGRAGRA  122 (131)
T ss_pred             CCHHHheecccccccC
Confidence            9998777555555544

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=99.50  E-value=2.8e-13  Score=124.15  Aligned_cols=87  Identities=28%  Similarity=0.349  Sum_probs=82.2

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecC-
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSL-  183 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~-  183 (233)
                      .+.+++|||++++.++.+++.|.+.|+++..+||++++.+|..+++.|+.|+.+++|||+.+++|+|+|++++||++|. 
T Consensus       445 ~g~~viIf~~t~~~ae~L~~~L~~~gi~~~~~h~~~~~~~R~~~l~~f~~g~i~vlV~t~~L~rGfdlp~v~lVii~d~e  524 (652)
T PRK05298        445 KGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDIPEVSLVAILDAD  524 (652)
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHhhcceeEEEEECCCCHHHHHHHHHHHHcCCceEEEEeCHHhCCccccCCcEEEEeCCc
Confidence            5678999999999999999999999999999999999999999999999999999999999999999999999999984 


Q ss_pred             ----CCCccccc
Q psy14082        184 ----QLSANHNI  191 (233)
Q Consensus       184 ----P~~~~~~i  191 (233)
                          |.+...||
T Consensus       525 ifG~~~~~~~yi  536 (652)
T PRK05298        525 KEGFLRSERSLI  536 (652)
T ss_pred             ccccCCCHHHHH
Confidence                77877666

>cd00268 DEADc DEAD-box helicases

Probab=99.45  E-value=2.4e-13  Score=107.37  Aligned_cols=78  Identities=35%  Similarity=0.573  Sum_probs=66.9

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEcC
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGG   79 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~gg   79 (233)
                      ++.+.+|+|+++.+|||+|||++|++|+++++....   ...+++++|++||++|+.|+.+.++.+  ..++++..+.|+
T Consensus        30 ~~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~---~~~~~~viii~p~~~L~~q~~~~~~~~~~~~~~~~~~~~~~  106 (203)
T cd00268          30 IPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSP---KKDGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGG  106 (203)
T ss_pred             HHHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhhc---ccCCceEEEEcCCHHHHHHHHHHHHHHhccCCceEEEEECC
Confidence            456778999999999999999999999999987642   135789999999999999999999999  347788888888


Q ss_pred             CCC
Q psy14082         80 TPK   82 (233)
Q Consensus        80 ~~~   82 (233)
                      .+.
T Consensus       107 ~~~  109 (203)
T cd00268         107 TSI  109 (203)
T ss_pred             CCH
Confidence            765

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.

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

Probab=99.42  E-value=6.6e-12  Score=114.56  Aligned_cols=65  Identities=17%  Similarity=0.111  Sum_probs=53.5

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCCC
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPK   82 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~   82 (233)
                      +-.+..+-||||||.+|+=.+-..+        ..|.++|+|+|-..|..|+.+.|+..+. .++..++++.+.
T Consensus       218 ~~~Ll~GvTGSGKTEvYl~~i~~~L--------~~GkqvLvLVPEI~Ltpq~~~rf~~rFg-~~v~vlHS~Ls~  282 (730)
T COG1198         218 APFLLDGVTGSGKTEVYLEAIAKVL--------AQGKQVLVLVPEIALTPQLLARFKARFG-AKVAVLHSGLSP  282 (730)
T ss_pred             cceeEeCCCCCcHHHHHHHHHHHHH--------HcCCEEEEEeccccchHHHHHHHHHHhC-CChhhhcccCCh
Confidence            4467788999999999876555544        3478999999999999999999999865 788888888665

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.42  E-value=4.4e-13  Score=123.68  Aligned_cols=81  Identities=10%  Similarity=-0.029  Sum_probs=70.7

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~g   78 (233)
                      +||.++.++|++++|+||+|||++|++|++..++..        ..++||+||+|||.|+++.+..+  +.++++.+++|
T Consensus       100 ~I~~i~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~g--------~~v~IVTpTrELA~Qdae~m~~L~k~lGLsV~~i~G  171 (970)
T PRK12899        100 ILGAIAMHKGFITEMQTGEGKTLTAVMPLYLNALTG--------KPVHLVTVNDYLAQRDCEWVGSVLRWLGLTTGVLVS  171 (970)
T ss_pred             HhhhhhcCCCeEEEeCCCCChHHHHHHHHHHHHhhc--------CCeEEEeCCHHHHHHHHHHHHHHHhhcCCeEEEEeC
Confidence            478899999999999999999999999999888642        23899999999999999999999  56789999999


Q ss_pred             CCCC-------CCeeEEe
Q psy14082         79 GTPK-------GPQDCLP   89 (233)
Q Consensus        79 g~~~-------~~~~lv~   89 (233)
                      |.+.       .+++++|
T Consensus       172 G~~~~eq~~~y~~DIVyg  189 (970)
T PRK12899        172 GSPLEKRKEIYQCDVVYG  189 (970)
T ss_pred             CCCHHHHHHHcCCCEEEE
Confidence            9765       4567777

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=99.40  E-value=7.4e-13  Score=88.77  Aligned_cols=76  Identities=34%  Similarity=0.511  Sum_probs=68.6

Q ss_pred             HHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCcccccceeeE
Q psy14082        121 DITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQVIE  196 (233)
Q Consensus       121 ~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i~~~~~  196 (233)
                      .+.+.|...++.+..+||+|+.++|..+++.|+++...+|++|+.+++|+|+|++++||.+++|.+...+++..++
T Consensus         2 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gi~~~~~~~vi~~~~~~~~~~~~Q~~gR   77 (82)
T smart00490        2 ELAELLKELGIKVARLHGGLSQEEREEILEKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGR   77 (82)
T ss_pred             HHHHHHHHCCCeEEEEECCCCHHHHHHHHHHHHcCCCeEEEECChhhCCcChhcCCEEEEeCCCCCHHHHHHhhcc
Confidence            4667788889999999999999999999999999999999999999999999999999999999999866644443

>KOG0385|consensus

Probab=99.40  E-value=1.4e-11  Score=110.37  Aligned_cols=109  Identities=14%  Similarity=0.272  Sum_probs=96.7

Q ss_pred             hcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCC---CCEEEecccCcCCcCCCCccEE
Q psy14082        102 AKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGK---APILVATDVAARGLDVEDVNTV  178 (233)
Q Consensus       102 ~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~---~~iLv~T~~~~~Gldi~~v~~V  178 (233)
                      ....++|++||..-....+-+.+++.-+++...-+.|.++.++|...++.|....   .-.|++|.+.+-|||+..+|+|
T Consensus       483 Lk~~GhRVLIFSQmt~mLDILeDyc~~R~y~ycRiDGSt~~eeR~~aI~~fn~~~s~~FiFlLSTRAGGLGINL~aADtV  562 (971)
T KOG0385|consen  483 LKEQGHRVLIFSQMTRMLDILEDYCMLRGYEYCRLDGSTSHEEREDAIEAFNAPPSEKFIFLLSTRAGGLGINLTAADTV  562 (971)
T ss_pred             HHhCCCeEEEeHHHHHHHHHHHHHHHhcCceeEeecCCCCcHHHHHHHHhcCCCCcceEEEEEeccccccccccccccEE
Confidence            4568899999999999999999999999999999999999999999999998765   3378999999999999999999


Q ss_pred             EEecCCCCcc---------cccc-----eeeEEeecchHHHHHHHH
Q psy14082        179 NIGSLQLSAN---------HNIS-----QVIEVVQDYEKEKRLFSL  210 (233)
Q Consensus       179 I~~d~P~~~~---------~~i~-----~~~~~~~~~~~~~~~~~~  210 (233)
                      |.||..+++.         ||||     +++++++++.-++++++-
T Consensus       563 IlyDSDWNPQ~DLQAmDRaHRIGQ~K~V~V~RLitentVEe~IveR  608 (971)
T KOG0385|consen  563 ILYDSDWNPQVDLQAMDRAHRIGQKKPVVVYRLITENTVEEKIVER  608 (971)
T ss_pred             EEecCCCCchhhhHHHHHHHhhCCcCceEEEEEeccchHHHHHHHH
Confidence            9999999985         8887     789999987766666554

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

Probab=99.38  E-value=2e-11  Score=115.33  Aligned_cols=79  Identities=16%  Similarity=0.229  Sum_probs=63.4

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCcc--EE
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVN--TV  178 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~--~V  178 (233)
                      ..++++||+++.+..+.++..|...    ++.  ++..+.. ..|.+++++|++++..||++|+.+.||+|+|+..  +|
T Consensus       673 ~~g~~LVlftS~~~l~~v~~~L~~~~~~~~~~--~l~q~~~-~~r~~ll~~F~~~~~~iLlgt~sf~EGVD~~g~~l~~v  749 (850)
T TIGR01407       673 TSPKILVLFTSYEMLHMVYDMLNELPEFEGYE--VLAQGIN-GSRAKIKKRFNNGEKAILLGTSSFWEGVDFPGNGLVCL  749 (850)
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHhhhccccCce--EEecCCC-ccHHHHHHHHHhCCCeEEEEcceeecccccCCCceEEE
Confidence            5578999999999999999999752    333  3333333 5788999999999999999999999999999876  57


Q ss_pred             EEecCCCC
Q psy14082        179 NIGSLQLS  186 (233)
Q Consensus       179 I~~d~P~~  186 (233)
                      |...+|..
T Consensus       750 iI~~LPf~  757 (850)
T TIGR01407       750 VIPRLPFA  757 (850)
T ss_pred             EEeCCCCC
Confidence            77777743

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.

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

Probab=99.38  E-value=1.4e-11  Score=111.60  Aligned_cols=184  Identities=18%  Similarity=0.186  Sum_probs=129.1

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCCCC--CeeE
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPKG--PQDC   87 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~~--~~~l   87 (233)
                      -++++++||||||-+ ++.++.+|++.     +...|+|+|+-++.|+.|.+..+..+.+.-....++.+...+  .++.
T Consensus       187 raLlvMATGTGKTrT-Aiaii~rL~r~-----~~~KRVLFLaDR~~Lv~QA~~af~~~~P~~~~~n~i~~~~~~~s~~i~  260 (875)
T COG4096         187 RALLVMATGTGKTRT-AIAIIDRLIKS-----GWVKRVLFLADRNALVDQAYGAFEDFLPFGTKMNKIEDKKGDTSSEIY  260 (875)
T ss_pred             eEEEEEecCCCccee-HHHHHHHHHhc-----chhheeeEEechHHHHHHHHHHHHHhCCCccceeeeecccCCcceeEE
Confidence            389999999999999 88899999976     557789999999999999999999995544444444333322  2443


Q ss_pred             Ee-------------------------------ccc--------------------------------------------
Q psy14082         88 LP-------------------------------LHR--------------------------------------------   92 (233)
Q Consensus        88 v~-------------------------------l~r--------------------------------------------   92 (233)
                      ++                               -+|                                            
T Consensus       261 lsTyqt~~~~~~~~~~~~~~f~~g~FDlIvIDEaHRgi~~~~~~I~dYFdA~~~gLTATP~~~~d~~T~~~F~g~Pt~~Y  340 (875)
T COG4096         261 LSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHRGIYSEWSSILDYFDAATQGLTATPKETIDRSTYGFFNGEPTYAY  340 (875)
T ss_pred             EeehHHHHhhhhccccccccCCCCceeEEEechhhhhHHhhhHHHHHHHHHHHHhhccCcccccccccccccCCCcceee
Confidence            33                               000                                            


Q ss_pred             --------------------------------------------------------------------hhhhchHHHhc-
Q psy14082         93 --------------------------------------------------------------------FVFNCQYEMAK-  103 (233)
Q Consensus        93 --------------------------------------------------------------------~~~~~~~~~~~-  103 (233)
                                                                                          +...+.+++.. 
T Consensus       341 sleeAV~DGfLvpy~vi~i~~~~~~~G~~~~~~serek~~g~~i~~dd~~~~~~d~dr~~v~~~~~~~V~r~~~~~l~~~  420 (875)
T COG4096         341 SLEEAVEDGFLVPYKVIRIDTDFDLDGWKPDAGSEREKLQGEAIDEDDQNFEARDFDRTLVIPFRTETVARELTEYLKRG  420 (875)
T ss_pred             cHHHHhhccccCCCCceEEeeeccccCcCcCccchhhhhhccccCcccccccccccchhccccchHHHHHHHHHHHhccc
Confidence                                                                                11111224444 


Q ss_pred             -C--CCCeEEEEecchhHHHHHHHHHhhC-----CCeeEEEeCCCCHHHHHHHHHHhhCC--CCCEEEecccCcCCcCCC
Q psy14082        104 -N--PAFKVIVFVETKKKVEDITRALRRE-----RHSAICIHGDKTQQDRDYVLNDFRQG--KAPILVATDVAARGLDVE  173 (233)
Q Consensus       104 -~--~~~k~iIf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g--~~~iLv~T~~~~~Gldi~  173 (233)
                       .  ...||||||.+..|++.+...|.+.     +--+..++|+-.+  -...++.|...  --+|-++.|++..|+|+|
T Consensus       421 ~~g~~~~KTIvFa~n~dHAe~i~~~~~~~ype~~~~~a~~IT~d~~~--~q~~Id~f~~ke~~P~IaitvdlL~TGiDvp  498 (875)
T COG4096         421 ATGDEIGKTIVFAKNHDHAERIREALVNEYPEYNGRYAMKITGDAEQ--AQALIDNFIDKEKYPRIAITVDLLTTGVDVP  498 (875)
T ss_pred             cCCCccCceEEEeeCcHHHHHHHHHHHHhCccccCceEEEEeccchh--hHHHHHHHHhcCCCCceEEehhhhhcCCCch
Confidence             2  2579999999999999999999765     3346667776333  33555666542  355889999999999999


Q ss_pred             CccEEEEecCCCCcc---cccceeeEEeecc
Q psy14082        174 DVNTVNIGSLQLSAN---HNISQVIEVVQDY  201 (233)
Q Consensus       174 ~v~~VI~~d~P~~~~---~~i~~~~~~~~~~  201 (233)
                      .|..++-+-.=.|..   |-+||..+++...
T Consensus       499 ev~nlVF~r~VrSktkF~QMvGRGTRl~~~~  529 (875)
T COG4096         499 EVVNLVFDRKVRSKTKFKQMVGRGTRLCPDL  529 (875)
T ss_pred             heeeeeehhhhhhHHHHHHHhcCccccCccc
Confidence            999888776666655   4447777766543

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.36  E-value=1.1e-11  Score=115.28  Aligned_cols=94  Identities=22%  Similarity=0.275  Sum_probs=76.4

Q ss_pred             hcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHh----hCCCCCEEEecccCcCCcCCCCccE
Q psy14082        102 AKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDF----RQGKAPILVATDVAARGLDVEDVNT  177 (233)
Q Consensus       102 ~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f----~~g~~~iLv~T~~~~~Gldi~~v~~  177 (233)
                      ....+.+++|-|||++.|..++..|++.+.++..+||.+...+|.+.++.+    +.++..|+|+|.+.+-|+|+ +.|+
T Consensus       436 ~~~~~~kvlvI~NTV~~Aie~Y~~Lk~~~~~v~LlHSRf~~~dR~~ke~~l~~~~~~~~~~IvVaTQVIEagvDi-dfd~  514 (733)
T COG1203         436 EVKEGKKVLVIVNTVDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQVIEAGVDI-DFDV  514 (733)
T ss_pred             hhccCCcEEEEEecHHHHHHHHHHHHhcCCCEEEEecccchhhHHHHHHHHHHHHhccCCeEEEEeeEEEEEecc-ccCe
Confidence            344778999999999999999999999988899999999999999888864    45678899999999999999 5888


Q ss_pred             EEE-ecCCCCcccccceeeE
Q psy14082        178 VNI-GSLQLSANHNISQVIE  196 (233)
Q Consensus       178 VI~-~d~P~~~~~~i~~~~~  196 (233)
                      +|- ..+..|..|+.||+-|
T Consensus       515 mITe~aPidSLIQR~GRv~R  534 (733)
T COG1203         515 LITELAPIDSLIQRAGRVNR  534 (733)
T ss_pred             eeecCCCHHHHHHHHHHHhh
Confidence            773 3333444466655444

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

Probab=99.36  E-value=9.1e-13  Score=100.81  Aligned_cols=74  Identities=24%  Similarity=0.328  Sum_probs=63.6

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhc--CCcEEEEEcC
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSS--ALRNICIFGG   79 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~--~~~~~~~~gg   79 (233)
                      ++.+.+|+|+++.+|||+|||++|.+|+++.+.+.      ...+++|++|+++|+.|.++.+..++.  ++++..++|+
T Consensus         8 ~~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~------~~~~~lii~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~   81 (169)
T PF00270_consen    8 IEAIISGKNVLISAPTGSGKTLAYILPALNRLQEG------KDARVLIIVPTRALAEQQFERLRKFFSNTNVRVVLLHGG   81 (169)
T ss_dssp             HHHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTT------SSSEEEEEESSHHHHHHHHHHHHHHTTTTTSSEEEESTT
T ss_pred             HHHHHcCCCEEEECCCCCccHHHHHHHHHhhhccC------CCceEEEEeeccccccccccccccccccccccccccccc
Confidence            34556899999999999999999999999988753      234899999999999999999999943  5788999988


Q ss_pred             CC
Q psy14082         80 TP   81 (233)
Q Consensus        80 ~~   81 (233)
                      .+
T Consensus        82 ~~   83 (169)
T PF00270_consen   82 QS   83 (169)
T ss_dssp             SC
T ss_pred             cc
Confidence            76

Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0008026 ATP-dependent helicase activity; PDB: 3RRM_A 3RRN_A 3PEW_A 2KBE_A 3PEY_A 3FHO_A 2ZJA_A 2ZJ8_A 2ZJ5_A 2ZJ2_A ....

>KOG0387|consensus

Probab=99.35  E-value=9.3e-11  Score=105.48  Aligned_cols=99  Identities=18%  Similarity=0.286  Sum_probs=86.3

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHh-hCCCeeEEEeCCCCHHHHHHHHHHhhCCCCC--EEEecccCcCCcCCCCccEEEE
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALR-RERHSAICIHGDKTQQDRDYVLNDFRQGKAP--ILVATDVAARGLDVEDVNTVNI  180 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~-~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~--iLv~T~~~~~Gldi~~v~~VI~  180 (233)
                      ..+.++++|..++...+-+...|. ..++++.-+.|..+...|...+++|++++.-  .|++|.+.+-|+|+..++-||.
T Consensus       544 kqg~rvllFsqs~~mLdilE~fL~~~~~ysylRmDGtT~~~~R~~lVd~Fne~~s~~VFLLTTrvGGLGlNLTgAnRVII  623 (923)
T KOG0387|consen  544 KQGDRVLLFSQSRQMLDILESFLRRAKGYSYLRMDGTTPAALRQKLVDRFNEDESIFVFLLTTRVGGLGLNLTGANRVII  623 (923)
T ss_pred             hCCCEEEEehhHHHHHHHHHHHHHhcCCceEEEecCCCccchhhHHHHhhcCCCceEEEEEEecccccccccccCceEEE
Confidence            366799999999999999999998 6899999999999999999999999988744  6789999999999999999999


Q ss_pred             ecCCCCcc---------cccc-----eeeEEeecch
Q psy14082        181 GSLQLSAN---------HNIS-----QVIEVVQDYE  202 (233)
Q Consensus       181 ~d~P~~~~---------~~i~-----~~~~~~~~~~  202 (233)
                      ||+.|++.         .|||     .+.++++..-
T Consensus       624 fDPdWNPStD~QAreRawRiGQkkdV~VYRL~t~gT  659 (923)
T KOG0387|consen  624 FDPDWNPSTDNQARERAWRIGQKKDVVVYRLMTAGT  659 (923)
T ss_pred             ECCCCCCccchHHHHHHHhhcCccceEEEEEecCCc
Confidence            99999986         3444     4667776544

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

Probab=99.34  E-value=3.6e-11  Score=110.66  Aligned_cols=81  Identities=22%  Similarity=0.306  Sum_probs=62.4

Q ss_pred             CCeEEEEecchhHHHHHHHHHhhC-----CCeeEEEeCCCCHH---------------------HHHHHHHHhhC-CCCC
Q psy14082        106 AFKVIVFVETKKKVEDITRALRRE-----RHSAICIHGDKTQQ---------------------DRDYVLNDFRQ-GKAP  158 (233)
Q Consensus       106 ~~k~iIf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~---------------------~r~~~~~~f~~-g~~~  158 (233)
                      +.+++|||.++.+|..+.+.|.+.     +..+.+++++.+.+                     ....++++|++ +..+
T Consensus       514 ~~kamvv~~sr~~a~~~~~~l~~~~~~~~~~~~vv~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Fk~~~~~~  593 (667)
T TIGR00348       514 KFKAMVVAISRYACVEEKNALDEELNEKFEASAIVMTGKESDDAEIRDYNKHIRTKFDKSDGFEIYYKDLERFKKEENPK  593 (667)
T ss_pred             cCceeEEEecHHHHHHHHHHHHhhcccccCCeeEEecCCccchhHHHHHHHHhccccccchhhhHHHHHHHHhcCCCCce
Confidence            589999999999999999988654     24556666654432                     12468889976 6789


Q ss_pred             EEEecccCcCCcCCCCccEEEEecCCCC
Q psy14082        159 ILVATDVAARGLDVEDVNTVNIGSLQLS  186 (233)
Q Consensus       159 iLv~T~~~~~Gldi~~v~~VI~~d~P~~  186 (233)
                      +||++|++..|+|.|.+++++..-+-.+
T Consensus       594 ilIVvdmllTGFDaP~l~tLyldKplk~  621 (667)
T TIGR00348       594 LLIVVDMLLTGFDAPILNTLYLDKPLKY  621 (667)
T ss_pred             EEEEEcccccccCCCccceEEEeccccc
Confidence            9999999999999999998875444343

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

>KOG0953|consensus

Probab=99.30  E-value=5.5e-11  Score=103.36  Aligned_cols=158  Identities=15%  Similarity=0.162  Sum_probs=116.6

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCCCC-------
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPKG-------   83 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~~-------   83 (233)
                      ++-.+||.||||.-    +++++.+.        ...++--|.|-||..+++.+...  ++.|.+++|.....       
T Consensus       194 i~H~GPTNSGKTy~----ALqrl~~a--------ksGvycGPLrLLA~EV~~r~na~--gipCdL~TGeE~~~~~~~~~~  259 (700)
T KOG0953|consen  194 IMHVGPTNSGKTYR----ALQRLKSA--------KSGVYCGPLRLLAHEVYDRLNAL--GIPCDLLTGEERRFVLDNGNP  259 (700)
T ss_pred             EEEeCCCCCchhHH----HHHHHhhh--------ccceecchHHHHHHHHHHHhhhc--CCCccccccceeeecCCCCCc
Confidence            45678999999976    57787653        45788999999999999999988  78888888874331       


Q ss_pred             CeeE-----------------Ee----c---cc-----------------------hhhhchH-----------------
Q psy14082         84 PQDC-----------------LP----L---HR-----------------------FVFNCQY-----------------   99 (233)
Q Consensus        84 ~~~l-----------------v~----l---~r-----------------------~~~~~~~-----------------   99 (233)
                      .+.+                 |.    +   .|                       .++++++                 
T Consensus       260 a~hvScTVEM~sv~~~yeVAViDEIQmm~Dp~RGwAWTrALLGl~AdEiHLCGepsvldlV~~i~k~TGd~vev~~YeRl  339 (700)
T KOG0953|consen  260 AQHVSCTVEMVSVNTPYEVAVIDEIQMMRDPSRGWAWTRALLGLAADEIHLCGEPSVLDLVRKILKMTGDDVEVREYERL  339 (700)
T ss_pred             ccceEEEEEEeecCCceEEEEehhHHhhcCcccchHHHHHHHhhhhhhhhccCCchHHHHHHHHHhhcCCeeEEEeeccc
Confidence            1110                 00    0   00                       1111111                 


Q ss_pred             -----------HHhcCCCCeEEEEecchhHHHHHHHHHhhCCCe-eEEEeCCCCHHHHHHHHHHhhC--CCCCEEEeccc
Q psy14082        100 -----------EMAKNPAFKVIVFVETKKKVEDITRALRRERHS-AICIHGDKTQQDRDYVLNDFRQ--GKAPILVATDV  165 (233)
Q Consensus       100 -----------~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~-~~~~~~~~~~~~r~~~~~~f~~--g~~~iLv~T~~  165 (233)
                                 .+..-..+-++|-+ +++....+...+.+.|.. +.+++|++|++.|.+--..|++  ++++||||||+
T Consensus       340 ~pL~v~~~~~~sl~nlk~GDCvV~F-Skk~I~~~k~kIE~~g~~k~aVIYGsLPPeTr~aQA~~FNd~~~e~dvlVAsDA  418 (700)
T KOG0953|consen  340 SPLVVEETALGSLSNLKPGDCVVAF-SKKDIFTVKKKIEKAGNHKCAVIYGSLPPETRLAQAALFNDPSNECDVLVASDA  418 (700)
T ss_pred             CcceehhhhhhhhccCCCCCeEEEe-ehhhHHHHHHHHHHhcCcceEEEecCCCCchhHHHHHHhCCCCCccceEEeecc
Confidence                       22223334444443 568899999999888755 9999999999999999999998  89999999999


Q ss_pred             CcCCcCCCCccEEEEecCC
Q psy14082        166 AARGLDVEDVNTVNIGSLQ  184 (233)
Q Consensus       166 ~~~Gldi~~v~~VI~~d~P  184 (233)
                      .+.|+|+ +++-||-|++-
T Consensus       419 IGMGLNL-~IrRiiF~sl~  436 (700)
T KOG0953|consen  419 IGMGLNL-NIRRIIFYSLI  436 (700)
T ss_pred             ccccccc-ceeEEEEeecc
Confidence            9999999 88888888754

>KOG0948|consensus

Probab=99.24  E-value=5.6e-11  Score=106.33  Aligned_cols=168  Identities=15%  Similarity=0.117  Sum_probs=130.5

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCC
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGT   80 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~   80 (233)
                      ||-.+-++.-|++.|.|.+|||++.-.++...+.        ...|+++=+|-++|.+|-|+.+..-+.  .+.+++|+.
T Consensus       137 aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr--------~kQRVIYTSPIKALSNQKYREl~~EF~--DVGLMTGDV  206 (1041)
T KOG0948|consen  137 AIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLR--------EKQRVIYTSPIKALSNQKYRELLEEFK--DVGLMTGDV  206 (1041)
T ss_pred             hhhhhcCCceEEEEeecCCCcchHHHHHHHHHHH--------hcCeEEeeChhhhhcchhHHHHHHHhc--ccceeecce
Confidence            4556778899999999999999998887777773        356899999999999999998877654  467788887


Q ss_pred             CCCCee--EEe---------------------------------------------------------------------
Q psy14082         81 PKGPQD--CLP---------------------------------------------------------------------   89 (233)
Q Consensus        81 ~~~~~~--lv~---------------------------------------------------------------------   89 (233)
                      ..++..  +|-                                                                     
T Consensus       207 TInP~ASCLVMTTEILRsMLYRGSEvmrEVaWVIFDEIHYMRDkERGVVWEETIIllP~~vr~VFLSATiPNA~qFAeWI  286 (1041)
T KOG0948|consen  207 TINPDASCLVMTTEILRSMLYRGSEVMREVAWVIFDEIHYMRDKERGVVWEETIILLPDNVRFVFLSATIPNARQFAEWI  286 (1041)
T ss_pred             eeCCCCceeeeHHHHHHHHHhccchHhheeeeEEeeeehhccccccceeeeeeEEeccccceEEEEeccCCCHHHHHHHH
Confidence            665544  222                                                                     


Q ss_pred             --ccc---------------------------------------------------------------------------
Q psy14082         90 --LHR---------------------------------------------------------------------------   92 (233)
Q Consensus        90 --l~r---------------------------------------------------------------------------   92 (233)
                        +++                                                                           
T Consensus       287 ~~ihkQPcHVVYTdyRPTPLQHyifP~ggdGlylvVDek~~FrednF~~am~~l~~~~~~~~~~~~~~k~~kG~~~~~~~  366 (1041)
T KOG0948|consen  287 CHIHKQPCHVVYTDYRPTPLQHYIFPAGGDGLYLVVDEKGKFREDNFQKAMSVLRKAGESDGKKKANKKGRKGGTGGKGP  366 (1041)
T ss_pred             HHHhcCCceEEeecCCCCcceeeeecCCCCeeEEEEecccccchHHHHHHHHHhhccCCCccccccccccccCCcCCCCC
Confidence              000                                                                           


Q ss_pred             ----hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCC-------------------------------------
Q psy14082         93 ----FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERH-------------------------------------  131 (233)
Q Consensus        93 ----~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~-------------------------------------  131 (233)
                          +..++. ..-.....++|||+-+++.|+.++-.+.++.+                                     
T Consensus       367 ~~s~i~kiVk-mi~~~~~~PVIvFSFSkkeCE~~Alqm~kldfN~deEk~~V~~iF~nAi~~LseeDr~LPqie~iLPLL  445 (1041)
T KOG0948|consen  367 GDSDIYKIVK-MIMERNYLPVIVFSFSKKECEAYALQMSKLDFNTDEEKELVETIFNNAIDQLSEEDRELPQIENILPLL  445 (1041)
T ss_pred             CcccHHHHHH-HHHhhcCCceEEEEecHhHHHHHHHhhccCcCCChhHHHHHHHHHHHHHHhcChhhccchHHHHHHHHH
Confidence                111111 11234566899999999999999999874311                                     


Q ss_pred             --eeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEE
Q psy14082        132 --SAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVN  179 (233)
Q Consensus       132 --~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI  179 (233)
                        .+.+.|||+-+--++.+.--|.+|-.++|+||..++.|+|.|.-.+|+
T Consensus       446 ~RGIGIHHsGLLPIlKE~IEILFqEGLvKvLFATETFsiGLNMPAkTVvF  495 (1041)
T KOG0948|consen  446 RRGIGIHHSGLLPILKEVIEILFQEGLVKVLFATETFSIGLNMPAKTVVF  495 (1041)
T ss_pred             HhccccccccchHHHHHHHHHHHhccHHHHHHhhhhhhhccCCcceeEEE
Confidence              467899999988888888899999999999999999999999988876

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

Probab=99.12  E-value=3.8e-10  Score=105.76  Aligned_cols=184  Identities=15%  Similarity=0.098  Sum_probs=133.9

Q ss_pred             CCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCC--cEEEEEcCCC
Q psy14082          4 PSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSAL--RNICIFGGTP   81 (233)
Q Consensus         4 ~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~--~~~~~~gg~~   81 (233)
                      .+.+|.-|+++||||+|||+..-.++...+.        .+.++++.+|.++|.+|.+..+...+..+  .+.+++|+..
T Consensus       130 ~Ler~esVlV~ApTssGKTvVaeyAi~~al~--------~~qrviYTsPIKALsNQKyrdl~~~fgdv~~~vGL~TGDv~  201 (1041)
T COG4581         130 ILERGESVLVCAPTSSGKTVVAEYAIALALR--------DGQRVIYTSPIKALSNQKYRDLLAKFGDVADMVGLMTGDVS  201 (1041)
T ss_pred             HHhCCCcEEEEccCCCCcchHHHHHHHHHHH--------cCCceEeccchhhhhhhHHHHHHHHhhhhhhhccceeccee
Confidence            4567899999999999999997777766663        35569999999999999999999886633  4688888877


Q ss_pred             CCCee--EEe---------------------------------------------ccc----------------------
Q psy14082         82 KGPQD--CLP---------------------------------------------LHR----------------------   92 (233)
Q Consensus        82 ~~~~~--lv~---------------------------------------------l~r----------------------   92 (233)
                      .++..  +|-                                             +.+                      
T Consensus       202 IN~~A~clvMTTEILRnMlyrg~~~~~~i~~ViFDEvHyi~D~eRG~VWEE~Ii~lP~~v~~v~LSATv~N~~EF~~Wi~  281 (1041)
T COG4581         202 INPDAPCLVMTTEILRNMLYRGSESLRDIEWVVFDEVHYIGDRERGVVWEEVIILLPDHVRFVFLSATVPNAEEFAEWIQ  281 (1041)
T ss_pred             eCCCCceEEeeHHHHHHHhccCcccccccceEEEEeeeeccccccchhHHHHHHhcCCCCcEEEEeCCCCCHHHHHHHHH
Confidence            65443  222                                             000                      


Q ss_pred             ----------------------------hhhhchH---------------------------------------------
Q psy14082         93 ----------------------------FVFNCQY---------------------------------------------   99 (233)
Q Consensus        93 ----------------------------~~~~~~~---------------------------------------------   99 (233)
                                                  +.++.++                                             
T Consensus       282 ~~~~~~~~vv~t~~RpvPL~~~~~~~~~l~~lvde~~~~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~a~~~~~~~~~~  361 (1041)
T COG4581         282 RVHSQPIHVVSTEHRPVPLEHFVYVGKGLFDLVDEKKKFNAENFPSANRSLSCFSEKVRETDDGDVGRYARRTKALRGSA  361 (1041)
T ss_pred             hccCCCeEEEeecCCCCCeEEEEecCCceeeeecccccchhhcchhhhhhhhccchhccccCccccccccccccccCCcc
Confidence                                        0000000                                             


Q ss_pred             -----------HHhcCCCCeEEEEecchhHHHHHHHHHhhC----------------------------CC---------
Q psy14082        100 -----------EMAKNPAFKVIVFVETKKKVEDITRALRRE----------------------------RH---------  131 (233)
Q Consensus       100 -----------~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~----------------------------~~---------  131 (233)
                                 .+......++|+|+-+++.|+..+..+...                            ++         
T Consensus       362 ~~~~~~~~iv~~l~~~~~lP~I~F~FSr~~Ce~~a~~~~~ldl~~~~~~e~~i~~ii~~~i~~L~~ed~~lp~~~~~~~~  441 (1041)
T COG4581         362 KGPAGRPEIVNKLDKDNLLPAIVFSFSRRGCEEAAQILSTLDLVLTEEKERAIREIIDHAIGDLAEEDRELPLQILEISA  441 (1041)
T ss_pred             cccccchHHHhhhhhhcCCceEEEEEchhhHHHHHHHhcccccccCCcHHHHHHHHHHHHHhhcChhhhcCcccHHHHHH
Confidence                       111234457899999999999888887621                            11         


Q ss_pred             ----eeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCcccccceeeEEeec
Q psy14082        132 ----SAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQVIEVVQD  200 (233)
Q Consensus       132 ----~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i~~~~~~~~~  200 (233)
                          ...+.|++|=+..+..+...|..|-.+++++|..++.|+|.|.-.+|+     .+..++=|...+++++
T Consensus       442 ~L~RGiavHH~GlLP~~K~~vE~Lfq~GLvkvvFaTeT~s~GiNmPartvv~-----~~l~K~dG~~~r~L~~  509 (1041)
T COG4581         442 LLLRGIAVHHAGLLPAIKELVEELFQEGLVKVVFATETFAIGINMPARTVVF-----TSLSKFDGNGHRWLSP  509 (1041)
T ss_pred             HHhhhhhhhccccchHHHHHHHHHHhccceeEEeehhhhhhhcCCcccceee-----eeeEEecCCceeecCh
Confidence                234789999999999999999999999999999999999999988876     3333333444444443

>KOG0384|consensus

Probab=99.11  E-value=1.2e-09  Score=102.24  Aligned_cols=108  Identities=17%  Similarity=0.278  Sum_probs=95.2

Q ss_pred             hcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCC---CEEEecccCcCCcCCCCccEE
Q psy14082        102 AKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKA---PILVATDVAARGLDVEDVNTV  178 (233)
Q Consensus       102 ~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~---~iLv~T~~~~~Gldi~~v~~V  178 (233)
                      .+..++|+|||..-+...+-|+++|..+++..--+.|.+..+.|..+++.|.....   -.|.||.+.+-|||+-.+|.|
T Consensus       695 Lk~~GHrVLIFSQMVRmLDIL~eYL~~r~ypfQRLDGsvrgelRq~AIDhFnap~SddFvFLLSTRAGGLGINLatADTV  774 (1373)
T KOG0384|consen  695 LKEGGHRVLIFSQMVRMLDILAEYLSLRGYPFQRLDGSVRGELRQQAIDHFNAPDSDDFVFLLSTRAGGLGINLATADTV  774 (1373)
T ss_pred             HhcCCceEEEhHHHHHHHHHHHHHHHHcCCcceeccCCcchHHHHHHHHhccCCCCCceEEEEecccCcccccccccceE
Confidence            34577999999999999999999999999999999999999999999999987654   489999999999999999999


Q ss_pred             EEecCCCCcc---------cccc-----eeeEEeecchHHHHHHH
Q psy14082        179 NIGSLQLSAN---------HNIS-----QVIEVVQDYEKEKRLFS  209 (233)
Q Consensus       179 I~~d~P~~~~---------~~i~-----~~~~~~~~~~~~~~~~~  209 (233)
                      |+||..+++.         ||||     .+.++++...-++.+++
T Consensus       775 IIFDSDWNPQNDLQAqARaHRIGQkk~VnVYRLVTk~TvEeEilE  819 (1373)
T KOG0384|consen  775 IIFDSDWNPQNDLQAQARAHRIGQKKHVNVYRLVTKNTVEEEILE  819 (1373)
T ss_pred             EEeCCCCCcchHHHHHHHHHhhcccceEEEEEEecCCchHHHHHH
Confidence            9999999985         8997     57888887655554444

>KOG0392|consensus

Probab=99.10  E-value=1.8e-09  Score=101.11  Aligned_cols=88  Identities=19%  Similarity=0.392  Sum_probs=76.1

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCCC-ee--EEEeCCCCHHHHHHHHHHhhCC-CCCEE-EecccCcCCcCCCCccEEE
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRERH-SA--ICIHGDKTQQDRDYVLNDFRQG-KAPIL-VATDVAARGLDVEDVNTVN  179 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~~-~~--~~~~~~~~~~~r~~~~~~f~~g-~~~iL-v~T~~~~~Gldi~~v~~VI  179 (233)
                      .++|++|||.-+...+-+.+.|.+... ++  ..+.|..++.+|.++.++|+++ .+++| .+|.+.+-|+|+.++|.||
T Consensus      1339 sqHRiLIFcQlK~mlDlVekDL~k~~mpsVtymRLDGSVpp~~R~kiV~~FN~DptIDvLlLTThVGGLGLNLTGADTVV 1418 (1549)
T KOG0392|consen 1339 SQHRILIFCQLKSMLDLVEKDLFKKYMPSVTYMRLDGSVPPGDRQKIVERFNEDPTIDVLLLTTHVGGLGLNLTGADTVV 1418 (1549)
T ss_pred             ccceeEEeeeHHHHHHHHHHHHhhhhcCceeEEEecCCCCcHHHHHHHHHhcCCCceeEEEEeeeccccccccCCCceEE
Confidence            568999999999999999999866533 33  3578999999999999999998 68876 6788999999999999999


Q ss_pred             EecCCCCc---------ccccc
Q psy14082        180 IGSLQLSA---------NHNIS  192 (233)
Q Consensus       180 ~~d~P~~~---------~~~i~  192 (233)
                      .++=.|++         .||||
T Consensus      1419 FvEHDWNPMrDLQAMDRAHRIG 1440 (1549)
T KOG0392|consen 1419 FVEHDWNPMRDLQAMDRAHRIG 1440 (1549)
T ss_pred             EEecCCCchhhHHHHHHHHhhc
Confidence            99988887         38887

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

Probab=99.08  E-value=3.9e-10  Score=102.16  Aligned_cols=71  Identities=8%  Similarity=0.055  Sum_probs=59.8

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh-----cCCcEEEEEcCC
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS-----SALRNICIFGGT   80 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~-----~~~~~~~~~gg~   80 (233)
                      ..+..+++.|+||+|||++|++|++..+...      .+.++||++||++|+.|+.+.+..+.     .++++..+.|+.
T Consensus        14 ~~~~~lliEA~TGtGKTlAYLlpal~~~~~~------~~~rvlIstpT~~Lq~Ql~~~l~~l~~~~l~~~i~~~~lkGr~   87 (636)
T TIGR03117        14 RQKRIGMLEASTGVGKTLAMIMAALTMLKER------PDQKIAIAVPTLALMGQLWSELERLTAEGLAGPVQAGFFPGSQ   87 (636)
T ss_pred             hcCCeEEEEcCCCCcHHHHHHHHHHHHHHhc------cCceEEEECCcHHHHHHHHHHHHHHHHhhcCCCeeEEEEECCc
Confidence            4578899999999999999999999887532      35789999999999999999888774     256778888887


Q ss_pred             CC
Q psy14082         81 PK   82 (233)
Q Consensus        81 ~~   82 (233)
                      ++
T Consensus        88 nY   89 (636)
T TIGR03117        88 EF   89 (636)
T ss_pred             cc
Confidence            66

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.

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=99.06  E-value=6.2e-10  Score=103.55  Aligned_cols=100  Identities=20%  Similarity=0.207  Sum_probs=85.1

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCC---Ccc---
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVE---DVN---  176 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~---~v~---  176 (233)
                      ...+.++||||+|++.++.++..|.+.|+++..+|+  .+.+|+..+.+|+.+...|+||||+++||+|++   +|.   
T Consensus       595 ~~~grpVLIft~Sve~sE~Ls~~L~~~gI~h~vLna--kq~~REa~Iia~AG~~g~VtIATNMAGRGtDIkl~~~V~~vG  672 (1025)
T PRK12900        595 QKKGQPVLVGTASVEVSETLSRMLRAKRIAHNVLNA--KQHDREAEIVAEAGQKGAVTIATNMAGRGTDIKLGEGVRELG  672 (1025)
T ss_pred             hhCCCCEEEEeCcHHHHHHHHHHHHHcCCCceeecC--CHHHhHHHHHHhcCCCCeEEEeccCcCCCCCcCCccchhhhC
Confidence            347889999999999999999999999999999997  588999999999999999999999999999999   554   


Q ss_pred             --EEEEecCCCCcc---ccc---------ceeeEEeecchHH
Q psy14082        177 --TVNIGSLQLSAN---HNI---------SQVIEVVQDYEKE  204 (233)
Q Consensus       177 --~VI~~d~P~~~~---~~i---------~~~~~~~~~~~~~  204 (233)
                        +||+++.|.|..   |++         |.+..|++..+.-
T Consensus       673 GL~VIgterhes~Rid~Ql~GRtGRqGdpGsS~ffvSleD~L  714 (1025)
T PRK12900        673 GLFILGSERHESRRIDRQLRGRAGRQGDPGESVFYVSLEDEL  714 (1025)
T ss_pred             CceeeCCCCCchHHHHHHHhhhhhcCCCCcceEEEechhHHH
Confidence              348888888884   555         4555677765533

>KOG1123|consensus

Probab=99.05  E-value=2.2e-09  Score=92.62  Aligned_cols=76  Identities=21%  Similarity=0.303  Sum_probs=63.4

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCC-CCCEEEecccCcCCcCCCCccEEEEe
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQG-KAPILVATDVAARGLDVEDVNTVNIG  181 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~iLv~T~~~~~Gldi~~v~~VI~~  181 (233)
                      ...+.|+|||..+.-...+.+-.|     .--+++|..++.+|..+++.|+-+ .++.++-+.+....+|+|..+++|+.
T Consensus       540 E~RgDKiIVFsDnvfALk~YAikl-----~KpfIYG~Tsq~ERm~ILqnFq~n~~vNTIFlSKVgDtSiDLPEAnvLIQI  614 (776)
T KOG1123|consen  540 ERRGDKIIVFSDNVFALKEYAIKL-----GKPFIYGPTSQNERMKILQNFQTNPKVNTIFLSKVGDTSIDLPEANVLIQI  614 (776)
T ss_pred             HhcCCeEEEEeccHHHHHHHHHHc-----CCceEECCCchhHHHHHHHhcccCCccceEEEeeccCccccCCcccEEEEE
Confidence            347789999998877777776665     234789999999999999999854 57888888999999999999999987


Q ss_pred             cC
Q psy14082        182 SL  183 (233)
Q Consensus       182 d~  183 (233)
                      ..
T Consensus       615 SS  616 (776)
T KOG1123|consen  615 SS  616 (776)
T ss_pred             cc
Confidence            53

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

Probab=99.03  E-value=7.3e-10  Score=104.05  Aligned_cols=68  Identities=21%  Similarity=0.215  Sum_probs=56.6

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHH-HHHHHh--hcCCcEEEEEcCCCC
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQ-TVAKEF--SSALRNICIFGGTPK   82 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~-~~~~~~--~~~~~~~~~~gg~~~   82 (233)
                      ..+.+++++|+||||||++|++|++...         .+.+++|++||++|++|+. +.+..+  ..++++.++.|+.++
T Consensus       262 ~~~~~~~~eA~tGtGKT~ayllp~l~~~---------~~~~vvI~t~T~~Lq~Ql~~~~i~~l~~~~~~~~~~~kg~~~y  332 (820)
T PRK07246        262 HDGPASFIEAQTGIGKTYGYLLPLLAQS---------DQRQIIVSVPTKILQDQIMAEEVKAIQEVFHIDCHSLKGPQNY  332 (820)
T ss_pred             hCCCcEEEECCCCCcHHHHHHHHHHHhc---------CCCcEEEEeCcHHHHHHHHHHHHHHHHHhcCCcEEEEECCccc
Confidence            3578899999999999999999988754         2467999999999999994 666666  456788899998766

>KOG0389|consensus

Probab=99.01  E-value=1.5e-08  Score=91.54  Aligned_cols=111  Identities=18%  Similarity=0.332  Sum_probs=94.2

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCC--CCEEEecccCcCCcCCCCccEEEE
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGK--APILVATDVAARGLDVEDVNTVNI  180 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~--~~iLv~T~~~~~Gldi~~v~~VI~  180 (233)
                      ...+.|++||.......+-+...|..++++..-+.|.....+|..++..|...+  .-+|.+|.+.+-|||+..+++||.
T Consensus       774 k~~G~RVLiFSQFTqmLDILE~~L~~l~~~ylRLDGsTqV~~RQ~lId~Fn~d~difVFLLSTKAGG~GINLt~An~VIi  853 (941)
T KOG0389|consen  774 KKKGDRVLIFSQFTQMLDILEVVLDTLGYKYLRLDGSTQVNDRQDLIDEFNTDKDIFVFLLSTKAGGFGINLTCANTVII  853 (941)
T ss_pred             hhcCCEEEEeeHHHHHHHHHHHHHHhcCceEEeecCCccchHHHHHHHhhccCCceEEEEEeeccCcceecccccceEEE
Confidence            346699999999999999999999999999999999999999999999998765  236789999999999999999999


Q ss_pred             ecCCCCc---------ccccc-----eeeEEeecchHHHHHHHHHHh
Q psy14082        181 GSLQLSA---------NHNIS-----QVIEVVQDYEKEKRLFSLIRE  213 (233)
Q Consensus       181 ~d~P~~~---------~~~i~-----~~~~~~~~~~~~~~~~~~i~~  213 (233)
                      ||...++         .||+|     .+++++++.--++.++++-++
T Consensus       854 hD~dFNP~dD~QAEDRcHRvGQtkpVtV~rLItk~TIEE~I~~lA~~  900 (941)
T KOG0389|consen  854 HDIDFNPYDDKQAEDRCHRVGQTKPVTVYRLITKSTIEEGILRLAKT  900 (941)
T ss_pred             eecCCCCcccchhHHHHHhhCCcceeEEEEEEecCcHHHHHHHHHHH
Confidence            9987766         38887     567888876666665555443

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=99.01  E-value=1.3e-08  Score=92.48  Aligned_cols=83  Identities=19%  Similarity=0.264  Sum_probs=63.6

Q ss_pred             hcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCC-CCEEEecccCcCCcCCCCc-----
Q psy14082        102 AKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGK-APILVATDVAARGLDVEDV-----  175 (233)
Q Consensus       102 ~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~-~~iLv~T~~~~~Gldi~~v-----  175 (233)
                      ....+.++||.+.+....+.+...|.+.|++..++++.-..++ .+++.+  .|+ ..|-|||++++||.|+.--     
T Consensus       423 ~~~~GrPVLVgt~sI~~SE~ls~~L~~~gI~h~vLNAk~~~~E-A~IIa~--AG~~gaVTIATNMAGRGTDIkLg~~~~~  499 (764)
T PRK12326        423 VHETGQPVLVGTHDVAESEELAERLRAAGVPAVVLNAKNDAEE-ARIIAE--AGKYGAVTVSTQMAGRGTDIRLGGSDEA  499 (764)
T ss_pred             HHHcCCCEEEEeCCHHHHHHHHHHHHhCCCcceeeccCchHhH-HHHHHh--cCCCCcEEEEecCCCCccCeecCCCccc
Confidence            3458899999999999999999999999999999998633322 444433  243 4588999999999998621     


Q ss_pred             ----------cEEEEecCCCCc
Q psy14082        176 ----------NTVNIGSLQLSA  187 (233)
Q Consensus       176 ----------~~VI~~d~P~~~  187 (233)
                                =+||--..|.|.
T Consensus       500 ~~~~V~~~GGLhVIgTerheSr  521 (764)
T PRK12326        500 DRDRVAELGGLHVIGTGRHRSE  521 (764)
T ss_pred             chHHHHHcCCcEEEeccCCchH
Confidence                      268877777665

>KOG0947|consensus

Probab=98.98  E-value=5e-09  Score=96.23  Aligned_cols=78  Identities=24%  Similarity=0.294  Sum_probs=67.0

Q ss_pred             hcCCCCeEEEEecchhHHHHHHHHHhhCCC---------------------------------------eeEEEeCCCCH
Q psy14082        102 AKNPAFKVIVFVETKKKVEDITRALRRERH---------------------------------------SAICIHGDKTQ  142 (233)
Q Consensus       102 ~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~---------------------------------------~~~~~~~~~~~  142 (233)
                      .....-++++||=+++.|++.++.|...++                                       ...++|||.=+
T Consensus       563 ~k~~lLP~VvFvFSkkrCde~a~~L~~~nL~~~~EKseV~lfl~k~~~rLk~~DR~LPQvl~m~~ll~RGiaVHH~GlLP  642 (1248)
T KOG0947|consen  563 RKKNLLPVVVFVFSKKRCDEYADYLTNLNLTDSKEKSEVHLFLSKAVARLKGEDRNLPQVLSMRSLLLRGIAVHHGGLLP  642 (1248)
T ss_pred             hhcccCceEEEEEccccHHHHHHHHhccCcccchhHHHHHHHHHHHHHhcChhhccchHHHHHHHHHhhcchhhcccchH
Confidence            334456899999999999999999984321                                       45778999988


Q ss_pred             HHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEE
Q psy14082        143 QDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVN  179 (233)
Q Consensus       143 ~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI  179 (233)
                      -.++-+.--|..|-++||+||..++.|+|.|.-.+|+
T Consensus       643 ivKE~VE~LFqrGlVKVLFATETFAMGVNMPARtvVF  679 (1248)
T KOG0947|consen  643 IVKEVVELLFQRGLVKVLFATETFAMGVNMPARTVVF  679 (1248)
T ss_pred             HHHHHHHHHHhcCceEEEeehhhhhhhcCCCceeEEe
Confidence            8888888889999999999999999999999988886

>KOG0390|consensus

Probab=98.97  E-value=4.2e-08  Score=89.89  Aligned_cols=79  Identities=10%  Similarity=0.277  Sum_probs=64.1

Q ss_pred             EEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCC---EEEecccCcCCcCCCCccEEEEecCCCC
Q psy14082        110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAP---ILVATDVAARGLDVEDVNTVNIGSLQLS  186 (233)
Q Consensus       110 iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~---iLv~T~~~~~Gldi~~v~~VI~~d~P~~  186 (233)
                      .+..|-+...+.+....+-.|+.+..+||.|+..+|..+++.|++....   .|.+|.+++.||++-+.+.||.||++++
T Consensus       599 v~Isny~~tldl~e~~~~~~g~~~~rLdG~~~~~qRq~~vd~FN~p~~~~~vfLlSsKAgg~GinLiGAsRlil~D~dWN  678 (776)
T KOG0390|consen  599 VLISNYTQTLDLFEQLCRWRGYEVLRLDGKTSIKQRQKLVDTFNDPESPSFVFLLSSKAGGEGLNLIGASRLILFDPDWN  678 (776)
T ss_pred             EEeccHHHHHHHHHHHHhhcCceEEEEcCCCchHHHHHHHHhccCCCCCceEEEEecccccCceeecccceEEEeCCCCC
Confidence            3333444444444444455699999999999999999999999986544   6688899999999999999999999999


Q ss_pred             cc
Q psy14082        187 AN  188 (233)
Q Consensus       187 ~~  188 (233)
                      ++
T Consensus       679 Pa  680 (776)
T KOG0390|consen  679 PA  680 (776)
T ss_pred             ch
Confidence            96

>KOG1002|consensus

Probab=98.92  E-value=6.4e-08  Score=83.69  Aligned_cols=114  Identities=18%  Similarity=0.286  Sum_probs=96.1

Q ss_pred             hcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCC-CCC-EEEecccCcCCcCCCCccEEE
Q psy14082        102 AKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQG-KAP-ILVATDVAARGLDVEDVNTVN  179 (233)
Q Consensus       102 ~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~-iLv~T~~~~~Gldi~~v~~VI  179 (233)
                      .+...-|.|||.......+.+...|.+.|++|+-+-|+|++..|...++.|++. +++ .|++-.+.+-.+|+...++|+
T Consensus       634 ~rd~t~KsIVFSQFTSmLDLi~~rL~kaGfscVkL~GsMs~~ardatik~F~nd~~c~vfLvSLkAGGVALNLteASqVF  713 (791)
T KOG1002|consen  634 ERDRTAKSIVFSQFTSMLDLIEWRLGKAGFSCVKLVGSMSPAARDATIKYFKNDIDCRVFLVSLKAGGVALNLTEASQVF  713 (791)
T ss_pred             HcccchhhhhHHHHHHHHHHHHHHhhccCceEEEeccCCChHHHHHHHHHhccCCCeEEEEEEeccCceEeeechhceeE
Confidence            344557899999999999999999999999999999999999999999999875 455 457777888889999999999


Q ss_pred             EecCCCCcc---------cccc-----eeeEEeecchHHHHHHHHHHhhc
Q psy14082        180 IGSLQLSAN---------HNIS-----QVIEVVQDYEKEKRLFSLIRELG  215 (233)
Q Consensus       180 ~~d~P~~~~---------~~i~-----~~~~~~~~~~~~~~~~~~i~~~~  215 (233)
                      ..|+=+++.         |+||     ++++|+=+..-+.+++++-++-.
T Consensus       714 mmDPWWNpaVe~Qa~DRiHRIGQ~rPvkvvrf~iEnsiE~kIieLQeKKa  763 (791)
T KOG1002|consen  714 MMDPWWNPAVEWQAQDRIHRIGQYRPVKVVRFCIENSIEEKIIELQEKKA  763 (791)
T ss_pred             eecccccHHHHhhhhhhHHhhcCccceeEEEeehhccHHHHHHHHHHHHh
Confidence            999988874         6776     67889877677788887776643

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=98.91  E-value=2.8e-08  Score=92.32  Aligned_cols=64  Identities=11%  Similarity=-0.044  Sum_probs=54.7

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEcCCCC
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGGTPK   82 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~gg~~~   82 (233)
                      -|+.+.||+|||++..+|++...+        .|..+-|++||.-||.|-++.+..+  +.++++.++.++.+.
T Consensus        98 ~iaEM~TGEGKTLvA~l~a~l~al--------~G~~VhvvT~ndyLA~RD~e~m~~l~~~lGl~v~~i~~~~~~  163 (913)
T PRK13103         98 KIAEMRTGEGKTLVGTLAVYLNAL--------SGKGVHVVTVNDYLARRDANWMRPLYEFLGLSVGIVTPFQPP  163 (913)
T ss_pred             ccccccCCCCChHHHHHHHHHHHH--------cCCCEEEEeCCHHHHHHHHHHHHHHhcccCCEEEEECCCCCH
Confidence            478899999999999999986664        3667999999999999999999998  568899998887543

>KOG0950|consensus

Probab=98.90  E-value=1.4e-08  Score=93.48  Aligned_cols=171  Identities=16%  Similarity=0.193  Sum_probs=126.4

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEcC
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGG   79 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~gg   79 (233)
                      .|.++.+++.|-.+||+.|||++.-+-++..++..       +..++.+.|-..-++.-...+..+  ..++.+...+|.
T Consensus       234 ~~~~~e~~nliys~Pts~gktlvaeilml~~~l~~-------rr~~llilp~vsiv~Ek~~~l~~~~~~~G~~ve~y~g~  306 (1008)
T KOG0950|consen  234 LPRLLERKNLIYSLPTSAGKTLVAEILMLREVLCR-------RRNVLLILPYVSIVQEKISALSPFSIDLGFPVEEYAGR  306 (1008)
T ss_pred             chhhhcccceEEeCCCccchHHHHHHHHHHHHHHH-------hhceeEecceeehhHHHHhhhhhhccccCCcchhhccc
Confidence            57778899999999999999999988888877753       446788888877777766666666  346677777776


Q ss_pred             CCCCC-----eeEEe-------------------------------------------------------------ccc-
Q psy14082         80 TPKGP-----QDCLP-------------------------------------------------------------LHR-   92 (233)
Q Consensus        80 ~~~~~-----~~lv~-------------------------------------------------------------l~r-   92 (233)
                      .+...     .+-|+                                                             +++ 
T Consensus       307 ~~p~~~~k~~sv~i~tiEkanslin~lie~g~~~~~g~vvVdElhmi~d~~rg~~lE~~l~k~~y~~~~~~~~iIGMSAT  386 (1008)
T KOG0950|consen  307 FPPEKRRKRESVAIATIEKANSLINSLIEQGRLDFLGMVVVDELHMIGDKGRGAILELLLAKILYENLETSVQIIGMSAT  386 (1008)
T ss_pred             CCCCCcccceeeeeeehHhhHhHHHHHHhcCCccccCcEEEeeeeeeeccccchHHHHHHHHHHHhccccceeEeeeecc
Confidence            54321     11222                                                             000 


Q ss_pred             --------------------------------------------------------------hhhhchHHHhcCCCCeEE
Q psy14082         93 --------------------------------------------------------------FVFNCQYEMAKNPAFKVI  110 (233)
Q Consensus        93 --------------------------------------------------------------~~~~~~~~~~~~~~~k~i  110 (233)
                                                                                    ++.+|.+  ....+.++|
T Consensus       387 i~N~~lL~~~L~A~~y~t~fRPv~L~E~ik~G~~i~~~~r~~~lr~ia~l~~~~~g~~dpD~~v~L~te--t~~e~~~~l  464 (1008)
T KOG0950|consen  387 IPNNSLLQDWLDAFVYTTRFRPVPLKEYIKPGSLIYESSRNKVLREIANLYSSNLGDEDPDHLVGLCTE--TAPEGSSVL  464 (1008)
T ss_pred             cCChHHHHHHhhhhheecccCcccchhccCCCcccccchhhHHHHHhhhhhhhhcccCCCcceeeehhh--hhhcCCeEE
Confidence                                                                          1111111  112556799


Q ss_pred             EEecchhHHHHHHHHHhhC--------------------------------------CCeeEEEeCCCCHHHHHHHHHHh
Q psy14082        111 VFVETKKKVEDITRALRRE--------------------------------------RHSAICIHGDKTQQDRDYVLNDF  152 (233)
Q Consensus       111 If~~~~~~~~~l~~~L~~~--------------------------------------~~~~~~~~~~~~~~~r~~~~~~f  152 (233)
                      |||++++.|+.++..+...                                      -..+.++|.+++.++|..+...|
T Consensus       465 vfc~sk~~ce~~a~~~~~~vpk~~~~e~~~~~~~~~s~s~~lr~~~~~ld~Vl~~ti~~GvAyHhaGLT~eER~~iE~af  544 (1008)
T KOG0950|consen  465 VFCPSKKNCENVASLIAKKVPKHIKSEKRLGLWELLSISNLLRRIPGILDPVLAKTIPYGVAYHHAGLTSEEREIIEAAF  544 (1008)
T ss_pred             EEcCcccchHHHHHHHHHHhhHhhhhhhhhhHHHHHHHHhHhhcCCcccchHHheeccccceecccccccchHHHHHHHH
Confidence            9999999999888666421                                      12567889999999999999999


Q ss_pred             hCCCCCEEEecccCcCCcCCCCccEEEEe
Q psy14082        153 RQGKAPILVATDVAARGLDVEDVNTVNIG  181 (233)
Q Consensus       153 ~~g~~~iLv~T~~~~~Gldi~~v~~VI~~  181 (233)
                      ++|-..+++||+.++-|.+.|...++|-.
T Consensus       545 r~g~i~vl~aTSTlaaGVNLPArRVIira  573 (1008)
T KOG0950|consen  545 REGNIFVLVATSTLAAGVNLPARRVIIRA  573 (1008)
T ss_pred             HhcCeEEEEecchhhccCcCCcceeEEeC
Confidence            99999999999999999999999988854

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=98.89  E-value=5.8e-08  Score=89.82  Aligned_cols=70  Identities=19%  Similarity=0.303  Sum_probs=55.6

Q ss_pred             hcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCC-CHHHHHHHHHHhhCCC-CCEEEecccCcCCcCCC
Q psy14082        102 AKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDK-TQQDRDYVLNDFRQGK-APILVATDVAARGLDVE  173 (233)
Q Consensus       102 ~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~-~~~~r~~~~~~f~~g~-~~iLv~T~~~~~Gldi~  173 (233)
                      ....+.++||-+.+.+..+.++..|.+.|++..++++.- ....-.+++..  .|. ..|-|||++++||.|+.
T Consensus       420 ~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLNAk~~~~~~EA~IIA~--AG~~G~VTIATNMAGRGTDI~  491 (870)
T CHL00122        420 MHQTGRPILIGTTTIEKSELLSQLLKEYRLPHQLLNAKPENVRRESEIVAQ--AGRKGSITIATNMAGRGTDII  491 (870)
T ss_pred             HHhcCCCEEEeeCCHHHHHHHHHHHHHcCCccceeeCCCccchhHHHHHHh--cCCCCcEEEeccccCCCcCee
Confidence            445889999999999999999999999999999999863 22333444444  344 55889999999999973

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

Probab=98.79  E-value=2.4e-07  Score=86.34  Aligned_cols=83  Identities=17%  Similarity=0.303  Sum_probs=73.2

Q ss_pred             hcCCCCeEEEEecchhHHHHHHHHHhh----CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccE
Q psy14082        102 AKNPAFKVIVFVETKKKVEDITRALRR----ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNT  177 (233)
Q Consensus       102 ~~~~~~k~iIf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~  177 (233)
                      .....+-++||.+-....+.+.+.|++    ....+..+||.++.+++..+++--..|.-+|+++|++++.++-+|++.+
T Consensus       255 ~~~~~GdILvFLpG~~EI~~~~~~L~~~~l~~~~~i~PLy~~L~~~eQ~rvF~p~~~~~RKVVlATNIAETSLTI~gIr~  334 (845)
T COG1643         255 LREGSGSILVFLPGQREIERTAEWLEKAELGDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATNIAETSLTIPGIRY  334 (845)
T ss_pred             ccCCCCCEEEECCcHHHHHHHHHHHHhccccCCcEEeeccccCCHHHHHhhcCCCCCCcceEEEEccccccceeeCCeEE
Confidence            445678899999999999999999987    3477889999999999999888877777779999999999999999999


Q ss_pred             EEEecCC
Q psy14082        178 VNIGSLQ  184 (233)
Q Consensus       178 VI~~d~P  184 (233)
                      ||.-++-
T Consensus       335 VIDsG~a  341 (845)
T COG1643         335 VIDSGLA  341 (845)
T ss_pred             EecCCcc
Confidence            9977754

>KOG4150|consensus

Probab=98.76  E-value=2.6e-08  Score=87.41  Aligned_cols=167  Identities=19%  Similarity=0.203  Sum_probs=122.3

Q ss_pred             CCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh----hcCCcEEEEEcCCCCCCee--------
Q psy14082         19 LLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF----SSALRNICIFGGTPKGPQD--------   86 (233)
Q Consensus        19 sGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~----~~~~~~~~~~gg~~~~~~~--------   86 (233)
                      .-|.++|-.|+.+.+...      -..-+|++-|+..+++.+.+.+.++    ..+.....+.|....+...        
T Consensus       400 L~~~~~~~~~~~~~~~~~------~~~~~~Y~~~~~~~~~~~~R~L~~L~~~F~~~~~~~~~~~~~~~K~~~~~~~~~~~  473 (1034)
T KOG4150|consen  400 LAKSLCYNVPVFEELCKD------TNSCALYLFPTKALAQDQLRALSDLIKGFEASINMGVYDGDTPYKDRTRLRSELAN  473 (1034)
T ss_pred             hhhccccccHHHHHHHhc------ccceeeeecchhhHHHHHHHHHHHHHHHHHhhcCcceEeCCCCcCCHHHHHHHhcC
Confidence            457778888888776642      3456899999999999988887777    4566667777776653322        


Q ss_pred             -----EEe------------------cc---c----hhhhchHHH--hcCCCCeEEEEecchhHHHHHHHHHhhC----C
Q psy14082         87 -----CLP------------------LH---R----FVFNCQYEM--AKNPAFKVIVFVETKKKVEDITRALRRE----R  130 (233)
Q Consensus        87 -----lv~------------------l~---r----~~~~~~~~~--~~~~~~k~iIf~~~~~~~~~l~~~L~~~----~  130 (233)
                           +|.                  +.   |    ++....+++  .-..+-++|-||..++.|+.+-..-++.    +
T Consensus       474 ~~E~~Li~~DGSPs~~K~~V~WNP~~~P~~~~~~~~~i~E~s~~~~~~i~~~~R~IAFC~~R~~CEL~~~~~R~I~~ET~  553 (1034)
T KOG4150|consen  474 LSELELVTIDGSPSSEKLFVLWNPSAPPTSKSEKSSKVVEVSHLFAEMVQHGLRCIAFCPSRKLCELVLCLTREILAETA  553 (1034)
T ss_pred             CcceEEEEecCCCCccceEEEeCCCCCCcchhhhhhHHHHHHHHHHHHHHcCCcEEEeccHHHHHHHHHHHHHHHHHHhh
Confidence                 222                  00   0    111111111  1236679999999999999876665542    1


Q ss_pred             ----CeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc
Q psy14082        131 ----HSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI  191 (233)
Q Consensus       131 ----~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i  191 (233)
                          -.+..+.||.+.++|.++.+..-.|...-+++|++++-|+|+...|.|++.++|-|....-
T Consensus       554 ~~LV~~i~SYRGGY~A~DRRKIE~~~F~G~L~giIaTNALELGIDIG~LDAVl~~GFP~S~aNl~  618 (1034)
T KOG4150|consen  554 PHLVEAITSYRGGYIAEDRRKIESDLFGGKLCGIIATNALELGIDIGHLDAVLHLGFPGSIANLW  618 (1034)
T ss_pred             HHHHHHHHhhcCccchhhHHHHHHHhhCCeeeEEEecchhhhccccccceeEEEccCchhHHHHH
Confidence                1345678999999999999999999999999999999999999999999999999987444

>COG4889 Predicted helicase [General function prediction only]

Probab=98.72  E-value=1.3e-08  Score=93.09  Aligned_cols=93  Identities=18%  Similarity=0.234  Sum_probs=69.8

Q ss_pred             CCeEEEEecchhHHHHHHHHHhh-------------CCCeeEE--EeCCCCHHHHHHHHHH---hhCCCCCEEEecccCc
Q psy14082        106 AFKVIVFVETKKKVEDITRALRR-------------ERHSAIC--IHGDKTQQDRDYVLND---FRQGKAPILVATDVAA  167 (233)
Q Consensus       106 ~~k~iIf~~~~~~~~~l~~~L~~-------------~~~~~~~--~~~~~~~~~r~~~~~~---f~~g~~~iLv~T~~~~  167 (233)
                      ..|+|-||.+.++.+.+++.+.+             .++.+.+  +.|.|+..+|...+..   |...+++||-....++
T Consensus       460 ~~RAIaF~k~I~tSK~i~~sFe~Vve~Y~~Elk~d~~nL~iSi~HvDGtmNal~R~~l~~l~~~~~~neckIlSNaRcLS  539 (1518)
T COG4889         460 MQRAIAFAKDIKTSKQIAESFETVVEAYDEELKKDFKNLKISIDHVDGTMNALERLDLLELKNTFEPNECKILSNARCLS  539 (1518)
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhcCCCceEEeecccccccHHHHHHHHhccCCCCcchheeeccchhhh
Confidence            35789999999888888776652             2444444  5588999999555443   5667899999999999


Q ss_pred             CCcCCCCccEEEEecCCCCcccccceeeEEe
Q psy14082        168 RGLDVEDVNTVNIGSLQLSANHNISQVIEVV  198 (233)
Q Consensus       168 ~Gldi~~v~~VI~~d~P~~~~~~i~~~~~~~  198 (233)
                      +|+|+|..|-||.||+-++.-.-++.+++++
T Consensus       540 EGVDVPaLDsViFf~pr~smVDIVQaVGRVM  570 (1518)
T COG4889         540 EGVDVPALDSVIFFDPRSSMVDIVQAVGRVM  570 (1518)
T ss_pred             cCCCccccceEEEecCchhHHHHHHHHHHHH
Confidence            9999999999999998887765554333333

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=98.66  E-value=1.1e-06  Score=81.61  Aligned_cols=70  Identities=17%  Similarity=0.275  Sum_probs=55.9

Q ss_pred             hcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCC-CCHHHHHHHHHHhhCCC-CCEEEecccCcCCcCCC
Q psy14082        102 AKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGD-KTQQDRDYVLNDFRQGK-APILVATDVAARGLDVE  173 (233)
Q Consensus       102 ~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~-~~~~~r~~~~~~f~~g~-~~iLv~T~~~~~Gldi~  173 (233)
                      ....+.++||-+.|.+..+.++..|.+.|+...+++.. .....-.+++..  .|+ ..|-|||++++||-|+.
T Consensus       435 ~~~~GrPVLIgT~SVe~SE~ls~~L~~~gi~h~vLNAk~~~~~~EA~IIa~--AG~~GaVTIATNMAGRGTDIk  506 (939)
T PRK12902        435 MHKQGRPVLVGTTSVEKSELLSALLQEQGIPHNLLNAKPENVEREAEIVAQ--AGRKGAVTIATNMAGRGTDII  506 (939)
T ss_pred             HHhCCCCEEEeeCCHHHHHHHHHHHHHcCCchheeeCCCcchHhHHHHHHh--cCCCCcEEEeccCCCCCcCEe
Confidence            34588999999999999999999999999999999986 333333444444  344 45889999999999973

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=98.59  E-value=3.1e-07  Score=66.94  Aligned_cols=68  Identities=28%  Similarity=0.278  Sum_probs=52.7

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhc-CCcEEEEEcCCCC
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSS-ALRNICIFGGTPK   82 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~-~~~~~~~~gg~~~   82 (233)
                      +.+++.++||+|||.+++..+.+....      ....+++|++|++.++.|+.+.+..... ...+..+.++...
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~------~~~~~~lv~~p~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~   69 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDS------LKGGQVLVLAPTRELANQVAERLKELFGEGIKVGYLIGGTSI   69 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhc------ccCCCEEEEcCcHHHHHHHHHHHHHHhhCCcEEEEEecCcch
Confidence            367899999999999977777665543      2456899999999999999999998843 4666666665443

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

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

Probab=98.53  E-value=2.7e-07  Score=88.21  Aligned_cols=69  Identities=14%  Similarity=0.116  Sum_probs=56.0

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHH----HHHh-hcCCcEEEEEcCCC
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTV----AKEF-SSALRNICIFGGTP   81 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~----~~~~-~~~~~~~~~~gg~~   81 (233)
                      .+.++++.|+||+|||++|++|++.....       .+.+++|-++|+.|-+|+.+.    +++. ..+++++++.|..+
T Consensus       275 ~~~~~~iEA~TGtGKTlaYLlpa~~~a~~-------~~~~vvIsT~T~~LQ~Ql~~kDiP~L~~~~~~~~~~~~lKGr~n  347 (928)
T PRK08074        275 DSEHALIEAGTGTGKSLAYLLPAAYFAKK-------KEEPVVISTYTIQLQQQLLEKDIPLLQKIFPFPVEAALLKGRSH  347 (928)
T ss_pred             cCCCEEEECCCCCchhHHHHHHHHHHhhc-------cCCeEEEEcCCHHHHHHHHHhhHHHHHHHcCCCceEEEEEcccc
Confidence            57789999999999999999999865542       367899999999999998763    4444 44778899998876


Q ss_pred             C
Q psy14082         82 K   82 (233)
Q Consensus        82 ~   82 (233)
                      +
T Consensus       348 Y  348 (928)
T PRK08074        348 Y  348 (928)
T ss_pred             c
Confidence            5

>KOG1000|consensus

Probab=98.52  E-value=2.2e-05  Score=68.36  Aligned_cols=112  Identities=18%  Similarity=0.359  Sum_probs=90.9

Q ss_pred             hcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCC-CC-EEEecccCcCCcCCCCccEEE
Q psy14082        102 AKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGK-AP-ILVATDVAARGLDVEDVNTVN  179 (233)
Q Consensus       102 ~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~-~~-iLv~T~~~~~Gldi~~v~~VI  179 (233)
                      ...++.|.+||+.-....+.+...+.+.++...-+.|..+..+|....+.|+..+ .. -+++-.+++.|+++...+.|+
T Consensus       488 ~d~~~~KflVFaHH~~vLd~Iq~~~~~r~vg~IRIDGst~s~~R~ll~qsFQ~seev~VAvlsItA~gvGLt~tAa~~VV  567 (689)
T KOG1000|consen  488 PDAPPRKFLVFAHHQIVLDTIQVEVNKRKVGSIRIDGSTPSHRRTLLCQSFQTSEEVRVAVLSITAAGVGLTLTAASVVV  567 (689)
T ss_pred             ccCCCceEEEEehhHHHHHHHHHHHHHcCCCeEEecCCCCchhHHHHHHHhccccceEEEEEEEeecccceeeeccceEE
Confidence            3457789999999999999999999999999999999999999999999998764 33 335567889999999999999


Q ss_pred             EecCCCCcc---------cccce-----eeEEeecchHHHHHHHHHHh
Q psy14082        180 IGSLQLSAN---------HNISQ-----VIEVVQDYEKEKRLFSLIRE  213 (233)
Q Consensus       180 ~~d~P~~~~---------~~i~~-----~~~~~~~~~~~~~~~~~i~~  213 (233)
                      ...+|+++.         |+||+     +..++...-..+..+.++.+
T Consensus       568 FaEL~wnPgvLlQAEDRaHRiGQkssV~v~ylvAKgT~Ddy~Wp~l~~  615 (689)
T KOG1000|consen  568 FAELHWNPGVLLQAEDRAHRIGQKSSVFVQYLVAKGTADDYMWPMLQQ  615 (689)
T ss_pred             EEEecCCCceEEechhhhhhccccceeeEEEEEecCchHHHHHHHHHH
Confidence            999999974         77764     33455554455666666654

>KOG0386|consensus

Probab=98.51  E-value=8.6e-07  Score=82.26  Aligned_cols=108  Identities=19%  Similarity=0.357  Sum_probs=90.3

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCC---EEEecccCcCCcCCCCccEEE
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAP---ILVATDVAARGLDVEDVNTVN  179 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~---iLv~T~~~~~Gldi~~v~~VI  179 (233)
                      +..+++++.||.-..-..-+..+|.-.++...-+.|....++|-..++.|+....+   .|.+|...+.|+|+...|.||
T Consensus       723 katgHRVLlF~qMTrlmdimEdyL~~~~~kYlRLDG~TK~~eRg~ll~~FN~Pds~yf~FllstragglglNlQtadtvi  802 (1157)
T KOG0386|consen  723 KATGHRVLLFSQMTRLMDILEDYLQIREYKYLRLDGQTKVEERGDLLEIFNAPDSPYFIFLLSTRAGGLGLNLQTADTVI  802 (1157)
T ss_pred             HhcCcchhhHHHHHHHHHHHHHHHhhhhhheeeecCCcchhhHHHHHHHhcCCCCceeeeeeeecccccccchhhcceEE
Confidence            34778999999999999999999988888989999999999999999999987644   678999999999999999999


Q ss_pred             EecCCCCcc---------cccc-----eeeEEeecchHHHHHHHH
Q psy14082        180 IGSLQLSAN---------HNIS-----QVIEVVQDYEKEKRLFSL  210 (233)
Q Consensus       180 ~~d~P~~~~---------~~i~-----~~~~~~~~~~~~~~~~~~  210 (233)
                      .||..+++.         |+||     ++.++++-...++.+++.
T Consensus       803 ifdsdwnp~~d~qaqdrahrigq~~evRv~rl~tv~sveE~il~~  847 (1157)
T KOG0386|consen  803 IFDSDWNPHQDLQAQDRAHRIGQKKEVRVLRLITVNSVEEKILAE  847 (1157)
T ss_pred             EecCCCCchhHHHHHHHHHHhhchhheeeeeeehhhHHHHHHHHH
Confidence            999999885         6675     566666654544444443

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=98.49  E-value=6.6e-06  Score=76.38  Aligned_cols=82  Identities=16%  Similarity=0.200  Sum_probs=64.5

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCC-CCEEEecccCcCCcCCCCcc-----
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGK-APILVATDVAARGLDVEDVN-----  176 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~-~~iLv~T~~~~~Gldi~~v~-----  176 (233)
                      ...+.++||.|.+.+..+.++..|.+.|+...++++.-.  +++..+-+ +.|. ..|.|||++++||.|+.--.     
T Consensus       423 ~~~gqPVLVgT~SIe~SE~ls~~L~~~gi~h~vLNAk~~--e~EA~IIa-~AG~~GaVTIATNMAGRGTDI~Lg~~V~~~  499 (925)
T PRK12903        423 HKKGQPILIGTAQVEDSETLHELLLEANIPHTVLNAKQN--AREAEIIA-KAGQKGAITIATNMAGRGTDIKLSKEVLEL  499 (925)
T ss_pred             HhcCCCEEEEeCcHHHHHHHHHHHHHCCCCceeecccch--hhHHHHHH-hCCCCCeEEEecccccCCcCccCchhHHHc
Confidence            357899999999999999999999999999999988633  33333332 3454 56899999999999986433     


Q ss_pred             ---EEEEecCCCCc
Q psy14082        177 ---TVNIGSLQLSA  187 (233)
Q Consensus       177 ---~VI~~d~P~~~  187 (233)
                         |||....|.|.
T Consensus       500 GGLhVIgTerheSr  513 (925)
T PRK12903        500 GGLYVLGTDKAESR  513 (925)
T ss_pred             CCcEEEecccCchH
Confidence               89988887665

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=98.49  E-value=4.2e-07  Score=75.77  Aligned_cols=60  Identities=5%  Similarity=-0.104  Sum_probs=48.4

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ..|.++++.||||+|||++|++|++..+...+..  .++.++++.++|..+..|....+++.
T Consensus        25 ~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~--~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00488       25 DRGKIGILESPTGTGKTLSLLCLTLTWLRSFPER--IQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             HcCCcEEEECCCCcchhHHHHHHHHHHHHhCccc--ccccceeEEeccHHHHHHHHHHHHhc
Confidence            4688999999999999999999999877653211  12358999999999999988887765

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=98.49  E-value=4.2e-07  Score=75.77  Aligned_cols=60  Identities=5%  Similarity=-0.104  Sum_probs=48.4

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ..|.++++.||||+|||++|++|++..+...+..  .++.++++.++|..+..|....+++.
T Consensus        25 ~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~--~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00489       25 DRGKIGILESPTGTGKTLSLLCLTLTWLRSFPER--IQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             HcCCcEEEECCCCcchhHHHHHHHHHHHHhCccc--ccccceeEEeccHHHHHHHHHHHHhc
Confidence            4688999999999999999999999877653211  12358999999999999988887765

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=98.47  E-value=3.6e-07  Score=70.71  Aligned_cols=59  Identities=29%  Similarity=0.262  Sum_probs=49.5

Q ss_pred             CCCC-CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhc
Q psy14082          5 SESG-CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSS   69 (233)
Q Consensus         5 ~~~g-~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~   69 (233)
                      +..+ +..++.++||||||.+++.+++..+...      ...++++++|++.++.|+.+.+..+..
T Consensus        20 ~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~------~~~~~l~~~p~~~~~~~~~~~~~~~~~   79 (201)
T smart00487       20 LLSGLRDVILAAPTGSGKTLAALLPALEALKRG------KGKRVLVLVPTRELAEQWAEELKKLGP   79 (201)
T ss_pred             HHcCCCcEEEECCCCCchhHHHHHHHHHHhccc------CCCcEEEEeCCHHHHHHHHHHHHHHhc
Confidence            3445 7899999999999999899888877643      245799999999999999999998843

>PF04851 ResIII: Type III restriction enzyme, res subunit; InterPro: IPR006935 This entry represents a domain found in the N terminus of several proteins, including helicases, the R subunit (HsdR) of type I restriction endonucleases (3

Probab=98.46  E-value=4.5e-07  Score=69.82  Aligned_cols=50  Identities=12%  Similarity=0.078  Sum_probs=41.6

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS   68 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~   68 (233)
                      ++.+++.+|||||||.+++. ++..+..          ++++++|+..|+.|+.+.+..+.
T Consensus        25 ~~~~ll~~~tGsGKT~~~~~-~~~~l~~----------~~l~~~p~~~l~~Q~~~~~~~~~   74 (184)
T PF04851_consen   25 ERRVLLNAPTGSGKTIIALA-LILELAR----------KVLIVAPNISLLEQWYDEFDDFG   74 (184)
T ss_dssp             CSEEEEEESTTSSHHHHHHH-HHHHHHC----------EEEEEESSHHHHHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCcChhhhh-hhhcccc----------ceeEecCHHHHHHHHHHHHHHhh
Confidence            57899999999999999664 4444432          79999999999999999998773

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

>KOG0922|consensus

Probab=98.38  E-value=1.9e-05  Score=70.79  Aligned_cols=83  Identities=17%  Similarity=0.345  Sum_probs=72.1

Q ss_pred             HhcCCCCeEEEEecchhHHHHHHHHHhhCC----C----eeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCC
Q psy14082        101 MAKNPAFKVIVFVETKKKVEDITRALRRER----H----SAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDV  172 (233)
Q Consensus       101 ~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~----~----~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi  172 (233)
                      ....+.+-++||-...++++...+.|.+.-    -    -+..+||.++.+++..+++.-..|..+++++|++++.-+-+
T Consensus       253 h~~E~~GDILvFLtGqeEIe~~~~~l~e~~~~~~~~~~~~~lply~aL~~e~Q~rvF~p~p~g~RKvIlsTNIAETSlTI  332 (674)
T KOG0922|consen  253 HLTEPPGDILVFLTGQEEIEAACELLRERAKSLPEDCPELILPLYGALPSEEQSRVFDPAPPGKRKVILSTNIAETSLTI  332 (674)
T ss_pred             HccCCCCCEEEEeCCHHHHHHHHHHHHHHhhhccccCcceeeeecccCCHHHhhccccCCCCCcceEEEEcceeeeeEEe
Confidence            345677899999999999999999997651    1    24679999999999999988888999999999999999999


Q ss_pred             CCccEEEEecC
Q psy14082        173 EDVNTVNIGSL  183 (233)
Q Consensus       173 ~~v~~VI~~d~  183 (233)
                      +++.+||.-++
T Consensus       333 ~GI~YVVDsG~  343 (674)
T KOG0922|consen  333 DGIRYVVDSGF  343 (674)
T ss_pred             cceEEEEcCCc
Confidence            99999997665

>KOG0391|consensus

Probab=98.37  E-value=2.7e-06  Score=80.20  Aligned_cols=108  Identities=14%  Similarity=0.324  Sum_probs=93.4

Q ss_pred             hcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCC--CCEEEecccCcCCcCCCCccEEE
Q psy14082        102 AKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGK--APILVATDVAARGLDVEDVNTVN  179 (233)
Q Consensus       102 ~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~--~~iLv~T~~~~~Gldi~~v~~VI  179 (233)
                      .+..+++++||+.-.+..+-+..+|.-+|+...-+.|....++|...+++|+...  .-.+.+|...+.|+|+-+.|.||
T Consensus      1272 Lk~eghRvLIfTQMtkmLDVLeqFLnyHgylY~RLDg~t~vEqRQaLmerFNaD~RIfcfILSTrSggvGiNLtgADTVv 1351 (1958)
T KOG0391|consen 1272 LKSEGHRVLIFTQMTKMLDVLEQFLNYHGYLYVRLDGNTSVEQRQALMERFNADRRIFCFILSTRSGGVGINLTGADTVV 1351 (1958)
T ss_pred             HHhcCceEEehhHHHHHHHHHHHHHhhcceEEEEecCCccHHHHHHHHHHhcCCCceEEEEEeccCCccccccccCceEE
Confidence            3568899999999999999999999999999999999999999999999998764  22567899999999999999999


Q ss_pred             EecCCCCcc---------cccc-----eeeEEeecchHHHHHHH
Q psy14082        180 IGSLQLSAN---------HNIS-----QVIEVVQDYEKEKRLFS  209 (233)
Q Consensus       180 ~~d~P~~~~---------~~i~-----~~~~~~~~~~~~~~~~~  209 (233)
                      .||..+++.         |+||     ...++++++--+..+++
T Consensus      1352 FYDsDwNPtMDaQAQDrChRIGqtRDVHIYRLISe~TIEeniLk 1395 (1958)
T KOG0391|consen 1352 FYDSDWNPTMDAQAQDRCHRIGQTRDVHIYRLISERTIEENILK 1395 (1958)
T ss_pred             EecCCCCchhhhHHHHHHHhhcCccceEEEEeeccchHHHHHHh
Confidence            999999874         8898     45778887765555544

>PRK14873 primosome assembly protein PriA; Provisional

Probab=98.36  E-value=3e-06  Score=77.96  Aligned_cols=100  Identities=19%  Similarity=0.153  Sum_probs=78.8

Q ss_pred             ecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCCCCCeeEEeccch
Q psy14082         14 KITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPKGPQDCLPLHRF   93 (233)
Q Consensus        14 ~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~~~~~lv~l~r~   93 (233)
                      .+.+|||||..|+-.+-..+.        .|.++|||+|...|+.|+.+.++..+.                        
T Consensus       166 ~~~~GSGKTevyl~~i~~~l~--------~Gk~vLvLvPEi~lt~q~~~rl~~~f~------------------------  213 (665)
T PRK14873        166 QALPGEDWARRLAAAAAATLR--------AGRGALVVVPDQRDVDRLEAALRALLG------------------------  213 (665)
T ss_pred             hcCCCCcHHHHHHHHHHHHHH--------cCCeEEEEecchhhHHHHHHHHHHHcC------------------------
Confidence            344699999998775555442        367899999999999999999976521                        


Q ss_pred             hhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCC
Q psy14082         94 VFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVE  173 (233)
Q Consensus        94 ~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~  173 (233)
                                                          +..+..+|++++..+|.+.+.+.++|+.+|+|.|..+. -.=++
T Consensus       214 ------------------------------------~~~v~~lhS~l~~~~R~~~w~~~~~G~~~IViGtRSAv-FaP~~  256 (665)
T PRK14873        214 ------------------------------------AGDVAVLSAGLGPADRYRRWLAVLRGQARVVVGTRSAV-FAPVE  256 (665)
T ss_pred             ------------------------------------CCcEEEECCCCCHHHHHHHHHHHhCCCCcEEEEcceeE-EeccC
Confidence                                                02567899999999999999999999999999997544 34456


Q ss_pred             CccEEEEec
Q psy14082        174 DVNTVNIGS  182 (233)
Q Consensus       174 ~v~~VI~~d  182 (233)
                      +..+||..|
T Consensus       257 ~LgLIIvdE  265 (665)
T PRK14873        257 DLGLVAIWD  265 (665)
T ss_pred             CCCEEEEEc
Confidence            777777665

>KOG0949|consensus

Probab=98.34  E-value=7.9e-06  Score=76.01  Aligned_cols=51  Identities=25%  Similarity=0.296  Sum_probs=47.3

Q ss_pred             eeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEec
Q psy14082        132 SAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGS  182 (233)
Q Consensus       132 ~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d  182 (233)
                      .+.+.|++|+...|..+.--||.|...||++|..++-|+|.|.-.+|+--|
T Consensus       964 GiG~HHaglNr~yR~~VEvLFR~g~L~VlfaT~TLsLGiNMPCrTVvF~gD 1014 (1330)
T KOG0949|consen  964 GIGVHHAGLNRKYRSLVEVLFRQGHLQVLFATETLSLGINMPCRTVVFAGD 1014 (1330)
T ss_pred             cccccccccchHHHHHHHHHhhcCceEEEEEeeehhcccCCCceeEEEecc
Confidence            456789999999999999999999999999999999999999998888777

>KOG4439|consensus

Probab=98.31  E-value=2.1e-05  Score=70.93  Aligned_cols=86  Identities=17%  Similarity=0.332  Sum_probs=71.9

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhC--CCCCEE-EecccCcCCcCCCCccEEE
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQ--GKAPIL-VATDVAARGLDVEDVNTVN  179 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~--g~~~iL-v~T~~~~~Gldi~~v~~VI  179 (233)
                      .....+++|...-.....-+...+++.|.....+||....++|..+++.|+.  |..+|+ ++-.+.+-|+|+-..+|+|
T Consensus       743 ~~skeK~viVSQwtsvLniv~~hi~~~g~~y~si~Gqv~vK~Rq~iv~~FN~~k~~~rVmLlSLtAGGVGLNL~GaNHli  822 (901)
T KOG4439|consen  743 TSSKEKVVIVSQWTSVLNIVRKHIQKGGHIYTSITGQVLVKDRQEIVDEFNQEKGGARVMLLSLTAGGVGLNLIGANHLI  822 (901)
T ss_pred             hcccceeeehhHHHHHHHHHHHHHhhCCeeeeeecCccchhHHHHHHHHHHhccCCceEEEEEEccCcceeeecccceEE
Confidence            4455667777777777777888888899999999999999999999999974  445655 6667888999999999999


Q ss_pred             EecCCCCcc
Q psy14082        180 IGSLQLSAN  188 (233)
Q Consensus       180 ~~d~P~~~~  188 (233)
                      ..|+=|++.
T Consensus       823 lvDlHWNPa  831 (901)
T KOG4439|consen  823 LVDLHWNPA  831 (901)
T ss_pred             EEecccCHH
Confidence            999999985

>KOG0924|consensus

Probab=98.27  E-value=1.5e-05  Score=71.69  Aligned_cols=81  Identities=14%  Similarity=0.235  Sum_probs=68.7

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhC----------CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCC
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRE----------RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDV  172 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~----------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi  172 (233)
                      ....+-.+||..-.+.++.....+.+.          ++.+..+++.++.+.+.++++.-..|..+++|||++++.-+.+
T Consensus       560 ~~~~GdilIfmtGqediE~t~~~i~~~l~ql~~~~~~~L~vlpiYSQLp~dlQ~kiFq~a~~~vRK~IvATNIAETSLTi  639 (1042)
T KOG0924|consen  560 SGPPGDILIFMTGQEDIECTCDIIKEKLEQLDSAPTTDLAVLPIYSQLPADLQAKIFQKAEGGVRKCIVATNIAETSLTI  639 (1042)
T ss_pred             cCCCCCEEEecCCCcchhHHHHHHHHHHHhhhcCCCCceEEEeehhhCchhhhhhhcccCCCCceeEEEeccchhhceee
Confidence            345578899998887777666665431          5788899999999999999999888999999999999999999


Q ss_pred             CCccEEEEecC
Q psy14082        173 EDVNTVNIGSL  183 (233)
Q Consensus       173 ~~v~~VI~~d~  183 (233)
                      |++.+||..++
T Consensus       640 ~gI~yVID~Gy  650 (1042)
T KOG0924|consen  640 PGIRYVIDTGY  650 (1042)
T ss_pred             cceEEEEecCc
Confidence            99999998764

>KOG0951|consensus

Probab=98.23  E-value=2.4e-05  Score=74.60  Aligned_cols=159  Identities=18%  Similarity=0.111  Sum_probs=111.9

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh---hcCCcEEEEEcCCCCC-
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF---SSALRNICIFGGTPKG-   83 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~---~~~~~~~~~~gg~~~~-   83 (233)
                      ...+++.+|+|||||++.-++++.         +....+++++.|..+.+...+..+.+-   ..+..+..+.|..+.+ 
T Consensus      1159 nd~v~vga~~gsgkt~~ae~a~l~---------~~~~~~~vyi~p~~~i~~~~~~~w~~~f~~~~G~~~~~l~ge~s~~l 1229 (1674)
T KOG0951|consen 1159 NDNVLVGAPNGSGKTACAELALLR---------PDTIGRAVYIAPLEEIADEQYRDWEKKFSKLLGLRIVKLTGETSLDL 1229 (1674)
T ss_pred             cceEEEecCCCCchhHHHHHHhcC---------CccceEEEEecchHHHHHHHHHHHHHhhccccCceEEecCCccccch
Confidence            345899999999999998887775         145678999999999998888777765   3466777777775542 


Q ss_pred             -----CeeEEe-------cc------------------------------c-----------------------------
Q psy14082         84 -----PQDCLP-------LH------------------------------R-----------------------------   92 (233)
Q Consensus        84 -----~~~lv~-------l~------------------------------r-----------------------------   92 (233)
                           .+++|+       ++                              |                             
T Consensus      1230 kl~~~~~vii~tpe~~d~lq~iQ~v~l~i~d~lh~igg~~g~v~evi~S~r~ia~q~~k~ir~v~ls~~lana~d~ig~s 1309 (1674)
T KOG0951|consen 1230 KLLQKGQVIISTPEQWDLLQSIQQVDLFIVDELHLIGGVYGAVYEVICSMRYIASQLEKKIRVVALSSSLANARDLIGAS 1309 (1674)
T ss_pred             HHhhhcceEEechhHHHHHhhhhhcceEeeehhhhhcccCCceEEEEeeHHHHHHHHHhheeEEEeehhhccchhhcccc
Confidence                 333444       00                              0                             


Q ss_pred             ---------------------------------------hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhC----
Q psy14082         93 ---------------------------------------FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRE----  129 (233)
Q Consensus        93 ---------------------------------------~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~----  129 (233)
                                                             +-.+++   ....+++++||+++++++..++..+...    
T Consensus      1310 ~~~v~Nf~p~~R~~Pl~i~i~~~~~~~~~~~~~am~~~~~~ai~~---~a~~~k~~~vf~p~rk~~~~~a~~~~~~s~~~ 1386 (1674)
T KOG0951|consen 1310 SSGVFNFSPSVRPVPLEIHIQSVDISHFESRMLAMTKPTYTAIVR---HAGNRKPAIVFLPTRKHARLVAVDLVTFSHAD 1386 (1674)
T ss_pred             ccceeecCcccCCCceeEEEEEeccchhHHHHHHhhhhHHHHHHH---HhcCCCCeEEEeccchhhhhhhhccchhhccC
Confidence                                                   111111   2346789999999999999888776521    


Q ss_pred             ------------------CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEE
Q psy14082        130 ------------------RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNI  180 (233)
Q Consensus       130 ------------------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~  180 (233)
                                        .++..+-|.+++..+..-+-+-|..|.++++|...- ..|+-.. .+.||.
T Consensus      1387 ~~~~l~~~~e~~~~~l~e~l~~gvg~e~~s~~d~~iv~~l~e~g~i~v~v~s~~-~~~~~~~-~~lVvv 1453 (1674)
T KOG0951|consen 1387 EPDYLLSELEECDETLRESLKHGVGHEGLSSNDQEIVQQLFEAGAIQVCVMSRD-CYGTKLK-AHLVVV 1453 (1674)
T ss_pred             cHHHHHHHHhcchHhhhhcccccccccccCcchHHHHHHHHhcCcEEEEEEEcc-ccccccc-ceEEEE
Confidence                              223333488999999988889999999999988766 5566543 334443

>KOG0920|consensus

Probab=98.21  E-value=2.6e-05  Score=73.23  Aligned_cols=82  Identities=17%  Similarity=0.307  Sum_probs=71.7

Q ss_pred             hcCCCCeEEEEecchhHHHHHHHHHhhC-------CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCC
Q psy14082        102 AKNPAFKVIVFVETKKKVEDITRALRRE-------RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVED  174 (233)
Q Consensus       102 ~~~~~~k~iIf~~~~~~~~~l~~~L~~~-------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~  174 (233)
                      .....+.+|||-+.-..+..+.+.|..+       .+-+..+|+.|+..++..+.+.--.|..+|+++|++++-.+-|++
T Consensus       409 ~~~~~GaILVFLPG~~eI~~~~~~L~~~~~f~~~~~~~ilplHs~~~s~eQ~~VF~~pp~g~RKIIlaTNIAETSITIdD  488 (924)
T KOG0920|consen  409 EREFEGAILVFLPGWEEILQLKELLEVNLPFADSLKFAILPLHSSIPSEEQQAVFKRPPKGTRKIILATNIAETSITIDD  488 (924)
T ss_pred             cCCCCceEEEEcCCHHHHHHHHHHhhhccccccccceEEEeccccCChHHHHHhcCCCCCCcchhhhhhhhHhhcccccC
Confidence            3345788999999999999999999753       245677899999999999999999999999999999999999999


Q ss_pred             ccEEEEecC
Q psy14082        175 VNTVNIGSL  183 (233)
Q Consensus       175 v~~VI~~d~  183 (233)
                      |-+||..+.
T Consensus       489 VvyVIDsG~  497 (924)
T KOG0920|consen  489 VVYVIDSGL  497 (924)
T ss_pred             eEEEEecCe
Confidence            999997653

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=98.21  E-value=3.9e-06  Score=78.06  Aligned_cols=68  Identities=10%  Similarity=0.009  Sum_probs=52.2

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHH-HHHh----hcCCcEEEEEcCCCC
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTV-AKEF----SSALRNICIFGGTPK   82 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~-~~~~----~~~~~~~~~~gg~~~   82 (233)
                      +..+++.|+||+|||++|++|++.....       .+.+++|=++|..|=+|+.+. +-.+    ..+++++++-|-.++
T Consensus        49 ~~~lviEAgTGtGKTlaYLlPai~~A~~-------~~k~vVIST~T~~LQeQL~~kDlP~l~~~l~~~~~~~llKGr~nY  121 (697)
T PRK11747         49 GRILVIEAGTGVGKTLSYLLAGIPIARA-------EKKKLVISTATVALQEQLVSKDLPLLLKISGLDFKFTLAKGRGRY  121 (697)
T ss_pred             cceEEEECCCCcchhHHHHHHHHHHHHH-------cCCeEEEEcCCHHHHHHHHhhhhhHHHHHcCCCceEEEEcCcccc
Confidence            4678999999999999999999876543       356799999999999998643 2222    345677777777665

>KOG0926|consensus

Probab=98.20  E-value=2.2e-05  Score=71.92  Aligned_cols=51  Identities=18%  Similarity=0.201  Sum_probs=41.1

Q ss_pred             eEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecC
Q psy14082        133 AICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSL  183 (233)
Q Consensus       133 ~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~  183 (233)
                      +..+++-++.+++..+++.--.|..-++|+|++++.-+.+|++.+||..+.
T Consensus       607 vLPLYSLLs~~~Q~RVF~~~p~g~RLcVVaTNVAETSLTIPgIkYVVD~Gr  657 (1172)
T KOG0926|consen  607 VLPLYSLLSTEKQMRVFDEVPKGERLCVVATNVAETSLTIPGIKYVVDCGR  657 (1172)
T ss_pred             EeehhhhcCHHHhhhhccCCCCCceEEEEeccchhcccccCCeeEEEeccc
Confidence            344455567777777777777788889999999999999999999998765

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

Probab=98.16  E-value=5.2e-05  Score=70.04  Aligned_cols=65  Identities=22%  Similarity=0.297  Sum_probs=52.5

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCC
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVED  174 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~  174 (233)
                      ..+.++-||++|...++.+++.....+.++..++|.-+..+.    +.|  ++++|++-|+.+.-|+++.+
T Consensus       280 ~~gknIcvfsSt~~~~~~v~~~~~~~~~~Vl~l~s~~~~~dv----~~W--~~~~VviYT~~itvG~Sf~~  344 (824)
T PF02399_consen  280 NAGKNICVFSSTVSFAEIVARFCARFTKKVLVLNSTDKLEDV----ESW--KKYDVVIYTPVITVGLSFEE  344 (824)
T ss_pred             hCCCcEEEEeChHHHHHHHHHHHHhcCCeEEEEcCCCCcccc----ccc--cceeEEEEeceEEEEeccch
Confidence            366778899999999999999998888899888887655532    234  57899999999999998853

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

>PF13245 AAA_19: Part of AAA domain

Probab=98.15  E-value=9.3e-06  Score=53.74  Aligned_cols=53  Identities=19%  Similarity=0.173  Sum_probs=38.3

Q ss_pred             CCc-eeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHH
Q psy14082          8 GCQ-NFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVA   64 (233)
Q Consensus         8 g~d-~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~   64 (233)
                      +.. +++++++|||||.+ ++..+..+.....   ..+.++++++||+..++++.+.+
T Consensus         9 ~~~~~vv~g~pGtGKT~~-~~~~i~~l~~~~~---~~~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen    9 GSPLFVVQGPPGTGKTTT-LAARIAELLAARA---DPGKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             hCCeEEEECCCCCCHHHH-HHHHHHHHHHHhc---CCCCeEEEECCCHHHHHHHHHHH
Confidence            444 44599999999977 4445555543210   12668999999999999998888

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

Probab=98.01  E-value=6.3e-05  Score=71.66  Aligned_cols=110  Identities=15%  Similarity=0.287  Sum_probs=91.7

Q ss_pred             CCCC--eEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCC-CCC-EEEecccCcCCcCCCCccEEE
Q psy14082        104 NPAF--KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQG-KAP-ILVATDVAARGLDVEDVNTVN  179 (233)
Q Consensus       104 ~~~~--k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~-iLv~T~~~~~Gldi~~v~~VI  179 (233)
                      ..+.  ++++|+......+-+...+...++....++|+++.+.|...+++|.++ +.. .++++.+++.|+|+...++||
T Consensus       707 ~~~~~~kvlifsq~t~~l~il~~~l~~~~~~~~~ldG~~~~~~r~~~i~~f~~~~~~~v~lls~kagg~glnLt~a~~vi  786 (866)
T COG0553         707 EEGHYHKVLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLKAGGLGLNLTGADTVI  786 (866)
T ss_pred             hhcccccEEEEeCcHHHHHHHHHHHHhcCCcEEEEeCCCChhhHHHHHHHhhcCCCCceEEEEecccccceeecccceEE
Confidence            3444  999999999999999999999998899999999999999999999986 334 667788999999999999999


Q ss_pred             EecCCCCcc---------cccc-----eeeEEeecchHHHHHHHHHHh
Q psy14082        180 IGSLQLSAN---------HNIS-----QVIEVVQDYEKEKRLFSLIRE  213 (233)
Q Consensus       180 ~~d~P~~~~---------~~i~-----~~~~~~~~~~~~~~~~~~i~~  213 (233)
                      +||+.+++.         |+||     .+.+++.....++++++..++
T Consensus       787 ~~d~~wnp~~~~Qa~dRa~RigQ~~~v~v~r~i~~~tiEe~i~~~~~~  834 (866)
T COG0553         787 LFDPWWNPAVELQAIDRAHRIGQKRPVKVYRLITRGTIEEKILELQEK  834 (866)
T ss_pred             EeccccChHHHHHHHHHHHHhcCcceeEEEEeecCCcHHHHHHHHHHH
Confidence            999999985         5665     566677665555666665544

>KOG0923|consensus

Probab=97.97  E-value=0.00011  Score=66.17  Aligned_cols=83  Identities=14%  Similarity=0.283  Sum_probs=70.8

Q ss_pred             hcCCCCeEEEEecchhHHHHHHHHHhhC---------CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCC
Q psy14082        102 AKNPAFKVIVFVETKKKVEDITRALRRE---------RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDV  172 (233)
Q Consensus       102 ~~~~~~k~iIf~~~~~~~~~l~~~L~~~---------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi  172 (233)
                      ...+.+-+|||..-.+..+...+.|++.         .+-+..+|+++|.+.+..+++---.|..+|++||++++.-+.+
T Consensus       469 ~tqp~GDILVFltGQeEIEt~~e~l~~~~~~LGski~eliv~PiYaNLPselQakIFePtP~gaRKVVLATNIAETSlTI  548 (902)
T KOG0923|consen  469 LTQPLGDILVFLTGQEEIETVKENLKERCRRLGSKIRELIVLPIYANLPSELQAKIFEPTPPGARKVVLATNIAETSLTI  548 (902)
T ss_pred             eccCCccEEEEeccHHHHHHHHHHHHHHHHHhccccceEEEeeccccCChHHHHhhcCCCCCCceeEEEeecchhhceee
Confidence            4456788999999998888888777643         2456789999999999999998888999999999999999999


Q ss_pred             CCccEEEEecCC
Q psy14082        173 EDVNTVNIGSLQ  184 (233)
Q Consensus       173 ~~v~~VI~~d~P  184 (233)
                      +++.+||.-++-
T Consensus       549 dgI~yViDpGf~  560 (902)
T KOG0923|consen  549 DGIKYVIDPGFV  560 (902)
T ss_pred             cCeEEEecCccc
Confidence            999999976653

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

Probab=97.90  E-value=1.7e-05  Score=73.53  Aligned_cols=55  Identities=16%  Similarity=0.190  Sum_probs=47.1

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      -.|..+++.||||+|||++|++|.+..-...       +..++|.++|+.|-+|+.+....+
T Consensus        32 ~~~~~~~iEapTGtGKTl~yL~~al~~~~~~-------~~~viist~t~~lq~q~~~~~~~~   86 (654)
T COG1199          32 KGGEGLLIEAPTGTGKTLAYLLPALAYAREE-------GKKVIISTRTKALQEQLLEEDLPI   86 (654)
T ss_pred             cCCCcEEEECCCCccHHHHHHHHHHHHHHHc-------CCcEEEECCCHHHHHHHHHhhcch
Confidence            3466699999999999999999999877643       477999999999999998887765

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

Probab=97.72  E-value=7.3e-05  Score=57.27  Aligned_cols=81  Identities=22%  Similarity=0.379  Sum_probs=59.8

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhCCC--eeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc--cCcCCcCCCC--cc
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRERH--SAICIHGDKTQQDRDYVLNDFRQGKAPILVATD--VAARGLDVED--VN  176 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~~~--~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~--~~~~Gldi~~--v~  176 (233)
                      ....+.++||+++.+..+.+.+.+.+...  ...++..  +..++...++.|+.++..+|+++.  .+.+|+|+|+  +.
T Consensus         6 ~~~~g~~lv~f~Sy~~l~~~~~~~~~~~~~~~~~v~~q--~~~~~~~~l~~~~~~~~~il~~v~~g~~~EGiD~~~~~~r   83 (167)
T PF13307_consen    6 SAVPGGVLVFFPSYRRLEKVYERLKERLEEKGIPVFVQ--GSKSRDELLEEFKRGEGAILLAVAGGSFSEGIDFPGDLLR   83 (167)
T ss_dssp             HCCSSEEEEEESSHHHHHHHHTT-TSS-E-ETSCEEES--TCCHHHHHHHHHCCSSSEEEEEETTSCCGSSS--ECESEE
T ss_pred             hcCCCCEEEEeCCHHHHHHHHHHHHhhcccccceeeec--CcchHHHHHHHHHhccCeEEEEEecccEEEeecCCCchhh
Confidence            34558999999999999999999987642  1122322  255788999999999999999998  9999999996  77


Q ss_pred             EEEEecCCC
Q psy14082        177 TVNIGSLQL  185 (233)
Q Consensus       177 ~VI~~d~P~  185 (233)
                      .||...+|-
T Consensus        84 ~vii~glPf   92 (167)
T PF13307_consen   84 AVIIVGLPF   92 (167)
T ss_dssp             EEEEES---
T ss_pred             eeeecCCCC
Confidence            899999984

>KOG0388|consensus

Probab=97.68  E-value=0.00033  Score=63.68  Aligned_cols=87  Identities=17%  Similarity=0.292  Sum_probs=79.6

Q ss_pred             hcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCC-CEEEecccCcCCcCCCCccEEEE
Q psy14082        102 AKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKA-PILVATDVAARGLDVEDVNTVNI  180 (233)
Q Consensus       102 ~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~-~iLv~T~~~~~Gldi~~v~~VI~  180 (233)
                      .+..++++++|+.-.+..+.+.++|.-.++...-+.|.....+|..++.+|+..++ -.|.+|.+.+-||++...|.||.
T Consensus      1040 LkaegHRvL~yfQMTkM~dl~EdYl~yr~Y~ylRLDGSsk~~dRrd~vrDwQ~sdiFvFLLSTRAGGLGINLTAADTViF 1119 (1185)
T KOG0388|consen 1040 LKAEGHRVLMYFQMTKMIDLIEDYLVYRGYTYLRLDGSSKASDRRDVVRDWQASDIFVFLLSTRAGGLGINLTAADTVIF 1119 (1185)
T ss_pred             hhcCCceEEehhHHHHHHHHHHHHHHhhccceEEecCcchhhHHHHHHhhccCCceEEEEEecccCcccccccccceEEE
Confidence            35578999999999999999999999999999999999999999999999998653 36789999999999999999999


Q ss_pred             ecCCCCcc
Q psy14082        181 GSLQLSAN  188 (233)
Q Consensus       181 ~d~P~~~~  188 (233)
                      ||..+++.
T Consensus      1120 YdSDWNPT 1127 (1185)
T KOG0388|consen 1120 YDSDWNPT 1127 (1185)
T ss_pred             ecCCCCcc
Confidence            99999885

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=97.62  E-value=0.00016  Score=67.73  Aligned_cols=58  Identities=5%  Similarity=-0.038  Sum_probs=49.3

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      +-.|.+.++.||||+|||++.+.|.+....+.     ...+++++.+.|..=..|..+++++.
T Consensus        26 l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~-----~~~~kIiy~sRThsQl~q~i~Elk~~   83 (705)
T TIGR00604        26 LDRGDEAILEMPSGTGKTISLLSLILAYQQEK-----PEVRKIIYASRTHSQLEQATEELRKL   83 (705)
T ss_pred             hccCCceEEeCCCCCCccHHHHHHHHHHHHhc-----cccccEEEEcccchHHHHHHHHHHhh
Confidence            35688999999999999999999999876543     23468999999999999999999986

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).

>KOG1015|consensus

Probab=97.51  E-value=0.00031  Score=65.74  Aligned_cols=89  Identities=19%  Similarity=0.242  Sum_probs=76.0

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhh----------------------CCCeeEEEeCCCCHHHHHHHHHHhhCCC---C
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRR----------------------ERHSAICIHGDKTQQDRDYVLNDFRQGK---A  157 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~----------------------~~~~~~~~~~~~~~~~r~~~~~~f~~g~---~  157 (233)
                      ..-+.+.|||..+..+.+.+..+|..                      .|...+-+.|..+..+|......|++-.   .
T Consensus      1139 eeIGDKlLVFSQSL~SLdLIe~fLe~v~r~gk~~~d~~~~~~~eGkW~~GkDyyriDGst~s~~R~k~~~~FNdp~NlRa 1218 (1567)
T KOG1015|consen 1139 EEIGDKLLVFSQSLISLDLIEDFLELVSREGKEDKDKPLIYKGEGKWLRGKDYYRLDGSTTSQSRKKWAEEFNDPTNLRA 1218 (1567)
T ss_pred             HHhcceeEEeecccchhHHHHHHHHhhcccCccccccccccccccceecCCceEEecCcccHHHHHHHHHHhcCccccee
Confidence            35788999999999999988888862                      2446677889999999999999998753   2


Q ss_pred             C-EEEecccCcCCcCCCCccEEEEecCCCCccccc
Q psy14082        158 P-ILVATDVAARGLDVEDVNTVNIGSLQLSANHNI  191 (233)
Q Consensus       158 ~-iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i  191 (233)
                      + .||+|.+.+-|+|+-.++.||+||..|++.+.+
T Consensus      1219 Rl~LISTRAGsLGiNLvAANRVIIfDasWNPSyDt 1253 (1567)
T KOG1015|consen 1219 RLFLISTRAGSLGINLVAANRVIIFDASWNPSYDT 1253 (1567)
T ss_pred             EEEEEeeccCccccceeecceEEEEecccCCccch
Confidence            2 789999999999999999999999999998665

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

Probab=97.44  E-value=0.00022  Score=52.74  Aligned_cols=53  Identities=19%  Similarity=0.133  Sum_probs=38.0

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      |.--++-..||+|||--.+.-++.....       ++.++|||.|||.++..+++.++..
T Consensus         4 g~~~~~d~hpGaGKTr~vlp~~~~~~i~-------~~~rvLvL~PTRvva~em~~aL~~~   56 (148)
T PF07652_consen    4 GELTVLDLHPGAGKTRRVLPEIVREAIK-------RRLRVLVLAPTRVVAEEMYEALKGL   56 (148)
T ss_dssp             TEEEEEE--TTSSTTTTHHHHHHHHHHH-------TT--EEEEESSHHHHHHHHHHTTTS
T ss_pred             CceeEEecCCCCCCcccccHHHHHHHHH-------ccCeEEEecccHHHHHHHHHHHhcC
Confidence            4456778899999998755445544443       4779999999999999999999766

The domain is related to the DEAD/DEAH box helicase domain which is found in a large family of ATPases.; GO: 0005524 ATP binding, 0008026 ATP-dependent helicase activity, 0019079 viral genome replication; PDB: 2QEQ_A 2V6J_A 2V6I_A 8OHM_A 4A92_B 1JR6_A 1HEI_A 1ONB_A 1A1V_A 1YMF_A ....

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

Probab=97.39  E-value=0.00017  Score=57.52  Aligned_cols=61  Identities=11%  Similarity=0.094  Sum_probs=42.1

Q ss_pred             CCCCCc-eeEecCCCCCchHHhHHHHHHhhhcc-CCCCCCCCceEEEEcCcHHHHHHHHHHHHH
Q psy14082          5 SESGCQ-NFSKITNYLLSPPQYMLPAAVHISHQ-EPVKQGDGPIALVLAPTRELAQQIQTVAKE   66 (233)
Q Consensus         5 ~~~g~d-~i~~a~tGsGKT~~~~lp~l~~l~~~-~~~~~~~~~~~lil~PtreL~~Q~~~~~~~   66 (233)
                      +++..+ .++++|+|||||.+ +..++..+... .......+.++|+++||..-++++.+.+.+
T Consensus        13 ~~~~~~~~~i~GpPGTGKT~~-l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen   13 ALSSNGITLIQGPPGTGKTTT-LASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             HCTSSE-EEEE-STTSSHHHH-HHHHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             HHcCCCCEEEECCCCCChHHH-HHHHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            355666 89999999999955 55566555211 001114578899999999999999999988

>PF00176 SNF2_N: SNF2 family N-terminal domain; InterPro: IPR000330 This domain is found in proteins involved in a variety of processes including transcription regulation (e

Probab=97.18  E-value=0.0014  Score=54.48  Aligned_cols=71  Identities=14%  Similarity=0.106  Sum_probs=45.1

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh-c-CCcEEEEEcCC
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS-S-ALRNICIFGGT   80 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~-~-~~~~~~~~gg~   80 (233)
                      ...+..++.-..|+|||+. ++.++..+....+.  .+...+||+||. .+..||.+++.++. + .+++....|+.
T Consensus        23 ~~~~g~lL~de~GlGKT~~-~i~~~~~l~~~~~~--~~~~~~LIv~P~-~l~~~W~~E~~~~~~~~~~~v~~~~~~~   95 (299)
T PF00176_consen   23 SPPRGGLLADEMGLGKTIT-AIALISYLKNEFPQ--RGEKKTLIVVPS-SLLSQWKEEIEKWFDPDSLRVIIYDGDS   95 (299)
T ss_dssp             TTT-EEEE---TTSSHHHH-HHHHHHHHHHCCTT--SS-S-EEEEE-T-TTHHHHHHHHHHHSGT-TS-EEEESSSC
T ss_pred             cCCCCEEEEECCCCCchhh-hhhhhhhhhhcccc--ccccceeEeecc-chhhhhhhhhcccccccccccccccccc
Confidence            3456678888899999988 55566655543110  112259999999 88899999999995 2 57777777665

g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1) [, ]. SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilises energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors. Proteins that contain this domain appear to be distantly related to the DEAX box helicases IPR001410 from INTERPRO, however no helicase activity has ever been demonstrated for these proteins. ; GO: 0003677 DNA binding, 0005524 ATP binding; PDB: 1Z63_B 1Z3I_X 3DMQ_A 3MWY_W.

>KOG0331|consensus

Probab=97.11  E-value=0.0031  Score=56.15  Aligned_cols=127  Identities=24%  Similarity=0.349  Sum_probs=91.3

Q ss_pred             hcCCCCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEec-----ccCcCC-cC
Q psy14082        102 AKNPAFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVAT-----DVAARG-LD  171 (233)
Q Consensus       102 ~~~~~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T-----~~~~~G-ld  171 (233)
                      .+..+.++||.++||+.+.++.+.+.+.    ++++.+++|+.+...+..-+++    ..+|+|+|     |.+.+| +|
T Consensus       161 ~~~~~P~vLVL~PTRELA~QV~~~~~~~~~~~~~~~~cvyGG~~~~~Q~~~l~~----gvdiviaTPGRl~d~le~g~~~  236 (519)
T KOG0331|consen  161 SRGDGPIVLVLAPTRELAVQVQAEAREFGKSLRLRSTCVYGGAPKGPQLRDLER----GVDVVIATPGRLIDLLEEGSLN  236 (519)
T ss_pred             cCCCCCeEEEEcCcHHHHHHHHHHHHHHcCCCCccEEEEeCCCCccHHHHHHhc----CCcEEEeCChHHHHHHHcCCcc
Confidence            3456778999999999999999998765    3568999999998888887765    58999999     233333 33


Q ss_pred             CCCccEEE-------------------------------EecCCCC--------------------------ccccccee
Q psy14082        172 VEDVNTVN-------------------------------IGSLQLS--------------------------ANHNISQV  194 (233)
Q Consensus       172 i~~v~~VI-------------------------------~~d~P~~--------------------------~~~~i~~~  194 (233)
                      +..+.+++                               .|...+.                          +.+.|.+.
T Consensus       237 l~~v~ylVLDEADrMldmGFe~qI~~Il~~i~~~~rQtlm~saTwp~~v~~lA~~fl~~~~~i~ig~~~~~~a~~~i~qi  316 (519)
T KOG0331|consen  237 LSRVTYLVLDEADRMLDMGFEPQIRKILSQIPRPDRQTLMFSATWPKEVRQLAEDFLNNPIQINVGNKKELKANHNIRQI  316 (519)
T ss_pred             ccceeEEEeccHHhhhccccHHHHHHHHHhcCCCcccEEEEeeeccHHHHHHHHHHhcCceEEEecchhhhhhhcchhhh
Confidence            33333333                               2221111                          12333577


Q ss_pred             eEEeecchHHHHHHHHHHhhc----CcccccccchhhHhhhc
Q psy14082        195 IEVVQDYEKEKRLFSLIRELG----KYTLITQESSSTLSEMV  232 (233)
Q Consensus       195 ~~~~~~~~~~~~~~~~i~~~~----~~~~~~~~~~~~~~~l~  232 (233)
                      +..+.+.++..++.++|+++.    +..++|.++++..++|+
T Consensus       317 ve~~~~~~K~~~l~~lL~~~~~~~~~KvIIFc~tkr~~~~l~  358 (519)
T KOG0331|consen  317 VEVCDETAKLRKLGKLLEDISSDSEGKVIIFCETKRTCDELA  358 (519)
T ss_pred             hhhcCHHHHHHHHHHHHHHHhccCCCcEEEEecchhhHHHHH
Confidence            777887788899999998873    57899999999998875

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

Probab=97.06  E-value=0.0022  Score=61.86  Aligned_cols=83  Identities=17%  Similarity=0.253  Sum_probs=65.3

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhCCC--eeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCC--ccEE
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRERH--SAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVED--VNTV  178 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~~~--~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~--v~~V  178 (233)
                      ...+++++||+++.+..+.+++.|.+...  ....+.-+++...|.+++++|+.++-.||++|+.+.+|+|+|+  ..+|
T Consensus       749 ~~~~g~~LVLFtSy~~l~~v~~~l~~~~~~~~~~ll~Qg~~~~~r~~l~~~F~~~~~~iLlG~~sFwEGVD~pg~~l~~v  828 (928)
T PRK08074        749 KATKGRMLVLFTSYEMLKKTYYNLKNEEELEGYVLLAQGVSSGSRARLTKQFQQFDKAILLGTSSFWEGIDIPGDELSCL  828 (928)
T ss_pred             HhCCCCEEEEECCHHHHHHHHHHHhhcccccCceEEecCCCCCCHHHHHHHHHhcCCeEEEecCcccCccccCCCceEEE
Confidence            34567999999999999999999975432  1223332444456889999999988889999999999999997  4789


Q ss_pred             EEecCCC
Q psy14082        179 NIGSLQL  185 (233)
Q Consensus       179 I~~d~P~  185 (233)
                      |...+|-
T Consensus       829 iI~kLPF  835 (928)
T PRK08074        829 VIVRLPF  835 (928)
T ss_pred             EEecCCC
Confidence            9888875

>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=97.04  E-value=0.0045  Score=54.31  Aligned_cols=86  Identities=16%  Similarity=0.213  Sum_probs=77.1

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc--cCcCCcCCCCccEEEE
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD--VAARGLDVEDVNTVNI  180 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~--~~~~Gldi~~v~~VI~  180 (233)
                      ......++||+++--.--.+.+.|++.+++...+|...+..+...+-..|..|+.++|+.|.  -.-+=..+.++..||-
T Consensus       297 ~~~~~~~LIfIPSYfDfVRlRN~lk~~~~sF~~i~EYts~~~isRAR~~F~~G~~~iLL~TER~HFfrRy~irGi~~viF  376 (442)
T PF06862_consen  297 DSKMSGTLIFIPSYFDFVRLRNYLKKENISFVQISEYTSNSDISRARSQFFHGRKPILLYTERFHFFRRYRIRGIRHVIF  376 (442)
T ss_pred             ccCCCcEEEEecchhhhHHHHHHHHhcCCeEEEecccCCHHHHHHHHHHHHcCCceEEEEEhHHhhhhhceecCCcEEEE
Confidence            66778999999999999999999999999999999999999999999999999999999995  2333456788999999


Q ss_pred             ecCCCCcc
Q psy14082        181 GSLQLSAN  188 (233)
Q Consensus       181 ~d~P~~~~  188 (233)
                      |++|..+.
T Consensus       377 Y~~P~~p~  384 (442)
T PF06862_consen  377 YGPPENPQ  384 (442)
T ss_pred             ECCCCChh
Confidence            99999986

; GO: 0005634 nucleus

>KOG1803|consensus

Probab=97.03  E-value=0.001  Score=59.52  Aligned_cols=47  Identities=13%  Similarity=0.006  Sum_probs=39.4

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHH
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAK   65 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~   65 (233)
                      .++++|+|||||.+ +.-+++++..+       +.++|+.+||.+-++.+.+.+.
T Consensus       204 ~~I~GPPGTGKT~T-lvEiI~qlvk~-------~k~VLVcaPSn~AVdNiverl~  250 (649)
T KOG1803|consen  204 LIIHGPPGTGKTRT-LVEIISQLVKQ-------KKRVLVCAPSNVAVDNIVERLT  250 (649)
T ss_pred             eEeeCCCCCCceee-HHHHHHHHHHc-------CCeEEEEcCchHHHHHHHHHhc
Confidence            67899999999988 55567666654       6789999999999999999765

>KOG2340|consensus

Probab=96.97  E-value=0.0071  Score=53.56  Aligned_cols=87  Identities=13%  Similarity=0.169  Sum_probs=72.0

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEeccc--CcCCcCCCCccEEEEec
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDV--AARGLDVEDVNTVNIGS  182 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~--~~~Gldi~~v~~VI~~d  182 (233)
                      ...-++|+.++--.--.+...+++.+++.+.+|...++..-..+-.-|-.|...+|+-|.=  .-|-.++.+|.-||.|.
T Consensus       551 t~s~~LiyIPSYfDFVRvRNy~K~e~i~F~~i~EYssk~~vsRAR~lF~qgr~~vlLyTER~hffrR~~ikGVk~vVfYq  630 (698)
T KOG2340|consen  551 TESGILIYIPSYFDFVRVRNYMKKEEISFVMINEYSSKSKVSRARELFFQGRKSVLLYTERAHFFRRYHIKGVKNVVFYQ  630 (698)
T ss_pred             ccCceEEEecchhhHHHHHHHhhhhhcchHHHhhhhhHhhhhHHHHHHHhcCceEEEEehhhhhhhhheecceeeEEEec
Confidence            3456799999988888899999988888888888777777777778899999999999953  44567899999999999


Q ss_pred             CCCCccccc
Q psy14082        183 LQLSANHNI  191 (233)
Q Consensus       183 ~P~~~~~~i  191 (233)
                      +|.++.=|.
T Consensus       631 pP~~P~FYs  639 (698)
T KOG2340|consen  631 PPNNPHFYS  639 (698)
T ss_pred             CCCCcHHHH
Confidence            999986443

>PF00580 UvrD-helicase: UvrD/REP helicase N-terminal domain; InterPro: IPR000212 Members of this family are helicases that catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA

Probab=96.97  E-value=0.0021  Score=53.66  Aligned_cols=57  Identities=14%  Similarity=-0.004  Sum_probs=41.3

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ....+++.|..|||||.+.+-=++..+....    -...+.|++++|+..+..+.+++...
T Consensus        12 ~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~----~~~~~Il~lTft~~aa~e~~~ri~~~   68 (315)
T PF00580_consen   12 TEGPLLVNAGAGSGKTTTLLERIAYLLYEGG----VPPERILVLTFTNAAAQEMRERIREL   68 (315)
T ss_dssp             -SSEEEEEE-TTSSHHHHHHHHHHHHHHTSS----STGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCchHHHHHHHHHhhcccc----CChHHheecccCHHHHHHHHHHHHHh
Confidence            3567899999999999884444443333321    23456999999999999999999886

THe family includes both Rep and UvrD helcases. The Rep family helicases are composed of four structural domains []. The Rep proteins function as dimers.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 1UAA_B 1W36_B 3K70_B 2IS6_B 3LFU_A 2IS2_B 2IS1_B 2IS4_A 1QHG_A 1PJR_A ....

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=96.94  E-value=0.005  Score=57.50  Aligned_cols=76  Identities=14%  Similarity=0.273  Sum_probs=64.9

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhh----CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEeccc-CcCCcCCCCccEE
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRR----ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDV-AARGLDVEDVNTV  178 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~-~~~Gldi~~v~~V  178 (233)
                      ..+.++++.++|+.-+.+.++.+++    .++++..+||+++..+|.+.++...+|+.+|+|+|.. +...+++.++.+|
T Consensus       308 ~~g~q~lilaPT~~LA~Q~~~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~v~~~~l~lv  387 (681)
T PRK10917        308 EAGYQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLV  387 (681)
T ss_pred             HcCCeEEEEeccHHHHHHHHHHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcccchhcccceE
Confidence            3577999999999999988888765    3689999999999999999999999999999999974 4445667788877


Q ss_pred             E
Q psy14082        179 N  179 (233)
Q Consensus       179 I  179 (233)
                      |
T Consensus       388 V  388 (681)
T PRK10917        388 I  388 (681)
T ss_pred             E
Confidence            6

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

Probab=96.92  E-value=0.0047  Score=58.77  Aligned_cols=79  Identities=18%  Similarity=0.205  Sum_probs=62.1

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCC--CccEEEEe
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVE--DVNTVNIG  181 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~--~v~~VI~~  181 (233)
                      ..+++++|++++.+..+.+++.|....... ...|.-.  .+..++++|++++..||++|+.+.+|+|+|  +...||..
T Consensus       645 ~~~g~~LVLFtS~~~l~~v~~~l~~~~~~~-l~Qg~~~--~~~~l~~~F~~~~~~vLlG~~sFwEGVD~p~~~~~~viI~  721 (820)
T PRK07246        645 QLQQPILVLFNSKKHLLAVSDLLDQWQVSH-LAQEKNG--TAYNIKKRFDRGEQQILLGLGSFWEGVDFVQADRMIEVIT  721 (820)
T ss_pred             hcCCCEEEEECcHHHHHHHHHHHhhcCCcE-EEeCCCc--cHHHHHHHHHcCCCeEEEecchhhCCCCCCCCCeEEEEEe
Confidence            456899999999999999999997665444 5555322  256689999998889999999999999997  35566777


Q ss_pred             cCCC
Q psy14082        182 SLQL  185 (233)
Q Consensus       182 d~P~  185 (233)
                      .+|-
T Consensus       722 kLPF  725 (820)
T PRK07246        722 RLPF  725 (820)
T ss_pred             cCCC
Confidence            7773

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=96.84  E-value=0.0074  Score=56.50  Aligned_cols=78  Identities=19%  Similarity=0.419  Sum_probs=60.1

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhh----CCCCCEEEecccCcCCcCCCC--ccEE
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFR----QGKAPILVATDVAARGLDVED--VNTV  178 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~----~g~~~iLv~T~~~~~Gldi~~--v~~V  178 (233)
                      ..+.++||+++.+..+.++..|....-.....+|..   .+..+++.|+    .++..||++|..+.+|+|+|+  ..+|
T Consensus       533 ~~gg~LVlFtSy~~l~~v~~~l~~~~~~~ll~Q~~~---~~~~ll~~f~~~~~~~~~~VL~g~~sf~EGVD~pGd~l~~v  609 (697)
T PRK11747        533 KHKGSLVLFASRRQMQKVADLLPRDLRLMLLVQGDQ---PRQRLLEKHKKRVDEGEGSVLFGLQSFAEGLDLPGDYLTQV  609 (697)
T ss_pred             cCCCEEEEeCcHHHHHHHHHHHHHhcCCcEEEeCCc---hHHHHHHHHHHHhccCCCeEEEEeccccccccCCCCceEEE
Confidence            344589999999999999999864322334556643   4667787776    467779999999999999986  7889


Q ss_pred             EEecCCC
Q psy14082        179 NIGSLQL  185 (233)
Q Consensus       179 I~~d~P~  185 (233)
                      |...+|-
T Consensus       610 II~kLPF  616 (697)
T PRK11747        610 IITKIPF  616 (697)
T ss_pred             EEEcCCC
Confidence            9999884

>TIGR00376 DNA helicase, putative

Probab=96.79  E-value=0.0018  Score=59.85  Aligned_cols=61  Identities=8%  Similarity=-0.075  Sum_probs=45.6

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcC
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGG   79 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg   79 (233)
                      ...++++|+|||||.+ +..++..+..       .+.++|+++||..-++++.+.+...  ++++..+...
T Consensus       174 ~~~lI~GpPGTGKT~t-~~~ii~~~~~-------~g~~VLv~a~sn~Avd~l~e~l~~~--~~~vvRlg~~  234 (637)
T TIGR00376       174 DLFLIHGPPGTGKTRT-LVELIRQLVK-------RGLRVLVTAPSNIAVDNLLERLALC--DQKIVRLGHP  234 (637)
T ss_pred             CeEEEEcCCCCCHHHH-HHHHHHHHHH-------cCCCEEEEcCcHHHHHHHHHHHHhC--CCcEEEeCCc
Confidence            4588999999999976 5556655553       2568999999999999999988765  4554444433

The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases.

