Psyllid ID: psy4275

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180--
Protein Sequence
MEDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFFFFLKYYIPS
Secondary Structure (PSIPRED)
ccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHccccEEEccccccHHHHHHHHHHHHHHcccccccEEEEEcccHHHHHHHHHHHHHHHcccccEEEEEEccccHHHHHHHHHccccEEEEccHHHHHHHccccccccccccEEEEEcccccccccccccHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cccccccHHHccccHHHHHHHHHcccccccHHHHHHHHHHHccccEHEEHcccccHHHHHHHHHHHHccccccccEEEEEccHHHHHHHHHHHHHHHHHccccEEEEEEcccccHHHHHHHHccccEEEEcccHHHHHHHHcccEcHccEEEEEEccHHHHccccccccHHHHHHHHHHccc
Coil and Loop (DISEMBL)
medpiksftdlklnpwlirqcqtigvktptEIQKAIiphvlndedcigcaktgsgktLAFALPILQkwcedpygifaLVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGkelakkphiviatpgrladhldtcntfslnriKFLVLDEADRLSLMTSLKFFFFFFFLKYYIPS
Flexible Loop (DISEMBL)
medpiksftdlklnpwlIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFFFFLKYYIPS
Low Complexity Region (SEG)
MEDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKfffffffLKYYIPS
Disordered region (IsUnstruct)
*******FTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFFFFLKYYI**
Disordered Region (DISOPRED)
****IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFFFFLKYYIPS
Disordered Region (DISEMBL)
MEDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFFFFLKYYIPS
Disordered Region (DISPRO)
*****KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFFFFLKYYIPS
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MEDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFFFFLKYYIPS
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	182	2.2.26 [Sep-21-2011]
Q9Y6V7	483	Probable ATP-dependent RN	yes	N/A	0.862	0.325	0.649	3e-57
Q4FZF3	480	Probable ATP-dependent RN	yes	N/A	0.862	0.327	0.636	1e-56
Q9HGM5	453	ATP-dependent RNA helicas	yes	N/A	0.879	0.353	0.558	2e-49
A5DLE0	433	ATP-dependent RNA helicas	N/A	N/A	0.840	0.353	0.575	2e-49
Q07886	521	Probable ATP-dependent RN	yes	N/A	0.846	0.295	0.564	2e-48
A5AA68	522	ATP-dependent RNA helicas	yes	N/A	0.884	0.308	0.542	3e-48
A3LP87	445	ATP-dependent RNA helicas	yes	N/A	0.851	0.348	0.594	3e-48
Q4I662	547	ATP-dependent RNA helicas	yes	N/A	0.873	0.290	0.530	4e-48
Q5B3H7	525	ATP-dependent RNA helicas	yes	N/A	0.851	0.295	0.544	6e-48
A6SFV4	545	ATP-dependent RNA helicas	N/A	N/A	0.873	0.291	0.555	1e-47

>sp|Q9Y6V7|DDX49_HUMAN Probable ATP-dependent RNA helicase DDX49 OS=Homo sapiens GN=DDX49 PE=1 SV=1

 Score =  220 bits (561), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 102/157 (64%), Positives = 123/157 (78%)

Query: 5   IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPI 64
           +  F +L L+ WL+ QC+ +G+K PT +Q   IP +L   DC+GCAKTGSGKT AF LPI
Sbjct: 1   MAGFAELGLSSWLVEQCRQLGLKQPTPVQLGCIPAILEGRDCLGCAKTGSGKTAAFVLPI 60

Query: 65  LQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKK 124
           LQK  EDPYGIF LVLTPTRELAYQI +QF VLGK + L+  II GGMDMV Q  EL++K
Sbjct: 61  LQKLSEDPYGIFCLVLTPTRELAYQIAEQFRVLGKPLGLKDCIIVGGMDMVAQALELSRK 120

Query: 125 PHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           PH+VIATPGRLADHL + NTFS+ +I+FLV+DEADRL
Sbjct: 121 PHVVIATPGRLADHLRSSNTFSIKKIRFLVMDEADRL 157

Homo sapiens (taxid: 9606)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q4FZF3|DDX49_MOUSE Probable ATP-dependent RNA helicase DDX49 OS=Mus musculus GN=Ddx49 PE=2 SV=1

 Score =  219 bits (557), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 100/157 (63%), Positives = 123/157 (78%)

Query: 5   IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPI 64
           +  F ++ L+ WL+ QC+ +G+K PT +Q   IP +L   DC+GCAKTGSGKT AF LPI
Sbjct: 1   MAGFAEIGLSSWLVEQCRQLGLKQPTPVQLGCIPAILEGRDCLGCAKTGSGKTAAFVLPI 60

Query: 65  LQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKK 124
           LQK  EDPYGIF LVLTPTRELAYQI +QF VLGK + L+  II GGMDMV Q  EL++K
Sbjct: 61  LQKLSEDPYGIFCLVLTPTRELAYQIAEQFRVLGKPLGLKDCIIVGGMDMVAQALELSRK 120

Query: 125 PHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           PH+VIATPGRLADHL + NTF++ +I+FLV+DEADRL
Sbjct: 121 PHVVIATPGRLADHLRSSNTFNMKKIQFLVMDEADRL 157

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9HGM5|DBP8_SCHPO ATP-dependent RNA helicase dbp8 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=dbp8 PE=3 SV=1

 Score =  194 bits (493), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 91/163 (55%), Positives = 121/163 (74%), Gaps = 3/163 (1%)

Query: 2   EDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFA 61
           E   KSF+DL ++PWLI   + + +  PT+IQ+ +I  +L   +CIG AKTGSGKT AFA
Sbjct: 3   EHTRKSFSDLGISPWLIDTLKALAIYEPTDIQEGVIAQILEGRNCIGGAKTGSGKTAAFA 62

Query: 62  LPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL 121
           LPI++KW +DP GIFAL+LTPTRELA QI +QF  LG  +NL+ ++I GGMDM+ Q  +L
Sbjct: 63  LPIIEKWSKDPSGIFALILTPTRELAIQIDEQFAALGANLNLKHALIVGGMDMIRQSIDL 122

Query: 122 AKKPHIVIATPGRLADHLDTCNTFS---LNRIKFLVLDEADRL 161
           +K+PH+V+ATPGRLAD + +    +   L RIKFLV+DEADRL
Sbjct: 123 SKRPHVVVATPGRLADLIRSNGEETIAGLRRIKFLVMDEADRL 165

ATP-binding RNA helicase involved in 40S ribosomal subunit biogenesis and is required for the normal formation of 18S rRNAs through pre-rRNA processing at A0, A1 and A2 sites. Required for vegetative growth.

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

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A5DLE0|DBP8_PICGU ATP-dependent RNA helicase DBP8 OS=Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) GN=DBP8 PE=3 SV=2

 Score =  194 bits (493), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 92/160 (57%), Positives = 114/160 (71%), Gaps = 7/160 (4%)

Query: 7   SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ 66
           SF DL ++ WL+     + +++PT IQ   IP +L   DCIG AKTGSGKT+AFA P++ 
Sbjct: 2   SFKDLGVSKWLLEALAAMKIRSPTSIQAECIPQILAGRDCIGGAKTGSGKTIAFAAPMMT 61

Query: 67  KWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPH 126
           KW EDP+GI+ LVLTPTRELA QI +QFL LG  MN++V+++ GG DMV Q  E+ K PH
Sbjct: 62  KWSEDPFGIYGLVLTPTRELALQIAEQFLALGASMNIKVAVVVGGEDMVKQALEIQKSPH 121

Query: 127 IVIATPGRLADHL-----DTCNTFSLNRIKFLVLDEADRL 161
            +IATPGRLADH+     DT     L RIKFLVLDEADRL
Sbjct: 122 FIIATPGRLADHILNSGDDTVG--GLKRIKFLVLDEADRL 159

ATP-binding RNA helicase involved in 40S ribosomal subunit biogenesis and is required for the normal formation of 18S rRNAs through pre-rRNA processing at A0, A1 and A2 sites. Required for vegetative growth.

Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) (taxid: 294746)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q07886|DDX49_DROME Probable ATP-dependent RNA helicase Dbp45A OS=Drosophila melanogaster GN=Dbp45A PE=2 SV=2

 Score =  191 bits (485), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 87/154 (56%), Positives = 116/154 (75%)

Query: 8   FTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQK 67
           F  L L PWL++Q   +G+K  T IQ+  IP +L  +DCIG AKTGSGKT AFALPIL++
Sbjct: 9   FQILGLRPWLVKQLTKLGLKGATPIQQKCIPAILAGQDCIGAAKTGSGKTFAFALPILER 68

Query: 68  WCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHI 127
             E+P   FALVLTPT ELAYQI +QFLV G+ M +RV +++GG D + + ++L ++PHI
Sbjct: 69  LSEEPVSHFALVLTPTHELAYQISEQFLVAGQAMGVRVCVVSGGTDQMVESQKLMQRPHI 128

Query: 128 VIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           V+A PGRLADHL  C+TFS + +K+LV+DEADR+
Sbjct: 129 VVAMPGRLADHLTGCDTFSFDNLKYLVVDEADRM 162

Probable ATP-binding RNA helicase.

Drosophila melanogaster (taxid: 7227)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A5AA68|DBP8_ASPNC ATP-dependent RNA helicase dbp8 OS=Aspergillus niger (strain CBS 513.88 / FGSC A1513) GN=dbp8 PE=3 SV=1

 Score =  191 bits (485), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 89/164 (54%), Positives = 117/164 (71%), Gaps = 3/164 (1%)

Query: 1   MEDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAF 60
           + D   SF  L + PWLI    T+ V+ PT IQKA IP +LN  DCIG ++TGSGKT+AF
Sbjct: 87  LNDAQNSFASLNVAPWLIGSLTTMAVRKPTAIQKACIPEILNGRDCIGGSRTGSGKTIAF 146

Query: 61  ALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKE 120
           ++P+LQKW EDP+GIF LVLTPTRELA QI +Q   +    +++  +ITGG DM  Q   
Sbjct: 147 SVPMLQKWAEDPFGIFGLVLTPTRELALQIYEQIKAISAPQSMKPLLITGGTDMRPQAVA 206

Query: 121 LAKKPHIVIATPGRLADHLDTCNTFS---LNRIKFLVLDEADRL 161
           LA++PH+VIATPGRLADH++T  + +   L R++ +VLDEADRL
Sbjct: 207 LAQRPHVVIATPGRLADHINTSGSDTIRGLKRVRMVVLDEADRL 250

ATP-binding RNA helicase involved in 40S ribosomal subunit biogenesis and is required for the normal formation of 18S rRNAs through pre-rRNA processing at A0, A1 and A2 sites. Required for vegetative growth.

Aspergillus niger (strain CBS 513.88 / FGSC A1513) (taxid: 425011)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A3LP87|DBP8_PICST ATP-dependent RNA helicase DBP8 OS=Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545) GN=DBP8 PE=3 SV=2

 Score =  191 bits (484), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 94/158 (59%), Positives = 112/158 (70%), Gaps = 3/158 (1%)

Query: 7   SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ 66
           SF DL ++ WL      + + TPT IQ   IP +L+  DCIG AKTGSGKT+AFA P+L 
Sbjct: 2   SFEDLGVSRWLSEALAAMKIHTPTAIQSGCIPKILSGHDCIGGAKTGSGKTIAFAAPMLT 61

Query: 67  KWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPH 126
           +W EDP+GIF LVLTPTRELA QI +QF  LG  MN+++S++ GG D V Q  EL KKPH
Sbjct: 62  QWSEDPFGIFGLVLTPTRELALQIAEQFAALGASMNIKISVVVGGEDFVKQTLELQKKPH 121

Query: 127 IVIATPGRLADHLDTC--NTFS-LNRIKFLVLDEADRL 161
            VIATPGRLADH+      T S L RIK+LVLDEADRL
Sbjct: 122 FVIATPGRLADHILNSGEETISGLRRIKYLVLDEADRL 159

ATP-binding RNA helicase involved in 40S ribosomal subunit biogenesis and is required for the normal formation of 18S rRNAs through pre-rRNA processing at A0, A1 and A2 sites. Required for vegetative growth.

Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545) (taxid: 322104)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q4I662|DBP8_GIBZE ATP-dependent RNA helicase DBP8 OS=Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) GN=DBP8 PE=3 SV=1

 Score =  190 bits (483), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 86/162 (53%), Positives = 116/162 (71%), Gaps = 3/162 (1%)

Query: 3   DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFAL 62
           DP  +F+ L + PWL++  + + +K PT IQK  IP +L   DCIG ++TGSGKT+AFA+
Sbjct: 113 DPNTTFSALDVRPWLVQSLENMAIKRPTGIQKGCIPEILKGRDCIGGSRTGSGKTMAFAV 172

Query: 63  PILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA 122
           PILQKW EDP  IFA+VLTPTRELA QI +QF  +    +L+  ++TGG DM  Q  E+ 
Sbjct: 173 PILQKWSEDPTAIFAVVLTPTRELALQIFEQFKAISSPQSLKAILVTGGSDMRTQAIEIG 232

Query: 123 KKPHIVIATPGRLADHLDTCNTFS---LNRIKFLVLDEADRL 161
           K+PH++IATPGRLADH+ T    +   L R++++VLDEADRL
Sbjct: 233 KRPHVIIATPGRLADHIRTSGEDTICGLRRVRYVVLDEADRL 274

ATP-binding RNA helicase involved in 40S ribosomal subunit biogenesis and is required for the normal formation of 18S rRNAs through pre-rRNA processing at A0, A1 and A2 sites. Required for vegetative growth.

Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) (taxid: 229533)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5B3H7|DBP8_EMENI ATP-dependent RNA helicase dbp8 OS=Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) GN=dbp8 PE=3 SV=1

 Score =  189 bits (481), Expect = 6e-48,   Method: Compositional matrix adjust.
 Identities = 86/158 (54%), Positives = 114/158 (72%), Gaps = 3/158 (1%)

Query: 7   SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ 66
           SF  L + PWL+    T+ V+ PT IQ+A IP +L   DCIG ++TGSGKT+AF++PILQ
Sbjct: 96  SFKALNVAPWLVGSLTTMAVRKPTAIQRACIPEILKGRDCIGGSRTGSGKTIAFSVPILQ 155

Query: 67  KWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPH 126
           KW EDP+GIFA++LTPTRELA QI +Q   +    +++  +ITGG DM  Q  ELA +PH
Sbjct: 156 KWAEDPFGIFAVILTPTRELALQIFEQIKAISAPQSMKPVLITGGTDMRSQAIELAGRPH 215

Query: 127 IVIATPGRLADHLDTCNT---FSLNRIKFLVLDEADRL 161
           +V+ATPGRLADH++T  T     L R++ +VLDEADRL
Sbjct: 216 VVVATPGRLADHINTSGTDTVAGLKRVRMVVLDEADRL 253

ATP-binding RNA helicase involved in 40S ribosomal subunit biogenesis and is required for the normal formation of 18S rRNAs through pre-rRNA processing at A0, A1 and A2 sites. Required for vegetative growth.

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

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A6SFV4|DBP8_BOTFB ATP-dependent RNA helicase dbp8 OS=Botryotinia fuckeliana (strain B05.10) GN=dbp8 PE=3 SV=1

 Score =  189 bits (479), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 90/162 (55%), Positives = 114/162 (70%), Gaps = 3/162 (1%)

Query: 3   DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFAL 62
           D   +F  L + PWL+    ++ +K PT IQK  IP +L   DCIG ++TGSGKT+AFA+
Sbjct: 113 DAQTTFAALNVKPWLVGSLGSMAIKRPTGIQKGCIPEILKGRDCIGGSRTGSGKTVAFAV 172

Query: 63  PILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA 122
           PILQKW EDP+GIFALVLTPTRELA QI +QF  +    +L+  +ITGG DM  Q   LA
Sbjct: 173 PILQKWAEDPFGIFALVLTPTRELALQIYEQFKAISSPQSLKAVLITGGSDMRPQATALA 232

Query: 123 KKPHIVIATPGRLADHLDTCNT---FSLNRIKFLVLDEADRL 161
           ++PHIVIATPGRLADH+ T       +L R++ +VLDEADRL
Sbjct: 233 QRPHIVIATPGRLADHIRTSGEDTIGALRRVRMVVLDEADRL 274

ATP-binding RNA helicase involved in 40S ribosomal subunit biogenesis and is required for the normal formation of 18S rRNAs through pre-rRNA processing at A0, A1 and A2 sites. Required for vegetative growth.

Botryotinia fuckeliana (strain B05.10) (taxid: 332648)

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	182
270005640	447	hypothetical protein TcasGA2_TC007723 [T	0.857	0.348	0.756	3e-66
322796322	420	hypothetical protein SINV_00745 [Solenop	0.884	0.383	0.726	2e-65
307167913	457	Probable ATP-dependent RNA helicase DDX4	0.873	0.347	0.729	3e-65
332016384	461	Putative ATP-dependent RNA helicase DDX4	0.884	0.349	0.720	5e-65
242005222	422	DEAD box ATP-dependent RNA helicase, put	0.857	0.369	0.705	4e-63
156549811	456	PREDICTED: probable ATP-dependent RNA he	0.851	0.339	0.735	6e-62
383851888	449	PREDICTED: probable ATP-dependent RNA he	0.851	0.345	0.716	2e-60
346466157	487	hypothetical protein [Amblyomma maculatu	0.851	0.318	0.703	3e-60
350415766	452	PREDICTED: probable ATP-dependent RNA he	0.851	0.342	0.716	6e-60
380026593	452	PREDICTED: probable ATP-dependent RNA he	0.851	0.342	0.709	7e-60

>gi|270005640|gb|EFA02088.1| hypothetical protein TcasGA2_TC007723 [Tribolium castaneum]

 Score =  256 bits (654), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 118/156 (75%), Positives = 136/156 (87%)

Query: 6   KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPIL 65
           KSF  L+LNPW+IRQC TIGV++PT IQ   IP +L   DCIG AKTGSGKTLAFALPIL
Sbjct: 4   KSFDKLQLNPWIIRQCATIGVRSPTPIQTNCIPPILAGRDCIGAAKTGSGKTLAFALPIL 63

Query: 66  QKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKP 125
           QK CEDPYGIFAL+LTPTRELA+QI DQF V+GKVMNLR  +I GGMDMV QGK+LA+KP
Sbjct: 64  QKLCEDPYGIFALILTPTRELAFQIADQFAVIGKVMNLRHCVIVGGMDMVVQGKDLARKP 123

Query: 126 HIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           HIV+ATPGRLADHL++CNTF+ N+++FLVLDEADRL
Sbjct: 124 HIVVATPGRLADHLESCNTFNFNKLRFLVLDEADRL 159

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322796322|gb|EFZ18887.1| hypothetical protein SINV_00745 [Solenopsis invicta]

 Score =  253 bits (646), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 117/161 (72%), Positives = 137/161 (85%)

Query: 1   MEDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAF 60
           M + +K F  LKLN WL+ QC+++G+K PT IQ+  IP +L  EDCIGCAKTGSGKTLAF
Sbjct: 1   MNEEVKDFLHLKLNSWLLAQCKSMGLKKPTPIQENCIPRILMGEDCIGCAKTGSGKTLAF 60

Query: 61  ALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKE 120
           ALPILQK CEDPYGIFALVLTPTRELA+QI DQF  +GKV+NL+  +I GGMDM+ QG E
Sbjct: 61  ALPILQKLCEDPYGIFALVLTPTRELAFQIADQFAAIGKVINLKKCVIVGGMDMMIQGLE 120

Query: 121 LAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           L+K+PHIV+ATPGRLADHLD+CNTFSL +IKFLVLDEADRL
Sbjct: 121 LSKRPHIVVATPGRLADHLDSCNTFSLQKIKFLVLDEADRL 161

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307167913|gb|EFN61290.1| Probable ATP-dependent RNA helicase DDX49 [Camponotus floridanus]

 Score =  253 bits (645), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 116/159 (72%), Positives = 136/159 (85%)

Query: 3   DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFAL 62
           + IK F+DLKLN WL+ QC T+G+K PT IQ+  IP +L  EDCIGCAKTGSGKTLAFAL
Sbjct: 2   NEIKDFSDLKLNSWLLAQCDTMGLKNPTLIQQNCIPRILAGEDCIGCAKTGSGKTLAFAL 61

Query: 63  PILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA 122
           PILQK CEDPYGIFALVLTPTRELA+QI DQF  +GK +NL+  ++ GGMDM+ QG EL+
Sbjct: 62  PILQKLCEDPYGIFALVLTPTRELAFQIADQFAAIGKAINLKKCVVVGGMDMMVQGLELS 121

Query: 123 KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           K+PHIV+ATPGRLADHLD+C+TFSL +IKFLVLDEADRL
Sbjct: 122 KRPHIVVATPGRLADHLDSCDTFSLQKIKFLVLDEADRL 160

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332016384|gb|EGI57297.1| Putative ATP-dependent RNA helicase DDX49 [Acromyrmex echinatior]

 Score =  252 bits (643), Expect = 5e-65,   Method: Compositional matrix adjust.
 Identities = 116/161 (72%), Positives = 136/161 (84%)

Query: 1   MEDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAF 60
           M   IK F+DLKLN WL+ QC+++G+K PT IQ+  IP +L  EDCIGCAKTGSGKTLAF
Sbjct: 6   MSKEIKHFSDLKLNSWLLAQCESMGLKKPTPIQQNCIPRILMGEDCIGCAKTGSGKTLAF 65

Query: 61  ALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKE 120
            LPILQK CEDPYGIFALVLTPTRELA+QI DQF  +GK +NL+  +I GGMDM+ QG E
Sbjct: 66  VLPILQKLCEDPYGIFALVLTPTRELAFQIADQFTAIGKAINLKKCVIVGGMDMMVQGLE 125

Query: 121 LAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           L+K+PHIV+ATPGRLADHLD+C+TFSL +IKFLVLDEADRL
Sbjct: 126 LSKRPHIVVATPGRLADHLDSCDTFSLQKIKFLVLDEADRL 166

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242005222|ref|XP_002423470.1| DEAD box ATP-dependent RNA helicase, putative [Pediculus humanus corporis] gi|212506558|gb|EEB10732.1| DEAD box ATP-dependent RNA helicase, putative [Pediculus humanus corporis]

 Score =  246 bits (627), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 110/156 (70%), Positives = 133/156 (85%)

Query: 6   KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPIL 65
           + F DL LN W++RQC + G+  PT IQ   IP +L   DCIGCAKTGSGKTLAFALPIL
Sbjct: 3   ERFEDLNLNKWIVRQCDSFGLTKPTPIQAHCIPKILEGNDCIGCAKTGSGKTLAFALPIL 62

Query: 66  QKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKP 125
           QK  E+P+GIFALVLTPTRELA+QIG+QFL  GKV+NL++ +I+GGMDMV QG+EL+K+P
Sbjct: 63  QKLSEEPFGIFALVLTPTRELAFQIGEQFLAYGKVINLKLCVISGGMDMVTQGQELSKRP 122

Query: 126 HIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           HIV++TPGRLADHLD+CNTFSL +I+FLVLDEADRL
Sbjct: 123 HIVVSTPGRLADHLDSCNTFSLKKIRFLVLDEADRL 158

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156549811|ref|XP_001606554.1| PREDICTED: probable ATP-dependent RNA helicase DDX49-like [Nasonia vitripennis]

 Score =  242 bits (617), Expect = 6e-62,   Method: Compositional matrix adjust.
 Identities = 114/155 (73%), Positives = 131/155 (84%)

Query: 7   SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ 66
            FTDL ++ W+I Q + IGVK PT IQ+  IP +L+ +DCIGCAKTGSGKTLAFALPILQ
Sbjct: 3   EFTDLNISSWIIDQLKLIGVKKPTPIQQNCIPAILSGKDCIGCAKTGSGKTLAFALPILQ 62

Query: 67  KWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPH 126
           K  EDPYGIFALVLTPTRELA+QIGDQF  +GK +NL+   I GGMDMV QG+ELA+ PH
Sbjct: 63  KLSEDPYGIFALVLTPTRELAFQIGDQFAAIGKTINLKKCTIVGGMDMVVQGQELARHPH 122

Query: 127 IVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           IV+ATPGRLADHL++CNTFSL RIKFLVLDEADRL
Sbjct: 123 IVVATPGRLADHLESCNTFSLARIKFLVLDEADRL 157

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383851888|ref|XP_003701463.1| PREDICTED: probable ATP-dependent RNA helicase DDX49-like [Megachile rotundata]

 Score =  236 bits (603), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 111/155 (71%), Positives = 127/155 (81%)

Query: 7   SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ 66
           +FT L LN WL+ QC  +G+K PT IQ+  IP +L  EDCIGCAKTGSGKTLAFALPILQ
Sbjct: 2   TFTTLNLNSWLVDQCNFMGLKNPTPIQQNCIPRILAGEDCIGCAKTGSGKTLAFALPILQ 61

Query: 67  KWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPH 126
           K  EDPYGIFAL+LTPTRELA+QI DQF  +GK + L+  +I GGMDMV QG EL+K PH
Sbjct: 62  KLSEDPYGIFALILTPTRELAFQIADQFSAIGKSIGLKKCVIVGGMDMVIQGLELSKHPH 121

Query: 127 IVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           IV+ATPGRLADHL +CNTFSL +IKFLVLDEADRL
Sbjct: 122 IVVATPGRLADHLTSCNTFSLKKIKFLVLDEADRL 156

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|346466157|gb|AEO32923.1| hypothetical protein [Amblyomma maculatum]

 Score =  236 bits (602), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 109/155 (70%), Positives = 130/155 (83%)

Query: 7   SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ 66
           +F DLKLN W+I Q  T+G+K P+ IQ+  IP +LN +DCIGCAKTGSGKTLAFALPILQ
Sbjct: 31  TFKDLKLNKWMIDQLDTLGIKNPSPIQENCIPAILNGKDCIGCAKTGSGKTLAFALPILQ 90

Query: 67  KWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPH 126
           K  EDPYGIFAL+LTPTRELA+QI +QF V+GK   LR  +I GGMDMV QG+ LA+ PH
Sbjct: 91  KLFEDPYGIFALILTPTRELAFQISEQFKVVGKAAGLRDCVIVGGMDMVTQGQILAESPH 150

Query: 127 IVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           +V+ATPGRLADHL++CNTF+L RI+FLVLDEADRL
Sbjct: 151 VVVATPGRLADHLESCNTFTLKRIRFLVLDEADRL 185

Source: Amblyomma maculatum

Species: Amblyomma maculatum

Genus: Amblyomma

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350415766|ref|XP_003490744.1| PREDICTED: probable ATP-dependent RNA helicase DDX49-like [Bombus impatiens]

 Score =  235 bits (599), Expect = 6e-60,   Method: Compositional matrix adjust.
 Identities = 111/155 (71%), Positives = 128/155 (82%)

Query: 7   SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ 66
           SF  L L+ WL++QC  +G+K PT IQK  IP +L  +DCIGCAKTGSGKTLAFALPILQ
Sbjct: 2   SFAALNLSSWLVQQCNFMGLKCPTPIQKNCIPKILAGDDCIGCAKTGSGKTLAFALPILQ 61

Query: 67  KWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPH 126
           K  EDPYGIFALVLTPTRELA+QI DQF  +GK + L+  +I GGMDMV QG EL+K PH
Sbjct: 62  KLSEDPYGIFALVLTPTRELAFQIADQFSAIGKSIGLKKCVIVGGMDMVVQGLELSKHPH 121

Query: 127 IVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           IV+ATPGRLADHL++CNTFSL +IKFLVLDEADRL
Sbjct: 122 IVVATPGRLADHLESCNTFSLKQIKFLVLDEADRL 156

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380026593|ref|XP_003697032.1| PREDICTED: probable ATP-dependent RNA helicase DDX49-like [Apis florea]

 Score =  235 bits (599), Expect = 7e-60,   Method: Compositional matrix adjust.
 Identities = 110/155 (70%), Positives = 129/155 (83%)

Query: 7   SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ 66
           +F DL L+ WL++QC  +G+K PT IQ+  IP +L  +DCIGCAKTGSGKTLAFALPILQ
Sbjct: 2   TFADLNLSLWLVQQCTFMGLKYPTSIQQNCIPRILAGDDCIGCAKTGSGKTLAFALPILQ 61

Query: 67  KWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPH 126
           K  EDPYGIFALVLTPTRELA+QI DQF  +GK + L+  +I GGMDMV QG EL+K PH
Sbjct: 62  KLSEDPYGIFALVLTPTRELAFQIADQFSAIGKSIGLKKCVIVGGMDMVIQGLELSKHPH 121

Query: 127 IVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           IV+ATPGRLADHL++CNTFSL +IKFLVLDEADRL
Sbjct: 122 IVVATPGRLADHLESCNTFSLKQIKFLVLDEADRL 156

Source: Apis florea

Species: Apis florea

Genus: Apis

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	182
RGD|1311124	480	Ddx49 "DEAD (Asp-Glu-Ala-Asp)	0.846	0.320	0.662	4.9e-53
UNIPROTKB|E2RBM7	488	DDX49 "Uncharacterized protein	0.846	0.315	0.662	1.3e-52
UNIPROTKB|Q9Y6V7	483	DDX49 "Probable ATP-dependent	0.846	0.318	0.662	1.3e-52
UNIPROTKB|F1S7D9	483	DDX49 "Uncharacterized protein	0.846	0.318	0.662	1.3e-52
ZFIN|ZDB-GENE-031030-3	468	ddx49 "DEAD (Asp-Glu-Ala-Asp)	0.851	0.331	0.638	2.1e-52
MGI|MGI:2136689	480	Ddx49 "DEAD (Asp-Glu-Ala-Asp)	0.846	0.320	0.649	5.6e-52
UNIPROTKB|F1NA53	402	DDX49 "Uncharacterized protein	0.851	0.385	0.632	6.5e-51
UNIPROTKB|F1NYX0	482	DDX49 "Uncharacterized protein	0.851	0.321	0.632	6.5e-51
POMBASE|SPBC543.06c	453	dbp8 "ATP-dependent RNA helica	0.857	0.344	0.572	1.5e-44
FB|FBgn0010220	521	Dbp45A "DEAD box protein 45A"	0.846	0.295	0.564	1.9e-44

RGD|1311124 Ddx49 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 49" [Rattus norvegicus (taxid:10116)]

 Score = 549 (198.3 bits), Expect = 4.9e-53, P = 4.9e-53
 Identities = 102/154 (66%), Positives = 123/154 (79%)

Query:     8 FTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQK 67
             F +L+L+ WL+ QC+ +G+K PT +Q   IP +L   DC+GCAKTGSGKT AF LPILQK
Sbjct:     4 FAELRLSSWLVEQCRQLGLKQPTPVQLGCIPAILEGRDCLGCAKTGSGKTAAFVLPILQK 63

Query:    68 WCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHI 127
               EDPYGIF LVLTPTRELAYQI +QF VLGK + L+  II GGMDMV Q  EL++KPH+
Sbjct:    64 LSEDPYGIFCLVLTPTRELAYQIAEQFRVLGKPLGLKDCIIVGGMDMVTQALELSRKPHV 123

Query:   128 VIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
             VIATPGRLADHL + NTF++ +I+FLVLDEADRL
Sbjct:   124 VIATPGRLADHLRSSNTFNMKKIRFLVLDEADRL 157

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

UNIPROTKB|E2RBM7 DDX49 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 545 (196.9 bits), Expect = 1.3e-52, P = 1.3e-52
 Identities = 102/154 (66%), Positives = 122/154 (79%)

Query:     8 FTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQK 67
             F +L L+ WL+ QC+ +G+K PT +Q   IP +L   DC+GCAKTGSGKT AF LPILQK
Sbjct:     4 FAELGLSSWLVEQCRQLGLKQPTPVQLGCIPAILEGRDCLGCAKTGSGKTAAFVLPILQK 63

Query:    68 WCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHI 127
               EDPYGIF LVLTPTRELAYQI +QF VLGK + L+  II GGMDMV Q  EL++KPH+
Sbjct:    64 LSEDPYGIFCLVLTPTRELAYQIAEQFRVLGKPLGLKDCIIVGGMDMVAQALELSRKPHV 123

Query:   128 VIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
             VIATPGRLADHL + NTFS+ +I+FLV+DEADRL
Sbjct:   124 VIATPGRLADHLRSSNTFSIKKIRFLVMDEADRL 157

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q9Y6V7 DDX49 "Probable ATP-dependent RNA helicase DDX49" [Homo sapiens (taxid:9606)]

 Score = 545 (196.9 bits), Expect = 1.3e-52, P = 1.3e-52
 Identities = 102/154 (66%), Positives = 122/154 (79%)

Query:     8 FTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQK 67
             F +L L+ WL+ QC+ +G+K PT +Q   IP +L   DC+GCAKTGSGKT AF LPILQK
Sbjct:     4 FAELGLSSWLVEQCRQLGLKQPTPVQLGCIPAILEGRDCLGCAKTGSGKTAAFVLPILQK 63

Query:    68 WCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHI 127
               EDPYGIF LVLTPTRELAYQI +QF VLGK + L+  II GGMDMV Q  EL++KPH+
Sbjct:    64 LSEDPYGIFCLVLTPTRELAYQIAEQFRVLGKPLGLKDCIIVGGMDMVAQALELSRKPHV 123

Query:   128 VIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
             VIATPGRLADHL + NTFS+ +I+FLV+DEADRL
Sbjct:   124 VIATPGRLADHLRSSNTFSIKKIRFLVMDEADRL 157

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|F1S7D9 DDX49 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 545 (196.9 bits), Expect = 1.3e-52, P = 1.3e-52
 Identities = 102/154 (66%), Positives = 122/154 (79%)

Query:     8 FTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQK 67
             F +L L+ WL+ QC+ +G+K PT +Q   IP +L   DC+GCAKTGSGKT AF LPILQK
Sbjct:     4 FAELGLSSWLVEQCRQLGLKQPTPVQLGCIPAILEGRDCLGCAKTGSGKTAAFVLPILQK 63

Query:    68 WCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHI 127
               EDPYGIF LVLTPTRELAYQI +QF VLGK + L+  II GGMDMV Q  EL++KPH+
Sbjct:    64 LSEDPYGIFCLVLTPTRELAYQIAEQFRVLGKPLGLKDCIIVGGMDMVAQALELSRKPHV 123

Query:   128 VIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
             VIATPGRLADHL + NTFS+ +I+FLV+DEADRL
Sbjct:   124 VIATPGRLADHLRSSNTFSIKKIRFLVMDEADRL 157

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

GO:0005524 "ATP binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

ZFIN|ZDB-GENE-031030-3 ddx49 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 49" [Danio rerio (taxid:7955)]

 Score = 543 (196.2 bits), Expect = 2.1e-52, P = 2.1e-52
 Identities = 99/155 (63%), Positives = 125/155 (80%)

Query:     7 SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ 66
             +F  L L+ WLI+QC+ +G+  PT +Q+  IP +L+  DC+GCAKTGSGKT AF LP+LQ
Sbjct:     3 TFESLGLSEWLIQQCKQMGISRPTAVQEKCIPAILDGRDCMGCAKTGSGKTAAFVLPVLQ 62

Query:    67 KWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPH 126
             K  EDPYG+F LVLTPTRELAYQI +QF VLGK + L+  II GGMDMV QG EL+KKPH
Sbjct:    63 KLSEDPYGVFCLVLTPTRELAYQIAEQFRVLGKPLGLKDCIIVGGMDMVTQGLELSKKPH 122

Query:   127 IVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
             +V+ATPGRLADH+ + +T +LNRI+FL++DEADRL
Sbjct:   123 VVVATPGRLADHIRSSDTINLNRIQFLIMDEADRL 157

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:0000166 "nucleotide binding" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

MGI|MGI:2136689 Ddx49 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 49" [Mus musculus (taxid:10090)]

 Score = 539 (194.8 bits), Expect = 5.6e-52, P = 5.6e-52
 Identities = 100/154 (64%), Positives = 122/154 (79%)

Query:     8 FTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQK 67
             F ++ L+ WL+ QC+ +G+K PT +Q   IP +L   DC+GCAKTGSGKT AF LPILQK
Sbjct:     4 FAEIGLSSWLVEQCRQLGLKQPTPVQLGCIPAILEGRDCLGCAKTGSGKTAAFVLPILQK 63

Query:    68 WCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHI 127
               EDPYGIF LVLTPTRELAYQI +QF VLGK + L+  II GGMDMV Q  EL++KPH+
Sbjct:    64 LSEDPYGIFCLVLTPTRELAYQIAEQFRVLGKPLGLKDCIIVGGMDMVAQALELSRKPHV 123

Query:   128 VIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
             VIATPGRLADHL + NTF++ +I+FLV+DEADRL
Sbjct:   124 VIATPGRLADHLRSSNTFNMKKIQFLVMDEADRL 157

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

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

GO:0008150 "biological_process" evidence=ND

GO:0016787 "hydrolase activity" evidence=IEA

UNIPROTKB|F1NA53 DDX49 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 529 (191.3 bits), Expect = 6.5e-51, P = 6.5e-51
 Identities = 98/155 (63%), Positives = 121/155 (78%)

Query:     7 SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ 66
             +F +L L PWL+ Q + +G+  PT +Q + IP +L   DC+GCAKTGSGKT AF LP+LQ
Sbjct:     3 AFRELGLAPWLVEQARQMGLSRPTPVQASCIPPILQGRDCLGCAKTGSGKTAAFVLPVLQ 62

Query:    67 KWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPH 126
                EDPYGIF LVLTPTRELAYQI +QF VLGK + L+  ++ GG+DMV Q  EL++KPH
Sbjct:    63 VLSEDPYGIFCLVLTPTRELAYQIAEQFRVLGKPLGLKDCVVVGGLDMVAQALELSRKPH 122

Query:   127 IVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
             +VIATPGRLADHL + NTFSL ++KFLVLDEADRL
Sbjct:   123 VVIATPGRLADHLRSSNTFSLKKLKFLVLDEADRL 157

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|F1NYX0 DDX49 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 529 (191.3 bits), Expect = 6.5e-51, P = 6.5e-51
 Identities = 98/155 (63%), Positives = 121/155 (78%)

Query:     7 SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ 66
             +F +L L PWL+ Q + +G+  PT +Q + IP +L   DC+GCAKTGSGKT AF LP+LQ
Sbjct:     6 AFRELGLAPWLVEQARQMGLSRPTPVQASCIPPILQGRDCLGCAKTGSGKTAAFVLPVLQ 65

Query:    67 KWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPH 126
                EDPYGIF LVLTPTRELAYQI +QF VLGK + L+  ++ GG+DMV Q  EL++KPH
Sbjct:    66 VLSEDPYGIFCLVLTPTRELAYQIAEQFRVLGKPLGLKDCVVVGGLDMVAQALELSRKPH 125

Query:   127 IVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
             +VIATPGRLADHL + NTFSL ++KFLVLDEADRL
Sbjct:   126 VVIATPGRLADHLRSSNTFSLKKLKFLVLDEADRL 160

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

POMBASE|SPBC543.06c dbp8 "ATP-dependent RNA helicase Dbp8 (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 469 (170.2 bits), Expect = 1.5e-44, P = 1.5e-44
 Identities = 91/159 (57%), Positives = 121/159 (76%)

Query:     6 KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPIL 65
             KSF+DL ++PWLI   + + +  PT+IQ+ +I  +L   +CIG AKTGSGKT AFALPI+
Sbjct:     7 KSFSDLGISPWLIDTLKALAIYEPTDIQEGVIAQILEGRNCIGGAKTGSGKTAAFALPII 66

Query:    66 QKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKP 125
             +KW +DP GIFAL+LTPTRELA QI +QF  LG  +NL+ ++I GGMDM+ Q  +L+K+P
Sbjct:    67 EKWSKDPSGIFALILTPTRELAIQIDEQFAALGANLNLKHALIVGGMDMIRQSIDLSKRP 126

Query:   126 HIVIATPGRLADHLDTCN--TFS-LNRIKFLVLDEADRL 161
             H+V+ATPGRLAD + +    T + L RIKFLV+DEADRL
Sbjct:   127 HVVVATPGRLADLIRSNGEETIAGLRRIKFLVMDEADRL 165

GO:0003723 "RNA binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=ISM

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=ISO;IDA

GO:0006364 "rRNA processing" evidence=ISO

FB|FBgn0010220 Dbp45A "DEAD box protein 45A" [Drosophila melanogaster (taxid:7227)]

 Score = 468 (169.8 bits), Expect = 1.9e-44, P = 1.9e-44
 Identities = 87/154 (56%), Positives = 116/154 (75%)

Query:     8 FTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQK 67
             F  L L PWL++Q   +G+K  T IQ+  IP +L  +DCIG AKTGSGKT AFALPIL++
Sbjct:     9 FQILGLRPWLVKQLTKLGLKGATPIQQKCIPAILAGQDCIGAAKTGSGKTFAFALPILER 68

Query:    68 WCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHI 127
               E+P   FALVLTPT ELAYQI +QFLV G+ M +RV +++GG D + + ++L ++PHI
Sbjct:    69 LSEEPVSHFALVLTPTHELAYQISEQFLVAGQAMGVRVCVVSGGTDQMVESQKLMQRPHI 128

Query:   128 VIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
             V+A PGRLADHL  C+TFS + +K+LV+DEADR+
Sbjct:   129 VVAMPGRLADHLTGCDTFSFDNLKYLVVDEADRM 162

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

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IC

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q756G5	DBP8_ASHGO	3, ., 6, ., 4, ., 1, 3	0.5426	0.8626	0.3609	yes	N/A
Q4I662	DBP8_GIBZE	3, ., 6, ., 4, ., 1, 3	0.5308	0.8736	0.2906	yes	N/A
Q9Y6V7	DDX49_HUMAN	3, ., 6, ., 4, ., 1, 3	0.6496	0.8626	0.3250	yes	N/A
P0CR00	RRP3_CRYNJ	3, ., 6, ., 4, ., -	0.5512	0.8571	0.3223	yes	N/A
Q4WJE9	RRP3_ASPFU	3, ., 6, ., 4, ., -	0.5641	0.8571	0.3305	yes	N/A
Q55BR9	DDX49_DICDI	3, ., 6, ., 4, ., 1, 3	0.5448	0.8571	0.3070	yes	N/A
Q5B3H7	DBP8_EMENI	3, ., 6, ., 4, ., 1, 3	0.5443	0.8516	0.2952	yes	N/A
Q4FZF3	DDX49_MOUSE	3, ., 6, ., 4, ., 1, 3	0.6369	0.8626	0.3270	yes	N/A
Q6CXW0	DBP8_KLULA	3, ., 6, ., 4, ., 1, 3	0.5477	0.8241	0.3448	yes	N/A
Q07886	DDX49_DROME	3, ., 6, ., 4, ., 1, 3	0.5649	0.8461	0.2955	yes	N/A
A5AA68	DBP8_ASPNC	3, ., 6, ., 4, ., 1, 3	0.5426	0.8846	0.3084	yes	N/A
Q6BGU8	DBP8_DEBHA	3, ., 6, ., 4, ., 1, 3	0.5569	0.8516	0.3514	yes	N/A
A3LP87	DBP8_PICST	3, ., 6, ., 4, ., 1, 3	0.5949	0.8516	0.3483	yes	N/A
P38719	DBP8_YEAST	3, ., 6, ., 4, ., 1, 3	0.5605	0.8241	0.3480	yes	N/A
Q9HGM5	DBP8_SCHPO	3, ., 6, ., 4, ., 1, 3	0.5582	0.8791	0.3532	yes	N/A
Q6FQZ0	DBP8_CANGA	3, ., 6, ., 4, ., 1, 3	0.5345	0.8351	0.3478	yes	N/A
Q6C799	DBP8_YARLI	3, ., 6, ., 4, ., 1, 3	0.5687	0.8406	0.3461	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4	0.691

---

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	182
cd00268	203	cd00268, DEADc, DEAD-box helicases	8e-66
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	2e-59
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	6e-50
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	7e-41
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	7e-39
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	6e-36
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	2e-34
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	1e-33
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	9e-33
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	1e-31
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	7e-29
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	2e-27
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	6e-27
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	1e-26
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	1e-22
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	8e-16
COG1204	766	COG1204, COG1204, Superfamily II helicase [General	9e-13
COG1205	851	COG1205, COG1205, Distinct helicase family with a	1e-10
PRK13767	876	PRK13767, PRK13767, ATP-dependent helicase; Provis	1e-07
TIGR04121	803	TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA	1e-05
TIGR03817	742	TIGR03817, DECH_helic, helicase/secretion neighbor	2e-05
COG1061	442	COG1061, SSL2, DNA or RNA helicases of superfamily	9e-05
TIGR00643	630	TIGR00643, recG, ATP-dependent DNA helicase RecG	0.004

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

 Score =  200 bits (510), Expect = 8e-66
 Identities = 75/156 (48%), Positives = 100/156 (64%), Gaps = 3/156 (1%)

Query: 8   FTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQK 67
           F +L L+P L+R    +G + PT IQ   IP +L+  D IG A+TGSGKT AF +PIL+K
Sbjct: 1   FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEK 60

Query: 68  W--CEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKP 125
                   G  AL+L PTRELA QI +    LGK  NL+V +I GG  +  Q ++L + P
Sbjct: 61  LDPSPKKDGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLKRGP 120

Query: 126 HIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           HIV+ATPGRL D L+      L+++K+LVLDEADR+
Sbjct: 121 HIVVATPGRLLDLLER-GKLDLSKVKYLVLDEADRM 155

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

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

 Score =  192 bits (490), Expect = 2e-59
 Identities = 69/163 (42%), Positives = 99/163 (60%), Gaps = 4/163 (2%)

Query: 2   EDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFA 61
           E     F  L L+P L++  + +G + PT IQ A IP +L   D +G A+TG+GKT AF 
Sbjct: 25  EKTPPEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFL 84

Query: 62  LPILQK--WCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQG 118
           LP+LQK     +   + AL+L PTRELA QI ++   LGK +  LRV+++ GG+ +  Q 
Sbjct: 85  LPLLQKILKSVERKYVSALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQI 144

Query: 119 KELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           + L +   IV+ATPGRL D +       L+ ++ LVLDEADR+
Sbjct: 145 EALKRGVDIVVATPGRLLDLIKR-GKLDLSGVETLVLDEADRM 186

Length = 513

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

 Score =  158 bits (402), Expect = 6e-50
 Identities = 66/136 (48%), Positives = 84/136 (61%), Gaps = 1/136 (0%)

Query: 30  TEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQ 89
           T IQ   IP +L+ +D +  A TGSGKTLAF LPILQ       G  ALVL PTRELA Q
Sbjct: 1   TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQ 60

Query: 90  IGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAK-KPHIVIATPGRLADHLDTCNTFSLN 148
           I ++   L K++ LRV+++TGG  + +Q ++L K K  I++ TPGRL D L       L 
Sbjct: 61  IYEELKKLFKILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKLKLLK 120

Query: 149 RIKFLVLDEADRLSLM 164
            +K LVLDEA RL  M
Sbjct: 121 NLKLLVLDEAHRLLDM 136

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

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

 Score =  143 bits (362), Expect = 7e-41
 Identities = 65/156 (41%), Positives = 88/156 (56%), Gaps = 2/156 (1%)

Query: 6   KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPIL 65
            +F+ L L P L+     +G    T IQ   +P +L  +D I  AKTGSGKT AF L +L
Sbjct: 4   TAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLL 63

Query: 66  QKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGKELAKK 124
           QK     + + ALVL PTRELA Q+  +   L + + N++V  + GG+ M  Q   L   
Sbjct: 64  QKLDVKRFRVQALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHG 123

Query: 125 PHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR 160
            HI++ TPGR+ DHL    T  L+ +  LVLDEADR
Sbjct: 124 AHIIVGTPGRILDHLRK-GTLDLDALNTLVLDEADR 158

Length = 460

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

 Score =  136 bits (346), Expect = 7e-39
 Identities = 64/158 (40%), Positives = 91/158 (57%), Gaps = 5/158 (3%)

Query: 8   FTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQK 67
           F++L+L+  L+   Q  G   PT IQ   IP  L+  D +G A TG+GKT AF LP LQ 
Sbjct: 3   FSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQH 62

Query: 68  WCEDP--YGIFA--LVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAK 123
             + P         L+LTPTRELA Q+ DQ   L K  +L ++ ITGG+  ++  +  ++
Sbjct: 63  LLDFPRRKSGPPRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVFSE 122

Query: 124 KPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
              IV+ATPGRL  ++   N F    ++ L+LDEADR+
Sbjct: 123 NQDIVVATPGRLLQYIKEEN-FDCRAVETLILDEADRM 159

Length = 434

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

 Score =  123 bits (311), Expect = 6e-36
 Identities = 55/142 (38%), Positives = 74/142 (52%), Gaps = 4/142 (2%)

Query: 25  GVKTPTEIQKAIIPHVL-NDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT 83
           G +     QK  I  +L    D I  A TGSGKTLA  LP L+       G   LVL PT
Sbjct: 5   GFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGR-VLVLVPT 63

Query: 84  RELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAK-KPHIVIATPGRLADHLDTC 142
           RELA Q  ++   LG  + L+V  + GG    +Q ++L   K  I++ TPGRL D L+  
Sbjct: 64  RELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLEN- 122

Query: 143 NTFSLNRIKFLVLDEADRLSLM 164
           +  SL+ +  ++LDEA RL   
Sbjct: 123 DKLSLSNVDLVILDEAHRLLDG 144

Length = 201

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

 Score =  125 bits (316), Expect = 2e-34
 Identities = 66/164 (40%), Positives = 94/164 (57%), Gaps = 7/164 (4%)

Query: 7   SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ 66
           SF  L L+P ++R     G + PT IQ+  IP VL   D +  A+TG+GKT  F LP+LQ
Sbjct: 2   SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQ 61

Query: 67  KWCEDPYG------IFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKE 120
                         + AL+LTPTRELA QIG+      K +N+R  ++ GG+ +  Q  +
Sbjct: 62  HLITRQPHAKGRRPVRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMK 121

Query: 121 LAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM 164
           L     +++ATPGRL D L+  N   L++++ LVLDEADR+  M
Sbjct: 122 LRGGVDVLVATPGRLLD-LEHQNAVKLDQVEILVLDEADRMLDM 164

Length = 456

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

 Score =  124 bits (313), Expect = 1e-33
 Identities = 66/165 (40%), Positives = 90/165 (54%), Gaps = 2/165 (1%)

Query: 1   MEDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAF 60
           M +   +F DL L   ++     +G + P+ IQ   IPH+LN  D +G A+TGSGKT AF
Sbjct: 1   MAEFETTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAF 60

Query: 61  ALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMN-LRVSIITGGMDMVDQGK 119
           +LP+L     +      LVL PTRELA Q+ +      K M  + V  + GG     Q +
Sbjct: 61  SLPLLHNLDPELKAPQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLR 120

Query: 120 ELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM 164
            L + P IV+ TPGRL DHL    T  L+++  LVLDEAD +  M
Sbjct: 121 ALRQGPQIVVGTPGRLLDHLKR-GTLDLSKLSGLVLDEADEMLRM 164

Length = 629

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

 Score =  113 bits (286), Expect = 9e-33
 Identities = 51/126 (40%), Positives = 66/126 (52%), Gaps = 3/126 (2%)

Query: 44  EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNL 103
            D +  A TGSGKTLA  LPIL+       G   LVL PTRELA Q+ ++   L     +
Sbjct: 1   RDVLLAAPTGSGKTLAALLPILELLDSLKGGQ-VLVLAPTRELANQVAERLKELFGE-GI 58

Query: 104 RVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL 163
           +V  + GG  +  Q K L+ K  IV+ TPGRL D L+     SL ++  L+LDEA RL  
Sbjct: 59  KVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELER-LKLSLKKLDLLILDEAHRLLN 117

Query: 164 MTSLKF 169
                 
Sbjct: 118 QGFGLL 123

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

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

 Score =  119 bits (299), Expect = 1e-31
 Identities = 66/166 (39%), Positives = 88/166 (53%), Gaps = 6/166 (3%)

Query: 4   PIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALP 63
           P+ SF       ++++  +  G   PT IQ    P  L+  D IG A+TGSGKTLAF LP
Sbjct: 128 PVVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLP 187

Query: 64  ILQKWCEDPY-----GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQG 118
            +      P      G   LVL PTRELA QI +Q    G    +R ++  GG+    Q 
Sbjct: 188 AIVHINAQPLLRYGDGPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQI 247

Query: 119 KELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM 164
             L +   I+IA PGRL D L++ N  +L R+ +LVLDEADR+  M
Sbjct: 248 YALRRGVEILIACPGRLIDFLES-NVTNLRRVTYLVLDEADRMLDM 292

Length = 545

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

 Score =  111 bits (278), Expect = 7e-29
 Identities = 61/164 (37%), Positives = 88/164 (53%), Gaps = 8/164 (4%)

Query: 3   DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFAL 62
            PI SF+   L P L+   +T G + PT IQ   IP  L+    +  A TGSGKT +F +
Sbjct: 118 PPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLV 177

Query: 63  PILQKWC-------EDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMV 115
           PI+ + C        +     A+VLTPTREL  Q+ DQ  VLGK +  + +++ GG  M 
Sbjct: 178 PIISRCCTIRSGHPSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMP 237

Query: 116 DQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEAD 159
            Q   + +   +++ TPGRL D L + +   L+ +  LVLDE D
Sbjct: 238 QQLYRIQQGVELIVGTPGRLIDLL-SKHDIELDNVSVLVLDEVD 280

Length = 518

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

 Score =  106 bits (267), Expect = 2e-27
 Identities = 61/165 (36%), Positives = 84/165 (50%), Gaps = 9/165 (5%)

Query: 8   FTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQK 67
           F D  L P L+     +G    T IQ  ++ + L   D IG A+TG+GKT AF + I+ +
Sbjct: 89  FHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQ 148

Query: 68  WCEDPYG-------IFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKE 120
             + P           AL++ PTREL  QI      L K   L V    GGMD   Q K+
Sbjct: 149 LLQTPPPKERYMGEPRALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQ 208

Query: 121 L-AKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM 164
           L A+   I++ATPGRL D  +      L+ ++ +VLDEADR+  M
Sbjct: 209 LEARFCDILVATPGRLLD-FNQRGEVHLDMVEVMVLDEADRMLDM 252

Length = 475

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

 Score =  104 bits (261), Expect = 6e-27
 Identities = 59/160 (36%), Positives = 87/160 (54%), Gaps = 1/160 (0%)

Query: 2   EDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFA 61
           ++ + SF  LKLN  L+R   + G + P+ IQ+  I  +L+  D IG A++G+GKT  F 
Sbjct: 24  DEIVDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFV 83

Query: 62  LPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL 121
           +  LQ    D     AL+L PTRELA QI    L LG  + +R     GG  + D   +L
Sbjct: 84  IAALQLIDYDLNACQALILAPTRELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKL 143

Query: 122 AKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
               H+V+ TPGR+ D +D      ++ +K  +LDEAD +
Sbjct: 144 KAGVHMVVGTPGRVYDMIDK-RHLRVDDLKLFILDEADEM 182

Length = 401

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

 Score =  105 bits (262), Expect = 1e-26
 Identities = 60/165 (36%), Positives = 89/165 (53%), Gaps = 13/165 (7%)

Query: 7   SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ 66
           +F+   L+P L+   ++ G    T IQ   +P  L   D  G A+TG+GKTLAF + ++ 
Sbjct: 10  TFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMN 69

Query: 67  KWC----------EDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVD 116
           +            EDP    AL+L PTRELA QI    +  G  + LR +++ GG+D   
Sbjct: 70  RLLSRPALADRKPEDPR---ALILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDK 126

Query: 117 QGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           Q + L +   ++IATPGRL D++      SL+  +  VLDEADR+
Sbjct: 127 QRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRM 171

Length = 572

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

 Score = 92.7 bits (231), Expect = 1e-22
 Identities = 58/171 (33%), Positives = 82/171 (47%), Gaps = 11/171 (6%)

Query: 6   KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALP-- 63
           + F+D  L+P ++   +  G    T IQ   +P  L   D  G A+TG+GKT+AF     
Sbjct: 8   QKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATF 67

Query: 64  --ILQKWCEDPYGIF---ALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQG 118
             +L     +   +    AL++ PTRELA QI      L +   L++ +  GG     Q 
Sbjct: 68  HYLLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQL 127

Query: 119 KELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKF 169
           K L     I+I T GRL D+    N  +L  I+ +VLDEADR   M  L F
Sbjct: 128 KVLESGVDILIGTTGRLIDYAKQ-NHINLGAIQVVVLDEADR---MFDLGF 174

Length = 423

>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction only]

 Score = 74.2 bits (183), Expect = 8e-16
 Identities = 41/152 (26%), Positives = 72/152 (47%), Gaps = 9/152 (5%)

Query: 13  LNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP 72
           L+P +    +     + T  Q+  IP + + E+ +  A TGSGKT A  LP++ +     
Sbjct: 8   LDPRVREWFKRKF-TSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLG 66

Query: 73  Y-----GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHI 127
                 GI+AL ++P + L   I  +     + + + V++  G     ++ K L   PHI
Sbjct: 67  KGKLEDGIYALYISPLKALNNDIRRRLEEPLRELGIEVAVRHGDTPQSEKQKMLKNPPHI 126

Query: 128 VIATPGRLADHLDTCNTFS--LNRIKFLVLDE 157
           +I TP  LA  L     F   L  ++++++DE
Sbjct: 127 LITTPESLAILL-NSPKFRELLRDVRYVIVDE 157

Length = 814

>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function prediction only]

 Score = 65.1 bits (159), Expect = 9e-13
 Identities = 40/128 (31%), Positives = 64/128 (50%), Gaps = 9/128 (7%)

Query: 32  IQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIG 91
            Q+A+   +L+DE+ +  A TGSGKTL   L IL    E   G   + + P + LA +  
Sbjct: 36  QQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLE--GGGKVVYIVPLKALAEEKY 93

Query: 92  DQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSL-NRI 150
           ++F  L + + +RV I TG  D+     E   +  +++ TP +L D L T    S    +
Sbjct: 94  EEFSRL-EELGIRVGISTGDYDL---DDERLARYDVIVTTPEKL-DSL-TRKRPSWIEEV 147

Query: 151 KFLVLDEA 158
             +V+DE 
Sbjct: 148 DLVVIDEI 155

Length = 766

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

 Score = 59.0 bits (143), Expect = 1e-10
 Identities = 38/129 (29%), Positives = 53/129 (41%), Gaps = 20/129 (15%)

Query: 42  NDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQ---FLVLG 98
              + +    TGSGKT +F LPIL     DP    AL+L PT  LA    DQ      L 
Sbjct: 84  EGRNVVVTTGTGSGKTESFLLPILDHLLRDPSAR-ALLLYPTNALAN---DQAERLRELI 139

Query: 99  KVM--NLRVSIITGGMDMVDQGKE---LAKKPHIVIATPGRLADHLDTCNT----FSLNR 149
             +   +     TG  D     +    +   P I++  P  L  +L   N     + L  
Sbjct: 140 SDLPGKVTFGRYTG--D-TPPEERRAIIRNPPDILLTNPDML-HYLLLRNHDAWLWLLRN 195

Query: 150 IKFLVLDEA 158
           +K+LV+DE 
Sbjct: 196 LKYLVVDEL 204

Length = 851

>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional

 Score = 50.3 bits (121), Expect = 1e-07
 Identities = 45/153 (29%), Positives = 72/153 (47%), Gaps = 25/153 (16%)

Query: 27  KTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPIL-------QKW-CEDPYGIFAL 78
            T T  Q+  IP +   ++ +  + TGSGKTLA  L I+       ++   ED   ++ L
Sbjct: 31  GTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELED--KVYCL 88

Query: 79  VLTPTRELA-----------YQIGDQFLVLG-KVMNLRVSIITGGMDMVDQGKELAKKPH 126
            ++P R L             +I +     G ++  +RV+I TG     ++ K L K PH
Sbjct: 89  YVSPLRALNNDIHRNLEEPLTEIREIAKERGEELPEIRVAIRTGDTSSYEKQKMLKKPPH 148

Query: 127 IVIATPGRLADHLDTCNTFS--LNRIKFLVLDE 157
           I+I TP  LA  L     F   L  +K++++DE
Sbjct: 149 ILITTPESLAILL-NSPKFREKLRTVKWVIVDE 180

Length = 876

>gnl|CDD|234478 TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA ligase-associated

 Score = 44.5 bits (106), Expect = 1e-05
 Identities = 38/114 (33%), Positives = 50/114 (43%), Gaps = 5/114 (4%)

Query: 28  TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQK--WCEDP-YGIFALVLTPTR 84
           TP   Q  +    L     +  A TGSGKTLA  LP L      E P  G+  L +TP R
Sbjct: 13  TPRPFQLEMWAAALEGRSGLLIAPTGSGKTLAGFLPSLIDLAGPEKPKKGLHTLYITPLR 72

Query: 85  ELAYQIGDQFLVLGKVMNL--RVSIITGGMDMVDQGKELAKKPHIVIATPGRLA 136
            LA  I        + + L  RV   TG     ++ ++  K P I++ TP  LA
Sbjct: 73  ALAVDIARNLQAPIEELGLPIRVETRTGDTSSSERARQRKKPPDILLTTPESLA 126

Members of this protein family are DEAD/DEAH box helicases found associated with a bacterial ATP-dependent DNA ligase, part of a four-gene system that occurs in about 12 % of prokaryotic reference genomes. The actual motif in this family is DE[VILW]H. Length = 803

>gnl|CDD|234365 TIGR03817, DECH_helic, helicase/secretion neighborhood putative DEAH-box helicase

 Score = 44.0 bits (104), Expect = 2e-05
 Identities = 24/79 (30%), Positives = 35/79 (44%), Gaps = 4/79 (5%)

Query: 15 PWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYG 74
          P ++   +  G+  P + Q             +    T SGK+LA+ LP+L    +DP  
Sbjct: 23 PDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADDP-R 81

Query: 75 IFALVLTPTRELAYQIGDQ 93
            AL L PT+ LA    DQ
Sbjct: 82 ATALYLAPTKALAA---DQ 97

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. Length = 742

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

 Score = 41.7 bits (98), Expect = 9e-05
 Identities = 31/113 (27%), Positives = 42/113 (37%), Gaps = 19/113 (16%)

Query: 52  TGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGG 111
           TG+GKT+  A  I +           LVL PT+EL  Q  +        +N  + I  GG
Sbjct: 64  TGAGKTVVAAEAIAE------LKRSTLVLVPTKELLDQWAEALKKFLL-LNDEIGIYGGG 116

Query: 112 MDMVDQGKELAKKPHIVIAT--PGRLADHLDTCNTFSLNRIKFLVLDEADRLS 162
                  KEL     + +AT         LD    F  N    ++ DE   L 
Sbjct: 117 E------KELEPA-KVTVATVQTLARRQLLD---EFLGNEFGLIIFDEVHHLP 159

Length = 442

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

 Score = 36.9 bits (86), Expect = 0.004
 Identities = 28/121 (23%), Positives = 52/121 (42%), Gaps = 13/121 (10%)

Query: 53  GSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGM 112
           GSGKTL  AL +L        G    ++ PT  LA Q  +    L   + + V+++TG +
Sbjct: 266 GSGKTLVAALAMLAAI---EAGYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSL 322

Query: 113 DMVDQGKELAK----KPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLK 168
               + + L      + H+V+ T   + + ++        R+  +++DE  R  +    K
Sbjct: 323 KGKRRKELLETIASGQIHLVVGTHALIQEKVE------FKRLALVIIDEQHRFGVEQRKK 376

Query: 169 F 169
            
Sbjct: 377 L 377

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	182
KOG0330|consensus	476		100.0
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	100.0
PTZ00110	545	helicase; Provisional	100.0
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	100.0
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	100.0
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	100.0
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	100.0
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.98
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.98
KOG0331|consensus	519		99.97
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.97
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.97
KOG0338|consensus	691		99.97
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.97
KOG0340|consensus	442		99.97
KOG0348|consensus	708		99.97
PTZ00424	401	helicase 45; Provisional	99.97
PRK02362	737	ski2-like helicase; Provisional	99.96
KOG0345|consensus	567		99.96
KOG0339|consensus	731		99.96
KOG0328|consensus	400		99.95
KOG0343|consensus	758		99.95
KOG0342|consensus	543		99.95
KOG0346|consensus	569		99.95
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.95
KOG0335|consensus	482		99.95
PRK00254	720	ski2-like helicase; Provisional	99.95
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.95
KOG0333|consensus	673		99.95
KOG0347|consensus	731		99.95
PRK01172	674	ski2-like helicase; Provisional	99.94
KOG0350|consensus	620		99.94
KOG0326|consensus	459		99.94
KOG0334|consensus	997		99.93
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.93
PRK13767	876	ATP-dependent helicase; Provisional	99.92
KOG0341|consensus	610		99.92
COG1205	851	Distinct helicase family with a unique C-terminal	99.91
COG1204	766	Superfamily II helicase [General function predicti	99.91
KOG0336|consensus	629		99.9
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.9
KOG0329|consensus	387		99.89
KOG0327|consensus	397		99.89
KOG0332|consensus	477		99.89
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.89
KOG4284|consensus	980		99.89
KOG0337|consensus	529		99.89
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.88
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.88
PRK09401	1176	reverse gyrase; Reviewed	99.87
KOG0952|consensus	1230		99.87
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.87
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.87
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.86
COG1202	830	Superfamily II helicase, archaea-specific [General	99.86
PRK14701	1638	reverse gyrase; Provisional	99.86
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.86
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.86
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.85
PHA02558	501	uvsW UvsW helicase; Provisional	99.84
PRK10689	1147	transcription-repair coupling factor; Provisional	99.83
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.83
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.83
PRK13766	773	Hef nuclease; Provisional	99.82
KOG0344|consensus	593		99.82
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.81
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.78
KOG0354|consensus	746		99.78
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.77
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.77
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.74
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.74
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.74
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.73
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.73
PRK05580	679	primosome assembly protein PriA; Validated	99.73
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.72
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.71
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	99.7
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.69
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.66
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.66
PHA02653	675	RNA helicase NPH-II; Provisional	99.66
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.65
KOG0951|consensus	1674		99.64
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.64
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.64
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.63
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.6
KOG0353|consensus	695		99.59
KOG0352|consensus	641		99.59
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.58
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	99.58
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.56
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.55
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.55
KOG0949|consensus	1330		99.53
PRK09694	878	helicase Cas3; Provisional	99.51
KOG0947|consensus	1248		99.51
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.5
KOG0351|consensus	941		99.48
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	99.47
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	99.46
COG4096	875	HsdR Type I site-specific restriction-modification	99.45
KOG0349|consensus	725		99.45
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	99.45
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	99.44
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	99.42
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	99.42
KOG0948|consensus	1041		99.41
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	99.4
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	99.38
COG1198	730	PriA Primosomal protein N' (replication factor Y)	99.38
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.35
KOG0951|consensus	1674		99.35
KOG0385|consensus	971		99.34
PRK12326	764	preprotein translocase subunit SecA; Reviewed	99.33
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.32
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	99.31
KOG0950|consensus	1008		99.31
PRK04914	956	ATP-dependent helicase HepA; Validated	99.3
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	99.26
KOG0389|consensus	941		99.25
KOG0391|consensus	1958		99.24
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.21
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	99.2
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	99.19
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	99.17
KOG0387|consensus	923		99.14
CHL00122	870	secA preprotein translocase subunit SecA; Validate	99.12
KOG1123|consensus	776		99.12
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	99.1
KOG0920|consensus	924		99.09
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	99.09
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.08
KOG0952|consensus	1230		99.07
KOG0922|consensus	674		99.04
KOG1802|consensus	935		98.99
KOG0390|consensus	776		98.97
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	98.96
KOG4439|consensus	901		98.95
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	98.93
COG4889	1518	Predicted helicase [General function prediction on	98.9
PRK14873	665	primosome assembly protein PriA; Provisional	98.89
KOG0384|consensus	1373		98.89
KOG0388|consensus	1185		98.88
KOG1000|consensus	689		98.88
COG0610	962	Type I site-specific restriction-modification syst	98.87
KOG1002|consensus	791		98.86
PRK15483	986	type III restriction-modification system StyLTI en	98.84
KOG0392|consensus	1549		98.82
KOG0925|consensus	699		98.77
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	98.76
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	98.74
KOG0923|consensus	902		98.74
KOG0386|consensus	1157		98.73
KOG0926|consensus	1172		98.71
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	98.68
TIGR00376	637	DNA helicase, putative. The gene product may repre	98.67
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	98.61
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	98.58
KOG0924|consensus	1042		98.53
KOG1803|consensus	649		98.49
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	98.45
PF13245	76	AAA_19: Part of AAA domain	98.44
PRK10536	262	hypothetical protein; Provisional	98.43
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	98.39
PRK10875	615	recD exonuclease V subunit alpha; Provisional	98.38
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	98.38
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	98.3
KOG1805|consensus	1100		98.3
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	98.23
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	98.21
PF13872	303	AAA_34: P-loop containing NTP hydrolase pore-1	98.21
COG3587	985	Restriction endonuclease [Defense mechanisms]	98.2
KOG1132|consensus	945		98.18
KOG1131|consensus	755		98.18
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	98.14
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	98.13
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	98.11
KOG0989|consensus	346		98.04
PRK13889	988	conjugal transfer relaxase TraA; Provisional	97.92
KOG1001|consensus	674		97.87
PRK13826	1102	Dtr system oriT relaxase; Provisional	97.85
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	97.84
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.83
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	97.82
PRK11054	684	helD DNA helicase IV; Provisional	97.81
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	97.79
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	97.77
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	97.75
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	97.72
PHA02533	534	17 large terminase protein; Provisional	97.7
smart00382	148	AAA ATPases associated with a variety of cellular	97.68
PRK04296	190	thymidine kinase; Provisional	97.68
KOG0953|consensus	700		97.61
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	97.59
PRK06526	254	transposase; Provisional	97.59
KOG1015|consensus	1567		97.58
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	97.58
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	97.56
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.56
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	97.54
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	97.51
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	97.44
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	97.43
PRK08181	269	transposase; Validated	97.4
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	97.39
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	97.35
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	97.29
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	97.27
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	97.27
KOG0298|consensus	1394		97.23
KOG0991|consensus	333		97.22
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	97.16
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	97.14
PHA03333	752	putative ATPase subunit of terminase; Provisional	97.13
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	97.13
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	97.11
PF05127	177	Helicase_RecD: Helicase; InterPro: IPR007807 This	97.1
PRK00411	394	cdc6 cell division control protein 6; Reviewed	97.1
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	97.09
PF03354	477	Terminase_1: Phage Terminase ; InterPro: IPR005021	97.09
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	97.09
COG3973	747	Superfamily I DNA and RNA helicases [General funct	97.09
PRK13833	323	conjugal transfer protein TrbB; Provisional	97.08
PRK05298	652	excinuclease ABC subunit B; Provisional	97.06
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	97.06
PRK06921	266	hypothetical protein; Provisional	97.06
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	97.04
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	97.03
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	97.03
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	97.01
KOG4150|consensus	1034		96.98
PRK14087	450	dnaA chromosomal replication initiation protein; P	96.97
PRK07952	244	DNA replication protein DnaC; Validated	96.96
KOG0333|consensus	673		96.96
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	96.93
PRK05707	328	DNA polymerase III subunit delta'; Validated	96.92
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	96.88
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	96.87
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	96.84
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	96.82
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	96.81
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	96.81
CHL00181	287	cbbX CbbX; Provisional	96.8
KOG2340|consensus	698		96.79
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	96.79
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	96.79
PLN03025	319	replication factor C subunit; Provisional	96.78
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	96.78
COG1444	758	Predicted P-loop ATPase fused to an acetyltransfer	96.75
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	96.73
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	96.71
KOG0921|consensus	1282		96.71
COG3421	812	Uncharacterized protein conserved in bacteria [Fun	96.7
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	96.7
PRK08903	227	DnaA regulatory inactivator Hda; Validated	96.7
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	96.7
PRK00149	450	dnaA chromosomal replication initiation protein; R	96.7
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	96.69
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	96.67
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	96.65
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	96.61
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	96.58
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	96.57
PRK04195	482	replication factor C large subunit; Provisional	96.57
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	96.57
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	96.57
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	96.56
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	96.55
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.55
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	96.54
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	96.53
PRK11823	446	DNA repair protein RadA; Provisional	96.49
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	96.48
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	96.47
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	96.47
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	96.45
PF03237	384	Terminase_6: Terminase-like family; InterPro: IPR0	96.43
PHA03368	738	DNA packaging terminase subunit 1; Provisional	96.42
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	96.42
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	96.42
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	96.41
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	96.41
PTZ00112	1164	origin recognition complex 1 protein; Provisional	96.39
PRK08727	233	hypothetical protein; Validated	96.38
COG4626	546	Phage terminase-like protein, large subunit [Gener	96.36
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	96.35
PRK14088	440	dnaA chromosomal replication initiation protein; P	96.35
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	96.33
KOG1016|consensus	1387		96.31
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	96.31
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	96.31
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	96.3
COG1435	201	Tdk Thymidine kinase [Nucleotide transport and met	96.29
PRK05973	237	replicative DNA helicase; Provisional	96.29
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	96.29
TIGR00959	428	ffh signal recognition particle protein. This mode	96.27
PRK08116	268	hypothetical protein; Validated	96.26
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	96.23
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	96.23
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	96.22
PRK13851	344	type IV secretion system protein VirB11; Provision	96.21
PRK00771	437	signal recognition particle protein Srp54; Provisi	96.19
TIGR02237	209	recomb_radB DNA repair and recombination protein R	96.19
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	96.17
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	96.17
PRK14974	336	cell division protein FtsY; Provisional	96.17
KOG0331|consensus	519		96.15
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	96.15
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	96.14
PF02456	369	Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR	96.13
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	96.12
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	96.11
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	96.11
PF12846	304	AAA_10: AAA-like domain	96.11
KOG1133|consensus	821		96.11
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	96.11
PRK08769	319	DNA polymerase III subunit delta'; Validated	96.11
COG1484	254	DnaC DNA replication protein [DNA replication, rec	96.09
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	96.07
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	96.04
PRK10689	1147	transcription-repair coupling factor; Provisional	96.03
PRK14086	617	dnaA chromosomal replication initiation protein; P	96.0
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	95.98
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	95.98
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	95.97
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	95.97
PF06733	174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	95.96
PHA02544	316	44 clamp loader, small subunit; Provisional	95.91
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	95.9
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	95.87
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	95.86
TIGR00064	272	ftsY signal recognition particle-docking protein F	95.85
PTZ00293	211	thymidine kinase; Provisional	95.83
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	95.79
COG5008	375	PilU Tfp pilus assembly protein, ATPase PilU [Cell	95.79
KOG2373|consensus	514		95.78
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	95.77
PRK10436	462	hypothetical protein; Provisional	95.75
PRK08939	306	primosomal protein DnaI; Reviewed	95.75
PRK10867	433	signal recognition particle protein; Provisional	95.75
PRK06964	342	DNA polymerase III subunit delta'; Validated	95.74
PRK13764	602	ATPase; Provisional	95.73
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	95.72
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	95.71
PRK07993	334	DNA polymerase III subunit delta'; Validated	95.71
cd01394	218	radB RadB. The archaeal protein radB shares simila	95.7
COG0210	655	UvrD Superfamily I DNA and RNA helicases [DNA repl	95.7
COG1702	348	PhoH Phosphate starvation-inducible protein PhoH,	95.68
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	95.67
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	95.64
PRK06835	329	DNA replication protein DnaC; Validated	95.56
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	95.55
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	95.54
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	95.54
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	95.53
cd03115	173	SRP The signal recognition particle (SRP) mediates	95.52
PRK00440	319	rfc replication factor C small subunit; Reviewed	95.51
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	95.51
PRK07471	365	DNA polymerase III subunit delta'; Validated	95.49
KOG0341|consensus	610		95.44
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	95.39
KOG0739|consensus	439		95.38
PHA00012	361	I assembly protein	95.38
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	95.35
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	95.33
PRK13700	732	conjugal transfer protein TraD; Provisional	95.3
PF02572	172	CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase	95.28
PRK13341	725	recombination factor protein RarA/unknown domain f	95.25
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	95.24
PF05729	166	NACHT: NACHT domain	95.24
PHA00350	399	putative assembly protein	95.23
TIGR00767	415	rho transcription termination factor Rho. Members	95.22
PRK12422	445	chromosomal replication initiation protein; Provis	95.21
PRK08533	230	flagellar accessory protein FlaH; Reviewed	95.21
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	95.2
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	95.18
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	95.18
TIGR02533	486	type_II_gspE general secretory pathway protein E.	95.17
PRK09183	259	transposase/IS protein; Provisional	95.16
PRK04328	249	hypothetical protein; Provisional	95.16
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	95.14
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	95.14
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	95.13
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	95.1
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	95.08
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	95.08
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	95.07
COG1221	403	PspF Transcriptional regulators containing an AAA-	95.07
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	95.05
PRK05748	448	replicative DNA helicase; Provisional	95.04
PRK08699	325	DNA polymerase III subunit delta'; Validated	95.01
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	95.0
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	94.99
PRK09376	416	rho transcription termination factor Rho; Provisio	94.99
cd01128	249	rho_factor Transcription termination factor rho is	94.94
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	94.92
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	94.9
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	94.87
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	94.87
TIGR03743	634	SXT_TraD conjugative coupling factor TraD, SXT/TOL	94.86
PRK12377	248	putative replication protein; Provisional	94.84
COG0552	340	FtsY Signal recognition particle GTPase [Intracell	94.82
TIGR00665	434	DnaB replicative DNA helicase. This model describe	94.77
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	94.75
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	94.71
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	94.65
COG1074	1139	RecB ATP-dependent exoDNAse (exonuclease V) beta s	94.62
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	94.59
KOG0058|consensus	716		94.58
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	94.56
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	94.53
TIGR02784	1141	addA_alphas double-strand break repair helicase Ad	94.52
COG1132	567	MdlB ABC-type multidrug transport system, ATPase a	94.51
PRK09112	351	DNA polymerase III subunit delta'; Validated	94.51
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	94.5
KOG2228|consensus	408		94.46
PRK08006	471	replicative DNA helicase; Provisional	94.46
PRK06904	472	replicative DNA helicase; Validated	94.45
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	94.45
PRK10263	1355	DNA translocase FtsK; Provisional	94.43
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	94.4
PRK13897	606	type IV secretion system component VirD4; Provisio	94.4
PRK08506	472	replicative DNA helicase; Provisional	94.39
PF14516	331	AAA_35: AAA-like domain	94.38
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	94.37
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	94.33
PF01935	229	DUF87: Domain of unknown function DUF87; InterPro:	94.32
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	94.26
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	94.26
TIGR03754	643	conj_TOL_TraD conjugative coupling factor TraD, TO	94.26
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	94.24
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	94.23
PRK07004	460	replicative DNA helicase; Provisional	94.23
KOG1807|consensus	1025		94.22
PF00004	132	AAA: ATPase family associated with various cellula	94.21
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	94.19
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	94.17
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	94.14
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	94.13
cd00983	325	recA RecA is a bacterial enzyme which has roles in	94.1
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	94.05
PF02283	167	CobU: Cobinamide kinase / cobinamide phosphate gua	94.0
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	93.99
PRK06871	325	DNA polymerase III subunit delta'; Validated	93.97
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	93.93
PRK10416	318	signal recognition particle-docking protein FtsY;	93.9
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	93.89
PRK13695	174	putative NTPase; Provisional	93.88
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	93.87
PRK06090	319	DNA polymerase III subunit delta'; Validated	93.87
PRK08058	329	DNA polymerase III subunit delta'; Validated	93.87
CHL00176	638	ftsH cell division protein; Validated	93.85
PRK06067	234	flagellar accessory protein FlaH; Validated	93.85
COG3972	660	Superfamily I DNA and RNA helicases [General funct	93.74
PF05894	333	Podovirus_Gp16: Podovirus DNA encapsidation protei	93.73
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	93.71
PRK09354	349	recA recombinase A; Provisional	93.7
PRK08840	464	replicative DNA helicase; Provisional	93.68
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	93.63
cd01127	410	TrwB Bacterial conjugation protein TrwB, ATP bindi	93.61
PTZ00110	545	helicase; Provisional	93.59
PRK05595	444	replicative DNA helicase; Provisional	93.56
COG3598	402	RepA RecA-family ATPase [DNA replication, recombin	93.56
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	93.54
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	93.54
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	93.51
PRK09165	497	replicative DNA helicase; Provisional	93.5
PF13555	62	AAA_29: P-loop containing region of AAA domain	93.5
KOG1806|consensus	1320		93.47
TIGR00609	1087	recB exodeoxyribonuclease V, beta subunit. All pro	93.43
KOG0344|consensus	593		93.4
PRK13850	670	type IV secretion system protein VirD4; Provisiona	93.29
PRK12608	380	transcription termination factor Rho; Provisional	93.28
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	93.25
PHA00149	331	DNA encapsidation protein	93.04
PRK08760	476	replicative DNA helicase; Provisional	93.02
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	93.0
PRK13822	641	conjugal transfer coupling protein TraG; Provision	92.99
KOG0328|consensus	400		92.98
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	92.93
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	92.92
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	92.88
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	92.87
COG2256	436	MGS1 ATPase related to the helicase subunit of the	92.86
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	92.86
) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF06309">PF06309	127	Torsin: Torsin; InterPro: IPR010448 This family co	92.85
PHA03372	668	DNA packaging terminase subunit 1; Provisional	92.76
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	92.76
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	92.75
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	92.7
COG2109	198	BtuR ATP:corrinoid adenosyltransferase [Coenzyme m	92.7
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	92.68
TIGR02759	566	TraD_Ftype type IV conjugative transfer system cou	92.67
KOG0744|consensus	423		92.65
PRK05636	505	replicative DNA helicase; Provisional	92.65
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	92.64
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	92.39

>KOG0330|consensus

Probab=100.00  E-value=1.7e-33  Score=213.61  Aligned_cols=173  Identities=54%  Similarity=0.820  Sum_probs=163.1

Q ss_pred             CccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcC
Q psy4275           3 DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTP   82 (182)
Q Consensus         3 ~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p   82 (182)
                      +...+|.+|++.+++.+++...++..|+++|.+++|.++.|++++..+.||||||.+|++|+++.+++++..++++|++|
T Consensus        58 e~~~sf~dLgv~~~L~~ac~~l~~~~PT~IQ~~aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p~~~~~lVLtP  137 (476)
T KOG0330|consen   58 ESFKSFADLGVHPELLEACQELGWKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQEPKLFFALVLTP  137 (476)
T ss_pred             hhhcchhhcCcCHHHHHHHHHhCcCCCchhhhhhcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHcCCCCceEEEecC
Confidence            34578999999999999999999999999999999999999999999999999999999999999999988899999999


Q ss_pred             CHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccc
Q psy4275          83 TRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLS  162 (182)
Q Consensus        83 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~  162 (182)
                      +++|+.|+++.++.++...|++++.+.|+.....+...+..+++|+|+||+.+.+++...+.++++.++++|+||||.++
T Consensus       138 tRELA~QI~e~fe~Lg~~iglr~~~lvGG~~m~~q~~~L~kkPhilVaTPGrL~dhl~~Tkgf~le~lk~LVlDEADrlL  217 (476)
T KOG0330|consen  138 TRELAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQANQLSKKPHILVATPGRLWDHLENTKGFSLEQLKFLVLDEADRLL  217 (476)
T ss_pred             cHHHHHHHHHHHHHhccccCeEEEEEecCchHHHHHHHhhcCCCEEEeCcHHHHHHHHhccCccHHHhHHHhhchHHhhh
Confidence            99999999999999999999999999999999888888899999999999999999998799999999999999999999


Q ss_pred             ccCChhHHHHHHH
Q psy4275         163 LMTSLKFFFFFFF  175 (182)
Q Consensus       163 ~~~~~~~~~~~~~  175 (182)
                      ++.+-..++.+.+
T Consensus       218 d~dF~~~ld~ILk  230 (476)
T KOG0330|consen  218 DMDFEEELDYILK  230 (476)
T ss_pred             hhhhHHHHHHHHH
Confidence            9988766555443

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=2.2e-32  Score=219.18  Aligned_cols=167  Identities=34%  Similarity=0.458  Sum_probs=150.0

Q ss_pred             CCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCC-------CCeeEE
Q psy4275           6 KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP-------YGIFAL   78 (182)
Q Consensus         6 ~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~-------~~~~~l   78 (182)
                      .+|+++++++++.+.+...|+..|+|+|.++++.+++|+++++++|||+|||.+|++++++.+...+       .+++++
T Consensus         8 ~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~~~~l   87 (423)
T PRK04837          8 QKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRAL   87 (423)
T ss_pred             CCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhcccccccccCCceEE
Confidence            5899999999999999999999999999999999999999999999999999999999998775432       246899


Q ss_pred             EEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecc
Q psy4275          79 VLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEA  158 (182)
Q Consensus        79 il~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~  158 (182)
                      |++|+++|+.|+++.+..+.+..++++..+.|+.........+.++++|+|+||+.+.+++.+ +.+.+++++++|+|||
T Consensus        88 il~PtreLa~Qi~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~TP~~l~~~l~~-~~~~l~~v~~lViDEa  166 (423)
T PRK04837         88 IMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQ-NHINLGAIQVVVLDEA  166 (423)
T ss_pred             EECCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhcCCCCEEEECHHHHHHHHHc-CCcccccccEEEEecH
Confidence            999999999999999999999999999999998877776667777899999999999999987 6678899999999999


Q ss_pred             ccccccCChhHHHHH
Q psy4275         159 DRLSLMTSLKFFFFF  173 (182)
Q Consensus       159 h~~~~~~~~~~~~~~  173 (182)
                      |++.++++......+
T Consensus       167 d~l~~~~f~~~i~~i  181 (423)
T PRK04837        167 DRMFDLGFIKDIRWL  181 (423)
T ss_pred             HHHhhcccHHHHHHH
Confidence            999998876554433

>PTZ00110 helicase; Provisional

Probab=100.00  E-value=4.6e-32  Score=222.52  Aligned_cols=169  Identities=38%  Similarity=0.536  Sum_probs=152.3

Q ss_pred             CCCccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccC-----CCCe
Q psy4275           1 MEDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCED-----PYGI   75 (182)
Q Consensus         1 ~~~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~-----~~~~   75 (182)
                      .|+++.+|+++++++.+.+.+.+.|+..|+|+|.++|+.+++|+++++++|||+|||++|+++++..+...     ..++
T Consensus       125 ~p~p~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~~~~~gp  204 (545)
T PTZ00110        125 VPKPVVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGP  204 (545)
T ss_pred             CCcccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEEeCCCChHHHHHHHHHHHHHHhcccccCCCCc
Confidence            37889999999999999999999999999999999999999999999999999999999999988776542     2367


Q ss_pred             eEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEE
Q psy4275          76 FALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVL  155 (182)
Q Consensus        76 ~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~  155 (182)
                      .+||++|+++|+.|+.+.++.+....++++.+++|+.....+...+.++++|+|+||+++.+++.. ....+++++++|+
T Consensus       205 ~~LIL~PTreLa~Qi~~~~~~~~~~~~i~~~~~~gg~~~~~q~~~l~~~~~IlVaTPgrL~d~l~~-~~~~l~~v~~lVi  283 (545)
T PTZ00110        205 IVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQIYALRRGVEILIACPGRLIDFLES-NVTNLRRVTYLVL  283 (545)
T ss_pred             EEEEECChHHHHHHHHHHHHHHhcccCccEEEEeCCCCHHHHHHHHHcCCCEEEECHHHHHHHHHc-CCCChhhCcEEEe
Confidence            899999999999999999999999889999999998887777777788999999999999999987 5667889999999


Q ss_pred             eccccccccCChhHH
Q psy4275         156 DEADRLSLMTSLKFF  170 (182)
Q Consensus       156 DE~h~~~~~~~~~~~  170 (182)
                      ||||+|.++++...+
T Consensus       284 DEAd~mld~gf~~~i  298 (545)
T PTZ00110        284 DEADRMLDMGFEPQI  298 (545)
T ss_pred             ehHHhhhhcchHHHH
Confidence            999999998865433

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

Probab=100.00  E-value=6.9e-32  Score=220.64  Aligned_cols=168  Identities=36%  Similarity=0.549  Sum_probs=151.2

Q ss_pred             CCCccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhcc-------CCC
Q psy4275           1 MEDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCE-------DPY   73 (182)
Q Consensus         1 ~~~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~-------~~~   73 (182)
                      .|+++.+|+++++++.+.+.+.+.|+..|+|+|.++++.+..|+++++++|||+|||.+|+++++..+..       ...
T Consensus       116 ~p~pi~~f~~~~l~~~l~~~L~~~g~~~ptpiQ~~aip~il~g~dviv~ApTGSGKTlayllPil~~l~~~~~~~~~~~~  195 (518)
T PLN00206        116 VPPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQR  195 (518)
T ss_pred             CCchhcCHHhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEecCCCCccHHHHHHHHHHHHhhccccccccC
Confidence            3789999999999999999999999999999999999999999999999999999999999999887642       124


Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEE
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFL  153 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~i  153 (182)
                      +++++|++|+++|+.|+.+.++.+.+..++++..+.|+.....+...+.++++|+|+||+++.+++.. +...+++++++
T Consensus       196 ~~~aLIL~PTreLa~Qi~~~~~~l~~~~~~~~~~~~gG~~~~~q~~~l~~~~~IiV~TPgrL~~~l~~-~~~~l~~v~~l  274 (518)
T PLN00206        196 NPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSK-HDIELDNVSVL  274 (518)
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHHHhcCCCCEEEECHHHHHHHHHc-CCccchheeEE
Confidence            67999999999999999999999998888999888888877776677778899999999999999987 56788999999


Q ss_pred             EEeccccccccCChhH
Q psy4275         154 VLDEADRLSLMTSLKF  169 (182)
Q Consensus       154 I~DE~h~~~~~~~~~~  169 (182)
                      |+||||+|.++++...
T Consensus       275 ViDEad~ml~~gf~~~  290 (518)
T PLN00206        275 VLDEVDCMLERGFRDQ  290 (518)
T ss_pred             EeecHHHHhhcchHHH
Confidence            9999999999886554

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=100.00  E-value=1.3e-31  Score=222.11  Aligned_cols=172  Identities=38%  Similarity=0.559  Sum_probs=154.1

Q ss_pred             CCCccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEE
Q psy4275           1 MEDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVL   80 (182)
Q Consensus         1 ~~~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil   80 (182)
                      |.+...+|+++++++.+.+++.+.|+.+|+|+|.++++.+.+++++++++|||+|||.++.+++++.+.....++++||+
T Consensus         1 ~~~~~~~f~~l~L~~~ll~al~~~G~~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~~~~~~~LIL   80 (629)
T PRK11634          1 MAEFETTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVL   80 (629)
T ss_pred             CCcccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhccCCCeEEEE
Confidence            34667789999999999999999999999999999999999999999999999999999999999887665556799999


Q ss_pred             cCCHHHHHHHHHHHHHhhccC-CceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccc
Q psy4275          81 TPTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEAD  159 (182)
Q Consensus        81 ~p~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h  159 (182)
                      +|+++|+.|+++.++.+.+.. ++++..++|+.+...+...+..+++|+|+||+.+.+++.. +.+.+++++++|+||||
T Consensus        81 ~PTreLa~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l~~~~~IVVgTPgrl~d~l~r-~~l~l~~l~~lVlDEAd  159 (629)
T PRK11634         81 APTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKR-GTLDLSKLSGLVLDEAD  159 (629)
T ss_pred             eCcHHHHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHhcCCCCEEEECHHHHHHHHHc-CCcchhhceEEEeccHH
Confidence            999999999999999887765 7889999999887777777778899999999999999987 66788999999999999


Q ss_pred             cccccCChhHHHHH
Q psy4275         160 RLSLMTSLKFFFFF  173 (182)
Q Consensus       160 ~~~~~~~~~~~~~~  173 (182)
                      +|+++++.+.+..+
T Consensus       160 ~ml~~gf~~di~~I  173 (629)
T PRK11634        160 EMLRMGFIEDVETI  173 (629)
T ss_pred             HHhhcccHHHHHHH
Confidence            99999887665544

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=100.00  E-value=2.8e-31  Score=214.82  Aligned_cols=167  Identities=40%  Similarity=0.565  Sum_probs=150.3

Q ss_pred             cCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCH
Q psy4275           5 IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTR   84 (182)
Q Consensus         5 ~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~   84 (182)
                      +.+|+++++++.+.+.+.+.|+..|+|+|.++++.+.+|+++++++|||+|||.+|.++++..+.....+.+++|++|++
T Consensus         3 ~~~f~~l~l~~~l~~~l~~~g~~~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~~~~~~~lil~Ptr   82 (460)
T PRK11776          3 MTAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTR   82 (460)
T ss_pred             CCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhhccCCceEEEEeCCH
Confidence            46899999999999999999999999999999999999999999999999999999999999886655566899999999


Q ss_pred             HHHHHHHHHHHHhhccC-CceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275          85 ELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus        85 ~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      +|+.|+.+.++.+.+.. ++++..++|+.+...+...+..+++|+|+||+.+.+++++ +.+.+++++++|+||||+|.+
T Consensus        83 eLa~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~~~~~IvV~Tp~rl~~~l~~-~~~~l~~l~~lViDEad~~l~  161 (460)
T PRK11776         83 ELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHGAHIIVGTPGRILDHLRK-GTLDLDALNTLVLDEADRMLD  161 (460)
T ss_pred             HHHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhcCCCCEEEEChHHHHHHHHc-CCccHHHCCEEEEECHHHHhC
Confidence            99999999999987755 6899999999988777777778899999999999999987 666788999999999999999


Q ss_pred             cCChhHHHH
Q psy4275         164 MTSLKFFFF  172 (182)
Q Consensus       164 ~~~~~~~~~  172 (182)
                      .++...+..
T Consensus       162 ~g~~~~l~~  170 (460)
T PRK11776        162 MGFQDAIDA  170 (460)
T ss_pred             cCcHHHHHH
Confidence            887655443

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=2.7e-31  Score=218.84  Aligned_cols=166  Identities=36%  Similarity=0.535  Sum_probs=148.8

Q ss_pred             CccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCC-------CCeeEEE
Q psy4275           7 SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP-------YGIFALV   79 (182)
Q Consensus         7 ~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~-------~~~~~li   79 (182)
                      +|++|++++.+.+.|.+.|+..++|+|.++++.+++|+++++++|||+|||.+|++++++.+...+       ..+++||
T Consensus        10 ~f~~l~l~~~l~~~L~~~g~~~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~raLI   89 (572)
T PRK04537         10 TFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRALI   89 (572)
T ss_pred             ChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCceEEE
Confidence            599999999999999999999999999999999999999999999999999999999998875421       2468999


Q ss_pred             EcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccc
Q psy4275          80 LTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEAD  159 (182)
Q Consensus        80 l~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h  159 (182)
                      ++|+++|+.|+++.++.+....++++..++|+.....+...+.++++|+|+||+.+.+++...+.+.++.++++|+||||
T Consensus        90 l~PTreLa~Qi~~~~~~l~~~~~i~v~~l~Gg~~~~~q~~~l~~~~dIiV~TP~rL~~~l~~~~~~~l~~v~~lViDEAh  169 (572)
T PRK04537         90 LAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEAD  169 (572)
T ss_pred             EeCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHHhCCCCEEEECHHHHHHHHHhccccchhheeeeEecCHH
Confidence            99999999999999999999999999999999888777777777899999999999999987556678889999999999


Q ss_pred             cccccCChhHHHH
Q psy4275         160 RLSLMTSLKFFFF  172 (182)
Q Consensus       160 ~~~~~~~~~~~~~  172 (182)
                      +|.++++...+..
T Consensus       170 ~lld~gf~~~i~~  182 (572)
T PRK04537        170 RMFDLGFIKDIRF  182 (572)
T ss_pred             HHhhcchHHHHHH
Confidence            9999886654433

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.98  E-value=5e-31  Score=211.96  Aligned_cols=168  Identities=38%  Similarity=0.534  Sum_probs=150.5

Q ss_pred             CCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccC----CCCeeEEEEc
Q psy4275           6 KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCED----PYGIFALVLT   81 (182)
Q Consensus         6 ~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~----~~~~~~lil~   81 (182)
                      .+|+++++++.+.+.+.+.|+..|+++|.++++.+.+++++++++|||+|||.+|+++++..+...    ....+++|++
T Consensus         1 ~~f~~l~l~~~l~~~l~~~g~~~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~~lil~   80 (434)
T PRK11192          1 TTFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILT   80 (434)
T ss_pred             CCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCceEEEEC
Confidence            369999999999999999999999999999999999999999999999999999999999877542    2246899999


Q ss_pred             CCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccc
Q psy4275          82 PTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL  161 (182)
Q Consensus        82 p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~  161 (182)
                      |+++|+.|+++.+..+.+..++++..++|+.........+.++++|+|+||+.+.+++.. +.+.+++++++|+||||+|
T Consensus        81 Pt~eLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~Tp~rl~~~~~~-~~~~~~~v~~lViDEah~~  159 (434)
T PRK11192         81 PTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVFSENQDIVVATPGRLLQYIKE-ENFDCRAVETLILDEADRM  159 (434)
T ss_pred             CcHHHHHHHHHHHHHHHccCCcEEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHc-CCcCcccCCEEEEECHHHH
Confidence            999999999999999999999999999999887777777777899999999999999987 6677889999999999999


Q ss_pred             cccCChhHHHHHH
Q psy4275         162 SLMTSLKFFFFFF  174 (182)
Q Consensus       162 ~~~~~~~~~~~~~  174 (182)
                      .++++......+.
T Consensus       160 l~~~~~~~~~~i~  172 (434)
T PRK11192        160 LDMGFAQDIETIA  172 (434)
T ss_pred             hCCCcHHHHHHHH
Confidence            9998766655443

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.98  E-value=3.6e-31  Score=213.73  Aligned_cols=163  Identities=40%  Similarity=0.595  Sum_probs=146.9

Q ss_pred             CccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCC------CCeeEEEE
Q psy4275           7 SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP------YGIFALVL   80 (182)
Q Consensus         7 ~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~------~~~~~lil   80 (182)
                      +|++|++++++.+.+.+.|+..|+|+|.++++.+.+++++++++|||+|||.+|++++++.+....      ...++||+
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~~~~~aLil   81 (456)
T PRK10590          2 SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALIL   81 (456)
T ss_pred             CHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhcccccccCCCceEEEE
Confidence            799999999999999999999999999999999999999999999999999999999998875432      13479999


Q ss_pred             cCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccc
Q psy4275          81 TPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR  160 (182)
Q Consensus        81 ~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~  160 (182)
                      +|+++|+.|+.+.++.+.+..++++..+.|+.+...+...+.++++|+|+||+.+++++.. +.+.+++++++|+||||+
T Consensus        82 ~PtreLa~Qi~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~IiV~TP~rL~~~~~~-~~~~l~~v~~lViDEah~  160 (456)
T PRK10590         82 TPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLEHQ-NAVKLDQVEILVLDEADR  160 (456)
T ss_pred             eCcHHHHHHHHHHHHHHhccCCCEEEEEECCcCHHHHHHHHcCCCcEEEEChHHHHHHHHc-CCcccccceEEEeecHHH
Confidence            9999999999999999999989999999999887777667778899999999999999877 566789999999999999


Q ss_pred             ccccCChhHH
Q psy4275         161 LSLMTSLKFF  170 (182)
Q Consensus       161 ~~~~~~~~~~  170 (182)
                      |.++++...+
T Consensus       161 ll~~~~~~~i  170 (456)
T PRK10590        161 MLDMGFIHDI  170 (456)
T ss_pred             HhccccHHHH
Confidence            9998875443

>KOG0331|consensus

Probab=99.97  E-value=3.7e-31  Score=210.46  Aligned_cols=162  Identities=40%  Similarity=0.570  Sum_probs=153.4

Q ss_pred             CccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhcc------CCCCeeEEEE
Q psy4275           7 SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCE------DPYGIFALVL   80 (182)
Q Consensus         7 ~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~------~~~~~~~lil   80 (182)
                      .|+.++++++..+++...|+..|+|+|.+.|+.++.|++++..+.||+|||++|+++++.++.+      +++++++|++
T Consensus        92 ~f~~~~ls~~~~~~lk~~g~~~PtpIQaq~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLVL  171 (519)
T KOG0331|consen   92 AFQELGLSEELMKALKEQGFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVL  171 (519)
T ss_pred             hhhcccccHHHHHHHHhcCCCCCchhhhcccceeccCCceEEEeccCCcchhhhhhHHHHHHHhccccccCCCCCeEEEE
Confidence            6889999999999999999999999999999999999999999999999999999999998876      3457899999


Q ss_pred             cCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccc
Q psy4275          81 TPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR  160 (182)
Q Consensus        81 ~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~  160 (182)
                      +||++||.|+...+..+.+.+++++.+++|+.....+.+.+.++.+|+|+||+.+.++++. +...+++++++|+||||+
T Consensus       172 ~PTRELA~QV~~~~~~~~~~~~~~~~cvyGG~~~~~Q~~~l~~gvdiviaTPGRl~d~le~-g~~~l~~v~ylVLDEADr  250 (519)
T KOG0331|consen  172 APTRELAVQVQAEAREFGKSLRLRSTCVYGGAPKGPQLRDLERGVDVVIATPGRLIDLLEE-GSLNLSRVTYLVLDEADR  250 (519)
T ss_pred             cCcHHHHHHHHHHHHHHcCCCCccEEEEeCCCCccHHHHHHhcCCcEEEeCChHHHHHHHc-CCccccceeEEEeccHHh
Confidence            9999999999999999999999999999999999999999999999999999999999999 788999999999999999


Q ss_pred             ccccCChhH
Q psy4275         161 LSLMTSLKF  169 (182)
Q Consensus       161 ~~~~~~~~~  169 (182)
                      |++.++..-
T Consensus       251 MldmGFe~q  259 (519)
T KOG0331|consen  251 MLDMGFEPQ  259 (519)
T ss_pred             hhccccHHH
Confidence            999996543

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

Probab=99.97  E-value=2.3e-30  Score=210.97  Aligned_cols=170  Identities=41%  Similarity=0.593  Sum_probs=153.8

Q ss_pred             CCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhcc-CCCCee-EEEEcCC
Q psy4275           6 KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCE-DPYGIF-ALVLTPT   83 (182)
Q Consensus         6 ~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~-~~~~~~-~lil~p~   83 (182)
                      .+|+++++++++.+++.+.||..|+|+|.+++|.++.|++++.+++||+|||.+|.+++++.+.. ...... ++|++||
T Consensus        29 ~~F~~l~l~~~ll~~l~~~gf~~pt~IQ~~~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~~~~~~~aLil~PT  108 (513)
T COG0513          29 PEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPT  108 (513)
T ss_pred             CCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhcccccCCCceEEECCC
Confidence            57999999999999999999999999999999999999999999999999999999999999763 222222 9999999


Q ss_pred             HHHHHHHHHHHHHhhccC-CceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccc
Q psy4275          84 RELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLS  162 (182)
Q Consensus        84 ~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~  162 (182)
                      ++||.|+++.+..+.+.. ++++..++|+.+...+...+..+++|+|+||+++++++.. +.++++++.++|+||||+|+
T Consensus       109 RELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~~~~~ivVaTPGRllD~i~~-~~l~l~~v~~lVlDEADrmL  187 (513)
T COG0513         109 RELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKR-GKLDLSGVETLVLDEADRML  187 (513)
T ss_pred             HHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHhcCCCEEEECccHHHHHHHc-CCcchhhcCEEEeccHhhhh
Confidence            999999999999999998 7999999999998888888877899999999999999998 58899999999999999999


Q ss_pred             ccCChhHHHHHHHH
Q psy4275         163 LMTSLKFFFFFFFL  176 (182)
Q Consensus       163 ~~~~~~~~~~~~~~  176 (182)
                      +.++.+....+...
T Consensus       188 d~Gf~~~i~~I~~~  201 (513)
T COG0513         188 DMGFIDDIEKILKA  201 (513)
T ss_pred             cCCCHHHHHHHHHh
Confidence            99887766655443

>cd00268 DEADc DEAD-box helicases

Probab=99.97  E-value=7.9e-30  Score=185.66  Aligned_cols=165  Identities=46%  Similarity=0.664  Sum_probs=146.4

Q ss_pred             ccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccC--CCCeeEEEEcCCHH
Q psy4275           8 FTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCED--PYGIFALVLTPTRE   85 (182)
Q Consensus         8 ~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~--~~~~~~lil~p~~~   85 (182)
                      |+++++++.+.+.+...|+..++++|.++++.+.+++++++++|||+|||.+++++++..+...  ..+++++|++|+++
T Consensus         1 ~~~~~~~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~~~~~~~viii~p~~~   80 (203)
T cd00268           1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTRE   80 (203)
T ss_pred             CCcCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhhcccCCceEEEEcCCHH
Confidence            7899999999999999999999999999999999999999999999999999999999888776  45779999999999


Q ss_pred             HHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccC
Q psy4275          86 LAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus        86 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~  165 (182)
                      |+.|+.+.++.+....++++..++|+.........+.++++|+|+||+.+..++.+ ....+++++++|+||+|++.+.+
T Consensus        81 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~-~~~~~~~l~~lIvDE~h~~~~~~  159 (203)
T cd00268          81 LALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLER-GKLDLSKVKYLVLDEADRMLDMG  159 (203)
T ss_pred             HHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHc-CCCChhhCCEEEEeChHHhhccC
Confidence            99999999999988888999999998887666666666899999999999999887 44778899999999999998776


Q ss_pred             ChhHHHHH
Q psy4275         166 SLKFFFFF  173 (182)
Q Consensus       166 ~~~~~~~~  173 (182)
                      +......+
T Consensus       160 ~~~~~~~~  167 (203)
T cd00268         160 FEDQIREI  167 (203)
T ss_pred             hHHHHHHH
Confidence            55544443

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.

>KOG0338|consensus

Probab=99.97  E-value=3.8e-31  Score=206.74  Aligned_cols=174  Identities=43%  Similarity=0.615  Sum_probs=160.7

Q ss_pred             cCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCC---eeEEEEc
Q psy4275           5 IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYG---IFALVLT   81 (182)
Q Consensus         5 ~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~---~~~lil~   81 (182)
                      ..+|.+++|+-.+.+++...||..|+|+|..++|-.+-|++++.|+.||+|||.+|++|++++++-++.+   -++||++
T Consensus       180 ~~sF~~mNLSRPlLka~~~lGy~~PTpIQ~a~IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~~~~TRVLVL~  259 (691)
T KOG0338|consen  180 NESFQSMNLSRPLLKACSTLGYKKPTPIQVATIPVALLGKDICACAATGSGKTAAFALPILERLLYRPKKVAATRVLVLV  259 (691)
T ss_pred             hhhHHhcccchHHHHHHHhcCCCCCCchhhhcccHHhhcchhhheecccCCchhhhHHHHHHHHhcCcccCcceeEEEEe
Confidence            5688999999999999999999999999999999999999999999999999999999999999877643   5899999


Q ss_pred             CCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccc
Q psy4275          82 PTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL  161 (182)
Q Consensus        82 p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~  161 (182)
                      ||++|+.|++...+++..++++.++++.|+.+...+.+.+.+.++|+|+||++|.++++....++++++..+|+||||+|
T Consensus       260 PTRELaiQv~sV~~qlaqFt~I~~~L~vGGL~lk~QE~~LRs~PDIVIATPGRlIDHlrNs~sf~ldsiEVLvlDEADRM  339 (691)
T KOG0338|consen  260 PTRELAIQVHSVTKQLAQFTDITVGLAVGGLDLKAQEAVLRSRPDIVIATPGRLIDHLRNSPSFNLDSIEVLVLDEADRM  339 (691)
T ss_pred             ccHHHHHHHHHHHHHHHhhccceeeeeecCccHHHHHHHHhhCCCEEEecchhHHHHhccCCCccccceeEEEechHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999988999999999999999999


Q ss_pred             cccCChhHHHHHHHHhhcCC
Q psy4275         162 SLMTSLKFFFFFFFLKYYIP  181 (182)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~~~  181 (182)
                      ++.++..-   +.++.++.|
T Consensus       340 LeegFade---mnEii~lcp  356 (691)
T KOG0338|consen  340 LEEGFADE---MNEIIRLCP  356 (691)
T ss_pred             HHHHHHHH---HHHHHHhcc
Confidence            99987654   444444443

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.97  E-value=1.2e-29  Score=206.02  Aligned_cols=164  Identities=37%  Similarity=0.514  Sum_probs=144.8

Q ss_pred             ccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCC-------Cee
Q psy4275           4 PIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPY-------GIF   76 (182)
Q Consensus         4 ~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~-------~~~   76 (182)
                      ....|.++++++.+.+++.+.|+..++++|.++++.+.+|+|+++++|||+|||++|+++++..+.+.+.       ..+
T Consensus        85 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~~  164 (475)
T PRK01297         85 GKTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPR  164 (475)
T ss_pred             CCCCHhHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCce
Confidence            4567899999999999999999999999999999999999999999999999999999999998866431       468


Q ss_pred             EEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhc-CCCcEEEEChHHHHHHHhcCCCCCCCCccEEEE
Q psy4275          77 ALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA-KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVL  155 (182)
Q Consensus        77 ~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~  155 (182)
                      ++|++|+++|+.|+.+.++.+.+..++++..++|+.........+. +.++|+|+||++++++... ....+++++++|+
T Consensus       165 aLil~PtreLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~~~~~~~~Iiv~TP~~Ll~~~~~-~~~~l~~l~~lVi  243 (475)
T PRK01297        165 ALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQR-GEVHLDMVEVMVL  243 (475)
T ss_pred             EEEEeCcHHHHHHHHHHHHHhhccCCCEEEEEEccCChHHHHHHHhCCCCCEEEECHHHHHHHHHc-CCcccccCceEEe
Confidence            9999999999999999999999999999999999877665555543 4689999999999998877 4567889999999


Q ss_pred             eccccccccCChh
Q psy4275         156 DEADRLSLMTSLK  168 (182)
Q Consensus       156 DE~h~~~~~~~~~  168 (182)
                      ||+|++.+.++..
T Consensus       244 DEah~l~~~~~~~  256 (475)
T PRK01297        244 DEADRMLDMGFIP  256 (475)
T ss_pred             chHHHHHhcccHH
Confidence            9999999887644

>KOG0340|consensus

Probab=99.97  E-value=1.2e-30  Score=196.05  Aligned_cols=172  Identities=57%  Similarity=0.937  Sum_probs=161.5

Q ss_pred             CccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcC
Q psy4275           3 DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTP   82 (182)
Q Consensus         3 ~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p   82 (182)
                      ....+|+.||+++|+.+.++..|+..|+|.|..|+|.++.|++++-++.||+|||.++.+++++++...+.+.++++++|
T Consensus         4 ~t~~~F~~LGl~~Wlve~l~~l~i~~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLsedP~giFalvlTP   83 (442)
T KOG0340|consen    4 KTAKPFSILGLSPWLVEQLKALGIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSEDPYGIFALVLTP   83 (442)
T ss_pred             cccCchhhcCccHHHHHHHHHhcCCCCCchHhhhhHHHhcccccccccccCCCcchhhhHHHHHhhccCCCcceEEEecc
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcC---CCCCCCCccEEEEeccc
Q psy4275          83 TRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTC---NTFSLNRIKFLVLDEAD  159 (182)
Q Consensus        83 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~---~~~~~~~~~~iI~DE~h  159 (182)
                      |++|+-|+++.+..+++..+.+++++.|+++...+...+..+++++|+||+.+.+++...   ..+.++++.++|+|||+
T Consensus        84 TrELA~QiaEQF~alGk~l~lK~~vivGG~d~i~qa~~L~~rPHvVvatPGRlad~l~sn~~~~~~~~~rlkflVlDEAD  163 (442)
T KOG0340|consen   84 TRELALQIAEQFIALGKLLNLKVSVIVGGTDMIMQAAILSDRPHVVVATPGRLADHLSSNLGVCSWIFQRLKFLVLDEAD  163 (442)
T ss_pred             hHHHHHHHHHHHHHhcccccceEEEEEccHHHhhhhhhcccCCCeEecCccccccccccCCccchhhhhceeeEEecchh
Confidence            999999999999999999999999999999999999999999999999999999999885   34578889999999999


Q ss_pred             cccccCChhHHHHHH
Q psy4275         160 RLSLMTSLKFFFFFF  174 (182)
Q Consensus       160 ~~~~~~~~~~~~~~~  174 (182)
                      .|++..+...+.-+.
T Consensus       164 rvL~~~f~d~L~~i~  178 (442)
T KOG0340|consen  164 RVLAGCFPDILEGIE  178 (442)
T ss_pred             hhhccchhhHHhhhh
Confidence            999998877766554

>KOG0348|consensus

Probab=99.97  E-value=3.6e-30  Score=202.21  Aligned_cols=172  Identities=39%  Similarity=0.558  Sum_probs=156.8

Q ss_pred             CCccCCCCCHHHHHHHHH-CCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccC------CCCeeEE
Q psy4275           6 KSFTDLKLNPWLIRQCQT-IGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCED------PYGIFAL   78 (182)
Q Consensus         6 ~~~~~~~l~~~i~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~------~~~~~~l   78 (182)
                      ..|..+|+++.+...+.. .++..|+..|++++|.+++|+++++.++||+|||++|++++.+.+.+.      .+|+.++
T Consensus       136 ~~f~~LGL~~~lv~~L~~~m~i~~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~G~~AL  215 (708)
T KOG0348|consen  136 AAFASLGLHPHLVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRSDGPYAL  215 (708)
T ss_pred             ccchhcCCCHHHHHHHHHHhccCccchHhhcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCccccccCCceEE
Confidence            468899999999999975 699999999999999999999999999999999999999999987653      4588999


Q ss_pred             EEcCCHHHHHHHHHHHHHhhccCCceE-EEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEec
Q psy4275          79 VLTPTRELAYQIGDQFLVLGKVMNLRV-SIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDE  157 (182)
Q Consensus        79 il~p~~~l~~q~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE  157 (182)
                      |++||++|+.|+++.+.++.+.+.+-| +.+.|+.....+.+.+.++++|+|+||+++++++++...+.+++++++|+||
T Consensus       216 VivPTREL~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARLRKGiNILIgTPGRLvDHLknT~~i~~s~LRwlVlDE  295 (708)
T KOG0348|consen  216 VIVPTRELALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKARLRKGINILIGTPGRLVDHLKNTKSIKFSRLRWLVLDE  295 (708)
T ss_pred             EEechHHHHHHHHHHHHHHhcCceEEeeceeecccccccHHHHHhcCceEEEcCchHHHHHHhccchheeeeeeEEEecc
Confidence            999999999999999999999877655 6778888888888899999999999999999999998999999999999999


Q ss_pred             cccccccCChhHHHHHHHHh
Q psy4275         158 ADRLSLMTSLKFFFFFFFLK  177 (182)
Q Consensus       158 ~h~~~~~~~~~~~~~~~~~~  177 (182)
                      +|.+++.++-+.+..+....
T Consensus       296 aDrlleLGfekdit~Il~~v  315 (708)
T KOG0348|consen  296 ADRLLELGFEKDITQILKAV  315 (708)
T ss_pred             hhHHHhccchhhHHHHHHHH
Confidence            99999999988887776655

>PTZ00424 helicase 45; Provisional

Probab=99.97  E-value=1.9e-29  Score=200.90  Aligned_cols=164  Identities=36%  Similarity=0.511  Sum_probs=145.8

Q ss_pred             ccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275           4 PIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus         4 ~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      ...+|+++++++.+.+.+.++|+..|+|+|.++++.+.++++.++++|||+|||.+++++++..+.....+.+++|++|+
T Consensus        26 ~~~~~~~l~l~~~~~~~l~~~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~~~~~~~lil~Pt  105 (401)
T PTZ00424         26 IVDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDLNACQALILAPT  105 (401)
T ss_pred             ccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCCCCCceEEEECCC
Confidence            45789999999999999999999999999999999999999999999999999999999999887654456789999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275          84 RELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus        84 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      ++|+.|+.+.+..+....+..+..+.|+.........+.++++|+|+||+.+.+.+.. +...+++++++|+||+|++.+
T Consensus       106 ~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~-~~~~l~~i~lvViDEah~~~~  184 (401)
T PTZ00424        106 RELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDK-RHLRVDDLKLFILDEADEMLS  184 (401)
T ss_pred             HHHHHHHHHHHHHHhhhcCceEEEEECCcCHHHHHHHHcCCCCEEEECcHHHHHHHHh-CCcccccccEEEEecHHHHHh
Confidence            9999999999999988888888888888776666666667889999999999998876 556788999999999999998


Q ss_pred             cCChh
Q psy4275         164 MTSLK  168 (182)
Q Consensus       164 ~~~~~  168 (182)
                      +++..
T Consensus       185 ~~~~~  189 (401)
T PTZ00424        185 RGFKG  189 (401)
T ss_pred             cchHH
Confidence            77654

>PRK02362 ski2-like helicase; Provisional

Probab=99.96  E-value=1.1e-27  Score=203.04  Aligned_cols=165  Identities=24%  Similarity=0.294  Sum_probs=138.7

Q ss_pred             CCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhh-hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCH
Q psy4275           6 KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPH-VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTR   84 (182)
Q Consensus         6 ~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~-~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~   84 (182)
                      ++|+++++++++.+.+.+.|+.+++|+|.++++. +..|+|+++++|||+|||.++.++++..+..   +.+++|++|++
T Consensus         1 ~~~~~l~lp~~~~~~l~~~g~~~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~~---~~kal~i~P~r   77 (737)
T PRK02362          1 MKIAELPLPEGVIEFYEAEGIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIAR---GGKALYIVPLR   77 (737)
T ss_pred             CChhhcCCCHHHHHHHHhCCCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHhc---CCcEEEEeChH
Confidence            4689999999999999999999999999999988 6779999999999999999999999988754   56899999999


Q ss_pred             HHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccccc
Q psy4275          85 ELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus        85 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~  164 (182)
                      +|+.|.++.++++.. .++++..++|+.....   .....++|+|+||+++..++++ ....+++++++|+||+|.+.+.
T Consensus        78 aLa~q~~~~~~~~~~-~g~~v~~~tGd~~~~~---~~l~~~~IiV~Tpek~~~llr~-~~~~l~~v~lvViDE~H~l~d~  152 (737)
T PRK02362         78 ALASEKFEEFERFEE-LGVRVGISTGDYDSRD---EWLGDNDIIVATSEKVDSLLRN-GAPWLDDITCVVVDEVHLIDSA  152 (737)
T ss_pred             HHHHHHHHHHHHhhc-CCCEEEEEeCCcCccc---cccCCCCEEEECHHHHHHHHhc-ChhhhhhcCEEEEECccccCCC
Confidence            999999999987653 5899999999875433   2235689999999999999886 3345788999999999999987


Q ss_pred             CChhHHHH-HHHHhh
Q psy4275         165 TSLKFFFF-FFFLKY  178 (182)
Q Consensus       165 ~~~~~~~~-~~~~~~  178 (182)
                      +....++. +.++++
T Consensus       153 ~rg~~le~il~rl~~  167 (737)
T PRK02362        153 NRGPTLEVTLAKLRR  167 (737)
T ss_pred             cchHHHHHHHHHHHh
Confidence            65554444 455544

>KOG0345|consensus

Probab=99.96  E-value=1.3e-27  Score=185.34  Aligned_cols=173  Identities=38%  Similarity=0.554  Sum_probs=145.8

Q ss_pred             CCccCCC--CCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCC-----CCeeEE
Q psy4275           6 KSFTDLK--LNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP-----YGIFAL   78 (182)
Q Consensus         6 ~~~~~~~--l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~-----~~~~~l   78 (182)
                      ..|++++  |++++.+++...|+...+|.|..++|.+.+++++++.++||||||++|++|+++.+.++.     ...-++
T Consensus         4 ~~~~~l~~~L~~~l~~~l~~~GF~~mTpVQa~tIPlll~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vgal   83 (567)
T KOG0345|consen    4 KSFSSLAPPLSPWLLEALDESGFEKMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGAL   83 (567)
T ss_pred             cchhhcCCCccHHHHHHHHhcCCcccCHHHHhhhHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCccceeEE
Confidence            4677775  559999999999999999999999999999999999999999999999999999985532     123689


Q ss_pred             EEcCCHHHHHHHHHHHHHhhcc-CCceEEEEEcCCchhhhhHHh-cCCCcEEEEChHHHHHHHhc-CCCCCCCCccEEEE
Q psy4275          79 VLTPTRELAYQIGDQFLVLGKV-MNLRVSIITGGMDMVDQGKEL-AKKPHIVIATPGRLADHLDT-CNTFSLNRIKFLVL  155 (182)
Q Consensus        79 il~p~~~l~~q~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~-~~~~~Ilv~T~~~l~~~~~~-~~~~~~~~~~~iI~  155 (182)
                      ||+||++|+.|+.+.+..+... .++++.++.|+.+.......+ .++++|+||||+++.+++++ ...++++++.++|+
T Consensus        84 IIsPTRELa~QI~~V~~~F~~~l~~l~~~l~vGG~~v~~Di~~fkee~~nIlVgTPGRL~di~~~~~~~l~~rsLe~LVL  163 (567)
T KOG0345|consen   84 IISPTRELARQIREVAQPFLEHLPNLNCELLVGGRSVEEDIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRSLEILVL  163 (567)
T ss_pred             EecCcHHHHHHHHHHHHHHHHhhhccceEEEecCccHHHHHHHHHHhCCcEEEeCchhHHHHHhchhhhccccccceEEe
Confidence            9999999999999999988777 578889999997765544444 45789999999999999987 34567889999999


Q ss_pred             eccccccccCChhHHHHHHHHhhcCC
Q psy4275         156 DEADRLSLMTSLKFFFFFFFLKYYIP  181 (182)
Q Consensus       156 DE~h~~~~~~~~~~~~~~~~~~~~~~  181 (182)
                      ||||.+++.++.+..   ..+...||
T Consensus       164 DEADrLldmgFe~~~---n~ILs~LP  186 (567)
T KOG0345|consen  164 DEADRLLDMGFEASV---NTILSFLP  186 (567)
T ss_pred             cchHhHhcccHHHHH---HHHHHhcc
Confidence            999999999987654   44555555

>KOG0339|consensus

Probab=99.96  E-value=3e-28  Score=190.60  Aligned_cols=166  Identities=39%  Similarity=0.557  Sum_probs=156.7

Q ss_pred             CCCccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccC-----CCCe
Q psy4275           1 MEDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCED-----PYGI   75 (182)
Q Consensus         1 ~~~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~-----~~~~   75 (182)
                      .|+++..|+.+++++.+..+.++..+..++|+|.++++..+.|++++-.+-||+|||.+++.+++..+...     ++++
T Consensus       218 ~~rpvtsfeh~gfDkqLm~airk~Ey~kptpiq~qalptalsgrdvigIAktgSgktaAfi~pm~~himdq~eL~~g~gP  297 (731)
T KOG0339|consen  218 PPRPVTSFEHFGFDKQLMTAIRKSEYEKPTPIQCQALPTALSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPELKPGEGP  297 (731)
T ss_pred             CCCCcchhhhcCchHHHHHHHhhhhcccCCcccccccccccccccchheeeccCcchhHHHHHHHHHhcchhhhcCCCCC
Confidence            47899999999999999999999999999999999999999999999999999999999999998877653     4588


Q ss_pred             eEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEE
Q psy4275          76 FALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVL  155 (182)
Q Consensus        76 ~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~  155 (182)
                      ..+|++||++|+.|++.+++++.+..++++++++|+.+.+++...+..++.|+|+||+++.++++. +..++.+++++|+
T Consensus       298 i~vilvPTrela~Qi~~eaKkf~K~ygl~~v~~ygGgsk~eQ~k~Lk~g~EivVaTPgRlid~Vkm-Katn~~rvS~LV~  376 (731)
T KOG0339|consen  298 IGVILVPTRELASQIFSEAKKFGKAYGLRVVAVYGGGSKWEQSKELKEGAEIVVATPGRLIDMVKM-KATNLSRVSYLVL  376 (731)
T ss_pred             eEEEEeccHHHHHHHHHHHHHhhhhccceEEEeecCCcHHHHHHhhhcCCeEEEechHHHHHHHHh-hcccceeeeEEEE
Confidence            999999999999999999999999999999999999999999999999999999999999999988 7788999999999


Q ss_pred             eccccccccCCh
Q psy4275         156 DEADRLSLMTSL  167 (182)
Q Consensus       156 DE~h~~~~~~~~  167 (182)
                      ||+++|.+.++-
T Consensus       377 DEadrmfdmGfe  388 (731)
T KOG0339|consen  377 DEADRMFDMGFE  388 (731)
T ss_pred             echhhhhccccH
Confidence            999999999874

>KOG0328|consensus

Probab=99.95  E-value=2.9e-28  Score=178.77  Aligned_cols=175  Identities=34%  Similarity=0.517  Sum_probs=159.7

Q ss_pred             CccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcC
Q psy4275           3 DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTP   82 (182)
Q Consensus         3 ~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p   82 (182)
                      +++++|+++|+++++.+..-..|++.|..+|+.+++.+++|++++.++.+|+|||..+.+.++..+.-+...-+++++.|
T Consensus        24 ~v~~~F~~Mgl~edlLrgiY~yGfekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~~si~vlq~~d~~~r~tQ~lilsP  103 (400)
T KOG0328|consen   24 KVIPTFDDMGLKEDLLRGIYAYGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSISVLQSLDISVRETQALILSP  103 (400)
T ss_pred             ccccchhhcCchHHHHHHHHHhccCCchHHHhhhhhhhhcccceEEEecCCCCceEEEEeeeeeecccccceeeEEEecC
Confidence            56889999999999999999999999999999999999999999999999999999998888887766655679999999


Q ss_pred             CHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccc
Q psy4275          83 TRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLS  162 (182)
Q Consensus        83 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~  162 (182)
                      +++|+.|+.+.+..++...++.+..+.|+++.-+....+.-+.+++.+||++++++++. +.++-+.+.++|+||+|.|+
T Consensus       104 TRELa~Qi~~vi~alg~~mnvq~hacigg~n~gedikkld~G~hvVsGtPGrv~dmikr-~~L~tr~vkmlVLDEaDemL  182 (400)
T KOG0328|consen  104 TRELAVQIQKVILALGDYMNVQCHACIGGKNLGEDIKKLDYGQHVVSGTPGRVLDMIKR-RSLRTRAVKMLVLDEADEML  182 (400)
T ss_pred             hHHHHHHHHHHHHHhcccccceEEEEecCCccchhhhhhcccceEeeCCCchHHHHHHh-ccccccceeEEEeccHHHHH
Confidence            99999999999999999999999999999998777777777899999999999999998 67788899999999999999


Q ss_pred             ccCChhHHHHHHHHhhcCC
Q psy4275         163 LMTSLKFFFFFFFLKYYIP  181 (182)
Q Consensus       163 ~~~~~~~~~~~~~~~~~~~  181 (182)
                      +.++   ...+..+-+|+|
T Consensus       183 ~kgf---k~Qiydiyr~lp  198 (400)
T KOG0328|consen  183 NKGF---KEQIYDIYRYLP  198 (400)
T ss_pred             HhhH---HHHHHHHHHhCC
Confidence            9954   467777777777

>KOG0343|consensus

Probab=99.95  E-value=5.8e-28  Score=190.54  Aligned_cols=174  Identities=37%  Similarity=0.539  Sum_probs=156.7

Q ss_pred             ccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccC----CCCeeEEE
Q psy4275           4 PIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCED----PYGIFALV   79 (182)
Q Consensus         4 ~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~----~~~~~~li   79 (182)
                      .+..|++||++....+.|+..++..++..|+++++..+.|++++-.+.||+|||++++.++++.+++.    .+|--+||
T Consensus        67 ~~~kF~dlpls~~t~kgLke~~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~kWs~~DGlGalI  146 (758)
T KOG0343|consen   67 TIKKFADLPLSQKTLKGLKEAKFVKMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLKWSPTDGLGALI  146 (758)
T ss_pred             hhhhHHhCCCchHHHHhHhhcCCccHHHHHHhhcchhccCcccccccccCCCceeeehHHHHHHHHHcCCCCCCCceeEE
Confidence            45689999999999999999999999999999999999999999999999999999999999998764    35667999


Q ss_pred             EcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccc
Q psy4275          80 LTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEAD  159 (182)
Q Consensus        80 l~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h  159 (182)
                      |.||++||.|..+.+.++++..++..+++.|+.....+...+ ++.+|+||||+++++++.+...++.+++.++|+||||
T Consensus       147 ISPTRELA~QtFevL~kvgk~h~fSaGLiiGG~~~k~E~eRi-~~mNILVCTPGRLLQHmde~~~f~t~~lQmLvLDEAD  225 (758)
T KOG0343|consen  147 ISPTRELALQTFEVLNKVGKHHDFSAGLIIGGKDVKFELERI-SQMNILVCTPGRLLQHMDENPNFSTSNLQMLVLDEAD  225 (758)
T ss_pred             ecchHHHHHHHHHHHHHHhhccccccceeecCchhHHHHHhh-hcCCeEEechHHHHHHhhhcCCCCCCcceEEEeccHH
Confidence            999999999999999999999999999999999866555443 6789999999999999999888899999999999999


Q ss_pred             cccccCChhHHHHHHHHhhcCC
Q psy4275         160 RLSLMTSLKFFFFFFFLKYYIP  181 (182)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~~~~~  181 (182)
                      +|+++++...++.   +..+||
T Consensus       226 R~LDMGFk~tL~~---Ii~~lP  244 (758)
T KOG0343|consen  226 RMLDMGFKKTLNA---IIENLP  244 (758)
T ss_pred             HHHHHhHHHHHHH---HHHhCC
Confidence            9999998876554   445554

>KOG0342|consensus

Probab=99.95  E-value=1.5e-27  Score=185.77  Aligned_cols=172  Identities=37%  Similarity=0.496  Sum_probs=157.9

Q ss_pred             cCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccC----CCCeeEEEE
Q psy4275           5 IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCED----PYGIFALVL   80 (182)
Q Consensus         5 ~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~----~~~~~~lil   80 (182)
                      ...|+.+.+++...+++...|+...++.|...++-++.|++++..+-||+|||+++++++++.+...    ..+..++|+
T Consensus        81 ~~~f~~~~LS~~t~kAi~~~GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r~~~~vlIi  160 (543)
T KOG0342|consen   81 TFRFEEGSLSPLTLKAIKEMGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFKPRNGTGVLII  160 (543)
T ss_pred             hhHhhccccCHHHHHHHHhcCccchhHHHHhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhcccCCCCCeeEEEe
Confidence            3457888999999999999999999999999999999999999999999999999999999988764    245689999


Q ss_pred             cCCHHHHHHHHHHHHHhhccC-CceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccc
Q psy4275          81 TPTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEAD  159 (182)
Q Consensus        81 ~p~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h  159 (182)
                      +||++|+.|.+.+++.+.+.. ++.+..+.|+.+.......+.++++|+|+||+.+++++++.+.+..++++++|+||||
T Consensus       161 ~PTRELA~Q~~~eak~Ll~~h~~~~v~~viGG~~~~~e~~kl~k~~niliATPGRLlDHlqNt~~f~~r~~k~lvlDEAD  240 (543)
T KOG0342|consen  161 CPTRELAMQIFAEAKELLKYHESITVGIVIGGNNFSVEADKLVKGCNILIATPGRLLDHLQNTSGFLFRNLKCLVLDEAD  240 (543)
T ss_pred             cccHHHHHHHHHHHHHHHhhCCCcceEEEeCCccchHHHHHhhccccEEEeCCchHHhHhhcCCcchhhccceeEeecch
Confidence            999999999999999999988 8999999999998888888888999999999999999999888888899999999999


Q ss_pred             cccccCChhHHHHHHHH
Q psy4275         160 RLSLMTSLKFFFFFFFL  176 (182)
Q Consensus       160 ~~~~~~~~~~~~~~~~~  176 (182)
                      ++++.++.+.+..+..+
T Consensus       241 rlLd~GF~~di~~Ii~~  257 (543)
T KOG0342|consen  241 RLLDIGFEEDVEQIIKI  257 (543)
T ss_pred             hhhhcccHHHHHHHHHh
Confidence            99999999887776543

>KOG0346|consensus

Probab=99.95  E-value=8.8e-28  Score=185.11  Aligned_cols=173  Identities=34%  Similarity=0.467  Sum_probs=149.6

Q ss_pred             CCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccC------CCCeeEEE
Q psy4275           6 KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCED------PYGIFALV   79 (182)
Q Consensus         6 ~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~------~~~~~~li   79 (182)
                      .+|++|++++.+.+++.+.|+..|+-+|..++|..+.|++++..+-||+|||.+|+++++..+.+.      +.++.++|
T Consensus        19 ktFe~~gLD~RllkAi~~lG~ekpTlIQs~aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~sa~i   98 (569)
T KOG0346|consen   19 KTFEEFGLDSRLLKAITKLGWEKPTLIQSSAIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSAVI   98 (569)
T ss_pred             ccHHHhCCCHHHHHHHHHhCcCCcchhhhcccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhhhcccccccceeEE
Confidence            589999999999999999999999999999999999999999999999999999999999988753      45788999


Q ss_pred             EcCCHHHHHHHHHHHHHhhccCC--ceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEec
Q psy4275          80 LTPTRELAYQIGDQFLVLGKVMN--LRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDE  157 (182)
Q Consensus        80 l~p~~~l~~q~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE  157 (182)
                      ++||++|+.|+++.+.++...++  +++.-+.++.+.......+...++|+|+||++++.++........+.++++|+||
T Consensus        99 LvPTkEL~qQvy~viekL~~~c~k~lr~~nl~s~~sdsv~~~~L~d~pdIvV~TP~~ll~~~~~~~~~~~~~l~~LVvDE  178 (569)
T KOG0346|consen   99 LVPTKELAQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNSVALMDLPDIVVATPAKLLRHLAAGVLEYLDSLSFLVVDE  178 (569)
T ss_pred             EechHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccchHHHHHHHccCCCeEEeChHHHHHHHhhccchhhhheeeEEech
Confidence            99999999999999999988775  4455555455555555667778999999999999999885446888999999999


Q ss_pred             cccccccCChhHHHHHHHHhhcCC
Q psy4275         158 ADRLSLMTSLKFFFFFFFLKYYIP  181 (182)
Q Consensus       158 ~h~~~~~~~~~~~~~~~~~~~~~~  181 (182)
                      ||.+++.+|-+   -+.++.+.||
T Consensus       179 ADLllsfGYee---dlk~l~~~LP  199 (569)
T KOG0346|consen  179 ADLLLSFGYEE---DLKKLRSHLP  199 (569)
T ss_pred             hhhhhhcccHH---HHHHHHHhCC
Confidence            99999998855   4566666666

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

Probab=99.95  E-value=2e-26  Score=194.57  Aligned_cols=174  Identities=20%  Similarity=0.257  Sum_probs=138.4

Q ss_pred             CCccCCccCCC--CCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEE
Q psy4275           2 EDPIKSFTDLK--LNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALV   79 (182)
Q Consensus         2 ~~~~~~~~~~~--l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~li   79 (182)
                      |.....+.+++  +++++.+++.+.|+..|+++|.++++.+.+|+|+++++|||||||.+|.+++++.+.+++ +.++||
T Consensus         8 p~~~a~~~~~~~~l~~~l~~~L~~~g~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~~~-~~~aL~   86 (742)
T TIGR03817         8 PARAGRTAPWPAWAHPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADDP-RATALY   86 (742)
T ss_pred             CCCCcccCCCCCcCCHHHHHHHHHcCCCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhhCC-CcEEEE
Confidence            34445566654  899999999999999999999999999999999999999999999999999999887644 569999


Q ss_pred             EcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhc-CCC--CCCCCccEEEEe
Q psy4275          80 LTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDT-CNT--FSLNRIKFLVLD  156 (182)
Q Consensus        80 l~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~-~~~--~~~~~~~~iI~D  156 (182)
                      ++|+++|+.|+.+.++.+. ..++++..+.|+....++ ..+.++++|+|+||+.+...+-. ...  ..+++++++|+|
T Consensus        87 l~PtraLa~q~~~~l~~l~-~~~i~v~~~~Gdt~~~~r-~~i~~~~~IivtTPd~L~~~~L~~~~~~~~~l~~l~~vViD  164 (742)
T TIGR03817        87 LAPTKALAADQLRAVRELT-LRGVRPATYDGDTPTEER-RWAREHARYVLTNPDMLHRGILPSHARWARFLRRLRYVVID  164 (742)
T ss_pred             EcChHHHHHHHHHHHHHhc-cCCeEEEEEeCCCCHHHH-HHHhcCCCEEEEChHHHHHhhccchhHHHHHHhcCCEEEEe
Confidence            9999999999999999886 447888889998875443 44556789999999998753321 111  137789999999


Q ss_pred             ccccccccCChhHHHHHHHHhh
Q psy4275         157 EADRLSLMTSLKFFFFFFFLKY  178 (182)
Q Consensus       157 E~h~~~~~~~~~~~~~~~~~~~  178 (182)
                      |+|.|.+.........+.++++
T Consensus       165 Eah~~~g~fg~~~~~il~rL~r  186 (742)
T TIGR03817       165 ECHSYRGVFGSHVALVLRRLRR  186 (742)
T ss_pred             ChhhccCccHHHHHHHHHHHHH
Confidence            9999976433344444444443

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.

>KOG0335|consensus

Probab=99.95  E-value=1.3e-27  Score=187.79  Aligned_cols=172  Identities=34%  Similarity=0.467  Sum_probs=155.3

Q ss_pred             CCccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCC---------
Q psy4275           2 EDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP---------   72 (182)
Q Consensus         2 ~~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~---------   72 (182)
                      |.++..|++-.+.+.+....+..++..++|+|+.+++.+..|++.++||+||+|||.+++++++..+....         
T Consensus        70 p~~i~~f~~~~l~~~l~~ni~~~~~~~ptpvQk~sip~i~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~~~~~~~~~  149 (482)
T KOG0335|consen   70 PPHIPTFDEAILGEALAGNIKRSGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAAFLIPIISYLLDEGPEDRGESGG  149 (482)
T ss_pred             CCCcccccccchhHHHhhccccccccCCCcceeeccceeecCCceEEEccCCCcchHHHHHHHHHHHHhcCcccCcccCC
Confidence            56777888888999999999999999999999999999999999999999999999999999999887642         


Q ss_pred             -CCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCcc
Q psy4275          73 -YGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIK  151 (182)
Q Consensus        73 -~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~  151 (182)
                       ..++++|++||++|++|++++.+++.-..+.+.+..+|+.+.-.+.+.+..+|+|+|+||+++.+++.. +.+.+.+++
T Consensus       150 ~~~P~~lIlapTReL~~Qi~nea~k~~~~s~~~~~~~ygg~~~~~q~~~~~~gcdIlvaTpGrL~d~~e~-g~i~l~~~k  228 (482)
T KOG0335|consen  150 GVYPRALILAPTRELVDQIYNEARKFSYLSGMKSVVVYGGTDLGAQLRFIKRGCDILVATPGRLKDLIER-GKISLDNCK  228 (482)
T ss_pred             CCCCceEEEeCcHHHhhHHHHHHHhhcccccceeeeeeCCcchhhhhhhhccCccEEEecCchhhhhhhc-ceeehhhCc
Confidence             148999999999999999999999999999999999999888888888889999999999999999988 888899999


Q ss_pred             EEEEeccccccc-cCChhHHHHHH
Q psy4275         152 FLVLDEADRLSL-MTSLKFFFFFF  174 (182)
Q Consensus       152 ~iI~DE~h~~~~-~~~~~~~~~~~  174 (182)
                      ++|+||||.|+| .++-..+..+.
T Consensus       229 ~~vLDEADrMlD~mgF~p~Ir~iv  252 (482)
T KOG0335|consen  229 FLVLDEADRMLDEMGFEPQIRKIV  252 (482)
T ss_pred             EEEecchHHhhhhccccccHHHHh
Confidence            999999999999 66665555443

>PRK00254 ski2-like helicase; Provisional

Probab=99.95  E-value=2.2e-26  Score=194.84  Aligned_cols=160  Identities=24%  Similarity=0.297  Sum_probs=136.2

Q ss_pred             CccCCCCCHHHHHHHHHCCCCCChHHHHhhhhh-hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHH
Q psy4275           7 SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPH-VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRE   85 (182)
Q Consensus         7 ~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~-~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~   85 (182)
                      +|+++++++.+.+.+.+.|+..++|+|.++++. +..|+|+++++|||+|||.++.++++..+..+  +.+++|++|+++
T Consensus         2 ~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~~--~~~~l~l~P~~a   79 (720)
T PRK00254          2 KVDELRVDERIKRVLKERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLRE--GGKAVYLVPLKA   79 (720)
T ss_pred             cHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHhc--CCeEEEEeChHH
Confidence            688999999999999999999999999999986 78899999999999999999999998887654  568999999999


Q ss_pred             HHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccC
Q psy4275          86 LAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus        86 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~  165 (182)
                      |+.|.++.++.+. ..++++..++|+.....   ...++++|+|+||+++..+++. +...+++++++|+||+|.+.+.+
T Consensus        80 La~q~~~~~~~~~-~~g~~v~~~~Gd~~~~~---~~~~~~~IiV~Tpe~~~~ll~~-~~~~l~~l~lvViDE~H~l~~~~  154 (720)
T PRK00254         80 LAEEKYREFKDWE-KLGLRVAMTTGDYDSTD---EWLGKYDIIIATAEKFDSLLRH-GSSWIKDVKLVVADEIHLIGSYD  154 (720)
T ss_pred             HHHHHHHHHHHHh-hcCCEEEEEeCCCCCch---hhhccCCEEEEcHHHHHHHHhC-CchhhhcCCEEEEcCcCccCCcc
Confidence            9999999988764 46899999999876432   2335789999999999998876 44467899999999999998876


Q ss_pred             ChhHHHHH
Q psy4275         166 SLKFFFFF  173 (182)
Q Consensus       166 ~~~~~~~~  173 (182)
                      ....++.+
T Consensus       155 rg~~le~i  162 (720)
T PRK00254        155 RGATLEMI  162 (720)
T ss_pred             chHHHHHH
Confidence            55544433

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

Probab=99.95  E-value=3.3e-26  Score=161.80  Aligned_cols=142  Identities=31%  Similarity=0.455  Sum_probs=120.4

Q ss_pred             hHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEE
Q psy4275          30 TEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIIT  109 (182)
Q Consensus        30 ~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~  109 (182)
                      +|+|.++++.+.+++++++.+|||+|||.++..+++..+.+. ...++++++|++++++|..+.+..+....++++..++
T Consensus         1 t~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~-~~~~~lii~P~~~l~~q~~~~~~~~~~~~~~~~~~~~   79 (169)
T PF00270_consen    1 TPLQQEAIEAIISGKNVLISAPTGSGKTLAYILPALNRLQEG-KDARVLIIVPTRALAEQQFERLRKFFSNTNVRVVLLH   79 (169)
T ss_dssp             -HHHHHHHHHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTT-SSSEEEEEESSHHHHHHHHHHHHHHTTTTTSSEEEES
T ss_pred             CHHHHHHHHHHHcCCCEEEECCCCCccHHHHHHHHHhhhccC-CCceEEEEeeccccccccccccccccccccccccccc
Confidence            689999999999999999999999999999999999888776 4459999999999999999999999888888999998


Q ss_pred             cCCchh-hhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHHHHH
Q psy4275         110 GGMDMV-DQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFF  173 (182)
Q Consensus       110 ~~~~~~-~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~~~~  173 (182)
                      |+.... .....+.++++|+|+||+++.+.++.... ++.+++++|+||+|++.++.+......+
T Consensus        80 ~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~-~~~~~~~iViDE~h~l~~~~~~~~~~~i  143 (169)
T PF00270_consen   80 GGQSISEDQREVLSNQADILVTTPEQLLDLISNGKI-NISRLSLIVIDEAHHLSDETFRAMLKSI  143 (169)
T ss_dssp             TTSCHHHHHHHHHHTTSSEEEEEHHHHHHHHHTTSS-TGTTESEEEEETHHHHHHTTHHHHHHHH
T ss_pred             ccccccccccccccccccccccCcchhhcccccccc-ccccceeeccCcccccccccHHHHHHHH
Confidence            888755 33344456899999999999999988433 6777999999999999998655544333

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 ....

>KOG0333|consensus

Probab=99.95  E-value=7e-27  Score=183.45  Aligned_cols=178  Identities=38%  Similarity=0.556  Sum_probs=159.5

Q ss_pred             CCCccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCC--------
Q psy4275           1 MEDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP--------   72 (182)
Q Consensus         1 ~~~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~--------   72 (182)
                      +|.|+.+|++.+++.++.+.+.+.|+..|+|+|.+++|..+.+++.|..+.||||||.+|+++++..+...+        
T Consensus       240 lpnplrnwEE~~~P~e~l~~I~~~~y~eptpIqR~aipl~lQ~rD~igvaETgsGktaaf~ipLl~~IsslP~~~~~en~  319 (673)
T KOG0333|consen  240 LPNPLRNWEESGFPLELLSVIKKPGYKEPTPIQRQAIPLGLQNRDPIGVAETGSGKTAAFLIPLLIWISSLPPMARLENN  319 (673)
T ss_pred             CCccccChhhcCCCHHHHHHHHhcCCCCCchHHHhhccchhccCCeeeEEeccCCccccchhhHHHHHHcCCCcchhhhc
Confidence            589999999999999999999999999999999999999999999999999999999999999987765532        


Q ss_pred             -CCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCcc
Q psy4275          73 -YGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIK  151 (182)
Q Consensus        73 -~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~  151 (182)
                       .++.+++++|++.|+.|+.++-.++++.+++++..+.|+.+.+++-..+..+|+|+|+||+.+.+-+.+ ..+-+++..
T Consensus       320 ~~gpyaiilaptReLaqqIeeEt~kf~~~lg~r~vsvigg~s~EEq~fqls~gceiviatPgrLid~Len-r~lvl~qct  398 (673)
T KOG0333|consen  320 IEGPYAIILAPTRELAQQIEEETNKFGKPLGIRTVSVIGGLSFEEQGFQLSMGCEIVIATPGRLIDSLEN-RYLVLNQCT  398 (673)
T ss_pred             ccCceeeeechHHHHHHHHHHHHHHhcccccceEEEEecccchhhhhhhhhccceeeecCchHHHHHHHH-HHHHhccCc
Confidence             378999999999999999999999999999999999999998888778888999999999999999987 666788899


Q ss_pred             EEEEeccccccccCChhHHHHHHHHhhcCCC
Q psy4275         152 FLVLDEADRLSLMTSLKFFFFFFFLKYYIPS  182 (182)
Q Consensus       152 ~iI~DE~h~~~~~~~~~~~~~~~~~~~~~~~  182 (182)
                      ++|+|||+.|.+.++-.   -...++.++||
T Consensus       399 yvvldeadrmiDmgfE~---dv~~iL~~mPs  426 (673)
T KOG0333|consen  399 YVVLDEADRMIDMGFEP---DVQKILEQMPS  426 (673)
T ss_pred             eEeccchhhhhcccccH---HHHHHHHhCCc
Confidence            99999999999998743   34444555553

>KOG0347|consensus

Probab=99.95  E-value=4.3e-27  Score=185.53  Aligned_cols=173  Identities=37%  Similarity=0.587  Sum_probs=152.8

Q ss_pred             ccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCC-CcEEEECCCCChHHHHHHHHHHHhhccCC----------
Q psy4275           4 PIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLND-EDCIGCAKTGSGKTLAFALPILQKWCEDP----------   72 (182)
Q Consensus         4 ~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~-~~~li~~~tg~GKT~~~~~~~~~~~~~~~----------   72 (182)
                      .+.-|..|+++.++.+++...||.+|+++|...+|....| .+++-.+.||||||++|-+++++.+....          
T Consensus       179 DvsAW~~l~lp~~iL~aL~~~gFs~Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e~~~~~  258 (731)
T KOG0347|consen  179 DVSAWKNLFLPMEILRALSNLGFSRPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLESSDDSQELSNTS  258 (731)
T ss_pred             ChHHHhcCCCCHHHHHHHHhcCCCCCccchhhcccHhhccchhcccccccCCCceeeecchhhhhhhhccchHhhhhhHH
Confidence            4667999999999999999999999999999999998887 68888999999999999999999655432          


Q ss_pred             -CCee--EEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCC--CC
Q psy4275          73 -YGIF--ALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTF--SL  147 (182)
Q Consensus        73 -~~~~--~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~--~~  147 (182)
                       .+++  .+|++||++|+.|+.++++.+.+..++++..+.|+.....+.+.+...++|+|+||++|..++.+.+..  .+
T Consensus       259 ~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQqRlL~~~p~IVVATPGRlweli~e~n~~l~~~  338 (731)
T KOG0347|consen  259 AKYVKPIALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQRLLNQRPDIVVATPGRLWELIEEDNTHLGNF  338 (731)
T ss_pred             hccCcceeEEecChHHHHHHHHHHHHHhccccCeEEEEeechhHHHHHHHHHhcCCCEEEecchHHHHHHHhhhhhhhhh
Confidence             1344  899999999999999999999999999999999999998888998889999999999999999885542  78


Q ss_pred             CCccEEEEeccccccccCChhHHHHHHHH
Q psy4275         148 NRIKFLVLDEADRLSLMTSLKFFFFFFFL  176 (182)
Q Consensus       148 ~~~~~iI~DE~h~~~~~~~~~~~~~~~~~  176 (182)
                      ++++++|+||+|+|...++-+-+..+..+
T Consensus       339 k~vkcLVlDEaDRmvekghF~Els~lL~~  367 (731)
T KOG0347|consen  339 KKVKCLVLDEADRMVEKGHFEELSKLLKH  367 (731)
T ss_pred             hhceEEEEccHHHHhhhccHHHHHHHHHH
Confidence            89999999999999999876655554443

>PRK01172 ski2-like helicase; Provisional

Probab=99.94  E-value=6.4e-26  Score=190.98  Aligned_cols=161  Identities=19%  Similarity=0.243  Sum_probs=134.8

Q ss_pred             CCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHH
Q psy4275           6 KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRE   85 (182)
Q Consensus         6 ~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~   85 (182)
                      ++|+++++++.+.+.+...++. ++++|.++++.+.+++++++++|||+|||.++.++++..+.+   +.+++|++|+++
T Consensus         1 ~~~~~~~l~~~~~~~~~~~~~~-l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~~---~~k~v~i~P~ra   76 (674)
T PRK01172          1 MKISDLGYDDEFLNLFTGNDFE-LYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLA---GLKSIYIVPLRS   76 (674)
T ss_pred             CcHhhcCCCHHHHHHHhhCCCC-CCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHHh---CCcEEEEechHH
Confidence            4688999999999999988875 999999999999999999999999999999999998887765   458999999999


Q ss_pred             HHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccC
Q psy4275          86 LAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus        86 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~  165 (182)
                      |+.|.++.++++. ..+.++....|+.....   ...+.++|+|+||+++..+++++ ...+++++++|+||+|++.+.+
T Consensus        77 La~q~~~~~~~l~-~~g~~v~~~~G~~~~~~---~~~~~~dIiv~Tpek~~~l~~~~-~~~l~~v~lvViDEaH~l~d~~  151 (674)
T PRK01172         77 LAMEKYEELSRLR-SLGMRVKISIGDYDDPP---DFIKRYDVVILTSEKADSLIHHD-PYIINDVGLIVADEIHIIGDED  151 (674)
T ss_pred             HHHHHHHHHHHHh-hcCCeEEEEeCCCCCCh---hhhccCCEEEECHHHHHHHHhCC-hhHHhhcCEEEEecchhccCCC
Confidence            9999999998764 46888888888775432   22356899999999999988774 3457889999999999998876


Q ss_pred             ChhHHHHHHH
Q psy4275         166 SLKFFFFFFF  175 (182)
Q Consensus       166 ~~~~~~~~~~  175 (182)
                      ....++.+..
T Consensus       152 rg~~le~ll~  161 (674)
T PRK01172        152 RGPTLETVLS  161 (674)
T ss_pred             ccHHHHHHHH
Confidence            6555554433

>KOG0350|consensus

Probab=99.94  E-value=2.2e-26  Score=179.70  Aligned_cols=173  Identities=35%  Similarity=0.510  Sum_probs=150.4

Q ss_pred             cCCccCCCCCHHHHHH----------HHHCCCCCChHHHHhhhhhhhC---------CCcEEEECCCCChHHHHHHHHHH
Q psy4275           5 IKSFTDLKLNPWLIRQ----------CQTIGVKTPTEIQKAIIPHVLN---------DEDCIGCAKTGSGKTLAFALPIL   65 (182)
Q Consensus         5 ~~~~~~~~l~~~i~~~----------l~~~~~~~~~~~Q~~~~~~~~~---------~~~~li~~~tg~GKT~~~~~~~~   65 (182)
                      .+-|+.++.++.+...          +.+.++.+..|.|...+++++.         .+++.+.+|||+|||++|.+++.
T Consensus       126 lq~~s~l~~se~k~~~d~lea~~~q~l~k~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIV  205 (620)
T KOG0350|consen  126 LQIFSVLGKSEMKNLEDTLEATIDQLLVKMAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIV  205 (620)
T ss_pred             eeeeeccchhHHHHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHH
Confidence            3446666666555544          8888999999999999988843         57899999999999999999999


Q ss_pred             HhhccCCC-CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCC-----CcEEEEChHHHHHHH
Q psy4275          66 QKWCEDPY-GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKK-----PHIVIATPGRLADHL  139 (182)
Q Consensus        66 ~~~~~~~~-~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~Ilv~T~~~l~~~~  139 (182)
                      ..+..++. --|++||+|++.|+.|+++.++.+....|+.|+...|..+...+.+++.+.     .+|+|+||+++.+++
T Consensus       206 Q~L~~R~v~~LRavVivPtr~L~~QV~~~f~~~~~~tgL~V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPGRLVDHl  285 (620)
T KOG0350|consen  206 QLLSSRPVKRLRAVVIVPTRELALQVYDTFKRLNSGTGLAVCSLSGQNSLEDEARQLASDPPECRIDILVATPGRLVDHL  285 (620)
T ss_pred             HHHccCCccceEEEEEeeHHHHHHHHHHHHHHhccCCceEEEecccccchHHHHHHHhcCCCccccceEEcCchHHHHhc
Confidence            99988753 359999999999999999999999999999999999999988887777663     389999999999999


Q ss_pred             hcCCCCCCCCccEEEEeccccccccCChhHHHHHHHHh
Q psy4275         140 DTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFFFFLK  177 (182)
Q Consensus       140 ~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~~~~~~~~  177 (182)
                      ...+.+.+++++++|+||||+|++..+..+...+....
T Consensus       286 ~~~k~f~Lk~LrfLVIDEADRll~qsfQ~Wl~~v~~~~  323 (620)
T KOG0350|consen  286 NNTKSFDLKHLRFLVIDEADRLLDQSFQEWLDTVMSLC  323 (620)
T ss_pred             cCCCCcchhhceEEEechHHHHHHHHHHHHHHHHHHHh
Confidence            98899999999999999999999999988888776554

>KOG0326|consensus

Probab=99.94  E-value=4.5e-27  Score=175.14  Aligned_cols=167  Identities=33%  Similarity=0.465  Sum_probs=156.9

Q ss_pred             CccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHH
Q psy4275           7 SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTREL   86 (182)
Q Consensus         7 ~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l   86 (182)
                      .|+++.+..++...+.+.|+..|.|+|++.+|..+.|++++..+.+|+|||.++.+++++.+....+..++++++|+++|
T Consensus        86 efEd~~Lkr~LLmgIfe~G~ekPSPiQeesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~~~~~IQ~~ilVPtrel  165 (459)
T KOG0326|consen   86 EFEDYCLKRELLMGIFEKGFEKPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLEKIDPKKNVIQAIILVPTREL  165 (459)
T ss_pred             cHHHhhhhHHHHHHHHHhccCCCCCccccccceeecchhhhhhccCCCCCccceechhhhhcCccccceeEEEEeecchh
Confidence            57889999999999999999999999999999999999999999999999999999999999998889999999999999


Q ss_pred             HHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCC
Q psy4275          87 AYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTS  166 (182)
Q Consensus        87 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~  166 (182)
                      |-|....++++.+..+++++..+|+++.....-.+.+..+++|+||++++++.++ +...+++..++|+||||.+++..+
T Consensus       166 ALQtSqvc~~lskh~~i~vmvttGGT~lrDDI~Rl~~~VH~~vgTPGRIlDL~~K-gVa~ls~c~~lV~DEADKlLs~~F  244 (459)
T KOG0326|consen  166 ALQTSQVCKELSKHLGIKVMVTTGGTSLRDDIMRLNQTVHLVVGTPGRILDLAKK-GVADLSDCVILVMDEADKLLSVDF  244 (459)
T ss_pred             hHHHHHHHHHHhcccCeEEEEecCCcccccceeeecCceEEEEcCChhHHHHHhc-ccccchhceEEEechhhhhhchhh
Confidence            9999999999999999999999999998888888888999999999999999988 777899999999999999999988


Q ss_pred             hhHHHHHH
Q psy4275         167 LKFFFFFF  174 (182)
Q Consensus       167 ~~~~~~~~  174 (182)
                      ....+.+.
T Consensus       245 ~~~~e~li  252 (459)
T KOG0326|consen  245 QPIVEKLI  252 (459)
T ss_pred             hhHHHHHH
Confidence            87766554

>KOG0334|consensus

Probab=99.93  E-value=1e-25  Score=188.40  Aligned_cols=167  Identities=40%  Similarity=0.598  Sum_probs=152.5

Q ss_pred             CCccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccC-----CCCee
Q psy4275           2 EDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCED-----PYGIF   76 (182)
Q Consensus         2 ~~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~-----~~~~~   76 (182)
                      |+|+.+|+.-|++..+...++++|+..++|+|.++||++..|+++|.++.||+|||++|+++++.+....     ++|+-
T Consensus       361 pkpv~sW~q~gl~~~il~tlkkl~y~k~~~IQ~qAiP~ImsGrdvIgvakTgSGKT~af~LPmirhi~dQr~~~~gdGPi  440 (997)
T KOG0334|consen  361 PKPVTSWTQCGLSSKILETLKKLGYEKPTPIQAQAIPAIMSGRDVIGVAKTGSGKTLAFLLPMIRHIKDQRPLEEGDGPI  440 (997)
T ss_pred             CcccchHhhCCchHHHHHHHHHhcCCCCcchhhhhcchhccCcceEEeeccCCccchhhhcchhhhhhcCCChhhCCCce
Confidence            7899999999999999999999999999999999999999999999999999999999999998665432     45889


Q ss_pred             EEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcC--CCCCCCCccEEE
Q psy4275          77 ALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTC--NTFSLNRIKFLV  154 (182)
Q Consensus        77 ~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~--~~~~~~~~~~iI  154 (182)
                      ++|++||++|+.|+.++++++.+.+++++++++|+....++...+..++.|+||||+.+.+.+-..  +..++.++.++|
T Consensus       441 ~li~aPtrela~QI~r~~~kf~k~l~ir~v~vygg~~~~~qiaelkRg~eIvV~tpGRmiD~l~~n~grvtnlrR~t~lv  520 (997)
T KOG0334|consen  441 ALILAPTRELAMQIHREVRKFLKLLGIRVVCVYGGSGISQQIAELKRGAEIVVCTPGRMIDILCANSGRVTNLRRVTYLV  520 (997)
T ss_pred             EEEEcCCHHHHHHHHHHHHHHHhhcCceEEEecCCccHHHHHHHHhcCCceEEeccchhhhhHhhcCCccccccccceee
Confidence            999999999999999999999999999999999999999999999999999999999999987542  344777888999


Q ss_pred             EeccccccccCChh
Q psy4275         155 LDEADRLSLMTSLK  168 (182)
Q Consensus       155 ~DE~h~~~~~~~~~  168 (182)
                      +||||.|.+.++-.
T Consensus       521 ~deaDrmfdmgfeP  534 (997)
T KOG0334|consen  521 LDEADRMFDMGFEP  534 (997)
T ss_pred             echhhhhheeccCc
Confidence            99999999877644

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

Probab=99.93  E-value=4.5e-25  Score=184.31  Aligned_cols=167  Identities=25%  Similarity=0.349  Sum_probs=146.1

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccC-----CCCeeEEEEcCCHHHH
Q psy4275          13 LNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCED-----PYGIFALVLTPTRELA   87 (182)
Q Consensus        13 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~-----~~~~~~lil~p~~~l~   87 (182)
                      +++.+.+.+... +..|+|.|.++++.+.+|+|+++.+|||+|||.++.++++..+...     ..+..++||+|.++|.
T Consensus         8 l~~~v~~~~~~~-~~~~t~~Q~~a~~~i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIsPLkALn   86 (814)
T COG1201           8 LDPRVREWFKRK-FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLKALN   86 (814)
T ss_pred             cCHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCceEEEcCCCCChHHHHHHHHHHHHHhccCCCCCCceEEEEeCcHHHHH
Confidence            788999999877 8899999999999999999999999999999999999999998776     3467999999999999


Q ss_pred             HHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCC-CCCCCccEEEEeccccccccC-
Q psy4275          88 YQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNT-FSLNRIKFLVLDEADRLSLMT-  165 (182)
Q Consensus        88 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~-~~~~~~~~iI~DE~h~~~~~~-  165 (182)
                      +.+...++...+..|+.+.+.+|++...++.+...+-++|+|+||+.+.-++...+. -.+++++++|+||+|.+.+.. 
T Consensus        87 ~Di~~rL~~~~~~~G~~v~vRhGDT~~~er~r~~~~PPdILiTTPEsL~lll~~~~~r~~l~~vr~VIVDEiHel~~sKR  166 (814)
T COG1201          87 NDIRRRLEEPLRELGIEVAVRHGDTPQSEKQKMLKNPPHILITTPESLAILLNSPKFRELLRDVRYVIVDEIHALAESKR  166 (814)
T ss_pred             HHHHHHHHHHHHHcCCccceecCCCChHHhhhccCCCCcEEEeChhHHHHHhcCHHHHHHhcCCcEEEeehhhhhhcccc
Confidence            999999999999999999999999999999999999999999999999877755211 268899999999999999554 


Q ss_pred             ChhHHHHHHHHhhcC
Q psy4275         166 SLKFFFFFFFLKYYI  180 (182)
Q Consensus       166 ~~~~~~~~~~~~~~~  180 (182)
                      .......+-+++++.
T Consensus       167 G~~Lsl~LeRL~~l~  181 (814)
T COG1201         167 GVQLALSLERLRELA  181 (814)
T ss_pred             chhhhhhHHHHHhhC
Confidence            555555666665543

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.92  E-value=2.6e-24  Score=184.78  Aligned_cols=166  Identities=27%  Similarity=0.349  Sum_probs=130.4

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccC------CCCeeEEEEcCCHHH
Q psy4275          13 LNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCED------PYGIFALVLTPTREL   86 (182)
Q Consensus        13 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~------~~~~~~lil~p~~~l   86 (182)
                      +++.+.+.+.. ++..|+|+|.++++.+.+|+|+++++|||+|||.++.+++++.+...      ..+.+++|++|+++|
T Consensus        18 l~~~v~~~~~~-~~~~~tpiQ~~Ai~~il~g~nvli~APTGSGKTlaa~Lpil~~l~~~~~~~~~~~~~~~LyIsPtraL   96 (876)
T PRK13767         18 LRPYVREWFKE-KFGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYVSPLRAL   96 (876)
T ss_pred             cCHHHHHHHHH-ccCCCCHHHHHHHHHHHcCCCEEEECCCCCcHHHHHHHHHHHHHHhhccccCCCCCeEEEEEcCHHHH
Confidence            67777777765 67899999999999999999999999999999999999999877542      235689999999999


Q ss_pred             HHHHHHHHHH-------hh----ccC-CceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCC-CCCCCccEE
Q psy4275          87 AYQIGDQFLV-------LG----KVM-NLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNT-FSLNRIKFL  153 (182)
Q Consensus        87 ~~q~~~~~~~-------~~----~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~-~~~~~~~~i  153 (182)
                      ++|+++.+..       +.    ... ++++...+|+.........+.+.++|+|+||+.+..++...+. ..++++++|
T Consensus        97 a~di~~~L~~~l~~i~~~~~~~g~~~~~i~v~v~~Gdt~~~~r~~~l~~~p~IlVtTPE~L~~ll~~~~~~~~l~~l~~V  176 (876)
T PRK13767         97 NNDIHRNLEEPLTEIREIAKERGEELPEIRVAIRTGDTSSYEKQKMLKKPPHILITTPESLAILLNSPKFREKLRTVKWV  176 (876)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCcCCeeEEEEcCCCCHHHHHHHHhCCCCEEEecHHHHHHHhcChhHHHHHhcCCEE
Confidence            9998765542       22    233 6788999999988777777777899999999999887765321 147889999


Q ss_pred             EEeccccccccCChh-HHHHHHHHhhc
Q psy4275         154 VLDEADRLSLMTSLK-FFFFFFFLKYY  179 (182)
Q Consensus       154 I~DE~h~~~~~~~~~-~~~~~~~~~~~  179 (182)
                      |+||+|.+.+..... +...+.+++++
T Consensus       177 VIDE~H~l~~~~RG~~l~~~L~rL~~l  203 (876)
T PRK13767        177 IVDEIHSLAENKRGVHLSLSLERLEEL  203 (876)
T ss_pred             EEechhhhccCccHHHHHHHHHHHHHh
Confidence            999999999765433 33344445443

>KOG0341|consensus

Probab=99.92  E-value=1e-25  Score=171.78  Aligned_cols=174  Identities=39%  Similarity=0.530  Sum_probs=153.5

Q ss_pred             CCCccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhcc--------CC
Q psy4275           1 MEDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCE--------DP   72 (182)
Q Consensus         1 ~~~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~--------~~   72 (182)
                      +|-|+++|.++.++..+.+.+++.|+..|+|+|.+.+|.+++|++.+-.+-||||||++|.++++...++        ..
T Consensus       165 ipPPIksF~eMKFP~~~L~~lk~KGI~~PTpIQvQGlPvvLsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~lPf~~~  244 (610)
T KOG0341|consen  165 IPPPIKSFKEMKFPKPLLRGLKKKGIVHPTPIQVQGLPVVLSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMMLPFARG  244 (610)
T ss_pred             CCCchhhhhhccCCHHHHHHHHhcCCCCCCceeecCcceEeecCceeeEEeecCCceEEEeHHHHHHHHHHHhcCccccC
Confidence            4789999999999999999999999999999999999999999999999999999999999998876654        24


Q ss_pred             CCeeEEEEcCCHHHHHHHHHHHHHhhccC------CceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCC
Q psy4275          73 YGIFALVLTPTRELAYQIGDQFLVLGKVM------NLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFS  146 (182)
Q Consensus        73 ~~~~~lil~p~~~l~~q~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~  146 (182)
                      .++..+|+||+++|+.|.++.+..+...+      .++..++.|+....++...+..+.+|+|+||+++.+++.+ +...
T Consensus       245 EGP~gLiicPSRELArQt~~iie~~~~~L~e~g~P~lRs~LciGG~~v~eql~~v~~GvHivVATPGRL~DmL~K-K~~s  323 (610)
T KOG0341|consen  245 EGPYGLIICPSRELARQTHDIIEQYVAALQEAGYPELRSLLCIGGVPVREQLDVVRRGVHIVVATPGRLMDMLAK-KIMS  323 (610)
T ss_pred             CCCeeEEEcCcHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhhcCccHHHHHHHHhcCeeEEEcCcchHHHHHHH-hhcc
Confidence            58899999999999999998888765543      2567888899998888888888999999999999999998 7778


Q ss_pred             CCCccEEEEeccccccccCChhHHHHHHH
Q psy4275         147 LNRIKFLVLDEADRLSLMTSLKFFFFFFF  175 (182)
Q Consensus       147 ~~~~~~iI~DE~h~~~~~~~~~~~~~~~~  175 (182)
                      +.-.+++++||||+|.+.++-..+-.++.
T Consensus       324 Ld~CRyL~lDEADRmiDmGFEddir~iF~  352 (610)
T KOG0341|consen  324 LDACRYLTLDEADRMIDMGFEDDIRTIFS  352 (610)
T ss_pred             HHHHHHhhhhhHHHHhhccchhhHHHHHH
Confidence            88889999999999999998665554443

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

Probab=99.91  E-value=2.8e-23  Score=176.77  Aligned_cols=167  Identities=23%  Similarity=0.276  Sum_probs=147.5

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHH
Q psy4275          13 LNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGD   92 (182)
Q Consensus        13 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~   92 (182)
                      .++.+...+.+.|..+++.+|.+++..+.+|+|++++.|||||||.+|++++++.+.+.+.+ ++|++-|+++|++...+
T Consensus        55 ~~~~l~~~l~~~g~~~lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~~a-~AL~lYPtnALa~DQ~~  133 (851)
T COG1205          55 RDESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSA-RALLLYPTNALANDQAE  133 (851)
T ss_pred             hhhHHHHHHHHhccccccHHHHHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhhCcCc-cEEEEechhhhHhhHHH
Confidence            45556888889999999999999999999999999999999999999999999999988755 89999999999999999


Q ss_pred             HHHHhhccCC--ceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCC---CCCCCccEEEEeccccccccCCh
Q psy4275          93 QFLVLGKVMN--LRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNT---FSLNRIKFLVLDEADRLSLMTSL  167 (182)
Q Consensus        93 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~---~~~~~~~~iI~DE~h~~~~~~~~  167 (182)
                      .+.++....+  ++...++|++........+.+.++|+++||+++...+..+..   +.++++++||+||+|-.-.....
T Consensus       134 rl~~~~~~~~~~v~~~~y~Gdt~~~~r~~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDElHtYrGv~GS  213 (851)
T COG1205         134 RLRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYRGVQGS  213 (851)
T ss_pred             HHHHHHHhCCCcceeeeecCCCChHHHHHHHhCCCCEEEeCHHHHHHHhccCcchHHHHHhcCcEEEEecceeccccchh
Confidence            9999988887  888999999988777777889999999999999885433222   35777999999999999998888


Q ss_pred             hHHHHHHHHhhcC
Q psy4275         168 KFFFFFFFLKYYI  180 (182)
Q Consensus       168 ~~~~~~~~~~~~~  180 (182)
                      +...+++++++.+
T Consensus       214 ~vA~llRRL~~~~  226 (851)
T COG1205         214 EVALLLRRLLRRL  226 (851)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999988754

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.91  E-value=2.8e-23  Score=174.76  Aligned_cols=163  Identities=24%  Similarity=0.310  Sum_probs=133.8

Q ss_pred             CCCCCHHHHHHHHHCCCCCChHHHHhhhhh-hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHH
Q psy4275          10 DLKLNPWLIRQCQTIGVKTPTEIQKAIIPH-VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAY   88 (182)
Q Consensus        10 ~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~-~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~   88 (182)
                      ...+++.+.+.++..++.++.+.|+.++.. +.+++|+++++|||+|||.+++++++..+.+.  +.+++|+||+++|++
T Consensus        13 ~~~~~~~v~~i~~~~~~~el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~--~~k~vYivPlkALa~   90 (766)
T COG1204          13 KVKLDDRVLEILKGDGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEG--GGKVVYIVPLKALAE   90 (766)
T ss_pred             cccccHHHHHHhccCChHHhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhc--CCcEEEEeChHHHHH
Confidence            344888999999988987777777776655 45579999999999999999999999988875  568999999999999


Q ss_pred             HHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccccc-CCh
Q psy4275          89 QIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM-TSL  167 (182)
Q Consensus        89 q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~-~~~  167 (182)
                      +.+++++ ....+|++|...+|+.....   ....+++|+|+||+++....+++.. ....++++|+||+|.+.+. ...
T Consensus        91 Ek~~~~~-~~~~~GirV~~~TgD~~~~~---~~l~~~~ViVtT~EK~Dsl~R~~~~-~~~~V~lvViDEiH~l~d~~RG~  165 (766)
T COG1204          91 EKYEEFS-RLEELGIRVGISTGDYDLDD---ERLARYDVIVTTPEKLDSLTRKRPS-WIEEVDLVVIDEIHLLGDRTRGP  165 (766)
T ss_pred             HHHHHhh-hHHhcCCEEEEecCCcccch---hhhccCCEEEEchHHhhHhhhcCcc-hhhcccEEEEeeeeecCCcccCc
Confidence            9999998 55777999999999987544   3346899999999999999998544 7788999999999999998 444


Q ss_pred             hHHHHHHHHhhc
Q psy4275         168 KFFFFFFFLKYY  179 (182)
Q Consensus       168 ~~~~~~~~~~~~  179 (182)
                      -......++++.
T Consensus       166 ~lE~iv~r~~~~  177 (766)
T COG1204         166 VLESIVARMRRL  177 (766)
T ss_pred             eehhHHHHHHhh
Confidence            444455555443

>KOG0336|consensus

Probab=99.90  E-value=9.5e-24  Score=162.07  Aligned_cols=166  Identities=39%  Similarity=0.524  Sum_probs=144.7

Q ss_pred             CCCccCCccC-CCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccC------CC
Q psy4275           1 MEDPIKSFTD-LKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCED------PY   73 (182)
Q Consensus         1 ~~~~~~~~~~-~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~------~~   73 (182)
                      +|.|.-+|++ |...+++.+.+.+.||..|+|+|.++||-+++|.+++.++.||+|||++++++.+..+...      ..
T Consensus       214 IPnP~ctFddAFq~~pevmenIkK~GFqKPtPIqSQaWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr~  293 (629)
T KOG0336|consen  214 IPNPVCTFDDAFQCYPEVMENIKKTGFQKPTPIQSQAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQRN  293 (629)
T ss_pred             CCCCcCcHHHHHhhhHHHHHHHHhccCCCCCcchhcccceeecCcceEEEEecCCCcCHHHhccceeeeeccchhhhccC
Confidence            4677777765 4778999999999999999999999999999999999999999999999999887766543      24


Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEE
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFL  153 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~i  153 (182)
                      ++.+++++|+++|+.|+.-+.++. ..-+.+..+++|+.+..++...+..+.+|+++||+.|.++... +.++++.+.++
T Consensus       294 ~p~~lvl~ptreLalqie~e~~ky-syng~ksvc~ygggnR~eqie~lkrgveiiiatPgrlndL~~~-n~i~l~siTYl  371 (629)
T KOG0336|consen  294 GPGVLVLTPTRELALQIEGEVKKY-SYNGLKSVCVYGGGNRNEQIEDLKRGVEIIIATPGRLNDLQMD-NVINLASITYL  371 (629)
T ss_pred             CCceEEEeccHHHHHHHHhHHhHh-hhcCcceEEEecCCCchhHHHHHhcCceEEeeCCchHhhhhhc-CeeeeeeeEEE
Confidence            678999999999999997666654 3337788888888888888889999999999999999999888 88899999999


Q ss_pred             EEeccccccccCChh
Q psy4275         154 VLDEADRLSLMTSLK  168 (182)
Q Consensus       154 I~DE~h~~~~~~~~~  168 (182)
                      |+||||.|++.++-.
T Consensus       372 VlDEADrMLDMgFEp  386 (629)
T KOG0336|consen  372 VLDEADRMLDMGFEP  386 (629)
T ss_pred             EecchhhhhcccccH
Confidence            999999999998744

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.90  E-value=6.8e-23  Score=166.22  Aligned_cols=150  Identities=22%  Similarity=0.254  Sum_probs=113.7

Q ss_pred             HHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccC
Q psy4275          22 QTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVM  101 (182)
Q Consensus        22 ~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~  101 (182)
                      ..+|+..++|+|.++++.+.+|+++++++|||+|||++|+++++..      ++.++|++|+++|+.|+.+.++..    
T Consensus         5 ~~~g~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~~------~~~~lVi~P~~~L~~dq~~~l~~~----   74 (470)
T TIGR00614         5 TVFGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALCS------DGITLVISPLISLMEDQVLQLKAS----   74 (470)
T ss_pred             hhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHHHc------CCcEEEEecHHHHHHHHHHHHHHc----
Confidence            3579999999999999999999999999999999999999998753      457999999999999887777643    


Q ss_pred             CceEEEEEcCCchhhhhH----HhcCCCcEEEEChHHHHHHHhcCCCC-CCCCccEEEEeccccccccC--ChhHHHHHH
Q psy4275         102 NLRVSIITGGMDMVDQGK----ELAKKPHIVIATPGRLADHLDTCNTF-SLNRIKFLVLDEADRLSLMT--SLKFFFFFF  174 (182)
Q Consensus       102 ~~~~~~~~~~~~~~~~~~----~~~~~~~Ilv~T~~~l~~~~~~~~~~-~~~~~~~iI~DE~h~~~~~~--~~~~~~~~~  174 (182)
                      ++.+..+.++....+...    ...+..+|+++||+.+....+....+ ...+++++|+||||++.+|+  +......+.
T Consensus        75 gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TPe~l~~~~~~~~~l~~~~~i~~iViDEaH~i~~~g~~fr~~~~~l~  154 (470)
T TIGR00614        75 GIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKCSASNRLLQTLEERKGITLIAVDEAHCISQWGHDFRPDYKALG  154 (470)
T ss_pred             CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHcCchhHHHHHHhcCCcCEEEEeCCcccCccccccHHHHHHHH
Confidence            677888877765443221    12346899999999975322111111 45778999999999999887  445555555


Q ss_pred             HHhhcCC
Q psy4275         175 FLKYYIP  181 (182)
Q Consensus       175 ~~~~~~~  181 (182)
                      .++..+|
T Consensus       155 ~l~~~~~  161 (470)
T TIGR00614       155 SLKQKFP  161 (470)
T ss_pred             HHHHHcC
Confidence            6666554

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=150.47  Aligned_cols=156  Identities=35%  Similarity=0.549  Sum_probs=143.8

Q ss_pred             ccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHH
Q psy4275           8 FTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELA   87 (182)
Q Consensus         8 ~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~   87 (182)
                      |.++=+.+++.+++...|+..|.+.|.+++|...-|-+++.++.+|-|||.++.++.+..+........++++|++++|+
T Consensus        44 frdfllkpellraivdcgfehpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqiepv~g~vsvlvmchtrela  123 (387)
T KOG0329|consen   44 FRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPVDGQVSVLVMCHTRELA  123 (387)
T ss_pred             hhhhhcCHHHHHHHHhccCCCchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcCCCCCeEEEEEEeccHHHH
Confidence            56777899999999999999999999999999999999999999999999999999999987766667899999999999


Q ss_pred             HHHHHHHHHhhccC-CceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccccc
Q psy4275          88 YQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus        88 ~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~  164 (182)
                      -|+.++..++.+.. ++++.+..|+.+.......+.+.++|+|+||+.++.+.++ +.++++++..+|+|||+.|+.+
T Consensus       124 fqi~~ey~rfskymP~vkvaVFfGG~~Ikkdee~lk~~PhivVgTPGrilALvr~-k~l~lk~vkhFvlDEcdkmle~  200 (387)
T KOG0329|consen  124 FQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELLKNCPHIVVGTPGRILALVRN-RSLNLKNVKHFVLDECDKMLEQ  200 (387)
T ss_pred             HHHHHHHHHHHhhCCCceEEEEEcceeccccHHHHhCCCeEEEcCcHHHHHHHHh-ccCchhhcceeehhhHHHHHHH
Confidence            99999999998887 4899999999998888888888999999999999999998 8889999999999999988754

>KOG0327|consensus

Probab=99.89  E-value=4.5e-23  Score=156.76  Aligned_cols=172  Identities=36%  Similarity=0.519  Sum_probs=152.0

Q ss_pred             ccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275           4 PIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus         4 ~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      ...+|++++|++++.+.+...||..|+.+|+.++.-+.+|.|+.+++++|+|||.++..+++..+.-.....++++++|+
T Consensus        24 vvdsfddm~L~e~LLrgiy~yGFekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~~ke~qalilaPt  103 (397)
T KOG0327|consen   24 VVDSFDDMNLKESLLRGIYAYGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMSVKETQALILAPT  103 (397)
T ss_pred             HhhhhhhcCCCHHHHhHHHhhccCCchHHHhccccccccCCceeEeeeccccchhhhHHHHHhhcCcchHHHHHHHhcch
Confidence            46789999999999999999999999999999999999999999999999999999999999887655556689999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh-cCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccc
Q psy4275          84 RELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL-AKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLS  162 (182)
Q Consensus        84 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~  162 (182)
                      ++|+.|..+..+.+....++++..+.|+...-.....+ ...++|+++||+++.+.++. ..+..+.+.++|+||+++|+
T Consensus       104 reLa~qi~~v~~~lg~~~~~~v~~~igg~~~~~~~~~i~~~~~hivvGTpgrV~dml~~-~~l~~~~iKmfvlDEaDEmL  182 (397)
T KOG0327|consen  104 RELAQQIQKVVRALGDHMDVSVHACIGGTNVRREDQALLKDKPHIVVGTPGRVFDMLNR-GSLSTDGIKMFVLDEADEML  182 (397)
T ss_pred             HHHHHHHHHHHHhhhcccceeeeeecCcccchhhhhhhhccCceeecCCchhHHHhhcc-ccccccceeEEeecchHhhh
Confidence            99999999999999999999999999888765444333 44689999999999999988 46778889999999999999


Q ss_pred             ccCChhHHHHHHHH
Q psy4275         163 LMTSLKFFFFFFFL  176 (182)
Q Consensus       163 ~~~~~~~~~~~~~~  176 (182)
                      ..++...+..++..
T Consensus       183 s~gfkdqI~~if~~  196 (397)
T KOG0327|consen  183 SRGFKDQIYDIFQE  196 (397)
T ss_pred             ccchHHHHHHHHHH
Confidence            99998877766553

>KOG0332|consensus

Probab=99.89  E-value=3.9e-23  Score=156.81  Aligned_cols=172  Identities=31%  Similarity=0.457  Sum_probs=146.2

Q ss_pred             cCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCC--CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcC
Q psy4275           5 IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLND--EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTP   82 (182)
Q Consensus         5 ~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~--~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p   82 (182)
                      +++|++|+|.+++.+.+...+|..|+.+|+.++|.++..  +|.+.++.+|+|||.+|.+.++.+.......++++.++|
T Consensus        89 ~ksFeeL~LkPellkgly~M~F~kPskIQe~aLPlll~~Pp~nlIaQsqsGtGKTaaFvL~MLsrvd~~~~~PQ~iCLaP  168 (477)
T KOG0332|consen   89 AKSFEELRLKPELLKGLYAMKFQKPSKIQETALPLLLAEPPQNLIAQSQSGTGKTAAFVLTMLSRVDPDVVVPQCICLAP  168 (477)
T ss_pred             cccHHhhCCCHHHHhHHHHhccCCcchHHHhhcchhhcCCchhhhhhhcCCCchhHHHHHHHHHhcCccccCCCceeeCc
Confidence            578999999999999999999999999999999999884  689999999999999999999999888777889999999


Q ss_pred             CHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccc
Q psy4275          83 TRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLS  162 (182)
Q Consensus        83 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~  162 (182)
                      +++|+.|+-+.+.+.+++.+++..+...+...... +.+  ..+|+|+||+.+.+++...+.+.++.++.+|+|||+.|.
T Consensus       169 trELA~Q~~eVv~eMGKf~~ita~yair~sk~~rG-~~i--~eqIviGTPGtv~Dlm~klk~id~~kikvfVlDEAD~Mi  245 (477)
T KOG0332|consen  169 TRELAPQTGEVVEEMGKFTELTASYAIRGSKAKRG-NKL--TEQIVIGTPGTVLDLMLKLKCIDLEKIKVFVLDEADVMI  245 (477)
T ss_pred             hHHHHHHHHHHHHHhcCceeeeEEEEecCcccccC-Ccc--hhheeeCCCccHHHHHHHHHhhChhhceEEEecchhhhh
Confidence            99999999999999999998888777655521111 111  358999999999999998888899999999999999999


Q ss_pred             ccCChhHHHHHHHHhhcCC
Q psy4275         163 LMTSLKFFFFFFFLKYYIP  181 (182)
Q Consensus       163 ~~~~~~~~~~~~~~~~~~~  181 (182)
                      +.....  ..-.++++.+|
T Consensus       246 ~tqG~~--D~S~rI~~~lP  262 (477)
T KOG0332|consen  246 DTQGFQ--DQSIRIMRSLP  262 (477)
T ss_pred             hccccc--ccchhhhhhcC
Confidence            866433  44455555555

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

Probab=99.89  E-value=5.4e-22  Score=169.74  Aligned_cols=165  Identities=23%  Similarity=0.262  Sum_probs=123.3

Q ss_pred             Ccc--CCCCCHHHHHHHHH-CCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275           7 SFT--DLKLNPWLIRQCQT-IGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus         7 ~~~--~~~l~~~i~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      +|+  .++.++.+...+++ +|+..++|.|.++++.++.|+++++.+|||+|||++|.++++..      ++.+|||+|+
T Consensus       436 ~W~~~~fpw~~~L~~~lk~~FG~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL~~------~GiTLVISPL  509 (1195)
T PLN03137        436 KWSSRNFPWTKKLEVNNKKVFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALIC------PGITLVISPL  509 (1195)
T ss_pred             cccccCCCchHHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHHHHHHHc------CCcEEEEeCH
Confidence            454  57788888888865 79999999999999999999999999999999999999999864      4579999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhc------CCCcEEEEChHHHHH---HHhcCCCC-CCCCccEE
Q psy4275          84 RELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA------KKPHIVIATPGRLAD---HLDTCNTF-SLNRIKFL  153 (182)
Q Consensus        84 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~Ilv~T~~~l~~---~~~~~~~~-~~~~~~~i  153 (182)
                      ++|+.+....+..    .+++...+.++.........+.      ...+|+++||+++..   +++....+ ....+++|
T Consensus       510 iSLmqDQV~~L~~----~GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTPERL~~~d~ll~~L~~L~~~~~LslI  585 (1195)
T PLN03137        510 VSLIQDQIMNLLQ----ANIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTPEKVAKSDSLLRHLENLNSRGLLARF  585 (1195)
T ss_pred             HHHHHHHHHHHHh----CCCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEChHHhhcchHHHHHHHhhhhcccccee
Confidence            9998754333333    3788888888876544433222      468999999999852   22211111 23458899


Q ss_pred             EEeccccccccC--ChhHHHHHHHHhhcCC
Q psy4275         154 VLDEADRLSLMT--SLKFFFFFFFLKYYIP  181 (182)
Q Consensus       154 I~DE~h~~~~~~--~~~~~~~~~~~~~~~~  181 (182)
                      ||||||++.+|+  +......+..++..+|
T Consensus       586 VIDEAHcVSqWGhDFRpdYr~L~~Lr~~fp  615 (1195)
T PLN03137        586 VIDEAHCVSQWGHDFRPDYQGLGILKQKFP  615 (1195)
T ss_pred             ccCcchhhhhcccchHHHHHHHHHHHHhCC
Confidence            999999999987  4454455555665554

>KOG4284|consensus

Probab=99.89  E-value=4.2e-23  Score=165.86  Aligned_cols=176  Identities=29%  Similarity=0.403  Sum_probs=151.2

Q ss_pred             CCccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275           2 EDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus         2 ~~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      +.+...|+.+-+...+...|+..++..|+++|..++|....+-+.|+++..|+|||.+|...+++.+..+...++.+|++
T Consensus        21 ~~~~~~fe~l~l~r~vl~glrrn~f~~ptkiQaaAIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~~~~~~q~~Iv~  100 (980)
T KOG4284|consen   21 SNCTPGFEQLALWREVLLGLRRNAFALPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDSRSSHIQKVIVT  100 (980)
T ss_pred             cCCCCCHHHHHHHHHHHHHHHhhcccCCCchhhhhhhhhhcccceEEEecCCCCceEEEEeeeehhcCcccCcceeEEEe
Confidence            44567889999999999999999999999999999999999999999999999999999999999887777778999999


Q ss_pred             CCHHHHHHHHHHHHHhhccC-CceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccc
Q psy4275          82 PTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR  160 (182)
Q Consensus        82 p~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~  160 (182)
                      ||++++.|+.+.+.+++..+ |.++.++.|++......-. .+.++|+||||+++.+++.. +.++.++++++|+||||.
T Consensus       101 PTREiaVQI~~tv~~v~~sf~g~~csvfIGGT~~~~d~~r-lk~~rIvIGtPGRi~qL~el-~~~n~s~vrlfVLDEADk  178 (980)
T KOG4284|consen  101 PTREIAVQIKETVRKVAPSFTGARCSVFIGGTAHKLDLIR-LKQTRIVIGTPGRIAQLVEL-GAMNMSHVRLFVLDEADK  178 (980)
T ss_pred             cchhhhhHHHHHHHHhcccccCcceEEEecCchhhhhhhh-hhhceEEecCchHHHHHHHh-cCCCccceeEEEeccHHh
Confidence            99999999999999988754 8999999999986554444 35788999999999999988 888999999999999999


Q ss_pred             ccccCChhHHHHHHHHhhcCC
Q psy4275         161 LSLMTSLKFFFFFFFLKYYIP  181 (182)
Q Consensus       161 ~~~~~~~~~~~~~~~~~~~~~  181 (182)
                      +++.+.-.  ..+..+...+|
T Consensus       179 L~~t~sfq--~~In~ii~slP  197 (980)
T KOG4284|consen  179 LMDTESFQ--DDINIIINSLP  197 (980)
T ss_pred             hhchhhHH--HHHHHHHHhcc
Confidence            99854322  34444444444

>KOG0337|consensus

Probab=99.89  E-value=5.5e-23  Score=158.03  Aligned_cols=164  Identities=39%  Similarity=0.574  Sum_probs=149.5

Q ss_pred             CCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCC-CCeeEEEEcCCH
Q psy4275           6 KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP-YGIFALVLTPTR   84 (182)
Q Consensus         6 ~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~-~~~~~lil~p~~   84 (182)
                      ..|..+||+..+.+++.+.|+..|+|+|+..+|.++.+++.+..+-||+|||.++++++++.+.... .+.+++++.|++
T Consensus        21 g~fqsmgL~~~v~raI~kkg~~~ptpiqRKTipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s~~g~Ralilsptr  100 (529)
T KOG0337|consen   21 GGFQSMGLDYKVLRAIHKKGFNTPTPIQRKTIPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHSQTGLRALILSPTR  100 (529)
T ss_pred             CCccccCCCHHHHHHHHHhhcCCCCchhcccccceeeccccceeeecCCcchhhHHHHHHHHHhhccccccceeeccCcH
Confidence            5789999999999999999999999999999999999999999999999999999999999987654 467999999999


Q ss_pred             HHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccccc
Q psy4275          85 ELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus        85 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~  164 (182)
                      +|+.|..+..+++++..+.+..++.|+-+..++...+..+++|+++||+.+.+...+ -.+.++.+.++||||++.+...
T Consensus       101 eLa~qtlkvvkdlgrgt~lr~s~~~ggD~~eeqf~~l~~npDii~ATpgr~~h~~ve-m~l~l~sveyVVfdEadrlfem  179 (529)
T KOG0337|consen  101 ELALQTLKVVKDLGRGTKLRQSLLVGGDSIEEQFILLNENPDIIIATPGRLLHLGVE-MTLTLSSVEYVVFDEADRLFEM  179 (529)
T ss_pred             HHHHHHHHHHHHhccccchhhhhhcccchHHHHHHHhccCCCEEEecCceeeeeehh-eeccccceeeeeehhhhHHHhh
Confidence            999999999999999999999999988888887778888999999999999988776 4467889999999999999998


Q ss_pred             CChhHH
Q psy4275         165 TSLKFF  170 (182)
Q Consensus       165 ~~~~~~  170 (182)
                      ++.+-+
T Consensus       180 gfqeql  185 (529)
T KOG0337|consen  180 GFQEQL  185 (529)
T ss_pred             hhHHHH
Confidence            876543

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.88  E-value=1.2e-21  Score=163.06  Aligned_cols=151  Identities=21%  Similarity=0.251  Sum_probs=115.8

Q ss_pred             HHHH-CCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhh
Q psy4275          20 QCQT-IGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLG   98 (182)
Q Consensus        20 ~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~   98 (182)
                      .|++ +|+.+++|.|.++++.+..|+++++++|||+|||++|.++++..      ++.++|++|+.+|+.|..+.++.. 
T Consensus         4 ~l~~~fg~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~lpal~~------~g~~lVisPl~sL~~dq~~~l~~~-   76 (591)
T TIGR01389         4 VLKRTFGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALLL------KGLTVVISPLISLMKDQVDQLRAA-   76 (591)
T ss_pred             HHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHHHHHHHc------CCcEEEEcCCHHHHHHHHHHHHHc-
Confidence            4543 79999999999999999999999999999999999999888753      457899999999998887777664 


Q ss_pred             ccCCceEEEEEcCCchhhhhH----HhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccC--ChhHHHH
Q psy4275          99 KVMNLRVSIITGGMDMVDQGK----ELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMT--SLKFFFF  172 (182)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~----~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~--~~~~~~~  172 (182)
                         ++.+..++++.+..+...    ...+..+|+++||+.+...... ......+++++|+||||++..|+  +......
T Consensus        77 ---gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe~l~~~~~~-~~l~~~~l~~iViDEaH~i~~~g~~frp~y~~  152 (591)
T TIGR01389        77 ---GVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQDYFL-NMLQRIPIALVAVDEAHCVSQWGHDFRPEYQR  152 (591)
T ss_pred             ---CCcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChhHhcChHHH-HHHhcCCCCEEEEeCCcccccccCccHHHHHH
Confidence               678888888776544332    2235789999999998642221 12245678999999999999876  4455555


Q ss_pred             HHHHhhcCC
Q psy4275         173 FFFLKYYIP  181 (182)
Q Consensus       173 ~~~~~~~~~  181 (182)
                      +..++..+|
T Consensus       153 l~~l~~~~~  161 (591)
T TIGR01389       153 LGSLAERFP  161 (591)
T ss_pred             HHHHHHhCC
Confidence            656655554

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.