>PRK05580 primosome assembly protein PriA; Validated

Probab=96.75  E-value=0.01  Score=55.45  Aligned_cols=77  Identities=12%  Similarity=0.173  Sum_probs=64.9

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhh-CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEec
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRR-ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGS  182 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~-~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d  182 (233)
                      .+.++++.++++..+.++.+.|++ .+.++..+||+++..+|.+.+.+..+|+.+|+|+|.... -..+.++.+||.-+
T Consensus       189 ~g~~vLvLvPt~~L~~Q~~~~l~~~fg~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal-~~p~~~l~liVvDE  266 (679)
T PRK05580        189 QGKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSAL-FLPFKNLGLIIVDE  266 (679)
T ss_pred             cCCeEEEEeCcHHHHHHHHHHHHHHhCCCEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHh-cccccCCCEEEEEC
Confidence            367999999999999999999976 478899999999999999999999999999999997432 24566778777543

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

Probab=96.72  E-value=0.004  Score=59.42  Aligned_cols=52  Identities=8%  Similarity=-0.104  Sum_probs=41.5

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHH
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAK   65 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~   65 (233)
                      ..++.+.++||||||.+|+-.+++....      .+..+.||+||+.+.-..+.+.+.
T Consensus        59 ~~n~~~~M~TGtGKT~~~~~~i~~l~~~------~~~~~fii~vp~~aI~egv~~~l~  110 (986)
T PRK15483         59 KANIDIKMETGTGKTYVYTRLMYELHQK------YGLFKFIIVVPTPAIKEGTRNFIQ  110 (986)
T ss_pred             cceEEEEeCCCCCHHHHHHHHHHHHHHH------cCCcEEEEEeCCHHHHHHHHHHhh
Confidence            4688999999999999988877665433      345679999999998888877665

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=96.60  E-value=0.01  Score=54.99  Aligned_cols=75  Identities=16%  Similarity=0.246  Sum_probs=63.1

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhh----CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccC-cCCcCCCCccEEE
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRR----ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVA-ARGLDVEDVNTVN  179 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~-~~Gldi~~v~~VI  179 (233)
                      .+.++++.++|+.-+++.++.+++    .|+++..+||+++..+|...++...+|+.+|+|+|... ...+++.++.+||
T Consensus       283 ~g~qvlilaPT~~LA~Q~~~~~~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~~~~~~~l~lvV  362 (630)
T TIGR00643       283 AGYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVI  362 (630)
T ss_pred             cCCcEEEECCHHHHHHHHHHHHHHHhcccCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhccccccccceEE
Confidence            567999999999999988887765    37899999999999999999999999999999999653 3345666777665

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=96.58  E-value=0.0073  Score=56.00  Aligned_cols=56  Identities=16%  Similarity=0.009  Sum_probs=43.5

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEE
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICI   76 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~   76 (233)
                      ..++.+.||||||++.+ -+++.+          +..+|||+|+..+|.|+++.++.|+++-.+..+
T Consensus        31 ~~~l~Gvtgs~kt~~~a-~~~~~~----------~~p~Lvi~~n~~~A~ql~~el~~f~p~~~V~~f   86 (655)
T TIGR00631        31 HQTLLGVTGSGKTFTMA-NVIAQV----------NRPTLVIAHNKTLAAQLYNEFKEFFPENAVEYF   86 (655)
T ss_pred             cEEEECCCCcHHHHHHH-HHHHHh----------CCCEEEEECCHHHHHHHHHHHHHhCCCCeEEEE
Confidence            55689999999998833 455433          224899999999999999999999776446666

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

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

Probab=96.56  E-value=0.0093  Score=55.49  Aligned_cols=80  Identities=21%  Similarity=0.328  Sum_probs=62.8

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCCCe-eEEEeCCCCHHHHHHHHHHhhCCCC-CEEEecccCcCCcCCCCc--cEEE
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRERHS-AICIHGDKTQQDRDYVLNDFRQGKA-PILVATDVAARGLDVEDV--NTVN  179 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~~~-~~~~~~~~~~~~r~~~~~~f~~g~~-~iLv~T~~~~~Gldi~~v--~~VI  179 (233)
                      ...++++||+++-+..+.+.+.+...... ....+|..+   +...++.|+.+.- .++|+|..+++|+|+|+=  .+||
T Consensus       477 ~~~~~~lvlF~Sy~~l~~~~~~~~~~~~~~~v~~q~~~~---~~~~l~~f~~~~~~~~lv~~gsf~EGVD~~g~~l~~vv  553 (654)
T COG1199         477 ASPGGVLVLFPSYEYLKRVAERLKDERSTLPVLTQGEDE---REELLEKFKASGEGLILVGGGSFWEGVDFPGDALRLVV  553 (654)
T ss_pred             hcCCCEEEEeccHHHHHHHHHHHhhcCccceeeecCCCc---HHHHHHHHHHhcCCeEEEeeccccCcccCCCCCeeEEE
Confidence            34449999999999999999999877652 444555443   4588888887765 899999999999999974  6788


Q ss_pred             EecCCCC
Q psy14082        180 IGSLQLS  186 (233)
Q Consensus       180 ~~d~P~~  186 (233)
                      ...+|--
T Consensus       554 I~~lPfp  560 (654)
T COG1199         554 IVGLPFP  560 (654)
T ss_pred             EEecCCC
Confidence            8888743

>TIGR00595 priA primosomal protein N'

Probab=96.51  E-value=0.015  Score=52.35  Aligned_cols=75  Identities=11%  Similarity=0.209  Sum_probs=62.7

Q ss_pred             CCeEEEEecchhHHHHHHHHHhhC-CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEe
Q psy14082        106 AFKVIVFVETKKKVEDITRALRRE-RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIG  181 (233)
Q Consensus       106 ~~k~iIf~~~~~~~~~l~~~L~~~-~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~  181 (233)
                      +.++++.++++.-+.++.+.|++. +.++..+||+++..+|.+.+.+.++|+.+|+|+|...- -..+++..+||.-
T Consensus        25 g~~vLvlvP~i~L~~Q~~~~l~~~f~~~v~vlhs~~~~~er~~~~~~~~~g~~~IVVGTrsal-f~p~~~l~lIIVD  100 (505)
T TIGR00595        25 GKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVVIGTRSAL-FLPFKNLGLIIVD  100 (505)
T ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhCCcEEEEECCCCHHHHHHHHHHHHcCCCCEEECChHHH-cCcccCCCEEEEE
Confidence            458999999999999999999764 67889999999999999999999999999999996533 2446677777744

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).

>smart00492 HELICc3 helicase superfamily c-terminal domain

Probab=96.42  E-value=0.018  Score=42.78  Aligned_cols=67  Identities=16%  Similarity=0.286  Sum_probs=47.9

Q ss_pred             HHHHHHHHhhCCC------eeEEEeCCCCHHHHHHHHHHhhCCCC-CEEEecccCcCCcCCCC--ccEEEEecCCC
Q psy14082        119 VEDITRALRRERH------SAICIHGDKTQQDRDYVLNDFRQGKA-PILVATDVAARGLDVED--VNTVNIGSLQL  185 (233)
Q Consensus       119 ~~~l~~~L~~~~~------~~~~~~~~~~~~~r~~~~~~f~~g~~-~iLv~T~~~~~Gldi~~--v~~VI~~d~P~  185 (233)
                      .+.+...+++.+.      .-.++..+.+..+..++++.|+...- .||+++.-+++|+|+|+  ...||...+|-
T Consensus         4 m~~v~~~~~~~~~~~~l~~~~~i~~e~~~~~~~~~~l~~f~~~~~~~iL~~~~~~~EGiD~~g~~~r~vii~glPf   79 (141)
T smart00492        4 MESFVQYWKENGILENINKNLLLLVQGEDGKETGKLLEKYVEACENAILLATARFSEGVDFPGDYLRAVIIDGLPF   79 (141)
T ss_pred             HHHHHHHHHHcCchhhHhcCCeEEEeCCChhHHHHHHHHHHHcCCCEEEEEccceecceecCCCCeeEEEEEecCC
Confidence            4555566655443      22344445666667899999987643 69999988999999997  56899999884

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

Probab=96.33  E-value=0.013  Score=55.67  Aligned_cols=66  Identities=17%  Similarity=0.263  Sum_probs=55.4

Q ss_pred             HHhcCCCCeEEEEecchhHHHHHHHHHhhCC-----CeeEE-EeCCCCHHHHHHHHHHhhCCCCCEEEeccc
Q psy14082        100 EMAKNPAFKVIVFVETKKKVEDITRALRRER-----HSAIC-IHGDKTQQDRDYVLNDFRQGKAPILVATDV  165 (233)
Q Consensus       100 ~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~-----~~~~~-~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~  165 (233)
                      .+....++++++.++|.--+.+.++.|++..     ..+.+ +||.|+.+++.+++++|.+|+.+|||+|+.
T Consensus       119 l~~a~kgkr~yii~PT~~Lv~Q~~~kl~~~~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~  190 (1187)
T COG1110         119 LYLAKKGKRVYIIVPTTTLVRQVYERLKKFAEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQ  190 (1187)
T ss_pred             HHHHhcCCeEEEEecCHHHHHHHHHHHHHHHhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHH
Confidence            3445677999999999999999999987652     33333 999999999999999999999999999954

>KOG1802|consensus

Probab=96.28  E-value=0.0096  Score=54.15  Aligned_cols=64  Identities=13%  Similarity=0.080  Sum_probs=49.6

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCCC
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPK   82 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~   82 (233)
                      =.++|+|+|+|||++-+- ++.++.++      ....+|+.+|+.--++|+.+.+.+-  ++++..+......
T Consensus       427 lsLIQGPPGTGKTvtsa~-IVyhl~~~------~~~~VLvcApSNiAVDqLaeKIh~t--gLKVvRl~aksRE  490 (935)
T KOG1802|consen  427 LSLIQGPPGTGKTVTSAT-IVYHLARQ------HAGPVLVCAPSNIAVDQLAEKIHKT--GLKVVRLCAKSRE  490 (935)
T ss_pred             ceeeecCCCCCceehhHH-HHHHHHHh------cCCceEEEcccchhHHHHHHHHHhc--CceEeeeehhhhh
Confidence            368899999999998544 55555543      2456899999999999999999887  6888877766443

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=96.21  E-value=0.025  Score=54.55  Aligned_cols=75  Identities=15%  Similarity=0.261  Sum_probs=64.1

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-cCcCCcCCCCccEEE
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-VAARGLDVEDVNTVN  179 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-~~~~Gldi~~v~~VI  179 (233)
                      .+.+++|.++|+.-+++.++.+++.    ++++..++|..+.+++...++.+++|+.+|+|+|. .+.+.+.+.++.++|
T Consensus       499 ~g~qvlvLvPT~~LA~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~ll~~~v~f~~L~llV  578 (926)
T TIGR00580       499 DGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLLQKDVKFKDLGLLI  578 (926)
T ss_pred             hCCeEEEEeCcHHHHHHHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHHhhCCCCcccCCEEE
Confidence            4579999999999999998887653    67888999999999999999999999999999997 344567777888776

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.

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

Probab=96.13  E-value=0.033  Score=51.33  Aligned_cols=84  Identities=17%  Similarity=0.206  Sum_probs=64.8

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCC----CCCEEEecccCcCCcCC------
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQG----KAPILVATDVAARGLDV------  172 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g----~~~iLv~T~~~~~Gldi------  172 (233)
                      ...+++++|.+.+....+.+++.|...--....+.|+.+  .+...+++|+..    +..||++|+.+-+|+|+      
T Consensus       467 ~~~~G~~lvLfTS~~~~~~~~~~l~~~l~~~~l~qg~~~--~~~~l~~~f~~~~~~~~~~vL~gt~sfweGvDv~~~~~~  544 (636)
T TIGR03117       467 RKAQGGTLVLTTAFSHISAIGQLVELGIPAEIVIQSEKN--RLASAEQQFLALYANGIQPVLIAAGGAWTGIDLTHKPVS  544 (636)
T ss_pred             HHcCCCEEEEechHHHHHHHHHHHHhhcCCCEEEeCCCc--cHHHHHHHHHHhhcCCCCcEEEeCCccccccccCCccCC
Confidence            345568999999999999999999654324456677543  356788888874    68899999999999999      


Q ss_pred             ----CCccEEEEecCCCCcc
Q psy14082        173 ----EDVNTVNIGSLQLSAN  188 (233)
Q Consensus       173 ----~~v~~VI~~d~P~~~~  188 (233)
                          ..+.+||+.-+|..+.
T Consensus       545 p~~G~~Ls~ViI~kLPF~~~  564 (636)
T TIGR03117       545 PDKDNLLTDLIITCAPFGLN  564 (636)
T ss_pred             CCCCCcccEEEEEeCCCCcC
Confidence                2488999988885543

Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein 1), as it lies farthest (fourth closest) from the repeats in the A. ferrooxidans genome.

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

Probab=96.11  E-value=0.038  Score=50.57  Aligned_cols=88  Identities=15%  Similarity=0.251  Sum_probs=71.9

Q ss_pred             HHhcCCCCeEEEEecchhHHH----HHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEeccc-CcCCcCCCC
Q psy14082        100 EMAKNPAFKVIVFVETKKKVE----DITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDV-AARGLDVED  174 (233)
Q Consensus       100 ~~~~~~~~k~iIf~~~~~~~~----~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~-~~~Gldi~~  174 (233)
                      +..-..+.++.+.++|.--++    .+.+.|...|+.+..+.|.+..+.|.+++....+|+.+++|.|.+ +...+++.+
T Consensus       305 l~ai~~G~Q~ALMAPTEILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALiQd~V~F~~  384 (677)
T COG1200         305 LAAIEAGYQAALMAPTEILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQDKVEFHN  384 (677)
T ss_pred             HHHHHcCCeeEEeccHHHHHHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhhhcceeecc
Confidence            445568889999999975555    455555567999999999999999999999999999999999986 456788888


Q ss_pred             ccEEEEecCCCCcccccc
Q psy14082        175 VNTVNIGSLQLSANHNIS  192 (233)
Q Consensus       175 v~~VI~~d~P~~~~~~i~  192 (233)
                      .-+||     .+..||.|
T Consensus       385 LgLVI-----iDEQHRFG  397 (677)
T COG1200         385 LGLVI-----IDEQHRFG  397 (677)
T ss_pred             eeEEE-----Eecccccc
Confidence            88888     45566664

>smart00491 HELICc2 helicase superfamily c-terminal domain

Probab=96.07  E-value=0.02  Score=42.53  Aligned_cols=67  Identities=15%  Similarity=0.256  Sum_probs=44.5

Q ss_pred             HHHHHHHHhhCCC---eeEEEeCCCCHHHHHHHHHHhhCCCC---CEEEeccc--CcCCcCCCC--ccEEEEecCCC
Q psy14082        119 VEDITRALRRERH---SAICIHGDKTQQDRDYVLNDFRQGKA---PILVATDV--AARGLDVED--VNTVNIGSLQL  185 (233)
Q Consensus       119 ~~~l~~~L~~~~~---~~~~~~~~~~~~~r~~~~~~f~~g~~---~iLv~T~~--~~~Gldi~~--v~~VI~~d~P~  185 (233)
                      .+.+.+.+.+.+.   ...++.-+....+..++++.|++...   .||+++.-  +++|+|+|+  ..+||..++|-
T Consensus         4 m~~v~~~~~~~~~~~~~~~i~~e~~~~~~~~~~l~~f~~~~~~~g~iL~~v~~G~~~EGiD~~g~~~r~vii~glPf   80 (142)
T smart00491        4 LEQVVEYWKENGILEINKPVFIEGKDSGETEELLEKYSAACEARGALLLAVARGKVSEGIDFPDDLGRAVIIVGIPF   80 (142)
T ss_pred             HHHHHHHHHhcCccccCceEEEECCCCchHHHHHHHHHHhcCCCCEEEEEEeCCeeecceecCCCccEEEEEEecCC
Confidence            4556666665543   12223322333355788999987543   58888876  899999997  57899999884

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=96.02  E-value=0.031  Score=52.58  Aligned_cols=82  Identities=20%  Similarity=0.316  Sum_probs=62.0

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhCCC-------eeEEEeCCCCHHHHHHHHHHhhC----CCCCEEEec--ccCcCC
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRERH-------SAICIHGDKTQQDRDYVLNDFRQ----GKAPILVAT--DVAARG  169 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~~~-------~~~~~~~~~~~~~r~~~~~~f~~----g~~~iLv~T--~~~~~G  169 (233)
                      ..-.+.++||+++-...+.+.+.+.+.+.       +..+.-+ -...++..++++|+.    |..-||+|+  ..+++|
T Consensus       519 ~~~pgg~lvfFpSy~~l~~v~~~~~~~~~~~~i~~~k~i~~E~-~~~~~~~~~l~~f~~~~~~~~gavL~av~gGk~sEG  597 (705)
T TIGR00604       519 KIIPDGIVVFFPSYSYLENIVSTWKEMGILENIEKKKLIFVET-KDAQETSDALERYKQAVSEGRGAVLLSVAGGKVSEG  597 (705)
T ss_pred             hcCCCcEEEEccCHHHHHHHHHHHHhcCHHHHHhcCCCEEEeC-CCcchHHHHHHHHHHHHhcCCceEEEEecCCcccCc
Confidence            33457899999999999999998876542       2223322 222577889999964    445699998  889999


Q ss_pred             cCCCC--ccEEEEecCCC
Q psy14082        170 LDVED--VNTVNIGSLQL  185 (233)
Q Consensus       170 ldi~~--v~~VI~~d~P~  185 (233)
                      +|+++  ...||..++|-
T Consensus       598 IDf~~~~~r~ViivGlPf  615 (705)
T TIGR00604       598 IDFCDDLGRAVIMVGIPY  615 (705)
T ss_pred             cccCCCCCcEEEEEccCC
Confidence            99997  68899999996

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).

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=96.01  E-value=0.0093  Score=51.81  Aligned_cols=48  Identities=10%  Similarity=0.071  Sum_probs=39.0

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ++++.|+||||||.++++|-+...          +..++|.=|--|+...+....+..
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll~~----------~~s~vv~D~Kge~~~~t~~~r~~~   48 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLLTW----------PGSVVVLDPKGENFELTSEHRRAL   48 (384)
T ss_pred             CeeEecCCCCCCccEEEccchhcC----------CCCEEEEccchhHHHHHHHHHHHc
Confidence            578999999999999999876532          246889999999998887776655

These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA transfer to plant cells and is required for virulence.

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

Probab=96.01  E-value=0.017  Score=45.30  Aligned_cols=47  Identities=15%  Similarity=0.097  Sum_probs=34.7

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHH
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVA   64 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~   64 (233)
                      -.+++++.|||||.+ +-.+...+..       .+.++++++||...+....+..
T Consensus        20 ~~~l~G~aGtGKT~~-l~~~~~~~~~-------~g~~v~~~apT~~Aa~~L~~~~   66 (196)
T PF13604_consen   20 VSVLQGPAGTGKTTL-LKALAEALEA-------AGKRVIGLAPTNKAAKELREKT   66 (196)
T ss_dssp             EEEEEESTTSTHHHH-HHHHHHHHHH-------TT--EEEEESSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCHHHH-HHHHHHHHHh-------CCCeEEEECCcHHHHHHHHHhh
Confidence            477889999999965 4455555543       3678999999999999877774

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=95.96  E-value=0.12  Score=49.81  Aligned_cols=83  Identities=16%  Similarity=0.181  Sum_probs=61.6

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCC--------C
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVE--------D  174 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~--------~  174 (233)
                      ...+.++||-+.+.+..+.+...|...|+...+++.....++ .+++.. ......|-|||++++||-|+.        +
T Consensus       625 ~~~GrPVLVGT~SVe~SE~lS~~L~~~gI~H~VLNAK~h~~E-AeIVA~-AG~~GaVTIATNMAGRGTDIkLg~~V~e~G  702 (1112)
T PRK12901        625 SEAGRPVLVGTTSVEISELLSRMLKMRKIPHNVLNAKLHQKE-AEIVAE-AGQPGTVTIATNMAGRGTDIKLSPEVKAAG  702 (1112)
T ss_pred             HHCCCCEEEEeCcHHHHHHHHHHHHHcCCcHHHhhccchhhH-HHHHHh-cCCCCcEEEeccCcCCCcCcccchhhHHcC
Confidence            458899999999999999999999999999888877643333 333332 222346889999999999986        1


Q ss_pred             ccEEEEecCCCCc
Q psy14082        175 VNTVNIGSLQLSA  187 (233)
Q Consensus       175 v~~VI~~d~P~~~  187 (233)
                      ==+||--..|.|.
T Consensus       703 GL~VIgTerheSr  715 (1112)
T PRK12901        703 GLAIIGTERHESR  715 (1112)
T ss_pred             CCEEEEccCCCcH
Confidence            2367766666654

>KOG0339|consensus

Probab=95.94  E-value=0.082  Score=46.95  Aligned_cols=68  Identities=18%  Similarity=0.204  Sum_probs=53.2

Q ss_pred             hhhhchH-HHhcCCCCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc
Q psy14082         93 FVFNCQY-EMAKNPAFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD  164 (233)
Q Consensus        93 ~~~~~~~-~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~  164 (233)
                      ++.+.++ .+....+.-.+|.|+|++.+.++....++.    |+.++++||+++..++...++    -...++|||+
T Consensus       282 ~~himdq~eL~~g~gPi~vilvPTrela~Qi~~eaKkf~K~ygl~~v~~ygGgsk~eQ~k~Lk----~g~EivVaTP  354 (731)
T KOG0339|consen  282 IVHIMDQPELKPGEGPIGVILVPTRELASQIFSEAKKFGKAYGLRVVAVYGGGSKWEQSKELK----EGAEIVVATP  354 (731)
T ss_pred             HHHhcchhhhcCCCCCeEEEEeccHHHHHHHHHHHHHhhhhccceEEEeecCCcHHHHHHhhh----cCCeEEEech
Confidence            4444443 355567777899999999999888777654    789999999999999888777    3578999993

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

Probab=95.94  E-value=0.015  Score=49.97  Aligned_cols=51  Identities=12%  Similarity=0.017  Sum_probs=39.8

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      +++.+.+|||||+. ++-++..+...     ..+..++++++...|...+.+.+..-
T Consensus         4 ~~I~G~aGTGKTvl-a~~l~~~l~~~-----~~~~~~~~l~~n~~l~~~l~~~l~~~   54 (352)
T PF09848_consen    4 ILITGGAGTGKTVL-ALNLAKELQNS-----EEGKKVLYLCGNHPLRNKLREQLAKK   54 (352)
T ss_pred             EEEEecCCcCHHHH-HHHHHHHhhcc-----ccCCceEEEEecchHHHHHHHHHhhh
Confidence            68899999999988 56566666211     34678999999999999888888654

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues

Probab=95.94  E-value=0.012  Score=52.52  Aligned_cols=49  Identities=14%  Similarity=0.154  Sum_probs=40.2

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      .++++.|+||||||..|++|.+-..         ++ .++|.=|-.||...+....++.
T Consensus        45 ~h~lvig~tgSGKt~~~viP~ll~~---------~~-s~iV~D~KgEl~~~t~~~r~~~   93 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNLLNY---------PG-SMIVTDPKGELYEKTAGYRKKR   93 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHHHhc---------cC-CEEEEECCCcHHHHHHHHHHHC
Confidence            4699999999999999999987422         12 5888889999999888877776

These proteins contain a P-loop and walker-B site for nucleotide binding. TraG is essential for DNA transfer in bacterial conjugation. These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems [, ].; GO: 0009291 unidirectional conjugation, 0016020 membrane

>PRK10689 transcription-repair coupling factor; Provisional

Probab=95.93  E-value=0.041  Score=54.28  Aligned_cols=76  Identities=16%  Similarity=0.188  Sum_probs=63.5

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEeccc-CcCCcCCCCccEE
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDV-AARGLDVEDVNTV  178 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~-~~~Gldi~~v~~V  178 (233)
                      ..+.+++|.++|+..+.+.++.+++.    ++++..++|..+.+++.++++..++|..+|+|+|.. +...+++.++.++
T Consensus       647 ~~g~qvlvLvPT~eLA~Q~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL~~~v~~~~L~lL  726 (1147)
T PRK10689        647 ENHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLL  726 (1147)
T ss_pred             HcCCeEEEEeCcHHHHHHHHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHHhCCCCHhhCCEE
Confidence            35789999999999999998888753    467888999999999999999999999999999963 4445666777776


Q ss_pred             E
Q psy14082        179 N  179 (233)
Q Consensus       179 I  179 (233)
                      |
T Consensus       727 V  727 (1147)
T PRK10689        727 I  727 (1147)
T ss_pred             E
Confidence            6

>KOG0335|consensus

Probab=95.70  E-value=0.037  Score=48.82  Aligned_cols=123  Identities=23%  Similarity=0.291  Sum_probs=86.8

Q ss_pred             CCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEec------------------
Q psy14082        106 AFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVAT------------------  163 (233)
Q Consensus       106 ~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T------------------  163 (233)
                      ..+.+|..+|++-+.++++.-++.    +.++...+|+.+....    ..+....++|+|||                  
T Consensus       152 ~P~~lIlapTReL~~Qi~nea~k~~~~s~~~~~~~ygg~~~~~q----~~~~~~gcdIlvaTpGrL~d~~e~g~i~l~~~  227 (482)
T KOG0335|consen  152 YPRALILAPTRELVDQIYNEARKFSYLSGMKSVVVYGGTDLGAQ----LRFIKRGCDILVATPGRLKDLIERGKISLDNC  227 (482)
T ss_pred             CCceEEEeCcHHHhhHHHHHHHhhcccccceeeeeeCCcchhhh----hhhhccCccEEEecCchhhhhhhcceeehhhC
Confidence            578999999999999999998765    4677888888443332    33445679999999                  


Q ss_pred             -----ccCcCCcC----CCCccEEEEec-CCC---------------Cc---------cccc--------------ceee
Q psy14082        164 -----DVAARGLD----VEDVNTVNIGS-LQL---------------SA---------NHNI--------------SQVI  195 (233)
Q Consensus       164 -----~~~~~Gld----i~~v~~VI~~d-~P~---------------~~---------~~~i--------------~~~~  195 (233)
                           |.+.|.+|    .|++++++.+. +|.               +.         +.|+              -+.+
T Consensus       228 k~~vLDEADrMlD~mgF~p~Ir~iv~~~~~~~~~~~qt~mFSAtfp~~iq~l~~~fl~~~yi~laV~rvg~~~~ni~q~i  307 (482)
T KOG0335|consen  228 KFLVLDEADRMLDEMGFEPQIRKIVEQLGMPPKNNRQTLLFSATFPKEIQRLAADFLKDNYIFLAVGRVGSTSENITQKI  307 (482)
T ss_pred             cEEEecchHHhhhhccccccHHHHhcccCCCCccceeEEEEeccCChhhhhhHHHHhhccceEEEEeeeccccccceeEe
Confidence                 44555566    45666655543 331               11         1133              4888


Q ss_pred             EEeecchHHHHHHHHHHhhc-----C-----cccccccchhhHhhhc
Q psy14082        196 EVVQDYEKEKRLFSLIRELG-----K-----YTLITQESSSTLSEMV  232 (233)
Q Consensus       196 ~~~~~~~~~~~~~~~i~~~~-----~-----~~~~~~~~~~~~~~l~  232 (233)
                      .++.+.++...+++++....     +     ..++|.|.++.+.+++
T Consensus       308 ~~V~~~~kr~~Lldll~~~~~~~~~~~~~~e~tlvFvEt~~~~d~l~  354 (482)
T KOG0335|consen  308 LFVNEMEKRSKLLDLLNKDDGPPSDGEPKWEKTLVFVETKRGADELA  354 (482)
T ss_pred             eeecchhhHHHHHHHhhcccCCcccCCcccceEEEEeeccchhhHHH
Confidence            89998899999999887532     2     5788999998887764

>PF07517 SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011115 SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane

Probab=95.65  E-value=0.048  Score=44.91  Aligned_cols=63  Identities=17%  Similarity=0.087  Sum_probs=51.4

Q ss_pred             eEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEcCCCC
Q psy14082         12 FSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGGTPK   82 (233)
Q Consensus        12 i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~gg~~~   82 (233)
                      +++..||=|||++..+|++-..+.        |..+=|++.+.-||..=++.+..+  +.++++.+..++.+.
T Consensus        94 laEm~TGEGKTli~~l~a~~~AL~--------G~~V~vvT~NdyLA~RD~~~~~~~y~~LGlsv~~~~~~~~~  158 (266)
T PF07517_consen   94 LAEMKTGEGKTLIAALPAALNALQ--------GKGVHVVTSNDYLAKRDAEEMRPFYEFLGLSVGIITSDMSS  158 (266)
T ss_dssp             EEEESTTSHHHHHHHHHHHHHHTT--------SS-EEEEESSHHHHHHHHHHHHHHHHHTT--EEEEETTTEH
T ss_pred             eEEecCCCCcHHHHHHHHHHHHHh--------cCCcEEEeccHHHhhccHHHHHHHHHHhhhccccCccccCH
Confidence            899999999999999888776653        556888999999999999999998  668999999988653

SecA protein achieves this translocation, in association with SecY protein, in an ATP-dependent manner [,]. This domain represents the N-terminal ATP-dependent helicase domain, which is related to the IPR0011545 from INTERPRO.; GO: 0005524 ATP binding, 0017038 protein import, 0016020 membrane; PDB: 1NL3_B 1NKT_B 3DIN_B 3JUX_A 2FSG_B 2VDA_A 2FSH_A 2FSF_A 2FSI_A 3BXZ_A ....

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=95.65  E-value=0.02  Score=52.57  Aligned_cols=50  Identities=6%  Similarity=-0.136  Sum_probs=42.3

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ..++++.||||||||..|++|-+...          +..++|+=|--|+...+....++.
T Consensus       158 ~~hvLviapTgSGKg~g~VIPnLL~~----------~~S~VV~DpKGEl~~~Ta~~R~~~  207 (606)
T PRK13897        158 FQHALLFAPTGSGKGVGFVIPNLLFW----------EDSVVVHDIKLENYELTSGWREKQ  207 (606)
T ss_pred             CceEEEEcCCCCCcceEEehhhHHhC----------CCCEEEEeCcHHHHHHHHHHHHHC
Confidence            45799999999999999999998754          234888999999999988888776

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

Probab=95.51  E-value=0.11  Score=50.43  Aligned_cols=89  Identities=12%  Similarity=0.190  Sum_probs=74.0

Q ss_pred             HHhcCCCCeEEEEecchhHHHHHHHHHhh----CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-cCcCCcCCCC
Q psy14082        100 EMAKNPAFKVIVFVETKKKVEDITRALRR----ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-VAARGLDVED  174 (233)
Q Consensus       100 ~~~~~~~~k~iIf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-~~~~Gldi~~  174 (233)
                      ...-..++++.|.++|.--+++-++.+++    ..+++..+..-.+.+++.++++..++|+++|+|.|. .++.++-+.+
T Consensus       637 FkAV~~GKQVAvLVPTTlLA~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTHrLL~kdv~Fkd  716 (1139)
T COG1197         637 FKAVMDGKQVAVLVPTTLLAQQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHRLLSKDVKFKD  716 (1139)
T ss_pred             HHHhcCCCeEEEEcccHHhHHHHHHHHHHHhcCCCeeEEEecccCCHHHHHHHHHHHhcCCccEEEechHhhCCCcEEec
Confidence            34455789999999998777766666654    467888999999999999999999999999999996 5778888999


Q ss_pred             ccEEEEecCCCCcccccce
Q psy14082        175 VNTVNIGSLQLSANHNISQ  193 (233)
Q Consensus       175 v~~VI~~d~P~~~~~~i~~  193 (233)
                      .-++|     -+.+|+.|.
T Consensus       717 LGLlI-----IDEEqRFGV  730 (1139)
T COG1197         717 LGLLI-----IDEEQRFGV  730 (1139)
T ss_pred             CCeEE-----EechhhcCc
Confidence            99888     467777774

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

Probab=95.45  E-value=0.054  Score=50.60  Aligned_cols=102  Identities=16%  Similarity=0.218  Sum_probs=78.0

Q ss_pred             CCcEEEEEcCCCCC-CeeEEeccchhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhC-CCeeEEEeCCCCHHHHHH
Q psy14082         70 ALRNICIFGGTPKG-PQDCLPLHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRE-RHSAICIHGDKTQQDRDY  147 (233)
Q Consensus        70 ~~~~~~~~gg~~~~-~~~lv~l~r~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~-~~~~~~~~~~~~~~~r~~  147 (233)
                      +....++.|-+... ..      -++..+.+.+.  .++++|+.++.......+.+.++.+ |.++.++|+++++.+|.+
T Consensus       216 ~~~~~Ll~GvTGSGKTE------vYl~~i~~~L~--~GkqvLvLVPEI~Ltpq~~~rf~~rFg~~v~vlHS~Ls~~er~~  287 (730)
T COG1198         216 GFAPFLLDGVTGSGKTE------VYLEAIAKVLA--QGKQVLVLVPEIALTPQLLARFKARFGAKVAVLHSGLSPGERYR  287 (730)
T ss_pred             cccceeEeCCCCCcHHH------HHHHHHHHHHH--cCCEEEEEeccccchHHHHHHHHHHhCCChhhhcccCChHHHHH
Confidence            35666666654432 22      26666766554  5689999999999999999999754 889999999999999999


Q ss_pred             HHHHhhCCCCCEEEecccCcCCcCCCCccEEEE
Q psy14082        148 VLNDFRQGKAPILVATDVAARGLDVEDVNTVNI  180 (233)
Q Consensus       148 ~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~  180 (233)
                      .+.+.++|+.+|+|.|..+- -.=+++..+||.
T Consensus       288 ~W~~~~~G~~~vVIGtRSAl-F~Pf~~LGLIIv  319 (730)
T COG1198         288 VWRRARRGEARVVIGTRSAL-FLPFKNLGLIIV  319 (730)
T ss_pred             HHHHHhcCCceEEEEechhh-cCchhhccEEEE
Confidence            99999999999999996533 233556666663

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

Probab=95.42  E-value=0.057  Score=48.86  Aligned_cols=67  Identities=25%  Similarity=0.381  Sum_probs=53.4

Q ss_pred             EEEEecchhHHHHHHHHHhhC-----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----cCcCC-cCCCCccE
Q psy14082        109 VIVFVETKKKVEDITRALRRE-----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----VAARG-LDVEDVNT  177 (233)
Q Consensus       109 ~iIf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----~~~~G-ldi~~v~~  177 (233)
                      +||+++|++.+.++++.+...     ++.+..++|+++...+...++.   | .+|+|+|+     .+.++ +|+..+.+
T Consensus       102 aLil~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~~---~-~~ivVaTPGRllD~i~~~~l~l~~v~~  177 (513)
T COG0513         102 ALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKR---G-VDIVVATPGRLLDLIKRGKLDLSGVET  177 (513)
T ss_pred             eEEECCCHHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHhc---C-CCEEEECccHHHHHHHcCCcchhhcCE
Confidence            999999999999999988753     5678999999998887755554   6 99999993     45555 67667776


Q ss_pred             EE
Q psy14082        178 VN  179 (233)
Q Consensus       178 VI  179 (233)
                      +|
T Consensus       178 lV  179 (513)
T COG0513         178 LV  179 (513)
T ss_pred             EE
Confidence            65

>PRK14701 reverse gyrase; Provisional

Probab=95.38  E-value=0.072  Score=54.28  Aligned_cols=61  Identities=16%  Similarity=0.239  Sum_probs=54.4

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhC------CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEeccc
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRE------RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDV  165 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~  165 (233)
                      .+.+++|.++|+.-+.++.+.++..      +..+..+||+++.+++.+.++.+++|+.+|||+|+.
T Consensus       121 ~g~~aLVl~PTreLa~Qi~~~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPg  187 (1638)
T PRK14701        121 KGKKCYIILPTTLLVKQTVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQ  187 (1638)
T ss_pred             cCCeEEEEECHHHHHHHHHHHHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCc
Confidence            5679999999999999999999863      467788999999999999999999999999999963

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=95.35  E-value=0.14  Score=48.18  Aligned_cols=70  Identities=19%  Similarity=0.249  Sum_probs=54.5

Q ss_pred             hcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCC
Q psy14082        102 AKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVE  173 (233)
Q Consensus       102 ~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~  173 (233)
                      ....+.|+||-+.+.+..+.+.+.|.+.|++..++...-.  .++.-+-+.....--+-|||++++||-|+.
T Consensus       425 ~~~~gqPvLvgT~sie~SE~ls~~L~~~~i~h~VLNAk~h--~~EA~Iia~AG~~gaVTiATNMAGRGTDIk  494 (822)
T COG0653         425 RHEKGQPVLVGTVSIEKSELLSKLLRKAGIPHNVLNAKNH--AREAEIIAQAGQPGAVTIATNMAGRGTDIK  494 (822)
T ss_pred             HHhcCCCEEEcCcceecchhHHHHHHhcCCCceeeccccH--HHHHHHHhhcCCCCccccccccccCCcccc
Confidence            5568899999999999999999999999999888877644  333333333322334779999999999974

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

Probab=95.24  E-value=0.049  Score=52.85  Aligned_cols=54  Identities=17%  Similarity=0.130  Sum_probs=43.7

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ++--+++=-||||||++ ++=+.+.+.+.     ...|.+++++-+++|-.|+.+.+..+
T Consensus       273 ~~~G~IWHtqGSGKTlT-m~~~A~~l~~~-----~~~~~v~fvvDR~dLd~Q~~~~f~~~  326 (962)
T COG0610         273 GKGGYIWHTQGSGKTLT-MFKLARLLLEL-----PKNPKVLFVVDRKDLDDQTSDEFQSF  326 (962)
T ss_pred             CCceEEEeecCCchHHH-HHHHHHHHHhc-----cCCCeEEEEechHHHHHHHHHHHHHH
Confidence            45577788899999999 44345555544     56789999999999999999999998

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=95.24  E-value=0.019  Score=49.09  Aligned_cols=42  Identities=10%  Similarity=-0.140  Sum_probs=30.9

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHH
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELA   57 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~   57 (233)
                      .+.++++.++||||||.. +-.++..+-        ...+.+.+=.+.||.
T Consensus       161 ~~~nilI~G~tGSGKTTl-l~aLl~~i~--------~~~rivtiEd~~El~  202 (344)
T PRK13851        161 GRLTMLLCGPTGSGKTTM-SKTLISAIP--------PQERLITIEDTLELV  202 (344)
T ss_pred             cCCeEEEECCCCccHHHH-HHHHHcccC--------CCCCEEEECCCcccc
Confidence            578899999999999954 555665542        244677788888874

>PF12340 DUF3638: Protein of unknown function (DUF3638); InterPro: IPR022099 This domain family is found in eukaryotes, and is approximately 230 amino acids in length

Probab=95.22  E-value=0.061  Score=43.11  Aligned_cols=54  Identities=13%  Similarity=0.171  Sum_probs=44.4

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      .+|.+.+.|.-.|.|||-+ ++|++..++.+      +..-+-++||. .|..|..+.++.-
T Consensus        39 ~~~~n~v~QlnMGeGKTsV-I~Pmla~~LAd------g~~LvrviVpk-~Ll~q~~~~L~~~   92 (229)
T PF12340_consen   39 PSGKNSVMQLNMGEGKTSV-IVPMLALALAD------GSRLVRVIVPK-ALLEQMRQMLRSR   92 (229)
T ss_pred             CCCCCeEeeecccCCccch-HHHHHHHHHcC------CCcEEEEEcCH-HHHHHHHHHHHHH
Confidence            4788999999999999977 89999988864      34456667774 7999999999887

There are two conserved sequence motifs: LLE and NMG.

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=95.22  E-value=0.063  Score=48.64  Aligned_cols=59  Identities=17%  Similarity=0.014  Sum_probs=43.2

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      .+.-+++|++.|||||.+.+--+.-.+..-+....  +..+||+.|.+-+..=+.+.+=.+
T Consensus       225 k~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l~--~k~vlvl~PN~vFleYis~VLPeL  283 (747)
T COG3973         225 KNKILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQ--AKPVLVLGPNRVFLEYISRVLPEL  283 (747)
T ss_pred             CCCeEEEecCCCCCchhHHHHHHHHHHhccccccc--cCceEEEcCcHHHHHHHHHhchhh
Confidence            45568999999999998866555444444332222  333999999999999998888777

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=95.16  E-value=0.078  Score=50.64  Aligned_cols=82  Identities=23%  Similarity=0.292  Sum_probs=62.1

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCC-CCEEEecccCcCCcCCCCc------
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGK-APILVATDVAARGLDVEDV------  175 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~-~~iLv~T~~~~~Gldi~~v------  175 (233)
                      ...+.++||-|.+....+.++..|.+.|+...+++..-..++ .+++..  .|+ ..|-|||++++||.|+.--      
T Consensus       565 ~~~grPvLigt~si~~se~ls~~L~~~gi~h~vLNak~~~~E-a~iia~--AG~~g~VTIATNmAGRGTDIkl~~~v~~~  641 (970)
T PRK12899        565 HRKGNPILIGTESVEVSEKLSRILRQNRIEHTVLNAKNHAQE-AEIIAG--AGKLGAVTVATNMAGRGTDIKLDEEAVAV  641 (970)
T ss_pred             HhCCCCEEEEeCcHHHHHHHHHHHHHcCCcceecccchhhhH-HHHHHh--cCCCCcEEEeeccccCCcccccCchHHhc
Confidence            457789999999999999999999999999999988633222 333332  344 5689999999999998422      


Q ss_pred             --cEEEEecCCCCc
Q psy14082        176 --NTVNIGSLQLSA  187 (233)
Q Consensus       176 --~~VI~~d~P~~~  187 (233)
                        =+||.-..|.|.
T Consensus       642 GGLhVIgTer~es~  655 (970)
T PRK12899        642 GGLYVIGTSRHQSR  655 (970)
T ss_pred             CCcEEEeeccCchH
Confidence              167777777665

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=95.13  E-value=0.075  Score=50.51  Aligned_cols=25  Identities=12%  Similarity=0.187  Sum_probs=21.9

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhh
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRR  128 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~  128 (233)
                      .+.+++||||+.+.+|..+.+.|..
T Consensus       293 ~~~~~iLI~~~d~~T~~qL~~~L~~  317 (814)
T TIGR00596       293 QGPGKVLIMCSDNRTCLQLRDYLTT  317 (814)
T ss_pred             CCCCcEEEEEcchHHHHHHHHHHHh
Confidence            4567899999999999999999855

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

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=95.09  E-value=0.042  Score=51.12  Aligned_cols=49  Identities=10%  Similarity=0.026  Sum_probs=39.5

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      .++++.||||||||..|++|-+-..          ...++|+=|--|+...+....++.
T Consensus       140 ~hvlviApTgSGKgvg~VIPnLL~~----------~gS~VV~DpKGE~~~~Ta~~R~~~  188 (670)
T PRK13850        140 PHSLVVAPTRAGKGVGVVIPTLLTF----------KGSVIALDVKGELFELTSRARKAS  188 (670)
T ss_pred             ceEEEEecCCCCceeeehHhHHhcC----------CCCEEEEeCCchHHHHHHHHHHhC
Confidence            4899999999999999999987643          225888889989888877666655

>KOG0952|consensus

Probab=95.05  E-value=0.024  Score=54.02  Aligned_cols=70  Identities=11%  Similarity=0.009  Sum_probs=57.8

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEcCCCCC
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGGTPKG   83 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~gg~~~~   83 (233)
                      ..+.++.+|||+|||++|.+.+...+..      .++.++++++|-..|+..-.+.+.+.  .+++++.-..|....+
T Consensus       943 d~~~~~g~ptgsgkt~~ae~a~~~~~~~------~p~~kvvyIap~kalvker~~Dw~~r~~~~g~k~ie~tgd~~pd 1014 (1230)
T KOG0952|consen  943 DLNFLLGAPTGSGKTVVAELAIFRALSY------YPGSKVVYIAPDKALVKERSDDWSKRDELPGIKVIELTGDVTPD 1014 (1230)
T ss_pred             chhhhhcCCccCcchhHHHHHHHHHhcc------CCCccEEEEcCCchhhcccccchhhhcccCCceeEeccCccCCC
Confidence            4567889999999999999988876654      35678999999999999988888876  4578888888887654

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=95.04  E-value=0.019  Score=47.66  Aligned_cols=25  Identities=4%  Similarity=-0.177  Sum_probs=22.0

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhhcc
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHISHQ   36 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~~~   36 (233)
                      ++|.+|||||||.+ +.+++..+.++
T Consensus       128 ILVTGpTGSGKSTT-lAamId~iN~~  152 (353)
T COG2805         128 ILVTGPTGSGKSTT-LAAMIDYINKH  152 (353)
T ss_pred             EEEeCCCCCcHHHH-HHHHHHHHhcc
Confidence            78999999999977 77899998875

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=95.01  E-value=0.049  Score=44.05  Aligned_cols=54  Identities=9%  Similarity=-0.154  Sum_probs=39.1

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ++.|.-+++.+++|+|||....--+.+.+        .++..+++++ +.|-..|+.+.+..+
T Consensus        18 ~~~gs~~lI~G~pGsGKT~la~~~l~~~~--------~~ge~~lyvs-~ee~~~~i~~~~~~~   71 (237)
T TIGR03877        18 IPERNVVLLSGGPGTGKSIFSQQFLWNGL--------QMGEPGIYVA-LEEHPVQVRRNMAQF   71 (237)
T ss_pred             CcCCeEEEEEcCCCCCHHHHHHHHHHHHH--------HcCCcEEEEE-eeCCHHHHHHHHHHh
Confidence            35788899999999999975433334444        2356688777 567788888888877

Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=95.00  E-value=0.036  Score=46.98  Aligned_cols=45  Identities=11%  Similarity=-0.079  Sum_probs=32.3

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHH
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELA   57 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~   57 (233)
                      .+.++++.++||||||.. +-.++..+...     ..+.+.+.+=.+.||.
T Consensus       143 ~~~nilI~G~tGSGKTTl-l~aL~~~i~~~-----~~~~rivtiEd~~El~  187 (323)
T PRK13833        143 SRLNIVISGGTGSGKTTL-ANAVIAEIVAS-----APEDRLVILEDTAEIQ  187 (323)
T ss_pred             cCCeEEEECCCCCCHHHH-HHHHHHHHhcC-----CCCceEEEecCCcccc
Confidence            467899999999999954 66666666432     1245778888888874

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=94.91  E-value=0.05  Score=45.70  Aligned_cols=45  Identities=11%  Similarity=-0.030  Sum_probs=32.6

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHH
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELA   57 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~   57 (233)
                      .+..+++.++||||||.. +-.++..+...     ....+++.+=.+.|+.
T Consensus       131 ~~~~ilI~G~tGSGKTTl-l~al~~~i~~~-----~~~~ri~tiEd~~El~  175 (299)
T TIGR02782       131 ARKNILVVGGTGSGKTTL-ANALLAEIAKN-----DPTDRVVIIEDTRELQ  175 (299)
T ss_pred             cCCeEEEECCCCCCHHHH-HHHHHHHhhcc-----CCCceEEEECCchhhc
Confidence            467899999999999954 66666655432     1245788888888874

The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=94.88  E-value=0.035  Score=47.01  Aligned_cols=46  Identities=7%  Similarity=-0.090  Sum_probs=33.3

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHH
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELA   57 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~   57 (233)
                      ..+..+++.++|||||| +++-.++..+...     .+..+.+++-.+.||.
T Consensus       146 ~~~~~ilI~G~tGSGKT-Tll~aL~~~~~~~-----~~~~rivtIEd~~El~  191 (319)
T PRK13894        146 RAHRNILVIGGTGSGKT-TLVNAIINEMVIQ-----DPTERVFIIEDTGEIQ  191 (319)
T ss_pred             HcCCeEEEECCCCCCHH-HHHHHHHHhhhhc-----CCCceEEEEcCCCccc
Confidence            35778999999999999 5566676655322     2345788888888873

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=94.79  E-value=0.045  Score=42.33  Aligned_cols=48  Identities=13%  Similarity=0.029  Sum_probs=31.2

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHH
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQT   62 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~   62 (233)
                      -.+..++..+++|+|||.. +..+...+...       +..+++ ++..+|..++..
T Consensus        45 ~~~~~l~l~G~~G~GKThL-a~ai~~~~~~~-------g~~v~f-~~~~~L~~~l~~   92 (178)
T PF01695_consen   45 ENGENLILYGPPGTGKTHL-AVAIANEAIRK-------GYSVLF-ITASDLLDELKQ   92 (178)
T ss_dssp             SC--EEEEEESTTSSHHHH-HHHHHHHHHHT-------T--EEE-EEHHHHHHHHHC
T ss_pred             ccCeEEEEEhhHhHHHHHH-HHHHHHHhccC-------CcceeE-eecCceeccccc
Confidence            4578899999999999987 55566666543       445555 566677776644

They are found associated with IS21 family insertion sequences []. Functionally they have not been characterised, but they may be involved in transposition [].; GO: 0005524 ATP binding; PDB: 3EC2_A 3ECC_A 2W58_A 2QGZ_A.

>PRK13822 conjugal transfer coupling protein TraG; Provisional

Probab=94.72  E-value=0.061  Score=49.85  Aligned_cols=50  Identities=16%  Similarity=0.236  Sum_probs=39.6

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ..++++.|+||||||..+++|-+-..          +..++++=|-.|+...+....++.
T Consensus       224 ~~H~Lv~ApTgsGKt~g~VIPnLL~~----------~gS~VV~DpKgEl~~~Ta~~R~~~  273 (641)
T PRK13822        224 STHGLVFAGSGGFKTTSVVVPTALKW----------GGPLVVLDPSTEVAPMVSEHRRDA  273 (641)
T ss_pred             CceEEEEeCCCCCccceEehhhhhcC----------CCCEEEEeCcHHHHHHHHHHHHHC
Confidence            46899999999999999999976422          234777889999988877766655

>cd01133 F1-ATPase_beta F1 ATP synthase beta subunit, nucleotide-binding domain

Probab=94.65  E-value=0.65  Score=38.44  Aligned_cols=31  Identities=10%  Similarity=-0.105  Sum_probs=22.6

Q ss_pred             CCCCCCCceeEecCCCCCchHHhHHHHHHhhh
Q psy14082          3 PPSESGCQNFSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus         3 p~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      -++-.|+-..+.++.|+|||.. +.-++....
T Consensus        64 ~pig~GQr~~If~~~G~GKTtL-a~~i~~~i~   94 (274)
T cd01133          64 APYAKGGKIGLFGGAGVGKTVL-IMELINNIA   94 (274)
T ss_pred             CCcccCCEEEEecCCCCChhHH-HHHHHHHHH
Confidence            3567889999999999999975 343444443

The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The beta subunit of ATP synthase is catalytic.

>cd01127 TrwB Bacterial conjugation protein TrwB, ATP binding domain

Probab=94.65  E-value=0.039  Score=48.45  Aligned_cols=51  Identities=14%  Similarity=0.165  Sum_probs=35.3

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHH
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQI   60 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~   60 (233)
                      ||.-...+++++.++||||||.. +..++..+...       +.+++|+=|..|+....
T Consensus        36 ~~~~~~~~h~~i~g~tGsGKt~~-i~~l~~~~~~~-------~~~~vi~D~kg~~~~~~   86 (410)
T cd01127          36 FPKDAEEAHTMIIGTTGTGKTTQ-IRELLASIRAR-------GDRAIIYDPNGGFVSKF   86 (410)
T ss_pred             CCcchhhccEEEEcCCCCCHHHH-HHHHHHHHHhc-------CCCEEEEeCCcchhHhh
Confidence            34455678999999999999975 55566655532       44677777777765443

TrwB is a homohexamer encoded by conjugative plasmids in Gram-negative bacteria. TrwB also has an all alpha domain which has been hypothesized to be responsible for DNA binding. TrwB is a component of Type IV secretion and is responsible for the horizontal transfer of DNA between bacteria.

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=94.62  E-value=0.043  Score=46.79  Aligned_cols=43  Identities=12%  Similarity=-0.103  Sum_probs=31.1

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHH
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQ   58 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~   58 (233)
                      .+.++++.++||||||.. +-.++..+-        ...+++.+=-+.||..
T Consensus       159 ~~~nili~G~tgSGKTTl-l~aL~~~ip--------~~~ri~tiEd~~El~l  201 (332)
T PRK13900        159 SKKNIIISGGTSTGKTTF-TNAALREIP--------AIERLITVEDAREIVL  201 (332)
T ss_pred             cCCcEEEECCCCCCHHHH-HHHHHhhCC--------CCCeEEEecCCCcccc
Confidence            578999999999999944 666666552        2346777767777754

>PRK11054 helD DNA helicase IV; Provisional

Probab=94.60  E-value=0.065  Score=50.10  Aligned_cols=55  Identities=13%  Similarity=0.007  Sum_probs=41.4

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ..+++.|..|||||.+ ++.-+..+.....   ..+.++|+++.|+..|..+.+++...
T Consensus       210 ~~~lV~agaGSGKT~v-l~~r~ayLl~~~~---~~~~~IL~ltft~~AA~em~eRL~~~  264 (684)
T PRK11054        210 DSLLVLAGAGSGKTSV-LVARAGWLLARGQ---AQPEQILLLAFGRQAAEEMDERIRER  264 (684)
T ss_pred             CCeEEEEeCCCCHHHH-HHHHHHHHHHhCC---CCHHHeEEEeccHHHHHHHHHHHHHh
Confidence            4588999999999988 4444444443211   23458999999999999999998876

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=94.60  E-value=0.064  Score=41.29  Aligned_cols=48  Identities=10%  Similarity=-0.067  Sum_probs=33.0

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      +++.+++|+|||.. ++-++.....       .+..+++++ +.|-..++.+.+..+
T Consensus         2 ~li~G~~G~GKT~l-~~~~~~~~~~-------~g~~v~~~s-~e~~~~~~~~~~~~~   49 (187)
T cd01124           2 TLLSGGPGTGKTTF-ALQFLYAGLA-------RGEPGLYVT-LEESPEELIENAESL   49 (187)
T ss_pred             EEEEcCCCCCHHHH-HHHHHHHHHH-------CCCcEEEEE-CCCCHHHHHHHHHHc
Confidence            57899999999965 4333333332       356677775 457788888888777

A related protein is found in archaea.

>cd00268 DEADc DEAD-box helicases

Probab=94.60  E-value=0.36  Score=37.58  Aligned_cols=72  Identities=19%  Similarity=0.233  Sum_probs=52.7

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEeccc-----CcC-CcCCC
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDV-----AAR-GLDVE  173 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~-----~~~-Gldi~  173 (233)
                      ..+.+++|.++++..+.+....++..    ++.+..++|+.+..+....++    +..+|+|+|..     +.+ -.+++
T Consensus        67 ~~~~~viii~p~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~iiv~T~~~l~~~l~~~~~~~~  142 (203)
T cd00268          67 KDGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLK----RGPHIVVATPGRLLDLLERGKLDLS  142 (203)
T ss_pred             cCCceEEEEcCCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhc----CCCCEEEEChHHHHHHHHcCCCChh
Confidence            35679999999999999887777554    678888999988766554433    56799999942     222 25667


Q ss_pred             CccEEE
Q psy14082        174 DVNTVN  179 (233)
Q Consensus       174 ~v~~VI  179 (233)
                      +++++|
T Consensus       143 ~l~~lI  148 (203)
T cd00268         143 KVKYLV  148 (203)
T ss_pred             hCCEEE
Confidence            777766

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.

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=94.55  E-value=0.071  Score=49.86  Aligned_cols=56  Identities=5%  Similarity=-0.112  Sum_probs=41.6

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      .-.+++.|.+|||||.+ +.--+.++.....   -...++|+|+.|+..|..+.+++..+
T Consensus        15 ~g~~lV~AgpGSGKT~v-L~~Ria~Li~~~~---v~p~~IL~lTFT~kAA~em~~Rl~~~   70 (672)
T PRK10919         15 TGPCLVLAGAGSGKTRV-ITNKIAHLIRGCG---YQARHIAAVTFTNKAAREMKERVAQT   70 (672)
T ss_pred             CCCEEEEecCCCCHHHH-HHHHHHHHHHhcC---CCHHHeeeEechHHHHHHHHHHHHHH
Confidence            34678999999999988 4444444443211   12457999999999999999999876

>PF10412 TrwB_AAD_bind: Type IV secretion-system coupling protein DNA-binding domain; InterPro: IPR019476 The plasmid conjugative coupling protein TraD (also known as TrwB) is a basic integral inner-membrane nucleoside-triphosphate-binding protein

Probab=94.50  E-value=0.039  Score=48.03  Aligned_cols=53  Identities=13%  Similarity=0.120  Sum_probs=36.2

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHH
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQT   62 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~   62 (233)
                      ||.-...+++++.+.||||||.+ +-+++..+...       +-+++|.=|.-+.....++
T Consensus         9 l~~~~e~~~~li~G~~GsGKT~~-i~~ll~~~~~~-------g~~~iI~D~kg~~~~~f~~   61 (386)
T PF10412_consen    9 LPKDSENRHILIIGATGSGKTQA-IRHLLDQIRAR-------GDRAIIYDPKGEFTERFYR   61 (386)
T ss_dssp             E-GGGGGG-EEEEE-TTSSHHHH-HHHHHHHHHHT-------T-EEEEEEETTHHHHHH--
T ss_pred             cccchhhCcEEEECCCCCCHHHH-HHHHHHHHHHc-------CCEEEEEECCchHHHHhcC
Confidence            35556788999999999999974 67788777653       5678888888777665444

It is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells []. This protein forms hexamers from six structurally very similar protomers []. This hexamer contains a central channel running from the cytosolic pole (formed by the all-alpha domains) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB all-alpha domain appears to be the DNA-binding domain of the structure. ; PDB: 1E9S_D 1E9R_F 1GKI_B 1GL7_G 1GL6_A.

>TIGR02767 TraG-Ti Ti-type conjugative transfer system protien TraG

Probab=94.33  E-value=0.088  Score=48.58  Aligned_cols=50  Identities=14%  Similarity=0.161  Sum_probs=38.4

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ..++++.||||||||..+++|-+-..          +..++++=|-.|+...+...-++.
T Consensus       211 ~~H~lv~ApTgsGKgvg~VIPnLL~~----------~gS~VV~DpKgE~~~~Ta~~R~~~  260 (623)
T TIGR02767       211 STHMIFFAGSGGFKTTSVVVPTALKY----------GGPLVCLDPSTEVAPMVCEHRRQA  260 (623)
T ss_pred             CceEEEEeCCCCCccceeehhhhhcC----------CCCEEEEEChHHHHHHHHHHHHHc
Confidence            36899999999999999999975422          234788888888887777655544

This protein is found in the Agrobacterium tumefaciens Ti plasmid tra region responsible for conjugative transfer of the entire plasmid among Agrobacterium strains. The protein is distantly related to the F-type conjugation system TraG protein. Both of these systems are examples of type IV secretion systems.

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=94.24  E-value=0.079  Score=41.89  Aligned_cols=41  Identities=7%  Similarity=-0.141  Sum_probs=26.5

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHH
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRE   55 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~Ptre   55 (233)
                      .-+++.+|.|||||+..+...++.+...      .--+.+|.-|..+
T Consensus        20 ~~v~~~G~AGTGKT~LA~a~Al~~v~~g------~~~kiii~Rp~v~   60 (205)
T PF02562_consen   20 DLVIVNGPAGTGKTFLALAAALELVKEG------EYDKIIITRPPVE   60 (205)
T ss_dssp             SEEEEE--TTSSTTHHHHHHHHHHHHTT------S-SEEEEEE-S--
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHHHhC------CCcEEEEEecCCC
Confidence            4588999999999999888888777652      3446677667643

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

>KOG0333|consensus

Probab=94.21  E-value=0.61  Score=41.81  Aligned_cols=128  Identities=18%  Similarity=0.259  Sum_probs=87.7

Q ss_pred             HHhcCCCCeEEEEecchhHHHHHHHHHhh----CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEec------------
Q psy14082        100 EMAKNPAFKVIVFVETKKKVEDITRALRR----ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVAT------------  163 (233)
Q Consensus       100 ~~~~~~~~k~iIf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T------------  163 (233)
                      ......++..+|..+|+..++.+.+.-.+    .|++++.+-|+.+.+++-.-+..    .+.|+|+|            
T Consensus       316 ~en~~~gpyaiilaptReLaqqIeeEt~kf~~~lg~r~vsvigg~s~EEq~fqls~----gceiviatPgrLid~Lenr~  391 (673)
T KOG0333|consen  316 LENNIEGPYAIILAPTRELAQQIEEETNKFGKPLGIRTVSVIGGLSFEEQGFQLSM----GCEIVIATPGRLIDSLENRY  391 (673)
T ss_pred             hhhcccCceeeeechHHHHHHHHHHHHHHhcccccceEEEEecccchhhhhhhhhc----cceeeecCchHHHHHHHHHH
Confidence            34567888999999999999888776544    47899999999998886544443    47888888            


Q ss_pred             -----------ccCcCCcCCC---CccEEEEecCCCC-------------------------------------------
Q psy14082        164 -----------DVAARGLDVE---DVNTVNIGSLQLS-------------------------------------------  186 (233)
Q Consensus       164 -----------~~~~~Gldi~---~v~~VI~~d~P~~-------------------------------------------  186 (233)
                                 |.++|.+|..   +|.-++- -+|.+                                           
T Consensus       392 lvl~qctyvvldeadrmiDmgfE~dv~~iL~-~mPssn~k~~tde~~~~~~~~~~~~~~k~yrqT~mftatm~p~verla  470 (673)
T KOG0333|consen  392 LVLNQCTYVVLDEADRMIDMGFEPDVQKILE-QMPSSNAKPDTDEKEGEERVRKNFSSSKKYRQTVMFTATMPPAVERLA  470 (673)
T ss_pred             HHhccCceEeccchhhhhcccccHHHHHHHH-hCCccccCCCccchhhHHHHHhhcccccceeEEEEEecCCChHHHHHH
Confidence                       3334444421   1111110 11211                                           


Q ss_pred             -----------------cccccceeeEEeecchHHHHHHHHHHhh-cCcccccccchhhHhhhc
Q psy14082        187 -----------------ANHNISQVIEVVQDYEKEKRLFSLIREL-GKYTLITQESSSTLSEMV  232 (233)
Q Consensus       187 -----------------~~~~i~~~~~~~~~~~~~~~~~~~i~~~-~~~~~~~~~~~~~~~~l~  232 (233)
                                       +..++.+.+..+++.++..++.+.+++. ....++|...+++.+.||
T Consensus       471 r~ylr~pv~vtig~~gk~~~rveQ~v~m~~ed~k~kkL~eil~~~~~ppiIIFvN~kk~~d~lA  534 (673)
T KOG0333|consen  471 RSYLRRPVVVTIGSAGKPTPRVEQKVEMVSEDEKRKKLIEILESNFDPPIIIFVNTKKGADALA  534 (673)
T ss_pred             HHHhhCCeEEEeccCCCCccchheEEEEecchHHHHHHHHHHHhCCCCCEEEEEechhhHHHHH
Confidence                             1122248888888888999999999997 466889999999988776

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=94.20  E-value=0.24  Score=44.13  Aligned_cols=71  Identities=20%  Similarity=0.292  Sum_probs=54.1

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhC-----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----cCcC-CcCCC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRE-----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----VAAR-GLDVE  173 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----~~~~-Gldi~  173 (233)
                      ...+++|.++|++-+.++++.++..     +..+..++|+.+...+...++    ...+|+|+|+     .+.+ .+++.
T Consensus        71 ~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~----~~~~IvV~Tp~rl~~~l~~~~~~l~  146 (460)
T PRK11776         71 FRVQALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLE----HGAHIIVGTPGRILDHLRKGTLDLD  146 (460)
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhc----CCCCEEEEChHHHHHHHHcCCccHH
Confidence            3458999999999999999888653     578889999999877655444    4679999993     3333 46777


Q ss_pred             CccEEE
Q psy14082        174 DVNTVN  179 (233)
Q Consensus       174 ~v~~VI  179 (233)
                      +++++|
T Consensus       147 ~l~~lV  152 (460)
T PRK11776        147 ALNTLV  152 (460)
T ss_pred             HCCEEE
Confidence            788776

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=94.20  E-value=0.15  Score=47.52  Aligned_cols=56  Identities=18%  Similarity=0.008  Sum_probs=42.5

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEE
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICI   76 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~   76 (233)
                      ..++.+.+|||||+..+ .++...          +..+|||+|+.+.|.|+++.+..++++-.+..+
T Consensus        34 ~~ll~Gl~gs~ka~lia-~l~~~~----------~r~vLIVt~~~~~A~~l~~dL~~~~~~~~v~~f   89 (652)
T PRK05298         34 HQTLLGVTGSGKTFTMA-NVIARL----------QRPTLVLAHNKTLAAQLYSEFKEFFPENAVEYF   89 (652)
T ss_pred             cEEEEcCCCcHHHHHHH-HHHHHh----------CCCEEEEECCHHHHHHHHHHHHHhcCCCeEEEe
Confidence            45688999999998733 344322          235999999999999999999999665445555

>TIGR01054 rgy reverse gyrase

Probab=94.14  E-value=0.16  Score=50.33  Aligned_cols=60  Identities=12%  Similarity=0.187  Sum_probs=51.2

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhC----CCee---EEEeCCCCHHHHHHHHHHhhCCCCCEEEecc
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRE----RHSA---ICIHGDKTQQDRDYVLNDFRQGKAPILVATD  164 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~----~~~~---~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~  164 (233)
                      .+.+++|.++|+.-+.++++.+.+.    ++.+   ..+||+++..++...++.+++|..+|+|+|+
T Consensus       120 ~g~~vLIL~PTreLa~Qi~~~l~~l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp  186 (1171)
T TIGR01054       120 KGKRCYIILPTTLLVIQVAEKISSLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTT  186 (1171)
T ss_pred             cCCeEEEEeCHHHHHHHHHHHHHHHHHhcCCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECH
Confidence            4689999999999999998888754    3333   3589999999999999999999999999994

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.

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=94.13  E-value=0.24  Score=46.04  Aligned_cols=72  Identities=18%  Similarity=0.242  Sum_probs=53.0

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhC-----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----cCcCC-cCC
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRE-----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----VAARG-LDV  172 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----~~~~G-ldi  172 (233)
                      ....++||.++|+.-+.++++.+...     ++.+..+||+.+.+.+...++    ...+|+|+|+     .+.++ +++
T Consensus        72 ~~~~~~LIL~PTreLa~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l~----~~~~IVVgTPgrl~d~l~r~~l~l  147 (629)
T PRK11634         72 LKAPQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALR----QGPQIVVGTPGRLLDHLKRGTLDL  147 (629)
T ss_pred             cCCCeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHhc----CCCCEEEECHHHHHHHHHcCCcch
Confidence            34568999999999999998887643     688899999988776655443    3578999993     33333 566


Q ss_pred             CCccEEE
Q psy14082        173 EDVNTVN  179 (233)
Q Consensus       173 ~~v~~VI  179 (233)
                      .++.+||
T Consensus       148 ~~l~~lV  154 (629)
T PRK11634        148 SKLSGLV  154 (629)
T ss_pred             hhceEEE
Confidence            6776655

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=94.12  E-value=0.11  Score=42.52  Aligned_cols=51  Identities=8%  Similarity=0.052  Sum_probs=39.4

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHH
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKE   66 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~   66 (233)
                      ++..++..+++|+|||.. +.++...+..       .|. .++++++-||+.++...+..
T Consensus       104 ~~~nl~l~G~~G~GKThL-a~Ai~~~l~~-------~g~-sv~f~~~~el~~~Lk~~~~~  154 (254)
T COG1484         104 RGENLVLLGPPGVGKTHL-AIAIGNELLK-------AGI-SVLFITAPDLLSKLKAAFDE  154 (254)
T ss_pred             cCCcEEEECCCCCcHHHH-HHHHHHHHHH-------cCC-eEEEEEHHHHHHHHHHHHhc
Confidence            678899999999999988 5566666663       244 45567888999999887764

>PRK13876 conjugal transfer coupling protein TraG; Provisional

Probab=94.06  E-value=0.065  Score=49.81  Aligned_cols=50  Identities=12%  Similarity=-0.057  Sum_probs=39.2

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ..++++.||||||||..+++|-+...          ...++|+=|-.|+...+....++.
T Consensus       144 ~~hvLviApTrSGKgvg~VIPnLL~~----------~~S~VV~D~KGEl~~~Ta~~R~~~  193 (663)
T PRK13876        144 PEHVLCFAPTRSGKGVGLVVPTLLTW----------PGSAIVHDIKGENWQLTAGFRARF  193 (663)
T ss_pred             CceEEEEecCCCCcceeEehhhHHhC----------CCCEEEEeCcchHHHHHHHHHHhC
Confidence            46899999999999999999987644          224788888888877776665554

>KOG0925|consensus

Probab=94.05  E-value=1.3  Score=39.59  Aligned_cols=79  Identities=16%  Similarity=0.300  Sum_probs=56.9

Q ss_pred             hcCCCCeEEEEecchhHHHHHHHHHhhC---------CCeeEEEeCCCCHHHHHHHHHHhh---CC--CCCEEEecccCc
Q psy14082        102 AKNPAFKVIVFVETKKKVEDITRALRRE---------RHSAICIHGDKTQQDRDYVLNDFR---QG--KAPILVATDVAA  167 (233)
Q Consensus       102 ~~~~~~k~iIf~~~~~~~~~l~~~L~~~---------~~~~~~~~~~~~~~~r~~~~~~f~---~g--~~~iLv~T~~~~  167 (233)
                      .....+.+++|-...+..+...+.+...         .+++..+|    +.++..+++-..   +|  ..+++|+|++++
T Consensus       249 ~~ee~GDilvFLtgeeeIe~aC~~i~re~~~L~~~~g~l~v~PLy----P~~qq~iFep~p~~~~~~~~RkvVvstniae  324 (699)
T KOG0925|consen  249 MCEEPGDILVFLTGEEEIEDACRKISREVDNLGPQVGPLKVVPLY----PAQQQRIFEPAPEKRNGAYGRKVVVSTNIAE  324 (699)
T ss_pred             hccCCCCEEEEecCHHHHHHHHHHHHHHHHhhccccCCceEEecC----chhhccccCCCCcccCCCccceEEEEecchh
Confidence            4456788999999999998888888632         25777788    223333332221   12  356999999999


Q ss_pred             CCcCCCCccEEEEecCC
Q psy14082        168 RGLDVEDVNTVNIGSLQ  184 (233)
Q Consensus       168 ~Gldi~~v~~VI~~d~P  184 (233)
                      .-+-++++.+||.-++-
T Consensus       325 tsltidgiv~VIDpGf~  341 (699)
T KOG0925|consen  325 TSLTIDGIVFVIDPGFS  341 (699)
T ss_pred             eeeeeccEEEEecCchh
Confidence            99999999999987764

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=94.02  E-value=0.11  Score=49.00  Aligned_cols=56  Identities=5%  Similarity=-0.063  Sum_probs=42.0

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ...+++.|..|||||.+ +.--+.++.....   -+..++|+|+-|+..|..+.+++.++
T Consensus        22 ~g~~lV~AgaGSGKT~v-l~~Ria~Li~~~~---v~p~~IL~lTFT~kAA~Em~~Rl~~~   77 (721)
T PRK11773         22 LGNMLVLAGAGSGKTRV-LVHRIAWLMQVEN---ASPYSIMAVTFTNKAAAEMRHRIEQL   77 (721)
T ss_pred             CCCEEEEecCCCCHHHH-HHHHHHHHHHcCC---CChhHeEeeeccHHHHHHHHHHHHHH
Confidence            34688999999999988 4444444443211   12457999999999999999999987

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=93.99  E-value=0.078  Score=37.88  Aligned_cols=41  Identities=10%  Similarity=-0.130  Sum_probs=26.7

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHH
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTREL   56 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL   56 (233)
                      +..+++.+|+|||||.. +.-++..+...       +..++++.+....
T Consensus         2 ~~~~~l~G~~G~GKTtl-~~~l~~~~~~~-------~~~~~~~~~~~~~   42 (148)
T smart00382        2 GEVILIVGPPGSGKTTL-ARALARELGPP-------GGGVIYIDGEDIL   42 (148)
T ss_pred             CCEEEEECCCCCcHHHH-HHHHHhccCCC-------CCCEEEECCEEcc
Confidence            56789999999999976 44454444321       1347777766433

AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=93.94  E-value=0.28  Score=43.86  Aligned_cols=59  Identities=20%  Similarity=0.282  Sum_probs=54.5

Q ss_pred             CCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc
Q psy14082        106 AFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD  164 (233)
Q Consensus       106 ~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~  164 (233)
                      .+.++|.++++.-++.....|...|+.+..++++.+..++..++...+.++.+++++|+
T Consensus        51 ~~~~lVi~P~~~L~~dq~~~l~~~gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TP  109 (470)
T TIGR00614        51 DGITLVISPLISLMEDQVLQLKASGIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTP  109 (470)
T ss_pred             CCcEEEEecHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECH
Confidence            45789999999999999999999999999999999999999999999999999999985

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

>PRK13880 conjugal transfer coupling protein TraG; Provisional

Probab=93.88  E-value=0.063  Score=49.78  Aligned_cols=47  Identities=9%  Similarity=-0.031  Sum_probs=37.2

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHH
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVA   64 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~   64 (233)
                      ..++++.||||||||..+++|-+...          +..++|+=|-.|+...+....
T Consensus       175 ~~HvlviapTgSGKgvg~ViPnLL~~----------~~S~VV~D~KGE~~~~Tag~R  221 (636)
T PRK13880        175 PEHVLTYAPTRSGKGVGLVVPTLLSW----------GHSSVITDLKGELWALTAGWR  221 (636)
T ss_pred             CceEEEEecCCCCCceEEEccchhhC----------CCCEEEEeCcHHHHHHHHHHH
Confidence            46799999999999999999988532          335888889999976665544

>TIGR01075 uvrD DNA helicase II

Probab=93.85  E-value=0.12  Score=48.73  Aligned_cols=56  Identities=5%  Similarity=-0.094  Sum_probs=42.5

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ...+++.|..|||||.+ +.-=+.++.....   -+..++|+|+-|+..|..+.+++.++
T Consensus        17 ~g~~lV~AgaGSGKT~~-L~~Ria~Li~~~~---v~p~~IL~lTFTnkAA~em~~Rl~~~   72 (715)
T TIGR01075        17 PGNLLVLAGAGSGKTRV-LTHRIAWLLSVEN---ASPHSIMAVTFTNKAAAEMRHRIGAL   72 (715)
T ss_pred             CCCEEEEecCCCCHHHH-HHHHHHHHHHcCC---CCHHHeEeeeccHHHHHHHHHHHHHH
Confidence            34689999999999988 4444445543311   12457999999999999999999988

Designed to identify uvrD members of the uvrD/rep subfamily.

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]

Probab=93.83  E-value=0.05  Score=44.81  Aligned_cols=44  Identities=7%  Similarity=-0.103  Sum_probs=30.6

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHH
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQ   58 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~   58 (233)
                      .+..+++.++||||||.. +-.++..+...       ..+++.+-.+.|+-.
T Consensus       126 ~~~~ili~G~tGSGKTT~-l~all~~i~~~-------~~~iv~iEd~~E~~l  169 (270)
T PF00437_consen  126 GRGNILISGPTGSGKTTL-LNALLEEIPPE-------DERIVTIEDPPELRL  169 (270)
T ss_dssp             TTEEEEEEESTTSSHHHH-HHHHHHHCHTT-------TSEEEEEESSS-S--
T ss_pred             cceEEEEECCCccccchH-HHHHhhhcccc-------ccceEEeccccceee
Confidence            467899999999999955 66677666431       357788877777743

These proteins are probably located in the cytoplasm and, on the basis of the presence of a conserved P-loop region IPR001687 from INTERPRO, bind ATP.; GO: 0005524 ATP binding, 0006810 transport, 0005622 intracellular; PDB: 1NLZ_C 2PT7_B 1OPX_A 1NLY_A 1G6O_B 2OAQ_2 2OAP_1 2JNQ_A 2JMZ_A 2GZA_B ....

>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain

Probab=93.82  E-value=2  Score=35.56  Aligned_cols=23  Identities=9%  Similarity=-0.045  Sum_probs=19.4

Q ss_pred             CCCCCCCCceeEecCCCCCchHH
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~   24 (233)
                      +-++-.|+...+.++.|+|||..
T Consensus        63 l~pigrGQr~~Ifg~~g~GKt~L   85 (274)
T cd01132          63 MIPIGRGQRELIIGDRQTGKTAI   85 (274)
T ss_pred             cCCcccCCEEEeeCCCCCCccHH
Confidence            34567899999999999999974

The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The alpha subunit of the F1 ATP synthase can bind nucleotides, but is non-catalytic.

>PRK04328 hypothetical protein; Provisional

Probab=93.63  E-value=0.15  Score=41.66  Aligned_cols=54  Identities=9%  Similarity=-0.141  Sum_probs=37.2

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ++.|.-+++.+++|+|||.-.+--+.+.+        .++..+++++ +.|-..++.+.++.+
T Consensus        20 ip~gs~ili~G~pGsGKT~l~~~fl~~~~--------~~ge~~lyis-~ee~~~~i~~~~~~~   73 (249)
T PRK04328         20 IPERNVVLLSGGPGTGKSIFSQQFLWNGL--------QMGEPGVYVA-LEEHPVQVRRNMRQF   73 (249)
T ss_pred             CcCCcEEEEEcCCCCCHHHHHHHHHHHHH--------hcCCcEEEEE-eeCCHHHHHHHHHHc
Confidence            45788899999999999965333333433        2355677666 666777788877777

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=93.59  E-value=0.07  Score=42.66  Aligned_cols=55  Identities=11%  Similarity=-0.039  Sum_probs=36.0

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ++.|.-+++.+++|||||.-..--+.+.+..       .+.++++++ +.|-..++.+.++.+
T Consensus        16 ip~gs~~li~G~~GsGKT~l~~q~l~~~~~~-------~ge~vlyvs-~ee~~~~l~~~~~s~   70 (226)
T PF06745_consen   16 IPKGSVVLISGPPGSGKTTLALQFLYNGLKN-------FGEKVLYVS-FEEPPEELIENMKSF   70 (226)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHHHHHHH-------HT--EEEEE-SSS-HHHHHHHHHTT
T ss_pred             CCCCcEEEEEeCCCCCcHHHHHHHHHHhhhh-------cCCcEEEEE-ecCCHHHHHHHHHHc
Confidence            4678889999999999996633334444432       044677776 456677877787776

More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=93.38  E-value=0.2  Score=46.87  Aligned_cols=56  Identities=4%  Similarity=-0.156  Sum_probs=42.1

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      +.++++.|.+|||||.+ ++--+.++.....   ....+.|+++.|+..+.++.+.+.+.
T Consensus        14 ~~~~~V~Ag~GSGKT~~-L~~ri~~ll~~~~---~~p~~IL~vTFt~~Aa~em~~Rl~~~   69 (664)
T TIGR01074        14 TGPCLVLAGAGSGKTRV-ITNKIAYLIQNCG---YKARNIAAVTFTNKAAREMKERVAKT   69 (664)
T ss_pred             CCCEEEEecCCCCHHHH-HHHHHHHHHHhcC---CCHHHeEEEeccHHHHHHHHHHHHHH
Confidence            45789999999999988 4444444443211   12457899999999999999999876

Designed to identify rep members of the uvrD/rep subfamily.

>PRK06921 hypothetical protein; Provisional

Probab=93.33  E-value=0.21  Score=41.18  Aligned_cols=50  Identities=12%  Similarity=-0.099  Sum_probs=32.9

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHH
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVA   64 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~   64 (233)
                      .+..++..++||+|||.. +..+...+..+      .+..++++ +..++..++.+.+
T Consensus       116 ~~~~l~l~G~~G~GKThL-a~aia~~l~~~------~g~~v~y~-~~~~l~~~l~~~~  165 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHL-LTAAANELMRK------KGVPVLYF-PFVEGFGDLKDDF  165 (266)
T ss_pred             CCCeEEEECCCCCcHHHH-HHHHHHHHhhh------cCceEEEE-EHHHHHHHHHHHH
Confidence            356799999999999966 45566666532      14455554 5567766665544

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=93.27  E-value=0.22  Score=40.17  Aligned_cols=54  Identities=7%  Similarity=-0.082  Sum_probs=36.2

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ++.|.-+++.+++|+|||.. ++-++.....       ++.++++++ +.+-..+..+.+..+
T Consensus        21 i~~g~~~~i~G~~G~GKTtl-~~~~~~~~~~-------~g~~~~yi~-~e~~~~~~~~~~~~~   74 (230)
T PRK08533         21 IPAGSLILIEGDESTGKSIL-SQRLAYGFLQ-------NGYSVSYVS-TQLTTTEFIKQMMSL   74 (230)
T ss_pred             CCCCcEEEEECCCCCCHHHH-HHHHHHHHHh-------CCCcEEEEe-CCCCHHHHHHHHHHh
Confidence            45688899999999999966 3333433432       356678887 445556666666665

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=93.23  E-value=0.2  Score=46.00  Aligned_cols=58  Identities=10%  Similarity=-0.002  Sum_probs=40.5

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHH
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKE   66 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~   66 (233)
                      +.++-.++.+++|||||.+ +..++..+....+.  ..+.++++.+||..-|..+.+....
T Consensus       158 l~~~~~vitGgpGTGKTt~-v~~ll~~l~~~~~~--~~~~~I~l~APTGkAA~rL~e~~~~  215 (586)
T TIGR01447       158 LKSNFSLITGGPGTGKTTT-VARLLLALVKQSPK--QGKLRIALAAPTGKAAARLAESLRK  215 (586)
T ss_pred             hhCCeEEEEcCCCCCHHHH-HHHHHHHHHHhccc--cCCCcEEEECCcHHHHHHHHHHHHh
Confidence            4567789999999999976 55566555443110  1135799999998888877766544

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

>PF12846 AAA_10: AAA-like domain

Probab=93.18  E-value=0.13  Score=42.42  Aligned_cols=42  Identities=7%  Similarity=0.048  Sum_probs=31.9

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHH
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQ   58 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~   58 (233)
                      +++++.++||||||.... .++..+..       .+..++++=|..+...
T Consensus         2 ~h~~i~G~tGsGKT~~~~-~l~~~~~~-------~g~~~~i~D~~g~~~~   43 (304)
T PF12846_consen    2 PHTLILGKTGSGKTTLLK-NLLEQLIR-------RGPRVVIFDPKGDYSP   43 (304)
T ss_pred             CeEEEECCCCCcHHHHHH-HHHHHHHH-------cCCCEEEEcCCchHHH
Confidence            578999999999997744 66666654       3678888888766665

>PRK06526 transposase; Provisional

Probab=93.07  E-value=0.1  Score=42.72  Aligned_cols=47  Identities=4%  Similarity=-0.087  Sum_probs=30.1

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHH
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQ   61 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~   61 (233)
                      -.+.++++.+|+|+|||.. +..+...+..       .|.++++. +..+|..+..
T Consensus        96 ~~~~nlll~Gp~GtGKThL-a~al~~~a~~-------~g~~v~f~-t~~~l~~~l~  142 (254)
T PRK06526         96 TGKENVVFLGPPGTGKTHL-AIGLGIRACQ-------AGHRVLFA-TAAQWVARLA  142 (254)
T ss_pred             hcCceEEEEeCCCCchHHH-HHHHHHHHHH-------CCCchhhh-hHHHHHHHHH
Confidence            4577899999999999976 4445554443       24455553 4445665553

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=93.05  E-value=0.59  Score=41.22  Aligned_cols=71  Identities=17%  Similarity=0.268  Sum_probs=53.5

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhh----CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc------cCcCCcCCCC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRR----ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD------VAARGLDVED  174 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~------~~~~Gldi~~  174 (233)
                      ...+++|.++|+..+.++++.+..    .++++..++|+.+...+...+.    +..+|+|+|.      .....++..+
T Consensus        72 ~~~~~lil~Pt~eLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~----~~~~IlV~Tp~rl~~~~~~~~~~~~~  147 (434)
T PRK11192         72 GPPRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVFS----ENQDIVVATPGRLLQYIKEENFDCRA  147 (434)
T ss_pred             CCceEEEECCcHHHHHHHHHHHHHHHccCCcEEEEEECCCCHHHHHHHhc----CCCCEEEEChHHHHHHHHcCCcCccc
Confidence            346899999999999888776654    4688999999999887765543    4678999995      1224567777


Q ss_pred             ccEEE
Q psy14082        175 VNTVN  179 (233)
Q Consensus       175 v~~VI  179 (233)
                      +++||
T Consensus       148 v~~lV  152 (434)
T PRK11192        148 VETLI  152 (434)
T ss_pred             CCEEE
Confidence            77766

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=92.98  E-value=0.19  Score=48.63  Aligned_cols=66  Identities=15%  Similarity=0.041  Sum_probs=49.1

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEcC
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGG   79 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~gg   79 (233)
                      |--++-.|.||+|||++=+= ++..+-..     ..|.|..|-.-.|-|..|+.+.+++-  ..+-..++++||
T Consensus       431 GfF~vNMASTGcGKT~aNAR-ImyaLsd~-----~~g~RfsiALGLRTLTLQTGda~r~rL~L~~ddLAVlIGs  498 (1110)
T TIGR02562       431 GAFGVNMASTGCGKTLANAR-AMYALRDD-----KQGARFAIALGLRSLTLQTGHALKTRLNLSDDDLAVLIGG  498 (1110)
T ss_pred             CeEEEEecCCCcchHHHHHH-HHHHhCCC-----CCCceEEEEccccceeccchHHHHHhcCCCccceEEEECH
Confidence            45577789999999988443 33333221     45778888889999999999999986  334568888887

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.

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=92.98  E-value=0.28  Score=40.22  Aligned_cols=55  Identities=11%  Similarity=-0.081  Sum_probs=32.8

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcC---cHHHHHHHHHHHHHh
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAP---TRELAQQIQTVAKEF   67 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~P---treL~~Q~~~~~~~~   67 (233)
                      ++.|.=+++.+++|+|||.. .+-++....       .++.++++++-   ...+.+++......+
T Consensus        33 ip~gs~~lI~G~pGtGKT~l-~~qf~~~~a-------~~Ge~vlyis~Ee~~~~~~~~l~~~a~~~   90 (259)
T TIGR03878        33 IPAYSVINITGVSDTGKSLM-VEQFAVTQA-------SRGNPVLFVTVESPANFVYTSLKERAKAM   90 (259)
T ss_pred             eECCcEEEEEcCCCCCHHHH-HHHHHHHHH-------hCCCcEEEEEecCCchHHHHHHHHHHHHc
Confidence            35688899999999999965 333332222       23567888873   233344444444444

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=92.88  E-value=0.54  Score=43.36  Aligned_cols=59  Identities=12%  Similarity=0.148  Sum_probs=53.8

Q ss_pred             CCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc
Q psy14082        106 AFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD  164 (233)
Q Consensus       106 ~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~  164 (233)
                      .+.++|.++++.-++.-...|+..|+.+..+|++++..++..+++....|+.++++.|+
T Consensus        53 ~g~~lVisPl~sL~~dq~~~l~~~gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tp  111 (591)
T TIGR01389        53 KGLTVVISPLISLMKDQVDQLRAAGVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAP  111 (591)
T ss_pred             CCcEEEEcCCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECh
Confidence            35688999999999988999999999999999999999999999999999999998874

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.

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=92.77  E-value=0.089  Score=46.75  Aligned_cols=25  Identities=4%  Similarity=-0.116  Sum_probs=20.7

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhhcc
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHISHQ   36 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~~~   36 (233)
                      +++.+|||||||.+ +..+++.+...
T Consensus       261 iLvTGPTGSGKTTT-LY~~L~~ln~~  285 (500)
T COG2804         261 ILVTGPTGSGKTTT-LYAALSELNTP  285 (500)
T ss_pred             EEEeCCCCCCHHHH-HHHHHHHhcCC
Confidence            67899999999977 77788877653

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=92.75  E-value=0.25  Score=49.45  Aligned_cols=57  Identities=14%  Similarity=-0.010  Sum_probs=43.1

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      .+|+++++.|+-|||||.+-+--++..+...     ..--+.|+++=|+.-|..+.+++.+.
T Consensus        12 ~~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~-----~~~~~il~~tFt~~aa~e~~~ri~~~   68 (1232)
T TIGR02785        12 TRGQNILVSASAGSGKTAVLVERIIKKILRG-----VDIDRLLVVTFTNAAAREMKERIEEA   68 (1232)
T ss_pred             CCCCCEEEEecCCCcHHHHHHHHHHHHHhcC-----CCHhhEEEEeccHHHHHHHHHHHHHH
Confidence            3588999999999999988555455555422     11235999999999999888888775

AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the Firmicutes (as modeled here) and the alphaproteobacteria, while the partner AddB proteins show no strong homology across the two groups of species.

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

Probab=92.71  E-value=0.094  Score=50.15  Aligned_cols=151  Identities=17%  Similarity=0.115  Sum_probs=83.1

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCc-EEEEEcCCCC-CCe
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALR-NICIFGGTPK-GPQ   85 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~-~~~~~gg~~~-~~~   85 (233)
                      +.+.+....-|.|||+. .+..+..+....   ....+.++|+||+ +++.+|.+.+.++.+.++ +....|.... +..
T Consensus       358 ~~~~ilaD~mglGKTiq-~i~~l~~~~~~~---~~~~~~~liv~p~-s~~~nw~~e~~k~~~~~~~~~~~~g~~~~~~~~  432 (866)
T COG0553         358 LLGGILADDMGLGKTVQ-TIALLLSLLESI---KVYLGPALIVVPA-SLLSNWKREFEKFAPDLRLVLVYHGEKSELDKK  432 (866)
T ss_pred             cCCCcccccccchhHHH-HHHHHHhhhhcc---cCCCCCeEEEecH-HHHHHHHHHHhhhCccccceeeeeCCcccccHH
Confidence            44556667899999988 444444433321   1114578999998 889999999999977777 6777766542 110


Q ss_pred             eEEeccchhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEeccc
Q psy14082         86 DCLPLHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDV  165 (233)
Q Consensus        86 ~lv~l~r~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~  165 (233)
                              .....+......   .++|+.-..+.+.+...+        ..|+.+...+...++-++...     +.++.
T Consensus       433 --------~~~~~~~~~~~~---~~~~~v~itty~~l~~~~--------~~~~~l~~~~~~~~v~DEa~~-----ikn~~  488 (866)
T COG0553         433 --------REALRDLLKLHL---VIIFDVVITTYELLRRFL--------VDHGGLKKIEWDRVVLDEAHR-----IKNDQ  488 (866)
T ss_pred             --------HHHHHHHhhhcc---cceeeEEechHHHHHHhh--------hhHHHHhhceeeeeehhhHHH-----Hhhhh
Confidence                    111111111111   566666666655555533        112222222222222222111     44455


Q ss_pred             CcCCcCCCCccEEEEecCCCCc
Q psy14082        166 AARGLDVEDVNTVNIGSLQLSA  187 (233)
Q Consensus       166 ~~~Gldi~~v~~VI~~d~P~~~  187 (233)
                      ..++..+......+.+++|.++
T Consensus       489 s~~~~~l~~~~~~~~~~LtgTP  510 (866)
T COG0553         489 SSEGKALQFLKALNRLDLTGTP  510 (866)
T ss_pred             hHHHHHHHHHhhcceeeCCCCh
Confidence            5556666666667777777777

>PRK08181 transposase; Validated

Probab=92.70  E-value=0.2  Score=41.40  Aligned_cols=47  Identities=13%  Similarity=0.031  Sum_probs=31.6

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHH
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQT   62 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~   62 (233)
                      .+.++++.+|+|+|||.. +..+...+..+       |..+ +..+..+|..++..
T Consensus       105 ~~~nlll~Gp~GtGKTHL-a~Aia~~a~~~-------g~~v-~f~~~~~L~~~l~~  151 (269)
T PRK08181        105 KGANLLLFGPPGGGKSHL-AAAIGLALIEN-------GWRV-LFTRTTDLVQKLQV  151 (269)
T ss_pred             cCceEEEEecCCCcHHHH-HHHHHHHHHHc-------CCce-eeeeHHHHHHHHHH
Confidence            467899999999999965 44455555432       4445 44566788887644

>TIGR03743 SXT_TraD conjugative coupling factor TraD, SXT/TOL subfamily

Probab=92.63  E-value=0.54  Score=43.72  Aligned_cols=56  Identities=14%  Similarity=0.116  Sum_probs=39.7

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHH--HHHHHHHHHHHhhc
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRE--LAQQIQTVAKEFSS   69 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~Ptre--L~~Q~~~~~~~~~~   69 (233)
                      -...|+++.++||+|||..+.. ++.....       .+..++++=|-.+  |...++..++..+.
T Consensus       174 ~~~~H~lv~G~TGsGKT~l~~~-l~~q~i~-------~g~~viv~DpKgD~~l~~~~~~~~~~~G~  231 (634)
T TIGR03743       174 HRVGHTLVLGTTGVGKTRLAEL-LITQDIR-------RGDVVIVIDPKGDADLKRRMRAEAKRAGR  231 (634)
T ss_pred             CCCCcEEEECCCCCCHHHHHHH-HHHHHHH-------cCCeEEEEeCCCchHHHHHHHHHHHHhCC
Confidence            3567899999999999977644 4444443       2456777777754  88888888877733

Members of this protein family are the putative conjugative coupling factor, TraD (or TraG), rather distantly related to the well-characterized TraD of the F plasmid. Members are associated with conjugative-transposon-like mobile genetic elements of the class that includes SXT, an antibiotic resistance transfer element in some Vibrio cholerae strains.

>PRK05973 replicative DNA helicase; Provisional

Probab=92.60  E-value=0.25  Score=39.98  Aligned_cols=54  Identities=11%  Similarity=0.007  Sum_probs=36.6

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      +..|.=+++.++||+|||.. ++-++.....       +|.+++|++ .-|=..|+.+.+..+
T Consensus        61 l~~Gsl~LIaG~PG~GKT~l-alqfa~~~a~-------~Ge~vlyfS-lEes~~~i~~R~~s~  114 (237)
T PRK05973         61 LKPGDLVLLGARPGHGKTLL-GLELAVEAMK-------SGRTGVFFT-LEYTEQDVRDRLRAL  114 (237)
T ss_pred             CCCCCEEEEEeCCCCCHHHH-HHHHHHHHHh-------cCCeEEEEE-EeCCHHHHHHHHHHc
Confidence            45677889999999999965 4433333322       255677775 335577888888777

>CHL00181 cbbX CbbX; Provisional

Probab=92.58  E-value=5.4  Score=33.27  Aligned_cols=52  Identities=12%  Similarity=0.086  Sum_probs=33.4

Q ss_pred             cCCCCeEEEEecchhHHHHHH---HHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCC
Q psy14082        103 KNPAFKVIVFVETKKKVEDIT---RALRRERHSAICIHGDKTQQDRDYVLNDFRQG  155 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~---~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g  155 (233)
                      .....-.+|++.+.+..+.+.   ..|..+ +...+.-..++.++..++++.|-+.
T Consensus       157 ~~~~~~~vI~ag~~~~~~~~~~~np~L~sR-~~~~i~F~~~t~~el~~I~~~~l~~  211 (287)
T CHL00181        157 NQRDDLVVIFAGYKDRMDKFYESNPGLSSR-IANHVDFPDYTPEELLQIAKIMLEE  211 (287)
T ss_pred             cCCCCEEEEEeCCcHHHHHHHhcCHHHHHh-CCceEEcCCcCHHHHHHHHHHHHHH
Confidence            344556778887766655443   334333 2444556678899999999998654

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=92.55  E-value=0.31  Score=39.24  Aligned_cols=49  Identities=16%  Similarity=0.223  Sum_probs=32.2

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEc---CcHHHHHHH
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLA---PTRELAQQI   60 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~---PtreL~~Q~   60 (233)
                      +..|.=+++.|+||+|||. +++-++.....+      .+..+++++   |..++...+
T Consensus        10 l~~G~l~lI~G~~G~GKT~-~~~~~~~~~~~~------~g~~vly~s~E~~~~~~~~r~   61 (242)
T cd00984          10 LQPGDLIIIAARPSMGKTA-FALNIAENIAKK------QGKPVLFFSLEMSKEQLLQRL   61 (242)
T ss_pred             CCCCeEEEEEeCCCCCHHH-HHHHHHHHHHHh------CCCceEEEeCCCCHHHHHHHH
Confidence            4567778999999999994 455555554432      256788887   344444443

The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.

>KOG0347|consensus

Probab=92.51  E-value=0.4  Score=43.16  Aligned_cols=53  Identities=23%  Similarity=0.349  Sum_probs=47.0

Q ss_pred             eEEEEecchhHHHHHHHHHhh----CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc
Q psy14082        108 KVIVFVETKKKVEDITRALRR----ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD  164 (233)
Q Consensus       108 k~iIf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~  164 (233)
                      -.+||++||+-+.++.+.|..    -++.+..+.|||+...++.+++.    .-+|+|||+
T Consensus       265 ~~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQqRlL~~----~p~IVVATP  321 (731)
T KOG0347|consen  265 IALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQRLLNQ----RPDIVVATP  321 (731)
T ss_pred             eeEEecChHHHHHHHHHHHHHhccccCeEEEEeechhHHHHHHHHHhc----CCCEEEecc
Confidence            389999999999999988864    37999999999999999999887    568999994

>PRK12377 putative replication protein; Provisional

Probab=92.45  E-value=0.26  Score=40.22  Aligned_cols=47  Identities=2%  Similarity=-0.080  Sum_probs=32.8

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHH
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVA   64 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~   64 (233)
                      ..++..+++|+|||.. +..+.+.+..+       +..+ +.++..+|..++...+
T Consensus       102 ~~l~l~G~~GtGKThL-a~AIa~~l~~~-------g~~v-~~i~~~~l~~~l~~~~  148 (248)
T PRK12377        102 TNFVFSGKPGTGKNHL-AAAIGNRLLAK-------GRSV-IVVTVPDVMSRLHESY  148 (248)
T ss_pred             CeEEEECCCCCCHHHH-HHHHHHHHHHc-------CCCe-EEEEHHHHHHHHHHHH
Confidence            4688999999999966 56667666542       3344 4556678888776554

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=92.38  E-value=0.36  Score=37.31  Aligned_cols=61  Identities=11%  Similarity=-0.001  Sum_probs=35.8

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCC---CCCCCceEEEEcCcHHHHHHHHHHHHHhh
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPV---KQGDGPIALVLAPTRELAQQIQTVAKEFS   68 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~---~~~~~~~~lil~PtreL~~Q~~~~~~~~~   68 (233)
                      ..|.-+++.|++|+|||.. ++-+...+....+.   ....+.++|++..-.. ..++.+.+....
T Consensus        30 ~~g~l~~i~g~~g~GKT~~-~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~-~~~~~~rl~~~~   93 (193)
T PF13481_consen   30 PRGELTLIAGPPGSGKTTL-ALQLAAALATGRPFLGELPPRPGRVLYISLEDS-ESQIARRLRALL   93 (193)
T ss_dssp             -TTSEEEEEECSTSSHHHH-HHHHHHHHHT---TT---------EEEEESSS--HHHHHHHHHHHH
T ss_pred             cCCeEEEEEeCCCCCHHHH-HHHHHHHHHhCCccCCcccccCceEEEEeccCC-HHHHHHHHHHHh
Confidence            3577799999999999955 66666666542111   1124567787766433 567777777763

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=92.37  E-value=0.19  Score=47.24  Aligned_cols=33  Identities=15%  Similarity=-0.033  Sum_probs=28.0

Q ss_pred             CCCEEEecccCcCCcCCCCccEEEEecCCCCcc
Q psy14082        156 KAPILVATDVAARGLDVEDVNTVNIGSLQLSAN  188 (233)
Q Consensus       156 ~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~  188 (233)
                      ..+.+.+--.+-+|.|-|+|=.++-.....|..
T Consensus       483 plRFIFS~waLrEGWDNPNVFtIckL~~S~Sei  515 (985)
T COG3587         483 PLRFIFSKWALREGWDNPNVFTICKLRSSGSEI  515 (985)
T ss_pred             cceeeeehhHHhhcCCCCCeeEEEEecCCCcch
Confidence            478899999999999999999888887776665

>cd01131 PilT Pilus retraction ATPase PilT

Probab=92.37  E-value=0.21  Score=39.25  Aligned_cols=39  Identities=8%  Similarity=-0.072  Sum_probs=24.7

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHH
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTREL   56 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL   56 (233)
                      +++.+|||||||.. +-.++..+...      .+.+++.+--..|+
T Consensus         4 ilI~GptGSGKTTl-l~~ll~~~~~~------~~~~i~t~e~~~E~   42 (198)
T cd01131           4 VLVTGPTGSGKSTT-LAAMIDYINKN------KTHHILTIEDPIEF   42 (198)
T ss_pred             EEEECCCCCCHHHH-HHHHHHHhhhc------CCcEEEEEcCCccc
Confidence            57889999999966 55566655422      23455666554454

PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=92.35  E-value=0.35  Score=38.63  Aligned_cols=54  Identities=17%  Similarity=-0.014  Sum_probs=33.9

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ++.|.-+++.+++|+|||.. +.-++.....       ++..++++.- .+...++.+..+.+
T Consensus        17 i~~G~~~~i~G~~G~GKT~l-~~~~~~~~~~-------~g~~~~~is~-e~~~~~i~~~~~~~   70 (229)
T TIGR03881        17 IPRGFFVAVTGEPGTGKTIF-CLHFAYKGLR-------DGDPVIYVTT-EESRESIIRQAAQF   70 (229)
T ss_pred             CcCCeEEEEECCCCCChHHH-HHHHHHHHHh-------cCCeEEEEEc-cCCHHHHHHHHHHh
Confidence            45688899999999999955 3333322222       2445666653 45566666666555

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>KOG0744|consensus

Probab=92.21  E-value=1.8  Score=36.78  Aligned_cols=145  Identities=12%  Similarity=0.012  Sum_probs=77.7

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCC-CceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCCCCCee
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGD-GPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPKGPQD   86 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~-~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~~~~~   86 (233)
                      .+=+++.+|+|+|||-. .-++.+++--.   ...+ ..-.+|=.....|-..|+.+--++-.                 
T Consensus       177 NRliLlhGPPGTGKTSL-CKaLaQkLSIR---~~~~y~~~~liEinshsLFSKWFsESgKlV~-----------------  235 (423)
T KOG0744|consen  177 NRLILLHGPPGTGKTSL-CKALAQKLSIR---TNDRYYKGQLIEINSHSLFSKWFSESGKLVA-----------------  235 (423)
T ss_pred             eeEEEEeCCCCCChhHH-HHHHHHhheee---ecCccccceEEEEehhHHHHHHHhhhhhHHH-----------------
Confidence            45578899999999944 55666665421   1122 22345545555565555555444300                 


Q ss_pred             EEeccchhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHH------HHHHHHhhCCCCCEE
Q psy14082         87 CLPLHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDR------DYVLNDFRQGKAPIL  160 (233)
Q Consensus        87 lv~l~r~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r------~~~~~~f~~g~~~iL  160 (233)
                           ++.+.++++.   ..+..+||+- .+.++.++..=..      ...+.-|.+..      ..-+++.+.-.--++
T Consensus       236 -----kmF~kI~ELv---~d~~~lVfvL-IDEVESLa~aR~s------~~S~~EpsDaIRvVNalLTQlDrlK~~~Nvli  300 (423)
T KOG0744|consen  236 -----KMFQKIQELV---EDRGNLVFVL-IDEVESLAAARTS------ASSRNEPSDAIRVVNALLTQLDRLKRYPNVLI  300 (423)
T ss_pred             -----HHHHHHHHHH---hCCCcEEEEE-eHHHHHHHHHHHh------hhcCCCCchHHHHHHHHHHHHHHhccCCCEEE
Confidence                 0222222222   2255667664 4667766655211      11122222211      122444555554566


Q ss_pred             EecccCcCCcCCCC---ccEEEEecCCCCcc
Q psy14082        161 VATDVAARGLDVED---VNTVNIGSLQLSAN  188 (233)
Q Consensus       161 v~T~~~~~Gldi~~---v~~VI~~d~P~~~~  188 (233)
                      .||+-+..-+|..-   .|.+.+.++|....
T Consensus       301 L~TSNl~~siD~AfVDRADi~~yVG~Pt~~a  331 (423)
T KOG0744|consen  301 LATSNLTDSIDVAFVDRADIVFYVGPPTAEA  331 (423)
T ss_pred             EeccchHHHHHHHhhhHhhheeecCCccHHH
Confidence            88988888899654   45788888887654

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=92.20  E-value=0.59  Score=42.94  Aligned_cols=70  Identities=9%  Similarity=0.112  Sum_probs=52.0

Q ss_pred             CCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----cCcC--CcCCCC
Q psy14082        106 AFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----VAAR--GLDVED  174 (233)
Q Consensus       106 ~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----~~~~--Gldi~~  174 (233)
                      ..++||.++|++.+.++.+.+.+.    ++.+..+||+.+.+.+...++    +..+|+|+|.     .+..  .+++..
T Consensus        84 ~~raLIl~PTreLa~Qi~~~~~~l~~~~~i~v~~l~Gg~~~~~q~~~l~----~~~dIiV~TP~rL~~~l~~~~~~~l~~  159 (572)
T PRK04537         84 DPRALILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQRELLQ----QGVDVIIATPGRLIDYVKQHKVVSLHA  159 (572)
T ss_pred             CceEEEEeCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHHh----CCCCEEEECHHHHHHHHHhccccchhh
Confidence            468999999999999988887653    678899999998877665554    3578999994     3222  355666


Q ss_pred             ccEEE
Q psy14082        175 VNTVN  179 (233)
Q Consensus       175 v~~VI  179 (233)
                      ++++|
T Consensus       160 v~~lV  164 (572)
T PRK04537        160 CEICV  164 (572)
T ss_pred             eeeeE
Confidence            66554

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=92.18  E-value=0.22  Score=40.40  Aligned_cols=25  Identities=0%  Similarity=-0.282  Sum_probs=18.9

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhh
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      -.+++.|++||||| ++++-++..+.
T Consensus        14 fr~viIG~sGSGKT-~li~~lL~~~~   38 (241)
T PF04665_consen   14 FRMVIIGKSGSGKT-TLIKSLLYYLR   38 (241)
T ss_pred             ceEEEECCCCCCHH-HHHHHHHHhhc
Confidence            35789999999999 44776765543

This is thought to be an ATPase involved in viral DNA packaging [].

>KOG1016|consensus

Probab=92.14  E-value=0.35  Score=45.30  Aligned_cols=89  Identities=18%  Similarity=0.307  Sum_probs=72.9

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCCC------------------eeEEEeCCCCHHHHHHHHHHhhCCC---CCEEEe
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRERH------------------SAICIHGDKTQQDRDYVLNDFRQGK---APILVA  162 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~~------------------~~~~~~~~~~~~~r~~~~~~f~~g~---~~iLv~  162 (233)
                      ..+.++|+|....-..+.+.+.|.+..+                  +-.-+.|..+..+|++.+++|++..   +-+|++
T Consensus       717 ~~g~kil~fSq~l~~Ld~ieeil~krq~pc~~gdnG~~aqkW~~n~sy~rldG~t~a~~rekLinqfN~e~~lsWlflls  796 (1387)
T KOG1016|consen  717 QIGEKILIFSQNLTALDMIEEILKKRQIPCKDGDNGCPAQKWEKNRSYLRLDGTTSAADREKLINQFNSEPGLSWLFLLS  796 (1387)
T ss_pred             ccCceEEEeecchhHHHHHHHHHhcccccCCCCCCCCchhhhhhccceecccCCcccchHHHHHHhccCCCCceeeeeeh
Confidence            3567899999999988888888876522                  2234678889999999999998643   458899


Q ss_pred             cccCcCCcCCCCccEEEEecCCCCcccccc
Q psy14082        163 TDVAARGLDVEDVNTVNIGSLQLSANHNIS  192 (233)
Q Consensus       163 T~~~~~Gldi~~v~~VI~~d~P~~~~~~i~  192 (233)
                      |...+-|+++-..+-++.||--+++.|..+
T Consensus       797 trag~lGinLIsanr~~ifda~wnpchdaq  826 (1387)
T KOG1016|consen  797 TRAGSLGINLISANRCIIFDACWNPCHDAQ  826 (1387)
T ss_pred             hccccccceeeccceEEEEEeecCccccch
Confidence            999999999999999999999999886664

>cd01134 V_A-ATPase_A V/A-type ATP synthase catalytic subunit A

Probab=92.14  E-value=5.3  Score=34.41  Aligned_cols=54  Identities=11%  Similarity=-0.006  Sum_probs=32.3

Q ss_pred             CCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          3 PPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         3 p~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      -++-.|.-..+.++.|+|||..- .-++    ++.    +..  ++|.+--=|-...+.+.+++|
T Consensus       152 ~Pi~kGqr~~I~G~~G~GKT~L~-~~Ia----k~~----~~d--vvVyv~iGERg~Ev~e~l~ef  205 (369)
T cd01134         152 FPVVKGGTAAIPGPFGCGKTVIQ-QSLS----KYS----NSD--IVIYVGCGERGNEMTEVLEEF  205 (369)
T ss_pred             ccccCCCEEEEECCCCCChHHHH-HHHH----hCC----CCC--EEEEEEeCCChHHHHHHHHHH
Confidence            35667888888999999999762 2222    221    223  344444445566666666665

These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria.

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=92.13  E-value=0.15  Score=43.00  Aligned_cols=24  Identities=4%  Similarity=-0.346  Sum_probs=18.5

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHH
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAV   31 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~   31 (233)
                      .|..+++.++||||||.. +-.++.
T Consensus       143 ~~~~ili~G~tGsGKTTl-l~al~~  166 (308)
T TIGR02788       143 SRKNIIISGGTGSGKTTF-LKSLVD  166 (308)
T ss_pred             CCCEEEEECCCCCCHHHH-HHHHHc
Confidence            588999999999999954 443443

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>PF01935 DUF87: Domain of unknown function DUF87; InterPro: IPR002789 The function of this domain is unknown

Probab=92.13  E-value=0.21  Score=39.96  Aligned_cols=47  Identities=11%  Similarity=-0.048  Sum_probs=34.2

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHH
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQI   60 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~   60 (233)
                      -++++.+.+.||||||.+ +--+++.+..      ..+..++|+=|.-|=+.-.
T Consensus        22 ~~~H~~I~G~TGsGKS~~-~~~ll~~l~~------~~~~~~ii~D~~GEY~~~~   68 (229)
T PF01935_consen   22 FNRHIAIFGTTGSGKSNT-VKVLLEELLK------KKGAKVIIFDPHGEYASLF   68 (229)
T ss_pred             ccceEEEECCCCCCHHHH-HHHHHHHHHh------cCCCCEEEEcCCCcchhhh
Confidence            368999999999999977 6668888873      2355677777776654443

It contains several conserved aspartates and histidines that could be metal ligands.

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=92.07  E-value=0.083  Score=44.40  Aligned_cols=20  Identities=5%  Similarity=-0.433  Sum_probs=16.7

Q ss_pred             CCCCceeEecCCCCCchHHh
Q psy14082          6 ESGCQNFSKITNYLLSPPQY   25 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~   25 (233)
                      +...+++..+|||||||+..
T Consensus        95 L~KSNILLiGPTGsGKTlLA  114 (408)
T COG1219          95 LSKSNILLIGPTGSGKTLLA  114 (408)
T ss_pred             eeeccEEEECCCCCcHHHHH
Confidence            45668999999999999763

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=92.01  E-value=0.25  Score=45.62  Aligned_cols=56  Identities=9%  Similarity=-0.056  Sum_probs=39.9

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHH
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAK   65 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~   65 (233)
                      +..+-.++.+++|||||.+ +.-++..+.+..   ..+..++++.+||..-|..+.+.+.
T Consensus       165 ~~~~~~vItGgpGTGKTt~-v~~ll~~l~~~~---~~~~~~i~l~APTgkAA~rL~e~~~  220 (615)
T PRK10875        165 LTRRISVISGGPGTGKTTT-VAKLLAALIQLA---DGERCRIRLAAPTGKAAARLTESLG  220 (615)
T ss_pred             hcCCeEEEEeCCCCCHHHH-HHHHHHHHHHhc---CCCCcEEEEECCcHHHHHHHHHHHH
Confidence            4566789999999999976 444555554321   0224578899999998888877664

>PRK09183 transposase/IS protein; Provisional

Probab=91.96  E-value=0.43  Score=39.21  Aligned_cols=48  Identities=8%  Similarity=-0.081  Sum_probs=30.4

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHH
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQ   61 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~   61 (233)
                      +.+|..+++.+|+|+|||.. +..+......       .|..++++ +..+|..++.
T Consensus        99 i~~~~~v~l~Gp~GtGKThL-a~al~~~a~~-------~G~~v~~~-~~~~l~~~l~  146 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHL-AIALGYEAVR-------AGIKVRFT-TAADLLLQLS  146 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHH-HHHHHHHHHH-------cCCeEEEE-eHHHHHHHHH
Confidence            45688899999999999965 3333333322       25556655 4456765543

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=91.91  E-value=1.1  Score=39.98  Aligned_cols=69  Identities=16%  Similarity=0.302  Sum_probs=51.5

Q ss_pred             CeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc------cCcCCcCCCCcc
Q psy14082        107 FKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD------VAARGLDVEDVN  176 (233)
Q Consensus       107 ~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~------~~~~Gldi~~v~  176 (233)
                      .++||.++|++.+.++.+.+.+.    ++.+..++|+.+.+.+...+    .+..+|+|+|.      .....+++.+++
T Consensus        76 ~~aLil~PtreLa~Qi~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l----~~~~~IiV~TP~rL~~~~~~~~~~l~~v~  151 (456)
T PRK10590         76 VRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMKL----RGGVDVLVATPGRLLDLEHQNAVKLDQVE  151 (456)
T ss_pred             ceEEEEeCcHHHHHHHHHHHHHHhccCCCEEEEEECCcCHHHHHHHH----cCCCcEEEEChHHHHHHHHcCCcccccce
Confidence            47999999999999888887653    57888899998877654433    25689999994      223446777777


Q ss_pred             EEE
Q psy14082        177 TVN  179 (233)
Q Consensus       177 ~VI  179 (233)
                      ++|
T Consensus       152 ~lV  154 (456)
T PRK10590        152 ILV  154 (456)
T ss_pred             EEE
Confidence            766

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=91.89  E-value=0.24  Score=42.92  Aligned_cols=42  Identities=5%  Similarity=-0.217  Sum_probs=27.0

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHH
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTREL   56 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL   56 (233)
                      --+++.+|||||||.. +-.+++.+...     ....+++.+=-..|+
T Consensus       150 GlilI~G~TGSGKTT~-l~al~~~i~~~-----~~~~~IvtiEdp~E~  191 (372)
T TIGR02525       150 GLGLICGETGSGKSTL-AASIYQHCGET-----YPDRKIVTYEDPIEY  191 (372)
T ss_pred             CEEEEECCCCCCHHHH-HHHHHHHHHhc-----CCCceEEEEecCchh
Confidence            3588999999999955 66777777543     123345555444444

Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).

>PRK08727 hypothetical protein; Validated

Probab=91.76  E-value=0.48  Score=38.21  Aligned_cols=50  Identities=10%  Similarity=0.018  Sum_probs=32.4

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      +-+++.+++|+|||.. +-.+...+.+       .+.+++++ |..++.....+.++.+
T Consensus        42 ~~l~l~G~~G~GKThL-~~a~~~~~~~-------~~~~~~y~-~~~~~~~~~~~~~~~l   91 (233)
T PRK08727         42 DWLYLSGPAGTGKTHL-ALALCAAAEQ-------AGRSSAYL-PLQAAAGRLRDALEAL   91 (233)
T ss_pred             CeEEEECCCCCCHHHH-HHHHHHHHHH-------cCCcEEEE-eHHHhhhhHHHHHHHH
Confidence            3489999999999965 4445555543       25566665 4556666655655555

>TIGR03754 conj_TOL_TraD conjugative coupling factor TraD, TOL family

Probab=91.75  E-value=0.88  Score=42.16  Aligned_cols=64  Identities=16%  Similarity=0.101  Sum_probs=43.3

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcH--HHHHHHHHHHHHhhcCCcEEEEE
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTR--ELAQQIQTVAKEFSSALRNICIF   77 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~Ptr--eL~~Q~~~~~~~~~~~~~~~~~~   77 (233)
                      ..-.|.++.++||+|||..+..-+.+.+ .       .+..++++=|-.  ++..-++..++..+..-....+.
T Consensus       178 ~~~gHtlV~GtTGsGKT~l~~~li~q~i-~-------~g~~vi~fDpkgD~el~~~~~~~~~~~GR~~~f~~~~  243 (643)
T TIGR03754       178 ERVGHTLVLGTTRVGKTRLAELLITQDI-R-------RGDVVIVFDPKGDADLLKRMYAEAKRAGRLDEFYVFH  243 (643)
T ss_pred             cccCceEEECCCCCCHHHHHHHHHHHHH-H-------cCCeEEEEeCCCCHHHHHHHHHHHHHhCCCCceEEec
Confidence            3567899999999999988666444444 2       355677777766  57777777777774433333333

Members of this protein are assigned by homology to the TraD family of conjugative coupling factor. This particular clade serves as a marker for an extended gene region that occurs occasionally on plasmids, including the toluene catabolism TOL plasmid. More commonly, the gene region is chromosomal, flanked by various markers of conjugative transfer and insertion.

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=91.75  E-value=1.7  Score=37.65  Aligned_cols=27  Identities=11%  Similarity=-0.182  Sum_probs=19.9

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhh
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      ..|.-++..+|||+|||.+.. -+..++
T Consensus       135 ~~g~ii~lvGptGvGKTTtia-kLA~~~  161 (374)
T PRK14722        135 ERGGVFALMGPTGVGKTTTTA-KLAARC  161 (374)
T ss_pred             cCCcEEEEECCCCCCHHHHHH-HHHHHH
Confidence            457789999999999998743 344443

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=91.72  E-value=0.96  Score=39.81  Aligned_cols=71  Identities=14%  Similarity=0.140  Sum_probs=50.9

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhh----CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----cC-cCCcCCCC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRR----ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----VA-ARGLDVED  174 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----~~-~~Gldi~~  174 (233)
                      .+.+++|.++|++-+.++.+.+..    .++++..++|+.+...+...++    ...+|+|+|.     .+ ...+++.+
T Consensus        82 ~~~~~lil~PtreLa~Qi~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~----~~~~IlV~TP~~l~~~l~~~~~~l~~  157 (423)
T PRK04837         82 NQPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKVLE----SGVDILIGTTGRLIDYAKQNHINLGA  157 (423)
T ss_pred             CCceEEEECCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhc----CCCCEEEECHHHHHHHHHcCCccccc
Confidence            346899999999999998776653    4788999999988766554432    3578999995     22 22356666


Q ss_pred             ccEEE
Q psy14082        175 VNTVN  179 (233)
Q Consensus       175 v~~VI  179 (233)
                      +.++|
T Consensus       158 v~~lV  162 (423)
T PRK04837        158 IQVVV  162 (423)
T ss_pred             ccEEE
Confidence            66665

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=91.58  E-value=0.34  Score=43.54  Aligned_cols=54  Identities=9%  Similarity=-0.116  Sum_probs=39.9

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ++.|.-+++.+++|+|||...+- .+....       .++.++++++ +.|-..|+...++.+
T Consensus       260 ~~~gs~~li~G~~G~GKt~l~~~-f~~~~~-------~~ge~~~y~s-~eEs~~~i~~~~~~l  313 (484)
T TIGR02655       260 FFKDSIILATGATGTGKTLLVSK-FLENAC-------ANKERAILFA-YEESRAQLLRNAYSW  313 (484)
T ss_pred             ccCCcEEEEECCCCCCHHHHHHH-HHHHHH-------HCCCeEEEEE-eeCCHHHHHHHHHHc
Confidence            45788899999999999965333 333332       2366788766 678899999999888

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=91.48  E-value=0.43  Score=39.03  Aligned_cols=54  Identities=15%  Similarity=0.047  Sum_probs=38.2

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ++.|+-+++.+++|||||.- .+=.+.....       .|-.++++ .+.|...++.+.+..+
T Consensus        20 ~p~g~~~lI~G~pGsGKT~f-~~qfl~~~~~-------~ge~vlyv-s~~e~~~~l~~~~~~~   73 (260)
T COG0467          20 LPRGSVVLITGPPGTGKTIF-ALQFLYEGAR-------EGEPVLYV-STEESPEELLENARSF   73 (260)
T ss_pred             CcCCcEEEEEcCCCCcHHHH-HHHHHHHHHh-------cCCcEEEE-EecCCHHHHHHHHHHc
Confidence            46789999999999999954 4433333332       24455554 5668888999999887

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=91.36  E-value=0.53  Score=37.53  Aligned_cols=54  Identities=15%  Similarity=-0.062  Sum_probs=36.2

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ++.|.-+++.+++|+|||.. ++-++.....       ++..++++.. .+-..|+.+.+..+
T Consensus        13 i~~g~~~li~G~~G~GKt~~-~~~~~~~~~~-------~g~~~~y~s~-e~~~~~l~~~~~~~   66 (224)
T TIGR03880        13 FPEGHVIVVIGEYGTGKTTF-SLQFLYQGLK-------NGEKAMYISL-EEREERILGYAKSK   66 (224)
T ss_pred             CCCCeEEEEECCCCCCHHHH-HHHHHHHHHh-------CCCeEEEEEC-CCCHHHHHHHHHHc
Confidence            35688889999999999854 3333322221       2556777654 56788888888777

This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.

>PTZ00185 ATPase alpha subunit; Provisional

Probab=91.29  E-value=9.2  Score=34.80  Aligned_cols=65  Identities=8%  Similarity=0.120  Sum_probs=36.6

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEE---cCcHHHHHHHHHHHHHh
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVL---APTRELAQQIQTVAKEF   67 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil---~PtreL~~Q~~~~~~~~   67 (233)
                      +-++-+|+-..+.+..|+|||...+=.+++...-+.....+....+++.   --.+|.++ +.+.+++.
T Consensus       183 LiPIGRGQR~lIfGd~GtGKTtLAld~IinQ~~~~~~~~~~~~~v~VyvaIGeR~rEV~e-i~~~L~e~  250 (574)
T PTZ00185        183 MIPIGRGQRELIVGDRQTGKTSIAVSTIINQVRINQQILSKNAVISIYVSIGQRCSNVAR-IHRLLRSY  250 (574)
T ss_pred             cccccCCCEEEeecCCCCChHHHHHHHHHhhhhhccccccCCCCEEEEEEeccchHHHHH-HHHHHHhc
Confidence            3457789999999999999997743334443311000000122233333   25666665 77777766

>PRK07952 DNA replication protein DnaC; Validated

Probab=91.28  E-value=0.49  Score=38.52  Aligned_cols=47  Identities=4%  Similarity=-0.038  Sum_probs=31.0

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHH
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVA   64 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~   64 (233)
                      ..++..+++|+|||.. +..+...+...       +..++++ +..+|...+...+
T Consensus       100 ~~~~l~G~~GtGKThL-a~aia~~l~~~-------g~~v~~i-t~~~l~~~l~~~~  146 (244)
T PRK07952        100 ASFIFSGKPGTGKNHL-AAAICNELLLR-------GKSVLII-TVADIMSAMKDTF  146 (244)
T ss_pred             ceEEEECCCCCCHHHH-HHHHHHHHHhc-------CCeEEEE-EHHHHHHHHHHHH
Confidence            3588999999999976 55666666542       4455544 6667766555443

>cd01394 radB RadB

Probab=91.27  E-value=0.64  Score=36.80  Aligned_cols=39  Identities=13%  Similarity=-0.037  Sum_probs=26.3

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEc
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLA   51 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~   51 (233)
                      ++.|.=+++.+++|+|||.. ++-++.....       .+.+++++.
T Consensus        16 i~~g~i~~i~G~~GsGKT~l-~~~~a~~~~~-------~g~~v~yi~   54 (218)
T cd01394          16 VERGTVTQVYGPPGTGKTNI-AIQLAVETAG-------QGKKVAYID   54 (218)
T ss_pred             ccCCeEEEEECCCCCCHHHH-HHHHHHHHHh-------cCCeEEEEE
Confidence            35577788999999999955 4444444432       255788874

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>PRK10536 hypothetical protein; Provisional

Probab=91.21  E-value=0.35  Score=39.60  Aligned_cols=29  Identities=17%  Similarity=-0.161  Sum_probs=21.6

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhc
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISH   35 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~   35 (233)
                      .+.-+++.+++|||||+......++.+..
T Consensus        73 ~~~lV~i~G~aGTGKT~La~a~a~~~l~~  101 (262)
T PRK10536         73 SKQLIFATGEAGCGKTWISAAKAAEALIH  101 (262)
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            34568889999999998866656655543

>TIGR02012 tigrfam_recA protein RecA

Probab=91.19  E-value=0.45  Score=40.33  Aligned_cols=44  Identities=14%  Similarity=-0.051  Sum_probs=29.8

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHH
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTREL   56 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL   56 (233)
                      +++|+=+.+.+|+|||||.. ++.++.....       .+..++++-.-..+
T Consensus        52 lp~G~iteI~G~~GsGKTtL-aL~~~~~~~~-------~g~~v~yId~E~~~   95 (321)
T TIGR02012        52 LPRGRIIEIYGPESSGKTTL-ALHAIAEAQK-------AGGTAAFIDAEHAL   95 (321)
T ss_pred             CcCCeEEEEECCCCCCHHHH-HHHHHHHHHH-------cCCcEEEEcccchh
Confidence            56788889999999999955 5555555543       25567776554333

This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.

>KOG0701|consensus

Probab=91.15  E-value=0.067  Score=53.69  Aligned_cols=89  Identities=20%  Similarity=0.246  Sum_probs=70.9

Q ss_pred             CeEEEEecchhHHHHHHHHHhhCC-CeeEEEeCCCC-----------HHHHHHHHHHhhCCCCCEEEecccCcCCcCCCC
Q psy14082        107 FKVIVFVETKKKVEDITRALRRER-HSAICIHGDKT-----------QQDRDYVLNDFRQGKAPILVATDVAARGLDVED  174 (233)
Q Consensus       107 ~k~iIf~~~~~~~~~l~~~L~~~~-~~~~~~~~~~~-----------~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~  174 (233)
                      --.++|++.+..+....+.+++.+ ..+..+.|.+.           ...+.+++..|...++++|++|.++.+|+|++.
T Consensus       293 l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~k~~~~~~~~~~~~vl~~~~~~~ln~L~~~~~~~e~~d~~~  372 (1606)
T KOG0701|consen  293 LSGIIFVDQRYTAYVLLELLREIFSNDPLFVTGASGANLWKSFKNELELRQAEVLRRFHFHELNLLIATSVLEEGVDVPK  372 (1606)
T ss_pred             hhheeecccchHHHHHHHHHHHhhccCcceeeccccCccchhhHHHHHhhhHHHHHHHhhhhhhHHHHHHHHHhhcchhh
Confidence            456899999999998888887653 23333555422           223578899999999999999999999999999


Q ss_pred             ccEEEEecCCCCcccccceee
Q psy14082        175 VNTVNIGSLQLSANHNISQVI  195 (233)
Q Consensus       175 v~~VI~~d~P~~~~~~i~~~~  195 (233)
                      ++.++.+|.|.....|+++.+
T Consensus       373 ~~~~~~~~~~~~~~~~vq~~~  393 (1606)
T KOG0701|consen  373 CNLVVLFDAPTYYRSYVQKKG  393 (1606)
T ss_pred             hhhheeccCcchHHHHHHhhc
Confidence            999999999999988885433

>KOG0338|consensus

Probab=91.11  E-value=1.4  Score=39.43  Aligned_cols=72  Identities=15%  Similarity=0.237  Sum_probs=55.1

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEeccc-------CcCCcCC
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDV-------AARGLDV  172 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~-------~~~Gldi  172 (233)
                      ....++||.|+|++-+-+++...++.    .+.+...-||++-+.++.+++.    ..+|+|||+-       -+-++|+
T Consensus       250 ~~~TRVLVL~PTRELaiQv~sV~~qlaqFt~I~~~L~vGGL~lk~QE~~LRs----~PDIVIATPGRlIDHlrNs~sf~l  325 (691)
T KOG0338|consen  250 VAATRVLVLVPTRELAIQVHSVTKQLAQFTDITVGLAVGGLDLKAQEAVLRS----RPDIVIATPGRLIDHLRNSPSFNL  325 (691)
T ss_pred             CcceeEEEEeccHHHHHHHHHHHHHHHhhccceeeeeecCccHHHHHHHHhh----CCCEEEecchhHHHHhccCCCccc
Confidence            35578999999999988887777654    5788888999999999999886    5799999952       2334556


Q ss_pred             CCccEEE
Q psy14082        173 EDVNTVN  179 (233)
Q Consensus       173 ~~v~~VI  179 (233)
                      .++.++|
T Consensus       326 dsiEVLv  332 (691)
T KOG0338|consen  326 DSIEVLV  332 (691)
T ss_pred             cceeEEE
Confidence            6666544

>PRK13764 ATPase; Provisional

Probab=91.06  E-value=0.3  Score=44.87  Aligned_cols=26  Identities=4%  Similarity=-0.222  Sum_probs=20.8

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      +..+++.++||||||. ++-.++..+.
T Consensus       257 ~~~ILIsG~TGSGKTT-ll~AL~~~i~  282 (602)
T PRK13764        257 AEGILIAGAPGAGKST-FAQALAEFYA  282 (602)
T ss_pred             CCEEEEECCCCCCHHH-HHHHHHHHHh
Confidence            5679999999999995 4677777764

>TIGR02759 TraD_Ftype type IV conjugative transfer system coupling protein TraD

Probab=91.06  E-value=0.25  Score=45.22  Aligned_cols=31  Identities=6%  Similarity=-0.245  Sum_probs=22.7

Q ss_pred             CCCCCCCceeEecCCCCCchHHhHHHHHHhhh
Q psy14082          3 PPSESGCQNFSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus         3 p~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      |.-...+++++.++||||||.+ +-.++..+.
T Consensus       171 ~~~~e~~h~li~G~tGsGKs~~-i~~ll~~~~  201 (566)
T TIGR02759       171 KFGSETQHILIHGTTGSGKSVA-IRKLLRWIR  201 (566)
T ss_pred             CCcccccceEEEcCCCCCHHHH-HHHHHHHHH
Confidence            4345678999999999999964 455555554

The TraD protein performs an essential coupling function in conjugative type IV secretion systems. This protein sits at the inner membrane in contact with the assembled pilus and its scaffold as well as the relaxosome-plasmid DNA complex (through TraM).

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=91.03  E-value=0.43  Score=45.14  Aligned_cols=56  Identities=9%  Similarity=-0.018  Sum_probs=41.3

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ...+++.|..|||||.+ +.--+.++......   ...++|.++-|+.-|..+.+++.++
T Consensus        17 ~g~~lV~AgaGSGKT~~-l~~ria~Li~~~~i---~P~~IL~lTFT~kAA~em~~Rl~~~   72 (726)
T TIGR01073        17 EGPLLIMAGAGSGKTRV-LTHRIAHLIAEKNV---APWNILAITFTNKAAREMKERVEKL   72 (726)
T ss_pred             CCCEEEEeCCCCCHHHH-HHHHHHHHHHcCCC---CHHHeeeeeccHHHHHHHHHHHHHH
Confidence            45689999999999988 44444444432111   2346999999999999999999877

Designed to identify pcrA members of the uvrD/rep subfamily.

>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]

Probab=90.94  E-value=0.58  Score=46.56  Aligned_cols=59  Identities=10%  Similarity=-0.056  Sum_probs=44.8

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ..+..+++.|..|||||.+-.-=++..++...   +-.-.+.|+++-|+.-+..+..++..-
T Consensus        14 ~~~~~~lveASAGSGKT~vL~~r~lrlLl~~~---~~~v~~ILvvTFT~aAa~Emk~RI~~~   72 (1139)
T COG1074          14 PPGQSVLVEASAGTGKTFVLAERVLRLLLEGG---PLDVDEILVVTFTKAAAAEMKERIRDR   72 (1139)
T ss_pred             CCCCcEEEEEcCCCCchhHHHHHHHHHHhhcC---CCChhHeeeeeccHHHHHHHHHHHHHH
Confidence            45779999999999999996666666666531   123457999999998888888777765

>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

Probab=90.89  E-value=0.66  Score=33.26  Aligned_cols=26  Identities=4%  Similarity=-0.314  Sum_probs=19.4

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhh
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      .+..+++.+++|+|||.. +--+...+
T Consensus        18 ~~~~v~i~G~~G~GKT~l-~~~i~~~~   43 (151)
T cd00009          18 PPKNLLLYGPPGTGKTTL-ARAIANEL   43 (151)
T ss_pred             CCCeEEEECCCCCCHHHH-HHHHHHHh
Confidence            367899999999999954 44455444

The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.

>PF00006 ATP-synt_ab: ATP synthase alpha/beta family, nucleotide-binding domain This Pfam entry corresponds to chains a,b,c,d,e and f; InterPro: IPR000194 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane

Probab=90.78  E-value=3.3  Score=33.03  Aligned_cols=27  Identities=11%  Similarity=-0.221  Sum_probs=20.9

Q ss_pred             CCCCCCceeEecCCCCCchHHhHHHHHH
Q psy14082          4 PSESGCQNFSKITNYLLSPPQYMLPAAV   31 (233)
Q Consensus         4 ~~~~g~d~i~~a~tGsGKT~~~~lp~l~   31 (233)
                      ++-.|+.+.+.++.|+|||.. +.-++.
T Consensus        11 Pig~Gqr~~I~g~~g~GKt~L-l~~i~~   37 (215)
T PF00006_consen   11 PIGRGQRIGIFGGAGVGKTVL-LQEIAN   37 (215)
T ss_dssp             CEETTSEEEEEESTTSSHHHH-HHHHHH
T ss_pred             ccccCCEEEEEcCcccccchh-hHHHHh
Confidence            566799999999999999976 333433

ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, ]. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself driven by the movement of protons through the F0 complex C subunit []. In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory. The structure of the alpha and beta subunits is almost identical. Each subunit consists of a N-terminal beta-barrel, a central domain containing the nucleotide-binding site and a C-terminal alpha bundle domain []. This entry represents the central domain. It is found in the alpha and beta subunits from F1, V1, and A1 complexes, as well as in flagellar ATPase and the termination factor Rho. ; GO: 0005524 ATP binding; PDB: 3OEE_N 2HLD_W 3FKS_N 3OE7_O 3OFN_M 2XOK_D 3OEH_V 2WPD_F 3ZRY_D 2OBL_A ....