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.88  E-value=1.6e-21  Score=162.33  Aligned_cols=160  Identities=23%  Similarity=0.238  Sum_probs=119.2

Q ss_pred             CCCCHHHHHHHHH-CCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHH
Q psy4275          11 LKLNPWLIRQCQT-IGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQ   89 (182)
Q Consensus        11 ~~l~~~i~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q   89 (182)
                      ++.++...+.+++ +|+..++|.|.++++.+.+|+++++++|||+|||++|+++++..      .+.++|++|+++|+.|
T Consensus         7 ~~~~~~~~~~l~~~fG~~~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y~lpal~~------~g~tlVisPl~sL~~d   80 (607)
T PRK11057          7 LNLESLAKQVLQETFGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVL------DGLTLVVSPLISLMKD   80 (607)
T ss_pred             CCchhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHc------CCCEEEEecHHHHHHH
Confidence            3455666666754 79999999999999999999999999999999999999988754      4479999999999999


Q ss_pred             HHHHHHHhhccCCceEEEEEcCCchhhhhHH----hcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccC
Q psy4275          90 IGDQFLVLGKVMNLRVSIITGGMDMVDQGKE----LAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~  165 (182)
                      +.+.++..    ++.+..+.+..........    ..+..+++++||+.+...... ..+...+++++|+||||++.+|+
T Consensus        81 qv~~l~~~----gi~~~~~~s~~~~~~~~~~~~~~~~g~~~il~~tPe~l~~~~~~-~~l~~~~l~~iVIDEaH~i~~~G  155 (607)
T PRK11057         81 QVDQLLAN----GVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMDNFL-EHLAHWNPALLAVDEAHCISQWG  155 (607)
T ss_pred             HHHHHHHc----CCcEEEEcCCCCHHHHHHHHHHHhCCCCcEEEEChHHhcChHHH-HHHhhCCCCEEEEeCcccccccc
Confidence            88777654    6777777766554332221    224578999999998632111 11234468999999999999876


Q ss_pred             --ChhHHHHHHHHhhcCC
Q psy4275         166 --SLKFFFFFFFLKYYIP  181 (182)
Q Consensus       166 --~~~~~~~~~~~~~~~~  181 (182)
                        +......+..+++.+|
T Consensus       156 ~~fr~~y~~L~~l~~~~p  173 (607)
T PRK11057        156 HDFRPEYAALGQLRQRFP  173 (607)
T ss_pred             CcccHHHHHHHHHHHhCC
Confidence              4444455666666554

>PRK09401 reverse gyrase; Reviewed

Probab=99.87  E-value=5.4e-21  Score=167.29  Aligned_cols=141  Identities=20%  Similarity=0.239  Sum_probs=109.1

Q ss_pred             HHHHHHHC-CCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHH
Q psy4275          17 LIRQCQTI-GVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFL   95 (182)
Q Consensus        17 i~~~l~~~-~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~   95 (182)
                      +.+.+.+. |+ +|+++|..+++.+..|+++++++|||+|||..++. +...+..  .+.+++|++||++|+.|+++.++
T Consensus        69 ~~~~f~~~~G~-~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~f~l~-~~~~l~~--~g~~alIL~PTreLa~Qi~~~l~  144 (1176)
T PRK09401         69 FEKFFKKKTGS-KPWSLQRTWAKRLLLGESFAIIAPTGVGKTTFGLV-MSLYLAK--KGKKSYIIFPTRLLVEQVVEKLE  144 (1176)
T ss_pred             HHHHHHHhcCC-CCcHHHHHHHHHHHCCCcEEEEcCCCCCHHHHHHH-HHHHHHh--cCCeEEEEeccHHHHHHHHHHHH
Confidence            33445443 55 89999999999999999999999999999975443 3333322  26799999999999999999999


Q ss_pred             HhhccCCceEEEEEcCCch--h---hhhHHhc-CCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccccc
Q psy4275          96 VLGKVMNLRVSIITGGMDM--V---DQGKELA-KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~--~---~~~~~~~-~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~  164 (182)
                      .+....++.+..+.|+...  .   .....+. ++++|+|+||+.+.+.++.   +...+++++|+||||+|+++
T Consensus       145 ~l~~~~~~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~~~~~---l~~~~~~~lVvDEaD~~L~~  216 (1176)
T PRK09401        145 KFGEKVGCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFDE---LPKKKFDFVFVDDVDAVLKS  216 (1176)
T ss_pred             HHhhhcCceEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECHHHHHHHHHh---ccccccCEEEEEChHHhhhc
Confidence            9999888888777765432  1   1122223 4689999999999988763   34566999999999999973

>KOG0952|consensus

Probab=99.87  E-value=4.3e-22  Score=166.66  Aligned_cols=153  Identities=20%  Similarity=0.252  Sum_probs=129.6

Q ss_pred             CCCCCChHHHHhhhhhhhC-CCcEEEECCCCChHHHHHHHHHHHhhccC-------CCCeeEEEEcCCHHHHHHHHHHHH
Q psy4275          24 IGVKTPTEIQKAIIPHVLN-DEDCIGCAKTGSGKTLAFALPILQKWCED-------PYGIFALVLTPTRELAYQIGDQFL   95 (182)
Q Consensus        24 ~~~~~~~~~Q~~~~~~~~~-~~~~li~~~tg~GKT~~~~~~~~~~~~~~-------~~~~~~lil~p~~~l~~q~~~~~~   95 (182)
                      +++.+++..|.+++|...+ +.|.++|+|||+|||..|++.+++.+.++       .++.+++||+|+++||.++.+.|.
T Consensus       106 f~f~~fN~iQS~vFp~aY~SneNMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKALa~Em~~~~~  185 (1230)
T KOG0952|consen  106 FSFEEFNRIQSEVFPVAYKSNENMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAAEMVDKFS  185 (1230)
T ss_pred             ccHHHHHHHHHHhhhhhhcCCCCEEEECCCCCCchHHHHHHHHHHHHhhccccccccCCceEEEEechHHHHHHHHHHHh
Confidence            5677899999999999876 78999999999999999999999877652       236789999999999999999998


Q ss_pred             HhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCC--CCCCCCccEEEEeccccccccCChhHHHHH
Q psy4275          96 VLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCN--TFSLNRIKFLVLDEADRLSLMTSLKFFFFF  173 (182)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~--~~~~~~~~~iI~DE~h~~~~~~~~~~~~~~  173 (182)
                      +.+..+|++|..++|++......   ..+++|+|+||+++.-.-+++.  ...++.++++|+||+|.+-++.+.-.....
T Consensus       186 kkl~~~gi~v~ELTGD~ql~~te---i~~tqiiVTTPEKwDvvTRk~~~d~~l~~~V~LviIDEVHlLhd~RGpvlEtiV  262 (1230)
T KOG0952|consen  186 KKLAPLGISVRELTGDTQLTKTE---IADTQIIVTTPEKWDVVTRKSVGDSALFSLVRLVIIDEVHLLHDDRGPVLETIV  262 (1230)
T ss_pred             hhcccccceEEEecCcchhhHHH---HHhcCEEEecccceeeeeeeeccchhhhhheeeEEeeeehhhcCcccchHHHHH
Confidence            88888899999999998765543   3479999999999966555543  235778999999999999999988888888


Q ss_pred             HHHhhc
Q psy4275         174 FFLKYY  179 (182)
Q Consensus       174 ~~~~~~  179 (182)
                      .|..+.
T Consensus       263 aRtlr~  268 (1230)
T KOG0952|consen  263 ARTLRL  268 (1230)
T ss_pred             HHHHHH
Confidence            887754

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.87  E-value=3.9e-21  Score=161.70  Aligned_cols=150  Identities=17%  Similarity=0.196  Sum_probs=125.1

Q ss_pred             CCCCCHHHHHHHH-----HCCCCCC---hHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275          10 DLKLNPWLIRQCQ-----TIGVKTP---TEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus        10 ~~~l~~~i~~~l~-----~~~~~~~---~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      .|.+..++.+.+.     ..|+..|   +|+|.++++.+..+++.+.+++||+|||+++.++++..+...   ..++||+
T Consensus        66 afal~re~~~r~lg~~~~~~G~~~p~~~tp~qvQ~I~~i~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~g---~~v~IVT  142 (970)
T PRK12899         66 AYGVVKNVCRRLAGTPVEVSGYHQQWDMVPYDVQILGAIAMHKGFITEMQTGEGKTLTAVMPLYLNALTG---KPVHLVT  142 (970)
T ss_pred             HhCCCHHHHHHHhccccccccccCCCCCChHHHHHhhhhhcCCCeEEEeCCCCChHHHHHHHHHHHHhhc---CCeEEEe
Confidence            3455556655554     4566666   999999999999999999999999999999999999877653   2489999


Q ss_pred             CCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHH-HHHHhcCCCCCCC-------CccEE
Q psy4275          82 PTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRL-ADHLDTCNTFSLN-------RIKFL  153 (182)
Q Consensus        82 p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l-~~~~~~~~~~~~~-------~~~~i  153 (182)
                      |++.||.|.++++..+.+.++++++++.|+.+...+...+  +++|+|+||+.+ .++++. +.+..+       .+.++
T Consensus       143 pTrELA~Qdae~m~~L~k~lGLsV~~i~GG~~~~eq~~~y--~~DIVygTPgRLgfDyLrd-~~~~~~~~~~vqr~~~~~  219 (970)
T PRK12899        143 VNDYLAQRDCEWVGSVLRWLGLTTGVLVSGSPLEKRKEIY--QCDVVYGTASEFGFDYLRD-NSIATRKEEQVGRGFYFA  219 (970)
T ss_pred             CCHHHHHHHHHHHHHHHhhcCCeEEEEeCCCCHHHHHHHc--CCCEEEECCChhHHHHhhC-CCCCcCHHHhhcccccEE
Confidence            9999999999999999999999999999998877665554  589999999999 999987 444333       55899


Q ss_pred             EEeccccccccC
Q psy4275         154 VLDEADRLSLMT  165 (182)
Q Consensus       154 I~DE~h~~~~~~  165 (182)
                      |+||||.|+-+.
T Consensus       220 IIDEADsmLiDE  231 (970)
T PRK12899        220 IIDEVDSILIDE  231 (970)
T ss_pred             EEechhhhhhhc
Confidence            999999998644

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.87  E-value=3.8e-21  Score=161.77  Aligned_cols=139  Identities=25%  Similarity=0.380  Sum_probs=113.3

Q ss_pred             HHHHHHH-HHCCCCCChHHHHhhhhhhhCC------CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHH
Q psy4275          15 PWLIRQC-QTIGVKTPTEIQKAIIPHVLND------EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELA   87 (182)
Q Consensus        15 ~~i~~~l-~~~~~~~~~~~Q~~~~~~~~~~------~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~   87 (182)
                      ..+.+.+ ..+++ +|++.|+++++.+.++      .+.+++++||+|||.+++++++..+.+   +.++++++||++|+
T Consensus       248 ~~~~~~~~~~l~f-~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~~---g~q~lilaPT~~LA  323 (681)
T PRK10917        248 GELLKKFLASLPF-ELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEA---GYQAALMAPTEILA  323 (681)
T ss_pred             hHHHHHHHHhCCC-CCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHHc---CCeEEEEeccHHHH
Confidence            3444444 55666 7999999999999885      378999999999999999999887654   67999999999999


Q ss_pred             HHHHHHHHHhhccCCceEEEEEcCCchhhhhH---Hhc-CCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275          88 YQIGDQFLVLGKVMNLRVSIITGGMDMVDQGK---ELA-KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus        88 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~-~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      .|+++.++++.+..++++..++|+.+..+...   .+. ++++|+|+||+.+.+      ...+++++++|+||+|++..
T Consensus       324 ~Q~~~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~------~v~~~~l~lvVIDE~Hrfg~  397 (681)
T PRK10917        324 EQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQD------DVEFHNLGLVIIDEQHRFGV  397 (681)
T ss_pred             HHHHHHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcc------cchhcccceEEEechhhhhH
Confidence            99999999999999999999999987544332   222 369999999987632      23577899999999999754

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.86  E-value=4.9e-21  Score=160.04  Aligned_cols=140  Identities=23%  Similarity=0.349  Sum_probs=113.6

Q ss_pred             HHHHHHHHHCCCCCChHHHHhhhhhhhCC------CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHH
Q psy4275          15 PWLIRQCQTIGVKTPTEIQKAIIPHVLND------EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAY   88 (182)
Q Consensus        15 ~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~------~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~   88 (182)
                      ..+.+.+..+++ ++++.|+++++.+.++      .+.+++++||+|||.+++++++..+.+   +.+++|++||++|+.
T Consensus       223 ~~~~~~~~~lpf-~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~---g~qvlilaPT~~LA~  298 (630)
T TIGR00643       223 ELLTKFLASLPF-KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEA---GYQVALMAPTEILAE  298 (630)
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHHc---CCcEEEECCHHHHHH
Confidence            334455667777 8999999999998874      258999999999999999888887655   668999999999999


Q ss_pred             HHHHHHHHhhccCCceEEEEEcCCchhhhhHH---h-cCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccccc
Q psy4275          89 QIGDQFLVLGKVMNLRVSIITGGMDMVDQGKE---L-AKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus        89 q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~-~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~  164 (182)
                      |+++.+++++...++++..++|+.........   + .++++|+|+||+.+.+      ...+++++++|+||+|++...
T Consensus       299 Q~~~~~~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~------~~~~~~l~lvVIDEaH~fg~~  372 (630)
T TIGR00643       299 QHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQE------KVEFKRLALVIIDEQHRFGVE  372 (630)
T ss_pred             HHHHHHHHHhcccCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhc------cccccccceEEEechhhccHH
Confidence            99999999999889999999998875543222   2 2367999999987642      235678999999999996543

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

Probab=99.86  E-value=4.4e-21  Score=152.76  Aligned_cols=171  Identities=22%  Similarity=0.230  Sum_probs=149.0

Q ss_pred             CccCCCCCHHHHHHHHHCCCCCChHHHHhhhhh-hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHH
Q psy4275           7 SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPH-VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRE   85 (182)
Q Consensus         7 ~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~-~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~   85 (182)
                      +.+++.+++.+.+.+...|+.++.|.|..+++. ++.|.|.+++.+|++|||++..++-+..+...  +.+.++++|..+
T Consensus       195 ~vdeLdipe~fk~~lk~~G~~eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgElAGi~~~l~~--g~KmlfLvPLVA  272 (830)
T COG1202         195 PVDELDIPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLSG--GKKMLFLVPLVA  272 (830)
T ss_pred             cccccCCcHHHHHHHHhcCcceecchhhhhhhhccccCCceEEEeccCCCcchHHHhhCcHHHHhC--CCeEEEEehhHH
Confidence            567889999999999999999999999999977 78899999999999999999999999888876  568999999999


Q ss_pred             HHHHHHHHHHHhhccCCceEEEEEcCCchhhhh----HHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccc
Q psy4275          86 LAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQG----KELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL  161 (182)
Q Consensus        86 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~  161 (182)
                      |++|-++.++.-...+++++..-.|........    ..-..+++|+|+|.+-+.++++..  ..+.+++.+|+||+|.+
T Consensus       273 LANQKy~dF~~rYs~LglkvairVG~srIk~~~~pv~~~t~~dADIIVGTYEGiD~lLRtg--~~lgdiGtVVIDEiHtL  350 (830)
T COG1202         273 LANQKYEDFKERYSKLGLKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEGIDYLLRTG--KDLGDIGTVVIDEIHTL  350 (830)
T ss_pred             hhcchHHHHHHHhhcccceEEEEechhhhcccCCccccCCCCCCcEEEeechhHHHHHHcC--CcccccceEEeeeeeec
Confidence            999999999998899999998888765543322    122236799999999999999884  46889999999999999


Q ss_pred             cc-cCChhHHHHHHHHhhcCC
Q psy4275         162 SL-MTSLKFFFFFFFLKYYIP  181 (182)
Q Consensus       162 ~~-~~~~~~~~~~~~~~~~~~  181 (182)
                      .+ ....+..-++.++++++|
T Consensus       351 ~deERG~RLdGLI~RLr~l~~  371 (830)
T COG1202         351 EDEERGPRLDGLIGRLRYLFP  371 (830)
T ss_pred             cchhcccchhhHHHHHHHhCC
Confidence            98 457888899999999988

>PRK14701 reverse gyrase; Provisional

Probab=99.86  E-value=1e-20  Score=169.04  Aligned_cols=143  Identities=17%  Similarity=0.163  Sum_probs=112.8

Q ss_pred             HHHHHHHHH-CCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHH
Q psy4275          15 PWLIRQCQT-IGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQ   93 (182)
Q Consensus        15 ~~i~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~   93 (182)
                      +++.+.+.+ .|+ +|++.|.++++.++.|+++++++|||+|||.+++.+.+....   .+.+++|++||++|+.|+.+.
T Consensus        66 ~~~~~~f~~~~G~-~pt~iQ~~~i~~il~G~d~li~APTGsGKTl~~~~~al~~~~---~g~~aLVl~PTreLa~Qi~~~  141 (1638)
T PRK14701         66 EEFEEFFEKITGF-EFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGAFIALFLAL---KGKKCYIILPTTLLVKQTVEK  141 (1638)
T ss_pred             HHHHHHHHHhhCC-CCCHHHHHHHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHHHh---cCCeEEEEECHHHHHHHHHHH
Confidence            344555655 688 799999999999999999999999999999976655544322   256899999999999999999


Q ss_pred             HHHhhccC--CceEEEEEcCCchhhhhH---Hhc-CCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccccc
Q psy4275          94 FLVLGKVM--NLRVSIITGGMDMVDQGK---ELA-KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus        94 ~~~~~~~~--~~~~~~~~~~~~~~~~~~---~~~-~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~  164 (182)
                      ++.+....  ++++..++|+.+..+...   .+. ++++|+|+||+.+.+.+...   ...+++++|+||||+|+.+
T Consensus       142 l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPgrL~~~~~~l---~~~~i~~iVVDEAD~ml~~  215 (1638)
T PRK14701        142 IESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQFLARNFPEM---KHLKFDFIFVDDVDAFLKA  215 (1638)
T ss_pred             HHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCchhHHhHHHH---hhCCCCEEEEECceecccc
Confidence            99988775  456778888877654432   233 35899999999998876542   1267899999999999874

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.86  E-value=1.3e-20  Score=161.57  Aligned_cols=142  Identities=22%  Similarity=0.229  Sum_probs=113.8

Q ss_pred             CCCCHHHHHHHH-HCCCCCChHHHHhhhhhhhCC------CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275          11 LKLNPWLIRQCQ-TIGVKTPTEIQKAIIPHVLND------EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus        11 ~~l~~~i~~~l~-~~~~~~~~~~Q~~~~~~~~~~------~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      ++.+....+.+. .+++ .++|.|.++++.+.++      .+.+++++||+|||.+++.+++..+.+   +.+++|++||
T Consensus       434 ~~~~~~~~~~~~~~~~f-~~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~---g~qvlvLvPT  509 (926)
T TIGR00580       434 FPPDLEWQQEFEDSFPF-EETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLD---GKQVAVLVPT  509 (926)
T ss_pred             CCCCHHHHHHHHHhCCC-CCCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHh---CCeEEEEeCc
Confidence            345555555554 4677 6999999999999874      689999999999999999998887765   5699999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHH---hc-CCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccc
Q psy4275          84 RELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKE---LA-KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEAD  159 (182)
Q Consensus        84 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~-~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h  159 (182)
                      ++|+.|.++.+++++..+++++..++|..+..+....   +. ++++|+|+||..+    .  +.+.+++++++|+||+|
T Consensus       510 ~~LA~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~ll----~--~~v~f~~L~llVIDEah  583 (926)
T TIGR00580       510 TLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLL----Q--KDVKFKDLGLLIIDEEQ  583 (926)
T ss_pred             HHHHHHHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHHh----h--CCCCcccCCEEEeeccc
Confidence            9999999999999988889999999887664433322   22 3689999999533    2  33568899999999999


Q ss_pred             ccc
Q psy4275         160 RLS  162 (182)
Q Consensus       160 ~~~  162 (182)
                      ++.
T Consensus       584 rfg  586 (926)
T TIGR00580       584 RFG  586 (926)
T ss_pred             ccc
Confidence            964

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.

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

Probab=99.86  E-value=2.1e-20  Score=157.31  Aligned_cols=150  Identities=17%  Similarity=0.113  Sum_probs=113.1

Q ss_pred             HHHHHH-CCCCCChHHHHhhhhhhhCCC-cEEEECCCCChHHHHHHHHHHHhhccCCCCe-eEEEEcCCHHHHHHHHHHH
Q psy4275          18 IRQCQT-IGVKTPTEIQKAIIPHVLNDE-DCIGCAKTGSGKTLAFALPILQKWCEDPYGI-FALVLTPTRELAYQIGDQF   94 (182)
Q Consensus        18 ~~~l~~-~~~~~~~~~Q~~~~~~~~~~~-~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~-~~lil~p~~~l~~q~~~~~   94 (182)
                      .+.+.. .|+. |+|+|.++++.++.|+ ..++++|||+|||.++.++++.. ..+...+ +.++++|+++|++|+++.+
T Consensus         5 ~~ff~~~~G~~-PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafll~~-~~~~~~~~rLv~~vPtReLa~Qi~~~~   82 (844)
T TIGR02621         5 DEWYQGLHGYS-PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWLLAV-EIGAKVPRRLVYVVNRRTVVDQVTEEA   82 (844)
T ss_pred             HHHHHHHhCCC-CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhhccc-cccccccceEEEeCchHHHHHHHHHHH
Confidence            334443 3775 9999999999999988 57778999999999765555533 2222233 5556889999999999999


Q ss_pred             HHhhccC-----------------------CceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCC-------
Q psy4275          95 LVLGKVM-----------------------NLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNT-------  144 (182)
Q Consensus        95 ~~~~~~~-----------------------~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~-------  144 (182)
                      +++.+.+                       ++++..+.|+.+...+...+..+++|+|+|++.+    .+...       
T Consensus        83 ~~~~k~l~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~GG~~~~~q~~~l~~~p~IIVgT~D~i----~sr~L~~gYg~~  158 (844)
T TIGR02621        83 EKIGERLPDVPEVEAALWALCSTRPEKKDRPLAISTLRGQFADNDEWMLDPHRPAVIVGTVDMI----GSRLLFSGYGCG  158 (844)
T ss_pred             HHHHHHhcccchhhhhhhhhhccccccccCCeEEEEEECCCChHHHHHhcCCCCcEEEECHHHH----cCCccccccccc
Confidence            9988765                       4888999999998888888888999999996544    33211       


Q ss_pred             -----C---CCCCccEEEEeccccccccCChhHHHHHHH
Q psy4275         145 -----F---SLNRIKFLVLDEADRLSLMTSLKFFFFFFF  175 (182)
Q Consensus       145 -----~---~~~~~~~iI~DE~h~~~~~~~~~~~~~~~~  175 (182)
                           +   .+++++++|+||||  ++.++......+..
T Consensus       159 ~~~~pi~ag~L~~v~~LVLDEAD--Ld~gF~~~l~~Il~  195 (844)
T TIGR02621       159 FKSRPLHAGFLGQDALIVHDEAH--LEPAFQELLKQIMN  195 (844)
T ss_pred             cccccchhhhhccceEEEEehhh--hccccHHHHHHHHH
Confidence                 1   26789999999999  56677666555555

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.

>TIGR01054 rgy reverse gyrase

Probab=99.85  E-value=4.1e-20  Score=161.95  Aligned_cols=142  Identities=20%  Similarity=0.204  Sum_probs=109.2

Q ss_pred             HHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHH
Q psy4275          16 WLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFL   95 (182)
Q Consensus        16 ~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~   95 (182)
                      ++.+.+.+.....|+++|..+++.+..|+++++++|||+|||..+ +++...+...  +++++|++||++|+.|+++.++
T Consensus        66 ~f~~~f~~~~g~~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~f~-l~~~~~l~~~--g~~vLIL~PTreLa~Qi~~~l~  142 (1171)
T TIGR01054        66 EFEEFFKKAVGSEPWSIQKMWAKRVLRGDSFAIIAPTGVGKTTFG-LAMSLFLAKK--GKRCYIILPTTLLVIQVAEKIS  142 (1171)
T ss_pred             HHHHHHHHhcCCCCcHHHHHHHHHHhCCCeEEEECCCCCCHHHHH-HHHHHHHHhc--CCeEEEEeCHHHHHHHHHHHHH
Confidence            344445544445899999999999999999999999999999844 4444433322  6799999999999999999999


Q ss_pred             HhhccCCceEE---EEEcCCchhhhhH---Hhc-CCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccccc
Q psy4275          96 VLGKVMNLRVS---IITGGMDMVDQGK---ELA-KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus        96 ~~~~~~~~~~~---~~~~~~~~~~~~~---~~~-~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~  164 (182)
                      .+....+++..   .++|+.+..++..   .+. ++++|+|+||+.+.+.+....   . +++++|+||||+|+++
T Consensus       143 ~l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~~~l~---~-~~~~iVvDEaD~~L~~  214 (1171)
T TIGR01054       143 SLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDELG---P-KFDFIFVDDVDALLKA  214 (1171)
T ss_pred             HHHHhcCCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHHHHhc---C-CCCEEEEeChHhhhhc
Confidence            99887776543   4678776554322   222 358999999999988876522   2 7899999999999983

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.

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.84  E-value=2.8e-20  Score=151.94  Aligned_cols=131  Identities=18%  Similarity=0.149  Sum_probs=98.7

Q ss_pred             CCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEE
Q psy4275          27 KTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVS  106 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~  106 (182)
                      ..|+++|.++++.+..+++.++++|||+|||.++...+ ....++. ..+++|++|+++|++|+.+.++++.......+.
T Consensus       113 ~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~l~-~~~~~~~-~~~vLilvpt~eL~~Q~~~~l~~~~~~~~~~~~  190 (501)
T PHA02558        113 IEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLLS-RYYLENY-EGKVLIIVPTTSLVTQMIDDFVDYRLFPREAMH  190 (501)
T ss_pred             CCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHHHH-HHHHhcC-CCeEEEEECcHHHHHHHHHHHHHhcccccccee
Confidence            48999999999999998899999999999999865432 2223322 348999999999999999999987654344454


Q ss_pred             EEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHH
Q psy4275         107 IITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFF  170 (182)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~  170 (182)
                      .+.++....       .+.+|+|+|++.+.+....    .+++++++|+||||++.+..+...+
T Consensus       191 ~i~~g~~~~-------~~~~I~VaT~qsl~~~~~~----~~~~~~~iIvDEaH~~~~~~~~~il  243 (501)
T PHA02558        191 KIYSGTAKD-------TDAPIVVSTWQSAVKQPKE----WFDQFGMVIVDECHLFTGKSLTSII  243 (501)
T ss_pred             EEecCcccC-------CCCCEEEeeHHHHhhchhh----hccccCEEEEEchhcccchhHHHHH
Confidence            454444321       3578999999998764432    3678999999999999876554433

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.83  E-value=2.1e-19  Score=157.07  Aligned_cols=138  Identities=25%  Similarity=0.235  Sum_probs=110.7

Q ss_pred             HHHHHHHHHCCCCCChHHHHhhhhhhhCC------CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHH
Q psy4275          15 PWLIRQCQTIGVKTPTEIQKAIIPHVLND------EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAY   88 (182)
Q Consensus        15 ~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~------~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~   88 (182)
                      .+..+....+++ .+++.|.++++.+..+      .+.+++++||+|||.+++.++...+..   +.+++|++||++|+.
T Consensus       588 ~~~~~~~~~~~~-~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~~---g~qvlvLvPT~eLA~  663 (1147)
T PRK10689        588 EQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVEN---HKQVAVLVPTTLLAQ  663 (1147)
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHHc---CCeEEEEeCcHHHHH
Confidence            344455566777 7999999999999886      789999999999999988776665443   679999999999999


Q ss_pred             HHHHHHHHhhccCCceEEEEEcCCchhhhhHHhc----CCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccc
Q psy4275          89 QIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA----KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLS  162 (182)
Q Consensus        89 q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~  162 (182)
                      |+++.+++.+...++++..++|..+..++...+.    +.++|+|+||+.+    .  +.+.+++++++|+||+|++.
T Consensus       664 Q~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL----~--~~v~~~~L~lLVIDEahrfG  735 (1147)
T PRK10689        664 QHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLL----Q--SDVKWKDLGLLIVDEEHRFG  735 (1147)
T ss_pred             HHHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHH----h--CCCCHhhCCEEEEechhhcc
Confidence            9999999888878889988888777655443332    4689999999743    2  23457789999999999983

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.83  E-value=6.5e-19  Score=126.54  Aligned_cols=142  Identities=36%  Similarity=0.456  Sum_probs=110.9

Q ss_pred             CCCCCChHHHHhhhhhhhCC-CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCC
Q psy4275          24 IGVKTPTEIQKAIIPHVLND-EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMN  102 (182)
Q Consensus        24 ~~~~~~~~~Q~~~~~~~~~~-~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~  102 (182)
                      .++..++++|.+++..+... ++.++.++||+|||.++..+++..+...+ ..++++++|+.+++.|+.+.+........
T Consensus         4 ~~~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~~-~~~~l~~~p~~~~~~~~~~~~~~~~~~~~   82 (201)
T smart00487        4 FGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGK-GKRVLVLVPTRELAEQWAEELKKLGPSLG   82 (201)
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhcccC-CCcEEEEeCCHHHHHHHHHHHHHHhccCC
Confidence            45678999999999999988 99999999999999998888888777654 35899999999999999988888776655


Q ss_pred             -ceEEEEEcCCchhhhhHHhcCCC-cEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChh
Q psy4275         103 -LRVSIITGGMDMVDQGKELAKKP-HIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLK  168 (182)
Q Consensus       103 -~~~~~~~~~~~~~~~~~~~~~~~-~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~  168 (182)
                       .....+.+..... ......++. +++++|++.+.+.... ......+++++|+||+|++.......
T Consensus        83 ~~~~~~~~~~~~~~-~~~~~~~~~~~v~~~t~~~l~~~~~~-~~~~~~~~~~iIiDE~h~~~~~~~~~  148 (201)
T smart00487       83 LKVVGLYGGDSKRE-QLRKLESGKTDILVTTPGRLLDLLEN-DLLELSNVDLVILDEAHRLLDGGFGD  148 (201)
T ss_pred             eEEEEEeCCcchHH-HHHHHhcCCCCEEEeChHHHHHHHHc-CCcCHhHCCEEEEECHHHHhcCCcHH
Confidence             3444444433333 333334444 9999999999999887 33556778899999999999754333

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.83  E-value=7.7e-20  Score=161.46  Aligned_cols=134  Identities=25%  Similarity=0.273  Sum_probs=107.2

Q ss_pred             EECCCCChHHHHHHHHHHHhhccC----------CCCeeEEEEcCCHHHHHHHHHHHHHhh------------ccCCceE
Q psy4275          48 GCAKTGSGKTLAFALPILQKWCED----------PYGIFALVLTPTRELAYQIGDQFLVLG------------KVMNLRV  105 (182)
Q Consensus        48 i~~~tg~GKT~~~~~~~~~~~~~~----------~~~~~~lil~p~~~l~~q~~~~~~~~~------------~~~~~~~  105 (182)
                      +++|||||||.++.++++..+..+          ..+.++|||+|+++|+.|+.+.++...            ...++++
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            478999999999999999888643          135799999999999999988876421            1247899


Q ss_pred             EEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccC-ChhHHHHHHHHhhcCC
Q psy4275         106 SIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMT-SLKFFFFFFFLKYYIP  181 (182)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~-~~~~~~~~~~~~~~~~  181 (182)
                      ...+|+++..++...+.+.++|+|+||+++..++.+.....++++++||+||+|.+.+.. ...+...+.+++.+++
T Consensus        81 ~vrtGDt~~~eR~rll~~ppdILVTTPEsL~~LLtsk~r~~L~~Vr~VIVDE~H~L~g~kRG~~Lel~LeRL~~l~~  157 (1490)
T PRK09751         81 GIRTGDTPAQERSKLTRNPPDILITTPESLYLMLTSRARETLRGVETVIIDEVHAVAGSKRGAHLALSLERLDALLH  157 (1490)
T ss_pred             EEEECCCCHHHHHHHhcCCCCEEEecHHHHHHHHhhhhhhhhccCCEEEEecHHHhcccccccHHHHHHHHHHHhCC
Confidence            999999998877777777899999999999998865333468999999999999999764 4455566667766553

>PRK13766 Hef nuclease; Provisional

Probab=99.82  E-value=6e-19  Score=151.03  Aligned_cols=139  Identities=24%  Similarity=0.311  Sum_probs=112.5

Q ss_pred             CCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCce
Q psy4275          25 GVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLR  104 (182)
Q Consensus        25 ~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~  104 (182)
                      +..++++||.+++...+.+ +.++++|||+|||.++++.+...+. .+ +.+++|++|+++|++|+.+.++.+....+.+
T Consensus        12 ~~~~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~-~~-~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~~~~   88 (773)
T PRK13766         12 NTIEARLYQQLLAATALKK-NTLVVLPTGLGKTAIALLVIAERLH-KK-GGKVLILAPTKPLVEQHAEFFRKFLNIPEEK   88 (773)
T ss_pred             CcCCccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHH-hC-CCeEEEEeCcHHHHHHHHHHHHHHhCCCCce
Confidence            4457999999999888776 8999999999999998888877663 22 5689999999999999999998876654567


Q ss_pred             EEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChh
Q psy4275         105 VSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLK  168 (182)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~  168 (182)
                      +..++|+.....+ ...+.+++|+|+||+.+...+.. +.+.+.+++++||||||++.......
T Consensus        89 v~~~~g~~~~~~r-~~~~~~~~iiv~T~~~l~~~l~~-~~~~~~~~~liVvDEaH~~~~~~~~~  150 (773)
T PRK13766         89 IVVFTGEVSPEKR-AELWEKAKVIVATPQVIENDLIA-GRISLEDVSLLIFDEAHRAVGNYAYV  150 (773)
T ss_pred             EEEEeCCCCHHHH-HHHHhCCCEEEECHHHHHHHHHc-CCCChhhCcEEEEECCccccccccHH
Confidence            8888888766543 34456789999999999877755 55678889999999999987655443

>KOG0344|consensus

Probab=99.82  E-value=7.9e-20  Score=145.56  Aligned_cols=170  Identities=36%  Similarity=0.500  Sum_probs=135.3

Q ss_pred             CCCccCCccC----CCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccC-----
Q psy4275           1 MEDPIKSFTD----LKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCED-----   71 (182)
Q Consensus         1 ~~~~~~~~~~----~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~-----   71 (182)
                      +|+++..|++    +..+..+.+.+...+|..|+|.|.++++.+..+++++.|+|||+|||+++.++++..+...     
T Consensus       127 ~~~~l~~f~~lt~~~~~~~~ll~nl~~~~F~~Pt~iq~~aipvfl~~r~~lAcapTGsgKtlaf~~Pil~~L~~~~~~~~  206 (593)
T KOG0344|consen  127 LPPPLLSFSDLTYDYSMNKRLLENLQELGFDEPTPIQKQAIPVFLEKRDVLACAPTGSGKTLAFNLPILQHLKDLSQEKH  206 (593)
T ss_pred             CCCccccccccchhhhhcHHHHHhHhhCCCCCCCcccchhhhhhhcccceEEeccCCCcchhhhhhHHHHHHHHhhcccC
Confidence            4788889987    5789999999999999999999999999999999999999999999999999999887553     


Q ss_pred             CCCeeEEEEcCCHHHHHHHHHHHHHhh--ccCCceEEEEEcCCchhh-hhHHhcCCCcEEEEChHHHHHHHhcCC-CCCC
Q psy4275          72 PYGIFALVLTPTRELAYQIGDQFLVLG--KVMNLRVSIITGGMDMVD-QGKELAKKPHIVIATPGRLADHLDTCN-TFSL  147 (182)
Q Consensus        72 ~~~~~~lil~p~~~l~~q~~~~~~~~~--~~~~~~~~~~~~~~~~~~-~~~~~~~~~~Ilv~T~~~l~~~~~~~~-~~~~  147 (182)
                      ..+.+++|+.|+++|+.|++.+..++.  +..+.+...........+ ........++++++||-.+...+.... .+.+
T Consensus       207 ~~gl~a~Il~ptreLa~Qi~re~~k~~~~~~t~~~a~~~~~~~~~~qk~a~~~~~k~dili~TP~ri~~~~~~~~~~idl  286 (593)
T KOG0344|consen  207 KVGLRALILSPTRELAAQIYREMRKYSIDEGTSLRAAQFSKPAYPSQKPAFLSDEKYDILISTPMRIVGLLGLGKLNIDL  286 (593)
T ss_pred             ccceEEEEecchHHHHHHHHHHHHhcCCCCCCchhhhhcccccchhhccchhHHHHHHHHhcCHHHHHHHhcCCCccchh
Confidence            346899999999999999999999887  444444443333211111 111222367899999999999887632 3588


Q ss_pred             CCccEEEEecccccccc-CChhHH
Q psy4275         148 NRIKFLVLDEADRLSLM-TSLKFF  170 (182)
Q Consensus       148 ~~~~~iI~DE~h~~~~~-~~~~~~  170 (182)
                      +.+.++|+||+|.+.+. .+.+-.
T Consensus       287 ~~V~~lV~dEaD~lfe~~~f~~Ql  310 (593)
T KOG0344|consen  287 SKVEWLVVDEADLLFEPEFFVEQL  310 (593)
T ss_pred             heeeeEeechHHhhhChhhHHHHH
Confidence            89999999999999998 444433

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

Probab=99.81  E-value=3.1e-19  Score=140.45  Aligned_cols=142  Identities=24%  Similarity=0.289  Sum_probs=119.6

Q ss_pred             CCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q psy4275          24 IGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNL  103 (182)
Q Consensus        24 ~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  103 (182)
                      .+..+++.||.......+.+ |++++.|||.|||++++..+..++...+ + ++|+++||+-|+.|.++.+.++..--..
T Consensus        11 p~~ie~R~YQ~~i~a~al~~-NtLvvlPTGLGKT~IA~~V~~~~l~~~~-~-kvlfLAPTKPLV~Qh~~~~~~v~~ip~~   87 (542)
T COG1111          11 PNTIEPRLYQLNIAAKALFK-NTLVVLPTGLGKTFIAAMVIANRLRWFG-G-KVLFLAPTKPLVLQHAEFCRKVTGIPED   87 (542)
T ss_pred             cccccHHHHHHHHHHHHhhc-CeEEEecCCccHHHHHHHHHHHHHHhcC-C-eEEEecCCchHHHHHHHHHHHHhCCChh
Confidence            34558999999998887765 8999999999999999988888877764 3 8999999999999999999998877667


Q ss_pred             eEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHH
Q psy4275         104 RVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFF  170 (182)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~  170 (182)
                      .++.++|......+. ..|++.+|+|+||+.+.+=+.. +.+++.++.++||||||+--.+..+-+.
T Consensus        88 ~i~~ltGev~p~~R~-~~w~~~kVfvaTPQvveNDl~~-Grid~~dv~~lifDEAHRAvGnyAYv~V  152 (542)
T COG1111          88 EIAALTGEVRPEERE-ELWAKKKVFVATPQVVENDLKA-GRIDLDDVSLLIFDEAHRAVGNYAYVFV  152 (542)
T ss_pred             heeeecCCCChHHHH-HHHhhCCEEEeccHHHHhHHhc-CccChHHceEEEechhhhccCcchHHHH
Confidence            888999988765544 4467889999999999888877 7889999999999999997766654443

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.78  E-value=2.1e-18  Score=144.02  Aligned_cols=135  Identities=21%  Similarity=0.195  Sum_probs=104.1

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSI  107 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  107 (182)
                      .++|+|.+++..+.-.+..+++++||+|||+++.++++.....   +..++|++|++.|+.|+++++..+.+.+|+++..
T Consensus        68 glrpydVQlig~l~l~~G~Iaem~TGeGKTLta~Lpa~l~aL~---g~~V~VVTpn~yLA~Rdae~m~~l~~~LGLsv~~  144 (762)
T TIGR03714        68 GMFPYDVQVLGAIVLHQGNIAEMKTGEGKTLTATMPLYLNALT---GKGAMLVTTNDYLAKRDAEEMGPVYEWLGLTVSL  144 (762)
T ss_pred             CCCccHHHHHHHHHhcCCceeEecCCcchHHHHHHHHHHHhhc---CCceEEeCCCHHHHHHHHHHHHHHHhhcCCcEEE
Confidence            4566777666665555557999999999999999998766555   4579999999999999999999999999999988


Q ss_pred             EEcCCc---hhhhhHHhcCCCcEEEEChHHH-HHHHhcC-----CCCCCCCccEEEEeccccccccC
Q psy4275         108 ITGGMD---MVDQGKELAKKPHIVIATPGRL-ADHLDTC-----NTFSLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus       108 ~~~~~~---~~~~~~~~~~~~~Ilv~T~~~l-~~~~~~~-----~~~~~~~~~~iI~DE~h~~~~~~  165 (182)
                      ..++..   .....+....+++|+++||+.+ .++++..     ....++.+.++|+||||.|+-+.
T Consensus       145 ~~~~s~~~~~~~~~rr~~y~~dIvygTp~~LgfDyLrD~l~~~~~~~~~r~l~~~IVDEaDsILiDe  211 (762)
T TIGR03714       145 GVVDDPDEEYDANEKRKIYNSDIVYTTNSALGFDYLIDNLASNKEGKFLRPFNYVIVDEVDSVLLDS  211 (762)
T ss_pred             EECCCCccccCHHHHHHhCCCCEEEECchhhhhhHHHHHhhcchhhcccccCcEEEEecHhhHhhcc
Confidence            776522   2222333345799999999999 5666432     22346788999999999997544

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.

>KOG0354|consensus

Probab=99.78  E-value=3.7e-18  Score=140.77  Aligned_cols=151  Identities=21%  Similarity=0.170  Sum_probs=116.5

Q ss_pred             CHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHH
Q psy4275          14 NPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQ   93 (182)
Q Consensus        14 ~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~   93 (182)
                      ++.....+.-.....+++||.+.....+ ++|+++++|||+|||.++...+.+++...+. .++++++|++-|+.|....
T Consensus        48 ~~s~~~~~~~p~~~~lR~YQ~eivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p~-~KiVF~aP~~pLv~QQ~a~  125 (746)
T KOG0354|consen   48 DESAAQRWIYPTNLELRNYQEELVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWRPK-GKVVFLAPTRPLVNQQIAC  125 (746)
T ss_pred             ChhhhccccccCcccccHHHHHHhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhcCCc-ceEEEeeCCchHHHHHHHH
Confidence            3333333333334479999999998878 9999999999999999999999998877664 5899999999999998866


Q ss_pred             HHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChh
Q psy4275          94 FLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLK  168 (182)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~  168 (182)
                      +...+..  ..+....|+.........+++..+|++.||+.+.+-+++...-.++.+.++||||||+-.....+.
T Consensus       126 ~~~~~~~--~~~T~~l~~~~~~~~r~~i~~s~~vff~TpQil~ndL~~~~~~~ls~fs~iv~DE~Hra~kn~~Y~  198 (746)
T KOG0354|consen  126 FSIYLIP--YSVTGQLGDTVPRSNRGEIVASKRVFFRTPQILENDLKSGLHDELSDFSLIVFDECHRTSKNHPYN  198 (746)
T ss_pred             HhhccCc--ccceeeccCccCCCchhhhhcccceEEeChHhhhhhcccccccccceEEEEEEcccccccccccHH
Confidence            6666554  556566666444444457778899999999999988877332236889999999999988766444

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.77  E-value=1e-17  Score=131.63  Aligned_cols=130  Identities=17%  Similarity=0.181  Sum_probs=95.7

Q ss_pred             HHHhhhhhhhCCCc--EEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccC----CceE
Q psy4275          32 IQKAIIPHVLNDED--CIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVM----NLRV  105 (182)
Q Consensus        32 ~Q~~~~~~~~~~~~--~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~----~~~~  105 (182)
                      +|.++++.+.++++  +++++|||+|||.+++++++..      +.++++++|+++|++++++.++.+...+    +..+
T Consensus         1 hQ~~~~~~~~~~~~~~~~i~apTGsGKT~~~~~~~l~~------~~~~~~~~P~~aL~~~~~~~~~~~~~~~~~~~~~~v   74 (357)
T TIGR03158         1 HQVATFEALQSKDADIIFNTAPTGAGKTLAWLTPLLHG------ENDTIALYPTNALIEDQTEAIKEFVDVFKPERDVNL   74 (357)
T ss_pred             CHHHHHHHHHcCCCCEEEEECCCCCCHHHHHHHHHHHc------CCCEEEEeChHHHHHHHHHHHHHHHHhcCCCCCceE
Confidence            58999999998764  7889999999999998888752      3478999999999999999888876433    4566


Q ss_pred             EEEEcCCchh--h------------------hhHHhcCCCcEEEEChHHHHHHHhcCC---C----CCCCCccEEEEecc
Q psy4275         106 SIITGGMDMV--D------------------QGKELAKKPHIVIATPGRLADHLDTCN---T----FSLNRIKFLVLDEA  158 (182)
Q Consensus       106 ~~~~~~~~~~--~------------------~~~~~~~~~~Ilv~T~~~l~~~~~~~~---~----~~~~~~~~iI~DE~  158 (182)
                      ..++|....+  .                  +.....+.+.|+++||+.+..+++.+.   .    ..+.+++++|+||+
T Consensus        75 ~~~~g~~~~d~~~~~~~~~~~~~g~~~~~~~r~~~~~~~p~illT~p~~l~~llr~~~~~~~~~~~~~~~~~~~iV~DE~  154 (357)
T TIGR03158        75 LHVSKATLKDIKEYANDKVGSSKGEKLYNLLRNPIGTSTPIILLTNPDIFVYLTRFAYIDRGDIAAGFYTKFSTVIFDEF  154 (357)
T ss_pred             EEecCCchHHHHHhhhhhcccCccchhhhhHHHHHhcCCCCEEEecHHHHHHHHhhhccCcccchhhhhcCCCEEEEecc
Confidence            6666653221  0                  011113467899999999987665421   1    12478999999999


Q ss_pred             ccccccCCh
Q psy4275         159 DRLSLMTSL  167 (182)
Q Consensus       159 h~~~~~~~~  167 (182)
                      |.+..+...
T Consensus       155 H~~~~~~~~  163 (357)
T TIGR03158       155 HLYDAKQLV  163 (357)
T ss_pred             cccCcccch
Confidence            998865543

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.

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.77  E-value=4.9e-18  Score=141.18  Aligned_cols=131  Identities=24%  Similarity=0.228  Sum_probs=108.6

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSI  107 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  107 (182)
                      .|++.|..+...+..|+  +.+++||+|||+++.++++-....   +..+.+++|+..||.|.++++..+.+.+|+++++
T Consensus        56 ~p~~vQlig~~~l~~G~--Iaem~TGeGKTLva~lpa~l~aL~---G~~V~VvTpt~~LA~qdae~~~~l~~~LGLsv~~  130 (745)
T TIGR00963        56 RPFDVQLIGGIALHKGK--IAEMKTGEGKTLTATLPAYLNALT---GKGVHVVTVNDYLAQRDAEWMGQVYRFLGLSVGL  130 (745)
T ss_pred             CccchHHhhhhhhcCCc--eeeecCCCccHHHHHHHHHHHHHh---CCCEEEEcCCHHHHHHHHHHHHHHhccCCCeEEE
Confidence            67888888877776665  999999999999999998644444   4479999999999999999999999999999999


Q ss_pred             EEcCCchhhhhHHhcCCCcEEEEChHHH-HHHHhcCC-----CCCCCCccEEEEeccccccccC
Q psy4275         108 ITGGMDMVDQGKELAKKPHIVIATPGRL-ADHLDTCN-----TFSLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~Ilv~T~~~l-~~~~~~~~-----~~~~~~~~~iI~DE~h~~~~~~  165 (182)
                      +.|+.+...+...+  .++|+++||..+ .++++..-     ...++.+.++|+||+|.|+-+.
T Consensus       131 i~g~~~~~~r~~~y--~~dIvyGT~~rlgfDyLrd~~~~~~~~~~~r~l~~aIIDEaDs~LIDe  192 (745)
T TIGR00963       131 ILSGMSPEERREAY--ACDITYGTNNELGFDYLRDNMAHSKEEKVQRPFHFAIIDEVDSILIDE  192 (745)
T ss_pred             EeCCCCHHHHHHhc--CCCEEEECCCchhhHHHhcccccchhhhhccccceeEeecHHHHhHHh
Confidence            99988765443333  589999999999 88987731     2467889999999999998744

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.

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.74  E-value=9.7e-17  Score=109.07  Aligned_cols=122  Identities=42%  Similarity=0.536  Sum_probs=96.7

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcC
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAK  123 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  123 (182)
                      ++.++.+|||+|||..++..+........ ..++++++|+.+++.++.+.+...... +..+..+.+.............
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~~~-~~~~lv~~p~~~l~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~   78 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDSLK-GGQVLVLAPTRELANQVAERLKELFGE-GIKVGYLIGGTSIKQQEKLLSG   78 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhccc-CCCEEEEcCcHHHHHHHHHHHHHHhhC-CcEEEEEecCcchhHHHHHhcC
Confidence            46899999999999998888777665532 458999999999999998888887765 6777777777665555445567


Q ss_pred             CCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChh
Q psy4275         124 KPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLK  168 (182)
Q Consensus       124 ~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~  168 (182)
                      ..+|+++|++.+........ ......+++|+||+|.+.......
T Consensus        79 ~~~i~i~t~~~~~~~~~~~~-~~~~~~~~iiiDE~h~~~~~~~~~  122 (144)
T cd00046          79 KTDIVVGTPGRLLDELERLK-LSLKKLDLLILDEAHRLLNQGFGL  122 (144)
T ss_pred             CCCEEEECcHHHHHHHHcCC-cchhcCCEEEEeCHHHHhhcchHH
Confidence            88999999999988876632 345568899999999998877544

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

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.74  E-value=4.1e-17  Score=137.30  Aligned_cols=133  Identities=21%  Similarity=0.255  Sum_probs=109.1

Q ss_pred             CCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCce
Q psy4275          25 GVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLR  104 (182)
Q Consensus        25 ~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~  104 (182)
                      |. .|++.|..+...+..|+  +.++.||+|||+++.++++.....   +..+.+++|+..||.|.++++..+.+.+|++
T Consensus        76 g~-~p~~vQl~~~~~l~~G~--Iaem~TGeGKTL~a~lp~~l~al~---G~~v~VvTpt~~LA~qd~e~~~~l~~~lGl~  149 (790)
T PRK09200         76 GM-RPYDVQLIGALVLHEGN--IAEMQTGEGKTLTATMPLYLNALE---GKGVHLITVNDYLAKRDAEEMGQVYEFLGLT  149 (790)
T ss_pred             CC-CCchHHHHhHHHHcCCc--eeeecCCCcchHHHHHHHHHHHHc---CCCeEEEeCCHHHHHHHHHHHHHHHhhcCCe
Confidence            44 78888988888777665  999999999999999998866665   6689999999999999999999999999999


Q ss_pred             EEEEEcCCc-hhhhhHHhcCCCcEEEEChHHH-HHHHhcCC-----CCCCCCccEEEEeccccccccC
Q psy4275         105 VSIITGGMD-MVDQGKELAKKPHIVIATPGRL-ADHLDTCN-----TFSLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus       105 ~~~~~~~~~-~~~~~~~~~~~~~Ilv~T~~~l-~~~~~~~~-----~~~~~~~~~iI~DE~h~~~~~~  165 (182)
                      ++++.|+.+ ..+.. . ..+++|+++||+.+ .++++..-     ....+.+.++|+||+|.|+=+.
T Consensus       150 v~~i~g~~~~~~~r~-~-~y~~dIvygT~~~l~fDyLrd~~~~~~~~~~~r~~~~~IvDEaDsiLiDe  215 (790)
T PRK09200        150 VGLNFSDIDDASEKK-A-IYEADIIYTTNSELGFDYLRDNLADSKEDKVQRPLNYAIIDEIDSILLDE  215 (790)
T ss_pred             EEEEeCCCCcHHHHH-H-hcCCCEEEECCccccchhHHhccccchhhhcccccceEEEeccccceecc
Confidence            999999887 33332 2 34689999999999 56665421     1355778999999999998554

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

Probab=99.74  E-value=2.3e-17  Score=132.83  Aligned_cols=135  Identities=21%  Similarity=0.233  Sum_probs=99.0

Q ss_pred             CCChHHHHhhhhhhhC----CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCC
Q psy4275          27 KTPTEIQKAIIPHVLN----DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMN  102 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~----~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~  102 (182)
                      ..++++|++++..+.+    ++..+++.|||+|||.+++..+...      +.+++||+|+.+|+.||++.+....... 
T Consensus        35 ~~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~~~------~~~~Lvlv~~~~L~~Qw~~~~~~~~~~~-  107 (442)
T COG1061          35 FELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAEL------KRSTLVLVPTKELLDQWAEALKKFLLLN-  107 (442)
T ss_pred             CCCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHHHh------cCCEEEEECcHHHHHHHHHHHHHhcCCc-
Confidence            3699999999999988    8899999999999999987766665      3359999999999999986666554431 


Q ss_pred             ceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHHHHHHHH
Q psy4275         103 LRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFFFFL  176 (182)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~~~~~~~  176 (182)
                      ..++.+.|+.....       ...|.|+|.+.+...- ....+..+.+++||+|||||+.+..+..+...+...
T Consensus       108 ~~~g~~~~~~~~~~-------~~~i~vat~qtl~~~~-~l~~~~~~~~~liI~DE~Hh~~a~~~~~~~~~~~~~  173 (442)
T COG1061         108 DEIGIYGGGEKELE-------PAKVTVATVQTLARRQ-LLDEFLGNEFGLIIFDEVHHLPAPSYRRILELLSAA  173 (442)
T ss_pred             cccceecCceeccC-------CCcEEEEEhHHHhhhh-hhhhhcccccCEEEEEccccCCcHHHHHHHHhhhcc
Confidence            23344444332111       1469999999997642 112223447899999999999998887777665543

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.73  E-value=7.8e-17  Score=133.16  Aligned_cols=131  Identities=23%  Similarity=0.208  Sum_probs=109.8

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSI  107 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  107 (182)
                      .|+|.|..+++.+..|+  +.++.||+|||+++.++++.....   +..++|++|++.||.|.++++..+.+.+|+++++
T Consensus       103 ~p~~VQ~~~~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al~---G~~v~VvTptreLA~qdae~~~~l~~~lGlsv~~  177 (656)
T PRK12898        103 RHFDVQLMGGLALLSGR--LAEMQTGEGKTLTATLPAGTAALA---GLPVHVITVNDYLAERDAELMRPLYEALGLTVGC  177 (656)
T ss_pred             CCChHHHHHHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhhc---CCeEEEEcCcHHHHHHHHHHHHHHHhhcCCEEEE
Confidence            79999999999999988  999999999999999999987665   6689999999999999999999999999999999


Q ss_pred             EEcCCchhhhhHHhcCCCcEEEEChHHH-HHHHhcCCC------------------------CCCCCccEEEEecccccc
Q psy4275         108 ITGGMDMVDQGKELAKKPHIVIATPGRL-ADHLDTCNT------------------------FSLNRIKFLVLDEADRLS  162 (182)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~Ilv~T~~~l-~~~~~~~~~------------------------~~~~~~~~iI~DE~h~~~  162 (182)
                      +.|+.+..  .+....+++|+++|+..+ .++++..-.                        .-.+.+.+.|+||+|.++
T Consensus       178 i~gg~~~~--~r~~~y~~dIvygT~~e~~FDyLrd~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~r~~~~aIvDEvDSiL  255 (656)
T PRK12898        178 VVEDQSPD--ERRAAYGADITYCTNKELVFDYLRDRLALGQRASDARLALESLHGRSSRSTQLLLRGLHFAIVDEADSVL  255 (656)
T ss_pred             EeCCCCHH--HHHHHcCCCEEEECCCchhhhhccccccccccccchhhhhhhhccccCchhhhcccccceeEeeccccee
Confidence            99987643  334445789999999998 566655311                        123557899999999987


Q ss_pred             ccC
Q psy4275         163 LMT  165 (182)
Q Consensus       163 ~~~  165 (182)
                      =+.
T Consensus       256 iDe  258 (656)
T PRK12898        256 IDE  258 (656)
T ss_pred             ecc
Confidence            544

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.73  E-value=3.5e-17  Score=136.63  Aligned_cols=131  Identities=15%  Similarity=0.126  Sum_probs=95.5

Q ss_pred             CChHHHHhhhhhhhC-C--CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCce
Q psy4275          28 TPTEIQKAIIPHVLN-D--EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLR  104 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~-~--~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~  104 (182)
                      .++|||++++..+.. +  ++.++++|||+|||++++..+...      +.++||+||+..|++||.+.++++.......
T Consensus       255 ~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa~~l------~k~tLILvps~~Lv~QW~~ef~~~~~l~~~~  328 (732)
T TIGR00603       255 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACTV------KKSCLVLCTSAVSVEQWKQQFKMWSTIDDSQ  328 (732)
T ss_pred             CcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHHHHh------CCCEEEEeCcHHHHHHHHHHHHHhcCCCCce
Confidence            589999999988764 3  478999999999999987665543      3479999999999999999999886544456


Q ss_pred             EEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcC-------CCCCCCCccEEEEeccccccccCChhH
Q psy4275         105 VSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTC-------NTFSLNRIKFLVLDEADRLSLMTSLKF  169 (182)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~-------~~~~~~~~~~iI~DE~h~~~~~~~~~~  169 (182)
                      +..+.|+...     .......|+|+|++++.....+.       ..+....++++|+||||++.+..+.+.
T Consensus       329 I~~~tg~~k~-----~~~~~~~VvVtTYq~l~~~~~r~~~~~~~l~~l~~~~~gLII~DEvH~lpA~~fr~i  395 (732)
T TIGR00603       329 ICRFTSDAKE-----RFHGEAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPAAMFRRV  395 (732)
T ss_pred             EEEEecCccc-----ccccCCcEEEEEHHHhhcccccchhhhHHHHHhccccCCEEEEEccccccHHHHHHH
Confidence            6666665322     11235789999999875432211       112335688999999999876555443

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).

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.73  E-value=9.9e-17  Score=134.99  Aligned_cols=122  Identities=23%  Similarity=0.288  Sum_probs=97.7

Q ss_pred             CChHHHHhhhhhhhCC---CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCce
Q psy4275          28 TPTEIQKAIIPHVLND---EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLR  104 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~---~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~  104 (182)
                      .+++.|.++++.+.++   ++.++.++||+|||.+++.++...+..   +.++++++|+++|+.|+.+.+++.   ++.+
T Consensus       144 ~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~---g~~vLvLvPt~~L~~Q~~~~l~~~---fg~~  217 (679)
T PRK05580        144 TLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLAQ---GKQALVLVPEIALTPQMLARFRAR---FGAP  217 (679)
T ss_pred             CCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHHc---CCeEEEEeCcHHHHHHHHHHHHHH---hCCC
Confidence            5899999999999873   789999999999999998776665544   568999999999999998888764   3578


Q ss_pred             EEEEEcCCchhhhhHH----hcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275         105 VSIITGGMDMVDQGKE----LAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus       105 ~~~~~~~~~~~~~~~~----~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      +..++|+.+..+....    ..++.+|+|+|+..+.        ..++++++||+||+|...-
T Consensus       218 v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~--------~p~~~l~liVvDEeh~~s~  272 (679)
T PRK05580        218 VAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALF--------LPFKNLGLIIVDEEHDSSY  272 (679)
T ss_pred             EEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHhc--------ccccCCCEEEEECCCcccc
Confidence            8889988765443322    2356899999987652        3477899999999998654

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.72  E-value=6.6e-17  Score=136.41  Aligned_cols=131  Identities=24%  Similarity=0.245  Sum_probs=105.7

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSI  107 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  107 (182)
                      .+.+.|....-.+..  .-+.+++||+|||+++.++++..+..   +..+.|++|++.||.|.++++..+.+.+|+++++
T Consensus        82 ~~ydvQliGg~~Lh~--G~Iaem~TGeGKTL~a~Lpa~~~al~---G~~V~VvTpn~yLA~qd~e~m~~l~~~lGLtv~~  156 (896)
T PRK13104         82 RHFDVQLIGGMVLHE--GNIAEMRTGEGKTLVATLPAYLNAIS---GRGVHIVTVNDYLAKRDSQWMKPIYEFLGLTVGV  156 (896)
T ss_pred             CcchHHHhhhhhhcc--CccccccCCCCchHHHHHHHHHHHhc---CCCEEEEcCCHHHHHHHHHHHHHHhcccCceEEE
Confidence            455555554444433  45889999999999999999977765   4469999999999999999999999999999999


Q ss_pred             EEcCCchhhhhHHhcCCCcEEEEChHHH-HHHHhcCCCCCC-----CCccEEEEeccccccccC
Q psy4275         108 ITGGMDMVDQGKELAKKPHIVIATPGRL-ADHLDTCNTFSL-----NRIKFLVLDEADRLSLMT  165 (182)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~Ilv~T~~~l-~~~~~~~~~~~~-----~~~~~iI~DE~h~~~~~~  165 (182)
                      +.|+.+.......+  .++|+++||+.+ .++++....+.+     +.+.++|+||+|.|+-+.
T Consensus       157 i~gg~~~~~r~~~y--~~dIvygT~grlgfDyLrd~~~~~~~~~v~r~l~~~IvDEaDsiLIDe  218 (896)
T PRK13104        157 IYPDMSHKEKQEAY--KADIVYGTNNEYGFDYLRDNMAFSLTDKVQRELNFAIVDEVDSILIDE  218 (896)
T ss_pred             EeCCCCHHHHHHHh--CCCEEEECChhhhHHHHhcCCccchHhhhccccceEEeccHhhhhhhc
Confidence            99987765554443  689999999999 999987433433     588999999999998544

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

Probab=99.71  E-value=3.8e-17  Score=132.92  Aligned_cols=152  Identities=20%  Similarity=0.247  Sum_probs=116.8

Q ss_pred             HHHHH-CCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHh
Q psy4275          19 RQCQT-IGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVL   97 (182)
Q Consensus        19 ~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~   97 (182)
                      ..|++ +|+..+++-|.+++..+.++++.++..|||+||++||.++.+-.      .+-+|||.|..+|.....+.++..
T Consensus         7 ~~L~~~fGy~~FR~gQ~evI~~~l~g~d~lvvmPTGgGKSlCyQiPAll~------~G~TLVVSPLiSLM~DQV~~l~~~   80 (590)
T COG0514           7 QVLKQVFGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLL------EGLTLVVSPLISLMKDQVDQLEAA   80 (590)
T ss_pred             HHHHHHhCccccCCCHHHHHHHHHcCCcEEEEccCCCCcchHhhhHHHhc------CCCEEEECchHHHHHHHHHHHHHc
Confidence            44544 68999999999999999999999999999999999999998876      347999999999955444444333


Q ss_pred             hccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccC--ChhHHH
Q psy4275          98 GKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMT--SLKFFF  171 (182)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~--~~~~~~  171 (182)
                          |+.+..+++..+..++...+    ....+++..+|+.+..--.. +.+.--+++++++|||||+..|+  ++....
T Consensus        81 ----Gi~A~~lnS~l~~~e~~~v~~~l~~g~~klLyisPErl~~~~f~-~~L~~~~i~l~vIDEAHCiSqWGhdFRP~Y~  155 (590)
T COG0514          81 ----GIRAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERLMSPRFL-ELLKRLPISLVAIDEAHCISQWGHDFRPDYR  155 (590)
T ss_pred             ----CceeehhhcccCHHHHHHHHHHHhcCceeEEEECchhhcChHHH-HHHHhCCCceEEechHHHHhhcCCccCHhHH
Confidence                78888888876655444332    23578999999998542111 11123457899999999999997  888888


Q ss_pred             HHHHHhhcCC
Q psy4275         172 FFFFLKYYIP  181 (182)
Q Consensus       172 ~~~~~~~~~~  181 (182)
                      .+..++..+|
T Consensus       156 ~lg~l~~~~~  165 (590)
T COG0514         156 RLGRLRAGLP  165 (590)
T ss_pred             HHHHHHhhCC
Confidence            8888887765

>PF04851 ResIII: Type III restriction enzyme, res subunit; InterPro: IPR006935 This entry represents a domain found in the N terminus of several proteins, including helicases, the R subunit (HsdR) of type I restriction endonucleases (3

Probab=99.70  E-value=1.1e-16  Score=114.21  Aligned_cols=132  Identities=22%  Similarity=0.247  Sum_probs=89.9

Q ss_pred             CChHHHHhhhhhhhC-------CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhcc
Q psy4275          28 TPTEIQKAIIPHVLN-------DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKV  100 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~-------~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~  100 (182)
                      +++++|.+++..+.+       .++.++.+|||+|||.+++..+.....      ++++++|+.++++|+.+.++.+...
T Consensus         3 ~lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~~------~~l~~~p~~~l~~Q~~~~~~~~~~~   76 (184)
T PF04851_consen    3 KLRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILELAR------KVLIVAPNISLLEQWYDEFDDFGSE   76 (184)
T ss_dssp             EE-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHHHC------EEEEEESSHHHHHHHHHHHHHHSTT
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhcccc------ceeEecCHHHHHHHHHHHHHHhhhh
Confidence            589999999988874       589999999999999998755555433      7999999999999999888665443


Q ss_pred             CCceEE-----------EEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCC----------CCCCCccEEEEeccc
Q psy4275         101 MNLRVS-----------IITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNT----------FSLNRIKFLVLDEAD  159 (182)
Q Consensus       101 ~~~~~~-----------~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~----------~~~~~~~~iI~DE~h  159 (182)
                      ......           ...................+++++|.+.+.........          ......+++|+||||
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~vI~DEaH  156 (184)
T PF04851_consen   77 KYNFFEKSIKPAYDSKEFISIQDDISDKSESDNNDKDIILTTYQSLQSDIKEEKKIDESARRSYKLLKNKFDLVIIDEAH  156 (184)
T ss_dssp             SEEEEE--GGGCCE-SEEETTTTEEEHHHHHCBSS-SEEEEEHHHHHHHHHH---------GCHHGGGGSESEEEEETGG
T ss_pred             hhhhcccccccccccccccccccccccccccccccccchhhHHHHHHhhcccccccccchhhhhhhccccCCEEEEehhh
Confidence            211100           00111111122223345778999999999887654211          133456899999999


Q ss_pred             cccccC
Q psy4275         160 RLSLMT  165 (182)
Q Consensus       160 ~~~~~~  165 (182)
                      ++.+..
T Consensus       157 ~~~~~~  162 (184)
T PF04851_consen  157 HYPSDS  162 (184)
T ss_dssp             CTHHHH
T ss_pred             hcCCHH
Confidence            987766

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 ....

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

Probab=99.69  E-value=2.6e-16  Score=134.30  Aligned_cols=139  Identities=20%  Similarity=0.204  Sum_probs=114.4

Q ss_pred             HCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCC
Q psy4275          23 TIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMN  102 (182)
Q Consensus        23 ~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~  102 (182)
                      ..++ .+.++|++++..+..+.++++++|||+|||+++.+++...+.+   +.+++|.+|.++|.+|.+..+...+....
T Consensus       115 ~~~F-~LD~fQ~~a~~~Ler~esVlV~ApTssGKTvVaeyAi~~al~~---~qrviYTsPIKALsNQKyrdl~~~fgdv~  190 (1041)
T COG4581         115 EYPF-ELDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIALALRD---GQRVIYTSPIKALSNQKYRDLLAKFGDVA  190 (1041)
T ss_pred             hCCC-CcCHHHHHHHHHHhCCCcEEEEccCCCCcchHHHHHHHHHHHc---CCceEeccchhhhhhhHHHHHHHHhhhhh
Confidence            3454 7999999999999999999999999999999998888877766   45799999999999999877666555433


Q ss_pred             ceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHHHHH
Q psy4275         103 LRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFF  173 (182)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~~~~  173 (182)
                      --+++++|+.+       +..++.++|.|.+.+.+++-. +...+..+..|||||+|.|.+....-.|+..
T Consensus       191 ~~vGL~TGDv~-------IN~~A~clvMTTEILRnMlyr-g~~~~~~i~~ViFDEvHyi~D~eRG~VWEE~  253 (1041)
T COG4581         191 DMVGLMTGDVS-------INPDAPCLVMTTEILRNMLYR-GSESLRDIEWVVFDEVHYIGDRERGVVWEEV  253 (1041)
T ss_pred             hhccceeccee-------eCCCCceEEeeHHHHHHHhcc-CcccccccceEEEEeeeeccccccchhHHHH
Confidence            34577788774       456788999999999998877 5667889999999999999998866655544

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.66  E-value=2.1e-15  Score=128.73  Aligned_cols=121  Identities=18%  Similarity=0.219  Sum_probs=94.8

Q ss_pred             hHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHH-hhccCCceEEEE
Q psy4275          30 TEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLV-LGKVMNLRVSII  108 (182)
Q Consensus        30 ~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~-~~~~~~~~~~~~  108 (182)
                      ...-.+.+..+.++++++++++||+|||+++..++++....   +++++++.|++.++.|+++.+.. +....+..+++.
T Consensus         7 ~~~~~~i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~~~---~~~ilvlqPrR~aA~qia~rva~~l~~~~g~~VGy~   83 (812)
T PRK11664          7 AAVLPELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGGI---NGKIIMLEPRRLAARNVAQRLAEQLGEKPGETVGYR   83 (812)
T ss_pred             HHHHHHHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHcCCc---CCeEEEECChHHHHHHHHHHHHHHhCcccCceEEEE
Confidence            33445566677778899999999999999999988876433   34899999999999999888754 555567777776


Q ss_pred             EcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccc
Q psy4275         109 TGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL  161 (182)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~  161 (182)
                      .++.+.      ..++.+|+|+||+.+++++...  ..++++++||+||+|+.
T Consensus        84 vr~~~~------~~~~t~I~v~T~G~Llr~l~~d--~~L~~v~~IIlDEaHER  128 (812)
T PRK11664         84 MRAESK------VGPNTRLEVVTEGILTRMIQRD--PELSGVGLVILDEFHER  128 (812)
T ss_pred             ecCccc------cCCCCcEEEEChhHHHHHHhhC--CCcCcCcEEEEcCCCcc
Confidence            654432      1235689999999999988763  36889999999999983

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.66  E-value=5.1e-15  Score=126.28  Aligned_cols=124  Identities=19%  Similarity=0.246  Sum_probs=95.7

Q ss_pred             HHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHH-HhhccCCceEEEEE
Q psy4275          31 EIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFL-VLGKVMNLRVSIIT  109 (182)
Q Consensus        31 ~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~-~~~~~~~~~~~~~~  109 (182)
                      .+-.+.+..+.++++++++++||+|||+.+..++++....   +++++++.|++.++.|+++.+. .+....|..|++..
T Consensus         5 ~~~~~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~~---~~~ilvlqPrR~aA~qiA~rva~~~~~~~g~~VGy~v   81 (819)
T TIGR01970         5 AVLPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPGI---GGKIIMLEPRRLAARSAAQRLASQLGEAVGQTVGYRV   81 (819)
T ss_pred             HHHHHHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhhcc---CCeEEEEeCcHHHHHHHHHHHHHHhCCCcCcEEEEEE
Confidence            3445566677778899999999999999999999887532   4589999999999999998875 45555566676554


Q ss_pred             cCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccc-ccccC
Q psy4275         110 GGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR-LSLMT  165 (182)
Q Consensus       110 ~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~-~~~~~  165 (182)
                      +..+      ...++.+|+|+|++.+++.++..  ..++++++||+||+|+ +.+.+
T Consensus        82 r~~~------~~s~~t~I~v~T~G~Llr~l~~d--~~L~~v~~VIiDEaHER~L~~D  130 (819)
T TIGR01970        82 RGEN------KVSRRTRLEVVTEGILTRMIQDD--PELDGVGALIFDEFHERSLDAD  130 (819)
T ss_pred             cccc------ccCCCCcEEEECCcHHHHHHhhC--cccccCCEEEEeccchhhhccc
Confidence            4332      22346789999999999988763  3688999999999995 44433

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.

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.66  E-value=2.1e-15  Score=126.02  Aligned_cols=127  Identities=14%  Similarity=0.046  Sum_probs=92.0

Q ss_pred             hHHHHhhhhhhhCCCcEEEECCCCChHHHHHH---------HHHHHhhc---cCCCCeeEEEEcCCHHHHHHHHHHHHHh
Q psy4275          30 TEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFA---------LPILQKWC---EDPYGIFALVLTPTRELAYQIGDQFLVL   97 (182)
Q Consensus        30 ~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~---------~~~~~~~~---~~~~~~~~lil~p~~~l~~q~~~~~~~~   97 (182)
                      ...|.++++.+.++++++++|+||+|||.+..         ++.+..+.   .+..+.++++++|+++++.|+.+.+.+.
T Consensus       166 ~~iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~~~~~~~~ilvt~PrreLa~qi~~~i~~~  245 (675)
T PHA02653        166 PDVQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKIDPNFIERPIVLSLPRVALVRLHSITLLKS  245 (675)
T ss_pred             HHHHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcccccCCcEEEEECcHHHHHHHHHHHHHHH
Confidence            45688999999999999999999999998732         22233221   1223568999999999999998888765


Q ss_pred             hcc---CCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccC
Q psy4275          98 GKV---MNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus        98 ~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~  165 (182)
                      ...   .+.++....|+.... .........+|+|+|++.        ....+++++++|+||+|++...+
T Consensus       246 vg~~~~~g~~v~v~~Gg~~~~-~~~t~~k~~~Ilv~T~~L--------~l~~L~~v~~VVIDEaHEr~~~~  307 (675)
T PHA02653        246 LGFDEIDGSPISLKYGSIPDE-LINTNPKPYGLVFSTHKL--------TLNKLFDYGTVIIDEVHEHDQIG  307 (675)
T ss_pred             hCccccCCceEEEEECCcchH-HhhcccCCCCEEEEeCcc--------cccccccCCEEEccccccCccch
Confidence            543   356677888887632 112223367899999652        11247789999999999998766

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

Probab=99.65  E-value=1.7e-15  Score=123.68  Aligned_cols=147  Identities=24%  Similarity=0.334  Sum_probs=118.3

Q ss_pred             CCCCHHHHHHH-HHCCCCCChHHHHhhhhhhhCC------CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275          11 LKLNPWLIRQC-QTIGVKTPTEIQKAIIPHVLND------EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus        11 ~~l~~~i~~~l-~~~~~~~~~~~Q~~~~~~~~~~------~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      ++.+.++.+.+ ....| +++..|++++..+..+      -+-+++|..|||||++++++++....+   |.++...+||
T Consensus       245 ~~~~~~l~~~~~~~LPF-~LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~~---G~Q~ALMAPT  320 (677)
T COG1200         245 LPANGELLAKFLAALPF-KLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEA---GYQAALMAPT  320 (677)
T ss_pred             CCccHHHHHHHHHhCCC-CccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHHc---CCeeEEeccH
Confidence            45566655555 55666 8999999999988762      378999999999999999999988777   7799999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHH---hc-CCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccc
Q psy4275          84 RELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKE---LA-KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEAD  159 (182)
Q Consensus        84 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~-~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h  159 (182)
                      .-||+|.++.+.++++.+|++|..+.|......+...   +. +..+|+|||..-+    +.  ...+++++++|+||-|
T Consensus       321 EILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALi----Qd--~V~F~~LgLVIiDEQH  394 (677)
T COG1200         321 EILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALI----QD--KVEFHNLGLVIIDEQH  394 (677)
T ss_pred             HHHHHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhh----hc--ceeecceeEEEEeccc
Confidence            9999999999999999999999999998765444333   23 3589999996543    32  3467889999999999


Q ss_pred             cccccCCh
Q psy4275         160 RLSLMTSL  167 (182)
Q Consensus       160 ~~~~~~~~  167 (182)
                      ++......
T Consensus       395 RFGV~QR~  402 (677)
T COG1200         395 RFGVHQRL  402 (677)
T ss_pred             cccHHHHH
Confidence            98765543

>KOG0951|consensus

Probab=99.64  E-value=9.9e-16  Score=130.92  Aligned_cols=154  Identities=20%  Similarity=0.269  Sum_probs=120.5

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHhhhhhhhC-CCcEEEECCCCChHHHHHHHHHHHhhccCCC--------CeeEEEEcCC
Q psy4275          13 LNPWLIRQCQTIGVKTPTEIQKAIIPHVLN-DEDCIGCAKTGSGKTLAFALPILQKWCEDPY--------GIFALVLTPT   83 (182)
Q Consensus        13 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~--------~~~~lil~p~   83 (182)
                      ++++-..++  +|...++++|......... ..|.++|||||+|||.++++.+++.+..+..        ..+++|++|.
T Consensus       296 lP~Wnq~aF--~g~~sLNrIQS~v~daAl~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAPm  373 (1674)
T KOG0951|consen  296 LPKWNQPAF--FGKQSLNRIQSKVYDAALRGDENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAPM  373 (1674)
T ss_pred             Ccchhhhhc--ccchhhhHHHHHHHHHHhcCcCcEEEeccCCCCchHHHHHHHHHHHhcccccccceecccceEEEEeeH
Confidence            444444444  3556799999999988766 6799999999999999999999998866422        3589999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCC-CCCccEEEEecccccc
Q psy4275          84 RELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFS-LNRIKFLVLDEADRLS  162 (182)
Q Consensus        84 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~-~~~~~~iI~DE~h~~~  162 (182)
                      ++|+.++...+.+....+|++|...+|+.....+   -..+.+|+||||+++.-.-++.+... .+-++++|+||+|.+-
T Consensus       374 KaLvqE~VgsfSkRla~~GI~V~ElTgD~~l~~~---qieeTqVIV~TPEK~DiITRk~gdraY~qlvrLlIIDEIHLLh  450 (1674)
T KOG0951|consen  374 KALVQEMVGSFSKRLAPLGITVLELTGDSQLGKE---QIEETQVIVTTPEKWDIITRKSGDRAYEQLVRLLIIDEIHLLH  450 (1674)
T ss_pred             HHHHHHHHHHHHhhccccCcEEEEecccccchhh---hhhcceeEEeccchhhhhhcccCchhHHHHHHHHhhhhhhhcc
Confidence            9999999999999999999999999998754332   13478999999999977766644432 3357899999999886


Q ss_pred             ccCChhHHH
Q psy4275         163 LMTSLKFFF  171 (182)
Q Consensus       163 ~~~~~~~~~  171 (182)
                      ++.+.....
T Consensus       451 DdRGpvLES  459 (1674)
T KOG0951|consen  451 DDRGPVLES  459 (1674)
T ss_pred             cccchHHHH
Confidence            666544433

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

Probab=99.64  E-value=9.5e-15  Score=126.14  Aligned_cols=94  Identities=22%  Similarity=0.322  Sum_probs=73.3

Q ss_pred             CHHHHHHHHHCCCCCChHHHHhhhh----hhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHH
Q psy4275          14 NPWLIRQCQTIGVKTPTEIQKAIIP----HVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQ   89 (182)
Q Consensus        14 ~~~i~~~l~~~~~~~~~~~Q~~~~~----~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q   89 (182)
                      ++...+.+...|+ +++|.|.+.+.    .+.++++.++.+|||+|||.+|+++++.....   +.+++|.+||++|++|
T Consensus       232 ~~~~~~~~~~~~~-~~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~~---~~~vvi~t~t~~Lq~Q  307 (850)
T TIGR01407       232 SSLFSKNIDRLGL-EYRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAIT---EKPVVISTNTKVLQSQ  307 (850)
T ss_pred             cHHHHHhhhhcCC-ccCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhcC---CCeEEEEeCcHHHHHH
Confidence            3466667766777 58999998665    55568899999999999999999999887652   4589999999999999


Q ss_pred             HH-HHHHHhhccCC--ceEEEEEcC
Q psy4275          90 IG-DQFLVLGKVMN--LRVSIITGG  111 (182)
Q Consensus        90 ~~-~~~~~~~~~~~--~~~~~~~~~  111 (182)
                      +. +.+..+.+.++  +++..+.|+
T Consensus       308 l~~~~~~~l~~~~~~~~~~~~~kG~  332 (850)
T TIGR01407       308 LLEKDIPLLNEILNFKINAALIKGK  332 (850)
T ss_pred             HHHHHHHHHHHHcCCCceEEEEEcc
Confidence            85 46776665554  666666654

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.

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.64  E-value=1.5e-15  Score=119.54  Aligned_cols=128  Identities=17%  Similarity=0.060  Sum_probs=85.5

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchh---------
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMV---------  115 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~---------  115 (182)
                      .+++++|||+|||.+++.++++.+.+. .+.+++|++|+++|++|+++.++.++..   ++...+++....         
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~~-~~~~ii~v~P~~~L~~q~~~~l~~~f~~---~~~~~~~~~~~~~~~~~~~~~   76 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKSQ-KADRVIIALPTRATINAMYRRAKELFGS---NLGLLHSSSSFKRIKEMGDSE   76 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhhC-CCCeEEEEeehHHHHHHHHHHHHHHhCc---ccEEeeccHHHHHHhccCCch
Confidence            368999999999999999999876543 3569999999999999999998887542   344444432210         


Q ss_pred             --hh-hHHh------cCCCcEEEEChHHHHHHHhcC-CC--CCC--CCccEEEEeccccccccCChhHHHHHHHH
Q psy4275         116 --DQ-GKEL------AKKPHIVIATPGRLADHLDTC-NT--FSL--NRIKFLVLDEADRLSLMTSLKFFFFFFFL  176 (182)
Q Consensus       116 --~~-~~~~------~~~~~Ilv~T~~~l~~~~~~~-~~--~~~--~~~~~iI~DE~h~~~~~~~~~~~~~~~~~  176 (182)
                        .. ....      .-..+|+|+||+.+...+... ..  +..  -..+++|+||+|.+.+.+.......+..+
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iViDE~h~~~~~~~~~l~~~l~~l  151 (358)
T TIGR01587        77 EFEHLFPLYIHSNDKLFLDPITVCTIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVHFYDEYTLALILAVLEVL  151 (358)
T ss_pred             hHHHHHHHHhhchhhhhhCCeeeCCHHHHHHHHhcccchHHHHHHHhcCCEEEEeCCCCCCHHHHHHHHHHHHHH
Confidence              00 0000      113679999999998876551 11  111  12378999999999886544444444333

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.

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.63  E-value=4.3e-15  Score=125.24  Aligned_cols=131  Identities=22%  Similarity=0.195  Sum_probs=105.6

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSI  107 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  107 (182)
                      .+++.|-...-.+..|  -+.++.||+|||+++.++++-....   +..+-+++|+..||.|.++++..+.+.+|+++++
T Consensus        81 ~~~dvQlig~l~L~~G--~Iaem~TGeGKTLva~lpa~l~aL~---G~~V~IvTpn~yLA~rd~e~~~~l~~~LGlsv~~  155 (830)
T PRK12904         81 RHFDVQLIGGMVLHEG--KIAEMKTGEGKTLVATLPAYLNALT---GKGVHVVTVNDYLAKRDAEWMGPLYEFLGLSVGV  155 (830)
T ss_pred             CCCccHHHhhHHhcCC--chhhhhcCCCcHHHHHHHHHHHHHc---CCCEEEEecCHHHHHHHHHHHHHHHhhcCCeEEE
Confidence            5677776666555444  4899999999999999988644444   3357799999999999999999999999999999


Q ss_pred             EEcCCchhhhhHHhcCCCcEEEEChHHH-HHHHhcCCC-----CCCCCccEEEEeccccccccC
Q psy4275         108 ITGGMDMVDQGKELAKKPHIVIATPGRL-ADHLDTCNT-----FSLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~Ilv~T~~~l-~~~~~~~~~-----~~~~~~~~iI~DE~h~~~~~~  165 (182)
                      +.|+.+...+...+  .++|+++||..+ .++++....     ...+.+.++|+||+|.|+=+.
T Consensus       156 i~~~~~~~er~~~y--~~dI~ygT~~elgfDyLrd~~~~~~~~~~~r~~~~aIvDEaDsiLIDe  217 (830)
T PRK12904        156 ILSGMSPEERREAY--AADITYGTNNEFGFDYLRDNMVFSLEERVQRGLNYAIVDEVDSILIDE  217 (830)
T ss_pred             EcCCCCHHHHHHhc--CCCeEEECCcchhhhhhhcccccchhhhcccccceEEEechhhheecc
Confidence            99988776655554  489999999999 899987432     246778899999999998554

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

Probab=99.60  E-value=1.3e-14  Score=127.03  Aligned_cols=132  Identities=17%  Similarity=0.113  Sum_probs=89.6

Q ss_pred             CChHHHHhhhhhhhC-----CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCC
Q psy4275          28 TPTEIQKAIIPHVLN-----DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMN  102 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~-----~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~  102 (182)
                      .++++|.+++..+.+     .++.+++++||+|||.+++. ++..+.......++|+++|+.+|+.|+.+.++......+
T Consensus       413 ~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai~-li~~L~~~~~~~rVLfLvDR~~L~~Qa~~~F~~~~~~~~  491 (1123)
T PRK11448        413 GLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAIA-LMYRLLKAKRFRRILFLVDRSALGEQAEDAFKDTKIEGD  491 (1123)
T ss_pred             CCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHHHH-HHHHHHhcCccCeEEEEecHHHHHHHHHHHHHhcccccc
Confidence            589999999977653     46799999999999988544 444455444456999999999999999988887633222


Q ss_pred             ceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcC----CCCCCCCccEEEEecccccc
Q psy4275         103 LRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTC----NTFSLNRIKFLVLDEADRLS  162 (182)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~----~~~~~~~~~~iI~DE~h~~~  162 (182)
                      .......+......  .......+|+|+|.+++...+...    ..+.+.++++||+||||+-.
T Consensus       492 ~~~~~i~~i~~L~~--~~~~~~~~I~iaTiQtl~~~~~~~~~~~~~~~~~~fdlIIiDEaHRs~  553 (1123)
T PRK11448        492 QTFASIYDIKGLED--KFPEDETKVHVATVQGMVKRILYSDDPMDKPPVDQYDCIIVDEAHRGY  553 (1123)
T ss_pred             cchhhhhchhhhhh--hcccCCCCEEEEEHHHHHHhhhccccccccCCCCcccEEEEECCCCCC
Confidence            11111111111001  112345789999999997765321    12456788999999999953

>KOG0353|consensus

Probab=99.59  E-value=1.2e-14  Score=111.75  Aligned_cols=163  Identities=20%  Similarity=0.218  Sum_probs=124.5

Q ss_pred             cCCCCCHHHHHHHHH-CCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHH
Q psy4275           9 TDLKLNPWLIRQCQT-IGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELA   87 (182)
Q Consensus         9 ~~~~l~~~i~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~   87 (182)
                      ++||++.+..+.++. +.+..++|.|..++.....+++.++..|||.||++||.++.+-.      .+.+++++|..+|.
T Consensus        74 d~fpws~e~~~ilk~~f~lekfrplq~~ain~~ma~ed~~lil~tgggkslcyqlpal~a------dg~alvi~plislm  147 (695)
T KOG0353|consen   74 DDFPWSDEAKDILKEQFHLEKFRPLQLAAINATMAGEDAFLILPTGGGKSLCYQLPALCA------DGFALVICPLISLM  147 (695)
T ss_pred             CCCCCchHHHHHHHHHhhHHhcChhHHHHhhhhhccCceEEEEeCCCccchhhhhhHHhc------CCceEeechhHHHH
Confidence            678999999999974 67889999999999999999999999999999999999998765      67899999999998


Q ss_pred             HHHHHHHHHhhccCCceEEEEEcCCchhhhh---HHhcC---CCcEEEEChHHHHHH---Hhc-CCCCCCCCccEEEEec
Q psy4275          88 YQIGDQFLVLGKVMNLRVSIITGGMDMVDQG---KELAK---KPHIVIATPGRLADH---LDT-CNTFSLNRIKFLVLDE  157 (182)
Q Consensus        88 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~---~~~Ilv~T~~~l~~~---~~~-~~~~~~~~~~~iI~DE  157 (182)
                      +...-.++.+    |+....+..+.+..+..   ..+.+   +..++..||+++...   +.+ .+.+....+.+|.+||
T Consensus       148 edqil~lkql----gi~as~lnansske~~k~v~~~i~nkdse~kliyvtpekiaksk~~mnkleka~~~~~~~~iaide  223 (695)
T KOG0353|consen  148 EDQILQLKQL----GIDASMLNANSSKEEAKRVEAAITNKDSEFKLIYVTPEKIAKSKKFMNKLEKALEAGFFKLIAIDE  223 (695)
T ss_pred             HHHHHHHHHh----CcchhhccCcccHHHHHHHHHHHcCCCceeEEEEecHHHHHHHHHHHHHHHHHhhcceeEEEeecc
Confidence            7665566655    66666666555543222   22222   457899999998642   211 1334567788999999


Q ss_pred             cccccccC--ChhHHHHHHHHhhcCC
Q psy4275         158 ADRLSLMT--SLKFFFFFFFLKYYIP  181 (182)
Q Consensus       158 ~h~~~~~~--~~~~~~~~~~~~~~~~  181 (182)
                      +|+-..|+  ++.....+..+++-+|
T Consensus       224 vhccsqwghdfr~dy~~l~ilkrqf~  249 (695)
T KOG0353|consen  224 VHCCSQWGHDFRPDYKALGILKRQFK  249 (695)
T ss_pred             eeehhhhCcccCcchHHHHHHHHhCC
Confidence            99999887  5566666777776665

>KOG0352|consensus

Probab=99.59  E-value=7.3e-15  Score=114.10  Aligned_cols=154  Identities=20%  Similarity=0.293  Sum_probs=112.8

Q ss_pred             HHHHHHHH-CCCCC-ChHHHHhhhhhhhC-CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHH
Q psy4275          16 WLIRQCQT-IGVKT-PTEIQKAIIPHVLN-DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGD   92 (182)
Q Consensus        16 ~i~~~l~~-~~~~~-~~~~Q~~~~~~~~~-~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~   92 (182)
                      .+.++|++ +|+.. -++.|++++..+.+ +.++.+++|||+||++||.++.+..      ++-+|++.|..+|+....+
T Consensus         6 ~VreaLKK~FGh~kFKs~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~~------~gITIV~SPLiALIkDQiD   79 (641)
T KOG0352|consen    6 KVREALKKLFGHKKFKSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPALVH------GGITIVISPLIALIKDQID   79 (641)
T ss_pred             HHHHHHHHHhCchhhcChHHHHHHHHHHhccCcEEEeccCCCchhhhhhchHHHh------CCeEEEehHHHHHHHHHHH
Confidence            45667765 56654 58999999988766 6699999999999999999998775      5689999999999877666


Q ss_pred             HHHHhhccCCceEEEEEcCCchhhhhHHhc------CCCcEEEEChHHHHH-----HHhcCCCCCCCCccEEEEeccccc
Q psy4275          93 QFLVLGKVMNLRVSIITGGMDMVDQGKELA------KKPHIVIATPGRLAD-----HLDTCNTFSLNRIKFLVLDEADRL  161 (182)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~Ilv~T~~~l~~-----~~~~~~~~~~~~~~~iI~DE~h~~  161 (182)
                      .+.++    -+++..+++..+..++.+.+-      ....++..||+....     +++.  ..+-+.++++|+||||++
T Consensus        80 HL~~L----KVp~~SLNSKlSt~ER~ri~~DL~~ekp~~K~LYITPE~AAt~~FQ~lLn~--L~~r~~L~Y~vVDEAHCV  153 (641)
T KOG0352|consen   80 HLKRL----KVPCESLNSKLSTVERSRIMGDLAKEKPTIKMLYITPEGAATDGFQKLLNG--LANRDVLRYIVVDEAHCV  153 (641)
T ss_pred             HHHhc----CCchhHhcchhhHHHHHHHHHHHHhcCCceeEEEEchhhhhhhhHHHHHHH--HhhhceeeeEEechhhhH
Confidence            66665    455666666666555444332      256789999997632     2222  113345789999999999


Q ss_pred             cccC--ChhHHHHHHHHhhcCC
Q psy4275         162 SLMT--SLKFFFFFFFLKYYIP  181 (182)
Q Consensus       162 ~~~~--~~~~~~~~~~~~~~~~  181 (182)
                      ..|+  ++.....+..+|..+|
T Consensus       154 SQWGHDFRPDYL~LG~LRS~~~  175 (641)
T KOG0352|consen  154 SQWGHDFRPDYLTLGSLRSVCP  175 (641)
T ss_pred             hhhccccCcchhhhhhHHhhCC
Confidence            9988  6677777777777664

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

Probab=99.58  E-value=1.3e-13  Score=118.49  Aligned_cols=157  Identities=22%  Similarity=0.181  Sum_probs=121.5

Q ss_pred             CCCCHHHHHHHHHCCCCCChHHHHhhhhhhhC----CC--cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCH
Q psy4275          11 LKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLN----DE--DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTR   84 (182)
Q Consensus        11 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~----~~--~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~   84 (182)
                      ++.+.+..+.+....-...+|-|..++..+.+    ++  +-++||..|.|||-+++.++......   |++|.++|||.
T Consensus       577 f~~d~~~q~~F~~~FPyeET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~~---GKQVAvLVPTT  653 (1139)
T COG1197         577 FPPDTEWQEEFEASFPYEETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVMD---GKQVAVLVPTT  653 (1139)
T ss_pred             CCCChHHHHHHHhcCCCcCCHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHHHHHHHHHhcC---CCeEEEEcccH
Confidence            44555555566443333789999999999877    22  78999999999999999988887777   67999999999


Q ss_pred             HHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccc
Q psy4275          85 ELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR  160 (182)
Q Consensus        85 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~  160 (182)
                      -|++|.++.+++-+..+++++..+..-.+..+....+    .+..+|+|||..-+    .  +.+.+++++++|+||-|+
T Consensus       654 lLA~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTHrLL----~--kdv~FkdLGLlIIDEEqR  727 (1139)
T COG1197         654 LLAQQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHRLL----S--KDVKFKDLGLLIIDEEQR  727 (1139)
T ss_pred             HhHHHHHHHHHHHhcCCCeeEEEecccCCHHHHHHHHHHHhcCCccEEEechHhh----C--CCcEEecCCeEEEechhh
Confidence            9999999999999999999998887665554444333    24789999995433    2  456788999999999999


Q ss_pred             ccccCChhHHHHHHHHhhcC
Q psy4275         161 LSLMTSLKFFFFFFFLKYYI  180 (182)
Q Consensus       161 ~~~~~~~~~~~~~~~~~~~~  180 (182)
                      +..    +..+.+..++...
T Consensus       728 FGV----k~KEkLK~Lr~~V  743 (1139)
T COG1197         728 FGV----KHKEKLKELRANV  743 (1139)
T ss_pred             cCc----cHHHHHHHHhccC
Confidence            654    4556677666543

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

Probab=99.58  E-value=9.1e-14  Score=117.45  Aligned_cols=143  Identities=17%  Similarity=0.171  Sum_probs=109.5

Q ss_pred             HHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHH
Q psy4275          17 LIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLV   96 (182)
Q Consensus        17 i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~   96 (182)
                      +.+.+.+....+|+..|+.....+..|+++-+.+|||.|||+..++..+....+   +.+++||+||..|+.|.++.+++
T Consensus        71 ~~~fF~k~~G~~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTfg~~~sl~~a~k---gkr~yii~PT~~Lv~Q~~~kl~~  147 (1187)
T COG1110          71 FEEFFKKATGFRPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFGLLMSLYLAKK---GKRVYIIVPTTTLVRQVYERLKK  147 (1187)
T ss_pred             HHHHHHHhhCCCchHHHHHHHHHHHcCCceEEEcCCCCchhHHHHHHHHHHHhc---CCeEEEEecCHHHHHHHHHHHHH
Confidence            334444443348999999999999999999999999999999876666665554   57999999999999999999999


Q ss_pred             hhccCC-ceEEE-EEcCCchhhhhH----HhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccC
Q psy4275          97 LGKVMN-LRVSI-ITGGMDMVDQGK----ELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus        97 ~~~~~~-~~~~~-~~~~~~~~~~~~----~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~  165 (182)
                      +....+ .++.. +|+..+..+...    .-.++.+|+|+|.+.+.+.+.....   -++++|.+|++|.++..+
T Consensus       148 ~~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~FL~k~~e~L~~---~kFdfifVDDVDA~Lkas  219 (1187)
T COG1110         148 FAEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLSKRFEELSK---LKFDFIFVDDVDAILKAS  219 (1187)
T ss_pred             HHhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHHHHhhHHHhcc---cCCCEEEEccHHHHHhcc
Confidence            987766 44433 666644433222    2234789999999999888876332   357899999999988655

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.56  E-value=1.6e-14  Score=122.06  Aligned_cols=132  Identities=23%  Similarity=0.218  Sum_probs=103.8

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSI  107 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  107 (182)
                      .+.+.|....-.+.  ..-+.+++||.|||+++.++++.....   +..+.||+|+..||.+.++++..+.+.+|++|.+
T Consensus        82 ~~ydVQliGgl~L~--~G~IaEm~TGEGKTL~a~lp~~l~al~---g~~VhIvT~ndyLA~RD~e~m~~l~~~lGlsv~~  156 (908)
T PRK13107         82 RHFDVQLLGGMVLD--SNRIAEMRTGEGKTLTATLPAYLNALT---GKGVHVITVNDYLARRDAENNRPLFEFLGLTVGI  156 (908)
T ss_pred             CcCchHHhcchHhc--CCccccccCCCCchHHHHHHHHHHHhc---CCCEEEEeCCHHHHHHHHHHHHHHHHhcCCeEEE
Confidence            45555554443333  345899999999999999998877666   4459999999999999999999999999999999


Q ss_pred             EEcCCchhhhhHHhcCCCcEEEEChHHH-HHHHhcCCCCCC-----CCccEEEEeccccccccCC
Q psy4275         108 ITGGMDMVDQGKELAKKPHIVIATPGRL-ADHLDTCNTFSL-----NRIKFLVLDEADRLSLMTS  166 (182)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~Ilv~T~~~l-~~~~~~~~~~~~-----~~~~~iI~DE~h~~~~~~~  166 (182)
                      +.++.+......  .-.++|+++||..+ .++++..-....     +.+.++|+||+|.++-+..
T Consensus       157 i~~~~~~~~r~~--~Y~~dI~YgT~~e~gfDyLrdnm~~~~~~~vqr~~~~aIvDEvDsiLiDEA  219 (908)
T PRK13107        157 NVAGLGQQEKKA--AYNADITYGTNNEFGFDYLRDNMAFSPQERVQRPLHYALIDEVDSILIDEA  219 (908)
T ss_pred             ecCCCCHHHHHh--cCCCCeEEeCCCcccchhhhccCccchhhhhccccceeeecchhhhccccC
Confidence            988876533322  22789999999999 899987423333     6788999999999987653

>TIGR00595 priA primosomal protein N'

Probab=99.55  E-value=5e-14  Score=115.08  Aligned_cols=103  Identities=23%  Similarity=0.284  Sum_probs=78.1

Q ss_pred             EEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHH----hc
Q psy4275          47 IGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKE----LA  122 (182)
Q Consensus        47 li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~  122 (182)
                      ++.|+||+|||.+++..+.+.+.+   +.+++|++|+.+|+.|+++.+++.+   +.++..++++.+..+....    ..
T Consensus         1 LL~g~TGsGKT~v~l~~i~~~l~~---g~~vLvlvP~i~L~~Q~~~~l~~~f---~~~v~vlhs~~~~~er~~~~~~~~~   74 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVLAL---GKSVLVLVPEIALTPQMIQRFKYRF---GSQVAVLHSGLSDSEKLQAWRKVKN   74 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHc---CCeEEEEeCcHHHHHHHHHHHHHHh---CCcEEEEECCCCHHHHHHHHHHHHc
Confidence            468999999999987665554433   5689999999999999988887643   5678888887765443222    23


Q ss_pred             CCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275         123 KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus       123 ~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      ++.+|+|||+..+.        ..++++++||+||.|...-
T Consensus        75 g~~~IVVGTrsalf--------~p~~~l~lIIVDEeh~~sy  107 (505)
T TIGR00595        75 GEILVVIGTRSALF--------LPFKNLGLIIVDEEHDSSY  107 (505)
T ss_pred             CCCCEEECChHHHc--------CcccCCCEEEEECCCcccc
Confidence            46799999987652        2477899999999998764

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).

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

Probab=99.55  E-value=1.2e-13  Score=118.40  Aligned_cols=130  Identities=25%  Similarity=0.331  Sum_probs=97.1

Q ss_pred             CChHHHHhhhhhhh----CCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHH-HHHHHHhhccCC
Q psy4275          28 TPTEIQKAIIPHVL----NDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQI-GDQFLVLGKVMN  102 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~----~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~-~~~~~~~~~~~~  102 (182)
                      +.++.|.+....+.    ++++.+++++||+|||++|+++++...    .+.+++|.+||++|++|+ .+.+..+.+.++
T Consensus       245 e~R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayllp~l~~~----~~~~vvI~t~T~~Lq~Ql~~~~i~~l~~~~~  320 (820)
T PRK07246        245 EERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLLAQS----DQRQIIVSVPTKILQDQIMAEEVKAIQEVFH  320 (820)
T ss_pred             ccCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHHHHHhc----CCCcEEEEeCcHHHHHHHHHHHHHHHHHhcC
Confidence            79999998665544    478899999999999999999988753    246899999999999999 577888888788


Q ss_pred             ceEEEEEcCCchh-------------------------------------------------------------------
Q psy4275         103 LRVSIITGGMDMV-------------------------------------------------------------------  115 (182)
Q Consensus       103 ~~~~~~~~~~~~~-------------------------------------------------------------------  115 (182)
                      +++..+.|+....                                                                   
T Consensus       321 ~~~~~~kg~~~ylcl~k~~~~l~~~~~~~~~~~~~~~il~Wl~~T~tGD~~El~~~~~~~~~w~~i~~~~~~~~~cp~~~  400 (820)
T PRK07246        321 IDCHSLKGPQNYLKLDAFYDSLQQNDDNRLVNRYKMQLLVWLTETETGDLDEIKQKQRYAAYFDQLKHDGNLSQSSLFYD  400 (820)
T ss_pred             CcEEEEECCcccccHHHHHHHhhccCcchHHHHHHHHHHHHHhcCCCCCHhhccCCccccHHHHHhhccCCCCCCCCcch
Confidence            8777766642210                                                                   


Q ss_pred             ----hhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275         116 ----DQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus       116 ----~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                          ...+.-...++|+|++...+...+....  .+...+.+||||||++.+
T Consensus       401 ~cf~~~ar~~a~~AdivItNHall~~~~~~~~--~~p~~~~lIiDEAH~l~~  450 (820)
T PRK07246        401 YDFWKRSYEKAKTARLLITNHAYFLTRVQDDK--DFARNKVLVFDEAQKLML  450 (820)
T ss_pred             hhHHHHHHHHHHhCCEEEEchHHHHHHHhhcc--CCCCCCEEEEECcchhHH
Confidence                0000011245899999988877665433  245688999999999984

>KOG0949|consensus

Probab=99.53  E-value=2.8e-14  Score=119.89  Aligned_cols=146  Identities=18%  Similarity=0.255  Sum_probs=109.4

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHH-HHHHHhhccCCceEE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIG-DQFLVLGKVMNLRVS  106 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~-~~~~~~~~~~~~~~~  106 (182)
                      .|..||.+.+..+-.+++.++++||.+|||.+ ..++++...+..+..-+++++|+++|++|+. +....+....-.+..
T Consensus       511 ~Pd~WQ~elLDsvDr~eSavIVAPTSaGKTfi-sfY~iEKVLResD~~VVIyvaPtKaLVnQvsa~VyaRF~~~t~~rg~  589 (1330)
T KOG0949|consen  511 CPDEWQRELLDSVDRNESAVIVAPTSAGKTFI-SFYAIEKVLRESDSDVVIYVAPTKALVNQVSANVYARFDTKTFLRGV  589 (1330)
T ss_pred             CCcHHHHHHhhhhhcccceEEEeeccCCceec-cHHHHHHHHhhcCCCEEEEecchHHHhhhhhHHHHHhhccCccccch
Confidence            58999999999999999999999999999988 4566666666666778999999999999995 444444233323333


Q ss_pred             EEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcC--CCCCCCCccEEEEeccccccccCChhHHHHHHHH
Q psy4275         107 IITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTC--NTFSLNRIKFLVLDEADRLSLMTSLKFFFFFFFL  176 (182)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~--~~~~~~~~~~iI~DE~h~~~~~~~~~~~~~~~~~  176 (182)
                      .+.|....+....  .-.|+|+|+.|+++..++-..  .....++++++|+||+|.+++..-...++.+--+
T Consensus       590 sl~g~ltqEYsin--p~nCQVLITvPecleslLlspp~~q~~cerIRyiIfDEVH~iG~~ed~l~~Eqll~l  659 (1330)
T KOG0949|consen  590 SLLGDLTQEYSIN--PWNCQVLITVPECLESLLLSPPHHQKFCERIRYIIFDEVHLIGNEEDGLLWEQLLLL  659 (1330)
T ss_pred             hhHhhhhHHhcCC--chhceEEEEchHHHHHHhcCchhhhhhhhcceEEEechhhhccccccchHHHHHHHh
Confidence            4444444333222  127999999999999988662  3346888999999999999988877777665443

>PRK09694 helicase Cas3; Provisional

Probab=99.51  E-value=2.7e-13  Score=116.15  Aligned_cols=137  Identities=17%  Similarity=0.093  Sum_probs=91.4

Q ss_pred             CCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccC--Cc
Q psy4275          26 VKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVM--NL  103 (182)
Q Consensus        26 ~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~--~~  103 (182)
                      ...|+|+|+.+..........++.+|||+|||.+++.++...+ ......+++|..|+.+.++++++.++++.+..  ..
T Consensus       284 ~~~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~~l~-~~~~~~gi~~aLPT~Atan~m~~Rl~~~~~~~f~~~  362 (878)
T PRK09694        284 GYQPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAWRLI-DQGLADSIIFALPTQATANAMLSRLEALASKLFPSP  362 (878)
T ss_pred             CCCChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHHHHH-HhCCCCeEEEECcHHHHHHHHHHHHHHHHHHhcCCC
Confidence            4489999998764434466789999999999999877655433 33334589999999999999998887644332  34


Q ss_pred             eEEEEEcCCchhhh--------------------hHHhcC-------CCcEEEEChHHHHHHHhcCCCCCCCCc----cE
Q psy4275         104 RVSIITGGMDMVDQ--------------------GKELAK-------KPHIVIATPGRLADHLDTCNTFSLNRI----KF  152 (182)
Q Consensus       104 ~~~~~~~~~~~~~~--------------------~~~~~~-------~~~Ilv~T~~~l~~~~~~~~~~~~~~~----~~  152 (182)
                      ++.+.+|.......                    ...+..       -.+|+|||.+.++...-..+-..++.+    ++
T Consensus       363 ~v~L~Hg~a~l~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~kr~llapi~V~TiDQlL~a~l~~kh~~lR~~~La~sv  442 (878)
T PRK09694        363 NLILAHGNSRFNHLFQSLKSRAATEQGQEEAWVQCCEWLSQSNKRVFLGQIGVCTIDQVLISVLPVKHRFIRGFGLGRSV  442 (878)
T ss_pred             ceEeecCcchhhhhhhhhhcccccccccchhhhHHHHHHhhhhhhhhcCCEEEcCHHHHHHHHHccchHHHHHHhhccCe
Confidence            67777775432110                    001111       158999999998754433221122222    48


Q ss_pred             EEEeccccccc
Q psy4275         153 LVLDEADRLSL  163 (182)
Q Consensus       153 iI~DE~h~~~~  163 (182)
                      |||||+|.+..
T Consensus       443 vIiDEVHAyD~  453 (878)
T PRK09694        443 LIVDEVHAYDA  453 (878)
T ss_pred             EEEechhhCCH
Confidence            99999998754

>KOG0947|consensus

Probab=99.51  E-value=1.5e-13  Score=115.29  Aligned_cols=129  Identities=18%  Similarity=0.185  Sum_probs=104.6

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSI  107 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  107 (182)
                      ++.++|++++-++..|.++++.|+|++|||+++.+++.-....   .-|++|..|-++|.+|-+..+++.+...|    +
T Consensus       297 elD~FQk~Ai~~lerg~SVFVAAHTSAGKTvVAEYAialaq~h---~TR~iYTSPIKALSNQKfRDFk~tF~Dvg----L  369 (1248)
T KOG0947|consen  297 ELDTFQKEAIYHLERGDSVFVAAHTSAGKTVVAEYAIALAQKH---MTRTIYTSPIKALSNQKFRDFKETFGDVG----L  369 (1248)
T ss_pred             CccHHHHHHHHHHHcCCeEEEEecCCCCcchHHHHHHHHHHhh---ccceEecchhhhhccchHHHHHHhccccc----e
Confidence            8999999999999999999999999999999987766543222   56899999999999998888777666433    7


Q ss_pred             EEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHHH
Q psy4275         108 ITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFF  171 (182)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~~  171 (182)
                      ++|+.       ++..+++.+|+|.+.+.+++=+ +.=-++++.+|||||+|-+.|....-.|+
T Consensus       370 lTGDv-------qinPeAsCLIMTTEILRsMLYr-gadliRDvE~VIFDEVHYiND~eRGvVWE  425 (1248)
T KOG0947|consen  370 LTGDV-------QINPEASCLIMTTEILRSMLYR-GADLIRDVEFVIFDEVHYINDVERGVVWE  425 (1248)
T ss_pred             eecce-------eeCCCcceEeehHHHHHHHHhc-ccchhhccceEEEeeeeecccccccccce
Confidence            78877       3455788999999999988755 33357789999999999998876544443

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

Probab=99.50  E-value=6e-13  Score=110.40  Aligned_cols=73  Identities=23%  Similarity=0.247  Sum_probs=56.7

Q ss_pred             hhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhh-ccC--CceEEEEEc
Q psy4275          37 IPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLG-KVM--NLRVSIITG  110 (182)
Q Consensus        37 ~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~-~~~--~~~~~~~~~  110 (182)
                      ...+.+++..++++|||+|||.+|+++++..+.... +.+++|.+||++|++|+.+.+..+. +..  ++++..+.|
T Consensus        10 ~~al~~~~~lliEA~TGtGKTlAYLlpal~~~~~~~-~~rvlIstpT~~Lq~Ql~~~l~~l~~~~l~~~i~~~~lkG   85 (636)
T TIGR03117        10 LTSLRQKRIGMLEASTGVGKTLAMIMAALTMLKERP-DQKIAIAVPTLALMGQLWSELERLTAEGLAGPVQAGFFPG   85 (636)
T ss_pred             HHHHhcCCeEEEEcCCCCcHHHHHHHHHHHHHHhcc-CceEEEECCcHHHHHHHHHHHHHHHHhhcCCCeeEEEEEC
Confidence            344555889999999999999999999988765322 4689999999999999998888877 332  455555444

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.

>KOG0351|consensus

Probab=99.48  E-value=1e-13  Score=118.79  Aligned_cols=156  Identities=22%  Similarity=0.237  Sum_probs=113.3

Q ss_pred             HHHHHH-HHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHH
Q psy4275          16 WLIRQC-QTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQF   94 (182)
Q Consensus        16 ~i~~~l-~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~   94 (182)
                      +....+ ..+|...+++-|.+++..++.|+++++.+|||.||++||.++++-.      ++-+++|.|..+|.....   
T Consensus       251 ~~~~~l~~~Fg~~~FR~~Q~eaI~~~l~Gkd~fvlmpTG~GKSLCYQlPA~l~------~gitvVISPL~SLm~DQv---  321 (941)
T KOG0351|consen  251 ELELLLKEVFGHKGFRPNQLEAINATLSGKDCFVLMPTGGGKSLCYQLPALLL------GGVTVVISPLISLMQDQV---  321 (941)
T ss_pred             HHHHHHHHHhccccCChhHHHHHHHHHcCCceEEEeecCCceeeEeecccccc------CCceEEeccHHHHHHHHH---
Confidence            344444 4579999999999999999999999999999999999998887665      558999999999965543   


Q ss_pred             HHhhccCCceEEEEEcCCchhhhh---HHhcC---CCcEEEEChHHHHHHHhcC-CCCCCCC---ccEEEEecccccccc
Q psy4275          95 LVLGKVMNLRVSIITGGMDMVDQG---KELAK---KPHIVIATPGRLADHLDTC-NTFSLNR---IKFLVLDEADRLSLM  164 (182)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~---~~~Ilv~T~~~l~~~~~~~-~~~~~~~---~~~iI~DE~h~~~~~  164 (182)
                      ..+ ...+++...+.++....++.   +.+.+   ..+|+..||+++.....-. ....+..   +.++|+||||++..|
T Consensus       322 ~~L-~~~~I~a~~L~s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~~~~~~L~~~~~lal~vIDEAHCVSqW  400 (941)
T KOG0351|consen  322 THL-SKKGIPACFLSSIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLYARGLLALFVIDEAHCVSQW  400 (941)
T ss_pred             Hhh-hhcCcceeeccccccHHHHHHHHHHHhCCCCeEEEEEeCHHHhhcccchhhHHHhccCCCeeEEEEecHHHHhhhh
Confidence            333 33378888888776653222   22222   5789999999996533221 1112333   789999999999998


Q ss_pred             C--ChhHHHHHHHHhhcCC
Q psy4275         165 T--SLKFFFFFFFLKYYIP  181 (182)
Q Consensus       165 ~--~~~~~~~~~~~~~~~~  181 (182)
                      +  ++..--.+..++.-+|
T Consensus       401 gHdFRp~Yk~l~~l~~~~~  419 (941)
T KOG0351|consen  401 GHDFRPSYKRLGLLRIRFP  419 (941)
T ss_pred             cccccHHHHHHHHHHhhCC
Confidence            8  6666666666665554

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

Probab=99.47  E-value=1.2e-12  Score=113.95  Aligned_cols=83  Identities=24%  Similarity=0.287  Sum_probs=62.7

Q ss_pred             CCChHHHHhhhhhhh----CCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHH-HHHHHhhccC
Q psy4275          27 KTPTEIQKAIIPHVL----NDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIG-DQFLVLGKVM  101 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~----~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~-~~~~~~~~~~  101 (182)
                      .++||.|.+....+.    ++++.++.+|||+|||++|+++++.....+  +.+++|-++|++|.+|+. +.+..+.+.+
T Consensus       256 ~e~R~~Q~~m~~~v~~~l~~~~~~~iEA~TGtGKTlaYLlpa~~~a~~~--~~~vvIsT~T~~LQ~Ql~~kDiP~L~~~~  333 (928)
T PRK08074        256 YEKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAYLLPAAYFAKKK--EEPVVISTYTIQLQQQLLEKDIPLLQKIF  333 (928)
T ss_pred             CcCCHHHHHHHHHHHHHHhcCCCEEEECCCCCchhHHHHHHHHHHhhcc--CCeEEEEcCCHHHHHHHHHhhHHHHHHHc
Confidence            489999999775554    478899999999999999999998766543  568999999999999984 4444443333


Q ss_pred             --CceEEEEEcC
Q psy4275         102 --NLRVSIITGG  111 (182)
Q Consensus       102 --~~~~~~~~~~  111 (182)
                        ++++.++.|.
T Consensus       334 ~~~~~~~~lKGr  345 (928)
T PRK08074        334 PFPVEAALLKGR  345 (928)
T ss_pred             CCCceEEEEEcc
Confidence              3455555553

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

Probab=99.46  E-value=6.5e-13  Score=112.00  Aligned_cols=130  Identities=21%  Similarity=0.256  Sum_probs=86.2

Q ss_pred             ChHHHHhhhhhhhC----------CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhh
Q psy4275          29 PTEIQKAIIPHVLN----------DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLG   98 (182)
Q Consensus        29 ~~~~Q~~~~~~~~~----------~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~   98 (182)
                      ++++|..++..+..          .+..+++.+||+|||.+++..+...+ .....+++++++|+.+|..|+.+.++.+.
T Consensus       239 ~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~~l~-~~~~~~~vl~lvdR~~L~~Q~~~~f~~~~  317 (667)
T TIGR00348       239 QRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKAL-ELLKNPKVFFVVDRRELDYQLMKEFQSLQ  317 (667)
T ss_pred             hHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHHHHH-hhcCCCeEEEEECcHHHHHHHHHHHHhhC
Confidence            78899888876532          25799999999999999765554433 43446799999999999999999988875


Q ss_pred             ccCCceEEEEEcCCchhhhhHHhc-CCCcEEEEChHHHHHHHhcC-CCCCCCC-ccEEEEeccccccccC
Q psy4275          99 KVMNLRVSIITGGMDMVDQGKELA-KKPHIVIATPGRLADHLDTC-NTFSLNR-IKFLVLDEADRLSLMT  165 (182)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~~Ilv~T~~~l~~~~~~~-~~~~~~~-~~~iI~DE~h~~~~~~  165 (182)
                      ....      .+..+.......+. ...+|+|+|.+++...+... ..+...+ -.+||+||||+.....
T Consensus       318 ~~~~------~~~~s~~~L~~~l~~~~~~iivtTiQk~~~~~~~~~~~~~~~~~~~lvIvDEaHrs~~~~  381 (667)
T TIGR00348       318 KDCA------ERIESIAELKRLLEKDDGGIIITTIQKFDKKLKEEEEKFPVDRKEVVVIFDEAHRSQYGE  381 (667)
T ss_pred             CCCC------cccCCHHHHHHHHhCCCCCEEEEEhHHhhhhHhhhhhccCCCCCCEEEEEEcCccccchH
Confidence            3210      11112222222222 34689999999998654331 1111111 1289999999976544

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

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

Probab=99.45  E-value=6.9e-13  Score=110.33  Aligned_cols=130  Identities=19%  Similarity=0.212  Sum_probs=99.0

Q ss_pred             CChHHHHhhhhhhhC----C-CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCC
Q psy4275          28 TPTEIQKAIIPHVLN----D-EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMN  102 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~----~-~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~  102 (182)
                      .++++|..++..+.+    | +..++++.||+|||.+ .+.+++++.+.....++|+++-.++|++|.+..+..+... +
T Consensus       165 ~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrT-Aiaii~rL~r~~~~KRVLFLaDR~~Lv~QA~~af~~~~P~-~  242 (875)
T COG4096         165 GPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRT-AIAIIDRLIKSGWVKRVLFLADRNALVDQAYGAFEDFLPF-G  242 (875)
T ss_pred             cchHHHHHHHHHHHHHHhcCCceEEEEEecCCCccee-HHHHHHHHHhcchhheeeEEechHHHHHHHHHHHHHhCCC-c
Confidence            689999999866544    3 4699999999999998 4677777888777789999999999999998888887665 3


Q ss_pred             ceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcC----CCCCCCCccEEEEeccccccccCCh
Q psy4275         103 LRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTC----NTFSLNRIKFLVLDEADRLSLMTSL  167 (182)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~----~~~~~~~~~~iI~DE~h~~~~~~~~  167 (182)
                      -.+..+.+...        .+.++|.|+|.+.+...+...    ..+....+++||+||||+=.-..+.
T Consensus       243 ~~~n~i~~~~~--------~~s~~i~lsTyqt~~~~~~~~~~~~~~f~~g~FDlIvIDEaHRgi~~~~~  303 (875)
T COG4096         243 TKMNKIEDKKG--------DTSSEIYLSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHRGIYSEWS  303 (875)
T ss_pred             cceeeeecccC--------CcceeEEEeehHHHHhhhhccccccccCCCCceeEEEechhhhhHHhhhH
Confidence            44444443322        126799999999999887653    2346667999999999984443333

>KOG0349|consensus

Probab=99.45  E-value=2.2e-13  Score=106.29  Aligned_cols=99  Identities=33%  Similarity=0.430  Sum_probs=82.3

Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhhccCC---ceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCcc
Q psy4275          75 IFALVLTPTRELAYQIGDQFLVLGKVMN---LRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIK  151 (182)
Q Consensus        75 ~~~lil~p~~~l~~q~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~  151 (182)
                      ++++|+-|+++|++|.++.++++.....   ++..+..|+.....+...+.++.+|+|+||+++.+.+.. ....+.+.+
T Consensus       287 p~avivepsrelaEqt~N~i~~Fk~h~~np~~r~lLmiggv~~r~Q~~ql~~g~~ivvGtpgRl~~~is~-g~~~lt~cr  365 (725)
T KOG0349|consen  287 PEAVIVEPSRELAEQTHNQIEEFKMHTSNPEVRSLLMIGGVLKRTQCKQLKDGTHIVVGTPGRLLQPISK-GLVTLTHCR  365 (725)
T ss_pred             cceeEecCcHHHHHHHHhhHHHHHhhcCChhhhhhhhhhhHHhHHHHHHhhcCceeeecCchhhhhhhhc-cceeeeeeE
Confidence            6789999999999999998888766542   344466676666677777888999999999999999988 777889999


Q ss_pred             EEEEeccccccccCChhHHHHHH
Q psy4275         152 FLVLDEADRLSLMTSLKFFFFFF  174 (182)
Q Consensus       152 ~iI~DE~h~~~~~~~~~~~~~~~  174 (182)
                      ++++||++-++..++...+..+.
T Consensus       366 FlvlDead~lL~qgy~d~I~r~h  388 (725)
T KOG0349|consen  366 FLVLDEADLLLGQGYDDKIYRFH  388 (725)
T ss_pred             EEEecchhhhhhcccHHHHHHHh
Confidence            99999999999998887766553

>PF00176 SNF2_N: SNF2 family N-terminal domain; InterPro: IPR000330 This domain is found in proteins involved in a variety of processes including transcription regulation (e

Probab=99.45  E-value=9.5e-13  Score=100.85  Aligned_cols=124  Identities=23%  Similarity=0.184  Sum_probs=79.5

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCC--eeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYG--IFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKE  120 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~--~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  120 (182)
                      .+.+++..++|.|||..++..+..........  ..+||++|. ++..+|..++.++......++..+.|..........
T Consensus        25 ~~g~lL~de~GlGKT~~~i~~~~~l~~~~~~~~~~~~LIv~P~-~l~~~W~~E~~~~~~~~~~~v~~~~~~~~~~~~~~~  103 (299)
T PF00176_consen   25 PRGGLLADEMGLGKTITAIALISYLKNEFPQRGEKKTLIVVPS-SLLSQWKEEIEKWFDPDSLRVIIYDGDSERRRLSKN  103 (299)
T ss_dssp             T-EEEE---TTSSHHHHHHHHHHHHHHCCTTSS-S-EEEEE-T-TTHHHHHHHHHHHSGT-TS-EEEESSSCHHHHTTSS
T ss_pred             CCCEEEEECCCCCchhhhhhhhhhhhhccccccccceeEeecc-chhhhhhhhhcccccccccccccccccccccccccc
Confidence            56889999999999998766655333222211  259999999 777999999999986556678777776623333333


Q ss_pred             hcCCCcEEEEChHHHH-----HHHhcCCCCCCCCccEEEEeccccccccCChhHH
Q psy4275         121 LAKKPHIVIATPGRLA-----DHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFF  170 (182)
Q Consensus       121 ~~~~~~Ilv~T~~~l~-----~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~  170 (182)
                      .....+++|+|.+.+.     .....   +..-+++++|+||+|.+-+.......
T Consensus       104 ~~~~~~vvi~ty~~~~~~~~~~~~~~---l~~~~~~~vIvDEaH~~k~~~s~~~~  155 (299)
T PF00176_consen  104 QLPKYDVVITTYETLRKARKKKDKED---LKQIKWDRVIVDEAHRLKNKDSKRYK  155 (299)
T ss_dssp             SCCCSSEEEEEHHHHH--TSTHTTHH---HHTSEEEEEEETTGGGGTTTTSHHHH
T ss_pred             ccccceeeeccccccccccccccccc---cccccceeEEEecccccccccccccc
Confidence            3457899999999998     21111   11223789999999999766654433

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.

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=99.44  E-value=1.4e-12  Score=110.46  Aligned_cols=131  Identities=22%  Similarity=0.157  Sum_probs=102.4

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSI  107 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  107 (182)
                      .+.+.|....-.+.  ..-+..+.||.|||+++.++++.....   |..+.+++|+..||.+-++++..+.+.+|++|++
T Consensus        82 ~~ydVQliGg~~Lh--~G~iaEM~TGEGKTLvA~l~a~l~al~---G~~VhvvT~ndyLA~RD~e~m~~l~~~lGl~v~~  156 (913)
T PRK13103         82 RHFDVQLIGGMTLH--EGKIAEMRTGEGKTLVGTLAVYLNALS---GKGVHVVTVNDYLARRDANWMRPLYEFLGLSVGI  156 (913)
T ss_pred             CcchhHHHhhhHhc--cCccccccCCCCChHHHHHHHHHHHHc---CCCEEEEeCCHHHHHHHHHHHHHHhcccCCEEEE
Confidence            56666665544444  345889999999999998888876666   5689999999999999999999999999999999


Q ss_pred             EEcCCchhhhhHHhcCCCcEEEEChHHH-HHHHhcCCC-----CCCCCccEEEEeccccccccC
Q psy4275         108 ITGGMDMVDQGKELAKKPHIVIATPGRL-ADHLDTCNT-----FSLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~Ilv~T~~~l-~~~~~~~~~-----~~~~~~~~iI~DE~h~~~~~~  165 (182)
                      +.++....++...+  .++|++||..-+ .++++..-.     .-.+.+.++|+||+|.++=+.
T Consensus       157 i~~~~~~~err~~Y--~~dI~YGT~~e~gFDYLrD~~~~~~~~~vqr~l~~aIVDEvDsiLIDE  218 (913)
T PRK13103        157 VTPFQPPEEKRAAY--AADITYGTNNEFGFDYLRDNMAFSLDDKFQRELNFAVIDEVDSILIDE  218 (913)
T ss_pred             ECCCCCHHHHHHHh--cCCEEEEcccccccchhhccceechhhhcccccceeEechhhheeccc
Confidence            98877665554444  489999999887 455554211     134678999999999987543

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=99.42  E-value=4.7e-12  Score=96.86  Aligned_cols=70  Identities=23%  Similarity=0.118  Sum_probs=55.5

Q ss_pred             CChHHHHhhhh----hhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCC---CeeEEEEcCCHHHHHHHHHHHHHh
Q psy4275          28 TPTEIQKAIIP----HVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPY---GIFALVLTPTRELAYQIGDQFLVL   97 (182)
Q Consensus        28 ~~~~~Q~~~~~----~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~---~~~~lil~p~~~l~~q~~~~~~~~   97 (182)
                      +++|.|.+...    .+.+++++++.+|||+|||++++.+++..+...+.   +.+++|.+++.++.+|....++++
T Consensus         8 ~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00488        8 EPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhc
Confidence            56999999554    44558899999999999999999999876655432   238999999999988876666654

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=99.42  E-value=4.7e-12  Score=96.86  Aligned_cols=70  Identities=23%  Similarity=0.118  Sum_probs=55.5

Q ss_pred             CChHHHHhhhh----hhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCC---CeeEEEEcCCHHHHHHHHHHHHHh
Q psy4275          28 TPTEIQKAIIP----HVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPY---GIFALVLTPTRELAYQIGDQFLVL   97 (182)
Q Consensus        28 ~~~~~Q~~~~~----~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~---~~~~lil~p~~~l~~q~~~~~~~~   97 (182)
                      +++|.|.+...    .+.+++++++.+|||+|||++++.+++..+...+.   +.+++|.+++.++.+|....++++
T Consensus         8 ~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00489        8 EPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhc
Confidence            56999999554    44558899999999999999999999876655432   238999999999988876666654

>KOG0948|consensus

Probab=99.41  E-value=6.6e-13  Score=109.27  Aligned_cols=124  Identities=19%  Similarity=0.214  Sum_probs=103.6

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSI  107 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  107 (182)
                      .+.|+|..++..+-++.++++.+.|++|||.++.+++...+..   +.|+||..|-++|.+|-+.++..-++.    |++
T Consensus       129 ~LDpFQ~~aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~---kQRVIYTSPIKALSNQKYREl~~EF~D----VGL  201 (1041)
T KOG0948|consen  129 TLDPFQSTAIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLRE---KQRVIYTSPIKALSNQKYRELLEEFKD----VGL  201 (1041)
T ss_pred             ccCchHhhhhhhhcCCceEEEEeecCCCcchHHHHHHHHHHHh---cCeEEeeChhhhhcchhHHHHHHHhcc----cce
Confidence            6899999999999999999999999999999999999888877   459999999999999998877765554    666


Q ss_pred             EEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCC
Q psy4275         108 ITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTS  166 (182)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~  166 (182)
                      .+|+-..       ...+.-+|+|.+.+..++=+ +.--++.+.++||||+|-|-|...
T Consensus       202 MTGDVTI-------nP~ASCLVMTTEILRsMLYR-GSEvmrEVaWVIFDEIHYMRDkER  252 (1041)
T KOG0948|consen  202 MTGDVTI-------NPDASCLVMTTEILRSMLYR-GSEVMREVAWVIFDEIHYMRDKER  252 (1041)
T ss_pred             eecceee-------CCCCceeeeHHHHHHHHHhc-cchHhheeeeEEeeeehhcccccc
Confidence            6676643       34567799999999888755 444577899999999999987653

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=99.40  E-value=5.6e-12  Score=109.40  Aligned_cols=134  Identities=16%  Similarity=0.097  Sum_probs=94.3

Q ss_pred             CChHHHHhhhhhhh----CCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q psy4275          28 TPTEIQKAIIPHVL----NDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNL  103 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~----~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  103 (182)
                      .++|||.+++.++.    ++.++|+...+|.|||+.++..+.......+..+.+|||||. ++..+|.++++++..  ..
T Consensus       169 ~Lr~YQleGlnWLi~l~~~g~gGILADEMGLGKTlQaIalL~~L~~~~~~~gp~LIVvP~-SlL~nW~~Ei~kw~p--~l  245 (1033)
T PLN03142        169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISLLGYLHEYRGITGPHMVVAPK-STLGNWMNEIRRFCP--VL  245 (1033)
T ss_pred             chHHHHHHHHHHHHHHHhcCCCEEEEeCCCccHHHHHHHHHHHHHHhcCCCCCEEEEeCh-HHHHHHHHHHHHHCC--CC
Confidence            68999999998875    477899999999999998665554433333334578999996 455889888988875  36


Q ss_pred             eEEEEEcCCchhhhhH---HhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCCh
Q psy4275         104 RVSIITGGMDMVDQGK---ELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSL  167 (182)
Q Consensus       104 ~~~~~~~~~~~~~~~~---~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~  167 (182)
                      ++..++|.........   ......+|+|+|.+.+........   --.+.+||+||||.+-+....
T Consensus       246 ~v~~~~G~~~eR~~~~~~~~~~~~~dVvITSYe~l~~e~~~L~---k~~W~~VIvDEAHrIKN~~Sk  309 (1033)
T PLN03142        246 RAVKFHGNPEERAHQREELLVAGKFDVCVTSFEMAIKEKTALK---RFSWRYIIIDEAHRIKNENSL  309 (1033)
T ss_pred             ceEEEeCCHHHHHHHHHHHhcccCCCcceecHHHHHHHHHHhc---cCCCCEEEEcCccccCCHHHH
Confidence            6777777654322111   123467899999998865433222   224679999999998876543

>PF07517 SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011115 SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane

Probab=99.38  E-value=2.6e-11  Score=91.03  Aligned_cols=131  Identities=24%  Similarity=0.269  Sum_probs=98.5

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSI  107 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  107 (182)
                      .|++.|..+.-.+..|+  +++..||-|||+++.+++......   |..|-|++.+..|+..-++++..+.+.+|++++.
T Consensus        77 ~p~~vQll~~l~L~~G~--laEm~TGEGKTli~~l~a~~~AL~---G~~V~vvT~NdyLA~RD~~~~~~~y~~LGlsv~~  151 (266)
T PF07517_consen   77 RPYDVQLLGALALHKGR--LAEMKTGEGKTLIAALPAALNALQ---GKGVHVVTSNDYLAKRDAEEMRPFYEFLGLSVGI  151 (266)
T ss_dssp             ---HHHHHHHHHHHTTS--EEEESTTSHHHHHHHHHHHHHHTT---SS-EEEEESSHHHHHHHHHHHHHHHHHTT--EEE
T ss_pred             cccHHHHhhhhhcccce--eEEecCCCCcHHHHHHHHHHHHHh---cCCcEEEeccHHHhhccHHHHHHHHHHhhhcccc
Confidence            68888888776665554  999999999999988777776666   5689999999999999999999999999999999


Q ss_pred             EEcCCchhhhhHHhcCCCcEEEEChHHHH-HHHhcCCC-----CCCCCccEEEEeccccccccC
Q psy4275         108 ITGGMDMVDQGKELAKKPHIVIATPGRLA-DHLDTCNT-----FSLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~-~~~~~~~~-----~~~~~~~~iI~DE~h~~~~~~  165 (182)
                      ..++.+...+...+  .++|+.+|...+. ++++..-.     ...+.+.++|+||+|.++-+.
T Consensus       152 ~~~~~~~~~r~~~Y--~~dI~Y~t~~~~~fD~Lrd~~~~~~~~~~~r~~~~~ivDEvDs~LiDe  213 (266)
T PF07517_consen  152 ITSDMSSEERREAY--AADIVYGTNSEFGFDYLRDNLALSKNEQVQRGFDFAIVDEVDSILIDE  213 (266)
T ss_dssp             EETTTEHHHHHHHH--HSSEEEEEHHHHHHHHHHHTT-SSGGG--SSSSSEEEECTHHHHTTTG
T ss_pred             CccccCHHHHHHHH--hCcccccccchhhHHHHHHHHhhccchhccCCCCEEEEeccceEEEec
Confidence            99888755544443  4679999999885 46654211     124678899999999988544

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 ....

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

Probab=99.38  E-value=1.7e-12  Score=108.80  Aligned_cols=120  Identities=21%  Similarity=0.305  Sum_probs=94.9

Q ss_pred             CChHHHHhhhhhhhCC----CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q psy4275          28 TPTEIQKAIIPHVLND----EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNL  103 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~----~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  103 (182)
                      .+++.|..++..+.+.    +..++.|.||+|||-+|+-.+...+.+   |.++|+++|..+|-.|+.+.++.   .++.
T Consensus       198 ~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~i~~~L~~---GkqvLvLVPEI~Ltpq~~~rf~~---rFg~  271 (730)
T COG1198         198 ALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLEAIAKVLAQ---GKQVLVLVPEIALTPQLLARFKA---RFGA  271 (730)
T ss_pred             ccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHHHHHHHHHc---CCEEEEEeccccchHHHHHHHHH---HhCC
Confidence            5788899999888765    689999999999999988777777666   67999999999998886655554   4457


Q ss_pred             eEEEEEcCCchhh----hhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccc
Q psy4275         104 RVSIITGGMDMVD----QGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL  161 (182)
Q Consensus       104 ~~~~~~~~~~~~~----~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~  161 (182)
                      ++.+++++.+..+    +.+...++.+|+|||        ++.-...++++++||+||-|.-
T Consensus       272 ~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGt--------RSAlF~Pf~~LGLIIvDEEHD~  325 (730)
T COG1198         272 KVAVLHSGLSPGERYRVWRRARRGEARVVIGT--------RSALFLPFKNLGLIIVDEEHDS  325 (730)
T ss_pred             ChhhhcccCChHHHHHHHHHHhcCCceEEEEe--------chhhcCchhhccEEEEeccccc
Confidence            7888887766543    344445688999999        6644558999999999999963

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.35  E-value=8.2e-12  Score=105.32  Aligned_cols=131  Identities=21%  Similarity=0.210  Sum_probs=103.6

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSI  107 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  107 (182)
                      .|++.|..+.-.+..|+  +.+..||.|||+++.++++.....   |..+-+++|+..||.+-++++..+.+.+|++|++
T Consensus        80 ~~~dvQlig~l~l~~G~--iaEm~TGEGKTLvA~l~a~l~al~---G~~v~vvT~neyLA~Rd~e~~~~~~~~LGl~vg~  154 (796)
T PRK12906         80 RPFDVQIIGGIVLHEGN--IAEMKTGEGKTLTATLPVYLNALT---GKGVHVVTVNEYLSSRDATEMGELYRWLGLTVGL  154 (796)
T ss_pred             CCchhHHHHHHHHhcCC--cccccCCCCCcHHHHHHHHHHHHc---CCCeEEEeccHHHHHhhHHHHHHHHHhcCCeEEE
Confidence            67777777665555454  999999999999998888887777   6689999999999999999999999999999999


Q ss_pred             EEcCCchhhhhHHhcCCCcEEEEChHHH-HHHHhcCC-----CCCCCCccEEEEeccccccccC
Q psy4275         108 ITGGMDMVDQGKELAKKPHIVIATPGRL-ADHLDTCN-----TFSLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~Ilv~T~~~l-~~~~~~~~-----~~~~~~~~~iI~DE~h~~~~~~  165 (182)
                      +.++.....+...+  .++|+.+|...+ .++++..-     ..-.+.+.+.|+||+|.++=+.
T Consensus       155 i~~~~~~~~r~~~y--~~dI~Y~t~~e~gfDyLRD~m~~~~~~~v~r~~~~aIvDEvDSiLiDe  216 (796)
T PRK12906        155 NLNSMSPDEKRAAY--NCDITYSTNSELGFDYLRDNMVVYKEQMVQRPLNYAIVDEVDSILIDE  216 (796)
T ss_pred             eCCCCCHHHHHHHh--cCCCeecCCccccccchhhccccchhhhhccCcceeeeccchheeecc
Confidence            98877665554443  679999999887 45665521     1134567899999999987544

>KOG0951|consensus

Probab=99.35  E-value=1.3e-12  Score=112.39  Aligned_cols=128  Identities=22%  Similarity=0.298  Sum_probs=102.2

Q ss_pred             CChHHHHhhhhhhhC-CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHH-HHHhhccCCceE
Q psy4275          28 TPTEIQKAIIPHVLN-DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQ-FLVLGKVMNLRV  105 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~-~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~-~~~~~~~~~~~~  105 (182)
                      ..+|.|.+.++.+.+ +.++++.+|+|+|||.|+-++++.    .....++++++|..+.+..++.. -+++.+..|..+
T Consensus      1143 ~~n~iqtqVf~~~y~~nd~v~vga~~gsgkt~~ae~a~l~----~~~~~~~vyi~p~~~i~~~~~~~w~~~f~~~~G~~~ 1218 (1674)
T KOG0951|consen 1143 DFNPIQTQVFTSLYNTNDNVLVGAPNGSGKTACAELALLR----PDTIGRAVYIAPLEEIADEQYRDWEKKFSKLLGLRI 1218 (1674)
T ss_pred             ccCCceEEEEeeeecccceEEEecCCCCchhHHHHHHhcC----CccceEEEEecchHHHHHHHHHHHHHhhccccCceE
Confidence            458999999999877 668888999999999999988887    22256999999999999888554 455666678888


Q ss_pred             EEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChh
Q psy4275         106 SIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLK  168 (182)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~  168 (182)
                      ..+.|..+...   .+.+..+|+|+||+.+..+ +     ....+++.|.||+|.+.+....-
T Consensus      1219 ~~l~ge~s~~l---kl~~~~~vii~tpe~~d~l-q-----~iQ~v~l~i~d~lh~igg~~g~v 1272 (1674)
T KOG0951|consen 1219 VKLTGETSLDL---KLLQKGQVIISTPEQWDLL-Q-----SIQQVDLFIVDELHLIGGVYGAV 1272 (1674)
T ss_pred             EecCCccccch---HHhhhcceEEechhHHHHH-h-----hhhhcceEeeehhhhhcccCCce
Confidence            88888877554   4455779999999999766 2     46778999999999988555433

>KOG0385|consensus

Probab=99.34  E-value=1e-11  Score=102.51  Aligned_cols=134  Identities=18%  Similarity=0.111  Sum_probs=97.2

Q ss_pred             CChHHHHhhhhhhhC----CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q psy4275          28 TPTEIQKAIIPHVLN----DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNL  103 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~----~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  103 (182)
                      .+++||.+.+.++.+    |-|+|+...+|.|||+..+..+.+........+..+|++|...| ..|.++++++..  ++
T Consensus       167 ~lr~YQveGlnWLi~l~engingILaDEMGLGKTlQtIs~l~yl~~~~~~~GPfLVi~P~StL-~NW~~Ef~rf~P--~l  243 (971)
T KOG0385|consen  167 ELRDYQLEGLNWLISLYENGINGILADEMGLGKTLQTISLLGYLKGRKGIPGPFLVIAPKSTL-DNWMNEFKRFTP--SL  243 (971)
T ss_pred             ccchhhhccHHHHHHHHhcCcccEeehhcccchHHHHHHHHHHHHHhcCCCCCeEEEeeHhhH-HHHHHHHHHhCC--Cc
Confidence            699999999988765    67899999999999988665555544433333468999998888 557888888877  58


Q ss_pred             eEEEEEcCCchhhhh---HHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCCh
Q psy4275         104 RVSIITGGMDMVDQG---KELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSL  167 (182)
Q Consensus       104 ~~~~~~~~~~~~~~~---~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~  167 (182)
                      ++.+++|+.......   -......+|+|+|.+..+.--   ..+.--+++++|+||+|++-+....
T Consensus       244 ~~~~~~Gdk~eR~~~~r~~~~~~~fdV~iTsYEi~i~dk---~~lk~~~W~ylvIDEaHRiKN~~s~  307 (971)
T KOG0385|consen  244 NVVVYHGDKEERAALRRDIMLPGRFDVCITSYEIAIKDK---SFLKKFNWRYLVIDEAHRIKNEKSK  307 (971)
T ss_pred             ceEEEeCCHHHHHHHHHHhhccCCCceEeehHHHHHhhH---HHHhcCCceEEEechhhhhcchhhH
Confidence            899999987432211   112337899999999886531   2122224789999999999887653

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=99.33  E-value=1.8e-11  Score=101.79  Aligned_cols=131  Identities=21%  Similarity=0.157  Sum_probs=104.7

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSI  107 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  107 (182)
                      .+++.|....-.+..|.  +.++.||.|||+++.+++......   |..+.+++|+..||.+-++++..+.+.+|+++++
T Consensus        78 r~ydvQlig~l~Ll~G~--VaEM~TGEGKTLvA~l~a~l~AL~---G~~VhvvT~NdyLA~RDae~m~~ly~~LGLsvg~  152 (764)
T PRK12326         78 RPFDVQLLGALRLLAGD--VIEMATGEGKTLAGAIAAAGYALQ---GRRVHVITVNDYLARRDAEWMGPLYEALGLTVGW  152 (764)
T ss_pred             CcchHHHHHHHHHhCCC--cccccCCCCHHHHHHHHHHHHHHc---CCCeEEEcCCHHHHHHHHHHHHHHHHhcCCEEEE
Confidence            67888888777777664  889999999999998888877666   6689999999999999999999999999999999


Q ss_pred             EEcCCchhhhhHHhcCCCcEEEEChHHH-HHHHhcC-----CCCCCCCccEEEEeccccccccC
Q psy4275         108 ITGGMDMVDQGKELAKKPHIVIATPGRL-ADHLDTC-----NTFSLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~Ilv~T~~~l-~~~~~~~-----~~~~~~~~~~iI~DE~h~~~~~~  165 (182)
                      +.++....+....+  .|+|..+|..-+ .++++..     ...-.+.+.+.|+||+|.++-+.
T Consensus       153 i~~~~~~~err~aY--~~DItYgTn~e~gFDyLRDnm~~~~~~~v~R~~~faIVDEvDSiLIDe  214 (764)
T PRK12326        153 ITEESTPEERRAAY--ACDVTYASVNEIGFDVLRDQLVTDVADLVSPNPDVAIIDEADSVLVDE  214 (764)
T ss_pred             ECCCCCHHHHHHHH--cCCCEEcCCcccccccchhhhccChHhhcCCccceeeecchhhheecc
Confidence            98887765554444  689999998876 3455442     11234567899999999988554

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.32  E-value=4.2e-11  Score=105.52  Aligned_cols=123  Identities=19%  Similarity=0.229  Sum_probs=77.2

Q ss_pred             hHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCH----HHHHHHHHHHHH-hhccCCce
Q psy4275          30 TEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTR----ELAYQIGDQFLV-LGKVMNLR  104 (182)
Q Consensus        30 ~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~----~l~~q~~~~~~~-~~~~~~~~  104 (182)
                      ...-.+.+..+.++..++++|+||||||+.....++.. .. +..+.+++.-|.+    +++.++++++.. ++...|+.
T Consensus        76 ~~~r~~Il~ai~~~~VviI~GeTGSGKTTqlPq~lle~-g~-g~~g~I~~TQPRRlAArsLA~RVA~El~~~lG~~VGY~  153 (1294)
T PRK11131         76 SQKKQDILEAIRDHQVVIVAGETGSGKTTQLPKICLEL-GR-GVKGLIGHTQPRRLAARTVANRIAEELETELGGCVGYK  153 (1294)
T ss_pred             HHHHHHHHHHHHhCCeEEEECCCCCCHHHHHHHHHHHc-CC-CCCCceeeCCCcHHHHHHHHHHHHHHHhhhhcceecee
Confidence            44455666777777888999999999999643333332 11 1123455555765    445555444442 33333333


Q ss_pred             EEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccc-ccccCC
Q psy4275         105 VSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR-LSLMTS  166 (182)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~-~~~~~~  166 (182)
                      +    .-.      ....++++|+++||+.+++.+....  .++++++||+||+|+ +.+.++
T Consensus       154 v----rf~------~~~s~~t~I~v~TpG~LL~~l~~d~--~Ls~~~~IIIDEAHERsLn~Df  204 (1294)
T PRK11131        154 V----RFN------DQVSDNTMVKLMTDGILLAEIQQDR--LLMQYDTIIIDEAHERSLNIDF  204 (1294)
T ss_pred             e----cCc------cccCCCCCEEEEChHHHHHHHhcCC--ccccCcEEEecCccccccccch
Confidence            2    111      1223578999999999999987633  488999999999995 555444

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=99.31  E-value=3.8e-11  Score=101.82  Aligned_cols=73  Identities=25%  Similarity=0.211  Sum_probs=58.0

Q ss_pred             CCChHHHHhhhhhhhC---C------CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHH-HHHHHH
Q psy4275          27 KTPTEIQKAIIPHVLN---D------EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQI-GDQFLV   96 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~---~------~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~-~~~~~~   96 (182)
                      .+.++.|.+....+.+   +      ++.++.||||+|||++|+++++.....+  +.+++|-++|.+|.+|+ .+.+..
T Consensus        24 ~e~R~~Q~~M~~~V~~al~~~~~~~~~~lviEAgTGtGKTlaYLlPai~~A~~~--~k~vVIST~T~~LQeQL~~kDlP~  101 (697)
T PRK11747         24 FIPRAGQRQMIAEVAKTLAGEYLKDGRILVIEAGTGVGKTLSYLLAGIPIARAE--KKKLVISTATVALQEQLVSKDLPL  101 (697)
T ss_pred             CCcCHHHHHHHHHHHHHHhcccccccceEEEECCCCcchhHHHHHHHHHHHHHc--CCeEEEEcCCHHHHHHHHhhhhhH
Confidence            4899999997766653   2      6789999999999999999998876654  56899999999999999 455555


Q ss_pred             hhccC
Q psy4275          97 LGKVM  101 (182)
Q Consensus        97 ~~~~~  101 (182)
                      +.+.+
T Consensus       102 l~~~l  106 (697)
T PRK11747        102 LLKIS  106 (697)
T ss_pred             HHHHc
Confidence            54433

>KOG0950|consensus

Probab=99.31  E-value=1.1e-11  Score=104.36  Aligned_cols=153  Identities=16%  Similarity=0.145  Sum_probs=119.4

Q ss_pred             HHHHHHHCCCCCChHHHHhhh--hhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHH
Q psy4275          17 LIRQCQTIGVKTPTEIQKAII--PHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQF   94 (182)
Q Consensus        17 i~~~l~~~~~~~~~~~Q~~~~--~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~   94 (182)
                      ..-.....|...+.+||.+++  +.+..++|.+...||+.|||+++.+.++....-.  ...++.+.|..+.+.+-...+
T Consensus       212 ~~~~~~~kgi~~~fewq~ecls~~~~~e~~nliys~Pts~gktlvaeilml~~~l~~--rr~~llilp~vsiv~Ek~~~l  289 (1008)
T KOG0950|consen  212 SHLYAKDKGILKLFEWQAECLSLPRLLERKNLIYSLPTSAGKTLVAEILMLREVLCR--RRNVLLILPYVSIVQEKISAL  289 (1008)
T ss_pred             HHHHHHhhhHHHHHHHHHHHhcchhhhcccceEEeCCCccchHHHHHHHHHHHHHHH--hhceeEecceeehhHHHHhhh
Confidence            333345568889999999998  5577889999999999999999998888776554  336889999998888878888


Q ss_pred             HHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcC-CCCCCCCccEEEEeccccccccCChhHHHHH
Q psy4275          95 LVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTC-NTFSLNRIKFLVLDEADRLSLMTSLKFFFFF  173 (182)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~-~~~~~~~~~~iI~DE~h~~~~~~~~~~~~~~  173 (182)
                      ..+....|+.+..+.|......    ..+.-++.|+|.++...++... ..=++..+++||+||.|.+.+.+....++.+
T Consensus       290 ~~~~~~~G~~ve~y~g~~~p~~----~~k~~sv~i~tiEkanslin~lie~g~~~~~g~vvVdElhmi~d~~rg~~lE~~  365 (1008)
T KOG0950|consen  290 SPFSIDLGFPVEEYAGRFPPEK----RRKRESVAIATIEKANSLINSLIEQGRLDFLGMVVVDELHMIGDKGRGAILELL  365 (1008)
T ss_pred             hhhccccCCcchhhcccCCCCC----cccceeeeeeehHhhHhHHHHHHhcCCccccCcEEEeeeeeeeccccchHHHHH
Confidence            8899999999988887664322    2345689999999987765432 1114778899999999999999977776665


Q ss_pred             HH
Q psy4275         174 FF  175 (182)
Q Consensus       174 ~~  175 (182)
                      ..
T Consensus       366 l~  367 (1008)
T KOG0950|consen  366 LA  367 (1008)
T ss_pred             HH
Confidence            43

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.30  E-value=1.5e-11  Score=106.36  Aligned_cols=131  Identities=22%  Similarity=0.173  Sum_probs=86.4

Q ss_pred             CChHHHHhhhhhhhC--CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceE
Q psy4275          28 TPTEIQKAIIPHVLN--DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRV  105 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~--~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~  105 (182)
                      .+.|+|......+..  ...+++..++|.|||+.+.+.+...+... ...++|||||. +|..||..++.+.   ++...
T Consensus       152 ~l~pHQl~~~~~vl~~~~~R~LLADEvGLGKTIeAglil~~l~~~g-~~~rvLIVvP~-sL~~QW~~El~~k---F~l~~  226 (956)
T PRK04914        152 SLIPHQLYIAHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQLLTG-RAERVLILVPE-TLQHQWLVEMLRR---FNLRF  226 (956)
T ss_pred             CCCHHHHHHHHHHhhccCCCEEEEeCCcCcHHHHHHHHHHHHHHcC-CCCcEEEEcCH-HHHHHHHHHHHHH---hCCCe
Confidence            599999998877654  45789999999999999876666655443 34589999996 7888887766543   34555


Q ss_pred             EEEEcCCchhhh--hHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275         106 SIITGGMDMVDQ--GKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus       106 ~~~~~~~~~~~~--~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      ..+.+.......  ....+...+++|+|.+.+...-.....+.-..++++|+||||++-.
T Consensus       227 ~i~~~~~~~~~~~~~~~pf~~~~~vI~S~~~l~~~~~~~~~l~~~~wdlvIvDEAH~lk~  286 (956)
T PRK04914        227 SLFDEERYAEAQHDADNPFETEQLVICSLDFLRRNKQRLEQALAAEWDLLVVDEAHHLVW  286 (956)
T ss_pred             EEEcCcchhhhcccccCccccCcEEEEEHHHhhhCHHHHHHHhhcCCCEEEEechhhhcc
Confidence            555443321110  0012235689999988775411110112234688999999999973

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

Probab=99.26  E-value=4.2e-11  Score=81.10  Aligned_cols=109  Identities=20%  Similarity=0.201  Sum_probs=69.6

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKE  120 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  120 (182)
                      .+|+-.++...+|+|||.-.+--++....+.  +.++|++.||+.+++++.+.++..    ++++.  . ....    ..
T Consensus         2 ~kg~~~~~d~hpGaGKTr~vlp~~~~~~i~~--~~rvLvL~PTRvva~em~~aL~~~----~~~~~--t-~~~~----~~   68 (148)
T PF07652_consen    2 RKGELTVLDLHPGAGKTRRVLPEIVREAIKR--RLRVLVLAPTRVVAEEMYEALKGL----PVRFH--T-NARM----RT   68 (148)
T ss_dssp             STTEEEEEE--TTSSTTTTHHHHHHHHHHHT--T--EEEEESSHHHHHHHHHHTTTS----SEEEE--S-TTSS------
T ss_pred             CCCceeEEecCCCCCCcccccHHHHHHHHHc--cCeEEEecccHHHHHHHHHHHhcC----CcccC--c-eeee----cc
Confidence            3466678899999999986555555544444  679999999999999888777543    33332  1 1110    12


Q ss_pred             hcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccccc
Q psy4275         121 LAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus       121 ~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~  164 (182)
                      ...+.-|-|+|...+.+++..  .....++++||+||||.....
T Consensus        69 ~~g~~~i~vMc~at~~~~~~~--p~~~~~yd~II~DEcH~~Dp~  110 (148)
T PF07652_consen   69 HFGSSIIDVMCHATYGHFLLN--PCRLKNYDVIIMDECHFTDPT  110 (148)
T ss_dssp             --SSSSEEEEEHHHHHHHHHT--SSCTTS-SEEEECTTT--SHH
T ss_pred             ccCCCcccccccHHHHHHhcC--cccccCccEEEEeccccCCHH
Confidence            235667899999999888765  334678999999999975443

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 ....

>KOG0389|consensus

Probab=99.25  E-value=1.1e-11  Score=102.60  Aligned_cols=142  Identities=18%  Similarity=0.148  Sum_probs=98.8

Q ss_pred             CChHHHHhhhhhhh----CCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q psy4275          28 TPTEIQKAIIPHVL----NDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNL  103 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~----~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  103 (182)
                      .+.+||.-.+.++.    .+-++|+...+|.|||...+.++.. +.+.+..+.-|||||+..| +.|..++.+|+..  +
T Consensus       399 ~LkdYQlvGvNWL~Llyk~~l~gILADEMGLGKTiQvIaFlay-Lkq~g~~gpHLVVvPsSTl-eNWlrEf~kwCPs--l  474 (941)
T KOG0389|consen  399 QLKDYQLVGVNWLLLLYKKKLNGILADEMGLGKTIQVIAFLAY-LKQIGNPGPHLVVVPSSTL-ENWLREFAKWCPS--L  474 (941)
T ss_pred             cccchhhhhHHHHHHHHHccccceehhhccCcchhHHHHHHHH-HHHcCCCCCcEEEecchhH-HHHHHHHHHhCCc--e
Confidence            58999999887753    2558899999999999875544443 3333334568999999887 4455566666553  7


Q ss_pred             eEEEEEcCCchhhhhHHhcC----CCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHHHHH
Q psy4275         104 RVSIITGGMDMVDQGKELAK----KPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFF  173 (182)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~~----~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~~~~  173 (182)
                      +|-.++|........+...+    ..+|+|+|...+..--..++.+.-.+++++|+||+|.+-+....++..++
T Consensus       475 ~Ve~YyGSq~ER~~lR~~i~~~~~~ydVllTTY~la~~~kdDRsflk~~~~n~viyDEgHmLKN~~SeRy~~LM  548 (941)
T KOG0389|consen  475 KVEPYYGSQDERRELRERIKKNKDDYDVLLTTYNLAASSKDDRSFLKNQKFNYVIYDEGHMLKNRTSERYKHLM  548 (941)
T ss_pred             EEEeccCcHHHHHHHHHHHhccCCCccEEEEEeecccCChHHHHHHHhccccEEEecchhhhhccchHHHHHhc
Confidence            88888988765444433322    67999999887753332323334456889999999999988877766554

>KOG0391|consensus

Probab=99.24  E-value=2.2e-11  Score=104.36  Aligned_cols=141  Identities=19%  Similarity=0.194  Sum_probs=112.9

Q ss_pred             CChHHHHhhhhhhhC----CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q psy4275          28 TPTEIQKAIIPHVLN----DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNL  103 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~----~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  103 (182)
                      .++.||...+.++..    +-|.|+...+|.|||+..+..+.+...+.++.+--|||+||..+. .|..++++|+.  ++
T Consensus       615 qLReYQkiGLdWLatLYeknlNGILADEmGLGKTIQtISllAhLACeegnWGPHLIVVpTsviL-nWEMElKRwcP--gl  691 (1958)
T KOG0391|consen  615 QLREYQKIGLDWLATLYEKNLNGILADEMGLGKTIQTISLLAHLACEEGNWGPHLIVVPTSVIL-NWEMELKRWCP--GL  691 (1958)
T ss_pred             HHHHHHHhhHHHHHHHHHhcccceehhhhcccchhHHHHHHHHHHhcccCCCCceEEeechhhh-hhhHHHhhhCC--cc
Confidence            589999999987654    558999999999999998888888888888888899999998874 48888999988  68


Q ss_pred             eEEEEEcCCchhhhhHHhcC---CCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHHHHHH
Q psy4275         104 RVSIITGGMDMVDQGKELAK---KPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFFF  174 (182)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~~---~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~~~~~  174 (182)
                      ++..++|........+.-|+   ..+|.|++...+..=+..   |.-+++.++|+||+|++-++...++-.+|+
T Consensus       692 KILTYyGs~kErkeKRqgW~kPnaFHVCItSYklv~qd~~A---FkrkrWqyLvLDEaqnIKnfksqrWQAlln  762 (1958)
T KOG0391|consen  692 KILTYYGSHKERKEKRQGWAKPNAFHVCITSYKLVFQDLTA---FKRKRWQYLVLDEAQNIKNFKSQRWQALLN  762 (1958)
T ss_pred             eEeeecCCHHHHHHHhhcccCCCeeEEeehhhHHHHhHHHH---HHhhccceeehhhhhhhcchhHHHHHHHhc
Confidence            99999998776555555554   457999998877654433   234567899999999999998877766554

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.21  E-value=2.4e-10  Score=101.00  Aligned_cols=127  Identities=19%  Similarity=0.170  Sum_probs=84.7

Q ss_pred             hHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHH-hhccCCceEEEE
Q psy4275          30 TEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLV-LGKVMNLRVSII  108 (182)
Q Consensus        30 ~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~-~~~~~~~~~~~~  108 (182)
                      .....+.+..+.++..++++|+||||||+.....+++.-  ....+++++.-|.+..+..++..+.. +....|..|++.
T Consensus        69 ~~~~~~Il~~l~~~~vvii~g~TGSGKTTqlPq~lle~~--~~~~~~I~~tQPRRlAA~svA~RvA~elg~~lG~~VGY~  146 (1283)
T TIGR01967        69 SAKREDIAEAIAENQVVIIAGETGSGKTTQLPKICLELG--RGSHGLIGHTQPRRLAARTVAQRIAEELGTPLGEKVGYK  146 (1283)
T ss_pred             HHHHHHHHHHHHhCceEEEeCCCCCCcHHHHHHHHHHcC--CCCCceEecCCccHHHHHHHHHHHHHHhCCCcceEEeeE
Confidence            333455667777788899999999999997654554421  11133667777988888887666554 333334444432


Q ss_pred             EcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccc-ccccCC
Q psy4275         109 TGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR-LSLMTS  166 (182)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~-~~~~~~  166 (182)
                      ....+      ....+++|.++|++.++..+....  .++++++||+||+|+ +.+.++
T Consensus       147 vR~~~------~~s~~T~I~~~TdGiLLr~l~~d~--~L~~~~~IIIDEaHERsL~~D~  197 (1283)
T TIGR01967       147 VRFHD------QVSSNTLVKLMTDGILLAETQQDR--FLSRYDTIIIDEAHERSLNIDF  197 (1283)
T ss_pred             EcCCc------ccCCCceeeeccccHHHHHhhhCc--ccccCcEEEEcCcchhhccchh
Confidence            22111      123467899999999999887643  478899999999995 555443

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.

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=99.20  E-value=3.4e-10  Score=96.02  Aligned_cols=131  Identities=24%  Similarity=0.206  Sum_probs=100.4

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSI  107 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  107 (182)
                      .+.+.|....-.+.  ...+..+.||-|||+++.+++.-..+.   |..+-||+++..||..-++++..+.+.+|++|++
T Consensus        85 r~ydVQliGgl~Lh--~G~IAEM~TGEGKTL~atlpaylnAL~---GkgVhVVTvNdYLA~RDae~m~~vy~~LGLtvg~  159 (939)
T PRK12902         85 RHFDVQLIGGMVLH--EGQIAEMKTGEGKTLVATLPSYLNALT---GKGVHVVTVNDYLARRDAEWMGQVHRFLGLSVGL  159 (939)
T ss_pred             CcchhHHHhhhhhc--CCceeeecCCCChhHHHHHHHHHHhhc---CCCeEEEeCCHHHHHhHHHHHHHHHHHhCCeEEE
Confidence            56666665554444  445899999999999998888776666   5579999999999999999999999999999999


Q ss_pred             EEcCCchhhhhHHhcCCCcEEEEChHHH-HHHHhcC-----CCCCCCCccEEEEeccccccccC
Q psy4275         108 ITGGMDMVDQGKELAKKPHIVIATPGRL-ADHLDTC-----NTFSLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~Ilv~T~~~l-~~~~~~~-----~~~~~~~~~~iI~DE~h~~~~~~  165 (182)
                      ..++.....+...  -.|+|+.+|+..+ .++++..     ...-.+.+.+.|+||+|.++=+.
T Consensus       160 i~~~~~~~err~a--Y~~DItYgTn~e~gFDYLRDnm~~~~~~~vqR~~~faIVDEvDSILIDE  221 (939)
T PRK12902        160 IQQDMSPEERKKN--YACDITYATNSELGFDYLRDNMATDISEVVQRPFNYCVIDEVDSILIDE  221 (939)
T ss_pred             ECCCCChHHHHHh--cCCCeEEecCCcccccchhhhhcccccccccCccceEEEecccceeecc
Confidence            8776655444333  3789999999988 3444331     22345678899999999988544

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=99.19  E-value=2e-10  Score=97.87  Aligned_cols=74  Identities=18%  Similarity=0.134  Sum_probs=62.2

Q ss_pred             CCCCCChHHHHhhhhhhhC----CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHh
Q psy4275          24 IGVKTPTEIQKAIIPHVLN----DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVL   97 (182)
Q Consensus        24 ~~~~~~~~~Q~~~~~~~~~----~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~   97 (182)
                      +.+..++|.|.+....+.+    +++.++.+|||+|||++.+.+++......+...+++|.+.|++-..|..+++++.
T Consensus         6 FPy~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~~~~kIiy~sRThsQl~q~i~Elk~~   83 (705)
T TIGR00604         6 FPYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKPEVRKIIYASRTHSQLEQATEELRKL   83 (705)
T ss_pred             cCCCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhccccccEEEEcccchHHHHHHHHHHhh
Confidence            4566679999887766544    8899999999999999999999987765544578999999999999999898885

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).

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

Probab=99.17  E-value=7.4e-10  Score=94.46  Aligned_cols=139  Identities=20%  Similarity=0.214  Sum_probs=101.0

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHH-hhccCCceEE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLV-LGKVMNLRVS  106 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~-~~~~~~~~~~  106 (182)
                      ..+....+....+.++.-++++|+||+|||+.....+++.-+  ..++++.+.-|.+--|..+++.+.+ +....|-.|+
T Consensus        50 Pv~~~~~~i~~ai~~~~vvii~getGsGKTTqlP~~lle~g~--~~~g~I~~tQPRRlAArsvA~RvAeel~~~~G~~VG  127 (845)
T COG1643          50 PVTAVRDEILKAIEQNQVVIIVGETGSGKTTQLPQFLLEEGL--GIAGKIGCTQPRRLAARSVAERVAEELGEKLGETVG  127 (845)
T ss_pred             CcHHHHHHHHHHHHhCCEEEEeCCCCCChHHHHHHHHHhhhc--ccCCeEEecCchHHHHHHHHHHHHHHhCCCcCceee
Confidence            345556667777788889999999999999998888888766  2245788888999888888766554 4444455554


Q ss_pred             EEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHHHHHHHHhhcC
Q psy4275         107 IITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFFFFLKYYI  180 (182)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~~~~~~~~~~~  180 (182)
                      +..--.      .....+..|-++|.+.|+..++...  .++.+++||+||+|+    ........+..+++.+
T Consensus       128 Y~iRfe------~~~s~~Trik~mTdGiLlrei~~D~--~Ls~ys~vIiDEaHE----RSl~tDilLgllk~~~  189 (845)
T COG1643         128 YSIRFE------SKVSPRTRIKVMTDGILLREIQNDP--LLSGYSVVIIDEAHE----RSLNTDILLGLLKDLL  189 (845)
T ss_pred             EEEEee------ccCCCCceeEEeccHHHHHHHhhCc--ccccCCEEEEcchhh----hhHHHHHHHHHHHHHH
Confidence            332111      1223467899999999999998644  488999999999998    5556666666666544

>KOG0387|consensus

Probab=99.14  E-value=6.1e-10  Score=92.53  Aligned_cols=137  Identities=18%  Similarity=0.116  Sum_probs=94.3

Q ss_pred             CChHHHHhhhhhhhC----CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q psy4275          28 TPTEIQKAIIPHVLN----DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNL  103 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~----~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  103 (182)
                      .+.++|++++.++.+    +...|+-..+|.|||+..+..+.........-..+|||||. .+..||.+++..+...  .
T Consensus       205 ~Lf~yQreGV~WL~~L~~q~~GGILgDeMGLGKTIQiisFLaaL~~S~k~~~paLIVCP~-Tii~qW~~E~~~w~p~--~  281 (923)
T KOG0387|consen  205 KLFPYQREGVQWLWELYCQRAGGILGDEMGLGKTIQIISFLAALHHSGKLTKPALIVCPA-TIIHQWMKEFQTWWPP--F  281 (923)
T ss_pred             HhhHHHHHHHHHHHHHHhccCCCeecccccCccchhHHHHHHHHhhcccccCceEEEccH-HHHHHHHHHHHHhCcc--e
Confidence            478999999987755    66789999999999987544443333331323579999995 5568898899888774  7


Q ss_pred             eEEEEEcCCch---------hh----hhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHH
Q psy4275         104 RVSIITGGMDM---------VD----QGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFF  170 (182)
Q Consensus       104 ~~~~~~~~~~~---------~~----~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~  170 (182)
                      +|..++|..+.         ..    ..+....+..|+|+|.+.+.-.  . ..+.-..++++|+||.|.+-+.+....+
T Consensus       282 rv~ilh~t~s~~r~~~~~~~~~~~~~L~r~~~~~~~ilitty~~~r~~--~-d~l~~~~W~y~ILDEGH~IrNpns~isl  358 (923)
T KOG0387|consen  282 RVFILHGTGSGARYDASHSSHKKDKLLIRKVATDGGILITTYDGFRIQ--G-DDLLGILWDYVILDEGHRIRNPNSKISL  358 (923)
T ss_pred             EEEEEecCCcccccccchhhhhhhhhheeeecccCcEEEEehhhhccc--C-cccccccccEEEecCcccccCCccHHHH
Confidence            88888876652         11    1111223567999998776332  1 2233445789999999999888775544

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=99.12  E-value=2.9e-10  Score=96.35  Aligned_cols=131  Identities=22%  Similarity=0.219  Sum_probs=99.1

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSI  107 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  107 (182)
                      ++++.|....-.+  .+..+.++.||.|||+++.+++.-....   |..|.|++++..||.+-+++...+.+.+|++|++
T Consensus        76 r~ydvQlig~l~L--~~G~IaEm~TGEGKTL~a~l~ayl~aL~---G~~VhVvT~NdyLA~RD~e~m~pvy~~LGLsvg~  150 (870)
T CHL00122         76 RHFDVQLIGGLVL--NDGKIAEMKTGEGKTLVATLPAYLNALT---GKGVHIVTVNDYLAKRDQEWMGQIYRFLGLTVGL  150 (870)
T ss_pred             CCCchHhhhhHhh--cCCccccccCCCCchHHHHHHHHHHHhc---CCceEEEeCCHHHHHHHHHHHHHHHHHcCCceee
Confidence            4666665554333  3557999999999999988888654444   5579999999999999999999999999999999


Q ss_pred             EEcCCchhhhhHHhcCCCcEEEEChHHH-HHHHhcCC-----CCCCCCccEEEEeccccccccC
Q psy4275         108 ITGGMDMVDQGKELAKKPHIVIATPGRL-ADHLDTCN-----TFSLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~Ilv~T~~~l-~~~~~~~~-----~~~~~~~~~iI~DE~h~~~~~~  165 (182)
                      ..++.+...+...+  .++|..+|..-+ .++++..-     ..-.+.+.+.|+||+|.++=+.
T Consensus       151 i~~~~~~~err~aY--~~DItYgTn~e~gFDyLRDnm~~~~~~~v~r~~~faIVDEvDSiLIDe  212 (870)
T CHL00122        151 IQEGMSSEERKKNY--LKDITYVTNSELGFDYLRDNMALSLSDVVQRPFNYCIIDEVDSILIDE  212 (870)
T ss_pred             eCCCCChHHHHHhc--CCCCEecCCccccccchhhccCcChHHhhccccceeeeecchhheecc
Confidence            88877665544443  579999998766 35555421     1134568899999999988554

>KOG1123|consensus

Probab=99.12  E-value=8.7e-11  Score=93.43  Aligned_cols=135  Identities=16%  Similarity=0.107  Sum_probs=99.3

Q ss_pred             CChHHHHhhhhhhhC---CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCce
Q psy4275          28 TPTEIQKAIIPHVLN---DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLR  104 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~---~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~  104 (182)
                      .++|+|+..+..+-.   .++.+++.|.|+|||++.+.++...      +.++|++|.+...++||...++.|..--+-.
T Consensus       302 ~iRpYQEksL~KMFGNgRARSGiIVLPCGAGKtLVGvTAa~ti------kK~clvLcts~VSVeQWkqQfk~wsti~d~~  375 (776)
T KOG1123|consen  302 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGVTAACTI------KKSCLVLCTSAVSVEQWKQQFKQWSTIQDDQ  375 (776)
T ss_pred             ccCchHHHHHHHHhCCCcccCceEEEecCCCCceeeeeeeeee------cccEEEEecCccCHHHHHHHHHhhcccCccc
Confidence            489999999988765   3589999999999999876555543      5589999999999999999999987666666


Q ss_pred             EEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcC-------CCCCCCCccEEEEeccccccccCChhHHHHH
Q psy4275         105 VSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTC-------NTFSLNRIKFLVLDEADRLSLMTSLKFFFFF  173 (182)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~-------~~~~~~~~~~iI~DE~h~~~~~~~~~~~~~~  173 (182)
                      ++.++++...     ....++.|+|+|..++.+--++.       ..+.-+.++++++||+|-+-..-+++.+...
T Consensus       376 i~rFTsd~Ke-----~~~~~~gvvvsTYsMva~t~kRS~eaek~m~~l~~~EWGllllDEVHvvPA~MFRRVlsiv  446 (776)
T KOG1123|consen  376 ICRFTSDAKE-----RFPSGAGVVVTTYSMVAYTGKRSHEAEKIMDFLRGREWGLLLLDEVHVVPAKMFRRVLSIV  446 (776)
T ss_pred             eEEeeccccc-----cCCCCCcEEEEeeehhhhcccccHHHHHHHHHHhcCeeeeEEeehhccchHHHHHHHHHHH
Confidence            7776655432     23457899999988874321110       0113445889999999987776666655443

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

Probab=99.10  E-value=5.4e-10  Score=94.65  Aligned_cols=73  Identities=30%  Similarity=0.306  Sum_probs=59.2

Q ss_pred             HHCCCCCChHHHHhhhhhhhC----CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHH
Q psy4275          22 QTIGVKTPTEIQKAIIPHVLN----DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLV   96 (182)
Q Consensus        22 ~~~~~~~~~~~Q~~~~~~~~~----~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~   96 (182)
                      ..+...++++.|.+....+..    ++..++++|||+|||++++.+++......  +.+++|.++|+.+.+|..+....
T Consensus         9 ~~~~~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~~--~~~viist~t~~lq~q~~~~~~~   85 (654)
T COG1199           9 VAFPGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREE--GKKVIISTRTKALQEQLLEEDLP   85 (654)
T ss_pred             hhCCCCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHHc--CCcEEEECCCHHHHHHHHHhhcc
Confidence            345556899999998866543    66699999999999999999999887665  36899999999999998655443

>KOG0920|consensus

Probab=99.09  E-value=2.7e-09  Score=91.18  Aligned_cols=142  Identities=18%  Similarity=0.243  Sum_probs=103.2

Q ss_pred             CCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHh-hccCCceE
Q psy4275          27 KTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVL-GKVMNLRV  105 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~-~~~~~~~~  105 (182)
                      ...+..+++.+..+.+++.++++|.||+|||+...-.+++....++...++++--|.+-.|..+++.+..- ....|-.|
T Consensus       172 LPa~~~r~~Il~~i~~~qVvvIsGeTGcGKTTQvpQfiLd~~~~~~~~~~IicTQPRRIsAIsvAeRVa~ER~~~~g~~V  251 (924)
T KOG0920|consen  172 LPAYKMRDTILDAIEENQVVVISGETGCGKTTQVPQFILDEAIESGAACNIICTQPRRISAISVAERVAKERGESLGEEV  251 (924)
T ss_pred             CccHHHHHHHHHHHHhCceEEEeCCCCCCchhhhhHHHHHHHHhcCCCCeEEecCCchHHHHHHHHHHHHHhccccCCee
Confidence            35678888899999999999999999999999988888888777665667788889988888888776653 33344444


Q ss_pred             EEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHHHHHHHHhhcC
Q psy4275         106 SIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFFFFLKYYI  180 (182)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~~~~~~~~~~~  180 (182)
                      +.-.+..+.      ......++.||.+.++..+...  ..+..+..+|+||+|+=.    .....++..++..+
T Consensus       252 GYqvrl~~~------~s~~t~L~fcTtGvLLr~L~~~--~~l~~vthiivDEVHER~----i~~DflLi~lk~lL  314 (924)
T KOG0920|consen  252 GYQVRLESK------RSRETRLLFCTTGVLLRRLQSD--PTLSGVTHIIVDEVHERS----INTDFLLILLKDLL  314 (924)
T ss_pred             eEEEeeecc------cCCceeEEEecHHHHHHHhccC--cccccCceeeeeeEEEcc----CCcccHHHHHHHHh
Confidence            443332221      1224689999999999999773  357789999999999843    33334444444443

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

Probab=99.09  E-value=1.6e-09  Score=79.98  Aligned_cols=68  Identities=24%  Similarity=0.231  Sum_probs=50.3

Q ss_pred             ChHHHHhhhhhhhCCCc-EEEECCCCChHHHHHHHHHHHhh-----ccCCCCeeEEEEcCCHHHHHHHHHHHHH
Q psy4275          29 PTEIQKAIIPHVLNDED-CIGCAKTGSGKTLAFALPILQKW-----CEDPYGIFALVLTPTRELAYQIGDQFLV   96 (182)
Q Consensus        29 ~~~~Q~~~~~~~~~~~~-~li~~~tg~GKT~~~~~~~~~~~-----~~~~~~~~~lil~p~~~l~~q~~~~~~~   96 (182)
                      +++.|.+++..+.+... .+++||+|+|||.+....+....     .....+.++++++|++..++.+.+.+.+
T Consensus         2 ln~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen    2 LNESQREAIQSALSSNGITLIQGPPGTGKTTTLASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             --HHHHHHHHHHCTSSE-EEEE-STTSSHHHHHHHHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHcCCCCEEEECCCCCChHHHHHHHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            68999999999998887 99999999999976544444331     1233467899999999999998887777

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

Probab=99.08  E-value=1.5e-09  Score=82.79  Aligned_cols=115  Identities=20%  Similarity=0.255  Sum_probs=89.7

Q ss_pred             CChHHHHhhhhhhh----CCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q psy4275          28 TPTEIQKAIIPHVL----NDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNL  103 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~----~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  103 (182)
                      .+++.|+.+-..+.    +.+..++.+-||+|||-. ++..++...+.  |.++.+..|..+.+-+++..+++-+..  .
T Consensus        97 ~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEM-if~~i~~al~~--G~~vciASPRvDVclEl~~Rlk~aF~~--~  171 (441)
T COG4098          97 TLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEM-IFQGIEQALNQ--GGRVCIASPRVDVCLELYPRLKQAFSN--C  171 (441)
T ss_pred             ccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhh-hHHHHHHHHhc--CCeEEEecCcccchHHHHHHHHHhhcc--C
Confidence            68999988765544    478999999999999987 55666666665  678999999999999999888886664  5


Q ss_pred             eEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccc
Q psy4275         104 RVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLS  162 (182)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~  162 (182)
                      +..+++|+.....       +.+++|+|...++.+.+.        ++++|+||+|.+-
T Consensus       172 ~I~~Lyg~S~~~f-------r~plvVaTtHQLlrFk~a--------FD~liIDEVDAFP  215 (441)
T COG4098         172 DIDLLYGDSDSYF-------RAPLVVATTHQLLRFKQA--------FDLLIIDEVDAFP  215 (441)
T ss_pred             CeeeEecCCchhc-------cccEEEEehHHHHHHHhh--------ccEEEEecccccc
Confidence            6667777764321       367999998888776655        6799999999754

>KOG0952|consensus

Probab=99.07  E-value=7.1e-11  Score=100.44  Aligned_cols=133  Identities=23%  Similarity=0.275  Sum_probs=108.7

Q ss_pred             CChHHHHhhhhhhhC-CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEE
Q psy4275          28 TPTEIQKAIIPHVLN-DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVS  106 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~-~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~  106 (182)
                      ..+|.|.+.+-.... ..++++-+|||+|||.++...+...+...+. .+++|++|.++|+..-.+.|++....-|+++.
T Consensus       927 ~fn~~q~~if~~~y~td~~~~~g~ptgsgkt~~ae~a~~~~~~~~p~-~kvvyIap~kalvker~~Dw~~r~~~~g~k~i 1005 (1230)
T KOG0952|consen  927 YFNPIQTQIFHCLYHTDLNFLLGAPTGSGKTVVAELAIFRALSYYPG-SKVVYIAPDKALVKERSDDWSKRDELPGIKVI 1005 (1230)
T ss_pred             ccCCccceEEEEEeecchhhhhcCCccCcchhHHHHHHHHHhccCCC-ccEEEEcCCchhhcccccchhhhcccCCceeE
Confidence            567778887766655 6789999999999999999999988777764 68999999999998887777776655599999


Q ss_pred             EEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCC-CCCCccEEEEecccccccc
Q psy4275         107 IITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTF-SLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~-~~~~~~~iI~DE~h~~~~~  164 (182)
                      -++|+...+.   .-..+++++|+||+++....++|... -+.+++++|+||.|+..++
T Consensus      1006 e~tgd~~pd~---~~v~~~~~~ittpek~dgi~Rsw~~r~~v~~v~~iv~de~hllg~~ 1061 (1230)
T KOG0952|consen 1006 ELTGDVTPDV---KAVREADIVITTPEKWDGISRSWQTRKYVQSVSLIVLDEIHLLGED 1061 (1230)
T ss_pred             eccCccCCCh---hheecCceEEcccccccCccccccchhhhccccceeecccccccCC
Confidence            9998876553   22347899999999999988876443 5778999999999988776

>KOG0922|consensus

Probab=99.04  E-value=4.5e-09  Score=86.11  Aligned_cols=139  Identities=20%  Similarity=0.175  Sum_probs=99.9

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHH-hhccCCceEE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLV-LGKVMNLRVS  106 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~-~~~~~~~~~~  106 (182)
                      ....+-.+.+..+.+++-.++.|+||||||+...-++.+.-+.+.  +++.+.-|.+..|..+++.... .....|-.|+
T Consensus        51 PI~~~r~~il~~ve~nqvlIviGeTGsGKSTQipQyL~eaG~~~~--g~I~~TQPRRVAavslA~RVAeE~~~~lG~~VG  128 (674)
T KOG0922|consen   51 PIYKYRDQILYAVEDNQVLIVIGETGSGKSTQIPQYLAEAGFASS--GKIACTQPRRVAAVSLAKRVAEEMGCQLGEEVG  128 (674)
T ss_pred             CHHHHHHHHHHHHHHCCEEEEEcCCCCCccccHhHHHHhcccccC--CcEEeecCchHHHHHHHHHHHHHhCCCcCceee
Confidence            345555677778888899999999999999997777777666653  3488888999998888766554 4444455554


Q ss_pred             EEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHHHHHHHHhhcC
Q psy4275         107 IITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFFFFLKYYI  180 (182)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~~~~~~~~~~~  180 (182)
                      +...-.+      .-.....|...|.+.++.-+....  .+++.++||+||||+    .......++..+|+.+
T Consensus       129 Y~IRFed------~ts~~TrikymTDG~LLRE~l~Dp--~LskYsvIIlDEAHE----Rsl~TDiLlGlLKki~  190 (674)
T KOG0922|consen  129 YTIRFED------STSKDTRIKYMTDGMLLREILKDP--LLSKYSVIILDEAHE----RSLHTDILLGLLKKIL  190 (674)
T ss_pred             eEEEecc------cCCCceeEEEecchHHHHHHhcCC--ccccccEEEEechhh----hhhHHHHHHHHHHHHH
Confidence            3221110      112367899999999998776544  588899999999997    6666667777777655

>KOG1802|consensus

Probab=98.99  E-value=2.1e-09  Score=88.14  Aligned_cols=86  Identities=19%  Similarity=0.178  Sum_probs=69.2

Q ss_pred             HHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhh
Q psy4275          19 RQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLG   98 (182)
Q Consensus        19 ~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~   98 (182)
                      +.+...++..++..|..+..+++.+.-.+++||+|+|||.+....+++....+  ++.+|+++|+...++|+++.+.+- 
T Consensus       401 ~~~s~~~lpkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa~IVyhl~~~~--~~~VLvcApSNiAVDqLaeKIh~t-  477 (935)
T KOG1802|consen  401 RRFSVPNLPKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSATIVYHLARQH--AGPVLVCAPSNIAVDQLAEKIHKT-  477 (935)
T ss_pred             hhhcCCCchhhchHHHHHHHHHHcCCceeeecCCCCCceehhHHHHHHHHHhc--CCceEEEcccchhHHHHHHHHHhc-
Confidence            35566788899999999999999999999999999999998665555554443  558999999999999998887664 


Q ss_pred             ccCCceEEEEEc
Q psy4275          99 KVMNLRVSIITG  110 (182)
Q Consensus        99 ~~~~~~~~~~~~  110 (182)
                         |++|..+..
T Consensus       478 ---gLKVvRl~a  486 (935)
T KOG1802|consen  478 ---GLKVVRLCA  486 (935)
T ss_pred             ---CceEeeeeh
Confidence               566655543

>KOG0390|consensus

Probab=98.97  E-value=1.3e-08  Score=85.78  Aligned_cols=135  Identities=20%  Similarity=0.103  Sum_probs=97.5

Q ss_pred             CChHHHHhhhhhhhC----------CCcEEEECCCCChHHHHHHHHHHHhhccCCC----CeeEEEEcCCHHHHHHHHHH
Q psy4275          28 TPTEIQKAIIPHVLN----------DEDCIGCAKTGSGKTLAFALPILQKWCEDPY----GIFALVLTPTRELAYQIGDQ   93 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~----------~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~----~~~~lil~p~~~l~~q~~~~   93 (182)
                      .++|+|++.+.-+.+          ...+++...+|+|||...+..+...+.+.+.    -.+.+||+|. .|+..|+++
T Consensus       238 ~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq~IsflwtlLrq~P~~~~~~~k~lVV~P~-sLv~nWkkE  316 (776)
T KOG0390|consen  238 ILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQCISFIWTLLRQFPQAKPLINKPLVVAPS-SLVNNWKKE  316 (776)
T ss_pred             hcCchHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHHHHHHHHHHHHhCcCccccccccEEEccH-HHHHHHHHH
Confidence            589999999976644          2357778899999999877777777666664    1478999994 667889999


Q ss_pred             HHHhhccCCceEEEEEcCCch-hhhhHHhc------CCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCC
Q psy4275          94 FLVLGKVMNLRVSIITGGMDM-VDQGKELA------KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTS  166 (182)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~------~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~  166 (182)
                      +.+|.....+....+++..+. +.....+.      -...|++.+.+.+.++++.-   ....++++|+||.|..=+...
T Consensus       317 F~KWl~~~~i~~l~~~~~~~~~w~~~~sil~~~~~~~~~~vli~sye~~~~~~~~i---l~~~~glLVcDEGHrlkN~~s  393 (776)
T KOG0390|consen  317 FGKWLGNHRINPLDFYSTKKSSWIKLKSILFLGYKQFTTPVLIISYETASDYCRKI---LLIRPGLLVCDEGHRLKNSDS  393 (776)
T ss_pred             HHHhccccccceeeeecccchhhhhhHHHHHhhhhheeEEEEeccHHHHHHHHHHH---hcCCCCeEEECCCCCccchhh
Confidence            988877656666666766653 11111111      13468999999998877663   356689999999998766554

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=98.96  E-value=8.7e-09  Score=87.43  Aligned_cols=131  Identities=21%  Similarity=0.161  Sum_probs=100.0

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSI  107 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  107 (182)
                      ++++.|....-.+..|  .+..+.||-|||+++.+++.-..+.   |..|-|++.+..||..-+++...+...+|++|++
T Consensus        78 r~ydVQliGglvLh~G--~IAEMkTGEGKTLvAtLpayLnAL~---GkgVhVVTvNdYLA~RDae~mg~vy~fLGLsvG~  152 (925)
T PRK12903         78 RPYDVQIIGGIILDLG--SVAEMKTGEGKTITSIAPVYLNALT---GKGVIVSTVNEYLAERDAEEMGKVFNFLGLSVGI  152 (925)
T ss_pred             CcCchHHHHHHHHhcC--CeeeecCCCCccHHHHHHHHHHHhc---CCceEEEecchhhhhhhHHHHHHHHHHhCCceee
Confidence            5666676655444444  5899999999999988887665555   5578999999999999999999999999999998


Q ss_pred             EEcCCchhhhhHHhcCCCcEEEEChHHH-HHHHhcCCC-----CCCCCccEEEEeccccccccC
Q psy4275         108 ITGGMDMVDQGKELAKKPHIVIATPGRL-ADHLDTCNT-----FSLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~Ilv~T~~~l-~~~~~~~~~-----~~~~~~~~iI~DE~h~~~~~~  165 (182)
                      ...+.........+  .|+|..+|..-| .++++..-.     .-.+.+.+.|+||+|.++=+.
T Consensus       153 i~~~~~~~~rr~aY--~~DItYgTn~E~gFDYLRDnm~~~~~~~vqR~~~faIVDEVDSILIDE  214 (925)
T PRK12903        153 NKANMDPNLKREAY--ACDITYSVHSELGFDYLRDNMVSSKEEKVQRGLNFCLIDEVDSILIDE  214 (925)
T ss_pred             eCCCCChHHHHHhc--cCCCeeecCcccchhhhhhcccccHHHhcCcccceeeeccchheeecc
Confidence            88766555444443  589999998877 457765311     134667899999999987544

>KOG4439|consensus

Probab=98.95  E-value=1.5e-09  Score=89.32  Aligned_cols=144  Identities=20%  Similarity=0.138  Sum_probs=99.2

Q ss_pred             CChHHHHhhhhhhhC-----CCcEEEECCCCChHHHHHHHHHHHhhccC-------CCCeeEEEEcCCHHHHHHHHHHHH
Q psy4275          28 TPTEIQKAIIPHVLN-----DEDCIGCAKTGSGKTLAFALPILQKWCED-------PYGIFALVLTPTRELAYQIGDQFL   95 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~-----~~~~li~~~tg~GKT~~~~~~~~~~~~~~-------~~~~~~lil~p~~~l~~q~~~~~~   95 (182)
                      ++-|+|+.++.++.+     ....|+....|.|||.+.+..+++.-.+.       +....++|||| .+|..||+.+++
T Consensus       325 ~LmpHQkaal~Wl~wRE~q~~~GGILaddmGLGKTlsmislil~qK~~~~~~~~~~~~a~~TLII~P-aSli~qW~~Ev~  403 (901)
T KOG4439|consen  325 ELMPHQKAALRWLLWRESQPPSGGILADDMGLGKTLSMISLILHQKAARKAREKKGESASKTLIICP-ASLIHQWEAEVA  403 (901)
T ss_pred             ecchhhhhhhhhhcccccCCCCCcccccccccccchHHHHHHHHHHHHHHhhcccccccCCeEEeCc-HHHHHHHHHHHH
Confidence            578999999988876     34688899999999998766666543221       11225899999 567799988888


Q ss_pred             HhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHH----HHhcCC---CCCCCCccEEEEeccccccccCChh
Q psy4275          96 VLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLAD----HLDTCN---TFSLNRIKFLVLDEADRLSLMTSLK  168 (182)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~----~~~~~~---~~~~~~~~~iI~DE~h~~~~~~~~~  168 (182)
                      .....--++|..++|.... .-.......++|+|+|..-+..    -....+   .+.--.++-||+||||.+-+.....
T Consensus       404 ~rl~~n~LsV~~~HG~n~r-~i~~~~L~~YDvViTTY~lva~~~~~e~~~~~~~spL~~I~W~RVILDEAH~IrN~~tq~  482 (901)
T KOG4439|consen  404 RRLEQNALSVYLYHGPNKR-EISAKELRKYDVVITTYNLVANKPDDELEEGKNSSPLARIAWSRVILDEAHNIRNSNTQC  482 (901)
T ss_pred             HHHhhcceEEEEecCCccc-cCCHHHHhhcceEEEeeeccccCCchhhhcccCccHHHHhhHHHhhhhhhhhhcccchhH
Confidence            8777767899999988752 2222334689999999876654    111111   1111123469999999998877766


Q ss_pred             HHHHH
Q psy4275         169 FFFFF  173 (182)
Q Consensus       169 ~~~~~  173 (182)
                      ....+
T Consensus       483 S~AVC  487 (901)
T KOG4439|consen  483 SKAVC  487 (901)
T ss_pred             HHHHH
Confidence            55544

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=98.93  E-value=6e-09  Score=89.10  Aligned_cols=148  Identities=16%  Similarity=0.054  Sum_probs=92.4

Q ss_pred             CChHHHHhhhhhhhC---CC-cEEEECCCCChHHHHHHHHHHHhhcc-CCCCeeEEEEcCCHHHHHHHHHHHHHhhccCC
Q psy4275          28 TPTEIQKAIIPHVLN---DE-DCIGCAKTGSGKTLAFALPILQKWCE-DPYGIFALVLTPTRELAYQIGDQFLVLGKVMN  102 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~---~~-~~li~~~tg~GKT~~~~~~~~~~~~~-~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~  102 (182)
                      ...+.|..++.....   .. .+++.+|||+|||.+++.++...+.. .....+++++.|++++.+++++.++......+
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~~~~~~r~i~vlP~~t~ie~~~~r~~~~~~~~~  274 (733)
T COG1203         195 EGYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIEDMYRRAKEIFGLFS  274 (733)
T ss_pred             hhhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhccccccceEEEEccHHHHHHHHHHHHHhhhcccc
Confidence            458888888877665   34 78899999999999999888887766 33567999999999999999999998777655


Q ss_pred             ceEEEEEcCCchhhhhHH---------h-----cCCCcEEEEChHHHHHHHhcCCCCC-CC--CccEEEEeccccccccC
Q psy4275         103 LRVSIITGGMDMVDQGKE---------L-----AKKPHIVIATPGRLADHLDTCNTFS-LN--RIKFLVLDEADRLSLMT  165 (182)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~---------~-----~~~~~Ilv~T~~~l~~~~~~~~~~~-~~--~~~~iI~DE~h~~~~~~  165 (182)
                      ......+|..........         .     ..-..+.++||.......-....+. +.  ..+++|+||+|.+.+..
T Consensus       275 ~~~~~~h~~~~~~~~~~~~~~~~~~~~~~ds~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~S~vIlDE~h~~~~~~  354 (733)
T COG1203         275 VIGKSLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILIFSVKGFKFEFLALLLTSLVILDEVHLYADET  354 (733)
T ss_pred             cccccccccccchhhhccccccceeEEecccccceeccccccCHhHhhhhhccccchHHHHHHHhhchhhccHHhhcccc
Confidence            444323333221110000         0     0012344455444433111111111 11  13689999999998885


Q ss_pred             ChhHHHHHHH
Q psy4275         166 SLKFFFFFFF  175 (182)
Q Consensus       166 ~~~~~~~~~~  175 (182)
                      ....+..+..
T Consensus       355 ~~~~l~~~i~  364 (733)
T COG1203         355 MLAALLALLE  364 (733)
T ss_pred             hHHHHHHHHH
Confidence            4344443333

>COG4889 Predicted helicase [General function prediction only]

Probab=98.90  E-value=9.3e-09  Score=86.85  Aligned_cols=141  Identities=19%  Similarity=0.185  Sum_probs=89.3

Q ss_pred             HHHHHHHHCCCCCChHHHHhhhhhhhC----CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHH
Q psy4275          16 WLIRQCQTIGVKTPTEIQKAIIPHVLN----DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIG   91 (182)
Q Consensus        16 ~i~~~l~~~~~~~~~~~Q~~~~~~~~~----~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~   91 (182)
                      +....+.-..-..|+|+|+.++....+    +...=+.+..|+|||..++- +.+.+.+    .++++++|+.+|..|..
T Consensus       149 e~~~nl~l~~~kk~R~hQq~Aid~a~~~F~~n~RGkLIMAcGTGKTfTsLk-isEala~----~~iL~LvPSIsLLsQTl  223 (1518)
T COG4889         149 ELQDNLPLKKPKKPRPHQQTAIDAAKEGFSDNDRGKLIMACGTGKTFTSLK-ISEALAA----ARILFLVPSISLLSQTL  223 (1518)
T ss_pred             ccccccccCCCCCCChhHHHHHHHHHhhcccccCCcEEEecCCCccchHHH-HHHHHhh----hheEeecchHHHHHHHH
Confidence            444445444556899999999988766    22333456689999998654 3333333    48999999999999876


Q ss_pred             HHHHHhhccCCceEEEEEcCCchh-------------------------hhhHHhcCCCcEEEEChHHHHHHHhcCCCCC
Q psy4275          92 DQFLVLGKVMNLRVSIITGGMDMV-------------------------DQGKELAKKPHIVIATPGRLADHLDTCNTFS  146 (182)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~-------------------------~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~  146 (182)
                      ..|..- +..+++...++++..-.                         ...+.-.++--|+.+|.+.+...-.. ...-
T Consensus       224 rew~~~-~~l~~~a~aVcSD~kvsrs~eDik~sdl~~p~sT~~~~il~~~~~~~k~~~~~vvFsTYQSl~~i~eA-Qe~G  301 (1518)
T COG4889         224 REWTAQ-KELDFRASAVCSDDKVSRSAEDIKASDLPIPVSTDLEDILSEMEHRQKANGLTVVFSTYQSLPRIKEA-QEAG  301 (1518)
T ss_pred             HHHhhc-cCccceeEEEecCccccccccccccccCCCCCcccHHHHHHHHHHhhccCCcEEEEEcccchHHHHHH-HHcC
Confidence            665543 22344444443321100                         11111223456899999988765443 2334


Q ss_pred             CCCccEEEEeccccccc
Q psy4275         147 LNRIKFLVLDEADRLSL  163 (182)
Q Consensus       147 ~~~~~~iI~DE~h~~~~  163 (182)
                      +..+++||.||||+...
T Consensus       302 ~~~fDliicDEAHRTtG  318 (1518)
T COG4889         302 LDEFDLIICDEAHRTTG  318 (1518)
T ss_pred             CCCccEEEecchhcccc
Confidence            77889999999998654

>PRK14873 primosome assembly protein PriA; Provisional

Probab=98.89  E-value=8.1e-09  Score=86.92  Aligned_cols=102  Identities=15%  Similarity=0.141  Sum_probs=76.5