>PRK13700 conjugal transfer protein TraD; Provisional

Probab=90.75  E-value=0.33  Score=45.32  Aligned_cols=50  Identities=8%  Similarity=-0.067  Sum_probs=34.4

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHH
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQ   59 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q   59 (233)
                      ||.-...++.++.+.||||||.+ +--++..+..       +|-+++|.=|+-+.+..
T Consensus       179 ip~~~E~~H~li~GttGSGKS~~-i~~LL~~ir~-------RGdrAIIyD~~GeFv~~  228 (732)
T PRK13700        179 IIRDSEIQNFCLHGTVGAGKSEV-IRRLANYARQ-------RGDMVVIYDRSGEFVKS  228 (732)
T ss_pred             CCcchhhcceEEeCCCCCCHHHH-HHHHHHHHHH-------cCCeEEEEeCCCchHHH
Confidence            45556789999999999999986 4556665543       34456666565555543

>PRK06835 DNA replication protein DnaC; Validated

Probab=90.60  E-value=0.51  Score=40.22  Aligned_cols=46  Identities=9%  Similarity=-0.113  Sum_probs=31.8

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHH
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQT   62 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~   62 (233)
                      +..++..++||+|||.. +..+...+..       .+..+++ .+..+|..+..+
T Consensus       183 ~~~Lll~G~~GtGKThL-a~aIa~~l~~-------~g~~V~y-~t~~~l~~~l~~  228 (329)
T PRK06835        183 NENLLFYGNTGTGKTFL-SNCIAKELLD-------RGKSVIY-RTADELIEILRE  228 (329)
T ss_pred             CCcEEEECCCCCcHHHH-HHHHHHHHHH-------CCCeEEE-EEHHHHHHHHHH
Confidence            46799999999999976 5556666653       2445554 556677776644

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=90.58  E-value=0.17  Score=31.84  Aligned_cols=27  Identities=15%  Similarity=-0.071  Sum_probs=19.0

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhh
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      ..|...++.+++|||||..  +-+++.++
T Consensus        21 ~~g~~tli~G~nGsGKSTl--lDAi~~~L   47 (62)
T PF13555_consen   21 PRGDVTLITGPNGSGKSTL--LDAIQTVL   47 (62)
T ss_pred             CCCcEEEEECCCCCCHHHH--HHHHHHHH
Confidence            3456789999999999965  33444444

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=90.50  E-value=0.82  Score=40.00  Aligned_cols=64  Identities=14%  Similarity=-0.060  Sum_probs=43.3

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcH-------HHHHHHHHHHHHhhcCCcEEEEE
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTR-------ELAQQIQTVAKEFSSALRNICIF   77 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~Ptr-------eL~~Q~~~~~~~~~~~~~~~~~~   77 (233)
                      ..+-+++.+++|+|||.. +-++-+.....     .+..+++++....       ++-+.-.+.|++.+ ++...++.
T Consensus       112 ~~nplfi~G~~GlGKTHL-l~Aign~~~~~-----~~~a~v~y~~se~f~~~~v~a~~~~~~~~Fk~~y-~~dlllID  182 (408)
T COG0593         112 AYNPLFIYGGVGLGKTHL-LQAIGNEALAN-----GPNARVVYLTSEDFTNDFVKALRDNEMEKFKEKY-SLDLLLID  182 (408)
T ss_pred             cCCcEEEECCCCCCHHHH-HHHHHHHHHhh-----CCCceEEeccHHHHHHHHHHHHHhhhHHHHHHhh-ccCeeeec
Confidence            356689999999999987 55566666554     4556788887755       44455555666666 66655554

>PRK09281 F0F1 ATP synthase subunit alpha; Validated

Probab=90.48  E-value=5.9  Score=35.82  Aligned_cols=22  Identities=9%  Similarity=-0.090  Sum_probs=18.9

Q ss_pred             CCCCCCCceeEecCCCCCchHH
Q psy14082          3 PPSESGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         3 p~~~~g~d~i~~a~tGsGKT~~   24 (233)
                      -++-+|+-..+.+..|+|||..
T Consensus       157 ~pigrGQr~~Ifg~~g~GKt~l  178 (502)
T PRK09281        157 IPIGRGQRELIIGDRQTGKTAI  178 (502)
T ss_pred             cccccCcEEEeecCCCCCchHH
Confidence            3567899999999999999976

>PTZ00110 helicase; Provisional

Probab=90.46  E-value=1.4  Score=40.18  Aligned_cols=71  Identities=17%  Similarity=0.217  Sum_probs=51.0

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----cCcCC-cCCCC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----VAARG-LDVED  174 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----~~~~G-ldi~~  174 (233)
                      .+..+||.++|++-+.++.+.+.+.    ++.+..++|+.+...+...+.   . ..+|+|+|+     .+.++ .++..
T Consensus       202 ~gp~~LIL~PTreLa~Qi~~~~~~~~~~~~i~~~~~~gg~~~~~q~~~l~---~-~~~IlVaTPgrL~d~l~~~~~~l~~  277 (545)
T PTZ00110        202 DGPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQIYALR---R-GVEILIACPGRLIDFLESNVTNLRR  277 (545)
T ss_pred             CCcEEEEECChHHHHHHHHHHHHHHhcccCccEEEEeCCCCHHHHHHHHH---c-CCCEEEECHHHHHHHHHcCCCChhh
Confidence            4567999999999999998888765    467888899988766554443   2 479999994     33333 45556


Q ss_pred             ccEEE
Q psy14082        175 VNTVN  179 (233)
Q Consensus       175 v~~VI  179 (233)
                      +++||
T Consensus       278 v~~lV  282 (545)
T PTZ00110        278 VTYLV  282 (545)
T ss_pred             CcEEE
Confidence            66554

>KOG0330|consensus

Probab=90.46  E-value=1.7  Score=37.61  Aligned_cols=68  Identities=18%  Similarity=0.110  Sum_probs=51.7

Q ss_pred             hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc
Q psy14082         93 FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD  164 (233)
Q Consensus        93 ~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~  164 (233)
                      .+-+++.++.......++|.++||+-+.++++.+...    |+.+..+-|||+...+.  .+.++  +..|||||+
T Consensus       116 aLPIl~~LL~~p~~~~~lVLtPtRELA~QI~e~fe~Lg~~iglr~~~lvGG~~m~~q~--~~L~k--kPhilVaTP  187 (476)
T KOG0330|consen  116 ALPILQRLLQEPKLFFALVLTPTRELAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQA--NQLSK--KPHILVATP  187 (476)
T ss_pred             HHHHHHHHHcCCCCceEEEecCcHHHHHHHHHHHHHhccccCeEEEEEecCchHHHHH--HHhhc--CCCEEEeCc
Confidence            3445555666667789999999999999999888765    67899999998865544  44443  567899993

>KOG0334|consensus

Probab=90.40  E-value=4.9  Score=38.96  Aligned_cols=58  Identities=19%  Similarity=0.366  Sum_probs=45.8

Q ss_pred             hcCCCCeEEEEecchhHHHHHHHHHhh----CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEec
Q psy14082        102 AKNPAFKVIVFVETKKKVEDITRALRR----ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVAT  163 (233)
Q Consensus       102 ~~~~~~k~iIf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T  163 (233)
                      ....+.-.||.++|++.+.++...++.    .++.++.++|+....++..   ..+.| ..|+|||
T Consensus       434 ~~gdGPi~li~aPtrela~QI~r~~~kf~k~l~ir~v~vygg~~~~~qia---elkRg-~eIvV~t  495 (997)
T KOG0334|consen  434 EEGDGPIALILAPTRELAMQIHREVRKFLKLLGIRVVCVYGGSGISQQIA---ELKRG-AEIVVCT  495 (997)
T ss_pred             hhCCCceEEEEcCCHHHHHHHHHHHHHHHhhcCceEEEecCCccHHHHHH---HHhcC-CceEEec
Confidence            445667789999999999988888764    4889999999977665544   45557 8999998

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=90.39  E-value=0.57  Score=39.80  Aligned_cols=46  Identities=11%  Similarity=-0.092  Sum_probs=31.6

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHH
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQ   58 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~   58 (233)
                      ++.|+=+.+.+|+|||||.. ++.++.....       .+..++++.+-..+-.
T Consensus        52 lp~G~iteI~Gp~GsGKTtL-al~~~~~~~~-------~g~~~vyId~E~~~~~   97 (325)
T cd00983          52 YPKGRIIEIYGPESSGKTTL-ALHAIAEAQK-------LGGTVAFIDAEHALDP   97 (325)
T ss_pred             ccCCeEEEEECCCCCCHHHH-HHHHHHHHHH-------cCCCEEEECccccHHH
Confidence            56788889999999999955 5555544443       2566788776544443

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK09280 F0F1 ATP synthase subunit beta; Validated

Probab=90.31  E-value=6.5  Score=35.14  Aligned_cols=100  Identities=16%  Similarity=0.131  Sum_probs=50.6

Q ss_pred             CCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh-hc-CC-cEEEEEcC
Q psy14082          3 PPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF-SS-AL-RNICIFGG   79 (233)
Q Consensus         3 p~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~-~~-~~-~~~~~~gg   79 (233)
                      -++-.|+-+.+.|+.|+|||... ..++......     ...  +.|++--=|-...+.+-++.+ .. .+ ++.++.+.
T Consensus       139 ~pigkGQR~gIfa~~GvGKt~Ll-~~i~~~~~~~-----~~~--v~V~~liGER~rEv~efi~~~~~~~~l~rsvvV~at  210 (463)
T PRK09280        139 APYAKGGKIGLFGGAGVGKTVLI-QELINNIAKE-----HGG--YSVFAGVGERTREGNDLYHEMKESGVLDKTALVFGQ  210 (463)
T ss_pred             CCcccCCEEEeecCCCCChhHHH-HHHHHHHHhc-----CCC--EEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEEC
Confidence            35677899999999999999763 3333333221     112  333333334444555555555 11 12 34444444


Q ss_pred             CCCCCeeEEeccchhh-----hchHHHhcCCCCeEEEEecc
Q psy14082         80 TPKGPQDCLPLHRFVF-----NCQYEMAKNPAFKVIVFVET  115 (233)
Q Consensus        80 ~~~~~~~lv~l~r~~~-----~~~~~~~~~~~~k~iIf~~~  115 (233)
                      .+..+     +.|+..     -+.+++....+..++++..+
T Consensus       211 sd~p~-----~~r~~a~~~a~tiAEyfrd~~G~~VLll~Ds  246 (463)
T PRK09280        211 MNEPP-----GARLRVALTGLTMAEYFRDVEGQDVLLFIDN  246 (463)
T ss_pred             CCCCH-----HHHHHHHHHHHHHHHHHHHhcCCceEEEecc
Confidence            33322     122111     12335554477777777755

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=90.30  E-value=0.51  Score=40.41  Aligned_cols=43  Identities=5%  Similarity=-0.126  Sum_probs=28.0

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHH
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELA   57 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~   57 (233)
                      +.-+++.+|||||||.. +-.++..+...      .+.+++.+--..|+.
T Consensus       122 ~g~ili~G~tGSGKTT~-l~al~~~i~~~------~~~~i~tiEdp~E~~  164 (343)
T TIGR01420       122 RGLILVTGPTGSGKSTT-LASMIDYINKN------AAGHIITIEDPIEYV  164 (343)
T ss_pred             CcEEEEECCCCCCHHHH-HHHHHHhhCcC------CCCEEEEEcCChhhh
Confidence            45588999999999966 55566655321      234566666555653

This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=90.30  E-value=1.5  Score=42.47  Aligned_cols=98  Identities=14%  Similarity=0.036  Sum_probs=65.1

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEcCCCC------
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGGTPK------   82 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~gg~~~------   82 (233)
                      -|+.++||=|||++..+|++-.-+.      ++|+.  |++..-=||.-=.++...+  +.++++.++..+.+.      
T Consensus       154 ~IAEM~TGEGKTLvatlp~yLnAL~------G~gVH--vVTvNDYLA~RDaewm~p~y~flGLtVg~i~~~~~~~~Rr~a  225 (1025)
T PRK12900        154 KISEMATGEGKTLVSTLPTFLNALT------GRGVH--VVTVNDYLAQRDKEWMNPVFEFHGLSVGVILNTMRPEERREQ  225 (1025)
T ss_pred             CccccCCCCCcchHhHHHHHHHHHc------CCCcE--EEeechHhhhhhHHHHHHHHHHhCCeeeeeCCCCCHHHHHHh
Confidence            4678889999999999998765554      33544  4455556887777777776  679999998765433      


Q ss_pred             -CCeeEEe---------------------ccc-----hhhhchHHHhcCCCCeEEEEecch
Q psy14082         83 -GPQDCLP---------------------LHR-----FVFNCQYEMAKNPAFKVIVFVETK  116 (233)
Q Consensus        83 -~~~~lv~---------------------l~r-----~~~~~~~~~~~~~~~k~iIf~~~~  116 (233)
                       ..+|.-|                     ..|     ++|.+...+-.....|.||--+..
T Consensus       226 Y~~DItYgTn~EfGFDYLRDnma~~~~~~vqR~~~faIVDEvDSvLIDeARTPLIISgp~~  286 (1025)
T PRK12900        226 YLCDITYGTNNEFGFDYLRDNMAGTPEEMVQRDFYFAIVDEVDSVLIDEARTPLIISGPVP  286 (1025)
T ss_pred             CCCcceecCCCccccccchhccccchhhhhccCCceEEEechhhhhhccccCceEEeCCCC
Confidence             3333222                     112     566666666666777888877633

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=90.18  E-value=0.71  Score=36.25  Aligned_cols=41  Identities=15%  Similarity=0.032  Sum_probs=27.1

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCc
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPT   53 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~Pt   53 (233)
                      ++.|.=+.+.+++|||||...+- ++.....       .+.+++++.-.
T Consensus         9 i~~g~i~~i~G~~GsGKT~l~~~-~~~~~~~-------~g~~v~yi~~e   49 (209)
T TIGR02237         9 VERGTITQIYGPPGSGKTNICMI-LAVNAAR-------QGKKVVYIDTE   49 (209)
T ss_pred             CCCCeEEEEECCCCCCHHHHHHH-HHHHHHh-------CCCeEEEEECC
Confidence            35677789999999999966433 3333322       25567777764

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=89.99  E-value=2.2  Score=38.20  Aligned_cols=71  Identities=14%  Similarity=0.150  Sum_probs=50.9

Q ss_pred             CCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEeccc-----Cc-CCcCCCCc
Q psy14082        106 AFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDV-----AA-RGLDVEDV  175 (233)
Q Consensus       106 ~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~-----~~-~Gldi~~v  175 (233)
                      ..++|+.++|++-+.++.+.++..    ++.+..++|+.+...+.   +.+..+..+|+|+|..     .. ..+.+.++
T Consensus       162 ~~~aLil~PtreLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~---~~~~~~~~~Iiv~TP~~Ll~~~~~~~~~l~~l  238 (475)
T PRK01297        162 EPRALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQL---KQLEARFCDILVATPGRLLDFNQRGEVHLDMV  238 (475)
T ss_pred             CceEEEEeCcHHHHHHHHHHHHHhhccCCCEEEEEEccCChHHHH---HHHhCCCCCEEEECHHHHHHHHHcCCcccccC
Confidence            468999999999999988877654    67888999998765544   3455677899999952     11 23445555


Q ss_pred             cEEE
Q psy14082        176 NTVN  179 (233)
Q Consensus       176 ~~VI  179 (233)
                      ++||
T Consensus       239 ~~lV  242 (475)
T PRK01297        239 EVMV  242 (475)
T ss_pred             ceEE
Confidence            5554

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=89.85  E-value=1.6  Score=40.52  Aligned_cols=59  Identities=17%  Similarity=0.222  Sum_probs=53.9

Q ss_pred             CCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc
Q psy14082        106 AFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD  164 (233)
Q Consensus       106 ~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~  164 (233)
                      .+.++|.++++.-+......++..|+.+..+++..+.+++..++...+.|+.+++++|+
T Consensus        65 ~g~tlVisPl~sL~~dqv~~l~~~gi~~~~~~s~~~~~~~~~~~~~~~~g~~~il~~tP  123 (607)
T PRK11057         65 DGLTLVVSPLISLMKDQVDQLLANGVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAP  123 (607)
T ss_pred             CCCEEEEecHHHHHHHHHHHHHHcCCcEEEEcCCCCHHHHHHHHHHHhCCCCcEEEECh
Confidence            45799999999999999999999999999999999999999999999999999998884

>PRK10436 hypothetical protein; Provisional

Probab=89.84  E-value=0.43  Score=42.60  Aligned_cols=24  Identities=4%  Similarity=-0.177  Sum_probs=18.6

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhhh
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      -+++.+|||||||.+ +..++..+.
T Consensus       220 liLvtGpTGSGKTTt-L~a~l~~~~  243 (462)
T PRK10436        220 LILVTGPTGSGKTVT-LYSALQTLN  243 (462)
T ss_pred             eEEEECCCCCChHHH-HHHHHHhhC
Confidence            478999999999976 556676664

>PRK08116 hypothetical protein; Validated

Probab=89.83  E-value=0.62  Score=38.48  Aligned_cols=47  Identities=9%  Similarity=-0.101  Sum_probs=32.3

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHH
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVA   64 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~   64 (233)
                      .-+++.+++|+|||.. +..+.+.+..+       +..++ ..+..+|..++...+
T Consensus       115 ~gl~l~G~~GtGKThL-a~aia~~l~~~-------~~~v~-~~~~~~ll~~i~~~~  161 (268)
T PRK08116        115 VGLLLWGSVGTGKTYL-AACIANELIEK-------GVPVI-FVNFPQLLNRIKSTY  161 (268)
T ss_pred             ceEEEECCCCCCHHHH-HHHHHHHHHHc-------CCeEE-EEEHHHHHHHHHHHH
Confidence            3489999999999977 55677777643       33444 445667777765543

>COG0630 VirB11 Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=89.79  E-value=0.4  Score=40.53  Aligned_cols=44  Identities=11%  Similarity=-0.114  Sum_probs=32.4

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHH
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQ   58 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~   58 (233)
                      ..+++++++++||||||.. +.+++..+-        +..+.+.+=-|.|+..
T Consensus       141 e~~~siii~G~t~sGKTt~-lnall~~Ip--------~~~rivtIEdt~E~~~  184 (312)
T COG0630         141 EARKSIIICGGTASGKTTL-LNALLDFIP--------PEERIVTIEDTPELKL  184 (312)
T ss_pred             HcCCcEEEECCCCCCHHHH-HHHHHHhCC--------chhcEEEEeccccccC
Confidence            4688999999999999955 777777663        3445666666666643

>PRK12597 F0F1 ATP synthase subunit beta; Provisional

Probab=89.70  E-value=9  Score=34.29  Aligned_cols=101  Identities=18%  Similarity=0.210  Sum_probs=52.4

Q ss_pred             CCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh-hc-CC-cEEEEEcC
Q psy14082          3 PPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF-SS-AL-RNICIFGG   79 (233)
Q Consensus         3 p~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~-~~-~~-~~~~~~gg   79 (233)
                      -++-.|+-+.+.|+.|+|||.. +..++.....+     ...  +.|++--=|-...+.+-++.+ .. .+ ++.++.+.
T Consensus       138 ~pigkGQR~gIfa~~G~GKt~L-l~~~~~~~~~~-----~~d--v~V~~liGER~rEv~ef~~~~~~~~~l~rsvvv~at  209 (461)
T PRK12597        138 CPIAKGGKTGLFGGAGVGKTVL-MMELIFNISKQ-----HSG--SSVFAGVGERSREGHELYHEMKESGVLDKTVMVYGQ  209 (461)
T ss_pred             CccccCCEEEeecCCCCChhHH-HHHHHHHHHhh-----CCC--EEEEEcCCcchHHHHHHHHHHHhcCCcceeEEEecC
Confidence            3566789999999999999976 33344444321     112  333443334445555555555 11 22 34445544


Q ss_pred             CCCCCeeEEeccch-----hhhchHHHhcCCCCeEEEEecch
Q psy14082         80 TPKGPQDCLPLHRF-----VFNCQYEMAKNPAFKVIVFVETK  116 (233)
Q Consensus        80 ~~~~~~~lv~l~r~-----~~~~~~~~~~~~~~k~iIf~~~~  116 (233)
                      .+..+-     .|+     ---+.+++....+..++++..+.
T Consensus       210 sd~~~~-----~R~~a~~~a~tiAEyfrd~~G~~VLl~~Dsl  246 (461)
T PRK12597        210 MNEPPG-----ARMRVVLTGLTIAEYLRDEEKEDVLLFIDNI  246 (461)
T ss_pred             CCCCHH-----HHHHHHHHHHHHHHHHHHhcCCceEEEeccc
Confidence            444321     121     11123345444477787777653

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

Probab=89.67  E-value=1.8  Score=42.79  Aligned_cols=59  Identities=14%  Similarity=0.112  Sum_probs=52.7

Q ss_pred             CCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhC--CCCCEEEecc
Q psy14082        106 AFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQ--GKAPILVATD  164 (233)
Q Consensus       106 ~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~--g~~~iLv~T~  164 (233)
                      .+.+||.++++.-+..-...|...|+.+..+.++++..++.++++.+..  |++++|++|+
T Consensus       500 ~GiTLVISPLiSLmqDQV~~L~~~GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTP  560 (1195)
T PLN03137        500 PGITLVISPLVSLIQDQIMNLLQANIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTP  560 (1195)
T ss_pred             CCcEEEEeCHHHHHHHHHHHHHhCCCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEECh
Confidence            4689999999999986677777889999999999999999999999877  8899999996

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

Probab=89.61  E-value=3.7  Score=30.52  Aligned_cols=72  Identities=22%  Similarity=0.366  Sum_probs=51.4

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHH-HHHHHHHHhhCCCCCEEEecc-----cCc-CCcCC
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQ-DRDYVLNDFRQGKAPILVATD-----VAA-RGLDV  172 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~-~r~~~~~~f~~g~~~iLv~T~-----~~~-~Gldi  172 (233)
                      .+..++++.++++..++...+.+.+.    +.++..+|++.+.. +....+    .++.+|+|+|.     ... ...++
T Consensus        42 ~~~~~~lii~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilv~T~~~l~~~~~~~~~~~  117 (169)
T PF00270_consen   42 GKDARVLIIVPTRALAEQQFERLRKFFSNTNVRVVLLHGGQSISEDQREVL----SNQADILVTTPEQLLDLISNGKINI  117 (169)
T ss_dssp             TSSSEEEEEESSHHHHHHHHHHHHHHTTTTTSSEEEESTTSCHHHHHHHHH----HTTSSEEEEEHHHHHHHHHTTSSTG
T ss_pred             CCCceEEEEeecccccccccccccccccccccccccccccccccccccccc----cccccccccCcchhhcccccccccc
Confidence            35569999999999999999888764    35788889988855 333333    56789999993     222 23466


Q ss_pred             CCccEEE
Q psy14082        173 EDVNTVN  179 (233)
Q Consensus       173 ~~v~~VI  179 (233)
                      ..+++||
T Consensus       118 ~~~~~iV  124 (169)
T PF00270_consen  118 SRLSLIV  124 (169)
T ss_dssp             TTESEEE
T ss_pred             ccceeec
Confidence            6677665

Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0008026 ATP-dependent helicase activity; PDB: 3RRM_A 3RRN_A 3PEW_A 2KBE_A 3PEY_A 3FHO_A 2ZJA_A 2ZJ8_A 2ZJ5_A 2ZJ2_A ....

>TIGR03324 alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit alpha

Probab=89.56  E-value=6.4  Score=35.47  Aligned_cols=23  Identities=13%  Similarity=-0.028  Sum_probs=19.2

Q ss_pred             CCCCCCCCceeEecCCCCCchHH
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~   24 (233)
                      +-++-+|+-..+.+..|+|||..
T Consensus       156 l~pigrGQR~~Ifg~~g~GKT~L  178 (497)
T TIGR03324       156 LIPIGRGQRELILGDRQTGKTAI  178 (497)
T ss_pred             cCCcccCCEEEeecCCCCCHHHH
Confidence            34567899999999999999975

A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 alpha subunit of this apparent second ATP synthase.

>PRK11823 DNA repair protein RadA; Provisional

Probab=89.52  E-value=0.71  Score=41.06  Aligned_cols=53  Identities=19%  Similarity=0.155  Sum_probs=37.0

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ..|.-+++.+++|+|||.. ++-+...+..       .+.+++++. +.|-..|+....+++
T Consensus        78 ~~Gs~~lI~G~pG~GKTtL-~lq~a~~~a~-------~g~~vlYvs-~Ees~~qi~~ra~rl  130 (446)
T PRK11823         78 VPGSVVLIGGDPGIGKSTL-LLQVAARLAA-------AGGKVLYVS-GEESASQIKLRAERL  130 (446)
T ss_pred             cCCEEEEEECCCCCCHHHH-HHHHHHHHHh-------cCCeEEEEE-ccccHHHHHHHHHHc
Confidence            4577788999999999954 4444444432       255788876 456778888877777

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=89.49  E-value=8.6  Score=33.72  Aligned_cols=110  Identities=6%  Similarity=0.087  Sum_probs=56.0

Q ss_pred             CCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCCC
Q psy14082          3 PPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPK   82 (233)
Q Consensus         3 p~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~   82 (233)
                      -++=.|+-..+.|+.|+|||.. +--+.+.+..+     ..... ++++-..|--..+.+..+.+. +   .++.+..+.
T Consensus       164 ~PIGkGQR~lIvgppGvGKTTL-aK~Ian~I~~n-----hFDv~-~~VvLIgER~~EVtdiqrsIl-g---~vv~st~d~  232 (416)
T PRK09376        164 APIGKGQRGLIVAPPKAGKTVL-LQNIANSITTN-----HPEVH-LIVLLIDERPEEVTDMQRSVK-G---EVVASTFDE  232 (416)
T ss_pred             cccccCceEEEeCCCCCChhHH-HHHHHHHHHhh-----cCCeE-EEEEEeCCchhHHHHHHHHhc-C---cEEEECCCC
Confidence            3566788889999999999954 55566655543     12333 333334444344444444442 1   233333333


Q ss_pred             CCe--eEEeccchhhhchHHHhcCCCCeEEEEecchhHHHHHHHHH
Q psy14082         83 GPQ--DCLPLHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRAL  126 (233)
Q Consensus        83 ~~~--~lv~l~r~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L  126 (233)
                      .+.  ..++ ...+...+ .+. ..+..+++|..+......-....
T Consensus       233 ~~~~~~~~a-~~~ie~Ae-~~~-e~G~dVlL~iDsItR~arAqrev  275 (416)
T PRK09376        233 PAERHVQVA-EMVIEKAK-RLV-EHGKDVVILLDSITRLARAYNTV  275 (416)
T ss_pred             CHHHHHHHH-HHHHHHHH-HHH-HcCCCEEEEEEChHHHHHHHHhh
Confidence            222  1110 00111112 222 56789999998866554444433

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=89.46  E-value=0.54  Score=40.56  Aligned_cols=28  Identities=4%  Similarity=-0.155  Sum_probs=20.8

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhc
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISH   35 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~   35 (233)
                      .+--+++.+|||||||.. +-.++..+..
T Consensus       133 ~~glilI~GpTGSGKTTt-L~aLl~~i~~  160 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTL-LAAIIRELAE  160 (358)
T ss_pred             cCCEEEEECCCCCCHHHH-HHHHHHHHhh
Confidence            355689999999999966 5556666643

Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems.

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=89.43  E-value=0.56  Score=35.90  Aligned_cols=46  Identities=7%  Similarity=-0.037  Sum_probs=31.2

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      +++.+++||||| +|+.-++..          .+.++++++..+.+-..+.+.+.+.
T Consensus         2 ~li~G~~~sGKS-~~a~~~~~~----------~~~~~~y~at~~~~d~em~~rI~~H   47 (169)
T cd00544           2 ILVTGGARSGKS-RFAERLAAE----------LGGPVTYIATAEAFDDEMAERIARH   47 (169)
T ss_pred             EEEECCCCCCHH-HHHHHHHHh----------cCCCeEEEEccCcCCHHHHHHHHHH
Confidence            478899999999 444433322          2457899988777766666665554

CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]

Probab=89.35  E-value=0.46  Score=40.40  Aligned_cols=127  Identities=9%  Similarity=0.002  Sum_probs=63.4

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCCCCCeeE
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPKGPQDC   87 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~~~~~l   87 (233)
                      .+++++++.||||||.. +-.+...+.        ..-|++.+=-|.||-.+.-...         .+..-..+....--
T Consensus       173 r~NILisGGTGSGKTTl-LNal~~~i~--------~~eRvItiEDtaELql~~ph~v---------rL~TR~~n~Eg~ge  234 (355)
T COG4962         173 RCNILISGGTGSGKTTL-LNALSGFID--------SDERVITIEDTAELQLAHPHVV---------RLETRPPNVEGTGE  234 (355)
T ss_pred             ceeEEEeCCCCCCHHHH-HHHHHhcCC--------CcccEEEEeehhhhccCCCceE---------EEeecCCCCCCcce
Confidence            35899999999999965 333333332        2338898888888843321111         11111111111111


Q ss_pred             EeccchhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHh-hCCCeeEEEeCCCCHHHHHHHHHHhhCCC
Q psy14082         88 LPLHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALR-RERHSAICIHGDKTQQDRDYVLNDFRQGK  156 (233)
Q Consensus        88 v~l~r~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~-~~~~~~~~~~~~~~~~~r~~~~~~f~~g~  156 (233)
                      |.   +-++++..+...+..-.+-=|.- ..+..+.+.+. .+.=....+|+..+.+.-....+.+..+.
T Consensus       235 vt---m~dLvkn~LRmRPDRIiVGEVRG-~Ea~dLL~AmnTGHdG~~~TlHans~~ea~~rle~l~~~~~  300 (355)
T COG4962         235 VT---MRDLVKNALRMRPDRIIVGEVRG-VEALDLLQAMNTGHDGGMGTLHANSPREALTRLEQLIAEGG  300 (355)
T ss_pred             EE---HHHHHHHHhhcCccceEEEEecC-ccHHHHHHHhccCCCCcceeeccCCHHHHHHHHHHHHHhhc
Confidence            22   23444444444444433333332 33444444441 22225677898877776666665555443

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=89.34  E-value=0.54  Score=36.41  Aligned_cols=26  Identities=4%  Similarity=-0.254  Sum_probs=19.1

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHh
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVH   32 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~   32 (233)
                      ..|..+++.++||||||.. +-.++..
T Consensus        23 ~~g~~i~I~G~tGSGKTTl-l~aL~~~   48 (186)
T cd01130          23 EARKNILISGGTGSGKTTL-LNALLAF   48 (186)
T ss_pred             hCCCEEEEECCCCCCHHHH-HHHHHhh
Confidence            3578899999999999965 3334433

The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.

>PRK04296 thymidine kinase; Provisional

Probab=89.31  E-value=0.48  Score=36.91  Aligned_cols=36  Identities=19%  Similarity=0.139  Sum_probs=25.4

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcC
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAP   52 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~P   52 (233)
                      .=.++.+++|+|||.. ++-.+.++..       .+.+++++-|
T Consensus         3 ~i~litG~~GsGKTT~-~l~~~~~~~~-------~g~~v~i~k~   38 (190)
T PRK04296          3 KLEFIYGAMNSGKSTE-LLQRAYNYEE-------RGMKVLVFKP   38 (190)
T ss_pred             EEEEEECCCCCHHHHH-HHHHHHHHHH-------cCCeEEEEec
Confidence            3457788999999965 5556665543       3667888877

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=89.31  E-value=0.72  Score=41.47  Aligned_cols=55  Identities=16%  Similarity=-0.032  Sum_probs=39.4

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      +++|+-+++.+++|||||.-.+--+.+.+.+       .+..+|+++- .|-..++.+.+..+
T Consensus        18 lp~g~~~Li~G~pGsGKT~la~qfl~~g~~~-------~ge~~lyvs~-eE~~~~l~~~~~~~   72 (484)
T TIGR02655        18 LPIGRSTLVSGTSGTGKTLFSIQFLYNGIIH-------FDEPGVFVTF-EESPQDIIKNARSF   72 (484)
T ss_pred             CCCCeEEEEEcCCCCCHHHHHHHHHHHHHHh-------CCCCEEEEEE-ecCHHHHHHHHHHc
Confidence            4678999999999999996644333443322       2456787774 47788888888888

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>PF05872 DUF853: Bacterial protein of unknown function (DUF853); InterPro: IPR008571 Members of this family have a P-loop containing nucleotide triphosphate hydrolases fold

Probab=89.31  E-value=0.16  Score=44.68  Aligned_cols=32  Identities=13%  Similarity=-0.034  Sum_probs=25.2

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhh
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      ||+-+..||-++.++||||||.+ +--+.+.+-
T Consensus        13 l~~~~~NRHGLIaGATGTGKTvT-LqvlAE~fS   44 (502)
T PF05872_consen   13 LPLKMANRHGLIAGATGTGKTVT-LQVLAEQFS   44 (502)
T ss_pred             cChhhccccceeeccCCCCceeh-HHHHHHHhh
Confidence            67778899999999999999988 333555443

This family is restricted to bacterial proteins, none of which have currently been characterised.

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=89.21  E-value=2.7  Score=36.72  Aligned_cols=135  Identities=8%  Similarity=-0.003  Sum_probs=71.9

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEc--CcHHHHHHHHHHHHHhhcCCcEEEEEcCCCCCCe
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLA--PTRELAQQIQTVAKEFSSALRNICIFGGTPKGPQ   85 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~--PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~~~~   85 (233)
                      ++-+...+|||.|||.+-+- +..+....     .+..++-||+  ..|-=|....+.+.+. .++.+...+...+-.. 
T Consensus       203 ~~vi~LVGPTGVGKTTTlAK-LAar~~~~-----~~~~kVaiITtDtYRIGA~EQLk~Ya~i-m~vp~~vv~~~~el~~-  274 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAK-LAARYVML-----KKKKKVAIITTDTYRIGAVEQLKTYADI-MGVPLEVVYSPKELAE-  274 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHH-HHHHHHhh-----ccCcceEEEEeccchhhHHHHHHHHHHH-hCCceEEecCHHHHHH-
Confidence            67788999999999987443 22222211     1233344443  3343333333333332 2444444443322111 


Q ss_pred             eEEeccchhhhchHHHhcCCCCeEEEEecch-------hHHHHHHHHHhhC-CC-eeEEEeCCCCHHHHHHHHHHhhCCC
Q psy14082         86 DCLPLHRFVFNCQYEMAKNPAFKVIVFVETK-------KKVEDITRALRRE-RH-SAICIHGDKTQQDRDYVLNDFRQGK  156 (233)
Q Consensus        86 ~lv~l~r~~~~~~~~~~~~~~~k~iIf~~~~-------~~~~~l~~~L~~~-~~-~~~~~~~~~~~~~r~~~~~~f~~g~  156 (233)
                                .+.     .-...=+|++.|.       ...+++...+..- .+ ...++...+..++-.++++.|+.-.
T Consensus       275 ----------ai~-----~l~~~d~ILVDTaGrs~~D~~~i~el~~~~~~~~~i~~~Lvlsat~K~~dlkei~~~f~~~~  339 (407)
T COG1419         275 ----------AIE-----ALRDCDVILVDTAGRSQYDKEKIEELKELIDVSHSIEVYLVLSATTKYEDLKEIIKQFSLFP  339 (407)
T ss_pred             ----------HHH-----HhhcCCEEEEeCCCCCccCHHHHHHHHHHHhccccceEEEEEecCcchHHHHHHHHHhccCC
Confidence                      000     0111235666664       3334444444322 33 3456677888899999999999988


Q ss_pred             CCEEEeccc
Q psy14082        157 APILVATDV  165 (233)
Q Consensus       157 ~~iLv~T~~  165 (233)
                      ++-+|-|-+
T Consensus       340 i~~~I~TKl  348 (407)
T COG1419         340 IDGLIFTKL  348 (407)
T ss_pred             cceeEEEcc
Confidence            888888743

>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=89.20  E-value=0.5  Score=37.08  Aligned_cols=134  Identities=13%  Similarity=0.047  Sum_probs=60.3

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEc--CcHHHHHHHHHHHHHhhcCCcEEEEEcCCCCCCeeEE
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLA--PTRELAQQIQTVAKEFSSALRNICIFGGTPKGPQDCL   88 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~--PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~~~~~lv   88 (233)
                      ++..+|||+|||.+. .=+..++..+       +.++.+++  ..|.=+.+   +++.+...+.+-........++.   
T Consensus         4 i~lvGptGvGKTTt~-aKLAa~~~~~-------~~~v~lis~D~~R~ga~e---QL~~~a~~l~vp~~~~~~~~~~~---   69 (196)
T PF00448_consen    4 IALVGPTGVGKTTTI-AKLAARLKLK-------GKKVALISADTYRIGAVE---QLKTYAEILGVPFYVARTESDPA---   69 (196)
T ss_dssp             EEEEESTTSSHHHHH-HHHHHHHHHT-------T--EEEEEESTSSTHHHH---HHHHHHHHHTEEEEESSTTSCHH---
T ss_pred             EEEECCCCCchHhHH-HHHHHHHhhc-------cccceeecCCCCCccHHH---HHHHHHHHhccccchhhcchhhH---
Confidence            577899999999873 3344444332       33455554  33433333   33333222333333322222221   


Q ss_pred             eccchhhhchHH---HhcCCCCeEEEEecch-----hHHHHHHHHHhhC-CC-eeEEEeCCCCHHHHHHHHHHhhCCCCC
Q psy14082         89 PLHRFVFNCQYE---MAKNPAFKVIVFVETK-----KKVEDITRALRRE-RH-SAICIHGDKTQQDRDYVLNDFRQGKAP  158 (233)
Q Consensus        89 ~l~r~~~~~~~~---~~~~~~~k~iIf~~~~-----~~~~~l~~~L~~~-~~-~~~~~~~~~~~~~r~~~~~~f~~g~~~  158 (233)
                            ++..+.   .......-++|=+.-+     ...+++.+.+... .. ...++.+.+.+++-..+.+.+....+.
T Consensus        70 ------~~~~~~l~~~~~~~~D~vlIDT~Gr~~~d~~~~~el~~~~~~~~~~~~~LVlsa~~~~~~~~~~~~~~~~~~~~  143 (196)
T PF00448_consen   70 ------EIAREALEKFRKKGYDLVLIDTAGRSPRDEELLEELKKLLEALNPDEVHLVLSATMGQEDLEQALAFYEAFGID  143 (196)
T ss_dssp             ------HHHHHHHHHHHHTTSSEEEEEE-SSSSTHHHHHHHHHHHHHHHSSSEEEEEEEGGGGGHHHHHHHHHHHHSSTC
T ss_pred             ------HHHHHHHHHHhhcCCCEEEEecCCcchhhHHHHHHHHHHhhhcCCccceEEEecccChHHHHHHHHHhhcccCc
Confidence                  111111   1122223334433321     2234444444332 33 334556666666666555555555677


Q ss_pred             EEEecc
Q psy14082        159 ILVATD  164 (233)
Q Consensus       159 iLv~T~  164 (233)
                      -+|-|.
T Consensus       144 ~lIlTK  149 (196)
T PF00448_consen  144 GLILTK  149 (196)
T ss_dssp             EEEEES
T ss_pred             eEEEEe
Confidence            677764

SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....

>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins

Probab=89.20  E-value=0.3  Score=42.02  Aligned_cols=28  Identities=7%  Similarity=-0.123  Sum_probs=20.6

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhh
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      ++|+-++..+|+|||||+. ++++.+.|-
T Consensus        48 ~aGr~iLiaGppGtGKTAl-A~~ia~eLG   75 (398)
T PF06068_consen   48 IAGRAILIAGPPGTGKTAL-AMAIAKELG   75 (398)
T ss_dssp             -TT-EEEEEE-TTSSHHHH-HHHHHHHCT
T ss_pred             ccCcEEEEeCCCCCCchHH-HHHHHHHhC
Confidence            5799999999999999966 676776664

The N-terminal domain contains the AAA ATPase, central region IPR003959 from INTERPRO domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway []. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases [].; GO: 0003678 DNA helicase activity, 0005524 ATP binding; PDB: 2XSZ_E 2CQA_A 2C9O_C.

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=89.15  E-value=0.44  Score=40.79  Aligned_cols=42  Identities=5%  Similarity=-0.100  Sum_probs=29.0

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHH
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELA   57 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~   57 (233)
                      .+..+++.++||||||.. +-.++..+.        ...+.+.+--+.||.
T Consensus       177 ~~~~ili~G~tGsGKTTl-l~al~~~i~--------~~~riv~iEd~~El~  218 (340)
T TIGR03819       177 ARLAFLISGGTGSGKTTL-LSALLALVA--------PDERIVLVEDAAELR  218 (340)
T ss_pred             CCCeEEEECCCCCCHHHH-HHHHHccCC--------CCCcEEEECCcceec
Confidence            467899999999999954 444444331        234577777777874

Members of this protein family comprise a distinct clade of putative ATPase associated with an integral membrane complex likely to act in pilus formation, secretion, or conjugal transfer. The association of most members with a nearby gene for a DEAH-box helicase suggests a role in conjugal transfer.

>KOG1533|consensus

Probab=89.09  E-value=0.45  Score=38.38  Aligned_cols=24  Identities=8%  Similarity=-0.168  Sum_probs=19.0

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhhc
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHISH   35 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~~   35 (233)
                      .++++|+||||| +|..-+.+.+..
T Consensus         5 qvVIGPPgSGKs-TYc~g~~~fls~   28 (290)
T KOG1533|consen    5 QVVIGPPGSGKS-TYCNGMSQFLSA   28 (290)
T ss_pred             eEEEcCCCCCcc-chhhhHHHHHHH
Confidence            478999999999 778777766654

>CHL00059 atpA ATP synthase CF1 alpha subunit

Probab=89.05  E-value=7  Score=35.12  Aligned_cols=22  Identities=9%  Similarity=-0.084  Sum_probs=19.0

Q ss_pred             CCCCCCCceeEecCCCCCchHH
Q psy14082          3 PPSESGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         3 p~~~~g~d~i~~a~tGsGKT~~   24 (233)
                      -++-+|+-..+.+..|+|||..
T Consensus       136 ~pigrGQR~~I~g~~g~GKt~L  157 (485)
T CHL00059        136 IPIGRGQRELIIGDRQTGKTAV  157 (485)
T ss_pred             cccccCCEEEeecCCCCCHHHH
Confidence            3567889999999999999976

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=88.99  E-value=0.38  Score=41.19  Aligned_cols=28  Identities=7%  Similarity=-0.166  Sum_probs=23.3

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhh
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      ++|+-++..+|+|||||+. ++.+.+-|-
T Consensus        63 ~aGrgiLi~GppgTGKTAl-A~gIa~eLG   90 (450)
T COG1224          63 MAGRGILIVGPPGTGKTAL-AMGIARELG   90 (450)
T ss_pred             ccccEEEEECCCCCcHHHH-HHHHHHHhC
Confidence            6799999999999999966 676776664

>COG4185 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=88.95  E-value=0.2  Score=37.93  Aligned_cols=38  Identities=21%  Similarity=0.152  Sum_probs=24.9

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHH
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQI   60 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~   60 (233)
                      .|+.++.|||||..|.......+          +  ..+.+.+-|+|.|+
T Consensus         5 ~IvaG~NGsGKstv~~~~~~~~~----------~--~~~~VN~D~iA~~i   42 (187)
T COG4185           5 DIVAGPNGSGKSTVYASTLAPLL----------P--GIVFVNADEIAAQI   42 (187)
T ss_pred             EEEecCCCCCceeeeeccchhhc----------C--CeEEECHHHHhhhc
Confidence            46789999999998876444322          1  45566666666554

>PRK09401 reverse gyrase; Reviewed

Probab=88.91  E-value=1.5  Score=43.84  Aligned_cols=60  Identities=20%  Similarity=0.325  Sum_probs=48.8

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCC----CeeEEE--eCCCCHHHHHHHHHHhhCCCCCEEEecc
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRER----HSAICI--HGDKTQQDRDYVLNDFRQGKAPILVATD  164 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~----~~~~~~--~~~~~~~~r~~~~~~f~~g~~~iLv~T~  164 (233)
                      .+.+++|.++|+.-+.++++.+++.+    ..+..+  |++++.+++.+..+.+++|..+|+|+|.
T Consensus       122 ~g~~alIL~PTreLa~Qi~~~l~~l~~~~~~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp  187 (1176)
T PRK09401        122 KGKKSYIIFPTRLLVEQVVEKLEKFGEKVGCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTS  187 (1176)
T ss_pred             cCCeEEEEeccHHHHHHHHHHHHHHhhhcCceEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECH
Confidence            57899999999999999999998653    344434  4556678888888999999999999993

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A

Probab=88.91  E-value=0.21  Score=41.29  Aligned_cols=25  Identities=4%  Similarity=-0.229  Sum_probs=19.2

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHH
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAV   31 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~   31 (233)
                      -+++.+++.+|||+|||.. +--.++
T Consensus        31 ~~~~pvLl~G~~GtGKT~l-i~~~l~   55 (272)
T PF12775_consen   31 SNGRPVLLVGPSGTGKTSL-IQNFLS   55 (272)
T ss_dssp             HCTEEEEEESSTTSSHHHH-HHHHHH
T ss_pred             HcCCcEEEECCCCCchhHH-HHhhhc
Confidence            3688899999999999976 333443

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=88.91  E-value=0.51  Score=38.88  Aligned_cols=24  Identities=4%  Similarity=-0.139  Sum_probs=18.6

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhhh
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      -+++.++||||||.. +-.+++.+.
T Consensus        82 lilisG~tGSGKTT~-l~all~~i~  105 (264)
T cd01129          82 IILVTGPTGSGKTTT-LYSALSELN  105 (264)
T ss_pred             EEEEECCCCCcHHHH-HHHHHhhhC
Confidence            488999999999965 566666663

It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=88.87  E-value=1.2  Score=35.67  Aligned_cols=54  Identities=4%  Similarity=-0.159  Sum_probs=35.5

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ++.|.=+++.+++|+|||.- +.-++....       .++.+++++.-. +-..++.+.+..+
T Consensus        22 ~~~g~~~~i~G~~GsGKt~l-~~~~~~~~~-------~~g~~~~y~~~e-~~~~~~~~~~~~~   75 (234)
T PRK06067         22 IPFPSLILIEGDHGTGKSVL-SQQFVYGAL-------KQGKKVYVITTE-NTSKSYLKQMESV   75 (234)
T ss_pred             CcCCcEEEEECCCCCChHHH-HHHHHHHHH-------hCCCEEEEEEcC-CCHHHHHHHHHHC
Confidence            46788899999999999955 333333222       235567776653 4556777777776

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=88.85  E-value=0.22  Score=35.71  Aligned_cols=26  Identities=8%  Similarity=-0.277  Sum_probs=15.5

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhh
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      .++-+++.+++|+|||.. +--+...+
T Consensus         3 ~~~~~~i~G~~G~GKT~~-~~~~~~~~   28 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTL-IKRLARQL   28 (131)
T ss_dssp             ----EEEEE-TTSSHHHH-HHHHHHHH
T ss_pred             CCcccEEEcCCCCCHHHH-HHHHHHHh
Confidence            356689999999999976 44444444

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=88.84  E-value=1  Score=40.01  Aligned_cols=49  Identities=6%  Similarity=-0.059  Sum_probs=32.1

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHH
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVA   64 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~   64 (233)
                      +.+++.+++|+|||.. +-.+.+.+.++     ..+.+++++ +..++..+....+
T Consensus       149 ~~l~l~G~~G~GKThL-~~ai~~~~~~~-----~~~~~v~yi-~~~~~~~~~~~~~  197 (450)
T PRK00149        149 NPLFIYGGVGLGKTHL-LHAIGNYILEK-----NPNAKVVYV-TSEKFTNDFVNAL  197 (450)
T ss_pred             CeEEEECCCCCCHHHH-HHHHHHHHHHh-----CCCCeEEEE-EHHHHHHHHHHHH
Confidence            4588999999999976 55666666543     235566665 5456665554443

>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type

Probab=88.83  E-value=1.2  Score=44.34  Aligned_cols=55  Identities=9%  Similarity=-0.082  Sum_probs=41.8

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      .+.+++.|+-|||||.+-.--++..+...     .....+++|+-|+.-|..+.+++...
T Consensus        10 ~~~~~~~a~agsgkt~~l~~~~~~~~~~~-----~~~~~i~~~t~t~~aa~em~~Ri~~~   64 (1141)
T TIGR02784        10 KTSAWVSANAGSGKTHVLTQRVIRLLLNG-----VPPSKILCLTYTKAAAAEMQNRVFDR   64 (1141)
T ss_pred             CCCEEEEEECCCCHHHHHHHHHHHHHHcC-----CCCCeEEEEecCHHHHHHHHHHHHHH
Confidence            35689999999999988655555555432     12347999999999999988888766

AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the alphaproteobacteria (as modeled here) and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species.

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=88.82  E-value=1  Score=39.37  Aligned_cols=48  Identities=6%  Similarity=-0.033  Sum_probs=31.4

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHH
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTV   63 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~   63 (233)
                      +-+++.+++|+|||.. +..+.+.+.++     ..+.+++++. ..++..++...
T Consensus       137 n~l~l~G~~G~GKThL-~~ai~~~l~~~-----~~~~~v~yi~-~~~~~~~~~~~  184 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHL-LHAIGNEILEN-----NPNAKVVYVS-SEKFTNDFVNA  184 (405)
T ss_pred             CeEEEECCCCCcHHHH-HHHHHHHHHHh-----CCCCcEEEEE-HHHHHHHHHHH
Confidence            4578999999999976 56667666543     2345677764 44555554443

DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=88.81  E-value=0.58  Score=37.38  Aligned_cols=48  Identities=15%  Similarity=0.065  Sum_probs=31.4

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHH
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVA   64 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~   64 (233)
                      -+++.+++|+|||.. +-++.+.+.+.     .++.+++++.. .+......+.+
T Consensus        36 ~l~l~G~~G~GKTHL-L~Ai~~~~~~~-----~~~~~v~y~~~-~~f~~~~~~~~   83 (219)
T PF00308_consen   36 PLFLYGPSGLGKTHL-LQAIANEAQKQ-----HPGKRVVYLSA-EEFIREFADAL   83 (219)
T ss_dssp             EEEEEESTTSSHHHH-HHHHHHHHHHH-----CTTS-EEEEEH-HHHHHHHHHHH
T ss_pred             ceEEECCCCCCHHHH-HHHHHHHHHhc-----cccccceeecH-HHHHHHHHHHH
Confidence            479999999999985 66677766654     34667777654 35555444433

DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=88.75  E-value=0.58  Score=38.40  Aligned_cols=54  Identities=9%  Similarity=-0.080  Sum_probs=32.8

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ..|.-+++.++||+|||.. +.-+...+..+      .+..++++.- -+-..++...+...
T Consensus        28 ~~g~~~~i~g~~G~GKT~l-~~~~~~~~~~~------~g~~vl~iS~-E~~~~~~~~r~~~~   81 (271)
T cd01122          28 RKGELIILTAGTGVGKTTF-LREYALDLITQ------HGVRVGTISL-EEPVVRTARRLLGQ   81 (271)
T ss_pred             cCCcEEEEEcCCCCCHHHH-HHHHHHHHHHh------cCceEEEEEc-ccCHHHHHHHHHHH
Confidence            4577788999999999954 44444444321      2566777763 23345555555443

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=88.47  E-value=1.5  Score=38.19  Aligned_cols=53  Identities=6%  Similarity=-0.049  Sum_probs=41.5

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHH-HHHHHHHHHHHh
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRE-LAQQIQTVAKEF   67 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~Ptre-L~~Q~~~~~~~~   67 (233)
                      -.+..+..|||||.+.+.-++..++..     .++.+++++-|+.. |..-++..+...
T Consensus         3 ~~i~~GgrgSGKS~~~~~~~~~~~~~~-----~~~~~~~~~r~~~~sl~~sv~~~l~~~   56 (396)
T TIGR01547         3 EIIAKGGRRSGKTFAIALKLVEKLAIN-----KKQQNILAARKVQNSIRDSVFKDIENL   56 (396)
T ss_pred             eEEEeCCCCcccHHHHHHHHHHHHHhc-----CCCcEEEEEehhhhHHHHHHHHHHHHH
Confidence            467889999999999888888888764     14678999989887 666667776654

This model detects members of a highly divergent family of the large subunit of phage terminase. All members are encoded by phage genomes or within prophage regions of bacterial genomes. This is a distinct family from pfam03354.

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=88.47  E-value=1.1  Score=37.36  Aligned_cols=52  Identities=6%  Similarity=0.030  Sum_probs=28.3

Q ss_pred             cCCCCeEEEEecchhHHHHHH---HHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCC
Q psy14082        103 KNPAFKVIVFVETKKKVEDIT---RALRRERHSAICIHGDKTQQDRDYVLNDFRQG  155 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~---~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g  155 (233)
                      .....-.+|++.+.+..+.+.   ..|..+ +...+.-..++.+++..+++.|-..
T Consensus       156 ~~~~~~~vI~a~~~~~~~~~~~~np~L~sR-~~~~i~fp~l~~edl~~I~~~~l~~  210 (284)
T TIGR02880       156 NQRDDLVVILAGYKDRMDSFFESNPGFSSR-VAHHVDFPDYSEAELLVIAGLMLKE  210 (284)
T ss_pred             cCCCCEEEEEeCCcHHHHHHHhhCHHHHhh-CCcEEEeCCcCHHHHHHHHHHHHHH
Confidence            334455677776655444432   222222 1222334556788888888887544

Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis.

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=88.39  E-value=6.1  Score=32.26  Aligned_cols=21  Identities=10%  Similarity=-0.012  Sum_probs=17.8

Q ss_pred             CCCCCCceeEecCCCCCchHH
Q psy14082          4 PSESGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         4 ~~~~g~d~i~~a~tGsGKT~~   24 (233)
                      ++-.|.-+.+.++.|+|||..
T Consensus        12 ~i~~Gqr~~I~G~~G~GKTTL   32 (249)
T cd01128          12 PIGKGQRGLIVAPPKAGKTTL   32 (249)
T ss_pred             ccCCCCEEEEECCCCCCHHHH
Confidence            456788999999999999953

It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=88.36  E-value=1.2  Score=39.59  Aligned_cols=49  Identities=10%  Similarity=-0.065  Sum_probs=31.9

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHH
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVA   64 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~   64 (233)
                      +-+++.+++|+|||.. +-.+.+.+...     .++.+++++.+ .++..++.+.+
T Consensus       142 npl~i~G~~G~GKTHL-l~Ai~~~l~~~-----~~~~~v~yv~~-~~f~~~~~~~l  190 (450)
T PRK14087        142 NPLFIYGESGMGKTHL-LKAAKNYIESN-----FSDLKVSYMSG-DEFARKAVDIL  190 (450)
T ss_pred             CceEEECCCCCcHHHH-HHHHHHHHHHh-----CCCCeEEEEEH-HHHHHHHHHHH
Confidence            4588999999999955 45566655543     33566766554 56666655443

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

Probab=88.34  E-value=2  Score=38.36  Aligned_cols=71  Identities=23%  Similarity=0.293  Sum_probs=55.1

Q ss_pred             eEEEEecchhHHHHHHHHHhhC-CC---eeEEEeCCCCHHHHHHHHHHhhCCCCCEEEec------ccCcCCcCCCCccE
Q psy14082        108 KVIVFVETKKKVEDITRALRRE-RH---SAICIHGDKTQQDRDYVLNDFRQGKAPILVAT------DVAARGLDVEDVNT  177 (233)
Q Consensus       108 k~iIf~~~~~~~~~l~~~L~~~-~~---~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T------~~~~~Gldi~~v~~  177 (233)
                      ++|+..+|+--+.+-+..+.+- ++   .+..++|..++++|.+.+..     .+|.|+|      |+.+-=+|+.++.+
T Consensus        60 kvlfLAPTKPLV~Qh~~~~~~v~~ip~~~i~~ltGev~p~~R~~~w~~-----~kVfvaTPQvveNDl~~Grid~~dv~~  134 (542)
T COG1111          60 KVLFLAPTKPLVLQHAEFCRKVTGIPEDEIAALTGEVRPEEREELWAK-----KKVFVATPQVVENDLKAGRIDLDDVSL  134 (542)
T ss_pred             eEEEecCCchHHHHHHHHHHHHhCCChhheeeecCCCChHHHHHHHhh-----CCEEEeccHHHHhHHhcCccChHHceE
Confidence            8999999997777766666542 44   56799999999999998774     6899999      44444499999998


Q ss_pred             EEEecCC
Q psy14082        178 VNIGSLQ  184 (233)
Q Consensus       178 VI~~d~P  184 (233)
                      +| ||--
T Consensus       135 li-fDEA  140 (542)
T COG1111         135 LI-FDEA  140 (542)
T ss_pred             EE-echh
Confidence            87 5543

>PF05729 NACHT: NACHT domain

Probab=88.32  E-value=0.9  Score=33.70  Aligned_cols=25  Identities=4%  Similarity=-0.146  Sum_probs=19.1

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhhcc
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHISHQ   36 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~~~   36 (233)
                      +++.+++|+|||.. +--++..+...
T Consensus         3 l~I~G~~G~GKStl-l~~~~~~~~~~   27 (166)
T PF05729_consen    3 LWISGEPGSGKSTL-LRKLAQQLAEE   27 (166)
T ss_pred             EEEECCCCCChHHH-HHHHHHHHHhc
Confidence            68899999999965 55666666554

>KOG1807|consensus

Probab=88.07  E-value=0.89  Score=42.60  Aligned_cols=70  Identities=11%  Similarity=-0.143  Sum_probs=45.1

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCCCC
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPKG   83 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~~   83 (233)
                      -.++++|+|+|||++- +-+++.++.+....... -..|+.|-|..-++|....+..  .+-...+..|+...+
T Consensus       395 lsliqgppGTgkt~vt-lkav~tLL~n~s~~~~~-epIlvvC~Tnhavdq~ligiy~--~qrpsImr~gsr~~s  464 (1025)
T KOG1807|consen  395 LSLIQGPPGTGKTLVT-LKAVDTLLLNSSGYTEP-EPILVVCLTNHAVDQYLIGIYY--HQRPSIMRQGSRFFS  464 (1025)
T ss_pred             hheeecCCCCCceeeh-HHHHHHHHhcccccccc-cceeeeehhhHHHHHHHHHHHh--cCCceEEEeccccCC
Confidence            3588999999999994 45777777765333222 3368889888888887666643  122334445554443

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=87.94  E-value=0.39  Score=39.35  Aligned_cols=28  Identities=7%  Similarity=-0.299  Sum_probs=19.7

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhh
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      .....+++..+|+|||||.. +-.+...+
T Consensus        39 ~~~~~~vll~GppGtGKTtl-A~~ia~~l   66 (261)
T TIGR02881        39 SKQVLHMIFKGNPGTGKTTV-ARILGKLF   66 (261)
T ss_pred             CCCcceEEEEcCCCCCHHHH-HHHHHHHH
Confidence            34567899999999999966 33344333

Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group.

>PF01580 FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR002543 The FtsK/SpoIIIE domain is found extensively in a wide variety of proteins from prokaryotes and plasmids [] some of which contain up to three copies

Probab=87.87  E-value=0.84  Score=35.79  Aligned_cols=27  Identities=0%  Similarity=-0.215  Sum_probs=17.9

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhc
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISH   35 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~   35 (233)
                      ..++++.++||||||.+ +..++..+..
T Consensus        38 ~~h~li~G~tgsGKS~~-l~~ll~~l~~   64 (205)
T PF01580_consen   38 NPHLLIAGATGSGKSTL-LRTLLLSLAL   64 (205)
T ss_dssp             S-SEEEE--TTSSHHHH-HHHHHHHHHT
T ss_pred             CceEEEEcCCCCCccHH-HHHHHHHHHH
Confidence            34899999999999976 5555555554

The domain contains a putative ATP binding P-loop motif. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification []. The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer []. ; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0005524 ATP binding, 0007049 cell cycle, 0007059 chromosome segregation, 0051301 cell division, 0016021 integral to membrane; PDB: 2IUS_E 2IUU_A 2IUT_A.

>KOG1942|consensus

Probab=87.74  E-value=0.51  Score=39.39  Aligned_cols=28  Identities=7%  Similarity=-0.110  Sum_probs=23.7

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhh
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      ++|+.++..+|+|+|||+. ++++.+.+-
T Consensus        62 maGravLlaGppgtGKTAl-AlaisqELG   89 (456)
T KOG1942|consen   62 MAGRAVLLAGPPGTGKTAL-ALAISQELG   89 (456)
T ss_pred             ccCcEEEEecCCCCchhHH-HHHHHHHhC
Confidence            6799999999999999966 777777664

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=87.71  E-value=1.3  Score=32.67  Aligned_cols=38  Identities=13%  Similarity=0.012  Sum_probs=23.6

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHH
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTREL   56 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL   56 (233)
                      +++.+++|+|||.. +.-++.....       .+..++++.....+
T Consensus         2 ~~i~G~~G~GKT~l-~~~i~~~~~~-------~~~~v~~~~~e~~~   39 (165)
T cd01120           2 ILVFGPTGSGKTTL-ALQLALNIAT-------KGGKVVYVDIEEEI   39 (165)
T ss_pred             eeEeCCCCCCHHHH-HHHHHHHHHh-------cCCEEEEEECCcch
Confidence            57899999999965 4434443322       35567777654333

This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta

Probab=87.68  E-value=12  Score=33.35  Aligned_cols=100  Identities=13%  Similarity=0.146  Sum_probs=52.5

Q ss_pred             CCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh-h-cCC-cEEEEEcC
Q psy14082          3 PPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF-S-SAL-RNICIFGG   79 (233)
Q Consensus         3 p~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~-~-~~~-~~~~~~gg   79 (233)
                      -++-.|+-+.+.++.|+|||.. +.-++.....+     ..  -+.|++--=|-...+.+.++.+ . ..+ ++.++.+.
T Consensus       133 ~pigkGQr~~Ifg~~G~GKt~l-~~~~~~~~~~~-----~~--~v~V~~~iGeR~rEv~e~~~~~~~~~~l~rtvvv~~t  204 (449)
T TIGR03305       133 VPLERGGKAGLFGGAGVGKTVL-LTEMIHNMVGQ-----HQ--GVSIFCGIGERCREGEELYREMKEAGVLDNTVMVFGQ  204 (449)
T ss_pred             cccccCCEEEeecCCCCChhHH-HHHHHHHHHhc-----CC--CEEEEEEeccCcHHHHHHHHHHhhccccceEEEEEeC
Confidence            3567899999999999999966 44344333211     11  2344444434455555555555 1 122 34445544


Q ss_pred             CCCCCeeEEeccchh-----hhchHHHhcCCCCeEEEEecc
Q psy14082         80 TPKGPQDCLPLHRFV-----FNCQYEMAKNPAFKVIVFVET  115 (233)
Q Consensus        80 ~~~~~~~lv~l~r~~-----~~~~~~~~~~~~~k~iIf~~~  115 (233)
                      .+..+-     .|+.     --+.+++....+..++++..+
T Consensus       205 s~~~~~-----~r~~~~~~a~tiAEyfrd~~G~~VLl~~Ds  240 (449)
T TIGR03305       205 MNEPPG-----ARFRVGHTALTMAEYFRDDEKQDVLLLIDN  240 (449)
T ss_pred             CCCCHH-----HHHHHHHHHHHHHHHHHHhcCCceEEEecC
Confidence            444321     1211     112335554466777777765

A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 beta subunit of this apparent second ATP synthase.

>PF07088 GvpD: GvpD gas vesicle protein; InterPro: IPR009788 This family consists of several archaeal GvpD gas vesicle proteins

Probab=87.56  E-value=0.44  Score=41.34  Aligned_cols=38  Identities=8%  Similarity=-0.008  Sum_probs=28.5

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCc
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPT   53 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~Pt   53 (233)
                      .|+-.++.+.+||||| .|.+-++..+...        .-+++|+++
T Consensus         9 ~G~TLLIKG~PGTGKT-tfaLelL~~l~~~--------~~v~YISTR   46 (484)
T PF07088_consen    9 PGQTLLIKGEPGTGKT-TFALELLNSLKDH--------GNVMYISTR   46 (484)
T ss_pred             CCcEEEEecCCCCCce-eeehhhHHHHhcc--------CCeEEEEec
Confidence            4788999999999999 6688888877543        235666654

GvpD is thought to be involved in the regulation of gas vesicle formation [,].; GO: 0005524 ATP binding

>KOG1132|consensus

Probab=87.55  E-value=1.5  Score=41.63  Aligned_cols=26  Identities=0%  Similarity=-0.171  Sum_probs=19.8

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHh
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVH   32 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~   32 (233)
                      +..+.+..+|||||||++-+...+..
T Consensus        39 ~~q~~llESPTGTGKSLsLLCS~LAW   64 (945)
T KOG1132|consen   39 RKQNGLLESPTGTGKSLSLLCSTLAW   64 (945)
T ss_pred             HhhhhhccCCCCCCccHHHHHHHHHH
Confidence            45678999999999998866544433

>cd01524 RHOD_Pyr_redox Member of the Rhodanese Homology Domain superfamily

Probab=87.49  E-value=1.2  Score=29.78  Aligned_cols=38  Identities=13%  Similarity=0.128  Sum_probs=32.4

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCC
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKT  141 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~  141 (233)
                      ....++++||.+-..+...+..|++.|+++..+.|+++
T Consensus        49 ~~~~~vvl~c~~g~~a~~~a~~L~~~G~~v~~l~GG~~   86 (90)
T cd01524          49 PKDKEIIVYCAVGLRGYIAARILTQNGFKVKNLDGGYK   86 (90)
T ss_pred             CCCCcEEEEcCCChhHHHHHHHHHHCCCCEEEecCCHH
Confidence            34578999999888888899999999998888999875

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.

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=87.47  E-value=15  Score=32.18  Aligned_cols=32  Identities=9%  Similarity=0.052  Sum_probs=23.9

Q ss_pred             eEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc
Q psy14082        133 AICIHGDKTQQDRDYVLNDFRQGKAPILVATD  164 (233)
Q Consensus       133 ~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~  164 (233)
                      +.++..++...+-..+++.|..-...-+|-|-
T Consensus       320 ~LVLsag~~~~d~~~i~~~f~~l~i~glI~TK  351 (407)
T PRK12726        320 CFTFSSGMKSADVMTILPKLAEIPIDGFIITK  351 (407)
T ss_pred             EEECCCcccHHHHHHHHHhcCcCCCCEEEEEc
Confidence            34556677888888888889877777777773

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=87.43  E-value=0.33  Score=35.41  Aligned_cols=23  Identities=4%  Similarity=-0.311  Sum_probs=16.4

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhh
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      ++++.+++|+|||.. +--+...+
T Consensus         1 ~vlL~G~~G~GKt~l-~~~la~~~   23 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTL-ARELAALL   23 (139)
T ss_dssp             EEEEEESSSSSHHHH-HHHHHHHH
T ss_pred             CEEEECCCCCCHHHH-HHHHHHHh
Confidence            478999999999966 33344433

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of this ATPase AAA domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. This ATPase domain includes some proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NBX_X 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>PRK08972 fliI flagellum-specific ATP synthase; Validated

Probab=87.32  E-value=8.9  Score=34.06  Aligned_cols=20  Identities=5%  Similarity=-0.318  Sum_probs=16.5

Q ss_pred             CCCCCceeEecCCCCCchHH
Q psy14082          5 SESGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~   24 (233)
                      +-.|.-+.+.+++|+|||..
T Consensus       159 i~~GqrigI~G~sG~GKSTL  178 (444)
T PRK08972        159 VGKGQRMGLFAGSGVGKSVL  178 (444)
T ss_pred             EcCCCEEEEECCCCCChhHH
Confidence            34677888999999999965

>PRK05642 DNA replication initiation factor; Validated

Probab=87.27  E-value=1.5  Score=35.39  Aligned_cols=43  Identities=14%  Similarity=0.050  Sum_probs=28.0

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHH
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQI   60 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~   60 (233)
                      +.+++.+++|+|||.. +-.+.+.+..       .+.+++++. ..++....
T Consensus        46 ~~l~l~G~~G~GKTHL-l~a~~~~~~~-------~~~~v~y~~-~~~~~~~~   88 (234)
T PRK05642         46 SLIYLWGKDGVGRSHL-LQAACLRFEQ-------RGEPAVYLP-LAELLDRG   88 (234)
T ss_pred             CeEEEECCCCCCHHHH-HHHHHHHHHh-------CCCcEEEee-HHHHHhhh
Confidence            4578999999999966 4445554432       245666654 46776554

>PTZ00301 uridine kinase; Provisional

Probab=87.26  E-value=0.91  Score=36.05  Aligned_cols=22  Identities=0%  Similarity=-0.369  Sum_probs=15.1

Q ss_pred             eEecCCCCCchHHhHHHHHHhhh
Q psy14082         12 FSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus        12 i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      -+.+++|||||.. +-.+.+.+.
T Consensus         7 gIaG~SgSGKTTl-a~~l~~~l~   28 (210)
T PTZ00301          7 GISGASGSGKSSL-STNIVSELM   28 (210)
T ss_pred             EEECCCcCCHHHH-HHHHHHHHH
Confidence            4567899999954 555555554

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=87.20  E-value=0.99  Score=37.54  Aligned_cols=26  Identities=8%  Similarity=-0.150  Sum_probs=18.3

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhh
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      .+.-+.+.+|||+|||.+ +.-+...+
T Consensus       193 ~~~vi~~vGptGvGKTTt-~~kLa~~~  218 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTT-LAKLAARF  218 (282)
T ss_pred             CCeEEEEECCCCCCHHHH-HHHHHHHH
Confidence            456788899999999976 33344444

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=87.20  E-value=0.47  Score=43.52  Aligned_cols=24  Identities=4%  Similarity=-0.198  Sum_probs=18.6

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhhh
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      -+++.+|||||||.+ +..++..+.
T Consensus       318 lilv~G~tGSGKTTt-l~a~l~~~~  341 (564)
T TIGR02538       318 MVLVTGPTGSGKTVS-LYTALNILN  341 (564)
T ss_pred             eEEEECCCCCCHHHH-HHHHHHhhC
Confidence            367999999999976 556776664

This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=87.08  E-value=21  Score=31.57  Aligned_cols=134  Identities=12%  Similarity=0.080  Sum_probs=65.0

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcC--cH-HHHHHHHHHHHHhhcCCcEEEEEcCCCCCC
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAP--TR-ELAQQIQTVAKEFSSALRNICIFGGTPKGP   84 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~P--tr-eL~~Q~~~~~~~~~~~~~~~~~~gg~~~~~   84 (233)
                      ++.+.+.++||+|||.+... +...+..       .+.++.++..  -| .-+.|+.......  ++.+.  ...   ++
T Consensus       241 ~~vI~LVGptGvGKTTTiaK-LA~~L~~-------~GkkVglI~aDt~RiaAvEQLk~yae~l--gipv~--v~~---d~  305 (436)
T PRK11889        241 VQTIALIGPTGVGKTTTLAK-MAWQFHG-------KKKTVGFITTDHSRIGTVQQLQDYVKTI--GFEVI--AVR---DE  305 (436)
T ss_pred             CcEEEEECCCCCcHHHHHHH-HHHHHHH-------cCCcEEEEecCCcchHHHHHHHHHhhhc--CCcEE--ecC---CH
Confidence            46788999999999976333 4334432       2445555543  33 3444544333322  22222  111   11


Q ss_pred             eeEEeccchhhhchHHHhcCCCCeEEEEecch-------hHHHHHHHHHhhCC-Cee-EEEeCCCCHHHHHHHHHHhhCC
Q psy14082         85 QDCLPLHRFVFNCQYEMAKNPAFKVIVFVETK-------KKVEDITRALRRER-HSA-ICIHGDKTQQDRDYVLNDFRQG  155 (233)
Q Consensus        85 ~~lv~l~r~~~~~~~~~~~~~~~k~iIf~~~~-------~~~~~l~~~L~~~~-~~~-~~~~~~~~~~~r~~~~~~f~~g  155 (233)
                      .      .+.+.+.. +... ...-+||+.|.       ....++...+.... ..+ .++.+.+...+-..+++.|+.-
T Consensus       306 ~------~L~~aL~~-lk~~-~~~DvVLIDTaGRs~kd~~lm~EL~~~lk~~~PdevlLVLsATtk~~d~~~i~~~F~~~  377 (436)
T PRK11889        306 A------AMTRALTY-FKEE-ARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASMKSKDMIEIITNFKDI  377 (436)
T ss_pred             H------HHHHHHHH-HHhc-cCCCEEEEeCccccCcCHHHHHHHHHHHhhcCCCeEEEEECCccChHHHHHHHHHhcCC
Confidence            1      01111111 1110 11223444332       23445555554322 223 3355556667777899999887


Q ss_pred             CCCEEEecc
Q psy14082        156 KAPILVATD  164 (233)
Q Consensus       156 ~~~iLv~T~  164 (233)
                      .+.-+|-|-
T Consensus       378 ~idglI~TK  386 (436)
T PRK11889        378 HIDGIVFTK  386 (436)
T ss_pred             CCCEEEEEc
Confidence            777777773

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=87.03  E-value=1.2  Score=39.48  Aligned_cols=49  Identities=4%  Similarity=-0.083  Sum_probs=32.2

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHH
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVA   64 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~   64 (233)
                      +.+++.+++|+|||.. +-.+.+.+.+.     ..+.+++++.. .++..+..+.+
T Consensus       131 n~l~lyG~~G~GKTHL-l~ai~~~l~~~-----~~~~~v~yi~~-~~f~~~~~~~~  179 (440)
T PRK14088        131 NPLFIYGGVGLGKTHL-LQSIGNYVVQN-----EPDLRVMYITS-EKFLNDLVDSM  179 (440)
T ss_pred             CeEEEEcCCCCcHHHH-HHHHHHHHHHh-----CCCCeEEEEEH-HHHHHHHHHHH
Confidence            4589999999999976 56677766543     23456676654 45555554433

>KOG1133|consensus

Probab=86.96  E-value=0.57  Score=43.25  Aligned_cols=23  Identities=9%  Similarity=0.186  Sum_probs=10.8

Q ss_pred             CeEEEEecchhHHHHHHHHHhhC
Q psy14082        107 FKVIVFVETKKKVEDITRALRRE  129 (233)
Q Consensus       107 ~k~iIf~~~~~~~~~l~~~L~~~  129 (233)
                      +-+++|+++-+-...+.+...+.
T Consensus       630 gGvV~FfPSy~yL~~v~k~w~~~  652 (821)
T KOG1133|consen  630 GGVVCFFPSYAYLGQVRKRWEQN  652 (821)
T ss_pred             CcEEEEeccHHHHHHHHHHHHhc
Confidence            34455555544444444444433

>PRK06893 DNA replication initiation factor; Validated

Probab=86.94  E-value=0.8  Score=36.79  Aligned_cols=34  Identities=6%  Similarity=-0.137  Sum_probs=22.7

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcC
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAP   52 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~P   52 (233)
                      +++.+|+|+|||.. +..+.+.+..+       +..+.++..
T Consensus        42 l~l~G~~G~GKThL-~~ai~~~~~~~-------~~~~~y~~~   75 (229)
T PRK06893         42 FYIWGGKSSGKSHL-LKAVSNHYLLN-------QRTAIYIPL   75 (229)
T ss_pred             EEEECCCCCCHHHH-HHHHHHHHHHc-------CCCeEEeeH
Confidence            68999999999966 45555555432       445666544

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=86.92  E-value=22  Score=32.07  Aligned_cols=54  Identities=11%  Similarity=0.052  Sum_probs=34.2

Q ss_pred             eeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCC
Q psy14082        132 SAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQL  185 (233)
Q Consensus       132 ~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~  185 (233)
                      ...++...+....-.++.+.|+.....-+|-|.+-+..---.-+++++.+++|-
T Consensus       368 ~~LVLdAt~~~~~l~~i~~~f~~~~~~g~IlTKlDet~~~G~~l~i~~~~~lPI  421 (484)
T PRK06995        368 RLLLLNATSHGDTLNEVVQAYRGPGLAGCILTKLDEAASLGGALDVVIRYKLPL  421 (484)
T ss_pred             eEEEEeCCCcHHHHHHHHHHhccCCCCEEEEeCCCCcccchHHHHHHHHHCCCe
Confidence            446667777788888899999988777777775433211112344555566664

>TIGR01039 atpD ATP synthase, F1 beta subunit

Probab=86.87  E-value=19  Score=32.21  Aligned_cols=101  Identities=14%  Similarity=0.134  Sum_probs=50.8

Q ss_pred             CCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh-hcC-C-cEEEEEcC
Q psy14082          3 PPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF-SSA-L-RNICIFGG   79 (233)
Q Consensus         3 p~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~-~~~-~-~~~~~~gg   79 (233)
                      -++-.|+-+.+.++.|+|||.. +..++......     .+.  +.|++--=|-...+.+-++.+ ..+ + +..++.+.
T Consensus       138 ~pig~GQr~~If~~~G~GKt~L-~~~~~~~~~~~-----~~~--v~V~alIGER~rEv~ef~~~~~~~~~l~rtvvV~at  209 (461)
T TIGR01039       138 APYAKGGKIGLFGGAGVGKTVL-IQELINNIAKE-----HGG--YSVFAGVGERTREGNDLYHEMKESGVIDKTALVYGQ  209 (461)
T ss_pred             CCcccCCEEEeecCCCCChHHH-HHHHHHHHHhc-----CCC--eEEEEEecCCchHHHHHHHHHHhcCCcceeEEEEEC
Confidence            3567789999999999999966 33343333221     112  333343333444444444444 112 2 34444444


Q ss_pred             CCCCCeeEEeccchhh-----hchHHHhcCCCCeEEEEecch
Q psy14082         80 TPKGPQDCLPLHRFVF-----NCQYEMAKNPAFKVIVFVETK  116 (233)
Q Consensus        80 ~~~~~~~lv~l~r~~~-----~~~~~~~~~~~~k~iIf~~~~  116 (233)
                      .+..+     +.|+..     -+.+++...++..++++..+.
T Consensus       210 sd~p~-----~~R~~a~~~a~tiAEyfrd~~G~~VLll~Dsl  246 (461)
T TIGR01039       210 MNEPP-----GARMRVALTGLTMAEYFRDEQGQDVLLFIDNI  246 (461)
T ss_pred             CCCCH-----HHHHHHHHHHHHHHHHHHHhcCCeeEEEecch
Confidence            44322     112111     123355544667777777553

The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. Proton translocating ATP synthase, F1 beta subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), A subunit.

>PRK08084 DNA replication initiation factor; Provisional

Probab=86.86  E-value=1.1  Score=36.12  Aligned_cols=38  Identities=8%  Similarity=-0.087  Sum_probs=25.0

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcC
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAP   52 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~P   52 (233)
                      .+..+++.+|+|+|||.. +..+.+.+..       .+.+++++.-
T Consensus        44 ~~~~l~l~Gp~G~GKThL-l~a~~~~~~~-------~~~~v~y~~~   81 (235)
T PRK08084         44 HSGYIYLWSREGAGRSHL-LHAACAELSQ-------RGRAVGYVPL   81 (235)
T ss_pred             CCCeEEEECCCCCCHHHH-HHHHHHHHHh-------CCCeEEEEEH
Confidence            346789999999999965 4445554443       2456666544

>PRK08939 primosomal protein DnaI; Reviewed

Probab=86.73  E-value=1.1  Score=37.87  Aligned_cols=48  Identities=8%  Similarity=-0.022  Sum_probs=30.9

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHH
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTV   63 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~   63 (233)
                      .++.+++.+++|+|||.. +.++...+...       +..+.++ ..-+|+.++...
T Consensus       155 ~~~gl~L~G~~G~GKThL-a~Aia~~l~~~-------g~~v~~~-~~~~l~~~lk~~  202 (306)
T PRK08939        155 KVKGLYLYGDFGVGKSYL-LAAIANELAKK-------GVSSTLL-HFPEFIRELKNS  202 (306)
T ss_pred             CCCeEEEECCCCCCHHHH-HHHHHHHHHHc-------CCCEEEE-EHHHHHHHHHHH
Confidence            356799999999999977 55566666532       4444444 333566665544

>PF04364 DNA_pol3_chi: DNA polymerase III chi subunit, HolC; InterPro: IPR007459 The DNA polymerase III holoenzyme (2

Probab=86.64  E-value=6.4  Score=28.94  Aligned_cols=88  Identities=17%  Similarity=0.215  Sum_probs=47.8

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQ  184 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P  184 (233)
                      .+.+++|+|.+.+.++.+-+.|-...-...+=|+-....         ......|+++++...  -..+..+++||.+..
T Consensus        28 ~g~rv~V~~~d~~~a~~lD~~LW~~~~~sFlPH~~~~~~---------~~~~~PV~i~~~~~~--~~~~~~~vLinL~~~   96 (137)
T PF04364_consen   28 QGQRVLVLCPDEEQAEALDELLWTFSPDSFLPHGLAGEP---------PAARQPVLITWDQEA--NPNNHADVLINLSGE   96 (137)
T ss_dssp             TT--EEEE-SSHHHHHHHHHHTTTSSTT----EEETT-S---------STT--SEEEE-TTS------S--SEEEE--SS
T ss_pred             cCCeEEEEeCCHHHHHHHHHHHHCCCCCCCCCCcccCCC---------CCCCCeEEEecCccc--CCCCCCCEEEECCCC
Confidence            578999999999999999999988766666666642211         112358999987643  122347889998743


Q ss_pred             C-CcccccceeeEEeecchH
Q psy14082        185 L-SANHNISQVIEVVQDYEK  203 (233)
Q Consensus       185 ~-~~~~~i~~~~~~~~~~~~  203 (233)
                      . ..-.+..+++.++...+.
T Consensus        97 ~p~~~~~f~rvieiv~~~~~  116 (137)
T PF04364_consen   97 VPPFFSRFERVIEIVDQDDE  116 (137)
T ss_dssp             --GGGGG-SEEEEEE-SSHH
T ss_pred             CcchhhcccEEEEEecCCHH
Confidence            3 222445899999987663

7.7.7 from EC) is the polymerase responsible for the replication of the Escherichia coli chromosome. The holoenzyme is composed of the DNA polymerase III core, the sliding clamp, and the DnaX clamp loading complex. The DnaX complex contains either the tau or gamma product of gene dnax, complexed to delta.delta and to chi psi. Chi forms a 1:1 heterodimer with psi. The chi psi complex functions by increasing the affinity of tau and gamma for delta.delta allowing a functional clamp-loading complex to form at physiological subunit concentrations. Psi is responsible for the interaction with DnaX (gamma/tau), but psi is insoluble unless it is in a complex with chi [].; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3SXU_A 1EM8_C.

>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A

Probab=86.56  E-value=0.4  Score=33.96  Aligned_cols=22  Identities=5%  Similarity=-0.313  Sum_probs=15.4

Q ss_pred             eeEecCCCCCchHHhHHHHHHhh
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      +++.+++|||||.. +--+.+++
T Consensus         2 I~I~G~~gsGKST~-a~~La~~~   23 (121)
T PF13207_consen    2 IIISGPPGSGKSTL-AKELAERL   23 (121)
T ss_dssp             EEEEESTTSSHHHH-HHHHHHHH
T ss_pred             EEEECCCCCCHHHH-HHHHHHHH
Confidence            57899999999955 44444443

...

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=86.52  E-value=0.65  Score=33.11  Aligned_cols=22  Identities=5%  Similarity=-0.313  Sum_probs=15.8

Q ss_pred             eeEecCCCCCchHHhHHHHHHhh
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      +++.+|+|+|||.. +--+.+.+
T Consensus         1 ill~G~~G~GKT~l-~~~la~~l   22 (132)
T PF00004_consen    1 ILLHGPPGTGKTTL-ARALAQYL   22 (132)
T ss_dssp             EEEESSTTSSHHHH-HHHHHHHT
T ss_pred             CEEECcCCCCeeHH-HHHHHhhc
Confidence            57889999999966 44444444

Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=86.49  E-value=0.36  Score=39.68  Aligned_cols=20  Identities=10%  Similarity=-0.167  Sum_probs=17.4

Q ss_pred             CCCCCceeEecCCCCCchHH
Q psy14082          5 SESGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~   24 (233)
                      +..|+++++.+++|+|||..
T Consensus        18 l~~g~~vLL~G~~GtGKT~l   37 (262)
T TIGR02640        18 LKSGYPVHLRGPAGTGKTTL   37 (262)
T ss_pred             HhcCCeEEEEcCCCCCHHHH
Confidence            34688999999999999976

Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=86.39  E-value=0.77  Score=41.30  Aligned_cols=23  Identities=4%  Similarity=-0.116  Sum_probs=17.8

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhh
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      +++.+|||||||.+ +-.+++.+.
T Consensus       245 ilitGptGSGKTTt-L~a~L~~l~  267 (486)
T TIGR02533       245 ILVTGPTGSGKTTT-LYAALSRLN  267 (486)
T ss_pred             EEEEcCCCCCHHHH-HHHHHhccC
Confidence            68999999999966 555666654

This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.

>TIGR00416 sms DNA repair protein RadA

Probab=86.38  E-value=1.4  Score=39.24  Aligned_cols=54  Identities=17%  Similarity=0.086  Sum_probs=36.8

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      +..|.=+++.+++|+|||.. ++-++..+..       .+.+++++.. .|-..|+.....++
T Consensus        91 i~~GsvilI~G~pGsGKTTL-~lq~a~~~a~-------~g~kvlYvs~-EEs~~qi~~ra~rl  144 (454)
T TIGR00416        91 IVPGSLILIGGDPGIGKSTL-LLQVACQLAK-------NQMKVLYVSG-EESLQQIKMRAIRL  144 (454)
T ss_pred             ccCCeEEEEEcCCCCCHHHH-HHHHHHHHHh-------cCCcEEEEEC-cCCHHHHHHHHHHc
Confidence            34577789999999999965 4444444432       2346888765 46677887777766

The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=86.34  E-value=0.76  Score=43.45  Aligned_cols=50  Identities=10%  Similarity=-0.162  Sum_probs=34.8

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHH
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQT   62 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~   62 (233)
                      .++-.++.+++|||||.+ +-.++..+...     .+...+++++||-.-|..+.+
T Consensus       337 ~~~~~iitGgpGTGKTt~-l~~i~~~~~~~-----~~~~~v~l~ApTg~AA~~L~e  386 (720)
T TIGR01448       337 QHKVVILTGGPGTGKTTI-TRAIIELAEEL-----GGLLPVGLAAPTGRAAKRLGE  386 (720)
T ss_pred             hCCeEEEECCCCCCHHHH-HHHHHHHHHHc-----CCCceEEEEeCchHHHHHHHH
Confidence            456789999999999966 44555555432     112568889999887776654

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=86.30  E-value=2.1  Score=34.97  Aligned_cols=39  Identities=13%  Similarity=0.079  Sum_probs=27.4

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcC
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAP   52 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~P   52 (233)
                      .|.=+++.|.||.||| +|++-+...+..+      .+..+++++.
T Consensus        18 ~g~L~vi~a~pg~GKT-~~~l~ia~~~a~~------~~~~vly~Sl   56 (259)
T PF03796_consen   18 PGELTVIAARPGVGKT-AFALQIALNAALN------GGYPVLYFSL   56 (259)
T ss_dssp             TT-EEEEEESTTSSHH-HHHHHHHHHHHHT------TSSEEEEEES
T ss_pred             cCcEEEEEecccCCch-HHHHHHHHHHHHh------cCCeEEEEcC
Confidence            3556788899999999 4566666666543      2467888885

Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=86.23  E-value=3.9  Score=40.01  Aligned_cols=99  Identities=14%  Similarity=0.085  Sum_probs=64.5

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEc-CCC------
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFG-GTP------   81 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~g-g~~------   81 (233)
                      -|+.++||=|||++..+|+.-.-+.      ++|+  =|++..-=||.-=.++...+  +.++++.++.. +.+      
T Consensus       185 ~IAEM~TGEGKTLvAtlp~yLnAL~------GkgV--HvVTVNDYLA~RDaewmgply~fLGLsvg~i~~~~~~~~~rr~  256 (1112)
T PRK12901        185 KIAEMATGEGKTLVATLPVYLNALT------GNGV--HVVTVNDYLAKRDSEWMGPLYEFHGLSVDCIDKHQPNSEARRK  256 (1112)
T ss_pred             ceeeecCCCCchhHHHHHHHHHHHc------CCCc--EEEEechhhhhccHHHHHHHHHHhCCceeecCCCCCCHHHHHH
Confidence            4778889999999999998866654      2344  44555666887766666666  56899988865 212      


Q ss_pred             -CCCeeEEe---------------------ccc-----hhhhchHHHhcCCCCeEEEEecchh
Q psy14082         82 -KGPQDCLP---------------------LHR-----FVFNCQYEMAKNPAFKVIVFVETKK  117 (233)
Q Consensus        82 -~~~~~lv~---------------------l~r-----~~~~~~~~~~~~~~~k~iIf~~~~~  117 (233)
                       +..+|.=|                     ..|     ++|.+...+-.....|.||--+...
T Consensus       257 aY~~DItYgTn~EfGFDYLRDnm~~~~~~~vqR~~~fAIVDEvDSILIDEARTPLIISGp~~~  319 (1112)
T PRK12901        257 AYNADITYGTNNEFGFDYLRDNMAHSPEDLVQRKHNYAIVDEVDSVLIDDARTPLIISGPVPK  319 (1112)
T ss_pred             hCCCcceecCCCccccccchhccccchHhhhCcCCceeEeechhhhhhccccCcEEEeCCCCC
Confidence             23333222                     112     5666666666667778888777443

>PF09439 SRPRB: Signal recognition particle receptor beta subunit; InterPro: IPR019009 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=86.16  E-value=0.41  Score=37.06  Aligned_cols=20  Identities=0%  Similarity=-0.348  Sum_probs=14.7

Q ss_pred             CCceeEecCCCCCchHHhHH
Q psy14082          8 GCQNFSKITNYLLSPPQYML   27 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~l   27 (233)
                      ...+++.+|.|||||..|..
T Consensus         3 ~~~vlL~Gps~SGKTaLf~~   22 (181)
T PF09439_consen    3 RPTVLLVGPSGSGKTALFSQ   22 (181)
T ss_dssp             --EEEEE-STTSSHHHHHHH
T ss_pred             CceEEEEcCCCCCHHHHHHH
Confidence            46789999999999987654

SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain []. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon []. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane []. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel. The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase, which anchors the alpha subunit to the endoplasmic reticulum membrane []. ; PDB: 2GED_B 1NRJ_B 2GO5_2 2FH5_B.

>PRK13766 Hef nuclease; Provisional

Probab=86.11  E-value=3.6  Score=39.21  Aligned_cols=69  Identities=26%  Similarity=0.357  Sum_probs=50.9

Q ss_pred             CCeEEEEecchhHHHHHHHHHhhC-CC---eeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc------cCcCCcCCCCc
Q psy14082        106 AFKVIVFVETKKKVEDITRALRRE-RH---SAICIHGDKTQQDRDYVLNDFRQGKAPILVATD------VAARGLDVEDV  175 (233)
Q Consensus       106 ~~k~iIf~~~~~~~~~l~~~L~~~-~~---~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~------~~~~Gldi~~v  175 (233)
                      +.++++.++++..+++..+.+++. +.   .+..++|+.+..+|...+.     +.+|+|+|.      ....-+++.++
T Consensus        58 ~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~~~~v~~~~g~~~~~~r~~~~~-----~~~iiv~T~~~l~~~l~~~~~~~~~~  132 (773)
T PRK13766         58 GGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIVVFTGEVSPEKRAELWE-----KAKVIVATPQVIENDLIAGRISLEDV  132 (773)
T ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhCCCCceEEEEeCCCCHHHHHHHHh-----CCCEEEECHHHHHHHHHcCCCChhhC
Confidence            358999999998888877777653 33   7888999999888766554     358999995      23344666677


Q ss_pred             cEEE
Q psy14082        176 NTVN  179 (233)
Q Consensus       176 ~~VI  179 (233)
                      ++||
T Consensus       133 ~liV  136 (773)
T PRK13766        133 SLLI  136 (773)
T ss_pred             cEEE
Confidence            7766

>TIGR00962 atpA proton translocating ATP synthase, F1 alpha subunit

Probab=86.02  E-value=17  Score=32.86  Aligned_cols=22  Identities=9%  Similarity=-0.084  Sum_probs=18.9

Q ss_pred             CCCCCCCceeEecCCCCCchHH
Q psy14082          3 PPSESGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         3 p~~~~g~d~i~~a~tGsGKT~~   24 (233)
                      -++-+|+-..+.+..|+|||..
T Consensus       156 ~pigrGQr~~I~g~~g~GKt~L  177 (501)
T TIGR00962       156 IPIGRGQRELIIGDRQTGKTAV  177 (501)
T ss_pred             CCcccCCEEEeecCCCCCccHH
Confidence            4567899999999999999975

The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. The alpha-subunit contains a highly conserved adenine-specific noncatalytic nucleotide-binding domain. The conserved amino acid sequence is Gly-X-X-X-X-Gly-Lys. Proton translocating ATP synthase F1, alpha subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), B subunit.

>PRK14974 cell division protein FtsY; Provisional

Probab=86.00  E-value=2.4  Score=36.25  Aligned_cols=51  Identities=12%  Similarity=-0.022  Sum_probs=30.3

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCc---HHHHHHHHHHHHHh
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPT---RELAQQIQTVAKEF   67 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~Pt---reL~~Q~~~~~~~~   67 (233)
                      .=+++.+++|+|||.+..- +...+..       .+.+++++...   ..-..|+......+
T Consensus       141 ~vi~~~G~~GvGKTTtiak-LA~~l~~-------~g~~V~li~~Dt~R~~a~eqL~~~a~~l  194 (336)
T PRK14974        141 VVIVFVGVNGTGKTTTIAK-LAYYLKK-------NGFSVVIAAGDTFRAGAIEQLEEHAERL  194 (336)
T ss_pred             eEEEEEcCCCCCHHHHHHH-HHHHHHH-------cCCeEEEecCCcCcHHHHHHHHHHHHHc
Confidence            4477899999999976332 3344432       24456665532   34556665555554

>PRK13343 F0F1 ATP synthase subunit alpha; Provisional

Probab=85.63  E-value=24  Score=31.97  Aligned_cols=23  Identities=13%  Similarity=-0.028  Sum_probs=19.4

Q ss_pred             CCCCCCCCceeEecCCCCCchHH
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~   24 (233)
                      +-++-+|+-..+.+..|+|||..
T Consensus       156 l~pigrGQR~~I~g~~g~GKt~L  178 (502)
T PRK13343        156 LIPIGRGQRELIIGDRQTGKTAI  178 (502)
T ss_pred             ccccccCCEEEeeCCCCCCccHH
Confidence            34567899999999999999966

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=85.62  E-value=1.3  Score=35.15  Aligned_cols=26  Identities=4%  Similarity=-0.269  Sum_probs=18.8

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhh
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      .+..+++.+++|+|||.. +..+....
T Consensus        37 ~~~~lll~G~~G~GKT~l-a~~~~~~~   62 (226)
T TIGR03420        37 GDRFLYLWGESGSGKSHL-LQAACAAA   62 (226)
T ss_pred             CCCeEEEECCCCCCHHHH-HHHHHHHH
Confidence            356799999999999966 44444444

Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.

>KOG0735|consensus

Probab=85.54  E-value=5.6  Score=37.44  Aligned_cols=145  Identities=10%  Similarity=0.000  Sum_probs=78.7

Q ss_pred             CCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh-----------hcCC
Q psy14082          3 PPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF-----------SSAL   71 (233)
Q Consensus         3 p~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~-----------~~~~   71 (233)
                      .++++..++++-+|.|||||.. +-.++..+-.       ..-.=+.++.-.+|...-.+.++++           .+.+
T Consensus       426 spv~~~~~Ill~G~~GsGKT~L-~kal~~~~~k-------~~~~hv~~v~Cs~l~~~~~e~iQk~l~~vfse~~~~~PSi  497 (952)
T KOG0735|consen  426 SPVFRHGNILLNGPKGSGKTNL-VKALFDYYSK-------DLIAHVEIVSCSTLDGSSLEKIQKFLNNVFSEALWYAPSI  497 (952)
T ss_pred             ccccccccEEEeCCCCCCHhHH-HHHHHHHhcc-------ccceEEEEEechhccchhHHHHHHHHHHHHHHHHhhCCcE
Confidence            4578899999999999999965 5555554431       1112233333333433333333333           2222


Q ss_pred             ----cEEEEEcCC-CCCCeeEEeccchhhhchHH-HhcCCCCeEEEEecchhHHHHHHHHHhhCC-CeeEEEeCCCCHHH
Q psy14082         72 ----RNICIFGGT-PKGPQDCLPLHRFVFNCQYE-MAKNPAFKVIVFVETKKKVEDITRALRRER-HSAICIHGDKTQQD  144 (233)
Q Consensus        72 ----~~~~~~gg~-~~~~~~lv~l~r~~~~~~~~-~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~-~~~~~~~~~~~~~~  144 (233)
                          .+.++.|+. +...|.=++-.|+.+.+.+. .......+.|.|..|.++-+.+...|.... +.+..--......+
T Consensus       498 IvLDdld~l~~~s~~e~~q~~~~~~rla~flnqvi~~y~~~~~~ia~Iat~qe~qtl~~~L~s~~~Fq~~~~L~ap~~~~  577 (952)
T KOG0735|consen  498 IVLDDLDCLASASSNENGQDGVVSERLAAFLNQVIKIYLKRNRKIAVIATGQELQTLNPLLVSPLLFQIVIALPAPAVTR  577 (952)
T ss_pred             EEEcchhhhhccCcccCCcchHHHHHHHHHHHHHHHHHHccCcEEEEEEechhhhhcChhhcCccceEEEEecCCcchhH
Confidence                233444422 23344333333333333221 112344455777778888888888885544 34444445677888


Q ss_pred             HHHHHHHhhCC
Q psy14082        145 RDYVLNDFRQG  155 (233)
Q Consensus       145 r~~~~~~f~~g  155 (233)
                      |.+++..+-+.
T Consensus       578 R~~IL~~~~s~  588 (952)
T KOG0735|consen  578 RKEILTTIFSK  588 (952)
T ss_pred             HHHHHHHHHHh
Confidence            88888876543

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=85.52  E-value=24  Score=30.85  Aligned_cols=137  Identities=9%  Similarity=-0.005  Sum_probs=67.9

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEc--CcHHHHHHHHHHHHHhhcCCcEEEEEcCCCCCC
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLA--PTRELAQQIQTVAKEFSSALRNICIFGGTPKGP   84 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~--PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~~~   84 (233)
                      .++-++..+|||+|||.+..- +..++....   ...+.++.++.  +.|.-+......+.+. .++.+.....   .  
T Consensus       173 ~~~vi~lvGptGvGKTTT~aK-LA~~~~~~~---~~~g~~V~lit~Dt~R~aa~eQL~~~a~~-lgvpv~~~~~---~--  242 (388)
T PRK12723        173 KKRVFILVGPTGVGKTTTIAK-LAAIYGINS---DDKSLNIKIITIDNYRIGAKKQIQTYGDI-MGIPVKAIES---F--  242 (388)
T ss_pred             CCeEEEEECCCCCCHHHHHHH-HHHHHHhhh---ccCCCeEEEEeccCccHHHHHHHHHHhhc-CCcceEeeCc---H--
Confidence            356788999999999987443 333332110   01233444444  3344444333333221 1333221111   0  


Q ss_pred             eeEEeccchhhhchHHHhcCCCCeEEEEecchh-------HHHHHHHHHhhCC---CeeEEEeCCCCHHHHHHHHHHhhC
Q psy14082         85 QDCLPLHRFVFNCQYEMAKNPAFKVIVFVETKK-------KVEDITRALRRER---HSAICIHGDKTQQDRDYVLNDFRQ  154 (233)
Q Consensus        85 ~~lv~l~r~~~~~~~~~~~~~~~k~iIf~~~~~-------~~~~l~~~L~~~~---~~~~~~~~~~~~~~r~~~~~~f~~  154 (233)
                                +-+.+.+... ...-+|++.|..       ...++...+...+   ....++.+.....+-.+++++|..
T Consensus       243 ----------~~l~~~L~~~-~~~DlVLIDTaGr~~~~~~~l~el~~~l~~~~~~~e~~LVlsat~~~~~~~~~~~~~~~  311 (388)
T PRK12723        243 ----------KDLKEEITQS-KDFDLVLVDTIGKSPKDFMKLAEMKELLNACGRDAEFHLAVSSTTKTSDVKEIFHQFSP  311 (388)
T ss_pred             ----------HHHHHHHHHh-CCCCEEEEcCCCCCccCHHHHHHHHHHHHhcCCCCeEEEEEcCCCCHHHHHHHHHHhcC
Confidence                      0011111111 223344444431       2345555555433   244667777778888899999987


Q ss_pred             CCCCEEEecc
Q psy14082        155 GKAPILVATD  164 (233)
Q Consensus       155 g~~~iLv~T~  164 (233)
                      -...-+|-|-
T Consensus       312 ~~~~~~I~TK  321 (388)
T PRK12723        312 FSYKTVIFTK  321 (388)
T ss_pred             CCCCEEEEEe
Confidence            6667676663

>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C

Probab=85.42  E-value=0.49  Score=33.62  Aligned_cols=14  Identities=0%  Similarity=-0.657  Sum_probs=12.1

Q ss_pred             eeEecCCCCCchHH
Q psy14082         11 NFSKITNYLLSPPQ   24 (233)
Q Consensus        11 ~i~~a~tGsGKT~~   24 (233)
                      +++.+++|||||..
T Consensus         1 I~i~G~~GsGKtTi   14 (129)
T PF13238_consen    1 IGISGIPGSGKTTI   14 (129)
T ss_dssp             EEEEESTTSSHHHH
T ss_pred             CEEECCCCCCHHHH
Confidence            57889999999966

...

>PRK12678 transcription termination factor Rho; Provisional

Probab=85.41  E-value=4.1  Score=37.48  Aligned_cols=32  Identities=13%  Similarity=-0.003  Sum_probs=24.2

Q ss_pred             CCCCCCCceeEecCCCCCchHHhHHHHHHhhhc
Q psy14082          3 PPSESGCQNFSKITNYLLSPPQYMLPAAVHISH   35 (233)
Q Consensus         3 p~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~   35 (233)
                      -++-.|+-.++.+++|+|||.. +..+++.+..
T Consensus       411 ~PIGkGQR~LIvgpp~aGKTtL-L~~IAn~i~~  442 (672)
T PRK12678        411 MPIGKGQRGLIVSPPKAGKTTI-LQNIANAITT  442 (672)
T ss_pred             cccccCCEeEEeCCCCCCHHHH-HHHHHHHHhh
Confidence            3556788899999999999976 5556665543

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=85.36  E-value=1.5  Score=39.71  Aligned_cols=55  Identities=11%  Similarity=-0.071  Sum_probs=36.9

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ++.|.-+++.+++|+|||.-..--+.+.+.+       .+..++++ .+-|-..|+.+.+..+
T Consensus        28 ~p~Gs~~li~G~pGsGKT~l~~qf~~~~~~~-------~ge~~lyi-s~ee~~~~i~~~~~~~   82 (509)
T PRK09302         28 LPKGRPTLVSGTAGTGKTLFALQFLVNGIKR-------FDEPGVFV-TFEESPEDIIRNVASF   82 (509)
T ss_pred             CCCCcEEEEEeCCCCCHHHHHHHHHHHHHHh-------cCCCEEEE-EccCCHHHHHHHHHHc
Confidence            4578889999999999995533223333321       14567666 4557777888888777

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=85.36  E-value=1.9  Score=40.92  Aligned_cols=47  Identities=13%  Similarity=-0.067  Sum_probs=33.7

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHH
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQT   62 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~   62 (233)
                      ++-.++++++|+|||.+ +-++.+.+..       .+.+++.++||---+..+.+
T Consensus       368 ~~~~il~G~aGTGKTtl-l~~i~~~~~~-------~g~~V~~~ApTg~Aa~~L~~  414 (744)
T TIGR02768       368 GDIAVVVGRAGTGKSTM-LKAAREAWEA-------AGYRVIGAALSGKAAEGLQA  414 (744)
T ss_pred             CCEEEEEecCCCCHHHH-HHHHHHHHHh-------CCCeEEEEeCcHHHHHHHHh
Confidence            34578999999999966 4445544432       36789999999877776654

This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=85.32  E-value=1.6  Score=39.52  Aligned_cols=54  Identities=15%  Similarity=-0.020  Sum_probs=37.2

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ++.|.-+++.+++|+|||.. +.-++.....       .+-++++++ +.+-..|+.+.+..+
T Consensus       270 ~~~g~~~li~G~~G~GKT~l-~~~~~~~~~~-------~g~~~~yis-~e~~~~~i~~~~~~~  323 (509)
T PRK09302        270 FFRGSIILVSGATGTGKTLL-ASKFAEAACR-------RGERCLLFA-FEESRAQLIRNARSW  323 (509)
T ss_pred             CCCCcEEEEEcCCCCCHHHH-HHHHHHHHHh-------CCCcEEEEE-ecCCHHHHHHHHHHc
Confidence            45688888999999999965 4333333322       355678775 446688888888777

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=85.24  E-value=1.3  Score=33.83  Aligned_cols=47  Identities=9%  Similarity=-0.051  Sum_probs=28.4

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      -+++.+++|||||.. +.-+....          +...+++......-.++.+++...
T Consensus         3 ~ili~G~~~sGKS~~-a~~l~~~~----------~~~~~~iat~~~~~~e~~~ri~~h   49 (170)
T PRK05800          3 LILVTGGARSGKSRF-AERLAAQS----------GLQVLYIATAQPFDDEMAARIAHH   49 (170)
T ss_pred             EEEEECCCCccHHHH-HHHHHHHc----------CCCcEeCcCCCCChHHHHHHHHHH
Confidence            478999999999944 44444332          223566766554455555555443

>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]

Probab=85.12  E-value=1.1  Score=36.79  Aligned_cols=54  Identities=17%  Similarity=0.041  Sum_probs=34.8

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEE------EcCcHHHHHHHHHHHHHh
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALV------LAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~li------l~PtreL~~Q~~~~~~~~   67 (233)
                      ..|--+...+|+|||||.+  +-+++++.+..     .| .++|      =.|-.+|-..+--.++..
T Consensus        25 ~~gef~vliGpSGsGKTTt--LkMINrLiept-----~G-~I~i~g~~i~~~d~~~LRr~IGYviQqi   84 (309)
T COG1125          25 EEGEFLVLIGPSGSGKTTT--LKMINRLIEPT-----SG-EILIDGEDISDLDPVELRRKIGYVIQQI   84 (309)
T ss_pred             cCCeEEEEECCCCCcHHHH--HHHHhcccCCC-----Cc-eEEECCeecccCCHHHHHHhhhhhhhhc
Confidence            3466678899999999966  56888887642     11 1111      125566766666666665

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=85.10  E-value=10  Score=33.45  Aligned_cols=32  Identities=9%  Similarity=0.140  Sum_probs=25.0

Q ss_pred             eEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc
Q psy14082        133 AICIHGDKTQQDRDYVLNDFRQGKAPILVATD  164 (233)
Q Consensus       133 ~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~  164 (233)
                      ..++...+..++-.++++.|+.-.+.-+|-|.
T Consensus       304 ~LVl~at~~~~~~~~~~~~f~~~~~~~~I~TK  335 (420)
T PRK14721        304 LLLLNATSSGDTLDEVISAYQGHGIHGCIITK  335 (420)
T ss_pred             EEEEcCCCCHHHHHHHHHHhcCCCCCEEEEEe
Confidence            45567777888889999999877777777774

>cd01523 RHOD_Lact_B Member of the Rhodanese Homology Domain superfamily

Probab=84.86  E-value=1.8  Score=29.51  Aligned_cols=38  Identities=11%  Similarity=0.073  Sum_probs=33.0

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCC
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKT  141 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~  141 (233)
                      .+..+++++|.+-..+...+..|++.|+.+..+.|++.
T Consensus        59 ~~~~~ivv~C~~G~rs~~aa~~L~~~G~~~~~l~GG~~   96 (100)
T cd01523          59 PDDQEVTVICAKEGSSQFVAELLAERGYDVDYLAGGMK   96 (100)
T ss_pred             CCCCeEEEEcCCCCcHHHHHHHHHHcCceeEEeCCcHH
Confidence            35678999999988899999999999999888888874

This CD includes predicted proteins with rhodanese-like domains found N-terminal of the metallo-beta-lactamase domain.

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=84.85  E-value=1.5  Score=32.94  Aligned_cols=35  Identities=3%  Similarity=-0.221  Sum_probs=22.7

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCc
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPT   53 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~Pt   53 (233)
                      +.+.+++|||||.. +--++..+..       .|.++.++-+.
T Consensus         2 i~i~G~~gsGKTtl-~~~l~~~l~~-------~G~~V~viK~~   36 (155)
T TIGR00176         2 LQIVGPKNSGKTTL-IERLVKALKA-------RGYRVATIKHD   36 (155)
T ss_pred             EEEECCCCCCHHHH-HHHHHHHHHh-------cCCeEEEEecc
Confidence            35678999999954 4555555532       35667777654

This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes.

>PF01583 APS_kinase: Adenylylsulphate kinase; InterPro: IPR002891 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases

Probab=84.81  E-value=13  Score=28.07  Aligned_cols=27  Identities=4%  Similarity=-0.239  Sum_probs=18.5

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhc
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISH   35 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~   35 (233)
                      |.=+|..+.+|||||.. +-.+-.+|..
T Consensus         2 g~vIwltGlsGsGKtTl-A~~L~~~L~~   28 (156)
T PF01583_consen    2 GFVIWLTGLSGSGKTTL-ARALERRLFA   28 (156)
T ss_dssp             -EEEEEESSTTSSHHHH-HHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHH-HHHHHHHHHH
Confidence            44578999999999954 4545555543

Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This domain contains an ATP binding P-loop motif [].; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity, transferring phosphorus-containing groups, 0000103 sulfate assimilation; PDB: 1M7H_B 1M7G_B 3CR7_B 1D6J_A 2OFW_G 1X6V_B 1XNJ_A 1XJQ_B 2PEY_A 2PEZ_B ....

>KOG1131|consensus

Probab=84.79  E-value=3.7  Score=37.08  Aligned_cols=58  Identities=7%  Similarity=0.014  Sum_probs=33.0

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      -++-+.+..+|+|+|||++ ++.++-..+..-+   ...-+.++-+-|..=.+....+++.+
T Consensus        33 DakGh~llEMPSGTGKTvs-LLSli~aYq~~~p---~~~~KliYCSRTvpEieK~l~El~~l   90 (755)
T KOG1131|consen   33 DAKGHCLLEMPSGTGKTVS-LLSLIIAYQLHYP---DEHRKLIYCSRTVPEIEKALEELKRL   90 (755)
T ss_pred             ccCCcEEEECCCCCCcchH-HHHHHHHHHHhCC---cccceEEEecCcchHHHHHHHHHHHH
Confidence            3466789999999999988 5656555554321   12233444444433334444444444

>PRK12608 transcription termination factor Rho; Provisional

Probab=84.76  E-value=1.6  Score=37.79  Aligned_cols=32  Identities=9%  Similarity=0.035  Sum_probs=24.5

Q ss_pred             CCCCCCCceeEecCCCCCchHHhHHHHHHhhhc
Q psy14082          3 PPSESGCQNFSKITNYLLSPPQYMLPAAVHISH   35 (233)
Q Consensus         3 p~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~   35 (233)
                      -++-.|+..++.++.|+|||.. +.-+++.+..
T Consensus       128 ~PiGkGQR~LIvG~pGtGKTTL-l~~la~~i~~  159 (380)
T PRK12608        128 APIGKGQRGLIVAPPRAGKTVL-LQQIAAAVAA  159 (380)
T ss_pred             eecCCCceEEEECCCCCCHHHH-HHHHHHHHHh
Confidence            3456789999999999999966 5556666654

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=84.73  E-value=1.6  Score=34.77  Aligned_cols=40  Identities=15%  Similarity=0.000  Sum_probs=25.9

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcC
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAP   52 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~P   52 (233)
                      ++.|.=+.+.+++|+|||.. ++-++.....       .+.+++++.-
T Consensus        20 i~~g~i~~i~G~~GsGKT~l-~~~la~~~~~-------~~~~v~yi~~   59 (225)
T PRK09361         20 FERGTITQIYGPPGSGKTNI-CLQLAVEAAK-------NGKKVIYIDT   59 (225)
T ss_pred             CCCCeEEEEECCCCCCHHHH-HHHHHHHHHH-------CCCeEEEEEC
Confidence            35677789999999999965 3434433332       2456777654

>PRK06936 type III secretion system ATPase; Provisional

Probab=84.46  E-value=16  Score=32.55  Aligned_cols=20  Identities=5%  Similarity=-0.356  Sum_probs=16.7

Q ss_pred             CCCCCceeEecCCCCCchHH
Q psy14082          5 SESGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~   24 (233)
                      +-.|.-+.+.++.|+|||..
T Consensus       159 i~~Gq~~~I~G~sG~GKStL  178 (439)
T PRK06936        159 CGEGQRMGIFAAAGGGKSTL  178 (439)
T ss_pred             ecCCCEEEEECCCCCChHHH
Confidence            45677888999999999965

>PRK09354 recA recombinase A; Provisional

Probab=84.35  E-value=2.2  Score=36.65  Aligned_cols=45  Identities=13%  Similarity=-0.048  Sum_probs=29.9

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHH
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELA   57 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~   57 (233)
                      +++|+=+.+.+|+|||||.. ++.++.....       .+..++++-.-..+-
T Consensus        57 ip~G~IteI~G~~GsGKTtL-al~~~~~~~~-------~G~~~~yId~E~s~~  101 (349)
T PRK09354         57 LPRGRIVEIYGPESSGKTTL-ALHAIAEAQK-------AGGTAAFIDAEHALD  101 (349)
T ss_pred             CcCCeEEEEECCCCCCHHHH-HHHHHHHHHH-------cCCcEEEECCccchH
Confidence            56788888999999999966 4444443332       356677776554444

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=84.29  E-value=0.84  Score=36.66  Aligned_cols=28  Identities=11%  Similarity=-0.152  Sum_probs=21.6

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhc
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISH   35 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~   35 (233)
                      ..|.-+.+.+|+|||||.  ++-++..+..
T Consensus        29 ~~Ge~vaI~GpSGSGKST--LLniig~ld~   56 (226)
T COG1136          29 EAGEFVAIVGPSGSGKST--LLNLLGGLDK   56 (226)
T ss_pred             cCCCEEEEECCCCCCHHH--HHHHHhcccC
Confidence            467788999999999994  4666766654

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=84.24  E-value=2.3  Score=36.88  Aligned_cols=53  Identities=17%  Similarity=0.149  Sum_probs=35.7

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ..|.=+++.+++|+|||.. ++-+...+..       .+.+++++.- .|-..|+.....++
T Consensus        80 ~~GslvLI~G~pG~GKStL-llq~a~~~a~-------~g~~VlYvs~-EEs~~qi~~Ra~rl  132 (372)
T cd01121          80 VPGSVILIGGDPGIGKSTL-LLQVAARLAK-------RGGKVLYVSG-EESPEQIKLRADRL  132 (372)
T ss_pred             cCCeEEEEEeCCCCCHHHH-HHHHHHHHHh-------cCCeEEEEEC-CcCHHHHHHHHHHc
Confidence            4467788999999999965 4444444432       2456888765 35667877777766

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=84.19  E-value=2  Score=37.10  Aligned_cols=54  Identities=22%  Similarity=0.118  Sum_probs=38.6

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHH--HHHHHHh
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQI--QTVAKEF   67 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~--~~~~~~~   67 (233)
                      ..|..+++.++-|+|||.. +-.+.+.+ .      ..+..+++.+||---|..+  ..++..+
T Consensus        20 ~~~~~~fv~G~~GtGKs~l-~~~i~~~~-~------~~~~~~~~~a~tg~AA~~i~~G~T~hs~   75 (364)
T PF05970_consen   20 EEGLNFFVTGPAGTGKSFL-IKAIIDYL-R------SRGKKVLVTAPTGIAAFNIPGGRTIHSF   75 (364)
T ss_pred             cCCcEEEEEcCCCCChhHH-HHHHHHHh-c------cccceEEEecchHHHHHhccCCcchHHh
Confidence            4578899999999999966 22344333 2      2467899999998888877  4555555

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>KOG1806|consensus

Probab=84.19  E-value=1.2  Score=43.08  Aligned_cols=55  Identities=5%  Similarity=-0.057  Sum_probs=44.7

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ..-+.++.+|||+|||-. +.-++.-+..+     .+.++++|++.+..-..|.++.+.+.
T Consensus       752 qpgltmvvgppgtgktd~-avqil~~lyhn-----~p~qrTlivthsnqaln~lfeKi~~~  806 (1320)
T KOG1806|consen  752 QPGLTMVVGPPGTGKTDV-AVQILSVLYHN-----SPNQRTLIVTHSNQALNQLFEKIMAL  806 (1320)
T ss_pred             CCCceeeecCCCCCCcch-hhhhhhhhhhc-----CCCcceEEEEecccchhHHHHHHHhc
Confidence            346789999999999977 55567666665     56889999999988888888888777

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=84.17  E-value=1.6  Score=34.76  Aligned_cols=38  Identities=11%  Similarity=-0.163  Sum_probs=24.0

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcC
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAP   52 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~P   52 (233)
                      .+..+++.+++|+|||.. +-.+......       .+..++++..
T Consensus        41 ~~~~~~l~G~~G~GKT~L-a~ai~~~~~~-------~~~~~~~i~~   78 (227)
T PRK08903         41 ADRFFYLWGEAGSGRSHL-LQALVADASY-------GGRNARYLDA   78 (227)
T ss_pred             CCCeEEEECCCCCCHHHH-HHHHHHHHHh-------CCCcEEEEeh
Confidence            345699999999999955 3444444332       2445666554

>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI

Probab=84.00  E-value=22  Score=31.50  Aligned_cols=53  Identities=13%  Similarity=-0.091  Sum_probs=31.1

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHH
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVA   64 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~   64 (233)
                      +-.|.-+.+.+++|+|||..+  -++......     ..+..+++=-..+|..+-+.+.+
T Consensus       137 i~~Gq~i~I~G~sG~GKTtLl--~~I~~~~~~-----~~gvi~~iGer~~ev~~~~~~~l  189 (418)
T TIGR03498       137 LCRGQRLGIFAGSGVGKSTLL--SMLARNTDA-----DVVVIALVGERGREVREFLEDDL  189 (418)
T ss_pred             ccCCcEEEEECCCCCChHHHH--HHHhCCCCC-----CEEEEEEEeeechHHHHHHHHhh
Confidence            446777889999999999663  334333221     22333444456677665554443

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein

Probab=83.98  E-value=19  Score=30.63  Aligned_cols=99  Identities=12%  Similarity=0.043  Sum_probs=48.3

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCC-cEEEEEcCCCCC
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSAL-RNICIFGGTPKG   83 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~-~~~~~~gg~~~~   83 (233)
                      +-.|.-+.+.+++|+|||..+  -++......     ..+..+++--..+|...-+.+....  ..+ ++.++.+..+..
T Consensus        66 i~~Gqri~I~G~sG~GKTtLl--~~Ia~~~~~-----~~~vi~~iGer~~ev~~~~~~~~~~--~~l~rtvvv~~t~d~~  136 (326)
T cd01136          66 VGKGQRLGIFAGSGVGKSTLL--GMIARGTTA-----DVNVIALIGERGREVREFIEKDLGE--EGLKRSVVVVATSDES  136 (326)
T ss_pred             EcCCcEEEEECCCCCChHHHH--HHHhCCCCC-----CEEEEEEEecCCccHHHHHHHHHhc--CccceEEEEEcCCCCC
Confidence            345777888999999999762  234333211     2233344444556665544333322  122 445555554443


Q ss_pred             Cee--EEeccchhhhchHHHhcCCCCeEEEEecc
Q psy14082         84 PQD--CLPLHRFVFNCQYEMAKNPAFKVIVFVET  115 (233)
Q Consensus        84 ~~~--lv~l~r~~~~~~~~~~~~~~~k~iIf~~~  115 (233)
                      +-.  .++  ..---+.+++. ..+..++++..+
T Consensus       137 ~~~r~~~~--~~a~~~AEyfr-~~g~~Vll~~Ds  167 (326)
T cd01136         137 PLLRVKAA--YTATAIAEYFR-DQGKDVLLLMDS  167 (326)
T ss_pred             HHHHHHHH--HHHHHHHHHHH-HcCCCeEEEecc
Confidence            211  000  01111233444 356677777765

This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway.

>KOG0348|consensus

Probab=83.89  E-value=4.9  Score=36.42  Aligned_cols=77  Identities=13%  Similarity=0.148  Sum_probs=48.6

Q ss_pred             hcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCC--CCHHHHHHHHHHhhCCCCCEEEeccc-------CcCCcCC
Q psy14082        102 AKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGD--KTQQDRDYVLNDFRQGKAPILVATDV-------AARGLDV  172 (233)
Q Consensus       102 ~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~--~~~~~r~~~~~~f~~g~~~iLv~T~~-------~~~Gldi  172 (233)
                      .+..+.=++|.++||+-|.++++.+++.-..+.++-.+  |.-+.|..--.+++.| ++|||+|+-       --..+++
T Consensus       207 ~Rs~G~~ALVivPTREL~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARLRKG-iNILIgTPGRLvDHLknT~~i~~  285 (708)
T KOG0348|consen  207 QRSDGPYALVIVPTRELALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKARLRKG-INILIGTPGRLVDHLKNTKSIKF  285 (708)
T ss_pred             cccCCceEEEEechHHHHHHHHHHHHHHhcCceEEeeceeecccccccHHHHHhcC-ceEEEcCchHHHHHHhccchhee
Confidence            34566678999999999999999998875443332211  1112233333445555 899999951       1234666


Q ss_pred             CCccEEE
Q psy14082        173 EDVNTVN  179 (233)
Q Consensus       173 ~~v~~VI  179 (233)
                      ..+.|+|
T Consensus       286 s~LRwlV  292 (708)
T KOG0348|consen  286 SRLRWLV  292 (708)
T ss_pred             eeeeEEE
Confidence            7777776

>KOG0745|consensus

Probab=83.86  E-value=0.65  Score=40.80  Aligned_cols=27  Identities=0%  Similarity=-0.336  Sum_probs=19.6

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhh
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      +..-++++.+|||||||+...  -+.+++
T Consensus       224 LeKSNvLllGPtGsGKTllaq--TLAr~l  250 (564)
T KOG0745|consen  224 LEKSNVLLLGPTGSGKTLLAQ--TLARVL  250 (564)
T ss_pred             eecccEEEECCCCCchhHHHH--HHHHHh
Confidence            456689999999999997632  344444

>TIGR00665 DnaB replicative DNA helicase

Probab=83.86  E-value=1.5  Score=38.72  Aligned_cols=58  Identities=10%  Similarity=0.021  Sum_probs=35.0

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCC
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSAL   71 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~   71 (233)
                      ..|.=+++.|+||+||| +|++-++..+...      .+..+++++. -.=..|+.+++.....++
T Consensus       193 ~~G~l~vi~g~pg~GKT-~~~l~~a~~~a~~------~g~~vl~~Sl-Em~~~~i~~R~~~~~~~v  250 (434)
T TIGR00665       193 QPSDLIILAARPSMGKT-AFALNIAENAAIK------EGKPVAFFSL-EMSAEQLAMRMLSSESRV  250 (434)
T ss_pred             CCCeEEEEEeCCCCChH-HHHHHHHHHHHHh------CCCeEEEEeC-cCCHHHHHHHHHHHhcCC
Confidence            44666788999999999 5566666554421      2445676653 344555555555443333

This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.

>smart00115 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues

Probab=83.86  E-value=16  Score=29.54  Aligned_cols=65  Identities=12%  Similarity=0.215  Sum_probs=51.0

Q ss_pred             cCCCCeEEEEecch-----------hHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCC----CCCEEEecccCc
Q psy14082        103 KNPAFKVIVFVETK-----------KKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQG----KAPILVATDVAA  167 (233)
Q Consensus       103 ~~~~~k~iIf~~~~-----------~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g----~~~iLv~T~~~~  167 (233)
                      ..+.+.+||+.|..           ..++.+++.|++.|+.+ .++.+++.++-.+.+++|.+.    ..+++++. .++
T Consensus         5 ~~p~g~alII~n~~f~~~~~r~g~~~D~~~l~~~f~~lgF~V-~~~~dlt~~em~~~l~~~~~~~~~~~~d~~v~~-~~s   82 (241)
T smart00115        5 SKPRGLALIINNENFHSLPRRNGTDVDAENLTELFQSLGYEV-HVKNNLTAEEMLEELKEFAERPEHSDSDSFVCV-LLS   82 (241)
T ss_pred             CCCCcEEEEEECccCCCCcCCCCcHHHHHHHHHHHHHCCCEE-EEecCCCHHHHHHHHHHHHhccccCCCCEEEEE-EcC
Confidence            45667788888863           57999999999999987 567889999999999999763    35666665 566


Q ss_pred             CC
Q psy14082        168 RG  169 (233)
Q Consensus       168 ~G  169 (233)
                      .|
T Consensus        83 HG   84 (241)
T smart00115       83 HG   84 (241)
T ss_pred             CC
Confidence            66

Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=83.80  E-value=2.8  Score=36.95  Aligned_cols=53  Identities=13%  Similarity=0.030  Sum_probs=31.8

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHH
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKE   66 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~   66 (233)
                      ..|.=+++.|+||+||| +|++-+...+..      ..+..+++++. -.-..|+..++..
T Consensus       192 ~~g~liviag~pg~GKT-~~al~ia~~~a~------~~g~~v~~fSl-Em~~~~l~~Rl~~  244 (421)
T TIGR03600       192 VKGDLIVIGARPSMGKT-TLALNIAENVAL------REGKPVLFFSL-EMSAEQLGERLLA  244 (421)
T ss_pred             CCCceEEEEeCCCCCHH-HHHHHHHHHHHH------hCCCcEEEEEC-CCCHHHHHHHHHH
Confidence            44666788999999999 556666655431      12445777762 2334454444433

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B

Probab=83.77  E-value=0.56  Score=34.19  Aligned_cols=14  Identities=0%  Similarity=-0.555  Sum_probs=12.0

Q ss_pred             eeEecCCCCCchHH
Q psy14082         11 NFSKITNYLLSPPQ   24 (233)
Q Consensus        11 ~i~~a~tGsGKT~~   24 (233)
                      +++.+++|||||..
T Consensus         2 ii~~G~pgsGKSt~   15 (143)
T PF13671_consen    2 IILCGPPGSGKSTL   15 (143)
T ss_dssp             EEEEESTTSSHHHH
T ss_pred             EEEECCCCCCHHHH
Confidence            57899999999944

...

>TIGR02746 TraC-F-type type-IV secretion system protein TraC

Probab=83.56  E-value=1.4  Score=42.05  Aligned_cols=41  Identities=12%  Similarity=-0.148  Sum_probs=29.0

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHH
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTREL   56 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL   56 (233)
                      +.+.++.++||||||.. +--++..++.       .+.+++|+=|..+-
T Consensus       430 n~n~~I~G~tGsGKS~~-~~~l~~~~~~-------~g~~v~iiD~~~sy  470 (797)
T TIGR02746       430 NYNIAVVGGSGAGKSFF-MQELIVDNLS-------RGGKVWVIDVGRSY  470 (797)
T ss_pred             ccceEEEcCCCCCHHHH-HHHHHHHHHh-------CCCEEEEEeCCCCH
Confidence            45799999999999977 4445555543       35677777776544

The protein family described here is common among the F, P and I-like type IV secretion systems. Gene symbols include TraC (F-type), TrbE/VirB4 (P-type) and TraU (I-type). The protein conyains the Walker A and B motifs and so is a putative nucleotide triphosphatase.