Q ss_pred             EEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhh----HHhc
Q psy4275          47 IGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQG----KELA  122 (182)
Q Consensus        47 li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~  122 (182)
                      +..+.+|+|||.+|+-.+-..+..   |.++|+++|..++..|+.+.++..+.  +..+..++++.+..++.    ....
T Consensus       164 i~~~~~GSGKTevyl~~i~~~l~~---Gk~vLvLvPEi~lt~q~~~rl~~~f~--~~~v~~lhS~l~~~~R~~~w~~~~~  238 (665)
T PRK14873        164 VWQALPGEDWARRLAAAAAATLRA---GRGALVVVPDQRDVDRLEAALRALLG--AGDVAVLSAGLGPADRYRRWLAVLR  238 (665)
T ss_pred             HhhcCCCCcHHHHHHHHHHHHHHc---CCeEEEEecchhhHHHHHHHHHHHcC--CCcEEEECCCCCHHHHHHHHHHHhC
Confidence            334446999999987777666555   66899999999999998888776553  25688888877654333    3334


Q ss_pred             CCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccc
Q psy4275         123 KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL  161 (182)
Q Consensus       123 ~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~  161 (182)
                      ++.+|+|||        ++.-...++++++||+||-|.-
T Consensus       239 G~~~IViGt--------RSAvFaP~~~LgLIIvdEEhd~  269 (665)
T PRK14873        239 GQARVVVGT--------RSAVFAPVEDLGLVAIWDDGDD  269 (665)
T ss_pred             CCCcEEEEc--------ceeEEeccCCCCEEEEEcCCch
Confidence            568999999        6644558999999999999853

>KOG0384|consensus

Probab=98.89  E-value=5.9e-09  Score=90.19  Aligned_cols=135  Identities=17%  Similarity=0.164  Sum_probs=95.0

Q ss_pred             CCChHHHHhhhhhhhC----CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCC
Q psy4275          27 KTPTEIQKAIIPHVLN----DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMN  102 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~----~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~  102 (182)
                      .+++++|-+.+.+++.    ++|+|+...+|.|||+..+..+.+.+......+-.|+|+|...+. .|...+..+.   +
T Consensus       369 ~~LRdyQLeGlNWl~~~W~~~~n~ILADEmgLgktvqti~fl~~l~~~~~~~gpflvvvplst~~-~W~~ef~~w~---~  444 (1373)
T KOG0384|consen  369 NELRDYQLEGLNWLLYSWYKRNNCILADEMGLGKTVQTITFLSYLFHSLQIHGPFLVVVPLSTIT-AWEREFETWT---D  444 (1373)
T ss_pred             chhhhhhcccchhHHHHHHhcccceehhhcCCCcchHHHHHHHHHHHhhhccCCeEEEeehhhhH-HHHHHHHHHh---h
Confidence            5799999999987654    789999999999999875555444443332233478899976663 3555566555   6


Q ss_pred             ceEEEEEcCCchhhhhHHhc----C-----CCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChh
Q psy4275         103 LRVSIITGGMDMVDQGKELA----K-----KPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLK  168 (182)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~----~-----~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~  168 (182)
                      .++++++|+....+..+.+.    .     ..+++++|.+.++.=....+   --+++++++||||++-+.....
T Consensus       445 mn~i~y~g~~~sr~~i~~ye~~~~~~~~~lkf~~lltTye~~LkDk~~L~---~i~w~~~~vDeahrLkN~~~~l  516 (1373)
T KOG0384|consen  445 MNVIVYHGNLESRQLIRQYEFYHSSNTKKLKFNALLTTYEIVLKDKAELS---KIPWRYLLVDEAHRLKNDESKL  516 (1373)
T ss_pred             hceeeeecchhHHHHHHHHHheecCCccccccceeehhhHHHhccHhhhc---cCCcceeeecHHhhcCchHHHH
Confidence            88999999887655554432    1     46899999998865333222   2236799999999998766543

>KOG0388|consensus

Probab=98.88  E-value=7e-09  Score=85.78  Aligned_cols=142  Identities=18%  Similarity=0.129  Sum_probs=105.0

Q ss_pred             CChHHHHhhhhhhhC----CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q psy4275          28 TPTEIQKAIIPHVLN----DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNL  103 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~----~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  103 (182)
                      .+.+||-..+.++.+    |=|.++...+|.|||+..+..+.+..-.+...+-.++|+|...| +.|++++.++..  .+
T Consensus       567 tLKEYQlkGLnWLvnlYdqGiNGILADeMGLGKTVQsisvlAhLaE~~nIwGPFLVVtpaStL-~NWaqEisrFlP--~~  643 (1185)
T KOG0388|consen  567 TLKEYQLKGLNWLVNLYDQGINGILADEMGLGKTVQSISVLAHLAETHNIWGPFLVVTPASTL-HNWAQEISRFLP--SF  643 (1185)
T ss_pred             hhHHHhhccHHHHHHHHHccccceehhhhccchhHHHHHHHHHHHHhccCCCceEEeehHHHH-hHHHHHHHHhCc--cc
Confidence            577899999888766    77999999999999999776666655555445568999997777 556667766666  37


Q ss_pred             eEEEEEcCCchhhhhHHhc---------CCCcEEEEChHHHH---HHHhcCCCCCCCCccEEEEeccccccccCChhHHH
Q psy4275         104 RVSIITGGMDMVDQGKELA---------KKPHIVIATPGRLA---DHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFF  171 (182)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~---------~~~~Ilv~T~~~l~---~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~~  171 (182)
                      +++-+.|+.+.....+..+         ...+|+|++.+.+.   +++++-      ++.+.|+|||+.+-+....++..
T Consensus       644 k~lpywGs~~eRkiLrKfw~rKnmY~rna~fhVviTSYQlvVtDeky~qkv------KWQYMILDEAQAIKSSsS~RWKt  717 (1185)
T KOG0388|consen  644 KVLPYWGSPSERKILRKFWNRKNMYRRNAPFHVVITSYQLVVTDEKYLQKV------KWQYMILDEAQAIKSSSSSRWKT  717 (1185)
T ss_pred             eeecCcCChhhhHHHHHhcchhhhhccCCCceEEEEeeeeeechHHHHHhh------hhhheehhHHHHhhhhhhhHHHH
Confidence            8888888876544333322         25689999988773   445441      25699999999999999888888


Q ss_pred             HHHHHhh
Q psy4275         172 FFFFLKY  178 (182)
Q Consensus       172 ~~~~~~~  178 (182)
                      ++..-++
T Consensus       718 LLsF~cR  724 (1185)
T KOG0388|consen  718 LLSFKCR  724 (1185)
T ss_pred             Hhhhhcc
Confidence            7765443

>KOG1000|consensus

Probab=98.88  E-value=4.3e-08  Score=78.24  Aligned_cols=136  Identities=13%  Similarity=0.105  Sum_probs=91.2

Q ss_pred             CCCChHHHHhhhhhhhC-CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCce
Q psy4275          26 VKTPTEIQKAIIPHVLN-DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLR  104 (182)
Q Consensus        26 ~~~~~~~Q~~~~~~~~~-~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~  104 (182)
                      +.++-|+|.+.+...++ |..+++...+|.|||+.++..+......   + -.+||||.... -.|++.+.++..-+.- 
T Consensus       196 vs~LlPFQreGv~faL~RgGR~llADeMGLGKTiQAlaIA~yyraE---w-plliVcPAsvr-ftWa~al~r~lps~~p-  269 (689)
T KOG1000|consen  196 VSRLLPFQREGVIFALERGGRILLADEMGLGKTIQALAIARYYRAE---W-PLLIVCPASVR-FTWAKALNRFLPSIHP-  269 (689)
T ss_pred             HHhhCchhhhhHHHHHhcCCeEEEecccccchHHHHHHHHHHHhhc---C-cEEEEecHHHh-HHHHHHHHHhcccccc-
Confidence            45788999999877554 7889999999999999975444443222   3 48999996444 5677788877665433 


Q ss_pred             EEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHHHHH
Q psy4275         105 VSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFF  173 (182)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~~~~  173 (182)
                      +.++.++...-.   .+.....|.|.+.+.+..+-..   ......+++|+||+|++-+...++....+
T Consensus       270 i~vv~~~~D~~~---~~~t~~~v~ivSye~ls~l~~~---l~~~~~~vvI~DEsH~Lk~sktkr~Ka~~  332 (689)
T KOG1000|consen  270 IFVVDKSSDPLP---DVCTSNTVAIVSYEQLSLLHDI---LKKEKYRVVIFDESHMLKDSKTKRTKAAT  332 (689)
T ss_pred             eEEEecccCCcc---ccccCCeEEEEEHHHHHHHHHH---HhcccceEEEEechhhhhccchhhhhhhh
Confidence            444444443211   1223456899998887654433   22445789999999999887766654433

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

Probab=98.87  E-value=1.6e-08  Score=88.47  Aligned_cols=118  Identities=19%  Similarity=0.196  Sum_probs=83.7

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA  122 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  122 (182)
                      ++..++..-+|||||++. +.+...+...+..+.+++|+-.++|-.|..+.++.+........    ...+..+....+.
T Consensus       273 ~~~G~IWHtqGSGKTlTm-~~~A~~l~~~~~~~~v~fvvDR~dLd~Q~~~~f~~~~~~~~~~~----~~~s~~~Lk~~l~  347 (962)
T COG0610         273 GKGGYIWHTQGSGKTLTM-FKLARLLLELPKNPKVLFVVDRKDLDDQTSDEFQSFGKVAFNDP----KAESTSELKELLE  347 (962)
T ss_pred             CCceEEEeecCCchHHHH-HHHHHHHHhccCCCeEEEEechHHHHHHHHHHHHHHHHhhhhcc----cccCHHHHHHHHh
Confidence            357999999999999984 45555555557788999999999999999999998866533322    3334444445555


Q ss_pred             CC-CcEEEEChHHHHHHHhcCCCC-CCCCccEEEEeccccccccC
Q psy4275         123 KK-PHIVIATPGRLADHLDTCNTF-SLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus       123 ~~-~~Ilv~T~~~l~~~~~~~~~~-~~~~~~~iI~DE~h~~~~~~  165 (182)
                      +. ..|+|+|-++|.......... .-++=-++|+||||+-....
T Consensus       348 ~~~~~ii~TTIQKf~~~~~~~~~~~~~~~~ivvI~DEaHRSQ~G~  392 (962)
T COG0610         348 DGKGKIIVTTIQKFNKAVKEDELELLKRKNVVVIIDEAHRSQYGE  392 (962)
T ss_pred             cCCCcEEEEEecccchhhhcccccccCCCcEEEEEechhhccccH
Confidence            43 589999999998887663111 12222379999999855433

>KOG1002|consensus

Probab=98.86  E-value=4.5e-08  Score=78.21  Aligned_cols=131  Identities=21%  Similarity=0.167  Sum_probs=95.3

Q ss_pred             CChHHHHhhhhhhhCC-----CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCC
Q psy4275          28 TPTEIQKAIIPHVLND-----EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMN  102 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~-----~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~  102 (182)
                      .+-|+|++.+.++...     ...++...+|-|||+.++..++.....    ...++++|+.++ .||.+++.+... -.
T Consensus       184 ~LL~fQkE~l~Wl~~QE~Ss~~GGiLADEMGMGKTIQtIaLllae~~r----a~tLVvaP~VAl-mQW~nEI~~~T~-gs  257 (791)
T KOG1002|consen  184 PLLPFQKEGLAWLTSQEESSVAGGILADEMGMGKTIQTIALLLAEVDR----APTLVVAPTVAL-MQWKNEIERHTS-GS  257 (791)
T ss_pred             cchhhhHHHHHHHHHhhhhhhccceehhhhccchHHHHHHHHHhcccc----CCeeEEccHHHH-HHHHHHHHHhcc-Cc
Confidence            6889999998776552     356788899999999987777764333    359999999888 789999999877 35


Q ss_pred             ceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcC-CCC-----------CCCC--ccEEEEeccccccccCC
Q psy4275         103 LRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTC-NTF-----------SLNR--IKFLVLDEADRLSLMTS  166 (182)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~-~~~-----------~~~~--~~~iI~DE~h~~~~~~~  166 (182)
                      .++-.++|......-  .-..+++++++|...+.+.+++. ..+           .+.+  +-=||+||||.+-+...
T Consensus       258 lkv~~YhG~~R~~ni--kel~~YDvVLTty~vvEs~yRk~~~GfrrKngv~ke~SlLHsi~~~RiIlDEAH~IK~R~s  333 (791)
T KOG1002|consen  258 LKVYIYHGAKRDKNI--KELMNYDVVLTTYAVVESVYRKQDYGFRRKNGVDKEKSLLHSIKFYRIILDEAHNIKDRQS  333 (791)
T ss_pred             eEEEEEecccccCCH--HHhhcCcEEEEecHHHHHHHHhccccccccCCcccccchhhhceeeeeehhhhcccccccc
Confidence            788888886643222  11347899999999998777652 111           1222  22499999999987654

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

Probab=98.84  E-value=3.6e-08  Score=85.09  Aligned_cols=119  Identities=13%  Similarity=0.159  Sum_probs=72.0

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHH-----Hh----hccCCceEEEEEcCC--
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFL-----VL----GKVMNLRVSIITGGM--  112 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~-----~~----~~~~~~~~~~~~~~~--  112 (182)
                      .++.+.++||+|||.+++..+++.....+ ..++||+||+.+..+.+.+.+.     ..    .....+....+.++.  
T Consensus        60 ~n~~~~M~TGtGKT~~~~~~i~~l~~~~~-~~~fii~vp~~aI~egv~~~l~s~~~k~hF~~~y~~~~~~~~~~~S~k~~  138 (986)
T PRK15483         60 ANIDIKMETGTGKTYVYTRLMYELHQKYG-LFKFIIVVPTPAIKEGTRNFIQSDYAKQHFSQFYENTRIELYVINAGDKK  138 (986)
T ss_pred             ceEEEEeCCCCCHHHHHHHHHHHHHHHcC-CcEEEEEeCCHHHHHHHHHHhhHHHHHHHHHHHcCCceeEEEEEecCccc
Confidence            48899999999999998887776544433 4589999999999877665544     22    222234445555432  


Q ss_pred             -----c-hhhhhHHhc------CCCcEEEEChHHHHHHHh--c--------CCCCCCCCc----cEEEEeccccccc
Q psy4275         113 -----D-MVDQGKELA------KKPHIVIATPGRLADHLD--T--------CNTFSLNRI----KFLVLDEADRLSL  163 (182)
Q Consensus       113 -----~-~~~~~~~~~------~~~~Ilv~T~~~l~~~~~--~--------~~~~~~~~~----~~iI~DE~h~~~~  163 (182)
                           + .........      +..+|+|+|.+.+..-..  .        .....+..+    -.+|+||.|++..
T Consensus       139 k~gr~~~~~~i~~Fa~~~~~~~~~I~Ilv~niqa~n~~~~~~~~~D~~l~~g~~~p~~~i~~~~PivIiDEPh~~~~  215 (986)
T PRK15483        139 KSGRKNFPAQLSNFVKASRQNSNTIHVLLINAGMLNSASMTRDDYDQTLLGGFTSPVDALAATRPVVIIDEPHRFPR  215 (986)
T ss_pred             ccccccChHHHHHHHhccccCCCceEEEEEehHHhcccccccchhhhhhccCCCChHHHHHhCCCEEEEECCCCCCc
Confidence                 1 111111111      146899999998865211  0        010111111    2699999999965

>KOG0392|consensus

Probab=98.82  E-value=1.7e-08  Score=87.55  Aligned_cols=133  Identities=16%  Similarity=0.170  Sum_probs=96.2

Q ss_pred             CChHHHHhhhhhhhC----CCcEEEECCCCChHHHHHHHHHHHhhccCC-----CC-eeEEEEcCCHHHHHHHHHHHHHh
Q psy4275          28 TPTEIQKAIIPHVLN----DEDCIGCAKTGSGKTLAFALPILQKWCEDP-----YG-IFALVLTPTRELAYQIGDQFLVL   97 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~----~~~~li~~~tg~GKT~~~~~~~~~~~~~~~-----~~-~~~lil~p~~~l~~q~~~~~~~~   97 (182)
                      .++.||.+.+.++.-    +-|.|+|..+|.|||+..+..+....+.+.     .. .-.+||||+ .|+.-|..+++++
T Consensus       975 ~LRkYQqEGVnWLaFLnky~LHGILcDDMGLGKTLQticilAsd~y~r~s~~~e~~~~PSLIVCPs-TLtGHW~~E~~kf 1053 (1549)
T KOG0392|consen  975 KLRKYQQEGVNWLAFLNKYKLHGILCDDMGLGKTLQTICILASDHYKRRSESSEFNRLPSLIVCPS-TLTGHWKSEVKKF 1053 (1549)
T ss_pred             HHHHHHHhccHHHHHHHHhcccceeeccccccHHHHHHHHHHHHHHhhcccchhhccCCeEEECCc-hhhhHHHHHHHHh
Confidence            479999999877643    569999999999999887766655544431     11 227999996 5667788888888


Q ss_pred             hccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCC
Q psy4275          98 GKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTS  166 (182)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~  166 (182)
                      +..  .+|..+.|........+.-.++++|+|++.+.+.+=+...   .-.++.++|+||.|-+-+...
T Consensus      1054 ~pf--L~v~~yvg~p~~r~~lR~q~~~~~iiVtSYDv~RnD~d~l---~~~~wNYcVLDEGHVikN~kt 1117 (1549)
T KOG0392|consen 1054 FPF--LKVLQYVGPPAERRELRDQYKNANIIVTSYDVVRNDVDYL---IKIDWNYCVLDEGHVIKNSKT 1117 (1549)
T ss_pred             cch--hhhhhhcCChHHHHHHHhhccccceEEeeHHHHHHHHHHH---HhcccceEEecCcceecchHH
Confidence            876  7888888877666666666678899999999885322211   122366999999997665443

>KOG0925|consensus

Probab=98.77  E-value=2.9e-08  Score=79.05  Aligned_cols=162  Identities=17%  Similarity=0.126  Sum_probs=105.6

Q ss_pred             ccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275           4 PIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus         4 ~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      .+..|...+.+....+.+++..-...+.++.+..+.+.+++-++++|.||+|||+...-++++......  ..+...-|.
T Consensus        23 ~~Npf~~~p~s~rY~~ilk~R~~LPvw~~k~~F~~~l~~nQ~~v~vGetgsGKttQiPq~~~~~~~~~~--~~v~CTQpr  100 (699)
T KOG0925|consen   23 AINPFNGKPYSQRYYDILKKRRELPVWEQKEEFLKLLLNNQIIVLVGETGSGKTTQIPQFVLEYELSHL--TGVACTQPR  100 (699)
T ss_pred             hcCCCCCCcCcHHHHHHHHHHhcCchHHhHHHHHHHHhcCceEEEEecCCCCccccCcHHHHHHHHhhc--cceeecCch
Confidence            467889999999999999887666788888888888888999999999999999987777777766654  357777899


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275          84 RELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus        84 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      +.-+.+++....+-+   +++.+--.| .+...+ ....++.-+-.+|.++++.-.....  .+.+.+.||+||||+   
T Consensus       101 rvaamsva~RVadEM---Dv~lG~EVG-ysIrfE-dC~~~~T~Lky~tDgmLlrEams~p--~l~~y~viiLDeahE---  170 (699)
T KOG0925|consen  101 RVAAMSVAQRVADEM---DVTLGEEVG-YSIRFE-DCTSPNTLLKYCTDGMLLREAMSDP--LLGRYGVIILDEAHE---  170 (699)
T ss_pred             HHHHHHHHHHHHHHh---ccccchhcc-cccccc-ccCChhHHHHHhcchHHHHHHhhCc--ccccccEEEechhhh---
Confidence            988888876554422   222221111 111100 0000011122345555544333322  577889999999997   


Q ss_pred             cCChhHHHHHHHHhh
Q psy4275         164 MTSLKFFFFFFFLKY  178 (182)
Q Consensus       164 ~~~~~~~~~~~~~~~  178 (182)
                       .......++..+++
T Consensus       171 -RtlATDiLmGllk~  184 (699)
T KOG0925|consen  171 -RTLATDILMGLLKE  184 (699)
T ss_pred             -hhHHHHHHHHHHHH
Confidence             44444455555444

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

Probab=98.76  E-value=1.8e-08  Score=72.97  Aligned_cols=63  Identities=21%  Similarity=0.269  Sum_probs=45.2

Q ss_pred             CChHHHHhhhhhhhC-C-CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHH
Q psy4275          28 TPTEIQKAIIPHVLN-D-EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQ   93 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~-~-~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~   93 (182)
                      ++++.|.+++..+.. + +-.+++|+.|+|||+.. ..+...+...  +.++++++||...+..+.+.
T Consensus         1 ~L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l-~~~~~~~~~~--g~~v~~~apT~~Aa~~L~~~   65 (196)
T PF13604_consen    1 TLNEEQREAVRAILTSGDRVSVLQGPAGTGKTTLL-KALAEALEAA--GKRVIGLAPTNKAAKELREK   65 (196)
T ss_dssp             -S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHHH-HHHHHHHHHT--T--EEEEESSHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHHH-HHHHHHHHhC--CCeEEEECCcHHHHHHHHHh
Confidence            478999999999864 3 46788899999999873 4444444444  57899999999988876555

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=98.74  E-value=2e-08  Score=86.38  Aligned_cols=128  Identities=22%  Similarity=0.169  Sum_probs=95.3

Q ss_pred             ChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEE
Q psy4275          29 PTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSII  108 (182)
Q Consensus        29 ~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~  108 (182)
                      +.+.|-..--.+.  ..-+..+.||-|||+++.+++.-..+.   |.-|-+|+....||..=++|...+...+|++|++.
T Consensus       139 ~ydVQLiGgivLh--~G~IAEM~TGEGKTLvatlp~yLnAL~---G~gVHvVTvNDYLA~RDaewm~p~y~flGLtVg~i  213 (1025)
T PRK12900        139 PYDVQLIGGIVLH--SGKISEMATGEGKTLVSTLPTFLNALT---GRGVHVVTVNDYLAQRDKEWMNPVFEFHGLSVGVI  213 (1025)
T ss_pred             ccchHHhhhHHhh--cCCccccCCCCCcchHhHHHHHHHHHc---CCCcEEEeechHhhhhhHHHHHHHHHHhCCeeeee
Confidence            4444544443343  445889999999999998888776666   44688999999999999999999999999999988


Q ss_pred             EcCCchhhhhHHhcCCCcEEEEChHHH-HHHHhcCCC-----CCCCCccEEEEeccccccc
Q psy4275         109 TGGMDMVDQGKELAKKPHIVIATPGRL-ADHLDTCNT-----FSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~Ilv~T~~~l-~~~~~~~~~-----~~~~~~~~iI~DE~h~~~~  163 (182)
                      ..+.....+..  .-.|+|..||..-| .++++..-.     .-.+.+.+.|+||+|.++=
T Consensus       214 ~~~~~~~~Rr~--aY~~DItYgTn~EfGFDYLRDnma~~~~~~vqR~~~faIVDEvDSvLI  272 (1025)
T PRK12900        214 LNTMRPEERRE--QYLCDITYGTNNEFGFDYLRDNMAGTPEEMVQRDFYFAIVDEVDSVLI  272 (1025)
T ss_pred             CCCCCHHHHHH--hCCCcceecCCCccccccchhccccchhhhhccCCceEEEechhhhhh
Confidence            76655444433  34789999998776 466655211     1345678999999999874

>KOG0923|consensus

Probab=98.74  E-value=7.4e-08  Score=79.26  Aligned_cols=141  Identities=18%  Similarity=0.159  Sum_probs=95.5

Q ss_pred             CCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHH-HHhhccCCce
Q psy4275          26 VKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQF-LVLGKVMNLR  104 (182)
Q Consensus        26 ~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~-~~~~~~~~~~  104 (182)
                      .....++-.+.+.++....-.++.|.||||||+...-++.+.=+..+ +.++-+.-|.+..|..++..+ +.+...+|-.
T Consensus       263 sLPVy~ykdell~av~e~QVLiI~GeTGSGKTTQiPQyL~EaGytk~-gk~IgcTQPRRVAAmSVAaRVA~EMgvkLG~e  341 (902)
T KOG0923|consen  263 SLPVYPYKDELLKAVKEHQVLIIVGETGSGKTTQIPQYLYEAGYTKG-GKKIGCTQPRRVAAMSVAARVAEEMGVKLGHE  341 (902)
T ss_pred             cCCchhhHHHHHHHHHhCcEEEEEcCCCCCccccccHHHHhcccccC-CceEeecCcchHHHHHHHHHHHHHhCcccccc
Confidence            34567777888888888999999999999999987766666555543 445888889999999885444 3444443333


Q ss_pred             EEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHHHHHHHHhhc
Q psy4275         105 VSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFFFFLKYY  179 (182)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~~~~~~~~~~  179 (182)
                      |++     +...+. .-.++.-+-++|.++++.-+..  ..++.+.++||+||||.    .......+|..+++.
T Consensus       342 VGY-----sIRFEd-cTSekTvlKYMTDGmLlREfL~--epdLasYSViiiDEAHE----RTL~TDILfgLvKDI  404 (902)
T KOG0923|consen  342 VGY-----SIRFED-CTSEKTVLKYMTDGMLLREFLS--EPDLASYSVIIVDEAHE----RTLHTDILFGLVKDI  404 (902)
T ss_pred             cce-----EEEecc-ccCcceeeeeecchhHHHHHhc--cccccceeEEEeehhhh----hhhhhhHHHHHHHHH
Confidence            321     111110 1123456788999999875543  23688899999999997    455555566655554

>KOG0386|consensus

Probab=98.73  E-value=9.3e-09  Score=87.50  Aligned_cols=134  Identities=15%  Similarity=0.102  Sum_probs=91.0

Q ss_pred             CCChHHHHhhhhhhhC----CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCC
Q psy4275          27 KTPTEIQKAIIPHVLN----DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMN  102 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~----~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~  102 (182)
                      .++.+||...+.++.+    +-|.++...+|.|||+..+..+.+.+-.....+-.+|+||+..|.+ |..++..|...  
T Consensus       393 G~Lk~YQl~GLqWmVSLyNNnLNGILADEMGLGKTIQtIsLitYLmE~K~~~GP~LvivPlstL~N-W~~Ef~kWaPS--  469 (1157)
T KOG0386|consen  393 GELKEYQLHGLQWMVSLYNNNLNGILADEMGLGKTIQTISLITYLMEHKQMQGPFLIIVPLSTLVN-WSSEFPKWAPS--  469 (1157)
T ss_pred             CCCchhhhhhhHHHhhccCCCcccccchhcccchHHHHHHHHHHHHHHcccCCCeEEeccccccCC-chhhccccccc--
Confidence            4799999999988765    4488999999999998866555555444443445789999988855 66677777553  


Q ss_pred             ceEEEEEcCCchh--hhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCC
Q psy4275         103 LRVSIITGGMDMV--DQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTS  166 (182)
Q Consensus       103 ~~~~~~~~~~~~~--~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~  166 (182)
                      +..+.+.|.....  ........+.+|+++|.+.+.+   ....+.--++.++|+||.|+|-+...
T Consensus       470 v~~i~YkGtp~~R~~l~~qir~gKFnVLlTtyEyiik---dk~lLsKI~W~yMIIDEGHRmKNa~~  532 (1157)
T KOG0386|consen  470 VQKIQYKGTPQQRSGLTKQQRHGKFNVLLTTYEYIIK---DKALLSKISWKYMIIDEGHRMKNAIC  532 (1157)
T ss_pred             eeeeeeeCCHHHHhhHHHHHhcccceeeeeeHHHhcC---CHHHHhccCCcceeecccccccchhh
Confidence            5556666654321  1112223678999999877644   11112222356899999999987543

>KOG0926|consensus

Probab=98.71  E-value=1.6e-07  Score=78.88  Aligned_cols=120  Identities=21%  Similarity=0.238  Sum_probs=84.3

Q ss_pred             HhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCC---CCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEc
Q psy4275          34 KAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP---YGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITG  110 (182)
Q Consensus        34 ~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~---~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~  110 (182)
                      .+..+++..+.-+++||.||+|||+...-.+.+.=+.++   .++.+-|.-|.+..+..+++....-...++-.|++...
T Consensus       262 q~IMEaIn~n~vvIIcGeTGsGKTTQvPQFLYEAGf~s~~~~~~gmIGITqPRRVAaiamAkRVa~EL~~~~~eVsYqIR  341 (1172)
T KOG0926|consen  262 QRIMEAINENPVVIICGETGSGKTTQVPQFLYEAGFASEQSSSPGMIGITQPRRVAAIAMAKRVAFELGVLGSEVSYQIR  341 (1172)
T ss_pred             HHHHHHhhcCCeEEEecCCCCCccccchHHHHHcccCCccCCCCCeeeecCchHHHHHHHHHHHHHHhccCccceeEEEE
Confidence            445566666778999999999999986666665544432   34577888899998888876666544445555543321


Q ss_pred             CCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccc
Q psy4275         111 GMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL  161 (182)
Q Consensus       111 ~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~  161 (182)
                      -      ...+.....|.++|.+.++.-+..  .+.++..+.||+||||.=
T Consensus       342 f------d~ti~e~T~IkFMTDGVLLrEi~~--DflL~kYSvIIlDEAHER  384 (1172)
T KOG0926|consen  342 F------DGTIGEDTSIKFMTDGVLLREIEN--DFLLTKYSVIILDEAHER  384 (1172)
T ss_pred             e------ccccCCCceeEEecchHHHHHHHH--hHhhhhceeEEechhhhc
Confidence            0      012234678999999999987765  356888999999999973

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=98.68  E-value=4e-08  Score=71.19  Aligned_cols=59  Identities=25%  Similarity=0.218  Sum_probs=41.7

Q ss_pred             CCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHH
Q psy4275          26 VKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRE   85 (182)
Q Consensus        26 ~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~   85 (182)
                      +...++.|...+..+.+.+.+++.||+|+|||+.++..+++.+.+. .-.+++|+-|...
T Consensus         2 I~p~~~~Q~~~~~al~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g-~~~kiii~Rp~v~   60 (205)
T PF02562_consen    2 IKPKNEEQKFALDALLNNDLVIVNGPAGTGKTFLALAAALELVKEG-EYDKIIITRPPVE   60 (205)
T ss_dssp             ----SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTT-S-SEEEEEE-S--
T ss_pred             ccCCCHHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHHHHhC-CCcEEEEEecCCC
Confidence            3467889999999999888899999999999999999998887763 3447888878764

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

>TIGR00376 DNA helicase, putative

Probab=98.67  E-value=4.4e-07  Score=76.58  Aligned_cols=67  Identities=21%  Similarity=0.219  Sum_probs=53.5

Q ss_pred             CCChHHHHhhhhhhhCC-CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHH
Q psy4275          27 KTPTEIQKAIIPHVLND-EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLV   96 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~~-~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~   96 (182)
                      ..+++.|.+++...... ...++.||+|+|||.+..-.+...+..   +.++++++||...++++.+.+..
T Consensus       156 ~~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~~~ii~~~~~~---g~~VLv~a~sn~Avd~l~e~l~~  223 (637)
T TIGR00376       156 PNLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTLVELIRQLVKR---GLRVLVTAPSNIAVDNLLERLAL  223 (637)
T ss_pred             CCCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHHHHHHHHHHHc---CCCEEEEcCcHHHHHHHHHHHHh
Confidence            46799999999888765 788999999999998755444444333   45899999999999998877765

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.

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=98.61  E-value=7.6e-08  Score=83.04  Aligned_cols=130  Identities=22%  Similarity=0.189  Sum_probs=94.0

Q ss_pred             ChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEE
Q psy4275          29 PTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSII  108 (182)
Q Consensus        29 ~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~  108 (182)
                      ++++=.+.+-.+.=...-+..+.||-|||+++.+++.-..+.   |.-|-+|+....||..=+++...+...+|++|++.
T Consensus       168 m~~yDVQliGgivLh~G~IAEM~TGEGKTLvAtlp~yLnAL~---GkgVHvVTVNDYLA~RDaewmgply~fLGLsvg~i  244 (1112)
T PRK12901        168 MVHYDVQLIGGVVLHQGKIAEMATGEGKTLVATLPVYLNALT---GNGVHVVTVNDYLAKRDSEWMGPLYEFHGLSVDCI  244 (1112)
T ss_pred             CcccchHHhhhhhhcCCceeeecCCCCchhHHHHHHHHHHHc---CCCcEEEEechhhhhccHHHHHHHHHHhCCceeec
Confidence            344444444333333456899999999999998888777666   44688899999999999999999999999999988


Q ss_pred             Ec-CCchhhhhHHhcCCCcEEEEChHHH-HHHHhcCC-----CCCCCCccEEEEeccccccc
Q psy4275         109 TG-GMDMVDQGKELAKKPHIVIATPGRL-ADHLDTCN-----TFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus       109 ~~-~~~~~~~~~~~~~~~~Ilv~T~~~l-~~~~~~~~-----~~~~~~~~~iI~DE~h~~~~  163 (182)
                      .. ......+  .-.-.|+|..+|..-| .++++..-     ..-.+.+.+.|+||+|.++=
T Consensus       245 ~~~~~~~~~r--r~aY~~DItYgTn~EfGFDYLRDnm~~~~~~~vqR~~~fAIVDEvDSILI  304 (1112)
T PRK12901        245 DKHQPNSEAR--RKAYNADITYGTNNEFGFDYLRDNMAHSPEDLVQRKHNYAIVDEVDSVLI  304 (1112)
T ss_pred             CCCCCCHHHH--HHhCCCcceecCCCccccccchhccccchHhhhCcCCceeEeechhhhhh
Confidence            65 3333332  2234789999998776 45665421     11345678999999998874

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

Probab=98.58  E-value=3.2e-07  Score=72.33  Aligned_cols=96  Identities=18%  Similarity=0.160  Sum_probs=60.9

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCC
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKK  124 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  124 (182)
                      -+++.|.+|+|||+.++..+... .....+.+++++++...+...+.+.+.....                      ...
T Consensus         3 v~~I~G~aGTGKTvla~~l~~~l-~~~~~~~~~~~l~~n~~l~~~l~~~l~~~~~----------------------~~~   59 (352)
T PF09848_consen    3 VILITGGAGTGKTVLALNLAKEL-QNSEEGKKVLYLCGNHPLRNKLREQLAKKYN----------------------PKL   59 (352)
T ss_pred             EEEEEecCCcCHHHHHHHHHHHh-hccccCCceEEEEecchHHHHHHHHHhhhcc----------------------cch
Confidence            47889999999999966555554 2222356899999999998877777655420                      001


Q ss_pred             CcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccccc
Q psy4275         125 PHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus       125 ~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~  164 (182)
                      ....+..+..+...... ........++||+||||.+...
T Consensus        60 ~~~~~~~~~~~i~~~~~-~~~~~~~~DviivDEAqrl~~~   98 (352)
T PF09848_consen   60 KKSDFRKPTSFINNYSE-SDKEKNKYDVIIVDEAQRLRTK   98 (352)
T ss_pred             hhhhhhhhHHHHhhccc-ccccCCcCCEEEEehhHhhhhc
Confidence            11222333333332221 2224567889999999999984

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>KOG0924|consensus

Probab=98.53  E-value=1.2e-06  Score=72.62  Aligned_cols=137  Identities=19%  Similarity=0.200  Sum_probs=87.1

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHH-hhccCCceEE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLV-LGKVMNLRVS  106 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~-~~~~~~~~~~  106 (182)
                      .....+.+.+..+..++-+++.+.||+|||+...-+++..=+..  ++.+-+.-|.+..|..+++.++. +...+|-.|+
T Consensus       356 Pvf~~R~~ll~~ir~n~vvvivgETGSGKTTQl~QyL~edGY~~--~GmIGcTQPRRvAAiSVAkrVa~EM~~~lG~~VG  433 (1042)
T KOG0924|consen  356 PVFACRDQLLSVIRENQVVVIVGETGSGKTTQLAQYLYEDGYAD--NGMIGCTQPRRVAAISVAKRVAEEMGVTLGDTVG  433 (1042)
T ss_pred             chHHHHHHHHHHHhhCcEEEEEecCCCCchhhhHHHHHhccccc--CCeeeecCchHHHHHHHHHHHHHHhCCccccccc
Confidence            34455666677777788899999999999998665555543333  44677777999999998776654 4344444443


Q ss_pred             EEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHHHHHHHHhh
Q psy4275         107 IITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFFFFLKY  178 (182)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~~~~~~~~~  178 (182)
                      +-..     ... .-.....|-..|.+.++.-.-..+  .+.+.+.||+||||+    .......+|..++.
T Consensus       434 YsIR-----FEd-vT~~~T~IkymTDGiLLrEsL~d~--~L~kYSviImDEAHE----RslNtDilfGllk~  493 (1042)
T KOG0924|consen  434 YSIR-----FED-VTSEDTKIKYMTDGILLRESLKDR--DLDKYSVIIMDEAHE----RSLNTDILFGLLKK  493 (1042)
T ss_pred             eEEE-----eee-cCCCceeEEEeccchHHHHHhhhh--hhhheeEEEechhhh----cccchHHHHHHHHH
Confidence            2211     000 111345688899999875332212  577899999999997    33344444444443

>KOG1803|consensus

Probab=98.49  E-value=4.4e-07  Score=74.09  Aligned_cols=64  Identities=25%  Similarity=0.206  Sum_probs=51.4

Q ss_pred             CCChHHHHhhhhhhhCC-CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHH
Q psy4275          27 KTPTEIQKAIIPHVLND-EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQ   93 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~~-~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~   93 (182)
                      .++++.|++++....+. .-.+++||+|+|||.+....+...+.+   +.++++.+||...++.+.+.
T Consensus       184 ~~ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvEiI~qlvk~---~k~VLVcaPSn~AVdNiver  248 (649)
T KOG1803|consen  184 KNLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVKQ---KKRVLVCAPSNVAVDNIVER  248 (649)
T ss_pred             ccccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHHHHHHHHHc---CCeEEEEcCchHHHHHHHHH
Confidence            46889999999887775 578889999999998855555555444   56999999999998888764

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=98.45  E-value=1.1e-06  Score=73.34  Aligned_cols=68  Identities=19%  Similarity=0.185  Sum_probs=49.9

Q ss_pred             hHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHH--hhccCCCCeeEEEEcCCHHHHHHHHHHHHHh
Q psy4275          30 TEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ--KWCEDPYGIFALVLTPTRELAYQIGDQFLVL   97 (182)
Q Consensus        30 ~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~--~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~   97 (182)
                      .++|+.++.....++..++.|++|+|||++....+..  .........++.+.+||.--+..+.+.....
T Consensus       147 ~~~Qk~A~~~al~~~~~vitGgpGTGKTt~v~~ll~~l~~~~~~~~~~~I~l~APTGkAA~rL~e~~~~~  216 (586)
T TIGR01447       147 QNWQKVAVALALKSNFSLITGGPGTGKTTTVARLLLALVKQSPKQGKLRIALAAPTGKAAARLAESLRKA  216 (586)
T ss_pred             cHHHHHHHHHHhhCCeEEEEcCCCCCHHHHHHHHHHHHHHhccccCCCcEEEECCcHHHHHHHHHHHHhh
Confidence            4899999999999999999999999999874333222  1111111357999999998888877766553

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.

>PF13245 AAA_19: Part of AAA domain

Probab=98.44  E-value=1.6e-06  Score=52.94  Aligned_cols=51  Identities=31%  Similarity=0.429  Sum_probs=39.2

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhcc--CCCCeeEEEEcCCHHHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCE--DPYGIFALVLTPTRELAYQIGDQF   94 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~--~~~~~~~lil~p~~~l~~q~~~~~   94 (182)
                      ++-+++.+|+|+|||....-.+.+.+..  .. +.++++++|++..++++.+.+
T Consensus        10 ~~~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~-~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen   10 SPLFVVQGPPGTGKTTTLAARIAELLAARADP-GKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHHhcCC-CCeEEEECCCHHHHHHHHHHH
Confidence            4456669999999998766666666532  23 568999999999999887776

>PRK10536 hypothetical protein; Provisional

Probab=98.43  E-value=3.7e-06  Score=62.88  Aligned_cols=60  Identities=15%  Similarity=0.113  Sum_probs=45.8

Q ss_pred             CCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHH
Q psy4275          25 GVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRE   85 (182)
Q Consensus        25 ~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~   85 (182)
                      ++...+..|...+..+.++..+++.||+|+|||+.+....++.+.+.. -.++++.-|...
T Consensus        56 ~i~p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~a~a~~~l~~~~-~~kIiI~RP~v~  115 (262)
T PRK10536         56 PILARNEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKAAEALIHKD-VDRIIVTRPVLQ  115 (262)
T ss_pred             cccCCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHhcCC-eeEEEEeCCCCC
Confidence            456788899999998888888999999999999998888877665532 335555555543

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

Probab=98.39  E-value=1.8e-06  Score=75.23  Aligned_cols=145  Identities=20%  Similarity=0.069  Sum_probs=97.7

Q ss_pred             CCChHHHHhhhhhhhC-----CCcEEEECCCCChHHHHHHHHHHHhhccCCC-CeeEEEEcCCHHHHHHHHHHHHHhhcc
Q psy4275          27 KTPTEIQKAIIPHVLN-----DEDCIGCAKTGSGKTLAFALPILQKWCEDPY-GIFALVLTPTRELAYQIGDQFLVLGKV  100 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~-----~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~-~~~~lil~p~~~l~~q~~~~~~~~~~~  100 (182)
                      ..++++|.+.+.++..     +.+.++...+|.|||...+..+......... .+.+++++|...+ .+|.+++.++...
T Consensus       337 ~~lr~yq~~g~~wl~~~l~~~~~~~ilaD~mglGKTiq~i~~l~~~~~~~~~~~~~~liv~p~s~~-~nw~~e~~k~~~~  415 (866)
T COG0553         337 AELRPYQLEGVNWLSELLRSNLLGGILADDMGLGKTVQTIALLLSLLESIKVYLGPALIVVPASLL-SNWKREFEKFAPD  415 (866)
T ss_pred             hhhHHHHHHHHHHHHHHHHhccCCCcccccccchhHHHHHHHHHhhhhcccCCCCCeEEEecHHHH-HHHHHHHhhhCcc
Confidence            4689999999877551     6678888999999998877666653333332 3578999996554 6677777777665


Q ss_pred             CCceEEEEEcCCch----hhhhHHhcCC-----CcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHHH
Q psy4275         101 MNLRVSIITGGMDM----VDQGKELAKK-----PHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFF  171 (182)
Q Consensus       101 ~~~~~~~~~~~~~~----~~~~~~~~~~-----~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~~  171 (182)
                      ... +...+|....    ......+...     .+++++|.+.+.........+.-..+..+|+||+|.+.+........
T Consensus       416 ~~~-~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~v~itty~~l~~~~~~~~~l~~~~~~~~v~DEa~~ikn~~s~~~~~  494 (866)
T COG0553         416 LRL-VLVYHGEKSELDKKREALRDLLKLHLVIIFDVVITTYELLRRFLVDHGGLKKIEWDRVVLDEAHRIKNDQSSEGKA  494 (866)
T ss_pred             ccc-eeeeeCCcccccHHHHHHHHHhhhcccceeeEEechHHHHHHhhhhHHHHhhceeeeeehhhHHHHhhhhhHHHHH
Confidence            432 6667776641    2222222222     78999999988774222222334457799999999988877666555


Q ss_pred             HH
Q psy4275         172 FF  173 (182)
Q Consensus       172 ~~  173 (182)
                      ..
T Consensus       495 l~  496 (866)
T COG0553         495 LQ  496 (866)
T ss_pred             HH
Confidence            44

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=98.38  E-value=7.6e-06  Score=68.70  Aligned_cols=71  Identities=15%  Similarity=0.045  Sum_probs=51.6

Q ss_pred             ChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccC-CCCeeEEEEcCCHHHHHHHHHHHHHhhc
Q psy4275          29 PTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCED-PYGIFALVLTPTRELAYQIGDQFLVLGK   99 (182)
Q Consensus        29 ~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~-~~~~~~lil~p~~~l~~q~~~~~~~~~~   99 (182)
                      ..++|+.++.....++-.++.|++|+|||++....+....... ....++.+.+||.--+..+.+.+.....
T Consensus       153 ~~d~Qk~Av~~a~~~~~~vItGgpGTGKTt~v~~ll~~l~~~~~~~~~~i~l~APTgkAA~rL~e~~~~~~~  224 (615)
T PRK10875        153 EVDWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLAAPTGKAAARLTESLGKALR  224 (615)
T ss_pred             CCHHHHHHHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCCcEEEEECCcHHHHHHHHHHHHhhhh
Confidence            3589999999888889999999999999987433322221111 1235788999999998888777665433

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=98.38  E-value=3.8e-06  Score=71.97  Aligned_cols=64  Identities=23%  Similarity=0.152  Sum_probs=48.5

Q ss_pred             CCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHH
Q psy4275          27 KTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIG   91 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~   91 (182)
                      ..+++.|++++..+..++..++.|++|+|||.+. ..++..+...+....+++++||...+..+.
T Consensus       322 ~~l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~l-~~i~~~~~~~~~~~~v~l~ApTg~AA~~L~  385 (720)
T TIGR01448       322 KGLSEEQKQALDTAIQHKVVILTGGPGTGKTTIT-RAIIELAEELGGLLPVGLAAPTGRAAKRLG  385 (720)
T ss_pred             CCCCHHHHHHHHHHHhCCeEEEECCCCCCHHHHH-HHHHHHHHHcCCCceEEEEeCchHHHHHHH
Confidence            4799999999999988889999999999999874 344444333321246888999988776544

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.

>PF00580 UvrD-helicase: UvrD/REP helicase N-terminal domain; InterPro: IPR000212 Members of this family are helicases that catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA

Probab=98.30  E-value=2.9e-06  Score=65.32  Aligned_cols=70  Identities=27%  Similarity=0.160  Sum_probs=53.8

Q ss_pred             ChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccC-CCCeeEEEEcCCHHHHHHHHHHHHHhhcc
Q psy4275          29 PTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCED-PYGIFALVLTPTRELAYQIGDQFLVLGKV  100 (182)
Q Consensus        29 ~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~-~~~~~~lil~p~~~l~~q~~~~~~~~~~~  100 (182)
                      +++.|.+++..  ..++.++.|++|||||.+.+.-+.+.+... -...+++++++|+..+.++.+.+......
T Consensus         1 l~~eQ~~~i~~--~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~~~~~~Il~lTft~~aa~e~~~ri~~~l~~   71 (315)
T PF00580_consen    1 LTDEQRRIIRS--TEGPLLVNAGAGSGKTTTLLERIAYLLYEGGVPPERILVLTFTNAAAQEMRERIRELLEE   71 (315)
T ss_dssp             S-HHHHHHHHS---SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHhC--CCCCEEEEeCCCCCchHHHHHHHHHhhccccCChHHheecccCHHHHHHHHHHHHHhcCc
Confidence            47889999877  567899999999999999777666666554 23458999999999999998888775443

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 ....

>KOG1805|consensus

Probab=98.30  E-value=5.2e-06  Score=71.17  Aligned_cols=127  Identities=16%  Similarity=0.152  Sum_probs=82.0

Q ss_pred             CCChHHHHhhhhhhhC-CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceE
Q psy4275          27 KTPTEIQKAIIPHVLN-DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRV  105 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~-~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~  105 (182)
                      ..++.-|++++..++. ....++.|=+|+|||.... .++..+...  +.++++.+-|...++.+-..++.+    ++..
T Consensus       668 ~~LN~dQr~A~~k~L~aedy~LI~GMPGTGKTTtI~-~LIkiL~~~--gkkVLLtsyThsAVDNILiKL~~~----~i~~  740 (1100)
T KOG1805|consen  668 LRLNNDQRQALLKALAAEDYALILGMPGTGKTTTIS-LLIKILVAL--GKKVLLTSYTHSAVDNILIKLKGF----GIYI  740 (1100)
T ss_pred             hhcCHHHHHHHHHHHhccchheeecCCCCCchhhHH-HHHHHHHHc--CCeEEEEehhhHHHHHHHHHHhcc----Ccce
Confidence            4788889998877665 5678889999999998843 344444443  668999999999988877776654    2222


Q ss_pred             EEE---------------EcCCchh--hhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccC
Q psy4275         106 SII---------------TGGMDMV--DQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus       106 ~~~---------------~~~~~~~--~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~  165 (182)
                      ..+               ...++..  .......+...|+.+|=--+.+     ..+..++++++|+|||-++...-
T Consensus       741 lRLG~~~kih~~v~e~~~~~~~s~ks~~~l~~~~~~~~IVa~TClgi~~-----plf~~R~FD~cIiDEASQI~lP~  812 (1100)
T KOG1805|consen  741 LRLGSEEKIHPDVEEFTLTNETSEKSYADLKKFLDQTSIVACTCLGINH-----PLFVNRQFDYCIIDEASQILLPL  812 (1100)
T ss_pred             eecCCccccchHHHHHhcccccchhhHHHHHHHhCCCcEEEEEccCCCc-----hhhhccccCEEEEccccccccch
Confidence            211               1111111  1112334577888888443333     23345668999999999887543

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=98.23  E-value=2.5e-06  Score=67.54  Aligned_cols=122  Identities=17%  Similarity=0.150  Sum_probs=71.3

Q ss_pred             ChHHHHhhhhhh------hCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHH--HHHHHHhhcc
Q psy4275          29 PTEIQKAIIPHV------LNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQI--GDQFLVLGKV  100 (182)
Q Consensus        29 ~~~~Q~~~~~~~------~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~--~~~~~~~~~~  100 (182)
                      +++.|++++..+      ..+.++++.|+.|+|||..+ -.+.+.+...  +..+++++||-..|..+  ...+..++  
T Consensus         2 Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~-~~i~~~~~~~--~~~~~~~a~tg~AA~~i~~G~T~hs~f--   76 (364)
T PF05970_consen    2 LNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFLI-KAIIDYLRSR--GKKVLVTAPTGIAAFNIPGGRTIHSFF--   76 (364)
T ss_pred             CCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChhHHH-HHHHHHhccc--cceEEEecchHHHHHhccCCcchHHhc--
Confidence            678899998887      56889999999999999884 3333333332  55788889987665544  11122211  


Q ss_pred             CCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHHHHHHHHhh
Q psy4275         101 MNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFFFFLKY  178 (182)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~~~~~~~~~  178 (182)
                       ++.+..    .          .....   .+..-..     ....++..+++|+||+-++...........+..++.
T Consensus        77 -~i~~~~----~----------~~~~~---~~~~~~~-----~~~~l~~~~~lIiDEism~~~~~l~~i~~~lr~i~~  131 (364)
T PF05970_consen   77 -GIPINN----N----------EKSQC---KISKNSR-----LRERLRKADVLIIDEISMVSADMLDAIDRRLRDIRK  131 (364)
T ss_pred             -Cccccc----c----------ccccc---cccccch-----hhhhhhhheeeecccccchhHHHHHHHHHhhhhhhc
Confidence             111100    0          00000   1111101     112466788999999998777766655555555544

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>PF12340 DUF3638: Protein of unknown function (DUF3638); InterPro: IPR022099 This domain family is found in eukaryotes, and is approximately 230 amino acids in length

Probab=98.21  E-value=4.7e-05  Score=55.97  Aligned_cols=153  Identities=18%  Similarity=0.285  Sum_probs=93.3

Q ss_pred             CccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhC---CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275           7 SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLN---DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus         7 ~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~---~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      +|.....+.++.=.+. .++ -+++-|.+....+.+   ++|.+.+.-+|.|||.+ +.|++....+++.. -+.+++| 
T Consensus         4 ~w~p~~~P~wLl~E~e-~~i-liR~~Q~~ia~~mi~~~~~~n~v~QlnMGeGKTsV-I~Pmla~~LAdg~~-LvrviVp-   78 (229)
T PF12340_consen    4 NWDPMEYPDWLLFEIE-SNI-LIRPVQVEIAREMISPPSGKNSVMQLNMGEGKTSV-IVPMLALALADGSR-LVRVIVP-   78 (229)
T ss_pred             CCCchhChHHHHHHHH-cCc-eeeHHHHHHHHHHhCCCCCCCeEeeecccCCccch-HHHHHHHHHcCCCc-EEEEEcC-
Confidence            5666666666654442 333 689999999888776   67999999999999999 56666666665422 4556666 


Q ss_pred             HHHHHHHHHHHHHh-hccCCceEEEE--EcCCchh----hhhH----HhcCCCcEEEEChHHHHHHHhc-------CCC-
Q psy4275          84 RELAYQIGDQFLVL-GKVMNLRVSII--TGGMDMV----DQGK----ELAKKPHIVIATPGRLADHLDT-------CNT-  144 (182)
Q Consensus        84 ~~l~~q~~~~~~~~-~~~~~~~~~~~--~~~~~~~----~~~~----~~~~~~~Ilv~T~~~l~~~~~~-------~~~-  144 (182)
                      ++|.+|..+.+... ..-++-++..+  .......    ....    .......|+++||+.++++.-.       .+. 
T Consensus        79 k~Ll~q~~~~L~~~lg~l~~r~i~~lpFsR~~~~~~~~~~~~~~l~~~~~~~~gill~~PEhilSf~L~~le~l~~~~~~  158 (229)
T PF12340_consen   79 KALLEQMRQMLRSRLGGLLNRRIYHLPFSRSTPLTPETLEKIRQLLEECMRSGGILLATPEHILSFKLKGLERLQDGKPE  158 (229)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCeeEEecccCCCCCCHHHHHHHHHHHHHHHHcCCEEEeChHHHHHHHHHHHHHHHhcCHH
Confidence            66888887776653 33333333222  1122111    1111    1123567999999999764211       010 


Q ss_pred             ---------CCCCCccEEEEecccccccc
Q psy4275         145 ---------FSLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus       145 ---------~~~~~~~~iI~DE~h~~~~~  164 (182)
                               ..++...-=|+||+|..+..
T Consensus       159 ~~~~l~~~q~~l~~~~rdilDEsDe~L~~  187 (229)
T PF12340_consen  159 EARELLKIQKWLDEHSRDILDESDEILSV  187 (229)
T ss_pred             HHHHHHHHHHHHHhcCCeEeECchhccCc
Confidence                     01223334699999988774

There are two conserved sequence motifs: LLE and NMG.

>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1

Probab=98.21  E-value=4e-05  Score=58.43  Aligned_cols=147  Identities=18%  Similarity=0.149  Sum_probs=89.1

Q ss_pred             CChHHHHhhhhhhh----------CCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHh
Q psy4275          28 TPTEIQKAIIPHVL----------NDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVL   97 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~----------~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~   97 (182)
                      .+...|-+++-..-          .+..+++-.+||.||--...-.+++...+.  ..+.+++..+..|-......++.+
T Consensus        37 ~LS~~QLEaV~yA~q~h~~~Lp~~~R~Gf~lGDGtGvGKGR~iAgiI~~n~l~G--r~r~vwvS~s~dL~~Da~RDl~DI  114 (303)
T PF13872_consen   37 LLSALQLEAVIYACQRHEQILPGGSRAGFFLGDGTGVGKGRQIAGIILENWLRG--RKRAVWVSVSNDLKYDAERDLRDI  114 (303)
T ss_pred             cccHHHHHHHHHHHHHHHhhcccccCcEEEeccCCCcCccchhHHHHHHHHHcC--CCceEEEECChhhhhHHHHHHHHh
Confidence            36777777663332          134677777999999877666677766654  347999999999988888888887


Q ss_pred             hccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcC---CCC--------CCCCccEEEEeccccccccCC
Q psy4275          98 GKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTC---NTF--------SLNRIKFLVLDEADRLSLMTS  166 (182)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~---~~~--------~~~~~~~iI~DE~h~~~~~~~  166 (182)
                      ... .+.+.-+..-.. ..   ...-+..|+.+|...+..--+..   +..        -...=++|||||||.+-+...
T Consensus       115 G~~-~i~v~~l~~~~~-~~---~~~~~~GvlF~TYs~L~~~~~~~~~~~sRl~ql~~W~g~dfdgvivfDEcH~akn~~~  189 (303)
T PF13872_consen  115 GAD-NIPVHPLNKFKY-GD---IIRLKEGVLFSTYSTLISESQSGGKYRSRLDQLVDWCGEDFDGVIVFDECHKAKNLSS  189 (303)
T ss_pred             CCC-cccceechhhcc-Cc---CCCCCCCccchhHHHHHhHHhccCCccchHHHHHHHHhcCCCceEEeccchhcCCCCc
Confidence            654 333332221110 00   01124469999999887654221   000        012235899999999988755


Q ss_pred             -----hhHHHHHHHHhhcCC
Q psy4275         167 -----LKFFFFFFFLKYYIP  181 (182)
Q Consensus       167 -----~~~~~~~~~~~~~~~  181 (182)
                           .+.-.....+.+-+|
T Consensus       190 ~~~~~sk~g~avl~LQ~~LP  209 (303)
T PF13872_consen  190 GSKKPSKTGIAVLELQNRLP  209 (303)
T ss_pred             cCccccHHHHHHHHHHHhCC
Confidence                 233334444444444

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=98.20  E-value=8.1e-06  Score=69.25  Aligned_cols=117  Identities=15%  Similarity=0.160  Sum_probs=69.2

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHH-------H-HHhhccCCceEEEEEcCCch
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQ-------F-LVLGKVMNLRVSIITGGMDM  114 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~-------~-~~~~~~~~~~~~~~~~~~~~  114 (182)
                      .-|+-+.+.||+|||.||+-.+.+.-..-+ -.+.||+||+.+.-+-+...       + +...+  +.+.-.+.-+...
T Consensus        74 ~lNiDI~METGTGKTy~YlrtmfeLhk~YG-~~KFIivVPs~AIkeGv~~~s~~~~ehF~k~~Ye--nt~~e~~i~~~~~  150 (985)
T COG3587          74 KLNIDILMETGTGKTYTYLRTMFELHKKYG-LFKFIIVVPSLAIKEGVFLTSKETTEHFFKSEYE--NTRLESYIYDEDI  150 (985)
T ss_pred             cceeeEEEecCCCceeeHHHHHHHHHHHhC-ceeEEEEeccHHHHhhhHHHHHHHHHHHhhhhcc--CcceeEEeechHH
Confidence            347889999999999999877776433332 45899999999985543222       2 22222  2333333222222


Q ss_pred             hhhhHHhcCCCcEEEEChHHHHHH------H-----hcCCCC-----------CCCCccEEEEecccccccc
Q psy4275         115 VDQGKELAKKPHIVIATPGRLADH------L-----DTCNTF-----------SLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus       115 ~~~~~~~~~~~~Ilv~T~~~l~~~------~-----~~~~~~-----------~~~~~~~iI~DE~h~~~~~  164 (182)
                      ........+.+.+++.|...+..-      +     ...+.+           ..+  -.+|+||-|.|..+
T Consensus       151 ~~~~~~~~~~~~vLl~~~~Afnk~~inan~iN~~s~~~~~~~~~~~spvd~la~~r--PIvIvDEPh~f~~~  220 (985)
T COG3587         151 EKFKFKSNNKPCVLLIFVSAFNKEEINANMINSESMENTNLFNGATSPVDALASMR--PIVIVDEPHRFLGD  220 (985)
T ss_pred             HHHhhccCCCceEEEEehhhhccccccccccchhhhcccCccccccCHHHHHHhcC--CEEEecChhhcccc
Confidence            223333345788898887776432      1     110100           111  16999999999884

>KOG1132|consensus

Probab=98.18  E-value=1.8e-05  Score=67.29  Aligned_cols=39  Identities=28%  Similarity=0.414  Sum_probs=31.6

Q ss_pred             CChHHHHhhhhhhhC----CCcEEEECCCCChHHHHHHHHHHH
Q psy4275          28 TPTEIQKAIIPHVLN----DEDCIGCAKTGSGKTLAFALPILQ   66 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~----~~~~li~~~tg~GKT~~~~~~~~~   66 (182)
                      .|++.|......++.    +.+.++..|||+|||++.+...+.
T Consensus        21 qpY~~Q~a~M~rvl~~L~~~q~~llESPTGTGKSLsLLCS~LA   63 (945)
T KOG1132|consen   21 QPYPTQLAFMTRVLSCLDRKQNGLLESPTGTGKSLSLLCSTLA   63 (945)
T ss_pred             CcchHHHHHHHHHHHHHHHhhhhhccCCCCCCccHHHHHHHHH
Confidence            678999887776655    678999999999999987766554

>KOG1131|consensus

Probab=98.18  E-value=2.4e-05  Score=63.34  Aligned_cols=73  Identities=12%  Similarity=0.028  Sum_probs=46.6

Q ss_pred             CCCCCChHHHHhhhhhhhC----CCcEEEECCCCChHHHHHHHHHHHhhccCCC-CeeEEEEcCCHHHHHHHHHHHHH
Q psy4275          24 IGVKTPTEIQKAIIPHVLN----DEDCIGCAKTGSGKTLAFALPILQKWCEDPY-GIFALVLTPTRELAYQIGDQFLV   96 (182)
Q Consensus        24 ~~~~~~~~~Q~~~~~~~~~----~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~-~~~~lil~p~~~l~~q~~~~~~~   96 (182)
                      +.+....|.|.+-...+.+    +.++++.+|+|+|||++.+..++......+. -.+.+|..-|..=++....+++.
T Consensus        12 FPY~~iYPEQ~~YM~elKrsLDakGh~llEMPSGTGKTvsLLSli~aYq~~~p~~~~KliYCSRTvpEieK~l~El~~   89 (755)
T KOG1131|consen   12 FPYDYIYPEQYEYMRELKRSLDAKGHCLLEMPSGTGKTVSLLSLIIAYQLHYPDEHRKLIYCSRTVPEIEKALEELKR   89 (755)
T ss_pred             cCCcccCHHHHHHHHHHHHhhccCCcEEEECCCCCCcchHHHHHHHHHHHhCCcccceEEEecCcchHHHHHHHHHHH
Confidence            4456778888776555443    7899999999999999977666655555443 33566655544333333334443

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=98.14  E-value=1.2e-05  Score=68.28  Aligned_cols=111  Identities=16%  Similarity=0.116  Sum_probs=70.1

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA  122 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  122 (182)
                      ++-.++.+|+|+|||....-++-+.+.+.  ..+++++...++|+.+++..++.-.-. |+.  .+......     .+.
T Consensus        49 ~~V~vVRSpMGTGKTtaLi~wLk~~l~~~--~~~VLvVShRrSL~~sL~~rf~~~~l~-gFv--~Y~d~~~~-----~i~  118 (824)
T PF02399_consen   49 RGVLVVRSPMGTGKTTALIRWLKDALKNP--DKSVLVVSHRRSLTKSLAERFKKAGLS-GFV--NYLDSDDY-----IID  118 (824)
T ss_pred             CCeEEEECCCCCCcHHHHHHHHHHhccCC--CCeEEEEEhHHHHHHHHHHHHhhcCCC-cce--eeeccccc-----ccc
Confidence            34567889999999998777666654322  458999999999999988877654211 111  11111111     111


Q ss_pred             -CCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCCh
Q psy4275         123 -KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSL  167 (182)
Q Consensus       123 -~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~  167 (182)
                       ...+-+++..+.+......    .+.+.+++|+||+-.....-+.
T Consensus       119 ~~~~~rLivqIdSL~R~~~~----~l~~yDvVIIDEv~svL~qL~S  160 (824)
T PF02399_consen  119 GRPYDRLIVQIDSLHRLDGS----LLDRYDVVIIDEVMSVLNQLFS  160 (824)
T ss_pred             ccccCeEEEEehhhhhcccc----cccccCEEEEehHHHHHHHHhH
Confidence             1345666666666443322    4667899999999888776443

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

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=98.13  E-value=1.3e-05  Score=68.46  Aligned_cols=131  Identities=22%  Similarity=0.217  Sum_probs=98.2

Q ss_pred             ChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEE
Q psy4275          29 PTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSII  108 (182)
Q Consensus        29 ~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~  108 (182)
                      .+|+=.+.+-.+.-....++.+-||-|||+++.+++.-..+.   +..+.+++...-|+..-+++...+....|.++++.
T Consensus        79 ~~~~dVQliG~i~lh~g~iaEM~TGEGKTL~atlp~ylnaL~---gkgVhvVTvNdYLA~RDae~m~~l~~~LGlsvG~~  155 (822)
T COG0653          79 MRHFDVQLLGGIVLHLGDIAEMRTGEGKTLVATLPAYLNALA---GKGVHVVTVNDYLARRDAEWMGPLYEFLGLSVGVI  155 (822)
T ss_pred             CChhhHHHhhhhhhcCCceeeeecCCchHHHHHHHHHHHhcC---CCCcEEeeehHHhhhhCHHHHHHHHHHcCCceeec
Confidence            444445555555555667899999999999998887766666   45789999999999999999999999999999998


Q ss_pred             EcCCchhhhhHHhcCCCcEEEEChHHH-HHHHhcCC-----CCCCCCccEEEEecccccccc
Q psy4275         109 TGGMDMVDQGKELAKKPHIVIATPGRL-ADHLDTCN-----TFSLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~Ilv~T~~~l-~~~~~~~~-----~~~~~~~~~iI~DE~h~~~~~  164 (182)
                      ..+.+..+....+  .|+|..+|..-+ .++++..-     ..-.+.+.+.|+||++.++=+
T Consensus       156 ~~~m~~~ek~~aY--~~DItY~TnnElGFDYLRDNm~~~~ee~vqr~~~faIvDEvDSILID  215 (822)
T COG0653         156 LAGMSPEEKRAAY--ACDITYGTNNELGFDYLRDNMVTSQEEKVQRGLNFAIVDEVDSILID  215 (822)
T ss_pred             cCCCChHHHHHHH--hcCceeccccccCcchhhhhhhccHHHhhhccCCeEEEcchhheeee
Confidence            8877655554443  689999998877 34444321     113446789999999988743

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=98.11  E-value=6.8e-05  Score=64.65  Aligned_cols=62  Identities=16%  Similarity=0.209  Sum_probs=46.5

Q ss_pred             CCChHHHHhhhhhhhC-CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHH
Q psy4275          27 KTPTEIQKAIIPHVLN-DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIG   91 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~-~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~   91 (182)
                      ..+++.|++++..+.. ++-+++.|++|+|||... -.+...+...  +.+++.++||.-.+..+.
T Consensus       351 ~~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtll-~~i~~~~~~~--g~~V~~~ApTg~Aa~~L~  413 (744)
T TIGR02768       351 YRLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTML-KAAREAWEAA--GYRVIGAALSGKAAEGLQ  413 (744)
T ss_pred             CCCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHHH-HHHHHHHHhC--CCeEEEEeCcHHHHHHHH
Confidence            3689999999999877 467899999999999873 3344433332  568999999977765543

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.

>KOG0989|consensus

Probab=98.04  E-value=1e-05  Score=61.44  Aligned_cols=27  Identities=19%  Similarity=0.070  Sum_probs=22.2

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      ..+.++.||+|+|||.++.+...+...
T Consensus        57 lp~~LFyGPpGTGKTStalafar~L~~   83 (346)
T KOG0989|consen   57 LPHYLFYGPPGTGKTSTALAFARALNC   83 (346)
T ss_pred             CceEEeeCCCCCcHhHHHHHHHHHhcC
Confidence            468999999999999998777666544

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=97.92  E-value=0.00015  Score=63.96  Aligned_cols=61  Identities=15%  Similarity=0.093  Sum_probs=45.7

Q ss_pred             CCChHHHHhhhhhhhCC-CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHH
Q psy4275          27 KTPTEIQKAIIPHVLND-EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQI   90 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~~-~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~   90 (182)
                      ..+++.|.+++..+..+ ..++++|+.|+|||+. +-.+...+...  +.+++.++||.-.+..+
T Consensus       345 ~~Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~-l~~~~~~~e~~--G~~V~~~ApTGkAA~~L  406 (988)
T PRK13889        345 LVLSGEQADALAHVTDGRDLGVVVGYAGTGKSAM-LGVAREAWEAA--GYEVRGAALSGIAAENL  406 (988)
T ss_pred             CCCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHH-HHHHHHHHHHc--CCeEEEecCcHHHHHHH
Confidence            37999999999998884 4678999999999987 33444433332  56899999997766544

>KOG1001|consensus

Probab=97.87  E-value=9.4e-05  Score=62.69  Aligned_cols=116  Identities=21%  Similarity=0.201  Sum_probs=78.6

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccCC------CCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhh
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCEDP------YGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQ  117 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~~------~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  117 (182)
                      ..+++....|-|||...+..++..-....      .+.-.+++||...+ .||...+.+..+.....+.+++|..    .
T Consensus       153 ~ggIladd~glgkt~~ti~l~l~~~~~~~~~~~~~~~kttLivcp~s~~-~qW~~elek~~~~~~l~v~v~~gr~----k  227 (674)
T KOG1001|consen  153 RGGILADDMGLGKTVKTIALILKQKLKSKEEDRQKEFKTTLIVCPTSLL-TQWKTELEKVTEEDKLSIYVYHGRT----K  227 (674)
T ss_pred             ccceEeeccccchHHHHHHHHHhcccCCcchhhccccCceeEecchHHH-HHHHHHHhccCCccceEEEEecccc----c
Confidence            46788889999999987766665544433      34457888886554 7787777666666567777778711    1


Q ss_pred             hHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhH
Q psy4275         118 GKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKF  169 (182)
Q Consensus       118 ~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~  169 (182)
                      .....+.++|+++|++.+..   . ..+.+..+ -+|+||+|.+.+.....+
T Consensus       228 d~~el~~~dVVltTy~il~~---~-~l~~i~w~-Riildea~~ikn~~tq~~  274 (674)
T KOG1001|consen  228 DKSELNSYDVVLTTYDILKN---S-PLVKIKWL-RIVLDEAHTIKNKDTQIF  274 (674)
T ss_pred             ccchhcCCceEEeeHHHhhc---c-cccceeEE-EEEeccccccCCcchHhh
Confidence            11224577899999998853   1 22223333 599999999988776543

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=97.85  E-value=0.00033  Score=62.32  Aligned_cols=75  Identities=16%  Similarity=0.139  Sum_probs=51.5

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHhhhhhhhC-CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHH
Q psy4275          13 LNPWLIRQCQTIGVKTPTEIQKAIIPHVLN-DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIG   91 (182)
Q Consensus        13 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~   91 (182)
                      .++...+.....+ ..+++.|.+++..+.. ++-.+++|+.|+|||+.. -.+...+...  +.+++-++|+..-+..+.
T Consensus       367 v~~~~l~a~~~~~-~~Ls~eQ~~Av~~i~~~~r~~~v~G~AGTGKTt~l-~~~~~~~e~~--G~~V~g~ApTgkAA~~L~  442 (1102)
T PRK13826        367 VREAVLAATFARH-ARLSDEQKTAIEHVAGPARIAAVVGRAGAGKTTMM-KAAREAWEAA--GYRVVGGALAGKAAEGLE  442 (1102)
T ss_pred             CCHHHHHHHHhcC-CCCCHHHHHHHHHHhccCCeEEEEeCCCCCHHHHH-HHHHHHHHHc--CCeEEEEcCcHHHHHHHH
Confidence            3444443332233 4799999999998754 677899999999999874 3444433332  568999999977765543

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=97.84  E-value=0.0002  Score=62.88  Aligned_cols=77  Identities=21%  Similarity=0.135  Sum_probs=41.6

Q ss_pred             HHHHHHCCCCCChHHHHhhhhhhhC------CCcE-EEE-CCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHH
Q psy4275          18 IRQCQTIGVKTPTEIQKAIIPHVLN------DEDC-IGC-AKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQ   89 (182)
Q Consensus        18 ~~~l~~~~~~~~~~~Q~~~~~~~~~------~~~~-li~-~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q   89 (182)
                      .+.+.+..-..-..||..++..+..      ...+ .+. +.||+|||.+=.-.+ +.+.....+.|..|..-.+.|--|
T Consensus       398 hk~~~~r~~~~rF~WQdkA~d~a~~~r~~~~~~GfF~vNMASTGcGKT~aNARIm-yaLsd~~~g~RfsiALGLRTLTLQ  476 (1110)
T TIGR02562       398 HKYFCQRSAHPRFRWQNKAFNLAQKLRQKSPEQGAFGVNMASTGCGKTLANARAM-YALRDDKQGARFAIALGLRSLTLQ  476 (1110)
T ss_pred             hhhhccCCCCCCcchHHHHHHHHHHHHhhcccCCeEEEEecCCCcchHHHHHHHH-HHhCCCCCCceEEEEccccceecc
Confidence            3444444444567899998877654      2223 333 799999998744333 333333334454444444444444


Q ss_pred             HHHHHH
Q psy4275          90 IGDQFL   95 (182)
Q Consensus        90 ~~~~~~   95 (182)
                      ..+.++
T Consensus       477 TGda~r  482 (1110)
T TIGR02562       477 TGHALK  482 (1110)
T ss_pred             chHHHH
Confidence            433333

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.

>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

Probab=97.83  E-value=0.00019  Score=48.40  Aligned_cols=21  Identities=19%  Similarity=0.165  Sum_probs=17.1

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      ++++++.||+|+|||..+...
T Consensus        19 ~~~v~i~G~~G~GKT~l~~~i   39 (151)
T cd00009          19 PKNLLLYGPPGTGKTTLARAI   39 (151)
T ss_pred             CCeEEEECCCCCCHHHHHHHH
Confidence            678999999999999764333

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.

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=97.82  E-value=3.2e-05  Score=51.95  Aligned_cols=26  Identities=23%  Similarity=0.103  Sum_probs=16.7

Q ss_pred             CCCcEEEECCCCChHHHHHHHHHHHh
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALPILQK   67 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~~~~~   67 (182)
                      +++..++.|++|+|||......+-..
T Consensus         3 ~~~~~~i~G~~G~GKT~~~~~~~~~~   28 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLIKRLARQL   28 (131)
T ss_dssp             ----EEEEE-TTSSHHHHHHHHHHHH
T ss_pred             CCcccEEEcCCCCCHHHHHHHHHHHh
Confidence            35678999999999999866555443

>PRK11054 helD DNA helicase IV; Provisional

Probab=97.81  E-value=0.00014  Score=62.03  Aligned_cols=83  Identities=13%  Similarity=0.055  Sum_probs=59.4

Q ss_pred             CCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCC-CCeeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q psy4275          25 GVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP-YGIFALVLTPTRELAYQIGDQFLVLGKVMNL  103 (182)
Q Consensus        25 ~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~-~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  103 (182)
                      .-..+++.|.+++..  ...+.++.|+.|||||.+...-+.+.+.... ...++++++.++..+..+.+.+.......++
T Consensus       193 e~~~L~~~Q~~av~~--~~~~~lV~agaGSGKT~vl~~r~ayLl~~~~~~~~~IL~ltft~~AA~em~eRL~~~lg~~~v  270 (684)
T PRK11054        193 ESSPLNPSQARAVVN--GEDSLLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRQAAEEMDERIRERLGTEDI  270 (684)
T ss_pred             cCCCCCHHHHHHHhC--CCCCeEEEEeCCCCHHHHHHHHHHHHHHhCCCCHHHeEEEeccHHHHHHHHHHHHHhcCCCCc
Confidence            335799999998853  3457899999999999997666555544332 2458999999999999998887765443344


Q ss_pred             eEEEEE
Q psy4275         104 RVSIIT  109 (182)
Q Consensus       104 ~~~~~~  109 (182)
                      .+..+|
T Consensus       271 ~v~TFH  276 (684)
T PRK11054        271 TARTFH  276 (684)
T ss_pred             EEEeHH
Confidence            444443

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=97.79  E-value=4.1e-05  Score=59.65  Aligned_cols=64  Identities=23%  Similarity=0.223  Sum_probs=50.3

Q ss_pred             CCCCCChHHHHhhhhhhhCC--CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHH
Q psy4275          24 IGVKTPTEIQKAIIPHVLND--EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELA   87 (182)
Q Consensus        24 ~~~~~~~~~Q~~~~~~~~~~--~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~   87 (182)
                      .|+...+..|..++..++..  +-+.+.|+.|+|||+.++.+.+++....+.-.++++.=|+..+.
T Consensus       224 wGi~prn~eQ~~ALdlLld~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~~y~KiiVtRp~vpvG  289 (436)
T COG1875         224 WGIRPRNAEQRVALDLLLDDDIDLVSLGGKAGTGKTLLALAAGLEQVLERKRYRKIIVTRPTVPVG  289 (436)
T ss_pred             hccCcccHHHHHHHHHhcCCCCCeEEeeccCCccHhHHHHHHHHHHHHHHhhhceEEEecCCcCcc
Confidence            47777788899999988874  34566789999999999999999887766555777777776554

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=97.77  E-value=0.00016  Score=55.13  Aligned_cols=52  Identities=17%  Similarity=0.240  Sum_probs=40.1

Q ss_pred             CCCccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccC
Q psy4275           1 MEDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCED   71 (182)
Q Consensus         1 ~~~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~   71 (182)
                      +|..+.+|+++++++.+.+.....                  ..-+++.||||||||+. +.++++.+.++
T Consensus       101 Ip~~i~~~e~LglP~i~~~~~~~~------------------~GLILVTGpTGSGKSTT-lAamId~iN~~  152 (353)
T COG2805         101 IPSKIPTLEELGLPPIVRELAESP------------------RGLILVTGPTGSGKSTT-LAAMIDYINKH  152 (353)
T ss_pred             cCccCCCHHHcCCCHHHHHHHhCC------------------CceEEEeCCCCCcHHHH-HHHHHHHHhcc
Confidence            578889999999999888855432                  12378899999999988 66777776655

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=97.75  E-value=9.6e-05  Score=63.15  Aligned_cols=69  Identities=19%  Similarity=0.092  Sum_probs=54.1

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCC-CCeeEEEEcCCHHHHHHHHHHHHHhh
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP-YGIFALVLTPTRELAYQIGDQFLVLG   98 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~-~~~~~lil~p~~~l~~q~~~~~~~~~   98 (182)
                      .+++.|.+++.+.  ..++++.|++|||||.+...-+.+.+...+ ...++++++.|+..+.++.+.+....
T Consensus         2 ~Ln~~Q~~av~~~--~g~~lV~AgpGSGKT~vL~~Ria~Li~~~~v~p~~IL~lTFT~kAA~em~~Rl~~~l   71 (672)
T PRK10919          2 RLNPGQQQAVEFV--TGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVAQTL   71 (672)
T ss_pred             CCCHHHHHHHhCC--CCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeeeEechHHHHHHHHHHHHHHh
Confidence            4789999988653  467899999999999997766666654433 23479999999999999988887654

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

Probab=97.72  E-value=0.00012  Score=59.68  Aligned_cols=71  Identities=24%  Similarity=0.211  Sum_probs=52.5

Q ss_pred             CChHHHHhhhhhhhC-----CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCC
Q psy4275          28 TPTEIQKAIIPHVLN-----DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMN  102 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~-----~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~  102 (182)
                      .|..-|-+++..+..     .++..+.|.||||||.+. ..++....     .-++|++|.+.||.|++.+++.++..-.
T Consensus        12 ~PaGDQP~AI~~Lv~gi~~g~~~QtLLGvTGSGKTfT~-AnVI~~~~-----rPtLV~AhNKTLAaQLy~Efk~fFP~Na   85 (663)
T COG0556          12 KPAGDQPEAIAELVEGIENGLKHQTLLGVTGSGKTFTM-ANVIAKVQ-----RPTLVLAHNKTLAAQLYSEFKEFFPENA   85 (663)
T ss_pred             CCCCCcHHHHHHHHHHHhcCceeeEEeeeccCCchhHH-HHHHHHhC-----CCeEEEecchhHHHHHHHHHHHhCcCcc
Confidence            455556666655544     357888999999999884 34444332     2589999999999999999999988754


Q ss_pred             ce
Q psy4275         103 LR  104 (182)
Q Consensus       103 ~~  104 (182)
                      +.
T Consensus        86 VE   87 (663)
T COG0556          86 VE   87 (663)
T ss_pred             eE
Confidence            43

>PHA02533 17 large terminase protein; Provisional

Probab=97.70  E-value=0.0004  Score=57.67  Aligned_cols=123  Identities=15%  Similarity=0.101  Sum_probs=77.6

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCc--eE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNL--RV  105 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~--~~  105 (182)
                      .++|+|++.+..+..++-.++..+=..|||..+...++......+ +..+++++|+...+..+.+.++...+..+.  +.
T Consensus        59 ~L~p~Q~~i~~~~~~~R~~ii~~aRq~GKStl~a~~al~~a~~~~-~~~v~i~A~~~~QA~~vF~~ik~~ie~~P~l~~~  137 (534)
T PHA02533         59 QMRDYQKDMLKIMHKNRFNACNLSRQLGKTTVVAIFLLHYVCFNK-DKNVGILAHKASMAAEVLDRTKQAIELLPDFLQP  137 (534)
T ss_pred             CCcHHHHHHHHHHhcCeEEEEEEcCcCChHHHHHHHHHHHHHhCC-CCEEEEEeCCHHHHHHHHHHHHHHHHhCHHHhhc
Confidence            588999999988766666788889999999987765555444333 458999999999998888887765554321  11


Q ss_pred             EEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275         106 SIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      .......    ..-.+.+++.|.+.|...        ....=.+..++++||+|.+-+
T Consensus       138 ~i~~~~~----~~I~l~NGS~I~~lss~~--------~t~rG~~~~~liiDE~a~~~~  183 (534)
T PHA02533        138 GIVEWNK----GSIELENGSKIGAYASSP--------DAVRGNSFAMIYIDECAFIPN  183 (534)
T ss_pred             ceeecCc----cEEEeCCCCEEEEEeCCC--------CccCCCCCceEEEeccccCCC
Confidence            1111111    011124566665555221        111222356899999997654

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.68  E-value=7.8e-05  Score=49.91  Aligned_cols=41  Identities=20%  Similarity=0.038  Sum_probs=26.9

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTREL   86 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l   86 (182)
                      +++.++.||+|+|||..+...+... ...  ...++++.+....
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l~~~~-~~~--~~~~~~~~~~~~~   42 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARALAREL-GPP--GGGVIYIDGEDIL   42 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHhcc-CCC--CCCEEEECCEEcc
Confidence            4678999999999999864443333 222  1246777766554

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.

>PRK04296 thymidine kinase; Provisional

Probab=97.68  E-value=0.00016  Score=52.19  Aligned_cols=36  Identities=19%  Similarity=0.136  Sum_probs=25.0

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcC
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTP   82 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p   82 (182)
                      .-.++.||+|+|||+.++-.+.....+   +.+++++-|
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~~~~~~---g~~v~i~k~   38 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAYNYEER---GMKVLVFKP   38 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHc---CCeEEEEec
Confidence            346789999999998866555544333   457777755

>KOG0953|consensus

Probab=97.61  E-value=8.3e-05  Score=60.69  Aligned_cols=98  Identities=18%  Similarity=0.161  Sum_probs=66.2

Q ss_pred             EEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCC
Q psy4275          46 CIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKP  125 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  125 (182)
                      ++-+|||.+|||..++--+..       ..+.+|..|.+-||.++++.+...    |+.+.+++|.........  .+.+
T Consensus       194 i~H~GPTNSGKTy~ALqrl~~-------aksGvycGPLrLLA~EV~~r~na~----gipCdL~TGeE~~~~~~~--~~~a  260 (700)
T KOG0953|consen  194 IMHVGPTNSGKTYRALQRLKS-------AKSGVYCGPLRLLAHEVYDRLNAL----GIPCDLLTGEERRFVLDN--GNPA  260 (700)
T ss_pred             EEEeCCCCCchhHHHHHHHhh-------hccceecchHHHHHHHHHHHhhhc----CCCccccccceeeecCCC--CCcc
Confidence            445689999999987433333       346799999999999999888776    677777777543221111  1235


Q ss_pred             cEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccC
Q psy4275         126 HIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus       126 ~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~  165 (182)
                      +.+=||-++.    .-     -..+.+.|+||+++|-+..
T Consensus       261 ~hvScTVEM~----sv-----~~~yeVAViDEIQmm~Dp~  291 (700)
T KOG0953|consen  261 QHVSCTVEMV----SV-----NTPYEVAVIDEIQMMRDPS  291 (700)
T ss_pred             cceEEEEEEe----ec-----CCceEEEEehhHHhhcCcc
Confidence            6677775543    11     2346799999999887654

>TIGR01075 uvrD DNA helicase II

Probab=97.59  E-value=0.00023  Score=61.35  Aligned_cols=71  Identities=17%  Similarity=0.078  Sum_probs=55.3

Q ss_pred             CCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCC-CCeeEEEEcCCHHHHHHHHHHHHHhhc
Q psy4275          27 KTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP-YGIFALVLTPTRELAYQIGDQFLVLGK   99 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~-~~~~~lil~p~~~l~~q~~~~~~~~~~   99 (182)
                      ..+++.|.+++.+.  ..++++.|++|||||.+...-+.+.+...+ ...++++++.|+..+.++.+.+..+..
T Consensus         3 ~~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~~L~~Ria~Li~~~~v~p~~IL~lTFTnkAA~em~~Rl~~~~~   74 (715)
T TIGR01075         3 DGLNDKQREAVAAP--PGNLLVLAGAGSGKTRVLTHRIAWLLSVENASPHSIMAVTFTNKAAAEMRHRIGALLG   74 (715)
T ss_pred             cccCHHHHHHHcCC--CCCEEEEecCCCCHHHHHHHHHHHHHHcCCCCHHHeEeeeccHHHHHHHHHHHHHHhc
Confidence            46899999988653  467999999999999997666666554332 234899999999999999888877654

Designed to identify uvrD members of the uvrD/rep subfamily.

>PRK06526 transposase; Provisional

Probab=97.59  E-value=0.0004  Score=52.37  Aligned_cols=40  Identities=20%  Similarity=0.103  Sum_probs=26.5

Q ss_pred             hhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEE
Q psy4275          38 PHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVL   80 (182)
Q Consensus        38 ~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil   80 (182)
                      ..+..++++++.||+|+|||..+..........   +.+++++
T Consensus        93 ~fi~~~~nlll~Gp~GtGKThLa~al~~~a~~~---g~~v~f~  132 (254)
T PRK06526         93 DFVTGKENVVFLGPPGTGKTHLAIGLGIRACQA---GHRVLFA  132 (254)
T ss_pred             chhhcCceEEEEeCCCCchHHHHHHHHHHHHHC---CCchhhh
Confidence            334457899999999999998865544443322   4455543

>KOG1015|consensus

Probab=97.58  E-value=0.00052  Score=59.50  Aligned_cols=138  Identities=17%  Similarity=0.030  Sum_probs=81.2

Q ss_pred             ChHHHHhhhhhhhC--CCcEEEECCCCChHHHHHHHHHHHhhccC-CCCeeEEEEcCCHHHHHHHHHHHHHhhccC----
Q psy4275          29 PTEIQKAIIPHVLN--DEDCIGCAKTGSGKTLAFALPILQKWCED-PYGIFALVLTPTRELAYQIGDQFLVLGKVM----  101 (182)
Q Consensus        29 ~~~~Q~~~~~~~~~--~~~~li~~~tg~GKT~~~~~~~~~~~~~~-~~~~~~lil~p~~~l~~q~~~~~~~~~~~~----  101 (182)
                      .|+...+.+.....  |-.+|+..-+|.|||+..+.++...+... ..-.++|||+|...+ ..|.+++.+|...+    
T Consensus       680 Mwd~~~eSlkr~~~~~GsGcILAHcMGLGKTlQVvtflhTvL~c~klg~ktaLvV~PlNt~-~NW~~EFekWm~~~e~~~  758 (1567)
T KOG1015|consen  680 MWDCCCESLKRTKKSPGSGCILAHCMGLGKTLQVVTFLHTVLLCDKLGFKTALVVCPLNTA-LNWMNEFEKWMEGLEDDE  758 (1567)
T ss_pred             HHHHHHHHHHhhcCCCCcchHHHHhhcccceehhhHHHHHHHHhhccCCceEEEEcchHHH-HHHHHHHHHhcccccccc
Confidence            34444444444332  55778888899999975333332222221 224589999998776 55888888887742    


Q ss_pred             CceEEEEEcCCchh---hhhHHhcCCCcEEEEChHHHHHHHhcCCCC------------CCCCccEEEEeccccccccCC
Q psy4275         102 NLRVSIITGGMDMV---DQGKELAKKPHIVIATPGRLADHLDTCNTF------------SLNRIKFLVLDEADRLSLMTS  166 (182)
Q Consensus       102 ~~~~~~~~~~~~~~---~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~------------~~~~~~~iI~DE~h~~~~~~~  166 (182)
                      .+.|.-+..-....   .....+.+...|.|.-.+.+..+-..+...            .-.--+++|.||+|.+-+...
T Consensus       759 ~leV~eL~~vkr~e~R~~~L~~W~~~ggVmIiGYdmyRnLa~gr~vk~rk~ke~f~k~lvdpGPD~vVCDE~HiLKNeks  838 (1567)
T KOG1015|consen  759 KLEVSELATVKRPEERSYMLQRWQEDGGVMIIGYDMYRNLAQGRNVKSRKLKEIFNKALVDPGPDFVVCDEGHILKNEKS  838 (1567)
T ss_pred             cceeehhhhccChHHHHHHHHHHHhcCCEEEEehHHHHHHhcccchhhhHHHHHHHHhccCCCCCeEEecchhhhccchH
Confidence            23343332222212   222344556789999988887665432211            111236999999998887664


Q ss_pred             h
Q psy4275         167 L  167 (182)
Q Consensus       167 ~  167 (182)
                      .
T Consensus       839 a  839 (1567)
T KOG1015|consen  839 A  839 (1567)
T ss_pred             H
Confidence            3

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.58  E-value=0.00064  Score=54.24  Aligned_cols=61  Identities=21%  Similarity=0.117  Sum_probs=34.5

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccC-CCCeeEEEEcCCH--HHHHHHHHHHHHhhccCCceEEE
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCED-PYGIFALVLTPTR--ELAYQIGDQFLVLGKVMNLRVSI  107 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~-~~~~~~lil~p~~--~l~~q~~~~~~~~~~~~~~~~~~  107 (182)
                      +.+++.||||+|||+++.-.+....... ..+.++.+++-..  .-+.   .+++.+.+..++.+..
T Consensus       175 ~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~---eQL~~~a~~lgvpv~~  238 (388)
T PRK12723        175 RVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAK---KQIQTYGDIMGIPVKA  238 (388)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHH---HHHHHHhhcCCcceEe
Confidence            4688899999999998654444333221 1244555555332  3222   2355565655665543

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=97.56  E-value=0.0019  Score=44.59  Aligned_cols=40  Identities=23%  Similarity=0.110  Sum_probs=27.2

Q ss_pred             EEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHH
Q psy4275          46 CIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAY   88 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~   88 (182)
                      .++.|++|+|||..+...+......   +..++++........
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~~~---~~~v~~~~~e~~~~~   41 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIATK---GGKVVYVDIEEEIEE   41 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHHhc---CCEEEEEECCcchHH
Confidence            5789999999999865554444332   557778776655533

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.

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.56  E-value=0.00092  Score=53.03  Aligned_cols=91  Identities=22%  Similarity=0.132  Sum_probs=49.7

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA  122 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  122 (182)
                      ++.+++.||||+|||+.+...+.......+ ..++.+++....- .--.+.++.+.+..++.+...............+.
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~~~~~~~G-~~~V~lit~D~~R-~ga~EqL~~~a~~~gv~~~~~~~~~~l~~~l~~l~  214 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAARCVMRFG-ASKVALLTTDSYR-IGGHEQLRIFGKILGVPVHAVKDGGDLQLALAELR  214 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcC-CCeEEEEeccccc-ccHHHHHHHHHHHcCCceEecCCcccHHHHHHHhc
Confidence            568899999999999986555544333322 1245555432221 11133455555555666655544443333333334


Q ss_pred             CCCcEEEEChHHH
Q psy4275         123 KKPHIVIATPGRL  135 (182)
Q Consensus       123 ~~~~Ilv~T~~~l  135 (182)
                      +..-|+|-|++..
T Consensus       215 ~~DlVLIDTaG~~  227 (374)
T PRK14722        215 NKHMVLIDTIGMS  227 (374)
T ss_pred             CCCEEEEcCCCCC
Confidence            4445777777644

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=97.54  E-value=0.0007  Score=51.85  Aligned_cols=110  Identities=14%  Similarity=0.060  Sum_probs=59.5

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccC-CC---CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCED-PY---GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGK  119 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~-~~---~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  119 (182)
                      .+.+++|+|+-|||...--..-.+-... .+   -+-+.+-+|...-....+..+-   ..++.....   .......  
T Consensus        62 p~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL---~~lgaP~~~---~~~~~~~--  133 (302)
T PF05621_consen   62 PNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAIL---EALGAPYRP---RDRVAKL--  133 (302)
T ss_pred             CceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHH---HHhCcccCC---CCCHHHH--
Confidence            5899999999999997654443332211 11   1334455566555444443322   222222100   0000000  


Q ss_pred             HhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHHHHHHHHhhc
Q psy4275         120 ELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFFFFLKYY  179 (182)
Q Consensus       120 ~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~~~~~~~~~~  179 (182)
                                  -....++++..      .++++||||+|+++..+..+-...+.-+|++
T Consensus       134 ------------~~~~~~llr~~------~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L  175 (302)
T PF05621_consen  134 ------------EQQVLRLLRRL------GVRMLIIDEFHNLLAGSYRKQREFLNALKFL  175 (302)
T ss_pred             ------------HHHHHHHHHHc------CCcEEEeechHHHhcccHHHHHHHHHHHHHH
Confidence                        01123444442      3679999999999998887766666666543

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=97.51  E-value=0.00035  Score=60.28  Aligned_cols=71  Identities=17%  Similarity=0.069  Sum_probs=54.9

Q ss_pred             CCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCC-CCeeEEEEcCCHHHHHHHHHHHHHhhc
Q psy4275          27 KTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP-YGIFALVLTPTRELAYQIGDQFLVLGK   99 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~-~~~~~lil~p~~~l~~q~~~~~~~~~~   99 (182)
                      ..++|.|.+++.+.  ..++++.|++|||||.+...-+.+.+...+ ...++++++-|+..+.++.+.+.++..
T Consensus         8 ~~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~vl~~Ria~Li~~~~v~p~~IL~lTFT~kAA~Em~~Rl~~~~~   79 (721)
T PRK11773          8 DSLNDKQREAVAAP--LGNMLVLAGAGSGKTRVLVHRIAWLMQVENASPYSIMAVTFTNKAAAEMRHRIEQLLG   79 (721)
T ss_pred             HhcCHHHHHHHhCC--CCCEEEEecCCCCHHHHHHHHHHHHHHcCCCChhHeEeeeccHHHHHHHHHHHHHHhc
Confidence            36999999988643  468999999999999997666665543322 234799999999999999888877654

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=97.44  E-value=0.00052  Score=58.69  Aligned_cols=69  Identities=17%  Similarity=0.046  Sum_probs=53.1

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCC-CCeeEEEEcCCHHHHHHHHHHHHHhh
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP-YGIFALVLTPTRELAYQIGDQFLVLG   98 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~-~~~~~lil~p~~~l~~q~~~~~~~~~   98 (182)
                      .+++.|.+++.+  ...++++.|++|||||.+...-+.+.+...+ ...++++++.++..+.++.+.+.+..
T Consensus         1 ~Ln~~Q~~av~~--~~~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~~~p~~IL~vTFt~~Aa~em~~Rl~~~l   70 (664)
T TIGR01074         1 KLNPQQQEAVEY--VTGPCLVLAGAGSGKTRVITNKIAYLIQNCGYKARNIAAVTFTNKAAREMKERVAKTL   70 (664)
T ss_pred             CCCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHh
Confidence            378899998854  3468999999999999997766666654322 23579999999999999988777654

Designed to identify rep members of the uvrD/rep subfamily.

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=97.43  E-value=0.0011  Score=50.21  Aligned_cols=66  Identities=18%  Similarity=0.066  Sum_probs=42.3

Q ss_pred             HHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcC
Q psy4275          15 PWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTP   82 (182)
Q Consensus        15 ~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p   82 (182)
                      +++.++|...++..-.+.-.+...-+..|...++.|++|+|||..+...+.....+.  +..++++.-
T Consensus         2 ~~~~~~~~~~~~~tg~~~Ld~~~gG~~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~~--g~~vl~iS~   67 (271)
T cd01122           2 EEIREALSNEEVWWPFPVLNKLTKGLRKGELIILTAGTGVGKTTFLREYALDLITQH--GVRVGTISL   67 (271)
T ss_pred             chhhccccccCCCCCcceeeeeeEEEcCCcEEEEEcCCCCCHHHHHHHHHHHHHHhc--CceEEEEEc
Confidence            455666664444443333333444566688899999999999998766665554432  446777764

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>PRK08181 transposase; Validated

Probab=97.40  E-value=0.003  Score=48.03  Aligned_cols=57  Identities=21%  Similarity=0.174  Sum_probs=33.8

Q ss_pred             ChHHHHhhhh----hhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHH
Q psy4275          29 PTEIQKAIIP----HVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQ   89 (182)
Q Consensus        29 ~~~~Q~~~~~----~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q   89 (182)
                      +...|...+.    .+..++++++.||+|+|||-.+....... ...  +.+++++. ...+..+
T Consensus        88 ~~~~~~~~L~~~~~~~~~~~nlll~Gp~GtGKTHLa~Aia~~a-~~~--g~~v~f~~-~~~L~~~  148 (269)
T PRK08181         88 VSKAQVMAIAAGDSWLAKGANLLLFGPPGGGKSHLAAAIGLAL-IEN--GWRVLFTR-TTDLVQK  148 (269)
T ss_pred             CCHHHHHHHHHHHHHHhcCceEEEEecCCCcHHHHHHHHHHHH-HHc--CCceeeee-HHHHHHH
Confidence            4455655552    33457899999999999997754443333 332  44565553 3444443

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=97.39  E-value=0.00094  Score=53.05  Aligned_cols=89  Identities=17%  Similarity=0.179  Sum_probs=50.1

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEE-cCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVL-TPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL  121 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil-~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  121 (182)
                      ++.+.+.||||.|||++..-.+........ +.++-+| +-+--.+  -.+.++..++-.++.+.++............+
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~~~~~-~~kVaiITtDtYRIG--A~EQLk~Ya~im~vp~~vv~~~~el~~ai~~l  279 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYVMLKK-KKKVAIITTDTYRIG--AVEQLKTYADIMGVPLEVVYSPKELAEAIEAL  279 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHhhcc-CcceEEEEeccchhh--HHHHHHHHHHHhCCceEEecCHHHHHHHHHHh
Confidence            678899999999999885544433332222 3344444 3332221  12344555555567777776666555555555


Q ss_pred             cCCCcEEEEChHH
Q psy4275         122 AKKPHIVIATPGR  134 (182)
Q Consensus       122 ~~~~~Ilv~T~~~  134 (182)
                      .+.--|+|-|.++
T Consensus       280 ~~~d~ILVDTaGr  292 (407)
T COG1419         280 RDCDVILVDTAGR  292 (407)
T ss_pred             hcCCEEEEeCCCC
Confidence            4444566666554

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.35  E-value=0.00053  Score=55.92  Aligned_cols=24  Identities=25%  Similarity=0.210  Sum_probs=19.0

Q ss_pred             EEEECCCCChHHHHHHHHHHHhhc
Q psy4275          46 CIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      .+++||.|+|||..+.+.+-....
T Consensus        43 ~Lf~GP~GtGKTTlAriLAk~Lnc   66 (484)
T PRK14956         43 YIFFGPRGVGKTTIARILAKRLNC   66 (484)
T ss_pred             EEEECCCCCCHHHHHHHHHHhcCc
Confidence            699999999999997666555433

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=97.29  E-value=0.0018  Score=52.47  Aligned_cols=34  Identities=21%  Similarity=0.258  Sum_probs=26.9

Q ss_pred             ChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHH
Q psy4275          29 PTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        29 ~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~   62 (182)
                      +.......+..+..+++++++||+|+|||..+..
T Consensus       180 ~e~~le~l~~~L~~~~~iil~GppGtGKT~lA~~  213 (459)
T PRK11331        180 PETTIETILKRLTIKKNIILQGPPGVGKTFVARR  213 (459)
T ss_pred             CHHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHH
Confidence            4445556667777899999999999999988653

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=97.27  E-value=0.00097  Score=57.66  Aligned_cols=71  Identities=20%  Similarity=0.113  Sum_probs=54.5

Q ss_pred             CCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCC-CCeeEEEEcCCHHHHHHHHHHHHHhhc
Q psy4275          27 KTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP-YGIFALVLTPTRELAYQIGDQFLVLGK   99 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~-~~~~~lil~p~~~l~~q~~~~~~~~~~   99 (182)
                      ..++|.|.+++.+.  ..++++.|+.|||||.+...-+.+.+...+ ...+++.++-|+..+.++.+.+.++..
T Consensus         3 ~~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~~l~~ria~Li~~~~i~P~~IL~lTFT~kAA~em~~Rl~~~~~   74 (726)
T TIGR01073         3 AHLNPEQREAVKTT--EGPLLIMAGAGSGKTRVLTHRIAHLIAEKNVAPWNILAITFTNKAAREMKERVEKLLG   74 (726)
T ss_pred             cccCHHHHHHHhCC--CCCEEEEeCCCCCHHHHHHHHHHHHHHcCCCCHHHeeeeeccHHHHHHHHHHHHHHhc
Confidence            46899999998653  467999999999999997666666554332 234799999999999998888776643

Designed to identify pcrA members of the uvrD/rep subfamily.

>PF14617 CMS1: U3-containing 90S pre-ribosomal complex subunit

Probab=97.27  E-value=0.0011  Score=49.67  Aligned_cols=85  Identities=25%  Similarity=0.321  Sum_probs=56.5

Q ss_pred             CCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcC-CchhhhhHHhc-CCCcEEEEChHHHHHHHhcCCCCCCCCc
Q psy4275          73 YGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGG-MDMVDQGKELA-KKPHIVIATPGRLADHLDTCNTFSLNRI  150 (182)
Q Consensus        73 ~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~-~~~~Ilv~T~~~l~~~~~~~~~~~~~~~  150 (182)
                      ..+.+|||+.+---+-.+...++.+... +..+.-+... ....+....+. +..+|.||||+++..++.. ..+.++++
T Consensus       125 gsP~~lvvs~SalRa~dl~R~l~~~~~k-~~~v~KLFaKH~Kl~eqv~~L~~~~~~i~vGTP~Rl~kLle~-~~L~l~~l  202 (252)
T PF14617_consen  125 GSPHVLVVSSSALRAADLIRALRSFKGK-DCKVAKLFAKHIKLEEQVKLLKKTRVHIAVGTPGRLSKLLEN-GALSLSNL  202 (252)
T ss_pred             CCCEEEEEcchHHHHHHHHHHHHhhccC-CchHHHHHHhhccHHHHHHHHHhCCceEEEeChHHHHHHHHc-CCCCcccC
Confidence            3578899988755555555555555211 2233323222 23334444444 4789999999999999977 77889999


Q ss_pred             cEEEEeccc
Q psy4275         151 KFLVLDEAD  159 (182)
Q Consensus       151 ~~iI~DE~h  159 (182)
                      .+||+|--|
T Consensus       203 ~~ivlD~s~  211 (252)
T PF14617_consen  203 KRIVLDWSY  211 (252)
T ss_pred             eEEEEcCCc
Confidence            999999754

>KOG0298|consensus

Probab=97.23  E-value=0.0015  Score=58.10  Aligned_cols=94  Identities=15%  Similarity=0.001  Sum_probs=61.9

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccC-----------C----CCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCED-----------P----YGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSI  107 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~-----------~----~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  107 (182)
                      |+.++..-..|+|||..-+...+......           .    ..+.+|||+|. ++..||.+++..-.... ++|..
T Consensus       374 g~~~~~ade~~~qk~~~~l~~~l~~~~k~~~~~cS~~~~e~~n~~~tgaTLII~P~-aIl~QW~~EI~kH~~~~-lKv~~  451 (1394)
T KOG0298|consen  374 GKRVQCADEMGWQKTSEKLILELSDLPKLCPSCCSELVKEGENLVETGATLIICPN-AILMQWFEEIHKHISSL-LKVLL  451 (1394)
T ss_pred             CcceeehhhhhccchHHHHHHHHhcccccchhhhhHHHhcccceeecCceEEECcH-HHHHHHHHHHHHhcccc-ceEEE
Confidence            55667777899999988765555443221           1    12468999995 56689888888776653 78888


Q ss_pred             EEcCCchhhhhHHhcCCCcEEEEChHHHHHH
Q psy4275         108 ITGGMDMVDQGKELAKKPHIVIATPGRLADH  138 (182)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~  138 (182)
                      +.|=....-......-.++|+++|...+..-
T Consensus       452 Y~Girk~~~~~~~el~~yDIVlTtYdiLr~E  482 (1394)
T KOG0298|consen  452 YFGIRKTFWLSPFELLQYDIVLTTYDILRNE  482 (1394)
T ss_pred             EechhhhcccCchhhhccCEEEeehHHHHhH
Confidence            8773322111112234789999999999653

>KOG0991|consensus

Probab=97.22  E-value=0.00053  Score=50.63  Aligned_cols=24  Identities=21%  Similarity=0.177  Sum_probs=18.9

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHh
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQK   67 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~   67 (182)
                      .|.++.||+|+|||++....+-..
T Consensus        49 P~liisGpPG~GKTTsi~~LAr~L   72 (333)
T KOG0991|consen   49 PNLIISGPPGTGKTTSILCLAREL   72 (333)
T ss_pred             CceEeeCCCCCchhhHHHHHHHHH
Confidence            589999999999999965444443

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=97.16  E-value=0.0022  Score=59.17  Aligned_cols=63  Identities=22%  Similarity=0.173  Sum_probs=46.1

Q ss_pred             CChHHHHhhhhhhhC--CCcEEEECCCCChHHHHHH--HHHHHhhccCCCCeeEEEEcCCHHHHHHHH
Q psy4275          28 TPTEIQKAIIPHVLN--DEDCIGCAKTGSGKTLAFA--LPILQKWCEDPYGIFALVLTPTRELAYQIG   91 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~--~~~~li~~~tg~GKT~~~~--~~~~~~~~~~~~~~~~lil~p~~~l~~q~~   91 (182)
                      .+++.|++++..++.  ++.++++|..|+|||+..-  +.++..+.. ..+..++.++||..-+..+.
T Consensus       835 ~Lt~~Qr~Av~~iLts~dr~~~IqG~AGTGKTT~l~~i~~~~~~l~e-~~g~~V~glAPTgkAa~~L~  901 (1623)
T PRK14712        835 KLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPE-SERPRVVGLGPTHRAVGEMR  901 (1623)
T ss_pred             ccCHHHHHHHHHHHhCCCceEEEEeCCCCCHHHHHHHHHHHHHHHhh-ccCceEEEEechHHHHHHHH
Confidence            689999999999875  5789999999999998742  222222222 22457888999988776653

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=97.14  E-value=0.0043  Score=58.91  Aligned_cols=63  Identities=16%  Similarity=0.108  Sum_probs=47.4

Q ss_pred             CChHHHHhhhhhhhC--CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHH
Q psy4275          28 TPTEIQKAIIPHVLN--DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQ   93 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~--~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~   93 (182)
                      .+++-|.+++..+..  ++-.+++|+.|+|||... -.+...+...  +.+++.++|+...+..+.+.
T Consensus       429 ~Ls~~Q~~Av~~il~s~~~v~ii~G~aGTGKTt~l-~~l~~~~~~~--G~~V~~lAPTgrAA~~L~e~  493 (1960)
T TIGR02760       429 ALSPSNKDAVSTLFTSTKRFIIINGFGGTGSTEIA-QLLLHLASEQ--GYEIQIITAGSLSAQELRQK  493 (1960)
T ss_pred             CCCHHHHHHHHHHHhCCCCeEEEEECCCCCHHHHH-HHHHHHHHhc--CCeEEEEeCCHHHHHHHHHH
Confidence            688999999988776  468899999999999873 3444433333  56899999998876665543

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>PHA03333 putative ATPase subunit of terminase; Provisional

Probab=97.13  E-value=0.0078  Score=51.08  Aligned_cols=57  Identities=11%  Similarity=0.024  Sum_probs=43.7

Q ss_pred             CCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhcc
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKV  100 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~  100 (182)
                      +.+-.++..|-|.|||.+..+.+...+...  +.+++|.+|...-+.++.+.++...+.
T Consensus       186 kq~~tV~taPRqrGKS~iVgi~l~~La~f~--Gi~IlvTAH~~~ts~evF~rv~~~le~  242 (752)
T PHA03333        186 GKCYTAATVPRRCGKTTIMAIILAAMISFL--EIDIVVQAQRKTMCLTLYNRVETVVHA  242 (752)
T ss_pred             hhcceEEEeccCCCcHHHHHHHHHHHHHhc--CCeEEEECCChhhHHHHHHHHHHHHHH
Confidence            356788899999999998765655444322  578999999999999988777776653

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=97.13  E-value=0.0018  Score=59.04  Aligned_cols=123  Identities=19%  Similarity=0.108  Sum_probs=76.0

Q ss_pred             ChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEE
Q psy4275          29 PTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSII  108 (182)
Q Consensus        29 ~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~  108 (182)
                      .++.|.+++.  ..++++++.|+.|||||.+..--++..+.....-.++++++-|+..+.++.+.+.......-..    
T Consensus         2 ~t~~Q~~ai~--~~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~~~~~~il~~tFt~~aa~e~~~ri~~~l~~~~~~----   75 (1232)
T TIGR02785         2 WTDEQWQAIY--TRGQNILVSASAGSGKTAVLVERIIKKILRGVDIDRLLVVTFTNAAAREMKERIEEALQKALQQ----   75 (1232)
T ss_pred             CCHHHHHHHh--CCCCCEEEEecCCCcHHHHHHHHHHHHHhcCCCHhhEEEEeccHHHHHHHHHHHHHHHHHHHhc----
Confidence            5788999986  3578999999999999999776666665544223479999999999998877766643321000    


Q ss_pred             EcCCchhhhhHHhcCCCcEEEEChHHHHHHH-hcCC-CCCCCCccEEEEecccc
Q psy4275         109 TGGMDMVDQGKELAKKPHIVIATPGRLADHL-DTCN-TFSLNRIKFLVLDEADR  160 (182)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~-~~~~-~~~~~~~~~iI~DE~h~  160 (182)
                        ........+.+..-...-|+|-..|...+ ++.. .+.++. ++=|.||...
T Consensus        76 --~p~~~~L~~q~~~~~~~~i~Tihsf~~~~~~~~~~~l~ldP-~F~i~de~e~  126 (1232)
T TIGR02785        76 --EPNSKHLRRQLALLNTANISTLHSFCLKVIRKHYYLLDLDP-SFRILTDTEQ  126 (1232)
T ss_pred             --CchhHHHHHHHhhccCCeEeeHHHHHHHHHHHhhhhcCCCC-CceeCCHHHH
Confidence              01111122223333456789988886443 4321 112221 2345777654

AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the Firmicutes (as modeled here) and the alphaproteobacteria, while the partner AddB proteins show no strong homology across the two groups of species.

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=97.11  E-value=0.0019  Score=51.84  Aligned_cols=111  Identities=15%  Similarity=0.145  Sum_probs=67.7

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHH-HHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcC
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRE-LAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAK  123 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~-l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  123 (182)
                      ..++.|+.|||||.++...++..+.....+.+++++-++.. +.+.+...++.....+++....-......  .. ...+
T Consensus         3 ~~i~~GgrgSGKS~~~~~~~~~~~~~~~~~~~~~~~r~~~~sl~~sv~~~l~~~i~~~g~~~~~~~~~~~~--~i-~~~~   79 (396)
T TIGR01547         3 EIIAKGGRRSGKTFAIALKLVEKLAINKKQQNILAARKVQNSIRDSVFKDIENLLSIEGINYEFKKSKSSM--EI-KILN   79 (396)
T ss_pred             eEEEeCCCCcccHHHHHHHHHHHHHhcCCCcEEEEEehhhhHHHHHHHHHHHHHHHHcCChhheeecCCcc--EE-EecC
Confidence            45788999999999988777777766422568888888877 55666777777666656532211111100  11 1122


Q ss_pred             -CCcEEEECh-HHHHHHHhcCCCCCCCCccEEEEecccccccc
Q psy4275         124 -KPHIVIATP-GRLADHLDTCNTFSLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus       124 -~~~Ilv~T~-~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~  164 (182)
                       +..|++... +...+      ......+.++.+|||..+...
T Consensus        80 ~g~~i~f~g~~d~~~~------ik~~~~~~~~~idEa~~~~~~  116 (396)
T TIGR01547        80 TGKKFIFKGLNDKPNK------LKSGAGIAIIWFEEASQLTFE  116 (396)
T ss_pred             CCeEEEeecccCChhH------hhCcceeeeehhhhhhhcCHH
Confidence             455666554 22211      112334689999999998543

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.

>PF05127 Helicase_RecD: Helicase; InterPro: IPR007807 This domain is about 350 amino acid residues long and appears to have a P-loop motif, suggesting this is an ATPase

Probab=97.10  E-value=0.00012  Score=51.93  Aligned_cols=102  Identities=21%  Similarity=0.154  Sum_probs=40.9

Q ss_pred             EEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCc
Q psy4275          47 IGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPH  126 (182)
Q Consensus        47 li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  126 (182)
                      ++.++-|.|||.+.-+.+.......  ..++++.+|+.+-+..+.+.+..-.+..+++....   ...........+...
T Consensus         1 VltA~RGRGKSa~lGl~~a~l~~~~--~~~I~vtAP~~~~~~~lf~~~~~~l~~~~~~~~~~---~~~~~~~~~~~~~~~   75 (177)
T PF05127_consen    1 VLTADRGRGKSAALGLAAAALIQKG--KIRILVTAPSPENVQTLFEFAEKGLKALGYKEEKK---KRIGQIIKLRFNKQR   75 (177)
T ss_dssp             -EEE-TTSSHHHHHHHCCCCSSS-------EEEE-SS--S-HHHHHCC-----------------------------CCC
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHhc--CceEEEecCCHHHHHHHHHHHHhhccccccccccc---cccccccccccccce
Confidence            4788999999988544444433332  25799999999988887777666555544444100   000000011122455


Q ss_pred             EEEEChHHHHHHHhcCCCCCCCCccEEEEeccccc
Q psy4275         127 IVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL  161 (182)
Q Consensus       127 Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~  161 (182)
                      |-...|+.+...-        ...+++|+|||=.+
T Consensus        76 i~f~~Pd~l~~~~--------~~~DlliVDEAAaI  102 (177)
T PF05127_consen   76 IEFVAPDELLAEK--------PQADLLIVDEAAAI  102 (177)
T ss_dssp             --B--HHHHCCT------------SCEEECTGGGS
T ss_pred             EEEECCHHHHhCc--------CCCCEEEEechhcC
Confidence            6666776553321        12478999999653

This domain is often N-terminal to a GCN5-related N-acetyltransferase domain IPR000182 from INTERPRO and C-terminal to IPR013562 from INTERPRO.; PDB: 2ZPA_B.

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=97.10  E-value=0.0051  Score=49.21  Aligned_cols=36  Identities=14%  Similarity=0.212  Sum_probs=22.9

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEE
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVL   80 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil   80 (182)
                      .++++.||+|+|||...- .++..+.....+..++++
T Consensus        56 ~~~lI~G~~GtGKT~l~~-~v~~~l~~~~~~~~~v~i   91 (394)
T PRK00411         56 LNVLIYGPPGTGKTTTVK-KVFEELEEIAVKVVYVYI   91 (394)
T ss_pred             CeEEEECCCCCCHHHHHH-HHHHHHHHhcCCcEEEEE
Confidence            579999999999999844 344433332223345555

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.09  E-value=0.0028  Score=54.59  Aligned_cols=90  Identities=19%  Similarity=0.127  Sum_probs=46.0

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA  122 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  122 (182)
                      ++-+.+.||||+|||+++...+.......+ +.++.+++....-+ -..+.++.+.+..++.+.................
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~~~~~G-~kkV~lit~Dt~Ri-gA~eQL~~~a~~~gvpv~~~~~~~~l~~al~~~~  262 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARCVAREG-ADQLALLTTDSFRI-GALEQLRIYGRILGVPVHAVKDAADLRFALAALG  262 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhHHHHcC-CCeEEEecCcccch-HHHHHHHHHHHhCCCCccccCCHHHHHHHHHHhc
Confidence            345788999999999886555444322321 23555555432221 0133455555555655543332222222222223


Q ss_pred             CCCcEEEEChHH
Q psy4275         123 KKPHIVIATPGR  134 (182)
Q Consensus       123 ~~~~Ilv~T~~~  134 (182)
                      +.--|+|-|++.
T Consensus       263 ~~D~VLIDTAGR  274 (767)
T PRK14723        263 DKHLVLIDTVGM  274 (767)
T ss_pred             CCCEEEEeCCCC
Confidence            333478888884

>PF03354 Terminase_1: Phage Terminase ; InterPro: IPR005021 This entry is represented by Lactococcus phage bIL285, Orf41 (terminase)

Probab=97.09  E-value=0.0033  Score=51.80  Aligned_cols=70  Identities=17%  Similarity=0.068  Sum_probs=51.6

Q ss_pred             HHHHhhhhhhhC-----C----CcEEEECCCCChHHHHHHHHHHHhhc-cCCCCeeEEEEcCCHHHHHHHHHHHHHhhcc
Q psy4275          31 EIQKAIIPHVLN-----D----EDCIGCAKTGSGKTLAFALPILQKWC-EDPYGIFALVLTPTRELAYQIGDQFLVLGKV  100 (182)
Q Consensus        31 ~~Q~~~~~~~~~-----~----~~~li~~~tg~GKT~~~~~~~~~~~~-~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~  100 (182)
                      |||+..+..+..     +    +.+++.-|=+-|||.......++.+. ....+..+++.++++..+..+.+.++.+.+.
T Consensus         1 PwQ~fi~~~i~G~~~~~g~rrf~~~~l~v~RkNGKS~l~a~i~ly~l~~~g~~~~~i~~~A~~~~QA~~~f~~~~~~i~~   80 (477)
T PF03354_consen    1 PWQKFILRSIFGWRKDDGRRRFREVYLEVPRKNGKSTLAAAIALYMLFLDGEPGAEIYCAANTRDQAKIVFDEAKKMIEA   80 (477)
T ss_pred             CcHHHHHHHHhceEcCCCCEEEEEEEEEEcCccCccHHHHHHHHHHHhcCCccCceEEEEeCCHHHHHHHHHHHHHHHHh
Confidence            567776665542     1    35778889999999876665555543 3344678999999999999999888887665

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=97.09  E-value=0.003  Score=53.90  Aligned_cols=67  Identities=24%  Similarity=0.259  Sum_probs=51.4

Q ss_pred             CChHHHHhhhhhhhC----C-CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhcc
Q psy4275          28 TPTEIQKAIIPHVLN----D-EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKV  100 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~----~-~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~  100 (182)
                      .|...|..++..+.+    + ++.++.|.||+|||..+.. ++...     +..+|||+|+..++.|+++.++.++..
T Consensus         9 ~~~~~Q~~ai~~l~~~~~~~~~~~~l~Gvtgs~kt~~~a~-~~~~~-----~~p~Lvi~~n~~~A~ql~~el~~f~p~   80 (655)
T TIGR00631         9 QPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMAN-VIAQV-----NRPTLVIAHNKTLAAQLYNEFKEFFPE   80 (655)
T ss_pred             CCChHHHHHHHHHHHhhhcCCCcEEEECCCCcHHHHHHHH-HHHHh-----CCCEEEEECCHHHHHHHHHHHHHhCCC
Confidence            577888888877654    2 3667999999999988543 33321     236899999999999999999998754

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

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=97.09  E-value=0.0018  Score=53.74  Aligned_cols=71  Identities=24%  Similarity=0.148  Sum_probs=51.6

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCC---CCeeEEEEcCCHHHHHHHHHHHHHhhc
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP---YGIFALVLTPTRELAYQIGDQFLVLGK   99 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~---~~~~~lil~p~~~l~~q~~~~~~~~~~   99 (182)
                      ++.+.|.+++.. ..++-.+++|..|||||.+++.=+.+.++...   .+..++++.|.+...+-+.+.+..++.
T Consensus       212 TIQkEQneIIR~-ek~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vlvl~PN~vFleYis~VLPeLGe  285 (747)
T COG3973         212 TIQKEQNEIIRF-EKNKILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLGPNRVFLEYISRVLPELGE  285 (747)
T ss_pred             HhhHhHHHHHhc-cCCCeEEEecCCCCCchhHHHHHHHHHHhccccccccCceEEEcCcHHHHHHHHHhchhhcc
Confidence            455666666633 23567889999999999999877766665532   244599999999998877777766644

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=97.08  E-value=0.0017  Score=50.61  Aligned_cols=63  Identities=22%  Similarity=0.173  Sum_probs=38.7

Q ss_pred             HHHCCCCCChHHHHhhhhhh-hCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHH
Q psy4275          21 CQTIGVKTPTEIQKAIIPHV-LNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTREL   86 (182)
Q Consensus        21 l~~~~~~~~~~~Q~~~~~~~-~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l   86 (182)
                      +.+.|.  +.+.|.+.+..+ ..+.+++++|+||+|||+.. .+++..+...+.+.+++.+-...++
T Consensus       123 lv~~g~--~~~~~~~~L~~~v~~~~nilI~G~tGSGKTTll-~aL~~~i~~~~~~~rivtiEd~~El  186 (323)
T PRK13833        123 YVTSKI--MTEAQASVIRSAIDSRLNIVISGGTGSGKTTLA-NAVIAEIVASAPEDRLVILEDTAEI  186 (323)
T ss_pred             HHHcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHH-HHHHHHHhcCCCCceEEEecCCccc
Confidence            334443  567777766554 44779999999999999884 5555555332223355555444433

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=97.06  E-value=0.0041  Score=53.14  Aligned_cols=67  Identities=25%  Similarity=0.262  Sum_probs=51.9

Q ss_pred             CChHHHHhhhhhhhC----C-CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhcc
Q psy4275          28 TPTEIQKAIIPHVLN----D-EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKV  100 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~----~-~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~  100 (182)
                      .|++.|...+..+.+    + ++.++.|.+|+||+..+.. ++...     +..+++|+|+...+.++++.++.+...
T Consensus        12 ~~~~~Q~~ai~~l~~~~~~~~~~~ll~Gl~gs~ka~lia~-l~~~~-----~r~vLIVt~~~~~A~~l~~dL~~~~~~   83 (652)
T PRK05298         12 KPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMAN-VIARL-----QRPTLVLAHNKTLAAQLYSEFKEFFPE   83 (652)
T ss_pred             CCChHHHHHHHHHHHhhhcCCCcEEEEcCCCcHHHHHHHH-HHHHh-----CCCEEEEECCHHHHHHHHHHHHHhcCC
Confidence            789999998888754    2 2577999999999988543 22221     336999999999999999999888653

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.06  E-value=0.0031  Score=51.89  Aligned_cols=24  Identities=21%  Similarity=0.185  Sum_probs=19.2

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHh
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQK   67 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~   67 (182)
                      +..+++||.|+|||.++.+.+...
T Consensus        36 ha~Lf~Gp~G~GKTT~ArilAk~L   59 (491)
T PRK14964         36 QSILLVGASGVGKTTCARIISLCL   59 (491)
T ss_pred             ceEEEECCCCccHHHHHHHHHHHH
Confidence            468999999999999876665443

>PRK06921 hypothetical protein; Provisional

Probab=97.06  E-value=0.018  Score=43.84  Aligned_cols=38  Identities=18%  Similarity=0.203  Sum_probs=24.8

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcC
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTP   82 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p   82 (182)
                      ++++++.|++|+|||..+. ++...+..+. +..++++..
T Consensus       117 ~~~l~l~G~~G~GKThLa~-aia~~l~~~~-g~~v~y~~~  154 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLT-AAANELMRKK-GVPVLYFPF  154 (266)
T ss_pred             CCeEEEECCCCCcHHHHHH-HHHHHHhhhc-CceEEEEEH
Confidence            5689999999999997754 3334343321 345666653

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=97.04  E-value=0.0043  Score=57.92  Aligned_cols=64  Identities=20%  Similarity=0.165  Sum_probs=46.3

Q ss_pred             CCChHHHHhhhhhhhC--CCcEEEECCCCChHHHHHHHHHHHhhc--cCCCCeeEEEEcCCHHHHHHHH
Q psy4275          27 KTPTEIQKAIIPHVLN--DEDCIGCAKTGSGKTLAFALPILQKWC--EDPYGIFALVLTPTRELAYQIG   91 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~--~~~~li~~~tg~GKT~~~~~~~~~~~~--~~~~~~~~lil~p~~~l~~q~~   91 (182)
                      ..+++.|++++..+..  ++-.+++|..|+|||+.. -.+...+.  ....+.+++.++||..-+..+.
T Consensus       966 ~~Lt~~Q~~Av~~il~s~dr~~~I~G~AGTGKTT~l-~~v~~~~~~l~~~~~~~V~glAPTgrAAk~L~ 1033 (1747)
T PRK13709        966 EGLTSGQRAATRMILESTDRFTVVQGYAGVGKTTQF-RAVMSAVNTLPESERPRVVGLGPTHRAVGEMR 1033 (1747)
T ss_pred             CCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHHH-HHHHHHHHHhhcccCceEEEECCcHHHHHHHH
Confidence            3689999999999886  468999999999999873 33333221  1222457888999987766543

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=97.03  E-value=0.0022  Score=50.81  Aligned_cols=26  Identities=23%  Similarity=0.321  Sum_probs=19.8

Q ss_pred             CCCcEEEECCCCChHHHHHHHHHHHhh
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALPILQKW   68 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~~~~~~   68 (182)
                      .+..++++||||+|||+.. ..++..+
T Consensus       133 ~~glilI~GpTGSGKTTtL-~aLl~~i  158 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTLL-AAIIREL  158 (358)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHH
Confidence            3678999999999999884 4455544

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.

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=97.03  E-value=0.0026  Score=50.55  Aligned_cols=27  Identities=30%  Similarity=0.315  Sum_probs=19.9

Q ss_pred             CCCcEEEECCCCChHHHHHHHHHHHhhc
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      .+..++++||||+|||+.. .+++..+.
T Consensus       148 ~~GlilI~G~TGSGKTT~l-~al~~~i~  174 (372)
T TIGR02525       148 AAGLGLICGETGSGKSTLA-ASIYQHCG  174 (372)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHHH
Confidence            3457899999999999884 45555443

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).

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=97.01  E-value=0.0048  Score=47.72  Aligned_cols=57  Identities=26%  Similarity=0.316  Sum_probs=35.7

Q ss_pred             ChHHHHhhhhh-hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHH
Q psy4275          29 PTEIQKAIIPH-VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTREL   86 (182)
Q Consensus        29 ~~~~Q~~~~~~-~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l   86 (182)
                      +.+.|.+.+.. +..+++++++|+||+|||+.. .+++..+.......+++.+-...++
T Consensus       117 ~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTll-~al~~~i~~~~~~~ri~tiEd~~El  174 (299)
T TIGR02782       117 MTAAQRDVLREAVLARKNILVVGGTGSGKTTLA-NALLAEIAKNDPTDRVVIIEDTREL  174 (299)
T ss_pred             CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHH-HHHHHHhhccCCCceEEEECCchhh
Confidence            44555555544 445789999999999999884 4555555442223356666555444

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.

>KOG4150|consensus

Probab=96.98  E-value=0.00038  Score=57.34  Aligned_cols=161  Identities=7%  Similarity=-0.123  Sum_probs=102.0

Q ss_pred             HHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHH
Q psy4275          17 LIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLV   96 (182)
Q Consensus        17 i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~   96 (182)
                      +.+.+.+....+...+|.+++..+..|++..+...+.+||.+++.......+...+ ....+++.|+.+++....+-++.
T Consensus       275 ~~~~~~~~~~E~~~~~~~~~~~~~~~G~~~~~~~~~~~GK~~~~~~~s~~~~~~~~-~s~~~~~~~~~~~~~~~~~~~~V  353 (1034)
T KOG4150|consen  275 IRSLLNKNTGESGIAISLELLKFASEGRADGGNEARQAGKGTCPTSGSRKFQTLCH-ATNSLLPSEMVEHLRNGSKGQVV  353 (1034)
T ss_pred             HHHHHhcccccchhhhhHHHHhhhhhcccccccchhhcCCccCcccchhhhhhcCc-ccceecchhHHHHhhccCCceEE
Confidence            34445555566889999999999999999999999999999998877777655543 23578888888876543222111


Q ss_pred             hhccCC----ceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhc-CCCC--CCCCccEEEEeccccccccCChhH
Q psy4275          97 LGKVMN----LRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDT-CNTF--SLNRIKFLVLDEADRLSLMTSLKF  169 (182)
Q Consensus        97 ~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~-~~~~--~~~~~~~iI~DE~h~~~~~~~~~~  169 (182)
                      ......    --|-...| .+.....+-...+.+++.+.|.......-- .-.+  .+=...++++||+|..........
T Consensus       354 ~~~~I~~~K~A~V~~~D~-~sE~~~~A~~R~~~~~~~s~~~~~~s~~L~~~~~~~~~~~~~~~~~~~~~~~Y~~~~~~~~  432 (1034)
T KOG4150|consen  354 HVEVIKARKSAYVEMSDK-LSETTKSALKRIGLNTLYSHQAEAISAALAKSLCYNVPVFEELCKDTNSCALYLFPTKALA  432 (1034)
T ss_pred             EEEehhhhhcceeecccC-CCchhHHHHHhcCcceeecCHHHHHHHHhhhccccccHHHHHHHhcccceeeeecchhhHH
Confidence            111111    11112222 222223333345788999999887654322 1111  122345789999999888877777


Q ss_pred             HHHHHHHhhc
Q psy4275         170 FFFFFFLKYY  179 (182)
Q Consensus       170 ~~~~~~~~~~  179 (182)
                      ...++++.++
T Consensus       433 ~~~~R~L~~L  442 (1034)
T KOG4150|consen  433 QDQLRALSDL  442 (1034)
T ss_pred             HHHHHHHHHH
Confidence            7777777664

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=96.97  E-value=0.0082  Score=49.09  Aligned_cols=45  Identities=13%  Similarity=0.046  Sum_probs=27.9

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQI   90 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~   90 (182)
                      +..++.|++|+|||-.+ .++.+.+.....+.+++++.. ..+...+
T Consensus       142 npl~i~G~~G~GKTHLl-~Ai~~~l~~~~~~~~v~yv~~-~~f~~~~  186 (450)
T PRK14087        142 NPLFIYGESGMGKTHLL-KAAKNYIESNFSDLKVSYMSG-DEFARKA  186 (450)
T ss_pred             CceEEECCCCCcHHHHH-HHHHHHHHHhCCCCeEEEEEH-HHHHHHH
Confidence            45889999999999653 444554443333557777765 3343333

>PRK07952 DNA replication protein DnaC; Validated

Probab=96.96  E-value=0.015  Score=43.61  Aligned_cols=34  Identities=24%  Similarity=0.178  Sum_probs=22.7

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEE
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVL   80 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil   80 (182)
                      .++++.|++|+|||..+...+.+ +...  +..++++
T Consensus       100 ~~~~l~G~~GtGKThLa~aia~~-l~~~--g~~v~~i  133 (244)
T PRK07952        100 ASFIFSGKPGTGKNHLAAAICNE-LLLR--GKSVLII  133 (244)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH-HHhc--CCeEEEE
Confidence            47899999999999875444333 3332  4456655

>KOG0333|consensus

Probab=96.96  E-value=0.019  Score=47.17  Aligned_cols=70  Identities=14%  Similarity=0.227  Sum_probs=53.5

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhc----CCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA----KKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      .+.+||.++++.-++.+++.+.+    .+++++.+||+.+.+++...+.    +..+|+|+|.-      .. +.+++.+
T Consensus       517 ~ppiIIFvN~kk~~d~lAk~LeK----~g~~~~tlHg~k~qeQRe~aL~~fr~~t~dIlVaTDv------Ag-RGIDIpn  585 (673)
T KOG0333|consen  517 DPPIIIFVNTKKGADALAKILEK----AGYKVTTLHGGKSQEQRENALADFREGTGDILVATDV------AG-RGIDIPN  585 (673)
T ss_pred             CCCEEEEEechhhHHHHHHHHhh----ccceEEEeeCCccHHHHHHHHHHHHhcCCCEEEEecc------cc-cCCCCCc
Confidence            46788998988777766655554    4899999999999988876653    37899999943      22 6678899


Q ss_pred             ccEEE
Q psy4275         150 IKFLV  154 (182)
Q Consensus       150 ~~~iI  154 (182)
                      ++++|
T Consensus       586 VSlVi  590 (673)
T KOG0333|consen  586 VSLVI  590 (673)
T ss_pred             cceee
Confidence            98876

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.93  E-value=0.013  Score=48.24  Aligned_cols=91  Identities=21%  Similarity=0.127  Sum_probs=47.9

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA  122 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  122 (182)
                      ++-+.+.||||+|||++....+......++ +.++.++.-...- .-..+.++.+.+..++.+...............+.
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~G-~~kV~LI~~Dt~R-igA~EQLr~~AeilGVpv~~~~~~~Dl~~aL~~L~  333 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAARCVMRHG-ASKVALLTTDSYR-IGGHEQLRIYGKILGVPVHAVKDAADLRLALSELR  333 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHHHHHhcC-CCeEEEEeCCccc-hhHHHHHHHHHHHhCCCeeccCCchhHHHHHHhcc
Confidence            456788999999999986655544433332 2245444322110 11134455555555555544333333223333344


Q ss_pred             CCCcEEEEChHHH
Q psy4275         123 KKPHIVIATPGRL  135 (182)
Q Consensus       123 ~~~~Ilv~T~~~l  135 (182)
                      +...++|-|++..
T Consensus       334 d~d~VLIDTaGr~  346 (484)
T PRK06995        334 NKHIVLIDTIGMS  346 (484)
T ss_pred             CCCeEEeCCCCcC
Confidence            4556889888844

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=96.92  E-value=0.0026  Score=49.78  Aligned_cols=44  Identities=14%  Similarity=0.103  Sum_probs=33.5

Q ss_pred             CChHHHHhhhhhhhCC----CcEEEECCCCChHHHHHHHHHHHhhccC
Q psy4275          28 TPTEIQKAIIPHVLND----EDCIGCAKTGSGKTLAFALPILQKWCED   71 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~----~~~li~~~tg~GKT~~~~~~~~~~~~~~   71 (182)
                      ...|||...|..+...    +..++.||.|.||+..+...+-..+..+
T Consensus         3 ~~yPWl~~~~~~~~~~~r~~ha~Lf~G~~G~GK~~~A~~~A~~llC~~   50 (328)
T PRK05707          3 EIYPWQQSLWQQLAGRGRHPHAYLLHGPAGIGKRALAERLAAALLCEA   50 (328)
T ss_pred             cCCCCcHHHHHHHHHCCCcceeeeeECCCCCCHHHHHHHHHHHHcCCC
Confidence            4579999999887752    2477999999999998776666655543

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA

Probab=96.88  E-value=0.0023  Score=53.66  Aligned_cols=127  Identities=14%  Similarity=0.084  Sum_probs=80.8

Q ss_pred             CChHHHHhhhhhhhCC--CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHH-HHHHHHhhccCCce
Q psy4275          28 TPTEIQKAIIPHVLND--EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQI-GDQFLVLGKVMNLR  104 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~--~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~-~~~~~~~~~~~~~~  104 (182)
                      ..+|+|.+....+...  +.+.+..++-+|||.+.+..+.+.+...+  ..++++.|+...+... .+.+..+.+....-
T Consensus        16 ~~~Py~~eimd~~~~~~v~~Vv~~k~aQ~GkT~~~~n~~g~~i~~~P--~~~l~v~Pt~~~a~~~~~~rl~Pmi~~sp~l   93 (557)
T PF05876_consen   16 DRTPYLREIMDALSDPSVREVVVMKSAQVGKTELLLNWIGYSIDQDP--GPMLYVQPTDDAAKDFSKERLDPMIRASPVL   93 (557)
T ss_pred             CCChhHHHHHHhcCCcCccEEEEEEcchhhHhHHHHhhceEEEEeCC--CCEEEEEEcHHHHHHHHHHHHHHHHHhCHHH
Confidence            6789999999888773  57888899999999987776666666654  3589999999999888 46677776655431


Q ss_pred             EEEEEc---CCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275         105 VSIITG---GMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus       105 ~~~~~~---~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      -..+.+   ..........-..+..+.+....       +-..+.-..++++++||++.+..
T Consensus        94 ~~~~~~~~~~~~~~t~~~k~f~gg~l~~~ga~-------S~~~l~s~~~r~~~~DEvD~~p~  148 (557)
T PF05876_consen   94 RRKLSPSKSRDSGNTILYKRFPGGFLYLVGAN-------SPSNLRSRPARYLLLDEVDRYPD  148 (557)
T ss_pred             HHHhCchhhcccCCchhheecCCCEEEEEeCC-------CCcccccCCcCEEEEechhhccc
Confidence            112221   00000001111123444444311       11233455678999999999853

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=96.87  E-value=0.0028  Score=48.57  Aligned_cols=38  Identities=21%  Similarity=0.048  Sum_probs=23.9

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      ++.+.+.||||+|||+.+...+......++ +.++.++.
T Consensus       194 ~~vi~~vGptGvGKTTt~~kLa~~~~~~~g-~~~V~li~  231 (282)
T TIGR03499       194 GGVIALVGPTGVGKTTTLAKLAARFVLEHG-NKKVALIT  231 (282)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHHcC-CCeEEEEE
Confidence            446888999999999986554444433211 23555554

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=96.84  E-value=0.011  Score=44.83  Aligned_cols=21  Identities=24%  Similarity=0.129  Sum_probs=17.3

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      ..++++.||+|+|||..+-..
T Consensus        42 ~~~vll~GppGtGKTtlA~~i   62 (261)
T TIGR02881        42 VLHMIFKGNPGTGKTTVARIL   62 (261)
T ss_pred             cceEEEEcCCCCCHHHHHHHH
Confidence            357899999999999986444

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.

>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair

Probab=96.82  E-value=0.0079  Score=44.35  Aligned_cols=23  Identities=17%  Similarity=0.130  Sum_probs=17.6

Q ss_pred             CcEEEECCCCChHHHHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQ   66 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~   66 (182)
                      .|+++.||+|+|||..+.+.+-+
T Consensus        51 ~h~lf~GPPG~GKTTLA~IIA~e   73 (233)
T PF05496_consen   51 DHMLFYGPPGLGKTTLARIIANE   73 (233)
T ss_dssp             -EEEEESSTTSSHHHHHHHHHHH
T ss_pred             ceEEEECCCccchhHHHHHHHhc
Confidence            37999999999999887444433

Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the N-terminal region of the proteins.; GO: 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1IQP_B 3PFI_B 1IXR_C 1HQC_B 1IXS_B.

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.81  E-value=0.0064  Score=50.35  Aligned_cols=124  Identities=15%  Similarity=0.125  Sum_probs=58.1

Q ss_pred             CccCCCCCHHHHHHHHHC-CC----CCChHHHHhhhh---------hhhCCCcEEEECCCCChHHHHHHHHHHHhhccCC
Q psy4275           7 SFTDLKLNPWLIRQCQTI-GV----KTPTEIQKAIIP---------HVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP   72 (182)
Q Consensus         7 ~~~~~~l~~~i~~~l~~~-~~----~~~~~~Q~~~~~---------~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~   72 (182)
                      .+.+.|+++.+.+.+... .-    ...+.+-...+.         .+.+++.+.+.||+|+|||+.+...+....... 
T Consensus       300 ~L~~~Gvs~~la~~L~~~l~~~~~~~~~~~~l~~~L~~~l~v~~~~~l~~G~vIaLVGPtGvGKTTtaakLAa~la~~~-  378 (559)
T PRK12727        300 LMDDYGFDAGLTRDVAMQIPADTELHRGRGLMLGLLSKRLPVAPVDPLERGGVIALVGPTGAGKTTTIAKLAQRFAAQH-  378 (559)
T ss_pred             HHHHCCCCHHHHHHHHHhhhcccchhhHHHHHHHHHHHhcCcCccccccCCCEEEEECCCCCCHHHHHHHHHHHHHHhc-
Confidence            345667888888777432 11    111222112221         123367888999999999988654444332222 


Q ss_pred             CCeeEEEEcC--CHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHH
Q psy4275          73 YGIFALVLTP--TRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGR  134 (182)
Q Consensus        73 ~~~~~lil~p--~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~  134 (182)
                      .+.++.++.-  .+..+   .+.++......++.+...............+.+..-|+|-|++.
T Consensus       379 ~gkkVaLIdtDtyRigA---~EQLk~ya~iLgv~v~~a~d~~~L~~aL~~l~~~DLVLIDTaG~  439 (559)
T PRK12727        379 APRDVALVTTDTQRVGG---REQLHSYGRQLGIAVHEADSAESLLDLLERLRDYKLVLIDTAGM  439 (559)
T ss_pred             CCCceEEEecccccccH---HHHHHHhhcccCceeEecCcHHHHHHHHHHhccCCEEEecCCCc
Confidence            1234555442  22211   12344444444554433322222222222222233466677764

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.81  E-value=0.0048  Score=52.33  Aligned_cols=25  Identities=20%  Similarity=0.143  Sum_probs=19.3

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhc
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      ..+++||.|+|||..+.+.+-....
T Consensus        39 AyLF~GPpGvGKTTlAriLAK~LnC   63 (702)
T PRK14960         39 AYLFTGTRGVGKTTIARILAKCLNC   63 (702)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCC
Confidence            4599999999999997666555433

>CHL00181 cbbX CbbX; Provisional

Probab=96.80  E-value=0.014  Score=44.81  Aligned_cols=23  Identities=17%  Similarity=-0.050  Sum_probs=18.3

Q ss_pred             CCcEEEECCCCChHHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPIL   65 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~   65 (182)
                      +.++++.||+|+|||.++-...-
T Consensus        59 ~~~ill~G~pGtGKT~lAr~la~   81 (287)
T CHL00181         59 GLHMSFTGSPGTGKTTVALKMAD   81 (287)
T ss_pred             CceEEEECCCCCCHHHHHHHHHH
Confidence            45789999999999998755433

>KOG2340|consensus

Probab=96.79  E-value=0.012  Score=48.31  Aligned_cols=142  Identities=22%  Similarity=0.262  Sum_probs=85.9

Q ss_pred             CCChHHHHhhhhhhhCCCcEEEEC-CCCChH--HHHHHHHHHHhhccC----------------------------CCCe
Q psy4275          27 KTPTEIQKAIIPHVLNDEDCIGCA-KTGSGK--TLAFALPILQKWCED----------------------------PYGI   75 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~~~~~li~~-~tg~GK--T~~~~~~~~~~~~~~----------------------------~~~~   75 (182)
                      ..+++.|.+.+..+-+.++++.-. ..+.|+  +.++.+.++.+++..                            -..+
T Consensus       215 ~pltalQ~~L~~~m~~YrDl~y~~~s~kn~~e~R~lYclH~lNHi~K~r~~IL~Nn~r~~Sqk~g~~~~~~frDQG~tRp  294 (698)
T KOG2340|consen  215 EPLTALQKELFKIMFNYRDLLYPTRSQKNGEEYRSLYCLHALNHILKTRDLILGNNRRLASQKEGENPDESFRDQGFTRP  294 (698)
T ss_pred             CcchHHHHHHHHHHHhhhhhccccccccccchhhhhHHHHHHHHHHHHHHHHhcchHhhhhhhcCCCCchhhhhcCCCCc
Confidence            468999999998888877766543 223343  233444444443321                            0137


Q ss_pred             eEEEEcCCHHHHHHHHHHHHHhhccCCce-E-----E-------------------------EEEcCCchh--------h
Q psy4275          76 FALVLTPTRELAYQIGDQFLVLGKVMNLR-V-----S-------------------------IITGGMDMV--------D  116 (182)
Q Consensus        76 ~~lil~p~~~l~~q~~~~~~~~~~~~~~~-~-----~-------------------------~~~~~~~~~--------~  116 (182)
                      +|+||||+++.|-.+.+.+..+....+-. .     .                         ++.|++...        .
T Consensus       295 kVLivvpfRe~A~riVn~lis~l~G~~q~k~~V~Nk~RF~~eys~~te~~~~~~~kP~D~~~lf~GNtDD~FriGl~ftk  374 (698)
T KOG2340|consen  295 KVLIVVPFRESAYRIVNLLISLLSGDDQGKSEVWNKKRFEGEYSGPTELPPPRAKKPEDFEELFSGNTDDAFRIGLAFTK  374 (698)
T ss_pred             eEEEEecchHHHHHHHHHHHHHhcCccccchhhhhhhhhchhcCCCcccCCCCCCCchhHHHHhcCCCcchhhhhHHHHH
Confidence            89999999999988888777663322110 0     0                         111111100        0


Q ss_pred             hhHH---hcCCCcEEEEChHHHHHHHhcC----CCC-CCCCccEEEEeccccccccCChh
Q psy4275         117 QGKE---LAKKPHIVIATPGRLADHLDTC----NTF-SLNRIKFLVLDEADRLSLMTSLK  168 (182)
Q Consensus       117 ~~~~---~~~~~~Ilv~T~~~l~~~~~~~----~~~-~~~~~~~iI~DE~h~~~~~~~~~  168 (182)
                      ..-.   -....+|+||+|--+.=.+...    +.+ .++++.++|+|-+|.|...++-.
T Consensus       375 KtikLys~fy~SDIlVaSPLGLRmil~n~gdkkrd~dfLSSIEl~iIDQa~~~l~QNwEh  434 (698)
T KOG2340|consen  375 KTIKLYSKFYKSDILVASPLGLRMILGNTGDKKRDFDFLSSIELLIIDQADIMLMQNWEH  434 (698)
T ss_pred             HHHHHHhhhcccCeEEecchhhhhhhcCCCcccccchhhhhhhhhhhhhHHHHHHhhHHH
Confidence            0111   1236799999998887666521    112 56778899999999998877743

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.79  E-value=0.0078  Score=52.67  Aligned_cols=23  Identities=22%  Similarity=-0.008  Sum_probs=18.0

Q ss_pred             EEEECCCCChHHHHHHHHHHHhh
Q psy4275          46 CIGCAKTGSGKTLAFALPILQKW   68 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~~   68 (182)
                      .+++||.|+|||..+.+.+-...
T Consensus        41 yLFtGPpGtGKTTLARiLAk~Ln   63 (944)
T PRK14949         41 YLFTGTRGVGKTSLARLFAKGLN   63 (944)
T ss_pred             EEEECCCCCCHHHHHHHHHHhcc
Confidence            48999999999999766555543

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.79  E-value=0.0057  Score=49.59  Aligned_cols=38  Identities=18%  Similarity=-0.018  Sum_probs=24.7

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhh-ccCCCCeeEEEEcC
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKW-CEDPYGIFALVLTP   82 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~-~~~~~~~~~lil~p   82 (182)
                      ++.+++.||||+|||+.+...+.... ...  +.++.++.-
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~--g~~V~li~~  259 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYG--KKKVALITL  259 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcC--CCeEEEEEC
Confidence            45788899999999988665544433 222  345655553

>PLN03025 replication factor C subunit; Provisional

Probab=96.78  E-value=0.017  Score=45.05  Aligned_cols=23  Identities=22%  Similarity=0.225  Sum_probs=18.1

Q ss_pred             CcEEEECCCCChHHHHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQ   66 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~   66 (182)
                      .+.+++||+|+|||..+...+-.
T Consensus        35 ~~lll~Gp~G~GKTtla~~la~~   57 (319)
T PLN03025         35 PNLILSGPPGTGKTTSILALAHE   57 (319)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH
Confidence            47899999999999886544433

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=96.78  E-value=0.0061  Score=47.55  Aligned_cols=64  Identities=23%  Similarity=0.219  Sum_probs=37.7

Q ss_pred             HHHHCCCCCChHHHHhhhhh-hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHH
Q psy4275          20 QCQTIGVKTPTEIQKAIIPH-VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTREL   86 (182)
Q Consensus        20 ~l~~~~~~~~~~~Q~~~~~~-~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l   86 (182)
                      .+...|.  +.+.|.+.+.. +..+++++++|+||+|||... ..++......+...+++.+-.+.++
T Consensus       126 ~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTll-~aL~~~~~~~~~~~rivtIEd~~El  190 (319)
T PRK13894        126 QYVERGI--MTAAQREAIIAAVRAHRNILVIGGTGSGKTTLV-NAIINEMVIQDPTERVFIIEDTGEI  190 (319)
T ss_pred             HHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHH-HHHHHhhhhcCCCceEEEEcCCCcc
Confidence            3334443  55677777765 455889999999999999764 4444433211112345555444443

>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]

Probab=96.75  E-value=0.014  Score=50.14  Aligned_cols=129  Identities=14%  Similarity=0.145  Sum_probs=77.1

Q ss_pred             HHHHHHCCCCCChHHHHhhhhhhhCCC--cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHH
Q psy4275          18 IRQCQTIGVKTPTEIQKAIIPHVLNDE--DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFL   95 (182)
Q Consensus        18 ~~~l~~~~~~~~~~~Q~~~~~~~~~~~--~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~   95 (182)
                      ...+...........|.+.+..+.+.+  -.++.+.-|-|||.+.-+++. .+.......++++.+|+.+-+..+.+.+.
T Consensus       204 ~~~l~~l~~T~dQ~~~l~~~~~l~~~~~~~~vlTAdRGRGKSA~lGi~~~-~~~~~~~~~~iiVTAP~~~nv~~Lf~fa~  282 (758)
T COG1444         204 PRELYELCLTEDQAEALEILERLLDAPKRALVLTADRGRGKSAALGIALA-AAARLAGSVRIIVTAPTPANVQTLFEFAG  282 (758)
T ss_pred             CHHHhhhhcChhHHHHHHHHHHHHcCCCceEEEEcCCCCcHhHHHhHHHH-HHHHhcCCceEEEeCCCHHHHHHHHHHHH
Confidence            333444444456666666777766633  577889999999998765552 22222114589999999999988887777


Q ss_pred             HhhccCCceEEEEEcCCc-hhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccc
Q psy4275          96 VLGKVMNLRVSIITGGMD-MVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL  161 (182)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~  161 (182)
                      +-....|++-.+...... ...   .......|-..+|....           ..-+++|+|||=-+
T Consensus       283 ~~l~~lg~~~~v~~d~~g~~~~---~~~~~~~i~y~~P~~a~-----------~~~DllvVDEAAaI  335 (758)
T COG1444         283 KGLEFLGYKRKVAPDALGEIRE---VSGDGFRIEYVPPDDAQ-----------EEADLLVVDEAAAI  335 (758)
T ss_pred             HhHHHhCCccccccccccceee---ecCCceeEEeeCcchhc-----------ccCCEEEEehhhcC
Confidence            766776765433222211 111   10122335555655432           11468999999643

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.73  E-value=0.0057  Score=50.23  Aligned_cols=23  Identities=22%  Similarity=0.150  Sum_probs=18.0

Q ss_pred             cEEEECCCCChHHHHHHHHHHHh
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQK   67 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~   67 (182)
                      ..+++||+|+|||..+...+-..
T Consensus        38 ~~Lf~GPpGtGKTTlA~~lA~~l   60 (472)
T PRK14962         38 AYIFAGPRGTGKTTVARILAKSL   60 (472)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            36999999999999876554443

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.71  E-value=0.0082  Score=49.80  Aligned_cols=25  Identities=20%  Similarity=0.137  Sum_probs=19.2

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhc
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      ..+++||.|+|||..+.+.+-....
T Consensus        40 a~Lf~Gp~G~GKTt~A~~lAk~l~c   64 (509)
T PRK14958         40 AYLFTGTRGVGKTTISRILAKCLNC   64 (509)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhcC
Confidence            3589999999999987666555443

>KOG0921|consensus

Probab=96.71  E-value=0.0076  Score=52.35  Aligned_cols=124  Identities=21%  Similarity=0.245  Sum_probs=80.0

Q ss_pred             HHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCe--eEEEEcCCHHHHHHHHHHHHHh-hccCCceEEEEE
Q psy4275          33 QKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGI--FALVLTPTRELAYQIGDQFLVL-GKVMNLRVSIIT  109 (182)
Q Consensus        33 Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~--~~lil~p~~~l~~q~~~~~~~~-~~~~~~~~~~~~  109 (182)
                      -...+..+..+.-.++.+.||+|||.-+.-.+++.+..+..+.  .+.+--|++..+..+++.+.+- ....+-.|++-.
T Consensus       383 ~~~i~q~v~dn~v~~I~getgcgk~tq~aq~iLe~~~~ns~g~~~na~v~qprrisaisiaerva~er~e~~g~tvgy~v  462 (1282)
T KOG0921|consen  383 RSEILQAVAENRVVIIKGETGCGKSTQVAQFLLESFLENSNGASFNAVVSQPRRISAISLAERVANERGEEVGETCGYNV  462 (1282)
T ss_pred             HHHHHHHHhcCceeeEeecccccchhHHHHHHHHHHhhccccccccceeccccccchHHHHHHHHHhhHHhhcccccccc
Confidence            3445555666778899999999999999999999888875432  3455557776666665554432 222233332111


Q ss_pred             cCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccC
Q psy4275         110 GGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus       110 ~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~  165 (182)
                           ......-.....|+.+|-+-++..+.. .   +.-++++|+||.|+.+.++
T Consensus       463 -----Rf~Sa~prpyg~i~fctvgvllr~~e~-g---lrg~sh~i~deiherdv~~  509 (1282)
T KOG0921|consen  463 -----RFDSATPRPYGSIMFCTVGVLLRMMEN-G---LRGISHVIIDEIHERDVDT  509 (1282)
T ss_pred             -----cccccccccccceeeeccchhhhhhhh-c---ccccccccchhhhhhccch
Confidence                 011111122446899999999888876 3   4457799999999877655

>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.70  E-value=0.0019  Score=53.62  Aligned_cols=119  Identities=22%  Similarity=0.152  Sum_probs=60.6

Q ss_pred             EECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHH-HHhhccCCceEEEEEcCCchh----hhhHHhc
Q psy4275          48 GCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQF-LVLGKVMNLRVSIITGGMDMV----DQGKELA  122 (182)
Q Consensus        48 i~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~-~~~~~~~~~~~~~~~~~~~~~----~~~~~~~  122 (182)
                      ..+.||+|||+++...+++.......  ..++.|......+.....+ ......+-+.-.+..++....    .......
T Consensus         2 f~matgsgkt~~ma~lil~~y~kgyr--~flffvnq~nilekt~~nftd~~s~kylf~e~i~~~d~~i~ikkvn~fsehn   79 (812)
T COG3421           2 FEMATGSGKTLVMAGLILECYKKGYR--NFLFFVNQANILEKTKLNFTDSVSSKYLFSENININDENIEIKKVNNFSEHN   79 (812)
T ss_pred             cccccCCChhhHHHHHHHHHHHhchh--hEEEEecchhHHHHHHhhcccchhhhHhhhhhhhcCCceeeeeeecccCccC
Confidence            45789999999988777776655322  3556665555443332111 111111101101111111100    0000123


Q ss_pred             CCCcEEEEChHHHHHHHhcC--CCC---CCCCcc-EEEEeccccccccCChh
Q psy4275         123 KKPHIVIATPGRLADHLDTC--NTF---SLNRIK-FLVLDEADRLSLMTSLK  168 (182)
Q Consensus       123 ~~~~Ilv~T~~~l~~~~~~~--~~~---~~~~~~-~iI~DE~h~~~~~~~~~  168 (182)
                      .+..|..+|.+.+..-+-..  +.+   ++.+.. +++-||+||+....-..
T Consensus        80 d~iei~fttiq~l~~d~~~~ken~itledl~~~klvfl~deahhln~~tkkk  131 (812)
T COG3421          80 DAIEIYFTTIQGLFSDFTRAKENAITLEDLKDQKLVFLADEAHHLNTETKKK  131 (812)
T ss_pred             CceEEEEeehHHHHHHHHhhccccccHhhHhhCceEEEechhhhhhhhhhhh
Confidence            46689999999997655321  222   333333 46779999998765433

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.70  E-value=0.0092  Score=47.41  Aligned_cols=22  Identities=23%  Similarity=0.119  Sum_probs=17.3

Q ss_pred             EEEECCCCChHHHHHHHHHHHh
Q psy4275          46 CIGCAKTGSGKTLAFALPILQK   67 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~   67 (182)
                      .++.||.|+|||..+...+-..
T Consensus        41 ~L~~Gp~G~GKTtla~~la~~l   62 (363)
T PRK14961         41 WLLSGTRGVGKTTIARLLAKSL   62 (363)
T ss_pred             EEEecCCCCCHHHHHHHHHHHh
Confidence            5899999999999876555443

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=96.70  E-value=0.01  Score=43.77  Aligned_cols=23  Identities=17%  Similarity=0.186  Sum_probs=17.8

Q ss_pred             CCcEEEECCCCChHHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPIL   65 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~   65 (182)
                      ++.+++.|++|+|||..+.....
T Consensus        42 ~~~~~l~G~~G~GKT~La~ai~~   64 (227)
T PRK08903         42 DRFFYLWGEAGSGRSHLLQALVA   64 (227)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHH
Confidence            46799999999999987544333

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]

Probab=96.70  E-value=0.0046  Score=48.15  Aligned_cols=59  Identities=19%  Similarity=0.094  Sum_probs=41.4

Q ss_pred             CCCCChHHHHhhhhhhhCCC-cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHH
Q psy4275          25 GVKTPTEIQKAIIPHVLNDE-DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELA   87 (182)
Q Consensus        25 ~~~~~~~~Q~~~~~~~~~~~-~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~   87 (182)
                      .+...++-|...+......+ |++++|+||||||+. +-.+.......+   +++.+--+.+|.
T Consensus       154 ~~gt~~~~~a~~L~~av~~r~NILisGGTGSGKTTl-LNal~~~i~~~e---RvItiEDtaELq  213 (355)
T COG4962         154 IFGTMIRRAAKFLRRAVGIRCNILISGGTGSGKTTL-LNALSGFIDSDE---RVITIEDTAELQ  213 (355)
T ss_pred             HcCCcCHHHHHHHHHHHhhceeEEEeCCCCCCHHHH-HHHHHhcCCCcc---cEEEEeehhhhc
Confidence            34568888888887776655 999999999999987 444444444432   677776666653

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=96.70  E-value=0.017  Score=47.26  Aligned_cols=38  Identities=18%  Similarity=0.043  Sum_probs=24.2

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcC
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTP   82 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p   82 (182)
                      +.+++.||+|+|||..+.. +...+..+..+.+++++..
T Consensus       149 ~~l~l~G~~G~GKThL~~a-i~~~~~~~~~~~~v~yi~~  186 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLLHA-IGNYILEKNPNAKVVYVTS  186 (450)
T ss_pred             CeEEEECCCCCCHHHHHHH-HHHHHHHhCCCCeEEEEEH
Confidence            4588999999999987543 3333333322446676644

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=96.69  E-value=0.013  Score=43.06  Aligned_cols=24  Identities=21%  Similarity=0.163  Sum_probs=18.8

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQ   66 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~   66 (182)
                      ++++++.||+|+|||..+....-.
T Consensus        38 ~~~lll~G~~G~GKT~la~~~~~~   61 (226)
T TIGR03420        38 DRFLYLWGESGSGKSHLLQAACAA   61 (226)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH
Confidence            568999999999999886544433

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.

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=96.67  E-value=0.0072  Score=52.85  Aligned_cols=25  Identities=20%  Similarity=0.183  Sum_probs=20.3

Q ss_pred             EEEECCCCChHHHHHHHHHHHhhcc
Q psy4275          46 CIGCAKTGSGKTLAFALPILQKWCE   70 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~~~~   70 (182)
                      .|++||.|+|||.++.+........
T Consensus        40 ~Lf~Gp~G~GKTt~A~~lAr~L~C~   64 (824)
T PRK07764         40 YLFSGPRGCGKTSSARILARSLNCV   64 (824)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCcc
Confidence            6899999999999987776665543

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=96.65  E-value=0.02  Score=46.10  Aligned_cols=38  Identities=16%  Similarity=0.081  Sum_probs=24.5

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcC
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTP   82 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p   82 (182)
                      +..++.||+|+|||..+ .++...+.++..+.+++++..
T Consensus       137 n~l~l~G~~G~GKThL~-~ai~~~l~~~~~~~~v~yi~~  174 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLL-HAIGNEILENNPNAKVVYVSS  174 (405)
T ss_pred             CeEEEECCCCCcHHHHH-HHHHHHHHHhCCCCcEEEEEH
Confidence            35789999999999875 344444443322446777743

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).

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=96.61  E-value=0.012  Score=48.75  Aligned_cols=26  Identities=19%  Similarity=0.169  Sum_probs=20.3

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhc
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      +..+++||.|+|||..+.+.+-....
T Consensus        44 ~a~Lf~Gp~G~GKTT~ArilAk~Lnc   69 (507)
T PRK06645         44 GGYLLTGIRGVGKTTSARIIAKAVNC   69 (507)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhcC
Confidence            46899999999999997666555433

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=96.58  E-value=0.0089  Score=56.87  Aligned_cols=63  Identities=27%  Similarity=0.278  Sum_probs=45.3

Q ss_pred             CCChHHHHhhhhhhhC--CCcEEEECCCCChHHHHHH---HHHHHhhccCCCCeeEEEEcCCHHHHHHHH
Q psy4275          27 KTPTEIQKAIIPHVLN--DEDCIGCAKTGSGKTLAFA---LPILQKWCEDPYGIFALVLTPTRELAYQIG   91 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~--~~~~li~~~tg~GKT~~~~---~~~~~~~~~~~~~~~~lil~p~~~l~~q~~   91 (182)
                      ..+++.|++++..+..  ++.++++|+.|+|||+...   -++... ... .+.+++.++||..-+..+.
T Consensus      1018 ~~Lt~~Q~~Ai~~il~~~~~~~~i~G~AGtGKTt~l~~~~~~i~~~-~~~-~g~~v~glApT~~Aa~~L~ 1085 (1960)
T TIGR02760      1018 ERLTHGQKQAIHLIISTKDRFVAVQGLAGVGKTTMLESRYKPVLQA-FES-EQLQVIGLAPTHEAVGELK 1085 (1960)
T ss_pred             CCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHhHHHHHHHHHHH-HHh-cCCeEEEEeChHHHHHHHH
Confidence            4689999999999765  4677889999999998752   122222 222 2567899999977766553

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=96.57  E-value=0.01  Score=51.14  Aligned_cols=25  Identities=20%  Similarity=0.141  Sum_probs=18.9

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhc
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      -.|++|+.|+|||..+....-....
T Consensus        40 AyLFtGPpGvGKTTlAriLAKaLnC   64 (830)
T PRK07003         40 AYLFTGTRGVGKTTLSRIFAKALNC   64 (830)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhcC
Confidence            3589999999999987665555443

>PRK04195 replication factor C large subunit; Provisional

Probab=96.57  E-value=0.038  Score=45.67  Aligned_cols=23  Identities=17%  Similarity=0.031  Sum_probs=18.2

Q ss_pred             CCcEEEECCCCChHHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPIL   65 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~   65 (182)
                      .+.+++.||+|+|||..+...+-
T Consensus        39 ~~~lLL~GppG~GKTtla~ala~   61 (482)
T PRK04195         39 KKALLLYGPPGVGKTSLAHALAN   61 (482)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999988644433

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=96.57  E-value=0.013  Score=49.33  Aligned_cols=26  Identities=23%  Similarity=0.221  Sum_probs=19.6

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhc
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      +..+++||.|+|||.++-..+-....
T Consensus        39 hayLf~Gp~GtGKTt~Ak~lAkal~c   64 (559)
T PRK05563         39 HAYLFSGPRGTGKTSAAKIFAKAVNC   64 (559)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhcC
Confidence            34688999999999997666555433

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=96.57  E-value=0.017  Score=45.69  Aligned_cols=24  Identities=25%  Similarity=0.364  Sum_probs=18.0

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhh
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKW   68 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~   68 (182)
                      .+.++.||+|+|||...- .++..+
T Consensus        41 ~~i~I~G~~GtGKT~l~~-~~~~~l   64 (365)
T TIGR02928        41 SNVFIYGKTGTGKTAVTK-YVMKEL   64 (365)
T ss_pred             CcEEEECCCCCCHHHHHH-HHHHHH
Confidence            589999999999998753 344333

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.

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.56  E-value=0.017  Score=46.07  Aligned_cols=86  Identities=20%  Similarity=0.169  Sum_probs=44.9

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC--HH-HHHHHHHHHHHhhccCCceEEEEEcCCchhhhhH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT--RE-LAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGK  119 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~--~~-l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  119 (182)
                      ++.+.+.||+|+|||..+.-.+... ...  +.++.+++-.  +. -++|    |+.+.+..++.+..............
T Consensus       206 ~~ii~lvGptGvGKTTt~akLA~~l-~~~--g~~V~lItaDtyR~gAveQ----Lk~yae~lgvpv~~~~dp~dL~~al~  278 (407)
T PRK12726        206 HRIISLIGQTGVGKTTTLVKLGWQL-LKQ--NRTVGFITTDTFRSGAVEQ----FQGYADKLDVELIVATSPAELEEAVQ  278 (407)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH-HHc--CCeEEEEeCCccCccHHHH----HHHHhhcCCCCEEecCCHHHHHHHHH
Confidence            5677899999999998866555443 232  3456555532  22 2334    44455555555543221111111111


Q ss_pred             Hhc--CC-CcEEEEChHHH
Q psy4275         120 ELA--KK-PHIVIATPGRL  135 (182)
Q Consensus       120 ~~~--~~-~~Ilv~T~~~l  135 (182)
                      ...  ++ --|+|-|++..
T Consensus       279 ~l~~~~~~D~VLIDTAGr~  297 (407)
T PRK12726        279 YMTYVNCVDHILIDTVGRN  297 (407)
T ss_pred             HHHhcCCCCEEEEECCCCC
Confidence            121  23 34888898874

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=96.55  E-value=0.03  Score=44.60  Aligned_cols=26  Identities=27%  Similarity=0.349  Sum_probs=19.0

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhcc
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCE   70 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~   70 (182)
                      .|+++.|+||+|||.+.- .++..+..
T Consensus        43 ~n~~iyG~~GTGKT~~~~-~v~~~l~~   68 (366)
T COG1474          43 SNIIIYGPTGTGKTATVK-FVMEELEE   68 (366)
T ss_pred             ccEEEECCCCCCHhHHHH-HHHHHHHh
Confidence            379999999999999854 44444433

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.55  E-value=0.031  Score=45.30  Aligned_cols=87  Identities=17%  Similarity=0.078  Sum_probs=45.6

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhh----hhHH
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVD----QGKE  120 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~  120 (182)
                      -+.++|++|+|||+++.-.+.. +...  +.++++++....-+ ...++++.+....++.+....+......    ....
T Consensus       102 vi~lvG~~GvGKTTtaaKLA~~-l~~~--G~kV~lV~~D~~R~-aA~eQLk~~a~~~~vp~~~~~~~~dp~~i~~~~l~~  177 (429)
T TIGR01425       102 VIMFVGLQGSGKTTTCTKLAYY-YQRK--GFKPCLVCADTFRA-GAFDQLKQNATKARIPFYGSYTESDPVKIASEGVEK  177 (429)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH-HHHC--CCCEEEEcCcccch-hHHHHHHHHhhccCCeEEeecCCCCHHHHHHHHHHH
Confidence            4678899999999886544443 2222  44677666432111 1223455555555666654333222100    1111


Q ss_pred             h-cCCCc-EEEEChHHH
Q psy4275         121 L-AKKPH-IVIATPGRL  135 (182)
Q Consensus       121 ~-~~~~~-Ilv~T~~~l  135 (182)
                      . .++++ |+|-||+..
T Consensus       178 ~~~~~~DvViIDTaGr~  194 (429)
T TIGR01425       178 FKKENFDIIIVDTSGRH  194 (429)
T ss_pred             HHhCCCCEEEEECCCCC
Confidence            1 12444 788999876

This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=96.54  E-value=0.032  Score=41.17  Aligned_cols=39  Identities=15%  Similarity=0.043  Sum_probs=28.4

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcC
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTP   82 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p   82 (182)
                      ..|...++.|++|+|||..+...+.+.+.+   +..++++..
T Consensus        18 ~~G~~~~i~G~~G~GKT~l~~~~~~~~~~~---g~~~~~is~   56 (229)
T TIGR03881        18 PRGFFVAVTGEPGTGKTIFCLHFAYKGLRD---GDPVIYVTT   56 (229)
T ss_pred             cCCeEEEEECCCCCChHHHHHHHHHHHHhc---CCeEEEEEc
Confidence            447789999999999999876666555433   446777764

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.

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.53  E-value=0.0095  Score=50.51  Aligned_cols=25  Identities=20%  Similarity=0.166  Sum_probs=19.7

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhc
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      -.|++|+.|+|||..+....-....
T Consensus        40 A~LFtGP~GvGKTTLAriLAkaLnC   64 (700)
T PRK12323         40 AYLFTGTRGVGKTTLSRILAKSLNC   64 (700)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhcC
Confidence            3589999999999997766665544

>PRK11823 DNA repair protein RadA; Provisional

Probab=96.49  E-value=0.026  Score=46.18  Aligned_cols=51  Identities=18%  Similarity=0.033  Sum_probs=33.7

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHh
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVL   97 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~   97 (182)
                      |.-.++.|++|+|||+.++..+.....+   +.+++|+.-... .+|+....+.+
T Consensus        80 Gs~~lI~G~pG~GKTtL~lq~a~~~a~~---g~~vlYvs~Ees-~~qi~~ra~rl  130 (446)
T PRK11823         80 GSVVLIGGDPGIGKSTLLLQVAARLAAA---GGKVLYVSGEES-ASQIKLRAERL  130 (446)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHhc---CCeEEEEEcccc-HHHHHHHHHHc
Confidence            5678899999999999866665554422   457899886543 34554444433

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=96.48  E-value=0.014  Score=49.86  Aligned_cols=25  Identities=20%  Similarity=0.189  Sum_probs=19.4

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhc
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      ..+++||.|+|||..+...+-....
T Consensus        40 a~Lf~GP~GvGKTTlAriLAk~LnC   64 (709)
T PRK08691         40 AYLLTGTRGVGKTTIARILAKSLNC   64 (709)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHhcc
Confidence            4699999999999987666555433

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=96.47  E-value=0.034  Score=41.33  Aligned_cols=42  Identities=17%  Similarity=-0.016  Sum_probs=30.8

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      +..|.-.++.|++|+|||..++-.+.+.+.+.  +..++++...
T Consensus        10 l~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~--g~~vly~s~E   51 (242)
T cd00984          10 LQPGDLIIIAARPSMGKTAFALNIAENIAKKQ--GKPVLFFSLE   51 (242)
T ss_pred             CCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhC--CCceEEEeCC
Confidence            44577889999999999998776666665553  3467888743

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.

>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=96.47  E-value=0.021  Score=42.15  Aligned_cols=37  Identities=19%  Similarity=0.101  Sum_probs=23.8

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcC
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTP   82 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p   82 (182)
                      .+++.||+|+|||-. +.++...+.+...+.+++|+..
T Consensus        36 ~l~l~G~~G~GKTHL-L~Ai~~~~~~~~~~~~v~y~~~   72 (219)
T PF00308_consen   36 PLFLYGPSGLGKTHL-LQAIANEAQKQHPGKRVVYLSA   72 (219)
T ss_dssp             EEEEEESTTSSHHHH-HHHHHHHHHHHCTTS-EEEEEH
T ss_pred             ceEEECCCCCCHHHH-HHHHHHHHHhccccccceeecH
Confidence            479999999999975 4455554443322457777754

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.

>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=96.45  E-value=0.011  Score=42.92  Aligned_cols=57  Identities=18%  Similarity=0.130  Sum_probs=31.9

Q ss_pred             EEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcC--CHHHHHHHHHHHHHhhccCCceEEEE
Q psy4275          46 CIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTP--TRELAYQIGDQFLVLGKVMNLRVSII  108 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p--~~~l~~q~~~~~~~~~~~~~~~~~~~  108 (182)
                      +++.||||+|||++..-.+.+...+   +.++.+++-  .+.-+   .+.++.+.+..++.+...
T Consensus         4 i~lvGptGvGKTTt~aKLAa~~~~~---~~~v~lis~D~~R~ga---~eQL~~~a~~l~vp~~~~   62 (196)
T PF00448_consen    4 IALVGPTGVGKTTTIAKLAARLKLK---GKKVALISADTYRIGA---VEQLKTYAEILGVPFYVA   62 (196)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHT---T--EEEEEESTSSTHH---HHHHHHHHHHHTEEEEES
T ss_pred             EEEECCCCCchHhHHHHHHHHHhhc---cccceeecCCCCCccH---HHHHHHHHHHhccccchh
Confidence            5789999999999866555444444   334544442  33222   234445555556666543

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 ....

>PF03237 Terminase_6: Terminase-like family; InterPro: IPR004921 The terminase is a component of the molecular motor that translocates genomic DNA into empty capsids during DNA packaging []

Probab=96.43  E-value=0.063  Score=42.09  Aligned_cols=106  Identities=17%  Similarity=0.149  Sum_probs=52.5

Q ss_pred             EEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHH---HHHHHhhccCCceEEEE--EcCCchhhhhHHh
Q psy4275          47 IGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIG---DQFLVLGKVMNLRVSII--TGGMDMVDQGKEL  121 (182)
Q Consensus        47 li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~---~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~  121 (182)
                      ++.++.|+|||......++..+...+....+++...+.++...+.   ..+..+... .+....-  .+..-      .+
T Consensus         1 ~i~~~r~~GKT~~~~~~~~~~~~~~~~~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~------~~   73 (384)
T PF03237_consen    1 LINGGRGSGKTTLIAIWFLWWALTRPPGRRVIIASTYRQARDIFGRFWKGIIELLPS-WFEIKFNEWNDRKI------IL   73 (384)
T ss_dssp             -EEE-SSS-HHHHHHHHHHHHHHSSSS--EEEEEESSHHHHHHHHHHHHHHHHTS-T-TTS--EEEE-SSEE------EE
T ss_pred             CCcCCccccHHHHHHHHHHHHHhhCCCCcEEEEecCHHHHHHHHHHhHHHHHHHHHH-hcCcccccCCCCcE------Ee
Confidence            467899999999988888877777654446666655555555432   333344333 2222221  11111      11


Q ss_pred             cCCCcEEEEChHHH--HHHHhcCCCCCCCCccEEEEeccccccccC
Q psy4275         122 AKKPHIVIATPGRL--ADHLDTCNTFSLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus       122 ~~~~~Ilv~T~~~l--~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~  165 (182)
                      .++..|.+.+...-  ..-++.      ...+++++||+-.+.+..
T Consensus        74 ~nG~~i~~~~~~~~~~~~~~~G------~~~~~i~iDE~~~~~~~~  113 (384)
T PF03237_consen   74 PNGSRIQFRGADSPDSGDNIRG------FEYDLIIIDEAAKVPDDA  113 (384)
T ss_dssp             TTS-EEEEES-----SHHHHHT------S--SEEEEESGGGSTTHH
T ss_pred             cCceEEEEeccccccccccccc------cccceeeeeecccCchHH
Confidence            45666666663321  122222      346799999998776544

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.

>PHA03368 DNA packaging terminase subunit 1; Provisional

Probab=96.42  E-value=0.033  Score=47.28  Aligned_cols=116  Identities=15%  Similarity=0.118  Sum_probs=70.1

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccC-Cce-EEEEEcCCchhhhhHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVM-NLR-VSIITGGMDMVDQGKE  120 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~-~~~-~~~~~~~~~~~~~~~~  120 (182)
                      .+-.++..|--.|||+... +++..+...-.+.++++++|....++.+.++++...+.. +-+ +....| ...   ...
T Consensus       254 qk~tVflVPRR~GKTwivv-~iI~~ll~s~~Gi~IgytAH~~~ts~~vF~eI~~~le~~f~~~~v~~vkG-e~I---~i~  328 (738)
T PHA03368        254 QRATVFLVPRRHGKTWFLV-PLIALALATFRGIKIGYTAHIRKATEPVFEEIGARLRQWFGASRVDHVKG-ETI---SFS  328 (738)
T ss_pred             ccceEEEecccCCchhhHH-HHHHHHHHhCCCCEEEEEcCcHHHHHHHHHHHHHHHhhhcchhheeeecC-cEE---EEE
Confidence            4678888999999999765 444444433227799999999999999988888765532 111 222223 111   001


Q ss_pred             hcCC--CcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHH
Q psy4275         121 LAKK--PHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFF  170 (182)
Q Consensus       121 ~~~~--~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~  170 (182)
                      ..++  ..|...+.       +..+...=..++++|+|||+.+.+.-....+
T Consensus       329 f~nG~kstI~FaSa-------rntNsiRGqtfDLLIVDEAqFIk~~al~~il  373 (738)
T PHA03368        329 FPDGSRSTIVFASS-------HNTNGIRGQDFNLLFVDEANFIRPDAVQTIM  373 (738)
T ss_pred             ecCCCccEEEEEec-------cCCCCccCCcccEEEEechhhCCHHHHHHHH
Confidence            1222  24555531       2223333346889999999988775444433

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.42  E-value=0.015  Score=46.91  Aligned_cols=91  Identities=23%  Similarity=0.153  Sum_probs=42.8

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA  122 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  122 (182)
                      ++.+.+.||||+|||+.....+...........-.++.+.+.-.  -..+.+..+.+..|+.+...............+.
T Consensus       191 g~vi~lvGpnG~GKTTtlakLA~~~~~~~~~~~v~~i~~d~~ri--galEQL~~~a~ilGvp~~~v~~~~dl~~al~~l~  268 (420)
T PRK14721        191 GGVYALIGPTGVGKTTTTAKLAARAVIRHGADKVALLTTDSYRI--GGHEQLRIYGKLLGVSVRSIKDIADLQLMLHELR  268 (420)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecCCcch--hHHHHHHHHHHHcCCceecCCCHHHHHHHHHHhc
Confidence            55688899999999998654443332222111123344443222  1122344444444555543333222222222223


Q ss_pred             CCCcEEEEChHHH
Q psy4275         123 KKPHIVIATPGRL  135 (182)
Q Consensus       123 ~~~~Ilv~T~~~l  135 (182)
                      +.-.|+|-|+++.
T Consensus       269 ~~d~VLIDTaGrs  281 (420)
T PRK14721        269 GKHMVLIDTVGMS  281 (420)
T ss_pred             CCCEEEecCCCCC
Confidence            3344666665443

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=96.42  E-value=0.017  Score=45.63  Aligned_cols=39  Identities=13%  Similarity=0.173  Sum_probs=25.1

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      +..++++||||+|||+.. ..++..+.... +.+++.+-..
T Consensus       122 ~g~ili~G~tGSGKTT~l-~al~~~i~~~~-~~~i~tiEdp  160 (343)
T TIGR01420       122 RGLILVTGPTGSGKSTTL-ASMIDYINKNA-AGHIITIEDP  160 (343)
T ss_pred             CcEEEEECCCCCCHHHHH-HHHHHhhCcCC-CCEEEEEcCC
Confidence            568899999999999985 44444443322 3355555443

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.

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.41  E-value=0.01  Score=50.30  Aligned_cols=24  Identities=21%  Similarity=0.195  Sum_probs=18.9

Q ss_pred             EEEECCCCChHHHHHHHHHHHhhc
Q psy4275          46 CIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      .+++||.|+|||..+.+..-....
T Consensus        41 ~Lf~Gp~GvGKTtlAr~lAk~LnC   64 (618)
T PRK14951         41 YLFTGTRGVGKTTVSRILAKSLNC   64 (618)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhcC
Confidence            489999999999998766555444

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.41  E-value=0.016  Score=46.45  Aligned_cols=85  Identities=20%  Similarity=0.132  Sum_probs=43.6

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC--H-HHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT--R-ELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKE  120 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~--~-~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  120 (182)
                      +.+.+.||+|+|||+.+...+.... ..  +.++.++...  + +.++|+.    .+....++.+...............
T Consensus       242 ~vI~LVGptGvGKTTTiaKLA~~L~-~~--GkkVglI~aDt~RiaAvEQLk----~yae~lgipv~v~~d~~~L~~aL~~  314 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAKMAWQFH-GK--KKTVGFITTDHSRIGTVQQLQ----DYVKTIGFEVIAVRDEAAMTRALTY  314 (436)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHH-Hc--CCcEEEEecCCcchHHHHHHH----HHhhhcCCcEEecCCHHHHHHHHHH
Confidence            4678999999999998665554432 22  4456555542  2 2344444    3333445555433222222111112


Q ss_pred             hcC--CC-cEEEEChHHH
Q psy4275         121 LAK--KP-HIVIATPGRL  135 (182)
Q Consensus       121 ~~~--~~-~Ilv~T~~~l  135 (182)
                      +..  ++ -|+|-|++..
T Consensus       315 lk~~~~~DvVLIDTaGRs  332 (436)
T PRK11889        315 FKEEARVDYILIDTAGKN  332 (436)
T ss_pred             HHhccCCCEEEEeCcccc
Confidence            221  22 3777777764

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=96.39  E-value=0.043  Score=48.33  Aligned_cols=21  Identities=24%  Similarity=0.248  Sum_probs=15.6

Q ss_pred             EEECCCCChHHHHHHHHHHHhh
Q psy4275          47 IGCAKTGSGKTLAFALPILQKW   68 (182)
Q Consensus        47 li~~~tg~GKT~~~~~~~~~~~   68 (182)
                      ++.|+||+|||++.-. ++..+
T Consensus       785 YIyG~PGTGKTATVK~-VLrEL  805 (1164)
T PTZ00112        785 YISGMPGTGKTATVYS-VIQLL  805 (1164)
T ss_pred             EEECCCCCCHHHHHHH-HHHHH
Confidence            5899999999998544 33433

>PRK08727 hypothetical protein; Validated

Probab=96.38  E-value=0.012  Score=43.84  Aligned_cols=35  Identities=17%  Similarity=-0.005  Sum_probs=22.4

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      +.+++.||+|+|||-.+.... ..+.+.  +.+++|+.
T Consensus        42 ~~l~l~G~~G~GKThL~~a~~-~~~~~~--~~~~~y~~   76 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLALALC-AAAEQA--GRSSAYLP   76 (233)
T ss_pred             CeEEEECCCCCCHHHHHHHHH-HHHHHc--CCcEEEEe
Confidence            458999999999997644333 333332  34666664

>COG4626 Phage terminase-like protein, large subunit [General function prediction only]

Probab=96.36  E-value=0.019  Score=47.46  Aligned_cols=73  Identities=16%  Similarity=0.053  Sum_probs=53.8

Q ss_pred             CChHHHHhhhhhhhC------C----CcEEEECCCCChHHHHHHHHHH-HhhccCCCCeeEEEEcCCHHHHHHHHHHHHH
Q psy4275          28 TPTEIQKAIIPHVLN------D----EDCIGCAKTGSGKTLAFALPIL-QKWCEDPYGIFALVLTPTRELAYQIGDQFLV   96 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~------~----~~~li~~~tg~GKT~~~~~~~~-~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~   96 (182)
                      .+-|||+..+..+..      +    +-++|..|-+-|||..+...++ ..+..+..+..+.+++|+...+.+..+.++.
T Consensus        61 ~l~PwQkFiia~l~G~~~k~T~~rrf~e~fI~v~RkngKt~l~A~i~~~~~l~~~~~~~~~~i~A~s~~qa~~~F~~ar~  140 (546)
T COG4626          61 SLEPWQKFIVAALFGFYDKQTGIRRFKEAFIFIPRKNGKSTLAAGIMMTALLLNWRSGAGIYILAPSVEQAANSFNPARD  140 (546)
T ss_pred             ccchHHHHHHHHHhceeecCCCceEEEEEEEEEecCCchHHHHHHHHHHHHHhhhhcCCcEEEEeccHHHHHHhhHHHHH
Confidence            678999999988773      1    2578889999999987663333 3344444566899999999988888777776


Q ss_pred             hhcc
Q psy4275          97 LGKV  100 (182)
Q Consensus        97 ~~~~  100 (182)
                      ....
T Consensus       141 mv~~  144 (546)
T COG4626         141 MVKR  144 (546)
T ss_pred             HHHh
Confidence            5444

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=96.35  E-value=0.022  Score=43.00  Aligned_cols=117  Identities=15%  Similarity=0.126  Sum_probs=61.7

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHH-HHHHHhhccCCceEEEE-EcCCchhhh
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIG-DQFLVLGKVMNLRVSII-TGGMDMVDQ  117 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~-~~~~~~~~~~~~~~~~~-~~~~~~~~~  117 (182)
                      +..|.-.++.|.+|.|||..++-.+.+.+.+.  +..++|+...-.- +++. ..+... .  ++....+ .|.....+.
T Consensus        16 ~~~g~L~vi~a~pg~GKT~~~l~ia~~~a~~~--~~~vly~SlEm~~-~~l~~R~la~~-s--~v~~~~i~~g~l~~~e~   89 (259)
T PF03796_consen   16 LRPGELTVIAARPGVGKTAFALQIALNAALNG--GYPVLYFSLEMSE-EELAARLLARL-S--GVPYNKIRSGDLSDEEF   89 (259)
T ss_dssp             B-TT-EEEEEESTTSSHHHHHHHHHHHHHHTT--SSEEEEEESSS-H-HHHHHHHHHHH-H--TSTHHHHHCCGCHHHHH
T ss_pred             CCcCcEEEEEecccCCchHHHHHHHHHHHHhc--CCeEEEEcCCCCH-HHHHHHHHHHh-h--cchhhhhhccccCHHHH
Confidence            44466788899999999999877777776654  3578888764332 2222 222222 1  1111111 121111111


Q ss_pred             h------HHhcCCCcEEE-E----ChHHHHHHHhcCCCCCCCCccEEEEecccccccc
Q psy4275         118 G------KELAKKPHIVI-A----TPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus       118 ~------~~~~~~~~Ilv-~----T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~  164 (182)
                      .      ..+ .+..+.+ .    |++.+...++.... ....+++||+|-+|.+...
T Consensus        90 ~~~~~~~~~l-~~~~l~i~~~~~~~~~~i~~~i~~~~~-~~~~~~~v~IDyl~ll~~~  145 (259)
T PF03796_consen   90 ERLQAAAEKL-SDLPLYIEDTPSLTIDDIESKIRRLKR-EGKKVDVVFIDYLQLLKSE  145 (259)
T ss_dssp             HHHHHHHHHH-HTSEEEEEESSS-BHHHHHHHHHHHHH-HSTTEEEEEEEEGGGSBTS
T ss_pred             HHHHHHHHHH-hhCcEEEECCCCCCHHHHHHHHHHHHh-hccCCCEEEechHHHhcCC
Confidence            1      112 2333443 3    44555555544221 1267889999999998874

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 ....

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=96.35  E-value=0.045  Score=44.73  Aligned_cols=38  Identities=16%  Similarity=0.117  Sum_probs=24.8

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcC
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTP   82 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p   82 (182)
                      +..++.||+|+|||-.+. ++...+.....+.+++|+..
T Consensus       131 n~l~lyG~~G~GKTHLl~-ai~~~l~~~~~~~~v~yi~~  168 (440)
T PRK14088        131 NPLFIYGGVGLGKTHLLQ-SIGNYVVQNEPDLRVMYITS  168 (440)
T ss_pred             CeEEEEcCCCCcHHHHHH-HHHHHHHHhCCCCeEEEEEH
Confidence            468999999999997754 33343433322446777754

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=96.33  E-value=0.0097  Score=48.61  Aligned_cols=42  Identities=26%  Similarity=0.218  Sum_probs=29.6

Q ss_pred             ChHHHHhhhhhhhCCC--cEEEECCCCChHHHHHHHHHHHhhccC
Q psy4275          29 PTEIQKAIIPHVLNDE--DCIGCAKTGSGKTLAFALPILQKWCED   71 (182)
Q Consensus        29 ~~~~Q~~~~~~~~~~~--~~li~~~tg~GKT~~~~~~~~~~~~~~   71 (182)
                      ..+.|...+..+.+..  =+++.||||||||+. ++.++..+...
T Consensus       242 ~~~~~~~~~~~~~~~p~GliLvTGPTGSGKTTT-LY~~L~~ln~~  285 (500)
T COG2804         242 MSPFQLARLLRLLNRPQGLILVTGPTGSGKTTT-LYAALSELNTP  285 (500)
T ss_pred             CCHHHHHHHHHHHhCCCeEEEEeCCCCCCHHHH-HHHHHHHhcCC
Confidence            4677777777776643  466779999999998 55666655543

>KOG1016|consensus

Probab=96.31  E-value=0.022  Score=48.99  Aligned_cols=124  Identities=15%  Similarity=0.163  Sum_probs=71.3

Q ss_pred             CCHHHHHHHHHC---CCCCChHHHHhhhhhhhC--CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHH
Q psy4275          13 LNPWLIRQCQTI---GVKTPTEIQKAIIPHVLN--DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELA   87 (182)
Q Consensus        13 l~~~i~~~l~~~---~~~~~~~~Q~~~~~~~~~--~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~   87 (182)
                      +-+++.+.++..   |+..+++--.+.+....+  |=.+|+...+|.|||+. .+...+.+.++-....+|+|+|-..|.
T Consensus       247 lapqla~v~kPHQiGGiRFlYDN~iESl~rykkSsGFGCILAHSMGLGKTlQ-VisF~diflRhT~AKtVL~ivPiNTlQ  325 (1387)
T KOG1016|consen  247 LAPQLAHVLKPHQIGGIRFLYDNTIESLGRYKKSSGFGCILAHSMGLGKTLQ-VISFSDIFLRHTKAKTVLVIVPINTLQ  325 (1387)
T ss_pred             ehhhhHhhcCccccCcEEEehhhHHHHHhhccccCCcceeeeeccccCceeE-EeehhHHHhhcCccceEEEEEehHHHH
Confidence            455566665433   222333333333333322  45788888999999986 344455555544466899999987774


Q ss_pred             HHHHHHHHHhhccC---------CceEEEEEcCCch-hhh---hHHhcCCCcEEEEChHHHHHH
Q psy4275          88 YQIGDQFLVLGKVM---------NLRVSIITGGMDM-VDQ---GKELAKKPHIVIATPGRLADH  138 (182)
Q Consensus        88 ~q~~~~~~~~~~~~---------~~~~~~~~~~~~~-~~~---~~~~~~~~~Ilv~T~~~l~~~  138 (182)
                      + |..++..|....         .+.+.++.++... ..+   ...+..+..|++.-.+++.-+
T Consensus       326 N-WlsEfnmWiP~y~sD~~vrpR~F~vf~LnD~~KT~~~Rakvi~~Wv~~GGVlLvGYemfRLL  388 (1387)
T KOG1016|consen  326 N-WLSEFNMWIPKYFSDTGVRPRSFEVFLLNDGVKTFDQRAKVIEQWVQTGGVLLVGYEMFRLL  388 (1387)
T ss_pred             H-HHHHhhhhcCCCcccCCCccceeEEEEecCchhhHHHHHHHHHHHhccCCEEEehHHHHHHH
Confidence            3 444444444331         2456666655433 222   233445778999888887543

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=96.31  E-value=0.0064  Score=43.37  Aligned_cols=47  Identities=21%  Similarity=0.220  Sum_probs=27.9

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHH
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQI   90 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~   90 (182)
                      +.+++++++.|++|+|||..+...+.+.+. .  +..++++ +..+|.+.+
T Consensus        44 ~~~~~~l~l~G~~G~GKThLa~ai~~~~~~-~--g~~v~f~-~~~~L~~~l   90 (178)
T PF01695_consen   44 IENGENLILYGPPGTGKTHLAVAIANEAIR-K--GYSVLFI-TASDLLDEL   90 (178)
T ss_dssp             -SC--EEEEEESTTSSHHHHHHHHHHHHHH-T--T--EEEE-EHHHHHHHH
T ss_pred             cccCeEEEEEhhHhHHHHHHHHHHHHHhcc-C--CcceeEe-ecCceeccc
Confidence            344789999999999999886555444433 2  4456655 444555544

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.

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.31  E-value=0.015  Score=48.97  Aligned_cols=24  Identities=21%  Similarity=0.217  Sum_probs=19.1

Q ss_pred             EEEECCCCChHHHHHHHHHHHhhc
Q psy4275          46 CIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      .+++||.|+|||..+.+.+-....
T Consensus        38 ~Lf~Gp~G~GKTt~A~~lAk~l~c   61 (584)
T PRK14952         38 YLFSGPRGCGKTSSARILARSLNC   61 (584)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhcc
Confidence            589999999999998766655443

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=96.30  E-value=0.042  Score=43.86  Aligned_cols=50  Identities=14%  Similarity=-0.047  Sum_probs=32.1

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLV   96 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~   96 (182)
                      |.-+++.|++|+|||..++..+......   +.+++|+.-... ..|+....++
T Consensus        82 GslvLI~G~pG~GKStLllq~a~~~a~~---g~~VlYvs~EEs-~~qi~~Ra~r  131 (372)
T cd01121          82 GSVILIGGDPGIGKSTLLLQVAARLAKR---GGKVLYVSGEES-PEQIKLRADR  131 (372)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHhc---CCeEEEEECCcC-HHHHHHHHHH
Confidence            5678889999999999866555444332   357888876433 3444433333

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.

>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]

Probab=96.29  E-value=0.073  Score=38.33  Aligned_cols=104  Identities=15%  Similarity=0.143  Sum_probs=58.3

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA  122 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  122 (182)
                      ++-.++++|+.+|||.-.+..+-....+   +.++++..|...-             .  +....+.+....        
T Consensus         4 g~l~~i~gpM~SGKT~eLl~r~~~~~~~---g~~v~vfkp~iD~-------------R--~~~~~V~Sr~G~--------   57 (201)
T COG1435           4 GWLEFIYGPMFSGKTEELLRRARRYKEA---GMKVLVFKPAIDT-------------R--YGVGKVSSRIGL--------   57 (201)
T ss_pred             EEEEEEEccCcCcchHHHHHHHHHHHHc---CCeEEEEeccccc-------------c--cccceeeeccCC--------
Confidence            3446889999999999755444444344   5678888884222             1  111111111111        


Q ss_pred             CCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHHHHHHHHhh
Q psy4275         123 KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFFFFLKY  178 (182)
Q Consensus       123 ~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~~~~~~~~~  178 (182)
                      +..-++|-.+..+.+.+.....  ..+++.+.+||||-+..    +....+.++.+
T Consensus        58 ~~~A~~i~~~~~i~~~i~~~~~--~~~~~~v~IDEaQF~~~----~~v~~l~~lad  107 (201)
T COG1435          58 SSEAVVIPSDTDIFDEIAALHE--KPPVDCVLIDEAQFFDE----ELVYVLNELAD  107 (201)
T ss_pred             cccceecCChHHHHHHHHhccc--CCCcCEEEEehhHhCCH----HHHHHHHHHHh
Confidence            1223556666777777765321  11277999999996554    44445554443

>PRK05973 replicative DNA helicase; Provisional

Probab=96.29  E-value=0.014  Score=43.60  Aligned_cols=83  Identities=18%  Similarity=0.183  Sum_probs=50.8

Q ss_pred             CCCCCHHHHHHHHHCCCC----------CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEE
Q psy4275          10 DLKLNPWLIRQCQTIGVK----------TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALV   79 (182)
Q Consensus        10 ~~~l~~~i~~~l~~~~~~----------~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~li   79 (182)
                      ..++++-+.+.=.+.||.          ..+|. .+...-+..|.-.++.|++|+|||+.++-.+.+.+.+   +.+++|
T Consensus        22 ~~~~~~~~~~~a~~~g~~~w~~~~~~~~~~~p~-~~l~GGl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~~---Ge~vly   97 (237)
T PRK05973         22 NIPLHEALDRIAAEEGFSSWSLLAAKAAATTPA-EELFSQLKPGDLVLLGARPGHGKTLLGLELAVEAMKS---GRTGVF   97 (237)
T ss_pred             CCcHHHHHHHHHHHhccchHHHHHHhccCCCCH-HHhcCCCCCCCEEEEEeCCCCCHHHHHHHHHHHHHhc---CCeEEE
Confidence            345555555555555654          24442 2233455567788999999999999987777766544   456888


Q ss_pred             EcCCHHHHHHHHHHHHHh
Q psy4275          80 LTPTRELAYQIGDQFLVL   97 (182)
Q Consensus        80 l~p~~~l~~q~~~~~~~~   97 (182)
                      +.-... .+++.+.+..+
T Consensus        98 fSlEes-~~~i~~R~~s~  114 (237)
T PRK05973         98 FTLEYT-EQDVRDRLRAL  114 (237)
T ss_pred             EEEeCC-HHHHHHHHHHc
Confidence            864433 34454444443

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

Probab=96.29  E-value=0.063  Score=48.12  Aligned_cols=123  Identities=13%  Similarity=0.168  Sum_probs=92.1

Q ss_pred             HHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhc--c----------------------------CCCCeeEEEEc
Q psy4275          32 IQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWC--E----------------------------DPYGIFALVLT   81 (182)
Q Consensus        32 ~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~--~----------------------------~~~~~~~lil~   81 (182)
                      -|++.++.+..+-+++--..|-.=+|+-+.+.-+..+.  .                            -..++++.||.
T Consensus       731 k~KEkLK~Lr~~VDvLTLSATPIPRTL~Msm~GiRdlSvI~TPP~~R~pV~T~V~~~d~~~ireAI~REl~RgGQvfYv~  810 (1139)
T COG1197         731 KHKEKLKELRANVDVLTLSATPIPRTLNMSLSGIRDLSVIATPPEDRLPVKTFVSEYDDLLIREAILRELLRGGQVFYVH  810 (1139)
T ss_pred             cHHHHHHHHhccCcEEEeeCCCCcchHHHHHhcchhhhhccCCCCCCcceEEEEecCChHHHHHHHHHHHhcCCEEEEEe
Confidence            37778888888888888888888888765544433221  0                            02378999999


Q ss_pred             CCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHH----hcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEec
Q psy4275          82 PTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKE----LAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDE  157 (182)
Q Consensus        82 p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE  157 (182)
                      |..+-.+++++.++.+...  .++++.||.+...+....    +.++.+|+|||.      +=+ ..+++.+...+|+|-
T Consensus       811 NrV~~Ie~~~~~L~~LVPE--arI~vaHGQM~e~eLE~vM~~F~~g~~dVLv~TT------IIE-tGIDIPnANTiIIe~  881 (1139)
T COG1197         811 NRVESIEKKAERLRELVPE--ARIAVAHGQMRERELEEVMLDFYNGEYDVLVCTT------IIE-TGIDIPNANTIIIER  881 (1139)
T ss_pred             cchhhHHHHHHHHHHhCCc--eEEEEeecCCCHHHHHHHHHHHHcCCCCEEEEee------eee-cCcCCCCCceEEEec
Confidence            9999999999999998775  678899998876544433    345899999993      123 567899999999999


Q ss_pred             cccccc
Q psy4275         158 ADRLSL  163 (182)
Q Consensus       158 ~h~~~~  163 (182)
                      ||++.-
T Consensus       882 AD~fGL  887 (1139)
T COG1197         882 ADKFGL  887 (1139)
T ss_pred             cccccH
Confidence            999764

>TIGR00959 ffh signal recognition particle protein

Probab=96.27  E-value=0.048  Score=44.28  Aligned_cols=86  Identities=23%  Similarity=0.208  Sum_probs=44.8

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC--HHHHHHHHHHHHHhhccCCceEEEEEcCCchhhh----h
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT--RELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQ----G  118 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~--~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~  118 (182)
                      -++++|++|+|||+++.-.+.....+.  +.+++++.-.  +..+   .+.++.+....++.+.......+....    .
T Consensus       101 vi~~vG~~GsGKTTtaakLA~~l~~~~--g~kV~lV~~D~~R~~a---~~QL~~~a~~~gvp~~~~~~~~~P~~i~~~al  175 (428)
T TIGR00959       101 VILMVGLQGSGKTTTCGKLAYYLKKKQ--GKKVLLVACDLYRPAA---IEQLKVLGQQVGVPVFALGKGQSPVEIARRAL  175 (428)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHhC--CCeEEEEeccccchHH---HHHHHHHHHhcCCceEecCCCCCHHHHHHHHH
Confidence            477889999999998765555532222  3456666533  2221   223444445455555433222221111    1


Q ss_pred             -HHhcCCCc-EEEEChHHH
Q psy4275         119 -KELAKKPH-IVIATPGRL  135 (182)
Q Consensus       119 -~~~~~~~~-Ilv~T~~~l  135 (182)
                       ....++++ |+|-||+.+
T Consensus       176 ~~~~~~~~DvVIIDTaGr~  194 (428)
T TIGR00959       176 EYAKENGFDVVIVDTAGRL  194 (428)
T ss_pred             HHHHhcCCCEEEEeCCCcc
Confidence             11123454 888999864

This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.

>PRK08116 hypothetical protein; Validated

Probab=96.26  E-value=0.033  Score=42.43  Aligned_cols=41  Identities=22%  Similarity=0.227  Sum_probs=25.0

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAY   88 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~   88 (182)
                      ..+++.|++|+|||..+. ++...+...  +..++++ +...+..
T Consensus       115 ~gl~l~G~~GtGKThLa~-aia~~l~~~--~~~v~~~-~~~~ll~  155 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAA-CIANELIEK--GVPVIFV-NFPQLLN  155 (268)
T ss_pred             ceEEEECCCCCCHHHHHH-HHHHHHHHc--CCeEEEE-EHHHHHH
Confidence            349999999999998754 344444443  3345555 3334433

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.23  E-value=0.029  Score=46.59  Aligned_cols=22  Identities=23%  Similarity=0.194  Sum_probs=17.4

Q ss_pred             EEEECCCCChHHHHHHHHHHHh
Q psy4275          46 CIGCAKTGSGKTLAFALPILQK   67 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~   67 (182)
                      .+++||+|+|||..+...+-..
T Consensus        39 ~Lf~GppGtGKTTlA~~lA~~l   60 (504)
T PRK14963         39 YLFSGPRGVGKTTTARLIAMAV   60 (504)
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            4999999999999976554443

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=96.23  E-value=0.015  Score=49.49  Aligned_cols=24  Identities=25%  Similarity=0.198  Sum_probs=18.5

Q ss_pred             EEEECCCCChHHHHHHHHHHHhhc
Q psy4275          46 CIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      .++.||.|+|||..+...+-....
T Consensus        41 yLf~Gp~GvGKTTlAr~lAk~L~c   64 (647)
T PRK07994         41 YLFSGTRGVGKTTIARLLAKGLNC   64 (647)
T ss_pred             EEEECCCCCCHHHHHHHHHHhhhh
Confidence            489999999999987666554433

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A

Probab=96.22  E-value=0.039  Score=38.70  Aligned_cols=28  Identities=21%  Similarity=0.229  Sum_probs=20.5

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhccCC
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWCEDP   72 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~~~~   72 (182)
                      ..++.||.|+||+..+...+...+....
T Consensus        21 a~L~~G~~g~gk~~~a~~~a~~ll~~~~   48 (162)
T PF13177_consen   21 ALLFHGPSGSGKKTLALAFARALLCSNP   48 (162)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHC-TT-
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCC
Confidence            4699999999999987766666555543

...

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=96.21  E-value=0.011  Score=46.60  Aligned_cols=31  Identities=26%  Similarity=0.291  Sum_probs=22.8

Q ss_pred             hhhCCCcEEEECCCCChHHHHHHHHHHHhhcc
Q psy4275          39 HVLNDEDCIGCAKTGSGKTLAFALPILQKWCE   70 (182)
Q Consensus        39 ~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~   70 (182)
                      .+..+++++++||||+|||+.. .+++..+..
T Consensus       158 ~v~~~~nilI~G~tGSGKTTll-~aLl~~i~~  188 (344)
T PRK13851        158 CVVGRLTMLLCGPTGSGKTTMS-KTLISAIPP  188 (344)
T ss_pred             HHHcCCeEEEECCCCccHHHHH-HHHHcccCC
Confidence            3455889999999999999884 445554433

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=96.19  E-value=0.033  Score=45.36  Aligned_cols=87  Identities=20%  Similarity=0.153  Sum_probs=43.4

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchh----hhhHH
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMV----DQGKE  120 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~  120 (182)
                      .++++|++|+|||+++.-.+.. +...  +.++.++.....-. ...+.++.+....++.+..........    .....
T Consensus        97 vI~lvG~~GsGKTTtaakLA~~-L~~~--g~kV~lV~~D~~R~-aa~eQL~~la~~~gvp~~~~~~~~d~~~i~~~al~~  172 (437)
T PRK00771         97 TIMLVGLQGSGKTTTAAKLARY-FKKK--GLKVGLVAADTYRP-AAYDQLKQLAEKIGVPFYGDPDNKDAVEIAKEGLEK  172 (437)
T ss_pred             EEEEECCCCCcHHHHHHHHHHH-HHHc--CCeEEEecCCCCCH-HHHHHHHHHHHHcCCcEEecCCccCHHHHHHHHHHH
Confidence            5788899999999986555443 3332  44666665432111 123344445555555543321111111    11111


Q ss_pred             hcCCCcEEEEChHHH
Q psy4275         121 LAKKPHIVIATPGRL  135 (182)
Q Consensus       121 ~~~~~~Ilv~T~~~l  135 (182)
                      .....-|+|-|++..
T Consensus       173 ~~~~DvVIIDTAGr~  187 (437)
T PRK00771        173 FKKADVIIVDTAGRH  187 (437)
T ss_pred             hhcCCEEEEECCCcc
Confidence            122234788888655

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=96.19  E-value=0.062  Score=39.03  Aligned_cols=40  Identities=15%  Similarity=0.056  Sum_probs=29.5

Q ss_pred             CCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCH
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTR   84 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~   84 (182)
                      .|.-..+.||+|+|||..++..+......   +.+++|+.-..
T Consensus        11 ~g~i~~i~G~~GsGKT~l~~~~~~~~~~~---g~~v~yi~~e~   50 (209)
T TIGR02237        11 RGTITQIYGPPGSGKTNICMILAVNAARQ---GKKVVYIDTEG   50 (209)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEECCC
Confidence            35678899999999999887666655433   45788887753

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.17  E-value=0.015  Score=49.01  Aligned_cols=24  Identities=17%  Similarity=0.018  Sum_probs=18.5

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhh
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKW   68 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~   68 (182)
                      ..+++||.|+|||.++...+-...
T Consensus        40 ayLf~Gp~G~GKtt~A~~lak~l~   63 (576)
T PRK14965         40 AFLFTGARGVGKTSTARILAKALN   63 (576)
T ss_pred             EEEEECCCCCCHHHHHHHHHHhhc
Confidence            358999999999999766555543

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=96.17  E-value=0.029  Score=46.72  Aligned_cols=25  Identities=28%  Similarity=0.252  Sum_probs=18.7

Q ss_pred             EEEECCCCChHHHHHHHHHHHhhcc
Q psy4275          46 CIGCAKTGSGKTLAFALPILQKWCE   70 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~~~~   70 (182)
                      .+++||.|+|||..+...+-.....
T Consensus        39 yLf~Gp~G~GKTt~Ar~LAk~L~c~   63 (535)
T PRK08451         39 YLFSGLRGSGKTSSARIFARALVCE   63 (535)
T ss_pred             EEEECCCCCcHHHHHHHHHHHhcCC
Confidence            4899999999999876655554433

>PRK14974 cell division protein FtsY; Provisional

Probab=96.17  E-value=0.067  Score=42.07  Aligned_cols=55  Identities=15%  Similarity=0.145  Sum_probs=31.9

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC---HHHHHHHHHHHHHhhccCCceEE
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT---RELAYQIGDQFLVLGKVMNLRVS  106 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~---~~l~~q~~~~~~~~~~~~~~~~~  106 (182)
                      -+++.|++|+|||++....+ ..+...  +.+++++...   ....+|+..+.    ...++.+.
T Consensus       142 vi~~~G~~GvGKTTtiakLA-~~l~~~--g~~V~li~~Dt~R~~a~eqL~~~a----~~lgv~v~  199 (336)
T PRK14974        142 VIVFVGVNGTGKTTTIAKLA-YYLKKN--GFSVVIAAGDTFRAGAIEQLEEHA----ERLGVKVI  199 (336)
T ss_pred             EEEEEcCCCCCHHHHHHHHH-HHHHHc--CCeEEEecCCcCcHHHHHHHHHHH----HHcCCcee
Confidence            57788999999999854444 333332  4467666544   33445544433    33455543

>KOG0331|consensus

Probab=96.15  E-value=0.038  Score=45.60  Aligned_cols=72  Identities=10%  Similarity=0.128  Sum_probs=56.6

Q ss_pred             CCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhc----CCCcEEEEChHHHHHHHhcCCCCCCC
Q psy4275          73 YGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA----KKPHIVIATPGRLADHLDTCNTFSLN  148 (182)
Q Consensus        73 ~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~Ilv~T~~~l~~~~~~~~~~~~~  148 (182)
                      .++++||.|.++--++++...++..    ++++..+||+.+..++...+.    .++.|+|+|.-      .. +.++++
T Consensus       340 ~~~KvIIFc~tkr~~~~l~~~l~~~----~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATdV------Aa-RGLDi~  408 (519)
T KOG0331|consen  340 SEGKVIIFCETKRTCDELARNLRRK----GWPAVAIHGDKSQSERDWVLKGFREGKSPVLVATDV------AA-RGLDVP  408 (519)
T ss_pred             CCCcEEEEecchhhHHHHHHHHHhc----CcceeeecccccHHHHHHHHHhcccCCcceEEEccc------cc-ccCCCc
Confidence            3568999999999998887776664    588999999999887776654    36889999932      22 667888


Q ss_pred             CccEEEE
Q psy4275         149 RIKFLVL  155 (182)
Q Consensus       149 ~~~~iI~  155 (182)
                      ++++||-
T Consensus       409 dV~lVIn  415 (519)
T KOG0331|consen  409 DVDLVIN  415 (519)
T ss_pred             cccEEEe
Confidence            9998874

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=96.15  E-value=0.04  Score=42.68  Aligned_cols=29  Identities=24%  Similarity=0.195  Sum_probs=22.1

Q ss_pred             CCc-EEEECCCCChHHHHHHHHHHHhhccC
Q psy4275          43 DED-CIGCAKTGSGKTLAFALPILQKWCED   71 (182)
Q Consensus        43 ~~~-~li~~~tg~GKT~~~~~~~~~~~~~~   71 (182)
                      ..+ .++.||+|+|||..+....-......
T Consensus        23 ~~halL~~Gp~G~Gktt~a~~lA~~l~~~~   52 (325)
T COG0470          23 LPHALLFYGPPGVGKTTAALALAKELLCEN   52 (325)
T ss_pred             CCceeeeeCCCCCCHHHHHHHHHHHHhCCC
Confidence            456 99999999999999766665555443

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.14  E-value=0.019  Score=47.99  Aligned_cols=23  Identities=22%  Similarity=-0.036  Sum_probs=18.3

Q ss_pred             EEEECCCCChHHHHHHHHHHHhh
Q psy4275          46 CIGCAKTGSGKTLAFALPILQKW   68 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~~   68 (182)
                      .+++||.|+|||..+...+-...
T Consensus        41 ~Lf~Gp~GvGKTTlAr~lAk~L~   63 (546)
T PRK14957         41 YLFTGTRGVGKTTLGRLLAKCLN   63 (546)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhC
Confidence            68999999999999766655443

>PF02456 Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR003389 Va2 protein can interact with the adenoviral packaging signal and this interaction involves DNA sequences that have previously been demonstrated to be required for packaging []

Probab=96.13  E-value=0.012  Score=45.26  Aligned_cols=41  Identities=22%  Similarity=0.282  Sum_probs=26.9

Q ss_pred             EEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHH
Q psy4275          46 CIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELA   87 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~   87 (182)
                      .++.||||+||+-..--.+...+.+ +-.-.+++|+|....+
T Consensus        90 ~~VYGPTG~GKSqLlRNLis~~lI~-P~PETVfFItP~~~mI  130 (369)
T PF02456_consen   90 GVVYGPTGSGKSQLLRNLISCQLIQ-PPPETVFFITPQKDMI  130 (369)
T ss_pred             EEEECCCCCCHHHHHHHhhhcCccc-CCCCceEEECCCCCCC
Confidence            5678999999986532222233322 2234799999998875

During the course of lytic infection, the adenovirus major late promoter (MLP) is induced to high levels after replication of viral DNA has started. IVa2 is a transcriptional activator of the major late promoter [].; GO: 0019083 viral transcription

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.12  E-value=0.013  Score=49.46  Aligned_cols=26  Identities=19%  Similarity=0.148  Sum_probs=20.3

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhc
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      +..|+.||.|+|||.++.+.+-....
T Consensus        39 ha~Lf~GPpG~GKTtiArilAk~L~C   64 (624)
T PRK14959         39 PAYLFSGTRGVGKTTIARIFAKALNC   64 (624)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHhccc
Confidence            45778999999999998766655543

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=96.11  E-value=0.033  Score=39.86  Aligned_cols=26  Identities=19%  Similarity=0.184  Sum_probs=19.5

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhc
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      +..++.||.|+|||..+...+-....
T Consensus        15 ~~~L~~G~~G~gkt~~a~~~~~~l~~   40 (188)
T TIGR00678        15 HAYLFAGPEGVGKELLALALAKALLC   40 (188)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHcC
Confidence            45889999999999887655554443

At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.11  E-value=0.025  Score=45.52  Aligned_cols=25  Identities=28%  Similarity=0.187  Sum_probs=19.6

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhc
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      ..+++||.|+|||.++...+-....
T Consensus        40 a~lf~Gp~G~GKtt~A~~~a~~l~c   64 (397)
T PRK14955         40 GYIFSGLRGVGKTTAARVFAKAVNC   64 (397)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhcC
Confidence            4789999999999998766555444

>PF12846 AAA_10: AAA-like domain

Probab=96.11  E-value=0.012  Score=44.96  Aligned_cols=25  Identities=32%  Similarity=0.270  Sum_probs=19.4

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHh
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQK   67 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~   67 (182)
                      ++|+++.|+||+|||..+...+...
T Consensus         1 n~h~~i~G~tGsGKT~~~~~l~~~~   25 (304)
T PF12846_consen    1 NPHTLILGKTGSGKTTLLKNLLEQL   25 (304)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHH
Confidence            4689999999999998876444433

>KOG1133|consensus

Probab=96.11  E-value=0.0053  Score=51.75  Aligned_cols=43  Identities=26%  Similarity=0.340  Sum_probs=35.7

Q ss_pred             CChHHHHhhhhhhhC----CCcEEEECCCCChHHHHHHHHHHHhhcc
Q psy4275          28 TPTEIQKAIIPHVLN----DEDCIGCAKTGSGKTLAFALPILQKWCE   70 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~----~~~~li~~~tg~GKT~~~~~~~~~~~~~   70 (182)
                      .|+++|.+....+..    |+-.++..|||+|||++.+...+..+..
T Consensus        15 ~PYdIQ~~lM~elyrvLe~GkIgIfESPTGTGKSLSLiCaaltWL~~   61 (821)
T KOG1133|consen   15 TPYDIQEDLMRELYRVLEEGKIGIFESPTGTGKSLSLICAALTWLRD   61 (821)
T ss_pred             CchhHHHHHHHHHHHHHhcCCeeeeeCCCCCCchHHHHHHHHHHHHH
Confidence            789999888766554    8899999999999999888777776654

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=96.11  E-value=0.021  Score=48.05  Aligned_cols=25  Identities=24%  Similarity=0.098  Sum_probs=19.2

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhc
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      ..+++||.|+|||..+...+-....
T Consensus        40 ayLf~Gp~G~GKTt~Ar~lAk~L~c   64 (563)
T PRK06647         40 AYIFSGPRGVGKTSSARAFARCLNC   64 (563)
T ss_pred             EEEEECCCCCCHHHHHHHHHHhhcc
Confidence            4789999999999997665555443

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=96.11  E-value=0.032  Score=43.53  Aligned_cols=45  Identities=11%  Similarity=0.083  Sum_probs=33.6

Q ss_pred             CCChHHHHhhhhhhhC----CC---cEEEECCCCChHHHHHHHHHHHhhccC
Q psy4275          27 KTPTEIQKAIIPHVLN----DE---DCIGCAKTGSGKTLAFALPILQKWCED   71 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~----~~---~~li~~~tg~GKT~~~~~~~~~~~~~~   71 (182)
                      ..+.|||...+..+..    ++   -.++.||.|.||+..+...+-..+..+
T Consensus         3 ~~~yPW~~~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~   54 (319)
T PRK08769          3 SAFSPWQQRAYDQTVAALDAGRLGHGLLICGPEGLGKRAVALALAEHVLASG   54 (319)
T ss_pred             ccccccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHhCCC
Confidence            3678999998877654    33   478999999999998776665555543

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=96.09  E-value=0.023  Score=42.95  Aligned_cols=50  Identities=16%  Similarity=0.168  Sum_probs=34.4

Q ss_pred             CCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFL   95 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~   95 (182)
                      ++.++++.||+|+|||..+.....+.. ..  + .-++.++..+++.++...+.
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai~~~l~-~~--g-~sv~f~~~~el~~~Lk~~~~  153 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAIGNELL-KA--G-ISVLFITAPDLLSKLKAAFD  153 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHHHH-Hc--C-CeEEEEEHHHHHHHHHHHHh
Confidence            478999999999999988655555554 42  4 34555566777776655443

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=96.07  E-value=0.017  Score=40.99  Aligned_cols=48  Identities=17%  Similarity=0.086  Sum_probs=32.7

Q ss_pred             EEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHh
Q psy4275          46 CIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVL   97 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~   97 (182)
                      .++.||+|+|||..++-.+...+.+   +.+++|+..... .+++.+.++.+
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~~---g~~v~~~s~e~~-~~~~~~~~~~~   49 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLAR---GEPGLYVTLEES-PEELIENAESL   49 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHC---CCcEEEEECCCC-HHHHHHHHHHc
Confidence            6889999999999887777666543   557888875433 44444444443

A related protein is found in archaea.

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=96.04  E-value=0.024  Score=48.03  Aligned_cols=27  Identities=19%  Similarity=0.074  Sum_probs=21.1

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhcc
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCE   70 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~   70 (182)
                      +..+++||.|+|||..+.+.+-.....
T Consensus        47 ha~L~~Gp~GvGKTt~Ar~lAk~L~c~   73 (598)
T PRK09111         47 QAFMLTGVRGVGKTTTARILARALNYE   73 (598)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHhhCcC
Confidence            358999999999999987666655443

>PRK10689 transcription-repair coupling factor; Provisional

Probab=96.03  E-value=0.04  Score=50.10  Aligned_cols=80  Identities=14%  Similarity=0.182  Sum_probs=60.8

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +++++|++|+..-++.+++.+++...  +.++..++|+.+..+....+    .++.+|+|+|.-      -. ..+++.+
T Consensus       809 ~gqv~vf~n~i~~ie~la~~L~~~~p--~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaTdI------ie-rGIDIP~  879 (1147)
T PRK10689        809 GGQVYYLYNDVENIQKAAERLAELVP--EARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTI------IE-TGIDIPT  879 (1147)
T ss_pred             CCeEEEEECCHHHHHHHHHHHHHhCC--CCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEECch------hh-ccccccc
Confidence            46899999999988888888877654  46788899998776544433    247899999932      22 5678999


Q ss_pred             ccEEEEecccccc
Q psy4275         150 IKFLVLDEADRLS  162 (182)
Q Consensus       150 ~~~iI~DE~h~~~  162 (182)
                      ++++|++.++++.
T Consensus       880 v~~VIi~~ad~fg  892 (1147)
T PRK10689        880 ANTIIIERADHFG  892 (1147)
T ss_pred             CCEEEEecCCCCC
Confidence            9999999888653

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=96.00  E-value=0.084  Score=44.68  Aligned_cols=38  Identities=16%  Similarity=-0.002  Sum_probs=23.7

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcC
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTP   82 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p   82 (182)
                      +.+++.|++|+|||-.+. ++.+.+.....+.+++|+..
T Consensus       315 NpL~LyG~sGsGKTHLL~-AIa~~a~~~~~g~~V~Yita  352 (617)
T PRK14086        315 NPLFIYGESGLGKTHLLH-AIGHYARRLYPGTRVRYVSS  352 (617)
T ss_pred             CcEEEECCCCCCHHHHHH-HHHHHHHHhCCCCeEEEeeH
Confidence            348899999999997643 33343333222456776654

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=95.98  E-value=0.039  Score=49.07  Aligned_cols=79  Identities=14%  Similarity=0.196  Sum_probs=60.5

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +.++++++|+..-++.+++.+++...  +.++..++|+.+..+....+    .++.+|+|+|.-      -. ..+++.+
T Consensus       660 g~qv~if~n~i~~~e~l~~~L~~~~p--~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~i------ie-~GIDIp~  730 (926)
T TIGR00580       660 GGQVFYVHNRIESIEKLATQLRELVP--EARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTI------IE-TGIDIPN  730 (926)
T ss_pred             CCeEEEEECCcHHHHHHHHHHHHhCC--CCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECCh------hh-ccccccc
Confidence            56899999999988888888887643  57899999998765554332    347899999942      22 5678889


Q ss_pred             ccEEEEeccccc
Q psy4275         150 IKFLVLDEADRL  161 (182)
Q Consensus       150 ~~~iI~DE~h~~  161 (182)
                      ++++|++.++++
T Consensus       731 v~~VIi~~a~~~  742 (926)
T TIGR00580       731 ANTIIIERADKF  742 (926)
T ss_pred             CCEEEEecCCCC
Confidence            999999888764

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.

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=95.98  E-value=0.015  Score=43.34  Aligned_cols=52  Identities=10%  Similarity=0.044  Sum_probs=36.2

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLV   96 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~   96 (182)
                      ..|..+++.|++|+|||..+.-.+...+.+   +.+++|++-.. -.+++.+.++.
T Consensus        19 ~~gs~~lI~G~pGsGKT~la~~~l~~~~~~---ge~~lyvs~ee-~~~~i~~~~~~   70 (237)
T TIGR03877        19 PERNVVLLSGGPGTGKSIFSQQFLWNGLQM---GEPGIYVALEE-HPVQVRRNMAQ   70 (237)
T ss_pred             cCCeEEEEEcCCCCCHHHHHHHHHHHHHHc---CCcEEEEEeeC-CHHHHHHHHHH
Confidence            347789999999999999887777776643   45788887443 33445444443

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.

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=95.97  E-value=0.034  Score=43.55  Aligned_cols=20  Identities=20%  Similarity=0.217  Sum_probs=16.9

Q ss_pred             CcEEEECCCCChHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~   63 (182)
                      +++++.||+|+|||..+...
T Consensus        52 ~~~ll~GppG~GKT~la~~i   71 (328)
T PRK00080         52 DHVLLYGPPGLGKTTLANII   71 (328)
T ss_pred             CcEEEECCCCccHHHHHHHH
Confidence            57999999999999986543

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.97  E-value=0.029  Score=46.82  Aligned_cols=24  Identities=21%  Similarity=0.184  Sum_probs=18.4

Q ss_pred             EEEECCCCChHHHHHHHHHHHhhc
Q psy4275          46 CIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      .++.||.|+|||..+...+-....
T Consensus        41 ~Lf~Gp~G~GKTt~A~~lAk~l~c   64 (527)
T PRK14969         41 YLFTGTRGVGKTTLARILAKSLNC   64 (527)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhcC
Confidence            589999999999987666555433

>PF06733 DEAD_2: DEAD_2; InterPro: IPR010614 This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin

Probab=95.96  E-value=0.004  Score=44.15  Aligned_cols=45  Identities=31%  Similarity=0.324  Sum_probs=28.5

Q ss_pred             HHhcCCCcEEEEChHHHHHHHhcCC--CCCCCCccEEEEecccccccc
Q psy4275         119 KELAKKPHIVIATPGRLADHLDTCN--TFSLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus       119 ~~~~~~~~Ilv~T~~~l~~~~~~~~--~~~~~~~~~iI~DE~h~~~~~  164 (182)
                      +.....++|+|++...+++-.....  .+.++ -.++||||||++.+.
T Consensus       114 r~~~~~adivi~~y~yl~~~~~~~~~~~~~~~-~~ivI~DEAHNL~~~  160 (174)
T PF06733_consen  114 RELAKNADIVICNYNYLFDPSIRKSLFGIDLK-DNIVIFDEAHNLEDA  160 (174)
T ss_dssp             HHCGGG-SEEEEETHHHHSHHHHHHHCT--CC-CEEEEETTGGGCGGG
T ss_pred             HHhcccCCEEEeCHHHHhhHHHHhhhcccccc-CcEEEEecccchHHH
Confidence            3445578999999998875432211  12333 358999999998764

RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast [].; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 3CRV_A 3CRW_1 2VL7_A 4A15_A 2VSF_A.

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=95.91  E-value=0.076  Score=41.17  Aligned_cols=19  Identities=21%  Similarity=0.235  Sum_probs=14.4

Q ss_pred             cEEE-ECCCCChHHHHHHHH
Q psy4275          45 DCIG-CAKTGSGKTLAFALP   63 (182)
Q Consensus        45 ~~li-~~~tg~GKT~~~~~~   63 (182)
                      +.++ .||+|+|||..+...
T Consensus        44 ~~lll~G~~G~GKT~la~~l   63 (316)
T PHA02544         44 NMLLHSPSPGTGKTTVAKAL   63 (316)
T ss_pred             eEEEeeCcCCCCHHHHHHHH
Confidence            4555 899999999885443

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=95.90  E-value=0.024  Score=47.75  Aligned_cols=25  Identities=24%  Similarity=0.149  Sum_probs=19.4

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhc
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      ..++.||.|+|||..+...+-....
T Consensus        40 A~Lf~GP~GvGKTTlA~~lAk~L~C   64 (605)
T PRK05896         40 AYIFSGPRGIGKTSIAKIFAKAINC   64 (605)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhcC
Confidence            4789999999999997666555443

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.87  E-value=0.028  Score=47.71  Aligned_cols=25  Identities=28%  Similarity=0.187  Sum_probs=19.9

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhc
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      ..+++||.|+|||.++...+-....
T Consensus        40 a~Lf~Gp~GvGKttlA~~lAk~L~c   64 (620)
T PRK14954         40 GYIFSGLRGVGKTTAARVFAKAVNC   64 (620)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCC
Confidence            4789999999999998766655544

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.86  E-value=0.041  Score=46.58  Aligned_cols=23  Identities=17%  Similarity=0.078  Sum_probs=18.0

Q ss_pred             cEEEECCCCChHHHHHHHHHHHh
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQK   67 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~   67 (182)
                      ..+++||.|+|||..+...+-..
T Consensus        40 a~Lf~Gp~G~GKTtlA~~lA~~l   62 (585)
T PRK14950         40 AYLFTGPRGVGKTSTARILAKAV   62 (585)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            35899999999999976665443

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=95.85  E-value=0.1  Score=39.83  Aligned_cols=36  Identities=19%  Similarity=0.098  Sum_probs=23.9

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcC
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTP   82 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p   82 (182)
                      +-+.+.|++|+|||+++.-.+... ...  +.++.++.-
T Consensus        73 ~vi~l~G~~G~GKTTt~akLA~~l-~~~--g~~V~li~~  108 (272)
T TIGR00064        73 NVILFVGVNGVGKTTTIAKLANKL-KKQ--GKSVLLAAG  108 (272)
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHH-Hhc--CCEEEEEeC
Confidence            356677999999999866555443 222  456777763

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.

>PTZ00293 thymidine kinase; Provisional

Probab=95.83  E-value=0.045  Score=40.05  Aligned_cols=38  Identities=13%  Similarity=-0.049  Sum_probs=26.4

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      |+=.++.||+++|||.-.+..+.....+   +.+++++-|.
T Consensus         4 G~i~vi~GpMfSGKTteLLr~i~~y~~a---g~kv~~~kp~   41 (211)
T PTZ00293          4 GTISVIIGPMFSGKTTELMRLVKRFTYS---EKKCVVIKYS   41 (211)
T ss_pred             eEEEEEECCCCChHHHHHHHHHHHHHHc---CCceEEEEec
Confidence            4456889999999998755554444333   4578888775

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=95.79  E-value=0.025  Score=44.42  Aligned_cols=30  Identities=23%  Similarity=0.203  Sum_probs=22.9

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhcc
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCE   70 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~   70 (182)
                      +..+++++++|+||+|||+.. -+++..+..
T Consensus       157 v~~~~nili~G~tgSGKTTll-~aL~~~ip~  186 (332)
T PRK13900        157 VISKKNIIISGGTSTGKTTFT-NAALREIPA  186 (332)
T ss_pred             HHcCCcEEEECCCCCCHHHHH-HHHHhhCCC
Confidence            445889999999999999884 555555543

>COG5008 PilU Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=95.79  E-value=0.019  Score=43.47  Aligned_cols=45  Identities=27%  Similarity=0.330  Sum_probs=27.9

Q ss_pred             CccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHH
Q psy4275           3 DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ   66 (182)
Q Consensus         3 ~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~   66 (182)
                      ..+.+|++|++++.+.+.-                  +.+..-++++|+||+||+.+. .+++.
T Consensus       105 ~~IPt~eeL~LPevlk~la------------------~~kRGLviiVGaTGSGKSTtm-AaMi~  149 (375)
T COG5008         105 TKIPTFEELKLPEVLKDLA------------------LAKRGLVIIVGATGSGKSTTM-AAMIG  149 (375)
T ss_pred             ccCCcHHhcCCcHHHHHhh------------------cccCceEEEECCCCCCchhhH-HHHhc
Confidence            3466666666666554422                  112334788999999999884 34443

>KOG2373|consensus

Probab=95.78  E-value=0.0033  Score=49.09  Aligned_cols=29  Identities=28%  Similarity=0.225  Sum_probs=22.9

Q ss_pred             CCCcEEEECCCCChHHHHHHHHHHHhhcc
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALPILQKWCE   70 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~~~~~~~~   70 (182)
                      .|.-.++.||||+|||+...-+.++.+.+
T Consensus       272 ~GElTvlTGpTGsGKTTFlsEYsLDL~~Q  300 (514)
T KOG2373|consen  272 PGELTVLTGPTGSGKTTFLSEYSLDLFTQ  300 (514)
T ss_pred             CCceEEEecCCCCCceeEehHhhHHHHhh
Confidence            36679999999999998766666666555

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=95.77  E-value=0.091  Score=37.15  Aligned_cols=46  Identities=9%  Similarity=0.024  Sum_probs=33.7

Q ss_pred             EEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHh
Q psy4275          46 CIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVL   97 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~   97 (182)
                      .++.|++|+|||..+.-.+..      .+.+++|+.........+.+.++..
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~------~~~~~~y~at~~~~d~em~~rI~~H   47 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAE------LGGPVTYIATAEAFDDEMAERIARH   47 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHh------cCCCeEEEEccCcCCHHHHHHHHHH
Confidence            578999999999987766544      1457889988777766666665543

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.

>PRK10436 hypothetical protein; Provisional

Probab=95.75  E-value=0.026  Score=46.28  Aligned_cols=39  Identities=31%  Similarity=0.294  Sum_probs=25.3

Q ss_pred             hHHHHhhhhhhhC--CCcEEEECCCCChHHHHHHHHHHHhhc
Q psy4275          30 TEIQKAIIPHVLN--DEDCIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        30 ~~~Q~~~~~~~~~--~~~~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      .+.|.+.+..+..  +.-++++||||+|||+.. ..++..+.
T Consensus       203 ~~~~~~~l~~~~~~~~GliLvtGpTGSGKTTtL-~a~l~~~~  243 (462)
T PRK10436        203 TPAQLAQFRQALQQPQGLILVTGPTGSGKTVTL-YSALQTLN  243 (462)
T ss_pred             CHHHHHHHHHHHHhcCCeEEEECCCCCChHHHH-HHHHHhhC
Confidence            4445555544433  456889999999999984 44555443

>PRK08939 primosomal protein DnaI; Reviewed

Probab=95.75  E-value=0.055  Score=42.02  Aligned_cols=35  Identities=17%  Similarity=0.176  Sum_probs=22.7

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEE
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVL   80 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil   80 (182)
                      +++.++.|++|+|||..+...+-. +...  +..+.++
T Consensus       156 ~~gl~L~G~~G~GKThLa~Aia~~-l~~~--g~~v~~~  190 (306)
T PRK08939        156 VKGLYLYGDFGVGKSYLLAAIANE-LAKK--GVSSTLL  190 (306)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH-HHHc--CCCEEEE
Confidence            468999999999999875444333 3332  3344444

>PRK10867 signal recognition particle protein; Provisional

Probab=95.75  E-value=0.19  Score=41.01  Aligned_cols=86  Identities=22%  Similarity=0.189  Sum_probs=44.2

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC--HHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhh----
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT--RELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQG----  118 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~--~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----  118 (182)
                      -++++|++|+|||+++.-.+.......  +.+++++.-.  +..+   .+.++.+....++.+.......+.....    
T Consensus       102 vI~~vG~~GsGKTTtaakLA~~l~~~~--G~kV~lV~~D~~R~aa---~eQL~~~a~~~gv~v~~~~~~~dp~~i~~~a~  176 (433)
T PRK10867        102 VIMMVGLQGAGKTTTAGKLAKYLKKKK--KKKVLLVAADVYRPAA---IEQLKTLGEQIGVPVFPSGDGQDPVDIAKAAL  176 (433)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHhc--CCcEEEEEccccchHH---HHHHHHHHhhcCCeEEecCCCCCHHHHHHHHH
Confidence            367889999999998765555433221  3456655532  2222   2234444555566654332122211111    


Q ss_pred             -HHhcCCC-cEEEEChHHH
Q psy4275         119 -KELAKKP-HIVIATPGRL  135 (182)
Q Consensus       119 -~~~~~~~-~Ilv~T~~~l  135 (182)
                       ....+++ -|+|-|++.+
T Consensus       177 ~~a~~~~~DvVIIDTaGrl  195 (433)
T PRK10867        177 EEAKENGYDVVIVDTAGRL  195 (433)
T ss_pred             HHHHhcCCCEEEEeCCCCc
Confidence             1112334 4888999865

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=95.74  E-value=0.041  Score=43.39  Aligned_cols=43  Identities=14%  Similarity=-0.019  Sum_probs=31.3

Q ss_pred             ChHHHHhhhhhhhC--C---CcEEEECCCCChHHHHHHHHHHHhhccC
Q psy4275          29 PTEIQKAIIPHVLN--D---EDCIGCAKTGSGKTLAFALPILQKWCED   71 (182)
Q Consensus        29 ~~~~Q~~~~~~~~~--~---~~~li~~~tg~GKT~~~~~~~~~~~~~~   71 (182)
                      +.|||...+..+..  +   +..++.||.|.||+..+...+...+...
T Consensus         2 ~yPW~~~~~~~l~~~~~rl~ha~Lf~Gp~G~GK~~lA~~~A~~LlC~~   49 (342)
T PRK06964          2 LYPWQTDDWNRLQALRARLPHALLLHGQAGIGKLDFAQHLAQGLLCET   49 (342)
T ss_pred             CCcccHHHHHHHHHhcCCcceEEEEECCCCCCHHHHHHHHHHHHcCCC
Confidence            35788888877654  2   3677899999999998776665555543

>PRK13764 ATPase; Provisional

Probab=95.73  E-value=0.029  Score=47.38  Aligned_cols=27  Identities=15%  Similarity=0.254  Sum_probs=20.5

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhcc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCE   70 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~   70 (182)
                      +++++++||||+|||+.. .+++..+..
T Consensus       257 ~~~ILIsG~TGSGKTTll-~AL~~~i~~  283 (602)
T PRK13764        257 AEGILIAGAPGAGKSTFA-QALAEFYAD  283 (602)
T ss_pred             CCEEEEECCCCCCHHHHH-HHHHHHHhh
Confidence            678999999999999874 445555443

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=95.72  E-value=0.035  Score=42.18  Aligned_cols=39  Identities=23%  Similarity=0.240  Sum_probs=25.7

Q ss_pred             hHHHHhhhhhhhC--CCcEEEECCCCChHHHHHHHHHHHhhc
Q psy4275          30 TEIQKAIIPHVLN--DEDCIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        30 ~~~Q~~~~~~~~~--~~~~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      .+.|.+.+..+..  +..+++.|+||+|||+.. ..++..+.
T Consensus        65 ~~~~~~~l~~~~~~~~GlilisG~tGSGKTT~l-~all~~i~  105 (264)
T cd01129          65 KPENLEIFRKLLEKPHGIILVTGPTGSGKTTTL-YSALSELN  105 (264)
T ss_pred             CHHHHHHHHHHHhcCCCEEEEECCCCCcHHHHH-HHHHhhhC
Confidence            4556665555443  446889999999999985 44444443

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.

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=95.71  E-value=0.077  Score=42.93  Aligned_cols=53  Identities=19%  Similarity=0.274  Sum_probs=33.1

Q ss_pred             CHHHHHHHHHCCCCC--ChHHH-----HhhhhhhhCCCcEEEECCCCChHHHHHHHHHHH
Q psy4275          14 NPWLIRQCQTIGVKT--PTEIQ-----KAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ   66 (182)
Q Consensus        14 ~~~i~~~l~~~~~~~--~~~~Q-----~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~   66 (182)
                      ++|+.=.+...|+..  +.+-|     ..+++.+.++.|++..||+|+|||-.+.....+
T Consensus       173 dEWid~LlrSiG~~P~~~~~r~k~~~L~rl~~fve~~~Nli~lGp~GTGKThla~~l~~~  232 (449)
T TIGR02688       173 EEWIDVLIRSIGYEPEGFEARQKLLLLARLLPLVEPNYNLIELGPKGTGKSYIYNNLSPY  232 (449)
T ss_pred             HHHHHHHHHhcCCCcccCChHHHHHHHHhhHHHHhcCCcEEEECCCCCCHHHHHHHHhHH
Confidence            456666666667642  22221     122255566889999999999999776543444

Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families TIGR00763 (ATP-dependent protease La) or pfam02190 (ATP-dependent protease La (LON) domain). This protein is repeatedly found downstream of another uncharacterized protein of about 880 amino acids in length, described by model TIGR02687.

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=95.71  E-value=0.024  Score=44.55  Aligned_cols=44  Identities=9%  Similarity=-0.020  Sum_probs=31.8

Q ss_pred             CChHHHHhhhhhhhC----C---CcEEEECCCCChHHHHHHHHHHHhhccC
Q psy4275          28 TPTEIQKAIIPHVLN----D---EDCIGCAKTGSGKTLAFALPILQKWCED   71 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~----~---~~~li~~~tg~GKT~~~~~~~~~~~~~~   71 (182)
                      +..|||...|..+.+    +   +-.++.||.|.||+..+...+...+..+
T Consensus         2 ~~yPWl~~~~~~l~~~~~~~rl~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~   52 (334)
T PRK07993          2 KWYPWLRPDYEQLVGSYQAGRGHHALLIQALPGMGDDALIYALSRWLMCQQ   52 (334)
T ss_pred             CCCCCChHHHHHHHHHHHcCCcceEEeeECCCCCCHHHHHHHHHHHHcCCC
Confidence            356788888777653    3   3567999999999998877666665543

>cd01394 radB RadB

Probab=95.70  E-value=0.057  Score=39.55  Aligned_cols=38  Identities=13%  Similarity=0.017  Sum_probs=28.1

Q ss_pred             CCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcC
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTP   82 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p   82 (182)
                      .|.-.++.|++|+|||..++..+.....+   +.+++++.-
T Consensus        18 ~g~i~~i~G~~GsGKT~l~~~~a~~~~~~---g~~v~yi~~   55 (218)
T cd01394          18 RGTVTQVYGPPGTGKTNIAIQLAVETAGQ---GKKVAYIDT   55 (218)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhc---CCeEEEEEC
Confidence            35668899999999999877776665433   457888843

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]

Probab=95.70  E-value=0.04  Score=47.23  Aligned_cols=70  Identities=23%  Similarity=0.147  Sum_probs=54.1

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCC-CeeEEEEcCCHHHHHHHHHHHHHhhc
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPY-GIFALVLTPTRELAYQIGDQFLVLGK   99 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~-~~~~lil~p~~~l~~q~~~~~~~~~~   99 (182)
                      .+++.|.+++...  ....++.++.|+|||.+...-+.+.+..... ..+++.++=|+-.+.++.+.+..+..
T Consensus         2 ~Ln~~Q~~av~~~--~gp~lV~AGaGsGKT~vlt~Ria~li~~~~v~p~~Il~vTFTnkAA~em~~Rl~~~~~   72 (655)
T COG0210           2 KLNPEQREAVLHP--DGPLLVLAGAGSGKTRVLTERIAYLIAAGGVDPEQILAITFTNKAAAEMRERLLKLLG   72 (655)
T ss_pred             CCCHHHHHHHhcC--CCCeEEEECCCCCchhhHHHHHHHHHHcCCcChHHeeeeechHHHHHHHHHHHHHHhC
Confidence            5789999988666  5678889999999999876666666555432 23688899999999988888877765

>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]

Probab=95.68  E-value=0.061  Score=41.97  Aligned_cols=56  Identities=14%  Similarity=0.134  Sum_probs=41.7

Q ss_pred             CCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcC
Q psy4275          26 VKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTP   82 (182)
Q Consensus        26 ~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p   82 (182)
                      +...++.|.+-..++.+..-.+-.||.|+|||+.+.....+.+.+..-. ++|..=|
T Consensus       126 I~~kt~~Q~~y~eai~~~di~fGiGpAGTGKTyLava~av~al~~~~v~-rIiLtRP  181 (348)
T COG1702         126 IIPKTPGQNMYPEAIEEHDIVFGIGPAGTGKTYLAVAKAVDALGAGQVR-RIILTRP  181 (348)
T ss_pred             eEecChhHHHHHHHHHhcCeeeeecccccCChhhhHHhHhhhhhhcccc-eeeecCc
Confidence            4467889999988888876677778999999999887777776664322 4454445

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=95.67  E-value=0.036  Score=40.79  Aligned_cols=45  Identities=11%  Similarity=-0.083  Sum_probs=30.9

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhhccC---CCCeeEEEEcCCHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKWCED---PYGIFALVLTPTRE   85 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~---~~~~~~lil~p~~~   85 (182)
                      ..|.-..+.|++|+|||..++..+.......   .....++++.....
T Consensus        17 ~~g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~~   64 (226)
T cd01393          17 PTGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEGA   64 (226)
T ss_pred             cCCcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecCCC
Confidence            3467789999999999998776666554332   01257888877543

RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=95.64  E-value=0.073  Score=41.92  Aligned_cols=22  Identities=18%  Similarity=0.110  Sum_probs=17.0

Q ss_pred             cEEEECCCCChHHHHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQ   66 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~   66 (182)
                      ..+++||+|+|||..+...+-.
T Consensus        38 ~~Ll~G~~G~GKt~~a~~la~~   59 (355)
T TIGR02397        38 AYLFSGPRGTGKTSIARIFAKA   59 (355)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4689999999999886544444

This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.

>PRK06835 DNA replication protein DnaC; Validated

Probab=95.56  E-value=0.032  Score=43.78  Aligned_cols=44  Identities=23%  Similarity=0.243  Sum_probs=28.4

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQI   90 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~   90 (182)
                      ++++++.|++|+|||..+... ...+...  +..++++.. ..+...+
T Consensus       183 ~~~Lll~G~~GtGKThLa~aI-a~~l~~~--g~~V~y~t~-~~l~~~l  226 (329)
T PRK06835        183 NENLLFYGNTGTGKTFLSNCI-AKELLDR--GKSVIYRTA-DELIEIL  226 (329)
T ss_pred             CCcEEEECCCCCcHHHHHHHH-HHHHHHC--CCeEEEEEH-HHHHHHH
Confidence            578999999999999865433 3333333  446666544 4555544

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=95.55  E-value=0.16  Score=41.22  Aligned_cols=124  Identities=15%  Similarity=0.153  Sum_probs=62.4

Q ss_pred             HHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEE-EcC
Q psy4275          33 QKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSII-TGG  111 (182)
Q Consensus        33 Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~-~~~  111 (182)
                      -.+.+.-+..|.-+++.|++|.|||..++-.+.+.....  +..++++.-. .-.+++...+-.  ...++....+ .|.
T Consensus       184 LD~~~~G~~~g~liviag~pg~GKT~~al~ia~~~a~~~--g~~v~~fSlE-m~~~~l~~Rl~~--~~~~v~~~~~~~~~  258 (421)
T TIGR03600       184 LDRLTNGLVKGDLIVIGARPSMGKTTLALNIAENVALRE--GKPVLFFSLE-MSAEQLGERLLA--SKSGINTGNIRTGR  258 (421)
T ss_pred             HHHHhcCCCCCceEEEEeCCCCCHHHHHHHHHHHHHHhC--CCcEEEEECC-CCHHHHHHHHHH--HHcCCCHHHHhcCC
Confidence            333444455577888999999999998776665654333  4457777532 223333222211  1112222111 222


Q ss_pred             Cchhhhh------HHhcCCCcEEEE-----ChHHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275         112 MDMVDQG------KELAKKPHIVIA-----TPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus       112 ~~~~~~~------~~~~~~~~Ilv~-----T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      ....++.      ..+ .+..+.|.     |++.+...++..+. ....+++||+|-.|.|..
T Consensus       259 l~~~~~~~~~~~~~~l-~~~~l~i~d~~~~t~~~i~~~~r~~~~-~~~~~~lvvIDyLql~~~  319 (421)
T TIGR03600       259 FNDSDFNRLLNAVDRL-SEKDLYIDDTGGLTVAQIRSIARRIKR-KKGGLDLIVVDYIQLMAP  319 (421)
T ss_pred             CCHHHHHHHHHHHHHH-hcCCEEEECCCCCCHHHHHHHHHHHHH-hcCCCCEEEEecccccCC
Confidence            2221111      111 23345553     34444444432111 122578999999999875

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.

>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=95.54  E-value=0.029  Score=42.58  Aligned_cols=44  Identities=23%  Similarity=0.239  Sum_probs=29.3

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHH
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTREL   86 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l   86 (182)
                      +..+.+++++|+||+|||+.. .+++..+...  ..+++.+-...++
T Consensus       124 v~~~~~ili~G~tGSGKTT~l-~all~~i~~~--~~~iv~iEd~~E~  167 (270)
T PF00437_consen  124 VRGRGNILISGPTGSGKTTLL-NALLEEIPPE--DERIVTIEDPPEL  167 (270)
T ss_dssp             HHTTEEEEEEESTTSSHHHHH-HHHHHHCHTT--TSEEEEEESSS-S
T ss_pred             cccceEEEEECCCccccchHH-HHHhhhcccc--ccceEEeccccce
Confidence            345789999999999999985 5555555543  2456666544433

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 ....

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.54  E-value=0.091  Score=44.79  Aligned_cols=26  Identities=19%  Similarity=0.202  Sum_probs=20.3

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhc
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      +..++.||.|+|||..+...+-....
T Consensus        39 ~a~Lf~Gp~G~GKttlA~~lAk~L~c   64 (620)
T PRK14948         39 PAYLFTGPRGTGKTSSARILAKSLNC   64 (620)
T ss_pred             ceEEEECCCCCChHHHHHHHHHHhcC
Confidence            46789999999999997666655544

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=95.53  E-value=0.028  Score=42.56  Aligned_cols=40  Identities=15%  Similarity=0.004  Sum_probs=30.0

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      ..|.-.++.|++|+|||..++-.+.+.+.+   +.+++|+.-.
T Consensus        34 p~gs~~lI~G~pGtGKT~l~~qf~~~~a~~---Ge~vlyis~E   73 (259)
T TIGR03878        34 PAYSVINITGVSDTGKSLMVEQFAVTQASR---GNPVLFVTVE   73 (259)
T ss_pred             ECCcEEEEEcCCCCCHHHHHHHHHHHHHhC---CCcEEEEEec
Confidence            346778999999999999887776665544   4477887743

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>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=95.52  E-value=0.27  Score=34.51  Aligned_cols=84  Identities=25%  Similarity=0.228  Sum_probs=41.4

Q ss_pred             EEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc--CCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhh-----hh
Q psy4275          46 CIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT--PTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVD-----QG  118 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~--p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~  118 (182)
                      .++.|++|+|||..+...+.... +.  +.+++++.  +.+.-   ..+.+..+....++.+...........     ..
T Consensus         3 ~~~~G~~G~GKTt~~~~la~~~~-~~--g~~v~~i~~D~~~~~---~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   76 (173)
T cd03115           3 ILLVGLQGVGKTTTAAKLALYLK-KK--GKKVLLVAADTYRPA---AIEQLRVLGEQVGVPVFEEGEGKDPVSIAKRAIE   76 (173)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHH-HC--CCcEEEEEcCCCChH---HHHHHHHhcccCCeEEEecCCCCCHHHHHHHHHH
Confidence            57889999999998655544432 22  34565554  22211   122344444444555433222111110     01


Q ss_pred             HHhcCCC-cEEEEChHHH
Q psy4275         119 KELAKKP-HIVIATPGRL  135 (182)
Q Consensus       119 ~~~~~~~-~Ilv~T~~~l  135 (182)
                      ....++. -|++-||+..
T Consensus        77 ~~~~~~~d~viiDt~g~~   94 (173)
T cd03115          77 HAREENFDVVIVDTAGRL   94 (173)
T ss_pred             HHHhCCCCEEEEECcccc
Confidence            1123344 4788888864

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.

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=95.51  E-value=0.17  Score=39.17  Aligned_cols=21  Identities=24%  Similarity=0.164  Sum_probs=16.8

Q ss_pred             CcEEEECCCCChHHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~   64 (182)
                      .+.++.||+|+|||..+....
T Consensus        39 ~~~ll~G~~G~GKt~~~~~l~   59 (319)
T PRK00440         39 PHLLFAGPPGTGKTTAALALA   59 (319)
T ss_pred             CeEEEECCCCCCHHHHHHHHH
Confidence            368999999999998864433

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=95.51  E-value=0.085  Score=37.31  Aligned_cols=45  Identities=13%  Similarity=0.116  Sum_probs=29.7

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFL   95 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~   95 (182)
                      .+++.|++|+|||..+...+...      +..++++......-+++.+.+.
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~~~------~~~~~~iat~~~~~~e~~~ri~   47 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAAQS------GLQVLYIATAQPFDDEMAARIA   47 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHHHc------CCCcEeCcCCCCChHHHHHHHH
Confidence            47899999999999876655442      2246677765555555544443

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=95.49  E-value=0.038  Score=44.01  Aligned_cols=27  Identities=11%  Similarity=-0.123  Sum_probs=21.2

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhccC
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWCED   71 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~~~   71 (182)
                      -.++.||.|+||+..+...+-..+..+
T Consensus        43 A~Lf~Gp~G~GK~~lA~~~A~~Llc~~   69 (365)
T PRK07471         43 AWLIGGPQGIGKATLAYRMARFLLATP   69 (365)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHhCCC
Confidence            488999999999998776666665544

>KOG0341|consensus

Probab=95.44  E-value=0.18  Score=40.31  Aligned_cols=138  Identities=15%  Similarity=0.214  Sum_probs=89.5

Q ss_pred             CccCCccCCCCCHHHHHHHHHCCCC---------CChHHHHhhhhhhhCCCcEEEECCCCCh-----------HHHHHHH
Q psy4275           3 DPIKSFTDLKLNPWLIRQCQTIGVK---------TPTEIQKAIIPHVLNDEDCIGCAKTGSG-----------KTLAFAL   62 (182)
Q Consensus         3 ~~~~~~~~~~l~~~i~~~l~~~~~~---------~~~~~Q~~~~~~~~~~~~~li~~~tg~G-----------KT~~~~~   62 (182)
                      |....+-++|+.+++...+..|+-.         -|..+|..+=.++.+ .-.+=+|-.|..           |.-+-+.
T Consensus       333 DEADRmiDmGFEddir~iF~~FK~QRQTLLFSATMP~KIQ~FAkSALVK-PvtvNVGRAGAAsldViQevEyVkqEaKiV  411 (610)
T KOG0341|consen  333 DEADRMIDMGFEDDIRTIFSFFKGQRQTLLFSATMPKKIQNFAKSALVK-PVTVNVGRAGAASLDVIQEVEYVKQEAKIV  411 (610)
T ss_pred             hhHHHHhhccchhhHHHHHHHHhhhhheeeeeccccHHHHHHHHhhccc-ceEEecccccccchhHHHHHHHHHhhhhhh
Confidence            3445667889999999998877543         367777766655543 223333444432           2222234


Q ss_pred             HHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhc----CCCcEEEEChHHHHHH
Q psy4275          63 PILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA----KKPHIVIATPGRLADH  138 (182)
Q Consensus        63 ~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~Ilv~T~~~l~~~  138 (182)
                      ++++.+...  .+.++|.+-.++=++.+++.+--.    |+....++|++....+...+.    ++.+|+|+|.-     
T Consensus       412 ylLeCLQKT--~PpVLIFaEkK~DVD~IhEYLLlK----GVEavaIHGGKDQedR~~ai~afr~gkKDVLVATDV-----  480 (610)
T KOG0341|consen  412 YLLECLQKT--SPPVLIFAEKKADVDDIHEYLLLK----GVEAVAIHGGKDQEDRHYAIEAFRAGKKDVLVATDV-----  480 (610)
T ss_pred             hHHHHhccC--CCceEEEeccccChHHHHHHHHHc----cceeEEeecCcchhHHHHHHHHHhcCCCceEEEecc-----
Confidence            455555554  568999999999888887775432    788999999998877665543    46799999943     


Q ss_pred             HhcCCCCCCCCccEEE
Q psy4275         139 LDTCNTFSLNRIKFLV  154 (182)
Q Consensus       139 ~~~~~~~~~~~~~~iI  154 (182)
                       .+ +.+++.++..+|
T Consensus       481 -AS-KGLDFp~iqHVI  494 (610)
T KOG0341|consen  481 -AS-KGLDFPDIQHVI  494 (610)
T ss_pred             -hh-ccCCCccchhhc
Confidence             22 555666655443

>TIGR00763 lon ATP-dependent protease La

Probab=95.39  E-value=0.11  Score=45.58  Aligned_cols=20  Identities=20%  Similarity=-0.069  Sum_probs=16.5

Q ss_pred             CCcEEEECCCCChHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~   62 (182)
                      +...++.||+|+|||..+-.
T Consensus       347 ~~~lll~GppG~GKT~lAk~  366 (775)
T TIGR00763       347 GPILCLVGPPGVGKTSLGKS  366 (775)
T ss_pred             CceEEEECCCCCCHHHHHHH
Confidence            45799999999999987543

This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.

>KOG0739|consensus

Probab=95.38  E-value=0.15  Score=39.49  Aligned_cols=39  Identities=10%  Similarity=0.114  Sum_probs=26.8

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQI   90 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~   90 (182)
                      .+++.||+|+||++.+-..+-+.      + .+.+-+.+..|+..|
T Consensus       168 giLLyGPPGTGKSYLAKAVATEA------n-STFFSvSSSDLvSKW  206 (439)
T KOG0739|consen  168 GILLYGPPGTGKSYLAKAVATEA------N-STFFSVSSSDLVSKW  206 (439)
T ss_pred             eEEEeCCCCCcHHHHHHHHHhhc------C-CceEEeehHHHHHHH
Confidence            68999999999987754333332      2 566777777776554

>PHA00012 I assembly protein

Probab=95.38  E-value=0.21  Score=39.03  Aligned_cols=25  Identities=32%  Similarity=0.363  Sum_probs=20.0

Q ss_pred             EEEECCCCChHHHHHHHHHHHhhcc
Q psy4275          46 CIGCAKTGSGKTLAFALPILQKWCE   70 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~~~~   70 (182)
                      .++.|..|+|||+.+..-+...+.+
T Consensus         4 ylITGkPGSGKSl~aV~~I~~~L~~   28 (361)
T PHA00012          4 YVVTGKLGAGKTLVAVSRIQDKLVK   28 (361)
T ss_pred             EEEecCCCCCchHHHHHHHHHHHHc
Confidence            4789999999999988766665554

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=95.35  E-value=0.043  Score=46.25  Aligned_cols=38  Identities=26%  Similarity=0.314  Sum_probs=25.6

Q ss_pred             hHHHHhhhhhhhC--CCcEEEECCCCChHHHHHHHHHHHhh
Q psy4275          30 TEIQKAIIPHVLN--DEDCIGCAKTGSGKTLAFALPILQKW   68 (182)
Q Consensus        30 ~~~Q~~~~~~~~~--~~~~li~~~tg~GKT~~~~~~~~~~~   68 (182)
                      .+.|.+.+..+..  +..++++||||+|||+.. ..++..+
T Consensus       301 ~~~~~~~l~~~~~~~~Glilv~G~tGSGKTTtl-~a~l~~~  340 (564)
T TIGR02538       301 EPDQKALFLEAIHKPQGMVLVTGPTGSGKTVSL-YTALNIL  340 (564)
T ss_pred             CHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHH-HHHHHhh
Confidence            4555555555443  456789999999999984 4555554

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.

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=95.33  E-value=0.034  Score=39.85  Aligned_cols=39  Identities=26%  Similarity=0.198  Sum_probs=27.9

Q ss_pred             CChHHHHhhhhhh-hCCCcEEEECCCCChHHHHHHHHHHHh
Q psy4275          28 TPTEIQKAIIPHV-LNDEDCIGCAKTGSGKTLAFALPILQK   67 (182)
Q Consensus        28 ~~~~~Q~~~~~~~-~~~~~~li~~~tg~GKT~~~~~~~~~~   67 (182)
                      ...+.|.+.+... ..+.++++.||||+|||+.. ..++..
T Consensus         9 ~~~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTll-~aL~~~   48 (186)
T cd01130           9 TFSPLQAAYLWLAVEARKNILISGGTGSGKTTLL-NALLAF   48 (186)
T ss_pred             CCCHHHHHHHHHHHhCCCEEEEECCCCCCHHHHH-HHHHhh
Confidence            4566677766554 44889999999999999874 334443

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.

>PRK13700 conjugal transfer protein TraD; Provisional

Probab=95.30  E-value=0.022  Score=48.75  Aligned_cols=70  Identities=13%  Similarity=0.136  Sum_probs=43.1

Q ss_pred             CHHHHHHHHHCCCCCChHHHHhhhhhh--hCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHH
Q psy4275          14 NPWLIRQCQTIGVKTPTEIQKAIIPHV--LNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAY   88 (182)
Q Consensus        14 ~~~i~~~l~~~~~~~~~~~Q~~~~~~~--~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~   88 (182)
                      ++++.+.+++.+..  .++....+|..  ...+|+++.|.||+|||.+ +..++..+.++  +.++||.-|.-+...
T Consensus       156 ~~~l~k~lk~~~~~--s~i~I~gvPip~~~E~~H~li~GttGSGKS~~-i~~LL~~ir~R--GdrAIIyD~~GeFv~  227 (732)
T PRK13700        156 PKDVARMLKKDGKD--SDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEV-IRRLANYARQR--GDMVVIYDRSGEFVK  227 (732)
T ss_pred             HHHHHHHHHhcCCC--CCeeEccccCCcchhhcceEEeCCCCCCHHHH-HHHHHHHHHHc--CCeEEEEeCCCchHH
Confidence            35677777765532  22333333332  3368999999999999997 56677666554  345555555544433

>PF02572 CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP; InterPro: IPR003724 ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2

Probab=95.28  E-value=0.23  Score=35.17  Aligned_cols=119  Identities=17%  Similarity=0.068  Sum_probs=55.3

Q ss_pred             EEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCC
Q psy4275          46 CIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKP  125 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  125 (182)
                      +.+..+.|-|||++++-.++..+-.   +.+|+++-=.+.-.  ..-+.+-+...-++.... .|....+.....-   .
T Consensus         6 i~vytG~GKGKTTAAlGlalRA~G~---G~rV~ivQFlKg~~--~~GE~~~l~~l~~~~~~~-~g~~f~~~~~~~~---~   76 (172)
T PF02572_consen    6 IQVYTGDGKGKTTAALGLALRAAGH---GMRVLIVQFLKGGR--YSGELKALKKLPNVEIER-FGKGFVWRMNEEE---E   76 (172)
T ss_dssp             EEEEESSSS-HHHHHHHHHHHHHCT---T--EEEEESS--SS----HHHHHHGGGT--EEEE---TT----GGGHH---H
T ss_pred             EEEEeCCCCCchHHHHHHHHHHHhC---CCEEEEEEEecCCC--CcCHHHHHHhCCeEEEEE-cCCcccccCCCcH---H
Confidence            5566789999999988777776655   66888887655511  112222222222233322 1111111000000   0


Q ss_pred             cEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHHHHHHHHh
Q psy4275         126 HIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFFFFLK  177 (182)
Q Consensus       126 ~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~~~~~~~~  177 (182)
                      +  ........+..++  .+.-...+++|+||+-...+.+.....+.+..+.
T Consensus        77 ~--~~~~~~~~~~a~~--~i~~~~~dlvILDEi~~a~~~gll~~~~v~~~l~  124 (172)
T PF02572_consen   77 D--RAAAREGLEEAKE--AISSGEYDLVILDEINYAVDYGLLSEEEVLDLLE  124 (172)
T ss_dssp             H--HHHHHHHHHHHHH--HTT-TT-SEEEEETHHHHHHTTSS-HHHHHHHHH
T ss_pred             H--HHHHHHHHHHHHH--HHhCCCCCEEEEcchHHHhHCCCccHHHHHHHHH
Confidence            0  0011112222222  1224568899999999999988877766666554

5.1.17 from EC), catalyse the conversion of cobalamin (vitamin B12) into its coenzyme form, adenosylcobalamin (coenzyme B12) []. Adenosylcobalamin (AdoCbl) is required for the ativity of certain enzymes. AdoCbl contains an adenosyl moiety liganded to the cobalt ion of cobalamin via a covalent Co-C bond, and its synthesis is unique to certain prokaryotes. ATP:cob(I)alamin adenosyltransferases are classed into three groups: CobA-type [], EutT-type [] and PduO-type []. Each of the three enzyme types appears to be specialised for particular AdoCbl-dependent enzymes or for the de novo synthesis AdoCbl. PduO and EutT are distantly related, sharing short conserved motifs, while CobA is evolutionarily unrelated and is an example of convergent evolution. This entry represents the ATP:cob(I)alamin adenosyltransferases CobA (Salmonella typhimurium), CobO (Pseudomonas denitrificans), and ButR (Escherichia coli). There is a high degree of sequence identity between these proteins []. CobA is responsible for attaching the adenosyl moiety from ATP to the cobalt ion of the corrin ring, necessary for the convertion of cobalamin to adenosylcobalamin [, ]. ; GO: 0005524 ATP binding, 0008817 cob(I)yrinic acid a,c-diamide adenosyltransferase activity, 0009236 cobalamin biosynthetic process; PDB: 1G64_A 1G5T_A 1G5R_A.

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=95.25  E-value=0.053  Score=46.97  Aligned_cols=21  Identities=24%  Similarity=0.148  Sum_probs=17.1

Q ss_pred             CcEEEECCCCChHHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~   64 (182)
                      .++++.||+|+|||..+....
T Consensus        53 ~slLL~GPpGtGKTTLA~aIA   73 (725)
T PRK13341         53 GSLILYGPPGVGKTTLARIIA   73 (725)
T ss_pred             ceEEEECCCCCCHHHHHHHHH
Confidence            489999999999998864443

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.24  E-value=0.096  Score=43.34  Aligned_cols=22  Identities=23%  Similarity=0.122  Sum_probs=17.1

Q ss_pred             EEEECCCCChHHHHHHHHHHHh
Q psy4275          46 CIGCAKTGSGKTLAFALPILQK   67 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~   67 (182)
                      .+++||.|+|||+++.+.+...
T Consensus        41 yLf~Gp~G~GKTtlAr~lAk~L   62 (486)
T PRK14953         41 YIFAGPRGTGKTTIARILAKVL   62 (486)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            5789999999998876655443

>PF05729 NACHT: NACHT domain

Probab=95.24  E-value=0.12  Score=35.64  Aligned_cols=26  Identities=23%  Similarity=0.015  Sum_probs=18.2

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhcc
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWCE   70 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~~   70 (182)
                      -+++.|++|+|||+.+...+......
T Consensus         2 ~l~I~G~~G~GKStll~~~~~~~~~~   27 (166)
T PF05729_consen    2 VLWISGEPGSGKSTLLRKLAQQLAEE   27 (166)
T ss_pred             EEEEECCCCCChHHHHHHHHHHHHhc
Confidence            36889999999999865444444333

>PHA00350 putative assembly protein

Probab=95.23  E-value=0.13  Score=41.27  Aligned_cols=25  Identities=12%  Similarity=-0.028  Sum_probs=17.9

Q ss_pred             EEEECCCCChHHHHHHHHHHHhhcc
Q psy4275          46 CIGCAKTGSGKTLAFALPILQKWCE   70 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~~~~   70 (182)
                      .++.|.+|+|||..++-..+....+
T Consensus         4 ~l~tG~pGSGKT~~aV~~~i~palk   28 (399)
T PHA00350          4 YAIVGRPGSYKSYEAVVYHIIPALK   28 (399)
T ss_pred             EEEecCCCCchhHHHHHHHHHHHHH
Confidence            4788999999999877644433343

>TIGR00767 rho transcription termination factor Rho

Probab=95.22  E-value=0.16  Score=40.89  Aligned_cols=28  Identities=21%  Similarity=0.214  Sum_probs=20.4

Q ss_pred             CCCcEEEECCCCChHHHHHHHHHHHhhcc
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALPILQKWCE   70 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~~~~~~~~   70 (182)
                      .|+.+.+.||+|+|||..+. .+...+..
T Consensus       167 ~Gq~~~IvG~~g~GKTtL~~-~i~~~I~~  194 (415)
T TIGR00767       167 KGQRGLIVAPPKAGKTVLLQ-KIAQAITR  194 (415)
T ss_pred             CCCEEEEECCCCCChhHHHH-HHHHhhcc
Confidence            47889999999999998643 34444433

Members of this family differ in the specificity of RNA binding.

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=95.21  E-value=0.11  Score=42.56  Aligned_cols=36  Identities=22%  Similarity=0.174  Sum_probs=23.8

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcC
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTP   82 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p   82 (182)
                      +.+++.||+|+|||-.+. ++...+...  +.+++++..
T Consensus       142 npl~L~G~~G~GKTHLl~-Ai~~~l~~~--~~~v~yi~~  177 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQ-AAVHALRES--GGKILYVRS  177 (445)
T ss_pred             ceEEEEcCCCCCHHHHHH-HHHHHHHHc--CCCEEEeeH
Confidence            458999999999997744 333333332  456777753

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=95.21  E-value=0.051  Score=40.41  Aligned_cols=42  Identities=7%  Similarity=-0.052  Sum_probs=30.2

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCH
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTR   84 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~   84 (182)
                      +..+...++.|++|+|||+.+...+...+.+   +.++++++...
T Consensus        21 i~~g~~~~i~G~~G~GKTtl~~~~~~~~~~~---g~~~~yi~~e~   62 (230)
T PRK08533         21 IPAGSLILIEGDESTGKSILSQRLAYGFLQN---GYSVSYVSTQL   62 (230)
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHHHhC---CCcEEEEeCCC
Confidence            3447788999999999999876665554333   45788888544

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

Probab=95.20  E-value=0.18  Score=42.13  Aligned_cols=81  Identities=14%  Similarity=0.268  Sum_probs=57.8

Q ss_pred             HHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhc----CCCcEEEEChHHHHHH
Q psy4275          63 PILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA----KKPHIVIATPGRLADH  138 (182)
Q Consensus        63 ~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~Ilv~T~~~l~~~  138 (182)
                      .++..+.......++||.+.++..++.++..+...    |+++..++|+.....+.+.+.    +..+|+|+|--.    
T Consensus       262 ~~L~~ll~~~~~~~~IVF~~tk~~~~~l~~~l~~~----g~~~~~lhG~l~q~~R~~~l~~F~~g~~~vLVaTDva----  333 (513)
T COG0513         262 ELLLKLLKDEDEGRVIVFVRTKRLVEELAESLRKR----GFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVA----  333 (513)
T ss_pred             HHHHHHHhcCCCCeEEEEeCcHHHHHHHHHHHHHC----CCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEEechh----
Confidence            33444444443447999999999999877666554    789999999998776665543    478999999443    


Q ss_pred             HhcCCCCCCCCccEEE
Q psy4275         139 LDTCNTFSLNRIKFLV  154 (182)
Q Consensus       139 ~~~~~~~~~~~~~~iI  154 (182)
                        . +.++++++++||
T Consensus       334 --a-RGiDi~~v~~Vi  346 (513)
T COG0513         334 --A-RGLDIPDVSHVI  346 (513)
T ss_pred             --h-ccCCccccceeE
Confidence              2 556777777665

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=95.18  E-value=0.047  Score=40.22  Aligned_cols=54  Identities=13%  Similarity=0.009  Sum_probs=35.6

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHh
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVL   97 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~   97 (182)
                      ..|...++.|++|+|||..++-.+.+.+.+.  +.++++++-.... .++.+.++.+
T Consensus        17 p~gs~~li~G~~GsGKT~l~~q~l~~~~~~~--ge~vlyvs~ee~~-~~l~~~~~s~   70 (226)
T PF06745_consen   17 PKGSVVLISGPPGSGKTTLALQFLYNGLKNF--GEKVLYVSFEEPP-EELIENMKSF   70 (226)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHHHHHH--T--EEEEESSS-H-HHHHHHHHTT
T ss_pred             CCCcEEEEEeCCCCCcHHHHHHHHHHhhhhc--CCcEEEEEecCCH-HHHHHHHHHc
Confidence            3467899999999999999887777776662  2267777754333 4444444443

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 ....

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=95.18  E-value=0.048  Score=41.31  Aligned_cols=30  Identities=13%  Similarity=-0.023  Sum_probs=22.8

Q ss_pred             hhhhhhhCCCcEEEECCCCChHHHHHHHHH
Q psy4275          35 AIIPHVLNDEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        35 ~~~~~~~~~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      ++...+..++++++.||+|+|||..+....
T Consensus        13 ~~l~~l~~g~~vLL~G~~GtGKT~lA~~la   42 (262)
T TIGR02640        13 RALRYLKSGYPVHLRGPAGTGKTTLAMHVA   42 (262)
T ss_pred             HHHHHHhcCCeEEEEcCCCCCHHHHHHHHH
Confidence            334445568899999999999999875443

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=95.17  E-value=0.056  Score=44.73  Aligned_cols=40  Identities=18%  Similarity=0.157  Sum_probs=26.4

Q ss_pred             ChHHHHhhhhhhhCC--CcEEEECCCCChHHHHHHHHHHHhhc
Q psy4275          29 PTEIQKAIIPHVLND--EDCIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        29 ~~~~Q~~~~~~~~~~--~~~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      +.+.|.+.+..+...  .-++++||||+|||+.. ..++..+.
T Consensus       226 ~~~~~~~~l~~~~~~~~GlilitGptGSGKTTtL-~a~L~~l~  267 (486)
T TIGR02533       226 MSPELLSRFERLIRRPHGIILVTGPTGSGKTTTL-YAALSRLN  267 (486)
T ss_pred             CCHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHH-HHHHhccC
Confidence            355566666555542  34689999999999985 44555544

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.

>PRK09183 transposase/IS protein; Provisional

Probab=95.16  E-value=0.042  Score=41.64  Aligned_cols=46  Identities=22%  Similarity=0.154  Sum_probs=29.5

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHH
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQ   89 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q   89 (182)
                      +..+.++++.||+|+|||..+..........   +..+.++. ...+..+
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa~al~~~a~~~---G~~v~~~~-~~~l~~~  144 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLAIALGYEAVRA---GIKVRFTT-AADLLLQ  144 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHHHHHHHHHHHc---CCeEEEEe-HHHHHHH
Confidence            4558899999999999998765554333222   44666654 3344433

>PRK04328 hypothetical protein; Provisional

Probab=95.16  E-value=0.045  Score=41.18  Aligned_cols=52  Identities=10%  Similarity=0.031  Sum_probs=34.4

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLV   96 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~   96 (182)
                      ..|...++.|++|+|||..++-.+.+.+.+   +..++|+.-.. -.+++.+.++.
T Consensus        21 p~gs~ili~G~pGsGKT~l~~~fl~~~~~~---ge~~lyis~ee-~~~~i~~~~~~   72 (249)
T PRK04328         21 PERNVVLLSGGPGTGKSIFSQQFLWNGLQM---GEPGVYVALEE-HPVQVRRNMRQ   72 (249)
T ss_pred             cCCcEEEEEcCCCCCHHHHHHHHHHHHHhc---CCcEEEEEeeC-CHHHHHHHHHH
Confidence            346788999999999999877777776544   44677776433 23344444443

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=95.14  E-value=0.2  Score=42.40  Aligned_cols=73  Identities=15%  Similarity=0.281  Sum_probs=52.8

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +.++||.|+++..++.+++.+...    ++.+..++|+.+..++...+    .++.+|+|+|.-      -. ..+++.+
T Consensus       257 ~~k~LVF~nt~~~ae~l~~~L~~~----g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaTdv------~a-rGIDip~  325 (572)
T PRK04537        257 GARTMVFVNTKAFVERVARTLERH----GYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDV------AA-RGLHIDG  325 (572)
T ss_pred             CCcEEEEeCCHHHHHHHHHHHHHc----CCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEehh------hh-cCCCccC
Confidence            568999999999999888877654    68899999988765544333    236789999932      12 4567777


Q ss_pred             ccEEEEec
Q psy4275         150 IKFLVLDE  157 (182)
Q Consensus       150 ~~~iI~DE  157 (182)
                      ++++|.-+
T Consensus       326 V~~VInyd  333 (572)
T PRK04537        326 VKYVYNYD  333 (572)
T ss_pred             CCEEEEcC
Confidence            77777543

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=95.14  E-value=0.016  Score=42.71  Aligned_cols=17  Identities=24%  Similarity=0.245  Sum_probs=13.5

Q ss_pred             EEEECCCCChHHHHHHH
Q psy4275          46 CIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~   62 (182)
                      +++.|++|+|||....-
T Consensus         1 ~vv~G~pGsGKSt~i~~   17 (234)
T PF01443_consen    1 IVVHGVPGSGKSTLIKK   17 (234)
T ss_pred             CEEEcCCCCCHHHHHHH
Confidence            36889999999987433

Some of the members are found in positive-strand single stranded RNA viruses. The helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis [].; GO: 0004386 helicase activity

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=95.13  E-value=0.082  Score=37.77  Aligned_cols=57  Identities=19%  Similarity=0.054  Sum_probs=36.7

Q ss_pred             CCCcEEEECCCCChHHHHHHHHHHHhhccC-------CCCeeEEEEcCCHHHHHHHHHHHHHhhc
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALPILQKWCED-------PYGIFALVLTPTRELAYQIGDQFLVLGK   99 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~~~~~~~~~-------~~~~~~lil~p~~~l~~q~~~~~~~~~~   99 (182)
                      .|.-.++.|++|+|||...+-.+.......       ..+.+++|+..... ..++.+.+..+..
T Consensus        31 ~g~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~-~~~~~~rl~~~~~   94 (193)
T PF13481_consen   31 RGELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS-ESQIARRLRALLQ   94 (193)
T ss_dssp             TTSEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS--HHHHHHHHHHHHT
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC-HHHHHHHHHHHhc
Confidence            477799999999999998766666555421       13568888887766 4566667766654

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.10  E-value=0.076  Score=42.95  Aligned_cols=35  Identities=26%  Similarity=0.155  Sum_probs=23.0

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      -+++.||+|+|||+.+.-.+.......  +.++.+++
T Consensus       225 vi~lvGptGvGKTTtaaKLA~~~~~~~--G~~V~Lit  259 (432)
T PRK12724        225 VVFFVGPTGSGKTTSIAKLAAKYFLHM--GKSVSLYT  259 (432)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHhc--CCeEEEec
Confidence            477889999999998766655443332  33455554

>TIGR00416 sms DNA repair protein RadA

Probab=95.08  E-value=0.27  Score=40.36  Aligned_cols=50  Identities=14%  Similarity=-0.001  Sum_probs=32.7

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLV   96 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~   96 (182)
                      |.-+++.|++|+|||+.++..+.....+   +.+++|+..... ..|+.....+
T Consensus        94 GsvilI~G~pGsGKTTL~lq~a~~~a~~---g~kvlYvs~EEs-~~qi~~ra~r  143 (454)
T TIGR00416        94 GSLILIGGDPGIGKSTLLLQVACQLAKN---QMKVLYVSGEES-LQQIKMRAIR  143 (454)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHHhc---CCcEEEEECcCC-HHHHHHHHHH
Confidence            5678889999999999876555544332   347888876543 3455444333

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)).

>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []

Probab=95.08  E-value=0.035  Score=39.21  Aligned_cols=25  Identities=16%  Similarity=0.222  Sum_probs=17.6

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhcc
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWCE   70 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~~   70 (182)
                      ++++.|+.|+|||+.. .-+++.+..
T Consensus         1 ~i~iTG~pG~GKTTll-~k~i~~l~~   25 (168)
T PF03266_consen    1 HIFITGPPGVGKTTLL-KKVIEELKK   25 (168)
T ss_dssp             EEEEES-TTSSHHHHH-HHHHHHHHH
T ss_pred             CEEEECcCCCCHHHHH-HHHHHHhhc
Confidence            4789999999999984 445555543

It includes proteins from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase []. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme []. The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue [].; GO: 0005524 ATP binding, 0016740 transferase activity, 0019204 nucleotide phosphatase activity; PDB: 1YE8_A 2I3B_A.

>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=95.07  E-value=0.15  Score=41.44  Aligned_cols=50  Identities=26%  Similarity=0.325  Sum_probs=38.1

Q ss_pred             CCcEEEEChHHHHHHHhc----CCC-CCCCCccEEEEeccccccccCChhHHHHH
Q psy4275         124 KPHIVIATPGRLADHLDT----CNT-FSLNRIKFLVLDEADRLSLMTSLKFFFFF  173 (182)
Q Consensus       124 ~~~Ilv~T~~~l~~~~~~----~~~-~~~~~~~~iI~DE~h~~~~~~~~~~~~~~  173 (182)
                      .++|+|++|=-+.-.+..    .+. -.++++.++|+|.+|.|.-.++-.....+
T Consensus       131 ~SDIIiASPLGLr~~i~~~~~~~~d~DFLSSIEv~iiD~ad~l~MQNW~Hv~~v~  185 (442)
T PF06862_consen  131 SSDIIIASPLGLRMIIGEEGEKKRDYDFLSSIEVLIIDQADVLLMQNWEHVLHVF  185 (442)
T ss_pred             cCCEEEEChHHHHHHhccccccccccchhheeeeEeechhhHHHHhhHHHHHHHH
Confidence            579999999999877763    122 25788999999999998888775554444

; GO: 0005634 nucleus

>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=95.07  E-value=0.11  Score=41.76  Aligned_cols=60  Identities=13%  Similarity=0.168  Sum_probs=34.5

Q ss_pred             CCCcEEEECCCCChHHHHHHHHHHHhhccC-CCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEc
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALPILQKWCED-PYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITG  110 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~~~~~~~~~-~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~  110 (182)
                      .+.++++.|+||+||+..+  ..++..... ..++++-+=|-      ...+..... ..+|..-+.++|
T Consensus       100 ~~~~vLi~GetGtGKel~A--~~iH~~s~r~~~~PFI~~NCa------~~~en~~~~-eLFG~~kGaftG  160 (403)
T COG1221         100 SGLPVLIIGETGTGKELFA--RLIHALSARRAEAPFIAFNCA------AYSENLQEA-ELFGHEKGAFTG  160 (403)
T ss_pred             CCCcEEEecCCCccHHHHH--HHHHHhhhcccCCCEEEEEHH------HhCcCHHHH-HHhccccceeec
Confidence            3789999999999999887  334443333 34554443322      122222221 145666666666

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=95.05  E-value=0.024  Score=45.32  Aligned_cols=56  Identities=27%  Similarity=0.335  Sum_probs=39.0

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEE
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIIT  109 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~  109 (182)
                      |+++.||||+|||..++++-+...     ...++++-|.-++....+...+..    |.+|.++.
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll~~-----~~s~vv~D~Kge~~~~t~~~r~~~----G~~V~v~n   56 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLLTW-----PGSVVVLDPKGENFELTSEHRRAL----GRKVFVFD   56 (384)
T ss_pred             CeeEecCCCCCCccEEEccchhcC-----CCCEEEEccchhHHHHHHHHHHHc----CCeEEEEc
Confidence            578999999999998776654432     246888989888876655554432    55555554

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.

>PRK05748 replicative DNA helicase; Provisional

Probab=95.04  E-value=0.38  Score=39.40  Aligned_cols=121  Identities=12%  Similarity=0.040  Sum_probs=60.6

Q ss_pred             hhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHH-HHhhccCCceEE-EEEcCCc
Q psy4275          36 IIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQF-LVLGKVMNLRVS-IITGGMD  113 (182)
Q Consensus        36 ~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~-~~~~~~~~~~~~-~~~~~~~  113 (182)
                      ...-+..|.-+++.|.+|.|||..++-.+.+...+.  +..++++... .-.+|+...+ ....   ++... ...|...
T Consensus       196 ~~~G~~~G~livIaarpg~GKT~~al~ia~~~a~~~--g~~v~~fSlE-ms~~~l~~R~l~~~~---~v~~~~i~~~~l~  269 (448)
T PRK05748        196 MTSGLQPNDLIIVAARPSVGKTAFALNIAQNVATKT--DKNVAIFSLE-MGAESLVMRMLCAEG---NIDAQRLRTGQLT  269 (448)
T ss_pred             hcCCCCCCceEEEEeCCCCCchHHHHHHHHHHHHhC--CCeEEEEeCC-CCHHHHHHHHHHHhc---CCCHHHhhcCCCC
Confidence            333344567788899999999998776666554332  3356666432 2233443332 2221   12211 1123222


Q ss_pred             hhhhhH-----HhcCCCcEEEE-----ChHHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275         114 MVDQGK-----ELAKKPHIVIA-----TPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus       114 ~~~~~~-----~~~~~~~Ilv~-----T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      ..++..     ....+..+.|.     |++.+...+++... ....+++||+|-.|.|..
T Consensus       270 ~~e~~~~~~a~~~l~~~~~~i~d~~~~ti~~i~~~~r~~~~-~~~~~~~vvIDyL~li~~  328 (448)
T PRK05748        270 DDDWPKLTIAMGSLSDAPIYIDDTPGIKVTEIRARCRRLAQ-EHGGLGLILIDYLQLIQG  328 (448)
T ss_pred             HHHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHH-hcCCCCEEEEccchhcCC
Confidence            222111     11123445553     44555544433211 112578999999998853

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=95.01  E-value=0.23  Score=38.99  Aligned_cols=39  Identities=13%  Similarity=0.085  Sum_probs=29.0

Q ss_pred             hHHHHhhhhhhhC--C---CcEEEECCCCChHHHHHHHHHHHhh
Q psy4275          30 TEIQKAIIPHVLN--D---EDCIGCAKTGSGKTLAFALPILQKW   68 (182)
Q Consensus        30 ~~~Q~~~~~~~~~--~---~~~li~~~tg~GKT~~~~~~~~~~~   68 (182)
                      .||+...|..+..  +   +..++.||.|.|||..+...+-..+
T Consensus         3 yPW~~~~w~~l~~~~~r~~hA~Lf~G~~G~GK~~la~~~a~~ll   46 (325)
T PRK08699          3 YPWHQEQWRQIAEHWERRPNAWLFAGKKGIGKTAFARFAAQALL   46 (325)
T ss_pred             CCccHHHHHHHHHhcCCcceEEEeECCCCCCHHHHHHHHHHHHc
Confidence            5788888877664  2   3578999999999988766655544

>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=95.00  E-value=0.041  Score=44.18  Aligned_cols=43  Identities=28%  Similarity=0.338  Sum_probs=27.0

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTREL   86 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l   86 (182)
                      ...+|+++.|.||+|||.+ +..++..+..+  +.+++|.-|.-+.
T Consensus        13 ~e~~~~li~G~~GsGKT~~-i~~ll~~~~~~--g~~~iI~D~kg~~   55 (386)
T PF10412_consen   13 SENRHILIIGATGSGKTQA-IRHLLDQIRAR--GDRAIIYDPKGEF   55 (386)
T ss_dssp             GGGG-EEEEE-TTSSHHHH-HHHHHHHHHHT--T-EEEEEEETTHH
T ss_pred             hhhCcEEEECCCCCCHHHH-HHHHHHHHHHc--CCEEEEEECCchH
Confidence            3468999999999999975 56666666554  3345555555444

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.

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=94.99  E-value=0.065  Score=39.63  Aligned_cols=44  Identities=14%  Similarity=-0.114  Sum_probs=30.1

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhhccCC---CCeeEEEEcCCH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKWCEDP---YGIFALVLTPTR   84 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~---~~~~~lil~p~~   84 (182)
                      ..|.-..+.|++|+|||..+...+.......+   .+..++++....
T Consensus        17 ~~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~   63 (235)
T cd01123          17 ETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEG   63 (235)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCC
Confidence            34677899999999999987766655433321   124688887544

This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=94.99  E-value=0.14  Score=41.10  Aligned_cols=27  Identities=19%  Similarity=0.183  Sum_probs=19.6

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhcc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCE   70 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~   70 (182)
                      |+..++.+|.|+|||+.+. .+...+..
T Consensus       169 GQR~lIvgppGvGKTTLaK-~Ian~I~~  195 (416)
T PRK09376        169 GQRGLIVAPPKAGKTVLLQ-NIANSITT  195 (416)
T ss_pred             CceEEEeCCCCCChhHHHH-HHHHHHHh
Confidence            7889999999999997643 34444433

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=94.94  E-value=0.13  Score=38.81  Aligned_cols=30  Identities=17%  Similarity=0.133  Sum_probs=21.3

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhcc
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCE   70 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~   70 (182)
                      +-+|+..++.||.|+|||+.+ -.+...+..
T Consensus        13 i~~Gqr~~I~G~~G~GKTTLl-r~I~n~l~~   42 (249)
T cd01128          13 IGKGQRGLIVAPPKAGKTTLL-QSIANAITK   42 (249)
T ss_pred             cCCCCEEEEECCCCCCHHHHH-HHHHhcccc
Confidence            345889999999999999753 344444433

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.

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=94.92  E-value=0.065  Score=40.97  Aligned_cols=43  Identities=16%  Similarity=-0.035  Sum_probs=32.4

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQ   89 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q   89 (182)
                      .=.=+.||.|+|||..++..+......   +..++|+....++-.+
T Consensus        61 ~ItEiyG~~gsGKT~lal~~~~~aq~~---g~~a~fIDtE~~l~p~  103 (279)
T COG0468          61 RITEIYGPESSGKTTLALQLVANAQKP---GGKAAFIDTEHALDPE  103 (279)
T ss_pred             eEEEEecCCCcchhhHHHHHHHHhhcC---CCeEEEEeCCCCCCHH
Confidence            345567999999999988877776555   4488998887776444

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=94.90  E-value=0.043  Score=41.46  Aligned_cols=54  Identities=13%  Similarity=0.081  Sum_probs=38.0

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHh
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVL   97 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~   97 (182)
                      +..|+..++.|++|+|||+.++-.+...+..   +..+++++-... ..++.+.+..+
T Consensus        20 ~p~g~~~lI~G~pGsGKT~f~~qfl~~~~~~---ge~vlyvs~~e~-~~~l~~~~~~~   73 (260)
T COG0467          20 LPRGSVVLITGPPGTGKTIFALQFLYEGARE---GEPVLYVSTEES-PEELLENARSF   73 (260)
T ss_pred             CcCCcEEEEEcCCCCcHHHHHHHHHHHHHhc---CCcEEEEEecCC-HHHHHHHHHHc
Confidence            3447889999999999999988777777666   456788775433 34444444443

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=94.87  E-value=0.054  Score=40.98  Aligned_cols=44  Identities=14%  Similarity=0.014  Sum_probs=30.2

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhcc---CCCCeeEEEEcCCHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCE---DPYGIFALVLTPTREL   86 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~---~~~~~~~lil~p~~~l   86 (182)
                      |.-.=++|++|+|||-.++-.++.....   .+.+.+++|+......
T Consensus        38 g~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f   84 (256)
T PF08423_consen   38 GSITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTF   84 (256)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS
T ss_pred             CcEEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCCCC
Confidence            4556788999999998776665554433   2235689999866543

It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues

Probab=94.87  E-value=0.042  Score=45.09  Aligned_cols=57  Identities=25%  Similarity=0.253  Sum_probs=40.0

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEE
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIIT  109 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~  109 (182)
                      .|+++.||||+|||..++++.+-.   .  +..+++.-|--++....+...++.    |.+|.++.
T Consensus        45 ~h~lvig~tgSGKt~~~viP~ll~---~--~~s~iV~D~KgEl~~~t~~~r~~~----G~~V~vld  101 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNLLN---Y--PGSMIVTDPKGELYEKTAGYRKKR----GYKVYVLD  101 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHHHh---c--cCCEEEEECCCcHHHHHHHHHHHC----CCEEEEee
Confidence            479999999999999987776532   2  226888889888876666555544    44555554

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

>TIGR03743 SXT_TraD conjugative coupling factor TraD, SXT/TOL subfamily

Probab=94.86  E-value=0.12  Score=44.24  Aligned_cols=53  Identities=25%  Similarity=0.254  Sum_probs=36.4

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHH--HHHHHHHHHHHhh
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRE--LAYQIGDQFLVLG   98 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~--l~~q~~~~~~~~~   98 (182)
                      .+|.++.|+||+|||..+...+.+.+..   +..++++-|-..  +...+...++..+
T Consensus       176 ~~H~lv~G~TGsGKT~l~~~l~~q~i~~---g~~viv~DpKgD~~l~~~~~~~~~~~G  230 (634)
T TIGR03743       176 VGHTLVLGTTGVGKTRLAELLITQDIRR---GDVVIVIDPKGDADLKRRMRAEAKRAG  230 (634)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEeCCCchHHHHHHHHHHHHhC
Confidence            5799999999999998864444444433   446888888765  5555555555543

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.

>PRK12377 putative replication protein; Provisional

Probab=94.84  E-value=0.12  Score=38.89  Aligned_cols=45  Identities=16%  Similarity=0.167  Sum_probs=27.6

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIG   91 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~   91 (182)
                      ..++++.||+|+|||..+... ...+...  +..++++ +..++...+.
T Consensus       101 ~~~l~l~G~~GtGKThLa~AI-a~~l~~~--g~~v~~i-~~~~l~~~l~  145 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLAAAI-GNRLLAK--GRSVIVV-TVPDVMSRLH  145 (248)
T ss_pred             CCeEEEECCCCCCHHHHHHHH-HHHHHHc--CCCeEEE-EHHHHHHHHH
Confidence            357899999999999875433 3333333  3345444 4455655543

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=94.82  E-value=0.22  Score=38.94  Aligned_cols=87  Identities=22%  Similarity=0.187  Sum_probs=46.9

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchh-----hhhH
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMV-----DQGK  119 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~  119 (182)
                      -++++|-+|+|||++. .-+.+.+.++  +.++++.+-..--+ --.+.++.|.+..|+.+.....+....     ....
T Consensus       141 Vil~vGVNG~GKTTTI-aKLA~~l~~~--g~~VllaA~DTFRA-aAiEQL~~w~er~gv~vI~~~~G~DpAaVafDAi~~  216 (340)
T COG0552         141 VILFVGVNGVGKTTTI-AKLAKYLKQQ--GKSVLLAAGDTFRA-AAIEQLEVWGERLGVPVISGKEGADPAAVAFDAIQA  216 (340)
T ss_pred             EEEEEecCCCchHhHH-HHHHHHHHHC--CCeEEEEecchHHH-HHHHHHHHHHHHhCCeEEccCCCCCcHHHHHHHHHH
Confidence            4677899999999984 3444444443  55666666432221 112345555555677776643222211     1112


Q ss_pred             HhcCCCc-EEEEChHHH
Q psy4275         120 ELAKKPH-IVIATPGRL  135 (182)
Q Consensus       120 ~~~~~~~-Ilv~T~~~l  135 (182)
                      ...++.+ +++-|.+++
T Consensus       217 Akar~~DvvliDTAGRL  233 (340)
T COG0552         217 AKARGIDVVLIDTAGRL  233 (340)
T ss_pred             HHHcCCCEEEEeCcccc
Confidence            2223444 566788777

>TIGR00665 DnaB replicative DNA helicase

Probab=94.77  E-value=0.35  Score=39.38  Aligned_cols=117  Identities=16%  Similarity=0.067  Sum_probs=59.5

Q ss_pred             hhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE-EEcCCchhhh
Q psy4275          39 HVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSI-ITGGMDMVDQ  117 (182)
Q Consensus        39 ~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~-~~~~~~~~~~  117 (182)
                      -+..|.-.++.|++|+|||..++-.+.+.....  +..++++...- -..++.+.+.....  ++.... ..|.....++
T Consensus       191 G~~~G~l~vi~g~pg~GKT~~~l~~a~~~a~~~--g~~vl~~SlEm-~~~~i~~R~~~~~~--~v~~~~~~~g~l~~~~~  265 (434)
T TIGR00665       191 GLQPSDLIILAARPSMGKTAFALNIAENAAIKE--GKPVAFFSLEM-SAEQLAMRMLSSES--RVDSQKLRTGKLSDEDW  265 (434)
T ss_pred             CCCCCeEEEEEeCCCCChHHHHHHHHHHHHHhC--CCeEEEEeCcC-CHHHHHHHHHHHhc--CCCHHHhccCCCCHHHH
Confidence            344567788899999999998776666554432  34566665432 22333333222211  222111 1222222211


Q ss_pred             h------HHhcCCCcEEE-----EChHHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275         118 G------KELAKKPHIVI-----ATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus       118 ~------~~~~~~~~Ilv-----~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      .      ..+ .+..+.|     .|++.+...++....  -..+++||+|=.+.|..
T Consensus       266 ~~~~~a~~~l-~~~~l~i~d~~~~~~~~i~~~i~~~~~--~~~~~~vvID~l~~i~~  319 (434)
T TIGR00665       266 EKLTSAAGKL-SEAPLYIDDTPGLTITELRAKARRLKR--EHGLGLIVIDYLQLMSG  319 (434)
T ss_pred             HHHHHHHHHH-hcCCEEEECCCCCCHHHHHHHHHHHHH--hcCCCEEEEcchHhcCC
Confidence            1      111 2334555     244555544433211  12378999999998854

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.

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=94.75  E-value=0.045  Score=47.91  Aligned_cols=55  Identities=18%  Similarity=0.118  Sum_probs=42.3

Q ss_pred             HhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHHHHHHH
Q psy4275         120 ELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFFFF  175 (182)
Q Consensus       120 ~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~~~~~~  175 (182)
                      .++....|++.||..+..=+-. +.++++++..+||||||++.......++..+.+
T Consensus         3 ~ly~~ggi~~~T~rIl~~DlL~-~ri~~~~itgiiv~~Ahr~~~~~~eaFI~rlyr   57 (814)
T TIGR00596         3 KVYLEGGIFSITSRILVVDLLT-GIIPPELITGILVLRADRIIESSQEAFILRLYR   57 (814)
T ss_pred             hHhhcCCEEEEechhhHhHHhc-CCCCHHHccEEEEeecccccccccHHHHHHHHH
Confidence            3456778999999999654434 557899999999999999987777676655543

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

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=94.71  E-value=0.26  Score=37.56  Aligned_cols=23  Identities=30%  Similarity=0.219  Sum_probs=18.2

Q ss_pred             CcEEEECCCCChHHHHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQ   66 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~   66 (182)
                      ....+.|++|+|||..+...+..
T Consensus        76 ~~i~~~G~~g~GKTtl~~~l~~~   98 (270)
T PRK06731         76 QTIALIGPTGVGKTTTLAKMAWQ   98 (270)
T ss_pred             CEEEEECCCCCcHHHHHHHHHHH
Confidence            57889999999999986655444

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=94.65  E-value=0.098  Score=38.50  Aligned_cols=52  Identities=15%  Similarity=0.014  Sum_probs=35.1

Q ss_pred             CCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHh
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVL   97 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~   97 (182)
                      .|...++.|++|+|||..+...+...+.+   +.+++|+..... .+++.+.+..+
T Consensus        15 ~g~~~li~G~~G~GKt~~~~~~~~~~~~~---g~~~~y~s~e~~-~~~l~~~~~~~   66 (224)
T TIGR03880        15 EGHVIVVIGEYGTGKTTFSLQFLYQGLKN---GEKAMYISLEER-EERILGYAKSK   66 (224)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEECCCC-HHHHHHHHHHc
Confidence            36678899999999998877666665544   457888876543 35554444443

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.

>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]

Probab=94.62  E-value=0.075  Score=48.49  Aligned_cols=54  Identities=24%  Similarity=0.201  Sum_probs=44.4

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCC--CCeeEEEEcCCHHHHHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDP--YGIFALVLTPTRELAYQIGDQFLV   96 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~--~~~~~lil~p~~~l~~q~~~~~~~   96 (182)
                      +.+.++.|..|||||.+..--++..+...+  .-.++++++.|++-+.++...+..
T Consensus        16 ~~~~lveASAGSGKT~vL~~r~lrlLl~~~~~~v~~ILvvTFT~aAa~Emk~RI~~   71 (1139)
T COG1074          16 GQSVLVEASAGTGKTFVLAERVLRLLLEGGPLDVDEILVVTFTKAAAAEMKERIRD   71 (1139)
T ss_pred             CCcEEEEEcCCCCchhHHHHHHHHHHhhcCCCChhHeeeeeccHHHHHHHHHHHHH
Confidence            679999999999999998777788777742  335899999999999888766554

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=94.59  E-value=0.29  Score=39.79  Aligned_cols=76  Identities=12%  Similarity=0.239  Sum_probs=52.8

Q ss_pred             hccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCC
Q psy4275          68 WCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCN  143 (182)
Q Consensus        68 ~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~  143 (182)
                      +.+.....++||.++++.-++.+++.++.    .++++..++|+.+..++...+    .+..+|+|+|.-      .. .
T Consensus       239 l~~~~~~~~~lVF~~s~~~~~~l~~~L~~----~~~~~~~l~g~~~~~~R~~~l~~f~~G~~~vLVaTd~------~~-~  307 (434)
T PRK11192        239 LLKQPEVTRSIVFVRTRERVHELAGWLRK----AGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDV------AA-R  307 (434)
T ss_pred             HHhcCCCCeEEEEeCChHHHHHHHHHHHh----CCCCEEEecCCCCHHHHHHHHHHHhCCCCcEEEEccc------cc-c
Confidence            33333356899999999999988887765    378899999988765554332    246789999932      12 4


Q ss_pred             CCCCCCccEEE
Q psy4275         144 TFSLNRIKFLV  154 (182)
Q Consensus       144 ~~~~~~~~~iI  154 (182)
                      .+++.++++||
T Consensus       308 GiDip~v~~VI  318 (434)
T PRK11192        308 GIDIDDVSHVI  318 (434)
T ss_pred             CccCCCCCEEE
Confidence            45677777666

>KOG0058|consensus

Probab=94.58  E-value=0.054  Score=46.17  Aligned_cols=29  Identities=21%  Similarity=0.266  Sum_probs=23.0

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhhccC
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKWCED   71 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~   71 (182)
                      ..|+.+-++||.|+|||.++  .++.++++-
T Consensus       492 ~pGe~vALVGPSGsGKSTia--sLL~rfY~P  520 (716)
T KOG0058|consen  492 RPGEVVALVGPSGSGKSTIA--SLLLRFYDP  520 (716)
T ss_pred             CCCCEEEEECCCCCCHHHHH--HHHHHhcCC
Confidence            34888999999999999987  666666653

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=94.56  E-value=0.28  Score=40.26  Aligned_cols=70  Identities=19%  Similarity=0.226  Sum_probs=49.0

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      ..++||.|+++.-++.+++.+...    ++++..++|+.+..++...+    .+..+|+|+|.-      -. ..+++.+
T Consensus       245 ~~~~lVF~~t~~~~~~l~~~L~~~----g~~~~~lhg~~~~~~R~~~l~~F~~g~~~iLVaTdv------~~-rGiDip~  313 (456)
T PRK10590        245 WQQVLVFTRTKHGANHLAEQLNKD----GIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDI------AA-RGLDIEE  313 (456)
T ss_pred             CCcEEEEcCcHHHHHHHHHHHHHC----CCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEccH------Hh-cCCCccc
Confidence            458999999999988887777553    78889999988765444332    236789999942      11 4456666


Q ss_pred             ccEEE
Q psy4275         150 IKFLV  154 (182)
Q Consensus       150 ~~~iI  154 (182)
                      +++||
T Consensus       314 v~~VI  318 (456)
T PRK10590        314 LPHVV  318 (456)
T ss_pred             CCEEE
Confidence            66655

>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=94.53  E-value=0.084  Score=38.28  Aligned_cols=43  Identities=19%  Similarity=0.279  Sum_probs=24.6

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhcc-CCCCeeEEEEcC
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCE-DPYGIFALVLTP   82 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~-~~~~~~~lil~p   82 (182)
                      +.+..|+++.|+||+|||......+...+.. ++...++.++-+
T Consensus        35 l~~~~h~li~G~tgsGKS~~l~~ll~~l~~~~~p~~~~l~iiD~   78 (205)
T PF01580_consen   35 LKKNPHLLIAGATGSGKSTLLRTLLLSLALTYSPDDVQLYIIDP   78 (205)
T ss_dssp             GGGS-SEEEE--TTSSHHHHHHHHHHHHHTT--TTTEEEEEE-T
T ss_pred             cCCCceEEEEcCCCCCccHHHHHHHHHHHHHhcCCccEEEEEcC
Confidence            3445699999999999999866555555442 233444444444

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.

>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type

Probab=94.52  E-value=0.13  Score=47.04  Aligned_cols=56  Identities=20%  Similarity=0.135  Sum_probs=42.7

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhh
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLG   98 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~   98 (182)
                      .+++++.++.|||||.+..--++..+.......++++|+.|+.-+.++.+.+....
T Consensus        10 ~~~~~~~a~agsgkt~~l~~~~~~~~~~~~~~~~i~~~t~t~~aa~em~~Ri~~~L   65 (1141)
T TIGR02784        10 KTSAWVSANAGSGKTHVLTQRVIRLLLNGVPPSKILCLTYTKAAAAEMQNRVFDRL   65 (1141)
T ss_pred             CCCEEEEEECCCCHHHHHHHHHHHHHHcCCCCCeEEEEecCHHHHHHHHHHHHHHH
Confidence            57899999999999998766666655543334589999999999988876655443

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.

>COG1132 MdlB ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]

Probab=94.51  E-value=0.098  Score=44.08  Aligned_cols=36  Identities=19%  Similarity=0.203  Sum_probs=23.7

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEE
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALV   79 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~li   79 (182)
                      ..|+.+-++||+|+|||+..  -++.+++... .+++++
T Consensus       353 ~~Ge~vaiVG~sGsGKSTl~--~LL~r~~~~~-~G~I~i  388 (567)
T COG1132         353 EPGEKVAIVGPSGSGKSTLI--KLLLRLYDPT-SGEILI  388 (567)
T ss_pred             cCCCEEEEECCCCCCHHHHH--HHHhccCCCC-CCeEEE
Confidence            34777789999999998765  4455555432 334555

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=94.51  E-value=0.29  Score=38.79  Aligned_cols=25  Identities=12%  Similarity=-0.114  Sum_probs=18.6

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhc
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      ..+++||.|+|||..+...+-..+.
T Consensus        47 a~L~~G~~G~GKttlA~~lA~~Llc   71 (351)
T PRK09112         47 ALLFEGPEGIGKATLAFHLANHILS   71 (351)
T ss_pred             eEeeECCCCCCHHHHHHHHHHHHcC
Confidence            4889999999999986555444433

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=94.50  E-value=0.14  Score=40.35  Aligned_cols=47  Identities=17%  Similarity=0.129  Sum_probs=30.4

Q ss_pred             HHHHHCCCCCChHHHHhhhhhhh-CCCcEEEECCCCChHHHHHHHHHHHhh
Q psy4275          19 RQCQTIGVKTPTEIQKAIIPHVL-NDEDCIGCAKTGSGKTLAFALPILQKW   68 (182)
Q Consensus        19 ~~l~~~~~~~~~~~Q~~~~~~~~-~~~~~li~~~tg~GKT~~~~~~~~~~~   68 (182)
                      +.+.+.|.  +.+.+.+.+..+. .+.+++++|+||+|||... ..++..+
T Consensus       155 ~~l~~~g~--~~~~~~~~L~~~v~~~~~ili~G~tGsGKTTll-~al~~~i  202 (340)
T TIGR03819       155 DELVASGT--FPPGVARLLRAIVAARLAFLISGGTGSGKTTLL-SALLALV  202 (340)
T ss_pred             HHHHHcCC--CCHHHHHHHHHHHhCCCeEEEECCCCCCHHHHH-HHHHccC
Confidence            33444443  4556666665544 4779999999999999874 3344433

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.

>KOG2228|consensus

Probab=94.46  E-value=0.53  Score=37.06  Aligned_cols=24  Identities=25%  Similarity=0.318  Sum_probs=18.6

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQ   66 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~   66 (182)
                      ++++++.||-|+|||+-.-..+..
T Consensus        49 snsviiigprgsgkT~li~~~Ls~   72 (408)
T KOG2228|consen   49 SNSVIIIGPRGSGKTILIDTRLSD   72 (408)
T ss_pred             CCceEEEccCCCCceEeeHHHHhh
Confidence            578999999999999864444444

>PRK08006 replicative DNA helicase; Provisional

Probab=94.46  E-value=0.86  Score=37.67  Aligned_cols=121  Identities=17%  Similarity=0.100  Sum_probs=61.8

Q ss_pred             hhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEE-EcCCchh
Q psy4275          37 IPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSII-TGGMDMV  115 (182)
Q Consensus        37 ~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~-~~~~~~~  115 (182)
                      ..-+..|.-+++.|.+|.|||..++-.+.+.....  +..++++... .-.+|+.+.+-...  .++....+ .|..+..
T Consensus       218 ~~Gl~~G~LiiIaarPgmGKTafalnia~~~a~~~--g~~V~~fSlE-M~~~ql~~Rlla~~--~~v~~~~i~~~~l~~~  292 (471)
T PRK08006        218 TAGLQPSDLIIVAARPSMGKTTFAMNLCENAAMLQ--DKPVLIFSLE-MPGEQIMMRMLASL--SRVDQTRIRTGQLDDE  292 (471)
T ss_pred             hcCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhc--CCeEEEEecc-CCHHHHHHHHHHHh--cCCCHHHhhcCCCCHH
Confidence            33445566778888999999998776665554332  3456666432 22344433322211  12222111 2333322


Q ss_pred             hhhH------HhcCCCcEEEE-----ChHHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275         116 DQGK------ELAKKPHIVIA-----TPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus       116 ~~~~------~~~~~~~Ilv~-----T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      ++.+      .+.+...+.|.     |+..+....++... ....+++||+|-.|.|..
T Consensus       293 e~~~~~~a~~~~~~~~~l~I~d~~~~t~~~i~~~~r~~~~-~~~~~~lvvIDYLqli~~  350 (471)
T PRK08006        293 DWARISGTMGILLEKRNMYIDDSSGLTPTEVRSRARRIFR-EHGGLSLIMIDYLQLMRV  350 (471)
T ss_pred             HHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHH-hcCCCCEEEEccHHHccC
Confidence            2211      12234456653     45555444433111 122578999999998863

>PRK06904 replicative DNA helicase; Validated

Probab=94.45  E-value=0.66  Score=38.36  Aligned_cols=121  Identities=19%  Similarity=0.127  Sum_probs=61.1

Q ss_pred             hhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEE-Ec-CCchh
Q psy4275          38 PHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSII-TG-GMDMV  115 (182)
Q Consensus        38 ~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~-~~-~~~~~  115 (182)
                      .-+..|.-+++.|.+|.|||..++-.+.......  +..++++... .-.+|+...+-...  .++....+ .| ..+..
T Consensus       216 ~Gl~~G~LiiIaarPg~GKTafalnia~~~a~~~--g~~Vl~fSlE-Ms~~ql~~Rlla~~--s~v~~~~i~~g~~l~~~  290 (472)
T PRK06904        216 AGLQPSDLIIVAARPSMGKTTFAMNLCENAAMAS--EKPVLVFSLE-MPAEQIMMRMLASL--SRVDQTKIRTGQNLDQQ  290 (472)
T ss_pred             hccCCCcEEEEEeCCCCChHHHHHHHHHHHHHhc--CCeEEEEecc-CCHHHHHHHHHHhh--CCCCHHHhccCCCCCHH
Confidence            3445566778888999999998765555444332  3456666533 33344433322211  12222111 23 22222


Q ss_pred             hhh------HHhcCCCcEEE-----EChHHHHHHHhcCCCCCCCCccEEEEecccccccc
Q psy4275         116 DQG------KELAKKPHIVI-----ATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus       116 ~~~------~~~~~~~~Ilv-----~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~  164 (182)
                      ++.      ..+.+...+.|     .|+..+....++... ....+++||||-.|.|...
T Consensus       291 e~~~~~~a~~~l~~~~~l~I~d~~~~t~~~i~~~~r~~~~-~~~~~~lvvIDYLqli~~~  349 (472)
T PRK06904        291 DWAKISSTVGMFKQKPNLYIDDSSGLTPTELRSRARRVYR-ENGGLSLIMVDYLQLMRAP  349 (472)
T ss_pred             HHHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHHH-hCCCCCEEEEecHHhcCCC
Confidence            221      12222344666     355555544433111 1124789999999988643

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP

Probab=94.45  E-value=0.56  Score=37.40  Aligned_cols=49  Identities=14%  Similarity=0.067  Sum_probs=27.7

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHh
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVL   97 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~   97 (182)
                      .+.+.+.|+.|+|||...-+. .+.+.. ..+.+    ++...-..++++.+.++
T Consensus        62 ~~GlYl~G~vG~GKT~Lmd~f-~~~lp~-~~k~R----~HFh~Fm~~vh~~l~~~  110 (362)
T PF03969_consen   62 PKGLYLWGPVGRGKTMLMDLF-YDSLPI-KRKRR----VHFHEFMLDVHSRLHQL  110 (362)
T ss_pred             CceEEEECCCCCchhHHHHHH-HHhCCc-ccccc----ccccHHHHHHHHHHHHH
Confidence            568899999999999874333 222222 11212    24445555555555554

AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding

>PRK10263 DNA translocase FtsK; Provisional

Probab=94.43  E-value=0.14  Score=46.73  Aligned_cols=41  Identities=22%  Similarity=0.345  Sum_probs=27.3

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhcc-CCCCeeEEEEcCC
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCE-DPYGIFALVLTPT   83 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~-~~~~~~~lil~p~   83 (182)
                      ..|.++.|.||+|||.+.-..++..+.. ++...+.++|-|.
T Consensus      1010 ~PHLLIAGaTGSGKSv~LntLIlSLl~~~sPeeVrl~LIDPK 1051 (1355)
T PRK10263       1010 MPHLLVAGTTGSGKSVGVNAMILSMLYKAQPEDVRFIMIDPK 1051 (1355)
T ss_pred             CCcEEEecCCCCCHHHHHHHHHHHHHHhCCccceEEEEECCC
Confidence            4699999999999999865555554443 2334455555554

>TIGR02012 tigrfam_recA protein RecA

Probab=94.40  E-value=0.11  Score=40.61  Aligned_cols=47  Identities=17%  Similarity=-0.017  Sum_probs=33.9

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHH
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQ   89 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q   89 (182)
                      +..|.-..+.||+|+|||..++..+......   +..++++.....+..+
T Consensus        52 lp~G~iteI~G~~GsGKTtLaL~~~~~~~~~---g~~v~yId~E~~~~~~   98 (321)
T TIGR02012        52 LPRGRIIEIYGPESSGKTTLALHAIAEAQKA---GGTAAFIDAEHALDPV   98 (321)
T ss_pred             CcCCeEEEEECCCCCCHHHHHHHHHHHHHHc---CCcEEEEcccchhHHH
Confidence            3446678899999999999977766665443   5578888776655443

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.

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=94.40  E-value=0.072  Score=45.20  Aligned_cols=59  Identities=22%  Similarity=0.134  Sum_probs=44.1

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITG  110 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~  110 (182)
                      ..|+++.||||+|||..++++-+-..     +..++++-|.-++....+...++    .|.+|.++..
T Consensus       158 ~~hvLviapTgSGKg~g~VIPnLL~~-----~~S~VV~DpKGEl~~~Ta~~R~~----~G~~V~vfdP  216 (606)
T PRK13897        158 FQHALLFAPTGSGKGVGFVIPNLLFW-----EDSVVVHDIKLENYELTSGWREK----QGQKVFVWEP  216 (606)
T ss_pred             CceEEEEcCCCCCcceEEehhhHHhC-----CCCEEEEeCcHHHHHHHHHHHHH----CCCeEEEEeC
Confidence            35899999999999999888876643     23689999999998776665554    3666666553

>PRK08506 replicative DNA helicase; Provisional

Probab=94.39  E-value=0.51  Score=39.01  Aligned_cols=119  Identities=17%  Similarity=0.082  Sum_probs=61.4

Q ss_pred             hhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE-EEcCCchhh
Q psy4275          38 PHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSI-ITGGMDMVD  116 (182)
Q Consensus        38 ~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~-~~~~~~~~~  116 (182)
                      .-+..|.-+++.|.+|.|||..++-.+.+...+   +..++++... .-..|+...+-..  ..++.... ..|..+...
T Consensus       187 ~G~~~G~LivIaarpg~GKT~fal~ia~~~~~~---g~~V~~fSlE-Ms~~ql~~Rlla~--~s~v~~~~i~~~~l~~~e  260 (472)
T PRK08506        187 KGFNKGDLIIIAARPSMGKTTLCLNMALKALNQ---DKGVAFFSLE-MPAEQLMLRMLSA--KTSIPLQNLRTGDLDDDE  260 (472)
T ss_pred             CCCCCCceEEEEcCCCCChHHHHHHHHHHHHhc---CCcEEEEeCc-CCHHHHHHHHHHH--hcCCCHHHHhcCCCCHHH
Confidence            334456678888999999999877666665422   4456666533 3334443332221  11222211 123322222


Q ss_pred             hh------HHhcCCCcEEEE-----ChHHHHHHHhcCCCCCCCCccEEEEecccccccc
Q psy4275         117 QG------KELAKKPHIVIA-----TPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus       117 ~~------~~~~~~~~Ilv~-----T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~  164 (182)
                      +.      ..+ .+..+.|-     |+..+...++.... ....+++||+|-.+.|...
T Consensus       261 ~~~~~~a~~~l-~~~~l~I~d~~~~ti~~I~~~~r~l~~-~~~~~~lvvIDyLql~~~~  317 (472)
T PRK08506        261 WERLSDACDEL-SKKKLFVYDSGYVNIHQVRAQLRKLKS-QHPEIGLAVIDYLQLMSGS  317 (472)
T ss_pred             HHHHHHHHHHH-HcCCeEEECCCCCCHHHHHHHHHHHHH-hCCCCCEEEEcChhhccCC
Confidence            21      112 23345552     45555544443211 1235789999999988643

>PF14516 AAA_35: AAA-like domain

Probab=94.38  E-value=0.29  Score=38.44  Aligned_cols=49  Identities=14%  Similarity=0.140  Sum_probs=36.8

Q ss_pred             hHHHHhhhhhhhC-CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275          30 TEIQKAIIPHVLN-DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus        30 ~~~Q~~~~~~~~~-~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      .|..++++..+.+ |..+.+.+|-..|||.. +..+++.+.+.  +.+++++-
T Consensus        17 ~~~e~~~~~~i~~~G~~~~I~apRq~GKTSl-l~~l~~~l~~~--~~~~v~id   66 (331)
T PF14516_consen   17 PPAEQECYQEIVQPGSYIRIKAPRQMGKTSL-LLRLLERLQQQ--GYRCVYID   66 (331)
T ss_pred             hHHHHHHHHHHhcCCCEEEEECcccCCHHHH-HHHHHHHHHHC--CCEEEEEE
Confidence            3588999999888 99999999999999988 44555555443  45565554

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=94.37  E-value=0.11  Score=39.92  Aligned_cols=20  Identities=20%  Similarity=0.071  Sum_probs=16.8

Q ss_pred             CCcEEEECCCCChHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~   62 (182)
                      +.++++.||+|+|||.++..
T Consensus        58 ~~~vll~G~pGTGKT~lA~~   77 (284)
T TIGR02880        58 TLHMSFTGNPGTGKTTVALR   77 (284)
T ss_pred             CceEEEEcCCCCCHHHHHHH
Confidence            45899999999999988643

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.

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=94.33  E-value=0.1  Score=40.54  Aligned_cols=28  Identities=25%  Similarity=0.347  Sum_probs=21.0

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhh
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKW   68 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~   68 (182)
                      +..+.++++.|+||+|||+.. ..++..+
T Consensus       141 v~~~~~ili~G~tGsGKTTll-~al~~~~  168 (308)
T TIGR02788       141 IASRKNIIISGGTGSGKTTFL-KSLVDEI  168 (308)
T ss_pred             hhCCCEEEEECCCCCCHHHHH-HHHHccC
Confidence            445889999999999999874 3344433

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=94.32  E-value=0.084  Score=38.95  Aligned_cols=40  Identities=20%  Similarity=0.351  Sum_probs=27.0

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTR   84 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~   84 (182)
                      ++|+.+.|.||+|||..... +++.+.+. .+..++++=|.-
T Consensus        23 ~~H~~I~G~TGsGKS~~~~~-ll~~l~~~-~~~~~ii~D~~G   62 (229)
T PF01935_consen   23 NRHIAIFGTTGSGKSNTVKV-LLEELLKK-KGAKVIIFDPHG   62 (229)
T ss_pred             cceEEEECCCCCCHHHHHHH-HHHHHHhc-CCCCEEEEcCCC
Confidence            57999999999999998544 44444421 144677776653

It contains several conserved aspartates and histidines that could be metal ligands.

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=94.26  E-value=0.014  Score=42.71  Aligned_cols=25  Identities=20%  Similarity=0.243  Sum_probs=18.6

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhh
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKW   68 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~   68 (182)
                      .+.+++.||.|+|||.. +..+....
T Consensus        20 ~~~~~l~G~rg~GKTsL-l~~~~~~~   44 (234)
T PF01637_consen   20 SQHILLYGPRGSGKTSL-LKEFINEL   44 (234)
T ss_dssp             SSEEEEEESTTSSHHHH-HHHHHHHC
T ss_pred             CcEEEEEcCCcCCHHHH-HHHHHHHh
Confidence            46889999999999986 44444444

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=94.26  E-value=0.085  Score=43.64  Aligned_cols=54  Identities=15%  Similarity=0.004  Sum_probs=36.1

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHh
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVL   97 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~   97 (182)
                      ..|...++.|++|+|||+.++-.+.+.+.+.  +.+++|++-. +-.+++.+..+.+
T Consensus        19 p~g~~~Li~G~pGsGKT~la~qfl~~g~~~~--ge~~lyvs~e-E~~~~l~~~~~~~   72 (484)
T TIGR02655        19 PIGRSTLVSGTSGTGKTLFSIQFLYNGIIHF--DEPGVFVTFE-ESPQDIIKNARSF   72 (484)
T ss_pred             CCCeEEEEEcCCCCCHHHHHHHHHHHHHHhC--CCCEEEEEEe-cCHHHHHHHHHHc
Confidence            3477899999999999999888877765542  2357777753 3334444444443

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.

>TIGR03754 conj_TOL_TraD conjugative coupling factor TraD, TOL family

Probab=94.26  E-value=0.21  Score=42.57  Aligned_cols=54  Identities=22%  Similarity=0.189  Sum_probs=38.6

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHH--HHHHHHHHHHHhhc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRE--LAYQIGDQFLVLGK   99 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~--l~~q~~~~~~~~~~   99 (182)
                      ..|.++.|+||+|||......+...+..   +..++++-|...  +...++..++...+
T Consensus       180 ~gHtlV~GtTGsGKT~l~~~li~q~i~~---g~~vi~fDpkgD~el~~~~~~~~~~~GR  235 (643)
T TIGR03754       180 VGHTLVLGTTRVGKTRLAELLITQDIRR---GDVVIVFDPKGDADLLKRMYAEAKRAGR  235 (643)
T ss_pred             cCceEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEeCCCCHHHHHHHHHHHHHhCC
Confidence            5689999999999999977665555543   457888888764  44555555555544

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.

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=94.24  E-value=0.46  Score=38.56  Aligned_cols=72  Identities=15%  Similarity=0.159  Sum_probs=51.7

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      ..++||.++++.-++.+++.+..    .++++..++|+....++...+    .++.+|+|+|.-      -. ..+++.+
T Consensus       255 ~~~~lVF~~t~~~~~~l~~~L~~----~g~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLVaTdv------~~-rGiDip~  323 (423)
T PRK04837        255 PDRAIIFANTKHRCEEIWGHLAA----DGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDV------AA-RGLHIPA  323 (423)
T ss_pred             CCeEEEEECCHHHHHHHHHHHHh----CCCcEEEecCCCChhHHHHHHHHHHcCCCcEEEEech------hh-cCCCccc
Confidence            45899999999998887777754    378899999987765544332    347899999942      12 4567777


Q ss_pred             ccEEEEe
Q psy4275         150 IKFLVLD  156 (182)
Q Consensus       150 ~~~iI~D  156 (182)
                      ++++|.-
T Consensus       324 v~~VI~~  330 (423)
T PRK04837        324 VTHVFNY  330 (423)
T ss_pred             cCEEEEe
Confidence            7766643

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=94.23  E-value=0.043  Score=42.62  Aligned_cols=56  Identities=20%  Similarity=0.160  Sum_probs=34.7

Q ss_pred             CCccCCCCCHHHHHHHHHCCCC----------CChHHHHhhhhh------hhCCCcEEEECCCCChHHHHHH
Q psy4275           6 KSFTDLKLNPWLIRQCQTIGVK----------TPTEIQKAIIPH------VLNDEDCIGCAKTGSGKTLAFA   61 (182)
Q Consensus         6 ~~~~~~~l~~~i~~~l~~~~~~----------~~~~~Q~~~~~~------~~~~~~~li~~~tg~GKT~~~~   61 (182)
                      ...+++|-+.++.+.|...-+.          ..+.+-++.-..      -+.+.|+++.||||||||+.+.
T Consensus        44 ~~~~~lPtP~eik~~Ld~YVIGQe~AKKvLsVAVYNHYKRl~~~~~~~dvEL~KSNILLiGPTGsGKTlLAq  115 (408)
T COG1219          44 KELSELPTPKEIKAHLDEYVIGQEQAKKVLSVAVYNHYKRLNNKEDNDDVELSKSNILLIGPTGSGKTLLAQ  115 (408)
T ss_pred             hhhccCCChHHHHHHhhhheecchhhhceeeeeehhHHHHHhccCCCCceeeeeccEEEECCCCCcHHHHHH
Confidence            3456678888888888765332          122222222111      1225689999999999998764

>PRK07004 replicative DNA helicase; Provisional

Probab=94.23  E-value=0.47  Score=39.08  Aligned_cols=122  Identities=16%  Similarity=0.114  Sum_probs=60.6

Q ss_pred             hhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHH-HHhhccCCceEEEE-EcCCc
Q psy4275          36 IIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQF-LVLGKVMNLRVSII-TGGMD  113 (182)
Q Consensus        36 ~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~-~~~~~~~~~~~~~~-~~~~~  113 (182)
                      ...-+..|.-+++.|.+|.|||..++-.+.+.....  +..++++.. ..-.+|+...+ ....   ++....+ .|..+
T Consensus       206 ~t~G~~~g~liviaarpg~GKT~~al~ia~~~a~~~--~~~v~~fSl-EM~~~ql~~R~la~~~---~v~~~~i~~g~l~  279 (460)
T PRK07004        206 MTSGMHGGELIIVAGRPSMGKTAFSMNIGEYVAVEY--GLPVAVFSM-EMPGTQLAMRMLGSVG---RLDQHRMRTGRLT  279 (460)
T ss_pred             cccCCCCCceEEEEeCCCCCccHHHHHHHHHHHHHc--CCeEEEEeC-CCCHHHHHHHHHHhhc---CCCHHHHhcCCCC
Confidence            333344566788889999999998776665544332  334555542 22233332222 2211   2222111 23333


Q ss_pred             hhhhhH-----HhcCCCcEEEE-----ChHHHHHHHhcCCCCCCCCccEEEEecccccccc
Q psy4275         114 MVDQGK-----ELAKKPHIVIA-----TPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus       114 ~~~~~~-----~~~~~~~Ilv~-----T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~  164 (182)
                      ..++..     ...++..+.|.     |+..+....++... ....+++||+|-.|.|...
T Consensus       280 ~~e~~~~~~a~~~l~~~~l~I~d~~~~~~~~i~~~~r~l~~-~~~~~~lviIDYLql~~~~  339 (460)
T PRK07004        280 DEDWPKLTHAVQKMSEAQLFIDETGGLNPMELRSRARRLAR-QCGKLGLIIIDYLQLMSGS  339 (460)
T ss_pred             HHHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHH-hCCCCCEEEEChhhhccCC
Confidence            222211     11224556662     44444444333111 1234789999999998743

>KOG1807|consensus

Probab=94.22  E-value=0.094  Score=45.16  Aligned_cols=67  Identities=18%  Similarity=-0.030  Sum_probs=52.0

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCC---CCeeEEEEcCCHHHHHHHHHHH
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP---YGIFALVLTPTRELAYQIGDQF   94 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~---~~~~~lil~p~~~l~~q~~~~~   94 (182)
                      -+...|..++......+-.+++||+|+|||.+.+.++-..+.++.   ..-.++++|-|...++|...-+
T Consensus       378 ildsSq~~A~qs~ltyelsliqgppGTgkt~vtlkav~tLL~n~s~~~~~epIlvvC~Tnhavdq~ligi  447 (1025)
T KOG1807|consen  378 ILDSSQQFAKQSKLTYELSLIQGPPGTGKTLVTLKAVDTLLLNSSGYTEPEPILVVCLTNHAVDQYLIGI  447 (1025)
T ss_pred             eecHHHHHHHHHHhhhhhheeecCCCCCceeehHHHHHHHHhcccccccccceeeeehhhHHHHHHHHHH
Confidence            466779999988888889999999999999997777666655541   2335899999999888865443

>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=94.21  E-value=0.2  Score=33.05  Aligned_cols=21  Identities=19%  Similarity=0.056  Sum_probs=16.1

Q ss_pred             EEEECCCCChHHHHHHHHHHH
Q psy4275          46 CIGCAKTGSGKTLAFALPILQ   66 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~   66 (182)
                      +++.||+|+|||..+-..+-.
T Consensus         1 ill~G~~G~GKT~l~~~la~~   21 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQY   21 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHH
T ss_pred             CEEECcCCCCeeHHHHHHHhh
Confidence            478999999999986544444

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 ....

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.19  E-value=0.33  Score=41.47  Aligned_cols=24  Identities=21%  Similarity=0.177  Sum_probs=18.3

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhh
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKW   68 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~   68 (182)
                      ..+++||.|+|||.++.+......
T Consensus        41 ayLf~Gp~G~GKtt~A~~lAk~l~   64 (614)
T PRK14971         41 AYLFCGPRGVGKTTCARIFAKTIN   64 (614)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhC
Confidence            378999999999997665555443

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=94.17  E-value=0.23  Score=40.73  Aligned_cols=26  Identities=19%  Similarity=0.158  Sum_probs=19.8

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhc
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      +..++.||.|+|||..+...+-....
T Consensus        40 ha~Lf~Gp~G~GKtt~A~~lAk~l~c   65 (451)
T PRK06305         40 HAYLFSGIRGTGKTTLARIFAKALNC   65 (451)
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHhcC
Confidence            34789999999999997666555443

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=94.14  E-value=0.19  Score=35.20  Aligned_cols=54  Identities=24%  Similarity=0.305  Sum_probs=33.6

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEE
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIIT  109 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~  109 (182)
                      ..+.+.|++|+|||+. +.-+.+.+...+-+ -.=+++|          ++..=.+..|+++.-+.
T Consensus         6 mki~ITG~PGvGKtTl-~~ki~e~L~~~g~k-vgGf~t~----------EVR~gGkR~GF~Ivdl~   59 (179)
T COG1618           6 MKIFITGRPGVGKTTL-VLKIAEKLREKGYK-VGGFITP----------EVREGGKRIGFKIVDLA   59 (179)
T ss_pred             eEEEEeCCCCccHHHH-HHHHHHHHHhcCce-eeeEEee----------eeecCCeEeeeEEEEcc
Confidence            3578999999999988 44555555554311 2234544          33455566677776655

>cd01131 PilT Pilus retraction ATPase PilT

Probab=94.13  E-value=0.11  Score=37.54  Aligned_cols=24  Identities=21%  Similarity=0.257  Sum_probs=17.5

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhc
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      -++++||||+|||+.. ..++..+.
T Consensus         3 lilI~GptGSGKTTll-~~ll~~~~   26 (198)
T cd01131           3 LVLVTGPTGSGKSTTL-AAMIDYIN   26 (198)
T ss_pred             EEEEECCCCCCHHHHH-HHHHHHhh
Confidence            4688999999999985 34444443

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.

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=94.10  E-value=0.13  Score=40.25  Aligned_cols=46  Identities=15%  Similarity=-0.063  Sum_probs=33.9

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQ   89 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q   89 (182)
                      ..|+-+.+.||+|+|||..++..+......   +..++|+.+...+-.+
T Consensus        53 p~G~iteI~Gp~GsGKTtLal~~~~~~~~~---g~~~vyId~E~~~~~~   98 (325)
T cd00983          53 PKGRIIEIYGPESSGKTTLALHAIAEAQKL---GGTVAFIDAEHALDPV   98 (325)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHHHHc---CCCEEEECccccHHHH
Confidence            335678899999999999877766665433   5578899887766543

RecA couples ATP hydrolysis to DNA strand exchange.

>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=94.05  E-value=0.055  Score=41.32  Aligned_cols=24  Identities=21%  Similarity=0.199  Sum_probs=19.5

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHH
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~   63 (182)
                      +..+++++++||+|+|||....-.
T Consensus        30 ~~~~~pvLl~G~~GtGKT~li~~~   53 (272)
T PF12775_consen   30 LSNGRPVLLVGPSGTGKTSLIQNF   53 (272)
T ss_dssp             HHCTEEEEEESSTTSSHHHHHHHH
T ss_pred             HHcCCcEEEECCCCCchhHHHHhh
Confidence            445889999999999999985443

>PF02283 CobU: Cobinamide kinase / cobinamide phosphate guanyltransferase; InterPro: IPR003203 This family is composed of a group of bifunctional cobalbumin biosynthesis enzymes which display cobinamide kinase and cobinamide phosphate guanyltransferase activity

Probab=94.00  E-value=1  Score=31.72  Aligned_cols=84  Identities=12%  Similarity=0.024  Sum_probs=50.8

Q ss_pred             EEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCC
Q psy4275          46 CIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKP  125 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  125 (182)
                      +++.|+..||||..+.-.+...      +.+.+|++.....-.++.+.+++..+.-+....++...............+.
T Consensus         1 ilv~GG~rSGKS~~Ae~la~~~------~~~~~YiAT~~~~D~em~~RI~~H~~~R~~~w~tiE~~~~l~~~~~~~~~~~   74 (167)
T PF02283_consen    1 ILVTGGARSGKSSFAERLALSF------GGPVTYIATARPFDEEMRERIARHRQRRPKGWITIEEPRDLAEALEELSPGD   74 (167)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS--------SCEEEEESSHHHHHHHHHHHHHHHHHSSTCEEEEE-SS-GGGTS-TTS-T-
T ss_pred             CEEeCCCCcchHHHHHHHHHhc------CCCcEEEeCCCCCCHHHHHHHHHHHHhCCCCcEEEecchhHHHHHHHhccCC
Confidence            4789999999998877666222      3578999999999777777777655444666666655444333332222223


Q ss_pred             cEEEEChHHH
Q psy4275         126 HIVIATPGRL  135 (182)
Q Consensus       126 ~Ilv~T~~~l  135 (182)
                      -|+|-.-..+
T Consensus        75 ~vLlDclt~w   84 (167)
T PF02283_consen   75 VVLLDCLTLW   84 (167)
T ss_dssp             EEEEE-HHHH
T ss_pred             eEEEeCHHHH
Confidence            4666554444

The crystal structure of the enzyme reveals the molecule to be a trimer with a propeller-like shape [].; GO: 0000166 nucleotide binding, 0043752 adenosylcobinamide kinase activity, 0051188 cofactor biosynthetic process; PDB: 1CBU_C 1C9K_B.

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=93.99  E-value=0.069  Score=44.56  Aligned_cols=28  Identities=21%  Similarity=0.218  Sum_probs=20.5

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhhcc
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKWCE   70 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~~~   70 (182)
                      ..|+...++||+|+|||+.+  -++..++.
T Consensus       359 ~~G~~vaIvG~SGsGKSTLl--~lL~g~~~  386 (529)
T TIGR02868       359 PPGERVAILGPSGSGKSTLL--MLLTGLLD  386 (529)
T ss_pred             cCCCEEEEECCCCCCHHHHH--HHHhcCCC
Confidence            34888999999999999764  44444444

The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=93.97  E-value=0.66  Score=36.41  Aligned_cols=84  Identities=13%  Similarity=0.039  Sum_probs=49.6

Q ss_pred             ChHHHHhhhhhhhC----C---CcEEEECCCCChHHHHHHHHHHHhhccCC------------------CCeeEEEEcCC
Q psy4275          29 PTEIQKAIIPHVLN----D---EDCIGCAKTGSGKTLAFALPILQKWCEDP------------------YGIFALVLTPT   83 (182)
Q Consensus        29 ~~~~Q~~~~~~~~~----~---~~~li~~~tg~GKT~~~~~~~~~~~~~~~------------------~~~~~lil~p~   83 (182)
                      ..||+...+..+.+    +   +-.++.||.|.||+..+...+...+..++                  ..+-+.++.|.
T Consensus         3 ~yPW~~~~~~~l~~~~~~~rl~HA~Lf~G~~G~GK~~lA~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~   82 (325)
T PRK06871          3 LYPWLQPTYQQITQAFQQGLGHHALLFKADSGLGTEQLIRALAQWLMCQTPQGDQPCGQCHSCHLFQAGNHPDFHILEPI   82 (325)
T ss_pred             CCcchHHHHHHHHHHHHcCCcceeEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEccc
Confidence            46777777766654    3   35668999999999887766555544321                  12335666673


Q ss_pred             ---HHHHHHHHHHHHHh---hccCCceEEEEEcCC
Q psy4275          84 ---RELAYQIGDQFLVL---GKVMNLRVSIITGGM  112 (182)
Q Consensus        84 ---~~l~~q~~~~~~~~---~~~~~~~~~~~~~~~  112 (182)
                         .--++|+.+..+.+   ....+.++..+.+..
T Consensus        83 ~~~~I~id~iR~l~~~~~~~~~~g~~KV~iI~~a~  117 (325)
T PRK06871         83 DNKDIGVDQVREINEKVSQHAQQGGNKVVYIQGAE  117 (325)
T ss_pred             cCCCCCHHHHHHHHHHHhhccccCCceEEEEechh
Confidence               12355655443333   233457887776543

>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=93.93  E-value=0.11  Score=40.47  Aligned_cols=42  Identities=26%  Similarity=0.182  Sum_probs=29.9

Q ss_pred             CChHHHHhhh-hhhhCCCcEEEECCCCChHHHHHHHHHHHhhcc
Q psy4275          28 TPTEIQKAII-PHVLNDEDCIGCAKTGSGKTLAFALPILQKWCE   70 (182)
Q Consensus        28 ~~~~~Q~~~~-~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~   70 (182)
                      .+.+.|..-+ -.+..+++.+++|+||+|||.. +.+++..+..
T Consensus       127 t~~~~~~ayL~~~ie~~~siii~G~t~sGKTt~-lnall~~Ip~  169 (312)
T COG0630         127 TISPEQAAYLWLAIEARKSIIICGGTASGKTTL-LNALLDFIPP  169 (312)
T ss_pred             CCCHHHHHHHHHHHHcCCcEEEECCCCCCHHHH-HHHHHHhCCc
Confidence            4566665544 4456689999999999999987 5555555443

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=93.90  E-value=0.59  Score=36.55  Aligned_cols=37  Identities=16%  Similarity=0.040  Sum_probs=23.9

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcC
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTP   82 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p   82 (182)
                      ++-+.+.||+|+|||+.+.-.+... ...  +.+++++.-
T Consensus       114 ~~vi~lvGpnGsGKTTt~~kLA~~l-~~~--g~~V~Li~~  150 (318)
T PRK10416        114 PFVILVVGVNGVGKTTTIGKLAHKY-KAQ--GKKVLLAAG  150 (318)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHH-Hhc--CCeEEEEec
Confidence            3457788999999998865444333 222  456777653

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=93.89  E-value=0.11  Score=42.90  Aligned_cols=52  Identities=17%  Similarity=0.116  Sum_probs=36.2

Q ss_pred             CCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHh
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVL   97 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~   97 (182)
                      .|.-+++.||+|+|||+.++..+...+.+   +.+++|+.-.. -.+|+....+.+
T Consensus       262 ~gs~~li~G~~G~GKt~l~~~f~~~~~~~---ge~~~y~s~eE-s~~~i~~~~~~l  313 (484)
T TIGR02655       262 KDSIILATGATGTGKTLLVSKFLENACAN---KERAILFAYEE-SRAQLLRNAYSW  313 (484)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHC---CCeEEEEEeeC-CHHHHHHHHHHc
Confidence            36688999999999999877776666544   45788887433 345555555544

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.

>PRK13695 putative NTPase; Provisional

Probab=93.88  E-value=1.2  Score=31.37  Aligned_cols=18  Identities=22%  Similarity=0.041  Sum_probs=14.9

Q ss_pred             cEEEECCCCChHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~   62 (182)
                      ++.+.|++|+|||+.+..
T Consensus         2 ~i~ltG~~G~GKTTll~~   19 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLK   19 (174)
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            467899999999998654

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=93.87  E-value=0.088  Score=43.64  Aligned_cols=24  Identities=17%  Similarity=0.074  Sum_probs=18.5

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHh
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQK   67 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~   67 (182)
                      +-.+++||-|+|||.++-+.+-..
T Consensus        39 hAYlfsG~RGvGKTt~Ari~Akal   62 (515)
T COG2812          39 HAYLFSGPRGVGKTTIARILAKAL   62 (515)
T ss_pred             hhhhhcCCCCcCchhHHHHHHHHh
Confidence            457889999999999875555444

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=93.87  E-value=0.77  Score=35.93  Aligned_cols=86  Identities=12%  Similarity=0.007  Sum_probs=51.3

Q ss_pred             CChHHHHhhhhhhhC----C---CcEEEECCCCChHHHHHHHHHHHhhccCC-----------------CCeeEEEEcCC
Q psy4275          28 TPTEIQKAIIPHVLN----D---EDCIGCAKTGSGKTLAFALPILQKWCEDP-----------------YGIFALVLTPT   83 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~----~---~~~li~~~tg~GKT~~~~~~~~~~~~~~~-----------------~~~~~lil~p~   83 (182)
                      +..|||...+..+.+    +   +-.+++||.|.||+..+...+...+..++                 ..+-+.++.|.
T Consensus         3 ~~yPWl~~~~~~l~~~~~~~rl~hA~L~~G~~G~Gk~~lA~~~a~~llC~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~   82 (319)
T PRK06090          3 NDYPWLVPVWQNWKAGLDAGRIPGALLLQSDEGLGVESLVELFSRALLCQNYQSEACGFCHSCELMQSGNHPDLHVIKPE   82 (319)
T ss_pred             cCcccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecC
Confidence            467888888877654    3   35889999999999887655554443221                 12345667774


Q ss_pred             H----HHHHHHHHHHHHh---hccCCceEEEEEcCCc
Q psy4275          84 R----ELAYQIGDQFLVL---GKVMNLRVSIITGGMD  113 (182)
Q Consensus        84 ~----~l~~q~~~~~~~~---~~~~~~~~~~~~~~~~  113 (182)
                      .    --++|+.+..+..   ....+.+|.++.+...
T Consensus        83 ~~~~~I~vdqiR~l~~~~~~~~~~~~~kV~iI~~ae~  119 (319)
T PRK06090         83 KEGKSITVEQIRQCNRLAQESSQLNGYRLFVIEPADA  119 (319)
T ss_pred             cCCCcCCHHHHHHHHHHHhhCcccCCceEEEecchhh
Confidence            2    1345554433222   1223578888776443

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=93.87  E-value=0.3  Score=38.35  Aligned_cols=26  Identities=15%  Similarity=0.161  Sum_probs=19.6

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhcc
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWCE   70 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~~   70 (182)
                      -.++.||.|+||+..+...+-..+..
T Consensus        30 a~Lf~G~~G~gk~~~a~~la~~l~c~   55 (329)
T PRK08058         30 AYLFEGAKGTGKKATALWLAKSLFCL   55 (329)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHCCC
Confidence            35899999999999876665555444

>CHL00176 ftsH cell division protein; Validated

Probab=93.85  E-value=0.49  Score=40.61  Aligned_cols=20  Identities=25%  Similarity=0.275  Sum_probs=16.8

Q ss_pred             CcEEEECCCCChHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~   63 (182)
                      +++++.||+|+|||..+-..
T Consensus       217 ~gVLL~GPpGTGKT~LAral  236 (638)
T CHL00176        217 KGVLLVGPPGTGKTLLAKAI  236 (638)
T ss_pred             ceEEEECCCCCCHHHHHHHH
Confidence            57999999999999886444

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=93.85  E-value=0.18  Score=37.44  Aligned_cols=52  Identities=13%  Similarity=-0.006  Sum_probs=35.5

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLV   96 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~   96 (182)
                      ..|.-+++.|++|+|||..+...+...+.+   +.+++|+.-.... +++.+.++.
T Consensus        23 ~~g~~~~i~G~~GsGKt~l~~~~~~~~~~~---g~~~~y~~~e~~~-~~~~~~~~~   74 (234)
T PRK06067         23 PFPSLILIEGDHGTGKSVLSQQFVYGALKQ---GKKVYVITTENTS-KSYLKQMES   74 (234)
T ss_pred             cCCcEEEEECCCCCChHHHHHHHHHHHHhC---CCEEEEEEcCCCH-HHHHHHHHH
Confidence            336678889999999999877776665543   5578888865444 344444444

>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=93.74  E-value=0.075  Score=43.61  Aligned_cols=72  Identities=15%  Similarity=-0.053  Sum_probs=55.2

Q ss_pred             CCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhh
Q psy4275          25 GVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLG   98 (182)
Q Consensus        25 ~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~   98 (182)
                      ++.++...|+++.-..-.|+. .+.|-.|+|||.....-+.+.-..+++. ++++.+-++.|+.++...+.+++
T Consensus       159 kIanfD~~Q~kaa~~~~~G~q-rIrGLAGSGKT~~La~Kaa~lh~knPd~-~I~~Tfftk~L~s~~r~lv~~F~  230 (660)
T COG3972         159 KIANFDTDQTKAAFQSGFGKQ-RIRGLAGSGKTELLAHKAAELHSKNPDS-RIAFTFFTKILASTMRTLVPEFF  230 (660)
T ss_pred             HHhcccchhheeeeecCCchh-hhhcccCCCchhHHHHHHHHHhcCCCCc-eEEEEeehHHHHHHHHHHHHHHH
Confidence            345677778776655555655 6788899999999777777766666655 89999999999999888777764

>PF05894 Podovirus_Gp16: Podovirus DNA encapsidation protein (Gp16); InterPro: IPR008784 This family consists of several DNA encapsidation protein (Gp16) sequences from the phi-29-like viruses

Probab=93.73  E-value=0.95  Score=35.15  Aligned_cols=101  Identities=17%  Similarity=0.091  Sum_probs=57.0

Q ss_pred             EEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHH-HHHHhhccCCceEEEEEcCCchhhhhHHhcCCC
Q psy4275          47 IGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGD-QFLVLGKVMNLRVSIITGGMDMVDQGKELAKKP  125 (182)
Q Consensus        47 li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  125 (182)
                      ++.|+-|.|||.+.--.++..+...  |.+.+++=-...=++.+.+ .+.++.+.++-.-..+.|..-       ..++-
T Consensus        21 ~viG~RgiGKtya~k~~~i~df~~~--G~qfiyLRr~k~E~~~~~n~~f~dv~~~f~~~~F~vk~~k~-------~idgk   91 (333)
T PF05894_consen   21 FVIGARGIGKTYALKKKLIKDFIEY--GEQFIYLRRYKTELDKMKNKFFNDVQQEFPNNEFEVKGNKI-------YIDGK   91 (333)
T ss_pred             EEEecccccchhHHHHHHHHHHHhc--CCEEEEEEecchHHHHHhhHHHHHHHHhCCCCcEEEEccEE-------EECCe
Confidence            4459999999999888888888776  5577887655554444443 444443333221122233221       11122


Q ss_pred             cEEEEChHHHHHHHhcCCCCCCCCccEEEEeccc
Q psy4275         126 HIVIATPGRLADHLDTCNTFSLNRIKFLVLDEAD  159 (182)
Q Consensus       126 ~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h  159 (182)
                      .+...+|-.-....   +....+++..||+||.-
T Consensus        92 ~~g~~~~Ls~~q~~---Ks~~Yp~V~~IvfDEfi  122 (333)
T PF05894_consen   92 LIGYFIPLSGWQKL---KSSSYPNVYTIVFDEFI  122 (333)
T ss_pred             EEEEEEecchhhhc---ccCCCCcEEEEEEEEEE
Confidence            22222222222222   44467889999999996

Gene product 16 catalyses the in vivo and in vitro genome-encapsidation reaction [].; GO: 0005524 ATP binding, 0019069 viral capsid assembly

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=93.71  E-value=0.13  Score=40.56  Aligned_cols=55  Identities=20%  Similarity=0.279  Sum_probs=35.9

Q ss_pred             CccCCccCCC-CCHHHHHHHHHC--CCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHH
Q psy4275           3 DPIKSFTDLK-LNPWLIRQCQTI--GVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus         3 ~~~~~~~~~~-l~~~i~~~l~~~--~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~   60 (182)
                      +|--+|++.| |++++.+.-.-.  .+.+|--+++-.+   ..-+.+++.||+|+|||+.+
T Consensus       145 ~PdvtY~dIGGL~~Qi~EirE~VELPL~~PElF~~~GI---~PPKGVLLYGPPGTGKTLLA  202 (406)
T COG1222         145 KPDVTYEDIGGLDEQIQEIREVVELPLKNPELFEELGI---DPPKGVLLYGPPGTGKTLLA  202 (406)
T ss_pred             CCCCChhhccCHHHHHHHHHHHhcccccCHHHHHHcCC---CCCCceEeeCCCCCcHHHHH
Confidence            3445677774 777777666443  3344444444444   22467999999999999885

>PRK09354 recA recombinase A; Provisional

Probab=93.70  E-value=0.17  Score=40.03  Aligned_cols=43  Identities=19%  Similarity=0.003  Sum_probs=33.0

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAY   88 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~   88 (182)
                      |.-+.+.||+|+|||..++..+......   +..++|+....++-.
T Consensus        60 G~IteI~G~~GsGKTtLal~~~~~~~~~---G~~~~yId~E~s~~~  102 (349)
T PRK09354         60 GRIVEIYGPESSGKTTLALHAIAEAQKA---GGTAAFIDAEHALDP  102 (349)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc---CCcEEEECCccchHH
Confidence            5578899999999999987777665543   557888888776654

>PRK08840 replicative DNA helicase; Provisional

Probab=93.68  E-value=1.4  Score=36.37  Aligned_cols=124  Identities=16%  Similarity=0.128  Sum_probs=61.4

Q ss_pred             HHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHH-HHHhhccCCceEEEE-Ec
Q psy4275          33 QKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQ-FLVLGKVMNLRVSII-TG  110 (182)
Q Consensus        33 Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~-~~~~~~~~~~~~~~~-~~  110 (182)
                      -.....-+..|.-+++.|.+|.|||..++-.+.......  +..++++... .-.+|+... +...   .++....+ .|
T Consensus       207 LD~~~~G~~~g~LiviaarPg~GKTafalnia~~~a~~~--~~~v~~fSlE-Ms~~ql~~Rlla~~---s~v~~~~i~~~  280 (464)
T PRK08840        207 LNKKTAGLQGSDLIIVAARPSMGKTTFAMNLCENAAMDQ--DKPVLIFSLE-MPAEQLMMRMLASL---SRVDQTKIRTG  280 (464)
T ss_pred             HHHhhcCCCCCceEEEEeCCCCchHHHHHHHHHHHHHhC--CCeEEEEecc-CCHHHHHHHHHHhh---CCCCHHHHhcC
Confidence            334444455577788889999999998765555544332  3456666433 223444322 2222   12222111 22


Q ss_pred             CCchhhhhH------HhcCCCcEEEE-----ChHHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275         111 GMDMVDQGK------ELAKKPHIVIA-----TPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus       111 ~~~~~~~~~------~~~~~~~Ilv~-----T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      ..+..++..      .+.+...+.|.     |...+....++... ....+++||+|-.|.|..
T Consensus       281 ~l~~~e~~~~~~a~~~l~~~~~l~I~d~~~~ti~~i~~~~r~~~~-~~~~~~lvvIDYLql~~~  343 (464)
T PRK08840        281 QLDDEDWARISSTMGILMEKKNMYIDDSSGLTPTEVRSRARRIAR-EHGGLSMIMVDYLQLMRV  343 (464)
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHH-hcCCCCEEEEccHHhcCC
Confidence            222222221      12123445553     34444433333211 112478999999998863

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=93.63  E-value=0.13  Score=37.88  Aligned_cols=40  Identities=15%  Similarity=0.005  Sum_probs=29.5

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      ..|.-..+.|++|+|||..++..+.+.+..   +.+++|+.-.
T Consensus        21 ~~g~i~~i~G~~GsGKT~l~~~la~~~~~~---~~~v~yi~~e   60 (225)
T PRK09361         21 ERGTITQIYGPPGSGKTNICLQLAVEAAKN---GKKVIYIDTE   60 (225)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHHC---CCeEEEEECC
Confidence            336678999999999999877766665543   4577887655

>cd01127 TrwB Bacterial conjugation protein TrwB, ATP binding domain

Probab=93.61  E-value=0.09  Score=42.55  Aligned_cols=23  Identities=26%  Similarity=0.400  Sum_probs=18.1

Q ss_pred             hhhhCCCcEEEECCCCChHHHHH
Q psy4275          38 PHVLNDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        38 ~~~~~~~~~li~~~tg~GKT~~~   60 (182)
                      +.-...+|+++.|+||+|||...
T Consensus        37 ~~~~~~~h~~i~g~tGsGKt~~i   59 (410)
T cd01127          37 PKDAEEAHTMIIGTTGTGKTTQI   59 (410)
T ss_pred             CcchhhccEEEEcCCCCCHHHHH
Confidence            33344679999999999999874

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.

>PTZ00110 helicase; Provisional

Probab=93.59  E-value=0.8  Score=38.57  Aligned_cols=71  Identities=18%  Similarity=0.208  Sum_probs=50.1

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +.++||.|+++.-++.+++.+..    .++.+..++|+....++...+    .+..+|+|+|.-      .. ..+++.+
T Consensus       377 ~~k~LIF~~t~~~a~~l~~~L~~----~g~~~~~ihg~~~~~eR~~il~~F~~G~~~ILVaTdv------~~-rGIDi~~  445 (545)
T PTZ00110        377 GDKILIFVETKKGADFLTKELRL----DGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDV------AS-RGLDVKD  445 (545)
T ss_pred             CCeEEEEecChHHHHHHHHHHHH----cCCcEEEEECCCcHHHHHHHHHHHhcCCCcEEEEcch------hh-cCCCccc
Confidence            56899999999999888777754    367888999988765544332    236789999942      12 4456777


Q ss_pred             ccEEEE
Q psy4275         150 IKFLVL  155 (182)
Q Consensus       150 ~~~iI~  155 (182)
                      +++||.
T Consensus       446 v~~VI~  451 (545)
T PTZ00110        446 VKYVIN  451 (545)
T ss_pred             CCEEEE
Confidence            776664

>PRK05595 replicative DNA helicase; Provisional

Probab=93.56  E-value=0.43  Score=39.06  Aligned_cols=124  Identities=14%  Similarity=0.054  Sum_probs=60.2

Q ss_pred             HhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEE-EcCC
Q psy4275          34 KAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSII-TGGM  112 (182)
Q Consensus        34 ~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~-~~~~  112 (182)
                      .+...-+..|.-+++.|.||.|||..++-.+.+...++  +..++++...- -.+|+...+-...  .++....+ .|..
T Consensus       192 d~~~~G~~~g~liviaarpg~GKT~~al~ia~~~a~~~--g~~vl~fSlEm-s~~~l~~R~~a~~--~~v~~~~~~~~~l  266 (444)
T PRK05595        192 DAKTSGFQKGDMILIAARPSMGKTTFALNIAEYAALRE--GKSVAIFSLEM-SKEQLAYKLLCSE--ANVDMLRLRTGNL  266 (444)
T ss_pred             HHhcCCCCCCcEEEEEecCCCChHHHHHHHHHHHHHHc--CCcEEEEecCC-CHHHHHHHHHHHh--cCCCHHHHhcCCC
Confidence            33333344566778889999999998776665543332  44677765431 2233332222111  12222111 2222


Q ss_pred             chhhhhHH-----hcCCCcEEEE-----ChHHHHHHHhcCCCCCCCCccEEEEecccccccc
Q psy4275         113 DMVDQGKE-----LAKKPHIVIA-----TPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus       113 ~~~~~~~~-----~~~~~~Ilv~-----T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~  164 (182)
                      ...++...     ...+..+.|-     |++.+...+++.+  .-..+++||+|-.|.|...
T Consensus       267 ~~~e~~~~~~~~~~l~~~~l~i~d~~~~t~~~i~~~~r~~~--~~~~~~~vvIDylql~~~~  326 (444)
T PRK05595        267 EDKDWENIARASGPLAAAKIFIDDTAGVSVMEMRSKCRRLK--IEHGIDMILIDYLQLMSGG  326 (444)
T ss_pred             CHHHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHH--HhcCCCEEEEeHHHhccCC
Confidence            22211110     0112344442     3344444343321  1234789999999998743

>COG3598 RepA RecA-family ATPase [DNA replication, recombination, and repair]

Probab=93.56  E-value=0.38  Score=37.57  Aligned_cols=135  Identities=16%  Similarity=0.076  Sum_probs=69.4

Q ss_pred             HHhhhhhh-hCCCcEEEECCCCChHHHHHHHHHHHhhcc-------CCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCce
Q psy4275          33 QKAIIPHV-LNDEDCIGCAKTGSGKTLAFALPILQKWCE-------DPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLR  104 (182)
Q Consensus        33 Q~~~~~~~-~~~~~~li~~~tg~GKT~~~~~~~~~~~~~-------~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~  104 (182)
                      |-+.++.+ ..+...++.|+.|.|||+..+...+.....       -++.+.++||.-...- +.+...++.+....++.
T Consensus        78 ~P~lId~~fr~g~~~~~~gdsg~GKttllL~l~IalaaG~~lfG~~v~epGkvlyvslEl~r-e~~L~Rl~~v~a~mgLs  156 (402)
T COG3598          78 SPQLIDEFFRKGYVSILYGDSGVGKTTLLLYLCIALAAGKNLFGNKVKEPGKVLYVSLELYR-EDILERLEPVRARMGLS  156 (402)
T ss_pred             ChhhhhHHhhcCeeEEEecCCcccHhHHHHHHHHHHHhhHHHhcccccCCCeEEEEEeccCh-HHHHHHHHHHHHHcCCC
Confidence            44445443 346678888999999999876555543221       1234578888643222 33344555555544432


Q ss_pred             E-----EEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEe------ccccccccCChhHHHHH
Q psy4275         105 V-----SIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLD------EADRLSLMTSLKFFFFF  173 (182)
Q Consensus       105 ~-----~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~D------E~h~~~~~~~~~~~~~~  173 (182)
                      -     .-+++-..         ....--+..| ++.+.+...  ....+-+++|+|      |-....+..-..+...+
T Consensus       157 Padvrn~dltd~~G---------aa~~~d~l~p-kl~rRfek~--~~Q~rp~~vViDp~v~f~~G~s~s~vqv~~fi~~~  224 (402)
T COG3598         157 PADVRNMDLTDVSG---------AADESDVLSP-KLYRRFEKI--LEQKRPDFVVIDPFVAFYEGKSISDVQVKEFIKKT  224 (402)
T ss_pred             hHhhhheecccccc---------CCCccccccH-HHHHHHHHH--HHHhCCCeEEEcchhhhcCCccchhHHHHHHHHHH
Confidence            1     11110000         1111122344 444433221  112335689999      44555556666777777


Q ss_pred             HHHhhcC
Q psy4275         174 FFLKYYI  180 (182)
Q Consensus       174 ~~~~~~~  180 (182)
                      .+++..+
T Consensus       225 rkla~~l  231 (402)
T COG3598         225 RKLARNL  231 (402)
T ss_pred             HHHHHhc
Confidence            7777655

>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor

Probab=93.54  E-value=0.35  Score=34.10  Aligned_cols=40  Identities=23%  Similarity=0.236  Sum_probs=27.4

Q ss_pred             CCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      ...+++++|++|+||+..+  -.++....+..++.+.+=|..
T Consensus        21 ~~~pVlI~GE~GtGK~~lA--~~IH~~s~r~~~pfi~vnc~~   60 (168)
T PF00158_consen   21 SDLPVLITGETGTGKELLA--RAIHNNSPRKNGPFISVNCAA   60 (168)
T ss_dssp             STS-EEEECSTTSSHHHHH--HHHHHCSTTTTS-EEEEETTT
T ss_pred             CCCCEEEEcCCCCcHHHHH--HHHHHhhhcccCCeEEEehhh
Confidence            3578999999999999886  455555444456667666654

These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....

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

Probab=93.54  E-value=0.31  Score=41.49  Aligned_cols=80  Identities=20%  Similarity=0.298  Sum_probs=55.5

Q ss_pred             CeeEEEEcCCHHH--------HHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhc
Q psy4275          74 GIFALVLTPTREL--------AYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDT  141 (182)
Q Consensus        74 ~~~~lil~p~~~l--------~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~  141 (182)
                      |.++.+|||..+=        +...++.++.+..  +.++..+||..+..+..+.+    .++.+|+|+|.-      =+
T Consensus       473 GrQaY~VcPLIeESE~l~l~~a~~~~~~L~~~~~--~~~vgL~HGrm~~~eKd~vM~~Fk~~e~~ILVaTTV------IE  544 (677)
T COG1200         473 GRQAYVVCPLIEESEKLELQAAEELYEELKSFLP--ELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTV------IE  544 (677)
T ss_pred             CCEEEEEeccccccccchhhhHHHHHHHHHHHcc--cceeEEEecCCChHHHHHHHHHHHcCCCcEEEEeeE------EE
Confidence            6789999997652        3444555554333  57899999998865554443    247899999921      12


Q ss_pred             CCCCCCCCccEEEEecccccc
Q psy4275         142 CNTFSLNRIKFLVLDEADRLS  162 (182)
Q Consensus       142 ~~~~~~~~~~~iI~DE~h~~~  162 (182)
                       ..++..+-+++|+..|+++.
T Consensus       545 -VGVdVPnATvMVIe~AERFG  564 (677)
T COG1200         545 -VGVDVPNATVMVIENAERFG  564 (677)
T ss_pred             -ecccCCCCeEEEEechhhhh
Confidence             45688888999999998764

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=93.51  E-value=0.61  Score=38.26  Aligned_cols=73  Identities=12%  Similarity=0.218  Sum_probs=51.4

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      ..++||.|+++.-++.+++.+...    ++.+..++|+.+..++...+    .+..+|+|+|.-      -. ..+++++
T Consensus       242 ~~~~lVF~~t~~~~~~l~~~L~~~----~~~v~~~hg~~~~~eR~~~l~~F~~g~~~vLVaTdv------~~-rGiDi~~  310 (460)
T PRK11776        242 PESCVVFCNTKKECQEVADALNAQ----GFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDV------AA-RGLDIKA  310 (460)
T ss_pred             CCceEEEECCHHHHHHHHHHHHhC----CCcEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEecc------cc-cccchhc
Confidence            457999999999999888877654    78899999988765444333    236789999932      12 4456777


Q ss_pred             ccEEEEec
Q psy4275         150 IKFLVLDE  157 (182)
Q Consensus       150 ~~~iI~DE  157 (182)
                      ++++|.-+
T Consensus       311 v~~VI~~d  318 (460)
T PRK11776        311 LEAVINYE  318 (460)
T ss_pred             CCeEEEec
Confidence            77666543

>PRK09165 replicative DNA helicase; Provisional

Probab=93.50  E-value=1.6  Score=36.43  Aligned_cols=120  Identities=15%  Similarity=0.054  Sum_probs=60.6

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhccC------------CCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCED------------PYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSI  107 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~------------~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  107 (182)
                      +..|.-+++.|.+|.|||..++-.+.+...+.            ..+..++|+.-. .-.+|+...+-....  ++....
T Consensus       214 ~~~g~livIaarpg~GKT~~al~ia~~~a~~~~~~~~~~~~~~~~~g~~vl~fSlE-Ms~~ql~~R~la~~s--~v~~~~  290 (497)
T PRK09165        214 LHPSDLIILAGRPSMGKTALATNIAFNAAKAYRREAQPDGSKKAVNGGVVGFFSLE-MSAEQLATRILSEQS--EISSSK  290 (497)
T ss_pred             CCCCceEEEEeCCCCChHHHHHHHHHHHHHhhcccccccccccccCCCeEEEEeCc-CCHHHHHHHHHHHhc--CCCHHH
Confidence            34456688889999999998776655544321            124466666432 223444333322211  222211


Q ss_pred             -EEcCCchhhhhH-----HhcCCCcEEEE-----ChHHHHHHHhcCCCCCCCCccEEEEecccccccc
Q psy4275         108 -ITGGMDMVDQGK-----ELAKKPHIVIA-----TPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus       108 -~~~~~~~~~~~~-----~~~~~~~Ilv~-----T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~  164 (182)
                       ..|.....++..     .......+.|.     |++.+...+++.+  .-..+++||||=.|.|...
T Consensus       291 i~~~~l~~~e~~~l~~a~~~l~~~~l~I~d~~~~ti~~i~~~ir~l~--~~~~~~lvvIDyLqli~~~  356 (497)
T PRK09165        291 IRRGKISEEDFEKLVDASQELQKLPLYIDDTPALSISQLRARARRLK--RQHGLDLLVVDYLQLIRGS  356 (497)
T ss_pred             HhcCCCCHHHHHHHHHHHHHHhcCCeEEeCCCCCCHHHHHHHHHHHH--HhcCCCEEEEcchHhccCC
Confidence             223332222211     11123445553     4555555554321  1234789999999988643

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=93.50  E-value=0.077  Score=30.87  Aligned_cols=18  Identities=22%  Similarity=0.320  Sum_probs=15.4

Q ss_pred             CCcEEEECCCCChHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~   60 (182)
                      +...++.+++|+|||...
T Consensus        23 g~~tli~G~nGsGKSTll   40 (62)
T PF13555_consen   23 GDVTLITGPNGSGKSTLL   40 (62)
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            457999999999999874

>KOG1806|consensus

Probab=93.47  E-value=0.15  Score=45.27  Aligned_cols=68  Identities=19%  Similarity=0.151  Sum_probs=51.2

Q ss_pred             ChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHh
Q psy4275          29 PTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVL   97 (182)
Q Consensus        29 ~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~   97 (182)
                      .+|-|.+++..-..-+...+.||+|+|||-.+. -++..++.+.-+.+++|++++....++..+.+.+.
T Consensus       739 ft~~qveai~sg~qpgltmvvgppgtgktd~av-qil~~lyhn~p~qrTlivthsnqaln~lfeKi~~~  806 (1320)
T KOG1806|consen  739 FTPTQVEAILSGMQPGLTMVVGPPGTGKTDVAV-QILSVLYHNSPNQRTLIVTHSNQALNQLFEKIMAL  806 (1320)
T ss_pred             cCHHHHHHHHhcCCCCceeeecCCCCCCcchhh-hhhhhhhhcCCCcceEEEEecccchhHHHHHHHhc
Confidence            467888888776666789999999999997754 33333444444679999999999888887776654

>TIGR00609 recB exodeoxyribonuclease V, beta subunit

Probab=93.43  E-value=0.23  Score=45.26  Aligned_cols=53  Identities=25%  Similarity=0.167  Sum_probs=41.7

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccC-C-CCeeEEEEcCCHHHHHHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCED-P-YGIFALVLTPTRELAYQIGDQFLV   96 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~-~-~~~~~lil~p~~~l~~q~~~~~~~   96 (182)
                      ...+|.+..|+|||.+.....+..+... . .-.++++|+=|++-+.++.+.+++
T Consensus        10 G~~lieAsAGtGKT~ti~~~~lrll~~~~~~~~~~iLvvTFT~aAt~el~~RIr~   64 (1087)
T TIGR00609        10 GTFLIEASAGTGKTFTIAQLYLRLLLEGGPLTVEEILVVTFTNAATEELKTRIRG   64 (1087)
T ss_pred             CCEEEEECCCCCHHHHHHHHHHHHHhcCCCCChhhEEEEehhHHHHHHHHHHHHH
Confidence            4689999999999998777777666654 2 235899999999988888777665

All proteins in this family for which functions are known are DNA-DNA helicases that are used as part of an exonuclease-helicase complex (made up of RecBCD homologs) that function to generate substrates for the initiation of recombination and recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>KOG0344|consensus

Probab=93.40  E-value=1.5  Score=36.83  Aligned_cols=98  Identities=15%  Similarity=0.174  Sum_probs=69.8

Q ss_pred             CCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhc----CCCc
Q psy4275          51 KTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA----KKPH  126 (182)
Q Consensus        51 ~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~  126 (182)
                      -.++|++..-++++...+. .+-.+.++|.+.+.+-+.|++..+.   ..-++++..++|..+..++...+.    +...
T Consensus       365 lvF~gse~~K~lA~rq~v~-~g~~PP~lIfVQs~eRak~L~~~L~---~~~~i~v~vIh~e~~~~qrde~~~~FR~g~Iw  440 (593)
T KOG0344|consen  365 LVFCGSEKGKLLALRQLVA-SGFKPPVLIFVQSKERAKQLFEELE---IYDNINVDVIHGERSQKQRDETMERFRIGKIW  440 (593)
T ss_pred             heeeecchhHHHHHHHHHh-ccCCCCeEEEEecHHHHHHHHHHhh---hccCcceeeEecccchhHHHHHHHHHhccCee
Confidence            3577787776666666544 4456789999999999998887776   334688999999877655554443    3567


Q ss_pred             EEEEChHHHHHHHhcCCCCCCCCccEEEEeccc
Q psy4275         127 IVIATPGRLADHLDTCNTFSLNRIKFLVLDEAD  159 (182)
Q Consensus       127 Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h  159 (182)
                      ++|||.     .+.  +.+++..+++||-++.-
T Consensus       441 vLicTd-----ll~--RGiDf~gvn~VInyD~p  466 (593)
T KOG0344|consen  441 VLICTD-----LLA--RGIDFKGVNLVINYDFP  466 (593)
T ss_pred             EEEehh-----hhh--ccccccCcceEEecCCC
Confidence            999992     232  34788899999988753

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=93.29  E-value=0.15  Score=43.90  Aligned_cols=57  Identities=18%  Similarity=0.099  Sum_probs=41.0

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEE
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIIT  109 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~  109 (182)
                      .|+++.||||+|||..++++-+-..     ...++++-|--++......+.++    .|.+|.++.
T Consensus       140 ~hvlviApTgSGKgvg~VIPnLL~~-----~gS~VV~DpKGE~~~~Ta~~R~~----~G~~V~~Fn  196 (670)
T PRK13850        140 PHSLVVAPTRAGKGVGVVIPTLLTF-----KGSVIALDVKGELFELTSRARKA----SGDAVFKFA  196 (670)
T ss_pred             ceEEEEecCCCCceeeehHhHHhcC-----CCCEEEEeCCchHHHHHHHHHHh----CCCEEEEec
Confidence            4899999999999999887765542     23688888988887666555544    355665544

>PRK12608 transcription termination factor Rho; Provisional

Probab=93.28  E-value=1.3  Score=35.47  Aligned_cols=36  Identities=17%  Similarity=0.165  Sum_probs=24.0

Q ss_pred             Hhhhhhhh---CCCcEEEECCCCChHHHHHHHHHHHhhcc
Q psy4275          34 KAIIPHVL---NDEDCIGCAKTGSGKTLAFALPILQKWCE   70 (182)
Q Consensus        34 ~~~~~~~~---~~~~~li~~~tg~GKT~~~~~~~~~~~~~   70 (182)
                      ..++..+.   +|+..++.||.|+|||+.... +...+.+
T Consensus       121 ~RvID~l~PiGkGQR~LIvG~pGtGKTTLl~~-la~~i~~  159 (380)
T PRK12608        121 MRVVDLVAPIGKGQRGLIVAPPRAGKTVLLQQ-IAAAVAA  159 (380)
T ss_pred             HhhhhheeecCCCceEEEECCCCCCHHHHHHH-HHHHHHh
Confidence            33444443   378999999999999988543 3343333

>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=93.25  E-value=0.077  Score=35.84  Aligned_cols=19  Identities=21%  Similarity=0.135  Sum_probs=15.3

Q ss_pred             cEEEECCCCChHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~   63 (182)
                      ++++.||+|+|||..+...
T Consensus         1 ~vlL~G~~G~GKt~l~~~l   19 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLAREL   19 (139)
T ss_dssp             EEEEEESSSSSHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHH
Confidence            4789999999999885433

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.

>PHA00149 DNA encapsidation protein

Probab=93.04  E-value=1.9  Score=33.19  Aligned_cols=103  Identities=17%  Similarity=0.122  Sum_probs=56.0

Q ss_pred             EEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCC
Q psy4275          46 CIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKP  125 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  125 (182)
                      .++.|+-|.|||.+..-.++..+...  |-+.+++=-...=.....+.+........-.-..+.|..       ...++-
T Consensus        20 ~fviG~RgiGKTya~k~~~~k~~i~k--geqfiYLRr~k~El~~k~~Ff~d~~~~~~~~~F~Vkg~k-------i~~~~k   90 (331)
T PHA00149         20 NFVIGARGIGKTYALKKYLIKRFIKK--GEQFIYLRRYKSELKKKSKFFADIAQEFPNTEFEVKGRK-------IYIKGK   90 (331)
T ss_pred             EEEEeccccchhhHHHHHHHHHHHhc--CcEEEEEEecchhhhhhhhhhHHHHHhCCCCceEEEccE-------EEEcCe
Confidence            34459999999999888888887776  446677654433322233333333333222222333321       111222


Q ss_pred             cEEEEChHHHHHHHhcCCCCCCCCccEEEEecccc
Q psy4275         126 HIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR  160 (182)
Q Consensus       126 ~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~  160 (182)
                      .|...-|-.-.+.+   +....+++..|++||.-.
T Consensus        91 ~igy~i~LS~~q~~---Ks~~Yp~V~~I~fDEfi~  122 (331)
T PHA00149         91 LIGYAIPLSTWQAL---KSSAYPNVSTIFFDEFIR  122 (331)
T ss_pred             EEEEEEehhhHHhh---cccCCCceEEEEeeeeee
Confidence            23333332222223   344678899999999976

>PRK08760 replicative DNA helicase; Provisional

Probab=93.02  E-value=0.98  Score=37.42  Aligned_cols=118  Identities=16%  Similarity=0.138  Sum_probs=60.1

Q ss_pred             hhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEE-EEEcCCchhhh
Q psy4275          39 HVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVS-IITGGMDMVDQ  117 (182)
Q Consensus        39 ~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~-~~~~~~~~~~~  117 (182)
                      -+..|.-+++.|.+|.|||..++-.+.....++  +..++++...- -.+|+...+.....  ++... ...|.....++
T Consensus       225 G~~~G~LivIaarPg~GKTafal~iA~~~a~~~--g~~V~~fSlEM-s~~ql~~Rl~a~~s--~i~~~~i~~g~l~~~e~  299 (476)
T PRK08760        225 GLQPTDLIILAARPAMGKTTFALNIAEYAAIKS--KKGVAVFSMEM-SASQLAMRLISSNG--RINAQRLRTGALEDEDW  299 (476)
T ss_pred             CCCCCceEEEEeCCCCChhHHHHHHHHHHHHhc--CCceEEEeccC-CHHHHHHHHHHhhC--CCcHHHHhcCCCCHHHH
Confidence            344466788889999999998776666654433  33566664322 22344333322211  12111 11222222221


Q ss_pred             hH-----HhcCCCcEEEE-----ChHHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275         118 GK-----ELAKKPHIVIA-----TPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus       118 ~~-----~~~~~~~Ilv~-----T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      ..     ....+..+.|.     |++.+...++..+  ....+++||||-.+.|..
T Consensus       300 ~~~~~a~~~l~~~~l~I~d~~~~t~~~I~~~~r~l~--~~~~~~lVvIDyLql~~~  353 (476)
T PRK08760        300 ARVTGAIKMLKETKIFIDDTPGVSPEVLRSKCRRLK--REHDLGLIVIDYLQLMSV  353 (476)
T ss_pred             HHHHHHHHHHhcCCEEEeCCCCCCHHHHHHHHHHHH--HhcCCCEEEEecHHhcCC
Confidence            11     11123445553     4555555444321  123478999999998853

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=93.00  E-value=0.61  Score=40.02  Aligned_cols=78  Identities=19%  Similarity=0.229  Sum_probs=52.2

Q ss_pred             CeeEEEEcCCHH--------HHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhc
Q psy4275          74 GIFALVLTPTRE--------LAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDT  141 (182)
Q Consensus        74 ~~~~lil~p~~~--------l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~  141 (182)
                      +.++++++|..+        -+.+.++.++...  .+.++..++|+.+..++...+    .++.+|+|+|.-      -.
T Consensus       448 g~q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~~--~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~v------ie  519 (630)
T TIGR00643       448 GRQAYVVYPLIEESEKLDLKAAEALYERLKKAF--PKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTV------IE  519 (630)
T ss_pred             CCcEEEEEccccccccchHHHHHHHHHHHHhhC--CCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECce------ee
Confidence            557899998752        2344455555433  367899999988765444332    247899999931      22


Q ss_pred             CCCCCCCCccEEEEecccc
Q psy4275         142 CNTFSLNRIKFLVLDEADR  160 (182)
Q Consensus       142 ~~~~~~~~~~~iI~DE~h~  160 (182)
                       ..+++.+++++|+..++.
T Consensus       520 -~GvDiP~v~~VIi~~~~r  537 (630)
T TIGR00643       520 -VGVDVPNATVMVIEDAER  537 (630)
T ss_pred             -cCcccCCCcEEEEeCCCc
Confidence             567888899988877764

>PRK13822 conjugal transfer coupling protein TraG; Provisional

Probab=92.99  E-value=0.19  Score=43.01  Aligned_cols=59  Identities=22%  Similarity=0.192  Sum_probs=42.3

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITG  110 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~  110 (182)
                      ..|.++.||||+|||...+++-+-.   .  +..++++-|..++........++    .|.+|.++..
T Consensus       224 ~~H~Lv~ApTgsGKt~g~VIPnLL~---~--~gS~VV~DpKgEl~~~Ta~~R~~----~G~~V~vfdP  282 (641)
T PRK13822        224 STHGLVFAGSGGFKTTSVVVPTALK---W--GGPLVVLDPSTEVAPMVSEHRRD----AGREVIVLDP  282 (641)
T ss_pred             CceEEEEeCCCCCccceEehhhhhc---C--CCCEEEEeCcHHHHHHHHHHHHH----CCCeEEEEeC
Confidence            3589999999999999988886532   1  23688888998887665555433    3666766654

>KOG0328|consensus

Probab=92.98  E-value=0.33  Score=37.17  Aligned_cols=68  Identities=16%  Similarity=0.251  Sum_probs=49.2

Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhc----CCCcEEEEChHHHHHHHhcC-CCCCCCC
Q psy4275          75 IFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA----KKPHIVIATPGRLADHLDTC-NTFSLNR  149 (182)
Q Consensus        75 ~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~Ilv~T~~~l~~~~~~~-~~~~~~~  149 (182)
                      .+++|.|.++.-++    |+.+..+..+..|...+|+....++.....    ...+|+++|.-        | +.++...
T Consensus       267 tQavIFcnTk~kVd----wLtekm~~~nftVssmHGDm~qkERd~im~dFRsg~SrvLitTDV--------waRGiDv~q  334 (400)
T KOG0328|consen  267 TQAVIFCNTKRKVD----WLTEKMREANFTVSSMHGDMEQKERDKIMNDFRSGKSRVLITTDV--------WARGIDVQQ  334 (400)
T ss_pred             heEEEEecccchhh----HHHHHHHhhCceeeeccCCcchhHHHHHHHHhhcCCceEEEEech--------hhccCCcce
Confidence            47999999988765    555555666899999999998776665543    36789999832        2 4556777


Q ss_pred             ccEEE
Q psy4275         150 IKFLV  154 (182)
Q Consensus       150 ~~~iI  154 (182)
                      ++++|
T Consensus       335 Vslvi  339 (400)
T KOG0328|consen  335 VSLVI  339 (400)
T ss_pred             eEEEE
Confidence            77666

>TIGR00602 rad24 checkpoint protein rad24

Probab=92.93  E-value=0.63  Score=39.86  Aligned_cols=20  Identities=15%  Similarity=0.213  Sum_probs=15.8

Q ss_pred             CcEEEECCCCChHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~   63 (182)
                      +-.++.||+|+|||..+-+.
T Consensus       111 ~illL~GP~GsGKTTl~~~l  130 (637)
T TIGR00602       111 RILLITGPSGCGKSTTIKIL  130 (637)
T ss_pred             cEEEEECCCCCCHHHHHHHH
Confidence            34889999999999886433

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

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=92.92  E-value=0.65  Score=39.85  Aligned_cols=71  Identities=17%  Similarity=0.242  Sum_probs=50.8

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      ..++||.|+++.-+.++++.+...    ++.+..++|+.+..++...+    .++.+|+|+|.-      -. ..+++++
T Consensus       245 ~~~~IVF~~tk~~a~~l~~~L~~~----g~~~~~lhgd~~q~~R~~il~~Fr~G~~~ILVATdv------~a-rGIDip~  313 (629)
T PRK11634        245 FDAAIIFVRTKNATLEVAEALERN----GYNSAALNGDMNQALREQTLERLKDGRLDILIATDV------AA-RGLDVER  313 (629)
T ss_pred             CCCEEEEeccHHHHHHHHHHHHhC----CCCEEEeeCCCCHHHHHHHHHHHhCCCCCEEEEcch------Hh-cCCCccc
Confidence            357999999999998888777653    78888999988765544332    247889999932      12 4466777


Q ss_pred             ccEEEE
Q psy4275         150 IKFLVL  155 (182)
Q Consensus       150 ~~~iI~  155 (182)
                      +++||.
T Consensus       314 V~~VI~  319 (629)
T PRK11634        314 ISLVVN  319 (629)
T ss_pred             CCEEEE
Confidence            777664

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=92.88  E-value=0.86  Score=37.59  Aligned_cols=72  Identities=14%  Similarity=0.262  Sum_probs=50.9

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHH----hcCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKE----LAKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +..+||.++++.-++.+++.++..    ++++..++++.+..++...    ..+..+|+|+|...      . ..+++++
T Consensus       226 ~~~~IIF~~s~~~~e~la~~L~~~----g~~~~~~H~~l~~~eR~~i~~~F~~g~~~vLVaT~~~------~-~GID~p~  294 (470)
T TIGR00614       226 GKSGIIYCPSRKKSEQVTASLQNL----GIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAF------G-MGINKPD  294 (470)
T ss_pred             CCceEEEECcHHHHHHHHHHHHhc----CCCeeEeeCCCCHHHHHHHHHHHHcCCCcEEEEechh------h-ccCCccc
Confidence            456799999999999988877654    7889999998876544332    23578999999431      1 4456666


Q ss_pred             ccEEEEe
Q psy4275         150 IKFLVLD  156 (182)
Q Consensus       150 ~~~iI~D  156 (182)
                      ++++|.-
T Consensus       295 V~~VI~~  301 (470)
T TIGR00614       295 VRFVIHY  301 (470)
T ss_pred             ceEEEEe
Confidence            7766654

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

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=92.87  E-value=0.94  Score=37.37  Aligned_cols=71  Identities=13%  Similarity=0.191  Sum_probs=46.8

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      ..++||.++++.-++.+++.+..    .++++..++|+....++....    .++.+|+|+|.--      . ..+++..
T Consensus       335 ~~~~IVF~~s~~~~~~l~~~L~~----~~~~~~~~~g~~~~~~R~~~~~~Fr~G~~~vLvaT~~l------~-~GIDi~~  403 (475)
T PRK01297        335 WERVMVFANRKDEVRRIEERLVK----DGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVA------G-RGIHIDG  403 (475)
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHH----cCCCEEEEECCCCHHHHHHHHHHHhCCCCcEEEEcccc------c-cCCcccC
Confidence            45899999999988887766654    367888889887765443322    2367889988321      1 3345555


Q ss_pred             ccEEEE
Q psy4275         150 IKFLVL  155 (182)
Q Consensus       150 ~~~iI~  155 (182)
                      ++++|.
T Consensus       404 v~~VI~  409 (475)
T PRK01297        404 ISHVIN  409 (475)
T ss_pred             CCEEEE
Confidence            555553

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=92.86  E-value=0.76  Score=36.93  Aligned_cols=22  Identities=27%  Similarity=0.150  Sum_probs=18.0

Q ss_pred             CcEEEECCCCChHHHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPIL   65 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~   65 (182)
                      .+.|+.||+|+|||..+.+..-
T Consensus        49 ~SmIl~GPPG~GKTTlA~liA~   70 (436)
T COG2256          49 HSMILWGPPGTGKTTLARLIAG   70 (436)
T ss_pred             ceeEEECCCCCCHHHHHHHHHH
Confidence            4899999999999998755443

>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=92.86  E-value=0.11  Score=34.13  Aligned_cols=20  Identities=25%  Similarity=0.081  Sum_probs=15.6

Q ss_pred             EEEECCCCChHHHHHHHHHH
Q psy4275          46 CIGCAKTGSGKTLAFALPIL   65 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~   65 (182)
                      +++.|++|+|||+.+-...-
T Consensus         2 I~I~G~~gsGKST~a~~La~   21 (121)
T PF13207_consen    2 IIISGPPGSGKSTLAKELAE   21 (121)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57899999999998654433

...

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=92.85  E-value=0.63  Score=31.21  Aligned_cols=54  Identities=15%  Similarity=0.093  Sum_probs=29.6

Q ss_pred             CcEE--EECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc-----CCHHHHHHHHHHHHHh
Q psy4275          44 EDCI--GCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT-----PTRELAYQIGDQFLVL   97 (182)
Q Consensus        44 ~~~l--i~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~-----p~~~l~~q~~~~~~~~   97 (182)
                      +..+  +.|+||+|||.++-+.+-......-.+..+....     |....+.+..++++.+
T Consensus        52 KpLVlSfHG~tGtGKn~v~~liA~~ly~~G~~S~~V~~f~~~~hFP~~~~v~~Yk~~L~~~  112 (127)
T PF06309_consen   52 KPLVLSFHGWTGTGKNFVSRLIAEHLYKSGMKSPFVHQFIATHHFPHNSNVDEYKEQLKSW  112 (127)
T ss_pred             CCEEEEeecCCCCcHHHHHHHHHHHHHhcccCCCceeeecccccCCCchHHHHHHHHHHHH
Confidence            4444  5689999999997665555443322333443333     4444444444444443

Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of AAA ATPase, central region containing proteins () proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor

>PHA03372 DNA packaging terminase subunit 1; Provisional

Probab=92.76  E-value=1.9  Score=36.63  Aligned_cols=59  Identities=12%  Similarity=0.124  Sum_probs=42.3

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHH-hhccCC
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLV-LGKVMN  102 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~-~~~~~~  102 (182)
                      .+-.+.--|--.|||+. +.+++..+..+-.+.++.|+++-+..++-+.+++.. ..+.++
T Consensus       202 QkaTVFLVPRRHGKTWf-~VpiIsllL~s~~gI~IGYvAHqKhvs~~Vf~EI~~~lrrwF~  261 (668)
T PHA03372        202 QKATVFLVPRRHGKTWF-IIPIISFLLKNIIGISIGYVAHQKHVSQFVLKEVEFRCRRMFP  261 (668)
T ss_pred             ccceEEEecccCCceeh-HHHHHHHHHHhhcCceEEEEeeHHHHHHHHHHHHHHHHhhhcC
Confidence            35667778999999987 556666666655588999999999888877655543 333343

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=92.76  E-value=0.67  Score=39.90  Aligned_cols=53  Identities=17%  Similarity=0.226  Sum_probs=34.6

Q ss_pred             HhcCCCcEEE-EChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHHHHHHHH
Q psy4275         120 ELAKKPHIVI-ATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFFFFL  176 (182)
Q Consensus       120 ~~~~~~~Ilv-~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~~~~~~~  176 (182)
                      .+.+.-+-.| +-|+++.+-+++.+..+    -++.+||+|.|.++....-...+.++
T Consensus       391 EIRGHRRTYIGamPGrIiQ~mkka~~~N----Pv~LLDEIDKm~ss~rGDPaSALLEV  444 (782)
T COG0466         391 EIRGHRRTYIGAMPGKIIQGMKKAGVKN----PVFLLDEIDKMGSSFRGDPASALLEV  444 (782)
T ss_pred             HhccccccccccCChHHHHHHHHhCCcC----CeEEeechhhccCCCCCChHHHHHhh
Confidence            3334334455 56999999988754322    37999999999987654444444443

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=92.75  E-value=0.42  Score=37.80  Aligned_cols=43  Identities=9%  Similarity=-0.171  Sum_probs=28.6

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhcc---CCCCeeEEEEcCCHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCE---DPYGIFALVLTPTRE   85 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~---~~~~~~~lil~p~~~   85 (182)
                      +.-..+.|++|+|||..++..+......   ...+.+++|+.-...
T Consensus       123 g~i~~i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE~~  168 (342)
T PLN03186        123 GSITEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGT  168 (342)
T ss_pred             ceEEEEECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEECCCC
Confidence            3457789999999998876555443322   122347999987664

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=92.70  E-value=0.77  Score=39.79  Aligned_cols=78  Identities=23%  Similarity=0.282  Sum_probs=51.9

Q ss_pred             CeeEEEEcCCHH--------HHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhc
Q psy4275          74 GIFALVLTPTRE--------LAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDT  141 (182)
Q Consensus        74 ~~~~lil~p~~~--------l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~  141 (182)
                      +.++++++|+.+        -+...++.+.....  ++++..++|+.+..++...+    .++.+|+|+|.-      -.
T Consensus       471 g~q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~~--~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~v------ie  542 (681)
T PRK10917        471 GRQAYVVCPLIEESEKLDLQSAEETYEELQEAFP--ELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTV------IE  542 (681)
T ss_pred             CCcEEEEEcccccccchhHHHHHHHHHHHHHHCC--CCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECcc------ee
Confidence            558999999542        23444555544432  37899999998765554433    236799999931      22


Q ss_pred             CCCCCCCCccEEEEecccc
Q psy4275         142 CNTFSLNRIKFLVLDEADR  160 (182)
Q Consensus       142 ~~~~~~~~~~~iI~DE~h~  160 (182)
                       ..+++.+++++|+..++.
T Consensus       543 -~GiDip~v~~VIi~~~~r  560 (681)
T PRK10917        543 -VGVDVPNATVMVIENAER  560 (681)
T ss_pred             -eCcccCCCcEEEEeCCCC
Confidence             556888899999887765

>COG2109 BtuR ATP:corrinoid adenosyltransferase [Coenzyme metabolism]

Probab=92.70  E-value=1.6  Score=31.37  Aligned_cols=29  Identities=21%  Similarity=0.194  Sum_probs=24.5

Q ss_pred             CccEEEEeccccccccCChhHHHHHHHHh
Q psy4275         149 RIKFLVLDEADRLSLMTSLKFFFFFFFLK  177 (182)
Q Consensus       149 ~~~~iI~DE~h~~~~~~~~~~~~~~~~~~  177 (182)
                      ..+++|+||+.-.+..++....+.+..+.
T Consensus       122 ~ydlviLDEl~~al~~g~l~~eeV~~~l~  150 (198)
T COG2109         122 KYDLVILDELNYALRYGLLPLEEVVALLK  150 (198)
T ss_pred             CCCEEEEehhhHHHHcCCCCHHHHHHHHh
Confidence            58899999999999999888877776654

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=92.68  E-value=1.2  Score=38.37  Aligned_cols=79  Identities=16%  Similarity=0.283  Sum_probs=55.9

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +.+++|.++++..++.+.+.+.+.    ++++..++|+....++...+    .++.+|+|+|.     .+ . ..+.+..
T Consensus       442 g~~vLIf~~tk~~ae~L~~~L~~~----gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t~-----~L-~-rGfDiP~  510 (655)
T TIGR00631       442 NERVLVTTLTKKMAEDLTDYLKEL----GIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGIN-----LL-R-EGLDLPE  510 (655)
T ss_pred             CCEEEEEECCHHHHHHHHHHHhhh----ccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEcC-----hh-c-CCeeeCC
Confidence            668999999999988887777654    67888888876543332222    24678998882     11 2 5678889


Q ss_pred             ccEEEEeccccccc
Q psy4275         150 IKFLVLDEADRLSL  163 (182)
Q Consensus       150 ~~~iI~DE~h~~~~  163 (182)
                      ++++|+-|++...-
T Consensus       511 v~lVvi~DadifG~  524 (655)
T TIGR00631       511 VSLVAILDADKEGF  524 (655)
T ss_pred             CcEEEEeCcccccC
Confidence            99988887766543

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

>TIGR02759 TraD_Ftype type IV conjugative transfer system coupling protein TraD

Probab=92.67  E-value=0.2  Score=42.32  Aligned_cols=28  Identities=25%  Similarity=0.302  Sum_probs=20.9

Q ss_pred             CCCcEEEECCCCChHHHHHHHHHHHhhcc
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALPILQKWCE   70 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~~~~~~~~   70 (182)
                      ..+|+++.|+||+|||.. +..++..+.+
T Consensus       175 e~~h~li~G~tGsGKs~~-i~~ll~~~~~  202 (566)
T TIGR02759       175 ETQHILIHGTTGSGKSVA-IRKLLRWIRQ  202 (566)
T ss_pred             cccceEEEcCCCCCHHHH-HHHHHHHHHh
Confidence            357999999999999975 4555555443

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).