>PRK05728 DNA polymerase III subunit chi; Validated

Probab=83.52  E-value=13  Score=27.41  Aligned_cols=85  Identities=18%  Similarity=0.207  Sum_probs=57.1

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEe-cccCcCCcCCCCccEEEEec
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVA-TDVAARGLDVEDVNTVNIGS  182 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~-T~~~~~Gldi~~v~~VI~~d  182 (233)
                      ..+.|++|.|.+.+.++.+-+.|-...-...+=|+-.....         .....|+++ ++.    -+.+..+++||.+
T Consensus        27 ~~g~rv~I~~~d~~~a~~lD~~LW~~~~~sFlPH~~~~~~~---------~~~~PV~l~~~~~----~~~~~~~~LinL~   93 (142)
T PRK05728         27 RAGWRVLVQCEDEEQAEALDEALWTFRDESFLPHGLAGEGP---------AAGQPVLLTWPGK----RNANHRDLLINLD   93 (142)
T ss_pred             HCCCEEEEEcCCHHHHHHHHHHhcCCCCCcCCCCCcCCCCC---------CCCCCEEEEcCCC----CCCCCCcEEEECC
Confidence            46889999999999999999999877656656666322110         124678887 321    2345667899887


Q ss_pred             C--CCCcccccceeeEEeecch
Q psy14082        183 L--QLSANHNISQVIEVVQDYE  202 (233)
Q Consensus       183 ~--P~~~~~~i~~~~~~~~~~~  202 (233)
                      .  |.... +..|++.++.+.+
T Consensus        94 ~~~p~~~~-~F~Rvieiv~~d~  114 (142)
T PRK05728         94 GAVPAFAA-AFERVVDFVGYDE  114 (142)
T ss_pred             CCCcchhh-cccEEEEEeCCCH
Confidence            4  44434 4489999996544

>PRK07004 replicative DNA helicase; Provisional

Probab=83.50  E-value=2.4  Score=37.87  Aligned_cols=52  Identities=8%  Similarity=-0.020  Sum_probs=30.8

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHH
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVA   64 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~   64 (233)
                      +..|.=+++.|.||+||| +|++-+.......      .+..+++++ ...=..|+..++
T Consensus       210 ~~~g~liviaarpg~GKT-~~al~ia~~~a~~------~~~~v~~fS-lEM~~~ql~~R~  261 (460)
T PRK07004        210 MHGGELIIVAGRPSMGKT-AFSMNIGEYVAVE------YGLPVAVFS-MEMPGTQLAMRM  261 (460)
T ss_pred             CCCCceEEEEeCCCCCcc-HHHHHHHHHHHHH------cCCeEEEEe-CCCCHHHHHHHH
Confidence            345666788899999999 5577666554321      244566665 223344444444

>KOG0741|consensus

Probab=83.44  E-value=15  Score=33.53  Aligned_cols=49  Identities=10%  Similarity=0.009  Sum_probs=31.4

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcH-------HHHHHHHHHHHHhh
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTR-------ELAQQIQTVAKEFS   68 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~Ptr-------eL~~Q~~~~~~~~~   68 (233)
                      -++..+|+|||||...+-..+.          ..-|-+=|++|..       +-|.-+.+.|+..+
T Consensus       540 SvLl~Gp~~sGKTaLAA~iA~~----------S~FPFvKiiSpe~miG~sEsaKc~~i~k~F~DAY  595 (744)
T KOG0741|consen  540 SVLLEGPPGSGKTALAAKIALS----------SDFPFVKIISPEDMIGLSESAKCAHIKKIFEDAY  595 (744)
T ss_pred             EEEEecCCCCChHHHHHHHHhh----------cCCCeEEEeChHHccCccHHHHHHHHHHHHHHhh
Confidence            4788999999999654332221          4467777777742       44556666666653

>KOG0329|consensus

Probab=83.26  E-value=3.2  Score=34.01  Aligned_cols=71  Identities=20%  Similarity=0.272  Sum_probs=53.2

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhC-----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc------cCcCCcCCC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRE-----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD------VAARGLDVE  173 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~------~~~~Gldi~  173 (233)
                      ..-.+++.|.|++.+..+.+...+.     +.++.++.||++-+.-.+.++.    -..|+|+|+      +-.+-+++.
T Consensus       109 g~vsvlvmchtrelafqi~~ey~rfskymP~vkvaVFfGG~~Ikkdee~lk~----~PhivVgTPGrilALvr~k~l~lk  184 (387)
T KOG0329|consen  109 GQVSVLVMCHTRELAFQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELLKN----CPHIVVGTPGRILALVRNRSLNLK  184 (387)
T ss_pred             CeEEEEEEeccHHHHHHHHHHHHHHHhhCCCceEEEEEcceeccccHHHHhC----CCeEEEcCcHHHHHHHHhccCchh
Confidence            3456799999999999988877654     5789999999998888887765    456889995      223456666


Q ss_pred             CccEEE
Q psy14082        174 DVNTVN  179 (233)
Q Consensus       174 ~v~~VI  179 (233)
                      ++.+.+
T Consensus       185 ~vkhFv  190 (387)
T KOG0329|consen  185 NVKHFV  190 (387)
T ss_pred             hcceee
Confidence            666544

>PRK05748 replicative DNA helicase; Provisional

Probab=82.80  E-value=2.1  Score=38.08  Aligned_cols=53  Identities=6%  Similarity=-0.035  Sum_probs=33.8

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHH
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKE   66 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~   66 (233)
                      ..|.=+++.|.||+||| +|++-++......      .+..+++++ ..+-..|+..++..
T Consensus       201 ~~G~livIaarpg~GKT-~~al~ia~~~a~~------~g~~v~~fS-lEms~~~l~~R~l~  253 (448)
T PRK05748        201 QPNDLIIVAARPSVGKT-AFALNIAQNVATK------TDKNVAIFS-LEMGAESLVMRMLC  253 (448)
T ss_pred             CCCceEEEEeCCCCCch-HHHHHHHHHHHHh------CCCeEEEEe-CCCCHHHHHHHHHH
Confidence            45666888999999999 5577676655321      244566664 33455666666643

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=82.74  E-value=2.2  Score=36.94  Aligned_cols=28  Identities=0%  Similarity=-0.263  Sum_probs=20.5

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhcc
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQ   36 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~   36 (233)
                      +.++++-++||||||++ +--+...+...
T Consensus        42 p~n~~iyG~~GTGKT~~-~~~v~~~l~~~   69 (366)
T COG1474          42 PSNIIIYGPTGTGKTAT-VKFVMEELEES   69 (366)
T ss_pred             CccEEEECCCCCCHhHH-HHHHHHHHHhh
Confidence            34589999999999988 44466666543

>COG4604 CeuD ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=82.66  E-value=2  Score=33.96  Aligned_cols=54  Identities=15%  Similarity=0.116  Sum_probs=34.7

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHH
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQI   60 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~   60 (233)
                      ++.|.=.=.++|.|.||+.  ++.+..++.......-.-..+-+-=.|+++||..+
T Consensus        24 i~~g~iTs~IGPNGAGKST--LLS~~sRL~~~d~G~i~i~g~~~~~~~s~~LAk~l   77 (252)
T COG4604          24 IPKGGITSIIGPNGAGKST--LLSMMSRLLKKDSGEITIDGLELTSTPSKELAKKL   77 (252)
T ss_pred             ecCCceeEEECCCCccHHH--HHHHHHHhccccCceEEEeeeecccCChHHHHHHH
Confidence            3456666678999999994  57788888865321111122334446899998654

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=82.62  E-value=1.3  Score=43.16  Aligned_cols=49  Identities=10%  Similarity=-0.129  Sum_probs=34.1

Q ss_pred             CCCCCc-eeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHH
Q psy14082          5 SESGCQ-NFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQ   61 (233)
Q Consensus         5 ~~~g~d-~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~   61 (233)
                      ++.+++ .++++..|||||.+ +-++.+.+ +      ..|.+++.++||---+..+.
T Consensus       358 il~s~~v~vv~G~AGTGKTT~-l~~~~~~~-e------~~G~~V~~~ApTGkAA~~L~  407 (988)
T PRK13889        358 VTDGRDLGVVVGYAGTGKSAM-LGVAREAW-E------AAGYEVRGAALSGIAAENLE  407 (988)
T ss_pred             HhcCCCeEEEEeCCCCCHHHH-HHHHHHHH-H------HcCCeEEEecCcHHHHHHHh
Confidence            345444 68899999999976 44444443 2      23778999999987776654

>PRK14729 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Provisional

Probab=82.52  E-value=0.77  Score=38.57  Aligned_cols=22  Identities=5%  Similarity=-0.218  Sum_probs=16.4

Q ss_pred             ceeEecCCCCCchHHhHHHHHHh
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVH   32 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~   32 (233)
                      =+++.+|||||||.. ++-+..+
T Consensus         6 ii~I~GpTasGKS~L-Al~LA~~   27 (300)
T PRK14729          6 IVFIFGPTAVGKSNI-LFHFPKG   27 (300)
T ss_pred             EEEEECCCccCHHHH-HHHHHHh
Confidence            378899999999965 5555543

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=82.51  E-value=5.5  Score=32.95  Aligned_cols=18  Identities=0%  Similarity=-0.476  Sum_probs=15.8

Q ss_pred             CCCceeEecCCCCCchHH
Q psy14082          7 SGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~   24 (233)
                      +.++|+--+|||+|||..
T Consensus       150 APknVLFyGppGTGKTm~  167 (368)
T COG1223         150 APKNVLFYGPPGTGKTMM  167 (368)
T ss_pred             CcceeEEECCCCccHHHH
Confidence            467899999999999976

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

Probab=82.46  E-value=5.9  Score=35.96  Aligned_cols=71  Identities=11%  Similarity=0.226  Sum_probs=47.4

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----cCcC-CcCCCC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----VAAR-GLDVED  174 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----~~~~-Gldi~~  174 (233)
                      .+.+++|.++|++-+.++.+.++..    ++.+..+.|+.+...+...   ++. ..+|+|+|.     .+.+ ++++.+
T Consensus       195 ~~~~aLIL~PTreLa~Qi~~~~~~l~~~~~~~~~~~~gG~~~~~q~~~---l~~-~~~IiV~TPgrL~~~l~~~~~~l~~  270 (518)
T PLN00206        195 RNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQLYR---IQQ-GVELIVGTPGRLIDLLSKHDIELDN  270 (518)
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHHH---hcC-CCCEEEECHHHHHHHHHcCCccchh
Confidence            5678999999999998877776543    4677778887665554332   333 478999993     3332 455556


Q ss_pred             ccEEE
Q psy14082        175 VNTVN  179 (233)
Q Consensus       175 v~~VI  179 (233)
                      +.++|
T Consensus       271 v~~lV  275 (518)
T PLN00206        271 VSVLV  275 (518)
T ss_pred             eeEEE
Confidence            66544

>KOG0743|consensus

Probab=82.39  E-value=17  Score=32.28  Aligned_cols=130  Identities=11%  Similarity=0.029  Sum_probs=73.6

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEcCCCC------
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGGTPK------   82 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~gg~~~------   82 (233)
                      -+.-+|+||||| +++.++.+.+.-        ...-|=|+-     .+--+.++++  ...-+..+++-+.+-      
T Consensus       238 YLLYGPPGTGKS-S~IaAmAn~L~y--------dIydLeLt~-----v~~n~dLr~LL~~t~~kSIivIEDIDcs~~l~~  303 (457)
T KOG0743|consen  238 YLLYGPPGTGKS-SFIAAMANYLNY--------DIYDLELTE-----VKLDSDLRHLLLATPNKSILLIEDIDCSFDLRE  303 (457)
T ss_pred             ceeeCCCCCCHH-HHHHHHHhhcCC--------ceEEeeecc-----ccCcHHHHHHHHhCCCCcEEEEeeccccccccc
Confidence            356799999999 556667666632        223332222     1222336666  222233333332111      


Q ss_pred             ---C----Ce---eEEeccchhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCC-CeeEEEeCCCCHHHHHHHHHH
Q psy14082         83 ---G----PQ---DCLPLHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRER-HSAICIHGDKTQQDRDYVLND  151 (233)
Q Consensus        83 ---~----~~---~lv~l~r~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~-~~~~~~~~~~~~~~r~~~~~~  151 (233)
                         +    .+   --|.|+-++..+.-........|++||+.  .+.+.+-..|-+.| ....++-|.-+...-....+.
T Consensus       304 ~~~~~~~~~~~~~~~VTlSGLLNfiDGlwSscg~ERIivFTT--Nh~EkLDPALlRpGRmDmhI~mgyCtf~~fK~La~n  381 (457)
T KOG0743|consen  304 RRKKKKENFEGDLSRVTLSGLLNFLDGLWSSCGDERIIVFTT--NHKEKLDPALLRPGRMDMHIYMGYCTFEAFKTLASN  381 (457)
T ss_pred             ccccccccccCCcceeehHHhhhhhccccccCCCceEEEEec--CChhhcCHhhcCCCcceeEEEcCCCCHHHHHHHHHH
Confidence               1    01   12555555555555555666788888875  56777777776655 455566666677777777777


Q ss_pred             hhCCC
Q psy14082        152 FRQGK  156 (233)
Q Consensus       152 f~~g~  156 (233)
                      |-..+
T Consensus       382 YL~~~  386 (457)
T KOG0743|consen  382 YLGIE  386 (457)
T ss_pred             hcCCC
Confidence            76554

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=82.38  E-value=35  Score=30.27  Aligned_cols=48  Identities=8%  Similarity=0.090  Sum_probs=33.2

Q ss_pred             hHHHHHHHHHhhCC-----CeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc
Q psy14082        117 KKVEDITRALRRER-----HSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD  164 (233)
Q Consensus       117 ~~~~~l~~~L~~~~-----~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~  164 (233)
                      ..++.+.+.+...+     ....++.+...+++-..+.+.|..-.++-+|-|.
T Consensus       316 ~~l~eL~~~~~~~~~~~~~e~~LVLsAt~~~~~~~~~~~~f~~~~~~glIlTK  368 (432)
T PRK12724        316 EQLERMQSFYSCFGEKDSVENLLVLSSTSSYHHTLTVLKAYESLNYRRILLTK  368 (432)
T ss_pred             HHHHHHHHHHHhhcCCCCCeEEEEEeCCCCHHHHHHHHHHhcCCCCCEEEEEc
Confidence            44555555554321     2456677888888889999999887788777774

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

Probab=82.28  E-value=4.2  Score=37.37  Aligned_cols=58  Identities=17%  Similarity=0.243  Sum_probs=51.5

Q ss_pred             CCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEec
Q psy14082        106 AFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVAT  163 (233)
Q Consensus       106 ~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T  163 (233)
                      .+-+||..+-..-.+.=.+.|+..|+.+..+++.++.++|..+++.+..|++++|--+
T Consensus        57 ~G~TLVVSPLiSLM~DQV~~l~~~Gi~A~~lnS~l~~~e~~~v~~~l~~g~~klLyis  114 (590)
T COG0514          57 EGLTLVVSPLISLMKDQVDQLEAAGIRAAYLNSTLSREERQQVLNQLKSGQLKLLYIS  114 (590)
T ss_pred             CCCEEEECchHHHHHHHHHHHHHcCceeehhhcccCHHHHHHHHHHHhcCceeEEEEC
Confidence            3478888888888888788899999999999999999999999999999999998555

>KOG1133|consensus

Probab=82.25  E-value=11  Score=35.38  Aligned_cols=32  Identities=25%  Similarity=0.415  Sum_probs=23.1

Q ss_pred             CCCCEEEe--cccCcCCcCCCC--ccEEEEecCCCC
Q psy14082        155 GKAPILVA--TDVAARGLDVED--VNTVNIGSLQLS  186 (233)
Q Consensus       155 g~~~iLv~--T~~~~~Gldi~~--v~~VI~~d~P~~  186 (233)
                      |.--+|.+  -.-+++|||+.+  ..+|+..++|-.
T Consensus       686 g~GaiLlaVVGGKlSEGINF~D~LgRaVvvVGlPyP  721 (821)
T KOG1133|consen  686 GRGAILLAVVGGKLSEGINFSDDLGRAVVVVGLPYP  721 (821)
T ss_pred             CCCeEEEEEeccccccccccccccccEEEEeecCCC
Confidence            34346644  467899999987  678999998743

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=82.13  E-value=1.6  Score=32.05  Aligned_cols=27  Identities=7%  Similarity=-0.189  Sum_probs=19.7

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhh
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      ..|.-+.+.++.|+||| +++-.+...+
T Consensus        20 ~~~~~i~l~G~lGaGKT-tl~~~l~~~l   46 (133)
T TIGR00150        20 DFGTVVLLKGDLGAGKT-TLVQGLLQGL   46 (133)
T ss_pred             CCCCEEEEEcCCCCCHH-HHHHHHHHHc
Confidence            34556778999999999 5566666654

Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity.

>KOG0991|consensus

Probab=82.11  E-value=1.3  Score=35.88  Aligned_cols=25  Identities=8%  Similarity=-0.200  Sum_probs=19.0

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhhhc
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHISH   35 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l~~   35 (233)
                      ++++.+|+|+|||.+ +..+...++.
T Consensus        50 ~liisGpPG~GKTTs-i~~LAr~LLG   74 (333)
T KOG0991|consen   50 NLIISGPPGTGKTTS-ILCLARELLG   74 (333)
T ss_pred             ceEeeCCCCCchhhH-HHHHHHHHhC
Confidence            578999999999988 4445555554

>PRK14530 adenylate kinase; Provisional

Probab=82.09  E-value=0.9  Score=36.00  Aligned_cols=18  Identities=11%  Similarity=-0.339  Sum_probs=15.5

Q ss_pred             CCCceeEecCCCCCchHH
Q psy14082          7 SGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~   24 (233)
                      .|..+++.+++|||||..
T Consensus         2 ~~~~I~i~G~pGsGKsT~   19 (215)
T PRK14530          2 SQPRILLLGAPGAGKGTQ   19 (215)
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            567799999999999965

>TIGR03496 FliI_clade1 flagellar protein export ATPase FliI

Probab=82.09  E-value=34  Score=30.18  Aligned_cols=20  Identities=5%  Similarity=-0.286  Sum_probs=16.7

Q ss_pred             CCCCCceeEecCCCCCchHH
Q psy14082          5 SESGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~   24 (233)
                      +..|.-+.+.+++|+|||..
T Consensus       134 i~~Gq~~~I~G~sG~GKTtL  153 (411)
T TIGR03496       134 VGRGQRMGIFAGSGVGKSTL  153 (411)
T ss_pred             EecCcEEEEECCCCCCHHHH
Confidence            45677788999999999975

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>KOG0391|consensus

Probab=82.08  E-value=2.9  Score=41.38  Aligned_cols=66  Identities=18%  Similarity=0.251  Sum_probs=49.2

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCC
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTP   81 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~   81 (233)
                      +-|..-.-|-|||.. .|.++.++.=.+.   +=||. ||+|||- ....|.-+|++|.+++++...+|...
T Consensus       636 NGILADEmGLGKTIQ-tISllAhLACeeg---nWGPH-LIVVpTs-viLnWEMElKRwcPglKILTYyGs~k  701 (1958)
T KOG0391|consen  636 NGILADEMGLGKTIQ-TISLLAHLACEEG---NWGPH-LIVVPTS-VILNWEMELKRWCPGLKILTYYGSHK  701 (1958)
T ss_pred             cceehhhhcccchhH-HHHHHHHHHhccc---CCCCc-eEEeech-hhhhhhHHHhhhCCcceEeeecCCHH
Confidence            345556689999987 6777777764321   22555 8889994 45678899999999999999999744

>COG5008 PilU Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=81.99  E-value=1.8  Score=35.83  Aligned_cols=25  Identities=4%  Similarity=-0.287  Sum_probs=18.7

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhhcc
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHISHQ   36 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~~~   36 (233)
                      +|+.++|||||+.+ +..++.+-.++
T Consensus       130 viiVGaTGSGKSTt-mAaMi~yRN~~  154 (375)
T COG5008         130 VIIVGATGSGKSTT-MAAMIGYRNKN  154 (375)
T ss_pred             EEEECCCCCCchhh-HHHHhcccccC
Confidence            77899999999977 55666655443

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=81.81  E-value=2.2  Score=36.98  Aligned_cols=26  Identities=0%  Similarity=-0.291  Sum_probs=19.7

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      +..+++.+++|+|||.+ +--++..+.
T Consensus        55 ~~~~lI~G~~GtGKT~l-~~~v~~~l~   80 (394)
T PRK00411         55 PLNVLIYGPPGTGKTTT-VKKVFEELE   80 (394)
T ss_pred             CCeEEEECCCCCCHHHH-HHHHHHHHH
Confidence            35699999999999977 555555554

>PF03029 ATP_bind_1: Conserved hypothetical ATP binding protein; InterPro: IPR004130 Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity

Probab=81.76  E-value=1.5  Score=35.52  Aligned_cols=23  Identities=0%  Similarity=-0.242  Sum_probs=17.2

Q ss_pred             EecCCCCCchHHhHHHHHHhhhcc
Q psy14082         13 SKITNYLLSPPQYMLPAAVHISHQ   36 (233)
Q Consensus        13 ~~a~tGsGKT~~~~lp~l~~l~~~   36 (233)
                      +.+|.||||| +|.-.+-+++..+
T Consensus         1 ViGpaGSGKT-T~~~~~~~~~~~~   23 (238)
T PF03029_consen    1 VIGPAGSGKT-TFCKGLSEWLESN   23 (238)
T ss_dssp             -EESTTSSHH-HHHHHHHHHHTTT
T ss_pred             CCCCCCCCHH-HHHHHHHHHHHhc
Confidence            4789999999 7777777766543

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>COG3451 VirB4 Type IV secretory pathway, VirB4 components [Intracellular trafficking and secretion]

Probab=81.71  E-value=1.6  Score=41.77  Aligned_cols=25  Identities=0%  Similarity=-0.343  Sum_probs=18.0

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhh
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      .+.++.++||+|||+. +-.++....
T Consensus       437 ghT~I~G~tGaGKTvL-l~~llaq~~  461 (796)
T COG3451         437 GHTLIIGPTGAGKTVL-LSFLLAQAL  461 (796)
T ss_pred             CCeEEECCCCCCHHHH-HHHHHHHHH
Confidence            3789999999999955 444554444

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=81.70  E-value=4.5  Score=33.50  Aligned_cols=35  Identities=14%  Similarity=-0.034  Sum_probs=21.6

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEc
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLA   51 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~   51 (233)
                      +=+.+.+++|+|||.+.+- +...+..       .+.+++++.
T Consensus        73 ~vi~l~G~~G~GKTTt~ak-LA~~l~~-------~g~~V~li~  107 (272)
T TIGR00064        73 NVILFVGVNGVGKTTTIAK-LANKLKK-------QGKSVLLAA  107 (272)
T ss_pred             eEEEEECCCCCcHHHHHHH-HHHHHHh-------cCCEEEEEe
Confidence            3466779999999977433 3333432       245666665

There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.

>TIGR01043 ATP_syn_A_arch ATP synthase archaeal, A subunit

Probab=81.67  E-value=35  Score=31.46  Aligned_cols=53  Identities=11%  Similarity=0.039  Sum_probs=32.2

Q ss_pred             CCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          4 PSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         4 ~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ++-.|.-+-+-++.|+|||..     ++.+.+.    .+....+.+.|=  |-...+.+.++.+
T Consensus       218 Pi~kGqr~~I~gg~G~GKT~l-----~~~lak~----~~adivVyvg~G--ERG~E~~e~le~f  270 (578)
T TIGR01043       218 PIAKGGTAAIPGPFGSGKTVT-----QHQLAKW----SDADIVVYIGCG--ERGNEMTDVLEEF  270 (578)
T ss_pred             cccCCCEEEEecCCCCCHHHH-----HHHHHhc----CCCCEEEEEEec--cChHHHHHHHHHh
Confidence            456677788899999999974     3333221    123333444443  4566777677666

Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases.

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=81.58  E-value=1.2  Score=33.76  Aligned_cols=29  Identities=3%  Similarity=-0.220  Sum_probs=16.5

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhc
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISH   35 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~   35 (233)
                      -.++-+++.+++|+|||.. +--++.++..
T Consensus        22 ~~~~~~ll~G~~G~GKT~l-l~~~~~~~~~   50 (185)
T PF13191_consen   22 GSPRNLLLTGESGSGKTSL-LRALLDRLAE   50 (185)
T ss_dssp             -----EEE-B-TTSSHHHH-HHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHH-HHHHHHHHHh
Confidence            3467799999999999955 5556655554

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=81.54  E-value=1.8  Score=31.95  Aligned_cols=24  Identities=0%  Similarity=-0.287  Sum_probs=17.9

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhhc
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHISH   35 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~~   35 (233)
                      +.+.++.|||||.. +--++..+.+
T Consensus         3 v~VvG~~~sGKTTl-~~~Li~~l~~   26 (140)
T PF03205_consen    3 VQVVGPKNSGKTTL-IRKLINELKR   26 (140)
T ss_dssp             EEEEESTTSSHHHH-HHHHHHHHHH
T ss_pred             EEEECCCCCCHHHH-HHHHHHHHhH
Confidence            46789999999944 6667776654

>TIGR03744 traC_PFL_4706 conjugative transfer ATPase, PFL_4706 family

Probab=81.54  E-value=1.7  Score=42.25  Aligned_cols=41  Identities=2%  Similarity=-0.039  Sum_probs=30.4

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHH
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRE   55 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~Ptre   55 (233)
                      ..+.++.++||||||+. +-.++..++..      .+++++|+=|-++
T Consensus       475 n~n~~I~G~TGSGKS~l-~~~li~q~~~~------~~~~v~IiD~g~s  515 (893)
T TIGR03744       475 NAHLLILGPTGAGKSAT-LTNLLMQVMAV------HRPRLFIVEAGNS  515 (893)
T ss_pred             cccEEEECCCCCCHHHH-HHHHHHHHHHh------cCCEEEEEcCCCC
Confidence            46789999999999976 55566555532      2678888888776

Members of this protein family are predicted ATP-binding proteins apparently associated with DNA conjugal transfer. Members are found both in plasmids and in bacterial chromosomal regions that appear to derive from integrative elements such as conjugative transposons. More distant homologs, outside the scope of this family, include type IV secretion/conjugal transfer proteins such as TraC, VirB4 and TrsE. The granularity of this protein family definition is chosen so as to represent one distinctive clade and act as a marker through which to define and recognize the class of mobile element it serves.

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes

Probab=81.51  E-value=2.3  Score=32.26  Aligned_cols=23  Identities=4%  Similarity=-0.211  Sum_probs=15.7

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhh
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      +++.+++|+|||.. ..-+...+.
T Consensus         3 ~~~~G~~G~GKTt~-~~~la~~~~   25 (173)
T cd03115           3 ILLVGLQGVGKTTT-AAKLALYLK   25 (173)
T ss_pred             EEEECCCCCCHHHH-HHHHHHHHH
Confidence            46789999999976 444444443

SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=81.46  E-value=1.4  Score=30.81  Aligned_cols=24  Identities=4%  Similarity=-0.234  Sum_probs=17.8

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhhc
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHISH   35 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~~   35 (233)
                      +++.+++|+|||.. +-.++..+.+
T Consensus         1 I~i~G~~G~GKS~l-~~~l~~~l~~   24 (107)
T PF00910_consen    1 IWIYGPPGIGKSTL-AKELAKDLLK   24 (107)
T ss_pred             CEEECCCCCCHHHH-HHHHHHHHHH
Confidence            57889999999976 5556665654

All of the proteins bind ATP and, consequently, all of them carry the classical Walker A (phosphate-binding loop or P-loop) and Walker B (Mg2+-binding aspartic acid) motifs. Superfamily 3 consists of helicases encoded mainly by small DNA viruses and some large nucleocytoplasmic DNA viruses [, ]. Small viruses are very dependent on the host-cell machinery to replicate. SF3 helicase in small viruses is associated with an origin-binding domain. By pairing a domain that recognises the ori with a helicase, the virus can bypass the host-cell-based regulation pathway and initiate its own replication. The protein binds to the viral ori leading to origin unwinding. Cellular replication proteins are then recruited to the ori and the viral DNA is replicated. In SF3 helicases the Walker A and Walker B motifs are separated by spacers of rather uniform, and relatively short, length. In addition to the A and B motifs this family is characterised by a third motif (C) which resides between the B motif and the C terminus of the conserved region. This motif consists of an Asn residue preceded by a run of hydrophobic residues []. Several structures of SF3 helicases have been solved []. They all possess the same core alpha/beta fold, consisting of a five-stranded parallel beta sheet flanked on both sides by several alpha helices. In contrast to SF1 and SF2 helicases, which have RecA-like core folds, the strand connectivity within the alpha/beta core domain is that of AAA+ proteins []. The SF3 helicase proteins assemble into a hexameric ring. Some proteins known to contain an SF3 helicase domain are listed below: Polyomavirus large T antigen. It initiates DNA unwinding and replication via interactions with the viral origin of replication. Papillomavirus E1 protein. An ATP-dependent DNA helicase required for initiation of viral DNA replication. Parvovirus Rep/NS1 protein, which is also required for the initiation of viral replication. Poxviridae and other large DNA viruses D5 protein. Bacteriophage DNA primase/helicase protein. Bacterial prophage DNA primase/helicase protein. The entry represents the core alpha/beta fold of the SF3 helicase domain found predominantly in DNA viruses.; GO: 0003723 RNA binding, 0003724 RNA helicase activity

>PRK07960 fliI flagellum-specific ATP synthase; Validated

Probab=81.38  E-value=20  Score=32.02  Aligned_cols=49  Identities=10%  Similarity=-0.085  Sum_probs=28.7

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHH
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQI   60 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~   60 (233)
                      +-.|.-+.+.+++|+|||...  -++..+...     ..-..+.|-...+|....+
T Consensus       172 I~~Gqri~I~G~sG~GKTTLL--~~Ia~~~~~-----d~iv~g~Igerg~ev~e~~  220 (455)
T PRK07960        172 VGRGQRMGLFAGSGVGKSVLL--GMMARYTQA-----DVIVVGLIGERGREVKDFI  220 (455)
T ss_pred             ccCCcEEEEECCCCCCccHHH--HHHhCCCCC-----CEEEEEEEEECCeEHHHHH
Confidence            456788899999999999652  233322211     1112345666777775433

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

Probab=81.36  E-value=6.7  Score=37.37  Aligned_cols=56  Identities=21%  Similarity=0.333  Sum_probs=44.6

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhC---CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRE---RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD  164 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~---~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~  164 (233)
                      .+..++|+.++|++-+......+++.   ++++..++|+.+.++|..+    + ...+|+++|+
T Consensus        79 ~~~~~aL~l~PtraLa~q~~~~l~~l~~~~i~v~~~~Gdt~~~~r~~i----~-~~~~IivtTP  137 (742)
T TIGR03817        79 DPRATALYLAPTKALAADQLRAVRELTLRGVRPATYDGDTPTEERRWA----R-EHARYVLTNP  137 (742)
T ss_pred             CCCcEEEEEcChHHHHHHHHHHHHHhccCCeEEEEEeCCCCHHHHHHH----h-cCCCEEEECh
Confidence            45679999999999999999998875   5788889999998776432    2 2368999995

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.

>PF03237 Terminase_6: Terminase-like family; InterPro: IPR004921 The terminase is a component of the molecular motor that translocates genomic DNA into empty capsids during DNA packaging []

Probab=81.31  E-value=4.5  Score=34.17  Aligned_cols=45  Identities=4%  Similarity=-0.134  Sum_probs=26.9

Q ss_pred             eEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHH
Q psy14082         12 FSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQ   61 (233)
Q Consensus        12 i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~   61 (233)
                      ++.++.|+|||.+.+.-++..+...+     ++..+++...+.++...+.
T Consensus         1 ~i~~~r~~GKT~~~~~~~~~~~~~~~-----~~~~vi~~~~~~~~~~~~~   45 (384)
T PF03237_consen    1 LINGGRGSGKTTLIAIWFLWWALTRP-----PGRRVIIASTYRQARDIFG   45 (384)
T ss_dssp             -EEE-SSS-HHHHHHHHHHHHHHSSS-----S--EEEEEESSHHHHHHHH
T ss_pred             CCcCCccccHHHHHHHHHHHHHhhCC-----CCcEEEEecCHHHHHHHHH
Confidence            35788999999998887887777641     2355666655555555433

The large subunit heterodimerises with the small terminase protein, which is docked on the capsid portal protein. The latter forms a ring through which genomic DNA is translocated into the capsid. The terminase protein may have or induce an endonuclease activity to cleave DNA after encapsidation. This entry represents a family of terminase large subunits found in a variety of the Caudovirales and prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) [], including ORFg2 (RCAP_rcc01683) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in ].; PDB: 2O0K_A 3CPE_A 2O0J_A 2O0H_A 3C6H_A 3C6A_A.

>PRK08506 replicative DNA helicase; Provisional

Probab=81.30  E-value=2.4  Score=38.08  Aligned_cols=52  Identities=10%  Similarity=-0.065  Sum_probs=32.7

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      .|.=+++.|.||.||| +|++-++.....       .+..+++++. -.=..|+..++...
T Consensus       191 ~G~LivIaarpg~GKT-~fal~ia~~~~~-------~g~~V~~fSl-EMs~~ql~~Rlla~  242 (472)
T PRK08506        191 KGDLIIIAARPSMGKT-TLCLNMALKALN-------QDKGVAFFSL-EMPAEQLMLRMLSA  242 (472)
T ss_pred             CCceEEEEcCCCCChH-HHHHHHHHHHHh-------cCCcEEEEeC-cCCHHHHHHHHHHH
Confidence            4555778888999999 557766666543       2445676653 24455666555443

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=81.27  E-value=3.6  Score=38.06  Aligned_cols=47  Identities=9%  Similarity=-0.056  Sum_probs=30.5

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHH
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTV   63 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~   63 (233)
                      -+++.+++|+|||.. +..+.+.+...     ..+.+++++ +..+++.+....
T Consensus       316 pL~LyG~sGsGKTHL-L~AIa~~a~~~-----~~g~~V~Yi-taeef~~el~~a  362 (617)
T PRK14086        316 PLFIYGESGLGKTHL-LHAIGHYARRL-----YPGTRVRYV-SSEEFTNEFINS  362 (617)
T ss_pred             cEEEECCCCCCHHHH-HHHHHHHHHHh-----CCCCeEEEe-eHHHHHHHHHHH
Confidence            488999999999976 55566665532     235566655 455666555443

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=81.27  E-value=7.8  Score=36.71  Aligned_cols=57  Identities=12%  Similarity=-0.031  Sum_probs=46.1

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhh----CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEeccc
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRR----ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDV  165 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~  165 (233)
                      ...+.++.|.++|..-+...++.+..    .|+++.+++|+++.++|...++      .+|+++|+.
T Consensus        94 aL~G~~V~VvTpt~~LA~qdae~~~~l~~~LGLsv~~i~g~~~~~~r~~~y~------~dIvyGT~~  154 (745)
T TIGR00963        94 ALTGKGVHVVTVNDYLAQRDAEWMGQVYRFLGLSVGLILSGMSPEERREAYA------CDITYGTNN  154 (745)
T ss_pred             HHhCCCEEEEcCCHHHHHHHHHHHHHHhccCCCeEEEEeCCCCHHHHHHhcC------CCEEEECCC
Confidence            34566899999999888888777754    5899999999999888776653      689999975

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.

>PRK04192 V-type ATP synthase subunit A; Provisional

Probab=81.24  E-value=39  Score=31.22  Aligned_cols=53  Identities=11%  Similarity=0.060  Sum_probs=31.5

Q ss_pred             CCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          4 PSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         4 ~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ++..|.-+-+-++.|+|||..     .+.+.++.    +..  ++|.+--=|-...+.+.+..|
T Consensus       223 Pi~kGq~~~Ipg~~G~GKTvl-----~~~iak~a----~ad--ivVyvg~GERg~E~~e~l~ef  275 (586)
T PRK04192        223 PVAKGGTAAIPGPFGSGKTVT-----QHQLAKWA----DAD--IVIYVGCGERGNEMTEVLEEF  275 (586)
T ss_pred             ccccCCeEEEecCCCCCHHHH-----HHHHHhcC----CCC--EEEEEEcCcChHHHHHHHHHH
Confidence            455677777888999999943     23333221    223  444444446666666666666

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=81.21  E-value=1.2  Score=33.43  Aligned_cols=21  Identities=5%  Similarity=-0.406  Sum_probs=14.2

Q ss_pred             eeEecCCCCCchHHhHHHHHHh
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVH   32 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~   32 (233)
                      +++.+++|||||.. +-.+...
T Consensus         1 i~l~G~~GsGKSTl-a~~l~~~   21 (163)
T TIGR01313         1 FVLMGVAGSGKSTI-ASALAHR   21 (163)
T ss_pred             CEEECCCCCCHHHH-HHHHHHh
Confidence            36789999999944 4434433

This model represents a subfamily of proteins that includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases.

>PRK05595 replicative DNA helicase; Provisional

Probab=81.18  E-value=2.2  Score=37.94  Aligned_cols=57  Identities=9%  Similarity=-0.001  Sum_probs=33.9

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCC
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSAL   71 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~   71 (233)
                      .|.=+++.|.||.||| +|++-+..++..      ..+..+++++. ..-..|+..++.....++
T Consensus       200 ~g~liviaarpg~GKT-~~al~ia~~~a~------~~g~~vl~fSl-Ems~~~l~~R~~a~~~~v  256 (444)
T PRK05595        200 KGDMILIAARPSMGKT-TFALNIAEYAAL------REGKSVAIFSL-EMSKEQLAYKLLCSEANV  256 (444)
T ss_pred             CCcEEEEEecCCCChH-HHHHHHHHHHHH------HcCCcEEEEec-CCCHHHHHHHHHHHhcCC
Confidence            3555677888999999 556666655432      12556777754 234555555554443333

>KOG0060|consensus

Probab=81.15  E-value=0.91  Score=41.24  Aligned_cols=29  Identities=10%  Similarity=-0.179  Sum_probs=22.0

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhc
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISH   35 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~   35 (233)
                      +++|+++++.+|+|+|||-.  +-++.-+..
T Consensus       458 V~~g~~LLItG~sG~GKtSL--lRvlggLWp  486 (659)
T KOG0060|consen  458 VPSGQNLLITGPSGCGKTSL--LRVLGGLWP  486 (659)
T ss_pred             ecCCCeEEEECCCCCchhHH--HHHHhcccc
Confidence            56899999999999999943  445555544

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=81.15  E-value=6  Score=40.48  Aligned_cols=72  Identities=22%  Similarity=0.240  Sum_probs=53.3

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhh----------------CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEeccc---
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRR----------------ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDV---  165 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~----------------~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~---  165 (233)
                      .+.++|+.++++.-+..+.+.|+.                .++++...||+.+.++|.+.++    ...+|||+|.-   
T Consensus        36 ~~~raLYISPLKALa~Dv~~~L~~pl~~i~~~~~~~g~~~~~i~V~vrtGDt~~~eR~rll~----~ppdILVTTPEsL~  111 (1490)
T PRK09751         36 KTSRILYISPIKALGTDVQRNLQIPLKGIADERRRRGETEVNLRVGIRTGDTPAQERSKLTR----NPPDILITTPESLY  111 (1490)
T ss_pred             CCCEEEEEeChHHHHHHHHHHHHHHHHhhhhhhhhcccccCceEEEEEECCCCHHHHHHHhc----CCCCEEEecHHHHH
Confidence            356899999999999988887752                3678899999999999877554    36789999942   


Q ss_pred             --Cc-CC-cCCCCccEEEE
Q psy14082        166 --AA-RG-LDVEDVNTVNI  180 (233)
Q Consensus       166 --~~-~G-ldi~~v~~VI~  180 (233)
                        +. ++ ..+.++++||.
T Consensus       112 ~LLtsk~r~~L~~Vr~VIV  130 (1490)
T PRK09751        112 LMLTSRARETLRGVETVII  130 (1490)
T ss_pred             HHHhhhhhhhhccCCEEEE
Confidence              22 22 24667777663

>KOG1015|consensus

Probab=81.04  E-value=2.5  Score=40.82  Aligned_cols=52  Identities=13%  Similarity=-0.043  Sum_probs=38.7

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      +|..=.-|.|||+. ++..++.++...+   ..-.++||+||- .-+..|.+.|.+|
T Consensus       699 cILAHcMGLGKTlQ-VvtflhTvL~c~k---lg~ktaLvV~Pl-Nt~~NW~~EFekW  750 (1567)
T KOG1015|consen  699 CILAHCMGLGKTLQ-VVTFLHTVLLCDK---LGFKTALVVCPL-NTALNWMNEFEKW  750 (1567)
T ss_pred             hHHHHhhcccceeh-hhHHHHHHHHhhc---cCCceEEEEcch-HHHHHHHHHHHHh
Confidence            44444568999988 6777777775432   446789999996 5677899999998

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=81.00  E-value=3  Score=35.09  Aligned_cols=19  Identities=5%  Similarity=-0.436  Sum_probs=15.4

Q ss_pred             CCCCceeEecCCCCCchHH
Q psy14082          6 ESGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~   24 (233)
                      +.|.=+.+.+++|+|||..
T Consensus        93 ~~g~i~ei~G~~g~GKT~l  111 (310)
T TIGR02236        93 ETQAITEVFGEFGSGKTQI  111 (310)
T ss_pred             CCCeEEEEECCCCCCHHHH
Confidence            4566678999999999955

This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.

>KOG1001|consensus

Probab=80.74  E-value=0.04  Score=51.14  Aligned_cols=82  Identities=13%  Similarity=0.123  Sum_probs=71.1

Q ss_pred             CeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCC-CCEE-EecccCcCCcCCCCccEEEEecCC
Q psy14082        107 FKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGK-APIL-VATDVAARGLDVEDVNTVNIGSLQ  184 (233)
Q Consensus       107 ~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~-~~iL-v~T~~~~~Gldi~~v~~VI~~d~P  184 (233)
                      .+++||+.-..-+..+.-.|...++....+.|.|+...|...+..|..+. ..+| ++..+..-|+++....+|+..|+=
T Consensus       540 ~kiiifsq~~~~l~l~~~~l~~~~~~~~~~~g~~~~~~r~~s~~~~~~~~~~~vll~Slkag~~glnlt~a~~v~~~d~~  619 (674)
T KOG1001|consen  540 PKIVIFSQLIWGLALVCLRLFFKGFVFLRYDGEMLMKIRTKSFTDFPCDPLVTALLMSLKAGKVGLNLTAASHVLLMDPW  619 (674)
T ss_pred             CceeeehhHHHHHHHhhhhhhhcccccchhhhhhHHHHHHhhhcccccCccHHHHHHHHHHhhhhhchhhhhHHHhhchh
Confidence            39999999999998888888888888888999999999999999998553 3344 677889999999999999999987


Q ss_pred             CCcc
Q psy14082        185 LSAN  188 (233)
Q Consensus       185 ~~~~  188 (233)
                      +++.
T Consensus       620 wnp~  623 (674)
T KOG1001|consen  620 WNPA  623 (674)
T ss_pred             cChH
Confidence            7764

>smart00450 RHOD Rhodanese Homology Domain

Probab=80.63  E-value=3.3  Score=27.46  Aligned_cols=39  Identities=13%  Similarity=0.192  Sum_probs=33.4

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhCCCe-eEEEeCCCC
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRERHS-AICIHGDKT  141 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~-~~~~~~~~~  141 (233)
                      ..+..+++++|.+...+...+..|.+.|+. +..+.|++.
T Consensus        53 ~~~~~~iv~~c~~g~~a~~~~~~l~~~G~~~v~~l~GG~~   92 (100)
T smart00450       53 LDKDKPVVVYCRSGNRSAKAAWLLRELGFKNVYLLDGGYK   92 (100)
T ss_pred             CCCCCeEEEEeCCCcHHHHHHHHHHHcCCCceEEecCCHH
Confidence            456689999999999999999999999987 888888864

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.

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=80.53  E-value=1.4  Score=35.15  Aligned_cols=28  Identities=11%  Similarity=-0.100  Sum_probs=20.7

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhc
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISH   35 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~   35 (233)
                      -.|.=+.+++|+|||||.  ++-+++.|-.
T Consensus        26 ~~Gevv~iiGpSGSGKST--lLRclN~LE~   53 (240)
T COG1126          26 EKGEVVVIIGPSGSGKST--LLRCLNGLEE   53 (240)
T ss_pred             cCCCEEEEECCCCCCHHH--HHHHHHCCcC
Confidence            356678899999999994  4556766643

>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=80.50  E-value=5.6  Score=35.76  Aligned_cols=55  Identities=20%  Similarity=-0.019  Sum_probs=41.1

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ..|.. -+.+--|||||...++-+.+..+.      ++.-+.+|=+-|+-|+.|+.+...+|
T Consensus       175 ~~G~q-rIrGLAGSGKT~~La~Kaa~lh~k------nPd~~I~~Tfftk~L~s~~r~lv~~F  229 (660)
T COG3972         175 GFGKQ-RIRGLAGSGKTELLAHKAAELHSK------NPDSRIAFTFFTKILASTMRTLVPEF  229 (660)
T ss_pred             CCchh-hhhcccCCCchhHHHHHHHHHhcC------CCCceEEEEeehHHHHHHHHHHHHHH
Confidence            34555 346668999998866555444433      45778999999999999999999988

>KOG0326|consensus

Probab=80.37  E-value=3.6  Score=34.80  Aligned_cols=126  Identities=17%  Similarity=0.266  Sum_probs=77.7

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhh----CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEec-----ccCcCCcC-C
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRR----ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVAT-----DVAARGLD-V  172 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T-----~~~~~Gld-i  172 (233)
                      ....-+++|.+++++-+-...+...+    .++.+.+.+|+.+-.  ..+++-.  +...++|+|     |...+|+- +
T Consensus       150 ~~~~IQ~~ilVPtrelALQtSqvc~~lskh~~i~vmvttGGT~lr--DDI~Rl~--~~VH~~vgTPGRIlDL~~KgVa~l  225 (459)
T KOG0326|consen  150 KKNVIQAIILVPTRELALQTSQVCKELSKHLGIKVMVTTGGTSLR--DDIMRLN--QTVHLVVGTPGRILDLAKKGVADL  225 (459)
T ss_pred             cccceeEEEEeecchhhHHHHHHHHHHhcccCeEEEEecCCcccc--cceeeec--CceEEEEcCChhHHHHHhcccccc
Confidence            44556899999999977665554433    478999999997744  3554432  457888988     45555542 2


Q ss_pred             CCccEEE------------------------------Eec--CCCCccccc---------------------ceeeEEee
Q psy14082        173 EDVNTVN------------------------------IGS--LQLSANHNI---------------------SQVIEVVQ  199 (233)
Q Consensus       173 ~~v~~VI------------------------------~~d--~P~~~~~~i---------------------~~~~~~~~  199 (233)
                      .++..++                              .|+  +|.....|.                     .+...|+.
T Consensus       226 s~c~~lV~DEADKlLs~~F~~~~e~li~~lP~~rQillySATFP~tVk~Fm~~~l~kPy~INLM~eLtl~GvtQyYafV~  305 (459)
T KOG0326|consen  226 SDCVILVMDEADKLLSVDFQPIVEKLISFLPKERQILLYSATFPLTVKGFMDRHLKKPYEINLMEELTLKGVTQYYAFVE  305 (459)
T ss_pred             hhceEEEechhhhhhchhhhhHHHHHHHhCCccceeeEEecccchhHHHHHHHhccCcceeehhhhhhhcchhhheeeec
Confidence            2222221                              121  233322222                     37778888


Q ss_pred             cchHHHHHHHHHHhhc-CcccccccchhhHhhhc
Q psy14082        200 DYEKEKRLFSLIRELG-KYTLITQESSSTLSEMV  232 (233)
Q Consensus       200 ~~~~~~~~~~~i~~~~-~~~~~~~~~~~~~~~l~  232 (233)
                      +..|.-++.-++.+.. +..++|..+..+.+-||
T Consensus       306 e~qKvhCLntLfskLqINQsIIFCNS~~rVELLA  339 (459)
T KOG0326|consen  306 ERQKVHCLNTLFSKLQINQSIIFCNSTNRVELLA  339 (459)
T ss_pred             hhhhhhhHHHHHHHhcccceEEEeccchHhHHHH
Confidence            8778877777777755 56666666666655443

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=80.35  E-value=1.6  Score=37.32  Aligned_cols=26  Identities=4%  Similarity=-0.243  Sum_probs=20.0

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      +..+++.+|+|+|||.+ +-.++..+.
T Consensus        40 ~~~i~I~G~~GtGKT~l-~~~~~~~l~   65 (365)
T TIGR02928        40 PSNVFIYGKTGTGKTAV-TKYVMKELE   65 (365)
T ss_pred             CCcEEEECCCCCCHHHH-HHHHHHHHH
Confidence            35799999999999976 555666554

Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.

>PRK06904 replicative DNA helicase; Validated

Probab=80.26  E-value=4.6  Score=36.28  Aligned_cols=58  Identities=10%  Similarity=-0.030  Sum_probs=34.1

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCc
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALR   72 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~   72 (233)
                      .|.=+++.|.||.|||. |++-+.......      .+..+++++.- --..|+..++-....++.
T Consensus       220 ~G~LiiIaarPg~GKTa-falnia~~~a~~------~g~~Vl~fSlE-Ms~~ql~~Rlla~~s~v~  277 (472)
T PRK06904        220 PSDLIIVAARPSMGKTT-FAMNLCENAAMA------SEKPVLVFSLE-MPAEQIMMRMLASLSRVD  277 (472)
T ss_pred             CCcEEEEEeCCCCChHH-HHHHHHHHHHHh------cCCeEEEEecc-CCHHHHHHHHHHhhCCCC
Confidence            35557778889999994 566666554321      24457776532 445565555554433333

>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX

Probab=80.22  E-value=1  Score=35.63  Aligned_cols=18  Identities=6%  Similarity=-0.313  Sum_probs=13.2

Q ss_pred             CCCceeEecCCCCCchHH
Q psy14082          7 SGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~   24 (233)
                      .+++++..+++|+|||..
T Consensus        21 G~h~lLl~GppGtGKTml   38 (206)
T PF01078_consen   21 GGHHLLLIGPPGTGKTML   38 (206)
T ss_dssp             CC--EEEES-CCCTHHHH
T ss_pred             CCCCeEEECCCCCCHHHH
Confidence            477899999999999965

This is the first unique step in the synthesis of (bacterio)chlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weights between 38-42 kDa.; GO: 0016851 magnesium chelatase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process; PDB: 2X31_J 1G8P_A 3K1J_B.

>KOG0345|consensus

Probab=80.20  E-value=5.2  Score=35.59  Aligned_cols=69  Identities=14%  Similarity=0.262  Sum_probs=51.7

Q ss_pred             eEEEEecchhHHHHHHHHHhh-----CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----cCcC---CcCCCC
Q psy14082        108 KVIVFVETKKKVEDITRALRR-----ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----VAAR---GLDVED  174 (233)
Q Consensus       108 k~iIf~~~~~~~~~l~~~L~~-----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----~~~~---Gldi~~  174 (233)
                      -.+|..+|++-+.++.+.+..     .++++..+-||++.+   +-++.|++...+|||+|+     ++.+   ++|+.+
T Consensus        81 galIIsPTRELa~QI~~V~~~F~~~l~~l~~~l~vGG~~v~---~Di~~fkee~~nIlVgTPGRL~di~~~~~~~l~~rs  157 (567)
T KOG0345|consen   81 GALIISPTRELARQIREVAQPFLEHLPNLNCELLVGGRSVE---EDIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRS  157 (567)
T ss_pred             eEEEecCcHHHHHHHHHHHHHHHHhhhccceEEEecCccHH---HHHHHHHHhCCcEEEeCchhHHHHHhchhhhccccc
Confidence            469999999998877766643     367899999996644   456778888899999994     4444   566667


Q ss_pred             ccEEE
Q psy14082        175 VNTVN  179 (233)
Q Consensus       175 v~~VI  179 (233)
                      .+++|
T Consensus       158 Le~LV  162 (567)
T KOG0345|consen  158 LEILV  162 (567)
T ss_pred             cceEE
Confidence            77665

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=80.19  E-value=3.7  Score=36.58  Aligned_cols=45  Identities=9%  Similarity=-0.021  Sum_probs=30.1

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHH
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQT   62 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~   62 (233)
                      +.+++.+++|+|||.. +-++.+.+...       +.+++++.. .++..+..+
T Consensus       142 npl~L~G~~G~GKTHL-l~Ai~~~l~~~-------~~~v~yi~~-~~f~~~~~~  186 (445)
T PRK12422        142 NPIYLFGPEGSGKTHL-MQAAVHALRES-------GGKILYVRS-ELFTEHLVS  186 (445)
T ss_pred             ceEEEEcCCCCCHHHH-HHHHHHHHHHc-------CCCEEEeeH-HHHHHHHHH
Confidence            4589999999999966 55666666532       456776654 455554433

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	233
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		2e-18
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		3e-18
2jgn_A	185	Ddx3 Helicase Domain Length = 185		2e-14
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		2e-14
3i32_A	300	Dimeric Structure Of A Hera Helicase Fragment Inclu		3e-13
3eaq_A	212	Novel Dimerization Motif In The Dead Box Rna Helica		5e-13
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		6e-12
1fuk_A	165	Crystal Structure Of The Carboxy Terminal Domain Of		6e-12
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		2e-11
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		3e-11
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		8e-11
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		8e-11
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		2e-10
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		2e-10
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		2e-10
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		2e-10
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		2e-10
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		2e-10
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		2e-10
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		2e-10
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		2e-10
2kbf_A	187	Solution Structure Of Carboxyl-Terminal Domain Of D		2e-10
3gfp_A	189	Structure Of The C-Terminal Domain Of The Dead-Box		3e-10
3peu_A	188	S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To		3e-10
2hjv_A	163	Structure Of The Second Domain (Residues 207-368) O		7e-10
2p6n_A	191	Human Dead-box Rna Helicase Ddx41, Helicase Domain		4e-09
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		5e-09
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		1e-07
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		1e-07
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		1e-07
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		1e-07
2wax_A	193	Structure Of The Human Ddx6 C-Terminal Domain In Co		2e-07
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		3e-07
2yjt_D	170	Crystal Structure Of E. Coli Dead-Box Protein Srmb		6e-07
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		7e-07
2rb4_A	175	Crystal Structure Of The Helicase Domain Of Human D		2e-06
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		2e-06
4db2_A	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		8e-05
4db4_A	256	Mss116p Dead-Box Helicase Domain 2 Bound To A Chima		8e-05
4db2_C	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		8e-05
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		1e-04
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		2e-04
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		2e-04
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		3e-04
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		4e-04
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		4e-04

>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I In Complex With Adp Length = 242

Iteration: 1
 Score = 89.0 bits (219), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 41/63 (65%), Positives = 51/63 (80%), Gaps = 2/63 (3%)
Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSA--LRNICIFGGTPK 82
           Y+LPA VHI+HQ  +++GDGPI LVLAPTRELAQQ+Q VA E+  A  L++ CI+GG PK
Sbjct: 83  YLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPK 142
Query: 83  GPQ 85
           GPQ
Sbjct: 143 GPQ 145

>pdb|4A4D|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human Dead-Box Rna Helicase Ddx5 (P68) Length = 253

Iteration: 1
 Score = 88.6 bits (218), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 41/63 (65%), Positives = 51/63 (80%), Gaps = 2/63 (3%)
Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSA--LRNICIFGGTPK 82
           Y+LPA VHI+HQ  +++GDGPI LVLAPTRELAQQ+Q VA E+  A  L++ CI+GG PK
Sbjct: 97  YLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPK 156
Query: 83  GPQ 85
           GPQ
Sbjct: 157 GPQ 159

>pdb|2JGN|A Chain A, Ddx3 Helicase Domain Length = 185

Iteration: 1
 Score = 76.3 bits (186), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 36/70 (51%), Positives = 49/70 (70%)
Query: 109 VIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAAR 168
            +VFVETKK  + +   L  E ++   IHGD++Q+DR+  L+ FR GK+PILVAT VAAR
Sbjct: 49  TLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAAR 108
Query: 169 GLDVEDVNTV 178
           GLD+ +V  V
Sbjct: 109 GLDISNVKHV 118

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score = 75.9 bits (185), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 49/69 (71%)
Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
           +VFVETKK  + +   L  E ++   IHGD++Q+DR+  L+ FR GK+PILVAT VAARG
Sbjct: 280 LVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARG 339
Query: 170 LDVEDVNTV 178
           LD+ +V  V
Sbjct: 340 LDISNVKHV 348

>pdb|3I32|A Chain A, Dimeric Structure Of A Hera Helicase Fragment Including The C-Terminal Reca Domain, The Dimerization Domain, And The Rna Binding Domain Length = 300

Iteration: 1
 Score = 72.0 bits (175), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 34/71 (47%), Positives = 48/71 (67%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           + +VF  TK + E+I + L R  H A  +HGD +Q +R+ V+  FRQG+  +LVATDVAA
Sbjct: 30  RAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAA 89
Query: 168 RGLDVEDVNTV 178
           RGLD+  V+ V
Sbjct: 90  RGLDIPQVDLV 100

>pdb|3EAQ|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase Hera Form 2, Complete Dimer, Symmetric Length = 212

Iteration: 1
 Score = 71.2 bits (173), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 35/71 (49%), Positives = 48/71 (67%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           + +VF  TK + E+I + L R  H A  +HGD +Q +R+ VL  FRQG+  +LVATDVAA
Sbjct: 33  RAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAA 92
Query: 168 RGLDVEDVNTV 178
           RGLD+  V+ V
Sbjct: 93  RGLDIPQVDLV 103

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score = 67.4 bits (163), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 28/71 (39%), Positives = 50/71 (70%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           + ++F  T++KVE++T  LR ++ +   I+ D  QQ+RD ++ +FR G + IL++TD+ A
Sbjct: 262 QAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLA 321
Query: 168 RGLDVEDVNTV 178
           RG+DV+ V+ V
Sbjct: 322 RGIDVQQVSLV 332

>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast Eif4a Length = 165

Iteration: 1
 Score = 67.4 bits (163), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 28/71 (39%), Positives = 50/71 (70%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           + ++F  T++KVE++T  LR ++ +   I+ D  QQ+RD ++ +FR G + IL++TD+ A
Sbjct: 32  QAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLA 91
Query: 168 RGLDVEDVNTV 178
           RG+DV+ V+ V
Sbjct: 92  RGIDVQQVSLV 102

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score = 65.5 bits (158), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 28/71 (39%), Positives = 49/71 (69%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           + ++F  T++KVE++T  LR ++ +   I+ D  QQ+RD +  +FR G + IL++TD+ A
Sbjct: 261 QAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIXKEFRSGSSRILISTDLLA 320
Query: 168 RGLDVEDVNTV 178
           RG+DV+ V+ V
Sbjct: 321 RGIDVQQVSLV 331

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score = 65.5 bits (158), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 36/88 (40%), Positives = 52/88 (59%), Gaps = 2/88 (2%)
Query: 91  HRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLN 150
            RF   C+  + KN  F  +VF +TK+  +++   LR     A  IHGD +Q  R+ V+ 
Sbjct: 225 ERFEALCR--LLKNKEFYGLVFCKTKRDTKELASXLRDIGFKAGAIHGDLSQSQREKVIR 282
Query: 151 DFRQGKAPILVATDVAARGLDVEDVNTV 178
            F+Q K  IL+ATDV +RG+DV D+N V
Sbjct: 283 LFKQKKIRILIATDVXSRGIDVNDLNCV 310

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 63.9 bits (154), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 28/69 (40%), Positives = 45/69 (65%)
Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
           I+FV TKK    +   L+ E H    +HGD   Q+RD +++DFR+G++ +L+ T+V ARG
Sbjct: 247 IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARG 306
Query: 170 LDVEDVNTV 178
           +D+  V+ V
Sbjct: 307 IDIPTVSMV 315

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 63.5 bits (153), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 28/69 (40%), Positives = 45/69 (65%)
Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
           I+FV TKK    +   L+ E H    +HGD   Q+RD +++DFR+G++ +L+ T+V ARG
Sbjct: 247 IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARG 306
Query: 170 LDVEDVNTV 178
           +D+  V+ V
Sbjct: 307 IDIPTVSMV 315

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score = 62.8 bits (151), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 47/71 (66%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           + ++F+ T++KV+ +T  +     +   +HGD  Q++RD ++ +FR G + +L+ TD+ A
Sbjct: 282 QAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLA 341
Query: 168 RGLDVEDVNTV 178
           RG+DV+ V+ V
Sbjct: 342 RGIDVQQVSLV 352

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score = 62.8 bits (151), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 47/71 (66%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           + ++F+ T++KV+ +T  +     +   +HGD  Q++RD ++ +FR G + +L+ TD+ A
Sbjct: 256 QAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLA 315
Query: 168 RGLDVEDVNTV 178
           RG+DV+ V+ V
Sbjct: 316 RGIDVQQVSLV 326

>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 = 62.4 bits (150), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 47/71 (66%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           + ++F  TK+KV+ +T  +R    +   +HGD  Q++R+ ++ +FR G + +L++TDV A
Sbjct: 279 QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWA 338
Query: 168 RGLDVEDVNTV 178
           RGLDV  V+ +
Sbjct: 339 RGLDVPQVSLI 349

>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 = 62.4 bits (150), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 47/71 (66%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           + ++F  TK+KV+ +T  +R    +   +HGD  Q++R+ ++ +FR G + +L++TDV A
Sbjct: 279 QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWA 338
Query: 168 RGLDVEDVNTV 178
           RGLDV  V+ +
Sbjct: 339 RGLDVPQVSLI 349

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score = 62.4 bits (150), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 47/71 (66%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           + ++F  TK+KV+ +T  +R    +   +HGD  Q++R+ ++ +FR G + +L++TDV A
Sbjct: 257 QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWA 316
Query: 168 RGLDVEDVNTV 178
           RGLDV  V+ +
Sbjct: 317 RGLDVPQVSLI 327

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 62.4 bits (150), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 47/71 (66%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           + ++F  TK+KV+ +T  +R    +   +HGD  Q++R+ ++ +FR G + +L++TDV A
Sbjct: 242 QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWA 301
Query: 168 RGLDVEDVNTV 178
           RGLDV  V+ +
Sbjct: 302 RGLDVPQVSLI 312

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score = 62.4 bits (150), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 47/71 (66%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           + ++F  TK+KV+ +T  +R    +   +HGD  Q++R+ ++ +FR G + +L++TDV A
Sbjct: 278 QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWA 337
Query: 168 RGLDVEDVNTV 178
           RGLDV  V+ +
Sbjct: 338 RGLDVPQVSLI 348

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 62.4 bits (150), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 47/71 (66%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           + ++F  TK+KV+ +T  +R    +   +HGD  Q++R+ ++ +FR G + +L++TDV A
Sbjct: 242 QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWA 301
Query: 168 RGLDVEDVNTV 178
           RGLDV  V+ +
Sbjct: 302 RGLDVPQVSLI 312

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score = 62.4 bits (150), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 42/128 (32%), Positives = 66/128 (51%), Gaps = 10/128 (7%)
Query: 58  QQIQTVAKEFSSALRN-----ICIFGGTPKG-PQDCLPLHRFVFNCQY-EMAKNPAFKVI 110
           ++IQ +A EF   L+N     I I GG      Q    ++++    +  E+    A   I
Sbjct: 248 EEIQRMAGEF---LKNYVFVAIGIVGGACSDVKQTIYEVNKYAKRSKLIEILSEQADGTI 304
Query: 111 VFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGL 170
           VFVETK+  + +   L  +      IHGD+ Q  R+  L DF+ G   +L+AT VA+RGL
Sbjct: 305 VFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGL 364
Query: 171 DVEDVNTV 178
           D++++  V
Sbjct: 365 DIKNIKHV 372

>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p Length = 187

Iteration: 1
 Score = 62.0 bits (149), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 28/69 (40%), Positives = 45/69 (65%)
Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
           I+FV TKK    +   L+ E H    +HGD   Q+RD +++DFR+G++ +L+ T+V ARG
Sbjct: 39  IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARG 98
Query: 170 LDVEDVNTV 178
           +D+  V+ V
Sbjct: 99  IDIPTVSMV 107

>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein Dbp5 Length = 189

Iteration: 1
 Score = 62.0 bits (149), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 28/69 (40%), Positives = 45/69 (65%)
Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
           I+FV TKK    +   L+ E H    +HGD   Q+RD +++DFR+G++ +L+ T+V ARG
Sbjct: 41  IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARG 100
Query: 170 LDVEDVNTV 178
           +D+  V+ V
Sbjct: 101 IDIPTVSXV 109

>pdb|3PEU|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1 H337r And Ip6 Length = 188

Iteration: 1
 Score = 61.6 bits (148), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 28/69 (40%), Positives = 45/69 (65%)
Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
           I+FV TKK    +   L+ E H    +HGD   Q+RD +++DFR+G++ +L+ T+V ARG
Sbjct: 40  IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARG 99
Query: 170 LDVEDVNTV 178
           +D+  V+ V
Sbjct: 100 IDIPTVSXV 108

>pdb|2HJV|A Chain A, Structure Of The Second Domain (Residues 207-368) Of The Bacillus Subtilis Yxin Protein Length = 163

Iteration: 1
 Score = 60.5 bits (145), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 33/78 (42%), Positives = 49/78 (62%), Gaps = 1/78 (1%)
Query: 101 MAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPIL 160
           M +NP    I+F  TK+ V  +T  L    +    IHG   Q+DR  V+N+F++G+   L
Sbjct: 31  MTENPD-SCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYL 89
Query: 161 VATDVAARGLDVEDVNTV 178
           VATDVAARG+D+E+++ V
Sbjct: 90  VATDVAARGIDIENISLV 107

>pdb|2P6N|A Chain A, Human Dead-box Rna Helicase Ddx41, Helicase Domain Length = 191

Iteration: 1
 Score = 58.2 bits (139), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 28/63 (44%), Positives = 40/63 (63%)
Query: 109 VIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAAR 168
           V++F E K  V+ I   L  +   A+ IHG K Q++R   +  FR+GK  +LVATDVA++
Sbjct: 57  VLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASK 116
Query: 169 GLD 171
           GLD
Sbjct: 117 GLD 119

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score = 53.1 bits (126), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/71 (35%), Positives = 40/71 (56%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           + ++F  T+K    +   L +E H    + G+   + R  V+  FR+GK  +LV T+V A
Sbjct: 268 QAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCA 327
Query: 168 RGLDVEDVNTV 178
           RG+DVE V+ V
Sbjct: 328 RGIDVEQVSVV 338

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score = 53.1 bits (126), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/71 (35%), Positives = 40/71 (56%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           + ++F  T+K    +   L +E H    + G+   + R  V+  FR+GK  +LV T+V A
Sbjct: 305 QAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCA 364
Query: 168 RGLDVEDVNTV 178
           RG+DVE V+ V
Sbjct: 365 RGIDVEQVSVV 375

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score = 53.1 bits (126), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/71 (35%), Positives = 40/71 (56%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           + ++F  T+K    +   L +E H    + G+   + R  V+  FR+GK  +LV T+V A
Sbjct: 284 QAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCA 343
Query: 168 RGLDVEDVNTV 178
           RG+DVE V+ V
Sbjct: 344 RGIDVEQVSVV 354

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score = 53.1 bits (126), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/71 (35%), Positives = 40/71 (56%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           + ++F  T+K    +   L +E H    + G+   + R  V+  FR+GK  +LV T+V A
Sbjct: 335 QAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCA 394
Query: 168 RGLDVEDVNTV 178
           RG+DVE V+ V
Sbjct: 395 RGIDVEQVSVV 405

>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 = 52.4 bits (124), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 24/69 (34%), Positives = 40/69 (57%)
Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
           I+F  + ++VE + + + +  +S   IH    Q+ R+ V +DFR G    LV TD+  RG
Sbjct: 48  IIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRG 107
Query: 170 LDVEDVNTV 178
           +D++ VN V
Sbjct: 108 IDIQAVNVV 116

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score = 52.0 bits (123), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 41/71 (57%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           + I+F  +  +VE + + +    +S    H    QQ+R+ V ++FRQGK   LV +D+  
Sbjct: 260 QAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLT 319
Query: 168 RGLDVEDVNTV 178
           RG+D++ VN V
Sbjct: 320 RGIDIQAVNVV 330

>pdb|2YJT|D Chain D, Crystal Structure Of E. Coli Dead-Box Protein Srmb Bound To Regulator Of Ribonuclease Activity A (Rraa) Length = 170

Iteration: 1
 Score = 50.8 bits (120), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 28/79 (35%), Positives = 46/79 (58%), Gaps = 1/79 (1%)
Query: 101 MAKNP-AFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPI 159
           + K P A + IVFV  +++V ++   LR    +   + G+  Q  R+  +    +G+  +
Sbjct: 24  LLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNV 83
Query: 160 LVATDVAARGLDVEDVNTV 178
           LVATDVAARG+D+ DV+ V
Sbjct: 84  LVATDVAARGIDIPDVSHV 102

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 50.8 bits (120), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 38/125 (30%), Positives = 62/125 (49%), Gaps = 24/125 (19%)
Query: 58  QQIQTVAKEFSSALRNICIFGGTPKGPQDCLPL----HRFVFNCQYEMAKNPAFK----- 108
           ++I+ V K+F +    I          + C+ L    H+FV       +K  A +     
Sbjct: 172 EEIRKVVKDFITNYEEI----------EACIGLANVEHKFVHVKDDWRSKVQALRENKDK 221
Query: 109 -VIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
            VIVFV T+ +V  + R       +AI + GD  Q  R+  ++ FR+G+  +L+ TDVA+
Sbjct: 222 GVIVFVRTRNRVAKLVRLF----DNAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVAS 277
Query: 168 RGLDV 172
           RGLD+
Sbjct: 278 RGLDI 282

>pdb|2RB4|A Chain A, Crystal Structure Of The Helicase Domain Of Human Ddx25 Rna Helicase Length = 175

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/71 (30%), Positives = 42/71 (59%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           + I+F +T++  + +T  + ++ H    + G+ T + R  ++  FR GK  +L+ T+V A
Sbjct: 36  QAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCA 95
Query: 168 RGLDVEDVNTV 178
           RG+DV+ V  V
Sbjct: 96  RGIDVKQVTIV 106

>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain Length = 228

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 38/58 (65%), Gaps = 4/58 (6%)
Query: 25  YMLPAAVHISHQEPV--KQGDGPIALVLAPTRELAQQIQTVAKEFS-SALRNICIFGG 79
           Y++P  +H+  Q P+  +Q +GP  LVL PTRELA  ++    ++S   L++ICI+GG
Sbjct: 74  YLMPGFIHLDSQ-PISREQRNGPGMLVLTPTRELALHVEAECSKYSYKGLKSICIYGG 130

>pdb|4DB2|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex Length = 257

Iteration: 1
 Score = 43.9 bits (102), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 30/91 (32%), Positives = 47/91 (51%), Gaps = 4/91 (4%)
Query: 103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICI---HGDKTQQDRDYVLNDFRQGKAPI 159
           ++  +K I+F  T K    +   L+ E    + I   HG  TQ  R  ++  F++ ++ I
Sbjct: 30  RDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGI 89
Query: 160 LVATDVAARGLDVEDVNTV-NIGSLQLSANH 189
           LV TDV ARG+D  +V+ V  IG     AN+
Sbjct: 90  LVCTDVGARGMDFPNVHEVLQIGVPSELANY 120

>pdb|4DB4|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric Rna-Dna Duplex Length = 256

Iteration: 1
 Score = 43.9 bits (102), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 30/91 (32%), Positives = 47/91 (51%), Gaps = 4/91 (4%)
Query: 103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICI---HGDKTQQDRDYVLNDFRQGKAPI 159
           ++  +K I+F  T K    +   L+ E    + I   HG  TQ  R  ++  F++ ++ I
Sbjct: 30  RDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGI 89
Query: 160 LVATDVAARGLDVEDVNTV-NIGSLQLSANH 189
           LV TDV ARG+D  +V+ V  IG     AN+
Sbjct: 90  LVCTDVGARGMDFPNVHEVLQIGVPSELANY 120

>pdb|4DB2|C Chain C, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex Length = 257

Iteration: 1
 Score = 43.9 bits (102), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 30/91 (32%), Positives = 47/91 (51%), Gaps = 4/91 (4%)
Query: 103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICI---HGDKTQQDRDYVLNDFRQGKAPI 159
           ++  +K I+F  T K    +   L+ E    + I   HG  TQ  R  ++  F++ ++ I
Sbjct: 30  RDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGI 89
Query: 160 LVATDVAARGLDVEDVNTV-NIGSLQLSANH 189
           LV TDV ARG+D  +V+ V  IG     AN+
Sbjct: 90  LVCTDVGARGMDFPNVHEVLQIGVPSELANY 120

>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion) Bound To Ssrna And Amp-Pnp Length = 512

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 42/79 (53%), Gaps = 3/79 (3%)
Query: 103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICI---HGDKTQQDRDYVLNDFRQGKAPI 159
           ++  +K I+F  T K    +   L+ E    + I   HG  TQ  R  ++  F++ ++ I
Sbjct: 285 RDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGI 344
Query: 160 LVATDVAARGLDVEDVNTV 178
           LV TDV ARG+D  +V+ V
Sbjct: 345 LVCTDVGARGMDFPNVHEV 363

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 42/79 (53%), Gaps = 3/79 (3%)
Query: 103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICI---HGDKTQQDRDYVLNDFRQGKAPI 159
           ++  +K I+F  T K    +   L+ E    + I   HG  TQ  R  ++  F++ ++ I
Sbjct: 336 RDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGI 395
Query: 160 LVATDVAARGLDVEDVNTV 178
           LV TDV ARG+D  +V+ V
Sbjct: 396 LVCTDVGARGMDFPNVHEV 414

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 42/79 (53%), Gaps = 3/79 (3%)
Query: 103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICI---HGDKTQQDRDYVLNDFRQGKAPI 159
           ++  +K I+F  T K    +   L+ E    + I   HG  TQ  R  ++  F++ ++ I
Sbjct: 285 RDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGI 344
Query: 160 LVATDVAARGLDVEDVNTV 178
           LV TDV ARG+D  +V+ V
Sbjct: 345 LVCTDVGARGMDFPNVHEV 363

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/69 (31%), Positives = 40/69 (57%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           +V++FV++ ++   + + L  +   AI IH    Q++R      F+  +  ILVAT++  
Sbjct: 252 QVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFG 311
Query: 168 RGLDVEDVN 176
           RG+D+E VN
Sbjct: 312 RGMDIERVN 320

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/69 (31%), Positives = 40/69 (57%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           +V++FV++ ++   + + L  +   AI IH    Q++R      F+  +  ILVAT++  
Sbjct: 252 QVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFG 311
Query: 168 RGLDVEDVN 176
           RG+D+E VN
Sbjct: 312 RGMDIERVN 320

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/69 (31%), Positives = 40/69 (57%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           +V++FV++ ++   + + L  +   AI IH    Q++R      F+  +  ILVAT++  
Sbjct: 251 QVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFG 310
Query: 168 RGLDVEDVN 176
           RG+D+E VN
Sbjct: 311 RGMDIERVN 319

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	233
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	1e-37
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	2e-08
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	1e-36
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	4e-25
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	2e-08
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	3e-36
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	4e-09
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	8e-36
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	1e-21
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	6e-07
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	5e-31
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	1e-07
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	1e-29
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	4e-29
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	9e-29
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	1e-28
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	7e-28
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	1e-27
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	3e-07
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	1e-27
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	2e-27
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	3e-27
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	8e-07
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	6e-27
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	5e-07
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	6e-27
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	3e-07
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	9e-27
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	1e-06
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	2e-26
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	5e-08
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	2e-26
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	8e-07
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	2e-26
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	4e-06
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	2e-26
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	3e-26
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	1e-06
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	1e-25
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	4e-25
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	2e-08
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	1e-24
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	3e-08
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	8e-24
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	2e-06
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	6e-21
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	1e-18
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	4e-09
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	2e-18
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	6e-13
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	6e-09
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	1e-08
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	3e-08
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	3e-08
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	4e-08
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	5e-08
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	5e-08
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	3e-07
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	4e-07
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	4e-07
3bor_A	237	Human initiation factor 4A-II; translation initiat	7e-07
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	8e-07
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	9e-07
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	3e-06
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	6e-06
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	1e-05
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	1e-05
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	2e-05
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	2e-05
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	3e-05
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	6e-05
1yks_A	440	Genome polyprotein [contains: flavivirin protease	3e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-04

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens} Length = 185

 Score =  128 bits (325), Expect = 1e-37
 Identities = 37/78 (47%), Positives = 50/78 (64%)

Query: 101 MAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPIL 160
            A       +VFVETKK  + +   L  E ++   IHGD++Q+DR+  L+ FR GK+PIL
Sbjct: 41  NATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPIL 100

Query: 161 VATDVAARGLDVEDVNTV 178
           VAT VAARGLD+ +V  V
Sbjct: 101 VATAVAARGLDISNVKHV 118

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens} Length = 185

 Score = 51.4 bits (124), Expect = 2e-08
 Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 1/43 (2%)

Query: 178 VNIGSLQLSANHNISQVIEVVQDYEKEKRLFSLIRELGKYTLI 220
            N+   Q S + NI+Q +  V++ +K   L  L+   GK +L 
Sbjct: 8   ENLY-FQGSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLT 49

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster} Length = 434

 Score =  132 bits (334), Expect = 1e-36
 Identities = 28/71 (39%), Positives = 42/71 (59%)

Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
             IVFVETK+  + +   L  +      IHGD+ Q  R+  L DF+ G   +L+AT VA+
Sbjct: 302 GTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVAS 361

Query: 168 RGLDVEDVNTV 178
           RGLD++++  V
Sbjct: 362 RGLDIKNIKHV 372

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster} Length = 434

 Score =  101 bits (253), Expect = 4e-25
 Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 2/63 (3%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS--SALRNICIFGGTPK 82
           ++LP    +       +   P  ++++PTRELA QI   A++F+  S L+   ++GGT  
Sbjct: 110 FLLPILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSF 169

Query: 83  GPQ 85
             Q
Sbjct: 170 RHQ 172

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster} Length = 434

 Score = 52.9 bits (128), Expect = 2e-08
 Identities = 12/43 (27%), Positives = 20/43 (46%), Gaps = 1/43 (2%)

Query: 178 VNIGSLQLSANHNISQVIEVVQDYEKEKRLFSLIRELGKYTLI 220
           V IG +   A  ++ Q I  V  Y K  +L  ++ E    T++
Sbjct: 264 VAIGIVG-GACSDVKQTIYEVNKYAKRSKLIEILSEQADGTIV 305

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens} Length = 191

 Score =  125 bits (316), Expect = 3e-36
 Identities = 29/71 (40%), Positives = 42/71 (59%)

Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
            V++F E K  V+ I   L  +   A+ IHG K Q++R   +  FR+GK  +LVATDVA+
Sbjct: 56  PVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVAS 115

Query: 168 RGLDVEDVNTV 178
           +GLD   +  V
Sbjct: 116 KGLDFPAIQHV 126

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens} Length = 191

 Score = 53.4 bits (129), Expect = 4e-09
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 6/49 (12%)

Query: 178 VNIGSLQL------SANHNISQVIEVVQDYEKEKRLFSLIRELGKYTLI 220
           V++G+  L      +A+ ++ Q +E V++  K   L   +++     LI
Sbjct: 11  VDLGTENLYFQSMGAASLDVIQEVEYVKEEAKMVYLLECLQKTPPPVLI 59

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  129 bits (328), Expect = 8e-36
 Identities = 36/71 (50%), Positives = 49/71 (69%)

Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
             +VFVETKK  + +   L  E ++   IHGD++Q+DR+  L+ FR GK+PILVAT VAA
Sbjct: 278 LTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAA 337

Query: 168 RGLDVEDVNTV 178
           RGLD+ +V  V
Sbjct: 338 RGLDISNVKHV 348

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score = 91.1 bits (227), Expect = 1e-21
 Identities = 27/76 (35%), Positives = 37/76 (48%), Gaps = 15/76 (19%)

Query: 25  YMLPAAVHISHQEPVK-------------QGDGPIALVLAPTRELAQQIQTVAKEFS--S 69
           ++LP    I    P +             +   PI+LVLAPTRELA QI   A++FS  S
Sbjct: 69  FLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRS 128

Query: 70  ALRNICIFGGTPKGPQ 85
            +R   ++GG   G Q
Sbjct: 129 RVRPCVVYGGADIGQQ 144

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score = 48.3 bits (116), Expect = 6e-07
 Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 1/43 (2%)

Query: 178 VNIGSLQLSANHNISQVIEVVQDYEKEKRLFSLIRELGKYTLI 220
           + +G +  S + NI+Q +  V++ +K   L  L+   GK +L 
Sbjct: 238 LAVGRVG-STSENITQKVVWVEESDKRSFLLDLLNATGKDSLT 279

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis} Length = 163

 Score =  107 bits (270), Expect = 1e-29
 Identities = 30/72 (41%), Positives = 45/72 (62%)

Query: 107 FKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVA 166
              I+F  TK+ V  +T  L    +    IHG   Q+DR  V+N+F++G+   LVATDVA
Sbjct: 36  DSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVA 95

Query: 167 ARGLDVEDVNTV 178
           ARG+D+E+++ V
Sbjct: 96  ARGIDIENISLV 107

>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 =  106 bits (267), Expect = 4e-29
 Identities = 22/69 (31%), Positives = 41/69 (59%)

Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
           I+F +T++  + +T  + ++ H    + G+ T + R  ++  FR GK  +L+ T+V ARG
Sbjct: 38  IIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARG 97

Query: 170 LDVEDVNTV 178
           +DV+ V  V
Sbjct: 98  IDVKQVTIV 106

>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 =  105 bits (264), Expect = 9e-29
 Identities = 22/70 (31%), Positives = 39/70 (55%)

Query: 109 VIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAAR 168
           V++FV++ ++   + + L  +   AI IH    Q++R      F+  +  ILVAT++  R
Sbjct: 34  VVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGR 93

Query: 169 GLDVEDVNTV 178
           G+D+E VN  
Sbjct: 94  GMDIERVNIA 103

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} Length = 242

 Score =  107 bits (269), Expect = 1e-28
 Identities = 41/63 (65%), Positives = 51/63 (80%), Gaps = 2/63 (3%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSA--LRNICIFGGTPK 82
           Y+LPA VHI+HQ  +++GDGPI LVLAPTRELAQQ+Q VA E+  A  L++ CI+GG PK
Sbjct: 83  YLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPK 142

Query: 83  GPQ 85
           GPQ
Sbjct: 143 GPQ 145

>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 =  104 bits (261), Expect = 7e-28
 Identities = 35/75 (46%), Positives = 48/75 (64%)

Query: 104 NPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVAT 163
               + +VF  TK + E+I + L R  H A  +HGD +Q +R+ VL  FRQG+  +LVAT
Sbjct: 29  ASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVAT 88

Query: 164 DVAARGLDVEDVNTV 178
           DVAARGLD+  V+ V
Sbjct: 89  DVAARGLDIPQVDLV 103

>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 =  107 bits (270), Expect = 1e-27
 Identities = 28/69 (40%), Positives = 45/69 (65%)

Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
           I+FV TKK    +   L+ E H    +HGD   Q+RD +++DFR+G++ +L+ T+V ARG
Sbjct: 247 IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARG 306

Query: 170 LDVEDVNTV 178
           +D+  V+ V
Sbjct: 307 IDIPTVSMV 315

>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 = 49.5 bits (119), Expect = 3e-07
 Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 3/42 (7%)

Query: 47  ALVLAPTRELAQQIQTVAKEFSSALRNI---CIFGGTPKGPQ 85
           A+ LAP+RELA+Q   V +E     +      +     K  Q
Sbjct: 78  AICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKNKQ 119

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus} Length = 300

 Score =  105 bits (264), Expect = 1e-27
 Identities = 34/75 (45%), Positives = 48/75 (64%)

Query: 104 NPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVAT 163
               + +VF  TK + E+I + L R  H A  +HGD +Q +R+ V+  FRQG+  +LVAT
Sbjct: 26  ASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVAT 85

Query: 164 DVAARGLDVEDVNTV 178
           DVAARGLD+  V+ V
Sbjct: 86  DVAARGLDIPQVDLV 100

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19 Length = 165

 Score =  101 bits (255), Expect = 2e-27
 Identities = 28/70 (40%), Positives = 49/70 (70%)

Query: 109 VIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAAR 168
            ++F  T++KVE++T  LR ++ +   I+ D  QQ+RD ++ +FR G + IL++TD+ AR
Sbjct: 33  AVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLAR 92

Query: 169 GLDVEDVNTV 178
           G+DV+ V+ V
Sbjct: 93  GIDVQQVSLV 102

>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 =  106 bits (268), Expect = 3e-27
 Identities = 25/69 (36%), Positives = 39/69 (56%)

Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
           ++F  T+K    +   L +E H    + G+   + R  V+  FR+GK  +LV T+V ARG
Sbjct: 270 MIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARG 329

Query: 170 LDVEDVNTV 178
           +DVE V+ V
Sbjct: 330 IDVEQVSVV 338

>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 = 47.9 bits (115), Expect = 8e-07
 Identities = 11/48 (22%), Positives = 15/48 (31%), Gaps = 9/48 (18%)

Query: 47  ALVLAPTRELAQQIQTVAKEFSSALRNI---CIFGGTP------KGPQ 85
            L L+PT ELA Q   V ++       +       G           Q
Sbjct: 98  CLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQ 145

>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 =  105 bits (265), Expect = 6e-27
 Identities = 28/69 (40%), Positives = 49/69 (71%)

Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
           ++F  T++KVE++T  LR ++ +   I+ D  QQ+RD ++ +FR G + IL++TD+ ARG
Sbjct: 263 VIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARG 322

Query: 170 LDVEDVNTV 178
           +DV+ V+ V
Sbjct: 323 IDVQQVSLV 331

>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 = 48.7 bits (117), Expect = 5e-07
 Identities = 17/41 (41%), Positives = 21/41 (51%), Gaps = 2/41 (4%)

Query: 47  ALVLAPTRELAQQIQTVAKEFSS--ALRNICIFGGTPKGPQ 85
           AL+LAPTRELA QIQ V    +    ++     GGT     
Sbjct: 92  ALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVED 132

>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 =  105 bits (265), Expect = 6e-27
 Identities = 24/70 (34%), Positives = 40/70 (57%)

Query: 109 VIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAAR 168
            I+F  +  +VE + + +    +S    H    QQ+R+ V ++FRQGK   LV +D+  R
Sbjct: 261 AIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTR 320

Query: 169 GLDVEDVNTV 178
           G+D++ VN V
Sbjct: 321 GIDIQAVNVV 330

>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 = 49.5 bits (119), Expect = 3e-07
 Identities = 13/41 (31%), Positives = 18/41 (43%), Gaps = 2/41 (4%)

Query: 47  ALVLAPTRELAQQIQTVAKEFSS--ALRNICIFGGTPKGPQ 85
           AL++ PTRELA Q   V +       +  +   GGT     
Sbjct: 92  ALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDD 132

>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 =  106 bits (266), Expect = 9e-27
 Identities = 25/69 (36%), Positives = 39/69 (56%)

Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
           ++F  T+K    +   L +E H    + G+   + R  V+  FR+GK  +LV T+V ARG
Sbjct: 337 MIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARG 396

Query: 170 LDVEDVNTV 178
           +DVE V+ V
Sbjct: 397 IDVEQVSVV 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 = 47.7 bits (114), Expect = 1e-06
 Identities = 11/48 (22%), Positives = 15/48 (31%), Gaps = 9/48 (18%)

Query: 47  ALVLAPTRELAQQIQTVAKEFSSALRNI---CIFGGTP------KGPQ 85
            L L+PT ELA Q   V ++       +       G           Q
Sbjct: 165 CLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQ 212

>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 =  104 bits (261), Expect = 2e-26
 Identities = 22/70 (31%), Positives = 39/70 (55%)

Query: 109 VIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAAR 168
           V++FV++ ++   + + L  +   AI IH    Q++R      F+  +  ILVAT++  R
Sbjct: 253 VVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGR 312

Query: 169 GLDVEDVNTV 178
           G+D+E VN  
Sbjct: 313 GMDIERVNIA 322

>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 = 51.4 bits (124), Expect = 5e-08
 Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 3/42 (7%)

Query: 47  ALVLAPTRELAQQIQTVAKEFSSALRNI---CIFGGTPKGPQ 85
            LV+  TRELA QI    + FS  + N+     FGG      
Sbjct: 79  VLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKD 120

>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 =  104 bits (262), Expect = 2e-26
 Identities = 24/69 (34%), Positives = 46/69 (66%)

Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
           ++F+ T++KV+ +T  +     +   +HGD  Q++RD ++ +FR G + +L+ TD+ ARG
Sbjct: 284 VIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARG 343

Query: 170 LDVEDVNTV 178
           +DV+ V+ V
Sbjct: 344 IDVQQVSLV 352

>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 = 47.9 bits (115), Expect = 8e-07
 Identities = 19/41 (46%), Positives = 21/41 (51%), Gaps = 2/41 (4%)

Query: 47  ALVLAPTRELAQQIQTVAKEFSSAL--RNICIFGGTPKGPQ 85
           ALVLAPTRELAQQIQ V       +        GGT    +
Sbjct: 111 ALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAE 151

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19 Length = 367

 Score =  103 bits (260), Expect = 2e-26
 Identities = 32/75 (42%), Positives = 46/75 (61%)

Query: 104 NPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVAT 163
           N  F  +VF +TK+  +++   LR     A  IHGD +Q  R+ V+  F+Q K  IL+AT
Sbjct: 236 NKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIAT 295

Query: 164 DVAARGLDVEDVNTV 178
           DV +RG+DV D+N V
Sbjct: 296 DVMSRGIDVNDLNCV 310

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19 Length = 367

 Score = 46.0 bits (110), Expect = 4e-06
 Identities = 22/54 (40%), Positives = 28/54 (51%), Gaps = 8/54 (14%)

Query: 37  EPVKQGDGPIALVLAPTRELAQQIQTVAKEFSS-----ALRNICIFGGTPKGPQ 85
           E V + +G  A++L PTRELA Q   VA E  S      L+   I+GG    PQ
Sbjct: 67  ELVNENNGIEAIILTPTRELAIQ---VADEIESLKGNKNLKIAKIYGGKAIYPQ 117

>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 = 99.2 bits (248), Expect = 2e-26
 Identities = 25/71 (35%), Positives = 42/71 (59%)

Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           + IVFV  +++V ++   LR    +   + G+  Q  R+  +    +G+  +LVATDVAA
Sbjct: 32  RSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAA 91

Query: 168 RGLDVEDVNTV 178
           RG+D+ DV+ V
Sbjct: 92  RGIDIPDVSHV 102

>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 =  104 bits (261), Expect = 3e-26
 Identities = 26/69 (37%), Positives = 46/69 (66%)

Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
           ++F  TK+KV+ +T  +R    +   +HGD  Q++R+ ++ +FR G + +L++TDV ARG
Sbjct: 280 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 339

Query: 170 LDVEDVNTV 178
           LDV  V+ +
Sbjct: 340 LDVPQVSLI 348

>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 = 47.6 bits (114), Expect = 1e-06
 Identities = 17/41 (41%), Positives = 20/41 (48%), Gaps = 2/41 (4%)

Query: 47  ALVLAPTRELAQQIQTVAKEFSSAL--RNICIFGGTPKGPQ 85
           AL+LAPTRELA QIQ         +  +     GGT  G  
Sbjct: 108 ALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGED 148

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens} Length = 228

 Score = 98.8 bits (247), Expect = 1e-25
 Identities = 24/63 (38%), Positives = 38/63 (60%), Gaps = 2/63 (3%)

Query: 25  YMLPAAVHISHQ-EPVKQGDGPIALVLAPTRELAQQIQTVAKEFS-SALRNICIFGGTPK 82
           Y++P  +H+  Q    +Q +GP  LVL PTRELA  ++    ++S   L++ICI+GG  +
Sbjct: 74  YLMPGFIHLDSQPISREQRNGPGMLVLTPTRELALHVEAECSKYSYKGLKSICIYGGRNR 133

Query: 83  GPQ 85
             Q
Sbjct: 134 NGQ 136

>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 =  101 bits (254), Expect = 4e-25
 Identities = 25/81 (30%), Positives = 41/81 (50%), Gaps = 3/81 (3%)

Query: 101 MAKNPAFKVIVFVETKKKVEDITRALRRERH---SAICIHGDKTQQDRDYVLNDFRQGKA 157
             ++  +K I+F  T K    +   L+ E       +  HG  TQ  R  ++  F++ ++
Sbjct: 283 KERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDES 342

Query: 158 PILVATDVAARGLDVEDVNTV 178
            ILV TDV ARG+D  +V+ V
Sbjct: 343 GILVCTDVGARGMDFPNVHEV 363

>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 = 52.9 bits (127), Expect = 2e-08
 Identities = 14/67 (20%), Positives = 25/67 (37%), Gaps = 7/67 (10%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSS------ALRNICIFG 78
           +++P                  A+++APTR+LA QI+   K+             + + G
Sbjct: 77  FLIPI-FQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVG 135

Query: 79  GTPKGPQ 85
           GT     
Sbjct: 136 GTDFRAA 142

>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 =  100 bits (251), Expect = 1e-24
 Identities = 25/81 (30%), Positives = 41/81 (50%), Gaps = 3/81 (3%)

Query: 101 MAKNPAFKVIVFVETKKKVEDITRALRRERH---SAICIHGDKTQQDRDYVLNDFRQGKA 157
             ++  +K I+F  T K    +   L+ E       +  HG  TQ  R  ++  F++ ++
Sbjct: 334 KERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDES 393

Query: 158 PILVATDVAARGLDVEDVNTV 178
            ILV TDV ARG+D  +V+ V
Sbjct: 394 GILVCTDVGARGMDFPNVHEV 414

>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 = 52.5 bits (126), Expect = 3e-08
 Identities = 14/65 (21%), Positives = 23/65 (35%), Gaps = 7/65 (10%)

Query: 27  LPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSS------ALRNICIFGGT 80
           +P                  A+++APTR+LA QI+   K+             + + GGT
Sbjct: 130 IPI-FQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGT 188

Query: 81  PKGPQ 85
                
Sbjct: 189 DFRAA 193

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii} Length = 337

 Score = 96.4 bits (241), Expect = 8e-24
 Identities = 28/70 (40%), Positives = 42/70 (60%), Gaps = 4/70 (5%)

Query: 109 VIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAAR 168
           VIVFV T+ +V  + R       +AI + GD  Q  R+  ++ FR+G+  +L+ TDVA+R
Sbjct: 223 VIVFVRTRNRVAKLVRLFD----NAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASR 278

Query: 169 GLDVEDVNTV 178
           GLD+  V  V
Sbjct: 279 GLDIPLVEKV 288

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii} Length = 337

 Score = 46.7 bits (112), Expect = 2e-06
 Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 8/44 (18%)

Query: 47 ALVLAPTRELAQQIQTVAKEFSS-----ALRNICIFGGTPKGPQ 85
          +LV+ PTREL +Q   VA            +   ++GG P   Q
Sbjct: 59 SLVVTPTRELTRQ---VASHIRDIGRYMDTKVAEVYGGMPYKAQ 99

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19 Length = 253

 Score = 87.2 bits (217), Expect = 6e-21
 Identities = 22/67 (32%), Positives = 38/67 (56%), Gaps = 6/67 (8%)

Query: 25  YMLPAAVHI----SHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS--SALRNICIFG 78
           +++P   H+     +Q+   +   P  L+LAPTRELA QI + +++FS  + LR+  ++G
Sbjct: 77  FLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYG 136

Query: 79  GTPKGPQ 85
           G     Q
Sbjct: 137 GADTHSQ 143

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score = 82.9 bits (205), Expect = 1e-18
 Identities = 14/72 (19%), Positives = 35/72 (48%), Gaps = 9/72 (12%)

Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDV-- 165
            +++F +T+++ +++   L+R +      +  +T  + +    DF+ GK  IL+      
Sbjct: 254 GILIFAQTEEEGKELYEYLKRFK-----FNVGETWSEFEKNFEDFKVGKINILIGVQAYY 308

Query: 166 --AARGLDVEDV 175
               RG+D+ + 
Sbjct: 309 GKLTRGVDLPER 320

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score = 55.1 bits (133), Expect = 4e-09
 Identities = 30/199 (15%), Positives = 57/199 (28%), Gaps = 25/199 (12%)

Query: 43  DGPIALVLAPTRELAQQIQTVAKEFS-SALRNICIFGGTPKGPQDCLPLHRFVFNCQ--- 98
            G  + ++ PT  L +Q     ++ +   ++    +    K  ++         +     
Sbjct: 63  KGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILV 122

Query: 99  ---------YEMAKNPAFKVIVFVETKK-----KVEDITRALRRERHSAICIHGDKTQQD 144
                     E      F  +   +        +  D    +       I       +Q 
Sbjct: 123 FSTQFVSKNREKLSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGIPEEIIRKAFSTIKQG 182

Query: 145 RDYVL-NDFRQGKAPILVATDVA--ARGLDVEDVNTVNIGSLQLSANHNISQVIEVVQDY 201
           + Y    + + G   +  AT      R L   D+    +G L  S   NI+ V    +  
Sbjct: 183 KIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLNFTVGRLV-SVARNITHVRISSRSK 241

Query: 202 EKEKRLFSLIRELGKYTLI 220
           EK   L  L+       LI
Sbjct: 242 EK---LVELLEIFRDGILI 257

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens} Length = 245

 Score = 80.3 bits (199), Expect = 2e-18
 Identities = 15/70 (21%), Positives = 26/70 (37%), Gaps = 6/70 (8%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS--SALRNICIFGGTPK 82
           + +P  + +          G  AL+++PTRELA QI     + S  +  R   I      
Sbjct: 83  FSIPILMQLKQP----ANKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVA 138

Query: 83  GPQDCLPLHR 92
             +      +
Sbjct: 139 AKKFGPKSSK 148

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19 Length = 494

 Score = 66.4 bits (161), Expect = 6e-13
 Identities = 23/89 (25%), Positives = 45/89 (50%), Gaps = 8/89 (8%)

Query: 98  QYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDK--------TQQDRDYVL 149
           + ++ +    K+IVF   ++  + I   L ++   A    G          +Q+++  +L
Sbjct: 353 REQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLIL 412

Query: 150 NDFRQGKAPILVATDVAARGLDVEDVNTV 178
           ++F +G+  +LVAT V   GLDV +V+ V
Sbjct: 413 DEFARGEFNVLVATSVGEEGLDVPEVDLV 441

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens} Length = 262

 Score = 53.9 bits (130), Expect = 6e-09
 Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 3/63 (4%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSS--ALRNICIFGGTPK 82
           +++PA V +  +      +G   L+L+PTRELA Q   V KE  +        I GG+ +
Sbjct: 108 FLIPA-VELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNR 166

Query: 83  GPQ 85
             +
Sbjct: 167 SAE 169

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A* Length = 230

 Score = 53.0 bits (128), Expect = 1e-08
 Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 3/42 (7%)

Query: 47  ALVLAPTRELAQQIQTVAKEFSSALRNI---CIFGGTPKGPQ 85
            L+LAPTRE+A QI +V       +  +      GGTP    
Sbjct: 95  ILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQD 136

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A* Length = 472

 Score = 52.5 bits (126), Expect = 3e-08
 Identities = 20/99 (20%), Positives = 45/99 (45%), Gaps = 9/99 (9%)

Query: 97  CQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGK 156
            +  + ++   K+I+F    + V  I++           I    ++++R+ +L  FR G+
Sbjct: 340 LREILERHRKDKIIIFTRHNELVYRISKVFLIP-----AITHRTSREEREEILEGFRTGR 394

Query: 157 APILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQVI 195
              +V++ V   G+DV D N      + +S + +  + I
Sbjct: 395 FRAIVSSQVLDEGIDVPDANVG----VIMSGSGSAREYI 429

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A Length = 207

 Score = 51.0 bits (123), Expect = 3e-08
 Identities = 22/59 (37%), Positives = 33/59 (55%), Gaps = 2/59 (3%)

Query: 27  LPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPKGPQ 85
           LP A  ++  +   +G  P ALVL PTRELA Q+ +     +  L+ + ++GGT  G Q
Sbjct: 57  LPIAERLAPSQE--RGRKPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQ 113

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens} Length = 236

 Score = 51.1 bits (123), Expect = 4e-08
 Identities = 15/63 (23%), Positives = 27/63 (42%), Gaps = 3/63 (4%)

Query: 25  YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSS--ALRNICIFGGTPK 82
           +++P  +   ++      DG   L+++PTRELA Q   V ++           I GG   
Sbjct: 79  FLVPV-LEALYRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDL 137

Query: 83  GPQ 85
             +
Sbjct: 138 KHE 140

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19 Length = 220

 Score = 50.7 bits (122), Expect = 5e-08
 Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 3/42 (7%)

Query: 47  ALVLAPTRELAQQIQTVAKEFSSALRNI---CIFGGTPKGPQ 85
            LV+  TRELA QI    + FS  + N+     FGG      
Sbjct: 85  VLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKD 126

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19 Length = 206

 Score = 50.6 bits (122), Expect = 5e-08
 Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 3/42 (7%)

Query: 47  ALVLAPTRELAQQIQTVAKEFSSALRNI---CIFGGTPKGPQ 85
           A+V+ PTRELA Q+  +  + S  +         GGT     
Sbjct: 74  AMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDD 115

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens} Length = 249

 Score = 48.8 bits (117), Expect = 3e-07
 Identities = 17/44 (38%), Positives = 21/44 (47%), Gaps = 2/44 (4%)

Query: 44  GPIALVLAPTRELAQQIQTVAKEFSS--ALRNICIFGGTPKGPQ 85
              ALVL PTRELA QI    +   S   +++  I GG     Q
Sbjct: 111 RLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQ 154

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A Length = 224

 Score = 48.3 bits (116), Expect = 4e-07
 Identities = 17/41 (41%), Positives = 21/41 (51%), Gaps = 2/41 (4%)

Query: 47  ALVLAPTRELAQQIQTVAKEFSS--ALRNICIFGGTPKGPQ 85
           AL+LAPTRELA QIQ V    +    ++     GGT     
Sbjct: 85  ALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVED 125

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score = 47.9 bits (115), Expect = 4e-07
 Identities = 15/45 (33%), Positives = 20/45 (44%), Gaps = 6/45 (13%)

Query: 47  ALVLAPTRELAQQIQTVAKEFSSALRN------ICIFGGTPKGPQ 85
           A++ APTRELA QI     + +            C+ GGT K   
Sbjct: 75  AVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKA 119

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A* Length = 237

 Score = 47.6 bits (114), Expect = 7e-07
 Identities = 19/41 (46%), Positives = 20/41 (48%), Gaps = 2/41 (4%)

Query: 47  ALVLAPTRELAQQIQTVAKEFSS--ALRNICIFGGTPKGPQ 85
           ALVLAPTRELAQQIQ V                GGT    +
Sbjct: 101 ALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNE 141

>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.70A {Anas platyrhynchos} Length = 936

 Score = 48.4 bits (114), Expect = 8e-07
 Identities = 21/102 (20%), Positives = 36/102 (35%), Gaps = 13/102 (12%)

Query: 90  LHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRER------------HSAICIH 137
           L   V         NP  + ++F +T+  V  + + +                       
Sbjct: 615 LEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQT 674

Query: 138 GDKTQQDRDYVLNDFRQGKA-PILVATDVAARGLDVEDVNTV 178
              T   +  VL+ F+  K   +L+AT VA  G+D+   N V
Sbjct: 675 TGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLV 716

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens} Length = 300

 Score = 47.8 bits (114), Expect = 9e-07
 Identities = 10/38 (26%), Positives = 14/38 (36%), Gaps = 3/38 (7%)

Query: 47  ALVLAPTRELAQQIQTVAKEFSSALRNI---CIFGGTP 81
            L L+PT ELA Q   V ++       +       G  
Sbjct: 165 CLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNK 202

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 46.5 bits (109), Expect = 3e-06
 Identities = 31/148 (20%), Positives = 51/148 (34%), Gaps = 24/148 (16%)

Query: 90  LHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRER------------HSAICIH 137
           L    F  Q E   NP    I+FV+T+  V+ +   +                      +
Sbjct: 382 LEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQN 441

Query: 138 GDKTQQDRDYVLNDFRQ-GKAPILVATDVAARGLDVEDVNTV--------NIGSLQ--LS 186
              T   +  +L+ F+  G   IL+AT VA  G+D+   N V         I  +Q    
Sbjct: 442 TGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR 501

Query: 187 ANHNISQVIEVV-QDYEKEKRLFSLIRE 213
                S+   +       EK   ++ +E
Sbjct: 502 GRARGSKCFLLTSNAGVIEKEQINMYKE 529

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A* Length = 556

 Score = 45.7 bits (107), Expect = 6e-06
 Identities = 21/102 (20%), Positives = 36/102 (35%), Gaps = 13/102 (12%)

Query: 90  LHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRER------------HSAICIH 137
           L   V         NP  + ++F +T+  V  + + +                       
Sbjct: 374 LEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQT 433

Query: 138 GDKTQQDRDYVLNDFRQGKA-PILVATDVAARGLDVEDVNTV 178
              T   +  VL+ F+  K   +L+AT VA  G+D+   N V
Sbjct: 434 TGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLV 475

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A* Length = 523

 Score = 44.8 bits (107), Expect = 1e-05
 Identities = 16/54 (29%), Positives = 25/54 (46%)

Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVAT 163
           I++  ++ KVED    L+ +  SA   H       R  V   F++    I+VAT
Sbjct: 240 IIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVAT 293

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A* Length = 591

 Score = 44.6 bits (106), Expect = 1e-05
 Identities = 12/54 (22%), Positives = 26/54 (48%)

Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVAT 163
           I++  ++K  E +T +L+     A   H +   +D+  V   +   +  ++VAT
Sbjct: 271 IIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVAT 324

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos} Length = 797

 Score = 44.6 bits (104), Expect = 2e-05
 Identities = 21/102 (20%), Positives = 36/102 (35%), Gaps = 13/102 (12%)

Query: 90  LHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRER------------HSAICIH 137
           L   V         NP  + ++F +T+  V  + + +                       
Sbjct: 615 LEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQT 674

Query: 138 GDKTQQDRDYVLNDFRQGKA-PILVATDVAARGLDVEDVNTV 178
              T   +  VL+ F+  K   +L+AT VA  G+D+   N V
Sbjct: 675 TGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLV 716

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 43.7 bits (102), Expect = 2e-05
 Identities = 26/102 (25%), Positives = 38/102 (37%), Gaps = 13/102 (12%)

Query: 90  LHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRER------------HSAICIH 137
           L       Q E    P  K I+FV+T+  V+ + + +                       
Sbjct: 373 LRDLYLVLQEEYHLKPETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRA 432

Query: 138 GDKTQQDRDYVLNDFRQ-GKAPILVATDVAARGLDVEDVNTV 178
              T   +  VL  FR  G   IL+AT VA  G+D+ + N V
Sbjct: 433 TGMTLPAQKCVLEAFRASGDNNILIATSVADEGIDIAECNLV 474

>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription factor, RNA polymerase recycling, activator, ATP-binding, DNA-binding; 3.20A {Escherichia coli K12} Length = 968

 Score = 43.5 bits (102), Expect = 3e-05
 Identities = 15/79 (18%), Positives = 33/79 (41%), Gaps = 3/79 (3%)

Query: 103 KNPAFKVIVFVETKKKVEDITRALR-RERHSAICIHGDKTQQDRDYVLNDFRQ--GKAPI 159
            + + KV+V          + + LR RE   A   H   +  +RD     F +    A +
Sbjct: 500 SHRSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQV 559

Query: 160 LVATDVAARGLDVEDVNTV 178
           L+ +++ + G + +  + +
Sbjct: 560 LLCSEIGSEGRNFQFASHM 578

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4} Length = 510

 Score = 42.6 bits (99), Expect = 6e-05
 Identities = 14/72 (19%), Positives = 31/72 (43%), Gaps = 1/72 (1%)

Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVAT-DVA 166
              V  +     + I   ++ E      + G+   + R+ +      GK  I+VA+  V 
Sbjct: 349 NAFVMFKHVSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVF 408

Query: 167 ARGLDVEDVNTV 178
           + G+ V++++ V
Sbjct: 409 STGISVKNLHHV 420

>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* Length = 440

 Score = 40.6 bits (95), Expect = 3e-04
 Identities = 13/71 (18%), Positives = 31/71 (43%), Gaps = 5/71 (7%)

Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
               F+ + +    +  +LR+   S + ++    +++        +Q K   ++ATD+A 
Sbjct: 179 PTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFERE----YPTIKQKKPDFILATDIAE 234

Query: 168 RGLDVEDVNTV 178
            G ++  V  V
Sbjct: 235 MGANL-CVERV 244

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 40.2 bits (93), Expect = 4e-04
 Identities = 24/214 (11%), Positives = 55/214 (25%), Gaps = 58/214 (27%)

Query: 48  LVLAPTRE---------LAQQIQTVAKEF------------SSALRNICIFGGTPKGPQD 86
           ++++             L  + + + ++F             S ++        P     
Sbjct: 54  IIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQR---QPSMMTR 110

Query: 87  CLPLHRFVFNCQYEMAKNPAFKVIV-----FVETKKKVEDITRALRRERHSA-ICIHGDK 140
                       Y   ++  +          V   +    + +AL   R +  + I G  
Sbjct: 111 -----------MYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVL 159

Query: 141 TQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQVIEVVQD 200
                         GK   +           V+      I  L L   ++   V+E++Q 
Sbjct: 160 G------------SGKT-WVALD--VCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQK 204

Query: 201 --YEKEKRLFSLIRELGKYTLITQESSSTLSEMV 232
             Y+ +    S         L      + L  ++
Sbjct: 205 LLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLL 238

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	233
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	100.0
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	100.0
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	100.0
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	100.0
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	100.0
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	100.0
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	100.0
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	100.0
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	100.0
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	100.0
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	100.0
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.98
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.97
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.97
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.97
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.97
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.97
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.97
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.97
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.97
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.96
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.96
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.96
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.95
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.95
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.95
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.95
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.95
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.95
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.95
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.95
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.95
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.94
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.94
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.94
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.94
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.94
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.94
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.94
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.94
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.94
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.93
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.93
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.93
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.93
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.92
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.92
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.91
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.91
3h1t_A	590	Type I site-specific restriction-modification syst	99.9
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	99.89
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.88
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	99.88
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.88
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	99.88
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.87
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	99.87
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.87
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.87
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.84
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.84
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	99.84
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.84
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.83
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	99.7
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.75
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.71
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.68
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.67
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.66
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.64
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.64
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.64
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.64
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.63
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.63
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.62
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.62
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.61
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.61
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.6
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.6
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.6
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.58
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.56
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.27
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.18
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.13
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.06
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.05
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	98.91
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	98.9
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	97.98
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	97.95
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	96.98
3hgt_A	328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	96.94
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	96.78
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	96.59
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	96.47
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	96.43
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	96.15
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	96.15
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	96.12
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	95.97
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	95.81
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	95.79
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	95.75
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	95.31
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	95.14
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	94.85
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	94.84
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	94.59
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	94.54
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	94.5
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	94.43
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	94.29
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	94.19
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	93.99
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	93.98
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	93.78
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	93.74
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	93.47
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	93.32
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	93.06
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	92.64
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	92.37
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	92.36
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	91.98
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	91.87
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	91.55
2l82_A	162	Designed protein OR32; structural genomics, northe	91.24
3bor_A	237	Human initiation factor 4A-II; translation initiat	91.15
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	90.98
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	90.82
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	90.66
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	90.51
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	90.5
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	90.41
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	89.83
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	89.67
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	89.66
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	89.66
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	89.42
3co5_A	143	Putative two-component system transcriptional RES	89.41
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	89.27
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	89.17
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	89.15
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	89.14
2qgz_A	308	Helicase loader, putative primosome component; str	88.82
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	88.59
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	88.38
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	88.11
1tue_A	212	Replication protein E1; helicase, replication, E1E	88.06
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	87.95
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	87.92
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	87.83
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	87.6
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	87.38
3ice_A	422	Transcription termination factor RHO; transcriptio	87.31
3bos_A	242	Putative DNA replication factor; P-loop containing	86.97
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	86.49
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	86.48
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	86.23
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	86.09
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	85.96
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	85.75
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	85.72
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	85.43
1xp8_A	366	RECA protein, recombinase A; recombination, radior	85.36
1u94_A	356	RECA protein, recombinase A; homologous recombinat	85.21
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	85.08
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	84.88
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	84.85
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	84.85
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	84.85
3u4q_B	1166	ATP-dependent helicase/deoxyribonuclease subunit;	84.84
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	84.67
3foj_A	100	Uncharacterized protein; protein SSP1007, structur	84.25
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	84.22
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	84.05
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	83.94
3eme_A	103	Rhodanese-like domain protein; alpha-beta-alpha sa	83.82
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	83.81
3gk5_A	108	Uncharacterized rhodanese-related protein TVG08686	83.74
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	83.7
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	83.65
3iwh_A	103	Rhodanese-like domain protein; alpha-beta-alpha sa	83.51
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	83.41
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	83.33
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	83.26
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	83.19
2r6a_A	454	DNAB helicase, replicative helicase; replication,	82.91
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	82.89
1w36_B	1180	RECB, exodeoxyribonuclease V beta chain; recombina	82.78
1fx0_A	507	ATP synthase alpha chain; latent ATPase, thermal s	82.77
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	82.47
3io5_A	333	Recombination and repair protein; storage dimer, i	82.26
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	82.0
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	81.92
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	81.71
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	81.46
2r9v_A	515	ATP synthase subunit alpha; TM1612, structural gen	81.28
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	81.18
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	81.17
2eyu_A	261	Twitching motility protein PILT; pilus retraction	81.16
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	81.14
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	81.08
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	81.03
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	81.01
2z43_A	324	DNA repair and recombination protein RADA; archaea	80.87
2qe7_A	502	ATP synthase subunit alpha; blockage of ATP hydrol	80.69
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	80.68
2chg_A	226	Replication factor C small subunit; DNA-binding pr	80.65
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	80.59
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	80.57
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	80.47
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	80.33
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	80.21
2ck3_A	510	ATP synthase subunit alpha\, mitochondrial; hydrol	80.06

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=100.00  E-value=3.3e-38  Score=275.53  Aligned_cols=200  Identities=26%  Similarity=0.373  Sum_probs=167.0

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~g   78 (233)
                      |||.+++|+|++++|+||||||++|++|++++++.........++++||++|||||+.|+++.++++  ..++++.+++|
T Consensus        86 ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~~~~~~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~~~~~g  165 (434)
T 2db3_A           86 SIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYG  165 (434)
T ss_dssp             HHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCCCCCTTCCSEEEECSSHHHHHHHHHHHHHHTTTSSCCCCEECT
T ss_pred             HHHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHhcccccccCCccEEEEecCHHHHHHHHHHHHHHhccCCcEEEEEEC
Confidence            4677889999999999999999999999999998764433456889999999999999999999999  35688999999


Q ss_pred             CCCC---------CCeeEEe--------c-------cc-----------------------hh-----------------
Q psy14082         79 GTPK---------GPQDCLP--------L-------HR-----------------------FV-----------------   94 (233)
Q Consensus        79 g~~~---------~~~~lv~--------l-------~r-----------------------~~-----------------   94 (233)
                      |.+.         ..+++|+        +       ++                       ++                 
T Consensus       166 g~~~~~~~~~l~~~~~Ivv~Tp~~l~~~l~~~~~~l~~~~~lVlDEah~~~~~gf~~~~~~i~~~~~~~~~~q~l~~SAT  245 (434)
T 2db3_A          166 GTSFRHQNECITRGCHVVIATPGRLLDFVDRTFITFEDTRFVVLDEADRMLDMGFSEDMRRIMTHVTMRPEHQTLMFSAT  245 (434)
T ss_dssp             TSCHHHHHHHHTTCCSEEEECHHHHHHHHHTTSCCCTTCCEEEEETHHHHTSTTTHHHHHHHHHCTTSCSSCEEEEEESC
T ss_pred             CCCHHHHHHHhhcCCCEEEEChHHHHHHHHhCCcccccCCeEEEccHhhhhccCcHHHHHHHHHhcCCCCCceEEEEecc
Confidence            9763         4567777        0       00                       00                 


Q ss_pred             --------------------------------------------hhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCC
Q psy14082         95 --------------------------------------------FNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRER  130 (233)
Q Consensus        95 --------------------------------------------~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~  130 (233)
                                                                  ..+.+.+.. ...++||||++++.++.+++.|.+.+
T Consensus       246 ~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~-~~~~~lVF~~t~~~a~~l~~~L~~~~  324 (434)
T 2db3_A          246 FPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTIYEVNKYAKRSKLIEILSE-QADGTIVFVETKRGADFLASFLSEKE  324 (434)
T ss_dssp             CCHHHHHHHHTTCSSCEEEEESSTTCCCTTEEEEEEECCGGGHHHHHHHHHHH-CCTTEEEECSSHHHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHhccCCEEEEeccccccccccceEEEEeCcHHHHHHHHHHHHh-CCCCEEEEEeCcHHHHHHHHHHHhCC
Confidence                                                        000002222 23459999999999999999999999


Q ss_pred             CeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc------------ceeeEEe
Q psy14082        131 HSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI------------SQVIEVV  198 (233)
Q Consensus       131 ~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i------------~~~~~~~  198 (233)
                      +.+..+||+|++++|..++++|++|+.+|||||+++++|+|+|++++|||||+|.+.+.|+            |.++.|+
T Consensus       325 ~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~v~~rGlDi~~v~~VI~~d~p~~~~~y~qriGR~gR~g~~G~a~~~~  404 (434)
T 2db3_A          325 FPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFF  404 (434)
T ss_dssp             CCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECGGGTSSCCCTTCCEEEESSCCSSHHHHHHHHTTSSCTTCCEEEEEEE
T ss_pred             CCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEchhhhCCCCcccCCEEEEECCCCCHHHHHHHhcccccCCCCCEEEEEE
Confidence            9999999999999999999999999999999999999999999999999999999998666            4667778


Q ss_pred             ecc
Q psy14082        199 QDY  201 (233)
Q Consensus       199 ~~~  201 (233)
                      ++.
T Consensus       405 ~~~  407 (434)
T 2db3_A          405 DPE  407 (434)
T ss_dssp             CTT
T ss_pred             ecc
Confidence            743

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=100.00  E-value=2.3e-35  Score=254.95  Aligned_cols=216  Identities=24%  Similarity=0.296  Sum_probs=177.1

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~g   78 (233)
                      |||.++.|+|+++.+|||||||++|++|+++.+...     ..++++||++||++|+.|+++.++++  ..++++..++|
T Consensus        67 ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~-----~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g  141 (410)
T 2j0s_A           67 AIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQ-----VRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIG  141 (410)
T ss_dssp             HHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTT-----SCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECT
T ss_pred             HHHHHhCCCCEEEECCCCCCchHHHHHHHHHHHhhc-----cCCceEEEEcCcHHHHHHHHHHHHHHhccCCeEEEEEEC
Confidence            356678899999999999999999999999988543     35678999999999999999999998  44678888888


Q ss_pred             CCCC---------CCeeEEe--------ccc-------------------------------------------------
Q psy14082         79 GTPK---------GPQDCLP--------LHR-------------------------------------------------   92 (233)
Q Consensus        79 g~~~---------~~~~lv~--------l~r-------------------------------------------------   92 (233)
                      |.+.         ..+++|+        +.+                                                 
T Consensus       142 ~~~~~~~~~~~~~~~~ivv~Tp~~l~~~l~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~  221 (410)
T 2j0s_A          142 GTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLP  221 (410)
T ss_dssp             TSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHTSTTTHHHHHHHHTTSCTTCEEEEEESCCC
T ss_pred             CCCHHHHHHHhhcCCCEEEcCHHHHHHHHHhCCccHhheeEEEEccHHHHHhhhhHHHHHHHHHhCccCceEEEEEcCCC
Confidence            8653         3455665        000                                                 


Q ss_pred             -----------------------------------------hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCC
Q psy14082         93 -----------------------------------------FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERH  131 (233)
Q Consensus        93 -----------------------------------------~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~  131 (233)
                                                               ..+.+.+.+......++||||++++.++.+++.|.+.++
T Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~  301 (410)
T 2j0s_A          222 HEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANF  301 (410)
T ss_dssp             HHHHTTGGGTCSSCEEECCCGGGCSCTTEEEEEEEESSTTHHHHHHHHHHHHHTSSEEEEECSSHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHcCCCEEEEecCccccCCCceEEEEEeCcHHhHHHHHHHHHHhcCCCcEEEEEcCHHHHHHHHHHHHhCCC
Confidence                                                     000111123334567999999999999999999999999


Q ss_pred             eeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc------------ceeeEEee
Q psy14082        132 SAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI------------SQVIEVVQ  199 (233)
Q Consensus       132 ~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i------------~~~~~~~~  199 (233)
                      .+..+||+|++++|..++++|++|+.+|||||+++++|+|+|++++||+||+|.+...|+            |.++.+++
T Consensus       302 ~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~  381 (410)
T 2j0s_A          302 TVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVK  381 (410)
T ss_dssp             CCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEE
T ss_pred             ceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECChhhCcCCcccCCEEEEECCCCCHHHHHHhcccccCCCCceEEEEEec
Confidence            999999999999999999999999999999999999999999999999999999987555            46777888


Q ss_pred             cchHHHHHHHHHHhhcCccccccc
Q psy14082        200 DYEKEKRLFSLIRELGKYTLITQE  223 (233)
Q Consensus       200 ~~~~~~~~~~~i~~~~~~~~~~~~  223 (233)
                      +.+  ...++.++++.+.+++..+
T Consensus       382 ~~~--~~~~~~i~~~~~~~~~~~~  403 (410)
T 2j0s_A          382 NDD--IRILRDIEQYYSTQIDEMP  403 (410)
T ss_dssp             GGG--HHHHHHHHHHTTCCCEECC
T ss_pred             HHH--HHHHHHHHHHhCCCceecc
Confidence            654  7788888887776665444

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=100.00  E-value=1e-34  Score=251.11  Aligned_cols=202  Identities=32%  Similarity=0.412  Sum_probs=165.1

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCC-------------CCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPV-------------KQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~-------------~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      |||.++.|+|++++||||||||++|++|+++.+......             ....++++||++||++|+.|+++.++++
T Consensus        45 ~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  124 (417)
T 2i4i_A           45 AIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKF  124 (417)
T ss_dssp             HHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCCCHHHHHHHHCBTTBSCSBCCSEEEECSSHHHHHHHHHHHHHH
T ss_pred             HHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHhccccchhhccccccccccccCCccEEEECCcHHHHHHHHHHHHHH
Confidence            356778999999999999999999999999998754211             1233578999999999999999999998


Q ss_pred             --hcCCcEEEEEcCCCC---------CCeeEEe---------------ccc-----------------------------
Q psy14082         68 --SSALRNICIFGGTPK---------GPQDCLP---------------LHR-----------------------------   92 (233)
Q Consensus        68 --~~~~~~~~~~gg~~~---------~~~~lv~---------------l~r-----------------------------   92 (233)
                        ..++++..++||.+.         ..+++|+               +.+                             
T Consensus       125 ~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~i~~~~~  204 (417)
T 2i4i_A          125 SYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDT  204 (417)
T ss_dssp             HTTSSCCEEEECSSSCHHHHHHHHTTCCSEEEECHHHHHHHHHTTSBCCTTCCEEEESSHHHHHHTTCHHHHHHHHTSSS
T ss_pred             hCcCCceEEEEECCCCHHHHHHHhhCCCCEEEEChHHHHHHHHcCCcChhhCcEEEEEChhHhhccCcHHHHHHHHHhcc
Confidence              356888999998653         3566776               000                             


Q ss_pred             ---------------------------------------------------------hhhhchHHHhc-CCCCeEEEEec
Q psy14082         93 ---------------------------------------------------------FVFNCQYEMAK-NPAFKVIVFVE  114 (233)
Q Consensus        93 ---------------------------------------------------------~~~~~~~~~~~-~~~~k~iIf~~  114 (233)
                                                                               ....+.+.+.. ..+.++||||+
T Consensus       205 ~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~l~~~l~~~~~~~~~lVf~~  284 (417)
T 2i4i_A          205 MPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVE  284 (417)
T ss_dssp             CCCBTTBEEEEEESCCCHHHHHHHHHHCSSCEEEEEC----CCSSEEEEEEECCGGGHHHHHHHHHHTCCTTCEEEEECS
T ss_pred             CCCcCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEeCCCCCCccCceEEEEEeccHhHHHHHHHHHHhcCCCCeEEEEEC
Confidence                                                                     00000112222 35789999999


Q ss_pred             chhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc---
Q psy14082        115 TKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI---  191 (233)
Q Consensus       115 ~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i---  191 (233)
                      +++.++.+++.|.+.++.+..+||+|++++|.+++++|++|+.+|||||+++++|+|+|++++||+||+|.+...|+   
T Consensus       285 ~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlvaT~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~  364 (417)
T 2i4i_A          285 TKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRI  364 (417)
T ss_dssp             SHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTSSCEEEECHHHHTTSCCCCEEEEEESSCCSSHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCCeeEecCCCCHHHHHHHHHHHHcCCCCEEEECChhhcCCCcccCCEEEEEcCCCCHHHHHHhc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999997665   


Q ss_pred             ---------ceeeEEeecch
Q psy14082        192 ---------SQVIEVVQDYE  202 (233)
Q Consensus       192 ---------~~~~~~~~~~~  202 (233)
                               |.++.++++.+
T Consensus       365 GR~gR~g~~g~~~~~~~~~~  384 (417)
T 2i4i_A          365 GRTGRVGNLGLATSFFNERN  384 (417)
T ss_dssp             TTBCC--CCEEEEEEECGGG
T ss_pred             CccccCCCCceEEEEEcccc
Confidence                     45666777544

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=100.00  E-value=7.9e-34  Score=243.43  Aligned_cols=216  Identities=21%  Similarity=0.276  Sum_probs=175.2

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh---cCCcEEEEE
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS---SALRNICIF   77 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~---~~~~~~~~~   77 (233)
                      |+|.++.|+|+++.+|||+|||++|++|++..+...     ..++++||++||++|+.|+++.++++.   +++++..+.
T Consensus        38 ~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~-----~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~  112 (391)
T 1xti_A           38 CIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPV-----TGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFF  112 (391)
T ss_dssp             HHHHHTTTCCEEEECSSCSSHHHHHHHHHHHHCCCC-----TTCCCEEEECSCHHHHHHHHHHHHHHTTTCTTCCEEEEC
T ss_pred             HHHHHhcCCcEEEECCCCCcHHHHHHHHHHHhhccc-----CCCeeEEEECCCHHHHHHHHHHHHHHHhhCCCeEEEEEe
Confidence            356678899999999999999999999999887643     346789999999999999999999983   378899999


Q ss_pred             cCCCC----------CCeeEEe---------------ccc----------------------------------------
Q psy14082         78 GGTPK----------GPQDCLP---------------LHR----------------------------------------   92 (233)
Q Consensus        78 gg~~~----------~~~~lv~---------------l~r----------------------------------------   92 (233)
                      ||.+.          ..+++|+               +.+                                        
T Consensus       113 g~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~vViDEaH~~~~~~~~~~~~~~~~~~~~~~~~~i~~SA  192 (391)
T 1xti_A          113 GGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSA  192 (391)
T ss_dssp             TTSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCSEEEECSHHHHTSSHHHHHHHHHHHHTSCSSSEEEEEES
T ss_pred             CCCCHHHHHHHHhcCCCCEEEECHHHHHHHHHcCCccccccCEEEEeCHHHHhhccchHHHHHHHHhhCCCCceEEEEEe
Confidence            98653          2466666               000                                        


Q ss_pred             --------------------------------------------hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhh
Q psy14082         93 --------------------------------------------FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRR  128 (233)
Q Consensus        93 --------------------------------------------~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~  128 (233)
                                                                  ....+.+.+.....+++||||++++.++.+++.|.+
T Consensus       193 T~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~lvf~~~~~~~~~l~~~L~~  272 (391)
T 1xti_A          193 TLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVE  272 (391)
T ss_dssp             SCCSTHHHHHHHHCSSCEEEECCCCCCCCCTTCEEEEEECCGGGHHHHHHHHHHHSCCSEEEEECSCHHHHHHHHHHHHH
T ss_pred             eCCHHHHHHHHHHcCCCeEEEecCccccCcccceEEEEEcCchhHHHHHHHHHHhcCCCcEEEEeCcHHHHHHHHHHHHh
Confidence                                                        000111134455778999999999999999999999


Q ss_pred             CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc------------ceeeE
Q psy14082        129 ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI------------SQVIE  196 (233)
Q Consensus       129 ~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i------------~~~~~  196 (233)
                      .++.+..+||+|+.++|..++++|++|+.++||||+++++|+|+|++++||+||+|.+...|+            |.++.
T Consensus       273 ~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~  352 (391)
T 1xti_A          273 QNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAIT  352 (391)
T ss_dssp             TTCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESCCCSSCBCCTTEEEEEESSCCSSHHHHHHHHCBCSSSCCCCEEEE
T ss_pred             CCCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHhcccccCCCCceEEEE
Confidence            999999999999999999999999999999999999999999999999999999999997555            35566


Q ss_pred             EeecchHHHHHHHHHHhhcCcccccc
Q psy14082        197 VVQDYEKEKRLFSLIRELGKYTLITQ  222 (233)
Q Consensus       197 ~~~~~~~~~~~~~~i~~~~~~~~~~~  222 (233)
                      ++++ +++..+++.+++..+..++..
T Consensus       353 ~~~~-~~~~~~~~~~~~~~~~~~~~~  377 (391)
T 1xti_A          353 FVSD-ENDAKILNDVQDRFEVNISEL  377 (391)
T ss_dssp             EECS-HHHHHHHHHHHHHTTCCCEEC
T ss_pred             EEcc-cchHHHHHHHHHHhcCChhhC
Confidence            7765 345667777777655544433

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=100.00  E-value=2.8e-34  Score=247.63  Aligned_cols=216  Identities=21%  Similarity=0.268  Sum_probs=171.3

Q ss_pred             CCCCCCC--CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh---hcCCcEEEE
Q psy14082          2 LPPSESG--CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF---SSALRNICI   76 (233)
Q Consensus         2 ip~~~~g--~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~---~~~~~~~~~   76 (233)
                      ||.++.|  +|+++.+|||||||++|++|+++.+...     ..++++||++||++|+.|+++.++++   ..++++...
T Consensus        56 i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~-----~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~  130 (412)
T 3fht_A           56 LPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPA-----NKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYA  130 (412)
T ss_dssp             HHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCCTT-----SCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEE
T ss_pred             HHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhhhc-----CCCCCEEEECCCHHHHHHHHHHHHHHHhhcccceEEEe
Confidence            4556666  9999999999999999999999988654     45678999999999999999999998   346788888


Q ss_pred             EcCCCCC------CeeEEe--------c--------cc------------------------------------------
Q psy14082         77 FGGTPKG------PQDCLP--------L--------HR------------------------------------------   92 (233)
Q Consensus        77 ~gg~~~~------~~~lv~--------l--------~r------------------------------------------   92 (233)
                      .|+....      .+++|+        +        .+                                          
T Consensus       131 ~~~~~~~~~~~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~  210 (412)
T 3fht_A          131 VRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATF  210 (412)
T ss_dssp             CTTCCCCTTCCCCCSEEEECHHHHHHHHTTSCSSCGGGCCEEEEETHHHHHSTTTTHHHHHHHHHTSCTTCEEEEEESCC
T ss_pred             ecCcchhhhhcCCCCEEEECchHHHHHHHhcCCcChhhCcEEEEeCHHHHhhcCCcHHHHHHHHhhCCCCceEEEEEeec
Confidence            8876542      356666        0        00                                          


Q ss_pred             ------------------------------------------hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCC
Q psy14082         93 ------------------------------------------FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRER  130 (233)
Q Consensus        93 ------------------------------------------~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~  130 (233)
                                                                ....+.+.+......++||||++++.++.++..|.+.+
T Consensus       211 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvf~~~~~~~~~l~~~L~~~~  290 (412)
T 3fht_A          211 EDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEG  290 (412)
T ss_dssp             CHHHHHHHHHHSSSCEEECCCGGGSSCTTEEEEEEECSSHHHHHHHHHHHHHHHSSSEEEEECSSHHHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHhcCCCeEEeeccccccccCceEEEEEcCChHHHHHHHHHHHhhcCCCCEEEEeCCHHHHHHHHHHHHhCC
Confidence                                                      00011113334466899999999999999999999999


Q ss_pred             CeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCc------cccc------------c
Q psy14082        131 HSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSA------NHNI------------S  192 (233)
Q Consensus       131 ~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~------~~~i------------~  192 (233)
                      +.+..+||+|++++|..+++.|++|+.+|||||+++++|+|+|++++||+||+|.+.      ..|+            |
T Consensus       291 ~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g  370 (412)
T 3fht_A          291 HQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRG  370 (412)
T ss_dssp             CCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECGGGTSSCCCTTEEEEEESSCCBCSSSSBCHHHHHHHHTTSSCTTCCE
T ss_pred             CeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcCccccCCCccCCCEEEEECCCCCCCCCcchheeecccCcccCCCCCc
Confidence            999999999999999999999999999999999999999999999999999999643      3444            3


Q ss_pred             eeeEEeecchHHHHHHHHHHhhcCccccccc
Q psy14082        193 QVIEVVQDYEKEKRLFSLIRELGKYTLITQE  223 (233)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~  223 (233)
                      .++.++++ +++...++.+++..+..++..+
T Consensus       371 ~~~~~~~~-~~~~~~~~~i~~~~~~~~~~~~  400 (412)
T 3fht_A          371 LAVNMVDS-KHSMNILNRIQEHFNKKIERLD  400 (412)
T ss_dssp             EEEEEECS-HHHHHHHHHHHHHHTCCCEEC-
T ss_pred             eEEEEEcC-hhhHHHHHHHHHHHCCccccCC
Confidence            55667765 3446777777776655554433

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=100.00  E-value=1.7e-34  Score=259.26  Aligned_cols=215  Identities=21%  Similarity=0.285  Sum_probs=172.8

Q ss_pred             CCCCC--CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh------cCCcE
Q psy14082          2 LPPSE--SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS------SALRN   73 (233)
Q Consensus         2 ip~~~--~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~------~~~~~   73 (233)
                      ||.++  .|+|+++.||||||||++|++|+++++...... ...++++|||+||++|+.|+++.++++.      ....+
T Consensus       103 i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~-~~~~~~~lil~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~  181 (563)
T 3i5x_A          103 IKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFD-SQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYAC  181 (563)
T ss_dssp             HHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTS-STTSCCEEEECSSHHHHHHHHHHHHHHHHHCGGGTTSCE
T ss_pred             HHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhcccc-ccCCeeEEEEcCcHHHHHHHHHHHHHHHhhccccCceeE
Confidence            45566  689999999999999999999999999865321 2346789999999999999999999972      24568


Q ss_pred             EEEEcCCCC----------CCeeEEe--------c--------cc-----------------------------------
Q psy14082         74 ICIFGGTPK----------GPQDCLP--------L--------HR-----------------------------------   92 (233)
Q Consensus        74 ~~~~gg~~~----------~~~~lv~--------l--------~r-----------------------------------   92 (233)
                      ..++||.+.          ..+++|+        +        ++                                   
T Consensus       182 ~~~~g~~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~l~~~~f~~~~~~i~~~l~~~~~~~  261 (563)
T 3i5x_A          182 VSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKS  261 (563)
T ss_dssp             EEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTCCEEEEETHHHHTSTTTHHHHHHHHHHHHHHCSSC
T ss_pred             EEEECCcCHHHHHHHHhcCCCCEEEECcHHHHHHHHhccccccccceEEEEeCHHHHhccchHHHHHHHHHhhhhccccC
Confidence            888888753          4567777        0        00                                   


Q ss_pred             ---------------------------------------------------------------hhhhchH-HHhcCCCCe
Q psy14082         93 ---------------------------------------------------------------FVFNCQY-EMAKNPAFK  108 (233)
Q Consensus        93 ---------------------------------------------------------------~~~~~~~-~~~~~~~~k  108 (233)
                                                                                     .+..+.+ ......+.+
T Consensus       262 ~~~~~~l~~SAT~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  341 (563)
T 3i5x_A          262 ADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYK  341 (563)
T ss_dssp             TTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEESSTTHHHHHHHHHHHHHHHHTTTCCE
T ss_pred             ccCceEEEEEccCCHHHHHHHHHhcCCCceEEEeccCCCCccccccCceEEEECchhHhhHHHHHHHHHHHHhhcCCCCc
Confidence                                                                           0000000 112256789


Q ss_pred             EEEEecchhHHHHHHHHHhhC---CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCC
Q psy14082        109 VIVFVETKKKVEDITRALRRE---RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQL  185 (233)
Q Consensus       109 ~iIf~~~~~~~~~l~~~L~~~---~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~  185 (233)
                      +||||++++.++.++..|.+.   ++.+..+||+|++.+|..+++.|++|+.+|||||+++++|+|+|++++||+||+|.
T Consensus       342 ~iVF~~s~~~~~~l~~~L~~~~~~~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLvaT~~~~~GiDip~v~~VI~~~~p~  421 (563)
T 3i5x_A          342 AIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPS  421 (563)
T ss_dssp             EEEECSCHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGGGTSSCCCTTCCEEEEESCCS
T ss_pred             EEEEcCcHHHHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcCCCCEEEEcchhhcCCCcccCCEEEEECCCC
Confidence            999999999999999999876   89999999999999999999999999999999999999999999999999999999


Q ss_pred             Cccccc------------ceeeEEeecchHHHHHHHHHHhhcCccc
Q psy14082        186 SANHNI------------SQVIEVVQDYEKEKRLFSLIRELGKYTL  219 (233)
Q Consensus       186 ~~~~~i------------~~~~~~~~~~~~~~~~~~~i~~~~~~~~  219 (233)
                      +...|+            |.++.++.+.+  ...++.+++..+..+
T Consensus       422 s~~~y~Qr~GRagR~g~~g~~i~~~~~~e--~~~~~~l~~~~~~~~  465 (563)
T 3i5x_A          422 ELANYIHRIGRTARSGKEGSSVLFICKDE--LPFVRELEDAKNIVI  465 (563)
T ss_dssp             STTHHHHHHTTSSCTTCCEEEEEEEEGGG--HHHHHHHHHHHCCCC
T ss_pred             chhhhhhhcCccccCCCCceEEEEEchhH--HHHHHHHHHHhCCCc
Confidence            998776            46677888654  777777877654433

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=100.00  E-value=1.3e-34  Score=249.97  Aligned_cols=213  Identities=26%  Similarity=0.357  Sum_probs=167.5

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEcC
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGG   79 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~gg   79 (233)
                      ||.++.|+|+++.+|||||||++|++|+++.+...     ..+.++||++||++|+.|+++.++.+  ..+..+...+||
T Consensus        71 i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~-----~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~  145 (414)
T 3eiq_A           71 ILPCIKGYDVIAQAQSGTGKTATFAISILQQIELD-----LKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGG  145 (414)
T ss_dssp             HHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCTT-----SCSCCEEEECSSHHHHHHHHHHHHHHGGGSCCCEEECCCC
T ss_pred             hHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhhc-----CCceeEEEEeChHHHHHHHHHHHHHHhcccCceEEEEECC
Confidence            56678899999999999999999999999988653     35778999999999999999999998  346788888887


Q ss_pred             CCC----------CCeeEEe--------c-------cc------------------------------------------
Q psy14082         80 TPK----------GPQDCLP--------L-------HR------------------------------------------   92 (233)
Q Consensus        80 ~~~----------~~~~lv~--------l-------~r------------------------------------------   92 (233)
                      .+.          ..+++|+        +       .+                                          
T Consensus       146 ~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~  225 (414)
T 3eiq_A          146 TNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMP  225 (414)
T ss_dssp             TTHHHHHHHHTTTCCSEEEECHHHHHHHHHHTSSCSTTCCEEEECSHHHHHHTTTHHHHHHHHTTSCTTCEEEEECSCCC
T ss_pred             cchHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccCcEEEEECHHHhhccCcHHHHHHHHHhCCCCCeEEEEEEecC
Confidence            653          4466666        0       00                                          


Q ss_pred             -----------------------------------------hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCC
Q psy14082         93 -----------------------------------------FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERH  131 (233)
Q Consensus        93 -----------------------------------------~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~  131 (233)
                                                               ....+.+.+......++||||++++.++.+++.|.+.++
T Consensus       226 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvf~~~~~~~~~l~~~l~~~~~  305 (414)
T 3eiq_A          226 SDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDF  305 (414)
T ss_dssp             HHHHHHHTTTCSSCEEECCCCCCCCTTSCCEEEEECSSSTTHHHHHHHHHHSSCCSSCEEECSCHHHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHcCCCEEEEecCCccCCCCceEEEEEeChHHhHHHHHHHHHHhCCCCcEEEEeCCHHHHHHHHHHHHhcCC
Confidence                                                     111111244555678999999999999999999999999


Q ss_pred             eeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc------------ceeeEEee
Q psy14082        132 SAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI------------SQVIEVVQ  199 (233)
Q Consensus       132 ~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i------------~~~~~~~~  199 (233)
                      .+..+||+|++++|..+++.|++|+.+|||||+++++|+|+|++++||+||+|.+...|+            |.++.+++
T Consensus       306 ~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~  385 (414)
T 3eiq_A          306 TVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVT  385 (414)
T ss_dssp             CCEEC---CHHHHHHHHHHHHSCC---CEEECSSCC--CCGGGCSCEEESSCCSSTHHHHHHSCCC-------CEEEEEC
T ss_pred             eEEEecCCCCHHHHHHHHHHHHcCCCcEEEECCccccCCCccCCCEEEEeCCCCCHHHhhhhcCcccCCCCCceEEEEEc
Confidence            999999999999999999999999999999999999999999999999999999987665            35666777


Q ss_pred             cchHHHHHHHHHHhhcCccccc
Q psy14082        200 DYEKEKRLFSLIRELGKYTLIT  221 (233)
Q Consensus       200 ~~~~~~~~~~~i~~~~~~~~~~  221 (233)
                      +.+  ...++.++++.+..++.
T Consensus       386 ~~~--~~~~~~~~~~~~~~~~~  405 (414)
T 3eiq_A          386 EED--KRTLRDIETFYNTSIEE  405 (414)
T ss_dssp             STH--HHHHHHHHHHTTCCCEE
T ss_pred             HHH--HHHHHHHHHHHcCCccc
Confidence            654  67778888876655443

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=100.00  E-value=2e-34  Score=259.94  Aligned_cols=215  Identities=21%  Similarity=0.312  Sum_probs=173.6

Q ss_pred             CCCCC--CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh------cCCcE
Q psy14082          2 LPPSE--SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS------SALRN   73 (233)
Q Consensus         2 ip~~~--~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~------~~~~~   73 (233)
                      ||.++  .|+|++++||||||||++|++|+++.+..... ....++++|||+||++|+.|+++.++++.      ..+.+
T Consensus        52 i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~-~~~~~~~~lvl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~  130 (579)
T 3sqw_A           52 IKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKF-DSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYAC  130 (579)
T ss_dssp             HHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTT-SSTTSCCEEEECSSHHHHHHHHHHHHHHHHHCGGGTTSCE
T ss_pred             HHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhccc-cccCCCeEEEEcchHHHHHHHHHHHHHHHhhcccccceEE
Confidence            45566  68999999999999999999999999986532 12346799999999999999999999973      34678


Q ss_pred             EEEEcCCCC----------CCeeEEe--------ccc-------------------------------------------
Q psy14082         74 ICIFGGTPK----------GPQDCLP--------LHR-------------------------------------------   92 (233)
Q Consensus        74 ~~~~gg~~~----------~~~~lv~--------l~r-------------------------------------------   92 (233)
                      ..++||.+.          ..+++|+        +.+                                           
T Consensus       131 ~~~~gg~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~l~~~gf~~~~~~i~~~l~~~~~~~  210 (579)
T 3sqw_A          131 VSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKS  210 (579)
T ss_dssp             EEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTCCEEEEETHHHHTSTTTHHHHHHHHHHHHHHCSSC
T ss_pred             EEEECCccHHHHHHHHhcCCCCEEEECHHHHHHHHHhccccccccCCEEEEEChHHhhcCCCHHHHHHHHHHhhhhhccc
Confidence            888888653          4567777        000                                           


Q ss_pred             ---------------------------------------------------------------hhhhchHHH-hcCCCCe
Q psy14082         93 ---------------------------------------------------------------FVFNCQYEM-AKNPAFK  108 (233)
Q Consensus        93 ---------------------------------------------------------------~~~~~~~~~-~~~~~~k  108 (233)
                                                                                     .+..+.+.+ ....+.+
T Consensus       211 ~~~~~~l~~SAT~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  290 (579)
T 3sqw_A          211 ADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYK  290 (579)
T ss_dssp             TTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEESSTTHHHHHHHHHHHHHHHHTTTCCE
T ss_pred             ccCceEEEEeccCChHHHHHHHHHcCCCceEEEeecCccccccccccceEEEEecchhhhHHHHHHHHHHHHhhcCCCCc
Confidence                                                                           000000011 2256789


Q ss_pred             EEEEecchhHHHHHHHHHhhC---CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCC
Q psy14082        109 VIVFVETKKKVEDITRALRRE---RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQL  185 (233)
Q Consensus       109 ~iIf~~~~~~~~~l~~~L~~~---~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~  185 (233)
                      +||||++++.++.++..|.+.   ++.+..+||+|++.+|..++++|++|+.+|||||+++++|+|+|++++||+||+|.
T Consensus       291 ~iVF~~t~~~~~~l~~~L~~~~~~~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVaT~~~~~GiDip~v~~VI~~~~p~  370 (579)
T 3sqw_A          291 AIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPS  370 (579)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGGGTSSCCCTTCCEEEEESCCS
T ss_pred             EEEECCcHHHHHHHHHHHHHhhcCCCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEEcchhhcCCCcccCCEEEEcCCCC
Confidence            999999999999999999876   89999999999999999999999999999999999999999999999999999999


Q ss_pred             Cccccc------------ceeeEEeecchHHHHHHHHHHhhcCccc
Q psy14082        186 SANHNI------------SQVIEVVQDYEKEKRLFSLIRELGKYTL  219 (233)
Q Consensus       186 ~~~~~i------------~~~~~~~~~~~~~~~~~~~i~~~~~~~~  219 (233)
                      +...|+            |.++.++.+.+  ...++.+++.....+
T Consensus       371 s~~~y~Qr~GRagR~g~~g~~i~~~~~~e--~~~~~~l~~~~~~~~  414 (579)
T 3sqw_A          371 ELANYIHRIGRTARSGKEGSSVLFICKDE--LPFVRELEDAKNIVI  414 (579)
T ss_dssp             STTHHHHHHTTSSCTTCCEEEEEEEEGGG--HHHHHHHHHHHCCCC
T ss_pred             CHHHhhhhccccccCCCCceEEEEEcccH--HHHHHHHHHHhCCCc
Confidence            998776            46777888654  777888877654443

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=100.00  E-value=9e-34  Score=242.86  Aligned_cols=209  Identities=25%  Similarity=0.325  Sum_probs=168.9

Q ss_pred             CCCCCCC--CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEE
Q psy14082          2 LPPSESG--CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIF   77 (233)
Q Consensus         2 ip~~~~g--~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~   77 (233)
                      +|.++.|  +++++++|||||||++|++|+++++...     ..++++||++||++|+.|+++.++++  ..++.+....
T Consensus        36 i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~-----~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~  110 (395)
T 3pey_A           36 LPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPE-----DASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIV  110 (395)
T ss_dssp             HHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTT-----CCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEES
T ss_pred             HHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccC-----CCCccEEEECCCHHHHHHHHHHHHHHhcccCeeEEEEe
Confidence            4455666  9999999999999999999999988654     45778999999999999999999998  4567777777


Q ss_pred             cCCCC-----CCeeEEe--------c-------cc---------------------------------------------
Q psy14082         78 GGTPK-----GPQDCLP--------L-------HR---------------------------------------------   92 (233)
Q Consensus        78 gg~~~-----~~~~lv~--------l-------~r---------------------------------------------   92 (233)
                      |+...     +.+++|+        +       .+                                             
T Consensus       111 ~~~~~~~~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~  190 (395)
T 3pey_A          111 PDSFEKNKQINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSATFADA  190 (395)
T ss_dssp             TTSSCTTSCBCCSEEEECHHHHHHHHHTTCBCCTTCCEEEEETHHHHHHSTTHHHHHHHHHHTSCTTCEEEEEESCCCHH
T ss_pred             cCchhhhccCCCCEEEEcHHHHHHHHHcCCcccccCCEEEEEChhhhcCccccHHHHHHHHHhCCCCcEEEEEEecCCHH
Confidence            77543     3456666        0       00                                             


Q ss_pred             ---------------------------------------hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCCee
Q psy14082         93 ---------------------------------------FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSA  133 (233)
Q Consensus        93 ---------------------------------------~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~  133 (233)
                                                             ....+.+.+......++||||++++.++.+++.|++.++.+
T Consensus       191 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvf~~~~~~~~~l~~~l~~~~~~~  270 (395)
T 3pey_A          191 VRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEV  270 (395)
T ss_dssp             HHHHHHHHSCSCEEECCCGGGCSCTTEEEEEEECSSHHHHHHHHHHHHTTTTSSEEEEECSCHHHHHHHHHHHHHTTCCC
T ss_pred             HHHHHHHhCCCCeEEEccccccccccccEEEEEcCchHHHHHHHHHHHHhccCCCEEEEeCCHHHHHHHHHHHHhcCCcE
Confidence                                                   01111113445567899999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCC------Cccccc------------ceee
Q psy14082        134 ICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQL------SANHNI------------SQVI  195 (233)
Q Consensus       134 ~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~------~~~~~i------------~~~~  195 (233)
                      ..+||+|+.++|.+++++|++|+.+|||||+++++|+|+|++++||+||+|.      +...|+            |.++
T Consensus       271 ~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~  350 (395)
T 3pey_A          271 SILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAI  350 (395)
T ss_dssp             EEECTTSCHHHHHHHHHHHHTTSCCEEEECGGGSSSCCCTTEEEEEESSCCBCTTSSBCHHHHHHHHTTSSCTTCCEEEE
T ss_pred             EEeCCCCCHHHHHHHHHHHHCCCCCEEEECChhhcCCCcccCCEEEEcCCCCCCcCCCCHHHhhHhccccccCCCCceEE
Confidence            9999999999999999999999999999999999999999999999999998      666444            3455


Q ss_pred             EEeecchHHHHHHHHHHhhcC
Q psy14082        196 EVVQDYEKEKRLFSLIRELGK  216 (233)
Q Consensus       196 ~~~~~~~~~~~~~~~i~~~~~  216 (233)
                      .++.+ ++....++.+++..+
T Consensus       351 ~~~~~-~~~~~~~~~i~~~~~  370 (395)
T 3pey_A          351 SFVHD-KNSFNILSAIQKYFG  370 (395)
T ss_dssp             EEECS-HHHHHHHHHHHHHTT
T ss_pred             EEEec-hHHHHHHHHHHHHhC
Confidence            56665 455677777777654

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=100.00  E-value=8.7e-34  Score=244.14  Aligned_cols=212  Identities=22%  Similarity=0.295  Sum_probs=172.6

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh--cCCcEEEEEcC
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS--SALRNICIFGG   79 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~--~~~~~~~~~gg   79 (233)
                      +|.++.|+|+++.+|||||||++|++|++..+...     ..+.++||++||++|+.|+++.++.+.  .++++....|+
T Consensus        52 i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~-----~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~  126 (400)
T 1s2m_A           52 IPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPK-----LNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGG  126 (400)
T ss_dssp             HHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTT-----SCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECSS
T ss_pred             HHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhhc-----cCCccEEEEcCCHHHHHHHHHHHHHHhcccCceEEEEeCC
Confidence            45567899999999999999999999999988643     356789999999999999999999994  36788888888


Q ss_pred             CCC---------CCeeEEe---------------ccc-------------------------------------------
Q psy14082         80 TPK---------GPQDCLP---------------LHR-------------------------------------------   92 (233)
Q Consensus        80 ~~~---------~~~~lv~---------------l~r-------------------------------------------   92 (233)
                      .+.         +.+++|+               +.+                                           
T Consensus       127 ~~~~~~~~~~~~~~~Ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~~~~~~~~~~i~~~~~~~~~~i~lSAT~~~  206 (400)
T 1s2m_A          127 TNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSLLFSATFPL  206 (400)
T ss_dssp             SCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEESHHHHSSHHHHHHHHHHHTTSCSSCEEEEEESCCCH
T ss_pred             cchHHHHHHhcCCCCEEEEchHHHHHHHHhCCcccccCCEEEEeCchHhhhhchHHHHHHHHHhCCcCceEEEEEecCCH
Confidence            652         3456666               000                                           


Q ss_pred             --------------------------------------hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeE
Q psy14082         93 --------------------------------------FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAI  134 (233)
Q Consensus        93 --------------------------------------~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~  134 (233)
                                                            ....+...+......++||||++++.++.+++.|.+.++.+.
T Consensus       207 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~  286 (400)
T 1s2m_A          207 TVKEFMVKHLHKPYEINLMEELTLKGITQYYAFVEERQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCY  286 (400)
T ss_dssp             HHHHHHHHHCSSCEEESCCSSCBCTTEEEEEEECCGGGHHHHHHHHHHHSCCSEEEEECSSHHHHHHHHHHHHHHTCCEE
T ss_pred             HHHHHHHHHcCCCeEEEeccccccCCceeEEEEechhhHHHHHHHHHhhcCCCcEEEEEecHHHHHHHHHHHHhcCCCeE
Confidence                                                  001111134455678999999999999999999999999999


Q ss_pred             EEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc------------ceeeEEeecch
Q psy14082        135 CIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI------------SQVIEVVQDYE  202 (233)
Q Consensus       135 ~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i------------~~~~~~~~~~~  202 (233)
                      .+||+|+..+|..+++.|++|+.+|||||+++++|+|+|++++||+||+|.+...|+            |.++.++++.+
T Consensus       287 ~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~~~~~Gidip~~~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~l~~~~~  366 (400)
T 1s2m_A          287 YSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWND  366 (400)
T ss_dssp             EECTTSCHHHHHHHHHHHHTTSSSEEEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGGG
T ss_pred             EecCCCCHHHHHHHHHHHhcCCCcEEEEcCccccCCCccCCCEEEEeCCCCCHHHHHHhcchhcCCCCCceEEEEeccch
Confidence            999999999999999999999999999999999999999999999999999987555            46677887654


Q ss_pred             HHHHHHHHHHhhcCcccc
Q psy14082        203 KEKRLFSLIRELGKYTLI  220 (233)
Q Consensus       203 ~~~~~~~~i~~~~~~~~~  220 (233)
                        ...++.+++..+.++.
T Consensus       367 --~~~~~~i~~~~~~~~~  382 (400)
T 1s2m_A          367 --RFNLYKIEQELGTEIA  382 (400)
T ss_dssp             --HHHHHHHHHHHTCCCE
T ss_pred             --HHHHHHHHHHhCCCcc
Confidence              5566667765555443

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens}

Probab=100.00  E-value=6.9e-35  Score=257.21  Aligned_cols=181  Identities=24%  Similarity=0.321  Sum_probs=69.4

Q ss_pred             CCCCCCCC--CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh---hcCCcEEE
Q psy14082          1 MLPPSESG--CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF---SSALRNIC   75 (233)
Q Consensus         1 aip~~~~g--~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~---~~~~~~~~   75 (233)
                      |||.++.|  +|++++|+||||||++|++|+++++...     ..++++|||+||++|+.|+++.++++   ..++.+..
T Consensus       122 ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l~~~-----~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~  196 (479)
T 3fmp_B          122 ALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPA-----NKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAY  196 (479)
T ss_dssp             HHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTCCTT-----SCSCCEEEECSSHHHHHHHHHHHHHHHTTSTTCCEEE
T ss_pred             HHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHHhhc-----CCCCcEEEEeChHHHHHHHHHHHHHHHhhCCCceEEE
Confidence            35666776  9999999999999999999999988654     35678999999999999999999998   34678888


Q ss_pred             EEcCCCC------CCeeEEe--------c--------cc----hhhh---------------------------------
Q psy14082         76 IFGGTPK------GPQDCLP--------L--------HR----FVFN---------------------------------   96 (233)
Q Consensus        76 ~~gg~~~------~~~~lv~--------l--------~r----~~~~---------------------------------   96 (233)
                      ..|+...      ..+++|+        +        .+    ++|.                                 
T Consensus       197 ~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT  276 (479)
T 3fmp_B          197 AVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSAT  276 (479)
T ss_dssp             ESTTCCCCTTCCCCCSEEEECHHHHHHHHTTSCCCCGGGCCEEEECCHHHHHTSTTHHHHHHHHHTTSCTTSEEEEEESC
T ss_pred             EeCCccccccccCCCCEEEECchHHHHHHHhcCCcCcccCCEEEEECHHHHhhcCCcHHHHHHHHhhCCccceEEEEeCC
Confidence            8887654      2356777        0        00    0000                                 


Q ss_pred             -------------------------------------c----------hHHHhcCCCCeEEEEecchhHHHHHHHHHhhC
Q psy14082         97 -------------------------------------C----------QYEMAKNPAFKVIVFVETKKKVEDITRALRRE  129 (233)
Q Consensus        97 -------------------------------------~----------~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~  129 (233)
                                                           +          ...+......++||||++++.++.++..|.+.
T Consensus       277 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvF~~s~~~~~~l~~~L~~~  356 (479)
T 3fmp_B          277 FEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKE  356 (479)
T ss_dssp             CCHHHHHHHHHHSSSEEEEEEC----------------------------------------------------------
T ss_pred             CCHHHHHHHHHHcCCCeEEeccccccCcCCceEEEEEeCCHHHHHHHHHHHHhhccCCceEEEeCcHHHHHHHHHHHHhC
Confidence                                                 0          00222335578999999999999999999999


Q ss_pred             CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCC
Q psy14082        130 RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLS  186 (233)
Q Consensus       130 ~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~  186 (233)
                      ++.+..+||+|++.+|..+++.|++|+.+|||||+++++|+|+|++++||+||+|.+
T Consensus       357 ~~~v~~lh~~~~~~~R~~~~~~f~~g~~~iLv~T~~~~~GlDip~v~~VI~~d~p~~  413 (479)
T 3fmp_B          357 GHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVD  413 (479)
T ss_dssp             ---------------------------------------------------------
T ss_pred             CccEEEecCCCCHHHHHHHHHHHHcCCCcEEEEccccccCCccccCCEEEEecCCCC
Confidence            999999999999999999999999999999999999999999999999999999953

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=100.00  E-value=8.9e-33  Score=234.49  Aligned_cols=210  Identities=26%  Similarity=0.363  Sum_probs=171.3

Q ss_pred             CCCCCCC-CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh--cCCcEEEEEc
Q psy14082          2 LPPSESG-CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS--SALRNICIFG   78 (233)
Q Consensus         2 ip~~~~g-~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~--~~~~~~~~~g   78 (233)
                      +|.++.| +++++.+|||||||++|++|+++.+..      .++.++||++||++|+.|+++.+.++.  .++++..+.|
T Consensus        37 i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~------~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~v~~~~~  110 (367)
T 1hv8_A           37 IPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNE------NNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYG  110 (367)
T ss_dssp             HHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCS------SSSCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEECT
T ss_pred             HHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhcc------cCCCcEEEEcCCHHHHHHHHHHHHHHhCCCCceEEEEEC
Confidence            3455666 799999999999999999999988754      347789999999999999999999983  4678888888


Q ss_pred             CCCC--------CCeeEEe---------------ccc-------------------------------------------
Q psy14082         79 GTPK--------GPQDCLP---------------LHR-------------------------------------------   92 (233)
Q Consensus        79 g~~~--------~~~~lv~---------------l~r-------------------------------------------   92 (233)
                      +.+.        +.+++|+               +.+                                           
T Consensus       111 ~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~  190 (367)
T 1hv8_A          111 GKAIYPQIKALKNANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRILLFSATMPR  190 (367)
T ss_dssp             TSCHHHHHHHHHTCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHTTTTHHHHHHHHHTSCSSCEEEEECSSCCH
T ss_pred             CcchHHHHhhcCCCCEEEecHHHHHHHHHcCCcccccCCEEEEeCchHhhhhchHHHHHHHHHhCCCCceEEEEeeccCH
Confidence            8653        3455555               000                                           


Q ss_pred             -----------------------------------hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEe
Q psy14082         93 -----------------------------------FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIH  137 (233)
Q Consensus        93 -----------------------------------~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~  137 (233)
                                                         ....+. .+....+.++||||++++.++.+++.|.+.++.+..+|
T Consensus       191 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-~~l~~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~  269 (367)
T 1hv8_A          191 EILNLAKKYMGDYSFIKAKINANIEQSYVEVNENERFEALC-RLLKNKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIH  269 (367)
T ss_dssp             HHHHHHHHHCCSEEEEECCSSSSSEEEEEECCGGGHHHHHH-HHHCSTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEEC
T ss_pred             HHHHHHHHHcCCCeEEEecCCCCceEEEEEeChHHHHHHHH-HHHhcCCCcEEEEECCHHHHHHHHHHHHhcCCCeEEee
Confidence                                               000000 12345778999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc------------ceeeEEeecchHHH
Q psy14082        138 GDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI------------SQVIEVVQDYEKEK  205 (233)
Q Consensus       138 ~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i------------~~~~~~~~~~~~~~  205 (233)
                      |+++.++|.++++.|++|+.++||||+++++|+|+|++++||+||+|.|...|+            |.++.++++.+  .
T Consensus       270 ~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~--~  347 (367)
T 1hv8_A          270 GDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRRE--Y  347 (367)
T ss_dssp             SSSCHHHHHHHHHHHHTTSSSEEEECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTTS--H
T ss_pred             CCCCHHHHHHHHHHHHcCCCeEEEECChhhcCCCcccCCEEEEecCCCCHHHhhhcccccccCCCccEEEEEEcHHH--H
Confidence            999999999999999999999999999999999999999999999999987555            45667777654  6


Q ss_pred             HHHHHHHhhcCcccc
Q psy14082        206 RLFSLIRELGKYTLI  220 (233)
Q Consensus       206 ~~~~~i~~~~~~~~~  220 (233)
                      ..++.+++..+.+++
T Consensus       348 ~~~~~i~~~~~~~~~  362 (367)
T 1hv8_A          348 KKLRYIERAMKLKIK  362 (367)
T ss_dssp             HHHHHHHHHHTCCCC
T ss_pred             HHHHHHHHHhCCCCc
Confidence            777888887666554

>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=99.98  E-value=4.1e-34  Score=245.30  Aligned_cols=186  Identities=28%  Similarity=0.411  Sum_probs=69.5

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEcC
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGG   79 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~gg   79 (233)
                      +|.++.|+|+++.+|||+|||++|++|+++.+...     ..++++||++||++|+.|+++.+.++  ..++++..++|+
T Consensus        52 i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~-----~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~  126 (394)
T 1fuu_A           52 IMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTS-----VKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGG  126 (394)
T ss_dssp             HHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTT-----CCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECSS
T ss_pred             HHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhcc-----CCCCCEEEEcCCHHHHHHHHHHHHHHhccCCeeEEEEeCC
Confidence            45667899999999999999999999999988653     35778999999999999999999998  346788889988


Q ss_pred             CCC--------CCeeEEe--------cc-------c--------------------------------------------
Q psy14082         80 TPK--------GPQDCLP--------LH-------R--------------------------------------------   92 (233)
Q Consensus        80 ~~~--------~~~~lv~--------l~-------r--------------------------------------------   92 (233)
                      .+.        +.+++|+        +.       +                                            
T Consensus       127 ~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~vIiDEah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~  206 (394)
T 1fuu_A          127 TSFVEDAEGLRDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPND  206 (394)
T ss_dssp             CCHHHHHHHHHHCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHTTCHHHHHHHHHHSCTTCEEEEECSSCCHH
T ss_pred             CchHHHHhhcCCCCEEEECHHHHHHHHHhCCcchhhCcEEEEEChHHhhCCCcHHHHHHHHHhCCCCceEEEEEEecCHH
Confidence            663        3445665        00       0                                            


Q ss_pred             ------------------------------h---------hhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCCee
Q psy14082         93 ------------------------------F---------VFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSA  133 (233)
Q Consensus        93 ------------------------------~---------~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~  133 (233)
                                                    +         ...+.+.+......++||||++++.++.+++.|++.++.+
T Consensus       207 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~  286 (394)
T 1fuu_A          207 VLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTV  286 (394)
T ss_dssp             HHHHHHHHCCSCEEEEECC-------------------------------------------------------------
T ss_pred             HHHHHHHhcCCCeEEEecCccccCCCceEEEEEcCchhhHHHHHHHHHhcCCCCcEEEEECCHHHHHHHHHHHHHcCCeE
Confidence                                          0         0000012233356799999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCcccccc
Q psy14082        134 ICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNIS  192 (233)
Q Consensus       134 ~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i~  192 (233)
                      ..+||+|+.++|..+++.|++|+.++||||+++++|+|+|++++||+||+|.+...|++
T Consensus       287 ~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gldi~~~~~Vi~~~~p~s~~~~~Q  345 (394)
T 1fuu_A          287 SAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIH  345 (394)
T ss_dssp             -----------------------------------------------------------
T ss_pred             EEeeCCCCHHHHHHHHHHHHCCCCcEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999886663

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A*

Probab=99.97  E-value=2.9e-31  Score=239.24  Aligned_cols=178  Identities=19%  Similarity=0.208  Sum_probs=149.4

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCC
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGT   80 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~   80 (233)
                      |||.++.|+|+++.+|||+|||++|++|++.           .+.++||++|+++|+.|+.+.+..+  ++++..+.|+.
T Consensus        52 ~i~~il~g~d~lv~~pTGsGKTl~~~lpal~-----------~~g~~lVisP~~~L~~q~~~~l~~~--gi~~~~l~~~~  118 (591)
T 2v1x_A           52 TINVTMAGKEVFLVMPTGGGKSLCYQLPALC-----------SDGFTLVICPLISLMEDQLMVLKQL--GISATMLNASS  118 (591)
T ss_dssp             HHHHHHTTCCEEEECCTTSCTTHHHHHHHHT-----------SSSEEEEECSCHHHHHHHHHHHHHH--TCCEEECCSSC
T ss_pred             HHHHHHcCCCEEEEECCCChHHHHHHHHHHH-----------cCCcEEEEeCHHHHHHHHHHHHHhc--CCcEEEEeCCC
Confidence            3566788999999999999999999999985           1348999999999999999999998  77888888875


Q ss_pred             CC---------------CCeeEEe----c----------c------c---------------------------------
Q psy14082         81 PK---------------GPQDCLP----L----------H------R---------------------------------   92 (233)
Q Consensus        81 ~~---------------~~~~lv~----l----------~------r---------------------------------   92 (233)
                      +.               ..+++++    +          .      +                                 
T Consensus       119 ~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L~~~~~~~~~l~~~~~~~~i~~iViDEAH~is~~g~dfr~~~~~l~~l~~~~  198 (591)
T 2v1x_A          119 SKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEKAYEARRFTRIAVDEVHCCSQWGHDFRPDYKALGILKRQF  198 (591)
T ss_dssp             CHHHHHHHHHHHHCTTCCCCEEEECHHHHHSCHHHHHHHHHHHHTTCEEEEEEETGGGGSTTCTTCCGGGGGGGHHHHHC
T ss_pred             CHHHHHHHHHHhhcccCCCCEEEEChhHhhccHHHHHHHHhhhhccCCcEEEEECcccccccccccHHHHHHHHHHHHhC
Confidence            32               3444444    0          0      0                                 


Q ss_pred             ------------------------------------------------------hhhhchHHHh-cCCCCeEEEEecchh
Q psy14082         93 ------------------------------------------------------FVFNCQYEMA-KNPAFKVIVFVETKK  117 (233)
Q Consensus        93 ------------------------------------------------------~~~~~~~~~~-~~~~~k~iIf~~~~~  117 (233)
                                                                            .+..+.+.+. ...+.++||||++++
T Consensus       199 ~~~~ii~lSAT~~~~v~~~i~~~l~~~~~~~~~~~~~r~nl~~~v~~~~~~~~~~~~~l~~~l~~~~~~~~~IVf~~sr~  278 (591)
T 2v1x_A          199 PNASLIGLTATATNHVLTDAQKILCIEKCFTFTASFNRPNLYYEVRQKPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQK  278 (591)
T ss_dssp             TTSEEEEEESSCCHHHHHHHHHHTTCCSCEEEECCCCCTTEEEEEEECCSSHHHHHHHHHHHHTTTTTTCEEEEECSSHH
T ss_pred             CCCcEEEEecCCCHHHHHHHHHHhCCCCcEEEecCCCCcccEEEEEeCCCcHHHHHHHHHHHHHHhccCCCeEEEeCcHH
Confidence                                                                  0000111222 236789999999999


Q ss_pred             HHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc
Q psy14082        118 KVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI  191 (233)
Q Consensus       118 ~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i  191 (233)
                      .++.++..|.+.|+.+..+||+|++++|..++++|++|+.+|||||+++++|+|+|++++||+||+|.|.+.|+
T Consensus       279 ~~e~la~~L~~~g~~~~~~h~~l~~~~R~~~~~~F~~g~~~VlVAT~a~~~GID~p~V~~VI~~~~p~s~~~y~  352 (591)
T 2v1x_A          279 DSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYY  352 (591)
T ss_dssp             HHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEECTTSCTTCCCSCEEEEEESSCCSSHHHHH
T ss_pred             HHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhcCCCcccccEEEEeCCCCCHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999998777

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.97  E-value=1.4e-31  Score=238.92  Aligned_cols=99  Identities=25%  Similarity=0.354  Sum_probs=65.6

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCC------------CeeEEEeCCCCHHHHHHHHHHhhC-CCCCEEEecccCcCCc
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRER------------HSAICIHGDKTQQDRDYVLNDFRQ-GKAPILVATDVAARGL  170 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~------------~~~~~~~~~~~~~~r~~~~~~f~~-g~~~iLv~T~~~~~Gl  170 (233)
                      ....++||||+++++++.++..|.+.+            .....+||+|++++|.+++++|++ |+.+|||||+++++|+
T Consensus       387 ~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~~~~Gl  466 (555)
T 3tbk_A          387 KPETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFRASGDNNILIATSVADEGI  466 (555)
T ss_dssp             CTTCCEEEECSSHHHHHHHHHHHHHCGGGTTCCEEECCC--------------------------CCSEEEECCCTTCCE
T ss_pred             CCCceEEEEeCcHHHHHHHHHHHhhCcCcCceeeeEEEecCCcccccccCHHHHHHHHHHHhcCCCeeEEEEcchhhcCC
Confidence            355899999999999999999998764            344555679999999999999999 9999999999999999


Q ss_pred             CCCCccEEEEecCCCCccccc----------ceeeEEeecch
Q psy14082        171 DVEDVNTVNIGSLQLSANHNI----------SQVIEVVQDYE  202 (233)
Q Consensus       171 di~~v~~VI~~d~P~~~~~~i----------~~~~~~~~~~~  202 (233)
                      |+|++++||+||+|+|+..|+          |.++.++++.+
T Consensus       467 Dlp~v~~VI~~d~p~s~~~~~Qr~GRgR~~~g~~~~l~~~~~  508 (555)
T 3tbk_A          467 DIAECNLVILYEYVGNVIKMIQTRGRGRARDSKCFLLTSSAD  508 (555)
T ss_dssp             ETTSCSEEEEESCCSSCCCEECSSCCCTTTSCEEEEEESCHH
T ss_pred             ccccCCEEEEeCCCCCHHHHHHhcCcCcCCCceEEEEEcCCC
Confidence            999999999999999998777          35666777654

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*

Probab=99.97  E-value=7.8e-32  Score=240.81  Aligned_cols=89  Identities=21%  Similarity=0.327  Sum_probs=46.9

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhC------------CCeeEEEeCCCCHHHHHHHHHHhhC-CCCCEEEecccCcCCc
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRE------------RHSAICIHGDKTQQDRDYVLNDFRQ-GKAPILVATDVAARGL  170 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~------------~~~~~~~~~~~~~~~r~~~~~~f~~-g~~~iLv~T~~~~~Gl  170 (233)
                      ..+.++||||+++++++.+++.|.+.            |.....+||+|++++|.+++++|++ |+.+|||||+++++|+
T Consensus       388 ~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~~~~Gi  467 (556)
T 4a2p_A          388 NPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGI  467 (556)
T ss_dssp             CTTCCEEEEESSHHHHHHHHHHHTTCSGGGSCCEEC------------------------------CCEEEEEC------
T ss_pred             CCCceEEEEEccHHHHHHHHHHHHhCCCcceeeeeEEEccCCcccccccCHHHHHHHHHHhcccCceEEEEEcCchhcCC
Confidence            46789999999999999999999876            5556667888999999999999999 9999999999999999


Q ss_pred             CCCCccEEEEecCCCCcccccc
Q psy14082        171 DVEDVNTVNIGSLQLSANHNIS  192 (233)
Q Consensus       171 di~~v~~VI~~d~P~~~~~~i~  192 (233)
                      |+|++++||+||+|+|+..|++
T Consensus       468 Dip~v~~VI~~d~p~s~~~~~Q  489 (556)
T 4a2p_A          468 DIVQCNLVVLYEYSGNVTKMIQ  489 (556)
T ss_dssp             -----CEEEEETCCSCHHHHHH
T ss_pred             CchhCCEEEEeCCCCCHHHHHH
Confidence            9999999999999999987763

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A*

Probab=99.97  E-value=5.9e-31  Score=234.49  Aligned_cols=177  Identities=16%  Similarity=0.153  Sum_probs=148.1

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCC
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTP   81 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~   81 (233)
                      |+.++.|+|+++.+|||+|||++|++|++..           ...+||++|+++|+.|+.+.++.+  ++.+..+.|+.+
T Consensus        34 i~~il~g~d~lv~apTGsGKTl~~~lp~l~~-----------~g~~lvi~P~~aL~~q~~~~l~~~--gi~~~~l~~~~~  100 (523)
T 1oyw_A           34 IDTVLSGRDCLVVMPTGGGKSLCYQIPALLL-----------NGLTVVVSPLISLMKDQVDQLQAN--GVAAACLNSTQT  100 (523)
T ss_dssp             HHHHHTTCCEEEECSCHHHHHHHHHHHHHHS-----------SSEEEEECSCHHHHHHHHHHHHHT--TCCEEEECTTSC
T ss_pred             HHHHHcCCCEEEECCCCcHHHHHHHHHHHHh-----------CCCEEEECChHHHHHHHHHHHHHc--CCcEEEEeCCCC
Confidence            5667889999999999999999999999842           246999999999999999999987  677777777654


Q ss_pred             C-------------CCeeEEe-------------------------------------------ccc-------------
Q psy14082         82 K-------------GPQDCLP-------------------------------------------LHR-------------   92 (233)
Q Consensus        82 ~-------------~~~~lv~-------------------------------------------l~r-------------   92 (233)
                      .             ..+++++                                           +.+             
T Consensus       101 ~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~~~~~~l~~~~~~~vViDEaH~i~~~g~~fr~~~~~l~~l~~~~~~~~~i~l  180 (523)
T 1oyw_A          101 REQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTLPFMAL  180 (523)
T ss_dssp             HHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGGGGCTTSSCCCHHHHGGGGHHHHCTTSCEEEE
T ss_pred             HHHHHHHHHHHhcCCCCEEEECHHHHhChHHHHHHhhCCCCEEEEeCccccCcCCCccHHHHHHHHHHHHhCCCCCEEEE
Confidence            2             1333333                                           000             


Q ss_pred             ------------------------------------------hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCC
Q psy14082         93 ------------------------------------------FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRER  130 (233)
Q Consensus        93 ------------------------------------------~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~  130 (233)
                                                                ....+.+.+....+.++||||++++.++.+++.|.+.|
T Consensus       181 SAT~~~~~~~~i~~~l~~~~~~~~~~~~~r~~l~~~v~~~~~~~~~l~~~l~~~~~~~~IVf~~sr~~~e~l~~~L~~~g  260 (523)
T 1oyw_A          181 TATADDTTRQDIVRLLGLNDPLIQISSFDRPNIRYMLMEKFKPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKG  260 (523)
T ss_dssp             ESCCCHHHHHHHHHHHTCCSCEEEECCCCCTTEEEEEEECSSHHHHHHHHHHHTTTCCEEEECSSHHHHHHHHHHHHHTT
T ss_pred             eCCCCHHHHHHHHHHhCCCCCeEEeCCCCCCceEEEEEeCCCHHHHHHHHHHhcCCCcEEEEeCCHHHHHHHHHHHHHCC
Confidence                                                      00111113445577899999999999999999999999


Q ss_pred             CeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc
Q psy14082        131 HSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI  191 (233)
Q Consensus       131 ~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i  191 (233)
                      +.+..+||+|++++|..++++|++|+.+|||||+++++|+|+|++++||+||+|.|.+.|+
T Consensus       261 ~~~~~~h~~l~~~~R~~~~~~f~~g~~~vlVaT~a~~~GiD~p~v~~VI~~~~p~s~~~y~  321 (523)
T 1oyw_A          261 ISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYY  321 (523)
T ss_dssp             CCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSCTTTCCTTCCEEEESSCCSSHHHHH
T ss_pred             CCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhCCCCccCccEEEEECCCCCHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999998666

>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=99.97  E-value=7.6e-31  Score=220.32  Aligned_cols=175  Identities=28%  Similarity=0.403  Sum_probs=145.4

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEcC
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGG   79 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~gg   79 (233)
                      +|.++.|+++++.+|||+|||++|++|+++.           +.++||++|+++|+.|+++.++++  ..++++..++|+
T Consensus        25 i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~-----------~~~~liv~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~   93 (337)
T 2z0m_A           25 IPLMLQGKNVVVRAKTGSGKTAAYAIPILEL-----------GMKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGG   93 (337)
T ss_dssp             HHHHHTTCCEEEECCTTSSHHHHHHHHHHHH-----------TCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECTT
T ss_pred             HHHHhcCCCEEEEcCCCCcHHHHHHHHHHhh-----------cCCEEEEeCCHHHHHHHHHHHHHHhhhcCCcEEEEECC
Confidence            4556789999999999999999999998863           457999999999999999999998  346788888888


Q ss_pred             CCC--------CCeeEEe---------------ccc--------------------------------------------
Q psy14082         80 TPK--------GPQDCLP---------------LHR--------------------------------------------   92 (233)
Q Consensus        80 ~~~--------~~~~lv~---------------l~r--------------------------------------------   92 (233)
                      .+.        +.+++|+               +.+                                            
T Consensus        94 ~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~~~~~~~~~~~~~~~SAT~~~~  173 (337)
T 2z0m_A           94 MPYKAQINRVRNADIVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITGLFSATIPEE  173 (337)
T ss_dssp             SCHHHHHHHHTTCSEEEECHHHHHHHHHTTSCCGGGCSEEEEESHHHHHHTTCHHHHHHHHHHCTTCSEEEEEESCCCHH
T ss_pred             cchHHHHhhcCCCCEEEECHHHHHHHHHcCCcchhhCcEEEEEChHHhhccccHHHHHHHHhhCCcccEEEEEeCcCCHH
Confidence            653        3456666               000                                            


Q ss_pred             ---------------------------hhh------hchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCC
Q psy14082         93 ---------------------------FVF------NCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGD  139 (233)
Q Consensus        93 ---------------------------~~~------~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~  139 (233)
                                                 ++.      ...+.+....+.++||||++++.++.+++.|.    ++..+||+
T Consensus       174 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lvf~~~~~~~~~l~~~l~----~~~~~~~~  249 (337)
T 2z0m_A          174 IRKVVKDFITNYEEIEACIGLANVEHKFVHVKDDWRSKVQALRENKDKGVIVFVRTRNRVAKLVRLFD----NAIELRGD  249 (337)
T ss_dssp             HHHHHHHHSCSCEEEECSGGGGGEEEEEEECSSSSHHHHHHHHTCCCSSEEEECSCHHHHHHHHTTCT----TEEEECTT
T ss_pred             HHHHHHHhcCCceeeecccccCCceEEEEEeChHHHHHHHHHHhCCCCcEEEEEcCHHHHHHHHHHhh----hhhhhcCC
Confidence                                       000      00013455678899999999999999988875    57899999


Q ss_pred             CCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc
Q psy14082        140 KTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI  191 (233)
Q Consensus       140 ~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i  191 (233)
                      |+..+|.+++++|++|+.++||||+++++|+|+|++++||+||+|.|...|+
T Consensus       250 ~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi~~~~~~s~~~~~  301 (337)
T 2z0m_A          250 LPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVINFDAPQDLRTYI  301 (337)
T ss_dssp             SCHHHHHHHHHHHHTTSCSEEEECHHHHTTCCCCCBSEEEESSCCSSHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCcEEEEcCccccCCCccCCCEEEEecCCCCHHHhh
Confidence            9999999999999999999999999999999999999999999999997555

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.97  E-value=7.4e-31  Score=227.32  Aligned_cols=176  Identities=14%  Similarity=0.144  Sum_probs=146.3

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhc-CCcEEEEEcC
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSS-ALRNICIFGG   79 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~-~~~~~~~~gg   79 (233)
                      |||.++.|+|+++++|||||||++|++|++..+        .+++++||++||++|+.|+++.++++.. ++++..++||
T Consensus        29 ~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~--------~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~v~~~~g~  100 (414)
T 3oiy_A           29 WAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLA--------RKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSS  100 (414)
T ss_dssp             HHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHH--------TTTCCEEEEESSHHHHHHHHHHHHHHCCSSCCEEECCTT
T ss_pred             HHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHh--------cCCCEEEEEECCHHHHHHHHHHHHHHccCCceEEEEECC
Confidence            457788999999999999999999999988766        3477999999999999999999999854 7899999999


Q ss_pred             CCC-------------CCeeEEe------------------------c----------cchhh--------------hch
Q psy14082         80 TPK-------------GPQDCLP------------------------L----------HRFVF--------------NCQ   98 (233)
Q Consensus        80 ~~~-------------~~~~lv~------------------------l----------~r~~~--------------~~~   98 (233)
                      .+.             +.+++|+                        .          .|+++              .+.
T Consensus       101 ~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~iViDEaH~~~~~~~~~d~~l~~~~~~~~~~~~i~~~~~  180 (414)
T 3oiy_A          101 MKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGIPEEIIRKAFSTIK  180 (414)
T ss_dssp             SCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHHHTTCCCSEEEESCHHHHHHCHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             CChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHHhccccccEEEEeChHhhhhccchhhhHHhhcCCcHHHHHHHHHhcc
Confidence            865             2677777                        1          01110              000


Q ss_pred             -----------H------------------------------------------------------HHhcCCCCeEEEEe
Q psy14082         99 -----------Y------------------------------------------------------EMAKNPAFKVIVFV  113 (233)
Q Consensus        99 -----------~------------------------------------------------------~~~~~~~~k~iIf~  113 (233)
                                 .                                                      .+.. .+.++||||
T Consensus       181 ~~~~~~~l~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~l~~~l~~-~~~~~lVF~  259 (414)
T 3oiy_A          181 QGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLNFTVGRLVSVARNITHVRISSRSKEKLVELLEI-FRDGILIFA  259 (414)
T ss_dssp             HTCCCCCCTTCCCCEEEESSCCSSCCSSTTHHHHHHHSCCSSCCCCCCCSEEEEEESSCCHHHHHHHHHH-HCSSEEEEE
T ss_pred             cchhhhhcccCCCceEEEEecCCCcchhHHHHHHHhhccCcCccccccccchheeeccCHHHHHHHHHHH-cCCCEEEEE
Confidence                       1                                                      1222 458999999


Q ss_pred             cchhHHHHHHHHHhhCCCeeE-EEeCCCCHHHHHHHHHHhhCCCCCEEEe----cccCcCCcCCCC-ccEEEEecCC--C
Q psy14082        114 ETKKKVEDITRALRRERHSAI-CIHGDKTQQDRDYVLNDFRQGKAPILVA----TDVAARGLDVED-VNTVNIGSLQ--L  185 (233)
Q Consensus       114 ~~~~~~~~l~~~L~~~~~~~~-~~~~~~~~~~r~~~~~~f~~g~~~iLv~----T~~~~~Gldi~~-v~~VI~~d~P--~  185 (233)
                      ++++.++.++..|.+.|+.+. .+||+    +|.  +++|++|+.+||||    |+++++|+|+|+ +++||+||+|  .
T Consensus       260 ~~~~~~~~l~~~L~~~~~~~~~~~h~~----~r~--~~~f~~g~~~vLvat~s~T~~~~~GiDip~~v~~VI~~~~p~~~  333 (414)
T 3oiy_A          260 QTEEEGKELYEYLKRFKFNVGETWSEF----EKN--FEDFKVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPSGP  333 (414)
T ss_dssp             SSHHHHHHHHHHHHHTTCCEEESSSCH----HHH--HHHHHTTSCSEEEEECCTTCCCCCCCCCTTTCCEEEEESCCTTT
T ss_pred             CCHHHHHHHHHHHHHcCCceehhhcCc----chH--HHHHhCCCCeEEEEecCcCchhhccCccccccCEEEEECCCCCC
Confidence            999999999999999999998 88985    333  99999999999999    999999999999 9999999999  8


Q ss_pred             Cccccc
Q psy14082        186 SANHNI  191 (233)
Q Consensus       186 ~~~~~i  191 (233)
                      +...|+
T Consensus       334 ~~~~y~  339 (414)
T 3oiy_A          334 DVYTYI  339 (414)
T ss_dssp             CHHHHH
T ss_pred             CHHHHH
Confidence            887665

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.97  E-value=1.2e-30  Score=239.56  Aligned_cols=88  Identities=24%  Similarity=0.338  Sum_probs=57.7

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCC----CeeEEE--------eCCCCHHHHHHHHHHhhC-CCCCEEEecccCcCCcC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRER----HSAICI--------HGDKTQQDRDYVLNDFRQ-GKAPILVATDVAARGLD  171 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~----~~~~~~--------~~~~~~~~r~~~~~~f~~-g~~~iLv~T~~~~~Gld  171 (233)
                      .+.++||||++++.++.+++.|.+.+    +++..+        ||+|++++|.+++++|++ |+.+|||||+++++|+|
T Consensus       397 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F~~~g~~~vLVaT~v~~~GiD  476 (696)
T 2ykg_A          397 PETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGID  476 (696)
T ss_dssp             TTCCEEEECSCHHHHHHHHHHHHHCTTCCSCCEEC-----------------------------CCSCSEEEESSCCC--
T ss_pred             CCCcEEEEeCcHHHHHHHHHHHHhCCCccccceeEEEccCCCccccCCCHHHHHHHHHHHHhcCCccEEEEechhhcCCc
Confidence            56799999999999999999999987    888888        559999999999999998 99999999999999999


Q ss_pred             CCCccEEEEecCCCCcccccc
Q psy14082        172 VEDVNTVNIGSLQLSANHNIS  192 (233)
Q Consensus       172 i~~v~~VI~~d~P~~~~~~i~  192 (233)
                      +|++++||+||+|.|...|++
T Consensus       477 ip~v~~VI~~d~p~s~~~~~Q  497 (696)
T 2ykg_A          477 IAQCNLVILYEYVGNVIKMIQ  497 (696)
T ss_dssp             -CCCSEEEEESCC--CCCC--
T ss_pred             CccCCEEEEeCCCCCHHHHHH
Confidence            999999999999999987774

>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=99.96  E-value=4.3e-30  Score=239.26  Aligned_cols=99  Identities=22%  Similarity=0.322  Sum_probs=57.0

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhC------------CCeeEEEeCCCCHHHHHHHHHHhhC-CCCCEEEecccCcCCc
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRE------------RHSAICIHGDKTQQDRDYVLNDFRQ-GKAPILVATDVAARGL  170 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~------------~~~~~~~~~~~~~~~r~~~~~~f~~-g~~~iLv~T~~~~~Gl  170 (233)
                      ..+.++||||+++++++.++..|.+.            |.....+||+|++++|..++++|++ |+.+|||||+++++|+
T Consensus       629 ~~~~kvLIF~~~~~~~~~L~~~L~~~~~~~~~~~~~l~G~~~~~~hg~~~~~eR~~~l~~F~~~g~~~vLVaT~~~~~GI  708 (797)
T 4a2q_A          629 NPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGI  708 (797)
T ss_dssp             CSSCCEEEEESSHHHHHHHHHHHHTCSTTCSCCCEEC----------------------------CCSEEEEECC-----
T ss_pred             CCCCeEEEEECcHHHHHHHHHHHHhCcccccccceEEEecCCcccCCCCCHHHHHHHHHHhhccCCceEEEEcCchhcCC
Confidence            45689999999999999999999874            5566777999999999999999999 9999999999999999


Q ss_pred             CCCCccEEEEecCCCCcccccc----------eeeEEeecch
Q psy14082        171 DVEDVNTVNIGSLQLSANHNIS----------QVIEVVQDYE  202 (233)
Q Consensus       171 di~~v~~VI~~d~P~~~~~~i~----------~~~~~~~~~~  202 (233)
                      |+|++++||+||+|+|+..|++          .++.++++.+
T Consensus       709 Dlp~v~~VI~yd~p~s~~~~iQr~GRGR~~~g~~i~l~~~~~  750 (797)
T 4a2q_A          709 DIVQCNLVVLYEYSGNVTKMIQVRGRGRAAGSKCILVTSKTE  750 (797)
T ss_dssp             --CCCSEEEEESCCSCHHHHHTC-------CCCEEEEECCHH
T ss_pred             CchhCCEEEEeCCCCCHHHHHHhcCCCCCCCceEEEEEeCCc
Confidence            9999999999999999987663          4555666544

>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.70A {Anas platyrhynchos}

Probab=99.96  E-value=1.2e-29  Score=239.29  Aligned_cols=89  Identities=21%  Similarity=0.327  Sum_probs=52.8

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhC------------CCeeEEEeCCCCHHHHHHHHHHhhC-CCCCEEEecccCcCCc
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRE------------RHSAICIHGDKTQQDRDYVLNDFRQ-GKAPILVATDVAARGL  170 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~------------~~~~~~~~~~~~~~~r~~~~~~f~~-g~~~iLv~T~~~~~Gl  170 (233)
                      ..+.++||||+++++++.++..|.+.            |.....+||+|++.+|.+++++|++ |+.+|||||+++++|+
T Consensus       629 ~~~~rvLIF~~t~~~ae~L~~~L~~~~~l~~ik~~~l~G~~~~~~hg~m~~~eR~~il~~Fr~~g~~~VLVaT~~~~eGI  708 (936)
T 4a2w_A          629 NPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGI  708 (936)
T ss_dssp             CTTCCEEEEESSHHHHHHHHHHHHHCSTTSSCCCEEC----------------------------CCSEEEEECC-----
T ss_pred             CCCCeEEEEeCCHHHHHHHHHHHhhCccccccceeEEecCCCcccCCCCCHHHHHHHHHHhhccCCeeEEEEeCchhcCC
Confidence            45689999999999999999999886            5566677899999999999999999 9999999999999999


Q ss_pred             CCCCccEEEEecCCCCcccccc
Q psy14082        171 DVEDVNTVNIGSLQLSANHNIS  192 (233)
Q Consensus       171 di~~v~~VI~~d~P~~~~~~i~  192 (233)
                      |+|++++||+||+|+|+..|++
T Consensus       709 Dlp~v~~VI~yD~p~s~~~~iQ  730 (936)
T 4a2w_A          709 DIVQCNLVVLYEYSGNVTKMIQ  730 (936)
T ss_dssp             -CCCCSEEEEESCCSCSHHHHC
T ss_pred             cchhCCEEEEeCCCCCHHHHHH
Confidence            9999999999999999986663

>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=99.96  E-value=2.4e-30  Score=237.72  Aligned_cols=86  Identities=27%  Similarity=0.392  Sum_probs=77.5

Q ss_pred             CCeEEEEecchhHHHHHHHHHhhC------CCeeEEEeCC--------CCHHHHHHHHHHhhCCCCCEEEecccCcCCcC
Q psy14082        106 AFKVIVFVETKKKVEDITRALRRE------RHSAICIHGD--------KTQQDRDYVLNDFRQGKAPILVATDVAARGLD  171 (233)
Q Consensus       106 ~~k~iIf~~~~~~~~~l~~~L~~~------~~~~~~~~~~--------~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gld  171 (233)
                      +.++||||++++.++.+++.|.+.      |+++..+||+        |++.+|.+++++|++|+.+|||||+++++|+|
T Consensus       400 ~~~~IVF~~s~~~~~~l~~~L~~~~~l~~~g~~~~~lhg~~~~~~~~~~~~~eR~~~~~~F~~g~~~VLVaT~~~~~GID  479 (699)
T 4gl2_A          400 SARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGKINLLIATTVAEEGLD  479 (699)
T ss_dssp             CCCEEEECSCHHHHHHHHHHHHSSCSCC-----CEECCCSCCCTTCCCCCHHHHHHHHHHHCC---CCSEEECSCCTTSC
T ss_pred             CCcEEEEECcHHHHHHHHHHHHhCccccccCcceEEEECCCCccCCCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCc
Confidence            789999999999999999999987      8999999999        99999999999999999999999999999999


Q ss_pred             CCCccEEEEecCCCCccccc
Q psy14082        172 VEDVNTVNIGSLQLSANHNI  191 (233)
Q Consensus       172 i~~v~~VI~~d~P~~~~~~i  191 (233)
                      +|++++||+||+|+|+..|+
T Consensus       480 ip~v~~VI~~d~p~s~~~~~  499 (699)
T 4gl2_A          480 IKECNIVIRYGLVTNEIAMV  499 (699)
T ss_dssp             CCSCCCCEEESCCCCHHHHH
T ss_pred             cccCCEEEEeCCCCCHHHHH
Confidence            99999999999999998666

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.95  E-value=1.5e-28  Score=234.34  Aligned_cols=170  Identities=14%  Similarity=0.129  Sum_probs=143.1

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh-hcCCcEEEEEcC
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF-SSALRNICIFGG   79 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~-~~~~~~~~~~gg   79 (233)
                      |||.++.|+|++++||||||||++|++|++..+        ..++++|||+||+|||.|+++.++++ ..++++..++||
T Consensus        86 ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~--------~~~~~~Lil~PtreLa~Q~~~~l~~l~~~~i~v~~l~Gg  157 (1104)
T 4ddu_A           86 WAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLA--------RKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSS  157 (1104)
T ss_dssp             HHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHH--------TTTCCEEEEESSHHHHHHHHHHHHTTSCTTSCEEEECTT
T ss_pred             HHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHH--------hcCCeEEEEechHHHHHHHHHHHHHhhCCCCeEEEEeCC
Confidence            467889999999999999999999888888776        34789999999999999999999997 357899999999


Q ss_pred             CCC-------------CCeeEEe------------------------c----------cchhh--------------hch
Q psy14082         80 TPK-------------GPQDCLP------------------------L----------HRFVF--------------NCQ   98 (233)
Q Consensus        80 ~~~-------------~~~~lv~------------------------l----------~r~~~--------------~~~   98 (233)
                      .+.             +.+++|+                        .          .|+++              .+.
T Consensus       158 ~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~l~~~~l~~lViDEaH~l~~~~r~~Dr~L~~~gf~~~~i~~il~~l~  237 (1104)
T 4ddu_A          158 MKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGIPEEIIRKAFSTIK  237 (1104)
T ss_dssp             CCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHHHHTSCCSEEEESCHHHHTTSSHHHHHHHHTSSCCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHhhcccCcCEEEEeCCCccccccccchhhhHhcCCCHHHHHHHHHhcc
Confidence            876             3677887                        1          11111              001


Q ss_pred             -----------H------------------------------------------------------HHhcCCCCeEEEEe
Q psy14082         99 -----------Y------------------------------------------------------EMAKNPAFKVIVFV  113 (233)
Q Consensus        99 -----------~------------------------------------------------------~~~~~~~~k~iIf~  113 (233)
                                 .                                                      .+.. .+.++||||
T Consensus       238 ~~~~~~~~~~~~~~q~ll~SAT~~p~~~~~~~~~~~l~i~v~~~~~~~~~i~~~~~~~~k~~~L~~ll~~-~~~~~LVF~  316 (1104)
T 4ddu_A          238 QGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLNFTVGRLVSVARNITHVRISSRSKEKLVELLEI-FRDGILIFA  316 (1104)
T ss_dssp             HTSCCCCCSSCCCCEEEEECBSSCCCSSTTHHHHHHTCCCCCBCCCCCCCEEEEEESCCCHHHHHHHHHH-HCSSEEEEE
T ss_pred             cchhhhhhccCCCceEEEEcCCCCcHHHHHHHhhcceeEEeccCCCCcCCceeEEEecCHHHHHHHHHHh-cCCCEEEEE
Confidence                       1                                                      1222 358999999


Q ss_pred             cchhHHHHHHHHHhhCCCeeE-EEeCCCCHHHHHHHHHHhhCCCCCEEEe----cccCcCCcCCCC-ccEEEEecCCC
Q psy14082        114 ETKKKVEDITRALRRERHSAI-CIHGDKTQQDRDYVLNDFRQGKAPILVA----TDVAARGLDVED-VNTVNIGSLQL  185 (233)
Q Consensus       114 ~~~~~~~~l~~~L~~~~~~~~-~~~~~~~~~~r~~~~~~f~~g~~~iLv~----T~~~~~Gldi~~-v~~VI~~d~P~  185 (233)
                      ++++.++.++..|.+.|+.+. .+||.     |.+ +++|++|+.+||||    |++++||+|+|+ |++|||||+|.
T Consensus       317 ~s~~~a~~l~~~L~~~g~~~~~~lhg~-----rr~-l~~F~~G~~~VLVatas~TdvlarGIDip~~V~~VI~~d~P~  388 (1104)
T 4ddu_A          317 QTEEEGKELYEYLKRFKFNVGETWSEF-----EKN-FEDFKVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPS  388 (1104)
T ss_dssp             SSSHHHHHHHHHHHHTTCCEEESSSSH-----HHH-HHHHHHTSCSEEEEETTTHHHHCCSCCCTTTCCEEEEESCCE
T ss_pred             CcHHHHHHHHHHHHhCCCCeeeEecCc-----HHH-HHHHHCCCCCEEEEecCCCCeeEecCcCCCCCCEEEEECCCC
Confidence            999999999999999999998 99993     555 99999999999999    999999999999 99999999998

>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=99.95  E-value=3.7e-29  Score=219.26  Aligned_cols=174  Identities=13%  Similarity=0.051  Sum_probs=132.9

Q ss_pred             CCCCCCCCCce-eEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcC
Q psy14082          1 MLPPSESGCQN-FSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGG   79 (233)
Q Consensus         1 aip~~~~g~d~-i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg   79 (233)
                      +||.+++|+|+ ++++|||||||++|++|+++.+..       .++++||++|||||+.|+++.+..+    .+..-.+.
T Consensus        11 ~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~-------~~~~~lvl~Ptr~La~Q~~~~l~g~----~v~~~~~~   79 (451)
T 2jlq_A           11 VDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALL-------RRLRTLILAPTRVVAAEMEEALRGL----PIRYQTPA   79 (451)
T ss_dssp             CCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHH-------TTCCEEEEESSHHHHHHHHHHTTTS----CEEECCTT
T ss_pred             HHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHh-------cCCcEEEECCCHHHHHHHHHHhcCc----eeeeeecc
Confidence            47899999998 999999999999999999988764       3678999999999999999998644    11111111


Q ss_pred             CC----CCCee------------------------EEe-ccc--------------------------------------
Q psy14082         80 TP----KGPQD------------------------CLP-LHR--------------------------------------   92 (233)
Q Consensus        80 ~~----~~~~~------------------------lv~-l~r--------------------------------------   92 (233)
                      ..    ....+                        ++- .++                                      
T Consensus        80 ~~~~~~~~~~i~~~t~~~l~~~l~~~~~l~~~~~iViDEah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~  159 (451)
T 2jlq_A           80 VKSDHTGREIVDLMCHATFTTRLLSSTRVPNYNLIVMDEAHFTDPCSVAARGYISTRVEMGEAAAIFMTATPPGSTDPFP  159 (451)
T ss_dssp             CSCCCCSSCCEEEEEHHHHHHHHHHCSCCCCCSEEEEETTTCCSHHHHHHHHHHHHHHHTTSCEEEEECSSCTTCCCSSC
T ss_pred             ccccCCCCceEEEEChHHHHHHhhCcccccCCCEEEEeCCccCCcchHHHHHHHHHhhcCCCceEEEEccCCCccchhhh
Confidence            00    00111                        111 000                                      


Q ss_pred             -----hh-----------hhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCC
Q psy14082         93 -----FV-----------FNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGK  156 (233)
Q Consensus        93 -----~~-----------~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~  156 (233)
                           ++           ....+.+. ...+++||||++++.++.+++.|.+.++.+..+||++.    .++++.|++|+
T Consensus       160 ~~~~~~~~~~~~~p~~~~~~~~~~l~-~~~~~~lVF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~----~~~~~~f~~g~  234 (451)
T 2jlq_A          160 QSNSPIEDIEREIPERSWNTGFDWIT-DYQGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRKTF----DTEYPKTKLTD  234 (451)
T ss_dssp             CCSSCEEEEECCCCSSCCSSSCHHHH-HCCSCEEEECSSHHHHHHHHHHHHTTTCCEEEECTTTH----HHHGGGGGSSC
T ss_pred             cCCCceEecCccCCchhhHHHHHHHH-hCCCCEEEEcCCHHHHHHHHHHHHHcCCeEEECCHHHH----HHHHHhhccCC
Confidence                 00           00001222 23569999999999999999999999999999999754    57899999999


Q ss_pred             CCEEEecccCcCCcCCCCccEEEEec--------------------CCCCccccc
Q psy14082        157 APILVATDVAARGLDVEDVNTVNIGS--------------------LQLSANHNI  191 (233)
Q Consensus       157 ~~iLv~T~~~~~Gldi~~v~~VI~~d--------------------~P~~~~~~i  191 (233)
                      .+|||||+++++|+|+|+ ++|||||                    +|.+...|+
T Consensus       235 ~~vLVaT~v~~~GiDip~-~~VI~~~~~~~~~~d~~~~~~l~~~~~~p~s~~~y~  288 (451)
T 2jlq_A          235 WDFVVTTDISEMGANFRA-GRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAA  288 (451)
T ss_dssp             CSEEEECGGGGSSCCCCC-SEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHH
T ss_pred             ceEEEECCHHHhCcCCCC-CEEEECCCcccccccccccceeeecccccCCHHHHH
Confidence            999999999999999999 9999999                    999988666

>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=99.95  E-value=3.2e-28  Score=232.18  Aligned_cols=178  Identities=13%  Similarity=0.060  Sum_probs=142.8

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCC
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGT   80 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~   80 (233)
                      |||.+..|+|++++|+||||||++|.+|+++.+.        .+.++||++||++|+.|+++.+.+++.  .+..++|+.
T Consensus       192 AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~--------~g~rvlvl~PtraLa~Q~~~~l~~~~~--~VglltGd~  261 (1108)
T 3l9o_A          192 AISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLK--------NKQRVIYTSPIKALSNQKYRELLAEFG--DVGLMTGDI  261 (1108)
T ss_dssp             HHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHH--------TTCEEEEEESSHHHHHHHHHHHHHHTS--SEEEECSSC
T ss_pred             HHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHh--------cCCeEEEEcCcHHHHHHHHHHHHHHhC--CccEEeCcc
Confidence            4567789999999999999999999999999884        367899999999999999999999855  678889987


Q ss_pred             CCC--CeeEEe--------------------------ccc-----------------------------------hhhh-
Q psy14082         81 PKG--PQDCLP--------------------------LHR-----------------------------------FVFN-   96 (233)
Q Consensus        81 ~~~--~~~lv~--------------------------l~r-----------------------------------~~~~-   96 (233)
                      +.+  .+++|+                          .++                                   +..+ 
T Consensus       262 ~~~~~~~IlV~Tpe~L~~~L~~~~~~l~~l~lVVIDEaH~l~d~~rg~~~e~ii~~l~~~~qvl~lSATipn~~e~a~~l  341 (1108)
T 3l9o_A          262 TINPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWI  341 (1108)
T ss_dssp             BCCCSCSEEEEEHHHHHHHHHHCSSHHHHEEEEEEETGGGTTSHHHHHHHHHHHHHSCTTSEEEEEECSCSSCHHHHHHH
T ss_pred             ccCCCCCEEEeChHHHHHHHHcCccccccCCEEEEhhhhhccccchHHHHHHHHHhcCCCceEEEEcCCCCCHHHHHHHH
Confidence            654  456666                          000                                   0000 


Q ss_pred             --------------------------------------------------------------------------------
Q psy14082         97 --------------------------------------------------------------------------------   96 (233)
Q Consensus        97 --------------------------------------------------------------------------------   96 (233)
                                                                                                      
T Consensus       342 ~~~~~~~~~vi~~~~rp~pl~~~~~~~~~~~~~~~vd~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  421 (1108)
T 3l9o_A          342 CKIHSQPCHIVYTNFRPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASISNQIGDDPNSTDSRGKKGQTYKGGSA  421 (1108)
T ss_dssp             HHHTCSCEEEEEECCCSSCEEEEEEETTSSCCEEEEETTTEECHHHHHHHHTTC--------------------------
T ss_pred             HhhcCCCeEEEecCCCcccceEEEeecCCcceeeeeccccchhhhhHHHHHHHHHhhhcccccccccccccccccccccc
Confidence                                                                                            


Q ss_pred             ----------chHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCCe----------------------------------
Q psy14082         97 ----------CQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHS----------------------------------  132 (233)
Q Consensus        97 ----------~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~----------------------------------  132 (233)
                                +-..+......++||||++++.++.++..|...++.                                  
T Consensus       422 ~~~~~~~l~~li~~l~~~~~~~vIVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~  501 (1108)
T 3l9o_A          422 KGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILP  501 (1108)
T ss_dssp             ---CHHHHHHHHHHHHHTTCCCEEEEESCHHHHHHHHHHTCSHHHHCC----CHHHHGGGSCTHHHHHTTCCHHHHHHTH
T ss_pred             cccchhHHHHHHHHHHhcCCCCEEEEeCcHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHhhcchhhhhhhhHHHHHH
Confidence                      000112234569999999999999999998654332                                  


Q ss_pred             -----eEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCcc
Q psy14082        133 -----AICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSAN  188 (233)
Q Consensus       133 -----~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~  188 (233)
                           +..+||+|++.+|..+++.|++|..+|||||+++++|+|+|++++||+++.|.+..
T Consensus       502 ~l~~gV~~~Hg~l~~~~R~~v~~~F~~G~ikVLVAT~vla~GIDiP~v~~VI~~~~~~d~~  562 (1108)
T 3l9o_A          502 LLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQ  562 (1108)
T ss_dssp             HHHHTEEEECSCSCHHHHHHHHHHHHHTCCCEEEEESCCCSCCCC--CEEEESCSEEESSS
T ss_pred             hhhcCeeeecCCCCHHHHHHHHHHHhCCCCeEEEECcHHhcCCCCCCceEEEecCcccCcc
Confidence                 68899999999999999999999999999999999999999999999988866544

>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=99.95  E-value=3.2e-28  Score=231.72  Aligned_cols=169  Identities=14%  Similarity=0.146  Sum_probs=135.8

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhc--CC----cEE
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSS--AL----RNI   74 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~--~~----~~~   74 (233)
                      |||.++.|+|++++||||||||+ |++|++..+..       +++++|||+||++|+.|+++.++.+..  ++    ++.
T Consensus        64 ai~~il~g~dvlv~apTGSGKTl-~~lp~l~~~~~-------~~~~~lil~PtreLa~Q~~~~l~~l~~~~~i~~~~~v~  135 (1054)
T 1gku_B           64 WAKRILRKESFAATAPTGVGKTS-FGLAMSLFLAL-------KGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIG  135 (1054)
T ss_dssp             HHHHHHTTCCEECCCCBTSCSHH-HHHHHHHHHHT-------TSCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEE
T ss_pred             HHHHHHhCCCEEEEcCCCCCHHH-HHHHHHHHHhh-------cCCeEEEEeccHHHHHHHHHHHHHHHhhcCCCccceEE
Confidence            46778899999999999999998 99999998864       367999999999999999999999943  56    789


Q ss_pred             EEEcCCCCC-----------CeeEEe--------cc---c-----------hhh--------------------------
Q psy14082         75 CIFGGTPKG-----------PQDCLP--------LH---R-----------FVF--------------------------   95 (233)
Q Consensus        75 ~~~gg~~~~-----------~~~lv~--------l~---r-----------~~~--------------------------   95 (233)
                      .++||.+..           .+++|+        +.   +           +.+                          
T Consensus       136 ~~~Gg~~~~~~~~~~~~l~~~~IlV~TP~~L~~~l~~L~~l~~lViDEah~~l~~~~~~~~i~~~lgf~~~~~~~~~~~~  215 (1054)
T 1gku_B          136 YYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHYRELGHFDFIFVDDVDAILKASKNVDKLLHLLGFHYDLKTKSWVGE  215 (1054)
T ss_dssp             ECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHHCSTTSCCCSEEEESCHHHHHTSTHHHHHHHHHTTEEEETTTTEEEEC
T ss_pred             EEeCCCChhhHHHHHhhccCCCEEEEcHHHHHHHHHHhccCCEEEEeChhhhhhccccHHHHHHHhCcchhhhhhhcccC
Confidence            999987653           356676        00   0           000                          


Q ss_pred             --------------------------------------------------hchHHHhcCCCCeEEEEecchhHHHHHHHH
Q psy14082         96 --------------------------------------------------NCQYEMAKNPAFKVIVFVETKKKVEDITRA  125 (233)
Q Consensus        96 --------------------------------------------------~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~  125 (233)
                                                                        .+. .+....+.++||||++++.++.++..
T Consensus       216 ~q~~l~SAT~t~~~~~~~~~~~~~~~i~v~~~~~~~~~i~~~~~~~~k~~~L~-~ll~~~~~~~LVF~~t~~~a~~l~~~  294 (1054)
T 1gku_B          216 ARGCLMVSTATAKKGKKAELFRQLLNFDIGSSRITVRNVEDVAVNDESISTLS-SILEKLGTGGIIYARTGEEAEEIYES  294 (1054)
T ss_dssp             CSSEEEECCCCSCCCTTHHHHHHHHCCCCSCCEECCCCEEEEEESCCCTTTTH-HHHTTSCSCEEEEESSHHHHHHHHHT
T ss_pred             CceEEEEecCCCchhHHHHHhhcceEEEccCcccCcCCceEEEechhHHHHHH-HHHhhcCCCEEEEEcCHHHHHHHHHH
Confidence                                                              000 12223367899999999999999999


Q ss_pred             HhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEe----cccCcCCcCCCCc-cEEEEecCC
Q psy14082        126 LRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVA----TDVAARGLDVEDV-NTVNIGSLQ  184 (233)
Q Consensus       126 L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~----T~~~~~Gldi~~v-~~VI~~d~P  184 (233)
                      |.+. +++..+||+|.     .++++|++|+.+||||    ||++++|+|+|+| ++||+||+|
T Consensus       295 L~~~-~~v~~lhg~~~-----~~l~~F~~G~~~VLVaTas~Tdv~~rGIDip~VI~~VI~~~~P  352 (1054)
T 1gku_B          295 LKNK-FRIGIVTATKK-----GDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCP  352 (1054)
T ss_dssp             TTTS-SCEEECTTSSS-----HHHHHHHHTSCSEEEEECC------CCSCCTTTCCEEEEESCC
T ss_pred             Hhhc-cCeeEEeccHH-----HHHHHHHcCCCcEEEEecCCCCeeEeccccCCcccEEEEeCCC
Confidence            9888 99999999983     7889999999999999    9999999999996 999999999

>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=99.95  E-value=7.9e-28  Score=210.25  Aligned_cols=106  Identities=26%  Similarity=0.401  Sum_probs=91.1

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeC--------CCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCc
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRERHSAICIHG--------DKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDV  175 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~--------~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v  175 (233)
                      ..+.++||||++++.++.+++.|.+.|+.+..+||        +|+.++|.+++++|++|+.+|||||+++++|+|+|++
T Consensus       359 ~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~~~~~vLv~T~~~~~Gldl~~~  438 (494)
T 1wp9_A          359 KQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEV  438 (494)
T ss_dssp             CTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECGGGGGGGGSTTC
T ss_pred             CCCCeEEEEEccHHHHHHHHHHHHHcCCCcEEEeccccccccccCCHHHHHHHHHHHhcCCceEEEECCccccCCCchhC
Confidence            46889999999999999999999999999999999        9999999999999999999999999999999999999


Q ss_pred             cEEEEecCCCCccccc-----------ceeeEEeecchHHHHHHH
Q psy14082        176 NTVNIGSLQLSANHNI-----------SQVIEVVQDYEKEKRLFS  209 (233)
Q Consensus       176 ~~VI~~d~P~~~~~~i-----------~~~~~~~~~~~~~~~~~~  209 (233)
                      ++||+||+|+++..|+           |.++.++.+...+++.+.
T Consensus       439 ~~Vi~~d~~~~~~~~~Qr~GR~~R~g~g~~~~l~~~~t~ee~~~~  483 (494)
T 1wp9_A          439 DLVVFYEPVPSAIRSIQRRGRTGRHMPGRVIILMAKGTRDEAYYW  483 (494)
T ss_dssp             CEEEESSCCHHHHHHHHHHTTSCSCCCSEEEEEEETTSHHHHHHH
T ss_pred             CEEEEeCCCCCHHHHHHHHhhccCCCCceEEEEEecCCHHHHHHH
Confidence            9999999999986444           456667776554444444

>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=99.95  E-value=2.2e-28  Score=213.62  Aligned_cols=170  Identities=15%  Similarity=0.148  Sum_probs=123.9

Q ss_pred             CCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCC---
Q psy14082          4 PSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGT---   80 (233)
Q Consensus         4 ~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~---   80 (233)
                      .++.|+|++++++||||||++|++|+++.+...       +++++|++||++||.|+++.+..+    .+....+..   
T Consensus         4 ~l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~~-------~~~~lil~Ptr~La~Q~~~~l~~~----~v~~~~~~~~~v   72 (440)
T 1yks_A            4 MLKKGMTTVLDFHPGAGKTRRFLPQILAECARR-------RLRTLVLAPTRVVLSEMKEAFHGL----DVKFHTQAFSAH   72 (440)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT-------TCCEEEEESSHHHHHHHHHHTTTS----CEEEESSCCCCC
T ss_pred             HhhCCCCEEEEcCCCCCHHHHHHHHHHHHHHhc-------CCeEEEEcchHHHHHHHHHHHhcC----CeEEecccceec
Confidence            467899999999999999999999999988643       678999999999999999999766    111111110   


Q ss_pred             --C----------------------CCCeeEEe--ccc------------------------------------------
Q psy14082         81 --P----------------------KGPQDCLP--LHR------------------------------------------   92 (233)
Q Consensus        81 --~----------------------~~~~~lv~--l~r------------------------------------------   92 (233)
                        +                      .+...+|-  .++                                          
T Consensus        73 ~Tp~~l~~~l~~~~l~~~~~~~~~~~~l~~vViDEah~~~~~~~~~~~~~~~~~~~~~~~~l~~SAT~~~~~~~~~~~~~  152 (440)
T 1yks_A           73 GSGREVIDAMCHATLTYRMLEPTRVVNWEVIIMDEAHFLDPASIAARGWAAHRARANESATILMTATPPGTSDEFPHSNG  152 (440)
T ss_dssp             CCSSCCEEEEEHHHHHHHHTSSSCCCCCSEEEETTTTCCSHHHHHHHHHHHHHHHTTSCEEEEECSSCTTCCCSSCCCSS
T ss_pred             cCCccceeeecccchhHhhhCcccccCccEEEEECccccCcchHHHHHHHHHHhccCCceEEEEeCCCCchhhhhhhcCC
Confidence              0                      00001111  000                                          


Q ss_pred             -------------hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCE
Q psy14082         93 -------------FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPI  159 (233)
Q Consensus        93 -------------~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~i  159 (233)
                                   ...... .+. ..+.++||||++++.++.+++.|++.++++..+||    ++|.+++++|++|+.+|
T Consensus       153 ~~~~~~~~~~~~~~~~~~~-~l~-~~~~~~lVF~~s~~~a~~l~~~L~~~~~~v~~lhg----~~R~~~~~~F~~g~~~v  226 (440)
T 1yks_A          153 EIEDVQTDIPSEPWNTGHD-WIL-ADKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNR----KTFEREYPTIKQKKPDF  226 (440)
T ss_dssp             CEEEEECCCCSSCCSSSCH-HHH-HCCSCEEEECSCHHHHHHHHHHHHHTTCCEEECCS----SSCC--------CCCSE
T ss_pred             CeeEeeeccChHHHHHHHH-HHH-hcCCCEEEEeCCHHHHHHHHHHHHHcCCCEEEecc----hhHHHHHhhhcCCCceE
Confidence                         000000 122 24679999999999999999999999999999999    36889999999999999


Q ss_pred             EEecccCcCCcCCCCccEEEE-------------------ecCCCCccccc
Q psy14082        160 LVATDVAARGLDVEDVNTVNI-------------------GSLQLSANHNI  191 (233)
Q Consensus       160 Lv~T~~~~~Gldi~~v~~VI~-------------------~d~P~~~~~~i  191 (233)
                      ||||+++++|+|+| +++||+                   ||+|.+..+|+
T Consensus       227 LVaT~v~e~GiDip-v~~VI~~g~~~~pv~~~~~~~~vi~~~~p~~~~~~~  276 (440)
T 1yks_A          227 ILATDIAEMGANLC-VERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAA  276 (440)
T ss_dssp             EEESSSTTCCTTCC-CSEEEECCEEEEEEEETTTTEEEEEEEEECCHHHHH
T ss_pred             EEECChhheeeccC-ceEEEeCCccceeeecccccceeeccccccCHHHHH
Confidence            99999999999999 999996                   89999988666

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.95  E-value=3.6e-28  Score=221.44  Aligned_cols=177  Identities=14%  Similarity=0.121  Sum_probs=133.4

Q ss_pred             CCCCCC------CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcE-
Q psy14082          1 MLPPSE------SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRN-   73 (233)
Q Consensus         1 aip~~~------~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~-   73 (233)
                      |||.++      .|+|++++++||||||++|++|+++.+..       +++++||++||++||.|+++.+..+.-+... 
T Consensus       228 aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~-------~~~~~lilaPTr~La~Q~~~~l~~~~i~~~~~  300 (673)
T 2wv9_A          228 PVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQ-------KRLRTAVLAPTRVVAAEMAEALRGLPVRYLTP  300 (673)
T ss_dssp             --CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHH-------TTCCEEEEESSHHHHHHHHHHTTTSCCEECCC
T ss_pred             chHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHh-------CCCcEEEEccHHHHHHHHHHHHhcCCeeeecc
Confidence            578888      89999999999999999999999998764       3678999999999999999999866111000 


Q ss_pred             ------------EEEEcCC---------C-CCCeeEEe--ccc-------------------------------------
Q psy14082         74 ------------ICIFGGT---------P-KGPQDCLP--LHR-------------------------------------   92 (233)
Q Consensus        74 ------------~~~~gg~---------~-~~~~~lv~--l~r-------------------------------------   92 (233)
                                  ..+..+.         . .+...+|-  .++                                     
T Consensus       301 ~l~~v~tp~~ll~~l~~~~l~~~l~~~~~l~~l~lvViDEaH~~~~~~~~~~~~l~~~~~~~~~~vl~~SAT~~~~i~~~  380 (673)
T 2wv9_A          301 AVQREHSGNEIVDVMCHATLTHRLMSPLRVPNYNLFVMDEAHFTDPASIAARGYIATRVEAGEAAAIFMTATPPGTSDPF  380 (673)
T ss_dssp             ---CCCCSCCCEEEEEHHHHHHHHHSSSCCCCCSEEEEESTTCCCHHHHHHHHHHHHHHHTTSCEEEEECSSCTTCCCSS
T ss_pred             cccccCCHHHHHHHHHhhhhHHHHhcccccccceEEEEeCCcccCccHHHHHHHHHHhccccCCcEEEEcCCCChhhhhh
Confidence                        0001000         0 00011111  000                                     


Q ss_pred             ------------------hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhC
Q psy14082         93 ------------------FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQ  154 (233)
Q Consensus        93 ------------------~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~  154 (233)
                                        +..... .+ ...+.++||||++++.++.+++.|++.++++..+||+    +|.+++++|++
T Consensus       381 ~~~~~~i~~v~~~~~~~~~~~~l~-~l-~~~~~~~lVF~~s~~~~e~la~~L~~~g~~v~~lHg~----eR~~v~~~F~~  454 (673)
T 2wv9_A          381 PDTNSPVHDVSSEIPDRAWSSGFE-WI-TDYAGKTVWFVASVKMSNEIAQCLQRAGKRVIQLNRK----SYDTEYPKCKN  454 (673)
T ss_dssp             CCCSSCEEEEECCCCSSCCSSCCH-HH-HSCCSCEEEECSSHHHHHHHHHHHHTTTCCEEEECSS----SHHHHGGGGGT
T ss_pred             cccCCceEEEeeecCHHHHHHHHH-HH-HhCCCCEEEEECCHHHHHHHHHHHHhCCCeEEEeChH----HHHHHHHHHHC
Confidence                              000000 12 2357899999999999999999999999999999994    78999999999


Q ss_pred             CCCCEEEecccCcCCcCCCCccEEEE--------------------ecCCCCccccc
Q psy14082        155 GKAPILVATDVAARGLDVEDVNTVNI--------------------GSLQLSANHNI  191 (233)
Q Consensus       155 g~~~iLv~T~~~~~Gldi~~v~~VI~--------------------~d~P~~~~~~i  191 (233)
                      |+.+|||||+++++|+|+| +++|||                    ||+|.+.++|+
T Consensus       455 g~~~VLVaTdv~e~GIDip-v~~VI~~g~~~~p~vi~da~~r~~ll~d~P~s~~~y~  510 (673)
T 2wv9_A          455 GDWDFVITTDISEMGANFG-ASRVIDCRKSVKPTILDEGEGRVILSVPSAITSASAA  510 (673)
T ss_dssp             CCCSEEEECGGGGTTCCCC-CSEEEECCEECCEEEECSTTCEEEECCSEECCHHHHH
T ss_pred             CCceEEEECchhhcceeeC-CcEEEECCCcccceeeecccccceecccCCCCHHHHH
Confidence            9999999999999999999 999998                    67888887666

>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=99.95  E-value=8.4e-28  Score=217.46  Aligned_cols=172  Identities=14%  Similarity=0.097  Sum_probs=133.0

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCC
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGT   80 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~   80 (233)
                      +||.++.|+|++++|+||||||++|++|+++++..       +++++||++||||||.|+++.+..+    .+. +.++.
T Consensus       179 ~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~-------~~~~vLvl~PtreLa~Qi~~~l~~~----~v~-~~~~~  246 (618)
T 2whx_A          179 DEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALK-------RRLRTLILAPTRVVAAEMEEALRGL----PIR-YQTPA  246 (618)
T ss_dssp             CGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHH-------TTCCEEEEESSHHHHHHHHHHTTTS----CEE-ECCTT
T ss_pred             CHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHh-------CCCeEEEEcChHHHHHHHHHHhcCC----cee-Eeccc
Confidence            36778999999999999999999999999999875       3678999999999999999988643    221 11110


Q ss_pred             ------CC----------------------CCeeE-Ee-ccc--------------------------------------
Q psy14082         81 ------PK----------------------GPQDC-LP-LHR--------------------------------------   92 (233)
Q Consensus        81 ------~~----------------------~~~~l-v~-l~r--------------------------------------   92 (233)
                            +.                      +-..+ +- .++                                      
T Consensus       247 l~~~~tp~~~i~~~t~~~l~~~l~~~~~l~~~~~iViDEah~~~~~~~~~~~~i~~~l~~~~~q~il~SAT~~~~~~~~~  326 (618)
T 2whx_A          247 VKSDHTGREIVDLMCHATFTTRLLSSTRVPNYNLIVMDEAHFTDPCSVAARGYISTRVEMGEAAAIFMTATPPGSTDPFP  326 (618)
T ss_dssp             SSCCCCSSSCEEEEEHHHHHHHHHHCSSCCCCSEEEEESTTCCSHHHHHHHHHHHHHHHHTSCEEEEECSSCTTCCCSSC
T ss_pred             ceeccCCCceEEEEChHHHHHHHhccccccCCeEEEEECCCCCCccHHHHHHHHHHHhcccCccEEEEECCCchhhhhhh
Confidence                  00                      00001 11 000                                      


Q ss_pred             -----------------hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCC
Q psy14082         93 -----------------FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQG  155 (233)
Q Consensus        93 -----------------~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g  155 (233)
                                       +..+.. .+.. ...++||||++++.++.+++.|.+.++++..+||+    +|.+++++|++|
T Consensus       327 ~~~~~~~~v~~~~~~~~~~~ll~-~l~~-~~~~~LVF~~s~~~a~~l~~~L~~~g~~v~~lhg~----~R~~~l~~F~~g  400 (618)
T 2whx_A          327 QSNSPIEDIEREIPERSWNTGFD-WITD-YQGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRK----TFDTEYPKTKLT  400 (618)
T ss_dssp             CCSSCEEEEECCCCSSCCSSSCH-HHHH-CCSCEEEECSSHHHHHHHHHHHHHTTCCEEEECTT----THHHHTTHHHHS
T ss_pred             ccCCceeeecccCCHHHHHHHHH-HHHh-CCCCEEEEECChhHHHHHHHHHHHcCCcEEEEChH----HHHHHHHhhcCC
Confidence                             000001 1222 46799999999999999999999999999999985    688899999999


Q ss_pred             CCCEEEecccCcCCcCCCCccEE--------------------EEecCCCCccccc
Q psy14082        156 KAPILVATDVAARGLDVEDVNTV--------------------NIGSLQLSANHNI  191 (233)
Q Consensus       156 ~~~iLv~T~~~~~Gldi~~v~~V--------------------I~~d~P~~~~~~i  191 (233)
                      +.+||||||++++|+|+| +++|                    ||||+|.+.++|+
T Consensus       401 ~~~VLVaTdv~~rGiDi~-v~~VId~g~~~~P~~~~~~~~~~~i~~d~P~s~~~yi  455 (618)
T 2whx_A          401 DWDFVVTTDISEMGANFR-AGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAA  455 (618)
T ss_dssp             CCSEEEECGGGGTTCCCC-CSEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHH
T ss_pred             CcEEEEECcHHHcCcccC-ceEEEECcceecceecccCCCceEEcccccCCHHHHH
Confidence            999999999999999997 9988                    8888899988666

>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=99.95  E-value=5.6e-28  Score=220.74  Aligned_cols=96  Identities=15%  Similarity=0.129  Sum_probs=83.9

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCC--------Ccc
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVE--------DVN  176 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~--------~v~  176 (233)
                      .+.++||||+|++.++.++..|.+.|+++.++||++++.++..+.++|+.|  .|+||||+++||+|++        ++.
T Consensus       431 ~~~pvLVft~s~~~se~Ls~~L~~~gi~~~vLhg~~~~rEr~ii~~ag~~g--~VlIATdmAgRG~DI~l~~~V~~~ggl  508 (844)
T 1tf5_A          431 TGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKG--AVTIATNMAGRGTDIKLGEGVKELGGL  508 (844)
T ss_dssp             HTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHHHHTTTTSTT--CEEEEETTSSTTCCCCCCTTSGGGTSE
T ss_pred             cCCcEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCccHHHHHHHHHcCCCC--eEEEeCCccccCcCccccchhhhcCCc
Confidence            356899999999999999999999999999999999888887666666655  7999999999999999        788


Q ss_pred             EEEEecCCCCccccc------------ceeeEEeecch
Q psy14082        177 TVNIGSLQLSANHNI------------SQVIEVVQDYE  202 (233)
Q Consensus       177 ~VI~~d~P~~~~~~i------------~~~~~~~~~~~  202 (233)
                      +|||||+|.|...|+            |.++.|++..+
T Consensus       509 ~VIn~d~p~s~r~y~hr~GRTGRqG~~G~s~~~vs~eD  546 (844)
T 1tf5_A          509 AVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMED  546 (844)
T ss_dssp             EEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTS
T ss_pred             EEEEecCCCCHHHHHhhcCccccCCCCCeEEEEecHHH
Confidence            999999999998666            46667887655

>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=99.94  E-value=3e-28  Score=213.91  Aligned_cols=174  Identities=13%  Similarity=0.090  Sum_probs=126.4

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEE-cCCCC-
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIF-GGTPK-   82 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~-gg~~~-   82 (233)
                      +..|+++++++|||||||++|++|+++.+..       .++++||++|||+|+.|+++.+..+.-......+. +..+. 
T Consensus        18 l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~-------~~~~~lvl~Ptr~La~Q~~~~l~g~~v~~~~~~~~~~~t~~~   90 (459)
T 2z83_A           18 LRKRQMTVLDLHPGSGKTRKILPQIIKDAIQ-------QRLRTAVLAPTRVVAAEMAEALRGLPVRYQTSAVQREHQGNE   90 (459)
T ss_dssp             GSTTCEEEECCCTTSCTTTTHHHHHHHHHHH-------TTCCEEEEECSHHHHHHHHHHTTTSCEEECC--------CCC
T ss_pred             HhcCCcEEEECCCCCCHHHHHHHHHHHHHHh-------CCCcEEEECchHHHHHHHHHHhcCceEeEEecccccCCCCCc
Confidence            4668999999999999999999999998864       36789999999999999999987541100000000 00000 


Q ss_pred             ---------------------CCeeEEe--ccc-------------------------------------------hh--
Q psy14082         83 ---------------------GPQDCLP--LHR-------------------------------------------FV--   94 (233)
Q Consensus        83 ---------------------~~~~lv~--l~r-------------------------------------------~~--   94 (233)
                                           +-..+|-  .++                                           +.  
T Consensus        91 ~i~~~~~~~l~~~l~~~~~l~~~~~iViDEaH~~~~~~~~~~~~~~~~~~~~~~~~il~SAT~~~~~~~~~~~~~pi~~~  170 (459)
T 2z83_A           91 IVDVMCHATLTHRLMSPNRVPNYNLFVMDEAHFTDPASIAARGYIATKVELGEAAAIFMTATPPGTTDPFPDSNAPIHDL  170 (459)
T ss_dssp             SEEEEEHHHHHHHHHSCC-CCCCSEEEESSTTCCSHHHHHHHHHHHHHHHTTSCEEEEECSSCTTCCCSSCCCSSCEEEE
T ss_pred             EEEEEchHHHHHHhhccccccCCcEEEEECCccCCchhhHHHHHHHHHhccCCccEEEEEcCCCcchhhhccCCCCeEEe
Confidence                                 0000111  000                                           00  


Q ss_pred             ---------hhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEeccc
Q psy14082         95 ---------FNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDV  165 (233)
Q Consensus        95 ---------~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~  165 (233)
                               ....+.+. ...+++||||++++.++.+++.|++.++.+..+||+    +|..++++|++|+.+|||||++
T Consensus       171 ~~~~~~~~~~~~~~~l~-~~~~~~LVF~~s~~~~~~l~~~L~~~g~~v~~lh~~----~R~~~~~~f~~g~~~iLVaT~v  245 (459)
T 2z83_A          171 QDEIPDRAWSSGYEWIT-EYAGKTVWFVASVKMGNEIAMCLQRAGKKVIQLNRK----SYDTEYPKCKNGDWDFVITTDI  245 (459)
T ss_dssp             ECCCCSSCCSSCCHHHH-HCCSCEEEECSCHHHHHHHHHHHHHTTCCEEEESTT----CCCCCGGGSSSCCCSEEEESSC
T ss_pred             cccCCcchhHHHHHHHH-hcCCCEEEEeCChHHHHHHHHHHHhcCCcEEecCHH----HHHHHHhhccCCCceEEEECCh
Confidence                     00000222 236799999999999999999999999999999995    6788999999999999999999


Q ss_pred             CcCCcCCCCccEEEE--------------------ecCCCCccccc
Q psy14082        166 AARGLDVEDVNTVNI--------------------GSLQLSANHNI  191 (233)
Q Consensus       166 ~~~Gldi~~v~~VI~--------------------~d~P~~~~~~i  191 (233)
                      +++|+|+|+ ++||+                    ||+|.|...|+
T Consensus       246 ~~~GiDip~-~~VI~~G~~~~~~~~~~~~~~~~~~~d~p~s~~~~~  290 (459)
T 2z83_A          246 SEMGANFGA-SRVIDCRKSVKPTILEEGEGRVILGNPSPITSASAA  290 (459)
T ss_dssp             C---CCCSC-SEEEECCEECCEEEECSSSCEEEECSCEECCHHHHH
T ss_pred             HHhCeecCC-CEEEECCcccccccccccccccccccCCCCCHHHHH
Confidence            999999999 99999                    77999988666

>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=99.94  E-value=2.8e-27  Score=213.63  Aligned_cols=170  Identities=15%  Similarity=0.066  Sum_probs=132.3

Q ss_pred             CCCC-CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCC
Q psy14082          2 LPPS-ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGT   80 (233)
Q Consensus         2 ip~~-~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~   80 (233)
                      ||.. ..++|++++|+||||||++|.+|+++           ++.++||++||||||.|+++.+.+.. +..+...+|+.
T Consensus       225 i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~-----------~g~~vLVl~PTReLA~Qia~~l~~~~-g~~vg~~vG~~  292 (666)
T 3o8b_A          225 PPAVPQSFQVAHLHAPTGSGKSTKVPAAYAA-----------QGYKVLVLNPSVAATLGFGAYMSKAH-GIDPNIRTGVR  292 (666)
T ss_dssp             CCCCCSSCEEEEEECCTTSCTTTHHHHHHHH-----------TTCCEEEEESCHHHHHHHHHHHHHHH-SCCCEEECSSC
T ss_pred             HHHHHHcCCeEEEEeCCchhHHHHHHHHHHH-----------CCCeEEEEcchHHHHHHHHHHHHHHh-CCCeeEEECcE
Confidence            4444 46888999999999999999999885           24589999999999999999887763 45566677775


Q ss_pred             C--CCCeeEEe-----ccc-----------------------------hhhhchH-------------------------
Q psy14082         81 P--KGPQDCLP-----LHR-----------------------------FVFNCQY-------------------------   99 (233)
Q Consensus        81 ~--~~~~~lv~-----l~r-----------------------------~~~~~~~-------------------------   99 (233)
                      .  .+.+++|+     +.+                             +...+..                         
T Consensus       293 ~~~~~~~IlV~TPGrLl~~~~l~l~~l~~lVlDEAH~l~~~~~~~l~~Il~~l~~~~~~llil~SAT~~~~i~~~~p~i~  372 (666)
T 3o8b_A          293 TITTGAPVTYSTYGKFLADGGCSGGAYDIIICDECHSTDSTTILGIGTVLDQAETAGARLVVLATATPPGSVTVPHPNIE  372 (666)
T ss_dssp             EECCCCSEEEEEHHHHHHTTSCCTTSCSEEEETTTTCCSHHHHHHHHHHHHHTTTTTCSEEEEEESSCTTCCCCCCTTEE
T ss_pred             eccCCCCEEEECcHHHHhCCCcccCcccEEEEccchhcCccHHHHHHHHHHhhhhcCCceEEEECCCCCcccccCCcceE
Confidence            3  34566666     000                             0000000                         


Q ss_pred             -----------------HHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEe
Q psy14082        100 -----------------EMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVA  162 (233)
Q Consensus       100 -----------------~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~  162 (233)
                                       .+.....+++||||++++.++.+++.|++.++++..+||+|++++       |+++..+||||
T Consensus       373 ~v~~~~~~~i~~~~~~~~l~~~~~~~vLVFv~Tr~~ae~la~~L~~~g~~v~~lHG~l~q~e-------r~~~~~~VLVA  445 (666)
T 3o8b_A          373 EVALSNTGEIPFYGKAIPIEAIRGGRHLIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVSV-------IPTIGDVVVVA  445 (666)
T ss_dssp             EEECBSCSSEEETTEEECGGGSSSSEEEEECSCHHHHHHHHHHHHTTTCCEEEECTTSCGGG-------SCSSSCEEEEE
T ss_pred             EEeecccchhHHHHhhhhhhhccCCcEEEEeCCHHHHHHHHHHHHhCCCcEEEecCCCCHHH-------HHhCCCcEEEE
Confidence                             122335679999999999999999999999999999999999875       55666799999


Q ss_pred             cccCcCCcCCCCccEEE----------Eec-----------CCCCccccc
Q psy14082        163 TDVAARGLDVEDVNTVN----------IGS-----------LQLSANHNI  191 (233)
Q Consensus       163 T~~~~~Gldi~~v~~VI----------~~d-----------~P~~~~~~i  191 (233)
                      ||++++|+|++ +++||          |||           +|.+.++|+
T Consensus       446 TdVaerGIDId-V~~VI~~Gl~~~~ViNyDydP~~gl~~~~~P~s~~syi  494 (666)
T 3o8b_A          446 TDALMTGYTGD-FDSVIDCNTCVTQTVDFSLDPTFTIETTTVPQDAVSRS  494 (666)
T ss_dssp             CTTHHHHCCCC-BSEEEECCEEEEEEEECCCSSSCEEEEEEEECBHHHHH
T ss_pred             CChHHccCCCC-CcEEEecCcccccccccccccccccccccCcCCHHHHH
Confidence            99999999997 99988          788           899987666

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.94  E-value=4.5e-27  Score=204.91  Aligned_cols=168  Identities=10%  Similarity=0.089  Sum_probs=126.4

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCCC--CC
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPK--GP   84 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~--~~   84 (233)
                      .|+|+++++|||||||++|++|+++.+..       .+.+++|++||++|+.|+++.+.    ++.+....|+...  .+
T Consensus         1 kg~~~lv~a~TGsGKT~~~l~~~l~~~~~-------~g~~~lvl~Pt~~La~Q~~~~~~----~~~v~~~~~~~~~~~~~   69 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVLPQLVREAVK-------KRLRTVILAPTRVVASEMYEALR----GEPIRYMTPAVQSERTG   69 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHHHHHHHHHHH-------TTCCEEEEESSHHHHHHHHHHTT----TSCEEEC---------C
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHh-------CCCCEEEECcHHHHHHHHHHHhC----CCeEEEEecCccccCCC
Confidence            47899999999999999999999977764       36789999999999999998875    3445444443111  00


Q ss_pred             -ee------------------------EE-e-ccc-----------hh--------------------------------
Q psy14082         85 -QD------------------------CL-P-LHR-----------FV--------------------------------   94 (233)
Q Consensus        85 -~~------------------------lv-~-l~r-----------~~--------------------------------   94 (233)
                       .+                        +| - .++           +.                                
T Consensus        70 ~~~~~~~~~~~l~~~l~~~~~~~~l~~vViDEaH~~~~~~~~~~~~l~~~~~~~~~~~l~~SAT~~~~~~~~~~~~~~i~  149 (431)
T 2v6i_A           70 NEIVDFMCHSTFTMKLLQGVRVPNYNLYIMDEAHFLDPASVAARGYIETRVSMGDAGAIFMTATPPGTTEAFPPSNSPII  149 (431)
T ss_dssp             CCSEEEEEHHHHHHHHHHTCCCCCCSEEEEESTTCCSHHHHHHHHHHHHHHHTTSCEEEEEESSCTTCCCSSCCCSSCCE
T ss_pred             CceEEEEchHHHHHHHhcCccccCCCEEEEeCCccCCccHHHHHHHHHHHhhCCCCcEEEEeCCCCcchhhhcCCCCcee
Confidence             01                        11 1 000           00                                


Q ss_pred             -----------hhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEec
Q psy14082         95 -----------FNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVAT  163 (233)
Q Consensus        95 -----------~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T  163 (233)
                                 ....+.+. ...+++||||++++.++.+++.|++.++++..+||+    +|.+++++|++|+.+|||||
T Consensus       150 ~~~~~~~~~~~~~~~~~l~-~~~~~~lVF~~~~~~~~~l~~~L~~~~~~v~~lhg~----~r~~~~~~f~~g~~~vLVaT  224 (431)
T 2v6i_A          150 DEETRIPDKAWNSGYEWIT-EFDGRTVWFVHSIKQGAEIGTCLQKAGKKVLYLNRK----TFESEYPKCKSEKWDFVITT  224 (431)
T ss_dssp             EEECCCCSSCCSSCCHHHH-SCSSCEEEECSSHHHHHHHHHHHHHTTCCEEEESTT----THHHHTTHHHHSCCSEEEEC
T ss_pred             eccccCCHHHHHHHHHHHH-cCCCCEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCc----cHHHHHHhhcCCCCeEEEEC
Confidence                       00001222 246789999999999999999999999999999997    57889999999999999999


Q ss_pred             ccCcCCcCCCCccE-----------------EEEecCCCCccccc
Q psy14082        164 DVAARGLDVEDVNT-----------------VNIGSLQLSANHNI  191 (233)
Q Consensus       164 ~~~~~Gldi~~v~~-----------------VI~~d~P~~~~~~i  191 (233)
                      +++++|+|+| +++                 ||+++.|.+..+|+
T Consensus       225 ~v~e~GiDip-~~~VI~~g~~~~~v~d~~~~vi~~~~p~~~~~~~  268 (431)
T 2v6i_A          225 DISEMGANFK-ADRVIDPRKTIKPILLDGRVSMQGPIAITPASAA  268 (431)
T ss_dssp             GGGGTSCCCC-CSEEEECCEEEEEEEETTEEEEEEEEECCHHHHH
T ss_pred             chHHcCcccC-CcEEEecCccccceecccceeecccccCCHHHHH
Confidence            9999999999 655                 67889999988666

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19

Probab=99.94  E-value=5.8e-28  Score=222.75  Aligned_cols=170  Identities=18%  Similarity=0.136  Sum_probs=137.7

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhc--CCcEEEEEcCCCC----
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSS--ALRNICIFGGTPK----   82 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~--~~~~~~~~gg~~~----   82 (233)
                      .|++++++||||||++|++|+++.+.        .+.+++|++||++|+.|+++.+.+++.  ++++..++|+.+.    
T Consensus       390 ~~~Ll~a~TGSGKTlvall~il~~l~--------~g~qvlvlaPtr~La~Q~~~~l~~~~~~~gi~v~~l~G~~~~~~r~  461 (780)
T 1gm5_A          390 MNRLLQGDVGSGKTVVAQLAILDNYE--------AGFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKE  461 (780)
T ss_dssp             CCCEEECCSSSSHHHHHHHHHHHHHH--------HTSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHH
T ss_pred             CcEEEEcCCCCCHHHHHHHHHHHHHH--------cCCeEEEEeCcHHHHHHHHHHHHHHhhhcCceEEEEeCCCCHHHHH
Confidence            58999999999999999999999874        367899999999999999999999854  6899999998653    


Q ss_pred             ---------CCeeEEe----c------cc---------------------------------------------------
Q psy14082         83 ---------GPQDCLP----L------HR---------------------------------------------------   92 (233)
Q Consensus        83 ---------~~~~lv~----l------~r---------------------------------------------------   92 (233)
                               +.+++|+    +      .+                                                   
T Consensus       462 ~~~~~l~~g~~~IvVgT~~ll~~~~~~~~l~lVVIDEaHr~g~~qr~~l~~~~~~~~vL~mSATp~p~tl~~~~~g~~~~  541 (780)
T 1gm5_A          462 KIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLVIIDEQHRFGVKQREALMNKGKMVDTLVMSATPIPRSMALAFYGDLDV  541 (780)
T ss_dssp             HHHHHHHSSCCCEEEECTTHHHHCCCCSCCCEEEEESCCCC-----CCCCSSSSCCCEEEEESSCCCHHHHHHHTCCSSC
T ss_pred             HHHHHHhcCCCCEEEECHHHHhhhhhccCCceEEecccchhhHHHHHHHHHhCCCCCEEEEeCCCCHHHHHHHHhCCcce
Confidence                     3566776    0      00                                                   


Q ss_pred             -hh--------------------hhchHHH--hcCCCCeEEEEecch--------hHHHHHHHHHhh---CCCeeEEEeC
Q psy14082         93 -FV--------------------FNCQYEM--AKNPAFKVIVFVETK--------KKVEDITRALRR---ERHSAICIHG  138 (233)
Q Consensus        93 -~~--------------------~~~~~~~--~~~~~~k~iIf~~~~--------~~~~~l~~~L~~---~~~~~~~~~~  138 (233)
                       .+                    ..+.+.+  ....+.+++|||++.        ..++.+++.|.+   .++.+..+||
T Consensus       542 s~i~~~p~~r~~i~~~~~~~~~~~~l~~~i~~~l~~g~qvlVf~~~ie~se~l~~~~a~~l~~~L~~~~~~~~~v~~lHG  621 (780)
T 1gm5_A          542 TVIDEMPPGRKEVQTMLVPMDRVNEVYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHG  621 (780)
T ss_dssp             EEECCCCSSCCCCEECCCCSSTHHHHHHHHHHHTTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCS
T ss_pred             eeeeccCCCCcceEEEEeccchHHHHHHHHHHHHhcCCcEEEEecchhhhhhhhHHHHHHHHHHHHhhhcCCCcEEEEeC
Confidence             00                    0000011  224678899999965        457888888887   4688999999


Q ss_pred             CCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCC
Q psy14082        139 DKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLS  186 (233)
Q Consensus       139 ~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~  186 (233)
                      +|++++|..++++|++|+.+|||||+++++|+|+|++++||++|.|..
T Consensus       622 ~m~~~eR~~v~~~F~~G~~~ILVaT~vie~GIDiP~v~~VIi~d~~r~  669 (780)
T 1gm5_A          622 RLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERF  669 (780)
T ss_dssp             SSCCSCSHHHHHHHTTTSSSBCCCSSCCCSCSCCTTCCEEEBCSCSSS
T ss_pred             CCCHHHHHHHHHHHHCCCCeEEEECCCCCccccCCCCCEEEEeCCCCC
Confidence            999999999999999999999999999999999999999999999963

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.94  E-value=1e-25  Score=207.69  Aligned_cols=183  Identities=15%  Similarity=0.099  Sum_probs=142.6

Q ss_pred             CCC-CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh-hcCCcEEEEEcC
Q psy14082          2 LPP-SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF-SSALRNICIFGG   79 (233)
Q Consensus         2 ip~-~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~-~~~~~~~~~~gg   79 (233)
                      ++. +..|+++++++|||||||++|.+|+++.+...       +.+++|++|+|+|+.|+++.++.+ ..++++...+|+
T Consensus        39 i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~-------~~~il~i~P~r~La~q~~~~~~~~~~~g~~v~~~~G~  111 (715)
T 2va8_A           39 VKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKN-------GGKAIYVTPLRALTNEKYLTFKDWELIGFKVAMTSGD  111 (715)
T ss_dssp             HHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHHS-------CSEEEEECSCHHHHHHHHHHHGGGGGGTCCEEECCSC
T ss_pred             HHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHHC-------CCeEEEEeCcHHHHHHHHHHHHHhhcCCCEEEEEeCC
Confidence            344 67899999999999999999999999887642       568999999999999999999766 337889999998


Q ss_pred             CCCC------CeeEEe---------------ccc----------------------------------------------
Q psy14082         80 TPKG------PQDCLP---------------LHR----------------------------------------------   92 (233)
Q Consensus        80 ~~~~------~~~lv~---------------l~r----------------------------------------------   92 (233)
                      ....      .+++|+               +++                                              
T Consensus       112 ~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~~~~~~l~~i~~~~~~~~ii~lSATl~n~~~~  191 (715)
T 2va8_A          112 YDTDDAWLKNYDIIITTYEKLDSLWRHRPEWLNEVNYFVLDELHYLNDPERGPVVESVTIRAKRRNLLALSATISNYKQI  191 (715)
T ss_dssp             SSSCCGGGGGCSEEEECHHHHHHHHHHCCGGGGGEEEEEECSGGGGGCTTTHHHHHHHHHHHHTSEEEEEESCCTTHHHH
T ss_pred             CCCchhhcCCCCEEEEcHHHHHHHHhCChhHhhccCEEEEechhhcCCcccchHHHHHHHhcccCcEEEEcCCCCCHHHH
Confidence            6653      355665               000                                              


Q ss_pred             ---------------------h-----------h-------------hhchHHH--hcCCCCeEEEEecchhHHHHHHHH
Q psy14082         93 ---------------------F-----------V-------------FNCQYEM--AKNPAFKVIVFVETKKKVEDITRA  125 (233)
Q Consensus        93 ---------------------~-----------~-------------~~~~~~~--~~~~~~k~iIf~~~~~~~~~l~~~  125 (233)
                                           +           +             +...+.+  ....++++||||++++.++.++..
T Consensus       192 ~~~l~~~~~~~~~r~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LVF~~s~~~~~~~a~~  271 (715)
T 2va8_A          192 AKWLGAEPVATNWRPVPLIEGVIYPERKKKEYNVIFKDNTTKKVHGDDAIIAYTLDSLSKNGQVLVFRNSRKMAESTALK  271 (715)
T ss_dssp             HHHHTCEEEECCCCSSCEEEEEEEECSSTTEEEEEETTSCEEEEESSSHHHHHHHHHHTTTCCEEEECSSHHHHHHHHHH
T ss_pred             HHHhCCCccCCCCCCCCceEEEEecCCcccceeeecCcchhhhcccchHHHHHHHHHHhcCCCEEEEECCHHHHHHHHHH
Confidence                                 0           0             0000000  113568999999999999999999


Q ss_pred             HhhCC------------------------------------CeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCC
Q psy14082        126 LRRER------------------------------------HSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG  169 (233)
Q Consensus       126 L~~~~------------------------------------~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~G  169 (233)
                      |.+..                                    ..+..+||+|+.++|..+++.|++|..+|||||+++++|
T Consensus       272 L~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~~~v~~~h~~l~~~~r~~v~~~f~~g~~~vlvaT~~l~~G  351 (715)
T 2va8_A          272 IANYMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSLISKGVAYHHAGLSKALRDLIEEGFRQRKIKVIVATPTLAAG  351 (715)
T ss_dssp             HHHTTTSSCCCHHHHHHHHHHHHTCCSSCHHHHHHHHHHHTTTEEEECTTSCHHHHHHHHHHHHTTCSCEEEECGGGGGS
T ss_pred             HHHHHhhccCChHHHHHHHHHHHHhhhccccccHHHHHHHhcCEEEECCCCCHHHHHHHHHHHHcCCCeEEEEChHHhcc
Confidence            97642                                    248899999999999999999999999999999999999


Q ss_pred             cCCCCccEEEE----ec-------CCCCccccc
Q psy14082        170 LDVEDVNTVNI----GS-------LQLSANHNI  191 (233)
Q Consensus       170 ldi~~v~~VI~----~d-------~P~~~~~~i  191 (233)
                      +|+|++++||+    ||       .|.|...|+
T Consensus       352 idip~~~~VI~~~~~~d~~~~~~~~~~s~~~~~  384 (715)
T 2va8_A          352 VNLPARTVIIGDIYRFNKKIAGYYDEIPIMEYK  384 (715)
T ss_dssp             SCCCBSEEEECCC--------------CHHHHH
T ss_pred             cCCCceEEEEeCCeeccccCCCCCCcCCHHHHH
Confidence            99999999999    99       788876444

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.94  E-value=5.2e-27  Score=208.28  Aligned_cols=181  Identities=15%  Similarity=0.126  Sum_probs=145.8

Q ss_pred             CCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEcCC
Q psy14082          3 PPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGGT   80 (233)
Q Consensus         3 p~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~gg~   80 (233)
                      +.++.++|+++.++||+|||++|+.|+...+..       .+.++|||+||++|+.|+++.++++  +++.++..+.|+.
T Consensus       123 ~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~-------~~~~vlvl~P~~~L~~Q~~~~~~~~~~~~~~~v~~~~~~~  195 (510)
T 2oca_A          123 FEGLVNRRRILNLPTSAGRSLIQALLARYYLEN-------YEGKILIIVPTTALTTQMADDFVDYRLFSHAMIKKIGGGA  195 (510)
T ss_dssp             HHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHH-------CSSEEEEEESSHHHHHHHHHHHHHTTSSCGGGEEECGGGC
T ss_pred             HHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhC-------CCCeEEEEECcHHHHHHHHHHHHHhhcCCccceEEEecCC
Confidence            345667899999999999999999998887753       2348999999999999999999998  5567888888887


Q ss_pred             CC------CCeeEEe-----------------------------------cc----------------------------
Q psy14082         81 PK------GPQDCLP-----------------------------------LH----------------------------   91 (233)
Q Consensus        81 ~~------~~~~lv~-----------------------------------l~----------------------------   91 (233)
                      +.      ..+++|+                                   +.                            
T Consensus       196 ~~~~~~~~~~~I~i~T~~~l~~~~~~~~~~~~liIiDE~H~~~~~~~~~il~~~~~~~~~l~lSATp~~~~~~~~~~~~~  275 (510)
T 2oca_A          196 SKDDKYKNDAPVVVGTWQTVVKQPKEWFSQFGMMMNDECHLATGKSISSIISGLNNCMFKFGLSGSLRDGKANIMQYVGM  275 (510)
T ss_dssp             CTTGGGCTTCSEEEEEHHHHTTSCGGGGGGEEEEEEETGGGCCHHHHHHHGGGCTTCCEEEEEESCGGGCSSCHHHHHHH
T ss_pred             ccccccccCCcEEEEeHHHHhhchhhhhhcCCEEEEECCcCCCcccHHHHHHhcccCcEEEEEEeCCCCCcccHHHhHHh
Confidence            65      3456666                                   00                            


Q ss_pred             ------------------------------------------chhh---h----------chHHH---hcCCCCeEEEEe
Q psy14082         92 ------------------------------------------RFVF---N----------CQYEM---AKNPAFKVIVFV  113 (233)
Q Consensus        92 ------------------------------------------r~~~---~----------~~~~~---~~~~~~k~iIf~  113 (233)
                                                                ++-.   .          +.+.+   ....+.+++||+
T Consensus       276 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~ivf~  355 (510)
T 2oca_A          276 FGEIFKPVTTSKLMEDGQVTELKINSIFLRYPDEFTTKLKGKTYQEEIKIITGLSKRNKWIAKLAIKLAQKDENAFVMFK  355 (510)
T ss_dssp             HCSEECCCCCC---------CCEEEEEEEECCHHHHHHHTTCCHHHHHHHHHTCHHHHHHHHHHHHHHHTTTCEEEEEES
T ss_pred             hCCeEEeeCHHHHhhCCcCCCceEEEEeecCChHHhccccccchHHHHHHHhccHHHHHHHHHHHHHHHhcCCCeEEEEe
Confidence                                                      0000   0          00011   112445566666


Q ss_pred             cchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEec-ccCcCCcCCCCccEEEEecCCCCccccc
Q psy14082        114 ETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVAT-DVAARGLDVEDVNTVNIGSLQLSANHNI  191 (233)
Q Consensus       114 ~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T-~~~~~Gldi~~v~~VI~~d~P~~~~~~i  191 (233)
                      + .++++.+++.|.+.+.++..+||+|+.++|.+++++|++|+.+||||| +++++|+|+|++++||++|+|.+...|+
T Consensus       356 ~-~~~~~~l~~~L~~~~~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv~T~~~~~~GiDip~v~~vi~~~~~~s~~~~~  433 (510)
T 2oca_A          356 H-VSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFSTGISVKNLHHVVLAHGVKSKIIVL  433 (510)
T ss_dssp             S-HHHHHHHHHHHHTTCSSEEEESSSTTHHHHHHHHHHHHHCCSCEEEEEHHHHHHSCCCCSEEEEEESSCCCSCCHHH
T ss_pred             c-HHHHHHHHHHHHHcCCCeEEEECCCCHHHHHHHHHHHhCCCCCEEEEEcChhhcccccccCcEEEEeCCCCCHHHHH
Confidence            6 888999999999998899999999999999999999999999999999 9999999999999999999999987555

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.94  E-value=1.4e-26  Score=219.28  Aligned_cols=180  Identities=14%  Similarity=0.050  Sum_probs=145.2

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCC
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTP   81 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~   81 (233)
                      |+.+.+|+++++++|||||||++|.+|++..+.        .+.++||++||++|+.|+++.+.+++.  ++..++|+.+
T Consensus        95 i~~l~~g~~vLV~apTGSGKTlva~lai~~~l~--------~g~rvL~l~PtkaLa~Q~~~~l~~~~~--~vglltGd~~  164 (1010)
T 2xgj_A           95 ISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLK--------NKQRVIYTSPIKALSNQKYRELLAEFG--DVGLMTGDIT  164 (1010)
T ss_dssp             HHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHH--------TTCEEEEEESSHHHHHHHHHHHHHHHS--CEEEECSSCE
T ss_pred             HHHHHcCCCEEEECCCCCChHHHHHHHHHHHhc--------cCCeEEEECChHHHHHHHHHHHHHHhC--CEEEEeCCCc
Confidence            445677999999999999999999999998773        367999999999999999999999865  7788888876


Q ss_pred             CC--CeeEEe---------------ccc----------------------------------------------hhhhch
Q psy14082         82 KG--PQDCLP---------------LHR----------------------------------------------FVFNCQ   98 (233)
Q Consensus        82 ~~--~~~lv~---------------l~r----------------------------------------------~~~~~~   98 (233)
                      .+  .+++|+               +++                                              +..++.
T Consensus       165 ~~~~~~IvV~Tpe~L~~~L~~~~~~l~~l~lVViDEaH~l~d~~rg~~~e~il~~l~~~~~il~LSATi~n~~e~a~~l~  244 (1010)
T 2xgj_A          165 INPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWIC  244 (1010)
T ss_dssp             ECTTCSEEEEEHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCTTTHHHHHHHHHHSCTTCEEEEEECCCTTHHHHHHHHH
T ss_pred             cCCCCCEEEEcHHHHHHHHHcCcchhhcCCEEEEechhhhcccchhHHHHHHHHhcCCCCeEEEEcCCCCCHHHHHHHHH
Confidence            43  456666               000                                              000000


Q ss_pred             --------------------------------------------------------------------------------
Q psy14082         99 --------------------------------------------------------------------------------   98 (233)
Q Consensus        99 --------------------------------------------------------------------------------   98 (233)
                                                                                                      
T Consensus       245 ~~~~~~~~vi~~~~rp~pl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~g~~~~~~k~~~~~  324 (1010)
T 2xgj_A          245 KIHSQPCHIVYTNFRPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASISNQIGDDPNSTDSRGKKGQTYKGGSAK  324 (1010)
T ss_dssp             HHHTSCEEEEEECCCSSCEEEEEEETTSSCCEEEECTTCCBCHHHHHHHHHTCC--------------------------
T ss_pred             hhcCCCeEEEecCCCcccceEEEEecCCcceeeeeccccccchHHHHHHHHHHhhhhccccccccccccccccccccccc
Confidence                                                                                            


Q ss_pred             -----------HHHhcCCCCeEEEEecchhHHHHHHHHHhhCCCe-----------------------------------
Q psy14082         99 -----------YEMAKNPAFKVIVFVETKKKVEDITRALRRERHS-----------------------------------  132 (233)
Q Consensus        99 -----------~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~-----------------------------------  132 (233)
                                 +.+......++||||++++.++.++..|.+.++.                                   
T Consensus       325 ~~~~~~l~~l~~~l~~~~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~  404 (1010)
T 2xgj_A          325 GDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPL  404 (1010)
T ss_dssp             ----CHHHHHHHHHHHHTCCSEEEEESSHHHHHHHHHTTTTSCCCCHHHHHHHHHHHHHHHTTSCGGGTTCHHHHHHHHH
T ss_pred             ccchHHHHHHHHHHHhcCCCCEEEEECCHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHH
Confidence                       0001112348999999999999999999775442                                   


Q ss_pred             ----eEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEE----ecC----CCCccccc
Q psy14082        133 ----AICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNI----GSL----QLSANHNI  191 (233)
Q Consensus       133 ----~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~----~d~----P~~~~~~i  191 (233)
                          +..+||+|++.+|..+++.|++|..+|||||+++++|+|+|++++||+    ||.    |.++.+|+
T Consensus       405 l~~gI~~~Hggl~~~eR~~ve~~F~~G~ikVLVAT~~la~GIDiP~~~vVI~~~~kfd~~~~rp~s~~~y~  475 (1010)
T 2xgj_A          405 LRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYI  475 (1010)
T ss_dssp             HHHTEEEESTTSCHHHHHHHHHHHHTTCCSEEEEEGGGGGSTTCCBSEEEESCSEEECSSCEEECCHHHHH
T ss_pred             HhCCeeEECCCCCHHHHHHHHHHHhcCCCcEEEEehHhhccCCCCCceEEEeCCcccCCcCCccCCHHHHh
Confidence                788999999999999999999999999999999999999999999999    999    88887555

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=99.94  E-value=5.3e-26  Score=209.70  Aligned_cols=183  Identities=17%  Similarity=0.173  Sum_probs=146.0

Q ss_pred             CCC-CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh-hcCCcEEEEEcC
Q psy14082          2 LPP-SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF-SSALRNICIFGG   79 (233)
Q Consensus         2 ip~-~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~-~~~~~~~~~~gg   79 (233)
                      ++. +..|+++++++|||||||++|.+|+++.+...       +.+++|++|+++|+.|+++.++++ ..++++..++|+
T Consensus        32 i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~-------~~~~l~i~P~raLa~q~~~~~~~l~~~g~~v~~~~G~  104 (720)
T 2zj8_A           32 LKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQ-------GGKAVYIVPLKALAEEKFQEFQDWEKIGLRVAMATGD  104 (720)
T ss_dssp             HTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHHH-------CSEEEEECSSGGGHHHHHHHTGGGGGGTCCEEEECSC
T ss_pred             HHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHhC-------CCEEEEEcCcHHHHHHHHHHHHHHHhcCCEEEEecCC
Confidence            455 67899999999999999999999999988743       578999999999999999999776 337899999998


Q ss_pred             CCCC------CeeEEe---------------c-----------------cc-----------------------------
Q psy14082         80 TPKG------PQDCLP---------------L-----------------HR-----------------------------   92 (233)
Q Consensus        80 ~~~~------~~~lv~---------------l-----------------~r-----------------------------   92 (233)
                      ...+      .+++|+               +                 .|                             
T Consensus       105 ~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~~r~~~~~~ll~~l~~~~~ii~lSATl~n~~~  184 (720)
T 2zj8_A          105 YDSKDEWLGKYDIIIATAEKFDSLLRHGSSWIKDVKILVADEIHLIGSRDRGATLEVILAHMLGKAQIIGLSATIGNPEE  184 (720)
T ss_dssp             SSCCCGGGGGCSEEEECHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCTTTHHHHHHHHHHHBTTBEEEEEECCCSCHHH
T ss_pred             CCccccccCCCCEEEECHHHHHHHHHcChhhhhcCCEEEEECCcccCCCcccHHHHHHHHHhhcCCeEEEEcCCcCCHHH
Confidence            6653      345665               0                 00                             


Q ss_pred             ------------------------------hhh-------hchHHH--hcCCCCeEEEEecchhHHHHHHHHHhhC----
Q psy14082         93 ------------------------------FVF-------NCQYEM--AKNPAFKVIVFVETKKKVEDITRALRRE----  129 (233)
Q Consensus        93 ------------------------------~~~-------~~~~~~--~~~~~~k~iIf~~~~~~~~~l~~~L~~~----  129 (233)
                                                    +.+       ...+.+  ....++++||||++++.++.++..|.+.    
T Consensus       185 ~~~~l~~~~~~~~~rp~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LVF~~sr~~~~~~a~~L~~~~~~~  264 (720)
T 2zj8_A          185 LAEWLNAELIVSDWRPVKLRRGVFYQGFVTWEDGSIDRFSSWEELVYDAIRKKKGALIFVNMRRKAERVALELSKKVKSL  264 (720)
T ss_dssp             HHHHTTEEEEECCCCSSEEEEEEEETTEEEETTSCEEECSSTTHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHHGGG
T ss_pred             HHHHhCCcccCCCCCCCcceEEEEeCCeeeccccchhhhhHHHHHHHHHHhCCCCEEEEecCHHHHHHHHHHHHHHHHHh
Confidence                                          000       000000  0125689999999999999999998753    


Q ss_pred             --------------C---------------CeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEE
Q psy14082        130 --------------R---------------HSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNI  180 (233)
Q Consensus       130 --------------~---------------~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~  180 (233)
                                    +               ..+..+||+|+.++|..+++.|++|..+|||||+.+++|+|+|++++||+
T Consensus       265 ~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~v~~~h~~l~~~~R~~v~~~f~~g~~~vlvaT~~l~~Gvdip~~~~VI~  344 (720)
T 2zj8_A          265 LTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHHAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTPAFRVIIR  344 (720)
T ss_dssp             SCHHHHHHHHHHHHTSCSCHHHHHHHHHHTTTEEEECTTSCHHHHHHHHHHHHTTSSCEEEECSTTGGGCCCCBSEEEEC
T ss_pred             cChhhHHHHHHHHHHHhcccchHHHHHHHhcCeeeecCCCCHHHHHHHHHHHHCCCCeEEEECcHhhccCCCCceEEEEc
Confidence                          1               24889999999999999999999999999999999999999999999999


Q ss_pred             ----ec----CCCCccccc
Q psy14082        181 ----GS----LQLSANHNI  191 (233)
Q Consensus       181 ----~d----~P~~~~~~i  191 (233)
                          ||    .|.+...|+
T Consensus       345 ~~~~yd~~g~~~~s~~~~~  363 (720)
T 2zj8_A          345 DIWRYSDFGMERIPIIEVH  363 (720)
T ss_dssp             CSEECCSSSCEECCHHHHH
T ss_pred             CCeeecCCCCccCCHHHHH
Confidence                77    577765444

>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=99.94  E-value=1.6e-27  Score=209.76  Aligned_cols=171  Identities=19%  Similarity=0.151  Sum_probs=143.0

Q ss_pred             CCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCc-EEEEEcCCC
Q psy14082          3 PPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALR-NICIFGGTP   81 (233)
Q Consensus         3 p~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~-~~~~~gg~~   81 (233)
                      +.++.+.++++.++||+|||++|+.++...           +.++||+||+++|+.||.+.+.+|  +++ +..+.|+.+
T Consensus       103 ~~i~~~~~~ll~~~TGsGKT~~~l~~i~~~-----------~~~~Lvl~P~~~L~~Q~~~~~~~~--~~~~v~~~~g~~~  169 (472)
T 2fwr_A          103 ERWLVDKRGCIVLPTGSGKTHVAMAAINEL-----------STPTLIVVPTLALAEQWKERLGIF--GEEYVGEFSGRIK  169 (472)
T ss_dssp             HHHTTTTEEEEECCTTSCHHHHHHHHHHHH-----------CSCEEEEESSHHHHHHHHHHGGGG--CGGGEEEBSSSCB
T ss_pred             HHHHhcCCEEEEeCCCCCHHHHHHHHHHHc-----------CCCEEEEECCHHHHHHHHHHHHhC--CCcceEEECCCcC
Confidence            345677889999999999999999987753           357999999999999999999996  677 888888888


Q ss_pred             CCCeeEEe--------------------------------------------------ccc-------------------
Q psy14082         82 KGPQDCLP--------------------------------------------------LHR-------------------   92 (233)
Q Consensus        82 ~~~~~lv~--------------------------------------------------l~r-------------------   92 (233)
                      ...+++|+                                                  ..|                   
T Consensus       170 ~~~~Ivv~T~~~l~~~~~~~~~~~~liIvDEaH~~~~~~~~~~~~~~~~~~~l~lSATp~~~~~~~~~l~~~~~~~~~~~  249 (472)
T 2fwr_A          170 ELKPLTVSTYDSAYVNAEKLGNRFMLLIFDEVHHLPAESYVQIAQMSIAPFRLGLTATFEREDGRHEILKEVVGGKVFEL  249 (472)
T ss_dssp             CCCSEEEEEHHHHHHTHHHHTTTCSEEEEETGGGTTSTTTHHHHHTCCCSEEEEEESCCCCTTSGGGSHHHHTCCEEEEC
T ss_pred             CcCCEEEEEcHHHHHHHHHhcCCCCEEEEECCcCCCChHHHHHHHhcCCCeEEEEecCccCCCCHHHHHHHHhCCeEeec
Confidence            77778777                                                  000                   


Q ss_pred             -hh-----------------------------------------------------------------------------
Q psy14082         93 -FV-----------------------------------------------------------------------------   94 (233)
Q Consensus        93 -~~-----------------------------------------------------------------------------   94 (233)
                       ..                                                                             
T Consensus       250 ~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  329 (472)
T 2fwr_A          250 FPDSLAGKHLAKYTIKRIFVPLAEDERVEYEKREKVYKQFLRARGITLRRAEDFNKIVMASGYDERAYEALRAWEEARRI  329 (472)
T ss_dssp             CHHHHTSCCCCSEEECCEEECCCHHHHHHTTTTTHHHHSCSSSCCCTTTCCSSSTTTTTTTCCSSSSSTTTHHHHHHHHH
T ss_pred             CHHHHhcCcCCCeEEEEEEcCCCHHHHHHHHHHHHHHHHHHHhcCccccchhhHHHHHHHhccCHHHHHHHHHHHHHHHH
Confidence             00                                                                             


Q ss_pred             --------hhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccC
Q psy14082         95 --------FNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVA  166 (233)
Q Consensus        95 --------~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~  166 (233)
                              ..+.+.+....+.++||||++++.++.+++.|.     +..+||+++..+|.+++++|++|+.+|||||+++
T Consensus       330 ~~~~~~k~~~l~~~l~~~~~~k~lvF~~~~~~~~~l~~~l~-----~~~~~g~~~~~~R~~~~~~F~~g~~~vLv~T~~~  404 (472)
T 2fwr_A          330 AFNSKNKIRKLREILERHRKDKIIIFTRHNELVYRISKVFL-----IPAITHRTSREEREEILEGFRTGRFRAIVSSQVL  404 (472)
T ss_dssp             HHSCSHHHHHHHHHHHHTSSSCBCCBCSCHHHHHHHHHHTT-----CCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCC
T ss_pred             hhcChHHHHHHHHHHHhCCCCcEEEEECCHHHHHHHHHHhC-----cceeeCCCCHHHHHHHHHHHhCCCCCEEEEcCch
Confidence                    001112344567899999999999999999873     5679999999999999999999999999999999