>KOG0744|consensus

Probab=92.65  E-value=0.5  Score=37.02  Aligned_cols=67  Identities=16%  Similarity=0.065  Sum_probs=36.5

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccC---CCCeeEEEEcCCHHH-----------HHHHHHHHHHhhccCCceEEEE
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCED---PYGIFALVLTPTREL-----------AYQIGDQFLVLGKVMNLRVSII  108 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~---~~~~~~lil~p~~~l-----------~~q~~~~~~~~~~~~~~~~~~~  108 (182)
                      ++-+++.||+|+|||... -++...+.-+   ....-.++=..+.+|           +.++.+.++++.+.-+.-|+++
T Consensus       177 NRliLlhGPPGTGKTSLC-KaLaQkLSIR~~~~y~~~~liEinshsLFSKWFsESgKlV~kmF~kI~ELv~d~~~lVfvL  255 (423)
T KOG0744|consen  177 NRLILLHGPPGTGKTSLC-KALAQKLSIRTNDRYYKGQLIEINSHSLFSKWFSESGKLVAKMFQKIQELVEDRGNLVFVL  255 (423)
T ss_pred             eeEEEEeCCCCCChhHHH-HHHHHhheeeecCccccceEEEEehhHHHHHHHhhhhhHHHHHHHHHHHHHhCCCcEEEEE
Confidence            567888999999999653 2333333211   112234454555554           3444455555555555555555


Q ss_pred             Ec
Q psy4275         109 TG  110 (182)
Q Consensus       109 ~~  110 (182)
                      .+
T Consensus       256 ID  257 (423)
T KOG0744|consen  256 ID  257 (423)
T ss_pred             eH
Confidence            43

>PRK05636 replicative DNA helicase; Provisional

Probab=92.65  E-value=0.62  Score=38.84  Aligned_cols=39  Identities=13%  Similarity=0.075  Sum_probs=25.5

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEE
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVL   80 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil   80 (182)
                      +..|.-+++.|.+|.|||..++-.+.....++  +..++++
T Consensus       262 l~~G~Liiiaarpg~GKT~~al~~a~~~a~~~--g~~v~~f  300 (505)
T PRK05636        262 LRGGQMIIVAARPGVGKSTLALDFMRSASIKH--NKASVIF  300 (505)
T ss_pred             CCCCceEEEEeCCCCCHHHHHHHHHHHHHHhC--CCeEEEE
Confidence            34456678889999999998775555444332  3355555

>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=92.64  E-value=0.24  Score=37.06  Aligned_cols=35  Identities=26%  Similarity=0.253  Sum_probs=22.0

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcC
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTP   82 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p   82 (182)
                      +.++.|++|||||..... ++..+...  -..+++++|
T Consensus        15 r~viIG~sGSGKT~li~~-lL~~~~~~--f~~I~l~t~   49 (241)
T PF04665_consen   15 RMVIIGKSGSGKTTLIKS-LLYYLRHK--FDHIFLITP   49 (241)
T ss_pred             eEEEECCCCCCHHHHHHH-HHHhhccc--CCEEEEEec
Confidence            788999999999987443 33333332  124455555

This is thought to be an ATPase involved in viral DNA packaging [].

>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=92.39  E-value=0.095  Score=34.51  Aligned_cols=19  Identities=26%  Similarity=-0.017  Sum_probs=14.9

Q ss_pred             EEEECCCCChHHHHHHHHH
Q psy4275          46 CIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~   64 (182)
                      +++.|++|+|||+++-...
T Consensus         1 I~i~G~~GsGKtTia~~L~   19 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELA   19 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHH
Confidence            4689999999999865433

...

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	182
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		8e-43
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		2e-27
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		3e-27
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		6e-25
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		7e-25
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		2e-24
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		4e-24
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		3e-23
3bor_A	237	Crystal Structure Of The Deadc Domain Of Human Tran		3e-21
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		4e-21
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		6e-21
1q0u_A	219	Crystal Structure Of The Bstdead N-Terminal Domain		1e-20
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		1e-20
1t6n_A	220	Crystal Structure Of The N-Terminal Domain Of Human		3e-20
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		5e-20
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		6e-20
3ly5_A	262	Ddx18 Dead-Domain Length = 262		9e-20
2g9n_A	221	Structure Of The Dead Domain Of Human Eukaryotic In		1e-19
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		2e-19
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		3e-19
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		3e-19
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		3e-19
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		3e-19
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		4e-19
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		4e-19
1qva_A	223	Yeast Initiation Factor 4a N-Terminal Domain Length		4e-19
1qde_A	224	Crystal Structure Of The Atpase Domain Of Translati		7e-19
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		7e-19
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		8e-19
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		8e-19
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		1e-18
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		1e-17
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		1e-17
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		6e-17
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		7e-16
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		9e-16
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		9e-16
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		1e-15
3fhc_B	235	Crystal Structure Of Human Dbp5 In Complex With Nup		6e-15
3fmo_B	300	Crystal Structure Of The Nucleoporin Nup214 In Comp		7e-15
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		1e-14
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		1e-14
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		1e-14
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		1e-14
2kbe_A	226	Solution Structure Of Amino-Terminal Domain Of Dbp5		1e-13
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		2e-13
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		2e-13
2oxc_A	230	Human Dead-Box Rna Helicase Ddx20, Dead Domain In C		2e-12
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		1e-10
1wp9_A	494	Crystal Structure Of Pyrococcus Furiosus Hef Helica		4e-04

>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In Complex With Amp Length = 249

Iteration: 1
 Score =  169 bits (428), Expect = 8e-43,   Method: Compositional matrix adjust.
 Identities = 84/160 (52%), Positives = 107/160 (66%)
Query: 2   EDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFA 61
           E+  K+F DL +   L   C  +G   PT+IQ   IP  L   D IG A+TGSGKT AFA
Sbjct: 39  EEETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFA 98
Query: 62  LPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL 121
           LPIL    E P  +FALVLTPTRELA+QI +QF  LG  + ++ ++I GG+D + Q   L
Sbjct: 99  LPILNALLETPQRLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLAL 158
Query: 122 AKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           AKKPHI+IATPGRL DHL+    F+L  +K+LV+DEADR+
Sbjct: 159 AKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRI 198

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score =  118 bits (295), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 64/154 (41%), Positives = 99/154 (64%), Gaps = 4/154 (2%)
Query: 7   SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDE-DCIGCAKTGSGKTLAFALPIL 65
           +F +L L+  ++   +  G + PT+IQ  +IP  LNDE + +  A+TGSGKT +FA+P++
Sbjct: 7   NFNELNLSDNILNAIRNKGFEKPTDIQXKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 66
Query: 66  QKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKP 125
           +   E+  GI A++LTPTRELA Q+ D+   L    NL+++ I GG  +  Q K L K  
Sbjct: 67  ELVNENN-GIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKAL-KNA 124
Query: 126 HIVIATPGRLADHLDTCNTFSLNRIKFLVLDEAD 159
           +IV+ TPGR+ DH++   T +L  +K+ +LDEAD
Sbjct: 125 NIVVGTPGRILDHINRG-TLNLKNVKYFILDEAD 157

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score =  117 bits (294), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 68/164 (41%), Positives = 94/164 (57%), Gaps = 8/164 (4%)
Query: 4   PIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALP 63
           PI+ FT   L   +I      G K PT IQK  IP + +  D + CA+TGSGKT AF LP
Sbjct: 54  PIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLP 113
Query: 64  ILQKWCEDPYGIF-----ALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQG 118
           IL K  EDP+ +       ++++PTRELA QI ++         L++ I+ GG     Q 
Sbjct: 114 ILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQN 173
Query: 119 KELAKKPHIVIATPGRLADHLDTCNTF-SLNRIKFLVLDEADRL 161
           + + +  H+VIATPGRL D +D   TF +    +F+VLDEADR+
Sbjct: 174 ECITRGCHVVIATPGRLLDFVD--RTFITFEDTRFVVLDEADRM 215

>pdb|1WRB|A Chain A, Crystal Structure Of The N-Terminal Reca-Like Domain Of Djvlgb, A Pranarian Vasa-Like Rna Helicase Length = 253

Iteration: 1
 Score =  110 bits (274), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 67/166 (40%), Positives = 93/166 (56%), Gaps = 10/166 (6%)
Query: 5   IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPI 64
           I++F +LKL+P +         + PT IQK  IP +L   D + CA+TGSGKT AF +PI
Sbjct: 22  IENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPI 81
Query: 65  LQKW-CED----PYGIFA----LVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMV 115
           +    C+D     Y   A    L+L PTRELA QI  +         LR  ++ GG D  
Sbjct: 82  INHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTH 141
Query: 116 DQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
            Q +E+    H+++ATPGRL D ++  N  SL   K++VLDEADR+
Sbjct: 142 SQIREVQMGCHLLVATPGRLVDFIEK-NKISLEFCKYIVLDEADRM 186

>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex With Adp Length = 236

Iteration: 1
 Score =  109 bits (273), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 61/164 (37%), Positives = 93/164 (56%), Gaps = 7/164 (4%)
Query: 3   DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFAL 62
           + I  F+D  L+   ++  Q    +  TEIQK  I   L  +D +G AKTGSGKTLAF +
Sbjct: 22  NEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLV 81
Query: 63  PILQ-----KWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQ 117
           P+L+     +W     G+  L+++PTRELAYQ  +    +GK  +    +I GG D+  +
Sbjct: 82  PVLEALYRLQWTSTD-GLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHE 140
Query: 118 GKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
            + +    +I++ TPGRL  H+D   +F    ++ LVLDEADR+
Sbjct: 141 AERI-NNINILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRI 183

>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score =  108 bits (270), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 64/157 (40%), Positives = 87/157 (55%), Gaps = 6/157 (3%)
Query: 8   FTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQK 67
           F D  L P ++      G+ TPT IQ A +P  L  +D IG A+TG+GKTLAFALPI ++
Sbjct: 3   FKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAER 62
Query: 68  WC---EDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKK 124
                E      ALVLTPTRELA Q+  +   +    +L+V  + GG     Q + L + 
Sbjct: 63  LAPSQERGRKPRALVLTPTRELALQVASELTAVAP--HLKVVAVYGGTGYGKQKEALLRG 120
Query: 125 PHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
              V+ATPGR  D+L       L+R++  VLDEAD +
Sbjct: 121 ADAVVATPGRALDYLRQ-GVLDLSRVEVAVLDEADEM 156

>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score =  107 bits (266), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 63/157 (40%), Positives = 87/157 (55%), Gaps = 6/157 (3%)
Query: 8   FTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQK 67
           F D  L P ++      G+ TPT I+ A +P  L  +D IG A+TG+GKTLAFALPI ++
Sbjct: 3   FKDFPLKPEILEALHGRGLTTPTPIEAAALPLALEGKDLIGQARTGTGKTLAFALPIAER 62
Query: 68  WC---EDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKK 124
                E      ALVLTPTRELA Q+  +   +    +L+V  + GG     Q + L + 
Sbjct: 63  LAPSQERGRKPRALVLTPTRELALQVASELTAVAP--HLKVVAVYGGTGYGKQKEALLRG 120
Query: 125 PHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
              V+ATPGR  D+L       L+R++  VLDEAD +
Sbjct: 121 ADAVVATPGRALDYLRQ-GVLDLSRVEVAVLDEADEM 156

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score =  104 bits (259), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 64/175 (36%), Positives = 96/175 (54%), Gaps = 19/175 (10%)
Query: 5   IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPI 64
           I+SF+D+++   ++   +      PT +QK  IP +    D + CA+TGSGKT AF LPI
Sbjct: 14  IESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPI 73
Query: 65  L-QKWCEDP------------YGI-----FALVLTPTRELAYQIGDQFLVLGKVMNLRVS 106
           L Q + + P            YG       +LVL PTRELA QI ++         +R  
Sbjct: 74  LSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPC 133
Query: 107 IITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           ++ GG D+  Q ++L +  H+++ATPGRL D ++      L+  K+LVLDEADR+
Sbjct: 134 VVYGGADIGQQIRDLERGCHLLVATPGRLVDMMER-GKIGLDFCKYLVLDEADRM 187

>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation Initiation Factor 4a-2 Length = 237

Iteration: 1
 Score = 97.8 bits (242), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 64/159 (40%), Positives = 89/159 (55%), Gaps = 4/159 (2%)
Query: 5   IKSFTDLKLNPWLIRQCQTIGVKTPTEIQ-KAIIPHVLNDEDCIGCAKTGSGKTLAFALP 63
           + +F D+ L   L+R     G + P+ IQ +AIIP  +   D I  A++G+GKT  FA+ 
Sbjct: 29  VDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIP-CIKGYDVIAQAQSGTGKTATFAIS 87
Query: 64  ILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL-A 122
           ILQ+   +     ALVL PTRELA QI    L LG  M        GG ++ ++ ++L A
Sbjct: 88  ILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQA 147
Query: 123 KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           + PHIV+ TPGR+ D L+     S   IK  VLDEAD +
Sbjct: 148 EAPHIVVGTPGRVFDMLNR-RYLSPKWIKMFVLDEADEM 185

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score = 97.4 bits (241), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 60/158 (37%), Positives = 85/158 (53%), Gaps = 2/158 (1%)
Query: 5   IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPI 64
           + SF D+ L+  L+R     G + P+ IQ+  I   +   D I  A++G+GKT  FA+ I
Sbjct: 39  VDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISI 98
Query: 65  LQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA-K 123
           LQ+   D     ALVL PTRELA QI    + LG  M        GG ++  + ++L  +
Sbjct: 99  LQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQME 158
Query: 124 KPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
            PHI++ TPGR+ D L+     S   IK  VLDEAD +
Sbjct: 159 APHIIVGTPGRVFDMLNR-RYLSPKYIKMFVLDEADEM 195

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score = 97.1 bits (240), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 60/158 (37%), Positives = 85/158 (53%), Gaps = 2/158 (1%)
Query: 5   IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPI 64
           + SF D+ L+  L+R     G + P+ IQ+  I   +   D I  A++G+GKT  FA+ I
Sbjct: 13  VDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISI 72
Query: 65  LQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA-K 123
           LQ+   D     ALVL PTRELA QI    + LG  M        GG ++  + ++L  +
Sbjct: 73  LQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQME 132
Query: 124 KPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
            PHI++ TPGR+ D L+     S   IK  VLDEAD +
Sbjct: 133 APHIIVGTPGRVFDMLNR-RYLSPKYIKMFVLDEADEM 169

>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain Length = 219

Iteration: 1
 Score = 95.9 bits (237), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 58/157 (36%), Positives = 84/157 (53%), Gaps = 5/157 (3%)
Query: 7   SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ 66
            FT     P++I   +T+    PTEIQ+ IIP  L  E  +G ++TG+GKT A+ LPI +
Sbjct: 5   QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESXVGQSQTGTGKTHAYLLPIXE 64
Query: 67  KWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIIT----GGMDMVDQGKELA 122
           K   +   + A++  PTRELA QI  + L + K       I+     GG D     ++L 
Sbjct: 65  KIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRXIVARCLIGGTDKQKALEKLN 124
Query: 123 KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEAD 159
            +PHIVI TPGR+ D +       ++    LV+DEAD
Sbjct: 125 VQPHIVIGTPGRINDFIRE-QALDVHTAHILVVDEAD 160

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score = 95.9 bits (237), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 58/160 (36%), Positives = 88/160 (55%), Gaps = 5/160 (3%)
Query: 5   IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPI 64
           +  F D  L P L+R     G + P+E+Q   IP  +   D +  AK+G GKT  F L  
Sbjct: 6   MSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLAT 65
Query: 65  LQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGKELAK 123
           LQ+       +  LV+  TRELA+QI  ++    K M N++V++  GG+  + + +E+ K
Sbjct: 66  LQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLS-IKKDEEVLK 124
Query: 124 K--PHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           K  PHIV+ TPGR+   L    + +L  IK  +LDEAD++
Sbjct: 125 KNCPHIVVGTPGRIL-ALARNKSLNLKHIKHFILDEADKM 163

>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56 Length = 220

Iteration: 1
 Score = 94.4 bits (233), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 57/157 (36%), Positives = 86/157 (54%), Gaps = 5/157 (3%)
Query: 8   FTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQK 67
           F D  L P L+R     G + P+E+Q   IP  +   D +  AK+G GKT  F L  LQ+
Sbjct: 16  FRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQ 75
Query: 68  WCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGKELAKK-- 124
                  +  LV+  TRELA+QI  ++    K M N++V++  GG+  + + +E+ KK  
Sbjct: 76  LEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLS-IKKDEEVLKKNC 134
Query: 125 PHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           PHIV+ TPGR+   L    + +L  IK  +LDE D++
Sbjct: 135 PHIVVGTPGRILA-LARNKSLNLKHIKHFILDECDKM 170

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score = 93.6 bits (231), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 57/157 (36%), Positives = 86/157 (54%), Gaps = 5/157 (3%)
Query: 8   FTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQK 67
           F D  L P L+R     G + P+E+Q   IP  +   D +  AK+G GKT  F L  LQ+
Sbjct: 10  FRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQ 69
Query: 68  WCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGKELAKK-- 124
                  +  LV+  TRELA+QI  ++    K M N++V++  GG+  + + +E+ KK  
Sbjct: 70  LEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLS-IKKDEEVLKKNC 128
Query: 125 PHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           PHIV+ TPGR+   L    + +L  IK  +LDE D++
Sbjct: 129 PHIVVGTPGRIL-ALARNKSLNLKHIKHFILDECDKM 164

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score = 93.6 bits (231), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 57/157 (36%), Positives = 86/157 (54%), Gaps = 5/157 (3%)
Query: 8   FTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQK 67
           F D  L P L+R     G + P+E+Q   IP  +   D +  AK+G GKT  F L  LQ+
Sbjct: 10  FRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQ 69
Query: 68  WCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGKELAKK-- 124
                  +  LV+  TRELA+QI  ++    K M N++V++  GG+  + + +E+ KK  
Sbjct: 70  LEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLS-IKKDEEVLKKNC 128
Query: 125 PHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           PHIV+ TPGR+   L    + +L  IK  +LDE D++
Sbjct: 129 PHIVVGTPGRIL-ALARNKSLNLKHIKHFILDECDKM 164

>pdb|3LY5|A Chain A, Ddx18 Dead-Domain Length = 262

Iteration: 1
 Score = 92.8 bits (229), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 57/156 (36%), Positives = 86/156 (55%), Gaps = 10/156 (6%)
Query: 13  LNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP 72
           +N   ++  + +G    TEIQ   I  +L   D +  AKTGSGKTLAF +P ++   +  
Sbjct: 61  VNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLR 120
Query: 73  Y----GIFALVLTPTRELAYQIGDQFLVLGKVMNLRV---SIITGGMDMVDQGKELAKKP 125
           +    G   L+L+PTRELA Q    F VL ++M   V    +I GG +   + ++L    
Sbjct: 121 FMPRNGTGVLILSPTRELAMQT---FGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGI 177
Query: 126 HIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           +I++ATPGRL DH+     F    ++ LV+DEADR+
Sbjct: 178 NIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRI 213

>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic Initiation Factor 4a, Eif4a Length = 221

Iteration: 1
 Score = 92.4 bits (228), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 58/158 (36%), Positives = 82/158 (51%), Gaps = 2/158 (1%)
Query: 5   IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPI 64
           + SF D+ L+  L+R     G + P+ IQ+  I   +   D I  A++G+G T  FA+ I
Sbjct: 14  VDSFDDMNLSESLLRGIYAYGFEXPSAIQQRAILPCIXGYDVIAQAQSGTGXTATFAISI 73
Query: 65  LQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA-K 123
           LQ+   D     ALVL PTRELA QI    + LG  M        GG ++  + + L  +
Sbjct: 74  LQQIELDLXATQALVLAPTRELAQQIQXVVMALGDYMGASCHACIGGTNVRAEVQXLQME 133
Query: 124 KPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
            PHI++ TPGR+ D L+     S   I   VLDEAD +
Sbjct: 134 APHIIVGTPGRVFDMLNR-RYLSPXYIXMFVLDEADEM 170

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 91.7 bits (226), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 54/147 (36%), Positives = 86/147 (58%), Gaps = 8/147 (5%)
Query: 13  LNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP 72
           +N  + +  + +G K  TE+Q   IP +L  ++ +  AKTGSGKT A+A+PIL+      
Sbjct: 1   MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILE------ 54
Query: 73  YGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATP 132
            G+ +LV+TPTREL  Q+      +G+ M+ +V+ + GGM    Q   + +   IV+ATP
Sbjct: 55  LGMKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRV-RNADIVVATP 113
Query: 133 GRLADHLDTCNTFSLNRIKFLVLDEAD 159
           GRL D L +     L+  + +++DEAD
Sbjct: 114 GRLLD-LWSKGVIDLSSFEIVIIDEAD 139

>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I In Complex With Adp Length = 242

Iteration: 1
 Score = 91.3 bits (225), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 57/138 (41%), Positives = 75/138 (54%), Gaps = 6/138 (4%)
Query: 29  PTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPY-----GIFALVLTPT 83
           PT IQ    P  L+  D +G A+TGSGKTL++ LP +      P+     G   LVL PT
Sbjct: 52  PTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPT 111
Query: 84  RELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCN 143
           RELA Q+        +   L+ + I GG     Q ++L +   I IATPGRL D L+ C 
Sbjct: 112 RELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLE-CG 170
Query: 144 TFSLNRIKFLVLDEADRL 161
             +L R  +LVLDEADR+
Sbjct: 171 KTNLRRTTYLVLDEADRM 188

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score = 91.3 bits (225), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 54/159 (33%), Positives = 82/159 (51%), Gaps = 1/159 (0%)
Query: 3   DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFAL 62
           D   +F  + L   L+R     G + P+ IQ+  I  ++   D I  +++G+GKT  F++
Sbjct: 34  DVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSI 93
Query: 63  PILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA 122
            +LQ          AL+L PTRELA QI    L LG  MN++     GG ++ +  ++L 
Sbjct: 94  SVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLD 153
Query: 123 KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
              H+V  TPGR+ D +    +     IK LVLDEAD +
Sbjct: 154 YGQHVVAGTPGRVFDMIRR-RSLRTRAIKMLVLDEADEM 191

>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 = 90.9 bits (224), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 57/138 (41%), Positives = 75/138 (54%), Gaps = 6/138 (4%)
Query: 29  PTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPY-----GIFALVLTPT 83
           PT IQ    P  L+  D +G A+TGSGKTL++ LP +      P+     G   LVL PT
Sbjct: 66  PTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPT 125
Query: 84  RELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCN 143
           RELA Q+        +   L+ + I GG     Q ++L +   I IATPGRL D L+ C 
Sbjct: 126 RELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLE-CG 184
Query: 144 TFSLNRIKFLVLDEADRL 161
             +L R  +LVLDEADR+
Sbjct: 185 KTNLRRTTYLVLDEADRM 202

>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 = 90.9 bits (224), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 54/159 (33%), Positives = 82/159 (51%), Gaps = 1/159 (0%)
Query: 3   DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFAL 62
           D   +F  + L   L+R     G + P+ IQ+  I  ++   D I  +++G+GKT  F++
Sbjct: 35  DVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSI 94
Query: 63  PILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA 122
            +LQ          AL+L PTRELA QI    L LG  MN++     GG ++ +  ++L 
Sbjct: 95  SVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLD 154
Query: 123 KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
              H+V  TPGR+ D +    +     IK LVLDEAD +
Sbjct: 155 YGQHVVAGTPGRVFDMIRR-RSLRTRAIKMLVLDEADEM 192

>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 = 90.9 bits (224), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 54/159 (33%), Positives = 82/159 (51%), Gaps = 1/159 (0%)
Query: 3   DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFAL 62
           D   +F  + L   L+R     G + P+ IQ+  I  ++   D I  +++G+GKT  F++
Sbjct: 35  DVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSI 94
Query: 63  PILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA 122
            +LQ          AL+L PTRELA QI    L LG  MN++     GG ++ +  ++L 
Sbjct: 95  SVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLD 154
Query: 123 KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
              H+V  TPGR+ D +    +     IK LVLDEAD +
Sbjct: 155 YGQHVVAGTPGRVFDMIRR-RSLRTRAIKMLVLDEADEM 192

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score = 90.9 bits (224), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 54/159 (33%), Positives = 82/159 (51%), Gaps = 1/159 (0%)
Query: 3   DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFAL 62
           D   +F  + L   L+R     G + P+ IQ+  I  ++   D I  +++G+GKT  F++
Sbjct: 13  DVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSI 72
Query: 63  PILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA 122
            +LQ          AL+L PTRELA QI    L LG  MN++     GG ++ +  ++L 
Sbjct: 73  SVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLD 132
Query: 123 KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
              H+V  TPGR+ D +    +     IK LVLDEAD +
Sbjct: 133 YGQHVVAGTPGRVFDMIRR-RSLRTRAIKMLVLDEADEM 170

>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain Length = 223

Iteration: 1
 Score = 90.5 bits (223), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 52/157 (33%), Positives = 85/157 (54%), Gaps = 2/157 (1%)
Query: 5   IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPI 64
           +  F D++L+  L+R     G + P+ IQ+  I  ++   D +  A++G+GKT  F++  
Sbjct: 20  VYKFDDMELDEQLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAA 79
Query: 65  LQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKK 124
           LQ+         AL+L PTRELA QI    + L   M+++V    GG   V+  + L + 
Sbjct: 80  LQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGL-RD 138
Query: 125 PHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
             IV+ TPGR+ D++     F  ++IK  +LDEAD +
Sbjct: 139 AQIVVGTPGRVFDNIQR-RRFRTDKIKMFILDEADEM 174

>pdb|1QDE|A Chain A, Crystal Structure Of The Atpase Domain Of Translation Initiation Factor 4a From Saccharomyces Cerevisiae-The Prototype Of The Dead Box Protein Family Length = 224

Iteration: 1
 Score = 90.1 bits (222), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 52/157 (33%), Positives = 85/157 (54%), Gaps = 2/157 (1%)
Query: 5   IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPI 64
           +  F D++L+  L+R     G + P+ IQ+  I  ++   D +  A++G+GKT  F++  
Sbjct: 13  VYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAA 72
Query: 65  LQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKK 124
           LQ+         AL+L PTRELA QI    + L   M+++V    GG   V+  + L + 
Sbjct: 73  LQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGL-RD 131
Query: 125 PHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
             IV+ TPGR+ D++     F  ++IK  +LDEAD +
Sbjct: 132 AQIVVGTPGRVFDNIQR-RRFRTDKIKMFILDEADEM 167

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score = 90.1 bits (222), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 52/157 (33%), Positives = 85/157 (54%), Gaps = 2/157 (1%)
Query: 5   IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPI 64
           +  F D++L+  L+R     G + P+ IQ+  I  ++   D +  A++G+GKT  F++  
Sbjct: 21  VYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAA 80
Query: 65  LQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKK 124
           LQ+         AL+L PTRELA QI    + L   M+++V    GG   V+  + L + 
Sbjct: 81  LQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGL-RD 139
Query: 125 PHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
             IV+ TPGR+ D++     F  ++IK  +LDEAD +
Sbjct: 140 AQIVVGTPGRVFDNIQR-RRFRTDKIKMFILDEADEM 175

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 89.7 bits (221), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 52/155 (33%), Positives = 81/155 (52%), Gaps = 1/155 (0%)
Query: 7   SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ 66
           +F  + L   L+R     G + P+ IQ+  I  ++   D I  +++G+GKT  F++ +LQ
Sbjct: 2   TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQ 61
Query: 67  KWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPH 126
                     AL+L PTRELA Q+    L LG  MN++     GG ++ +  ++L    H
Sbjct: 62  CLDIQVRETQALILAPTRELAVQVQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQH 121
Query: 127 IVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           +V  TPGR+ D +    +     IK LVLDEAD +
Sbjct: 122 VVAGTPGRVFDMIRR-RSLRTRAIKMLVLDEADEM 155

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 89.7 bits (221), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 52/155 (33%), Positives = 81/155 (52%), Gaps = 1/155 (0%)
Query: 7   SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ 66
           +F  + L   L+R     G + P+ IQ+  I  ++   D I  +++G+GKT  F++ +LQ
Sbjct: 2   TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQ 61
Query: 67  KWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPH 126
                     AL+L PTRELA Q+    L LG  MN++     GG ++ +  ++L    H
Sbjct: 62  CLDIQVRETQALILAPTRELAVQVQKGLLALGDYMNVQSHACIGGTNVGEDIRKLDYGQH 121
Query: 127 IVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           +V  TPGR+ D +    +     IK LVLDEAD +
Sbjct: 122 VVAGTPGRVFDMIRR-RSLRTRAIKMLVLDEADEM 155

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score = 89.0 bits (219), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 53/155 (34%), Positives = 79/155 (50%), Gaps = 1/155 (0%)
Query: 7   SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ 66
           +F D  L   L+      G + P+ IQ+  IP  +   D +  AK G+GKT AF +P L+
Sbjct: 22  TFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLE 81
Query: 67  KWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPH 126
           K       I AL++ PTRELA Q       LGK   +   + TGG ++ D    L +  H
Sbjct: 82  KVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVH 141
Query: 127 IVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           I++ TPGR+ D L +     L+     ++DEAD++
Sbjct: 142 ILVGTPGRVLD-LASRKVADLSDCSLFIMDEADKM 175

>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A Human Dead-Box Protein Length = 206

Iteration: 1
 Score = 85.9 bits (211), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 55/156 (35%), Positives = 85/156 (54%), Gaps = 2/156 (1%)
Query: 7   SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ 66
            F D  L   L+     +G + P+ IQ+  IP  L+  D +  AK G+GK+ A+ +P+L+
Sbjct: 4   EFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLE 63
Query: 67  KWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGKELAKKP 125
           +       I A+V+ PTRELA Q+    + + K M   +V   TGG ++ D    L    
Sbjct: 64  RLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTV 123
Query: 126 HIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           H+VIATPGR+ D L       ++ ++ +VLDEAD+L
Sbjct: 124 HVVIATPGRILD-LIKKGVAKVDHVQMIVLDEADKL 158

>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In Complex With Adp Length = 245

Iteration: 1
 Score = 85.9 bits (211), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 58/168 (34%), Positives = 92/168 (54%), Gaps = 7/168 (4%)
Query: 1   MEDPIKSFTDL----KLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGK 56
           + DPI +F  L    K+N  L++     G + PT IQ   IP +L+  + +  A TGSGK
Sbjct: 20  LPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGK 79
Query: 57  TLAFALPILQKWCEDPY-GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMV 115
           TLAF++PIL +  +    G  AL+++PTRELA QI  + + + +    R+ +I       
Sbjct: 80  TLAFSIPILMQLKQPANKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAA 139
Query: 116 DQ-GKELAKKPHIVIATPGRLADHLDT-CNTFSLNRIKFLVLDEADRL 161
            + G + +KK  I++ TP RL   L        L  +++LV+DE+D+L
Sbjct: 140 KKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKL 187

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score = 83.6 bits (205), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 51/155 (32%), Positives = 80/155 (51%), Gaps = 2/155 (1%)
Query: 5   IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPI 64
           +  F D +L+  L+R     G + P+ IQ+  I  ++   D +  A++G+GKT  F++  
Sbjct: 20  VYKFDDXELDENLLRGVFGYGFEEPSAIQQRAIXPIIEGHDVLAQAQSGTGKTGTFSIAA 79
Query: 65  LQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKK 124
           LQ+         AL L PTRELA QI      L    +++V    GG   V+  + L + 
Sbjct: 80  LQRIDTSVKAPQALXLAPTRELALQIQKVVXALAFHXDIKVHACIGGTSFVEDAEGL-RD 138
Query: 125 PHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEAD 159
             IV+ TPGR+ D++     F  ++IK  +LDEAD
Sbjct: 139 AQIVVGTPGRVFDNIQR-RRFRTDKIKXFILDEAD 172

>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain Length = 228

Iteration: 1
 Score = 80.1 bits (196), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 56/153 (36%), Positives = 81/153 (52%), Gaps = 8/153 (5%)
Query: 15  PWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPY- 73
           P L++    +G+  PT IQ    P +L   D I  A+TG+GKTL++ +P        P  
Sbjct: 29  PDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPIS 88
Query: 74  -----GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIV 128
                G   LVLTPTRELA  +  +         L+   I GG +   Q ++++K   I+
Sbjct: 89  REQRNGPGMLVLTPTRELALHVEAECSKYS-YKGLKSICIYGGRNRNGQIEDISKGVDII 147
Query: 129 IATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           IATPGRL D L   N+ +L  I +LV+DEAD++
Sbjct: 148 IATPGRLND-LQMNNSVNLRSITYLVIDEADKM 179

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score = 79.7 bits (195), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 53/146 (36%), Positives = 80/146 (54%), Gaps = 17/146 (11%)
Query: 30  TEIQKAIIPHVLN--DEDCIGCAKTGSGKTLAFALPILQKWC----EDPYGIFALVLTPT 83
           T +Q+  I  +L+  D D I  AKTG+GKT AF +PI Q       +  Y + A+++ PT
Sbjct: 45  TPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPT 104
Query: 84  RELAYQIGDQFLVLGKVMNLRVSI-------ITGGMDMVDQGKELAK-KPHIVIATPGRL 135
           R+LA QI  +   + K+ ++   +       + GG D      ++ K +P+IVIATPGRL
Sbjct: 105 RDLALQIEAE---VKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRL 161
Query: 136 ADHLDTCNTFSLNRIKFLVLDEADRL 161
            D L+  +      + + VLDEADRL
Sbjct: 162 IDVLEKYSNKFFRFVDYKVLDEADRL 187

>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 = 79.3 bits (194), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 53/146 (36%), Positives = 80/146 (54%), Gaps = 17/146 (11%)
Query: 30  TEIQKAIIPHVLN--DEDCIGCAKTGSGKTLAFALPILQKWC----EDPYGIFALVLTPT 83
           T +Q+  I  +L+  D D I  AKTG+GKT AF +PI Q       +  Y + A+++ PT
Sbjct: 45  TPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPT 104
Query: 84  RELAYQIGDQFLVLGKVMNLRVSI-------ITGGMDMVDQGKELAK-KPHIVIATPGRL 135
           R+LA QI  +   + K+ ++   +       + GG D      ++ K +P+IVIATPGRL
Sbjct: 105 RDLALQIEAE---VKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRL 161
Query: 136 ADHLDTCNTFSLNRIKFLVLDEADRL 161
            D L+  +      + + VLDEADRL
Sbjct: 162 IDVLEKYSNKFFRFVDYKVLDEADRL 187

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 79.3 bits (194), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 53/146 (36%), Positives = 80/146 (54%), Gaps = 17/146 (11%)
Query: 30  TEIQKAIIPHVLN--DEDCIGCAKTGSGKTLAFALPILQKWC----EDPYGIFALVLTPT 83
           T +Q+  I  +L+  D D I  AKTG+GKT AF +PI Q       +  Y + A+++ PT
Sbjct: 96  TPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPT 155
Query: 84  RELAYQIGDQFLVLGKVMNLRVSI-------ITGGMDMVDQGKELAK-KPHIVIATPGRL 135
           R+LA QI  +   + K+ ++   +       + GG D      ++ K +P+IVIATPGRL
Sbjct: 156 RDLALQIEAE---VKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRL 212
Query: 136 ADHLDTCNTFSLNRIKFLVLDEADRL 161
            D L+  +      + + VLDEADRL
Sbjct: 213 IDVLEKYSNKFFRFVDYKVLDEADRL 238

>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214 Length = 235

Iteration: 1
 Score = 77.0 bits (188), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 52/160 (32%), Positives = 90/160 (56%), Gaps = 10/160 (6%)
Query: 5   IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLND--EDCIGCAKTGSGKTLAFAL 62
           +KSF +L+L P L++    +G   P++IQ+  +P +L +  ++ I  +++G+GKT AF L
Sbjct: 24  VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 83
Query: 63  PILQKWCEDPYGIFA--LVLTPTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGK 119
            +L +   +P   +   L L+PT ELA Q G     +GK    L+++    G + +++G+
Sbjct: 84  AMLSQV--EPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRG-NKLERGQ 140
Query: 120 ELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEAD 159
           ++++   IVI TPG + D           +IK  VLDEAD
Sbjct: 141 KISE--QIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEAD 178

>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 300

Iteration: 1
 Score = 76.6 bits (187), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 52/160 (32%), Positives = 90/160 (56%), Gaps = 10/160 (6%)
Query: 5   IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLND--EDCIGCAKTGSGKTLAFAL 62
           +KSF +L+L P L++    +G   P++IQ+  +P +L +  ++ I  +++G+GKT AF L
Sbjct: 91  VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 150
Query: 63  PILQKWCEDPYGIFA--LVLTPTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGK 119
            +L +   +P   +   L L+PT ELA Q G     +GK    L+++    G + +++G+
Sbjct: 151 AMLSQV--EPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRG-NKLERGQ 207
Query: 120 ELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEAD 159
           ++++   IVI TPG + D           +IK  VLDEAD
Sbjct: 208 KISE--QIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEAD 245

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score = 76.3 bits (186), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 52/160 (32%), Positives = 91/160 (56%), Gaps = 10/160 (6%)
Query: 5   IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLND--EDCIGCAKTGSGKTLAFAL 62
           +KSF +L+L P L++    +G   P++IQ+  +P +L +  ++ I  +++G+GKT AF L
Sbjct: 61  VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 120
Query: 63  PILQKWCEDPYGIF--ALVLTPTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGK 119
            +L +   +P   +   L L+PT ELA Q G     +GK    L+++    G + +++G+
Sbjct: 121 AMLSQV--EPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRG-NKLERGQ 177
Query: 120 ELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEAD 159
           +++++  IVI TPG + D           +IK  VLDEAD
Sbjct: 178 KISEQ--IVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEAD 215

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score = 76.3 bits (186), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 52/160 (32%), Positives = 91/160 (56%), Gaps = 10/160 (6%)
Query: 5   IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLND--EDCIGCAKTGSGKTLAFAL 62
           +KSF +L+L P L++    +G   P++IQ+  +P +L +  ++ I  +++G+GKT AF L
Sbjct: 40  VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 99
Query: 63  PILQKWCEDPYGIF--ALVLTPTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGK 119
            +L +   +P   +   L L+PT ELA Q G     +GK    L+++    G + +++G+
Sbjct: 100 AMLSQV--EPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRG-NKLERGQ 156
Query: 120 ELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEAD 159
           +++++  IVI TPG + D           +IK  VLDEAD
Sbjct: 157 KISEQ--IVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEAD 194

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score = 76.3 bits (186), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 52/160 (32%), Positives = 91/160 (56%), Gaps = 10/160 (6%)
Query: 5   IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLND--EDCIGCAKTGSGKTLAFAL 62
           +KSF +L+L P L++    +G   P++IQ+  +P +L +  ++ I  +++G+GKT AF L
Sbjct: 24  VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 83
Query: 63  PILQKWCEDPYGIF--ALVLTPTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGK 119
            +L +   +P   +   L L+PT ELA Q G     +GK    L+++    G + +++G+
Sbjct: 84  AMLSQV--EPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRG-NKLERGQ 140
Query: 120 ELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEAD 159
           +++++  IVI TPG + D           +IK  VLDEAD
Sbjct: 141 KISEQ--IVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEAD 178

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score = 75.9 bits (185), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 52/160 (32%), Positives = 91/160 (56%), Gaps = 10/160 (6%)
Query: 5   IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLND--EDCIGCAKTGSGKTLAFAL 62
           +KSF +L+L P L++    +G   P++IQ+  +P +L +  ++ I  +++G+GKT AF L
Sbjct: 91  VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 150
Query: 63  PILQKWCEDPYGIF--ALVLTPTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGK 119
            +L +   +P   +   L L+PT ELA Q G     +GK    L+++    G + +++G+
Sbjct: 151 AMLSQV--EPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRG-NKLERGQ 207
Query: 120 ELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEAD 159
           +++++  IVI TPG + D           +IK  VLDEAD
Sbjct: 208 KISEQ--IVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEAD 245

>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p Length = 226

Iteration: 1
 Score = 72.4 bits (176), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 48/158 (30%), Positives = 85/158 (53%), Gaps = 7/158 (4%)
Query: 6   KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLND--EDCIGCAKTGSGKTLAFALP 63
           KSF +L L P L++    +  + P++IQ+  +P +L++   + I  +++G+GKT AF+L 
Sbjct: 22  KSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLT 81
Query: 64  ILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAK 123
           +L +   +     A+ L P+RELA Q  +    +GK   +   +I    D  ++ K++  
Sbjct: 82  MLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVP--DSFEKNKQI-- 137
Query: 124 KPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
              +++ TPG + D L       L +IK  VLDEAD +
Sbjct: 138 NAQVIVGTPGTVLD-LMRRKLMQLQKIKIFVLDEADNM 174

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 71.6 bits (174), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 48/158 (30%), Positives = 85/158 (53%), Gaps = 7/158 (4%)
Query: 6   KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLND--EDCIGCAKTGSGKTLAFALP 63
           KSF +L L P L++    +  + P++IQ+  +P +L++   + I  +++G+GKT AF+L 
Sbjct: 5   KSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLT 64
Query: 64  ILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAK 123
           +L +   +     A+ L P+RELA Q  +    +GK   +   +I    D  ++ K++  
Sbjct: 65  MLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVP--DSFEKNKQI-- 120
Query: 124 KPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
              +++ TPG + D L       L +IK  VLDEAD +
Sbjct: 121 NAQVIVGTPGTVLD-LMRRKLMQLQKIKIFVLDEADNM 157

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 71.6 bits (174), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 48/158 (30%), Positives = 85/158 (53%), Gaps = 7/158 (4%)
Query: 6   KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLND--EDCIGCAKTGSGKTLAFALP 63
           KSF +L L P L++    +  + P++IQ+  +P +L++   + I  +++G+GKT AF+L 
Sbjct: 5   KSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLT 64
Query: 64  ILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAK 123
           +L +   +     A+ L P+RELA Q  +    +GK   +   +I    D  ++ K++  
Sbjct: 65  MLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVP--DSFEKNKQI-- 120
Query: 124 KPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
              +++ TPG + D L       L +IK  VLDEAD +
Sbjct: 121 NAQVIVGTPGTVLD-LMRRKLMQLQKIKIFVLDEADNM 157

>pdb|2OXC|A Chain A, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex With Adp Length = 230

Iteration: 1
 Score = 68.6 bits (166), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/157 (33%), Positives = 75/157 (47%), Gaps = 7/157 (4%)
Query: 8   FTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQK 67
           F  L L+  ++   +  G + P+ +Q   IP      D I  AK+G+GKT  F+   L  
Sbjct: 26  FESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDS 85
Query: 68  WCEDPYGIFALVLTPTRELAYQIGDQFLVLG-KVMNLRVSIITGGMDMVDQGKELAKKPH 126
              +      L+L PTRE+A QI      +G K+  L   +  GG  +  Q K   KK H
Sbjct: 86  LVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPL-SQDKTRLKKCH 144
Query: 127 IVIATPGRLAD--HLDTCNTFSLNRIKFLVLDEADRL 161
           I + +PGR+     LD  N  S   I+  +LDEAD+L
Sbjct: 145 IAVGSPGRIKQLIELDYLNPGS---IRLFILDEADKL 178

>pdb|1WP9|A Chain A, Crystal Structure Of Pyrococcus Furiosus Hef Helicase Domain Length = 494

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 34/129 (26%), Positives = 60/129 (46%), Gaps = 4/129 (3%)
Query: 32  IQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIG 91
           I + +I     + +C+    TG GKTL   +  + ++    YG   L+L PT+ L  Q  
Sbjct: 12  IYQEVIYAKCKETNCLIVLPTGLGKTLIAMM--IAEYRLTKYGGKVLMLAPTKPLVLQHA 69
Query: 92  DQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIK 151
           + F  L  +   ++  +TG     ++ K  A +  +++ATP  + + L      SL  + 
Sbjct: 70  ESFRRLFNLPPEKIVALTGEKSPEERSKAWA-RAKVIVATPQTIENDL-LAGRISLEDVS 127
Query: 152 FLVLDEADR 160
            +V DEA R
Sbjct: 128 LIVFDEAHR 136

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	182
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	6e-86
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	1e-68
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	1e-67
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	9e-60
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	6e-59
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	9e-59
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	3e-58
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	2e-57
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	5e-57
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	5e-56
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	5e-56
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	1e-55
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	6e-55
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	1e-54
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	1e-54
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	5e-54
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	6e-54
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	7e-54
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	4e-53
3bor_A	237	Human initiation factor 4A-II; translation initiat	4e-53
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	6e-53
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	1e-52
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	2e-52
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	2e-51
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	3e-50
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	1e-47
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	1e-47
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	5e-47
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	9e-46
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	2e-45
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	8e-45
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	6e-18
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	6e-15
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	1e-13
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	2e-13
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	2e-13
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	3e-13
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	4e-13
3b6e_A	216	Interferon-induced helicase C domain-containing P;	7e-13
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	1e-12
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	5e-12
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	5e-08
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	1e-06
1yks_A	440	Genome polyprotein [contains: flavivirin protease	9e-06
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	2e-05
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	6e-05
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	7e-05
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	1e-04
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	5e-04
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	7e-04

>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 =  252 bits (645), Expect = 6e-86
 Identities = 84/160 (52%), Positives = 107/160 (66%)

Query: 2   EDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFA 61
           E+  K+F DL +   L   C  +G   PT+IQ   IP  L   D IG A+TGSGKT AFA
Sbjct: 39  EEETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFA 98

Query: 62  LPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL 121
           LPIL    E P  +FALVLTPTRELA+QI +QF  LG  + ++ ++I GG+D + Q   L
Sbjct: 99  LPILNALLETPQRLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLAL 158

Query: 122 AKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           AKKPHI+IATPGRL DHL+    F+L  +K+LV+DEADR+
Sbjct: 159 AKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRI 198

>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 =  207 bits (530), Expect = 1e-68
 Identities = 60/164 (36%), Positives = 91/164 (55%), Gaps = 5/164 (3%)

Query: 2   EDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFA 61
            + I  F+D  L+   ++  Q    +  TEIQK  I   L  +D +G AKTGSGKTLAF 
Sbjct: 21  VNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFL 80

Query: 62  LPILQKWCED----PYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQ 117
           +P+L+           G+  L+++PTRELAYQ  +    +GK  +    +I GG D+  +
Sbjct: 81  VPVLEALYRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHE 140

Query: 118 GKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
            + +    +I++ TPGRL  H+D   +F    ++ LVLDEADR+
Sbjct: 141 AERI-NNINILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRI 183

>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 =  206 bits (525), Expect = 1e-67
 Identities = 56/162 (34%), Positives = 83/162 (51%), Gaps = 6/162 (3%)

Query: 6   KSFTDL--KLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALP 63
            SF  L   +N   ++  + +G    TEIQ   I  +L   D +  AKTGSGKTLAF +P
Sbjct: 52  TSFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIP 111

Query: 64  ILQKWCEDPY----GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGK 119
            ++   +  +    G   L+L+PTRELA Q       L         +I GG +   + +
Sbjct: 112 AVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQ 171

Query: 120 ELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           +L    +I++ATPGRL DH+     F    ++ LV+DEADR+
Sbjct: 172 KLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRI 213

>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 =  194 bits (494), Expect = 9e-60
 Identities = 53/167 (31%), Positives = 82/167 (49%), Gaps = 11/167 (6%)

Query: 6   KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDE--DCIGCAKTGSGKTLAFALP 63
               +  L+  + +    +     T +Q+  I  +L+ E  D I  AKTG+GKT AF +P
Sbjct: 72  SLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIP 131

Query: 64  ILQK----WCEDPYGIFALVLTPTRELAYQIGDQFLVLGK----VMNLRVSIITGGMDMV 115
           I Q       +  Y + A+++ PTR+LA QI  +   +      +       + GG D  
Sbjct: 132 IFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFR 191

Query: 116 DQGKELAK-KPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
               ++ K +P+IVIATPGRL D L+  +      + + VLDEADRL
Sbjct: 192 AAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRL 238

>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 =  183 bits (467), Expect = 6e-59
 Identities = 58/166 (34%), Positives = 91/166 (54%), Gaps = 7/166 (4%)

Query: 3   DPIKSFTDL----KLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTL 58
           DPI +F  L    K+N  L++     G + PT IQ   IP +L+  + +  A TGSGKTL
Sbjct: 22  DPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTL 81

Query: 59  AFALPILQKWCEDP-YGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQ 117
           AF++PIL +  +    G  AL+++PTRELA QI  + + + +    R+ +I        +
Sbjct: 82  AFSIPILMQLKQPANKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKK 141

Query: 118 -GKELAKKPHIVIATPGRLADHLDTCNTF-SLNRIKFLVLDEADRL 161
            G + +KK  I++ TP RL   L        L  +++LV+DE+D+L
Sbjct: 142 FGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKL 187

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score =  181 bits (463), Expect = 9e-59
 Identities = 58/164 (35%), Positives = 87/164 (53%), Gaps = 7/164 (4%)

Query: 1   MEDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAF 60
           M +    FT     P++I   +T+    PTEIQ+ IIP  L  E  +G ++TG+GKT A+
Sbjct: 1   MAE--TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAY 58

Query: 61  ALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVM----NLRVSIITGGMDMVD 116
            LPI++K   +   + A++  PTRELA QI  + L + K       +    + GG D   
Sbjct: 59  LLPIMEKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQK 118

Query: 117 QGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR 160
             ++L  +PHIVI TPGR+ D +       ++    LV+DEAD 
Sbjct: 119 ALEKLNVQPHIVIGTPGRINDFIRE-QALDVHTAHILVVDEADL 161

>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 =  181 bits (463), Expect = 3e-58
 Identities = 62/167 (37%), Positives = 87/167 (52%), Gaps = 10/167 (5%)

Query: 3   DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFAL 62
           + I++F +LKL+P +         + PT IQK  IP +L   D + CA+TGSGKT AF +
Sbjct: 20  NVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLI 79

Query: 63  PILQKWCEDPY---------GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMD 113
           PI+                     L+L PTRELA QI  +         LR  ++ GG D
Sbjct: 80  PIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGAD 139

Query: 114 MVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR 160
              Q +E+    H+++ATPGRL D ++     SL   K++VLDEADR
Sbjct: 140 THSQIREVQMGCHLLVATPGRLVDFIEKNKI-SLEFCKYIVLDEADR 185

>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 =  179 bits (456), Expect = 2e-57
 Identities = 59/163 (36%), Positives = 81/163 (49%), Gaps = 6/163 (3%)

Query: 3   DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFAL 62
            P+ +F +      ++          PT IQ    P  L+  D +G A+TGSGKTL++ L
Sbjct: 26  KPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLL 85

Query: 63  PIL-----QKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQ 117
           P +     Q + E   G   LVL PTRELA Q+        +   L+ + I GG     Q
Sbjct: 86  PAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQ 145

Query: 118 GKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR 160
            ++L +   I IATPGRL D L+     +L R  +LVLDEADR
Sbjct: 146 IRDLERGVEICIATPGRLIDFLEC-GKTNLRRTTYLVLDEADR 187

>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 =  187 bits (476), Expect = 5e-57
 Identities = 52/167 (31%), Positives = 81/167 (48%), Gaps = 11/167 (6%)

Query: 6   KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDE--DCIGCAKTGSGKTLAFALP 63
               +  L+  + +    +     T +Q+  I  +L+ E  D I  AKTG+GKT AF +P
Sbjct: 21  SLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIP 80

Query: 64  ILQKWCEDPY----GIFALVLTPTRELAYQIGDQFLVLGK----VMNLRVSIITGGMDMV 115
           I Q      +     + A+++ PTR+LA QI  +   +      +       + GG D  
Sbjct: 81  IFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFR 140

Query: 116 DQGKELAK-KPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
               ++ K +P+IVIATPGRL D L+  +      + + VLDEADRL
Sbjct: 141 AAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRL 187

>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 =  181 bits (461), Expect = 5e-56
 Identities = 66/163 (40%), Positives = 90/163 (55%), Gaps = 6/163 (3%)

Query: 3   DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFAL 62
            PI+ FT   L   +I      G K PT IQK  IP + +  D + CA+TGSGKT AF L
Sbjct: 53  QPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLL 112

Query: 63  PILQKWCEDPY-----GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQ 117
           PIL K  EDP+         ++++PTRELA QI ++         L++ I+ GG     Q
Sbjct: 113 PILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQ 172

Query: 118 GKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR 160
            + + +  H+VIATPGRL D +D     +    +F+VLDEADR
Sbjct: 173 NECITRGCHVVIATPGRLLDFVDRTFI-TFEDTRFVVLDEADR 214

>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 =  179 bits (457), Expect = 5e-56
 Identities = 63/160 (39%), Positives = 99/160 (61%), Gaps = 4/160 (2%)

Query: 1   MEDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLN-DEDCIGCAKTGSGKTLA 59
           ME    +F +L L+  ++   +  G + PT+IQ  +IP  LN + + +  A+TGSGKT +
Sbjct: 1   MEVEYMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTAS 60

Query: 60  FALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGK 119
           FA+P+++    +  GI A++LTPTRELA Q+ D+   L    NL+++ I GG  +  Q K
Sbjct: 61  FAIPLIEL-VNENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIK 119

Query: 120 ELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEAD 159
            L K  +IV+ TPGR+ DH++   T +L  +K+ +LDEAD
Sbjct: 120 AL-KNANIVVGTPGRILDHINR-GTLNLKNVKYFILDEAD 157

>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 =  173 bits (442), Expect = 1e-55
 Identities = 63/157 (40%), Positives = 85/157 (54%), Gaps = 6/157 (3%)

Query: 7   SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ 66
            F D  L P ++      G+ TPT IQ A +P  L  +D IG A+TG+GKTLAFALPI +
Sbjct: 2   EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAE 61

Query: 67  KWCEDPY---GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAK 123
           +            ALVLTPTRELA Q+  +   +    +L+V  + GG     Q + L +
Sbjct: 62  RLAPSQERGRKPRALVLTPTRELALQVASELTAVAP--HLKVVAVYGGTGYGKQKEALLR 119

Query: 124 KPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR 160
               V+ATPGR  D+L       L+R++  VLDEAD 
Sbjct: 120 GADAVVATPGRALDYLRQ-GVLDLSRVEVAVLDEADE 155

>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 =  175 bits (447), Expect = 6e-55
 Identities = 53/148 (35%), Positives = 84/148 (56%), Gaps = 8/148 (5%)

Query: 13  LNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP 72
           +N  + +  + +G K  TE+Q   IP +L  ++ +  AKTGSGKT A+A+PIL+      
Sbjct: 1   MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL----- 55

Query: 73  YGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATP 132
            G+ +LV+TPTREL  Q+      +G+ M+ +V+ + GGM    Q   + +   IV+ATP
Sbjct: 56  -GMKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRV-RNADIVVATP 113

Query: 133 GRLADHLDTCNTFSLNRIKFLVLDEADR 160
           GRL D         L+  + +++DEAD 
Sbjct: 114 GRLLDLWSK-GVIDLSSFEIVIIDEADL 140

>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 =  177 bits (451), Expect = 1e-54
 Identities = 54/160 (33%), Positives = 82/160 (51%), Gaps = 1/160 (0%)

Query: 2   EDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFA 61
            D   +F  + L   L+R     G + P+ IQ+  I  ++   D I  +++G+GKT  F+
Sbjct: 33  VDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFS 92

Query: 62  LPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL 121
           + +LQ          AL+L PTRELA QI    L LG  MN++     GG ++ +  ++L
Sbjct: 93  ISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKL 152

Query: 122 AKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
               H+V  TPGR+ D +    +     IK LVLDEAD +
Sbjct: 153 DYGQHVVAGTPGRVFDMIR-RRSLRTRAIKMLVLDEADEM 191

>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 =  177 bits (450), Expect = 1e-54
 Identities = 52/155 (33%), Positives = 77/155 (49%), Gaps = 1/155 (0%)

Query: 7   SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ 66
           +F D  L   L+      G + P+ IQ+  IP  +   D +  AK G+GKT AF +P L+
Sbjct: 22  TFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLE 81

Query: 67  KWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPH 126
           K       I AL++ PTRELA Q       LGK   +   + TGG ++ D    L +  H
Sbjct: 82  KVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVH 141

Query: 127 IVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           I++ TPGR+ D         L+     ++DEAD++
Sbjct: 142 ILVGTPGRVLDLASR-KVADLSDCSLFIMDEADKM 175

>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 =  170 bits (433), Expect = 5e-54
 Identities = 58/165 (35%), Positives = 83/165 (50%), Gaps = 9/165 (5%)

Query: 3   DPIKSFTD-LKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFA 61
            P   F D  +  P L++    +G+  PT IQ    P +L   D I  A+TG+GKTL++ 
Sbjct: 16  KPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYL 75

Query: 62  LPILQKWCEDPY------GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMV 115
           +P        P       G   LVLTPTRELA  +  +         L+   I GG +  
Sbjct: 76  MPGFIHLDSQPISREQRNGPGMLVLTPTRELALHVEAECSKYSY-KGLKSICIYGGRNRN 134

Query: 116 DQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR 160
            Q ++++K   I+IATPGRL D     N+ +L  I +LV+DEAD+
Sbjct: 135 GQIEDISKGVDIIIATPGRLNDLQMN-NSVNLRSITYLVIDEADK 178

>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 =  175 bits (445), Expect = 6e-54
 Identities = 52/160 (32%), Positives = 86/160 (53%), Gaps = 2/160 (1%)

Query: 2   EDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFA 61
           +  +  F D++L+  L+R     G + P+ IQ+  I  ++   D +  A++G+GKT  F+
Sbjct: 17  DKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFS 76

Query: 62  LPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL 121
           +  LQ+         AL+L PTRELA QI    + L   M+++V    GG   V+  + L
Sbjct: 77  IAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGL 136

Query: 122 AKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
            +   IV+ TPGR+ D++     F  ++IK  +LDEAD +
Sbjct: 137 -RDAQIVVGTPGRVFDNIQR-RRFRTDKIKMFILDEADEM 174

>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 =  169 bits (430), Expect = 7e-54
 Identities = 54/156 (34%), Positives = 85/156 (54%), Gaps = 2/156 (1%)

Query: 7   SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ 66
            F D  L   L+     +G + P+ IQ+  IP  L+  D +  AK G+GK+ A+ +P+L+
Sbjct: 4   EFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLE 63

Query: 67  KWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGKELAKKP 125
           +       I A+V+ PTRELA Q+    + + K M   +V   TGG ++ D    L    
Sbjct: 64  RLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTV 123

Query: 126 HIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           H+VIATPGR+ D +       ++ ++ +VLDEAD+L
Sbjct: 124 HVVIATPGRILDLIKK-GVAKVDHVQMIVLDEADKL 158

>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 =  168 bits (427), Expect = 4e-53
 Identities = 52/158 (32%), Positives = 85/158 (53%), Gaps = 2/158 (1%)

Query: 2   EDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFA 61
           +  +  F D++L+  L+R     G + P+ IQ+  I  ++   D +  A++G+GKT  F+
Sbjct: 10  DKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFS 69

Query: 62  LPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL 121
           +  LQ+         AL+L PTRELA QI    + L   M+++V    GG   V+  + L
Sbjct: 70  IAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGL 129

Query: 122 AKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEAD 159
            +   IV+ TPGR+ D++     F  ++IK  +LDEAD
Sbjct: 130 -RDAQIVVGTPGRVFDNIQR-RRFRTDKIKMFILDEAD 165

>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 =  168 bits (428), Expect = 4e-53
 Identities = 61/159 (38%), Positives = 86/159 (54%), Gaps = 2/159 (1%)

Query: 2   EDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFA 61
            + + +F D+ L   L+R     G + P+ IQ+  I   +   D I  A++G+GKT  FA
Sbjct: 26  NEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFA 85

Query: 62  LPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL 121
           + ILQ+   +     ALVL PTRELA QI    L LG  M        GG ++ ++ ++L
Sbjct: 86  ISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKL 145

Query: 122 -AKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEAD 159
            A+ PHIV+ TPGR+ D L+     S   IK  VLDEAD
Sbjct: 146 QAEAPHIVVGTPGRVFDMLNR-RYLSPKWIKMFVLDEAD 183

>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 =  167 bits (424), Expect = 6e-53
 Identities = 56/167 (33%), Positives = 84/167 (50%), Gaps = 4/167 (2%)

Query: 1   MEDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAF 60
           +      F D  L P L+R     G + P+E+Q   IP  +   D +  AK+G GKT  F
Sbjct: 9   VSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVF 68

Query: 61  ALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGK 119
            L  LQ+       +  LV+  TRELA+QI  ++    K M N++V++  GG+ +    +
Sbjct: 69  VLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEE 128

Query: 120 ELAKK-PHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR-LSLM 164
            L K  PHIV+ TPGR+        + +L  IK  +LDE D+ L  +
Sbjct: 129 VLKKNCPHIVVGTPGRILALARN-KSLNLKHIKHFILDECDKMLEQL 174

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  171 bits (437), Expect = 1e-52
 Identities = 61/176 (34%), Positives = 91/176 (51%), Gaps = 19/176 (10%)

Query: 3   DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFAL 62
             I+SF+D+++   ++   +      PT +QK  IP +    D + CA+TGSGKT AF L
Sbjct: 12  PHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLL 71

Query: 63  PILQKWCEDPY------------------GIFALVLTPTRELAYQIGDQFLVLGKVMNLR 104
           PIL +   D                       +LVL PTRELA QI ++         +R
Sbjct: 72  PILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVR 131

Query: 105 VSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR 160
             ++ GG D+  Q ++L +  H+++ATPGRL D ++      L+  K+LVLDEADR
Sbjct: 132 PCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKI-GLDFCKYLVLDEADR 186

>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 =  171 bits (436), Expect = 2e-52
 Identities = 60/161 (37%), Positives = 86/161 (53%), Gaps = 2/161 (1%)

Query: 2   EDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFA 61
            + + SF D+ L+  L+R     G + P+ IQ+  I   +   D I  A++G+GKT  FA
Sbjct: 36  NEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFA 95

Query: 62  LPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL 121
           + ILQ+   D     ALVL PTRELA QI    + LG  M        GG ++  + ++L
Sbjct: 96  ISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKL 155

Query: 122 AKK-PHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
             + PHI++ TPGR+ D L+     S   IK  VLDEAD +
Sbjct: 156 QMEAPHIIVGTPGRVFDMLNR-RYLSPKYIKMFVLDEADEM 195

>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 =  163 bits (416), Expect = 2e-51
 Identities = 47/162 (29%), Positives = 74/162 (45%), Gaps = 3/162 (1%)

Query: 1   MEDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAF 60
           +      F  L L+  ++   +  G + P+ +Q   IP      D I  AK+G+GKT  F
Sbjct: 19  LLAEPADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVF 78

Query: 61  ALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGK 119
           +   L     +      L+L PTRE+A QI      +G  M  L   +  GG  +     
Sbjct: 79  STIALDSLVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKT 138

Query: 120 ELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
            L KK HI + +PGR+   ++  +  +   I+  +LDEAD+L
Sbjct: 139 RL-KKCHIAVGSPGRIKQLIEL-DYLNPGSIRLFILDEADKL 178

>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 =  165 bits (420), Expect = 3e-50
 Identities = 56/161 (34%), Positives = 83/161 (51%), Gaps = 4/161 (2%)

Query: 7   SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ 66
            F D  L P L+R     G + P+E+Q   IP  +   D +  AK+G GKT  F L  LQ
Sbjct: 9   GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 68

Query: 67  KWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGKELAKK- 124
           +       +  LV+  TRELA+QI  ++    K M N++V++  GG+ +    + L K  
Sbjct: 69  QLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNC 128

Query: 125 PHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR-LSLM 164
           PHIV+ TPGR+        + +L  IK  +LDE D+ L  +
Sbjct: 129 PHIVVGTPGRILALARN-KSLNLKHIKHFILDECDKMLEQL 168

>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 =  159 bits (404), Expect = 1e-47
 Identities = 50/164 (30%), Positives = 79/164 (48%), Gaps = 7/164 (4%)

Query: 5   IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDE--DCIGCAKTGSGKTLAFAL 62
           +KSF +L+L P L++    +G   P++IQ+  +P +L +   + I  +++G+GKT AF L
Sbjct: 24  VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 83

Query: 63  PILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGKEL 121
            +L +          L L+PT ELA Q G     +GK    L+++    G  +       
Sbjct: 84  AMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG---Q 140

Query: 122 AKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR-LSLM 164
                IVI TPG + D           +IK  VLDEAD  ++  
Sbjct: 141 KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQ 184

>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 =  156 bits (395), Expect = 1e-47
 Identities = 51/166 (30%), Positives = 80/166 (48%), Gaps = 7/166 (4%)

Query: 3   DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDE--DCIGCAKTGSGKTLAF 60
             +KSF +L+L P L++    +G   P++IQ+  +P +L +   + I  +++G+GKT AF
Sbjct: 89  YSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAF 148

Query: 61  ALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGK 119
            L +L +          L L+PT ELA Q G     +GK    L+++    G  +    K
Sbjct: 149 VLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQK 208

Query: 120 ELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR-LSLM 164
                  IVI TPG + D           +IK  VLDEAD  ++  
Sbjct: 209 ---ISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQ 251

>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 =  158 bits (402), Expect = 5e-47
 Identities = 50/164 (30%), Positives = 79/164 (48%), Gaps = 7/164 (4%)

Query: 5   IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDE--DCIGCAKTGSGKTLAFAL 62
           +KSF +L+L P L++    +G   P++IQ+  +P +L +   + I  +++G+GKT AF L
Sbjct: 91  VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 150

Query: 63  PILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGKEL 121
            +L +          L L+PT ELA Q G     +GK    L+++    G  +       
Sbjct: 151 AMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG---Q 207

Query: 122 AKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR-LSLM 164
                IVI TPG + D           +IK  VLDEAD  ++  
Sbjct: 208 KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQ 251

>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 =  153 bits (390), Expect = 9e-46
 Identities = 46/157 (29%), Positives = 79/157 (50%), Gaps = 7/157 (4%)

Query: 5   IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDE--DCIGCAKTGSGKTLAFAL 62
            KSF +L L P L++    +  + P++IQ+  +P +L++   + I  +++G+GKT AF+L
Sbjct: 4   AKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSL 63

Query: 63  PILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA 122
            +L +   +     A+ L P+RELA Q  +    +GK   +   +I          K   
Sbjct: 64  TMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDS----FEKNKQ 119

Query: 123 KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEAD 159
               +++ TPG + D +       L +IK  VLDEAD
Sbjct: 120 INAQVIVGTPGTVLDLMRR-KLMQLQKIKIFVLDEAD 155

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score =  153 bits (389), Expect = 2e-45
 Identities = 24/139 (17%), Positives = 51/139 (36%), Gaps = 11/139 (7%)

Query: 27  KTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTREL 86
           K  T  Q+     ++  +     A TG GKT    +  L    +      + ++ PT  L
Sbjct: 20  KDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKGKK---SALVFPTVTL 76

Query: 87  AYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAK----KPHIVIATPGRLADHLDTC 142
             Q  ++   L     +++      M   ++ K          HI++ +   ++ + +  
Sbjct: 77  VKQTLERLQKLAD-EKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKL 135

Query: 143 NTFSLNRIKFLVLDEADRL 161
              S  R  F+ +D+ D +
Sbjct: 136 ---SQKRFDFVFVDDVDAV 151

>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 = 79.5 bits (195), Expect = 6e-18
 Identities = 34/149 (22%), Positives = 57/149 (38%), Gaps = 9/149 (6%)

Query: 28  TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELA 87
            P   Q+ I        +C+    TG GKTL   +    ++    YG   L+L PT+ L 
Sbjct: 9   QPRIYQEVIYAKCKE-TNCLIVLPTGLGKTLIAMMIA--EYRLTKYGGKVLMLAPTKPLV 65

Query: 88  YQIGDQFLVLGKVMNLRVSIITG--GMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTF 145
            Q         ++ NL    I    G    ++  +   +  +++ATP  + + L      
Sbjct: 66  LQ---HAESFRRLFNLPPEKIVALTGEKSPEERSKAWARAKVIVATPQTIENDL-LAGRI 121

Query: 146 SLNRIKFLVLDEADRLSLMTSLKFFFFFF 174
           SL  +  +V DEA R     +  F    +
Sbjct: 122 SLEDVSLIVFDEAHRAVGNYAYVFIAREY 150

>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 = 70.7 bits (172), Expect = 6e-15
 Identities = 25/157 (15%), Positives = 50/157 (31%), Gaps = 8/157 (5%)

Query: 26  VKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ--KWCEDPYGIFALVLTPT 83
            K     Q  +    +N ++ + CA TGSGKT    L      +          + L   
Sbjct: 5   TKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATK 64

Query: 84  RELAYQIGDQFLVLGKVMNLRVSIITGGM-DMVDQG--KELAKKPHIVIATPGRLADHLD 140
             +  Q   Q  V       +   + G   +       +++ +   I++ TP  L +  +
Sbjct: 65  VPVYEQ---QKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFE 121

Query: 141 TCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFFFFLK 177
                SL+    ++ DE    +           +  +
Sbjct: 122 DGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQ 158

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 67.3 bits (163), Expect = 1e-13
 Identities = 30/153 (19%), Positives = 51/153 (33%), Gaps = 2/153 (1%)

Query: 28  TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ--KWCEDPYGIFALVLTPTRE 85
            P   Q  +    +  ++ I CA TG GKT    L      K          +       
Sbjct: 13  KPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIP 72

Query: 86  LAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTF 145
           +  Q    F    +    RV+ I+G        +++ +   I+I TP  L ++L      
Sbjct: 73  VYEQNKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIP 132

Query: 146 SLNRIKFLVLDEADRLSLMTSLKFFFFFFFLKY 178
           SL+    ++ DE    S         F +  + 
Sbjct: 133 SLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQK 165

>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 = 66.9 bits (162), Expect = 2e-13
 Identities = 28/187 (14%), Positives = 61/187 (32%), Gaps = 13/187 (6%)

Query: 1   MEDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAF 60
           + + + S  +    P  +        K     Q  +    +N ++ + CA TGSGKT   
Sbjct: 226 LSENLGSAAEGIGKPPPVY-----ETKKARSYQIELAQPAINGKNALICAPTGSGKTFVS 280

Query: 61  ALPILQ--KWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITG--GMDMVD 116
            L      +          + L     +  Q   Q  V       +   + G  G +  +
Sbjct: 281 ILICEHHFQNMPAGRKAKVVFLATKVPVYEQ---QKNVFKHHFERQGYSVQGISGENFSN 337

Query: 117 QG-KELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFFFF 175
              +++ +   I++ TP  L +  +     SL+    ++ DE    +           + 
Sbjct: 338 VSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYL 397

Query: 176 LKYYIPS 182
            + +  +
Sbjct: 398 EQKFNSA 404

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 66.5 bits (161), Expect = 2e-13
 Identities = 25/130 (19%), Positives = 45/130 (34%), Gaps = 2/130 (1%)

Query: 33  QKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ--KWCEDPYGIFALVLTPTRELAYQI 90
           Q  +       ++ I CA TG GKT    L      K          +       +  Q 
Sbjct: 9   QLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQ 68

Query: 91  GDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRI 150
              F    + +   ++ I+G        + + +   I+I TP  L ++L+     SL+  
Sbjct: 69  ATVFSRYFERLGYNIASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNNGAIPSLSVF 128

Query: 151 KFLVLDEADR 160
             ++ DE   
Sbjct: 129 TLMIFDECHN 138

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus} Length = 715

 Score = 66.3 bits (162), Expect = 3e-13
 Identities = 39/150 (26%), Positives = 61/150 (40%), Gaps = 8/150 (5%)

Query: 9   TDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLN-DEDCIGCAKTGSGKTLAFALPILQK 67
            DLKL   +I   +  G+K     Q   +   L      +  + TGSGKTL   + I+  
Sbjct: 11  EDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISF 70

Query: 68  WCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHI 127
             ++  G  A+ +TP R L  +    F      +  +V++ +G  D         K   I
Sbjct: 71  LLKN--GGKAIYVTPLRALTNEKYLTFKDWEL-IGFKVAMTSGDYDT---DDAWLKNYDI 124

Query: 128 VIATPGRLADHLDTCNTFSLNRIKFLVLDE 157
           +I T  +  D L       LN + + VLDE
Sbjct: 125 IITTYEK-LDSLWRHRPEWLNEVNYFVLDE 153

>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 = 65.7 bits (159), Expect = 4e-13
 Identities = 27/182 (14%), Positives = 57/182 (31%), Gaps = 13/182 (7%)

Query: 1   MEDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAF 60
           + + + S  +    P  +        K     Q  +    +N ++ + CA TGSGKT   
Sbjct: 226 LSENLGSAAEGIGKPPPVY-----ETKKARSYQIELAQPAINGKNALICAPTGSGKTFVS 280

Query: 61  ALPILQ--KWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGM-DMVDQ 117
            L      +          + L     +  Q   Q  V       +   + G   +    
Sbjct: 281 ILICEHHFQNMPAGRKAKVVFLATKVPVYEQ---QKNVFKHHFERQGYSVQGISGENFSN 337

Query: 118 G--KELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFFFF 175
              +++ +   I++ TP  L +  +     SL+    ++ DE    +           + 
Sbjct: 338 VSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYL 397

Query: 176 LK 177
            +
Sbjct: 398 EQ 399

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens} Length = 216

 Score = 63.3 bits (154), Expect = 7e-13
 Identities = 29/134 (21%), Positives = 47/134 (35%), Gaps = 8/134 (5%)

Query: 33  QKAIIPHVLNDEDCIGCAKTGSGKTLAFALPI---LQKWCEDPYGIFALVLTPTRELAYQ 89
           Q  +    L  ++ I C  TGSGKT          L K  +       +VL     L  Q
Sbjct: 38  QMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQ 97

Query: 90  IGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNT----- 144
           +  +          RV  ++G   +     E+ K   I+I+T   L + L          
Sbjct: 98  LFRKEFQPFLKKWYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAG 157

Query: 145 FSLNRIKFLVLDEA 158
             L+    +++DE 
Sbjct: 158 VQLSDFSLIIIDEC 171

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A Length = 702

 Score = 64.1 bits (156), Expect = 1e-12
 Identities = 29/145 (20%), Positives = 62/145 (42%), Gaps = 8/145 (5%)

Query: 13  LNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP 72
           ++ + +   +  G++     Q   +  V + ++ +    T +GKTL   + ++++  +  
Sbjct: 10  ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGG 69

Query: 73  YGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATP 132
             ++   + P R LA +  + F    K + LR+ I TG  +      E      I++ T 
Sbjct: 70  KSLY---VVPLRALAGEKYESFKKWEK-IGLRIGISTGDYES---RDEHLGDCDIIVTTS 122

Query: 133 GRLADHLDTCNTFSLNRIKFLVLDE 157
            + AD L       +  +  LV+DE
Sbjct: 123 EK-ADSLIRNRASWIKAVSCLVVDE 146

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A* Length = 720

 Score = 62.2 bits (151), Expect = 5e-12
 Identities = 36/149 (24%), Positives = 67/149 (44%), Gaps = 8/149 (5%)

Query: 10  DLKLNPWLIRQCQTIGVKTPTEIQKAIIP-HVLNDEDCIGCAKTGSGKTLAFALPILQKW 68
           +L+++  +    +  G+++    Q   +   +L  ++ +    T SGKTL   + ++ + 
Sbjct: 5   ELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRI 64

Query: 69  CEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIV 128
                G  A+ + P + LA +   +F    K + LRV++ TG  D      E   K  I+
Sbjct: 65  LTQ--GGKAVYIVPLKALAEEKFQEFQDWEK-IGLRVAMATGDYDS---KDEWLGKYDII 118

Query: 129 IATPGRLADHLDTCNTFSLNRIKFLVLDE 157
           IAT  +  D L    +  +  +K LV DE
Sbjct: 119 IATAEK-FDSLLRHGSSWIKDVKILVADE 146

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4a92_A* 1cu1_A 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A 8ohm_A 2f55_A 1jr6_A 1onb_A Length = 666

 Score = 50.8 bits (121), Expect = 5e-08
 Identities = 26/158 (16%), Positives = 44/158 (27%), Gaps = 21/158 (13%)

Query: 22  QTIGVKTPTEIQKAIIPHVLND-EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVL 80
               +++P     +  P V    +     A TGSGK+         +      G   LVL
Sbjct: 210 METTMRSPVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAAQ------GYKVLVL 263

Query: 81  TPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLD 140
            P+       G     + K   +  +I TG   +            +  +T G+      
Sbjct: 264 NPSVAATLGFGAY---MSKAHGIDPNIRTGVRTITTGAP-------VTYSTYGKFLADGG 313

Query: 141 TCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFFFFLKY 178
                S      ++ DE       T L         + 
Sbjct: 314 C----SGGAYDIIICDECHSTDSTTILGIGTVLDQAET 347

>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 = 46.7 bits (111), Expect = 1e-06
 Identities = 33/160 (20%), Positives = 52/160 (32%), Gaps = 34/160 (21%)

Query: 8   FTDLKLNPWLIRQCQTIGVKTPTEI---QKAIIPHVLNDEDCIGCAKTGSGKTL--AFAL 62
           F D   +P                +   Q+  +   L D+       TGSGKT     A+
Sbjct: 75  FVDNAADPIPT-----PYFDAEISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAI 129

Query: 63  PILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA 122
             L            L++ PT  LA Q  ++  + G      V   +G +      KEL 
Sbjct: 130 NELSTPT--------LIVVPTLALAEQWKERLGIFG---EEYVGEFSGRI------KELK 172

Query: 123 KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLS 162
               + ++T      + +       NR   L+ DE   L 
Sbjct: 173 P---LTVSTYDSAYVNAEKLG----NRFMLLIFDEVHHLP 205

>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 = 44.1 bits (104), Expect = 9e-06
 Identities = 25/118 (21%), Positives = 40/118 (33%), Gaps = 15/118 (12%)

Query: 50  AKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIIT 109
              G+GKT  F   IL +          LVL PTR +  ++ + F        L V   T
Sbjct: 15  FHPGAGKTRRFLPQILAECARRRLRT--LVLAPTRVVLSEMKEAFH------GLDVKFHT 66

Query: 110 GGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSL 167
                   G+E+     I       L   +       +   + +++DEA  L   +  
Sbjct: 67  QAFSAHGSGREV-----IDAMCHATLTYRMLEPT--RVVNWEVIIMDEAHFLDPASIA 117

>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 Length = 237

 Score = 42.7 bits (101), Expect = 2e-05
 Identities = 31/154 (20%), Positives = 53/154 (34%), Gaps = 30/154 (19%)

Query: 8   FTDLKLNPWLIRQCQTIGVKTPTEI---QKAIIPHVLNDEDCIGCAKTGSGKTLAFALPI 64
           F D   +P                +   Q+  +   L D+       TGSGKT   A+  
Sbjct: 75  FVDNAADPIPT-----PYFDAEISLRDYQEKALERWLVDKRGCIVLPTGSGKTH-VAMAA 128

Query: 65  LQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKK 124
           + +          L++ PT  LA Q  ++  + G+     V   +G +      KEL   
Sbjct: 129 INE-----LSTPTLIVVPTLALAEQWKERLGIFGEEY---VGEFSGRI------KELKP- 173

Query: 125 PHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEA 158
             + ++T      + +       NR   L+ DE 
Sbjct: 174 --LTVSTYDSAYVNAEK----LGNRFMLLIFDEV 201

>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 Length = 451

 Score = 41.8 bits (98), Expect = 6e-05
 Identities = 24/135 (17%), Positives = 43/135 (31%), Gaps = 24/135 (17%)

Query: 29  PTEIQKAIIPHVLND-EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFA--LVLTPTRE 85
             E    +   +       I     G+GKT      IL     +        L+L PTR 
Sbjct: 4   MGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKR----ILPSIVREALLRRLRTLILAPTRV 59

Query: 86  LAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHL--DTCN 143
           +A ++ +       +  L +   T  +     G+E+     + +         L   T  
Sbjct: 60  VAAEMEEA------LRGLPIRYQTPAVKSDHTGREI-----VDLMCHATFTTRLLSSTR- 107

Query: 144 TFSLNRIKFLVLDEA 158
              +     +V+DEA
Sbjct: 108 ---VPNYNLIVMDEA 119

>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* Length = 1054

 Score = 41.6 bits (98), Expect = 7e-05
 Identities = 37/152 (24%), Positives = 56/152 (36%), Gaps = 22/152 (14%)

Query: 26  VKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKT---LAFALPILQKWCEDPYGIFALVLTP 82
           V  P  IQK     +L  E     A TG GKT   LA +L +  K      G    V+ P
Sbjct: 54  VGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALK------GKRCYVIFP 107

Query: 83  TRELAYQIGDQFLVLGKVMNLRVSIITGGMD--MVDQGKELAKKP----HIVIATPGRLA 136
           T  L  Q  +      +   +    + G     +  + KE   +      IVI T   L+
Sbjct: 108 TSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLS 167

Query: 137 DHLDTCNTFSLNRIKFLVLDEADRLSLMTSLK 168
            H        L    F+ +D+ D  +++ + K
Sbjct: 168 KHYR-----ELGHFDFIFVDDVD--AILKASK 192

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A* Length = 620

 Score = 40.8 bits (96), Expect = 1e-04
 Identities = 17/80 (21%), Positives = 26/80 (32%), Gaps = 2/80 (2%)

Query: 31  EIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQI 90
           E    +   +         + TGSGKT+      LQ   E    +    L  T     Q+
Sbjct: 10  EAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSERKLKVL--YLVRTNSQEEQV 67

Query: 91  GDQFLVLGKVMNLRVSIITG 110
             +   L   M +R   + G
Sbjct: 68  IKELRSLSSTMKIRAIPMQG 87

>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} Length = 1108

 Score = 39.1 bits (90), Expect = 5e-04
 Identities = 25/127 (19%), Positives = 46/127 (36%), Gaps = 19/127 (14%)

Query: 33  QKAIIPHVLNDEDCIGCAKTGSGKTLA--FALPILQKWCEDPYGIFALVLTPTRELAYQI 90
           Q   I  +   E  +  A T +GKT+   +A  I Q        I+    +P + L+ Q 
Sbjct: 189 QDTAISCIDRGESVLVSAHTSAGKTVVAEYA--IAQSLKNKQRVIY---TSPIKALSNQK 243

Query: 91  GDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRI 150
             + L         V ++TG  D+             ++ T   L   L    +  +  +
Sbjct: 244 YRELLAEFG----DVGLMTG--DITINPDA-----GCLVMTTEILRSMLYR-GSEVMREV 291

Query: 151 KFLVLDE 157
            +++ DE
Sbjct: 292 AWVIFDE 298

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae} Length = 1010

 Score = 38.6 bits (89), Expect = 7e-04
 Identities = 25/127 (19%), Positives = 46/127 (36%), Gaps = 19/127 (14%)

Query: 33  QKAIIPHVLNDEDCIGCAKTGSGKTLA--FALPILQKWCEDPYGIFALVLTPTRELAYQI 90
           Q   I  +   E  +  A T +GKT+   +A  I Q        I+    +P + L+ Q 
Sbjct: 91  QDTAISCIDRGESVLVSAHTSAGKTVVAEYA--IAQSLKNKQRVIY---TSPIKALSNQK 145

Query: 91  GDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRI 150
             + L         V ++TG  D+             ++ T   L   L    +  +  +
Sbjct: 146 YRELLAEFG----DVGLMTG--DITINPDA-----GCLVMTTEILRSMLYR-GSEVMREV 193

Query: 151 KFLVLDE 157
            +++ DE
Sbjct: 194 AWVIFDE 200

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	182
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	100.0
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	100.0
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	100.0
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	100.0
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	100.0
3bor_A	237	Human initiation factor 4A-II; translation initiat	100.0
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	100.0
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	100.0
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	100.0
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	100.0
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	100.0
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	100.0
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	100.0
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	100.0
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	100.0
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	100.0
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.98
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.97
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.97
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.97
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.97
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.97
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.96
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.96
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.96
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.96
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.95
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.95
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.94
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.94
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.93
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.93
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.93
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.93
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.93
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.93
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.93
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.93
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.92
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.92
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.91
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.91
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.9
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.9
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.89
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.88
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.88
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.88
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.88
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.87
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.87
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.87
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.85
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.85
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.85
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.85
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.83
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.83
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.82
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.82
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.82
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.75
3h1t_A	590	Type I site-specific restriction-modification syst	99.73
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.73
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.72
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.71
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.71
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.7
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.67
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.66
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.65
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.63
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.63
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.62
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.58
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.57
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.57
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.51
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.35
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.18
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	99.0
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	98.94
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	98.86
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	98.77
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	98.75
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	98.66
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	98.63
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	97.98
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	97.88
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	97.79
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	97.79
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	97.69
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	97.6
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	97.43
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	97.32
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	97.31
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	97.24
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	97.19
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	97.18
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	97.14
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	97.08
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	96.97
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	96.94
2chg_A	226	Replication factor C small subunit; DNA-binding pr	96.93
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	96.89
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	96.85
3bos_A	242	Putative DNA replication factor; P-loop containing	96.79
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	96.73
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	96.72
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	96.66
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	96.62
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	96.61
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	96.53
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	96.51
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	96.45
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	96.32
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	96.3
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	96.28
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	96.27
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	96.18
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	96.17
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	96.16
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	96.14
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	96.09
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	96.08
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	95.94
2r6a_A	454	DNAB helicase, replicative helicase; replication,	95.93
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	95.88
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	95.87
3pvs_A	447	Replication-associated recombination protein A; ma	95.87
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	95.85
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	95.8
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	95.75
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	95.74
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	95.71
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	95.71
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	95.51
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	95.49
2fna_A	357	Conserved hypothetical protein; structural genomic	95.47
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	95.43
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	95.32
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	95.27
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	95.25
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	95.1
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	95.01
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	94.91
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	94.85
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	94.83
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	94.75
3co5_A	143	Putative two-component system transcriptional RES	94.71
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	94.69
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	94.68
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	94.45
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	94.37
2eyu_A	261	Twitching motility protein PILT; pilus retraction	94.3
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	94.25
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	94.24
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	94.16
1w36_B	1180	RECB, exodeoxyribonuclease V beta chain; recombina	94.05
2qgz_A	308	Helicase loader, putative primosome component; str	93.93
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	93.81
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	93.73
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	93.68
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	93.65
1p9r_A	418	General secretion pathway protein E; bacterial typ	93.58
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	93.57
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	93.55
3u4q_B	1166	ATP-dependent helicase/deoxyribonuclease subunit;	93.4
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	93.34
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	93.3
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	93.24
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	93.21
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	93.21
1yks_A	440	Genome polyprotein [contains: flavivirin protease	93.14
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	93.11
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	93.09
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	92.97
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	92.93
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	92.92
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	92.91
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	92.9
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	92.85
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	92.84
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	92.61
2r44_A	331	Uncharacterized protein; putative ATPase, structur	92.6
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	92.59
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	92.5
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	92.44
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	92.39
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	92.36
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	92.28
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	92.26
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	92.21
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	92.19
1tue_A	212	Replication protein E1; helicase, replication, E1E	92.18
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	92.12
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	91.33
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	92.0
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	91.95
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	91.8
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	91.73
2cvh_A	220	DNA repair and recombination protein RADB; filamen	91.71
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	91.69
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	91.68
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	91.67
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	91.67
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	91.64
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	91.56
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	91.51
2z43_A	324	DNA repair and recombination protein RADA; archaea	91.51
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	91.44
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	91.43
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	91.43
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	91.4
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	91.39
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	91.34
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	91.29
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	91.27
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	91.23
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	91.17
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	91.11
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	91.05
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	91.04
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	91.01
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	91.0
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	90.99
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	90.97
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	90.96
1u94_A	356	RECA protein, recombinase A; homologous recombinat	90.96
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	90.91
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	90.9
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	90.87
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	90.82
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	90.73
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	90.72
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	90.65
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	90.64
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	90.63
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	90.6
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	90.58
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	90.48
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	90.48
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	90.46
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	90.39
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	90.27
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	90.25
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	90.18
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	90.13
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	90.1
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	90.09
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	90.08
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	89.9
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	89.9
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	89.81
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	89.76
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	89.73
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	89.71
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	89.65
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	89.43
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	89.41
2ewv_A	372	Twitching motility protein PILT; pilus retraction	89.41
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	89.39
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	89.23
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	89.18
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	89.12
1xp8_A	366	RECA protein, recombinase A; recombination, radior	89.06
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	89.03
4dzz_A	206	Plasmid partitioning protein PARF; deviant walker	89.01
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	88.99
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	88.99
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	88.95
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	88.9
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	88.86
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	88.82
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	88.77
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	88.74
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	88.72
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	88.64
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	88.63
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	88.55
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	88.5
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	88.48
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	88.46
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	88.4
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	88.39
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	88.26
3io5_A	333	Recombination and repair protein; storage dimer, i	88.19
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	88.16
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	88.12
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	88.11
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	88.06
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	88.01
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	87.88
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	87.6
1via_A	175	Shikimate kinase; structural genomics, transferase	87.54
2chq_A	319	Replication factor C small subunit; DNA-binding pr	87.54
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	87.54
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	87.43
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	87.42
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	87.41
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	87.33
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	87.29
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	87.23
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	87.15
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	87.14
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	87.1
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	87.07
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	87.06
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	87.04
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	87.01
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	86.92
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	86.92
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	86.91
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	86.88
4anj_A	1052	Unconventional myosin-VI, green fluorescent prote;	86.87
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	86.81
4a74_A	231	DNA repair and recombination protein RADA; hydrola	86.72
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	86.67
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	86.33
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	86.22
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	86.12
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	86.12
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	86.11
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	86.09
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	86.08
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	86.04
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	85.95
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	85.93
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	85.85
3kta_A	182	Chromosome segregation protein SMC; structural mai	85.81
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	85.71
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	85.71
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	85.57
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	85.53
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	85.5
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	85.37
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	85.33
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	85.33
4gl2_A	699	Interferon-induced helicase C domain-containing P;	85.32
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	85.27
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	85.24
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	85.16
2og2_A	359	Putative signal recognition particle receptor; nuc	85.15
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	85.11
3nwn_A	359	Kinesin-like protein KIF9; motor domain, ADP, stru	85.09
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	85.02
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	84.99
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	84.92
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	84.91
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	84.88
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	84.83
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	84.77
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	84.7
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	84.69
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	84.67
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	84.66
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	84.52
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	84.41
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	84.27
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	84.26
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	84.15
1bg2_A	325	Kinesin; motor protein, ATPase, microtubule associ	84.05
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	84.04
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	83.99
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	83.97
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	83.95
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	83.87
4db1_A	783	Myosin-7; S1DC, cardiac, beta isoform, MYH7, myhcb	83.79
1f9v_A	347	Kinesin-like protein KAR3; kinesin-related protein	83.72
3bs4_A	260	Uncharacterized protein PH0321; structural genomic	83.7
1g8x_A	1010	Myosin II heavy chain fused to alpha-actinin 3; mo	83.64
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	83.58
3dc4_A	344	Kinesin-like protein NOD; catalytic domain, ATPase	83.56
1lkx_A	697	Myosin IE heavy chain; myosin motor domain, lever	83.55
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	83.53
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	83.51
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	83.46
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	83.45
2vli_A	183	Antibiotic resistance protein; transferase, tunica	83.42
3t0q_A	349	AGR253WP; kinesin, alpha and beta proteins, P-loop	83.39
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	83.39
1w7j_A	795	Myosin VA; motor protein, unconventional myosin, m	83.31
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	83.28
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	83.26
1w9i_A	770	Myosin II heavy chain; molecular motor, ATPase, mo	83.19
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	83.17
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	83.16
2vvg_A	350	Kinesin-2; motor protein, nucleotide-binding, micr	83.13
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	83.09
3lre_A	355	Kinesin-like protein KIF18A; motor protein, nucleo	83.06
2zfi_A	366	Kinesin-like protein KIF1A, kinesin heavy chain is	82.91
2y65_A	365	Kinesin, kinesin heavy chain; motor protein; HET:	82.9
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	82.88
3qf7_A	365	RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.	82.86
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	82.82
2h58_A	330	Kinesin-like protein KIFC3 variant; motor domain,	82.76
4a14_A	344	Kinesin, kinesin-like protein KIF7; motor protein,	82.72
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	82.66
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	82.62
1v8k_A	410	Kinesin-like protein KIF2C; microtubule destabiliz	82.6
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	82.58
1goj_A	355	Kinesin, kinesin heavy chain; motor protein, ATPas	82.51
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	82.51
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	82.48
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	82.39
3b6u_A	372	Kinesin-like protein KIF3B; structural genomics co	82.3
3qks_A	203	DNA double-strand break repair RAD50 ATPase; RECA-	82.3
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	82.28
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	82.18
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	82.17
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	82.17
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	82.17
3gbj_A	354	KIF13B protein; kinesin, motor domain, ADP, struct	82.1
1sgw_A	214	Putative ABC transporter; structural genomics, P p	82.05
2nr8_A	358	Kinesin-like protein KIF9; motor domain, ADP, stru	81.89
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	81.72
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	81.7
2heh_A	387	KIF2C protein; kinesin, motor domain, ADP, structu	81.65
1x88_A	359	Kinesin-like protein KIF11; switch II, motor domai	81.63
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	81.63
1t5c_A	349	CENP-E protein, centromeric protein E; kinesin mot	81.62
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	81.6
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	81.58
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	81.55
1kk8_A	837	Myosin heavy chain, striated muscle; actin-detache	81.55
3auy_A	371	DNA double-strand break repair RAD50 ATPase; DNA r	81.46
1ry6_A	360	Internal kinesin; kinesin motor domain, nucleotide	81.46
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	81.45
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	81.44
2owm_A	443	Nckin3-434, related to kinesin-like protein KIF1C;	81.39
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	81.38
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	81.37
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	81.34
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	81.32
2ycu_A	995	Non muscle myosin 2C, alpha-actinin; motor protein	81.29
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	81.29
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	81.28
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	81.26
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	81.24
3u06_A	412	Protein claret segregational; motor domain, stalk	81.23
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	81.21
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	81.1
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	81.08
1g6h_A	257	High-affinity branched-chain amino acid transport	81.07
1ji0_A	240	ABC transporter; ATP binding protein, structural g	81.02
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	81.01
1b0u_A	262	Histidine permease; ABC transporter, transport pro	80.97
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	80.8
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	80.79
2wbe_C	373	Bipolar kinesin KRP-130; EG5, KLP61F, tubulin, mit	80.73
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	80.72
2ghi_A	260	Transport protein; multidrug resistance protein, M	80.63
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	80.6
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	80.48
3bfn_A	388	Kinesin-like protein KIF22; limited proteolysis, s	80.33
3cob_A	369	Kinesin heavy chain-like protein; motor, switch II	80.31
2rep_A	376	Kinesin-like protein KIFC1; structural genomics co	80.29
2v26_A	784	Myosin VI; calmodulin-binding, nucleotide-binding,	80.27
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	80.21
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	80.2
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	80.18
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	80.01

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=100.00  E-value=1.4e-34  Score=214.90  Aligned_cols=172  Identities=34%  Similarity=0.439  Sum_probs=154.6

Q ss_pred             CCCccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccC-----CCCe
Q psy4275           1 MEDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCED-----PYGI   75 (182)
Q Consensus         1 ~~~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~-----~~~~   75 (182)
                      .|+++.+|+++++++.+.+.+.+.|+..|+++|.++++.+.+|+++++++|||+|||.+++++++..+...     ..++
T Consensus        24 ~p~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~~~l~~l~~l~~~~~~~~~~~~  103 (242)
T 3fe2_A           24 CPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGP  103 (242)
T ss_dssp             CCCCCSSTTTTTCCHHHHHHHHTTTCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHHHHHHHHHHHHHTSCCCCTTCCC
T ss_pred             CCCccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHHHHHHHHHHHHHhccccccCCCC
Confidence            37889999999999999999999999999999999999999999999999999999999999999887643     2467


Q ss_pred             eEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEE
Q psy4275          76 FALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVL  155 (182)
Q Consensus        76 ~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~  155 (182)
                      +++|++|+++|+.|+++.++.+.+..++++..++|+.........+.++++|+|+||+++.+++.. ....+++++++|+
T Consensus       104 ~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~-~~~~~~~~~~lVi  182 (242)
T 3fe2_A          104 ICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLEC-GKTNLRRTTYLVL  182 (242)
T ss_dssp             SEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHH-TSCCCTTCCEEEE
T ss_pred             EEEEEeCcHHHHHHHHHHHHHHHhhcCceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHc-CCCCcccccEEEE
Confidence            899999999999999999999999999999999999988777777777899999999999999987 5567889999999


Q ss_pred             eccccccccCChhHHHHH
Q psy4275         156 DEADRLSLMTSLKFFFFF  173 (182)
Q Consensus       156 DE~h~~~~~~~~~~~~~~  173 (182)
                      ||||++.++++......+
T Consensus       183 DEah~l~~~~~~~~~~~i  200 (242)
T 3fe2_A          183 DEADRMLDMGFEPQIRKI  200 (242)
T ss_dssp             TTHHHHHHTTCHHHHHHH
T ss_pred             eCHHHHhhhCcHHHHHHH
Confidence            999999998866554433

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=100.00  E-value=6.2e-34  Score=212.37  Aligned_cols=170  Identities=49%  Similarity=0.749  Sum_probs=153.3

Q ss_pred             ccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275           4 PIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus         4 ~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      +..+|+++++++.+.+.+...|+..++++|.++++.+.+++++++++|||+|||.+++++++..+.....+.+++|++|+
T Consensus        41 ~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~il~~l~~~~~~~~~lil~Pt  120 (249)
T 3ber_A           41 ETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETPQRLFALVLTPT  120 (249)
T ss_dssp             HHCCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHSCCSSCEEEECSS
T ss_pred             ccCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHhHHHHHHHHhcCCCCceEEEEeCC
Confidence            46789999999999999999999999999999999999999999999999999999999999988777667789999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275          84 RELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus        84 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      ++|+.|+++.++++....++++..+.|+.........+.++++|+|+||+++.+.+...+.+.+++++++|+||||++.+
T Consensus       121 r~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~l~~~~~lViDEah~l~~  200 (249)
T 3ber_A          121 RELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRILN  200 (249)
T ss_dssp             HHHHHHHHHHHHHHHGGGTCCEEEECTTSCHHHHHHHHHTCCSEEEECHHHHHHHHHHSTTCCCTTCCEEEECSHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccCCeeEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCcCccccCEEEEcChhhhhc
Confidence            99999999999999998899999999998877766677788999999999999998875666788999999999999999


Q ss_pred             cCChhHHHHH
Q psy4275         164 MTSLKFFFFF  173 (182)
Q Consensus       164 ~~~~~~~~~~  173 (182)
                      +++...+..+
T Consensus       201 ~~~~~~l~~i  210 (249)
T 3ber_A          201 MDFETEVDKI  210 (249)
T ss_dssp             TTCHHHHHHH
T ss_pred             cChHHHHHHH
Confidence            8776554443

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=100.00  E-value=2.4e-33  Score=203.22  Aligned_cols=167  Identities=32%  Similarity=0.491  Sum_probs=148.9

Q ss_pred             CCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHH
Q psy4275           6 KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRE   85 (182)
Q Consensus         6 ~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~   85 (182)
                      .+|+++++++++.+.+.+.|+..|+|+|.++++.+.+++++++++|||+|||.+++++++..+.....+.+++|++|+++
T Consensus         3 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~   82 (206)
T 1vec_A            3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRE   82 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHH
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEECCCCCchHHHHHHHHHHHhcccCCCeeEEEEeCcHH
Confidence            57999999999999999999999999999999999999999999999999999999999998776666779999999999


Q ss_pred             HHHHHHHHHHHhhccC-CceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccccc
Q psy4275          86 LAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus        86 l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~  164 (182)
                      |+.|+++.++.+.+.. +.++..+.|+.........+.++++|+|+||+.+.+.+.. +...+++++++|+||||++.+.
T Consensus        83 L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~-~~~~~~~~~~lViDEah~~~~~  161 (206)
T 1vec_A           83 LALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKK-GVAKVDHVQMIVLDEADKLLSQ  161 (206)
T ss_dssp             HHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHT-TCSCCTTCCEEEEETHHHHTST
T ss_pred             HHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHhcCCCCCEEEeCHHHHHHHHHc-CCcCcccCCEEEEEChHHhHhh
Confidence            9999999999998877 7889999998887766666777899999999999999877 5567888999999999999987


Q ss_pred             CChhHHHHH
Q psy4275         165 TSLKFFFFF  173 (182)
Q Consensus       165 ~~~~~~~~~  173 (182)
                      ++...+..+
T Consensus       162 ~~~~~l~~i  170 (206)
T 1vec_A          162 DFVQIMEDI  170 (206)
T ss_dssp             TTHHHHHHH
T ss_pred             CcHHHHHHH
Confidence            765544443

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=100.00  E-value=1.3e-33  Score=206.74  Aligned_cols=169  Identities=34%  Similarity=0.513  Sum_probs=147.5

Q ss_pred             ccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275           4 PIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus         4 ~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      +..+|+++++++.+.+.+.+.|+..++++|.++++.+.+++++++++|||+|||.+++++++..+.....+.+++|++|+
T Consensus         2 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt   81 (219)
T 1q0u_A            2 AETQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPT   81 (219)
T ss_dssp             --CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSS
T ss_pred             CCCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhCcCCceEEEEcCc
Confidence            34789999999999999999999999999999999999999999999999999999999999988776667799999999


Q ss_pred             HHHHHHHHHHHHHhhccC----CceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccc
Q psy4275          84 RELAYQIGDQFLVLGKVM----NLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEAD  159 (182)
Q Consensus        84 ~~l~~q~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h  159 (182)
                      ++|+.|+++.++++....    ++++..+.|+.........+.++++|+|+||+.+.+.++. +...+++++++|+||||
T Consensus        82 ~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~-~~~~~~~~~~lViDEah  160 (219)
T 1q0u_A           82 RELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIRE-QALDVHTAHILVVDEAD  160 (219)
T ss_dssp             HHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHT-TCCCGGGCCEEEECSHH
T ss_pred             HHHHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHHHHHcCCCCCEEEeCHHHHHHHHHc-CCCCcCcceEEEEcCch
Confidence            999999999999988776    6888888888876655555556889999999999999877 55677889999999999


Q ss_pred             cccccCChhHHHHH
Q psy4275         160 RLSLMTSLKFFFFF  173 (182)
Q Consensus       160 ~~~~~~~~~~~~~~  173 (182)
                      ++.++++......+
T Consensus       161 ~~~~~~~~~~l~~i  174 (219)
T 1q0u_A          161 LMLDMGFITDVDQI  174 (219)
T ss_dssp             HHHHTTCHHHHHHH
T ss_pred             HHhhhChHHHHHHH
Confidence            99988876544433

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=100.00  E-value=3.7e-33  Score=204.74  Aligned_cols=170  Identities=31%  Similarity=0.511  Sum_probs=144.2

Q ss_pred             CCccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275           2 EDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus         2 ~~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      ++++.+|+++++++.+.+.+.+.|+..++++|.++++.+.+++++++++|||+|||.+++++++..+.....+.+++|++
T Consensus        10 ~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~~~~~~~lil~   89 (224)
T 1qde_A           10 DKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLA   89 (224)
T ss_dssp             CCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEEC
T ss_pred             CcccCChhhcCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhccCCCceEEEEE
Confidence            67788999999999999999999999999999999999999999999999999999999999999887766677999999


Q ss_pred             CCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccc
Q psy4275          82 PTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL  161 (182)
Q Consensus        82 p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~  161 (182)
                      |+++|+.|+++.++.+....+.++..+.|+.........+ .+++|+|+||+.+.+.+.. +...+++++++|+||||++
T Consensus        90 Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~iiv~Tp~~l~~~~~~-~~~~~~~~~~iViDEah~~  167 (224)
T 1qde_A           90 PTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGL-RDAQIVVGTPGRVFDNIQR-RRFRTDKIKMFILDEADEM  167 (224)
T ss_dssp             SSHHHHHHHHHHHHHHTTTSCCCEEEECC----------C-TTCSEEEECHHHHHHHHHT-TSSCCTTCCEEEEETHHHH
T ss_pred             CCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHhcC-CCCCEEEECHHHHHHHHHh-CCcchhhCcEEEEcChhHH
Confidence            9999999999999999888899999998887655444443 3489999999999999877 5567888999999999999


Q ss_pred             cccCChhHHHHH
Q psy4275         162 SLMTSLKFFFFF  173 (182)
Q Consensus       162 ~~~~~~~~~~~~  173 (182)
                      .++++...+..+
T Consensus       168 ~~~~~~~~l~~i  179 (224)
T 1qde_A          168 LSSGFKEQIYQI  179 (224)
T ss_dssp             HHTTCHHHHHHH
T ss_pred             hhhhhHHHHHHH
Confidence            998876644443

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=100.00  E-value=2.5e-33  Score=207.63  Aligned_cols=171  Identities=35%  Similarity=0.504  Sum_probs=141.8

Q ss_pred             CCccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275           2 EDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus         2 ~~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      |+++.+|+++++++.+.+.+...|+..|+++|.++++.+.+++++++++|||+|||.+++++++..+.....+.+++|++
T Consensus        26 ~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~  105 (237)
T 3bor_A           26 NEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLA  105 (237)
T ss_dssp             -CCCCSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCTTSCSCCEEEEC
T ss_pred             CCccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEE
Confidence            56788999999999999999999999999999999999999999999999999999999999999887655577999999


Q ss_pred             CCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCC-CcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccc
Q psy4275          82 PTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKK-PHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR  160 (182)
Q Consensus        82 p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~  160 (182)
                      |+++|+.|+++.++.+....+.++..+.|+.........+..+ ++|+|+||+.+.+.+.. +...+++++++|+||||+
T Consensus       106 Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~Ilv~Tp~~l~~~l~~-~~~~~~~~~~lViDEah~  184 (237)
T 3bor_A          106 PTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNR-RYLSPKWIKMFVLDEADE  184 (237)
T ss_dssp             SSHHHHHHHHHHHHHHTTTTTCCEEEECC-------------CCCSEEEECHHHHHHHHHT-TSSCSTTCCEEEEESHHH
T ss_pred             CcHHHHHHHHHHHHHHhhhcCceEEEEECCCchHHHHHHHhcCCCCEEEECHHHHHHHHHh-CCcCcccCcEEEECCchH
Confidence            9999999999999999888888998888887655544444444 89999999999999877 556788899999999999


Q ss_pred             ccccCChhHHHHH
Q psy4275         161 LSLMTSLKFFFFF  173 (182)
Q Consensus       161 ~~~~~~~~~~~~~  173 (182)
                      +.++++...+..+
T Consensus       185 ~~~~~~~~~l~~i  197 (237)
T 3bor_A          185 MLSRGFKDQIYEI  197 (237)
T ss_dssp             HHHTTCHHHHHHH
T ss_pred             hhccCcHHHHHHH
Confidence            9988876544433

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=100.00  E-value=6.7e-33  Score=204.41  Aligned_cols=168  Identities=28%  Similarity=0.395  Sum_probs=144.7

Q ss_pred             CCccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275           2 EDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus         2 ~~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      |.+..+|+++++++.+.+.+.+.|+..++++|.++++.+.+++++++++|||+|||.+++++++..+.....+.+++|++
T Consensus        20 ~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~lil~   99 (230)
T 2oxc_A           20 LAEPADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILILA   99 (230)
T ss_dssp             ----CCGGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEEC
T ss_pred             CCCCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEe
Confidence            45678899999999999999999999999999999999999999999999999999999999999887665577999999


Q ss_pred             CCHHHHHHHHHHHHHhhccC-CceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccc
Q psy4275          82 PTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR  160 (182)
Q Consensus        82 p~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~  160 (182)
                      |+++|+.|+++.++.+.... ++++..+.|+.....+...+ ++++|+|+||+.+.++++. +.+.+++++++|+||||+
T Consensus       100 Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~Iiv~Tp~~l~~~~~~-~~~~~~~~~~lViDEah~  177 (230)
T 2oxc_A          100 PTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRL-KKCHIAVGSPGRIKQLIEL-DYLNPGSIRLFILDEADK  177 (230)
T ss_dssp             SSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHT-TSCSEEEECHHHHHHHHHT-TSSCGGGCCEEEESSHHH
T ss_pred             CCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhc-cCCCEEEECHHHHHHHHhc-CCcccccCCEEEeCCchH
Confidence            99999999999999988765 78999999988765554443 5789999999999999876 556678899999999999


Q ss_pred             ccccC-ChhHHH
Q psy4275         161 LSLMT-SLKFFF  171 (182)
Q Consensus       161 ~~~~~-~~~~~~  171 (182)
                      +.+++ +.....
T Consensus       178 ~~~~~~~~~~~~  189 (230)
T 2oxc_A          178 LLEEGSFQEQIN  189 (230)
T ss_dssp             HHSTTSSHHHHH
T ss_pred             hhcCcchHHHHH
Confidence            99886 554443

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=100.00  E-value=2.9e-33  Score=205.92  Aligned_cols=171  Identities=34%  Similarity=0.456  Sum_probs=144.6

Q ss_pred             CCCccCCccC-CCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccC------CC
Q psy4275           1 MEDPIKSFTD-LKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCED------PY   73 (182)
Q Consensus         1 ~~~~~~~~~~-~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~------~~   73 (182)
                      +|++..+|++ +++++++.+.+.+.|+..|+++|.++++.+.+++++++++|||+|||.+++++++..+...      ..
T Consensus        14 ~p~p~~~f~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~~~~~   93 (228)
T 3iuy_A           14 IPKPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRN   93 (228)
T ss_dssp             CCCCCCSHHHHHTTCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC---------C
T ss_pred             CCCChhhHhhhhccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccchhhccC
Confidence            4889999999 7999999999999999999999999999999999999999999999999999998876542      24


Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEE
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFL  153 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~i  153 (182)
                      +++++|++|+++|+.|+++.++.+. ..+.++..+.|+.........+.++++|+|+||+++.+++.. ....+++++++
T Consensus        94 ~~~~lil~Pt~~L~~q~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~Tp~~l~~~~~~-~~~~~~~~~~l  171 (228)
T 3iuy_A           94 GPGMLVLTPTRELALHVEAECSKYS-YKGLKSICIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMN-NSVNLRSITYL  171 (228)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHC-CTTCCEEEECC------CHHHHHSCCSEEEECHHHHHHHHHT-TCCCCTTCCEE
T ss_pred             CCcEEEEeCCHHHHHHHHHHHHHhc-ccCceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHc-CCcCcccceEE
Confidence            6789999999999999999999986 447888888888877766677778899999999999998877 55678899999


Q ss_pred             EEeccccccccCChhHHHHH
Q psy4275         154 VLDEADRLSLMTSLKFFFFF  173 (182)
Q Consensus       154 I~DE~h~~~~~~~~~~~~~~  173 (182)
                      |+||||++.++++......+
T Consensus       172 ViDEah~~~~~~~~~~~~~i  191 (228)
T 3iuy_A          172 VIDEADKMLDMEFEPQIRKI  191 (228)
T ss_dssp             EECCHHHHHHTTCHHHHHHH
T ss_pred             EEECHHHHhccchHHHHHHH
Confidence            99999999998866655444

>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=8.8e-33  Score=221.02  Aligned_cols=173  Identities=39%  Similarity=0.556  Sum_probs=155.4

Q ss_pred             CCccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCC-----CCee
Q psy4275           2 EDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP-----YGIF   76 (182)
Q Consensus         2 ~~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~-----~~~~   76 (182)
                      |+++.+|+++++++.+.+.+.+.|+..|+|+|.++++.+.+++++++++|||+|||.+++++++..+...+     .+++
T Consensus        52 p~~~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~~~~~~~~~~~  131 (434)
T 2db3_A           52 PQPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQ  131 (434)
T ss_dssp             CCCCCCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCCCCCTTCCS
T ss_pred             CCCcCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHhcccccccCCcc
Confidence            67899999999999999999999999999999999999999999999999999999999999998876542     3568


Q ss_pred             EEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEe
Q psy4275          77 ALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLD  156 (182)
Q Consensus        77 ~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~D  156 (182)
                      ++|++|+++|+.|+++.++++....++++..++|+.....+...+.++++|+|+||+++.+++.+ ....+++++++|+|
T Consensus       132 ~lil~PtreLa~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Ivv~Tp~~l~~~l~~-~~~~l~~~~~lVlD  210 (434)
T 2db3_A          132 VVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDR-TFITFEDTRFVVLD  210 (434)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTSSCCCCEECTTSCHHHHHHHHTTCCSEEEECHHHHHHHHHT-TSCCCTTCCEEEEE
T ss_pred             EEEEecCHHHHHHHHHHHHHHhccCCcEEEEEECCCCHHHHHHHhhcCCCEEEEChHHHHHHHHh-CCcccccCCeEEEc
Confidence            99999999999999999999998888999999999988777777778999999999999999987 55678899999999


Q ss_pred             ccccccccCChhHHHHHHH
Q psy4275         157 EADRLSLMTSLKFFFFFFF  175 (182)
Q Consensus       157 E~h~~~~~~~~~~~~~~~~  175 (182)
                      |||+|.++++......+..
T Consensus       211 Eah~~~~~gf~~~~~~i~~  229 (434)
T 2db3_A          211 EADRMLDMGFSEDMRRIMT  229 (434)
T ss_dssp             THHHHTSTTTHHHHHHHHH
T ss_pred             cHhhhhccCcHHHHHHHHH
Confidence            9999999987665544433

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19

Probab=100.00  E-value=3.7e-33  Score=208.41  Aligned_cols=172  Identities=37%  Similarity=0.515  Sum_probs=151.9

Q ss_pred             CccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCC---------C
Q psy4275           3 DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP---------Y   73 (182)
Q Consensus         3 ~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~---------~   73 (182)
                      +++.+|+++++++.+.+.+...|+..|+++|.++++.+.+++++++++|||+|||.+++++++..+....         .
T Consensus        20 ~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~~   99 (253)
T 1wrb_A           20 NVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTA   99 (253)
T ss_dssp             SCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCB
T ss_pred             CccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhhccccccccccC
Confidence            3788999999999999999999999999999999999999999999999999999999999998875432         2


Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEE
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFL  153 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~i  153 (182)
                      +++++|++|+++|+.|+++.++.+....++++..+.|+.........+.++++|+|+||+++.+++.. ....+++++++
T Consensus       100 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~-~~~~~~~~~~l  178 (253)
T 1wrb_A          100 YPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEK-NKISLEFCKYI  178 (253)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHT-TSBCCTTCCEE
T ss_pred             CceEEEEECCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhCCCCCEEEECHHHHHHHHHc-CCCChhhCCEE
Confidence            46899999999999999999999988888999999998887777677778899999999999999987 55678889999


Q ss_pred             EEeccccccccCChhHHHHHHH
Q psy4275         154 VLDEADRLSLMTSLKFFFFFFF  175 (182)
Q Consensus       154 I~DE~h~~~~~~~~~~~~~~~~  175 (182)
                      |+||||++.++++......+..
T Consensus       179 ViDEah~~~~~~~~~~~~~i~~  200 (253)
T 1wrb_A          179 VLDEADRMLDMGFEPQIRKIIE  200 (253)
T ss_dssp             EEETHHHHHHTTCHHHHHHHHH
T ss_pred             EEeCHHHHHhCchHHHHHHHHh
Confidence            9999999999887665555443

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=100.00  E-value=1.7e-32  Score=202.78  Aligned_cols=169  Identities=36%  Similarity=0.551  Sum_probs=145.4

Q ss_pred             CCccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccC----CCCeeE
Q psy4275           2 EDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCED----PYGIFA   77 (182)
Q Consensus         2 ~~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~----~~~~~~   77 (182)
                      ++++.+|+++++++.+.+.+.+.|+..|+++|.++++.+.+++++++++|||+|||.+++++++..+...    ..+.++
T Consensus        21 ~~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~  100 (236)
T 2pl3_A           21 VNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGV  100 (236)
T ss_dssp             GGGCSBGGGSCCCHHHHHHHHHTTCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCE
T ss_pred             CcccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHHHHHHHHHHHhhcccccCCceE
Confidence            3567889999999999999999999999999999999999999999999999999999999998876542    235689


Q ss_pred             EEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEec
Q psy4275          78 LVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDE  157 (182)
Q Consensus        78 lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE  157 (182)
                      +|++|+++|+.|+++.++.+....++++..+.|+.........+ ++++|+|+||+.+.+.+.....+.+++++++|+||
T Consensus       101 lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~iiv~Tp~~l~~~l~~~~~~~~~~~~~lViDE  179 (236)
T 2pl3_A          101 LIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERI-NNINILVCTPGRLLQHMDETVSFHATDLQMLVLDE  179 (236)
T ss_dssp             EEECSSHHHHHHHHHHHHHHTTTSSCCEEEECCC--CHHHHHHH-TTCSEEEECHHHHHHHHHHCSSCCCTTCCEEEETT
T ss_pred             EEEeCCHHHHHHHHHHHHHHhCCCCeeEEEEECCCCHHHHHHhC-CCCCEEEECHHHHHHHHHhcCCcccccccEEEEeC
Confidence            99999999999999999999988889999999887765544443 57899999999999998775556788899999999


Q ss_pred             cccccccCChhHHH
Q psy4275         158 ADRLSLMTSLKFFF  171 (182)
Q Consensus       158 ~h~~~~~~~~~~~~  171 (182)
                      ||++.++++...+.
T Consensus       180 ah~~~~~~~~~~~~  193 (236)
T 2pl3_A          180 ADRILDMGFADTMN  193 (236)
T ss_dssp             HHHHHHTTTHHHHH
T ss_pred             hHHHhcCCcHHHHH
Confidence            99999888665443

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=100.00  E-value=5.6e-32  Score=197.98  Aligned_cols=160  Identities=34%  Similarity=0.547  Sum_probs=140.3

Q ss_pred             ccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275           4 PIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus         4 ~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      ...+|+++++++.+.+.+...|+..|+++|.++++.+.+++++++++|||+|||.+++++++..+.....+.+++|++|+
T Consensus        12 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt   91 (220)
T 1t6n_A           12 HSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHT   91 (220)
T ss_dssp             --CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSC
T ss_pred             cCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhccCCCEEEEEEeCC
Confidence            34679999999999999999999999999999999999999999999999999999999999987765556689999999


Q ss_pred             HHHHHHHHHHHHHhhccC-CceEEEEEcCCchhhhhHHhc-CCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccc
Q psy4275          84 RELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGKELA-KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL  161 (182)
Q Consensus        84 ~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~-~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~  161 (182)
                      ++|+.|+++.++++.+.. +.++..+.|+.........+. +.++|+|+||+.+.+.++. ....+++++++|+||||++
T Consensus        92 ~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~-~~~~~~~~~~lViDEah~~  170 (220)
T 1t6n_A           92 RELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARN-KSLNLKHIKHFILDECDKM  170 (220)
T ss_dssp             HHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHT-TSSCCTTCCEEEEESHHHH
T ss_pred             HHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHHHhcCCCCEEEeCHHHHHHHHHh-CCCCcccCCEEEEcCHHHH
Confidence            999999999999998776 789999999887655555444 3579999999999999887 5567889999999999999


Q ss_pred             ccc
Q psy4275         162 SLM  164 (182)
Q Consensus       162 ~~~  164 (182)
                      .++
T Consensus       171 ~~~  173 (220)
T 1t6n_A          171 LEQ  173 (220)
T ss_dssp             HSS
T ss_pred             hcc
Confidence            874

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=100.00  E-value=2.7e-32  Score=208.54  Aligned_cols=173  Identities=29%  Similarity=0.443  Sum_probs=146.7

Q ss_pred             ccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCC--CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275           4 PIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLND--EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus         4 ~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~--~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      ...+|+++++++.+.+.+...|+..|+++|.++++.+..+  +++++++|||+|||.+|+++++..+.....+++++|++
T Consensus        90 ~~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~~~~~~~lil~  169 (300)
T 3fmo_B           90 SVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLS  169 (300)
T ss_dssp             CCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEEC
T ss_pred             CcCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhhhccCCCceEEEEc
Confidence            4678999999999999999999999999999999999987  89999999999999999999999988776677999999


Q ss_pred             CCHHHHHHHHHHHHHhhccC-CceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccc
Q psy4275          82 PTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR  160 (182)
Q Consensus        82 p~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~  160 (182)
                      |+++|+.|+++.++.+.+.. ++++....|+......   ...+++|+|+||+++.+++.+.+.+.+++++++|+||||+
T Consensus       170 PtreLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~---~~~~~~IlV~TP~~l~~~l~~~~~~~l~~l~~lVlDEad~  246 (300)
T 3fmo_B          170 PTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADV  246 (300)
T ss_dssp             SSHHHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTT---CCCCCSEEEECHHHHHHHHTTTCCCCGGGCSEEEETTHHH
T ss_pred             CcHHHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhh---hcCCCCEEEECHHHHHHHHHhcCCCChhhceEEEEeCHHH
Confidence            99999999999999998765 6788888877654332   2457899999999999999776677889999999999999


Q ss_pred             ccccCChhHHHHHHHHhhcCC
Q psy4275         161 LSLMTSLKFFFFFFFLKYYIP  181 (182)
Q Consensus       161 ~~~~~~~~~~~~~~~~~~~~~  181 (182)
                      |.+...  +...+..+.+.+|
T Consensus       247 l~~~~~--~~~~~~~i~~~~~  265 (300)
T 3fmo_B          247 MIATQG--HQDQSIRIQRMLP  265 (300)
T ss_dssp             HHHSTT--HHHHHHHHHTTSC
T ss_pred             HhhccC--cHHHHHHHHHhCC
Confidence            997332  3344445555443

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=100.00  E-value=7.3e-32  Score=195.42  Aligned_cols=164  Identities=39%  Similarity=0.548  Sum_probs=143.8

Q ss_pred             CccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccC---CCCeeEEEEcCC
Q psy4275           7 SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCED---PYGIFALVLTPT   83 (182)
Q Consensus         7 ~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~---~~~~~~lil~p~   83 (182)
                      +|+++++++.+.+.+.+.|+..|+|+|.++++.+.+++++++++|||+|||.+++++++..+...   ..+++++|++|+
T Consensus         2 ~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~l~~~~~~~~~~~~lil~P~   81 (207)
T 2gxq_A            2 EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPT   81 (207)
T ss_dssp             CGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCCCTTCCCSEEEECSS
T ss_pred             ChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCcEEEEECC
Confidence            69999999999999999999999999999999999999999999999999999999999887642   236789999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275          84 RELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus        84 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      ++|+.|+++.++.+...  .++..++|+.........+.++++|+|+||+.+.+.+.. +...+++++++|+||||++.+
T Consensus        82 ~~L~~q~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~-~~~~~~~~~~iViDEah~~~~  158 (207)
T 2gxq_A           82 RELALQVASELTAVAPH--LKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQ-GVLDLSRVEVAVLDEADEMLS  158 (207)
T ss_dssp             HHHHHHHHHHHHHHCTT--SCEEEECSSSCSHHHHHHHHHCCSEEEECHHHHHHHHHH-TSSCCTTCSEEEEESHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhc--ceEEEEECCCChHHHHHHhhCCCCEEEECHHHHHHHHHc-CCcchhhceEEEEEChhHhhc
Confidence            99999999999998764  677888888876666666667899999999999999887 566788899999999999998


Q ss_pred             cCChhHHHHH
Q psy4275         164 MTSLKFFFFF  173 (182)
Q Consensus       164 ~~~~~~~~~~  173 (182)
                      +++......+
T Consensus       159 ~~~~~~~~~i  168 (207)
T 2gxq_A          159 MGFEEEVEAL  168 (207)
T ss_dssp             TTCHHHHHHH
T ss_pred             cchHHHHHHH
Confidence            8776655444

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=100.00  E-value=1.6e-32  Score=204.04  Aligned_cols=178  Identities=33%  Similarity=0.492  Sum_probs=148.5

Q ss_pred             CCCccCCccCC----CCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccC-CCCe
Q psy4275           1 MEDPIKSFTDL----KLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCED-PYGI   75 (182)
Q Consensus         1 ~~~~~~~~~~~----~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~-~~~~   75 (182)
                      .|+++.+|+++    ++++.+.+.+.+.|+..|+|+|.++++.+.+++++++++|||+|||.+++++++..+... ..+.
T Consensus        20 ~p~~~~~f~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~   99 (245)
T 3dkp_A           20 LPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPANKGF   99 (245)
T ss_dssp             CCCCCSSHHHHHHHHCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHCSCCSSSC
T ss_pred             CCCcccCHHHhhhccCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHhhcccCCc
Confidence            47888999987    899999999999999999999999999999999999999999999999999999887653 2466


Q ss_pred             eEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhh-hHHhcCCCcEEEEChHHHHHHHhcCC-CCCCCCccEE
Q psy4275          76 FALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQ-GKELAKKPHIVIATPGRLADHLDTCN-TFSLNRIKFL  153 (182)
Q Consensus        76 ~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~Ilv~T~~~l~~~~~~~~-~~~~~~~~~i  153 (182)
                      +++|++|+++|+.|+++.++++....++++..+.|+...... .....++++|+|+||+++.++++... .+.+++++++
T Consensus       100 ~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~~~l  179 (245)
T 3dkp_A          100 RALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWL  179 (245)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTSCCCEECCCHHHHHHTTTSTTSCCCCCEEEECHHHHHHHHHSSSCSCCCTTCCEE
T ss_pred             eEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEecCccHHHHhhhhhcCCCCEEEECHHHHHHHHHhCCCCcccccCcEE
Confidence            899999999999999999999999888888877765543222 12234578999999999999998743 4678899999


Q ss_pred             EEeccccccccCChhHHHHHHHHhh
Q psy4275         154 VLDEADRLSLMTSLKFFFFFFFLKY  178 (182)
Q Consensus       154 I~DE~h~~~~~~~~~~~~~~~~~~~  178 (182)
                      |+||||++.+++...+...+..+..
T Consensus       180 ViDEah~~~~~~~~~~~~~~~~i~~  204 (245)
T 3dkp_A          180 VVDESDKLFEDGKTGFRDQLASIFL  204 (245)
T ss_dssp             EESSHHHHHHHC--CHHHHHHHHHH
T ss_pred             EEeChHHhcccccccHHHHHHHHHH
Confidence            9999999999776666666665543

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=100.00  E-value=3.2e-32  Score=204.54  Aligned_cols=167  Identities=34%  Similarity=0.444  Sum_probs=144.4

Q ss_pred             CccCCC--CCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCC----CCeeEEEE
Q psy4275           7 SFTDLK--LNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP----YGIFALVL   80 (182)
Q Consensus         7 ~~~~~~--l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~----~~~~~lil   80 (182)
                      +|++++  +++.+.+.+...|+..++++|.++++.+..++++++++|||+|||.+++++++..+....    .+.+++|+
T Consensus        53 ~f~~l~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~~~~lil  132 (262)
T 3ly5_A           53 SFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLIL  132 (262)
T ss_dssp             CC-----CCCHHHHHHHHHTTCCBCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEE
T ss_pred             ChhHhccccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhccccccCCceEEEE
Confidence            466666  999999999999999999999999999999999999999999999999999998776522    35689999


Q ss_pred             cCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccc
Q psy4275          81 TPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR  160 (182)
Q Consensus        81 ~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~  160 (182)
                      +|+++|+.|+++.++++....+.++..+.|+.........+.++++|+|+||+++.+++.....+.+++++++|+||||+
T Consensus       133 ~Pt~~La~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~~~~~~~~~~~~l~~lViDEah~  212 (262)
T 3ly5_A          133 SPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADR  212 (262)
T ss_dssp             CSSHHHHHHHHHHHHHHTTTCCSCEEEECSSSCHHHHHHHHHHCCSEEEECHHHHHHHHHHCTTCCCTTCCEEEECSHHH
T ss_pred             eCCHHHHHHHHHHHHHHHhhcCceEEEEECCCCHHHHHHHhcCCCCEEEEcHHHHHHHHHccCCcccccCCEEEEcChHH
Confidence            99999999999999999999899999999988877766666678999999999999999876667788999999999999


Q ss_pred             ccccCChhHHHHH
Q psy4275         161 LSLMTSLKFFFFF  173 (182)
Q Consensus       161 ~~~~~~~~~~~~~  173 (182)
                      +.++++...+..+
T Consensus       213 l~~~~~~~~l~~i  225 (262)
T 3ly5_A          213 ILDVGFEEELKQI  225 (262)
T ss_dssp             HHHTTCHHHHHHH
T ss_pred             HhhhhHHHHHHHH
Confidence            9998866554443

>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-31  Score=212.92  Aligned_cols=173  Identities=36%  Similarity=0.516  Sum_probs=153.4

Q ss_pred             CCCccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCC--------
Q psy4275           1 MEDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP--------   72 (182)
Q Consensus         1 ~~~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~--------   72 (182)
                      .|+++.+|+++++++.+.+.+...|+..|+|+|.++++.+.+++++++++|||+|||.+++++++..+....        
T Consensus        10 ~p~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~~~~~~   89 (417)
T 2i4i_A           10 CPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAM   89 (417)
T ss_dssp             CCCCCSSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCCCHHHHHH
T ss_pred             CCcccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHhccccchhhcc
Confidence            378899999999999999999999999999999999999999999999999999999999999988765432        


Q ss_pred             ----------CCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcC
Q psy4275          73 ----------YGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTC  142 (182)
Q Consensus        73 ----------~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~  142 (182)
                                .+++++|++|+++|+.|+++.++++....++++..+.|+.........+.++++|+|+||+.+.+++.. 
T Consensus        90 ~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~-  168 (417)
T 2i4i_A           90 KENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMER-  168 (417)
T ss_dssp             HHCBTTBSCSBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCHHHHHHHHTTCCSEEEECHHHHHHHHHT-
T ss_pred             ccccccccccCCccEEEECCcHHHHHHHHHHHHHHhCcCCceEEEEECCCCHHHHHHHhhCCCCEEEEChHHHHHHHHc-
Confidence                      136799999999999999999999998889999999999887777777778899999999999999987 


Q ss_pred             CCCCCCCccEEEEeccccccccCChhHHHHHH
Q psy4275         143 NTFSLNRIKFLVLDEADRLSLMTSLKFFFFFF  174 (182)
Q Consensus       143 ~~~~~~~~~~iI~DE~h~~~~~~~~~~~~~~~  174 (182)
                      ..+.+++++++|+||+|++.++++......+.
T Consensus       169 ~~~~~~~~~~iViDEah~~~~~~~~~~~~~i~  200 (417)
T 2i4i_A          169 GKIGLDFCKYLVLDEADRMLDMGFEPQIRRIV  200 (417)
T ss_dssp             TSBCCTTCCEEEESSHHHHHHTTCHHHHHHHH
T ss_pred             CCcChhhCcEEEEEChhHhhccCcHHHHHHHH
Confidence            55678889999999999999988666554443

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=99.98  E-value=8e-31  Score=207.64  Aligned_cols=167  Identities=32%  Similarity=0.481  Sum_probs=150.4

Q ss_pred             CccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcC
Q psy4275           3 DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTP   82 (182)
Q Consensus         3 ~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p   82 (182)
                      ++..+|+++++++.+.+.+...|+..|+|+|.++++.+.+++++++++|||+|||.+++++++..+.....+.+++|++|
T Consensus        34 ~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P  113 (410)
T 2j0s_A           34 DVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAP  113 (410)
T ss_dssp             CCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECS
T ss_pred             cCCCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHHHHHHHHHhhccCCceEEEEcC
Confidence            45678999999999999999999999999999999999999999999999999999999999988765555779999999


Q ss_pred             CHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccc
Q psy4275          83 TRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLS  162 (182)
Q Consensus        83 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~  162 (182)
                      +++|+.|+++.++.+....++++..+.|+.........+..+++|+|+||+.+.+.+.. ......+++++|+||+|++.
T Consensus       114 t~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ivv~Tp~~l~~~l~~-~~~~~~~~~~vViDEah~~~  192 (410)
T 2j0s_A          114 TRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRR-RSLRTRAIKMLVLDEADEML  192 (410)
T ss_dssp             SHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHT-TSSCCTTCCEEEEETHHHHT
T ss_pred             cHHHHHHHHHHHHHHhccCCeEEEEEECCCCHHHHHHHhhcCCCEEEcCHHHHHHHHHh-CCccHhheeEEEEccHHHHH
Confidence            99999999999999999889999999999887777667777889999999999999987 55677889999999999999


Q ss_pred             ccCChhHH
Q psy4275         163 LMTSLKFF  170 (182)
Q Consensus       163 ~~~~~~~~  170 (182)
                      ++++...+
T Consensus       193 ~~~~~~~~  200 (410)
T 2j0s_A          193 NKGFKEQI  200 (410)
T ss_dssp             STTTHHHH
T ss_pred             hhhhHHHH
Confidence            88865433

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=99.97  E-value=4.9e-30  Score=202.44  Aligned_cols=164  Identities=32%  Similarity=0.466  Sum_probs=145.7

Q ss_pred             ccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275           4 PIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus         4 ~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      ...+|+++++++.+.+.+...|+..|+|+|.++++.+.+++++++++|||+|||.+++++++..+.....+.+++|++|+
T Consensus        19 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~   98 (400)
T 1s2m_A           19 KGNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPT   98 (400)
T ss_dssp             --CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSS
T ss_pred             ccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhhccCCccEEEEcCC
Confidence            34689999999999999999999999999999999999999999999999999999999999887765556789999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275          84 RELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus        84 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      ++|+.|+.+.++.+....++++....|+............+++|+|+||+.+.+.+.. ....+.+++++|+||||++.+
T Consensus        99 ~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~T~~~l~~~~~~-~~~~~~~~~~vIiDEaH~~~~  177 (400)
T 1s2m_A           99 RELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASR-KVADLSDCSLFIMDEADKMLS  177 (400)
T ss_dssp             HHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHT-TCSCCTTCCEEEEESHHHHSS
T ss_pred             HHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHHHhcCCCCEEEEchHHHHHHHHh-CCcccccCCEEEEeCchHhhh
Confidence            9999999999999999889999999998877666666667899999999999998876 556688899999999999988


Q ss_pred             cCChh
Q psy4275         164 MTSLK  168 (182)
Q Consensus       164 ~~~~~  168 (182)
                      .++..
T Consensus       178 ~~~~~  182 (400)
T 1s2m_A          178 RDFKT  182 (400)
T ss_dssp             HHHHH
T ss_pred             hchHH
Confidence            65443

>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=99.97  E-value=6.1e-30  Score=201.19  Aligned_cols=170  Identities=31%  Similarity=0.505  Sum_probs=149.1

Q ss_pred             CCccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275           2 EDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus         2 ~~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      .++..+|+++++++.+.+.+...|+..|+|+|.++++.+.+++++++++|||+|||.+++++++..+.....+++++|++
T Consensus        17 ~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~   96 (394)
T 1fuu_A           17 DKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLA   96 (394)
T ss_dssp             CCCCCSSGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTTCCSCCEEEEC
T ss_pred             ccccCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhccCCCCCEEEEc
Confidence            46678899999999999999999999999999999999999999999999999999999999999887766677999999


Q ss_pred             CCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccc
Q psy4275          82 PTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL  161 (182)
Q Consensus        82 p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~  161 (182)
                      |+++|+.|+++.++++....++++..+.|+.........+. +++|+|+||+.+.+.+.. ......+++++|+||+|++
T Consensus        97 P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-~~~i~v~T~~~l~~~~~~-~~~~~~~~~~vIiDEah~~  174 (394)
T 1fuu_A           97 PTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQR-RRFRTDKIKMFILDEADEM  174 (394)
T ss_dssp             SSHHHHHHHHHHHHHHTTTSCCCEEEECSSCCHHHHHHHHH-HCSEEEECHHHHHHHHHT-TSSCCTTCCEEEEETHHHH
T ss_pred             CCHHHHHHHHHHHHHHhccCCeeEEEEeCCCchHHHHhhcC-CCCEEEECHHHHHHHHHh-CCcchhhCcEEEEEChHHh
Confidence            99999999999999999888999999999887654444333 689999999999998877 5566788999999999999


Q ss_pred             cccCChhHHHHH
Q psy4275         162 SLMTSLKFFFFF  173 (182)
Q Consensus       162 ~~~~~~~~~~~~  173 (182)
                      .++++......+
T Consensus       175 ~~~~~~~~~~~~  186 (394)
T 1fuu_A          175 LSSGFKEQIYQI  186 (394)
T ss_dssp             HHTTCHHHHHHH
T ss_pred             hCCCcHHHHHHH
Confidence            988866554443

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=99.97  E-value=1.7e-29  Score=199.98  Aligned_cols=169  Identities=36%  Similarity=0.517  Sum_probs=149.2

Q ss_pred             CCccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275           2 EDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus         2 ~~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      ++...+|+++++++.+.+.+.++|+..|+++|.++++.+.+++++++++|||+|||.+++++++..+.....+.+++|++
T Consensus        36 ~~~~~~f~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~  115 (414)
T 3eiq_A           36 NEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLA  115 (414)
T ss_dssp             CCCCCCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCTTSCSCCEEEEC
T ss_pred             cchhcCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhhcCCceeEEEEe
Confidence            35568899999999999999999999999999999999999999999999999999999999999887765677999999


Q ss_pred             CCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhc-CCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccc
Q psy4275          82 PTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA-KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR  160 (182)
Q Consensus        82 p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~  160 (182)
                      |+++|+.|+.+.++.+....+..+....|+.........+. ++++|+|+||+.+.+.+.. +.....+++++|+||||+
T Consensus       116 P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~-~~~~~~~~~~vViDEah~  194 (414)
T 3eiq_A          116 PTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNR-RYLSPKYIKMFVLDEADE  194 (414)
T ss_dssp             SSHHHHHHHHHHHHHHGGGSCCCEEECCCCTTHHHHHHHHTTTCCSEEEECHHHHHHHHHH-TSSCSTTCCEEEECSHHH
T ss_pred             ChHHHHHHHHHHHHHHhcccCceEEEEECCcchHHHHHHHhcCCCCEEEECHHHHHHHHHc-CCcccccCcEEEEECHHH
Confidence            99999999999999999988999998888877655554544 6789999999999999987 556778899999999999


Q ss_pred             ccccCChhHHH
Q psy4275         161 LSLMTSLKFFF  171 (182)
Q Consensus       161 ~~~~~~~~~~~  171 (182)
                      +.++++...+.
T Consensus       195 ~~~~~~~~~~~  205 (414)
T 3eiq_A          195 MLSRGFKDQIY  205 (414)
T ss_dssp             HHHTTTHHHHH
T ss_pred             hhccCcHHHHH
Confidence            98887655443

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=99.97  E-value=3.2e-29  Score=197.01  Aligned_cols=158  Identities=34%  Similarity=0.560  Sum_probs=139.6

Q ss_pred             CCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHH
Q psy4275           6 KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRE   85 (182)
Q Consensus         6 ~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~   85 (182)
                      .+|+++++++.+.+.+.+.|+..|+|+|.++++.+..++++++++|||+|||.+++++++..+.....+.+++|++|+++
T Consensus         8 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~   87 (391)
T 1xti_A            8 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE   87 (391)
T ss_dssp             -CGGGGCCCHHHHHHHHHHSCCSCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHHHHHHHHCCCCTTCCCEEEECSCHH
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHhhcccCCCeeEEEECCCHH
Confidence            57999999999999999999999999999999999999999999999999999999999988776655679999999999


Q ss_pred             HHHHHHHHHHHhhccC-CceEEEEEcCCchhhhhHHhc-CCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275          86 LAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGKELA-KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus        86 l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~-~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      |+.|+++.++++.... ++++..+.|+.........+. +.++|+|+||+.+...+.. ....+.+++++|+||||++.+
T Consensus        88 L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~-~~~~~~~~~~vViDEaH~~~~  166 (391)
T 1xti_A           88 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARN-KSLNLKHIKHFILDECDKMLE  166 (391)
T ss_dssp             HHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHHHHHSCCSEEEECHHHHHHHHHT-TSSCCTTCSEEEECSHHHHTS
T ss_pred             HHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHHHhcCCCCEEEECHHHHHHHHHc-CCccccccCEEEEeCHHHHhh
Confidence            9999999999998776 789999999887655554444 3579999999999998877 556688899999999999987


Q ss_pred             c
Q psy4275         164 M  164 (182)
Q Consensus       164 ~  164 (182)
                      +
T Consensus       167 ~  167 (391)
T 1xti_A          167 Q  167 (391)
T ss_dssp             S
T ss_pred             c
Confidence            5

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=99.97  E-value=4.9e-29  Score=195.82  Aligned_cols=157  Identities=29%  Similarity=0.455  Sum_probs=138.1

Q ss_pred             CccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCC--CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEE
Q psy4275           3 DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLND--EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVL   80 (182)
Q Consensus         3 ~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~--~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil   80 (182)
                      +...+|+++++++.+.+.+.+.|+..|+|+|.++++.+..+  +++++++|||+|||.+++++++..+.....+.+++|+
T Consensus         2 ~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil   81 (395)
T 3pey_A            2 AMAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICL   81 (395)
T ss_dssp             --CCSSTTSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTCCSCCEEEE
T ss_pred             ccccCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccCCCCccEEEE
Confidence            56789999999999999999999999999999999999987  8999999999999999999999988776667799999


Q ss_pred             cCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccc
Q psy4275          81 TPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR  160 (182)
Q Consensus        81 ~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~  160 (182)
                      +|+++|+.|+++.++++....++.+....++.....    ...+++|+|+||+.+.+.+.. ....+.+++++|+||||+
T Consensus        82 ~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~iiv~T~~~l~~~~~~-~~~~~~~~~~iIiDEah~  156 (395)
T 3pey_A           82 APSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKN----KQINAQVIVGTPGTVLDLMRR-KLMQLQKIKIFVLDEADN  156 (395)
T ss_dssp             CSSHHHHHHHHHHHHHHTTTSCCCEEEESTTSSCTT----SCBCCSEEEECHHHHHHHHHT-TCBCCTTCCEEEEETHHH
T ss_pred             CCCHHHHHHHHHHHHHHhcccCeeEEEEecCchhhh----ccCCCCEEEEcHHHHHHHHHc-CCcccccCCEEEEEChhh
Confidence            999999999999999998888888888777654322    134689999999999999877 556788899999999999


Q ss_pred             cccc
Q psy4275         161 LSLM  164 (182)
Q Consensus       161 ~~~~  164 (182)
                      +.+.
T Consensus       157 ~~~~  160 (395)
T 3pey_A          157 MLDQ  160 (395)
T ss_dssp             HHHS
T ss_pred             hcCc
Confidence            9874

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=99.96  E-value=8.8e-29  Score=195.59  Aligned_cols=166  Identities=30%  Similarity=0.445  Sum_probs=141.5

Q ss_pred             CccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCC--CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEE
Q psy4275           3 DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLND--EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVL   80 (182)
Q Consensus         3 ~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~--~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil   80 (182)
                      ..+.+|+++++++.+.+.+.+.|+..|+|+|.++++.+.++  +++++++|||+|||.+++++++..+.....+++++|+
T Consensus        22 ~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil  101 (412)
T 3fht_A           22 YSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCL  101 (412)
T ss_dssp             CCSSCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEE
T ss_pred             cccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhhhcCCCCCEEEE
Confidence            35778999999999999999999999999999999999986  8999999999999999999999988776667799999


Q ss_pred             cCCHHHHHHHHHHHHHhhccC-CceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccc
Q psy4275          81 TPTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEAD  159 (182)
Q Consensus        81 ~p~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h  159 (182)
                      +|+++|+.|+++.++++.... +.++....++......   ....++|+|+||+.+.+++...+.+.+++++++|+||||
T Consensus       102 ~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~~iViDEah  178 (412)
T 3fht_A          102 SPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEAD  178 (412)
T ss_dssp             CSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTCCCCTT---CCCCCSEEEECHHHHHHHHTTSCSSCGGGCCEEEEETHH
T ss_pred             CCCHHHHHHHHHHHHHHHhhcccceEEEeecCcchhhh---hcCCCCEEEECchHHHHHHHhcCCcChhhCcEEEEeCHH
Confidence            999999999999999987765 5777777776654332   234679999999999999977666778899999999999


Q ss_pred             cccc-cCChhHHH
Q psy4275         160 RLSL-MTSLKFFF  171 (182)
Q Consensus       160 ~~~~-~~~~~~~~  171 (182)
                      ++.+ .++.....
T Consensus       179 ~~~~~~~~~~~~~  191 (412)
T 3fht_A          179 VMIATQGHQDQSI  191 (412)
T ss_dssp             HHHSTTTTHHHHH
T ss_pred             HHhhcCCcHHHHH
Confidence            9987 44444333

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=99.96  E-value=2.7e-28  Score=189.88  Aligned_cols=167  Identities=39%  Similarity=0.600  Sum_probs=143.9

Q ss_pred             CccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCC-CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275           3 DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLND-EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus         3 ~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~-~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      -...+|+++++++.+.+.+.+.|+..|+|+|.++++.+.++ +++++.+|||+|||.+++.+++..+... .+.+++|++
T Consensus         3 ~~~~~f~~~~l~~~~~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~~-~~~~~lil~   81 (367)
T 1hv8_A            3 VEYMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNEN-NGIEAIILT   81 (367)
T ss_dssp             CCCCCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSS-SSCCEEEEC
T ss_pred             cccCchhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhccc-CCCcEEEEc
Confidence            34578999999999999999999999999999999999887 6999999999999999999988876553 356899999


Q ss_pred             CCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccc
Q psy4275          82 PTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL  161 (182)
Q Consensus        82 p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~  161 (182)
                      |+++|+.|+++.++.+....++++....|+.........+ .+++|+|+||+.+.+.+.. ....+++++++|+||+|++
T Consensus        82 P~~~L~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~-~~~~iiv~T~~~l~~~~~~-~~~~~~~~~~iIiDEah~~  159 (367)
T 1hv8_A           82 PTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKAL-KNANIVVGTPGRILDHINR-GTLNLKNVKYFILDEADEM  159 (367)
T ss_dssp             SCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHH-HTCSEEEECHHHHHHHHHT-TCSCTTSCCEEEEETHHHH
T ss_pred             CCHHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHhhc-CCCCEEEecHHHHHHHHHc-CCcccccCCEEEEeCchHh
Confidence            9999999999999999888888999999888765544443 3789999999999998877 5567888999999999999


Q ss_pred             cccCChhHHHH
Q psy4275         162 SLMTSLKFFFF  172 (182)
Q Consensus       162 ~~~~~~~~~~~  172 (182)
                      .++++......
T Consensus       160 ~~~~~~~~~~~  170 (367)
T 1hv8_A          160 LNMGFIKDVEK  170 (367)
T ss_dssp             HTTTTHHHHHH
T ss_pred             hhhchHHHHHH
Confidence            98886554433

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens}

Probab=99.96  E-value=3.8e-28  Score=196.18  Aligned_cols=159  Identities=31%  Similarity=0.486  Sum_probs=137.4

Q ss_pred             ccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCC--CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275           4 PIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLND--EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus         4 ~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~--~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      .+.+|+++++++.+.+.+...|+..|+|+|.++++.+..+  +++++++|||+|||.+|+++++..+.....+++++|++
T Consensus        90 ~~~~f~~~~l~~~l~~~l~~~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~  169 (479)
T 3fmp_B           90 SVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLS  169 (479)
T ss_dssp             CCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTCCTTSCSCCEEEEC
T ss_pred             CcCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHHhhcCCCCcEEEEe
Confidence            3578999999999999999999999999999999999986  89999999999999999999999887766667999999


Q ss_pred             CCHHHHHHHHHHHHHhhccC-CceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccc
Q psy4275          82 PTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR  160 (182)
Q Consensus        82 p~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~  160 (182)
                      |+++|+.|+++.++.+.+.. +..+....++......   ....++|+|+||+.+.+++.+.+.+.++++++||+||+|+
T Consensus       170 Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEah~  246 (479)
T 3fmp_B          170 PTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADV  246 (479)
T ss_dssp             SSHHHHHHHHHHHHHHHTTSTTCCEEEESTTCCCCTT---CCCCCSEEEECHHHHHHHHTTSCCCCGGGCCEEEECCHHH
T ss_pred             ChHHHHHHHHHHHHHHHhhCCCceEEEEeCCcccccc---ccCCCCEEEECchHHHHHHHhcCCcCcccCCEEEEECHHH
Confidence            99999999999999987764 5677777666543322   1346789999999999999876777889999999999999


Q ss_pred             ccccC
Q psy4275         161 LSLMT  165 (182)
Q Consensus       161 ~~~~~  165 (182)
                      +.+..
T Consensus       247 ~~~~~  251 (479)
T 3fmp_B          247 MIATQ  251 (479)
T ss_dssp             HHTST
T ss_pred             HhhcC
Confidence            98743

>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=99.96  E-value=1.6e-27  Score=183.68  Aligned_cols=153  Identities=35%  Similarity=0.544  Sum_probs=133.4

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHH
Q psy4275          13 LNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGD   92 (182)
Q Consensus        13 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~   92 (182)
                      +++++.+.+.++|+..|+|+|.++++.+.+++++++.+|||+|||.+++.+++..      +.+++|++|+++|+.|+++
T Consensus         1 l~~~i~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~------~~~~liv~P~~~L~~q~~~   74 (337)
T 2z0m_A            1 MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL------GMKSLVVTPTRELTRQVAS   74 (337)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHH------TCCEEEECSSHHHHHHHHH
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEcCCCCcHHHHHHHHHHhh------cCCEEEEeCCHHHHHHHHH
Confidence            5789999999999999999999999999999999999999999999999888774      5689999999999999999


Q ss_pred             HHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHHHH
Q psy4275          93 QFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFF  172 (182)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~~~  172 (182)
                      .++++....+.++..++|+.........+ .+++|+|+||+.+.+.+.. ....+.+++++|+||+|++.++++......
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~i~v~T~~~l~~~~~~-~~~~~~~~~~iViDEah~~~~~~~~~~~~~  152 (337)
T 2z0m_A           75 HIRDIGRYMDTKVAEVYGGMPYKAQINRV-RNADIVVATPGRLLDLWSK-GVIDLSSFEIVIIDEADLMFEMGFIDDIKI  152 (337)
T ss_dssp             HHHHHTTTSCCCEEEECTTSCHHHHHHHH-TTCSEEEECHHHHHHHHHT-TSCCGGGCSEEEEESHHHHHHTTCHHHHHH
T ss_pred             HHHHHhhhcCCcEEEEECCcchHHHHhhc-CCCCEEEECHHHHHHHHHc-CCcchhhCcEEEEEChHHhhccccHHHHHH
Confidence            99999988899999999888765554444 3589999999999998876 555678899999999999998887654443


Q ss_pred             H
Q psy4275         173 F  173 (182)
Q Consensus       173 ~  173 (182)
                      +
T Consensus       153 ~  153 (337)
T 2z0m_A          153 I  153 (337)
T ss_dssp             H
T ss_pred             H
Confidence            3

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.95  E-value=7.5e-28  Score=198.63  Aligned_cols=171  Identities=31%  Similarity=0.434  Sum_probs=139.8

Q ss_pred             CCccCCC----CCHHHHHHHHHCCCCCChHHHHhhhhhhh--CCCcEEEECCCCChHHHHHHHHHHHhhccCC----CCe
Q psy4275           6 KSFTDLK----LNPWLIRQCQTIGVKTPTEIQKAIIPHVL--NDEDCIGCAKTGSGKTLAFALPILQKWCEDP----YGI   75 (182)
Q Consensus         6 ~~~~~~~----l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~--~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~----~~~   75 (182)
                      .+|+++.    +++++.+++..+|+..|+|+|.++++.+.  .++++++++|||+|||.+++++++..+....    .+.
T Consensus        17 ~~~~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~   96 (579)
T 3sqw_A           17 VTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMV   96 (579)
T ss_dssp             CCHHHHHHTTSSCHHHHHHHHTTTCSSCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSC
T ss_pred             cCHHHHhhcCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhccccccCCC
Confidence            3455553    99999999999999999999999999998  6789999999999999999999998876542    346


Q ss_pred             eEEEEcCCHHHHHHHHHHHHHhhcc----CCceEEEEEcCCchhhhhHHhc-CCCcEEEEChHHHHHHHhcCCCCCCCCc
Q psy4275          76 FALVLTPTRELAYQIGDQFLVLGKV----MNLRVSIITGGMDMVDQGKELA-KKPHIVIATPGRLADHLDTCNTFSLNRI  150 (182)
Q Consensus        76 ~~lil~p~~~l~~q~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~-~~~~Ilv~T~~~l~~~~~~~~~~~~~~~  150 (182)
                      +++|++|+++|+.|+++.++.+...    ....+....|+.........+. .+++|+|+||+.+.+++.......++++
T Consensus        97 ~~lvl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~~~  176 (579)
T 3sqw_A           97 KAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFV  176 (579)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTC
T ss_pred             eEEEEcchHHHHHHHHHHHHHHHhhcccccceEEEEEECCccHHHHHHHHhcCCCCEEEECHHHHHHHHHhccccccccC
Confidence            8999999999999999999987632    3466777788776555444443 4789999999999998876434457889


Q ss_pred             cEEEEeccccccccCChhHHHHHHHH
Q psy4275         151 KFLVLDEADRLSLMTSLKFFFFFFFL  176 (182)
Q Consensus       151 ~~iI~DE~h~~~~~~~~~~~~~~~~~  176 (182)
                      +++|+||||++.++++......+...
T Consensus       177 ~~lViDEah~l~~~gf~~~~~~i~~~  202 (579)
T 3sqw_A          177 DYKVLDEADRLLEIGFRDDLETISGI  202 (579)
T ss_dssp             CEEEEETHHHHTSTTTHHHHHHHHHH
T ss_pred             CEEEEEChHHhhcCCCHHHHHHHHHH
Confidence            99999999999999977766655544

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=99.95  E-value=3.6e-27  Score=193.83  Aligned_cols=164  Identities=32%  Similarity=0.444  Sum_probs=135.4

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHhhhhhhh--CCCcEEEECCCCChHHHHHHHHHHHhhccCC----CCeeEEEEcCCHHH
Q psy4275          13 LNPWLIRQCQTIGVKTPTEIQKAIIPHVL--NDEDCIGCAKTGSGKTLAFALPILQKWCEDP----YGIFALVLTPTREL   86 (182)
Q Consensus        13 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~--~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~----~~~~~lil~p~~~l   86 (182)
                      +++++.+.+.+.|+..|+|+|.++++.+.  .++++++++|||+|||.+++++++..+....    .+.+++|++|+++|
T Consensus        79 l~~~l~~~l~~~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lil~Ptr~L  158 (563)
T 3i5x_A           79 LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDL  158 (563)
T ss_dssp             SCHHHHHHHHTTCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhccccccCCeeEEEEcCcHHH
Confidence            99999999999999999999999999998  5789999999999999999999998876643    24589999999999


Q ss_pred             HHHHHHHHHHhhcc----CCceEEEEEcCCchhhhhHHh-cCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccc
Q psy4275          87 AYQIGDQFLVLGKV----MNLRVSIITGGMDMVDQGKEL-AKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL  161 (182)
Q Consensus        87 ~~q~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~-~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~  161 (182)
                      +.|+++.++.+...    ....+..+.|+.........+ ..+++|+|+||+.+.+++.+.....+++++++|+||||++
T Consensus       159 a~Q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~l  238 (563)
T 3i5x_A          159 ALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRL  238 (563)
T ss_dssp             HHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTCCEEEEETHHHH
T ss_pred             HHHHHHHHHHHHhhccccCceeEEEEECCcCHHHHHHHHhcCCCCEEEECcHHHHHHHHhccccccccceEEEEeCHHHH
Confidence            99999999987543    245677777777655444443 3478999999999999887643345778999999999999


Q ss_pred             cccCChhHHHHHHHH
Q psy4275         162 SLMTSLKFFFFFFFL  176 (182)
Q Consensus       162 ~~~~~~~~~~~~~~~  176 (182)
                      .++++......+...
T Consensus       239 ~~~~f~~~~~~i~~~  253 (563)
T 3i5x_A          239 LEIGFRDDLETISGI  253 (563)
T ss_dssp             TSTTTHHHHHHHHHH
T ss_pred             hccchHHHHHHHHHh
Confidence            999877766655444

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=99.94  E-value=1.7e-26  Score=194.76  Aligned_cols=162  Identities=22%  Similarity=0.281  Sum_probs=136.4

Q ss_pred             CCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhh-hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCH
Q psy4275           6 KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPH-VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTR   84 (182)
Q Consensus         6 ~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~-~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~   84 (182)
                      .+|+++++++++.+.+.+.|+..++|+|.++++. +.+++++++++|||+|||.++.++++..+..+  +.+++|++|++
T Consensus         1 ~~f~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~--~~~~l~i~P~r   78 (720)
T 2zj8_A            1 MRVDELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQ--GGKAVYIVPLK   78 (720)
T ss_dssp             CBGGGCCSCHHHHHHHHHTTCCBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHHH--CSEEEEECSSG
T ss_pred             CcHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHhC--CCEEEEEcCcH
Confidence            3689999999999999999999999999999998 78899999999999999999999998877643  56999999999


Q ss_pred             HHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccccc
Q psy4275          85 ELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus        85 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~  164 (182)
                      +|+.|+++.++.+.+ .++++..++|+......   ..++++|+|+||+++...++. ....++++++||+||+|++.++
T Consensus        79 aLa~q~~~~~~~l~~-~g~~v~~~~G~~~~~~~---~~~~~~Iiv~Tpe~l~~~~~~-~~~~l~~~~~vIiDE~H~l~~~  153 (720)
T 2zj8_A           79 ALAEEKFQEFQDWEK-IGLRVAMATGDYDSKDE---WLGKYDIIIATAEKFDSLLRH-GSSWIKDVKILVADEIHLIGSR  153 (720)
T ss_dssp             GGHHHHHHHTGGGGG-GTCCEEEECSCSSCCCG---GGGGCSEEEECHHHHHHHHHH-TCTTGGGEEEEEEETGGGGGCT
T ss_pred             HHHHHHHHHHHHHHh-cCCEEEEecCCCCcccc---ccCCCCEEEECHHHHHHHHHc-ChhhhhcCCEEEEECCcccCCC
Confidence            999999999865544 48999999997654332   234789999999999998887 4445788999999999999986


Q ss_pred             CChhHHHHHH
Q psy4275         165 TSLKFFFFFF  174 (182)
Q Consensus       165 ~~~~~~~~~~  174 (182)
                      .....++.+.
T Consensus       154 ~r~~~~~~ll  163 (720)
T 2zj8_A          154 DRGATLEVIL  163 (720)
T ss_dssp             TTHHHHHHHH
T ss_pred             cccHHHHHHH
Confidence            6555444443

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.94  E-value=5.3e-26  Score=191.62  Aligned_cols=162  Identities=25%  Similarity=0.271  Sum_probs=136.4

Q ss_pred             cCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhh-hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275           5 IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPH-VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus         5 ~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~-~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      ..+|+++++++++.+.+.+.|+..++|+|.++++. +.+++++++++|||+|||+++.+++++.+..+  +.+++|++|+
T Consensus         7 ~~~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~--~~~il~i~P~   84 (715)
T 2va8_A            7 WMPIEDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKN--GGKAIYVTPL   84 (715)
T ss_dssp             CCBGGGSSSCHHHHHHHHTTSCCBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHHS--CSEEEEECSC
T ss_pred             cCcHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHHC--CCeEEEEeCc
Confidence            45799999999999999999999999999999999 77899999999999999999999999877643  5699999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275          84 RELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus        84 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      ++|+.|+++.++.+ ...++++...+|+......   ..++++|+|+||+++...++. ....++++++||+||+|++.+
T Consensus        85 r~La~q~~~~~~~~-~~~g~~v~~~~G~~~~~~~---~~~~~~Iiv~Tpe~l~~~~~~-~~~~l~~~~~vIiDE~H~l~~  159 (715)
T 2va8_A           85 RALTNEKYLTFKDW-ELIGFKVAMTSGDYDTDDA---WLKNYDIIITTYEKLDSLWRH-RPEWLNEVNYFVLDELHYLND  159 (715)
T ss_dssp             HHHHHHHHHHHGGG-GGGTCCEEECCSCSSSCCG---GGGGCSEEEECHHHHHHHHHH-CCGGGGGEEEEEECSGGGGGC
T ss_pred             HHHHHHHHHHHHHh-hcCCCEEEEEeCCCCCchh---hcCCCCEEEEcHHHHHHHHhC-ChhHhhccCEEEEechhhcCC
Confidence            99999999888644 4458899999987764432   124789999999999999887 444578899999999999987


Q ss_pred             cCChhHHHHH
Q psy4275         164 MTSLKFFFFF  173 (182)
Q Consensus       164 ~~~~~~~~~~  173 (182)
                      +.....+..+
T Consensus       160 ~~~~~~l~~i  169 (715)
T 2va8_A          160 PERGPVVESV  169 (715)
T ss_dssp             TTTHHHHHHH
T ss_pred             cccchHHHHH
Confidence            6665544443

>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=1.9e-26  Score=194.09  Aligned_cols=159  Identities=18%  Similarity=0.248  Sum_probs=132.3

Q ss_pred             CccCCC--CCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCH
Q psy4275           7 SFTDLK--LNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTR   84 (182)
Q Consensus         7 ~~~~~~--l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~   84 (182)
                      +|++++  +++.+.+.+.+.|+..++|+|.++++.+.+++++++++|||+|||+++.++++..+.+   +.+++|++|++
T Consensus         2 ~f~~l~~~l~~~~~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~~l~il~~~~~---~~~~l~i~P~r   78 (702)
T 2p6r_A            2 KVEELAESISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK---GGKSLYVVPLR   78 (702)
T ss_dssp             CSHHHHHHHHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT---TCCEEEEESSH
T ss_pred             chhhhhhccCHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCcEEEEcCCccHHHHHHHHHHHHHHHh---CCcEEEEeCcH
Confidence            688888  9999999999999999999999999999999999999999999999999999987664   56899999999


Q ss_pred             HHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccccc
Q psy4275          85 ELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus        85 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~  164 (182)
                      +|+.|+++.++.+ ...|+++...+|+......   ..++++|+|+||+++..+++. ....+++++++|+||+|++.++
T Consensus        79 ~La~q~~~~~~~~-~~~g~~v~~~~G~~~~~~~---~~~~~~Iiv~Tpe~l~~~l~~-~~~~l~~~~~vIiDE~H~l~~~  153 (702)
T 2p6r_A           79 ALAGEKYESFKKW-EKIGLRIGISTGDYESRDE---HLGDCDIIVTTSEKADSLIRN-RASWIKAVSCLVVDEIHLLDSE  153 (702)
T ss_dssp             HHHHHHHHHHTTT-TTTTCCEEEECSSCBCCSS---CSTTCSEEEEEHHHHHHHHHT-TCSGGGGCCEEEETTGGGGGCT
T ss_pred             HHHHHHHHHHHHH-HhcCCEEEEEeCCCCcchh---hccCCCEEEECHHHHHHHHHc-ChhHHhhcCEEEEeeeeecCCC
Confidence            9999999988644 3458899999998764332   234789999999999999887 4445778999999999999987


Q ss_pred             CChhHHHHH
Q psy4275         165 TSLKFFFFF  173 (182)
Q Consensus       165 ~~~~~~~~~  173 (182)
                      +.....+.+
T Consensus       154 ~r~~~~~~l  162 (702)
T 2p6r_A          154 KRGATLEIL  162 (702)
T ss_dssp             TTHHHHHHH
T ss_pred             CcccHHHHH
Confidence            655544443

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.93  E-value=2.8e-25  Score=186.57  Aligned_cols=149  Identities=19%  Similarity=0.190  Sum_probs=123.7

Q ss_pred             HHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCC--CeeEEEEcCCHHHHHHHHHHHH
Q psy4275          18 IRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPY--GIFALVLTPTRELAYQIGDQFL   95 (182)
Q Consensus        18 ~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~--~~~~lil~p~~~l~~q~~~~~~   95 (182)
                      .+.+..+|+..|+|+|.++++.+..++++++++|||+|||++++++++..+...+.  +++++|++|+++|+.|+.+.++
T Consensus         3 ~~~l~~~g~~~lr~~Q~~~i~~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~lvl~Pt~~L~~Q~~~~~~   82 (696)
T 2ykg_A            3 VSDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQNKSVFS   82 (696)
T ss_dssp             ----CTTC--CCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCTTCCCCEEEECSSHHHHHHHHHHHH
T ss_pred             CCcccccCCCCccHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHHHHhCccCCCCeEEEEECCHHHHHHHHHHHH
Confidence            45677889999999999999999999999999999999999999999987765432  3689999999999999999999


Q ss_pred             HhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCC
Q psy4275          96 VLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTS  166 (182)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~  166 (182)
                      ++....++++..++|+.........+..+++|+|+||+.+.+.+.......+.+++++|+||||++.+...
T Consensus        83 ~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~L~~~l~~~~~~~l~~~~~vViDEaH~~~~~~~  153 (696)
T 2ykg_A           83 KYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHP  153 (696)
T ss_dssp             HHTTTTTCCEEEECSSSCSSSCHHHHHHTCSEEEECHHHHHHHHHTTSSCCGGGCSEEEEETGGGCSTTCH
T ss_pred             HHhccCCceEEEEeCCccccccHHHhccCCCEEEECHHHHHHHHhcCcccccccccEEEEeCCCcccCccc
Confidence            99988889999999988665555555567999999999999999873332678899999999999986653

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.93  E-value=4.1e-26  Score=181.10  Aligned_cols=141  Identities=18%  Similarity=0.177  Sum_probs=116.7

Q ss_pred             HHHHHHHH-CCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHH
Q psy4275          16 WLIRQCQT-IGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQF   94 (182)
Q Consensus        16 ~i~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~   94 (182)
                      ++.+.+.+ +++ +|+|+|.++++.+.+++++++++|||+|||.+++.+++.....   +++++|++|+++|+.|+++.+
T Consensus         9 ~~~~~l~~~~~~-~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~~~---~~~~lil~Pt~~L~~q~~~~~   84 (414)
T 3oiy_A            9 DFRSFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARK---GKKSALVFPTVTLVKQTLERL   84 (414)
T ss_dssp             HHHHHHHHHHSS-CCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHHTT---TCCEEEEESSHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCC-CCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHhcC---CCEEEEEECCHHHHHHHHHHH
Confidence            44555655 355 8999999999999999999999999999999988887776533   679999999999999999999


Q ss_pred             HHhhccCCceEEEEEcCCchh---hhhHHhcC-CCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccccc
Q psy4275          95 LVLGKVMNLRVSIITGGMDMV---DQGKELAK-KPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~-~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~  164 (182)
                      +.+.. .++++..++|+....   .....+.+ .++|+|+||+.+.+.+..   +...+++++|+||||++..+
T Consensus        85 ~~~~~-~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~---~~~~~~~~iViDEaH~~~~~  154 (414)
T 3oiy_A           85 QKLAD-EKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK---LSQKRFDFVFVDDVDAVLKA  154 (414)
T ss_dssp             HHHCC-SSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHH---HTTCCCSEEEESCHHHHHHC
T ss_pred             HHHcc-CCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHH---hccccccEEEEeChHhhhhc
Confidence            99888 889999999998763   33334444 489999999999888765   34668999999999987653

>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=99.93  E-value=3.2e-25  Score=181.36  Aligned_cols=142  Identities=19%  Similarity=0.201  Sum_probs=118.7

Q ss_pred             CCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCC--CeeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q psy4275          26 VKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPY--GIFALVLTPTRELAYQIGDQFLVLGKVMNL  103 (182)
Q Consensus        26 ~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~--~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  103 (182)
                      ..+|+|+|.++++.+.+++++++++|||+|||.+++++++..+...+.  +.+++|++|+++|+.|+.+.++.+....++
T Consensus         5 ~~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~   84 (556)
T 4a2p_A            5 TKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGY   84 (556)
T ss_dssp             ---CCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGGGTC
T ss_pred             CCCCCHHHHHHHHHHHcCCCEEEEcCCCChHHHHHHHHHHHHHHhCcccCCCeEEEEeCCHHHHHHHHHHHHHHhcccCc
Confidence            357999999999999999999999999999999999999888776542  568999999999999999999999998899


Q ss_pred             eEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCCh
Q psy4275         104 RVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSL  167 (182)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~  167 (182)
                      ++..++|+.........+..+++|+|+||+.+.+.+.......+.+++++|+||||++.+++..
T Consensus        85 ~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~~~  148 (556)
T 4a2p_A           85 SVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPY  148 (556)
T ss_dssp             CEEECCCC-----CHHHHHHHCSEEEECHHHHHHHHHSSSCCCSTTCSEEEEETGGGCSTTSHH
T ss_pred             eEEEEeCCCCcchhHHHhhCCCCEEEECHHHHHHHHHhCcccccccCCEEEEECCcccCCcchH
Confidence            9999999887665555556678999999999999998733337889999999999999987753

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.93  E-value=3.8e-25  Score=180.63  Aligned_cols=140  Identities=19%  Similarity=0.202  Sum_probs=122.9

Q ss_pred             CCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCC--CeeEEEEcCCHHHHHHHHHHHHHhhccCCce
Q psy4275          27 KTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPY--GIFALVLTPTRELAYQIGDQFLVLGKVMNLR  104 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~--~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~  104 (182)
                      ..|+|+|.++++.+.+++++++++|||+|||.+++++++..+...+.  +.+++|++|+++|+.|+.+.+++++...+++
T Consensus         3 ~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~   82 (555)
T 3tbk_A            3 LKPRNYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQATVFSRYFERLGYN   82 (555)
T ss_dssp             CCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHTTTCC
T ss_pred             CCCcHHHHHHHHHHhCCCCEEEEeCCCChHHHHHHHHHHHHHHhcccCCCCEEEEEeCCHHHHHHHHHHHHHHhccCCcE
Confidence            37999999999999999999999999999999999999988776542  5689999999999999999999999988999


Q ss_pred             EEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCC
Q psy4275         105 VSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTS  166 (182)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~  166 (182)
                      +..++|+.........+.++++|+|+||+.+.+.+.......+.+++++|+||||++.+.+.
T Consensus        83 ~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~~  144 (555)
T 3tbk_A           83 IASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNNGAIPSLSVFTLMIFDECHNTSKNHP  144 (555)
T ss_dssp             EEEECTTTGGGSCHHHHHHHCSEEEECHHHHHHHHHTSSSCCGGGCSEEEETTGGGCSTTCH
T ss_pred             EEEEcCCCcchhhHHHHhcCCCEEEECHHHHHHHHhcCcccccccCCEEEEECccccCCcch
Confidence            99999998766555556667999999999999999873333688899999999999988764

>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=99.93  E-value=1.5e-25  Score=182.78  Aligned_cols=166  Identities=20%  Similarity=0.195  Sum_probs=130.1

Q ss_pred             cCCccCCCCCHHHHHHHHH-CCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275           5 IKSFTDLKLNPWLIRQCQT-IGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus         5 ~~~~~~~~l~~~i~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      +.+|+++++++.+.+.+.+ +|+..++|+|.++++.+.+++++++.+|||+|||.++.++++..      ++.++|++|+
T Consensus         1 ~~~fe~l~L~~~~~~~l~~~~g~~~~r~~Q~~~i~~il~g~d~lv~apTGsGKTl~~~lp~l~~------~g~~lvi~P~   74 (523)
T 1oyw_A            1 MAQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL------NGLTVVVSPL   74 (523)
T ss_dssp             CCCCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS------SSEEEEECSC
T ss_pred             CCChhhCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHHh------CCCEEEECCh
Confidence            4689999999999999998 89999999999999999999999999999999999999888754      3579999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhH----HhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccc
Q psy4275          84 RELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGK----ELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEAD  159 (182)
Q Consensus        84 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h  159 (182)
                      ++|+.|+.+.++.+    ++++..++++........    ...+..+|+++||+.+...... ..+...+++++|+||||
T Consensus        75 ~aL~~q~~~~l~~~----gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~~~~-~~l~~~~~~~vViDEaH  149 (523)
T 1oyw_A           75 ISLMKDQVDQLQAN----GVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFL-EHLAHWNPVLLAVDEAH  149 (523)
T ss_dssp             HHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHH-HHHTTSCEEEEEESSGG
T ss_pred             HHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhChHHH-HHHhhCCCCEEEEeCcc
Confidence            99999998888764    778888888766543322    2235689999999998532111 11234678999999999


Q ss_pred             cccccC--ChhHHHHHHHHhhcCC
Q psy4275         160 RLSLMT--SLKFFFFFFFLKYYIP  181 (182)
Q Consensus       160 ~~~~~~--~~~~~~~~~~~~~~~~  181 (182)
                      ++.+++  +......+..++..+|
T Consensus       150 ~i~~~g~~fr~~~~~l~~l~~~~~  173 (523)
T 1oyw_A          150 CISQWGHDFRPEYAALGQLRQRFP  173 (523)
T ss_dssp             GGCTTSSCCCHHHHGGGGHHHHCT
T ss_pred             ccCcCCCccHHHHHHHHHHHHhCC
Confidence            999887  4444444444444443

>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=99.93  E-value=5.9e-25  Score=181.43  Aligned_cols=165  Identities=18%  Similarity=0.208  Sum_probs=131.1

Q ss_pred             cCCcc--CCCCCHHHHHHHHH-CCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275           5 IKSFT--DLKLNPWLIRQCQT-IGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus         5 ~~~~~--~~~l~~~i~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      ...|+  ++++++.+.+.+.+ +|+..++|+|.++++.+.+|+++++.+|||+|||++|+++++..      .++++|++
T Consensus        18 ~~~w~~~~~~l~~~l~~~L~~~fg~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~lpal~~------~g~~lVis   91 (591)
T 2v1x_A           18 PAAWNKEDFPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCS------DGFTLVIC   91 (591)
T ss_dssp             GGGGCCSCSTTHHHHHHHHHHTSCCCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHHHHHHTS------SSEEEEEC
T ss_pred             hhccccccCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHHHHHHHc------CCcEEEEe
Confidence            34554  58899999999998 79999999999999999999999999999999999999998763      45899999


Q ss_pred             CCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHH------hcCCCcEEEEChHHHH------HHHhcCCCCCCCC
Q psy4275          82 PTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKE------LAKKPHIVIATPGRLA------DHLDTCNTFSLNR  149 (182)
Q Consensus        82 p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~Ilv~T~~~l~------~~~~~~~~~~~~~  149 (182)
                      |+++|+.|+.+.++.+    ++++..++|+.........      ....++|+|+||+++.      +.++.  .....+
T Consensus        92 P~~~L~~q~~~~l~~~----gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L~~~~~~~~~l~~--~~~~~~  165 (591)
T 2v1x_A           92 PLISLMEDQLMVLKQL----GISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEK--AYEARR  165 (591)
T ss_dssp             SCHHHHHHHHHHHHHH----TCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHHHHHSCHHHHHHHHH--HHHTTC
T ss_pred             CHHHHHHHHHHHHHhc----CCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChhHhhccHHHHHHHHh--hhhccC
Confidence            9999999999888876    7888888888765443322      2457899999999874      22222  224667


Q ss_pred             ccEEEEeccccccccC--ChhHHHHHHHHhhcCC
Q psy4275         150 IKFLVLDEADRLSLMT--SLKFFFFFFFLKYYIP  181 (182)
Q Consensus       150 ~~~iI~DE~h~~~~~~--~~~~~~~~~~~~~~~~  181 (182)
                      ++++|+||||++.+|+  +......+..+++.+|
T Consensus       166 i~~iViDEAH~is~~g~dfr~~~~~l~~l~~~~~  199 (591)
T 2v1x_A          166 FTRIAVDEVHCCSQWGHDFRPDYKALGILKRQFP  199 (591)
T ss_dssp             EEEEEEETGGGGSTTCTTCCGGGGGGGHHHHHCT
T ss_pred             CcEEEEECcccccccccccHHHHHHHHHHHHhCC
Confidence            8999999999999887  5555555555555443

>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=99.92  E-value=4.7e-25  Score=160.21  Aligned_cols=145  Identities=20%  Similarity=0.155  Sum_probs=107.4

Q ss_pred             CCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccC---CCCeeEEEEcCCHHHHHH-HHHHHHHhhc
Q psy4275          24 IGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCED---PYGIFALVLTPTRELAYQ-IGDQFLVLGK   99 (182)
Q Consensus        24 ~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~---~~~~~~lil~p~~~l~~q-~~~~~~~~~~   99 (182)
                      .....++++|.++++.+.+++++++.+|||+|||.+++.++...+...   ..+.+++|++|+++|++| +.+.++.+..
T Consensus        29 ~~~~~l~~~Q~~~i~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~~lil~p~~~L~~q~~~~~~~~~~~  108 (216)
T 3b6e_A           29 EPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLK  108 (216)
T ss_dssp             SCCCCCCHHHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCCCEEEEESSHHHHHHHHHHTHHHHHT
T ss_pred             cCCCCchHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhcccccCCCcEEEEECHHHHHHHHHHHHHHHHhc
Confidence            345689999999999999999999999999999999998888765432   225689999999999999 7788888766


Q ss_pred             cCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCC-----CCCCCccEEEEeccccccccCChhH
Q psy4275         100 VMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNT-----FSLNRIKFLVLDEADRLSLMTSLKF  169 (182)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~-----~~~~~~~~iI~DE~h~~~~~~~~~~  169 (182)
                      . ++++..+.|+...........++++|+|+||+.+.+.+.....     ..+.+++++|+||||++.+.+....
T Consensus       109 ~-~~~v~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~~~  182 (216)
T 3b6e_A          109 K-WYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNN  182 (216)
T ss_dssp             T-TSCEEECCC---CCCCHHHHHHHCSEEEEEHHHHHHHHHC-------CCCGGGCSEEEETTC-------CHHH
T ss_pred             c-CceEEEEeCCcccchhHHhhccCCCEEEECHHHHHHHHhccCcccccccchhcccEEEEECchhhccCCcHHH
Confidence            5 6788888887665444444445789999999999998876432     4567889999999999987654443

>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=99.92  E-value=1.7e-24  Score=184.33  Aligned_cols=144  Identities=19%  Similarity=0.194  Sum_probs=119.4

Q ss_pred             HCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCC--CeeEEEEcCCHHHHHHHHHHHHHhhcc
Q psy4275          23 TIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPY--GIFALVLTPTRELAYQIGDQFLVLGKV  100 (182)
Q Consensus        23 ~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~--~~~~lil~p~~~l~~q~~~~~~~~~~~  100 (182)
                      ..|+..|+|+|.++++.+.+++++++++|||+|||.+++++++..+...+.  +++++|++|+++|+.|+.+.+++++..
T Consensus       243 ~~g~~~l~~~Q~~~i~~~l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~Lvl~Pt~~L~~Q~~~~~~~~~~~  322 (797)
T 4a2q_A          243 VYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFER  322 (797)
T ss_dssp             -----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGG
T ss_pred             hcCCCCCCHHHHHHHHHHHhCCCEEEEeCCCChHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHhccc
Confidence            346778999999999999999999999999999999999999988776542  568999999999999999999999988


Q ss_pred             CCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCC
Q psy4275         101 MNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTS  166 (182)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~  166 (182)
                      .++++..++|+.........+.++++|+|+||+.+.+.++......+.++++||+||||++.+.+.
T Consensus       323 ~~~~v~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEaH~~~~~~~  388 (797)
T 4a2q_A          323 QGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHP  388 (797)
T ss_dssp             GTCCEEEECCC-----CHHHHHHTCSEEEECHHHHHHHHHSSSCCCGGGCSEEEETTGGGCSTTSH
T ss_pred             CCceEEEEeCCcchhhhHHHhhCCCCEEEEchHHHHHHHHhccccccccCCEEEEECccccCCCcc
Confidence            899999999998766655666678999999999999999873333788899999999999998764

>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=3.2e-24  Score=193.06  Aligned_cols=162  Identities=22%  Similarity=0.233  Sum_probs=131.1

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHhhhhhhhC-CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHH
Q psy4275          13 LNPWLIRQCQTIGVKTPTEIQKAIIPHVLN-DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIG   91 (182)
Q Consensus        13 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~   91 (182)
                      +.....+.+...++..++|+|.++++.+.+ ++|+++++|||+|||+++.++++..+.+++ +.+++|++|+++|+.|.+
T Consensus       911 L~~~~~e~l~~~~f~~fnpiQ~q~~~~l~~~~~nvlv~APTGSGKTliaelail~~l~~~~-~~kavyi~P~raLa~q~~  989 (1724)
T 4f92_B          911 LRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSS-EGRCVYITPMEALAEQVY  989 (1724)
T ss_dssp             SCCHHHHTTTTTTCSBCCHHHHHHHHHHHSCCSCEEEECCTTSCCHHHHHHHHHHHHHHCT-TCCEEEECSCHHHHHHHH
T ss_pred             ccCHHHHHHHHhcCCCCCHHHHHHHHHHhcCCCcEEEEeCCCCCchHHHHHHHHHHHHhCC-CCEEEEEcChHHHHHHHH
Confidence            345566666666788999999999999876 678999999999999999999999887654 458999999999999998


Q ss_pred             HHHHH-hhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCC-CCCCccEEEEeccccccccCChhH
Q psy4275          92 DQFLV-LGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTF-SLNRIKFLVLDEADRLSLMTSLKF  169 (182)
Q Consensus        92 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~-~~~~~~~iI~DE~h~~~~~~~~~~  169 (182)
                      +.+++ +.+..|.+|..++|+...+..   ...+++|+|+||+++..+++++... .+++++++|+||+|.+.+..+...
T Consensus       990 ~~~~~~f~~~~g~~V~~ltGd~~~~~~---~~~~~~IiV~TPEkld~llr~~~~~~~l~~v~lvViDE~H~l~d~rg~~l 1066 (1724)
T 4f92_B          990 MDWYEKFQDRLNKKVVLLTGETSTDLK---LLGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLIGGENGPVL 1066 (1724)
T ss_dssp             HHHHHHHTTTSCCCEEECCSCHHHHHH---HHHHCSEEEECHHHHHHHHTTTTTCHHHHSCSEEEECCGGGGGSTTHHHH
T ss_pred             HHHHHHhchhcCCEEEEEECCCCcchh---hcCCCCEEEECHHHHHHHHhCcccccccceeeEEEeechhhcCCCCCccH
Confidence            88865 556689999999998764332   2346799999999998888775432 467899999999999988766555


Q ss_pred             HHHHHHHhh
Q psy4275         170 FFFFFFLKY  178 (182)
Q Consensus       170 ~~~~~~~~~  178 (182)
                      ...+.++++
T Consensus      1067 e~il~rl~~ 1075 (1724)
T 4f92_B         1067 EVICSRMRY 1075 (1724)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            666666654

>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=99.91  E-value=6.3e-24  Score=183.29  Aligned_cols=144  Identities=19%  Similarity=0.194  Sum_probs=118.6

Q ss_pred             HCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCC--CeeEEEEcCCHHHHHHHHHHHHHhhcc
Q psy4275          23 TIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPY--GIFALVLTPTRELAYQIGDQFLVLGKV  100 (182)
Q Consensus        23 ~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~--~~~~lil~p~~~l~~q~~~~~~~~~~~  100 (182)
                      ..+...|+|+|.++++.+.+|+++++++|||+|||.+++++++..+...+.  +.+++|++|+++|+.|+.+.+++++..
T Consensus       243 l~~~~~~r~~Q~~ai~~il~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~~~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~  322 (936)
T 4a2w_A          243 VYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFER  322 (936)
T ss_dssp             -----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHTTTTTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHT
T ss_pred             ccCCCCCCHHHHHHHHHHHcCCCEEEEeCCCchHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHHhcc
Confidence            345678999999999999999999999999999999999999888766532  568999999999999999999999988


Q ss_pred             CCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCC
Q psy4275         101 MNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTS  166 (182)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~  166 (182)
                      .++++..++|+.........+..+++|+|+||+.+.+.+.......+++++++|+||||++.+.+.
T Consensus       323 ~~~~v~~~~G~~~~~~~~~~~~~~~~IvI~Tp~~L~~~l~~~~~~~l~~~~liViDEaH~~~~~~~  388 (936)
T 4a2w_A          323 QGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHP  388 (936)
T ss_dssp             TTCCEEEECCC-----CCHHHHHHCSEEEECHHHHHHHHHSSSCCCGGGCSEEEEETGGGCSTTCH
T ss_pred             cCceEEEEECCcchhhHHHHhccCCCEEEecHHHHHHHHHcCccccccCCCEEEEECccccCCCcc
Confidence            899999999998766555555667899999999999999874333678899999999999998764

>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=99.90  E-value=5.1e-24  Score=185.90  Aligned_cols=152  Identities=15%  Similarity=0.121  Sum_probs=126.3

Q ss_pred             CCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHH
Q psy4275           6 KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRE   85 (182)
Q Consensus         6 ~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~   85 (182)
                      ..|+.++++..+...+...+...++|+|.++++.+.+++++++++|||+|||+++.++++..+..   +.+++|++|+++
T Consensus       162 ~~~~~~~l~~~~~~~~~~~~~f~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~~---g~rvlvl~Ptra  238 (1108)
T 3l9o_A          162 PNYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKN---KQRVIYTSPIKA  238 (1108)
T ss_dssp             SCCCSSTTTTTCCCSCSSCCSSCCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHHT---TCEEEEEESSHH
T ss_pred             CCcccCCCChhhhHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHhc---CCeEEEEcCcHH
Confidence            45666777777666666666668999999999999999999999999999999999999988755   569999999999


Q ss_pred             HHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccC
Q psy4275          86 LAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus        86 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~  165 (182)
                      |+.|+++.++..+.    .++.++|+...       ..+++|+|+||+.+.+++.. ....++++++||+||||++.+++
T Consensus       239 La~Q~~~~l~~~~~----~VglltGd~~~-------~~~~~IlV~Tpe~L~~~L~~-~~~~l~~l~lVVIDEaH~l~d~~  306 (1108)
T 3l9o_A          239 LSNQKYRELLAEFG----DVGLMTGDITI-------NPDAGCLVMTTEILRSMLYR-GSEVMREVAWVIFDEVHYMRDKE  306 (1108)
T ss_dssp             HHHHHHHHHHHHTS----SEEEECSSCBC-------CCSCSEEEEEHHHHHHHHHH-CSSHHHHEEEEEEETGGGTTSHH
T ss_pred             HHHHHHHHHHHHhC----CccEEeCcccc-------CCCCCEEEeChHHHHHHHHc-CccccccCCEEEEhhhhhccccc
Confidence            99999999988765    57778887752       34689999999999999877 44557789999999999998876


Q ss_pred             ChhHHHH
Q psy4275         166 SLKFFFF  172 (182)
Q Consensus       166 ~~~~~~~  172 (182)
                      +...+..
T Consensus       307 rg~~~e~  313 (1108)
T 3l9o_A          307 RGVVWEE  313 (1108)
T ss_dssp             HHHHHHH
T ss_pred             hHHHHHH
Confidence            5544443

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B

Probab=99.90  E-value=2.5e-23  Score=187.25  Aligned_cols=150  Identities=20%  Similarity=0.235  Sum_probs=121.9

Q ss_pred             CCCCChHHHHhhhhhhhC-CCcEEEECCCCChHHHHHHHHHHHhhccC--------CCCeeEEEEcCCHHHHHHHHHHHH
Q psy4275          25 GVKTPTEIQKAIIPHVLN-DEDCIGCAKTGSGKTLAFALPILQKWCED--------PYGIFALVLTPTRELAYQIGDQFL   95 (182)
Q Consensus        25 ~~~~~~~~Q~~~~~~~~~-~~~~li~~~tg~GKT~~~~~~~~~~~~~~--------~~~~~~lil~p~~~l~~q~~~~~~   95 (182)
                      |+..++++|.++++.+.. ++|+++++|||+|||.++.++++..+.+.        ..+.+++|++|+++|+.|..+.+.
T Consensus        76 g~~~ln~iQs~~~~~al~~~~N~lv~APTGsGKTlva~l~il~~l~~~~~~~~~~~~~~~k~lyiaP~kALa~e~~~~l~  155 (1724)
T 4f92_B           76 GFKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMVGSFG  155 (1724)
T ss_dssp             TCSBCCHHHHHTHHHHHTCCCCEEEECCTTSCCHHHHHHHHHHHHGGGCCTTSSCCTTSCEEEEECSSHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHcCCCcEEEEeCCcchHHHHHHHHHHHHHHhhccccccccCCCCEEEEECCHHHHHHHHHHHHH
Confidence            688999999999998765 88999999999999999999999887642        236689999999999999999999


Q ss_pred             HhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCC-CCCCCccEEEEeccccccccCChhHHHHHH
Q psy4275          96 VLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNT-FSLNRIKFLVLDEADRLSLMTSLKFFFFFF  174 (182)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~-~~~~~~~~iI~DE~h~~~~~~~~~~~~~~~  174 (182)
                      +.+...|++|..++|+.......   ..+++|+|+|||++..++++... ..+++++++|+||+|.+.+..+......+.
T Consensus       156 ~~~~~~gi~V~~~tGd~~~~~~~---~~~~~IlVtTpEkld~llr~~~~~~~l~~v~~vIiDEvH~l~d~RG~~lE~~l~  232 (1724)
T 4f92_B          156 KRLATYGITVAELTGDHQLCKEE---ISATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLHDDRGPVLEALVA  232 (1724)
T ss_dssp             HHHTTTTCCEEECCSSCSSCCTT---GGGCSEEEECHHHHHHHTTSSTTHHHHTTEEEEEETTGGGGGSTTHHHHHHHHH
T ss_pred             HHHhhCCCEEEEEECCCCCCccc---cCCCCEEEECHHHHHHHHcCCccchhhcCcCEEEEecchhcCCccHHHHHHHHH
Confidence            98888999999999988654321   34689999999999777766332 246789999999999887754434444455


Q ss_pred             HHh
Q psy4275         175 FLK  177 (182)
Q Consensus       175 ~~~  177 (182)
                      +++
T Consensus       233 rl~  235 (1724)
T 4f92_B          233 RAI  235 (1724)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            554

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.89  E-value=1.5e-22  Score=176.59  Aligned_cols=133  Identities=19%  Similarity=0.200  Sum_probs=113.2

Q ss_pred             HCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCC
Q psy4275          23 TIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMN  102 (182)
Q Consensus        23 ~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~  102 (182)
                      ..|+ +|+|+|.++++.+.+|+++++++|||+|||.+++.+++..+..   +.+++|++|+++|+.|+++.++.+. ..+
T Consensus        74 ~~gf-~pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~~~---~~~~Lil~PtreLa~Q~~~~l~~l~-~~~  148 (1104)
T 4ddu_A           74 KFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARK---GKKSALVFPTVTLVKQTLERLQKLA-DEK  148 (1104)
T ss_dssp             HSSS-CCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHHTT---TCCEEEEESSHHHHHHHHHHHHTTS-CTT
T ss_pred             hcCC-CCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHHhc---CCeEEEEechHHHHHHHHHHHHHhh-CCC
Confidence            3566 7999999999999999999999999999999888887776633   6799999999999999999999977 678


Q ss_pred             ceEEEEEcCCch---hhhhHHhcC-CCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275         103 LRVSIITGGMDM---VDQGKELAK-KPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus       103 ~~~~~~~~~~~~---~~~~~~~~~-~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      +++..++|+.+.   ......+.+ .++|+|+||+.+.+++..   +.+++++++|+||||++..
T Consensus       149 i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~---l~~~~l~~lViDEaH~l~~  210 (1104)
T 4ddu_A          149 VKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK---LSQKRFDFVFVDDVDAVLK  210 (1104)
T ss_dssp             SCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHH---HHTSCCSEEEESCHHHHTT
T ss_pred             CeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHh---hcccCcCEEEEeCCCcccc
Confidence            999999999876   334444544 499999999999888764   4567899999999988765

>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=99.88  E-value=7.8e-22  Score=157.94  Aligned_cols=134  Identities=25%  Similarity=0.354  Sum_probs=112.3

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSI  107 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  107 (182)
                      .|+|+|.++++.+.++ ++++.+|||+|||.+++.++...+..  .+.+++|++|+++|+.|+.+.++++....+.++..
T Consensus         9 ~l~~~Q~~~i~~~~~~-~~ll~~~tG~GKT~~~~~~~~~~~~~--~~~~~liv~P~~~L~~q~~~~~~~~~~~~~~~v~~   85 (494)
T 1wp9_A            9 QPRIYQEVIYAKCKET-NCLIVLPTGLGKTLIAMMIAEYRLTK--YGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVA   85 (494)
T ss_dssp             CCCHHHHHHHHHGGGS-CEEEECCTTSCHHHHHHHHHHHHHHH--SCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEE
T ss_pred             CccHHHHHHHHHHhhC-CEEEEcCCCCCHHHHHHHHHHHHHhc--CCCeEEEEECCHHHHHHHHHHHHHHhCcchhheEE
Confidence            6999999999999988 99999999999999999888877652  25689999999999999999999887544568888


Q ss_pred             EEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCC
Q psy4275         108 ITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTS  166 (182)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~  166 (182)
                      ++|+....... ...++++|+|+||+.+...+.. ..+...+++++|+||||++.+...
T Consensus        86 ~~g~~~~~~~~-~~~~~~~ivv~T~~~l~~~~~~-~~~~~~~~~~vIiDEaH~~~~~~~  142 (494)
T 1wp9_A           86 LTGEKSPEERS-KAWARAKVIVATPQTIENDLLA-GRISLEDVSLIVFDEAHRAVGNYA  142 (494)
T ss_dssp             ECSCSCHHHHH-HHHHHCSEEEECHHHHHHHHHT-TSCCTTSCSEEEEETGGGCSTTCH
T ss_pred             eeCCcchhhhh-hhccCCCEEEecHHHHHHHHhc-CCcchhhceEEEEECCcccCCCCc
Confidence            88887655433 3345789999999999998876 556778899999999999986543

>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=99.88  E-value=2.9e-22  Score=174.53  Aligned_cols=135  Identities=24%  Similarity=0.306  Sum_probs=114.4

Q ss_pred             HHHH-HCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHh
Q psy4275          19 RQCQ-TIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVL   97 (182)
Q Consensus        19 ~~l~-~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~   97 (182)
                      +.+. .+|+. | ++|.++++.+.+|+++++++|||+|||. +.++++..+...  +++++|++|+++|+.|+++.++.+
T Consensus        48 ~~~~~~~g~~-p-~iQ~~ai~~il~g~dvlv~apTGSGKTl-~~lp~l~~~~~~--~~~~lil~PtreLa~Q~~~~l~~l  122 (1054)
T 1gku_B           48 EFFRKCVGEP-R-AIQKMWAKRILRKESFAATAPTGVGKTS-FGLAMSLFLALK--GKRCYVIFPTSLLVIQAAETIRKY  122 (1054)
T ss_dssp             HHHHTTTCSC-C-HHHHHHHHHHHTTCCEECCCCBTSCSHH-HHHHHHHHHHTT--SCCEEEEESCHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCCC-H-HHHHHHHHHHHhCCCEEEEcCCCCCHHH-HHHHHHHHHhhc--CCeEEEEeccHHHHHHHHHHHHHH
Confidence            4443 47888 9 9999999999999999999999999998 677777666543  678999999999999999999999