Q ss_pred             cCCcCCCCccEEEEecCCCCccccc
Q psy14082        167 ARGLDVEDVNTVNIGSLQLSANHNI  191 (233)
Q Consensus       167 ~~Gldi~~v~~VI~~d~P~~~~~~i  191 (233)
                      ++|+|+|++++||+||+|+++..|+
T Consensus       405 ~~Gldlp~~~~Vi~~~~~~s~~~~~  429 (472)
T 2fwr_A          405 DEGIDVPDANVGVIMSGSGSAREYI  429 (472)
T ss_dssp             CSSSCSCCBSEEEEECCSSCCHHHH
T ss_pred             hcCcccccCcEEEEECCCCCHHHHH
Confidence            9999999999999999999997555

>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=99.93  E-value=2.1e-26  Score=220.69  Aligned_cols=173  Identities=17%  Similarity=0.119  Sum_probs=140.1

Q ss_pred             CC--ceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhc--CCcEEEEEcCCCC-
Q psy14082          8 GC--QNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSS--ALRNICIFGGTPK-   82 (233)
Q Consensus         8 g~--d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~--~~~~~~~~gg~~~-   82 (233)
                      |+  |++++++||+|||++|+.+++..+.        .+.+++|++||++|+.|+++.+.+++.  ++++..+.|..+. 
T Consensus       622 g~p~d~ll~~~TGsGKT~val~aa~~~~~--------~g~~vlvlvPt~~La~Q~~~~~~~~~~~~~i~v~~l~~~~~~~  693 (1151)
T 2eyq_A          622 PLAMDRLVCGDVGFGKTEVAMRAAFLAVD--------NHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAK  693 (1151)
T ss_dssp             SSCCEEEEECCCCTTTHHHHHHHHHHHHT--------TTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHH
T ss_pred             CCcCcEEEECCCCCCHHHHHHHHHHHHHH--------hCCeEEEEechHHHHHHHHHHHHHHhhcCCCeEEEEeCCCCHH
Confidence            55  9999999999999999999887663        366999999999999999999998743  5677777765332 


Q ss_pred             ------------CCeeEEec----------cc------------------------------------------------
Q psy14082         83 ------------GPQDCLPL----------HR------------------------------------------------   92 (233)
Q Consensus        83 ------------~~~~lv~l----------~r------------------------------------------------   92 (233)
                                  +.+++|+-          ++                                                
T Consensus       694 ~~~~~~~~l~~g~~dIvV~T~~ll~~~~~~~~l~lvIiDEaH~~g~~~~~~l~~l~~~~~vl~lSATp~p~~l~~~~~~~  773 (1151)
T 2eyq_A          694 EQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLIVDEEHRFGVRHKERIKAMRANVDILTLTATPIPRTLNMAMSGM  773 (1151)
T ss_dssp             HHHHHHHHHHTTCCSEEEECTHHHHSCCCCSSEEEEEEESGGGSCHHHHHHHHHHHTTSEEEEEESSCCCHHHHHHHTTT
T ss_pred             HHHHHHHHHhcCCCCEEEECHHHHhCCccccccceEEEechHhcChHHHHHHHHhcCCCCEEEEcCCCChhhHHHHHhcC
Confidence                        35566660          00                                                


Q ss_pred             ------------------hhh------hchHH-HhcCCCCeEEEEecchhHHHHHHHHHhhC--CCeeEEEeCCCCHHHH
Q psy14082         93 ------------------FVF------NCQYE-MAKNPAFKVIVFVETKKKVEDITRALRRE--RHSAICIHGDKTQQDR  145 (233)
Q Consensus        93 ------------------~~~------~~~~~-~~~~~~~k~iIf~~~~~~~~~l~~~L~~~--~~~~~~~~~~~~~~~r  145 (233)
                                        ++.      +.... .....+++++|||+++++++.+++.|++.  +.++..+||+|++++|
T Consensus       774 ~~~~~i~~~~~~r~~i~~~~~~~~~~~i~~~il~~l~~g~qvlvf~~~v~~~~~l~~~L~~~~p~~~v~~lhg~~~~~eR  853 (1151)
T 2eyq_A          774 RDLSIIATPPARRLAVKTFVREYDSMVVREAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMREREL  853 (1151)
T ss_dssp             SEEEECCCCCCBCBCEEEEEEECCHHHHHHHHHHHHTTTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHH
T ss_pred             CCceEEecCCCCccccEEEEecCCHHHHHHHHHHHHhcCCeEEEEECCHHHHHHHHHHHHHhCCCCeEEEEeCCCCHHHH
Confidence                              000      00001 12235789999999999999999999887  7899999999999999


Q ss_pred             HHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCC-CCcc
Q psy14082        146 DYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQ-LSAN  188 (233)
Q Consensus       146 ~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P-~~~~  188 (233)
                      .+++++|++|+.+|||||+++++|+|+|++++||+++.+ .+..
T Consensus       854 ~~il~~F~~g~~~VLVaT~v~e~GiDip~v~~VIi~~~~~~~l~  897 (1151)
T 2eyq_A          854 ERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLA  897 (1151)
T ss_dssp             HHHHHHHHTTSCCEEEESSTTGGGSCCTTEEEEEETTTTSSCHH
T ss_pred             HHHHHHHHcCCCcEEEECCcceeeecccCCcEEEEeCCCCCCHH
Confidence            999999999999999999999999999999999999884 4544

>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=99.93  E-value=4e-26  Score=209.94  Aligned_cols=180  Identities=18%  Similarity=0.135  Sum_probs=144.3

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh-hcCCcEEEEEcCC
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF-SSALRNICIFGGT   80 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~-~~~~~~~~~~gg~   80 (233)
                      +|.+..|+++++++|||||||++|.+|+++.+..        +.+++|++|+|+|+.|+++.++.+ ..++++..++|+.
T Consensus        34 i~~i~~~~~~lv~apTGsGKT~~~~l~il~~~~~--------~~~~l~i~P~r~La~q~~~~~~~~~~~g~~v~~~~G~~  105 (702)
T 2p6r_A           34 VEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK--------GGKSLYVVPLRALAGEKYESFKKWEKIGLRIGISTGDY  105 (702)
T ss_dssp             HHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT--------TCCEEEEESSHHHHHHHHHHHTTTTTTTCCEEEECSSC
T ss_pred             HHHHhCCCcEEEEcCCccHHHHHHHHHHHHHHHh--------CCcEEEEeCcHHHHHHHHHHHHHHHhcCCEEEEEeCCC
Confidence            3446789999999999999999999999988753        568999999999999999999766 3378999999986


Q ss_pred             CC------CCeeEEe---------------cc-----------------c------------------------------
Q psy14082         81 PK------GPQDCLP---------------LH-----------------R------------------------------   92 (233)
Q Consensus        81 ~~------~~~~lv~---------------l~-----------------r------------------------------   92 (233)
                      ..      +.+++|+               ++                 |                              
T Consensus       106 ~~~~~~~~~~~Iiv~Tpe~l~~~l~~~~~~l~~~~~vIiDE~H~l~~~~r~~~~~~ll~~l~~~~~~~~ii~lSATl~n~  185 (702)
T 2p6r_A          106 ESRDEHLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTKMRRMNKALRVIGLSATAPNV  185 (702)
T ss_dssp             BCCSSCSTTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCTTTHHHHHHHHHHHHHHCTTCEEEEEECCCTTH
T ss_pred             CcchhhccCCCEEEECHHHHHHHHHcChhHHhhcCEEEEeeeeecCCCCcccHHHHHHHHHHhcCcCceEEEECCCcCCH
Confidence            54      3455665               00                 0                              


Q ss_pred             --------------------------------hh-------------hhchHHHhcCCCCeEEEEecchhHHHHHHHHHh
Q psy14082         93 --------------------------------FV-------------FNCQYEMAKNPAFKVIVFVETKKKVEDITRALR  127 (233)
Q Consensus        93 --------------------------------~~-------------~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~  127 (233)
                                                      +.             ..+.+.  ...++++||||++++.++.++..|.
T Consensus       186 ~~~~~~l~~~~~~~~~r~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~LVF~~s~~~~~~~a~~L~  263 (702)
T 2p6r_A          186 TEIAEWLDADYYVSDWRPVPLVEGVLCEGTLELFDGAFSTSRRVKFEELVEEC--VAENGGVLVFESTRRGAEKTAVKLS  263 (702)
T ss_dssp             HHHHHHTTCEEEECCCCSSCEEEEEECSSEEEEEETTEEEEEECCHHHHHHHH--HHTTCCEEEECSSHHHHHHHHHHHH
T ss_pred             HHHHHHhCCCcccCCCCCccceEEEeeCCeeeccCcchhhhhhhhHHHHHHHH--HhcCCCEEEEcCCHHHHHHHHHHHH
Confidence                                            00             000001  1256899999999999999999987


Q ss_pred             hC------------------------------CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccE
Q psy14082        128 RE------------------------------RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNT  177 (233)
Q Consensus       128 ~~------------------------------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~  177 (233)
                      +.                              +..+..+||+|+.++|..+.+.|++|+.+|||||+.+++|+|+|++++
T Consensus       264 ~~~~~~~~~~~~~~~i~~~~~~~~~~~l~~~~~~~v~~~h~~l~~~~R~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~  343 (702)
T 2p6r_A          264 AITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRV  343 (702)
T ss_dssp             HHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHHHHHHHHHHHHTTSCCEEEECSTTTSSSCCCBSEE
T ss_pred             HHHHhhcChHHHHHHHHhhccccccHHHHHHHhcCeEEecCCCCHHHHHHHHHHHHCCCCeEEEECcHHhccCCCCceEE
Confidence            53                              135778999999999999999999999999999999999999999999


Q ss_pred             EEE----ec---CCCCccccc
Q psy14082        178 VNI----GS---LQLSANHNI  191 (233)
Q Consensus       178 VI~----~d---~P~~~~~~i  191 (233)
                      ||+    ||   .|.|...|+
T Consensus       344 VI~~~~~yd~~~~~~s~~~~~  364 (702)
T 2p6r_A          344 IVRSLYRFDGYSKRIKVSEYK  364 (702)
T ss_dssp             EECCSEEESSSEEECCHHHHH
T ss_pred             EEcCceeeCCCCCcCCHHHHH
Confidence            999    77   677766444

>2fsf_A Preprotein translocase SECA subunit; ATPase, DNA-RNA helicase, protein translocation, protein transport; 2.00A {Escherichia coli} PDB: 2fsg_A* 2fsh_A* 2fsi_A* 2vda_A 3bxz_A*

Probab=99.93  E-value=5.3e-26  Score=207.37  Aligned_cols=97  Identities=14%  Similarity=0.051  Sum_probs=85.5

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCC----------
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVED----------  174 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~----------  174 (233)
                      .+.++||||+|++.++.++..|.+.|+++.++||++.+.++..+.++|+.|  .|+||||+++||+|++.          
T Consensus       440 ~gqpvLVft~sie~se~Ls~~L~~~gi~~~vLnak~~~rEa~iia~agr~G--~VtIATnmAgRGtDI~l~gn~~~~~~~  517 (853)
T 2fsf_A          440 KGQPVLVGTISIEKSELVSNELTKAGIKHNVLNAKFHANEAAIVAQAGYPA--AVTIATNMAGRGTDIVLGGSWQAEVAA  517 (853)
T ss_dssp             TTCCEEEEESSHHHHHHHHHHHHHTTCCCEECCTTCHHHHHHHHHTTTSTT--CEEEEESCCSSCSCCCTTCCHHHHHHH
T ss_pred             CCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCChhHHHHHHHHhcCCCC--eEEEecccccCCcCccCCCchHhhhhh
Confidence            567899999999999999999999999999999999988888888889888  69999999999999987          


Q ss_pred             ----------------------c-----cEEEEecCCCCccccc------------ceeeEEeecchH
Q psy14082        175 ----------------------V-----NTVNIGSLQLSANHNI------------SQVIEVVQDYEK  203 (233)
Q Consensus       175 ----------------------v-----~~VI~~d~P~~~~~~i------------~~~~~~~~~~~~  203 (233)
                                            |     .+||+||+|.|...|+            |.+..|++..+.
T Consensus       518 ~~~~~~~~~~~~~~~~~~~~~~V~~~GGl~VI~te~pes~riy~qr~GRTGRqGd~G~s~~fls~eD~  585 (853)
T 2fsf_A          518 LENPTAEQIEKIKADWQVRHDAVLEAGGLHIIGTERHESRRIDNQLRGRSGRQGDAGSSRFYLSMEDA  585 (853)
T ss_dssp             CSSCCSSHHHHHHHHHHHHHHHHHHTTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTSG
T ss_pred             cccchhHHHHHHHHHhhhhhhHHHhcCCcEEEEccCCCCHHHHHhhccccccCCCCeeEEEEecccHH
Confidence                                  4     6999999999987555            456668876553

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.93  E-value=3e-26  Score=216.82  Aligned_cols=81  Identities=14%  Similarity=-0.014  Sum_probs=67.1

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCC
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGT   80 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~   80 (233)
                      |||.+++|+|+++.+|||||||++|++|+...+.        .+.++||++|+++|+.|+++.+.+++.++++..++|+.
T Consensus        47 aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~--------~g~~vlvl~PtraLa~Q~~~~l~~~~~~~~v~~l~G~~  118 (997)
T 4a4z_A           47 AVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHR--------NMTKTIYTSPIKALSNQKFRDFKETFDDVNIGLITGDV  118 (997)
T ss_dssp             HHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHH--------TTCEEEEEESCGGGHHHHHHHHHTTC--CCEEEECSSC
T ss_pred             HHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHh--------cCCeEEEEeCCHHHHHHHHHHHHHHcCCCeEEEEeCCC
Confidence            3566788999999999999999999999887653        36789999999999999999999987788999999987


Q ss_pred             CCC--CeeEEe
Q psy14082         81 PKG--PQDCLP   89 (233)
Q Consensus        81 ~~~--~~~lv~   89 (233)
                      +.+  .+++|+
T Consensus       119 ~~~~~~~IlV~  129 (997)
T 4a4z_A          119 QINPDANCLIM  129 (997)
T ss_dssp             EECTTSSEEEE
T ss_pred             ccCCCCCEEEE
Confidence            543  445555

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.92  E-value=4.3e-25  Score=200.89  Aligned_cols=163  Identities=13%  Similarity=0.066  Sum_probs=128.4

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCCCC-
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPKG-   83 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~~-   83 (233)
                      .+.|+|++++||||||||+    ++++.+...        ..++|++|||+||.|+++.+.+.  ++++..++|+...- 
T Consensus       152 ~l~rk~vlv~apTGSGKT~----~al~~l~~~--------~~gl~l~PtR~LA~Qi~~~l~~~--g~~v~lltG~~~~iv  217 (677)
T 3rc3_A          152 AMQRKIIFHSGPTNSGKTY----HAIQKYFSA--------KSGVYCGPLKLLAHEIFEKSNAA--GVPCDLVTGEERVTV  217 (677)
T ss_dssp             TSCCEEEEEECCTTSSHHH----HHHHHHHHS--------SSEEEEESSHHHHHHHHHHHHHT--TCCEEEECSSCEECC
T ss_pred             hcCCCEEEEEcCCCCCHHH----HHHHHHHhc--------CCeEEEeCHHHHHHHHHHHHHhc--CCcEEEEECCeeEEe
Confidence            3678999999999999998    455555442        23599999999999999999987  77888888885431 


Q ss_pred             ------CeeEEe------------------ccc-----------------------------hhhhchH-----------
Q psy14082         84 ------PQDCLP------------------LHR-----------------------------FVFNCQY-----------   99 (233)
Q Consensus        84 ------~~~lv~------------------l~r-----------------------------~~~~~~~-----------   99 (233)
                            .+++++                  .++                             .......           
T Consensus       218 ~TpGr~~~il~~T~e~~~l~~~v~lvVIDEaH~l~d~~~g~~~~~~l~~l~~~~i~il~~SAT~~~i~~l~~~~~~~~~v  297 (677)
T 3rc3_A          218 QPNGKQASHVSCTVEMCSVTTPYEVAVIDEIQMIRDPARGWAWTRALLGLCAEEVHLCGEPAAIDLVMELMYTTGEEVEV  297 (677)
T ss_dssp             STTCCCCSEEEEEGGGCCSSSCEEEEEECSGGGGGCTTTHHHHHHHHHHCCEEEEEEEECGGGHHHHHHHHHHHTCCEEE
T ss_pred             cCCCcccceeEecHhHhhhcccCCEEEEecceecCCccchHHHHHHHHccCccceEEEeccchHHHHHHHHHhcCCceEE
Confidence                  222222                  000                             0000000           


Q ss_pred             -----------------HHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhC--CCCCEE
Q psy14082        100 -----------------EMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQ--GKAPIL  160 (233)
Q Consensus       100 -----------------~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~--g~~~iL  160 (233)
                                       .+.. .....+|||++++.++.+++.|.+.++.+..+||+|++++|.++++.|++  |..+||
T Consensus       298 ~~~~r~~~l~~~~~~l~~l~~-~~~g~iIf~~s~~~ie~la~~L~~~g~~v~~lHG~L~~~~R~~~~~~F~~~~g~~~VL  376 (677)
T 3rc3_A          298 RDYKRLTPISVLDHALESLDN-LRPGDCIVCFSKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKIL  376 (677)
T ss_dssp             EECCCSSCEEECSSCCCSGGG-CCTTEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHCTTSSCCEE
T ss_pred             EEeeecchHHHHHHHHHHHHh-cCCCCEEEEcCHHHHHHHHHHHHhcCCCeeeeeccCCHHHHHHHHHHHHccCCCeEEE
Confidence                             1111 23455899999999999999999999999999999999999999999999  889999


Q ss_pred             EecccCcCCcCCCCccEEEEecC
Q psy14082        161 VATDVAARGLDVEDVNTVNIGSL  183 (233)
Q Consensus       161 v~T~~~~~Gldi~~v~~VI~~d~  183 (233)
                      |||+++++|+|+ ++++||++|+
T Consensus       377 VATdi~e~GlDi-~v~~VI~~~~  398 (677)
T 3rc3_A          377 VATDAIGMGLNL-SIRRIIFYSL  398 (677)
T ss_dssp             EECGGGGSSCCC-CBSEEEESCS
T ss_pred             EeCcHHHCCcCc-CccEEEECCc
Confidence            999999999999 9999999999

>1nkt_A Preprotein translocase SECA 1 subunit; preprotein translocation, ATPase, transmembrane transport, helicase-like motor domain; HET: ADP; 2.60A {Mycobacterium tuberculosis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1nl3_A

Probab=99.92  E-value=4.7e-25  Score=201.63  Aligned_cols=98  Identities=16%  Similarity=0.106  Sum_probs=85.3

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCc---------
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDV---------  175 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v---------  175 (233)
                      .+.++||||+|++.++.++..|.+.|+++.++||++.+.++..+.++|+.|  .|+||||+++||+|++.+         
T Consensus       459 ~gqpvLVft~Sie~sE~Ls~~L~~~Gi~~~vLnak~~~rEa~iia~agr~G--~VtIATnmAgRGtDI~l~~~~~~~~~~  536 (922)
T 1nkt_A          459 KGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQEATIIAVAGRRG--GVTVATNMAGRGTDIVLGGNVDFLTDQ  536 (922)
T ss_dssp             TTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHHHHHHHHTTTSTT--CEEEEETTCSTTCCCCTTCCHHHHHHH
T ss_pred             cCCcEEEEECCHHHHHHHHHHHHHCCCCEEEecCChhHHHHHHHHhcCCCC--eEEEecchhhcCccccCCCCHHHHHHH
Confidence            456899999999999999999999999999999999888887777888877  799999999999999975         


Q ss_pred             -------------------------------------------cEEEEecCCCCccccc------------ceeeEEeec
Q psy14082        176 -------------------------------------------NTVNIGSLQLSANHNI------------SQVIEVVQD  200 (233)
Q Consensus       176 -------------------------------------------~~VI~~d~P~~~~~~i------------~~~~~~~~~  200 (233)
                                                                 .+||+||+|.|...|+            |.+..|++.
T Consensus       537 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGlhVI~te~pes~riy~qr~GRTGRqGdpG~s~fflSl  616 (922)
T 1nkt_A          537 RLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQLRGRSGRQGDPGESRFYLSL  616 (922)
T ss_dssp             HHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHHHHHHHTSSGGGCCEEEEEEEET
T ss_pred             HHhhccccccccchhhHHHHHHHHHHHHHHHHHhhhHHHhcCCcEEEeccCCCCHHHHHHHhcccccCCCCeeEEEEech
Confidence                                                       5999999999987555            566778886


Q ss_pred             chHH
Q psy14082        201 YEKE  204 (233)
Q Consensus       201 ~~~~  204 (233)
                      .++.
T Consensus       617 eD~l  620 (922)
T 1nkt_A          617 GDEL  620 (922)
T ss_dssp             TSHH
T ss_pred             hHHH
Confidence            5543

>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=99.91  E-value=4.6e-24  Score=210.19  Aligned_cols=175  Identities=18%  Similarity=0.135  Sum_probs=139.1

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCC---CCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEcCC
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEP---VKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGGT   80 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~---~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~gg~   80 (233)
                      .++.+++++||||||||++|.+|+++.+.+...   .....+.++||++|+|+||.|+++.+.+.  ..++++..++|+.
T Consensus        93 ~~~~N~lv~APTGsGKTlva~l~il~~l~~~~~~~~~~~~~~~k~lyiaP~kALa~e~~~~l~~~~~~~gi~V~~~tGd~  172 (1724)
T 4f92_B           93 ETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMVGSFGKRLATYGITVAELTGDH  172 (1724)
T ss_dssp             TCCCCEEEECCTTSCCHHHHHHHHHHHHGGGCCTTSSCCTTSCEEEEECSSHHHHHHHHHHHHHHHTTTTCCEEECCSSC
T ss_pred             cCCCcEEEEeCCcchHHHHHHHHHHHHHHhhccccccccCCCCEEEEECCHHHHHHHHHHHHHHHHhhCCCEEEEEECCC
Confidence            357889999999999999999999999986432   22245789999999999999999999886  3478999999997


Q ss_pred             CCC------CeeEEe--------cc-------------------------c-----------------------------
Q psy14082         81 PKG------PQDCLP--------LH-------------------------R-----------------------------   92 (233)
Q Consensus        81 ~~~------~~~lv~--------l~-------------------------r-----------------------------   92 (233)
                      +.+      .+++|+        ++                         |                             
T Consensus       173 ~~~~~~~~~~~IlVtTpEkld~llr~~~~~~~l~~v~~vIiDEvH~l~d~RG~~lE~~l~rl~~~~~~~~~~~riI~LSA  252 (1724)
T 4f92_B          173 QLCKEEISATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLHDDRGPVLEALVARAIRNIEMTQEDVRLIGLSA  252 (1724)
T ss_dssp             SSCCTTGGGCSEEEECHHHHHHHTTSSTTHHHHTTEEEEEETTGGGGGSTTHHHHHHHHHHHHHHHHHHTCCCEEEEEEC
T ss_pred             CCCccccCCCCEEEECHHHHHHHHcCCccchhhcCcCEEEEecchhcCCccHHHHHHHHHHHHHHHHhCCCCCcEEEEec
Confidence            653      456777        00                         0                             


Q ss_pred             ----------hh----------------------------------------hhchH-HHhcCCCCeEEEEecchhHHHH
Q psy14082         93 ----------FV----------------------------------------FNCQY-EMAKNPAFKVIVFVETKKKVED  121 (233)
Q Consensus        93 ----------~~----------------------------------------~~~~~-~~~~~~~~k~iIf~~~~~~~~~  121 (233)
                                ++                                        ..+.+ ......++++||||++++.++.
T Consensus       253 Tl~N~~dvA~wL~~~~~~~~~~~~~~~RPvpL~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~LVF~~sR~~~~~  332 (1724)
T 4f92_B          253 TLPNYEDVATFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKRFQIMNEIVYEKIMEHAGKNQVLVFVHSRKETGK  332 (1724)
T ss_dssp             SCTTHHHHHHHTTCCHHHHEEECCGGGCSSCEEEECCEECCCCHHHHHHHHHHHHHHHHTTCCSSCCEEEECSSTTTTHH
T ss_pred             ccCCHHHHHHHhCCCCCCCeEEECCCCccCccEEEEeccCCcchhhhhHHHHHHHHHHHHHHhcCCcEEEECCCHHHHHH
Confidence                      00                                        00000 1122356789999999999999


Q ss_pred             HHHHHhhC-------------------------------------CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc
Q psy14082        122 ITRALRRE-------------------------------------RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD  164 (233)
Q Consensus       122 l~~~L~~~-------------------------------------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~  164 (233)
                      ++..|.+.                                     ...+.++||+|++++|..+.+.|++|.++|||||+
T Consensus       333 ~A~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Gva~HHagL~~~~R~~vE~~F~~G~i~vlvaTs  412 (1724)
T 4f92_B          333 TARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHAGMTRVDRTLVEDLFADKHIQVLVSTA  412 (1724)
T ss_dssp             HHHHHHHHHHHTTSTTCCSSCCTTCSSHHHHTTSCCSTHHHHHHTTTTEEEECSSSCTHHHHHHHHHHHTTCCCEEEECH
T ss_pred             HHHHHHHHHhhccchhhhcccchhHHHHHHhhhcccccHHHHHHhhcCEEEEcCCCCHHHHHHHHHHHHCCCCeEEEEcc
Confidence            88887531                                     12478899999999999999999999999999999


Q ss_pred             cCcCCcCCCCccEEEE
Q psy14082        165 VAARGLDVEDVNTVNI  180 (233)
Q Consensus       165 ~~~~Gldi~~v~~VI~  180 (233)
                      .+++|+|+|++++||.
T Consensus       413 TLa~GVNlPa~~vVI~  428 (1724)
T 4f92_B          413 TLAWGVNLPAHTVIIK  428 (1724)
T ss_dssp             HHHHHSCCCBSEEEEE
T ss_pred             hhHhhCCCCCceEEEe
Confidence            9999999999999995

>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=99.91  E-value=5.7e-24  Score=209.52  Aligned_cols=168  Identities=15%  Similarity=0.116  Sum_probs=134.5

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh-h--cCCcEEEEEcCCCC-
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF-S--SALRNICIFGGTPK-   82 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~-~--~~~~~~~~~gg~~~-   82 (233)
                      .+.+++++||||||||++|.+|+++.+.+.      ++.++||++|+|+||.|.++.+.+. .  .++++..++|+... 
T Consensus       941 ~~~nvlv~APTGSGKTliaelail~~l~~~------~~~kavyi~P~raLa~q~~~~~~~~f~~~~g~~V~~ltGd~~~~ 1014 (1724)
T 4f92_B          941 SDDNVFVGAPTGSGKTICAEFAILRMLLQS------SEGRCVYITPMEALAEQVYMDWYEKFQDRLNKKVVLLTGETSTD 1014 (1724)
T ss_dssp             CCSCEEEECCTTSCCHHHHHHHHHHHHHHC------TTCCEEEECSCHHHHHHHHHHHHHHHTTTSCCCEEECCSCHHHH
T ss_pred             CCCcEEEEeCCCCCchHHHHHHHHHHHHhC------CCCEEEEEcChHHHHHHHHHHHHHHhchhcCCEEEEEECCCCcc
Confidence            467799999999999999999999999764      4668999999999999999999875 2  46789999998653 


Q ss_pred             -----CCeeEEe--------ccc-----------------------------------hh--------------------
Q psy14082         83 -----GPQDCLP--------LHR-----------------------------------FV--------------------   94 (233)
Q Consensus        83 -----~~~~lv~--------l~r-----------------------------------~~--------------------   94 (233)
                           +.+++|+        +++                                   +.                    
T Consensus      1015 ~~~~~~~~IiV~TPEkld~llr~~~~~~~l~~v~lvViDE~H~l~d~rg~~le~il~rl~~i~~~~~~~~riI~lSATl~ 1094 (1724)
T 4f92_B         1015 LKLLGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLIGGENGPVLEVICSRMRYISSQIERPIRIVALSSSLS 1094 (1724)
T ss_dssp             HHHHHHCSEEEECHHHHHHHHTTTTTCHHHHSCSEEEECCGGGGGSTTHHHHHHHHHHHHHHHHTTSSCCEEEEEESCBT
T ss_pred             hhhcCCCCEEEECHHHHHHHHhCcccccccceeeEEEeechhhcCCCCCccHHHHHHHHHHHHhhcCCCceEEEEeCCCC
Confidence                 3456666        000                                   00                    


Q ss_pred             ---------------------------------------------hhch----HHHhcCCCCeEEEEecchhHHHHHHHH
Q psy14082         95 ---------------------------------------------FNCQ----YEMAKNPAFKVIVFVETKKKVEDITRA  125 (233)
Q Consensus        95 ---------------------------------------------~~~~----~~~~~~~~~k~iIf~~~~~~~~~l~~~  125 (233)
                                                                   .+..    .......++++||||++++.++.++..
T Consensus      1095 N~~dla~WL~~~~~~~~~~~~~~RPvpL~~~i~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~lVF~~sR~~~~~~A~~ 1174 (1724)
T 4f92_B         1095 NAKDVAHWLGCSATSTFNFHPNVRPVPLELHIQGFNISHTQTRLLSMAKPVYHAITKHSPKKPVIVFVPSRKQTRLTAID 1174 (1724)
T ss_dssp             THHHHHHHHTCCSTTEEECCGGGCSSCEEEEEEEECCCSHHHHHHTTHHHHHHHHHHHCSSSCEEEEESSHHHHHHHHHH
T ss_pred             CHHHHHHHhCCCCCCeEEeCCCCCCCCeEEEEEeccCCCchhhhhhhcchHHHHHHHhcCCCCeeeeCCCHHHHHHHHHH
Confidence                                                         0000    012345678999999999999998877


Q ss_pred             HhhC----------------------------------CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcC
Q psy14082        126 LRRE----------------------------------RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLD  171 (233)
Q Consensus       126 L~~~----------------------------------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gld  171 (233)
                      |...                                  ...+.++||+|++.+|..+.+.|++|.++|||||+.+++|+|
T Consensus      1175 L~~~~~~~~~~~~~~~~~~~~l~~~l~~~~d~~L~~~l~~GIa~hHagL~~~~R~~VE~lF~~G~i~VLvaT~tlA~GVn 1254 (1724)
T 4f92_B         1175 ILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYLHEGLSPMERRLVEQLFSSGAIQVVVASRSLCWGMN 1254 (1724)
T ss_dssp             HHHHHHHTTCTTTTBCSCHHHHHHHHTTCCCHHHHHHHHTTEEEECTTSCHHHHHHHHHHHHHTSBCEEEEEGGGSSSCC
T ss_pred             HHHHHhhccchhhhhcccHHHHHHHHhhcccHHHHHHHhCCEEEECCCCCHHHHHHHHHHHHCCCCeEEEEChHHHcCCC
Confidence            7421                                  124788999999999999999999999999999999999999


Q ss_pred             CCCccEEEE
Q psy14082        172 VEDVNTVNI  180 (233)
Q Consensus       172 i~~v~~VI~  180 (233)
                      +|+..+||.
T Consensus      1255 lPa~~VVI~ 1263 (1724)
T 4f92_B         1255 VAAHLVIIM 1263 (1724)
T ss_dssp             CCBSEEEEE
T ss_pred             CCccEEEEe
Confidence            999999983

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.90  E-value=9.4e-24  Score=190.60  Aligned_cols=95  Identities=16%  Similarity=0.221  Sum_probs=81.0

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCCC--------eeEEEeCCCCHHHHHHHHHHhhCCCCC---EEEecccCcCCcCC
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRERH--------SAICIHGDKTQQDRDYVLNDFRQGKAP---ILVATDVAARGLDV  172 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~~--------~~~~~~~~~~~~~r~~~~~~f~~g~~~---iLv~T~~~~~Gldi  172 (233)
                      ...+|+||||+++++++.+++.|.+.+.        .+..+||+++. +|.+++++|++|+.+   |||||+++++|+|+
T Consensus       437 ~~~~k~lVF~~~~~~a~~l~~~L~~~~~~~~~~~~~~~~~i~g~~~~-~r~~~l~~F~~~~~~~~~ilvtt~~l~~GiDi  515 (590)
T 3h1t_A          437 DRFAKTIVFCVDQEHADEMRRALNNLNSDLSRKHPDYVARVTSEEGK-IGKGHLSRFQELETSTPVILTTSQLLTTGVDA  515 (590)
T ss_dssp             CTTSEEEEEESSHHHHHHHHHHHHHHTHHHHTTCTTSEEECSSTTHH-HHHHHHHHHHCTTCCCCCEEEESSTTTTTCCC
T ss_pred             CCCccEEEEECCHHHHHHHHHHHHHhhhhhhccCCCeEEEEeCCChH-HHHHHHHHHhCCCCCCCEEEEECChhhcCccc
Confidence            4568999999999999999999987543        26788998764 799999999998866   89999999999999


Q ss_pred             CCccEEEEecCCCCccccc---ceeeEEee
Q psy14082        173 EDVNTVNIGSLQLSANHNI---SQVIEVVQ  199 (233)
Q Consensus       173 ~~v~~VI~~d~P~~~~~~i---~~~~~~~~  199 (233)
                      |++++||++++|.|...|+   ||+.+...
T Consensus       516 p~v~~Vi~~~~~~s~~~~~Q~iGR~~R~~~  545 (590)
T 3h1t_A          516 PTCKNVVLARVVNSMSEFKQIVGRGTRLRE  545 (590)
T ss_dssp             TTEEEEEEESCCCCHHHHHHHHTTSCCCBG
T ss_pred             hheeEEEEEecCCChHHHHHHHhhhcccCc
Confidence            9999999999999998544   66666553

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=99.89  E-value=1.9e-22  Score=153.18  Aligned_cols=120  Identities=33%  Similarity=0.458  Sum_probs=105.9

Q ss_pred             HhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEE
Q psy14082        101 MAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNI  180 (233)
Q Consensus       101 ~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~  180 (233)
                      +......++||||++++.++.+++.|.+.|+.+..+||+|++.+|..++++|++|+.++||||+++++|+|+|++++||+
T Consensus        30 l~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gld~~~~~~Vi~  109 (163)
T 2hjv_A           30 LMTENPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVIN  109 (163)
T ss_dssp             HHHHCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECGGGTTTCCCSCCSEEEE
T ss_pred             HHhcCCCcEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEECChhhcCCchhcCCEEEE
Confidence            33456679999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCccccc------------ceeeEEeecchHHHHHHHHHHhhcCcccccc
Q psy14082        181 GSLQLSANHNI------------SQVIEVVQDYEKEKRLFSLIRELGKYTLITQ  222 (233)
Q Consensus       181 ~d~P~~~~~~i------------~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~  222 (233)
                      ||+|+++..|+            |.++.++.+.+  ...++.+++..+.+++..
T Consensus       110 ~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~--~~~~~~i~~~~~~~~~~~  161 (163)
T 2hjv_A          110 YDLPLEKESYVHRTGRTGRAGNKGKAISFVTAFE--KRFLADIEEYIGFEIQKI  161 (163)
T ss_dssp             SSCCSSHHHHHHHTTTSSCTTCCEEEEEEECGGG--HHHHHHHHHHHTSCCEEC
T ss_pred             eCCCCCHHHHHHhccccCcCCCCceEEEEecHHH--HHHHHHHHHHHCCCcCcc
Confidence            99999998665            46777888654  778888888776666543

>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=99.88  E-value=2.1e-23  Score=192.97  Aligned_cols=81  Identities=14%  Similarity=0.253  Sum_probs=76.1

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhh-----------CCCeeEEEeCCCCHHHHHHHHHHhh-----CCCCCEEEecccC
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRR-----------ERHSAICIHGDKTQQDRDYVLNDFR-----QGKAPILVATDVA  166 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~-----------~~~~~~~~~~~~~~~~r~~~~~~f~-----~g~~~iLv~T~~~  166 (233)
                      ....+++||||++++.++.++..|.+           .++.+..+||+|++++|..+++.|+     +|..+|||||+++
T Consensus       300 ~~~~g~iLVF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~~~eR~~v~~~f~~~~~~~g~~kVlVAT~ia  379 (773)
T 2xau_A          300 TEEAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNGRPGRKVVISTNIA  379 (773)
T ss_dssp             HSCSCEEEEECSCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECTTCCHHHHGGGGSCCCCCSSSSCCEEEEEECTHH
T ss_pred             hcCCCCEEEECCCHHHHHHHHHHHHHHHHhhcccccCCCeEEEEeCCCCCHHHHHHHHhhcccccCCCCceEEEEeCcHH
Confidence            34678999999999999999999975           5788999999999999999999999     9999999999999


Q ss_pred             cCCcCCCCccEEEEecC
Q psy14082        167 ARGLDVEDVNTVNIGSL  183 (233)
Q Consensus       167 ~~Gldi~~v~~VI~~d~  183 (233)
                      ++|+|+|++++||++|+
T Consensus       380 e~GidIp~v~~VId~g~  396 (773)
T 2xau_A          380 ETSLTIDGIVYVVDPGF  396 (773)
T ss_dssp             HHTCCCTTEEEEEECSE
T ss_pred             HhCcCcCCeEEEEeCCC
Confidence            99999999999999888

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19

Probab=99.88  E-value=6.2e-22  Score=151.73  Aligned_cols=123  Identities=20%  Similarity=0.294  Sum_probs=105.9

Q ss_pred             HHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEE
Q psy14082        100 EMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVN  179 (233)
Q Consensus       100 ~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI  179 (233)
                      ++......++||||++++.++.++..|.+.|+.+..+||+|++.+|..++++|++|+.++||||+++++|+|+|++++||
T Consensus        25 ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldi~~~~~Vi  104 (172)
T 1t5i_A           25 LLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAF  104 (172)
T ss_dssp             HHHHSCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSCCSTTCCGGGCSEEE
T ss_pred             HHHhCCCCcEEEEECCHHHHHHHHHHHHhcCCCEEEEECCCCHHHHHHHHHHHHCCCCcEEEECCchhcCcchhhCCEEE
Confidence            34455678999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCccccc------------ceeeEEeecchHHHHHHHHHHhhcCccccccc
Q psy14082        180 IGSLQLSANHNI------------SQVIEVVQDYEKEKRLFSLIRELGKYTLITQE  223 (233)
Q Consensus       180 ~~d~P~~~~~~i------------~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~  223 (233)
                      +||+|++...|+            |.++.++++. ++...++.+++..+.+++..+
T Consensus       105 ~~d~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~  159 (172)
T 1t5i_A          105 NYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDE-NDAKILNDVQDRFEVNISELP  159 (172)
T ss_dssp             ESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSH-HHHHHHHHHHHHHCCCEEECC
T ss_pred             EECCCCCHHHHHHHhcccccCCCCcEEEEEEcCh-hHHHHHHHHHHHHhcchhhCC
Confidence            999999998666            4577777753 345677777776666554443

>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=99.88  E-value=1.1e-21  Score=185.77  Aligned_cols=110  Identities=15%  Similarity=0.204  Sum_probs=94.3

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhh-CCCeeEEEeCCCCHHHHHHHHHHhhCCC--CCEEEecccCcCCcCCCCccEEEE
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRR-ERHSAICIHGDKTQQDRDYVLNDFRQGK--APILVATDVAARGLDVEDVNTVNI  180 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~-~~~~~~~~~~~~~~~~r~~~~~~f~~g~--~~iLv~T~~~~~Gldi~~v~~VI~  180 (233)
                      ..+.++||||+++..++.++..|.+ .|+++..+||+|++.+|..++++|++|+  .+|||||+++++|+|+|++++||+
T Consensus       501 ~~~~k~iVF~~~~~~~~~l~~~L~~~~g~~~~~lhG~~~~~~R~~~l~~F~~g~~~~~vLvaT~v~~~GlDl~~~~~VI~  580 (968)
T 3dmq_A          501 HRSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEIGSEGRNFQFASHMVM  580 (968)
T ss_dssp             TSSSCCCEECSSTHHHHHHHHHHHTTTCCCEEEECTTSCTTHHHHHHHHHHSTTSSCEEEECSCCTTCSSCCTTCCEEEC
T ss_pred             CCCCCEEEEeCcHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhCCCCcccEEEecchhhcCCCcccCcEEEE
Confidence            4578999999999999999999985 6999999999999999999999999998  999999999999999999999999


Q ss_pred             ecCCCCccccc---ce-----------eeEEeecchHHHHHHHHHHh
Q psy14082        181 GSLQLSANHNI---SQ-----------VIEVVQDYEKEKRLFSLIRE  213 (233)
Q Consensus       181 ~d~P~~~~~~i---~~-----------~~~~~~~~~~~~~~~~~i~~  213 (233)
                      ||+|+++..|+   ||           ++.++.+...+.++++.+.+
T Consensus       581 ~d~p~~~~~~~Q~~GR~~R~Gq~~~v~v~~~~~~~t~ee~i~~~~~~  627 (968)
T 3dmq_A          581 FDLPFNPDLLEQRIGRLDRIGQAHDIQIHVPYLEKTAQSVLVRWYHE  627 (968)
T ss_dssp             SSCCSSHHHHHHHHHTTSCSSSCSCCEEEEEEETTSHHHHHHHHHHH
T ss_pred             ecCCCCHHHHHHHhhccccCCCCceEEEEEecCCChHHHHHHHHHHh
Confidence            99999997555   22           33444554555666666654

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=99.88  E-value=2.2e-21  Score=147.62  Aligned_cols=122  Identities=26%  Similarity=0.410  Sum_probs=105.4

Q ss_pred             HHHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEE
Q psy14082         99 YEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTV  178 (233)
Q Consensus        99 ~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~V  178 (233)
                      +.+......++||||++++.++.++..|.+.++.+..+||+|++.+|..+++.|++|+.++||||+++++|+|+|++++|
T Consensus        23 ~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~G~d~~~~~~V  102 (165)
T 1fuk_A           23 DLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLV  102 (165)
T ss_dssp             HHHHHTTCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGGGTTTCCCCSCSEE
T ss_pred             HHHHhCCCCCEEEEECCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEEcChhhcCCCcccCCEE
Confidence            34445577899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEecCCCCccccc------------ceeeEEeecchHHHHHHHHHHhhcCcccccc
Q psy14082        179 NIGSLQLSANHNI------------SQVIEVVQDYEKEKRLFSLIRELGKYTLITQ  222 (233)
Q Consensus       179 I~~d~P~~~~~~i------------~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~  222 (233)
                      |+||+|.+...|+            |.++.++++.+  ...+..+++..+.+++..
T Consensus       103 i~~~~p~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~--~~~~~~~~~~~~~~~~~~  156 (165)
T 1fuk_A          103 INYDLPANKENYIHRIGRGGRFGRKGVAINFVTNED--VGAMRELEKFYSTQIEEL  156 (165)
T ss_dssp             EESSCCSSGGGGGGSSCSCC-----CEEEEEEETTT--HHHHHHHHHHSSCCCEEC
T ss_pred             EEeCCCCCHHHHHHHhcccccCCCCceEEEEEcchH--HHHHHHHHHHHccCcccc
Confidence            9999999998666            35566777544  666777877766655443

>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=99.87  E-value=4.8e-21  Score=169.49  Aligned_cols=109  Identities=14%  Similarity=0.197  Sum_probs=90.7

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhC-CCeeEEEeCCCCHHHHHHHHHHhhCC-CCC-EEEecccCcCCcCCCCccEEEEe
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRE-RHSAICIHGDKTQQDRDYVLNDFRQG-KAP-ILVATDVAARGLDVEDVNTVNIG  181 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~-~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~-iLv~T~~~~~Gldi~~v~~VI~~  181 (233)
                      .+.++||||+++..++.+...|.+. |..+..+||+|+.++|.+++++|+++ ..+ +|++|+++++|+|++++++||+|
T Consensus       340 ~~~k~lvF~~~~~~~~~l~~~l~~~~~~~~~~~~g~~~~~~R~~~~~~F~~~~~~~vil~st~~~~~Glnl~~~~~vi~~  419 (500)
T 1z63_A          340 EGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIHF  419 (500)
T ss_dssp             TTCCEEEECSCHHHHHHHHHHHHHHHTCCCCEEETTSCHHHHHHHHHHHHHCTTCCCCEEECCCC-CCCCCTTCSEEEES
T ss_pred             cCCcEEEEEehHHHHHHHHHHHHHhhCCCeEEEECCCCHHHHHHHHHHhcCCCCCCEEEEecccccCCCchhhCCEEEEe
Confidence            5779999999999999999999875 99999999999999999999999998 455 78999999999999999999999


Q ss_pred             cCCCCccccc---c-----------eeeEEeecchHHHHHHHHHHh
Q psy14082        182 SLQLSANHNI---S-----------QVIEVVQDYEKEKRLFSLIRE  213 (233)
Q Consensus       182 d~P~~~~~~i---~-----------~~~~~~~~~~~~~~~~~~i~~  213 (233)
                      |+|+|+..++   |           .+.+++.+..-++++++.+++
T Consensus       420 d~~~~~~~~~Q~~gR~~R~Gq~~~v~v~~lv~~~tiee~i~~~~~~  465 (500)
T 1z63_A          420 DRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEEKIDQLLAF  465 (500)
T ss_dssp             SCCSCC---CHHHHTTTTTTTTSCEEEEEEEETTSHHHHTHHHHTT
T ss_pred             CCCCCcchHHHHHHHHHHcCCCCeeEEEEEEeCCCHHHHHHHHHHH
Confidence            9999997554   2           346677665555677776655

>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=99.87  E-value=1.6e-21  Score=154.41  Aligned_cols=123  Identities=33%  Similarity=0.397  Sum_probs=106.3

Q ss_pred             chHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCcc
Q psy14082         97 CQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVN  176 (233)
Q Consensus        97 ~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~  176 (233)
                      +.+.+....+.++||||++++.++.++..|.+.|+.+..+||+|++.+|..+++.|++|+.+|||||+++++|+|+|+++
T Consensus        22 l~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~~~~~Gidi~~v~  101 (212)
T 3eaq_A           22 LSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAARGLDIPQVD  101 (212)
T ss_dssp             HHHHHHHHCCSCEEEECSSHHHHHHHHHHHHHHTCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECTTTTCSSSCCCBS
T ss_pred             HHHHHHhCCCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecChhhcCCCCccCc
Confidence            33344455678999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEecCCCCccccc------------ceeeEEeecchHHHHHHHHHHhhcCccccc
Q psy14082        177 TVNIGSLQLSANHNI------------SQVIEVVQDYEKEKRLFSLIRELGKYTLIT  221 (233)
Q Consensus       177 ~VI~~d~P~~~~~~i------------~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~  221 (233)
                      +||+||+|.+...|+            |.++.++++.+  ...++.+++..+..+..
T Consensus       102 ~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~l~~~~~--~~~~~~i~~~~~~~~~~  156 (212)
T 3eaq_A          102 LVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRE--RRDVEALERAVGRRFKR  156 (212)
T ss_dssp             EEEESSCCSSHHHHHHHHTTBCCCC--BEEEEEECGGG--HHHHHHHHHHHSSCCEE
T ss_pred             EEEECCCCcCHHHHHHHhcccCCCCCCCeEEEEEchhH--HHHHHHHHHHhcCcCee
Confidence            999999999998666            46677887654  77777888766554443

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens}

Probab=99.87  E-value=2.6e-21  Score=148.56  Aligned_cols=121  Identities=21%  Similarity=0.302  Sum_probs=102.5

Q ss_pred             HHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEE
Q psy14082        100 EMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVN  179 (233)
Q Consensus       100 ~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI  179 (233)
                      .+......++||||++++.++.++..|.+.|+.+..+||+|++.+|..+++.|++|+.++||||+++++|+|+|++++||
T Consensus        28 ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~~~~~Gid~~~~~~Vi  107 (175)
T 2rb4_A           28 IYGSITIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVV  107 (175)
T ss_dssp             HHTTSCCSEEEEECSCHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECCSCCTTTCCTTEEEEE
T ss_pred             HHHhCCCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEecchhcCCCcccCCEEE
Confidence            33445678999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCC------CCccccc------------ceeeEEeecchHHHHHHHHHHhhcCcccccc
Q psy14082        180 IGSLQ------LSANHNI------------SQVIEVVQDYEKEKRLFSLIRELGKYTLITQ  222 (233)
Q Consensus       180 ~~d~P------~~~~~~i------------~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~  222 (233)
                      +||+|      .+...|+            |.++.++++.+  ...+..+++..+..++..
T Consensus       108 ~~d~p~~~~~~~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~--~~~~~~i~~~~~~~~~~~  166 (175)
T 2rb4_A          108 NFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDE--LPSLMKIQDHFNSSIKQL  166 (175)
T ss_dssp             ESSCCC--CCSCCHHHHHHHHCBC----CCEEEEEEECGGG--HHHHHHHHHHHTCCCEEE
T ss_pred             EeCCCCCccccCCHHHHHHHhcccccCCCCceEEEEEccch--HHHHHHHHHHhcCccccc
Confidence            99999      7776555            34566777544  666777777655554433

>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=99.87  E-value=4.4e-21  Score=172.53  Aligned_cols=98  Identities=15%  Similarity=0.147  Sum_probs=83.0

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCC--------Ccc
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVE--------DVN  176 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~--------~v~  176 (233)
                      .+.++||||+|++.++.++..|.+.|+++.++||++.+.++..+.++|+.|  .|+||||+++||+|++        +..
T Consensus       473 ~gqpVLVFt~S~e~sE~Ls~~L~~~Gi~~~vLhgkq~~rE~~ii~~ag~~g--~VtVATdmAgRGtDI~lg~~V~~~Ggl  550 (822)
T 3jux_A          473 KGQPVLVGTTSIEKSELLSSMLKKKGIPHQVLNAKYHEKEAEIVAKAGQKG--MVTIATNMAGRGTDIKLGPGVAELGGL  550 (822)
T ss_dssp             HTCCEEEEESSHHHHHHHHHHHHTTTCCCEEECSCHHHHHHHHHHHHHSTT--CEEEEETTTTTTCCCCCCTTTTTTTSC
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCchHHHHHHHHhCCCCC--eEEEEcchhhCCcCccCCcchhhcCCC
Confidence            578999999999999999999999999999999996666666666666655  6999999999999998        667


Q ss_pred             EEEEecCCCCccccc------------ceeeEEeecchHH
Q psy14082        177 TVNIGSLQLSANHNI------------SQVIEVVQDYEKE  204 (233)
Q Consensus       177 ~VI~~d~P~~~~~~i------------~~~~~~~~~~~~~  204 (233)
                      +||||++|.|...|+            |.++.|++..+..
T Consensus       551 hVInte~Pes~r~y~qriGRTGRqG~~G~a~~fvsleD~l  590 (822)
T 3jux_A          551 CIIGTERHESRRIDNQLRGRAGRQGDPGESIFFLSLEDDL  590 (822)
T ss_dssp             EEEESSCCSSHHHHHHHHTTSSCSSCCCEEEEEEETTSHH
T ss_pred             EEEecCCCCCHHHHHHhhCccccCCCCeeEEEEechhHHH
Confidence            999999999998665            4666788775533

>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=99.84  E-value=5.4e-21  Score=148.18  Aligned_cols=124  Identities=35%  Similarity=0.447  Sum_probs=87.7

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQ  184 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P  184 (233)
                      .+.++||||++++.++.++..|...|+.+..+||+|++.+|..++++|++|+.++||||+++++|+|+|++++||+||+|
T Consensus        45 ~~~k~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldi~~~~~VI~~d~p  124 (185)
T 2jgn_A           45 KDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLP  124 (185)
T ss_dssp             CCSCEEEEESCHHHHHHHHHHHHHTTCCEEEEC--------CHHHHHHHHTSSSEEEEEC------CCCSBSEEEESSCC
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHHcCCceEEEeCCCCHHHHHHHHHHHHcCCCeEEEEcChhhcCCCcccCCEEEEeCCC
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCccccc------------ceeeEEeecchHHHHHHHHHHhhcCcccccccchhhHhhhc
Q psy14082        185 LSANHNI------------SQVIEVVQDYEKEKRLFSLIRELGKYTLITQESSSTLSEMV  232 (233)
Q Consensus       185 ~~~~~~i------------~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~l~  232 (233)
                      ++...|+            |.++.++++.+  ...++.+++..+..  .++.+..+.++|
T Consensus       125 ~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~--~~~~~~l~~~l~~~--~~~~~~~l~~~a  180 (185)
T 2jgn_A          125 SDIEEYVHRIGRTGRVGNLGLATSFFNERN--INITKDLLDLLVEA--KQEVPSWLENMA  180 (185)
T ss_dssp             SSHHHHHHHHTTBCCTTSCEEEEEEECGGG--GGGHHHHHHHHHHT--TCCCCHHHHHHH
T ss_pred             CCHHHHHHHccccCCCCCCcEEEEEEchhh--HHHHHHHHHHHHhc--cCCCCHHHHHHH
Confidence            9998666            46677887644  34444444433221  233344455443

>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=99.84  E-value=1.7e-19  Score=164.30  Aligned_cols=109  Identities=11%  Similarity=0.214  Sum_probs=95.2

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCC---EEEecccCcCCcCCCCccEEEEe
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAP---ILVATDVAARGLDVEDVNTVNIG  181 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~---iLv~T~~~~~Gldi~~v~~VI~~  181 (233)
                      .+.|+|||++.+..++.+...|...|+.+..+||+|+.++|.+++++|++++..   +|++|+++++|+|++++++||+|
T Consensus       415 ~~~k~lIFs~~~~~~~~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~v~L~st~a~g~Glnl~~a~~Vi~~  494 (644)
T 1z3i_X          415 TSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLVMF  494 (644)
T ss_dssp             CCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGGGSCTTCCCTTEEEEEEC
T ss_pred             CCCEEEEEEccHHHHHHHHHHHHHCCCCEEEEeCCCCHHHHHHHHHHhcCCCCCcEEEEEecccccCCcccccCCEEEEE
Confidence            468999999999999999999999999999999999999999999999998764   89999999999999999999999


Q ss_pred             cCCCCcc---------cccc-----eeeEEeecchHHHHHHHHHHh
Q psy14082        182 SLQLSAN---------HNIS-----QVIEVVQDYEKEKRLFSLIRE  213 (233)
Q Consensus       182 d~P~~~~---------~~i~-----~~~~~~~~~~~~~~~~~~i~~  213 (233)
                      |+|+|+.         +|+|     .+.+++....-++++++..++
T Consensus       495 d~~wnp~~~~Qa~gR~~R~Gq~~~v~v~~lv~~~tiEe~i~~~~~~  540 (644)
T 1z3i_X          495 DPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTGTIEEKILQRQAH  540 (644)
T ss_dssp             SCCSSHHHHHHHHTTSSSTTCCSCEEEEEEEETTSHHHHHHHHHHH
T ss_pred             CCCCCccHHHHHHHhhhhcCCCCceEEEEEEECCCHHHHHHHHHHH
Confidence            9999986         3333     456677766556777776655

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=99.84  E-value=1.5e-20  Score=155.99  Aligned_cols=121  Identities=31%  Similarity=0.403  Sum_probs=105.7

Q ss_pred             HHHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEE
Q psy14082         99 YEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTV  178 (233)
Q Consensus        99 ~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~V  178 (233)
                      +.+....+.++||||++++.++.++..|.+.++.+..+||+|++.+|..+++.|++|+.+|||||+++++|+|+|++++|
T Consensus        21 ~ll~~~~~~~~LVF~~t~~~~~~l~~~L~~~g~~~~~lhg~l~~~~r~~~~~~f~~g~~~vLVaT~va~~Gidi~~v~~V  100 (300)
T 3i32_A           21 DLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLV  100 (300)
T ss_dssp             HHHHHHCCSSEEEECSSHHHHHHHHHHHHTTTCCEEEECSCCCTHHHHHHHHHHHHTSCCEEEECSTTTCSTTCCCCSEE
T ss_pred             HHHHhcCCCCEEEEECCHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhcCCceEEEEechhhcCccccceeEE
Confidence            34444558899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEecCCCCccccc------------ceeeEEeecchHHHHHHHHHHhhcCccccc
Q psy14082        179 NIGSLQLSANHNI------------SQVIEVVQDYEKEKRLFSLIRELGKYTLIT  221 (233)
Q Consensus       179 I~~d~P~~~~~~i------------~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~  221 (233)
                      |+||+|.+...|+            |.++.++++.+  ...++.+++..+..+..
T Consensus       101 I~~d~p~s~~~y~Qr~GRagR~g~~G~~i~l~~~~e--~~~~~~ie~~~~~~~~~  153 (300)
T 3i32_A          101 VHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRE--RRDVEALERAVGRRFKR  153 (300)
T ss_dssp             EESSCCSSTTHHHHHHTCCC-----CEEEEEECSST--HHHHHHHHHHHTCCCEE
T ss_pred             EEcCCCCCHHHHHHHccCcCcCCCCceEEEEeChHH--HHHHHHHHHHhCCcceE
Confidence            9999999998666            46667887655  67778888766555443

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=99.84  E-value=8.9e-21  Score=147.69  Aligned_cols=124  Identities=26%  Similarity=0.375  Sum_probs=100.6

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQ  184 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P  184 (233)
                      .+.++||||++++.++.++..|.+.|+.+..+||+|++.+|..++++|++|+.+|||||+++++|+|+|++++||+||+|
T Consensus        53 ~~~~~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~~~~~Gldi~~v~~VI~~d~p  132 (191)
T 2p6n_A           53 TPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMP  132 (191)
T ss_dssp             SCSCEEEECSCHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHHTSCSEEEECHHHHTTCCCCCCSEEEESSCC
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEcCchhcCCCcccCCEEEEeCCC
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCccccc------------ceeeEEeecchHHHHHHHHHHhhcCcccccccchhhHhhh
Q psy14082        185 LSANHNI------------SQVIEVVQDYEKEKRLFSLIRELGKYTLITQESSSTLSEM  231 (233)
Q Consensus       185 ~~~~~~i------------~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~l  231 (233)
                      .+...|+            |.++.|+++.+ +....+.+++....  ..++.|..+.++
T Consensus       133 ~~~~~~~qr~GR~gR~g~~g~~i~l~~~~~-~~~~~~~l~~~l~~--~~~~~p~~l~~~  188 (191)
T 2p6n_A          133 EEIENYVHRIGRTGCSGNTGIATTFINKAC-DESVLMDLKALLLE--AKQKVPPVLQVL  188 (191)
T ss_dssp             SSHHHHHHHHTTSCC---CCEEEEEECTTS-CHHHHHHHHHHHHH--TTCCCCHHHHST
T ss_pred             CCHHHHHHHhCccccCCCCcEEEEEEcCch-hHHHHHHHHHHHHH--ccCcCCHHHHhh
Confidence            9988666            45667787542 23444445443211  123344445554

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=99.83  E-value=2.2e-19  Score=167.17  Aligned_cols=111  Identities=16%  Similarity=0.262  Sum_probs=96.7

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCC---EEEecccCcCCcCCCCccEEEE
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAP---ILVATDVAARGLDVEDVNTVNI  180 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~---iLv~T~~~~~Gldi~~v~~VI~  180 (233)
                      ..+.|+|||+.....++.+...|...|+.+..+||+++..+|..++++|+++..+   +|++|+++++|+|++.+++||+
T Consensus       570 ~~g~kvLIFsq~~~~ld~L~~~L~~~g~~~~~i~G~~~~~eR~~~i~~F~~~~~~~~v~LlSt~agg~GlNL~~a~~VI~  649 (800)
T 3mwy_W          570 KDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRAGGLGINLMTADTVVI  649 (800)
T ss_dssp             TTTCCEEEEESCHHHHHHHHHHHHHHTCCCEEESTTSCHHHHHHHHHTTSSTTCSCCCEEEEHHHHTTTCCCTTCCEEEE
T ss_pred             hCCCeEEEEechHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhCCCCCceEEEEecccccCCCCccccceEEE
Confidence            3567999999999999999999999999999999999999999999999987654   9999999999999999999999


Q ss_pred             ecCCCCcc---------cccc-----eeeEEeecchHHHHHHHHHHhh
Q psy14082        181 GSLQLSAN---------HNIS-----QVIEVVQDYEKEKRLFSLIREL  214 (233)
Q Consensus       181 ~d~P~~~~---------~~i~-----~~~~~~~~~~~~~~~~~~i~~~  214 (233)
                      ||+|+|+.         +|+|     .+.+++....-++++++..++-
T Consensus       650 ~D~~wnp~~~~Qa~gR~~RiGQ~k~V~Vyrlv~~~TiEe~i~~~~~~K  697 (800)
T 3mwy_W          650 FDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTVEEEVLERARKK  697 (800)
T ss_dssp             SSCCSCSHHHHHHHTTTSCSSCCSCEEEEEEEETTSHHHHHHHHHHHH
T ss_pred             ecCCCChhhHHHHHHHHHhcCCCceEEEEEEecCCCHHHHHHHHHHHH
Confidence            99999996         3333     4566777766667777777663

>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=99.70  E-value=1.4e-21  Score=149.38  Aligned_cols=91  Identities=30%  Similarity=0.471  Sum_probs=85.9

Q ss_pred             hcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEe
Q psy14082        102 AKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIG  181 (233)
Q Consensus       102 ~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~  181 (233)
                      ....+.++||||++++.++.++..|.+.++.+..+||+|++.+|..++++|++|+.++||||+++++|+|+|++++||+|
T Consensus        26 ~~~~~~~~iVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gid~~~~~~Vi~~  105 (170)
T 2yjt_D           26 KQPEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNF  105 (170)
Confidence            34566899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCcccccc
Q psy14082        182 SLQLSANHNIS  192 (233)
Q Consensus       182 d~P~~~~~~i~  192 (233)
                      |+|++...|++
T Consensus       106 ~~p~~~~~~~q  116 (170)
T 2yjt_D          106 DMPRSGDTYLH  116 (170)
Confidence            99999987773

>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=99.75  E-value=4.2e-18  Score=161.12  Aligned_cols=86  Identities=8%  Similarity=0.086  Sum_probs=69.7

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCC------------Cee-EEEeCC----------C----------CHH--------
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRER------------HSA-ICIHGD----------K----------TQQ--------  143 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~------------~~~-~~~~~~----------~----------~~~--------  143 (233)
                      .+.++||||+++.+|..++..|.+.+            +++ .++||+          +          ++.        
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            34689999999999999999997654            455 445542          2          322        


Q ss_pred             ---------------------HHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCCCCccccc
Q psy14082        144 ---------------------DRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNI  191 (233)
Q Consensus       144 ---------------------~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P~~~~~~i  191 (233)
                                           .|..++++|++|++++||+||++.+|+|+|.+ .++++|.|.+...++
T Consensus       616 I~dyn~~f~~~~~~~~~~~~~~R~~i~~~Fk~g~i~ILIvvd~lltGfDiP~l-~tlylDkpl~~~~li  683 (1038)
T 2w00_A          616 IREYNSHFKTNFSTDSNGFQNYYRDLAQRVKNQDIDLLIVVGMFLTGFDAPTL-NTLFVDKNLRYHGLM  683 (1038)
T ss_dssp             HHHHHHHHTCCCCSSHHHHHHHHHHHHHHHHTTSSSEEEESSTTSSSCCCTTE-EEEEEESCCCHHHHH
T ss_pred             HHHHHHHhcccccccchhhhHHHHHHHHHHHcCCCeEEEEcchHHhCcCcccc-cEEEEccCCCcccee
Confidence                                 47888999999999999999999999999999 678999998876444

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=99.71  E-value=5.7e-17  Score=130.42  Aligned_cols=148  Identities=32%  Similarity=0.485  Sum_probs=98.9

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~g   78 (233)
                      |||.++.|+|++++||||||||++|++|+++++...+......++++||++||++|+.|+++.++++  ..++++..++|
T Consensus        59 ~i~~~~~g~~~l~~apTGsGKT~~~~l~~l~~l~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g  138 (242)
T 3fe2_A           59 GWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYG  138 (242)
T ss_dssp             HHHHHHHTCCEEEEECTTSCHHHHHHHHHHHHHHTSCCCCTTCCCSEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEECT
T ss_pred             HHHHHhCCCCEEEECCCcCHHHHHHHHHHHHHHHhccccccCCCCEEEEEeCcHHHHHHHHHHHHHHHhhcCceEEEEEC
Confidence            3567788999999999999999999999999998765444456889999999999999999999998  45789999999


Q ss_pred             CCCC---------CCeeEEe-ccchhhhchHHHhcCCCCeEEEEecchhH-----HHHHHHHHhh--CCCeeEEEeCCCC
Q psy14082         79 GTPK---------GPQDCLP-LHRFVFNCQYEMAKNPAFKVIVFVETKKK-----VEDITRALRR--ERHSAICIHGDKT  141 (233)
Q Consensus        79 g~~~---------~~~~lv~-l~r~~~~~~~~~~~~~~~k~iIf~~~~~~-----~~~l~~~L~~--~~~~~~~~~~~~~  141 (233)
                      |.+.         ..+++|+ ..|+.+...........-+.+|+-+--..     ...+...+..  .+.....+.+-++
T Consensus       139 ~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~i~~~~~~~~q~~~~SAT~~  218 (242)
T 3fe2_A          139 GAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWP  218 (242)
T ss_dssp             TSCHHHHHHHHHHCCSEEEECHHHHHHHHHHTSCCCTTCCEEEETTHHHHHHTTCHHHHHHHHTTSCSSCEEEEEESCCC
T ss_pred             CCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCCcccccEEEEeCHHHHhhhCcHHHHHHHHHhCCccceEEEEEeecC
Confidence            9765         3466777 34444443321112223344554332111     1112222222  2345666777777


Q ss_pred             HHHHHHH
Q psy14082        142 QQDRDYV  148 (233)
Q Consensus       142 ~~~r~~~  148 (233)
                      ...+..+
T Consensus       219 ~~~~~~~  225 (242)
T 3fe2_A          219 KEVRQLA  225 (242)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            6654433

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=99.68  E-value=3.9e-17  Score=135.64  Aligned_cols=91  Identities=18%  Similarity=0.135  Sum_probs=74.3

Q ss_pred             CCCCCCCC--CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh---cCCcEEE
Q psy14082          1 MLPPSESG--CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS---SALRNIC   75 (233)
Q Consensus         1 aip~~~~g--~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~---~~~~~~~   75 (233)
                      |||.++.|  +|++++|+||||||++|++|+++++...     .+++++|||+||||||.|+++.++.+.   .++++..
T Consensus       122 ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~-----~~~~~~lil~PtreLa~Q~~~~~~~l~~~~~~~~~~~  196 (300)
T 3fmo_B          122 ALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPA-----NKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAY  196 (300)
T ss_dssp             HHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHCCTT-----SCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEE
T ss_pred             HHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhhhcc-----CCCceEEEEcCcHHHHHHHHHHHHHHHhhCCCcEEEE
Confidence            46777887  9999999999999999999999998754     457899999999999999999999983   4688999


Q ss_pred             EEcCCCCC------CeeEEe-ccchhhh
Q psy14082         76 IFGGTPKG------PQDCLP-LHRFVFN   96 (233)
Q Consensus        76 ~~gg~~~~------~~~lv~-l~r~~~~   96 (233)
                      .+||.+..      .+++|+ -.|+.+.
T Consensus       197 ~~~~~~~~~~~~~~~~IlV~TP~~l~~~  224 (300)
T 3fmo_B          197 AVRGNKLERGQKISEQIVIGTPGTVLDW  224 (300)
T ss_dssp             ESTTCCCCTTCCCCCSEEEECHHHHHHH
T ss_pred             EeCCccHhhhhcCCCCEEEECHHHHHHH
Confidence            99987643      356777 3333333

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=99.67  E-value=2.4e-16  Score=125.47  Aligned_cols=83  Identities=29%  Similarity=0.503  Sum_probs=64.2

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCC-CCCCCCceEEEEcCcHHHHHHHHHHHHHh-hcCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEP-VKQGDGPIALVLAPTRELAQQIQTVAKEF-SSALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~-~~~~~~~~~lil~PtreL~~Q~~~~~~~~-~~~~~~~~~~g   78 (233)
                      |||.++.|+|+++++|||||||++|++|++.++..... .....++++||++||++|+.|+++.++++ ..++++..++|
T Consensus        50 ~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~  129 (228)
T 3iuy_A           50 AWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPGMLVLTPTRELALHVEAECSKYSYKGLKSICIYG  129 (228)
T ss_dssp             HHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC---------CCCSEEEECSSHHHHHHHHHHHHHHCCTTCCEEEECC
T ss_pred             HHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccchhhccCCCcEEEEeCCHHHHHHHHHHHHHhcccCceEEEEEC
Confidence            35667899999999999999999999999998875421 12246789999999999999999999998 56789999999


Q ss_pred             CCCCC
Q psy14082         79 GTPKG   83 (233)
Q Consensus        79 g~~~~   83 (233)
                      |.+.+
T Consensus       130 ~~~~~  134 (228)
T 3iuy_A          130 GRNRN  134 (228)
T ss_dssp             -----
T ss_pred             CCChH
Confidence            87654

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=99.66  E-value=9.6e-16  Score=125.41  Aligned_cols=109  Identities=14%  Similarity=0.197  Sum_probs=93.1

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhC-CCeeEEEeCCCCHHHHHHHHHHhhCC-CCC-EEEecccCcCCcCCCCccEEEEe
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRE-RHSAICIHGDKTQQDRDYVLNDFRQG-KAP-ILVATDVAARGLDVEDVNTVNIG  181 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~-~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~-iLv~T~~~~~Gldi~~v~~VI~~  181 (233)
                      .+.|+||||+++..++.+...|.+. |+.+..+||++++++|.+++++|+++ +.+ +|++|+++++|+|++++++||+|
T Consensus       111 ~~~kvlIFs~~~~~~~~l~~~L~~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~v~L~st~~~g~Glnl~~a~~VI~~  190 (271)
T 1z5z_A          111 EGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIHF  190 (271)
T ss_dssp             TTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEECCTTCCCCCCTTCSEEEEC
T ss_pred             CCCeEEEEeccHHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHhcCCCCCCEEEEehhhhcCCcCcccCCEEEEE
Confidence            6789999999999999999999885 99999999999999999999999998 677 78999999999999999999999


Q ss_pred             cCCCCccccc---c-----------eeeEEeecchHHHHHHHHHHh
Q psy14082        182 SLQLSANHNI---S-----------QVIEVVQDYEKEKRLFSLIRE  213 (233)
Q Consensus       182 d~P~~~~~~i---~-----------~~~~~~~~~~~~~~~~~~i~~  213 (233)
                      |+|+++..|+   |           .+.+++....-++++++.+++
T Consensus       191 d~~wnp~~~~Q~~gR~~R~Gq~~~v~v~~li~~~TiEe~i~~~~~~  236 (271)
T 1z5z_A          191 DRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEEKIDQLLAF  236 (271)
T ss_dssp             SCCSCTTTC--------------CCEEEEEEETTSHHHHHHHHHHH
T ss_pred             CCCCChhHHHHHHHhccccCCCCceEEEEEeeCCCHHHHHHHHHHH
Confidence            9999997554   2           234566655455677776655

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19

Probab=99.64  E-value=1.6e-15  Score=122.55  Aligned_cols=153  Identities=20%  Similarity=0.262  Sum_probs=98.8

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCC----CCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEE
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPV----KQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNI   74 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~----~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~   74 (233)
                      |||.++.|+|+++++|||||||++|++|+++++......    ....++++||++||++|+.|+++.++++  ..++++.
T Consensus        53 ~i~~i~~~~~~l~~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~  132 (253)
T 1wrb_A           53 AIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSC  132 (253)
T ss_dssp             HHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEE
T ss_pred             HHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhhccccccccccCCceEEEEECCHHHHHHHHHHHHHHhccCCceEE
Confidence            356678899999999999999999999999998754211    1234679999999999999999999998  3467888


Q ss_pred             EEEcCCCC---------CCeeEEe-ccchhhhchHHHhcCCCCeEEEEecchhH-----HHHHHHHHhhC------CCee
Q psy14082         75 CIFGGTPK---------GPQDCLP-LHRFVFNCQYEMAKNPAFKVIVFVETKKK-----VEDITRALRRE------RHSA  133 (233)
Q Consensus        75 ~~~gg~~~---------~~~~lv~-l~r~~~~~~~~~~~~~~~k~iIf~~~~~~-----~~~l~~~L~~~------~~~~  133 (233)
                      .++||.+.         ..+++|+ ..++.+.+.........-+.+|+-+--..     ...+...+...      +...
T Consensus       133 ~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~i~~~~~~~~~~~~q~  212 (253)
T 1wrb_A          133 VVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEESNMPSGINRQT  212 (253)
T ss_dssp             EECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCTTCCEEEEETHHHHHHTTCHHHHHHHHHSSCCCCGGGCEE
T ss_pred             EEECCCCHHHHHHHhCCCCCEEEECHHHHHHHHHcCCCChhhCCEEEEeCHHHHHhCchHHHHHHHHhhccCCCCCCcEE
Confidence            99998764         3466777 34444333221111223345665443221     12233333321      2346


Q ss_pred             EEEeCCCCHHHHHHHHHHhhC
Q psy14082        134 ICIHGDKTQQDRDYVLNDFRQ  154 (233)
Q Consensus       134 ~~~~~~~~~~~r~~~~~~f~~  154 (233)
                      ..+++-++.+. .+..+.|-.
T Consensus       213 l~~SAT~~~~~-~~~~~~~l~  232 (253)
T 1wrb_A          213 LMFSATFPKEI-QKLAADFLY  232 (253)
T ss_dssp             EEEESSCCHHH-HHHHHHHCS
T ss_pred             EEEEEeCCHHH-HHHHHHHcC
Confidence            66777776554 344444443

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=99.64  E-value=4.5e-16  Score=125.22  Aligned_cols=148  Identities=15%  Similarity=0.148  Sum_probs=94.1

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh--cCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS--SALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~--~~~~~~~~~g   78 (233)
                      |||.++.|+|++++||||||||++|++|+++++...    ...++++||++||++|+.|+++.++++.  .++++..+.|
T Consensus        59 ~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~----~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~  134 (245)
T 3dkp_A           59 AIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQP----ANKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHK  134 (245)
T ss_dssp             HHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHCSC----CSSSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEECCCH
T ss_pred             HHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHhhc----ccCCceEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEec
Confidence            356778899999999999999999999999988643    1457799999999999999999999983  3667777776


Q ss_pred             CC----------CCCCeeEEe-ccchhhhchHH--HhcCCCCeEEEEecchhHH--------HHHHHHHhh---CCCeeE
Q psy14082         79 GT----------PKGPQDCLP-LHRFVFNCQYE--MAKNPAFKVIVFVETKKKV--------EDITRALRR---ERHSAI  134 (233)
Q Consensus        79 g~----------~~~~~~lv~-l~r~~~~~~~~--~~~~~~~k~iIf~~~~~~~--------~~l~~~L~~---~~~~~~  134 (233)
                      +.          ..+.+++|+ ..++.+.....  ......-+.+|+-+--...        +.+...+..   .+....
T Consensus       135 ~~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~~~~i~~~~~~~~~~~~  214 (245)
T 3dkp_A          135 AAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRA  214 (245)
T ss_dssp             HHHHHTTTSTTSCCCCCEEEECHHHHHHHHHSSSCSCCCTTCCEEEESSHHHHHHHC--CHHHHHHHHHHHCCCTTCEEE
T ss_pred             CccHHHHhhhhhcCCCCEEEECHHHHHHHHHhCCCCcccccCcEEEEeChHHhcccccccHHHHHHHHHHhcCCCCcEEE
Confidence            53          124467777 33333333211  0111223455554322111        122222222   345667


Q ss_pred             EEeCCCCHHHHHHHHHHhh
Q psy14082        135 CIHGDKTQQDRDYVLNDFR  153 (233)
Q Consensus       135 ~~~~~~~~~~r~~~~~~f~  153 (233)
                      .+.+-++.+-+ +..+.|.
T Consensus       215 ~~SAT~~~~v~-~~~~~~l  232 (245)
T 3dkp_A          215 MFSATFAYDVE-QWCKLNL  232 (245)
T ss_dssp             EEESSCCHHHH-HHHHHHS
T ss_pred             EEeccCCHHHH-HHHHHhC
Confidence            77777766544 3444443

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=99.64  E-value=2.5e-15  Score=117.49  Aligned_cols=76  Identities=26%  Similarity=0.386  Sum_probs=65.8

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh---cCCcEEEEEc
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS---SALRNICIFG   78 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~---~~~~~~~~~g   78 (233)
                      +|.++.|+|+++.+|||||||++|++|+++++...     ..++++||++||++|+.|+++.++++.   +++++..++|
T Consensus        34 i~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~-----~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g  108 (206)
T 1vec_A           34 IPIALSGRDILARAKNGTGKSGAYLIPLLERLDLK-----KDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTG  108 (206)
T ss_dssp             HHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTT-----SCSCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECS
T ss_pred             HHHHccCCCEEEECCCCCchHHHHHHHHHHHhccc-----CCCeeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEeC
Confidence            45677899999999999999999999999988643     356789999999999999999999983   2678888998


Q ss_pred             CCCC
Q psy14082         79 GTPK   82 (233)
Q Consensus        79 g~~~   82 (233)
                      +.+.
T Consensus       109 ~~~~  112 (206)
T 1vec_A          109 GTNL  112 (206)
T ss_dssp             SSCH
T ss_pred             CccH
Confidence            8654

>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=99.64  E-value=1.2e-15  Score=139.21  Aligned_cols=98  Identities=28%  Similarity=0.325  Sum_probs=90.3

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecC-
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSL-  183 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~-  183 (233)
                      .+.++||||+|++.++.+++.|.+.|+++..+||+|++.+|..++++|++|+.+|||||+++++|+|+|++++||++|. 
T Consensus       444 ~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~~l~~GlDip~v~lVi~~d~d  523 (661)
T 2d7d_A          444 RNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDAD  523 (661)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESCCCSTTCCCTTEEEEEETTTT
T ss_pred             cCCeEEEEECCHHHHHHHHHHHHhcCCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecchhhCCcccCCCCEEEEeCcc
Confidence            5679999999999999999999999999999999999999999999999999999999999999999999999999997 


Q ss_pred             ----CCCccccc-----------ceeeEEeecch
Q psy14082        184 ----QLSANHNI-----------SQVIEVVQDYE  202 (233)
Q Consensus       184 ----P~~~~~~i-----------~~~~~~~~~~~  202 (233)
                          |.+...|+           |.++.++++.+
T Consensus       524 ~~G~p~s~~~~iQr~GRagR~~~G~~i~~~~~~~  557 (661)
T 2d7d_A          524 KEGFLRSERSLIQTIGRAARNAEGRVIMYADKIT  557 (661)
T ss_dssp             CCTTTTSHHHHHHHHHTTTTSTTCEEEEECSSCC
T ss_pred             cccCCCCHHHHHHHhCcccCCCCCEEEEEEeCCC
Confidence                88887666           46677887644

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=99.63  E-value=1e-15  Score=122.77  Aligned_cols=148  Identities=20%  Similarity=0.189  Sum_probs=93.8

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh--cCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS--SALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~--~~~~~~~~~g   78 (233)
                      |||.++.|+|+++.+|||||||++|++|+++.+...     ..++++||++||++|+.|+++.++++.  .++++..++|
T Consensus        60 ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~~-----~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g  134 (237)
T 3bor_A           60 AIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIE-----FKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIG  134 (237)
T ss_dssp             HHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCTT-----SCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECC
T ss_pred             HHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhc-----CCCceEEEEECcHHHHHHHHHHHHHHhhhcCceEEEEEC
Confidence            356678899999999999999999999999988643     356789999999999999999999993  3678888888


Q ss_pred             CCCCC----------CeeEEe-ccchhhhchHHHhcCCCCeEEEEecchhH-----HHHHHHHHhhC--CCeeEEEeCCC
Q psy14082         79 GTPKG----------PQDCLP-LHRFVFNCQYEMAKNPAFKVIVFVETKKK-----VEDITRALRRE--RHSAICIHGDK  140 (233)
Q Consensus        79 g~~~~----------~~~lv~-l~r~~~~~~~~~~~~~~~k~iIf~~~~~~-----~~~l~~~L~~~--~~~~~~~~~~~  140 (233)
                      |.+..          .+++|+ ..++.+...........-+.+|+-+--..     ...+...++..  +.....+.+-+
T Consensus       135 ~~~~~~~~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~~~~~~~~~l~~i~~~~~~~~~~i~~SAT~  214 (237)
T 3bor_A          135 GTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATM  214 (237)
T ss_dssp             -------------CCCSEEEECHHHHHHHHHTTSSCSTTCCEEEEESHHHHHHTTCHHHHHHHHHHSCTTCEEEEECSSC
T ss_pred             CCchHHHHHHHhcCCCCEEEECHHHHHHHHHhCCcCcccCcEEEECCchHhhccCcHHHHHHHHHhCCCCCeEEEEEEec
Confidence            86642          456666 23333333221111223455665432211     11233333332  35566667767


Q ss_pred             CHHHHHHHHHHhhC
Q psy14082        141 TQQDRDYVLNDFRQ  154 (233)
Q Consensus       141 ~~~~r~~~~~~f~~  154 (233)
                      +.+.+ +..+.|-.
T Consensus       215 ~~~~~-~~~~~~l~  227 (237)
T 3bor_A          215 PTDVL-EVTKKFMR  227 (237)
T ss_dssp             CHHHH-HHHHHHCS
T ss_pred             CHHHH-HHHHHHCC
Confidence            65543 34444543

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=99.63  E-value=3.8e-15  Score=120.40  Aligned_cols=148  Identities=18%  Similarity=0.211  Sum_probs=97.4

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh--cCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS--SALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~--~~~~~~~~~g   78 (233)
                      |||.++.|+|+++.+|||||||++|++|+++.+...     ..++++||++||++|+.|+++.++++.  .++++..++|
T Consensus        73 ~i~~i~~~~~~lv~a~TGsGKT~~~~~~il~~l~~~-----~~~~~~lil~Ptr~L~~q~~~~~~~~~~~~~~~~~~~~g  147 (249)
T 3ber_A           73 AIPLALQGRDIIGLAETGSGKTGAFALPILNALLET-----PQRLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVG  147 (249)
T ss_dssp             HHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHS-----CCSSCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEEECT
T ss_pred             HHHHHhCCCCEEEEcCCCCCchhHhHHHHHHHHhcC-----CCCceEEEEeCCHHHHHHHHHHHHHHhccCCeeEEEEEC
Confidence            356678899999999999999999999999998765     346789999999999999999999983  4788999999


Q ss_pred             CCCC---------CCeeEEe-ccchhhhchHH-HhcCCCCeEEEEecchhHHH-----HHHHHHhhC--CCeeEEEeCCC
Q psy14082         79 GTPK---------GPQDCLP-LHRFVFNCQYE-MAKNPAFKVIVFVETKKKVE-----DITRALRRE--RHSAICIHGDK  140 (233)
Q Consensus        79 g~~~---------~~~~lv~-l~r~~~~~~~~-~~~~~~~k~iIf~~~~~~~~-----~l~~~L~~~--~~~~~~~~~~~  140 (233)
                      |.+.         +.+++|+ ..++.+.+... ......-+.+|+-+--...+     .+...+...  +.....+.+-+
T Consensus       148 ~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~l~~~~~lViDEah~l~~~~~~~~l~~i~~~~~~~~~~l~~SAT~  227 (249)
T 3ber_A          148 GIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRILNMDFETEVDKILKVIPRDRKTFLFSATM  227 (249)
T ss_dssp             TSCHHHHHHHHHTCCSEEEECHHHHHHHHHHSTTCCCTTCCEEEECSHHHHHHTTCHHHHHHHHHSSCSSSEEEEEESSC
T ss_pred             CCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCcCccccCEEEEcChhhhhccChHHHHHHHHHhCCCCCeEEEEeccC
Confidence            8763         4567777 34443333220 00112234555543221111     122222222  35666777777


Q ss_pred             CHHHHHHHHHHhhC
Q psy14082        141 TQQDRDYVLNDFRQ  154 (233)
Q Consensus       141 ~~~~r~~~~~~f~~  154 (233)
                      +.+.+ +..+.|-.
T Consensus       228 ~~~v~-~~~~~~l~  240 (249)
T 3ber_A          228 TKKVQ-KLQRAALK  240 (249)
T ss_dssp             CHHHH-HHHHHHCS
T ss_pred             CHHHH-HHHHHHCC
Confidence            76544 34444443

>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=99.62  E-value=1.9e-15  Score=137.96  Aligned_cols=98  Identities=23%  Similarity=0.256  Sum_probs=89.6

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecC-
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSL-  183 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~-  183 (233)
                      .+.++||||+|++.++.+++.|.+.|+++..+||+|++.+|.+++++|++|+.+|||||+++++|+|+|++++||++|. 
T Consensus       438 ~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~~l~~GlDip~v~lVI~~d~d  517 (664)
T 1c4o_A          438 RGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDAD  517 (664)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEEEEEETTTT
T ss_pred             cCCEEEEEECCHHHHHHHHHHHHhcCCCceeecCCCCHHHHHHHHHHhhcCCceEEEccChhhcCccCCCCCEEEEeCCc
Confidence            4679999999999999999999999999999999999999999999999999999999999999999999999999997 


Q ss_pred             ----CCCccccc-----------ceeeEEeecch
Q psy14082        184 ----QLSANHNI-----------SQVIEVVQDYE  202 (233)
Q Consensus       184 ----P~~~~~~i-----------~~~~~~~~~~~  202 (233)
                          |.|...|+           |.++.++++.+
T Consensus       518 ~~G~p~s~~~~iQr~GRagR~~~G~~i~~~~~~~  551 (664)
T 1c4o_A          518 KEGFLRSERSLIQTIGRAARNARGEVWLYADRVS  551 (664)
T ss_dssp             SCSGGGSHHHHHHHHGGGTTSTTCEEEEECSSCC
T ss_pred             ccCCCCCHHHHHHHHCccCcCCCCEEEEEEcCCC
Confidence                88887666           46677776543

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=99.62  E-value=4.3e-15  Score=118.79  Aligned_cols=87  Identities=18%  Similarity=0.175  Sum_probs=70.2

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh--cCCcEEEEEcC
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS--SALRNICIFGG   79 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~--~~~~~~~~~gg   79 (233)
                      +|.++.|+|+++.+|||||||++|++|+++.+..... ....++++||++||++|+.|+++.++++.  .++++..++||
T Consensus        56 i~~~~~~~~~li~a~TGsGKT~~~~~~~l~~l~~~~~-~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~  134 (236)
T 2pl3_A           56 IGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQW-TSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGG  134 (236)
T ss_dssp             HHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHTTC-CGGGCCCEEEECSSHHHHHHHHHHHHHHTTTSSCCEEEECCC
T ss_pred             HHHHhCCCCEEEEeCCCCcHHHHHHHHHHHHHHhhcc-cccCCceEEEEeCCHHHHHHHHHHHHHHhCCCCeeEEEEECC
Confidence            5667889999999999999999999999998875421 12347889999999999999999999984  35889999998


Q ss_pred             CCC--------CCeeEEe
Q psy14082         80 TPK--------GPQDCLP   89 (233)
Q Consensus        80 ~~~--------~~~~lv~   89 (233)
                      .+.        +.+++|+
T Consensus       135 ~~~~~~~~~~~~~~iiv~  152 (236)
T 2pl3_A          135 KDLKHEAERINNINILVC  152 (236)
T ss_dssp             --CHHHHHHHTTCSEEEE
T ss_pred             CCHHHHHHhCCCCCEEEE
Confidence            765        3456666

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=99.61  E-value=5.2e-16  Score=123.82  Aligned_cols=76  Identities=25%  Similarity=0.294  Sum_probs=66.4

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh---cCCcEEEEEc
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS---SALRNICIFG   78 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~---~~~~~~~~~g   78 (233)
                      +|.++.|+|+++++|||||||++|++|+++++...     ..++++||++||++|+.|+++.++++.   .++++..++|
T Consensus        55 i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~-----~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g  129 (230)
T 2oxc_A           55 IPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLE-----NLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIG  129 (230)
T ss_dssp             HHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTT-----SCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECT
T ss_pred             HHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhc-----CCCceEEEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeC
Confidence            56677899999999999999999999999988654     356799999999999999999999983   3788999999


Q ss_pred             CCCC
Q psy14082         79 GTPK   82 (233)
Q Consensus        79 g~~~   82 (233)
                      |.+.
T Consensus       130 ~~~~  133 (230)
T 2oxc_A          130 GTPL  133 (230)
T ss_dssp             TSCH
T ss_pred             CCCH
Confidence            8763

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=99.61  E-value=5e-15  Score=117.34  Aligned_cols=147  Identities=22%  Similarity=0.228  Sum_probs=91.5

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEcC
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGG   79 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~gg   79 (233)
                      +|.++.|+|+++.+|||||||++|++|+++++...     .+++++||++||++|+.|+++.++.+  ..++++..+.||
T Consensus        45 i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~-----~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~  119 (224)
T 1qde_A           45 IMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTS-----VKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGG  119 (224)
T ss_dssp             HHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTT-----CCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC-
T ss_pred             HHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhcc-----CCCceEEEEECCHHHHHHHHHHHHHHhcccCceEEEEeCC
Confidence            56678899999999999999999999999988654     45779999999999999999999998  346788899998


Q ss_pred             CCCC--------CeeEEe-ccchhhhchHHHhcCCCCeEEEEecchhH-----HHHHHHHHhh--CCCeeEEEeCCCCHH
Q psy14082         80 TPKG--------PQDCLP-LHRFVFNCQYEMAKNPAFKVIVFVETKKK-----VEDITRALRR--ERHSAICIHGDKTQQ  143 (233)
Q Consensus        80 ~~~~--------~~~lv~-l~r~~~~~~~~~~~~~~~k~iIf~~~~~~-----~~~l~~~L~~--~~~~~~~~~~~~~~~  143 (233)
                      .+..        .+++|+ ..++.+...........-..+|+-+--..     ...+...+..  .+.....+.+-++.+
T Consensus       120 ~~~~~~~~~~~~~~iiv~Tp~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~~~~~l~~i~~~~~~~~~~i~lSAT~~~~  199 (224)
T 1qde_A          120 TSFVEDAEGLRDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPND  199 (224)
T ss_dssp             ---------CTTCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHTTCHHHHHHHHHHSCTTCEEEEEESSCCHH
T ss_pred             cchHHHHhcCCCCCEEEECHHHHHHHHHhCCcchhhCcEEEEcChhHHhhhhhHHHHHHHHHhCCccCeEEEEEeecCHH
Confidence            7643        355666 23333322211111122345555432111     1112222222  234566677767655


Q ss_pred             HHHHHHHHhhC
Q psy14082        144 DRDYVLNDFRQ  154 (233)
Q Consensus       144 ~r~~~~~~f~~  154 (233)
                      .+ +..+.|-.
T Consensus       200 ~~-~~~~~~~~  209 (224)
T 1qde_A          200 VL-EVTTKFMR  209 (224)
T ss_dssp             HH-HHHHHHCS
T ss_pred             HH-HHHHHHCC
Confidence            43 44444543

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.60  E-value=1.4e-15  Score=120.41  Aligned_cols=75  Identities=27%  Similarity=0.369  Sum_probs=65.1

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhc------CCcEEE
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSS------ALRNIC   75 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~------~~~~~~   75 (233)
                      +|.++.|+|+++.+|||||||++|++|+++.+...     ..++++||++||++|+.|+++.++++..      ++++..
T Consensus        35 i~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~-----~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~  109 (219)
T 1q0u_A           35 IPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPE-----RAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARC  109 (219)
T ss_dssp             HHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTT-----SCSCCEEEECSSHHHHHHHHHHHHHHHTTSCGGGCCCEEE
T ss_pred             HHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhC-----cCCceEEEEcCcHHHHHHHHHHHHHHhhhcccccceEEEE
Confidence            45677899999999999999999999999988653     3568899999999999999999999832      678888


Q ss_pred             EEcCCC
Q psy14082         76 IFGGTP   81 (233)
Q Consensus        76 ~~gg~~   81 (233)
                      ++||.+
T Consensus       110 ~~g~~~  115 (219)
T 1q0u_A          110 LIGGTD  115 (219)
T ss_dssp             ECCCSH
T ss_pred             EeCCCC
Confidence            898864

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=99.60  E-value=9.7e-15  Score=114.16  Aligned_cols=149  Identities=20%  Similarity=0.284  Sum_probs=96.8

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCC
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTP   81 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~   81 (233)
                      +|.++.|+|+++.+|||||||++|++|+++.+....  ...+++++||++||++|+.|+++.++++...+++..++||.+
T Consensus        32 i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~l~~~~--~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~  109 (207)
T 2gxq_A           32 LPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQ--ERGRKPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTG  109 (207)
T ss_dssp             HHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCC--CTTCCCSEEEECSSHHHHHHHHHHHHHHCTTSCEEEECSSSC
T ss_pred             HHHHcCCCCEEEECCCCChHHHHHHHHHHHHHhhcc--ccCCCCcEEEEECCHHHHHHHHHHHHHHhhcceEEEEECCCC
Confidence            456778999999999999999999999999887532  124578999999999999999999999977789999999876


Q ss_pred             C---------CCeeEEe-ccchhhhchHHHhcCCCCeEEEEecchhH-----HHHHHHHHhhC--CCeeEEEeCCCCHHH
Q psy14082         82 K---------GPQDCLP-LHRFVFNCQYEMAKNPAFKVIVFVETKKK-----VEDITRALRRE--RHSAICIHGDKTQQD  144 (233)
Q Consensus        82 ~---------~~~~lv~-l~r~~~~~~~~~~~~~~~k~iIf~~~~~~-----~~~l~~~L~~~--~~~~~~~~~~~~~~~  144 (233)
                      .         ..+++|+ ..++.+...........-+.+|+-+--..     ...+...+...  +.....+++-++...
T Consensus       110 ~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~  189 (207)
T 2gxq_A          110 YGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLLFSATLPSWA  189 (207)
T ss_dssp             SHHHHHHHHHCCSEEEECHHHHHHHHHHTSSCCTTCSEEEEESHHHHHHTTCHHHHHHHHHTSCTTSEEEEECSSCCHHH
T ss_pred             hHHHHHHhhCCCCEEEECHHHHHHHHHcCCcchhhceEEEEEChhHhhccchHHHHHHHHHhCCccCeEEEEEEecCHHH
Confidence            4         3556666 33333333321112233455665432211     11122222222  345556666665543


Q ss_pred             HHHHHHHhh
Q psy14082        145 RDYVLNDFR  153 (233)
Q Consensus       145 r~~~~~~f~  153 (233)
                       .+..+.|-
T Consensus       190 -~~~~~~~~  197 (207)
T 2gxq_A          190 -KRLAERYM  197 (207)
T ss_dssp             -HHHHHHHC
T ss_pred             -HHHHHHHc
Confidence             34445553

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=99.60  E-value=4.9e-16  Score=126.53  Aligned_cols=81  Identities=26%  Similarity=0.292  Sum_probs=67.8

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~g   78 (233)
                      |+|.++.|+|++++||||||||++|++|+++.+...+. ....+.++||++||++|+.|+++.++++  ..+..+..++|
T Consensus        84 ~i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~-~~~~~~~~lil~Pt~~La~q~~~~~~~~~~~~~~~~~~~~g  162 (262)
T 3ly5_A           84 SIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRF-MPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMG  162 (262)
T ss_dssp             HHHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTC-CGGGCCCEEEECSSHHHHHHHHHHHHHHTTTCCSCEEEECS
T ss_pred             HHHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhccc-cccCCceEEEEeCCHHHHHHHHHHHHHHHhhcCceEEEEEC
Confidence            35667889999999999999999999999999876421 1234788999999999999999999998  34678888999


Q ss_pred             CCCC
Q psy14082         79 GTPK   82 (233)
Q Consensus        79 g~~~   82 (233)
                      |...
T Consensus       163 ~~~~  166 (262)
T 3ly5_A          163 GSNR  166 (262)
T ss_dssp             SSCH
T ss_pred             CCCH
Confidence            8764

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=99.58  E-value=2.1e-15  Score=119.28  Aligned_cols=76  Identities=22%  Similarity=0.312  Sum_probs=65.7

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh---cCCcEEEEEc
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS---SALRNICIFG   78 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~---~~~~~~~~~g   78 (233)
                      +|.++.|+|+++.+|||+|||++|++|+++.+...     .+++++||++||++|+.|+++.++++.   +++++..++|
T Consensus        45 i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~-----~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g  119 (220)
T 1t6n_A           45 IPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPV-----TGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFG  119 (220)
T ss_dssp             HHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCC-----TTCCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESC
T ss_pred             HHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhcc-----CCCEEEEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeC
Confidence            45677899999999999999999999999987543     346789999999999999999999993   3788999999


Q ss_pred             CCCC
Q psy14082         79 GTPK   82 (233)
Q Consensus        79 g~~~   82 (233)
                      |.+.
T Consensus       120 ~~~~  123 (220)
T 1t6n_A          120 GLSI  123 (220)
T ss_dssp             CSCH
T ss_pred             CCCh
Confidence            8763

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.56  E-value=6.2e-15  Score=135.21  Aligned_cols=70  Identities=13%  Similarity=-0.036  Sum_probs=60.7

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEcC
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGG   79 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~gg   79 (233)
                      ||.++.|+  +++++||+|||++|++|++...+        .+.+++|++||++||.|.++.+..+  +.++++.+++||
T Consensus        88 ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~aL--------~G~qv~VvTPTreLA~Qdae~m~~l~~~lGLsv~~i~Gg  157 (997)
T 2ipc_A           88 GAVLHEGK--IAEMKTGEGKTLVATLAVALNAL--------TGKGVHVVTVNDYLARRDAEWMGPVYRGLGLSVGVIQHA  157 (997)
T ss_dssp             HHHHHTTS--EEECCSTHHHHHHHHHHHHHHHT--------TCSCCEEEESSHHHHHHHHHHHHHHHHTTTCCEEECCTT
T ss_pred             cccccCCc--eeeccCCCchHHHHHHHHHHHHH--------hCCCEEEEeCCHHHHHHHHHHHHHHHHhcCCeEEEEeCC
Confidence            57788888  99999999999999999965443        2457999999999999999999999  568999999998


Q ss_pred             CC
Q psy14082         80 TP   81 (233)
Q Consensus        80 ~~   81 (233)
                      .+
T Consensus       158 ~~  159 (997)
T 2ipc_A          158 ST  159 (997)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}

Probab=99.27  E-value=8.9e-13  Score=103.34  Aligned_cols=81  Identities=16%  Similarity=0.097  Sum_probs=62.3

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHH-HHHHHHHh-hcCCcEEEEEcC
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQ-IQTVAKEF-SSALRNICIFGG   79 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q-~~~~~~~~-~~~~~~~~~~gg   79 (233)
                      ++.++.|+++++.+|||+|||++|++++.+.+.....  ...+.++||++|+++|+.| +.+.+..+ ..++++..+.|+
T Consensus        42 i~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~--~~~~~~~lil~p~~~L~~q~~~~~~~~~~~~~~~v~~~~g~  119 (216)
T 3b6e_A           42 AQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKK--ASEPGKVIVLVNKVLLVEQLFRKEFQPFLKKWYRVIGLSGD  119 (216)
T ss_dssp             HHHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHH--TTCCCCEEEEESSHHHHHHHHHHTHHHHHTTTSCEEECCC-
T ss_pred             HHHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhccc--ccCCCcEEEEECHHHHHHHHHHHHHHHHhccCceEEEEeCC
Confidence            3445678999999999999999999999987764311  1236789999999999999 88888888 336788888888


Q ss_pred             CCCCC
Q psy14082         80 TPKGP   84 (233)
Q Consensus        80 ~~~~~   84 (233)
                      .+...
T Consensus       120 ~~~~~  124 (216)
T 3b6e_A          120 TQLKI  124 (216)
T ss_dssp             --CCC
T ss_pred             cccch
Confidence            76544

>1rif_A DAR protein, DNA helicase UVSW; bacteriophage, RECG, SF2, DNA binding protein; HET: DNA; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.23

Probab=99.18  E-value=1e-11  Score=101.89  Aligned_cols=71  Identities=17%  Similarity=0.093  Sum_probs=57.5

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh--cCCcEEEEEcCCCC
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS--SALRNICIFGGTPK   82 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~--~~~~~~~~~gg~~~   82 (233)
                      ++.+.+.++.++||+|||++++.++...+..       .+.++||++||++|+.|+.+.++++.  ....+..+.||.+.
T Consensus       125 ~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~-------~~~~~lil~Pt~~L~~q~~~~l~~~~~~~~~~~~~~~~~~~~  197 (282)
T 1rif_A          125 GLVNRRRILNLPTSAGRSLIQALLARYYLEN-------YEGKILIIVPTTALTTQMADDFVDYRLFSHAMIKKIGGGASK  197 (282)
T ss_dssp             HHHHSEEEECCCTTSCHHHHHHHHHHHHHHH-------CSSEEEEECSSHHHHHHHHHHHHHHTSCCGGGEEECSTTCSS
T ss_pred             HHhcCCeEEEcCCCCCcHHHHHHHHHHHHHc-------CCCeEEEEECCHHHHHHHHHHHHHhcccccceEEEEeCCCcc
Confidence            4556788999999999999998887776643       23489999999999999999999983  34577888887654

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=99.13  E-value=4.7e-11  Score=108.12  Aligned_cols=70  Identities=13%  Similarity=-0.003  Sum_probs=60.9

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEcCCC
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGGTP   81 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~gg~~   81 (233)
                      +..|+|++++||||+|||++|++|++..+...       +.+++|++||++|+.|+.+.+..+  ..++++..+.|+.+
T Consensus        19 l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~~-------~~kvli~t~T~~l~~Qi~~el~~l~~~~~~~~~~l~gr~~   90 (620)
T 4a15_A           19 LQKSYGVALESPTGSGKTIMALKSALQYSSER-------KLKVLYLVRTNSQEEQVIKELRSLSSTMKIRAIPMQGRVN   90 (620)
T ss_dssp             HHHSSEEEEECCTTSCHHHHHHHHHHHHHHHH-------TCEEEEEESSHHHHHHHHHHHHHHHHHSCCCEEECCCHHH
T ss_pred             HHcCCCEEEECCCCCCHHHHHHHHHHHhhhhc-------CCeEEEECCCHHHHHHHHHHHHHHhhccCeEEEEEECCCc
Confidence            35799999999999999999999999988643       568999999999999999999998  34788888887754

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.06  E-value=7.3e-11  Score=105.60  Aligned_cols=65  Identities=9%  Similarity=-0.056  Sum_probs=55.9

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEcCCC
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGGTP   81 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~gg~~   81 (233)
                      ..|+|++++||||+|||++|++|++.           .+++++|++||++|+.|+.+.+..+  ..++++..+.|+.+
T Consensus        20 ~~~~~~~~~a~TGtGKT~~~l~p~l~-----------~~~~v~i~~pt~~l~~q~~~~~~~l~~~~~~~~~~l~gr~~   86 (551)
T 3crv_A           20 RNNFLVALNAPTGSGKTLFSLLVSLE-----------VKPKVLFVVRTHNEFYPIYRDLTKIREKRNITFSFLVGKPS   86 (551)
T ss_dssp             HTTCEEEEECCTTSSHHHHHHHHHHH-----------HCSEEEEEESSGGGHHHHHHHHTTCCCSSCCCEEECCCHHH
T ss_pred             HcCCcEEEECCCCccHHHHHHHHHHh-----------CCCeEEEEcCCHHHHHHHHHHHHHHhhhcCccEEEEccccc
Confidence            47899999999999999999999997           2568999999999999999999888  33677777777543

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=99.05  E-value=1.5e-10  Score=92.71  Aligned_cols=73  Identities=12%  Similarity=-0.069  Sum_probs=59.3

Q ss_pred             CCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCc-EEEEEcCCCC
Q psy14082          4 PSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALR-NICIFGGTPK   82 (233)
Q Consensus         4 ~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~-~~~~~gg~~~   82 (233)
                      .++.++++++.++||+|||.+++.++...           +.++||++|+++|+.|+.+.+.++  +++ +..+.|+.+.
T Consensus       104 ~~~~~~~~ll~~~tG~GKT~~a~~~~~~~-----------~~~~liv~P~~~L~~q~~~~~~~~--~~~~v~~~~g~~~~  170 (237)
T 2fz4_A          104 RWLVDKRGCIVLPTGSGKTHVAMAAINEL-----------STPTLIVVPTLALAEQWKERLGIF--GEEYVGEFSGRIKE  170 (237)
T ss_dssp             HHTTTSEEEEEESSSTTHHHHHHHHHHHS-----------CSCEEEEESSHHHHHHHHHHHGGG--CGGGEEEESSSCBC
T ss_pred             HHHhCCCEEEEeCCCCCHHHHHHHHHHHc-----------CCCEEEEeCCHHHHHHHHHHHHhC--CCCeEEEEeCCCCC
Confidence            35567889999999999999988776542           346999999999999999999985  677 8888888776


Q ss_pred             CCeeEEe
Q psy14082         83 GPQDCLP   89 (233)
Q Consensus        83 ~~~~lv~   89 (233)
                      ..+++|+
T Consensus       171 ~~~i~v~  177 (237)
T 2fz4_A          171 LKPLTVS  177 (237)
T ss_dssp             CCSEEEE
T ss_pred             cCCEEEE
Confidence            6666555

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=98.91  E-value=1.4e-09  Score=97.13  Aligned_cols=61  Identities=15%  Similarity=0.043  Sum_probs=50.1

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEc
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFG   78 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~g   78 (233)
                      +..|++++++||||+|||++|++|++..           +.+++|++||++|+.|+.+.+..+  ++++..+.|
T Consensus        23 ~~~~~~~~~~a~TGtGKT~~~l~~~~~~-----------~~~~~~~~~t~~l~~q~~~~~~~l--~~~~~~l~g   83 (540)
T 2vl7_A           23 LKHGKTLLLNAKPGLGKTVFVEVLGMQL-----------KKKVLIFTRTHSQLDSIYKNAKLL--GLKTGFLIG   83 (540)
T ss_dssp             HHTTCEEEEECCTTSCHHHHHHHHHHHH-----------TCEEEEEESCHHHHHHHHHHHGGG--TCCEEEC--
T ss_pred             HHcCCCEEEEcCCCCcHHHHHHHHHHhC-----------CCcEEEEcCCHHHHHHHHHHHHhc--CCcEEEecC
Confidence            3578999999999999999999998752           468999999999999999988876  455555544

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=98.90  E-value=5.1e-10  Score=89.28  Aligned_cols=63  Identities=10%  Similarity=-0.115  Sum_probs=52.7

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      +|.+..|+++++.|+||||||.+|.+++++.......   ..+.++++++|+++|+.|+.+.+...
T Consensus        70 i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~---~~~~~~l~~~p~~~la~q~~~~~~~~  132 (235)
T 3llm_A           70 LEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDR---AAECNIVVTQPRRISAVSVAERVAFE  132 (235)
T ss_dssp             HHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTC---GGGCEEEEEESSHHHHHHHHHHHHHT
T ss_pred             HHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCC---CCceEEEEeccchHHHHHHHHHHHHH
Confidence            3456679999999999999999999999987765421   23568999999999999999999876

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=97.98  E-value=2.9e-06  Score=76.66  Aligned_cols=60  Identities=12%  Similarity=0.012  Sum_probs=47.9

Q ss_pred             CCCCCCCCceeEecCCCCCch--HHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          2 LPPSESGCQNFSKITNYLLSP--PQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT--~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ++.++.++++++++++|||||  ++++++.+..+..      ..+.++++++||.++|.++.+.+...
T Consensus       158 i~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~------~~~~~vll~APTg~AA~~L~e~~~~~  219 (608)
T 1w36_D          158 AAVALTRRISVISGGPGTGKTTTVAKLLAALIQMAD------GERCRIRLAAPTGKAAARLTESLGKA  219 (608)
T ss_dssp             HHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCS------SCCCCEEEEBSSHHHHHHHHHHHTHH
T ss_pred             HHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhh------cCCCeEEEEeCChhHHHHHHHHHHHH
Confidence            344567899999999999999  6777777765532      23678999999999999998887754

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=97.95  E-value=7.8e-06  Score=72.82  Aligned_cols=78  Identities=17%  Similarity=0.312  Sum_probs=52.0

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEE--ecccCcCCcCCCC----ccE
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILV--ATDVAARGLDVED----VNT  177 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv--~T~~~~~Gldi~~----v~~  177 (233)
                      ...+.++||++|...++.+++.+..   .....++..  .+|.+++++|+++. .||+  +|+.+++|+|+|+    +++
T Consensus       382 ~~~g~~lvff~S~~~~~~v~~~l~~---~~~~~q~~~--~~~~~~l~~f~~~~-~il~~V~~~~~~EGiD~~~~~~~~~~  455 (540)
T 2vl7_A          382 NSSKSVLVFFPSYEMLESVRIHLSG---IPVIEENKK--TRHEEVLELMKTGK-YLVMLVMRAKESEGVEFREKENLFES  455 (540)
T ss_dssp             TCSSEEEEEESCHHHHHHHHTTCTT---SCEEESTTT--CCHHHHHHHHHTSC-CEEEEEC---------------CEEE
T ss_pred             hCCCCEEEEeCCHHHHHHHHHHhcc---CceEecCCC--CcHHHHHHHHhcCC-eEEEEEecCceecceecCCCcccccE
Confidence            4567999999999999999988865   234566654  46889999999864 6777  8899999999997    899


Q ss_pred             EEEecCCCCc
Q psy14082        178 VNIGSLQLSA  187 (233)
Q Consensus       178 VI~~d~P~~~  187 (233)
                      ||++++|...
T Consensus       456 Vii~~lPf~~  465 (540)
T 2vl7_A          456 LVLAGLPYPN  465 (540)
T ss_dssp             EEEESCCCCC
T ss_pred             EEEECCCCCC
Confidence            9999999544

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=96.98  E-value=0.00093  Score=60.68  Aligned_cols=52  Identities=10%  Similarity=-0.017  Sum_probs=41.0

Q ss_pred             CCc-eeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          8 GCQ-NFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         8 g~d-~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      .++ .++++|+|||||.+ +.-++..+..+       +.++|+.+||..-++++.+.+...
T Consensus       204 ~~~~~lI~GPPGTGKT~t-i~~~I~~l~~~-------~~~ILv~a~TN~AvD~i~erL~~~  256 (646)
T 4b3f_X          204 QKELAIIHGPPGTGKTTT-VVEIILQAVKQ-------GLKVLCCAPSNIAVDNLVERLALC  256 (646)
T ss_dssp             CSSEEEEECCTTSCHHHH-HHHHHHHHHHT-------TCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             CCCceEEECCCCCCHHHH-HHHHHHHHHhC-------CCeEEEEcCchHHHHHHHHHHHhc
Confidence            344 68999999999988 44455555543       568999999999999999988765

>3hgt_A HDA1 complex subunit 3; RECA-like domain, SWI2/SNF2 helical domain, chromatin regulator, coiled coil, nucleus, repressor, transcription; 2.20A {Saccharomyces cerevisiae} PDB: 3hgq_A

Probab=96.94  E-value=0.009  Score=49.38  Aligned_cols=97  Identities=3%  Similarity=0.000  Sum_probs=68.2

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcC-----CCCccE
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLD-----VEDVNT  177 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gld-----i~~v~~  177 (233)
                      ...+.+++||++..+..+-+...+...+++..-+.|....+++ +.    .++...+.+.|...+-|+|     ....|.
T Consensus       122 ~~~~~kVLIfsq~t~~LDilE~~l~~~~~~y~RlDG~~~~~~~-k~----~~~~~~i~Lltsag~~gin~~~~nl~~aD~  196 (328)
T 3hgt_A          122 QEYETETAIVCRPGRTMDLLEALLLGNKVHIKRYDGHSIKSAA-AA----NDFSCTVHLFSSEGINFTKYPIKSKARFDM  196 (328)
T ss_dssp             TTSCEEEEEEECSTHHHHHHHHHHTTSSCEEEESSSCCC------------CCSEEEEEEESSCCCTTTSCCCCCSCCSE
T ss_pred             HhCCCEEEEEECChhHHHHHHHHHhcCCCceEeCCCCchhhhh-hc----ccCCceEEEEECCCCCCcCcccccCCCCCE
Confidence            3477899999999999999999999999999999988554322 11    2344455555776666675     678999


Q ss_pred             EEEecCCCCccc----------ccc-------eeeEEeecchHH
Q psy14082        178 VNIGSLQLSANH----------NIS-------QVIEVVQDYEKE  204 (233)
Q Consensus       178 VI~~d~P~~~~~----------~i~-------~~~~~~~~~~~~  204 (233)
                      ||.||..+++..          |+|       .+++++...--+
T Consensus       197 VI~~DsdwNp~~d~iQa~~r~~R~~~gq~k~v~V~RLvt~~TiE  240 (328)
T 3hgt_A          197 LICLDTTVDTSQKDIQYLLQYKRERKGLERYAPIVRLVAINSID  240 (328)
T ss_dssp             EEECSTTCCTTSHHHHHHHCCC---------CCEEEEEETTSHH
T ss_pred             EEEECCCCCCCChHHHHHHHHhhhccCCCCcceEEEEeCCCCHH
Confidence            999999888763          552       567777664433

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=96.78  E-value=0.0013  Score=59.46  Aligned_cols=78  Identities=13%  Similarity=0.206  Sum_probs=55.9

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc--cCcCCcCCCC--ccEEEE
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD--VAARGLDVED--VNTVNI  180 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~--~~~~Gldi~~--v~~VI~  180 (233)
                      .++.++||+++....+.+++.++..+.+   ...+++..++..++++|+ ++.-||+++.  .+.+|+|+|+  ..+||.
T Consensus       447 ~~g~~lvlF~Sy~~l~~v~~~l~~~~~~---~~q~~~~~~~~~ll~~f~-~~~~vL~~v~~gsf~EGiD~~g~~l~~viI  522 (620)
T 4a15_A          447 VKKNTIVYFPSYSLMDRVENRVSFEHMK---EYRGIDQKELYSMLKKFR-RDHGTIFAVSGGRLSEGINFPGNELEMIIL  522 (620)
T ss_dssp             HCSCEEEEESCHHHHHHHTSSCCSCCEE---CCTTCCSHHHHHHHHHHT-TSCCEEEEETTSCC--------CCCCEEEE
T ss_pred             CCCCEEEEeCCHHHHHHHHHHHHhcchh---ccCCCChhHHHHHHHHhc-cCCcEEEEEecCceeccccCCCCceEEEEE
Confidence            3557999999999999999888732222   555677778999999999 8888999974  8999999996  668999


Q ss_pred             ecCCCC
Q psy14082        181 GSLQLS  186 (233)
Q Consensus       181 ~d~P~~  186 (233)
                      ..+|--
T Consensus       523 ~~lPfp  528 (620)
T 4a15_A          523 AGLPFP  528 (620)
T ss_dssp             SSCCCC
T ss_pred             EcCCCC
Confidence            998844

>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=96.59  E-value=0.0038  Score=56.85  Aligned_cols=57  Identities=18%  Similarity=0.002  Sum_probs=42.7

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEE
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIF   77 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~   77 (233)
                      ...+.+.||||||++++ .++..+.          ..+|||+|+..+|.|+++.++.|+++-.+..+.
T Consensus        30 ~~~l~g~tgs~kt~~~a-~~~~~~~----------~~~lvv~~~~~~A~ql~~el~~~~~~~~V~~fp   86 (664)
T 1c4o_A           30 FVTLLGATGTGKTVTMA-KVIEALG----------RPALVLAPNKILAAQLAAEFRELFPENAVEYFI   86 (664)
T ss_dssp             EEEEEECTTSCHHHHHH-HHHHHHT----------CCEEEEESSHHHHHHHHHHHHHHCTTSEEEECC
T ss_pred             cEEEEcCCCcHHHHHHH-HHHHHhC----------CCEEEEecCHHHHHHHHHHHHHHCCCCeEEEcC
Confidence            45678999999998844 3444441          138999999999999999999996554444443

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=96.47  E-value=0.0029  Score=57.25  Aligned_cols=54  Identities=13%  Similarity=0.025  Sum_probs=42.2

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      .+.-.++++|+|||||.+ +..++..+...      .+.++|+++||...++++.+.+.+.
T Consensus       194 ~~~~~li~GppGTGKT~~-~~~~i~~l~~~------~~~~ilv~a~tn~A~~~l~~~l~~~  247 (624)
T 2gk6_A          194 QRPLSLIQGPPGTGKTVT-SATIVYHLARQ------GNGPVLVCAPSNIAVDQLTEKIHQT  247 (624)
T ss_dssp             TCSEEEEECCTTSCHHHH-HHHHHHHHHTS------SSCCEEEEESSHHHHHHHHHHHHTT
T ss_pred             cCCCeEEECCCCCCHHHH-HHHHHHHHHHc------CCCeEEEEeCcHHHHHHHHHHHHhc
Confidence            344578999999999987 45566665532      3568999999999999999988765

>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=96.43  E-value=0.0084  Score=55.58  Aligned_cols=75  Identities=13%  Similarity=0.217  Sum_probs=62.7

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhh----CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEeccc-CcCCcCCCCccEEE
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRR----ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDV-AARGLDVEDVNTVN  179 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~-~~~Gldi~~v~~VI  179 (233)
                      .+.++++.++|+.-+.+.++.+.+    .++++..+||+++..++...++.+.+|+.+|+|+|.. +...+++.++++||
T Consensus       416 ~g~qvlvlaPtr~La~Q~~~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~~~~~~l~lVV  495 (780)
T 1gm5_A          416 AGFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLVI  495 (780)
T ss_dssp             HTSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCSCCCEEE
T ss_pred             cCCeEEEEeCcHHHHHHHHHHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhhhhhccCCceEE
Confidence            457999999999998888877764    3789999999999999999999999999999999964 23346667777666

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=96.15  E-value=0.014  Score=49.53  Aligned_cols=61  Identities=15%  Similarity=0.199  Sum_probs=55.9

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhh---CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRR---ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD  164 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~---~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~  164 (233)
                      ..+.+++|.++++.-+.+.++.+++   .++++..+||+.+..++...++.+..|+.+|+|+|+
T Consensus        62 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp  125 (414)
T 3oiy_A           62 RKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFST  125 (414)
T ss_dssp             TTTCCEEEEESSHHHHHHHHHHHHHHCCSSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEH
T ss_pred             cCCCEEEEEECCHHHHHHHHHHHHHHccCCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECH
Confidence            4678999999999999999999988   588999999999999999999999999999999994

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=96.15  E-value=0.006  Score=56.77  Aligned_cols=53  Identities=11%  Similarity=0.038  Sum_probs=41.7

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      +.-.++++|+|||||.+ +..++..+...      ++.++|+++||...++++.+.+.+.
T Consensus       375 ~~~~lI~GppGTGKT~~-i~~~i~~l~~~------~~~~ILv~a~tn~A~d~l~~rL~~~  427 (802)
T 2xzl_A          375 RPLSLIQGPPGTGKTVT-SATIVYHLSKI------HKDRILVCAPSNVAVDHLAAKLRDL  427 (802)
T ss_dssp             CSEEEEECSTTSSHHHH-HHHHHHHHHHH------HCCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             CCCEEEECCCCCCHHHH-HHHHHHHHHhC------CCCeEEEEcCcHHHHHHHHHHHHhh
Confidence            44579999999999977 44555555432      2567999999999999999999876

>3lfu_A DNA helicase II; SF1 helicase, ATP-binding, DNA damage, DNA REP replication, DNA-binding, hydrolase, nucleotide-B SOS response; HET: DNA; 1.80A {Escherichia coli} PDB: 2is6_A* 2is2_A* 2is1_A* 2is4_A*

Probab=96.12  E-value=0.0095  Score=53.75  Aligned_cols=56  Identities=5%  Similarity=-0.072  Sum_probs=41.8

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      +..+++.|++|||||.+ ++--+.++.....   .+..++|++++|+..+.++.+.+.++
T Consensus        22 ~~~~lV~a~aGsGKT~~-l~~ri~~l~~~~~---~~~~~iL~ltft~~aa~e~~~rl~~~   77 (647)
T 3lfu_A           22 RSNLLVLAGAGSGKTRV-LVHRIAWLMSVEN---CSPYSIMAVTFTNKAAAEMRHRIGQL   77 (647)
T ss_dssp             SSCEEEEECTTSCHHHH-HHHHHHHHHHTSC---CCGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCHHHH-HHHHHHHHHHhCC---CChhhEEEEeccHHHHHHHHHHHHHH
Confidence            45689999999999987 4434444443211   12357999999999999999999887

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A

Probab=95.97  E-value=0.0074  Score=56.12  Aligned_cols=53  Identities=13%  Similarity=0.024  Sum_probs=42.0

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      +.-.++++|+|||||.+ +..++..+...      .+.++|+++||..-+.++.+.+...
T Consensus       371 ~~~~lI~GppGTGKT~t-i~~~i~~l~~~------~~~~ilv~a~tn~A~~~l~~~l~~~  423 (800)
T 2wjy_A          371 RPLSLIQGPPGTGKTVT-SATIVYHLARQ------GNGPVLVCAPSNIAVDQLTEKIHQT  423 (800)
T ss_dssp             SSEEEEECCTTSCHHHH-HHHHHHHHHTT------CSSCEEEEESSHHHHHHHHHHHHTT
T ss_pred             CCeEEEEcCCCCCHHHH-HHHHHHHHHHc------CCCcEEEEcCcHHHHHHHHHHHHHh
Confidence            44578999999999987 55566666542      3568999999999999999888765

>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=95.81  E-value=0.021  Score=51.92  Aligned_cols=57  Identities=16%  Similarity=-0.010  Sum_probs=42.5

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEE
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIF   77 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~   77 (233)
                      ...+.+.||||||++.+ .++....          ..+|||+|+.++|.|+++.++.|+++-.+..+.
T Consensus        34 ~~~l~g~~gs~k~~~~a-~~~~~~~----------~~~lvv~~~~~~A~~l~~el~~~~~~~~v~~fp   90 (661)
T 2d7d_A           34 HQTLLGATGTGKTFTVS-NLIKEVN----------KPTLVIAHNKTLAGQLYSEFKEFFPNNAVEYFV   90 (661)
T ss_dssp             EEEEEECTTSCHHHHHH-HHHHHHC----------CCEEEECSSHHHHHHHHHHHHHHCTTSEEEEEC
T ss_pred             cEEEECcCCcHHHHHHH-HHHHHhC----------CCEEEEECCHHHHHHHHHHHHHHcCCCcEEEcc
Confidence            45678999999998743 3444431          138999999999999999999996554555444

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=95.79  E-value=0.036  Score=49.19  Aligned_cols=77  Identities=9%  Similarity=0.143  Sum_probs=56.2

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEec--ccCcCCcCCC-----Ccc
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVAT--DVAARGLDVE-----DVN  176 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T--~~~~~Gldi~-----~v~  176 (233)
                      ...+.++||+++....+.+++.   .+..+..-..+++   +.+.++.|+..+.-||+++  ..+.+|+|+|     ...
T Consensus       391 ~~~g~~lvlF~Sy~~l~~v~~~---~~~~v~~q~~~~~---~~~~~~~~~~~~~~vl~~v~gg~~~EGiD~~d~~g~~l~  464 (551)
T 3crv_A          391 QAKANVLVVFPSYEIMDRVMSR---ISLPKYVESEDSS---VEDLYSAISANNKVLIGSVGKGKLAEGIELRNNDRSLIS  464 (551)
T ss_dssp             HCSSEEEEEESCHHHHHHHHTT---CCSSEEECCSSCC---HHHHHHHTTSSSSCEEEEESSCCSCCSSCCEETTEESEE
T ss_pred             hCCCCEEEEecCHHHHHHHHHh---cCCcEEEcCCCCC---HHHHHHHHHhcCCeEEEEEecceecccccccccCCccee
Confidence            3556999999999999988862   3444433333455   4557778864445799998  6999999999     378


Q ss_pred             EEEEecCCCC
Q psy14082        177 TVNIGSLQLS  186 (233)
Q Consensus       177 ~VI~~d~P~~  186 (233)
                      +||...+|--
T Consensus       465 ~viI~~lPfp  474 (551)
T 3crv_A          465 DVVIVGIPYP  474 (551)
T ss_dssp             EEEEESCCCC
T ss_pred             EEEEEcCCCC
Confidence            8999998743

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=95.75  E-value=0.02  Score=55.19  Aligned_cols=75  Identities=15%  Similarity=0.184  Sum_probs=63.4

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhh---CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEeccc-----CcCCcCCCCc
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRR---ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDV-----AARGLDVEDV  175 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~---~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~-----~~~Gldi~~v  175 (233)
                      ..+.+++|.++++.-+.++++.+++   .++++..+||+++..+|...++.+.+|..+|+|+|.-     +.. ++..++
T Consensus       119 ~~~~~~Lil~PtreLa~Q~~~~l~~l~~~~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~-l~~~~l  197 (1104)
T 4ddu_A          119 RKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK-LSQKRF  197 (1104)
T ss_dssp             TTTCCEEEEESSHHHHHHHHHHHHTTSCTTSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHH-HHTSCC
T ss_pred             hcCCeEEEEechHHHHHHHHHHHHHhhCCCCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHh-hcccCc
Confidence            5678999999999999999999988   5679999999999989999999999999999999952     222 445677


Q ss_pred             cEEE
Q psy14082        176 NTVN  179 (233)
Q Consensus       176 ~~VI  179 (233)
                      ++||
T Consensus       198 ~~lV  201 (1104)
T 4ddu_A          198 DFVF  201 (1104)
T ss_dssp             SEEE
T ss_pred             CEEE
Confidence            7766

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=95.31  E-value=0.022  Score=51.01  Aligned_cols=50  Identities=14%  Similarity=-0.093  Sum_probs=38.2

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHH
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTV   63 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~   63 (233)
                      +.+..+++.+++|||||.+ +..++..+..       .+.++++++||...+..+.+.
T Consensus       202 ~~~~~~~I~G~pGTGKTt~-i~~l~~~l~~-------~g~~Vl~~ApT~~Aa~~L~e~  251 (574)
T 3e1s_A          202 AGHRLVVLTGGPGTGKSTT-TKAVADLAES-------LGLEVGLCAPTGKAARRLGEV  251 (574)
T ss_dssp             TTCSEEEEECCTTSCHHHH-HHHHHHHHHH-------TTCCEEEEESSHHHHHHHHHH
T ss_pred             HhCCEEEEEcCCCCCHHHH-HHHHHHHHHh-------cCCeEEEecCcHHHHHHhHhh
Confidence            3467789999999999976 4455555543       356799999999999888764

>3u4q_A ATP-dependent helicase/nuclease subunit A; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_A*

Probab=95.14  E-value=0.031  Score=54.42  Aligned_cols=59  Identities=15%  Similarity=0.019  Sum_probs=43.7

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      .+.++++.|+.|||||.+-+--++..+....  .+-...++|++++|+..+..+.+.+...
T Consensus        22 ~~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~--~~~~~~~il~~Tft~~aa~e~~~ri~~~   80 (1232)
T 3u4q_A           22 TGQDILVAAAAGSGKTAVLVERMIRKITAEE--NPIDVDRLLVVTFTNASAAEMKHRIAEA   80 (1232)
T ss_dssp             CSSCEEEEECTTCCHHHHHHHHHHHHHSCSS--SCCCGGGEEEECSSHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEecCCCcHHHHHHHHHHHHHhcCC--CCCCccceEEEeccHHHHHHHHHHHHHH
Confidence            3778999999999999885444555444321  1113457999999999999999988874

>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=94.85  E-value=0.081  Score=51.19  Aligned_cols=76  Identities=17%  Similarity=0.216  Sum_probs=63.7

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhh----CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-cCcCCcCCCCccEE
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRR----ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-VAARGLDVEDVNTV  178 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-~~~~Gldi~~v~~V  178 (233)
                      ..+.+++|.++|+..+.+.++.+.+    .++++..+++..+..++...++.+.+|+.+|+|+|. .+...+++.++++|
T Consensus       650 ~~g~~vlvlvPt~~La~Q~~~~~~~~~~~~~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~~~~~~~~l~lv  729 (1151)
T 2eyq_A          650 DNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLL  729 (1151)
T ss_dssp             TTTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCSSEEEE
T ss_pred             HhCCeEEEEechHHHHHHHHHHHHHHhhcCCCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhCCccccccceE
Confidence            4567999999999999888888764    367889999999999999999999999999999995 34555777777776


Q ss_pred             E
Q psy14082        179 N  179 (233)
Q Consensus       179 I  179 (233)
                      |
T Consensus       730 I  730 (1151)
T 2eyq_A          730 I  730 (1151)
T ss_dssp             E
T ss_pred             E
Confidence            6

>1uaa_A REP helicase, protein (ATP-dependent DNA helicase REP.); complex (helicase/DNA), DNA unwinding, hydrolase/DNA complex; HET: DNA; 3.00A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19

Probab=94.84  E-value=0.037  Score=50.32  Aligned_cols=56  Identities=7%  Similarity=-0.171  Sum_probs=41.4

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      +..+++.|+.|||||.+-+--+...+....    -...++|+++.|+..+.++.+.+.+.
T Consensus        15 ~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~----~~~~~IL~lTfT~~Aa~em~~Rl~~~   70 (673)
T 1uaa_A           15 TGPCLVLAGAGSGKTRVITNKIAHLIRGCG----YQARHIAAVTFTNKAAREMKERVGQT   70 (673)
T ss_dssp             SSEEEECCCTTSCHHHHHHHHHHHHHHHHC----CCGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCChHHHHHHHHHHHHHhcC----CCHHHeEEEeccHHHHHHHHHHHHHH
Confidence            456889999999999874433333333211    12457999999999999999999887

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=94.59  E-value=0.047  Score=47.27  Aligned_cols=48  Identities=6%  Similarity=-0.096  Sum_probs=36.4

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHH
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVA   64 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~   64 (233)
                      .+++.++.|||||.+ +..++..+...      ....+++++||...+..+.+.+
T Consensus        47 ~~li~G~aGTGKT~l-l~~~~~~l~~~------~~~~il~~a~T~~Aa~~l~~~~   94 (459)
T 3upu_A           47 HVTINGPAGTGATTL-TKFIIEALIST------GETGIILAAPTHAAKKILSKLS   94 (459)
T ss_dssp             EEEEECCTTSCHHHH-HHHHHHHHHHT------TCCCEEEEESSHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHH-HHHHHHHHHhc------CCceEEEecCcHHHHHHHHhhh
Confidence            789999999999965 55666666543      1246899999998888776554

>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=94.54  E-value=0.21  Score=38.18  Aligned_cols=71  Identities=18%  Similarity=0.280  Sum_probs=53.6

Q ss_pred             CCeEEEEecchhHHHHHHHHHhhC-----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEeccc-----C-cCCcCCCC
Q psy14082        106 AFKVIVFVETKKKVEDITRALRRE-----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDV-----A-ARGLDVED  174 (233)
Q Consensus       106 ~~k~iIf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~-----~-~~Gldi~~  174 (233)
                      ..+++|.++++..+++.++.+++.     +.++..++|+.+...+...+   ..+..+|+|+|..     + ...+++.+
T Consensus        82 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~---~~~~~~i~v~T~~~l~~~~~~~~~~~~~  158 (220)
T 1t6n_A           82 QVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVL---KKNCPHIVVGTPGRILALARNKSLNLKH  158 (220)
T ss_dssp             CCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHH---HHSCCSEEEECHHHHHHHHHTTSSCCTT
T ss_pred             CEEEEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHHH---hcCCCCEEEeCHHHHHHHHHhCCCCccc
Confidence            458999999999999988888764     68899999999877665544   4466799999942     1 23356677


Q ss_pred             ccEEE
Q psy14082        175 VNTVN  179 (233)
Q Consensus       175 v~~VI  179 (233)
                      ++++|
T Consensus       159 ~~~lV  163 (220)
T 1t6n_A          159 IKHFI  163 (220)
T ss_dssp             CCEEE
T ss_pred             CCEEE
Confidence            77766

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=94.50  E-value=0.034  Score=47.99  Aligned_cols=45  Identities=16%  Similarity=0.088  Sum_probs=33.3

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHH
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKE   66 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~   66 (233)
                      +=.++.++.|||||...    .+.+..         ...+|++||++++..+.+.+.+
T Consensus       162 ~v~~I~G~aGsGKTt~I----~~~~~~---------~~~lVlTpT~~aa~~l~~kl~~  206 (446)
T 3vkw_A          162 KVVLVDGVPGCGKTKEI----LSRVNF---------EEDLILVPGRQAAEMIRRRANA  206 (446)
T ss_dssp             EEEEEEECTTSCHHHHH----HHHCCT---------TTCEEEESCHHHHHHHHHHHTT
T ss_pred             cEEEEEcCCCCCHHHHH----HHHhcc---------CCeEEEeCCHHHHHHHHHHhhh
Confidence            34678999999999762    222211         2369999999999999988853

>1pjr_A PCRA; DNA repair, DNA replication, SOS response, helicase, ATP- binding, DNA-binding; 2.50A {Geobacillus stearothermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1qhg_A* 3pjr_A* 2pjr_A* 1qhh_B* 1qhh_D* 1qhh_A* 1qhh_C* 2pjr_B*

Probab=94.43  E-value=0.071  Score=48.99  Aligned_cols=56  Identities=5%  Similarity=-0.126  Sum_probs=40.9

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      +..+++.|..|||||.+-.- -+.++.....   -...++|+++.|+..|.++.+++.++
T Consensus        24 ~g~~lV~AgAGSGKT~vL~~-ri~~ll~~~~---~~p~~IL~vTFTnkAA~Em~~Rl~~~   79 (724)
T 1pjr_A           24 EGPLLIMAGAGSGKTRVLTH-RIAYLMAEKH---VAPWNILAITFTNKAAREMRERVQSL   79 (724)
T ss_dssp             SSCEEEEECTTSCHHHHHHH-HHHHHHHTTC---CCGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEcCCCCHHHHHHH-HHHHHHHhcC---CCHHHeEEEeccHHHHHHHHHHHHHH
Confidence            45688999999999988433 3333433211   12357999999999999999999887

>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=94.29  E-value=0.2  Score=39.05  Aligned_cols=72  Identities=14%  Similarity=0.169  Sum_probs=54.9

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhh----CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----cCc-CCcCCC
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRR----ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----VAA-RGLDVE  173 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----~~~-~Gldi~  173 (233)
                      ..+.+++|.++++..+.++.+.+++    .++.+..++|+.+...+...++.    ..+|+|+|.     .+. ..+++.
T Consensus       100 ~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~----~~~I~v~Tp~~l~~~l~~~~~~~~  175 (242)
T 3fe2_A          100 GDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLER----GVEICIATPGRLIDFLECGKTNLR  175 (242)
T ss_dssp             TCCCSEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHH----CCSEEEECHHHHHHHHHHTSCCCT
T ss_pred             CCCCEEEEEeCcHHHHHHHHHHHHHHHhhcCceEEEEECCCChHHHHHHhcC----CCCEEEECHHHHHHHHHcCCCCcc
Confidence            3567899999999999988777765    47899999999998877666554    579999994     222 235677


Q ss_pred             CccEEE
Q psy14082        174 DVNTVN  179 (233)
Q Consensus       174 ~v~~VI  179 (233)
                      +++++|
T Consensus       176 ~~~~lV  181 (242)
T 3fe2_A          176 RTTYLV  181 (242)
T ss_dssp             TCCEEE
T ss_pred             cccEEE
Confidence            788776

>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=94.19  E-value=0.14  Score=45.13  Aligned_cols=59  Identities=17%  Similarity=0.247  Sum_probs=55.0

Q ss_pred             CCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc
Q psy14082        106 AFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD  164 (233)
Q Consensus       106 ~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~  164 (233)
                      .++++|.++++.-++.....|.+.|+.+..+||+.+..++......+..|..+++++|+
T Consensus        65 ~g~~lvi~P~~aL~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tp  123 (523)
T 1oyw_A           65 NGLTVVVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAP  123 (523)
T ss_dssp             SSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECH
T ss_pred             CCCEEEECChHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECH
Confidence            36899999999999999999999999999999999999999999999999999999984

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=93.99  E-value=0.31  Score=38.32  Aligned_cols=74  Identities=15%  Similarity=0.214  Sum_probs=54.9

Q ss_pred             hcCCCCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEeccc-----Cc--CCc
Q psy14082        102 AKNPAFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDV-----AA--RGL  170 (233)
Q Consensus       102 ~~~~~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~-----~~--~Gl  170 (233)
                      ....+.+++|.++++..+.++++.+++.    ++.+..++|+.+...+...+.    +..+|+|+|..     +.  .++
T Consensus       107 ~~~~~~~~lil~Ptr~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~I~v~Tp~~l~~~l~~~~~~  182 (249)
T 3ber_A          107 ETPQRLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLALA----KKPHIIIATPGRLIDHLENTKGF  182 (249)
T ss_dssp             HSCCSSCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEEECTTSCHHHHHHHHH----TCCSEEEECHHHHHHHHHHSTTC
T ss_pred             cCCCCceEEEEeCCHHHHHHHHHHHHHHhccCCeeEEEEECCCChHHHHHHhc----CCCCEEEECHHHHHHHHHcCCCc
Confidence            3445678999999999999888887654    788999999988766554433    46899999942     21  356


Q ss_pred             CCCCccEEE
Q psy14082        171 DVEDVNTVN  179 (233)
Q Consensus       171 di~~v~~VI  179 (233)
                      ++.++++||
T Consensus       183 ~l~~~~~lV  191 (249)
T 3ber_A          183 NLRALKYLV  191 (249)
T ss_dssp             CCTTCCEEE
T ss_pred             CccccCEEE
Confidence            777788776

>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=93.98  E-value=0.24  Score=42.36  Aligned_cols=124  Identities=18%  Similarity=0.215  Sum_probs=79.6

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----cCcCC-cCCCC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----VAARG-LDVED  174 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----~~~~G-ldi~~  174 (233)
                      .+.+++|.++|+.-+.++++.+++.    ++++..++|+.+...+...+.    ...+|+|+|.     .+.++ +++.+
T Consensus       128 ~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~----~~~~Ivv~Tp~~l~~~l~~~~~~l~~  203 (434)
T 2db3_A          128 GRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECIT----RGCHVVIATPGRLLDFVDRTFITFED  203 (434)
T ss_dssp             TCCSEEEECSSHHHHHHHHHHHHHHTTTSSCCCCEECTTSCHHHHHHHHT----TCCSEEEECHHHHHHHHHTTSCCCTT
T ss_pred             CCccEEEEecCHHHHHHHHHHHHHHhccCCcEEEEEECCCCHHHHHHHhh----cCCCEEEEChHHHHHHHHhCCccccc
Confidence            3568999999999999998888763    577889999998776654432    3579999993     22222 34455


Q ss_pred             ccEEEE--------------------------------ec--CCCC----------------------cccccceeeEEe
Q psy14082        175 VNTVNI--------------------------------GS--LQLS----------------------ANHNISQVIEVV  198 (233)
Q Consensus       175 v~~VI~--------------------------------~d--~P~~----------------------~~~~i~~~~~~~  198 (233)
                      ++++|.                                +.  +|..                      ....+.+.+..+
T Consensus       204 ~~~lVlDEah~~~~~gf~~~~~~i~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~  283 (434)
T 2db3_A          204 TRFVVLDEADRMLDMGFSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTIYEV  283 (434)
T ss_dssp             CCEEEEETHHHHTSTTTHHHHHHHHHCTTSCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEEESSTTCCCTTEEEEEEEC
T ss_pred             CCeEEEccHhhhhccCcHHHHHHHHHhcCCCCCceEEEEeccCCHHHHHHHHHhccCCEEEEeccccccccccceEEEEe
Confidence            555442                                11  0000                      001112344455


Q ss_pred             ecchHHHHHHHHHHhhcCcccccccchhhHhhhc
Q psy14082        199 QDYEKEKRLFSLIRELGKYTLITQESSSTLSEMV  232 (233)
Q Consensus       199 ~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~l~  232 (233)
                      .+.++...+.+.+.+.....+.+.+.+..++.++
T Consensus       284 ~~~~k~~~l~~~l~~~~~~~lVF~~t~~~a~~l~  317 (434)
T 2db3_A          284 NKYAKRSKLIEILSEQADGTIVFVETKRGADFLA  317 (434)
T ss_dssp             CGGGHHHHHHHHHHHCCTTEEEECSSHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHhCCCCEEEEEeCcHHHHHHH
Confidence            6666777788888777666778888777776553

>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=93.78  E-value=0.15  Score=45.75  Aligned_cols=60  Identities=13%  Similarity=0.175  Sum_probs=54.8

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHh--hCCCCCEEEecc
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDF--RQGKAPILVATD  164 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f--~~g~~~iLv~T~  164 (233)
                      ..+++||.++++.-++...+.|.+.|+.+..++|+++..++...++.+  ..+..+|+++|+
T Consensus        83 ~~g~~lVisP~~~L~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tp  144 (591)
T 2v1x_A           83 SDGFTLVICPLISLMEDQLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTP  144 (591)
T ss_dssp             SSSEEEEECSCHHHHHHHHHHHHHHTCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECH
T ss_pred             cCCcEEEEeCHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEECh
Confidence            356999999999999999999999999999999999999999998888  578899999996

>1e9r_A Conjugal transfer protein TRWB; coupling protein, bacterial conjugation, F1-ATPase-like quaternary structure, ring helicases; 2.4A {Escherichia coli} SCOP: c.37.1.11 PDB: 1e9s_A 1gki_A* 1gl7_A* 1gl6_A*

Probab=93.74  E-value=0.053  Score=46.52  Aligned_cols=48  Identities=8%  Similarity=0.012  Sum_probs=35.7

Q ss_pred             CCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHH
Q psy14082          3 PPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQ   58 (233)
Q Consensus         3 p~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~   58 (233)
                      |.-....++++.++||||||.. +-+++..+...       +..++|+=|..|+..
T Consensus        48 ~~~~~~~h~~i~G~tGsGKs~~-~~~li~~~~~~-------g~~viv~Dpkge~~~   95 (437)
T 1e9r_A           48 PRDAEPRHLLVNGATGTGKSVL-LRELAYTGLLR-------GDRMVIVDPNGDMLS   95 (437)
T ss_dssp             CGGGGGGCEEEEECTTSSHHHH-HHHHHHHHHHT-------TCEEEEEEETTHHHH
T ss_pred             ccccCcceEEEECCCCCCHHHH-HHHHHHHHHHC-------CCcEEEEeCCCchhH
Confidence            4444678999999999999987 45566555542       567888889888864

>3hjh_A Transcription-repair-coupling factor; MFD, mutation frequency decline, ATP-binding, DNA DAMA repair, DNA-binding, helicase, hydrolase; 1.95A {Escherichia coli} PDB: 2b2n_A* 4dfc_A

Probab=93.47  E-value=0.15  Score=44.54  Aligned_cols=53  Identities=13%  Similarity=0.112  Sum_probs=40.4

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcC
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSA   70 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~   70 (233)
                      .|....+.+.||||||++ +..++...          +..+|||+|+...|.|+++.++.|.+.
T Consensus        13 ~~~~~~l~g~~gs~ka~~-~a~l~~~~----------~~p~lvv~~~~~~A~~l~~~l~~~~~~   65 (483)
T 3hjh_A           13 AGEQRLLGELTGAACATL-VAEIAERH----------AGPVVLIAPDMQNALRLHDEISQFTDQ   65 (483)
T ss_dssp             TTCEEEEECCCTTHHHHH-HHHHHHHS----------SSCEEEEESSHHHHHHHHHHHHHTCSS
T ss_pred             CCCeEEEeCCCchHHHHH-HHHHHHHh----------CCCEEEEeCCHHHHHHHHHHHHhhCCC
Confidence            466788899999999987 33333322          223899999999999999999998543

>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=93.32  E-value=0.26  Score=38.06  Aligned_cols=72  Identities=13%  Similarity=0.113  Sum_probs=53.6

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhC-----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEeccc-----C-cCCcC
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRE-----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDV-----A-ARGLD  171 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~-----~-~~Gld  171 (233)
                      ...+.+++|.++++..+++..+.+++.     ++++..++|+.+..++...+     ...+|+|+|..     + ...++
T Consensus        89 ~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-----~~~~Iiv~Tp~~l~~~~~~~~~~  163 (230)
T 2oxc_A           89 ENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRL-----KKCHIAVGSPGRIKQLIELDYLN  163 (230)
T ss_dssp             TSCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHT-----TSCSEEEECHHHHHHHHHTTSSC
T ss_pred             cCCCceEEEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhc-----cCCCEEEECHHHHHHHHhcCCcc
Confidence            345679999999999999999888764     67889999999877665543     25799999952     1 23456


Q ss_pred             CCCccEEE
Q psy14082        172 VEDVNTVN  179 (233)
Q Consensus       172 i~~v~~VI  179 (233)
                      ..+++++|
T Consensus       164 ~~~~~~lV  171 (230)
T 2oxc_A          164 PGSIRLFI  171 (230)
T ss_dssp             GGGCCEEE
T ss_pred             cccCCEEE
Confidence            66777665

>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=93.06  E-value=0.28  Score=37.72  Aligned_cols=72  Identities=13%  Similarity=0.247  Sum_probs=48.7

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhC---CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----c-CcCCcCCCC
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRE---RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----V-AARGLDVED  174 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~---~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----~-~~~Gldi~~  174 (233)
                      ..+.++++.++++..+.++.+.+.+.   +..+..++|+.+...+...+   .. ..+|+|+|.     . ....+++.+
T Consensus        92 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~-~~~iiv~Tp~~l~~~~~~~~~~~~~  167 (228)
T 3iuy_A           92 RNGPGMLVLTPTRELALHVEAECSKYSYKGLKSICIYGGRNRNGQIEDI---SK-GVDIIIATPGRLNDLQMNNSVNLRS  167 (228)
T ss_dssp             -CCCSEEEECSSHHHHHHHHHHHHHHCCTTCCEEEECC------CHHHH---HS-CCSEEEECHHHHHHHHHTTCCCCTT
T ss_pred             cCCCcEEEEeCCHHHHHHHHHHHHHhcccCceEEEEECCCChHHHHHHh---cC-CCCEEEECHHHHHHHHHcCCcCccc
Confidence            36678999999999999999988764   67888999987766554443   32 489999994     1 223456777


Q ss_pred             ccEEE
Q psy14082        175 VNTVN  179 (233)
Q Consensus       175 v~~VI  179 (233)
                      +++||
T Consensus       168 ~~~lV  172 (228)
T 3iuy_A          168 ITYLV  172 (228)
T ss_dssp             CCEEE
T ss_pred             ceEEE
Confidence            88776

>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=92.64  E-value=0.46  Score=35.69  Aligned_cols=72  Identities=17%  Similarity=0.163  Sum_probs=52.9

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhC--CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----cCc-CCcCCCCc
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRE--RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----VAA-RGLDVEDV  175 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----~~~-~Gldi~~v  175 (233)
                      ..+.++++.++++..+....+.+.+.  +.++..++|+.+...+...+..    ..+|+|+|.     .+. ..+++.++
T Consensus        70 ~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~i~v~T~~~l~~~~~~~~~~~~~~  145 (207)
T 2gxq_A           70 GRKPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALLR----GADAVVATPGRALDYLRQGVLDLSRV  145 (207)
T ss_dssp             TCCCSEEEECSSHHHHHHHHHHHHHHCTTSCEEEECSSSCSHHHHHHHHH----CCSEEEECHHHHHHHHHHTSSCCTTC
T ss_pred             CCCCcEEEEECCHHHHHHHHHHHHHHhhcceEEEEECCCChHHHHHHhhC----CCCEEEECHHHHHHHHHcCCcchhhc
Confidence            35678999999999999999999775  4678889998876655544432    578999994     222 23566777


Q ss_pred             cEEE
Q psy14082        176 NTVN  179 (233)
Q Consensus       176 ~~VI  179 (233)
                      ++||
T Consensus       146 ~~iV  149 (207)
T 2gxq_A          146 EVAV  149 (207)
T ss_dssp             SEEE
T ss_pred             eEEE
Confidence            7766

>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=92.37  E-value=0.63  Score=38.54  Aligned_cols=72  Identities=17%  Similarity=0.254  Sum_probs=53.3

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhC-----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccC------cCCcCCC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRE-----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVA------ARGLDVE  173 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~------~~Gldi~  173 (233)
                      .+.+++|.++++..+++..+.+.+.     ++++..++|+.+.......+   ..+..+|+|+|...      ...++..
T Consensus        75 ~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~---~~~~~~iiv~T~~~l~~~~~~~~~~~~  151 (391)
T 1xti_A           75 GQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVL---KKNCPHIVVGTPGRILALARNKSLNLK  151 (391)
T ss_dssp             TCCCEEEECSCHHHHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHHH---HHSCCSEEEECHHHHHHHHHTTSSCCT
T ss_pred             CCeeEEEECCCHHHHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHHH---hcCCCCEEEECHHHHHHHHHcCCcccc
Confidence            4569999999999999988888764     78899999999877765544   34668999999421      2234566


Q ss_pred             CccEEE
Q psy14082        174 DVNTVN  179 (233)
Q Consensus       174 ~v~~VI  179 (233)
                      ++++||
T Consensus       152 ~~~~vV  157 (391)
T 1xti_A          152 HIKHFI  157 (391)
T ss_dssp             TCSEEE
T ss_pred             ccCEEE
Confidence            666665

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=92.36  E-value=0.26  Score=38.14  Aligned_cols=71  Identities=20%  Similarity=0.220  Sum_probs=49.9

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEeccc-----CcC--CcCC
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDV-----AAR--GLDV  172 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~-----~~~--Gldi  172 (233)
                      ..+.+++|.++++..+.+..+.+++.    ++.+..++|+.+.......+     +..+|+|+|..     +.+  .++.
T Consensus        95 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-----~~~~iiv~Tp~~l~~~l~~~~~~~~  169 (236)
T 2pl3_A           95 TDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERI-----NNINILVCTPGRLLQHMDETVSFHA  169 (236)
T ss_dssp             GGCCCEEEECSSHHHHHHHHHHHHHHTTTSSCCEEEECCC--CHHHHHHH-----TTCSEEEECHHHHHHHHHHCSSCCC
T ss_pred             cCCceEEEEeCCHHHHHHHHHHHHHHhCCCCeeEEEEECCCCHHHHHHhC-----CCCCEEEECHHHHHHHHHhcCCccc
Confidence            35678999999999999999888764    47888999987765544433     36799999942     112  3566


Q ss_pred             CCccEEE
Q psy14082        173 EDVNTVN  179 (233)
Q Consensus       173 ~~v~~VI  179 (233)
                      .++++||
T Consensus       170 ~~~~~lV  176 (236)
T 2pl3_A          170 TDLQMLV  176 (236)
T ss_dssp             TTCCEEE
T ss_pred             ccccEEE
Confidence            6777666

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=91.98  E-value=0.1  Score=38.74  Aligned_cols=51  Identities=12%  Similarity=0.021  Sum_probs=30.9

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHH
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVA   64 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~   64 (233)
                      ..|..+++.+|+|+|||.. +-.+...+...      .+..++ .++..++..++...+
T Consensus        36 ~~g~~~~l~G~~G~GKTtL-~~~i~~~~~~~------~g~~~~-~~~~~~~~~~~~~~~   86 (180)
T 3ec2_A           36 EEGKGLTFVGSPGVGKTHL-AVATLKAIYEK------KGIRGY-FFDTKDLIFRLKHLM   86 (180)
T ss_dssp             GGCCEEEECCSSSSSHHHH-HHHHHHHHHHH------SCCCCC-EEEHHHHHHHHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH-HHHHHHHHHHH------cCCeEE-EEEHHHHHHHHHHHh
Confidence            3478899999999999966 44455554322      132333 345556666655444

>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=91.87  E-value=0.74  Score=34.51  Aligned_cols=72  Identities=13%  Similarity=0.216  Sum_probs=51.5

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhC-----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----cCcC-CcCC
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRE-----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----VAAR-GLDV  172 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----~~~~-Gldi  172 (233)
                      ..+.++++.++++..+++..+.+.+.     +..+..++|+.+..+....   + .+..+|+|+|.     .+.+ ..++
T Consensus        69 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~-~~~~~i~v~T~~~l~~~~~~~~~~~  144 (206)
T 1vec_A           69 KDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMR---L-DDTVHVVIATPGRILDLIKKGVAKV  144 (206)
T ss_dssp             SCSCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHH---T-TSCCSEEEECHHHHHHHHHTTCSCC
T ss_pred             CCCeeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHh---c-CCCCCEEEeCHHHHHHHHHcCCcCc
Confidence            34568999999999999888888653     5788889999887654433   2 24679999995     2222 3456


Q ss_pred             CCccEEE
Q psy14082        173 EDVNTVN  179 (233)
Q Consensus       173 ~~v~~VI  179 (233)
                      .+++++|
T Consensus       145 ~~~~~lV  151 (206)
T 1vec_A          145 DHVQMIV  151 (206)
T ss_dssp             TTCCEEE
T ss_pred             ccCCEEE
Confidence            6777766

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=91.55  E-value=0.15  Score=39.57  Aligned_cols=53  Identities=9%  Similarity=-0.147  Sum_probs=33.3

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ..|.-+++.+++|+|||.. ++-++.....       .+..++++.. .+-..++.+.+..+
T Consensus        21 ~~G~~~~i~G~~GsGKTtl-~~~~~~~~~~-------~~~~v~~~~~-e~~~~~~~~~~~~~   73 (247)
T 2dr3_A           21 PERNVVLLSGGPGTGKTIF-SQQFLWNGLK-------MGEPGIYVAL-EEHPVQVRQNMAQF   73 (247)
T ss_dssp             ETTCEEEEEECTTSSHHHH-HHHHHHHHHH-------TTCCEEEEES-SSCHHHHHHHHHTT
T ss_pred             CCCcEEEEECCCCCCHHHH-HHHHHHHHHh-------cCCeEEEEEc-cCCHHHHHHHHHHc
Confidence            4677789999999999965 4444444332       2445777663 34456666666544

>2l82_A Designed protein OR32; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, de novo protein; NMR {Artificial gene}

Probab=91.24  E-value=1.5  Score=29.79  Aligned_cols=50  Identities=18%  Similarity=0.399  Sum_probs=44.0

Q ss_pred             EEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCC
Q psy14082        109 VIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAP  158 (233)
Q Consensus       109 ~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~  158 (233)
                      .++|.+...-...+...++..|..++.++++.+.+.|.+-++.|.....+
T Consensus         5 fvvfssdpeilkeivreikrqgvrvvllysdqdekrrrerleefekqgvd   54 (162)
T 2l82_A            5 FVVFSSDPEILKEIVREIKRQGVRVVLLYSDQDEKRRRERLEEFEKQGVD   54 (162)
T ss_dssp             EEEEESCHHHHHHHHHHHHHTTCEEEEEECCSCHHHHHHHHHHHHTTTCE
T ss_pred             EEEecCCHHHHHHHHHHHHhCCeEEEEEecCchHHHHHHHHHHHHHcCCc
Confidence            46888889999999999999999999999999999999999998765443

>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=91.15  E-value=0.48  Score=36.74  Aligned_cols=72  Identities=13%  Similarity=0.188  Sum_probs=45.5

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----cCcC-CcCCCC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----VAAR-GLDVED  174 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----~~~~-Gldi~~  174 (233)
                      .+.+++|.++++..+..+.+.+++.    +..+..++|+.+....   .+.+..+..+|+|+|.     .+.+ .++...
T Consensus        97 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~---~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~  173 (237)
T 3bor_A           97 KETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNE---MQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKW  173 (237)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECC----------------CCCSEEEECHHHHHHHHHTTSSCSTT
T ss_pred             CCceEEEEECcHHHHHHHHHHHHHHhhhcCceEEEEECCCchHHH---HHHHhcCCCCEEEECHHHHHHHHHhCCcCccc
Confidence            5679999999999999998888754    5677888888654433   3445567789999993     3333 356667


Q ss_pred             ccEEE
Q psy14082        175 VNTVN  179 (233)
Q Consensus       175 v~~VI  179 (233)
                      +++||
T Consensus       174 ~~~lV  178 (237)
T 3bor_A          174 IKMFV  178 (237)
T ss_dssp             CCEEE
T ss_pred             CcEEE
Confidence            77766

>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=90.98  E-value=1.2  Score=35.16  Aligned_cols=71  Identities=18%  Similarity=0.241  Sum_probs=52.8

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhh----CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----cC--cCCcCCC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRR----ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----VA--ARGLDVE  173 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----~~--~~Gldi~  173 (233)
                      .+.++++.++++.-+++..+.+++    .+..+..++|+.+.......+..   + .+|+|+|.     .+  ..++++.
T Consensus       125 ~~~~~lil~Pt~~La~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~---~-~~Iiv~Tp~~l~~~~~~~~~~~~~  200 (262)
T 3ly5_A          125 NGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGN---G-INIIVATPGRLLDHMQNTPGFMYK  200 (262)
T ss_dssp             GCCCEEEECSSHHHHHHHHHHHHHHTTTCCSCEEEECSSSCHHHHHHHHHH---C-CSEEEECHHHHHHHHHHCTTCCCT
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHHhhcCceEEEEECCCCHHHHHHHhcC---C-CCEEEEcHHHHHHHHHccCCcccc
Confidence            567899999999999999888876    35678889999887665544432   3 89999993     11  1246777


Q ss_pred             CccEEE
Q psy14082        174 DVNTVN  179 (233)
Q Consensus       174 ~v~~VI  179 (233)
                      ++++||
T Consensus       201 ~l~~lV  206 (262)
T 3ly5_A          201 NLQCLV  206 (262)
T ss_dssp             TCCEEE
T ss_pred             cCCEEE
Confidence            888776

>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=90.82  E-value=3.3  Score=30.25  Aligned_cols=37  Identities=14%  Similarity=0.195  Sum_probs=31.7

Q ss_pred             CceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCCC
Q psy14082         44 GPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPK   82 (233)
Q Consensus        44 ~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~   82 (233)
                      +.++||.|++++-+..+++.+...  ++.+..++|+.+.
T Consensus        31 ~~~~lVF~~~~~~~~~l~~~L~~~--~~~~~~~hg~~~~   67 (172)
T 1t5i_A           31 FNQVVIFVKSVQRCIALAQLLVEQ--NFPAIAIHRGMPQ   67 (172)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHHT--TCCEEEECTTSCH
T ss_pred             CCcEEEEECCHHHHHHHHHHHHhc--CCCEEEEECCCCH
Confidence            457999999999999999999877  7788899998653

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19

Probab=90.66  E-value=0.92  Score=35.38  Aligned_cols=71  Identities=14%  Similarity=0.101  Sum_probs=50.8

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEeccc-----Cc-CCcCCCC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDV-----AA-RGLDVED  174 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~-----~~-~Gldi~~  174 (233)
                      .+.+++|.++++..+.+..+.+++.    ++.+..++|+.+.......+    ....+|+|+|..     +. ..+++.+
T Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~----~~~~~Ivv~Tp~~l~~~l~~~~~~~~~  174 (253)
T 1wrb_A           99 AYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREV----QMGCHLLVATPGRLVDFIEKNKISLEF  174 (253)
T ss_dssp             BCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHH----SSCCSEEEECHHHHHHHHHTTSBCCTT
T ss_pred             CCceEEEEECCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHh----CCCCCEEEECHHHHHHHHHcCCCChhh
Confidence            3468999999999999988887653    57788899988766554433    246799999942     22 2356677


Q ss_pred             ccEEE
Q psy14082        175 VNTVN  179 (233)
Q Consensus       175 v~~VI  179 (233)
                      ++++|
T Consensus       175 ~~~lV  179 (253)
T 1wrb_A          175 CKYIV  179 (253)
T ss_dssp             CCEEE
T ss_pred             CCEEE
Confidence            77766

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=90.51  E-value=0.52  Score=38.53  Aligned_cols=54  Identities=6%  Similarity=-0.106  Sum_probs=34.8

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      +..|.=+++.+++|+|||. |++-+......+       +..+++++.- +-..|+..++...
T Consensus        65 l~~G~l~li~G~pG~GKTt-l~l~ia~~~a~~-------g~~vl~~slE-~s~~~l~~R~~~~  118 (315)
T 3bh0_A           65 YKRRNFVLIAARPSMGKTA-FALKQAKNMSDN-------DDVVNLHSLE-MGKKENIKRLIVT  118 (315)
T ss_dssp             BCTTCEEEEECCTTSSHHH-HHHHHHHHHHTT-------TCEEEEEESS-SCHHHHHHHHHHH
T ss_pred             CCCCcEEEEEeCCCCCHHH-HHHHHHHHHHHc-------CCeEEEEECC-CCHHHHHHHHHHH
Confidence            4567778999999999994 455555444332       3567777643 4455666665544

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=90.50  E-value=0.25  Score=37.13  Aligned_cols=38  Identities=13%  Similarity=0.038  Sum_probs=27.2

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCc
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPT   53 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~Pt   53 (233)
                      |+=.+..++.|+|||.. ++-++.++..       .+.+++++.|.
T Consensus         3 g~i~vi~G~~gsGKTT~-ll~~~~~~~~-------~g~~v~~~~~~   40 (184)
T 2orw_A            3 GKLTVITGPMYSGKTTE-LLSFVEIYKL-------GKKKVAVFKPK   40 (184)
T ss_dssp             CCEEEEEESTTSSHHHH-HHHHHHHHHH-------TTCEEEEEEEC
T ss_pred             cEEEEEECCCCCCHHHH-HHHHHHHHHH-------CCCeEEEEeec
Confidence            56677899999999977 4445555443       25578888887

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=90.41  E-value=0.13  Score=36.86  Aligned_cols=19  Identities=5%  Similarity=-0.293  Sum_probs=16.5

Q ss_pred             CCCCceeEecCCCCCchHH
Q psy14082          6 ESGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~   24 (233)
                      ..+..+++.+++|+|||..
T Consensus        22 ~~~~~vll~G~~GtGKt~l   40 (145)
T 3n70_A           22 ETDIAVWLYGAPGTGRMTG   40 (145)
T ss_dssp             TCCSCEEEESSTTSSHHHH
T ss_pred             CCCCCEEEECCCCCCHHHH
Confidence            4567899999999999976

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=89.83  E-value=0.26  Score=40.61  Aligned_cols=28  Identities=0%  Similarity=-0.231  Sum_probs=22.3

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhc
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISH   35 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~   35 (233)
                      .+..+++.+|||+|||++ +-.++..+..
T Consensus        44 ~~~~lli~GpPGTGKT~~-v~~v~~~L~~   71 (318)
T 3te6_A           44 QNKLFYITNADDSTKFQL-VNDVMDELIT   71 (318)
T ss_dssp             CCCEEEEECCCSHHHHHH-HHHHHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHH-HHHHHHHHHH
Confidence            467899999999999977 5566766654

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=89.67  E-value=0.24  Score=38.60  Aligned_cols=40  Identities=13%  Similarity=0.115  Sum_probs=28.6

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcH
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTR   54 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~Ptr   54 (233)
                      .|.=.++.+++|+|||.+ ++-.+.++..       .+.+++++.|..
T Consensus        11 ~G~i~litG~mGsGKTT~-ll~~~~r~~~-------~g~kVli~~~~~   50 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAE-LIRRLHRLEY-------ADVKYLVFKPKI   50 (223)
T ss_dssp             CCEEEEEECSTTSCHHHH-HHHHHHHHHH-------TTCCEEEEEECC
T ss_pred             CcEEEEEECCCCCcHHHH-HHHHHHHHHh-------cCCEEEEEEecc
Confidence            355677889999999977 5556666543       366788887754

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=89.66  E-value=0.13  Score=39.93  Aligned_cols=53  Identities=9%  Similarity=-0.006  Sum_probs=32.5

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHh-hhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVH-ISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~-l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      +.|.=+++.+++|+|||.- ++-++.. ...       .+..+++++- .+-..|+.+.+..+
T Consensus        28 ~~G~l~~i~G~pG~GKT~l-~l~~~~~~~~~-------~~~~v~~~s~-E~~~~~~~~~~~~~   81 (251)
T 2zts_A           28 PEGTTVLLTGGTGTGKTTF-AAQFIYKGAEE-------YGEPGVFVTL-EERARDLRREMASF   81 (251)
T ss_dssp             ETTCEEEEECCTTSSHHHH-HHHHHHHHHHH-------HCCCEEEEES-SSCHHHHHHHHHTT
T ss_pred             CCCeEEEEEeCCCCCHHHH-HHHHHHHHHHh-------cCCCceeecc-cCCHHHHHHHHHHc
Confidence            4577789999999999944 4443332 222       1334666653 34466666666554

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=89.66  E-value=0.55  Score=35.84  Aligned_cols=71  Identities=14%  Similarity=0.137  Sum_probs=45.3

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhh----CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccC------cCCcCCC
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRR----ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVA------ARGLDVE  173 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~------~~Gldi~  173 (233)
                      ..+.++++.++++..+.+..+.+.+    .+..+..++|+.+..++...   +.  ..+|+|+|...      ...++..
T Consensus        80 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~~--~~~iiv~Tp~~l~~~~~~~~~~~~  154 (224)
T 1qde_A           80 VKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEG---LR--DAQIVVGTPGRVFDNIQRRRFRTD  154 (224)
T ss_dssp             CCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC-------------CT--TCSEEEECHHHHHHHHHTTSSCCT
T ss_pred             CCCceEEEEECCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHhc---CC--CCCEEEECHHHHHHHHHhCCcchh
Confidence            4567999999999999988888765    36788889998776554432   22  37899999521      2345666


Q ss_pred             CccEEE
Q psy14082        174 DVNTVN  179 (233)
Q Consensus       174 ~v~~VI  179 (233)
                      .+++||
T Consensus       155 ~~~~iV  160 (224)
T 1qde_A          155 KIKMFI  160 (224)
T ss_dssp             TCCEEE
T ss_pred             hCcEEE
Confidence            777766

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=89.42  E-value=0.41  Score=35.00  Aligned_cols=27  Identities=7%  Similarity=-0.241  Sum_probs=20.0

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhc
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISH   35 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~   35 (233)
                      +..+++.+++|+|||.. +-.+...+..
T Consensus        43 ~~~~ll~G~~G~GKT~l-~~~~~~~~~~   69 (195)
T 1jbk_A           43 KNNPVLIGEPGVGKTAI-VEGLAQRIIN   69 (195)
T ss_dssp             SCEEEEECCTTSCHHHH-HHHHHHHHHH
T ss_pred             CCceEEECCCCCCHHHH-HHHHHHHHHh
Confidence            46799999999999966 4555555543

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=89.41  E-value=0.14  Score=36.59  Aligned_cols=18  Identities=6%  Similarity=-0.304  Sum_probs=15.6

Q ss_pred             CCCceeEecCCCCCchHH
Q psy14082          7 SGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~   24 (233)
                      .+..+++.+++|+|||..
T Consensus        26 ~~~~vll~G~~GtGKt~l   43 (143)
T 3co5_A           26 RTSPVFLTGEAGSPFETV   43 (143)
T ss_dssp             CSSCEEEEEETTCCHHHH
T ss_pred             CCCcEEEECCCCccHHHH
Confidence            467899999999999965

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=89.27  E-value=0.38  Score=36.19  Aligned_cols=25  Identities=4%  Similarity=-0.194  Sum_probs=19.2

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhh
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      ..+++.+++|+|||.. +-.+...+.
T Consensus        55 ~~~~l~G~~GtGKT~l-a~~i~~~~~   79 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYL-LAAIANELA   79 (202)
T ss_dssp             CEEEEECSTTSSHHHH-HHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHH-HHHHHHHHH
Confidence            6799999999999976 445555554

>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=89.17  E-value=0.97  Score=43.32  Aligned_cols=70  Identities=13%  Similarity=0.186  Sum_probs=55.7

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhC----CC----eeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----cCcCCcC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRE----RH----SAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----VAARGLD  171 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~----~~----~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----~~~~Gld  171 (233)
                      .+.+++|.++|+..+.++++.+++.    ++    .+..+||+.+..++....+.+++  .+|+|+|+     .+.+   
T Consensus        98 ~~~~~lil~PtreLa~Q~~~~l~~l~~~~~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~--~~IlV~TP~~L~~~l~~---  172 (1054)
T 1gku_B           98 KGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRN--FKIVITTTQFLSKHYRE---  172 (1054)
T ss_dssp             TSCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGG--CSEEEEEHHHHHHCSTT---
T ss_pred             cCCeEEEEeccHHHHHHHHHHHHHHHhhcCCCccceEEEEeCCCChhhHHHHHhhccC--CCEEEEcHHHHHHHHHH---
Confidence            5679999999999999988888643    56    78999999999998888888877  89999995     2222   


Q ss_pred             CCCccEEE
Q psy14082        172 VEDVNTVN  179 (233)
Q Consensus       172 i~~v~~VI  179 (233)
                      +.++++||
T Consensus       173 L~~l~~lV  180 (1054)
T 1gku_B          173 LGHFDFIF  180 (1054)
T ss_dssp             SCCCSEEE
T ss_pred             hccCCEEE
Confidence            44666665

>3cpe_A Terminase, DNA packaging protein GP17; large terminase, alternative initiation, ATP-binding, DNA- binding, hydrolase, nuclease; HET: DNA; 2.80A {Bacteriophage T4} PDB: 3ezk_A*

Probab=89.15  E-value=0.85  Score=40.73  Aligned_cols=54  Identities=9%  Similarity=0.058  Sum_probs=42.5

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      .+-+++..+.|+|||.+.+.-++..+..      .++..+++++|+++.|..+++.++.+
T Consensus       178 ~r~~~i~~~Rq~GKS~~~a~~~l~~~~~------~~~~~i~~va~t~~qA~~~~~~i~~~  231 (592)
T 3cpe_A          178 KRMTVCNLSRQLGKTTVVAIFLAHFVCF------NKDKAVGILAHKGSMSAEVLDRTKQA  231 (592)
T ss_dssp             CSEEEEEECSSSCHHHHHHHHHHHHHHT------SSSCEEEEEESSHHHHHHHHHHHHHH
T ss_pred             ccEEEEEEcCccChHHHHHHHHHHHHHh------CCCCeEEEEECCHHHHHHHHHHHHHH
Confidence            4568899999999998866545544443      23568999999999999999888877

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=89.14  E-value=0.51  Score=34.43  Aligned_cols=27  Identities=7%  Similarity=-0.162  Sum_probs=19.7

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhc
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISH   35 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~   35 (233)
                      +..+++.+++|+|||.. +-.+...+..
T Consensus        43 ~~~vll~G~~G~GKT~l-a~~~~~~~~~   69 (187)
T 2p65_A           43 KNNPILLGDPGVGKTAI-VEGLAIKIVQ   69 (187)
T ss_dssp             SCEEEEESCGGGCHHHH-HHHHHHHHHT
T ss_pred             CCceEEECCCCCCHHHH-HHHHHHHHHh
Confidence            56789999999999965 4445555543

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=88.82  E-value=0.36  Score=39.38  Aligned_cols=26  Identities=8%  Similarity=-0.207  Sum_probs=20.3

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      +..+++.+|||+|||.. +..+...+.
T Consensus       152 ~~~lll~G~~GtGKT~L-a~aia~~~~  177 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYL-LAAMAHELS  177 (308)
T ss_dssp             CCEEEEECSTTSSHHHH-HHHHHHHHH
T ss_pred             CceEEEECCCCCCHHHH-HHHHHHHHH
Confidence            57899999999999976 445555554

>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=88.59  E-value=1  Score=39.29  Aligned_cols=70  Identities=16%  Similarity=0.139  Sum_probs=47.2

Q ss_pred             CCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----cCcCC-c-CCCC
Q psy14082        106 AFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----VAARG-L-DVED  174 (233)
Q Consensus       106 ~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----~~~~G-l-di~~  174 (233)
                      +.+++|.++++..+......+.+.    ++.+..+||+.+...+...+..    ..+|+|+|.     .+..+ + ++.+
T Consensus        55 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~----~~~i~v~T~~~l~~~~~~~~~~~~~~  130 (556)
T 4a2p_A           55 KAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIE----DSDIIVVTPQILVNSFEDGTLTSLSI  130 (556)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEECCCC-----CHHHHHH----HCSEEEECHHHHHHHHHSSSCCCSTT
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEeCCCCcchhHHHhhC----CCCEEEECHHHHHHHHHhCccccccc
Confidence            678999999999998888888764    8899999999876665433332    478999994     22222 3 5667


Q ss_pred             ccEEE
Q psy14082        175 VNTVN  179 (233)
Q Consensus       175 v~~VI  179 (233)
                      +++||
T Consensus       131 ~~~vV  135 (556)
T 4a2p_A          131 FTLMI  135 (556)
T ss_dssp             CSEEE
T ss_pred             CCEEE
Confidence            77766

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=88.38  E-value=0.46  Score=36.00  Aligned_cols=39  Identities=10%  Similarity=0.030  Sum_probs=28.9

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCc
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPT   53 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~Pt   53 (233)
                      .|+=.+..++.|||||.+ ++-++.+...       .+.+++++.|.
T Consensus         7 ~g~i~v~~G~mgsGKTT~-ll~~a~r~~~-------~g~kV~v~k~~   45 (191)
T 1xx6_A            7 HGWVEVIVGPMYSGKSEE-LIRRIRRAKI-------AKQKIQVFKPE   45 (191)
T ss_dssp             CCEEEEEECSTTSSHHHH-HHHHHHHHHH-------TTCCEEEEEEC
T ss_pred             CCEEEEEECCCCCcHHHH-HHHHHHHHHH-------CCCEEEEEEec
Confidence            456677788899999977 5556665543       36789999987

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=88.11  E-value=1.9  Score=35.95  Aligned_cols=70  Identities=17%  Similarity=0.159  Sum_probs=49.9

Q ss_pred             CCeEEEEecchhHHHHHHHHHhh----CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----cCcC-CcCCCCc
Q psy14082        106 AFKVIVFVETKKKVEDITRALRR----ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----VAAR-GLDVEDV  175 (233)
Q Consensus       106 ~~k~iIf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----~~~~-Gldi~~v  175 (233)
                      ..+++|.++++..+.++++.+++    .++++..++|+.+..+....+   . ...+|+|+|.     .+.+ .+++.++
T Consensus       101 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~---~-~~~~I~v~Tp~~l~~~l~~~~~~~~~~  176 (417)
T 2i4i_A          101 YPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDL---E-RGCHLLVATPGRLVDMMERGKIGLDFC  176 (417)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCHHHHHHHH---T-TCCSEEEECHHHHHHHHHTTSBCCTTC
T ss_pred             CccEEEECCcHHHHHHHHHHHHHHhCcCCceEEEEECCCCHHHHHHHh---h-CCCCEEEEChHHHHHHHHcCCcChhhC
Confidence            36799999999999998888865    467889999998876654433   2 3578999994     1112 2455566


Q ss_pred             cEEE
Q psy14082        176 NTVN  179 (233)
Q Consensus       176 ~~VI  179 (233)
                      ++||
T Consensus       177 ~~iV  180 (417)
T 2i4i_A          177 KYLV  180 (417)
T ss_dssp             CEEE
T ss_pred             cEEE
Confidence            6555

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=88.06  E-value=0.26  Score=37.99  Aligned_cols=26  Identities=4%  Similarity=-0.409  Sum_probs=19.7

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhh
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      ..+.+++.+|+|+|||.. +..++..+
T Consensus        57 kkn~ili~GPPGtGKTt~-a~ala~~l   82 (212)
T 1tue_A           57 KKNCLVFCGPANTGKSYF-GMSFIHFI   82 (212)
T ss_dssp             TCSEEEEESCGGGCHHHH-HHHHHHHH
T ss_pred             cccEEEEECCCCCCHHHH-HHHHHHHh
Confidence            345689999999999955 56666655

>2o0j_A Terminase, DNA packaging protein GP17; nucleotide-binding fold, hydrolase; HET: DNA ADP; 1.80A {Enterobacteria phage T4} PDB: 2o0h_A* 2o0k_A*

Probab=87.95  E-value=1.3  Score=37.47  Aligned_cols=53  Identities=9%  Similarity=0.066  Sum_probs=41.6

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      +-+++..+.+.|||.+.+.-++..+..      .++..+++++||++-|..+++.++.+
T Consensus       179 R~~vi~~sRq~GKT~l~a~~~l~~a~~------~~g~~v~~vA~t~~qA~~vf~~i~~m  231 (385)
T 2o0j_A          179 RMTVCNLSRQLGKTTVVAIFLAHFVCF------NKDKAVGILAHKGSMSAEVLDRTKQA  231 (385)
T ss_dssp             SEEEEEECSSSCHHHHHHHHHHHHHHS------SSSCEEEEEESSHHHHHHHHHHHHHH
T ss_pred             cEEEEEEcCcCChhHHHHHHHHHHHHh------CCCCeEEEEeCCHHHHHHHHHHHHHH
Confidence            457899999999998766655544443      24668999999999999999888877

>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=87.92  E-value=1.4  Score=40.76  Aligned_cols=70  Identities=16%  Similarity=0.120  Sum_probs=47.5

Q ss_pred             CCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEeccc-----CcCC-c-CCCC
Q psy14082        106 AFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDV-----AARG-L-DVED  174 (233)
Q Consensus       106 ~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~-----~~~G-l-di~~  174 (233)
                      +.+++|.++++..+......+++.    ++++..+||+.+...+...+.    +..+|+|+|.-     +.++ + ++.+
T Consensus       296 ~~~~Lvl~Pt~~L~~Q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~----~~~~Ivv~Tp~~l~~~l~~~~~~~~~~  371 (797)
T 4a2q_A          296 KAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVI----EDSDIIVVTPQILVNSFEDGTLTSLSI  371 (797)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEEECCC-----CHHHHH----HTCSEEEECHHHHHHHHHSSSCCCGGG
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHhcccCCceEEEEeCCcchhhhHHHhh----CCCCEEEEchHHHHHHHHhcccccccc
Confidence            679999999999998888877664    899999999987666544333    25789999942     2222 3 5566


Q ss_pred             ccEEE
Q psy14082        175 VNTVN  179 (233)
Q Consensus       175 v~~VI  179 (233)
                      +++||
T Consensus       372 ~~~iV  376 (797)
T 4a2q_A          372 FTLMI  376 (797)
T ss_dssp             CSEEE
T ss_pred             CCEEE
Confidence            77766

>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=87.83  E-value=1.4  Score=37.11  Aligned_cols=101  Identities=21%  Similarity=0.241  Sum_probs=75.0

Q ss_pred             CCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCCCC
Q psy14082          4 PSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPKG   83 (233)
Q Consensus         4 ~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~~   83 (233)
                      .++.+ ++++.++||+|||++++++++..+.                                -                
T Consensus        20 ~~~~~-~~ll~~~tG~GKT~~~~~~~~~~~~--------------------------------~----------------   50 (494)
T 1wp9_A           20 KCKET-NCLIVLPTGLGKTLIAMMIAEYRLT--------------------------------K----------------   50 (494)
T ss_dssp             HGGGS-CEEEECCTTSCHHHHHHHHHHHHHH--------------------------------H----------------
T ss_pred             HHhhC-CEEEEcCCCCCHHHHHHHHHHHHHh--------------------------------c----------------
Confidence            35566 9999999999999999888775320                                0                


Q ss_pred             CeeEEeccchhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhC-CC---eeEEEeCCCCHHHHHHHHHHhhCCCCCE
Q psy14082         84 PQDCLPLHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRE-RH---SAICIHGDKTQQDRDYVLNDFRQGKAPI  159 (233)
Q Consensus        84 ~~~lv~l~r~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~-~~---~~~~~~~~~~~~~r~~~~~~f~~g~~~i  159 (233)
                                           .+.+++|.++++..+....+.+.+. +.   .+..+||+.+..++.....     ..+|
T Consensus        51 ---------------------~~~~~liv~P~~~L~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~-----~~~i  104 (494)
T 1wp9_A           51 ---------------------YGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWA-----RAKV  104 (494)
T ss_dssp             ---------------------SCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEEECSCSCHHHHHHHHH-----HCSE
T ss_pred             ---------------------CCCeEEEEECCHHHHHHHHHHHHHHhCcchhheEEeeCCcchhhhhhhcc-----CCCE
Confidence                                 2358999999999999888888765 55   8899999999887665543     3689


Q ss_pred             EEeccc------CcCCcCCCCccEEE
Q psy14082        160 LVATDV------AARGLDVEDVNTVN  179 (233)
Q Consensus       160 Lv~T~~------~~~Gldi~~v~~VI  179 (233)
                      +|+|.-      ....++..+.++||
T Consensus       105 vv~T~~~l~~~~~~~~~~~~~~~~vI  130 (494)
T 1wp9_A          105 IVATPQTIENDLLAGRISLEDVSLIV  130 (494)
T ss_dssp             EEECHHHHHHHHHTTSCCTTSCSEEE
T ss_pred             EEecHHHHHHHHhcCCcchhhceEEE
Confidence            999942      11234566677666

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=87.60  E-value=0.55  Score=40.45  Aligned_cols=54  Identities=6%  Similarity=-0.106  Sum_probs=34.6

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      +..|.=+++.|++|+|||. |++-+......+       +..+++++-- +-..|+..++...
T Consensus       194 l~~G~liiIaG~pG~GKTt-lal~ia~~~a~~-------g~~vl~fSlE-ms~~ql~~R~~~~  247 (444)
T 3bgw_A          194 YKRRNFVLIAARPSMGKTA-FALKQAKNMSDN-------DDVVNLHSLE-MGKKENIKRLIVT  247 (444)
T ss_dssp             BCSSCEEEEEECSSSSHHH-HHHHHHHHHHHT-------TCEEEEECSS-SCTTHHHHHHHHH
T ss_pred             CCCCcEEEEEeCCCCChHH-HHHHHHHHHHHc-------CCEEEEEECC-CCHHHHHHHHHHH
Confidence            3457778999999999994 466566555432       4567777643 3445555555443

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=87.38  E-value=0.59  Score=35.63  Aligned_cols=71  Identities=15%  Similarity=0.216  Sum_probs=49.2

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhC--------CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----cCcC-Cc
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRE--------RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----VAAR-GL  170 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~--------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----~~~~-Gl  170 (233)
                      .+.+++|.++++..+.+..+.+++.        +..+..++|+.+..+..+   .+ ....+|+|+|.     .+.+ .+
T Consensus        71 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~---~~-~~~~~Iiv~Tp~~l~~~l~~~~~  146 (219)
T 1q0u_A           71 AEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALE---KL-NVQPHIVIGTPGRINDFIREQAL  146 (219)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTC---CC-SSCCSEEEECHHHHHHHHHTTCC
T ss_pred             CCceEEEEcCcHHHHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHHHH---Hc-CCCCCEEEeCHHHHHHHHHcCCC
Confidence            4578999999999999888877653        578888899876443322   12 23578999994     2222 35


Q ss_pred             CCCCccEEE
Q psy14082        171 DVEDVNTVN  179 (233)
Q Consensus       171 di~~v~~VI  179 (233)
                      +..+++++|
T Consensus       147 ~~~~~~~lV  155 (219)
T 1q0u_A          147 DVHTAHILV  155 (219)
T ss_dssp             CGGGCCEEE
T ss_pred             CcCcceEEE
Confidence            666777766

>3ice_A Transcription termination factor RHO; transcription, ATPase, hexamer, helicase, RNA, RECA, OB fold ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A

Probab=87.31  E-value=0.77  Score=38.99  Aligned_cols=102  Identities=11%  Similarity=0.098  Sum_probs=50.9

Q ss_pred             CCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCCCC
Q psy14082          4 PSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPKG   83 (233)
Q Consensus         4 ~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~~   83 (233)
                      ++-.|+-+.+.+++|+|||.... -+...+..+     ..+..++|+     ++-|-.++...+...++..++.+..+..
T Consensus       170 pi~rGQr~~IvG~sG~GKTtLl~-~Iar~i~~~-----~~~v~~I~~-----lIGER~~Ev~~~~~~~~~~vV~atadep  238 (422)
T 3ice_A          170 PIGRGQRGLIVAPPKAGKTMLLQ-NIAQSIAYN-----HPDCVLMVL-----LIDERPEEVTEMQRLVKGEVVASTFDEP  238 (422)
T ss_dssp             CCBTTCEEEEECCSSSSHHHHHH-HHHHHHHHH-----CTTSEEEEE-----EESSCHHHHHHHHTTCSSEEEEECTTSC
T ss_pred             eecCCcEEEEecCCCCChhHHHH-HHHHHHhhc-----CCCeeEEEE-----EecCChHHHHHHHHHhCeEEEEeCCCCC
Confidence            45678999999999999997633 233333332     234444442     2333333444443444555555554443


Q ss_pred             CeeEEeccchhhhchHHHhcCCCCeEEEEecchh
Q psy14082         84 PQDCLPLHRFVFNCQYEMAKNPAFKVIVFVETKK  117 (233)
Q Consensus        84 ~~~lv~l~r~~~~~~~~~~~~~~~k~iIf~~~~~  117 (233)
                      +..-+......--..+++. ..+..++|+..+.-
T Consensus       239 ~~~r~~~a~~alt~AEyfr-d~G~dVLil~DslT  271 (422)
T 3ice_A          239 ASRHVQVAEMVIEKAKRLV-EHKKDVIILLDSIT  271 (422)
T ss_dssp             HHHHHHHHHHHHHHHHHHH-HTSCEEEEEEECHH
T ss_pred             HHHHHHHHHHHHHHHHHHH-hcCCCEEEEEeCch
Confidence            3210000001111222344 36778888876643

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=86.97  E-value=0.61  Score=35.64  Aligned_cols=27  Identities=4%  Similarity=-0.271  Sum_probs=20.0

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhh
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      .+..+++.+|+|+|||.. +-.+...+.
T Consensus        51 ~~~~~ll~G~~G~GKT~l-a~~l~~~~~   77 (242)
T 3bos_A           51 GVQAIYLWGPVKSGRTHL-IHAACARAN   77 (242)
T ss_dssp             SCSEEEEECSTTSSHHHH-HHHHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHH-HHHHHHHHH
Confidence            467899999999999965 444555443

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=86.49  E-value=0.52  Score=37.91  Aligned_cols=28  Identities=7%  Similarity=-0.268  Sum_probs=20.2

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhh
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      ..+..+++.+|+|+|||.. +-.+...+.
T Consensus        65 ~~~~~vll~G~~GtGKT~l-a~~la~~l~   92 (309)
T 3syl_A           65 TPTLHMSFTGNPGTGKTTV-ALKMAGLLH   92 (309)
T ss_dssp             CCCCEEEEEECTTSSHHHH-HHHHHHHHH
T ss_pred             CCCceEEEECCCCCCHHHH-HHHHHHHHH
Confidence            3456799999999999976 444555443

>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=86.48  E-value=3.1  Score=34.24  Aligned_cols=71  Identities=14%  Similarity=0.125  Sum_probs=51.7

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhh----CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEeccc-----C-cCCcCCC
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRR----ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDV-----A-ARGLDVE  173 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~-----~-~~Gldi~  173 (233)
                      ..+.++++.++++..+.+..+.+.+    .++.+..++|+.+..+....+.     ..+|+|+|..     + ...++..
T Consensus        87 ~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-----~~~i~v~T~~~l~~~~~~~~~~~~  161 (394)
T 1fuu_A           87 VKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-----DAQIVVGTPGRVFDNIQRRRFRTD  161 (394)
T ss_dssp             CCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECSSCCHHHHHHHHH-----HCSEEEECHHHHHHHHHTTSSCCT
T ss_pred             CCCCCEEEEcCCHHHHHHHHHHHHHHhccCCeeEEEEeCCCchHHHHhhcC-----CCCEEEECHHHHHHHHHhCCcchh
Confidence            3567999999999999988887765    4678899999998777665544     4689999932     1 1234455


Q ss_pred             CccEEE
Q psy14082        174 DVNTVN  179 (233)
Q Consensus       174 ~v~~VI  179 (233)
                      ++++||
T Consensus       162 ~~~~vI  167 (394)
T 1fuu_A          162 KIKMFI  167 (394)
T ss_dssp             TCCEEE
T ss_pred             hCcEEE
Confidence            666665

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=86.23  E-value=0.58  Score=37.75  Aligned_cols=30  Identities=7%  Similarity=-0.395  Sum_probs=20.6

Q ss_pred             CCCCCCCceeEecCCCCCchHHhHHHHHHhh
Q psy14082          3 PPSESGCQNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus         3 p~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      |.....+-+++.+|+|+|||.. +-.+...+
T Consensus        31 ~~~~~p~~lLl~GppGtGKT~l-a~aiA~~l   60 (293)
T 3t15_A           31 PNIKVPLILGIWGGKGQGKSFQ-CELVFRKM   60 (293)
T ss_dssp             TTCCCCSEEEEEECTTSCHHHH-HHHHHHHH
T ss_pred             CCCCCCeEEEEECCCCCCHHHH-HHHHHHHh
Confidence            3333456688899999999966 44455544

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=86.09  E-value=0.39  Score=35.41  Aligned_cols=22  Identities=9%  Similarity=-0.303  Sum_probs=17.9

Q ss_pred             CCCCCCCceeEecCCCCCchHH
Q psy14082          3 PPSESGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         3 p~~~~g~d~i~~a~tGsGKT~~   24 (233)
                      |....+..+++.+++|||||..
T Consensus         6 ~~~~~~~~i~i~G~~GsGKst~   27 (180)
T 3iij_A            6 PEFMLLPNILLTGTPGVGKTTL   27 (180)
T ss_dssp             CTTCCCCCEEEECSTTSSHHHH
T ss_pred             cccccCCeEEEEeCCCCCHHHH
Confidence            3445677899999999999965

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=85.96  E-value=0.54  Score=35.85  Aligned_cols=54  Identities=15%  Similarity=-0.044  Sum_probs=30.6

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      +..|.-+.+.+++|+|||.. +.-+...+...       +..++++... ....++...+..+
T Consensus        20 i~~G~~~~i~G~~GsGKTtl-~~~l~~~~~~~-------~~~v~~~~~~-~~~~~~~~~~~~~   73 (235)
T 2w0m_A           20 IPQGFFIALTGEPGTGKTIF-SLHFIAKGLRD-------GDPCIYVTTE-ESRDSIIRQAKQF   73 (235)
T ss_dssp             EETTCEEEEECSTTSSHHHH-HHHHHHHHHHH-------TCCEEEEESS-SCHHHHHHHHHHT
T ss_pred             CcCCCEEEEEcCCCCCHHHH-HHHHHHHHHHC-------CCeEEEEEcc-cCHHHHHHHHHHh
Confidence            45677788999999999954 33344333322       2345665432 2344555555444

>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=85.75  E-value=4.9  Score=32.55  Aligned_cols=72  Identities=18%  Similarity=0.218  Sum_probs=51.2

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhh----CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEeccc-----Cc-CCcCC
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRR----ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDV-----AA-RGLDV  172 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~-----~~-~Gldi  172 (233)
                      ...+.++++.++++.-+++.++.+.+    .+..+..++|+.+.......+.     ..+|+|+|..     +. ..+++
T Consensus        71 ~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~-----~~~iiv~T~~~l~~~~~~~~~~~  145 (367)
T 1hv8_A           71 ENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-----NANIVVGTPGRILDHINRGTLNL  145 (367)
T ss_dssp             SSSSCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHH-----TCSEEEECHHHHHHHHHTTCSCT
T ss_pred             ccCCCcEEEEcCCHHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHhhcC-----CCCEEEecHHHHHHHHHcCCccc
Confidence            34677999999999999988888875    3678888999988766544443     4789999942     11 12445


Q ss_pred             CCccEEE
Q psy14082        173 EDVNTVN  179 (233)
Q Consensus       173 ~~v~~VI  179 (233)
                      .++++||
T Consensus       146 ~~~~~iI  152 (367)
T 1hv8_A          146 KNVKYFI  152 (367)
T ss_dssp             TSCCEEE
T ss_pred             ccCCEEE
Confidence            6666655

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=85.72  E-value=1  Score=32.37  Aligned_cols=18  Identities=6%  Similarity=-0.298  Sum_probs=15.7

Q ss_pred             CCCceeEecCCCCCchHH
Q psy14082          7 SGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~   24 (233)
                      .|.-+++.+++|+|||..
T Consensus        35 ~g~~~~l~G~~G~GKTtL   52 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHL   52 (149)
T ss_dssp             CCSEEEEESSSTTTTCHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            577889999999999965

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=85.43  E-value=0.8  Score=37.96  Aligned_cols=53  Identities=13%  Similarity=0.031  Sum_probs=33.9

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHH
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKE   66 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~   66 (233)
                      +..|.=+++.+++|+||| +|++-+...+..       .+..++|++.- .-..|+..++..
T Consensus        43 l~~G~LiiIaG~pG~GKT-t~al~ia~~~a~-------~g~~Vl~fSlE-ms~~ql~~Rlls   95 (338)
T 4a1f_A           43 FNKGSLVIIGARPSMGKT-SLMMNMVLSALN-------DDRGVAVFSLE-MSAEQLALRALS   95 (338)
T ss_dssp             BCTTCEEEEEECTTSCHH-HHHHHHHHHHHH-------TTCEEEEEESS-SCHHHHHHHHHH
T ss_pred             CCCCcEEEEEeCCCCCHH-HHHHHHHHHHHH-------cCCeEEEEeCC-CCHHHHHHHHHH
Confidence            345667889999999999 446656555543       25567877643 334555555543

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=85.36  E-value=0.62  Score=39.09  Aligned_cols=41  Identities=7%  Similarity=-0.084  Sum_probs=28.2

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCc
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPT   53 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~Pt   53 (233)
                      ++.|.-+++.+++|+|||. +++.++..+...       +..++++..-
T Consensus        71 l~~G~li~I~G~pGsGKTt-lal~la~~~~~~-------g~~vlyi~~E  111 (366)
T 1xp8_A           71 IPRGRITEIYGPESGGKTT-LALAIVAQAQKA-------GGTCAFIDAE  111 (366)
T ss_dssp             EETTSEEEEEESTTSSHHH-HHHHHHHHHHHT-------TCCEEEEESS
T ss_pred             ccCCcEEEEEcCCCCChHH-HHHHHHHHHHHC-------CCeEEEEECC
Confidence            4567889999999999994 466666555432       3456666643

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=85.21  E-value=0.64  Score=38.82  Aligned_cols=40  Identities=8%  Similarity=-0.110  Sum_probs=27.9

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcC
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAP   52 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~P   52 (233)
                      ++.|.-+++.+++|+|||.. ++-++..+...       +..++++..
T Consensus        60 l~~G~ii~I~G~pGsGKTtL-al~la~~~~~~-------g~~vlyid~   99 (356)
T 1u94_A           60 LPMGRIVEIYGPESSGKTTL-TLQVIAAAQRE-------GKTCAFIDA   99 (356)
T ss_dssp             EETTSEEEEECSTTSSHHHH-HHHHHHHHHHT-------TCCEEEEES
T ss_pred             ccCCeEEEEECCCCCCHHHH-HHHHHHHHHHC-------CCeEEEEeC
Confidence            45678899999999999955 55555554432       446777765

>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=85.08  E-value=4.2  Score=33.83  Aligned_cols=72  Identities=11%  Similarity=0.127  Sum_probs=51.6

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----cCcC-CcCCC
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----VAAR-GLDVE  173 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----~~~~-Gldi~  173 (233)
                      ..+.+++|.++++.-+.+..+.+.+.    ++.+..++|+.+..+....+..    ..+|+|+|.     .+.+ .++..
T Consensus       103 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~----~~~ivv~Tp~~l~~~l~~~~~~~~  178 (410)
T 2j0s_A          103 VRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY----GQHVVAGTPGRVFDMIRRRSLRTR  178 (410)
T ss_dssp             SCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHH----CCSEEEECHHHHHHHHHTTSSCCT
T ss_pred             cCCceEEEEcCcHHHHHHHHHHHHHHhccCCeEEEEEECCCCHHHHHHHhhc----CCCEEEcCHHHHHHHHHhCCccHh
Confidence            45689999999999999998888653    5788889999887776555442    468999983     2222 34455


Q ss_pred             CccEEE
Q psy14082        174 DVNTVN  179 (233)
Q Consensus       174 ~v~~VI  179 (233)
                      .+++||
T Consensus       179 ~~~~vV  184 (410)
T 2j0s_A          179 AIKMLV  184 (410)
T ss_dssp             TCCEEE
T ss_pred             heeEEE
Confidence            566554

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=84.88  E-value=0.84  Score=39.20  Aligned_cols=53  Identities=13%  Similarity=0.051  Sum_probs=33.1

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHH
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAK   65 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~   65 (233)
                      +..|.=+++.|++|+||| +|++-+.......      .+..++++..- .-..|+..++.
T Consensus       197 l~~G~l~ii~G~pg~GKT-~lal~ia~~~a~~------~g~~vl~~slE-~~~~~l~~R~~  249 (444)
T 2q6t_A          197 LGPGSLNIIAARPAMGKT-AFALTIAQNAALK------EGVGVGIYSLE-MPAAQLTLRMM  249 (444)
T ss_dssp             CCTTCEEEEEECTTSCHH-HHHHHHHHHHHHT------TCCCEEEEESS-SCHHHHHHHHH
T ss_pred             cCCCcEEEEEeCCCCCHH-HHHHHHHHHHHHh------CCCeEEEEECC-CCHHHHHHHHH
Confidence            455777899999999999 4566565555431      24457777643 23445555543

>4ag6_A VIRB4 ATPase, type IV secretory pathway VIRB4 components-like P; hydrolase, type IV secretion, conjugation; 2.35A {Thermoanaerobacter pseudethanolicus} PDB: 4ag5_A

Probab=84.85  E-value=0.8  Score=38.47  Aligned_cols=42  Identities=10%  Similarity=-0.020  Sum_probs=29.8

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHH
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTREL   56 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL   56 (233)
                      .+.++++.++||+|||.. +--++..+..       .+.+++++=|..+.
T Consensus        34 ~~~~~~i~G~~G~GKs~~-~~~~~~~~~~-------~~~~~~~~D~~~~~   75 (392)
T 4ag6_A           34 TNSNWTILAKPGAGKSFT-AKMLLLREYM-------QGSRVIIIDPEREY   75 (392)
T ss_dssp             CCCCEEEECCTTSSHHHH-HHHHHHHHHT-------TTCCEEEEESSCCS
T ss_pred             ccCceEEEcCCCCCHHHH-HHHHHHHHHH-------CCCEEEEEeCCcCH
Confidence            567899999999999966 4445444432       35677888887664

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=84.85  E-value=0.53  Score=39.37  Aligned_cols=41  Identities=12%  Similarity=-0.072  Sum_probs=28.1

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCc
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPT   53 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~Pt   53 (233)
                      ++.|.=+.+.+|+|+|||.. ++.++..+...       +.+++++...
T Consensus        58 i~~G~i~~I~GppGsGKSTL-al~la~~~~~~-------gg~VlyId~E   98 (356)
T 3hr8_A           58 YPRGRIVEIFGQESSGKTTL-ALHAIAEAQKM-------GGVAAFIDAE   98 (356)
T ss_dssp             EETTEEEEEEESTTSSHHHH-HHHHHHHHHHT-------TCCEEEEESS
T ss_pred             ccCCcEEEEECCCCCCHHHH-HHHHHHHHHhc-------CCeEEEEecc
Confidence            45677789999999999954 66666555432       3457777654

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=84.85  E-value=9.7  Score=28.30  Aligned_cols=37  Identities=19%  Similarity=0.296  Sum_probs=31.8

Q ss_pred             CceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCCC
Q psy14082         44 GPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPK   82 (233)
Q Consensus        44 ~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~   82 (233)
                      +.++||.|++++-+..+.+.+...  ++.+..+.|+.+.
T Consensus        54 ~~~~lVF~~~~~~~~~l~~~L~~~--g~~~~~lhg~~~~   90 (191)
T 2p6n_A           54 PPPVLIFAEKKADVDAIHEYLLLK--GVEAVAIHGGKDQ   90 (191)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHH--TCCEEEECTTSCH
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHc--CCcEEEEeCCCCH
Confidence            347999999999999999999877  7888999998654

>3u4q_B ATP-dependent helicase/deoxyribonuclease subunit; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_B*

Probab=84.84  E-value=0.73  Score=44.61  Aligned_cols=49  Identities=8%  Similarity=-0.015  Sum_probs=31.0

Q ss_pred             eEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHH
Q psy14082         12 FSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKE   66 (233)
Q Consensus        12 i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~   66 (233)
                      ++.|..|||||.+.+--+...+...     ..+.++|+|||.+ ...+..+.+..
T Consensus         5 lV~agAGSGKT~~l~~ri~~ll~~~-----~~~~~il~lVP~q-~TFt~~~rl~~   53 (1166)
T 3u4q_B            5 FLVGRSGSGKTKLIINSIQDELRRA-----PFGKPIIFLVPDQ-MTFLMEYELAK   53 (1166)
T ss_dssp             EEEECTTSSHHHHHHHHHHHHHHHC-----TTSSCEEEECCGG-GHHHHHHHHTC
T ss_pred             EEEeCCCCChHHHHHHHHHHHHHhC-----CCCCcEEEEecCc-ccHHHHHHHHH
Confidence            6789999999987444343333332     2346799999986 55554444443

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=84.67  E-value=1.2  Score=38.75  Aligned_cols=70  Identities=14%  Similarity=0.142  Sum_probs=49.6

Q ss_pred             CCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----cCcCC-c-CCCC
Q psy14082        106 AFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----VAARG-L-DVED  174 (233)
Q Consensus       106 ~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----~~~~G-l-di~~  174 (233)
                      +.+++|.++++..+......+.+.    ++.+..++|+.+...+...+..    ..+|+|+|.     .+..+ + ++.+
T Consensus        52 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~----~~~i~v~T~~~l~~~~~~~~~~~~~~  127 (555)
T 3tbk_A           52 KGKVVFFANQIPVYEQQATVFSRYFERLGYNIASISGATSDSVSVQHIIE----DNDIIILTPQILVNNLNNGAIPSLSV  127 (555)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHHHHHTTTCCEEEECTTTGGGSCHHHHHH----HCSEEEECHHHHHHHHHTSSSCCGGG
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHHhccCCcEEEEEcCCCcchhhHHHHhc----CCCEEEECHHHHHHHHhcCccccccc
Confidence            678999999999888888777654    8999999999876554333322    478999983     22222 3 4556


Q ss_pred             ccEEE
Q psy14082        175 VNTVN  179 (233)
Q Consensus       175 v~~VI  179 (233)
                      +++||
T Consensus       128 ~~~vV  132 (555)
T 3tbk_A          128 FTLMI  132 (555)
T ss_dssp             CSEEE
T ss_pred             CCEEE
Confidence            67665

>3foj_A Uncharacterized protein; protein SSP1007, structural genomics, PSI-2, protein structure initiative; 1.60A {Staphylococcus saprophyticus subsp}

Probab=84.25  E-value=1.2  Score=29.51  Aligned_cols=38  Identities=11%  Similarity=0.205  Sum_probs=33.4

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCC
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKT  141 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~  141 (233)
                      .+..+++++|.+-..+...+..|++.|+++..+.|++.
T Consensus        54 ~~~~~ivvyC~~g~rs~~a~~~L~~~G~~v~~l~GG~~   91 (100)
T 3foj_A           54 NDNETYYIICKAGGRSAQVVQYLEQNGVNAVNVEGGMD   91 (100)
T ss_dssp             CTTSEEEEECSSSHHHHHHHHHHHTTTCEEEEETTHHH
T ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHCCCCEEEecccHH
Confidence            45678999999999999999999999998888888854

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=84.22  E-value=0.75  Score=38.27  Aligned_cols=40  Identities=15%  Similarity=-0.049  Sum_probs=27.2

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcC
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAP   52 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~P   52 (233)
                      ++.|.-+.+.+++|+|||.. ++-++..+..       .+..++++..
T Consensus        58 l~~G~iv~I~G~pGsGKTtL-al~la~~~~~-------~g~~vlyi~~   97 (349)
T 2zr9_A           58 LPRGRVIEIYGPESSGKTTV-ALHAVANAQA-------AGGIAAFIDA   97 (349)
T ss_dssp             EETTSEEEEEESTTSSHHHH-HHHHHHHHHH-------TTCCEEEEES
T ss_pred             ccCCeEEEEECCCCCCHHHH-HHHHHHHHHh-------CCCeEEEEEC
Confidence            45678899999999999955 5545544433       2445777764

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=84.05  E-value=0.79  Score=40.27  Aligned_cols=18  Identities=0%  Similarity=-0.300  Sum_probs=15.7

Q ss_pred             CCCceeEecCCCCCchHH
Q psy14082          7 SGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~   24 (233)
                      .|..+.+.+|||||||..
T Consensus       259 ~g~~i~I~GptGSGKTTl  276 (511)
T 2oap_1          259 HKFSAIVVGETASGKTTT  276 (511)
T ss_dssp             TTCCEEEEESTTSSHHHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            577799999999999965

>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=83.94  E-value=4  Score=33.79  Aligned_cols=71  Identities=20%  Similarity=0.243  Sum_probs=50.7

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----cCcC-CcCCCC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----VAAR-GLDVED  174 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----~~~~-Gldi~~  174 (233)
                      .+.++++.++++..+++..+.+++.    ++.+..++|+.........    ..+..+|+|+|.     .+.+ ..++.+
T Consensus        88 ~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~----~~~~~~Ivv~T~~~l~~~~~~~~~~~~~  163 (400)
T 1s2m_A           88 NKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILR----LNETVHILVGTPGRVLDLASRKVADLSD  163 (400)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHH----TTSCCSEEEECHHHHHHHHHTTCSCCTT
T ss_pred             CCccEEEEcCCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHHH----hcCCCCEEEEchHHHHHHHHhCCccccc
Confidence            4568999999999998888888653    6788889999876654332    235689999994     2222 355666


Q ss_pred             ccEEE
Q psy14082        175 VNTVN  179 (233)
Q Consensus       175 v~~VI  179 (233)
                      +++||
T Consensus       164 ~~~vI  168 (400)
T 1s2m_A          164 CSLFI  168 (400)
T ss_dssp             CCEEE
T ss_pred             CCEEE
Confidence            77665

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=83.81  E-value=1.1  Score=36.49  Aligned_cols=27  Identities=7%  Similarity=-0.284  Sum_probs=20.1

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhh
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      .++.+++.+|+|+|||.. +-.+...+.
T Consensus        36 ~~~~lll~G~~GtGKT~l-a~~i~~~~~   62 (324)
T 1l8q_A           36 LYNPIFIYGSVGTGKTHL-LQAAGNEAK   62 (324)
T ss_dssp             SCSSEEEECSSSSSHHHH-HHHHHHHHH
T ss_pred             CCCeEEEECCCCCcHHHH-HHHHHHHHH
Confidence            356899999999999966 444555554

>3gk5_A Uncharacterized rhodanese-related protein TVG0868615; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.40A {Thermoplasma volcanium GSS1}

Probab=83.74  E-value=1.1  Score=30.17  Aligned_cols=38  Identities=11%  Similarity=0.072  Sum_probs=33.5

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCC
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKT  141 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~  141 (233)
                      .+..+++++|.+-..+...+..|++.|+++..+.||+.
T Consensus        53 ~~~~~ivvyC~~G~rs~~aa~~L~~~G~~v~~l~GG~~   90 (108)
T 3gk5_A           53 ERDKKYAVICAHGNRSAAAVEFLSQLGLNIVDVEGGIQ   90 (108)
T ss_dssp             CTTSCEEEECSSSHHHHHHHHHHHTTTCCEEEETTHHH
T ss_pred             CCCCeEEEEcCCCcHHHHHHHHHHHcCCCEEEEcCcHH
Confidence            45678999999999999999999999999888999854

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=83.70  E-value=0.86  Score=36.87  Aligned_cols=69  Identities=7%  Similarity=0.049  Sum_probs=48.8

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhC-----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEeccc-----Cc--CCcC
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRE-----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDV-----AA--RGLD  171 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~-----~~--~Gld  171 (233)
                      ..+.+++|.++|+..+.+++..++..     ++.+...+|+.+...+.       ....+|+|+|.-     +.  ..++
T Consensus       160 ~~~~~~lil~PtreLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~-------~~~~~IlV~TP~~l~~~l~~~~~~~  232 (300)
T 3fmo_B          160 NKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ-------KISEQIVIGTPGTVLDWCSKLKFID  232 (300)
T ss_dssp             SCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTTC-------CCCCSEEEECHHHHHHHHTTTCCCC
T ss_pred             CCCceEEEEcCcHHHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhhh-------cCCCCEEEECHHHHHHHHHhcCCCC
Confidence            45568999999999999988887653     46777787775532221       345789999952     21  3577


Q ss_pred             CCCccEEE
Q psy14082        172 VEDVNTVN  179 (233)
Q Consensus       172 i~~v~~VI  179 (233)
                      +.++.++|
T Consensus       233 l~~l~~lV  240 (300)
T 3fmo_B          233 PKKIKVFV  240 (300)
T ss_dssp             GGGCSEEE
T ss_pred             hhhceEEE
Confidence            78888776

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=83.65  E-value=1.1  Score=35.91  Aligned_cols=40  Identities=8%  Similarity=-0.070  Sum_probs=25.1

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEc
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLA   51 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~   51 (233)
                      +..|.=+.+.+++|+|||.. +.-+...+...      .|..++++.
T Consensus        32 l~~G~~~~i~G~~G~GKTTl-~~~ia~~~~~~------~G~~v~~~~   71 (296)
T 1cr0_A           32 ARGGEVIMVTSGSGMGKSTF-VRQQALQWGTA------MGKKVGLAM   71 (296)
T ss_dssp             BCTTCEEEEEESTTSSHHHH-HHHHHHHHHHT------SCCCEEEEE
T ss_pred             CCCCeEEEEEeCCCCCHHHH-HHHHHHHHHHH------cCCeEEEEe
Confidence            45677788999999999954 44344433321      233566664

>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=83.51  E-value=1.2  Score=29.89  Aligned_cols=37  Identities=11%  Similarity=0.114  Sum_probs=32.6

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCC
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDK  140 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~  140 (233)
                      .+..+++++|.+-..+...+..|++.|++...+.||+
T Consensus        54 ~~~~~ivv~C~~G~rS~~aa~~L~~~G~~~~~l~GG~   90 (103)
T 3iwh_A           54 NKNEIYYIVCAGGVRSAKVVEYLEANGIDAVNVEGGM   90 (103)
T ss_dssp             CTTSEEEEECSSSSHHHHHHHHHHTTTCEEEEETTHH
T ss_pred             cCCCeEEEECCCCHHHHHHHHHHHHcCCCEEEecChH
Confidence            4567899999999999999999999999988888875

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=83.41  E-value=1.7  Score=33.60  Aligned_cols=72  Identities=21%  Similarity=0.288  Sum_probs=48.6

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----cCcC---CcCC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----VAAR---GLDV  172 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----~~~~---Gldi  172 (233)
                      .+.++++.++++.-+.++++.+.+.    ++.+..++|+.....   .......+..+|+|+|.     .+.+   .+++
T Consensus        97 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~  173 (245)
T 3dkp_A           97 KGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAK---KFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDL  173 (245)
T ss_dssp             SSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEECCCHHHHHHT---TTSTTSCCCCCEEEECHHHHHHHHHSSSCSCCC
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEecCccHHH---HhhhhhcCCCCEEEECHHHHHHHHHhCCCCccc
Confidence            5568999999999999999988764    567766766532211   11223356689999993     2212   4677


Q ss_pred             CCccEEE
Q psy14082        173 EDVNTVN  179 (233)
Q Consensus       173 ~~v~~VI  179 (233)
                      .+++++|
T Consensus       174 ~~~~~lV  180 (245)
T 3dkp_A          174 ASVEWLV  180 (245)
T ss_dssp             TTCCEEE
T ss_pred             ccCcEEE
Confidence            7888776

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=83.33  E-value=0.5  Score=35.01  Aligned_cols=19  Identities=0%  Similarity=-0.440  Sum_probs=15.9

Q ss_pred             CCCCceeEecCCCCCchHH
Q psy14082          6 ESGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~   24 (233)
                      ..|+-+.+.+|+|+|||..
T Consensus         3 ~~g~~i~i~GpsGsGKSTL   21 (180)
T 1kgd_A            3 HMRKTLVLLGAHGVGRRHI   21 (180)
T ss_dssp             CCCCEEEEECCTTSSHHHH
T ss_pred             CCCCEEEEECCCCCCHHHH
Confidence            3577788999999999965

>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=83.26  E-value=4.3  Score=32.52  Aligned_cols=69  Identities=19%  Similarity=0.205  Sum_probs=50.1

Q ss_pred             CCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEeccc-----Cc-CCcCCCCc
Q psy14082        106 AFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDV-----AA-RGLDVEDV  175 (233)
Q Consensus       106 ~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~-----~~-~Gldi~~v  175 (233)
                      +.++++.++++.-+++.++.+++.    +..+..++|+.+...+...+   .  ..+|+|+|..     .. ..++..++
T Consensus        56 ~~~~liv~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~--~~~i~v~T~~~l~~~~~~~~~~~~~~  130 (337)
T 2z0m_A           56 GMKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRV---R--NADIVVATPGRLLDLWSKGVIDLSSF  130 (337)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECTTSCHHHHHHHH---T--TCSEEEECHHHHHHHHHTTSCCGGGC
T ss_pred             cCCEEEEeCCHHHHHHHHHHHHHHhhhcCCcEEEEECCcchHHHHhhc---C--CCCEEEECHHHHHHHHHcCCcchhhC
Confidence            678999999999999998888753    57888999998877654433   2  3789999942     12 23456667


Q ss_pred             cEEE
Q psy14082        176 NTVN  179 (233)
Q Consensus       176 ~~VI  179 (233)
                      ++||
T Consensus       131 ~~iV  134 (337)
T 2z0m_A          131 EIVI  134 (337)
T ss_dssp             SEEE
T ss_pred             cEEE
Confidence            7665

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=83.19  E-value=0.8  Score=36.36  Aligned_cols=26  Identities=8%  Similarity=-0.313  Sum_probs=19.0

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHh
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVH   32 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~   32 (233)
                      ..++.+++.+|+|+|||.. +-.+...
T Consensus        49 ~~~~~~ll~G~~GtGKT~l-a~~la~~   74 (285)
T 3h4m_A           49 EPPKGILLYGPPGTGKTLL-AKAVATE   74 (285)
T ss_dssp             CCCSEEEEESSSSSSHHHH-HHHHHHH
T ss_pred             CCCCeEEEECCCCCcHHHH-HHHHHHH
Confidence            3467799999999999966 4444443

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=82.91  E-value=0.83  Score=39.33  Aligned_cols=52  Identities=10%  Similarity=0.008  Sum_probs=32.3

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHH
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVA   64 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~   64 (233)
                      +..|.=+++.+++|+|||. +++-+...+...      .+..++++... .-..|+..++
T Consensus       200 l~~G~liiI~G~pG~GKTt-l~l~ia~~~~~~------~g~~Vl~~s~E-~s~~~l~~r~  251 (454)
T 2r6a_A          200 FQRSDLIIVAARPSVGKTA-FALNIAQNVATK------TNENVAIFSLE-MSAQQLVMRM  251 (454)
T ss_dssp             BCTTCEEEEECCTTSCHHH-HHHHHHHHHHHH------SSCCEEEEESS-SCHHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCHHH-HHHHHHHHHHHh------CCCcEEEEECC-CCHHHHHHHH
Confidence            4567778999999999994 456555555432      24457777643 2234555544

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=82.89  E-value=0.7  Score=38.16  Aligned_cols=25  Identities=8%  Similarity=-0.157  Sum_probs=19.8

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      ++.+++.+|+|+|||.. +-.+...+
T Consensus        70 ~~~vLl~GppGtGKT~l-a~~la~~l   94 (368)
T 3uk6_A           70 GRAVLIAGQPGTGKTAI-AMGMAQAL   94 (368)
T ss_dssp             TCEEEEEESTTSSHHHH-HHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHH-HHHHHHHh
Confidence            67899999999999976 55555555

>1w36_B RECB, exodeoxyribonuclease V beta chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 c.52.1.24 PDB: 3k70_B*

Probab=82.78  E-value=2.6  Score=40.92  Aligned_cols=60  Identities=7%  Similarity=-0.145  Sum_probs=41.9

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccC----CCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQE----PVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~----~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      .|.. ++.|+-|||||.+-+-=++..+....    ...+-.-.+.|+++=|+.-|..+.+++.+.
T Consensus        16 ~g~~-lV~AsAGSGKT~~L~~r~lrLll~~g~~~~~~~~~~~~~ILvvTFT~aAA~EMr~RI~~~   79 (1180)
T 1w36_B           16 QGER-LIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSN   79 (1180)
T ss_dssp             SSCE-EEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHH
T ss_pred             CCCE-EEEECCCCCHHHHHHHHHHHHHhcCCcccccCCCCCHHHEEEEeccHHHHHHHHHHHHHH
Confidence            4555 89999999999885555555554321    001122357999999999888888888775

>1fx0_A ATP synthase alpha chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_A*

Probab=82.77  E-value=11  Score=32.95  Aligned_cols=23  Identities=9%  Similarity=-0.028  Sum_probs=19.4

Q ss_pred             CCCCCCCCceeEecCCCCCchHH
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~   24 (233)
                      +-++-+|+-..+.++.|+|||..
T Consensus       157 l~PigrGQR~~Ifg~~g~GKT~L  179 (507)
T 1fx0_A          157 MIPVGRGQRELIIGDRQTGKTAV  179 (507)
T ss_dssp             TSCCBTTCBCBEEESSSSSHHHH
T ss_pred             ccccccCCEEEEecCCCCCccHH
Confidence            34567889999999999999976

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=82.47  E-value=0.88  Score=36.76  Aligned_cols=25  Identities=4%  Similarity=-0.399  Sum_probs=18.5

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHH
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAV   31 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~   31 (233)
                      ..++.+++.+|+|+|||.. +-.+..
T Consensus        47 ~~~~~vLL~Gp~GtGKT~l-a~ala~   71 (301)
T 3cf0_A           47 TPSKGVLFYGPPGCGKTLL-AKAIAN   71 (301)
T ss_dssp             CCCSEEEEECSSSSSHHHH-HHHHHH
T ss_pred             CCCceEEEECCCCcCHHHH-HHHHHH
Confidence            3467799999999999976 333443

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=82.26  E-value=0.89  Score=37.48  Aligned_cols=45  Identities=11%  Similarity=-0.023  Sum_probs=29.4

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHH
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTREL   56 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL   56 (233)
                      ++.| =+.+.+++|+|||.. ++.++......     ..+.+++++..-..+
T Consensus        26 l~~G-iteI~G~pGsGKTtL-~Lq~~~~~~~~-----g~g~~vlyId~E~s~   70 (333)
T 3io5_A           26 MQSG-LLILAGPSKSFKSNF-GLTMVSSYMRQ-----YPDAVCLFYDSEFGI   70 (333)
T ss_dssp             BCSE-EEEEEESSSSSHHHH-HHHHHHHHHHH-----CTTCEEEEEESSCCC
T ss_pred             CcCC-eEEEECCCCCCHHHH-HHHHHHHHHhc-----CCCceEEEEeccchh
Confidence            3456 478999999999955 55555555432     225578887765444

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=82.00  E-value=1.2  Score=34.67  Aligned_cols=28  Identities=21%  Similarity=0.040  Sum_probs=19.9

Q ss_pred             CCC-ceeEecCCCCCchHHhHHHHHHhhhc
Q psy14082          7 SGC-QNFSKITNYLLSPPQYMLPAAVHISH   35 (233)
Q Consensus         7 ~g~-d~i~~a~tGsGKT~~~~lp~l~~l~~   35 (233)
                      +|+ .+++.+++|+|||.+ ++.+...+..
T Consensus         4 ~g~l~I~~~~kgGvGKTt~-a~~la~~l~~   32 (228)
T 2r8r_A            4 RGRLKVFLGAAPGVGKTYA-MLQAAHAQLR   32 (228)
T ss_dssp             CCCEEEEEESSTTSSHHHH-HHHHHHHHHH
T ss_pred             CceEEEEEECCCCCcHHHH-HHHHHHHHHH
Confidence            344 488899999999977 5555555554

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=81.92  E-value=0.64  Score=36.62  Aligned_cols=18  Identities=0%  Similarity=-0.509  Sum_probs=15.7

Q ss_pred             CCCceeEecCCCCCchHH
Q psy14082          7 SGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~   24 (233)
                      .+..+++.+++|+|||..
T Consensus        28 ~~~~vll~G~~GtGKt~l   45 (265)
T 2bjv_A           28 LDKPVLIIGERGTGKELI   45 (265)
T ss_dssp             SCSCEEEECCTTSCHHHH
T ss_pred             CCCCEEEECCCCCcHHHH
Confidence            467899999999999965

>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=81.71  E-value=5  Score=33.26  Aligned_cols=72  Identities=15%  Similarity=0.196  Sum_probs=51.0

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----cCcC-CcCCCC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----VAAR-GLDVED  174 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----~~~~-Gldi~~  174 (233)
                      .+.+++|.++++..+.+..+.+++.    +..+...+|+.+....   .+.+..+..+|+|+|.     .+.+ .++...
T Consensus       107 ~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~  183 (414)
T 3eiq_A          107 KATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAE---VQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKY  183 (414)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHGGGSCCCEEECCCCTTHHHH---HHHHTTTCCSEEEECHHHHHHHHHHTSSCSTT
T ss_pred             CceeEEEEeChHHHHHHHHHHHHHHhcccCceEEEEECCcchHHH---HHHHhcCCCCEEEECHHHHHHHHHcCCccccc
Confidence            5678999999999999888888754    5677888888765544   4455667889999994     2222 244555


Q ss_pred             ccEEE
Q psy14082        175 VNTVN  179 (233)
Q Consensus       175 v~~VI  179 (233)
                      +++||
T Consensus       184 ~~~vV  188 (414)
T 3eiq_A          184 IKMFV  188 (414)
T ss_dssp             CCEEE
T ss_pred             CcEEE
Confidence            66554

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=81.46  E-value=0.66  Score=38.50  Aligned_cols=25  Identities=8%  Similarity=-0.217  Sum_probs=19.0

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhh
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      .-+++.+|||||||.. .+-+..++.
T Consensus        41 ~lIvI~GPTgsGKTtL-a~~LA~~l~   65 (339)
T 3a8t_A           41 KLLVLMGATGTGKSRL-SIDLAAHFP   65 (339)
T ss_dssp             EEEEEECSTTSSHHHH-HHHHHTTSC
T ss_pred             ceEEEECCCCCCHHHH-HHHHHHHCC
Confidence            3588999999999966 565666553

>2r9v_A ATP synthase subunit alpha; TM1612, structural genomics, JOI for structural genomics, JCSG, protein structure initiative ATP synthesis; HET: ATP PG4; 2.10A {Thermotoga maritima MSB8}

Probab=81.28  E-value=10  Score=33.23  Aligned_cols=21  Identities=10%  Similarity=-0.053  Sum_probs=18.2

Q ss_pred             CCCCCCceeEecCCCCCchHH
Q psy14082          4 PSESGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         4 ~~~~g~d~i~~a~tGsGKT~~   24 (233)
                      ++-+|+-..+.++.|+|||..
T Consensus       171 PigrGQR~~I~g~~g~GKT~L  191 (515)
T 2r9v_A          171 PIGRGQRELIIGDRQTGKTAI  191 (515)
T ss_dssp             CEETTCBEEEEEETTSSHHHH
T ss_pred             ccccCCEEEEEcCCCCCccHH
Confidence            456788999999999999976

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=81.18  E-value=1  Score=36.06  Aligned_cols=25  Identities=4%  Similarity=-0.366  Sum_probs=18.4

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      +..+++.+|+|+|||.. +-.+...+
T Consensus        50 ~~~vll~G~~GtGKT~l-a~~la~~l   74 (310)
T 1ofh_A           50 PKNILMIGPTGVGKTEI-ARRLAKLA   74 (310)
T ss_dssp             CCCEEEECCTTSSHHHH-HHHHHHHH
T ss_pred             CceEEEECCCCCCHHHH-HHHHHHHh
Confidence            56799999999999966 33344433

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=81.17  E-value=0.67  Score=33.92  Aligned_cols=17  Identities=0%  Similarity=-0.439  Sum_probs=14.5

Q ss_pred             CCceeEecCCCCCchHH
Q psy14082          8 GCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~   24 (233)
                      ++-+++.+++|||||..
T Consensus         3 ~~~i~l~G~~GsGKST~   19 (178)
T 1qhx_A            3 TRMIILNGGSSAGKSGI   19 (178)
T ss_dssp             CCEEEEECCTTSSHHHH
T ss_pred             ceEEEEECCCCCCHHHH
Confidence            45689999999999965

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=81.16  E-value=0.58  Score=37.24  Aligned_cols=19  Identities=0%  Similarity=-0.384  Sum_probs=15.7

Q ss_pred             CCCCceeEecCCCCCchHH
Q psy14082          6 ESGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~   24 (233)
                      ..|.-+.+.+|||||||..
T Consensus        23 ~~g~~v~i~Gp~GsGKSTl   41 (261)
T 2eyu_A           23 RKMGLILVTGPTGSGKSTT   41 (261)
T ss_dssp             CSSEEEEEECSTTCSHHHH
T ss_pred             CCCCEEEEECCCCccHHHH
Confidence            4566788999999999965

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=81.14  E-value=5.8  Score=33.90  Aligned_cols=25  Identities=4%  Similarity=-0.379  Sum_probs=19.1

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      .+-++..+|+|||||+. +-++...+
T Consensus       206 prGiLL~GPPGtGKT~l-akAiA~~~  230 (428)
T 4b4t_K          206 PRGVLLYGPPGTGKTML-VKAVANST  230 (428)
T ss_dssp             CCEEEEESCTTTTHHHH-HHHHHHHH
T ss_pred             CceEEEECCCCCCHHHH-HHHHHHHh
Confidence            45689999999999976 55555544

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=81.08  E-value=0.85  Score=35.93  Aligned_cols=21  Identities=5%  Similarity=-0.167  Sum_probs=15.0

Q ss_pred             eeEecCCCCCchHHhHHHHHHh
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVH   32 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~   32 (233)
                      +++.++||||||.. +-.+...
T Consensus         4 i~I~G~~GSGKSTl-a~~La~~   24 (253)
T 2ze6_A            4 HLIYGPTCSGKTDM-AIQIAQE   24 (253)
T ss_dssp             EEEECCTTSSHHHH-HHHHHHH
T ss_pred             EEEECCCCcCHHHH-HHHHHhc
Confidence            57899999999955 4444443

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=81.03  E-value=0.87  Score=36.25  Aligned_cols=29  Identities=14%  Similarity=-0.101  Sum_probs=20.5

Q ss_pred             CCCCCCceeEecCCCCCchHHhHHHHHHhh
Q psy14082          4 PSESGCQNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus         4 ~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      -+..|.=+.+.+++|+|||.. +.-++..+
T Consensus        26 gl~~G~i~~i~G~~GsGKTtl-~~~l~~~~   54 (279)
T 1nlf_A           26 NMVAGTVGALVSPGGAGKSML-ALQLAAQI   54 (279)
T ss_dssp             TEETTSEEEEEESTTSSHHHH-HHHHHHHH
T ss_pred             CccCCCEEEEEcCCCCCHHHH-HHHHHHHH
Confidence            345788899999999999955 44344333

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=81.01  E-value=0.68  Score=36.15  Aligned_cols=26  Identities=4%  Similarity=-0.358  Sum_probs=18.4

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhh
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      ..+.+++.+|+|+|||.. +-.+...+
T Consensus        38 ~~~~vll~G~~GtGKT~l-a~~la~~~   63 (262)
T 2qz4_A           38 VPKGALLLGPPGCGKTLL-AKAVATEA   63 (262)
T ss_dssp             CCCEEEEESCTTSSHHHH-HHHHHHHH
T ss_pred             CCceEEEECCCCCCHHHH-HHHHHHHh
Confidence            356689999999999966 33344433

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=80.87  E-value=2  Score=35.12  Aligned_cols=61  Identities=13%  Similarity=-0.026  Sum_probs=34.2

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHH-HHHHHHHHHHh
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTREL-AQQIQTVAKEF   67 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL-~~Q~~~~~~~~   67 (233)
                      +..|.-+++.+++|+|||.. ++-++....... .....+..++++.-...+ ..++.+.++.+
T Consensus       104 l~~G~i~~i~G~~GsGKT~l-a~~la~~~~~~~-~~gg~~~~vlyi~~e~~~~~~~l~~~~~~~  165 (324)
T 2z43_A          104 IETRTMTEFFGEFGSGKTQL-CHQLSVNVQLPP-EKGGLSGKAVYIDTEGTFRWERIENMAKAL  165 (324)
T ss_dssp             EETTSEEEEEESTTSSHHHH-HHHHHHHTTSCG-GGTCCSCEEEEEESSSCCCHHHHHHHHHHT
T ss_pred             CCCCcEEEEECCCCCCHhHH-HHHHHHHHhccc-ccCCCCCeEEEEECCCCCCHHHHHHHHHHh
Confidence            35678899999999999955 444443332110 000114577887654322 44555555555

>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase, single analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} PDB: 1sky_B

Probab=80.69  E-value=13  Score=32.42  Aligned_cols=22  Identities=9%  Similarity=-0.093  Sum_probs=19.0

Q ss_pred             CCCCCCCceeEecCCCCCchHH
Q psy14082          3 PPSESGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         3 p~~~~g~d~i~~a~tGsGKT~~   24 (233)
                      -++-+|+-..+.++.|+|||..
T Consensus       157 ~PigrGQR~~Ifg~~g~GKT~L  178 (502)
T 2qe7_A          157 IPIGRGQRELIIGDRQTGKTTI  178 (502)
T ss_dssp             SCCBTTCBCEEEECSSSCHHHH
T ss_pred             cccccCCEEEEECCCCCCchHH
Confidence            3567889999999999999976

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=80.68  E-value=0.84  Score=34.95  Aligned_cols=24  Identities=8%  Similarity=-0.132  Sum_probs=17.6

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHH
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAV   31 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~   31 (233)
                      .|+-+++.++||+|||.. ++.+.+
T Consensus        33 ~g~~ilI~GpsGsGKStL-A~~La~   56 (205)
T 2qmh_A           33 YGLGVLITGDSGVGKSET-ALELVQ   56 (205)
T ss_dssp             TTEEEEEECCCTTTTHHH-HHHHHT
T ss_pred             CCEEEEEECCCCCCHHHH-HHHHHH
Confidence            366689999999999855 444443

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=80.65  E-value=1.1  Score=33.40  Aligned_cols=23  Identities=4%  Similarity=-0.174  Sum_probs=17.3

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhh
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      .+++.+++|+|||.. +-.+...+
T Consensus        40 ~~ll~G~~G~GKT~l-~~~l~~~~   62 (226)
T 2chg_A           40 HLLFSGPPGTGKTAT-AIALARDL   62 (226)
T ss_dssp             CEEEECSTTSSHHHH-HHHHHHHH
T ss_pred             eEEEECCCCCCHHHH-HHHHHHHH
Confidence            499999999999965 44455544

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=80.59  E-value=0.64  Score=34.46  Aligned_cols=20  Identities=5%  Similarity=-0.321  Sum_probs=16.7

Q ss_pred             CCCCCceeEecCCCCCchHH
Q psy14082          5 SESGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~   24 (233)
                      +..|.-+++.+++|||||..
T Consensus         6 i~~g~~i~l~G~~GsGKSTl   25 (191)
T 1zp6_A            6 DLGGNILLLSGHPGSGKSTI   25 (191)
T ss_dssp             CCTTEEEEEEECTTSCHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHH
Confidence            45677789999999999965

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=80.57  E-value=0.77  Score=34.95  Aligned_cols=19  Identities=0%  Similarity=-0.368  Sum_probs=16.7

Q ss_pred             CCCCceeEecCCCCCchHH
Q psy14082          6 ESGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~   24 (233)
                      ..|+-+++.+|+|+|||..
T Consensus        17 ~~g~~ivl~GPSGaGKsTL   35 (197)
T 3ney_A           17 QGRKTLVLIGASGVGRSHI   35 (197)
T ss_dssp             CSCCEEEEECCTTSSHHHH
T ss_pred             CCCCEEEEECcCCCCHHHH
Confidence            5788899999999999965

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=80.47  E-value=0.66  Score=37.15  Aligned_cols=23  Identities=4%  Similarity=-0.434  Sum_probs=17.6

Q ss_pred             CCceeEecCCCCCchHHhHHHHHH
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAV   31 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~   31 (233)
                      ++.+++.+|+|+|||.. +-.+..
T Consensus        54 ~~~vll~Gp~GtGKT~l-a~~la~   76 (297)
T 3b9p_A           54 AKGLLLFGPPGNGKTLL-ARAVAT   76 (297)
T ss_dssp             CSEEEEESSSSSCHHHH-HHHHHH
T ss_pred             CCeEEEECcCCCCHHHH-HHHHHH
Confidence            57899999999999966 333443

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=80.33  E-value=2.3  Score=32.80  Aligned_cols=40  Identities=10%  Similarity=0.096  Sum_probs=26.8

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHH
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRE   55 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~Ptre   55 (233)
                      |+=.+..++-|||||.+ ++-.+.+...       .+.+++++.|...
T Consensus        28 G~l~vitG~MgsGKTT~-lL~~a~r~~~-------~g~kVli~k~~~d   67 (214)
T 2j9r_A           28 GWIEVICGSMFSGKSEE-LIRRVRRTQF-------AKQHAIVFKPCID   67 (214)
T ss_dssp             CEEEEEECSTTSCHHHH-HHHHHHHHHH-------TTCCEEEEECC--
T ss_pred             CEEEEEECCCCCcHHHH-HHHHHHHHHH-------CCCEEEEEEeccC
Confidence            44345677779999977 5556655543       3678999999753

>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A

Probab=80.21  E-value=0.87  Score=37.42  Aligned_cols=24  Identities=4%  Similarity=-0.283  Sum_probs=17.6

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhh
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      .-+++.+|||||||.. +..+.+.+
T Consensus         4 ~~i~i~GptgsGKt~l-a~~La~~~   27 (322)
T 3exa_A            4 KLVAIVGPTAVGKTKT-SVMLAKRL   27 (322)
T ss_dssp             EEEEEECCTTSCHHHH-HHHHHHTT
T ss_pred             cEEEEECCCcCCHHHH-HHHHHHhC
Confidence            3467899999999966 55566554

>2ck3_A ATP synthase subunit alpha\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1bmf_A* 1e1q_A* 1e1r_A* 1e79_A* 1h8h_A* 1nbm_A* 1ohh_A* 1qo1_A 1w0j_A* 1w0k_A* 1h8e_A* 2jdi_A* 2wss_A* 2w6j_A 2w6e_A 2w6g_A 2w6f_A 2w6h_A 2w6i_A 1cow_A* ...

Probab=80.06  E-value=23  Score=30.89  Aligned_cols=30  Identities=7%  Similarity=-0.127  Sum_probs=22.1

Q ss_pred             CCCCCCceeEecCCCCCchHHhHHHHHHhh
Q psy14082          4 PSESGCQNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus         4 ~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      ++-+|+-..+.++.|+|||...+=.+.+..
T Consensus       158 PigrGQR~~I~g~~g~GKT~Lal~~I~~q~  187 (510)
T 2ck3_A          158 PIGRGQRELIIGDRQTGKTSIAIDTIINQK  187 (510)
T ss_dssp             CCBTTCBCEEEESTTSSHHHHHHHHHHHTH
T ss_pred             ccccCCEEEEecCCCCCchHHHHHHHHHHH
Confidence            567788999999999999977333344443

---

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	233
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	5e-18
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	6e-13
d1wp9a2	286	c.37.1.19 (A:201-486) putative ATP-dependent RNA h	1e-10
d1c4oa2	174	c.37.1.19 (A:410-583) Nucleotide excision repair e	2e-09
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	3e-08
d1t5la2	181	c.37.1.19 (A:415-595) Nucleotide excision repair e	4e-08
d1oywa3	200	c.37.1.19 (A:207-406) RecQ helicase domain {Escher	5e-07
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	5e-06
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	4e-04
d1yksa2	299	c.37.1.14 (A:325-623) YFV helicase domain {Yellow	5e-06
d1jr6a_	138	c.37.1.14 (A:) HCV helicase domain {Human hepatiti	6e-06
d1hv8a2	155	c.37.1.19 (A:211-365) Putative DEAD box RNA helica	2e-05
d2j0sa2	168	c.37.1.19 (A:244-411) Probable ATP-dependent RNA h	8e-05
d1gm5a4	206	c.37.1.19 (A:550-755) RecG helicase domain {Thermo	7e-04
d1wi9a_	72	a.4.5.47 (A:) Hypothetical protein C20orf116 homol	0.002
d2fwra1	200	c.37.1.19 (A:257-456) DNA repair protein RAD25 {Ar	0.003
d2eyqa5	211	c.37.1.19 (A:779-989) Transcription-repair couplin	0.004

>d1a1va2 c.37.1.14 (A:326-624) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 299

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

 Score = 78.8 bits (194), Expect = 5e-18
 Identities = 8/81 (9%), Positives = 23/81 (28%), Gaps = 10/81 (12%)

Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQ----------QDRDYVLNDFRQGKA 157
           + ++F  +KKK +++   L     +A+  +                     L     G  
Sbjct: 38  RHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDF 97

Query: 158 PILVATDVAARGLDVEDVNTV 178
             ++  +          ++  
Sbjct: 98  DSVIDCNTCVTQTVDFSLDPT 118

>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 = 64.0 bits (155), Expect = 6e-13
 Identities = 14/76 (18%), Positives = 28/76 (36%), Gaps = 11/76 (14%)

Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVAT---- 163
             I++  T ++ E+I  +L+ +               +      F +G+   L+ T    
Sbjct: 27  GGIIYARTGEEAEEIYESLKNK------FRIGIVTATKKGDYEKFVEGEIDHLIGTAHYY 80

Query: 164 DVAARGLDV-EDVNTV 178
               RGLD+ E +   
Sbjct: 81  GTLVRGLDLPERIRFA 96

>d1wp9a2 c.37.1.19 (A:201-486) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 286

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 57.6 bits (138), Expect = 1e-10
 Identities = 22/90 (24%), Positives = 44/90 (48%), Gaps = 8/90 (8%)

Query: 97  CQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDY--------V 148
            + ++ +    K+IVF   ++  + I   L ++   A    G  ++++           +
Sbjct: 152 IREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLI 211

Query: 149 LNDFRQGKAPILVATDVAARGLDVEDVNTV 178
           L++F +G+  +LVAT V   GLDV +V+ V
Sbjct: 212 LDEFARGEFNVLVATSVGEEGLDVPEVDLV 241

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]} Length = 174

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

 Score = 52.8 bits (126), Expect = 2e-09
 Identities = 20/90 (22%), Positives = 36/90 (40%)

Query: 107 FKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVA 166
            + +V V T +  E++T  L      A  +H +     R  ++ D R G    LV  ++ 
Sbjct: 32  ERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLL 91

Query: 167 ARGLDVEDVNTVNIGSLQLSANHNISQVIE 196
             GLD+ +V+ V I            + + 
Sbjct: 92  REGLDIPEVSLVAILDADKEGFLRSERSLI 121

>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 = 49.1 bits (116), Expect = 3e-08
 Identities = 30/92 (32%), Positives = 56/92 (60%)

Query: 103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVA 162
                + ++F  T++KVE++T  LR ++ +   I+ D  QQ+RD ++ +FR G + IL++
Sbjct: 24  SISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILIS 83

Query: 163 TDVAARGLDVEDVNTVNIGSLQLSANHNISQV 194
           TD+ ARG+DV+ V+ V    L  +  + I ++
Sbjct: 84  TDLLARGIDVQQVSLVINYDLPANKENYIHRI 115

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]} Length = 181

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

 Score = 49.4 bits (117), Expect = 4e-08
 Identities = 21/72 (29%), Positives = 36/72 (50%)

Query: 107 FKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVA 166
            + +V   TKK  ED+T  L+        +H +    +R  ++ D R GK  +LV  ++ 
Sbjct: 32  ERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLL 91

Query: 167 ARGLDVEDVNTV 178
             GLD+ +V+ V
Sbjct: 92  REGLDIPEVSLV 103

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

 Score = 46.6 bits (109), Expect = 5e-07
 Identities = 21/100 (21%), Positives = 37/100 (37%), Gaps = 4/100 (4%)

Query: 101 MAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPIL 160
           + +      I++  ++ KVED    L+ +  SA   H       R  V   F++    I+
Sbjct: 25  VQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIV 84

Query: 161 VATDVAARGLDVEDVNTVNIGSLQLSANHNISQVIEVVQD 200
           VAT     G++  +V  V    +      NI    +    
Sbjct: 85  VATVAFGMGINKPNVRFV----VHFDIPRNIESYYQETGR 120

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]} Length = 305

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

 Score = 44.1 bits (103), Expect = 5e-06
 Identities = 15/84 (17%), Positives = 29/84 (34%), Gaps = 4/84 (4%)

Query: 99  YEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAP 158
           +E   +   K + FV + K   DI   LR+     I +       +        R     
Sbjct: 171 HEWVTDFKGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSRKTFDSEYIK----TRTNDWD 226

Query: 159 ILVATDVAARGLDVEDVNTVNIGS 182
            +V TD++  G + +    ++   
Sbjct: 227 FVVTTDISEMGANFKAERVIDPRR 250

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]} Length = 305

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

 Score = 38.4 bits (88), Expect = 4e-04
 Identities = 14/73 (19%), Positives = 25/73 (34%)

Query: 42  GDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPKGPQDCLPLHRFVFNCQYEM 101
             G   L+LAPTR +A +++   +      +   I           L  H          
Sbjct: 36  KRGLRTLILAPTRVVAAEMEEALRGLPIRYQTPAIRAEHTGREIVDLMCHATFTMRLLSP 95

Query: 102 AKNPAFKVIVFVE 114
            + P + +I+  E
Sbjct: 96  IRVPNYNLIIMDE 108

>d1yksa2 c.37.1.14 (A:325-623) YFV helicase domain {Yellow fever virus [TaxId: 11089]} Length = 299

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

 Score = 44.2 bits (104), Expect = 5e-06
 Identities = 11/74 (14%), Positives = 31/74 (41%), Gaps = 4/74 (5%)

Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
               F+ + +    +  +LR+   S + ++    +++        +Q K   ++ATD+A 
Sbjct: 38  PTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYP----TIKQKKPDFILATDIAE 93

Query: 168 RGLDVEDVNTVNIG 181
            G ++     ++  
Sbjct: 94  MGANLCVERVLDCR 107

>d1jr6a_ c.37.1.14 (A:) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 138

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

 Score = 42.4 bits (99), Expect = 6e-06
 Identities = 12/64 (18%), Positives = 26/64 (40%), Gaps = 7/64 (10%)

Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
           + ++F  +KKK +++   L     +A+  +       R   ++        ++VATD   
Sbjct: 37  RHLIFCHSKKKCDELAAKLVALGINAVAYY-------RGLDVSVIPTNGDVVVVATDALM 89

Query: 168 RGLD 171
            G  
Sbjct: 90  TGFT 93

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 155

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 41.5 bits (96), Expect = 2e-05
 Identities = 42/135 (31%), Positives = 66/135 (48%), Gaps = 3/135 (2%)

Query: 99  YEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAP 158
             + KN  F  +VF +TK+  +++   LR     A  IHGD +Q  R+ V+  F+Q K  
Sbjct: 21  CRLLKNKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIR 80

Query: 159 ILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQVIEVVQDYEKEKRLFSLI--RELGK 216
           IL+ATDV +RG+DV D+N V    L  +    +   I       K+ +  S+I  RE  K
Sbjct: 81  ILIATDVMSRGIDVNDLNCVINYHLPQNPESYM-HRIGRTGRAGKKGKAISIINRREYKK 139

Query: 217 YTLITQESSSTLSEM 231
              I +     + ++
Sbjct: 140 LRYIERAMKLKIKKL 154

>d2j0sa2 c.37.1.19 (A:244-411) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]} Length = 168

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.5 bits (91), Expect = 8e-05
 Identities = 26/76 (34%), Positives = 47/76 (61%)

Query: 103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVA 162
                + ++F  TK+KV+ +T  +R    +   +HGD  Q++R+ ++ +FR G + +L++
Sbjct: 31  TLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLIS 90

Query: 163 TDVAARGLDVEDVNTV 178
           TDV ARGLDV  V+ +
Sbjct: 91  TDVWARGLDVPQVSLI 106

>d1gm5a4 c.37.1.19 (A:550-755) RecG helicase domain {Thermotoga maritima [TaxId: 2336]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

 Score = 37.5 bits (86), Expect = 7e-04
 Identities = 17/46 (36%), Positives = 29/46 (63%)

Query: 135 CIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNI 180
            +HG  +Q+++D V+ +F +G+  ILV+T V   G+DV   N + I
Sbjct: 69  LMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVI 114

>d1wi9a_ a.4.5.47 (A:) Hypothetical protein C20orf116 homolog {Mouse (Mus musculus) [TaxId: 10090]} Length = 72

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PCI domain (PINT motif)
domain: Hypothetical protein C20orf116 homolog
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 33.5 bits (77), Expect = 0.002
 Identities = 12/45 (26%), Positives = 19/45 (42%), Gaps = 2/45 (4%)

Query: 185 LSANHNIS--QVIEVVQDYEKEKRLFSLIRELGKYTLITQESSST 227
           L+    +     I  +QD   E  L  +I + GK+  IT    S+
Sbjct: 27  LAFQMGLRTQDAINRIQDLLTEGTLTGVIDDRGKFIYITPSGPSS 71

>d2fwra1 c.37.1.19 (A:257-456) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 35.3 bits (80), Expect = 0.003
 Identities = 18/78 (23%), Positives = 37/78 (47%), Gaps = 5/78 (6%)

Query: 101 MAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPIL 160
           + ++   K+I+F    + V  I+     +      I    ++++R+ +L  FR G+   +
Sbjct: 88  LERHRKDKIIIFTRHNELVYRIS-----KVFLIPAITHRTSREEREEILEGFRTGRFRAI 142

Query: 161 VATDVAARGLDVEDVNTV 178
           V++ V   G+DV D N  
Sbjct: 143 VSSQVLDEGIDVPDANVG 160

>d2eyqa5 c.37.1.19 (A:779-989) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]} Length = 211

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

 Score = 35.0 bits (80), Expect = 0.004
 Identities = 14/46 (30%), Positives = 25/46 (54%)

Query: 135 CIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNI 180
             HG   +++ + V+NDF   +  +LV T +   G+D+   NT+ I
Sbjct: 62  IGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIII 107

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	233
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	99.94
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.92
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	99.92
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.92
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	99.91
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	99.9
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.9
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.9
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.9
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	99.88
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	99.82
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	99.8
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	99.79
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.79
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	99.78
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.77
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	99.75
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	99.75
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	99.68
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.65
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.62
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.61
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	99.58
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.58
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.5
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	99.49
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.49
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	99.46
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.45
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.42
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.42
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.35
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.32
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.31
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.28
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	99.04
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	98.96
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	98.94
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	98.84
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	98.76
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	98.04
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	97.56
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	97.4
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	97.2
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	97.16
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	97.01
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	96.72
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	96.1
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	95.71
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	95.26
d2qy9a2	211	GTPase domain of the signal recognition particle r	95.02
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	94.98
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	94.73
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	94.45
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	94.13
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	94.09
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	93.94
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	93.58
d1okkd2	207	GTPase domain of the signal recognition particle r	93.15
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	92.33
d1ls1a2	207	GTPase domain of the signal sequence recognition p	92.2
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	91.99
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	91.5
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	91.21
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	90.67
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	90.6
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	90.56
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	90.5
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	90.39
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	89.81
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	89.6
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	89.57
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	89.11
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	89.1
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	88.91
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	88.79
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	88.57
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	88.53
d1yt8a4	130	Thiosulfate sulfurtransferase PA2603 {Pseudomonas	88.31
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	88.2
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	87.95
d1j8yf2	211	GTPase domain of the signal sequence recognition p	87.38
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	87.25
d2eyqa2	117	Transcription-repair coupling factor, TRCF {Escher	87.21
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	87.06
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	87.02
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	86.93
d1em8a_	147	DNA polymerase III chi subunit {Escherichia coli [	86.62
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	86.62
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	86.57
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	86.56
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	86.53
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	86.37
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	86.32
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	85.93
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	85.82
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	85.75
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	85.75
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	85.57
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	85.52
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	85.51
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	85.41
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	85.37
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	85.1
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	85.09
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	85.03
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	84.9
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	84.13
d1vmaa2	213	GTPase domain of the signal recognition particle r	84.11
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	83.66
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	83.61
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	83.43
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	83.0
d1xpua3	289	Transcription termination factor Rho, ATPase domai	82.92
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	82.85
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	82.59
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	82.45
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	82.17
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	82.08
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	81.9
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	81.73
d1tq1a_	119	Thiosulfate sulfurtransferase/Senescence-associate	81.6
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	81.5
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	81.28
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	80.56
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	80.49
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	80.48
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	80.42
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	80.03

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.94  E-value=9.9e-26  Score=169.34  Aligned_cols=133  Identities=26%  Similarity=0.389  Sum_probs=113.6

Q ss_pred             hhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCC
Q psy14082         95 FNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVED  174 (233)
Q Consensus        95 ~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~  174 (233)
                      +.+.+++...+..|+||||+++.+++.+++.|...++.+..+||+|++++|..+++.|+.|+.++|||||+++||+|+|+
T Consensus        16 ~~L~~ll~~~~~~k~iIF~~s~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Tdv~~rGiDi~~   95 (162)
T d1fuka_          16 ECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQ   95 (162)
T ss_dssp             HHHHHHHHHTTCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGGGTTTCCCCS
T ss_pred             HHHHHHHHhCCCCcEEEEEEEEchHHHHHHHHhhcCceEEEeccCCchhhHHHHHHHHhhcccceeeccccccccccCCC
Confidence            34444556678899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccEEEEecCCCCccccc------------ceeeEEeecchHHHHHHHHHHhhcCcccccccchhhHhhh
Q psy14082        175 VNTVNIGSLQLSANHNI------------SQVIEVVQDYEKEKRLFSLIRELGKYTLITQESSSTLSEM  231 (233)
Q Consensus       175 v~~VI~~d~P~~~~~~i------------~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~l  231 (233)
                      +++|||||+|++++.|+            |.++.++++.+  ...+..+++..+.+++  +.|.+++++
T Consensus        96 v~~VI~~d~P~~~~~yihR~GR~gR~g~~g~~i~~~~~~d--~~~~~~i~~~~~~~~~--~ip~~~~~l  160 (162)
T d1fuka_          96 VSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNED--VGAMRELEKFYSTQIE--ELPSDIATL  160 (162)
T ss_dssp             CSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETTT--HHHHHHHHHHSSCCCE--ECCSCCTTT
T ss_pred             ceEEEEeccchhHHHHHhhccccccCCCccEEEEEcCHHH--HHHHHHHHHHHcCcCC--CCChHHHHh
Confidence            99999999999999887            45778888654  6777888887665544  344444443

>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=99.92  E-value=3.5e-26  Score=187.94  Aligned_cols=163  Identities=17%  Similarity=0.163  Sum_probs=118.4

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCCCCC
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPKGP   84 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~~~   84 (233)
                      +..|+++++.||||||||++|+.|++......       +.++||++||||||.|+++.++.+..+.......+......
T Consensus         6 ~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~-------~~~~lvi~Ptr~La~q~~~~l~~~~~~~~~~~~~~~~~~~~   78 (305)
T d2bmfa2           6 FRKKRLTIMDLHPGAGKTKRYLPAIVREAIKR-------GLRTLILAPTRVVAAEMEEALRGLPIRYQTPAIRAEHTGRE   78 (305)
T ss_dssp             SSTTCEEEECCCTTSSTTTTHHHHHHHHHHHH-------TCCEEEEESSHHHHHHHHHHTTTSCCBCCC--------CCC
T ss_pred             hhcCCcEEEEECCCCCHHHHHHHHHHHHHHhc-------CCEEEEEccHHHHHHHHHHHHhcCCcceeeeEEeecccCcc
Confidence            45789999999999999999988998777643       67899999999999999999887733333222233323333


Q ss_pred             eeEEe--------------ccc----hhhhc--------------hH---------------------------------
Q psy14082         85 QDCLP--------------LHR----FVFNC--------------QY---------------------------------   99 (233)
Q Consensus        85 ~~lv~--------------l~r----~~~~~--------------~~---------------------------------   99 (233)
                      .++++              +.+    ++|.+              ..                                 
T Consensus        79 ~i~~~t~~~l~~~~~~~~~~~~~~~vViDE~H~~~~~~~~~~~~l~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~  158 (305)
T d2bmfa2          79 IVDLMCHATFTMRLLSPIRVPNYNLIIMDEAHFTDPASIAARGYISTRVEMGEAAGIFMTATPPGSRDPFPQSNAPIMDE  158 (305)
T ss_dssp             SEEEEEHHHHHHHHTSSSCCCCCSEEEEESTTCCSHHHHHHHHHHHHHHHHTSCEEEEECSSCTTCCCSSCCCSSCEEEE
T ss_pred             ccccCCcHHHHHHHhcCccccceeEEEeeeeeecchhhHHHHHHHHHhhccccceEEEeecCCCcceeeecccCCcceEE
Confidence            33333              000    00000              00                                 


Q ss_pred             -------------HHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccC
Q psy14082        100 -------------EMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVA  166 (233)
Q Consensus       100 -------------~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~  166 (233)
                                   ........+++|||++++.++.+++.|.+.++++..+||++++..+    ..|++|..+++|+|+.+
T Consensus       159 ~~~~~~~~~~~~~~~~~~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~l~~~~~~~~~----~~~~~~~~~~lvaT~~~  234 (305)
T d2bmfa2         159 EREIPERSWNSGHEWVTDFKGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSRKTFDSEY----IKTRTNDWDFVVTTDIS  234 (305)
T ss_dssp             ECCCCCSCCSSCCHHHHSSCSCEEEECSCHHHHHHHHHHHHHHTCCCEECCTTCHHHHG----GGGGTSCCSEEEECGGG
T ss_pred             EEeccHHHHHHHHHHHHhhCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeCCcChHHHH----hhhhccchhhhhhhHHH
Confidence                         2334567899999999999999999999999999999999876544    46899999999999999


Q ss_pred             cCCcCCCCccEEE
Q psy14082        167 ARGLDVEDVNTVN  179 (233)
Q Consensus       167 ~~Gldi~~v~~VI  179 (233)
                      ++|+|+ ++++||
T Consensus       235 ~~G~~~-~~~~Vi  246 (305)
T d2bmfa2         235 EMGANF-KAERVI  246 (305)
T ss_dssp             GTTCCC-CCSEEE
T ss_pred             HhcCCC-CccEEE
Confidence            999999 455554

>d2j0sa2 c.37.1.19 (A:244-411) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.92  E-value=5.7e-25  Score=166.06  Aligned_cols=119  Identities=27%  Similarity=0.418  Sum_probs=106.4

Q ss_pred             HHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEE
Q psy14082        100 EMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVN  179 (233)
Q Consensus       100 ~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI  179 (233)
                      ++......++||||++++.++.++..|+..++++..+||+|++++|..+++.|++|+.++|||||+++||+|+|++++||
T Consensus        28 ll~~~~~~k~iiF~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~fk~g~~~iLv~Td~~~rGiDi~~v~~VI  107 (168)
T d2j0sa2          28 LYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLII  107 (168)
T ss_dssp             HHHHHTSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGGSSSCCCTTEEEEE
T ss_pred             HHHhCCCCceEEEeeeHHHHHHHHHHhhhcccchhhhhhhhhHHHHHHHHHHHhcCCccEEeccchhcccccccCcceEE
Confidence            44456778999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCccccc------------ceeeEEeecchHHHHHHHHHHhhcCcccc
Q psy14082        180 IGSLQLSANHNI------------SQVIEVVQDYEKEKRLFSLIRELGKYTLI  220 (233)
Q Consensus       180 ~~d~P~~~~~~i------------~~~~~~~~~~~~~~~~~~~i~~~~~~~~~  220 (233)
                      |||+|++...|+            |.++.++.+++  ...++.+++..+.+++
T Consensus       108 n~d~P~~~~~yihR~GR~gR~g~~G~~i~~~~~~d--~~~~~~i~~~~~~~i~  158 (168)
T d2j0sa2         108 NYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDD--IRILRDIEQYYSTQID  158 (168)
T ss_dssp             ESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGGG--HHHHHHHHHHTTCCCE
T ss_pred             EecCCcCHHHHHhhhccccccCCCcEEEEEECHHH--HHHHHHHHHHHcCcCC
Confidence            999999998777            57788888765  6777888876655443

>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.92  E-value=1.5e-24  Score=164.41  Aligned_cols=119  Identities=24%  Similarity=0.322  Sum_probs=106.8

Q ss_pred             HHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEE
Q psy14082        100 EMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVN  179 (233)
Q Consensus       100 ~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI  179 (233)
                      ++...+..++||||+++++++.++..|...|+.+..+||+|++++|..++++|++|+.++||||++++||+|+|++++||
T Consensus        26 ll~~~~~~k~iVF~~~~~~~~~l~~~L~~~g~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~Td~~~~Gid~~~v~~VI  105 (171)
T d1s2ma2          26 LFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVI  105 (171)
T ss_dssp             HHHHSCCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCSSSSCCCTTEEEEE
T ss_pred             HHHhCCCCceEEEEeeeehhhHhHHhhhcccccccccccccchhhhhhhhhhcccCccccccchhHhhhccccceeEEEE
Confidence            44566788999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCccccc------------ceeeEEeecchHHHHHHHHHHhhcCcccc
Q psy14082        180 IGSLQLSANHNI------------SQVIEVVQDYEKEKRLFSLIRELGKYTLI  220 (233)
Q Consensus       180 ~~d~P~~~~~~i------------~~~~~~~~~~~~~~~~~~~i~~~~~~~~~  220 (233)
                      |||+|+++..|+            |.++.|+.+.+  .+.+..+++..+.+++
T Consensus       106 ~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~v~~~e--~~~~~~i~~~l~~~~~  156 (171)
T d1s2ma2         106 NFDFPKTAETYLHRIGRSGRFGHLGLAINLINWND--RFNLYKIEQELGTEIA  156 (171)
T ss_dssp             ESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGGG--HHHHHHHHHHHTCCCE
T ss_pred             ecCCcchHHHHHHHhhhcccCCCccEEEEEeCHHH--HHHHHHHHHHHCCCCC
Confidence            999999998776            56777888755  7788888876665544

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.91  E-value=5.2e-24  Score=158.86  Aligned_cols=115  Identities=32%  Similarity=0.459  Sum_probs=103.5

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecC
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSL  183 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~  183 (233)
                      ..+.++||||+++++++.++..|++.|+.+..+||++++.+|..++++|++|+.++|||||++++|+|+|++++|||||+
T Consensus        26 ~~~~k~IIF~~s~~~~~~l~~~L~~~g~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~~~~~Gid~~~v~~Vi~~d~  105 (155)
T d1hv8a2          26 NKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHL  105 (155)
T ss_dssp             STTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTHHHHCCCSCCSEEEESSC
T ss_pred             cCCCCEEEEECchHHHHHHHhhhcccccccccccccchhhhhhhhhhhhhcccceeeeehhHHhhhhhhccCcEEEEecC
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCccccc------------ceeeEEeecchHHHHHHHHHHhhcCcccc
Q psy14082        184 QLSANHNI------------SQVIEVVQDYEKEKRLFSLIRELGKYTLI  220 (233)
Q Consensus       184 P~~~~~~i------------~~~~~~~~~~~~~~~~~~~i~~~~~~~~~  220 (233)
                      |+|+..|+            |.++.++.+.+  ...++.+++..+.+++
T Consensus       106 p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~d--~~~~~~i~~~~~~~i~  152 (155)
T d1hv8a2         106 PQNPESYMHRIGRTGRAGKKGKAISIINRRE--YKKLRYIERAMKLKIK  152 (155)
T ss_dssp             CSCHHHHHHHSTTTCCSSSCCEEEEEECTTS--HHHHHHHHHHHTCCCC
T ss_pred             CCCHHHHHHHHHhcCcCCCCceEEEEEchHH--HHHHHHHHHHHCCCcc
Confidence            99998777            46777888654  6777888876666554

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.90  E-value=2e-23  Score=157.59  Aligned_cols=121  Identities=21%  Similarity=0.304  Sum_probs=105.1

Q ss_pred             HHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEE
Q psy14082        100 EMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVN  179 (233)
Q Consensus       100 ~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI  179 (233)
                      .+......|+||||++++.++.+++.|.+.|+.+..+||+|++++|..++++|++|+.++||||+++++|+|+|++++||
T Consensus        21 ll~~~~~~k~iIF~~~~~~~~~l~~~L~~~~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T~~~~~Gid~~~~~~vi  100 (168)
T d1t5ia_          21 LLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAF  100 (168)
T ss_dssp             HHHHSCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSCCSTTCCGGGCSEEE
T ss_pred             HHHhCCCCeEEEEEeeeecchhhhhhhccccccccccccccchhhhhhhhhhhccccceeeeccccccchhhcccchhhh
Confidence            44556778999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCccccc------------ceeeEEeecchHHHHHHHHHHhhcCccccc
Q psy14082        180 IGSLQLSANHNI------------SQVIEVVQDYEKEKRLFSLIRELGKYTLIT  221 (233)
Q Consensus       180 ~~d~P~~~~~~i------------~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~  221 (233)
                      +||+|+++..|+            |.++.++++. .+.+++..+++..+..+..
T Consensus       101 ~~~~p~~~~~yiqr~GR~gR~g~~g~~i~l~~~~-~~~~~~~~i~~~~~~~~~e  153 (168)
T d1t5ia_         101 NYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDE-NDAKILNDVQDRFEVNISE  153 (168)
T ss_dssp             ESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSH-HHHHHHHHHHHHHCCCEEE
T ss_pred             hhhcccchhhHhhhhhhcccCCCccEEEEEECch-HHHHHHHHHHHHHcCCccc
Confidence            999999998776            3566677763 3467777777765554443

>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=99.90  E-value=2e-24  Score=164.46  Aligned_cols=87  Identities=28%  Similarity=0.358  Sum_probs=82.4

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQ  184 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P  184 (233)
                      .+.++||||+++++++.++..|.+.|+++..+||+|++.+|.+++++|++|+.+||||||+++||+|+|+|++|||||+|
T Consensus        30 ~~~~~iif~~~~~~~~~~~~~l~~~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTdv~~rGiDip~v~~VI~~d~p  109 (181)
T d1t5la2          30 RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDAD  109 (181)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESCCCSSSCCCTTEEEEEETTTT
T ss_pred             cCCeEEEEeehhhhhHHHHHHHHhCCcceeEecCCccHHHHHHHHHHHHCCCCCEEEehhHHHccCCCCCCCEEEEecCC
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             C-----Cccccc
Q psy14082        185 L-----SANHNI  191 (233)
Q Consensus       185 ~-----~~~~~i  191 (233)
                      .     |..+|+
T Consensus       110 ~~~~~~s~~~yi  121 (181)
T d1t5la2         110 KEGFLRSERSLI  121 (181)
T ss_dssp             SCSGGGSHHHHH
T ss_pred             cccccccHHHHH
Confidence            6     445566

>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=99.90  E-value=2.7e-23  Score=160.84  Aligned_cols=114  Identities=18%  Similarity=0.191  Sum_probs=99.5

Q ss_pred             HHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEE
Q psy14082        100 EMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVN  179 (233)
Q Consensus       100 ~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI  179 (233)
                      ++....+.++||||+|++.++.++..|...++.+..+||+|++++|..+++.|++|+.++|||||++++|+|+|+|++||
T Consensus        24 ~l~~~~~~~~IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd~~~~GiD~p~v~~VI  103 (200)
T d1oywa3          24 YVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVV  103 (200)
T ss_dssp             HHHHTTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSCTTTCCTTCCEEE
T ss_pred             HHHhcCCCCEEEEEeeehhhHHhhhhhccCCceeEEecCCCcHHHHHHHHHHHhcccceEEEecchhhhccCCCCCCEEE
Confidence            44456778999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCccccc------------ceeeEEeecchHHHHHHHHHHhh
Q psy14082        180 IGSLQLSANHNI------------SQVIEVVQDYEKEKRLFSLIREL  214 (233)
Q Consensus       180 ~~d~P~~~~~~i------------~~~~~~~~~~~~~~~~~~~i~~~  214 (233)
                      |||+|.+...|+            |.++.|+.+.+ ...+.+.+++.
T Consensus       104 ~~~~P~~~~~y~qr~GR~gR~g~~g~ai~~~~~~d-~~~l~~~i~~~  149 (200)
T d1oywa3         104 HFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPAD-MAWLRRCLEEK  149 (200)
T ss_dssp             ESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHH-HHHHHHHHHTS
T ss_pred             ECCCccchHHHHHHhhhhhcCCCCceEEEecCHHH-HHHHHhhhhcc
Confidence            999999999888            46667887633 33343445543

>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=99.88  E-value=1.4e-22  Score=152.16  Aligned_cols=84  Identities=24%  Similarity=0.299  Sum_probs=80.8