Q ss_pred             hccCCc----eEEEEEcCCchhhh---hHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccccc
Q psy4275          98 GKVMNL----RVSIITGGMDMVDQ---GKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus        98 ~~~~~~----~~~~~~~~~~~~~~---~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~  164 (182)
                      ....++    ++..++|+.+...+   ...+.+ ++|+|+||+.+.+++..     +++++++|+||||+|.++
T Consensus       123 ~~~~~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~-~~IlV~TP~~L~~~l~~-----L~~l~~lViDEah~~l~~  190 (1054)
T 1gku_B          123 AEKAGVGTENLIGYYHGRIPKREKENFMQNLRN-FKIVITTTQFLSKHYRE-----LGHFDFIFVDDVDAILKA  190 (1054)
T ss_dssp             HTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGG-CSEEEEEHHHHHHCSTT-----SCCCSEEEESCHHHHHTS
T ss_pred             HhhcCCCccceEEEEeCCCChhhHHHHHhhccC-CCEEEEcHHHHHHHHHH-----hccCCEEEEeChhhhhhc
Confidence            988888    89999998876553   233344 99999999999987765     568999999999999984

>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=99.88  E-value=6.5e-22  Score=165.93  Aligned_cols=134  Identities=25%  Similarity=0.246  Sum_probs=114.3

Q ss_pred             HCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCC
Q psy4275          23 TIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMN  102 (182)
Q Consensus        23 ~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~  102 (182)
                      ..|+ .|+|.|..+++.+..|+  +.+++||+|||+++.++++.....   +..++|++|+++||.|.++++..+.+.+|
T Consensus        79 ~lG~-~pt~VQ~~~ip~ll~G~--Iaea~TGeGKTlaf~LP~~l~aL~---g~~vlVltptreLA~qd~e~~~~l~~~lg  152 (844)
T 1tf5_A           79 VTGM-FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALT---GKGVHVVTVNEYLASRDAEQMGKIFEFLG  152 (844)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTT---SSCEEEEESSHHHHHHHHHHHHHHHHHTT
T ss_pred             HcCC-CCcHHHHHhhHHHhCCC--EEEccCCcHHHHHHHHHHHHHHHc---CCCEEEEeCCHHHHHHHHHHHHHHHhhcC
Confidence            5788 99999999999999988  999999999999999999854443   55899999999999999999999999999


Q ss_pred             ceEEEEEcCCchhhhhHHhcCCCcEEEEChHHH-HHHHhcC-----CCCCCCCccEEEEecccccc-cc
Q psy4275         103 LRVSIITGGMDMVDQGKELAKKPHIVIATPGRL-ADHLDTC-----NTFSLNRIKFLVLDEADRLS-LM  164 (182)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l-~~~~~~~-----~~~~~~~~~~iI~DE~h~~~-~~  164 (182)
                      +++.++.|+.+...+..  ..+++|+|+||+.+ .++++..     ....++.+.++|+||||.|+ +.
T Consensus       153 l~v~~i~gg~~~~~r~~--~~~~dIv~gTpgrlgfD~L~D~m~~~~~~l~lr~~~~lVlDEaD~mLiDe  219 (844)
T 1tf5_A          153 LTVGLNLNSMSKDEKRE--AYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDE  219 (844)
T ss_dssp             CCEEECCTTSCHHHHHH--HHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTT
T ss_pred             CeEEEEeCCCCHHHHHH--hcCCCEEEECchhhhHHHHHHhhhcchhhhcccCCCEEEECchhhhhhhc
Confidence            99999999887544333  34689999999999 6776653     13467889999999999998 54

>4gl2_A Interferon-induced helicase C domain-containing P; MDA5, dsRNA, anti-viral signaling, RIG-I, MAVS, oligomerizat helicase, ATPase; HET: ANP; 3.56A {Homo sapiens}

Probab=99.88  E-value=7.5e-23  Score=171.88  Aligned_cols=139  Identities=20%  Similarity=0.168  Sum_probs=112.0

Q ss_pred             CCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCC---CCeeEEEEcCCHHHHHHH-HHHHHHhhccCC
Q psy4275          27 KTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP---YGIFALVLTPTRELAYQI-GDQFLVLGKVMN  102 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~---~~~~~lil~p~~~l~~q~-~~~~~~~~~~~~  102 (182)
                      ..|+|+|.++++.+.+++++++.+|||+|||+++++++...+....   .+.+++|++|+++|+.|+ .+.+++++.. +
T Consensus         6 ~~l~~~Q~~~i~~il~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~vlvl~P~~~L~~Q~~~~~l~~~~~~-~   84 (699)
T 4gl2_A            6 LQLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKK-W   84 (699)
T ss_dssp             -CCCHHHHHHHHHHHSSCCEEECCCTTSCHHHHHHHHHHHHHHHHHHHTCCCCBCCEESCSHHHHHHHHHTHHHHHTT-T
T ss_pred             CCccHHHHHHHHHHHhCCCEEEEcCCCCcHHHHHHHHHHHHHHhccccCCCCeEEEEECCHHHHHHHHHHHHHHHcCc-C
Confidence            3799999999999999999999999999999999999988765432   236899999999999999 9999998775 5


Q ss_pred             ceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhc-----CCCCCCCCccEEEEeccccccccCC
Q psy4275         103 LRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDT-----CNTFSLNRIKFLVLDEADRLSLMTS  166 (182)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~-----~~~~~~~~~~~iI~DE~h~~~~~~~  166 (182)
                      +++..++|+.........+.++++|+|+||+.+.+.+..     ...+.+.++++||+||||++.....
T Consensus        85 ~~v~~~~g~~~~~~~~~~~~~~~~Ilv~Tp~~L~~~l~~~~~~~~~~~~~~~~~lvViDEaH~~~~~~~  153 (699)
T 4gl2_A           85 YRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAV  153 (699)
T ss_dssp             SCEEEEC----CCCCHHHHHHSCSEEEEEHHHHHHHTC--------CCCGGGCSEEEEESGGGCBTTBS
T ss_pred             ceEEEEeCCcchhhHHHhhhcCCCEEEECHHHHHHHHhccccccccceecccCcEEEEECccccCccch
Confidence            889999988776555555567899999999999988842     2445678899999999999976553

>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=99.87  E-value=1e-21  Score=165.96  Aligned_cols=139  Identities=22%  Similarity=0.290  Sum_probs=114.8

Q ss_pred             HHHHHHHHHCCCCCChHHHHhhhhhhhCC------CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHH
Q psy4275          15 PWLIRQCQTIGVKTPTEIQKAIIPHVLND------EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAY   88 (182)
Q Consensus        15 ~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~------~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~   88 (182)
                      +.+.+.+..+++ +++++|.++++.+.++      .+.++++|||+|||.+++++++..+.+   +.++++++|+++|+.
T Consensus       356 ~~~~~~~~~lpf-~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~---g~qvlvlaPtr~La~  431 (780)
T 1gm5_A          356 KLAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA---GFQTAFMVPTSILAI  431 (780)
T ss_dssp             HHHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH---TSCEEEECSCHHHHH
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHc---CCeEEEEeCcHHHHH
Confidence            455566678888 9999999999988764      589999999999999999999987765   568999999999999


Q ss_pred             HHHHHHHHhhccCCceEEEEEcCCchhhhhHH---h-cCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275          89 QIGDQFLVLGKVMNLRVSIITGGMDMVDQGKE---L-AKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus        89 q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~-~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      |+++.++++....++++..++|+.........   + .+.++|+|+||+.+.+      ...+++++++|+||+|++..
T Consensus       432 Q~~~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~------~~~~~~l~lVVIDEaHr~g~  504 (780)
T 1gm5_A          432 QHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE------DVHFKNLGLVIIDEQHRFGV  504 (780)
T ss_dssp             HHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH------CCCCSCCCEEEEESCCCC--
T ss_pred             HHHHHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhh------hhhccCCceEEecccchhhH
Confidence            99999999998889999999998876543322   2 2368999999987743      23577899999999999754

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.87  E-value=1.1e-21  Score=170.00  Aligned_cols=135  Identities=18%  Similarity=0.169  Sum_probs=113.3

Q ss_pred             HCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCC
Q psy4275          23 TIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMN  102 (182)
Q Consensus        23 ~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~  102 (182)
                      .+++ +++|+|.++++.+.+++++++++|||+|||+++.+++...+..   +.+++|++|+++|++|+++.++..+.   
T Consensus        82 ~~~f-~L~~~Q~eai~~l~~g~~vLV~apTGSGKTlva~lai~~~l~~---g~rvL~l~PtkaLa~Q~~~~l~~~~~---  154 (1010)
T 2xgj_A           82 TYPF-TLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKN---KQRVIYTSPIKALSNQKYRELLAEFG---  154 (1010)
T ss_dssp             CCSS-CCCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHHT---TCEEEEEESSHHHHHHHHHHHHHHHS---
T ss_pred             hCCC-CCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhcc---CCeEEEECChHHHHHHHHHHHHHHhC---
Confidence            3455 5999999999999999999999999999999998888876644   56999999999999999999888765   


Q ss_pred             ceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHHHHH
Q psy4275         103 LRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFF  173 (182)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~~~~  173 (182)
                       +++.++|+....       .+++|+|+||+.+.+++.+ ....++++++||+||+|++.+++....+..+
T Consensus       155 -~vglltGd~~~~-------~~~~IvV~Tpe~L~~~L~~-~~~~l~~l~lVViDEaH~l~d~~rg~~~e~i  216 (1010)
T 2xgj_A          155 -DVGLMTGDITIN-------PDAGCLVMTTEILRSMLYR-GSEVMREVAWVIFDEVHYMRDKERGVVWEET  216 (1010)
T ss_dssp             -CEEEECSSCEEC-------TTCSEEEEEHHHHHHHHHH-TCTTGGGEEEEEEETGGGGGCTTTHHHHHHH
T ss_pred             -CEEEEeCCCccC-------CCCCEEEEcHHHHHHHHHc-CcchhhcCCEEEEechhhhcccchhHHHHHH
Confidence             677888877532       3678999999999988876 4456788999999999999988765555443

>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=99.87  E-value=3.2e-22  Score=151.41  Aligned_cols=128  Identities=20%  Similarity=0.160  Sum_probs=102.4

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSI  107 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  107 (182)
                      .++++|.++++.+.++++.++++|||+|||.+++.++...+...  ..+++|++|+++|++|+.+.++++....+..+..
T Consensus       113 ~l~~~Q~~ai~~~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~--~~~~lil~Pt~~L~~q~~~~l~~~~~~~~~~~~~  190 (282)
T 1rif_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENY--EGKILIIVPTTALTTQMADDFVDYRLFSHAMIKK  190 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHC--SSEEEEECSSHHHHHHHHHHHHHHTSCCGGGEEE
T ss_pred             CccHHHHHHHHHHHhcCCeEEEcCCCCCcHHHHHHHHHHHHHcC--CCeEEEEECCHHHHHHHHHHHHHhcccccceEEE
Confidence            79999999999988888899999999999999977776655432  3489999999999999999999987766677777


Q ss_pred             EEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccccc
Q psy4275         108 ITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~  164 (182)
                      +.++.....   ....+.+|+|+||+.+....    ....++++++|+||||++.+.
T Consensus       191 ~~~~~~~~~---~~~~~~~I~v~T~~~l~~~~----~~~~~~~~~vIiDEaH~~~~~  240 (282)
T 1rif_A          191 IGGGASKDD---KYKNDAPVVVGTWQTVVKQP----KEWFSQFGMMMNDECHLATGK  240 (282)
T ss_dssp             CSTTCSSTT---CCCTTCSEEEECHHHHTTSC----GGGGGGEEEEEEETGGGCCHH
T ss_pred             EeCCCcchh---hhccCCcEEEEchHHHHhhH----HHHHhhCCEEEEECCccCCcc
Confidence            777664332   22357899999999874432    224667899999999999854

>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=99.85  E-value=4.3e-21  Score=160.79  Aligned_cols=133  Identities=23%  Similarity=0.179  Sum_probs=113.4

Q ss_pred             CCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q psy4275          24 IGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNL  103 (182)
Q Consensus        24 ~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  103 (182)
                      .|. +|+|.|..+++.+..|+  +.+++||+|||+++.++++.....   +.+++|++||+.||.|.++++..+.+.+++
T Consensus        71 lg~-~p~~VQ~~~i~~ll~G~--Iaem~TGsGKTlaf~LP~l~~~l~---g~~vlVltPTreLA~Q~~e~~~~l~~~lgl  144 (853)
T 2fsf_A           71 FGM-RHFDVQLLGGMVLNERC--IAEMRTGEGKTLTATLPAYLNALT---GKGVHVVTVNDYLAQRDAENNRPLFEFLGL  144 (853)
T ss_dssp             HSC-CCCHHHHHHHHHHHSSE--EEECCTTSCHHHHHHHHHHHHHTT---SSCCEEEESSHHHHHHHHHHHHHHHHHTTC
T ss_pred             cCC-CCChHHHhhcccccCCe--eeeecCCchHHHHHHHHHHHHHHc---CCcEEEEcCCHHHHHHHHHHHHHHHHhcCC
Confidence            464 89999999999999987  999999999999999999865544   558999999999999999999999999999


Q ss_pred             eEEEEEcCCchhhhhHHhcCCCcEEEEChHHH-HHHHhcCC-----CCCCCCccEEEEecccccccc
Q psy4275         104 RVSIITGGMDMVDQGKELAKKPHIVIATPGRL-ADHLDTCN-----TFSLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l-~~~~~~~~-----~~~~~~~~~iI~DE~h~~~~~  164 (182)
                      ++.++.|+.+....  ....+++|+|+||+.+ .++++..-     ...++++.++|+||+|.|+.+
T Consensus       145 ~v~~i~GG~~~~~r--~~~~~~dIvvgTpgrl~fDyLrd~~~~~~~~~~~~~l~~lVlDEaD~mLiD  209 (853)
T 2fsf_A          145 TVGINLPGMPAPAK--REAYAADITYGTNNEYGFDYLRDNMAFSPEERVQRKLHYALVDEVDSILID  209 (853)
T ss_dssp             CEEECCTTCCHHHH--HHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCSCCEEEESCHHHHTTT
T ss_pred             eEEEEeCCCCHHHH--HHhcCCCEEEECCchhhHHHHHhhhhccHhHhcccCCcEEEECchHHHHHh
Confidence            99999998875433  3334689999999999 78887632     246788999999999999943

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.85  E-value=3.5e-21  Score=166.75  Aligned_cols=132  Identities=17%  Similarity=0.197  Sum_probs=110.8

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSI  107 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  107 (182)
                      +++|+|.++++.+.+++++++++|||+|||+++.+++......   +.+++|++|+++|+.|+++.++..+.  ++++..
T Consensus        39 ~l~~~Q~~aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~~---g~~vlvl~PtraLa~Q~~~~l~~~~~--~~~v~~  113 (997)
T 4a4z_A           39 ELDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHRN---MTKTIYTSPIKALSNQKFRDFKETFD--DVNIGL  113 (997)
T ss_dssp             CCCHHHHHHHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHHT---TCEEEEEESCGGGHHHHHHHHHTTC----CCEEE
T ss_pred             CCCHHHHHHHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHhc---CCeEEEEeCCHHHHHHHHHHHHHHcC--CCeEEE
Confidence            6999999999999999999999999999999988887776544   56899999999999999998888654  578888


Q ss_pred             EEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHHHH
Q psy4275         108 ITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFF  172 (182)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~~~  172 (182)
                      ++|+...       ..+.+|+|+||+.+.+.+.. ....++++++||+||+|++.++++...+..
T Consensus       114 l~G~~~~-------~~~~~IlV~Tpe~L~~~l~~-~~~~l~~l~lvViDEaH~l~d~~~g~~~e~  170 (997)
T 4a4z_A          114 ITGDVQI-------NPDANCLIMTTEILRSMLYR-GADLIRDVEFVIFDEVHYVNDQDRGVVWEE  170 (997)
T ss_dssp             ECSSCEE-------CTTSSEEEEEHHHHHHHHHH-TCSGGGGEEEEEECCTTCCCTTCTTCCHHH
T ss_pred             EeCCCcc-------CCCCCEEEECHHHHHHHHHh-CchhhcCCCEEEEECcccccccchHHHHHH
Confidence            8887753       24579999999999998876 445678899999999999999876554443

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.85  E-value=6.2e-21  Score=155.02  Aligned_cols=128  Identities=20%  Similarity=0.163  Sum_probs=105.7

Q ss_pred             CCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEE
Q psy4275          27 KTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVS  106 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~  106 (182)
                      .+++|+|.++++.+.++++.++++|||+|||.+++.++...+...  +.+++|++|+++|+.|+.+.++++....+.++.
T Consensus       112 ~~l~~~Q~~ai~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~--~~~vlvl~P~~~L~~Q~~~~~~~~~~~~~~~v~  189 (510)
T 2oca_A          112 IEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENY--EGKILIIVPTTALTTQMADDFVDYRLFSHAMIK  189 (510)
T ss_dssp             ECCCHHHHHHHHHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHHC--SSEEEEEESSHHHHHHHHHHHHHTTSSCGGGEE
T ss_pred             CCCCHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhCC--CCeEEEEECcHHHHHHHHHHHHHhhcCCccceE
Confidence            379999999999999989999999999999999988877765442  349999999999999999999888666667888


Q ss_pred             EEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275         107 IITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      .+.|+......   ...+.+|+|+||+.+...    ....++++++||+||+|++.+
T Consensus       190 ~~~~~~~~~~~---~~~~~~I~i~T~~~l~~~----~~~~~~~~~liIiDE~H~~~~  239 (510)
T 2oca_A          190 KIGGGASKDDK---YKNDAPVVVGTWQTVVKQ----PKEWFSQFGMMMNDECHLATG  239 (510)
T ss_dssp             ECGGGCCTTGG---GCTTCSEEEEEHHHHTTS----CGGGGGGEEEEEEETGGGCCH
T ss_pred             EEecCCccccc---cccCCcEEEEeHHHHhhc----hhhhhhcCCEEEEECCcCCCc
Confidence            88887655443   456789999999976432    223567899999999999887

>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=99.85  E-value=1.2e-20  Score=158.48  Aligned_cols=134  Identities=20%  Similarity=0.217  Sum_probs=113.9

Q ss_pred             HCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCC
Q psy4275          23 TIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMN  102 (182)
Q Consensus        23 ~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~  102 (182)
                      ..|+ +|+|.|..+++.+..|+  +.+++||+|||+++.++++.....   +..++|++|++.||.|.++++..+.+.+|
T Consensus       107 ~lG~-rP~~VQ~~~ip~Ll~G~--Iaem~TGeGKTLa~~LP~~l~aL~---g~~v~VvTpTreLA~Qdae~m~~l~~~lG  180 (922)
T 1nkt_A          107 VLDQ-RPFDVQVMGAAALHLGN--VAEMKTGEGKTLTCVLPAYLNALA---GNGVHIVTVNDYLAKRDSEWMGRVHRFLG  180 (922)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTTE--EEECCTTSCHHHHTHHHHHHHHTT---TSCEEEEESSHHHHHHHHHHHHHHHHHTT
T ss_pred             HcCC-CCCHHHHHHHHhHhcCC--EEEecCCCccHHHHHHHHHHHHHh---CCCeEEEeCCHHHHHHHHHHHHHHHhhcC
Confidence            4577 99999999999999887  999999999999999999755444   45799999999999999999999999999


Q ss_pred             ceEEEEEcCCchhhhhHHhcCCCcEEEEChHHH-HHHHhcCC-----CCCCCCccEEEEecccccccc
Q psy4275         103 LRVSIITGGMDMVDQGKELAKKPHIVIATPGRL-ADHLDTCN-----TFSLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l-~~~~~~~~-----~~~~~~~~~iI~DE~h~~~~~  164 (182)
                      ++++++.|+.+......  ..+++|+++||+.+ .++++..-     ...++.+.++|+||+|.|+.+
T Consensus       181 Lsv~~i~gg~~~~~r~~--~y~~DIvygTpgrlgfDyLrD~m~~~~~~l~lr~l~~lIVDEaDsmLiD  246 (922)
T 1nkt_A          181 LQVGVILATMTPDERRV--AYNADITYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVDEVDSILID  246 (922)
T ss_dssp             CCEEECCTTCCHHHHHH--HHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEETTHHHHHTT
T ss_pred             CeEEEEeCCCCHHHHHH--hcCCCEEEECchHhhHHHHHhhhhccHhhhccCCCCEEEEeChHHHHHh
Confidence            99999999887543333  33689999999999 78887631     356778999999999999843

>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=99.83  E-value=2.8e-20  Score=149.81  Aligned_cols=118  Identities=21%  Similarity=0.232  Sum_probs=99.8

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCce-EE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLR-VS  106 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~-~~  106 (182)
                      .|+|+|.++++.+.+++++++++|||+|||.+++.++...      +.+++|++|+++|+.|+.+.++++    +.+ +.
T Consensus        93 ~l~~~Q~~ai~~i~~~~~~ll~~~TGsGKT~~~l~~i~~~------~~~~Lvl~P~~~L~~Q~~~~~~~~----~~~~v~  162 (472)
T 2fwr_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL------STPTLIVVPTLALAEQWKERLGIF----GEEYVG  162 (472)
T ss_dssp             CBCHHHHHHHHHHTTTTEEEEECCTTSCHHHHHHHHHHHH------CSCEEEEESSHHHHHHHHHHGGGG----CGGGEE
T ss_pred             CcCHHHHHHHHHHHhcCCEEEEeCCCCCHHHHHHHHHHHc------CCCEEEEECCHHHHHHHHHHHHhC----CCcceE
Confidence            6999999999999998899999999999999998887765      458999999999999998888773    777 88


Q ss_pred             EEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChh
Q psy4275         107 IITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLK  168 (182)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~  168 (182)
                      .++|+..         ...+|+|+|++.+.......    .+++++||+||+|++.+..+..
T Consensus       163 ~~~g~~~---------~~~~Ivv~T~~~l~~~~~~~----~~~~~liIvDEaH~~~~~~~~~  211 (472)
T 2fwr_A          163 EFSGRIK---------ELKPLTVSTYDSAYVNAEKL----GNRFMLLIFDEVHHLPAESYVQ  211 (472)
T ss_dssp             EBSSSCB---------CCCSEEEEEHHHHHHTHHHH----TTTCSEEEEETGGGTTSTTTHH
T ss_pred             EECCCcC---------CcCCEEEEEcHHHHHHHHHh----cCCCCEEEEECCcCCCChHHHH
Confidence            8887664         25789999999998766541    2458999999999999887754

>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=99.83  E-value=5.7e-20  Score=135.84  Aligned_cols=118  Identities=21%  Similarity=0.232  Sum_probs=97.2

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCce-EE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLR-VS  106 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~-~~  106 (182)
                      .++++|.+++..+.++++.++++|||+|||.+++.++...      +.+++|++|+++|+.|+.+.++++    +.+ +.
T Consensus        93 ~l~~~Q~~ai~~~~~~~~~ll~~~tG~GKT~~a~~~~~~~------~~~~liv~P~~~L~~q~~~~~~~~----~~~~v~  162 (237)
T 2fz4_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL------STPTLIVVPTLALAEQWKERLGIF----GEEYVG  162 (237)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHHS------CSCEEEEESSHHHHHHHHHHHGGG----CGGGEE
T ss_pred             CcCHHHHHHHHHHHhCCCEEEEeCCCCCHHHHHHHHHHHc------CCCEEEEeCCHHHHHHHHHHHHhC----CCCeEE
Confidence            7899999999999998889999999999999988777654      457999999999999998887773    677 77


Q ss_pred             EEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChh
Q psy4275         107 IITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLK  168 (182)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~  168 (182)
                      .+.|+..         ...+|+|+|++.+.......    ..+++++|+||+|++.+..+..
T Consensus       163 ~~~g~~~---------~~~~i~v~T~~~l~~~~~~~----~~~~~llIiDEaH~l~~~~~~~  211 (237)
T 2fz4_A          163 EFSGRIK---------ELKPLTVSTYDSAYVNAEKL----GNRFMLLIFDEVHHLPAESYVQ  211 (237)
T ss_dssp             EESSSCB---------CCCSEEEEEHHHHHHTHHHH----TTTCSEEEEECSSCCCTTTHHH
T ss_pred             EEeCCCC---------CcCCEEEEeHHHHHhhHHHh----cccCCEEEEECCccCCChHHHH
Confidence            7777653         25689999999987766541    2458899999999998776544

>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=99.82  E-value=2.6e-19  Score=157.06  Aligned_cols=144  Identities=24%  Similarity=0.197  Sum_probs=113.0

Q ss_pred             CCCCCHHHHHHHH-HCCCCCChHHHHhhhhhhhC----CC--cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcC
Q psy4275          10 DLKLNPWLIRQCQ-TIGVKTPTEIQKAIIPHVLN----DE--DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTP   82 (182)
Q Consensus        10 ~~~l~~~i~~~l~-~~~~~~~~~~Q~~~~~~~~~----~~--~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p   82 (182)
                      .++.+....+.+. .+++ +++|+|.++++.+.+    ++  +.+++++||+|||.+++.++......   +.+++|++|
T Consensus       585 ~~~~~~~~~~~~~~~f~~-~~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~~---g~~vlvlvP  660 (1151)
T 2eyq_A          585 AFKHDREQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDN---HKQVAVLVP  660 (1151)
T ss_dssp             CCCCCHHHHHHHHHTCCS-CCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTT---TCEEEEECS
T ss_pred             CCCCCHHHHHHHHHhCCC-CCCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHHh---CCeEEEEec
Confidence            3456666666664 4566 579999999998876    55  89999999999999998887776544   569999999


Q ss_pred             CHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHH---hc-CCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecc
Q psy4275          83 TRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKE---LA-KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEA  158 (182)
Q Consensus        83 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~-~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~  158 (182)
                      +++|+.|+++.+++.+...++++..+++..+.......   +. +.++|+|+||+.+.      +...+++++++|+||+
T Consensus       661 t~~La~Q~~~~~~~~~~~~~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~------~~~~~~~l~lvIiDEa  734 (1151)
T 2eyq_A          661 TTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ------SDVKFKDLGLLIVDEE  734 (1151)
T ss_dssp             SHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH------SCCCCSSEEEEEEESG
T ss_pred             hHHHHHHHHHHHHHHhhcCCCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHh------CCccccccceEEEech
Confidence            99999999999999888888999998876654433222   22 36899999998652      2345788999999999


Q ss_pred             ccccc
Q psy4275         159 DRLSL  163 (182)
Q Consensus       159 h~~~~  163 (182)
                      |++..
T Consensus       735 H~~g~  739 (1151)
T 2eyq_A          735 HRFGV  739 (1151)
T ss_dssp             GGSCH
T ss_pred             HhcCh
Confidence            99643

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.82  E-value=1.1e-19  Score=152.57  Aligned_cols=134  Identities=22%  Similarity=0.219  Sum_probs=113.9

Q ss_pred             CCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q psy4275          24 IGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNL  103 (182)
Q Consensus        24 ~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  103 (182)
                      .|+ .|++.|..+++.+..|+  +.++.||+|||+++.++++.....   +.+++|++||+.||.|.++++..+.+.+|+
T Consensus        76 lG~-~Pt~VQ~~~ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~aL~---G~qv~VvTPTreLA~Qdae~m~~l~~~lGL  149 (997)
T 2ipc_A           76 LGM-RHFDVQLIGGAVLHEGK--IAEMKTGEGKTLVATLAVALNALT---GKGVHVVTVNDYLARRDAEWMGPVYRGLGL  149 (997)
T ss_dssp             TCC-CCCHHHHHHHHHHHTTS--EEECCSTHHHHHHHHHHHHHHHTT---CSCCEEEESSHHHHHHHHHHHHHHHHTTTC
T ss_pred             hCC-CCcHHHHhhcccccCCc--eeeccCCCchHHHHHHHHHHHHHh---CCCEEEEeCCHHHHHHHHHHHHHHHHhcCC
Confidence            577 89999999999999987  999999999999999999654444   457999999999999999999999999999


Q ss_pred             eEEEEEcCCchhhhhHHhcCCCcEEEEChHHH-HHHHhcCC-----CCCCC---CccEEEEeccccccccC
Q psy4275         104 RVSIITGGMDMVDQGKELAKKPHIVIATPGRL-ADHLDTCN-----TFSLN---RIKFLVLDEADRLSLMT  165 (182)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l-~~~~~~~~-----~~~~~---~~~~iI~DE~h~~~~~~  165 (182)
                      +++++.|+.+......  ..+++|+|+||+.+ .++++...     ...++   .+.++|+||+|.|+.+.
T Consensus       150 sv~~i~Gg~~~~~r~~--ay~~DIvyGTpgrlgfDyLrd~m~~~~~~l~~r~d~~l~~lIIDEaDsmLiDe  218 (997)
T 2ipc_A          150 SVGVIQHASTPAERRK--AYLADVTYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAIIDEVDSILIDE  218 (997)
T ss_dssp             CEEECCTTCCHHHHHH--HHTSSEEEEEHHHHHHHHHHHTSCSSTTTCCSCSSSSSCEEEETTHHHHTTSS
T ss_pred             eEEEEeCCCCHHHHHH--HcCCCEEEECchhhhhHHHHHhhhcchhhcccccCCCcceEEEechHHHHHhC
Confidence            9999999887543333  34689999999999 88887742     24567   89999999999998443

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=99.82  E-value=1.4e-19  Score=133.44  Aligned_cols=127  Identities=17%  Similarity=0.164  Sum_probs=97.6

Q ss_pred             CCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCC--CeeEEEEcCCHHHHHHHHHHHHHhhc-cCC
Q psy4275          26 VKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPY--GIFALVLTPTRELAYQIGDQFLVLGK-VMN  102 (182)
Q Consensus        26 ~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~--~~~~lil~p~~~l~~q~~~~~~~~~~-~~~  102 (182)
                      ...++++|.++++.+.+|++++++||||+|||+.+..+++......+.  +.++++++|+++++.|+.+.+..... ..+
T Consensus        59 ~~p~~~~q~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~~~~~~~~~~~~~~  138 (235)
T 3llm_A           59 LLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPG  138 (235)
T ss_dssp             TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHHHHHHHHTTTCCTT
T ss_pred             cCChHHHHHHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHHHHHHHHHhccccC
Confidence            346899999999999999999999999999999888888876655433  45899999999999999877765433 334


Q ss_pred             ceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccc
Q psy4275         103 LRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL  161 (182)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~  161 (182)
                      ..++......     ......+++|+|+||+.+.+.+..    .+++++++|+||+|++
T Consensus       139 ~~~g~~~~~~-----~~~~~~~~~Ivv~Tpg~l~~~l~~----~l~~~~~lVlDEah~~  188 (235)
T 3llm_A          139 KSCGYSVRFE-----SILPRPHASIMFCTVGVLLRKLEA----GIRGISHVIVDEIHER  188 (235)
T ss_dssp             SSEEEEETTE-----EECCCSSSEEEEEEHHHHHHHHHH----CCTTCCEEEECCTTSC
T ss_pred             ceEEEeechh-----hccCCCCCeEEEECHHHHHHHHHh----hhcCCcEEEEECCccC
Confidence            4443322111     111124678999999999999876    3788999999999985

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.75  E-value=4.8e-18  Score=139.45  Aligned_cols=130  Identities=22%  Similarity=0.079  Sum_probs=100.9

Q ss_pred             CChHHHHhhhhhh----hCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q psy4275          28 TPTEIQKAIIPHV----LNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNL  103 (182)
Q Consensus        28 ~~~~~Q~~~~~~~----~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  103 (182)
                      +++|+|.+++..+    ..++++++++|||+|||.+++++++..      +.+++|++||++|+.|+.+.++.+.+..++
T Consensus         3 ~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~~------~~~v~i~~pt~~l~~q~~~~~~~l~~~~~~   76 (551)
T 3crv_A            3 KLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLEV------KPKVLFVVRTHNEFYPIYRDLTKIREKRNI   76 (551)
T ss_dssp             SCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHHH------CSEEEEEESSGGGHHHHHHHHTTCCCSSCC
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHhC------CCeEEEEcCCHHHHHHHHHHHHHHhhhcCc
Confidence            6899999977654    458999999999999999999999882      569999999999999999999988877788


Q ss_pred             eEEEEEcCCch---------------------------------hhh------------------hHHhcCCCcEEEECh
Q psy4275         104 RVSIITGGMDM---------------------------------VDQ------------------GKELAKKPHIVIATP  132 (182)
Q Consensus       104 ~~~~~~~~~~~---------------------------------~~~------------------~~~~~~~~~Ilv~T~  132 (182)
                      ++..+.|....                                 +..                  .+.....++|+|+|+
T Consensus        77 ~~~~l~gr~~~c~~~~~~~~~~~~~c~~c~~~~~~~~~g~~~~~~~~~~~~~~~G~~~~~Cpy~~ar~~~~~adIVV~~~  156 (551)
T 3crv_A           77 TFSFLVGKPSSCLYAEKGAESEDIPCKYCELKGSIVEVKTDDSPLSLVKKLKKDGLQDKFCPYYSLLNSLYKADVIALTY  156 (551)
T ss_dssp             CEEECCCHHHHCTTBCTTCCGGGCCGGGCTTTTCCCCCCCCSCHHHHHHHHHHHHHHHTCCHHHHHHHHGGGCSEEEEET
T ss_pred             cEEEEccccccCcCchhcCCCcccccCCCCCccccccccccCCHHHHHHHHHHcCCcCCcCccHHHHhhhhcCCEEEeCc
Confidence            88887763321                                 000                  122234679999999


Q ss_pred             HHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275         133 GRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus       133 ~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      ..+.+...+...........+||||||++.+
T Consensus       157 ~~l~~~~~~~~~~~~~~~~~vIiDEAHnl~d  187 (551)
T 3crv_A          157 PYFFIDRYREFIDIDLREYMIVIDEAHNLDK  187 (551)
T ss_dssp             HHHHCHHHHTTSCCCSTTEEEEETTGGGGGG
T ss_pred             hHhcCHHHHHhcCCCcCCeEEEEecccchHH
Confidence            9998875432211223567899999999998

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.73  E-value=2.4e-18  Score=142.16  Aligned_cols=125  Identities=19%  Similarity=0.185  Sum_probs=74.0

Q ss_pred             CChHHHHhhhhhhhC-----CCcEEEECCCCChHHHHHHHHHHHhhccCC-------CCeeEEEEcCCHHHHHHHH-HHH
Q psy4275          28 TPTEIQKAIIPHVLN-----DEDCIGCAKTGSGKTLAFALPILQKWCEDP-------YGIFALVLTPTRELAYQIG-DQF   94 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~-----~~~~li~~~tg~GKT~~~~~~~~~~~~~~~-------~~~~~lil~p~~~l~~q~~-~~~   94 (182)
                      .++|+|.++++.+..     +++++++++||+|||.+++..+.. +....       .+.+++|++|+++|+.|+. +.+
T Consensus       178 ~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~~~~~~~-l~~~~~~~~~~~~~~~vlil~P~~~L~~Q~~~~~~  256 (590)
T 3h1t_A          178 SPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVAFQISWK-LWSARWNRTGDYRKPRILFLADRNVLVDDPKDKTF  256 (590)
T ss_dssp             -CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHHHH-HHHTTCCSSCSSSCCCEEEEEC-----------CC
T ss_pred             CchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHHHHHHHH-HHhcccccccccCCCeEEEEeCCHHHHHHHHHHHH
Confidence            699999999998765     467899999999999996554444 33332       4679999999999999987 655


Q ss_pred             HHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcC---CCCCCCCccEEEEeccccccccC
Q psy4275          95 LVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTC---NTFSLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~---~~~~~~~~~~iI~DE~h~~~~~~  165 (182)
                      +.+    +..+..+.++        ....+.+|+|+||+.+.......   ..+...++++||+||||++....
T Consensus       257 ~~~----~~~~~~~~~~--------~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~lvIiDEaH~~~~~~  318 (590)
T 3h1t_A          257 TPF----GDARHKIEGG--------KVVKSREIYFAIYQSIASDERRPGLYKEFPQDFFDLIIIDECHRGSARD  318 (590)
T ss_dssp             TTT----CSSEEECCC----------CCSSCSEEEEEGGGC------CCGGGGSCTTSCSEEEESCCC------
T ss_pred             Hhc----chhhhhhhcc--------CCCCCCcEEEEEhhhhccccccccccccCCCCccCEEEEECCccccccc
Confidence            544    3344333322        22357799999999998765421   22356678999999999998753

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4b71_A* 4b73_A* 4b74_A* 4b76_A* 4b75_A* 4a92_A* 1cu1_A 4b6e_A* 4b6f_A* 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A ...

Probab=99.73  E-value=3.2e-18  Score=141.83  Aligned_cols=115  Identities=17%  Similarity=0.134  Sum_probs=90.7

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSI  107 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  107 (182)
                      .++++|+++++.+.+++++++++|||+|||.++.+++++.      +.+++|++|+++|+.|+++.+.+..   +.++..
T Consensus       217 P~~~~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~~------g~~vLVl~PTReLA~Qia~~l~~~~---g~~vg~  287 (666)
T 3o8b_A          217 PVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAAQ------GYKVLVLNPSVAATLGFGAYMSKAH---GIDPNI  287 (666)
T ss_dssp             CSCCCCCSCCCCCSSCEEEEEECCTTSCTTTHHHHHHHHT------TCCEEEEESCHHHHHHHHHHHHHHH---SCCCEE
T ss_pred             CcHHHHHHHHHHHHcCCeEEEEeCCchhHHHHHHHHHHHC------CCeEEEEcchHHHHHHHHHHHHHHh---CCCeeE
Confidence            4566777777777788999999999999999998888763      5589999999999999987665543   455666


Q ss_pred             EEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccc
Q psy4275         108 ITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLS  162 (182)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~  162 (182)
                      ..|+..       ...+.+|+|+||+.++   +. ..+.+++++++|+||+|++.
T Consensus       288 ~vG~~~-------~~~~~~IlV~TPGrLl---~~-~~l~l~~l~~lVlDEAH~l~  331 (666)
T 3o8b_A          288 RTGVRT-------ITTGAPVTYSTYGKFL---AD-GGCSGGAYDIIICDECHSTD  331 (666)
T ss_dssp             ECSSCE-------ECCCCSEEEEEHHHHH---HT-TSCCTTSCSEEEETTTTCCS
T ss_pred             EECcEe-------ccCCCCEEEECcHHHH---hC-CCcccCcccEEEEccchhcC
Confidence            666543       3457899999999973   33 55678889999999997654

>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=99.72  E-value=2e-17  Score=143.36  Aligned_cols=129  Identities=18%  Similarity=0.208  Sum_probs=95.7

Q ss_pred             CChHHHHhhhhhhhC--------------CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHH
Q psy4275          28 TPTEIQKAIIPHVLN--------------DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQ   93 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~--------------~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~   93 (182)
                      .|+|+|.++++.+..              +++++++++||+|||.++ ++++..+...+...++|+|+|+++|+.|+.+.
T Consensus       271 ~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~-~~l~~ll~~~~~~~rvLvlvpr~eL~~Q~~~~  349 (1038)
T 2w00_A          271 VMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTS-FKAARLATELDFIDKVFFVVDRKDLDYQTMKE  349 (1038)
T ss_dssp             ECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHH-HHHHHHHTTCTTCCEEEEEECGGGCCHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHH-HHHHHHHHhcCCCceEEEEeCcHHHHHHHHHH
Confidence            599999999988764              368999999999999997 55555554444456999999999999999998


Q ss_pred             HHHhhccCCceEEEEEcCCchhhhhHHh-cCCCcEEEEChHHHHHHHhcCCC-CCCCCccEEEEeccccccc
Q psy4275          94 FLVLGKVMNLRVSIITGGMDMVDQGKEL-AKKPHIVIATPGRLADHLDTCNT-FSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~Ilv~T~~~l~~~~~~~~~-~~~~~~~~iI~DE~h~~~~  163 (182)
                      ++.+....      +.+..+.......+ ..+++|+|+||+++...++.... ..++...+||+||||++..
T Consensus       350 f~~f~~~~------v~~~~s~~~l~~~L~~~~~~IiVtTiqkl~~~l~~~~~~~~~~~~~lvIiDEAHrs~~  415 (1038)
T 2w00_A          350 YQRFSPDS------VNGSENTAGLKRNLDKDDNKIIVTTIQKLNNLMKAESDLPVYNQQVVFIFDECHRSQF  415 (1038)
T ss_dssp             HHTTSTTC------SSSSCCCHHHHHHHHCSSCCEEEEEHHHHHHHHHHCCCCGGGGSCEEEEEESCCTTHH
T ss_pred             HHHhcccc------cccccCHHHHHHHhcCCCCCEEEEEHHHHHHHHhcccchhccccccEEEEEccchhcc
Confidence            88875431      12333333333334 34689999999999998765321 2345678999999999764

>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=99.71  E-value=1e-16  Score=135.90  Aligned_cols=149  Identities=18%  Similarity=0.154  Sum_probs=107.9

Q ss_pred             CccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhC-CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275           3 DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLN-DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus         3 ~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      .++.+|+++++++.+.+.+...+ ..|.+.|++.++.... ++++++++|||+|||+.....+.........+.++++++
T Consensus        69 ~~~~~f~~~~l~~~~~~~l~~r~-~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTtllp~ll~~~~~~~~~g~~ilvl~  147 (773)
T 2xau_A           69 GKINPFTGREFTPKYVDILKIRR-ELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTTQIPQFVLFDEMPHLENTQVACTQ  147 (773)
T ss_dssp             SSBCTTTCSBCCHHHHHHHHHHT-TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHCGGGGTCEEEEEE
T ss_pred             CCCCCccccCCCHHHHHHHHHhh-cCChHHHHHHHHHHHhCCCeEEEECCCCCCHHHHHHHHHHHhccccCCCceEEecC
Confidence            45778999999999999998887 5788888888877665 678999999999999954444443333322255799999


Q ss_pred             CCHHHHHHHHHHHHHhh-ccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccc
Q psy4275          82 PTRELAYQIGDQFLVLG-KVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR  160 (182)
Q Consensus        82 p~~~l~~q~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~  160 (182)
                      |+++++.|+++.+.... ...+..++......      .....+.+|+++||+.+...+...  ..+.+++++|+||+|.
T Consensus       148 P~r~La~q~~~~l~~~~~~~v~~~vG~~i~~~------~~~~~~~~I~v~T~G~l~r~l~~~--~~l~~~~~lIlDEah~  219 (773)
T 2xau_A          148 PRRVAAMSVAQRVAEEMDVKLGEEVGYSIRFE------NKTSNKTILKYMTDGMLLREAMED--HDLSRYSCIILDEAHE  219 (773)
T ss_dssp             SCHHHHHHHHHHHHHHTTCCBTTTEEEEETTE------EECCTTCSEEEEEHHHHHHHHHHS--TTCTTEEEEEECSGGG
T ss_pred             chHHHHHHHHHHHHHHhCCchhheecceeccc------cccCCCCCEEEECHHHHHHHHhhC--ccccCCCEEEecCccc
Confidence            99999999987665432 22233333211111      111346789999999999877653  3578899999999996

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A

Probab=99.71  E-value=9.7e-18  Score=134.56  Aligned_cols=121  Identities=17%  Similarity=0.208  Sum_probs=90.9

Q ss_pred             CCCCChHHHHhhhhhhhCCCcE-EEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q psy4275          25 GVKTPTEIQKAIIPHVLNDEDC-IGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNL  103 (182)
Q Consensus        25 ~~~~~~~~Q~~~~~~~~~~~~~-li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  103 (182)
                      |...++|.|+ +++.+.++++. ++++|||+|||.+++++++..+...  +.+++|++|+++|+.|+++.+.      +.
T Consensus         1 G~~q~~~iq~-~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~--~~~~lvl~Ptr~La~Q~~~~l~------g~   71 (451)
T 2jlq_A            1 GSAMGEPDYE-VDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALLR--RLRTLILAPTRVVAAEMEEALR------GL   71 (451)
T ss_dssp             CCCCCSCCCC-CCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTT------TS
T ss_pred             CCCCCCCcHH-HHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHhc--CCcEEEECCCHHHHHHHHHHhc------Cc
Confidence            4567788874 78998887776 8999999999999888988766654  5689999999999999988764      33


Q ss_pred             eEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccc
Q psy4275         104 RVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL  161 (182)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~  161 (182)
                      .+....+....     ....+..|.++|++.+.+.+...  ..+++++++|+||||++
T Consensus        72 ~v~~~~~~~~~-----~~~~~~~i~~~t~~~l~~~l~~~--~~l~~~~~iViDEah~~  122 (451)
T 2jlq_A           72 PIRYQTPAVKS-----DHTGREIVDLMCHATFTTRLLSS--TRVPNYNLIVMDEAHFT  122 (451)
T ss_dssp             CEEECCTTCSC-----CCCSSCCEEEEEHHHHHHHHHHC--SCCCCCSEEEEETTTCC
T ss_pred             eeeeeeccccc-----cCCCCceEEEEChHHHHHHhhCc--ccccCCCEEEEeCCccC
Confidence            33221111100     12345679999999998877653  35778999999999987

>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex, hydrolase/DNA complex complex; 3.00A {Sulfolobus solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A

Probab=99.70  E-value=5.7e-17  Score=131.41  Aligned_cols=127  Identities=15%  Similarity=0.098  Sum_probs=94.6

Q ss_pred             CChHHHHhhhhhh----hCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q psy4275          28 TPTEIQKAIIPHV----LNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNL  103 (182)
Q Consensus        28 ~~~~~Q~~~~~~~----~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  103 (182)
                      .++|+|.++++.+    ..++++++..+||+|||++++..+... .......+++||||. +++.||.++++++..  +.
T Consensus        37 ~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai~~i~~~-~~~~~~~~~LIv~P~-~l~~qw~~e~~~~~~--~~  112 (500)
T 1z63_A           37 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDA-KKENELTPSLVICPL-SVLKNWEEELSKFAP--HL  112 (500)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHHHH-HHTTCCSSEEEEECS-TTHHHHHHHHHHHCT--TS
T ss_pred             cchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHHHHHHHH-HhcCCCCCEEEEccH-HHHHHHHHHHHHHCC--Cc
Confidence            6999999999776    347889999999999999976555544 333334589999995 588999999998875  35


Q ss_pred             eEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCCh
Q psy4275         104 RVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSL  167 (182)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~  167 (182)
                      ++..++|+...     ......+|+|+|++.+.....    +...+++++|+||||++.+....
T Consensus       113 ~v~~~~g~~~~-----~~~~~~~ivi~t~~~l~~~~~----l~~~~~~~vIvDEaH~~kn~~~~  167 (500)
T 1z63_A          113 RFAVFHEDRSK-----IKLEDYDIILTTYAVLLRDTR----LKEVEWKYIVIDEAQNIKNPQTK  167 (500)
T ss_dssp             CEEECSSSTTS-----CCGGGSSEEEEEHHHHTTCHH----HHTCCEEEEEEETGGGGSCTTSH
T ss_pred             eEEEEecCchh-----ccccCCcEEEeeHHHHhccch----hcCCCcCEEEEeCccccCCHhHH
Confidence            66666665421     123467899999999865433    22345789999999999876643

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.67  E-value=9.9e-17  Score=131.33  Aligned_cols=128  Identities=18%  Similarity=0.083  Sum_probs=86.2

Q ss_pred             CCCCChHHHHhhhhh----hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhcc
Q psy4275          25 GVKTPTEIQKAIIPH----VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKV  100 (182)
Q Consensus        25 ~~~~~~~~Q~~~~~~----~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~  100 (182)
                      |+ +++|+|.+++..    +..+++.++++|||+|||.+++++++..      +.+++|++||++|++|+.+.++.+   
T Consensus         5 ~~-~~r~~Q~~~~~~v~~~~~~~~~~~~~a~TGtGKT~~~l~~~~~~------~~~~~~~~~t~~l~~q~~~~~~~l---   74 (540)
T 2vl7_A            5 KL-QLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQL------KKKVLIFTRTHSQLDSIYKNAKLL---   74 (540)
T ss_dssp             -----CCHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHHHHHHHH------TCEEEEEESCHHHHHHHHHHHGGG---
T ss_pred             CC-CCCHHHHHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHhC------CCcEEEEcCCHHHHHHHHHHHHhc---
Confidence            45 799999998654    4568999999999999999999988764      568999999999999998777664   


Q ss_pred             CCceEEEEEcCCch--------h---------------------------------------hhhHHhcCCCcEEEEChH
Q psy4275         101 MNLRVSIITGGMDM--------V---------------------------------------DQGKELAKKPHIVIATPG  133 (182)
Q Consensus       101 ~~~~~~~~~~~~~~--------~---------------------------------------~~~~~~~~~~~Ilv~T~~  133 (182)
                       ++++..+.|....        .                                       ...+.....++|+|+|+.
T Consensus        75 -~~~~~~l~gr~~lC~~~~~~~~~~~~~c~~c~~~~~~~~~gd~~~~~~~~~~~~~~~~Cpy~~~r~~~~~adiVV~n~~  153 (540)
T 2vl7_A           75 -GLKTGFLIGKSASCIYAQGDEEPDEINCSKCRLKDKIKTIEDKEPSKLIEEFKDAVDYCPYYSLRANLKDKDVIAMTYP  153 (540)
T ss_dssp             -TCCEEEC---------------------------------------------------------CTTGGGCSEEEEETH
T ss_pred             -CCcEEEecCCccccCCchhcccccccCCCCCCchhcccccccCCcHHHHHHHhhhcCCChHHHHHHHhhcCCEEEEChH
Confidence             4445444432210        0                                       000111235799999999


Q ss_pred             HHHHHHhcCC-C-----CCCCCccEEEEeccccccc
Q psy4275         134 RLADHLDTCN-T-----FSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus       134 ~l~~~~~~~~-~-----~~~~~~~~iI~DE~h~~~~  163 (182)
                      .+.+-..... .     -.......+||||||++.+
T Consensus       154 ~l~~~~~~~~~~~~~~~~~~~~~~~vIiDEAHnl~~  189 (540)
T 2vl7_A          154 YLFQKPIRNSVFCNKDDCLKLEDYLIVIDEAHNLLE  189 (540)
T ss_dssp             HHHSHHHHHHHSCSSTTSCCGGGEEEEETTGGGGGG
T ss_pred             HhcCHHHHHhhCcccccccCcCCCEEEEEccccHHH
Confidence            9986432211 0     0234567999999999943

>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=99.66  E-value=8.3e-17  Score=139.42  Aligned_cols=135  Identities=19%  Similarity=0.132  Sum_probs=95.9

Q ss_pred             CChHHHHhhhhhhhC--CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceE
Q psy4275          28 TPTEIQKAIIPHVLN--DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRV  105 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~--~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~  105 (182)
                      .++|+|.+++..+..  +.+++++++||+|||.+++..+........ ..+++||||+ +|+.||.+.+.+.+   +.++
T Consensus       153 ~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g~-~~rvLIVvP~-sLl~Qw~~E~~~~f---~l~v  227 (968)
T 3dmq_A          153 SLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSGA-AERVLIIVPE-TLQHQWLVEMLRRF---NLRF  227 (968)
T ss_dssp             CCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHTSS-CCCEEEECCT-TTHHHHHHHHHHHS---CCCC
T ss_pred             CCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHhCC-CCeEEEEeCH-HHHHHHHHHHHHHh---CCCE
Confidence            699999999988776  458899999999999998777766554432 4489999999 99999888876554   5667


Q ss_pred             EEEEcCCchhhhh--HHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCCh
Q psy4275         106 SIITGGMDMVDQG--KELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSL  167 (182)
Q Consensus       106 ~~~~~~~~~~~~~--~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~  167 (182)
                      ..++++.......  .......+|+|+|++.+.........+...++++||+||||++.+.+..
T Consensus       228 ~v~~~~~~~~~~~~~~~~~~~~dIvI~T~~~L~~~~~~~~~l~~~~~dlVIvDEAH~~kn~~~~  291 (968)
T 3dmq_A          228 ALFDDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLVWSEDA  291 (968)
T ss_dssp             EECCHHHHHHHHHTTCSSSTTCSEEEECHHHHHTSTTTTHHHHTSCCCEEEECCSSCCCCBTTB
T ss_pred             EEEccchhhhhhhhcccccccCCEEEEcHHHHhhCHHHHHHhhhcCCCEEEehhhHhhcCCCCc
Confidence            6666544322111  1223467999999998854322111233456899999999999876643

>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=99.65  E-value=4.5e-17  Score=135.06  Aligned_cols=135  Identities=13%  Similarity=0.107  Sum_probs=94.0

Q ss_pred             CCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHH
Q psy4275          11 LKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQI   90 (182)
Q Consensus        11 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~   90 (182)
                      +++++.+.+++... ...+.|.|++.++.+.+++++++++|||+|||.+++++++..+...  +.+++|++|+++|+.|+
T Consensus       155 l~~~~~~~~~l~~~-~~~~lpiq~~~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~~--~~~vLvl~PtreLa~Qi  231 (618)
T 2whx_A          155 VTKSGDYVSAITQA-ERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALKR--RLRTLILAPTRVVAAEM  231 (618)
T ss_dssp             -------CEECBCC-CCCCCCCCCCCGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHH
T ss_pred             ccchHHHHHHHhhc-cccCCCccccCHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHhC--CCeEEEEcChHHHHHHH
Confidence            34555554444432 2567788777899999999999999999999999999998877653  56899999999999999


Q ss_pred             HHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccc
Q psy4275          91 GDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL  161 (182)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~  161 (182)
                      .+.++      +..+. +.+... .   .....+..+.++|.+.+...+...  ..+++++++|+||||++
T Consensus       232 ~~~l~------~~~v~-~~~~~l-~---~~~tp~~~i~~~t~~~l~~~l~~~--~~l~~~~~iViDEah~~  289 (618)
T 2whx_A          232 EEALR------GLPIR-YQTPAV-K---SDHTGREIVDLMCHATFTTRLLSS--TRVPNYNLIVMDEAHFT  289 (618)
T ss_dssp             HHHTT------TSCEE-ECCTTS-S---CCCCSSSCEEEEEHHHHHHHHHHC--SSCCCCSEEEEESTTCC
T ss_pred             HHHhc------CCcee-Eecccc-e---eccCCCceEEEEChHHHHHHHhcc--ccccCCeEEEEECCCCC
Confidence            87765      23333 222110 0   011224467788888887766553  35788999999999998

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=99.63  E-value=9.3e-16  Score=130.76  Aligned_cols=133  Identities=18%  Similarity=0.123  Sum_probs=99.1

Q ss_pred             CChHHHHhhhhhhh----CCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q psy4275          28 TPTEIQKAIIPHVL----NDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNL  103 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~----~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  103 (182)
                      .++|+|.+++..+.    .++++++..+||.|||+.++..+............+||||| .+++.||.+.++++..  +.
T Consensus       236 ~Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~l~~~~~~~~~~LIV~P-~sll~qW~~E~~~~~p--~~  312 (800)
T 3mwy_W          236 ELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVP-LSTMPAWLDTFEKWAP--DL  312 (800)
T ss_dssp             CCCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHHHHHHHSCCSCEEEECC-TTTHHHHHHHHHHHST--TC
T ss_pred             CcCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHHHHHhcCCCCCEEEEEC-chHHHHHHHHHHHHCC--Cc
Confidence            68999999998665    68899999999999999987776665544333557999999 6678999999988875  46


Q ss_pred             eEEEEEcCCchhhhhHH------------hcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCC
Q psy4275         104 RVSIITGGMDMVDQGKE------------LAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTS  166 (182)
Q Consensus       104 ~~~~~~~~~~~~~~~~~------------~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~  166 (182)
                      ++..++|..........            ....++|+|+|++.+.......   ...++++||+||||++-+...
T Consensus       313 ~v~~~~g~~~~r~~~~~~~~~~~~~~~~~~~~~~dvvitTy~~l~~~~~~l---~~~~w~~vIvDEaH~lkn~~s  384 (800)
T 3mwy_W          313 NCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRAEL---GSIKWQFMAVDEAHRLKNAES  384 (800)
T ss_dssp             CEEECCCSSHHHHHHHHHHSCSCC-----CCCCCSEEEECTTHHHHTHHHH---HTSEEEEEEETTGGGGCCSSS
T ss_pred             eEEEEeCCHHHHHHHHHHHhhccccccccccccCCEEEecHHHHHhhHHHH---hcCCcceeehhhhhhhcCchh
Confidence            77777777654332221            1235789999999997654331   123578999999999976554

>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=99.63  E-value=6.3e-15  Score=122.94  Aligned_cols=136  Identities=18%  Similarity=0.159  Sum_probs=96.7

Q ss_pred             CChHHHHhhhhhhh---------CCCcEEEECCCCChHHHHHHHHHHHhhccCC----CCeeEEEEcCCHHHHHHHHHHH
Q psy4275          28 TPTEIQKAIIPHVL---------NDEDCIGCAKTGSGKTLAFALPILQKWCEDP----YGIFALVLTPTRELAYQIGDQF   94 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~---------~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~----~~~~~lil~p~~~l~~q~~~~~   94 (182)
                      .++|+|.+++..+.         .++++++..+||+|||+.++..+...+...+    ...++|||+|+ +++.||.+++
T Consensus        55 ~LrpyQ~~gv~~l~~~~~~~~~~~~~g~ILad~mGlGKT~~~i~~i~~l~~~~~~~~p~~~~~LiV~P~-sll~qW~~E~  133 (644)
T 1z3i_X           55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPS-SLVRNWYNEV  133 (644)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECH-HHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHhhhcccccCCCCeEeeeCCCchHHHHHHHHHHHHHHhCccccCCCCcEEEEecH-HHHHHHHHHH
Confidence            68999999998763         3567899999999999998777766554432    23469999996 7889999999


Q ss_pred             HHhhccCCceEEEEEcCCchhhh--hHHh-c-----CCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCC
Q psy4275          95 LVLGKVMNLRVSIITGGMDMVDQ--GKEL-A-----KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTS  166 (182)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~--~~~~-~-----~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~  166 (182)
                      +++... .+.+..++++......  .... .     ...+|+|+|++.+......   +....+++||+||||++-+...
T Consensus       134 ~~~~~~-~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~vvi~ty~~l~~~~~~---l~~~~~~~vI~DEaH~ikn~~~  209 (644)
T 1z3i_X          134 GKWLGG-RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAEV---LHKGKVGLVICDEGHRLKNSDN  209 (644)
T ss_dssp             HHHHGG-GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTTT---TTTSCCCEEEETTGGGCCTTCH
T ss_pred             HHHcCC-CeeEEEEeCCCHHHHHHHHHHHHHhcCCCCCCcEEEeeHHHHHhhHHH---hhcCCccEEEEECceecCChhh
Confidence            998765 4556666655432211  1111 1     1478999999998764432   3345688999999999987654


Q ss_pred             hh
Q psy4275         167 LK  168 (182)
Q Consensus       167 ~~  168 (182)
                      ..
T Consensus       210 ~~  211 (644)
T 1z3i_X          210 QT  211 (644)
T ss_dssp             HH
T ss_pred             HH
Confidence            33

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.62  E-value=1.5e-15  Score=121.19  Aligned_cols=104  Identities=16%  Similarity=0.198  Sum_probs=75.3

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA  122 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  122 (182)
                      ++++++++|||+|||.+++++++..+..+  +.+++|++|+++|+.|+++.++      +..+....|....     .-.
T Consensus         2 g~~~lv~a~TGsGKT~~~l~~~l~~~~~~--g~~~lvl~Pt~~La~Q~~~~~~------~~~v~~~~~~~~~-----~~~   68 (431)
T 2v6i_A            2 RELTVLDLHPGAGKTRRVLPQLVREAVKK--RLRTVILAPTRVVASEMYEALR------GEPIRYMTPAVQS-----ERT   68 (431)
T ss_dssp             CCEEEEECCTTSCTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTT------TSCEEEC--------------
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHhC--CCCEEEECcHHHHHHHHHHHhC------CCeEEEEecCccc-----cCC
Confidence            68899999999999999988888665544  5689999999999999887664      4455554443211     111


Q ss_pred             CCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccc
Q psy4275         123 KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL  161 (182)
Q Consensus       123 ~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~  161 (182)
                      .+.-+.+.|.+.+.+.+..  ...+++++++|+||+|++
T Consensus        69 ~~~~~~~~~~~~l~~~l~~--~~~~~~l~~vViDEaH~~  105 (431)
T 2v6i_A           69 GNEIVDFMCHSTFTMKLLQ--GVRVPNYNLYIMDEAHFL  105 (431)
T ss_dssp             CCCSEEEEEHHHHHHHHHH--TCCCCCCSEEEEESTTCC
T ss_pred             CCceEEEEchHHHHHHHhc--CccccCCCEEEEeCCccC
Confidence            2445777888888766555  235788999999999997

>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=99.58  E-value=1.6e-16  Score=127.11  Aligned_cols=108  Identities=21%  Similarity=0.226  Sum_probs=71.2

Q ss_pred             hhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhh
Q psy4275          39 HVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQG  118 (182)
Q Consensus        39 ~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  118 (182)
                      .+.+++++++++|||+|||.+++++++..+..+  +.+++|++|+++|+.|+++.++.+      .+....+....    
T Consensus         4 ~l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~~--~~~~lil~Ptr~La~Q~~~~l~~~------~v~~~~~~~~~----   71 (440)
T 1yks_A            4 MLKKGMTTVLDFHPGAGKTRRFLPQILAECARR--RLRTLVLAPTRVVLSEMKEAFHGL------DVKFHTQAFSA----   71 (440)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTTTS------CEEEESSCCCC----
T ss_pred             HhhCCCCEEEEcCCCCCHHHHHHHHHHHHHHhc--CCeEEEEcchHHHHHHHHHHHhcC------CeEEeccccee----
Confidence            456789999999999999999999988876654  568999999999999998877643      22221111100    


Q ss_pred             HHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccc
Q psy4275         119 KELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL  161 (182)
Q Consensus       119 ~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~  161 (182)
                       ....+.-+-..+.+.+...+..  ...+++++++|+||+|++
T Consensus        72 -v~Tp~~l~~~l~~~~l~~~~~~--~~~~~~l~~vViDEah~~  111 (440)
T 1yks_A           72 -HGSGREVIDAMCHATLTYRMLE--PTRVVNWEVIIMDEAHFL  111 (440)
T ss_dssp             -CCCSSCCEEEEEHHHHHHHHTS--SSCCCCCSEEEETTTTCC
T ss_pred             -ccCCccceeeecccchhHhhhC--cccccCccEEEEECcccc
Confidence             0000111222233333333222  235788999999999998

>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=99.57  E-value=3.9e-15  Score=119.68  Aligned_cols=110  Identities=20%  Similarity=0.204  Sum_probs=78.5

Q ss_pred             hhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhh
Q psy4275          37 IPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVD  116 (182)
Q Consensus        37 ~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~  116 (182)
                      ...+.+++++++++|||+|||.+++++++..+...  +.+++|++|+++|+.|+++.++      +..+....+....  
T Consensus        15 ~~~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~~--~~~~lvl~Ptr~La~Q~~~~l~------g~~v~~~~~~~~~--   84 (459)
T 2z83_A           15 PNMLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQQ--RLRTAVLAPTRVVAAEMAEALR------GLPVRYQTSAVQR--   84 (459)
T ss_dssp             CGGGSTTCEEEECCCTTSCTTTTHHHHHHHHHHHT--TCCEEEEECSHHHHHHHHHHTT------TSCEEECC-------
T ss_pred             HHHHhcCCcEEEECCCCCCHHHHHHHHHHHHHHhC--CCcEEEECchHHHHHHHHHHhc------CceEeEEeccccc--
Confidence            34456688999999999999999999998877653  5689999999999999988775      3333222111110  


Q ss_pred             hhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccc
Q psy4275         117 QGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL  161 (182)
Q Consensus       117 ~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~  161 (182)
                         .-..+..+.++|.+.+...+...  ..++++++||+||||++
T Consensus        85 ---~~t~~~~i~~~~~~~l~~~l~~~--~~l~~~~~iViDEaH~~  124 (459)
T 2z83_A           85 ---EHQGNEIVDVMCHATLTHRLMSP--NRVPNYNLFVMDEAHFT  124 (459)
T ss_dssp             ------CCCSEEEEEHHHHHHHHHSC--C-CCCCSEEEESSTTCC
T ss_pred             ---CCCCCcEEEEEchHHHHHHhhcc--ccccCCcEEEEECCccC
Confidence               01224457788888887766552  35788999999999984

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.57  E-value=1.5e-15  Score=126.92  Aligned_cols=119  Identities=19%  Similarity=0.262  Sum_probs=82.3

Q ss_pred             CChHHHH-----hhhhhhh------CCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHH
Q psy4275          28 TPTEIQK-----AIIPHVL------NDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLV   96 (182)
Q Consensus        28 ~~~~~Q~-----~~~~~~~------~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~   96 (182)
                      .++++|+     ++++.++      ++++.++++|||+|||.+++++++..+..+  +.+++|++|+++|+.|+++.++.
T Consensus       215 ~pt~IQ~~~r~~~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~~--~~~~lilaPTr~La~Q~~~~l~~  292 (673)
T 2wv9_A          215 YVSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQK--RLRTAVLAPTRVVAAEMAEALRG  292 (673)
T ss_dssp             EEEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTTT
T ss_pred             ccCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhC--CCcEEEEccHHHHHHHHHHHHhc
Confidence            7888888     8888877      799999999999999999999998876654  56899999999999999887764


Q ss_pred             hhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccc
Q psy4275          97 LGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL  161 (182)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~  161 (182)
                      +    ++.  ...+...     .....+.-+-+.+.+.+.+.+...  ..+++++++|+||+|++
T Consensus       293 ~----~i~--~~~~~l~-----~v~tp~~ll~~l~~~~l~~~l~~~--~~l~~l~lvViDEaH~~  344 (673)
T 2wv9_A          293 L----PVR--YLTPAVQ-----REHSGNEIVDVMCHATLTHRLMSP--LRVPNYNLFVMDEAHFT  344 (673)
T ss_dssp             S----CCE--ECCC--------CCCCSCCCEEEEEHHHHHHHHHSS--SCCCCCSEEEEESTTCC
T ss_pred             C----Cee--eeccccc-----ccCCHHHHHHHHHhhhhHHHHhcc--cccccceEEEEeCCccc
Confidence            3    222  1111000     000112234455556655544442  45788999999999998

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.51  E-value=5e-14  Score=117.62  Aligned_cols=108  Identities=16%  Similarity=0.084  Sum_probs=78.2

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKE  120 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  120 (182)
                      .+++++++++|||+|||..++..+..    .   .+.+|++|+++|+.|+++.++..    ++++..+.|+.....  ..
T Consensus       153 l~rk~vlv~apTGSGKT~~al~~l~~----~---~~gl~l~PtR~LA~Qi~~~l~~~----g~~v~lltG~~~~iv--~T  219 (677)
T 3rc3_A          153 MQRKIIFHSGPTNSGKTYHAIQKYFS----A---KSGVYCGPLKLLAHEIFEKSNAA----GVPCDLVTGEERVTV--QP  219 (677)
T ss_dssp             SCCEEEEEECCTTSSHHHHHHHHHHH----S---SSEEEEESSHHHHHHHHHHHHHT----TCCEEEECSSCEECC--ST
T ss_pred             cCCCEEEEEcCCCCCHHHHHHHHHHh----c---CCeEEEeCHHHHHHHHHHHHHhc----CCcEEEEECCeeEEe--cC
Confidence            45789999999999999954444333    2   24599999999999999888775    778888888765411  01


Q ss_pred             hcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHH
Q psy4275         121 LAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFF  170 (182)
Q Consensus       121 ~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~  170 (182)
                      -....+++++|++.+.         ....++++|+||+|++.+.++...+
T Consensus       220 pGr~~~il~~T~e~~~---------l~~~v~lvVIDEaH~l~d~~~g~~~  260 (677)
T 3rc3_A          220 NGKQASHVSCTVEMCS---------VTTPYEVAVIDEIQMIRDPARGWAW  260 (677)
T ss_dssp             TCCCCSEEEEEGGGCC---------SSSCEEEEEECSGGGGGCTTTHHHH
T ss_pred             CCcccceeEecHhHhh---------hcccCCEEEEecceecCCccchHHH
Confidence            1113678999976441         2456799999999999877655433

>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=99.35  E-value=1.6e-11  Score=102.01  Aligned_cols=134  Identities=21%  Similarity=0.181  Sum_probs=103.1

Q ss_pred             CCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q psy4275          24 IGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNL  103 (182)
Q Consensus        24 ~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  103 (182)
                      .|+ ++++.|....-.+..|+  +.++.||.|||+++.++++-..+.   |..+.+++|+..||.+-++++..+.+.+|+
T Consensus        72 lg~-r~~dvQligg~~L~~G~--iaEM~TGEGKTLva~lp~~lnAL~---G~~vhVvT~ndyLA~rdae~m~~l~~~Lgl  145 (822)
T 3jux_A           72 LGM-RPFDVQVMGGIALHEGK--VAEMKTGEGKTLAATMPIYLNALI---GKGVHLVTVNDYLARRDALWMGPVYLFLGL  145 (822)
T ss_dssp             TSC-CCCHHHHHHHHHHHTTC--EEECCTTSCHHHHTHHHHHHHHTT---SSCEEEEESSHHHHHHHHHHHHHHHHHTTC
T ss_pred             hCC-CCcHHHHHHHHHHhCCC--hhhccCCCCccHHHHHHHHHHHhc---CCceEEEeccHHHHHhHHHHHHHHHHHhCC
Confidence            354 78888888887777665  999999999999999998766665   557999999999999999999999999999


Q ss_pred             eEEEEEcC--------------------------------------------------CchhhhhHHhcCCCcEEEEChH
Q psy4275         104 RVSIITGG--------------------------------------------------MDMVDQGKELAKKPHIVIATPG  133 (182)
Q Consensus       104 ~~~~~~~~--------------------------------------------------~~~~~~~~~~~~~~~Ilv~T~~  133 (182)
                      +|+++.+.                                                  .+..++...+  .|+|..+|..
T Consensus       146 svg~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~err~aY--~~DItYgTn~  223 (822)
T 3jux_A          146 RVGVINSLGKSYEVVWKNPDLARKAIEENWSVWPDGFNGEVLKEESMNKEAVEAFQVELKEITRKEAY--LCDVTYGTNN  223 (822)
T ss_dssp             CEEEEETTTEEEEEEESSHHHHHHHHHTTCCSSCTTCCSSSCCGGGSCHHHHTTTCEECCBCCHHHHH--HSSEEEEEHH
T ss_pred             EEEEEcCCCcccccccccchhhhhhhcccccccccccccccccccccccccchhccccCCHHHHHHHh--cCCCEEccCc
Confidence            99988872                                                  1111111222  5799999988


Q ss_pred             HH-HHHHhcCC-----CCCCCCccEEEEeccccccccC
Q psy4275         134 RL-ADHLDTCN-----TFSLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus       134 ~l-~~~~~~~~-----~~~~~~~~~iI~DE~h~~~~~~  165 (182)
                      -| .++++..-     ..-.+.+.+.|+||+|.++=+.
T Consensus       224 EfgFDYLRDnm~~~~~~~vqR~~~~aIVDEvDSiLIDe  261 (822)
T 3jux_A          224 EFGFDYLRDNLVLDYNDKVQRGHFYAIVDEADSVLIDE  261 (822)
T ss_dssp             HHHHHHHHHTSCSSTTSCCCCCCCEEEEETHHHHHTTG
T ss_pred             chhhHhHHhhccCCHHHhccCCCCeEEEecccceeecC
Confidence            87 56776531     2234668899999999987543

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=99.18  E-value=4.5e-11  Score=99.26  Aligned_cols=81  Identities=23%  Similarity=0.192  Sum_probs=67.2

Q ss_pred             CChHHHHhhhhhh----hCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q psy4275          28 TPTEIQKAIIPHV----LNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNL  103 (182)
Q Consensus        28 ~~~~~Q~~~~~~~----~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  103 (182)
                      +++|.|.+....+    .+++++++++|||+|||.+++++++..+...  +.+++|++||++++.|+.+.++.+....++
T Consensus         3 ~~R~~Q~~~~~~v~~~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~~--~~kvli~t~T~~l~~Qi~~el~~l~~~~~~   80 (620)
T 4a15_A            3 ENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSER--KLKVLYLVRTNSQEEQVIKELRSLSSTMKI   80 (620)
T ss_dssp             --CHHHHHHHHHHHHHHHHSSEEEEECCTTSCHHHHHHHHHHHHHHHH--TCEEEEEESSHHHHHHHHHHHHHHHHHSCC
T ss_pred             CCCHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHhhhhc--CCeEEEECCCHHHHHHHHHHHHHHhhccCe
Confidence            6899999988654    4589999999999999999999999877543  468999999999999999999998776677


Q ss_pred             eEEEEEc
Q psy4275         104 RVSIITG  110 (182)
Q Consensus       104 ~~~~~~~  110 (182)
                      ++..+.|
T Consensus        81 ~~~~l~g   87 (620)
T 4a15_A           81 RAIPMQG   87 (620)
T ss_dssp             CEEECCC
T ss_pred             EEEEEEC
Confidence            7766555

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=99.00  E-value=4.2e-09  Score=87.37  Aligned_cols=86  Identities=16%  Similarity=0.111  Sum_probs=61.9

Q ss_pred             HHHHHHHHCC-CCCChHHHHhhhhhhhCCCcEEEECCCCChHHHH--HHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHH
Q psy4275          16 WLIRQCQTIG-VKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLA--FALPILQKWCEDPYGIFALVLTPTRELAYQIGD   92 (182)
Q Consensus        16 ~i~~~l~~~~-~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~--~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~   92 (182)
                      .+.+.+.... .....++|+++++.+..++.++++|++|+|||..  +++..+...... .+.++++++||...+.++.+
T Consensus       136 ~~~~~l~~~~~~~~~~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~~-~~~~vll~APTg~AA~~L~e  214 (608)
T 1w36_D          136 LLAQTLDKLFPVSDEINWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMADG-ERCRIRLAAPTGKAAARLTE  214 (608)
T ss_dssp             HHHHHHHTTCCCTTSCCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCSS-CCCCEEEEBSSHHHHHHHHH
T ss_pred             HHHHHHHHHhccCCCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhhc-CCCeEEEEeCChhHHHHHHH
Confidence            4455555432 2233789999999999999999999999999954  444444433222 25689999999999999988


Q ss_pred             HHHHhhccCC
Q psy4275          93 QFLVLGKVMN  102 (182)
Q Consensus        93 ~~~~~~~~~~  102 (182)
                      .+.......+
T Consensus       215 ~~~~~~~~l~  224 (608)
T 1w36_D          215 SLGKALRQLP  224 (608)
T ss_dssp             HHTHHHHHSS
T ss_pred             HHHHHHhcCC
Confidence            8776655444

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=98.94  E-value=2.1e-09  Score=89.82  Aligned_cols=67  Identities=22%  Similarity=0.219  Sum_probs=53.6

Q ss_pred             CChHHHHhhhhhhhC-CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHh
Q psy4275          28 TPTEIQKAIIPHVLN-DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVL   97 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~-~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~   97 (182)
                      .+++.|.+++..++. ..-.+++||+|+|||.+....+...+.+   +.++++++||+..++++.+.+...
T Consensus       189 ~LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti~~~I~~l~~~---~~~ILv~a~TN~AvD~i~erL~~~  256 (646)
T 4b3f_X          189 CLDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAVKQ---GLKVLCCAPSNIAVDNLVERLALC  256 (646)
T ss_dssp             TCCHHHHHHHHHHHHCSSEEEEECCTTSCHHHHHHHHHHHHHHT---TCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHhcCCCceEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEcCchHHHHHHHHHHHhc
Confidence            589999999988775 4478999999999998865555444433   568999999999999988777653

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=98.86  E-value=2.4e-08  Score=83.09  Aligned_cols=70  Identities=17%  Similarity=0.113  Sum_probs=55.1

Q ss_pred             CCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHh
Q psy4275          26 VKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVL   97 (182)
Q Consensus        26 ~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~   97 (182)
                      ...+++.|.+++..+..+...+++||+|+|||.+....+. .+... .+.++++++||...++++.+.+...
T Consensus       178 ~~~ln~~Q~~av~~~l~~~~~li~GppGTGKT~~~~~~i~-~l~~~-~~~~ilv~a~tn~A~~~l~~~l~~~  247 (624)
T 2gk6_A          178 LPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVY-HLARQ-GNGPVLVCAPSNIAVDQLTEKIHQT  247 (624)
T ss_dssp             SCCCCHHHHHHHHHHHTCSEEEEECCTTSCHHHHHHHHHH-HHHTS-SSCCEEEEESSHHHHHHHHHHHHTT
T ss_pred             cCCCCHHHHHHHHHHhcCCCeEEECCCCCCHHHHHHHHHH-HHHHc-CCCeEEEEeCcHHHHHHHHHHHHhc
Confidence            3468999999999988888899999999999988554443 33332 2558999999999999988777653

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=98.77  E-value=5.3e-08  Score=83.02  Aligned_cols=69  Identities=19%  Similarity=0.132  Sum_probs=54.7

Q ss_pred             CCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHh
Q psy4275          27 KTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVL   97 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~   97 (182)
                      ..+++.|.+++..+..+...+++||+|+|||.+....+.......  +.++++++||...++++.+.+.+.
T Consensus       359 ~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~~i~~~i~~l~~~~--~~~ILv~a~tn~A~d~l~~rL~~~  427 (802)
T 2xzl_A          359 AQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSATIVYHLSKIH--KDRILVCAPSNVAVDHLAAKLRDL  427 (802)
T ss_dssp             CCCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHHHHHHHHHHHHH--CCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             ccCCHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHHHhCC--CCeEEEEcCcHHHHHHHHHHHHhh
Confidence            468999999999988888899999999999988554443322211  458999999999999998887664

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A

Probab=98.75  E-value=8.7e-08  Score=81.66  Aligned_cols=69  Identities=17%  Similarity=0.097  Sum_probs=54.4

Q ss_pred             CCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHh
Q psy4275          27 KTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVL   97 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~   97 (182)
                      ..+++.|.+++..+..++..+++||+|+|||.+....+ ..+... .+.++++++||...++++.+.+...
T Consensus       355 ~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~ti~~~i-~~l~~~-~~~~ilv~a~tn~A~~~l~~~l~~~  423 (800)
T 2wjy_A          355 PDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIV-YHLARQ-GNGPVLVCAPSNIAVDQLTEKIHQT  423 (800)
T ss_dssp             CCCCHHHHHHHHHHHTSSEEEEECCTTSCHHHHHHHHH-HHHHTT-CSSCEEEEESSHHHHHHHHHHHHTT
T ss_pred             cCCCHHHHHHHHHhccCCeEEEEcCCCCCHHHHHHHHH-HHHHHc-CCCcEEEEcCcHHHHHHHHHHHHHh
Confidence            46899999999998888889999999999998854433 333332 2458999999999999988777653

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=98.66  E-value=1.1e-07  Score=78.40  Aligned_cols=64  Identities=17%  Similarity=0.200  Sum_probs=50.6

Q ss_pred             CCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHH
Q psy4275          27 KTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQ   93 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~   93 (182)
                      ..+++.|++++..+..++.+++.||+|+|||.... .++..+...  +.++++++||...+..+.+.
T Consensus       188 ~~L~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~i~-~l~~~l~~~--g~~Vl~~ApT~~Aa~~L~e~  251 (574)
T 3e1s_A          188 KGLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTTK-AVADLAESL--GLEVGLCAPTGKAARRLGEV  251 (574)
T ss_dssp             TTCCHHHHHHHHHHTTCSEEEEECCTTSCHHHHHH-HHHHHHHHT--TCCEEEEESSHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHhCCEEEEEcCCCCCHHHHHH-HHHHHHHhc--CCeEEEecCcHHHHHHhHhh
Confidence            36899999999999989999999999999998743 334433333  56899999999988776554

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=98.63  E-value=1.4e-07  Score=75.68  Aligned_cols=72  Identities=15%  Similarity=0.076  Sum_probs=51.2

Q ss_pred             HHHCCCCCChHHHHhhhhhhhC-----CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHH
Q psy4275          21 CQTIGVKTPTEIQKAIIPHVLN-----DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQF   94 (182)
Q Consensus        21 l~~~~~~~~~~~Q~~~~~~~~~-----~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~   94 (182)
                      +....+..+++.|++++..+..     ...+++.|++|+|||.+. ..++..+...+ ...+++++||...+..+.+.+
T Consensus        18 ~~p~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll-~~~~~~l~~~~-~~~il~~a~T~~Aa~~l~~~~   94 (459)
T 3upu_A           18 GSHMTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLT-KFIIEALISTG-ETGIILAAPTHAAKKILSKLS   94 (459)
T ss_dssp             ---CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHH-HHHHHHHHHTT-CCCEEEEESSHHHHHHHHHHH
T ss_pred             cCCCccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHH-HHHHHHHHhcC-CceEEEecCcHHHHHHHHhhh
Confidence            4456677899999999987643     248999999999999874 44444444432 236999999998887765544

>3lfu_A DNA helicase II; SF1 helicase, ATP-binding, DNA damage, DNA REP replication, DNA-binding, hydrolase, nucleotide-B SOS response; HET: DNA; 1.80A {Escherichia coli} PDB: 2is6_A* 2is2_A* 2is1_A* 2is4_A*

Probab=97.98  E-value=2e-05  Score=65.54  Aligned_cols=81  Identities=16%  Similarity=0.097  Sum_probs=59.9

Q ss_pred             CCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCC-CCeeEEEEcCCHHHHHHHHHHHHHhhcc--CCc
Q psy4275          27 KTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP-YGIFALVLTPTRELAYQIGDQFLVLGKV--MNL  103 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~-~~~~~lil~p~~~l~~q~~~~~~~~~~~--~~~  103 (182)
                      ..+++.|.+++..  .++..++.|++|||||.+...-+.+.+...+ ...+++++++|+..+.++.+.+......  .++
T Consensus         8 ~~Ln~~Q~~av~~--~~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~~~~~~iL~ltft~~aa~e~~~rl~~~~~~~~~~~   85 (647)
T 3lfu_A            8 DSLNDKQREAVAA--PRSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFTNKAAAEMRHRIGQLMGTSQGGM   85 (647)
T ss_dssp             TTCCHHHHHHHTC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTSCCCGGGEEEEESSHHHHHHHHHHHHHHHCSCCTTC
T ss_pred             hcCCHHHHHHHhC--CCCCEEEEECCCCCHHHHHHHHHHHHHHhCCCChhhEEEEeccHHHHHHHHHHHHHHhccccCCc
Confidence            4789999999973  3568999999999999997666666554432 2348999999999999998888776432  234


Q ss_pred             eEEEEE
Q psy4275         104 RVSIIT  109 (182)
Q Consensus       104 ~~~~~~  109 (182)
                      .+..++
T Consensus        86 ~v~Tfh   91 (647)
T 3lfu_A           86 WVGTFH   91 (647)
T ss_dssp             EEEEHH
T ss_pred             EEEcHH
Confidence            444443

>2o0j_A Terminase, DNA packaging protein GP17; nucleotide-binding fold, hydrolase; HET: DNA ADP; 1.80A {Enterobacteria phage T4} PDB: 2o0h_A* 2o0k_A*

Probab=97.88  E-value=5.3e-05  Score=59.33  Aligned_cols=122  Identities=11%  Similarity=0.068  Sum_probs=77.5

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCc--eE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNL--RV  105 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~--~~  105 (182)
                      .+.|+|...+..+...+..++..+-+.|||......++..+...+ +..+++++|+...+..+.+.++.+.+..+.  +-
T Consensus       163 ~L~p~Qk~il~~l~~~R~~vi~~sRq~GKT~l~a~~~l~~a~~~~-g~~v~~vA~t~~qA~~vf~~i~~mi~~~P~ll~~  241 (385)
T 2o0j_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFNK-DKAVGILAHKGSMSAEVLDRTKQAIELLPDFLQP  241 (385)
T ss_dssp             CCCHHHHHHHHHHHHSSEEEEEECSSSCHHHHHHHHHHHHHHSSS-SCEEEEEESSHHHHHHHHHHHHHHHHHSCTTTSC
T ss_pred             CCCHHHHHHHHhhccCcEEEEEEcCcCChhHHHHHHHHHHHHhCC-CCeEEEEeCCHHHHHHHHHHHHHHHHhChHhhhh
Confidence            689999999987655566889999999999987766666444433 458999999999988887777776654331  10


Q ss_pred             -EEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275         106 -SIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus       106 -~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                       ........    . .+.++..|.+.+..  .+-++.      .+..++|+||+|.+-+
T Consensus       242 ~~~~~~~~~----I-~f~nGs~i~~lsa~--~~slrG------~~~~~viiDE~a~~~~  287 (385)
T 2o0j_A          242 GIVEWNKGS----I-ELDNGSSIGAYASS--PDAVRG------NSFAMIYIEDCAFIPN  287 (385)
T ss_dssp             CEEEECSSE----E-EETTSCEEEEEECS--HHHHHT------SCCSEEEEESGGGSTT
T ss_pred             hhccCCccE----E-EeCCCCEEEEEECC--CCCccC------CCCCEEEechhhhcCC
Confidence             01111110    0 12245555444321  112233      1246899999998764

>1uaa_A REP helicase, protein (ATP-dependent DNA helicase REP.); complex (helicase/DNA), DNA unwinding, hydrolase/DNA complex; HET: DNA; 3.00A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19

Probab=97.79  E-value=4.6e-05  Score=63.86  Aligned_cols=81  Identities=19%  Similarity=0.076  Sum_probs=59.5

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCC-CCeeEEEEcCCHHHHHHHHHHHHHhhccC---Cc
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP-YGIFALVLTPTRELAYQIGDQFLVLGKVM---NL  103 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~-~~~~~lil~p~~~l~~q~~~~~~~~~~~~---~~  103 (182)
                      .+++.|.+++...  +++.++.|+.|||||.+...-+.+.+...+ ...++++++.|+..+.++.+.+.......   ++
T Consensus         2 ~L~~~Q~~av~~~--~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~~~~~~IL~lTfT~~Aa~em~~Rl~~~l~~~~~~~~   79 (673)
T 1uaa_A            2 RLNPGQQQAVEFV--TGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLGRKEARGL   79 (673)
T ss_dssp             CCCHHHHHHHHCC--SSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHSCTTTTTTS
T ss_pred             CCCHHHHHHHhCC--CCCEEEEeCCCCChHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHcCcccccCC
Confidence            5789999998753  578899999999999987655555544322 24579999999999999988887764432   35


Q ss_pred             eEEEEEc
Q psy4275         104 RVSIITG  110 (182)
Q Consensus       104 ~~~~~~~  110 (182)
                      .+..+++
T Consensus        80 ~v~Tfhs   86 (673)
T 1uaa_A           80 MISTFHT   86 (673)
T ss_dssp             EEEEHHH
T ss_pred             EEEeHHH
Confidence            5555443

>3cpe_A Terminase, DNA packaging protein GP17; large terminase, alternative initiation, ATP-binding, DNA- binding, hydrolase, nuclease; HET: DNA; 2.80A {Bacteriophage T4} PDB: 3ezk_A*

Probab=97.79  E-value=0.00024  Score=58.71  Aligned_cols=120  Identities=12%  Similarity=0.106  Sum_probs=79.1

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCC--ceE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMN--LRV  105 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~--~~~  105 (182)
                      .+.|+|+..+..+-..+..++..+-|.|||......++..+...+ +..++++.|+...+..+.+.++.+.+..+  ++.
T Consensus       163 ~l~p~Q~~i~~~l~~~r~~~i~~~Rq~GKS~~~a~~~l~~~~~~~-~~~i~~va~t~~qA~~~~~~i~~~i~~~p~~~~~  241 (592)
T 3cpe_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFNK-DKAVGILAHKGSMSAEVLDRTKQAIELLPDFLQP  241 (592)
T ss_dssp             CCCHHHHHHHHHHHHCSEEEEEECSSSCHHHHHHHHHHHHHHTSS-SCEEEEEESSHHHHHHHHHHHHHHHTTSCTTTSC
T ss_pred             cCCHHHHHHHHhhccccEEEEEEcCccChHHHHHHHHHHHHHhCC-CCeEEEEECCHHHHHHHHHHHHHHHHhChHhhcc
Confidence            589999999987644677899999999999987766666555543 45899999999999988888887766554  111


Q ss_pred             EEE-EcCCchhhhhHHhcCCCcEEEEC--hHHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275         106 SII-TGGMDMVDQGKELAKKPHIVIAT--PGRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus       106 ~~~-~~~~~~~~~~~~~~~~~~Ilv~T--~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      ... .....    . .+.++..|...+  |+.+    +..      +.+++|+||+|.+-+
T Consensus       242 ~~~~~~~~~----i-~~~nGs~i~~~s~~~~~l----rG~------~~~~~iiDE~~~~~~  287 (592)
T 3cpe_A          242 GIVEWNKGS----I-ELDNGSSIGAYASSPDAV----RGN------SFAMIYIEDCAFIPN  287 (592)
T ss_dssp             CEEEECSSE----E-EETTSCEEEEEECCHHHH----HHS------CCSEEEEETGGGCTT
T ss_pred             ccccCCccE----E-EecCCCEEEEEeCCCCCc----cCC------CcceEEEehhccCCc
Confidence            111 11111    1 123455554433  3332    331      256899999998755

>1pjr_A PCRA; DNA repair, DNA replication, SOS response, helicase, ATP- binding, DNA-binding; 2.50A {Geobacillus stearothermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1qhg_A* 3pjr_A* 2pjr_A* 1qhh_B* 1qhh_D* 1qhh_A* 1qhh_C* 2pjr_B*

Probab=97.69  E-value=0.00011  Score=62.20  Aligned_cols=81  Identities=19%  Similarity=0.111  Sum_probs=59.6

Q ss_pred             CCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCC-CCeeEEEEcCCHHHHHHHHHHHHHhhcc--CCc
Q psy4275          27 KTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP-YGIFALVLTPTRELAYQIGDQFLVLGKV--MNL  103 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~-~~~~~lil~p~~~l~~q~~~~~~~~~~~--~~~  103 (182)
                      ..+++.|.+++..  .+.+.++.|+.|||||.+...-+.+.+...+ ...++++++.|+..+.++.+.+......  .++
T Consensus        10 ~~Ln~~Q~~av~~--~~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~~~p~~IL~vTFTnkAA~Em~~Rl~~~l~~~~~~~   87 (724)
T 1pjr_A           10 AHLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLLGGAAEDV   87 (724)
T ss_dssp             TTSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHHHGGGGTTS
T ss_pred             hhCCHHHHHHHhC--CCCCEEEEEcCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHhcccccCc
Confidence            4789999999865  3568999999999999987665665554332 2347999999999999998887776432  234


Q ss_pred             eEEEEE
Q psy4275         104 RVSIIT  109 (182)
Q Consensus       104 ~~~~~~  109 (182)
                      .+..++
T Consensus        88 ~v~Tfh   93 (724)
T 1pjr_A           88 WISTFH   93 (724)
T ss_dssp             EEEEHH
T ss_pred             EEeeHH
Confidence            555444

>3u4q_A ATP-dependent helicase/nuclease subunit A; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_A*

Probab=97.60  E-value=0.00016  Score=64.55  Aligned_cols=69  Identities=25%  Similarity=0.155  Sum_probs=55.8

Q ss_pred             CCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCC---CCeeEEEEcCCHHHHHHHHHHHHHh
Q psy4275          27 KTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP---YGIFALVLTPTRELAYQIGDQFLVL   97 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~---~~~~~lil~p~~~l~~q~~~~~~~~   97 (182)
                      ..+++.|.+++..-  ++++++.|+.|||||.+.+--++..+....   ...+++++++|++.+.++.+.+...
T Consensus         9 ~~~t~eQ~~~i~~~--~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~~~~~~~il~~Tft~~aa~e~~~ri~~~   80 (1232)
T 3u4q_A            9 STWTDDQWNAIVST--GQDILVAAAAGSGKTAVLVERMIRKITAEENPIDVDRLLVVTFTNASAAEMKHRIAEA   80 (1232)
T ss_dssp             -CCCHHHHHHHHCC--SSCEEEEECTTCCHHHHHHHHHHHHHSCSSSCCCGGGEEEECSSHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHhCC--CCCEEEEecCCCcHHHHHHHHHHHHHhcCCCCCCccceEEEeccHHHHHHHHHHHHHH
Confidence            36899999998654  779999999999999997766777666532   3458999999999999998877764

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=97.43  E-value=0.00019  Score=57.07  Aligned_cols=86  Identities=19%  Similarity=0.106  Sum_probs=51.8

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA  122 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  122 (182)
                      .+-.++.|+.|+|||....-.+ .   .    .+.++++|++++++.+.+.+...    +.        .          
T Consensus       161 ~~v~~I~G~aGsGKTt~I~~~~-~---~----~~~lVlTpT~~aa~~l~~kl~~~----~~--------~----------  210 (446)
T 3vkw_A          161 AKVVLVDGVPGCGKTKEILSRV-N---F----EEDLILVPGRQAAEMIRRRANAS----GI--------I----------  210 (446)
T ss_dssp             SEEEEEEECTTSCHHHHHHHHC-C---T----TTCEEEESCHHHHHHHHHHHTTT----SC--------C----------
T ss_pred             ccEEEEEcCCCCCHHHHHHHHh-c---c----CCeEEEeCCHHHHHHHHHHhhhc----Cc--------c----------
Confidence            3456789999999998753322 1   1    25799999999998877665332    00        0          


Q ss_pred             CCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccc
Q psy4275         123 KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL  161 (182)
Q Consensus       123 ~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~  161 (182)
                      .....-|.|-+.++-  +. .....-..+.+|+||+.++
T Consensus       211 ~~~~~~V~T~dsfL~--~~-~~~~~~~~d~liiDE~sm~  246 (446)
T 3vkw_A          211 VATKDNVRTVDSFLM--NY-GKGARCQFKRLFIDEGLML  246 (446)
T ss_dssp             CCCTTTEEEHHHHHH--TT-TSSCCCCCSEEEEETGGGS
T ss_pred             ccccceEEEeHHhhc--CC-CCCCCCcCCEEEEeCcccC
Confidence            011233556555432  22 2112224789999999854

>1c4o_A DNA nucleotide excision repair enzyme UVRB; uvrabc, helicase, hypertherm protein, replication; HET: DNA BOG; 1.50A {Thermus thermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1d2m_A*

Probab=97.32  E-value=0.00051  Score=57.54  Aligned_cols=66  Identities=33%  Similarity=0.361  Sum_probs=50.6

Q ss_pred             CChHHHHhhhhhhhC----CC-cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhc
Q psy4275          28 TPTEIQKAIIPHVLN----DE-DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGK   99 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~----~~-~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~   99 (182)
                      .|++.|.+++..+.+    |. ..++.|.||+|||.++...+ ...     +..+|||+|+..++.|+++.++.++.
T Consensus         8 ~~~~~q~~ai~~l~~~~~~~~~~~~l~g~tgs~kt~~~a~~~-~~~-----~~~~lvv~~~~~~A~ql~~el~~~~~   78 (664)
T 1c4o_A            8 SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMAKVI-EAL-----GRPALVLAPNKILAAQLAAEFRELFP   78 (664)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHH-HHH-----TCCEEEEESSHHHHHHHHHHHHHHCT
T ss_pred             CCCCCChHHHHHHHHHHhcCCCcEEEEcCCCcHHHHHHHHHH-HHh-----CCCEEEEecCHHHHHHHHHHHHHHCC
Confidence            788889888776543    32 46788999999998864333 322     22599999999999999999999864

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=97.31  E-value=0.0013  Score=45.51  Aligned_cols=21  Identities=19%  Similarity=0.102  Sum_probs=17.5

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      ++.+++.||+|+|||..+...
T Consensus        38 g~~~~l~G~~G~GKTtL~~~i   58 (180)
T 3ec2_A           38 GKGLTFVGSPGVGKTHLAVAT   58 (180)
T ss_dssp             CCEEEECCSSSSSHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHH
Confidence            678999999999999875433

>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=97.24  E-value=0.0014  Score=54.88  Aligned_cols=67  Identities=22%  Similarity=0.210  Sum_probs=50.4

Q ss_pred             CChHHHHhhhhhhhC----CC-cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhcc
Q psy4275          28 TPTEIQKAIIPHVLN----DE-DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKV  100 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~----~~-~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~  100 (182)
                      .|+..|..++..+.+    +. ...+.|.||+|||.++.-.+ ...     +..+++|+|+..++.|+++.++.+...
T Consensus        12 ~p~~~Q~~~i~~l~~~~~~~~~~~~l~g~~gs~k~~~~a~~~-~~~-----~~~~lvv~~~~~~A~~l~~el~~~~~~   83 (661)
T 2d7d_A           12 QPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTVSNLI-KEV-----NKPTLVIAHNKTLAGQLYSEFKEFFPN   83 (661)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHH-HHH-----CCCEEEECSSHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEECcCCcHHHHHHHHHH-HHh-----CCCEEEEECCHHHHHHHHHHHHHHcCC
Confidence            688888887765543    43 46788999999998854333 322     125999999999999999999998653

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=97.19  E-value=0.0069  Score=46.15  Aligned_cols=25  Identities=8%  Similarity=-0.068  Sum_probs=18.9

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhh
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKW   68 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~   68 (182)
                      +.++++.||+|+|||.++-. ++..+
T Consensus        45 ~~~lli~GpPGTGKT~~v~~-v~~~L   69 (318)
T 3te6_A           45 NKLFYITNADDSTKFQLVND-VMDEL   69 (318)
T ss_dssp             CCEEEEECCCSHHHHHHHHH-HHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHH-HHHHH
Confidence            56899999999999988543 34444

>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=97.18  E-value=0.0008  Score=47.52  Aligned_cols=39  Identities=15%  Similarity=-0.059  Sum_probs=27.7

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTR   84 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~   84 (182)
                      |+-.++.|++|+|||+.++-.+.....+   +.+++++.|..
T Consensus         8 g~i~v~~G~mgsGKTT~ll~~a~r~~~~---g~kV~v~k~~~   46 (191)
T 1xx6_A            8 GWVEVIVGPMYSGKSEELIRRIRRAKIA---KQKIQVFKPEI   46 (191)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHT---TCCEEEEEEC-
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHHC---CCEEEEEEecc
Confidence            5567888999999998866554444333   56899998873

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=97.14  E-value=0.00043  Score=46.86  Aligned_cols=28  Identities=14%  Similarity=0.191  Sum_probs=20.4

Q ss_pred             HhhhhhhhCCCcEEEECCCCChHHHHHHH
Q psy4275          34 KAIIPHVLNDEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        34 ~~~~~~~~~~~~~li~~~tg~GKT~~~~~   62 (182)
                      ..++..+ .++...+.||+|+|||..+-.
T Consensus        28 ~~~l~~~-~g~~~~l~G~~G~GKTtL~~~   55 (149)
T 2kjq_A           28 VYVLRHK-HGQFIYVWGEEGAGKSHLLQA   55 (149)
T ss_dssp             HHHCCCC-CCSEEEEESSSTTTTCHHHHH
T ss_pred             HHHHHhc-CCCEEEEECCCCCCHHHHHHH
Confidence            3333333 678899999999999987543

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=97.08  E-value=0.00082  Score=51.52  Aligned_cols=40  Identities=8%  Similarity=-0.126  Sum_probs=27.3

Q ss_pred             ChHHHHhhhhhhh----CCC---cEEEECCCCChHHHHHHHHHHHhh
Q psy4275          29 PTEIQKAIIPHVL----NDE---DCIGCAKTGSGKTLAFALPILQKW   68 (182)
Q Consensus        29 ~~~~Q~~~~~~~~----~~~---~~li~~~tg~GKT~~~~~~~~~~~   68 (182)
                      ..|||.+.+..+.    +++   ..++.||.|+|||..+...+-...
T Consensus         3 ~~pw~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~~la~~l~   49 (334)
T 1a5t_A            3 WYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLL   49 (334)
T ss_dssp             CCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             CCCchHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHHHHHHHHHh
Confidence            3577777665543    332   389999999999998765554443

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=96.97  E-value=0.0053  Score=44.35  Aligned_cols=91  Identities=11%  Similarity=0.068  Sum_probs=51.4

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA  122 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  122 (182)
                      |.-.++.|++|+|||+.++-.+.....+   +.+++++.|...-  .   ....+....|+.                  
T Consensus        12 G~i~litG~mGsGKTT~ll~~~~r~~~~---g~kVli~~~~~d~--r---~~~~i~srlG~~------------------   65 (223)
T 2b8t_A           12 GWIEFITGPMFAGKTAELIRRLHRLEYA---DVKYLVFKPKIDT--R---SIRNIQSRTGTS------------------   65 (223)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHHT---TCCEEEEEECCCG--G---GCSSCCCCCCCS------------------
T ss_pred             cEEEEEECCCCCcHHHHHHHHHHHHHhc---CCEEEEEEeccCc--h---HHHHHHHhcCCC------------------
Confidence            5567888999999999865554444333   4578888765321  0   000111211111                  


Q ss_pred             CCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccc
Q psy4275         123 KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLS  162 (182)
Q Consensus       123 ~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~  162 (182)
                       ...+-+.+...+.+.+....  .-.+.++||+||++.+.
T Consensus        66 -~~~~~~~~~~~i~~~i~~~~--~~~~~dvViIDEaQ~l~  102 (223)
T 2b8t_A           66 -LPSVEVESAPEILNYIMSNS--FNDETKVIGIDEVQFFD  102 (223)
T ss_dssp             -SCCEEESSTHHHHHHHHSTT--SCTTCCEEEECSGGGSC
T ss_pred             -ccccccCCHHHHHHHHHHHh--hCCCCCEEEEecCccCc
Confidence             11233455666666665521  12346899999999754

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=96.94  E-value=0.0014  Score=47.08  Aligned_cols=40  Identities=18%  Similarity=0.141  Sum_probs=28.3

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRE   85 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~   85 (182)
                      |+-.+++|++|+|||+.++-.+.....+   +.+++++.|...
T Consensus        28 G~l~vitG~MgsGKTT~lL~~a~r~~~~---g~kVli~k~~~d   67 (214)
T 2j9r_A           28 GWIEVICGSMFSGKSEELIRRVRRTQFA---KQHAIVFKPCID   67 (214)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHHT---TCCEEEEECC--
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHHC---CCEEEEEEeccC
Confidence            4455688999999999866665555444   568999998754

>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=96.93  E-value=0.0069  Score=42.62  Aligned_cols=19  Identities=21%  Similarity=0.205  Sum_probs=15.8

Q ss_pred             CcEEEECCCCChHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~   62 (182)
                      .++++.||+|+|||..+..
T Consensus        39 ~~~ll~G~~G~GKT~l~~~   57 (226)
T 2chg_A           39 PHLLFSGPPGTGKTATAIA   57 (226)
T ss_dssp             CCEEEECSTTSSHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHH
Confidence            4699999999999987543

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=96.89  E-value=0.0041  Score=45.95  Aligned_cols=22  Identities=23%  Similarity=-0.068  Sum_probs=17.5

Q ss_pred             CCcEEEECCCCChHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      .+++++.||+|+|||..+....
T Consensus        64 ~~~vLl~G~~GtGKT~la~~ia   85 (272)
T 1d2n_A           64 LVSVLLEGPPHSGKTALAAKIA   85 (272)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHH
T ss_pred             CeEEEEECCCCCcHHHHHHHHH
Confidence            3579999999999998864433

>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=96.85  E-value=0.0057  Score=46.39  Aligned_cols=36  Identities=14%  Similarity=0.067  Sum_probs=23.2

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      ++++++.||+|+|||..+-.. ...+...  +..++++.
T Consensus        37 ~~~lll~G~~GtGKT~la~~i-~~~~~~~--~~~~~~i~   72 (324)
T 1l8q_A           37 YNPIFIYGSVGTGKTHLLQAA-GNEAKKR--GYRVIYSS   72 (324)
T ss_dssp             CSSEEEECSSSSSHHHHHHHH-HHHHHHT--TCCEEEEE
T ss_pred             CCeEEEECCCCCcHHHHHHHH-HHHHHHC--CCEEEEEE
Confidence            468999999999999885433 3333322  33455554

>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=96.79  E-value=0.0024  Score=45.82  Aligned_cols=22  Identities=14%  Similarity=0.013  Sum_probs=17.9

Q ss_pred             CCCcEEEECCCCChHHHHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~   63 (182)
                      .++++++.||+|+|||..+...
T Consensus        51 ~~~~~ll~G~~G~GKT~la~~l   72 (242)
T 3bos_A           51 GVQAIYLWGPVKSGRTHLIHAA   72 (242)
T ss_dssp             SCSEEEEECSTTSSHHHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHHHH
Confidence            3678999999999999885433

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=96.73  E-value=0.0025  Score=45.09  Aligned_cols=38  Identities=13%  Similarity=-0.034  Sum_probs=28.2

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      ++-.++.||+|+|||...+-.+-....+   +.+++++.|.
T Consensus        20 g~l~fiyG~MgsGKTt~Ll~~i~n~~~~---~~kvl~~kp~   57 (195)
T 1w4r_A           20 GQIQVILGPMFSGKSTELMRRVRRFQIA---QYKCLVIKYA   57 (195)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHHHHT---TCCEEEEEET
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHHHc---CCeEEEEccc
Confidence            5677889999999998755555554444   4578888876

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=96.72  E-value=0.0034  Score=45.60  Aligned_cols=39  Identities=13%  Similarity=-0.010  Sum_probs=29.1

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTR   84 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~   84 (182)
                      |+-.++.|++|+|||+.++-.+.....+   +.+++++.|..
T Consensus        19 g~l~v~~G~MgsGKTT~lL~~~~r~~~~---g~kvli~kp~~   57 (234)
T 2orv_A           19 GQIQVILGPMFSGKSTELMRRVRRFQIA---QYKCLVIKYAK   57 (234)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHHHTT---TCCEEEEEETT
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHHHC---CCeEEEEeecC
Confidence            5667888999999999866665555444   56888888764

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=96.66  E-value=0.016  Score=39.55  Aligned_cols=21  Identities=24%  Similarity=0.145  Sum_probs=17.2

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      .+++++.||+|+|||..+...
T Consensus        43 ~~~vll~G~~G~GKT~la~~~   63 (187)
T 2p65_A           43 KNNPILLGDPGVGKTAIVEGL   63 (187)
T ss_dssp             SCEEEEESCGGGCHHHHHHHH
T ss_pred             CCceEEECCCCCCHHHHHHHH
Confidence            468999999999999886443

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=96.62  E-value=0.016  Score=43.88  Aligned_cols=18  Identities=22%  Similarity=0.259  Sum_probs=13.2

Q ss_pred             EEEECCCCChHHHHHHHH
Q psy4275          46 CIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~   63 (182)
                      .++.||+|+|||..+...
T Consensus        51 ~L~~G~~G~GKT~la~~l   68 (324)
T 3u61_B           51 ILHSPSPGTGKTTVAKAL   68 (324)
T ss_dssp             EEECSSTTSSHHHHHHHH
T ss_pred             EEeeCcCCCCHHHHHHHH
Confidence            455667999999886443

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=96.61  E-value=0.009  Score=45.97  Aligned_cols=21  Identities=29%  Similarity=0.313  Sum_probs=17.3

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      ++++++.||+|+|||..+-..
T Consensus        44 ~~~vll~G~~G~GKT~l~~~~   64 (387)
T 2v1u_A           44 PSNALLYGLTGTGKTAVARLV   64 (387)
T ss_dssp             CCCEEECBCTTSSHHHHHHHH
T ss_pred             CCcEEEECCCCCCHHHHHHHH
Confidence            568999999999999885433

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=96.53  E-value=0.0047  Score=44.36  Aligned_cols=40  Identities=13%  Similarity=-0.041  Sum_probs=27.4

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRE   85 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~   85 (182)
                      |.-.+++|++|+|||+..+-.+.....+   +.+++++.|...
T Consensus        28 G~I~vitG~M~sGKTT~Llr~~~r~~~~---g~kvli~kp~~D   67 (219)
T 3e2i_A           28 GWIECITGSMFSGKSEELIRRLRRGIYA---KQKVVVFKPAID   67 (219)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHHHHT---TCCEEEEEEC--
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHHc---CCceEEEEeccC
Confidence            5567889999999998765554433333   457899988754

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=96.51  E-value=0.033  Score=40.00  Aligned_cols=52  Identities=12%  Similarity=0.100  Sum_probs=33.5

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHH
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFL   95 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~   95 (182)
                      +..|.-.++.|++|+|||..+...+......   +..++++..... ..++.+.+.
T Consensus        20 l~~G~~~~i~G~~GsGKTtl~~~~~~~~~~~---~~~v~~~~~e~~-~~~~~~~~~   71 (247)
T 2dr3_A           20 IPERNVVLLSGGPGTGKTIFSQQFLWNGLKM---GEPGIYVALEEH-PVQVRQNMA   71 (247)
T ss_dssp             EETTCEEEEEECTTSSHHHHHHHHHHHHHHT---TCCEEEEESSSC-HHHHHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHHHhc---CCeEEEEEccCC-HHHHHHHHH
Confidence            3457788999999999999866555554433   346777765433 244444443

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=96.45  E-value=0.011  Score=47.00  Aligned_cols=21  Identities=19%  Similarity=0.036  Sum_probs=17.0

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      .+++++.||+|+|||..+-..
T Consensus       130 ~~~lll~Gp~G~GKTtLa~ai  150 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLLQSI  150 (440)
T ss_dssp             SCCEEEECSSSSSHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHH
Confidence            357999999999999875433

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=96.32  E-value=0.032  Score=42.73  Aligned_cols=20  Identities=25%  Similarity=0.322  Sum_probs=16.9

Q ss_pred             CCcEEEECCCCChHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~   62 (182)
                      ++.+++.||+|+|||..+-.
T Consensus        45 ~~~vli~G~~G~GKTtl~~~   64 (386)
T 2qby_A           45 PNNIFIYGLTGTGKTAVVKF   64 (386)
T ss_dssp             CCCEEEEECTTSSHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHH
Confidence            56899999999999988544

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=96.30  E-value=0.03  Score=39.78  Aligned_cols=41  Identities=17%  Similarity=0.056  Sum_probs=27.6

Q ss_pred             hhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcC
Q psy4275          39 HVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTP   82 (182)
Q Consensus        39 ~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p   82 (182)
                      .+..|..+++.||+|+|||..+...+......   +..++++..
T Consensus        19 gi~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~---~~~v~~~~~   59 (235)
T 2w0m_A           19 GIPQGFFIALTGEPGTGKTIFSLHFIAKGLRD---GDPCIYVTT   59 (235)
T ss_dssp             SEETTCEEEEECSTTSSHHHHHHHHHHHHHHH---TCCEEEEES
T ss_pred             CCcCCCEEEEEcCCCCCHHHHHHHHHHHHHHC---CCeEEEEEc
Confidence            34557788999999999998765554443333   335676654

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=96.28  E-value=0.032  Score=39.42  Aligned_cols=36  Identities=22%  Similarity=0.024  Sum_probs=29.2

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      ...+++.+++|.|||.+++-.++..+..   +.+++++-
T Consensus        28 ~g~i~v~tG~GkGKTTaA~GlalRA~g~---G~rV~~vQ   63 (196)
T 1g5t_A           28 RGIIIVFTGNGKGKTTAAFGTAARAVGH---GKNVGVVQ   63 (196)
T ss_dssp             CCCEEEEESSSSCHHHHHHHHHHHHHHT---TCCEEEEE
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHC---CCeEEEEE
Confidence            4578888999999999988777776655   66888884

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=96.27  E-value=0.0052  Score=51.32  Aligned_cols=59  Identities=17%  Similarity=0.219  Sum_probs=42.5

Q ss_pred             CChHHHHhhhhhhhC--CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHH
Q psy4275          28 TPTEIQKAIIPHVLN--DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGD   92 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~--~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~   92 (182)
                      .++.-|.+++..+..  ....++.|+-|.|||...-+.+.. +..     +++|.+|+..-+..+.+
T Consensus       175 ~~T~dQ~~al~~~~~~~~~~~vlta~RGRGKSa~lG~~~a~-~~~-----~~~vtAP~~~a~~~l~~  235 (671)
T 2zpa_A          175 APQPEQQQLLKQLMTMPPGVAAVTAARGRGKSALAGQLISR-IAG-----RAIVTAPAKASTDVLAQ  235 (671)
T ss_dssp             SCCHHHHHHHHHHTTCCSEEEEEEECTTSSHHHHHHHHHHH-SSS-----CEEEECSSCCSCHHHHH
T ss_pred             CCCHHHHHHHHHHHHhhhCeEEEecCCCCCHHHHHHHHHHH-HHh-----CcEEECCCHHHHHHHHH
Confidence            578899999988776  446789999999999765444443 332     46899999877654433

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=96.18  E-value=0.025  Score=42.42  Aligned_cols=19  Identities=26%  Similarity=0.160  Sum_probs=16.0

Q ss_pred             cEEEECCCCChHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~   63 (182)
                      +.++.||+|+|||..+...
T Consensus        48 ~~ll~G~~G~GKT~la~~l   66 (327)
T 1iqp_A           48 HLLFAGPPGVGKTTAALAL   66 (327)
T ss_dssp             EEEEESCTTSSHHHHHHHH
T ss_pred             eEEEECcCCCCHHHHHHHH
Confidence            7999999999999886433

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=96.17  E-value=0.031  Score=37.92  Aligned_cols=73  Identities=18%  Similarity=0.203  Sum_probs=52.2

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +.++||.++++.-++.+++.++..    ++.+..++|+.+..++...+    .+..+|+|+|.-      -. ..+++..
T Consensus        35 ~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T~~------~~-~Gld~~~  103 (163)
T 2hjv_A           35 PDSCIIFCRTKEHVNQLTDELDDL----GYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDV------AA-RGIDIEN  103 (163)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECGG------GT-TTCCCSC
T ss_pred             CCcEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEECCh------hh-cCCchhc
Confidence            347999999999999888877664    78899999988765444332    246789999932      12 4566777


Q ss_pred             ccEEEEec
Q psy4275         150 IKFLVLDE  157 (182)
Q Consensus       150 ~~~iI~DE  157 (182)
                      ++++|.-+
T Consensus       104 ~~~Vi~~~  111 (163)
T 2hjv_A          104 ISLVINYD  111 (163)
T ss_dssp             CSEEEESS
T ss_pred             CCEEEEeC
Confidence            77777543

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=96.16  E-value=0.021  Score=43.97  Aligned_cols=18  Identities=22%  Similarity=0.355  Sum_probs=15.6

Q ss_pred             cEEEECCCCChHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~   62 (182)
                      ++++.||+|+|||..+-.
T Consensus        46 ~~li~G~~G~GKTtl~~~   63 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTLRK   63 (389)
T ss_dssp             EEEEECCTTSSHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHH
Confidence            799999999999988643

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=96.14  E-value=0.015  Score=44.20  Aligned_cols=20  Identities=20%  Similarity=0.204  Sum_probs=16.9

Q ss_pred             CcEEEECCCCChHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~   63 (182)
                      .++++.||+|+|||..+-..
T Consensus        56 ~~vll~G~~GtGKT~la~~i   75 (338)
T 3pfi_A           56 DHILFSGPAGLGKTTLANII   75 (338)
T ss_dssp             CCEEEECSTTSSHHHHHHHH
T ss_pred             CeEEEECcCCCCHHHHHHHH
Confidence            58999999999999886443

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=96.09  E-value=0.0071  Score=46.69  Aligned_cols=21  Identities=24%  Similarity=0.145  Sum_probs=16.8

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      .+++++.||+|+|||..+...
T Consensus        45 ~~~vll~G~~G~GKT~la~~l   65 (384)
T 2qby_B           45 KFSNLFLGLTGTGKTFVSKYI   65 (384)
T ss_dssp             CCEEEEEECTTSSHHHHHHHH
T ss_pred             CCcEEEECCCCCCHHHHHHHH
Confidence            457999999999999885433

>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=96.08  E-value=0.046  Score=37.48  Aligned_cols=71  Identities=15%  Similarity=0.199  Sum_probs=51.8

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +.++||.++++..++.+++.+...    ++.+..++|+.+...+...+    .+..+|+|+|.-      -. ..+++..
T Consensus        34 ~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~~------~~-~Gid~~~  102 (175)
T 2rb4_A           34 IGQAIIFCQTRRNAKWLTVEMIQD----GHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNV------CA-RGIDVKQ  102 (175)
T ss_dssp             CSEEEEECSCHHHHHHHHHHHHTT----TCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECCS------CC-TTTCCTT
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEecc------hh-cCCCccc
Confidence            458999999999988888777653    78899999988765544332    246789999922      12 4567778


Q ss_pred             ccEEEE
Q psy4275         150 IKFLVL  155 (182)
Q Consensus       150 ~~~iI~  155 (182)
                      ++++|.
T Consensus       103 ~~~Vi~  108 (175)
T 2rb4_A          103 VTIVVN  108 (175)
T ss_dssp             EEEEEE
T ss_pred             CCEEEE
Confidence            888774

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=95.94  E-value=0.019  Score=43.42  Aligned_cols=21  Identities=5%  Similarity=-0.417  Sum_probs=16.8

Q ss_pred             CcEEEECCCCChHHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~   64 (182)
                      ++.++.||.|+|||..+...+
T Consensus        19 ~~~Lf~Gp~G~GKtt~a~~la   39 (305)
T 2gno_A           19 ISILINGEDLSYPREVSLELP   39 (305)
T ss_dssp             EEEEEECSSSSHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHH
Confidence            478999999999998765443

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=95.93  E-value=0.053  Score=43.21  Aligned_cols=43  Identities=12%  Similarity=-0.056  Sum_probs=30.6

Q ss_pred             hhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275          39 HVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus        39 ~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      .+..|.-+++.|++|+|||..++..+.......  +..++|+...
T Consensus       199 Gl~~G~liiI~G~pG~GKTtl~l~ia~~~~~~~--g~~Vl~~s~E  241 (454)
T 2r6a_A          199 GFQRSDLIIVAARPSVGKTAFALNIAQNVATKT--NENVAIFSLE  241 (454)
T ss_dssp             SBCTTCEEEEECCTTSCHHHHHHHHHHHHHHHS--SCCEEEEESS
T ss_pred             CCCCCCEEEEECCCCCCHHHHHHHHHHHHHHhC--CCcEEEEECC
Confidence            345577899999999999998776666655432  3367777644

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=95.88  E-value=0.058  Score=36.57  Aligned_cols=72  Identities=13%  Similarity=0.150  Sum_probs=51.4

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +.++||.++++.-++.+++.++..    ++.+..++|+.+..++...+    .+..+|+|+|.-      -. ..+++..
T Consensus        30 ~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~------~~-~G~d~~~   98 (165)
T 1fuk_A           30 VTQAVIFCNTRRKVEELTTKLRND----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDL------LA-RGIDVQQ   98 (165)
T ss_dssp             CSCEEEEESSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGG------GT-TTCCCCS
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHc----CCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEEcCh------hh-cCCCccc
Confidence            458999999999998888877664    67889999988765444332    246789999932      12 4456777


Q ss_pred             ccEEEEe
Q psy4275         150 IKFLVLD  156 (182)
Q Consensus       150 ~~~iI~D  156 (182)
                      ++++|.-
T Consensus        99 ~~~Vi~~  105 (165)
T 1fuk_A           99 VSLVINY  105 (165)
T ss_dssp             CSEEEES
T ss_pred             CCEEEEe
Confidence            7776654

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=95.87  E-value=0.055  Score=40.97  Aligned_cols=45  Identities=9%  Similarity=-0.146  Sum_probs=32.1

Q ss_pred             hhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275          36 IIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus        36 ~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      .+.-+..|.-+++.|++|+|||..++-.+.....+   +..++++.-.
T Consensus        61 ~lgGl~~G~l~li~G~pG~GKTtl~l~ia~~~a~~---g~~vl~~slE  105 (315)
T 3bh0_A           61 MTYGYKRRNFVLIAARPSMGKTAFALKQAKNMSDN---DDVVNLHSLE  105 (315)
T ss_dssp             HHSSBCTTCEEEEECCTTSSHHHHHHHHHHHHHTT---TCEEEEEESS
T ss_pred             hcCCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHc---CCeEEEEECC
Confidence            33445557789999999999998877666665544   3468887744

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=95.87  E-value=0.014  Score=46.62  Aligned_cols=20  Identities=25%  Similarity=0.225  Sum_probs=16.4

Q ss_pred             CcEEEECCCCChHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~   63 (182)
                      .++++.||+|+|||..+-..
T Consensus        51 ~~vLL~GppGtGKTtlAr~i   70 (447)
T 3pvs_A           51 HSMILWGPPGTGKTTLAEVI   70 (447)
T ss_dssp             CEEEEECSTTSSHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHHHH
Confidence            36899999999999886433

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=95.85  E-value=0.077  Score=40.41  Aligned_cols=19  Identities=16%  Similarity=0.179  Sum_probs=15.8

Q ss_pred             CcEEEECCCCChHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~   62 (182)
                      .+.++.||+|+|||..+-.
T Consensus        37 ~~~ll~Gp~G~GKTtl~~~   55 (354)
T 1sxj_E           37 PHLLLYGPNGTGKKTRCMA   55 (354)
T ss_dssp             CCEEEECSTTSSHHHHHHT
T ss_pred             CeEEEECCCCCCHHHHHHH
Confidence            4599999999999988543

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=95.80  E-value=0.076  Score=42.17  Aligned_cols=42  Identities=14%  Similarity=-0.031  Sum_probs=29.8

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      +..|.-+++.|++|+|||..++-.+.......  +..++++...
T Consensus       197 l~~G~l~ii~G~pg~GKT~lal~ia~~~a~~~--g~~vl~~slE  238 (444)
T 2q6t_A          197 LGPGSLNIIAARPAMGKTAFALTIAQNAALKE--GVGVGIYSLE  238 (444)
T ss_dssp             CCTTCEEEEEECTTSCHHHHHHHHHHHHHHTT--CCCEEEEESS
T ss_pred             cCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhC--CCeEEEEECC
Confidence            44467789999999999998776666655432  3467777654

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=95.75  E-value=0.15  Score=36.46  Aligned_cols=44  Identities=9%  Similarity=-0.172  Sum_probs=28.8

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhccC---CCCeeEEEEcCC
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCED---PYGIFALVLTPT   83 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~---~~~~~~lil~p~   83 (182)
                      +..|.-+.+.||+|+|||..+...+...+...   ..+..++++...
T Consensus        21 i~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~   67 (243)
T 1n0w_A           21 IETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTE   67 (243)
T ss_dssp             EETTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESS
T ss_pred             CcCCeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECC
Confidence            44577899999999999998766665433321   012356666543

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=95.74  E-value=0.024  Score=42.71  Aligned_cols=21  Identities=24%  Similarity=0.105  Sum_probs=17.2

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      ..++++.||+|+|||..+-..
T Consensus        38 ~~~vll~G~~GtGKT~la~~i   58 (324)
T 1hqc_A           38 LEHLLLFGPPGLGKTTLAHVI   58 (324)
T ss_dssp             CCCCEEECCTTCCCHHHHHHH
T ss_pred             CCcEEEECCCCCCHHHHHHHH
Confidence            468999999999999886433

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=95.71  E-value=0.16  Score=35.41  Aligned_cols=71  Identities=17%  Similarity=0.264  Sum_probs=50.4

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +.++||.++++.-++.+++.++..    ++.+..++|+.+..++...+    .+..+|+|+|.-      .. ..+++..
T Consensus        54 ~~~~lVF~~~~~~~~~l~~~L~~~----g~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~~------~~-~Gldi~~  122 (191)
T 2p6n_A           54 PPPVLIFAEKKADVDAIHEYLLLK----GVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDV------AS-KGLDFPA  122 (191)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHH----TCCEEEECTTSCHHHHHHHHHHHHHTSCSEEEECHH------HH-TTCCCCC
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEcCc------hh-cCCCccc
Confidence            347999999999999888887765    78899999988765544332    246889999932      11 3455666


Q ss_pred             ccEEEE
Q psy4275         150 IKFLVL  155 (182)
Q Consensus       150 ~~~iI~  155 (182)
                      ++++|.
T Consensus       123 v~~VI~  128 (191)
T 2p6n_A          123 IQHVIN  128 (191)
T ss_dssp             CSEEEE
T ss_pred             CCEEEE
Confidence            666655

>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=95.71  E-value=0.051  Score=38.63  Aligned_cols=71  Identities=17%  Similarity=0.252  Sum_probs=50.8

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +.++||.++++.-++.+++.+...    ++.+..++|+.+..++...+    .+..+|+|+|.-      .. ..+++..
T Consensus        31 ~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~~------~~-~Gidi~~   99 (212)
T 3eaq_A           31 PDRAMVFTRTKAETEEIAQGLLRL----GHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDV------AA-RGLDIPQ   99 (212)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHH----TCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECTT------TT-CSSSCCC
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHc----CCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecCh------hh-cCCCCcc
Confidence            448999999999999888877664    78899999998765544333    246789999932      12 4456667


Q ss_pred             ccEEEE
Q psy4275         150 IKFLVL  155 (182)
Q Consensus       150 ~~~iI~  155 (182)
                      ++++|.
T Consensus       100 v~~Vi~  105 (212)
T 3eaq_A          100 VDLVVH  105 (212)
T ss_dssp             BSEEEE
T ss_pred             CcEEEE
Confidence            766653

>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=95.51  E-value=0.056  Score=37.03  Aligned_cols=73  Identities=11%  Similarity=0.098  Sum_probs=52.0

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +.++||.++++.-++.+++.+...    ++.+..++|+.+..++...+    .+..+|+|+|.-      -. ..+++..
T Consensus        31 ~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vLvaT~~------~~-~Gldi~~   99 (172)
T 1t5i_A           31 FNQVVIFVKSVQRCIALAQLLVEQ----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNL------FG-RGMDIER   99 (172)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSC------CS-TTCCGGG
T ss_pred             CCcEEEEECCHHHHHHHHHHHHhc----CCCEEEEECCCCHHHHHHHHHHHHCCCCcEEEECCc------hh-cCcchhh
Confidence            458999999999999888887664    78889999988765544332    246789999932      11 4456777


Q ss_pred             ccEEEEec
Q psy4275         150 IKFLVLDE  157 (182)
Q Consensus       150 ~~~iI~DE  157 (182)
                      ++++|.-+
T Consensus       100 ~~~Vi~~d  107 (172)
T 1t5i_A          100 VNIAFNYD  107 (172)
T ss_dssp             CSEEEESS
T ss_pred             CCEEEEEC
Confidence            77776543

>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=95.49  E-value=0.26  Score=40.06  Aligned_cols=89  Identities=11%  Similarity=0.079  Sum_probs=60.8

Q ss_pred             HHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHH
Q psy4275          61 ALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLA  136 (182)
Q Consensus        61 ~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~  136 (182)
                      +..+...+.....+.++||.++++.-++.+++.++..... ++.+..++|+.....+...+    .+..+|+|+|.-   
T Consensus       326 ~~~l~~~~~~~~~~~~~iVF~~s~~~~~~l~~~L~~~~~~-~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLvaT~~---  401 (563)
T 3i5x_A          326 VEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKK-DLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDV---  401 (563)
T ss_dssp             HHHHHHHHHHTTTCCEEEEECSCHHHHHHHHHHHHHHHTT-TSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGG---
T ss_pred             HHHHHHHHhhcCCCCcEEEEcCcHHHHHHHHHHHHHhccC-CceEEEecCCCCHHHHHHHHHHHhcCCCCEEEEcch---
Confidence            3334444443344668999999999999999888876442 67888999988765544332    247889999942   


Q ss_pred             HHHhcCCCCCCCCccEEEEec
Q psy4275         137 DHLDTCNTFSLNRIKFLVLDE  157 (182)
Q Consensus       137 ~~~~~~~~~~~~~~~~iI~DE  157 (182)
                         -. ..+++.++++||.-.
T Consensus       402 ---~~-~GiDip~v~~VI~~~  418 (563)
T 3i5x_A          402 ---GA-RGMDFPNVHEVLQIG  418 (563)
T ss_dssp             ---GT-SSCCCTTCCEEEEES
T ss_pred             ---hh-cCCCcccCCEEEEEC
Confidence               22 456777787777554

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=95.47  E-value=0.56  Score=35.25  Aligned_cols=20  Identities=10%  Similarity=0.037  Sum_probs=16.5

Q ss_pred             CcEEEECCCCChHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~   63 (182)
                      +.+++.||.|+|||......
T Consensus        31 ~~v~i~G~~G~GKT~L~~~~   50 (357)
T 2fna_A           31 PITLVLGLRRTGKSSIIKIG   50 (357)
T ss_dssp             SEEEEEESTTSSHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHH
Confidence            67899999999999875433

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=95.43  E-value=0.042  Score=36.50  Aligned_cols=21  Identities=14%  Similarity=0.097  Sum_probs=18.0

Q ss_pred             hCCCcEEEECCCCChHHHHHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~   61 (182)
                      ..+.++++.||+|+|||..+-
T Consensus        22 ~~~~~vll~G~~GtGKt~lA~   42 (145)
T 3n70_A           22 ETDIAVWLYGAPGTGRMTGAR   42 (145)
T ss_dssp             TCCSCEEEESSTTSSHHHHHH
T ss_pred             CCCCCEEEECCCCCCHHHHHH
Confidence            347799999999999998864

>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=95.32  E-value=0.18  Score=40.56  Aligned_cols=86  Identities=12%  Similarity=0.060  Sum_probs=55.1

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcC-------Cch-
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGG-------MDM-  114 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~-------~~~-  114 (182)
                      +....+.|-+|+||+..+...+ .. .    +..+++|+|+...+.++++.++.+...   .|..+-..       .+. 
T Consensus        14 ~~~~~l~g~~gs~ka~~~a~l~-~~-~----~~p~lvv~~~~~~A~~l~~~l~~~~~~---~v~~fp~~e~lpyd~~~p~   84 (483)
T 3hjh_A           14 GEQRLLGELTGAACATLVAEIA-ER-H----AGPVVLIAPDMQNALRLHDEISQFTDQ---MVMNLADWETLPYDSFSPH   84 (483)
T ss_dssp             TCEEEEECCCTTHHHHHHHHHH-HH-S----SSCEEEEESSHHHHHHHHHHHHHTCSS---CEEECCCCCSCTTCSSCCC
T ss_pred             CCeEEEeCCCchHHHHHHHHHH-HH-h----CCCEEEEeCCHHHHHHHHHHHHhhCCC---cEEEEeCcccccccccCCC
Confidence            5577889999999998743322 22 1    235899999999999999999988653   24333221       000 


Q ss_pred             ----hhhh----HHhcCCCcEEEEChHHHHH
Q psy4275         115 ----VDQG----KELAKKPHIVIATPGRLAD  137 (182)
Q Consensus       115 ----~~~~----~~~~~~~~Ilv~T~~~l~~  137 (182)
                          ..+.    +....+..|+|+|...++.
T Consensus        85 ~~~~~~Rl~~l~~L~~~~~~ivv~sv~al~~  115 (483)
T 3hjh_A           85 QDIISSRLSTLYQLPTMQRGVLIVPVNTLMQ  115 (483)
T ss_dssp             HHHHHHHHHHHHHGGGCCSSEEEEEHHHHHB
T ss_pred             hHHHHHHHHHHHHHHhCCCCEEEEEHHHHhh
Confidence                0111    1122356799999888864

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.27  E-value=0.017  Score=45.86  Aligned_cols=60  Identities=17%  Similarity=0.163  Sum_probs=38.1

Q ss_pred             CccCCccCCCCCHHHHHHHHHC---CCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHH
Q psy4275           3 DPIKSFTDLKLNPWLIRQCQTI---GVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPIL   65 (182)
Q Consensus         3 ~~~~~~~~~~l~~~i~~~l~~~---~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~   65 (182)
                      +|-.+|++.+--++..+.+.+.   .+..|.-++...+   ...+.+++.||+|+|||..+-..+-
T Consensus       175 ~p~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~---~~prGvLLyGPPGTGKTllAkAiA~  237 (434)
T 4b4t_M          175 KPTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGI---RAPKGALMYGPPGTGKTLLARACAA  237 (434)
T ss_dssp             SCSCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCC---CCCCEEEEESCTTSSHHHHHHHHHH
T ss_pred             CCCCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCCeeEEECcCCCCHHHHHHHHHH
Confidence            4566899997666666666542   1223443433333   2256899999999999988644433

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=95.25  E-value=0.34  Score=39.64  Aligned_cols=86  Identities=12%  Similarity=0.096  Sum_probs=59.7

Q ss_pred             HHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHH
Q psy4275          64 ILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHL  139 (182)
Q Consensus        64 ~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~  139 (182)
                      +...+.....+.++||.++++.-++.+++.++..... ++.+..++|+.....+...+    .+..+|+|+|.-      
T Consensus       278 l~~~~~~~~~~~~~iVF~~t~~~~~~l~~~L~~~~~~-~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVaT~~------  350 (579)
T 3sqw_A          278 IKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKK-DLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDV------  350 (579)
T ss_dssp             HHHHHHHTTTCCEEEEECSSHHHHHHHHHHHHHHHTT-TSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGG------
T ss_pred             HHHHHhhcCCCCcEEEECCcHHHHHHHHHHHHHhhcC-CCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEEcch------
Confidence            3333333333568999999999999999888876442 67888999988765443332    247889999942      


Q ss_pred             hcCCCCCCCCccEEEEec
Q psy4275         140 DTCNTFSLNRIKFLVLDE  157 (182)
Q Consensus       140 ~~~~~~~~~~~~~iI~DE  157 (182)
                      -. ..++++++++||.-.
T Consensus       351 ~~-~GiDip~v~~VI~~~  367 (579)
T 3sqw_A          351 GA-RGMDFPNVHEVLQIG  367 (579)
T ss_dssp             GT-SSCCCTTCCEEEEES
T ss_pred             hh-cCCCcccCCEEEEcC
Confidence            22 556778888877655

>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=95.10  E-value=0.1  Score=36.20  Aligned_cols=88  Identities=20%  Similarity=0.221  Sum_probs=48.3

Q ss_pred             CChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEE
Q psy4275          53 GSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIV  128 (182)
Q Consensus        53 g~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Il  128 (182)
                      ...|... +.-++...   ..+.++||.++++.-++.+++.++..    ++.+..++|+.+..++...+    .+..+|+
T Consensus        29 ~~~K~~~-L~~ll~~~---~~~~k~lVF~~~~~~~~~l~~~L~~~----g~~~~~lhg~~~~~~r~~~~~~f~~g~~~vL  100 (185)
T 2jgn_A           29 ESDKRSF-LLDLLNAT---GKDSLTLVFVETKKGADSLEDFLYHE----GYACTSIHGDRSQRDREEALHQFRSGKSPIL  100 (185)
T ss_dssp             GGGHHHH-HHHHHHHC----CCSCEEEEESCHHHHHHHHHHHHHT----TCCEEEEC--------CHHHHHHHHTSSSEE
T ss_pred             cHHHHHH-HHHHHHhc---CCCCeEEEEECCHHHHHHHHHHHHHc----CCceEEEeCCCCHHHHHHHHHHHHcCCCeEE
Confidence            4456443 33344332   22558999999999998888777664    67888899877654433222    2467899


Q ss_pred             EEChHHHHHHHhcCCCCCCCCccEEEE
Q psy4275         129 IATPGRLADHLDTCNTFSLNRIKFLVL  155 (182)
Q Consensus       129 v~T~~~l~~~~~~~~~~~~~~~~~iI~  155 (182)
                      |+|.- +     . ..+++..++++|.
T Consensus       101 vaT~~-~-----~-~Gldi~~~~~VI~  120 (185)
T 2jgn_A          101 VATAV-A-----A-RGLDISNVKHVIN  120 (185)
T ss_dssp             EEEC-------------CCCSBSEEEE
T ss_pred             EEcCh-h-----h-cCCCcccCCEEEE
Confidence            99832 1     1 3345556665554

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=95.01  E-value=0.1  Score=41.49  Aligned_cols=57  Identities=23%  Similarity=-0.003  Sum_probs=33.5

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc--CCHHHHHHHHHHHHHhhccCCceEEE
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT--PTRELAYQIGDQFLVLGKVMNLRVSI  107 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~--p~~~l~~q~~~~~~~~~~~~~~~~~~  107 (182)
                      -+++.|++|+|||+.+.-.+... ...  +.+++++.  |.+.-+   .+.++.+....++.+..
T Consensus       102 vIlivG~~G~GKTTt~~kLA~~l-~~~--G~kVllv~~D~~R~aa---~eqL~~~~~~~gvpv~~  160 (443)
T 3dm5_A          102 ILLMVGIQGSGKTTTVAKLARYF-QKR--GYKVGVVCSDTWRPGA---YHQLRQLLDRYHIEVFG  160 (443)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH-HTT--TCCEEEEECCCSSTHH---HHHHHHHHGGGTCEEEC
T ss_pred             EEEEECcCCCCHHHHHHHHHHHH-HHC--CCeEEEEeCCCcchhH---HHHHHHHHHhcCCcEEe
Confidence            57788999999999865444333 332  45676665  333322   23445555555666543

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=94.91  E-value=0.021  Score=42.85  Aligned_cols=21  Identities=24%  Similarity=0.151  Sum_probs=16.6

Q ss_pred             CcEEEECCCCChHHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~   64 (182)
                      .+.++.||+|+|||..+....
T Consensus        43 ~~~ll~G~~G~GKt~la~~l~   63 (323)
T 1sxj_B           43 PHMIISGMPGIGKTTSVHCLA   63 (323)
T ss_dssp             CCEEEECSTTSSHHHHHHHHH
T ss_pred             CeEEEECcCCCCHHHHHHHHH
Confidence            359999999999998754433

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=94.85  E-value=0.25  Score=38.27  Aligned_cols=72  Identities=19%  Similarity=0.254  Sum_probs=51.6

Q ss_pred             CCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCC
Q psy4275          73 YGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLN  148 (182)
Q Consensus        73 ~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~  148 (182)
                      .+.+++|.++++.-++.+++.++..    ++.+..++|+.+..++...+    .+..+|+|+|.-      -. ..+++.
T Consensus       275 ~~~~~lVf~~~~~~~~~l~~~L~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlvaT~~------~~-~Gidip  343 (417)
T 2i4i_A          275 KDSLTLVFVETKKGADSLEDFLYHE----GYACTSIHGDRSQRDREEALHQFRSGKSPILVATAV------AA-RGLDIS  343 (417)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHHTSSCEEEECHH------HH-TTSCCC
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHHC----CCCeeEecCCCCHHHHHHHHHHHHcCCCCEEEECCh------hh-cCCCcc
Confidence            3568999999999999888887664    78899999988765443332    246789999942      12 445666


Q ss_pred             CccEEEE
Q psy4275         149 RIKFLVL  155 (182)
Q Consensus       149 ~~~~iI~  155 (182)
                      .++++|.
T Consensus       344 ~v~~Vi~  350 (417)
T 2i4i_A          344 NVKHVIN  350 (417)
T ss_dssp             CEEEEEE
T ss_pred             cCCEEEE
Confidence            7776664

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=94.83  E-value=0.091  Score=40.21  Aligned_cols=20  Identities=25%  Similarity=0.174  Sum_probs=16.0

Q ss_pred             cEEEECCCCChHHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~   64 (182)
                      ..++.||+|+|||..+....
T Consensus        40 ~~ll~G~~G~GKT~la~~la   59 (373)
T 1jr3_A           40 AYLFSGTRGVGKTSIARLLA   59 (373)
T ss_dssp             EEEEESCTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            47899999999998864443

>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=94.75  E-value=0.17  Score=37.30  Aligned_cols=28  Identities=14%  Similarity=0.150  Sum_probs=22.2

Q ss_pred             hhhhCCCcEEEECCCCChHHHHHHHHHH
Q psy4275          38 PHVLNDEDCIGCAKTGSGKTLAFALPIL   65 (182)
Q Consensus        38 ~~~~~~~~~li~~~tg~GKT~~~~~~~~   65 (182)
                      ..+..|.-+++.||+|+|||+.+...+.
T Consensus        25 ggl~~G~i~~i~G~~GsGKTtl~~~l~~   52 (279)
T 1nlf_A           25 PNMVAGTVGALVSPGGAGKSMLALQLAA   52 (279)
T ss_dssp             TTEETTSEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCccCCCEEEEEcCCCCCHHHHHHHHHH
Confidence            3456688899999999999988665554

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=94.71  E-value=0.025  Score=37.55  Aligned_cols=20  Identities=10%  Similarity=-0.057  Sum_probs=17.1

Q ss_pred             hCCCcEEEECCCCChHHHHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~   60 (182)
                      ..+.++++.|++|+|||..+
T Consensus        25 ~~~~~vll~G~~GtGKt~lA   44 (143)
T 3co5_A           25 KRTSPVFLTGEAGSPFETVA   44 (143)
T ss_dssp             TCSSCEEEEEETTCCHHHHH
T ss_pred             CCCCcEEEECCCCccHHHHH
Confidence            44678999999999999775

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=94.69  E-value=0.038  Score=38.49  Aligned_cols=39  Identities=15%  Similarity=-0.066  Sum_probs=27.1

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTR   84 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~   84 (182)
                      ++-.++.|++|+|||+.++-.+.....+   +.+++++.|..
T Consensus         3 g~i~vi~G~~gsGKTT~ll~~~~~~~~~---g~~v~~~~~~~   41 (184)
T 2orw_A            3 GKLTVITGPMYSGKTTELLSFVEIYKLG---KKKVAVFKPKI   41 (184)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHHT---TCEEEEEEEC-
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHHHHC---CCeEEEEeecc
Confidence            4557889999999999865444443333   45788888873

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=94.68  E-value=0.084  Score=36.82  Aligned_cols=19  Identities=26%  Similarity=0.207  Sum_probs=16.4

Q ss_pred             CcEEEECCCCChHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~   62 (182)
                      +++++.||+|+|||..+..
T Consensus        55 ~~~~l~G~~GtGKT~la~~   73 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLAA   73 (202)
T ss_dssp             CEEEEECSTTSSHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHH
Confidence            6899999999999987543

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=94.45  E-value=0.064  Score=50.16  Aligned_cols=43  Identities=19%  Similarity=0.003  Sum_probs=32.9

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTREL   86 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l   86 (182)
                      ..++++++.||+|+|||..+...+.....+   +.+++++.....+
T Consensus      1425 ~~g~~vll~GppGtGKT~LA~ala~ea~~~---G~~v~Fi~~e~~~ 1467 (2050)
T 3cmu_A         1425 PMGRIVEIYGPESSGKTTLTLQVIAAAQRE---GKTCAFIDAEHAL 1467 (2050)
T ss_dssp             ETTSEEEEECCTTSSHHHHHHHHHHHHHTT---TCCEEEECTTSCC
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHHHHc---CCcEEEEEccccc
Confidence            347899999999999999877766665443   5678888876544

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=94.37  E-value=0.031  Score=41.33  Aligned_cols=57  Identities=12%  Similarity=0.102  Sum_probs=32.0

Q ss_pred             cCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhh--hhCCCcEEEECCCCChHHHHHHHH
Q psy4275           5 IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPH--VLNDEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus         5 ~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~--~~~~~~~li~~~tg~GKT~~~~~~   63 (182)
                      -.+|+++.-.+...+.+...-.. + -...+.+..  +...+++++.||+|+|||..+-..
T Consensus        13 ~~~~~~i~G~~~~~~~l~~~~~~-~-~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~l   71 (285)
T 3h4m_A           13 NVRYEDIGGLEKQMQEIREVVEL-P-LKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAV   71 (285)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHTHH-H-HHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHH
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHH-H-hhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHH
Confidence            34677776566666655432110 0 000111111  234678999999999999886443

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=94.30  E-value=0.044  Score=40.41  Aligned_cols=22  Identities=27%  Similarity=0.182  Sum_probs=17.9

Q ss_pred             hhCCCcEEEECCCCChHHHHHH
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~   61 (182)
                      +..|..+.+.||||+|||+..-
T Consensus        22 i~~g~~v~i~Gp~GsGKSTll~   43 (261)
T 2eyu_A           22 HRKMGLILVTGPTGSGKSTTIA   43 (261)
T ss_dssp             GCSSEEEEEECSTTCSHHHHHH
T ss_pred             hCCCCEEEEECCCCccHHHHHH
Confidence            4557788999999999998743

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=94.25  E-value=0.11  Score=40.02  Aligned_cols=22  Identities=32%  Similarity=0.303  Sum_probs=17.9

Q ss_pred             CCCcEEEECCCCChHHHHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~   63 (182)
                      ...++++.||+|+|||..+-..
T Consensus        50 ~~~~vll~GppGtGKT~la~~i   71 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTLLAETL   71 (363)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHHHH
Confidence            3568999999999999986443

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=94.24  E-value=0.14  Score=38.51  Aligned_cols=71  Identities=17%  Similarity=0.254  Sum_probs=50.6

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +.++||.++++.-++.+++.+...    ++.+..++|+.+..++...+    .+..+|+|+|.-      .. ..+++..
T Consensus        28 ~~~~LVF~~t~~~~~~l~~~L~~~----g~~~~~lhg~l~~~~r~~~~~~f~~g~~~vLVaT~v------a~-~Gidi~~   96 (300)
T 3i32_A           28 PDRAMVFTRTKAETEEIAQGLLRL----GHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDV------AA-RGLDIPQ   96 (300)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHTT----TCCEEEECSCCCTHHHHHHHHHHHHTSCCEEEECST------TT-CSTTCCC
T ss_pred             CCCEEEEECCHHHHHHHHHHHHhC----CCCEEEEeCCCCHHHHHHHHHHhhcCCceEEEEech------hh-cCccccc
Confidence            458999999999988877776553    78899999998765544333    246789999932      22 4556777


Q ss_pred             ccEEEE
Q psy4275         150 IKFLVL  155 (182)
Q Consensus       150 ~~~iI~  155 (182)
                      ++++|.
T Consensus        97 v~~VI~  102 (300)
T 3i32_A           97 VDLVVH  102 (300)
T ss_dssp             CSEEEE
T ss_pred             eeEEEE
Confidence            776664

>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=94.16  E-value=0.38  Score=36.74  Aligned_cols=75  Identities=12%  Similarity=0.177  Sum_probs=54.4

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +.+++|.++++.-++.+++.++..    +..+..++|+.+..++...+    .+..+|+|+|.-      -. ..+++++
T Consensus       243 ~~~~lvf~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~------~~-~Gidip~  311 (395)
T 3pey_A          243 IGSSIIFVATKKTANVLYGKLKSE----GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNV------LA-RGIDIPT  311 (395)
T ss_dssp             SSEEEEECSCHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECGG------GS-SSCCCTT
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhc----CCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECCh------hh-cCCCccc
Confidence            468999999999998888887664    67888999987765443332    246789999932      22 5567888


Q ss_pred             ccEEEEeccc
Q psy4275         150 IKFLVLDEAD  159 (182)
Q Consensus       150 ~~~iI~DE~h  159 (182)
                      ++++|.-+..
T Consensus       312 ~~~Vi~~~~p  321 (395)
T 3pey_A          312 VSMVVNYDLP  321 (395)
T ss_dssp             EEEEEESSCC
T ss_pred             CCEEEEcCCC
Confidence            8888865443

>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=94.05  E-value=0.13  Score=45.95  Aligned_cols=54  Identities=20%  Similarity=0.064  Sum_probs=41.7

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccCC---------CCeeEEEEcCCHHHHHHHHHHHHHh
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCEDP---------YGIFALVLTPTRELAYQIGDQFLVL   97 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~~---------~~~~~lil~p~~~l~~q~~~~~~~~   97 (182)
                      .+.++.|+.|||||.+...-++..+...+         .-.++|+|+=|++-+.++.+.+...
T Consensus        17 g~~lV~AsAGSGKT~~L~~r~lrLll~~g~~~~~~~~~~~~~ILvvTFT~aAA~EMr~RI~~~   79 (1180)
T 1w36_B           17 GERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSN   79 (1180)
T ss_dssp             SCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCHHHHHHHHHHHHHhcCCcccccCCCCCHHHEEEEeccHHHHHHHHHHHHHH
Confidence            45699999999999987777777665421         1347999999999999887776653

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=93.93  E-value=0.064  Score=40.52  Aligned_cols=24  Identities=17%  Similarity=0.144  Sum_probs=18.7

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQ   66 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~   66 (182)
                      ++++++.||+|+|||..+......
T Consensus       152 ~~~lll~G~~GtGKT~La~aia~~  175 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLLAAMAHE  175 (308)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHHHHH
Confidence            578999999999999876544333

>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=93.81  E-value=0.48  Score=39.08  Aligned_cols=72  Identities=13%  Similarity=0.150  Sum_probs=52.4

Q ss_pred             CCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCC
Q psy4275          73 YGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLN  148 (182)
Q Consensus        73 ~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~  148 (182)
                      .+.++||.++++.-++++++.++..    ++.+..++|+.+..++....    .+..+|+|+|..      -. ..++.+
T Consensus       266 ~~~~~IVf~~sr~~~e~la~~L~~~----g~~~~~~h~~l~~~~R~~~~~~F~~g~~~VlVAT~a------~~-~GID~p  334 (591)
T 2v1x_A          266 KGQSGIIYCFSQKDSEQVTVSLQNL----GIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVA------FG-MGIDKP  334 (591)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEECTT------SC-TTCCCS
T ss_pred             cCCCeEEEeCcHHHHHHHHHHHHHC----CCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEech------hh-cCCCcc
Confidence            3568999999999999988888764    78899999998765443322    346789999932      12 455677


Q ss_pred             CccEEEE
Q psy4275         149 RIKFLVL  155 (182)
Q Consensus       149 ~~~~iI~  155 (182)
                      ++++||.
T Consensus       335 ~V~~VI~  341 (591)
T 2v1x_A          335 DVRFVIH  341 (591)
T ss_dssp             CEEEEEE
T ss_pred             cccEEEE
Confidence            7777664

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=93.73  E-value=0.089  Score=40.65  Aligned_cols=19  Identities=26%  Similarity=0.296  Sum_probs=15.9

Q ss_pred             CCCcEEEECCCCChHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~   60 (182)
                      .+..+++.||||+|||+..
T Consensus       122 ~~g~i~I~GptGSGKTTlL  140 (356)
T 3jvv_A          122 PRGLVLVTGPTGSGKSTTL  140 (356)
T ss_dssp             SSEEEEEECSTTSCHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            3557899999999999874

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=93.68  E-value=0.1  Score=40.98  Aligned_cols=60  Identities=20%  Similarity=0.190  Sum_probs=33.8

Q ss_pred             ccCCccCCCCCHHHHHHHHHC-C--CCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHH
Q psy4275           4 PIKSFTDLKLNPWLIRQCQTI-G--VKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ   66 (182)
Q Consensus         4 ~~~~~~~~~l~~~i~~~l~~~-~--~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~   66 (182)
                      |--+|++.+=-++..+.+.+. .  +..|.-++...+   ...+.+++.||+|+|||..+-..+-+
T Consensus       143 p~v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi---~~prGvLL~GPPGTGKTllAkAiA~e  205 (405)
T 4b4t_J          143 PDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLGI---AQPKGVILYGPPGTGKTLLARAVAHH  205 (405)
T ss_dssp             CSCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTC---CCCCCEEEESCSSSSHHHHHHHHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCCceEEeCCCCCCHHHHHHHHHHh
Confidence            345778875344444444332 1  122333333222   23568999999999999886444433

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=93.65  E-value=0.095  Score=41.91  Aligned_cols=60  Identities=15%  Similarity=0.131  Sum_probs=35.6

Q ss_pred             CccCCccCCCCCHHHHHHHHHCC---CCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHH
Q psy4275           3 DPIKSFTDLKLNPWLIRQCQTIG---VKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPIL   65 (182)
Q Consensus         3 ~~~~~~~~~~l~~~i~~~l~~~~---~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~   65 (182)
                      .|--+|++.+=-+++.+.+.+.-   +..+.-++...   +..-+.+++.||+|+|||..+-..+-
T Consensus       203 ~P~vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~G---i~pprGILLyGPPGTGKTlLAkAiA~  265 (467)
T 4b4t_H          203 KPDVTYSDVGGCKDQIEKLREVVELPLLSPERFATLG---IDPPKGILLYGPPGTGKTLCARAVAN  265 (467)
T ss_dssp             SCSCCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHT---CCCCSEEEECSCTTSSHHHHHHHHHH
T ss_pred             CCCCCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHCC---CCCCCceEeeCCCCCcHHHHHHHHHh
Confidence            34457888875556666665421   11222222222   22357899999999999988644433

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=93.58  E-value=0.13  Score=40.63  Aligned_cols=35  Identities=20%  Similarity=0.222  Sum_probs=21.9

Q ss_pred             HHhhhhhhh--CCCcEEEECCCCChHHHHHHHHHHHhh
Q psy4275          33 QKAIIPHVL--NDEDCIGCAKTGSGKTLAFALPILQKW   68 (182)
Q Consensus        33 Q~~~~~~~~--~~~~~li~~~tg~GKT~~~~~~~~~~~   68 (182)
                      +...+..+.  .+..+++.||||+|||+.. ..++..+
T Consensus       155 ~~~~L~~l~~~~ggii~I~GpnGSGKTTlL-~allg~l  191 (418)
T 1p9r_A          155 NHDNFRRLIKRPHGIILVTGPTGSGKSTTL-YAGLQEL  191 (418)
T ss_dssp             HHHHHHHHHTSSSEEEEEECSTTSCHHHHH-HHHHHHH
T ss_pred             HHHHHHHHHHhcCCeEEEECCCCCCHHHHH-HHHHhhc
Confidence            344444333  3556789999999999874 3344433

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=93.57  E-value=0.056  Score=42.98  Aligned_cols=60  Identities=20%  Similarity=0.172  Sum_probs=33.3

Q ss_pred             ccCCccCCCCCHHHHHHHHHC-C--CCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHH
Q psy4275           4 PIKSFTDLKLNPWLIRQCQTI-G--VKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ   66 (182)
Q Consensus         4 ~~~~~~~~~l~~~i~~~l~~~-~--~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~   66 (182)
                      |--+|++.+=-++..+.+... .  +..|.-++...+   ..-+.+++.||+|+|||..+-..+-+
T Consensus       176 p~v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~---~~prGvLL~GPPGtGKTllAkAiA~e  238 (437)
T 4b4t_L          176 GEITFDGIGGLTEQIRELREVIELPLKNPEIFQRVGI---KPPKGVLLYGPPGTGKTLLAKAVAAT  238 (437)
T ss_dssp             CSSCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCC---CCCCEEEEESCTTSSHHHHHHHHHHH
T ss_pred             CCCChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCCeEEEECCCCCcHHHHHHHHHHH
Confidence            445677776444444444332 1  122222222222   23578999999999999986544433

>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=93.55  E-value=0.077  Score=41.88  Aligned_cols=18  Identities=22%  Similarity=0.388  Sum_probs=16.3

Q ss_pred             CCcEEEECCCCChHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~   60 (182)
                      ..|+++.|+||+|||...
T Consensus        53 ~~h~~i~G~tGsGKs~~~   70 (437)
T 1e9r_A           53 PRHLLVNGATGTGKSVLL   70 (437)
T ss_dssp             GGCEEEEECTTSSHHHHH
T ss_pred             cceEEEECCCCCCHHHHH
Confidence            679999999999999974

>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=93.40  E-value=0.065  Score=47.76  Aligned_cols=41  Identities=24%  Similarity=0.332  Sum_probs=31.9

Q ss_pred             EEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHH
Q psy4275          46 CIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTREL   86 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l   86 (182)
                      -++.|+.|||||.+.+.-+.+.+.+...+.++++++|.+.-
T Consensus         4 ~lV~agAGSGKT~~l~~ri~~ll~~~~~~~~il~lVP~q~T   44 (1166)
T 3u4q_B            4 EFLVGRSGSGKTKLIINSIQDELRRAPFGKPIIFLVPDQMT   44 (1166)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHHHCTTSSCEEEECCGGGH
T ss_pred             EEEEeCCCCChHHHHHHHHHHHHHhCCCCCcEEEEecCccc
Confidence            47889999999999877777666555555689999997653

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=93.34  E-value=0.15  Score=34.61  Aligned_cols=21  Identities=19%  Similarity=0.148  Sum_probs=17.0

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      .+++++.||+|+|||..+...
T Consensus        43 ~~~~ll~G~~G~GKT~l~~~~   63 (195)
T 1jbk_A           43 KNNPVLIGEPGVGKTAIVEGL   63 (195)
T ss_dssp             SCEEEEECCTTSCHHHHHHHH
T ss_pred             CCceEEECCCCCCHHHHHHHH
Confidence            467999999999999885433

>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=93.30  E-value=0.11  Score=40.31  Aligned_cols=25  Identities=24%  Similarity=0.413  Sum_probs=19.5

Q ss_pred             CCCcEEEECCCCChHHHHHHHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALPILQ   66 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~~~~   66 (182)
                      .+.|.++.|+||+|||...-..+..
T Consensus        34 ~~~~~~i~G~~G~GKs~~~~~~~~~   58 (392)
T 4ag6_A           34 TNSNWTILAKPGAGKSFTAKMLLLR   58 (392)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             ccCceEEEcCCCCCHHHHHHHHHHH
Confidence            4679999999999999875544443

>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=93.24  E-value=0.34  Score=37.33  Aligned_cols=71  Identities=13%  Similarity=0.209  Sum_probs=52.5

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +.+++|.++++.-++.+++.+...    +..+..++|+....++...+    .+..+|+|+|.-      -. ..+++.+
T Consensus       266 ~~~~lvf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~------~~-~Gidip~  334 (412)
T 3fht_A          266 IAQAMIFCHTRKTASWLAAELSKE----GHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNV------CA-RGIDVEQ  334 (412)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECGG------GT-SSCCCTT
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhC----CCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcCc------cc-cCCCccC
Confidence            458999999999999888887765    67888999988765544332    246789999932      22 5567888


Q ss_pred             ccEEEE
Q psy4275         150 IKFLVL  155 (182)
Q Consensus       150 ~~~iI~  155 (182)
                      ++++|.
T Consensus       335 ~~~Vi~  340 (412)
T 3fht_A          335 VSVVIN  340 (412)
T ss_dssp             EEEEEE
T ss_pred             CCEEEE
Confidence            888774

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=93.21  E-value=0.09  Score=41.66  Aligned_cols=58  Identities=12%  Similarity=0.074  Sum_probs=32.3

Q ss_pred             ccCCccCCCCCHHHHHHHHHC---CCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHH
Q psy4275           4 PIKSFTDLKLNPWLIRQCQTI---GVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus         4 ~~~~~~~~~l~~~i~~~l~~~---~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      |--+|++.+=-+++.+.+...   .+..+.-++...+   ...+.+++.||+|+|||..+-..+
T Consensus       167 p~v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~---~~prGiLL~GPPGtGKT~lakAiA  227 (428)
T 4b4t_K          167 PDVTYADVGGLDMQKQEIREAVELPLVQADLYEQIGI---DPPRGVLLYGPPGTGKTMLVKAVA  227 (428)
T ss_dssp             CSCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCC---CCCCEEEEESCTTTTHHHHHHHHH
T ss_pred             CCCCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCceEEEECCCCCCHHHHHHHHH
Confidence            345677775444444444321   1122322332222   235679999999999998864433

>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=93.21  E-value=0.044  Score=41.13  Aligned_cols=58  Identities=19%  Similarity=0.145  Sum_probs=31.6

Q ss_pred             ccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhh--hhCCCcEEEECCCCChHHHHHHHH
Q psy4275           4 PIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPH--VLNDEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus         4 ~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~--~~~~~~~li~~~tg~GKT~~~~~~   63 (182)
                      +-.+|++++-.+.+.+.+...-. .+..+. +.+..  +..++.+++.||+|+|||..+-..
T Consensus        10 ~~~~~~di~G~~~~~~~l~~~v~-~~~~~~-~~~~~~~~~~~~~vLL~Gp~GtGKT~la~al   69 (301)
T 3cf0_A           10 PQVTWEDIGGLEDVKRELQELVQ-YPVEHP-DKFLKFGMTPSKGVLFYGPPGCGKTLLAKAI   69 (301)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHHH-HHHHCH-HHHHHHCCCCCSEEEEECSSSSSHHHHHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHH-HHhhCH-HHHHHcCCCCCceEEEECCCCcCHHHHHHHH
Confidence            33467777655555555543210 000000 11111  234678999999999999886433

>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=93.14  E-value=0.27  Score=38.97  Aligned_cols=69  Identities=13%  Similarity=0.043  Sum_probs=46.7

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEE
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFL  153 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~i  153 (182)
                      +.+++|++|++.-++.+++.++..    ++++..++|+...........+..+|+|+|.-      -. ..++++ +++|
T Consensus       177 ~~~~lVF~~s~~~a~~l~~~L~~~----~~~v~~lhg~~R~~~~~~F~~g~~~vLVaT~v------~e-~GiDip-v~~V  244 (440)
T 1yks_A          177 KRPTAWFLPSIRAANVMAASLRKA----GKSVVVLNRKTFEREYPTIKQKKPDFILATDI------AE-MGANLC-VERV  244 (440)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHT----TCCEEECCSSSCC--------CCCSEEEESSS------TT-CCTTCC-CSEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHc----CCCEEEecchhHHHHHhhhcCCCceEEEECCh------hh-eeeccC-ceEE
Confidence            458999999999999988888765    68898999854332222222346899999932      22 456777 8877


Q ss_pred             E
Q psy4275         154 V  154 (182)
Q Consensus       154 I  154 (182)
                      |
T Consensus       245 I  245 (440)
T 1yks_A          245 L  245 (440)
T ss_dssp             E
T ss_pred             E
Confidence            6

>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=93.11  E-value=1.2  Score=37.15  Aligned_cols=78  Identities=12%  Similarity=0.211  Sum_probs=58.0

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +.+++|.++++..++.+++.++..    ++++..++|+....++...+    .+..+|+|+|.-      -. ..+++..
T Consensus       445 ~~~vlVf~~t~~~ae~L~~~L~~~----gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~~------l~-~GlDip~  513 (661)
T 2d7d_A          445 NERVLVTTLTKKMSEDLTDYLKEI----GIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINL------LR-EGLDIPE  513 (661)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESCC------CS-TTCCCTT
T ss_pred             CCeEEEEECCHHHHHHHHHHHHhc----CCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecch------hh-CCcccCC
Confidence            568999999999998888777664    67888889887655444332    246789999831      12 5678889


Q ss_pred             ccEEEEecccccc
Q psy4275         150 IKFLVLDEADRLS  162 (182)
Q Consensus       150 ~~~iI~DE~h~~~  162 (182)
                      ++++|+-|++...
T Consensus       514 v~lVi~~d~d~~G  526 (661)
T 2d7d_A          514 VSLVAILDADKEG  526 (661)
T ss_dssp             EEEEEETTTTCCT
T ss_pred             CCEEEEeCccccc
Confidence            9999998886544

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=93.09  E-value=0.07  Score=38.34  Aligned_cols=41  Identities=24%  Similarity=0.107  Sum_probs=28.2

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      ..|.-.++.|++|+|||..++-.+.+...+.  +..++|+.-.
T Consensus        28 ~~G~l~~i~G~pG~GKT~l~l~~~~~~~~~~--~~~v~~~s~E   68 (251)
T 2zts_A           28 PEGTTVLLTGGTGTGKTTFAAQFIYKGAEEY--GEPGVFVTLE   68 (251)
T ss_dssp             ETTCEEEEECCTTSSHHHHHHHHHHHHHHHH--CCCEEEEESS
T ss_pred             CCCeEEEEEeCCCCCHHHHHHHHHHHHHHhc--CCCceeeccc
Confidence            3467789999999999988776666544432  3356776643

>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=92.97  E-value=0.49  Score=36.39  Aligned_cols=71  Identities=8%  Similarity=0.077  Sum_probs=50.7

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +.+++|.+++..-++.+++.++..    ++.+..++|+.+..++...+    .+..+|+|+|.-      -. ..++++.
T Consensus       258 ~~~~lVf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~~------~~-~Gidip~  326 (400)
T 1s2m_A          258 INQAIIFCNSTNRVELLAKKITDL----GYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDL------LT-RGIDIQA  326 (400)
T ss_dssp             CSEEEEECSSHHHHHHHHHHHHHH----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSC------SS-SSCCCTT
T ss_pred             CCcEEEEEecHHHHHHHHHHHHhc----CCCeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCc------cc-cCCCccC
Confidence            458999999999998888887765    67888899988765443322    246789999931      11 4567777


Q ss_pred             ccEEEE
Q psy4275         150 IKFLVL  155 (182)
Q Consensus       150 ~~~iI~  155 (182)
                      ++++|.
T Consensus       327 ~~~Vi~  332 (400)
T 1s2m_A          327 VNVVIN  332 (400)
T ss_dssp             EEEEEE
T ss_pred             CCEEEE
Confidence            777664

>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=92.93  E-value=0.75  Score=36.17  Aligned_cols=69  Identities=16%  Similarity=0.164  Sum_probs=51.3

Q ss_pred             eEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCCcc
Q psy4275          76 FALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNRIK  151 (182)
Q Consensus        76 ~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~  151 (182)
                      ++||.++++.-++.+++.+...    ++.+..++|+....++...+    .+..+|+|+|.-      -. ..+++.+++
T Consensus       302 ~~lVF~~t~~~a~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~v------~~-rGlDi~~v~  370 (434)
T 2db3_A          302 GTIVFVETKRGADFLASFLSEK----EFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSV------AS-RGLDIKNIK  370 (434)
T ss_dssp             TEEEECSSHHHHHHHHHHHHHT----TCCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECGG------GT-SSCCCTTCC
T ss_pred             CEEEEEeCcHHHHHHHHHHHhC----CCCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEchh------hh-CCCCcccCC
Confidence            4999999999998888777664    78899999998765554433    246789999942      22 556788888


Q ss_pred             EEEE
Q psy4275         152 FLVL  155 (182)
Q Consensus       152 ~iI~  155 (182)
                      ++|.
T Consensus       371 ~VI~  374 (434)
T 2db3_A          371 HVIN  374 (434)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            7774

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=92.92  E-value=0.13  Score=38.93  Aligned_cols=54  Identities=15%  Similarity=0.005  Sum_probs=34.4

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccC---------CCC----eeEEEEcCCHHH-HHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCED---------PYG----IFALVLTPTREL-AYQIGDQFLV   96 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~---------~~~----~~~lil~p~~~l-~~q~~~~~~~   96 (182)
                      |.-.++.|++|+|||..++..+.......         ..+    .+++|+.-.... .+++.+.++.
T Consensus        98 g~i~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~~~~~~  165 (322)
T 2i1q_A           98 QSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQMAEH  165 (322)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHHHHHHH
Confidence            45789999999999998776666543221         112    578888866542 3444444443

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=92.91  E-value=0.12  Score=36.65  Aligned_cols=35  Identities=26%  Similarity=0.201  Sum_probs=27.6

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHH
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~   62 (182)
                      .-+..|..++..+..|.-+.+.||+|+|||+..-+
T Consensus         7 pk~~g~~~~l~~i~~Ge~~~liG~nGsGKSTLl~~   41 (208)
T 3b85_A            7 PKTLGQKHYVDAIDTNTIVFGLGPAGSGKTYLAMA   41 (208)
T ss_dssp             CCSHHHHHHHHHHHHCSEEEEECCTTSSTTHHHHH
T ss_pred             cCCHhHHHHHHhccCCCEEEEECCCCCCHHHHHHH
Confidence            34455677888888898899999999999987543

>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=92.90  E-value=0.6  Score=36.47  Aligned_cols=95  Identities=17%  Similarity=0.209  Sum_probs=57.1

Q ss_pred             CCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEc--------CCchhhhhHHh--
Q psy4275          52 TGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITG--------GMDMVDQGKEL--  121 (182)
Q Consensus        52 tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~--  121 (182)
                      ..++|.... .-++........+.++||.+++...++.+++.++..    ++++..++|        +.+..++...+  
T Consensus       340 ~~~~k~~~l-~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~----~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~  414 (494)
T 1wp9_A          340 LDHPKMDKL-KEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKD----GIKAKRFVGQASKENDRGLSQREQKLILDE  414 (494)
T ss_dssp             CSCHHHHHH-HHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHT----TCCEEEECCSSCC-------CCHHHHHHHH
T ss_pred             CCChHHHHH-HHHHHHHhccCCCCeEEEEEccHHHHHHHHHHHHHc----CCCcEEEeccccccccccCCHHHHHHHHHH
Confidence            445565443 333333322122568999999999988888877765    788888888        44443332222  


Q ss_pred             --cCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecc
Q psy4275         122 --AKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEA  158 (182)
Q Consensus       122 --~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~  158 (182)
                        .+..+|+|+|.-      -. ..+++..++++|+-+.
T Consensus       415 F~~~~~~vLv~T~~------~~-~Gldl~~~~~Vi~~d~  446 (494)
T 1wp9_A          415 FARGEFNVLVATSV------GE-EGLDVPEVDLVVFYEP  446 (494)
T ss_dssp             HHHTSCSEEEECGG------GG-GGGGSTTCCEEEESSC
T ss_pred             HhcCCceEEEECCc------cc-cCCCchhCCEEEEeCC
Confidence              246789999932      12 4456777777775443

>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=92.85  E-value=0.37  Score=35.69  Aligned_cols=21  Identities=24%  Similarity=0.147  Sum_probs=17.4

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      .+++++.||+|+|||..+-..
T Consensus        50 ~~~vll~G~~GtGKT~la~~l   70 (310)
T 1ofh_A           50 PKNILMIGPTGVGKTEIARRL   70 (310)
T ss_dssp             CCCEEEECCTTSSHHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHH
Confidence            568999999999999886433

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=92.84  E-value=0.17  Score=40.97  Aligned_cols=36  Identities=17%  Similarity=0.185  Sum_probs=26.5

Q ss_pred             CCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHH
Q psy4275          25 GVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        25 ~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~   60 (182)
                      .+..-...-..+...+..+.++++.||+|+|||..+
T Consensus        23 ~ivGq~~~i~~l~~al~~~~~VLL~GpPGtGKT~LA   58 (500)
T 3nbx_X           23 GLYERSHAIRLCLLAALSGESVFLLGPPGIAKSLIA   58 (500)
T ss_dssp             TCSSCHHHHHHHHHHHHHTCEEEEECCSSSSHHHHH
T ss_pred             hhHHHHHHHHHHHHHHhcCCeeEeecCchHHHHHHH
Confidence            333444444555566677899999999999999875

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=92.61  E-value=0.042  Score=40.80  Aligned_cols=56  Identities=13%  Similarity=0.145  Sum_probs=28.1

Q ss_pred             ccCCccCCCCCHHHHHHHHHCCCCCChHHH-Hhhhhhh--hCCCcEEEECCCCChHHHHHHH
Q psy4275           4 PIKSFTDLKLNPWLIRQCQTIGVKTPTEIQ-KAIIPHV--LNDEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus         4 ~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q-~~~~~~~--~~~~~~li~~~tg~GKT~~~~~   62 (182)
                      +--+|++++--+++.+.+...-.   .|+. .+.+..+  .-.+.+++.||+|+|||+.+-.
T Consensus         5 ~~~~~~di~g~~~~~~~l~~~i~---~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLaka   63 (274)
T 2x8a_A            5 PNVTWADIGALEDIREELTMAIL---APVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKA   63 (274)
T ss_dssp             -------CCHHHHHHHHHHHHHT---HHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHH---HHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHHHH
Confidence            44578888766667766654211   1111 1122221  1134599999999999987543

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=92.60  E-value=0.14  Score=38.69  Aligned_cols=33  Identities=12%  Similarity=0.094  Sum_probs=23.6

Q ss_pred             hHHHHhhhhhhhCCCcEEEECCCCChHHHHHHH
Q psy4275          30 TEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        30 ~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~   62 (182)
                      ...-..+...+..++++++.||+|+|||..+-.
T Consensus        33 ~~~~~~l~~~l~~~~~vll~G~pGtGKT~la~~   65 (331)
T 2r44_A           33 KYMINRLLIGICTGGHILLEGVPGLAKTLSVNT   65 (331)
T ss_dssp             HHHHHHHHHHHHHTCCEEEESCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCeEEEECCCCCcHHHHHHH
Confidence            333344444555688999999999999987543

>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=92.59  E-value=0.57  Score=35.78  Aligned_cols=73  Identities=11%  Similarity=0.094  Sum_probs=52.2

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +.+++|.+++..-++.+++.++..    ++.+..++|+.+..++...+    .+..+|+|+|.-      - ...+++..
T Consensus       250 ~~~~lvf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~------~-~~Gidi~~  318 (391)
T 1xti_A          250 FNQVVIFVKSVQRCIALAQLLVEQ----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNL------F-GRGMDIER  318 (391)
T ss_dssp             CSEEEEECSCHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESCC------C-SSCBCCTT
T ss_pred             CCcEEEEeCcHHHHHHHHHHHHhC----CCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECCh------h-hcCCCccc
Confidence            458999999999999888877664    67888999987754443322    236789999921      1 14567777


Q ss_pred             ccEEEEec
Q psy4275         150 IKFLVLDE  157 (182)
Q Consensus       150 ~~~iI~DE  157 (182)
                      ++++|.-+
T Consensus       319 ~~~Vi~~~  326 (391)
T 1xti_A          319 VNIAFNYD  326 (391)
T ss_dssp             EEEEEESS
T ss_pred             CCEEEEeC
Confidence            88777644

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=92.50  E-value=0.4  Score=36.94  Aligned_cols=21  Identities=33%  Similarity=0.316  Sum_probs=17.4

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      ..++++.||+|+|||..+-..
T Consensus        72 ~~~ill~Gp~GtGKT~la~~l   92 (376)
T 1um8_A           72 KSNILLIGPTGSGKTLMAQTL   92 (376)
T ss_dssp             CCCEEEECCTTSSHHHHHHHH
T ss_pred             CCCEEEECCCCCCHHHHHHHH
Confidence            468999999999999886443

>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=92.44  E-value=0.37  Score=35.09  Aligned_cols=20  Identities=25%  Similarity=0.346  Sum_probs=17.2

Q ss_pred             CCCcEEEECCCCChHHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~   61 (182)
                      .+.++++.||+|+|||..+-
T Consensus        28 ~~~~vll~G~~GtGKt~la~   47 (265)
T 2bjv_A           28 LDKPVLIIGERGTGKELIAS   47 (265)
T ss_dssp             SCSCEEEECCTTSCHHHHHH
T ss_pred             CCCCEEEECCCCCcHHHHHH
Confidence            46789999999999998753

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=92.39  E-value=0.17  Score=41.01  Aligned_cols=38  Identities=21%  Similarity=0.083  Sum_probs=24.6

Q ss_pred             hHHHHhhhh-hhhCCCcEEEECCCCChHHHHHHHHHHHhh
Q psy4275          30 TEIQKAIIP-HVLNDEDCIGCAKTGSGKTLAFALPILQKW   68 (182)
Q Consensus        30 ~~~Q~~~~~-~~~~~~~~li~~~tg~GKT~~~~~~~~~~~   68 (182)
                      .+.+...+. .+..|.++++.||||+|||+.. ..++..+
T Consensus       246 ~~~~l~~l~~~v~~g~~i~I~GptGSGKTTlL-~aL~~~i  284 (511)
T 2oap_1          246 PSGVLAYLWLAIEHKFSAIVVGETASGKTTTL-NAIMMFI  284 (511)
T ss_dssp             CHHHHHHHHHHHHTTCCEEEEESTTSSHHHHH-HHHGGGS
T ss_pred             CHHHHHHHHHHHhCCCEEEEECCCCCCHHHHH-HHHHhhC
Confidence            333333333 3456888999999999999874 3344433

>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=92.36  E-value=0.52  Score=36.39  Aligned_cols=72  Identities=13%  Similarity=0.174  Sum_probs=52.0

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      ..+++|.+++..-++.+++.+...    ++.+..++|+....++...+    .+..+|+|+|.-      -. ..+++..
T Consensus       276 ~~~~lVf~~~~~~~~~l~~~L~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~------~~-~Gidi~~  344 (410)
T 2j0s_A          276 ITQAVIFCNTKRKVDWLTEKMREA----NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDV------WA-RGLDVPQ  344 (410)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGG------GS-SSCCCTT
T ss_pred             CCcEEEEEcCHHHHHHHHHHHHhC----CCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECCh------hh-CcCCccc
Confidence            348999999999988888777664    67888999988765443332    246789999942      22 5567888


Q ss_pred             ccEEEEe
Q psy4275         150 IKFLVLD  156 (182)
Q Consensus       150 ~~~iI~D  156 (182)
                      ++++|.-
T Consensus       345 v~~Vi~~  351 (410)
T 2j0s_A          345 VSLIINY  351 (410)
T ss_dssp             EEEEEES
T ss_pred             CCEEEEE
Confidence            8877753

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=92.28  E-value=0.1  Score=36.40  Aligned_cols=24  Identities=17%  Similarity=-0.130  Sum_probs=18.6

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      ..++.+++.|++|+|||+.+-...
T Consensus        23 ~~~~~i~l~G~~GsGKsTl~~~La   46 (199)
T 3vaa_A           23 NAMVRIFLTGYMGAGKTTLGKAFA   46 (199)
T ss_dssp             -CCCEEEEECCTTSCHHHHHHHHH
T ss_pred             CCCCEEEEEcCCCCCHHHHHHHHH
Confidence            346789999999999999864443

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=92.26  E-value=0.45  Score=37.72  Aligned_cols=57  Identities=25%  Similarity=0.146  Sum_probs=31.8

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc--CCHHHHHHHHHHHHHhhccCCceEE
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT--PTRELAYQIGDQFLVLGKVMNLRVS  106 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~--p~~~l~~q~~~~~~~~~~~~~~~~~  106 (182)
                      .-+++.|++|+|||+.+...+... ...  +.+++++.  +.+.-+   .+.+..+....++.+.
T Consensus        98 ~vI~lvG~~GsGKTTt~~kLA~~l-~~~--G~kVllv~~D~~r~~a---~eqL~~~~~~~gv~~~  156 (433)
T 3kl4_A           98 FIIMLVGVQGSGKTTTAGKLAYFY-KKR--GYKVGLVAADVYRPAA---YDQLLQLGNQIGVQVY  156 (433)
T ss_dssp             EEEEECCCTTSCHHHHHHHHHHHH-HHT--TCCEEEEEECCSCHHH---HHHHHHHHHTTTCCEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH-HHc--CCeEEEEecCccchhH---HHHHHHHHHhcCCcee
Confidence            356778999999998865444333 232  45676665  333222   2334444444455443

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=92.21  E-value=0.13  Score=38.84  Aligned_cols=58  Identities=9%  Similarity=0.008  Sum_probs=32.0

Q ss_pred             ccCCccCCCCCHHHHHHHHHCCCCCChHHHH-hhhhh-hhCCCcEEEECCCCChHHHHHHHHH
Q psy4275           4 PIKSFTDLKLNPWLIRQCQTIGVKTPTEIQK-AIIPH-VLNDEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus         4 ~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~-~~~~~-~~~~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      +-.+|+++.-.+...+.+...-.   .|... +.+.. ....+++++.||+|+|||..+-...
T Consensus        13 ~~~~~~di~G~~~~~~~l~~~i~---~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia   72 (322)
T 3eie_A           13 PNVKWEDVAGLEGAKEALKEAVI---LPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVA   72 (322)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHTH---HHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHH
T ss_pred             CCCCHHHhcChHHHHHHHHHHHH---HHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHH
Confidence            34467777666666666653211   11110 01111 1124579999999999998864443

>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=92.19  E-value=0.56  Score=38.03  Aligned_cols=71  Identities=13%  Similarity=0.162  Sum_probs=51.6

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +.++||.++++.-++.+++.++..    ++.+..++|+.+..++....    .++.+|+|+|..      -. ..+++++
T Consensus       236 ~~~~IVf~~sr~~~e~l~~~L~~~----g~~~~~~h~~l~~~~R~~~~~~f~~g~~~vlVaT~a------~~-~GiD~p~  304 (523)
T 1oyw_A          236 GKSGIIYCNSRAKVEDTAARLQSK----GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVA------FG-MGINKPN  304 (523)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTT------SC-TTTCCTT
T ss_pred             CCcEEEEeCCHHHHHHHHHHHHHC----CCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEech------hh-CCCCccC
Confidence            457999999999999988888764    77899999988764443322    346889999942      12 4556777


Q ss_pred             ccEEEE
Q psy4275         150 IKFLVL  155 (182)
Q Consensus       150 ~~~iI~  155 (182)
                      ++++|.
T Consensus       305 v~~VI~  310 (523)
T 1oyw_A          305 VRFVVH  310 (523)
T ss_dssp             CCEEEE
T ss_pred             ccEEEE
Confidence            777765

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=92.18  E-value=0.096  Score=37.35  Aligned_cols=19  Identities=16%  Similarity=0.160  Sum_probs=15.8

Q ss_pred             CcEEEECCCCChHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~   62 (182)
                      ++.++.||+|+|||..+..
T Consensus        59 n~ili~GPPGtGKTt~a~a   77 (212)
T 1tue_A           59 NCLVFCGPANTGKSYFGMS   77 (212)
T ss_dssp             SEEEEESCGGGCHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHH
Confidence            4689999999999988643

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=92.12  E-value=0.13  Score=40.70  Aligned_cols=61  Identities=21%  Similarity=0.197  Sum_probs=34.3

Q ss_pred             CccCCccCCCCCHHHHHHHHHC---CCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHH
Q psy4275           3 DPIKSFTDLKLNPWLIRQCQTI---GVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ   66 (182)
Q Consensus         3 ~~~~~~~~~~l~~~i~~~l~~~---~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~   66 (182)
                      .+--+|++.+==++..+.+.+.   .+..+.-++...+   ...+.+++.||+|+|||..+-..+-+
T Consensus       176 ~p~v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi---~~prGvLLyGPPGTGKTlLAkAiA~e  239 (437)
T 4b4t_I          176 SPTESYSDIGGLESQIQEIKESVELPLTHPELYEEMGI---KPPKGVILYGAPGTGKTLLAKAVANQ  239 (437)
T ss_dssp             SCCCCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTC---CCCSEEEEESSTTTTHHHHHHHHHHH
T ss_pred             CCCCcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCCCCceECCCCchHHHHHHHHHHH
Confidence            3455788885333333333321   1223333333332   22568999999999999986444433

>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=91.33  E-value=0.027  Score=38.45  Aligned_cols=54  Identities=13%  Similarity=0.230  Sum_probs=38.8

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIAT  131 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T  131 (182)
                      +.++||.++++..++.+++.++..    ++.+..++|+.+..++...+    .+..+|+|+|
T Consensus        30 ~~~~iVF~~~~~~~~~l~~~L~~~----~~~~~~~~g~~~~~~r~~~~~~f~~g~~~vLvaT   87 (170)
T 2yjt_D           30 ATRSIVFVRKRERVHELANWLREA----GINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVAT   87 (170)
Confidence            458999999999888877777654    67788888877654443332    2356789988

>1c9k_A COBU, adenosylcobinamide kinase; alpha/beta structure rossmann fold P-loop, transferase; HET: 5GP; 2.20A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1cbu_A

Probab=92.00  E-value=0.2  Score=34.84  Aligned_cols=44  Identities=14%  Similarity=0.066  Sum_probs=25.4

Q ss_pred             EEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHH
Q psy4275          46 CIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLV   96 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~   96 (182)
                      .++.|++|||||..+.-.+..       +..++|++.....-.++.+.+..
T Consensus         2 ilV~Gg~~SGKS~~A~~la~~-------~~~~~yiaT~~~~d~e~~~rI~~   45 (180)
T 1c9k_A            2 ILVTGGARSGKSRHAEALIGD-------APQVLYIATSQILDDEMAARIQH   45 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHHCS-------CSSEEEEECCCC------CHHHH
T ss_pred             EEEECCCCCcHHHHHHHHHhc-------CCCeEEEecCCCCCHHHHHHHHH
Confidence            578999999999887544322       23578888755444444444443

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=91.95  E-value=0.72  Score=38.70  Aligned_cols=69  Identities=10%  Similarity=-0.026  Sum_probs=47.9

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEE
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFL  153 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~i  153 (182)
                      +.+++|++|++.-++.+++.++..    ++++..++|+...........++.+|+|+|.-      -. ..+++. +++|
T Consensus       410 ~~~~lVF~~s~~~~e~la~~L~~~----g~~v~~lHg~eR~~v~~~F~~g~~~VLVaTdv------~e-~GIDip-v~~V  477 (673)
T 2wv9_A          410 AGKTVWFVASVKMSNEIAQCLQRA----GKRVIQLNRKSYDTEYPKCKNGDWDFVITTDI------SE-MGANFG-ASRV  477 (673)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHTT----TCCEEEECSSSHHHHGGGGGTCCCSEEEECGG------GG-TTCCCC-CSEE
T ss_pred             CCCEEEEECCHHHHHHHHHHHHhC----CCeEEEeChHHHHHHHHHHHCCCceEEEECch------hh-cceeeC-CcEE
Confidence            458999999999998888777664    78899999854322222222347899999932      22 455677 7776


Q ss_pred             E
Q psy4275         154 V  154 (182)
Q Consensus       154 I  154 (182)
                      |
T Consensus       478 I  478 (673)
T 2wv9_A          478 I  478 (673)
T ss_dssp             E
T ss_pred             E
Confidence            6

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=91.80  E-value=0.1  Score=38.94  Aligned_cols=20  Identities=20%  Similarity=0.072  Sum_probs=16.7

Q ss_pred             CCcEEEECCCCChHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~   62 (182)
                      +.++++.||+|+|||..+-.
T Consensus        67 ~~~vll~G~~GtGKT~la~~   86 (309)
T 3syl_A           67 TLHMSFTGNPGTGKTTVALK   86 (309)
T ss_dssp             CCEEEEEECTTSSHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHH
Confidence            45799999999999988643

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=91.73  E-value=0.14  Score=35.25  Aligned_cols=21  Identities=10%  Similarity=0.023  Sum_probs=16.9

Q ss_pred             CCCcEEEECCCCChHHHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~   62 (182)
                      .|+-+.+.||+|+|||+.+-.
T Consensus         4 ~g~~i~i~GpsGsGKSTL~~~   24 (180)
T 1kgd_A            4 MRKTLVLLGAHGVGRRHIKNT   24 (180)
T ss_dssp             CCCEEEEECCTTSSHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHH
Confidence            356788999999999987543

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=91.71  E-value=0.13  Score=36.16  Aligned_cols=38  Identities=16%  Similarity=-0.081  Sum_probs=26.9

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      +..|.-.++.|++|+|||..+...+.   ..   +..++++...
T Consensus        17 i~~G~~~~i~G~~GsGKTtl~~~l~~---~~---~~~v~~i~~~   54 (220)
T 2cvh_A           17 FAPGVLTQVYGPYASGKTTLALQTGL---LS---GKKVAYVDTE   54 (220)
T ss_dssp             BCTTSEEEEECSTTSSHHHHHHHHHH---HH---CSEEEEEESS
T ss_pred             CcCCEEEEEECCCCCCHHHHHHHHHH---Hc---CCcEEEEECC
Confidence            44577889999999999988665555   11   3467777643

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=91.69  E-value=0.43  Score=37.62  Aligned_cols=55  Identities=15%  Similarity=0.011  Sum_probs=40.9

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEECh
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATP  132 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~  132 (182)
                      +.+++|++|++.-++.+++.++..    ++++..++|+...........+..+|+|+|.
T Consensus       171 ~~~~lVF~~~~~~~~~l~~~L~~~----~~~v~~lhg~~r~~~~~~f~~g~~~vLVaT~  225 (431)
T 2v6i_A          171 DGRTVWFVHSIKQGAEIGTCLQKA----GKKVLYLNRKTFESEYPKCKSEKWDFVITTD  225 (431)
T ss_dssp             SSCEEEECSSHHHHHHHHHHHHHT----TCCEEEESTTTHHHHTTHHHHSCCSEEEECG
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHc----CCeEEEeCCccHHHHHHhhcCCCCeEEEECc
Confidence            458999999999999888888765    7889999987543322233345788999983

>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=91.68  E-value=2.3  Score=35.56  Aligned_cols=77  Identities=12%  Similarity=0.152  Sum_probs=56.1

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +.++||.++++..++.+.+.+...    ++++..++|+....++...+    .+..+|+|+|.-      -. ..+++..
T Consensus       439 ~~~vlVf~~t~~~ae~L~~~L~~~----gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~~------l~-~GlDip~  507 (664)
T 1c4o_A          439 GERTLVTVLTVRMAEELTSFLVEH----GIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINL------LR-EGLDIPE  507 (664)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCC------CC-TTCCCTT
T ss_pred             CCEEEEEECCHHHHHHHHHHHHhc----CCCceeecCCCCHHHHHHHHHHhhcCCceEEEccCh------hh-cCccCCC
Confidence            568999999999998888777664    67888888887654443332    246789999822      12 5678888


Q ss_pred             ccEEEEeccccc
Q psy4275         150 IKFLVLDEADRL  161 (182)
Q Consensus       150 ~~~iI~DE~h~~  161 (182)
                      ++++|+=+++..
T Consensus       508 v~lVI~~d~d~~  519 (664)
T 1c4o_A          508 VSLVAILDADKE  519 (664)
T ss_dssp             EEEEEETTTTSC
T ss_pred             CCEEEEeCCccc
Confidence            998888777544

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=91.67  E-value=0.13  Score=35.27  Aligned_cols=22  Identities=18%  Similarity=-0.031  Sum_probs=17.7

Q ss_pred             CCcEEEECCCCChHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      .+.+++.|++|+|||+.+-...
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La   26 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLA   26 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHH
Confidence            4578999999999999865443

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=91.67  E-value=0.63  Score=45.66  Aligned_cols=48  Identities=13%  Similarity=0.133  Sum_probs=32.8

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHh-hh---hhhhCCCcEEEECCCCChHHHHHH
Q psy4275          13 LNPWLIRQCQTIGVKTPTEIQKA-II---PHVLNDEDCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        13 l~~~i~~~l~~~~~~~~~~~Q~~-~~---~~~~~~~~~li~~~tg~GKT~~~~   61 (182)
                      +.+.+.+.+.+.|+. +.+.+.. ++   +.+.-.+.++++||||+|||.++-
T Consensus       873 l~~ai~~~~~~~~L~-~~~~~v~KviQLye~~~vRhGvmlVGp~gsGKTt~~~  924 (3245)
T 3vkg_A          873 LRKKIQEIAKQRHLV-TKQEWVEKILQLHQILNINHGVMMVGPSGGGKTTSWE  924 (3245)
T ss_dssp             HHHHHHHHHHHTTCC-CCHHHHHHHHHHHHHHTTCSEEEEECSSSSSHHHHHH
T ss_pred             HHHHHHHHHHHcCCc-cCHHHHHHHHHHHHHHHheeeEEEECCCCCCHHHHHH
Confidence            446667777788874 4444433 33   333347789999999999999864

>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=91.64  E-value=0.14  Score=34.99  Aligned_cols=23  Identities=17%  Similarity=-0.002  Sum_probs=18.5

Q ss_pred             hCCCcEEEECCCCChHHHHHHHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~   63 (182)
                      ..++.+++.|++|+|||+.+-..
T Consensus         9 ~~~~~i~i~G~~GsGKst~~~~l   31 (180)
T 3iij_A            9 MLLPNILLTGTPGVGKTTLGKEL   31 (180)
T ss_dssp             CCCCCEEEECSTTSSHHHHHHHH
T ss_pred             ccCCeEEEEeCCCCCHHHHHHHH
Confidence            34678999999999999986543

>2iut_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- cell division, DNA translocation, KOPS, membrane; HET: DNA SAP; 2.25A {Pseudomonas aeruginosa} PDB: 2iuu_A*

Probab=91.56  E-value=0.38  Score=39.53  Aligned_cols=42  Identities=19%  Similarity=0.276  Sum_probs=29.8

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhcc-CCCCeeEEEEcCCH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCE-DPYGIFALVLTPTR   84 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~-~~~~~~~lil~p~~   84 (182)
                      ..|.++.|.||+|||.+.-..++..+.. .+...+++++-|..
T Consensus       214 ~pHlLIaG~TGSGKS~~L~tlI~sLl~~~sP~ev~lilIDpKg  256 (574)
T 2iut_A          214 MPHLLVAGTTGSGKSVGVNAMLLSILFKSTPSEARLIMIDPKM  256 (574)
T ss_dssp             SCCEEEECCTTSSHHHHHHHHHHHHHTTCCTTTEEEEEECSSS
T ss_pred             CCeeEEECCCCCCHHHHHHHHHHHHHHhCCCcceEEEEeCCCh
Confidence            5799999999999999866555555443 34455677776653

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=91.51  E-value=0.14  Score=35.80  Aligned_cols=21  Identities=14%  Similarity=0.249  Sum_probs=16.1

Q ss_pred             CCCcEEEECCCCChHHHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~   62 (182)
                      .|+.+.+.||+|+|||+..-.
T Consensus         3 ~g~~i~lvGpsGaGKSTLl~~   23 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTLLKK   23 (198)
T ss_dssp             --CCEEEECCTTSSHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHH
Confidence            467789999999999987543

>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=91.51  E-value=0.19  Score=38.11  Aligned_cols=43  Identities=14%  Similarity=-0.082  Sum_probs=29.7

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccC---CCCeeEEEEcCCHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCED---PYGIFALVLTPTRE   85 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~---~~~~~~lil~p~~~   85 (182)
                      |.-+++.|++|+|||..+...+.......   ..+..++|+.-...
T Consensus       107 G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~  152 (324)
T 2z43_A          107 RTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGT  152 (324)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSC
T ss_pred             CcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCC
Confidence            56789999999999998776666543321   11347888876543

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=91.44  E-value=0.14  Score=35.81  Aligned_cols=24  Identities=17%  Similarity=0.216  Sum_probs=19.1

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHH
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~   63 (182)
                      +..++-++++||+|+|||+.+-..
T Consensus         9 ~~~~~~i~l~G~sGsGKsTl~~~L   32 (204)
T 2qor_A            9 MARIPPLVVCGPSGVGKGTLIKKV   32 (204)
T ss_dssp             CCCCCCEEEECCTTSCHHHHHHHH
T ss_pred             cccCCEEEEECCCCCCHHHHHHHH
Confidence            445778999999999999875443

>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=91.43  E-value=0.14  Score=37.14  Aligned_cols=21  Identities=24%  Similarity=0.226  Sum_probs=17.2

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      .+++++.||+|+|||..+-..
T Consensus        39 ~~~vll~G~~GtGKT~la~~l   59 (262)
T 2qz4_A           39 PKGALLLGPPGCGKTLLAKAV   59 (262)
T ss_dssp             CCEEEEESCTTSSHHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHH
Confidence            567999999999999886443

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=91.43  E-value=0.53  Score=34.80  Aligned_cols=49  Identities=10%  Similarity=-0.053  Sum_probs=30.3

Q ss_pred             CHHHHHHHHHCCCCCChHHHHh-hhhhhhCC-----CcEEEECCCCChHHHHHHHHHH
Q psy4275          14 NPWLIRQCQTIGVKTPTEIQKA-IIPHVLND-----EDCIGCAKTGSGKTLAFALPIL   65 (182)
Q Consensus        14 ~~~i~~~l~~~~~~~~~~~Q~~-~~~~~~~~-----~~~li~~~tg~GKT~~~~~~~~   65 (182)
                      ...+.+.|+.-|+   .+.+.. .+..++++     +.+++.||+|+|||..+...+.
T Consensus        72 ~n~i~~~l~~qg~---~~~~~~~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~ala~  126 (267)
T 1u0j_A           72 SNRIYKILELNGY---DPQYAASVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAH  126 (267)
T ss_dssp             GCHHHHHHHHTTC---CHHHHHHHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHH
T ss_pred             hHHHHHHHHHcCC---CHHHHHHHHHHHHhCCCCCCcEEEEECCCCCCHHHHHHHHHh
Confidence            3456667765554   354433 23444443     2589999999999998764443