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecC
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSL  183 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~  183 (233)
                      ..+.++||||+++++++.++..|.+.|+++..+||+|++.+|.+++++|++|+++|||||++++||+|+|+|++|||||+
T Consensus        29 ~~g~r~lvfc~t~~~~~~l~~~L~~~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~v~~~GiDip~V~~Vi~~~~  108 (174)
T d1c4oa2          29 ARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDA  108 (174)
T ss_dssp             HTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEEEEEETTT
T ss_pred             hcCCcEEEEEcchhHHHHHHHHHHhcCCceEEEecccchHHHHHHHHHHHCCCeEEEEeeeeeeeeccCCCCcEEEEecc
Confidence            36789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCc
Q psy14082        184 QLSA  187 (233)
Q Consensus       184 P~~~  187 (233)
                      |.+.
T Consensus       109 ~~~~  112 (174)
T d1c4oa2         109 DKEG  112 (174)
T ss_dssp             TSCS
T ss_pred             cccc
Confidence            8754

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=2.7e-21  Score=151.99  Aligned_cols=109  Identities=22%  Similarity=0.184  Sum_probs=85.0

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~g   78 (233)
                      |||.++.|+|++++|+||||||+||++|+++++...     ..+++++|++||||||.|+++.++.+  +.++++..++|
T Consensus        47 aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~~-----~~~~~~lil~PtreLa~Qi~~~~~~l~~~~~i~~~~~~g  121 (222)
T d2j0sa1          47 AIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQ-----VRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIG  121 (222)
T ss_dssp             HHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTT-----SCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECT
T ss_pred             HHHHHHCCCCeEEEcCcchhhhhhhccccccccccc-----ccCceeEEecchHHHHHHHHHHHHHHhCccceeEEEEee
Confidence            578999999999999999999999999999999765     45789999999999999999999999  56789999999


Q ss_pred             CCCC---------CCeeEEe-ccchhhhchHHHhcCCCCeEEEEec
Q psy14082         79 GTPK---------GPQDCLP-LHRFVFNCQYEMAKNPAFKVIVFVE  114 (233)
Q Consensus        79 g~~~---------~~~~lv~-l~r~~~~~~~~~~~~~~~k~iIf~~  114 (233)
                      |.+.         ..+++|| ..|+.+...........-+.+|+-+
T Consensus       122 ~~~~~~~~~~l~~~~~Ilv~TPgrl~~~~~~~~~~~~~l~~lVlDE  167 (222)
T d2j0sa1         122 GTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDE  167 (222)
T ss_dssp             TSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEET
T ss_pred             cccchhhHHHhccCCeEEeCCCCcHHhcccccccccccceeeeecc
Confidence            9765         4555666 3444444433222233345555544

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=99.80  E-value=3.3e-19  Score=141.47  Aligned_cols=154  Identities=20%  Similarity=0.271  Sum_probs=103.5

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCC----CCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEE
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEP----VKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNI   74 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~----~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~   74 (233)
                      |||.+++|+|++++|+||||||++|++|++++++....    .....++++|||+||+|||.|+++.+..+  ..++++.
T Consensus        51 ~ip~il~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~~~~~~~~~alil~pt~el~~q~~~~~~~~~~~~~~~~~  130 (238)
T d1wrba1          51 AIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSC  130 (238)
T ss_dssp             HHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEE
T ss_pred             HhhhhhCCCCEEEECCCCCCcceeeHHHHHHHHHhcccccccccCCCCceEEEeccchhhhcchheeeeecccCCCcEEE
Confidence            57889999999999999999999999999999986532    22356899999999999999999999999  4578899


Q ss_pred             EEEcCCCC---------CCeeEEe-ccchhhhchHHHhcCCCCeEEEEecchhHH-----HHHHHHHhhC------CCee
Q psy14082         75 CIFGGTPK---------GPQDCLP-LHRFVFNCQYEMAKNPAFKVIVFVETKKKV-----EDITRALRRE------RHSA  133 (233)
Q Consensus        75 ~~~gg~~~---------~~~~lv~-l~r~~~~~~~~~~~~~~~k~iIf~~~~~~~-----~~l~~~L~~~------~~~~  133 (233)
                      .++|+...         .++++|+ ..|+.+++.........-+.+|+-+-....     +.+...+++.      ....
T Consensus       131 ~~~g~~~~~~~~~~~~~~~~ivV~TP~~l~~~~~~~~~~l~~v~~lViDEaD~ll~~~f~~~i~~Il~~~~~~~~~~~Q~  210 (238)
T d1wrba1         131 VVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEESNMPSGINRQT  210 (238)
T ss_dssp             EECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCTTCCEEEEETHHHHHHTTCHHHHHHHHHSSCCCCGGGCEE
T ss_pred             EEeccchhhHHHhhcccCCceeecCHHHHHhHHccCceeccccceeeeehhhhhhhhccHHHHHHHHHHhcCCCCCCCEE
Confidence            99888664         4567888 344444443322223344556654432221     2333333322      1244


Q ss_pred             EEEeCCCCHHHHHHHHHHhhCC
Q psy14082        134 ICIHGDKTQQDRDYVLNDFRQG  155 (233)
Q Consensus       134 ~~~~~~~~~~~r~~~~~~f~~g  155 (233)
                      .++.+-|+.+- ....+.|-..
T Consensus       211 il~SAT~~~~v-~~l~~~~~~~  231 (238)
T d1wrba1         211 LMFSATFPKEI-QKLAADFLYN  231 (238)
T ss_dssp             EEEESSCCHHH-HHHHHHHCSS
T ss_pred             EEEeeeCCHHH-HHHHHHHCCC
Confidence            56666666544 4455556543

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=2.1e-19  Score=140.79  Aligned_cols=109  Identities=25%  Similarity=0.231  Sum_probs=81.1

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~g   78 (233)
                      |||.++.|+|++++|+||||||++|++|+++++...     ..++++||++||+|||.|+++.+..+  ..+++...+.+
T Consensus        42 aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~~-----~~~~~alil~Pt~eL~~Q~~~~~~~~~~~~~~~~~~~~~  116 (218)
T d2g9na1          42 AILPCIKGYDVIAQAQSGTGKTATFAISILQQIELD-----LKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIG  116 (218)
T ss_dssp             HHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCTT-----CCSCCEEEECSSHHHHHHHHHHHHHHHTTTTCCEEEECC
T ss_pred             HHHHHHcCCCEEEEcccchhhhhhhhhhhhheeccc-----ccCccEEEEcccchhhhhHHHHHhhhccccceeEEeeec
Confidence            578899999999999999999999999999999654     56899999999999999999999999  45667777777


Q ss_pred             CCCC----------CCeeEEe-ccchhhhchHHHhcCCCCeEEEEec
Q psy14082         79 GTPK----------GPQDCLP-LHRFVFNCQYEMAKNPAFKVIVFVE  114 (233)
Q Consensus        79 g~~~----------~~~~lv~-l~r~~~~~~~~~~~~~~~k~iIf~~  114 (233)
                      +...          .++++|+ -.|+.+...+.......-+.+|+-+
T Consensus       117 ~~~~~~~~~~~~~~~~~IvV~TP~rl~~~l~~~~~~~~~l~~lVlDE  163 (218)
T d2g9na1         117 GTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDE  163 (218)
T ss_dssp             --CCCSTTTSSSSCCCSEEEECHHHHHHHHHTTSSCSTTCCEEEEES
T ss_pred             ccchhHHHHHHhcCCCEEEEeCChhHHHHHhcCCcccccceEEEeee
Confidence            6543          3456777 3444444433222233345566543

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=8e-20  Score=142.12  Aligned_cols=109  Identities=19%  Similarity=0.235  Sum_probs=81.7

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh---cCCcEEEEE
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS---SALRNICIF   77 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~---~~~~~~~~~   77 (233)
                      |||.+++|+|++++|+||||||++|++|+++++...     ..+++++|++|||||+.|+++.++.+.   ..+++.+++
T Consensus        31 aip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~~~-----~~~~~~lil~PtreL~~qi~~~~~~~~~~~~~~~~~~~~  105 (207)
T d1t6na_          31 CIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPV-----TGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFF  105 (207)
T ss_dssp             HHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCC-----TTCCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEES
T ss_pred             HHHHHHcCCCeEEEeccccccccccccceeeeeccc-----CCCceEEEEeccchhhHHHHHHHHHHHhhCCCceeEEEe
Confidence            578999999999999999999999999999998764     567899999999999999999999993   346788888


Q ss_pred             cCCCC----------CCeeEEe-ccchhhhchHHHhcCCCCeEEEEec
Q psy14082         78 GGTPK----------GPQDCLP-LHRFVFNCQYEMAKNPAFKVIVFVE  114 (233)
Q Consensus        78 gg~~~----------~~~~lv~-l~r~~~~~~~~~~~~~~~k~iIf~~  114 (233)
                      |+.+.          .++++|+ -.|+.+.++.....-..-+.+|+-+
T Consensus       106 g~~~~~~~~~~l~~~~~~ilI~TP~rl~~~~~~~~~~l~~l~~lVlDE  153 (207)
T d1t6na_         106 GGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDE  153 (207)
T ss_dssp             CCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEES
T ss_pred             ccccHHHHHHHHHhcCCCEEEeCcchhhhhccCCceeccccceeehhh
Confidence            88654          3556676 3344444332111223344555444

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=4.9e-19  Score=137.53  Aligned_cols=84  Identities=23%  Similarity=0.324  Sum_probs=72.0

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh---hcCCcEEEEE
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF---SSALRNICIF   77 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~---~~~~~~~~~~   77 (233)
                      |||.+++|+|++++|+||||||++|++|+++++...     .+++++||++||+||+.|+++.+..+   ..++.+....
T Consensus        33 aip~il~g~dvl~~a~TGsGKTlayllP~l~~~~~~-----~~~~~~lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~  107 (206)
T d1veca_          33 SIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLK-----KDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATT  107 (206)
T ss_dssp             HHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTT-----SCSCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEEC
T ss_pred             HHHHHHcCCCEEeeccCccccccccccchhhccccc-----ccCcceEEEeecchhhHHHHHHHHHHhhcccCccccccc
Confidence            578999999999999999999999999999998765     56889999999999999999999988   3456777777


Q ss_pred             cCCCC---------CCeeEEe
Q psy14082         78 GGTPK---------GPQDCLP   89 (233)
Q Consensus        78 gg~~~---------~~~~lv~   89 (233)
                      |+.+.         ..+++|+
T Consensus       108 g~~~~~~~~~~l~~~~~ivv~  128 (206)
T d1veca_         108 GGTNLRDDIMRLDDTVHVVIA  128 (206)
T ss_dssp             SSSCHHHHHHHTTSCCSEEEE
T ss_pred             CCccHHHHHHHHHhccCeEEe
Confidence            77533         5666777

>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=99.77  E-value=3.6e-19  Score=144.93  Aligned_cols=110  Identities=25%  Similarity=0.358  Sum_probs=92.0

Q ss_pred             hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeC--------CCCHHHHHHHHHHhhCCCCCEEEecc
Q psy14082         93 FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHG--------DKTQQDRDYVLNDFRQGKAPILVATD  164 (233)
Q Consensus        93 ~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~--------~~~~~~r~~~~~~f~~g~~~iLv~T~  164 (233)
                      +..++.+.+....+.++||||+++++++.+++.|.+.++++..+||        +|+..+|..+++.|++|++++||||+
T Consensus       148 l~~~l~~~~~~~~~~k~iiF~~~~~~~~~~~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~vLv~T~  227 (286)
T d1wp9a2         148 LKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATS  227 (286)
T ss_dssp             HHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECG
T ss_pred             HHHHHHHHHHhCCCCcEEEEeCcHHhHHHHHHHHHHcCCceEEeeccccccccchhchHHHHHHHHHHHcCCCcEEEEcc
Confidence            3444444556678899999999999999999999999999988876        57777899999999999999999999


Q ss_pred             cCcCCcCCCCccEEEEecCCCCccccc-----------ceeeEEeecch
Q psy14082        165 VAARGLDVEDVNTVNIGSLQLSANHNI-----------SQVIEVVQDYE  202 (233)
Q Consensus       165 ~~~~Gldi~~v~~VI~~d~P~~~~~~i-----------~~~~~~~~~~~  202 (233)
                      ++++|+|+|++++||+||+|+|+..|+           |.++.++++..
T Consensus       228 ~~~~Gld~~~~~~Vi~~d~~~~~~~~~Qr~GR~gR~~~~~~~~l~~~~~  276 (286)
T d1wp9a2         228 VGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMPGRVIILMAKGT  276 (286)
T ss_dssp             GGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCCCSEEEEEEETTS
T ss_pred             ceeccccCCCCCEEEEeCCCCCHHHHHHHHHhCCCCCCCEEEEEEeCCC
Confidence            999999999999999999999998666           35556666543

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.75  E-value=1.4e-18  Score=135.37  Aligned_cols=147  Identities=22%  Similarity=0.236  Sum_probs=95.3

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~g   78 (233)
                      |||.++.|+|++++|+||||||++|++|+++++...     .++++++|++||+||+.|++..+..+  ...+......|
T Consensus        40 aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~-----~~~~~~lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~  114 (212)
T d1qdea_          40 AIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTS-----VKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIG  114 (212)
T ss_dssp             HHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTT-----CCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC
T ss_pred             HHHHHHcCCCEEeecccccchhhhhHhhhHhhhhcc-----CCCcceEEEcccHHHhhhhhhhhcccccccccceeeEee
Confidence            578899999999999999999999999999999754     56899999999999999999999998  45667777777


Q ss_pred             CCCC--------CCeeEEe-ccchhhhchHHHhcCCCCeEEEEecch--------hHHHHHHHHHhhCCCeeEEEeCCCC
Q psy14082         79 GTPK--------GPQDCLP-LHRFVFNCQYEMAKNPAFKVIVFVETK--------KKVEDITRALRRERHSAICIHGDKT  141 (233)
Q Consensus        79 g~~~--------~~~~lv~-l~r~~~~~~~~~~~~~~~k~iIf~~~~--------~~~~~l~~~L~~~~~~~~~~~~~~~  141 (233)
                      +.+.        +++++|+ ..|+..+..+.-..-..-+.+|+-+-.        +..+.+.+.+. .+.....+.+-++
T Consensus       115 ~~~~~~~~~~~~~~~IvI~TP~~l~~~~~~~~~~l~~l~~lVlDEad~lld~~f~~~v~~I~~~~~-~~~Q~vl~SAT~~  193 (212)
T d1qdea_         115 GTSFVEDAEGLRDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLP-PTTQVVLLSATMP  193 (212)
T ss_dssp             ----------CTTCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHTTCHHHHHHHHHHSC-TTCEEEEEESSCC
T ss_pred             ccchhHHHHHhcCCcEEEECCCccccccccCceecCcceEEeehhhhhhcccchHHHHHHHHHhCC-CCCeEEEEEeeCC
Confidence            7544        4466887 233333332211122334445544322        12222222221 2345566667776


Q ss_pred             HHHHHHHHHHhhC
Q psy14082        142 QQDRDYVLNDFRQ  154 (233)
Q Consensus       142 ~~~r~~~~~~f~~  154 (233)
                      .+- .+..++|-.
T Consensus       194 ~~v-~~l~~~~l~  205 (212)
T d1qdea_         194 NDV-LEVTTKFMR  205 (212)
T ss_dssp             HHH-HHHHHHHCS
T ss_pred             HHH-HHHHHHHCC
Confidence            653 335555543

>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=99.75  E-value=1.5e-19  Score=131.25  Aligned_cols=83  Identities=17%  Similarity=0.157  Sum_probs=74.3

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEec
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGS  182 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d  182 (233)
                      ...++++||||+|++.++.+++.|++.|+++..+|++|+.+       .|++|+.++|||||++++|+| |++++|||||
T Consensus        32 ~~~~~k~IVFc~t~~~ae~la~~L~~~G~~~~~~H~~~~~~-------~~~~~~~~vlvaTd~~~~GiD-~~v~~Vi~~~  103 (138)
T d1jr6a_          32 VIKGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVS-------VIPTNGDVVVVATDALMTGFT-GDFDSVIDCN  103 (138)
T ss_dssp             HHTTSCEEEECSCHHHHHHHHHHHHHHTCEEEEECTTCCSC-------CCTTSSCEEEEESSSSCSSSC-CCBSEEEECS
T ss_pred             hcCCCCEEEEeCcHHHHHHHHHHHhccccchhhhhccchhh-------hhhhhhcceeehhHHHHhccc-cccceEEEEE
Confidence            44677999999999999999999999999999999999854       478999999999999999999 9999999965


Q ss_pred             ----CCCCcccccce
Q psy14082        183 ----LQLSANHNISQ  193 (233)
Q Consensus       183 ----~P~~~~~~i~~  193 (233)
                          +|.+.+.|+++
T Consensus       104 ~~~~~P~~~~~y~qr  118 (138)
T d1jr6a_         104 TSDGKPQDAVSRTQR  118 (138)
T ss_dssp             EETTEECCHHHHHHH
T ss_pred             ecCCCCCCHHHHHhH
Confidence                69998866643

>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=99.68  E-value=5.7e-18  Score=135.05  Aligned_cols=86  Identities=16%  Similarity=0.222  Sum_probs=71.2

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEec----ccCcCCcCCCC-ccEE
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVAT----DVAARGLDVED-VNTV  178 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T----~~~~~Gldi~~-v~~V  178 (233)
                      ..+.++||||++++.++.+++.|.+.      +||++++.+|.+++++|++|+++|||||    ++++||+|+|+ |++|
T Consensus        23 ~~~~~~iif~~~~~~~~~l~~~l~~~------~hg~~~~~~R~~~~~~f~~g~~~vLVaT~a~~~v~~rGlDip~~v~~V   96 (248)
T d1gkub2          23 KLGTGGIIYARTGEEAEEIYESLKNK------FRIGIVTATKKGDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFA   96 (248)
T ss_dssp             TSCSCEEEEESSHHHHHHHHHTTTTS------SCEEECTTSSSHHHHHHHHTSCSEEEEECC------CCSCCTTTCCEE
T ss_pred             HhCCCEEEEECCHHHHHHHHHHHHHh------ccCCCCHHHHHHHHHHHHhCCCeEEEEeccccchhhhccCccccccEE
Confidence            34678999999999999999999764      7999999999999999999999999999    78999999996 9999


Q ss_pred             EEecCCCCcccccceeeE
Q psy14082        179 NIGSLQLSANHNISQVIE  196 (233)
Q Consensus       179 I~~d~P~~~~~~i~~~~~  196 (233)
                      ||||+|+.. |++|++++
T Consensus        97 I~~d~P~~~-~r~gR~~R  113 (248)
T d1gkub2          97 VFVGCPSFR-VTIEDIDS  113 (248)
T ss_dssp             EEESCCEEE-EECSCGGG
T ss_pred             EEeCCCcch-hhhhhhhc
Confidence            999999633 44444333

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.65  E-value=2.8e-16  Score=121.85  Aligned_cols=91  Identities=19%  Similarity=0.269  Sum_probs=74.4

Q ss_pred             CCCCCCCC-CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEE
Q psy14082          1 MLPPSESG-CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIF   77 (233)
Q Consensus         1 aip~~~~g-~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~   77 (233)
                      |||.+++| +|++++|+||||||++|++|++++...      .+++++||++||++||.|+++.++.+  ..+.++...+
T Consensus        34 ~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~------~~~~~~lil~pt~~l~~q~~~~~~~~~~~~~~~v~~~~  107 (208)
T d1hv8a1          34 VIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNE------NNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIY  107 (208)
T ss_dssp             HHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCS------SSSCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEEC
T ss_pred             HHHHHHcCCCCeeeechhcccccceeeccccccccc------ccCcceEEEeeccccchhhhhhhhhhcccCCeEEEEee
Confidence            46778887 499999999999999999999998765      46889999999999999999999999  4567889999


Q ss_pred             cCCCC--------CCeeEEe-ccchhhhc
Q psy14082         78 GGTPK--------GPQDCLP-LHRFVFNC   97 (233)
Q Consensus        78 gg~~~--------~~~~lv~-l~r~~~~~   97 (233)
                      |+.+.        +++++|+ ..|+.+++
T Consensus       108 g~~~~~~~~~~l~~~~IlV~TP~~l~~~l  136 (208)
T d1hv8a1         108 GGKAIYPQIKALKNANIVVGTPGRILDHI  136 (208)
T ss_dssp             TTSCHHHHHHHHHTCSEEEECHHHHHHHH
T ss_pred             CCCChHHHHHhcCCCCEEEEChHHHHHHH
Confidence            98754        3566777 34444443

>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=99.62  E-value=2.4e-17  Score=127.16  Aligned_cols=99  Identities=23%  Similarity=0.343  Sum_probs=84.8

Q ss_pred             hchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCc
Q psy14082         96 NCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDV  175 (233)
Q Consensus        96 ~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v  175 (233)
                      .+.+++....+.++||||++...++.+.+.|     .+..+||+++.++|..++++|++|+.++||+|+++++|+|+|.+
T Consensus        83 ~l~~ll~~~~~~k~lvf~~~~~~~~~l~~~l-----~~~~i~g~~~~~~R~~~l~~F~~~~~~vLv~~~~~~~Gidl~~~  157 (200)
T d2fwra1          83 KLREILERHRKDKIIIFTRHNELVYRISKVF-----LIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDA  157 (200)
T ss_dssp             HHHHHHHHTSSSCBCCBCSCHHHHHHHHHHT-----TCCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSSCSCCB
T ss_pred             HHHHHHHhCCCCcEEEEeCcHHHHHHHHhhc-----CcceeeCCCCHHHHHHHHHHhhcCCeeeeeecchhhcccCCCCC
Confidence            3444556677889999999999999998876     34458999999999999999999999999999999999999999


Q ss_pred             cEEEEecCCCCcccccceeeEEee
Q psy14082        176 NTVNIGSLQLSANHNISQVIEVVQ  199 (233)
Q Consensus       176 ~~VI~~d~P~~~~~~i~~~~~~~~  199 (233)
                      ++||+||+|+|+.+|+++.++..+
T Consensus       158 ~~vi~~~~~~s~~~~~Q~iGR~~R  181 (200)
T d2fwra1         158 NVGVIMSGSGSAREYIQRLGRILR  181 (200)
T ss_dssp             SEEEEECCSSCCHHHHHHHHHSBC
T ss_pred             CEEEEeCCCCCHHHHHHHHHhcCC
Confidence            999999999999866644444443

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.61  E-value=6.5e-16  Score=119.58  Aligned_cols=84  Identities=20%  Similarity=0.294  Sum_probs=74.5

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEc
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFG   78 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~g   78 (233)
                      |||.++.|+|++++|+||||||++|++|+++++...     .+++++++++|+++++.|.+..+..+  ..++++...+|
T Consensus        31 aip~il~g~dvi~~a~tGsGKTlay~lp~i~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g  105 (206)
T d1s2ma1          31 AIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPK-----LNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTG  105 (206)
T ss_dssp             HHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTT-----SCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECS
T ss_pred             HHHHHHcCCCEEEecCCcchhhhhhccccccccccc-----cccccceeeccchhhhhhhhhhhhhcccccCeeEEeecC
Confidence            578899999999999999999999999999998765     56788999999999999999999998  66889999999


Q ss_pred             CCCC---------CCeeEEe
Q psy14082         79 GTPK---------GPQDCLP   89 (233)
Q Consensus        79 g~~~---------~~~~lv~   89 (233)
                      +.+.         .++++|+
T Consensus       106 ~~~~~~~~~~l~~~~~Ili~  125 (206)
T d1s2ma1         106 GTNLRDDILRLNETVHILVG  125 (206)
T ss_dssp             SSCHHHHHHHTTSCCSEEEE
T ss_pred             ccchhhHHHHhcccceEEEE
Confidence            8643         5677888

>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=99.58  E-value=1e-16  Score=128.14  Aligned_cols=87  Identities=13%  Similarity=0.114  Sum_probs=77.0

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHH----------HHHHHHhhCCCCCEEEecccCcC---CcC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDR----------DYVLNDFRQGKAPILVATDVAAR---GLD  171 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r----------~~~~~~f~~g~~~iLv~T~~~~~---Gld  171 (233)
                      .++|+||||++++.++.++..|++.|+++..+|++++++.|          ..+++.|+.|+.+++|+|+..++   |+|
T Consensus        35 kggk~LVFcnSR~~aE~La~~L~~~Gi~a~~~Hgglsq~~R~~~gd~~i~~~~aLe~f~~G~~dvVVaT~~~a~g~~giD  114 (299)
T d1a1va2          35 KGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFS  114 (299)
T ss_dssp             HSSEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCGGGSCSSSSEEEEECTTC---CCCCBSEEEECCEEEEEEEECC
T ss_pred             cCCCEEEECCcHHHHHHHHHHHHHCCCCEEEEeCCchHHHHHhccchHHHHHHHHHHHhcCCCcEEEEEeehhccCCCCC
Confidence            56799999999999999999999999999999999999887          56788999999999999999988   677


Q ss_pred             CCCccEEEEecCCCCccccc
Q psy14082        172 VEDVNTVNIGSLQLSANHNI  191 (233)
Q Consensus       172 i~~v~~VI~~d~P~~~~~~i  191 (233)
                      ++.+.+||+||+|.|.+.|+
T Consensus       115 id~V~~VI~~d~P~SvesyI  134 (299)
T d1a1va2         115 LDPTFTIETTTLPQDAVSRT  134 (299)
T ss_dssp             CSSSCEEEEEEEECBHHHHH
T ss_pred             CCcceEEEeCCCCCCHHHHH
Confidence            88888999999999998666

>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=99.58  E-value=1.1e-15  Score=117.78  Aligned_cols=97  Identities=22%  Similarity=0.219  Sum_probs=80.5

Q ss_pred             hhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCC------------------------------CeeEEEeCCCCH
Q psy14082         93 FVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRER------------------------------HSAICIHGDKTQ  142 (233)
Q Consensus        93 ~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~------------------------------~~~~~~~~~~~~  142 (233)
                      +.+++.+.+.  .+.++||||+|++.++.++..|.+..                              ..+.++||+|++
T Consensus        29 ~~~l~~~~i~--~~~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~  106 (201)
T d2p6ra4          29 FEELVEECVA--ENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLN  106 (201)
T ss_dssp             HHHHHHHHHH--TTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCH
T ss_pred             HHHHHHHHHH--cCCcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhh
Confidence            4455555444  45789999999999999998886420                              126789999999


Q ss_pred             HHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEE-------ecCCCCccccc
Q psy14082        143 QDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNI-------GSLQLSANHNI  191 (233)
Q Consensus       143 ~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~-------~d~P~~~~~~i  191 (233)
                      ++|..+.+.|++|.+++||||+.+++|+|+|..++||+       ++.|.+..+|+
T Consensus       107 ~~r~~ie~~f~~g~i~vlvaT~~l~~Gin~p~~~vvi~~~~~~d~~~~~~~~~~~~  162 (201)
T d2p6ra4         107 GQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYK  162 (201)
T ss_dssp             HHHHHHHHHHHTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHH
T ss_pred             hhHHHHHHHHhCCCceEEEechHHHhhcCCCCceEEEecceeccCCcCCCCHHHHH
Confidence            99999999999999999999999999999999999996       66777776555

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=99.50  E-value=1.2e-14  Score=112.48  Aligned_cols=84  Identities=26%  Similarity=0.368  Sum_probs=69.0

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh------hcCCcEE
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF------SSALRNI   74 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~------~~~~~~~   74 (233)
                      |||.++.|+|++++||||||||++|++|+++++...     ...+..++++|+++++.|.++.+...      .....+.
T Consensus        31 aip~~l~G~dvii~a~TGSGKTlayllp~l~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  105 (209)
T d1q0ua_          31 IIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPE-----RAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVAR  105 (209)
T ss_dssp             HHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTT-----SCSCCEEEECSSHHHHHHHHHHHHHHHTTSCGGGCCCEE
T ss_pred             HHHHHHCCCCeEeecccccccceeeeeeeccccccc-----cccccccccccccchhHHHHHHHHhhhcccccccccccc
Confidence            578899999999999999999999999999988765     45778999999999999999999887      2234566


Q ss_pred             EEEcCCCC---------CCeeEEe
Q psy14082         75 CIFGGTPK---------GPQDCLP   89 (233)
Q Consensus        75 ~~~gg~~~---------~~~~lv~   89 (233)
                      ++.|+.+.         .++++|+
T Consensus       106 ~~~~~~~~~~~~~~~~~~~~Ilv~  129 (209)
T d1q0ua_         106 CLIGGTDKQKALEKLNVQPHIVIG  129 (209)
T ss_dssp             EECCCSHHHHTTCCCSSCCSEEEE
T ss_pred             ccccchhhHHHHHHhccCceEEEe
Confidence            66666432         4567887

>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=99.49  E-value=2.2e-15  Score=115.90  Aligned_cols=85  Identities=22%  Similarity=0.318  Sum_probs=67.1

Q ss_pred             CCCCeEEEEecchhHHH--------HHHHHHhhC---CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCC
Q psy14082        104 NPAFKVIVFVETKKKVE--------DITRALRRE---RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDV  172 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~--------~l~~~L~~~---~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi  172 (233)
                      ..++++.+.||..+..+        ...+.|.+.   ++++..+||+|++++|+.++++|++|+++|||||+++++|+|+
T Consensus        27 ~~g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~~~iLVaTtViE~GIDi  106 (206)
T d1gm5a4          27 MRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDV  106 (206)
T ss_dssp             TTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSSCCCSCSCC
T ss_pred             HcCCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCCEEEEEEehhhhccccc
Confidence            46677777787654443        334444332   5678889999999999999999999999999999999999999


Q ss_pred             CCccEEEEecCCCCcc
Q psy14082        173 EDVNTVNIGSLQLSAN  188 (233)
Q Consensus       173 ~~v~~VI~~d~P~~~~  188 (233)
                      |++++||++|.|....
T Consensus       107 p~a~~iii~~a~~fgl  122 (206)
T d1gm5a4         107 PRANVMVIENPERFGL  122 (206)
T ss_dssp             TTCCEEEBCSCSSSCT
T ss_pred             cCCcEEEEEccCCccH
Confidence            9999999999998654

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.49  E-value=2.7e-15  Score=118.42  Aligned_cols=60  Identities=10%  Similarity=-0.032  Sum_probs=53.5

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS   68 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~   68 (233)
                      |||.++.|+|++++||||+|||++|++|++....        ++.++||++||++|+.|+++.+++++
T Consensus        51 ~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~--------~~~rvliv~Pt~~La~Q~~~~l~~~~  110 (237)
T d1gkub1          51 WAKRILRKESFAATAPTGVGKTSFGLAMSLFLAL--------KGKRCYVIFPTSLLVIQAAETIRKYA  110 (237)
T ss_dssp             HHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHT--------TSCCEEEEESCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHH--------hcCeEEEEeccHHHHHHHHHHHHHHH
Confidence            3577889999999999999999999999887663        35689999999999999999999983

>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=99.46  E-value=9.1e-14  Score=106.18  Aligned_cols=83  Identities=19%  Similarity=0.283  Sum_probs=77.5

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhC--CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEe
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRE--RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIG  181 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~  181 (233)
                      ..++++.+.||..+..+.+++.+++.  ++++.++||.|+.+++++++.+|++|+++|||||++.+.|+|+|+++++|.+
T Consensus        29 ~rGgQvy~V~p~I~~~e~~~~~l~~~~p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~TtvIEvGiDvpnA~~iiI~  108 (211)
T d2eyqa5          29 LRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIE  108 (211)
T ss_dssp             TTTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSCCTTEEEEEET
T ss_pred             HcCCeEEEEEcCccchhhHHHHHHHhCCceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEehhhhhccCCCCCcEEEEe
Confidence            57899999999999999999999874  6789999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy14082        182 SLQLS  186 (233)
Q Consensus       182 d~P~~  186 (233)
                      |.+.-
T Consensus       109 ~a~rf  113 (211)
T d2eyqa5         109 RADHF  113 (211)
T ss_dssp             TTTSS
T ss_pred             cchhc
Confidence            87753

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.45  E-value=3.2e-14  Score=109.41  Aligned_cols=73  Identities=16%  Similarity=0.069  Sum_probs=60.5

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhc-CCcEEEEEcCC
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSS-ALRNICIFGGT   80 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~-~~~~~~~~gg~   80 (233)
                      ++.+.+|+|+++++|||||||.++.++++..+..        +.++|+++|+++|+.|+++.++++.. ..++....|+.
T Consensus        34 i~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~~--------~~~vl~l~P~~~L~~q~~~~~~~~~~~~~~v~~~~~~~  105 (202)
T d2p6ra3          34 VEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK--------GGKSLYVVPLRALAGEKYESFKKWEKIGLRIGISTGDY  105 (202)
T ss_dssp             HHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT--------TCCEEEEESSHHHHHHHHHHHTTTTTTTCCEEEECSSC
T ss_pred             HHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhhc--------cCcceeecccHHHHHHHHHHHHHHhhccccceeeccCc
Confidence            4567889999999999999999999999987753        45799999999999999999998844 45666666665


Q ss_pred             CC
Q psy14082         81 PK   82 (233)
Q Consensus        81 ~~   82 (233)
                      ..
T Consensus       106 ~~  107 (202)
T d2p6ra3         106 ES  107 (202)
T ss_dssp             BC
T ss_pred             cc
Confidence            44

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=99.42  E-value=5.3e-13  Score=106.13  Aligned_cols=105  Identities=14%  Similarity=0.103  Sum_probs=89.9

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCCCCCeeEE
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPKGPQDCL   88 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~~~~~lv   88 (233)
                      .+-++++-||||||.+|+..+...+.        .|.++++++||..|+.|+++.+++++.                   
T Consensus       105 m~rLL~GdvGSGKT~Va~~a~~~~~~--------~g~q~~~m~Pt~~La~Qh~~~~~~~f~-------------------  157 (264)
T d1gm5a3         105 MNRLLQGDVGSGKTVVAQLAILDNYE--------AGFQTAFMVPTSILAIQHYRRTVESFS-------------------  157 (264)
T ss_dssp             CCCEEECCSSSSHHHHHHHHHHHHHH--------HTSCEEEECSCHHHHHHHHHHHHHHHT-------------------
T ss_pred             ceeeeeccccccccHHHHHHHHHHHh--------cccceeEEeehHhhhHHHHHHHHHhhh-------------------
Confidence            45689999999999999999988774        367899999999999999999988743                   


Q ss_pred             eccchhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCc-
Q psy14082         89 PLHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA-  167 (233)
Q Consensus        89 ~l~r~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~-  167 (233)
                                                             ..|+.+..+||+++..+|.+++++.++|+.+|+|+|..+- 
T Consensus       158 ---------------------------------------~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~  198 (264)
T d1gm5a3         158 ---------------------------------------KFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQ  198 (264)
T ss_dssp             ---------------------------------------CSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHH
T ss_pred             ---------------------------------------hccccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhc
Confidence                                                   2346778899999999999999999999999999997654 


Q ss_pred             CCcCCCCccEEE
Q psy14082        168 RGLDVEDVNTVN  179 (233)
Q Consensus       168 ~Gldi~~v~~VI  179 (233)
                      ..+.+.+..+||
T Consensus       199 ~~~~f~~Lglvi  210 (264)
T d1gm5a3         199 EDVHFKNLGLVI  210 (264)
T ss_dssp             HCCCCSCCCEEE
T ss_pred             CCCCccccceee
Confidence            457777888777

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=99.42  E-value=1.7e-12  Score=101.34  Aligned_cols=106  Identities=17%  Similarity=0.118  Sum_probs=91.4

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCCCCCeeE
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPKGPQDC   87 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~~~~~l   87 (233)
                      ..+.++++-||||||.+|+..+...+        ..|.++++|+||..|+.|+++.+++++..                 
T Consensus        76 ~~~~LL~GdvGsGKT~V~~~a~~~~~--------~~g~qv~~l~Pt~~La~Q~~~~~~~~~~~-----------------  130 (233)
T d2eyqa3          76 AMDRLVCGDVGFGKTEVAMRAAFLAV--------DNHKQVAVLVPTTLLAQQHYDNFRDRFAN-----------------  130 (233)
T ss_dssp             CCEEEEECCCCTTTHHHHHHHHHHHH--------TTTCEEEEECSSHHHHHHHHHHHHHHSTT-----------------
T ss_pred             ccCeEEEcCCCCCcHHHHHHHHHHHH--------HcCCceEEEccHHHhHHHHHHHHHHHHhh-----------------
Confidence            34779999999999999999988877        45889999999999999999999887332                 


Q ss_pred             EeccchhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccC-
Q psy14082         88 LPLHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVA-  166 (233)
Q Consensus        88 v~l~r~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~-  166 (233)
                                                               .+.++..+||.++..+|.++++.+.+|+.+|+|.|..+ 
T Consensus       131 -----------------------------------------~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l  169 (233)
T d2eyqa3         131 -----------------------------------------WPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLL  169 (233)
T ss_dssp             -----------------------------------------TTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHH
T ss_pred             -----------------------------------------CCCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhh
Confidence                                                     24577889999999999999999999999999999854 


Q ss_pred             cCCcCCCCccEEE
Q psy14082        167 ARGLDVEDVNTVN  179 (233)
Q Consensus       167 ~~Gldi~~v~~VI  179 (233)
                      ...+.+++..+||
T Consensus       170 ~~~~~f~~LgLiI  182 (233)
T d2eyqa3         170 QSDVKFKDLGLLI  182 (233)
T ss_dssp             HSCCCCSSEEEEE
T ss_pred             ccCCcccccccee
Confidence            4467888888887

>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=99.35  E-value=5.5e-12  Score=104.37  Aligned_cols=111  Identities=11%  Similarity=0.212  Sum_probs=95.5

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCC---EEEecccCcCCcCCCCccEEE
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAP---ILVATDVAARGLDVEDVNTVN  179 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~---iLv~T~~~~~Gldi~~v~~VI  179 (233)
                      ...+.|+|||++.....+.+...|...|+.+..++|+++..+|..++++|+++...   +|++|.+++.|+|++.+++||
T Consensus       115 ~~~g~KvlIFs~~~~~ld~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~vlLls~~agg~GlnL~~a~~vi  194 (346)
T d1z3ix1         115 TTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLV  194 (346)
T ss_dssp             HHCCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGGGSCTTCCCTTEEEEE
T ss_pred             HhcCCceeEEeehhhhhHHHHHHHhhhhccccccccchhHHHHHHHHHhhhcccccceeeeecchhhhhccccccceEEE
Confidence            35678999999999999999999999999999999999999999999999987543   678899999999999999999


Q ss_pred             EecCCCCcc---------cccc-----eeeEEeecchHHHHHHHHHHh
Q psy14082        180 IGSLQLSAN---------HNIS-----QVIEVVQDYEKEKRLFSLIRE  213 (233)
Q Consensus       180 ~~d~P~~~~---------~~i~-----~~~~~~~~~~~~~~~~~~i~~  213 (233)
                      +||+++++.         +|+|     .+.+++....-++++++...+
T Consensus       195 ~~d~~wnp~~~~Qa~~R~~R~GQ~~~V~v~rli~~~TiEe~i~~~~~~  242 (346)
T d1z3ix1         195 MFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTGTIEEKILQRQAH  242 (346)
T ss_dssp             ECSCCSSHHHHHHHHTTSSSTTCCSCEEEEEEEETTSHHHHHHHHHHH
T ss_pred             EecCCCccchHhHhhhcccccCCCCceEEEEEEeCCCHHHHHHHHHHH
Confidence            999999986         4444     556677765566777776655

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=99.32  E-value=3.6e-12  Score=97.88  Aligned_cols=56  Identities=14%  Similarity=0.137  Sum_probs=50.2

Q ss_pred             CCCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          1 MLPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         1 aip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      |||.++.|+|+++++|||||||++|.+|++.+           ..++++++|+++|+.|+.+.++.+
T Consensus        33 ai~~~l~g~~vlv~apTGsGKT~~~~~~~~~~-----------~~~~~~v~P~~~L~~q~~~~l~~~   88 (206)
T d1oywa2          33 IIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL-----------NGLTVVVSPLISLMKDQVDQLQAN   88 (206)
T ss_dssp             HHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS-----------SSEEEEECSCHHHHHHHHHHHHHT
T ss_pred             HHHHHHcCCCEEEEcCCCCCCcchhhhhhhhc-----------cCceEEeccchhhhhhHHHHHHhh
Confidence            45677899999999999999999999998752           457999999999999999999888

>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=99.31  E-value=1.1e-11  Score=97.68  Aligned_cols=110  Identities=15%  Similarity=0.220  Sum_probs=88.4

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhC-CCeeEEEeCCCCHHHHHHHHHHhhCCC-CCEEE-ecccCcCCcCCCCccEEEE
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRE-RHSAICIHGDKTQQDRDYVLNDFRQGK-APILV-ATDVAARGLDVEDVNTVNI  180 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~-~~~~~~~~~~~~~~~r~~~~~~f~~g~-~~iLv-~T~~~~~Gldi~~v~~VI~  180 (233)
                      ..+.|+||||+.....+.+...+.+. +.++..+||+++.++|..++++|+++. ..+++ +|...+.|+|++.+++||+
T Consensus        83 ~~g~kviIFs~~~~~~~~l~~~l~~~~~~~~~~i~G~~~~~~R~~~i~~F~~~~~~~vll~~~~~~g~Glnl~~a~~vi~  162 (244)
T d1z5za1          83 DEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIH  162 (244)
T ss_dssp             HTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEECCTTCCCCCCTTCSEEEE
T ss_pred             ccccceEEEeeceehHHHHHHHHHhhccceEEEEecccchhccchhhhhhhccccchhccccccccccccccchhhhhhh
Confidence            36789999999999999999888654 888889999999999999999998764 66665 4578999999999999999


Q ss_pred             ecCCCCccc---------ccc-----eeeEEeecchHHHHHHHHHHh
Q psy14082        181 GSLQLSANH---------NIS-----QVIEVVQDYEKEKRLFSLIRE  213 (233)
Q Consensus       181 ~d~P~~~~~---------~i~-----~~~~~~~~~~~~~~~~~~i~~  213 (233)
                      ||+|+|+..         |+|     .+.+++....-++++++.+++
T Consensus       163 ~~~~wn~~~~~Qa~~R~~R~Gq~~~v~i~~l~~~~Tiee~i~~~~~~  209 (244)
T d1z5za1         163 FDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEEKIDQLLAF  209 (244)
T ss_dssp             CSCCSCTTTC--------------CCEEEEEEETTSHHHHHHHHHHH
T ss_pred             cCchhhhHHHhhhcceeeecCCCCceEEEEEeeCCCHHHHHHHHHHH
Confidence            999999872         333     334566665556777777665

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=99.28  E-value=3.5e-12  Score=97.31  Aligned_cols=68  Identities=18%  Similarity=0.176  Sum_probs=54.8

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEcCCC
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGGTP   81 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~gg~~   81 (233)
                      .++++++++|||||||+++++++...+..       .+.++||++|+++|+.|+++.+.++  ..+.++....++..
T Consensus        22 ~~~n~lv~~pTGsGKT~i~~~~~~~~~~~-------~~~~il~i~P~~~L~~q~~~~~~~~~~~~~~~v~~~~~~~~   91 (200)
T d1wp9a1          22 KETNCLIVLPTGLGKTLIAMMIAEYRLTK-------YGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVALTGEKS   91 (200)
T ss_dssp             GGSCEEEECCTTSCHHHHHHHHHHHHHHH-------SCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEEECSCSC
T ss_pred             hcCCeEEEeCCCCcHHHHHHHHHHHHHHh-------cCCcEEEEcCchHHHHHHHHHHHHhhcccccceeeeecccc
Confidence            46789999999999999999888776653       2457999999999999999999998  34566666555544

>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=99.04  E-value=1.2e-10  Score=94.00  Aligned_cols=75  Identities=17%  Similarity=0.246  Sum_probs=62.7

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecCC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQ  184 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~P  184 (233)
                      .++++++||++...++.++..|++.|.++..+||.++..++.    +|++++.+++||||+++.|+|+ ++++||..+++
T Consensus        35 ~~g~~~~F~~s~~~~~~~a~~L~~~g~~V~~l~~~~~~~e~~----~~~~~~~~~~~~t~~~~~~~~~-~~~~vid~g~~  109 (299)
T d1yksa2          35 DKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYP----TIKQKKPDFILATDIAEMGANL-CVERVLDCRTA  109 (299)
T ss_dssp             CCSCEEEECSCHHHHHHHHHHHHHTTCCEEECCSSSCC------------CCCSEEEESSSTTCCTTC-CCSEEEECCEE
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHHhcCCeEEEEcCcCcHhHHh----hhhcCCcCEEEEechhhhceec-CceEEEecCce
Confidence            467899999999999999999999999999999999977755    4788999999999999999999 69999987763

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=98.96  E-value=8.6e-10  Score=78.65  Aligned_cols=56  Identities=13%  Similarity=0.064  Sum_probs=41.7

Q ss_pred             CCCCCCCc-eeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhc
Q psy14082          3 PPSESGCQ-NFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSS   69 (233)
Q Consensus         3 p~~~~g~d-~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~   69 (233)
                      |..+.+.+ .++.+|||||||..+...    +.       ..+.+++|++|+++|++|+.+.+.+++.
T Consensus         2 p~~~~~~~~~ll~apTGsGKT~~~~~~----~~-------~~~~~vli~~P~~~l~~q~~~~~~~~~~   58 (136)
T d1a1va1           2 PAVPQSFQVAHLHAPTGSGKSTKVPAA----YA-------AQGYKVLVLNPSVAATLGFGAYMSKAHG   58 (136)
T ss_dssp             CCCCSSCEEEEEECCTTSCTTTHHHHH----HH-------TTTCCEEEEESCHHHHHHHHHHHHHHHS
T ss_pred             CCCccCCCEEEEEeCCCCCHHHHHHHH----HH-------HcCCcEEEEcChHHHHHHHHHHHHHHhh
Confidence            33444444 688999999999763222    12       2366899999999999999999998843

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=98.94  E-value=2.8e-10  Score=80.96  Aligned_cols=55  Identities=15%  Similarity=0.176  Sum_probs=45.4

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      -.|+++++.+|||||||.++..+++....+       .+.++++++|+++|++|+++.+...
T Consensus         5 ~~~~~~il~~~tGsGKT~~~~~~~~~~~~~-------~~~~vli~~p~~~l~~q~~~~~~~~   59 (140)
T d1yksa1           5 KKGMTTVLDFHPGAGKTRRFLPQILAECAR-------RRLRTLVLAPTRVVLSEMKEAFHGL   59 (140)
T ss_dssp             STTCEEEECCCTTSSTTTTHHHHHHHHHHH-------TTCCEEEEESSHHHHHHHHHHTTTS
T ss_pred             HcCCcEEEEcCCCCChhHHHHHHHHHHhhh-------cCceeeeeecchhHHHHHHHHhhhh
Confidence            458999999999999999876666666654       3678999999999999998877544

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=98.84  E-value=3e-09  Score=81.32  Aligned_cols=73  Identities=14%  Similarity=-0.035  Sum_probs=51.4

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCCCCC
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPKGP   84 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~~~   84 (233)
                      +..+...++.+|||+|||++.+ .++.++          +.++||+||+++|+.||.+.++.+.. ..+....|+.....
T Consensus        82 ~~~~~~~ll~~~tG~GKT~~a~-~~~~~~----------~~~~Liv~p~~~L~~q~~~~~~~~~~-~~~~~~~~~~~~~~  149 (206)
T d2fz4a1          82 WLVDKRGCIVLPTGSGKTHVAM-AAINEL----------STPTLIVVPTLALAEQWKERLGIFGE-EYVGEFSGRIKELK  149 (206)
T ss_dssp             HTTTSEEEEEESSSTTHHHHHH-HHHHHS----------CSCEEEEESSHHHHHHHHHHHGGGCG-GGEEEESSSCBCCC
T ss_pred             HHhCCCcEEEeCCCCCceehHH-hHHHHh----------cCceeEEEcccchHHHHHHHHHhhcc-cchhhccccccccc
Confidence            3456678899999999998844 444433          34689999999999999999988732 34555555554444


Q ss_pred             eeEEe
Q psy14082         85 QDCLP   89 (233)
Q Consensus        85 ~~lv~   89 (233)
                      .++++
T Consensus       150 ~i~i~  154 (206)
T d2fz4a1         150 PLTVS  154 (206)
T ss_dssp             SEEEE
T ss_pred             ccccc
Confidence            44443

>d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: DNA helicase UvsW
domain: DNA helicase UvsW
species: Bacteriophage T4 [TaxId: 10665]

Probab=98.76  E-value=3.6e-09  Score=84.82  Aligned_cols=70  Identities=17%  Similarity=0.068  Sum_probs=51.0

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh--cCCcEEEEEcCCCC
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS--SALRNICIFGGTPK   82 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~--~~~~~~~~~gg~~~   82 (233)
                      +..+..++.+|||+|||++... ++..+...      ...++|||||+++|+.|+++.+.+++  ....+..+.+|...
T Consensus       126 l~~~~~il~~pTGsGKT~i~~~-i~~~~~~~------~~~k~Liivp~~~Lv~Q~~~~f~~~~~~~~~~~~~~~~g~~~  197 (282)
T d1rifa_         126 LVNRRRILNLPTSAGRSLIQAL-LARYYLEN------YEGKILIIVPTTALTTQMADDFVDYRLFSHAMIKKIGGGASK  197 (282)
T ss_dssp             HHHSEEEECCCTTSCHHHHHHH-HHHHHHHH------CSSEEEEECSSHHHHHHHHHHHHHHTSCCGGGEEECSTTCSS
T ss_pred             HhcCCceeEEEcccCccHHHHH-HHHHhhhc------ccceEEEEEcCchhHHHHHHHHHHhhccccccceeecceecc
Confidence            3455678999999999988543 44444432      24589999999999999999999983  23345666666544

>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=98.04  E-value=7.6e-06  Score=59.76  Aligned_cols=84  Identities=19%  Similarity=0.182  Sum_probs=64.9

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCC---cc---
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVED---VN---  176 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~---v~---  176 (233)
                      ...+.++||++.|.+..+.++..|.+.+++..+++.....  ++..+-........|.|||++++||.|+.-   |.   
T Consensus        31 ~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLnAk~~~--~Ea~II~~Ag~~g~VtIATNmAGRGtDikl~~~v~~~G  108 (175)
T d1tf5a4          31 YMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHE--REAQIIEEAGQKGAVTIATNMAGRGTDIKLGEGVKELG  108 (175)
T ss_dssp             HHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHH--HHHHHHTTTTSTTCEEEEETTSSTTCCCCCCTTSGGGT
T ss_pred             HhcCCCEEEEeCcHHHHHHHHHHHHHcCCCceeehhhhHH--HHHHHHHhccCCCceeehhhHHHcCCCccchHHHHhCC
Confidence            4577899999999999999999999999999999987543  333333333334569999999999999742   22   


Q ss_pred             --EEEEecCCCCcc
Q psy14082        177 --TVNIGSLQLSAN  188 (233)
Q Consensus       177 --~VI~~d~P~~~~  188 (233)
                        |||.-..|.|..
T Consensus       109 GLhVI~t~~~~s~R  122 (175)
T d1tf5a4         109 GLAVVGTERHESRR  122 (175)
T ss_dssp             SEEEEESSCCSSHH
T ss_pred             CcEEEEeccCcchh
Confidence              688777887763

>d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=97.56  E-value=0.00011  Score=58.22  Aligned_cols=71  Identities=14%  Similarity=0.127  Sum_probs=49.4

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhh-cCCcEEEEEcCC
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS-SALRNICIFGGT   80 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~-~~~~~~~~~gg~   80 (233)
                      +.-+|..=..|+|||+. ++.++..+..+.........++||+||. .|..||.+++.++. .......++|+.
T Consensus        79 ~~g~iLaDemGlGKT~q-aia~l~~l~~~~~~~~~~~~~~LIV~P~-sl~~qW~~Ei~k~~~~~~~~v~~~~~~  150 (298)
T d1z3ix2          79 SYGCIMADEMGLGKTLQ-CITLIWTLLKQSPDCKPEIDKVIVVSPS-SLVRNWYNEVGKWLGGRVQPVAIDGGS  150 (298)
T ss_dssp             CCEEEECCCTTSCHHHH-HHHHHHHHHHCCTTSSCSCSCEEEEECH-HHHHHHHHHHHHHHGGGCCEEEECSSC
T ss_pred             CCceEEEeCCCCCHHHH-HHHHHHHHHHhcccccCCCCcEEEEccc-hhhHHHHHHHHhhcCCceeEEEEeCch
Confidence            44466666899999987 5566666665433222334579999998 58999999999984 345566666654

>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=97.40  E-value=0.00031  Score=52.21  Aligned_cols=68  Identities=16%  Similarity=0.269  Sum_probs=54.4

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCC
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDV  172 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi  172 (233)
                      ...+.++||.+.|.+..+.+...|.+.+++..+++..-. +.-.+++.+ ......|-|||++++||.||
T Consensus        31 h~~GqPVLVGT~SVe~SE~lS~lL~~~gi~h~vLNAK~h-erEAeIIAq-AG~~GaVTIATNMAGRGTDI   98 (219)
T d1nkta4          31 YAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYH-EQEATIIAV-AGRRGGVTVATNMAGRGTDI   98 (219)
T ss_dssp             HHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCH-HHHHHHHHT-TTSTTCEEEEETTCSTTCCC
T ss_pred             HhcCCCEEEeeCcHHHHHHHHHHHHHhccchhccchhhH-HHHHHHHHh-cccCCcEEeeccccCCCCce
Confidence            457899999999999999999999999999999999633 332334433 22235689999999999998

>d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=97.20  E-value=0.00033  Score=53.23  Aligned_cols=63  Identities=14%  Similarity=0.102  Sum_probs=46.1

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEE
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIF   77 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~   77 (233)
                      +..+|+.-++|+|||+. ++.++..+...     ....++||+||. .+..||.+++.++.....+....
T Consensus        31 ~~g~iLaDe~GlGKT~~-~i~~~~~~~~~-----~~~~~~LIv~p~-~l~~~W~~e~~~~~~~~~~~~~~   93 (230)
T d1z63a1          31 GFGICLADDMGLGKTLQ-TIAVFSDAKKE-----NELTPSLVICPL-SVLKNWEEELSKFAPHLRFAVFH   93 (230)
T ss_dssp             TCCEEECCCTTSCHHHH-HHHHHHHHHHT-----TCCSSEEEEECS-TTHHHHHHHHHHHCTTSCEEECS
T ss_pred             CCCEEEEeCCCCChHHH-HHHhhhhhhhc-----ccccccceecch-hhhhHHHHHHHhhcccccceeec
Confidence            34467777999999998 56666666654     334578999995 78899999999996555544433

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=97.16  E-value=0.00024  Score=55.85  Aligned_cols=55  Identities=5%  Similarity=-0.140  Sum_probs=39.6

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ..+++.|++|||||.+.+- -+..+..+..   .+..++|++++|+.++..+.+.+.++
T Consensus        15 ~~~lI~g~aGTGKTt~l~~-rv~~ll~~~~---~~~~~ILvlt~tn~a~~~i~~~~~~~   69 (306)
T d1uaaa1          15 GPCLVLAGAGSGKTRVITN-KIAHLIRGCG---YQARHIAAVTFTNKAAREMKERVGQT   69 (306)
T ss_dssp             SEEEECCCTTSCHHHHHHH-HHHHHHHHHC---CCGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred             CCEEEEeeCCccHHHHHHH-HHHHHHHhcC---CChhHEEEEeCcHHHHHHHHHHHHHh
Confidence            3478999999999987433 3333333211   12347999999999999999988876

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=97.01  E-value=0.00062  Score=53.90  Aligned_cols=55  Identities=7%  Similarity=-0.112  Sum_probs=39.9

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ..+++.|+.|||||.+.+--+. .++....   -..-++|++++|+..+..+.+.+...
T Consensus        25 g~~lV~g~aGSGKTt~l~~ri~-~ll~~~~---~~p~~il~lt~t~~aa~~~~~~~~~~   79 (318)
T d1pjra1          25 GPLLIMAGAGSGKTRVLTHRIA-YLMAEKH---VAPWNILAITFTNKAAREMRERVQSL   79 (318)
T ss_dssp             SCEEEEECTTSCHHHHHHHHHH-HHHHTTC---CCGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred             CCEEEEecCCccHHHHHHHHHH-HHHHcCC---CCHHHeEeEeccHHHHHHHHHHHHhh
Confidence            3588999999999988443333 3333211   12247999999999999999999876

>d1t5la1 c.37.1.19 (A:2-414) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=96.72  E-value=0.0019  Score=53.37  Aligned_cols=59  Identities=15%  Similarity=0.015  Sum_probs=44.4

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEc
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFG   78 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~g   78 (233)
                      ++..+.+.||||||++ +..++...          +..+|||+|+..+|.|+++.++.|+++-.+..+..
T Consensus        32 ~~q~l~GltGS~ka~~-iA~l~~~~----------~rp~LVVt~n~~~A~qL~~dL~~~l~~~~v~~f~~   90 (413)
T d1t5la1          32 KHQTLLGATGTGKTFT-ISNVIAQV----------NKPTLVIAHNKTLAGQLYSELKEFFPHNAVEYFVS   90 (413)
T ss_dssp             SEEEEEECTTSCHHHH-HHHHHHHH----------TCCEEEECSSHHHHHHHHHHHHHHCTTSEEEEECC
T ss_pred             CcEEEeCCCCcHHHHH-HHHHHHHh----------CCCEEEEeCCHHHHHHHHHHHHHHcCCCceeeccc
Confidence            5678889999999977 33444443          22389999999999999999999966555554443

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=95.71  E-value=0.0067  Score=49.04  Aligned_cols=58  Identities=9%  Similarity=-0.056  Sum_probs=42.1

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      +.++-+++++++|||||.+ +.-++..+....   ..++.++++.+||..-+..+.+.....
T Consensus       161 l~~~~~vI~G~pGTGKTt~-i~~~l~~l~~~~---~~~~~~I~l~ApTgkAA~~L~e~~~~~  218 (359)
T d1w36d1         161 LTRRISVISGGPGTGKTTT-VAKLLAALIQMA---DGERCRIRLAAPTGKAAARLTESLGKA  218 (359)
T ss_dssp             HTBSEEEEECCTTSTHHHH-HHHHHHHHHHTC---SSCCCCEEEEBSSHHHHHHHHHHHTHH
T ss_pred             HcCCeEEEEcCCCCCceeh-HHHHHHHHHHHH---hccCCeEEEecCcHHHHHHHHHHHHHH
Confidence            4567789999999999977 444444444321   135678999999999998888777654

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=95.26  E-value=0.004  Score=49.64  Aligned_cols=115  Identities=10%  Similarity=-0.045  Sum_probs=61.9

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCCCCCee
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPKGPQD   86 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~~~~~   86 (233)
                      .++++++.++||||||.. +-.++..+        ....+.+.+--+.||...         ..-.+..+.++.+..   
T Consensus       165 ~~~nili~G~tgSGKTT~-l~al~~~i--------~~~~rivtiEd~~El~l~---------~~~~~~~~~~~~~~~---  223 (323)
T d1g6oa_         165 IGKNVIVCGGTGSGKTTY-IKSIMEFI--------PKEERIISIEDTEEIVFK---------HHKNYTQLFFGGNIT---  223 (323)
T ss_dssp             HTCCEEEEESTTSSHHHH-HHHHGGGS--------CTTCCEEEEESSCCCCCS---------SCSSEEEEECBTTBC---
T ss_pred             hCCCEEEEeeccccchHH-HHHHhhhc--------ccccceeeccchhhhhcc---------cccccceeccccchh---
Confidence            467899999999999955 55555544        234568888888887321         122233333322211   


Q ss_pred             EEeccchhhhchHHHhcCCCCeEEEEecchhHHHHHHHHHh--hCCC--eeEEEeCCCCHHHHHHHHHHh
Q psy14082         87 CLPLHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALR--RERH--SAICIHGDKTQQDRDYVLNDF  152 (233)
Q Consensus        87 lv~l~r~~~~~~~~~~~~~~~k~iIf~~~~~~~~~l~~~L~--~~~~--~~~~~~~~~~~~~r~~~~~~f  152 (233)
                            +-+++...+.  .....|++-+-+.. +. ...++  ..|.  ....+|++-+...-......+
T Consensus       224 ------~~~ll~~~lR--~~pd~iivgEiR~~-ea-~~~l~a~~tGh~g~~tT~Ha~s~~~a~~Rl~~l~  283 (323)
T d1g6oa_         224 ------SADCLKSCLR--MRPDRIILGELRSS-EA-YDFYNVLCSGHKGTLTTLHAGSSEEAFIRLANMS  283 (323)
T ss_dssp             ------HHHHHHHHTT--SCCSEEEESCCCST-HH-HHHHHHHHTTCSCEEEEECCSSHHHHHHHHHHHH
T ss_pred             ------HHHHHHHHhc--cCCCcccCCccCch-hH-HHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHhc
Confidence                  2233332222  34455666665533 22 22332  3343  467899986665555544443

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=95.02  E-value=0.35  Score=35.44  Aligned_cols=33  Identities=9%  Similarity=-0.097  Sum_probs=26.4

Q ss_pred             eeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc
Q psy14082        132 SAICIHGDKTQQDRDYVLNDFRQGKAPILVATD  164 (233)
Q Consensus       132 ~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~  164 (233)
                      ...++.+.+.+++-.++...|+.-.++-+|-|.
T Consensus       131 ~~LVl~a~~~~~~~~~~~~~~~~~~~~~lIlTK  163 (211)
T d2qy9a2         131 VMLTIDASTGQNAVSQAKLFHEAVGLTGITLTK  163 (211)
T ss_dssp             EEEEEEGGGTHHHHHHHHHHHHHSCCCEEEEEC
T ss_pred             eeeehhcccCcchHHHHhhhhhccCCceEEEee
Confidence            456677888899999999999877788777774

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

Probab=94.98  E-value=0.009  Score=49.03  Aligned_cols=49  Identities=8%  Similarity=0.030  Sum_probs=35.9

Q ss_pred             CCCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHH
Q psy14082          2 LPPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQ   58 (233)
Q Consensus         2 ip~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~   58 (233)
                      +|.-...+|+++.++||||||.+ +..++..+...       +..++|+=|.-|+..
T Consensus        44 ~~~~~~~~H~~I~G~tGsGKT~~-l~~li~~~~~~-------g~~~iiiD~kge~~~   92 (433)
T d1e9ra_          44 MPRDAEPRHLLVNGATGTGKSVL-LRELAYTGLLR-------GDRMVIVDPNGDMLS   92 (433)
T ss_dssp             CCGGGGGGCEEEEECTTSSHHHH-HHHHHHHHHHT-------TCEEEEEEETTHHHH
T ss_pred             cCCCcccceEEEEeCCCCcHHHH-HHHHHHHHHhC-------CCCEEEEeCChhHHH
Confidence            45556678999999999999976 45555555532       557888889887643

>d1tf5a3 c.37.1.19 (A:1-226,A:349-395) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=94.45  E-value=0.057  Score=41.33  Aligned_cols=63  Identities=13%  Similarity=-0.000  Sum_probs=50.3

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh--hcCCcEEEEEcCCC
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGGTP   81 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~--~~~~~~~~~~gg~~   81 (233)
                      -|+++.||=|||++..+|+.-.-+.        |..+=|+...--||.-=.+++..+  +.++++.+...+.+
T Consensus        96 ~iaem~TGEGKTL~a~l~a~l~al~--------g~~vhvvTvNdyLA~RDae~m~~iy~~lGlsvg~~~~~~~  160 (273)
T d1tf5a3          96 NIAEMKTGEGKTLTSTLPVYLNALT--------GKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVGLNLNSMS  160 (273)
T ss_dssp             SEEECCTTSCHHHHHHHHHHHHHTT--------SSCEEEEESSHHHHHHHHHHHHHHHHHTTCCEEECCTTSC
T ss_pred             hheeecCCCcchhHHHHHHHHHHhc--------CCCceEEecCccccchhhhHHhHHHHHcCCCccccccccC
Confidence            4889999999999999988876653        445777888888999888888887  56889888876544

>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=94.13  E-value=0.12  Score=37.73  Aligned_cols=73  Identities=18%  Similarity=0.200  Sum_probs=56.2

Q ss_pred             hcCCCCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----cC-cCCcC
Q psy14082        102 AKNPAFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----VA-ARGLD  171 (233)
Q Consensus       102 ~~~~~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----~~-~~Gld  171 (233)
                      ....+.+++|.++|++.+.++.+.+.+.    +..+...+|+.+..++.+.++     ..+|+|+|+     .+ ...++
T Consensus        68 ~~~~~~~~lil~pt~~l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~-----~~~IlV~TP~~l~~~l~~~~~~  142 (208)
T d1hv8a1          68 NENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-----NANIVVGTPGRILDHINRGTLN  142 (208)
T ss_dssp             CSSSSCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHH-----TCSEEEECHHHHHHHHHTTCSC
T ss_pred             ccccCcceEEEeeccccchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhcC-----CCCEEEEChHHHHHHHHcCCCC
Confidence            3456779999999999999988887653    578888999988877665553     368999994     23 34578


Q ss_pred             CCCccEEE
Q psy14082        172 VEDVNTVN  179 (233)
Q Consensus       172 i~~v~~VI  179 (233)
                      +.++.++|
T Consensus       143 ~~~l~~lV  150 (208)
T d1hv8a1         143 LKNVKYFI  150 (208)
T ss_dssp             TTSCCEEE
T ss_pred             cccCcEEE
Confidence            88888877

>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=94.09  E-value=0.096  Score=38.92  Aligned_cols=73  Identities=11%  Similarity=0.140  Sum_probs=56.0

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc------cCcCCcCC
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD------VAARGLDV  172 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~------~~~~Gldi  172 (233)
                      .....+++|+++|++.+.++.+.+.+.    ++++..++|+.+..+....++.    ..+|+|+|+      .-...+++
T Consensus        82 ~~~~~~~lil~PtreLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l~~----~~~Ilv~TPgrl~~~~~~~~~~~  157 (222)
T d2j0sa1          82 QVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY----GQHVVAGTPGRVFDMIRRRSLRT  157 (222)
T ss_dssp             TSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHH----CCSEEEECHHHHHHHHHTTSSCC
T ss_pred             cccCceeEEecchHHHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHhcc----CCeEEeCCCCcHHhccccccccc
Confidence            345678999999999999999888653    5788899999988777666553    468999994      22445777


Q ss_pred             CCccEEE
Q psy14082        173 EDVNTVN  179 (233)
Q Consensus       173 ~~v~~VI  179 (233)
                      .++.++|
T Consensus       158 ~~l~~lV  164 (222)
T d2j0sa1         158 RAIKMLV  164 (222)
T ss_dssp             TTCCEEE
T ss_pred             ccceeee
Confidence            8888876

>d1c4oa1 c.37.1.19 (A:2-409) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=93.94  E-value=0.063  Score=43.85  Aligned_cols=56  Identities=21%  Similarity=0.057  Sum_probs=41.0

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEE
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICI   76 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~   76 (233)
                      ...+.+.+||+|+++ +..++...          +..+|||+|+.+.|.|+++.++.+.++-.+..+
T Consensus        30 ~~~L~GlsgS~ka~~-~A~l~~~~----------~rp~LvVt~~~~~A~~l~~dL~~~l~~~~v~~f   85 (408)
T d1c4oa1          30 FVTLLGATGTGKTVT-MAKVIEAL----------GRPALVLAPNKILAAQLAAEFRELFPENAVEYF   85 (408)
T ss_dssp             EEEEEECTTSCHHHH-HHHHHHHH----------TCCEEEEESSHHHHHHHHHHHHHHCTTSEEEEC
T ss_pred             cEEEecCCCCHHHHH-HHHHHHHh----------CCCEEEEeCCHHHHHHHHHHHHHhcCccceeeC
Confidence            467889999999976 33344433          223799999999999999999999554444433

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.58  E-value=0.036  Score=38.98  Aligned_cols=26  Identities=8%  Similarity=-0.114  Sum_probs=20.6

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhhhc
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHISH   35 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l~~   35 (233)
                      +++++.+++|+|||.. +--++..+..
T Consensus         2 k~v~ItG~~GtGKTtl-~~~i~~~l~~   27 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTL-IHKASEVLKS   27 (189)
T ss_dssp             CCEEEESCCSSCHHHH-HHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHH-HHHHHHHHHH
Confidence            6799999999999964 6666666654

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=93.15  E-value=1.1  Score=32.62  Aligned_cols=139  Identities=13%  Similarity=0.014  Sum_probs=70.3

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEc--CcHHHHHHHHHHHHHhhcCCcEEEEEcCCCCC
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLA--PTRELAQQIQTVAKEFSSALRNICIFGGTPKG   83 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~--PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~~   83 (233)
                      ..++=++..+|||+|||.+.+- +..++..       .+.++.+++  ..|.=+.+..+.+.+.   +.+-+.......+
T Consensus         4 ~~~~vi~lvGptGvGKTTTiaK-LA~~~~~-------~g~kV~lit~Dt~R~gA~eQL~~~a~~---l~i~~~~~~~~~d   72 (207)
T d1okkd2           4 PKGRVVLVVGVNGVGKTTTIAK-LGRYYQN-------LGKKVMFCAGDTFRAAGGTQLSEWGKR---LSIPVIQGPEGTD   72 (207)
T ss_dssp             CSSSEEEEECSTTSSHHHHHHH-HHHHHHT-------TTCCEEEECCCCSSTTHHHHHHHHHHH---HTCCEECCCTTCC
T ss_pred             CCCEEEEEECCCCCCHHHHHHH-HHHHHHH-------CCCcEEEEEeccccccchhhHhhcccc---cCceEEeccCCcc
Confidence            4455567799999999988443 3333332       234555555  2355554433333333   2333333333332


Q ss_pred             CeeEEeccchhhhchHHH-hcCCCCeEEEEecchh-------HHHHHHHHHhh-------C-CCeeEEEeCCCCHHHHHH
Q psy14082         84 PQDCLPLHRFVFNCQYEM-AKNPAFKVIVFVETKK-------KVEDITRALRR-------E-RHSAICIHGDKTQQDRDY  147 (233)
Q Consensus        84 ~~~lv~l~r~~~~~~~~~-~~~~~~k~iIf~~~~~-------~~~~l~~~L~~-------~-~~~~~~~~~~~~~~~r~~  147 (233)
                      +.         ..+.+.. .......-+||+.|..       ..+++.+....       . .....++.+.+.+++-.+
T Consensus        73 ~~---------~~~~~~~~~~~~~~~d~ilIDTaGr~~~d~~l~~el~~~~~~~~~~~~~~p~~~~LVl~a~~~~~~~~~  143 (207)
T d1okkd2          73 PA---------ALAYDAVQAMKARGYDLLFVDTAGRLHTKHNLMEELKKVKRAIAKADPEEPKEVWLVLDAVTGQNGLEQ  143 (207)
T ss_dssp             HH---------HHHHHHHHHHHHHTCSEEEECCCCCCTTCHHHHHHHHHHHHHHHHHCTTCCSEEEEEEETTBCTHHHHH
T ss_pred             HH---------HHHHHHHHHHHHCCCCEEEcCccccchhhHHHHHHHHHHHHHhhhcccCCCceEEEEeecccCchHHHH
Confidence            21         1111100 0001112345554432       23333333221       1 224567788888889899


Q ss_pred             HHHHhhCCCCCEEEecc
Q psy14082        148 VLNDFRQGKAPILVATD  164 (233)
Q Consensus       148 ~~~~f~~g~~~iLv~T~  164 (233)
                      +.+.|..-..+-+|-|.
T Consensus       144 ~~~~~~~~~~~~lI~TK  160 (207)
T d1okkd2         144 AKKFHEAVGLTGVIVTK  160 (207)
T ss_dssp             HHHHHHHHCCSEEEEEC
T ss_pred             HHHhhhccCCceEEEec
Confidence            99988877777777774

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=92.33  E-value=0.025  Score=46.86  Aligned_cols=19  Identities=0%  Similarity=-0.366  Sum_probs=16.7

Q ss_pred             CCCCceeEecCCCCCchHH
Q psy14082          6 ESGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~   24 (233)
                      +..++++..+|||+|||+.
T Consensus        47 i~ksNILliGPTGvGKTlL   65 (443)
T d1g41a_          47 VTPKNILMIGPTGVGKTEI   65 (443)
T ss_dssp             CCCCCEEEECCTTSSHHHH
T ss_pred             cccccEEEECCCCCCHHHH
Confidence            4467999999999999977

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=92.20  E-value=0.071  Score=39.29  Aligned_cols=54  Identities=17%  Similarity=0.040  Sum_probs=29.2

Q ss_pred             CCCCCCCCce-eEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcC--cHHHHHHHHHHH
Q psy14082          2 LPPSESGCQN-FSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAP--TRELAQQIQTVA   64 (233)
Q Consensus         2 ip~~~~g~d~-i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~P--treL~~Q~~~~~   64 (233)
                      +|..- .+.+ +..+|||+|||.+.+- +..++..       ++.++.+++.  .|.-+.+..+.+
T Consensus         4 lp~~~-~~~vi~lvGp~GvGKTTTiaK-LA~~~~~-------~g~kV~lit~Dt~R~gA~eQL~~~   60 (207)
T d1ls1a2           4 LPVLK-DRNLWFLVGLQGSGKTTTAAK-LALYYKG-------KGRRPLLVAADTQRPAAREQLRLL   60 (207)
T ss_dssp             CCCCC-SSEEEEEECCTTTTHHHHHHH-HHHHHHH-------TTCCEEEEECCSSCHHHHHHHHHH
T ss_pred             CCCCC-CCcEEEEECCCCCCHHHHHHH-HHHHHHH-------CCCcEEEEecccccchHHHHHHHH
Confidence            45444 4454 5589999999977443 3333432       2345565553  455554433333

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=91.99  E-value=0.3  Score=36.72  Aligned_cols=50  Identities=16%  Similarity=0.202  Sum_probs=31.2

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCC-CeeEEEeCCCCHHHHHHHHHHhhCC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRER-HSAICIHGDKTQQDRDYVLNDFRQG  155 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~-~~~~~~~~~~~~~~r~~~~~~f~~g  155 (233)
                      ...+++|++.|. ..+.+-..|.+.+ +...+.-+..+.++|.++++.+...
T Consensus       144 ~~~~vivi~tTn-~~~~ld~al~R~~Rf~~~i~~~~P~~~eR~~il~~~l~~  194 (247)
T d1ixza_         144 KDTAIVVMAATN-RPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARG  194 (247)
T ss_dssp             TTCCEEEEEEES-CGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTT
T ss_pred             CCCCEEEEEeCC-CccccCHhHcCCCCCcEEEEECCcCHHHHHHHHHHHhcc
Confidence            334566665443 3445555554322 5555566778899999999988754

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=91.50  E-value=0.066  Score=43.59  Aligned_cols=24  Identities=0%  Similarity=-0.146  Sum_probs=19.6

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhhc
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHISH   35 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~~   35 (233)
                      +++.+|||||||.+ +-.+++.+..
T Consensus       161 iLvtGpTGSGKSTT-l~~~l~~~~~  184 (401)
T d1p9ra_         161 ILVTGPTGSGKSTT-LYAGLQELNS  184 (401)
T ss_dssp             EEEECSTTSCHHHH-HHHHHHHHCC
T ss_pred             EEEEcCCCCCccHH-HHHHhhhhcC
Confidence            78899999999977 6667777753

>d2jdia3 c.37.1.11 (A:95-379) Central domain of alpha subunit of F1 ATP synthase {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Cow (Bos taurus) [TaxId: 9913]

Probab=91.21  E-value=1.1  Score=34.27  Aligned_cols=21  Identities=10%  Similarity=-0.051  Sum_probs=17.9

Q ss_pred             CCCCCCceeEecCCCCCchHH
Q psy14082          4 PSESGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         4 ~~~~g~d~i~~a~tGsGKT~~   24 (233)
                      ++-.|+-..+.++.|+|||..
T Consensus        64 pig~GQr~~If~~~g~GKt~l   84 (285)
T d2jdia3          64 PIGRGQRELIIGDRQTGKTSI   84 (285)
T ss_dssp             CCBTTCBCEEEESTTSSHHHH
T ss_pred             CccCCCEEEeecCCCCChHHH
Confidence            466788889999999999965

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=90.67  E-value=0.2  Score=37.31  Aligned_cols=26  Identities=0%  Similarity=-0.488  Sum_probs=19.6

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      ...+++.+|+|+|||.+ +-.+...+.
T Consensus        43 ~~~lll~GppGtGKT~l-~~~l~~~l~   68 (276)
T d1fnna2          43 YPRATLLGRPGTGKTVT-LRKLWELYK   68 (276)
T ss_dssp             CCEEEEECCTTSSHHHH-HHHHHHHHT
T ss_pred             CCceEEECCCCCCHHHH-HHHHHHHHh
Confidence            36799999999999976 444555553

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=90.60  E-value=0.051  Score=38.02  Aligned_cols=19  Identities=11%  Similarity=-0.167  Sum_probs=16.8

Q ss_pred             CCCCceeEecCCCCCchHH
Q psy14082          6 ESGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~   24 (233)
                      +.+.++++.+++|||||..
T Consensus         3 pk~~~I~i~G~~GsGKTT~   21 (174)
T d1y63a_           3 PKGINILITGTPGTGKTSM   21 (174)
T ss_dssp             CSSCEEEEECSTTSSHHHH
T ss_pred             CCCCEEEEEeCCCCCHHHH
Confidence            5678899999999999966

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=90.56  E-value=0.1  Score=36.08  Aligned_cols=34  Identities=3%  Similarity=-0.227  Sum_probs=22.5

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcC
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAP   52 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~P   52 (233)
                      +++.++.||||| +++--++..+..       +|.++.++.+
T Consensus         5 i~itG~~GSGKT-TL~~~L~~~l~~-------~g~~v~v~~~   38 (170)
T d1np6a_           5 LAFAAWSGTGKT-TLLKKLIPALCA-------RGIRPGLIKH   38 (170)
T ss_dssp             EEEECCTTSCHH-HHHHHHHHHHHH-------TTCCEEEEEE
T ss_pred             EEEEcCCCCCHH-HHHHHHHHHHHH-------CCCeEEEecc
Confidence            567899999999 446666666653       2555555543

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=90.50  E-value=0.48  Score=35.73  Aligned_cols=50  Identities=18%  Similarity=0.192  Sum_probs=31.5

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhCC-CeeEEEeCCCCHHHHHHHHHHhhCC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRER-HSAICIHGDKTQQDRDYVLNDFRQG  155 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~~-~~~~~~~~~~~~~~r~~~~~~f~~g  155 (233)
                      ...++++++.|. ..+.+-..|.+.| +.-.+.-+-.+.++|.++++.+..+
T Consensus       147 ~~~~v~vIatTn-~~~~ld~al~R~gRfd~~i~i~~P~~~~R~~il~~~l~~  197 (256)
T d1lv7a_         147 GNEGIIVIAATN-RPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRR  197 (256)
T ss_dssp             SSSCEEEEEEES-CTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTT
T ss_pred             CCCCEEEEEeCC-CcccCCHhHcCCCCCCEEEECCCcCHHHHHHHHHHhccC
Confidence            344566665543 4455555555432 5555666778899999999988644

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.39  E-value=0.72  Score=34.59  Aligned_cols=51  Identities=24%  Similarity=0.180  Sum_probs=31.6

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCC-CeeEEEeCCCCHHHHHHHHHHhhCC
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRER-HSAICIHGDKTQQDRDYVLNDFRQG  155 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~-~~~~~~~~~~~~~~r~~~~~~f~~g  155 (233)
                      ....+++|++.| .+.+.+-..+...| +.-.+.-+-.+.++|..+++.+..+
T Consensus       136 ~~~~~vlvi~tT-n~~~~ld~al~r~gRfd~~i~~~~P~~~~R~~il~~~l~~  187 (258)
T d1e32a2         136 KQRAHVIVMAAT-NRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKN  187 (258)
T ss_dssp             CCSSCEEEEEEE-SCGGGSCGGGTSTTSSCEEEECCCCCHHHHHHHHHHTTTT
T ss_pred             cccCCccEEEeC-CCccccchhhhhcccccceeECCCCCHHHHHHHhhhhccC
Confidence            344455555544 34445555555433 5566666778888999999887643

>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=89.81  E-value=0.74  Score=33.24  Aligned_cols=74  Identities=18%  Similarity=0.267  Sum_probs=53.3

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhCC-----CeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----cCc-CCcC
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRER-----HSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----VAA-RGLD  171 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~~-----~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----~~~-~Gld  171 (233)
                      ...+.+++|.+++++.+..+.+.++..+     ..+..++|+.+.......+.   ....+|+|+|+     .+. ..++
T Consensus        66 ~~~~~~~lil~PtreL~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~---~~~~~ilI~TP~rl~~~~~~~~~~  142 (207)
T d1t6na_          66 VTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLK---KNCPHIVVGTPGRILALARNKSLN  142 (207)
T ss_dssp             CTTCCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHH---HSCCSEEEECHHHHHHHHHTTSSC
T ss_pred             cCCCceEEEEeccchhhHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHHHH---hcCCCEEEeCcchhhhhccCCcee
Confidence            3455689999999999999988886542     45677888888766554433   35689999995     222 3467


Q ss_pred             CCCccEEE
Q psy14082        172 VEDVNTVN  179 (233)
Q Consensus       172 i~~v~~VI  179 (233)
                      +.++.++|
T Consensus       143 l~~l~~lV  150 (207)
T d1t6na_         143 LKHIKHFI  150 (207)
T ss_dssp             CTTCCEEE
T ss_pred             ccccceee
Confidence            77888776

>d1w36b1 c.37.1.19 (B:1-485) Exodeoxyribonuclease V beta chain (RecB), N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V beta chain (RecB), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=89.60  E-value=0.47  Score=38.36  Aligned_cols=59  Identities=5%  Similarity=-0.166  Sum_probs=36.8

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhccCCCC----CCCCceEEEEcCcHHHHHHHHHHHHH
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQEPVK----QGDGPIALVLAPTRELAQQIQTVAKE   66 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~----~~~~~~~lil~PtreL~~Q~~~~~~~   66 (233)
                      .-.+++.|.-|||||.+-+-=++..+.......    .-..-.+|+|+=|+.-|..+.+++..
T Consensus        16 ~g~~lv~A~AGsGKT~~l~~r~~~ll~~~~~~~~~~~~~~~~~IL~lTFT~kAA~Emk~RI~~   78 (485)
T d1w36b1          16 QGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRS   78 (485)
T ss_dssp             SSCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHH
T ss_pred             CCCeEEEEcCchHHHHHHHHHHHHHHhhCcccccccCCCCcccEeEeccHHHHHHHHHHHHHH
Confidence            344888999999999885444444444321110    01123589999998777776666544

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=89.57  E-value=0.11  Score=36.12  Aligned_cols=31  Identities=13%  Similarity=0.003  Sum_probs=23.1

Q ss_pred             CCCCCCCceeEecCCCCCchHHhHHHHHHhhh
Q psy14082          3 PPSESGCQNFSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus         3 p~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      |....|.=++..+.+|||||.. +-.+..+|.
T Consensus         1 ~~~~~g~~I~l~G~~GsGKTTi-a~~La~~L~   31 (183)
T d1m8pa3           1 PRATQGFTIFLTGYMNSGKDAI-ARALQVTLN   31 (183)
T ss_dssp             CTTTCCEEEEEECSTTSSHHHH-HHHHHHHHH
T ss_pred             CCCCCCeEEEEECCCCCCHHHH-HHHHHHHHh
Confidence            5566788899999999999966 444555553

>d2jdid3 c.37.1.11 (D:82-357) Central domain of beta subunit of F1 ATP synthase {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of beta subunit of F1 ATP synthase
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=89.11  E-value=2.9  Score=31.64  Aligned_cols=29  Identities=7%  Similarity=-0.138  Sum_probs=21.5

Q ss_pred             CCCCCCceeEecCCCCCchHHhHHHHHHhh
Q psy14082          4 PSESGCQNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus         4 ~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      ++-.|+-..+.++.|+|||.. +.-++...
T Consensus        64 pigkGQr~~If~~~g~GKt~l-~~~i~~~~   92 (276)
T d2jdid3          64 PYAKGGKIGLFGGAGVGKTVL-IMELINNV   92 (276)
T ss_dssp             CEETTCEEEEEECTTSSHHHH-HHHHHHHH
T ss_pred             cccCCCEEEeeCCCCCCHHHH-HHHHHHHH
Confidence            456788899999999999955 45455443

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=89.10  E-value=0.064  Score=37.48  Aligned_cols=19  Identities=5%  Similarity=-0.347  Sum_probs=16.5

Q ss_pred             CCCCceeEecCCCCCchHH
Q psy14082          6 ESGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~   24 (233)
                      +.|+=+++.+++|||||..
T Consensus         2 ~~g~iI~l~G~~GsGKSTi   20 (176)
T d1zp6a1           2 LGGNILLLSGHPGSGKSTI   20 (176)
T ss_dssp             CTTEEEEEEECTTSCHHHH
T ss_pred             CCCeEEEEECCCCCCHHHH
Confidence            4678889999999999975

>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=88.91  E-value=2.5  Score=29.16  Aligned_cols=37  Identities=14%  Similarity=0.195  Sum_probs=31.7

Q ss_pred             CceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCCC
Q psy14082         44 GPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPK   82 (233)
Q Consensus        44 ~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~   82 (233)
                      +.++||.|++++-++.+++.+.+.  +..+..++|+.+.
T Consensus        27 ~~k~iIF~~~~~~~~~l~~~L~~~--~~~~~~ihg~~~~   63 (168)
T d1t5ia_          27 FNQVVIFVKSVQRCIALAQLLVEQ--NFPAIAIHRGMPQ   63 (168)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHHT--TCCEEEECTTSCH
T ss_pred             CCeEEEEEeeeecchhhhhhhccc--cccccccccccch
Confidence            457999999999999999988876  7788999998665

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=88.79  E-value=0.17  Score=37.42  Aligned_cols=45  Identities=9%  Similarity=-0.167  Sum_probs=26.5

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEc
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLA   51 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~   51 (233)
                      ++.|+=+++.+++|||||.- ++=++.....+.. ....+..++++.
T Consensus        33 lp~G~~~li~G~pGsGKT~~-~lq~~~~~~~~~~-~~~~~~~~~~~~   77 (254)
T d1pzna2          33 IETQAITEVFGEFGSGKTQL-AHTLAVMVQLPPE-EGGLNGSVIWID   77 (254)
T ss_dssp             EESSEEEEEEESTTSSHHHH-HHHHHHHTTSCGG-GTSCSCEEEEEE
T ss_pred             ccCCEEEEEEcCCCCCHHHH-HHHHHHHhhchHH-hcCCCceEEEEe
Confidence            45788899999999999955 4444433332110 112244566664

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=88.57  E-value=0.13  Score=35.08  Aligned_cols=25  Identities=8%  Similarity=-0.288  Sum_probs=18.0

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      .+.+++.+++|||||.. +--+..++
T Consensus         2 ~k~I~l~G~~GsGKSTv-ak~La~~L   26 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTI-GRQLAQQL   26 (169)
T ss_dssp             CCCEEEECCTTSCHHHH-HHHHHHHT
T ss_pred             CCeEEEECCCCCCHHHH-HHHHHHHh
Confidence            36789999999999966 33344444

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=88.53  E-value=0.35  Score=35.38  Aligned_cols=46  Identities=11%  Similarity=-0.030  Sum_probs=30.1

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHH
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVA   64 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~   64 (233)
                      -+++.+++|+|||.. +.++.+.+...       +..++++ +..++..+..+.+
T Consensus        38 ~l~l~G~~G~GKTHL-l~A~~~~~~~~-------~~~~~~~-~~~~~~~~~~~~~   83 (213)
T d1l8qa2          38 PIFIYGSVGTGKTHL-LQAAGNEAKKR-------GYRVIYS-SADDFAQAMVEHL   83 (213)
T ss_dssp             SEEEECSSSSSHHHH-HHHHHHHHHHT-------TCCEEEE-EHHHHHHHHHHHH
T ss_pred             cEEEECCCCCcHHHH-HHHHHHHhccC-------ccceEEe-chHHHHHHHHHHH
Confidence            389999999999976 55566665532       4455544 5556666655544

>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=88.31  E-value=0.35  Score=32.35  Aligned_cols=41  Identities=7%  Similarity=0.066  Sum_probs=35.9

Q ss_pred             HhcCCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCC
Q psy14082        101 MAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKT  141 (233)
Q Consensus       101 ~~~~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~  141 (233)
                      +...+..++++||.+-..+...+..|+++|+++..+.|++.
T Consensus        75 ~~~~~~~~ivl~C~~G~rS~~aa~~L~~~G~~v~~l~GG~~  115 (130)
T d1yt8a4          75 VASVRGARLVLVDDDGVRANMSASWLAQMGWQVAVLDGLSE  115 (130)
T ss_dssp             HCCSBTCEEEEECSSSSHHHHHHHHHHHTTCEEEEECSCCG
T ss_pred             ccCCccceEEeecCCCccHHHHHHHHHHcCCCeEEEcCchH
Confidence            34467789999999999999999999999999999999865

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=88.20  E-value=0.14  Score=37.94  Aligned_cols=24  Identities=8%  Similarity=-0.234  Sum_probs=17.8

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhh
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      .+++..+|+|+|||.+ +-.+...+
T Consensus        36 ~~~L~~GPpGtGKT~l-A~~la~~~   59 (238)
T d1in4a2          36 DHVLLAGPPGLGKTTL-AHIIASEL   59 (238)
T ss_dssp             CCEEEESSTTSSHHHH-HHHHHHHH
T ss_pred             CeEEEECCCCCcHHHH-HHHHHhcc
Confidence            3689999999999976 44455444

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=87.95  E-value=0.21  Score=36.79  Aligned_cols=54  Identities=9%  Similarity=-0.107  Sum_probs=34.6

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      ++.|.=+++.+++|+|||.. ++-++.....       .+..+++++-. +-..++.+.+..+
T Consensus        23 i~~gsl~li~G~pGsGKT~l-~~qia~~~~~-------~~~~~~~is~e-~~~~~~~~~~~~~   76 (242)
T d1tf7a2          23 FFKDSIILATGATGTGKTLL-VSRFVENACA-------NKERAILFAYE-ESRAQLLRNAYSW   76 (242)
T ss_dssp             EESSCEEEEEECTTSSHHHH-HHHHHHHHHT-------TTCCEEEEESS-SCHHHHHHHHHTT
T ss_pred             CcCCeEEEEEeCCCCCHHHH-HHHHHHHHHH-------hccccceeecc-CCHHHHHHHHHHc
Confidence            35677899999999999965 5545554443       35567777642 3345555555554

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=87.38  E-value=0.23  Score=36.52  Aligned_cols=32  Identities=16%  Similarity=0.128  Sum_probs=21.4

Q ss_pred             eeEEEeCCCCHHHHHHHHHHhhCCCCCEEEec
Q psy14082        132 SAICIHGDKTQQDRDYVLNDFRQGKAPILVAT  163 (233)
Q Consensus       132 ~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T  163 (233)
                      ...++.+.+.++....+...|+...++-+|-|
T Consensus       130 ~~LVl~a~~~~~~~~~~~~~~~~~~~~~lI~T  161 (211)
T d1j8yf2         130 VTLVIDASIGQKAYDLASKFNQASKIGTIIIT  161 (211)
T ss_dssp             EEEEEEGGGGGGHHHHHHHHHHHCTTEEEEEE
T ss_pred             EEEEEecccCcchHHHHhhhhcccCcceEEEe
Confidence            34555666666777777777777666766666

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=87.25  E-value=0.11  Score=40.58  Aligned_cols=25  Identities=4%  Similarity=-0.366  Sum_probs=18.5

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      +..++..+|||+|||.. +-.+...+
T Consensus        49 ~~~iLl~GPpG~GKT~l-AkalA~~~   73 (309)
T d1ofha_          49 PKNILMIGPTGVGKTEI-ARRLAKLA   73 (309)
T ss_dssp             CCCEEEECCTTSSHHHH-HHHHHHHH
T ss_pred             CceEEEECCCCCCHHHH-HHHHhhcc
Confidence            46788999999999977 34444443

>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=87.21  E-value=0.41  Score=31.50  Aligned_cols=65  Identities=17%  Similarity=0.056  Sum_probs=49.6

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEE
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNI  180 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~  180 (233)
                      ....++|+.|++....+.+.+.|.+.++.+..+.+. +         .|.++.  +-++...+..|+-+|+..++|.
T Consensus        32 ~~~~~Vli~a~s~g~~erl~e~L~~~~i~~~~~~~~-~---------~~~~~~--~~i~~~~l~~GF~~~~~~l~vI   96 (117)
T d2eyqa2          32 TFDGPVVFSVESEGRREALGELLARIKIAPQRIMRL-D---------EASDRG--RYLMIGAAEHGFVDTVRNLALI   96 (117)
T ss_dssp             TCCSCCCEEESSHHHHHHHHHHHGGGTCCCEECSSG-G---------GCCTTC--CEEEECCCCSCEEETTTTEEEE
T ss_pred             hCCCeEEEEECCccHHHHHHHHHHHcCCCceEecCh-h---------hhcCce--EEEEEecCccccccCCCCEEEE
Confidence            345689999999999999999999999987665442 2         233343  5566677899998898888774

>d1fx0a3 c.37.1.11 (A:97-372) Central domain of alpha subunit of F1 ATP synthase {Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]

Probab=87.06  E-value=3.5  Score=31.12  Aligned_cols=21  Identities=10%  Similarity=-0.034  Sum_probs=17.8

Q ss_pred             CCCCCCceeEecCCCCCchHH
Q psy14082          4 PSESGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         4 ~~~~g~d~i~~a~tGsGKT~~   24 (233)
                      ++-.|+...+.++.|+|||..
T Consensus        63 pig~GQr~~Ifg~~g~GKt~l   83 (276)
T d1fx0a3          63 PVGRGQRELIIGDRQTGKTAV   83 (276)
T ss_dssp             CCBTTCBCBEEESSSSSHHHH
T ss_pred             cccCCceEeeccCCCCChHHH
Confidence            456788899999999999965

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=87.02  E-value=0.11  Score=35.47  Aligned_cols=14  Identities=0%  Similarity=-0.470  Sum_probs=12.1

Q ss_pred             eeEecCCCCCchHH
Q psy14082         11 NFSKITNYLLSPPQ   24 (233)
Q Consensus        11 ~i~~a~tGsGKT~~   24 (233)
                      +++.+++|||||..
T Consensus         5 Iii~G~pGsGKTTl   18 (152)
T d1ly1a_           5 ILTIGCPGSGKSTW   18 (152)
T ss_dssp             EEEECCTTSSHHHH
T ss_pred             EEEECCCCCCHHHH
Confidence            67799999999964

>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=86.93  E-value=3.2  Score=28.41  Aligned_cols=37  Identities=16%  Similarity=0.268  Sum_probs=31.7

Q ss_pred             CceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCCC
Q psy14082         44 GPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPK   82 (233)
Q Consensus        44 ~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~   82 (233)
                      ..++||.|.++.-++++++.+...  ++.+..++|+.+.
T Consensus        27 ~~k~iIF~~s~~~~~~l~~~L~~~--~~~~~~~~~~~~~   63 (162)
T d1fuka_          27 VTQAVIFCNTRRKVEELTTKLRND--KFTVSAIYSDLPQ   63 (162)
T ss_dssp             CSCEEEEESSHHHHHHHHHHHHHT--TCCEEEECTTSCH
T ss_pred             CCcEEEEEEEEchHHHHHHHHhhc--CceEEEeccCCch
Confidence            457999999999999999988776  7788999998664

>d1em8a_ c.128.1.1 (A:) DNA polymerase III chi subunit {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: DNA polymerase III chi subunit
superfamily: DNA polymerase III chi subunit
family: DNA polymerase III chi subunit
domain: DNA polymerase III chi subunit
species: Escherichia coli [TaxId: 562]

Probab=86.62  E-value=1.7  Score=29.53  Aligned_cols=86  Identities=15%  Similarity=0.143  Sum_probs=55.5

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecccCcCCcCCCCccEEEEecC
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSL  183 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~~~~Gldi~~v~~VI~~d~  183 (233)
                      ..+.+++|+|++.+.++.+-+.|-...-...+=|+-.....         .....|+++|+...   ..++.+++||.+.
T Consensus        34 ~~g~ri~I~~~d~~~~~~lD~~LWt~~~~sFiPH~~~~~~~---------~~~~PI~l~~~~~~---~~~~~dvlinl~~  101 (147)
T d1em8a_          34 RSGKRVLIACEDEKQAYRLDEALWARPAESFVPHNLAGEGP---------RGGAPVEIAWPQKR---SSSRRDILISLRT  101 (147)
T ss_dssp             HTTCCEEEECSSHHHHHHHHHHHHHCSTTCCCCEEETTCSS---------TTCCSEEEECTTSC---CCSCCSEEEECCS
T ss_pred             HCCCEEEEEeCCHHHHHHHHHHHhCCCCcccccccccCCCc---------cCCCCEEecCCCCC---CCccceEEEECCC
Confidence            35779999999999999999999766443333343211110         13468999886322   1235678899873


Q ss_pred             --CCCcccccceeeEEeecch
Q psy14082        184 --QLSANHNISQVIEVVQDYE  202 (233)
Q Consensus       184 --P~~~~~~i~~~~~~~~~~~  202 (233)
                        |..... ..+++.++...+
T Consensus       102 ~~p~~~~~-f~Rvieiv~~de  121 (147)
T d1em8a_         102 SFADFATA-FTEVVDFVPYED  121 (147)
T ss_dssp             SCCGGGGG-CSEEEEEECSSH
T ss_pred             CCchhhhc-cCEEEEEECcCH
Confidence              444444 478999997544

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=86.62  E-value=0.12  Score=38.33  Aligned_cols=22  Identities=9%  Similarity=-0.360  Sum_probs=16.6

Q ss_pred             CceeEecCCCCCchHHhHHHHHH
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAV   31 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~   31 (233)
                      .+++..+|+|+|||.. +-.+..
T Consensus        36 ~~~Ll~GPpG~GKTtl-a~~la~   57 (239)
T d1ixsb2          36 EHLLLFGPPGLGKTTL-AHVIAH   57 (239)
T ss_dssp             CCEEEECCTTSCHHHH-HHHHHH
T ss_pred             CeEEEECCCCCCHHHH-HHHHHH
Confidence            4689999999999966 443443

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=86.57  E-value=0.19  Score=37.40  Aligned_cols=24  Identities=4%  Similarity=-0.230  Sum_probs=18.1

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhh
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      ..++..+|+|+|||.+ +-.+...+
T Consensus        53 ~~lll~GPpG~GKTt~-a~~la~~~   76 (253)
T d1sxja2          53 RAAMLYGPPGIGKTTA-AHLVAQEL   76 (253)
T ss_dssp             SEEEEECSTTSSHHHH-HHHHHHHT
T ss_pred             ceEEEECCCCCCHHHH-HHHHHHHH
Confidence            4689999999999966 44455544

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric replicative helicase repA
species: Escherichia coli [TaxId: 562]

Probab=86.56  E-value=0.36  Score=36.22  Aligned_cols=63  Identities=13%  Similarity=0.009  Sum_probs=36.6

Q ss_pred             CCCCCCCceeEecCCCCCchHHhHHHHHHhhhccCC---CCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082          3 PPSESGCQNFSKITNYLLSPPQYMLPAAVHISHQEP---VKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus         3 p~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~---~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      |-++.|.=.++.+++|+|||.. ++-+...+.....   .....+.+++++.- -+-..++..++..+
T Consensus        24 ~G~~pg~~~~i~G~~G~GKS~l-~l~la~~ia~g~~~~~~~~~~~~~vl~~~~-E~~~~~~~~Rl~~~   89 (274)
T d1nlfa_          24 PNMVAGTVGALVSPGGAGKSML-ALQLAAQIAGGPDLLEVGELPTGPVIYLPA-EDPPTAIHHRLHAL   89 (274)
T ss_dssp             TTEETTSEEEEEESTTSSHHHH-HHHHHHHHHTCCCTTCCCCCCCCCEEEEES-SSCHHHHHHHHHHH
T ss_pred             CCccCCcEEEEEeCCCCCHHHH-HHHHHHHHHcCCCcccccccCCCceEEEec-cchHHHHHHHHHHH
Confidence            3345588889999999999944 5555555443211   11123446777653 23345566666555

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=86.53  E-value=0.59  Score=33.72  Aligned_cols=46  Identities=13%  Similarity=-0.108  Sum_probs=29.0

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCc
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPT   53 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~Pt   53 (233)
                      ..++++..+++|.|||.. +--+.+++........-.+.+..-+-+.
T Consensus        42 ~k~n~lLvG~pGVGKTal-v~~LA~ri~~~~vp~~L~~~~i~~ld~~   87 (195)
T d1jbka_          42 TKNNPVLIGEPGVGKTAI-VEGLAQRIINGEVPEGLKGRRVLALDMG   87 (195)
T ss_dssp             SSCEEEEECCTTSCHHHH-HHHHHHHHHHTCSCGGGTTCEEEEECHH
T ss_pred             CCCCeEEEecCCcccHHH-HHHHHHHHHhCCCCHHHcCceEEEeeHH
Confidence            356799999999999976 5556666665432222334554444444

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=86.37  E-value=0.84  Score=33.77  Aligned_cols=72  Identities=14%  Similarity=0.133  Sum_probs=52.5

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhh----CCCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc------cCcCCcCCC
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRR----ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD------VAARGLDVE  173 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~------~~~~Gldi~  173 (233)
                      ....+++|.+++++.+.++...+..    .++++..+.|+.....+...    .....+|+|+|+      .-...+++.
T Consensus        96 ~~~~~alil~pt~el~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~----~~~~~~ivV~TP~~l~~~~~~~~~~l~  171 (238)
T d1wrba1          96 TAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIRE----VQMGCHLLVATPGRLVDFIEKNKISLE  171 (238)
T ss_dssp             CBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHH----HSSCCSEEEECHHHHHHHHHTTSBCCT
T ss_pred             CCCceEEEeccchhhhcchheeeeecccCCCcEEEEEeccchhhHHHhh----cccCCceeecCHHHHHhHHccCceecc
Confidence            4557899999999999999877753    46788888888776665432    334689999994      123356677


Q ss_pred             CccEEE
Q psy14082        174 DVNTVN  179 (233)
Q Consensus       174 ~v~~VI  179 (233)
                      ++.++|
T Consensus       172 ~v~~lV  177 (238)
T d1wrba1         172 FCKYIV  177 (238)
T ss_dssp             TCCEEE
T ss_pred             ccceee
Confidence            888776

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=86.32  E-value=0.13  Score=38.64  Aligned_cols=23  Identities=9%  Similarity=-0.315  Sum_probs=16.8

Q ss_pred             eeEecCCCCCchHHhHHHHHHhhh
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      +++.+|+|+|||.+ +-.++..+.
T Consensus        49 l~l~GppGtGKT~l-~~~l~~~l~   71 (287)
T d1w5sa2          49 YGSIGRVGIGKTTL-AKFTVKRVS   71 (287)
T ss_dssp             EECTTCCSSSHHHH-HHHHHHHHH
T ss_pred             EEeECCCCCCHHHH-HHHHHHHHH
Confidence            35579999999977 555666554

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.93  E-value=0.98  Score=32.54  Aligned_cols=73  Identities=15%  Similarity=0.228  Sum_probs=52.7

Q ss_pred             cCCCCeEEEEecchhHHHHHHHHHhhC-----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----c-CcCCcC
Q psy14082        103 KNPAFKVIVFVETKKKVEDITRALRRE-----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----V-AARGLD  171 (233)
Q Consensus       103 ~~~~~k~iIf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----~-~~~Gld  171 (233)
                      ...+.+++|.+++++.+..+...+...     +..+...+|+.+...+...++    ...+++|+|+     . -...++
T Consensus        68 ~~~~~~~lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~----~~~~ivv~TPgrl~~~~~~~~~~  143 (206)
T d1veca_          68 KKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLD----DTVHVVIATPGRILDLIKKGVAK  143 (206)
T ss_dssp             TSCSCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTT----SCCSEEEECHHHHHHHHHTTCSC
T ss_pred             cccCcceEEEeecchhhHHHHHHHHHHhhcccCcccccccCCccHHHHHHHHH----hccCeEEeCCccccccccchhcc
Confidence            456678999999999999998888643     356677788887766655543    4689999994     2 223466


Q ss_pred             CCCccEEE
Q psy14082        172 VEDVNTVN  179 (233)
Q Consensus       172 i~~v~~VI  179 (233)
                      +.++.++|
T Consensus       144 ~~~l~~lV  151 (206)
T d1veca_         144 VDHVQMIV  151 (206)
T ss_dssp             CTTCCEEE
T ss_pred             ccccceEE
Confidence            77788776

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=85.82  E-value=0.4  Score=36.09  Aligned_cols=40  Identities=8%  Similarity=-0.028  Sum_probs=26.6

Q ss_pred             CCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcC
Q psy14082          6 ESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAP   52 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~P   52 (233)
                      ..|.=+++.|+||+|||. |++-+...+..      ..+.++++++.
T Consensus        33 ~~G~l~vi~G~~G~GKT~-~~~~la~~~a~------~~g~~v~~~s~   72 (277)
T d1cr2a_          33 RGGEVIMVTSGSGMGKST-FVRQQALQWGT------AMGKKVGLAML   72 (277)
T ss_dssp             CTTCEEEEECSTTSSHHH-HHHHHHHHHHH------TSCCCEEEEES
T ss_pred             CCCeEEEEEeCCCCCHHH-HHHHHHHhhhh------hcccceeEeee
Confidence            346678889999999994 45555544322      23567888874

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=85.75  E-value=0.14  Score=38.34  Aligned_cols=24  Identities=0%  Similarity=-0.421  Sum_probs=17.1

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhh
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      +-++..+|||||||.. +-.+...+
T Consensus        33 ~~ilL~GpPGtGKT~l-a~~la~~~   56 (273)
T d1gvnb_          33 TAFLLGGQPGSGKTSL-RSAIFEET   56 (273)
T ss_dssp             EEEEEECCTTSCTHHH-HHHHHHHT
T ss_pred             EEEEEECCCCCCHHHH-HHHHHHHh
Confidence            3488999999999966 34344433

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=85.75  E-value=0.3  Score=35.70  Aligned_cols=20  Identities=10%  Similarity=-0.270  Sum_probs=16.9

Q ss_pred             CCCCCceeEecCCCCCchHH
Q psy14082          5 SESGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~   24 (233)
                      ++.|+=+++.+++|||||..
T Consensus        31 i~~G~~~li~G~pGsGKT~l   50 (251)
T d1szpa2          31 VETGSITELFGEFRTGKSQL   50 (251)
T ss_dssp             EESSSEEEEEESTTSSHHHH
T ss_pred             CcCCeEEEEEcCCCCCHHHH
Confidence            35688899999999999954

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.57  E-value=0.45  Score=34.87  Aligned_cols=58  Identities=7%  Similarity=-0.183  Sum_probs=32.8

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHH
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVA   64 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~   64 (233)
                      ++.|+=+++.+++|+|||.. ++-++....... ........++++.....+..+....+
T Consensus        34 ip~G~~~~i~G~~GsGKT~l-alq~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~   91 (258)
T d1v5wa_          34 IESMAITEAFGEFRTGKTQL-SHTLCVTAQLPG-AGGYPGGKIIFIDTENTFRPDRLRDI   91 (258)
T ss_dssp             BCSSEEEEEECCTTCTHHHH-HHHHHHHTTSCB-TTTBCCCEEEEEESSSCCCHHHHHHH
T ss_pred             CcCCEEEEEECCCCCCHHHH-HHHHHHHHHhhh-hcccccceEEEechHHHHHHHHHHHH
Confidence            46788899999999999965 433333222211 01123455666665554444444433

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=85.52  E-value=0.21  Score=36.68  Aligned_cols=24  Identities=8%  Similarity=-0.162  Sum_probs=17.7

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhh
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      .+++..+|+|+|||.+ +-.+...+
T Consensus        46 ~~lll~Gp~G~GKTtl-a~~iak~l   69 (231)
T d1iqpa2          46 PHLLFAGPPGVGKTTA-ALALAREL   69 (231)
T ss_dssp             CEEEEESCTTSSHHHH-HHHHHHHH
T ss_pred             CeEEEECCCCCcHHHH-HHHHHHHH
Confidence            3589999999999966 44455544

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.51  E-value=0.21  Score=35.59  Aligned_cols=28  Identities=14%  Similarity=-0.194  Sum_probs=20.0

Q ss_pred             CCCCCceeEecCCCCCchHHhHHHHHHhh
Q psy14082          5 SESGCQNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus         5 ~~~g~d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      ++.|.=+.+.+++|+|||.. ++-++.+.
T Consensus        20 i~~G~v~~i~G~~GsGKT~l-~l~la~~~   47 (242)
T d1n0wa_          20 IETGSITEMFGEFRTGKTQI-CHTLAVTC   47 (242)
T ss_dssp             EETTSEEEEECCTTSSHHHH-HHHHHHHT
T ss_pred             CcCCEEEEEEeCCCCCHHHH-HHHHHHHH
Confidence            35678889999999999954 44444433

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=85.41  E-value=0.23  Score=36.43  Aligned_cols=23  Identities=4%  Similarity=-0.151  Sum_probs=17.3

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhh
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      +++..+|+|+|||.. +-.+...+
T Consensus        35 ~lll~Gp~G~GKTtl-~~~i~~~l   57 (237)
T d1sxjd2          35 HMLFYGPPGTGKTST-ILALTKEL   57 (237)
T ss_dssp             CEEEECSTTSSHHHH-HHHHHHHH
T ss_pred             eEEEECCCCCChHHH-HHHHHHHH
Confidence            479999999999965 44455554

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=85.37  E-value=0.15  Score=35.19  Aligned_cols=14  Identities=0%  Similarity=-0.301  Sum_probs=12.4

Q ss_pred             eeEecCCCCCchHH
Q psy14082         11 NFSKITNYLLSPPQ   24 (233)
Q Consensus        11 ~i~~a~tGsGKT~~   24 (233)
                      +++.+++|||||..
T Consensus         5 I~i~G~~GsGKTTv   18 (176)
T d2bdta1           5 YIITGPAGVGKSTT   18 (176)
T ss_dssp             EEEECSTTSSHHHH
T ss_pred             EEEECCCCCCHHHH
Confidence            67899999999965

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=85.10  E-value=0.17  Score=35.97  Aligned_cols=20  Identities=10%  Similarity=-0.205  Sum_probs=16.4

Q ss_pred             CCCCceeEecCCCCCchHHh
Q psy14082          6 ESGCQNFSKITNYLLSPPQY   25 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~~   25 (233)
                      |.|-.+++.+|+|||||...
T Consensus         1 p~~~riil~G~pGSGKsT~a   20 (190)
T d1ak2a1           1 PKGVRAVLLGPPGAGKGTQA   20 (190)
T ss_dssp             CCCCEEEEECCTTSSHHHHH
T ss_pred             CCccEEEEECCCCCCHHHHH
Confidence            35677889999999999763

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=85.09  E-value=0.32  Score=33.37  Aligned_cols=16  Identities=6%  Similarity=-0.330  Sum_probs=13.6

Q ss_pred             CceeEecCCCCCchHH
Q psy14082          9 CQNFSKITNYLLSPPQ   24 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~   24 (233)
                      -.+++.+++|||||..
T Consensus         5 ~~I~i~G~pGsGKTTi   20 (173)
T d1rkba_           5 PNILLTGTPGVGKTTL   20 (173)
T ss_dssp             CCEEEECSTTSSHHHH
T ss_pred             CEEEEECCCCCCHHHH
Confidence            4678999999999965

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=85.03  E-value=0.37  Score=33.29  Aligned_cols=22  Identities=5%  Similarity=-0.342  Sum_probs=16.2

Q ss_pred             EecCCCCCchHHhHHHHHHhhhc
Q psy14082         13 SKITNYLLSPPQYMLPAAVHISH   35 (233)
Q Consensus        13 ~~a~tGsGKT~~~~lp~l~~l~~   35 (233)
                      +.+..|||||.. +--++.++..
T Consensus         6 I~G~~gSGKTTl-i~~l~~~L~~   27 (165)
T d1xjca_           6 VVGYKHSGKTTL-MEKWVAAAVR   27 (165)
T ss_dssp             EECCTTSSHHHH-HHHHHHHHHH
T ss_pred             EEeCCCCCHHHH-HHHHHHHHHh
Confidence            788999999944 5556666654

>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=84.90  E-value=1.1  Score=32.85  Aligned_cols=74  Identities=12%  Similarity=0.184  Sum_probs=51.8

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhC----CC----eeEEEeCCCCHHHHHHHHHHhhCCCCCEEEeccc-CcCC-cCCC
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRE----RH----SAICIHGDKTQQDRDYVLNDFRQGKAPILVATDV-AARG-LDVE  173 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~----~~----~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~~-~~~G-ldi~  173 (233)
                      .++.++++.++++.-+++..+.+++.    ++    ....++++.+...+.+.++...  ..+|+|+|.. +.+. .+..
T Consensus        84 ~~~~rvliv~Pt~~La~Q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~--~~~Ilv~Tp~~l~~~~~~~~  161 (237)
T d1gkub1          84 LKGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLR--NFKIVITTTQFLSKHYRELG  161 (237)
T ss_dssp             TTSCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGG--GCSEEEEEHHHHHHCSTTSC
T ss_pred             HhcCeEEEEeccHHHHHHHHHHHHHHHHHcCCceEEEEeeeecccchhhhhhhhcccc--ccceeccChHHHHHhhhhcC
Confidence            45679999999999999998888652    33    3456677777777777766553  4679999853 2222 3455


Q ss_pred             CccEEE
Q psy14082        174 DVNTVN  179 (233)
Q Consensus       174 ~v~~VI  179 (233)
                      ++++||
T Consensus       162 ~~~~vV  167 (237)
T d1gkub1         162 HFDFIF  167 (237)
T ss_dssp             CCSEEE
T ss_pred             CCCEEE
Confidence            677766

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=84.13  E-value=0.19  Score=34.96  Aligned_cols=25  Identities=4%  Similarity=-0.375  Sum_probs=17.8

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhh
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      -+.+++.+++|||||.. +-.+..++
T Consensus         7 ~K~I~i~G~~GsGKTTl-a~~La~~~   31 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVL-VNKLAAVF   31 (192)
T ss_dssp             CEEEEEECCTTSHHHHH-HHHHHHHT
T ss_pred             ceEEEEECCCCCCHHHH-HHHHHHHh
Confidence            35689999999999955 44444443

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=84.11  E-value=5.8  Score=28.57  Aligned_cols=33  Identities=9%  Similarity=-0.076  Sum_probs=24.9

Q ss_pred             eeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc
Q psy14082        132 SAICIHGDKTQQDRDYVLNDFRQGKAPILVATD  164 (233)
Q Consensus       132 ~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~  164 (233)
                      ...++.+.+.+++-.++.+.|+.-...-+|-|.
T Consensus       133 ~~LVl~a~~~~~~~~~~~~~~~~~~~~~lI~TK  165 (213)
T d1vmaa2         133 TLLVIDATTGQNGLVQAKIFKEAVNVTGIILTK  165 (213)
T ss_dssp             EEEEEEGGGHHHHHHHHHHHHHHSCCCEEEEEC
T ss_pred             eEEeeccccCcchhhhhhhhccccCCceEEEec
Confidence            456677777788888888888877777777774

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=83.66  E-value=0.2  Score=34.77  Aligned_cols=24  Identities=4%  Similarity=-0.413  Sum_probs=17.4

Q ss_pred             CceeEecCCCCCchHHhHHHHHHhh
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      +++++.+++|+|||.. .--+.+++
T Consensus         1 k~I~liG~~GsGKsTi-~k~La~~l   24 (161)
T d1viaa_           1 KNIVFIGFMGSGKSTL-ARALAKDL   24 (161)
T ss_dssp             CCEEEECCTTSCHHHH-HHHHHHHH
T ss_pred             CcEEEECCCCCCHHHH-HHHHHHHh
Confidence            4688899999999966 33344554

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=83.61  E-value=0.42  Score=36.39  Aligned_cols=28  Identities=7%  Similarity=-0.226  Sum_probs=21.4

Q ss_pred             CCceeEecCCCCCchHHhHHHHHHhhhcc
Q psy14082          8 GCQNFSKITNYLLSPPQYMLPAAVHISHQ   36 (233)
Q Consensus         8 g~d~i~~a~tGsGKT~~~~lp~l~~l~~~   36 (233)
                      .+++++.+++|.|||.. +--+.+++...
T Consensus        39 k~n~lLVG~~GvGKTal-v~~la~ri~~~   66 (268)
T d1r6bx2          39 KNNPLLVGESGVGKTAI-AEGLAWRIVQG   66 (268)
T ss_dssp             SCEEEEECCTTSSHHHH-HHHHHHHHHHT
T ss_pred             cCCcEEECCCCCcHHHH-HHHHHHHHHhC
Confidence            56799999999999966 55566666553

>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=83.43  E-value=4  Score=29.04  Aligned_cols=38  Identities=8%  Similarity=0.173  Sum_probs=32.2

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhhcCCcEEEEEcCCCC
Q psy14082         43 DGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPK   82 (233)
Q Consensus        43 ~~~~~lil~PtreL~~Q~~~~~~~~~~~~~~~~~~gg~~~   82 (233)
                      ++.++||.|+|+.-+..+++.+...  ++.+..++|+.+.
T Consensus        29 ~~~~~IIF~~t~~~~~~l~~~l~~~--~~~~~~~h~~~~~   66 (200)
T d1oywa3          29 RGKSGIIYCNSRAKVEDTAARLQSK--GISAAAYHAGLEN   66 (200)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHHHT--TCCEEEECTTSCH
T ss_pred             CCCCEEEEEeeehhhHHhhhhhccC--CceeEEecCCCcH
Confidence            3567999999999999999888876  7889999998664

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=83.00  E-value=2.6  Score=29.43  Aligned_cols=72  Identities=25%  Similarity=0.333  Sum_probs=53.3

Q ss_pred             CCCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc------cCcCCcCCCC
Q psy14082        105 PAFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD------VAARGLDVED  174 (233)
Q Consensus       105 ~~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~------~~~~Gldi~~  174 (233)
                      .+.++++.++++.-+++.++.+.+.    +..+..+|++....++......     .+++++|.      .....+...+
T Consensus        51 ~~~~il~i~P~~~L~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~-----~~i~i~t~~~~~~~~~~~~~~~~~  125 (200)
T d1wp9a1          51 YGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWAR-----AKVIVATPQTIENDLLAGRISLED  125 (200)
T ss_dssp             SCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEEECSCSCHHHHHHHHHH-----CSEEEECHHHHHHHHHTTSCCTTS
T ss_pred             cCCcEEEEcCchHHHHHHHHHHHHhhcccccceeeeecccchhHHHHhhhc-----ccccccccchhHHHHhhhhhhccc
Confidence            4578999999999998888888764    5678888999999988877654     47888883      1223345567


Q ss_pred             ccEEEEec
Q psy14082        175 VNTVNIGS  182 (233)
Q Consensus       175 v~~VI~~d  182 (233)
                      +++|| +|
T Consensus       126 ~~~vI-iD  132 (200)
T d1wp9a1         126 VSLIV-FD  132 (200)
T ss_dssp             CSEEE-EE
T ss_pred             cceEE-EE
Confidence            77766 45

>d1xpua3 c.37.1.11 (A:129-417) Transcription termination factor Rho, ATPase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Transcription termination factor Rho, ATPase domain
species: Escherichia coli [TaxId: 562]

Probab=82.92  E-value=0.46  Score=36.55  Aligned_cols=29  Identities=14%  Similarity=0.008  Sum_probs=22.1

Q ss_pred             CCCCCCceeEecCCCCCchHHhHHHHHHhh
Q psy14082          4 PSESGCQNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus         4 ~~~~g~d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      ++-+|+-..+.++.|+|||.. +.-++...
T Consensus        39 PigrGQr~~I~g~~g~GKT~l-~~~i~~~~   67 (289)
T d1xpua3          39 PIGRGQRGLIVAPPKAGKTML-LQNIAQSI   67 (289)
T ss_dssp             CCBTTCEEEEEECSSSSHHHH-HHHHHHHH
T ss_pred             cccCCCeeeEeCCCCCCHHHH-HHHHHHHH
Confidence            577899999999999999976 44444433

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=82.85  E-value=0.21  Score=37.57  Aligned_cols=23  Identities=4%  Similarity=-0.263  Sum_probs=16.7

Q ss_pred             CceeEecCCCCCchHHhHHHHHHh
Q psy14082          9 CQNFSKITNYLLSPPQYMLPAAVH   32 (233)
Q Consensus         9 ~d~i~~a~tGsGKT~~~~lp~l~~   32 (233)
                      +-++..+|+|||||.. +-.+...
T Consensus        41 ~~vLL~GppGtGKT~l-a~alA~~   63 (246)
T d1d2na_          41 VSVLLEGPPHSGKTAL-AAKIAEE   63 (246)
T ss_dssp             EEEEEECSTTSSHHHH-HHHHHHH
T ss_pred             eEEEEECcCCCCHHHH-HHHHhhc
Confidence            4589999999999966 3334443

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=82.59  E-value=0.36  Score=35.15  Aligned_cols=23  Identities=9%  Similarity=-0.155  Sum_probs=16.8

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhh
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      +++..+|+|+|||.+ +-.++..+
T Consensus        37 ~lLl~Gp~G~GKttl-~~~la~~l   59 (227)
T d1sxjc2          37 HLLFYGPPGTGKTST-IVALAREI   59 (227)
T ss_dssp             CEEEECSSSSSHHHH-HHHHHHHH
T ss_pred             eEEEECCCCCChhHH-HHHHHHHh
Confidence            478999999999965 44455444

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.45  E-value=1.9  Score=32.27  Aligned_cols=26  Identities=4%  Similarity=-0.391  Sum_probs=19.2

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhh
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      ..+-++..+|+|||||.. +-.+...+
T Consensus        40 ~~~giLL~Gp~GtGKT~l-~~ala~~~   65 (265)
T d1r7ra3          40 PSKGVLFYGPPGCGKTLL-AKAIANEC   65 (265)
T ss_dssp             CCCEEEEBCCTTSSHHHH-HHHHHHHT
T ss_pred             CCCeEEEECCCCCcchhH-HHHHHHHh
Confidence            356799999999999966 44455444

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=82.17  E-value=0.37  Score=33.41  Aligned_cols=23  Identities=0%  Similarity=-0.224  Sum_probs=16.4

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhh
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      .+++.+|+|+|||.. +-.++..+
T Consensus         2 ki~I~G~~G~GKSTL-l~~i~~~l   24 (178)
T d1ye8a1           2 KIIITGEPGVGKTTL-VKKIVERL   24 (178)
T ss_dssp             EEEEECCTTSSHHHH-HHHHHHHH
T ss_pred             EEEEECCCCcHHHHH-HHHHHhcC
Confidence            478999999999964 44444444

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=82.08  E-value=0.31  Score=36.04  Aligned_cols=24  Identities=8%  Similarity=-0.196  Sum_probs=18.7

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhhh
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHIS   34 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l~   34 (233)
                      .++..+|+|+|||.. +..+++.+.
T Consensus        35 ~lll~Gp~G~GKTt~-~~~la~~l~   58 (252)
T d1sxje2          35 HLLLYGPNGTGKKTR-CMALLESIF   58 (252)
T ss_dssp             CEEEECSTTSSHHHH-HHTHHHHHS
T ss_pred             eEEEECCCCCCHHHH-HHHHHHhhc
Confidence            589999999999966 555666654

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=81.90  E-value=0.51  Score=34.10  Aligned_cols=19  Identities=11%  Similarity=-0.200  Sum_probs=16.2

Q ss_pred             CCCCceeEecCCCCCchHH
Q psy14082          6 ESGCQNFSKITNYLLSPPQ   24 (233)
Q Consensus         6 ~~g~d~i~~a~tGsGKT~~   24 (233)
                      +.|.=+++.+++|+|||..
T Consensus        24 ~~G~~~~I~G~~G~GKT~l   42 (242)
T d1tf7a1          24 PIGRSTLVSGTSGTGKTLF   42 (242)
T ss_dssp             ETTSEEEEEESTTSSHHHH
T ss_pred             cCCeEEEEEeCCCCCHHHH
Confidence            5678889999999999954

>d1ckea_ c.37.1.1 (A:) CMP kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=81.73  E-value=0.3  Score=35.24  Aligned_cols=43  Identities=7%  Similarity=-0.119  Sum_probs=25.7

Q ss_pred             eeEe-cCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy14082         11 NFSK-ITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF   67 (233)
Q Consensus        11 ~i~~-a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~~Q~~~~~~~~   67 (233)
                      +|++ +|+||||+... --+.+++.             +.-..|=+|-.+......+.
T Consensus         5 iI~I~GppGSGKgT~a-k~La~~~g-------------l~~iStGdLlR~~a~~~~~~   48 (225)
T d1ckea_           5 VITIDGPSGAGKGTLC-KAMAEALQ-------------WHLLDSGAIYRVLALAALHH   48 (225)
T ss_dssp             EEEEECCTTSSHHHHH-HHHHHHHT-------------CEEEEHHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHH-HHHHHHhC-------------CcEECHHHHHHHHHHHHHHc
Confidence            5555 99999999773 33555552             33345656666555444444

>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=81.60  E-value=0.52  Score=30.82  Aligned_cols=38  Identities=16%  Similarity=0.083  Sum_probs=33.0

Q ss_pred             CCCCeEEEEecchhHHHHHHHHHhhCCC-eeEEEeCCCC
Q psy14082        104 NPAFKVIVFVETKKKVEDITRALRRERH-SAICIHGDKT  141 (233)
Q Consensus       104 ~~~~k~iIf~~~~~~~~~l~~~L~~~~~-~~~~~~~~~~  141 (233)
                      .+..+++++|.+-.++...+..|.+.|+ ++..+.||+.
T Consensus        70 ~~~~~iv~~C~~G~rs~~a~~~L~~~G~~nv~~l~GG~~  108 (119)
T d1tq1a_          70 GQSDNIIVGCQSGGRSIKATTDLLHAGFTGVKDIVGGYS  108 (119)
T ss_dssp             CTTSSEEEEESSCSHHHHHHHHHHHHHCCSEEEEECCHH
T ss_pred             CCCcEEEEEcCCcCcHHHHHHHHHhcccCCeEEecChHH
Confidence            3567899999999999999999999998 5888999974

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=81.50  E-value=0.42  Score=34.85  Aligned_cols=23  Identities=4%  Similarity=-0.197  Sum_probs=16.7

Q ss_pred             ceeEecCCCCCchHHhHHHHHHhh
Q psy14082         10 QNFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus        10 d~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      +++..+|+|+|||.+ +--++..+
T Consensus        38 ~~ll~Gp~G~GKTt~-a~~la~~l   60 (224)
T d1sxjb2          38 HMIISGMPGIGKTTS-VHCLAHEL   60 (224)
T ss_dssp             CEEEECSTTSSHHHH-HHHHHHHH
T ss_pred             eEEEECCCCCCchhh-HHHHHHHH
Confidence            478999999999976 33344444

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=81.28  E-value=0.31  Score=33.56  Aligned_cols=25  Identities=0%  Similarity=-0.386  Sum_probs=17.0

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHh
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVH   32 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~   32 (233)
                      +.+=+++.+++|||||.. +-.+.++
T Consensus         2 ~~kiI~l~G~~GsGKsTv-a~~L~~~   26 (178)
T d1qhxa_           2 TTRMIILNGGSSAGKSGI-VRCLQSV   26 (178)
T ss_dssp             CCCEEEEECCTTSSHHHH-HHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHH-HHHHHHH
Confidence            445577889999999965 3334443

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=80.56  E-value=0.47  Score=33.06  Aligned_cols=22  Identities=5%  Similarity=-0.437  Sum_probs=16.0

Q ss_pred             eeEecCCCCCchHHhHHHHHHhh
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      +++.+|+|||||... --+.+++
T Consensus         3 I~i~G~pGSGKsT~a-~~La~~~   24 (182)
T d1zina1           3 LVLMGLPGAGKGTQA-EKIVAAY   24 (182)
T ss_dssp             EEEECSTTSSHHHHH-HHHHHHH
T ss_pred             EEEECCCCCCHHHHH-HHHHHHH
Confidence            788999999999763 3344444

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.49  E-value=0.58  Score=34.25  Aligned_cols=75  Identities=15%  Similarity=0.160  Sum_probs=48.8

Q ss_pred             hcCCCCeEEEEecchhHHHHHHHHHhhC----CCeeEEEeCCCCHHHHHHHHHHhhCCCCCEEEecc-----cC-cCCcC
Q psy14082        102 AKNPAFKVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD-----VA-ARGLD  171 (233)
Q Consensus       102 ~~~~~~k~iIf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~iLv~T~-----~~-~~Gld  171 (233)
                      ......+++|+++|++.+.++.+.+...    +..+..++++....+   .......+..+|+|+|+     .+ ....+
T Consensus        76 ~~~~~~~alil~Pt~eL~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~IvV~TP~rl~~~l~~~~~~  152 (218)
T d2g9na1          76 LDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRA---EVQKLQMEAPHIIVGTPGRVFDMLNRRYLS  152 (218)
T ss_dssp             TTCCSCCEEEECSSHHHHHHHHHHHHHHHTTTTCCEEEECC--CCCS---TTTSSSSCCCSEEEECHHHHHHHHHTTSSC
T ss_pred             ccccCccEEEEcccchhhhhHHHHHhhhccccceeEEeeecccchhH---HHHHHhcCCCEEEEeCChhHHHHHhcCCcc
Confidence            3456788999999999999888877643    556666666533222   12223445678999995     22 33466


Q ss_pred             CCCccEEE
Q psy14082        172 VEDVNTVN  179 (233)
Q Consensus       172 i~~v~~VI  179 (233)
                      +.++.++|
T Consensus       153 ~~~l~~lV  160 (218)
T d2g9na1         153 PKYIKMFV  160 (218)
T ss_dssp             STTCCEEE
T ss_pred             cccceEEE
Confidence            77777776

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=80.48  E-value=1.2  Score=35.69  Aligned_cols=50  Identities=12%  Similarity=-0.106  Sum_probs=29.8

Q ss_pred             CCCceeEecCCCCCchHHhHHHHHHhhhccCCCCCCCCceEEEEcCcHHHH
Q psy14082          7 SGCQNFSKITNYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVLAPTRELA   57 (233)
Q Consensus         7 ~g~d~i~~a~tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil~PtreL~   57 (233)
                      ..+++++.+++|.|||.. +--+.+++....-+..-.+.++.-+-+.+=++
T Consensus        42 ~k~n~llvG~~GvGKtai-v~~la~~i~~~~vp~~l~~~~i~~ld~~~l~a   91 (387)
T d1qvra2          42 TKNNPVLIGEPGVGKTAI-VEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLA   91 (387)
T ss_dssp             SCCCCEEEECTTSCHHHH-HHHHHHHHHHTCSCTTSTTCEEEEECC-----
T ss_pred             CCCCCeEECCCCCCHHHH-HHHHHHHHHhCCCCHHHcCceEEEeeHhhhhc
Confidence            356789999999999966 44556666654333334455666666654444

>d1byia_ c.37.1.10 (A:) Dethiobiotin synthetase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Dethiobiotin synthetase
species: Escherichia coli [TaxId: 562]

Probab=80.42  E-value=0.62  Score=33.31  Aligned_cols=32  Identities=9%  Similarity=-0.161  Sum_probs=20.5

Q ss_pred             eeEecC-CCCCchHHhHHHHHHhhhccCCCCCCCCceEEEE
Q psy14082         11 NFSKIT-NYLLSPPQYMLPAAVHISHQEPVKQGDGPIALVL   50 (233)
Q Consensus        11 ~i~~a~-tGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~lil   50 (233)
                      .++.+. ||.|||.+ ..-+...+.+       +|.+++++
T Consensus         4 ~~i~gt~~GVGKTtv-s~~La~aLa~-------~G~rVl~i   36 (224)
T d1byia_           4 YFVTGTDTEVGKTVA-SCALLQAAKA-------AGYRTAGY   36 (224)
T ss_dssp             EEEEESSTTSCHHHH-HHHHHHHHHH-------TTCCEEEE
T ss_pred             EEEEECCCCccHHHH-HHHHHHHHHH-------CCCeEEEE
Confidence            455555 79999977 4445555543       36677776

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=80.03  E-value=0.31  Score=33.58  Aligned_cols=22  Identities=5%  Similarity=-0.275  Sum_probs=15.7

Q ss_pred             eeEecCCCCCchHHhHHHHHHhh
Q psy14082         11 NFSKITNYLLSPPQYMLPAAVHI   33 (233)
Q Consensus        11 ~i~~a~tGsGKT~~~~lp~l~~l   33 (233)
                      +++.+++|||||.. +-.+..++
T Consensus         9 ivl~G~~GsGKsT~-a~~La~~l   30 (171)
T d1knqa_           9 YVLMGVSGSGKSAV-ASEVAHQL   30 (171)
T ss_dssp             EEEECSTTSCHHHH-HHHHHHHH
T ss_pred             EEEECCCCCCHHHH-HHHHHHHh
Confidence            67799999999966 33344444