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=91.40  E-value=0.13  Score=38.17  Aligned_cols=21  Identities=24%  Similarity=0.221  Sum_probs=17.6

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      .+++++.||+|+|||..+-..
T Consensus        54 ~~~vll~Gp~GtGKT~la~~l   74 (297)
T 3b9p_A           54 AKGLLLFGPPGNGKTLLARAV   74 (297)
T ss_dssp             CSEEEEESSSSSCHHHHHHHH
T ss_pred             CCeEEEECcCCCCHHHHHHHH
Confidence            578999999999999886443

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=91.39  E-value=0.14  Score=37.18  Aligned_cols=57  Identities=14%  Similarity=0.038  Sum_probs=31.6

Q ss_pred             CccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhh--hCCCcEEEECCCCChHHHHHHH
Q psy4275           3 DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHV--LNDEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus         3 ~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~--~~~~~~li~~~tg~GKT~~~~~   62 (182)
                      .+-.+|+++.-.+.....+...... +.  ....+..+  .-.+++++.||+|+|||..+-.
T Consensus        10 ~~~~~~~~i~g~~~~~~~l~~l~~~-~~--~~~~~~~~~~~~~~g~ll~G~~G~GKTtl~~~   68 (254)
T 1ixz_A           10 APKVTFKDVAGAEEAKEELKEIVEF-LK--NPSRFHEMGARIPKGVLLVGPPGVGKTHLARA   68 (254)
T ss_dssp             CCSCCGGGCCSCHHHHHHHHHHHHH-HH--CHHHHHHTTCCCCSEEEEECCTTSSHHHHHHH
T ss_pred             CCCCCHHHhCCcHHHHHHHHHHHHH-HH--CHHHHHHcCCCCCCeEEEECCCCCCHHHHHHH
Confidence            3456788886666665555432110 00  01122221  1134589999999999987543

>2ius_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- binding, cell division, transmembrane, inner membrane; HET: DNA; 2.7A {Escherichia coli} PDB: 2j5p_A*

Probab=91.34  E-value=0.33  Score=39.35  Aligned_cols=42  Identities=19%  Similarity=0.315  Sum_probs=26.8

Q ss_pred             CCCcEEEECCCCChHHHHHHHHHHHhhcc-CCCCeeEEEEcCC
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALPILQKWCE-DPYGIFALVLTPT   83 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~~~~~~~~-~~~~~~~lil~p~   83 (182)
                      ++.|.++.|+||+|||.+.-..+...+.. .+...+++++-|.
T Consensus       166 ~~pHlLIaG~TGSGKSt~L~~li~sLl~~~~p~~v~l~liDpK  208 (512)
T 2ius_A          166 KMPHLLVAGTTGSGASVGVNAMILSMLYKAQPEDVRFIMIDPK  208 (512)
T ss_dssp             GSCSEEEECCTTSSHHHHHHHHHHHHHTTCCTTTEEEEEECCS
T ss_pred             cCceEEEECCCCCCHHHHHHHHHHHHHHhCCCceEEEEEECCc
Confidence            36799999999999999855544444333 2233445554443

>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=91.29  E-value=1.1  Score=35.60  Aligned_cols=69  Identities=10%  Similarity=-0.020  Sum_probs=48.4

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEE
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFL  153 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~i  153 (182)
                      +.++||.+|++.-++.+++.++..    ++++..++++.........-.+..+|+|+|.-      -. ..++++. ++|
T Consensus       188 ~~~~lVF~~s~~~a~~l~~~L~~~----g~~~~~lh~~~~~~~~~~f~~g~~~vLVaT~v------~~-~GiDip~-~~V  255 (451)
T 2jlq_A          188 QGKTVWFVPSIKAGNDIANCLRKS----GKRVIQLSRKTFDTEYPKTKLTDWDFVVTTDI------SE-MGANFRA-GRV  255 (451)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHTT----TCCEEEECTTTHHHHGGGGGSSCCSEEEECGG------GG-SSCCCCC-SEE
T ss_pred             CCCEEEEcCCHHHHHHHHHHHHHc----CCeEEECCHHHHHHHHHhhccCCceEEEECCH------HH-hCcCCCC-CEE
Confidence            348999999999999888887654    67888888876643333333457899999932      23 4556776 665


Q ss_pred             E
Q psy4275         154 V  154 (182)
Q Consensus       154 I  154 (182)
                      |
T Consensus       256 I  256 (451)
T 2jlq_A          256 I  256 (451)
T ss_dssp             E
T ss_pred             E
Confidence            5

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=91.27  E-value=0.15  Score=39.43  Aligned_cols=21  Identities=33%  Similarity=0.360  Sum_probs=18.2

Q ss_pred             hhCCCcEEEECCCCChHHHHH
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~   60 (182)
                      +..|..+.+.||||+|||+..
T Consensus       172 i~~G~~i~ivG~sGsGKSTll  192 (361)
T 2gza_A          172 VQLERVIVVAGETGSGKTTLM  192 (361)
T ss_dssp             HHTTCCEEEEESSSSCHHHHH
T ss_pred             HhcCCEEEEECCCCCCHHHHH
Confidence            455889999999999999874

>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=91.23  E-value=0.12  Score=35.23  Aligned_cols=20  Identities=15%  Similarity=0.013  Sum_probs=16.2

Q ss_pred             CCcEEEECCCCChHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~   62 (182)
                      +..+++.|++|+|||+++-.
T Consensus         3 ~~~i~l~G~~GsGKST~a~~   22 (178)
T 1qhx_A            3 TRMIILNGGSSAGKSGIVRC   22 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHH
Confidence            34678999999999998644

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=91.17  E-value=0.16  Score=35.77  Aligned_cols=22  Identities=14%  Similarity=-0.003  Sum_probs=17.3

Q ss_pred             CCCcEEEECCCCChHHHHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~   63 (182)
                      .|+-+++.||+|+|||+.+-..
T Consensus         7 ~g~~i~l~GpsGsGKsTl~~~L   28 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVREAV   28 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHH
T ss_pred             CCcEEEEECcCCCCHHHHHHHH
Confidence            3667889999999999885433

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=91.11  E-value=0.45  Score=35.71  Aligned_cols=20  Identities=25%  Similarity=0.403  Sum_probs=17.1

Q ss_pred             CCCcEEEECCCCChHHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~   61 (182)
                      .+.++++.|++|+|||..+-
T Consensus        24 ~~~~vLi~Ge~GtGKt~lAr   43 (304)
T 1ojl_A           24 SDATVLIHGDSGTGKELVAR   43 (304)
T ss_dssp             TTSCEEEESCTTSCHHHHHH
T ss_pred             CCCcEEEECCCCchHHHHHH
Confidence            36789999999999998863

>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=91.05  E-value=0.2  Score=38.54  Aligned_cols=42  Identities=14%  Similarity=0.042  Sum_probs=30.0

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCH
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTR   84 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~   84 (182)
                      +..|.-+++.|++|+|||..++..+......   +..++|+....
T Consensus        58 l~~G~iv~I~G~pGsGKTtLal~la~~~~~~---g~~vlyi~~E~   99 (349)
T 2zr9_A           58 LPRGRVIEIYGPESSGKTTVALHAVANAQAA---GGIAAFIDAEH   99 (349)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHHHHHHT---TCCEEEEESSC
T ss_pred             ccCCeEEEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEECCC
Confidence            3446778999999999999877666555433   44678877543

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=91.04  E-value=0.16  Score=35.35  Aligned_cols=22  Identities=14%  Similarity=-0.032  Sum_probs=17.6

Q ss_pred             hCCCcEEEECCCCChHHHHHHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~   62 (182)
                      ..|..+.+.||+|+|||+.+-.
T Consensus         4 ~~g~~i~l~G~~GsGKSTl~~~   25 (207)
T 2j41_A            4 EKGLLIVLSGPSGVGKGTVRKR   25 (207)
T ss_dssp             CCCCEEEEECSTTSCHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHH
Confidence            3466788999999999988543

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=91.01  E-value=0.17  Score=35.25  Aligned_cols=21  Identities=29%  Similarity=0.232  Sum_probs=16.9

Q ss_pred             CCCcEEEECCCCChHHHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~   62 (182)
                      .|.-+.+.||+|+|||+.+-.
T Consensus         6 ~g~ii~l~Gp~GsGKSTl~~~   26 (205)
T 3tr0_A            6 KANLFIISAPSGAGKTSLVRA   26 (205)
T ss_dssp             CCCEEEEECCTTSCHHHHHHH
T ss_pred             CCcEEEEECcCCCCHHHHHHH
Confidence            466788999999999987543

>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=91.00  E-value=0.11  Score=35.69  Aligned_cols=22  Identities=23%  Similarity=0.193  Sum_probs=17.7

Q ss_pred             hhCCCcEEEECCCCChHHHHHH
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~   61 (182)
                      +..|..+.+.||+|+|||+.+-
T Consensus         6 i~~g~~i~l~G~~GsGKSTl~~   27 (191)
T 1zp6_A            6 DLGGNILLLSGHPGSGKSTIAE   27 (191)
T ss_dssp             CCTTEEEEEEECTTSCHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHH
Confidence            3456778899999999998753

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=90.99  E-value=0.28  Score=37.55  Aligned_cols=42  Identities=10%  Similarity=-0.085  Sum_probs=29.4

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCC---CCeeEEEEcCCH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDP---YGIFALVLTPTR   84 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~---~~~~~lil~p~~   84 (182)
                      |.-+++.|++|+|||..+...+........   .+..++|+....
T Consensus       122 G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~  166 (343)
T 1v5w_A          122 MAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTEN  166 (343)
T ss_dssp             SEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCC
Confidence            456889999999999987766665433211   245788887655

>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=90.97  E-value=0.3  Score=43.60  Aligned_cols=78  Identities=14%  Similarity=0.208  Sum_probs=57.4

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +.+++|++++..-++.+++.++....  +.++..++|+.+..++...+    .++.+|+|+|.      +-. ..+++++
T Consensus       812 g~qvlvf~~~v~~~~~l~~~L~~~~p--~~~v~~lhg~~~~~eR~~il~~F~~g~~~VLVaT~------v~e-~GiDip~  882 (1151)
T 2eyq_A          812 GGQVYYLYNDVENIQKAAERLAELVP--EARIAIGHGQMRERELERVMNDFHHQRFNVLVCTT------IIE-TGIDIPT  882 (1151)
T ss_dssp             TCEEEEECCCSSCHHHHHHHHHHHCT--TSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESS------TTG-GGSCCTT
T ss_pred             CCeEEEEECCHHHHHHHHHHHHHhCC--CCeEEEEeCCCCHHHHHHHHHHHHcCCCcEEEECC------cce-eeecccC
Confidence            56899999999988888888887643  57788999988765443332    34789999994      122 4568888


Q ss_pred             ccEEEEecccc
Q psy4275         150 IKFLVLDEADR  160 (182)
Q Consensus       150 ~~~iI~DE~h~  160 (182)
                      ++++|+..++.
T Consensus       883 v~~VIi~~~~~  893 (1151)
T 2eyq_A          883 ANTIIIERADH  893 (1151)
T ss_dssp             EEEEEETTTTS
T ss_pred             CcEEEEeCCCC
Confidence            99888876654

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=90.96  E-value=0.13  Score=39.33  Aligned_cols=22  Identities=18%  Similarity=0.137  Sum_probs=17.6

Q ss_pred             CCcEEEECCCCChHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      ++++++.||+|+|||..+-...
T Consensus        70 ~~~vLl~GppGtGKT~la~~la   91 (368)
T 3uk6_A           70 GRAVLIAGQPGTGKTAIAMGMA   91 (368)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHH
Confidence            3579999999999999864443

>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=90.96  E-value=0.23  Score=38.31  Aligned_cols=42  Identities=17%  Similarity=-0.014  Sum_probs=30.4

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCH
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTR   84 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~   84 (182)
                      +..+.-+++.|++|+|||..++..+......   +.+++|+....
T Consensus        60 l~~G~ii~I~G~pGsGKTtLal~la~~~~~~---g~~vlyid~E~  101 (356)
T 1u94_A           60 LPMGRIVEIYGPESSGKTTLTLQVIAAAQRE---GKTCAFIDAEH  101 (356)
T ss_dssp             EETTSEEEEECSTTSSHHHHHHHHHHHHHHT---TCCEEEEESSC
T ss_pred             ccCCeEEEEECCCCCCHHHHHHHHHHHHHHC---CCeEEEEeCCC
Confidence            3446789999999999999877666655433   44688887643

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=90.91  E-value=0.19  Score=33.89  Aligned_cols=20  Identities=15%  Similarity=0.125  Sum_probs=16.6

Q ss_pred             CCcEEEECCCCChHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~   62 (182)
                      +..+.+.|++|+|||+.+-.
T Consensus         4 ~~~i~l~G~~GsGKSTl~~~   23 (173)
T 1kag_A            4 KRNIFLVGPMGAGKSTIGRQ   23 (173)
T ss_dssp             CCCEEEECCTTSCHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHH
Confidence            46789999999999988643

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=90.90  E-value=0.12  Score=34.70  Aligned_cols=19  Identities=26%  Similarity=0.125  Sum_probs=15.6

Q ss_pred             cEEEECCCCChHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~   63 (182)
                      .+++.|++|+|||+.+-..
T Consensus         3 ~I~l~G~~GsGKsT~a~~L   21 (179)
T 3lw7_A            3 VILITGMPGSGKSEFAKLL   21 (179)
T ss_dssp             EEEEECCTTSCHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            4688999999999986544

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=90.87  E-value=0.63  Score=45.03  Aligned_cols=48  Identities=21%  Similarity=0.115  Sum_probs=31.8

Q ss_pred             CHHHHHHHHHCCCCCChHHHHh----hhhhhhCCCcEEEECCCCChHHHHHHH
Q psy4275          14 NPWLIRQCQTIGVKTPTEIQKA----IIPHVLNDEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        14 ~~~i~~~l~~~~~~~~~~~Q~~----~~~~~~~~~~~li~~~tg~GKT~~~~~   62 (182)
                      .+.+.+.+.+.++. +.+.+..    .+..+..++.++++||||+|||.++-.
T Consensus       891 ~~~i~~~~~~~~l~-~~~~~~~K~~ql~e~~~~r~gvmlvGptgsGKTt~~~~  942 (2695)
T 4akg_A          891 VQCLKDAGQRSGFS-MSEEFLKKCMQFYYMQKTQQALILVGKAGCGKTATWKT  942 (2695)
T ss_dssp             HHHHHHHHHHHTCC-CCHHHHHHHHHHHHHHHHCSEEEEECSTTSSHHHHHHH
T ss_pred             HHHHHHHHHHcCCc-ccHHHHHHHHHHHHHHHhcceEEEECCCCCCHHHHHHH
Confidence            34566666677764 4444422    233344478899999999999998643

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=90.82  E-value=0.34  Score=37.56  Aligned_cols=21  Identities=19%  Similarity=0.192  Sum_probs=17.8

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      .+++++.||+|+|||..+-..
T Consensus       148 ~~~vLL~GppGtGKT~la~ai  168 (389)
T 3vfd_A          148 ARGLLLFGPPGNGKTMLAKAV  168 (389)
T ss_dssp             CSEEEEESSTTSCHHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHH
Confidence            478999999999999886544

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=90.73  E-value=0.24  Score=34.94  Aligned_cols=23  Identities=30%  Similarity=0.444  Sum_probs=17.8

Q ss_pred             cEEEECCCCChHHHHHHHHHHHh
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQK   67 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~   67 (182)
                      -.+++|++|+|||..+...+...
T Consensus         7 i~l~tG~pGsGKT~~a~~~~~~~   29 (199)
T 2r2a_A            7 ICLITGTPGSGKTLKMVSMMAND   29 (199)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHC
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHH
Confidence            36899999999999876555444

>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein transport, biosynthetic protein; HET: GNP; 3.00A {Bacillus subtilis} PDB: 2px3_A* 3syn_A*

Probab=90.72  E-value=0.28  Score=36.75  Aligned_cols=37  Identities=22%  Similarity=0.115  Sum_probs=23.7

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      ++.+.+.|++|+|||+.+...+......+  |.+++++.
T Consensus       105 g~vi~lvG~~GsGKTTl~~~LA~~l~~~~--G~~V~lv~  141 (296)
T 2px0_A          105 SKYIVLFGSTGAGKTTTLAKLAAISMLEK--HKKIAFIT  141 (296)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHHHHHTT--CCCEEEEE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhc--CCEEEEEe
Confidence            55788889999999988654443332222  34566554

>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=90.65  E-value=0.26  Score=36.60  Aligned_cols=42  Identities=17%  Similarity=-0.022  Sum_probs=27.8

Q ss_pred             hhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcC
Q psy4275          39 HVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTP   82 (182)
Q Consensus        39 ~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p   82 (182)
                      .+..|.-+++.|++|+|||+.+...+......+  +..++++..
T Consensus        31 ~l~~G~~~~i~G~~G~GKTTl~~~ia~~~~~~~--G~~v~~~~~   72 (296)
T 1cr0_A           31 GARGGEVIMVTSGSGMGKSTFVRQQALQWGTAM--GKKVGLAML   72 (296)
T ss_dssp             SBCTTCEEEEEESTTSSHHHHHHHHHHHHHHTS--CCCEEEEES
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHHc--CCeEEEEeC
Confidence            345578889999999999988655554443332  325666643

>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=90.63  E-value=0.91  Score=34.19  Aligned_cols=71  Identities=18%  Similarity=0.294  Sum_probs=48.6

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +.+++|.+++..-++.+++.++..    +..+..++|+.+...+...+    .+..+|+|+|.-.-       ..+++++
T Consensus       238 ~~~~lvf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~-------~Gid~~~  306 (367)
T 1hv8_A          238 EFYGLVFCKTKRDTKELASMLRDI----GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMS-------RGIDVND  306 (367)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTHH-------HHCCCSC
T ss_pred             CCcEEEEECCHHHHHHHHHHHHhc----CCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECChhh-------cCCCccc
Confidence            557999999999998888887764    67888999987765443322    24678999994211       2234555


Q ss_pred             ccEEEE
Q psy4275         150 IKFLVL  155 (182)
Q Consensus       150 ~~~iI~  155 (182)
                      ++++|.
T Consensus       307 ~~~Vi~  312 (367)
T 1hv8_A          307 LNCVIN  312 (367)
T ss_dssp             CSEEEE
T ss_pred             CCEEEE
Confidence            665554

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=90.60  E-value=0.16  Score=39.00  Aligned_cols=22  Identities=18%  Similarity=0.064  Sum_probs=17.4

Q ss_pred             CCcEEEECCCCChHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      ++.+++.||||+|||..+...+
T Consensus        40 ~~lIvI~GPTgsGKTtLa~~LA   61 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLSIDLA   61 (339)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHHH
Confidence            3468899999999999865444

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=90.58  E-value=0.17  Score=36.73  Aligned_cols=21  Identities=24%  Similarity=0.265  Sum_probs=16.9

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      .+++++.||+|+|||..+-..
T Consensus        45 ~~~vll~G~~GtGKT~la~~l   65 (257)
T 1lv7_A           45 PKGVLMVGPPGTGKTLLAKAI   65 (257)
T ss_dssp             CCEEEEECCTTSCHHHHHHHH
T ss_pred             CCeEEEECcCCCCHHHHHHHH
Confidence            457999999999999875433

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=90.48  E-value=0.18  Score=38.26  Aligned_cols=58  Identities=10%  Similarity=0.001  Sum_probs=32.9

Q ss_pred             ccCCccCCCCCHHHHHHHHHCCCCCChHHHH-hhhhh-hhCCCcEEEECCCCChHHHHHHHHH
Q psy4275           4 PIKSFTDLKLNPWLIRQCQTIGVKTPTEIQK-AIIPH-VLNDEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus         4 ~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~-~~~~~-~~~~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      +--+|++++=-+.+.+.+...-.   .|... +.+.. ....+++++.||+|+|||..+-..+
T Consensus         7 ~~~~~~di~G~~~~k~~l~~~v~---~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala   66 (322)
T 1xwi_A            7 PNVKWSDVAGLEGAKEALKEAVI---LPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVA   66 (322)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHHH---HHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHHHHH
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHH---HHHhCHHHHhCCCCCCceEEEECCCCccHHHHHHHHH
Confidence            44578888766666666643210   11110 11111 1224689999999999998864443

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=90.48  E-value=0.27  Score=37.24  Aligned_cols=20  Identities=20%  Similarity=0.190  Sum_probs=16.4

Q ss_pred             CcEEEECCCCChHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~   63 (182)
                      .++++.||+|+|||..+-..
T Consensus        59 ~~~ll~G~~G~GKT~la~~l   78 (353)
T 1sxj_D           59 PHMLFYGPPGTGKTSTILAL   78 (353)
T ss_dssp             CCEEEECSTTSSHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            57999999999999875433

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=90.46  E-value=0.38  Score=36.96  Aligned_cols=22  Identities=14%  Similarity=0.135  Sum_probs=17.7

Q ss_pred             CCcEEEECCCCChHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      .+++++.||+|+|||..+-..+
T Consensus        84 ~~~iLL~GppGtGKT~la~ala  105 (355)
T 2qp9_X           84 TSGILLYGPPGTGKSYLAKAVA  105 (355)
T ss_dssp             CCCEEEECSTTSCHHHHHHHHH
T ss_pred             CceEEEECCCCCcHHHHHHHHH
Confidence            4579999999999998864443

>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=90.39  E-value=0.16  Score=39.30  Aligned_cols=43  Identities=19%  Similarity=0.030  Sum_probs=29.4

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTREL   86 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l   86 (182)
                      ..|.-+++.||+|+|||..+...+......   +.+++|+......
T Consensus        59 ~~G~i~~I~GppGsGKSTLal~la~~~~~~---gg~VlyId~E~s~  101 (356)
T 3hr8_A           59 PRGRIVEIFGQESSGKTTLALHAIAEAQKM---GGVAAFIDAEHAL  101 (356)
T ss_dssp             ETTEEEEEEESTTSSHHHHHHHHHHHHHHT---TCCEEEEESSCCC
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHHHhc---CCeEEEEeccccc
Confidence            335678899999999998866555544332   4468888765443

>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=90.27  E-value=0.17  Score=35.84  Aligned_cols=22  Identities=14%  Similarity=0.107  Sum_probs=17.6

Q ss_pred             CCcEEEECCCCChHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      ++.+++.||||+|||..++-.+
T Consensus        34 g~~ilI~GpsGsGKStLA~~La   55 (205)
T 2qmh_A           34 GLGVLITGDSGVGKSETALELV   55 (205)
T ss_dssp             TEEEEEECCCTTTTHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHH
Confidence            6678999999999998764443

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=90.25  E-value=0.22  Score=34.28  Aligned_cols=22  Identities=18%  Similarity=0.179  Sum_probs=17.8

Q ss_pred             CCcEEEECCCCChHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      +..+++.|++|+|||+++-...
T Consensus        10 ~~~I~l~G~~GsGKSTv~~~La   31 (184)
T 1y63_A           10 GINILITGTPGTGKTSMAEMIA   31 (184)
T ss_dssp             SCEEEEECSTTSSHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHH
Confidence            5678999999999999865443

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=90.18  E-value=0.2  Score=36.94  Aligned_cols=55  Identities=15%  Similarity=0.048  Sum_probs=29.8

Q ss_pred             ccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhh--hCCCcEEEECCCCChHHHHHH
Q psy4275           4 PIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHV--LNDEDCIGCAKTGSGKTLAFA   61 (182)
Q Consensus         4 ~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~--~~~~~~li~~~tg~GKT~~~~   61 (182)
                      +-.+|+++.-.+...+.+...... +.  ....+..+  .-.+++++.||+|+|||..+-
T Consensus        35 ~~~~~~~i~g~~~~~~~l~~l~~~-~~--~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~~   91 (278)
T 1iy2_A           35 PKVTFKDVAGAEEAKEELKEIVEF-LK--NPSRFHEMGARIPKGVLLVGPPGVGKTHLAR   91 (278)
T ss_dssp             CCCCGGGSSSCHHHHHHHHHHHHH-HH--CHHHHHHTTCCCCCEEEEECCTTSSHHHHHH
T ss_pred             CCCCHHHhCChHHHHHHHHHHHHH-HH--CHHHHHHcCCCCCCeEEEECCCcChHHHHHH
Confidence            445677776666665555432110 00  01122221  113458999999999998754

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=90.13  E-value=0.19  Score=39.99  Aligned_cols=22  Identities=18%  Similarity=0.138  Sum_probs=17.8

Q ss_pred             CCcEEEECCCCChHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      ++++++.||+|+|||..+....
T Consensus        63 ~~~iLl~GppGtGKT~la~ala   84 (456)
T 2c9o_A           63 GRAVLLAGPPGTGKTALALAIA   84 (456)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHH
T ss_pred             CCeEEEECCCcCCHHHHHHHHH
Confidence            4689999999999998865443

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=90.10  E-value=0.17  Score=37.73  Aligned_cols=21  Identities=19%  Similarity=0.061  Sum_probs=16.5

Q ss_pred             CcEEEECCCCChHHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~   64 (182)
                      +.+++.||+|+|||..+-..+
T Consensus        37 ~~lLl~GppGtGKT~la~aiA   57 (293)
T 3t15_A           37 LILGIWGGKGQGKSFQCELVF   57 (293)
T ss_dssp             SEEEEEECTTSCHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHH
Confidence            568889999999998864433

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=90.09  E-value=0.35  Score=34.87  Aligned_cols=25  Identities=24%  Similarity=0.166  Sum_probs=19.1

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhc
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      ++++.++.|+|||..++........
T Consensus         8 ~I~~~~kgGvGKTt~a~~la~~l~~   32 (228)
T 2r8r_A            8 KVFLGAAPGVGKTYAMLQAAHAQLR   32 (228)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHH
Confidence            6888899999999997655555443

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=90.08  E-value=0.41  Score=33.63  Aligned_cols=19  Identities=26%  Similarity=0.197  Sum_probs=15.7

Q ss_pred             cEEEECCCCChHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~   63 (182)
                      .+++.||+|+|||..+...
T Consensus        47 ~~ll~G~~G~GKT~l~~~~   65 (250)
T 1njg_A           47 AYLFSGTRGVGKTSIARLL   65 (250)
T ss_dssp             EEEEECSTTSCHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            5899999999999875433

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=89.90  E-value=0.55  Score=37.31  Aligned_cols=42  Identities=10%  Similarity=-0.147  Sum_probs=31.5

Q ss_pred             hhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275          39 HVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus        39 ~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      -+..|.-+++.|++|+|||..++-.+.+...+   +..++|+.-.
T Consensus       193 Gl~~G~liiIaG~pG~GKTtlal~ia~~~a~~---g~~vl~fSlE  234 (444)
T 3bgw_A          193 GYKRRNFVLIAARPSMGKTAFALKQAKNMSDN---DDVVNLHSLE  234 (444)
T ss_dssp             SBCSSCEEEEEECSSSSHHHHHHHHHHHHHHT---TCEEEEECSS
T ss_pred             CCCCCcEEEEEeCCCCChHHHHHHHHHHHHHc---CCEEEEEECC
Confidence            34557789999999999999877777666554   4578888744

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=89.90  E-value=0.13  Score=35.06  Aligned_cols=21  Identities=19%  Similarity=0.071  Sum_probs=17.2

Q ss_pred             hCCCcEEEECCCCChHHHHHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~   61 (182)
                      ..|.-+.+.||+|+|||+.+-
T Consensus         7 ~~gei~~l~G~nGsGKSTl~~   27 (171)
T 4gp7_A            7 PELSLVVLIGSSGSGKSTFAK   27 (171)
T ss_dssp             ESSEEEEEECCTTSCHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHH
Confidence            346678899999999998865

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=89.81  E-value=0.075  Score=44.14  Aligned_cols=43  Identities=23%  Similarity=0.173  Sum_probs=27.7

Q ss_pred             HhcCCCcEEEEChHHHHHHH-hcC----CCCCCCCccEEEEeccccccc
Q psy4275         120 ELAKKPHIVIATPGRLADHL-DTC----NTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus       120 ~~~~~~~Ilv~T~~~l~~~~-~~~----~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      .....++|+|++...+++-. +..    -.+. ..-..+||||||++.+
T Consensus       171 ~~~~~ADvVV~ny~ylld~~~r~~~~~~~~i~-p~~~ivI~DEAHNL~d  218 (620)
T 4a15_A          171 AALPDADIVIAPYAYFLNRSVAEKFLSHWGVS-RNQIVIILDEAHNLPD  218 (620)
T ss_dssp             HHGGGCSEEEEEHHHHTCHHHHHHHHHHHTCC-GGGEEEEETTGGGHHH
T ss_pred             HHhhcCCEEEeCchhhcCHHHHHHHHHhhccC-cCCeEEEEECCCchHH
Confidence            34457899999998765432 110    0112 2345899999999976

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=89.76  E-value=0.65  Score=37.56  Aligned_cols=22  Identities=27%  Similarity=0.200  Sum_probs=17.8

Q ss_pred             CcEEEECCCCChHHHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPIL   65 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~   65 (182)
                      +.+++.||+|+|||..+...+-
T Consensus        78 ~~lLL~GppGtGKTtla~~la~   99 (516)
T 1sxj_A           78 RAAMLYGPPGIGKTTAAHLVAQ   99 (516)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            6899999999999998654433

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=89.73  E-value=0.28  Score=34.89  Aligned_cols=22  Identities=23%  Similarity=0.268  Sum_probs=17.0

Q ss_pred             hhCCCcEEEECCCCChHHHHHH
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~   61 (182)
                      +..|+-+.+.||+|+|||+..-
T Consensus        20 i~~G~~~~lvGpsGsGKSTLl~   41 (218)
T 1z6g_A           20 MNNIYPLVICGPSGVGKGTLIK   41 (218)
T ss_dssp             --CCCCEEEECSTTSSHHHHHH
T ss_pred             cCCCCEEEEECCCCCCHHHHHH
Confidence            3457788999999999998753

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=89.71  E-value=0.23  Score=36.28  Aligned_cols=20  Identities=25%  Similarity=-0.087  Sum_probs=15.8

Q ss_pred             cEEEECCCCChHHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~   64 (182)
                      .+++.||+|+|||+.+...+
T Consensus         3 li~I~G~~GSGKSTla~~La   22 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMAIQIA   22 (253)
T ss_dssp             EEEEECCTTSSHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHH
Confidence            36789999999999865443

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=89.65  E-value=0.34  Score=36.89  Aligned_cols=21  Identities=38%  Similarity=0.561  Sum_probs=17.7

Q ss_pred             hhCCCcEEEECCCCChHHHHH
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~   60 (182)
                      +..|..+.+.||||+|||+..
T Consensus       168 i~~g~~v~i~G~~GsGKTTll  188 (330)
T 2pt7_A          168 IAIGKNVIVCGGTGSGKTTYI  188 (330)
T ss_dssp             HHHTCCEEEEESTTSCHHHHH
T ss_pred             ccCCCEEEEECCCCCCHHHHH
Confidence            345889999999999999863

>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; HET: G3D; 2.20A {Bacillus subtilis} SCOP: c.37.1.1 PDB: 2axp_A*

Probab=89.43  E-value=0.25  Score=33.17  Aligned_cols=19  Identities=16%  Similarity=-0.286  Sum_probs=15.4

Q ss_pred             cEEEECCCCChHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~   63 (182)
                      .+++.|++|+|||+.+-..
T Consensus         3 ~i~l~G~~GsGKsT~~~~L   21 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAAKL   21 (173)
T ss_dssp             EEEEECSSSSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            4688999999999986543

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=89.41  E-value=0.14  Score=37.33  Aligned_cols=22  Identities=23%  Similarity=0.240  Sum_probs=17.5

Q ss_pred             CCcEEEECCCCChHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      .+++++.||+|+|||..+-...
T Consensus        44 ~~~vll~G~~GtGKT~la~~la   65 (268)
T 2r62_A           44 PKGVLLVGPPGTGKTLLAKAVA   65 (268)
T ss_dssp             CSCCCCBCSSCSSHHHHHHHHH
T ss_pred             CceEEEECCCCCcHHHHHHHHH
Confidence            4578999999999998865443

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=89.41  E-value=0.2  Score=38.83  Aligned_cols=21  Identities=29%  Similarity=0.222  Sum_probs=17.3

Q ss_pred             hCCCcEEEECCCCChHHHHHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~   61 (182)
                      ..+..+++.||||+|||+..-
T Consensus       134 ~~g~~i~ivG~~GsGKTTll~  154 (372)
T 2ewv_A          134 RKMGLILVTGPTGSGKSTTIA  154 (372)
T ss_dssp             SSSEEEEEECSSSSSHHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHHH
Confidence            446788999999999998743

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=89.23  E-value=0.2  Score=34.22  Aligned_cols=21  Identities=19%  Similarity=0.129  Sum_probs=16.9

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      +..+++.|++|+|||+.+-..
T Consensus         4 g~~I~l~G~~GsGKST~~~~L   24 (186)
T 3cm0_A            4 GQAVIFLGPPGAGKGTQASRL   24 (186)
T ss_dssp             EEEEEEECCTTSCHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHH
Confidence            456889999999999986544

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=89.18  E-value=0.29  Score=33.45  Aligned_cols=20  Identities=20%  Similarity=0.240  Sum_probs=16.2

Q ss_pred             CCcEEEECCCCChHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~   62 (182)
                      +..+++.|++|+|||+.+-.
T Consensus         3 ~~~I~i~G~~GsGKsT~~~~   22 (192)
T 1kht_A            3 NKVVVVTGVPGVGSTTSSQL   22 (192)
T ss_dssp             CCEEEEECCTTSCHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            45688999999999988543

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=89.12  E-value=0.3  Score=34.88  Aligned_cols=23  Identities=22%  Similarity=0.234  Sum_probs=17.5

Q ss_pred             hhCCCcEEEECCCCChHHHHHHH
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~   62 (182)
                      +..|.-+.+.||+|+|||+..-.
T Consensus        13 ~~~G~ii~l~GpsGsGKSTLlk~   35 (219)
T 1s96_A           13 MAQGTLYIVSAPSGAGKSSLIQA   35 (219)
T ss_dssp             --CCCEEEEECCTTSCHHHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHHHH
Confidence            45577889999999999987543

>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=89.06  E-value=0.36  Score=37.37  Aligned_cols=43  Identities=12%  Similarity=-0.041  Sum_probs=30.2

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHH
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRE   85 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~   85 (182)
                      +..+.-+++.|++|+|||..++..+......   +..++|+.....
T Consensus        71 l~~G~li~I~G~pGsGKTtlal~la~~~~~~---g~~vlyi~~E~s  113 (366)
T 1xp8_A           71 IPRGRITEIYGPESGGKTTLALAIVAQAQKA---GGTCAFIDAEHA  113 (366)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHHHHHHT---TCCEEEEESSCC
T ss_pred             ccCCcEEEEEcCCCCChHHHHHHHHHHHHHC---CCeEEEEECCCC
Confidence            3446778999999999999877666554433   346788776543

>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=89.03  E-value=0.27  Score=37.39  Aligned_cols=21  Identities=19%  Similarity=0.028  Sum_probs=16.3

Q ss_pred             CcEEEECCCCChHHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~   64 (182)
                      +-+++.||||+|||..+...+
T Consensus         4 ~~i~i~GptgsGKt~la~~La   24 (322)
T 3exa_A            4 KLVAIVGPTAVGKTKTSVMLA   24 (322)
T ss_dssp             EEEEEECCTTSCHHHHHHHHH
T ss_pred             cEEEEECCCcCCHHHHHHHHH
Confidence            346789999999998865444

>4dzz_A Plasmid partitioning protein PARF; deviant walker BOX, DNA segregation, unknown function; HET: ADP; 1.80A {Escherichia coli} PDB: 4e03_A* 4e07_A* 4e09_A*

Probab=89.01  E-value=1.5  Score=30.17  Aligned_cols=31  Identities=29%  Similarity=0.141  Sum_probs=20.3

Q ss_pred             ECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcC
Q psy4275          49 CAKTGSGKTLAFALPILQKWCEDPYGIFALVLTP   82 (182)
Q Consensus        49 ~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p   82 (182)
                      .+.-|.|||+.+...+......   +.+++++-.
T Consensus         8 s~kgG~GKTt~a~~la~~la~~---g~~vlliD~   38 (206)
T 4dzz_A            8 NPKGGSGKTTAVINIATALSRS---GYNIAVVDT   38 (206)
T ss_dssp             CSSTTSSHHHHHHHHHHHHHHT---TCCEEEEEC
T ss_pred             eCCCCccHHHHHHHHHHHHHHC---CCeEEEEEC
Confidence            3568899999876555544332   557777753

>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=88.99  E-value=0.33  Score=34.20  Aligned_cols=22  Identities=9%  Similarity=0.087  Sum_probs=17.5

Q ss_pred             CCCcEEEECCCCChHHHHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~   63 (182)
                      .++-+++.||+|+|||...-..
T Consensus        18 ~g~~ivl~GPSGaGKsTL~~~L   39 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIKNAL   39 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHH
T ss_pred             CCCEEEEECcCCCCHHHHHHHH
Confidence            4677889999999999875433

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=88.99  E-value=0.29  Score=33.09  Aligned_cols=19  Identities=21%  Similarity=-0.011  Sum_probs=15.3

Q ss_pred             cEEEECCCCChHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~   63 (182)
                      .+++.|++|+|||+.+-..
T Consensus         4 ~I~i~G~~GsGKST~a~~L   22 (181)
T 1ly1_A            4 IILTIGCPGSGKSTWAREF   22 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHH
T ss_pred             EEEEecCCCCCHHHHHHHH
Confidence            4688999999999986443

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=88.95  E-value=0.16  Score=41.94  Aligned_cols=16  Identities=13%  Similarity=0.223  Sum_probs=14.9

Q ss_pred             cEEEECCCCChHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAF   60 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~   60 (182)
                      ++++.||+|+|||..+
T Consensus       329 ~vLL~GppGtGKT~LA  344 (595)
T 3f9v_A          329 HILIIGDPGTAKSQML  344 (595)
T ss_dssp             CEEEEESSCCTHHHHH
T ss_pred             ceEEECCCchHHHHHH
Confidence            8999999999999875

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=88.90  E-value=1.5  Score=35.10  Aligned_cols=94  Identities=19%  Similarity=0.189  Sum_probs=52.1

Q ss_pred             ChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEc--------CCchhhhhHH---hc
Q psy4275          54 SGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITG--------GMDMVDQGKE---LA  122 (182)
Q Consensus        54 ~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~---~~  122 (182)
                      ++|.... .-++........+.++||.++++..++.+++.++......++++..++|        +.+..++...   ..
T Consensus       370 ~~k~~~l-~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~  448 (555)
T 3tbk_A          370 NPKLRDL-YLVLQEEYHLKPETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFR  448 (555)
T ss_dssp             CHHHHHH-HHHHHHHHHHCTTCCEEEECSSHHHHHHHHHHHHHCGGGTTCCEEECCC-----------------------
T ss_pred             CHHHHHH-HHHHHHHhccCCCceEEEEeCcHHHHHHHHHHHhhCcCcCceeeeEEEecCCcccccccCHHHHHHHHHHHh
Confidence            4565443 3333333322235689999999999999999998765433445555544        4333332222   12


Q ss_pred             --CCCcEEEEChHHHHHHHhcCCCCCCCCccEEEE
Q psy4275         123 --KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVL  155 (182)
Q Consensus       123 --~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~  155 (182)
                        +..+|+|+|.-      -. ..+++..+++||.
T Consensus       449 ~~g~~~vLvaT~~------~~-~GlDlp~v~~VI~  476 (555)
T 3tbk_A          449 ASGDNNILIATSV------AD-EGIDIAECNLVIL  476 (555)
T ss_dssp             ---CCSEEEECCC------TT-CCEETTSCSEEEE
T ss_pred             cCCCeeEEEEcch------hh-cCCccccCCEEEE
Confidence              35689999931      12 4567778887765

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=88.86  E-value=0.31  Score=33.94  Aligned_cols=22  Identities=23%  Similarity=0.135  Sum_probs=17.5

Q ss_pred             CCCcEEEECCCCChHHHHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~   63 (182)
                      .+..+.+.|++|+|||+.+-..
T Consensus        28 ~g~~i~l~G~~GsGKSTl~~~L   49 (200)
T 4eun_A           28 PTRHVVVMGVSGSGKTTIAHGV   49 (200)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHH
Confidence            3667889999999999885433

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A*

Probab=88.82  E-value=0.29  Score=37.15  Aligned_cols=21  Identities=19%  Similarity=0.202  Sum_probs=17.1

Q ss_pred             CcEEEECCCCChHHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~   64 (182)
                      .++++.||+|+|||..+-..+
T Consensus        52 ~~~ll~Gp~G~GKTTLa~~ia   72 (334)
T 1in4_A           52 DHVLLAGPPGLGKTTLAHIIA   72 (334)
T ss_dssp             CCEEEESSTTSSHHHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHH
Confidence            679999999999998754443

>3foz_A TRNA delta(2)-isopentenylpyrophosphate transferas; nucleoside modification, isopentenyl-tRNA transferase, transferase-RNA complex; 2.50A {Escherichia coli k-12} PDB: 2zxu_A* 2zm5_A

Probab=88.77  E-value=0.29  Score=37.14  Aligned_cols=20  Identities=25%  Similarity=-0.019  Sum_probs=16.0

Q ss_pred             cEEEECCCCChHHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~   64 (182)
                      -+++.||||+|||..+...+
T Consensus        12 ~i~i~GptgsGKt~la~~La   31 (316)
T 3foz_A           12 AIFLMGPTASGKTALAIELR   31 (316)
T ss_dssp             EEEEECCTTSCHHHHHHHHH
T ss_pred             EEEEECCCccCHHHHHHHHH
Confidence            46789999999998865444

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=88.74  E-value=0.29  Score=37.57  Aligned_cols=22  Identities=23%  Similarity=0.157  Sum_probs=17.9

Q ss_pred             CCcEEEECCCCChHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      .+++++.||+|+|||..+-...
T Consensus       117 ~~~vLl~GppGtGKT~la~aia  138 (357)
T 3d8b_A          117 PKGILLFGPPGTGKTLIGKCIA  138 (357)
T ss_dssp             CSEEEEESSTTSSHHHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHHH
Confidence            5689999999999998865443

>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=88.72  E-value=2.3  Score=36.32  Aligned_cols=74  Identities=15%  Similarity=0.143  Sum_probs=52.3

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhh-------ccCCceEEEEEcCCchhhhhHHhc---------CCCcEEEEChHHHHH
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLG-------KVMNLRVSIITGGMDMVDQGKELA---------KKPHIVIATPGRLAD  137 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~Ilv~T~~~l~~  137 (182)
                      ++++||.+|++.-++.+++.++...       ...++.+..++|+.+..++.....         +..+|+|+|.-    
T Consensus       303 ~g~iLVF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~~~eR~~v~~~f~~~~~~~g~~kVlVAT~i----  378 (773)
T 2xau_A          303 AGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNGRPGRKVVISTNI----  378 (773)
T ss_dssp             SCEEEEECSCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECTTCCHHHHGGGGSCCCCCSSSSCCEEEEEECTH----
T ss_pred             CCCEEEECCCHHHHHHHHHHHHHHHHhhcccccCCCeEEEEeCCCCCHHHHHHHHhhcccccCCCCceEEEEeCcH----
Confidence            5589999999999999888887532       224788999999987665554432         24579999943    


Q ss_pred             HHhcCCCCCCCCccEEE
Q psy4275         138 HLDTCNTFSLNRIKFLV  154 (182)
Q Consensus       138 ~~~~~~~~~~~~~~~iI  154 (182)
                        .. ..+++..+++||
T Consensus       379 --ae-~GidIp~v~~VI  392 (773)
T 2xau_A          379 --AE-TSLTIDGIVYVV  392 (773)
T ss_dssp             --HH-HTCCCTTEEEEE
T ss_pred             --HH-hCcCcCCeEEEE
Confidence              22 345677887655

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=88.64  E-value=0.34  Score=33.99  Aligned_cols=23  Identities=9%  Similarity=0.039  Sum_probs=17.2

Q ss_pred             hhhCCCcEEEECCCCChHHHHHH
Q psy4275          39 HVLNDEDCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        39 ~~~~~~~~li~~~tg~GKT~~~~   61 (182)
                      .+..|+-+.+.||+|+|||+..-
T Consensus        16 ~i~~Gei~~l~GpnGsGKSTLl~   38 (207)
T 1znw_A           16 PAAVGRVVVLSGPSAVGKSTVVR   38 (207)
T ss_dssp             ---CCCEEEEECSTTSSHHHHHH
T ss_pred             CCCCCCEEEEECCCCCCHHHHHH
Confidence            45668888999999999998753

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=88.63  E-value=0.27  Score=36.55  Aligned_cols=19  Identities=26%  Similarity=0.130  Sum_probs=16.0

Q ss_pred             CcEEEECCCCChHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~   62 (182)
                      .++++.||+|+|||..+-.
T Consensus        48 ~~~ll~G~~GtGKt~la~~   66 (311)
T 4fcw_A           48 GSFLFLGPTGVGKTELAKT   66 (311)
T ss_dssp             EEEEEESCSSSSHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHH
Confidence            4789999999999988643

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=88.55  E-value=0.32  Score=33.74  Aligned_cols=22  Identities=18%  Similarity=-0.097  Sum_probs=17.5

Q ss_pred             CCCcEEEECCCCChHHHHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~   63 (182)
                      .+..+++.|+.|+|||+.+-..
T Consensus         3 ~~~~I~l~G~~GsGKsT~~~~L   24 (204)
T 2v54_A            3 RGALIVFEGLDKSGKTTQCMNI   24 (204)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHH
Confidence            3567899999999999986433

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=88.50  E-value=0.81  Score=35.03  Aligned_cols=46  Identities=15%  Similarity=0.008  Sum_probs=32.3

Q ss_pred             hhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275          35 AIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus        35 ~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      ....-+..|.-+++.|++|.|||..++-.+......   +..++|+...
T Consensus        38 ~~~gGl~~G~LiiIaG~pG~GKTt~al~ia~~~a~~---g~~Vl~fSlE   83 (338)
T 4a1f_A           38 NYTSGFNKGSLVIIGARPSMGKTSLMMNMVLSALND---DRGVAVFSLE   83 (338)
T ss_dssp             HHHCSBCTTCEEEEEECTTSCHHHHHHHHHHHHHHT---TCEEEEEESS
T ss_pred             HHhcCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHc---CCeEEEEeCC
Confidence            333345557789999999999999877666655442   4577777653

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=88.48  E-value=0.3  Score=33.08  Aligned_cols=20  Identities=20%  Similarity=0.162  Sum_probs=16.4

Q ss_pred             CCcEEEECCCCChHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~   62 (182)
                      +..+.+.|++|+|||+.+-.
T Consensus         8 g~~i~l~G~~GsGKSTl~~~   27 (175)
T 1knq_A            8 HHIYVLMGVSGSGKSAVASE   27 (175)
T ss_dssp             SEEEEEECSTTSCHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHH
Confidence            45688999999999988644

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=88.46  E-value=0.33  Score=33.34  Aligned_cols=23  Identities=17%  Similarity=0.037  Sum_probs=18.1

Q ss_pred             hCCCcEEEECCCCChHHHHHHHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~   63 (182)
                      .++..+++.|++|+|||+.+-..
T Consensus         7 ~~~~~I~l~G~~GsGKsT~~~~L   29 (196)
T 2c95_A            7 KKTNIIFVVGGPGSGKGTQCEKI   29 (196)
T ss_dssp             TTSCEEEEEECTTSSHHHHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHHHHH
Confidence            34567899999999999986443

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=88.40  E-value=0.29  Score=34.10  Aligned_cols=19  Identities=16%  Similarity=0.267  Sum_probs=15.4

Q ss_pred             CcEEEECCCCChHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~   62 (182)
                      +-++++||+|+|||...-.
T Consensus         2 RpIVi~GPSG~GK~Tl~~~   20 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKK   20 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            4578999999999987533

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=88.39  E-value=0.49  Score=35.67  Aligned_cols=35  Identities=14%  Similarity=0.064  Sum_probs=22.3

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      +-+.+.|++|+|||+.+...+.... ..  +.+++++.
T Consensus       105 ~vi~ivG~~GsGKTTl~~~LA~~l~-~~--g~kV~lv~  139 (306)
T 1vma_A          105 FVIMVVGVNGTGKTTSCGKLAKMFV-DE--GKSVVLAA  139 (306)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHH-HT--TCCEEEEE
T ss_pred             eEEEEEcCCCChHHHHHHHHHHHHH-hc--CCEEEEEc
Confidence            4577889999999987654443322 22  44666654

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=88.26  E-value=0.35  Score=32.48  Aligned_cols=21  Identities=19%  Similarity=-0.005  Sum_probs=17.0

Q ss_pred             CcEEEECCCCChHHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~   64 (182)
                      +++++.|+.|+|||+++-...
T Consensus         8 ~~i~l~G~~GsGKSTva~~La   28 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLAQELG   28 (168)
T ss_dssp             CEEEEESCTTSSHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHH
Confidence            478999999999999875443

>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=88.19  E-value=0.33  Score=36.98  Aligned_cols=43  Identities=12%  Similarity=-0.093  Sum_probs=31.0

Q ss_pred             CCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTREL   86 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l   86 (182)
                      .| -+++.||+|+|||..++-.+.....+.+ +.+++|+....++
T Consensus        28 ~G-iteI~G~pGsGKTtL~Lq~~~~~~~~g~-g~~vlyId~E~s~   70 (333)
T 3io5_A           28 SG-LLILAGPSKSFKSNFGLTMVSSYMRQYP-DAVCLFYDSEFGI   70 (333)
T ss_dssp             SE-EEEEEESSSSSHHHHHHHHHHHHHHHCT-TCEEEEEESSCCC
T ss_pred             CC-eEEEECCCCCCHHHHHHHHHHHHHhcCC-CceEEEEeccchh
Confidence            35 5789999999999987776666543311 4578998876665

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=88.16  E-value=0.47  Score=40.68  Aligned_cols=59  Identities=14%  Similarity=0.013  Sum_probs=33.7

Q ss_pred             cCCccCCCCCHHHHHHHHHCC-CCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHH
Q psy4275           5 IKSFTDLKLNPWLIRQCQTIG-VKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus         5 ~~~~~~~~l~~~i~~~l~~~~-~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      .-+|++++--+++.+.+.+.- +.-.+|.+...+ .+...+.+++.||+|+|||+.+-..+
T Consensus       473 ~v~w~diggl~~~k~~l~e~v~~p~~~p~~f~~~-g~~~~~gvLl~GPPGtGKT~lAkaiA  532 (806)
T 3cf2_A          473 QVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKF-GMTPSKGVLFYGPPGCGKTLLAKAIA  532 (806)
T ss_dssp             CCCSTTCCSCHHHHHHHTTTTTTTTTCSGGGSSS-CCCCCSCCEEESSTTSSHHHHHHHHH
T ss_pred             CCCHHHhCCHHHHHHHHHHHHHhhhhCHHHHHhc-CCCCCceEEEecCCCCCchHHHHHHH
Confidence            346777776777777776542 111111111100 11224679999999999998764433

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=88.12  E-value=6  Score=31.48  Aligned_cols=88  Identities=16%  Similarity=0.100  Sum_probs=53.4

Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCCc
Q psy4275          75 IFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNRI  150 (182)
Q Consensus        75 ~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~  150 (182)
                      .+.+++.....-+..+++.+..    .+.++..++|+.+...+...+    .++.+|+|+|+..+.      ..++++++
T Consensus       348 ~~~~ivf~~~~~~~~l~~~L~~----~~~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv~T~~~~~------~GiDip~v  417 (510)
T 2oca_A          348 ENAFVMFKHVSHGKAIFDLIKN----EYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFS------TGISVKNL  417 (510)
T ss_dssp             CEEEEEESSHHHHHHHHHHHHT----TCSSEEEESSSTTHHHHHHHHHHHHHCCSCEEEEEHHHHH------HSCCCCSE
T ss_pred             CCeEEEEecHHHHHHHHHHHHH----cCCCeEEEECCCCHHHHHHHHHHHhCCCCCEEEEEcChhh------cccccccC
Confidence            3444555555555555555544    345888999988755433222    346789999977663      23467788


Q ss_pred             cEEEEeccccccccCChhHHHHHHHH
Q psy4275         151 KFLVLDEADRLSLMTSLKFFFFFFFL  176 (182)
Q Consensus       151 ~~iI~DE~h~~~~~~~~~~~~~~~~~  176 (182)
                      +++|+.+..    ++...+.-...|.
T Consensus       418 ~~vi~~~~~----~s~~~~~Q~~GR~  439 (510)
T 2oca_A          418 HHVVLAHGV----KSKIIVLQTIGRV  439 (510)
T ss_dssp             EEEEESSCC----CSCCHHHHHHHHH
T ss_pred             cEEEEeCCC----CCHHHHHHHHhcc
Confidence            888887766    2444444444444

>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=88.11  E-value=0.47  Score=36.59  Aligned_cols=71  Identities=14%  Similarity=0.222  Sum_probs=42.7

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +.++||.++++.-++.+++.++..    ++.+..++|+.....+...+    .+..+|+|+|.-      -. ..+++..
T Consensus       280 ~~~~lvf~~~~~~~~~l~~~l~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~------~~-~Gidip~  348 (414)
T 3eiq_A          280 ITQAVIFINTRRKVDWLTEKMHAR----DFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDL------LA-RGIDVQQ  348 (414)
T ss_dssp             CSSCEEECSCHHHHHHHHHHHHTT----TCCCEEC---CHHHHHHHHHHHHSCC---CEEECSS------CC---CCGGG
T ss_pred             CCcEEEEeCCHHHHHHHHHHHHhc----CCeEEEecCCCCHHHHHHHHHHHHcCCCcEEEECCc------cc-cCCCccC
Confidence            457999999999988887777653    67888889887765443332    235689999932      11 3456666


Q ss_pred             ccEEEE
Q psy4275         150 IKFLVL  155 (182)
Q Consensus       150 ~~~iI~  155 (182)
                      ++++|.
T Consensus       349 v~~Vi~  354 (414)
T 3eiq_A          349 VSLVIN  354 (414)
T ss_dssp             CSCEEE
T ss_pred             CCEEEE
Confidence            666654

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=88.06  E-value=0.62  Score=31.86  Aligned_cols=21  Identities=24%  Similarity=-0.012  Sum_probs=16.9

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      +..+++.|++|+|||+.+-..
T Consensus        13 ~~~i~l~G~~GsGKsT~~~~L   33 (186)
T 2yvu_A           13 GIVVWLTGLPGSGKTTIATRL   33 (186)
T ss_dssp             CEEEEEECCTTSSHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHH
Confidence            557889999999999886443

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=88.01  E-value=0.71  Score=34.74  Aligned_cols=36  Identities=17%  Similarity=0.002  Sum_probs=22.4

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      +..+.+.||+|+|||+..-..+... ...  ++++.+..
T Consensus       102 g~vi~lvG~nGsGKTTll~~Lagll-~~~--~g~V~l~g  137 (304)
T 1rj9_A          102 GRVVLVVGVNGVGKTTTIAKLGRYY-QNL--GKKVMFCA  137 (304)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHHHH-HTT--TCCEEEEC
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHH-Hhc--CCEEEEEe
Confidence            4567788999999998754333222 222  44666665

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=87.88  E-value=0.35  Score=36.83  Aligned_cols=22  Identities=18%  Similarity=-0.094  Sum_probs=17.2

Q ss_pred             CcEEEECCCCChHHHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPIL   65 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~   65 (182)
                      +.+++.||||+|||..+...+-
T Consensus         6 ~~i~i~GptGsGKTtla~~La~   27 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAMALAD   27 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            3578999999999998654443

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=87.60  E-value=0.35  Score=38.41  Aligned_cols=22  Identities=14%  Similarity=0.055  Sum_probs=17.7

Q ss_pred             CCcEEEECCCCChHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      .+++++.||+|+|||..+-...
T Consensus       167 ~~~vLL~GppGtGKT~lA~aia  188 (444)
T 2zan_A          167 WRGILLFGPPGTGKSYLAKAVA  188 (444)
T ss_dssp             CSEEEEECSTTSSHHHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHHH
Confidence            4689999999999998864333

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=87.54  E-value=0.45  Score=32.22  Aligned_cols=20  Identities=20%  Similarity=0.084  Sum_probs=16.2

Q ss_pred             cEEEECCCCChHHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~   64 (182)
                      .+++.|++|+|||+.+-...
T Consensus         6 ~i~i~G~~GsGKsTla~~La   25 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALA   25 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHH
Confidence            58899999999999865443

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=87.54  E-value=0.83  Score=33.83  Aligned_cols=19  Identities=21%  Similarity=0.174  Sum_probs=15.9

Q ss_pred             cEEEECCCCChHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~   63 (182)
                      +.++.||+|+|||..+...
T Consensus        40 ~~ll~G~~G~GKt~la~~l   58 (319)
T 2chq_A           40 HLLFSGPPGTGKTATAIAL   58 (319)
T ss_dssp             CEEEESSSSSSHHHHHHHH
T ss_pred             eEEEECcCCcCHHHHHHHH
Confidence            6999999999999875443

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=87.54  E-value=0.37  Score=33.54  Aligned_cols=21  Identities=19%  Similarity=0.047  Sum_probs=17.0

Q ss_pred             CCCcEEEECCCCChHHHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~   62 (182)
                      .+..+.+.|++|+|||+.+-.
T Consensus        24 ~g~~i~l~G~sGsGKSTl~~~   44 (200)
T 3uie_A           24 KGCVIWVTGLSGSGKSTLACA   44 (200)
T ss_dssp             CCEEEEEECSTTSSHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHH
Confidence            366788899999999988543

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=87.43  E-value=0.61  Score=35.35  Aligned_cols=20  Identities=20%  Similarity=0.197  Sum_probs=16.2

Q ss_pred             cEEEECCCCChHHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~   64 (182)
                      +.++.||+|+|||..+...+
T Consensus        48 ~~ll~Gp~G~GKTtla~~la   67 (340)
T 1sxj_C           48 HLLFYGPPGTGKTSTIVALA   67 (340)
T ss_dssp             CEEEECSSSSSHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHH
Confidence            48999999999998865443

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=87.42  E-value=0.62  Score=35.02  Aligned_cols=36  Identities=17%  Similarity=0.155  Sum_probs=22.5

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      +.-+.+.||+|+|||+..-..+-. +...  ++++.+..
T Consensus       100 g~vi~lvG~nGsGKTTll~~Lag~-l~~~--~g~V~l~g  135 (302)
T 3b9q_A          100 PAVIMIVGVNGGGKTTSLGKLAHR-LKNE--GTKVLMAA  135 (302)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHH-HHHT--TCCEEEEC
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHH-HHHc--CCeEEEEe
Confidence            456778999999999875433222 2222  44666665

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=87.41  E-value=0.44  Score=33.09  Aligned_cols=20  Identities=20%  Similarity=0.117  Sum_probs=16.4

Q ss_pred             CcEEEECCCCChHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~   63 (182)
                      ..+++.|++|+|||+.+-..
T Consensus        19 ~~I~l~G~~GsGKSTla~~L   38 (202)
T 3t61_A           19 GSIVVMGVSGSGKSSVGEAI   38 (202)
T ss_dssp             SCEEEECSTTSCHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHH
Confidence            46899999999999986443

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=87.33  E-value=0.64  Score=35.24  Aligned_cols=36  Identities=22%  Similarity=0.071  Sum_probs=23.0

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      ++-+.+.+++|+|||+.+...+.... ..  +.+++++.
T Consensus       105 ~~vI~ivG~~G~GKTT~~~~LA~~l~-~~--g~kVllid  140 (320)
T 1zu4_A          105 LNIFMLVGVNGTGKTTSLAKMANYYA-EL--GYKVLIAA  140 (320)
T ss_dssp             CEEEEEESSTTSSHHHHHHHHHHHHH-HT--TCCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHH-HC--CCeEEEEe
Confidence            34577889999999988654443322 22  45677664

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=87.29  E-value=0.31  Score=33.38  Aligned_cols=21  Identities=19%  Similarity=0.017  Sum_probs=16.6

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      +..+++.|++|+|||+.+-..
T Consensus         5 ~~~I~l~G~~GsGKST~~~~L   25 (193)
T 2rhm_A            5 PALIIVTGHPATGKTTLSQAL   25 (193)
T ss_dssp             CEEEEEEESTTSSHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHH
Confidence            456789999999999986443

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=87.23  E-value=0.23  Score=37.63  Aligned_cols=21  Identities=19%  Similarity=0.185  Sum_probs=17.2

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      ..++++.||+|+|||..+-..
T Consensus        45 ~~~vLl~G~~GtGKT~la~~l   65 (350)
T 1g8p_A           45 IGGVLVFGDRGTGKSTAVRAL   65 (350)
T ss_dssp             GCCEEEECCGGGCTTHHHHHH
T ss_pred             CceEEEECCCCccHHHHHHHH
Confidence            457999999999999886433

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=87.15  E-value=0.31  Score=33.49  Aligned_cols=20  Identities=20%  Similarity=0.114  Sum_probs=15.6

Q ss_pred             CcEEEECCCCChHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~   63 (182)
                      .-+.+.||+|+|||+.+-..
T Consensus         3 ~ii~l~G~~GaGKSTl~~~L   22 (189)
T 2bdt_A            3 KLYIITGPAGVGKSTTCKRL   22 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHH
Confidence            34678999999999876444

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=87.14  E-value=1.2  Score=36.82  Aligned_cols=24  Identities=13%  Similarity=0.184  Sum_probs=19.9

Q ss_pred             hhhhCCCcEEEECCCCChHHHHHH
Q psy4275          38 PHVLNDEDCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        38 ~~~~~~~~~li~~~tg~GKT~~~~   61 (182)
                      ..+..+.++++.||+|+|||+.+-
T Consensus        55 ~~i~~g~~vll~Gp~GtGKTtlar   78 (604)
T 3k1j_A           55 TAANQKRHVLLIGEPGTGKSMLGQ   78 (604)
T ss_dssp             HHHHTTCCEEEECCTTSSHHHHHH
T ss_pred             ccccCCCEEEEEeCCCCCHHHHHH
Confidence            345568899999999999998863

>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid biosynthesis, P-loop kinase, metal- binding, shikimate pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis} SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A* 2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A* 1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A* 3baf_A*

Probab=87.10  E-value=0.52  Score=32.14  Aligned_cols=20  Identities=20%  Similarity=0.092  Sum_probs=16.1

Q ss_pred             CcEEEECCCCChHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~   63 (182)
                      ..+++.|++|+|||+++-..
T Consensus         3 ~~I~l~G~~GsGKsT~a~~L   22 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRL   22 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHH
Confidence            45789999999999986443

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=87.07  E-value=0.25  Score=34.53  Aligned_cols=25  Identities=20%  Similarity=-0.210  Sum_probs=18.4

Q ss_pred             hhhCCCcEEEECCCCChHHHHHHHH
Q psy4275          39 HVLNDEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        39 ~~~~~~~~li~~~tg~GKT~~~~~~   63 (182)
                      .+..+.-+.+.|++|+|||+.+-..
T Consensus        17 ~~~~~~~i~i~G~~GsGKSTl~~~L   41 (207)
T 2qt1_A           17 RGSKTFIIGISGVTNSGKTTLAKNL   41 (207)
T ss_dssp             CSCCCEEEEEEESTTSSHHHHHHHH
T ss_pred             cCCCCeEEEEECCCCCCHHHHHHHH
Confidence            3444566789999999999886443

>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11

Probab=87.06  E-value=0.47  Score=36.41  Aligned_cols=41  Identities=12%  Similarity=-0.064  Sum_probs=26.1

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhcc--C-CCCeeEEEEcCC
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCE--D-PYGIFALVLTPT   83 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~--~-~~~~~~lil~p~   83 (182)
                      |.-+.+.||+|+|||..+...+......  . ..+.+++++.-.
T Consensus       131 G~i~~I~G~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~~e  174 (349)
T 1pzn_A          131 QAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTE  174 (349)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEeCC
Confidence            4568889999999998866555443211  1 113477777654

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=87.04  E-value=0.38  Score=38.42  Aligned_cols=22  Identities=18%  Similarity=0.093  Sum_probs=18.0

Q ss_pred             CCcEEEECCCCChHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      .++.++.||+|+|||..+-...
T Consensus       201 ~~~~LL~G~pG~GKT~la~~la  222 (468)
T 3pxg_A          201 KNNPVLIGEPGVGKTAIAEGLA  222 (468)
T ss_dssp             SCEEEEESCTTTTTHHHHHHHH
T ss_pred             CCCeEEECCCCCCHHHHHHHHH
Confidence            5689999999999999865433

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=87.01  E-value=0.25  Score=35.28  Aligned_cols=23  Identities=17%  Similarity=0.014  Sum_probs=14.0

Q ss_pred             hhCCCcEEEECCCCChHHHHHHH
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~   62 (182)
                      +..|.-+.+.||+|+|||+.+-.
T Consensus        24 v~~G~ii~l~Gp~GsGKSTl~~~   46 (231)
T 3lnc_A           24 KSVGVILVLSSPSGCGKTTVANK   46 (231)
T ss_dssp             EECCCEEEEECSCC----CHHHH
T ss_pred             cCCCCEEEEECCCCCCHHHHHHH
Confidence            34477788999999999987543

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=86.92  E-value=0.42  Score=36.67  Aligned_cols=21  Identities=24%  Similarity=-0.064  Sum_probs=16.5

Q ss_pred             cEEEECCCCChHHHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALPIL   65 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~   65 (182)
                      -+++.||||+|||..+...+-
T Consensus         9 lI~I~GptgSGKTtla~~La~   29 (340)
T 3d3q_A            9 LIVIVGPTASGKTELSIEVAK   29 (340)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEECCCcCcHHHHHHHHHH
Confidence            578999999999998654443

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=86.92  E-value=0.43  Score=32.86  Aligned_cols=22  Identities=18%  Similarity=-0.003  Sum_probs=17.4

Q ss_pred             CCCcEEEECCCCChHHHHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~   63 (182)
                      .+..+++.|++|+|||+.+-..
T Consensus        11 ~~~~I~l~G~~GsGKsT~a~~L   32 (199)
T 2bwj_A           11 KCKIIFIIGGPGSGKGTQCEKL   32 (199)
T ss_dssp             HSCEEEEEECTTSSHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHH
Confidence            3567889999999999886433

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=86.91  E-value=0.5  Score=33.34  Aligned_cols=21  Identities=14%  Similarity=0.031  Sum_probs=16.9

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      +..+++.|++|+|||+.+-..
T Consensus         4 ~~~I~l~G~~GsGKsT~a~~L   24 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGTQAPNL   24 (220)
T ss_dssp             CCEEEEECCTTSSHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHH
Confidence            456889999999999886543

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=86.88  E-value=0.42  Score=33.53  Aligned_cols=19  Identities=16%  Similarity=0.104  Sum_probs=15.4

Q ss_pred             cEEEECCCCChHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~   63 (182)
                      .+++.|++|+|||+.+-..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L   20 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQI   20 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            3688999999999986544

>4anj_A Unconventional myosin-VI, green fluorescent prote; motor protein-metal-bindng protein complex, molecular motor, metal-binding protein, transition state; HET: CR2 ADP; 2.60A {Sus scrofa}

Probab=86.87  E-value=0.81  Score=40.39  Aligned_cols=63  Identities=17%  Similarity=0.227  Sum_probs=40.9

Q ss_pred             cCCccCCC--CCHHHHHHHHHCCCCC--C--hHHHHhhhhhhhC---CCcEEEECCCCChHHHHHHHHHHHh
Q psy4275           5 IKSFTDLK--LNPWLIRQCQTIGVKT--P--TEIQKAIIPHVLN---DEDCIGCAKTGSGKTLAFALPILQK   67 (182)
Q Consensus         5 ~~~~~~~~--l~~~i~~~l~~~~~~~--~--~~~Q~~~~~~~~~---~~~~li~~~tg~GKT~~~~~~~~~~   67 (182)
                      +.+|.++|  .+++..+.+......+  |  ...-..++..+..   ++.+++.|.+|+|||.++-..+-+.
T Consensus        97 VNPyk~lp~iY~~~~~~~Y~g~~~~~lpPHIfaiA~~AY~~M~~~~~nQsIiiSGESGAGKTestK~im~yL  168 (1052)
T 4anj_A           97 VNPYFDIPKIYSSETIKSYQGKSLGTMPPHVFAIADKAFRDMKVLKLSQSIIVSGESGAGKTENTKFVLRYL  168 (1052)
T ss_dssp             ECCSSCCTTTTSHHHHHHHTTCCBTTBCSCHHHHHHHHHHHHHHHTCCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             ECCCCCccccCCHHHHHHhcCCCCCCCCCcHHHHHHHHHHHHHHhCCCceEEEecCCCCCHHHHHHHHHHHH
Confidence            45677775  4788888886543333  2  3333445555543   5689999999999998865444443

>3dl0_A Adenylate kinase; phosphotransferase, zinc coordination, ATP-binding, binding, nucleotide biosynthesis, nucleotide-binding, trans; HET: AP5; 1.58A {Bacillus subtilis} PDB: 1p3j_A* 2ori_A* 2eu8_A* 2oo7_A* 2p3s_A* 2qaj_A* 2osb_A* 3dkv_A* 1zin_A* 1zio_A* 1zip_A* 1s3g_A*

Probab=86.81  E-value=0.43  Score=33.54  Aligned_cols=19  Identities=16%  Similarity=0.036  Sum_probs=15.5

Q ss_pred             cEEEECCCCChHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~   63 (182)
                      .+++.|++|+|||+.+-..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L   20 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERI   20 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            3688999999999986544

>4a74_A DNA repair and recombination protein RADA; hydrolase, recombinase; HET: DNA ANP; 1.48A {Pyrococcus furiosus} PDB: 4a6x_A* 4a6p_A* 4a7o_A*

Probab=86.72  E-value=0.32  Score=34.32  Aligned_cols=44  Identities=11%  Similarity=-0.079  Sum_probs=27.3

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhccC---CCCeeEEEEcCC
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCED---PYGIFALVLTPT   83 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~---~~~~~~lil~p~   83 (182)
                      +..|.-+.+.||+|+|||+.+...+.......   ..+..++++...
T Consensus        22 i~~G~~~~l~G~nGsGKSTll~~l~g~~~~~~~~g~~~~~~i~~~~~   68 (231)
T 4a74_A           22 IETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTE   68 (231)
T ss_dssp             EESSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESS
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCEEEEEECC
Confidence            44577889999999999988655444332211   013356666543

>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway, P-loop protein, transferase; 1.8A {Erwinia chrysanthemi} SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*

Probab=86.67  E-value=0.55  Score=31.52  Aligned_cols=20  Identities=20%  Similarity=0.027  Sum_probs=16.1

Q ss_pred             CcEEEECCCCChHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~   63 (182)
                      +.+++.|++|+|||+.+-..
T Consensus         3 ~~I~l~G~~GsGKsT~a~~L   22 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGREL   22 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHH
Confidence            35789999999999986443

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=86.33  E-value=0.66  Score=33.47  Aligned_cols=22  Identities=27%  Similarity=0.081  Sum_probs=17.6

Q ss_pred             CCcEEEECCCCChHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      ...+++.||+|+|||+.+-...
T Consensus        29 ~~~I~l~G~~GsGKsT~a~~L~   50 (243)
T 3tlx_A           29 DGRYIFLGAPGSGKGTQSLNLK   50 (243)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHH
Confidence            4568999999999999865443

>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA translocation, nucleotide-binding, DNA-binding; 3.00A {Bovine papillomavirus type 1} PDB: 2gxa_A*

Probab=86.22  E-value=0.5  Score=35.64  Aligned_cols=21  Identities=10%  Similarity=0.031  Sum_probs=17.3

Q ss_pred             hCCCcEEEECCCCChHHHHHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~   61 (182)
                      ..|+.+.+.||+|+|||+..-
T Consensus       124 ~~Ge~vaIvGpsGsGKSTLl~  144 (305)
T 2v9p_A          124 PKKNCLAFIGPPNTGKSMLCN  144 (305)
T ss_dssp             TTCSEEEEECSSSSSHHHHHH
T ss_pred             cCCCEEEEECCCCCcHHHHHH
Confidence            347888999999999998743

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=86.12  E-value=0.62  Score=33.99  Aligned_cols=21  Identities=24%  Similarity=0.132  Sum_probs=18.1

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      +..+.+.|++|+|||+.+-..
T Consensus        48 g~~i~l~G~~GsGKSTl~~~L   68 (250)
T 3nwj_A           48 GRSMYLVGMMGSGKTTVGKIM   68 (250)
T ss_dssp             TCCEEEECSTTSCHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHH
Confidence            889999999999999986443

>1f2t_A RAD50 ABC-ATPase; DNA double-strand break repair, replication; 1.60A {Pyrococcus furiosus} SCOP: c.37.1.12 PDB: 1f2u_A* 1us8_A*

Probab=86.12  E-value=0.61  Score=31.01  Aligned_cols=17  Identities=24%  Similarity=0.239  Sum_probs=14.2

Q ss_pred             CcEEEECCCCChHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~   60 (182)
                      .-.++.||+|+|||...
T Consensus        24 g~~~I~G~NGsGKStil   40 (149)
T 1f2t_A           24 GINLIIGQNGSGKSSLL   40 (149)
T ss_dssp             EEEEEECCTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            35788999999999874

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=86.11  E-value=0.55  Score=32.31  Aligned_cols=16  Identities=31%  Similarity=0.329  Sum_probs=13.5

Q ss_pred             cEEEECCCCChHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAF   60 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~   60 (182)
                      .+.+.||+|+|||+..
T Consensus         2 ~i~l~G~nGsGKTTLl   17 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLV   17 (178)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4678999999999874

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=86.09  E-value=0.49  Score=33.59  Aligned_cols=21  Identities=19%  Similarity=0.020  Sum_probs=16.9

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      ...+++.|++|+|||+.+-..
T Consensus         7 ~~~I~l~G~~GsGKsT~a~~L   27 (227)
T 1zd8_A            7 LLRAVIMGAPGSGKGTVSSRI   27 (227)
T ss_dssp             CCEEEEEECTTSSHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHH
Confidence            456899999999999986443

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=86.08  E-value=0.54  Score=32.11  Aligned_cols=19  Identities=21%  Similarity=0.078  Sum_probs=15.6

Q ss_pred             CcEEEECCCCChHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~   62 (182)
                      ..+++.|++|+|||+.+-.
T Consensus         4 ~~I~l~G~~GsGKsT~a~~   22 (196)
T 1tev_A            4 LVVFVLGGPGAGKGTQCAR   22 (196)
T ss_dssp             EEEEEECCTTSSHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHH
Confidence            4578899999999988643

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=86.04  E-value=1.6  Score=36.35  Aligned_cols=76  Identities=22%  Similarity=0.282  Sum_probs=42.0

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEc--------CCchhhhhHH---h-c-CCCcEEEEChHHHHHHHh
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITG--------GMDMVDQGKE---L-A-KKPHIVIATPGRLADHLD  140 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~---~-~-~~~~Ilv~T~~~l~~~~~  140 (182)
                      +.++||.++++.-++.+++.++......++++..++|        +.+..++...   . . +..+|+|+|.-      -
T Consensus       398 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F~~~g~~~vLVaT~v------~  471 (696)
T 2ykg_A          398 ETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSV------A  471 (696)
T ss_dssp             TCCEEEECSCHHHHHHHHHHHHHCTTCCSCCEEC-----------------------------CCSCSEEEES------S
T ss_pred             CCcEEEEeCcHHHHHHHHHHHHhCCCccccceeEEEccCCCccccCCCHHHHHHHHHHHHhcCCccEEEEech------h
Confidence            5689999999999999998888764333367776654        4433322222   2 2 35789999921      2


Q ss_pred             cCCCCCCCCccEEEEe
Q psy4275         141 TCNTFSLNRIKFLVLD  156 (182)
Q Consensus       141 ~~~~~~~~~~~~iI~D  156 (182)
                      . ..+++..+++||.=
T Consensus       472 ~-~GiDip~v~~VI~~  486 (696)
T 2ykg_A          472 D-EGIDIAQCNLVILY  486 (696)
T ss_dssp             C-CC---CCCSEEEEE
T ss_pred             h-cCCcCccCCEEEEe
Confidence            2 45677788877753

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=85.95  E-value=0.48  Score=32.30  Aligned_cols=18  Identities=28%  Similarity=0.204  Sum_probs=14.8

Q ss_pred             cEEEECCCCChHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~   62 (182)
                      .+++.|++|+|||+.+-.
T Consensus         3 ~I~i~G~~GsGKsT~~~~   20 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVLAK   20 (194)
T ss_dssp             EEEEEECTTSCHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            468899999999988643

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=85.93  E-value=0.47  Score=35.30  Aligned_cols=21  Identities=24%  Similarity=0.137  Sum_probs=16.6

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      +..+++.||+|+|||+.+-..
T Consensus        33 ~~livl~G~sGsGKSTla~~L   53 (287)
T 1gvn_B           33 PTAFLLGGQPGSGKTSLRSAI   53 (287)
T ss_dssp             CEEEEEECCTTSCTHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHH
Confidence            346889999999999986443

>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2

Probab=85.85  E-value=0.61  Score=37.52  Aligned_cols=42  Identities=12%  Similarity=-0.126  Sum_probs=30.5

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      +..|.-+++.|++|+|||..++-.+.+...+.  +..++++.-.
T Consensus       239 l~~G~l~li~G~pG~GKT~lal~~a~~~a~~~--g~~vl~~s~E  280 (503)
T 1q57_A          239 ARGGEVIMVTSGSGMVMSTFVRQQALQWGTAM--GKKVGLAMLE  280 (503)
T ss_dssp             CCTTCEEEEEESSCHHHHHHHHHHHHHHTTTS--CCCEEEEESS
T ss_pred             cCCCeEEEEeecCCCCchHHHHHHHHHHHHhc--CCcEEEEecc
Confidence            44577889999999999998777766655442  3467777654

>3kta_A Chromosome segregation protein SMC; structural maintenance of chromosomes, ABC ATPase, CFTR adenylate kinase, AP5A, transferase; HET: AP5; 1.63A {Pyrococcus furiosus} PDB: 1xex_A* 1xew_X*

Probab=85.81  E-value=0.55  Score=31.95  Aligned_cols=17  Identities=24%  Similarity=0.024  Sum_probs=14.4

Q ss_pred             cEEEECCCCChHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~   61 (182)
                      -.++.||+|+|||...-
T Consensus        28 ~~~i~G~NGsGKStll~   44 (182)
T 3kta_A           28 FTAIVGANGSGKSNIGD   44 (182)
T ss_dssp             EEEEEECTTSSHHHHHH
T ss_pred             cEEEECCCCCCHHHHHH
Confidence            57889999999998753

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=85.71  E-value=0.56  Score=33.12  Aligned_cols=21  Identities=19%  Similarity=0.094  Sum_probs=16.9

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      ...+++.|++|+|||+.+-..
T Consensus         5 ~~~I~l~G~~GsGKsT~~~~L   25 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQCELI   25 (222)
T ss_dssp             SCCEEEEESTTSSHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHH
Confidence            356899999999999986543

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=85.71  E-value=0.56  Score=31.88  Aligned_cols=20  Identities=20%  Similarity=0.076  Sum_probs=16.2

Q ss_pred             CCcEEEECCCCChHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~   62 (182)
                      |..+.+.|++|+|||+.+-.
T Consensus         5 g~~i~l~G~~GsGKST~~~~   24 (179)
T 2pez_A            5 GCTVWLTGLSGAGKTTVSMA   24 (179)
T ss_dssp             CEEEEEECCTTSSHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHH
Confidence            55678999999999987543

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=85.57  E-value=0.53  Score=33.05  Aligned_cols=31  Identities=10%  Similarity=-0.033  Sum_probs=21.3

Q ss_pred             HHHHhhhhhhhCCCcEEEECCCCChHHHHHHH
Q psy4275          31 EIQKAIIPHVLNDEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        31 ~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~   62 (182)
                      +.+.... ....+..+++.|++|+|||+.+-.
T Consensus        14 ~~~r~~~-~~~~~~~i~~~G~~GsGKsT~~~~   44 (211)
T 1m7g_A           14 RSERTEL-RNQRGLTIWLTGLSASGKSTLAVE   44 (211)
T ss_dssp             HHHHHHH-HTSSCEEEEEECSTTSSHHHHHHH
T ss_pred             HHHhhcc-cCCCCCEEEEECCCCCCHHHHHHH
Confidence            3444442 344567788999999999987643

>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=85.53  E-value=1.5  Score=34.79  Aligned_cols=54  Identities=11%  Similarity=-0.037  Sum_probs=39.1

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIAT  131 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T  131 (182)
                      +.++||.+|++.-++.+++.++..    ++++..+++..........-.+..+|+|+|
T Consensus       190 ~~~~LVF~~s~~~~~~l~~~L~~~----g~~v~~lh~~~R~~~~~~f~~g~~~iLVaT  243 (459)
T 2z83_A          190 AGKTVWFVASVKMGNEIAMCLQRA----GKKVIQLNRKSYDTEYPKCKNGDWDFVITT  243 (459)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHT----TCCEEEESTTCCCCCGGGSSSCCCSEEEES
T ss_pred             CCCEEEEeCChHHHHHHHHHHHhc----CCcEEecCHHHHHHHHhhccCCCceEEEEC
Confidence            458999999999999888888765    778888888643222222223467899999

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=85.50  E-value=0.61  Score=32.89  Aligned_cols=20  Identities=15%  Similarity=-0.036  Sum_probs=15.9

Q ss_pred             CcEEEECCCCChHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~   63 (182)
                      ..+.+.||+|+|||+.+-..
T Consensus         6 ~~i~i~G~~GsGKSTl~~~L   25 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKAM   25 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHH
Confidence            45788999999999876543

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=85.37  E-value=0.55  Score=32.61  Aligned_cols=21  Identities=24%  Similarity=0.007  Sum_probs=16.7

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      +..+++.|++|+|||+.+-..
T Consensus         4 ~~~I~i~G~~GsGKsT~~~~L   24 (213)
T 2plr_A            4 GVLIAFEGIDGSGKSSQATLL   24 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHH
T ss_pred             CeEEEEEcCCCCCHHHHHHHH
Confidence            456789999999999986443

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=85.33  E-value=0.53  Score=32.08  Aligned_cols=20  Identities=25%  Similarity=0.097  Sum_probs=15.9

Q ss_pred             CcEEEECCCCChHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~   63 (182)
                      ..+++.|++|+|||+.+-..
T Consensus         7 ~~I~l~G~~GsGKsT~~~~L   26 (194)
T 1qf9_A            7 NVVFVLGGPGSGKGTQCANI   26 (194)
T ss_dssp             EEEEEEESTTSSHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHH
Confidence            35788999999999986443

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=85.33  E-value=0.64  Score=33.18  Aligned_cols=22  Identities=14%  Similarity=0.052  Sum_probs=17.6

Q ss_pred             CCcEEEECCCCChHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      ...+++.|++|+|||+.+-...
T Consensus        16 ~~~I~l~G~~GsGKsT~a~~La   37 (233)
T 1ak2_A           16 GVRAVLLGPPGAGKGTQAPKLA   37 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHH
Confidence            4578999999999999865443

>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=85.32  E-value=0.46  Score=39.64  Aligned_cols=74  Identities=16%  Similarity=0.255  Sum_probs=44.6

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHh--hccCCceEEEEEcC--------CchhhhhHHh----cCCCcEEEEChHHHHHHH
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVL--GKVMNLRVSIITGG--------MDMVDQGKEL----AKKPHIVIATPGRLADHL  139 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~--~~~~~~~~~~~~~~--------~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~  139 (182)
                      +.++||.++++..++.+++.++..  ....|+++..++|+        .+..++...+    .+..+|+|+|.-      
T Consensus       400 ~~~~IVF~~s~~~~~~l~~~L~~~~~l~~~g~~~~~lhg~~~~~~~~~~~~~eR~~~~~~F~~g~~~VLVaT~~------  473 (699)
T 4gl2_A          400 SARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGKINLLIATTV------  473 (699)
T ss_dssp             CCCEEEECSCHHHHHHHHHHHHSSCSCC-----CEECCCSCCCTTCCCCCHHHHHHHHHHHCC---CCSEEECS------
T ss_pred             CCcEEEEECcHHHHHHHHHHHHhCccccccCcceEEEECCCCccCCCCCCHHHHHHHHHHHhcCCCcEEEEccc------
Confidence            568999999999999998888764  33346888889988        5544433322    235678888831      


Q ss_pred             hcCCCCCCCCccEEE
Q psy4275         140 DTCNTFSLNRIKFLV  154 (182)
Q Consensus       140 ~~~~~~~~~~~~~iI  154 (182)
                      -. ..+++..+++||
T Consensus       474 ~~-~GIDip~v~~VI  487 (699)
T 4gl2_A          474 AE-EGLDIKECNIVI  487 (699)
T ss_dssp             CC-TTSCCCSCCCCE
T ss_pred             cc-cCCccccCCEEE
Confidence            11 345566666555

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=85.27  E-value=0.73  Score=36.11  Aligned_cols=41  Identities=7%  Similarity=-0.214  Sum_probs=27.7

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccC---CCCeeEEEEcCC
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCED---PYGIFALVLTPT   83 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~---~~~~~~lil~p~   83 (182)
                      |.-+.+.||+|+|||..+...++......   ..+..++++.-.
T Consensus       178 Gei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E  221 (400)
T 3lda_A          178 GSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTE  221 (400)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESS
T ss_pred             CcEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCC
Confidence            56788999999999998765555544321   124467887654

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=85.24  E-value=0.66  Score=32.14  Aligned_cols=20  Identities=15%  Similarity=0.051  Sum_probs=16.2

Q ss_pred             CcEEEECCCCChHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~   63 (182)
                      ..+++.|++|+|||+.+-..
T Consensus        21 ~~I~l~G~~GsGKST~a~~L   40 (201)
T 2cdn_A           21 MRVLLLGPPGAGKGTQAVKL   40 (201)
T ss_dssp             CEEEEECCTTSSHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHH
Confidence            46889999999999986443

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=85.16  E-value=0.59  Score=32.53  Aligned_cols=22  Identities=18%  Similarity=-0.008  Sum_probs=17.6

Q ss_pred             CCCcEEEECCCCChHHHHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~   63 (182)
                      .+..+++.|+.|+|||+.+-..
T Consensus         9 ~~~~I~l~G~~GsGKST~~~~L   30 (212)
T 2wwf_A            9 KGKFIVFEGLDRSGKSTQSKLL   30 (212)
T ss_dssp             CSCEEEEEESTTSSHHHHHHHH
T ss_pred             cCCEEEEEcCCCCCHHHHHHHH
Confidence            3567889999999999986443

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=85.15  E-value=0.91  Score=35.05  Aligned_cols=36  Identities=17%  Similarity=0.166  Sum_probs=22.5

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      +.-+.+.||+|+|||+..-..+- .+...  ++++.+..
T Consensus       157 g~vi~lvG~nGsGKTTll~~Lag-~l~~~--~G~V~l~g  192 (359)
T 2og2_A          157 PAVIMIVGVNGGGKTTSLGKLAH-RLKNE--GTKVLMAA  192 (359)
T ss_dssp             SEEEEEECCTTSCHHHHHHHHHH-HHHHT--TCCEEEEC
T ss_pred             CeEEEEEcCCCChHHHHHHHHHh-hcccc--CCEEEEec
Confidence            44677899999999987533322 22222  44666665

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=85.11  E-value=0.63  Score=37.05  Aligned_cols=20  Identities=25%  Similarity=0.192  Sum_probs=16.9

Q ss_pred             CCcEEEECCCCChHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~   62 (182)
                      .+++++.||+|+|||..+-.
T Consensus        50 ~~~iLl~GppGtGKT~lar~   69 (444)
T 1g41_A           50 PKNILMIGPTGVGKTEIARR   69 (444)
T ss_dssp             CCCEEEECCTTSSHHHHHHH
T ss_pred             CceEEEEcCCCCCHHHHHHH
Confidence            46899999999999988643

>3nwn_A Kinesin-like protein KIF9; motor domain, ADP, structural genomics, structural consortium, SGC, contractIle protein; HET: ADP; 2.00A {Homo sapiens}

Probab=85.09  E-value=0.66  Score=35.85  Aligned_cols=23  Identities=26%  Similarity=0.481  Sum_probs=16.0

Q ss_pred             hhhhCCCc--EEEECCCCChHHHHH
Q psy4275          38 PHVLNDED--CIGCAKTGSGKTLAF   60 (182)
Q Consensus        38 ~~~~~~~~--~li~~~tg~GKT~~~   60 (182)
                      ..+++|.|  ++..|.||+|||.+.
T Consensus        98 ~~~l~G~N~tifAYGQTGSGKTyTM  122 (359)
T 3nwn_A           98 SQALDGYNGTIMCYGQTGAGKTYTM  122 (359)
T ss_dssp             HHHHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HHHhCCCCEEEEEeCCCCCCccEEe
Confidence            33445654  555679999999885

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=85.02  E-value=0.98  Score=34.37  Aligned_cols=36  Identities=19%  Similarity=0.072  Sum_probs=22.1

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      +.-+.+.||+|+|||+..-..+-. +...  ++++.+..
T Consensus       129 g~vi~lvG~nGaGKTTll~~Lag~-l~~~--~g~V~l~g  164 (328)
T 3e70_C          129 PYVIMFVGFNGSGKTTTIAKLANW-LKNH--GFSVVIAA  164 (328)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHH-HHHT--TCCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH-HHhc--CCEEEEEe
Confidence            456788899999999875333322 2222  34565554

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=84.99  E-value=0.65  Score=32.01  Aligned_cols=19  Identities=21%  Similarity=0.090  Sum_probs=15.2

Q ss_pred             cEEEECCCCChHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~   63 (182)
                      .+++.|++|+|||+.+-..
T Consensus         2 ~I~i~G~~GsGKsT~~~~L   20 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEI   20 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHH
T ss_pred             EEEEECCCccCHHHHHHHH
Confidence            3678999999999986443

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=84.92  E-value=0.6  Score=37.61  Aligned_cols=21  Identities=24%  Similarity=0.229  Sum_probs=17.4

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      .+++++.||+|+|||..+-..
T Consensus       238 ~~~vLL~GppGtGKT~lArai  258 (489)
T 3hu3_A          238 PRGILLYGPPGTGKTLIARAV  258 (489)
T ss_dssp             CCEEEEECSTTSSHHHHHHHH
T ss_pred             CCcEEEECcCCCCHHHHHHHH
Confidence            467999999999999986443

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=84.91  E-value=0.79  Score=31.86  Aligned_cols=19  Identities=21%  Similarity=0.216  Sum_probs=15.2

Q ss_pred             CCcEEEECCCCChHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~   61 (182)
                      |..+.+.||+|+|||+..-
T Consensus         1 G~~i~i~G~nG~GKTTll~   19 (189)
T 2i3b_A            1 ARHVFLTGPPGVGKTTLIH   19 (189)
T ss_dssp             CCCEEEESCCSSCHHHHHH
T ss_pred             CCEEEEECCCCChHHHHHH
Confidence            3457889999999998753

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=84.88  E-value=0.56  Score=33.48  Aligned_cols=25  Identities=16%  Similarity=0.108  Sum_probs=18.1

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHH
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      +.+.+-+++.||+|+||++.+-...
T Consensus        26 ~~k~kiI~llGpPGsGKgTqa~~L~   50 (217)
T 3umf_A           26 LAKAKVIFVLGGPGSGKGTQCEKLV   50 (217)
T ss_dssp             TTSCEEEEEECCTTCCHHHHHHHHH
T ss_pred             ccCCcEEEEECCCCCCHHHHHHHHH
Confidence            3344567788999999998765443

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=84.83  E-value=1.3  Score=37.64  Aligned_cols=22  Identities=18%  Similarity=0.093  Sum_probs=18.0

Q ss_pred             CCcEEEECCCCChHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      ..+.++.||+|+|||..+-...
T Consensus       201 ~~~vLL~G~pGtGKT~la~~la  222 (758)
T 3pxi_A          201 KNNPVLIGEPGVGKTAIAEGLA  222 (758)
T ss_dssp             SCEEEEESCTTTTTHHHHHHHH
T ss_pred             CCCeEEECCCCCCHHHHHHHHH
Confidence            5689999999999999864443

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=84.77  E-value=0.62  Score=32.46  Aligned_cols=22  Identities=9%  Similarity=-0.120  Sum_probs=17.5

Q ss_pred             CCCcEEEECCCCChHHHHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~   63 (182)
                      ++..+++.|+.|+|||+.+-..
T Consensus         8 ~~~~I~l~G~~GsGKsT~~~~L   29 (215)
T 1nn5_A            8 RGALIVLEGVDRAGKSTQSRKL   29 (215)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHH
Confidence            3567889999999999986443

>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation, ATP-binding, cytoplasm, mitochondrion, nucleotide-binding, nucleus; 2.95A {Saccharomyces cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*

Probab=84.70  E-value=0.54  Score=36.94  Aligned_cols=20  Identities=20%  Similarity=0.069  Sum_probs=15.8

Q ss_pred             cEEEECCCCChHHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~   64 (182)
                      -+++.||||+|||..+...+
T Consensus         4 ~i~i~GptgsGKttla~~La   23 (409)
T 3eph_A            4 VIVIAGTTGVGKSQLSIQLA   23 (409)
T ss_dssp             EEEEEECSSSSHHHHHHHHH
T ss_pred             EEEEECcchhhHHHHHHHHH
Confidence            46789999999998865444

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=84.69  E-value=0.59  Score=32.74  Aligned_cols=18  Identities=22%  Similarity=0.137  Sum_probs=15.1

Q ss_pred             CCcEEEECCCCChHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~   60 (182)
                      +.-+.+.||+|+|||+.+
T Consensus        22 g~~v~I~G~sGsGKSTl~   39 (208)
T 3c8u_A           22 RQLVALSGAPGSGKSTLS   39 (208)
T ss_dssp             CEEEEEECCTTSCTHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            556778899999999875

>3tif_A Uncharacterized ABC transporter ATP-binding prote; nucleotide-binding domain, ABC transporter ATPase; HET: ADP; 1.80A {Methanocaldococcus jannaschii dsm 2661ORGANISM_TAXID} PDB: 1l2t_A* 1f3o_A*

Probab=84.67  E-value=0.47  Score=34.23  Aligned_cols=26  Identities=23%  Similarity=0.163  Sum_probs=18.9

Q ss_pred             CCCcEEEECCCCChHHHHHHHHHHHhhc
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      .|.-+.+.||+|+|||+..  -++..+.
T Consensus        30 ~Ge~~~iiG~nGsGKSTLl--~~l~Gl~   55 (235)
T 3tif_A           30 EGEFVSIMGPSGSGKSTML--NIIGCLD   55 (235)
T ss_dssp             TTCEEEEECSTTSSHHHHH--HHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHH--HHHhcCC
Confidence            4778889999999999763  3444433

>1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2 function project, S2F, structural genomics, transferase; HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1

Probab=84.66  E-value=0.66  Score=32.25  Aligned_cols=19  Identities=32%  Similarity=0.041  Sum_probs=14.9

Q ss_pred             cEEEECCCCChHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~   63 (182)
                      .+.+.|++|+|||+.+-..
T Consensus         4 ~i~l~G~~GsGKST~~~~L   22 (206)
T 1jjv_A            4 IVGLTGGIGSGKTTIANLF   22 (206)
T ss_dssp             EEEEECSTTSCHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            3578899999999886443

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=84.52  E-value=0.69  Score=32.05  Aligned_cols=19  Identities=16%  Similarity=0.071  Sum_probs=15.3

Q ss_pred             CcEEEECCCCChHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~   62 (182)
                      ..+++.|++|+|||+.+-.
T Consensus        16 ~~I~l~G~~GsGKsT~~~~   34 (203)
T 1ukz_A           16 SVIFVLGGPGAGKGTQCEK   34 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHH
Confidence            3578899999999988643

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=84.27  E-value=0.76  Score=30.67  Aligned_cols=19  Identities=21%  Similarity=-0.052  Sum_probs=15.2

Q ss_pred             cEEEECCCCChHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~   63 (182)
                      .+++.|++|+|||+.+-..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L   20 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLL   20 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHH
Confidence            3688999999999886443

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=84.26  E-value=0.72  Score=31.48  Aligned_cols=18  Identities=28%  Similarity=0.017  Sum_probs=14.6

Q ss_pred             EEEECCCCChHHHHHHHH
Q psy4275          46 CIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~   63 (182)
                      +++.|+.|+|||+.+-..
T Consensus         3 I~l~G~~GsGKsT~~~~L   20 (195)
T 2pbr_A            3 IAFEGIDGSGKTTQAKKL   20 (195)
T ss_dssp             EEEECSTTSCHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            678999999999986433

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=84.15  E-value=0.6  Score=32.78  Aligned_cols=20  Identities=15%  Similarity=0.024  Sum_probs=15.7

Q ss_pred             cEEEECCCCChHHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~   64 (182)
                      .+++.|++|+|||+.+-...
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~   21 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIM   21 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            36889999999998865443

>1bg2_A Kinesin; motor protein, ATPase, microtubule associated; HET: ADP; 1.80A {Homo sapiens} SCOP: c.37.1.9 PDB: 2p4n_K* 1mkj_A* 2kin_A* 3kin_A*

Probab=84.05  E-value=0.89  Score=34.60  Aligned_cols=22  Identities=32%  Similarity=0.424  Sum_probs=16.0

Q ss_pred             hhhCCCc--EEEECCCCChHHHHH
Q psy4275          39 HVLNDED--CIGCAKTGSGKTLAF   60 (182)
Q Consensus        39 ~~~~~~~--~li~~~tg~GKT~~~   60 (182)
                      .+.+|.|  ++..|+||+|||.+.
T Consensus        72 ~~l~G~n~tifAYGqTGSGKTyTm   95 (325)
T 1bg2_A           72 DVLEGYNGTIFAYGQTSSGKTHTM   95 (325)
T ss_dssp             HHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHhCCCeEEEEEECCCCCCCceEe
Confidence            3445655  555689999999985

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=84.04  E-value=0.62  Score=32.52  Aligned_cols=19  Identities=26%  Similarity=-0.088  Sum_probs=15.1

Q ss_pred             CCcEEEECCCCChHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~   61 (182)
                      +.-+.+.||+|+|||+.+-
T Consensus         6 ~~~i~i~G~~GsGKSTl~~   24 (211)
T 3asz_A            6 PFVIGIAGGTASGKTTLAQ   24 (211)
T ss_dssp             CEEEEEEESTTSSHHHHHH
T ss_pred             cEEEEEECCCCCCHHHHHH
Confidence            4456788999999998753

>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B

Probab=83.99  E-value=0.81  Score=36.26  Aligned_cols=35  Identities=20%  Similarity=0.081  Sum_probs=23.6

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      ..+++.|++|+|||+.+...+.....+   +.+++++.
T Consensus       100 ~vI~ivG~~GvGKTTla~~La~~l~~~---G~kVllv~  134 (432)
T 2v3c_C          100 NVILLVGIQGSGKTTTAAKLARYIQKR---GLKPALIA  134 (432)
T ss_dssp             CCEEEECCSSSSTTHHHHHHHHHHHHH---HCCEEEEC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEe
Confidence            368889999999998865544443322   44677665

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=83.97  E-value=0.67  Score=37.82  Aligned_cols=19  Identities=21%  Similarity=0.024  Sum_probs=16.7

Q ss_pred             CCcEEEECCCCChHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~   61 (182)
                      +.++++.||+|+|||..+-
T Consensus       108 g~~vll~Gp~GtGKTtlar  126 (543)
T 3m6a_A          108 GPILCLAGPPGVGKTSLAK  126 (543)
T ss_dssp             SCEEEEESSSSSSHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHH
Confidence            6789999999999998854

>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding motif, ATP- binding, nucleotide-binding, transferase; HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB: 3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*

Probab=83.95  E-value=0.55  Score=34.26  Aligned_cols=20  Identities=20%  Similarity=-0.075  Sum_probs=16.1

Q ss_pred             CcEEEECCCCChHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~   63 (182)
                      ..++++|++|+|||+.+-..
T Consensus         5 ~lIvl~G~pGSGKSTla~~L   24 (260)
T 3a4m_A            5 MLIILTGLPGVGKSTFSKNL   24 (260)
T ss_dssp             EEEEEECCTTSSHHHHHHHH
T ss_pred             EEEEEEcCCCCCHHHHHHHH
Confidence            45789999999999986443

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=83.87  E-value=0.8  Score=32.93  Aligned_cols=20  Identities=20%  Similarity=0.062  Sum_probs=16.4

Q ss_pred             CCcEEEECCCCChHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~   62 (182)
                      ...+.+.||+|+|||+.+-.
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~   46 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQR   46 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHH
Confidence            45788999999999987543

>4db1_A Myosin-7; S1DC, cardiac, beta isoform, MYH7, myhcb, MYHC-beta, contractIle protein; HET: ANP; 2.60A {Homo sapiens} PDB: 2w4a_M 2w4g_M 2w4h_M 2mys_A* 1m8q_A* 1mvw_A* 1o18_A* 1o19_A* 1o1a_A* 1o1b_A* 1o1c_A* 1o1d_A* 1o1e_A* 1o1f_A* 1o1g_A*

Probab=83.79  E-value=1.1  Score=38.32  Aligned_cols=63  Identities=14%  Similarity=0.156  Sum_probs=38.9

Q ss_pred             cCCccCCC-CCHHHHHHHHHCCCC--C--ChHHHHhhhhhhhC---CCcEEEECCCCChHHHHHHHHHHHh
Q psy4275           5 IKSFTDLK-LNPWLIRQCQTIGVK--T--PTEIQKAIIPHVLN---DEDCIGCAKTGSGKTLAFALPILQK   67 (182)
Q Consensus         5 ~~~~~~~~-l~~~i~~~l~~~~~~--~--~~~~Q~~~~~~~~~---~~~~li~~~tg~GKT~~~~~~~~~~   67 (182)
                      +.+|..++ .++++.+.+......  .  +...-..++..+..   ++.+++.|.+|+|||.++-..+-+.
T Consensus       125 vNPyk~l~iY~~~~~~~Y~g~~~~~~pPHifaiA~~Ay~~m~~~~~nQsIiiSGESGAGKTe~tK~im~yl  195 (783)
T 4db1_A          125 VNPYKWLPVYTPEVVAAYRGKKRSEAPPHIFSISDNAYQYMLTDRENQSILITGESGAGKTVNTKRVIQYF  195 (783)
T ss_dssp             ECCSSCCSCSSHHHHHHHTTCCGGGSCCCHHHHHHHHHHHHHHHTCCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             cCCCccCCCCCHHHHHHhcCCCcCCCCchhhHHHHHHHHHHHhhCCCceEEEeCCCCCCCchHHHHHHHhh
Confidence            44566666 366777777543222  2  23334455555543   5689999999999998865544433

>1f9v_A Kinesin-like protein KAR3; kinesin-related protein, motor protein, microtubinding proteinbule, contractIle protein; HET: ADP; 1.30A {Saccharomyces cerevisiae} SCOP: c.37.1.9 PDB: 1f9t_A* 1f9w_A* 1f9u_A* 3kar_A*

Probab=83.72  E-value=1  Score=34.56  Aligned_cols=25  Identities=28%  Similarity=0.481  Sum_probs=17.3

Q ss_pred             hhhhhCCCc--EEEECCCCChHHHHHH
Q psy4275          37 IPHVLNDED--CIGCAKTGSGKTLAFA   61 (182)
Q Consensus        37 ~~~~~~~~~--~li~~~tg~GKT~~~~   61 (182)
                      +..+.+|.|  ++..|+||+|||..+.
T Consensus        77 v~~~l~G~n~tifAYGqTGSGKTyTM~  103 (347)
T 1f9v_A           77 VQSSLDGYNVCIFAYGQTGSGKTFTML  103 (347)
T ss_dssp             HGGGGGTCCEEEEEECCTTSSHHHHHH
T ss_pred             HHHhcCCceeEEEEECCCCCCCcEecc
Confidence            334455665  4556899999998863

>3bs4_A Uncharacterized protein PH0321; structural genomics, unknown function, PSI-2, protein struct initiative; 1.60A {Pyrococcus horikoshii}

Probab=83.70  E-value=1.5  Score=32.30  Aligned_cols=42  Identities=10%  Similarity=-0.077  Sum_probs=28.2

Q ss_pred             CCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTREL   86 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l   86 (182)
                      .|...++.+++|+|||+.++-.+.+.+.+   +-+++|++-....
T Consensus        20 ~gs~~li~g~p~~~~~~l~~qfl~~g~~~---Ge~~~~~~~~e~~   61 (260)
T 3bs4_A           20 HSLILIHEEDASSRGKDILFYILSRKLKS---DNLVGMFSISYPL   61 (260)
T ss_dssp             TCEEEEEECSGGGCHHHHHHHHHHHHHHT---TCEEEEEECSSCH
T ss_pred             CCcEEEEEeCCCccHHHHHHHHHHHHHHC---CCcEEEEEEeCCH
Confidence            35678888888888886655566665544   4577887754433

>1g8x_A Myosin II heavy chain fused to alpha-actinin 3; motor, lever ARM, protein engineering, structural protein; HET: ADP; 2.80A {Dictyostelium discoideum} SCOP: k.1.1.1

Probab=83.64  E-value=1.4  Score=38.83  Aligned_cols=62  Identities=15%  Similarity=0.208  Sum_probs=38.8

Q ss_pred             cCCccCCC-CCHHHHHHHHHCCCCC--C--hHHHHhhhhhhhC---CCcEEEECCCCChHHHHHHHHHHH
Q psy4275           5 IKSFTDLK-LNPWLIRQCQTIGVKT--P--TEIQKAIIPHVLN---DEDCIGCAKTGSGKTLAFALPILQ   66 (182)
Q Consensus         5 ~~~~~~~~-l~~~i~~~l~~~~~~~--~--~~~Q~~~~~~~~~---~~~~li~~~tg~GKT~~~~~~~~~   66 (182)
                      +.+|..++ .++++.+.+......+  |  ...=..++..+..   +..+++.|.+|+|||.+.-..+-+
T Consensus       126 vNPyk~l~iy~~~~~~~Y~~~~~~~~pPHifaiA~~Ay~~m~~~~~~QsIiisGESGAGKTe~~K~i~~y  195 (1010)
T 1g8x_A          126 VNPFKRIPIYTQEMVDIFKGRRRNEVAPHIFAISDVAYRSMLDDRQNQSLLITGESGAGKTENTKKVIQY  195 (1010)
T ss_dssp             ECCSSCCSCCSHHHHHHHTTCCTTTSCCCHHHHHHHHHHHHHHHTCCEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             ecCCccccCCCHHHHHHhcCCCccCCCccHHHHHHHHHHHHHhcCCCeEEEEeCCCCCCcchHHHHHHHH
Confidence            45667776 4677777776543332  3  2233445555443   568999999999999875544433

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=83.58  E-value=0.72  Score=31.98  Aligned_cols=18  Identities=17%  Similarity=0.132  Sum_probs=14.7

Q ss_pred             cEEEECCCCChHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~   62 (182)
                      .+.+.|++|+|||+.+-.
T Consensus         3 ~i~i~G~~GsGKSTl~~~   20 (204)
T 2if2_A            3 RIGLTGNIGCGKSTVAQM   20 (204)
T ss_dssp             EEEEEECTTSSHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHH
Confidence            467899999999988643

>3dc4_A Kinesin-like protein NOD; catalytic domain, ATPase, microtubule, ADP, nucleotide-binding protein, ATP-binding, coiled coil, motor protein; HET: ADP; 1.90A {Drosophila melanogaster} PDB: 3dcb_A* 3dco_N* 3pxn_A*

Probab=83.56  E-value=0.8  Score=35.16  Aligned_cols=20  Identities=25%  Similarity=0.532  Sum_probs=14.9

Q ss_pred             hCCCc--EEEECCCCChHHHHH
Q psy4275          41 LNDED--CIGCAKTGSGKTLAF   60 (182)
Q Consensus        41 ~~~~~--~li~~~tg~GKT~~~   60 (182)
                      .+|.|  ++..|+||+|||.++
T Consensus        91 l~G~N~tifAYGQTGSGKTyTM  112 (344)
T 3dc4_A           91 LEGFQCTALAYGQTGTGKSYSM  112 (344)
T ss_dssp             HHTCCEEEEEESSTTSSHHHHH
T ss_pred             hCCCceEEEEecCCCCCCCeEE
Confidence            44554  456689999999985

>1lkx_A Myosin IE heavy chain; myosin motor domain, lever ARM, converter domain, contractIle protein; HET: ADP; 3.00A {Dictyostelium discoideum} SCOP: c.37.1.9

Probab=83.55  E-value=1  Score=37.93  Aligned_cols=64  Identities=16%  Similarity=0.107  Sum_probs=39.3

Q ss_pred             cCCccCCCC-CHHHHHHHHHCCCC--CC--hHHHHhhhhhhhC---CCcEEEECCCCChHHHHHHHHHHHhh
Q psy4275           5 IKSFTDLKL-NPWLIRQCQTIGVK--TP--TEIQKAIIPHVLN---DEDCIGCAKTGSGKTLAFALPILQKW   68 (182)
Q Consensus         5 ~~~~~~~~l-~~~i~~~l~~~~~~--~~--~~~Q~~~~~~~~~---~~~~li~~~tg~GKT~~~~~~~~~~~   68 (182)
                      +.+|..+++ +++..+.+......  .|  ...-..++..+..   ++.+++.|++|+|||...-..+-+..
T Consensus        48 vNPyk~l~iY~~~~~~~Y~g~~~~~~pPHifaiA~~Ay~~m~~~~~nQsIiisGESGAGKTe~tK~i~~yla  119 (697)
T 1lkx_A           48 TNPFKNLNIYKESDIKAYNGRYKYEMPPHMYALANDAYRSMRQSQENQCVIISGESGAGKTEASKKIMQFLT  119 (697)
T ss_dssp             ECCSSCCSCCSHHHHHHHSSCCGGGSCCCHHHHHHHHHHHHHHHCCCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             EcCCcCCCCCCHHHHHHHhCCCCCCCCchHHHHHHHHHHHHHhcCCCcEEEecCCCCCCchhhHHHHHHHHH
Confidence            456677764 67777776543222  23  2333455555543   56899999999999988655444433

>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=83.53  E-value=2.4  Score=31.44  Aligned_cols=69  Identities=10%  Similarity=0.124  Sum_probs=46.3

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +.+++|.+++..-++.+++.++        ++..++|+.+...+...+    .+..+|+|+|.-      -. ..++++.
T Consensus       220 ~~~~lvf~~~~~~~~~l~~~l~--------~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~------~~-~Gid~~~  284 (337)
T 2z0m_A          220 DKGVIVFVRTRNRVAKLVRLFD--------NAIELRGDLPQSVRNRNIDAFREGEYDMLITTDV------AS-RGLDIPL  284 (337)
T ss_dssp             CSSEEEECSCHHHHHHHHTTCT--------TEEEECTTSCHHHHHHHHHHHHTTSCSEEEECHH------HH-TTCCCCC
T ss_pred             CCcEEEEEcCHHHHHHHHHHhh--------hhhhhcCCCCHHHHHHHHHHHHcCCCcEEEEcCc------cc-cCCCccC
Confidence            5579999999988776655443        466778877654443332    246789999942      12 4567788


Q ss_pred             ccEEEEec
Q psy4275         150 IKFLVLDE  157 (182)
Q Consensus       150 ~~~iI~DE  157 (182)
                      ++++|.-+
T Consensus       285 ~~~Vi~~~  292 (337)
T 2z0m_A          285 VEKVINFD  292 (337)
T ss_dssp             BSEEEESS
T ss_pred             CCEEEEec
Confidence            88777643

>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=83.51  E-value=2.9  Score=34.71  Aligned_cols=55  Identities=13%  Similarity=0.014  Sum_probs=40.6

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEECh
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATP  132 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~  132 (182)
                      +.++||.++++.-++.+++.++..    ++++..++|+.........-.+..+|+|+|.
T Consensus       355 ~~~~LVF~~s~~~a~~l~~~L~~~----g~~v~~lhg~~R~~~l~~F~~g~~~VLVaTd  409 (618)
T 2whx_A          355 QGKTVWFVPSIKAGNDIANCLRKS----GKRVIQLSRKTFDTEYPKTKLTDWDFVVTTD  409 (618)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTTHHHHTTHHHHSCCSEEEECG
T ss_pred             CCCEEEEECChhHHHHHHHHHHHc----CCcEEEEChHHHHHHHHhhcCCCcEEEEECc
Confidence            458999999999999888888765    6788888886433322233345788999994

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=83.46  E-value=0.93  Score=35.59  Aligned_cols=26  Identities=27%  Similarity=0.498  Sum_probs=18.0

Q ss_pred             hhhhhhCCCc--EEEECCCCChHHHHHH
Q psy4275          36 IIPHVLNDED--CIGCAKTGSGKTLAFA   61 (182)
Q Consensus        36 ~~~~~~~~~~--~li~~~tg~GKT~~~~   61 (182)
                      .+..+.+|.|  ++..|.||+|||.++.
T Consensus       132 lv~~~l~G~N~tifAYGqTGSGKTyTM~  159 (403)
T 4etp_A          132 LVQSSLDGYNVAIFAYGQTGSGKTFTML  159 (403)
T ss_dssp             HHHHHHTTCCEEEEEESCTTSSHHHHHH
T ss_pred             HHHHHhCCcceEEEEECCCCCCCceEeC
Confidence            3344556665  4556899999999863

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=83.45  E-value=1.3  Score=33.04  Aligned_cols=36  Identities=25%  Similarity=0.107  Sum_probs=22.7

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      ++-+.+.+++|+|||+.+...+......   +.+++++.
T Consensus        98 ~~~i~i~g~~G~GKTT~~~~la~~~~~~---~~~v~l~~  133 (295)
T 1ls1_A           98 RNLWFLVGLQGSGKTTTAAKLALYYKGK---GRRPLLVA  133 (295)
T ss_dssp             SEEEEEECCTTTTHHHHHHHHHHHHHHT---TCCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEec
Confidence            4456677999999998765444333222   44666665

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=83.42  E-value=0.61  Score=31.60  Aligned_cols=21  Identities=19%  Similarity=-0.083  Sum_probs=12.7

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      +..+++.|++|+|||+.+-..
T Consensus         5 ~~~I~l~G~~GsGKST~a~~L   25 (183)
T 2vli_A            5 SPIIWINGPFGVGKTHTAHTL   25 (183)
T ss_dssp             CCEEEEECCC----CHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHH
Confidence            346789999999999986543

>3t0q_A AGR253WP; kinesin, alpha and beta proteins, P-loop containing nucleosi triphosphate hydrolases, microtubule motor protein; HET: ADP; 2.35A {Ashbya gossypii}

Probab=83.39  E-value=0.98  Score=34.72  Aligned_cols=26  Identities=27%  Similarity=0.473  Sum_probs=18.0

Q ss_pred             hhhhhhCCCc--EEEECCCCChHHHHHH
Q psy4275          36 IIPHVLNDED--CIGCAKTGSGKTLAFA   61 (182)
Q Consensus        36 ~~~~~~~~~~--~li~~~tg~GKT~~~~   61 (182)
                      .+..+.+|.|  ++..|+||+|||.+..
T Consensus        77 lv~~~l~G~n~tifAYGqTGSGKTyTm~  104 (349)
T 3t0q_A           77 LVQSSLDGYNVCIFAYGQTGSGKTYTML  104 (349)
T ss_dssp             HHHGGGTTCEEEEEEECSTTSSHHHHHH
T ss_pred             HHHHHHCCcceeEEEeCCCCCCCceEeC
Confidence            3444555665  4556899999999863

>3sr0_A Adenylate kinase; phosphoryl transfer analogue, ALF4, transferase (phosphotran phosphoryl transfer, nucleotide-binding; HET: ADP AMP; 1.56A {Aquifex aeolicus} PDB: 2rh5_A 2rgx_A*

Probab=83.39  E-value=0.82  Score=32.28  Aligned_cols=20  Identities=15%  Similarity=-0.003  Sum_probs=15.7

Q ss_pred             EEEECCCCChHHHHHHHHHH
Q psy4275          46 CIGCAKTGSGKTLAFALPIL   65 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~   65 (182)
                      +++.||+|+||++.+....-
T Consensus         3 Iil~GpPGsGKgTqa~~La~   22 (206)
T 3sr0_A            3 LVFLGPPGAGKGTQAKRLAK   22 (206)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57889999999988755443

>1w7j_A Myosin VA; motor protein, unconventional myosin, myosin V, chicken, molecular motor, ATPase, ELC, IQ motif, muscle protein, ATP-binding; HET: ADP; 2A {Gallus gallus} SCOP: b.34.3.1 c.37.1.9 PDB: 1w7i_A* 1oe9_A* 1w8j_A

Probab=83.31  E-value=1.2  Score=38.18  Aligned_cols=64  Identities=14%  Similarity=0.223  Sum_probs=39.4

Q ss_pred             cCCccCCC-CCHHHHHHHHHCCCC--CC--hHHHHhhhhhhhC---CCcEEEECCCCChHHHHHHHHHHHhh
Q psy4275           5 IKSFTDLK-LNPWLIRQCQTIGVK--TP--TEIQKAIIPHVLN---DEDCIGCAKTGSGKTLAFALPILQKW   68 (182)
Q Consensus         5 ~~~~~~~~-l~~~i~~~l~~~~~~--~~--~~~Q~~~~~~~~~---~~~~li~~~tg~GKT~~~~~~~~~~~   68 (182)
                      +.+|..++ .++++.+.+......  .|  ...-..++..+..   ++.+++.|++|+|||...-..+-+..
T Consensus       110 vNPyk~l~iY~~~~~~~Y~g~~~~~~pPHifaiA~~Ay~~m~~~~~nQsIiisGESGAGKTe~tK~i~~yla  181 (795)
T 1w7j_A          110 INPYEQLPIYGEDIINAYSGQNMGDMDPHIFAVAEEAYKQMARDERNQSIIVSGESGAGKTVSAKYAMRYFA  181 (795)
T ss_dssp             ECCSSCCSCCSHHHHHHHTTCCGGGSCCCHHHHHHHHHHHHHHHTCCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             ecCccccCcCCHHHHHHHcCCCccCCCccHhHHHHHHHHHhHhcCCCeEEEEeCCCCCCcchHHHHHHHHHH
Confidence            45667766 466777777543322  22  2333455555543   56899999999999988655544433

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E*

Probab=83.28  E-value=0.76  Score=36.90  Aligned_cols=21  Identities=24%  Similarity=0.243  Sum_probs=16.8

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      .+++++.||+|+|||..+-..
T Consensus        49 p~gvLL~GppGtGKT~Larai   69 (476)
T 2ce7_A           49 PKGILLVGPPGTGKTLLARAV   69 (476)
T ss_dssp             CSEEEEECCTTSSHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHH
Confidence            356999999999999875433

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=83.26  E-value=1.1  Score=41.65  Aligned_cols=44  Identities=18%  Similarity=0.017  Sum_probs=33.7

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHH
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTREL   86 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l   86 (182)
                      +..+...++.|++|+|||..++..+...+.+   +.+++|+.-....
T Consensus        31 i~~G~i~lI~G~pGsGKT~LAlqla~~~~~~---G~~vlYI~te~~~   74 (1706)
T 3cmw_A           31 LPMGRIVEIYGPESSGKTTLTLQVIAAAQRE---GKTCAFIDAEHAL   74 (1706)
T ss_dssp             EETTSEEEEECSTTSSHHHHHHHHHHHHHHT---TCCEEEECTTSCC
T ss_pred             cCCCeEEEEECCCCCCHHHHHHHHHHHHhhC---CCceEEEEecCcc
Confidence            4557899999999999999887777766544   4578888865443

>1w9i_A Myosin II heavy chain; molecular motor, ATPase, motor domain, mutant, muscle contraction; HET: ADP; 1.75A {Dictyostelium discoideum} PDB: 1w9j_A* 1w9l_A* 1w9k_A* 1mma_A* 2aka_A 1d0x_A* 1d0y_A* 1d0z_A* 1d1a_A* 1d1b_A* 1d1c_A* 2xel_A* 1yv3_A* 3bz7_A* 3bz8_A* 3bz9_A* 1jwy_A* 1jx2_A* 3mjx_A* 2jhr_A* ...

Probab=83.19  E-value=1.2  Score=37.94  Aligned_cols=62  Identities=15%  Similarity=0.212  Sum_probs=38.1

Q ss_pred             cCCccCCC-CCHHHHHHHHHCCCC--CC--hHHHHhhhhhhhC---CCcEEEECCCCChHHHHHHHHHHH
Q psy4275           5 IKSFTDLK-LNPWLIRQCQTIGVK--TP--TEIQKAIIPHVLN---DEDCIGCAKTGSGKTLAFALPILQ   66 (182)
Q Consensus         5 ~~~~~~~~-l~~~i~~~l~~~~~~--~~--~~~Q~~~~~~~~~---~~~~li~~~tg~GKT~~~~~~~~~   66 (182)
                      +.+|..++ .++++.+.+......  .|  ...-..++..+..   ++.+++.|++|+|||...-..+-+
T Consensus       126 vNPyk~l~iY~~~~~~~Y~~~~~~~~pPHifaiA~~Ay~~m~~~~~nQsIiisGESGAGKTe~tK~i~~y  195 (770)
T 1w9i_A          126 VNPFKRIPIYTQEMVDIFKGRRRNEVAPHIFAISDVAYRSMLDDRQNQSLLITGESGAGKTENTKKVIQY  195 (770)
T ss_dssp             ECCSSCCSCCSHHHHHHHTTCCGGGSCCCHHHHHHHHHHHHHHHCCCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             ecCCccccCCCHHHHHHhcCCCcCCCCccHHHHHHHHHHHHHhhcCCcEEEEecCCCCcchHHHHHHHHH
Confidence            45666666 466777776543322  22  2333445555443   568999999999999886544433

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=83.17  E-value=0.8  Score=32.27  Aligned_cols=22  Identities=23%  Similarity=0.196  Sum_probs=17.0

Q ss_pred             CCcEEEECCCCChHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      +..+++.|++|+|||+.+-...
T Consensus         5 ~~~I~l~G~~GsGKsT~a~~La   26 (217)
T 3be4_A            5 KHNLILIGAPGSGKGTQCEFIK   26 (217)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHH
Confidence            3468899999999999865443

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=83.16  E-value=1.2  Score=42.12  Aligned_cols=44  Identities=16%  Similarity=-0.024  Sum_probs=33.9

Q ss_pred             hhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHH
Q psy4275          39 HVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRE   85 (182)
Q Consensus        39 ~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~   85 (182)
                      .+..++++++.+|+|+|||..+...+.+...+   +.+++++.-...
T Consensus      1077 gi~~g~~vll~G~~GtGKT~la~~~~~ea~k~---Ge~~~Fit~ee~ 1120 (2050)
T 3cmu_A         1077 GLPMGRIVEIYGPESSGKTTLTLQVIAAAQRE---GKTCAFIDAEHA 1120 (2050)
T ss_dssp             SEETTSEEEEECCTTSSHHHHHHHHHHHHHTT---TCCEEEECTTSC
T ss_pred             CcCCCcEEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEEcccc
Confidence            34568899999999999999987777776655   557888875543

>2vvg_A Kinesin-2; motor protein, nucleotide-binding, microtubule, ATP-binding; HET: ADP; 1.60A {Giardia intestinalis}

Probab=83.13  E-value=1  Score=34.67  Aligned_cols=21  Identities=33%  Similarity=0.518  Sum_probs=15.2

Q ss_pred             hhCCCc--EEEECCCCChHHHHH
Q psy4275          40 VLNDED--CIGCAKTGSGKTLAF   60 (182)
Q Consensus        40 ~~~~~~--~li~~~tg~GKT~~~   60 (182)
                      +.+|.|  ++..|+||+|||...
T Consensus        85 ~l~G~n~tifAYGqTGSGKTyTm  107 (350)
T 2vvg_A           85 VLEGFNSTIFAYGQTGAGKTWTM  107 (350)
T ss_dssp             HHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HhCCCceeEEeecCCCCCCCEEe
Confidence            345554  555689999999885

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=83.09  E-value=1.7  Score=33.02  Aligned_cols=16  Identities=13%  Similarity=-0.112  Sum_probs=13.3

Q ss_pred             cEEEECCCCChHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAF   60 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~   60 (182)
                      -+-+.||+|+|||+.+
T Consensus        94 iigI~GpsGSGKSTl~  109 (321)
T 3tqc_A           94 IIGIAGSVAVGKSTTS  109 (321)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3667799999999885

>3lre_A Kinesin-like protein KIF18A; motor protein, nucleotide binding, microtubule binding, ATP- cell projection, cytoskeleton, glycoprotein, microtubule; HET: ADP; 2.20A {Homo sapiens} SCOP: c.37.1.0

Probab=83.06  E-value=1  Score=34.70  Aligned_cols=21  Identities=33%  Similarity=0.528  Sum_probs=15.3

Q ss_pred             hhCCCc--EEEECCCCChHHHHH
Q psy4275          40 VLNDED--CIGCAKTGSGKTLAF   60 (182)
Q Consensus        40 ~~~~~~--~li~~~tg~GKT~~~   60 (182)
                      +.+|.|  ++..|+||+|||.+.
T Consensus       101 ~l~G~n~tifAYGqTGSGKTyTm  123 (355)
T 3lre_A          101 FLNGYNCTVLAYGATGAGKTHTM  123 (355)
T ss_dssp             HTTTCCEEEEEECCTTSSHHHHH
T ss_pred             HhCCCceEEEEeCCCCCCceeee
Confidence            345654  456689999999885

>2zfi_A Kinesin-like protein KIF1A, kinesin heavy chain isoform 5C; alpha and beta protein, enzyme, ATPase, P-loop, motor protein, ATP-binding, coiled coil; HET: ADP; 1.55A {Mus musculus} SCOP: c.37.1.9 PDB: 1vfw_A* 1vfx_A* 1vfz_A* 1vfv_A* 2zfj_A* 2zfk_A* 2zfl_A* 2zfm_A* 1i5s_A* 1i6i_A* 2hxf_C* 1ia0_K* 2hxh_C*

Probab=82.91  E-value=1  Score=34.84  Aligned_cols=22  Identities=23%  Similarity=0.519  Sum_probs=15.6

Q ss_pred             hhhCCCc--EEEECCCCChHHHHH
Q psy4275          39 HVLNDED--CIGCAKTGSGKTLAF   60 (182)
Q Consensus        39 ~~~~~~~--~li~~~tg~GKT~~~   60 (182)
                      .+.+|.|  ++..|.||+|||...
T Consensus        84 ~~l~G~N~tifAYGqTGSGKTyTm  107 (366)
T 2zfi_A           84 HAFEGYNVCIFAYGQTGAGKSYTM  107 (366)
T ss_dssp             HHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHhcCCeeEEEEeCCCCCCCceEe
Confidence            3445654  455689999999875

>2y65_A Kinesin, kinesin heavy chain; motor protein; HET: ADP; 2.20A {Drosophila melanogaster} PDB: 2y5w_A*

Probab=82.90  E-value=1  Score=34.82  Aligned_cols=22  Identities=32%  Similarity=0.406  Sum_probs=15.8

Q ss_pred             hhhCCCc--EEEECCCCChHHHHH
Q psy4275          39 HVLNDED--CIGCAKTGSGKTLAF   60 (182)
Q Consensus        39 ~~~~~~~--~li~~~tg~GKT~~~   60 (182)
                      .+..|.|  ++..|+||+|||.+.
T Consensus        79 ~~l~G~n~tifAYGqTGSGKTyTm  102 (365)
T 2y65_A           79 DVLAGYNGTIFAYGQTSSGKTHTM  102 (365)
T ss_dssp             HHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHhCCCceEEEeecCCCCCCceEE
Confidence            3445654  455689999999985

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=82.88  E-value=0.88  Score=32.26  Aligned_cols=20  Identities=25%  Similarity=0.162  Sum_probs=15.7

Q ss_pred             cEEEECCCCChHHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~   64 (182)
                      .+++.|++|+|||+.+-...
T Consensus         2 ~I~l~G~~GsGKsT~a~~La   21 (223)
T 2xb4_A            2 NILIFGPNGSGKGTQGNLVK   21 (223)
T ss_dssp             EEEEECCTTSCHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            36889999999998865443

>3qf7_A RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.90A {Thermotoga maritima} PDB: 3qg5_A 3tho_A*

Probab=82.86  E-value=0.88  Score=35.07  Aligned_cols=17  Identities=24%  Similarity=0.307  Sum_probs=14.2

Q ss_pred             cEEEECCCCChHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~   61 (182)
                      -.++.||+|+|||..+-
T Consensus        25 ~~~i~G~NGaGKTTll~   41 (365)
T 3qf7_A           25 ITVVEGPNGAGKSSLFE   41 (365)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            57789999999998743

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=82.82  E-value=1.2  Score=36.00  Aligned_cols=35  Identities=14%  Similarity=0.144  Sum_probs=22.0

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEE
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVL   80 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil   80 (182)
                      +.-+.+.|++|+|||+..-..+ ..+...  ++++++.
T Consensus       293 GeVI~LVGpNGSGKTTLl~~LA-gll~~~--~G~V~l~  327 (503)
T 2yhs_A          293 PFVILMVGVNGVGKTTTIGKLA-RQFEQQ--GKSVMLA  327 (503)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHH-HHHHHT--TCCEEEE
T ss_pred             CeEEEEECCCcccHHHHHHHHH-HHhhhc--CCeEEEe
Confidence            4467788999999998754332 222222  4467666

>2h58_A Kinesin-like protein KIFC3 variant; motor domain, ADP, structural genomics, structur Al genomics consortium, SGC; HET: ADP; 1.85A {Homo sapiens}

Probab=82.76  E-value=1.1  Score=34.20  Aligned_cols=23  Identities=22%  Similarity=0.434  Sum_probs=16.4

Q ss_pred             hhhhCCCc--EEEECCCCChHHHHH
Q psy4275          38 PHVLNDED--CIGCAKTGSGKTLAF   60 (182)
Q Consensus        38 ~~~~~~~~--~li~~~tg~GKT~~~   60 (182)
                      ..+.+|.|  ++..|+||+|||...
T Consensus        74 ~~~l~G~n~tifAYGqTGSGKTyTm   98 (330)
T 2h58_A           74 TSCIDGFNVCIFAYGQTGAGKTYTM   98 (330)
T ss_dssp             HHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHHhCCCEEEEEeECCCCCCCcEEE
Confidence            34455655  555689999999885

>4a14_A Kinesin, kinesin-like protein KIF7; motor protein, motor domain; HET: ADP; 1.60A {Homo sapiens} SCOP: c.37.1.0 PDB: 2xt3_A*

Probab=82.72  E-value=1.1  Score=34.41  Aligned_cols=22  Identities=27%  Similarity=0.446  Sum_probs=15.8

Q ss_pred             hhhCCCc--EEEECCCCChHHHHH
Q psy4275          39 HVLNDED--CIGCAKTGSGKTLAF   60 (182)
Q Consensus        39 ~~~~~~~--~li~~~tg~GKT~~~   60 (182)
                      .+.+|.|  ++..|+||+|||.+.
T Consensus        78 ~~l~G~n~tifAYGqTGSGKTyTm  101 (344)
T 4a14_A           78 AFFEGFNATVFAYGQTGSGKTYTM  101 (344)
T ss_dssp             HHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHHhhcCeeEEEecccCCCceEee
Confidence            3345654  456689999999885

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=82.66  E-value=0.72  Score=44.64  Aligned_cols=24  Identities=29%  Similarity=0.451  Sum_probs=19.3

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHH
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~   63 (182)
                      +..+++++++||||+|||..+--.
T Consensus      1264 l~~~~~vLL~GPpGtGKT~la~~~ 1287 (2695)
T 4akg_A         1264 LNSKRGIILCGPPGSGKTMIMNNA 1287 (2695)
T ss_dssp             HHHTCEEEEECSTTSSHHHHHHHH
T ss_pred             HHCCCeEEEECCCCCCHHHHHHHH
Confidence            344889999999999999876333

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=82.62  E-value=0.94  Score=32.86  Aligned_cols=22  Identities=14%  Similarity=-0.029  Sum_probs=17.3

Q ss_pred             CCcEEEECCCCChHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      +..+.+.||+|+|||+.+-...
T Consensus        27 g~~I~I~G~~GsGKSTl~k~La   48 (252)
T 4e22_A           27 APVITVDGPSGAGKGTLCKALA   48 (252)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHH
Confidence            5678899999999998864443

>1v8k_A Kinesin-like protein KIF2C; microtubule destabilizer, structural P; HET: ANP; 2.25A {Mus musculus} SCOP: c.37.1.9 PDB: 1v8j_A* 2gry_A*

Probab=82.60  E-value=0.93  Score=35.66  Aligned_cols=23  Identities=30%  Similarity=0.644  Sum_probs=16.0

Q ss_pred             hhhCCCc--EEEECCCCChHHHHHH
Q psy4275          39 HVLNDED--CIGCAKTGSGKTLAFA   61 (182)
Q Consensus        39 ~~~~~~~--~li~~~tg~GKT~~~~   61 (182)
                      .+..|.|  ++..|.||+|||.+..
T Consensus       149 ~~l~G~N~tifAYGQTGSGKTyTM~  173 (410)
T 1v8k_A          149 TIFEGGKATCFAYGQTGSGKTHTMG  173 (410)
T ss_dssp             HHHTTCEEEEEEEESTTSSHHHHHH
T ss_pred             HHhcCCceeEEeecCCCCCCCeEee
Confidence            3445654  4556799999998853

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=82.58  E-value=0.69  Score=33.37  Aligned_cols=20  Identities=15%  Similarity=0.157  Sum_probs=16.6

Q ss_pred             hCCCcEEEECCCCChHHHHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~   60 (182)
                      ..|.-..+.||+|+|||+..
T Consensus        29 ~~Ge~~~i~G~nGsGKSTLl   48 (237)
T 2cbz_A           29 PEGALVAVVGQVGCGKSSLL   48 (237)
T ss_dssp             CTTCEEEEECSTTSSHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHH
Confidence            34778889999999999874

>1goj_A Kinesin, kinesin heavy chain; motor protein, ATPase; HET: ADP; 2.3A {Neurospora crassa} SCOP: c.37.1.9

Probab=82.51  E-value=1.1  Score=34.57  Aligned_cols=22  Identities=27%  Similarity=0.570  Sum_probs=15.7

Q ss_pred             hhhCCCc--EEEECCCCChHHHHH
Q psy4275          39 HVLNDED--CIGCAKTGSGKTLAF   60 (182)
Q Consensus        39 ~~~~~~~--~li~~~tg~GKT~~~   60 (182)
                      .+.+|.|  ++..|+||+|||.+.
T Consensus        75 ~~l~G~n~tifAYGqTGSGKTyTm   98 (355)
T 1goj_A           75 DILNGYNGTVFAYGQTGAGKSYTM   98 (355)
T ss_dssp             HHTTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHhCCCcceEEEECCCCCCcceEe
Confidence            3445654  555689999999885

>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=82.51  E-value=2.7  Score=33.63  Aligned_cols=96  Identities=17%  Similarity=0.152  Sum_probs=42.7

Q ss_pred             CChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEE--------EcCCchhhhhHHh---
Q psy4275          53 GSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSII--------TGGMDMVDQGKEL---  121 (182)
Q Consensus        53 g~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~---  121 (182)
                      .++|-....-.+...+.. ..+.++||.++++..++.+++.++......++++..+        +|+.+..++...+   
T Consensus       370 ~~~K~~~L~~~l~~~~~~-~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F  448 (556)
T 4a2p_A          370 ENPKLEELVCILDDAYRY-NPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAF  448 (556)
T ss_dssp             CCHHHHHHHHHHHHHHHH-CTTCCEEEEESSHHHHHHHHHHHTTCSGGGSCCEEC-------------------------
T ss_pred             CChHHHHHHHHHHHHhcC-CCCceEEEEEccHHHHHHHHHHHHhCCCcceeeeeEEEccCCcccccccCHHHHHHHHHHh
Confidence            466655533333332221 2256899999999999998888876532223444433        3334333222222   


Q ss_pred             -c-CCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEe
Q psy4275         122 -A-KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLD  156 (182)
Q Consensus       122 -~-~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~D  156 (182)
                       . +..+|+|+|.-      -. ..+++..+++||.=
T Consensus       449 ~~~g~~~vLvaT~~------~~-~GiDip~v~~VI~~  478 (556)
T 4a2p_A          449 KTSKDNRLLIATSV------AD-EGIDIVQCNLVVLY  478 (556)
T ss_dssp             -----CCEEEEEC------------------CEEEEE
T ss_pred             cccCceEEEEEcCc------hh-cCCCchhCCEEEEe
Confidence             1 35689999932      12 44567777777653

>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=82.48  E-value=4.9  Score=35.05  Aligned_cols=97  Identities=20%  Similarity=0.142  Sum_probs=47.5

Q ss_pred             CChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceE--------EEEEcCCchhhhhHHh---
Q psy4275          53 GSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRV--------SIITGGMDMVDQGKEL---  121 (182)
Q Consensus        53 g~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~---  121 (182)
                      .++|.... .-++........+.++||.++++..++.+.+.++......++++        ..++|+.+..++...+   
T Consensus       611 ~~~K~~~L-~~lL~~~~~~~~~~rvLIF~~t~~~ae~L~~~L~~~~~l~~ik~~~l~G~~~~~~hg~m~~~eR~~il~~F  689 (936)
T 4a2w_A          611 ENPKLEEL-VCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAF  689 (936)
T ss_dssp             CCHHHHHH-HHHHHHTTTSCTTCCEEEEESSHHHHHHHHHHHHHCSTTSSCCCEEC------------------------
T ss_pred             CCHHHHHH-HHHHHHHhccCCCCeEEEEeCCHHHHHHHHHHHhhCccccccceeEEecCCCcccCCCCCHHHHHHHHHHh
Confidence            35665543 33333333223357999999999999999999887532223333        3334444443332222   


Q ss_pred             c--CCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEec
Q psy4275         122 A--KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDE  157 (182)
Q Consensus       122 ~--~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE  157 (182)
                      .  +..+|+|+|.-      -. ..+++..+++||.=+
T Consensus       690 r~~g~~~VLVaT~~------~~-eGIDlp~v~~VI~yD  720 (936)
T 4a2w_A          690 KTSKDNRLLIATSV------AD-EGIDIVQCNLVVLYE  720 (936)
T ss_dssp             ----CCSEEEEECC-------------CCCCSEEEEES
T ss_pred             hccCCeeEEEEeCc------hh-cCCcchhCCEEEEeC
Confidence            2  35689999931      12 456777888777543

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=82.39  E-value=0.77  Score=31.79  Aligned_cols=24  Identities=13%  Similarity=-0.007  Sum_probs=19.3

Q ss_pred             CCCcEEEECCCCChHHHHHHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALPIL   65 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~~~   65 (182)
                      .|+.+++.|++|+|||..++..+.
T Consensus        15 ~G~gvli~G~SGaGKStlal~L~~   38 (181)
T 3tqf_A           15 DKMGVLITGEANIGKSELSLALID   38 (181)
T ss_dssp             TTEEEEEEESSSSSHHHHHHHHHH
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHH
Confidence            367899999999999988655544

>3b6u_A Kinesin-like protein KIF3B; structural genomics consortium, motor domain, ADP, SGC, ATP-binding, coiled coil, microtubule, motor protein; HET: ADP; 1.80A {Homo sapiens} PDB: 3b6v_A*

Probab=82.30  E-value=1  Score=35.00  Aligned_cols=21  Identities=33%  Similarity=0.533  Sum_probs=15.2

Q ss_pred             hhCCCc--EEEECCCCChHHHHH
Q psy4275          40 VLNDED--CIGCAKTGSGKTLAF   60 (182)
Q Consensus        40 ~~~~~~--~li~~~tg~GKT~~~   60 (182)
                      +.+|.|  ++..|+||+|||.+.
T Consensus        97 ~l~G~n~tifAYGqTGSGKTyTM  119 (372)
T 3b6u_A           97 VLQGFNGTIFAYGQTGTGKTYTM  119 (372)
T ss_dssp             HHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HhCCCeeeEEeecCCCCCCCEeE
Confidence            445654  455689999999885

>3qks_A DNA double-strand break repair RAD50 ATPase; RECA-like fold, coiled-coils, ATPase, exonuclease, endonucle binding, DNA binding; HET: DNA; 2.10A {Pyrococcus furiosus} PDB: 3qkr_A*

Probab=82.30  E-value=1.1  Score=31.48  Aligned_cols=17  Identities=24%  Similarity=0.239  Sum_probs=14.3

Q ss_pred             CcEEEECCCCChHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~   60 (182)
                      .-.++.||+|+|||...
T Consensus        24 ~~~~I~G~NgsGKStil   40 (203)
T 3qks_A           24 GINLIIGQNGSGKSSLL   40 (203)
T ss_dssp             EEEEEECCTTSSHHHHH
T ss_pred             CeEEEEcCCCCCHHHHH
Confidence            45788999999999874

>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; HET: ADP; 1.70A {Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A

Probab=82.28  E-value=0.87  Score=30.67  Aligned_cols=20  Identities=20%  Similarity=0.004  Sum_probs=16.3

Q ss_pred             hCCCcEEEECCCCChHHHHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~   60 (182)
                      ..|.-+.+.||.|+|||+..
T Consensus        31 ~~Ge~v~L~G~nGaGKTTLl   50 (158)
T 1htw_A           31 EKAIMVYLNGDLGAGKTTLT   50 (158)
T ss_dssp             SSCEEEEEECSTTSSHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHH
Confidence            44667888999999999874

>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=82.18  E-value=0.27  Score=39.13  Aligned_cols=70  Identities=13%  Similarity=0.227  Sum_probs=0.0

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      ..+++|.|+++.-++.+++.+...    +..+..++|+.....+...+    .+..+|+|+|.-      -. ..+++.+
T Consensus       333 ~~~~lvF~~s~~~~~~l~~~L~~~----~~~v~~lh~~~~~~~R~~~~~~f~~g~~~iLv~T~~------~~-~GlDip~  401 (479)
T 3fmp_B          333 IAQAMIFCHTRKTASWLAAELSKE----GHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNV------CA-RGIDVEQ  401 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCceEEEeCcHHHHHHHHHHHHhC----CccEEEecCCCCHHHHHHHHHHHHcCCCcEEEEccc------cc-cCCcccc
Confidence            457999999999888777776654    67788888887654443332    235789999932      11 3456666


Q ss_pred             ccEEE
Q psy4275         150 IKFLV  154 (182)
Q Consensus       150 ~~~iI  154 (182)
                      +++||
T Consensus       402 v~~VI  406 (479)
T 3fmp_B          402 VSVVI  406 (479)
T ss_dssp             -----
T ss_pred             CCEEE
Confidence            76665

>2vhj_A Ntpase P4, P4; non- hydrolysable ATP analogue, hydrolase, virus dsRNA, molecular motor, packaging ATPase, hexameric helicase; HET: ADP; 1.80A {Pseudomonas phage PHI12} PDB: 2vhq_A* 1w44_A* 1w46_A* 1w47_A* 1w48_A* 1w49_A* 1w4a_A* 1w4b_A* 1w4c_A 2vht_A* 2vhu_A* 2vhc_A*

Probab=82.17  E-value=0.94  Score=34.55  Aligned_cols=26  Identities=23%  Similarity=-0.011  Sum_probs=19.9

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQ   66 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~   66 (182)
                      ..+...++.||+|+|||..+...+..
T Consensus       121 ~~gsviLI~GpPGsGKTtLAlqlA~~  146 (331)
T 2vhj_A          121 YASGMVIVTGKGNSGKTPLVHALGEA  146 (331)
T ss_dssp             EESEEEEEECSCSSSHHHHHHHHHHH
T ss_pred             CCCcEEEEEcCCCCCHHHHHHHHHHh
Confidence            34566799999999999887665544

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus}

Probab=82.17  E-value=1.3  Score=39.29  Aligned_cols=64  Identities=14%  Similarity=0.223  Sum_probs=39.3

Q ss_pred             cCCccCCC-CCHHHHHHHHHCCCC--CC--hHHHHhhhhhhhC---CCcEEEECCCCChHHHHHHHHHHHhh
Q psy4275           5 IKSFTDLK-LNPWLIRQCQTIGVK--TP--TEIQKAIIPHVLN---DEDCIGCAKTGSGKTLAFALPILQKW   68 (182)
Q Consensus         5 ~~~~~~~~-l~~~i~~~l~~~~~~--~~--~~~Q~~~~~~~~~---~~~~li~~~tg~GKT~~~~~~~~~~~   68 (182)
                      +.+|..++ .++++.+.+......  .|  ...=..++..+..   +..+++.|.+|+|||.+.-..+-+..
T Consensus       110 vNPyk~l~iy~~~~~~~Y~~~~~~~~pPHifaiA~~Ay~~m~~~~~~QsIiisGESGAGKTe~~K~i~~yla  181 (1080)
T 2dfs_A          110 INPYEQLPIYGEDIINAYSGQNMGDMDPHIFAVAEEAYKQMARDERNQSIIVSGESGAGKTVSAKYAMRYFA  181 (1080)
T ss_dssp             ECCSSCCSCSSHHHHHHHTTCCGGGSCCCHHHHHHHHHHHHHHHTCCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             ecCCcccccCCHHHHHHhcCCCCCCCCCcHHHHHHHHHHHHHhcCCCcEEEEcCCCCCCccchHHHHHHHHH
Confidence            45667766 466777766543322  23  2333445555543   56899999999999988655554443

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=82.17  E-value=1.1  Score=33.46  Aligned_cols=35  Identities=14%  Similarity=-0.011  Sum_probs=22.3

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcC
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTP   82 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p   82 (182)
                      -+.+.+++|+|||+.+...+......   +.+++++..
T Consensus       100 vi~i~G~~G~GKTT~~~~la~~~~~~---g~~v~l~~~  134 (297)
T 1j8m_F          100 VIMLVGVQGTGKTTTAGKLAYFYKKK---GFKVGLVGA  134 (297)
T ss_dssp             EEEEECSSCSSTTHHHHHHHHHHHHT---TCCEEEEEC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC---CCeEEEEec
Confidence            46677999999998765444333222   446666653

>3gbj_A KIF13B protein; kinesin, motor domain, ADP, structural genomics, structural genomics consortium, SGC, ATP-binding, microtubule, motor protein; HET: ADP; 2.10A {Homo sapiens} SCOP: c.37.1.9

Probab=82.10  E-value=1.1  Score=34.62  Aligned_cols=23  Identities=22%  Similarity=0.459  Sum_probs=16.5

Q ss_pred             hhhhCCCc--EEEECCCCChHHHHH
Q psy4275          38 PHVLNDED--CIGCAKTGSGKTLAF   60 (182)
Q Consensus        38 ~~~~~~~~--~li~~~tg~GKT~~~   60 (182)
                      ..+.+|.|  ++..|+||+|||.++
T Consensus        86 ~~~l~G~n~tifAYGqTGSGKTyTm  110 (354)
T 3gbj_A           86 QNAFDGYNACIFAYGQTGSGKSYTM  110 (354)
T ss_dssp             HHHHTTCCEEEEEEECTTSSHHHHH
T ss_pred             HHHhCCceeEEEeeCCCCCCCceEE
Confidence            34455665  455689999999985

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=82.05  E-value=0.83  Score=32.48  Aligned_cols=20  Identities=20%  Similarity=0.066  Sum_probs=16.8

Q ss_pred             hCCCcEEEECCCCChHHHHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~   60 (182)
                      ..|.-+.+.||+|+|||+..
T Consensus        33 ~~Ge~~~iiG~NGsGKSTLl   52 (214)
T 1sgw_A           33 EKGNVVNFHGPNGIGKTTLL   52 (214)
T ss_dssp             ETTCCEEEECCTTSSHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHH
Confidence            34778889999999999874

>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=81.72  E-value=2.2  Score=37.33  Aligned_cols=76  Identities=12%  Similarity=0.239  Sum_probs=53.5

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh---cC-C--CcEEEEChHHHHHHHhcCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL---AK-K--PHIVIATPGRLADHLDTCNTFSL  147 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~-~--~~Ilv~T~~~l~~~~~~~~~~~~  147 (182)
                      +.+++|.+++..-++.+.+.+..   ..|+++..++|+.+..++...+   .+ .  .+|+|+| ..     -. ..+++
T Consensus       503 ~~k~iVF~~~~~~~~~l~~~L~~---~~g~~~~~lhG~~~~~~R~~~l~~F~~g~~~~~vLvaT-~v-----~~-~GlDl  572 (968)
T 3dmq_A          503 SQKVLVICAKAATALQLEQVLRE---REGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCS-EI-----GS-EGRNF  572 (968)
T ss_dssp             SSCCCEECSSTHHHHHHHHHHHT---TTCCCEEEECTTSCTTHHHHHHHHHHSTTSSCEEEECS-CC-----TT-CSSCC
T ss_pred             CCCEEEEeCcHHHHHHHHHHHHH---HcCCcEEEEeCCCCHHHHHHHHHHHhCCCCcccEEEec-ch-----hh-cCCCc
Confidence            56899999999988887777664   2378999999998765444332   22 3  8899999 21     12 45677


Q ss_pred             CCccEEEEeccc
Q psy4275         148 NRIKFLVLDEAD  159 (182)
Q Consensus       148 ~~~~~iI~DE~h  159 (182)
                      ..++++|+-+..
T Consensus       573 ~~~~~VI~~d~p  584 (968)
T 3dmq_A          573 QFASHMVMFDLP  584 (968)
T ss_dssp             TTCCEEECSSCC
T ss_pred             ccCcEEEEecCC
Confidence            788888776554

>2heh_A KIF2C protein; kinesin, motor domain, ADP, structural genomics, structural genomics consortium, SGC, structural protein; HET: ADP; 2.15A {Homo sapiens} PDB: 3edl_D*

Probab=81.65  E-value=1.2  Score=34.85  Aligned_cols=23  Identities=30%  Similarity=0.644  Sum_probs=16.1

Q ss_pred             hhhCCCc--EEEECCCCChHHHHHH
Q psy4275          39 HVLNDED--CIGCAKTGSGKTLAFA   61 (182)
Q Consensus        39 ~~~~~~~--~li~~~tg~GKT~~~~   61 (182)
                      .+.+|.|  ++..|.||+|||.+..
T Consensus       129 ~~l~G~N~tifAYGQTGSGKTyTM~  153 (387)
T 2heh_A          129 TIFEGGKATCFAYGQTGSGKTHTMG  153 (387)
T ss_dssp             HHHTTCEEEEEEESCTTSSHHHHHC
T ss_pred             HHhcCCceEEEEecCCCCCCCeEec
Confidence            3445654  5556899999998853

>1x88_A Kinesin-like protein KIF11; switch II, motor domain, NECK linker, cell cycle; HET: ADP NAT; 1.80A {Homo sapiens} SCOP: c.37.1.9 PDB: 3hqd_A* 3ken_A* 2pg2_A* 1yrs_A* 2fme_A* 2g1q_A* 2gm1_A* 1ii6_A* 2uyi_A* 2uym_A* 2wog_A* 2x2r_A* 2x7c_A* 2x7d_A* 2x7e_A* 2xae_A* 3k3b_A* 3k5e_A* 3l9h_A* 1q0b_A* ...

Probab=81.63  E-value=1  Score=34.77  Aligned_cols=22  Identities=27%  Similarity=0.501  Sum_probs=15.8

Q ss_pred             hhhCCCc--EEEECCCCChHHHHH
Q psy4275          39 HVLNDED--CIGCAKTGSGKTLAF   60 (182)
Q Consensus        39 ~~~~~~~--~li~~~tg~GKT~~~   60 (182)
                      .+..|.|  ++..|.||+|||.++
T Consensus        83 ~~l~G~n~tifAYGqTGSGKTyTM  106 (359)
T 1x88_A           83 EVIMGYNCTIFAYGQTGTGKTFTM  106 (359)
T ss_dssp             HHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             HHhCCCceEEEEeCCCCCCCceEE
Confidence            3445664  455689999999885

>1np6_A Molybdopterin-guanine dinucleotide biosynthesis protein B; mixed alpha-beta fold, elongated beta-sheet, walker A motif, P-loop structural motif; 1.90A {Escherichia coli} SCOP: c.37.1.10 PDB: 1p9n_A

Probab=81.63  E-value=2.8  Score=28.67  Aligned_cols=18  Identities=28%  Similarity=0.158  Sum_probs=14.3

Q ss_pred             CcEEEECCCCChHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~   61 (182)
                      +-+.+.|++|+|||+...
T Consensus         7 ~~i~i~G~sGsGKTTl~~   24 (174)
T 1np6_A            7 PLLAFAAWSGTGKTTLLK   24 (174)
T ss_dssp             CEEEEECCTTSCHHHHHH
T ss_pred             eEEEEEeCCCCCHHHHHH
Confidence            346788999999998743

>1t5c_A CENP-E protein, centromeric protein E; kinesin motor-domain-ADP complex, stranded beta-sheet core with solvent exposed alpha-helices; HET: ADP PIN; 2.50A {Homo sapiens}

Probab=81.62  E-value=1.1  Score=34.44  Aligned_cols=21  Identities=24%  Similarity=0.395  Sum_probs=15.2

Q ss_pred             hhCCCc--EEEECCCCChHHHHH
Q psy4275          40 VLNDED--CIGCAKTGSGKTLAF   60 (182)
Q Consensus        40 ~~~~~~--~li~~~tg~GKT~~~   60 (182)
                      +.+|.|  ++..|+||+|||..+
T Consensus        73 ~l~G~n~tifAYGqTGSGKTyTM   95 (349)
T 1t5c_A           73 AIQGYNGTIFAYGQTASGKTYTM   95 (349)
T ss_dssp             HHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HHcCCccceeeecCCCCCCCeEE
Confidence            345654  455689999999885

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=81.60  E-value=0.94  Score=31.17  Aligned_cols=18  Identities=33%  Similarity=0.174  Sum_probs=14.8

Q ss_pred             cEEEECCCCChHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~   62 (182)
                      .+.+.|++|+|||+++-.
T Consensus        10 ~I~i~G~~GsGKST~~~~   27 (203)
T 1uf9_A           10 IIGITGNIGSGKSTVAAL   27 (203)
T ss_dssp             EEEEEECTTSCHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            477889999999988644

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=81.58  E-value=0.64  Score=33.20  Aligned_cols=19  Identities=26%  Similarity=0.244  Sum_probs=15.9

Q ss_pred             CCCcEEEECCCCChHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~   60 (182)
                      .|.-..+.||+|+|||+..
T Consensus        29 ~Ge~~~iiG~nGsGKSTLl   47 (224)
T 2pcj_A           29 KGEFVSIIGASGSGKSTLL   47 (224)
T ss_dssp             TTCEEEEEECTTSCHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4677889999999999764

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=81.55  E-value=1.4  Score=35.60  Aligned_cols=42  Identities=19%  Similarity=0.230  Sum_probs=28.1

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCH
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTR   84 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~   84 (182)
                      +..|.-..+.|++|+|||+.+...+..... .  +.+++++++..
T Consensus       278 i~~G~i~~i~G~~GsGKSTLl~~l~g~~~~-~--G~~vi~~~~ee  319 (525)
T 1tf7_A          278 FFKDSIILATGATGTGKTLLVSRFVENACA-N--KERAILFAYEE  319 (525)
T ss_dssp             EESSCEEEEEECTTSSHHHHHHHHHHHHHT-T--TCCEEEEESSS
T ss_pred             CCCCcEEEEEeCCCCCHHHHHHHHHHHHHh-C--CCCEEEEEEeC
Confidence            455778899999999999876554433322 2  44577776544

>1kk8_A Myosin heavy chain, striated muscle; actin-detached, mechanics of motor, contractIle PROT; HET: ADP; 2.30A {Argopecten irradians} SCOP: b.34.3.1 c.37.1.9 PDB: 1kk7_A* 1qvi_A* 1s5g_A* 1sr6_A 1b7t_A* 1kqm_A* 1kwo_A* 1l2o_A* 1dfl_A* 2w4t_C 2w4v_C 2w4w_C 1dfk_A 2ec6_A 2otg_A* 2os8_A* 2ovk_A 2ekv_A 2ekw_A 2oy6_A* ...

Probab=81.55  E-value=1.2  Score=38.32  Aligned_cols=63  Identities=14%  Similarity=0.283  Sum_probs=38.7

Q ss_pred             cCCccCCC-CCHHHHHHHHHCCCC--CC--hHHHHhhhhhhhC---CCcEEEECCCCChHHHHHHHHHHHh
Q psy4275           5 IKSFTDLK-LNPWLIRQCQTIGVK--TP--TEIQKAIIPHVLN---DEDCIGCAKTGSGKTLAFALPILQK   67 (182)
Q Consensus         5 ~~~~~~~~-l~~~i~~~l~~~~~~--~~--~~~Q~~~~~~~~~---~~~~li~~~tg~GKT~~~~~~~~~~   67 (182)
                      +.+|..++ .++++.+.+......  .|  ...=..++..+..   ++.+++.|++|+|||.+.-..+-+.
T Consensus       123 vNPyk~l~iY~~~~~~~Y~g~~~~~~pPHifaiA~~Ay~~m~~~~~nQsIiiSGESGAGKTe~tK~i~~yl  193 (837)
T 1kk8_A          123 VNPYRRLPIYTDSVIAKYRGKRKTEIPPHLFSVADNAYQNMVTDRENQSCLITGESGAGKTENTKKVIMYL  193 (837)
T ss_dssp             ECCSSCCSTTSHHHHHHHTTCCGGGSCCCHHHHHHHHHHHHHHHTSEEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             eCCCcCCCCCCHHHHHHhcCCCcCCCCCcHHHHHHHHHHHHHhcCCCcEEEEeCCCCCCchhhHHHHHHHH
Confidence            45666776 467777777543322  23  2333445555543   5679999999999998865444433

>3auy_A DNA double-strand break repair RAD50 ATPase; DNA repair, ABC transporter ATPase domain-like; HET: DNA ADP; 2.70A {Methanocaldococcus jannaschii} PDB: 3aux_A* 3av0_B*

Probab=81.46  E-value=0.95  Score=34.89  Aligned_cols=18  Identities=28%  Similarity=0.287  Sum_probs=14.8

Q ss_pred             CcEEEECCCCChHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~   61 (182)
                      +-.++.|+||+|||...-
T Consensus        26 gl~vi~G~NGaGKT~ile   43 (371)
T 3auy_A           26 GIVAIIGENGSGKSSIFE   43 (371)
T ss_dssp             EEEEEEECTTSSHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHH
Confidence            457899999999998743

>1ry6_A Internal kinesin; kinesin motor domain, nucleotide-free, transport protein; 1.60A {Plasmodium falciparum} SCOP: c.37.1.9

Probab=81.46  E-value=1.1  Score=34.70  Aligned_cols=19  Identities=37%  Similarity=0.585  Sum_probs=15.1

Q ss_pred             CCc--EEEECCCCChHHHHHH
Q psy4275          43 DED--CIGCAKTGSGKTLAFA   61 (182)
Q Consensus        43 ~~~--~li~~~tg~GKT~~~~   61 (182)
                      |.+  ++..|+||+|||.++.
T Consensus        83 G~n~tifAYGqTGSGKTyTM~  103 (360)
T 1ry6_A           83 GCVCSCFAYGQTGSGKTYTML  103 (360)
T ss_dssp             CCEEEEEEECCTTSSHHHHHH
T ss_pred             CceeEEEeeCCCCCCCCEEEe
Confidence            665  4777899999998853

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10

Probab=81.45  E-value=2.4  Score=28.94  Aligned_cols=17  Identities=24%  Similarity=0.034  Sum_probs=13.6

Q ss_pred             cEEEECCCCChHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~   61 (182)
                      -+.+.|++|+|||+...
T Consensus         6 ~i~i~G~sGsGKTTl~~   22 (169)
T 1xjc_A            6 VWQVVGYKHSGKTTLME   22 (169)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            36788999999998743

>2owm_A Nckin3-434, related to kinesin-like protein KIF1C; motor domain, ADP, NECK linker, motor PR; HET: ADP; 3.25A {Neurospora crassa}

Probab=81.39  E-value=1.2  Score=35.32  Aligned_cols=21  Identities=24%  Similarity=0.401  Sum_probs=15.4

Q ss_pred             hhCCCc--EEEECCCCChHHHHH
Q psy4275          40 VLNDED--CIGCAKTGSGKTLAF   60 (182)
Q Consensus        40 ~~~~~~--~li~~~tg~GKT~~~   60 (182)
                      +.+|.|  ++..|.||+|||.++
T Consensus       132 ~l~GyN~tIfAYGQTGSGKTyTM  154 (443)
T 2owm_A          132 NFEGYHTCIFAYGQTGSGKSYTM  154 (443)
T ss_dssp             HHTTCCEEEEEESSTTSSHHHHH
T ss_pred             hhcCCceEEEEeCCCCCCCCEEe
Confidence            345654  555689999999886

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=81.38  E-value=1.7  Score=31.91  Aligned_cols=18  Identities=39%  Similarity=0.431  Sum_probs=15.6

Q ss_pred             CCcEEEECCCCChHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~   60 (182)
                      |....+.||+|+|||+..
T Consensus        30 Ge~~~i~G~NGsGKSTLl   47 (263)
T 2pjz_A           30 GEKVIILGPNGSGKTTLL   47 (263)
T ss_dssp             SSEEEEECCTTSSHHHHH
T ss_pred             CEEEEEECCCCCCHHHHH
Confidence            667889999999999874

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=81.37  E-value=1  Score=41.72  Aligned_cols=44  Identities=18%  Similarity=-0.003  Sum_probs=34.5

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQ   89 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q   89 (182)
                      |+-+.+.+|.|+|||+.++..+.+...+   +..++++.+..++...
T Consensus      1431 g~~iei~g~~~sGkttl~~~~~a~~~~~---g~~~~~i~~e~~~~~~ 1474 (1706)
T 3cmw_A         1431 GRIVEIYGPESSGKTTLTLQVIAAAQRE---GKTCAFIDAEHALDPI 1474 (1706)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHT---TCCEEEECTTSCCCHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHhc---CCeEEEEecCCCCCHH
Confidence            5678999999999999987777665444   5689999998777544

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=81.34  E-value=10  Score=27.75  Aligned_cols=91  Identities=14%  Similarity=0.192  Sum_probs=53.1

Q ss_pred             CCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh---cC--CCc
Q psy4275          52 TGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL---AK--KPH  126 (182)
Q Consensus        52 tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~--~~~  126 (182)
                      ..+||... +.-++..+...  +.++||.+.+...++.+.+.+...   .++.+..++|+.+..++...+   .+  ...
T Consensus        93 ~~s~K~~~-L~~ll~~~~~~--~~kvlIFs~~~~~~~~l~~~L~~~---~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~  166 (271)
T 1z5z_A           93 RRSGKMIR-TMEIIEEALDE--GDKIAIFTQFVDMGKIIRNIIEKE---LNTEVPFLYGELSKKERDDIISKFQNNPSVK  166 (271)
T ss_dssp             TTCHHHHH-HHHHHHHHHHT--TCCEEEEESCHHHHHHHHHHHHHH---HCSCCCEECTTSCHHHHHHHHHHHHHCTTCC
T ss_pred             ccCHHHHH-HHHHHHHHHhC--CCeEEEEeccHHHHHHHHHHHHHh---cCCcEEEEECCCCHHHHHHHHHHhcCCCCCC
Confidence            45667554 33333333222  458999999999888777776552   257788899988765444332   12  345


Q ss_pred             -EEEEChHHHHHHHhcCCCCCCCCccEEEE
Q psy4275         127 -IVIATPGRLADHLDTCNTFSLNRIKFLVL  155 (182)
Q Consensus       127 -Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~  155 (182)
                       ++++| ...      ...+++...+.+|+
T Consensus       167 v~L~st-~~~------g~Glnl~~a~~VI~  189 (271)
T 1z5z_A          167 FIVLSV-KAG------GFGINLTSANRVIH  189 (271)
T ss_dssp             EEEEEC-CTT------CCCCCCTTCSEEEE
T ss_pred             EEEEeh-hhh------cCCcCcccCCEEEE
Confidence             45555 211      13456666665554

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=81.32  E-value=0.81  Score=33.90  Aligned_cols=19  Identities=26%  Similarity=0.267  Sum_probs=16.2

Q ss_pred             CCCcEEEECCCCChHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~   60 (182)
                      .|.-+.+.||+|+|||+..
T Consensus        33 ~Ge~~~iiGpnGsGKSTLl   51 (275)
T 3gfo_A           33 RGEVTAILGGNGVGKSTLF   51 (275)
T ss_dssp             TTSEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4777889999999999874

>2ycu_A Non muscle myosin 2C, alpha-actinin; motor protein; HET: AOV; 2.25A {Homo sapiens} PDB: 1br1_A* 1br4_A* 1br2_A*

Probab=81.29  E-value=1.4  Score=38.76  Aligned_cols=62  Identities=16%  Similarity=0.251  Sum_probs=38.7

Q ss_pred             cCCccCCC-CCHHHHHHHHHCCCC--CC--hHHHHhhhhhhhC---CCcEEEECCCCChHHHHHHHHHHH
Q psy4275           5 IKSFTDLK-LNPWLIRQCQTIGVK--TP--TEIQKAIIPHVLN---DEDCIGCAKTGSGKTLAFALPILQ   66 (182)
Q Consensus         5 ~~~~~~~~-l~~~i~~~l~~~~~~--~~--~~~Q~~~~~~~~~---~~~~li~~~tg~GKT~~~~~~~~~   66 (182)
                      +.+|..++ .++++.+.+......  .|  ...=..++..+..   +..+++.|.+|+|||.+.-..+-+
T Consensus       100 vNPyk~l~iy~~~~~~~Y~~~~~~~~pPHifaiA~~Ay~~m~~~~~~QsIiisGESGAGKTe~~K~i~~y  169 (995)
T 2ycu_A          100 INPYKQLPIYTEAIVEMYRGKKRHEVPPHVYAVTEGAYRSMLQDREDQSILCTGESGAGKTENTKKVIQY  169 (995)
T ss_dssp             ECCSSCCSCCSHHHHHHHTTCCGGGSCCCHHHHHHHHHHHHHHHCCCEEEEEECBTTSSHHHHHHHHHHH
T ss_pred             eCCccccCCCCHHHHHHhcCCccCCCCchHHHHhHHHHHHHHhcCCCcEEEecCCCCCCchhhHHHHHHH
Confidence            45667776 467777777543322  23  2333445555543   568999999999999886544443

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=81.29  E-value=1.5  Score=37.19  Aligned_cols=19  Identities=32%  Similarity=0.123  Sum_probs=15.9

Q ss_pred             cEEEECCCCChHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~   63 (182)
                      ++++.||+|+|||..+-..
T Consensus       523 ~~Ll~Gp~GtGKT~lA~al  541 (758)
T 3pxi_A          523 SFIFLGPTGVGKTELARAL  541 (758)
T ss_dssp             EEEEESCTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            5999999999999886433

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=81.28  E-value=1.6  Score=34.44  Aligned_cols=35  Identities=26%  Similarity=0.117  Sum_probs=22.4

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      +.+.+.+++|+|||+.+...+.... ..  +.+++++.
T Consensus        99 ~vi~i~G~~GsGKTT~~~~LA~~l~-~~--g~~Vllvd  133 (425)
T 2ffh_A           99 NLWFLVGLQGSGKTTTAAKLALYYK-GK--GRRPLLVA  133 (425)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHH-TT--TCCEEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHH-Hc--CCeEEEee
Confidence            3466779999999988654443332 22  44666665

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=81.26  E-value=0.65  Score=33.67  Aligned_cols=21  Identities=19%  Similarity=0.232  Sum_probs=16.6

Q ss_pred             CCcEEEECCCCChHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~   63 (182)
                      +..+++.|++|+|||+.+-..
T Consensus        32 ~~~i~l~G~~GsGKSTla~~L   52 (253)
T 2p5t_B           32 PIAILLGGQSGAGKTTIHRIK   52 (253)
T ss_dssp             CEEEEEESCGGGTTHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHH
Confidence            446889999999999886443

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=81.24  E-value=1  Score=33.08  Aligned_cols=19  Identities=26%  Similarity=0.135  Sum_probs=16.2

Q ss_pred             CCCcEEEECCCCChHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~   60 (182)
                      .|.-+.+.||+|+|||+..
T Consensus        45 ~Ge~~~l~G~NGsGKSTLl   63 (267)
T 2zu0_C           45 PGEVHAIMGPNGSGKSTLS   63 (267)
T ss_dssp             TTCEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4677889999999999874

>3u06_A Protein claret segregational; motor domain, stalk rotation, power stroke, kinesin-14, MICR binding, NCD, transport, molecular motor; HET: ADP GOL; 2.35A {Drosophila melanogaster} PDB: 2ncd_A* 1n6m_A* 1cz7_A* 3l1c_A*

Probab=81.23  E-value=1.2  Score=35.17  Aligned_cols=23  Identities=30%  Similarity=0.482  Sum_probs=16.4

Q ss_pred             hhhhCCCc--EEEECCCCChHHHHH
Q psy4275          38 PHVLNDED--CIGCAKTGSGKTLAF   60 (182)
Q Consensus        38 ~~~~~~~~--~li~~~tg~GKT~~~   60 (182)
                      ..+..|.|  ++..|+||+|||.+.
T Consensus       132 ~~~l~G~n~tifAYGqTGSGKTyTM  156 (412)
T 3u06_A          132 QSALDGYNICIFAYGQTGSGKTYTM  156 (412)
T ss_dssp             HHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHHHCCCceEEEEecCCCCCCeeEe
Confidence            44455654  455689999999985

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=81.21  E-value=0.83  Score=32.74  Aligned_cols=19  Identities=26%  Similarity=0.261  Sum_probs=16.3

Q ss_pred             CCCcEEEECCCCChHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~   60 (182)
                      .|.-..+.||+|+|||+..
T Consensus        33 ~Ge~~~i~G~nGsGKSTLl   51 (229)
T 2pze_A           33 RGQLLAVAGSTGAGKTSLL   51 (229)
T ss_dssp             TTCEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4778889999999999874

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=81.10  E-value=0.81  Score=33.23  Aligned_cols=19  Identities=26%  Similarity=0.204  Sum_probs=16.3

Q ss_pred             CCCcEEEECCCCChHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~   60 (182)
                      .|.-+.+.||+|+|||+..
T Consensus        34 ~Ge~~~i~G~nGsGKSTLl   52 (247)
T 2ff7_A           34 QGEVIGIVGRSGSGKSTLT   52 (247)
T ss_dssp             TTCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4778889999999999874

>2grj_A Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosphocoenzyme kinase, structural genomics, joint center for structural GE JCSG; HET: ADP COD; 2.60A {Thermotoga maritima}

Probab=81.08  E-value=1.1  Score=31.13  Aligned_cols=20  Identities=20%  Similarity=0.112  Sum_probs=15.2

Q ss_pred             cEEEECCCCChHHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~   64 (182)
                      .+.+.|++|||||+++-...
T Consensus        14 iIgltG~~GSGKSTva~~L~   33 (192)
T 2grj_A           14 VIGVTGKIGTGKSTVCEILK   33 (192)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            35678999999999865443

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=81.07  E-value=0.75  Score=33.58  Aligned_cols=19  Identities=21%  Similarity=0.289  Sum_probs=16.1

Q ss_pred             CCCcEEEECCCCChHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~   60 (182)
                      .|.-..+.||+|+|||+..
T Consensus        32 ~Ge~~~liG~nGsGKSTLl   50 (257)
T 1g6h_A           32 KGDVTLIIGPNGSGKSTLI   50 (257)
T ss_dssp             TTCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4777889999999999874

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=81.02  E-value=0.77  Score=33.18  Aligned_cols=19  Identities=21%  Similarity=0.249  Sum_probs=16.2

Q ss_pred             CCCcEEEECCCCChHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~   60 (182)
                      .|.-+.+.||+|+|||+..
T Consensus        31 ~Ge~~~l~G~nGsGKSTLl   49 (240)
T 1ji0_A           31 RGQIVTLIGANGAGKTTTL   49 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4777889999999999874

>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=81.01  E-value=3.6  Score=34.49  Aligned_cols=52  Identities=15%  Similarity=0.179  Sum_probs=40.9

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEECh
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATP  132 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~  132 (182)
                      +.++||.++++.-++.+++.+++.    ++++..++|+....+.   ..++.+|+|+|.
T Consensus       396 ~~~vLVFv~Tr~~ae~la~~L~~~----g~~v~~lHG~l~q~er---~~~~~~VLVATd  447 (666)
T 3o8b_A          396 GGRHLIFCHSKKKCDELAAKLSGL----GINAVAYYRGLDVSVI---PTIGDVVVVATD  447 (666)
T ss_dssp             SSEEEEECSCHHHHHHHHHHHHTT----TCCEEEECTTSCGGGS---CSSSCEEEEECT
T ss_pred             CCcEEEEeCCHHHHHHHHHHHHhC----CCcEEEecCCCCHHHH---HhCCCcEEEECC
Confidence            458999999999999888877654    7889999998876542   234569999994

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=80.97  E-value=0.8  Score=33.58  Aligned_cols=19  Identities=21%  Similarity=0.207  Sum_probs=16.0

Q ss_pred             CCCcEEEECCCCChHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~   60 (182)
                      .|.-+.+.||+|+|||+..
T Consensus        31 ~Ge~~~liG~nGsGKSTLl   49 (262)
T 1b0u_A           31 AGDVISIIGSSGSGKSTFL   49 (262)
T ss_dssp             TTCEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4677889999999999874

>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=80.80  E-value=4.5  Score=34.45  Aligned_cols=96  Identities=17%  Similarity=0.104  Sum_probs=44.7

Q ss_pred             CChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCc--------eEEEEEcCCchhhhhHHh---
Q psy4275          53 GSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNL--------RVSIITGGMDMVDQGKEL---  121 (182)
Q Consensus        53 g~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~---  121 (182)
                      .++|.....-.+...+... .+.++||.++++..++.+.+.++......++        ....++|+.+..++...+   
T Consensus       611 ~~~K~~~L~~lL~~~~~~~-~~~kvLIF~~~~~~~~~L~~~L~~~~~~~~~~~~~l~G~~~~~~hg~~~~~eR~~~l~~F  689 (797)
T 4a2q_A          611 ENPKLEELVCILDDAYRYN-PQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAF  689 (797)
T ss_dssp             CCHHHHHHHHHHHHHHHHC-SSCCEEEEESSHHHHHHHHHHHHTCSTTCSCCCEEC------------------------
T ss_pred             CChHHHHHHHHHHHHhccC-CCCeEEEEECcHHHHHHHHHHHHhCcccccccceEEEecCCcccCCCCCHHHHHHHHHHh
Confidence            4667655333333322222 2568999999999999999888774322223        333334444433332222   


Q ss_pred             c--CCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEe
Q psy4275         122 A--KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLD  156 (182)
Q Consensus       122 ~--~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~D  156 (182)
                      .  +..+|+|+|.-      -. ..+++..+++||.=
T Consensus       690 ~~~g~~~vLVaT~~------~~-~GIDlp~v~~VI~y  719 (797)
T 4a2q_A          690 KTSKDNRLLIATSV------AD-EGIDIVQCNLVVLY  719 (797)
T ss_dssp             ----CCSEEEEECC--------------CCCSEEEEE
T ss_pred             hccCCceEEEEcCc------hh-cCCCchhCCEEEEe
Confidence            2  35689999932      11 45677778877753

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=80.79  E-value=1.1  Score=32.65  Aligned_cols=19  Identities=21%  Similarity=0.106  Sum_probs=16.3

Q ss_pred             CCCcEEEECCCCChHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~   60 (182)
                      .|.-+.+.||+|+|||+..
T Consensus        28 ~Ge~~~l~G~nGsGKSTLl   46 (250)
T 2d2e_A           28 KGEVHALMGPNGAGKSTLG   46 (250)
T ss_dssp             TTCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4777889999999999874

>2wbe_C Bipolar kinesin KRP-130; EG5, KLP61F, tubulin, mitosis, GTP-binding, motor protein, cell division, cell cycle, microtubule, ATP-binding; HET: GTP ANP GDP TA1; 9.40A {Drosophila melanogaster}

Probab=80.73  E-value=1.1  Score=34.68  Aligned_cols=21  Identities=38%  Similarity=0.588  Sum_probs=15.1

Q ss_pred             hhCCCc--EEEECCCCChHHHHH
Q psy4275          40 VLNDED--CIGCAKTGSGKTLAF   60 (182)
Q Consensus        40 ~~~~~~--~li~~~tg~GKT~~~   60 (182)
                      +.+|.|  ++..|.||+|||...
T Consensus        96 ~l~G~n~tifAYGqTGSGKTyTm  118 (373)
T 2wbe_C           96 VLNGYNCTVFAYGQTGTGKTHTM  118 (373)
T ss_dssp             HHHTCCEEEEEECSTTSSHHHHH
T ss_pred             HhCCceEEEEeecCCCCCcceec
Confidence            344554  555689999999885

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=80.72  E-value=1  Score=38.09  Aligned_cols=22  Identities=18%  Similarity=0.126  Sum_probs=17.9

Q ss_pred             CCcEEEECCCCChHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      +++.++.||+|+|||..+-...
T Consensus       207 ~~~vlL~G~~GtGKT~la~~la  228 (758)
T 1r6b_X          207 KNNPLLVGESGVGKTAIAEGLA  228 (758)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHH
T ss_pred             CCCeEEEcCCCCCHHHHHHHHH
Confidence            5789999999999998854433

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=80.63  E-value=0.88  Score=33.32  Aligned_cols=19  Identities=32%  Similarity=0.466  Sum_probs=16.4

Q ss_pred             CCCcEEEECCCCChHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~   60 (182)
                      .|.-+.+.||+|+|||+..
T Consensus        45 ~Ge~~~i~G~nGsGKSTLl   63 (260)
T 2ghi_A           45 SGTTCALVGHTGSGKSTIA   63 (260)
T ss_dssp             TTCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4778889999999999874

>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C

Probab=80.60  E-value=0.82  Score=33.29  Aligned_cols=20  Identities=20%  Similarity=0.139  Sum_probs=16.6

Q ss_pred             hCCCcEEEECCCCChHHHHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~   60 (182)
                      ..|....+.||+|+|||+..
T Consensus        24 ~~Ge~~~liG~NGsGKSTLl   43 (249)
T 2qi9_C           24 RAGEILHLVGPNGAGKSTLL   43 (249)
T ss_dssp             ETTCEEEEECCTTSSHHHHH
T ss_pred             cCCCEEEEECCCCCcHHHHH
Confidence            34777889999999999874

>1vht_A Dephospho-COA kinase; structural genomics, transferase; HET: BA3; 1.59A {Escherichia coli} SCOP: c.37.1.1 PDB: 1vhl_A* 1viy_A 1t3h_A 1n3b_A

Probab=80.48  E-value=1.2  Score=31.20  Aligned_cols=20  Identities=20%  Similarity=-0.032  Sum_probs=15.7

Q ss_pred             CcEEEECCCCChHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~   63 (182)
                      ..+.+.|++|+|||+.+-..
T Consensus         5 ~~I~i~G~~GSGKST~~~~L   24 (218)
T 1vht_A            5 YIVALTGGIGSGKSTVANAF   24 (218)
T ss_dssp             EEEEEECCTTSCHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHH
Confidence            35788999999999876443

>3bfn_A Kinesin-like protein KIF22; limited proteolysis, structural genomics consortium domain, ADP, SGC, ATP-binding, DNA-binding, microtubule, MO protein; HET: ADP; 2.30A {Homo sapiens}

Probab=80.33  E-value=1.2  Score=34.77  Aligned_cols=32  Identities=25%  Similarity=0.430  Sum_probs=20.8

Q ss_pred             ChHHHHhhhhh--------hhCCCc--EEEECCCCChHHHHH
Q psy4275          29 PTEIQKAIIPH--------VLNDED--CIGCAKTGSGKTLAF   60 (182)
Q Consensus        29 ~~~~Q~~~~~~--------~~~~~~--~li~~~tg~GKT~~~   60 (182)
                      +..-|.+.+..        +.+|.|  ++..|+||+|||.+.
T Consensus        75 ~~~tQ~~Vy~~~~~plv~~~l~G~N~tifAYGqTGSGKTyTM  116 (388)
T 3bfn_A           75 ERSTQQDIYAGSVQPILRHLLEGQNASVLAYGPTGAGKTHTM  116 (388)
T ss_dssp             TTCCHHHHHHHHTGGGHHHHTTTCCEEEEEESCTTSSHHHHH
T ss_pred             CCCCHhHHHHHHHHHHHHHhhcCceeeEeeecCCCCCCCeEe
Confidence            34456665543        344654  455689999999885

>3cob_A Kinesin heavy chain-like protein; motor, switch II, loop L11, conformation, nucleotide, ATP-binding, microtubule, motor protein; HET: ADP; 2.20A {Solanum tuberosum} SCOP: c.37.1.9 PDB: 3cnz_A* 1sdm_A* 3h4s_A*

Probab=80.31  E-value=1.1  Score=34.79  Aligned_cols=23  Identities=26%  Similarity=0.471  Sum_probs=16.1

Q ss_pred             hhhhCCCc--EEEECCCCChHHHHH
Q psy4275          38 PHVLNDED--CIGCAKTGSGKTLAF   60 (182)
Q Consensus        38 ~~~~~~~~--~li~~~tg~GKT~~~   60 (182)
                      ..+.+|.|  ++..|+||+|||.+.
T Consensus        73 ~~~l~G~n~tifAYGqTGSGKTyTM   97 (369)
T 3cob_A           73 QSAVDGYNVCIFAYGQTGSGKTFTI   97 (369)
T ss_dssp             HHHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             HhhhcCCceEEEEECCCCCCCeEee
Confidence            33445654  455689999999885

>2rep_A Kinesin-like protein KIFC1; structural genomics consortium, motor domain, ADP, binding, cell cycle, cell division, endosome, microtubule; HET: ADP; 2.60A {Homo sapiens}

Probab=80.29  E-value=1.3  Score=34.44  Aligned_cols=23  Identities=30%  Similarity=0.469  Sum_probs=16.1

Q ss_pred             hhhhCCCc--EEEECCCCChHHHHH
Q psy4275          38 PHVLNDED--CIGCAKTGSGKTLAF   60 (182)
Q Consensus        38 ~~~~~~~~--~li~~~tg~GKT~~~   60 (182)
                      ..+.+|.|  ++..|.||+|||..+
T Consensus       109 ~~~l~G~N~tifAYGqTGSGKTyTM  133 (376)
T 2rep_A          109 QSALDGYPVCIFAYGQTGSGKTFTM  133 (376)
T ss_dssp             HGGGGTCCEEEEEECSTTSSHHHHH
T ss_pred             HHhcCCCceEEEEeCCCCCCCceEe
Confidence            33445654  455689999999885

>2v26_A Myosin VI; calmodulin-binding, nucleotide-binding, membrane, vanadate, transport, PRE- powerstroke, transition state, protein transport; HET: ADP; 1.75A {Sus scrofa} PDB: 2bki_A 2bkh_A 3l9i_A 2x51_A 2vb6_A* 2vas_A*

Probab=80.27  E-value=2.6  Score=36.08  Aligned_cols=63  Identities=19%  Similarity=0.247  Sum_probs=39.2

Q ss_pred             cCCccCC-C-CCHHHHHHHHHCCCCC--C--hHHHHhhhhhhhC---CCcEEEECCCCChHHHHHHHHHHHh
Q psy4275           5 IKSFTDL-K-LNPWLIRQCQTIGVKT--P--TEIQKAIIPHVLN---DEDCIGCAKTGSGKTLAFALPILQK   67 (182)
Q Consensus         5 ~~~~~~~-~-l~~~i~~~l~~~~~~~--~--~~~Q~~~~~~~~~---~~~~li~~~tg~GKT~~~~~~~~~~   67 (182)
                      +.+|..+ + .+++..+.+......+  |  ...-..++..+..   ++.+++.|++|+|||.+.-..+-+.
T Consensus        93 VNPyk~l~~iY~~~~~~~Y~g~~~~~~pPHifaiA~~Ay~~m~~~~~nQsIiiSGESGAGKTe~tK~i~~yl  164 (784)
T 2v26_A           93 VNPYFDIPKIYSSETIKSYQGKSLGTMPPHVFAIADKAFRDMKVLKLSQSIIVSGESGAGKTENTKFVLRYL  164 (784)
T ss_dssp             ECCSSCCTTTTSHHHHHHHTTCCTTSSCSCHHHHHHHHHHHHHHHTCCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             ecCCcCcCCCCCHHHHHHHhCCCcccCCchHHHHHHHHHHHHHhcCCCcEEEEcCCCCCCceehHHHHHHHH
Confidence            4567777 3 4677777776443322  2  3333455555543   5689999999999998755444433

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=80.21  E-value=0.81  Score=33.08  Aligned_cols=19  Identities=21%  Similarity=0.277  Sum_probs=16.2

Q ss_pred             CCCcEEEECCCCChHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~   60 (182)
                      .|..+.+.||+|+|||+..
T Consensus        27 ~Ge~~~i~G~nGsGKSTLl   45 (243)
T 1mv5_A           27 PNSIIAFAGPSGGGKSTIF   45 (243)
T ss_dssp             TTEEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4777889999999999874

>4g1u_C Hemin import ATP-binding protein HMUV; membrane transporter, type II ABC importer, HMUT, plasma MEM transport protein-hydrolase complex; 3.01A {Yersinia pestis}

Probab=80.20  E-value=0.92  Score=33.38  Aligned_cols=19  Identities=21%  Similarity=0.249  Sum_probs=16.1

Q ss_pred             CCCcEEEECCCCChHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~   60 (182)
                      .|.-+.+.||+|+|||+..
T Consensus        36 ~Ge~~~liG~nGsGKSTLl   54 (266)
T 4g1u_C           36 SGEMVAIIGPNGAGKSTLL   54 (266)
T ss_dssp             TTCEEEEECCTTSCHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHH
Confidence            4777889999999999874

>1svm_A Large T antigen; AAA+ fold, viral protein; HET: ATP; 1.94A {Simian virus 40} SCOP: c.37.1.20 PDB: 1svl_A* 1svo_A 1n25_A 2h1l_A

Probab=80.18  E-value=1.2  Score=34.59  Aligned_cols=21  Identities=24%  Similarity=0.050  Sum_probs=17.2

Q ss_pred             CCCcEEEECCCCChHHHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~   62 (182)
                      .++.+.+.||+|+|||+.+-.
T Consensus       168 ~~~~i~l~G~~GsGKSTl~~~  188 (377)
T 1svm_A          168 KKRYWLFKGPIDSGKTTLAAA  188 (377)
T ss_dssp             TCCEEEEECSTTSSHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHH
Confidence            367889999999999987543

>1vpl_A ABC transporter, ATP-binding protein; TM0544, structural GENO joint center for structural genomics, JCSG, protein structu initiative, PSI; 2.10A {Thermotoga maritima} SCOP: c.37.1.12

Probab=80.01  E-value=0.91  Score=33.22  Aligned_cols=19  Identities=26%  Similarity=0.207  Sum_probs=16.1

Q ss_pred             CCCcEEEECCCCChHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~   60 (182)
                      .|.-+.+.||+|+|||+..
T Consensus        40 ~Gei~~l~G~NGsGKSTLl   58 (256)
T 1vpl_A           40 EGEIFGLIGPNGAGKTTTL   58 (256)
T ss_dssp             TTCEEEEECCTTSSHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            4677889999999999874

---

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	182
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	8e-33
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	8e-27
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	1e-26
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	2e-25
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	7e-25
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	4e-24
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	2e-23
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	1e-22
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	5e-21
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	1e-16
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	4e-16
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	1e-14
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	8e-14
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	2e-08
d1a1va1	136	c.37.1.14 (A:190-325) HCV helicase domain {Human h	7e-05

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 208

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score =  114 bits (286), Expect = 8e-33
 Identities = 63/156 (40%), Positives = 99/156 (63%), Gaps = 4/156 (2%)

Query: 7   SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDE-DCIGCAKTGSGKTLAFALPIL 65
           +F +L L+  ++   +  G + PT+IQ  +IP  LNDE + +  A+TGSGKT +FA+P++
Sbjct: 5   NFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 64

Query: 66  QKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKP 125
           +    +  GI A++LTPTRELA Q+ D+   L    NL+++ I GG  +  Q K L K  
Sbjct: 65  ELVN-ENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKAL-KNA 122

Query: 126 HIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
           +IV+ TPGR+ DH++   T +L  +K+ +LDEAD +
Sbjct: 123 NIVVGTPGRILDHINR-GTLNLKNVKYFILDEADEM 157

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]} Length = 218

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 99.2 bits (246), Expect = 8e-27
 Identities = 60/164 (36%), Positives = 83/164 (50%), Gaps = 2/164 (1%)

Query: 2   EDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFA 61
            + + SF D+ L+  L+R     G + P+ IQ+  I   +   D I  A++G+GKT  FA
Sbjct: 8   NEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFA 67

Query: 62  LPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRV-SIITGGMDMVDQGKE 120
           + ILQ+   D     ALVL PTRELA QI    + LG  M     + I G     +  K 
Sbjct: 68  ISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKL 127

Query: 121 LAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM 164
             + PHI++ TPGR+ D L+     S   IK  VLDEAD +   
Sbjct: 128 QMEAPHIIVGTPGRVFDMLNR-RYLSPKYIKMFVLDEADEMLSR 170

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]} Length = 222

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 98.4 bits (244), Expect = 1e-26
 Identities = 54/162 (33%), Positives = 81/162 (50%), Gaps = 1/162 (0%)

Query: 3   DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFAL 62
           D   +F  + L   L+R     G + P+ IQ+  I  ++   D I  +++G+GKT  F++
Sbjct: 14  DVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSI 73

Query: 63  PILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA 122
            +LQ          AL+L PTRELA QI    L LG  MN++     GG ++ +  ++L 
Sbjct: 74  SVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLD 133

Query: 123 KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM 164
              H+V  TPGR+ D      +     IK LVLDEAD +   
Sbjct: 134 YGQHVVAGTPGRVFDM-IRRRSLRTRAIKMLVLDEADEMLNK 174

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]} Length = 238

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

 Score = 95.7 bits (237), Expect = 2e-25
 Identities = 61/165 (36%), Positives = 86/165 (52%), Gaps = 10/165 (6%)

Query: 3   DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFAL 62
           + I++F +LKL+P +         + PT IQK  IP +L   D + CA+TGSGKT AF +
Sbjct: 18  NVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLI 77

Query: 63  PILQKWCEDPY---------GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMD 113
           PI+                     L+L PTRELA QI  +         LR  ++ GG D
Sbjct: 78  PIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGAD 137

Query: 114 MVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEA 158
              Q +E+    H+++ATPGRL D ++  N  SL   K++VLDEA
Sbjct: 138 THSQIREVQMGCHLLVATPGRLVDFIE-KNKISLEFCKYIVLDEA 181

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 212

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 93.7 bits (232), Expect = 7e-25
 Identities = 52/159 (32%), Positives = 84/159 (52%), Gaps = 2/159 (1%)

Query: 2   EDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFA 61
           +  +  F D++L+  L+R     G + P+ IQ+  I  ++   D +  A++G+GKT  F+
Sbjct: 6   DKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFS 65

Query: 62  LPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL 121
           +  LQ+         AL+L PTRELA QI    + L   M+++V    GG   V+  + L
Sbjct: 66  IAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGL 125

Query: 122 AKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR 160
            +   IV+ TPGR+ D+      F  ++IK  +LDEAD 
Sbjct: 126 -RDAQIVVGTPGRVFDN-IQRRRFRTDKIKMFILDEADE 162

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]} Length = 207

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 91.9 bits (227), Expect = 4e-24
 Identities = 52/153 (33%), Positives = 75/153 (49%), Gaps = 3/153 (1%)

Query: 7   SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ 66
            F D  L P L+R     G + P+E+Q   IP  +   D +  AK+G GKT  F L  LQ
Sbjct: 2   GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 61

Query: 67  KWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKK-- 124
           +       +  LV+  TRELA+QI  ++    K M      +  G   + + +E+ KK  
Sbjct: 62  QLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNC 121

Query: 125 PHIVIATPGRLADHLDTCNTFSLNRIKFLVLDE 157
           PHIV+ TPGR+        + +L  IK  +LDE
Sbjct: 122 PHIVVGTPGRILALARN-KSLNLKHIKHFILDE 153

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 237

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score = 90.7 bits (224), Expect = 2e-23
 Identities = 31/143 (21%), Positives = 45/143 (31%), Gaps = 14/143 (9%)

Query: 25  GVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTR 84
            V  P  IQK     +L  E     A TG GKT       L    +        V+ PT 
Sbjct: 40  CVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALKGK---RCYVIFPTS 96

Query: 85  ELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL------AKKPHIVIATPGRLADH 138
            L  Q  +      +   +    + G        +E        +   IVI T   L+ H
Sbjct: 97  LLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKH 156

Query: 139 LDTCNTFSLNRIKFLVLDEADRL 161
                   L    F+ +D+ D +
Sbjct: 157 Y-----RELGHFDFIFVDDVDAI 174

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 87.7 bits (216), Expect = 1e-22
 Identities = 53/155 (34%), Positives = 82/155 (52%), Gaps = 2/155 (1%)

Query: 6   KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPIL 65
             F D  L   L+     +G + P+ IQ+  IP  L+  D +  AK G+GK+ A+ +P+L
Sbjct: 3   NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLL 62

Query: 66  QKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGKELAKK 124
           ++       I A+V+ PTRELA Q+    + + K M   +V   TGG ++ D    L   
Sbjct: 63  ERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDT 122

Query: 125 PHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEAD 159
            H+VIATPGR+ D         ++ ++ +VLDEAD
Sbjct: 123 VHVVIATPGRILDL-IKKGVAKVDHVQMIVLDEAD 156

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 83.5 bits (205), Expect = 5e-21
 Identities = 50/151 (33%), Positives = 74/151 (49%), Gaps = 1/151 (0%)

Query: 7   SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ 66
           +F D  L   L+      G + P+ IQ+  IP  +   D +  AK G+GKT AF +P L+
Sbjct: 2   TFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLE 61

Query: 67  KWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPH 126
           K       I AL++ PTRELA Q       LGK   +   + TGG ++ D    L +  H
Sbjct: 62  KVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVH 121

Query: 127 IVIATPGRLADHLDTCNTFSLNRIKFLVLDE 157
           I++ TPGR+ D   +     L+     ++DE
Sbjct: 122 ILVGTPGRVLDL-ASRKVADLSDCSLFIMDE 151

>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 = 73.4 bits (179), Expect = 1e-16
 Identities = 18/122 (14%), Positives = 40/122 (32%), Gaps = 15/122 (12%)

Query: 44  EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNL 103
              I     G+GKT  +   I+++  +   G+  L+L PTR +A ++ +           
Sbjct: 10  RLTIMDLHPGAGKTKRYLPAIVREAIKR--GLRTLILAPTRVVAAEMEEAL--------- 58

Query: 104 RVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL 163
               +           E   +  + +         L   +   +     +++DEA     
Sbjct: 59  --RGLPIRYQTPAIRAEHTGREIVDLMCHATFTMRLL--SPIRVPNYNLIIMDEAHFTDP 114

Query: 164 MT 165
            +
Sbjct: 115 AS 116

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

 Score = 70.8 bits (172), Expect = 4e-16
 Identities = 34/159 (21%), Positives = 53/159 (33%), Gaps = 8/159 (5%)

Query: 7   SFTDLKLNPWLIRQCQTI-GVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPIL 65
               L L     +  Q   G +     Q+ II  VL+  DC+    TG GK+L + +P L
Sbjct: 3   QAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPAL 62

Query: 66  QKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKP 125
                       +V++P   L     DQ    G       S  T    +         + 
Sbjct: 63  LLNGL------TVVVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQI 116

Query: 126 HIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM 164
            ++   P RL    +     +      L +DEA  +S  
Sbjct: 117 RLLYIAPERLMLD-NFLEHLAHWNPVLLAVDEAHCISQW 154

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]} Length = 202

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 66.5 bits (161), Expect = 1e-14
 Identities = 24/160 (15%), Positives = 57/160 (35%), Gaps = 10/160 (6%)

Query: 7   SFTDL--KLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPI 64
              +L   ++ + +   +  G++     Q   +  V + ++ +    T +GKTL   + +
Sbjct: 2   KVEELAESISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAM 61

Query: 65  LQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKK 124
           +++  +    ++   + P R LA +  + F    K+               +        
Sbjct: 62  VREAIKGGKSLY---VVPLRALAGEKYESFKKWEKIGLRIGISTGDYESRDEHL----GD 114

Query: 125 PHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM 164
             I++ T  +  D L       +  +  LV+DE   L   
Sbjct: 115 CDIIVTTSEKA-DSLIRNRASWIKAVSCLVVDEIHLLDSE 153

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]} Length = 209

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 64.7 bits (156), Expect = 8e-14
 Identities = 44/154 (28%), Positives = 68/154 (44%), Gaps = 4/154 (2%)

Query: 7   SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPI-- 64
            FT     P++I   +T+    PTEIQ+ IIP  L  E  +G ++TG+GKT A+ LPI  
Sbjct: 2   QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIME 61

Query: 65  --LQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA 122
               +  E    I A       ++ ++         K   +    + GG D     ++L 
Sbjct: 62  KIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLN 121

Query: 123 KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLD 156
            +PHIVI TPGR+ D +             +V +
Sbjct: 122 VQPHIVIGTPGRINDFIREQALDVHTAHILVVDE 155

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 49.8 bits (117), Expect = 2e-08
 Identities = 32/135 (23%), Positives = 52/135 (38%), Gaps = 5/135 (3%)

Query: 28  TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELA 87
            P   Q+ I        +C+    TG GKTL   +    +  +   G   L+L PT+ L 
Sbjct: 9   QPRIYQEVIYAKCKE-TNCLIVLPTGLGKTLIAMMIAEYRLTKY--GGKVLMLAPTKPLV 65

Query: 88  YQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSL 147
            Q  + F  L  +   ++  +TG     ++ K  A+   IV        ++       SL
Sbjct: 66  LQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWARAKVIVATPQTI--ENDLLAGRISL 123

Query: 148 NRIKFLVLDEADRLS 162
             +  +V DEA R  
Sbjct: 124 EDVSLIVFDEAHRAV 138

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 136

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 = 38.7 bits (89), Expect = 7e-05
 Identities = 19/133 (14%), Positives = 27/133 (20%), Gaps = 21/133 (15%)

Query: 38  PHVLNDEDC-IGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLV 96
           P V          A TGSGK+         +      G   LVL P+       G     
Sbjct: 2   PAVPQSFQVAHLHAPTGSGKSTKVPAAYAAQ------GYKVLVLNPSVAATLGFGAYMSK 55

Query: 97  LGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLD 156
              V           +    +                            S      ++ D
Sbjct: 56  AHGVDP--------NIRTGVRTITTGSPITYSTYG------KFLADGGCSGGAYDIIICD 101

Query: 157 EADRLSLMTSLKF 169
           E       + L  
Sbjct: 102 ECHSTDATSILGI 114

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	182
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	100.0
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	100.0
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	100.0
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	100.0
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	100.0
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	100.0
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	100.0
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	100.0
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.97
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.94
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.94
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.93
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.93
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.83
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.83
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.82
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.82
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.73
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	99.7
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.65
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.51
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.41
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	99.32
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	99.25
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	98.59
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	98.4
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	98.2
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	97.97
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	97.81
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	97.4
d1ls1a2	207	GTPase domain of the signal sequence recognition p	97.34
d2qy9a2	211	GTPase domain of the signal recognition particle r	97.27
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	97.26
d1okkd2	207	GTPase domain of the signal recognition particle r	97.23
d1vmaa2	213	GTPase domain of the signal recognition particle r	97.19
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	97.19
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	97.07
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	97.05
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	97.02
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	97.0
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.88
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	96.85
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	96.81
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	96.66
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	96.59
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	96.45
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	96.36
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	96.33
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	96.17
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	96.17
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	96.12
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	96.09
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	96.02
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	95.98
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	95.94
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	95.94
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	95.85
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	95.76
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	95.74
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	95.52
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	95.37
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	95.3
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	95.21
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	94.96
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	94.95
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	94.94
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	94.92
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	94.9
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	94.78
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	94.63
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	94.55
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	94.54
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	94.5
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	94.45
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	94.3
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	94.15
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	94.13
d1g5ta_	157	ATP:corrinoid adenosyltransferase CobA {Salmonella	94.0
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	93.96
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	93.92
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	93.89
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	93.88
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	93.84
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	93.67
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	93.54
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	93.42
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	93.18
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	93.14
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	93.12
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	93.05
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	93.03
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	93.02
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	92.86
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	92.76
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	92.51
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	92.41
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	92.25
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	92.24
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	92.03
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	91.96
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	91.92
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	91.89
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	91.81
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	91.75
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	91.63
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	91.6
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	91.39
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	91.34
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	91.29
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	91.25
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	91.24
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	91.12
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	91.07
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	91.06
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	90.99
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	90.82
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	90.82
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	90.77
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	90.71
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	90.41
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	90.11
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	90.07
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	90.03
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	90.0
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	89.92
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	89.81
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	89.69
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	89.52
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	89.41
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	89.3
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	89.23
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	88.83
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	88.42
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	87.81
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	87.62
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	87.46
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	87.34
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	87.23
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	87.15
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	86.66
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	86.46
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	86.42
d1d0xa2	712	Myosin S1, motor domain {Dictyostelium discoideum	86.4
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	86.32
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	86.22
d1c9ka_	180	Adenosylcobinamide kinase/adenosylcobinamide phosp	86.04
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	85.89
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	85.86
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	85.81
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	85.67
d1lkxa_	684	Myosin S1, motor domain {Dictyostelium discoideum,	85.22
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	84.99
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	84.89
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	84.75
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	84.45
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	84.22
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	84.12
d1br2a2	710	Myosin S1, motor domain {Chicken (Gallus gallus),	83.82
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	83.82
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	83.72
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	83.54
d1kk8a2	789	Myosin S1, motor domain {Bay scallop (Aequipecten	83.53
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	83.35
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	83.33
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	83.33
d1w7ja2	730	Myosin S1, motor domain {Chicken (Gallus gallus),	83.31
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	83.03
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	82.79
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	82.7
d1goja_	354	Kinesin {Neurospora crassa [TaxId: 5141]}	82.58
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	82.31
d2mysa2	794	Myosin S1, motor domain {Chicken (Gallus gallus),	82.23
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	82.16
d2awna2	232	Maltose transport protein MalK, N-terminal domain	81.88
d1g2912	240	Maltose transport protein MalK, N-terminal domain	81.8
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	81.7
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	81.66
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	80.91
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	80.72
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	80.68
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	80.66
d1tuea_	205	Replication protein E1 helicase domain {Human papi	80.46
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	80.14
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	80.03

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=8.3e-37  Score=222.04  Aligned_cols=175  Identities=32%  Similarity=0.491  Sum_probs=159.6

Q ss_pred             CccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcC
Q psy4275           3 DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTP   82 (182)
Q Consensus         3 ~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p   82 (182)
                      +...+|+++++++.+.+++.+.|+..|+|.|.+++|.+++|+|++++++||+|||.+|++++++.+.....+++++|++|
T Consensus        14 ~~~~sF~~l~L~~~l~~~L~~~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~~~~~~~~lil~P   93 (222)
T d2j0sa1          14 DVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAP   93 (222)
T ss_dssp             CCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECS
T ss_pred             CCCCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhcccccccccccccCceeEEecc
Confidence            45678999999999999999999999999999999999999999999999999999999999999988877889999999


Q ss_pred             CHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccc
Q psy4275          83 TRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLS  162 (182)
Q Consensus        83 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~  162 (182)
                      +++|+.|+++.++.+.+..++++..+.|+.........+..+++|+|+||+++.+++.. +...+++++++|+||||.|.
T Consensus        94 treLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l~~~~~Ilv~TPgrl~~~~~~-~~~~~~~l~~lVlDEaD~ll  172 (222)
T d2j0sa1          94 TRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRR-RSLRTRAIKMLVLDEADEML  172 (222)
T ss_dssp             SHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHT-TSSCCTTCCEEEEETHHHHT
T ss_pred             hHHHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHhccCCeEEeCCCCcHHhcccc-cccccccceeeeecchhHhh
Confidence            99999999999999999999999999999988877777778899999999999999988 66789999999999999999


Q ss_pred             ccCChhHHHHHHHHhhcCC
Q psy4275         163 LMTSLKFFFFFFFLKYYIP  181 (182)
Q Consensus       163 ~~~~~~~~~~~~~~~~~~~  181 (182)
                      +.++...   +..+.+.+|
T Consensus       173 ~~~f~~~---i~~I~~~l~  188 (222)
T d2j0sa1         173 NKGFKEQ---IYDVYRYLP  188 (222)
T ss_dssp             STTTHHH---HHHHHTTSC
T ss_pred             hcCcHHH---HHHHHHhCC
Confidence            9987654   444455554

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=4.4e-35  Score=211.02  Aligned_cols=168  Identities=32%  Similarity=0.480  Sum_probs=151.3

Q ss_pred             cCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCH
Q psy4275           5 IKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTR   84 (182)
Q Consensus         5 ~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~   84 (182)
                      -.+|+++++++++.+++.+.|+..|+|.|+++++.+++|+|+++++|||+|||.+|+++++.++..+..++++++++|++
T Consensus         2 ~~~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllP~l~~~~~~~~~~~~lil~pt~   81 (206)
T d1veca_           2 GNEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTR   81 (206)
T ss_dssp             CSSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCH
T ss_pred             CCChhccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeeccCccccccccccchhhcccccccCcceEEEeecc
Confidence            36899999999999999999999999999999999999999999999999999999999999998888889999999999


Q ss_pred             HHHHHHHHHHHHhhccC-CceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275          85 ELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus        85 ~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      +++.|+++.++.+.+.. +..+....|+.........+..+++|+|+||+++.+++.. +...+++++++|+||||.|.+
T Consensus        82 el~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~ivv~TPgrl~~~~~~-~~~~~~~l~~lVlDEaD~ll~  160 (206)
T d1veca_          82 ELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKK-GVAKVDHVQMIVLDEADKLLS  160 (206)
T ss_dssp             HHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHT-TCSCCTTCCEEEEETHHHHTS
T ss_pred             hhhHHHHHHHHHHhhcccCcccccccCCccHHHHHHHHHhccCeEEeCCccccccccc-hhccccccceEEEeccccccc
Confidence            99999999998887654 4667777788877777777788999999999999999987 667889999999999999999


Q ss_pred             cCChhHHHHH
Q psy4275         164 MTSLKFFFFF  173 (182)
Q Consensus       164 ~~~~~~~~~~  173 (182)
                      .++.+.+..+
T Consensus       161 ~~f~~~i~~I  170 (206)
T d1veca_         161 QDFVQIMEDI  170 (206)
T ss_dssp             TTTHHHHHHH
T ss_pred             cchHHHHHHH
Confidence            9876654443

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.7e-35  Score=214.81  Aligned_cols=176  Identities=34%  Similarity=0.467  Sum_probs=153.4

Q ss_pred             CCccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275           2 EDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus         2 ~~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      ++++.+|+++++++.+.+++.+.|+.+|+|.|.++++.++.|+++++++|||+|||.+|++++++.+..+..+++++|++
T Consensus         8 ~e~i~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~~~~~~~alil~   87 (218)
T d2g9na1           8 NEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLA   87 (218)
T ss_dssp             CCCCCCGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEEC
T ss_pred             CCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhhhhheecccccCccEEEEc
Confidence            67899999999999999999999999999999999999999999999999999999999999999998777788999999


Q ss_pred             CCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhh-HHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccc
Q psy4275          82 PTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQG-KELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR  160 (182)
Q Consensus        82 p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~  160 (182)
                      |+++|+.|+++.++.+.+..+.++..+.++....... ....+.++|+|+||+++.+++.+ +...+++++++|+||||.
T Consensus        88 Pt~eL~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IvV~TP~rl~~~l~~-~~~~~~~l~~lVlDEaD~  166 (218)
T d2g9na1          88 PTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNR-RYLSPKYIKMFVLDEADE  166 (218)
T ss_dssp             SSHHHHHHHHHHHHHHHTTTTCCEEEECC--CCCSTTTSSSSCCCSEEEECHHHHHHHHHT-TSSCSTTCCEEEEESHHH
T ss_pred             ccchhhhhHHHHHhhhccccceeEEeeecccchhHHHHHHhcCCCEEEEeCChhHHHHHhc-CCcccccceEEEeeecch
Confidence            9999999999999999999999888887766544333 23335789999999999999987 667889999999999999


Q ss_pred             ccccCChhHHHHHHHHhhcCC
Q psy4275         161 LSLMTSLKFFFFFFFLKYYIP  181 (182)
Q Consensus       161 ~~~~~~~~~~~~~~~~~~~~~  181 (182)
                      |.+.++.....   ++.+++|
T Consensus       167 ll~~~f~~~~~---~Il~~~~  184 (218)
T d2g9na1         167 MLSRGFKDQIY---DIFQKLN  184 (218)
T ss_dssp             HHHTTCHHHHH---HHHHHSC
T ss_pred             hhcCchHHHHH---HHHHhCC
Confidence            99998765444   4444444

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=3.6e-35  Score=212.25  Aligned_cols=169  Identities=30%  Similarity=0.502  Sum_probs=147.4

Q ss_pred             CCccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275           2 EDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus         2 ~~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      |+++.+|++|++++++.+++.+.|+.+|+|.|.++++.++.|+++++++|||+|||.+|+++++.++.....++++++++
T Consensus         6 ~~~~~sF~~l~l~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~~~~~~~lil~   85 (212)
T d1qdea_           6 DKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLA   85 (212)
T ss_dssp             CCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEEC
T ss_pred             cccccChhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhhccCCCcceEEEc
Confidence            78899999999999999999999999999999999999999999999999999999999999999998888889999999


Q ss_pred             CCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccc
Q psy4275          82 PTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL  161 (182)
Q Consensus        82 p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~  161 (182)
                      |+++++.|....+..+......++....++.....+... .++++|+|+||+++.+++.. +.+.+++++++|+||||.|
T Consensus        86 pt~el~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~IvI~TP~~l~~~~~~-~~~~l~~l~~lVlDEad~l  163 (212)
T d1qdea_          86 PTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEG-LRDAQIVVGTPGRVFDNIQR-RRFRTDKIKMFILDEADEM  163 (212)
T ss_dssp             SSHHHHHHHHHHHHHHTTTSCCCEEEECC-----------CTTCSEEEECHHHHHHHHHT-TSSCCTTCCEEEEETHHHH
T ss_pred             ccHHHhhhhhhhhcccccccccceeeEeeccchhHHHHH-hcCCcEEEECCCcccccccc-CceecCcceEEeehhhhhh
Confidence            999999999999999988888888888777665444443 35789999999999999988 6678999999999999999


Q ss_pred             cccCChhHHHH
Q psy4275         162 SLMTSLKFFFF  172 (182)
Q Consensus       162 ~~~~~~~~~~~  172 (182)
                      .+.++......
T Consensus       164 ld~~f~~~v~~  174 (212)
T d1qdea_         164 LSSGFKEQIYQ  174 (212)
T ss_dssp             HHTTCHHHHHH
T ss_pred             cccchHHHHHH
Confidence            99887664433

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=2.6e-34  Score=207.10  Aligned_cols=172  Identities=31%  Similarity=0.480  Sum_probs=149.7

Q ss_pred             CCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHH
Q psy4275           6 KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRE   85 (182)
Q Consensus         6 ~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~   85 (182)
                      ..|++|++++++.+++.+.|+..|+|.|.++++.+++|+|+++++|||+|||.+|++++++.......++++++++|+++
T Consensus         1 s~F~dl~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~~~~~~~~~lil~Ptre   80 (207)
T d1t6na_           1 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE   80 (207)
T ss_dssp             CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHH
T ss_pred             CCccccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCeEEEeccccccccccccceeeeecccCCCceEEEEeccch
Confidence            36999999999999999999999999999999999999999999999999999999999999888777889999999999


Q ss_pred             HHHHHHHHHHHhhccCC-ceEEEEEcCCchhhhhHHh-cCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccc
Q psy4275          86 LAYQIGDQFLVLGKVMN-LRVSIITGGMDMVDQGKEL-AKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus        86 l~~q~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~-~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      |+.|+.+.++.+....+ .++..+.|+.........+ .+.++|+|+||+++.++++. +.+.++++.++|+||||.|.+
T Consensus        81 L~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~ilI~TP~rl~~~~~~-~~~~l~~l~~lVlDEaD~ll~  159 (207)
T d1t6na_          81 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARN-KSLNLKHIKHFILDECDKMLE  159 (207)
T ss_dssp             HHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHT-TSSCCTTCCEEEEESHHHHHS
T ss_pred             hhHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHHHHhcCCCEEEeCcchhhhhccC-Cceeccccceeehhhhhhhhh
Confidence            99999999999988764 5677778887766555544 46789999999999999987 677899999999999999987


Q ss_pred             c-CChhHHHHHHHHhhcCC
Q psy4275         164 M-TSLKFFFFFFFLKYYIP  181 (182)
Q Consensus       164 ~-~~~~~~~~~~~~~~~~~  181 (182)
                      . ++.   ..+.++.+++|
T Consensus       160 ~~~~~---~~i~~I~~~~~  175 (207)
T d1t6na_         160 QLDMR---RDVQEIFRMTP  175 (207)
T ss_dssp             SHHHH---HHHHHHHHTSC
T ss_pred             cCCcH---HHHHHHHHhCC
Confidence            4 443   34555555554

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=100.00  E-value=4.7e-35  Score=215.08  Aligned_cols=172  Identities=37%  Similarity=0.524  Sum_probs=155.9

Q ss_pred             CCccCCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccC---------C
Q psy4275           2 EDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCED---------P   72 (182)
Q Consensus         2 ~~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~---------~   72 (182)
                      |+++.+|+++++++++.+++.+.|+..|+|.|.++++.+++|+|+++++|||+|||.+|+++++..+...         .
T Consensus        17 ~~~~~~F~~l~l~~~l~~~L~~~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~~~~~   96 (238)
T d1wrba1          17 TNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKT   96 (238)
T ss_dssp             CSCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CC
T ss_pred             CCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeHHHHHHHHHhcccccccccCC
Confidence            5778999999999999999999999999999999999999999999999999999999999999987542         2


Q ss_pred             CCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccE
Q psy4275          73 YGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKF  152 (182)
Q Consensus        73 ~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~  152 (182)
                      .+++++|++|+++|+.|+.+.+..+....++++..+.|+.......+....+++|+|+||+.+.+++.. +...++++++
T Consensus        97 ~~~~alil~pt~el~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ivV~TP~~l~~~~~~-~~~~l~~v~~  175 (238)
T d1wrba1          97 AYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEK-NKISLEFCKY  175 (238)
T ss_dssp             BCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHT-TSBCCTTCCE
T ss_pred             CCceEEEeccchhhhcchheeeeecccCCCcEEEEEeccchhhHHHhhcccCCceeecCHHHHHhHHcc-Cceeccccce
Confidence            357899999999999999999999999999999999998887777777788999999999999999988 6678899999


Q ss_pred             EEEeccccccccCChhHHHHHH
Q psy4275         153 LVLDEADRLSLMTSLKFFFFFF  174 (182)
Q Consensus       153 iI~DE~h~~~~~~~~~~~~~~~  174 (182)
                      +|+||+|.+.+.++......+.
T Consensus       176 lViDEaD~ll~~~f~~~i~~Il  197 (238)
T d1wrba1         176 IVLDEADRMLDMGFEPQIRKII  197 (238)
T ss_dssp             EEEETHHHHHHTTCHHHHHHHH
T ss_pred             eeeehhhhhhhhccHHHHHHHH
Confidence            9999999999998776655443

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=100.00  E-value=6.3e-34  Score=205.27  Aligned_cols=164  Identities=40%  Similarity=0.620  Sum_probs=145.7

Q ss_pred             CCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCC-CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCH
Q psy4275           6 KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLND-EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTR   84 (182)
Q Consensus         6 ~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~-~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~   84 (182)
                      .+|+++++++++.+++.+.|+.+|+|.|.++++.+++| ++.++++|||+|||.++.++++.....+ .+++++|++|++
T Consensus         4 msf~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~~-~~~~~lil~pt~   82 (208)
T d1hv8a1           4 MNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNEN-NGIEAIILTPTR   82 (208)
T ss_dssp             CCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSS-SSCCEEEECSCH
T ss_pred             cCHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeecccccccccc-cCcceEEEeecc
Confidence            58999999999999999999999999999999998886 4999999999999999999999876554 367999999999


Q ss_pred             HHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccccc
Q psy4275          85 ELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM  164 (182)
Q Consensus        85 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~  164 (182)
                      +|+.|+.+.++.+....+.++....|+.....+...+ ++++|+|+||+++.+++++ +.+.+++++++|+||||+|.+.
T Consensus        83 ~l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l-~~~~IlV~TP~~l~~~l~~-~~~~~~~l~~lViDEad~l~~~  160 (208)
T d1hv8a1          83 ELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKAL-KNANIVVGTPGRILDHINR-GTLNLKNVKYFILDEADEMLNM  160 (208)
T ss_dssp             HHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHH-HTCSEEEECHHHHHHHHHT-TCSCTTSCCEEEEETHHHHHTT
T ss_pred             ccchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhc-CCCCEEEEChHHHHHHHHc-CCCCcccCcEEEEEChHHhhcC
Confidence            9999999999999999999999999988776655544 5799999999999999987 6678999999999999999988


Q ss_pred             CChhHHHH
Q psy4275         165 TSLKFFFF  172 (182)
Q Consensus       165 ~~~~~~~~  172 (182)
                      ++...+..
T Consensus       161 ~~~~~i~~  168 (208)
T d1hv8a1         161 GFIKDVEK  168 (208)
T ss_dssp             TTHHHHHH
T ss_pred             CChHHHHH
Confidence            87654433

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=6.4e-33  Score=199.70  Aligned_cols=172  Identities=31%  Similarity=0.474  Sum_probs=157.4

Q ss_pred             CCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHH
Q psy4275           6 KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRE   85 (182)
Q Consensus         6 ~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~   85 (182)
                      .+|++|++++.+.+++.+.|+..|+|.|.++++.+++|+++++++|||+|||.+|++++++....+..+.++++++|+..
T Consensus         1 ~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTlay~lp~i~~~~~~~~~~~~~~~~~~~~   80 (206)
T d1s2ma1           1 NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRE   80 (206)
T ss_dssp             CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHH
T ss_pred             CChHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhhhccccccccccccccccceeeccchh
Confidence            37999999999999999999999999999999999999999999999999999999999999988887889999999999


Q ss_pred             HHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccC
Q psy4275          86 LAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus        86 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~  165 (182)
                      ++.+............++++....|+.........+..+++|+|+||+.+.++++. +.+.+++++++|+||||.|.+.+
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~-~~~~l~~l~~lV~DEaD~l~~~~  159 (206)
T d1s2ma1          81 LALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASR-KVADLSDCSLFIMDEADKMLSRD  159 (206)
T ss_dssp             HHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHT-TCSCCTTCCEEEEESHHHHSSHH
T ss_pred             hhhhhhhhhhhcccccCeeEEeecCccchhhHHHHhcccceEEEECCccccccccc-ceeecccceEEEeechhhhhhhh
Confidence            99999999999999999999999999988888888888999999999999999987 67789999999999999999886


Q ss_pred             ChhHHHHHHHHhhcCC
Q psy4275         166 SLKFFFFFFFLKYYIP  181 (182)
Q Consensus       166 ~~~~~~~~~~~~~~~~  181 (182)
                      +..   .+..+.+.+|
T Consensus       160 f~~---~v~~I~~~l~  172 (206)
T d1s2ma1         160 FKT---IIEQILSFLP  172 (206)
T ss_dssp             HHH---HHHHHHTTSC
T ss_pred             hHH---HHHHHHHhCC
Confidence            544   4555555555

>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=99.97  E-value=5.4e-31  Score=189.91  Aligned_cols=172  Identities=34%  Similarity=0.523  Sum_probs=146.2

Q ss_pred             CCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHH
Q psy4275           6 KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRE   85 (182)
Q Consensus         6 ~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~   85 (182)
                      .+|+++|+++++.+++.+.|+.+|+|.|.++++.+++|+|+++++|||+|||++|++++++...........++++|...
T Consensus         1 t~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTlayllp~l~~~~~~~~~~~~~~~~~~~~   80 (209)
T d1q0ua_           1 TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRE   80 (209)
T ss_dssp             CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHH
T ss_pred             CccccCCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEeecccccccceeeeeeeccccccccccccccccccccc
Confidence            47999999999999999999999999999999999999999999999999999999999999988777788999999999


Q ss_pred             HHHHHHHHHHHhhccC----CceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccc
Q psy4275          86 LAYQIGDQFLVLGKVM----NLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL  161 (182)
Q Consensus        86 l~~q~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~  161 (182)
                      ++.+.+.......+..    ...+....+..+..........+++|+|+||+++..++.+ .....++++++|+||||.+
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~TP~~l~~~~~~-~~~~~~~l~~lViDEad~l  159 (209)
T d1q0ua_          81 LATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIRE-QALDVHTAHILVVDEADLM  159 (209)
T ss_dssp             HHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHT-TCCCGGGCCEEEECSHHHH
T ss_pred             hhHHHHHHHHhhhccccccccccccccccchhhHHHHHHhccCceEEEecCchhhhhhhh-hccccccceEEEEeecccc
Confidence            9999888877765554    3455666666666555555667899999999999999887 5567889999999999999


Q ss_pred             cccCChhHHHHHHHHhhcCC
Q psy4275         162 SLMTSLKFFFFFFFLKYYIP  181 (182)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~~~  181 (182)
                      .++++...   +..+.+.+|
T Consensus       160 l~~~f~~~---v~~I~~~~~  176 (209)
T d1q0ua_         160 LDMGFITD---VDQIAARMP  176 (209)
T ss_dssp             HHTTCHHH---HHHHHHTSC
T ss_pred             cccccHHH---HHHHHHHCC
Confidence            99987654   444444444

>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=99.94  E-value=1.1e-26  Score=170.04  Aligned_cols=143  Identities=22%  Similarity=0.218  Sum_probs=110.0

Q ss_pred             CHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHH
Q psy4275          14 NPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQ   93 (182)
Q Consensus        14 ~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~   93 (182)
                      .+++.+.+ +.++.+|+++|+++++.++.|+++++++|||+|||.+++++++.....   +.+++|++|+++|++|++++
T Consensus        30 ~~~~~~~~-~~~~~~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~~---~~rvliv~Pt~~La~Q~~~~  105 (237)
T d1gkub1          30 LKEFVEFF-RKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALK---GKRCYVIFPTSLLVIQAAET  105 (237)
T ss_dssp             HHHHHHHH-HTTTCSCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHTT---SCCEEEEESCHHHHHHHHHH
T ss_pred             HHHHHHHH-HhccCCCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHHh---cCeEEEEeccHHHHHHHHHH
Confidence            33444444 456779999999999999999999999999999999988888776554   56899999999999999999


Q ss_pred             HHHhhccCCceE----EEEEcCCchhhhhHHh--cCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccC
Q psy4275          94 FLVLGKVMNLRV----SIITGGMDMVDQGKEL--AKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus        94 ~~~~~~~~~~~~----~~~~~~~~~~~~~~~~--~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~  165 (182)
                      ++++.+..++++    ....+..........+  ..+++|+|+||+.+.+...     ..++++++|+||+|.|++.+
T Consensus       106 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Ilv~Tp~~l~~~~~-----~~~~~~~vVvDE~d~~l~~~  178 (237)
T d1gkub1         106 IRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHYR-----ELGHFDFIFVDDVDAILKAS  178 (237)
T ss_dssp             HHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHHCST-----TSCCCSEEEESCHHHHHTST
T ss_pred             HHHHHHHcCCceEEEEeeeecccchhhhhhhhccccccceeccChHHHHHhhh-----hcCCCCEEEEEChhhhhhcc
Confidence            999988776553    3333333333222222  3467899999998765433     36788999999999987654

>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=99.94  E-value=1.1e-26  Score=166.25  Aligned_cols=148  Identities=20%  Similarity=0.266  Sum_probs=119.6

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHH
Q psy4275          13 LNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGD   92 (182)
Q Consensus        13 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~   92 (182)
                      +++.+...+.+.|+.+++|+|.++++.+.+++++++++|||+|||.++.++++..+..   ++++++++|+++|++|+.+
T Consensus        10 ~~~~~~~~l~~~g~~~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~~---~~~vl~l~P~~~L~~q~~~   86 (202)
T d2p6ra3          10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK---GGKSLYVVPLRALAGEKYE   86 (202)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT---TCCEEEEESSHHHHHHHHH
T ss_pred             hhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhhc---cCcceeecccHHHHHHHHH
Confidence            6778889999999999999999999999999999999999999999998888877665   4589999999999999998


Q ss_pred             HHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChh
Q psy4275          93 QFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLK  168 (182)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~  168 (182)
                      .++++... ..++....|+.....   ...+.+.++++||..+...++. ....+.+++++|+||+|.+.++....
T Consensus        87 ~~~~~~~~-~~~v~~~~~~~~~~~---~~~~~~~ii~~~~~~~~~~~~~-~~~~~~~~~~ii~DE~h~~~~~~r~~  157 (202)
T d2p6ra3          87 SFKKWEKI-GLRIGISTGDYESRD---EHLGDCDIIVTTSEKADSLIRN-RASWIKAVSCLVVDEIHLLDSEKRGA  157 (202)
T ss_dssp             HHTTTTTT-TCCEEEECSSCBCCS---SCSTTCSEEEEEHHHHHHHHHT-TCSGGGGCCEEEETTGGGGGCTTTHH
T ss_pred             HHHHHhhc-cccceeeccCccccc---ccccccceeeeccHHHHHHHhc-cchhhhhhhhccccHHHHhcccccch
Confidence            88877554 355656666554322   3345788999999999998877 44567789999999999998876443

>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=99.93  E-value=7e-25  Score=156.33  Aligned_cols=138  Identities=25%  Similarity=0.338  Sum_probs=113.4

Q ss_pred             CCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEE
Q psy4275          27 KTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVS  106 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~  106 (182)
                      .+|+++|.+++..+. ++|.++++|||+|||.+++.++...+.+.  +.++++++|+++|++|+.+.++++....+.++.
T Consensus         8 ~~pr~~Q~~~~~~~~-~~n~lv~~pTGsGKT~i~~~~~~~~~~~~--~~~il~i~P~~~L~~q~~~~~~~~~~~~~~~v~   84 (200)
T d1wp9a1           8 IQPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKY--GGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIV   84 (200)
T ss_dssp             HCCCHHHHHHHHHGG-GSCEEEECCTTSCHHHHHHHHHHHHHHHS--CSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEE
T ss_pred             CCCCHHHHHHHHHHh-cCCeEEEeCCCCcHHHHHHHHHHHHHHhc--CCcEEEEcCchHHHHHHHHHHHHhhccccccee
Confidence            379999999998876 46799999999999999887777665544  458999999999999999999999888888888


Q ss_pred             EEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhH
Q psy4275         107 IITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKF  169 (182)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~  169 (182)
                      ...++.....+... ..+++++++||+.+.+.+.. .....++++++|+||||++........
T Consensus        85 ~~~~~~~~~~~~~~-~~~~~i~i~t~~~~~~~~~~-~~~~~~~~~~vIiDE~H~~~~~~~~~~  145 (200)
T d1wp9a1          85 ALTGEKSPEERSKA-WARAKVIVATPQTIENDLLA-GRISLEDVSLIVFDEAHRAVGNYAYVF  145 (200)
T ss_dssp             EECSCSCHHHHHHH-HHHCSEEEECHHHHHHHHHT-TSCCTTSCSEEEEETGGGCSTTCHHHH
T ss_pred             eeecccchhHHHHh-hhcccccccccchhHHHHhh-hhhhccccceEEEEehhhhhcchhHHH
Confidence            88777765544433 35678999999999988877 556788899999999999887664443

>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=99.93  E-value=1.6e-26  Score=165.90  Aligned_cols=150  Identities=21%  Similarity=0.206  Sum_probs=116.8

Q ss_pred             CCccCCCCCHHHHHHHHHC-CCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCH
Q psy4275           6 KSFTDLKLNPWLIRQCQTI-GVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTR   84 (182)
Q Consensus         6 ~~~~~~~l~~~i~~~l~~~-~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~   84 (182)
                      .+.+.++|++-..+.+++. |+..++|+|.++++.+.+|+|+++++|||+|||.++.++++..      ..++++++|++
T Consensus         2 ~~~e~~~l~~~~~~~l~~~fg~~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~~~~~~~~~------~~~~~~v~P~~   75 (206)
T d1oywa2           2 AQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL------NGLTVVVSPLI   75 (206)
T ss_dssp             CCCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS------SSEEEEECSCH
T ss_pred             CchhhCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcchhhhhhhhc------cCceEEeccch
Confidence            4567789999999999875 9999999999999999999999999999999999998888764      55899999999


Q ss_pred             HHHHHHHHHHHHhhccCCceEEEEEcCCch----hhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccc
Q psy4275          85 ELAYQIGDQFLVLGKVMNLRVSIITGGMDM----VDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR  160 (182)
Q Consensus        85 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~  160 (182)
                      +|+.|+.+.++.....    .....+....    ...........+|+++||+.+...... ......+++++|+||+|+
T Consensus        76 ~L~~q~~~~l~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~t~~~~~~~~~~-~~~~~~~v~~lviDEaH~  150 (206)
T d1oywa2          76 SLMKDQVDQLQANGVA----AACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFL-EHLAHWNPVLLAVDEAHC  150 (206)
T ss_dssp             HHHHHHHHHHHHTTCC----EEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHH-HHHTTSCEEEEEESSGGG
T ss_pred             hhhhhHHHHHHhhccc----ccccccccccccchhHHHHHhcCCceEEEEechhhhchhhc-ccchhheeeeeeeeeeee
Confidence            9999999888777443    3333222221    222233445789999999988544333 223466799999999999


Q ss_pred             ccccCC
Q psy4275         161 LSLMTS  166 (182)
Q Consensus       161 ~~~~~~  166 (182)
                      +.+++.
T Consensus       151 ~~~~~~  156 (206)
T d1oywa2         151 ISQWGH  156 (206)
T ss_dssp             GCTTSS
T ss_pred             eecccc
Confidence            988764

>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=99.83  E-value=2.4e-19  Score=129.48  Aligned_cols=144  Identities=23%  Similarity=0.160  Sum_probs=115.2

Q ss_pred             CCCCHHHHHHHHHCCCCCChHHHHhhhhhhhC----CC--cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCH
Q psy4275          11 LKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLN----DE--DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTR   84 (182)
Q Consensus        11 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~----~~--~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~   84 (182)
                      +..+.+..+.+.+.-...+++-|..++..+.+    ++  +.+++|.||+|||.+|+.++...+.+   +.++++++|+.
T Consensus        38 ~~~~~~~~~~~~~~lP~~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~---g~qv~~l~Pt~  114 (233)
T d2eyqa3          38 FKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDN---HKQVAVLVPTT  114 (233)
T ss_dssp             CCCCHHHHHHHHHTCCSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTT---TCEEEEECSSH
T ss_pred             CCCCHHHHHhhhhccccccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHc---CCceEEEccHH
Confidence            45567776777655445899999999987754    33  68999999999999999998888766   67999999999


Q ss_pred             HHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhH----HhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccc
Q psy4275          85 ELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGK----ELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR  160 (182)
Q Consensus        85 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~  160 (182)
                      .|+.|.++.+++.+..+++++..+++..+..++..    ...+..+|+|||-..+    .  ....++++++||+||-|.
T Consensus       115 ~La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l----~--~~~~f~~LgLiIiDEeH~  188 (233)
T d2eyqa3         115 LLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLL----Q--SDVKFKDLGLLIVDEEHR  188 (233)
T ss_dssp             HHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHH----H--SCCCCSSEEEEEEESGGG
T ss_pred             HhHHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhh----c--cCCccccccceeeechhh
Confidence            99999999999999999999999999887654332    3345789999995544    2  334678899999999997


Q ss_pred             ccc
Q psy4275         161 LSL  163 (182)
Q Consensus       161 ~~~  163 (182)
                      +.-
T Consensus       189 fg~  191 (233)
T d2eyqa3         189 FGV  191 (233)
T ss_dssp             SCH
T ss_pred             hhh
Confidence            443

>d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: DNA helicase UvsW
domain: DNA helicase UvsW
species: Bacteriophage T4 [TaxId: 10665]

Probab=99.83  E-value=7e-21  Score=142.19  Aligned_cols=129  Identities=19%  Similarity=0.174  Sum_probs=97.1

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSI  107 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  107 (182)
                      .|+++|.+++..+.++++.++.+|||+|||.++...+.......  +.++|+++|+.+|++|+++.+.++.......+..
T Consensus       113 ~~rdyQ~~av~~~l~~~~~il~~pTGsGKT~i~~~i~~~~~~~~--~~k~Liivp~~~Lv~Q~~~~f~~~~~~~~~~~~~  190 (282)
T d1rifa_         113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENY--EGKILIIVPTTALTTQMADDFVDYRLFSHAMIKK  190 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHC--SSEEEEECSSHHHHHHHHHHHHHHTSCCGGGEEE
T ss_pred             ccchHHHHHHHHHHhcCCceeEEEcccCccHHHHHHHHHhhhcc--cceEEEEEcCchhHHHHHHHHHHhhcccccccee
Confidence            79999999999999988999999999999998655443332322  3489999999999999999999886655555555


Q ss_pred             EEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccC
Q psy4275         108 ITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~  165 (182)
                      ..++.....   .......++++|++.+....+.    .++++++||+||||++.+..
T Consensus       191 ~~~g~~~~~---~~~~~~~i~i~t~qs~~~~~~~----~~~~f~~VIvDEaH~~~a~~  241 (282)
T d1rifa_         191 IGGGASKDD---KYKNDAPVVVGTWQTVVKQPKE----WFSQFGMMMNDECHLATGKS  241 (282)
T ss_dssp             CSTTCSSTT---CCCTTCSEEEECHHHHTTSCGG----GGGGEEEEEEETGGGCCHHH
T ss_pred             ecceecccc---cccccceEEEEeeehhhhhccc----ccCCCCEEEEECCCCCCchh
Confidence            555443221   2234678999999887554333    35679999999999976543

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.82  E-value=4.8e-20  Score=131.78  Aligned_cols=117  Identities=22%  Similarity=0.239  Sum_probs=90.5

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSI  107 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  107 (182)
                      .++++|.+++..+.++++.++.+|||+|||.+++..+...      +.++||++|+.+|++|+.+.++.+...   .+..
T Consensus        70 ~Lr~yQ~eav~~~~~~~~~ll~~~tG~GKT~~a~~~~~~~------~~~~Liv~p~~~L~~q~~~~~~~~~~~---~~~~  140 (206)
T d2fz4a1          70 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL------STPTLIVVPTLALAEQWKERLGIFGEE---YVGE  140 (206)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHHS------CSCEEEEESSHHHHHHHHHHHGGGCGG---GEEE
T ss_pred             CcCHHHHHHHHHHHhCCCcEEEeCCCCCceehHHhHHHHh------cCceeEEEcccchHHHHHHHHHhhccc---chhh
Confidence            5999999999999998899999999999999876555433      347999999999999999888776442   3444


Q ss_pred             EEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCC
Q psy4275         108 ITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTS  166 (182)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~  166 (182)
                      ..|..         ....+++++|.+.+....+..    .+++++||+||||++.+..+
T Consensus       141 ~~~~~---------~~~~~i~i~t~~~~~~~~~~~----~~~~~lvIiDEaH~~~a~~~  186 (206)
T d2fz4a1         141 FSGRI---------KELKPLTVSTYDSAYVNAEKL----GNRFMLLIFDEVHHLPAESY  186 (206)
T ss_dssp             ESSSC---------BCCCSEEEEEHHHHHHTHHHH----TTTCSEEEEECSSCCCTTTH
T ss_pred             ccccc---------ccccccccceehhhhhhhHhh----CCcCCEEEEECCeeCCcHHH
Confidence            44432         234579999999887665542    35688999999999875544

>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=99.82  E-value=8.6e-20  Score=134.11  Aligned_cols=143  Identities=20%  Similarity=0.283  Sum_probs=111.1

Q ss_pred             CCHHHHHHH-HHCCCCCChHHHHhhhhhhhC----C--CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHH
Q psy4275          13 LNPWLIRQC-QTIGVKTPTEIQKAIIPHVLN----D--EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRE   85 (182)
Q Consensus        13 l~~~i~~~l-~~~~~~~~~~~Q~~~~~~~~~----~--~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~   85 (182)
                      .+..+.+.+ +.+.+ ++++.|++++..+.+    +  .+.+++|.+|||||.+|+.++...+.+   |.++++++|+..
T Consensus        68 ~~~~l~~~f~~~LPF-eLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~---g~q~~~m~Pt~~  143 (264)
T d1gm5a3          68 IEGKLAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA---GFQTAFMVPTSI  143 (264)
T ss_dssp             CCTHHHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH---TSCEEEECSCHH
T ss_pred             CChHHHHHHHhhccc-cCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhc---ccceeEEeehHh
Confidence            333444444 45565 899999999988764    2  378999999999999999999888777   679999999999


Q ss_pred             HHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccc
Q psy4275          86 LAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL  161 (182)
Q Consensus        86 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~  161 (182)
                      |+.|.++.+++++..+++++..++|+.+..++...+    .++.+|+|||..-+    ..  ...+++++++|+||-|.+
T Consensus       144 La~Qh~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~----~~--~~~f~~LglviiDEqH~f  217 (264)
T d1gm5a3         144 LAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALI----QE--DVHFKNLGLVIIDEQHRF  217 (264)
T ss_dssp             HHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHH----HH--CCCCSCCCEEEEESCCCC
T ss_pred             hhHHHHHHHHHhhhhccccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHh----cC--CCCccccceeeecccccc
Confidence            999999999999999999999999988765443332    34789999996644    22  234678999999999987


Q ss_pred             cccC
Q psy4275         162 SLMT  165 (182)
Q Consensus       162 ~~~~  165 (182)
                      ....
T Consensus       218 gv~Q  221 (264)
T d1gm5a3         218 GVKQ  221 (264)
T ss_dssp             ----
T ss_pred             chhh
Confidence            6543

>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=99.73  E-value=2e-18  Score=129.54  Aligned_cols=112  Identities=18%  Similarity=0.202  Sum_probs=80.6

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhH
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGK  119 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  119 (182)
                      +.++++.++.+|||+|||.+++.+++.....+  +.+++|++|+++|++|+++.++.+..    .+....       ...
T Consensus         6 ~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~--~~~~lvi~Ptr~La~q~~~~l~~~~~----~~~~~~-------~~~   72 (305)
T d2bmfa2           6 FRKKRLTIMDLHPGAGKTKRYLPAIVREAIKR--GLRTLILAPTRVVAAEMEEALRGLPI----RYQTPA-------IRA   72 (305)
T ss_dssp             SSTTCEEEECCCTTSSTTTTHHHHHHHHHHHH--TCCEEEEESSHHHHHHHHHHTTTSCC----BCCC------------
T ss_pred             hhcCCcEEEEECCCCCHHHHHHHHHHHHHHhc--CCEEEEEccHHHHHHHHHHHHhcCCc----ceeeeE-------Eee
Confidence            45689999999999999998877777665544  56899999999999998877665422    211111       111


Q ss_pred             HhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCC
Q psy4275         120 ELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTS  166 (182)
Q Consensus       120 ~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~  166 (182)
                      .......++++|++.+..+....  ..+.+++++|+||+|++..++.
T Consensus        73 ~~~~~~~i~~~t~~~l~~~~~~~--~~~~~~~~vViDE~H~~~~~~~  117 (305)
T d2bmfa2          73 EHTGREIVDLMCHATFTMRLLSP--IRVPNYNLIIMDEAHFTDPASI  117 (305)
T ss_dssp             ---CCCSEEEEEHHHHHHHHTSS--SCCCCCSEEEEESTTCCSHHHH
T ss_pred             cccCccccccCCcHHHHHHHhcC--ccccceeEEEeeeeeecchhhH
Confidence            22345679999999888776542  3467899999999999876653

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=99.70  E-value=3.8e-17  Score=108.99  Aligned_cols=104  Identities=21%  Similarity=0.181  Sum_probs=74.1

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA  122 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  122 (182)
                      .+..++.+|||+|||..+...+...      +.+++|++|+++|++|+++.+++....   ......++..       ..
T Consensus         8 ~~~~ll~apTGsGKT~~~~~~~~~~------~~~vli~~P~~~l~~q~~~~~~~~~~~---~~~~~~~~~~-------~~   71 (136)
T d1a1va1           8 FQVAHLHAPTGSGKSTKVPAAYAAQ------GYKVLVLNPSVAATLGFGAYMSKAHGV---DPNIRTGVRT-------IT   71 (136)
T ss_dssp             CEEEEEECCTTSCTTTHHHHHHHTT------TCCEEEEESCHHHHHHHHHHHHHHHSC---CCEEECSSCE-------EC
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHHHc------CCcEEEEcChHHHHHHHHHHHHHHhhc---cccccccccc-------cc
Confidence            4578999999999998765444332      568999999999999999888776443   2233333221       12


Q ss_pred             CCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCC
Q psy4275         123 KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTS  166 (182)
Q Consensus       123 ~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~  166 (182)
                      ....+.++|.+........    .+++++++|+||+|++.....
T Consensus        72 ~~~~~~~~~~~~~~~~~~~----~~~~~~~vIiDE~H~~~~~~~  111 (136)
T d1a1va1          72 TGSPITYSTYGKFLADGGC----SGGAYDIIICDECHSTDATSI  111 (136)
T ss_dssp             CCCSEEEEEHHHHHHTTGG----GGCCCSEEEEETTTCCSHHHH
T ss_pred             cccceEEEeeeeeccccch----hhhcCCEEEEecccccCHHHH
Confidence            3557889998877654433    477899999999998765443

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=99.65  E-value=1.6e-16  Score=105.71  Aligned_cols=111  Identities=19%  Similarity=0.202  Sum_probs=76.6

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhH
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGK  119 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  119 (182)
                      +.+|++.++++|||+|||.+++..++......  +.++++++|++++++|+.+.+...    +..+....+..       
T Consensus         4 l~~~~~~il~~~tGsGKT~~~~~~~~~~~~~~--~~~vli~~p~~~l~~q~~~~~~~~----~~~~~~~~~~~-------   70 (140)
T d1yksa1           4 LKKGMTTVLDFHPGAGKTRRFLPQILAECARR--RLRTLVLAPTRVVLSEMKEAFHGL----DVKFHTQAFSA-------   70 (140)
T ss_dssp             TSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTTTS----CEEEESSCCCC-------
T ss_pred             HHcCCcEEEEcCCCCChhHHHHHHHHHHhhhc--CceeeeeecchhHHHHHHHHhhhh----hhhhccccccc-------
Confidence            34588999999999999988776666665554  568999999999999887665332    22322111111       


Q ss_pred             HhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccC
Q psy4275         120 ELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMT  165 (182)
Q Consensus       120 ~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~  165 (182)
                      ....+..+.+.|...+......  ...+.+++++|+||||++...+
T Consensus        71 ~~~~~~~~~~~~~~~l~~~~~~--~~~~~~~~lvIiDEaH~~~~~~  114 (140)
T d1yksa1          71 HGSGREVIDAMCHATLTYRMLE--PTRVVNWEVIIMDEAHFLDPAS  114 (140)
T ss_dssp             CCCSSCCEEEEEHHHHHHHHTS--SSCCCCCSEEEETTTTCCSHHH
T ss_pred             ccccccchhhhhHHHHHHHHhc--cccccceeEEEEccccccChhh
Confidence            1123456777887777665433  3467789999999999885544

>d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=99.51  E-value=1.7e-13  Score=102.46  Aligned_cols=139  Identities=18%  Similarity=0.171  Sum_probs=92.4

Q ss_pred             CChHHHHhhhhhhh---------CCCcEEEECCCCChHHHHHHHHHHHhhccCC----CCeeEEEEcCCHHHHHHHHHHH
Q psy4275          28 TPTEIQKAIIPHVL---------NDEDCIGCAKTGSGKTLAFALPILQKWCEDP----YGIFALVLTPTRELAYQIGDQF   94 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~---------~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~----~~~~~lil~p~~~l~~q~~~~~   94 (182)
                      .++|+|.+++..+.         .+.++++...+|.|||+.++..+...+.+..    ...++|||||.. +..||.+++
T Consensus        55 ~Lr~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qaia~l~~l~~~~~~~~~~~~~~LIV~P~s-l~~qW~~Ei  133 (298)
T d1z3ix2          55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPSS-LVRNWYNEV  133 (298)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECHH-HHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHHHHHHHHHHHhcccccCCCCcEEEEccch-hhHHHHHHH
Confidence            58999999997652         2557899999999999986655544443332    234699999965 778999999


Q ss_pred             HHhhccCCceEEEEEcCCchhhhhH---Hh-----cCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCC
Q psy4275          95 LVLGKVMNLRVSIITGGMDMVDQGK---EL-----AKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTS  166 (182)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~---~~-----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~  166 (182)
                      +++.... ..+..++++........   ..     .....++++|.+.+......   +...+++++|+||+|++-+...
T Consensus       134 ~k~~~~~-~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i~sy~~~~~~~~~---l~~~~~~~vI~DEaH~ikn~~s  209 (298)
T d1z3ix2         134 GKWLGGR-VQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAEV---LHKGKVGLVICDEGHRLKNSDN  209 (298)
T ss_dssp             HHHHGGG-CCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTTT---TTTSCCCEEEETTGGGCCTTCH
T ss_pred             HhhcCCc-eeEEEEeCchHHHHHHHHHHhhhccCccccceEEEEeecccccchhc---ccccceeeeecccccccccccc
Confidence            8887642 34445555443221111   11     12457999998888654433   2233577999999999987776


Q ss_pred             hhHHH
Q psy4275         167 LKFFF  171 (182)
Q Consensus       167 ~~~~~  171 (182)
                      .....
T Consensus       210 ~~~~a  214 (298)
T d1z3ix2         210 QTYLA  214 (298)
T ss_dssp             HHHHH
T ss_pred             hhhhh
Confidence            55443

>d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.41  E-value=6e-13  Score=95.83  Aligned_cols=130  Identities=15%  Similarity=0.096  Sum_probs=86.7

Q ss_pred             CChHHHHhhhhhhhC----CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCc
Q psy4275          28 TPTEIQKAIIPHVLN----DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNL  103 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~----~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  103 (182)
                      +++|+|.+++..+..    +..+++..++|.|||..++..+.... ......+++|++|. .+..+|.+++.++...  .
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i~~~~~~~-~~~~~~~~LIv~p~-~l~~~W~~e~~~~~~~--~   87 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAK-KENELTPSLVICPL-SVLKNWEEELSKFAPH--L   87 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHHHHH-HTTCCSSEEEEECS-TTHHHHHHHHHHHCTT--S
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHHHhhhhhh-hcccccccceecch-hhhhHHHHHHHhhccc--c
Confidence            689999999976533    55689999999999999765554443 33334478999994 5568888888877653  3


Q ss_pred             eEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHH
Q psy4275         104 RVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFF  170 (182)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~  170 (182)
                      .+....+.....     ...+.+|+++|.+.+.....-    .--.+.++|+||+|.+.+.......
T Consensus        88 ~~~~~~~~~~~~-----~~~~~~vvi~~~~~~~~~~~l----~~~~~~~vI~DEah~~k~~~s~~~~  145 (230)
T d1z63a1          88 RFAVFHEDRSKI-----KLEDYDIILTTYAVLLRDTRL----KEVEWKYIVIDEAQNIKNPQTKIFK  145 (230)
T ss_dssp             CEEECSSSTTSC-----CGGGSSEEEEEHHHHTTCHHH----HTCCEEEEEEETGGGGSCTTSHHHH
T ss_pred             cceeeccccchh-----hccCcCEEEeeHHHHHhHHHH----hcccceEEEEEhhhcccccchhhhh
Confidence            333332222111     123568999998887543221    1224678999999999887765543

>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=99.32  E-value=2.6e-11  Score=87.64  Aligned_cols=132  Identities=23%  Similarity=0.233  Sum_probs=104.8

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEE
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSI  107 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  107 (182)
                      ++.+.|....-.+..|  -+.+..||-|||+++.+++.-....   |..+-+|+.+..||..=++|+..+.+.+|++|++
T Consensus        80 RhyDVQLiGgi~L~~G--~iaem~TGEGKTL~a~l~a~l~al~---g~~vhvvTvNdyLA~RDae~m~~iy~~lGlsvg~  154 (273)
T d1tf5a3          80 FPFKVQLMGGVALHDG--NIAEMKTGEGKTLTSTLPVYLNALT---GKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVGL  154 (273)
T ss_dssp             CCCHHHHHHHHHHHTT--SEEECCTTSCHHHHHHHHHHHHHTT---SSCEEEEESSHHHHHHHHHHHHHHHHHTTCCEEE
T ss_pred             EEehhHHHHHHHHHhh--hheeecCCCcchhHHHHHHHHHHhc---CCCceEEecCccccchhhhHHhHHHHHcCCCccc
Confidence            5677776666556555  4899999999999988888777666   5579999999999999999999999999999999


Q ss_pred             EEcCCchhhhhHHhcCCCcEEEEChHHH-HHHHhcCC-----CCCCCCccEEEEeccccccccCC
Q psy4275         108 ITGGMDMVDQGKELAKKPHIVIATPGRL-ADHLDTCN-----TFSLNRIKFLVLDEADRLSLMTS  166 (182)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~Ilv~T~~~l-~~~~~~~~-----~~~~~~~~~iI~DE~h~~~~~~~  166 (182)
                      ...+....++...+  .|+|+.+|+..+ .++++..-     ..-.+.+.+.|+||+|.++=+..
T Consensus       155 ~~~~~~~~~r~~~Y--~~di~Ygt~~e~~fDyLrd~~~~~~~~~~~r~~~~aIvDEvDsiliDea  217 (273)
T d1tf5a3         155 NLNSMSKDEKREAY--AADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEA  217 (273)
T ss_dssp             CCTTSCHHHHHHHH--HSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTT
T ss_pred             cccccCHHHHHHHh--hCCceecchhhhhhhhcchhhhcChhhhccCCCCEEEEEcchhhhhhcc
Confidence            88877766655554  679999999887 56776532     12356688999999999875543

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=98.59  E-value=5.7e-08  Score=73.74  Aligned_cols=72  Identities=18%  Similarity=0.114  Sum_probs=53.9

Q ss_pred             CCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHH--HHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhh
Q psy4275          26 VKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPI--LQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLG   98 (182)
Q Consensus        26 ~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~--~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~   98 (182)
                      .....++|++++.....++-.+++||+|+|||......+  +..... ..+.++++.+||..-+..+.+......
T Consensus       146 ~~~~~~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i~~~l~~l~~~~~-~~~~~I~l~ApTgkAA~~L~e~~~~~~  219 (359)
T d1w36d1         146 VSDEINWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMAD-GERCRIRLAAPTGKAAARLTESLGKAL  219 (359)
T ss_dssp             CTTSCCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCS-SCCCCEEEEBSSHHHHHHHHHHHTHHH
T ss_pred             CcccccHHHHHHHHHHcCCeEEEEcCCCCCceehHHHHHHHHHHHHh-ccCCeEEEecCcHHHHHHHHHHHHHHH
Confidence            345788999999999999999999999999998753322  222222 235689999999999888876665443

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=98.40  E-value=4e-07  Score=66.84  Aligned_cols=70  Identities=17%  Similarity=0.037  Sum_probs=52.0

Q ss_pred             CChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccC-CCCeeEEEEcCCHHHHHHHHHHHHHhhc
Q psy4275          28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCED-PYGIFALVLTPTRELAYQIGDQFLVLGK   99 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~-~~~~~~lil~p~~~l~~q~~~~~~~~~~   99 (182)
                      .++|.|.+++..  ...++++.|++|||||.+.+.-+.+.+.+. ....+++++++++++++.+.+.+.+...
T Consensus         1 ~L~~eQ~~av~~--~~~~~lI~g~aGTGKTt~l~~rv~~ll~~~~~~~~~ILvlt~tn~a~~~i~~~~~~~~~   71 (306)
T d1uaaa1           1 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLG   71 (306)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHSC
T ss_pred             CcCHHHHHHHhC--CCCCEEEEeeCCccHHHHHHHHHHHHHHhcCCChhHEEEEeCcHHHHHHHHHHHHHhcC
Confidence            378999999965  245689999999999998765544443331 1234799999999999998877766543

>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=98.20  E-value=2.8e-06  Score=62.75  Aligned_cols=69  Identities=20%  Similarity=0.142  Sum_probs=52.9

Q ss_pred             CCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCC-CCeeEEEEcCCHHHHHHHHHHHHHh
Q psy4275          27 KTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP-YGIFALVLTPTRELAYQIGDQFLVL   97 (182)
Q Consensus        27 ~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~-~~~~~lil~p~~~l~~q~~~~~~~~   97 (182)
                      .++++.|.+++.+.  +.+++|.|++|||||.+++.-+.+.+.+.. ...+++++++++..++.+.+.+...
T Consensus        10 ~~L~~eQ~~~v~~~--~g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~lt~t~~aa~~~~~~~~~~   79 (318)
T d1pjra1          10 AHLNKEQQEAVRTT--EGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSL   79 (318)
T ss_dssp             TTSCHHHHHHHHCC--SSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred             HhCCHHHHHHHhCC--CCCEEEEecCCccHHHHHHHHHHHHHHcCCCCHHHeEeEeccHHHHHHHHHHHHhh
Confidence            35899999999753  457999999999999997765555544332 2348999999999999987777654

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=97.81  E-value=1.2e-05  Score=55.92  Aligned_cols=43  Identities=9%  Similarity=-0.011  Sum_probs=30.1

Q ss_pred             CChHHHHhhhhhhhC----C--Cc-EEEECCCCChHHHHHHHHHHHhhcc
Q psy4275          28 TPTEIQKAIIPHVLN----D--ED-CIGCAKTGSGKTLAFALPILQKWCE   70 (182)
Q Consensus        28 ~~~~~Q~~~~~~~~~----~--~~-~li~~~tg~GKT~~~~~~~~~~~~~   70 (182)
                      +.+|||...+..+.+    +  .+ .++.||.|+|||..+...+-..+..
T Consensus         2 ~~yPw~~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~   51 (207)
T d1a5ta2           2 RWYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQ   51 (207)
T ss_dssp             CCCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHTCS
T ss_pred             CCCcccHHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHHHHHHHhcccc
Confidence            345788777766543    2  24 8899999999999876666555433

>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=97.40  E-value=0.00018  Score=49.72  Aligned_cols=80  Identities=14%  Similarity=0.182  Sum_probs=63.1

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +.++.||+|...-.+...+.+++...  +.++..+||..+..+....+    .++.+|+|+|.-      =+ ..+++++
T Consensus        31 GgQvy~V~p~I~~~e~~~~~l~~~~p--~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~Ttv------IE-vGiDvpn  101 (211)
T d2eyqa5          31 GGQVYYLYNDVENIQKAAERLAELVP--EARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTI------IE-TGIDIPT  101 (211)
T ss_dssp             TCEEEEECCCSSCHHHHHHHHHHHCT--TSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESST------TG-GGSCCTT
T ss_pred             CCeEEEEEcCccchhhHHHHHHHhCC--ceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEehh------hh-hccCCCC
Confidence            67999999998888888888888766  57899999998876555443    357899999932      22 4568999


Q ss_pred             ccEEEEecccccc
Q psy4275         150 IKFLVLDEADRLS  162 (182)
Q Consensus       150 ~~~iI~DE~h~~~  162 (182)
                      ..++|+.+|+++.
T Consensus       102 A~~iiI~~a~rfG  114 (211)
T d2eyqa5         102 ANTIIIERADHFG  114 (211)
T ss_dssp             EEEEEETTTTSSC
T ss_pred             CcEEEEecchhcc
Confidence            9999999999854

>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=97.34  E-value=0.00015  Score=50.24  Aligned_cols=85  Identities=26%  Similarity=0.262  Sum_probs=46.2

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC--HHHHHHHHHHHHHhhccCCceEEEEEcCCchhhh-----
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT--RELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQ-----  117 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~--~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----  117 (182)
                      -++++||||+|||++..-.+... ..+  +.++.+++..  +.-+   .+.++.+.+..++.+............     
T Consensus        12 vi~lvGp~GvGKTTTiaKLA~~~-~~~--g~kV~lit~Dt~R~gA---~eQL~~~a~~l~v~~~~~~~~~~~~~~~~~~~   85 (207)
T d1ls1a2          12 LWFLVGLQGSGKTTTAAKLALYY-KGK--GRRPLLVAADTQRPAA---REQLRLLGEKVGVPVLEVMDGESPESIRRRVE   85 (207)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHHH-HHT--TCCEEEEECCSSCHHH---HHHHHHHHHHHTCCEEECCTTCCHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH-HHC--CCcEEEEecccccchH---HHHHHHHHHhcCCccccccccchhhHHHHHHH
Confidence            35668999999998865544433 333  3456666542  3332   234555555556776665544332211     


Q ss_pred             -hHHhcCCCcEEEEChHHH
Q psy4275         118 -GKELAKKPHIVIATPGRL  135 (182)
Q Consensus       118 -~~~~~~~~~Ilv~T~~~l  135 (182)
                       .....+.--|+|-|+++.
T Consensus        86 ~~~~~~~~d~vlIDTaGr~  104 (207)
T d1ls1a2          86 EKARLEARDLILVDTAGRL  104 (207)
T ss_dssp             HHHHHHTCCEEEEECCCCS
T ss_pred             HHHhhccCcceeecccccc
Confidence             112223345778888754

>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=97.27  E-value=0.0014  Score=45.24  Aligned_cols=85  Identities=20%  Similarity=0.176  Sum_probs=46.4

Q ss_pred             EEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHH-----
Q psy4275          46 CIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKE-----  120 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----  120 (182)
                      ++++||||+|||++..-.+. ++..+  +.++.+++....-+- -.+.++.+.+..++.+...............     
T Consensus        12 i~lvGptGvGKTTTiAKLA~-~~~~~--g~kV~lit~Dt~R~g-A~eQL~~~a~~l~v~~~~~~~~~d~~~~l~~~~~~a   87 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTIGKLAR-QFEQQ--GKSVMLAAGDTFRAA-AVEQLQVWGQRNNIPVIAQHTGADSASVIFDAIQAA   87 (211)
T ss_dssp             EEEECCTTSCHHHHHHHHHH-HHHTT--TCCEEEECCCTTCHH-HHHHHHHHHHHTTCCEECCSTTCCHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH-HHHHC--CCcEEEEeccccccc-chhhhhhhhhhcCCcccccccCCCHHHHHHHHHHHH
Confidence            45689999999998665443 33333  345666654322111 1335556666667777655544433222111     


Q ss_pred             hcCCC-cEEEEChHH
Q psy4275         121 LAKKP-HIVIATPGR  134 (182)
Q Consensus       121 ~~~~~-~Ilv~T~~~  134 (182)
                      ..+++ -|+|-|+++
T Consensus        88 ~~~~~d~ilIDTaGr  102 (211)
T d2qy9a2          88 KARNIDVLIADTAGR  102 (211)
T ss_dssp             HHTTCSEEEECCCCC
T ss_pred             HHcCCCEEEeccCCC
Confidence            11233 478899874

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.26  E-value=0.0003  Score=49.57  Aligned_cols=48  Identities=17%  Similarity=0.108  Sum_probs=32.2

Q ss_pred             CCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHH
Q psy4275           6 KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPIL   65 (182)
Q Consensus         6 ~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~   65 (182)
                      ++|+++.-.+++.+.+...--.            -....+.++.||+|+|||..+...+-
T Consensus         8 ~~~~diig~~~~~~~L~~~~~~------------~~~~~~lll~Gp~G~GKTt~~~~la~   55 (252)
T d1sxje2           8 KSLNALSHNEELTNFLKSLSDQ------------PRDLPHLLLYGPNGTGKKTRCMALLE   55 (252)
T ss_dssp             CSGGGCCSCHHHHHHHHTTTTC------------TTCCCCEEEECSTTSSHHHHHHTHHH
T ss_pred             CCHHHccCcHHHHHHHHHHHHc------------CCCCCeEEEECCCCCCHHHHHHHHHH
Confidence            4677877778887777643211            11234689999999999998644333

>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=97.23  E-value=0.0009  Score=46.16  Aligned_cols=86  Identities=20%  Similarity=0.145  Sum_probs=45.9

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC--HHH-HHHHHHHHHHhhccCCceEEEEEcCCchhhhhH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT--REL-AYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGK  119 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~--~~l-~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  119 (182)
                      ++-++++||||+|||++..-.+.+ +..+  +.++.+++-.  +.- .+|    ++.+.+..++.+..............
T Consensus         6 ~~vi~lvGptGvGKTTTiaKLA~~-~~~~--g~kV~lit~Dt~R~gA~eQ----L~~~a~~l~i~~~~~~~~~d~~~~~~   78 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTIAKLGRY-YQNL--GKKVMFCAGDTFRAAGGTQ----LSEWGKRLSIPVIQGPEGTDPAALAY   78 (207)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHHH-HHTT--TCCEEEECCCCSSTTHHHH----HHHHHHHHTCCEECCCTTCCHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHH-HHHC--CCcEEEEEeccccccchhh----HhhcccccCceEEeccCCccHHHHHH
Confidence            345677999999999986654433 3333  3456666533  333 344    34444444666554443333222111


Q ss_pred             ------HhcCCCcEEEEChHHH
Q psy4275         120 ------ELAKKPHIVIATPGRL  135 (182)
Q Consensus       120 ------~~~~~~~Ilv~T~~~l  135 (182)
                            ...+.--|+|-|+++.
T Consensus        79 ~~~~~~~~~~~d~ilIDTaGr~  100 (207)
T d1okkd2          79 DAVQAMKARGYDLLFVDTAGRL  100 (207)
T ss_dssp             HHHHHHHHHTCSEEEECCCCCC
T ss_pred             HHHHHHHHCCCCEEEcCccccc
Confidence                  1123345788898853

>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=97.19  E-value=0.0027  Score=43.88  Aligned_cols=83  Identities=22%  Similarity=0.308  Sum_probs=43.2

Q ss_pred             EEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc-C-CHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhh-----h
Q psy4275          46 CIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT-P-TRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQ-----G  118 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~-p-~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~  118 (182)
                      ++++||||+|||++..-.+.+ +..+  +.++.+++ . .+.-+.   +.++.+.+..++.+.....+......     .
T Consensus        14 i~lvGptGvGKTTTiAKLAa~-~~~~--~~kV~lit~Dt~R~gA~---eQL~~~a~~l~i~~~~~~~~~d~~~~~~~~~~   87 (213)
T d1vmaa2          14 IMVVGVNGTGKTTSCGKLAKM-FVDE--GKSVVLAAADTFRAAAI---EQLKIWGERVGATVISHSEGADPAAVAFDAVA   87 (213)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH-HHHT--TCCEEEEEECTTCHHHH---HHHHHHHHHHTCEEECCSTTCCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH-HHHC--CCceEEEeecccccchh---HHHHHHhhhcCccccccCCCCcHHHHHHHHHH
Confidence            567899999999986544443 3333  33454444 2 333332   24445555556666554433322111     1


Q ss_pred             HHhcCC-CcEEEEChHH
Q psy4275         119 KELAKK-PHIVIATPGR  134 (182)
Q Consensus       119 ~~~~~~-~~Ilv~T~~~  134 (182)
                      ....++ --|+|-|+++
T Consensus        88 ~~~~~~~d~ilIDTaGr  104 (213)
T d1vmaa2          88 HALARNKDVVIIDTAGR  104 (213)
T ss_dssp             HHHHTTCSEEEEEECCC
T ss_pred             HHHHcCCCEEEEecccc
Confidence            111223 3488899973

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=97.19  E-value=0.0056  Score=42.71  Aligned_cols=46  Identities=15%  Similarity=0.099  Sum_probs=28.8

Q ss_pred             CCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCC---CcEEEECCCCChHHHHHHHHHHH
Q psy4275           6 KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLND---EDCIGCAKTGSGKTLAFALPILQ   66 (182)
Q Consensus         6 ~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~---~~~li~~~tg~GKT~~~~~~~~~   66 (182)
                      ++|+++-..+.+.+.+...               +.++   +..++.||+|+|||..+...+-.
T Consensus         9 ~~~~dlig~~~~~~~L~~~---------------i~~~~~~~~~Ll~Gp~G~GKtt~a~~~~~~   57 (239)
T d1njfa_           9 QTFADVVGQEHVLTALANG---------------LSLGRIHHAYLFSGTRGVGKTSIARLLAKG   57 (239)
T ss_dssp             SSGGGSCSCHHHHHHHHHH---------------HHTTCCCSEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCHHHccChHHHHHHHHHH---------------HHcCCCCeeEEEECCCCCcHHHHHHHHHHH
Confidence            4566665566666655421               2222   24789999999999987644433

>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=97.07  E-value=0.0013  Score=43.97  Aligned_cols=76  Identities=12%  Similarity=0.169  Sum_probs=59.4

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhc----CCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA----KKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +.++||.|+++..++.+++.+...    |+++..++|+.+..++...+.    ++.+|+|+|.-      .. ..++.++
T Consensus        31 g~r~lvfc~t~~~~~~l~~~L~~~----Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~v------~~-~GiDip~   99 (174)
T d1c4oa2          31 GERTLVTVLTVRMAEELTSFLVEH----GIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINL------LR-EGLDIPE   99 (174)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCC------CC-TTCCCTT
T ss_pred             CCcEEEEEcchhHHHHHHHHHHhc----CCceEEEecccchHHHHHHHHHHHCCCeEEEEeeee------ee-eeccCCC
Confidence            568999999999998888777664    899999999998766655443    47899999922      22 6678999


Q ss_pred             ccEEEEecccc
Q psy4275         150 IKFLVLDEADR  160 (182)
Q Consensus       150 ~~~iI~DE~h~  160 (182)
                      ++++|+=.++.
T Consensus       100 V~~Vi~~~~~~  110 (174)
T d1c4oa2         100 VSLVAILDADK  110 (174)
T ss_dssp             EEEEEETTTTS
T ss_pred             CcEEEEecccc
Confidence            99988865554

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.05  E-value=0.00038  Score=48.40  Aligned_cols=23  Identities=22%  Similarity=0.135  Sum_probs=18.2

Q ss_pred             CcEEEECCCCChHHHHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQ   66 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~   66 (182)
                      .+.++.||+|+|||..+...+-.
T Consensus        37 ~~~ll~Gp~G~GKTt~a~~la~~   59 (224)
T d1sxjb2          37 PHMIISGMPGIGKTTSVHCLAHE   59 (224)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCchhhHHHHHHH
Confidence            47999999999999987554433

>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=97.02  E-value=0.003  Score=43.71  Aligned_cols=21  Identities=24%  Similarity=0.124  Sum_probs=17.2

Q ss_pred             CcEEEECCCCChHHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~   64 (182)
                      .+.++.||+|+|||..+-..+
T Consensus        46 ~~lll~Gp~G~GKTtla~~ia   66 (231)
T d1iqpa2          46 PHLLFAGPPGVGKTTAALALA   66 (231)
T ss_dssp             CEEEEESCTTSSHHHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHH
Confidence            579999999999998865443

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.00  E-value=0.0013  Score=45.03  Aligned_cols=51  Identities=10%  Similarity=-0.144  Sum_probs=29.6

Q ss_pred             HHhhhhhhhC---CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275          33 QKAIIPHVLN---DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus        33 Q~~~~~~~~~---~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      |.+.+..+.+   +.+.+++||.|+|||..+....-.........+-++++.|.
T Consensus         2 ~~~~l~~~i~~~~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~~~i~~~   55 (198)
T d2gnoa2           2 QLETLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPE   55 (198)
T ss_dssp             HHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCS
T ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHhccccCCCCEEEEeCC
Confidence            3444444433   56899999999999998765443221111112235666664

>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=96.88  E-value=0.0023  Score=44.18  Aligned_cols=83  Identities=23%  Similarity=0.245  Sum_probs=38.9

Q ss_pred             EEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcC--CHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhH----
Q psy4275          46 CIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTP--TRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGK----  119 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p--~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----  119 (182)
                      ++++||||+|||++..-.+.. +..+  +.++.+++-  .+.-+.   +.++.+.+..++.+..............    
T Consensus        15 i~lvGptGvGKTTTiAKLA~~-~~~~--g~kV~lit~Dt~R~ga~---eQL~~~a~~l~v~~~~~~~~~~~~~~~~~a~~   88 (211)
T d1j8yf2          15 IMLVGVQGTGKATTAGKLAYF-YKKK--GFKVGLVGADVYRPAAL---EQLQQLGQQIGVPVYGEPGEKDVVGIAKRGVE   88 (211)
T ss_dssp             EEEECSCCC----HHHHHHHH-HHHT--TCCEEEEECCCSSHHHH---HHHHHHHHHHTCCEECCTTCCCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH-HHHC--CCceEEEEeeccccchh---HHHHHhccccCcceeecccchhhhHHHHHHHH
Confidence            456899999999986544433 3333  335555554  233322   2344444545666654443333211111    


Q ss_pred             --HhcCCCcEEEEChHH
Q psy4275         120 --ELAKKPHIVIATPGR  134 (182)
Q Consensus       120 --~~~~~~~Ilv~T~~~  134 (182)
                        ...+.--|+|-|+++
T Consensus        89 ~~~~~~~d~IlIDTaGr  105 (211)
T d1j8yf2          89 KFLSEKMEIIIVDTAGR  105 (211)
T ss_dssp             HHHHTTCSEEEEECCCS
T ss_pred             HhhccCCceEEEecCCc
Confidence              122234578888874

>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=96.85  E-value=0.0018  Score=49.29  Aligned_cols=66  Identities=20%  Similarity=0.200  Sum_probs=46.1

Q ss_pred             ChHHHHhhhhh----hhCC-CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhcc
Q psy4275          29 PTEIQKAIIPH----VLND-EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKV  100 (182)
Q Consensus        29 ~~~~Q~~~~~~----~~~~-~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~  100 (182)
                      |..-|=+++..    +.+| ++.++.|-||+|||..+. .++...     +..++||+|+...|.++++.++.+...
T Consensus        12 p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~~iA-~l~~~~-----~rp~LVVt~n~~~A~qL~~dL~~~l~~   82 (413)
T d1t5la1          12 PQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTIS-NVIAQV-----NKPTLVIAHNKTLAGQLYSELKEFFPH   82 (413)
T ss_dssp             CCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHHHHH-HHHHHH-----TCCEEEECSSHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHHHHH-HHHHHh-----CCCEEEEeCCHHHHHHHHHHHHHHcCC
Confidence            44444444433    3334 568889999999997743 333322     235999999999999999999988654

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=96.81  E-value=0.0025  Score=42.89  Aligned_cols=76  Identities=13%  Similarity=0.223  Sum_probs=58.6

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhc----CCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA----KKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +.++++.++++.-++.++..++.    .|+++..++|+.+..++...+.    +..+|+|+|.-      .. ..+++.+
T Consensus        31 ~~~~iif~~~~~~~~~~~~~l~~----~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTdv------~~-rGiDip~   99 (181)
T d1t5la2          31 NERTLVTTLTKKMAEDLTDYLKE----AGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINL------LR-EGLDIPE   99 (181)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHT----TTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESCC------CS-SSCCCTT
T ss_pred             CCeEEEEeehhhhhHHHHHHHHh----CCcceeEecCCccHHHHHHHHHHHHCCCCCEEEehhH------HH-ccCCCCC
Confidence            45899999999988877666654    4899999999998766655443    48899999932      22 6678999


Q ss_pred             ccEEEEecccc
Q psy4275         150 IKFLVLDEADR  160 (182)
Q Consensus       150 ~~~iI~DE~h~  160 (182)
                      +++||.-++..
T Consensus       100 v~~VI~~d~p~  110 (181)
T d1t5la2         100 VSLVAILDADK  110 (181)
T ss_dssp             EEEEEETTTTS
T ss_pred             CCEEEEecCCc
Confidence            99998776654

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=96.66  E-value=0.0023  Score=47.09  Aligned_cols=53  Identities=25%  Similarity=0.246  Sum_probs=33.5

Q ss_pred             ChHHHHhhhhh-hhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHH
Q psy4275          29 PTEIQKAIIPH-VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRE   85 (182)
Q Consensus        29 ~~~~Q~~~~~~-~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~   85 (182)
                      ..+.+...+.. +..++|++++|+||+|||+. +-+++..+..   ..+++.+-.+.+
T Consensus       151 ~~~~~~~~l~~~v~~~~nili~G~tgSGKTT~-l~al~~~i~~---~~rivtiEd~~E  204 (323)
T d1g6oa_         151 NKEQAISAIKDGIAIGKNVIVCGGTGSGKTTY-IKSIMEFIPK---EERIISIEDTEE  204 (323)
T ss_dssp             SHHHHHHHHHHHHHHTCCEEEEESTTSSHHHH-HHHHGGGSCT---TCCEEEEESSCC
T ss_pred             cHHHHHHHHHHHHHhCCCEEEEeeccccchHH-HHHHhhhccc---ccceeeccchhh
Confidence            34445555544 45588999999999999998 4555555443   335555544433

>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=96.59  E-value=0.0062  Score=40.02  Aligned_cols=73  Identities=12%  Similarity=0.160  Sum_probs=54.2

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      ..++||.|.++.-++++++.+...    ++++..++|+.+..++...+    .++.+|+|+|.-      .. +.+++.+
T Consensus        27 ~~k~iIF~~s~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Tdv------~~-rGiDi~~   95 (162)
T d1fuka_          27 VTQAVIFCNTRRKVEELTTKLRND----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDL------LA-RGIDVQQ   95 (162)
T ss_dssp             CSCEEEEESSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGG------GT-TTCCCCS
T ss_pred             CCcEEEEEEEEchHHHHHHHHhhc----CceEEEeccCCchhhHHHHHHHHhhcccceeecccc------cc-ccccCCC
Confidence            447999999999999887776554    78899999998876555443    347889999943      22 5677888


Q ss_pred             ccEEEEec
Q psy4275         150 IKFLVLDE  157 (182)
Q Consensus       150 ~~~iI~DE  157 (182)
                      ++++|.=+
T Consensus        96 v~~VI~~d  103 (162)
T d1fuka_          96 VSLVINYD  103 (162)
T ss_dssp             CSEEEESS
T ss_pred             ceEEEEec
Confidence            88777643

>d2b8ta1 c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-terminal domain {Ureaplasma urealyticum [TaxId: 2130]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

Probab=96.45  E-value=0.0033  Score=40.40  Aligned_cols=89  Identities=13%  Similarity=0.101  Sum_probs=50.8

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCC
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKK  124 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  124 (182)
                      =-++.||+.+|||.-.+..+-.....   +.+++++-|...-.            . +-.+....|.           ..
T Consensus         4 L~~i~GpMfsGKTteLi~~~~~~~~~---~~kv~~ikp~~D~R------------~-~~~i~s~~g~-----------~~   56 (139)
T d2b8ta1           4 IEFITGPMFAGKTAELIRRLHRLEYA---DVKYLVFKPKIDTR------------S-IRNIQSRTGT-----------SL   56 (139)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHHT---TCCEEEEEECCCGG------------G-CSSCCCCCCC-----------SS
T ss_pred             EEEEEccccCHHHHHHHHHHHHHHHC---CCcEEEEEEccccc------------c-cceEEcccCc-----------ee
Confidence            35789999999999855444333222   45788888864320            0 0011110110           12


Q ss_pred             CcEEEEChHHHHHHHhcCCCCCCCCccEEEEecccccc
Q psy4275         125 PHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLS  162 (182)
Q Consensus       125 ~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~  162 (182)
                      ..+.+.+...+.+.+....  ...+.++|.+||+|-+.
T Consensus        57 ~~~~~~~~~~~~~~~~~~~--~~~~~dvI~IDE~QFf~   92 (139)
T d2b8ta1          57 PSVEVESAPEILNYIMSNS--FNDETKVIGIDEVQFFD   92 (139)
T ss_dssp             CCEEESSTHHHHHHHHSTT--SCTTCCEEEECSGGGSC
T ss_pred             eeEEeccchhhHHHHHhhc--cccCcCEEEechhhhcc
Confidence            2355666666666655422  23467899999999764

>d1xbta1 c.37.1.24 (A:18-150) Thymidine kinase, TK1, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.36  E-value=0.0041  Score=39.61  Aligned_cols=39  Identities=13%  Similarity=0.012  Sum_probs=26.1

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRE   85 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~   85 (182)
                      .=.++.||+.+|||.-.+..+-.....   +.+++++-|...
T Consensus         3 ~L~li~GpMfsGKTt~Li~~~~~~~~~---g~~v~~ikp~~D   41 (133)
T d1xbta1           3 QIQVILGPMFSGKSTELMRRVRRFQIA---QYKCLVIKYAKD   41 (133)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHHTT---TCCEEEEEETTC
T ss_pred             EEEEEEecccCHHHHHHHHHHHHHHHc---CCcEEEEecccc
Confidence            345789999999999754444333233   457888888643

>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=96.33  E-value=0.016  Score=38.18  Aligned_cols=73  Identities=7%  Similarity=0.053  Sum_probs=53.3

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +.++||.|+++.-++.++..+...    ++.+..++|+.+..++...+    .+..+|+|+|..      - ...+++.+
T Consensus        32 ~~k~iVF~~~~~~~~~l~~~L~~~----g~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~Td~------~-~~Gid~~~  100 (171)
T d1s2ma2          32 INQAIIFCNSTNRVELLAKKITDL----GYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDL------L-TRGIDIQA  100 (171)
T ss_dssp             CSEEEEECSSHHHHHHHHHHHHHH----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSC------S-SSSCCCTT
T ss_pred             CCceEEEEeeeehhhHhHHhhhcc----cccccccccccchhhhhhhhhhcccCccccccchhH------h-hhccccce
Confidence            458999999999988888777665    78899999988865554433    247889999943      1 25567777


Q ss_pred             ccEEEEec
Q psy4275         150 IKFLVLDE  157 (182)
Q Consensus       150 ~~~iI~DE  157 (182)
                      ++++|.=+
T Consensus       101 v~~VI~~d  108 (171)
T d1s2ma2         101 VNVVINFD  108 (171)
T ss_dssp             EEEEEESS
T ss_pred             eEEEEecC
Confidence            77776543

>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=96.17  E-value=0.0096  Score=39.28  Aligned_cols=73  Identities=11%  Similarity=0.098  Sum_probs=50.7

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +.++||.|+++.-++.+.+.+.+.    ++++..++|+.+..++...+    .+..+|+|+|..      .. ..+++..
T Consensus        27 ~~k~iIF~~~~~~~~~l~~~L~~~----~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T~~------~~-~Gid~~~   95 (168)
T d1t5ia_          27 FNQVVIFVKSVQRCIALAQLLVEQ----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNL------FG-RGMDIER   95 (168)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSC------CS-TTCCGGG
T ss_pred             CCeEEEEEeeeecchhhhhhhccc----cccccccccccchhhhhhhhhhhccccceeeecccc------cc-chhhccc
Confidence            347999999999988877776554    78899999998776554333    346889999932      11 4456666


Q ss_pred             ccEEEEec
Q psy4275         150 IKFLVLDE  157 (182)
Q Consensus       150 ~~~iI~DE  157 (182)
                      ++++|.=+
T Consensus        96 ~~~vi~~~  103 (168)
T d1t5ia_          96 VNIAFNYD  103 (168)
T ss_dssp             CSEEEESS
T ss_pred             chhhhhhh
Confidence            66665443

>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=96.17  E-value=0.007  Score=46.04  Aligned_cols=54  Identities=20%  Similarity=0.088  Sum_probs=40.4

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCC---------CCeeEEEEcCCHHHHHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDP---------YGIFALVLTPTRELAYQIGDQFLV   96 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~---------~~~~~lil~p~~~l~~q~~~~~~~   96 (182)
                      ..+.++.|+.|||||.+...-+++.+....         .-.++++|+=|+.-+.++.+.+..
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            567899999999999987766666664321         113689999999988888766544

>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=96.12  E-value=0.0048  Score=46.69  Aligned_cols=40  Identities=20%  Similarity=0.176  Sum_probs=26.4

Q ss_pred             ChHHHHhhhhhhhC--CCcEEEECCCCChHHHHHHHHHHHhhc
Q psy4275          29 PTEIQKAIIPHVLN--DEDCIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        29 ~~~~Q~~~~~~~~~--~~~~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      +.+.|.+.+..+..  +.-+++.||||+|||+.. ..++..+.
T Consensus       142 ~~~~~~~~l~~l~~~~~GliLvtGpTGSGKSTTl-~~~l~~~~  183 (401)
T d1p9ra_         142 MTAHNHDNFRRLIKRPHGIILVTGPTGSGKSTTL-YAGLQELN  183 (401)
T ss_dssp             CCHHHHHHHHHHHTSSSEEEEEECSTTSCHHHHH-HHHHHHHC
T ss_pred             ccHHHHHHHHHHHhhhhceEEEEcCCCCCccHHH-HHHhhhhc
Confidence            44555555655554  345788899999999984 44555443

>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=96.02  E-value=0.017  Score=39.52  Aligned_cols=33  Identities=15%  Similarity=0.081  Sum_probs=20.5

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEE
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVL   80 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil   80 (182)
                      .+++.||+|+|||--.. ++...+.+.  +..++++
T Consensus        38 ~l~l~G~~G~GKTHLl~-A~~~~~~~~--~~~~~~~   70 (213)
T d1l8qa2          38 PIFIYGSVGTGKTHLLQ-AAGNEAKKR--GYRVIYS   70 (213)
T ss_dssp             SEEEECSSSSSHHHHHH-HHHHHHHHT--TCCEEEE
T ss_pred             cEEEECCCCCcHHHHHH-HHHHHhccC--ccceEEe
Confidence            48999999999996533 333333333  3345554

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=95.98  E-value=0.019  Score=38.92  Aligned_cols=70  Identities=13%  Similarity=0.173  Sum_probs=51.3

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +.++||.++++..++.+++.+...    ++.+..++|+.+..++...+    .++.+|+|+|..      .. ..+++.+
T Consensus        30 ~~~~IIF~~t~~~~~~l~~~l~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd~------~~-~GiD~p~   98 (200)
T d1oywa3          30 GKSGIIYCNSRAKVEDTAARLQSK----GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVA------FG-MGINKPN   98 (200)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTT------SC-TTTCCTT
T ss_pred             CCCEEEEEeeehhhHHhhhhhccC----CceeEEecCCCcHHHHHHHHHHHhcccceEEEecch------hh-hccCCCC
Confidence            457999999999988887766654    78899999988765544333    247789999942      12 5567778


Q ss_pred             ccEEE
Q psy4275         150 IKFLV  154 (182)
Q Consensus       150 ~~~iI  154 (182)
                      +++||
T Consensus        99 v~~VI  103 (200)
T d1oywa3          99 VRFVV  103 (200)
T ss_dssp             CCEEE
T ss_pred             CCEEE
Confidence            87776

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=95.94  E-value=0.0044  Score=46.28  Aligned_cols=19  Identities=37%  Similarity=0.412  Sum_probs=16.4

Q ss_pred             CCcEEEECCCCChHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~   61 (182)
                      -.++++.||||+|||..+-
T Consensus        68 ~~niLfiGPTGvGKTElAk   86 (364)
T d1um8a_          68 KSNILLIGPTGSGKTLMAQ   86 (364)
T ss_dssp             CCCEEEECCTTSSHHHHHH
T ss_pred             CcceeeeCCCCccHHHHHH
Confidence            4689999999999998863

>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=95.94  E-value=0.013  Score=40.57  Aligned_cols=53  Identities=13%  Similarity=-0.016  Sum_probs=31.2

Q ss_pred             CCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHHHH
Q psy4275           6 KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ   66 (182)
Q Consensus         6 ~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~~~   66 (182)
                      ++|+++.-.+.+.+.+...-        ......-...++.++.||+|+|||..+-..+-+
T Consensus         6 ~~~~divGqe~~~~~l~~~i--------~~~~~~~~~~~~~L~~GPpGtGKT~lA~~la~~   58 (238)
T d1in4a2           6 KSLDEFIGQENVKKKLSLAL--------EAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASE   58 (238)
T ss_dssp             SSGGGCCSCHHHHHHHHHHH--------HHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHH
T ss_pred             CcHHHcCChHHHHHHHHHHH--------HHHHhcCCCCCeEEEECCCCCcHHHHHHHHHhc
Confidence            46777766666666554210        000000011358999999999999987554443

>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=95.85  E-value=0.0046  Score=40.60  Aligned_cols=27  Identities=15%  Similarity=0.079  Sum_probs=20.0

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhccC
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWCED   71 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~~~   71 (182)
                      +++++.||+|+|||+.+. .++..+...
T Consensus         2 k~v~ItG~~GtGKTtl~~-~i~~~l~~~   28 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIH-KASEVLKSS   28 (189)
T ss_dssp             CCEEEESCCSSCHHHHHH-HHHHHHHHT
T ss_pred             cEEEEECCCCCcHHHHHH-HHHHHHHHC
Confidence            689999999999999644 444544444

>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=95.76  E-value=0.022  Score=37.52  Aligned_cols=93  Identities=11%  Similarity=0.110  Sum_probs=61.2

Q ss_pred             EEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----c
Q psy4275          47 IGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----A  122 (182)
Q Consensus        47 li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~  122 (182)
                      .+.-+..-.|... +..++...    .+.++++.|.++.-++.+++.+...    ++.+..++|+.+..++...+    .
T Consensus        12 ~v~v~~~~~K~~~-L~~ll~~~----~~~k~iiF~~~~~~~~~~~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~fk~   82 (168)
T d2j0sa2          12 FVAVEREEWKFDT-LCDLYDTL----TITQAVIFCNTKRKVDWLTEKMREA----NFTVSSMHGDMPQKERESIMKEFRS   82 (168)
T ss_dssp             EEEESSTTHHHHH-HHHHHHHH----TSSEEEEECSSHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHH
T ss_pred             EEEecChHHHHHH-HHHHHHhC----CCCceEEEeeeHHHHHHHHHHhhhc----ccchhhhhhhhhHHHHHHHHHHHhc
Confidence            3333444456433 33333332    2458999999999998887776654    67888999998876654443    2


Q ss_pred             CCCcEEEEChHHHHHHHhcCCCCCCCCccEEEE
Q psy4275         123 KKPHIVIATPGRLADHLDTCNTFSLNRIKFLVL  155 (182)
Q Consensus       123 ~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~  155 (182)
                      +..+|+|+|.-      -. +.+++.+++++|.
T Consensus        83 g~~~iLv~Td~------~~-rGiDi~~v~~VIn  108 (168)
T d2j0sa2          83 GASRVLISTDV------WA-RGLDVPQVSLIIN  108 (168)
T ss_dssp             TSSCEEEECGG------GS-SSCCCTTEEEEEE
T ss_pred             CCccEEeccch------hc-ccccccCcceEEE
Confidence            46789999943      22 5667778877664

>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=95.74  E-value=0.055  Score=36.83  Aligned_cols=21  Identities=19%  Similarity=0.153  Sum_probs=17.1

Q ss_pred             cEEEECCCCChHHHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALPIL   65 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~   65 (182)
                      +.++.||+|+|||..+...+-
T Consensus        37 ~lLl~Gp~G~GKttl~~~la~   57 (227)
T d1sxjc2          37 HLLFYGPPGTGKTSTIVALAR   57 (227)
T ss_dssp             CEEEECSSSSSHHHHHHHHHH
T ss_pred             eEEEECCCCCChhHHHHHHHH
Confidence            689999999999987655443

>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=95.52  E-value=0.014  Score=40.73  Aligned_cols=25  Identities=16%  Similarity=0.288  Sum_probs=19.0

Q ss_pred             CcEEEECCCCChHHHHHHHHHHHhhc
Q psy4275          44 EDCIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      .++++.||+|+|||.++ -.+...+.
T Consensus        44 ~~lll~GppGtGKT~l~-~~l~~~l~   68 (276)
T d1fnna2          44 PRATLLGRPGTGKTVTL-RKLWELYK   68 (276)
T ss_dssp             CEEEEECCTTSSHHHHH-HHHHHHHT
T ss_pred             CceEEECCCCCCHHHHH-HHHHHHHh
Confidence            58999999999999885 34444443

>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=95.37  E-value=0.0059  Score=39.21  Aligned_cols=23  Identities=13%  Similarity=0.042  Sum_probs=18.4

Q ss_pred             CCcEEEECCCCChHHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPIL   65 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~   65 (182)
                      ++++++.||+|+|||+++-...-
T Consensus         2 ~k~I~l~G~~GsGKSTvak~La~   24 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIGRQLAQ   24 (169)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999998654443

>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=95.30  E-value=0.056  Score=34.77  Aligned_cols=56  Identities=21%  Similarity=0.332  Sum_probs=41.7

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHh----cCCCcEEEEChH
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL----AKKPHIVIATPG  133 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~  133 (182)
                      +.++||.|+++.-++.++..++..    ++.+..++|+.+..++...+    .+...|+|+|..
T Consensus        28 ~~k~IIF~~s~~~~~~l~~~L~~~----g~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~~   87 (155)
T d1hv8a2          28 EFYGLVFCKTKRDTKELASMLRDI----GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDV   87 (155)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTT
T ss_pred             CCCEEEEECchHHHHHHHhhhccc----ccccccccccchhhhhhhhhhhhhcccceeeeehhH
Confidence            447999999999988877777653    78899999987765554333    346789999843

>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=95.21  E-value=0.026  Score=42.61  Aligned_cols=67  Identities=31%  Similarity=0.376  Sum_probs=45.2

Q ss_pred             CChHHHHhhhhh----hhCCCc-EEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhcc
Q psy4275          28 TPTEIQKAIIPH----VLNDED-CIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKV  100 (182)
Q Consensus        28 ~~~~~Q~~~~~~----~~~~~~-~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~  100 (182)
                      +|+.-|-+++..    +.+|.. ..+.|.+|++|+.+.. .+... .    +..++||+|+...|.++++.++.+...
T Consensus         8 ~p~~dqp~aI~~l~~~L~~g~~~~~L~GlsgS~ka~~~A-~l~~~-~----~rp~LvVt~~~~~A~~l~~dL~~~l~~   79 (408)
T d1c4oa1           8 SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMA-KVIEA-L----GRPALVLAPNKILAAQLAAEFRELFPE   79 (408)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHH-HHHHH-H----TCCEEEEESSHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEecCCCCHHHHHHH-HHHHH-h----CCCEEEEeCCHHHHHHHHHHHHHhcCc
Confidence            344444444443    444554 5788999999997643 23322 2    225899999999999999999988653

>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=94.96  E-value=0.008  Score=41.69  Aligned_cols=22  Identities=23%  Similarity=0.120  Sum_probs=18.0

Q ss_pred             CcEEEECCCCChHHHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPIL   65 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~~   65 (182)
                      +++++.||+|+|||..+-..+-
T Consensus        36 ~~~Ll~GPpG~GKTtla~~la~   57 (239)
T d1ixsb2          36 EHLLLFGPPGLGKTTLAHVIAH   57 (239)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999988755443

>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=94.95  E-value=0.015  Score=43.91  Aligned_cols=43  Identities=14%  Similarity=0.215  Sum_probs=27.8

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTREL   86 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l   86 (182)
                      ...+|+++.|+||+|||..+ ..++..+...  +..++|+-|..++
T Consensus        48 ~~~~H~~I~G~tGsGKT~~l-~~li~~~~~~--g~~~iiiD~kge~   90 (433)
T d1e9ra_          48 AEPRHLLVNGATGTGKSVLL-RELAYTGLLR--GDRMVIVDPNGDM   90 (433)
T ss_dssp             GGGGCEEEEECTTSSHHHHH-HHHHHHHHHT--TCEEEEEEETTHH
T ss_pred             cccceEEEEeCCCCcHHHHH-HHHHHHHHhC--CCCEEEEeCChhH
Confidence            34679999999999999874 3344444443  3345555555443

>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=94.94  E-value=0.021  Score=40.10  Aligned_cols=60  Identities=18%  Similarity=0.166  Sum_probs=35.5

Q ss_pred             CCccCCccCCCCCHHHHHHHHHC-C-CCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHH
Q psy4275           2 EDPIKSFTDLKLNPWLIRQCQTI-G-VKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus         2 ~~~~~~~~~~~l~~~i~~~l~~~-~-~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      +.|--+|.+++--+.+.+.+.+. . +..+..++...   ....+++++.||+|+|||..+-..+
T Consensus         2 ~~p~~~~~di~G~~~~k~~l~~~i~~l~~~~~~~~~g---~~~~~giLl~GppGtGKT~la~aia   63 (247)
T d1ixza_           2 EAPKVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMG---ARIPKGVLLVGPPGVGKTHLARAVA   63 (247)
T ss_dssp             CCCSCCGGGCCSCHHHHHHHHHHHHHHHCHHHHHHTT---CCCCSEEEEECCTTSSHHHHHHHHH
T ss_pred             CCCCCcHHHHccHHHHHHHHHHHHHHHHCHHHHHHcC---CCCCceEEEecCCCCChhHHHHHHH
Confidence            34556899997666666666432 0 11222222221   1223579999999999999864444

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=94.92  E-value=0.0064  Score=44.27  Aligned_cols=19  Identities=26%  Similarity=0.240  Sum_probs=16.9

Q ss_pred             CCcEEEECCCCChHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~   61 (182)
                      .++++++||||+|||..+-
T Consensus        49 ~~~iLl~GPpG~GKT~lAk   67 (309)
T d1ofha_          49 PKNILMIGPTGVGKTEIAR   67 (309)
T ss_dssp             CCCEEEECCTTSSHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            5789999999999999864

>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=94.90  E-value=0.25  Score=33.05  Aligned_cols=115  Identities=10%  Similarity=0.041  Sum_probs=59.4

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhcc----CCCCeeEEEEcCCHHHH------HHHHHHHHHhhccC---CceEEEEE
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCE----DPYGIFALVLTPTRELA------YQIGDQFLVLGKVM---NLRVSIIT  109 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~----~~~~~~~lil~p~~~l~------~q~~~~~~~~~~~~---~~~~~~~~  109 (182)
                      +.|.++.|++|.|||....-.+......    ...+.+ ++-+....+.      -++.+.++.+....   .-++.++.
T Consensus        43 k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~-i~~ld~~~LiAg~~~rG~~E~rl~~il~e~~~~~~~iILfI  121 (195)
T d1jbka_          43 KNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRR-VLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFI  121 (195)
T ss_dssp             SCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCE-EEEECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEE
T ss_pred             CCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCce-EEEeeHHHHhccCCccHHHHHHHHHHHHHHhcCCCcEEEEc
Confidence            5699999999999998854444332221    112334 4444444443      24544454433221   12233333


Q ss_pred             cCCch-------------hhhh-HHh-cCCCc-EEEEChHHHHHHHhcCCCCCCCCccEEEEeccc
Q psy4275         110 GGMDM-------------VDQG-KEL-AKKPH-IVIATPGRLADHLDTCNTFSLNRIKFLVLDEAD  159 (182)
Q Consensus       110 ~~~~~-------------~~~~-~~~-~~~~~-Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h  159 (182)
                      +..-.             .... -.+ ..+-+ |.-+||+.+..+++. ..-..+.+.-|-++|-.
T Consensus       122 Deih~l~~~g~~~g~~d~~~~Lkp~L~rg~l~~IgatT~eey~~~~e~-d~aL~rrF~~I~V~Ep~  186 (195)
T d1jbka_         122 DELHTMVGAGKADGAMDAGNMLKPALARGELHCVGATTLDEYRQYIEK-DAALERRFQKVFVAEPS  186 (195)
T ss_dssp             ETGGGGTT------CCCCHHHHHHHHHTTSCCEEEEECHHHHHHHTTT-CHHHHTTEEEEECCCCC
T ss_pred             chHHHHhcCCCCCCcccHHHHHHHHHhCCCceEEecCCHHHHHHHHHc-CHHHHhcCCEeecCCCC
Confidence            22110             0000 011 12334 445899999888776 33345567788888864

>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=94.78  E-value=0.012  Score=41.64  Aligned_cols=56  Identities=18%  Similarity=0.146  Sum_probs=31.9

Q ss_pred             CCccCCCCCHHHHHHHHHC--CCCCChHHHHhhhhhhhCCCcEEEECCCCChHHHHHHHHH
Q psy4275           6 KSFTDLKLNPWLIRQCQTI--GVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus         6 ~~~~~~~l~~~i~~~l~~~--~~~~~~~~Q~~~~~~~~~~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      -+|+|.+--+.+.+.+.+.  .+..+..++...   ....+.+++.||+|+|||..+-..+
T Consensus         9 ~t~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g---~~~~~~iLL~GppGtGKT~la~~iA   66 (256)
T d1lv7a_           9 TTFADVAGCDEAKEEVAELVEYLREPSRFQKLG---GKIPKGVLMVGPPGTGKTLLAKAIA   66 (256)
T ss_dssp             CCGGGSCSCHHHHHHTHHHHHHHHCGGGC--------CCCCEEEEECCTTSCHHHHHHHHH
T ss_pred             CCHHHHhchHHHHHHHHHHHHHHHCHHHHHHcC---CCCCCeEEeeCCCCCCccHHHHHHH
Confidence            4788887666666666432  011111111111   1224679999999999999865444

>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=94.63  E-value=0.0081  Score=46.01  Aligned_cols=19  Identities=26%  Similarity=0.240  Sum_probs=16.9

Q ss_pred             CCcEEEECCCCChHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~   61 (182)
                      .+|+|+.||||+|||..+-
T Consensus        49 ksNILliGPTGvGKTlLAr   67 (443)
T d1g41a_          49 PKNILMIGPTGVGKTEIAR   67 (443)
T ss_dssp             CCCEEEECCTTSSHHHHHH
T ss_pred             cccEEEECCCCCCHHHHHH
Confidence            5699999999999998864

>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=94.55  E-value=0.051  Score=34.48  Aligned_cols=66  Identities=14%  Similarity=0.231  Sum_probs=48.6

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCCccEE
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFL  153 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~i  153 (182)
                      +.++||.|+++.-++++++.++..    ++++..++++......   -.+..+|+|+|.-      -. ..++ .++++|
T Consensus        35 ~~k~IVFc~t~~~ae~la~~L~~~----G~~~~~~H~~~~~~~~---~~~~~~vlvaTd~------~~-~GiD-~~v~~V   99 (138)
T d1jr6a_          35 GGRHLIFCHSKKKCDELAAKLVAL----GINAVAYYRGLDVSVI---PTNGDVVVVATDA------LM-TGFT-GDFDSV   99 (138)
T ss_dssp             TSCEEEECSCHHHHHHHHHHHHHH----TCEEEEECTTCCSCCC---TTSSCEEEEESSS------SC-SSSC-CCBSEE
T ss_pred             CCCEEEEeCcHHHHHHHHHHHhcc----ccchhhhhccchhhhh---hhhhcceeehhHH------HH-hccc-cccceE
Confidence            458999999999999988888765    7899999998875443   2457899999932      12 3355 567766


Q ss_pred             E
Q psy4275         154 V  154 (182)
Q Consensus       154 I  154 (182)
                      |
T Consensus       100 i  100 (138)
T d1jr6a_         100 I  100 (138)
T ss_dssp             E
T ss_pred             E
Confidence            4

>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=94.54  E-value=0.044  Score=38.54  Aligned_cols=46  Identities=15%  Similarity=-0.039  Sum_probs=31.9

Q ss_pred             hhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCH
Q psy4275          37 IPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTR   84 (182)
Q Consensus        37 ~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~   84 (182)
                      +--+..|.-.++.|+||+|||..+.-.+.+.....  +.+++++...-
T Consensus        29 ~~G~~~G~l~vi~G~~G~GKT~~~~~la~~~a~~~--g~~v~~~s~E~   74 (277)
T d1cr2a_          29 TLGARGGEVIMVTSGSGMGKSTFVRQQALQWGTAM--GKKVGLAMLEE   74 (277)
T ss_dssp             HCSBCTTCEEEEECSTTSSHHHHHHHHHHHHHHTS--CCCEEEEESSS
T ss_pred             hcCCCCCeEEEEEeCCCCCHHHHHHHHHHhhhhhc--ccceeEeeecc
Confidence            33456688899999999999987665555544333  44688887543

>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=94.50  E-value=0.033  Score=40.24  Aligned_cols=55  Identities=15%  Similarity=0.070  Sum_probs=39.4

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEECh
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATP  132 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~  132 (182)
                      .++++|++|+..-++++++.+++.    |.+|..++|.....+......++.+|+|+|.
T Consensus        36 ~g~~~~F~~s~~~~~~~a~~L~~~----g~~V~~l~~~~~~~e~~~~~~~~~~~~~~t~   90 (299)
T d1yksa2          36 KRPTAWFLPSIRAANVMAASLRKA----GKSVVVLNRKTFEREYPTIKQKKPDFILATD   90 (299)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHT----TCCEEECCSSSCC--------CCCSEEEESS
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhc----CCeEEEEcCcCcHhHHhhhhcCCcCEEEEec
Confidence            457999999999999888888764    6789999998876666555556788999993

>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=94.45  E-value=0.013  Score=37.93  Aligned_cols=21  Identities=19%  Similarity=0.052  Sum_probs=16.9

Q ss_pred             CcEEEECCCCChHHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~   64 (182)
                      .++++.||+|+|||+.+-...
T Consensus         5 ~~I~i~G~pGsGKTTia~~La   25 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGKELA   25 (173)
T ss_dssp             CCEEEECSTTSSHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHH
Confidence            468999999999999865443

>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=94.30  E-value=0.029  Score=38.88  Aligned_cols=58  Identities=16%  Similarity=-0.003  Sum_probs=32.7

Q ss_pred             CCccCCCCCHHHHHHHHHCCCCCChHHHHhhhhh-----hhCCCcEEEECCCCChHHHHHHHHH
Q psy4275           6 KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPH-----VLNDEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus         6 ~~~~~~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~-----~~~~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      ++|+++...+...+.+...=- .........+..     ....++.++.||+|+|||..+-..+
T Consensus        11 ~~~~dlig~~~~~~~L~~~l~-~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la   73 (253)
T d1sxja2          11 TNLQQVCGNKGSVMKLKNWLA-NWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVA   73 (253)
T ss_dssp             SSGGGCCSCHHHHHHHHHHHH-THHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHH
T ss_pred             CCHHHhcCCHHHHHHHHHHHH-hhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHH
Confidence            467888777777776654210 000001111111     1113579999999999998865443

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=94.15  E-value=0.022  Score=39.25  Aligned_cols=40  Identities=20%  Similarity=0.227  Sum_probs=29.5

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      ..|.-.++.|++|+|||..++-.+.+...+   +..++++.-.
T Consensus        24 ~~gsl~li~G~pGsGKT~l~~qia~~~~~~---~~~~~~is~e   63 (242)
T d1tf7a2          24 FKDSIILATGATGTGKTLLVSRFVENACAN---KERAILFAYE   63 (242)
T ss_dssp             ESSCEEEEEECTTSSHHHHHHHHHHHHHTT---TCCEEEEESS
T ss_pred             cCCeEEEEEeCCCCCHHHHHHHHHHHHHHh---ccccceeecc
Confidence            346789999999999999987777775444   4467777643

>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=94.13  E-value=0.011  Score=40.52  Aligned_cols=83  Identities=16%  Similarity=0.334  Sum_probs=51.6

Q ss_pred             CeeEEEEcCCHHHHHHH-----HHHHHHhhccC--CceEEEEEcCCchhhhhHHh----cCCCcEEEEChHHHHHHHhcC
Q psy4275          74 GIFALVLTPTRELAYQI-----GDQFLVLGKVM--NLRVSIITGGMDMVDQGKEL----AKKPHIVIATPGRLADHLDTC  142 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~-----~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~T~~~l~~~~~~~  142 (182)
                      +.++.+|||..+-.+..     .+..+.+.+..  ++++..+||..+..+....+    .++.+|+|+|.-      -. 
T Consensus        29 g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~~~iLVaTtV------iE-  101 (206)
T d1gm5a4          29 GGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTV------IE-  101 (206)
T ss_dssp             SCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSSC------CC-
T ss_pred             CCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCCEEEEEEehh------hh-
Confidence            66899999976433221     22333333332  57788999998765544333    347899999922      22 


Q ss_pred             CCCCCCCccEEEEeccccccc
Q psy4275         143 NTFSLNRIKFLVLDEADRLSL  163 (182)
Q Consensus       143 ~~~~~~~~~~iI~DE~h~~~~  163 (182)
                      ..+++++++++|+.+++.+.-
T Consensus       102 ~GIDip~a~~iii~~a~~fgl  122 (206)
T d1gm5a4         102 VGIDVPRANVMVIENPERFGL  122 (206)
T ss_dssp             SCSCCTTCCEEEBCSCSSSCT
T ss_pred             ccccccCCcEEEEEccCCccH
Confidence            567899999999999987543

>d1g5ta_ c.37.1.11 (A:) ATP:corrinoid adenosyltransferase CobA {Salmonella typhimurium [TaxId: 90371]}

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: ATP:corrinoid adenosyltransferase CobA
species: Salmonella typhimurium [TaxId: 90371]

Probab=94.00  E-value=0.032  Score=36.30  Aligned_cols=118  Identities=16%  Similarity=0.046  Sum_probs=61.4

Q ss_pred             EEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHH-hcCC
Q psy4275          46 CIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKE-LAKK  124 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~  124 (182)
                      +.+..+.|-|||++++-.++..+-.   +.+++++-=.+.-...  .. ....+..++.......+......... ... 
T Consensus         5 i~vytG~GKGKTTAAlG~alRA~G~---G~rV~ivQFlKg~~~~--ge-~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~-   77 (157)
T d1g5ta_           5 IIVFTGNGKGKTTAAFGTAARAVGH---GKNVGVVQFIKGTWPN--GE-RNLLEPHGVEFQVMATGFTWETQNREADTA-   77 (157)
T ss_dssp             EEEEESSSSCHHHHHHHHHHHHHHT---TCCEEEEESSCCSSCC--HH-HHHHGGGTCEEEECCTTCCCCGGGHHHHHH-
T ss_pred             EEEEeCCCCCcHHHHHHHHHHHhcC---CCEEEEEEEecCCccc--ch-hhhhcccCcEEEEecCCCcccCCChHHHHH-
Confidence            5566789999999988888877665   5678877533221000  00 11122223333221111111000000 000 


Q ss_pred             CcEEEEChHHHHHHHhcCCCCCCCCccEEEEeccccccccCChhHHHHHHHHhh
Q psy4275         125 PHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFFFFFFLKY  178 (182)
Q Consensus       125 ~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~~~~~~~~~~~~~~~~~~~  178 (182)
                            ..+...+..+.  .+.-...+++|+||+-...+.+.......+..+..
T Consensus        78 ------~a~~~~~~a~~--~~~~~~~dllILDEi~~Ai~~gli~~~~v~~ll~~  123 (157)
T d1g5ta_          78 ------ACMAVWQHGKR--MLADPLLDMVVLDELTYMVAYDYLPLEEVISALNA  123 (157)
T ss_dssp             ------HHHHHHHHHHH--HTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHT
T ss_pred             ------HHHHHHHHHHH--HhhcCccCEEeHHHHHHHHHcCCCCHHHHHHHHHh
Confidence                  01111222221  12234578999999999999998887777776643

>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=93.96  E-value=0.013  Score=37.93  Aligned_cols=20  Identities=20%  Similarity=0.114  Sum_probs=15.9

Q ss_pred             CcEEEECCCCChHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~   63 (182)
                      +-+++.||+|+|||+++-..
T Consensus         3 klI~i~G~~GsGKTTva~~L   22 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRL   22 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHH
Confidence            34788999999999986433

>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=93.92  E-value=0.02  Score=37.17  Aligned_cols=22  Identities=18%  Similarity=0.179  Sum_probs=17.7

Q ss_pred             CCcEEEECCCCChHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      +.++++.||+|+|||+.+-...
T Consensus         5 ~~~I~i~G~~GsGKTT~~~~La   26 (174)
T d1y63a_           5 GINILITGTPGTGKTSMAEMIA   26 (174)
T ss_dssp             SCEEEEECSTTSSHHHHHHHHH
T ss_pred             CCEEEEEeCCCCCHHHHHHHHH
Confidence            4579999999999999864443

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {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: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=93.89  E-value=0.42  Score=32.68  Aligned_cols=26  Identities=23%  Similarity=0.379  Sum_probs=19.7

Q ss_pred             cEEEEeccccccccCChhHHHHHHHH
Q psy4275         151 KFLVLDEADRLSLMTSLKFFFFFFFL  176 (182)
Q Consensus       151 ~~iI~DE~h~~~~~~~~~~~~~~~~~  176 (182)
                      -++++||.|.+.+.....+...+...
T Consensus       138 ~~i~id~~~~~~~~~~~~~~~~l~~~  163 (283)
T d2fnaa2         138 VIIVLDEAQELVKLRGVNLLPALAYA  163 (283)
T ss_dssp             EEEEEETGGGGGGCTTCCCHHHHHHH
T ss_pred             cccccchhhhhcccchHHHHHHHHHH
Confidence            47999999999887776666555544

>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=93.88  E-value=0.012  Score=38.51  Aligned_cols=20  Identities=15%  Similarity=0.096  Sum_probs=16.8

Q ss_pred             CCcEEEECCCCChHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~   62 (182)
                      -+.+++.||+|+|||+.+-.
T Consensus         7 ~K~I~i~G~~GsGKTTla~~   26 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVNK   26 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHH
Confidence            36799999999999988644

>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=93.84  E-value=0.015  Score=37.07  Aligned_cols=18  Identities=22%  Similarity=0.058  Sum_probs=14.7

Q ss_pred             cEEEECCCCChHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~   62 (182)
                      -++++|++|+|||+.+-.
T Consensus         4 lIii~G~pGsGKTTla~~   21 (152)
T d1ly1a_           4 IILTIGCPGSGKSTWARE   21 (152)
T ss_dssp             EEEEECCTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            467899999999997643

>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=93.67  E-value=0.17  Score=35.75  Aligned_cols=116  Identities=15%  Similarity=0.099  Sum_probs=57.8

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccC-----CCCeeEEEEcCCHHHH-----HHHHHHHHHhhccC--CceEEEEEc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCED-----PYGIFALVLTPTRELA-----YQIGDQFLVLGKVM--NLRVSIITG  110 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~-----~~~~~~lil~p~~~l~-----~q~~~~~~~~~~~~--~~~~~~~~~  110 (182)
                      .+|.+++||+|.|||....-.+. ++.+.     ..+.+++.+-+..-++     .++.+.++.+....  .-++..+.+
T Consensus        39 k~n~lLVG~~GvGKTalv~~la~-ri~~~~vp~~l~~~~i~~l~~~~liag~~~~g~~e~r~~~i~~~~~~~~~iIlfiD  117 (268)
T d1r6bx2          39 KNNPLLVGESGVGKTAIAEGLAW-RIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFID  117 (268)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHH-HHHHTCSCGGGTTCEEEECCCC---CCCCCSSCHHHHHHHHHHHHSSSSCEEEEET
T ss_pred             cCCcEEECCCCCcHHHHHHHHHH-HHHhCCcccccccceeEEeeechHhccCccchhHHHHHHHHHHHhhccCCceEEec
Confidence            56899999999999988544333 33222     1233444444433332     22333333322221  122333332


Q ss_pred             C---------Cc--hhhhhHHhc---C--CCc-EEEEChHHHHHHHhcCCCCCCCCccEEEEecccc
Q psy4275         111 G---------MD--MVDQGKELA---K--KPH-IVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR  160 (182)
Q Consensus       111 ~---------~~--~~~~~~~~~---~--~~~-Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~DE~h~  160 (182)
                      .         ..  .......+.   .  +-+ |.-+||+.+..+++. ..-..+.+..|-++|-+.
T Consensus       118 eih~l~~~g~~~g~~~d~a~~Lkp~L~rg~i~vIgatT~eey~~~~e~-d~al~rrF~~I~V~Eps~  183 (268)
T d1r6bx2         118 EIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIGSTTYQEFSNIFEK-DRALARRFQKIDITEPSI  183 (268)
T ss_dssp             TTTTTTTSCCSSSCHHHHHHHHSSCSSSCCCEEEEEECHHHHHCCCCC-TTSSGGGEEEEECCCCCH
T ss_pred             chHHHhcCCCCCCccccHHHHhhHHHhCCCCeEEEeCCHHHHHHHHhh-cHHHHhhhcccccCCCCH
Confidence            1         11  111122221   1  233 455888888877766 333456688899998763

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=93.54  E-value=0.049  Score=40.36  Aligned_cols=42  Identities=12%  Similarity=-0.024  Sum_probs=26.1

Q ss_pred             CCCCCChHHHHhhhhhhhC----CCcEEEECCCCChHHHHHHHHHH
Q psy4275          24 IGVKTPTEIQKAIIPHVLN----DEDCIGCAKTGSGKTLAFALPIL   65 (182)
Q Consensus        24 ~~~~~~~~~Q~~~~~~~~~----~~~~li~~~tg~GKT~~~~~~~~   65 (182)
                      .++......-.+.+..+..    ++..++.||+|+|||..+...+-
T Consensus       131 ~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~g~~~~gk~~~~~~~~~  176 (362)
T d1svma_         131 CLLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLE  176 (362)
T ss_dssp             TTSTTHHHHHHHHHHHHHHCCTTCCEEEEECSTTSSHHHHHHHHHH
T ss_pred             hcccchHHHHHHHHHHHHhCCCCcCeEEEECCCCCCHHHHHHHHHH
Confidence            3454444443344433333    56899999999999988654433

>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=93.42  E-value=0.018  Score=40.28  Aligned_cols=19  Identities=26%  Similarity=0.209  Sum_probs=15.8

Q ss_pred             CcEEEECCCCChHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~   62 (182)
                      +.+++.||+|+|||..+-.
T Consensus        33 ~~ilL~GpPGtGKT~la~~   51 (273)
T d1gvnb_          33 TAFLLGGQPGSGKTSLRSA   51 (273)
T ss_dssp             EEEEEECCTTSCTHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHH
Confidence            3588999999999998643

>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=93.18  E-value=0.023  Score=36.90  Aligned_cols=19  Identities=21%  Similarity=0.197  Sum_probs=15.8

Q ss_pred             CCcEEEECCCCChHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~   61 (182)
                      |+-+++.||+|+|||+++-
T Consensus         4 g~iI~l~G~~GsGKSTia~   22 (176)
T d1zp6a1           4 GNILLLSGHPGSGKSTIAE   22 (176)
T ss_dssp             TEEEEEEECTTSCHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            5567889999999999863

>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=93.14  E-value=0.03  Score=38.34  Aligned_cols=21  Identities=19%  Similarity=0.172  Sum_probs=16.9

Q ss_pred             CcEEEECCCCChHHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~   64 (182)
                      .+.++.||+|+|||..+-..+
T Consensus        34 ~~lll~Gp~G~GKTtl~~~i~   54 (237)
T d1sxjd2          34 PHMLFYGPPGTGKTSTILALT   54 (237)
T ss_dssp             CCEEEECSTTSSHHHHHHHHH
T ss_pred             CeEEEECCCCCChHHHHHHHH
Confidence            468999999999998854444

>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=93.12  E-value=0.034  Score=37.98  Aligned_cols=44  Identities=9%  Similarity=-0.191  Sum_probs=28.8

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhccC---CCCeeEEEEcCC
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCED---PYGIFALVLTPT   83 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~---~~~~~~lil~p~   83 (182)
                      +..|+-.++.|++|+|||..++-.+.......   ..+..++++.-.
T Consensus        31 i~~G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~   77 (251)
T d1szpa2          31 VETGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTE   77 (251)
T ss_dssp             EESSSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESS
T ss_pred             CcCCeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeec
Confidence            34477899999999999998766555443321   224456666533

>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=93.05  E-value=0.024  Score=39.67  Aligned_cols=20  Identities=25%  Similarity=0.004  Sum_probs=16.4

Q ss_pred             CcEEEECCCCChHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~   63 (182)
                      +++++.||+|+|||..+-..
T Consensus        41 ~~vLL~GppGtGKT~la~al   60 (246)
T d1d2na_          41 VSVLLEGPPHSGKTALAAKI   60 (246)
T ss_dssp             EEEEEECSTTSSHHHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHHHH
Confidence            36899999999999886443

>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=93.03  E-value=0.028  Score=36.41  Aligned_cols=22  Identities=14%  Similarity=-0.093  Sum_probs=17.0

Q ss_pred             CCCcEEEECCCCChHHHHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~   63 (182)
                      +|.-+++.|++|+|||+++-..
T Consensus         5 ~g~~I~l~G~~GsGKTTia~~L   26 (183)
T d1m8pa3           5 QGFTIFLTGYMNSGKDAIARAL   26 (183)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHH
Confidence            3556778999999999986433

>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=93.02  E-value=0.032  Score=37.93  Aligned_cols=41  Identities=17%  Similarity=0.045  Sum_probs=28.9

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCC
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT   83 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~   83 (182)
                      ..|.-.++.|++|+|||..++-.+...+...  +..++++...
T Consensus        24 ~~G~~~~I~G~~G~GKT~la~~~~~~~~~~~--~~~~~~~s~e   64 (242)
T d1tf7a1          24 PIGRSTLVSGTSGTGKTLFSIQFLYNGIIEF--DEPGVFVTFE   64 (242)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHHHHHH--CCCEEEEESS
T ss_pred             cCCeEEEEEeCCCCCHHHHHHHHHHHHHHhc--CCCccccccc
Confidence            3477899999999999988766555544443  2357777654

>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=92.86  E-value=0.038  Score=35.77  Aligned_cols=21  Identities=19%  Similarity=0.099  Sum_probs=16.8

Q ss_pred             CcEEEECCCCChHHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~   64 (182)
                      +++++.|++|+|||+++-...
T Consensus         1 k~I~liG~~GsGKsTi~k~La   21 (161)
T d1viaa_           1 KNIVFIGFMGSGKSTLARALA   21 (161)
T ss_dssp             CCEEEECCTTSCHHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHHH
Confidence            468899999999999864433

>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=92.76  E-value=0.04  Score=36.68  Aligned_cols=28  Identities=11%  Similarity=-0.153  Sum_probs=22.4

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhh
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKW   68 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~   68 (182)
                      ..|.-.++.||+|+|||..++-.+.+..
T Consensus        21 ~~G~v~~i~G~~GsGKT~l~l~la~~~~   48 (242)
T d1n0wa_          21 ETGSITEMFGEFRTGKTQICHTLAVTCQ   48 (242)
T ss_dssp             ETTSEEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             cCCEEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            3477899999999999998776666544

>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=92.51  E-value=0.056  Score=37.93  Aligned_cols=19  Identities=26%  Similarity=0.305  Sum_probs=16.1

Q ss_pred             CCcEEEECCCCChHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~   61 (182)
                      .+.+++.||+|+|||..+-
T Consensus        38 ~~giLL~GppGtGKT~l~~   56 (258)
T d1e32a2          38 PRGILLYGPPGTGKTLIAR   56 (258)
T ss_dssp             CCEEEEECCTTSSHHHHHH
T ss_pred             CceeEEecCCCCCchHHHH
Confidence            4679999999999998753

>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=92.41  E-value=0.031  Score=36.13  Aligned_cols=20  Identities=20%  Similarity=0.125  Sum_probs=15.7

Q ss_pred             CcEEEECCCCChHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~   63 (182)
                      +-+++.|++|+|||+.+-..
T Consensus         7 ~iivl~G~~GsGKsT~a~~L   26 (171)
T d1knqa_           7 HIYVLMGVSGSGKSAVASEV   26 (171)
T ss_dssp             EEEEEECSTTSCHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHH
Confidence            34677899999999986543

>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=92.25  E-value=0.052  Score=34.98  Aligned_cols=20  Identities=15%  Similarity=0.013  Sum_probs=16.1

Q ss_pred             CCcEEEECCCCChHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~   62 (182)
                      ++-+++.|++|+|||+++-.
T Consensus         3 ~kiI~l~G~~GsGKsTva~~   22 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRC   22 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            45578889999999988644

>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=92.24  E-value=0.065  Score=36.78  Aligned_cols=42  Identities=12%  Similarity=-0.083  Sum_probs=28.5

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhccC---CCCeeEEEEc
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCED---PYGIFALVLT   81 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~---~~~~~~lil~   81 (182)
                      +..|+-+++.|++|+|||..++-.+.+...+.   ..+..++++.
T Consensus        33 lp~G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~   77 (254)
T d1pzna2          33 IETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWID   77 (254)
T ss_dssp             EESSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEE
T ss_pred             ccCCEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEe
Confidence            34467899999999999999877776655331   2234555554

>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=92.03  E-value=0.063  Score=36.02  Aligned_cols=34  Identities=18%  Similarity=0.065  Sum_probs=21.5

Q ss_pred             CcEEEEC-CCCChHHHHHHHHHHHhhccCCCCeeEEEE
Q psy4275          44 EDCIGCA-KTGSGKTLAFALPILQKWCEDPYGIFALVL   80 (182)
Q Consensus        44 ~~~li~~-~tg~GKT~~~~~~~~~~~~~~~~~~~~lil   80 (182)
                      +..+++| .||.|||++....+......   |.+++++
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aLa~~---G~rVl~i   36 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAAKAA---GYRTAGY   36 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHHT---TCCEEEE
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHHHHC---CCeEEEE
Confidence            3456666 47999999865444443333   5567765

>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=91.96  E-value=0.049  Score=35.37  Aligned_cols=16  Identities=31%  Similarity=0.329  Sum_probs=13.8

Q ss_pred             cEEEECCCCChHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAF   60 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~   60 (182)
                      ++++.||+|+|||+.+
T Consensus         2 ki~I~G~~G~GKSTLl   17 (178)
T d1ye8a1           2 KIIITGEPGVGKTTLV   17 (178)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEECCCCcHHHHHH
Confidence            3789999999999874

>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=91.92  E-value=0.088  Score=33.64  Aligned_cols=34  Identities=24%  Similarity=0.313  Sum_probs=21.5

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      -+.++|+.|||||+.+- .++..+..+  +.++.++.
T Consensus         4 vi~itG~~GSGKTTL~~-~L~~~l~~~--g~~v~v~~   37 (170)
T d1np6a_           4 LLAFAAWSGTGKTTLLK-KLIPALCAR--GIRPGLIK   37 (170)
T ss_dssp             EEEEECCTTSCHHHHHH-HHHHHHHHT--TCCEEEEE
T ss_pred             EEEEEcCCCCCHHHHHH-HHHHHHHHC--CCeEEEec
Confidence            36788999999998743 444444443  34455544

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=91.89  E-value=0.064  Score=34.84  Aligned_cols=21  Identities=19%  Similarity=0.014  Sum_probs=17.2

Q ss_pred             CcEEEECCCCChHHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~   64 (182)
                      +.+++.|++|+|||+++-..+
T Consensus         3 ~~Iil~G~~GsGKSTia~~LA   23 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRELA   23 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHHHH
Confidence            568889999999999875544

>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=91.81  E-value=0.061  Score=35.55  Aligned_cols=22  Identities=14%  Similarity=0.052  Sum_probs=17.6

Q ss_pred             CCcEEEECCCCChHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      |-.+++.||+|||||+.+-..+
T Consensus         3 ~~riil~G~pGSGKsT~a~~La   24 (190)
T d1ak2a1           3 GVRAVLLGPPGAGKGTQAPKLA   24 (190)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHHHHH
Confidence            4567889999999999875544

>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=91.75  E-value=0.052  Score=35.46  Aligned_cols=19  Identities=16%  Similarity=0.088  Sum_probs=15.7

Q ss_pred             cEEEECCCCChHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~   63 (182)
                      ++++.||+|+|||+.+-..
T Consensus         2 ~I~i~G~pGSGKsT~a~~L   20 (182)
T d1zina1           2 NLVLMGLPGAGKGTQAEKI   20 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            4789999999999987544

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=91.63  E-value=0.28  Score=34.01  Aligned_cols=39  Identities=13%  Similarity=0.204  Sum_probs=24.8

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      ..+..+++.|++|+||+.++  -.++..........+.+-+
T Consensus        21 ~~~~pvlI~Ge~GtGK~~~A--~~ih~~s~~~~~~~~~~~~   59 (247)
T d1ny5a2          21 CAECPVLITGESGVGKEVVA--RLIHKLSDRSKEPFVALNV   59 (247)
T ss_dssp             TCCSCEEEECSTTSSHHHHH--HHHHHHSTTTTSCEEEEET
T ss_pred             CCCCCEEEECCCCcCHHHHH--HHHHHhcCCcccccccchh
Confidence            34778999999999999876  3444433333344444444

>d1xx6a1 c.37.1.24 (A:2-142) Thymidine kinase, TK1, N-terminal domain {Clostridium acetobutylicum [TaxId: 1488]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Clostridium acetobutylicum [TaxId: 1488]

Probab=91.60  E-value=0.095  Score=33.31  Aligned_cols=40  Identities=15%  Similarity=-0.035  Sum_probs=26.9

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRE   85 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~   85 (182)
                      |.=-++.||+.+|||.-.+..+-.....   +.+++++.|...
T Consensus         7 G~l~lI~GpMfSGKTteLi~~~~~~~~~---g~~vl~i~~~~D   46 (141)
T d1xx6a1           7 GWVEVIVGPMYSGKSEELIRRIRRAKIA---KQKIQVFKPEID   46 (141)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHT---TCCEEEEEEC--
T ss_pred             eeEEEEEeccccHHHHHHHHHHHHhhhc---CCcEEEEEeccc
Confidence            4456889999999999855444333233   457999999744

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=91.39  E-value=0.061  Score=35.24  Aligned_cols=20  Identities=15%  Similarity=0.071  Sum_probs=16.3

Q ss_pred             cEEEECCCCChHHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~   64 (182)
                      ++++.||+|+|||+.+-...
T Consensus         2 ~I~i~G~pGsGKsT~a~~La   21 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLA   21 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            46889999999999876544

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=91.34  E-value=0.059  Score=35.64  Aligned_cols=19  Identities=21%  Similarity=0.165  Sum_probs=15.8

Q ss_pred             cEEEECCCCChHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~   63 (182)
                      .+++.||+|+|||+.+-..
T Consensus         5 ~I~i~GppGsGKsT~a~~L   23 (189)
T d1zaka1           5 KVMISGAPASGKGTQCELI   23 (189)
T ss_dssp             CEEEEESTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            5789999999999987544

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=91.29  E-value=0.13  Score=33.14  Aligned_cols=19  Identities=21%  Similarity=0.214  Sum_probs=15.3

Q ss_pred             CcEEEECCCCChHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~   62 (182)
                      +-+++.|++|+|||+.+-.
T Consensus         2 kiI~i~G~~GsGKsT~~~~   20 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQL   20 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            4578899999999988543

>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=91.25  E-value=0.068  Score=36.66  Aligned_cols=46  Identities=9%  Similarity=-0.070  Sum_probs=30.5

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhccCC---CCeeEEEEcCCHH
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP---YGIFALVLTPTRE   85 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~---~~~~~lil~p~~~   85 (182)
                      +..|.-.++.|++|+|||..++-.+.+......   ....++++.....
T Consensus        34 ip~G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (258)
T d1v5wa_          34 IESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENT   82 (258)
T ss_dssp             BCSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSC
T ss_pred             CcCCEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEechHHH
Confidence            344678999999999999998777766544321   1234555555443

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

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: Pig (Sus scrofa) [TaxId: 9823]

Probab=91.24  E-value=0.075  Score=35.26  Aligned_cols=25  Identities=16%  Similarity=0.110  Sum_probs=19.1

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHH
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      +.+.+-+++.||+|||||+.+-..+
T Consensus         5 ~~~~~iI~l~G~pGSGKsT~a~~La   29 (194)
T d3adka_           5 LKKSKIIFVVGGPGSGKGTQCEKIV   29 (194)
T ss_dssp             HHTSCEEEEEECTTSSHHHHHHHHH
T ss_pred             ccCCcEEEEECCCCCCHHHHHHHHH
Confidence            4456678889999999999865443

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.12  E-value=0.053  Score=35.59  Aligned_cols=17  Identities=18%  Similarity=0.280  Sum_probs=14.1

Q ss_pred             cEEEECCCCChHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~   61 (182)
                      -++++|++|+|||+.+-
T Consensus        16 liil~G~pGsGKST~a~   32 (172)
T d1yj5a2          16 VVVAVGFPGAGKSTFIQ   32 (172)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47888999999998653

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

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 globisporus [TaxId: 1459]

Probab=91.07  E-value=0.067  Score=35.10  Aligned_cols=21  Identities=14%  Similarity=0.085  Sum_probs=16.4

Q ss_pred             cEEEECCCCChHHHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALPIL   65 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~   65 (182)
                      .+++.||+|||||+.+-..+-
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~   22 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIVE   22 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            368899999999998754443

>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=91.06  E-value=0.2  Score=34.83  Aligned_cols=62  Identities=15%  Similarity=0.068  Sum_probs=37.3

Q ss_pred             hhhhhCCCcEEEECCCCChHHHHHHHHHHHhhccC-------CCCeeEEEEcCCHHHHHHHHHHHHHhhc
Q psy4275          37 IPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCED-------PYGIFALVLTPTRELAYQIGDQFLVLGK   99 (182)
Q Consensus        37 ~~~~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~~-------~~~~~~lil~p~~~l~~q~~~~~~~~~~   99 (182)
                      ++-+..|.-.++.|++|+|||..++-.++......       ..+.+++|+.-... ..++...+..+..
T Consensus        23 i~G~~pg~~~~i~G~~G~GKS~l~l~la~~ia~g~~~~~~~~~~~~~vl~~~~E~~-~~~~~~Rl~~~~~   91 (274)
T d1nlfa_          23 LPNMVAGTVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAEDP-PTAIHHRLHALGA   91 (274)
T ss_dssp             ETTEETTSEEEEEESTTSSHHHHHHHHHHHHHTCCCTTCCCCCCCCCEEEEESSSC-HHHHHHHHHHHHT
T ss_pred             hCCccCCcEEEEEeCCCCCHHHHHHHHHHHHHcCCCcccccccCCCceEEEeccch-HHHHHHHHHHHhh
Confidence            44455678899999999999988766555433221       12346777765432 3344444444433

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=90.99  E-value=0.083  Score=34.10  Aligned_cols=21  Identities=19%  Similarity=0.075  Sum_probs=16.7

Q ss_pred             CcEEEECCCCChHHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~   64 (182)
                      +++++.|++|+|||+++-...
T Consensus         2 p~IvliG~~G~GKSTig~~La   22 (165)
T d2iyva1           2 PKAVLVGLPGSGKSTIGRRLA   22 (165)
T ss_dssp             CSEEEECSTTSSHHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHHH
Confidence            467888999999999865443

>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=90.82  E-value=0.11  Score=36.62  Aligned_cols=23  Identities=22%  Similarity=0.153  Sum_probs=18.1

Q ss_pred             CCcEEEECCCCChHHHHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPIL   65 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~   65 (182)
                      .+.+++.||+|+|||..+-..+-
T Consensus        41 ~~giLL~Gp~GtGKT~l~~ala~   63 (265)
T d1r7ra3          41 SKGVLFYGPPGCGKTLLAKAIAN   63 (265)
T ss_dssp             CCEEEEBCCTTSSHHHHHHHHHH
T ss_pred             CCeEEEECCCCCcchhHHHHHHH
Confidence            46799999999999988544433

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate 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: Adenylate kinase
species: Escherichia coli [TaxId: 562]

Probab=90.82  E-value=0.065  Score=35.05  Aligned_cols=20  Identities=15%  Similarity=0.024  Sum_probs=15.8

Q ss_pred             cEEEECCCCChHHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~   64 (182)
                      ++++.||+|||||+.+-...
T Consensus         2 ~I~i~G~pGSGKsT~~~~La   21 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQFIM   21 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            46789999999999875443

>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=90.77  E-value=0.71  Score=32.28  Aligned_cols=74  Identities=16%  Similarity=0.188  Sum_probs=47.8

Q ss_pred             CCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchh--------hhhHH----hcCCCcEEEEChHHHHHHHh
Q psy4275          73 YGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMV--------DQGKE----LAKKPHIVIATPGRLADHLD  140 (182)
Q Consensus        73 ~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~----~~~~~~Ilv~T~~~l~~~~~  140 (182)
                      .+.++|+.+++..-++.+++.+.+.    ++++..++|.....        .+...    -.++++|+|+|.-      -
T Consensus       160 ~~~k~iiF~~~~~~~~~~~~~L~~~----~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~vLv~T~~------~  229 (286)
T d1wp9a2         160 QNSKIIVFTNYRETAKKIVNELVKD----GIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSV------G  229 (286)
T ss_dssp             TTCCEEEECSCHHHHHHHHHHHHHT----TCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECGG------G
T ss_pred             CCCcEEEEeCcHHhHHHHHHHHHHc----CCceEEeeccccccccchhchHHHHHHHHHHHcCCCcEEEEccc------e
Confidence            3568999999999988887776653    67777777643321        11111    1236789999932      2


Q ss_pred             cCCCCCCCCccEEEEec
Q psy4275         141 TCNTFSLNRIKFLVLDE  157 (182)
Q Consensus       141 ~~~~~~~~~~~~iI~DE  157 (182)
                      . ..+++..+++||.=+
T Consensus       230 ~-~Gld~~~~~~Vi~~d  245 (286)
T d1wp9a2         230 E-EGLDVPEVDLVVFYE  245 (286)
T ss_dssp             G-GGGGSTTCCEEEESS
T ss_pred             e-ccccCCCCCEEEEeC
Confidence            2 456777888777533

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.71  E-value=0.033  Score=36.77  Aligned_cols=21  Identities=19%  Similarity=-0.008  Sum_probs=16.1

Q ss_pred             CcEEEECCCCChHHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~   64 (182)
                      .-++++|++|+|||+.+-...
T Consensus        20 ~vI~L~G~pGSGKTTiAk~La   40 (195)
T d1x6va3          20 CTVWLTGLSGAGKTTVSMALE   40 (195)
T ss_dssp             EEEEEESSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHH
Confidence            356688999999999875443

>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=90.41  E-value=0.05  Score=37.91  Aligned_cols=17  Identities=24%  Similarity=0.225  Sum_probs=13.3

Q ss_pred             EEEECCCCChHHHHHHH
Q psy4275          46 CIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~   62 (182)
                      .++.||+|+|||.++-.
T Consensus        49 l~l~GppGtGKT~l~~~   65 (287)
T d1w5sa2          49 YGSIGRVGIGKTTLAKF   65 (287)
T ss_dssp             EECTTCCSSSHHHHHHH
T ss_pred             EEeECCCCCCHHHHHHH
Confidence            45679999999988543

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

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: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=90.11  E-value=0.085  Score=34.90  Aligned_cols=20  Identities=25%  Similarity=0.134  Sum_probs=15.7

Q ss_pred             cEEEECCCCChHHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~   64 (182)
                      -+++.||+|+|||+.+-..+
T Consensus         8 iI~i~G~pGSGKsT~a~~La   27 (194)
T d1qf9a_           8 VVFVLGGPGSGKGTQCANIV   27 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            46778999999999865444

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.07  E-value=0.097  Score=34.69  Aligned_cols=21  Identities=14%  Similarity=0.041  Sum_probs=16.2

Q ss_pred             cEEEECCCCChHHHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALPIL   65 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~   65 (182)
                      -+++.||+|+|||+.+-...-
T Consensus        10 iI~i~GppGSGKsT~a~~La~   30 (196)
T d1ukza_          10 VIFVLGGPGAGKGTQCEKLVK   30 (196)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            467789999999988755443

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, 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: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=90.03  E-value=0.16  Score=35.77  Aligned_cols=42  Identities=19%  Similarity=0.037  Sum_probs=30.3

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELA   87 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~   87 (182)
                      |+-..+.||+|+|||..++..+.....+   +..++|+--.....
T Consensus        54 g~itei~G~~gsGKTtl~l~~~~~~q~~---g~~~vyidtE~~~~   95 (263)
T d1u94a1          54 GRIVEIYGPESSGKTTLTLQVIAAAQRE---GKTCAFIDAEHALD   95 (263)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHT---TCCEEEEESSCCCC
T ss_pred             ceEEEEecCCCcHHHHHHHHHHHHHHcC---CCEEEEEccccccC
Confidence            5678899999999999877666665433   45677777665543

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=90.00  E-value=0.044  Score=39.84  Aligned_cols=20  Identities=20%  Similarity=0.258  Sum_probs=17.0

Q ss_pred             CCCcEEEECCCCChHHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~   61 (182)
                      .++|+++.|++|+|||+.+-
T Consensus        27 ~~h~vLl~G~pG~GKT~lar   46 (333)
T d1g8pa_          27 GIGGVLVFGDRGTGKSTAVR   46 (333)
T ss_dssp             GGCCEEEECCGGGCTTHHHH
T ss_pred             CCCeEEEECCCCccHHHHHH
Confidence            35789999999999998853

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.92  E-value=0.085  Score=34.88  Aligned_cols=20  Identities=15%  Similarity=0.215  Sum_probs=16.1

Q ss_pred             CcEEEECCCCChHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALP   63 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~   63 (182)
                      +.++++||+|+|||...-..
T Consensus         2 rpIvl~GpsG~GK~tl~~~L   21 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKL   21 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHH
Confidence            45799999999999975443

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=89.81  E-value=0.11  Score=33.99  Aligned_cols=20  Identities=10%  Similarity=0.092  Sum_probs=16.3

Q ss_pred             CCcEEEECCCCChHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~   62 (182)
                      |+-+++.||+|+|||...-.
T Consensus         2 G~iivl~GpsG~GK~tl~~~   21 (182)
T d1znwa1           2 GRVVVLSGPSAVGKSTVVRC   21 (182)
T ss_dssp             CCEEEEECSTTSSHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            55678999999999998543

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {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: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=89.69  E-value=0.1  Score=34.24  Aligned_cols=21  Identities=19%  Similarity=-0.061  Sum_probs=15.2

Q ss_pred             CCcEE-EECCCCChHHHHHHHH
Q psy4275          43 DEDCI-GCAKTGSGKTLAFALP   63 (182)
Q Consensus        43 ~~~~l-i~~~tg~GKT~~~~~~   63 (182)
                      ++-++ +.||+|+|||+.+-..
T Consensus        21 ~~~iIgI~G~~GSGKSTla~~L   42 (198)
T d1rz3a_          21 GRLVLGIDGLSRSGKTTLANQL   42 (198)
T ss_dssp             SSEEEEEEECTTSSHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHH
Confidence            44344 7899999999886443

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=89.52  E-value=0.096  Score=35.57  Aligned_cols=31  Identities=16%  Similarity=-0.004  Sum_probs=24.6

Q ss_pred             hhCCCcEEEECCCCChHHHHHHHHHHHhhcc
Q psy4275          40 VLNDEDCIGCAKTGSGKTLAFALPILQKWCE   70 (182)
Q Consensus        40 ~~~~~~~li~~~tg~GKT~~~~~~~~~~~~~   70 (182)
                      +..|.-.++.|++|+|||..++-.+.+.+..
T Consensus        31 l~~G~l~~i~G~~G~GKT~~~l~~a~~~~~~   61 (258)
T d2i1qa2          31 LESQSVTEFAGVFGSGKTQIMHQSCVNLQNP   61 (258)
T ss_dssp             EETTEEEEEEESTTSSHHHHHHHHHHHTTCG
T ss_pred             ccCCeEEEEEeCCCCCHHHHHHHHHHHHHhc
Confidence            4446789999999999999988777766543

>d1teva_ c.37.1.1 (A:) UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.41  E-value=0.12  Score=34.07  Aligned_cols=19  Identities=21%  Similarity=0.186  Sum_probs=15.3

Q ss_pred             EEEECCCCChHHHHHHHHH
Q psy4275          46 CIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~   64 (182)
                      +++.||+|+|||+.+-..+
T Consensus         4 I~i~GppGSGKsT~a~~La   22 (194)
T d1teva_           4 VFVLGGPGAGKGTQCARIV   22 (194)
T ss_dssp             EEEECCTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            5788999999999875443

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [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-3 [TaxId: 9913]

Probab=89.30  E-value=0.12  Score=34.32  Aligned_cols=21  Identities=19%  Similarity=0.023  Sum_probs=17.0

Q ss_pred             cEEEECCCCChHHHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALPIL   65 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~   65 (182)
                      .+++.||+|+|||+.+-..+-
T Consensus         8 rIiliG~PGSGKtT~a~~La~   28 (189)
T d2ak3a1           8 RAAIMGAPGSGKGTVSSRITK   28 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHH
Confidence            678899999999998755443

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.23  E-value=0.12  Score=33.77  Aligned_cols=20  Identities=15%  Similarity=0.037  Sum_probs=16.0

Q ss_pred             cEEEECCCCChHHHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~   64 (182)
                      .+++.||+|||||+.+-..+
T Consensus         4 rIvl~G~pGSGKtT~a~~La   23 (180)
T d1akya1           4 RMVLIGPPGAGKGTQAPNLQ   23 (180)
T ss_dssp             EEEEECCTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            46788999999999875443

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=88.83  E-value=0.25  Score=31.94  Aligned_cols=16  Identities=31%  Similarity=0.351  Sum_probs=13.4

Q ss_pred             EEEECCCCChHHHHHH
Q psy4275          46 CIGCAKTGSGKTLAFA   61 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~   61 (182)
                      +++.|++|+|||+.+-
T Consensus         4 ivi~G~~GsGKTT~~~   19 (194)
T d1nksa_           4 GIVTGIPGVGKSTVLA   19 (194)
T ss_dssp             EEEEECTTSCHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            4678999999998853

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.42  E-value=0.17  Score=33.48  Aligned_cols=18  Identities=17%  Similarity=0.289  Sum_probs=14.9

Q ss_pred             cEEEECCCCChHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~   62 (182)
                      -+++.||+|+|||..+-.
T Consensus         2 pIvl~GPsGsGK~tl~~~   19 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLLKK   19 (190)
T ss_dssp             CEEEECCTTSSHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHH
Confidence            478999999999997543

>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=87.81  E-value=0.79  Score=32.61  Aligned_cols=38  Identities=13%  Similarity=0.296  Sum_probs=31.3

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchh
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMV  115 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~  115 (182)
                      +.++||.++++.-++++++.+++.    |+++..++++.+..
T Consensus        36 ggk~LVFcnSR~~aE~La~~L~~~----Gi~a~~~Hgglsq~   73 (299)
T d1a1va2          36 GGRHLIFCHSKKKCDELAAKLVAL----GINAVAYYRGLDVS   73 (299)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCGG
T ss_pred             CCCEEEECCcHHHHHHHHHHHHHC----CCCEEEEeCCchHH
Confidence            458999999999999988887664    78888888876653

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC 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: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.62  E-value=0.26  Score=34.38  Aligned_cols=28  Identities=25%  Similarity=0.241  Sum_probs=20.4

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhhcc
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKWCE   70 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~~~   70 (182)
                      ..|..+.+.||+|+|||+..  -++..++.
T Consensus        38 ~~Ge~vaivG~sGsGKSTLl--~li~gl~~   65 (251)
T d1jj7a_          38 RPGEVTALVGPNGSGKSTVA--ALLQNLYQ   65 (251)
T ss_dssp             CTTCEEEEECSTTSSHHHHH--HHHTTSSC
T ss_pred             cCCCEEEEECCCCCcHHHHH--HHHhcccC
Confidence            34788999999999998874  44444443

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {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: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=87.46  E-value=0.26  Score=34.76  Aligned_cols=43  Identities=16%  Similarity=0.067  Sum_probs=30.4

Q ss_pred             CCCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELA   87 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~   87 (182)
                      .|+-..+.||+|+|||..++..+......   +..++|+-....+.
T Consensus        59 ~g~i~e~~G~~~~GKT~l~l~~~~~~q~~---g~~~vyIDtE~~~~  101 (269)
T d1mo6a1          59 RGRVIEIYGPESSGKTTVALHAVANAQAA---GGVAAFIDAEHALD  101 (269)
T ss_dssp             SSSEEEEECSSSSSHHHHHHHHHHHHHHT---TCEEEEEESSCCCC
T ss_pred             cceeEEEecCCCcHHHHHHHHHHHHHhcC---CCEEEEEECCccCC
Confidence            36678889999999999876665544333   45778877665553

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=87.34  E-value=0.22  Score=33.53  Aligned_cols=20  Identities=25%  Similarity=0.250  Sum_probs=16.4

Q ss_pred             CCcEEEECCCCChHHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~   62 (182)
                      |+-++++||+|+|||...-.
T Consensus         2 G~livi~GPSG~GK~tl~~~   21 (205)
T d1s96a_           2 GTLYIVSAPSGAGKSSLIQA   21 (205)
T ss_dssp             CCEEEEECCTTSCHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            56688999999999988543

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.23  E-value=0.16  Score=33.34  Aligned_cols=19  Identities=11%  Similarity=0.086  Sum_probs=15.8

Q ss_pred             CCcEEEECCCCChHHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~   61 (182)
                      ++-++++||+|+||+...-
T Consensus         3 ~k~ivl~Gpsg~GK~tl~~   21 (178)
T d1kgda_           3 RKTLVLLGAHGVGRRHIKN   21 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHH
T ss_pred             CCcEEEECCCCCCHHHHHH
Confidence            3568899999999998854

>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=87.15  E-value=0.72  Score=32.17  Aligned_cols=55  Identities=11%  Similarity=-0.028  Sum_probs=42.9

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhcCCCcEEEECh
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATP  132 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T~  132 (182)
                      +.++++.++++.-++.+++.+++.    ++++..++|+...........+..+++|+|.
T Consensus       178 ~~~~lvf~~~~~~~~~l~~~L~~~----~~~~~~l~~~~~~~~~~~~~~~~~~~lvaT~  232 (305)
T d2bmfa2         178 KGKTVWFVPSIKAGNDIAACLRKN----GKKVIQLSRKTFDSEYIKTRTNDWDFVVTTD  232 (305)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHH----TCCCEECCTTCHHHHGGGGGTSCCSEEEECG
T ss_pred             CCCEEEEeccHHHHHHHHHHHHhC----CCCEEEeCCcChHHHHhhhhccchhhhhhhH
Confidence            457999999999999888888765    5677888888766555555556788999995

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

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: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=86.66  E-value=0.13  Score=37.25  Aligned_cols=21  Identities=29%  Similarity=0.029  Sum_probs=15.4

Q ss_pred             CcEEEECCCCChHHHHHHHHH
Q psy4275          44 EDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        44 ~~~li~~~tg~GKT~~~~~~~   64 (182)
                      .+.++.||+|+|||..+-...
T Consensus       124 g~~l~~G~pG~GKT~la~ala  144 (321)
T d1w44a_         124 GMVIVTGKGNSGKTPLVHALG  144 (321)
T ss_dssp             EEEEEECSSSSCHHHHHHHHH
T ss_pred             ceEEEECCCCccHHHHHHHHH
Confidence            345568999999998864333

>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=86.46  E-value=0.4  Score=30.54  Aligned_cols=32  Identities=16%  Similarity=0.005  Sum_probs=20.3

Q ss_pred             EEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275          47 IGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus        47 li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      -+.|..|||||+.. -.++..+.+.  +.++.++-
T Consensus         5 ~I~G~~gSGKTTli-~~l~~~L~~~--g~~v~vik   36 (165)
T d1xjca_           5 QVVGYKHSGKTTLM-EKWVAAAVRE--GWRVGTVK   36 (165)
T ss_dssp             EEECCTTSSHHHHH-HHHHHHHHHT--TCCEEEEE
T ss_pred             EEEeCCCCCHHHHH-HHHHHHHHhC--CCeEEEEE
Confidence            47899999999884 3444444443  34555554

>d1r6bx3 c.37.1.20 (X:437-751) 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=86.42  E-value=0.2  Score=36.05  Aligned_cols=18  Identities=28%  Similarity=0.218  Sum_probs=15.3

Q ss_pred             cEEEECCCCChHHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFAL   62 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~   62 (182)
                      +++++||||+|||..+-.
T Consensus        54 ~~lf~Gp~GvGKT~lak~   71 (315)
T d1r6bx3          54 SFLFAGPTGVGKTEVTVQ   71 (315)
T ss_dssp             EEEEECSTTSSHHHHHHH
T ss_pred             EEEEECCCcchhHHHHHH
Confidence            588999999999987644

>d1d0xa2 c.37.1.9 (A:2-33,A:80-759) Myosin S1, motor domain {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Dictyostelium discoideum [TaxId: 44689]

Probab=86.40  E-value=0.33  Score=39.04  Aligned_cols=61  Identities=13%  Similarity=0.177  Sum_probs=37.5

Q ss_pred             CCccCCC-CCHHHHHHHHHCCCC--CChHH--HHhhhhhhhC---CCcEEEECCCCChHHHHHHHHHHH
Q psy4275           6 KSFTDLK-LNPWLIRQCQTIGVK--TPTEI--QKAIIPHVLN---DEDCIGCAKTGSGKTLAFALPILQ   66 (182)
Q Consensus         6 ~~~~~~~-l~~~i~~~l~~~~~~--~~~~~--Q~~~~~~~~~---~~~~li~~~tg~GKT~~~~~~~~~   66 (182)
                      .+|..++ .+++..+.+......  +|..+  -..++..+..   ++.+++.|.+|+|||.++-..+-+
T Consensus        80 NP~k~l~iy~~~~~~~y~~~~~~~~~PHifaiA~~Ay~~m~~~~~nQsIiisGeSGaGKTe~~k~il~y  148 (712)
T d1d0xa2          80 NPFKRIPIYTQEMVDIFKGRRRNEVAPHIFAISDVAYRSMLDDRQNQSLLITGESGAGKTENTKKVIQY  148 (712)
T ss_dssp             CCSSCCSCCSHHHHHHHTTCCGGGSCCCHHHHHHHHHHHHHHHTCCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHcCCCcCCCCCcHHHHHHHHHHHHHHhCCCceEEEeCCCCCCHHHHHHHHHHH
Confidence            4556666 467777777644332  33333  3345555443   568999999999999885544433

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {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: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=86.32  E-value=0.18  Score=33.81  Aligned_cols=30  Identities=17%  Similarity=0.039  Sum_probs=20.7

Q ss_pred             CCCccEEEEeccccccccCChh-HHHHHHHH
Q psy4275         147 LNRIKFLVLDEADRLSLMTSLK-FFFFFFFL  176 (182)
Q Consensus       147 ~~~~~~iI~DE~h~~~~~~~~~-~~~~~~~~  176 (182)
                      ..+-.++++||--.-+|..... ....+..+
T Consensus       141 ~~~~~llllDEPt~gLD~~~~~~i~~~l~~~  171 (200)
T d1sgwa_         141 LVNAEIYVLDDPVVAIDEDSKHKVLKSILEI  171 (200)
T ss_dssp             TSCCSEEEEESTTTTSCTTTHHHHHHHHHHH
T ss_pred             hcCCCEEEEcCcccccCHHHHHHHHHHHHHH
Confidence            4456799999998777776654 45555554

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {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: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.22  E-value=0.14  Score=34.27  Aligned_cols=14  Identities=36%  Similarity=0.294  Sum_probs=12.0

Q ss_pred             EECCCCChHHHHHH
Q psy4275          48 GCAKTGSGKTLAFA   61 (182)
Q Consensus        48 i~~~tg~GKT~~~~   61 (182)
                      +.|++|||||+.+-
T Consensus         7 I~G~~gSGKSTla~   20 (213)
T d1uj2a_           7 VSGGTASGKSSVCA   20 (213)
T ss_dssp             EECSTTSSHHHHHH
T ss_pred             EECCCCCCHHHHHH
Confidence            67999999998863

>d1c9ka_ c.37.1.11 (A:) Adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU {Salmonella typhimurium [TaxId: 90371]}

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: Adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU
species: Salmonella typhimurium [TaxId: 90371]

Probab=86.04  E-value=0.47  Score=31.23  Aligned_cols=83  Identities=12%  Similarity=0.006  Sum_probs=41.5

Q ss_pred             EEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHH-hcCC
Q psy4275          46 CIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKE-LAKK  124 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~  124 (182)
                      +++.|+..|||+..+.-.+     ..  +++++||+.....-..+.+.++.....-+-....+............ ..+.
T Consensus         2 iLVtGGarSGKS~~AE~l~-----~~--~~~~~YiAT~~~~D~em~~RI~~Hr~rR~~~w~tiE~~~~l~~~l~~~~~~~   74 (180)
T d1c9ka_           2 ILVTGGARSGKSRHAEALI-----GD--APQVLYIATSQILDDEMAARIQHHKDGRPAHWRTAECWRHLDTLITADLAPD   74 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHH-----CS--CSSEEEEECCCC------CHHHHHHHTSCTTEEEECCSSCGGGTSCTTSCTT
T ss_pred             EEEECCCCccHHHHHHHHH-----hc--CCCcEEEEccCCCCHHHHHHHHHHHhcCcCCCEEecccccHHHHHHhhcCcc
Confidence            5789999999998765321     22  44689998877665556555554433334444444433332222211 1223


Q ss_pred             CcEEEEChHHH
Q psy4275         125 PHIVIATPGRL  135 (182)
Q Consensus       125 ~~Ilv~T~~~l  135 (182)
                      .-|+|-.-..+
T Consensus        75 ~~vLlDclt~~   85 (180)
T d1c9ka_          75 DAILLECITTM   85 (180)
T ss_dssp             CEEEEECHHHH
T ss_pred             cchhhhhhhHH
Confidence            34666444444

>d1kkma_ c.91.1.2 (A:) HPr kinase HprK C-terminal domain {Lactobacillus casei [TaxId: 1582]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Lactobacillus casei [TaxId: 1582]

Probab=85.89  E-value=0.24  Score=32.58  Aligned_cols=23  Identities=13%  Similarity=0.082  Sum_probs=18.7

Q ss_pred             CCCcEEEECCCCChHHHHHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      .|+.+++.|+.|+|||..++..+
T Consensus        13 ~g~gvl~~G~sG~GKStlal~l~   35 (176)
T d1kkma_          13 YGLGVLITGDSGVGKSETALELV   35 (176)
T ss_dssp             TTEEEEEECCTTSCHHHHHHHHH
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHH
Confidence            47789999999999998865433

>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=85.86  E-value=3.4  Score=27.87  Aligned_cols=92  Identities=12%  Similarity=0.146  Sum_probs=53.3

Q ss_pred             CCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhhhhHHhc-----CCCc
Q psy4275          52 TGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELA-----KKPH  126 (182)
Q Consensus        52 tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~  126 (182)
                      ..+||..... -++......  +.+++|.+....-.+.+...+...   .+..+..++|+.+...+...+.     .+..
T Consensus        66 ~~S~K~~~l~-~~l~~~~~~--g~kviIFs~~~~~~~~l~~~l~~~---~~~~~~~i~G~~~~~~R~~~i~~F~~~~~~~  139 (244)
T d1z5za1          66 RRSGKMIRTM-EIIEEALDE--GDKIAIFTQFVDMGKIIRNIIEKE---LNTEVPFLYGELSKKERDDIISKFQNNPSVK  139 (244)
T ss_dssp             TTCHHHHHHH-HHHHHHHHT--TCCEEEEESCHHHHHHHHHHHHHH---HCSCCCEECTTSCHHHHHHHHHHHHHCTTCC
T ss_pred             hhhhHHHHHH-HHHHhhccc--ccceEEEeeceehHHHHHHHHHhh---ccceEEEEecccchhccchhhhhhhccccch
Confidence            4577866533 333333332  558999999888766555544432   3567778899987655443322     2467


Q ss_pred             EEEEChHHHHHHHhcCCCCCCCCccEEEE
Q psy4275         127 IVIATPGRLADHLDTCNTFSLNRIKFLVL  155 (182)
Q Consensus       127 Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~  155 (182)
                      ++++++...      ...+++...+.+|+
T Consensus       140 vll~~~~~~------g~Glnl~~a~~vi~  162 (244)
T d1z5za1         140 FIVLSVKAG------GFGINLTSANRVIH  162 (244)
T ss_dssp             EEEEECCTT------CCCCCCTTCSEEEE
T ss_pred             hcccccccc------ccccccchhhhhhh
Confidence            888876532      13344554444443

>d1knxa2 c.91.1.2 (A:133-309) HPr kinase HprK C-terminal domain {Mycoplasma pneumoniae [TaxId: 2104]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Mycoplasma pneumoniae [TaxId: 2104]

Probab=85.81  E-value=0.22  Score=32.86  Aligned_cols=23  Identities=17%  Similarity=0.086  Sum_probs=18.7

Q ss_pred             CCCcEEEECCCCChHHHHHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      .|+.++++|++|+|||..++..+
T Consensus        14 ~g~gvli~G~sG~GKS~lal~l~   36 (177)
T d1knxa2          14 FGVGVLLTGRSGIGKSECALDLI   36 (177)
T ss_dssp             TTEEEEEEESSSSSHHHHHHHHH
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHH
Confidence            47789999999999998865443

>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=85.67  E-value=0.27  Score=32.79  Aligned_cols=20  Identities=15%  Similarity=-0.039  Sum_probs=15.0

Q ss_pred             EEEECCCCChHHHHHHHHHH
Q psy4275          46 CIGCAKTGSGKTLAFALPIL   65 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~~   65 (182)
                      +.+.||+|+||++.+-..+-
T Consensus         6 I~I~GppGSGKgT~ak~La~   25 (225)
T d1ckea_           6 ITIDGPSGAGKGTLCKAMAE   25 (225)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45569999999998755443

>d1lkxa_ c.37.1.9 (A:) Myosin S1, motor domain {Dictyostelium discoideum, class-I myosin MyoE [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Dictyostelium discoideum, class-I myosin MyoE [TaxId: 44689]

Probab=85.22  E-value=0.37  Score=38.59  Aligned_cols=62  Identities=16%  Similarity=0.097  Sum_probs=37.5

Q ss_pred             CCccCCC-CCHHHHHHHHHCCCC--CChHH--HHhhhhhhhC---CCcEEEECCCCChHHHHHHHHHHHh
Q psy4275           6 KSFTDLK-LNPWLIRQCQTIGVK--TPTEI--QKAIIPHVLN---DEDCIGCAKTGSGKTLAFALPILQK   67 (182)
Q Consensus         6 ~~~~~~~-l~~~i~~~l~~~~~~--~~~~~--Q~~~~~~~~~---~~~~li~~~tg~GKT~~~~~~~~~~   67 (182)
                      .+|..++ .+++..+.+......  +|..+  =..++..+..   ++.+++.|.+|+|||.++-..+-+.
T Consensus        41 NP~~~l~~y~~~~~~~y~~~~~~~~~PHif~iA~~Ay~~l~~~~~~QsIiisGeSGsGKTe~~k~il~yL  110 (684)
T d1lkxa_          41 NPFKNLNIYKESDIKAYNGRYKYEMPPHMYALANDAYRSMRQSQENQCVIISGESGAGKTEASKKIMQFL  110 (684)
T ss_dssp             CCSSCCSCCSHHHHHHHSSCCGGGSCCCHHHHHHHHHHHHHHHCCCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHcCCCCCCCCChHHHHHHHHHHHHHHcCCCeEEEEEcCCCCCHHHHHHHHHHHH
Confidence            4556666 466667766543322  23333  3345555443   5578999999999999865544443

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {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: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=84.99  E-value=0.22  Score=32.87  Aligned_cols=19  Identities=16%  Similarity=0.013  Sum_probs=15.0

Q ss_pred             EEEECCCCChHHHHHHHHH
Q psy4275          46 CIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        46 ~li~~~tg~GKT~~~~~~~   64 (182)
                      ++++|.+|+|||+.+-...
T Consensus         5 i~l~GlpgsGKSTla~~L~   23 (213)
T d1bifa1           5 IVMVGLPARGKTYISKKLT   23 (213)
T ss_dssp             EEEECCTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            5788999999999875443

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {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: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=84.89  E-value=0.22  Score=34.49  Aligned_cols=28  Identities=21%  Similarity=0.242  Sum_probs=20.3

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhhcc
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKWCE   70 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~~~   70 (182)
                      ..|..+-+.|++|+|||+..  -++..++.
T Consensus        27 ~~Ge~vaIvG~sGsGKSTLl--~ll~gl~~   54 (241)
T d2pmka1          27 KQGEVIGIVGRSGSGKSTLT--KLIQRFYI   54 (241)
T ss_dssp             ETTCEEEEECSTTSSHHHHH--HHHTTSSC
T ss_pred             cCCCEEEEECCCCCCHHHHH--HHHHhcCC
Confidence            34788999999999999764  44444443

>d1q3ta_ c.37.1.1 (A:) CMP kinase {Streptococcus pneumoniae [TaxId: 1313]}

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: Streptococcus pneumoniae [TaxId: 1313]

Probab=84.75  E-value=0.36  Score=32.26  Aligned_cols=20  Identities=15%  Similarity=0.006  Sum_probs=15.1

Q ss_pred             EEECCCCChHHHHHHHHHHH
Q psy4275          47 IGCAKTGSGKTLAFALPILQ   66 (182)
Q Consensus        47 li~~~tg~GKT~~~~~~~~~   66 (182)
                      .+-||+|+|||+.+-..+-+
T Consensus         7 aIdGp~GsGKgT~ak~La~~   26 (223)
T d1q3ta_           7 AIDGPASSGKSTVAKIIAKD   26 (223)
T ss_dssp             EEECSSCSSHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHH
Confidence            45699999999987655543

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

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: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=84.45  E-value=0.46  Score=33.35  Aligned_cols=43  Identities=14%  Similarity=-0.045  Sum_probs=29.6

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEcCCHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAY   88 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~   88 (182)
                      |+-..+.||.|+|||..++..+......   +..++|+-.......
T Consensus        57 g~itei~G~~~sGKT~l~l~~~~~aqk~---g~~v~yiDtE~~~~~   99 (268)
T d1xp8a1          57 GRITEIYGPESGGKTTLALAIVAQAQKA---GGTCAFIDAEHALDP   99 (268)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHT---TCCEEEEESSCCCCH
T ss_pred             ceEEEEecCCccchHHHHHHHHHHHHhC---CCEEEEEECCccCCH
Confidence            4567788999999999876655554322   457888876655533

>d1nn5a_ c.37.1.1 (A:) Thymidylate kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.22  E-value=0.52  Score=31.57  Aligned_cols=29  Identities=10%  Similarity=0.141  Sum_probs=19.3

Q ss_pred             CCCcEEEECCCCChHHHHHHHHHHHhhccC
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALPILQKWCED   71 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~~~~~~~~~   71 (182)
                      +|.-+.+.|+.|+|||+.+- .+.+.+...
T Consensus         2 rG~lI~ieG~dGsGKsT~~~-~L~~~L~~~   30 (209)
T d1nn5a_           2 RGALIVLEGVDRAGKSTQSR-KLVEALCAA   30 (209)
T ss_dssp             CCCEEEEEESTTSSHHHHHH-HHHHHHHHT
T ss_pred             CeeEEEEECCCCCCHHHHHH-HHHHHHHHC
Confidence            35556777999999999854 334444443

>d1ko7a2 c.91.1.2 (A:130-298) HPr kinase HprK C-terminal domain {Staphylococcus xylosus [TaxId: 1288]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Staphylococcus xylosus [TaxId: 1288]

Probab=84.12  E-value=0.3  Score=31.90  Aligned_cols=23  Identities=17%  Similarity=0.096  Sum_probs=18.5

Q ss_pred             CCCcEEEECCCCChHHHHHHHHH
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALPI   64 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~~   64 (182)
                      .|+.+++.|+.|+|||..++..+
T Consensus        14 ~g~gvli~G~sg~GKS~la~~l~   36 (169)
T d1ko7a2          14 YGVGVLITGDSGIGKSETALELI   36 (169)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHH
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHH
Confidence            47789999999999998764433

>d1br2a2 c.37.1.9 (A:80-789) Myosin S1, motor domain {Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]

Probab=83.82  E-value=0.43  Score=38.32  Aligned_cols=62  Identities=19%  Similarity=0.255  Sum_probs=36.7

Q ss_pred             cCCccCCC-CCHHHHHHHHHCCCC--CC--hHHHHhhhhhhhC---CCcEEEECCCCChHHHHHHHHHHH
Q psy4275           5 IKSFTDLK-LNPWLIRQCQTIGVK--TP--TEIQKAIIPHVLN---DEDCIGCAKTGSGKTLAFALPILQ   66 (182)
Q Consensus         5 ~~~~~~~~-l~~~i~~~l~~~~~~--~~--~~~Q~~~~~~~~~---~~~~li~~~tg~GKT~~~~~~~~~   66 (182)
                      +.+|.+++ .+++..+.+......  .|  ...=..++..+..   ++.+++.|.+|+|||.+.-..+-+
T Consensus        45 vNP~k~l~~y~~~~~~~y~~~~~~~~~PHif~vA~~Ay~~m~~~~~~Q~IiisGeSGaGKTe~~k~il~y  114 (710)
T d1br2a2          45 INPYKQLPIYSEKIIDMYKGKKRHEMPPHIYAIADTAYRSMLQDREDQSILCTGESGAGKTENTKKVIQY  114 (710)
T ss_dssp             ECCSSCCTTCCHHHHHHTTTCCGGGSCCCHHHHHHHHHHHHHHHTCCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             ECCCCCCCCCCHHHHHHHcCCCCCCCCChHHHHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHHHHHHHHH
Confidence            34566665 466666665433222  23  2333445555544   567999999999999885444433

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=83.82  E-value=0.24  Score=34.53  Aligned_cols=20  Identities=20%  Similarity=0.233  Sum_probs=16.9

Q ss_pred             hCCCcEEEECCCCChHHHHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~   60 (182)
                      ..|..+-+.||+|+|||+.+
T Consensus        39 ~~Ge~iaivG~sGsGKSTLl   58 (253)
T d3b60a1          39 PAGKTVALVGRSGSGKSTIA   58 (253)
T ss_dssp             CTTCEEEEEECTTSSHHHHH
T ss_pred             cCCCEEEEECCCCChHHHHH
Confidence            34788999999999999774

>d1odfa_ c.37.1.6 (A:) Hypothetical protein Ygr205W {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: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein Ygr205W
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=83.72  E-value=0.3  Score=34.72  Aligned_cols=13  Identities=31%  Similarity=0.378  Sum_probs=10.8

Q ss_pred             EECCCCChHHHHH
Q psy4275          48 GCAKTGSGKTLAF   60 (182)
Q Consensus        48 i~~~tg~GKT~~~   60 (182)
                      +.|++|||||+.+
T Consensus        32 i~G~qGSGKSTl~   44 (286)
T d1odfa_          32 FSGPQGSGKSFTS   44 (286)
T ss_dssp             EECCTTSSHHHHH
T ss_pred             eECCCCCCHHHHH
Confidence            4699999999764

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=83.54  E-value=0.26  Score=34.43  Aligned_cols=20  Identities=20%  Similarity=0.220  Sum_probs=16.8

Q ss_pred             hCCCcEEEECCCCChHHHHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~   60 (182)
                      ..|..+.+.|++|+|||+..
T Consensus        42 ~~Ge~vaivG~sGsGKSTLl   61 (255)
T d2hyda1          42 EKGETVAFVGMSGGGKSTLI   61 (255)
T ss_dssp             CTTCEEEEECSTTSSHHHHH
T ss_pred             cCCCEEEEECCCCCcHHHHH
Confidence            34788999999999998764

>d1kk8a2 c.37.1.9 (A:1-28,A:77-837) Myosin S1, motor domain {Bay scallop (Aequipecten irradians) [TaxId: 31199]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Bay scallop (Aequipecten irradians) [TaxId: 31199]

Probab=83.53  E-value=0.43  Score=38.83  Aligned_cols=61  Identities=15%  Similarity=0.285  Sum_probs=36.6

Q ss_pred             CCccCCCC-CHHHHHHHHHCCCC--CChHH--HHhhhhhhhC---CCcEEEECCCCChHHHHHHHHHHH
Q psy4275           6 KSFTDLKL-NPWLIRQCQTIGVK--TPTEI--QKAIIPHVLN---DEDCIGCAKTGSGKTLAFALPILQ   66 (182)
Q Consensus         6 ~~~~~~~l-~~~i~~~l~~~~~~--~~~~~--Q~~~~~~~~~---~~~~li~~~tg~GKT~~~~~~~~~   66 (182)
                      .+|.++++ +++..+........  +|..+  -..++..+..   ++.+++.|.+|+|||.++-..+-+
T Consensus        76 NP~k~l~iy~~~~~~~y~~~~~~~~~PHiyavA~~Ay~~m~~~~~nQ~IiisGESGaGKTe~~K~il~y  144 (789)
T d1kk8a2          76 NPYRRLPIYTDSVIAKYRGKRKTEIPPHLFSVADNAYQNMVTDRENQSCLITGESGAGKTENTKKVIMY  144 (789)
T ss_dssp             CCSSCCSTTSHHHHHHHTTCCGGGSCCCHHHHHHHHHHHHHHHTSEEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHHHHHHHHH
Confidence            45555553 66666666543222  23333  3445555443   468999999999999885544443

>d1l2ta_ c.37.1.12 (A:) MJ0796 {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: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=83.35  E-value=0.27  Score=33.78  Aligned_cols=28  Identities=21%  Similarity=0.141  Sum_probs=20.6

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhhcc
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKWCE   70 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~~~   70 (182)
                      .+|..+-+.||+|+|||+..  -++..+..
T Consensus        29 ~~Ge~~~iiG~sGsGKSTLl--~~i~gl~~   56 (230)
T d1l2ta_          29 KEGEFVSIMGPSGSGKSTML--NIIGCLDK   56 (230)
T ss_dssp             CTTCEEEEECSTTSSHHHHH--HHHTTSSC
T ss_pred             cCCCEEEEECCCCCCcchhh--HhccCCCC
Confidence            34788899999999999663  45555443

>d1qvra3 c.37.1.20 (A:536-850) 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=83.33  E-value=0.31  Score=35.05  Aligned_cols=17  Identities=29%  Similarity=0.186  Sum_probs=14.6

Q ss_pred             cEEEECCCCChHHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~   61 (182)
                      ..+++||||+|||..+-
T Consensus        55 ~~lf~Gp~G~GKt~lak   71 (315)
T d1qvra3          55 SFLFLGPTGVGKTELAK   71 (315)
T ss_dssp             EEEEBSCSSSSHHHHHH
T ss_pred             EEEEECCCcchHHHHHH
Confidence            56888999999998864

>d4tmka_ c.37.1.1 (A:) Thymidylate 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: Thymidylate kinase
species: Escherichia coli [TaxId: 562]

Probab=83.33  E-value=1.3  Score=29.22  Aligned_cols=27  Identities=19%  Similarity=0.197  Sum_probs=19.2

Q ss_pred             CCcEEEECCCCChHHHHHHHHHHHhhcc
Q psy4275          43 DEDCIGCAKTGSGKTLAFALPILQKWCE   70 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~~~~~~~~~~~   70 (182)
                      |+-+++.|+.|+|||+.+-. +.+.+..
T Consensus         2 gkfIviEG~dGsGKsT~~~~-L~~~L~~   28 (210)
T d4tmka_           2 SKYIVIEGLEGAGKTTARNV-VVETLEQ   28 (210)
T ss_dssp             CCEEEEEECTTSCHHHHHHH-HHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHH-HHHHHHh
Confidence            66788899999999998543 3333433

>d1w7ja2 c.37.1.9 (A:63-792) Myosin S1, motor domain {Chicken (Gallus gallus), Va isoform [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Chicken (Gallus gallus), Va isoform [TaxId: 9031]

Probab=83.31  E-value=0.55  Score=37.82  Aligned_cols=62  Identities=15%  Similarity=0.252  Sum_probs=37.9

Q ss_pred             cCCccCCC-CCHHHHHHHHHCCCC--CChHH--HHhhhhhhhC---CCcEEEECCCCChHHHHHHHHHHH
Q psy4275           5 IKSFTDLK-LNPWLIRQCQTIGVK--TPTEI--QKAIIPHVLN---DEDCIGCAKTGSGKTLAFALPILQ   66 (182)
Q Consensus         5 ~~~~~~~~-l~~~i~~~l~~~~~~--~~~~~--Q~~~~~~~~~---~~~~li~~~tg~GKT~~~~~~~~~   66 (182)
                      +.+|..++ .+++..+........  +|..+  =..++..+..   +..+++.|.+|+|||.+.-..+-+
T Consensus        48 iNP~~~~~~y~~~~~~~y~~~~~~~~~PHif~vA~~Ay~~l~~~~~~Q~IiisGeSGsGKTe~~k~il~~  117 (730)
T d1w7ja2          48 INPYEQLPIYGEDIINAYSGQNMGDMDPHIFAVAEEAYKQMARDERNQSIIVSGESGAGKTVSAKYAMRY  117 (730)
T ss_dssp             ECCSSCCSCCSHHHHHHHTTCCGGGSCCCHHHHHHHHHHHHHHHTCCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             ECCCCCCCCCCHHHHHHHcCCCcCCCCCcHHHHHHHHHHHHHHhCCCeEEEEEeCCCCCHHHHHHHHHHH
Confidence            34566666 467777766543322  33333  3445555443   568999999999999976554433

>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=83.03  E-value=1.7  Score=28.70  Aligned_cols=75  Identities=16%  Similarity=0.085  Sum_probs=44.4

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccC--------------------------CceEEEEEcCCchhhhhHH----hcC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVM--------------------------NLRVSIITGGMDMVDQGKE----LAK  123 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~--------------------------~~~~~~~~~~~~~~~~~~~----~~~  123 (182)
                      +..+||.+|++.-++..+..+.......                          ...++..+++.+...+...    -.+
T Consensus        40 ~~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~~~r~~ie~~f~~g  119 (201)
T d2p6ra4          40 NGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRG  119 (201)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHHHHHHHHHHHHTT
T ss_pred             CCcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhhhhHHHHHHHHhCC
Confidence            4578999999888777776666533221                          0125677787765433321    134


Q ss_pred             CCcEEEEChHHHHHHHhcCCCCCCCCccEEEE
Q psy4275         124 KPHIVIATPGRLADHLDTCNTFSLNRIKFLVL  155 (182)
Q Consensus       124 ~~~Ilv~T~~~l~~~~~~~~~~~~~~~~~iI~  155 (182)
                      ..+|+|+|...      . ..+++....+||.
T Consensus       120 ~i~vlvaT~~l------~-~Gin~p~~~vvi~  144 (201)
T d2p6ra4         120 NIKVVVATPTL------A-AGVNLPARRVIVR  144 (201)
T ss_dssp             SCCEEEECSTT------T-SSSCCCBSEEEEC
T ss_pred             CceEEEechHH------H-hhcCCCCceEEEe
Confidence            67899999431      1 3456666655553

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=82.79  E-value=0.27  Score=34.01  Aligned_cols=26  Identities=19%  Similarity=0.391  Sum_probs=19.1

Q ss_pred             CCCcEEEECCCCChHHHHHHHHHHHhhc
Q psy4275          42 NDEDCIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        42 ~~~~~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      .|..+-+.||+|+|||+.+  -++..+.
T Consensus        27 ~Ge~vaivG~sGsGKSTLl--~ll~gl~   52 (242)
T d1mv5a_          27 PNSIIAFAGPSGGGKSTIF--SLLERFY   52 (242)
T ss_dssp             TTEEEEEECCTTSSHHHHH--HHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHH--HHHHHhh
Confidence            3778889999999999754  4444444

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.70  E-value=0.35  Score=34.27  Aligned_cols=18  Identities=39%  Similarity=0.303  Sum_probs=15.6

Q ss_pred             CCcEEEECCCCChHHHHH
Q psy4275          43 DEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        43 ~~~~li~~~tg~GKT~~~   60 (182)
                      |.-+.+.||+|+|||+..
T Consensus        62 Ge~vaivG~nGsGKSTLl   79 (281)
T d1r0wa_          62 GEMLAITGSTGSGKTSLL   79 (281)
T ss_dssp             TCEEEEEESTTSSHHHHH
T ss_pred             CCEEEEECCCCChHHHHH
Confidence            677889999999999764

>d1goja_ c.37.1.9 (A:) Kinesin {Neurospora crassa [TaxId: 5141]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Neurospora crassa [TaxId: 5141]

Probab=82.58  E-value=0.5  Score=34.47  Aligned_cols=23  Identities=26%  Similarity=0.536  Sum_probs=16.5

Q ss_pred             hhhhCCCc--EEEECCCCChHHHHH
Q psy4275          38 PHVLNDED--CIGCAKTGSGKTLAF   60 (182)
Q Consensus        38 ~~~~~~~~--~li~~~tg~GKT~~~   60 (182)
                      ..+.+|.+  ++..|+||+|||.+.
T Consensus        73 ~~~l~G~n~ti~aYG~tgSGKT~Tm   97 (354)
T d1goja_          73 DDILNGYNGTVFAYGQTGAGKSYTM   97 (354)
T ss_dssp             HHHTTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHhhccCceeEEecccCCCCcceee
Confidence            34455665  556689999999885

>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=82.31  E-value=0.28  Score=33.86  Aligned_cols=72  Identities=19%  Similarity=0.169  Sum_probs=42.1

Q ss_pred             CeeEEEEcCCHHHHHHHHHHHHHhhccCCceEEEEEcCCchhh----hhHHhcCCCcEEEEChHHHHHHHhcCCCCCCCC
Q psy4275          74 GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVD----QGKELAKKPHIVIATPGRLADHLDTCNTFSLNR  149 (182)
Q Consensus        74 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~Ilv~T~~~l~~~~~~~~~~~~~~  149 (182)
                      +..+||.|+++..++.+++.++..     +     +|+.....    ......++.+|+|+|...- +.+  ...+++++
T Consensus        25 ~~~~iif~~~~~~~~~l~~~l~~~-----~-----hg~~~~~~R~~~~~~f~~g~~~vLVaT~a~~-~v~--~rGlDip~   91 (248)
T d1gkub2          25 GTGGIIYARTGEEAEEIYESLKNK-----F-----RIGIVTATKKGDYEKFVEGEIDHLIGTAHYY-GTL--VRGLDLPE   91 (248)
T ss_dssp             CSCEEEEESSHHHHHHHHHTTTTS-----S-----CEEECTTSSSHHHHHHHHTSCSEEEEECC---------CCSCCTT
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHh-----c-----cCCCCHHHHHHHHHHHHhCCCeEEEEecccc-chh--hhccCccc
Confidence            346899999999988887776542     2     33332221    2222345789999995411 111  14567764


Q ss_pred             -ccEEEEecc
Q psy4275         150 -IKFLVLDEA  158 (182)
Q Consensus       150 -~~~iI~DE~  158 (182)
                       ++++|.=++
T Consensus        92 ~v~~VI~~d~  101 (248)
T d1gkub2          92 RIRFAVFVGC  101 (248)
T ss_dssp             TCCEEEEESC
T ss_pred             cccEEEEeCC
Confidence             888885433

>d2mysa2 c.37.1.9 (A:4-33,A:80-843) Myosin S1, motor domain {Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]

Probab=82.23  E-value=0.4  Score=39.03  Aligned_cols=62  Identities=16%  Similarity=0.207  Sum_probs=35.7

Q ss_pred             CCccCCC-CCHHHHHHHHHCCCC--CChHH--HHhhhhhhhC---CCcEEEECCCCChHHHHHHHHHHHh
Q psy4275           6 KSFTDLK-LNPWLIRQCQTIGVK--TPTEI--QKAIIPHVLN---DEDCIGCAKTGSGKTLAFALPILQK   67 (182)
Q Consensus         6 ~~~~~~~-l~~~i~~~l~~~~~~--~~~~~--Q~~~~~~~~~---~~~~li~~~tg~GKT~~~~~~~~~~   67 (182)
                      .+|..++ .+++..+........  +|..+  =..++..+..   ++.+++.|.+|+|||.++-..+-+.
T Consensus        78 NPyk~l~ly~~~~~~~y~~~~~~~~pPHifaiA~~Ay~~m~~~~~~QsIiisGeSGaGKTe~~K~il~yL  147 (794)
T d2mysa2          78 NPYKWLPVYNPKVVLAYRGKKRQEAPPHIFSISDNAYQFMLTDRENQSILITGESGAGKTVNTKRVIQYF  147 (794)
T ss_dssp             CCSSCCGGGCTTHHHHTTTCCTTSSCSCHHHHHHHHHHHHHHHTCCEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHcCCCcEEEEEcCCCCCHHHHHHHHHHHH
Confidence            3455554 355566655543322  23333  3345555443   4579999999999998865444443

>d1sq5a_ c.37.1.6 (A:) Pantothenate kinase PanK {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: Phosphoribulokinase/pantothenate kinase
domain: Pantothenate kinase PanK
species: Escherichia coli [TaxId: 562]

Probab=82.16  E-value=0.64  Score=33.31  Aligned_cols=15  Identities=13%  Similarity=0.047  Sum_probs=12.1

Q ss_pred             EEECCCCChHHHHHH
Q psy4275          47 IGCAKTGSGKTLAFA   61 (182)
Q Consensus        47 li~~~tg~GKT~~~~   61 (182)
                      -++|+.|+|||+.+-
T Consensus        84 GIaG~sgSGKSTla~   98 (308)
T d1sq5a_          84 SIAGSVAVGKSTTAR   98 (308)
T ss_dssp             EEEECTTSSHHHHHH
T ss_pred             EEeCCCCCCCcHHHH
Confidence            356899999998763

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, 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: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=81.88  E-value=0.46  Score=32.61  Aligned_cols=20  Identities=20%  Similarity=0.252  Sum_probs=16.3

Q ss_pred             hCCCcEEEECCCCChHHHHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~   60 (182)
                      .+|.-+-+.||+|+|||+..
T Consensus        24 ~~Gei~~liGpsGsGKSTLl   43 (232)
T d2awna2          24 HEGEFVVFVGPSGCGKSTLL   43 (232)
T ss_dssp             CTTCEEEEECCTTSSHHHHH
T ss_pred             cCCCEEEEECCCCChHHHHH
Confidence            34778889999999999763

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=81.80  E-value=0.44  Score=32.90  Aligned_cols=20  Identities=30%  Similarity=0.305  Sum_probs=16.5

Q ss_pred             hCCCcEEEECCCCChHHHHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~   60 (182)
                      .+|.-+-+.||+|+|||+..
T Consensus        27 ~~Ge~~~liG~sGaGKSTll   46 (240)
T d1g2912          27 KDGEFMILLGPSGCGKTTTL   46 (240)
T ss_dssp             ETTCEEEEECSTTSSHHHHH
T ss_pred             cCCCEEEEECCCCChHHHHH
Confidence            34778889999999999764

>d2vp4a1 c.37.1.1 (A:12-208) Deoxyribonucleoside kinase {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

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: Deoxyribonucleoside kinase
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=81.70  E-value=0.36  Score=31.63  Aligned_cols=16  Identities=31%  Similarity=0.326  Sum_probs=13.3

Q ss_pred             cEEEECCCCChHHHHH
Q psy4275          45 DCIGCAKTGSGKTLAF   60 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~   60 (182)
                      -+.+.|+.|+|||+.+
T Consensus        11 ~I~ieG~~GsGKTTl~   26 (197)
T d2vp4a1          11 TVLIEGNIGSGKTTYL   26 (197)
T ss_dssp             EEEEECSTTSCHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3677899999999864

>d1bg2a_ c.37.1.9 (A:) Kinesin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.66  E-value=0.53  Score=33.84  Aligned_cols=23  Identities=30%  Similarity=0.365  Sum_probs=16.5

Q ss_pred             hhhhCCC--cEEEECCCCChHHHHH
Q psy4275          38 PHVLNDE--DCIGCAKTGSGKTLAF   60 (182)
Q Consensus        38 ~~~~~~~--~~li~~~tg~GKT~~~   60 (182)
                      +.+.+|.  .++..|+||+|||...
T Consensus        69 ~~~l~G~n~~i~aYGqtgSGKTyT~   93 (323)
T d1bg2a_          69 KDVLEGYNGTIFAYGQTSSGKTHTM   93 (323)
T ss_dssp             HHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHcCCCcceeeecccCCCCceec
Confidence            3445565  4566689999999885

>d1ihua1 c.37.1.10 (A:1-296) Arsenite-translocating ATPase ArsA {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: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=80.91  E-value=0.88  Score=31.58  Aligned_cols=34  Identities=21%  Similarity=0.122  Sum_probs=22.6

Q ss_pred             cEEEECCCCChHHHHHHHHHHHhhccCCCCeeEEEEc
Q psy4275          45 DCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLT   81 (182)
Q Consensus        45 ~~li~~~tg~GKT~~~~~~~~~~~~~~~~~~~~lil~   81 (182)
                      -+++.|.=|.|||+++...+.....+   |.++++|-
T Consensus        10 ~i~~sGKGGVGKTTvaa~lA~~lA~~---G~rVLlvD   43 (296)
T d1ihua1          10 YLFFTGKGGVGKTSISCATAIRLAEQ---GKRVLLVS   43 (296)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHT---TCCEEEEE
T ss_pred             EEEEECCCcChHHHHHHHHHHHHHHC---CCCEEEEe
Confidence            45677888999999876655554333   44566554

>d1uf9a_ c.37.1.1 (A:) Dephospho-CoA kinase {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: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Thermus thermophilus [TaxId: 274]

Probab=80.72  E-value=0.3  Score=31.96  Aligned_cols=15  Identities=40%  Similarity=0.417  Sum_probs=12.4

Q ss_pred             EECCCCChHHHHHHH
Q psy4275          48 GCAKTGSGKTLAFAL   62 (182)
Q Consensus        48 i~~~tg~GKT~~~~~   62 (182)
                      ++|+.|||||+++-+
T Consensus         8 itG~~gSGKstva~~   22 (191)
T d1uf9a_           8 ITGNIGSGKSTVAAL   22 (191)
T ss_dssp             EEECTTSCHHHHHHH
T ss_pred             EECCCCCCHHHHHHH
Confidence            569999999998643

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {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: ABC transporter ATPase domain-like
domain: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=80.68  E-value=0.35  Score=33.47  Aligned_cols=27  Identities=11%  Similarity=0.000  Sum_probs=19.6

Q ss_pred             hCCCcEEEECCCCChHHHHHHHHHHHhhc
Q psy4275          41 LNDEDCIGCAKTGSGKTLAFALPILQKWC   69 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~~~~~~~~~~   69 (182)
                      .+|.-+-+.||+|+|||+..  -++..+.
T Consensus        29 ~~Ge~~~iiG~sGsGKSTLl--~~i~Gl~   55 (240)
T d3dhwc1          29 PAGQIYGVIGASGAGKSTLI--RCVNLLE   55 (240)
T ss_dssp             CSSCEEEEEESTTSSHHHHH--HHHTTSS
T ss_pred             cCCCEEEEECCCCCCHHHHH--HHHcCCc
Confidence            34778889999999999763  4444443

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=80.66  E-value=0.54  Score=32.42  Aligned_cols=20  Identities=25%  Similarity=0.280  Sum_probs=16.6

Q ss_pred             hCCCcEEEECCCCChHHHHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~   60 (182)
                      .+|.-+-+.||+|+|||+..
T Consensus        30 ~~Ge~~~liGpsGaGKSTLl   49 (239)
T d1v43a3          30 KDGEFLVLLGPSGCGKTTTL   49 (239)
T ss_dssp             CTTCEEEEECCTTSSHHHHH
T ss_pred             CCCCEEEEECCCCChHHHHH
Confidence            34777889999999999874

>d1tuea_ c.37.1.20 (A:) Replication protein E1 helicase domain {Human papillomavirus type 18 [TaxId: 333761]}

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 protein E1 helicase domain
species: Human papillomavirus type 18 [TaxId: 333761]

Probab=80.46  E-value=1.9  Score=28.80  Aligned_cols=46  Identities=9%  Similarity=0.053  Sum_probs=25.7

Q ss_pred             HHHHHHHHHCCCCCChHHHHhh---hhhhhCCCcEEEECCCCChHHHHHH
Q psy4275          15 PWLIRQCQTIGVKTPTEIQKAI---IPHVLNDEDCIGCAKTGSGKTLAFA   61 (182)
Q Consensus        15 ~~i~~~l~~~~~~~~~~~Q~~~---~~~~~~~~~~li~~~tg~GKT~~~~   61 (182)
                      +.|.+.|+.-++ ++.+.-...   +...-+.+..++.||+++|||+.+.
T Consensus        23 ~~I~~~l~~q~i-~~~~Fl~~l~~~l~~~PKkn~i~~~GP~~TGKS~f~~   71 (205)
T d1tuea_          23 RPIVQFLRYQQI-EFITFLGALKSFLKGTPKKNCLVFCGPANTGKSYFGM   71 (205)
T ss_dssp             HHHHHHHHHTTC-CHHHHHHHHHHHHHTCTTCSEEEEESCGGGCHHHHHH
T ss_pred             HHHHHHHHhcCc-cHHHHHHHHHHHHcCCCCceEEEEECCCCccHHHHHH
Confidence            455565654444 233332222   1222224567888999999998753

>d3d31a2 c.37.1.12 (A:1-229) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=80.14  E-value=0.46  Score=32.56  Aligned_cols=20  Identities=35%  Similarity=0.358  Sum_probs=16.5

Q ss_pred             hCCCcEEEECCCCChHHHHH
Q psy4275          41 LNDEDCIGCAKTGSGKTLAF   60 (182)
Q Consensus        41 ~~~~~~li~~~tg~GKT~~~   60 (182)
                      .+|.-+-+.||+|+|||+..
T Consensus        24 ~~Ge~~~liGpsGaGKSTll   43 (229)
T d3d31a2          24 ESGEYFVILGPTGAGKTLFL   43 (229)
T ss_dssp             CTTCEEEEECCCTHHHHHHH
T ss_pred             CCCCEEEEECCCCCcHHHHH
Confidence            34777889999999999874

>d1nija1 c.37.1.10 (A:2-223) Hypothetical protein YjiA, 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: Nitrogenase iron protein-like
domain: Hypothetical protein YjiA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=80.03  E-value=0.65  Score=31.43  Aligned_cols=14  Identities=29%  Similarity=0.259  Sum_probs=12.1

Q ss_pred             EEEECCCCChHHHH
Q psy4275          46 CIGCAKTGSGKTLA   59 (182)
Q Consensus        46 ~li~~~tg~GKT~~   59 (182)
                      .++.|.-|+|||+.
T Consensus         6 ~iitGFLGaGKTTl   19 (222)
T d1nija1           6 TLLTGFLGAGKTTL   19 (222)
T ss_dssp             EEEEESSSSSCHHH
T ss_pred             EEEeeCCCCCHHHH
Confidence            57889999999985